500-fold higher than the unfunctionalized \"naked\" virions (<104 IU/ml). The ability of the DARPin-conjugated lentivirus to transduce HER2+ cells correlated with the surface expression level of HER2. Furthermore, these lentiviruses preferentially transduced HER2+ cells in cocultures containing HER2+ and HER2- cells. To enable the use of commercially available monoclonal antibodies (MAbs) as the CBP, we developed a convenient click chemistry-based approach to conjugate MAb-derived Fab fragments to a variant SpyCatcherΔ protein containing a nonnatural amino acid, 4-azido-l-phenylalanine (AzF). Using the HER2-binding trastuzumab as a model cell-specific MAb, we created Fab-conjugated lentiviral vectors that transduced HER2+ SKOV3 cells with an infectious titer of 2.8 × 106 IU/ml, on par with the result achieved using the DARPin-SpyCatcherΔ fusion protein. The ability to create cell-specific lentiviral vectors through chemical conjugation of a CBP should make this approach generalizable to any antibody, giving it broad utility for a wide range of research and clinical applications. IMPORTANCE Lentiviral vectors hold great potential in gene therapy. However, it remains a major hurdle to robustly engineer cell-specific lentiviral vectors. This article reports a simple and effective strategy to functionalize lentiviral vectors with cell-binding proteins, thus retargeting these viruses to cells expressing the binding partner of the CBP. The CBP is genetically or chemically linked to the SpyCatcher. The SpyTag is displayed on the virion surface as a fusion to an engineered Sindbis virus envelope protein and is used as the anchorage site for SpyCatcher-linked CBP. Using this strategy, we created lentiviral vectors highly infectious toward HER2+ cancer cells. The ability to rapidly create cell-specific lentiviral vectors targeting a wide range of cell types should accelerate the development of custom lentiviral vectors for many research and clinical applications.","corpus_id":23106579,"score":0}],"string":"[\n {\n \"doc_id\": \"22366317\",\n \"title\": \"Peptide tag forming a rapid covalent bond to a protein, through engineering a bacterial adhesin.\",\n \"abstract\": \"Protein interactions with peptides generally have low thermodynamic and mechanical stability. Streptococcus pyogenes fibronectin-binding protein FbaB contains a domain with a spontaneous isopeptide bond between Lys and Asp. By splitting this domain and rational engineering of the fragments, we obtained a peptide (SpyTag) which formed an amide bond to its protein partner (SpyCatcher) in minutes. Reaction occurred in high yield simply upon mixing and amidst diverse conditions of pH, temperature, and buffer. SpyTag could be fused at either terminus or internally and reacted specifically at the mammalian cell surface. Peptide binding was not reversed by boiling or competing peptide. Single-molecule dynamic force spectroscopy showed that SpyTag did not separate from SpyCatcher until the force exceeded 1 nN, where covalent bonds snap. The robust reaction conditions and irreversible linkage of SpyTag shed light on spontaneous isopeptide bond formation and should provide a targetable lock in cells and a stable module for new protein architectures.\",\n \"corpus_id\": 13927823,\n \"score\": 2\n },\n {\n \"doc_id\": \"24056174\",\n \"title\": \"Plug-and-play pairing via defined divalent streptavidins.\",\n \"abstract\": \"Streptavidin is one of the most important hubs for molecular biology, either multimerizing biomolecules, bridging one molecule to another, or anchoring to a biotinylated surface/nanoparticle. Streptavidin has the advantage of rapid ultra-stable binding to biotin. However, the ability of streptavidin to bind four biotinylated molecules in a heterogeneous manner is often limiting. Here, we present an efficient approach to isolate streptavidin tetramers with two biotin-binding sites in a precise arrangement, cis or trans. We genetically modified specific subunits with negatively charged tags, refolded a mixture of monomers, and used ion-exchange chromatography to resolve tetramers according to the number and orientation of tags. We solved the crystal structures of cis-divalent streptavidin to 1.4Å resolution and trans-divalent streptavidin to 1.6Å resolution, validating the isolation strategy and explaining the behavior of the Dead streptavidin variant. cis- and trans-divalent streptavidins retained tetravalent streptavidin's high thermostability and low off-rate. These defined divalent streptavidins enabled us to uncover how streptavidin binding depends on the nature of the biotin ligand. Biotinylated DNA showed strong negative cooperativity of binding to cis-divalent but not trans-divalent streptavidin. A small biotinylated protein bound readily to cis and trans binding sites. We also solved the structure of trans-divalent streptavidin bound to biotin-4-fluorescein, showing how one ligand obstructs binding to an adjacent biotin-binding site. Using a hexaglutamate tag proved a more powerful way to isolate monovalent streptavidin, for ultra-stable labeling without undesired clustering. These forms of streptavidin allow this key hub to be used with a new level of precision, for homogeneous molecular assembly.\",\n \"corpus_id\": 9595969,\n \"score\": 2\n },\n {\n \"doc_id\": \"24873508\",\n \"title\": \"Dynamic supramolecular complexes constructed by orthogonal self-assembly.\",\n \"abstract\": \"CONSPECTUS: Supramolecular complexes, including various low-molecular-mass structures and large molecular aggregates that are assembled by reversible and highly directional noncovalent interactions, have attracted more and more attention due to their fascinating and unconventional chemical and physical properties that are different from those of traditional architectures encountered by covalently linked backbones. Supramolecular complexes are by nature dynamic architectures considering the reversibility of noncovalent interactions by which small molecular monomers can assemble into specific architectures that are able to be repeatably reorganized through the assembly/disassembly processes under certain environmental factors such as temperature, concentration, and solvent conditions. The construction of supramolecular complexes by orthogonal self-assembly with different types of highly specific, noninterfering interactions is currently attracting considerable interest since they not only can dynamically self-assemble, but also can be tuned by various external stimuli through addressing each type of noncovalent interaction separately. Therefore, these dynamic supramolecular complexes, especially with external responsiveness, represent the most outstanding candidates for the future development of functional and smart materials, and even mimic the assembling process of natural systems. In this Account, we will summarize the recent advances of dynamic supramolecular complexes constructed by orthogonal self-assembly in soluiton in two sections: (1) Construction strategies for supramolecular complexes based on orthogonal self-assembly, whose dynamic behaviors with external responsiveness were not experimentally investigated but potentially existed due to the intrinsic reversibility of noncovalent bonds; (2) dynamic behaviors of multiresponsive supramolecular complexes, which were experimentally reported to exhibit reversible multi-responsiveness to external stimuli. Dynamic nature is one of intrinsic properties of supramolecular complexes constructed by self-assembly. Therefore, in the first section, we will describe the dynamic self-assembly in the construction of supramolecular complexes, but will focus on their external responsive dynamic behaviors in the second section. In addition, considering that an increasing number of supramolecular complexes constructed by biological building blocks through bio-orthogonal assembly as mimics of biological systems have been reported in recent years, in the second section we will also present some typical examples on such special dynamic biological supramolecular complexes. The final part of this Account is devoted to foreseeing the rapid development of dynamic supramolecular complexes toward applications in functional and smart materials and fundamental questions facing dynamic supramolecular complexes in the future.\",\n \"corpus_id\": 5283533,\n \"score\": 2\n },\n {\n \"doc_id\": \"26787909\",\n \"title\": \"Programmable polyproteams built using twin peptide superglues.\",\n \"abstract\": \"Programmed connection of amino acids or nucleotides into chains introduced a revolution in control of biological function. Reacting proteins together is more complex because of the number of reactive groups and delicate stability. Here we achieved sequence-programmed irreversible connection of protein units, forming polyprotein teams by sequential amidation and transamidation. SpyTag peptide is engineered to spontaneously form an isopeptide bond with SpyCatcher protein. By engineering the adhesin RrgA from Streptococcus pneumoniae, we developed the peptide SnoopTag, which formed a spontaneous isopeptide bond to its protein partner SnoopCatcher with >99% yield and no cross-reaction to SpyTag/SpyCatcher. Solid-phase attachment followed by sequential SpyTag or SnoopTag reaction between building-blocks enabled iterative extension. Linear, branched, and combinatorial polyproteins were synthesized, identifying optimal combinations of ligands against death receptors and growth factor receptors for cancer cell death signal activation. This simple and modular route to programmable \\\"polyproteams\\\" should enable exploration of a new area of biological space.\",\n \"corpus_id\": 4687927,\n \"score\": 2\n },\n {\n \"doc_id\": \"28989685\",\n \"title\": \"Tuning SpyTag-SpyCatcher mutant pairs toward orthogonal reactivity encryption.\",\n \"abstract\": \"Genetically encoded covalent peptide tagging technology, such as the SpyTag-SpyCatcher reaction, has emerged as a unique way to do chemistry with proteins. Herein, we report the reactivity engineering of SpyTag-SpyCatcher mutant pairs and show that distinct reactivity can be encrypted for the same reaction based on protein sequences of high similarity. Valuable features, including high selectivity, inverse temperature dependence and (nearly) orthogonal reactivity, could be achieved based on as few as three mutations. This demonstrates the robustness of the SpyTag-SpyCatcher reaction and the plasticity of its sequence specificity, pointing to a family of engineered protein chemistry tools.\",\n \"corpus_id\": 23949264,\n \"score\": 2\n },\n {\n \"doc_id\": \"29662234\",\n \"title\": \"Modular assembly of proteins on nanoparticles.\",\n \"abstract\": \"Generally, the high diversity of protein properties necessitates the development of unique nanoparticle bio-conjugation methods, optimized for each different protein. Here we describe a universal bio-conjugation approach which makes use of a new recombinant fusion protein combining two distinct domains. The N-terminal part is Glutathione S-Transferase (GST) from Schistosoma japonicum, for which we identify and characterize the remarkable ability to bind gold nanoparticles (GNPs) by forming gold-sulfur bonds (Au-S). The C-terminal part of this multi-domain construct is the SpyCatcher from Streptococcus pyogenes, which provides the ability to capture recombinant proteins encoding a SpyTag. Here we show that SpyCatcher can be immobilized covalently on GNPs through GST without the loss of its full functionality. We then show that GST-SpyCatcher activated particles are able to covalently bind a SpyTag modified protein by simple mixing, through the spontaneous formation of an unusual isopeptide bond.\",\n \"corpus_id\": 4901820,\n \"score\": 2\n },\n {\n \"doc_id\": \"19259577\",\n \"title\": \"Supramolecular self-assembly of dendrimers containing orthogonal binding motifs.\",\n \"abstract\": \"Two orthogonal non-covalent binding sites, namely metal-ligand complexation of Ru and bipyridine and intermolecular hydrogen bonding, facilitate the self-assembly of a new type of supramolecular dendrimers.\",\n \"corpus_id\": 262929368,\n \"score\": 1\n },\n {\n \"doc_id\": \"19425108\",\n \"title\": \"Engineering monomeric streptavidin and its ligands with infinite affinity in binding but reversibility in interaction.\",\n \"abstract\": \"Natural tetrameric streptavidin captures and immobilizes biotinylated molecules with ultra-tight binding (K(d) approximately 10(-13) to 10(-14) M). In contrast, engineered monomeric streptavidin offers reversible binding (K(d) approximately 10(-7) M). To develop an ideal engineered streptavidin which possesses both the immobilization capability of the natural streptavidin and the reversible interaction reactivity of the monomeric streptavidin, a pair of engineered biomaterials was designed through molecular modeling. This system consists of two recombinant components: an engineered monomeric streptavidin M6, which has a cysteine residue (C118) near the biotin binding site, and a cysteine containing biotinylation tag. Interactions between M6 and the biotinylated peptide tag go through a two-stage process (capture and immobilization) to generate a covalently linked complex. Biotinylation is essential in the capture stage. Once the biotin moiety in the biotinylated tag is captured by M6, the biotinylated tag can fold back and rotate on the surface of the complex with the biotinylated lysine in the peptide tag as the axis until the formationof a disulfide bond. Consequently, cysteine residue in different positions flanking the biotin residue in the biotinylation tag can successfully form a disulfide bond with M6. Intermolecular disulfide bond formation between M6 and the tag containing protein offers the immobilization capability to M6. In the presence of reducing agent and biotin, bound ligands can be dissociated. This system has the potential to extend the biotin-streptavidin technology to develop reusable biosensor/protein chips and bioreactors.\",\n \"corpus_id\": 26377763,\n \"score\": 1\n },\n {\n \"doc_id\": \"20383133\",\n \"title\": \"A streptavidin variant with slower biotin dissociation and increased mechanostability.\",\n \"abstract\": \"Streptavidin binds biotin conjugates with exceptional stability but dissociation does occur, limiting its use in imaging, DNA amplification and nanotechnology. We identified a mutant streptavidin, traptavidin, with more than tenfold slower biotin dissociation, increased mechanical strength and improved thermostability; this resilience should enable diverse applications. FtsK, a motor protein important in chromosome segregation, rapidly displaced streptavidin from biotinylated DNA, whereas traptavidin resisted displacement, indicating the force generated by Ftsk translocation.\",\n \"corpus_id\": 2988461,\n \"score\": 1\n },\n {\n \"doc_id\": \"20462407\",\n \"title\": \"Binary polypeptide system for permanent and oriented protein immobilization.\",\n \"abstract\": \"BACKGROUND: Many techniques in molecular biology, clinical diagnostics and biotechnology rely on binary affinity tags. The existing tags are based on either small molecules (e.g., biotin/streptavidin or glutathione/GST) or peptide tags (FLAG, Myc, HA, Strep-tag and His-tag). Among these, the biotin-streptavidin system is most popular due to the nearly irreversible interaction of biotin with the tetrameric protein, streptavidin. The major drawback of the stable biotin-streptavidin system, however, is that neither of the two tags can be added to a protein of interest via recombinant means (except for the Strep-tag case) leading to the requirement for chemical coupling. RESULTS: Here we report a new immobilization system which utilizes two monomeric polypeptides which self-assemble to produce non-covalent yet nearly irreversible complex which is stable in strong detergents, chaotropic agents, as well as in acids and alkali. Our system is based on the core region of the tetra-helical bundle known as the SNARE (soluble N-ethylmaleimide-sensitive factor attachment protein receptor) complex. This irreversible protein attachment system (IPAS) uses either a shortened syntaxin helix and fused SNAP25-synaptobrevin or a fused syntaxin-synaptobrevin and SNAP25 allowing a two-component system suitable for recombinant protein tagging, capture and immobilization. We also show that IPAS is suitable for use with traditional beads and chromatography, planar surfaces and Biacore, gold nanoparticles and for protein-protein interaction in solution. CONCLUSIONS: IPAS offers an alternative to chemical cross-linking, streptavidin-biotin system and to traditional peptide affinity tags and can be used for a wide range of applications in nanotechnology and molecular sciences.\",\n \"corpus_id\": 3040277,\n \"score\": 1\n },\n {\n \"doc_id\": \"21241253\",\n \"title\": \"How the biotin-streptavidin interaction was made even stronger: investigation via crystallography and a chimaeric tetramer.\",\n \"abstract\": \"The interaction between SA (streptavidin) and biotin is one of the strongest non-covalent interactions in Nature. SA is a widely used tool and a paradigm for protein-ligand interactions. We previously developed a SA mutant, termed Tr (traptavidin), possessing a 10-fold lower off-rate for biotin, with increased mechanical and thermal stability. In the present study, we determined the crystal structures of apo-Tr and biotin-Tr at 1.5 Å resolution. In apo-SA the loop (L3/4), near biotin's valeryl tail, is typically disordered and open, but closes upon biotin binding. In contrast, L3/4 was shut in both apo-Tr and biotin-Tr. The reduced flexibility of L3/4 and decreased conformational change on biotin binding provide an explanation for Tr's reduced biotin off- and on-rates. L3/4 includes Ser45, which forms a hydrogen bond to biotin consistently in Tr, but erratically in SA. Reduced breakage of the biotin-Ser45 hydrogen bond in Tr is likely to inhibit the initiating event in biotin's dissociation pathway. We generated a Tr with a single biotin-binding site rather than four, which showed a simi-larly low off-rate, demonstrating that Tr's low off-rate was governed by intrasubunit effects. Understanding the structural features of this tenacious interaction may assist the design of even stronger affinity tags and inhibitors.\",\n \"corpus_id\": 28492457,\n \"score\": 1\n },\n {\n \"doc_id\": \"21551057\",\n \"title\": \"Scaffold proteins: hubs for controlling the flow of cellular information.\",\n \"abstract\": \"The spatial and temporal organization of molecules within a cell is critical for coordinating the many distinct activities carried out by the cell. In an increasing number of biological signaling processes, scaffold proteins have been found to play a central role in physically assembling the relevant molecular components. Although most scaffolds use a simple tethering mechanism to increase the efficiency of interaction between individual partner molecules, these proteins can also exert complex allosteric control over their partners and are themselves the target of regulation. Scaffold proteins offer a simple, flexible strategy for regulating selectivity in pathways, shaping output behaviors, and achieving new responses from preexisting signaling components. As a result, scaffold proteins have been exploited by evolution, pathogens, and cellular engineers to reshape cellular behavior.\",\n \"corpus_id\": 6512196,\n \"score\": 1\n },\n {\n \"doc_id\": \"22102445\",\n \"title\": \"Nanomechanics of streptavidin hubs for molecular materials.\",\n \"abstract\": \"A new strategy is reported for creating protein-based nanomaterials by genetically fusing large polypeptides to monomeric streptavidin and exploiting the propensity of streptavidin monomers(SM) to self-assemble into stable tetramers. We have characterized the mechanical properties of streptavidin-linked structures and measured, for the first time, the mechanical strength of streptavidin tetramers themselves. Using streptavidin tetramers as molecular hubs offers a unique opportunity to create a variety of well-defined, self-assembled protein-based (nano)materials with unusual mechanical properties.\",\n \"corpus_id\": 205242517,\n \"score\": 1\n },\n {\n \"doc_id\": \"22170585\",\n \"title\": \"Advances in switchable supramolecular nanoassemblies.\",\n \"abstract\": \"Supramolecular nanoassemblies are gaining increasing importance as promising new materials with considerable potential for novel and promising applications. Within supramolecular nanoassemblies the connectivity of the monomeric units is based on reversible noncovalent interactions, like van der Waals interactions, hydrogen bonding, or ionic interactions. As the strength of these interactions depends on the molecular surrounding, the formation of nanoassemblies in principle can be controlled externally by changing the environment and/or the molecular shape of the underlying monomer. This way it is not only possible to switch the self-assembly on or off, but also to change between different aggregation states. In this minireview we present some recent selected approaches to supramolecular stimuli-responsive nanoassemblies.\",\n \"corpus_id\": 205595932,\n \"score\": 1\n },\n {\n \"doc_id\": \"22806584\",\n \"title\": \"Stable, high-affinity streptavidin monomer for protein labeling and monovalent biotin detection.\",\n \"abstract\": \"The coupling between the quaternary structure, stability and function of streptavidin makes it difficult to engineer a stable, high affinity monomer for biotechnology applications. For example, the binding pocket of streptavidin tetramer is comprised of residues from multiple subunits, which cannot be replicated in a single domain protein. However, rhizavidin from Rhizobium etli was recently shown to bind biotin with high affinity as a dimer without the hydrophobic tryptophan lid donated by an adjacent subunit. In particular, the binding site of rhizavidin uses residues from a single subunit to interact with bound biotin. We therefore postulated that replacing the binding site residues of streptavidin monomer with corresponding rhizavidin residues would lead to the design of a high affinity monomer useful for biotechnology applications. Here, we report the construction and characterization of a structural monomer, mSA, which combines the streptavidin and rhizavidin sequences to achieve optimized biophysical properties. First, the biotin affinity of mSA (K(d) = 2.8 nM) is the highest among nontetrameric streptavidin, allowing sensitive monovalent detection of biotinylated ligands. The monomer also has significantly higher stability (T(m) = 59.8 °C) and solubility than all other previously engineered monomers to ensure the molecule remains folded and functional during its application. Using fluorescence correlation spectroscopy, we show that mSA binds biotinylated targets as a monomer. We also show that the molecule can be used as a genetic tag to introduce biotin binding capability to a heterologous protein. For example, recombinantly fusing the monomer to a cell surface receptor allows direct labeling and imaging of transfected cells using biotinylated fluorophores. A stable and functional streptavidin monomer, such as mSA, should be a useful reagent for designing novel detection systems based on monovalent biotin interaction.\",\n \"corpus_id\": 5140258,\n \"score\": 1\n },\n {\n \"doc_id\": \"22984964\",\n \"title\": \"Kinetic stability of the streptavidin-biotin interaction enhanced in the gas phase.\",\n \"abstract\": \"Results of the first detailed study of the structure and kinetic stability of the model high-affinity protein-ligand interaction between biotin (B) and the homotetrameric protein complex streptavidin (S(4)) in the gas phase are described. Collision cross sections (Ω) measured for protonated gaseous ions of free and ligand-bound truncated (residues 13-139) wild-type (WT) streptavidin, i.e., S(4)(n+) and (S(4)+4B)(n+) at charge states n = 12-16, were found to be independent of charge state and in agreement (within 10%) with values estimated for crystal structures reported for S(4) and (S(4)+4B). These results suggest that significant structural changes do not occur upon transfer of the complexes from solution to the gas phase by electrospray ionization. Temperature-dependent rate constants were measured for the loss of B from the protonated (S(4)+4B)(n+) ions. Over the temperature range investigated, the kinetic stability increases with decreasing charge state, from n = 16 to 13, but is indistinguishable for n = 12 and 13. A comparison of the activation energies (E(a)) measured for the loss of B from the (S(4)+4B)(13+) ions composed of WT streptavidin and five binding site mutants (Trp79Phe, Trp108Phe, Trp120Phe, Ser27Ala, and Tyr43Ala) suggests that at least some of the specific intermolecular interactions are preserved in the gas phase. The results of molecular dynamics simulations performed on WT (S(4)+4B)(12+) ions with different charge configurations support this conclusion. The most significant finding of this study is that the gaseous WT (S(4)+4B)(n+) ions at n = 12-14, owing to a much larger E(a) (by as much as 13 kcal mol(-1)) for the loss of B, are dramatically more stable kinetically at 25 °C than the (S(4)+4B) complex in aqueous neutral solution. The differences in E(a) values measured for the gaseous (S(4)+4B)(n+) ions and solvated (S(4)+4B) complex can be largely accounted for by a late dissociative transition state and the rehydration of B and the protein binding cavity in solution.\",\n \"corpus_id\": 207085543,\n \"score\": 1\n },\n {\n \"doc_id\": \"22989197\",\n \"title\": \"A new modular approach to nanoassembly: stable and addressable DNA nanoconstructs via orthogonal click chemistries.\",\n \"abstract\": \"Thermodynamic instability is a problem when assembling and purifying complex DNA nanostructures formed by hybridization alone. To address this issue, we have used photochemical fixation and orthogonal copper-free, ring-strain-promoted, click chemistry for the synthesis of dimeric, trimeric, and oligomeric modular DNA scaffolds from cyclic, double-stranded, 80-mer DNA nanoconstructs. This particular combination of orthogonal click reactions was more effective for nanoassembly than others explored. The complex nanostructures are stable to heat and denaturation agents and can therefore be purified and characterized. They are addressable in a sequence-specific manner by triplex formation, and they can be reversibly and selectively deconstructed. Nanostructures utilizing this orthogonal, chemical fixation methodology can be used as building blocks for nanomachines and functional DNA nanoarchitectures.\",\n \"corpus_id\": 10768662,\n \"score\": 1\n },\n {\n \"doc_id\": \"23282586\",\n \"title\": \"Orthogonality in organic, polymer, and supramolecular chemistry: from Merrifield to click chemistry.\",\n \"abstract\": \"The concept of orthogonality has been applied to many areas of chemistry, ranging from wave functions to chromatography. But it was Barany and Merrifield's orthogonal protecting group strategy that paved the way for solid phase peptide syntheses, other important classes of biomaterials such as oligosaccharides and oligonucleotides, and ultimately to a term in widespread usage that is focused on chemical reactivity and binding selectivity. The orthogonal protection strategy has been extended to the development of orthogonal activation, and recently the click reaction, for streamlining organic synthesis. The click reaction and its variants are considered orthogonal as the components react together in high yield and in the presence of many other functional groups. Likewise, supramolecular building blocks can also be orthogonal, thereby enabling programmed self-assembly, a superb strategy to create complex architectures. Overall, orthogonal reactions and supramolecular interactions have dramatically improved the syntheses, the preparation of functional materials, and the self-assembly of nanoscale structures.\",\n \"corpus_id\": 3027284,\n \"score\": 1\n },\n {\n \"doc_id\": \"23670729\",\n \"title\": \"Structure-based engineering of streptavidin monomer with a reduced biotin dissociation rate.\",\n \"abstract\": \"We recently reported the engineering of monomeric streptavidin, mSA, corresponding to one subunit of wild type (wt) streptavidin tetramer. The monomer was designed by homology modeling, in which the streptavidin and rhizavidin sequences were combined to engineer a high affinity binding pocket containing residues from a single subunit only. Although mSA is stable and binds biotin with nanomolar affinity, its fast off rate (koff ) creates practical challenges during applications. We obtained a 1.9 Å crystal structure of mSA bound to biotin to understand their interaction in detail, and used the structure to introduce targeted mutations to improve its binding kinetics. To this end, we compared mSA to shwanavidin, which contains a hydrophobic lid containing F43 in the binding pocket and binds biotin tightly. However, the T48F mutation in mSA, which introduces a comparable hydrophobic lid, only resulted in a modest 20-40% improvement in the measured koff . On the other hand, introducing the S25H mutation near the bicyclic ring of bound biotin increased the dissociation half life (t½ ) from 11 to 83 min at 20°C. Molecular dynamics (MD) simulations suggest that H25 stabilizes the binding loop L3,4 by interacting with A47, and protects key intermolecular hydrogen bonds by limiting solvent entry into the binding pocket. Concurrent T48F or T48W mutation clashes with H25 and partially abrogates the beneficial effects of H25. Taken together, this study suggests that stabilization of the binding loop and solvation of the binding pocket are important determinants of the dissociation kinetics in mSA.\",\n \"corpus_id\": 206407422,\n \"score\": 1\n },\n {\n \"doc_id\": \"23964715\",\n \"title\": \"Controlling macromolecular topology with genetically encoded SpyTag-SpyCatcher chemistry.\",\n \"abstract\": \"Control of molecular topology constitutes a fundamental challenge in macromolecular chemistry. Here we describe the synthesis and characterization of artificial elastin-like proteins (ELPs) with unconventional nonlinear topologies including circular, tadpole, star, and H-shaped proteins using genetically encoded SpyTag-SpyCatcher chemistry. SpyTag is a short polypeptide that binds its protein partner SpyCatcher and forms isopeptide bonds under physiological conditions. Sequences encoding SpyTag and SpyCatcher can be strategically placed into ELP genes to direct post-translational topological modification in situ. Placement of SpyTag at the N-terminus and SpyCatcher at the C-terminus directs formation of circular ELPs. Induction of expression at 16 °C with 10 μM IPTG yields 80% monomeric cyclic protein. When SpyTag is placed in the middle of the chain, it exhibits an even stronger tendency toward cyclization, yielding up to 94% monomeric tadpole proteins. Telechelic ELPs containing either SpyTag or SpyCatcher can be expressed, purified, and then coupled spontaneously upon mixing in vitro. Block proteins, 3-arm or 4-arm star proteins, and H-shaped proteins have been prepared, with the folded CnaB2 domain that results from the SpyTag-SpyCatcher reaction as the molecular core or branch junction. The modular character of the SpyTag-SpyCatcher strategy should make it useful for preparing nonlinear macromolecules of diverse sequence and structure.\",\n \"corpus_id\": 262965573,\n \"score\": 1\n },\n {\n \"doc_id\": \"24161952\",\n \"title\": \"Structural analysis and optimization of the covalent association between SpyCatcher and a peptide Tag.\",\n \"abstract\": \"Peptide tagging is a key strategy for observing and isolating proteins. However, the interactions of proteins with peptides are nearly all rapidly reversible. Proteins tagged with the peptide SpyTag form an irreversible covalent bond to the SpyCatcher protein via a spontaneous isopeptide linkage, thereby offering a genetically encoded way to create peptide interactions that resist force and harsh conditions. Here, we determined the crystal structure of the reconstituted covalent complex of SpyTag and SpyCatcher at 2.1Å resolution. The structure showed the expected reformation of the β-sandwich domain seen in the parental streptococcal adhesin, but flanking sequences at both N- and C-termini of SpyCatcher were disordered. In addition, only 10 out of 13 amino acids of the SpyTag peptide were observed to interact with SpyCatcher, pointing to specific contacts important for rapid split protein reconstitution. Based on these structural insights, we expressed a range of SpyCatcher variants and identified a minimized SpyCatcher, 32 residues shorter, that maintained rapid reaction with SpyTag. Together, these results give insight into split protein β-strand complementation and enhance a distinct approach to ultrastable molecular interaction.\",\n \"corpus_id\": 42121602,\n \"score\": 1\n },\n {\n \"doc_id\": \"24639550\",\n \"title\": \"SpyLigase peptide-peptide ligation polymerizes affibodies to enhance magnetic cancer cell capture.\",\n \"abstract\": \"Individual proteins can now often be modified with atomic precision, but there are still major obstacles to connecting proteins into larger assemblies. To direct protein assembly, ideally, peptide tags would be used, providing the minimal perturbation to protein function. However, binding to peptides is generally weak, so assemblies are unstable over time and disassemble with force or harsh conditions. We have recently developed an irreversible protein-peptide interaction (SpyTag/SpyCatcher), based on a protein domain from Streptococcus pyogenes, that locks itself together via spontaneous isopeptide bond formation. Here we develop irreversible peptide-peptide interaction, through redesign of this domain and genetic dissection into three parts: a protein domain termed SpyLigase, which now ligates two peptide tags to each other. All components expressed efficiently in Escherichia coli and peptide tags were reactive at the N terminus, at the C terminus, or at internal sites. Peptide-peptide ligation enabled covalent and site-specific polymerization of affibodies or antibodies against the tumor markers epidermal growth factor receptor (EGFR) and HER2. Magnetic capture of circulating tumor cells (CTCs) is one of the most promising approaches to improve cancer prognosis and management, but CTC capture is limited by inefficient recovery of cells expressing low levels of tumor antigen. SpyLigase-assembled protein polymers made possible the isolation of cancerous cells expressing lower levels of tumor antigen and should have general application in enhancing molecular capture.\",\n \"corpus_id\": 7349100,\n \"score\": 1\n },\n {\n \"doc_id\": \"24817566\",\n \"title\": \"SpyTag/SpyCatcher cyclization confers resilience to boiling on a mesophilic enzyme.\",\n \"abstract\": \"SpyTag is a peptide that spontaneously forms an amide bond with its protein partner SpyCatcher. SpyTag was fused at the N terminus of β-lactamase and SpyCatcher at the C terminus so that the partners could react to lock together the termini of the enzyme. The wild-type enzyme aggregates above 37 °C, with irreversible loss of activity. Cyclized β-lactamase was soluble even after heating at 100 °C; after cooling, the catalytic activity was restored. SpyTag/SpyCatcher cyclization led to a much larger increase in stability than that achieved through point mutation or alternative approaches to cyclization. Cyclized dihydrofolate reductase was similarly resilient. Analyzing unfolding through calorimetry indicated that cyclization did not increase the unfolding temperature but rather facilitated refolding after thermal stress. SpyTag/SpyCatcher sandwiching represents a simple and efficient route to enzyme cyclization, with potential to greatly enhance the robustness of biocatalysts.\",\n \"corpus_id\": 205380547,\n \"score\": 1\n },\n {\n \"doc_id\": \"24905869\",\n \"title\": \"Engineering orthogonality in supramolecular polymers: from simple scaffolds to complex materials.\",\n \"abstract\": \"Owing to the mastery exhibited by Nature in integrating both covalent and noncovalent interactions in a highly efficient manner, the quest to construct polymeric systems that rival not only the precision and fidelity but also the structure of natural systems has remained a daunting challenge. Supramolecular chemists have long endeavored to control the interplay between covalent and noncovalent bond formation, so as to examine and fully comprehend how function is predicated on self-assembly. The ability to reliably control polymer self-assembly is essential to generate \\\"smart\\\" materials and has the potential to tailor polymer properties (i.e., viscosity, electronic properties) through fine-tuning the noncovalent interactions that comprise the polymer architecture. In this context, supramolecular polymers have a distinct advantage over fully covalent systems in that they are dynamically modular, since noncovalent recognition motifs can be engineered to either impart a desired functionality within the overall architecture or provide a designed bias for the self-assembly process. In this Account, we describe engineering principles being developed and pursued by our group that exploit the orthogonal nature of noncovalent interactions, such as hydrogen bonding, metal coordination, and Coulombic interactions, to direct the self-assembly of functionalized macromolecules, resulting in the formation of supramolecular polymers. To begin, we describe our efforts to fabricate a modular poly(norbornene)-based scaffold via ring-opening metathesis polymerization (ROMP), wherein pendant molecular recognition elements based upon nucleobase-mimicking elements (e.g., thymine, diaminotriazine) or SCS-Pd(II) pincer were integrated within covalent monofunctional or symmetrically functionalized polymers. The simple polymer backbones exhibited reliable self-assembly with complementary polymers or small molecules. Within these systems, we applied successful protecting group strategies and template polymerizations to enhance the control afforded by ROMP. Main-chain-functionalized alternating block polymers based upon SCS-Pd(II) pincer-pyridine motifs were achieved through the combined exploitation of bimetallic initiators and supramolecularly functionalized terminators. Our initial design principles led to the successful fabrication of both main-chain- and side-chain-functionalized poly(norbornenes) via ROMP. Utilizing all of these techniques in concert led to engineering orthogonality while achieving complexity through the installation of multiple supramolecular motifs within the side chain, main chain, or both in our polymer systems. The exploitation and modification of design principles based upon functional ROMP initiators and terminators has resulted in the first synthesis of main-chain heterotelechelic polymers that self-assemble into A/B/C supramolecular triblock polymers composed of orthogonal cyanuric acid-Hamilton wedge and SCS-Pd(II) pincer-pyridine motifs. Furthermore, supramolecular A/B/A triblock copolymers were realized through the amalgamation of functionalized monomers, ROMP initiators, and terminators. To date, this ROMP-fabricated system represents the only known method to afford polymer main chains and side chains studded with orthogonal motifs. We end by discussing the impetus to attain functional materials via orthogonal self-assembly. Collectively, our studies suggest that combining covalent and noncovalent bonds in a well-defined and precise manner is an essential design element to achieve complex architectures. The results discussed in this Account illustrate the finesse associated with engineering orthogonal interactions within supramolecular systems and are considered essential steps toward developing complex biomimetic materials with high precision and fidelity.\",\n \"corpus_id\": 37347553,\n \"score\": 1\n },\n {\n \"doc_id\": \"25082796\",\n \"title\": \"\\\"Plug-and-go\\\" strategy to manipulate streptavidin valencies.\",\n \"abstract\": \"The streptavidin-biotin set is one of the most widely utilized conjugation pairs in biotechnological applications. The tetravalent nature of streptavidin and its homologues, however, tends to result in such undesirable complications as cross-linking or ill-defined stoichiometry. Here, we describe a mutagenesis-free strategy to manipulate the valencies of wild-type streptavidin that only requires commercially available reagents. The basic idea is simple: one obtains the desired streptavidin valency by blocking off unwanted binding sites using ancillary biotin (\\\"plug\\\"); this way, the extraordinary fM-biotin-binding affinity is fully retained for the remaining sites in streptavidin. In the present implementation, the ancillary biotin is attached to an auxiliary separation handle, negatively charged DNA or His-tagged protein, via a photochemically or enzymatically cleavable linker. Mixing streptavidin with the ancillary biotin construct produces a distribution of streptavidin valencies. The subsequent chromatographic separation readily isolates the construct of desired streptavidin valency, and the auxiliary handles are easily removed afterward (\\\"go\\\"). We demonstrate how this \\\"plug-and-go\\\" strategy allows a precise control for the compositions of streptavidin-biotin conjugates at the single-molecule level. This low-entry-barrier protocol could further expand the application scope of the streptavidin technology.\",\n \"corpus_id\": 31997189,\n \"score\": 1\n },\n {\n \"doc_id\": \"25168413\",\n \"title\": \"Superglue from bacteria: unbreakable bridges for protein nanotechnology.\",\n \"abstract\": \"Biotechnology is often limited by weak interactions. We suggest that an ideal interaction between proteins would be covalent, specific, require addition of only a peptide tag to the protein of interest, and form under a wide range of conditions. Here we summarize peptide tags that are able to form spontaneous amide bonds, based on harnessing reactions of adhesion proteins from the bacterium Streptococcus pyogenes. These include the irreversible peptide-protein interaction of SpyTag with SpyCatcher, as well as irreversible peptide-peptide interactions via SpyLigase. We describe existing applications, including polymerization to enhance cancer cell capture, assembly of living biomaterial, access to diverse protein shapes, and improved enzyme resilience. We also indicate future opportunities for resisting biological force and extending the scope of protein nanotechnology.\",\n \"corpus_id\": 22873894,\n \"score\": 1\n },\n {\n \"doc_id\": \"25357135\",\n \"title\": \"Programming supramolecular biohybrids as precision therapeutics.\",\n \"abstract\": \"CONSPECTUS: Chemical programming of macromolecular structures to instill a set of defined chemical properties designed to behave in a sequential and precise manner is a characteristic vision for creating next generation nanomaterials. In this context, biopolymers such as proteins and nucleic acids provide an attractive platform for the integration of complex chemical design due to their sequence specificity and geometric definition, which allows accurate translation of chemical functionalities to biological activity. Coupled with the advent of amino acid specific modification techniques, \\\"programmable\\\" areas of a protein chain become exclusively available for any synthetic customization. We envision that chemically reprogrammed hybrid proteins will bridge the vital link to overcome the limitations of synthetic and biological materials, providing a unique strategy for tailoring precision therapeutics. In this Account, we present our work toward the chemical design of protein- derived hybrid polymers and their supramolecular responsiveness, while summarizing their impact and the advancement in biomedicine. Proteins, in their native form, represent the central framework of all biological processes and are an unrivaled class of macromolecular drugs with immense specificity. Nonetheless, the route of administration of protein therapeutics is often vastly different from Nature's biosynthesis. Therefore, it is imperative to chemically reprogram these biopolymers to direct their entry and activity toward the designated target. As a consequence of the innate structural regularity of proteins, we show that supramolecular interactions facilitated by stimulus responsive chemistry can be intricately designed as a powerful tool to customize their functions, stability, activity profiles, and transportation capabilities. From another perspective, a protein in its denatured, unfolded form serves as a monodispersed, biodegradable polymer scaffold decorated with functional side chains available for grafting with molecules of interest. Additionally, we are equipped with analytical tools to map the fingerprint of the protein chain, directly elucidating the structure at the molecular level. Contrary to conventional polymers, these biopolymers facilitate a more systematic avenue to investigate engineered macromolecules, with greater detail and accuracy. In this regard, we focus on denaturing serum albumin, an abundant blood protein, and exploit its peptidic array of functionalities to program supramolecular architectures for bioimaging, drug and gene delivery. Ultimately, we seek to assimilate the evolutionary advantage of these protein based biopolymers with the limitless versatility of synthetic chemistry to merge the best of both worlds.\",\n \"corpus_id\": 5073559,\n \"score\": 1\n },\n {\n \"doc_id\": \"26020143\",\n \"title\": \"Protein-induced supramolecular disassembly of amphiphilic polypeptide nanoassemblies.\",\n \"abstract\": \"Mimicking noncovalent interaction based processes in nature has been an important goal of supramolecular chemistry. Here, we report on amphiphilic polypeptides that self-assemble to form nanoscale supramolecular assemblies and are programmed to disassemble in response to a specific protein. Benzenesulfonamide and carbonic anhydrase have been chosen as the ligand and protein, respectively, to demonstrate this possibility. Since the amphiphilic nanoassembly sequesters hydrophobic guest molecules, the protein-specific disassembly event provides a protein-sensitive molecular release as well. We envision that the binding induced disassembly and guest release might open up new opportunities for the next generation of supramolecular assemblies for protein-specific delivery and diagnostics.\",\n \"corpus_id\": 207156156,\n \"score\": 1\n },\n {\n \"doc_id\": \"26278701\",\n \"title\": \"Synthetic Biology: A New Tool for the Trade.\",\n \"abstract\": \"Protein-protein interactions are fundamental to many biological processes. Yet, the weak and transient noncovalent bonds that characterize most protein-protein interactions found in nature impose limits on many bioengineering experiments. Here, a new class of genetically encodable peptide-protein pairs--isopeptag-N/pilin-N, isopeptag/pilin-C, and SpyTag/SpyCatcher--that interact through autocatalytic intermolecular isopeptide bond formation is described. Reactions between peptide-protein pairs are specific, robust, orthogonal, and able to proceed under most biologically relevant conditions both in vitro and in vivo. As fusion constructs, they provide a handle on molecules of interest, both organic and inorganic, that can be grasped with an iron grip. Such stable interactions provide robust post-translational control over biological processes and open new opportunities in synthetic biology for engineering programmable and self-assembling protein nanoarchitectures.\",\n \"corpus_id\": 44982914,\n \"score\": 1\n },\n {\n \"doc_id\": \"26517567\",\n \"title\": \"Secrets of a covalent interaction for biomaterials and biotechnology: SpyTag and SpyCatcher.\",\n \"abstract\": \"SpyTag is a short peptide that forms an isopeptide bond upon encountering its protein partner SpyCatcher. This covalent peptide interaction is a simple and powerful tool for bioconjugation and extending what protein architectures are accessible. Here we review the origin and mechanism of SpyTag/SpyCatcher, focusing on recent innovative applications. Ligation of targeting-antibody with antigen provided a simple route to vaccine generation. SpyRings, from head-to-tail cyclisation, gave major enhancements in enzyme resilience. Linking multiple SpyCatchers gave dendrimers for T-cell activation or Spy networks forming hydrogels for stem cell culture. Synthetic biology applications include integrating amyloid biomaterials with living bacteria, for irreversible derivatisation of biofilms with enzymes or nanoparticles. We also discuss further opportunities to apply and enhance SpyTag/SpyCatcher technology.\",\n \"corpus_id\": 9799436,\n \"score\": 1\n },\n {\n \"doc_id\": \"26781591\",\n \"title\": \"Plug-and-Display: decoration of Virus-Like Particles via isopeptide bonds for modular immunization.\",\n \"abstract\": \"Virus-like particles (VLPs) are non-infectious self-assembling nanoparticles, useful in medicine and nanotechnology. Their repetitive molecularly-defined architecture is attractive for engineering multivalency, notably for vaccination. However, decorating VLPs with target-antigens by genetic fusion or chemical modification is time-consuming and often leads to capsid misassembly or antigen misfolding, hindering generation of protective immunity. Here we establish a platform for irreversibly decorating VLPs simply by mixing with protein antigen. SpyCatcher is a genetically-encoded protein designed to spontaneously form a covalent bond to its peptide-partner SpyTag. We expressed in E. coli VLPs from the bacteriophage AP205 genetically fused to SpyCatcher. We demonstrated quantitative covalent coupling to SpyCatcher-VLPs after mixing with SpyTag-linked to malaria antigens, including CIDR and Pfs25. In addition, we showed coupling to the VLPs for peptides relevant to cancer from epidermal growth factor receptor and telomerase. Injecting SpyCatcher-VLPs decorated with a malarial antigen efficiently induced antibody responses after only a single immunization. This simple, efficient and modular decoration of nanoparticles should accelerate vaccine development, as well as other applications of nanoparticle devices.\",\n \"corpus_id\": 1730573,\n \"score\": 1\n },\n {\n \"doc_id\": \"27034717\",\n \"title\": \"Enhanced thermal stability of lichenase from Bacillus subtilis 168 by SpyTag/SpyCatcher-mediated spontaneous cyclization.\",\n \"abstract\": \"BACKGROUND: SpyTag is a peptide that can form an irreversible covalent linkage to its 12 kDa partner SpyCatcher via a spontaneous isopeptide bond. Herein, we fused SpyTag at the N-terminal of lichenase and SpyCatcher at C-terminal so that the termini of lichenase were locked together by the covalent interaction between the partners. In addition, an elastin-like polypeptides tag was subsequently attached to the C-terminus of SpyCatcher, thereby facilitating the non-chromatographic purification of cyclized lichenase. RESULTS: The study showed that the optimum temperature of the cyclized lichenase was about 5 °C higher in comparison to its linear counterpart. Moreover, nearly 80 % of the cyclized lichenase activities were retained after 100 °C exposure, whereas the linear form lost almost all of its activities. Therefore, the cyclized variant displayed a significantly higher thermal stability as temperature elevated and was resistant to hyperthermal denaturation. Besides, the Km value of the cyclized lichenase (7.58 ± 0.92 mg/mL) was approximately 1.7-fold lower than that of the linear one (12.96 ± 1.93 mg/mL), indicating a higher affinity with substrates. CONCLUSIONS: This new SpyTag/SpyCatcher cyclization strategy is deemed as a generalized reference for enhancing enzyme stability and can be effectively customized to the cyclization of various enzymes, hence a tremendous potential for successful application in the biocatalytic conversion of biomass to produce fuels and chemicals.\",\n \"corpus_id\": 15396810,\n \"score\": 1\n },\n {\n \"doc_id\": \"27117585\",\n \"title\": \"Bacterial superglue enables easy development of efficient virus-like particle based vaccines.\",\n \"abstract\": \"BACKGROUND: Virus-like particles (VLPs) represent a significant advance in the development of subunit vaccines, combining high safety and efficacy. Their particulate nature and dense repetitive subunit organization makes them ideal scaffolds for display of vaccine antigens. Traditional approaches for VLP-based antigen display require labor-intensive trial-and-error optimization, and often fail to generate dense antigen display. Here we utilize the split-intein (SpyTag/SpyCatcher) conjugation system to generate stable isopeptide bound antigen-VLP complexes by simply mixing of the antigen and VLP components. RESULTS: Genetic fusion of SpyTag or SpyCatcher to the N-terminus and/or C-terminus of the Acinetobacter phage AP205 capsid protein resulted in formation of stable, nonaggregated VLPs expressing one SpyCatcher, one SpyTag or two SpyTags per capsid protein. Mixing of spy-VLPs with eleven different vaccine antigens fused to SpyCatcher or SpyTag resulted in formation of antigen-VLP complexes with coupling efficiencies (% occupancy of total VLP binding sites) ranging from 22-88 %. In mice, spy-VLP vaccines presenting the malaria proteins Pfs25 or VAR2CSA markedly increased antibody titer, affinity, longevity and functional efficacy compared to corresponding vaccines employing monomeric proteins. The spy-VLP vaccines also effectively broke B cell self-tolerance and induced potent and durable antibody responses upon vaccination with cancer or allergy-associated self-antigens (PD-L1, CTLA-4 and IL-5). CONCLUSIONS: The spy-VLP system constitutes a versatile and rapid method to develop highly immunogenic VLP-based vaccines. Our data provide proof-of-concept for the technology's ability to present complex vaccine antigens to the immune system and elicit robust functional antibody responses as well as to efficiently break B cell self-tolerance. The spy-VLP-system may serve as a generic tool for the cost-effective development of effective VLP-vaccines against both infectious- and non-communicable diseases and could facilitate rapid and unbiased screening of vaccine candidate antigens.\",\n \"corpus_id\": 217519352,\n \"score\": 1\n },\n {\n \"doc_id\": \"27249579\",\n \"title\": \"Geometrical assembly of ultrastable protein templates for nanomaterials.\",\n \"abstract\": \"The fabrication of nanoscale devices requires architectural templates on which to position functional molecules in complex arrangements. Protein scaffolds are particularly promising templates for nanomaterials due to inherent molecular recognition and self-assembly capabilities combined with genetically encoded functionalities. However, difficulties in engineering protein quaternary structure into stable and well-ordered shapes have hampered progress. Here we report the development of an ultrastable biomolecular construction kit for the assembly of filamentous proteins into geometrically defined templates of controllable size and symmetry. The strategy combines redesign of protein-protein interaction specificity with the creation of tunable connector proteins that govern the assembly and projection angles of the filaments. The functionality of these nanoarchitectures is illustrated by incorporation of nanoparticles at specific locations and orientations to create hybrid materials such as conductive nanowires. These new structural components facilitate the manufacturing of nanomaterials with diverse shapes and functional properties over a wide range of processing conditions.\",\n \"corpus_id\": 5664344,\n \"score\": 1\n },\n {\n \"doc_id\": \"27477779\",\n \"title\": \"Engineering Protein Hydrogels Using SpyCatcher-SpyTag Chemistry.\",\n \"abstract\": \"Constructing hydrogels from engineered proteins has attracted significant attention within the material sciences, owing to their myriad potential applications in biomedical engineering. Developing efficient methods to cross-link tailored protein building blocks into hydrogels with desirable mechanical, physical, and functional properties is of paramount importance. By making use of the recently developed SpyCatcher-SpyTag chemistry, we successfully engineered protein hydrogels on the basis of engineered tandem modular elastomeric proteins. Our resultant protein hydrogels are soft but stable, and show excellent biocompatibility. As the first step, we tested the use of these hydrogels as a drug carrier, as well as in encapsulating human lung fibroblast cells. Our results demonstrate the robustness of the SpyCatcher-SpyTag chemistry, even when the SpyTag (or SpyCatcher) is flanked by folded globular domains. These results demonstrate that SpyCatcher-SpyTag chemistry can be used to engineer protein hydrogels from tandem modular elastomeric proteins that can find applications in tissue engineering, in fundamental mechano-biological studies, and as a controlled drug release vehicle.\",\n \"corpus_id\": 2616636,\n \"score\": 1\n },\n {\n \"doc_id\": \"27503402\",\n \"title\": \"Protein-like Nanoparticles Based on Orthogonal Self-Assembly of Chimeric Peptides.\",\n \"abstract\": \"A novel two-component self-assembling chimeric peptide is designed where two orthogonal protein folding motifs are linked side by side with precisely defined position relative to one another. The self-assembly is driven by a combination of symmetry controlled molecular packing, intermolecular interactions, and geometric constraint to limit the assembly into compact dodecameric protein nanoparticles.\",\n \"corpus_id\": 46851353,\n \"score\": 1\n },\n {\n \"doc_id\": \"27658030\",\n \"title\": \"SpyTag/SpyCatcher Cyclization Enhances the Thermostability of Firefly Luciferase.\",\n \"abstract\": \"SpyTag can spontaneously form a covalent isopeptide bond with its protein partner SpyCatcher. Firefly luciferase from Photinus pyralis was cyclized in vivo by fusing SpyCatcher at the N terminus and SpyTag at the C terminus. Circular LUC was more thermostable and alkali-tolerant than the wild type, without compromising the specific activity. Structural analysis indicated that the cyclized LUC increased the thermodynamic stability of the structure and remained more properly folded at high temperatures when compared with the wild type. We also prepared an N-terminally and C-terminally shortened form of the SpyCatcher protein and cyclization using this truncated form led to even more thermostability than the original form. Our findings suggest that cyclization with SpyTag and SpyCatcher is a promising and effective strategy to enhance thermostability of enzymes.\",\n \"corpus_id\": 8477179,\n \"score\": 1\n },\n {\n \"doc_id\": \"27783674\",\n \"title\": \"Kinetic Controlled Tag-Catcher Interactions for Directed Covalent Protein Assembly.\",\n \"abstract\": \"Over the last few years, a number of different protein assembly strategies have been developed, greatly expanding the toolbox for controlling macromolecular assembly. One of the most promising developments is a rapid protein ligation approach using a short polypeptide SpyTag and its partner, SpyCatcher derived from Streptococcus pyogenes fibronectin-binding protein, FbaB. To extend this technology, we have engineered and characterized a new Tag-Catcher pair from a related fibronectin-binding protein in Streptococcus dysgalactiae. The polypeptide Tag, named SdyTag, was constructed based on the native Cna protein B-type (CnaB) domain and was found to be highly unreactive to SpyCatcher. SpyCatcher has 320-fold specificity for its native SpyTag compared to SdyTag. Similarly, SdyTag has a 75-fold specificity for its optimized Catcher, named SdyCatcherDANG short, compared to SpyCatcher. These Tag-Catcher pairs were used in combination to demonstrate specific sequential assembly of tagged proteins in vitro. We also demonstrated that the in vivo generation of circularized proteins in a Tag-Catcher specific manner where specific Tags can be left unreacted for use in subsequent ligation reactions. From the success of these experiments, we foresee the application of SdyTags and SpyTags, not only, for multiplexed control of protein assembly but also for the construction of novel protein architectures.\",\n \"corpus_id\": 1537692,\n \"score\": 1\n },\n {\n \"doc_id\": \"27982100\",\n \"title\": \"Spontaneous Isopeptide Bond Formation as a Powerful Tool for Engineering Site-Specific Antibody-Drug Conjugates.\",\n \"abstract\": \"Spontaneous isopeptide bond formation, a stabilizing posttranslational modification that can be found in gram-positive bacterial cell surface proteins, has previously been used to develop a peptide-peptide ligation technology that enables the polymerization of tagged-proteins catalyzed by SpyLigase. Here we adapted this technology to establish a novel modular antibody labeling approach which is based on isopeptide bond formation between two recognition peptides, SpyTag and KTag. Our labeling strategy allows the attachment of a reporting cargo of interest to an antibody scaffold by fusing it chemically to KTag, available via semi-automated solid-phase peptide synthesis (SPPS), while equipping the antibody with SpyTag. This strategy was successfully used to engineer site-specific antibody-drug conjugates (ADCs) that exhibit cytotoxicities in the subnanomolar range. Our approach may lead to a new class of antibody conjugates based on peptide-tags that have minimal effects on protein structure and function, thus expanding the toolbox of site-specific antibody conjugation.\",\n \"corpus_id\": 18992987,\n \"score\": 1\n },\n {\n \"doc_id\": \"28105787\",\n \"title\": \"Orthogonal Surface Tags for Whole-Cell Biocatalysis.\",\n \"abstract\": \"We herein describe the engineering of E. coli strains that display orthogonal tags for immobilization on their surface and overexpress a functional heterologous \\\"protein content\\\" in their cytosol at the same time. Using the outer membrane protein Lpp-ompA, cell-surface display of the streptavidin-binding peptide, the SpyTag/SpyCatcher system, or a HaloTag variant allowed us to generate bacterial strains that can selectively bind to solid substrates, as demonstrated with magnetic microbeads. The simultaneous cytosolic expression of functional content was demonstrated for fluorescent proteins or stereoselective ketoreductase enzymes. The latter strains gave high selectivities for specific immobilization onto complementary surfaces and also in the whole-cell stereospecific transformation of a prochiral CS -symmetric nitrodiketone.\",\n \"corpus_id\": 205398168,\n \"score\": 1\n },\n {\n \"doc_id\": \"28437083\",\n \"title\": \"Dual Plug-and-Display Synthetic Assembly Using Orthogonal Reactive Proteins for Twin Antigen Immunization.\",\n \"abstract\": \"Engineering modular platforms to control biomolecular architecture can advance both the understanding and the manipulation of biological systems. Icosahedral particles uniformly displaying single antigens stimulate potent immune activation and have been successful in various licensed vaccines. However, it remains challenging to display multiple antigens on a single particle and to induce broader immunity protective across strains or even against distinct diseases. Here, we design a dually addressable synthetic nanoparticle by engineering the multimerizing coiled-coil IMX313 and two orthogonally reactive split proteins. SpyCatcher protein forms an isopeptide bond with SpyTag peptide through spontaneous amidation. SnoopCatcher forms an isopeptide bond with SnoopTag peptide through transamidation. SpyCatcher-IMX-SnoopCatcher provides a modular platform, whereby SpyTag-antigen and SnoopTag-antigen can be multimerized on opposite faces of the particle simply upon mixing. We demonstrate efficient derivatization of the platform with model proteins and complex pathogen-derived antigens. SpyCatcher-IMX-SnoopCatcher was expressed in Escherichia coli and was resilient to lyophilization or extreme temperatures. For the next generation of malaria vaccines, blocking the transmission of the parasite from human to mosquito is an important goal. SpyCatcher-IMX-SnoopCatcher multimerization of the leading transmission-blocking antigens Pfs25 and Pfs28 greatly enhanced the antibody response to both antigens in comparison to the monomeric proteins. This dual plug-and-display architecture should help to accelerate vaccine development for malaria and other diseases.\",\n \"corpus_id\": 206520806,\n \"score\": 1\n },\n {\n \"doc_id\": \"28757182\",\n \"title\": \"Amine Landscaping to Maximize Protein-Dye Fluorescence and Ultrastable Protein-Ligand Interaction.\",\n \"abstract\": \"Chemical modification of proteins provides great opportunities to control and visualize living systems. The most common way to modify proteins is reaction of their abundant amines with N-hydroxysuccinimide (NHS) esters. Here we explore the impact of amine number and positioning on protein-conjugate behavior using streptavidin-biotin, a central research tool. Dye-NHS modification of streptavidin severely damaged ligand binding, necessitating development of a new streptavidin-retaining ultrastable binding after labeling. Exploring the ideal level of dye modification, we engineered a panel bearing 1-6 amines per subunit: \\\"amine landscaping.\\\" Surprisingly, brightness increased as amine number decreased, revealing extensive quenching following conventional labeling. We ultimately selected Flavidin (fluorophore-friendly streptavidin), combining ultrastable ligand binding with increased brightness after conjugation. Flavidin enhanced fluorescent imaging, allowing more sensitive and specific cell labeling in tissues. Flavidin should have wide application in molecular detection, providing a general insight into how to optimize simultaneously the behavior of the biomolecule and the chemical probe.\",\n \"corpus_id\": 20816884,\n \"score\": 1\n },\n {\n \"doc_id\": \"29024296\",\n \"title\": \"Evolving Accelerated Amidation by SpyTag/SpyCatcher to Analyze Membrane Dynamics.\",\n \"abstract\": \"SpyTag is a peptide that forms a spontaneous amide bond with its protein partner SpyCatcher. This protein superglue is a broadly useful tool for molecular assembly, locking together biological building blocks efficiently and irreversibly in diverse architectures. We initially developed SpyTag and SpyCatcher by rational design, through splitting a domain from a Gram-positive bacterial adhesin. In this work, we established a phage-display platform to select for specific amidation, leading to an order of magnitude acceleration for interaction of the SpyTag002 variant with the SpyCatcher002 variant. We show that the 002 pair bonds rapidly under a wide range of conditions and at either protein terminus. SpyCatcher002 was fused to an intimin derived from enterohemorrhagic Escherichia coli. SpyTag002 reaction enabled specific and covalent decoration of intimin for live cell fluorescent imaging of the dynamics of the bacterial outer membrane as cells divide.\",\n \"corpus_id\": 3598641,\n \"score\": 1\n },\n {\n \"doc_id\": \"29039416\",\n \"title\": \"Antibodies to biotin enable large-scale detection of biotinylation sites on proteins.\",\n \"abstract\": \"Although purification of biotinylated molecules is highly efficient, identifying specific sites of biotinylation remains challenging. We show that anti-biotin antibodies enable unprecedented enrichment of biotinylated peptides from complex peptide mixtures. Live-cell proximity labeling using APEX peroxidase followed by anti-biotin enrichment and mass spectrometry yielded over 1,600 biotinylation sites on hundreds of proteins, an increase of more than 30-fold in the number of biotinylation sites identified compared to streptavidin-based enrichment of proteins.\",\n \"corpus_id\": 21738454,\n \"score\": 1\n },\n {\n \"doc_id\": \"29625006\",\n \"title\": \"SpyCatcher-NTEV: A Circularly Permuted, Disordered SpyCatcher Variant for Less Trace Ligation.\",\n \"abstract\": \"The SpyTag/SpyCatcher reaction has emerged as a powerful way for bioconjugation, but it leaves a folded complex in the product after the formation of the isopeptide bond. To vary the location of the reactive residue and reduce the size of the complex and its potential immunogenicity, we engineer two circularly permuted SpyCatcher variants, SpyCatcher-N and SpyCatcher-NTEV, the latter of which possesses a TEV-recognition site for removal of the fragment containing the catalytic site. Surprisingly, both variants are found to be disordered in solution, yet still retain the ability to form an ordered complex upon reaction with SpyTag with second-order rate constants of ∼10 M-1 s-1. Cellular expression of a telechelic protein bearing SpyCatcher-NTEV at the N-terminus and SpyTag at the C-terminus gives both cyclized and chain-extended products. Notably, the monomers exist almost exclusively in the cyclic form owing to its high reactivity in vivo. The fragment containing the catalytic site of SpyCatcher-NTEV can then be removed by TEV digestion, giving a circular protein with minimal trace from the ligation reaction. The plasticity of SpyTag/SpyCatcher reactive pair has promised an ever-expanding toolbox of genetically encoded peptide-protein reaction with versatile features.\",\n \"corpus_id\": 4645665,\n \"score\": 1\n },\n {\n \"doc_id\": \"18668104\",\n \"title\": \"Functionalizing hydrogen-bonded surface networks with self-assembled monolayers.\",\n \"abstract\": \"One of the central challenges in nanotechnology is the development of flexible and efficient methods for creating ordered structures with nanometre precision over an extended length scale. Supramolecular self-assembly on surfaces offers attractive features in this regard: it is a 'bottom-up' approach and thus allows the simple and rapid creation of surface assemblies, which are readily tuned through the choice of molecular building blocks used and stabilized by hydrogen bonding, van der Waals interactions, pi-pi bonding or metal coordination between the blocks. Assemblies in the form of two-dimensional open networks are of particular interest for possible applications because well-defined pores can be used for the precise localization and confinement of guest entities such as molecules or clusters, which can add functionality to the supramolecular network. Another widely used method for producing surface structures involves self-assembled monolayers (SAMs), which have introduced unprecedented flexibility in our ability to tailor interfaces and generate patterned surfaces. But SAMs are part of a top-down technology that is limited in terms of the spatial resolution that can be achieved. We therefore rationalized that a particularly powerful fabrication platform might be realized by combining non-covalent self-assembly of porous networks and SAMs, with the former providing nanometre-scale precision and the latter allowing versatile functionalization. Here we show that the two strategies can indeed be combined to create integrated network-SAM hybrid systems that are sufficiently robust for further processing. We show that the supramolecular network and the SAM can both be deposited from solution, which should enable the widespread and flexible use of this combined fabrication method.\",\n \"corpus_id\": 205213948,\n \"score\": 0\n },\n {\n \"doc_id\": \"19374419\",\n \"title\": \"Dynamics of the streptavidin-biotin complex in solution and in its crystal lattice: distinct behavior revealed by molecular simulations.\",\n \"abstract\": \"We present a 250 ns simulation of the wild-type, biotin-liganded streptavidin tetramer in the solution phase and compare the trajectory to two previously published simulations of the protein in its crystal lattice. By performing both types of simulations, we are able to interpret the protein's behavior in solution in the context of its X-ray structure. We find that the rate of conformational sampling is increased in solution over the lattice environment, although the relevant conformational space in solution is also much larger, as indicated by overall fluctuations in the positions of backbone atoms. We also compare the distributions of chi1 angles sampled by side chains exposed to solvent in the lattice and in the solution phase, obtaining overall good agreement between the distributions obtained in our most rigorous lattice simulation and the crystallographic chi1 angles. We observe changes in the chi1 distributions in the solution phase, and note an apparent progression of the distributions as the environment changes from a tightly packed lattice filled with crystallization media to a bath of pure water. Finally, we examine the interaction of biotin and streptavidin in each simulation, uncovering a possible alternate conformation of the biotin carboxylate tail. We also note that a hydrogen bond observed to break transiently in previous solution-phase simulations is predominantly broken in this much longer solution-phase trajectory; in the lattice simulations, the lattice environment appears to help maintain the hydrogen bond, but more sampling will be needed to confirm whether the simulation model truly gives good agreement with the X-ray data in the lattice simulations. We expect that pairing solution-phase biomolecular simulations with crystal lattice simulations will help to validate simulation models and improve the interpretation of experimentally determined structures.\",\n \"corpus_id\": 8825566,\n \"score\": 0\n },\n {\n \"doc_id\": \"20462252\",\n \"title\": \"A distal point mutation in the streptavidin-biotin complex preserves structure but diminishes binding affinity: experimental evidence of electronic polarization effects?\",\n \"abstract\": \"We have identified a distal point mutation in streptavidin that causes a 1000-fold reduction in biotin binding affinity without disrupting the equilibrium complex structure. The F130L mutation creates a small cavity occupied by a water molecule; however, all neighboring side chain positions are preserved, and protein-biotin hydrogen bonds are unperturbed. Molecular dynamics simulations reveal a reduced mobility of biotin binding residues but no observable destabilization of protein-ligand interactions. Our combined structural and computational studies suggest that the additional water molecule may affect binding affinity through an electronic polarization effect that impacts the highly cooperative hydrogen bonding network in the biotin binding pocket.\",\n \"corpus_id\": 22733513,\n \"score\": 0\n },\n {\n \"doc_id\": \"21892837\",\n \"title\": \"Engineered streptavidin monomer and dimer with improved stability and function.\",\n \"abstract\": \"Although streptavidin's high affinity for biotin has made it a widely used and studied binding protein and labeling tool, its tetrameric structure may interfere with some assays. A streptavidin mutant with a simpler quaternary structure would demonstrate a molecular-level understanding of its structural organization and lead to the development of a novel molecular reagent. However, modulating the tetrameric structure without disrupting biotin binding has been extremely difficult. In this study, we describe the design of a stable monomer that binds biotin both in vitro and in vivo. To this end, we constructed and characterized monomers containing rationally designed mutations. The mutations improved the stability of the monomer (increase in T(m) from 31 to 47 °C) as well as its affinity (increase in K(d) from 123 to 38 nM). We also used the stability-improved monomer to construct a dimer consisting of two streptavidin subunits that interact across the dimer-dimer interface, which we call the A/D dimer. The biotin binding pocket is conserved between the tetramer and the A/D dimer, and therefore, the dimer is expected to have a significantly higher affinity than the monomer. The affinity of the dimer (K(d) = 17 nM) is higher than that of the monomer but is still many orders of magnitude lower than that of the wild-type tetramer, which suggests there are other factors important for high-affinity biotin binding. We show that the engineered streptavidin monomer and dimer can selectively bind biotinylated targets in vivo by labeling the cells displaying biotinylated receptors. Therefore, the designed mutants may be useful in novel applications as well as in future studies in elucidating the role of oligomerization in streptavidin function.\",\n \"corpus_id\": 21622029,\n \"score\": 0\n },\n {\n \"doc_id\": \"22802499\",\n \"title\": \"Ultra-precision: enabling our future.\",\n \"abstract\": \"This paper provides a perspective on the development of ultra-precision technologies: What drove their evolution and what do they now promise for the future as we face the consequences of consumption of the Earth's finite resources? Improved application of measurement is introduced as a major enabler of mass production, and its resultant impact on wealth generation is considered. This paper identifies the ambitions of the defence, automotive and microelectronics sectors as important drivers of improved manufacturing accuracy capability and ever smaller feature creation. It then describes how science fields such as astronomy have presented significant precision engineering challenges, illustrating how these fields of science have achieved unprecedented levels of accuracy, sensitivity and sheer scale. Notwithstanding their importance to science understanding, many science-driven ultra-precision technologies became key enablers for wealth generation and other well-being issues. Specific ultra-precision machine tools important to major astronomy programmes are discussed, as well as the way in which subsequently evolved machine tools made at the beginning of the twenty-first century, now provide much wider benefits.\",\n \"corpus_id\": 6059560,\n \"score\": 0\n },\n {\n \"doc_id\": \"23534402\",\n \"title\": \"Affinity capture of biotinylated proteins at acidic conditions to facilitate hydrogen/deuterium exchange mass spectrometry analysis of multimeric protein complexes.\",\n \"abstract\": \"Characterization of conformational and dynamic changes associated with protein interactions can be done by hydrogen/deuterium exchange mass spectrometry (HDX-MS) by comparing the deuterium uptake in the bound and unbound state of the proteins. Investigation of local hydrogen/deuterium exchange in heteromultimeric protein complexes poses a challenge for the method due to the increased complexity of the mixture of peptides originating from all interaction partners in the complex. Previously, interference of peptides from one interaction partner has been removed by immobilizing the intact protein on beads prior to the HDX-MS experiment. However, when studying protein complexes of more than two proteins, immobilization can possibly introduce steric limitations to the interactions. Here, we present a method based on the high affinity biotin-streptavidin interaction that allows selective capture of biotinylated proteins even under the extreme conditions for hydrogen/deuterium exchange quenching i.e. pH 2.5 and 0 °C. This biotin-streptavidin capture strategy allows hydrogen/deuterium exchange to occur in proteins in solution and enables characterization of specific proteins in heteromultimeric protein complexes without interference of peptides originating from other interaction partners in the complex. The biotin-streptavidin strategy has been successfully implemented in a model system with two recombinant monoclonal antibodies that target nonoverlapping epitopes on the human epidermal growth factor receptor (EGFR). We present a workflow for biotinylation and characterization of recombinant antibodies and demonstrate affinity capture of biotinylated antibodies under hydrogen/deuterium exchange quench conditions by the biotin-streptavidin strategy.\",\n \"corpus_id\": 27269560,\n \"score\": 0\n },\n {\n \"doc_id\": \"24790550\",\n \"title\": \"Fluorescence enhancement of fluorescent unnatural streptavidin by binding of a biotin analogue with spacer tail and its application to biotin sensing.\",\n \"abstract\": \"We designed a novel molecular biosensing system for the detection of biotin, an important vitamin by the combination of fluorescent unnatural streptavidin with a commercialized biotin-(AC5)2-hydrazide. A fluorescent unnatural amino acid, BODIPY-FL-aminophenylalanine (BFLAF), was position-specifically incorporated into Trp120 of streptavidin by four-base codon method. Fluorescence of the Trp120BFLAF mutant streptavidin was enhanced by the addition of biotin-(AC5)2-hydrazide with the concentration dependent, whereas fluorescence enhancement was not observed at all by the addition of natural biotin. It was considered that the spacer tail of biotin-(AC5)2-hydrazide may disturb the fluorescence quenching of the Trp120BFLAF by Trp79 and Trp108 of the neighbor subunit. Therefore, biotin sensing was carried out by the competitive binding reaction of biotin-(AC5)2-hydrazide and natural biotin to the fluorescent mutant streptavidin. The fluorescence intensity decreased by increasing free biotin concentration. The result suggested that molecular biosensor for small ligand could be successfully designed by the pair of fluorescent mutant binding protein and ligand analogue.\",\n \"corpus_id\": 15608490,\n \"score\": 0\n },\n {\n \"doc_id\": \"25049400\",\n \"title\": \"Synthesis of bioactive protein hydrogels by genetically encoded SpyTag-SpyCatcher chemistry.\",\n \"abstract\": \"Protein-based hydrogels have emerged as promising alternatives to synthetic hydrogels for biomedical applications, owing to the precise control of structure and function enabled by protein engineering. Nevertheless, strategies for assembling 3D molecular networks that carry the biological information encoded in full-length proteins remain underdeveloped. Here we present a robust protein gelation strategy based on a pair of genetically encoded reactive partners, SpyTag and SpyCatcher, that spontaneously form covalent isopeptide linkages under physiological conditions. The resulting \\\"network of Spies\\\" may be designed to include cell-adhesion ligands, matrix metalloproteinase-1 cleavage sites, and full-length globular proteins [mCherry and leukemia inhibitory factor (LIF)]. The LIF network was used to encapsulate mouse embryonic stem cells; the encapsulated cells remained pluripotent in the absence of added LIF. These results illustrate a versatile strategy for the creation of information-rich biomaterials.\",\n \"corpus_id\": 16197967,\n \"score\": 0\n },\n {\n \"doc_id\": \"25119814\",\n \"title\": \"Increasing and decreasing the ultrastability of bacterial chemotaxis core signaling complexes by modifying protein-protein contacts.\",\n \"abstract\": \"The chemosensory signaling array of bacterial chemotaxis is composed of functional core units containing two receptor trimers of dimers, a homodimeric CheA kinase, and two CheW adaptor proteins. In vitro reconstitutions generate individual, functional core units and larger functional assemblies, including dimers, hexagons, and hexagonal arrays. Such reconstituted complexes have been shown to have both quasi-stable and ultrastable populations that decay with lifetimes of 1-2 days and ∼3 weeks at 22 °C, respectively, where decay results primarily from proteolysis of the bound kinase [Erbse, A. H., and Falke, J. J. (2009) Biochemistry 48, 6975-6987; Slivka, P. F., and Falke, J. J. (2012) Biochemistry 51, 10218-10228]. In this work, we show that the ultrastable population can be destabilized to the quasi-stable level via the introduction of a bulky tryptophan residue at either one of two essential protein-protein interfaces within the core unit: the receptor-kinase contact or kinase-adaptor interface 1. Moreover, we demonstrate that the quasi-stable population can be made ultrastable via the introduction of a disulfide bond that covalently stabilizes the latter interface. The resulting disulfide at least doubles the functional lifetime of the ultrastable population, to ≥5.9 weeks at 22 °C, by protecting the kinase from endogenous and exogenous proteases. Together, these results indicate that the ultrastability of reconstituted core complexes requires well-formed contacts among the receptor, kinase, and adaptor proteins, whereas quasi-stability arises from less perfect contacts that allow slow proteolysis of the bound kinase. Furthermore, the results reveal that ultrastability, and perhaps the size or order of chemosensory complexes and arrays, can be increased by an engineered disulfide bond that covalently cross-links a key interface. Overall, it appears that native ultrastability has evolved to provide an optimal rather than maximal level of kinetic durability, suggesting that altered selective pressure could either increase or decrease the functional lifetime of core complexes.\",\n \"corpus_id\": 8321829,\n \"score\": 0\n },\n {\n \"doc_id\": \"25482395\",\n \"title\": \"Ultrastable cellulosome-adhesion complex tightens under load.\",\n \"abstract\": \"Challenging environments have guided nature in the development of ultrastable protein complexes. Specialized bacteria produce discrete multi-component protein networks called cellulosomes to effectively digest lignocellulosic biomass. While network assembly is enabled by protein interactions with commonplace affinities, we show that certain cellulosomal ligand-receptor interactions exhibit extreme resistance to applied force. Here, we characterize the ligand-receptor complex responsible for substrate anchoring in the Ruminococcus flavefaciens cellulosome using single-molecule force spectroscopy and steered molecular dynamics simulations. The complex withstands forces of 600-750 pN, making it one of the strongest bimolecular interactions reported, equivalent to half the mechanical strength of a covalent bond. Our findings demonstrate force activation and inter-domain stabilization of the complex, and suggest that certain network components serve as mechanical effectors for maintaining network integrity. This detailed understanding of cellulosomal network components may help in the development of biocatalysts for production of fuels and chemicals from renewable plant-derived biomass.\",\n \"corpus_id\": 465374,\n \"score\": 0\n },\n {\n \"doc_id\": \"25560523\",\n \"title\": \"SWATH enables precise label-free quantification on proteome scale.\",\n \"abstract\": \"MS-based proteomics has emerged as a powerful tool in biological studies. The shotgun proteomics strategy, in which proteolytic peptides are analyzed in data-dependent mode, enables a detection of the most comprehensive proteome (>10 000 proteins from whole-cell lysate). The quantitative proteomics uses stable isotopes or label-free method to measure relative protein abundance. The isotope labeling strategies are more precise and accurate compared to label-free methods, but labeling procedures are complicated and expensive, and the sample number and types are also limited. Sequential window acquisition of all theoretical mass spectra (SWATH) is a recently developed technique, in which data-independent acquisition is coupled with peptide spectral library match. In principle SWATH method is able to do label-free quantification in an MRM-like manner, which has higher quantification accuracy and precision. Previous data have demonstrated that SWATH can be used to quantify less complex systems, such as spiked-in peptide mixture or protein complex. Our study first time assessed the quantification performance of SWATH method on proteome scale using a complex mouse-cell lysate sample. In total 3600 proteins got identified and quantified without sample prefractionation. The SWATH method shows outstanding quantification precision, whereas the quantification accuracy becomes less perfect when protein abundances differ greatly. However, this inaccuracy does not prevent discovering biological correlates, because the measured signal intensities had linear relationship to the sample loading amounts; thus the SWATH method can predict precisely the significance of a protein. Our results prove that SWATH can provide precise label-free quantification on proteome scale.\",\n \"corpus_id\": 5498735,\n \"score\": 0\n },\n {\n \"doc_id\": \"26709829\",\n \"title\": \"Chemotactic Signaling by Single-Chain Chemoreceptors.\",\n \"abstract\": \"Bacterial chemoreceptors of the methyl-accepting chemotaxis protein (MCP) family operate in commingled clusters that enable cells to detect and track environmental chemical gradients with high sensitivity and precision. MCP homodimers of different detection specificities form mixed trimers of dimers that facilitate inter-receptor communication in core signaling complexes, which in turn assemble into a large signaling network. The two subunits of each homodimeric receptor molecule occupy different locations in the core complexes. One subunit participates in trimer-stabilizing interactions at the trimer axis, the other lies on the periphery of the trimer, where it can interact with two cytoplasmic proteins: CheA, a signaling autokinase, and CheW, which couples CheA activity to receptor control. As a possible tool for independently manipulating receptor subunits in these two structural environments, we constructed and characterized fused genes for the E. coli serine chemoreceptor Tsr that encoded single-chain receptor molecules in which the C-terminus of the first Tsr subunit was covalently connected to the N-terminus of the second with a polypeptide linker. We showed with soft agar assays and with a FRET-based in vivo CheA kinase assay that single-chain Tsr~Tsr molecules could promote serine sensing and chemotaxis responses. The length of the connection between the joined subunits was critical. Linkers nine residues or shorter locked the receptor in a kinase-on state, most likely by distorting the native structure of the receptor HAMP domain. Linkers 22 or more residues in length permitted near-normal Tsr function. Few single-chain molecules were found as monomer-sized proteolytic fragments in cells, indicating that covalently joined receptor subunits were responsible for mediating the signaling responses we observed. However, cysteine-directed crosslinking, spoiling by dominant-negative Tsr subunits, and rearrangement of ligand-binding site lesions revealed subunit swapping interactions that will need to be taken into account in experimental applications of single-chain chemoreceptors.\",\n \"corpus_id\": 13263204,\n \"score\": 0\n },\n {\n \"doc_id\": \"28551501\",\n \"title\": \"The role of CH/π interactions in the high affinity binding of streptavidin and biotin.\",\n \"abstract\": \"The streptavidin-biotin complex has an extraordinarily high affinity (Ka: 10(15)mol(-1)) and contains one of the strongest non-covalent interactions known. This strong interaction is widely used in biological tools, including for affinity tags, detection, and immobilization of proteins. Although hydrogen bond networks and hydrophobic interactions have been proposed to explain this high affinity, the reasons for it remain poorly understood. Inspired by the deceased affinity of biotin observed for point mutations of streptavidin at tryptophan residues, we hypothesized that a CH/π interaction may also contribute to the strong interaction between streptavidin and biotin. CH/π interactions were explored and analyzed at the biotin-binding site and at the interface of the subunits by the fragment molecular orbital method (FMO) and extended applications: PIEDA and FMO4. The results show that CH/π interactions are involved in the high affinity for biotin at the binding site of streptavidin. We further suggest that the involvement of CH/π interactions at the subunit interfaces and an extended CH/π network play more critical roles in determining the high affinity, rather than involvement at the binding site.\",\n \"corpus_id\": 5472834,\n \"score\": 0\n },\n {\n \"doc_id\": \"29206886\",\n \"title\": \"Monodisperse measurement of the biotin-streptavidin interaction strength in a well-defined pulling geometry.\",\n \"abstract\": \"The widely used interaction of the homotetramer streptavidin with the small molecule biotin has been intensively studied by force spectroscopy and has become a model system for receptor ligand interaction. However, streptavidin's tetravalency results in diverse force propagation pathways through the different binding interfaces. This multiplicity gives rise to polydisperse force spectroscopy data. Here, we present an engineered monovalent streptavidin tetramer with a single cysteine in its functional subunit that allows for site-specific immobilization of the molecule, orthogonal to biotin binding. Functionality of streptavidin and its binding properties for biotin remain unaffected. We thus created a stable and reliable molecular anchor with a unique high-affinity binding site for biotinylated molecules or nanoparticles, which we expect to be useful for many single-molecule applications. To characterize the mechanical properties of the bond between biotin and our monovalent streptavidin, we performed force spectroscopy experiments using an atomic force microscope. We were able to conduct measurements at the single-molecule level with 1:1-stoichiometry and a well-defined geometry, in which force exclusively propagates through a single subunit of the streptavidin tetramer. For different force loading rates, we obtained narrow force distributions of the bond rupture forces ranging from 200 pN at 1,500 pN/s to 230 pN at 110,000 pN/s. The data are in very good agreement with the standard Bell-Evans model with a single potential barrier at Δx0 = 0.38 nm and a zero-force off-rate koff,0 in the 10-6 s-1 range.\",\n \"corpus_id\": 13408524,\n \"score\": 0\n },\n {\n \"doc_id\": \"29233896\",\n \"title\": \"Retargeting Lentiviruses via SpyCatcher-SpyTag Chemistry for Gene Delivery into Specific Cell Types.\",\n \"abstract\": \"We report a simple strategy for the creation of lentiviral vectors specific to any desired target cells. SpyTag is inserted into an engineered Sindbis virus envelope protein and displayed on the lentivirus surface to create Sindbis virus-SpyTag pseudoparticles (Sind-SpyTag-pp). The SpyTag serves as the covalent anchoring site for a target-cell-specific cell-binding protein (CBP) that is fused to a truncated SpyCatcher (SpyCatcherΔ). Target-cell-specific lentiviruses are created by mixing the Sind-SpyTag-pp and CBP-SpyCatcherΔ in vitro We first used a HER2-binding designed ankyrin repeat protein (DARPin.9.26) as the model CBP. The DARPin-conjugated lentivirus transduced HER2+ SKOV3 cells with an infectious titer of 5.2 × 106 IU/ml, >500-fold higher than the unfunctionalized \\\"naked\\\" virions (<104 IU/ml). The ability of the DARPin-conjugated lentivirus to transduce HER2+ cells correlated with the surface expression level of HER2. Furthermore, these lentiviruses preferentially transduced HER2+ cells in cocultures containing HER2+ and HER2- cells. To enable the use of commercially available monoclonal antibodies (MAbs) as the CBP, we developed a convenient click chemistry-based approach to conjugate MAb-derived Fab fragments to a variant SpyCatcherΔ protein containing a nonnatural amino acid, 4-azido-l-phenylalanine (AzF). Using the HER2-binding trastuzumab as a model cell-specific MAb, we created Fab-conjugated lentiviral vectors that transduced HER2+ SKOV3 cells with an infectious titer of 2.8 × 106 IU/ml, on par with the result achieved using the DARPin-SpyCatcherΔ fusion protein. The ability to create cell-specific lentiviral vectors through chemical conjugation of a CBP should make this approach generalizable to any antibody, giving it broad utility for a wide range of research and clinical applications. IMPORTANCE Lentiviral vectors hold great potential in gene therapy. However, it remains a major hurdle to robustly engineer cell-specific lentiviral vectors. This article reports a simple and effective strategy to functionalize lentiviral vectors with cell-binding proteins, thus retargeting these viruses to cells expressing the binding partner of the CBP. The CBP is genetically or chemically linked to the SpyCatcher. The SpyTag is displayed on the virion surface as a fusion to an engineered Sindbis virus envelope protein and is used as the anchorage site for SpyCatcher-linked CBP. Using this strategy, we created lentiviral vectors highly infectious toward HER2+ cancer cells. The ability to rapidly create cell-specific lentiviral vectors targeting a wide range of cell types should accelerate the development of custom lentiviral vectors for many research and clinical applications.\",\n \"corpus_id\": 23106579,\n \"score\": 0\n }\n]","isConversational":false}}},{"rowIdx":48,"cells":{"query":{"kind":"string","value":"{\n \"doc_id\": \"26670244\",\n \"title\": \"Structure of the Receptor-Binding Carboxy-Terminal Domain of the Bacteriophage T5 L-Shaped Tail Fibre with and without Its Intra-Molecular Chaperone.\",\n \"abstract\": \"Bacteriophage T5, a Siphovirus belonging to the order Caudovirales, has a flexible, three-fold symmetric tail, to which three L-shaped fibres are attached. These fibres recognize oligo-mannose units on the bacterial cell surface prior to infection and are composed of homotrimers of the pb1 protein. Pb1 has 1396 amino acids, of which the carboxy-terminal 133 residues form a trimeric intra-molecular chaperone that is auto-proteolyzed after correct folding. The structure of a trimer of residues 970-1263 was determined by single anomalous dispersion phasing using incorporated selenomethionine residues and refined at 2.3 Å resolution using crystals grown from native, methionine-containing, protein. The protein inhibits phage infection by competition. The phage-distal receptor-binding domain resembles a bullet, with the walls formed by partially intertwined beta-sheets, conferring stability to the structure. The fold of the domain is novel and the topology unique to the pb1 structure. A site-directed mutant (Ser1264 to Ala), in which auto-proteolysis is impeded, was also produced, crystallized and its 2.5 Å structure solved by molecular replacement. The additional chaperone domain (residues 1263-1396) consists of a central trimeric alpha-helical coiled-coil flanked by a mixed alpha-beta domain. Three long beta-hairpin tentacles, one from each chaperone monomer, extend into long curved grooves of the bullet-shaped domain. The chaperone-containing mutant did not inhibit infection by competition.\",\n \"corpus_id\": 14888611\n}"},"candidates":{"kind":"list like","value":[{"doc_id":"18077713","title":"Structure of the receptor-binding protein of bacteriophage det7: a podoviral tail spike in a myovirus.","abstract":"A new Salmonella enterica phage, Det7, was isolated from sewage and shown by electron microscopy to belong to the Myoviridae morphogroup of bacteriophages. Det7 contains a 75-kDa protein with 50% overall sequence identity to the tail spike endorhamnosidase of podovirus P22. Adsorption of myoviruses to their bacterial hosts is normally mediated by long and short tail fibers attached to a contractile tail, whereas podoviruses do not contain fibers but attach to host cells through stubby tail spikes attached to a very short, noncontractile tail. The amino-terminal 150 residues of the Det7 protein lack homology to the P22 tail spike and are probably responsible for binding to the base plate of the myoviral tail. Det7 tail spike lacking this putative particle-binding domain was purified from Escherichia coli, and well-diffracting crystals of the protein were obtained. The structure, determined by molecular replacement and refined at a 1.6-A resolution, is very similar to that of bacteriophage P22 tail spike. Fluorescence titrations with an octasaccharide suggest Det7 tail spike to bind its receptor lipopolysaccharide somewhat less tightly than the P22 tail spike. The Det7 tail spike is even more resistant to thermal unfolding than the already exceptionally stable homologue from P22. Folding and assembly of both trimeric proteins are equally temperature sensitive and equally slow. Despite the close structural, biochemical, and sequence similarities between both proteins, the Det7 tail spike lacks both carboxy-terminal cysteines previously proposed to form a transient disulfide during P22 tail spike assembly. Our data suggest receptor-binding module exchange between podoviruses and myoviruses in the course of bacteriophage evolution.","corpus_id":22593104,"score":2},{"doc_id":"18160394","title":"Structure of the bacteriophage phi KZ lytic transglycosylase gp144.","abstract":"Lytic transglycosylases are enzymes that act on the peptidoglycan of bacterial cell walls. They cleave the glycosidic linkage between N-acetylmuramoyl and N-acetylglucosaminyl residues with the concomitant formation of a 1,6-anhydromuramoyl product. The x-ray structure of the lytic transglycosylase gp144 from the Pseudomonas bacteriophage phi KZ has been determined to 2.5-A resolution. This protein is probably employed by the bacteriophage in the late stage of the virus reproduction cycle to destroy the bacterial cell wall to release the phage progeny. phi KZ gp144 is a 260-residue alpha-helical protein composed of a 70-residue N-terminal cell wall-binding domain and a C-terminal catalytic domain. The fold of the N-terminal domain is similar to the peptidoglycan-binding domain from Streptomyces albus G D-Ala-D-Ala carboxypeptidase and to the N-terminal prodomain of human metalloproteinases that act on extracellular matrices. The C-terminal catalytic domain of gp144 has a structural similarity to the catalytic domain of the transglycosylase Slt70 from Escherichia coli and to lysozymes. The gp144 catalytic domain has an elongated groove that can bind at least five sugar residues at sites A-E. As in other lysozymes, the peptidoglycan cleavage (catalyzed by Glu 115 in gp144) occurs between sugar-binding subsites D and E. The x-ray structure of the phi KZ transglycosylase complexed with the chitotetraose (N-acetylglucosamine)(4) has been determined to 2.6-A resolution. The N-acetylglucosamine residues of the chitotetraose bind in sites A-D.","corpus_id":37782816,"score":2},{"doc_id":"18462681","title":"An intersubunit active site between supercoiled parallel beta helices in the trimeric tailspike endorhamnosidase of Shigella flexneri Phage Sf6.","abstract":"Sf6 belongs to the Podoviridae family of temperate bacteriophages that infect gram-negative bacteria by insertion of their double-stranded DNA. They attach to their hosts specifically via their tailspike proteins. The 1.25 A crystal structure of Shigella phage Sf6 tailspike protein (Sf6 TSP) reveals a conserved architecture with a central, right-handed beta helix. In the trimer of Sf6 TSP, the parallel beta helices form a left-handed, coiled-beta coil with a pitch of 340 A. The C-terminal domain consists of a beta sandwich reminiscent of viral capsid proteins. Further crystallographic and biochemical analyses show a Shigella cell wall O-antigen fragment to bind to an endorhamnosidase active site located between two beta-helix subunits each anchoring one catalytic carboxylate. The functionally and structurally related bacteriophage, P22 TSP, lacks sequence identity with Sf6 TSP and has its active sites on single subunits. Sf6 TSP may serve as an example for the evolution of different host specificities on a similar general architecture.","corpus_id":205258558,"score":2},{"doc_id":"19189967","title":"Proteolytic release of the intramolecular chaperone domain confers processivity to endosialidase F.","abstract":"Endosialidases (endoNs), as identified so far, are tailspike proteins of bacteriophages that specifically bind and degrade the alpha2,8-linked polysialic acid (polySia) capsules of their hosts. The crystal structure solved for the catalytic domain of endoN from coliphage K1F (endoNF) revealed a functional trimer. Folding of the catalytic trimer is mediated by an intramolecular C-terminal chaperone domain. Release of the chaperone from the folded protein confers kinetic stability to endoNF. In mutant c(S), the replacement of serine 911 by alanine prevents proteolysis and generates an enzyme that varies in activity from wild type. Using soluble polySia as substrate a 3-times higher activity was detected while evaluation with immobilized polySia revealed a 190-fold reduced activity. Importantly, activity of c(S) did not differ from wild type with tetrameric sialic acid, the minimal endoNF substrate. Furthermore, we show that the presence of the chaperone domain in c(S) destabilizes binding to polySia in a similar way as did selective disruption of a polySia binding site in the stalk domain. The improved catalytic efficiency toward soluble polySia observed in these mutants can be explained by higher dissociation and association probabilities, whereas inversely, an impaired processivity was found. The fact that endoNF is a processive enzyme introduces a new molecular basis to explain capsule degradation by bacteriophages, which until now has been regarded as a result of cooperative interaction of tailspike proteins. Moreover, knowing that release of the chaperone domain confers kinetic stability and processivity, conservation of the proteolytic process can be explained by its importance in phage evolution.","corpus_id":205377694,"score":2},{"doc_id":"19780551","title":"Observation of the membrane binding activity and domain structure of gpV, which comprises the tail spike of bacteriophage P2.","abstract":"The P2 phage virion has tail spike proteins beneath the baseplate and uses them to adsorb to the outer membrane of Escherichia coli during the infection process. Previous immunoelectron microscopic studies suggested that the tail spikes are composed of the gene V product (gpV); however, experimental evidence of its membrane binding activity has yet to be reported. In this study, we purified and characterized recombinant full-length gpV and its C-terminal domain. Limited chymotrypsin proteolysis of gpV produced a C-terminal domain composed of Ser86-Leu211. Our experiments demonstrated that the N- and C-terminal domains have very different melting temperatures: 50 and 74 degrees C, respectively. We also found that gpV binds the E. coli membrane via its C-terminal domain. We conclude that the C-terminal domain of gpV is a stable trimer and serves as the receptor-binding domain for the second step in the phage adsorption process.","corpus_id":14722,"score":2},{"doc_id":"19913618","title":"Two-chaperone assisted soluble expression and purification of the bacteriophage T4 long tail fibre protein gp37.","abstract":"Bacteriophage T4 recognises its host cells through its long tail fibre protein gene product (gp) 37. Gp37 is a protein containing 1026 amino acids per monomer, forming a fibrous parallel homotrimer at the distal end of the long tail fibres. The other distal half-fibre protein, gp36, is much smaller, forming a trimer of 221 amino acids per monomer. Functional and structural studies of gp37 have been hampered by the inability to produce suitable amounts of it. We produced soluble gp37 by co-expression with two bacteriophage T4-encoded chaperones in a two-vector system; co-expression with each chaperone separately did not lead to good amounts of correctly folded, trimeric protein. An expression vector for the bacteriophage T4 fibrous protein chaperone gp57 was co-transformed into bacteria with a compatible bi-cistronic expression vector containing bacteriophage T4 genes 37 and 38. A six-histidine tag is encoded amino-terminal to the gp37 gene. Recombinant trimeric gp37, containing the histidine tag and residues 12-1026 of gp37, was purified from lysed bacteria by subsequent nickel-affinity, size exclusion and strong anion exchange column chromatography. Yields of approximately 4 mg of purified protein per litre of bacterial culture were achieved. Electron microscopy confirmed the protein to form fibres around 63 nm long, presumably gp36 makes up the remaining 11 nm in the intact distal half-fibre. Purified, correctly folded, gp37 will be useful for receptor-binding studies, high-resolution structural studies and for specific binding and detection of bacteria.","corpus_id":38077951,"score":2},{"doc_id":"20478417","title":"The C-terminal domain is sufficient for host-binding activity of the Mu phage tail-spike protein.","abstract":"The Mu phage virion contains tail-spike proteins beneath the baseplate, which it uses to adsorb to the outer membrane of Escherichia coli during the infection process. The tail spikes are composed of gene product 45 (gp45), which contains 197 amino acid residues. In this study, we purified and characterized both the full-length and the C-terminal domains of recombinant gp45 to identify the functional and structural domains. Limited proteolysis resulted in a Ser64-Gln197 sequence, which was composed of a stable C-terminal domain. Analytical ultracentrifugation of the recombinant C-terminal domain (gp45-C) indicated that the molecular weight of gp45-C was about 58 kDa and formed a trimeric protomer in solution. Coprecipitation experiments and a quartz crystal microbalance (QCM) demonstrated that gp45-C irreversibly binds to the E. coli membrane. These results indicate that gp45 shows behaviors similar to tail-spike proteins of other phages; however, gp45 did not show significant sequence homology with the other phage tail-spike structures that have been identified.","corpus_id":5160019,"score":2},{"doc_id":"20531477","title":"[The beta-helical domain of bacteriophage T4 controls the folding of the fragment of long tail fibers in a chimeric protein].","abstract":"The key stage of the infection of the Escherichia coli cell with bacteriophage T4, the binding to the surface of the host cell, is determined by the specificity of the long tail fiber proteins of the phage, in particular, gp37. The assembly and oligomerization of this protein under natural conditions requires the participation of at least two additional protein factors, gp57A and gp38, which strongly hinders the production of the recombinant form of gp37. To overcome this problem, a modern protein engineering strategy was used, which involves the construction of a chimeric protein containing a carrier protein that drives the correct folding of the target protein. For this purpose, the trimeric beta-helical domain of another protein of phage T4, gp5, was used. It was shown that this domain, represented as a rigid trimeric polypeptide prism, has properties favorable for use as a protein carrier. A fragment of protein gp37 containing five pentapeptides repeats, Gly-X-His-X-His, which determine the binding to the receptors on the bacterial cell surface, was fused in a continuous reading frame to the C-terminus of the domain of gp5. The resulting chimeric protein forms a trimer that has the native conformation of gp37 and exhibits biological activity.","corpus_id":36456702,"score":2},{"doc_id":"20843802","title":"Crystal structure of bacteriophage SPP1 distal tail protein (gp19.1): a baseplate hub paradigm in gram-positive infecting phages.","abstract":"Siphophage SPP1 infects the gram-positive bacterium Bacillus subtilis using its long non-contractile tail and tail-tip. Electron microscopy (EM) previously allowed a low resolution assignment of most orf products belonging to these regions. We report here the structure of the SPP1 distal tail protein (Dit, gp19.1). The combination of x-ray crystallography, EM, and light scattering established that Dit is a back-to-back dimer of hexamers. However, Dit fitting in the virion EM maps was only possible with a hexamer located between the tail-tube and the tail-tip. Structure comparison revealed high similarity between Dit and a central component of lactophage baseplates. Sequence similarity search expanded its relatedness to several phage proteins, suggesting that Dit is a docking platform for the tail adsorption apparatus in Siphoviridae infecting gram-positive bacteria and that its architecture is a paradigm for these hub proteins. Dit structural similarity extends also to non-contractile and contractile phage tail proteins (gpV(N) and XkdM) as well as to components of the bacterial type 6 secretion system, supporting an evolutionary connection between all these devices.","corpus_id":21515226,"score":2},{"doc_id":"21041684","title":"Structure of the bacteriophage T4 long tail fiber receptor-binding tip.","abstract":"Bacteriophages are the most numerous organisms in the biosphere. In spite of their biological significance and the spectrum of potential applications, little high-resolution structural detail is available on their receptor-binding fibers. Here we present the crystal structure of the receptor-binding tip of the bacteriophage T4 long tail fiber, which is highly homologous to the tip of the bacteriophage lambda side tail fibers. This structure reveals an unusual elongated six-stranded antiparallel beta-strand needle domain containing seven iron ions coordinated by histidine residues arranged colinearly along the core of the biological unit. At the end of the tip, the three chains intertwine forming a broader head domain, which contains the putative receptor interaction site. The structure reveals a previously unknown beta-structured fibrous fold, provides insights into the remarkable stability of the fiber, and suggests a framework for mutations to expand or modulate receptor-binding specificity.","corpus_id":11209758,"score":2},{"doc_id":"21705802","title":"Atomic structure of bacteriophage Sf6 tail needle knob.","abstract":"Podoviridae are double-stranded DNA bacteriophages that use short, non-contractile tails to adsorb to the host cell surface. Within the tail apparatus of P22-like phages, a dedicated fiber known as the \"tail needle\" likely functions as a cell envelope-penetrating device to promote ejection of viral DNA inside the host. In Sf6, a P22-like phage that infects Shigella flexneri, the tail needle presents a C-terminal globular knob. This knob, absent in phage P22 but shared in other members of the P22-like genus, represents the outermost exposed tip of the virion that contacts the host cell surface. Here, we report a crystal structure of the Sf6 tail needle knob determined at 1.0 Å resolution. The structure reveals a trimeric globular domain of the TNF fold structurally superimposable with that of the tail-less phage PRD1 spike protein P5 and the adenovirus knob, domains that in both viruses function in receptor binding. However, P22-like phages are not known to utilize a protein receptor and are thought to directly penetrate the host surface. At 1.0 Å resolution, we identified three equivalents of l-glutamic acid (l-Glu) bound to each subunit interface. Although intimately bound to the protein, l-Glu does not increase the structural stability of the trimer nor it affects its ability to self-trimerize in vitro. In analogy to P22 gp26, we suggest the tail needle of phage Sf6 is ejected through the bacterial cell envelope during infection and its C-terminal knob is threaded through peptidoglycan pores formed by glycan strands.","corpus_id":19334689,"score":2},{"doc_id":"21821878","title":"The host-binding domain of the P2 phage tail spike reveals a trimeric iron-binding structure.","abstract":"The adsorption and infection of bacteriophage P2 is mediated by tail fibres and tail spikes. The tail spikes on the tail baseplate are used to irreversibly adsorb to the host cells. Recently, a P2 phage tail-spike protein, gpV, was purified and it was shown that a C-terminal domain, Ser87-Leu211, is sufficient for the binding of gpV to host Escherichia coli membranes [Kageyama et al. (2009), Biochemistry, 48, 10129-10135]. In this paper, the crystal structure of the C-terminal domain of P2 gpV is reported. The structure is a triangular pyramid and looks like a spearhead composed of an intertwined β-sheet, a triple β-helix and a metal-binding region containing iron, calcium and chloride ions.","corpus_id":5282916,"score":2},{"doc_id":"21885679","title":"A common evolutionary origin for tailed-bacteriophage functional modules and bacterial machineries.","abstract":"Bacteriophages belonging to the order Caudovirales possess a tail acting as a molecular nanomachine used during infection to recognize the host cell wall, attach to it, pierce it, and ensure the high-efficiency delivery of the genomic DNA to the host cytoplasm. In this review, we provide a comprehensive analysis of the various proteins constituting tailed bacteriophages from a structural viewpoint. To this end, we had in mind to pinpoint the resemblances within and between functional modules such as capsid/tail connectors, the tails themselves, or the tail distal host recognition devices, termed baseplates. This comparison has been extended to bacterial machineries embedded in the cell wall, for which shared molecular homology with phages has been recently revealed. This is the case for the type VI secretion system (T6SS), an inverted phage tail at the bacterial surface, or bacteriocins. Gathering all these data, we propose that a unique ancestral protein fold may have given rise to a large number of bacteriophage modules as well as to some related bacterial machinery components.","corpus_id":9299498,"score":2},{"doc_id":"22297990","title":"Crystallization of the C-terminal domain of the bacteriophage T7 fibre protein gp17.","abstract":"Bacteriophage T7 attaches to its host using the C-terminal domains of its six fibres, which are trimers of the gp17 protein. A C-terminal fragment of gp17 consisting of amino acids 371-553 has been expressed, purified and crystallized. Crystals of two forms were obtained, belonging to space group P2(1)2(1)2(1) (unit-cell parameters a = 61.2, b = 86.0, c = 118.4 Å) and space group C222(1) (unit-cell parameters a = 68.3, b = 145.6, c = 172.1 Å). They diffracted to 1.9 and 2.0 Å resolution, respectively. Both crystals are expected to contain one trimer in the asymmetric unit. Multiwavelength anomalous dispersion phasing with a mercury derivative is in progress.","corpus_id":9817331,"score":2},{"doc_id":"22303017","title":"Structural basis for antifreeze activity of ice-binding protein from arctic yeast.","abstract":"Arctic yeast Leucosporidium sp. produces a glycosylated ice-binding protein (LeIBP) with a molecular mass of ∼25 kDa, which can lower the freezing point below the melting point once it binds to ice. LeIBP is a member of a large class of ice-binding proteins, the structures of which are unknown. Here, we report the crystal structures of non-glycosylated LeIBP and glycosylated LeIBP at 1.57- and 2.43-Å resolution, respectively. Structural analysis of the LeIBPs revealed a dimeric right-handed β-helix fold, which is composed of three parts: a large coiled structural domain, a long helix region (residues 96-115 form a long α-helix that packs along one face of the β-helix), and a C-terminal hydrophobic loop region ((243)PFVPAPEVV(251)). Unexpectedly, the C-terminal hydrophobic loop region has an extended conformation pointing away from the body of the coiled structural domain and forms intertwined dimer interactions. In addition, structural analysis of glycosylated LeIBP with sugar moieties attached to Asn(185) provides a basis for interpreting previous biochemical analyses as well as the increased stability and secretion of glycosylated LeIBP. We also determined that the aligned Thr/Ser/Ala residues are critical for ice binding within the B face of LeIBP using site-directed mutagenesis. Although LeIBP has a common β-helical fold similar to that of canonical hyperactive antifreeze proteins, the ice-binding site is more complex and does not have a simple ice-binding motif. In conclusion, we could identify the ice-binding site of LeIBP and discuss differences in the ice-binding modes compared with other known antifreeze proteins and ice-binding proteins.","corpus_id":26030063,"score":2},{"doc_id":"22611190","title":"Structure of the phage TP901-1 1.8 MDa baseplate suggests an alternative host adhesion mechanism.","abstract":"Phages of the Caudovirales order possess a tail that recognizes the host and ensures genome delivery upon infection. The X-ray structure of the approximately 1.8 MDa host adsorption device (baseplate) from the lactococcal phage TP901-1 shows that the receptor-binding proteins are pointing in the direction of the host, suggesting that this organelle is in a conformation ready for host adhesion. This result is in marked contrast with the lactococcal phage p2 situation, whose baseplate is known to undergo huge conformational changes in the presence of Ca(2+) to reach its active state. In vivo infection experiments confirmed these structural observations by demonstrating that Ca(2+) ions are required for host adhesion among p2-like phages (936-species) but have no influence on TP901-1-like phages (P335-species). These data suggest that these two families rely on diverse adhesion strategies which may lead to different signaling for genome release.","corpus_id":863683,"score":2},{"doc_id":"22645347","title":"Structure of the receptor-binding carboxy-terminal domain of bacteriophage T7 tail fibers.","abstract":"The six bacteriophage T7 tail fibers, homo-trimers of gene product 17, are thought to be responsible for the first specific, albeit reversible, attachment to Escherichia coli lipopolysaccharide. The protein trimer forms kinked fibers comprised of an amino-terminal tail-attachment domain, a slender shaft, and a carboxyl-terminal domain composed of several nodules. Previously, we expressed, purified, and crystallized a carboxyl-terminal fragment comprising residues 371-553. Here, we report the structure of this protein trimer, solved using anomalous diffraction and refined at 2 Å resolution. Amino acids 371-447 form a tapered pyramid with a triangular cross-section composed of interlocked β-sheets from each of the three chains. The triangular pyramid domain has three α-helices at its narrow end, which are connected to a carboxyl-terminal three-blade β-propeller tip domain by flexible loops. The monomers of this tip domain each contain an eight-stranded β-sandwich. The exact topology of the β-sandwich fold is novel, but similar to that of knob domains of other viral fibers and the phage Sf6 needle. Several host-range change mutants have been mapped to loops located on the top of this tip domain, suggesting that this surface of the tip domain interacts with receptors on the cell surface.","corpus_id":22597494,"score":2},{"doc_id":"22659573","title":"New insights into pb5, the receptor binding protein of bacteriophage T5, and its interaction with its Escherichia coli receptor FhuA.","abstract":"The majority of bacterial viruses are bacteriophages bearing a tail that serves to recognise the bacterial surface and deliver the genome into the host cell. Infection is initiated by the irreversible interaction between the viral receptor binding protein (RBP) and a receptor at the surface of the bacterium. This interaction results ultimately in the phage DNA release in the host cytoplasm. Phage T5 infects Escherichia coli after binding of its RBP pb5 to the outer membrane ferrichrome transporter FhuA. Here, we have studied the complex formed by pb5 and FhuA by a variety of biophysical and biochemical techniques. We show that unlike RBPs of known structures, pb5 probably folds as a unique domain fulfilling both functions of binding to the host receptor and interaction with the rest of the phage. Pb5 likely binds to the domain occluding the β-barrel of FhuA as well as to external loops of the barrel. Furthermore, upon binding to FhuA, pb5 undergoes conformational changes, at the secondary and tertiary structure level that would be the key to the transmission of the signal through the tail to the capsid, triggering DNA release. This is the first structural information regarding the binding of a RBP to a proteic receptor.","corpus_id":20354844,"score":2},{"doc_id":"22666655","title":"The C-terminal cysteine annulus participates in auto-chaperone function for Salmonella phage P22 tailspike folding and assembly.","abstract":"Elongated trimeric adhesins are a distinct class of proteins employed by phages and viruses to recognize and bind to their host cells, and by bacteria to bind to their target cells and tissues. The tailspikes of E. coli phage K1F and Bacillus phage Ø29 exhibit auto-chaperone activity in their trimeric C-terminal domains. The P22 tailspike is structurally homologous to those adhesins. Though there are no disulfide bonds or reactive cysteines in the native P22 tailspikes, a set of C-terminal cysteines are very reactive in partially folded intermediates, implying an unusual local conformation in the domain. This is likely to be involved in the auto-chaperone function. We examined the unusual reactivity of C-terminal tailspike cysteines during folding and assembly as a potential reporter of auto-chaperone function. Reaction with IAA blocked productive refolding in vitro, but not off-pathway aggregation. Two-dimensional PAGE revealed that the predominant intermediate exhibiting reactive cysteine side chains was a partially folded monomer. Treatment with reducing reagent promoted native trimer formation from these species, consistent with transient disulfide bonds in the auto-chaperone domain. Limited enzymatic digestion and mass spectrometry of folding and assembly intermediates indicated that the C-terminal domain was compact in the protrimer species. These results indicate that the C-terminal domain of the P22 tailspike folds itself and associates prior to formation of the protrimer intermediate, and not after, as previously proposed. The C-terminal cysteines and triple β-helix domains apparently provide the staging for the correct auto-chaperone domain formation, needed for alignment of P22 tailspike native trimer.","corpus_id":17799096,"score":2},{"doc_id":"24155371","title":"Crystal structure of pb9, the distal tail protein of bacteriophage T5: a conserved structural motif among all siphophages.","abstract":"The tail of Caudovirales bacteriophages serves as an adsorption device, a host cell wall-perforating machine, and a genome delivery pathway. In Siphoviridae, the assembly of the long and flexible tail is a highly cooperative and regulated process that is initiated from the proteins forming the distal tail tip complex. In Gram-positive-bacterium-infecting siphophages, the distal tail (Dit) protein has been structurally characterized and is proposed to represent a baseplate hub docking structure. It is organized as a hexameric ring that connects the tail tube and the adsorption device. In this study, we report the characterization of pb9, a tail tip protein of Escherichia coli bacteriophage T5. By immunolocalization, we show that pb9 is located in the upper part of the cone of the T5 tail tip, at the end of the tail tube. The crystal structure of pb9 reveals a two-domain protein. Domain A exhibits remarkable structural similarity with the N-terminal domain of known Dit proteins, while domain B adopts an oligosaccharide/oligonucleotide-binding fold (OB-fold) that is not shared by these proteins. We thus propose that pb9 is the Dit protein of T5, making it the first Dit protein described for a Gram-negative-bacterium-infecting siphophage. Multiple sequence alignments suggest that pb9 is a paradigm for a large family of Dit proteins of siphophages infecting mostly Gram-negative hosts. The modular structure of the Dit protein maintains the basic building block that would be conserved among all siphophages, combining it with a more divergent domain that might serve specific host adhesion properties.","corpus_id":25872618,"score":2},{"doc_id":"24316831","title":"Crystallization of the C-terminal domain of the bacteriophage T5 L-shaped fibre.","abstract":"Tails of bacteriophage T5 (a member of the Siphoviridae family) were studied by electron microscopy. For the distal parts of the L-shaped tail fibres, which are involved in host cell receptor binding, a low-resolution volume was calculated. Several C-terminal fragments of the fibre were expressed and purified. Crystals of two of them were obtained that belonged to space groups P63 and R32 and diffracted synchrotron radiation to 2.3 and 2.9 Å resolution, respectively. A single-wavelength anomalous dispersion data set to 2.5 Å resolution was also collected from a selenomethionine-derivatized crystal of one of the fragments, which belonged to space group C2.","corpus_id":22403299,"score":2},{"doc_id":"24816102","title":"Bacteriophage P22 tailspike: structure of the complete protein and function of the interdomain linker.","abstract":"Attachment of phages to host cells, followed by phage DNA ejection, represents the first stage of viral infection of bacteria. Salmonella phage P22 has been extensively studied, serving as an experimental model for bacterial infection by phages. P22 engages bacteria by binding to the sugar moiety of lipopolysaccharides using the viral tailspike protein for attachment. While the structures of the N-terminal particle-binding domain and the major receptor-binding domain of the tailspike have been analyzed individually, the three-dimensional organization of the intact protein, including the highly conserved linker region between the two domains, remained unknown. A single amino-acid exchange in the linker sequence made it possible to crystallize the full-length protein. Two crystal structures of the linker region are presented: one attached to the N-terminal domain and the other present within the complete tailspike protein. Both retain their biological function, but the mutated full-length tailspike displays a retarded folding pathway. Fitting of the full-length tailspike into a published cryo-electron microscopy map of the P22 virion requires an elastic distortion of the crystal structure. The conservation of the linker suggests a role in signal transmission from the distal tip of the molecule to the phage head, eventually leading to DNA ejection.","corpus_id":19300673,"score":2},{"doc_id":"25005101","title":"Crystallization of the carboxy-terminal region of the bacteriophage T4 proximal long tail fibre protein gp34.","abstract":"The phage-proximal part of the long tail fibres of bacteriophage T4 consists of a trimer of the 1289 amino-acid gene product 34 (gp34). Different carboxy-terminal parts of gp34 have been produced and crystallized. Crystals of gp34(726-1289) diffracting X-rays to 2.9 Å resolution, crystals of gp34(781-1289) diffracting to 1.9 Å resolution and crystals of gp34(894-1289) diffracting to 3.0 and 2.0 Å resolution and belonging to different crystal forms were obtained. Native data were collected for gp34(726-1289) and gp34(894-1289), while single-wavelength anomalous diffraction data were collected for selenomethionine-containing gp34(781-1289) and gp34(894-1289). For the latter, high-quality anomalous signal was obtained.","corpus_id":26376710,"score":2},{"doc_id":"26805872","title":"Branched Lateral Tail Fiber Organization in T5-Like Bacteriophages DT57C and DT571/2 is Revealed by Genetic and Functional Analysis.","abstract":"The T5-like siphoviruses DT57C and DT571/2, isolated from horse feces, are very closely related to each other, and most of their structural proteins are also nearly identical to T5 phage. Their LTFs (L-shaped tail fibers), however, are composed of two proteins, LtfA and LtfB, instead of the single Ltf of bacteriophage T5. In silico and mutant analysis suggests a possible branched structure of DT57C and DT571/2 LTFs, where the LtfB protein is connected to the phage tail via the LtfA protein and with both proteins carrying receptor recognition domains. Such adhesin arrangement has not been previously recognized in siphoviruses. The LtfA proteins of our phages are found to recognize different host O-antigen types: E. coli O22-like for DT57C phage and E. coli O87 for DT571/2. LtfB proteins are identical in both phages and recognize another host receptor, most probably lipopolysaccharide (LPS) of E. coli O81 type. In these two bacteriophages, LTF function is essential to penetrate the shield of the host's O-antigens. We also demonstrate that LTF-mediated adsorption becomes superfluous when the non-specific cell protection by O-antigen is missing, allowing the phages to bind directly to their common secondary receptor, the outer membrane protein BtuB. The LTF independent adsorption was also demonstrated on an O22-like host mutant missing O-antigen O-acetylation, thus showing the biological value of this O-antigen modification for cell protection against phages.","corpus_id":334754,"score":2},{"doc_id":"28510021","title":"Molecular assembly and structure of the bacteriophage T4 tail.","abstract":"The tail of bacteriophage T4 undergoes large structural changes upon infection while delivering the phage genome into the host cell. The baseplate is located at the distal end of the contractile tail and plays a central role in transmitting the signal to the tail sheath that the tailfibers have been adsorbed by a host bacterium. This then triggers the sheath contraction. In order to understand the mechanism of assembly and conformational changes of the baseplate upon infection, we have determined the structure of an in vitro assembled baseplate through the three-dimensional reconstruction of cryo-electron microscopy images to a resolution of 3.8 Å from electron micrographs. The atomic structure was fitted to the baseplate structure before and after sheath contraction in order to elucidate the conformational changes that occur after bacteriophage T4 has attached itself to a cell surface. The structure was also used to investigate the protease digestion of the assembly intermediates and the mutation sites of the tail genes, resulting in a number of phenotypes.","corpus_id":9922995,"score":2},{"doc_id":"28665339","title":"Crystal Structure of the Carboxy-Terminal Region of the Bacteriophage T4 Proximal Long Tail Fiber Protein Gp34.","abstract":"Long tail fibers of bacteriophage T4 are formed by proteins gp34, gp35, gp36, and gp37, with gp34 located at the phage-proximal end and gp37 at the phage-distal, receptor-binding end. We have solved the structure of the carboxy-terminal region of gp34, consisting of amino acids 894-1289, by single-wavelength anomalous diffraction and extended the structure to amino acids 744-1289 using data collected from crystals containing longer gp34-fragments. The structure reveals three repeats of a mixed α-β fibrous domain in residues 744 to 877. A triple-helical neck connects to an extended triple β-helix domain (amino acids 900-1127) punctuated by two β-prism domains. Next, a β-prism domain decorated with short helices and extended β-helices is present (residues 1146-1238), while the C-terminal end is capped with another short β-helical region and three β-hairpins. The structure provides insight into the stability of the fibrous gp34 protein.","corpus_id":2193886,"score":2},{"doc_id":"29204885","title":"Bacteriophage T4 long tail fiber domains.","abstract":"Bacteriophage T4 initially recognizes its host cells using its long tail fibers. Long tail fibers consist of a phage-proximal and a phage-distal rod, each around 80 nm long and attached to each other at a slight angle. The phage-proximal rod is formed by a homo-trimer of gene product 34 (gp34) and is attached to the phage-distal rod by a monomer of gp35. The phage-distal rod consists of two protein trimers: a trimer of gp36, attached to gp35, although most of the phage-distal rod, including the receptor-binding domain, is formed by a trimer of gp37. In this review, we discuss what is known about the detailed structure and function of the different long tail fiber domains. Partial crystal structures of gp34 and gp37 have revealed the presence of new protein folds, some of which are present in several repeats, while others are apparently unique. Gp38, a phage chaperone protein necessary for folding of gp37, is thought to act on an α-helical coiled-coil region in gp37. Future studies should reveal the remaining structure of the long tail fibers, how they assemble into a functional unit, and how the long tail fibers trigger the infection process after successful recognition of a suitable host bacterium.","corpus_id":4871689,"score":2},{"doc_id":"29209037","title":"Bacteriophage T5 tail tube structure suggests a trigger mechanism for Siphoviridae DNA ejection.","abstract":"The vast majority of phages, bacterial viruses, possess a tail ensuring host recognition, cell wall perforation and safe viral DNA transfer from the capsid to the host cytoplasm. Long flexible tails are formed from the tail tube protein (TTP) polymerised as hexameric rings around and stacked along the tape measure protein (TMP). Here, we report the crystal structure of T5 TTP pb6 at 2.2 Å resolution. Pb6 is unusual in forming a trimeric ring, although structure analysis reveals homology with all classical TTPs and related tube proteins of bacterial puncturing devices (type VI secretion system and R-pyocin). Structures of T5 tail tubes before and after interaction with the host receptor were determined by cryo-electron microscopy at 6 Å resolution. Comparison of these two structures reveals that host-binding information is not propagated to the capsid through conformational changes in the tail tube, suggesting a role of the TMP in this information transduction process.","corpus_id":21264668,"score":2},{"doc_id":"18189419","title":"Crystal structure of a novel bacterial cell-surface flagellin binding to a polysaccharide.","abstract":"Bacterial flagellins are generally self-assembled into extracellular flagella for cell motility. However, the flagellin homologue p5 is found on the cell surface of Sphingomonas sp. A1 (strain A1) and binds tightly to the alginate polysaccharide. To assimilate alginate, strain A1 forms a mouthlike pit on the cell surface and concentrates the polymer in the pit. p5 is a candidate receptor that recognizes extracellular alginate and controls pit formation. To improve our understanding of the structure and function of p5, we determined the crystal structure of truncated p5 (p5DeltaN53C45) at 2.0 A resolution. This, to our knowledge, is the first structure of flagellin_IN motif-containing flagellin. p5DeltaN53C45 consists of two domains: an alpha-domain rich in alpha-helices that forms the N- and C-terminal regions and a beta-domain rich in beta-strands that constitutes the central region. The alpha-domain is structurally similar to the D1 domain of Salmonella typhimurium flagellin, while the beta-domain is structurally similar to the finger domain of the bacteriophage T4 baseplate protein that is important for intermolecular interactions between baseplate and a long or short tail fiber. Results from the deletion mutant analysis suggest that residues 20-40 and 353-363 are responsible for alginate binding. Truncated N- and C-terminal regions are thought to constitute alpha-helices extending from the alpha-domain. On the basis of the size and surface charge, the cleft in extended alpha-helices is proposed as an alginate binding site of p5. Structural similarity in the beta-domain suggests that the beta-domain is involved in the proper localization and/or orientation of p5 on the cell surface.","corpus_id":11163721,"score":1},{"doc_id":"18201719","title":"Structure and molecular dynamics simulation of archaeal prefoldin: the molecular mechanism for binding and recognition of nonnative substrate proteins.","abstract":"Prefoldin (PFD) is a heterohexameric molecular chaperone complex in the eukaryotic cytosol and archaea with a jellyfish-like structure containing six long coiled-coil tentacles. PFDs capture protein folding intermediates or unfolded polypeptides and transfer them to group II chaperonins for facilitated folding. Although detailed studies on the mechanisms for interaction with unfolded proteins or cooperation with chaperonins of archaeal PFD have been performed, it is still unclear how PFD captures the unfolded protein. In this study, we determined the X-ray structure of Pyrococcus horikoshii OT3 PFD (PhPFD) at 3.0 A resolution and examined the molecular mechanism for binding and recognition of nonnative substrate proteins by molecular dynamics (MD) simulation and mutation analyses. PhPFD has a jellyfish-like structure with six long coiled-coil tentacles and a large central cavity. Each subunit has a hydrophobic groove at the distal region where an unfolded substrate protein is bound. During MD simulation at 330 K, each coiled coil was highly flexible, enabling it to widen its central cavity and capture various nonnative proteins. Docking MD simulation of PhPFD with unfolded insulin showed that the beta subunit is essentially involved in substrate binding and that the alpha subunit modulates the shape and width of the central cavity. Analyses of mutant PhPFDs with amino acid replacement of the hydrophobic residues of the beta subunit in the hydrophobic groove have shown that beta Ile107 has a critical role in forming the hydrophobic groove.","corpus_id":43335465,"score":1},{"doc_id":"19218213","title":"Crystallographic structure of the alpha-helical triple coiled-coil domain of avian reovirus S1133 fibre.","abstract":"Avian reovirus fibre, a homo-trimer of the sigmaC protein, is a minor component of the avian reovirus outer capsid. It is anchored via a short N-terminal sequence to the inner capsid lambdaC pentamer, and its protruding globular C-terminal domain is responsible for primary host cell attachment. We have previously solved the structure of a receptor-binding fragment in which residues 160-191 form a triple beta-spiral and 196-326 a beta-barrel head domain. Here we have expressed, purified and crystallized a major sigmaC fragment comprising residues 117-326. Its structure, which was solved by molecular replacement using the previously determined receptor-binding domain structure and refined to 1.75 A (0.175 nm) resolution, reveals an alpha-helical triple coiled-coil connected to the previously solved structure by a zinc-ion-containing linker. The coiled-coil domain contains two chloride ion binding sites, as well as specific trimerization and registration sequences. The linker may act as a functionally important hinge.","corpus_id":206211556,"score":1},{"doc_id":"19241380","title":"Structural plasticity of the phage P22 tail needle gp26 probed with xenon gas.","abstract":"The tail needle, gp26, is a highly stable homo-trimeric fiber found in the tail apparatus of bacteriophage P22. In the mature virion, gp26 is responsible for plugging the DNA exit channel, and likely plays an important role in penetrating the host cell envelope. In this article, we have determined the 1.98 A resolution crystal structure of gp26 bound to xenon gas. The structure led us to identify a calcium and a chloride ion intimately bound at the interior of alpha-helical core, as well as seven small cavities occupied by xenon atoms. The two ions engage in buried polar interactions with gp26 side chains that provide specificity and register to gp26 helical core, thus enhancing its stability. Conversely, the distribution of xenon accessible cavities correlates well with the flexibility of the fiber observed in solution and in the crystal structure. We suggest that small internal cavities in gp26 between the helical core and the C-terminal tip allow for flexible swinging of the latter, without affecting the overall stability of the protein. The C-terminal tip may be important in scanning the bacterial surface in search of a cell-envelope penetration site, or for recognition of a yet unidentified receptor on the surface of the host.","corpus_id":25594438,"score":1},{"doc_id":"19482036","title":"An evolutionarily conserved family of virion tail needles related to bacteriophage P22 gp26: correlation between structural stability and length of the alpha-helical trimeric coiled coil.","abstract":"Bacteriophages of the Podoviridae family use short noncontractile tails to inject their genetic material into Gram-negative bacteria. In phage P22, the tail contains a thin needle, encoded by the phage gene 26, which is essential both for stabilization and for ejection of the packaged viral genome. Bioinformatic analysis of the N-terminal domain of gp26 (residues 1-60) led us to identify a family of genes encoding putative homologues of the tail needle gp26. To validate this idea experimentally and to explore their diversity, we cloned the gp26-like gene from phages HK620, Sf6 and HS1, and characterized these gene products in solution. All gp26-like factors contain an elongated alpha-helical coiled-coil core consisting of repeating, adjacent trimerization heptads and form trimeric fibers with length ranging between about 240 to 300 A. gp26 tail needles display a high level of structural stability in solution, with T(m) (temperature of melting) between 85 and 95 degrees C. To determine how the structural stability of these phage fibers correlates with the length of the alpha-helical core, we investigated the effect of insertions and deletions in the helical core. In the P22 tail needle, we identified an 85-residue-long helical domain, termed MiCRU (minimal coiled-coil repeat unit), that can be inserted in-frame inside the gp26 helical core, preserving the straight morphology of the fiber. Likewise, we were able to remove three quarters of the helical core of the HS1 tail needle, minimally decreasing the stability of the fiber. We conclude that in the gp26 family of tail needles, structural stability increases nonlinearly with the length of the alpha-helical core. Thus, the overall stability of these bacteriophage fibers is not solely dependent on the number of trimerization repeats in the alpha-helical core.","corpus_id":27199806,"score":1},{"doc_id":"19895817","title":"The crystal structure of bacteriophage HK97 gp6: defining a large family of head-tail connector proteins.","abstract":"The final step in the morphogenesis of long-tailed double-stranded DNA bacteriophages is the joining of the DNA-filled head to the tail. The connector is a specialized structure of the head that serves as the interface for tail attachment and the point of egress for DNA from the head during infection. Here, we report the determination of a 2.1 A crystal structure of gp6 of bacteriophage HK97. Through structural comparisons, functional studies, and bioinformatic analysis, gp6 has been determined to be a component of the connector of phage HK97 that is evolutionarily related to gp15, a well-characterized connector component of bacteriophage SPP1. Whereas the structure of gp15 was solved in a monomeric form, gp6 crystallized as an oligomeric ring with the dimensions expected for a connector protein. Although this ring is composed of 13 subunits, which does not match the symmetry of the connector within the phage, sequence conservation and modeling of this structure into the cryo-electron microscopy density of the SPP1 connector indicate that this oligomeric structure represents the arrangement of gp6 subunits within the mature phage particle. Through sequence searches and genomic position analysis, we determined that gp6 is a member of a large family of connector proteins that are present in long-tailed phages. We have also identified gp7 of HK97 as a homologue of gp16 of phage SPP1, which is the second component of the connector of this phage. These proteins are members of another large protein family involved in connector assembly.","corpus_id":6534193,"score":1},{"doc_id":"20693685","title":"Structure of the N-terminal fragment of Escherichia coli Lon protease.","abstract":"The structure of a recombinant construct consisting of residues 1-245 of Escherichia coli Lon protease, the prototypical member of the A-type Lon family, is reported. This construct encompasses all or most of the N-terminal domain of the enzyme. The structure was solved by SeMet SAD to 2.6 A resolution utilizing trigonal crystals that contained one molecule in the asymmetric unit. The molecule consists of two compact subdomains and a very long C-terminal alpha-helix. The structure of the first subdomain (residues 1-117), which consists mostly of beta-strands, is similar to that of the shorter fragment previously expressed and crystallized, whereas the second subdomain is almost entirely helical. The fold and spatial relationship of the two subdomains, with the exception of the C-terminal helix, closely resemble the structure of BPP1347, a 203-amino-acid protein of unknown function from Bordetella parapertussis, and more distantly several other proteins. It was not possible to refine the structure to satisfactory convergence; however, since almost all of the Se atoms could be located on the basis of their anomalous scattering the correctness of the overall structure is not in question. The structure reported here was also compared with the structures of the putative substrate-binding domains of several proteins, showing topological similarities that should help in defining the binding sites used by Lon substrates.","corpus_id":10466829,"score":1},{"doc_id":"20826161","title":"The solution structure of the C-terminal Ig-like domain of the bacteriophage λ tail tube protein.","abstract":"Immunoglobulin (Ig)-like domains are found frequently on the surface of tailed double-stranded DNA bacteriophages, yet their functional role remains obscure. Here, we have investigated the structure and function of the C-terminal Ig-like domain of gpV (gpV(C)), the tail tube protein of phage λ. This domain has been predicted through sequence similarity to be a member of the bacterial Ig-like domain 2 (Big_2) family, which is composed of more than 1300 phage and bacterial sequences. Using trypsin proteolysis, we have delineated the boundaries of gpV(C) and have shown that its removal reduces the biological activity of gpV by 100-fold; thus providing a definitive demonstration of a functional role for this domain. Determination of the solution structure of gpV(C) by NMR spectroscopy showed that it adopts a canonical Ig-like fold of the I-set class. This represents the first structure of a phage-encoded Ig-like domain and only the second structure of a Big_2 domain. Structural and sequence comparisons indicate that the gpV(C) structure is more representative of both the phage-encoded Big_2 domains and Big_2 domains in general than the other available Big_2 structure. Bioinformatics analyses have identified two conserved clusters of residues on the surface of gpV(C) that may be important in mediating the function of this domain.","corpus_id":45685977,"score":1},{"doc_id":"21646642","title":"Unraveling lactococcal phage baseplate assembly by mass spectrometry.","abstract":"Bacteriophages belonging to the Caudovirales order possess a tail acting as a molecular machine used during infection to recognize the host and ensure high-efficiency genome delivery to the cell cytoplasm. They bear a large and sophisticated multiprotein organelle at their distal tail end, either a baseplate or a tail-tip, which is the control center for infectivity. We report here insights into the baseplate assembly pathways of two lactoccocal phages (p2 and TP901-1) using electrospray ionization-mass spectrometry. Based on our \"block cloning\" strategy we have expressed large complexes of their baseplates as well as several significant structural subcomplexes. Previous biophysical characterization using size-exclusion chromatography coupled with on-line light scattering and refractometry demonstrated that the overproduced recombinant proteins interact with each other to form large (up to 1.9 MDa) and stable assemblies. The structures of several of these complexes have been determined by x-ray diffraction or by electron microscopy. In this contribution, we demonstrate that electrospray ionization-mass spectrometry yields accurate mass measurements for the different baseplate complexes studied from which their stoichiometries can be discerned, and that the subspecies observed in the spectra provide valuable information on the assembly mechanisms of these large organelles.","corpus_id":20813814,"score":1},{"doc_id":"21805520","title":"Crystal structure of the read-through domain from bacteriophage Qβ A1 protein.","abstract":"Bacteriophage Qβ is a small RNA virus that infects Escherichia coli. The virus particle contains a few copies of the minor coat protein A1, a C-terminally prolonged version of the coat protein, which is formed when ribosomes occasionally read-through the leaky stop codon of the coat protein. The crystal structure of the read-through domain from bacteriophage Qβ A1 protein was determined at a resolution of 1.8 Å. The domain consists of a heavily deformed five-stranded β-barrel on one side of the protein and a β-hairpin and a three-stranded β-sheet on the other. Several short helices and well-ordered loops are also present throughout the protein. The N-terminal part of the read-through domain contains a prominent polyproline type II helix. The overall fold of the domain is not similar to any published structure in the Protein Data Bank.","corpus_id":3418824,"score":1},{"doc_id":"22153511","title":"Structural conservation of the myoviridae phage tail sheath protein fold.","abstract":"Bacteriophage phiKZ is a giant phage that infects Pseudomonas aeruginosa, a human pathogen. The phiKZ virion consists of a 1450 Å diameter icosahedral head and a 2000 Å-long contractile tail. The structure of the whole virus was previously reported, showing that its tail organization in the extended state is similar to the well-studied Myovirus bacteriophage T4 tail. The crystal structure of a tail sheath protein fragment of phiKZ was determined to 2.4 Å resolution. Furthermore, crystal structures of two prophage tail sheath proteins were determined to 1.9 and 3.3 Å resolution. Despite low sequence identity between these proteins, all of these structures have a similar fold. The crystal structure of the phiKZ tail sheath protein has been fitted into cryo-electron-microscopy reconstructions of the extended tail sheath and of a polysheath. The structural rearrangement of the phiKZ tail sheath contraction was found to be similar to that of phage T4.","corpus_id":5103216,"score":1},{"doc_id":"23530214","title":"Viral infection modulation and neutralization by camelid nanobodies.","abstract":"Lactococcal phages belong to a large family of Siphoviridae and infect Lactococcus lactis, a gram-positive bacterium used in commercial dairy fermentations. These phages are believed to recognize and bind specifically to pellicle polysaccharides covering the entire bacterium. The phage TP901-1 baseplate, located at the tip of the tail, harbors 18 trimeric receptor binding proteins (RBPs) promoting adhesion to a specific lactococcal strain. Phage TP901-1 adhesion does not require major conformational changes or Ca(2+), which contrasts other lactococcal phages. Here, we produced and characterized llama nanobodies raised against the purified baseplate and the Tal protein of phage TP901-1 as tools to dissect the molecular determinants of phage TP901-1 infection. Using a set of complementary techniques, surface plasmon resonance, EM, and X-ray crystallography in a hybrid approach, we identified binders to the three components of the baseplate, analyzed their affinity for their targets, and determined their epitopes as well as their functional impact on TP901-1 phage infectivity. We determined the X-ray structures of three nanobodies in complex with the RBP. Two of them bind to the saccharide binding site of the RBP and are able to fully neutralize TP901-1 phage infectivity, even after 15 passages. These results provide clear evidence for a practical use of nanobodies in circumventing lactococcal phages viral infection in dairy fermentation.","corpus_id":33331946,"score":1},{"doc_id":"24100566","title":"Crystallization of the C-terminal head domain of the fibre protein from a siadenovirus, turkey adenovirus 3.","abstract":"Turkey adenovirus 3 belongs to the genus Siadenovirus. Its predicted fibre protein consists of an N-terminal virus-attachment domain, a central shaft domain and a head domain at the C-terminus. The head domain has little sequence identity to known adenovirus fibre head structures. Crystals of the fibre head domain consisting of amino acids 304-454 with an N-terminal purification tag were produced. Crystals of native and selenomethionine-derivatized protein belonged to space group I23 (unit-cell parameter 99 Å). They diffracted synchrotron radiation to 2.0 and 2.14 Å resolution, respectively, and are expected to contain one monomer in the asymmetric unit.","corpus_id":6477287,"score":1},{"doc_id":"24316834","title":"Crystallization of the C-terminal domain of the fibre protein from snake adenovirus 1, an atadenovirus.","abstract":"Adenovirus fibre proteins play an important role in determining viral tropism. The C-terminal domain of the fibre protein from snake adenovirus type 1, a member of the Atadenovirus genus, has been expressed, purified and crystallized. Crystals were obtained belonging to space groups P2(1)2(1)2(1) (two different forms), I2(1)3 and F23. The best of these diffracted synchrotron radiation to a resolution of 1.4 Å. As the protein lacks methionines or cysteines, site-directed mutagenesis was performed to change two leucine residues to methionines. Crystals of selenomethionine-derivatized crystals of the I2(1)3 form were also obtained and a multi-wavelength anomalous dispersion data set was collected.","corpus_id":35326870,"score":1},{"doc_id":"24336205","title":"Icosahedral bacteriophage ΦX174 forms a tail for DNA transport during infection.","abstract":"Prokaryotic viruses have evolved various mechanisms to transport their genomes across bacterial cell walls. Many bacteriophages use a tail to perform this function, whereas tail-less phages rely on host organelles. However, the tail-less, icosahedral, single-stranded DNA ΦX174-like coliphages do not fall into these well-defined infection processes. For these phages, DNA delivery requires a DNA pilot protein. Here we show that the ΦX174 pilot protein H oligomerizes to form a tube whose function is most probably to deliver the DNA genome across the host's periplasmic space to the cytoplasm. The 2.4 Å resolution crystal structure of the in vitro assembled H protein's central domain consists of a 170 Å-long α-helical barrel. The tube is constructed of ten α-helices with their amino termini arrayed in a right-handed super-helical coiled-coil and their carboxy termini arrayed in a left-handed super-helical coiled-coil. Genetic and biochemical studies demonstrate that the tube is essential for infectivity but does not affect in vivo virus assembly. Cryo-electron tomograms show that tubes span the periplasmic space and are present while the genome is being delivered into the host cell's cytoplasm. Both ends of the H protein contain transmembrane domains, which anchor the assembled tubes into the inner and outer cell membranes. The central channel of the H-protein tube is lined with amide and guanidinium side chains. This may be a general property of viral DNA conduits and is likely to be critical for efficient genome translocation into the host.","corpus_id":205236687,"score":1},{"doc_id":"24531468","title":"Exploring the atomic structure and conformational flexibility of a 320 Å long engineered viral fiber using X-ray crystallography.","abstract":"Protein fibers are widespread in nature, but only a limited number of high-resolution structures have been determined experimentally. Unlike globular proteins, fibers are usually recalcitrant to form three-dimensional crystals, preventing single-crystal X-ray diffraction analysis. In the absence of three-dimensional crystals, X-ray fiber diffraction is a powerful tool to determine the internal symmetry of a fiber, but it rarely yields atomic resolution structural information on complex protein fibers. An 85-residue-long minimal coiled-coil repeat unit (MiCRU) was previously identified in the trimeric helical core of tail needle gp26, a fibrous protein emanating from the tail apparatus of the bacteriophage P22 virion. Here, evidence is provided that an MiCRU can be inserted in frame inside the gp26 helical core to generate a rationally extended fiber (gp26-2M) which, like gp26, retains a trimeric quaternary structure in solution. The 2.7 Å resolution crystal structure of this engineered fiber, which measures ∼320 Å in length and is only 20-35 Å wide, was determined. This structure, the longest for a trimeric protein fiber to be determined to such a high resolution, reveals the architecture of 22 consecutive trimerization heptads and provides a framework to decipher the structural determinants for protein fiber assembly, stability and flexibility.","corpus_id":22279907,"score":1},{"doc_id":"24598932","title":"Combining secondary-structure and protein solvent-accessibility predictions in methionine substitution for anomalous dispersion.","abstract":"In X-ray crystallographic analysis, the single-wavelength and multi-wavelength anomalous diffraction (SAD and MAD) methods have been widely used in order to solve the phase problem. Selenium-labelled methionine has been shown to be very effective for anomalous dispersion phasing, and at least one selenomethionine is required for every 100 amino acids. Some proteins, such as the Arabidopsis thaliana thylakoid lumen protein AtTLP18.3, can be overexpressed in an Escherichia coli system and high-quality protein crystals can be obtained. However, AtTLP18.3 contains no methionine residues, and site-directed mutagenesis was required in order to introduce methionine residues into the protein. A criterion for the mutated residues is that they should avoid affecting the structure and function. In this study, several leucine and isoleucine residues were selected for methionine substitution by combining secondary-structure and solvent-accessibility predictions. From the secondary-structure prediction, mutated residues were first determined in the coil or loop regions at the junction of two secondary structures. Since leucine and isoleucine residues are hydrophobic and are normally buried within the protein core, these residues should have a higher solvent-accessibility prediction so that they would be partially buried or exposed in the protein. In addition, five residues (Leu107, Leu202, Ile133, Leu128 and Ile159) of AtTLP18.3 were mutated to methionine residues. After overexpression and purification, only two single-mutant lines, L128M and I159M, could be crystallized. Finally, a double-mutation line of truncated AtTLP18.3 with L128M and I159M mutations was constructed. The structure of the double mutant AtTLP18.3 protein was resolved using the single-wavelength anomalous diffraction method at 2.6 Å resolution. The results indicated that a combination of secondary-structure and solvent-accessibility prediction for methionine substitution is a useful method in SAD and MAD phasing.","corpus_id":22549296,"score":1},{"doc_id":"25064136","title":"Crystal structure of the lytic CHAP(K) domain of the endolysin LysK from Staphylococcus aureus bacteriophage K.","abstract":"BACKGROUND: Bacteriophages encode endolysins to lyse their host cell and allow escape of their progeny. Endolysins are also active against Gram-positive bacteria when applied from the outside and are thus attractive anti-bacterial agents. LysK, an endolysin from staphylococcal phage K, contains an N-terminal cysteine-histidine dependent amido-hydrolase/peptidase domain (CHAP(K)), a central amidase domain and a C-terminal SH3b cell wall-binding domain. CHAP(K) cleaves bacterial peptidoglycan between the tetra-peptide stem and the penta-glycine bridge. METHODS: The CHAP(K) domain of LysK was crystallized and high-resolution diffraction data was collected both from a native protein crystal and a methylmercury chloride derivatized crystal. The anomalous signal contained in the derivative data allowed the location of heavy atom sites and phase determination. The resulting structures were completed, refined and analyzed. The presence of calcium and zinc ions in the structure was confirmed by X-ray fluorescence emission spectroscopy. Zymogram analysis was performed on the enzyme and selected site-directed mutants. RESULTS: The structure of CHAP(K) revealed a papain-like topology with a hydrophobic cleft, where the catalytic triad is located. Ordered buffer molecules present in this groove may mimic the peptidoglycan substrate. When compared to previously solved CHAP domains, CHAP(K) contains an additional lobe in its N-terminal domain, with a structural calcium ion, coordinated by residues Asp45, Asp47, Tyr49, His51 and Asp56. The presence of a zinc ion in the active site was also apparent, coordinated by the catalytic residue Cys54 and a possible substrate analogue. Site-directed mutagenesis was used to demonstrate that residues involved in calcium binding and of the proposed active site were important for enzyme activity. CONCLUSIONS: The high-resolution structure of the CHAP(K) domain of LysK was determined, suggesting the location of the active site, the substrate-binding groove and revealing the presence of a structurally important calcium ion. A zinc ion was found more loosely bound. Based on the structure, we propose a possible reaction mechanism. Future studies will be aimed at co-crystallizing CHAP(K) with substrate analogues and elucidating its role in the complete LysK protein. This, in turn, may lead to the design of site-directed mutants with altered activity or substrate specificity.","corpus_id":1380517,"score":1},{"doc_id":"25994880","title":"Crystal structure of the fibre head domain of bovine adenovirus 4, a ruminant atadenovirus.","abstract":"BACKGROUND: In adenoviruses, primary host cell recognition is generally performed by the head domains of their homo-trimeric fibre proteins. This first interaction is reversible. A secondary, irreversible interaction subsequently takes place via other adenovirus capsid proteins and leads to a productive infection. Although many fibre head structures are known for human mastadenoviruses, not many animal adenovirus fibre head structures have been determined, especially not from those belonging to adenovirus genera other than Mastadenovirus. METHODS: We constructed an expression vector for the fibre head domain from a ruminant atadenovirus, bovine adenovirus 4 (BAdV-4), consisting of amino acids 414-535, expressed the protein in Escherichia coli, purified it by metal affinity and cation exchange chromatography and crystallized it. The structure was solved using single isomorphous replacement plus anomalous dispersion of a mercury derivative and refined against native data that extended to 1.2 Å resolution. RESULTS: Like in other adenoviruses, the BAdV-4 fibre head monomer contains a beta-sandwich consisting of ABCJ and GHID sheets. The topology is identical to the fibre head of the other studied atadenovirus, snake adenovirus 1 (SnAdV-1), including the alpha-helix in the DG-loop, despite of them having a sequence identity of only 15 %. There are also differences which may have implications for ligand binding. Beta-strands G and H are longer and differences in several surface-loops and surface charge are observed. CONCLUSIONS: Chimeric adenovirus fibres have been used to retarget adenovirus-based anti-cancer and gene therapy vectors. Ovine adenovirus 7 (OAdV-7), another ruminant atadenovirus, is intensively tested as a basis for such a vector. Here, we present the high-resolution atomic structure of the BAdV-4 fibre head domain, the second atadenovirus fibre head structure known and the first of an atadenovirus that infects a mammalian host. Future research should focus on the receptor-binding properties of these fibre head domains.","corpus_id":8568594,"score":1},{"doc_id":"26418008","title":"Structure and Sialyllactose Binding of the Carboxy-Terminal Head Domain of the Fibre from a Siadenovirus, Turkey Adenovirus 3.","abstract":"The virulent form of turkey adenovirus 3 (TAdV-3), also known as turkey hemorrhagic enteritis virus (THEV), is an economically important poultry pathogen, while the avirulent form is used as a vaccine. TAdV-3 belongs to the genus Siadenovirus. The carboxy-terminal region of its fibre does not have significant sequence similarity to any other adenovirus fibre heads of known structure. Two amino acid sequence differences between virulent and avirulent TAdV-3 map on the fibre head: where virulent TAdV-3 contains Ile354 and Thr376, avirulent TAdV-3 contains Met354 and Met376. We determined the crystal structures of the trimeric virulent and avirulent TAdV-3 fibre head domains at 2.2 Å resolution. Each monomer contains a beta-sandwich, which, surprisingly, resembles reovirus fibre head more than other adenovirus fibres, although the ABCJ-GHID topology is conserved in all. A beta-hairpin insertion in the C-strand of each trimer subunit embraces its neighbouring monomer. The avirulent and virulent TAdV-3 fibre heads are identical apart from the exact orientation of the beta-hairpin insertion. In vitro, sialyllactose was identified as a ligand by glycan microarray analysis, nuclear magnetic resonance spectroscopy, and crystallography. Its dissociation constant was measured to be in the mM range by isothermal titration calorimetry. The ligand binds to the side of the fibre head, involving amino acids Glu392, Thr419, Val420, Lys421, Asn422, and Gly423 binding to the sialic acid group. It binds slightly more strongly to the avirulent form. We propose that, in vivo, the TAdV-3 fibre may bind a sialic acid-containing cell surface component.","corpus_id":23279362,"score":1},{"doc_id":"26574546","title":"Structural Plasticity of the Protein Plug That Traps Newly Packaged Genomes in Podoviridae Virions.","abstract":"Bacterial viruses of the P22-like family encode a specialized tail needle essential for genome stabilization after DNA packaging and implicated in Gram-negative cell envelope penetration. The atomic structure of P22 tail needle (gp26) crystallized at acidic pH reveals a slender fiber containing an N-terminal \"trimer of hairpins\" tip. Although the length and composition of tail needles vary significantly in Podoviridae, unexpectedly, the amino acid sequence of the N-terminal tip is exceptionally conserved in more than 200 genomes of P22-like phages and prophages. In this paper, we used x-ray crystallography and EM to investigate the neutral pH structure of three tail needles from bacteriophage P22, HK620, and Sf6. In all cases, we found that the N-terminal tip is poorly structured, in stark contrast to the compact trimer of hairpins seen in gp26 crystallized at acidic pH. Hydrogen-deuterium exchange mass spectrometry, limited proteolysis, circular dichroism spectroscopy, and gel filtration chromatography revealed that the N-terminal tip is highly dynamic in solution and unlikely to adopt a stable trimeric conformation at physiological pH. This is supported by the cryo-EM reconstruction of P22 mature virion tail, where the density of gp26 N-terminal tip is incompatible with a trimer of hairpins. We propose the tail needle N-terminal tip exists in two conformations: a pre-ejection extended conformation, which seals the portal vertex after genome packaging, and a postejection trimer of hairpins, which forms upon its release from the virion. The conformational plasticity of the tail needle N-terminal tip is built in the amino acid sequence, explaining its extraordinary conservation in nature.","corpus_id":34346428,"score":1},{"doc_id":"26814179","title":"The Atomic Structure of the Phage Tuc2009 Baseplate Tripod Suggests that Host Recognition Involves Two Different Carbohydrate Binding Modules.","abstract":"UNLABELLED: The Gram-positive bacterium Lactococcus lactis, used for the production of cheeses and other fermented dairy products, falls victim frequently to fortuitous infection by tailed phages. The accompanying risk of dairy fermentation failures in industrial facilities has prompted in-depth investigations of these phages. Lactococcal phage Tuc2009 possesses extensive genomic homology to phage TP901-1. However, striking differences in the baseplate-encoding genes stimulated our interest in solving the structure of this host's adhesion device. We report here the X-ray structures of phage Tuc2009 receptor binding protein (RBP) and of a \"tripod\" assembly of three baseplate components, BppU, BppA, and BppL (the RBP). These structures made it possible to generate a realistic atomic model of the complete Tuc2009 baseplate that consists of an 84-protein complex: 18 BppU, 12 BppA, and 54 BppL proteins. The RBP head domain possesses a different fold than those of phages p2, TP901-1, and 1358, while the so-called \"stem\" and \"neck\" domains share structural features with their equivalents in phage TP901-1. The BppA module interacts strongly with the BppU N-terminal domain. Unlike other characterized lactococcal phages, Tuc2009 baseplate harbors two different carbohydrate recognition sites: one in the bona fide RBP head domain and the other in BppA. These findings represent a major step forward in deciphering the molecular mechanism by which Tuc2009 recognizes its saccharidic receptor(s) on its host. IMPORTANCE: Understanding how siphophages infect Lactococcus lactis is of commercial importance as they cause milk fermentation failures in the dairy industry. In addition, such knowledge is crucial in a general sense in order to understand how viruses recognize their host through protein-glycan interactions. We report here the lactococcal phage Tuc2009 receptor binding protein (RBP) structure as well as that of its baseplate. The RBP head domain has a different fold than those of phages p2, TP901-1, and 1358, while the so-called \"stem\" and \"neck\" share the fold characteristics also found in the equivalent baseplate proteins of phage TP901-1. The baseplate structure contains, in contrast to other characterized lactococcal phages, two different carbohydrate binding modules that may bind different motifs of the host's surface polysaccharide.","corpus_id":15144214,"score":1},{"doc_id":"27334597","title":"Crystal structure of raptor adenovirus 1 fibre head and role of the beta-hairpin in siadenovirus fibre head domains.","abstract":"BACKGROUND: Most adenoviruses recognize their host cells via an interaction of their fibre head domains with a primary receptor. The structural framework of adenovirus fibre heads is conserved between the different adenovirus genera for which crystal structures have been determined (Mastadenovirus, Aviadenovirus, Atadenovirus and Siadenovirus), but genus-specific differences have also been observed. The only known siadenovirus fibre head structure, that of turkey adenovirus 3 (TAdV-3), revealed a twisted beta-sandwich resembling the reovirus fibre head architecture more than that of other adenovirus fibre heads, plus a unique beta-hairpin embracing a neighbouring monomer. The TAdV-3 fibre head was shown to bind sialyllactose. METHODS: Raptor adenovirus 1 (RAdV-1) fibre head was expressed, crystallized and its structure was solved and refined at 1.5 Å resolution. The structure could be solved by molecular replacement using the TAdV-3 fibre head structure as a search model, despite them sharing a sequence identity of only 19 %. Versions of both the RAdV-1 and TAdV-3 fibre heads with their beta-hairpin arm deleted were prepared and their stabilities were compared with the non-mutated proteins by a thermal unfolding assay. RESULTS: The structure of the RAdV-1 fibre head contains the same twisted ABCJ-GHID beta-sandwich and beta-hairpin arm as the TAdV-3 fibre head. However, while the predicted electro-potential surface charge of the TAdV-3 fibre head is mainly positive, the RAdV-1 fibre head shows positively and negatively charged patches and does not appear to bind sialyllactose. Deletion of the beta-hairpin arm does not affect the structure of the raptor adenovirus 1 fibre head and only affects the stability of the RAdV-1 and TAdV-3 fibre heads slightly. CONCLUSIONS: The high-resolution structure of RAdV-1 fibre head is the second known structure of a siadenovirus fibre head domain. The structure shows that the siadenovirus fibre head structure is conserved, but differences in the predicted surface charge suggest that RAdV-1 uses a different natural receptor for cell attachment than TAdV-3. Deletion of the beta-hairpin arm shows little impact on the structure and stability of the siadenovirus fibre heads.","corpus_id":11335559,"score":1},{"doc_id":"29695426","title":"Structural and Functional Features of the Reovirus σ1 Tail.","abstract":"Mammalian orthoreovirus attachment to target cells is mediated by the outer capsid protein σ1, which projects from the virion surface. The σ1 protein is a homotrimer consisting of a filamentous tail, which is partly inserted into the virion; a body domain constructed from β-spiral repeats; and a globular head with receptor-binding properties. The σ1 tail is predicted to form an α-helical coiled coil. Although σ1 undergoes a conformational change during cell entry, the nature of this change and its contributions to viral replication are unknown. Electron micrographs of σ1 molecules released from virions identified three regions of flexibility, including one at the midpoint of the molecule, that may be involved in its structural rearrangement. To enable a detailed understanding of essential σ1 tail organization and properties, we determined high-resolution structures of the reovirus type 1 Lang (T1L) and type 3 Dearing (T3D) σ1 tail domains. Both molecules feature extended α-helical coiled coils, with T1L σ1 harboring central chloride ions. Each molecule displays a discontinuity (stutter) within the coiled coil and an unexpectedly seamless transition to the body domain. The transition region features conserved interdomain interactions and appears rigid rather than highly flexible. Functional analyses of reoviruses containing engineered σ1 mutations suggest that conserved residues predicted to stabilize the coiled-coil-to-body junction are essential for σ1 folding and encapsidation, whereas central chloride ion coordination and the stutter are dispensable for efficient replication. Together, these findings enable modeling of full-length reovirus σ1 and provide insight into the stabilization of a multidomain virus attachment protein. IMPORTANCE While it is established that different conformational states of attachment proteins of enveloped viruses mediate receptor binding and membrane fusion, less is understood about how such proteins mediate attachment and entry of nonenveloped viruses. The filamentous reovirus attachment protein σ1 binds cellular receptors; contains regions of predicted flexibility, including one at the fiber midpoint; and undergoes a conformational change during cell entry. Neither the nature of the structural change nor its contribution to viral infection is understood. We determined crystal structures of large σ1 fragments for two different reovirus serotypes. We observed an unexpectedly tight transition between two domains spanning the fiber midpoint, which allows for little flexibility. Studies of reoviruses with engineered changes near the σ1 midpoint suggest that the stabilization of this region is critical for function. Together with a previously determined structure, we now have a complete model of the full-length, elongated reovirus σ1 attachment protein.","corpus_id":25113018,"score":1},{"doc_id":"18096638","title":"Solution structure of the C-terminal domain of Ole e 9, a major allergen of olive pollen.","abstract":"Ole e 9 is an olive pollen allergen belonging to group 2 of pathogenesis-related proteins. The protein is composed of two immunological independent domains: an N-terminal domain (NtD) with 1,3-beta-glucanase activity, and a C-terminal domain (CtD) that binds 1,3-beta-glucans. We have determined the three-dimensional structure of CtD-Ole e 9 (101 amino acids), which consists of two parallel alpha-helices forming an angle of approximately 55 degrees , a small antiparallel beta-sheet with two short strands, and a 3-10 helix turn, all connected by long coil segments, resembling a novel type of folding among allergens. Two regions surrounded by aromatic residues (F49, Y60, F96, Y91 and Y31, H68, Y65, F78) have been localized on the protein surface, and a role for sugar binding is suggested. The epitope mapping of CtD-Ole e 9 shows that B-cell epitopes are mainly located on loops, although some of them are contained in secondary structural elements. Interestingly, the IgG and IgE epitopes are contiguous or overlapped, rather than coincident. The three-dimensional structure of CtD-Ole e 9 might help to understand the underlying mechanism of its biochemical function and to determine possible structure-allergenicity relationships.","corpus_id":23733055,"score":0},{"doc_id":"18373550","title":"Structural models and binding site prediction of the C-terminal domain of human Hsp90: a new target for anticancer drugs.","abstract":"Heat shock protein 90 is a valuable target for anticancer drugs because of its role in the activation and stabilization of multiple oncogenic signalling proteins. While several compounds inhibit heat shock protein 90 by binding the N-terminal domain, recent studies have proved that the C-terminal domain is important for dimerization of the chaperone and contains an additional binding site for inhibitors. Heat shock protein 90 inhibition achieved with molecules binding to the C-terminal domain provides an additional and novel opportunity to design and develop drugs. Therefore, for the first time, we have investigated the structure and the dynamic behaviour of the C-terminal domain of human heat shock protein 90 with and without the small-middle domain, using homology modelling and molecular dynamics simulations. In addition, secondary structure predictions and peptide folding simulations proved useful to investigate a putative additional alpha-helix located between H18 and beta20 of the C-terminal domain. Finally, we used the structural information to infer the location of the binding site located in the C-terminal domain by using a number of computational tools. The predicted pocket is formed by two grooves located between helix H18, the loop downstream of H18 and the loop connecting helices H20 and H21 of each monomer of the C-terminal domain, with only two amino acids contributing from each middle domain.","corpus_id":31018983,"score":0},{"doc_id":"18552768","title":"Crystal structure of human ERp44 shows a dynamic functional modulation by its carboxy-terminal tail.","abstract":"ERp44 mediates thiol-dependent retention in the early secretory pathway, forming mixed disulphides with substrate proteins through its conserved CRFS motif. Here, we present its crystal structure at a resolution of 2.6 A. Three thioredoxin domains-a, b and b'-are arranged in a clover-like structure. A flexible carboxy-terminal tail turns back to the b' and a domains, shielding a hydrophobic pocket in domain b' and a hydrophobic patch around the CRFS motif in domain a. Mutational and functional studies indicate that the C-terminal tail gates the CRFS area and the adjacent hydrophobic pocket, dynamically regulating protein quality control.","corpus_id":19426181,"score":0},{"doc_id":"19324050","title":"NMR structure of the amino-terminal domain of the lambda integrase protein in complex with DNA: immobilization of a flexible tail facilitates beta-sheet recognition of the major groove.","abstract":"The integrase protein (Int) from bacteriophage lambda is the archetypal member of the tyrosine recombinase family, a large group of enzymes that rearrange DNA in all domains of life. Int catalyzes the insertion and excision of the viral genome into and out of the Escherichia coli chromosome. Recombination transpires within higher-order nucleoprotein complexes that form when its amino-terminal domain binds to arm-type DNA sequences that are located distal to the site of strand exchange. Arm-site binding by Int is essential for catalysis, as it promotes Int-mediated bridge structures that stabilize the recombination machinery. We have elucidated how Int is able to sequence specifically recognize the arm-type site sequence by determining the solution structure of its amino-terminal domain (Int(N), residues Met1 to Leu64) in complex with its P'2 DNA binding site. Previous studies have shown that Int(N) adopts a rare monomeric DNA binding fold that consists of a three-stranded antiparallel beta-sheet that is packed against a carboxy-terminal alpha helix. A low-resolution crystal structure of the full-length protein also revealed that the sheet is inserted into the major groove of the arm-type site. The solution structure presented here reveals how Int(N) specifically recognizes the arm-type site sequence. A novel feature of the new solution structure is the use of an 11-residue tail that is located at the amino terminus. DNA binding induces the folding of a 3(10) helix in the tail that projects the amino terminus of the protein deep into the minor groove for stabilizing DNA contacts. This finding reveals the structural basis for the observation that the \"unstructured\" amino terminus is required for recombination.","corpus_id":25344386,"score":0},{"doc_id":"19447113","title":"Structure of the alkalohyperthermophilic Archaeoglobus fulgidus lipase contains a unique C-terminal domain essential for long-chain substrate binding.","abstract":"Several crystal structures of AFL, a novel lipase from the archaeon Archaeoglobus fulgidus, complexed with various ligands, have been determined at about 1.8 A resolution. This enzyme has optimal activity in the temperature range of 70-90 degrees C and pH 10-11. AFL consists of an N-terminal alpha/beta-hydrolase fold domain, a small lid domain, and a C-terminal beta-barrel domain. The N-terminal catalytic domain consists of a 6-stranded beta-sheet flanked by seven alpha-helices, four on one side and three on the other side. The C-terminal lipid binding domain consists of a beta-sheet of 14 strands and a substrate covering motif on top of the highly hydrophobic substrate binding site. The catalytic triad residues (Ser136, Asp163, and His210) and the residues forming the oxyanion hole (Leu31 and Met137) are in positions similar to those of other lipases. Long-chain lipid is located across the two domains in the AFL-substrate complex. Structural comparison of the catalytic domain of AFL with a homologous lipase from Bacillus subtilis reveals an opposite substrate binding orientation in the two enzymes. AFL has a higher preference toward long-chain substrates whose binding site is provided by a hydrophobic tunnel in the C-terminal domain. The unusually large interacting surface area between the two domains may contribute to thermostability of the enzyme. Two amino acids, Asp61 and Lys101, are identified as hinge residues regulating movement of the lid domain. The hydrogen-bonding pattern associated with these two residues is pH dependent, which may account for the optimal enzyme activity at high pH. Further engineering of this novel lipase with high temperature and alkaline stability will find its use in industrial applications.","corpus_id":5604880,"score":0},{"doc_id":"22708907","title":"Crystal structure of the Yersinia enterocolitica type III secretion chaperone SycD in complex with a peptide of the minor translocator YopD.","abstract":"BACKGROUND: Type III secretion systems are used by Gram-negative bacteria as \"macromolecular syringes\" to inject effector proteins into eukaryotic cells. Two hydrophobic proteins called translocators form the necessary pore in the host cell membrane. Both translocators depend on binding to a single chaperone in the bacterial cytoplasm to ensure their stability and efficient transport through the secretion needle. It was suggested that the conserved chaperones bind the more divergent translocators via a hexapeptide motif that is found in both translocators and conserved between species. RESULTS: We crystallized a synthetic decapeptide from the Yersinia enterocolitica minor type III secretion translocator YopD bound to its cognate chaperone SycD and determined the complex structure at 2.5 Å resolution. The structure of peptide-bound SycD is almost identical to that of apo SycD with an all helical fold consisting of three tetratricopeptide repeats (TPRs) and an additional C-terminal helix. Peptide-bound SycD formed a kinked head-to-head dimer that had previously been observed for the apo form of SycD. The homodimer interface comprises both helices of the first tetratricopeptide repeat. The YopD peptide bound in extended conformation into a mainly hydrophobic groove on the concave side of SycD. TPRs 1 and 2 of SycD form three hydrophobic pockets that accommodated the conserved hydrophobic residues at position 1, 3 and 6 of the translocator hexapeptide sequence. Two tyrosines that are highly conserved among translocator chaperones contribute to the hydrophobic patches but also form hydrogen bonds to the peptide backbone. CONCLUSIONS: The interaction between SycD and YopD is very similar to the binding of the Pseudomonas minor translocator PopD to its chaperone PcrH and the Shigella major translocator IpaB to its chaperone IpgC. This confirms the prediction made by Kolbe and co-workers that a hexapeptide with hydrophobic residues at three positions is a conserved chaperone binding motif. Because the hydrophobic groove on the concave side of translocator chaperones is involved in binding of the major and the minor translocator, simultaneous binding of both translocators to a single type III secretion class II chaperone appears unlikely.","corpus_id":15764038,"score":0},{"doc_id":"25982270","title":"Crystal structure of the C-terminal domain of tubulin-binding cofactor C from Leishmania major.","abstract":"Tubulin-binding cofactor C stimulates GTPase activity and contributes to the release of the heterodimeric α/β-tubulin from a super-complex of tubulin monomers and two ancillary cofactors. We have determined the 2.2 Å resolution crystal structure of the C-terminal domain of tubulin-binding cofactor C from Leishmania major based on single wavelength anomalous dispersion measurements targeting a selenomethionine derivative. Although previously predicted to consist of two domains the structure is best described as a single domain dominated by a right-handed β-helix of five turns that form a triangular prism. One face of the prism is covered by the C-terminal residues leaving another face solvent exposed. Comparisons with an orthologous human GTPase activating protein match key residues involved in binding nucleotide and identify the face of the β-helix fold likely involved in interacting with the β-tubulin:GTP complex.","corpus_id":7615194,"score":0},{"doc_id":"29223729","title":"Structure-Function Analysis of the C-Terminal Domain of the Type VI Secretion TssB Tail Sheath Subunit.","abstract":"The type VI secretion system (T6SS) is a specialized macromolecular complex dedicated to the delivery of protein effectors into both eukaryotic and bacterial cells. The general mechanism of action of the T6SS is similar to the injection of DNA by contractile bacteriophages. The cytoplasmic portion of the T6SS is evolutionarily, structurally and functionally related to the phage tail complex. It is composed of an inner tube made of stacked Hcp hexameric rings, engulfed within a sheath and built on a baseplate. This sheath undergoes cycles of extension and contraction, and the current model proposes that the sheath contraction propels the inner tube toward the target cell for effector delivery. The sheath comprises two subunits: TssB and TssC that polymerize under an extended conformation. Here, we show that isolated TssB forms trimers, and we report the crystal structure of a C-terminal fragment of TssB. This fragment comprises a long helix followed by a helical hairpin that presents surface-exposed charged residues. Site-directed mutagenesis coupled to functional assay further showed that these charges are required for proper assembly of the sheath. Positioning of these residues in the extended T6SS sheath structure suggests that they may mediate contacts with the baseplate.","corpus_id":46881667,"score":0}],"string":"[\n {\n \"doc_id\": \"18077713\",\n \"title\": \"Structure of the receptor-binding protein of bacteriophage det7: a podoviral tail spike in a myovirus.\",\n \"abstract\": \"A new Salmonella enterica phage, Det7, was isolated from sewage and shown by electron microscopy to belong to the Myoviridae morphogroup of bacteriophages. Det7 contains a 75-kDa protein with 50% overall sequence identity to the tail spike endorhamnosidase of podovirus P22. Adsorption of myoviruses to their bacterial hosts is normally mediated by long and short tail fibers attached to a contractile tail, whereas podoviruses do not contain fibers but attach to host cells through stubby tail spikes attached to a very short, noncontractile tail. The amino-terminal 150 residues of the Det7 protein lack homology to the P22 tail spike and are probably responsible for binding to the base plate of the myoviral tail. Det7 tail spike lacking this putative particle-binding domain was purified from Escherichia coli, and well-diffracting crystals of the protein were obtained. The structure, determined by molecular replacement and refined at a 1.6-A resolution, is very similar to that of bacteriophage P22 tail spike. Fluorescence titrations with an octasaccharide suggest Det7 tail spike to bind its receptor lipopolysaccharide somewhat less tightly than the P22 tail spike. The Det7 tail spike is even more resistant to thermal unfolding than the already exceptionally stable homologue from P22. Folding and assembly of both trimeric proteins are equally temperature sensitive and equally slow. Despite the close structural, biochemical, and sequence similarities between both proteins, the Det7 tail spike lacks both carboxy-terminal cysteines previously proposed to form a transient disulfide during P22 tail spike assembly. Our data suggest receptor-binding module exchange between podoviruses and myoviruses in the course of bacteriophage evolution.\",\n \"corpus_id\": 22593104,\n \"score\": 2\n },\n {\n \"doc_id\": \"18160394\",\n \"title\": \"Structure of the bacteriophage phi KZ lytic transglycosylase gp144.\",\n \"abstract\": \"Lytic transglycosylases are enzymes that act on the peptidoglycan of bacterial cell walls. They cleave the glycosidic linkage between N-acetylmuramoyl and N-acetylglucosaminyl residues with the concomitant formation of a 1,6-anhydromuramoyl product. The x-ray structure of the lytic transglycosylase gp144 from the Pseudomonas bacteriophage phi KZ has been determined to 2.5-A resolution. This protein is probably employed by the bacteriophage in the late stage of the virus reproduction cycle to destroy the bacterial cell wall to release the phage progeny. phi KZ gp144 is a 260-residue alpha-helical protein composed of a 70-residue N-terminal cell wall-binding domain and a C-terminal catalytic domain. The fold of the N-terminal domain is similar to the peptidoglycan-binding domain from Streptomyces albus G D-Ala-D-Ala carboxypeptidase and to the N-terminal prodomain of human metalloproteinases that act on extracellular matrices. The C-terminal catalytic domain of gp144 has a structural similarity to the catalytic domain of the transglycosylase Slt70 from Escherichia coli and to lysozymes. The gp144 catalytic domain has an elongated groove that can bind at least five sugar residues at sites A-E. As in other lysozymes, the peptidoglycan cleavage (catalyzed by Glu 115 in gp144) occurs between sugar-binding subsites D and E. The x-ray structure of the phi KZ transglycosylase complexed with the chitotetraose (N-acetylglucosamine)(4) has been determined to 2.6-A resolution. The N-acetylglucosamine residues of the chitotetraose bind in sites A-D.\",\n \"corpus_id\": 37782816,\n \"score\": 2\n },\n {\n \"doc_id\": \"18462681\",\n \"title\": \"An intersubunit active site between supercoiled parallel beta helices in the trimeric tailspike endorhamnosidase of Shigella flexneri Phage Sf6.\",\n \"abstract\": \"Sf6 belongs to the Podoviridae family of temperate bacteriophages that infect gram-negative bacteria by insertion of their double-stranded DNA. They attach to their hosts specifically via their tailspike proteins. The 1.25 A crystal structure of Shigella phage Sf6 tailspike protein (Sf6 TSP) reveals a conserved architecture with a central, right-handed beta helix. In the trimer of Sf6 TSP, the parallel beta helices form a left-handed, coiled-beta coil with a pitch of 340 A. The C-terminal domain consists of a beta sandwich reminiscent of viral capsid proteins. Further crystallographic and biochemical analyses show a Shigella cell wall O-antigen fragment to bind to an endorhamnosidase active site located between two beta-helix subunits each anchoring one catalytic carboxylate. The functionally and structurally related bacteriophage, P22 TSP, lacks sequence identity with Sf6 TSP and has its active sites on single subunits. Sf6 TSP may serve as an example for the evolution of different host specificities on a similar general architecture.\",\n \"corpus_id\": 205258558,\n \"score\": 2\n },\n {\n \"doc_id\": \"19189967\",\n \"title\": \"Proteolytic release of the intramolecular chaperone domain confers processivity to endosialidase F.\",\n \"abstract\": \"Endosialidases (endoNs), as identified so far, are tailspike proteins of bacteriophages that specifically bind and degrade the alpha2,8-linked polysialic acid (polySia) capsules of their hosts. The crystal structure solved for the catalytic domain of endoN from coliphage K1F (endoNF) revealed a functional trimer. Folding of the catalytic trimer is mediated by an intramolecular C-terminal chaperone domain. Release of the chaperone from the folded protein confers kinetic stability to endoNF. In mutant c(S), the replacement of serine 911 by alanine prevents proteolysis and generates an enzyme that varies in activity from wild type. Using soluble polySia as substrate a 3-times higher activity was detected while evaluation with immobilized polySia revealed a 190-fold reduced activity. Importantly, activity of c(S) did not differ from wild type with tetrameric sialic acid, the minimal endoNF substrate. Furthermore, we show that the presence of the chaperone domain in c(S) destabilizes binding to polySia in a similar way as did selective disruption of a polySia binding site in the stalk domain. The improved catalytic efficiency toward soluble polySia observed in these mutants can be explained by higher dissociation and association probabilities, whereas inversely, an impaired processivity was found. The fact that endoNF is a processive enzyme introduces a new molecular basis to explain capsule degradation by bacteriophages, which until now has been regarded as a result of cooperative interaction of tailspike proteins. Moreover, knowing that release of the chaperone domain confers kinetic stability and processivity, conservation of the proteolytic process can be explained by its importance in phage evolution.\",\n \"corpus_id\": 205377694,\n \"score\": 2\n },\n {\n \"doc_id\": \"19780551\",\n \"title\": \"Observation of the membrane binding activity and domain structure of gpV, which comprises the tail spike of bacteriophage P2.\",\n \"abstract\": \"The P2 phage virion has tail spike proteins beneath the baseplate and uses them to adsorb to the outer membrane of Escherichia coli during the infection process. Previous immunoelectron microscopic studies suggested that the tail spikes are composed of the gene V product (gpV); however, experimental evidence of its membrane binding activity has yet to be reported. In this study, we purified and characterized recombinant full-length gpV and its C-terminal domain. Limited chymotrypsin proteolysis of gpV produced a C-terminal domain composed of Ser86-Leu211. Our experiments demonstrated that the N- and C-terminal domains have very different melting temperatures: 50 and 74 degrees C, respectively. We also found that gpV binds the E. coli membrane via its C-terminal domain. We conclude that the C-terminal domain of gpV is a stable trimer and serves as the receptor-binding domain for the second step in the phage adsorption process.\",\n \"corpus_id\": 14722,\n \"score\": 2\n },\n {\n \"doc_id\": \"19913618\",\n \"title\": \"Two-chaperone assisted soluble expression and purification of the bacteriophage T4 long tail fibre protein gp37.\",\n \"abstract\": \"Bacteriophage T4 recognises its host cells through its long tail fibre protein gene product (gp) 37. Gp37 is a protein containing 1026 amino acids per monomer, forming a fibrous parallel homotrimer at the distal end of the long tail fibres. The other distal half-fibre protein, gp36, is much smaller, forming a trimer of 221 amino acids per monomer. Functional and structural studies of gp37 have been hampered by the inability to produce suitable amounts of it. We produced soluble gp37 by co-expression with two bacteriophage T4-encoded chaperones in a two-vector system; co-expression with each chaperone separately did not lead to good amounts of correctly folded, trimeric protein. An expression vector for the bacteriophage T4 fibrous protein chaperone gp57 was co-transformed into bacteria with a compatible bi-cistronic expression vector containing bacteriophage T4 genes 37 and 38. A six-histidine tag is encoded amino-terminal to the gp37 gene. Recombinant trimeric gp37, containing the histidine tag and residues 12-1026 of gp37, was purified from lysed bacteria by subsequent nickel-affinity, size exclusion and strong anion exchange column chromatography. Yields of approximately 4 mg of purified protein per litre of bacterial culture were achieved. Electron microscopy confirmed the protein to form fibres around 63 nm long, presumably gp36 makes up the remaining 11 nm in the intact distal half-fibre. Purified, correctly folded, gp37 will be useful for receptor-binding studies, high-resolution structural studies and for specific binding and detection of bacteria.\",\n \"corpus_id\": 38077951,\n \"score\": 2\n },\n {\n \"doc_id\": \"20478417\",\n \"title\": \"The C-terminal domain is sufficient for host-binding activity of the Mu phage tail-spike protein.\",\n \"abstract\": \"The Mu phage virion contains tail-spike proteins beneath the baseplate, which it uses to adsorb to the outer membrane of Escherichia coli during the infection process. The tail spikes are composed of gene product 45 (gp45), which contains 197 amino acid residues. In this study, we purified and characterized both the full-length and the C-terminal domains of recombinant gp45 to identify the functional and structural domains. Limited proteolysis resulted in a Ser64-Gln197 sequence, which was composed of a stable C-terminal domain. Analytical ultracentrifugation of the recombinant C-terminal domain (gp45-C) indicated that the molecular weight of gp45-C was about 58 kDa and formed a trimeric protomer in solution. Coprecipitation experiments and a quartz crystal microbalance (QCM) demonstrated that gp45-C irreversibly binds to the E. coli membrane. These results indicate that gp45 shows behaviors similar to tail-spike proteins of other phages; however, gp45 did not show significant sequence homology with the other phage tail-spike structures that have been identified.\",\n \"corpus_id\": 5160019,\n \"score\": 2\n },\n {\n \"doc_id\": \"20531477\",\n \"title\": \"[The beta-helical domain of bacteriophage T4 controls the folding of the fragment of long tail fibers in a chimeric protein].\",\n \"abstract\": \"The key stage of the infection of the Escherichia coli cell with bacteriophage T4, the binding to the surface of the host cell, is determined by the specificity of the long tail fiber proteins of the phage, in particular, gp37. The assembly and oligomerization of this protein under natural conditions requires the participation of at least two additional protein factors, gp57A and gp38, which strongly hinders the production of the recombinant form of gp37. To overcome this problem, a modern protein engineering strategy was used, which involves the construction of a chimeric protein containing a carrier protein that drives the correct folding of the target protein. For this purpose, the trimeric beta-helical domain of another protein of phage T4, gp5, was used. It was shown that this domain, represented as a rigid trimeric polypeptide prism, has properties favorable for use as a protein carrier. A fragment of protein gp37 containing five pentapeptides repeats, Gly-X-His-X-His, which determine the binding to the receptors on the bacterial cell surface, was fused in a continuous reading frame to the C-terminus of the domain of gp5. The resulting chimeric protein forms a trimer that has the native conformation of gp37 and exhibits biological activity.\",\n \"corpus_id\": 36456702,\n \"score\": 2\n },\n {\n \"doc_id\": \"20843802\",\n \"title\": \"Crystal structure of bacteriophage SPP1 distal tail protein (gp19.1): a baseplate hub paradigm in gram-positive infecting phages.\",\n \"abstract\": \"Siphophage SPP1 infects the gram-positive bacterium Bacillus subtilis using its long non-contractile tail and tail-tip. Electron microscopy (EM) previously allowed a low resolution assignment of most orf products belonging to these regions. We report here the structure of the SPP1 distal tail protein (Dit, gp19.1). The combination of x-ray crystallography, EM, and light scattering established that Dit is a back-to-back dimer of hexamers. However, Dit fitting in the virion EM maps was only possible with a hexamer located between the tail-tube and the tail-tip. Structure comparison revealed high similarity between Dit and a central component of lactophage baseplates. Sequence similarity search expanded its relatedness to several phage proteins, suggesting that Dit is a docking platform for the tail adsorption apparatus in Siphoviridae infecting gram-positive bacteria and that its architecture is a paradigm for these hub proteins. Dit structural similarity extends also to non-contractile and contractile phage tail proteins (gpV(N) and XkdM) as well as to components of the bacterial type 6 secretion system, supporting an evolutionary connection between all these devices.\",\n \"corpus_id\": 21515226,\n \"score\": 2\n },\n {\n \"doc_id\": \"21041684\",\n \"title\": \"Structure of the bacteriophage T4 long tail fiber receptor-binding tip.\",\n \"abstract\": \"Bacteriophages are the most numerous organisms in the biosphere. In spite of their biological significance and the spectrum of potential applications, little high-resolution structural detail is available on their receptor-binding fibers. Here we present the crystal structure of the receptor-binding tip of the bacteriophage T4 long tail fiber, which is highly homologous to the tip of the bacteriophage lambda side tail fibers. This structure reveals an unusual elongated six-stranded antiparallel beta-strand needle domain containing seven iron ions coordinated by histidine residues arranged colinearly along the core of the biological unit. At the end of the tip, the three chains intertwine forming a broader head domain, which contains the putative receptor interaction site. The structure reveals a previously unknown beta-structured fibrous fold, provides insights into the remarkable stability of the fiber, and suggests a framework for mutations to expand or modulate receptor-binding specificity.\",\n \"corpus_id\": 11209758,\n \"score\": 2\n },\n {\n \"doc_id\": \"21705802\",\n \"title\": \"Atomic structure of bacteriophage Sf6 tail needle knob.\",\n \"abstract\": \"Podoviridae are double-stranded DNA bacteriophages that use short, non-contractile tails to adsorb to the host cell surface. Within the tail apparatus of P22-like phages, a dedicated fiber known as the \\\"tail needle\\\" likely functions as a cell envelope-penetrating device to promote ejection of viral DNA inside the host. In Sf6, a P22-like phage that infects Shigella flexneri, the tail needle presents a C-terminal globular knob. This knob, absent in phage P22 but shared in other members of the P22-like genus, represents the outermost exposed tip of the virion that contacts the host cell surface. Here, we report a crystal structure of the Sf6 tail needle knob determined at 1.0 Å resolution. The structure reveals a trimeric globular domain of the TNF fold structurally superimposable with that of the tail-less phage PRD1 spike protein P5 and the adenovirus knob, domains that in both viruses function in receptor binding. However, P22-like phages are not known to utilize a protein receptor and are thought to directly penetrate the host surface. At 1.0 Å resolution, we identified three equivalents of l-glutamic acid (l-Glu) bound to each subunit interface. Although intimately bound to the protein, l-Glu does not increase the structural stability of the trimer nor it affects its ability to self-trimerize in vitro. In analogy to P22 gp26, we suggest the tail needle of phage Sf6 is ejected through the bacterial cell envelope during infection and its C-terminal knob is threaded through peptidoglycan pores formed by glycan strands.\",\n \"corpus_id\": 19334689,\n \"score\": 2\n },\n {\n \"doc_id\": \"21821878\",\n \"title\": \"The host-binding domain of the P2 phage tail spike reveals a trimeric iron-binding structure.\",\n \"abstract\": \"The adsorption and infection of bacteriophage P2 is mediated by tail fibres and tail spikes. The tail spikes on the tail baseplate are used to irreversibly adsorb to the host cells. Recently, a P2 phage tail-spike protein, gpV, was purified and it was shown that a C-terminal domain, Ser87-Leu211, is sufficient for the binding of gpV to host Escherichia coli membranes [Kageyama et al. (2009), Biochemistry, 48, 10129-10135]. In this paper, the crystal structure of the C-terminal domain of P2 gpV is reported. The structure is a triangular pyramid and looks like a spearhead composed of an intertwined β-sheet, a triple β-helix and a metal-binding region containing iron, calcium and chloride ions.\",\n \"corpus_id\": 5282916,\n \"score\": 2\n },\n {\n \"doc_id\": \"21885679\",\n \"title\": \"A common evolutionary origin for tailed-bacteriophage functional modules and bacterial machineries.\",\n \"abstract\": \"Bacteriophages belonging to the order Caudovirales possess a tail acting as a molecular nanomachine used during infection to recognize the host cell wall, attach to it, pierce it, and ensure the high-efficiency delivery of the genomic DNA to the host cytoplasm. In this review, we provide a comprehensive analysis of the various proteins constituting tailed bacteriophages from a structural viewpoint. To this end, we had in mind to pinpoint the resemblances within and between functional modules such as capsid/tail connectors, the tails themselves, or the tail distal host recognition devices, termed baseplates. This comparison has been extended to bacterial machineries embedded in the cell wall, for which shared molecular homology with phages has been recently revealed. This is the case for the type VI secretion system (T6SS), an inverted phage tail at the bacterial surface, or bacteriocins. Gathering all these data, we propose that a unique ancestral protein fold may have given rise to a large number of bacteriophage modules as well as to some related bacterial machinery components.\",\n \"corpus_id\": 9299498,\n \"score\": 2\n },\n {\n \"doc_id\": \"22297990\",\n \"title\": \"Crystallization of the C-terminal domain of the bacteriophage T7 fibre protein gp17.\",\n \"abstract\": \"Bacteriophage T7 attaches to its host using the C-terminal domains of its six fibres, which are trimers of the gp17 protein. A C-terminal fragment of gp17 consisting of amino acids 371-553 has been expressed, purified and crystallized. Crystals of two forms were obtained, belonging to space group P2(1)2(1)2(1) (unit-cell parameters a = 61.2, b = 86.0, c = 118.4 Å) and space group C222(1) (unit-cell parameters a = 68.3, b = 145.6, c = 172.1 Å). They diffracted to 1.9 and 2.0 Å resolution, respectively. Both crystals are expected to contain one trimer in the asymmetric unit. Multiwavelength anomalous dispersion phasing with a mercury derivative is in progress.\",\n \"corpus_id\": 9817331,\n \"score\": 2\n },\n {\n \"doc_id\": \"22303017\",\n \"title\": \"Structural basis for antifreeze activity of ice-binding protein from arctic yeast.\",\n \"abstract\": \"Arctic yeast Leucosporidium sp. produces a glycosylated ice-binding protein (LeIBP) with a molecular mass of ∼25 kDa, which can lower the freezing point below the melting point once it binds to ice. LeIBP is a member of a large class of ice-binding proteins, the structures of which are unknown. Here, we report the crystal structures of non-glycosylated LeIBP and glycosylated LeIBP at 1.57- and 2.43-Å resolution, respectively. Structural analysis of the LeIBPs revealed a dimeric right-handed β-helix fold, which is composed of three parts: a large coiled structural domain, a long helix region (residues 96-115 form a long α-helix that packs along one face of the β-helix), and a C-terminal hydrophobic loop region ((243)PFVPAPEVV(251)). Unexpectedly, the C-terminal hydrophobic loop region has an extended conformation pointing away from the body of the coiled structural domain and forms intertwined dimer interactions. In addition, structural analysis of glycosylated LeIBP with sugar moieties attached to Asn(185) provides a basis for interpreting previous biochemical analyses as well as the increased stability and secretion of glycosylated LeIBP. We also determined that the aligned Thr/Ser/Ala residues are critical for ice binding within the B face of LeIBP using site-directed mutagenesis. Although LeIBP has a common β-helical fold similar to that of canonical hyperactive antifreeze proteins, the ice-binding site is more complex and does not have a simple ice-binding motif. In conclusion, we could identify the ice-binding site of LeIBP and discuss differences in the ice-binding modes compared with other known antifreeze proteins and ice-binding proteins.\",\n \"corpus_id\": 26030063,\n \"score\": 2\n },\n {\n \"doc_id\": \"22611190\",\n \"title\": \"Structure of the phage TP901-1 1.8 MDa baseplate suggests an alternative host adhesion mechanism.\",\n \"abstract\": \"Phages of the Caudovirales order possess a tail that recognizes the host and ensures genome delivery upon infection. The X-ray structure of the approximately 1.8 MDa host adsorption device (baseplate) from the lactococcal phage TP901-1 shows that the receptor-binding proteins are pointing in the direction of the host, suggesting that this organelle is in a conformation ready for host adhesion. This result is in marked contrast with the lactococcal phage p2 situation, whose baseplate is known to undergo huge conformational changes in the presence of Ca(2+) to reach its active state. In vivo infection experiments confirmed these structural observations by demonstrating that Ca(2+) ions are required for host adhesion among p2-like phages (936-species) but have no influence on TP901-1-like phages (P335-species). These data suggest that these two families rely on diverse adhesion strategies which may lead to different signaling for genome release.\",\n \"corpus_id\": 863683,\n \"score\": 2\n },\n {\n \"doc_id\": \"22645347\",\n \"title\": \"Structure of the receptor-binding carboxy-terminal domain of bacteriophage T7 tail fibers.\",\n \"abstract\": \"The six bacteriophage T7 tail fibers, homo-trimers of gene product 17, are thought to be responsible for the first specific, albeit reversible, attachment to Escherichia coli lipopolysaccharide. The protein trimer forms kinked fibers comprised of an amino-terminal tail-attachment domain, a slender shaft, and a carboxyl-terminal domain composed of several nodules. Previously, we expressed, purified, and crystallized a carboxyl-terminal fragment comprising residues 371-553. Here, we report the structure of this protein trimer, solved using anomalous diffraction and refined at 2 Å resolution. Amino acids 371-447 form a tapered pyramid with a triangular cross-section composed of interlocked β-sheets from each of the three chains. The triangular pyramid domain has three α-helices at its narrow end, which are connected to a carboxyl-terminal three-blade β-propeller tip domain by flexible loops. The monomers of this tip domain each contain an eight-stranded β-sandwich. The exact topology of the β-sandwich fold is novel, but similar to that of knob domains of other viral fibers and the phage Sf6 needle. Several host-range change mutants have been mapped to loops located on the top of this tip domain, suggesting that this surface of the tip domain interacts with receptors on the cell surface.\",\n \"corpus_id\": 22597494,\n \"score\": 2\n },\n {\n \"doc_id\": \"22659573\",\n \"title\": \"New insights into pb5, the receptor binding protein of bacteriophage T5, and its interaction with its Escherichia coli receptor FhuA.\",\n \"abstract\": \"The majority of bacterial viruses are bacteriophages bearing a tail that serves to recognise the bacterial surface and deliver the genome into the host cell. Infection is initiated by the irreversible interaction between the viral receptor binding protein (RBP) and a receptor at the surface of the bacterium. This interaction results ultimately in the phage DNA release in the host cytoplasm. Phage T5 infects Escherichia coli after binding of its RBP pb5 to the outer membrane ferrichrome transporter FhuA. Here, we have studied the complex formed by pb5 and FhuA by a variety of biophysical and biochemical techniques. We show that unlike RBPs of known structures, pb5 probably folds as a unique domain fulfilling both functions of binding to the host receptor and interaction with the rest of the phage. Pb5 likely binds to the domain occluding the β-barrel of FhuA as well as to external loops of the barrel. Furthermore, upon binding to FhuA, pb5 undergoes conformational changes, at the secondary and tertiary structure level that would be the key to the transmission of the signal through the tail to the capsid, triggering DNA release. This is the first structural information regarding the binding of a RBP to a proteic receptor.\",\n \"corpus_id\": 20354844,\n \"score\": 2\n },\n {\n \"doc_id\": \"22666655\",\n \"title\": \"The C-terminal cysteine annulus participates in auto-chaperone function for Salmonella phage P22 tailspike folding and assembly.\",\n \"abstract\": \"Elongated trimeric adhesins are a distinct class of proteins employed by phages and viruses to recognize and bind to their host cells, and by bacteria to bind to their target cells and tissues. The tailspikes of E. coli phage K1F and Bacillus phage Ø29 exhibit auto-chaperone activity in their trimeric C-terminal domains. The P22 tailspike is structurally homologous to those adhesins. Though there are no disulfide bonds or reactive cysteines in the native P22 tailspikes, a set of C-terminal cysteines are very reactive in partially folded intermediates, implying an unusual local conformation in the domain. This is likely to be involved in the auto-chaperone function. We examined the unusual reactivity of C-terminal tailspike cysteines during folding and assembly as a potential reporter of auto-chaperone function. Reaction with IAA blocked productive refolding in vitro, but not off-pathway aggregation. Two-dimensional PAGE revealed that the predominant intermediate exhibiting reactive cysteine side chains was a partially folded monomer. Treatment with reducing reagent promoted native trimer formation from these species, consistent with transient disulfide bonds in the auto-chaperone domain. Limited enzymatic digestion and mass spectrometry of folding and assembly intermediates indicated that the C-terminal domain was compact in the protrimer species. These results indicate that the C-terminal domain of the P22 tailspike folds itself and associates prior to formation of the protrimer intermediate, and not after, as previously proposed. The C-terminal cysteines and triple β-helix domains apparently provide the staging for the correct auto-chaperone domain formation, needed for alignment of P22 tailspike native trimer.\",\n \"corpus_id\": 17799096,\n \"score\": 2\n },\n {\n \"doc_id\": \"24155371\",\n \"title\": \"Crystal structure of pb9, the distal tail protein of bacteriophage T5: a conserved structural motif among all siphophages.\",\n \"abstract\": \"The tail of Caudovirales bacteriophages serves as an adsorption device, a host cell wall-perforating machine, and a genome delivery pathway. In Siphoviridae, the assembly of the long and flexible tail is a highly cooperative and regulated process that is initiated from the proteins forming the distal tail tip complex. In Gram-positive-bacterium-infecting siphophages, the distal tail (Dit) protein has been structurally characterized and is proposed to represent a baseplate hub docking structure. It is organized as a hexameric ring that connects the tail tube and the adsorption device. In this study, we report the characterization of pb9, a tail tip protein of Escherichia coli bacteriophage T5. By immunolocalization, we show that pb9 is located in the upper part of the cone of the T5 tail tip, at the end of the tail tube. The crystal structure of pb9 reveals a two-domain protein. Domain A exhibits remarkable structural similarity with the N-terminal domain of known Dit proteins, while domain B adopts an oligosaccharide/oligonucleotide-binding fold (OB-fold) that is not shared by these proteins. We thus propose that pb9 is the Dit protein of T5, making it the first Dit protein described for a Gram-negative-bacterium-infecting siphophage. Multiple sequence alignments suggest that pb9 is a paradigm for a large family of Dit proteins of siphophages infecting mostly Gram-negative hosts. The modular structure of the Dit protein maintains the basic building block that would be conserved among all siphophages, combining it with a more divergent domain that might serve specific host adhesion properties.\",\n \"corpus_id\": 25872618,\n \"score\": 2\n },\n {\n \"doc_id\": \"24316831\",\n \"title\": \"Crystallization of the C-terminal domain of the bacteriophage T5 L-shaped fibre.\",\n \"abstract\": \"Tails of bacteriophage T5 (a member of the Siphoviridae family) were studied by electron microscopy. For the distal parts of the L-shaped tail fibres, which are involved in host cell receptor binding, a low-resolution volume was calculated. Several C-terminal fragments of the fibre were expressed and purified. Crystals of two of them were obtained that belonged to space groups P63 and R32 and diffracted synchrotron radiation to 2.3 and 2.9 Å resolution, respectively. A single-wavelength anomalous dispersion data set to 2.5 Å resolution was also collected from a selenomethionine-derivatized crystal of one of the fragments, which belonged to space group C2.\",\n \"corpus_id\": 22403299,\n \"score\": 2\n },\n {\n \"doc_id\": \"24816102\",\n \"title\": \"Bacteriophage P22 tailspike: structure of the complete protein and function of the interdomain linker.\",\n \"abstract\": \"Attachment of phages to host cells, followed by phage DNA ejection, represents the first stage of viral infection of bacteria. Salmonella phage P22 has been extensively studied, serving as an experimental model for bacterial infection by phages. P22 engages bacteria by binding to the sugar moiety of lipopolysaccharides using the viral tailspike protein for attachment. While the structures of the N-terminal particle-binding domain and the major receptor-binding domain of the tailspike have been analyzed individually, the three-dimensional organization of the intact protein, including the highly conserved linker region between the two domains, remained unknown. A single amino-acid exchange in the linker sequence made it possible to crystallize the full-length protein. Two crystal structures of the linker region are presented: one attached to the N-terminal domain and the other present within the complete tailspike protein. Both retain their biological function, but the mutated full-length tailspike displays a retarded folding pathway. Fitting of the full-length tailspike into a published cryo-electron microscopy map of the P22 virion requires an elastic distortion of the crystal structure. The conservation of the linker suggests a role in signal transmission from the distal tip of the molecule to the phage head, eventually leading to DNA ejection.\",\n \"corpus_id\": 19300673,\n \"score\": 2\n },\n {\n \"doc_id\": \"25005101\",\n \"title\": \"Crystallization of the carboxy-terminal region of the bacteriophage T4 proximal long tail fibre protein gp34.\",\n \"abstract\": \"The phage-proximal part of the long tail fibres of bacteriophage T4 consists of a trimer of the 1289 amino-acid gene product 34 (gp34). Different carboxy-terminal parts of gp34 have been produced and crystallized. Crystals of gp34(726-1289) diffracting X-rays to 2.9 Å resolution, crystals of gp34(781-1289) diffracting to 1.9 Å resolution and crystals of gp34(894-1289) diffracting to 3.0 and 2.0 Å resolution and belonging to different crystal forms were obtained. Native data were collected for gp34(726-1289) and gp34(894-1289), while single-wavelength anomalous diffraction data were collected for selenomethionine-containing gp34(781-1289) and gp34(894-1289). For the latter, high-quality anomalous signal was obtained.\",\n \"corpus_id\": 26376710,\n \"score\": 2\n },\n {\n \"doc_id\": \"26805872\",\n \"title\": \"Branched Lateral Tail Fiber Organization in T5-Like Bacteriophages DT57C and DT571/2 is Revealed by Genetic and Functional Analysis.\",\n \"abstract\": \"The T5-like siphoviruses DT57C and DT571/2, isolated from horse feces, are very closely related to each other, and most of their structural proteins are also nearly identical to T5 phage. Their LTFs (L-shaped tail fibers), however, are composed of two proteins, LtfA and LtfB, instead of the single Ltf of bacteriophage T5. In silico and mutant analysis suggests a possible branched structure of DT57C and DT571/2 LTFs, where the LtfB protein is connected to the phage tail via the LtfA protein and with both proteins carrying receptor recognition domains. Such adhesin arrangement has not been previously recognized in siphoviruses. The LtfA proteins of our phages are found to recognize different host O-antigen types: E. coli O22-like for DT57C phage and E. coli O87 for DT571/2. LtfB proteins are identical in both phages and recognize another host receptor, most probably lipopolysaccharide (LPS) of E. coli O81 type. In these two bacteriophages, LTF function is essential to penetrate the shield of the host's O-antigens. We also demonstrate that LTF-mediated adsorption becomes superfluous when the non-specific cell protection by O-antigen is missing, allowing the phages to bind directly to their common secondary receptor, the outer membrane protein BtuB. The LTF independent adsorption was also demonstrated on an O22-like host mutant missing O-antigen O-acetylation, thus showing the biological value of this O-antigen modification for cell protection against phages.\",\n \"corpus_id\": 334754,\n \"score\": 2\n },\n {\n \"doc_id\": \"28510021\",\n \"title\": \"Molecular assembly and structure of the bacteriophage T4 tail.\",\n \"abstract\": \"The tail of bacteriophage T4 undergoes large structural changes upon infection while delivering the phage genome into the host cell. The baseplate is located at the distal end of the contractile tail and plays a central role in transmitting the signal to the tail sheath that the tailfibers have been adsorbed by a host bacterium. This then triggers the sheath contraction. In order to understand the mechanism of assembly and conformational changes of the baseplate upon infection, we have determined the structure of an in vitro assembled baseplate through the three-dimensional reconstruction of cryo-electron microscopy images to a resolution of 3.8 Å from electron micrographs. The atomic structure was fitted to the baseplate structure before and after sheath contraction in order to elucidate the conformational changes that occur after bacteriophage T4 has attached itself to a cell surface. The structure was also used to investigate the protease digestion of the assembly intermediates and the mutation sites of the tail genes, resulting in a number of phenotypes.\",\n \"corpus_id\": 9922995,\n \"score\": 2\n },\n {\n \"doc_id\": \"28665339\",\n \"title\": \"Crystal Structure of the Carboxy-Terminal Region of the Bacteriophage T4 Proximal Long Tail Fiber Protein Gp34.\",\n \"abstract\": \"Long tail fibers of bacteriophage T4 are formed by proteins gp34, gp35, gp36, and gp37, with gp34 located at the phage-proximal end and gp37 at the phage-distal, receptor-binding end. We have solved the structure of the carboxy-terminal region of gp34, consisting of amino acids 894-1289, by single-wavelength anomalous diffraction and extended the structure to amino acids 744-1289 using data collected from crystals containing longer gp34-fragments. The structure reveals three repeats of a mixed α-β fibrous domain in residues 744 to 877. A triple-helical neck connects to an extended triple β-helix domain (amino acids 900-1127) punctuated by two β-prism domains. Next, a β-prism domain decorated with short helices and extended β-helices is present (residues 1146-1238), while the C-terminal end is capped with another short β-helical region and three β-hairpins. The structure provides insight into the stability of the fibrous gp34 protein.\",\n \"corpus_id\": 2193886,\n \"score\": 2\n },\n {\n \"doc_id\": \"29204885\",\n \"title\": \"Bacteriophage T4 long tail fiber domains.\",\n \"abstract\": \"Bacteriophage T4 initially recognizes its host cells using its long tail fibers. Long tail fibers consist of a phage-proximal and a phage-distal rod, each around 80 nm long and attached to each other at a slight angle. The phage-proximal rod is formed by a homo-trimer of gene product 34 (gp34) and is attached to the phage-distal rod by a monomer of gp35. The phage-distal rod consists of two protein trimers: a trimer of gp36, attached to gp35, although most of the phage-distal rod, including the receptor-binding domain, is formed by a trimer of gp37. In this review, we discuss what is known about the detailed structure and function of the different long tail fiber domains. Partial crystal structures of gp34 and gp37 have revealed the presence of new protein folds, some of which are present in several repeats, while others are apparently unique. Gp38, a phage chaperone protein necessary for folding of gp37, is thought to act on an α-helical coiled-coil region in gp37. Future studies should reveal the remaining structure of the long tail fibers, how they assemble into a functional unit, and how the long tail fibers trigger the infection process after successful recognition of a suitable host bacterium.\",\n \"corpus_id\": 4871689,\n \"score\": 2\n },\n {\n \"doc_id\": \"29209037\",\n \"title\": \"Bacteriophage T5 tail tube structure suggests a trigger mechanism for Siphoviridae DNA ejection.\",\n \"abstract\": \"The vast majority of phages, bacterial viruses, possess a tail ensuring host recognition, cell wall perforation and safe viral DNA transfer from the capsid to the host cytoplasm. Long flexible tails are formed from the tail tube protein (TTP) polymerised as hexameric rings around and stacked along the tape measure protein (TMP). Here, we report the crystal structure of T5 TTP pb6 at 2.2 Å resolution. Pb6 is unusual in forming a trimeric ring, although structure analysis reveals homology with all classical TTPs and related tube proteins of bacterial puncturing devices (type VI secretion system and R-pyocin). Structures of T5 tail tubes before and after interaction with the host receptor were determined by cryo-electron microscopy at 6 Å resolution. Comparison of these two structures reveals that host-binding information is not propagated to the capsid through conformational changes in the tail tube, suggesting a role of the TMP in this information transduction process.\",\n \"corpus_id\": 21264668,\n \"score\": 2\n },\n {\n \"doc_id\": \"18189419\",\n \"title\": \"Crystal structure of a novel bacterial cell-surface flagellin binding to a polysaccharide.\",\n \"abstract\": \"Bacterial flagellins are generally self-assembled into extracellular flagella for cell motility. However, the flagellin homologue p5 is found on the cell surface of Sphingomonas sp. A1 (strain A1) and binds tightly to the alginate polysaccharide. To assimilate alginate, strain A1 forms a mouthlike pit on the cell surface and concentrates the polymer in the pit. p5 is a candidate receptor that recognizes extracellular alginate and controls pit formation. To improve our understanding of the structure and function of p5, we determined the crystal structure of truncated p5 (p5DeltaN53C45) at 2.0 A resolution. This, to our knowledge, is the first structure of flagellin_IN motif-containing flagellin. p5DeltaN53C45 consists of two domains: an alpha-domain rich in alpha-helices that forms the N- and C-terminal regions and a beta-domain rich in beta-strands that constitutes the central region. The alpha-domain is structurally similar to the D1 domain of Salmonella typhimurium flagellin, while the beta-domain is structurally similar to the finger domain of the bacteriophage T4 baseplate protein that is important for intermolecular interactions between baseplate and a long or short tail fiber. Results from the deletion mutant analysis suggest that residues 20-40 and 353-363 are responsible for alginate binding. Truncated N- and C-terminal regions are thought to constitute alpha-helices extending from the alpha-domain. On the basis of the size and surface charge, the cleft in extended alpha-helices is proposed as an alginate binding site of p5. Structural similarity in the beta-domain suggests that the beta-domain is involved in the proper localization and/or orientation of p5 on the cell surface.\",\n \"corpus_id\": 11163721,\n \"score\": 1\n },\n {\n \"doc_id\": \"18201719\",\n \"title\": \"Structure and molecular dynamics simulation of archaeal prefoldin: the molecular mechanism for binding and recognition of nonnative substrate proteins.\",\n \"abstract\": \"Prefoldin (PFD) is a heterohexameric molecular chaperone complex in the eukaryotic cytosol and archaea with a jellyfish-like structure containing six long coiled-coil tentacles. PFDs capture protein folding intermediates or unfolded polypeptides and transfer them to group II chaperonins for facilitated folding. Although detailed studies on the mechanisms for interaction with unfolded proteins or cooperation with chaperonins of archaeal PFD have been performed, it is still unclear how PFD captures the unfolded protein. In this study, we determined the X-ray structure of Pyrococcus horikoshii OT3 PFD (PhPFD) at 3.0 A resolution and examined the molecular mechanism for binding and recognition of nonnative substrate proteins by molecular dynamics (MD) simulation and mutation analyses. PhPFD has a jellyfish-like structure with six long coiled-coil tentacles and a large central cavity. Each subunit has a hydrophobic groove at the distal region where an unfolded substrate protein is bound. During MD simulation at 330 K, each coiled coil was highly flexible, enabling it to widen its central cavity and capture various nonnative proteins. Docking MD simulation of PhPFD with unfolded insulin showed that the beta subunit is essentially involved in substrate binding and that the alpha subunit modulates the shape and width of the central cavity. Analyses of mutant PhPFDs with amino acid replacement of the hydrophobic residues of the beta subunit in the hydrophobic groove have shown that beta Ile107 has a critical role in forming the hydrophobic groove.\",\n \"corpus_id\": 43335465,\n \"score\": 1\n },\n {\n \"doc_id\": \"19218213\",\n \"title\": \"Crystallographic structure of the alpha-helical triple coiled-coil domain of avian reovirus S1133 fibre.\",\n \"abstract\": \"Avian reovirus fibre, a homo-trimer of the sigmaC protein, is a minor component of the avian reovirus outer capsid. It is anchored via a short N-terminal sequence to the inner capsid lambdaC pentamer, and its protruding globular C-terminal domain is responsible for primary host cell attachment. We have previously solved the structure of a receptor-binding fragment in which residues 160-191 form a triple beta-spiral and 196-326 a beta-barrel head domain. Here we have expressed, purified and crystallized a major sigmaC fragment comprising residues 117-326. Its structure, which was solved by molecular replacement using the previously determined receptor-binding domain structure and refined to 1.75 A (0.175 nm) resolution, reveals an alpha-helical triple coiled-coil connected to the previously solved structure by a zinc-ion-containing linker. The coiled-coil domain contains two chloride ion binding sites, as well as specific trimerization and registration sequences. The linker may act as a functionally important hinge.\",\n \"corpus_id\": 206211556,\n \"score\": 1\n },\n {\n \"doc_id\": \"19241380\",\n \"title\": \"Structural plasticity of the phage P22 tail needle gp26 probed with xenon gas.\",\n \"abstract\": \"The tail needle, gp26, is a highly stable homo-trimeric fiber found in the tail apparatus of bacteriophage P22. In the mature virion, gp26 is responsible for plugging the DNA exit channel, and likely plays an important role in penetrating the host cell envelope. In this article, we have determined the 1.98 A resolution crystal structure of gp26 bound to xenon gas. The structure led us to identify a calcium and a chloride ion intimately bound at the interior of alpha-helical core, as well as seven small cavities occupied by xenon atoms. The two ions engage in buried polar interactions with gp26 side chains that provide specificity and register to gp26 helical core, thus enhancing its stability. Conversely, the distribution of xenon accessible cavities correlates well with the flexibility of the fiber observed in solution and in the crystal structure. We suggest that small internal cavities in gp26 between the helical core and the C-terminal tip allow for flexible swinging of the latter, without affecting the overall stability of the protein. The C-terminal tip may be important in scanning the bacterial surface in search of a cell-envelope penetration site, or for recognition of a yet unidentified receptor on the surface of the host.\",\n \"corpus_id\": 25594438,\n \"score\": 1\n },\n {\n \"doc_id\": \"19482036\",\n \"title\": \"An evolutionarily conserved family of virion tail needles related to bacteriophage P22 gp26: correlation between structural stability and length of the alpha-helical trimeric coiled coil.\",\n \"abstract\": \"Bacteriophages of the Podoviridae family use short noncontractile tails to inject their genetic material into Gram-negative bacteria. In phage P22, the tail contains a thin needle, encoded by the phage gene 26, which is essential both for stabilization and for ejection of the packaged viral genome. Bioinformatic analysis of the N-terminal domain of gp26 (residues 1-60) led us to identify a family of genes encoding putative homologues of the tail needle gp26. To validate this idea experimentally and to explore their diversity, we cloned the gp26-like gene from phages HK620, Sf6 and HS1, and characterized these gene products in solution. All gp26-like factors contain an elongated alpha-helical coiled-coil core consisting of repeating, adjacent trimerization heptads and form trimeric fibers with length ranging between about 240 to 300 A. gp26 tail needles display a high level of structural stability in solution, with T(m) (temperature of melting) between 85 and 95 degrees C. To determine how the structural stability of these phage fibers correlates with the length of the alpha-helical core, we investigated the effect of insertions and deletions in the helical core. In the P22 tail needle, we identified an 85-residue-long helical domain, termed MiCRU (minimal coiled-coil repeat unit), that can be inserted in-frame inside the gp26 helical core, preserving the straight morphology of the fiber. Likewise, we were able to remove three quarters of the helical core of the HS1 tail needle, minimally decreasing the stability of the fiber. We conclude that in the gp26 family of tail needles, structural stability increases nonlinearly with the length of the alpha-helical core. Thus, the overall stability of these bacteriophage fibers is not solely dependent on the number of trimerization repeats in the alpha-helical core.\",\n \"corpus_id\": 27199806,\n \"score\": 1\n },\n {\n \"doc_id\": \"19895817\",\n \"title\": \"The crystal structure of bacteriophage HK97 gp6: defining a large family of head-tail connector proteins.\",\n \"abstract\": \"The final step in the morphogenesis of long-tailed double-stranded DNA bacteriophages is the joining of the DNA-filled head to the tail. The connector is a specialized structure of the head that serves as the interface for tail attachment and the point of egress for DNA from the head during infection. Here, we report the determination of a 2.1 A crystal structure of gp6 of bacteriophage HK97. Through structural comparisons, functional studies, and bioinformatic analysis, gp6 has been determined to be a component of the connector of phage HK97 that is evolutionarily related to gp15, a well-characterized connector component of bacteriophage SPP1. Whereas the structure of gp15 was solved in a monomeric form, gp6 crystallized as an oligomeric ring with the dimensions expected for a connector protein. Although this ring is composed of 13 subunits, which does not match the symmetry of the connector within the phage, sequence conservation and modeling of this structure into the cryo-electron microscopy density of the SPP1 connector indicate that this oligomeric structure represents the arrangement of gp6 subunits within the mature phage particle. Through sequence searches and genomic position analysis, we determined that gp6 is a member of a large family of connector proteins that are present in long-tailed phages. We have also identified gp7 of HK97 as a homologue of gp16 of phage SPP1, which is the second component of the connector of this phage. These proteins are members of another large protein family involved in connector assembly.\",\n \"corpus_id\": 6534193,\n \"score\": 1\n },\n {\n \"doc_id\": \"20693685\",\n \"title\": \"Structure of the N-terminal fragment of Escherichia coli Lon protease.\",\n \"abstract\": \"The structure of a recombinant construct consisting of residues 1-245 of Escherichia coli Lon protease, the prototypical member of the A-type Lon family, is reported. This construct encompasses all or most of the N-terminal domain of the enzyme. The structure was solved by SeMet SAD to 2.6 A resolution utilizing trigonal crystals that contained one molecule in the asymmetric unit. The molecule consists of two compact subdomains and a very long C-terminal alpha-helix. The structure of the first subdomain (residues 1-117), which consists mostly of beta-strands, is similar to that of the shorter fragment previously expressed and crystallized, whereas the second subdomain is almost entirely helical. The fold and spatial relationship of the two subdomains, with the exception of the C-terminal helix, closely resemble the structure of BPP1347, a 203-amino-acid protein of unknown function from Bordetella parapertussis, and more distantly several other proteins. It was not possible to refine the structure to satisfactory convergence; however, since almost all of the Se atoms could be located on the basis of their anomalous scattering the correctness of the overall structure is not in question. The structure reported here was also compared with the structures of the putative substrate-binding domains of several proteins, showing topological similarities that should help in defining the binding sites used by Lon substrates.\",\n \"corpus_id\": 10466829,\n \"score\": 1\n },\n {\n \"doc_id\": \"20826161\",\n \"title\": \"The solution structure of the C-terminal Ig-like domain of the bacteriophage λ tail tube protein.\",\n \"abstract\": \"Immunoglobulin (Ig)-like domains are found frequently on the surface of tailed double-stranded DNA bacteriophages, yet their functional role remains obscure. Here, we have investigated the structure and function of the C-terminal Ig-like domain of gpV (gpV(C)), the tail tube protein of phage λ. This domain has been predicted through sequence similarity to be a member of the bacterial Ig-like domain 2 (Big_2) family, which is composed of more than 1300 phage and bacterial sequences. Using trypsin proteolysis, we have delineated the boundaries of gpV(C) and have shown that its removal reduces the biological activity of gpV by 100-fold; thus providing a definitive demonstration of a functional role for this domain. Determination of the solution structure of gpV(C) by NMR spectroscopy showed that it adopts a canonical Ig-like fold of the I-set class. This represents the first structure of a phage-encoded Ig-like domain and only the second structure of a Big_2 domain. Structural and sequence comparisons indicate that the gpV(C) structure is more representative of both the phage-encoded Big_2 domains and Big_2 domains in general than the other available Big_2 structure. Bioinformatics analyses have identified two conserved clusters of residues on the surface of gpV(C) that may be important in mediating the function of this domain.\",\n \"corpus_id\": 45685977,\n \"score\": 1\n },\n {\n \"doc_id\": \"21646642\",\n \"title\": \"Unraveling lactococcal phage baseplate assembly by mass spectrometry.\",\n \"abstract\": \"Bacteriophages belonging to the Caudovirales order possess a tail acting as a molecular machine used during infection to recognize the host and ensure high-efficiency genome delivery to the cell cytoplasm. They bear a large and sophisticated multiprotein organelle at their distal tail end, either a baseplate or a tail-tip, which is the control center for infectivity. We report here insights into the baseplate assembly pathways of two lactoccocal phages (p2 and TP901-1) using electrospray ionization-mass spectrometry. Based on our \\\"block cloning\\\" strategy we have expressed large complexes of their baseplates as well as several significant structural subcomplexes. Previous biophysical characterization using size-exclusion chromatography coupled with on-line light scattering and refractometry demonstrated that the overproduced recombinant proteins interact with each other to form large (up to 1.9 MDa) and stable assemblies. The structures of several of these complexes have been determined by x-ray diffraction or by electron microscopy. In this contribution, we demonstrate that electrospray ionization-mass spectrometry yields accurate mass measurements for the different baseplate complexes studied from which their stoichiometries can be discerned, and that the subspecies observed in the spectra provide valuable information on the assembly mechanisms of these large organelles.\",\n \"corpus_id\": 20813814,\n \"score\": 1\n },\n {\n \"doc_id\": \"21805520\",\n \"title\": \"Crystal structure of the read-through domain from bacteriophage Qβ A1 protein.\",\n \"abstract\": \"Bacteriophage Qβ is a small RNA virus that infects Escherichia coli. The virus particle contains a few copies of the minor coat protein A1, a C-terminally prolonged version of the coat protein, which is formed when ribosomes occasionally read-through the leaky stop codon of the coat protein. The crystal structure of the read-through domain from bacteriophage Qβ A1 protein was determined at a resolution of 1.8 Å. The domain consists of a heavily deformed five-stranded β-barrel on one side of the protein and a β-hairpin and a three-stranded β-sheet on the other. Several short helices and well-ordered loops are also present throughout the protein. The N-terminal part of the read-through domain contains a prominent polyproline type II helix. The overall fold of the domain is not similar to any published structure in the Protein Data Bank.\",\n \"corpus_id\": 3418824,\n \"score\": 1\n },\n {\n \"doc_id\": \"22153511\",\n \"title\": \"Structural conservation of the myoviridae phage tail sheath protein fold.\",\n \"abstract\": \"Bacteriophage phiKZ is a giant phage that infects Pseudomonas aeruginosa, a human pathogen. The phiKZ virion consists of a 1450 Å diameter icosahedral head and a 2000 Å-long contractile tail. The structure of the whole virus was previously reported, showing that its tail organization in the extended state is similar to the well-studied Myovirus bacteriophage T4 tail. The crystal structure of a tail sheath protein fragment of phiKZ was determined to 2.4 Å resolution. Furthermore, crystal structures of two prophage tail sheath proteins were determined to 1.9 and 3.3 Å resolution. Despite low sequence identity between these proteins, all of these structures have a similar fold. The crystal structure of the phiKZ tail sheath protein has been fitted into cryo-electron-microscopy reconstructions of the extended tail sheath and of a polysheath. The structural rearrangement of the phiKZ tail sheath contraction was found to be similar to that of phage T4.\",\n \"corpus_id\": 5103216,\n \"score\": 1\n },\n {\n \"doc_id\": \"23530214\",\n \"title\": \"Viral infection modulation and neutralization by camelid nanobodies.\",\n \"abstract\": \"Lactococcal phages belong to a large family of Siphoviridae and infect Lactococcus lactis, a gram-positive bacterium used in commercial dairy fermentations. These phages are believed to recognize and bind specifically to pellicle polysaccharides covering the entire bacterium. The phage TP901-1 baseplate, located at the tip of the tail, harbors 18 trimeric receptor binding proteins (RBPs) promoting adhesion to a specific lactococcal strain. Phage TP901-1 adhesion does not require major conformational changes or Ca(2+), which contrasts other lactococcal phages. Here, we produced and characterized llama nanobodies raised against the purified baseplate and the Tal protein of phage TP901-1 as tools to dissect the molecular determinants of phage TP901-1 infection. Using a set of complementary techniques, surface plasmon resonance, EM, and X-ray crystallography in a hybrid approach, we identified binders to the three components of the baseplate, analyzed their affinity for their targets, and determined their epitopes as well as their functional impact on TP901-1 phage infectivity. We determined the X-ray structures of three nanobodies in complex with the RBP. Two of them bind to the saccharide binding site of the RBP and are able to fully neutralize TP901-1 phage infectivity, even after 15 passages. These results provide clear evidence for a practical use of nanobodies in circumventing lactococcal phages viral infection in dairy fermentation.\",\n \"corpus_id\": 33331946,\n \"score\": 1\n },\n {\n \"doc_id\": \"24100566\",\n \"title\": \"Crystallization of the C-terminal head domain of the fibre protein from a siadenovirus, turkey adenovirus 3.\",\n \"abstract\": \"Turkey adenovirus 3 belongs to the genus Siadenovirus. Its predicted fibre protein consists of an N-terminal virus-attachment domain, a central shaft domain and a head domain at the C-terminus. The head domain has little sequence identity to known adenovirus fibre head structures. Crystals of the fibre head domain consisting of amino acids 304-454 with an N-terminal purification tag were produced. Crystals of native and selenomethionine-derivatized protein belonged to space group I23 (unit-cell parameter 99 Å). They diffracted synchrotron radiation to 2.0 and 2.14 Å resolution, respectively, and are expected to contain one monomer in the asymmetric unit.\",\n \"corpus_id\": 6477287,\n \"score\": 1\n },\n {\n \"doc_id\": \"24316834\",\n \"title\": \"Crystallization of the C-terminal domain of the fibre protein from snake adenovirus 1, an atadenovirus.\",\n \"abstract\": \"Adenovirus fibre proteins play an important role in determining viral tropism. The C-terminal domain of the fibre protein from snake adenovirus type 1, a member of the Atadenovirus genus, has been expressed, purified and crystallized. Crystals were obtained belonging to space groups P2(1)2(1)2(1) (two different forms), I2(1)3 and F23. The best of these diffracted synchrotron radiation to a resolution of 1.4 Å. As the protein lacks methionines or cysteines, site-directed mutagenesis was performed to change two leucine residues to methionines. Crystals of selenomethionine-derivatized crystals of the I2(1)3 form were also obtained and a multi-wavelength anomalous dispersion data set was collected.\",\n \"corpus_id\": 35326870,\n \"score\": 1\n },\n {\n \"doc_id\": \"24336205\",\n \"title\": \"Icosahedral bacteriophage ΦX174 forms a tail for DNA transport during infection.\",\n \"abstract\": \"Prokaryotic viruses have evolved various mechanisms to transport their genomes across bacterial cell walls. Many bacteriophages use a tail to perform this function, whereas tail-less phages rely on host organelles. However, the tail-less, icosahedral, single-stranded DNA ΦX174-like coliphages do not fall into these well-defined infection processes. For these phages, DNA delivery requires a DNA pilot protein. Here we show that the ΦX174 pilot protein H oligomerizes to form a tube whose function is most probably to deliver the DNA genome across the host's periplasmic space to the cytoplasm. The 2.4 Å resolution crystal structure of the in vitro assembled H protein's central domain consists of a 170 Å-long α-helical barrel. The tube is constructed of ten α-helices with their amino termini arrayed in a right-handed super-helical coiled-coil and their carboxy termini arrayed in a left-handed super-helical coiled-coil. Genetic and biochemical studies demonstrate that the tube is essential for infectivity but does not affect in vivo virus assembly. Cryo-electron tomograms show that tubes span the periplasmic space and are present while the genome is being delivered into the host cell's cytoplasm. Both ends of the H protein contain transmembrane domains, which anchor the assembled tubes into the inner and outer cell membranes. The central channel of the H-protein tube is lined with amide and guanidinium side chains. This may be a general property of viral DNA conduits and is likely to be critical for efficient genome translocation into the host.\",\n \"corpus_id\": 205236687,\n \"score\": 1\n },\n {\n \"doc_id\": \"24531468\",\n \"title\": \"Exploring the atomic structure and conformational flexibility of a 320 Å long engineered viral fiber using X-ray crystallography.\",\n \"abstract\": \"Protein fibers are widespread in nature, but only a limited number of high-resolution structures have been determined experimentally. Unlike globular proteins, fibers are usually recalcitrant to form three-dimensional crystals, preventing single-crystal X-ray diffraction analysis. In the absence of three-dimensional crystals, X-ray fiber diffraction is a powerful tool to determine the internal symmetry of a fiber, but it rarely yields atomic resolution structural information on complex protein fibers. An 85-residue-long minimal coiled-coil repeat unit (MiCRU) was previously identified in the trimeric helical core of tail needle gp26, a fibrous protein emanating from the tail apparatus of the bacteriophage P22 virion. Here, evidence is provided that an MiCRU can be inserted in frame inside the gp26 helical core to generate a rationally extended fiber (gp26-2M) which, like gp26, retains a trimeric quaternary structure in solution. The 2.7 Å resolution crystal structure of this engineered fiber, which measures ∼320 Å in length and is only 20-35 Å wide, was determined. This structure, the longest for a trimeric protein fiber to be determined to such a high resolution, reveals the architecture of 22 consecutive trimerization heptads and provides a framework to decipher the structural determinants for protein fiber assembly, stability and flexibility.\",\n \"corpus_id\": 22279907,\n \"score\": 1\n },\n {\n \"doc_id\": \"24598932\",\n \"title\": \"Combining secondary-structure and protein solvent-accessibility predictions in methionine substitution for anomalous dispersion.\",\n \"abstract\": \"In X-ray crystallographic analysis, the single-wavelength and multi-wavelength anomalous diffraction (SAD and MAD) methods have been widely used in order to solve the phase problem. Selenium-labelled methionine has been shown to be very effective for anomalous dispersion phasing, and at least one selenomethionine is required for every 100 amino acids. Some proteins, such as the Arabidopsis thaliana thylakoid lumen protein AtTLP18.3, can be overexpressed in an Escherichia coli system and high-quality protein crystals can be obtained. However, AtTLP18.3 contains no methionine residues, and site-directed mutagenesis was required in order to introduce methionine residues into the protein. A criterion for the mutated residues is that they should avoid affecting the structure and function. In this study, several leucine and isoleucine residues were selected for methionine substitution by combining secondary-structure and solvent-accessibility predictions. From the secondary-structure prediction, mutated residues were first determined in the coil or loop regions at the junction of two secondary structures. Since leucine and isoleucine residues are hydrophobic and are normally buried within the protein core, these residues should have a higher solvent-accessibility prediction so that they would be partially buried or exposed in the protein. In addition, five residues (Leu107, Leu202, Ile133, Leu128 and Ile159) of AtTLP18.3 were mutated to methionine residues. After overexpression and purification, only two single-mutant lines, L128M and I159M, could be crystallized. Finally, a double-mutation line of truncated AtTLP18.3 with L128M and I159M mutations was constructed. The structure of the double mutant AtTLP18.3 protein was resolved using the single-wavelength anomalous diffraction method at 2.6 Å resolution. The results indicated that a combination of secondary-structure and solvent-accessibility prediction for methionine substitution is a useful method in SAD and MAD phasing.\",\n \"corpus_id\": 22549296,\n \"score\": 1\n },\n {\n \"doc_id\": \"25064136\",\n \"title\": \"Crystal structure of the lytic CHAP(K) domain of the endolysin LysK from Staphylococcus aureus bacteriophage K.\",\n \"abstract\": \"BACKGROUND: Bacteriophages encode endolysins to lyse their host cell and allow escape of their progeny. Endolysins are also active against Gram-positive bacteria when applied from the outside and are thus attractive anti-bacterial agents. LysK, an endolysin from staphylococcal phage K, contains an N-terminal cysteine-histidine dependent amido-hydrolase/peptidase domain (CHAP(K)), a central amidase domain and a C-terminal SH3b cell wall-binding domain. CHAP(K) cleaves bacterial peptidoglycan between the tetra-peptide stem and the penta-glycine bridge. METHODS: The CHAP(K) domain of LysK was crystallized and high-resolution diffraction data was collected both from a native protein crystal and a methylmercury chloride derivatized crystal. The anomalous signal contained in the derivative data allowed the location of heavy atom sites and phase determination. The resulting structures were completed, refined and analyzed. The presence of calcium and zinc ions in the structure was confirmed by X-ray fluorescence emission spectroscopy. Zymogram analysis was performed on the enzyme and selected site-directed mutants. RESULTS: The structure of CHAP(K) revealed a papain-like topology with a hydrophobic cleft, where the catalytic triad is located. Ordered buffer molecules present in this groove may mimic the peptidoglycan substrate. When compared to previously solved CHAP domains, CHAP(K) contains an additional lobe in its N-terminal domain, with a structural calcium ion, coordinated by residues Asp45, Asp47, Tyr49, His51 and Asp56. The presence of a zinc ion in the active site was also apparent, coordinated by the catalytic residue Cys54 and a possible substrate analogue. Site-directed mutagenesis was used to demonstrate that residues involved in calcium binding and of the proposed active site were important for enzyme activity. CONCLUSIONS: The high-resolution structure of the CHAP(K) domain of LysK was determined, suggesting the location of the active site, the substrate-binding groove and revealing the presence of a structurally important calcium ion. A zinc ion was found more loosely bound. Based on the structure, we propose a possible reaction mechanism. Future studies will be aimed at co-crystallizing CHAP(K) with substrate analogues and elucidating its role in the complete LysK protein. This, in turn, may lead to the design of site-directed mutants with altered activity or substrate specificity.\",\n \"corpus_id\": 1380517,\n \"score\": 1\n },\n {\n \"doc_id\": \"25994880\",\n \"title\": \"Crystal structure of the fibre head domain of bovine adenovirus 4, a ruminant atadenovirus.\",\n \"abstract\": \"BACKGROUND: In adenoviruses, primary host cell recognition is generally performed by the head domains of their homo-trimeric fibre proteins. This first interaction is reversible. A secondary, irreversible interaction subsequently takes place via other adenovirus capsid proteins and leads to a productive infection. Although many fibre head structures are known for human mastadenoviruses, not many animal adenovirus fibre head structures have been determined, especially not from those belonging to adenovirus genera other than Mastadenovirus. METHODS: We constructed an expression vector for the fibre head domain from a ruminant atadenovirus, bovine adenovirus 4 (BAdV-4), consisting of amino acids 414-535, expressed the protein in Escherichia coli, purified it by metal affinity and cation exchange chromatography and crystallized it. The structure was solved using single isomorphous replacement plus anomalous dispersion of a mercury derivative and refined against native data that extended to 1.2 Å resolution. RESULTS: Like in other adenoviruses, the BAdV-4 fibre head monomer contains a beta-sandwich consisting of ABCJ and GHID sheets. The topology is identical to the fibre head of the other studied atadenovirus, snake adenovirus 1 (SnAdV-1), including the alpha-helix in the DG-loop, despite of them having a sequence identity of only 15 %. There are also differences which may have implications for ligand binding. Beta-strands G and H are longer and differences in several surface-loops and surface charge are observed. CONCLUSIONS: Chimeric adenovirus fibres have been used to retarget adenovirus-based anti-cancer and gene therapy vectors. Ovine adenovirus 7 (OAdV-7), another ruminant atadenovirus, is intensively tested as a basis for such a vector. Here, we present the high-resolution atomic structure of the BAdV-4 fibre head domain, the second atadenovirus fibre head structure known and the first of an atadenovirus that infects a mammalian host. Future research should focus on the receptor-binding properties of these fibre head domains.\",\n \"corpus_id\": 8568594,\n \"score\": 1\n },\n {\n \"doc_id\": \"26418008\",\n \"title\": \"Structure and Sialyllactose Binding of the Carboxy-Terminal Head Domain of the Fibre from a Siadenovirus, Turkey Adenovirus 3.\",\n \"abstract\": \"The virulent form of turkey adenovirus 3 (TAdV-3), also known as turkey hemorrhagic enteritis virus (THEV), is an economically important poultry pathogen, while the avirulent form is used as a vaccine. TAdV-3 belongs to the genus Siadenovirus. The carboxy-terminal region of its fibre does not have significant sequence similarity to any other adenovirus fibre heads of known structure. Two amino acid sequence differences between virulent and avirulent TAdV-3 map on the fibre head: where virulent TAdV-3 contains Ile354 and Thr376, avirulent TAdV-3 contains Met354 and Met376. We determined the crystal structures of the trimeric virulent and avirulent TAdV-3 fibre head domains at 2.2 Å resolution. Each monomer contains a beta-sandwich, which, surprisingly, resembles reovirus fibre head more than other adenovirus fibres, although the ABCJ-GHID topology is conserved in all. A beta-hairpin insertion in the C-strand of each trimer subunit embraces its neighbouring monomer. The avirulent and virulent TAdV-3 fibre heads are identical apart from the exact orientation of the beta-hairpin insertion. In vitro, sialyllactose was identified as a ligand by glycan microarray analysis, nuclear magnetic resonance spectroscopy, and crystallography. Its dissociation constant was measured to be in the mM range by isothermal titration calorimetry. The ligand binds to the side of the fibre head, involving amino acids Glu392, Thr419, Val420, Lys421, Asn422, and Gly423 binding to the sialic acid group. It binds slightly more strongly to the avirulent form. We propose that, in vivo, the TAdV-3 fibre may bind a sialic acid-containing cell surface component.\",\n \"corpus_id\": 23279362,\n \"score\": 1\n },\n {\n \"doc_id\": \"26574546\",\n \"title\": \"Structural Plasticity of the Protein Plug That Traps Newly Packaged Genomes in Podoviridae Virions.\",\n \"abstract\": \"Bacterial viruses of the P22-like family encode a specialized tail needle essential for genome stabilization after DNA packaging and implicated in Gram-negative cell envelope penetration. The atomic structure of P22 tail needle (gp26) crystallized at acidic pH reveals a slender fiber containing an N-terminal \\\"trimer of hairpins\\\" tip. Although the length and composition of tail needles vary significantly in Podoviridae, unexpectedly, the amino acid sequence of the N-terminal tip is exceptionally conserved in more than 200 genomes of P22-like phages and prophages. In this paper, we used x-ray crystallography and EM to investigate the neutral pH structure of three tail needles from bacteriophage P22, HK620, and Sf6. In all cases, we found that the N-terminal tip is poorly structured, in stark contrast to the compact trimer of hairpins seen in gp26 crystallized at acidic pH. Hydrogen-deuterium exchange mass spectrometry, limited proteolysis, circular dichroism spectroscopy, and gel filtration chromatography revealed that the N-terminal tip is highly dynamic in solution and unlikely to adopt a stable trimeric conformation at physiological pH. This is supported by the cryo-EM reconstruction of P22 mature virion tail, where the density of gp26 N-terminal tip is incompatible with a trimer of hairpins. We propose the tail needle N-terminal tip exists in two conformations: a pre-ejection extended conformation, which seals the portal vertex after genome packaging, and a postejection trimer of hairpins, which forms upon its release from the virion. The conformational plasticity of the tail needle N-terminal tip is built in the amino acid sequence, explaining its extraordinary conservation in nature.\",\n \"corpus_id\": 34346428,\n \"score\": 1\n },\n {\n \"doc_id\": \"26814179\",\n \"title\": \"The Atomic Structure of the Phage Tuc2009 Baseplate Tripod Suggests that Host Recognition Involves Two Different Carbohydrate Binding Modules.\",\n \"abstract\": \"UNLABELLED: The Gram-positive bacterium Lactococcus lactis, used for the production of cheeses and other fermented dairy products, falls victim frequently to fortuitous infection by tailed phages. The accompanying risk of dairy fermentation failures in industrial facilities has prompted in-depth investigations of these phages. Lactococcal phage Tuc2009 possesses extensive genomic homology to phage TP901-1. However, striking differences in the baseplate-encoding genes stimulated our interest in solving the structure of this host's adhesion device. We report here the X-ray structures of phage Tuc2009 receptor binding protein (RBP) and of a \\\"tripod\\\" assembly of three baseplate components, BppU, BppA, and BppL (the RBP). These structures made it possible to generate a realistic atomic model of the complete Tuc2009 baseplate that consists of an 84-protein complex: 18 BppU, 12 BppA, and 54 BppL proteins. The RBP head domain possesses a different fold than those of phages p2, TP901-1, and 1358, while the so-called \\\"stem\\\" and \\\"neck\\\" domains share structural features with their equivalents in phage TP901-1. The BppA module interacts strongly with the BppU N-terminal domain. Unlike other characterized lactococcal phages, Tuc2009 baseplate harbors two different carbohydrate recognition sites: one in the bona fide RBP head domain and the other in BppA. These findings represent a major step forward in deciphering the molecular mechanism by which Tuc2009 recognizes its saccharidic receptor(s) on its host. IMPORTANCE: Understanding how siphophages infect Lactococcus lactis is of commercial importance as they cause milk fermentation failures in the dairy industry. In addition, such knowledge is crucial in a general sense in order to understand how viruses recognize their host through protein-glycan interactions. We report here the lactococcal phage Tuc2009 receptor binding protein (RBP) structure as well as that of its baseplate. The RBP head domain has a different fold than those of phages p2, TP901-1, and 1358, while the so-called \\\"stem\\\" and \\\"neck\\\" share the fold characteristics also found in the equivalent baseplate proteins of phage TP901-1. The baseplate structure contains, in contrast to other characterized lactococcal phages, two different carbohydrate binding modules that may bind different motifs of the host's surface polysaccharide.\",\n \"corpus_id\": 15144214,\n \"score\": 1\n },\n {\n \"doc_id\": \"27334597\",\n \"title\": \"Crystal structure of raptor adenovirus 1 fibre head and role of the beta-hairpin in siadenovirus fibre head domains.\",\n \"abstract\": \"BACKGROUND: Most adenoviruses recognize their host cells via an interaction of their fibre head domains with a primary receptor. The structural framework of adenovirus fibre heads is conserved between the different adenovirus genera for which crystal structures have been determined (Mastadenovirus, Aviadenovirus, Atadenovirus and Siadenovirus), but genus-specific differences have also been observed. The only known siadenovirus fibre head structure, that of turkey adenovirus 3 (TAdV-3), revealed a twisted beta-sandwich resembling the reovirus fibre head architecture more than that of other adenovirus fibre heads, plus a unique beta-hairpin embracing a neighbouring monomer. The TAdV-3 fibre head was shown to bind sialyllactose. METHODS: Raptor adenovirus 1 (RAdV-1) fibre head was expressed, crystallized and its structure was solved and refined at 1.5 Å resolution. The structure could be solved by molecular replacement using the TAdV-3 fibre head structure as a search model, despite them sharing a sequence identity of only 19 %. Versions of both the RAdV-1 and TAdV-3 fibre heads with their beta-hairpin arm deleted were prepared and their stabilities were compared with the non-mutated proteins by a thermal unfolding assay. RESULTS: The structure of the RAdV-1 fibre head contains the same twisted ABCJ-GHID beta-sandwich and beta-hairpin arm as the TAdV-3 fibre head. However, while the predicted electro-potential surface charge of the TAdV-3 fibre head is mainly positive, the RAdV-1 fibre head shows positively and negatively charged patches and does not appear to bind sialyllactose. Deletion of the beta-hairpin arm does not affect the structure of the raptor adenovirus 1 fibre head and only affects the stability of the RAdV-1 and TAdV-3 fibre heads slightly. CONCLUSIONS: The high-resolution structure of RAdV-1 fibre head is the second known structure of a siadenovirus fibre head domain. The structure shows that the siadenovirus fibre head structure is conserved, but differences in the predicted surface charge suggest that RAdV-1 uses a different natural receptor for cell attachment than TAdV-3. Deletion of the beta-hairpin arm shows little impact on the structure and stability of the siadenovirus fibre heads.\",\n \"corpus_id\": 11335559,\n \"score\": 1\n },\n {\n \"doc_id\": \"29695426\",\n \"title\": \"Structural and Functional Features of the Reovirus σ1 Tail.\",\n \"abstract\": \"Mammalian orthoreovirus attachment to target cells is mediated by the outer capsid protein σ1, which projects from the virion surface. The σ1 protein is a homotrimer consisting of a filamentous tail, which is partly inserted into the virion; a body domain constructed from β-spiral repeats; and a globular head with receptor-binding properties. The σ1 tail is predicted to form an α-helical coiled coil. Although σ1 undergoes a conformational change during cell entry, the nature of this change and its contributions to viral replication are unknown. Electron micrographs of σ1 molecules released from virions identified three regions of flexibility, including one at the midpoint of the molecule, that may be involved in its structural rearrangement. To enable a detailed understanding of essential σ1 tail organization and properties, we determined high-resolution structures of the reovirus type 1 Lang (T1L) and type 3 Dearing (T3D) σ1 tail domains. Both molecules feature extended α-helical coiled coils, with T1L σ1 harboring central chloride ions. Each molecule displays a discontinuity (stutter) within the coiled coil and an unexpectedly seamless transition to the body domain. The transition region features conserved interdomain interactions and appears rigid rather than highly flexible. Functional analyses of reoviruses containing engineered σ1 mutations suggest that conserved residues predicted to stabilize the coiled-coil-to-body junction are essential for σ1 folding and encapsidation, whereas central chloride ion coordination and the stutter are dispensable for efficient replication. Together, these findings enable modeling of full-length reovirus σ1 and provide insight into the stabilization of a multidomain virus attachment protein. IMPORTANCE While it is established that different conformational states of attachment proteins of enveloped viruses mediate receptor binding and membrane fusion, less is understood about how such proteins mediate attachment and entry of nonenveloped viruses. The filamentous reovirus attachment protein σ1 binds cellular receptors; contains regions of predicted flexibility, including one at the fiber midpoint; and undergoes a conformational change during cell entry. Neither the nature of the structural change nor its contribution to viral infection is understood. We determined crystal structures of large σ1 fragments for two different reovirus serotypes. We observed an unexpectedly tight transition between two domains spanning the fiber midpoint, which allows for little flexibility. Studies of reoviruses with engineered changes near the σ1 midpoint suggest that the stabilization of this region is critical for function. Together with a previously determined structure, we now have a complete model of the full-length, elongated reovirus σ1 attachment protein.\",\n \"corpus_id\": 25113018,\n \"score\": 1\n },\n {\n \"doc_id\": \"18096638\",\n \"title\": \"Solution structure of the C-terminal domain of Ole e 9, a major allergen of olive pollen.\",\n \"abstract\": \"Ole e 9 is an olive pollen allergen belonging to group 2 of pathogenesis-related proteins. The protein is composed of two immunological independent domains: an N-terminal domain (NtD) with 1,3-beta-glucanase activity, and a C-terminal domain (CtD) that binds 1,3-beta-glucans. We have determined the three-dimensional structure of CtD-Ole e 9 (101 amino acids), which consists of two parallel alpha-helices forming an angle of approximately 55 degrees , a small antiparallel beta-sheet with two short strands, and a 3-10 helix turn, all connected by long coil segments, resembling a novel type of folding among allergens. Two regions surrounded by aromatic residues (F49, Y60, F96, Y91 and Y31, H68, Y65, F78) have been localized on the protein surface, and a role for sugar binding is suggested. The epitope mapping of CtD-Ole e 9 shows that B-cell epitopes are mainly located on loops, although some of them are contained in secondary structural elements. Interestingly, the IgG and IgE epitopes are contiguous or overlapped, rather than coincident. The three-dimensional structure of CtD-Ole e 9 might help to understand the underlying mechanism of its biochemical function and to determine possible structure-allergenicity relationships.\",\n \"corpus_id\": 23733055,\n \"score\": 0\n },\n {\n \"doc_id\": \"18373550\",\n \"title\": \"Structural models and binding site prediction of the C-terminal domain of human Hsp90: a new target for anticancer drugs.\",\n \"abstract\": \"Heat shock protein 90 is a valuable target for anticancer drugs because of its role in the activation and stabilization of multiple oncogenic signalling proteins. While several compounds inhibit heat shock protein 90 by binding the N-terminal domain, recent studies have proved that the C-terminal domain is important for dimerization of the chaperone and contains an additional binding site for inhibitors. Heat shock protein 90 inhibition achieved with molecules binding to the C-terminal domain provides an additional and novel opportunity to design and develop drugs. Therefore, for the first time, we have investigated the structure and the dynamic behaviour of the C-terminal domain of human heat shock protein 90 with and without the small-middle domain, using homology modelling and molecular dynamics simulations. In addition, secondary structure predictions and peptide folding simulations proved useful to investigate a putative additional alpha-helix located between H18 and beta20 of the C-terminal domain. Finally, we used the structural information to infer the location of the binding site located in the C-terminal domain by using a number of computational tools. The predicted pocket is formed by two grooves located between helix H18, the loop downstream of H18 and the loop connecting helices H20 and H21 of each monomer of the C-terminal domain, with only two amino acids contributing from each middle domain.\",\n \"corpus_id\": 31018983,\n \"score\": 0\n },\n {\n \"doc_id\": \"18552768\",\n \"title\": \"Crystal structure of human ERp44 shows a dynamic functional modulation by its carboxy-terminal tail.\",\n \"abstract\": \"ERp44 mediates thiol-dependent retention in the early secretory pathway, forming mixed disulphides with substrate proteins through its conserved CRFS motif. Here, we present its crystal structure at a resolution of 2.6 A. Three thioredoxin domains-a, b and b'-are arranged in a clover-like structure. A flexible carboxy-terminal tail turns back to the b' and a domains, shielding a hydrophobic pocket in domain b' and a hydrophobic patch around the CRFS motif in domain a. Mutational and functional studies indicate that the C-terminal tail gates the CRFS area and the adjacent hydrophobic pocket, dynamically regulating protein quality control.\",\n \"corpus_id\": 19426181,\n \"score\": 0\n },\n {\n \"doc_id\": \"19324050\",\n \"title\": \"NMR structure of the amino-terminal domain of the lambda integrase protein in complex with DNA: immobilization of a flexible tail facilitates beta-sheet recognition of the major groove.\",\n \"abstract\": \"The integrase protein (Int) from bacteriophage lambda is the archetypal member of the tyrosine recombinase family, a large group of enzymes that rearrange DNA in all domains of life. Int catalyzes the insertion and excision of the viral genome into and out of the Escherichia coli chromosome. Recombination transpires within higher-order nucleoprotein complexes that form when its amino-terminal domain binds to arm-type DNA sequences that are located distal to the site of strand exchange. Arm-site binding by Int is essential for catalysis, as it promotes Int-mediated bridge structures that stabilize the recombination machinery. We have elucidated how Int is able to sequence specifically recognize the arm-type site sequence by determining the solution structure of its amino-terminal domain (Int(N), residues Met1 to Leu64) in complex with its P'2 DNA binding site. Previous studies have shown that Int(N) adopts a rare monomeric DNA binding fold that consists of a three-stranded antiparallel beta-sheet that is packed against a carboxy-terminal alpha helix. A low-resolution crystal structure of the full-length protein also revealed that the sheet is inserted into the major groove of the arm-type site. The solution structure presented here reveals how Int(N) specifically recognizes the arm-type site sequence. A novel feature of the new solution structure is the use of an 11-residue tail that is located at the amino terminus. DNA binding induces the folding of a 3(10) helix in the tail that projects the amino terminus of the protein deep into the minor groove for stabilizing DNA contacts. This finding reveals the structural basis for the observation that the \\\"unstructured\\\" amino terminus is required for recombination.\",\n \"corpus_id\": 25344386,\n \"score\": 0\n },\n {\n \"doc_id\": \"19447113\",\n \"title\": \"Structure of the alkalohyperthermophilic Archaeoglobus fulgidus lipase contains a unique C-terminal domain essential for long-chain substrate binding.\",\n \"abstract\": \"Several crystal structures of AFL, a novel lipase from the archaeon Archaeoglobus fulgidus, complexed with various ligands, have been determined at about 1.8 A resolution. This enzyme has optimal activity in the temperature range of 70-90 degrees C and pH 10-11. AFL consists of an N-terminal alpha/beta-hydrolase fold domain, a small lid domain, and a C-terminal beta-barrel domain. The N-terminal catalytic domain consists of a 6-stranded beta-sheet flanked by seven alpha-helices, four on one side and three on the other side. The C-terminal lipid binding domain consists of a beta-sheet of 14 strands and a substrate covering motif on top of the highly hydrophobic substrate binding site. The catalytic triad residues (Ser136, Asp163, and His210) and the residues forming the oxyanion hole (Leu31 and Met137) are in positions similar to those of other lipases. Long-chain lipid is located across the two domains in the AFL-substrate complex. Structural comparison of the catalytic domain of AFL with a homologous lipase from Bacillus subtilis reveals an opposite substrate binding orientation in the two enzymes. AFL has a higher preference toward long-chain substrates whose binding site is provided by a hydrophobic tunnel in the C-terminal domain. The unusually large interacting surface area between the two domains may contribute to thermostability of the enzyme. Two amino acids, Asp61 and Lys101, are identified as hinge residues regulating movement of the lid domain. The hydrogen-bonding pattern associated with these two residues is pH dependent, which may account for the optimal enzyme activity at high pH. Further engineering of this novel lipase with high temperature and alkaline stability will find its use in industrial applications.\",\n \"corpus_id\": 5604880,\n \"score\": 0\n },\n {\n \"doc_id\": \"22708907\",\n \"title\": \"Crystal structure of the Yersinia enterocolitica type III secretion chaperone SycD in complex with a peptide of the minor translocator YopD.\",\n \"abstract\": \"BACKGROUND: Type III secretion systems are used by Gram-negative bacteria as \\\"macromolecular syringes\\\" to inject effector proteins into eukaryotic cells. Two hydrophobic proteins called translocators form the necessary pore in the host cell membrane. Both translocators depend on binding to a single chaperone in the bacterial cytoplasm to ensure their stability and efficient transport through the secretion needle. It was suggested that the conserved chaperones bind the more divergent translocators via a hexapeptide motif that is found in both translocators and conserved between species. RESULTS: We crystallized a synthetic decapeptide from the Yersinia enterocolitica minor type III secretion translocator YopD bound to its cognate chaperone SycD and determined the complex structure at 2.5 Å resolution. The structure of peptide-bound SycD is almost identical to that of apo SycD with an all helical fold consisting of three tetratricopeptide repeats (TPRs) and an additional C-terminal helix. Peptide-bound SycD formed a kinked head-to-head dimer that had previously been observed for the apo form of SycD. The homodimer interface comprises both helices of the first tetratricopeptide repeat. The YopD peptide bound in extended conformation into a mainly hydrophobic groove on the concave side of SycD. TPRs 1 and 2 of SycD form three hydrophobic pockets that accommodated the conserved hydrophobic residues at position 1, 3 and 6 of the translocator hexapeptide sequence. Two tyrosines that are highly conserved among translocator chaperones contribute to the hydrophobic patches but also form hydrogen bonds to the peptide backbone. CONCLUSIONS: The interaction between SycD and YopD is very similar to the binding of the Pseudomonas minor translocator PopD to its chaperone PcrH and the Shigella major translocator IpaB to its chaperone IpgC. This confirms the prediction made by Kolbe and co-workers that a hexapeptide with hydrophobic residues at three positions is a conserved chaperone binding motif. Because the hydrophobic groove on the concave side of translocator chaperones is involved in binding of the major and the minor translocator, simultaneous binding of both translocators to a single type III secretion class II chaperone appears unlikely.\",\n \"corpus_id\": 15764038,\n \"score\": 0\n },\n {\n \"doc_id\": \"25982270\",\n \"title\": \"Crystal structure of the C-terminal domain of tubulin-binding cofactor C from Leishmania major.\",\n \"abstract\": \"Tubulin-binding cofactor C stimulates GTPase activity and contributes to the release of the heterodimeric α/β-tubulin from a super-complex of tubulin monomers and two ancillary cofactors. We have determined the 2.2 Å resolution crystal structure of the C-terminal domain of tubulin-binding cofactor C from Leishmania major based on single wavelength anomalous dispersion measurements targeting a selenomethionine derivative. Although previously predicted to consist of two domains the structure is best described as a single domain dominated by a right-handed β-helix of five turns that form a triangular prism. One face of the prism is covered by the C-terminal residues leaving another face solvent exposed. Comparisons with an orthologous human GTPase activating protein match key residues involved in binding nucleotide and identify the face of the β-helix fold likely involved in interacting with the β-tubulin:GTP complex.\",\n \"corpus_id\": 7615194,\n \"score\": 0\n },\n {\n \"doc_id\": \"29223729\",\n \"title\": \"Structure-Function Analysis of the C-Terminal Domain of the Type VI Secretion TssB Tail Sheath Subunit.\",\n \"abstract\": \"The type VI secretion system (T6SS) is a specialized macromolecular complex dedicated to the delivery of protein effectors into both eukaryotic and bacterial cells. The general mechanism of action of the T6SS is similar to the injection of DNA by contractile bacteriophages. The cytoplasmic portion of the T6SS is evolutionarily, structurally and functionally related to the phage tail complex. It is composed of an inner tube made of stacked Hcp hexameric rings, engulfed within a sheath and built on a baseplate. This sheath undergoes cycles of extension and contraction, and the current model proposes that the sheath contraction propels the inner tube toward the target cell for effector delivery. The sheath comprises two subunits: TssB and TssC that polymerize under an extended conformation. Here, we show that isolated TssB forms trimers, and we report the crystal structure of a C-terminal fragment of TssB. This fragment comprises a long helix followed by a helical hairpin that presents surface-exposed charged residues. Site-directed mutagenesis coupled to functional assay further showed that these charges are required for proper assembly of the sheath. Positioning of these residues in the extended T6SS sheath structure suggests that they may mediate contacts with the baseplate.\",\n \"corpus_id\": 46881667,\n \"score\": 0\n }\n]","isConversational":false}}},{"rowIdx":49,"cells":{"query":{"kind":"string","value":"{\n \"doc_id\": \"28358005\",\n \"title\": \"Structural intermediates and directionality of the swiveling motion of Pyruvate Phosphate Dikinase.\",\n \"abstract\": \"Pyruvate phosphate dikinase (PPDK) is a vital enzyme in cellular energy metabolism catalyzing the ATP- and Pi-dependent formation of phosphoenolpyruvate from pyruvate in C4 -plants, but the reverse reaction forming ATP in bacteria and protozoa. The multi-domain enzyme is considered an efficient molecular machine that performs one of the largest single domain movements in proteins. However, a comprehensive understanding of the proposed swiveling domain motion has been limited by not knowing structural intermediates or molecular dynamics of the catalytic process. Here, we present crystal structures of PPDKs from Flaveria, a model genus for studying the evolution of C4 -enzymes from phylogenetic ancestors. These structures resolve yet unknown conformational intermediates and provide the first detailed view on the large conformational transitions of the protein in the catalytic cycle. Independently performed unrestrained MD simulations and configurational free energy calculations also identified these intermediates. In all, our experimental and computational data reveal strict coupling of the CD swiveling motion to the conformational state of the NBD. Moreover, structural asymmetries and nucleotide binding states in the PPDK dimer support an alternate binding change mechanism for this intriguing bioenergetic enzyme.\",\n \"corpus_id\": 9682014\n}"},"candidates":{"kind":"list like","value":[{"doc_id":"17996018","title":"The pyruvate, orthophosphate dikinase regulatory proteins of Arabidopsis possess a novel, unprecedented Ser/Thr protein kinase primary structure.","abstract":"Pyruvate, orthophosphate dikinase (PPDK) is a ubiquitous, low-abundance metabolic enzyme of undetermined function in C3 plants. Its activity in C3 chloroplasts is light-regulated via reversible phosphorylation of an active-site Thr residue by the PPDK regulatory protein (RP), a most unusual bifunctional protein kinase (PK)/protein phosphatase (PP). In this paper we document the molecular cloning and functional analysis of the two unique C3 RPs in Arabidopsis thaliana. The first of these, AtRP1, encodes a typical chloroplast-targeted, bifunctional C4-like RP. The second RP gene, AtRP2, encodes a monofunctional polypeptide that possesses in vitro RP-like PK activity but lacks PP activity, and is localized in the cytosol. Notably, the deduced primary structures of these two highly homologous polypeptides are devoid of any canonical subdomain structure that unifies all known eukaryotic and prokaryotic Ser/Thr PKs into one of three superfamilies, despite the direct demonstration that AtRP1 is functionally a member of this group. Instead, these C3 RPs and the related C4 plant homologues encode a conserved, centrally positioned, approximately 260-residue sequence currently described as the 'domain of unknown function 299' (DUF 299). We propose that vascular plant RPs form a unique protein kinase family now designated as the DUF 299 gene family.","corpus_id":20245121,"score":2},{"doc_id":"18831048","title":"Opening of the ADP-bound active site in the ABC transporter ATPase dimer: evidence for a constant contact, alternating sites model for the catalytic cycle.","abstract":"ABC transporters are ubiquitous, ATP-dependent transmembrane pumps. The mechanism by which ATP hydrolysis in the nucleotide-binding domain (NBD) effects conformational changes in the transmembrane domain that lead to allocrite translocation remains largely unknown. A possible aspect of this mechanism was suggested by previous molecular dynamics simulations of the MJ0796 NBD dimer, which revealed a novel, nucleotide-dependent intrasubunit conformational change involving the relative rotation of the helical and catalytic subdomains. Here, we find that in four of five simulations of the ADP/ATP-bound dimer, the relative rotation of the helical and catalytic subdomains in the ADP-bound monomer results in opening of the ADP-bound active site, probably sufficient or close to sufficient to allow nucleotide exchange. We also observe that in all five simulations of the ADP/ATP-bound dimer, the intimate contact of the LSGGQ signature sequence with the ATP gamma-phosphate is weakened by the intrasubunit conformational change within the ADP-bound monomer. We discuss how these results support a constant contact model for the function of the NBD dimer in contrast to switch models, in which the NBDs are proposed to fully disassociate during the catalytic cycle.","corpus_id":10494245,"score":2},{"doc_id":"19914167","title":"Structures of asymmetric ClpX hexamers reveal nucleotide-dependent motions in a AAA+ protein-unfolding machine.","abstract":"ClpX is a AAA+ machine that uses the energy of ATP binding and hydrolysis to unfold native proteins and translocate unfolded polypeptides into the ClpP peptidase. The crystal structures presented here reveal striking asymmetry in ring hexamers of nucleotide-free and nucleotide-bound ClpX. Asymmetry arises from large changes in rotation between the large and small AAA+ domains of individual subunits. These differences prevent nucleotide binding to two subunits, generate a staggered arrangement of ClpX subunits and pore loops around the hexameric ring, and provide a mechanism for coupling conformational changes caused by ATP binding or hydrolysis in one subunit to flexing motions of the entire ring. Our structures explain numerous solution studies of ClpX function, predict mechanisms for pore elasticity during translocation of irregular polypeptides, and suggest how repetitive conformational changes might be coupled to mechanical work during the ATPase cycle of ClpX and related molecular machines.","corpus_id":7976574,"score":2},{"doc_id":"19996093","title":"The conformational transition pathway of ATP binding cassette transporter MsbA revealed by atomistic simulations.","abstract":"ATP binding cassette transporters are integral membrane proteins that use the energy released from ATP hydrolysis at the two nucleotide binding domains (NBDs) to translocate a wide variety of substrates through a channel at the two transmembrane domains (TMDs) across the cell membranes. MsbA from Gram-negative bacteria is a lipid and multidrug resistance ATP binding cassette exporter that can undergo large scale conformational changes between the outward-facing and the inward-facing conformations revealed by crystal structures in different states. Here, we use targeted molecular dynamics simulation methods to explore the atomic details of the conformational transition from the outward-facing to the inward-facing states of MsbA. The molecular dynamics trajectories revealed a clear spatiotemporal order of the conformational movements. The disruption of the nucleotide binding sites at the NBD dimer interface is the very first event that initiates the following conformational changes, verifying the assumption that the conformational conversion is triggered by ATP hydrolysis. The conserved x-loops of the NBDs were identified to participate in the interaction network that stabilizes the cytoplasmic tetrahelix bundle of the TMDs and play an important role in mediating the cross-talk between the NBD and TMD. The movement of the NBD dimer is transmitted through x-loops to break the tetrahelix bundle, inducing the packing rearrangements of the transmembrane helices at the cytoplasmic side and the periplasmic side sequentially. The packing rearrangement within each periplasmic wing of TMD that results in exposure of the substrate binding sites occurred at the end stage of the trajectory, preventing the wrong timing of the binding site accessibility.","corpus_id":2829607,"score":2},{"doc_id":"20369870","title":"Insights into the molecular mechanism of an ABC transporter: conformational changes in the NBD dimer of MJ0796.","abstract":"Despite the rapid advances in the study of ABC transporters, many fundamental questions linked to ATP binding/hydrolysis and its relation to the transport cycle remain unanswered. In particular, it is still neither clear nor consensual how the ATP energy is used by the nucleotide binding domains (NBDs) to produce mechanical work and drive the substrate translocation. The major conformational changes in the NBDs following ATP hydrolysis during the transport cycle and the role played by the conserved family motifs in harnessing the energy associated with nucleotide hydrolysis are yet unknown. Additionally, the way energy is transmitted from the catalytic to the membrane domains, in order to drive substrate translocation, is also a fundamental question that remains unanswered. Due to the high structure similarities of the NBD architecture throughout the whole ABC family, it is likely that the mechanism of ATP binding, hydrolysis, and communication with the transmembrane domains is similar in all family members, independently of the nature of the transported substrate. In this work, we focused our attention on the consequences of ATP hydrolysis in the NBDs, especially on the structural changes that occur during this process. For that, we use molecular dynamics simulation techniques taking as a starting point the X-ray structure of the MJ0796 dimer from Methanococcus jannaschii. Several potential intermediate states of the ATP hydrolytic cycle are investigated, each consisting of different combinations of nucleotide-bound forms. The results obtained allowed us to identify the conformational rearrangements induced by hydrolysis on the catalytic subunits, as well as the residues involved in this reorganization. The major changes are localized at specific regions of the protein, namely, involving segments 11-19 and 93-124. Additionally, our results together with the knowledge of complete ABC transporter X-ray structures suggest a possible NBD:TMD signal transmission interface.","corpus_id":26818665,"score":2},{"doc_id":"21414960","title":"Functional evolution of C(4) pyruvate, orthophosphate dikinase.","abstract":"Pyruvate,orthophosphate dikinase (PPDK) plays a controlling role in the PEP-regeneration phase of the C(4) photosynthetic pathway. Earlier studies have fully documented its biochemical properties and its post-translational regulation by the PPDK regulatory protein (PDRP). However, the question of its evolution into the C(4) pathway has, until recently, received little attention. One assumption concerning this evolution is that changes in catalytic and regulatory properties of PPDK were necessary for the enzyme to fulfil its role in the C(4) pathway. In this study, the functional evolution of PPDK from its ancient origins in the Archaea to its ascension as a photosynthetic enzyme in modern C(4) angiosperms is reviewed. This analysis is accompanied by a comparative investigation into key catalytic and regulatory properties of a C(3) PPDK isoform from Arabidopsis and the C(4) PPDK isoform from Zea mays. From these analyses, it is proposed that PPDK first became functionally seated in C(3) plants as an ancillary glycolytic enzyme and that its transition into a C(4) pathway enzyme involved only minor changes in enzyme properties per se.","corpus_id":15123166,"score":2},{"doc_id":"21421406","title":"What can enzymes of C₄ photosynthesis do for C₃ plants under stress?","abstract":"Phosphoenolpyruvate carboxylase (PEPC), NADP-malic enzyme (NADP-ME), and pyruvate, phosphate dikinase (PPDK) participate in the process of concentrating CO₂ in C₄ photosynthesis. Non-photosynthetic counterparts of these enzymes, which are present in all plants, play important roles in the maintenance of pH and replenishment of Krebs cycle intermediates, thereby contributing to the biosynthesis of amino acids and other compounds and providing NADPH for biosynthesis and the antioxidant system. Enhanced activities of PEPC and/or NADP-ME and/or PPDK were found in plants under various types of abiotic stress, such as drought, high salt concentration, ozone, the absence of phosphate and iron or the presence of heavy metals in the soil. Moreover, the activities of all of these enzymes were enhanced in plants under biotic stress caused by viral infection. The functions of PEPC, NADP-ME and PPDK appear to be more important for plants under stress than under optimal growth conditions.","corpus_id":3083252,"score":2},{"doc_id":"21883547","title":"The pyruvate, orthophosphate dikinase regulatory proteins of Arabidopsis are both bifunctional and interact with the catalytic and nucleotide-binding domains of pyruvate, orthophosphate dikinase.","abstract":"Pyruvate orthophosphate dikinase (PPDK) is a key enzyme in C(4) photosynthesis and is also found in C(3) plants. It is post-translationally modified by the PPDK regulatory protein (RP) that possesses both kinase and phosphotransferase activities. Phosphorylation and dephosphorylation of PPDK lead to inactivation and activation respectively. Arabidopsis thaliana contains two genes that encode chloroplastic (RP1) and cytosolic (RP2) isoforms of RP, and although RP1 has both kinase and phosphotransferase activities, to date RP2 has only been shown to act as a kinase. Here we demonstrate that RP2 is able to catalyse the dephosphorylation of PPDK, although at a slower rate than RP1 under the conditions of our assay. From yeast two-hybrid analysis we propose that RP1 binds to the central catalytic domain of PPDK, and that additional regions towards the carboxy and amino termini are required for a stable interaction between RP2 and PPDK. For 21 highly conserved amino acids in RP1, mutation of 15 of these reduced kinase and phosphotransferase activity, while mutation of six residues had no impact on either activity. We found no mutant in which only one activity was abolished. However, in some chimaeric fusions that comprised the amino and carboxy termini of RP1 and RP2 respectively, the kinase reaction was severely compromised but phosphotransferase activity remained unaffected. These findings are consistent with the findings that both RP1 and RP2 modulate reversibly the activity of PPDK, and possess one bifunctional active site or two separate sites in close proximity.","corpus_id":45178923,"score":2},{"doc_id":"23214920","title":"The power stroke driven by ATP binding in CFTR as studied by molecular dynamics simulations.","abstract":"Cystic fibrosis transmembrane conductance regulator (CFTR) is a chloride channel belonging to the ATP binding cassette (ABC) protein superfamily. Currently, it remains unclear how ATP binding causes the opening of the channel gate at the molecular level. To clarify this mechanism, we first constructed an atomic model of the inward-facing CFTR using the X-ray structures of other ABC proteins. Molecular dynamics (MD) simulations were then performed to explore the structure and dynamics of the inward-facing CFTR in a membrane environment. In the MgATP-bound state, two nucleotide-binding domains (NBDs) formed a head-to-tail type of dimer, in which the ATP molecules were sandwiched between the Walker A and signature motifs. Alternatively, one of the final MD structures in the apo state was similar to that of a \"closed-apo\" conformation found in the X-ray analysis of ATP-free MsbA. Principal component analysis for the MD trajectory indicated that NBD dimerization causes significant structural and dynamical changes in the transmembrane domains (TMDs), which is likely indicative of the formation of a chloride ion access path. This study suggests that the free energy gain from ATP binding acts as a driving force not only for NBD dimerization but also for NBD-TMD concerted motions.","corpus_id":11312616,"score":2},{"doc_id":"23912807","title":"Macromolecular crowding: chemistry and physics meet biology (Ascona, Switzerland, 10-14 June 2012).","abstract":"More than 60 years of biochemical and biophysical studies have accustomed us to think of proteins as highly purified entities that act in isolation, more or less freely diffusing until they find their cognate partner to bind to. While in vitro experiments that reproduce these conditions largely remain the only way to investigate the intrinsic properties of molecules, this approach ignores an important factor: in their natural milieu , proteins are surrounded by several other molecules of different chemical nature, and this crowded environment can considerably modify their behaviour. About 40% of the cellular volume on average is occupied by all sorts of molecules. Furthermore, biological macromolecules live and operate in an extremely structured and complex environment within the cell (endoplasmic reticulum, Golgi apparatus, cytoskeletal structures, etc). Hence, to further complicate the picture, the interior of the cell is by no means a simply crowded medium, rather, a most crowded and confining one. In recent times, several approaches have been developed in the attempt to take into account important factors such as the ones mentioned above, at both theoretical and experimental levels, so that this field of research is now emerging as one of the most thriving in molecular and cell biology (see figure 1). [ Formula: see text] Figure 1. Left: number of articles containing the word 'crowding' as a keyword limited to the biological and chemical science domains (source: ISI Web of Science). The arrow flags the 2003 'EMBO Workshop on Biological Implications of Macromolecular Crowding' (Embo, 2012). Right: number of citations to articles containing the word 'crowding' limited to the same domains (bars) and an exponential regression curve (source: Elsevier Scopus). To promote the importance of molecular crowding and confinement and provide researchers active in this field an interdisciplinary forum for meeting and exchanging ideas, we recently organized an international conference held in Ascona from 10 to 14 June 2012. In the unique scenario of the Maggiore lake and absorbed in the magic atmosphere of the Centro Stefano Franscini (CSF) at Monte Verità, we enjoyed three-and-a-half days of intense and inspiring activity, where not only many of the most prominent scientists working on macromolecular crowding, but also experts in closely related fields such as colloids and soft matter presented their work. The meeting was intended and has been organized to bring theoreticians and experimentalists together in the attempt to promote an active dialogue. Moreover, we wanted different disciplines to be represented, notably physics and chemistry, besides biology, as cross-fertilization is proving an increasingly fundamental source of inspiration and advancement. This issue of Physical Biology (PB) features a selection of the oral contributions presented at the conference, expanded in the form of research or review articles. PB, one of the scientific journals of the Institute of Physics (IOP), is one of the most dynamic and lively forums active at the interface between biology on one side, and physics and mathematics on the other. As its mission is stated by IOP, PB 'focuses on research in which physics-based approaches lead to new insights into biological systems at all scales of space and time, and all levels of complexity'. For these reasons, and also in view of its high reputation and broad readership, PB appears to be the ideal place for disseminating the thriving pieces of research presented at the conference. We are extremely grateful to PB and its kind and efficient editorial staff who helped make this issue a great scientific follow-up to the conference. The opening lecture of the conference, the first of four day-opening keynote lectures, was given by Allen P Minton from NIH (USA), possibly the most influential among the pioneers in the field. He provided a lucid and well-thought-out overview of the concept of macromolecular crowding through an exhaustive chronological account of the major milestones. It is clear that the concept of excluded volume as a key factor remains central to the concept of molecular crowding. As a consequence, simple descriptive paradigms borrowed essentially from colloid physics may still provide useful tools to understand the subtle effects of crowding and confinement in living matter. The contiguity between crowding, colloids and soft matter further emerged as an important concept in the course of the conference in several theoretical lectures and a few experimental ones. Dave Thirumalai, from the University of Maryland (USA), one of the most active theoreticians in the field of theoretical biophysics, outlined scaling theories, concepts from colloid literature and different simulation techniques to describe scenarios for crowding-induced changes in the structure and dynamics of proteins and RNA. In particular, he showed the importance of the shape of crowding particles in affecting folding oligomerization of amyloidogenic peptides. Johannes Schöneberg, from IMPRS, Mathematics Institute (Germany), illustrated ReaDDy , a newly developed particle-based simulation software tool for reaction-diffusion dynamics, developed in the group of Frank Noe at EMPRS. He showed that ReaDDy makes it possible to bridge the gap between soft matter and molecular dynamics (MD) simulations on the one hand and particle-based stochastic reaction-diffusion simulations on the other. We asked Johannes to organize a tutorial session to lead interested participants into the package and 'get their hands wet' under the guidance of the developers. The tutorial session was indeed successful and the broad possibilities offered by the simulation toolkit appeared to be clear to the participants. Paolo De Los Rios, from the Ecole Polytechnique Fédérale de Lausanne (EPFL, Switzerland), examined the complexity of the effects caused by crowding conditions from the point of view of statistical physics. Starting from a modification of the well-known Smoluchowski approach to calculate the encounter rate of diffusion-limited reactions, he showed how more realistic situations accounting for crowding effects could be treated equally well on the same theoretical grounds. This talk marked an important point in the conference as it reinforced the idea that simple models of theoretical physics still have the power to provide inspiring results in spite of the intrinsic simplifications of such theoretical approaches. Along the same lines, Nicolas Dorsaz, from the University of Cambridge (UK), proposed an extension of the Smoluchowski framework that incorporates repulsive and attracting interactions between the reactants. This approach was illustrated by reaction rates obtained from event-driven Brownian dynamics and dynamical Monte Carlo simulations. Another striking example of the physical subtleties associated with modelling crowding effects was provided by Jeffrey Skolnick, from the Georgia Institute of Technology (USA). He examined the role of hydrodynamic interactions in the self-organization of biological assemblies in the presence of crowding. His results strongly suggest that hydrodynamic interactions greatly affect the kinetics of self-assembly reactions, so that including them in the picture appears crucial for understanding the dynamics of biological systems in vivo . Margareth Cheung, from the University of Houston (USA), emphasized that how the crowded environment inside a cell affects the structural conformation of a protein with a spherical shape is a vital question because the geometry of proteins and protein-protein complexes are far from globules in vivo . Her work demonstrates the malleability of 'native' proteins and implies that crowding-induced shape changes may be important for protein function and malfunction in vivo . Huan-Xiang Zhou, from the Florida State University (USA), focused on atomistic simulations of protein folding and binding under crowding conditions. His lab has developed a post-processing method that allows the atomistic representation of proteins in folding and binding processes under crowding. A comparison with experimental results was also presented. Other lecturers pointed out that there are still aspects not entirely explored in the effects of both crowding and confinement. As suggested in the talk by Gary Pielak, from the University of North Carolina (USA), the currently used synthetic crowding agents are far from being satisfactory in replicating naturally occurring effects associated with crowded environments. For example, non-specific binding seems to play a subtle role in the cell, as natural macromolecules can induce both stabilization and destabilization when used as crowders. It is indeed possible to fine-tune the effect of proteins, as crowders, on the stability of other proteins. Another aspect that became clear is that new, more powerful methods need to be developed to study the effect of crowding, but even more to compare crowding and confinement. Indeed, it appeared clear from the lecture by Pierandrea Temussi, from the University of Naples (Italy), that a reliable comparison of the effects of crowding and confinement on the stability of proteins can only be based on the measurement of the whole stability curve of the same protein. Controversial aspects do not pertain only to the influence of crowding on protein stability, but also to aggregation phenomena in natural fluids. Domenico Sanfelice, from NIMR (London, UK), reported an interesting case of the apparent influence of crowding on aggregation. Hen egg white, a possible natural medium to study macromolecules in crowded conditions can dramatically increase the aggregation kinetics of proteins with an inbuilt tendency to associate. By carefully dissecting the phenomenology, it was shown that only part of this effect is due to crowding, while another factor playing an important role is the interaction with proteins from the milieu . In other words, high-molecular-weight glycoproteins can act as efficient molecular seeds for aggregation. A special topic of great relevance in the conference appeared to be the direct study of crowding in living systems. Alan Verkman, from the University of California, San Francisco (USA), one of the world's leading scientific personalities in the field of experimental investigation of crowding and confinement, was invited to give the second plenary lecture devoted to the experimental study of crowding effects in vivo . In his keynote lecture, Dr Verkman led us on a wide and compelling tour, exploring the main experimental approaches to study molecular crowding in and around cells. After a thorough examination of methods such as fluorescence recovery after photo-bleaching, fluorescence correlation spectroscopy, photo-activation localization microscopy and stochastic reconstruction microscopy, he concluded that the general consensus emerging from experimental studies is that the notion of universally anomalous diffusion in and around cells as a consequence of molecular crowding may not be correct, and that the slowing of diffusion in cells is less marked than has been widely assumed and can be simply described through a five- to sixfold reduction of the normal diffusion coefficient. A Soranno, from the University of Zürich (Switzerland), described how, by employing FRET measurements, it is possible to quantify the effect of molecular crowding on the dimensions of the highly charged, intrinsically disordered protein human prothymosin alpha. For a large variety of polymeric crowders (PEG, PVP, Ficoll, Dextran, PVA, PAA), a collapse of the polypeptide chain is observed with increasing polymer size and polymer concentration. The largest extent of collapse is observed for polymer radii comparable to the dimensions of the protein, in agreement with theoretical considerations. For his contribution, A Soranno was awarded the CSF Award for the best contributed talk. In his most inspiring talk, Clifford Brangwynne, from Princeton University (USA), drew attention to very important objects, namely Ribonucleoprotein (RNP) bodies. These are non-membrane-bound macromolecular assemblies that form from the dynamic interactions of RNA and proteins. The assembly of RNP bodies may sensitively depend on the biophysical features of the surrounding cytoplasm, including the degree of crowding, transport coefficients and mechanical properties. This dependency may have important implications for the RNA processing reactions involved in fundamental biological processes such as developmental cell growth. Remarkably, Brangwynne showed how RNPs behave in the cell as liquid droplets, pointing to a possible entirely new means that the cell could use to control and fine-tune its internal processes, in fact, more than that, a completely unexplored, new state of organization of living matter, and a functional one. Giuseppe Zaccai, from Institut Laue Langevin, Grenoble (France), showed that protein dynamics is more sensitive than structure to environmental factors such as crowding, solvent, temperature or pressure. Furthermore, he convincingly explained how neutron scattering provides unique experimental data to underpin MD calculations in this context. Following up on environment-induced modulations of protein functional dynamics, Ruth Nussinov, from Tel Aviv University (Israel), addressed the important problem of whether cellular signals can travel long distances in a crowded environment. She proposed a model based on the evolution of at least three properties: a modular functional organization of the cellular network, sequences in some key regions of proteins, such as linkers or loops, and compact interactions between proteins, possibly favoured by a crowded environment. The workshop ended on a keynote lecture by Jean-Marie Lehn, from the Université de Strasbourg (France). Lehn, 1987 Nobel Laureate in chemistry, offered a 'supramolecular view' of the field of molecular interactions. Supramolecular chemistry explores the design of systems undergoing self-organization , i.e. systems capable of generating well-defined functional supramolecular architectures by self-assembling from their components, thus behaving as programmed chemical systems . Chemistry may therefore be considered an information science , the science of informed matter. Supramolecular chemistry is intrinsically a dynamic chemistry in view of the ability of the interactions connecting the molecular components of a supramolecular entity and the resulting ability of supramolecular species to exchange their constituents. The same holds for molecular chemistry when the molecular entity contains covalent bonds that may form and break reversibly, so as to allow a continuous change in constitution by the reorganization and exchange of building blocks. These features define a constitutional dynamic chemistry (CDC) on both the molecular and supramolecular levels. CDC takes advantage of dynamic constitutional diversity to allow variation and selection in response to either internal or external factors to achieve adaptation . The merging of the features-information and programmability, dynamics and reversibility, constitution and structural diversity-points towards the emergence of adaptive and evolutive chemistry . The whole workshop could have not taken place without the help of the Centro Stefano Franscini. The CSF is the congress centre of the Swiss Federal Institute of Technology of Zurich (ETH Zurich) and has been situated at Monte Verità since 1989. It is an ideal meeting point for all members of the international scientific community who wish to discuss the state-of-the-art and new challenges of any field of research. The CSF supports 20-25 international conferences every year and, since 2010, up to ten winter doctoral schools1. The competence and professionalism of the staff were at the same level of beauty and inspiring character as that of Monte Verità. A meeting of this sort, if successful, leaves the audience with more open questions than settled answers, and this was definitely the case for Crowding 2012. Excluded volume is clearly a fundamental concept that has allowed crowding, a very familiar concept in soft matter, to enter into the domain of biological sciences. However, the complexity of the biological milieu calls for more refined descriptions. What is the role of electrostatic and electrodynamic interactions? What is the role of hydrodynamics interactions? To what extent does the strong spatial inhomogeneity (clustering of molecules, cellular compartmentalization, etc) have to be taken into account? Or, more generally, what are the minimal elements that prove crucial to describe reactions within a cell? How does the diffusion proceed (diffusion, slow diffusion, sub-diffusion) given that the experimental evidences are still controversial? In conclusion, we knew that allowing scientists with very different backgrounds and ideas to mingle was a hazardous attempt. Despite that, the workshop turned out to be a very successful experiment, which was highly enjoyed both by the participants and the organizers. Discussions sparked regularly among ever-changing groups, comprising senior scientists and students, despite the rather tight schedule, adding to the sense of fulfilment ignited by the outstanding level of the presentations. Given the success of the meeting Crowding 2012, a new event has been organized and will take place on the same themes during fall 2013, this time in the beautiful scenery of the Loire valley in France. The workshop 'Macromolecular crowding effects in cell biology: models and experiments' will be held on the CNRS campus in Orléans, France, on 24-25 October 2013. More information can be found on the workshop website: http://dirac.cnrs-orleans.fr/∼piazza/. 1Source: www.csf.ethz.ch/","corpus_id":3008401,"score":2},{"doc_id":"24348227","title":"Decipher the mechanisms of protein conformational changes induced by nucleotide binding through free-energy landscape analysis: ATP binding to Hsp70.","abstract":"ATP regulates the function of many proteins in the cell by transducing its binding and hydrolysis energies into protein conformational changes by mechanisms which are challenging to identify at the atomic scale. Based on molecular dynamics (MD) simulations, a method is proposed to analyze the structural changes induced by ATP binding to a protein by computing the effective free-energy landscape (FEL) of a subset of its coordinates along its amino-acid sequence. The method is applied to characterize the mechanism by which the binding of ATP to the nucleotide-binding domain (NBD) of Hsp70 propagates a signal to its substrate-binding domain (SBD). Unbiased MD simulations were performed for Hsp70-DnaK chaperone in nucleotide-free, ADP-bound and ATP-bound states. The simulations revealed that the SBD does not interact with the NBD for DnaK in its nucleotide-free and ADP-bound states whereas the docking of the SBD was found in the ATP-bound state. The docked state induced by ATP binding found in MD is an intermediate state between the initial nucleotide-free and final ATP-bound states of Hsp70. The analysis of the FEL projected along the amino-acid sequence permitted to identify a subset of 27 protein internal coordinates corresponding to a network of 91 key residues involved in the conformational change induced by ATP binding. Among the 91 residues, 26 are identified for the first time, whereas the others were shown relevant for the allosteric communication of Hsp70 s in several experiments and bioinformatics analysis. The FEL analysis revealed also the origin of the ATP-induced structural modifications of the SBD recently measured by Electron Paramagnetic Resonance. The pathway between the nucleotide-free and the intermediate state of DnaK was extracted by applying principal component analysis to the subset of internal coordinates describing the transition. The methodology proposed is general and could be applied to analyze allosteric communication in other proteins.","corpus_id":6375359,"score":2},{"doc_id":"24710069","title":"Posttranslational Modification of Maize Chloroplast Pyruvate Orthophosphate Dikinase Reveals the Precise Regulatory Mechanism of Its Enzymatic Activity.","abstract":"In C4 plants, pyruvate orthophosphate dikinase (PPDK) activity is tightly dark/light regulated by reversible phosphorylation of an active-site threonine (Thr) residue; this process is catalyzed by PPDK regulatory protein (PDRP). Phosphorylation and dephosphorylation of PPDK lead to its inactivation and activation, respectively. Here, we show that light intensity rather than the light/dark transition regulates PPDK activity by modulating the reversible phosphorylation at Thr-527 (previously termed Thr-456) of PPDK in maize (Zea mays). The amount of PPDK (unphosphorylated) involved in C4 photosynthesis is indeed strictly controlled by light intensity, despite the high levels of PPDK protein that accumulate in mesophyll chloroplasts. In addition, we identified a transit peptide cleavage site, uncovered partial amino-terminal acetylation, and detected phosphorylation at four serine (Ser)/Thr residues, two of which were previously unknown in maize. In vitro experiments indicated that Thr-527 and Ser-528, but not Thr-309 and Ser-506, are targets of PDRP. Modeling suggests that the two hydrogen bonds between the highly conserved residues Ser-528 and glycine-525 are required for PDRP-mediated phosphorylation of the active-site Thr-527 of PPDK. Taken together, our results suggest that the regulation of maize plastid PPDK isoform (C4PPDK) activity is much more complex than previously reported. These diverse regulatory pathways may work alone or in combination to fine-tune C4PPDK activity in response to changes in lighting.","corpus_id":1247803,"score":2},{"doc_id":"25302667","title":"ATP-induced conformational changes of nucleotide-binding domains in an ABC transporter. Importance of the water-mediated entropic force.","abstract":"ATP binding cassette (ABC) proteins belong to a superfamily of active transporters. Recent experimental and computational studies have shown that binding of ATP to the nucleotide binding domains (NBDs) of ABC proteins drives the dimerization of NBDs, which, in turn, causes large conformational changes within the transmembrane domains (TMDs). To elucidate the active substrate transport mechanism of ABC proteins, it is first necessary to understand how the NBD dimerization is driven by ATP binding. In this study, we selected MalKs (NBDs of a maltose transporter) as a representative NBD and calculated the free-energy change upon dimerization using molecular mechanics calculations combined with a statistical thermodynamic theory of liquids, as well as a method to calculate the translational, rotational, and vibrational entropy change. This combined method is applied to a large number of snapshot structures obtained from molecular dynamics simulations containing explicit water molecules. The results suggest that the NBD dimerization proceeds with a large gain of water entropy when ATP molecules bind to the NBDs. The energetic gain arising from direct NBD-NBD interactions is canceled by the dehydration penalty and the configurational-entropy loss. ATP hydrolysis induces a loss of the shape complementarity between the NBDs, which leads to the dissociation of the dimer, due to a decrease in the water-entropy gain and an increase in the configurational-entropy loss. This interpretation of the NBD dimerization mechanism in concert with ATP, especially focused on the water-mediated entropy force, is potentially applicable to a wide variety of the ABC transporters.","corpus_id":45723390,"score":2},{"doc_id":"25430456","title":"Structural and evolutionary characteristics of pyruvate phosphate dikinase in Giardia lamblia and other amitochondriate protozoa.","abstract":"BACKGROUND: Pyruvate phosphate dikinase (PPDK) reversibly catalyzes the interconversion of phosphoenolpyruvate (PEP) and pyruvic acid, leading to catabolism and adenosine triphosphate (ATP) synthesis or gluconeogenesis and ATP consumption. Molecular modeling of PPDKs from divergent organisms demonstrates that the orientation of the phosphorylatable histidine residue within the central domain of PPDK determines whether this enzyme promotes catabolism or gluconeogenesis. The goal of this study was to determine whether PDDK from Giardia underwent adaptive evolution in order to produce more energy under anaerobic conditions. METHODS: A total of 123 PPDK sequences from protozoans, proteobacteria, plants, and algae were selected, based upon sequence similarities to Giardia lamblia PPDK and Zea mays PPDK. Three-dimensional (3-D) models were generated for PPDKs from divergent organisms and were used to compare the orientation of the phosphorylatable histidine residue within the central domain of PPDKs. These PPDKs were compared using a maximum-likelihood tree. RESULTS: For PPDK from Giardia, as well as from other anaerobic protozoans, the central domain tilted toward the N-terminal nucleotide-binding domain, indicating that this enzyme catalyzed ATP synthesis. Furthermore, the orientation of this central domain was determined by interactions between the N- and C-terminal domains. Phylogenetic analysis of the N- and C-terminal sequences of PPDKs from different species suggested that PPDK has likely undergone adaptive evolution in response to differences in environmental and metabolic conditions. CONCLUSION: These results suggested that PPDK in anaerobic organisms is functionally adapted to generate energy more efficiently in an anaerobic environment.","corpus_id":1896825,"score":2},{"doc_id":"26148295","title":"Motion Tree Delineates Hierarchical Structure of Protein Dynamics Observed in Molecular Dynamics Simulation.","abstract":"Molecular dynamics (MD) simulations of proteins provide important information to understand their functional mechanisms, which are, however, likely to be hidden behind their complicated motions with a wide range of spatial and temporal scales. A straightforward and intuitive analysis of protein dynamics observed in MD simulation trajectories is therefore of growing significance with the large increase in both the simulation time and system size. In this study, we propose a novel description of protein motions based on the hierarchical clustering of fluctuations in the inter-atomic distances calculated from an MD trajectory, which constructs a single tree diagram, named a \"Motion Tree\", to determine a set of rigid-domain pairs hierarchically along with associated inter-domain fluctuations. The method was first applied to the MD trajectory of substrate-free adenylate kinase to clarify the usefulness of the Motion Tree, which illustrated a clear-cut dynamics picture of the inter-domain motions involving the ATP/AMP lid and the core domain together with the associated amplitudes and correlations. The comparison of two Motion Trees calculated from MD simulations of ligand-free and -bound glutamine binding proteins clarified changes in inherent dynamics upon ligand binding appeared in both large domains and a small loop that stabilized ligand molecule. Another application to a huge protein, a multidrug ATP binding cassette (ABC) transporter, captured significant increases of fluctuations upon binding a drug molecule observed in both large scale inter-subunit motions and a motion localized at a transmembrane helix, which may be a trigger to the subsequent structural change from inward-open to outward-open states to transport the drug molecule. These applications demonstrated the capabilities of Motion Trees to provide an at-a-glance view of various sizes of functional motions inherent in the complicated MD trajectory.","corpus_id":8385214,"score":2},{"doc_id":"26158224","title":"Analysis of the Free Energy Landscapes for the Opening-Closing Dynamics of the Maltose Transporter ATPase MalK2 Using Enhanced-Sampling Molecular Dynamics Simulation.","abstract":"Protein dynamics are considered significant for many physiological processes, such as metabolism, biomolecular recognition, and the regulation of several vital cellular processes. Due to their flexibility, proteins may stay in different substates with or without the existence of the cognate substrates. To describe these phenomena, two models have been proposed: the \"induced fit\" and the \"conformational selection\" mechanisms. In this study, we used MalK2, the subunits that mainly include the nucleotide-binding domains (NBDs) of the maltose transporter from Escherichia coli, as a target to understand the NBD dimerization mechanism. Accelerated and conventional molecular dynamics have been performed. The results revealed that Mg-ATP binding to MalK2 led to a significant change in the free energy profile and thus stabilized the closed conformation. On the contrary, when Mg-ATP was removed, the open conformation would be favored. The fact that ligand binding induces a drastic free energy change leads to a significant inference: MalK2 dimerization would occur through the induced-fit mechanism rather than the conformational selection mechanism. This study sheds new light on the NBD dimerization mechanism and would be of wide applicability to other ABC transporters.","corpus_id":206649349,"score":2},{"doc_id":"27003459","title":"Kinetic and molecular characterization of the pyruvate phosphate dikinase from Trypanosoma cruzi.","abstract":"Trypanosoma cruzi, like other trypanosomatids analyzed so far, can use both glucose and amino acids as carbon and energy source. In these parasites, glycolysis is compartmentalized in glycosomes, authentic but specialized peroxisomes. The major part of this pathway, as well as a two-branched glycolytic auxiliary system, are present in these organelles. The first enzyme of one branch of this auxiliary system is the PPi-dependent pyruvate phosphate dikinase (PPDK) that converts phosphoenolpyruvate (PEP), inorganic pyrophosphate (PPi) and AMP into pyruvate, inorganic phosphate (Pi) and ATP, thus contributing to the ATP/ADP balance within the glycosomes. In this work we cloned, expressed and purified the T. cruzi PPDK. It kinetic parameters were determined, finding KM values for PEP, PPi and AMP of 320, 70 and 17 μM, respectively. Using molecular exclusion chromatography, two native forms of the enzyme were found with estimated molecular weights of 200 and 100 kDa, corresponding to a homodimer and monomer, respectively. It was established that T. cruzi PPDK's specific activity can be enhanced up to 2.6 times by the presence of ammonium in the assay mixture. During growth of epimastigotes in batch culture an apparent decrease in the specific activity of PPDK was observed. However, when its activity is normalized for the presence of ammonium in the medium, no significant modification of the enzyme activity per cell in time was found.","corpus_id":33222461,"score":2},{"doc_id":"27622975","title":"GPCR Dynamics: Structures in Motion.","abstract":"The function of G protein-coupled receptors (GPCRs)-which represent the largest class of both human membrane proteins and drug targets-depends critically on their ability to change shape, transitioning among distinct conformations. Determining the structural dynamics of GPCRs is thus essential both for understanding the physiology of these receptors and for the rational design of GPCR-targeted drugs. Here we review what is currently known about the flexibility and dynamics of GPCRs, as determined through crystallography, spectroscopy, and computer simulations. We first provide an overview of the types of motion exhibited by a GPCR and then discuss GPCR dynamics in the context of ligand binding, activation, allosteric modulation, and biased signaling. Finally, we discuss the implications of GPCR conformational plasticity for drug design.","corpus_id":26075206,"score":2},{"doc_id":"28470715","title":"Trapped intermediate state of plant pyruvate phosphate dikinase indicates substeps in catalytic swiveling domain mechanism.","abstract":"Pyruvate phosphate dikinase (PPDK) is an essential enzyme of both the C4 photosynthetic pathway and cellular energy metabolism of some bacteria and unicellular protists. In C4 plants, it catalyzes the ATP- and Pi -dependent formation of phosphoenolpyruvate (PEP) while in bacteria and protozoa the ATP-forming direction is used. PPDK is composed out of three distinct domains and exhibits one of the largest single domain movements known today during its catalytic cycle. However, little information about potential intermediate steps of this movement was available. A recent study resolved a discrete intermediate step of PPDK's swiveling movement, shedding light on the details of this intriguing mechanism. Here we present an additional structural intermediate that possibly represents another crucial step in the catalytic cycle of PPDK, providing means to get a more detailed understanding of PPDK's mode of function.","corpus_id":46462162,"score":2},{"doc_id":"28808308","title":"On the potential alternate binding change mechanism in a dimeric structure of Pyruvate Phosphate Dikinase.","abstract":"The pyruvate phosphate dikinase (PPDK) reaction mechanism is characterized by a distinct spatial separation of reaction centers and large conformational changes involving an opening-closing motion of the nucleotide-binding domain (NBD) and a swiveling motion of the central domain (CD). However, why PPDK is active only in a dimeric form and to what extent an alternate binding change mechanism could underlie this fact has remained elusive. We performed unbiased molecular dynamics simulations, configurational free energy computations, and rigidity analysis to address this question. Our results support the hypothesis that PPDK dimerization influences the opening-closing motion of the NBDs, and that this influence is mediated via the CDs of both chains. Such an influence would be a prerequisite for an alternate binding change mechanism to occur. To the best of our knowledge, this is the first time that a possible explanation has been suggested as to why only dimeric PPDK is active.","corpus_id":3288206,"score":2},{"doc_id":"29547697","title":"Atomistic Mechanism of Large-Scale Conformational Transition in a Heterodimeric ABC Exporter.","abstract":"ATP-binding cassette (ABC) transporters are ATP-driven molecular machines, in which ATP binding and hydrolysis in the nucleotide-binding domains (NBDs) is chemomechanically coupled to large-scale, alternating access conformational changes in the transmembrane domains (TMDs), ultimately leading to the translocation of substrates across biological membranes. The precise nature of the structural dynamics behind the large-scale conformational transition as well as the coupling of NBD and TMD motions is still unresolved. In this work, we combine all-atom molecular dynamics (MD) simulations with electron paramagnetic resonance (EPR) spectroscopy to unravel the atomic-level mechanism of the dynamic conformational transitions underlying the functional working cycle of the heterodimeric ABC exporter TM287/288. Extensive multimicrosecond simulations in an explicit membrane/water environment show how in response to ATP binding, TM287/288 undergoes spontaneous conformational transitions from the inward-facing (IF) state via an occluded (Occ) intermediate to an outward-facing (OF) state. The latter two states have thus far not been characterized at atomic level. ATP-induced tightening of the NBD dimer involves closing and reorientation of the two NBD monomers concomitant with a closure of the intracellular TMD gate, which leads to the occluded state. Subsequently, opening at the extracellular TMD gate yields the OF conformer. The obtained mechanism imposes NBD-TMD coupling via a tight orchestration of conformational transitions, between both the two domains and also within the TMDs, ensuring that the cytoplasmic and periplasmic gate regions are never open simultaneously.","corpus_id":4583810,"score":2},{"doc_id":"29664234","title":"Characterization of maize leaf pyruvate orthophosphate dikinase using high throughput sequencing.","abstract":"In C4 photosynthesis, pyruvate orthophosphate dikinase (PPDK) catalyzes the regeneration of phosphoenolpyruvate in the carbon shuttle pathway. Although the biochemical function of PPDK in maize is well characterized, a genetic analysis of PPDK has not been reported. In this study, we use the maize transposable elements Mutator and Ds to generate multiple mutant alleles of PPDK. Loss-of-function mutants are seedling lethal, even when plants were grown under 2% CO2 , and they show very low capacity for CO2 assimilation, indicating C4 photosynthesis is essential in maize. Using RNA-seq and GC-MS technologies, we examined the transcriptional and metabolic responses to a deficiency in PPDK activity. These results indicate loss of PPDK results in downregulation of gene expression of enzymes of the C4 cycle, the Calvin cycle, and components of photochemistry. Furthermore, the loss of PPDK did not change Kranz anatomy, indicating that this metabolic defect in the C4 cycle did not impinge on the morphological differentiation of C4 characters. However, sugar metabolism and nitrogen utilization were altered in the mutants. An interaction between light intensity and genotype was also detected from transcriptome profiling, suggesting altered transcriptional and metabolic responses to environmental and endogenous signals in the PPDK mutants.","corpus_id":4884084,"score":2},{"doc_id":"17710553","title":"Molecular modeling on pyruvate phosphate dikinase of Entamoeba histolytica and in silico virtual screening for novel inhibitors.","abstract":"Pyruvate phosphate dikinase (PPDK) is the key enzyme essential for the glycolytic pathway in most common and perilous parasite Entamoeba histolytica. Inhibiting the function of this enzyme could control the wide spread of intestinal infections caused by Entamoeba histolytica in humans. With this objective, we modeled the three dimensional structure of the PPDK protein. We used templates with 51% identity and 67% similarity to employ homology-modeling approach. Stereo chemical quality of protein structure was validated by protein structure validation program PROCHECK and VERIFY3D. Experimental proof available in literature along with the in silico studies indicated Lys21, Arg91, Asp323, Glu325 and Gln337 to be the probable active sites in the target protein. Virtual screening was carried out using the genetic docking algorithm GOLD and a consensus scoring function X-Score to substantiate the prediction. The small molecule libraries (ChemDivision database, Diversity dataset, Kinase inhibitor database) were used for screening process. Along with the high scoring results, the interaction studies provided promising ligands for future experimental screening to inhibit the function of PPDK in Entamoeba histolytica. Further, the phylogeny study was carried out to assess the possibility of using the proposed ligands as inhibitors in related pathogens.","corpus_id":25026913,"score":1},{"doc_id":"18167307","title":"The catalyzing role of PPDK in Giardia lamblia.","abstract":"Giardia lamblia is an early branching eukaryotic microorganism that derives its metabolic energy primarily from anaerobic glycolysis. In most organisms, glycolysis is catalyzed by pyruvate kinase (PK), allowing the generation of two ATP molecules from one molecule of pyruvate. Giardia has both PK and pyrophosphate-dependent pyruvate phosphate dikinase (PPDK), which catalyzes the generation of five ATP molecules from pyruvate by pyrophosphate-dependent glycolysis and offers a potential selective advantage. In order to evaluate the importance of pyrophosphate-dependent glycolysis, we used ribozyme-mediated cleavage of the PPDK transcript to decrease PPDK transcript levels to 20% of normal. The accompanying decrease in PPDK enzyme activity decreased ATP levels to 3% of normal and increased glycogen deposition, confirming the importance pyrophosphate-mediated glycolysis that was previously suggested by cell lysate studies. PPDK is not found in vertebrates, so specific inhibitors may be useful for treatment of infections caused by anaerobic protists that depend on pyrophosphate-dependent glycolysis.","corpus_id":16126604,"score":1},{"doc_id":"18539347","title":"The Wolbachia endosymbiont of Brugia malayi has an active pyruvate phosphate dikinase.","abstract":"Genome analysis of the glycolytic/gluconeogenic pathway in the Wolbachia endosymbiont from the filarial parasite Brugia malayi (wBm) has revealed that wBm lacks pyruvate kinase (PK) and may instead utilize the enzyme pyruvate phosphate dikinase (PPDK; ATP:pyruvate, orthophosphate phosphotransferase, EC 2.7.9.1). PPDK catalyses the reversible conversion of AMP, PPi and phosphoenolpyruvate (PEP) into ATP, Pi and pyruvate. The glycolytic pathway of most organisms, including mammals, contains exclusively PK for the production of pyruvate from PEP. Therefore, the absence of PPDK in mammals makes the enzyme an attractive Wolbachia drug target. In the present study, we have cloned and expressed an active wBm-PPDK, thereby providing insight into the energy metabolism of the endosymbiont. Our results support the development of wBm-PPDK as a promising new drug target in an anti-symbiotic approach to controlling filarial infection.","corpus_id":11317709,"score":1},{"doc_id":"18539777","title":"Cool C4 photosynthesis: pyruvate Pi dikinase expression and activity corresponds to the exceptional cold tolerance of carbon assimilation in Miscanthus x giganteus.","abstract":"The bioenergy feedstock grass Miscanthus x giganteus is exceptional among C(4) species for its high productivity in cold climates. It can maintain photosynthetically active leaves at temperatures 6 degrees C below the minimum for maize (Zea mays), which allows it a longer growing season in cool climates. Understanding the basis for this difference between these two closely related plants may be critical in adapting maize to colder weather. When M. x giganteus and maize grown at 25 degrees C were transferred to 14 degrees C, light-saturated CO(2) assimilation and quantum yield of photosystem II declined by 30% and 40%, respectively, in the first 48 h in these two species. The decline continued in maize but arrested and then recovered partially in M. x giganteus. Within 24 h of the temperature transition, the pyruvate phosphate dikinase (PPDK) protein content per leaf area transiently declined in M. x giganteus but then steadily increased, such that after 7 d the enzyme content was significantly higher than in leaves growing in 25 degrees C. By contrast it declined throughout the chilling period in maize leaves. Rubisco levels remained constant in M. x giganteus but declined in maize. Consistent with increased PPDK protein content, the extractable PPDK activity per unit leaf area (V(max)(,ppdk)) in cold-grown M. x giganteus leaves was higher than in warm-grown leaves, while V(max,ppdk) was lower in cold-grown than in warm-grown maize. The rate of light activation of PPDK was also slower in cold-grown maize than M. x giganteus. The energy of activation (E(a)) of extracted PPDK was lower in cold-grown than warm-grown M. x giganteus but not in maize. The specific activities and E(a) of purified recombinant PPDK from M. x giganteus and maize cloned into Escherichia coli were similar. The increase in PPDK protein in the M. x giganteus leaves corresponded to an increase in PPDK mRNA level. These results indicate that of the two enzymes known to limit C(4) photosynthesis, increase of PPDK, not Rubisco content, corresponds to the recovery and maintenance of photosynthetic capacity. Functionally, increased enzyme concentration is shown to increase stability of M. x giganteus PPDK at low temperature. The results suggest that increases in either PPDK RNA transcription and/or the stability of this RNA are important for the increase in PPDK protein content and activity in M. x giganteus under chilling conditions relative to maize.","corpus_id":5116393,"score":1},{"doc_id":"18926491","title":"Molecular and biochemical mechanisms in maize endosperm development: the role of pyruvate-Pi-dikinase and Opaque-2 in the control of C/N ratio.","abstract":"A combined transcriptomic, proteomic and metabolic analysis provided an overview of the main changes occurring in gene expression during maize kernel development. It allowed identifying genes expressed at each developmental stage and the shift occurring from one stage to the other. A major change occurred at the transition from lag phase where final grain size is established to grain filling where starch and protein are accumulated in the endosperm storage tissue. Although the expression of enzymes involved in storage product synthesis is dominant in the accumulation phase, the proportion of protein destination and protein synthesis gene products is still important. Detailed proteomic analysis of metabolism shows an upsurge of the pyruvate-Pi-dikinase (PPDK) in the late filing period (21 DAP onwards) that is interpreted as a switch in the starch/protein balance. This hypothesis is based on biochemical arguments involving the negative effect of PPi on the ADP-glucose pyrophosphorylase (Agpase), a key-enzyme of starch synthesis, and the role of phosphoenolpyruvate (PEP) in aromatic amino acid synthesis. It is substantiated by the data on the Opaque-2 gene encoding a transcription factor with pleiotropic effect affecting lysine content and carbohydrate metabolism, thus acting indirectly on starch/amino acid ratio. The direct effect of O2 on PPDK gene expression provides a clue for explaining the competition between C and N metabolisms. This epistatic relationship between PPDK and O2 is further supported by quantitative and association genetics.","corpus_id":34076948,"score":1},{"doc_id":"19754142","title":"Molecular dynamics and quantum mechanics of RNA: conformational and chemical change we can believe in.","abstract":"Structure and dynamics are both critical to RNA's vital functions in biology. Numerous techniques can elucidate the structural dynamics of RNA, but computational approaches based on experimental data arguably hold the promise of providing the most detail. In this Account, we highlight areas wherein molecular dynamics (MD) and quantum mechanical (QM) techniques are applied to RNA, particularly in relation to complementary experimental studies. We have expanded on atomic-resolution crystal structures of RNAs in functionally relevant states by applying explicit solvent MD simulations to explore their dynamics and conformational changes on the submicrosecond time scale. MD relies on simplified atomistic, pairwise additive interaction potentials (force fields). Because of limited sampling, due to the finite accessible simulation time scale and the approximated force field, high-quality starting structures are required. Despite their imperfection, we find that currently available force fields empower MD to provide meaningful and predictive information on RNA dynamics around a crystallographically defined energy minimum. The performance of force fields can be estimated by precise QM calculations on small model systems. Such calculations agree reasonably well with the Cornell et al. AMBER force field, particularly for stacking and hydrogen-bonding interactions. A final verification of any force field is accomplished by simulations of complex nucleic acid structures. The performance of the Cornell et al. AMBER force field generally corresponds well with and augments experimental data, but one notable exception could be the capping loops of double-helical stems. In addition, the performance of pairwise additive force fields is obviously unsatisfactory for inclusion of divalent cations, because their interactions lead to major polarization and charge-transfer effects neglected by the force field. Neglect of polarization also limits, albeit to a lesser extent, the description accuracy of other contributions, such as interactions with monovalent ions, conformational flexibility of the anionic sugar-phosphate backbone, hydrogen bonding, and solute polarization by solvent. Still, despite limitations, MD simulations are a valid tool for analyzing the structural dynamics of existing experimental structures. Careful analysis of MD simulations can identify problematic aspects of an experimental RNA structure, unveil structural characteristics masked by experimental constraints, reveal functionally significant stochastic fluctuations, evaluate the structural role of base ionization, and predict structurally and potentially functionally important details of the solvent behavior, including the presence of tightly bound water molecules. Moreover, combining classical MD simulations with QM calculations in hybrid QM/MM approaches helps in the assessment of the plausibility of chemical mechanisms of catalytic RNAs (ribozymes). In contrast, the reliable prediction of structure from sequence information is beyond the applicability of MD tools. The ultimate utility of computational studies in understanding RNA function thus requires that the results are neither blindly accepted nor flatly rejected, but rather considered in the context of all available experimental data, with great care given to assessing limitations through the available starting structures, force field approximations, and sampling limitations. The examples given in this Account showcase how the judicious use of basic MD simulations has already served as a powerful tool to help evaluate the role of structural dynamics in biological function of RNA.","corpus_id":9121507,"score":1},{"doc_id":"20202167","title":"Cytosolic pyruvate,orthophosphate dikinase functions in nitrogen remobilization during leaf senescence and limits individual seed growth and nitrogen content.","abstract":"The protein content of seeds determines their nutritive value, downstream processing properties and market value. Up to 95% of seed protein is derived from amino acids that are exported to the seed after degradation of existing protein in leaves, but the pathways responsible for this nitrogen metabolism are poorly defined. The enzyme pyruvate,orthophosphate dikinase (PPDK) interconverts pyruvate and phosphoenolpyruvate, and is found in both plastids and the cytosol in plants. PPDK plays a cardinal role in C(4) photosynthesis, but its role in the leaves of C(3) species has remained unclear. We demonstrate that both the cytosolic and chloroplastic isoforms of PPDK are up-regulated in naturally senescing leaves. Cytosolic PPDK accumulates preferentially in the veins, while chloroplastic PPDK also accumulates in mesophyll cells. Analysis of microarrays and labelling patterns after feeding (13)C-labelled pyruvate indicated that PPDK functions in a pathway that generates the transport amino acid glutamine, which is then loaded into the phloem. In Arabidopsis thaliana, over-expression of PPDK during senescence can significantly accelerate nitrogen remobilization from leaves, and thereby increase rosette growth rate and the weight and nitrogen content of seeds. This indicates an important role for cytosolic PPDK in the leaves of C(3) plants, and allows us to propose a metabolic pathway that is responsible for production of transport amino acids during natural leaf senescence. Given that increased seed size and nitrogen content are desirable agronomic traits, and that efficient remobilization of nitrogen within the plant reduces the demand for fertiliser applications, PPDK and the pathway in which it operates are targets for crop improvement.","corpus_id":23973453,"score":1},{"doc_id":"22024416","title":"Robust control of PEP formation rate in the carbon fixation pathway of C(4) plants by a bi-functional enzyme.","abstract":"BACKGROUND: C(4) plants such as corn and sugarcane assimilate atmospheric CO(2) into biomass by means of the C(4) carbon fixation pathway. We asked how PEP formation rate, a key step in the carbon fixation pathway, might work at a precise rate, regulated by light, despite fluctuations in substrate and enzyme levels constituting and regulating this process. RESULTS: We present a putative mechanism for robustness in C(4) carbon fixation, involving a key enzyme in the pathway, pyruvate orthophosphate dikinase (PPDK), which is regulated by a bifunctional enzyme, Regulatory Protein (RP). The robust mechanism is based on avidity of the bifunctional enzyme RP to its multimeric substrate PPDK, and on a product-inhibition feedback loop that couples the system output to the activity of the bifunctional regulator. The model provides an explanation for several unusual biochemical characteristics of the system and predicts that the system's output, phosphoenolpyruvate (PEP) formation rate, is insensitive to fluctuations in enzyme levels (PPDK and RP), substrate levels (ATP and pyruvate) and the catalytic rate of PPDK, while remaining sensitive to the system's input (light levels). CONCLUSIONS: The presented PPDK mechanism is a new way to achieve robustness using product inhibition as a feedback loop on a bifunctional regulatory enzyme. This mechanism exhibits robustness to protein and metabolite levels as well as to catalytic rate changes. At the same time, the output of the system remains tuned to input levels.","corpus_id":5003497,"score":1},{"doc_id":"22392278","title":"Preliminary analysis to target pyruvate phosphate dikinase from wolbachia endosymbiont of Brugia malayi for designing anti-filarial agents.","abstract":"Filariasis causing nematode Brugia malayi is shown to harbor wolbachia bacteria as symbionts. The sequenced genome of the wolbachia endosymbiont from B.malayi (wBm) offers an unprecedented opportunity to identify new wolbachia drug targets. Genome analysis of the glycolytic/gluconeogenic pathway has revealed that wBm lacks pyruvate kinase (PK) and may instead utilize the enzyme pyruvate phosphate dikinase (PPDK; ATP: pyruvate, orthophosphate phosphotransferase, EC 2.7.9.1). PPDK catalyses the reversible conversion of AMP, PPi and phosphoenolpyruvate into ATP, Pi and pyruvate. Most organisms including mammals exclusively possess PK. Therefore the absence of PPDK in mammals makes this enzyme as attractive wolbachia drug target. In the present study we have modeled the three dimensional structure of wBm PPDK. The template with 50% identity and 67% similarity in amino acid sequence was employed for homology-modeling approach. The putative active site consists of His476, Arg360, Glu358, Asp344, Arg112, Lys43 and Glu346 was selected as site of interest for designing suitable inhibitor molecules. Docking studies were carried out using induced fit algorithms with OPLS force field of Schrödinger's Glide. The lead molecules which inhibit the PPDK activity are taken from the small molecule library (Pubchem database) and the interaction analysis showed that these compounds may inhibit the function of PPDK in wBm.","corpus_id":15776013,"score":1},{"doc_id":"23030682","title":"Phosphoproteomic analysis of Rhodopseudomonas palustris reveals the role of pyruvate phosphate dikinase phosphorylation in lipid production.","abstract":"Rhodopseudomonas palustris (R. palustris) is a purple nonsulfur anoxygenic phototrophic bacterium with metabolic versatility and is able to grow under photoheterotrophic and chemoheterotrophic states. It has uses in carbon management, carbon recycling, hydrogen generation, and lipid production; therefore, it has the potential for bioenergy production and biodegradation. This study is the first to identify the phosphoproteome of R. palustris including 100 phosphopeptides from 54 phosphoproteins and 74 phosphopeptides from 42 phosphoproteins in chemoheterotrophic and photoheterotrophic growth conditions, respectively. In the identified phosphoproteome, phosphorylation at the threonine residue, Thr487, of pyruvate phosphate dikinase (PPDK, RPA1051) was found to participate in the regulation of carbon metabolism. Here, we show that PPDK enzyme activity is higher in photoheterotrophic growth, with Thr487 phosphorylation as a possible mediator. Under the same photoheterotrophic conditions, R. palustris with overexpressed wild-type PPDK showed an enhanced accumulation of total lipids than those with mutant PPDK (T487V) form. This study reveals the role of the PPDK in the production of biodiesel material, lipid content, with threonyl-phosphorylation as one of the possible regulatory events during photoheterotrophic growth in R. palustris.","corpus_id":26046855,"score":1},{"doc_id":"23094589","title":"Design, synthesis, and evaluation of inhibitors of pyruvate phosphate dikinase.","abstract":"Pyruvate phosphate dikinase (PPDK) catalyzes the phosphorylation reaction of pyruvate that forms phosphoenolpyruvate (PEP) via two partial reactions: PPDK + ATP + P(i) → PPDK-P + AMP + PP(i) and PPDK-P + pyruvate → PEP + PPDK. Based on its role in the metabolism of microbial human pathogens, PPDK is a potential drug target. A screen of substances that bind to the PPDK ATP-grasp domain active site revealed that flavone analogues are potent inhibitors of the Clostridium symbiosum PPDK. In silico modeling studies suggested that placement of a 3–6 carbon-tethered ammonium substituent at the 3′- or 4′-positions of 5,7-dihydroxyflavones would result in favorable electrostatic interactions with the PPDK Mg-ATP binding site. As a result, polymethylene-tethered amine derivatives of 5,7-dihydroxyflavones were prepared. Steady-state kinetic analysis of these substances demonstrates that the 4′-aminohexyl-5,7-dyhydroxyflavone 10 is a potent competitive PPDK inhibitor (K(i) = 1.6 ± 0.1 μM). Single turnover experiments were conducted using 4′-aminopropyl-5,7-dihydroxyflavone 7 to show that this flavone specifically targets the ATP binding site and inhibits catalysis of only the PPDK + ATP + P(i) → PPDK-P + AMP PP(i) partial reaction. Finally, the 4′-aminopbutyl-5,7-dihydroxyflavone 8 displays selectivity for inhibition of PPDK versus other enzymes that utilize ATP and NAD.","corpus_id":13391283,"score":1},{"doc_id":"23573213","title":"An asymmetric post-hydrolysis state of the ABC transporter ATPase dimer.","abstract":"ABC transporters are a superfamily of enzyme pumps that hydrolyse ATP in exchange for translocation of substrates across cellular membranes. Architecturally, ABC transporters are a dimer of transmembrane domains coupled to a dimer of nucleotide binding domains (NBDs): the NBD dimer contains two ATP-binding sites at the intersubunit interface. A current controversy is whether the protomers of the NBD dimer separate during ATP hydrolysis cycling, or remain in constant contact. In order to investigate the ABC ATPase catalytic mechanism, MD simulations using the recent structure of the ADP+Pi-bound MJ0796 isolated NBD dimer were performed. In three independent simulations of the ADP+Pi/apo state, comprising a total of >0.5 µs, significant opening of the apo (empty) active site was observed; occurring by way of intrasubunit rotations between the core and helical subdomains within both NBD monomers. In contrast, in three equivalent simulations of the ATP/apo state, the NBD dimer remained close to the crystal structure, and no opening of either active site occurred. The results thus showed allosteric coupling between the active sites, mediated by intrasubunit conformational changes. Opening of the apo site is exquisitely tuned to the nature of the ligand, and thus to the stage of the reaction cycle, in the opposite site. In addition to this, in also showing how one active site can open, sufficient to bind nucleotide, while the opposite site remains occluded and bound to the hydrolysis products ADP+Pi, the results are consistent with a Constant Contact Model. Conversely, they show how there may be no requirement for the NBD protomers to separate to complete the catalytic cycle.","corpus_id":4031916,"score":1},{"doc_id":"23737004","title":"Activities of principal photosynthetic enzymes in green macroalga Ulva linza: functional implication of C₄ pathway in CO₂ assimilation.","abstract":"The green-tide-forming macroalga Ulva linza was profiled by transcriptome sequencing to ascertain whether the alga carries both C3 and C4 photosynthesis genes. The key enzymes involved in C4 metabolism including pyruvate orthophosphate dikinase (PPDK), phosphoenolpyruvate carboxylase (PEPC), and phosphoenolpyruvate carboxykinase (PCK) were found. When measured under normal and different stress conditions, expression of rbcL was higher under normal conditions and lower under the adverse conditions, whereas that of PPDK was higher under some adverse conditions, namely desiccation, high salinity, and low salinity. Both ribulose-1, 5-biphosphate carboxylase (RuBPCase) and PPDK were found to play a role in carbon fixation, with significantly higher PPDK activity across the stress conditions. These results suggest that elevated PPDK activity alters carbon metabolism in U. linza leading to partial operation of the C4 carbon metabolism, a pathway that, under stress conditions, probably contributes to the hardy character of U. linza and thus to its wide distribution.","corpus_id":1450913,"score":1},{"doc_id":"23936827","title":"Molecular dynamics studies on the conformational transitions of adenylate kinase: a computational evidence for the conformational selection mechanism.","abstract":"Escherichia coli adenylate kinase (ADK) is a monomeric phosphotransferase enzyme that catalyzes reversible transfer of phosphoryl group from ATP to AMP with a large-scale domain motion. The detailed mechanism for this conformational transition remains unknown. In the current study, we performed long time-scale molecular dynamics simulations on both open and closed states of ADK. Based on the structural analyses of the simulation trajectories, we detected over 20 times conformational transitions between the open and closed states of ADK and identified two novel conformations as intermediate states in the catalytic processes. With these findings, we proposed a possible mechanism for the large-scale domain motion of Escherichia coli ADK and its catalytic process: (1) the substrate free ADK adopted an open conformation; (2) ATP bound with LID domain closure; (3) AMP bound with NMP domain closure; (4) phosphoryl transfer occurred with ATP, and AMP converted into two ADPs, and no conformational transition was detected in the enzyme; (5) LID domain opened with one ADP released; (6) another ADP released with NMP domain open. As both open and closed states sampled a wide range of conformation transitions, our simulation strongly supported the conformational selection mechanism for Escherichia coli ADK.","corpus_id":61270,"score":1},{"doc_id":"24060543","title":"Post-translational modification of the pyruvate phosphate dikinase from Trypanosoma cruzi.","abstract":"In kinetoplastids such as Trypanosoma cruzi, glycolysis is compartmentalized in peroxisome-like organelles called glycosomes. Pyruvate phosphate dikinase (PPDK), an auxiliary enzyme of glycolysis, is also located in the glycosomes. We have detected that this protein is post-translationally modified by phosphorylation and proteolytic cleavage. On western blots of T. cruzi epimastigotes, two PPDK forms were found with apparent MW of 100 kDa and 75 kDa, the latter one being phosphorylated at Thr481, a residue present in a highly conserved region. In subcellular localization assays the 75 kDa PPDK was located peripherally at the glycosomal membrane. Both PPDK forms were found in all life-cycle stages of the parasite. When probing for both PPDK forms during a growth of epimastigotes in batch culture, an increase in the level of the 75 kDa form and a decrease of the 100 kDa one were observed by western blot analysis, signifying that glucose starvation and the concomitant switch of the metabolism to amino acid catabolism may play a role in the post-translational processing of the PPDK. Either one or both of the processes, phosphorylation and proteolytic cleavage of PPDK, result in inactivation of the enzyme. It remains to be established whether the phenomenon exerts a regulatory function.","corpus_id":116325,"score":1},{"doc_id":"24062450","title":"Phosphate release coupled to rotary motion of F1-ATPase.","abstract":"F1-ATPase, the catalytic domain of ATP synthase, synthesizes most of the ATP in living organisms. Running in reverse powered by ATP hydrolysis, this hexameric ring-shaped molecular motor formed by three αβ-dimers creates torque on its central γ-subunit. This reverse operation enables detailed explorations of the mechanochemical coupling mechanisms in experiment and simulation. Here, we use molecular dynamics simulations to construct a first atomistic conformation of the intermediate state following the 40° substep of rotary motion, and to study the timing and molecular mechanism of inorganic phosphate (Pi) release coupled to the rotation. In response to torque-driven rotation of the γ-subunit in the hydrolysis direction, the nucleotide-free αβE interface forming the \"empty\" E site loosens and singly charged Pi readily escapes to the P loop. By contrast, the interface stays closed with doubly charged Pi. The γ-rotation tightens the ATP-bound αβTP interface, as required for hydrolysis. The calculated rate for the outward release of doubly charged Pi from the αβE interface 120° after ATP hydrolysis closely matches the ~1-ms functional timescale. Conversely, Pi release from the ADP-bound αβDP interface postulated in earlier models would occur through a kinetically infeasible inward-directed pathway. Our simulations help reconcile conflicting interpretations of single-molecule experiments and crystallographic studies by clarifying the timing of Pi exit, its pathway and kinetics, associated changes in Pi protonation, and changes of the F1-ATPase structure in the 40° substep. Important elements of the molecular mechanism of Pi release emerging from our simulations appear to be conserved in myosin despite the different functional motions.","corpus_id":205263440,"score":1},{"doc_id":"24484954","title":"Phosphoenolpyruvate carboxylase, NADP-malic enzyme, and pyruvate, phosphate dikinase are involved in the acclimation of Nicotiana tabacum L. to drought stress.","abstract":"Drought stress is one of the most frequent forms of abiotic stresses, which occurs under condition of limited water availability. In this work, the possible participation of phosphoenolpyruvate carboxylase (EC 4.1.1.31; PEPC), NADP-malic enzyme (EC 1.1.1.40; NADP-ME), and pyruvate, phosphate dikinase (EC 2.7.9.1; PPDK) in response to drought of tobacco plants (Nicotiana tabacum L., cv. W38) was investigated. Enzyme specific activities in tobacco leaves of drought stressed plants were significantly increased after 11 days of stress, PEPC 2.3-fold, NADP-ME 3.9-fold, and PPDK 2.7-fold compared to control plants. The regulation of PEPC and NADP-ME activities were studied on transcriptional level by the quantitative RT PCR and on translational level - immunochemically. The amount of NADP-ME protein and transcription of mRNA for chloroplastic NADP-ME isoform were increased indicating their enhanced synthesis de novo. On the other hand, mRNA for cytosolic isoform of NADP-ME was decreased. The changes in PEPC protein and PEPC mRNA were not substantial. Therefore regulation of PEPC activity by phosphorylation was evaluated and found to be involved in the stress response. During recovery, activities of the tested enzymes returned close to their basal levels.","corpus_id":20050452,"score":1},{"doc_id":"24632881","title":"Structural characterization of two metastable ATP-bound states of P-glycoprotein.","abstract":"ATP Binding Cassette (ABC) transporters couple the binding and hydrolysis of ATP to the transport of substrate molecules across the membrane. The mechanism by which ATP binding and/or hydrolysis drives the conformational changes associated with substrate transport has not yet been characterized fully. Here, changes in the conformation of the ABC export protein P-glycoprotein on ATP binding are examined in a series of molecular dynamics simulations. When one molecule of ATP is placed at the ATP binding site associated with each of the two nucleotide binding domains (NBDs), the membrane-embedded P-glycoprotein crystal structure adopts two distinct metastable conformations. In one, each ATP molecule interacts primarily with the Walker A motif of the corresponding NBD. In the other, the ATP molecules interacts with both Walker A motif of one NBD and the Signature motif of the opposite NBD inducing the partial dimerization of the NBDs. This interaction is more extensive in one of the two ATP binding site, leading to an asymmetric structure. The overall conformation of the transmembrane domains is not altered in either of these metastable states, indicating that the conformational changes associated with ATP binding observed in the simulations in the absence of substrate do not lead to the outward-facing conformation and thus would be insufficient in themselves to drive transport. Nevertheless, the metastable intermediate ATP-bound conformations observed are compatible with a wide range of experimental cross-linking data demonstrating the simulations do capture physiologically important conformations. Analysis of the interaction between ATP and its cofactor Mg(2+) with each NBD indicates that the coordination of ATP and Mg(2+) differs between the two NBDs. The role structural asymmetry may play in ATP binding and hydrolysis is discussed. Furthermore, we demonstrate that our results are not heavily influenced by the crystal structure chosen for initiation of the simulations.","corpus_id":18460867,"score":1},{"doc_id":"24794874","title":"Contribution of pyruvate phosphate dikinase in the maintenance of the glycosomal ATP/ADP balance in the Trypanosoma brucei procyclic form.","abstract":"Trypanosoma brucei belongs to a group of protists that sequester the first six or seven glycolytic steps inside specialized peroxisomes, named glycosomes. Because of the glycosomal membrane impermeability to nucleotides, ATP molecules consumed by the first glycolytic steps need to be regenerated in the glycosomes by kinases, such as phosphoenolpyruvate carboxykinase (PEPCK). The glycosomal pyruvate phosphate dikinase (PPDK), which reversibly converts phosphoenolpyruvate into pyruvate, could also be involved in this process. To address this question, we analyzed the metabolism of the main carbon sources used by the procyclic trypanosomes (glucose, proline, and threonine) after deletion of the PPDK gene in the wild-type (Δppdk) and PEPCK null (Δppdk/Δpepck) backgrounds. The rate of acetate production from glucose is 30% reduced in the Δppdk mutant, whereas threonine-derived acetate production is not affected, showing that PPDK function in the glycolytic direction with production of ATP in the glycosomes. The Δppdk/Δpepck mutant incubated in glucose as the only carbon source showed a 3.8-fold reduction of the glycolytic rate compared with the Δpepck mutant, as a consequence of the imbalanced glycosomal ATP/ADP ratio. The role of PPDK in maintenance of the ATP/ADP balance was confirmed by expressing the glycosomal phosphoglycerate kinase (PGKC) in the Δppdk/Δpepck cell line, which restored the glycolytic flux. We also observed that expression of PGKC is lethal for procyclic trypanosomes, as a consequence of ATP depletion, due to glycosomal relocation of cytosolic ATP production. This illustrates the key roles played by glycosomal and cytosolic kinases, including PPDK, to maintain the cellular ATP/ADP homeostasis.","corpus_id":43731412,"score":1},{"doc_id":"25046577","title":"Low CO2 results in a rearrangement of carbon metabolism to support C4 photosynthetic carbon assimilation in Thalassiosira pseudonana.","abstract":"The mechanisms of carbon concentration in marine diatoms are controversial. At low CO2 , decreases in O2 evolution after inhibition of phosphoenolpyruvate carboxylases (PEPCs), and increases in PEPC transcript abundances, have been interpreted as evidence for a C4 mechanism in Thalassiosira pseudonana, but the ascertainment of which proteins are responsible for the subsequent decarboxylation and PEP regeneration steps has been elusive. We evaluated the responses of T. pseudonana to steady-state differences in CO2 availability, as well as to transient shifts to low CO2 , by integrated measurements of photosynthetic parameters, transcript abundances and quantitative proteomics. On shifts to low CO2 , two PEPC transcript abundances increased and then declined on timescales consistent with recoveries of Fv /Fm , non-photochemical quenching (NPQ) and maximum chlorophyll a-specific carbon fixation (Pmax ), but transcripts for archetypical decarboxylation enzymes phosphoenolpyruvate carboxykinase (PEPCK) and malic enzyme (ME) did not change. Of 3688 protein abundances measured, 39 were up-regulated under low CO2 , including both PEPCs and pyruvate carboxylase (PYC), whereas ME abundance did not change and PEPCK abundance declined. We propose a closed-loop biochemical model, whereby T. pseudonana produces and subsequently decarboxylates a C4 acid via PEPC2 and PYC, respectively, regenerates phosphoenolpyruvate (PEP) from pyruvate in a pyruvate phosphate dikinase-independent (but glycine decarboxylase (GDC)-dependent) manner, and recuperates photorespiratory CO2 as oxaloacetate (OAA).","corpus_id":1080606,"score":1},{"doc_id":"25288791","title":"Gluconeogenesis in Leishmania mexicana: contribution of glycerol kinase, phosphoenolpyruvate carboxykinase, and pyruvate phosphate dikinase.","abstract":"Gluconeogenesis is an active pathway in Leishmania amastigotes and is essential for their survival within the mammalian cells. However, our knowledge about this pathway in trypanosomatids is very limited. We investigated the role of glycerol kinase (GK), phosphoenolpyruvate carboxykinase (PEPCK), and pyruvate phosphate dikinase (PPDK) in gluconeogenesis by generating the respective Leishmania mexicana Δgk, Δpepck, and Δppdk null mutants. Our results demonstrated that indeed GK, PEPCK, and PPDK are key players in the gluconeogenesis pathway in Leishmania, although stage-specific differences in their contribution to this pathway were found. GK participates in the entry of glycerol in promastigotes and amastigotes; PEPCK participates in the entry of aspartate in promastigotes, and PPDK is involved in the entry of alanine in amastigotes. Furthermore, the majority of alanine enters into the pathway via decarboxylation of pyruvate in promastigotes, whereas pathway redundancy is suggested for the entry of aspartate in amastigotes. Interestingly, we also found that l-lactate, an abundant glucogenic precursor in mammals, was used by Leishmania amastigotes to synthesize mannogen, entering the pathway through PPDK. On the basis of these new results, we propose a revision in the current model of gluconeogenesis in Leishmania, emphasizing the differences between amastigotes and promastigotes. This work underlines the importance of studying the trypanosomatid intracellular life cycle stages to gain a better understanding of the pathologies caused in humans.","corpus_id":7844378,"score":1},{"doc_id":"25537000","title":"Decrypting the structural, dynamic, and energetic basis of a monomeric kinesin interacting with a tubulin dimer in three ATPase states by all-atom molecular dynamics simulation.","abstract":"We have employed molecular dynamics (MD) simulation to investigate, with atomic details, the structural dynamics and energetics of three major ATPase states (ADP, APO, and ATP state) of a human kinesin-1 monomer in complex with a tubulin dimer. Starting from a recently solved crystal structure of ATP-like kinesin-tubulin complex by the Knossow lab, we have used flexible fitting of cryo-electron-microscopy maps to construct new structural models of the kinesin-tubulin complex in APO and ATP state, and then conducted extensive MD simulations (total 400 ns for each state), followed by flexibility analysis, principal component analysis, hydrogen bond analysis, and binding free energy analysis. Our modeling and simulation have revealed key nucleotide-dependent changes in the structure and flexibility of the nucleotide-binding pocket (featuring a highly flexible and open switch I in APO state) and the tubulin-binding site, and allosterically coupled motions driving the APO to ATP transition. In addition, our binding free energy analysis has identified a set of key residues involved in kinesin-tubulin binding. On the basis of our simulation, we have attempted to address several outstanding issues in kinesin study, including the possible roles of β-sheet twist and neck linker docking in regulating nucleotide release and binding, the structural mechanism of ADP release, and possible extension and shortening of α4 helix during the ATPase cycle. This study has provided a comprehensive structural and dynamic picture of kinesin's major ATPase states, and offered promising targets for future mutational and functional studies to investigate the molecular mechanism of kinesin motors.","corpus_id":2983740,"score":1},{"doc_id":"26620526","title":"Structural basis of reversible phosphorylation by maize pyruvate orthophosphate dikinase regulatory protein (PDRP).","abstract":"Pyruvate orthophosphate dikinase (PPDK) is one of the most important enzymes in C4 photosynthesis. PPDK regulatory protein (PDRP) regulates the Pi-dependent activation and ADP-dependent inactivation of PPDK by reversible phosphorylation. PDRP shares no significant sequence similarity with other protein kinases or phosphatases. To investigate the molecular mechanism by which PDRP carries out its dual and competing activities, we determined the first crystal structure of PDRP from maize (Zea mays). PDRP forms a compact homo-dimer in which each protomer contains two separate N-terminal (NTD) and C-terminal (CTD) domains. The CTD includes several key elements for performing both phosphorylation and dephosphorylation activities: the P-loop for binding the ADP and inorganic phosphate substrates, residues Lys274 and Lys299 for neutralizing the negative charge, and residue Asp277 for protonating and deprotonating the target threonine residue of PPDK to promote nucleophilic attack. Surprisingly, the NTD shares the same protein fold as the CTD, and also includes a putative P-loop with AMP bound but lacking enzymatic activities. Structural analysis indicated that this loop may participate in the interaction with and regulation of PPDK. The NTD has conserved intramolecular and intermolecular disulfide bonds for PDRP dimerization. Moreover, PDRP is the first structure of the DUF299 (domain of unknown function 299) enzyme family. This study provides a structural basis for understanding the catalytic mechanism of PDRP and offers a foundation for development of selective activators or inhibitors that regulate photosynthesis.","corpus_id":21143557,"score":1},{"doc_id":"26968775","title":"Trypanosoma evansi contains two auxiliary enzymes of glycolytic metabolism: Phosphoenolpyruvate carboxykinase and pyruvate phosphate dikinase.","abstract":"Trypanosoma evansi is a monomorphic protist that can infect horses and other animal species of economic importance for man. Like the bloodstream form of the closely related species Trypanosoma brucei, T. evansi depends exclusively on glycolysis for its free-energy generation. In T. evansi as in other kinetoplastid organisms, the enzymes of the major part of the glycolytic pathway are present within organelles called glycosomes, which are authentic but specialized peroxisomes. Since T. evansi does not undergo stage-dependent differentiations, it occurs only as bloodstream forms, it has been assumed that the metabolic pattern of this parasite is identical to that of the bloodstream form of T. brucei. However, we report here the presence of two additional enzymes, phosphoenolpyruvate carboxykinase and PPi-dependent pyruvate phosphate dikinase in T. evansi glycosomes. Their colocalization with glycolytic enzymes within the glycosomes of this parasite has not been reported before. Both enzymes can make use of PEP for contributing to the production of ATP within the organelles. The activity of these enzymes in T. evansi glycosomes drastically changes the model assumed for the oxidation of glucose by this parasite.","corpus_id":26726736,"score":1},{"doc_id":"27933791","title":"Mechanistic Insights from the Crystal Structure of Bacillus subtilis o-Succinylbenzoyl-CoA Synthetase Complexed with the Adenylate Intermediate.","abstract":"o-Succinylbenzoyl-CoA (OSB-CoA) synthetase, or MenE, catalyzes an essential step in vitamin K biosynthesis and is a valuable drug target. Like many other adenylating enzymes, it changes its structure to accommodate substrate binding, catalysis, and product release along the path of a domain alternation catalytic mechanism. We have determined the crystal structure of its complex with the adenylation product, o-succinylbenzoyl-adenosine monophosphate (OSB-AMP), and captured a new postadenylation state. This structure presents unique features such as a strained conformation for the bound adenylate intermediate to indicate that it represents the enzyme state after completion of the adenylation reaction but before release of the C domain in its transition to the thioesterification conformation. By comparison to the ATP-bound preadenylation conformation, structural changes are identified in both the reactants and the active site to allow inference about how these changes accommodate and facilitate the adenylation reaction and to directly support an in-line backside attack nucleophilic substitution mechanism for the first half-reaction. Mutational analysis suggests that the conserved His196 plays an important role in desolvation of the active site rather than stabilizing the transition state of the adenylation reaction. In addition, comparison of the new structure with a previously determined OSB-AMP-bound structure of the same enzyme allows us to propose a release mechanism of the C domain in its alteration to form the thioesterification conformation. These findings allow us to better understand the domain alternation catalytic mechanism of MenE as well as many other adenylating enzymes.","corpus_id":11442071,"score":1},{"doc_id":"28240893","title":"How Intrinsic Dynamics Mediates the Allosteric Mechanism in the ABC Transporter Nucleotide Binding Domain Dimer.","abstract":"A protein's architecture facilitates specific motions-intrinsic dynamic modes-that are employed to effect function. Here we used molecular dynamics (MD) simulations to investigate the dynamics of the MJ0796 ABC transporter nucleotide-binding domain (NBD). ABC transporter NBDs form a rotationally symmetric dimer whereby two equivalent active sites are formed at their interface; in complex with a dimer of transmembrane domains they hydrolyze ATP to energize translocation of substrates across cellular membranes. Our data suggest the ABC NBD's ensemble of functional states can be understood predominately in terms of conformational changes between its major subdomains, occurring along two orthogonal dynamic modes. The data show that ligands and oligomeric interactions modulate the equilibrium conformation of the NBD with respect to these motions, suggesting that allostery is achieved by affecting the energetic profile along these two modes. The observed dynamics and allostery integrate consonantly and logically within a mechanistic framework for the ABC NBD dimer, which is supported by a large body of experimental and theoretical data, providing a higher resolution view of the enzyme's dynamic cycle. Our study shows how valuable mechanistic inferences can be derived from accessible short-time scale MD simulations of an enzyme's substructures.","corpus_id":46784601,"score":1},{"doc_id":"28271481","title":"\"Pyruvate Carboxylase, Structure and Function\".","abstract":"Pyruvate carboxylase is a metabolic enzyme that fuels the tricarboxylic acid cycle with one of its intermediates and also participates in the first step of gluconeogenesis. This large enzyme is multifunctional, and each subunit contains two active sites that catalyze two consecutive reactions that lead to the carboxylation of pyruvate into oxaloacetate, and a binding site for acetyl-CoA, an allosteric regulator of the enzyme. Pyruvate carboxylase oligomers arrange in tetramers and covalently attached biotins mediate the transfer of carboxyl groups between distant active sites. In this chapter, some of the recent findings on pyruvate carboxylase functioning are presented, with special focus on the structural studies of the full length enzyme. The emerging picture reveals large movements of domains that even change the overall quaternary organization of pyruvate carboxylase tetramers during catalysis.","corpus_id":6166593,"score":1},{"doc_id":"28700696","title":"Small-molecule inhibition of pyruvate phosphate dikinase targeting the nucleotide binding site.","abstract":"Pyruvate phosphate dikinase (PPDK) is an essential enzyme of C4 photosynthesis in plants, catalyzing the ATP-driven conversion of pyruvate to phosphoenolpyruvate (PEP). It is further used by some bacteria and unicellular protists in the reverse, ATP-forming direction. Many weed species use C4 photosynthesis in contrast to world's major crops, which are C3 plants. Hence inhibitors of PPDK may be used as C4-specific herbicides. By screening a library of 80 commercially available kinase inhibitors, we identified compounds derived from bisindolylmaleimide (bisindolylmaleimide IV, IC50 = 0.76 ± 0.13 μM) and indirubin (indirubin-3'-monoxime, IC50 = 4.2 ± 0.9 μM) that showed high inhibitory potency towards PPDK and are among the most effective PPDK inhibitors described today. Physiological studies on leaf tissues of a C4 model plant confirmed in vivo inhibition of C4-driven photosynthesis by these substances. Moreover, comparative docking studies of non-inhibitory bisindolylmaleimide derivatives suggest that the selectivity towards PPDK may be increased by addition of functional groups to the core structure.","corpus_id":1033705,"score":1},{"doc_id":"28820699","title":"In Vitro Testing of Potential Entamoeba histolytica Pyruvate Phosphate Dikinase Inhibitors.","abstract":"Adverse effects and resistance to metronidazole have motivated the search for new antiamoebic agents against Entamoeba histolytica. Control of amoeba growth may be achieved by inhibiting the function of the glycolytic enzyme and pyruvate phosphate dikinase (PPDK). In this study, we screened 10 compounds using an in vitro PPDK enzyme assay. These compounds were selected from a virtual screening of compounds in the National Cancer Institute database. The antiamoebic activity of the selected compounds was also evaluated by determining minimal inhibitory concentrations (MICs) and IC50 values using the nitro-blue tetrazolium reduction assay. Seven of the 10 compounds showed inhibitory activities against the ATP/Pi binding site of the ATP-grasp domain. Two compounds, NSC349156 (pancratistatin) and NSC228137 (7-ethoxy-4-[4-methylphenyl] sulfonyl-3-oxido-2, 1, 3-benzoxadiazol-3-ium), exhibited inhibitory effects on the growth of E. histolytica trophozoites with MIC values of 25 and 50 μM, and IC50 values of 14 and 20.7 μM, respectively.","corpus_id":13949376,"score":1},{"doc_id":"29239025","title":"Fine structure of conformational ensembles in adenylate kinase.","abstract":"Adenylate kinase (ADK) catalyzes the reversible Mg2+ -dependent phosphoryl transfer reaction Mg2+ +2ADP ↔Mg2+ +ATP + AMP in essential cellular systems. This reaction is a major player in cellular energy homeostasis and the isoform network of ADK plays an important role in AMP metabolic signaling circuits. ADK has 3 domains, the LID, NMP, and CORE domains, that undergo large conformational rearrangements during ADK's catalytic cycle. In spite of extensive experimental and computational studies, details of the conformational pathway from open to closed forms remain uncertain. In this paper we explore this pathway using coarse-grained molecular dynamics (MD) trajectories of ADK calculated by GROMACS using a SMOG model and classify the conformations within the resultant trajectories by K-means clustering. ADK conformations segregate naturally into open; intermediate; and closed forms with long-term residence in the intermediate state. Structural clustering divides the intermediate conformation into 3 sub-states that are distinguished from one another on the basis of differences in both structure and dynamics. These distinctions are defined on the basis of a number of different metrics including radius of gyration, dihedral angle fluctuation, and fluctuations of interatomic pair distances. Furthermore, differences in the sub-states appear to correspond to the distinct ways each sub-state contributes to the molecular mechanism of catalysis: One sub-state acts as a gate-way to the open conformation; one sub-state a gate-way to the closed conformation. A third intermediate sub-state appears to represent a metastable off-pathway structure that is nevertheless frequently visited during the passage from open to closed state.","corpus_id":46771857,"score":1},{"doc_id":"29255019","title":"Functions of maize genes encoding pyruvate phosphate dikinase in developing endosperm.","abstract":"Maize opaque2 (o2) mutations are beneficial for endosperm nutritional quality but cause negative pleiotropic effects for reasons that are not fully understood. Direct targets of the bZIP transcriptional regulator encoded by o2 include pdk1 and pdk2 that specify pyruvate phosphate dikinase (PPDK). This enzyme reversibly converts AMP, pyrophosphate, and phosphoenolpyruvate to ATP, orthophosphate, and pyruvate and provides diverse functions in plants. This study addressed PPDK function in maize starchy endosperm where it is highly abundant during grain fill. pdk1 and pdk2 were inactivated individually by transposon insertions, and both genes were simultaneously targeted by endosperm-specific RNAi. pdk2 accounts for the large majority of endosperm PPDK, whereas pdk1 specifies the abundant mesophyll form. The pdk1- mutation is seedling-lethal, indicating that C4 photosynthesis is essential in maize. RNAi expression in transgenic endosperm eliminated detectable PPDK protein and enzyme activity. Transgenic kernels weighed the same on average as nontransgenic siblings, with normal endosperm starch and total N contents, indicating that PPDK is not required for net storage compound synthesis. An opaque phenotype resulted from complete PPDK knockout, including loss of vitreous endosperm character similar to the phenotype conditioned by o2-. Concentrations of multiple glycolytic intermediates were elevated in transgenic endosperm, energy charge was altered, and starch granules were more numerous but smaller on average than normal. The data indicate that PPDK modulates endosperm metabolism, potentially through reversible adjustments to energy charge, and reveal that o2- mutations can affect the opaque phenotype through regulation of PPDK in addition to their previously demonstrated effects on storage protein gene expression.","corpus_id":26347092,"score":1},{"doc_id":"29362701","title":"Analysis of an ATP-induced conformational transition of ABC transporter MsbA using a coarse-grained model.","abstract":"Upon the binding of ATP molecules to nucleotide binding domains (NBDs), ATP-binding cassette (ABC) exporters undergo a conformational transition from an inward-facing (IF) to an outward-facing (OF) state. This molecular event is a typical example of chemo-mechanical coupling. However, the underlying mechanism remains unclear. In this study, we analyzed the IF→OF transition of a representative ABC exporter, MsbA, by solving the equation of motion under an elastic network model (ENM). ATP was represented as a single node in ENM or replaced by external forces. When two ATP nodes were added to the ENM of the IF state protein, the two NBDs dimerized; subsequently, the two transmembrane domains opened toward the extracellular side, resulting in the formation of the OF structure. Such a conformational transition was also reproduced by applying external forces, which caused the rotational motion of the NBDs instead of the addition of ATP nodes. The process of the conformational transition was analyzed in detail using cross-correlation maps for node-node interactions. More importantly, it was revealed that the ATP binding energy is converted into distortion energy of several transmembrane helices. These results are useful for understanding the chemo-mechanical coupling in ABC transporters.","corpus_id":6570778,"score":1},{"doc_id":"18477462","title":"Development of bioluminescent pyrophosphate assay using pyruvate phosphate dikinase and its application to single-nucleotide polymorphism analysis.","abstract":"DNA analysis is an important technology with respect to diagnosis of infectious disease and tailored medication. In this study, we developed a novel bioluminescent assay for pyrophosphate, and it was applied to single-nucleotide polymorphism (SNP) analysis using one-base extension reaction. The principle of this method is as follows. A specific primer within each aliquot possessing a short 3' end of the base of interest was hybridized to the single-stranded DNA template. Subsequently, (exo-)Klenow DNA polymerase and one of either alpha-thio-dATP, dTTP, dGTP, or dCTP were added and incubated for 1 min. Pyrophosphate released by DNA polymerase is converted to ATP by pyruvate phosphate dikinase (PPDK), and the concentration of ATP is determined using the firefly luciferase reaction. This method, which does not require expensive equipment, can be used to rapidly monitor one point mutation in the gene.","corpus_id":41285191,"score":0},{"doc_id":"18616182","title":"[Expression of PPDK from Microbispora rosea subsp. aerata in Escherichia coli and its application in pyrosequencing].","abstract":"Pyruvate phosphate dikinase (PPDK; EC 2.7.9.1) is found in certain microorganisms and plants, and catalyzes the conversion of AMP, PPi and phosphoenolpyruvate (PEP) to ATP, Pi and pyruvate. Using the genomic DNA of Microbispora rosea subsp. aerata as the template, a DNA fragment encoding the gene PPDK was amplified by PCR and inserted into the expression vector pET28a(+), yielding pET28a (+)-PPDK. The E. coli BL21 (DE3) was transformed with the pET28a (+)-PPDK. After inducing with IPTG, the E. coli BL21 (DE3) [pET28a (+)-PPDK] expressed recombinant PPDK fused to an N-terminal sequence of 6-His Tag. The molecular weight of PPDK was estimated to be 101 kD by SDS-PAGE. The PPDK was purified by His * Bind Resin affinity chromatography and ultrafiltration using 10 kD cut-off membrane. The successful application of PPDK in pyrosequencing was also demonstrated.","corpus_id":38104293,"score":0},{"doc_id":"19170242","title":"Nano-sized bacterial magnetic particles displaying pyruvate phosphate dikinase for pyrosequencing.","abstract":"There is a high demand for inexpensive and high-throughput DNA sequencing technologies in molecular biology and applied biosciences. In this study, novel nano-sized magnetic particles displaying enzymes for pyrosequencing, a rather novel bioluminometric DNA sequencing method based on the sequencing-by-synthesis principle by employing a cascade of several enzymatic reactions, was developed. A highly thermostable enzyme, pyruvate phosphate dikinase (PPDK) which converts PPi to ATP was successfully expressed onto bacterial magnetic particles (BacMPs) using a novel protein display system of Magnetospirillum magneticum AMB-1. The enzymatic stability of BacMPs displaying PPDK (PPDK-BacMPs) to pH and temperature was evaluated and its broad range of properties was shown. Subsequently, PPDK-BacMPs were applied in pyrosequencing and a target oligonucleotide was successfully sequenced. The PPDK enzyme displayed on BacMPs was shown to be recyclable in each sequence reaction as they can be manipulated by magnetic force. It was concluded that nano-sized PPDK-BacMPs are useful for the scale down of pyrosequencing reaction volumes, thus, permitting high-throughput. The recycling of enzymes was also shown to be promising and applicable for the development of an inexpensive DNA sequencing at a low running cost.","corpus_id":23319960,"score":0},{"doc_id":"22272354","title":"The conformational transition pathways of ATP-binding cassette transporter BtuCD revealed by targeted molecular dynamics simulation.","abstract":"BtuCD is a member of the ATP-binding cassette transporters in Escherichia coli that imports vitamin B(12) into the cell by utilizing the energy of ATP hydrolysis. Crystal structures of BtuCD and its homologous protein HI1470/1 in various conformational states support the \"alternating access\" mechanism which proposes the conformational transitions of the substrate translocation pathway at transmembrane domain (TMD) between the outward-facing and inward-facing states. The conformational transition at TMD is assumed to couple with the movement of the cytoplasmic nucleotide-binding domains (NBDs) driven by ATP hydrolysis/binding. In this study, we performed targeted molecular dynamics (MD) simulations to explore the atomic details of the conformational transitions of BtuCD importer. The outward-facing to inward-facing (O→I) transition was found to be initiated by the conformational movement of NBDs. The subsequent reorientation of the substrate translocation pathway at TMD began with the closing of the periplasmic gate, followed by the opening of the cytoplamic gate in the last stage of the conformational transition due to the extensive hydrophobic interactions at this region, consistent with the functional requirement of unidirectional transport of the substrates. The reverse inward-facing to outward-facing (I→O) transition was found to exhibit intrinsic diversity of the conformational transition pathways and significant structural asymmetry, suggesting that the asymmetric crystal structure of BtuCD-F is an intermediate state in this process.","corpus_id":723175,"score":0},{"doc_id":"26920481","title":"Metabolic networks to generate pyruvate, PEP and ATP from glycerol in Pseudomonas fluorescens.","abstract":"Glycerol is a major by-product of the biodiesel industry. In this study we report on the metabolic networks involved in its transformation into pyruvate, phosphoenolpyruvate (PEP) and ATP. When the nutritionally-versatile Pseudomonas fluorescens was exposed to hydrogen peroxide (H2O2) in a mineral medium with glycerol as the sole carbon source, the microbe reconfigured its metabolism to generate adenosine triphosphate (ATP) primarily via substrate-level phosphorylation (SLP). This alternative ATP-producing stratagem resulted in the synthesis of copious amounts of PEP and pyruvate. The production of these metabolites was mediated via the enhanced activities of such enzymes as pyruvate carboxylase (PC) and phosphoenolpyruvate carboxylase (PEPC). The high energy PEP was subsequently converted into ATP with the aid of pyruvate phosphate dikinase (PPDK), phosphoenolpyruvate synthase (PEPS) and pyruvate kinase (PK) with the concomitant formation of pyruvate. The participation of the phospho-transfer enzymes like adenylate kinase (AK) and acetate kinase (ACK) ensured the efficiency of this O2-independent energy-generating machinery. The increased activity of glycerol dehydrogenase (GDH) in the stressed bacteria provided the necessary precursors to fuel this process. This H2O2-induced anaerobic life-style fortuitously evokes metabolic networks to an effective pathway that can be harnessed into the synthesis of ATP, PEP and pyruvate. The bioconversion of glycerol to pyruvate will offer interesting economic benefit.","corpus_id":21877431,"score":0},{"doc_id":"27886288","title":"Exploring the mechanochemical cycle of dynein motor proteins: structural evidence of crucial intermediates.","abstract":"Dyneins, a class of motor proteins consisting of six AAA+ modules (AAA1-AAA6), convert chemical energy derived from the hydrolysis of ATP into mechanical energy to walk along the microtubule track towards its minus end while accomplishing various cellular tasks including the transportation of various intracellular cargos. In a full mechanochemical cycle, dynein goes through ATP binding induced open to closed state transition of AAA1, hydrolysis of that ATP and closed to open state transition induced by the release of hydrolysed products along with linker remodelling in different nucleotide states. Here we built structure based models (SBMs) to explore the sequence of events of this mechanochemical cycle from structural aspects. Free energy and kinetic simulation approaches on a multi-basin SBM of dynein reveal the following pathways: (1) in the closing pathway, the AAA1 domain first converts to a closed state followed by the movement of the linker and (2) in the opening transition, initially the AAA1 domain partially opens up and then the complete linker movement takes place followed by the complete opening of the AAA1 domain. In the opening transition, we have observed two intermediate states from our simulations where the AAA1 domain is partially opened. However, in one state the linker is at a closed position and in the other the linker is at an open position. The existence of such intermediates (Pi released, ADP bound state) of dynein has been suggested by numerous experimental studies earlier. Finally, we discuss the biological relevance of this sequence of events in terms of processivity and efficiency of the cycle. The current study also shows how the basic principle of protein folding can be extended to understand complex phenomena like the stepping mechanism of motor proteins.","corpus_id":22021572,"score":0}],"string":"[\n {\n \"doc_id\": \"17996018\",\n \"title\": \"The pyruvate, orthophosphate dikinase regulatory proteins of Arabidopsis possess a novel, unprecedented Ser/Thr protein kinase primary structure.\",\n \"abstract\": \"Pyruvate, orthophosphate dikinase (PPDK) is a ubiquitous, low-abundance metabolic enzyme of undetermined function in C3 plants. Its activity in C3 chloroplasts is light-regulated via reversible phosphorylation of an active-site Thr residue by the PPDK regulatory protein (RP), a most unusual bifunctional protein kinase (PK)/protein phosphatase (PP). In this paper we document the molecular cloning and functional analysis of the two unique C3 RPs in Arabidopsis thaliana. The first of these, AtRP1, encodes a typical chloroplast-targeted, bifunctional C4-like RP. The second RP gene, AtRP2, encodes a monofunctional polypeptide that possesses in vitro RP-like PK activity but lacks PP activity, and is localized in the cytosol. Notably, the deduced primary structures of these two highly homologous polypeptides are devoid of any canonical subdomain structure that unifies all known eukaryotic and prokaryotic Ser/Thr PKs into one of three superfamilies, despite the direct demonstration that AtRP1 is functionally a member of this group. Instead, these C3 RPs and the related C4 plant homologues encode a conserved, centrally positioned, approximately 260-residue sequence currently described as the 'domain of unknown function 299' (DUF 299). We propose that vascular plant RPs form a unique protein kinase family now designated as the DUF 299 gene family.\",\n \"corpus_id\": 20245121,\n \"score\": 2\n },\n {\n \"doc_id\": \"18831048\",\n \"title\": \"Opening of the ADP-bound active site in the ABC transporter ATPase dimer: evidence for a constant contact, alternating sites model for the catalytic cycle.\",\n \"abstract\": \"ABC transporters are ubiquitous, ATP-dependent transmembrane pumps. The mechanism by which ATP hydrolysis in the nucleotide-binding domain (NBD) effects conformational changes in the transmembrane domain that lead to allocrite translocation remains largely unknown. A possible aspect of this mechanism was suggested by previous molecular dynamics simulations of the MJ0796 NBD dimer, which revealed a novel, nucleotide-dependent intrasubunit conformational change involving the relative rotation of the helical and catalytic subdomains. Here, we find that in four of five simulations of the ADP/ATP-bound dimer, the relative rotation of the helical and catalytic subdomains in the ADP-bound monomer results in opening of the ADP-bound active site, probably sufficient or close to sufficient to allow nucleotide exchange. We also observe that in all five simulations of the ADP/ATP-bound dimer, the intimate contact of the LSGGQ signature sequence with the ATP gamma-phosphate is weakened by the intrasubunit conformational change within the ADP-bound monomer. We discuss how these results support a constant contact model for the function of the NBD dimer in contrast to switch models, in which the NBDs are proposed to fully disassociate during the catalytic cycle.\",\n \"corpus_id\": 10494245,\n \"score\": 2\n },\n {\n \"doc_id\": \"19914167\",\n \"title\": \"Structures of asymmetric ClpX hexamers reveal nucleotide-dependent motions in a AAA+ protein-unfolding machine.\",\n \"abstract\": \"ClpX is a AAA+ machine that uses the energy of ATP binding and hydrolysis to unfold native proteins and translocate unfolded polypeptides into the ClpP peptidase. The crystal structures presented here reveal striking asymmetry in ring hexamers of nucleotide-free and nucleotide-bound ClpX. Asymmetry arises from large changes in rotation between the large and small AAA+ domains of individual subunits. These differences prevent nucleotide binding to two subunits, generate a staggered arrangement of ClpX subunits and pore loops around the hexameric ring, and provide a mechanism for coupling conformational changes caused by ATP binding or hydrolysis in one subunit to flexing motions of the entire ring. Our structures explain numerous solution studies of ClpX function, predict mechanisms for pore elasticity during translocation of irregular polypeptides, and suggest how repetitive conformational changes might be coupled to mechanical work during the ATPase cycle of ClpX and related molecular machines.\",\n \"corpus_id\": 7976574,\n \"score\": 2\n },\n {\n \"doc_id\": \"19996093\",\n \"title\": \"The conformational transition pathway of ATP binding cassette transporter MsbA revealed by atomistic simulations.\",\n \"abstract\": \"ATP binding cassette transporters are integral membrane proteins that use the energy released from ATP hydrolysis at the two nucleotide binding domains (NBDs) to translocate a wide variety of substrates through a channel at the two transmembrane domains (TMDs) across the cell membranes. MsbA from Gram-negative bacteria is a lipid and multidrug resistance ATP binding cassette exporter that can undergo large scale conformational changes between the outward-facing and the inward-facing conformations revealed by crystal structures in different states. Here, we use targeted molecular dynamics simulation methods to explore the atomic details of the conformational transition from the outward-facing to the inward-facing states of MsbA. The molecular dynamics trajectories revealed a clear spatiotemporal order of the conformational movements. The disruption of the nucleotide binding sites at the NBD dimer interface is the very first event that initiates the following conformational changes, verifying the assumption that the conformational conversion is triggered by ATP hydrolysis. The conserved x-loops of the NBDs were identified to participate in the interaction network that stabilizes the cytoplasmic tetrahelix bundle of the TMDs and play an important role in mediating the cross-talk between the NBD and TMD. The movement of the NBD dimer is transmitted through x-loops to break the tetrahelix bundle, inducing the packing rearrangements of the transmembrane helices at the cytoplasmic side and the periplasmic side sequentially. The packing rearrangement within each periplasmic wing of TMD that results in exposure of the substrate binding sites occurred at the end stage of the trajectory, preventing the wrong timing of the binding site accessibility.\",\n \"corpus_id\": 2829607,\n \"score\": 2\n },\n {\n \"doc_id\": \"20369870\",\n \"title\": \"Insights into the molecular mechanism of an ABC transporter: conformational changes in the NBD dimer of MJ0796.\",\n \"abstract\": \"Despite the rapid advances in the study of ABC transporters, many fundamental questions linked to ATP binding/hydrolysis and its relation to the transport cycle remain unanswered. In particular, it is still neither clear nor consensual how the ATP energy is used by the nucleotide binding domains (NBDs) to produce mechanical work and drive the substrate translocation. The major conformational changes in the NBDs following ATP hydrolysis during the transport cycle and the role played by the conserved family motifs in harnessing the energy associated with nucleotide hydrolysis are yet unknown. Additionally, the way energy is transmitted from the catalytic to the membrane domains, in order to drive substrate translocation, is also a fundamental question that remains unanswered. Due to the high structure similarities of the NBD architecture throughout the whole ABC family, it is likely that the mechanism of ATP binding, hydrolysis, and communication with the transmembrane domains is similar in all family members, independently of the nature of the transported substrate. In this work, we focused our attention on the consequences of ATP hydrolysis in the NBDs, especially on the structural changes that occur during this process. For that, we use molecular dynamics simulation techniques taking as a starting point the X-ray structure of the MJ0796 dimer from Methanococcus jannaschii. Several potential intermediate states of the ATP hydrolytic cycle are investigated, each consisting of different combinations of nucleotide-bound forms. The results obtained allowed us to identify the conformational rearrangements induced by hydrolysis on the catalytic subunits, as well as the residues involved in this reorganization. The major changes are localized at specific regions of the protein, namely, involving segments 11-19 and 93-124. Additionally, our results together with the knowledge of complete ABC transporter X-ray structures suggest a possible NBD:TMD signal transmission interface.\",\n \"corpus_id\": 26818665,\n \"score\": 2\n },\n {\n \"doc_id\": \"21414960\",\n \"title\": \"Functional evolution of C(4) pyruvate, orthophosphate dikinase.\",\n \"abstract\": \"Pyruvate,orthophosphate dikinase (PPDK) plays a controlling role in the PEP-regeneration phase of the C(4) photosynthetic pathway. Earlier studies have fully documented its biochemical properties and its post-translational regulation by the PPDK regulatory protein (PDRP). However, the question of its evolution into the C(4) pathway has, until recently, received little attention. One assumption concerning this evolution is that changes in catalytic and regulatory properties of PPDK were necessary for the enzyme to fulfil its role in the C(4) pathway. In this study, the functional evolution of PPDK from its ancient origins in the Archaea to its ascension as a photosynthetic enzyme in modern C(4) angiosperms is reviewed. This analysis is accompanied by a comparative investigation into key catalytic and regulatory properties of a C(3) PPDK isoform from Arabidopsis and the C(4) PPDK isoform from Zea mays. From these analyses, it is proposed that PPDK first became functionally seated in C(3) plants as an ancillary glycolytic enzyme and that its transition into a C(4) pathway enzyme involved only minor changes in enzyme properties per se.\",\n \"corpus_id\": 15123166,\n \"score\": 2\n },\n {\n \"doc_id\": \"21421406\",\n \"title\": \"What can enzymes of C₄ photosynthesis do for C₃ plants under stress?\",\n \"abstract\": \"Phosphoenolpyruvate carboxylase (PEPC), NADP-malic enzyme (NADP-ME), and pyruvate, phosphate dikinase (PPDK) participate in the process of concentrating CO₂ in C₄ photosynthesis. Non-photosynthetic counterparts of these enzymes, which are present in all plants, play important roles in the maintenance of pH and replenishment of Krebs cycle intermediates, thereby contributing to the biosynthesis of amino acids and other compounds and providing NADPH for biosynthesis and the antioxidant system. Enhanced activities of PEPC and/or NADP-ME and/or PPDK were found in plants under various types of abiotic stress, such as drought, high salt concentration, ozone, the absence of phosphate and iron or the presence of heavy metals in the soil. Moreover, the activities of all of these enzymes were enhanced in plants under biotic stress caused by viral infection. The functions of PEPC, NADP-ME and PPDK appear to be more important for plants under stress than under optimal growth conditions.\",\n \"corpus_id\": 3083252,\n \"score\": 2\n },\n {\n \"doc_id\": \"21883547\",\n \"title\": \"The pyruvate, orthophosphate dikinase regulatory proteins of Arabidopsis are both bifunctional and interact with the catalytic and nucleotide-binding domains of pyruvate, orthophosphate dikinase.\",\n \"abstract\": \"Pyruvate orthophosphate dikinase (PPDK) is a key enzyme in C(4) photosynthesis and is also found in C(3) plants. It is post-translationally modified by the PPDK regulatory protein (RP) that possesses both kinase and phosphotransferase activities. Phosphorylation and dephosphorylation of PPDK lead to inactivation and activation respectively. Arabidopsis thaliana contains two genes that encode chloroplastic (RP1) and cytosolic (RP2) isoforms of RP, and although RP1 has both kinase and phosphotransferase activities, to date RP2 has only been shown to act as a kinase. Here we demonstrate that RP2 is able to catalyse the dephosphorylation of PPDK, although at a slower rate than RP1 under the conditions of our assay. From yeast two-hybrid analysis we propose that RP1 binds to the central catalytic domain of PPDK, and that additional regions towards the carboxy and amino termini are required for a stable interaction between RP2 and PPDK. For 21 highly conserved amino acids in RP1, mutation of 15 of these reduced kinase and phosphotransferase activity, while mutation of six residues had no impact on either activity. We found no mutant in which only one activity was abolished. However, in some chimaeric fusions that comprised the amino and carboxy termini of RP1 and RP2 respectively, the kinase reaction was severely compromised but phosphotransferase activity remained unaffected. These findings are consistent with the findings that both RP1 and RP2 modulate reversibly the activity of PPDK, and possess one bifunctional active site or two separate sites in close proximity.\",\n \"corpus_id\": 45178923,\n \"score\": 2\n },\n {\n \"doc_id\": \"23214920\",\n \"title\": \"The power stroke driven by ATP binding in CFTR as studied by molecular dynamics simulations.\",\n \"abstract\": \"Cystic fibrosis transmembrane conductance regulator (CFTR) is a chloride channel belonging to the ATP binding cassette (ABC) protein superfamily. Currently, it remains unclear how ATP binding causes the opening of the channel gate at the molecular level. To clarify this mechanism, we first constructed an atomic model of the inward-facing CFTR using the X-ray structures of other ABC proteins. Molecular dynamics (MD) simulations were then performed to explore the structure and dynamics of the inward-facing CFTR in a membrane environment. In the MgATP-bound state, two nucleotide-binding domains (NBDs) formed a head-to-tail type of dimer, in which the ATP molecules were sandwiched between the Walker A and signature motifs. Alternatively, one of the final MD structures in the apo state was similar to that of a \\\"closed-apo\\\" conformation found in the X-ray analysis of ATP-free MsbA. Principal component analysis for the MD trajectory indicated that NBD dimerization causes significant structural and dynamical changes in the transmembrane domains (TMDs), which is likely indicative of the formation of a chloride ion access path. This study suggests that the free energy gain from ATP binding acts as a driving force not only for NBD dimerization but also for NBD-TMD concerted motions.\",\n \"corpus_id\": 11312616,\n \"score\": 2\n },\n {\n \"doc_id\": \"23912807\",\n \"title\": \"Macromolecular crowding: chemistry and physics meet biology (Ascona, Switzerland, 10-14 June 2012).\",\n \"abstract\": \"More than 60 years of biochemical and biophysical studies have accustomed us to think of proteins as highly purified entities that act in isolation, more or less freely diffusing until they find their cognate partner to bind to. While in vitro experiments that reproduce these conditions largely remain the only way to investigate the intrinsic properties of molecules, this approach ignores an important factor: in their natural milieu , proteins are surrounded by several other molecules of different chemical nature, and this crowded environment can considerably modify their behaviour. About 40% of the cellular volume on average is occupied by all sorts of molecules. Furthermore, biological macromolecules live and operate in an extremely structured and complex environment within the cell (endoplasmic reticulum, Golgi apparatus, cytoskeletal structures, etc). Hence, to further complicate the picture, the interior of the cell is by no means a simply crowded medium, rather, a most crowded and confining one. In recent times, several approaches have been developed in the attempt to take into account important factors such as the ones mentioned above, at both theoretical and experimental levels, so that this field of research is now emerging as one of the most thriving in molecular and cell biology (see figure 1). [ Formula: see text] Figure 1. Left: number of articles containing the word 'crowding' as a keyword limited to the biological and chemical science domains (source: ISI Web of Science). The arrow flags the 2003 'EMBO Workshop on Biological Implications of Macromolecular Crowding' (Embo, 2012). Right: number of citations to articles containing the word 'crowding' limited to the same domains (bars) and an exponential regression curve (source: Elsevier Scopus). To promote the importance of molecular crowding and confinement and provide researchers active in this field an interdisciplinary forum for meeting and exchanging ideas, we recently organized an international conference held in Ascona from 10 to 14 June 2012. In the unique scenario of the Maggiore lake and absorbed in the magic atmosphere of the Centro Stefano Franscini (CSF) at Monte Verità, we enjoyed three-and-a-half days of intense and inspiring activity, where not only many of the most prominent scientists working on macromolecular crowding, but also experts in closely related fields such as colloids and soft matter presented their work. The meeting was intended and has been organized to bring theoreticians and experimentalists together in the attempt to promote an active dialogue. Moreover, we wanted different disciplines to be represented, notably physics and chemistry, besides biology, as cross-fertilization is proving an increasingly fundamental source of inspiration and advancement. This issue of Physical Biology (PB) features a selection of the oral contributions presented at the conference, expanded in the form of research or review articles. PB, one of the scientific journals of the Institute of Physics (IOP), is one of the most dynamic and lively forums active at the interface between biology on one side, and physics and mathematics on the other. As its mission is stated by IOP, PB 'focuses on research in which physics-based approaches lead to new insights into biological systems at all scales of space and time, and all levels of complexity'. For these reasons, and also in view of its high reputation and broad readership, PB appears to be the ideal place for disseminating the thriving pieces of research presented at the conference. We are extremely grateful to PB and its kind and efficient editorial staff who helped make this issue a great scientific follow-up to the conference. The opening lecture of the conference, the first of four day-opening keynote lectures, was given by Allen P Minton from NIH (USA), possibly the most influential among the pioneers in the field. He provided a lucid and well-thought-out overview of the concept of macromolecular crowding through an exhaustive chronological account of the major milestones. It is clear that the concept of excluded volume as a key factor remains central to the concept of molecular crowding. As a consequence, simple descriptive paradigms borrowed essentially from colloid physics may still provide useful tools to understand the subtle effects of crowding and confinement in living matter. The contiguity between crowding, colloids and soft matter further emerged as an important concept in the course of the conference in several theoretical lectures and a few experimental ones. Dave Thirumalai, from the University of Maryland (USA), one of the most active theoreticians in the field of theoretical biophysics, outlined scaling theories, concepts from colloid literature and different simulation techniques to describe scenarios for crowding-induced changes in the structure and dynamics of proteins and RNA. In particular, he showed the importance of the shape of crowding particles in affecting folding oligomerization of amyloidogenic peptides. Johannes Schöneberg, from IMPRS, Mathematics Institute (Germany), illustrated ReaDDy , a newly developed particle-based simulation software tool for reaction-diffusion dynamics, developed in the group of Frank Noe at EMPRS. He showed that ReaDDy makes it possible to bridge the gap between soft matter and molecular dynamics (MD) simulations on the one hand and particle-based stochastic reaction-diffusion simulations on the other. We asked Johannes to organize a tutorial session to lead interested participants into the package and 'get their hands wet' under the guidance of the developers. The tutorial session was indeed successful and the broad possibilities offered by the simulation toolkit appeared to be clear to the participants. Paolo De Los Rios, from the Ecole Polytechnique Fédérale de Lausanne (EPFL, Switzerland), examined the complexity of the effects caused by crowding conditions from the point of view of statistical physics. Starting from a modification of the well-known Smoluchowski approach to calculate the encounter rate of diffusion-limited reactions, he showed how more realistic situations accounting for crowding effects could be treated equally well on the same theoretical grounds. This talk marked an important point in the conference as it reinforced the idea that simple models of theoretical physics still have the power to provide inspiring results in spite of the intrinsic simplifications of such theoretical approaches. Along the same lines, Nicolas Dorsaz, from the University of Cambridge (UK), proposed an extension of the Smoluchowski framework that incorporates repulsive and attracting interactions between the reactants. This approach was illustrated by reaction rates obtained from event-driven Brownian dynamics and dynamical Monte Carlo simulations. Another striking example of the physical subtleties associated with modelling crowding effects was provided by Jeffrey Skolnick, from the Georgia Institute of Technology (USA). He examined the role of hydrodynamic interactions in the self-organization of biological assemblies in the presence of crowding. His results strongly suggest that hydrodynamic interactions greatly affect the kinetics of self-assembly reactions, so that including them in the picture appears crucial for understanding the dynamics of biological systems in vivo . Margareth Cheung, from the University of Houston (USA), emphasized that how the crowded environment inside a cell affects the structural conformation of a protein with a spherical shape is a vital question because the geometry of proteins and protein-protein complexes are far from globules in vivo . Her work demonstrates the malleability of 'native' proteins and implies that crowding-induced shape changes may be important for protein function and malfunction in vivo . Huan-Xiang Zhou, from the Florida State University (USA), focused on atomistic simulations of protein folding and binding under crowding conditions. His lab has developed a post-processing method that allows the atomistic representation of proteins in folding and binding processes under crowding. A comparison with experimental results was also presented. Other lecturers pointed out that there are still aspects not entirely explored in the effects of both crowding and confinement. As suggested in the talk by Gary Pielak, from the University of North Carolina (USA), the currently used synthetic crowding agents are far from being satisfactory in replicating naturally occurring effects associated with crowded environments. For example, non-specific binding seems to play a subtle role in the cell, as natural macromolecules can induce both stabilization and destabilization when used as crowders. It is indeed possible to fine-tune the effect of proteins, as crowders, on the stability of other proteins. Another aspect that became clear is that new, more powerful methods need to be developed to study the effect of crowding, but even more to compare crowding and confinement. Indeed, it appeared clear from the lecture by Pierandrea Temussi, from the University of Naples (Italy), that a reliable comparison of the effects of crowding and confinement on the stability of proteins can only be based on the measurement of the whole stability curve of the same protein. Controversial aspects do not pertain only to the influence of crowding on protein stability, but also to aggregation phenomena in natural fluids. Domenico Sanfelice, from NIMR (London, UK), reported an interesting case of the apparent influence of crowding on aggregation. Hen egg white, a possible natural medium to study macromolecules in crowded conditions can dramatically increase the aggregation kinetics of proteins with an inbuilt tendency to associate. By carefully dissecting the phenomenology, it was shown that only part of this effect is due to crowding, while another factor playing an important role is the interaction with proteins from the milieu . In other words, high-molecular-weight glycoproteins can act as efficient molecular seeds for aggregation. A special topic of great relevance in the conference appeared to be the direct study of crowding in living systems. Alan Verkman, from the University of California, San Francisco (USA), one of the world's leading scientific personalities in the field of experimental investigation of crowding and confinement, was invited to give the second plenary lecture devoted to the experimental study of crowding effects in vivo . In his keynote lecture, Dr Verkman led us on a wide and compelling tour, exploring the main experimental approaches to study molecular crowding in and around cells. After a thorough examination of methods such as fluorescence recovery after photo-bleaching, fluorescence correlation spectroscopy, photo-activation localization microscopy and stochastic reconstruction microscopy, he concluded that the general consensus emerging from experimental studies is that the notion of universally anomalous diffusion in and around cells as a consequence of molecular crowding may not be correct, and that the slowing of diffusion in cells is less marked than has been widely assumed and can be simply described through a five- to sixfold reduction of the normal diffusion coefficient. A Soranno, from the University of Zürich (Switzerland), described how, by employing FRET measurements, it is possible to quantify the effect of molecular crowding on the dimensions of the highly charged, intrinsically disordered protein human prothymosin alpha. For a large variety of polymeric crowders (PEG, PVP, Ficoll, Dextran, PVA, PAA), a collapse of the polypeptide chain is observed with increasing polymer size and polymer concentration. The largest extent of collapse is observed for polymer radii comparable to the dimensions of the protein, in agreement with theoretical considerations. For his contribution, A Soranno was awarded the CSF Award for the best contributed talk. In his most inspiring talk, Clifford Brangwynne, from Princeton University (USA), drew attention to very important objects, namely Ribonucleoprotein (RNP) bodies. These are non-membrane-bound macromolecular assemblies that form from the dynamic interactions of RNA and proteins. The assembly of RNP bodies may sensitively depend on the biophysical features of the surrounding cytoplasm, including the degree of crowding, transport coefficients and mechanical properties. This dependency may have important implications for the RNA processing reactions involved in fundamental biological processes such as developmental cell growth. Remarkably, Brangwynne showed how RNPs behave in the cell as liquid droplets, pointing to a possible entirely new means that the cell could use to control and fine-tune its internal processes, in fact, more than that, a completely unexplored, new state of organization of living matter, and a functional one. Giuseppe Zaccai, from Institut Laue Langevin, Grenoble (France), showed that protein dynamics is more sensitive than structure to environmental factors such as crowding, solvent, temperature or pressure. Furthermore, he convincingly explained how neutron scattering provides unique experimental data to underpin MD calculations in this context. Following up on environment-induced modulations of protein functional dynamics, Ruth Nussinov, from Tel Aviv University (Israel), addressed the important problem of whether cellular signals can travel long distances in a crowded environment. She proposed a model based on the evolution of at least three properties: a modular functional organization of the cellular network, sequences in some key regions of proteins, such as linkers or loops, and compact interactions between proteins, possibly favoured by a crowded environment. The workshop ended on a keynote lecture by Jean-Marie Lehn, from the Université de Strasbourg (France). Lehn, 1987 Nobel Laureate in chemistry, offered a 'supramolecular view' of the field of molecular interactions. Supramolecular chemistry explores the design of systems undergoing self-organization , i.e. systems capable of generating well-defined functional supramolecular architectures by self-assembling from their components, thus behaving as programmed chemical systems . Chemistry may therefore be considered an information science , the science of informed matter. Supramolecular chemistry is intrinsically a dynamic chemistry in view of the ability of the interactions connecting the molecular components of a supramolecular entity and the resulting ability of supramolecular species to exchange their constituents. The same holds for molecular chemistry when the molecular entity contains covalent bonds that may form and break reversibly, so as to allow a continuous change in constitution by the reorganization and exchange of building blocks. These features define a constitutional dynamic chemistry (CDC) on both the molecular and supramolecular levels. CDC takes advantage of dynamic constitutional diversity to allow variation and selection in response to either internal or external factors to achieve adaptation . The merging of the features-information and programmability, dynamics and reversibility, constitution and structural diversity-points towards the emergence of adaptive and evolutive chemistry . The whole workshop could have not taken place without the help of the Centro Stefano Franscini. The CSF is the congress centre of the Swiss Federal Institute of Technology of Zurich (ETH Zurich) and has been situated at Monte Verità since 1989. It is an ideal meeting point for all members of the international scientific community who wish to discuss the state-of-the-art and new challenges of any field of research. The CSF supports 20-25 international conferences every year and, since 2010, up to ten winter doctoral schools1. The competence and professionalism of the staff were at the same level of beauty and inspiring character as that of Monte Verità. A meeting of this sort, if successful, leaves the audience with more open questions than settled answers, and this was definitely the case for Crowding 2012. Excluded volume is clearly a fundamental concept that has allowed crowding, a very familiar concept in soft matter, to enter into the domain of biological sciences. However, the complexity of the biological milieu calls for more refined descriptions. What is the role of electrostatic and electrodynamic interactions? What is the role of hydrodynamics interactions? To what extent does the strong spatial inhomogeneity (clustering of molecules, cellular compartmentalization, etc) have to be taken into account? Or, more generally, what are the minimal elements that prove crucial to describe reactions within a cell? How does the diffusion proceed (diffusion, slow diffusion, sub-diffusion) given that the experimental evidences are still controversial? In conclusion, we knew that allowing scientists with very different backgrounds and ideas to mingle was a hazardous attempt. Despite that, the workshop turned out to be a very successful experiment, which was highly enjoyed both by the participants and the organizers. Discussions sparked regularly among ever-changing groups, comprising senior scientists and students, despite the rather tight schedule, adding to the sense of fulfilment ignited by the outstanding level of the presentations. Given the success of the meeting Crowding 2012, a new event has been organized and will take place on the same themes during fall 2013, this time in the beautiful scenery of the Loire valley in France. The workshop 'Macromolecular crowding effects in cell biology: models and experiments' will be held on the CNRS campus in Orléans, France, on 24-25 October 2013. More information can be found on the workshop website: http://dirac.cnrs-orleans.fr/∼piazza/. 1Source: www.csf.ethz.ch/\",\n \"corpus_id\": 3008401,\n \"score\": 2\n },\n {\n \"doc_id\": \"24348227\",\n \"title\": \"Decipher the mechanisms of protein conformational changes induced by nucleotide binding through free-energy landscape analysis: ATP binding to Hsp70.\",\n \"abstract\": \"ATP regulates the function of many proteins in the cell by transducing its binding and hydrolysis energies into protein conformational changes by mechanisms which are challenging to identify at the atomic scale. Based on molecular dynamics (MD) simulations, a method is proposed to analyze the structural changes induced by ATP binding to a protein by computing the effective free-energy landscape (FEL) of a subset of its coordinates along its amino-acid sequence. The method is applied to characterize the mechanism by which the binding of ATP to the nucleotide-binding domain (NBD) of Hsp70 propagates a signal to its substrate-binding domain (SBD). Unbiased MD simulations were performed for Hsp70-DnaK chaperone in nucleotide-free, ADP-bound and ATP-bound states. The simulations revealed that the SBD does not interact with the NBD for DnaK in its nucleotide-free and ADP-bound states whereas the docking of the SBD was found in the ATP-bound state. The docked state induced by ATP binding found in MD is an intermediate state between the initial nucleotide-free and final ATP-bound states of Hsp70. The analysis of the FEL projected along the amino-acid sequence permitted to identify a subset of 27 protein internal coordinates corresponding to a network of 91 key residues involved in the conformational change induced by ATP binding. Among the 91 residues, 26 are identified for the first time, whereas the others were shown relevant for the allosteric communication of Hsp70 s in several experiments and bioinformatics analysis. The FEL analysis revealed also the origin of the ATP-induced structural modifications of the SBD recently measured by Electron Paramagnetic Resonance. The pathway between the nucleotide-free and the intermediate state of DnaK was extracted by applying principal component analysis to the subset of internal coordinates describing the transition. The methodology proposed is general and could be applied to analyze allosteric communication in other proteins.\",\n \"corpus_id\": 6375359,\n \"score\": 2\n },\n {\n \"doc_id\": \"24710069\",\n \"title\": \"Posttranslational Modification of Maize Chloroplast Pyruvate Orthophosphate Dikinase Reveals the Precise Regulatory Mechanism of Its Enzymatic Activity.\",\n \"abstract\": \"In C4 plants, pyruvate orthophosphate dikinase (PPDK) activity is tightly dark/light regulated by reversible phosphorylation of an active-site threonine (Thr) residue; this process is catalyzed by PPDK regulatory protein (PDRP). Phosphorylation and dephosphorylation of PPDK lead to its inactivation and activation, respectively. Here, we show that light intensity rather than the light/dark transition regulates PPDK activity by modulating the reversible phosphorylation at Thr-527 (previously termed Thr-456) of PPDK in maize (Zea mays). The amount of PPDK (unphosphorylated) involved in C4 photosynthesis is indeed strictly controlled by light intensity, despite the high levels of PPDK protein that accumulate in mesophyll chloroplasts. In addition, we identified a transit peptide cleavage site, uncovered partial amino-terminal acetylation, and detected phosphorylation at four serine (Ser)/Thr residues, two of which were previously unknown in maize. In vitro experiments indicated that Thr-527 and Ser-528, but not Thr-309 and Ser-506, are targets of PDRP. Modeling suggests that the two hydrogen bonds between the highly conserved residues Ser-528 and glycine-525 are required for PDRP-mediated phosphorylation of the active-site Thr-527 of PPDK. Taken together, our results suggest that the regulation of maize plastid PPDK isoform (C4PPDK) activity is much more complex than previously reported. These diverse regulatory pathways may work alone or in combination to fine-tune C4PPDK activity in response to changes in lighting.\",\n \"corpus_id\": 1247803,\n \"score\": 2\n },\n {\n \"doc_id\": \"25302667\",\n \"title\": \"ATP-induced conformational changes of nucleotide-binding domains in an ABC transporter. Importance of the water-mediated entropic force.\",\n \"abstract\": \"ATP binding cassette (ABC) proteins belong to a superfamily of active transporters. Recent experimental and computational studies have shown that binding of ATP to the nucleotide binding domains (NBDs) of ABC proteins drives the dimerization of NBDs, which, in turn, causes large conformational changes within the transmembrane domains (TMDs). To elucidate the active substrate transport mechanism of ABC proteins, it is first necessary to understand how the NBD dimerization is driven by ATP binding. In this study, we selected MalKs (NBDs of a maltose transporter) as a representative NBD and calculated the free-energy change upon dimerization using molecular mechanics calculations combined with a statistical thermodynamic theory of liquids, as well as a method to calculate the translational, rotational, and vibrational entropy change. This combined method is applied to a large number of snapshot structures obtained from molecular dynamics simulations containing explicit water molecules. The results suggest that the NBD dimerization proceeds with a large gain of water entropy when ATP molecules bind to the NBDs. The energetic gain arising from direct NBD-NBD interactions is canceled by the dehydration penalty and the configurational-entropy loss. ATP hydrolysis induces a loss of the shape complementarity between the NBDs, which leads to the dissociation of the dimer, due to a decrease in the water-entropy gain and an increase in the configurational-entropy loss. This interpretation of the NBD dimerization mechanism in concert with ATP, especially focused on the water-mediated entropy force, is potentially applicable to a wide variety of the ABC transporters.\",\n \"corpus_id\": 45723390,\n \"score\": 2\n },\n {\n \"doc_id\": \"25430456\",\n \"title\": \"Structural and evolutionary characteristics of pyruvate phosphate dikinase in Giardia lamblia and other amitochondriate protozoa.\",\n \"abstract\": \"BACKGROUND: Pyruvate phosphate dikinase (PPDK) reversibly catalyzes the interconversion of phosphoenolpyruvate (PEP) and pyruvic acid, leading to catabolism and adenosine triphosphate (ATP) synthesis or gluconeogenesis and ATP consumption. Molecular modeling of PPDKs from divergent organisms demonstrates that the orientation of the phosphorylatable histidine residue within the central domain of PPDK determines whether this enzyme promotes catabolism or gluconeogenesis. The goal of this study was to determine whether PDDK from Giardia underwent adaptive evolution in order to produce more energy under anaerobic conditions. METHODS: A total of 123 PPDK sequences from protozoans, proteobacteria, plants, and algae were selected, based upon sequence similarities to Giardia lamblia PPDK and Zea mays PPDK. Three-dimensional (3-D) models were generated for PPDKs from divergent organisms and were used to compare the orientation of the phosphorylatable histidine residue within the central domain of PPDKs. These PPDKs were compared using a maximum-likelihood tree. RESULTS: For PPDK from Giardia, as well as from other anaerobic protozoans, the central domain tilted toward the N-terminal nucleotide-binding domain, indicating that this enzyme catalyzed ATP synthesis. Furthermore, the orientation of this central domain was determined by interactions between the N- and C-terminal domains. Phylogenetic analysis of the N- and C-terminal sequences of PPDKs from different species suggested that PPDK has likely undergone adaptive evolution in response to differences in environmental and metabolic conditions. CONCLUSION: These results suggested that PPDK in anaerobic organisms is functionally adapted to generate energy more efficiently in an anaerobic environment.\",\n \"corpus_id\": 1896825,\n \"score\": 2\n },\n {\n \"doc_id\": \"26148295\",\n \"title\": \"Motion Tree Delineates Hierarchical Structure of Protein Dynamics Observed in Molecular Dynamics Simulation.\",\n \"abstract\": \"Molecular dynamics (MD) simulations of proteins provide important information to understand their functional mechanisms, which are, however, likely to be hidden behind their complicated motions with a wide range of spatial and temporal scales. A straightforward and intuitive analysis of protein dynamics observed in MD simulation trajectories is therefore of growing significance with the large increase in both the simulation time and system size. In this study, we propose a novel description of protein motions based on the hierarchical clustering of fluctuations in the inter-atomic distances calculated from an MD trajectory, which constructs a single tree diagram, named a \\\"Motion Tree\\\", to determine a set of rigid-domain pairs hierarchically along with associated inter-domain fluctuations. The method was first applied to the MD trajectory of substrate-free adenylate kinase to clarify the usefulness of the Motion Tree, which illustrated a clear-cut dynamics picture of the inter-domain motions involving the ATP/AMP lid and the core domain together with the associated amplitudes and correlations. The comparison of two Motion Trees calculated from MD simulations of ligand-free and -bound glutamine binding proteins clarified changes in inherent dynamics upon ligand binding appeared in both large domains and a small loop that stabilized ligand molecule. Another application to a huge protein, a multidrug ATP binding cassette (ABC) transporter, captured significant increases of fluctuations upon binding a drug molecule observed in both large scale inter-subunit motions and a motion localized at a transmembrane helix, which may be a trigger to the subsequent structural change from inward-open to outward-open states to transport the drug molecule. These applications demonstrated the capabilities of Motion Trees to provide an at-a-glance view of various sizes of functional motions inherent in the complicated MD trajectory.\",\n \"corpus_id\": 8385214,\n \"score\": 2\n },\n {\n \"doc_id\": \"26158224\",\n \"title\": \"Analysis of the Free Energy Landscapes for the Opening-Closing Dynamics of the Maltose Transporter ATPase MalK2 Using Enhanced-Sampling Molecular Dynamics Simulation.\",\n \"abstract\": \"Protein dynamics are considered significant for many physiological processes, such as metabolism, biomolecular recognition, and the regulation of several vital cellular processes. Due to their flexibility, proteins may stay in different substates with or without the existence of the cognate substrates. To describe these phenomena, two models have been proposed: the \\\"induced fit\\\" and the \\\"conformational selection\\\" mechanisms. In this study, we used MalK2, the subunits that mainly include the nucleotide-binding domains (NBDs) of the maltose transporter from Escherichia coli, as a target to understand the NBD dimerization mechanism. Accelerated and conventional molecular dynamics have been performed. The results revealed that Mg-ATP binding to MalK2 led to a significant change in the free energy profile and thus stabilized the closed conformation. On the contrary, when Mg-ATP was removed, the open conformation would be favored. The fact that ligand binding induces a drastic free energy change leads to a significant inference: MalK2 dimerization would occur through the induced-fit mechanism rather than the conformational selection mechanism. This study sheds new light on the NBD dimerization mechanism and would be of wide applicability to other ABC transporters.\",\n \"corpus_id\": 206649349,\n \"score\": 2\n },\n {\n \"doc_id\": \"27003459\",\n \"title\": \"Kinetic and molecular characterization of the pyruvate phosphate dikinase from Trypanosoma cruzi.\",\n \"abstract\": \"Trypanosoma cruzi, like other trypanosomatids analyzed so far, can use both glucose and amino acids as carbon and energy source. In these parasites, glycolysis is compartmentalized in glycosomes, authentic but specialized peroxisomes. The major part of this pathway, as well as a two-branched glycolytic auxiliary system, are present in these organelles. The first enzyme of one branch of this auxiliary system is the PPi-dependent pyruvate phosphate dikinase (PPDK) that converts phosphoenolpyruvate (PEP), inorganic pyrophosphate (PPi) and AMP into pyruvate, inorganic phosphate (Pi) and ATP, thus contributing to the ATP/ADP balance within the glycosomes. In this work we cloned, expressed and purified the T. cruzi PPDK. It kinetic parameters were determined, finding KM values for PEP, PPi and AMP of 320, 70 and 17 μM, respectively. Using molecular exclusion chromatography, two native forms of the enzyme were found with estimated molecular weights of 200 and 100 kDa, corresponding to a homodimer and monomer, respectively. It was established that T. cruzi PPDK's specific activity can be enhanced up to 2.6 times by the presence of ammonium in the assay mixture. During growth of epimastigotes in batch culture an apparent decrease in the specific activity of PPDK was observed. However, when its activity is normalized for the presence of ammonium in the medium, no significant modification of the enzyme activity per cell in time was found.\",\n \"corpus_id\": 33222461,\n \"score\": 2\n },\n {\n \"doc_id\": \"27622975\",\n \"title\": \"GPCR Dynamics: Structures in Motion.\",\n \"abstract\": \"The function of G protein-coupled receptors (GPCRs)-which represent the largest class of both human membrane proteins and drug targets-depends critically on their ability to change shape, transitioning among distinct conformations. Determining the structural dynamics of GPCRs is thus essential both for understanding the physiology of these receptors and for the rational design of GPCR-targeted drugs. Here we review what is currently known about the flexibility and dynamics of GPCRs, as determined through crystallography, spectroscopy, and computer simulations. We first provide an overview of the types of motion exhibited by a GPCR and then discuss GPCR dynamics in the context of ligand binding, activation, allosteric modulation, and biased signaling. Finally, we discuss the implications of GPCR conformational plasticity for drug design.\",\n \"corpus_id\": 26075206,\n \"score\": 2\n },\n {\n \"doc_id\": \"28470715\",\n \"title\": \"Trapped intermediate state of plant pyruvate phosphate dikinase indicates substeps in catalytic swiveling domain mechanism.\",\n \"abstract\": \"Pyruvate phosphate dikinase (PPDK) is an essential enzyme of both the C4 photosynthetic pathway and cellular energy metabolism of some bacteria and unicellular protists. In C4 plants, it catalyzes the ATP- and Pi -dependent formation of phosphoenolpyruvate (PEP) while in bacteria and protozoa the ATP-forming direction is used. PPDK is composed out of three distinct domains and exhibits one of the largest single domain movements known today during its catalytic cycle. However, little information about potential intermediate steps of this movement was available. A recent study resolved a discrete intermediate step of PPDK's swiveling movement, shedding light on the details of this intriguing mechanism. Here we present an additional structural intermediate that possibly represents another crucial step in the catalytic cycle of PPDK, providing means to get a more detailed understanding of PPDK's mode of function.\",\n \"corpus_id\": 46462162,\n \"score\": 2\n },\n {\n \"doc_id\": \"28808308\",\n \"title\": \"On the potential alternate binding change mechanism in a dimeric structure of Pyruvate Phosphate Dikinase.\",\n \"abstract\": \"The pyruvate phosphate dikinase (PPDK) reaction mechanism is characterized by a distinct spatial separation of reaction centers and large conformational changes involving an opening-closing motion of the nucleotide-binding domain (NBD) and a swiveling motion of the central domain (CD). However, why PPDK is active only in a dimeric form and to what extent an alternate binding change mechanism could underlie this fact has remained elusive. We performed unbiased molecular dynamics simulations, configurational free energy computations, and rigidity analysis to address this question. Our results support the hypothesis that PPDK dimerization influences the opening-closing motion of the NBDs, and that this influence is mediated via the CDs of both chains. Such an influence would be a prerequisite for an alternate binding change mechanism to occur. To the best of our knowledge, this is the first time that a possible explanation has been suggested as to why only dimeric PPDK is active.\",\n \"corpus_id\": 3288206,\n \"score\": 2\n },\n {\n \"doc_id\": \"29547697\",\n \"title\": \"Atomistic Mechanism of Large-Scale Conformational Transition in a Heterodimeric ABC Exporter.\",\n \"abstract\": \"ATP-binding cassette (ABC) transporters are ATP-driven molecular machines, in which ATP binding and hydrolysis in the nucleotide-binding domains (NBDs) is chemomechanically coupled to large-scale, alternating access conformational changes in the transmembrane domains (TMDs), ultimately leading to the translocation of substrates across biological membranes. The precise nature of the structural dynamics behind the large-scale conformational transition as well as the coupling of NBD and TMD motions is still unresolved. In this work, we combine all-atom molecular dynamics (MD) simulations with electron paramagnetic resonance (EPR) spectroscopy to unravel the atomic-level mechanism of the dynamic conformational transitions underlying the functional working cycle of the heterodimeric ABC exporter TM287/288. Extensive multimicrosecond simulations in an explicit membrane/water environment show how in response to ATP binding, TM287/288 undergoes spontaneous conformational transitions from the inward-facing (IF) state via an occluded (Occ) intermediate to an outward-facing (OF) state. The latter two states have thus far not been characterized at atomic level. ATP-induced tightening of the NBD dimer involves closing and reorientation of the two NBD monomers concomitant with a closure of the intracellular TMD gate, which leads to the occluded state. Subsequently, opening at the extracellular TMD gate yields the OF conformer. The obtained mechanism imposes NBD-TMD coupling via a tight orchestration of conformational transitions, between both the two domains and also within the TMDs, ensuring that the cytoplasmic and periplasmic gate regions are never open simultaneously.\",\n \"corpus_id\": 4583810,\n \"score\": 2\n },\n {\n \"doc_id\": \"29664234\",\n \"title\": \"Characterization of maize leaf pyruvate orthophosphate dikinase using high throughput sequencing.\",\n \"abstract\": \"In C4 photosynthesis, pyruvate orthophosphate dikinase (PPDK) catalyzes the regeneration of phosphoenolpyruvate in the carbon shuttle pathway. Although the biochemical function of PPDK in maize is well characterized, a genetic analysis of PPDK has not been reported. In this study, we use the maize transposable elements Mutator and Ds to generate multiple mutant alleles of PPDK. Loss-of-function mutants are seedling lethal, even when plants were grown under 2% CO2 , and they show very low capacity for CO2 assimilation, indicating C4 photosynthesis is essential in maize. Using RNA-seq and GC-MS technologies, we examined the transcriptional and metabolic responses to a deficiency in PPDK activity. These results indicate loss of PPDK results in downregulation of gene expression of enzymes of the C4 cycle, the Calvin cycle, and components of photochemistry. Furthermore, the loss of PPDK did not change Kranz anatomy, indicating that this metabolic defect in the C4 cycle did not impinge on the morphological differentiation of C4 characters. However, sugar metabolism and nitrogen utilization were altered in the mutants. An interaction between light intensity and genotype was also detected from transcriptome profiling, suggesting altered transcriptional and metabolic responses to environmental and endogenous signals in the PPDK mutants.\",\n \"corpus_id\": 4884084,\n \"score\": 2\n },\n {\n \"doc_id\": \"17710553\",\n \"title\": \"Molecular modeling on pyruvate phosphate dikinase of Entamoeba histolytica and in silico virtual screening for novel inhibitors.\",\n \"abstract\": \"Pyruvate phosphate dikinase (PPDK) is the key enzyme essential for the glycolytic pathway in most common and perilous parasite Entamoeba histolytica. Inhibiting the function of this enzyme could control the wide spread of intestinal infections caused by Entamoeba histolytica in humans. With this objective, we modeled the three dimensional structure of the PPDK protein. We used templates with 51% identity and 67% similarity to employ homology-modeling approach. Stereo chemical quality of protein structure was validated by protein structure validation program PROCHECK and VERIFY3D. Experimental proof available in literature along with the in silico studies indicated Lys21, Arg91, Asp323, Glu325 and Gln337 to be the probable active sites in the target protein. Virtual screening was carried out using the genetic docking algorithm GOLD and a consensus scoring function X-Score to substantiate the prediction. The small molecule libraries (ChemDivision database, Diversity dataset, Kinase inhibitor database) were used for screening process. Along with the high scoring results, the interaction studies provided promising ligands for future experimental screening to inhibit the function of PPDK in Entamoeba histolytica. Further, the phylogeny study was carried out to assess the possibility of using the proposed ligands as inhibitors in related pathogens.\",\n \"corpus_id\": 25026913,\n \"score\": 1\n },\n {\n \"doc_id\": \"18167307\",\n \"title\": \"The catalyzing role of PPDK in Giardia lamblia.\",\n \"abstract\": \"Giardia lamblia is an early branching eukaryotic microorganism that derives its metabolic energy primarily from anaerobic glycolysis. In most organisms, glycolysis is catalyzed by pyruvate kinase (PK), allowing the generation of two ATP molecules from one molecule of pyruvate. Giardia has both PK and pyrophosphate-dependent pyruvate phosphate dikinase (PPDK), which catalyzes the generation of five ATP molecules from pyruvate by pyrophosphate-dependent glycolysis and offers a potential selective advantage. In order to evaluate the importance of pyrophosphate-dependent glycolysis, we used ribozyme-mediated cleavage of the PPDK transcript to decrease PPDK transcript levels to 20% of normal. The accompanying decrease in PPDK enzyme activity decreased ATP levels to 3% of normal and increased glycogen deposition, confirming the importance pyrophosphate-mediated glycolysis that was previously suggested by cell lysate studies. PPDK is not found in vertebrates, so specific inhibitors may be useful for treatment of infections caused by anaerobic protists that depend on pyrophosphate-dependent glycolysis.\",\n \"corpus_id\": 16126604,\n \"score\": 1\n },\n {\n \"doc_id\": \"18539347\",\n \"title\": \"The Wolbachia endosymbiont of Brugia malayi has an active pyruvate phosphate dikinase.\",\n \"abstract\": \"Genome analysis of the glycolytic/gluconeogenic pathway in the Wolbachia endosymbiont from the filarial parasite Brugia malayi (wBm) has revealed that wBm lacks pyruvate kinase (PK) and may instead utilize the enzyme pyruvate phosphate dikinase (PPDK; ATP:pyruvate, orthophosphate phosphotransferase, EC 2.7.9.1). PPDK catalyses the reversible conversion of AMP, PPi and phosphoenolpyruvate (PEP) into ATP, Pi and pyruvate. The glycolytic pathway of most organisms, including mammals, contains exclusively PK for the production of pyruvate from PEP. Therefore, the absence of PPDK in mammals makes the enzyme an attractive Wolbachia drug target. In the present study, we have cloned and expressed an active wBm-PPDK, thereby providing insight into the energy metabolism of the endosymbiont. Our results support the development of wBm-PPDK as a promising new drug target in an anti-symbiotic approach to controlling filarial infection.\",\n \"corpus_id\": 11317709,\n \"score\": 1\n },\n {\n \"doc_id\": \"18539777\",\n \"title\": \"Cool C4 photosynthesis: pyruvate Pi dikinase expression and activity corresponds to the exceptional cold tolerance of carbon assimilation in Miscanthus x giganteus.\",\n \"abstract\": \"The bioenergy feedstock grass Miscanthus x giganteus is exceptional among C(4) species for its high productivity in cold climates. It can maintain photosynthetically active leaves at temperatures 6 degrees C below the minimum for maize (Zea mays), which allows it a longer growing season in cool climates. Understanding the basis for this difference between these two closely related plants may be critical in adapting maize to colder weather. When M. x giganteus and maize grown at 25 degrees C were transferred to 14 degrees C, light-saturated CO(2) assimilation and quantum yield of photosystem II declined by 30% and 40%, respectively, in the first 48 h in these two species. The decline continued in maize but arrested and then recovered partially in M. x giganteus. Within 24 h of the temperature transition, the pyruvate phosphate dikinase (PPDK) protein content per leaf area transiently declined in M. x giganteus but then steadily increased, such that after 7 d the enzyme content was significantly higher than in leaves growing in 25 degrees C. By contrast it declined throughout the chilling period in maize leaves. Rubisco levels remained constant in M. x giganteus but declined in maize. Consistent with increased PPDK protein content, the extractable PPDK activity per unit leaf area (V(max)(,ppdk)) in cold-grown M. x giganteus leaves was higher than in warm-grown leaves, while V(max,ppdk) was lower in cold-grown than in warm-grown maize. The rate of light activation of PPDK was also slower in cold-grown maize than M. x giganteus. The energy of activation (E(a)) of extracted PPDK was lower in cold-grown than warm-grown M. x giganteus but not in maize. The specific activities and E(a) of purified recombinant PPDK from M. x giganteus and maize cloned into Escherichia coli were similar. The increase in PPDK protein in the M. x giganteus leaves corresponded to an increase in PPDK mRNA level. These results indicate that of the two enzymes known to limit C(4) photosynthesis, increase of PPDK, not Rubisco content, corresponds to the recovery and maintenance of photosynthetic capacity. Functionally, increased enzyme concentration is shown to increase stability of M. x giganteus PPDK at low temperature. The results suggest that increases in either PPDK RNA transcription and/or the stability of this RNA are important for the increase in PPDK protein content and activity in M. x giganteus under chilling conditions relative to maize.\",\n \"corpus_id\": 5116393,\n \"score\": 1\n },\n {\n \"doc_id\": \"18926491\",\n \"title\": \"Molecular and biochemical mechanisms in maize endosperm development: the role of pyruvate-Pi-dikinase and Opaque-2 in the control of C/N ratio.\",\n \"abstract\": \"A combined transcriptomic, proteomic and metabolic analysis provided an overview of the main changes occurring in gene expression during maize kernel development. It allowed identifying genes expressed at each developmental stage and the shift occurring from one stage to the other. A major change occurred at the transition from lag phase where final grain size is established to grain filling where starch and protein are accumulated in the endosperm storage tissue. Although the expression of enzymes involved in storage product synthesis is dominant in the accumulation phase, the proportion of protein destination and protein synthesis gene products is still important. Detailed proteomic analysis of metabolism shows an upsurge of the pyruvate-Pi-dikinase (PPDK) in the late filing period (21 DAP onwards) that is interpreted as a switch in the starch/protein balance. This hypothesis is based on biochemical arguments involving the negative effect of PPi on the ADP-glucose pyrophosphorylase (Agpase), a key-enzyme of starch synthesis, and the role of phosphoenolpyruvate (PEP) in aromatic amino acid synthesis. It is substantiated by the data on the Opaque-2 gene encoding a transcription factor with pleiotropic effect affecting lysine content and carbohydrate metabolism, thus acting indirectly on starch/amino acid ratio. The direct effect of O2 on PPDK gene expression provides a clue for explaining the competition between C and N metabolisms. This epistatic relationship between PPDK and O2 is further supported by quantitative and association genetics.\",\n \"corpus_id\": 34076948,\n \"score\": 1\n },\n {\n \"doc_id\": \"19754142\",\n \"title\": \"Molecular dynamics and quantum mechanics of RNA: conformational and chemical change we can believe in.\",\n \"abstract\": \"Structure and dynamics are both critical to RNA's vital functions in biology. Numerous techniques can elucidate the structural dynamics of RNA, but computational approaches based on experimental data arguably hold the promise of providing the most detail. In this Account, we highlight areas wherein molecular dynamics (MD) and quantum mechanical (QM) techniques are applied to RNA, particularly in relation to complementary experimental studies. We have expanded on atomic-resolution crystal structures of RNAs in functionally relevant states by applying explicit solvent MD simulations to explore their dynamics and conformational changes on the submicrosecond time scale. MD relies on simplified atomistic, pairwise additive interaction potentials (force fields). Because of limited sampling, due to the finite accessible simulation time scale and the approximated force field, high-quality starting structures are required. Despite their imperfection, we find that currently available force fields empower MD to provide meaningful and predictive information on RNA dynamics around a crystallographically defined energy minimum. The performance of force fields can be estimated by precise QM calculations on small model systems. Such calculations agree reasonably well with the Cornell et al. AMBER force field, particularly for stacking and hydrogen-bonding interactions. A final verification of any force field is accomplished by simulations of complex nucleic acid structures. The performance of the Cornell et al. AMBER force field generally corresponds well with and augments experimental data, but one notable exception could be the capping loops of double-helical stems. In addition, the performance of pairwise additive force fields is obviously unsatisfactory for inclusion of divalent cations, because their interactions lead to major polarization and charge-transfer effects neglected by the force field. Neglect of polarization also limits, albeit to a lesser extent, the description accuracy of other contributions, such as interactions with monovalent ions, conformational flexibility of the anionic sugar-phosphate backbone, hydrogen bonding, and solute polarization by solvent. Still, despite limitations, MD simulations are a valid tool for analyzing the structural dynamics of existing experimental structures. Careful analysis of MD simulations can identify problematic aspects of an experimental RNA structure, unveil structural characteristics masked by experimental constraints, reveal functionally significant stochastic fluctuations, evaluate the structural role of base ionization, and predict structurally and potentially functionally important details of the solvent behavior, including the presence of tightly bound water molecules. Moreover, combining classical MD simulations with QM calculations in hybrid QM/MM approaches helps in the assessment of the plausibility of chemical mechanisms of catalytic RNAs (ribozymes). In contrast, the reliable prediction of structure from sequence information is beyond the applicability of MD tools. The ultimate utility of computational studies in understanding RNA function thus requires that the results are neither blindly accepted nor flatly rejected, but rather considered in the context of all available experimental data, with great care given to assessing limitations through the available starting structures, force field approximations, and sampling limitations. The examples given in this Account showcase how the judicious use of basic MD simulations has already served as a powerful tool to help evaluate the role of structural dynamics in biological function of RNA.\",\n \"corpus_id\": 9121507,\n \"score\": 1\n },\n {\n \"doc_id\": \"20202167\",\n \"title\": \"Cytosolic pyruvate,orthophosphate dikinase functions in nitrogen remobilization during leaf senescence and limits individual seed growth and nitrogen content.\",\n \"abstract\": \"The protein content of seeds determines their nutritive value, downstream processing properties and market value. Up to 95% of seed protein is derived from amino acids that are exported to the seed after degradation of existing protein in leaves, but the pathways responsible for this nitrogen metabolism are poorly defined. The enzyme pyruvate,orthophosphate dikinase (PPDK) interconverts pyruvate and phosphoenolpyruvate, and is found in both plastids and the cytosol in plants. PPDK plays a cardinal role in C(4) photosynthesis, but its role in the leaves of C(3) species has remained unclear. We demonstrate that both the cytosolic and chloroplastic isoforms of PPDK are up-regulated in naturally senescing leaves. Cytosolic PPDK accumulates preferentially in the veins, while chloroplastic PPDK also accumulates in mesophyll cells. Analysis of microarrays and labelling patterns after feeding (13)C-labelled pyruvate indicated that PPDK functions in a pathway that generates the transport amino acid glutamine, which is then loaded into the phloem. In Arabidopsis thaliana, over-expression of PPDK during senescence can significantly accelerate nitrogen remobilization from leaves, and thereby increase rosette growth rate and the weight and nitrogen content of seeds. This indicates an important role for cytosolic PPDK in the leaves of C(3) plants, and allows us to propose a metabolic pathway that is responsible for production of transport amino acids during natural leaf senescence. Given that increased seed size and nitrogen content are desirable agronomic traits, and that efficient remobilization of nitrogen within the plant reduces the demand for fertiliser applications, PPDK and the pathway in which it operates are targets for crop improvement.\",\n \"corpus_id\": 23973453,\n \"score\": 1\n },\n {\n \"doc_id\": \"22024416\",\n \"title\": \"Robust control of PEP formation rate in the carbon fixation pathway of C(4) plants by a bi-functional enzyme.\",\n \"abstract\": \"BACKGROUND: C(4) plants such as corn and sugarcane assimilate atmospheric CO(2) into biomass by means of the C(4) carbon fixation pathway. We asked how PEP formation rate, a key step in the carbon fixation pathway, might work at a precise rate, regulated by light, despite fluctuations in substrate and enzyme levels constituting and regulating this process. RESULTS: We present a putative mechanism for robustness in C(4) carbon fixation, involving a key enzyme in the pathway, pyruvate orthophosphate dikinase (PPDK), which is regulated by a bifunctional enzyme, Regulatory Protein (RP). The robust mechanism is based on avidity of the bifunctional enzyme RP to its multimeric substrate PPDK, and on a product-inhibition feedback loop that couples the system output to the activity of the bifunctional regulator. The model provides an explanation for several unusual biochemical characteristics of the system and predicts that the system's output, phosphoenolpyruvate (PEP) formation rate, is insensitive to fluctuations in enzyme levels (PPDK and RP), substrate levels (ATP and pyruvate) and the catalytic rate of PPDK, while remaining sensitive to the system's input (light levels). CONCLUSIONS: The presented PPDK mechanism is a new way to achieve robustness using product inhibition as a feedback loop on a bifunctional regulatory enzyme. This mechanism exhibits robustness to protein and metabolite levels as well as to catalytic rate changes. At the same time, the output of the system remains tuned to input levels.\",\n \"corpus_id\": 5003497,\n \"score\": 1\n },\n {\n \"doc_id\": \"22392278\",\n \"title\": \"Preliminary analysis to target pyruvate phosphate dikinase from wolbachia endosymbiont of Brugia malayi for designing anti-filarial agents.\",\n \"abstract\": \"Filariasis causing nematode Brugia malayi is shown to harbor wolbachia bacteria as symbionts. The sequenced genome of the wolbachia endosymbiont from B.malayi (wBm) offers an unprecedented opportunity to identify new wolbachia drug targets. Genome analysis of the glycolytic/gluconeogenic pathway has revealed that wBm lacks pyruvate kinase (PK) and may instead utilize the enzyme pyruvate phosphate dikinase (PPDK; ATP: pyruvate, orthophosphate phosphotransferase, EC 2.7.9.1). PPDK catalyses the reversible conversion of AMP, PPi and phosphoenolpyruvate into ATP, Pi and pyruvate. Most organisms including mammals exclusively possess PK. Therefore the absence of PPDK in mammals makes this enzyme as attractive wolbachia drug target. In the present study we have modeled the three dimensional structure of wBm PPDK. The template with 50% identity and 67% similarity in amino acid sequence was employed for homology-modeling approach. The putative active site consists of His476, Arg360, Glu358, Asp344, Arg112, Lys43 and Glu346 was selected as site of interest for designing suitable inhibitor molecules. Docking studies were carried out using induced fit algorithms with OPLS force field of Schrödinger's Glide. The lead molecules which inhibit the PPDK activity are taken from the small molecule library (Pubchem database) and the interaction analysis showed that these compounds may inhibit the function of PPDK in wBm.\",\n \"corpus_id\": 15776013,\n \"score\": 1\n },\n {\n \"doc_id\": \"23030682\",\n \"title\": \"Phosphoproteomic analysis of Rhodopseudomonas palustris reveals the role of pyruvate phosphate dikinase phosphorylation in lipid production.\",\n \"abstract\": \"Rhodopseudomonas palustris (R. palustris) is a purple nonsulfur anoxygenic phototrophic bacterium with metabolic versatility and is able to grow under photoheterotrophic and chemoheterotrophic states. It has uses in carbon management, carbon recycling, hydrogen generation, and lipid production; therefore, it has the potential for bioenergy production and biodegradation. This study is the first to identify the phosphoproteome of R. palustris including 100 phosphopeptides from 54 phosphoproteins and 74 phosphopeptides from 42 phosphoproteins in chemoheterotrophic and photoheterotrophic growth conditions, respectively. In the identified phosphoproteome, phosphorylation at the threonine residue, Thr487, of pyruvate phosphate dikinase (PPDK, RPA1051) was found to participate in the regulation of carbon metabolism. Here, we show that PPDK enzyme activity is higher in photoheterotrophic growth, with Thr487 phosphorylation as a possible mediator. Under the same photoheterotrophic conditions, R. palustris with overexpressed wild-type PPDK showed an enhanced accumulation of total lipids than those with mutant PPDK (T487V) form. This study reveals the role of the PPDK in the production of biodiesel material, lipid content, with threonyl-phosphorylation as one of the possible regulatory events during photoheterotrophic growth in R. palustris.\",\n \"corpus_id\": 26046855,\n \"score\": 1\n },\n {\n \"doc_id\": \"23094589\",\n \"title\": \"Design, synthesis, and evaluation of inhibitors of pyruvate phosphate dikinase.\",\n \"abstract\": \"Pyruvate phosphate dikinase (PPDK) catalyzes the phosphorylation reaction of pyruvate that forms phosphoenolpyruvate (PEP) via two partial reactions: PPDK + ATP + P(i) → PPDK-P + AMP + PP(i) and PPDK-P + pyruvate → PEP + PPDK. Based on its role in the metabolism of microbial human pathogens, PPDK is a potential drug target. A screen of substances that bind to the PPDK ATP-grasp domain active site revealed that flavone analogues are potent inhibitors of the Clostridium symbiosum PPDK. In silico modeling studies suggested that placement of a 3–6 carbon-tethered ammonium substituent at the 3′- or 4′-positions of 5,7-dihydroxyflavones would result in favorable electrostatic interactions with the PPDK Mg-ATP binding site. As a result, polymethylene-tethered amine derivatives of 5,7-dihydroxyflavones were prepared. Steady-state kinetic analysis of these substances demonstrates that the 4′-aminohexyl-5,7-dyhydroxyflavone 10 is a potent competitive PPDK inhibitor (K(i) = 1.6 ± 0.1 μM). Single turnover experiments were conducted using 4′-aminopropyl-5,7-dihydroxyflavone 7 to show that this flavone specifically targets the ATP binding site and inhibits catalysis of only the PPDK + ATP + P(i) → PPDK-P + AMP PP(i) partial reaction. Finally, the 4′-aminopbutyl-5,7-dihydroxyflavone 8 displays selectivity for inhibition of PPDK versus other enzymes that utilize ATP and NAD.\",\n \"corpus_id\": 13391283,\n \"score\": 1\n },\n {\n \"doc_id\": \"23573213\",\n \"title\": \"An asymmetric post-hydrolysis state of the ABC transporter ATPase dimer.\",\n \"abstract\": \"ABC transporters are a superfamily of enzyme pumps that hydrolyse ATP in exchange for translocation of substrates across cellular membranes. Architecturally, ABC transporters are a dimer of transmembrane domains coupled to a dimer of nucleotide binding domains (NBDs): the NBD dimer contains two ATP-binding sites at the intersubunit interface. A current controversy is whether the protomers of the NBD dimer separate during ATP hydrolysis cycling, or remain in constant contact. In order to investigate the ABC ATPase catalytic mechanism, MD simulations using the recent structure of the ADP+Pi-bound MJ0796 isolated NBD dimer were performed. In three independent simulations of the ADP+Pi/apo state, comprising a total of >0.5 µs, significant opening of the apo (empty) active site was observed; occurring by way of intrasubunit rotations between the core and helical subdomains within both NBD monomers. In contrast, in three equivalent simulations of the ATP/apo state, the NBD dimer remained close to the crystal structure, and no opening of either active site occurred. The results thus showed allosteric coupling between the active sites, mediated by intrasubunit conformational changes. Opening of the apo site is exquisitely tuned to the nature of the ligand, and thus to the stage of the reaction cycle, in the opposite site. In addition to this, in also showing how one active site can open, sufficient to bind nucleotide, while the opposite site remains occluded and bound to the hydrolysis products ADP+Pi, the results are consistent with a Constant Contact Model. Conversely, they show how there may be no requirement for the NBD protomers to separate to complete the catalytic cycle.\",\n \"corpus_id\": 4031916,\n \"score\": 1\n },\n {\n \"doc_id\": \"23737004\",\n \"title\": \"Activities of principal photosynthetic enzymes in green macroalga Ulva linza: functional implication of C₄ pathway in CO₂ assimilation.\",\n \"abstract\": \"The green-tide-forming macroalga Ulva linza was profiled by transcriptome sequencing to ascertain whether the alga carries both C3 and C4 photosynthesis genes. The key enzymes involved in C4 metabolism including pyruvate orthophosphate dikinase (PPDK), phosphoenolpyruvate carboxylase (PEPC), and phosphoenolpyruvate carboxykinase (PCK) were found. When measured under normal and different stress conditions, expression of rbcL was higher under normal conditions and lower under the adverse conditions, whereas that of PPDK was higher under some adverse conditions, namely desiccation, high salinity, and low salinity. Both ribulose-1, 5-biphosphate carboxylase (RuBPCase) and PPDK were found to play a role in carbon fixation, with significantly higher PPDK activity across the stress conditions. These results suggest that elevated PPDK activity alters carbon metabolism in U. linza leading to partial operation of the C4 carbon metabolism, a pathway that, under stress conditions, probably contributes to the hardy character of U. linza and thus to its wide distribution.\",\n \"corpus_id\": 1450913,\n \"score\": 1\n },\n {\n \"doc_id\": \"23936827\",\n \"title\": \"Molecular dynamics studies on the conformational transitions of adenylate kinase: a computational evidence for the conformational selection mechanism.\",\n \"abstract\": \"Escherichia coli adenylate kinase (ADK) is a monomeric phosphotransferase enzyme that catalyzes reversible transfer of phosphoryl group from ATP to AMP with a large-scale domain motion. The detailed mechanism for this conformational transition remains unknown. In the current study, we performed long time-scale molecular dynamics simulations on both open and closed states of ADK. Based on the structural analyses of the simulation trajectories, we detected over 20 times conformational transitions between the open and closed states of ADK and identified two novel conformations as intermediate states in the catalytic processes. With these findings, we proposed a possible mechanism for the large-scale domain motion of Escherichia coli ADK and its catalytic process: (1) the substrate free ADK adopted an open conformation; (2) ATP bound with LID domain closure; (3) AMP bound with NMP domain closure; (4) phosphoryl transfer occurred with ATP, and AMP converted into two ADPs, and no conformational transition was detected in the enzyme; (5) LID domain opened with one ADP released; (6) another ADP released with NMP domain open. As both open and closed states sampled a wide range of conformation transitions, our simulation strongly supported the conformational selection mechanism for Escherichia coli ADK.\",\n \"corpus_id\": 61270,\n \"score\": 1\n },\n {\n \"doc_id\": \"24060543\",\n \"title\": \"Post-translational modification of the pyruvate phosphate dikinase from Trypanosoma cruzi.\",\n \"abstract\": \"In kinetoplastids such as Trypanosoma cruzi, glycolysis is compartmentalized in peroxisome-like organelles called glycosomes. Pyruvate phosphate dikinase (PPDK), an auxiliary enzyme of glycolysis, is also located in the glycosomes. We have detected that this protein is post-translationally modified by phosphorylation and proteolytic cleavage. On western blots of T. cruzi epimastigotes, two PPDK forms were found with apparent MW of 100 kDa and 75 kDa, the latter one being phosphorylated at Thr481, a residue present in a highly conserved region. In subcellular localization assays the 75 kDa PPDK was located peripherally at the glycosomal membrane. Both PPDK forms were found in all life-cycle stages of the parasite. When probing for both PPDK forms during a growth of epimastigotes in batch culture, an increase in the level of the 75 kDa form and a decrease of the 100 kDa one were observed by western blot analysis, signifying that glucose starvation and the concomitant switch of the metabolism to amino acid catabolism may play a role in the post-translational processing of the PPDK. Either one or both of the processes, phosphorylation and proteolytic cleavage of PPDK, result in inactivation of the enzyme. It remains to be established whether the phenomenon exerts a regulatory function.\",\n \"corpus_id\": 116325,\n \"score\": 1\n },\n {\n \"doc_id\": \"24062450\",\n \"title\": \"Phosphate release coupled to rotary motion of F1-ATPase.\",\n \"abstract\": \"F1-ATPase, the catalytic domain of ATP synthase, synthesizes most of the ATP in living organisms. Running in reverse powered by ATP hydrolysis, this hexameric ring-shaped molecular motor formed by three αβ-dimers creates torque on its central γ-subunit. This reverse operation enables detailed explorations of the mechanochemical coupling mechanisms in experiment and simulation. Here, we use molecular dynamics simulations to construct a first atomistic conformation of the intermediate state following the 40° substep of rotary motion, and to study the timing and molecular mechanism of inorganic phosphate (Pi) release coupled to the rotation. In response to torque-driven rotation of the γ-subunit in the hydrolysis direction, the nucleotide-free αβE interface forming the \\\"empty\\\" E site loosens and singly charged Pi readily escapes to the P loop. By contrast, the interface stays closed with doubly charged Pi. The γ-rotation tightens the ATP-bound αβTP interface, as required for hydrolysis. The calculated rate for the outward release of doubly charged Pi from the αβE interface 120° after ATP hydrolysis closely matches the ~1-ms functional timescale. Conversely, Pi release from the ADP-bound αβDP interface postulated in earlier models would occur through a kinetically infeasible inward-directed pathway. Our simulations help reconcile conflicting interpretations of single-molecule experiments and crystallographic studies by clarifying the timing of Pi exit, its pathway and kinetics, associated changes in Pi protonation, and changes of the F1-ATPase structure in the 40° substep. Important elements of the molecular mechanism of Pi release emerging from our simulations appear to be conserved in myosin despite the different functional motions.\",\n \"corpus_id\": 205263440,\n \"score\": 1\n },\n {\n \"doc_id\": \"24484954\",\n \"title\": \"Phosphoenolpyruvate carboxylase, NADP-malic enzyme, and pyruvate, phosphate dikinase are involved in the acclimation of Nicotiana tabacum L. to drought stress.\",\n \"abstract\": \"Drought stress is one of the most frequent forms of abiotic stresses, which occurs under condition of limited water availability. In this work, the possible participation of phosphoenolpyruvate carboxylase (EC 4.1.1.31; PEPC), NADP-malic enzyme (EC 1.1.1.40; NADP-ME), and pyruvate, phosphate dikinase (EC 2.7.9.1; PPDK) in response to drought of tobacco plants (Nicotiana tabacum L., cv. W38) was investigated. Enzyme specific activities in tobacco leaves of drought stressed plants were significantly increased after 11 days of stress, PEPC 2.3-fold, NADP-ME 3.9-fold, and PPDK 2.7-fold compared to control plants. The regulation of PEPC and NADP-ME activities were studied on transcriptional level by the quantitative RT PCR and on translational level - immunochemically. The amount of NADP-ME protein and transcription of mRNA for chloroplastic NADP-ME isoform were increased indicating their enhanced synthesis de novo. On the other hand, mRNA for cytosolic isoform of NADP-ME was decreased. The changes in PEPC protein and PEPC mRNA were not substantial. Therefore regulation of PEPC activity by phosphorylation was evaluated and found to be involved in the stress response. During recovery, activities of the tested enzymes returned close to their basal levels.\",\n \"corpus_id\": 20050452,\n \"score\": 1\n },\n {\n \"doc_id\": \"24632881\",\n \"title\": \"Structural characterization of two metastable ATP-bound states of P-glycoprotein.\",\n \"abstract\": \"ATP Binding Cassette (ABC) transporters couple the binding and hydrolysis of ATP to the transport of substrate molecules across the membrane. The mechanism by which ATP binding and/or hydrolysis drives the conformational changes associated with substrate transport has not yet been characterized fully. Here, changes in the conformation of the ABC export protein P-glycoprotein on ATP binding are examined in a series of molecular dynamics simulations. When one molecule of ATP is placed at the ATP binding site associated with each of the two nucleotide binding domains (NBDs), the membrane-embedded P-glycoprotein crystal structure adopts two distinct metastable conformations. In one, each ATP molecule interacts primarily with the Walker A motif of the corresponding NBD. In the other, the ATP molecules interacts with both Walker A motif of one NBD and the Signature motif of the opposite NBD inducing the partial dimerization of the NBDs. This interaction is more extensive in one of the two ATP binding site, leading to an asymmetric structure. The overall conformation of the transmembrane domains is not altered in either of these metastable states, indicating that the conformational changes associated with ATP binding observed in the simulations in the absence of substrate do not lead to the outward-facing conformation and thus would be insufficient in themselves to drive transport. Nevertheless, the metastable intermediate ATP-bound conformations observed are compatible with a wide range of experimental cross-linking data demonstrating the simulations do capture physiologically important conformations. Analysis of the interaction between ATP and its cofactor Mg(2+) with each NBD indicates that the coordination of ATP and Mg(2+) differs between the two NBDs. The role structural asymmetry may play in ATP binding and hydrolysis is discussed. Furthermore, we demonstrate that our results are not heavily influenced by the crystal structure chosen for initiation of the simulations.\",\n \"corpus_id\": 18460867,\n \"score\": 1\n },\n {\n \"doc_id\": \"24794874\",\n \"title\": \"Contribution of pyruvate phosphate dikinase in the maintenance of the glycosomal ATP/ADP balance in the Trypanosoma brucei procyclic form.\",\n \"abstract\": \"Trypanosoma brucei belongs to a group of protists that sequester the first six or seven glycolytic steps inside specialized peroxisomes, named glycosomes. Because of the glycosomal membrane impermeability to nucleotides, ATP molecules consumed by the first glycolytic steps need to be regenerated in the glycosomes by kinases, such as phosphoenolpyruvate carboxykinase (PEPCK). The glycosomal pyruvate phosphate dikinase (PPDK), which reversibly converts phosphoenolpyruvate into pyruvate, could also be involved in this process. To address this question, we analyzed the metabolism of the main carbon sources used by the procyclic trypanosomes (glucose, proline, and threonine) after deletion of the PPDK gene in the wild-type (Δppdk) and PEPCK null (Δppdk/Δpepck) backgrounds. The rate of acetate production from glucose is 30% reduced in the Δppdk mutant, whereas threonine-derived acetate production is not affected, showing that PPDK function in the glycolytic direction with production of ATP in the glycosomes. The Δppdk/Δpepck mutant incubated in glucose as the only carbon source showed a 3.8-fold reduction of the glycolytic rate compared with the Δpepck mutant, as a consequence of the imbalanced glycosomal ATP/ADP ratio. The role of PPDK in maintenance of the ATP/ADP balance was confirmed by expressing the glycosomal phosphoglycerate kinase (PGKC) in the Δppdk/Δpepck cell line, which restored the glycolytic flux. We also observed that expression of PGKC is lethal for procyclic trypanosomes, as a consequence of ATP depletion, due to glycosomal relocation of cytosolic ATP production. This illustrates the key roles played by glycosomal and cytosolic kinases, including PPDK, to maintain the cellular ATP/ADP homeostasis.\",\n \"corpus_id\": 43731412,\n \"score\": 1\n },\n {\n \"doc_id\": \"25046577\",\n \"title\": \"Low CO2 results in a rearrangement of carbon metabolism to support C4 photosynthetic carbon assimilation in Thalassiosira pseudonana.\",\n \"abstract\": \"The mechanisms of carbon concentration in marine diatoms are controversial. At low CO2 , decreases in O2 evolution after inhibition of phosphoenolpyruvate carboxylases (PEPCs), and increases in PEPC transcript abundances, have been interpreted as evidence for a C4 mechanism in Thalassiosira pseudonana, but the ascertainment of which proteins are responsible for the subsequent decarboxylation and PEP regeneration steps has been elusive. We evaluated the responses of T. pseudonana to steady-state differences in CO2 availability, as well as to transient shifts to low CO2 , by integrated measurements of photosynthetic parameters, transcript abundances and quantitative proteomics. On shifts to low CO2 , two PEPC transcript abundances increased and then declined on timescales consistent with recoveries of Fv /Fm , non-photochemical quenching (NPQ) and maximum chlorophyll a-specific carbon fixation (Pmax ), but transcripts for archetypical decarboxylation enzymes phosphoenolpyruvate carboxykinase (PEPCK) and malic enzyme (ME) did not change. Of 3688 protein abundances measured, 39 were up-regulated under low CO2 , including both PEPCs and pyruvate carboxylase (PYC), whereas ME abundance did not change and PEPCK abundance declined. We propose a closed-loop biochemical model, whereby T. pseudonana produces and subsequently decarboxylates a C4 acid via PEPC2 and PYC, respectively, regenerates phosphoenolpyruvate (PEP) from pyruvate in a pyruvate phosphate dikinase-independent (but glycine decarboxylase (GDC)-dependent) manner, and recuperates photorespiratory CO2 as oxaloacetate (OAA).\",\n \"corpus_id\": 1080606,\n \"score\": 1\n },\n {\n \"doc_id\": \"25288791\",\n \"title\": \"Gluconeogenesis in Leishmania mexicana: contribution of glycerol kinase, phosphoenolpyruvate carboxykinase, and pyruvate phosphate dikinase.\",\n \"abstract\": \"Gluconeogenesis is an active pathway in Leishmania amastigotes and is essential for their survival within the mammalian cells. However, our knowledge about this pathway in trypanosomatids is very limited. We investigated the role of glycerol kinase (GK), phosphoenolpyruvate carboxykinase (PEPCK), and pyruvate phosphate dikinase (PPDK) in gluconeogenesis by generating the respective Leishmania mexicana Δgk, Δpepck, and Δppdk null mutants. Our results demonstrated that indeed GK, PEPCK, and PPDK are key players in the gluconeogenesis pathway in Leishmania, although stage-specific differences in their contribution to this pathway were found. GK participates in the entry of glycerol in promastigotes and amastigotes; PEPCK participates in the entry of aspartate in promastigotes, and PPDK is involved in the entry of alanine in amastigotes. Furthermore, the majority of alanine enters into the pathway via decarboxylation of pyruvate in promastigotes, whereas pathway redundancy is suggested for the entry of aspartate in amastigotes. Interestingly, we also found that l-lactate, an abundant glucogenic precursor in mammals, was used by Leishmania amastigotes to synthesize mannogen, entering the pathway through PPDK. On the basis of these new results, we propose a revision in the current model of gluconeogenesis in Leishmania, emphasizing the differences between amastigotes and promastigotes. This work underlines the importance of studying the trypanosomatid intracellular life cycle stages to gain a better understanding of the pathologies caused in humans.\",\n \"corpus_id\": 7844378,\n \"score\": 1\n },\n {\n \"doc_id\": \"25537000\",\n \"title\": \"Decrypting the structural, dynamic, and energetic basis of a monomeric kinesin interacting with a tubulin dimer in three ATPase states by all-atom molecular dynamics simulation.\",\n \"abstract\": \"We have employed molecular dynamics (MD) simulation to investigate, with atomic details, the structural dynamics and energetics of three major ATPase states (ADP, APO, and ATP state) of a human kinesin-1 monomer in complex with a tubulin dimer. Starting from a recently solved crystal structure of ATP-like kinesin-tubulin complex by the Knossow lab, we have used flexible fitting of cryo-electron-microscopy maps to construct new structural models of the kinesin-tubulin complex in APO and ATP state, and then conducted extensive MD simulations (total 400 ns for each state), followed by flexibility analysis, principal component analysis, hydrogen bond analysis, and binding free energy analysis. Our modeling and simulation have revealed key nucleotide-dependent changes in the structure and flexibility of the nucleotide-binding pocket (featuring a highly flexible and open switch I in APO state) and the tubulin-binding site, and allosterically coupled motions driving the APO to ATP transition. In addition, our binding free energy analysis has identified a set of key residues involved in kinesin-tubulin binding. On the basis of our simulation, we have attempted to address several outstanding issues in kinesin study, including the possible roles of β-sheet twist and neck linker docking in regulating nucleotide release and binding, the structural mechanism of ADP release, and possible extension and shortening of α4 helix during the ATPase cycle. This study has provided a comprehensive structural and dynamic picture of kinesin's major ATPase states, and offered promising targets for future mutational and functional studies to investigate the molecular mechanism of kinesin motors.\",\n \"corpus_id\": 2983740,\n \"score\": 1\n },\n {\n \"doc_id\": \"26620526\",\n \"title\": \"Structural basis of reversible phosphorylation by maize pyruvate orthophosphate dikinase regulatory protein (PDRP).\",\n \"abstract\": \"Pyruvate orthophosphate dikinase (PPDK) is one of the most important enzymes in C4 photosynthesis. PPDK regulatory protein (PDRP) regulates the Pi-dependent activation and ADP-dependent inactivation of PPDK by reversible phosphorylation. PDRP shares no significant sequence similarity with other protein kinases or phosphatases. To investigate the molecular mechanism by which PDRP carries out its dual and competing activities, we determined the first crystal structure of PDRP from maize (Zea mays). PDRP forms a compact homo-dimer in which each protomer contains two separate N-terminal (NTD) and C-terminal (CTD) domains. The CTD includes several key elements for performing both phosphorylation and dephosphorylation activities: the P-loop for binding the ADP and inorganic phosphate substrates, residues Lys274 and Lys299 for neutralizing the negative charge, and residue Asp277 for protonating and deprotonating the target threonine residue of PPDK to promote nucleophilic attack. Surprisingly, the NTD shares the same protein fold as the CTD, and also includes a putative P-loop with AMP bound but lacking enzymatic activities. Structural analysis indicated that this loop may participate in the interaction with and regulation of PPDK. The NTD has conserved intramolecular and intermolecular disulfide bonds for PDRP dimerization. Moreover, PDRP is the first structure of the DUF299 (domain of unknown function 299) enzyme family. This study provides a structural basis for understanding the catalytic mechanism of PDRP and offers a foundation for development of selective activators or inhibitors that regulate photosynthesis.\",\n \"corpus_id\": 21143557,\n \"score\": 1\n },\n {\n \"doc_id\": \"26968775\",\n \"title\": \"Trypanosoma evansi contains two auxiliary enzymes of glycolytic metabolism: Phosphoenolpyruvate carboxykinase and pyruvate phosphate dikinase.\",\n \"abstract\": \"Trypanosoma evansi is a monomorphic protist that can infect horses and other animal species of economic importance for man. Like the bloodstream form of the closely related species Trypanosoma brucei, T. evansi depends exclusively on glycolysis for its free-energy generation. In T. evansi as in other kinetoplastid organisms, the enzymes of the major part of the glycolytic pathway are present within organelles called glycosomes, which are authentic but specialized peroxisomes. Since T. evansi does not undergo stage-dependent differentiations, it occurs only as bloodstream forms, it has been assumed that the metabolic pattern of this parasite is identical to that of the bloodstream form of T. brucei. However, we report here the presence of two additional enzymes, phosphoenolpyruvate carboxykinase and PPi-dependent pyruvate phosphate dikinase in T. evansi glycosomes. Their colocalization with glycolytic enzymes within the glycosomes of this parasite has not been reported before. Both enzymes can make use of PEP for contributing to the production of ATP within the organelles. The activity of these enzymes in T. evansi glycosomes drastically changes the model assumed for the oxidation of glucose by this parasite.\",\n \"corpus_id\": 26726736,\n \"score\": 1\n },\n {\n \"doc_id\": \"27933791\",\n \"title\": \"Mechanistic Insights from the Crystal Structure of Bacillus subtilis o-Succinylbenzoyl-CoA Synthetase Complexed with the Adenylate Intermediate.\",\n \"abstract\": \"o-Succinylbenzoyl-CoA (OSB-CoA) synthetase, or MenE, catalyzes an essential step in vitamin K biosynthesis and is a valuable drug target. Like many other adenylating enzymes, it changes its structure to accommodate substrate binding, catalysis, and product release along the path of a domain alternation catalytic mechanism. We have determined the crystal structure of its complex with the adenylation product, o-succinylbenzoyl-adenosine monophosphate (OSB-AMP), and captured a new postadenylation state. This structure presents unique features such as a strained conformation for the bound adenylate intermediate to indicate that it represents the enzyme state after completion of the adenylation reaction but before release of the C domain in its transition to the thioesterification conformation. By comparison to the ATP-bound preadenylation conformation, structural changes are identified in both the reactants and the active site to allow inference about how these changes accommodate and facilitate the adenylation reaction and to directly support an in-line backside attack nucleophilic substitution mechanism for the first half-reaction. Mutational analysis suggests that the conserved His196 plays an important role in desolvation of the active site rather than stabilizing the transition state of the adenylation reaction. In addition, comparison of the new structure with a previously determined OSB-AMP-bound structure of the same enzyme allows us to propose a release mechanism of the C domain in its alteration to form the thioesterification conformation. These findings allow us to better understand the domain alternation catalytic mechanism of MenE as well as many other adenylating enzymes.\",\n \"corpus_id\": 11442071,\n \"score\": 1\n },\n {\n \"doc_id\": \"28240893\",\n \"title\": \"How Intrinsic Dynamics Mediates the Allosteric Mechanism in the ABC Transporter Nucleotide Binding Domain Dimer.\",\n \"abstract\": \"A protein's architecture facilitates specific motions-intrinsic dynamic modes-that are employed to effect function. Here we used molecular dynamics (MD) simulations to investigate the dynamics of the MJ0796 ABC transporter nucleotide-binding domain (NBD). ABC transporter NBDs form a rotationally symmetric dimer whereby two equivalent active sites are formed at their interface; in complex with a dimer of transmembrane domains they hydrolyze ATP to energize translocation of substrates across cellular membranes. Our data suggest the ABC NBD's ensemble of functional states can be understood predominately in terms of conformational changes between its major subdomains, occurring along two orthogonal dynamic modes. The data show that ligands and oligomeric interactions modulate the equilibrium conformation of the NBD with respect to these motions, suggesting that allostery is achieved by affecting the energetic profile along these two modes. The observed dynamics and allostery integrate consonantly and logically within a mechanistic framework for the ABC NBD dimer, which is supported by a large body of experimental and theoretical data, providing a higher resolution view of the enzyme's dynamic cycle. Our study shows how valuable mechanistic inferences can be derived from accessible short-time scale MD simulations of an enzyme's substructures.\",\n \"corpus_id\": 46784601,\n \"score\": 1\n },\n {\n \"doc_id\": \"28271481\",\n \"title\": \"\\\"Pyruvate Carboxylase, Structure and Function\\\".\",\n \"abstract\": \"Pyruvate carboxylase is a metabolic enzyme that fuels the tricarboxylic acid cycle with one of its intermediates and also participates in the first step of gluconeogenesis. This large enzyme is multifunctional, and each subunit contains two active sites that catalyze two consecutive reactions that lead to the carboxylation of pyruvate into oxaloacetate, and a binding site for acetyl-CoA, an allosteric regulator of the enzyme. Pyruvate carboxylase oligomers arrange in tetramers and covalently attached biotins mediate the transfer of carboxyl groups between distant active sites. In this chapter, some of the recent findings on pyruvate carboxylase functioning are presented, with special focus on the structural studies of the full length enzyme. The emerging picture reveals large movements of domains that even change the overall quaternary organization of pyruvate carboxylase tetramers during catalysis.\",\n \"corpus_id\": 6166593,\n \"score\": 1\n },\n {\n \"doc_id\": \"28700696\",\n \"title\": \"Small-molecule inhibition of pyruvate phosphate dikinase targeting the nucleotide binding site.\",\n \"abstract\": \"Pyruvate phosphate dikinase (PPDK) is an essential enzyme of C4 photosynthesis in plants, catalyzing the ATP-driven conversion of pyruvate to phosphoenolpyruvate (PEP). It is further used by some bacteria and unicellular protists in the reverse, ATP-forming direction. Many weed species use C4 photosynthesis in contrast to world's major crops, which are C3 plants. Hence inhibitors of PPDK may be used as C4-specific herbicides. By screening a library of 80 commercially available kinase inhibitors, we identified compounds derived from bisindolylmaleimide (bisindolylmaleimide IV, IC50 = 0.76 ± 0.13 μM) and indirubin (indirubin-3'-monoxime, IC50 = 4.2 ± 0.9 μM) that showed high inhibitory potency towards PPDK and are among the most effective PPDK inhibitors described today. Physiological studies on leaf tissues of a C4 model plant confirmed in vivo inhibition of C4-driven photosynthesis by these substances. Moreover, comparative docking studies of non-inhibitory bisindolylmaleimide derivatives suggest that the selectivity towards PPDK may be increased by addition of functional groups to the core structure.\",\n \"corpus_id\": 1033705,\n \"score\": 1\n },\n {\n \"doc_id\": \"28820699\",\n \"title\": \"In Vitro Testing of Potential Entamoeba histolytica Pyruvate Phosphate Dikinase Inhibitors.\",\n \"abstract\": \"Adverse effects and resistance to metronidazole have motivated the search for new antiamoebic agents against Entamoeba histolytica. Control of amoeba growth may be achieved by inhibiting the function of the glycolytic enzyme and pyruvate phosphate dikinase (PPDK). In this study, we screened 10 compounds using an in vitro PPDK enzyme assay. These compounds were selected from a virtual screening of compounds in the National Cancer Institute database. The antiamoebic activity of the selected compounds was also evaluated by determining minimal inhibitory concentrations (MICs) and IC50 values using the nitro-blue tetrazolium reduction assay. Seven of the 10 compounds showed inhibitory activities against the ATP/Pi binding site of the ATP-grasp domain. Two compounds, NSC349156 (pancratistatin) and NSC228137 (7-ethoxy-4-[4-methylphenyl] sulfonyl-3-oxido-2, 1, 3-benzoxadiazol-3-ium), exhibited inhibitory effects on the growth of E. histolytica trophozoites with MIC values of 25 and 50 μM, and IC50 values of 14 and 20.7 μM, respectively.\",\n \"corpus_id\": 13949376,\n \"score\": 1\n },\n {\n \"doc_id\": \"29239025\",\n \"title\": \"Fine structure of conformational ensembles in adenylate kinase.\",\n \"abstract\": \"Adenylate kinase (ADK) catalyzes the reversible Mg2+ -dependent phosphoryl transfer reaction Mg2+ +2ADP ↔Mg2+ +ATP + AMP in essential cellular systems. This reaction is a major player in cellular energy homeostasis and the isoform network of ADK plays an important role in AMP metabolic signaling circuits. ADK has 3 domains, the LID, NMP, and CORE domains, that undergo large conformational rearrangements during ADK's catalytic cycle. In spite of extensive experimental and computational studies, details of the conformational pathway from open to closed forms remain uncertain. In this paper we explore this pathway using coarse-grained molecular dynamics (MD) trajectories of ADK calculated by GROMACS using a SMOG model and classify the conformations within the resultant trajectories by K-means clustering. ADK conformations segregate naturally into open; intermediate; and closed forms with long-term residence in the intermediate state. Structural clustering divides the intermediate conformation into 3 sub-states that are distinguished from one another on the basis of differences in both structure and dynamics. These distinctions are defined on the basis of a number of different metrics including radius of gyration, dihedral angle fluctuation, and fluctuations of interatomic pair distances. Furthermore, differences in the sub-states appear to correspond to the distinct ways each sub-state contributes to the molecular mechanism of catalysis: One sub-state acts as a gate-way to the open conformation; one sub-state a gate-way to the closed conformation. A third intermediate sub-state appears to represent a metastable off-pathway structure that is nevertheless frequently visited during the passage from open to closed state.\",\n \"corpus_id\": 46771857,\n \"score\": 1\n },\n {\n \"doc_id\": \"29255019\",\n \"title\": \"Functions of maize genes encoding pyruvate phosphate dikinase in developing endosperm.\",\n \"abstract\": \"Maize opaque2 (o2) mutations are beneficial for endosperm nutritional quality but cause negative pleiotropic effects for reasons that are not fully understood. Direct targets of the bZIP transcriptional regulator encoded by o2 include pdk1 and pdk2 that specify pyruvate phosphate dikinase (PPDK). This enzyme reversibly converts AMP, pyrophosphate, and phosphoenolpyruvate to ATP, orthophosphate, and pyruvate and provides diverse functions in plants. This study addressed PPDK function in maize starchy endosperm where it is highly abundant during grain fill. pdk1 and pdk2 were inactivated individually by transposon insertions, and both genes were simultaneously targeted by endosperm-specific RNAi. pdk2 accounts for the large majority of endosperm PPDK, whereas pdk1 specifies the abundant mesophyll form. The pdk1- mutation is seedling-lethal, indicating that C4 photosynthesis is essential in maize. RNAi expression in transgenic endosperm eliminated detectable PPDK protein and enzyme activity. Transgenic kernels weighed the same on average as nontransgenic siblings, with normal endosperm starch and total N contents, indicating that PPDK is not required for net storage compound synthesis. An opaque phenotype resulted from complete PPDK knockout, including loss of vitreous endosperm character similar to the phenotype conditioned by o2-. Concentrations of multiple glycolytic intermediates were elevated in transgenic endosperm, energy charge was altered, and starch granules were more numerous but smaller on average than normal. The data indicate that PPDK modulates endosperm metabolism, potentially through reversible adjustments to energy charge, and reveal that o2- mutations can affect the opaque phenotype through regulation of PPDK in addition to their previously demonstrated effects on storage protein gene expression.\",\n \"corpus_id\": 26347092,\n \"score\": 1\n },\n {\n \"doc_id\": \"29362701\",\n \"title\": \"Analysis of an ATP-induced conformational transition of ABC transporter MsbA using a coarse-grained model.\",\n \"abstract\": \"Upon the binding of ATP molecules to nucleotide binding domains (NBDs), ATP-binding cassette (ABC) exporters undergo a conformational transition from an inward-facing (IF) to an outward-facing (OF) state. This molecular event is a typical example of chemo-mechanical coupling. However, the underlying mechanism remains unclear. In this study, we analyzed the IF→OF transition of a representative ABC exporter, MsbA, by solving the equation of motion under an elastic network model (ENM). ATP was represented as a single node in ENM or replaced by external forces. When two ATP nodes were added to the ENM of the IF state protein, the two NBDs dimerized; subsequently, the two transmembrane domains opened toward the extracellular side, resulting in the formation of the OF structure. Such a conformational transition was also reproduced by applying external forces, which caused the rotational motion of the NBDs instead of the addition of ATP nodes. The process of the conformational transition was analyzed in detail using cross-correlation maps for node-node interactions. More importantly, it was revealed that the ATP binding energy is converted into distortion energy of several transmembrane helices. These results are useful for understanding the chemo-mechanical coupling in ABC transporters.\",\n \"corpus_id\": 6570778,\n \"score\": 1\n },\n {\n \"doc_id\": \"18477462\",\n \"title\": \"Development of bioluminescent pyrophosphate assay using pyruvate phosphate dikinase and its application to single-nucleotide polymorphism analysis.\",\n \"abstract\": \"DNA analysis is an important technology with respect to diagnosis of infectious disease and tailored medication. In this study, we developed a novel bioluminescent assay for pyrophosphate, and it was applied to single-nucleotide polymorphism (SNP) analysis using one-base extension reaction. The principle of this method is as follows. A specific primer within each aliquot possessing a short 3' end of the base of interest was hybridized to the single-stranded DNA template. Subsequently, (exo-)Klenow DNA polymerase and one of either alpha-thio-dATP, dTTP, dGTP, or dCTP were added and incubated for 1 min. Pyrophosphate released by DNA polymerase is converted to ATP by pyruvate phosphate dikinase (PPDK), and the concentration of ATP is determined using the firefly luciferase reaction. This method, which does not require expensive equipment, can be used to rapidly monitor one point mutation in the gene.\",\n \"corpus_id\": 41285191,\n \"score\": 0\n },\n {\n \"doc_id\": \"18616182\",\n \"title\": \"[Expression of PPDK from Microbispora rosea subsp. aerata in Escherichia coli and its application in pyrosequencing].\",\n \"abstract\": \"Pyruvate phosphate dikinase (PPDK; EC 2.7.9.1) is found in certain microorganisms and plants, and catalyzes the conversion of AMP, PPi and phosphoenolpyruvate (PEP) to ATP, Pi and pyruvate. Using the genomic DNA of Microbispora rosea subsp. aerata as the template, a DNA fragment encoding the gene PPDK was amplified by PCR and inserted into the expression vector pET28a(+), yielding pET28a (+)-PPDK. The E. coli BL21 (DE3) was transformed with the pET28a (+)-PPDK. After inducing with IPTG, the E. coli BL21 (DE3) [pET28a (+)-PPDK] expressed recombinant PPDK fused to an N-terminal sequence of 6-His Tag. The molecular weight of PPDK was estimated to be 101 kD by SDS-PAGE. The PPDK was purified by His * Bind Resin affinity chromatography and ultrafiltration using 10 kD cut-off membrane. The successful application of PPDK in pyrosequencing was also demonstrated.\",\n \"corpus_id\": 38104293,\n \"score\": 0\n },\n {\n \"doc_id\": \"19170242\",\n \"title\": \"Nano-sized bacterial magnetic particles displaying pyruvate phosphate dikinase for pyrosequencing.\",\n \"abstract\": \"There is a high demand for inexpensive and high-throughput DNA sequencing technologies in molecular biology and applied biosciences. In this study, novel nano-sized magnetic particles displaying enzymes for pyrosequencing, a rather novel bioluminometric DNA sequencing method based on the sequencing-by-synthesis principle by employing a cascade of several enzymatic reactions, was developed. A highly thermostable enzyme, pyruvate phosphate dikinase (PPDK) which converts PPi to ATP was successfully expressed onto bacterial magnetic particles (BacMPs) using a novel protein display system of Magnetospirillum magneticum AMB-1. The enzymatic stability of BacMPs displaying PPDK (PPDK-BacMPs) to pH and temperature was evaluated and its broad range of properties was shown. Subsequently, PPDK-BacMPs were applied in pyrosequencing and a target oligonucleotide was successfully sequenced. The PPDK enzyme displayed on BacMPs was shown to be recyclable in each sequence reaction as they can be manipulated by magnetic force. It was concluded that nano-sized PPDK-BacMPs are useful for the scale down of pyrosequencing reaction volumes, thus, permitting high-throughput. The recycling of enzymes was also shown to be promising and applicable for the development of an inexpensive DNA sequencing at a low running cost.\",\n \"corpus_id\": 23319960,\n \"score\": 0\n },\n {\n \"doc_id\": \"22272354\",\n \"title\": \"The conformational transition pathways of ATP-binding cassette transporter BtuCD revealed by targeted molecular dynamics simulation.\",\n \"abstract\": \"BtuCD is a member of the ATP-binding cassette transporters in Escherichia coli that imports vitamin B(12) into the cell by utilizing the energy of ATP hydrolysis. Crystal structures of BtuCD and its homologous protein HI1470/1 in various conformational states support the \\\"alternating access\\\" mechanism which proposes the conformational transitions of the substrate translocation pathway at transmembrane domain (TMD) between the outward-facing and inward-facing states. The conformational transition at TMD is assumed to couple with the movement of the cytoplasmic nucleotide-binding domains (NBDs) driven by ATP hydrolysis/binding. In this study, we performed targeted molecular dynamics (MD) simulations to explore the atomic details of the conformational transitions of BtuCD importer. The outward-facing to inward-facing (O→I) transition was found to be initiated by the conformational movement of NBDs. The subsequent reorientation of the substrate translocation pathway at TMD began with the closing of the periplasmic gate, followed by the opening of the cytoplamic gate in the last stage of the conformational transition due to the extensive hydrophobic interactions at this region, consistent with the functional requirement of unidirectional transport of the substrates. The reverse inward-facing to outward-facing (I→O) transition was found to exhibit intrinsic diversity of the conformational transition pathways and significant structural asymmetry, suggesting that the asymmetric crystal structure of BtuCD-F is an intermediate state in this process.\",\n \"corpus_id\": 723175,\n \"score\": 0\n },\n {\n \"doc_id\": \"26920481\",\n \"title\": \"Metabolic networks to generate pyruvate, PEP and ATP from glycerol in Pseudomonas fluorescens.\",\n \"abstract\": \"Glycerol is a major by-product of the biodiesel industry. In this study we report on the metabolic networks involved in its transformation into pyruvate, phosphoenolpyruvate (PEP) and ATP. When the nutritionally-versatile Pseudomonas fluorescens was exposed to hydrogen peroxide (H2O2) in a mineral medium with glycerol as the sole carbon source, the microbe reconfigured its metabolism to generate adenosine triphosphate (ATP) primarily via substrate-level phosphorylation (SLP). This alternative ATP-producing stratagem resulted in the synthesis of copious amounts of PEP and pyruvate. The production of these metabolites was mediated via the enhanced activities of such enzymes as pyruvate carboxylase (PC) and phosphoenolpyruvate carboxylase (PEPC). The high energy PEP was subsequently converted into ATP with the aid of pyruvate phosphate dikinase (PPDK), phosphoenolpyruvate synthase (PEPS) and pyruvate kinase (PK) with the concomitant formation of pyruvate. The participation of the phospho-transfer enzymes like adenylate kinase (AK) and acetate kinase (ACK) ensured the efficiency of this O2-independent energy-generating machinery. The increased activity of glycerol dehydrogenase (GDH) in the stressed bacteria provided the necessary precursors to fuel this process. This H2O2-induced anaerobic life-style fortuitously evokes metabolic networks to an effective pathway that can be harnessed into the synthesis of ATP, PEP and pyruvate. The bioconversion of glycerol to pyruvate will offer interesting economic benefit.\",\n \"corpus_id\": 21877431,\n \"score\": 0\n },\n {\n \"doc_id\": \"27886288\",\n \"title\": \"Exploring the mechanochemical cycle of dynein motor proteins: structural evidence of crucial intermediates.\",\n \"abstract\": \"Dyneins, a class of motor proteins consisting of six AAA+ modules (AAA1-AAA6), convert chemical energy derived from the hydrolysis of ATP into mechanical energy to walk along the microtubule track towards its minus end while accomplishing various cellular tasks including the transportation of various intracellular cargos. In a full mechanochemical cycle, dynein goes through ATP binding induced open to closed state transition of AAA1, hydrolysis of that ATP and closed to open state transition induced by the release of hydrolysed products along with linker remodelling in different nucleotide states. Here we built structure based models (SBMs) to explore the sequence of events of this mechanochemical cycle from structural aspects. Free energy and kinetic simulation approaches on a multi-basin SBM of dynein reveal the following pathways: (1) in the closing pathway, the AAA1 domain first converts to a closed state followed by the movement of the linker and (2) in the opening transition, initially the AAA1 domain partially opens up and then the complete linker movement takes place followed by the complete opening of the AAA1 domain. In the opening transition, we have observed two intermediate states from our simulations where the AAA1 domain is partially opened. However, in one state the linker is at a closed position and in the other the linker is at an open position. The existence of such intermediates (Pi released, ADP bound state) of dynein has been suggested by numerous experimental studies earlier. Finally, we discuss the biological relevance of this sequence of events in terms of processivity and efficiency of the cycle. The current study also shows how the basic principle of protein folding can be extended to understand complex phenomena like the stepping mechanism of motor proteins.\",\n \"corpus_id\": 22021572,\n \"score\": 0\n }\n]","isConversational":false}}},{"rowIdx":50,"cells":{"query":{"kind":"string","value":"{\n \"doc_id\": \"28943338\",\n \"title\": \"Structure of a Reptilian Adenovirus Reveals a Phage Tailspike Fold Stabilizing a Vertebrate Virus Capsid.\",\n \"abstract\": \"Although non-human adenoviruses (AdVs) might offer solutions to problems posed by human AdVs as therapeutic vectors, little is known about their basic biology. In particular, there are no structural studies on the complete virion of any AdV with a non-mammalian host. We combine mass spectrometry, cryo-electron microscopy, and protein crystallography to characterize the composition and structure of a snake AdV (SnAdV-1, Atadenovirus genus). SnAdV-1 particles contain the genus-specific proteins LH3, p32k, and LH2, a previously unrecognized structural component. Remarkably, the cementing protein LH3 has a trimeric β helix fold typical of bacteriophage host attachment proteins. The organization of minor coat proteins differs from that in human AdVs, correlating with higher thermostability in SnAdV-1. These findings add a new piece to the intriguing puzzle of virus evolution, hint at the use of cell entry pathways different from those in human AdVs, and will help development of new, thermostable SnAdV-1-based vectors.\",\n \"corpus_id\": 4022975\n}"},"candidates":{"kind":"list like","value":[{"doc_id":"18166240","title":"Completion of the genome analysis of snake adenovirus type 1, a representative of the reptilian lineage within the novel genus Atadenovirus.","abstract":"Genome sequencing and analysis of snake adenovirus type 1 (SnAdV-1), originating from corn snake, were completed. This is the first full genomic sequence of an adenovirus from reptilian hosts. The presence of characteristic genus-common genes and transcription units, showed that SnAdV-1 shares similar genome organisation with members of the recently established genus Atadenovirus. Three novel open reading frames of yet unknown functions were found. One of these seemed to be related to a putative gene, the so-called 105R that has recently been described from the genome of the tree shrew adenovirus. The other two putative genes were found to be unique for SnAdV-1. On phylogenetic trees, SnAdV-1 clustered within the atadenovirus clade. Thereby the hypothesis on the reptilian origin of atadenoviruses was further strengthened. Interestingly, however, one of the most striking features of atadenoviruses, namely the base content heavily biased towards A+T, is not characteristic for SnAdV-1 having a genome of balanced composition with a G+C value of 50.21%.","corpus_id":205654171,"score":2},{"doc_id":"18216088","title":"Three-dimensional structure of canine adenovirus serotype 2 capsid.","abstract":"There are more than 100 known adenovirus (AdV) serotypes, including 50 human serotypes. Because AdV-induced disease is relatively species specific, vectors derived from nonhuman serotypes may have wider clinical potential based, in part, on the lack of ubiquitous memory immunity. Whereas a few of the human serotype capsids have been studied at the structural level, none of the nonhuman serotypes has been analyzed. The basis laid by the analysis of human AdV (hAdV) has allowed us to determine and compare the three-dimensional structure of the capsid of canine serotype 2 (CAV-2) to that of hAdV serotype 5 (hAdV-5). We show that CAV-2 capsid has a smoother structure than the human serotypes. Many of the external loops found in the hAdV-5 penton base and the hexon, against which the antibody response is directed, are shorter or absent in CAV-2. On the other hand, the CAV-2 fiber appears to be more complex, with two bends in the shaft. An interesting difference between the human and canine viruses is that the C-terminal part of protein IX is in a different position, making an antenna sticking out of the CAV-2 capsid. The comparison between the two viruses allows the identification of sites that should be easy to modify on the CAV-2 capsid for altering tissue tropism or other biological activities.","corpus_id":7712466,"score":2},{"doc_id":"18508893","title":"Cryoelectron microscopy map of Atadenovirus reveals cross-genus structural differences from human adenovirus.","abstract":"A three-dimensional (3D) cryoelectron microscopy reconstruction of the prototype Atadenovirus (OAdV [an ovine adenovirus isolate]) showing information at a 10.6-A resolution (0.5 Fourier shell correlation) was derived by single-particle analysis. This is the first 3D structure solved for any adenovirus that is not a Mastadenovirus, allowing cross-genus comparisons between structures and the assignment of genus-specific capsid proteins. Viable OAdV mutants that lacked the genus-specific LH3 and p32k proteins in purified virions were also generated. Negatively stained 3D reconstructions of these mutants were used to identify the location of protein LH3 and infer that of p32k within the capsid. The key finding was that LH3 is a critical protein that holds the outer capsid of the virus together. In its absence, the outer viral capsid is unstable. LH3 is located in the same position among the hexon subunits as its protein IX equivalent from mastadenoviruses but sits on top of the hexon trimers, forming prominent \"knobs\" on the virion surface that visually distinguish OAdV from other known AdVs. Electron density was also assigned to hexon and penton subunits and to proteins IIIa and VIII. There was good correspondence between OAdV density and human AdV hexon structures, which also validated the significant differences that were observed between the penton base protein structures.","corpus_id":29949421,"score":2},{"doc_id":"18786402","title":"Bacteriophage lambda stabilization by auxiliary protein gpD: timing, location, and mechanism of attachment determined by cryo-EM.","abstract":"We report the cryo-EM structure of bacteriophage lambda and the mechanism for stabilizing the 20-A-thick capsid containing the dsDNA genome. The crystal structure of the HK97 bacteriophage capsid fits most of the T = 7 lambda particle density with only minor adjustment. A prominent surface feature at the 3-fold axes corresponds to the cementing protein gpD, which is necessary for stabilization of the capsid shell. Its position coincides with the location of the covalent cross-link formed in the docked HK97 crystal structure, suggesting an evolutionary replacement of this gene product in lambda by autocatalytic chemistry in HK97. The crystal structure of the trimeric gpD, in which the 14 N-terminal residues required for capsid binding are disordered, fits precisely into the corresponding EM density. The N-terminal residues of gpD are well ordered in the cryo-EM density, adding a strand to a beta-sheet formed by the capsid proteins and explaining the mechanism of particle stabilization.","corpus_id":205258718,"score":2},{"doc_id":"20798312","title":"Atomic structure of human adenovirus by cryo-EM reveals interactions among protein networks.","abstract":"Construction of a complex virus may involve a hierarchy of assembly elements. Here, we report the structure of the whole human adenovirus virion at 3.6 angstroms resolution by cryo-electron microscopy (cryo-EM), revealing in situ atomic models of three minor capsid proteins (IIIa, VIII, and IX), extensions of the (penton base and hexon) major capsid proteins, and interactions within three protein-protein networks. One network is mediated by protein IIIa at the vertices, within group-of-six (GOS) tiles--a penton base and its five surrounding hexons. Another is mediated by ropes (protein IX) that lash hexons together to form group-of-nine (GON) tiles and bind GONs to GONs. The third, mediated by IIIa and VIII, binds each GOS to five surrounding GONs. Optimization of adenovirus for cancer and gene therapy could target these networks.","corpus_id":206525577,"score":2},{"doc_id":"20798318","title":"Crystal structure of human adenovirus at 3.5 A resolution.","abstract":"Rational development of adenovirus vectors for therapeutic gene transfer is hampered by the lack of accurate structural information. Here, we report the x-ray structure at 3.5 angstrom resolution of the 150-megadalton adenovirus capsid containing nearly 1 million amino acids. We describe interactions between the major capsid protein (hexon) and several accessory molecules that stabilize the capsid. The virus structure also reveals an altered association between the penton base and the trimeric fiber protein, perhaps reflecting an early event in cell entry. The high-resolution structure provides a substantial advance toward understanding the assembly and cell entry mechanisms of a large double-stranded DNA virus and provides new opportunities for improving adenovirus-mediated gene transfer.","corpus_id":38763893,"score":2},{"doc_id":"21071053","title":"The host outer membrane proteins OmpA and OmpC are associated with the Shigella phage Sf6 virion.","abstract":"Assembly of dsDNA bacteriophage is a precisely programmed process. Potential roles of host cell components in phage assembly haven't been well understood. It was previously reported that two unidentified proteins were present in bacteriophage Sf6 virion (Casjens et al, 2004, J.Mol. Biol. 339, 379-394, Fig. 2A). Using tandem mass spectrometry, we have identified the two proteins as outer membrane proteins (OMPs) OmpA and OmpC from its host Shigella flexneri. The transmission electron cryo-microscopy structure of Sf6 shows significant density at specific sites at the phage capsid inner surface. This density fit well with the characteristic beta-barrel domains of OMPs, thus may be due to the two host proteins. Locations of this density suggest a role in Sf6 morphogenesis reminiscent of phage-encoded cementing proteins. These data indicate a new, OMP-related phage:host linkage, adding to previous knowledge that some lambdoid bacteriophage genomes contain OmpC-like genes that express phage-encoded porins in the lysogenic state.","corpus_id":15371524,"score":2},{"doc_id":"22754652","title":"Latest insights on adenovirus structure and assembly.","abstract":"Adenovirus (AdV) capsid organization is considerably complex, not only because of its large size (~950 Å) and triangulation number (pseudo T = 25), but also because it contains four types of minor proteins in specialized locations modulating the quasi-equivalent icosahedral interactions. Up until 2009, only its major components (hexon, penton, and fiber) had separately been described in atomic detail. Their relationships within the virion, and the location of minor coat proteins, were inferred from combining the known crystal structures with increasingly more detailed cryo-electron microscopy (cryoEM) maps. There was no structural information on assembly intermediates. Later on that year, two reports described the structural differences between the mature and immature adenoviral particle, starting to shed light on the different stages of viral assembly, and giving further insights into the roles of core and minor coat proteins during morphogenesis [1,2]. Finally, in 2010, two papers describing the atomic resolution structure of the complete virion appeared [3,4]. These reports represent a veritable tour de force for two structural biology techniques: X-ray crystallography and cryoEM, as this is the largest macromolecular complex solved at high resolution by either of them. In particular, the cryoEM analysis provided an unprecedented clear picture of the complex protein networks shaping the icosahedral shell. Here I review these latest developments in the field of AdV structural studies.","corpus_id":15455524,"score":2},{"doc_id":"25056898","title":"Molecular characterization of a lizard adenovirus reveals the first atadenovirus with two fiber genes and the first adenovirus with either one short or three long fibers per penton.","abstract":"UNLABELLED: Although adenoviruses (AdVs) have been found in a wide variety of reptiles, including numerous squamate species, turtles, and crocodiles, the number of reptilian adenovirus isolates is still scarce. The only fully sequenced reptilian adenovirus, snake adenovirus 1 (SnAdV-1), belongs to the Atadenovirus genus. Recently, two new atadenoviruses were isolated from a captive Gila monster (Heloderma suspectum) and Mexican beaded lizards (Heloderma horridum). Here we report the full genomic and proteomic characterization of the latter, designated lizard adenovirus 2 (LAdV-2). The double-stranded DNA (dsDNA) genome of LAdV-2 is 32,965 bp long, with an average G+C content of 44.16%. The overall arrangement and gene content of the LAdV-2 genome were largely concordant with those in other atadenoviruses, except for four novel open reading frames (ORFs) at the right end of the genome. Phylogeny reconstructions and plesiomorphic traits shared with SnAdV-1 further supported the assignment of LAdV-2 to the Atadenovirus genus. Surprisingly, two fiber genes were found for the first time in an atadenovirus. After optimizing the production of LAdV-2 in cell culture, we determined the protein compositions of the virions. The two fiber genes produce two fiber proteins of different sizes that are incorporated into the viral particles. Interestingly, the two different fiber proteins assemble as either one short or three long fiber projections per vertex. Stoichiometry estimations indicate that the long fiber triplet is present at only one or two vertices per virion. Neither triple fibers nor a mixed number of fibers per vertex had previously been reported for adenoviruses or any other virus. IMPORTANCE: Here we show that a lizard adenovirus, LAdV-2, has a penton architecture never observed before. LAdV-2 expresses two fiber proteins-one short and one long. In the virion, most vertices have one short fiber, but a few of them have three long fibers attached to the same penton base. This observation raises new intriguing questions on virus structure. How can the triple fiber attach to a pentameric vertex? What determines the number and location of each vertex type in the icosahedral particle? Since fibers are responsible for primary attachment to the host, this novel architecture also suggests a novel mode of cell entry for LAdV-2. Adenoviruses have a recognized potential in nanobiomedicine, but only a few of the more than 200 types found so far in nature have been characterized in detail. Exploring the taxonomic wealth of adenoviruses should improve our chances to successfully use them as therapeutic tools.","corpus_id":44788628,"score":2},{"doc_id":"27807242","title":"Evolution and Cryo-electron Microscopy Capsid Structure of a North American Bat Adenovirus and Its Relationship to Other Mastadenoviruses.","abstract":"Since the first description of adenoviruses in bats in 2006, a number of micro- and megabat species in Europe, Africa, and Asia have been shown to carry a wide diversity of adenoviruses. Here, we report on the evolutionary, biological, and structural characterization of a novel bat adenovirus (BtAdV) recovered from a Rafinesque's big-eared bat (Corynorhinus rafinesquii) in Kentucky, USA, which is the first adenovirus isolated from North American bats. This virus (BtAdV 250-A) exhibits a close phylogenetic relationship with Canine mastadenovirus A (CAdV A), as previously observed with other BtAdVs. To further investigate the relationships between BtAdVs and CAdVs, we conducted mass spectrometric analysis and single-particle cryo-electron microscopy reconstructions of the BtAdV 250-A capsid and also analyzed the in vitro host ranges of both viruses. Our results demonstrate that BtAdV 250-A represents a new mastadenovirus species that, in contrast to CAdV, has a unique capsid morphology that contains more prominent extensions of protein IX and can replicate efficiently in a phylogenetically diverse range of species. These findings, in addition to the recognition that both the genetic diversity of BtAdVs and the number of different bat species from disparate geographic regions infected with BtAdVs appears to be extensive, tentatively suggest that bats may have served as a potential reservoir for the cross-species transfer of adenoviruses to other hosts, as theorized for CAdV. IMPORTANCE: Although many adenoviruses are host specific and likely codiverged with their hosts over millions of years, other adenoviruses appear to have emerged through successful cross-species transmission events on more recent time scales. The wide geographic distribution and genetic diversity of adenoviruses in bats and their close phylogenetic relationship to Canine mastadenovirus A (CAdV A) has raised important questions about how CAdV A, and possibly other mammalian adenoviruses, may have emerged. Although most adenoviruses tend to cause limited disease in their natural hosts, CAdV A is unusual in that it may cause high morbidity and sometimes fatal infections in immunocompetent hosts and is thus an important pathogen of carnivores. Here, we performed a comparative evolutionary and structural study of representative bat and canine adenoviruses to better understand the relationship between these two viral groups.","corpus_id":29423462,"score":2},{"doc_id":"28456019","title":"Dual host specificity of phage SP6 is facilitated by tailspike rotation.","abstract":"Bacteriophage SP6 exhibits dual-host adsorption specificity. The SP6 tailspikes are recognized as important in host range determination but the mechanisms underlying dual host specificity are unknown. Cryo-electron tomography and sub-tomogram classification were used to analyze the SP6 virion with a particular focus on the interaction of tailspikes with host membranes. The SP6 tail is surrounded by six V-shaped structures that interconnect in forming a hand-over-hand hexameric garland. Each V-shaped structure consists of two trimeric tailspike proteins: gp46 and gp47, connected through the adaptor protein gp37. SP6 infection of Salmonella enterica serovars Typhimurium and Newport results in distinguishable changes in tailspike orientation, providing the first direct demonstration how tailspikes can confer dual host adsorption specificity. SP6 also infects S. Typhimurium strains lacking O antigen; in these infections tailspikes have no apparent specific role and the phage tail must therefore interact with a distinct host receptor to allow infection.","corpus_id":22528751,"score":2},{"doc_id":"18547389","title":"Crystal structure of Escherichia coli phage HK620 tailspike: podoviral tailspike endoglycosidase modules are evolutionarily related.","abstract":"Bacteriophage HK620 infects Escherichia coli H and is closely related to Shigella phage Sf6 and Salmonella phage P22. All three Podoviridae recognize and cleave their respective host cell receptor polysaccharide by homotrimeric tailspike proteins. The three proteins exhibit high sequence identity in the 110 residues of their N-terminal particle-binding domains, but no apparent sequence similarity in their major, receptor-binding parts. We have biochemically characterized the receptor-binding part of HK620 tailspike and determined its crystal structure to 1.38 A resolution. Its major domain is a right-handed parallel beta-helix, as in Sf6 and P22 tailspikes. HK620 tailspike has endo-N-acetylglucosaminidase activity and produces hexasaccharides of an O18A1-type O-antigen. As indicated by the structure of a hexasaccharide complex determined at 1.6 A resolution, the endoglycosidase-active sites are located intramolecularly, as in P22, and not between subunits, as in Sf6 tailspike. In contrast, the extreme C-terminal domain of HK620 tailspike forms a beta-sandwich, as in Sf6 and unlike P22 tailspike. Despite the different folds, structure-based sequence alignments of the C-termini reveal motifs conserved between the three proteins. We propose that the tailspike genes of P22, Sf6 and HK620 have a common precursor and are not mosaics of unrelated gene fragments.","corpus_id":34854199,"score":1},{"doc_id":"18824312","title":"PCR-sequence characterization of new adenoviruses found in reptiles and the first successful isolation of a lizard adenovirus.","abstract":"A consensus nested PCR was used to screen diagnostic samples from approximately 70 reptiles for the presence of adenoviruses (AdV) in the years 2006-2007. Classical virus isolation methods were also used with all samples. After adenoviruses were detected in a group of helodermatid lizards in a Danish zoo, a follow-up study was also carried out on lizards from this group (10 Mexican beaded lizards and 24 Gila monsters) over the period of a year. Adenoviruses were detected in a total of 26 lizards and snakes by PCR. The PCR amplicons from all positive animals were sequenced and the resulting polymerase gene sequences were used for phylogenetic analysis. Altogether six Agamid AdVs were amplified, with a minimal sequence variation between one another and between these and GenBank Agamid AdVs. The sequence obtained from one of the Gila monsters is identical with the GenBank Helodermatid AdV, while the sequences from the Mexican beaded lizards differ from this. In a snake collection we have detected a new AdV from an Asp viper. All of the above mentioned adenoviruses cluster in the Atadenovirus genus. However, the sequence from a new Varanid AdV detected in this study clusters outside this genus. On cell culture, viruses were isolated from three of the AdV positive helodermatid lizards (one Mexican beaded lizard and two Gila monsters) and identified as AdVs based on electron microscopy and PCR and sequencing using cell culture supernatant. This is the first report of the successful isolation of a lizard AdV.","corpus_id":19811017,"score":1},{"doc_id":"20376613","title":"Adenovirus.","abstract":"Of the 53 different human adenovirus (HAdV) serotypes belonging to species A-G, a significant number are associated with acute respiratory, gastrointestinal and ocular infections. Replication-defective HAdV-5-based vectors also continue to play a significant role in gene transfer trials and in vaccine delivery efforts in the clinic. Although significant progress has been made from studies of AdV biology, we still have an incomplete understanding of AdV's structure as well as its multifactorial interactions with the host. Continuing efforts to improve knowledge in these areas, as discussed in this chapter, will be crucial for revealing the mechanisms of AdV pathogenesis and for allowing optimal use of AdV vectors for biomedical applications.","corpus_id":260626758,"score":1},{"doc_id":"21146538","title":"Model of the trimeric fiber and its interactions with the pentameric penton base of human adenovirus by cryo-electron microscopy.","abstract":"Adenovirus invades host cells by first binding to host receptors through a trimeric fiber, which contains three domains: a receptor-binding knob domain, a long flexible shaft domain, and a penton base-attachment tail domain. Although the structure of the knob domain associated with a portion of the shaft has been solved by X-ray crystallography, the in situ structure of the fiber in the virion is not known; thus, it remains a mystery how the trimeric fiber attaches to its underlying pentameric penton base. By high-resolution cryo-electron microscopy, we have determined the structure of the human adenovirus type 5 (Ad5) to 3.6-Å resolution and have reported the full atomic models for its capsid proteins, but not for the fiber whose density cannot be directly interpreted due to symmetry mismatch with the penton base. Here, we report the determination of the Ad5 fiber structure and its mode of attachment to the pentameric penton base by using an integrative approach of multi-resolution filtering, homology modeling, computational simulation of mismatched symmetries, and fitting of atomic models into cryo-electron microscopy density maps. Our structure reveals that the interactions between the trimeric fiber and the pentameric penton base are mediated by a hydrophobic ring on the top surface of the penton base and three flexible tails inserted into three of the five available grooves formed by neighboring subunits of penton base. These interaction sites provide the molecular basis for the symmetry mismatch and can be targeted for optimizing adenovirus for gene therapy applications.","corpus_id":32786422,"score":1},{"doc_id":"21742267","title":"Insights into the evolution of a complex virus from the crystal structure of vaccinia virus D13.","abstract":"The morphogenesis of poxviruses such as vaccinia virus (VACV) sees the virion shape mature from spherical to brick-shaped. Trimeric capsomers of the VACV D13 protein form a transitory, stabilizing lattice on the surface of the initial spherical immature virus particle. The crystal structure of D13 reveals that this major scaffolding protein comprises a double β barrel \"jelly-roll\" subunit arranged as pseudo-hexagonal trimers. These structural features are characteristic of the major capsid proteins of a lineage of large icosahedral double-stranded DNA viruses including human adenovirus and the bacteriophages PRD1 and PM2. Structure-based phylogenetic analysis confirms that VACV belongs to this lineage, suggesting that (analogously to higher organism embryogenesis) early poxvirus morphogenesis reflects their evolution from a lineage of viruses sharing a common icosahedral ancestor.","corpus_id":13923660,"score":1},{"doc_id":"22153511","title":"Structural conservation of the myoviridae phage tail sheath protein fold.","abstract":"Bacteriophage phiKZ is a giant phage that infects Pseudomonas aeruginosa, a human pathogen. The phiKZ virion consists of a 1450 Å diameter icosahedral head and a 2000 Å-long contractile tail. The structure of the whole virus was previously reported, showing that its tail organization in the extended state is similar to the well-studied Myovirus bacteriophage T4 tail. The crystal structure of a tail sheath protein fragment of phiKZ was determined to 2.4 Å resolution. Furthermore, crystal structures of two prophage tail sheath proteins were determined to 1.9 and 3.3 Å resolution. Despite low sequence identity between these proteins, all of these structures have a similar fold. The crystal structure of the phiKZ tail sheath protein has been fitted into cryo-electron-microscopy reconstructions of the extended tail sheath and of a polysheath. The structural rearrangement of the phiKZ tail sheath contraction was found to be similar to that of phage T4.","corpus_id":5103216,"score":1},{"doc_id":"22386055","title":"Structural evolution of the P22-like phages: comparison of Sf6 and P22 procapsid and virion architectures.","abstract":"Coat proteins of tailed, dsDNA phages and in herpesviruses include a conserved core similar to the bacteriophage HK97 subunit. This core is often embellished with other domains such as the telokin Ig-like domain of phage P22. Eighty-six P22-like phages and prophages with sequenced genomes share a similar set of virion assembly genes and, based on comparisons of twelve viral assembly proteins (structural and assembly/packaging chaperones), these phages are classified into three groups (P22-like, Sf6-like, and CUS-3-like). We used cryo-electron microscopy and 3D image reconstruction to determine the structures of Sf6 procapsids and virions (~7Å resolution), and the structure of the entire, asymmetric Sf6 virion (16-Å resolution). The Sf6 coat protein is similar to that of P22 yet it has differences in the telokin domain and in its overall quaternary organization. Thermal stability and agarose gel experiments show that Sf6 virions are slightly less stable than those of P22. Finally, bacterial host outer membrane proteins A and C were identified in lipid vesicles that co-purify with Sf6 particles, but are not components of the capsid.","corpus_id":14670556,"score":1},{"doc_id":"22482707","title":"Structure of human adenovirus.","abstract":"A detailed structural analysis of the entire human adenovirus capsid has been stymied by the complexity and size of this 150 MDa macromolecular complex. Over the past 10 years, the steady improvements in viral genome manipulation concomitant with advances in crystallographic techniques and data processing software has allowed structure determination of this virus by X-ray diffraction at 3.5 Å resolution. The virus structure revealed the location, folds, and interactions of major and minor (cement proteins) on the inner and outer capsid surface. This new structural information sheds further light on the process of adenovirus capsid assembly and virus-host cell interactions.","corpus_id":29436951,"score":1},{"doc_id":"22514336","title":"Capsid structure and its stability at the late stages of bacteriophage SPP1 assembly.","abstract":"The structure of the bacteriophage SPP1 capsid was determined at subnanometer resolution by cryo-electron microscopy and single-particle analysis. The icosahedral capsid is composed of the major capsid protein gp13 and the auxiliary protein gp12, which are organized in a T=7 lattice. DNA is arranged in layers with a distance of ~24.5 Å. gp12 forms spikes that are anchored at the center of gp13 hexamers. In a gp12-deficient mutant, the centers of hexamers are closed by loops of gp13 coming together to protect the SPP1 genome from the outside environment. The HK97-like fold was used to build a pseudoatomic model of gp13. Its structural organization remains unchanged upon tail binding and following DNA release. gp13 exhibits enhanced thermostability in the DNA-filled capsid. A remarkable convergence between the thermostability of the capsid and those of the other virion components was found, revealing that the overall architecture of the SPP1 infectious particle coevolved toward high robustness.","corpus_id":34601670,"score":1},{"doc_id":"23091035","title":"Structure of Sputnik, a virophage, at 3.5-Å resolution.","abstract":"\"Sputnik\" is a dsDNA virus, referred to as a virophage, that is coassembled with Mimivirus in the host amoeba. We have used cryo-EM to produce an electron density map of the icosahedral Sputnik virus at 3.5-Å resolution, sufficient to verify the identity of most amino acids in the capsid proteins and to establish the identity of the pentameric protein forming the fivefold vertices. It was also shown that the virus lacks an internal membrane. The capsid is organized into a T = 27 lattice in which there are 260 trimeric capsomers and 12 pentameric capsomers. The trimeric capsomers consist of three double \"jelly-roll\" major capsid proteins creating pseudohexameric capsomer symmetry. The pentameric capsomers consist of five single jelly-roll proteins. The release of the genome by displacing one or more of the pentameric capsomers may be the result of a low-pH environment. These results suggest a mechanism of Sputnik DNA ejection that probably also occurs in other big icosahedral double jelly-roll viruses such as Adenovirus. In this study, the near-atomic resolution structure of a virus has been established where crystallization for X-ray crystallography was not feasible.","corpus_id":22281949,"score":1},{"doc_id":"24316834","title":"Crystallization of the C-terminal domain of the fibre protein from snake adenovirus 1, an atadenovirus.","abstract":"Adenovirus fibre proteins play an important role in determining viral tropism. The C-terminal domain of the fibre protein from snake adenovirus type 1, a member of the Atadenovirus genus, has been expressed, purified and crystallized. Crystals were obtained belonging to space groups P2(1)2(1)2(1) (two different forms), I2(1)3 and F23. The best of these diffracted synchrotron radiation to a resolution of 1.4 Å. As the protein lacks methionines or cysteines, site-directed mutagenesis was performed to change two leucine residues to methionines. Crystals of selenomethionine-derivatized crystals of the I2(1)3 form were also obtained and a multi-wavelength anomalous dispersion data set was collected.","corpus_id":35326870,"score":1},{"doc_id":"24889614","title":"Single-particle EM reveals plasticity of interactions between the adenovirus penton base and integrin αVβ3.","abstract":"Human adenoviruses are double-stranded DNA viruses responsible for numerous infections, some of which can be fatal. Furthermore, adenoviruses are currently used in clinical trials as vectors for gene therapy applications. Although initial binding of adenoviruses to host attachment receptors has been extensively characterized, the interactions with the entry receptor (integrins) remain poorly understood at the structural level. We characterized the interactions between the adenovirus 9 penton base subunit and αVβ3 integrin using fluorescence correlation spectroscopy and single-particle electron microscopy to understand the mechanisms underlying virus internalization and infection. Our results indicate that the penton base subunit can bind integrins with high affinity and in several different orientations. These outcomes correlate with the requirement of the pentameric penton base to simultaneously bind several integrins to enable their clustering and promote virus entry into the host cell.","corpus_id":33854643,"score":1},{"doc_id":"25043589","title":"Three-dimensional reconstructions of the bacteriophage CUS-3 virion reveal a conserved coat protein I-domain but a distinct tailspike receptor-binding domain.","abstract":"CUS-3 is a short-tailed, dsDNA bacteriophage that infects serotype K1 Escherichia coli. We report icosahedrally averaged and asymmetric, three-dimensional, cryo-electron microscopic reconstructions of the CUS-3 virion. Its coat protein structure adopts the \"HK97-fold\" shared by other tailed phages and is quite similar to that in phages P22 and Sf6 despite only weak amino acid sequence similarity. In addition, these coat proteins share a unique extra external domain (\"I-domain\"), suggesting that the group of P22-like phages has evolved over a very long time period without acquiring a new coat protein gene from another phage group. On the other hand, the morphology of the CUS-3 tailspike differs significantly from that of P22 or Sf6, but is similar to the tailspike of phage K1F, a member of the extremely distantly related T7 group of phages. We conclude that CUS-3 obtained its tailspike gene from a distantly related phage quite recently.","corpus_id":7603381,"score":1},{"doc_id":"25071205","title":"Structures and organization of adenovirus cement proteins provide insights into the role of capsid maturation in virus entry and infection.","abstract":"Adenovirus cement proteins play crucial roles in virion assembly, disassembly, cell entry, and infection. Based on a refined crystal structure of the adenovirus virion at 3.8-Å resolution, we have determined the structures of all of the cement proteins (IIIa, VI, VIII, and IX) and their organization in two distinct layers. We have significantly revised the recent cryoelectron microscopy models for proteins IIIa and IX and show that both are located on the capsid exterior. Together, the cement proteins exclusively stabilize the hexon shell, thus rendering penton vertices the weakest links of the adenovirus capsid. We describe, for the first time to our knowledge, the structure of protein VI, a key membrane-lytic molecule, and unveil its associations with VIII and core protein V, which together glue peripentonal hexons beneath the vertex region and connect them to the rest of the capsid on the interior. Following virion maturation, the cleaved N-terminal propeptide of VI is observed, reaching deep into the peripentonal hexon cavity, detached from the membrane-lytic domain, so that the latter can be released. Our results thus provide the molecular basis for the requirement of maturation cleavage of protein VI. This process is essential for untethering and release of the membrane-lytic region, which is known to mediate endosome rupture and delivery of partially disassembled virions into the host cell cytoplasm.","corpus_id":1492945,"score":1},{"doc_id":"25254384","title":"The adenovirus genome contributes to the structural stability of the virion.","abstract":"Adenovirus (Ad) vectors are currently the most commonly used platform for therapeutic gene delivery in human gene therapy clinical trials. Although these vectors are effective, many researchers seek to further improve the safety and efficacy of Ad-based vectors through detailed characterization of basic Ad biology relevant to its function as a vector system. Most Ad vectors are deleted of key, or all, viral protein coding sequences, which functions to not only prevent virus replication but also increase the cloning capacity of the vector for foreign DNA. However, radical modifications to the genome size significantly decreases virion stability, suggesting that the virus genome plays a role in maintaining the physical stability of the Ad virion. Indeed, a similar relationship between genome size and virion stability has been noted for many viruses. This review discusses the impact of the genome size on Ad virion stability and emphasizes the need to consider this aspect of virus biology in Ad-based vector design.","corpus_id":1212474,"score":1},{"doc_id":"25486282","title":"Crystal structure of the fibre head domain of the Atadenovirus Snake Adenovirus 1.","abstract":"Adenoviruses are non-enveloped icosahedral viruses with trimeric fibre proteins protruding from their vertices. There are five known genera, from which only Mastadenoviruses have been widely studied. Apart from studying adenovirus as a biological model system and with a view to prevent or combat viral infection, there is a major interest in using adenovirus for vaccination, cancer therapy and gene therapy purposes. Adenoviruses from the Atadenovirus genus have been isolated from squamate reptile hosts, ruminants and birds and have a characteristic gene organization and capsid morphology. The carboxy-terminal virus-distal fibre head domains are likely responsible for primary receptor recognition. We determined the high-resolution crystal structure of the Snake Adenovirus 1 (SnAdV-1) fibre head using the multi-wavelength anomalous dispersion (MAD) method. Despite the absence of significant sequence homology, this Atadenovirus fibre head has the same beta-sandwich propeller topology as other adenovirus fibre heads. However, it is about half the size, mainly due to much shorter loops connecting the beta-strands. The detailed structure of the SnAdV-1 fibre head and other animal adenovirus fibre heads, together with the future identification of their natural receptors, may lead to the development of new strategies to target adenovirus vectors to cells of interest.","corpus_id":10741158,"score":1},{"doc_id":"25994880","title":"Crystal structure of the fibre head domain of bovine adenovirus 4, a ruminant atadenovirus.","abstract":"BACKGROUND: In adenoviruses, primary host cell recognition is generally performed by the head domains of their homo-trimeric fibre proteins. This first interaction is reversible. A secondary, irreversible interaction subsequently takes place via other adenovirus capsid proteins and leads to a productive infection. Although many fibre head structures are known for human mastadenoviruses, not many animal adenovirus fibre head structures have been determined, especially not from those belonging to adenovirus genera other than Mastadenovirus. METHODS: We constructed an expression vector for the fibre head domain from a ruminant atadenovirus, bovine adenovirus 4 (BAdV-4), consisting of amino acids 414-535, expressed the protein in Escherichia coli, purified it by metal affinity and cation exchange chromatography and crystallized it. The structure was solved using single isomorphous replacement plus anomalous dispersion of a mercury derivative and refined against native data that extended to 1.2 Å resolution. RESULTS: Like in other adenoviruses, the BAdV-4 fibre head monomer contains a beta-sandwich consisting of ABCJ and GHID sheets. The topology is identical to the fibre head of the other studied atadenovirus, snake adenovirus 1 (SnAdV-1), including the alpha-helix in the DG-loop, despite of them having a sequence identity of only 15 %. There are also differences which may have implications for ligand binding. Beta-strands G and H are longer and differences in several surface-loops and surface charge are observed. CONCLUSIONS: Chimeric adenovirus fibres have been used to retarget adenovirus-based anti-cancer and gene therapy vectors. Ovine adenovirus 7 (OAdV-7), another ruminant atadenovirus, is intensively tested as a basis for such a vector. Here, we present the high-resolution atomic structure of the BAdV-4 fibre head domain, the second atadenovirus fibre head structure known and the first of an atadenovirus that infects a mammalian host. Future research should focus on the receptor-binding properties of these fibre head domains.","corpus_id":8568594,"score":1},{"doc_id":"26178997","title":"Structures of Adenovirus Incomplete Particles Clarify Capsid Architecture and Show Maturation Changes of Packaging Protein L1 52/55k.","abstract":"UNLABELLED: Adenovirus is one of the most complex icosahedral, nonenveloped viruses. Even after its structure was solved at near-atomic resolution by both cryo-electron microscopy and X-ray crystallography, the location of minor coat proteins is still a subject of debate. The elaborated capsid architecture is the product of a correspondingly complex assembly process, about which many aspects remain unknown. Genome encapsidation involves the concerted action of five virus proteins, and proteolytic processing by the virus protease is needed to prime the virion for sequential uncoating. Protein L1 52/55k is required for packaging, and multiple cleavages by the maturation protease facilitate its release from the nascent virion. Light-density particles are routinely produced in adenovirus infections and are thought to represent assembly intermediates. Here, we present the molecular and structural characterization of two different types of human adenovirus light particles produced by a mutant with delayed packaging. We show that these particles lack core polypeptide V but do not lack the density corresponding to this protein in the X-ray structure, thereby adding support to the adenovirus cryo-electron microscopy model. The two types of light particles present different degrees of proteolytic processing. Their structures provide the first glimpse of the organization of L1 52/55k protein inside the capsid shell and of how this organization changes upon partial maturation. Immature, full-length L1 52/55k is poised beneath the vertices to engage the virus genome. Upon proteolytic processing, L1 52/55k disengages from the capsid shell, facilitating genome release during uncoating. IMPORTANCE: Adenoviruses have been extensively characterized as experimental systems in molecular biology, as human pathogens, and as therapeutic vectors. However, a clear picture of many aspects of their basic biology is still lacking. Two of these aspects are the location of minor coat proteins in the capsid and the molecular details of capsid assembly. Here, we provide evidence supporting one of the two current models for capsid architecture. We also show for the first time the location of the packaging protein L1 52/55k in particles lacking the virus genome and how this location changes during maturation. Our results contribute to clarifying standing questions in adenovirus capsid architecture and provide new details on the role of L1 52/55k protein in assembly.","corpus_id":5903737,"score":1},{"doc_id":"26269173","title":"A Molecular Staple: D-Loops in the I Domain of Bacteriophage P22 Coat Protein Make Important Intercapsomer Contacts Required for Procapsid Assembly.","abstract":"UNLABELLED: Bacteriophage P22, a double-stranded DNA (dsDNA) virus, has a nonconserved 124-amino-acid accessory domain inserted into its coat protein, which has the canonical HK97 protein fold. This I domain is involved in virus capsid size determination and stability, as well as protein folding. The nuclear magnetic resonance (NMR) solution structure of the I domain revealed the presence of a D-loop, which was hypothesized to make important intersubunit contacts between coat proteins in adjacent capsomers. Here we show that amino acid substitutions of residues near the tip of the D-loop result in aberrant assembly products, including tubes and broken particles, highlighting the significance of the D-loops in proper procapsid assembly. Using disulfide cross-linking, we showed that the tips of the D-loops are positioned directly across from each other both in the procapsid and the mature virion, suggesting their importance in both states. Our results indicate that D-loop interactions act as \"molecular staples\" at the icosahedral 2-fold symmetry axis and significantly contribute to stabilizing the P22 capsid for DNA packaging. IMPORTANCE: Many dsDNA viruses have morphogenic pathways utilizing an intermediate capsid, known as a procapsid. These procapsids are assembled from a coat protein having the HK97 fold in a reaction driven by scaffolding proteins or delta domains. Maturation of the capsid occurs during DNA packaging. Bacteriophage HK97 uniquely stabilizes its capsid during maturation by intercapsomer cross-linking, but most virus capsids are stabilized by alternate means. Here we show that the I domain that is inserted into the coat protein of bacteriophage P22 is important in the process of proper procapsid assembly. Specifically, the I domain allows for stabilizing interactions across the capsid 2-fold axis of symmetry via a D-loop. When amino acid residues at the tip of the D-loop are mutated, aberrant assembly products, including tubes, are formed instead of procapsids, consequently phage production is affected, indicating the importance of stabilizing interactions during the assembly and maturation reactions.","corpus_id":40613704,"score":1},{"doc_id":"26996963","title":"New Structural Insights into the Genome and Minor Capsid Proteins of BK Polyomavirus using Cryo-Electron Microscopy.","abstract":"BK polyomavirus is the causative agent of several diseases in transplant patients and the immunosuppressed. In order to better understand the structure and life cycle of BK, we produced infectious virions and VP1-only virus-like particles in cell culture, and determined their three-dimensional structures using cryo-electron microscopy (EM) and single-particle image processing. The resulting 7.6-Å resolution structure of BK and 9.1-Å resolution of the virus-like particles are the highest-resolution cryo-EM structures of any polyomavirus. These structures confirm that the architecture of the major structural protein components of these human polyomaviruses are similar to previous structures from other hosts, but give new insight into the location and role of the enigmatic minor structural proteins, VP2 and VP3. We also observe two shells of electron density, which we attribute to a structurally ordered part of the viral genome, and discrete contacts between this density and both VP1 and the minor capsid proteins.","corpus_id":18131435,"score":1},{"doc_id":"27671640","title":"Asymmetric cryo-EM structure of the canonical Allolevivirus Qβ reveals a single maturation protein and the genomic ssRNA in situ.","abstract":"Single-stranded (ss) RNA viruses infect all domains of life. To date, for most ssRNA virions, only the structures of the capsids and their associated protein components have been resolved to high resolution. Qβ, an ssRNA phage specific for the conjugative F-pilus, has a T = 3 icosahedral lattice of coat proteins assembled around its 4,217 nucleotides of genomic RNA (gRNA). In the mature virion, the maturation protein, A2, binds to the gRNA and is required for adsorption to the F-pilus. Here, we report the cryo-electron microscopy (cryo-EM) structures of Qβ with and without symmetry applied. The icosahedral structure, at 3.7-Å resolution, resolves loops not previously seen in the published X-ray structure, whereas the asymmetric structure, at 7-Å resolution, reveals A2 and the gRNA. A2 contains a bundle of α-helices and replaces one dimer of coat proteins at a twofold axis. The helix bundle binds gRNA, causing denser packing of RNA in its proximity, which asymmetrically expands the surrounding coat protein shell to potentially facilitate RNA release during infection. We observe a fixed pattern of gRNA organization among all viral particles, with the major and minor grooves of RNA helices clearly visible. A single layer of RNA directly contacts every copy of the coat protein, with one-third of the interactions occurring at operator-like RNA hairpins. These RNA-coat interactions stabilize the tertiary structure of gRNA within the virion, which could further provide a roadmap for capsid assembly.","corpus_id":885877,"score":1},{"doc_id":"28344575","title":"Identification of Capsid/Coat Related Protein Folds and Their Utility for Virus Classification.","abstract":"The viral supergroup includes the entire collection of known and unknown viruses that roam our planet and infect life forms. The supergroup is remarkably diverse both in its genetics and morphology and has historically remained difficult to study and classify. The accumulation of protein structure data in the past few years now provides an excellent opportunity to re-examine the classification and evolution of viruses. Here we scan completely sequenced viral proteomes from all genome types and identify protein folds involved in the formation of viral capsids and virion architectures. Viruses encoding similar capsid/coat related folds were pooled into lineages, after benchmarking against published literature. Remarkably, the in silico exercise reproduced all previously described members of known structure-based viral lineages, along with several proposals for new additions, suggesting it could be a useful supplement to experimental approaches and to aid qualitative assessment of viral diversity in metagenome samples.","corpus_id":17549486,"score":1},{"doc_id":"19680644","title":"Viruses: incredible nanomachines. New advances with filamentous phages.","abstract":"During recent decades, bacteriophages have been at the cutting edge of new developments in molecular biology, biophysics, and, more recently, bionanotechnology. In particular filamentous viruses, for example bacteriophage M13, have a virion architecture that enables precision building of ordered and defect-free two and three-dimensional structures on a nanometre scale. This could not have been possible without detailed knowledge of coat protein structure and dynamics during the virus reproduction cycle. The results of the spectroscopic studies conducted in our group compellingly demonstrate a critical role of membrane embedment of the protein both during infectious entry of the virus into the host cell and during assembly of the new virion in the host membrane. The protein is effectively embedded in the membrane by a strong C-terminal interfacial anchor, which together with a simple tilt mechanism and a subtle structural adjustment of the extreme end of its N terminus provides favourable thermodynamical association of the protein in the lipid bilayer. This basic physicochemical rule cannot be violated and any new bionanotechnology that will emerge from bacteriophage M13 should take this into account.","corpus_id":12721091,"score":0},{"doc_id":"19835886","title":"Structure of the small outer capsid protein, Soc: a clamp for stabilizing capsids of T4-like phages.","abstract":"Many viruses need to stabilize their capsid structure against DNA pressure and for survival in hostile environments. The 9-kDa outer capsid protein (Soc) of bacteriophage T4, which stabilizes the virus, attaches to the capsid during the final stage of maturation. There are 870 Soc molecules that act as a \"glue\" between neighboring hexameric capsomers, forming a \"cage\" that stabilizes the T4 capsid against extremes of pH and temperature. Here we report a 1.9 A resolution crystal structure of Soc from the bacteriophage RB69, a close relative of T4. The RB69 crystal structure and a homology model of T4 Soc were fitted into the cryoelectron microscopy reconstruction of the T4 capsid. This established the region of Soc that interacts with the major capsid protein and suggested a mechanism, verified by extensive mutational and biochemical studies, for stabilization of the capsid in which the Soc trimers act as clamps between neighboring capsomers. The results demonstrate the factors involved in stabilizing not only the capsids of T4-like bacteriophages but also many other virus capsids.","corpus_id":13071755,"score":0},{"doc_id":"20463071","title":"The T=1 capsid protein of Penicillium chrysogenum virus is formed by a repeated helix-rich core indicative of gene duplication.","abstract":"Penicillium chrysogenum virus (PcV), a member of the Chrysoviridae family, is a double-stranded RNA (dsRNA) fungal virus with a multipartite genome, with each RNA molecule encapsidated in a separate particle. Chrysoviruses lack an extracellular route and are transmitted during sporogenesis and cell fusion. The PcV capsid, based on a T=1 lattice containing 60 subunits of the 982-amino-acid capsid protein, remains structurally undisturbed throughout the viral cycle, participates in genome metabolism, and isolates the virus genome from host defense mechanisms. Using three-dimensional cryoelectron microscopy, we determined the structure of the PcV virion at 8.0 A resolution. The capsid protein has a high content of rod-like densities characteristic of alpha-helices, forming a repeated alpha-helical core indicative of gene duplication. Whereas the PcV capsid protein has two motifs with the same fold, most dsRNA virus capsid subunits consist of dimers of a single protein with similar folds. The spatial arrangement of the alpha-helical core resembles that found in the capsid protein of the L-A virus, a fungal totivirus with an undivided genome, suggesting a conserved basic fold. The encapsidated genome is organized in concentric shells; whereas the inner dsRNA shells are well defined, the outermost layer is dense due to numerous interactions with the inner capsid surface, specifically, six interacting areas per monomer. The outermost genome layer is arranged in an icosahedral cage, sufficiently well ordered to allow for modeling of an A-form dsRNA. The genome ordering might constitute a framework for dsRNA transcription at the capsid interior and/or have a structural role for capsid stability.","corpus_id":37639100,"score":0},{"doc_id":"20861247","title":"Structural characterization of the dual glycan binding adeno-associated virus serotype 6.","abstract":"The three-dimensional structure of adeno-associated virus (AAV) serotype 6 (AAV6) was determined using cryo-electron microscopy and image reconstruction and using X-ray crystallography to 9.7- and 3.0-Å resolution, respectively. The AAV6 capsid contains a highly conserved, eight-stranded (βB to βI) β-barrel core and large loop regions between the strands which form the capsid surface, as observed in other AAV structures. The loops show conformational variation compared to other AAVs, consistent with previous reports that amino acids in these loop regions are involved in differentiating AAV receptor binding, transduction efficiency, and antigenicity properties. Toward structure-function annotation of AAV6 with respect to its unique dual glycan receptor (heparan sulfate and sialic acid) utilization for cellular recognition, and its enhanced lung epithelial transduction compared to other AAVs, the capsid structure was compared to that of AAV1, which binds sialic acid and differs from AAV6 in only 6 out of 736 amino acids. Five of these residues are located at or close to the icosahedral 3-fold axis of the capsid, thereby identifying this region as imparting important functions, such as receptor attachment and transduction phenotype. Two of the five observed amino acids are located in the capsid interior, suggesting that differential AAV infection properties are also controlled by postentry intracellular events. Density ordered inside the capsid, under the 3-fold axis in a previously reported, conserved AAV DNA binding pocket, was modeled as a nucleotide and a base, further implicating this capsid region in AAV genome recognition and/or stabilization.","corpus_id":25791007,"score":0},{"doc_id":"21038867","title":"Discrete structure of an RNA folding intermediate revealed by cryo-electron microscopy.","abstract":"RNA folding occurs via a series of transitions between metastable intermediate states. It is unknown whether folding intermediates are discrete structures folding along defined pathways or heterogeneous ensembles folding along broad landscapes. We use cryo-electron microscopy and single-particle image reconstruction to determine the structure of the major folding intermediate of the specificity domain of a ribonuclease P ribozyme. Our results support the existence of a discrete conformation for this folding intermediate.","corpus_id":22344761,"score":0},{"doc_id":"21858752","title":"Adenovirus.","abstract":"Adenoviruses (AdV) are DNA viruses that typically cause mild infections involving the upper or lower respiratory tract, gastrointestinal (GI) tract, or conjunctiva. Rare manifestations of AdV infections include hemorrhagic cystitis, hepatitis, hemorrhagic colitis, pancreatitis, nephritis, or encephalitis. Adenovirus infections are more common in young children, owing to lack of humoral immunity. Epidemics of AdV infections may occur in healthy children or adults in closed or crowded settings (particularly military recruits). The disease is more severe, and dissemination is more likely in patients with impaired immunity (eg, organ transplant recipients, human immunodeficiency virus infection, congenital immunodeficiency syndromes). Fatality rates for untreated severe AdV pneumonia or disseminated disease may exceed 50%. More than 50 serotypes of AdV have been identified. Different serotypes display different tissue trophisms and correlate with clinical manifestations of infection. The predominant serotypes differ among countries or regions and change over time. Transmission of novel strains between countries or across continents and replacement of dominant serotypes by new strains may occur. Treatment of AdV infections is controversial because prospective, randomized therapeutic trials have not been done. Cidofovir is considered the drug of choice for severe AdV infections, but not all patients require treatment. Vaccines have been shown to be highly efficacious in reducing the risk of respiratory AdV infection but are currently not available.","corpus_id":260317561,"score":0},{"doc_id":"23695247","title":"Structure of the Triatoma virus capsid.","abstract":"The members of the Dicistroviridae family are non-enveloped positive-sense single-stranded RNA (+ssRNA) viruses pathogenic to beneficial arthropods as well as insect pests of medical importance. Triatoma virus (TrV), a member of this family, infects several species of triatomine insects (popularly named kissing bugs), which are vectors for human trypanosomiasis, more commonly known as Chagas disease. The potential use of dicistroviruses as biological control agents has drawn considerable attention in the past decade, and several viruses of this family have been identified, with their targets covering honey bees, aphids and field crickets, among others. Here, the crystal structure of the TrV capsid at 2.5 Å resolution is reported, showing that as expected it is very similar to that of Cricket paralysis virus (CrPV). Nevertheless, a number of distinguishing structural features support the introduction of a new genus (Triatovirus; type species TrV) under the Dicistroviridae family. The most striking differences are the absence of icosahedrally ordered VP4 within the infectious particle and the presence of prominent projections that surround the fivefold axis. Furthermore, the structure identifies a second putative autoproteolytic DDF motif in protein VP3, in addition to the conserved one in VP1 which is believed to be responsible for VP0 cleavage during capsid maturation. The potential meaning of these new findings is discussed.","corpus_id":18244528,"score":0},{"doc_id":"23719463","title":"Mature HIV-1 capsid structure by cryo-electron microscopy and all-atom molecular dynamics.","abstract":"Retroviral capsid proteins are conserved structurally but assemble into different morphologies. The mature human immunodeficiency virus-1 (HIV-1) capsid is best described by a 'fullerene cone' model, in which hexamers of the capsid protein are linked to form a hexagonal surface lattice that is closed by incorporating 12 capsid-protein pentamers. HIV-1 capsid protein contains an amino-terminal domain (NTD) comprising seven α-helices and a β-hairpin, a carboxy-terminal domain (CTD) comprising four α-helices, and a flexible linker with a 310-helix connecting the two structural domains. Structures of the capsid-protein assembly units have been determined by X-ray crystallography; however, structural information regarding the assembled capsid and the contacts between the assembly units is incomplete. Here we report the cryo-electron microscopy structure of a tubular HIV-1 capsid-protein assembly at 8 Å resolution and the three-dimensional structure of a native HIV-1 core by cryo-electron tomography. The structure of the tubular assembly shows, at the three-fold interface, a three-helix bundle with critical hydrophobic interactions. Mutagenesis studies confirm that hydrophobic residues in the centre of the three-helix bundle are crucial for capsid assembly and stability, and for viral infectivity. The cryo-electron-microscopy structures enable modelling by large-scale molecular dynamics simulation, resulting in all-atom models for the hexamer-of-hexamer and pentamer-of-hexamer elements as well as for the entire capsid. Incorporation of pentamers results in closer trimer contacts and induces acute surface curvature. The complete atomic HIV-1 capsid model provides a platform for further studies of capsid function and for targeted pharmacological intervention.","corpus_id":4373417,"score":0},{"doc_id":"23810697","title":"The asymmetric structure of an icosahedral virus bound to its receptor suggests a mechanism for genome release.","abstract":"Simple, spherical RNA viruses have well-understood, symmetric protein capsids, but little structural information is available for their asymmetric components, such as minor proteins and their genomes, which are vital for infection. Here, we report an asymmetric structure of bacteriophage MS2, attached to its receptor, the F-pilus. Cryo-electron tomography and subtomographic averaging of such complexes result in a structure containing clear density for the packaged genome, implying that the conformation of the genome is the same in each virus particle. The data also suggest that the single-copy viral maturation protein breaks the symmetry of the capsid, occupying a position that would be filled by a coat protein dimer in an icosahedral shell. This capsomere can thus fulfill its known biological roles in receptor and genome binding and suggests an exit route for the genome during infection.","corpus_id":18515668,"score":0},{"doc_id":"23827137","title":"Structure of the pseudorabies virus capsid: comparison with herpes simplex virus type 1 and differential binding of essential minor proteins.","abstract":"The structure of pseudorabies virus (PRV) capsids isolated from the nucleus of infected cells and from PRV virions was determined by cryo-electron microscopy (cryo-EM) and compared to herpes simplex virus type 1 (HSV-1) capsids. PRV capsid structures closely resemble those of HSV-1, including distribution of the capsid vertex specific component (CVSC) of HSV-1, which is a heterodimer of the pUL17 and pUL25 proteins. Occupancy of CVSC on all PRV capsids is near 100%, compared to ~50% reported for HSV-1 C-capsids and 25% or less that we measure for HSV-1 A- and B-capsids. A PRV mutant lacking pUL25 does not produce C-capsids and lacks visible CVSC density in the cryo-EM-based reconstruction. A reconstruction of PRV capsids in which green fluorescent protein was fused within the N-terminus of pUL25 confirmed previous studies with a similar HSV-1 capsid mutant localizing pUL25 to the CVSC density region that is distal to the penton. However, comparison of the CVSC density in a 9-Å-resolution PRV C-capsid map with the available crystal structure of HSV-1 pUL25 failed to find a satisfactory fit, suggesting either a different fold for PRV pUL25 or a capsid-bound conformation for pUL25 that does not match the X-ray model determined from protein crystallized in solution. The PRV capsid imaged within virions closely resembles C-capsids with the addition of weak but significant density shrouding the pentons that we attribute to tegument proteins. Our results demonstrate significant structure conservation between the PRV and HSV capsids.","corpus_id":19884115,"score":0},{"doc_id":"23966856","title":"The smallest capsid protein mediates binding of the essential tegument protein pp150 to stabilize DNA-containing capsids in human cytomegalovirus.","abstract":"Human cytomegalovirus (HCMV) is a ubiquitous herpesvirus that causes birth defects in newborns and life-threatening complications in immunocompromised individuals. Among all human herpesviruses, HCMV contains a much larger dsDNA genome within a similarly-sized capsid compared to the others, and it was proposed to require pp150, a tegument protein only found in cytomegaloviruses, to stabilize its genome-containing capsid. However, little is known about how pp150 interacts with the underlying capsid. Moreover, the smallest capsid protein (SCP), while dispensable in herpes simplex virus type 1, was shown to play essential, yet undefined, role in HCMV infection. Here, by cryo electron microscopy (cryoEM), we determine three-dimensional structures of HCMV capsid (no pp150) and virion (with pp150) at sub-nanometer resolution. Comparison of these two structures reveals that each pp150 tegument density is composed of two helix bundles connected by a long central helix. Correlation between the resolved helices and sequence-based secondary structure prediction maps the tegument density to the N-terminal half of pp150. The structures also show that SCP mediates interactions between the capsid and pp150 at the upper helix bundle of pp150. Consistent with this structural observation, ribozyme inhibition of SCP expression in HCMV-infected cells impairs the formation of DNA-containing viral particles and reduces viral yield by 10,000 fold. By cryoEM reconstruction of the resulting \"SCP-deficient\" viral particles, we further demonstrate that SCP is required for pp150 functionally binding to the capsid. Together, our structural and biochemical results point to a mechanism whereby SCP recruits pp150 to stabilize genome-containing capsid for the production of infectious HCMV virion.","corpus_id":753089,"score":0},{"doc_id":"24027306","title":"The structure and host entry of an invertebrate parvovirus.","abstract":"The 3.5-Å resolution X-ray crystal structure of mature cricket parvovirus (Acheta domesticus densovirus [AdDNV]) has been determined. Structural comparisons show that vertebrate and invertebrate parvoviruses have evolved independently, although there are common structural features among all parvovirus capsid proteins. It was shown that raising the temperature of the AdDNV particles caused a loss of their genomes. The structure of these emptied particles was determined by cryo-electron microscopy to 5.5-Å resolution, and the capsid structure was found to be the same as that for the full, mature virus except for the absence of the three ordered nucleotides observed in the crystal structure. The viral protein 1 (VP1) amino termini could be externalized without significant damage to the capsid. In vitro, this externalization of the VP1 amino termini is accompanied by the release of the viral genome.","corpus_id":25223900,"score":0},{"doc_id":"24282305","title":"Rubella virus capsid protein structure and its role in virus assembly and infection.","abstract":"Rubella virus (RV) is a leading cause of birth defects due to infectious agents. When contracted during pregnancy, RV infection leads to severe damage in fetuses. Despite its medical importance, compared with the related alphaviruses, very little is known about the structure of RV. The RV capsid protein is an essential structural component of virions as well as a key factor in virus-host interactions. Here we describe three crystal structures of the structural domain of the RV capsid protein. The polypeptide fold of the RV capsid protomer has not been observed previously. Combining the atomic structure of the RV capsid protein with the cryoelectron tomograms of RV particles established a low-resolution structure of the virion. Mutational studies based on this structure confirmed the role of amino acid residues in the capsid that function in the assembly of infectious virions.","corpus_id":28331583,"score":0},{"doc_id":"24582831","title":"Structure and assembly of filamentous bacteriophages.","abstract":"Filamentous bacteriophages are interesting paradigms in structural molecular biology, in part because of the unusual mechanism of filamentous phage assembly. During assembly, several thousand copies of an intracellular DNA-binding protein bind to each copy of the replicating phage DNA, and are then displaced by membrane-spanning phage coat proteins as the nascent phage is extruded through the bacterial plasma membrane. This complicated process takes place without killing the host bacterium. The bacteriophage is a semi-flexible worm-like nucleoprotein filament. The virion comprises a tube of several thousand identical major coat protein subunits around a core of single-stranded circular DNA. Each protein subunit is a polymer of about 50 amino-acid residues, largely arranged in an α-helix. The subunits assemble into a helical sheath, with each subunit oriented at a small angle to the virion axis and interdigitated with neighbouring subunits. A few copies of \"minor\" phage proteins necessary for infection and/or extrusion of the virion are located at each end of the completed virion. Here we review both the structure of the virion and aspects of its function, such as the way the virion enters the host, multiplies, and exits to prey on further hosts. In particular we focus on our understanding of the way the components of the virion come together during assembly at the membrane. We try to follow a basic rule of empirical science, that one should chose the simplest theoretical explanation for experiments, but be prepared to modify or even abandon this explanation as new experiments add more detail.","corpus_id":207336143,"score":0},{"doc_id":"24648455","title":"Limits of structural plasticity in a picornavirus capsid revealed by a massively expanded equine rhinitis A virus particle.","abstract":"UNLABELLED: The Picornaviridae family of small, nonenveloped viruses includes major pathogens of humans and animals. They have positive-sense, single-stranded RNA genomes, and the mechanism(s) by which these genomes are introduced into cells to initiate infection remains poorly understood. The structures of presumed uncoating intermediate particles of several picornaviruses show limited expansion and some increased porosity compared to the mature virions. Here, we present the cryo-electron microscopy structure of native equine rhinitis A virus (ERAV), together with the structure of a massively expanded ERAV particle, each at ∼17-Å resolution. The expanded structure has large pores on the particle 3-fold axes and has lost the RNA genome and the capsid protein VP4. The expanded structure thus illustrates both the limits of structural plasticity in such capsids and a plausible route by which genomic RNA might exit. IMPORTANCE: Picornaviruses are important animal and human pathogens that protect their genomic RNAs within a protective protein capsid. Upon infection, this genomic RNA must be able to leave the capsid to initiate a new round of infection. We describe here the structure of a unique, massively expanded state of equine rhinitis A virus that provides insight into how this exit might occur.","corpus_id":14749439,"score":0},{"doc_id":"26167882","title":"The molecular basis for flexibility in the flexible filamentous plant viruses.","abstract":"Flexible filamentous plant viruses cause more than half the viral crop damage in the world but are also potentially useful for biotechnology. Structural studies began more than 75 years ago but have failed, owing to the virion's extreme flexibility. We have used cryo-EM to generate an atomic model for bamboo mosaic virus, which reveals flexible N- and C-terminal extensions that allow deformation while still maintaining structural integrity.","corpus_id":6551037,"score":0},{"doc_id":"26374901","title":"Electron microscopic imaging revealed the flexible filamentous structure of the cell attachment protein P2 of Rice dwarf virus located around the icosahedral 5-fold axes.","abstract":"The minor outer capsid protein P2 of Rice dwarf virus (RDV), a member of the genus Phytoreovirus in the family Reoviridae, is essential for viral cell entry. Here, we clarified the structure of P2 and the interactions to host insect cells. Negative stain electron microscopy (EM) showed that P2 proteins are monomeric and flexible L-shaped filamentous structures of ∼20 nm in length. Cryo-EM structure revealed the spatial arrangement of P2 in the capsid, which was prescribed by the characteristic virion structure. The P2 proteins were visualized as partial rod-shaped structures of ∼10 nm in length in the cryo-EM map and accommodated in crevasses on the viral surface around icosahedral 5-fold axes with hydrophobic interactions. The remaining disordered region of P2 assumed to be extended to the radial direction towards exterior. Electron tomography clearly showed that RDV particles were away from the cellular membrane at a uniform distance and several spike-like densities, probably corresponding to P2, connecting a viral particle to the host cellular membrane during cell entry. By combining the in vitro and in vivo structural information, we could gain new insights into the detailed mechanism of the cell entry of RDV.","corpus_id":34250693,"score":0},{"doc_id":"26446437","title":"Structure of Ljungan virus provides insight into genome packaging of this picornavirus.","abstract":"Picornaviruses are responsible for a range of human and animal diseases, but how their RNA genome is packaged remains poorly understood. A particularly poorly studied group within this family are those that lack the internal coat protein, VP4. Here we report the atomic structure of one such virus, Ljungan virus, the type member of the genus Parechovirus B, which has been linked to diabetes and myocarditis in humans. The 3.78-Å resolution cryo-electron microscopy structure shows remarkable features, including an extended VP1 C terminus, forming a major protuberance on the outer surface of the virus, and a basic motif at the N terminus of VP3, binding to which orders some 12% of the viral genome. This apparently charge-driven RNA attachment suggests that this branch of the picornaviruses uses a different mechanism of genome encapsidation, perhaps explored early in the evolution of picornaviruses.","corpus_id":12160583,"score":0},{"doc_id":"26939061","title":"Morphology and Molecular Composition of Purified Bovine Viral Diarrhea Virus Envelope.","abstract":"The family Flaviviridae includes viruses that have different virion structures and morphogenesis mechanisms. Most cellular and molecular studies have been so far performed with viruses of the Hepacivirus and Flavivirus genera. Here, we studied bovine viral diarrhea virus (BVDV), a member of the Pestivirus genus. We set up a method to purify BVDV virions and analyzed their morphology by electron microscopy and their protein and lipid composition by mass spectrometry. Cryo-electron microscopy showed near spherical viral particles displaying an electron-dense capsid surrounded by a phospholipid bilayer with no visible spikes. Most particles had a diameter of 50 nm and about 2% were larger with a diameter of up to 65 nm, suggesting some size flexibility during BVDV morphogenesis. Morphological and biochemical data suggested a low envelope glycoprotein content of BVDV particles, E1 and E2 being apparently less abundant than Erns. Lipid content of BVDV particles displayed a ~2.3 to 3.5-fold enrichment in cholesterol, sphingomyelin and hexosyl-ceramide, concomitant with a 1.5 to 5-fold reduction of all glycerophospholipid classes, as compared to lipid content of MDBK cells. Although BVDV buds in the endoplasmic reticulum, its lipid content differs from a typical endoplasmic reticulum membrane composition. This suggests that BVDV morphogenesis includes a mechanism of lipid sorting. Functional analyses confirmed the importance of cholesterol and sphingomyelin for BVDV entry. Surprisingly, despite a high cholesterol and sphingolipid content of BVDV envelope, E2 was not found in detergent-resistant membranes. Our results indicate that there are differences between the structure and molecular composition of viral particles of Flaviviruses, Pestiviruses and Hepaciviruses within the Flaviviridae family.","corpus_id":285662,"score":0},{"doc_id":"27021160","title":"Crystal Structure and Proteomics Analysis of Empty Virus-like Particles of Cowpea Mosaic Virus.","abstract":"Empty virus-like particles (eVLPs) of Cowpea mosaic virus (CPMV) are currently being utilized as reagents in various biomedical and nanotechnology applications. Here, we report the crystal structure of CPMV eVLPs determined using X-ray crystallography at 2.3 Å resolution and compare it with previously reported cryo-electron microscopy (cryo-EM) of eVLPs and virion crystal structures. Although the X-ray and cryo-EM structures of eVLPs are mostly similar, there exist significant differences at the C terminus of the small (S) subunit. The intact C terminus of the S subunit plays a critical role in enabling the efficient assembly of CPMV virions and eVLPs, but undergoes proteolysis after particle formation. In addition, we report the results of mass spectrometry-based proteomics analysis of coat protein subunits from CPMV eVLPs and virions that identify the C termini of S subunits undergo proteolytic cleavages at multiple sites instead of a single cleavage site as previously observed.","corpus_id":12343799,"score":0},{"doc_id":"27111889","title":"Extensive subunit contacts underpin herpesvirus capsid stability and interior-to-exterior allostery.","abstract":"The herpesvirus capsid is a complex protein assembly that includes hundreds of copies of four major subunits and lesser numbers of several minor proteins, all of which are essential for infectivity. Cryo-electron microscopy is uniquely suited for studying interactions that govern the assembly and function of such large functional complexes. Here we report two high-quality capsid structures, from human herpes simplex virus type 1 (HSV-1) and the animal pseudorabies virus (PRV), imaged inside intact virions at ~7-Å resolution. From these, we developed a complete model of subunit and domain organization and identified extensive networks of subunit contacts that underpin capsid stability and form a pathway that may signal the completion of DNA packaging from the capsid interior to outer surface, thereby initiating nuclear egress. Differences in the folding and orientation of subunit domains between herpesvirus capsids suggest that common elements have been modified for specific functions.","corpus_id":16786704,"score":0},{"doc_id":"27561669","title":"Asymmetric cryo-EM reconstruction of phage MS2 reveals genome structure in situ.","abstract":"In single-stranded ribonucleic acid (RNA) viruses, virus capsid assembly and genome packaging are intertwined processes. Using cryo-electron microscopy and single particle analysis we determined the asymmetric virion structure of bacteriophage MS2, which includes 178 copies of the coat protein, a single copy of the A-protein and the RNA genome. This reveals that in situ, the viral RNA genome can adopt a defined conformation. The RNA forms a branched network of stem-loops that almost all allocate near the capsid inner surface, while predominantly binding to coat protein dimers that are located in one-half of the capsid. This suggests that genomic RNA is highly involved in genome packaging and virion assembly.","corpus_id":6903077,"score":0},{"doc_id":"27591890","title":"Structure of AP205 Coat Protein Reveals Circular Permutation in ssRNA Bacteriophages.","abstract":"AP205 is a single-stranded RNA bacteriophage that has a coat protein sequence not similar to any other known single-stranded RNA phage. Here, we report an atomic-resolution model of the AP205 virus-like particle based on a crystal structure of an unassembled coat protein dimer and a cryo-electron microscopy reconstruction of the assembled particle, together with secondary structure information from site-specific solid-state NMR data. The AP205 coat protein dimer adopts the conserved Leviviridae coat protein fold except for the N-terminal region, which forms a beta-hairpin in the other known single-stranded RNA phages. AP205 has a similar structure at the same location formed by N- and C-terminal beta-strands, making it a circular permutant compared to the other coat proteins. The permutation moves the coat protein termini to the most surface-exposed part of the assembled particle, which explains its increased tolerance to long N- and C-terminal fusions.","corpus_id":31201789,"score":0},{"doc_id":"28065506","title":"Cryoelectron Microscopy Maps of Human Papillomavirus 16 Reveal L2 Densities and Heparin Binding Site.","abstract":"Human papillomavirus (HPV) is a significant health burden and leading cause of virus-induced cancers. The current commercial vaccines are genotype specific and provide little therapeutic benefit to patients with existing HPV infections. Host entry mechanisms represent an excellent target for alternative therapeutics, but HPV receptor use, the details of cell attachment, and host entry are inadequately understood. Here we present near-atomic resolution structures of the HPV16 capsid and HPV16 in complex with heparin, both determined from cryoelectron micrographs collected with direct electron detection technology. The structures clarify details of capsid architecture for the first time, including variation in L1 major capsid protein conformation and putative location of L2 minor protein. Heparin binds specifically around the capsid icosahedral vertices and may recapitulate the earliest stage of infection, providing a framework for continuing biochemical, genetic, and biophysical studies.","corpus_id":10097476,"score":0},{"doc_id":"28320961","title":"Structure of a headful DNA-packaging bacterial virus at 2.9 Å resolution by electron cryo-microscopy.","abstract":"The enormous prevalence of tailed DNA bacteriophages on this planet is enabled by highly efficient self-assembly of hundreds of protein subunits into highly stable capsids. These capsids can stand with an internal pressure as high as ∼50 atmospheres as a result of the phage DNA-packaging process. Here we report the complete atomic model of the headful DNA-packaging bacteriophage Sf6 at 2.9 Å resolution determined by electron cryo-microscopy. The structure reveals the DNA-inflated, tensed state of a robust protein shell assembled via noncovalent interactions. Remarkable global conformational polymorphism of capsid proteins, a network formed by extended N arms, mortise-and-tenon-like intercapsomer joints, and abundant β-sheet-like mainchain:mainchain intermolecular interactions, confers significant strength yet also flexibility required for capsid assembly and DNA packaging. Differential formations of the hexon and penton are mediated by a drastic α-helix-to-β-strand structural transition. The assembly scheme revealed here may be common among tailed DNA phages and herpesviruses.","corpus_id":205282017,"score":0},{"doc_id":"29190455","title":"Structural features of the salivary gland hypertrophy virus of the tsetse fly revealed by cryo-electron microscopy and tomography.","abstract":"Glossina palipides salivary gland hypertrophy virus (GpSGHV) infects tsetse flies, which are vectors for African trypanosomosis. This virus represents a major challenge in insect mass rearing and has hampered the implementation of the sterile insect technique programs in the Member States of the International Atomic Energy Agency. GpSGHV virions consist of long rod-shaped particles over 9000Å in length, but little is known about their detailed structural organization. We show by cryo electron microscopy and cryo electron tomography that the GpSGHV virion has a unique, non-icosahedral helical structure. Its envelope exhibits regularly spaced spikes that protrude from the lipid bilayer and are arranged on a four-start helix. This study provides a detailed insight into the 3D architecture of GpSGHV, which will help to understand the viral life cycle and possibly allow the design of antiviral strategies in the context of tsetse fly infections.","corpus_id":4863623,"score":0},{"doc_id":"29211815","title":"Bacteria and bacterial envelope components enhance mammalian reovirus thermostability.","abstract":"Enteric viruses encounter diverse environments as they migrate through the gastrointestinal tract to infect their hosts. The interaction of eukaryotic viruses with members of the host microbiota can greatly impact various aspects of virus biology, including the efficiency with which viruses can infect their hosts. Mammalian orthoreovirus, a human enteric virus that infects most humans during childhood, is negatively affected by antibiotic treatment prior to infection. However, it is not known how components of the host microbiota affect reovirus infectivity. In this study, we show that reovirus virions directly interact with Gram positive and Gram negative bacteria. Reovirus interaction with bacterial cells conveys enhanced virion thermostability that translates into enhanced attachment and infection of cells following an environmental insult. Enhanced virion thermostability was also conveyed by bacterial envelope components lipopolysaccharide (LPS) and peptidoglycan (PG). Lipoteichoic acid and N-acetylglucosamine-containing polysaccharides enhanced virion stability in a serotype-dependent manner. LPS and PG also enhanced the thermostability of an intermediate reovirus particle (ISVP) that is associated with primary infection in the gut. Although LPS and PG alter reovirus thermostability, these bacterial envelope components did not affect reovirus utilization of its proteinaceous cellular receptor junctional adhesion molecule-A or cell entry kinetics. LPS and PG also did not affect the overall number of reovirus capsid proteins σ1 and σ3, suggesting their effect on virion thermostability is not mediated through altering the overall number of major capsid proteins on the virus. Incubation of reovirus with LPS and PG did not significantly affect the neutralizing efficiency of reovirus-specific antibodies. These data suggest that bacteria enhance reovirus infection of the intestinal tract by enhancing the thermal stability of the reovirus particle at a variety of temperatures through interactions between the viral particle and bacterial envelope components.","corpus_id":4035645,"score":0}],"string":"[\n {\n \"doc_id\": \"18166240\",\n \"title\": \"Completion of the genome analysis of snake adenovirus type 1, a representative of the reptilian lineage within the novel genus Atadenovirus.\",\n \"abstract\": \"Genome sequencing and analysis of snake adenovirus type 1 (SnAdV-1), originating from corn snake, were completed. This is the first full genomic sequence of an adenovirus from reptilian hosts. The presence of characteristic genus-common genes and transcription units, showed that SnAdV-1 shares similar genome organisation with members of the recently established genus Atadenovirus. Three novel open reading frames of yet unknown functions were found. One of these seemed to be related to a putative gene, the so-called 105R that has recently been described from the genome of the tree shrew adenovirus. The other two putative genes were found to be unique for SnAdV-1. On phylogenetic trees, SnAdV-1 clustered within the atadenovirus clade. Thereby the hypothesis on the reptilian origin of atadenoviruses was further strengthened. Interestingly, however, one of the most striking features of atadenoviruses, namely the base content heavily biased towards A+T, is not characteristic for SnAdV-1 having a genome of balanced composition with a G+C value of 50.21%.\",\n \"corpus_id\": 205654171,\n \"score\": 2\n },\n {\n \"doc_id\": \"18216088\",\n \"title\": \"Three-dimensional structure of canine adenovirus serotype 2 capsid.\",\n \"abstract\": \"There are more than 100 known adenovirus (AdV) serotypes, including 50 human serotypes. Because AdV-induced disease is relatively species specific, vectors derived from nonhuman serotypes may have wider clinical potential based, in part, on the lack of ubiquitous memory immunity. Whereas a few of the human serotype capsids have been studied at the structural level, none of the nonhuman serotypes has been analyzed. The basis laid by the analysis of human AdV (hAdV) has allowed us to determine and compare the three-dimensional structure of the capsid of canine serotype 2 (CAV-2) to that of hAdV serotype 5 (hAdV-5). We show that CAV-2 capsid has a smoother structure than the human serotypes. Many of the external loops found in the hAdV-5 penton base and the hexon, against which the antibody response is directed, are shorter or absent in CAV-2. On the other hand, the CAV-2 fiber appears to be more complex, with two bends in the shaft. An interesting difference between the human and canine viruses is that the C-terminal part of protein IX is in a different position, making an antenna sticking out of the CAV-2 capsid. The comparison between the two viruses allows the identification of sites that should be easy to modify on the CAV-2 capsid for altering tissue tropism or other biological activities.\",\n \"corpus_id\": 7712466,\n \"score\": 2\n },\n {\n \"doc_id\": \"18508893\",\n \"title\": \"Cryoelectron microscopy map of Atadenovirus reveals cross-genus structural differences from human adenovirus.\",\n \"abstract\": \"A three-dimensional (3D) cryoelectron microscopy reconstruction of the prototype Atadenovirus (OAdV [an ovine adenovirus isolate]) showing information at a 10.6-A resolution (0.5 Fourier shell correlation) was derived by single-particle analysis. This is the first 3D structure solved for any adenovirus that is not a Mastadenovirus, allowing cross-genus comparisons between structures and the assignment of genus-specific capsid proteins. Viable OAdV mutants that lacked the genus-specific LH3 and p32k proteins in purified virions were also generated. Negatively stained 3D reconstructions of these mutants were used to identify the location of protein LH3 and infer that of p32k within the capsid. The key finding was that LH3 is a critical protein that holds the outer capsid of the virus together. In its absence, the outer viral capsid is unstable. LH3 is located in the same position among the hexon subunits as its protein IX equivalent from mastadenoviruses but sits on top of the hexon trimers, forming prominent \\\"knobs\\\" on the virion surface that visually distinguish OAdV from other known AdVs. Electron density was also assigned to hexon and penton subunits and to proteins IIIa and VIII. There was good correspondence between OAdV density and human AdV hexon structures, which also validated the significant differences that were observed between the penton base protein structures.\",\n \"corpus_id\": 29949421,\n \"score\": 2\n },\n {\n \"doc_id\": \"18786402\",\n \"title\": \"Bacteriophage lambda stabilization by auxiliary protein gpD: timing, location, and mechanism of attachment determined by cryo-EM.\",\n \"abstract\": \"We report the cryo-EM structure of bacteriophage lambda and the mechanism for stabilizing the 20-A-thick capsid containing the dsDNA genome. The crystal structure of the HK97 bacteriophage capsid fits most of the T = 7 lambda particle density with only minor adjustment. A prominent surface feature at the 3-fold axes corresponds to the cementing protein gpD, which is necessary for stabilization of the capsid shell. Its position coincides with the location of the covalent cross-link formed in the docked HK97 crystal structure, suggesting an evolutionary replacement of this gene product in lambda by autocatalytic chemistry in HK97. The crystal structure of the trimeric gpD, in which the 14 N-terminal residues required for capsid binding are disordered, fits precisely into the corresponding EM density. The N-terminal residues of gpD are well ordered in the cryo-EM density, adding a strand to a beta-sheet formed by the capsid proteins and explaining the mechanism of particle stabilization.\",\n \"corpus_id\": 205258718,\n \"score\": 2\n },\n {\n \"doc_id\": \"20798312\",\n \"title\": \"Atomic structure of human adenovirus by cryo-EM reveals interactions among protein networks.\",\n \"abstract\": \"Construction of a complex virus may involve a hierarchy of assembly elements. Here, we report the structure of the whole human adenovirus virion at 3.6 angstroms resolution by cryo-electron microscopy (cryo-EM), revealing in situ atomic models of three minor capsid proteins (IIIa, VIII, and IX), extensions of the (penton base and hexon) major capsid proteins, and interactions within three protein-protein networks. One network is mediated by protein IIIa at the vertices, within group-of-six (GOS) tiles--a penton base and its five surrounding hexons. Another is mediated by ropes (protein IX) that lash hexons together to form group-of-nine (GON) tiles and bind GONs to GONs. The third, mediated by IIIa and VIII, binds each GOS to five surrounding GONs. Optimization of adenovirus for cancer and gene therapy could target these networks.\",\n \"corpus_id\": 206525577,\n \"score\": 2\n },\n {\n \"doc_id\": \"20798318\",\n \"title\": \"Crystal structure of human adenovirus at 3.5 A resolution.\",\n \"abstract\": \"Rational development of adenovirus vectors for therapeutic gene transfer is hampered by the lack of accurate structural information. Here, we report the x-ray structure at 3.5 angstrom resolution of the 150-megadalton adenovirus capsid containing nearly 1 million amino acids. We describe interactions between the major capsid protein (hexon) and several accessory molecules that stabilize the capsid. The virus structure also reveals an altered association between the penton base and the trimeric fiber protein, perhaps reflecting an early event in cell entry. The high-resolution structure provides a substantial advance toward understanding the assembly and cell entry mechanisms of a large double-stranded DNA virus and provides new opportunities for improving adenovirus-mediated gene transfer.\",\n \"corpus_id\": 38763893,\n \"score\": 2\n },\n {\n \"doc_id\": \"21071053\",\n \"title\": \"The host outer membrane proteins OmpA and OmpC are associated with the Shigella phage Sf6 virion.\",\n \"abstract\": \"Assembly of dsDNA bacteriophage is a precisely programmed process. Potential roles of host cell components in phage assembly haven't been well understood. It was previously reported that two unidentified proteins were present in bacteriophage Sf6 virion (Casjens et al, 2004, J.Mol. Biol. 339, 379-394, Fig. 2A). Using tandem mass spectrometry, we have identified the two proteins as outer membrane proteins (OMPs) OmpA and OmpC from its host Shigella flexneri. The transmission electron cryo-microscopy structure of Sf6 shows significant density at specific sites at the phage capsid inner surface. This density fit well with the characteristic beta-barrel domains of OMPs, thus may be due to the two host proteins. Locations of this density suggest a role in Sf6 morphogenesis reminiscent of phage-encoded cementing proteins. These data indicate a new, OMP-related phage:host linkage, adding to previous knowledge that some lambdoid bacteriophage genomes contain OmpC-like genes that express phage-encoded porins in the lysogenic state.\",\n \"corpus_id\": 15371524,\n \"score\": 2\n },\n {\n \"doc_id\": \"22754652\",\n \"title\": \"Latest insights on adenovirus structure and assembly.\",\n \"abstract\": \"Adenovirus (AdV) capsid organization is considerably complex, not only because of its large size (~950 Å) and triangulation number (pseudo T = 25), but also because it contains four types of minor proteins in specialized locations modulating the quasi-equivalent icosahedral interactions. Up until 2009, only its major components (hexon, penton, and fiber) had separately been described in atomic detail. Their relationships within the virion, and the location of minor coat proteins, were inferred from combining the known crystal structures with increasingly more detailed cryo-electron microscopy (cryoEM) maps. There was no structural information on assembly intermediates. Later on that year, two reports described the structural differences between the mature and immature adenoviral particle, starting to shed light on the different stages of viral assembly, and giving further insights into the roles of core and minor coat proteins during morphogenesis [1,2]. Finally, in 2010, two papers describing the atomic resolution structure of the complete virion appeared [3,4]. These reports represent a veritable tour de force for two structural biology techniques: X-ray crystallography and cryoEM, as this is the largest macromolecular complex solved at high resolution by either of them. In particular, the cryoEM analysis provided an unprecedented clear picture of the complex protein networks shaping the icosahedral shell. Here I review these latest developments in the field of AdV structural studies.\",\n \"corpus_id\": 15455524,\n \"score\": 2\n },\n {\n \"doc_id\": \"25056898\",\n \"title\": \"Molecular characterization of a lizard adenovirus reveals the first atadenovirus with two fiber genes and the first adenovirus with either one short or three long fibers per penton.\",\n \"abstract\": \"UNLABELLED: Although adenoviruses (AdVs) have been found in a wide variety of reptiles, including numerous squamate species, turtles, and crocodiles, the number of reptilian adenovirus isolates is still scarce. The only fully sequenced reptilian adenovirus, snake adenovirus 1 (SnAdV-1), belongs to the Atadenovirus genus. Recently, two new atadenoviruses were isolated from a captive Gila monster (Heloderma suspectum) and Mexican beaded lizards (Heloderma horridum). Here we report the full genomic and proteomic characterization of the latter, designated lizard adenovirus 2 (LAdV-2). The double-stranded DNA (dsDNA) genome of LAdV-2 is 32,965 bp long, with an average G+C content of 44.16%. The overall arrangement and gene content of the LAdV-2 genome were largely concordant with those in other atadenoviruses, except for four novel open reading frames (ORFs) at the right end of the genome. Phylogeny reconstructions and plesiomorphic traits shared with SnAdV-1 further supported the assignment of LAdV-2 to the Atadenovirus genus. Surprisingly, two fiber genes were found for the first time in an atadenovirus. After optimizing the production of LAdV-2 in cell culture, we determined the protein compositions of the virions. The two fiber genes produce two fiber proteins of different sizes that are incorporated into the viral particles. Interestingly, the two different fiber proteins assemble as either one short or three long fiber projections per vertex. Stoichiometry estimations indicate that the long fiber triplet is present at only one or two vertices per virion. Neither triple fibers nor a mixed number of fibers per vertex had previously been reported for adenoviruses or any other virus. IMPORTANCE: Here we show that a lizard adenovirus, LAdV-2, has a penton architecture never observed before. LAdV-2 expresses two fiber proteins-one short and one long. In the virion, most vertices have one short fiber, but a few of them have three long fibers attached to the same penton base. This observation raises new intriguing questions on virus structure. How can the triple fiber attach to a pentameric vertex? What determines the number and location of each vertex type in the icosahedral particle? Since fibers are responsible for primary attachment to the host, this novel architecture also suggests a novel mode of cell entry for LAdV-2. Adenoviruses have a recognized potential in nanobiomedicine, but only a few of the more than 200 types found so far in nature have been characterized in detail. Exploring the taxonomic wealth of adenoviruses should improve our chances to successfully use them as therapeutic tools.\",\n \"corpus_id\": 44788628,\n \"score\": 2\n },\n {\n \"doc_id\": \"27807242\",\n \"title\": \"Evolution and Cryo-electron Microscopy Capsid Structure of a North American Bat Adenovirus and Its Relationship to Other Mastadenoviruses.\",\n \"abstract\": \"Since the first description of adenoviruses in bats in 2006, a number of micro- and megabat species in Europe, Africa, and Asia have been shown to carry a wide diversity of adenoviruses. Here, we report on the evolutionary, biological, and structural characterization of a novel bat adenovirus (BtAdV) recovered from a Rafinesque's big-eared bat (Corynorhinus rafinesquii) in Kentucky, USA, which is the first adenovirus isolated from North American bats. This virus (BtAdV 250-A) exhibits a close phylogenetic relationship with Canine mastadenovirus A (CAdV A), as previously observed with other BtAdVs. To further investigate the relationships between BtAdVs and CAdVs, we conducted mass spectrometric analysis and single-particle cryo-electron microscopy reconstructions of the BtAdV 250-A capsid and also analyzed the in vitro host ranges of both viruses. Our results demonstrate that BtAdV 250-A represents a new mastadenovirus species that, in contrast to CAdV, has a unique capsid morphology that contains more prominent extensions of protein IX and can replicate efficiently in a phylogenetically diverse range of species. These findings, in addition to the recognition that both the genetic diversity of BtAdVs and the number of different bat species from disparate geographic regions infected with BtAdVs appears to be extensive, tentatively suggest that bats may have served as a potential reservoir for the cross-species transfer of adenoviruses to other hosts, as theorized for CAdV. IMPORTANCE: Although many adenoviruses are host specific and likely codiverged with their hosts over millions of years, other adenoviruses appear to have emerged through successful cross-species transmission events on more recent time scales. The wide geographic distribution and genetic diversity of adenoviruses in bats and their close phylogenetic relationship to Canine mastadenovirus A (CAdV A) has raised important questions about how CAdV A, and possibly other mammalian adenoviruses, may have emerged. Although most adenoviruses tend to cause limited disease in their natural hosts, CAdV A is unusual in that it may cause high morbidity and sometimes fatal infections in immunocompetent hosts and is thus an important pathogen of carnivores. Here, we performed a comparative evolutionary and structural study of representative bat and canine adenoviruses to better understand the relationship between these two viral groups.\",\n \"corpus_id\": 29423462,\n \"score\": 2\n },\n {\n \"doc_id\": \"28456019\",\n \"title\": \"Dual host specificity of phage SP6 is facilitated by tailspike rotation.\",\n \"abstract\": \"Bacteriophage SP6 exhibits dual-host adsorption specificity. The SP6 tailspikes are recognized as important in host range determination but the mechanisms underlying dual host specificity are unknown. Cryo-electron tomography and sub-tomogram classification were used to analyze the SP6 virion with a particular focus on the interaction of tailspikes with host membranes. The SP6 tail is surrounded by six V-shaped structures that interconnect in forming a hand-over-hand hexameric garland. Each V-shaped structure consists of two trimeric tailspike proteins: gp46 and gp47, connected through the adaptor protein gp37. SP6 infection of Salmonella enterica serovars Typhimurium and Newport results in distinguishable changes in tailspike orientation, providing the first direct demonstration how tailspikes can confer dual host adsorption specificity. SP6 also infects S. Typhimurium strains lacking O antigen; in these infections tailspikes have no apparent specific role and the phage tail must therefore interact with a distinct host receptor to allow infection.\",\n \"corpus_id\": 22528751,\n \"score\": 2\n },\n {\n \"doc_id\": \"18547389\",\n \"title\": \"Crystal structure of Escherichia coli phage HK620 tailspike: podoviral tailspike endoglycosidase modules are evolutionarily related.\",\n \"abstract\": \"Bacteriophage HK620 infects Escherichia coli H and is closely related to Shigella phage Sf6 and Salmonella phage P22. All three Podoviridae recognize and cleave their respective host cell receptor polysaccharide by homotrimeric tailspike proteins. The three proteins exhibit high sequence identity in the 110 residues of their N-terminal particle-binding domains, but no apparent sequence similarity in their major, receptor-binding parts. We have biochemically characterized the receptor-binding part of HK620 tailspike and determined its crystal structure to 1.38 A resolution. Its major domain is a right-handed parallel beta-helix, as in Sf6 and P22 tailspikes. HK620 tailspike has endo-N-acetylglucosaminidase activity and produces hexasaccharides of an O18A1-type O-antigen. As indicated by the structure of a hexasaccharide complex determined at 1.6 A resolution, the endoglycosidase-active sites are located intramolecularly, as in P22, and not between subunits, as in Sf6 tailspike. In contrast, the extreme C-terminal domain of HK620 tailspike forms a beta-sandwich, as in Sf6 and unlike P22 tailspike. Despite the different folds, structure-based sequence alignments of the C-termini reveal motifs conserved between the three proteins. We propose that the tailspike genes of P22, Sf6 and HK620 have a common precursor and are not mosaics of unrelated gene fragments.\",\n \"corpus_id\": 34854199,\n \"score\": 1\n },\n {\n \"doc_id\": \"18824312\",\n \"title\": \"PCR-sequence characterization of new adenoviruses found in reptiles and the first successful isolation of a lizard adenovirus.\",\n \"abstract\": \"A consensus nested PCR was used to screen diagnostic samples from approximately 70 reptiles for the presence of adenoviruses (AdV) in the years 2006-2007. Classical virus isolation methods were also used with all samples. After adenoviruses were detected in a group of helodermatid lizards in a Danish zoo, a follow-up study was also carried out on lizards from this group (10 Mexican beaded lizards and 24 Gila monsters) over the period of a year. Adenoviruses were detected in a total of 26 lizards and snakes by PCR. The PCR amplicons from all positive animals were sequenced and the resulting polymerase gene sequences were used for phylogenetic analysis. Altogether six Agamid AdVs were amplified, with a minimal sequence variation between one another and between these and GenBank Agamid AdVs. The sequence obtained from one of the Gila monsters is identical with the GenBank Helodermatid AdV, while the sequences from the Mexican beaded lizards differ from this. In a snake collection we have detected a new AdV from an Asp viper. All of the above mentioned adenoviruses cluster in the Atadenovirus genus. However, the sequence from a new Varanid AdV detected in this study clusters outside this genus. On cell culture, viruses were isolated from three of the AdV positive helodermatid lizards (one Mexican beaded lizard and two Gila monsters) and identified as AdVs based on electron microscopy and PCR and sequencing using cell culture supernatant. This is the first report of the successful isolation of a lizard AdV.\",\n \"corpus_id\": 19811017,\n \"score\": 1\n },\n {\n \"doc_id\": \"20376613\",\n \"title\": \"Adenovirus.\",\n \"abstract\": \"Of the 53 different human adenovirus (HAdV) serotypes belonging to species A-G, a significant number are associated with acute respiratory, gastrointestinal and ocular infections. Replication-defective HAdV-5-based vectors also continue to play a significant role in gene transfer trials and in vaccine delivery efforts in the clinic. Although significant progress has been made from studies of AdV biology, we still have an incomplete understanding of AdV's structure as well as its multifactorial interactions with the host. Continuing efforts to improve knowledge in these areas, as discussed in this chapter, will be crucial for revealing the mechanisms of AdV pathogenesis and for allowing optimal use of AdV vectors for biomedical applications.\",\n \"corpus_id\": 260626758,\n \"score\": 1\n },\n {\n \"doc_id\": \"21146538\",\n \"title\": \"Model of the trimeric fiber and its interactions with the pentameric penton base of human adenovirus by cryo-electron microscopy.\",\n \"abstract\": \"Adenovirus invades host cells by first binding to host receptors through a trimeric fiber, which contains three domains: a receptor-binding knob domain, a long flexible shaft domain, and a penton base-attachment tail domain. Although the structure of the knob domain associated with a portion of the shaft has been solved by X-ray crystallography, the in situ structure of the fiber in the virion is not known; thus, it remains a mystery how the trimeric fiber attaches to its underlying pentameric penton base. By high-resolution cryo-electron microscopy, we have determined the structure of the human adenovirus type 5 (Ad5) to 3.6-Å resolution and have reported the full atomic models for its capsid proteins, but not for the fiber whose density cannot be directly interpreted due to symmetry mismatch with the penton base. Here, we report the determination of the Ad5 fiber structure and its mode of attachment to the pentameric penton base by using an integrative approach of multi-resolution filtering, homology modeling, computational simulation of mismatched symmetries, and fitting of atomic models into cryo-electron microscopy density maps. Our structure reveals that the interactions between the trimeric fiber and the pentameric penton base are mediated by a hydrophobic ring on the top surface of the penton base and three flexible tails inserted into three of the five available grooves formed by neighboring subunits of penton base. These interaction sites provide the molecular basis for the symmetry mismatch and can be targeted for optimizing adenovirus for gene therapy applications.\",\n \"corpus_id\": 32786422,\n \"score\": 1\n },\n {\n \"doc_id\": \"21742267\",\n \"title\": \"Insights into the evolution of a complex virus from the crystal structure of vaccinia virus D13.\",\n \"abstract\": \"The morphogenesis of poxviruses such as vaccinia virus (VACV) sees the virion shape mature from spherical to brick-shaped. Trimeric capsomers of the VACV D13 protein form a transitory, stabilizing lattice on the surface of the initial spherical immature virus particle. The crystal structure of D13 reveals that this major scaffolding protein comprises a double β barrel \\\"jelly-roll\\\" subunit arranged as pseudo-hexagonal trimers. These structural features are characteristic of the major capsid proteins of a lineage of large icosahedral double-stranded DNA viruses including human adenovirus and the bacteriophages PRD1 and PM2. Structure-based phylogenetic analysis confirms that VACV belongs to this lineage, suggesting that (analogously to higher organism embryogenesis) early poxvirus morphogenesis reflects their evolution from a lineage of viruses sharing a common icosahedral ancestor.\",\n \"corpus_id\": 13923660,\n \"score\": 1\n },\n {\n \"doc_id\": \"22153511\",\n \"title\": \"Structural conservation of the myoviridae phage tail sheath protein fold.\",\n \"abstract\": \"Bacteriophage phiKZ is a giant phage that infects Pseudomonas aeruginosa, a human pathogen. The phiKZ virion consists of a 1450 Å diameter icosahedral head and a 2000 Å-long contractile tail. The structure of the whole virus was previously reported, showing that its tail organization in the extended state is similar to the well-studied Myovirus bacteriophage T4 tail. The crystal structure of a tail sheath protein fragment of phiKZ was determined to 2.4 Å resolution. Furthermore, crystal structures of two prophage tail sheath proteins were determined to 1.9 and 3.3 Å resolution. Despite low sequence identity between these proteins, all of these structures have a similar fold. The crystal structure of the phiKZ tail sheath protein has been fitted into cryo-electron-microscopy reconstructions of the extended tail sheath and of a polysheath. The structural rearrangement of the phiKZ tail sheath contraction was found to be similar to that of phage T4.\",\n \"corpus_id\": 5103216,\n \"score\": 1\n },\n {\n \"doc_id\": \"22386055\",\n \"title\": \"Structural evolution of the P22-like phages: comparison of Sf6 and P22 procapsid and virion architectures.\",\n \"abstract\": \"Coat proteins of tailed, dsDNA phages and in herpesviruses include a conserved core similar to the bacteriophage HK97 subunit. This core is often embellished with other domains such as the telokin Ig-like domain of phage P22. Eighty-six P22-like phages and prophages with sequenced genomes share a similar set of virion assembly genes and, based on comparisons of twelve viral assembly proteins (structural and assembly/packaging chaperones), these phages are classified into three groups (P22-like, Sf6-like, and CUS-3-like). We used cryo-electron microscopy and 3D image reconstruction to determine the structures of Sf6 procapsids and virions (~7Å resolution), and the structure of the entire, asymmetric Sf6 virion (16-Å resolution). The Sf6 coat protein is similar to that of P22 yet it has differences in the telokin domain and in its overall quaternary organization. Thermal stability and agarose gel experiments show that Sf6 virions are slightly less stable than those of P22. Finally, bacterial host outer membrane proteins A and C were identified in lipid vesicles that co-purify with Sf6 particles, but are not components of the capsid.\",\n \"corpus_id\": 14670556,\n \"score\": 1\n },\n {\n \"doc_id\": \"22482707\",\n \"title\": \"Structure of human adenovirus.\",\n \"abstract\": \"A detailed structural analysis of the entire human adenovirus capsid has been stymied by the complexity and size of this 150 MDa macromolecular complex. Over the past 10 years, the steady improvements in viral genome manipulation concomitant with advances in crystallographic techniques and data processing software has allowed structure determination of this virus by X-ray diffraction at 3.5 Å resolution. The virus structure revealed the location, folds, and interactions of major and minor (cement proteins) on the inner and outer capsid surface. This new structural information sheds further light on the process of adenovirus capsid assembly and virus-host cell interactions.\",\n \"corpus_id\": 29436951,\n \"score\": 1\n },\n {\n \"doc_id\": \"22514336\",\n \"title\": \"Capsid structure and its stability at the late stages of bacteriophage SPP1 assembly.\",\n \"abstract\": \"The structure of the bacteriophage SPP1 capsid was determined at subnanometer resolution by cryo-electron microscopy and single-particle analysis. The icosahedral capsid is composed of the major capsid protein gp13 and the auxiliary protein gp12, which are organized in a T=7 lattice. DNA is arranged in layers with a distance of ~24.5 Å. gp12 forms spikes that are anchored at the center of gp13 hexamers. In a gp12-deficient mutant, the centers of hexamers are closed by loops of gp13 coming together to protect the SPP1 genome from the outside environment. The HK97-like fold was used to build a pseudoatomic model of gp13. Its structural organization remains unchanged upon tail binding and following DNA release. gp13 exhibits enhanced thermostability in the DNA-filled capsid. A remarkable convergence between the thermostability of the capsid and those of the other virion components was found, revealing that the overall architecture of the SPP1 infectious particle coevolved toward high robustness.\",\n \"corpus_id\": 34601670,\n \"score\": 1\n },\n {\n \"doc_id\": \"23091035\",\n \"title\": \"Structure of Sputnik, a virophage, at 3.5-Å resolution.\",\n \"abstract\": \"\\\"Sputnik\\\" is a dsDNA virus, referred to as a virophage, that is coassembled with Mimivirus in the host amoeba. We have used cryo-EM to produce an electron density map of the icosahedral Sputnik virus at 3.5-Å resolution, sufficient to verify the identity of most amino acids in the capsid proteins and to establish the identity of the pentameric protein forming the fivefold vertices. It was also shown that the virus lacks an internal membrane. The capsid is organized into a T = 27 lattice in which there are 260 trimeric capsomers and 12 pentameric capsomers. The trimeric capsomers consist of three double \\\"jelly-roll\\\" major capsid proteins creating pseudohexameric capsomer symmetry. The pentameric capsomers consist of five single jelly-roll proteins. The release of the genome by displacing one or more of the pentameric capsomers may be the result of a low-pH environment. These results suggest a mechanism of Sputnik DNA ejection that probably also occurs in other big icosahedral double jelly-roll viruses such as Adenovirus. In this study, the near-atomic resolution structure of a virus has been established where crystallization for X-ray crystallography was not feasible.\",\n \"corpus_id\": 22281949,\n \"score\": 1\n },\n {\n \"doc_id\": \"24316834\",\n \"title\": \"Crystallization of the C-terminal domain of the fibre protein from snake adenovirus 1, an atadenovirus.\",\n \"abstract\": \"Adenovirus fibre proteins play an important role in determining viral tropism. The C-terminal domain of the fibre protein from snake adenovirus type 1, a member of the Atadenovirus genus, has been expressed, purified and crystallized. Crystals were obtained belonging to space groups P2(1)2(1)2(1) (two different forms), I2(1)3 and F23. The best of these diffracted synchrotron radiation to a resolution of 1.4 Å. As the protein lacks methionines or cysteines, site-directed mutagenesis was performed to change two leucine residues to methionines. Crystals of selenomethionine-derivatized crystals of the I2(1)3 form were also obtained and a multi-wavelength anomalous dispersion data set was collected.\",\n \"corpus_id\": 35326870,\n \"score\": 1\n },\n {\n \"doc_id\": \"24889614\",\n \"title\": \"Single-particle EM reveals plasticity of interactions between the adenovirus penton base and integrin αVβ3.\",\n \"abstract\": \"Human adenoviruses are double-stranded DNA viruses responsible for numerous infections, some of which can be fatal. Furthermore, adenoviruses are currently used in clinical trials as vectors for gene therapy applications. Although initial binding of adenoviruses to host attachment receptors has been extensively characterized, the interactions with the entry receptor (integrins) remain poorly understood at the structural level. We characterized the interactions between the adenovirus 9 penton base subunit and αVβ3 integrin using fluorescence correlation spectroscopy and single-particle electron microscopy to understand the mechanisms underlying virus internalization and infection. Our results indicate that the penton base subunit can bind integrins with high affinity and in several different orientations. These outcomes correlate with the requirement of the pentameric penton base to simultaneously bind several integrins to enable their clustering and promote virus entry into the host cell.\",\n \"corpus_id\": 33854643,\n \"score\": 1\n },\n {\n \"doc_id\": \"25043589\",\n \"title\": \"Three-dimensional reconstructions of the bacteriophage CUS-3 virion reveal a conserved coat protein I-domain but a distinct tailspike receptor-binding domain.\",\n \"abstract\": \"CUS-3 is a short-tailed, dsDNA bacteriophage that infects serotype K1 Escherichia coli. We report icosahedrally averaged and asymmetric, three-dimensional, cryo-electron microscopic reconstructions of the CUS-3 virion. Its coat protein structure adopts the \\\"HK97-fold\\\" shared by other tailed phages and is quite similar to that in phages P22 and Sf6 despite only weak amino acid sequence similarity. In addition, these coat proteins share a unique extra external domain (\\\"I-domain\\\"), suggesting that the group of P22-like phages has evolved over a very long time period without acquiring a new coat protein gene from another phage group. On the other hand, the morphology of the CUS-3 tailspike differs significantly from that of P22 or Sf6, but is similar to the tailspike of phage K1F, a member of the extremely distantly related T7 group of phages. We conclude that CUS-3 obtained its tailspike gene from a distantly related phage quite recently.\",\n \"corpus_id\": 7603381,\n \"score\": 1\n },\n {\n \"doc_id\": \"25071205\",\n \"title\": \"Structures and organization of adenovirus cement proteins provide insights into the role of capsid maturation in virus entry and infection.\",\n \"abstract\": \"Adenovirus cement proteins play crucial roles in virion assembly, disassembly, cell entry, and infection. Based on a refined crystal structure of the adenovirus virion at 3.8-Å resolution, we have determined the structures of all of the cement proteins (IIIa, VI, VIII, and IX) and their organization in two distinct layers. We have significantly revised the recent cryoelectron microscopy models for proteins IIIa and IX and show that both are located on the capsid exterior. Together, the cement proteins exclusively stabilize the hexon shell, thus rendering penton vertices the weakest links of the adenovirus capsid. We describe, for the first time to our knowledge, the structure of protein VI, a key membrane-lytic molecule, and unveil its associations with VIII and core protein V, which together glue peripentonal hexons beneath the vertex region and connect them to the rest of the capsid on the interior. Following virion maturation, the cleaved N-terminal propeptide of VI is observed, reaching deep into the peripentonal hexon cavity, detached from the membrane-lytic domain, so that the latter can be released. Our results thus provide the molecular basis for the requirement of maturation cleavage of protein VI. This process is essential for untethering and release of the membrane-lytic region, which is known to mediate endosome rupture and delivery of partially disassembled virions into the host cell cytoplasm.\",\n \"corpus_id\": 1492945,\n \"score\": 1\n },\n {\n \"doc_id\": \"25254384\",\n \"title\": \"The adenovirus genome contributes to the structural stability of the virion.\",\n \"abstract\": \"Adenovirus (Ad) vectors are currently the most commonly used platform for therapeutic gene delivery in human gene therapy clinical trials. Although these vectors are effective, many researchers seek to further improve the safety and efficacy of Ad-based vectors through detailed characterization of basic Ad biology relevant to its function as a vector system. Most Ad vectors are deleted of key, or all, viral protein coding sequences, which functions to not only prevent virus replication but also increase the cloning capacity of the vector for foreign DNA. However, radical modifications to the genome size significantly decreases virion stability, suggesting that the virus genome plays a role in maintaining the physical stability of the Ad virion. Indeed, a similar relationship between genome size and virion stability has been noted for many viruses. This review discusses the impact of the genome size on Ad virion stability and emphasizes the need to consider this aspect of virus biology in Ad-based vector design.\",\n \"corpus_id\": 1212474,\n \"score\": 1\n },\n {\n \"doc_id\": \"25486282\",\n \"title\": \"Crystal structure of the fibre head domain of the Atadenovirus Snake Adenovirus 1.\",\n \"abstract\": \"Adenoviruses are non-enveloped icosahedral viruses with trimeric fibre proteins protruding from their vertices. There are five known genera, from which only Mastadenoviruses have been widely studied. Apart from studying adenovirus as a biological model system and with a view to prevent or combat viral infection, there is a major interest in using adenovirus for vaccination, cancer therapy and gene therapy purposes. Adenoviruses from the Atadenovirus genus have been isolated from squamate reptile hosts, ruminants and birds and have a characteristic gene organization and capsid morphology. The carboxy-terminal virus-distal fibre head domains are likely responsible for primary receptor recognition. We determined the high-resolution crystal structure of the Snake Adenovirus 1 (SnAdV-1) fibre head using the multi-wavelength anomalous dispersion (MAD) method. Despite the absence of significant sequence homology, this Atadenovirus fibre head has the same beta-sandwich propeller topology as other adenovirus fibre heads. However, it is about half the size, mainly due to much shorter loops connecting the beta-strands. The detailed structure of the SnAdV-1 fibre head and other animal adenovirus fibre heads, together with the future identification of their natural receptors, may lead to the development of new strategies to target adenovirus vectors to cells of interest.\",\n \"corpus_id\": 10741158,\n \"score\": 1\n },\n {\n \"doc_id\": \"25994880\",\n \"title\": \"Crystal structure of the fibre head domain of bovine adenovirus 4, a ruminant atadenovirus.\",\n \"abstract\": \"BACKGROUND: In adenoviruses, primary host cell recognition is generally performed by the head domains of their homo-trimeric fibre proteins. This first interaction is reversible. A secondary, irreversible interaction subsequently takes place via other adenovirus capsid proteins and leads to a productive infection. Although many fibre head structures are known for human mastadenoviruses, not many animal adenovirus fibre head structures have been determined, especially not from those belonging to adenovirus genera other than Mastadenovirus. METHODS: We constructed an expression vector for the fibre head domain from a ruminant atadenovirus, bovine adenovirus 4 (BAdV-4), consisting of amino acids 414-535, expressed the protein in Escherichia coli, purified it by metal affinity and cation exchange chromatography and crystallized it. The structure was solved using single isomorphous replacement plus anomalous dispersion of a mercury derivative and refined against native data that extended to 1.2 Å resolution. RESULTS: Like in other adenoviruses, the BAdV-4 fibre head monomer contains a beta-sandwich consisting of ABCJ and GHID sheets. The topology is identical to the fibre head of the other studied atadenovirus, snake adenovirus 1 (SnAdV-1), including the alpha-helix in the DG-loop, despite of them having a sequence identity of only 15 %. There are also differences which may have implications for ligand binding. Beta-strands G and H are longer and differences in several surface-loops and surface charge are observed. CONCLUSIONS: Chimeric adenovirus fibres have been used to retarget adenovirus-based anti-cancer and gene therapy vectors. Ovine adenovirus 7 (OAdV-7), another ruminant atadenovirus, is intensively tested as a basis for such a vector. Here, we present the high-resolution atomic structure of the BAdV-4 fibre head domain, the second atadenovirus fibre head structure known and the first of an atadenovirus that infects a mammalian host. Future research should focus on the receptor-binding properties of these fibre head domains.\",\n \"corpus_id\": 8568594,\n \"score\": 1\n },\n {\n \"doc_id\": \"26178997\",\n \"title\": \"Structures of Adenovirus Incomplete Particles Clarify Capsid Architecture and Show Maturation Changes of Packaging Protein L1 52/55k.\",\n \"abstract\": \"UNLABELLED: Adenovirus is one of the most complex icosahedral, nonenveloped viruses. Even after its structure was solved at near-atomic resolution by both cryo-electron microscopy and X-ray crystallography, the location of minor coat proteins is still a subject of debate. The elaborated capsid architecture is the product of a correspondingly complex assembly process, about which many aspects remain unknown. Genome encapsidation involves the concerted action of five virus proteins, and proteolytic processing by the virus protease is needed to prime the virion for sequential uncoating. Protein L1 52/55k is required for packaging, and multiple cleavages by the maturation protease facilitate its release from the nascent virion. Light-density particles are routinely produced in adenovirus infections and are thought to represent assembly intermediates. Here, we present the molecular and structural characterization of two different types of human adenovirus light particles produced by a mutant with delayed packaging. We show that these particles lack core polypeptide V but do not lack the density corresponding to this protein in the X-ray structure, thereby adding support to the adenovirus cryo-electron microscopy model. The two types of light particles present different degrees of proteolytic processing. Their structures provide the first glimpse of the organization of L1 52/55k protein inside the capsid shell and of how this organization changes upon partial maturation. Immature, full-length L1 52/55k is poised beneath the vertices to engage the virus genome. Upon proteolytic processing, L1 52/55k disengages from the capsid shell, facilitating genome release during uncoating. IMPORTANCE: Adenoviruses have been extensively characterized as experimental systems in molecular biology, as human pathogens, and as therapeutic vectors. However, a clear picture of many aspects of their basic biology is still lacking. Two of these aspects are the location of minor coat proteins in the capsid and the molecular details of capsid assembly. Here, we provide evidence supporting one of the two current models for capsid architecture. We also show for the first time the location of the packaging protein L1 52/55k in particles lacking the virus genome and how this location changes during maturation. Our results contribute to clarifying standing questions in adenovirus capsid architecture and provide new details on the role of L1 52/55k protein in assembly.\",\n \"corpus_id\": 5903737,\n \"score\": 1\n },\n {\n \"doc_id\": \"26269173\",\n \"title\": \"A Molecular Staple: D-Loops in the I Domain of Bacteriophage P22 Coat Protein Make Important Intercapsomer Contacts Required for Procapsid Assembly.\",\n \"abstract\": \"UNLABELLED: Bacteriophage P22, a double-stranded DNA (dsDNA) virus, has a nonconserved 124-amino-acid accessory domain inserted into its coat protein, which has the canonical HK97 protein fold. This I domain is involved in virus capsid size determination and stability, as well as protein folding. The nuclear magnetic resonance (NMR) solution structure of the I domain revealed the presence of a D-loop, which was hypothesized to make important intersubunit contacts between coat proteins in adjacent capsomers. Here we show that amino acid substitutions of residues near the tip of the D-loop result in aberrant assembly products, including tubes and broken particles, highlighting the significance of the D-loops in proper procapsid assembly. Using disulfide cross-linking, we showed that the tips of the D-loops are positioned directly across from each other both in the procapsid and the mature virion, suggesting their importance in both states. Our results indicate that D-loop interactions act as \\\"molecular staples\\\" at the icosahedral 2-fold symmetry axis and significantly contribute to stabilizing the P22 capsid for DNA packaging. IMPORTANCE: Many dsDNA viruses have morphogenic pathways utilizing an intermediate capsid, known as a procapsid. These procapsids are assembled from a coat protein having the HK97 fold in a reaction driven by scaffolding proteins or delta domains. Maturation of the capsid occurs during DNA packaging. Bacteriophage HK97 uniquely stabilizes its capsid during maturation by intercapsomer cross-linking, but most virus capsids are stabilized by alternate means. Here we show that the I domain that is inserted into the coat protein of bacteriophage P22 is important in the process of proper procapsid assembly. Specifically, the I domain allows for stabilizing interactions across the capsid 2-fold axis of symmetry via a D-loop. When amino acid residues at the tip of the D-loop are mutated, aberrant assembly products, including tubes, are formed instead of procapsids, consequently phage production is affected, indicating the importance of stabilizing interactions during the assembly and maturation reactions.\",\n \"corpus_id\": 40613704,\n \"score\": 1\n },\n {\n \"doc_id\": \"26996963\",\n \"title\": \"New Structural Insights into the Genome and Minor Capsid Proteins of BK Polyomavirus using Cryo-Electron Microscopy.\",\n \"abstract\": \"BK polyomavirus is the causative agent of several diseases in transplant patients and the immunosuppressed. In order to better understand the structure and life cycle of BK, we produced infectious virions and VP1-only virus-like particles in cell culture, and determined their three-dimensional structures using cryo-electron microscopy (EM) and single-particle image processing. The resulting 7.6-Å resolution structure of BK and 9.1-Å resolution of the virus-like particles are the highest-resolution cryo-EM structures of any polyomavirus. These structures confirm that the architecture of the major structural protein components of these human polyomaviruses are similar to previous structures from other hosts, but give new insight into the location and role of the enigmatic minor structural proteins, VP2 and VP3. We also observe two shells of electron density, which we attribute to a structurally ordered part of the viral genome, and discrete contacts between this density and both VP1 and the minor capsid proteins.\",\n \"corpus_id\": 18131435,\n \"score\": 1\n },\n {\n \"doc_id\": \"27671640\",\n \"title\": \"Asymmetric cryo-EM structure of the canonical Allolevivirus Qβ reveals a single maturation protein and the genomic ssRNA in situ.\",\n \"abstract\": \"Single-stranded (ss) RNA viruses infect all domains of life. To date, for most ssRNA virions, only the structures of the capsids and their associated protein components have been resolved to high resolution. Qβ, an ssRNA phage specific for the conjugative F-pilus, has a T = 3 icosahedral lattice of coat proteins assembled around its 4,217 nucleotides of genomic RNA (gRNA). In the mature virion, the maturation protein, A2, binds to the gRNA and is required for adsorption to the F-pilus. Here, we report the cryo-electron microscopy (cryo-EM) structures of Qβ with and without symmetry applied. The icosahedral structure, at 3.7-Å resolution, resolves loops not previously seen in the published X-ray structure, whereas the asymmetric structure, at 7-Å resolution, reveals A2 and the gRNA. A2 contains a bundle of α-helices and replaces one dimer of coat proteins at a twofold axis. The helix bundle binds gRNA, causing denser packing of RNA in its proximity, which asymmetrically expands the surrounding coat protein shell to potentially facilitate RNA release during infection. We observe a fixed pattern of gRNA organization among all viral particles, with the major and minor grooves of RNA helices clearly visible. A single layer of RNA directly contacts every copy of the coat protein, with one-third of the interactions occurring at operator-like RNA hairpins. These RNA-coat interactions stabilize the tertiary structure of gRNA within the virion, which could further provide a roadmap for capsid assembly.\",\n \"corpus_id\": 885877,\n \"score\": 1\n },\n {\n \"doc_id\": \"28344575\",\n \"title\": \"Identification of Capsid/Coat Related Protein Folds and Their Utility for Virus Classification.\",\n \"abstract\": \"The viral supergroup includes the entire collection of known and unknown viruses that roam our planet and infect life forms. The supergroup is remarkably diverse both in its genetics and morphology and has historically remained difficult to study and classify. The accumulation of protein structure data in the past few years now provides an excellent opportunity to re-examine the classification and evolution of viruses. Here we scan completely sequenced viral proteomes from all genome types and identify protein folds involved in the formation of viral capsids and virion architectures. Viruses encoding similar capsid/coat related folds were pooled into lineages, after benchmarking against published literature. Remarkably, the in silico exercise reproduced all previously described members of known structure-based viral lineages, along with several proposals for new additions, suggesting it could be a useful supplement to experimental approaches and to aid qualitative assessment of viral diversity in metagenome samples.\",\n \"corpus_id\": 17549486,\n \"score\": 1\n },\n {\n \"doc_id\": \"19680644\",\n \"title\": \"Viruses: incredible nanomachines. New advances with filamentous phages.\",\n \"abstract\": \"During recent decades, bacteriophages have been at the cutting edge of new developments in molecular biology, biophysics, and, more recently, bionanotechnology. In particular filamentous viruses, for example bacteriophage M13, have a virion architecture that enables precision building of ordered and defect-free two and three-dimensional structures on a nanometre scale. This could not have been possible without detailed knowledge of coat protein structure and dynamics during the virus reproduction cycle. The results of the spectroscopic studies conducted in our group compellingly demonstrate a critical role of membrane embedment of the protein both during infectious entry of the virus into the host cell and during assembly of the new virion in the host membrane. The protein is effectively embedded in the membrane by a strong C-terminal interfacial anchor, which together with a simple tilt mechanism and a subtle structural adjustment of the extreme end of its N terminus provides favourable thermodynamical association of the protein in the lipid bilayer. This basic physicochemical rule cannot be violated and any new bionanotechnology that will emerge from bacteriophage M13 should take this into account.\",\n \"corpus_id\": 12721091,\n \"score\": 0\n },\n {\n \"doc_id\": \"19835886\",\n \"title\": \"Structure of the small outer capsid protein, Soc: a clamp for stabilizing capsids of T4-like phages.\",\n \"abstract\": \"Many viruses need to stabilize their capsid structure against DNA pressure and for survival in hostile environments. The 9-kDa outer capsid protein (Soc) of bacteriophage T4, which stabilizes the virus, attaches to the capsid during the final stage of maturation. There are 870 Soc molecules that act as a \\\"glue\\\" between neighboring hexameric capsomers, forming a \\\"cage\\\" that stabilizes the T4 capsid against extremes of pH and temperature. Here we report a 1.9 A resolution crystal structure of Soc from the bacteriophage RB69, a close relative of T4. The RB69 crystal structure and a homology model of T4 Soc were fitted into the cryoelectron microscopy reconstruction of the T4 capsid. This established the region of Soc that interacts with the major capsid protein and suggested a mechanism, verified by extensive mutational and biochemical studies, for stabilization of the capsid in which the Soc trimers act as clamps between neighboring capsomers. The results demonstrate the factors involved in stabilizing not only the capsids of T4-like bacteriophages but also many other virus capsids.\",\n \"corpus_id\": 13071755,\n \"score\": 0\n },\n {\n \"doc_id\": \"20463071\",\n \"title\": \"The T=1 capsid protein of Penicillium chrysogenum virus is formed by a repeated helix-rich core indicative of gene duplication.\",\n \"abstract\": \"Penicillium chrysogenum virus (PcV), a member of the Chrysoviridae family, is a double-stranded RNA (dsRNA) fungal virus with a multipartite genome, with each RNA molecule encapsidated in a separate particle. Chrysoviruses lack an extracellular route and are transmitted during sporogenesis and cell fusion. The PcV capsid, based on a T=1 lattice containing 60 subunits of the 982-amino-acid capsid protein, remains structurally undisturbed throughout the viral cycle, participates in genome metabolism, and isolates the virus genome from host defense mechanisms. Using three-dimensional cryoelectron microscopy, we determined the structure of the PcV virion at 8.0 A resolution. The capsid protein has a high content of rod-like densities characteristic of alpha-helices, forming a repeated alpha-helical core indicative of gene duplication. Whereas the PcV capsid protein has two motifs with the same fold, most dsRNA virus capsid subunits consist of dimers of a single protein with similar folds. The spatial arrangement of the alpha-helical core resembles that found in the capsid protein of the L-A virus, a fungal totivirus with an undivided genome, suggesting a conserved basic fold. The encapsidated genome is organized in concentric shells; whereas the inner dsRNA shells are well defined, the outermost layer is dense due to numerous interactions with the inner capsid surface, specifically, six interacting areas per monomer. The outermost genome layer is arranged in an icosahedral cage, sufficiently well ordered to allow for modeling of an A-form dsRNA. The genome ordering might constitute a framework for dsRNA transcription at the capsid interior and/or have a structural role for capsid stability.\",\n \"corpus_id\": 37639100,\n \"score\": 0\n },\n {\n \"doc_id\": \"20861247\",\n \"title\": \"Structural characterization of the dual glycan binding adeno-associated virus serotype 6.\",\n \"abstract\": \"The three-dimensional structure of adeno-associated virus (AAV) serotype 6 (AAV6) was determined using cryo-electron microscopy and image reconstruction and using X-ray crystallography to 9.7- and 3.0-Å resolution, respectively. The AAV6 capsid contains a highly conserved, eight-stranded (βB to βI) β-barrel core and large loop regions between the strands which form the capsid surface, as observed in other AAV structures. The loops show conformational variation compared to other AAVs, consistent with previous reports that amino acids in these loop regions are involved in differentiating AAV receptor binding, transduction efficiency, and antigenicity properties. Toward structure-function annotation of AAV6 with respect to its unique dual glycan receptor (heparan sulfate and sialic acid) utilization for cellular recognition, and its enhanced lung epithelial transduction compared to other AAVs, the capsid structure was compared to that of AAV1, which binds sialic acid and differs from AAV6 in only 6 out of 736 amino acids. Five of these residues are located at or close to the icosahedral 3-fold axis of the capsid, thereby identifying this region as imparting important functions, such as receptor attachment and transduction phenotype. Two of the five observed amino acids are located in the capsid interior, suggesting that differential AAV infection properties are also controlled by postentry intracellular events. Density ordered inside the capsid, under the 3-fold axis in a previously reported, conserved AAV DNA binding pocket, was modeled as a nucleotide and a base, further implicating this capsid region in AAV genome recognition and/or stabilization.\",\n \"corpus_id\": 25791007,\n \"score\": 0\n },\n {\n \"doc_id\": \"21038867\",\n \"title\": \"Discrete structure of an RNA folding intermediate revealed by cryo-electron microscopy.\",\n \"abstract\": \"RNA folding occurs via a series of transitions between metastable intermediate states. It is unknown whether folding intermediates are discrete structures folding along defined pathways or heterogeneous ensembles folding along broad landscapes. We use cryo-electron microscopy and single-particle image reconstruction to determine the structure of the major folding intermediate of the specificity domain of a ribonuclease P ribozyme. Our results support the existence of a discrete conformation for this folding intermediate.\",\n \"corpus_id\": 22344761,\n \"score\": 0\n },\n {\n \"doc_id\": \"21858752\",\n \"title\": \"Adenovirus.\",\n \"abstract\": \"Adenoviruses (AdV) are DNA viruses that typically cause mild infections involving the upper or lower respiratory tract, gastrointestinal (GI) tract, or conjunctiva. Rare manifestations of AdV infections include hemorrhagic cystitis, hepatitis, hemorrhagic colitis, pancreatitis, nephritis, or encephalitis. Adenovirus infections are more common in young children, owing to lack of humoral immunity. Epidemics of AdV infections may occur in healthy children or adults in closed or crowded settings (particularly military recruits). The disease is more severe, and dissemination is more likely in patients with impaired immunity (eg, organ transplant recipients, human immunodeficiency virus infection, congenital immunodeficiency syndromes). Fatality rates for untreated severe AdV pneumonia or disseminated disease may exceed 50%. More than 50 serotypes of AdV have been identified. Different serotypes display different tissue trophisms and correlate with clinical manifestations of infection. The predominant serotypes differ among countries or regions and change over time. Transmission of novel strains between countries or across continents and replacement of dominant serotypes by new strains may occur. Treatment of AdV infections is controversial because prospective, randomized therapeutic trials have not been done. Cidofovir is considered the drug of choice for severe AdV infections, but not all patients require treatment. Vaccines have been shown to be highly efficacious in reducing the risk of respiratory AdV infection but are currently not available.\",\n \"corpus_id\": 260317561,\n \"score\": 0\n },\n {\n \"doc_id\": \"23695247\",\n \"title\": \"Structure of the Triatoma virus capsid.\",\n \"abstract\": \"The members of the Dicistroviridae family are non-enveloped positive-sense single-stranded RNA (+ssRNA) viruses pathogenic to beneficial arthropods as well as insect pests of medical importance. Triatoma virus (TrV), a member of this family, infects several species of triatomine insects (popularly named kissing bugs), which are vectors for human trypanosomiasis, more commonly known as Chagas disease. The potential use of dicistroviruses as biological control agents has drawn considerable attention in the past decade, and several viruses of this family have been identified, with their targets covering honey bees, aphids and field crickets, among others. Here, the crystal structure of the TrV capsid at 2.5 Å resolution is reported, showing that as expected it is very similar to that of Cricket paralysis virus (CrPV). Nevertheless, a number of distinguishing structural features support the introduction of a new genus (Triatovirus; type species TrV) under the Dicistroviridae family. The most striking differences are the absence of icosahedrally ordered VP4 within the infectious particle and the presence of prominent projections that surround the fivefold axis. Furthermore, the structure identifies a second putative autoproteolytic DDF motif in protein VP3, in addition to the conserved one in VP1 which is believed to be responsible for VP0 cleavage during capsid maturation. The potential meaning of these new findings is discussed.\",\n \"corpus_id\": 18244528,\n \"score\": 0\n },\n {\n \"doc_id\": \"23719463\",\n \"title\": \"Mature HIV-1 capsid structure by cryo-electron microscopy and all-atom molecular dynamics.\",\n \"abstract\": \"Retroviral capsid proteins are conserved structurally but assemble into different morphologies. The mature human immunodeficiency virus-1 (HIV-1) capsid is best described by a 'fullerene cone' model, in which hexamers of the capsid protein are linked to form a hexagonal surface lattice that is closed by incorporating 12 capsid-protein pentamers. HIV-1 capsid protein contains an amino-terminal domain (NTD) comprising seven α-helices and a β-hairpin, a carboxy-terminal domain (CTD) comprising four α-helices, and a flexible linker with a 310-helix connecting the two structural domains. Structures of the capsid-protein assembly units have been determined by X-ray crystallography; however, structural information regarding the assembled capsid and the contacts between the assembly units is incomplete. Here we report the cryo-electron microscopy structure of a tubular HIV-1 capsid-protein assembly at 8 Å resolution and the three-dimensional structure of a native HIV-1 core by cryo-electron tomography. The structure of the tubular assembly shows, at the three-fold interface, a three-helix bundle with critical hydrophobic interactions. Mutagenesis studies confirm that hydrophobic residues in the centre of the three-helix bundle are crucial for capsid assembly and stability, and for viral infectivity. The cryo-electron-microscopy structures enable modelling by large-scale molecular dynamics simulation, resulting in all-atom models for the hexamer-of-hexamer and pentamer-of-hexamer elements as well as for the entire capsid. Incorporation of pentamers results in closer trimer contacts and induces acute surface curvature. The complete atomic HIV-1 capsid model provides a platform for further studies of capsid function and for targeted pharmacological intervention.\",\n \"corpus_id\": 4373417,\n \"score\": 0\n },\n {\n \"doc_id\": \"23810697\",\n \"title\": \"The asymmetric structure of an icosahedral virus bound to its receptor suggests a mechanism for genome release.\",\n \"abstract\": \"Simple, spherical RNA viruses have well-understood, symmetric protein capsids, but little structural information is available for their asymmetric components, such as minor proteins and their genomes, which are vital for infection. Here, we report an asymmetric structure of bacteriophage MS2, attached to its receptor, the F-pilus. Cryo-electron tomography and subtomographic averaging of such complexes result in a structure containing clear density for the packaged genome, implying that the conformation of the genome is the same in each virus particle. The data also suggest that the single-copy viral maturation protein breaks the symmetry of the capsid, occupying a position that would be filled by a coat protein dimer in an icosahedral shell. This capsomere can thus fulfill its known biological roles in receptor and genome binding and suggests an exit route for the genome during infection.\",\n \"corpus_id\": 18515668,\n \"score\": 0\n },\n {\n \"doc_id\": \"23827137\",\n \"title\": \"Structure of the pseudorabies virus capsid: comparison with herpes simplex virus type 1 and differential binding of essential minor proteins.\",\n \"abstract\": \"The structure of pseudorabies virus (PRV) capsids isolated from the nucleus of infected cells and from PRV virions was determined by cryo-electron microscopy (cryo-EM) and compared to herpes simplex virus type 1 (HSV-1) capsids. PRV capsid structures closely resemble those of HSV-1, including distribution of the capsid vertex specific component (CVSC) of HSV-1, which is a heterodimer of the pUL17 and pUL25 proteins. Occupancy of CVSC on all PRV capsids is near 100%, compared to ~50% reported for HSV-1 C-capsids and 25% or less that we measure for HSV-1 A- and B-capsids. A PRV mutant lacking pUL25 does not produce C-capsids and lacks visible CVSC density in the cryo-EM-based reconstruction. A reconstruction of PRV capsids in which green fluorescent protein was fused within the N-terminus of pUL25 confirmed previous studies with a similar HSV-1 capsid mutant localizing pUL25 to the CVSC density region that is distal to the penton. However, comparison of the CVSC density in a 9-Å-resolution PRV C-capsid map with the available crystal structure of HSV-1 pUL25 failed to find a satisfactory fit, suggesting either a different fold for PRV pUL25 or a capsid-bound conformation for pUL25 that does not match the X-ray model determined from protein crystallized in solution. The PRV capsid imaged within virions closely resembles C-capsids with the addition of weak but significant density shrouding the pentons that we attribute to tegument proteins. Our results demonstrate significant structure conservation between the PRV and HSV capsids.\",\n \"corpus_id\": 19884115,\n \"score\": 0\n },\n {\n \"doc_id\": \"23966856\",\n \"title\": \"The smallest capsid protein mediates binding of the essential tegument protein pp150 to stabilize DNA-containing capsids in human cytomegalovirus.\",\n \"abstract\": \"Human cytomegalovirus (HCMV) is a ubiquitous herpesvirus that causes birth defects in newborns and life-threatening complications in immunocompromised individuals. Among all human herpesviruses, HCMV contains a much larger dsDNA genome within a similarly-sized capsid compared to the others, and it was proposed to require pp150, a tegument protein only found in cytomegaloviruses, to stabilize its genome-containing capsid. However, little is known about how pp150 interacts with the underlying capsid. Moreover, the smallest capsid protein (SCP), while dispensable in herpes simplex virus type 1, was shown to play essential, yet undefined, role in HCMV infection. Here, by cryo electron microscopy (cryoEM), we determine three-dimensional structures of HCMV capsid (no pp150) and virion (with pp150) at sub-nanometer resolution. Comparison of these two structures reveals that each pp150 tegument density is composed of two helix bundles connected by a long central helix. Correlation between the resolved helices and sequence-based secondary structure prediction maps the tegument density to the N-terminal half of pp150. The structures also show that SCP mediates interactions between the capsid and pp150 at the upper helix bundle of pp150. Consistent with this structural observation, ribozyme inhibition of SCP expression in HCMV-infected cells impairs the formation of DNA-containing viral particles and reduces viral yield by 10,000 fold. By cryoEM reconstruction of the resulting \\\"SCP-deficient\\\" viral particles, we further demonstrate that SCP is required for pp150 functionally binding to the capsid. Together, our structural and biochemical results point to a mechanism whereby SCP recruits pp150 to stabilize genome-containing capsid for the production of infectious HCMV virion.\",\n \"corpus_id\": 753089,\n \"score\": 0\n },\n {\n \"doc_id\": \"24027306\",\n \"title\": \"The structure and host entry of an invertebrate parvovirus.\",\n \"abstract\": \"The 3.5-Å resolution X-ray crystal structure of mature cricket parvovirus (Acheta domesticus densovirus [AdDNV]) has been determined. Structural comparisons show that vertebrate and invertebrate parvoviruses have evolved independently, although there are common structural features among all parvovirus capsid proteins. It was shown that raising the temperature of the AdDNV particles caused a loss of their genomes. The structure of these emptied particles was determined by cryo-electron microscopy to 5.5-Å resolution, and the capsid structure was found to be the same as that for the full, mature virus except for the absence of the three ordered nucleotides observed in the crystal structure. The viral protein 1 (VP1) amino termini could be externalized without significant damage to the capsid. In vitro, this externalization of the VP1 amino termini is accompanied by the release of the viral genome.\",\n \"corpus_id\": 25223900,\n \"score\": 0\n },\n {\n \"doc_id\": \"24282305\",\n \"title\": \"Rubella virus capsid protein structure and its role in virus assembly and infection.\",\n \"abstract\": \"Rubella virus (RV) is a leading cause of birth defects due to infectious agents. When contracted during pregnancy, RV infection leads to severe damage in fetuses. Despite its medical importance, compared with the related alphaviruses, very little is known about the structure of RV. The RV capsid protein is an essential structural component of virions as well as a key factor in virus-host interactions. Here we describe three crystal structures of the structural domain of the RV capsid protein. The polypeptide fold of the RV capsid protomer has not been observed previously. Combining the atomic structure of the RV capsid protein with the cryoelectron tomograms of RV particles established a low-resolution structure of the virion. Mutational studies based on this structure confirmed the role of amino acid residues in the capsid that function in the assembly of infectious virions.\",\n \"corpus_id\": 28331583,\n \"score\": 0\n },\n {\n \"doc_id\": \"24582831\",\n \"title\": \"Structure and assembly of filamentous bacteriophages.\",\n \"abstract\": \"Filamentous bacteriophages are interesting paradigms in structural molecular biology, in part because of the unusual mechanism of filamentous phage assembly. During assembly, several thousand copies of an intracellular DNA-binding protein bind to each copy of the replicating phage DNA, and are then displaced by membrane-spanning phage coat proteins as the nascent phage is extruded through the bacterial plasma membrane. This complicated process takes place without killing the host bacterium. The bacteriophage is a semi-flexible worm-like nucleoprotein filament. The virion comprises a tube of several thousand identical major coat protein subunits around a core of single-stranded circular DNA. Each protein subunit is a polymer of about 50 amino-acid residues, largely arranged in an α-helix. The subunits assemble into a helical sheath, with each subunit oriented at a small angle to the virion axis and interdigitated with neighbouring subunits. A few copies of \\\"minor\\\" phage proteins necessary for infection and/or extrusion of the virion are located at each end of the completed virion. Here we review both the structure of the virion and aspects of its function, such as the way the virion enters the host, multiplies, and exits to prey on further hosts. In particular we focus on our understanding of the way the components of the virion come together during assembly at the membrane. We try to follow a basic rule of empirical science, that one should chose the simplest theoretical explanation for experiments, but be prepared to modify or even abandon this explanation as new experiments add more detail.\",\n \"corpus_id\": 207336143,\n \"score\": 0\n },\n {\n \"doc_id\": \"24648455\",\n \"title\": \"Limits of structural plasticity in a picornavirus capsid revealed by a massively expanded equine rhinitis A virus particle.\",\n \"abstract\": \"UNLABELLED: The Picornaviridae family of small, nonenveloped viruses includes major pathogens of humans and animals. They have positive-sense, single-stranded RNA genomes, and the mechanism(s) by which these genomes are introduced into cells to initiate infection remains poorly understood. The structures of presumed uncoating intermediate particles of several picornaviruses show limited expansion and some increased porosity compared to the mature virions. Here, we present the cryo-electron microscopy structure of native equine rhinitis A virus (ERAV), together with the structure of a massively expanded ERAV particle, each at ∼17-Å resolution. The expanded structure has large pores on the particle 3-fold axes and has lost the RNA genome and the capsid protein VP4. The expanded structure thus illustrates both the limits of structural plasticity in such capsids and a plausible route by which genomic RNA might exit. IMPORTANCE: Picornaviruses are important animal and human pathogens that protect their genomic RNAs within a protective protein capsid. Upon infection, this genomic RNA must be able to leave the capsid to initiate a new round of infection. We describe here the structure of a unique, massively expanded state of equine rhinitis A virus that provides insight into how this exit might occur.\",\n \"corpus_id\": 14749439,\n \"score\": 0\n },\n {\n \"doc_id\": \"26167882\",\n \"title\": \"The molecular basis for flexibility in the flexible filamentous plant viruses.\",\n \"abstract\": \"Flexible filamentous plant viruses cause more than half the viral crop damage in the world but are also potentially useful for biotechnology. Structural studies began more than 75 years ago but have failed, owing to the virion's extreme flexibility. We have used cryo-EM to generate an atomic model for bamboo mosaic virus, which reveals flexible N- and C-terminal extensions that allow deformation while still maintaining structural integrity.\",\n \"corpus_id\": 6551037,\n \"score\": 0\n },\n {\n \"doc_id\": \"26374901\",\n \"title\": \"Electron microscopic imaging revealed the flexible filamentous structure of the cell attachment protein P2 of Rice dwarf virus located around the icosahedral 5-fold axes.\",\n \"abstract\": \"The minor outer capsid protein P2 of Rice dwarf virus (RDV), a member of the genus Phytoreovirus in the family Reoviridae, is essential for viral cell entry. Here, we clarified the structure of P2 and the interactions to host insect cells. Negative stain electron microscopy (EM) showed that P2 proteins are monomeric and flexible L-shaped filamentous structures of ∼20 nm in length. Cryo-EM structure revealed the spatial arrangement of P2 in the capsid, which was prescribed by the characteristic virion structure. The P2 proteins were visualized as partial rod-shaped structures of ∼10 nm in length in the cryo-EM map and accommodated in crevasses on the viral surface around icosahedral 5-fold axes with hydrophobic interactions. The remaining disordered region of P2 assumed to be extended to the radial direction towards exterior. Electron tomography clearly showed that RDV particles were away from the cellular membrane at a uniform distance and several spike-like densities, probably corresponding to P2, connecting a viral particle to the host cellular membrane during cell entry. By combining the in vitro and in vivo structural information, we could gain new insights into the detailed mechanism of the cell entry of RDV.\",\n \"corpus_id\": 34250693,\n \"score\": 0\n },\n {\n \"doc_id\": \"26446437\",\n \"title\": \"Structure of Ljungan virus provides insight into genome packaging of this picornavirus.\",\n \"abstract\": \"Picornaviruses are responsible for a range of human and animal diseases, but how their RNA genome is packaged remains poorly understood. A particularly poorly studied group within this family are those that lack the internal coat protein, VP4. Here we report the atomic structure of one such virus, Ljungan virus, the type member of the genus Parechovirus B, which has been linked to diabetes and myocarditis in humans. The 3.78-Å resolution cryo-electron microscopy structure shows remarkable features, including an extended VP1 C terminus, forming a major protuberance on the outer surface of the virus, and a basic motif at the N terminus of VP3, binding to which orders some 12% of the viral genome. This apparently charge-driven RNA attachment suggests that this branch of the picornaviruses uses a different mechanism of genome encapsidation, perhaps explored early in the evolution of picornaviruses.\",\n \"corpus_id\": 12160583,\n \"score\": 0\n },\n {\n \"doc_id\": \"26939061\",\n \"title\": \"Morphology and Molecular Composition of Purified Bovine Viral Diarrhea Virus Envelope.\",\n \"abstract\": \"The family Flaviviridae includes viruses that have different virion structures and morphogenesis mechanisms. Most cellular and molecular studies have been so far performed with viruses of the Hepacivirus and Flavivirus genera. Here, we studied bovine viral diarrhea virus (BVDV), a member of the Pestivirus genus. We set up a method to purify BVDV virions and analyzed their morphology by electron microscopy and their protein and lipid composition by mass spectrometry. Cryo-electron microscopy showed near spherical viral particles displaying an electron-dense capsid surrounded by a phospholipid bilayer with no visible spikes. Most particles had a diameter of 50 nm and about 2% were larger with a diameter of up to 65 nm, suggesting some size flexibility during BVDV morphogenesis. Morphological and biochemical data suggested a low envelope glycoprotein content of BVDV particles, E1 and E2 being apparently less abundant than Erns. Lipid content of BVDV particles displayed a ~2.3 to 3.5-fold enrichment in cholesterol, sphingomyelin and hexosyl-ceramide, concomitant with a 1.5 to 5-fold reduction of all glycerophospholipid classes, as compared to lipid content of MDBK cells. Although BVDV buds in the endoplasmic reticulum, its lipid content differs from a typical endoplasmic reticulum membrane composition. This suggests that BVDV morphogenesis includes a mechanism of lipid sorting. Functional analyses confirmed the importance of cholesterol and sphingomyelin for BVDV entry. Surprisingly, despite a high cholesterol and sphingolipid content of BVDV envelope, E2 was not found in detergent-resistant membranes. Our results indicate that there are differences between the structure and molecular composition of viral particles of Flaviviruses, Pestiviruses and Hepaciviruses within the Flaviviridae family.\",\n \"corpus_id\": 285662,\n \"score\": 0\n },\n {\n \"doc_id\": \"27021160\",\n \"title\": \"Crystal Structure and Proteomics Analysis of Empty Virus-like Particles of Cowpea Mosaic Virus.\",\n \"abstract\": \"Empty virus-like particles (eVLPs) of Cowpea mosaic virus (CPMV) are currently being utilized as reagents in various biomedical and nanotechnology applications. Here, we report the crystal structure of CPMV eVLPs determined using X-ray crystallography at 2.3 Å resolution and compare it with previously reported cryo-electron microscopy (cryo-EM) of eVLPs and virion crystal structures. Although the X-ray and cryo-EM structures of eVLPs are mostly similar, there exist significant differences at the C terminus of the small (S) subunit. The intact C terminus of the S subunit plays a critical role in enabling the efficient assembly of CPMV virions and eVLPs, but undergoes proteolysis after particle formation. In addition, we report the results of mass spectrometry-based proteomics analysis of coat protein subunits from CPMV eVLPs and virions that identify the C termini of S subunits undergo proteolytic cleavages at multiple sites instead of a single cleavage site as previously observed.\",\n \"corpus_id\": 12343799,\n \"score\": 0\n },\n {\n \"doc_id\": \"27111889\",\n \"title\": \"Extensive subunit contacts underpin herpesvirus capsid stability and interior-to-exterior allostery.\",\n \"abstract\": \"The herpesvirus capsid is a complex protein assembly that includes hundreds of copies of four major subunits and lesser numbers of several minor proteins, all of which are essential for infectivity. Cryo-electron microscopy is uniquely suited for studying interactions that govern the assembly and function of such large functional complexes. Here we report two high-quality capsid structures, from human herpes simplex virus type 1 (HSV-1) and the animal pseudorabies virus (PRV), imaged inside intact virions at ~7-Å resolution. From these, we developed a complete model of subunit and domain organization and identified extensive networks of subunit contacts that underpin capsid stability and form a pathway that may signal the completion of DNA packaging from the capsid interior to outer surface, thereby initiating nuclear egress. Differences in the folding and orientation of subunit domains between herpesvirus capsids suggest that common elements have been modified for specific functions.\",\n \"corpus_id\": 16786704,\n \"score\": 0\n },\n {\n \"doc_id\": \"27561669\",\n \"title\": \"Asymmetric cryo-EM reconstruction of phage MS2 reveals genome structure in situ.\",\n \"abstract\": \"In single-stranded ribonucleic acid (RNA) viruses, virus capsid assembly and genome packaging are intertwined processes. Using cryo-electron microscopy and single particle analysis we determined the asymmetric virion structure of bacteriophage MS2, which includes 178 copies of the coat protein, a single copy of the A-protein and the RNA genome. This reveals that in situ, the viral RNA genome can adopt a defined conformation. The RNA forms a branched network of stem-loops that almost all allocate near the capsid inner surface, while predominantly binding to coat protein dimers that are located in one-half of the capsid. This suggests that genomic RNA is highly involved in genome packaging and virion assembly.\",\n \"corpus_id\": 6903077,\n \"score\": 0\n },\n {\n \"doc_id\": \"27591890\",\n \"title\": \"Structure of AP205 Coat Protein Reveals Circular Permutation in ssRNA Bacteriophages.\",\n \"abstract\": \"AP205 is a single-stranded RNA bacteriophage that has a coat protein sequence not similar to any other known single-stranded RNA phage. Here, we report an atomic-resolution model of the AP205 virus-like particle based on a crystal structure of an unassembled coat protein dimer and a cryo-electron microscopy reconstruction of the assembled particle, together with secondary structure information from site-specific solid-state NMR data. The AP205 coat protein dimer adopts the conserved Leviviridae coat protein fold except for the N-terminal region, which forms a beta-hairpin in the other known single-stranded RNA phages. AP205 has a similar structure at the same location formed by N- and C-terminal beta-strands, making it a circular permutant compared to the other coat proteins. The permutation moves the coat protein termini to the most surface-exposed part of the assembled particle, which explains its increased tolerance to long N- and C-terminal fusions.\",\n \"corpus_id\": 31201789,\n \"score\": 0\n },\n {\n \"doc_id\": \"28065506\",\n \"title\": \"Cryoelectron Microscopy Maps of Human Papillomavirus 16 Reveal L2 Densities and Heparin Binding Site.\",\n \"abstract\": \"Human papillomavirus (HPV) is a significant health burden and leading cause of virus-induced cancers. The current commercial vaccines are genotype specific and provide little therapeutic benefit to patients with existing HPV infections. Host entry mechanisms represent an excellent target for alternative therapeutics, but HPV receptor use, the details of cell attachment, and host entry are inadequately understood. Here we present near-atomic resolution structures of the HPV16 capsid and HPV16 in complex with heparin, both determined from cryoelectron micrographs collected with direct electron detection technology. The structures clarify details of capsid architecture for the first time, including variation in L1 major capsid protein conformation and putative location of L2 minor protein. Heparin binds specifically around the capsid icosahedral vertices and may recapitulate the earliest stage of infection, providing a framework for continuing biochemical, genetic, and biophysical studies.\",\n \"corpus_id\": 10097476,\n \"score\": 0\n },\n {\n \"doc_id\": \"28320961\",\n \"title\": \"Structure of a headful DNA-packaging bacterial virus at 2.9 Å resolution by electron cryo-microscopy.\",\n \"abstract\": \"The enormous prevalence of tailed DNA bacteriophages on this planet is enabled by highly efficient self-assembly of hundreds of protein subunits into highly stable capsids. These capsids can stand with an internal pressure as high as ∼50 atmospheres as a result of the phage DNA-packaging process. Here we report the complete atomic model of the headful DNA-packaging bacteriophage Sf6 at 2.9 Å resolution determined by electron cryo-microscopy. The structure reveals the DNA-inflated, tensed state of a robust protein shell assembled via noncovalent interactions. Remarkable global conformational polymorphism of capsid proteins, a network formed by extended N arms, mortise-and-tenon-like intercapsomer joints, and abundant β-sheet-like mainchain:mainchain intermolecular interactions, confers significant strength yet also flexibility required for capsid assembly and DNA packaging. Differential formations of the hexon and penton are mediated by a drastic α-helix-to-β-strand structural transition. The assembly scheme revealed here may be common among tailed DNA phages and herpesviruses.\",\n \"corpus_id\": 205282017,\n \"score\": 0\n },\n {\n \"doc_id\": \"29190455\",\n \"title\": \"Structural features of the salivary gland hypertrophy virus of the tsetse fly revealed by cryo-electron microscopy and tomography.\",\n \"abstract\": \"Glossina palipides salivary gland hypertrophy virus (GpSGHV) infects tsetse flies, which are vectors for African trypanosomosis. This virus represents a major challenge in insect mass rearing and has hampered the implementation of the sterile insect technique programs in the Member States of the International Atomic Energy Agency. GpSGHV virions consist of long rod-shaped particles over 9000Å in length, but little is known about their detailed structural organization. We show by cryo electron microscopy and cryo electron tomography that the GpSGHV virion has a unique, non-icosahedral helical structure. Its envelope exhibits regularly spaced spikes that protrude from the lipid bilayer and are arranged on a four-start helix. This study provides a detailed insight into the 3D architecture of GpSGHV, which will help to understand the viral life cycle and possibly allow the design of antiviral strategies in the context of tsetse fly infections.\",\n \"corpus_id\": 4863623,\n \"score\": 0\n },\n {\n \"doc_id\": \"29211815\",\n \"title\": \"Bacteria and bacterial envelope components enhance mammalian reovirus thermostability.\",\n \"abstract\": \"Enteric viruses encounter diverse environments as they migrate through the gastrointestinal tract to infect their hosts. The interaction of eukaryotic viruses with members of the host microbiota can greatly impact various aspects of virus biology, including the efficiency with which viruses can infect their hosts. Mammalian orthoreovirus, a human enteric virus that infects most humans during childhood, is negatively affected by antibiotic treatment prior to infection. However, it is not known how components of the host microbiota affect reovirus infectivity. In this study, we show that reovirus virions directly interact with Gram positive and Gram negative bacteria. Reovirus interaction with bacterial cells conveys enhanced virion thermostability that translates into enhanced attachment and infection of cells following an environmental insult. Enhanced virion thermostability was also conveyed by bacterial envelope components lipopolysaccharide (LPS) and peptidoglycan (PG). Lipoteichoic acid and N-acetylglucosamine-containing polysaccharides enhanced virion stability in a serotype-dependent manner. LPS and PG also enhanced the thermostability of an intermediate reovirus particle (ISVP) that is associated with primary infection in the gut. Although LPS and PG alter reovirus thermostability, these bacterial envelope components did not affect reovirus utilization of its proteinaceous cellular receptor junctional adhesion molecule-A or cell entry kinetics. LPS and PG also did not affect the overall number of reovirus capsid proteins σ1 and σ3, suggesting their effect on virion thermostability is not mediated through altering the overall number of major capsid proteins on the virus. Incubation of reovirus with LPS and PG did not significantly affect the neutralizing efficiency of reovirus-specific antibodies. These data suggest that bacteria enhance reovirus infection of the intestinal tract by enhancing the thermal stability of the reovirus particle at a variety of temperatures through interactions between the viral particle and bacterial envelope components.\",\n \"corpus_id\": 4035645,\n \"score\": 0\n }\n]","isConversational":false}}},{"rowIdx":51,"cells":{"query":{"kind":"string","value":"{\n \"doc_id\": \"25175027\",\n \"title\": \"The molecular architecture of the TRAMP complex reveals the organization and interplay of its two catalytic activities.\",\n \"abstract\": \"The TRAMP complex is involved in the nuclear surveillance and turnover of noncoding RNAs and intergenic transcripts. TRAMP is associated with the nuclear exosome and consists of a poly(A)polymerase subcomplex (Trf4-Air2) and a helicase (Mtr4). We found that N-terminal low-complexity regions of Trf4 and Air2 bind Mtr4 in a cooperative manner. The 2.4 Å resolution crystal structure of the corresponding ternary complex reveals how Trf4 and Air2 wrap around the DExH core of the helicase. Structure-based mutations on the DExH core impair binding to Trf4 and Air2, and also to Trf5 and Air1. The combination of structural, biochemical, and biophysical data suggests that the poly(A)polymerase core of Trf4-Air2 is positioned below the base of the helicase, where the unwound 3' end of an RNA substrate is expected to emerge. The results reveal conceptual similarities between the two major regulators of the exosome, the nuclear TRAMP and cytoplasmic Ski complexes.\",\n \"corpus_id\": 31161047\n}"},"candidates":{"kind":"list like","value":[{"doc_id":"18000032","title":"Degradation of hypomodified tRNA(iMet) in vivo involves RNA-dependent ATPase activity of the DExH helicase Mtr4p.","abstract":"Effective turnover of many incorrectly processed RNAs in yeast, including hypomodified tRNA(iMet), requires the TRAMP complex, which appends a short poly(A) tail to RNA designated for decay. The poly(A) tail stimulates degradation by the exosome. The TRAMP complex contains the poly(A) polymerase Trf4p, the RNA-binding protein Air2p, and the DExH RNA helicase Mtr4p. The role of Mtr4p in RNA degradation processes involving the TRAMP complex has been unclear. Here we show through a genetic analysis that MTR4 is required for degradation but not for polyadenylation of hypomodified tRNA(iMet). A suppressor of the trm6-504 mutation in the tRNA m(1)A58 methyltransferase (Trm6p/Trm61p), which causes a reduced level of tRNA(iMet), was mapped to MTR4. This mtr4-20 mutation changed a single amino acid in the conserved helicase motif VI of Mtr4p. The mutation stabilizes hypomodified tRNA(iMet) in vivo but has no effect on TRAMP complex stability or polyadenylation activity in vivo or in vitro. We further show that purified recombinant Mtr4p displays RNA-dependent ATPase activity and unwinds RNA duplexes with a 3'-to-5' polarity in an ATP-dependent fashion. Unwinding and RNA-stimulated ATPase activities are strongly reduced in the recombinant mutant Mtr4-20p, suggesting that these activities of Mtr4p are critical for degradation of polyadenylated hypomodified tRNA(iMet).","corpus_id":19996245,"score":2},{"doc_id":"18025105","title":"Global role for polyadenylation-assisted nuclear RNA degradation in posttranscriptional gene silencing.","abstract":"Fission yeast Cid14, a component of the TRAMP (Cid14/Trf4-Air1-Mtr4 polyadenylation) complex, polyadenylates nuclear RNA and stimulates degradation by the exosome for RNA quality control. Here, we analyze patterns of global gene expression in cells lacking the Cid14 or the Dis3/Rpr44 subunit of the nuclear exosome. We found that transcripts from many genes induced during meiosis, including key regulators, accumulated in the absence of Cid14 or Dis3. Moreover, our data suggest that additional substrates include transcripts involved in heterochromatin assembly. Mutant cells lacking Cid14 and/or Dis3 accumulate transcripts corresponding to naturally silenced repeat elements within heterochromatic domains, reflecting defects in centromeric gene silencing and derepression of subtelomeric gene expression. We also uncover roles for Cid14 and Dis3 in maintaining the genomic integrity of ribosomal DNA. Our data indicate that polyadenylation-assisted nuclear RNA turnover functions in eliminating a variety of RNA targets to control diverse processes, such as heterochromatic gene silencing, meiotic differentiation, and maintenance of genomic integrity.","corpus_id":15469514,"score":2},{"doc_id":"18591258","title":"A yeast exosome cofactor, Mpp6, functions in RNA surveillance and in the degradation of noncoding RNA transcripts.","abstract":"A genome-wide screen for synthetic lethal (SL) interactions with loss of the nuclear exosome cofactors Rrp47/Lrp1 or Air1 identified 3'-->5' exonucleases, the THO complex required for mRNP assembly, and Ynr024w (Mpp6). SL interactions with mpp6Delta were confirmed for rrp47Delta and nuclear exosome component Rrp6. The results of bioinformatic analyses revealed homology between Mpp6 and a human exosome cofactor, underlining the high conservation of the RNA surveillance system. Mpp6 is an RNA binding protein that physically associates with the exosome and was localized throughout the nucleus. The results of functional analyses demonstrated roles for Mpp6 in the surveillance of both pre-rRNA and pre-mRNAs and in the degradation of \"cryptic\" noncoding RNAs (ncRNAs) derived from intergenic regions and the ribosomal DNA spacer heterochromatin. Strikingly, these ncRNAs are also targeted by other exosome cofactors, including Rrp47, the TRAMP complex (which includes Air1), and the Nrd1/Nab3 complex, and are degraded by both Rrp6 and the core exosome. Heterochromatic transcripts and other ncRNAs are characterized by very rapid degradation, and we predict that functional redundancy is an important feature of ncRNA metabolism.","corpus_id":14385449,"score":2},{"doc_id":"18765642","title":"TRF4 is involved in polyadenylation of snRNAs in Drosophila melanogaster.","abstract":"The Saccharomyces cerevisiae poly(A) polymerases Trf4 and Trf5 are involved in an RNA quality control mechanism, where polyadenylated RNAs are degraded by the nuclear exosome. Although Trf4/5 homologue genes are distributed throughout multicellular organisms, their biological roles remain to be elucidated. We isolated here the two homologues of Trf4/5 in Drosophila melanogaster, named DmTRF4-1 and DmTRF4-2, and investigated their biological function. DmTRF4-1 displayed poly(A) polymerase activity in vitro, whereas DmTRF4-2 did not. Gene knockdown of DmTRF4-1 by RNA interference is lethal in flies, as is the case for the trf4 trf5 double mutants. In contrast, disruption of DmTRF4-2 results in viable flies. Cellular localization analysis suggested that DmTRF4-1 localizes in the nucleolus. Abnormal polyadenylation of snRNAs was observed in transgenic flies overexpressing DmTRF4-1 and was slightly increased by the suppression of DmRrp6, the 3'-5' exonuclease of the nuclear exosome. These results suggest that DmTRF4-1 and DmRrp6 are involved in the polyadenylation-mediated degradation of snRNAs in vivo.","corpus_id":7961480,"score":2},{"doc_id":"19369424","title":"Regulation of NAB2 mRNA 3'-end formation requires the core exosome and the Trf4p component of the TRAMP complex.","abstract":"The nuclear exosome functions in a variety of pathways catalyzing formation of mature RNA 3'-ends or the destruction of aberrant RNA transcripts. The RNA 3'-end formation activity of the exosome appeared restricted to small noncoding RNAs. However, the nuclear exosome controls the level of the mRNA encoding the poly(A)-binding protein Nab2p in a manner requiring an A(26) sequence in the mRNA 3' untranslated regions (UTR), and the activities of Nab2p and the exosome-associated exoribonuclease Rrp6p. Here we show that the A(26) sequence inhibits normal 3'-end processing of NAB2 mRNA in vivo and in vitro, and makes formation of the mature 3'-end dependent on trimming of the transcript by the core exosome and the Trf4p component of the TRAMP complex from a downstream site. The detection of mature, polyadenylated transcripts ending at, or within, the A(26) sequence indicates that exosome trimming sometimes gives way to polyadenylation of the mRNA. Alternatively, Rrp6p and the TRAMP-associated Mtr4p degrade these transcripts thereby limiting the amount of Nab2p in the cell. These findings suggest that NAB2 mRNA 3'-end formation requires the exosome and TRAMP complex, and that competition between polyadenylation and Rrp6p-dependent degradation controls the level of this mRNA.","corpus_id":25961000,"score":2},{"doc_id":"19593367","title":"Distinct roles of non-canonical poly(A) polymerases in RNA metabolism.","abstract":"Trf4p and Trf5p are non-canonical poly(A) polymerases and are part of the heteromeric protein complexes TRAMP4 and TRAMP5 that promote the degradation of aberrant and short-lived RNA substrates by interacting with the nuclear exosome. To assess the level of functional redundancy between the paralogous Trf4 and Trf5 proteins and to investigate the role of the Trf4-dependent polyadenylation in vivo, we used DNA microarrays to compare gene expression of the wild-type yeast strain of S. cerevisiae with either that of trf4Delta or trf5Delta mutant strains or the trf4Delta mutant expressing the polyadenylation-defective Trf4(DADA) protein. We found little overlap between the sets of transcripts with altered expression in the trf4Delta or the trf5Delta mutants, suggesting that Trf4p and Trf5p target distinct groups of RNAs for degradation. Surprisingly, most RNAs the expression of which was altered by the trf4 deletion were restored to wild-type levels by overexpression of TRF4(DADA), showing that the polyadenylation activity of Trf4p is dispensable in vivo. Apart from previously reported Trf4p and Trf5p target RNAs, this analysis along with in vivo cross-linking and RNA immunopurification-chip experiments revealed that both the TRAMP4 and the TRAMP5 complexes stimulate the degradation of spliced-out introns via a mechanism that is independent of the polyadenylation activity of Trf4p. In addition, we show that disruption of trf4 causes severe shortening of telomeres suggesting that TRF4 functions in the maintenance of telomere length. Finally, our study demonstrates that TRF4, the exosome, and TRF5 participate in antisense RNA-mediated regulation of genes involved in phosphate metabolism. In conclusion, our results suggest that paralogous TRAMP complexes have distinct RNA selectivities with functional implications in RNA surveillance as well as other RNA-related processes. This indicates widespread and integrative functions of TRAMP complexes for the coordination of different gene expression regulatory processes.","corpus_id":11210046,"score":2},{"doc_id":"19707589","title":"The CCR4-NOT complex physically and functionally interacts with TRAMP and the nuclear exosome.","abstract":"BACKGROUND: Ccr4-Not is a highly conserved multi-protein complex consisting in yeast of 9 subunits, including Not5 and the major yeast deadenylase Ccr4. It has been connected functionally in the nucleus to transcription by RNA polymerase II and in the cytoplasm to mRNA degradation. However, there has been no evidence so far that this complex is important for RNA degradation in the nucleus. METHODOLOGY/PRINCIPAL FINDINGS: In this work we point to a new role for the Ccr4-Not complex in nuclear RNA metabolism. We determine the importance of the Ccr4-Not complex for the levels of non-coding nuclear RNAs, such as mis-processed and polyadenylated snoRNAs, whose turnover depends upon the nuclear exosome and TRAMP. Consistently, mutation of both the Ccr4-Not complex and the nuclear exosome results in synthetic slow growth phenotypes. We demonstrate physical interactions between the Ccr4-Not complex and the exosome. First, Not5 co-purifies with the exosome. Second, several exosome subunits co-purify with the Ccr4-Not complex. Third, the Ccr4-Not complex is important for the integrity of large exosome-containing complexes. Finally, we reveal a connection between the Ccr4-Not complex and TRAMP through the association of the Mtr4 helicase with the Ccr4-Not complex and the importance of specific subunits of Ccr4-Not for the association of Mtr4 with the nuclear exosome subunit Rrp6. CONCLUSIONS/SIGNIFICANCE: We propose a model in which the Ccr4-Not complex may provide a platform contributing to dynamic interactions between the nuclear exosome and its co-factor TRAMP. Our findings connect for the first time the different players involved in nuclear and cytoplasmic RNA degradation.","corpus_id":7014268,"score":2},{"doc_id":"19955569","title":"TRAMP complex enhances RNA degradation by the nuclear exosome component Rrp6.","abstract":"The RNA-processing exosome contains ribonucleases that degrade aberrant RNAs in archael and eukaryotic cells. In Saccharomyces cerevisiae, the nuclear/nucleolar 3'-5' exoribonuclease Rrp6 distinguishes the nuclear exosome from the cytoplasmic exosome. In vivo, the TRAMP complex enhances the ability of the nuclear exosome to destroy some aberrant RNAs. Previous reports showed that purified TRAMP enhanced RNA degradation by the nuclear exosome in vitro. However, the exoribonucleolytic component(s) of the nuclear exosome enhanced by TRAMP remain unidentified. We show that TRAMP does not significantly enhance RNA degradation by purified exosomes lacking Rrp6 in vitro, suggesting that TRAMP activation experiments with nuclear exosome preparations reflect, in part, effects on the activity of Rrp6. Consistent with this, we show that incubation of purified TRAMP with recombinant Rrp6 results in a 10-fold enhancement of the rate of RNA degradation. This increased activity results from enhancement of the hydrolytic activity of Rrp6 because TRAMP cannot enhance the activity of an Rrp6 mutant lacking a key amino acid side chain in its active site. We observed no ATP or polyadenylation dependence for the enhancement of Rrp6 activity by TRAMP, suggesting that neither the poly(A) polymerase activity of Trf4 nor the helicase activity of Mtr4 plays a role in the enhancement. These findings identify TRAMP as an exosome-independent enhancer of Rrp6 activity.","corpus_id":1313810,"score":2},{"doc_id":"20512111","title":"The crystal structure of Mtr4 reveals a novel arch domain required for rRNA processing.","abstract":"The essential RNA helicase, Mtr4, performs a critical role in RNA processing and degradation as an activator of the nuclear exosome. The molecular basis for this vital function is not understood and detailed analysis is significantly limited by the lack of structural data. In this study, we present the crystal structure of Mtr4. The structure reveals a new arch-like domain that is specific to Mtr4 and Ski2 (the cytosolic homologue of Mtr4). In vivo and in vitro analyses demonstrate that the Mtr4 arch domain is required for proper 5.8S rRNA processing, and suggest that the arch functions independently of canonical helicase activity. In addition, extensive conservation along the face of the putative RNA exit site highlights a potential interface with the exosome. These studies provide a molecular framework for understanding fundamental aspects of helicase function in exosome activation, and more broadly define the molecular architecture of Ski2-like helicases.","corpus_id":24491250,"score":2},{"doc_id":"20566885","title":"Structural analysis reveals the characteristic features of Mtr4, a DExH helicase involved in nuclear RNA processing and surveillance.","abstract":"Mtr4 is a conserved RNA helicase that functions together with the nuclear exosome. It participates in the processing of structured RNAs, including the maturation of 5.8S ribosomal RNA (rRNA). It also interacts with the polyadenylating Trf4-Air2 heterodimer to form the so-called TRAMP (Trf4-Air2-Mtr4 Polyadenylation) complex. TRAMP is involved in exosome-mediated degradation of aberrant RNAs in nuclear surveillance pathways. We report the 2.9-A resolution crystal structure of Saccharomyces cerevisiae Mtr4 in complex with ADP and RNA. The structure shows a central ATPase core similar to that of other DExH helicases. Inserted in the DExH core is a region characteristic of Mtr4 orthologues that folds into an elongated stalk connected to a beta-barrel domain. This domain shows unexpected similarity to the KOW domain of L24, a ribosomal protein that binds 23S rRNA. We find that indeed the KOW domain of Mtr4 is able to bind in vitro transcribed tRNA(iMet), suggesting it might assist in presenting RNA substrates to the helicase core. The interaction of Mtr4 with Trf4-Air2 is mediated not by the stalk/KOW insertion but by the DExH core. We find that in the context of the TRAMP complex, the DExH core functions independently in vitro as an RNA helicase and a protein-binding platform. Mtr4 has thus evolved specific structural and surface features to perform its multiple functions.","corpus_id":21161196,"score":2},{"doc_id":"20634320","title":"Loss of Topoisomerase I leads to R-loop-mediated transcriptional blocks during ribosomal RNA synthesis.","abstract":"Pre-rRNA transcription by RNA Polymerase I (Pol I) is very robust on active rDNA repeats. Loss of yeast Topoisomerase I (Top1) generated truncated pre-rRNA fragments, which were stabilized in strains lacking TRAMP (Trf4/Trf5-Air1/Air2-Mtr4 polyadenylation complexes) or exosome degradation activities. Loss of both Top1 and Top2 blocked pre-rRNA synthesis, with pre-rRNAs truncated predominately in the 18S 5' region. Positive supercoils in front of Pol I are predicted to slow elongation, while rDNA opening in its wake might cause R-loop formation. Chromatin immunoprecipitation analysis showed substantial levels of RNA/DNA hybrids in the wild type, particularly over the 18S 5' region. The absence of RNase H1 and H2 in cells depleted of Top1 increased the accumulation of RNA/DNA hybrids and reduced pre-rRNA truncation and pre-rRNA synthesis. Hybrid accumulation over the rDNA was greatly exacerbated when Top1, Top2, and RNase H were all absent. Electron microscopy (EM) analysis revealed Pol I pileups in the wild type, particularly over the 18S. Pileups were longer and more frequent in the absence of Top1, and their frequency was exacerbated when RNase H activity was also lacking. We conclude that the loss of Top1 enhances inherent R-loop formation, particularly over the 5' region of the rDNA, imposing persistent transcription blocks when RNase H is limiting.","corpus_id":21483556,"score":2},{"doc_id":"20696927","title":"Structure and function of the polymerase core of TRAMP, a RNA surveillance complex.","abstract":"The Trf4p/Air2p/Mtr4p polyadenylation (TRAMP) complex recognizes aberrant RNAs in Saccharomyces cerevisiae and targets them for degradation. A TRAMP subcomplex consisting of a noncanonical poly(A) RNA polymerase in the Pol ss superfamily of nucleotidyl transferases, Trf4p, and a zinc knuckle protein, Air2p, mediates initial substrate recognition. Trf4p and related eukaryotic poly(A) and poly(U) polymerases differ from other characterized enzymes in the Pol ss superfamily both in sequence and in the lack of recognizable nucleic acid binding motifs. Here we report, at 2.7-A resolution, the structure of Trf4p in complex with a fragment of Air2p comprising two zinc knuckle motifs. Trf4p consists of a catalytic and central domain similar in fold to those of other noncanonical Pol beta RNA polymerases, and the two zinc knuckle motifs of Air2p interact with the Trf4p central domain. The interaction surface on Trf4p is highly conserved across eukaryotes, providing evidence that the Trf4p/Air2p complex is conserved in higher eukaryotes as well as in yeast and that the TRAMP complex may also function in RNA surveillance in higher eukaryotes. We show that Air2p, and in particular sequences encompassing a zinc knuckle motif near its N terminus, modulate Trf4p activity, and we present data supporting a role for this zinc knuckle in RNA binding. Finally, we show that the RNA 3' end plays a role in substrate recognition.","corpus_id":20249410,"score":2},{"doc_id":"21460797","title":"The nuclear RNA polymerase II surveillance system targets polymerase III transcripts.","abstract":"A key question in nuclear RNA surveillance is how target RNAs are recognized. To address this, we identified in vivo binding sites for nuclear RNA surveillance factors, Nrd1, Nab3 and the Trf4/5–Air1/2–Mtr4 polyadenylation (TRAMP) complex poly(A) polymerase Trf4, by UV crosslinking. Hit clusters were reproducibly found over known binding sites on small nucleolar RNAs (snoRNAs), pre-mRNAs and cryptic, unstable non-protein-coding RNAs (ncRNAs) ('CUTs'), along with ~642 predicted long anti-sense ncRNAs (asRNAs), ~178 intergenic ncRNAs and, surprisingly, ~1384 mRNAs. Five putative asRNAs tested were confirmed to exist and were stabilized by loss of Nrd1, Nab3 or Trf4. Mapping of micro-deletions and substitutions allowed clear definition of preferred, in vivo Nab3 and Nrd1 binding sites. Nrd1 and Nab3 were believed to be Pol II specific but, unexpectedly, bound many oligoadenylated Pol III transcripts, predominately pre-tRNAs. Depletion of Nrd1 or Nab3 stabilized tested Pol III transcripts and their oligoadenylation was dependent on Nrd1–Nab3 and TRAMP. Surveillance targets were enriched for non-encoded A-rich tails. These were generally very short (1–5 nt), potentially explaining why adenylation destabilizes these RNAs while stabilizing mRNAs with long poly(A) tails.","corpus_id":14260193,"score":2},{"doc_id":"21663793","title":"The RNA helicase Mtr4p modulates polyadenylation in the TRAMP complex.","abstract":"Many steps in nuclear RNA processing, surveillance, and degradation require TRAMP, a complex containing the poly(A) polymerase Trf4p, the Zn-knuckle protein Air2p, and the RNA helicase Mtr4p. TRAMP polyadenylates RNAs designated for decay or trimming by the nuclear exosome. It has been unclear how polyadenylation by TRAMP differs from polyadenylation by conventional poly(A) polymerase, which produces poly(A) tails that stabilize RNAs. Using reconstituted S. cerevisiae TRAMP, we show that TRAMP inherently suppresses poly(A) addition after only 3-4 adenosines. This poly(A) tail length restriction is controlled by Mtr4p. The helicase detects the number of 3'-terminal adenosines and, over several adenylation steps, elicits precisely tuned adjustments of ATP affinities and rate constants for adenylation and TRAMP dissociation. Our data establish Mtr4p as a critical regulator of polyadenylation by TRAMP and reveal that an RNA helicase can control the activity of another enzyme in a highly complex fashion and in response to features in RNA.","corpus_id":17613517,"score":2},{"doc_id":"21878619","title":"Air1 zinc knuckles 4 and 5 and a conserved IWRXY motif are critical for the function and integrity of the Trf4/5-Air1/2-Mtr4 polyadenylation (TRAMP) RNA quality control complex.","abstract":"In Saccharomyces cerevisiae, non-coding RNAs, including cryptic unstable transcripts (CUTs), are subject to degradation by the exosome. The Trf4/5-Air1/2-Mtr4 polyadenylation (TRAMP) complex in S. cerevisiae is a nuclear exosome cofactor that recruits the exosome to degrade RNAs. Trf4/5 are poly(A) polymerases, Mtr4 is an RNA helicase, and Air1/2 are putative RNA-binding proteins that contain five CCHC zinc knuckles (ZnKs). One central question is how the TRAMP complex, especially the Air1/2 protein, recognizes its RNA substrates. To characterize the function of the Air1/2 protein, we used random mutagenesis of the AIR1/2 gene to identify residues critical for Air protein function. We identified air1-C178R and air2-C167R alleles encoding air1/2 mutant proteins with a substitution in the second cysteine of ZnK5. Mutagenesis of the second cysteine in AIR1/2 ZnK1-5 reveals that Air1/2 ZnK4 and -5 are critical for Air protein function in vivo. In addition, we find that the level of CUT, NEL025c, in air1 ZnK1-5 mutants is stabilized, particularly in air1 ZnK4, suggesting a role for Air1 ZnK4 in the degradation of CUTs. We also find that Air1/2 ZnK4 and -5 are critical for Trf4 interaction and that the Air1-Trf4 interaction and Air1 level are critical for TRAMP complex integrity. We identify a conserved IWRXY motif in the Air1 ZnK4-5 linker that is important for Trf4 interaction. We also find that hZCCHC7, a putative human orthologue of Air1 that contains the IWRXY motif, localizes to the nucleolus in human cells and interacts with both mammalian Trf4 orthologues, PAPD5 and PAPD7 (PAP-associated domain containing 5 and 7), suggesting that hZCCHC7 is the Air component of a human TRAMP complex.","corpus_id":22629431,"score":2},{"doc_id":"22114319","title":"The crystal structure of S. cerevisiae Ski2, a DExH helicase associated with the cytoplasmic functions of the exosome.","abstract":"Ski2 is a cytoplasmic RNA helicase that functions together with the exosome in the turnover and quality control of mRNAs. Ski2 is conserved in eukaryotes and is related to the helicase Mtr4, a cofactor of the nuclear exosome involved in the processing and quality control of a variety of structured RNAs. We have determined the 2.4 Å resolution crystal structure of the 113 kDa helicase region of Saccharomyces cerevisiae Ski2. The structure shows that Ski2 has an overall architecture similar to that of Mtr4, with a core DExH region and an extended insertion domain. The insertion is not required for the formation of the Ski2-Ski3-Ski8 complex, but is instead an RNA-binding domain. While this is reminiscent of the Mtr4 insertion, there are specific structural and biochemical differences between the two helicases. The insertion of yeast Mtr4 consists of a β-barrel domain that is flexibly attached to a helical stalk, contains a KOW signature motif, and binds in vitro-transcribed tRNA(i)(Met), but not single-stranded RNA. The β-barrel domain of yeast Ski2 does not contain a KOW motif and is tightly packed against the helical stalk, forming a single structural unit maintained by a zinc-binding site. Biochemically, the Ski2 insertion has broad substrate specificity, binding both single-stranded and double-stranded RNAs. We speculate that the Ski2 and Mtr4 insertion domains have evolved with different properties tailored to the type of transcripts that are the substrates of the cytoplasmic and nuclear exosome.","corpus_id":22357595,"score":2},{"doc_id":"22319136","title":"The TRAMP complex shows tRNA editing activity in S. cerevisiae.","abstract":"Transfer RNA (tRNA) editing is a widespread processing phenomenon that alters the sequence of primary transcripts by base substitutions as well as nucleotide deletions and insertions at internal or terminal transcript positions. In the corresponding tRNAs, these events are an important prerequisite for the generation of functional transcripts. Although many editing events are well characterized at the reaction level, it is unclear in most cases from which ancestral activities the modern editing enzymes evolved. Here, we show that in Saccharomyces cerevisiae, the noncanonical poly(A) polymerase Trf4p in the TRAMP complex can be recruited for such an editing reaction at an introduced tRNA transcript. As a distributive polymerase involved in RNA surveillance and quality control, it has a broad substrate spectrum and binds only transiently to the transcripts, limiting the number of added nucleotides at the editing position. These features exactly meet the criteria for an ancestral enzyme of a modern editing activity. Accordingly, our observations are a strong experimental support for the hypothesis that enzymatic promiscuity serves as an evolutionary starting point for the emergence of new functions and activities.","corpus_id":1502516,"score":2},{"doc_id":"22336707","title":"Tri-snRNP-associated proteins interact with subunits of the TRAMP and nuclear exosome complexes, linking RNA decay and pre-mRNA splicing.","abstract":"Nuclear RNA decay factors are involved in many different pathways including rRNA processing, snRNA and snoRNA biogenesis, pre-mRNA processing, and the rapid decay of cryptic intergenic transcripts. In contrast to its yeast counterpart, the mammalian nuclear decay machinery is largely uncharacterized. Here we report interactions of several putative components of the human nuclear RNA decay machinery, including the TRAMP complex protein Mtr4 and the nuclear exosome constituents PM/Scl-100 and PM/Scl-75, with components of the U4/U6.U5 tri-snRNP complex required for pre-mRNA splicing. The tri-snRNP component Prp31 interacts indirectly with Mtr4 and PM/Scl-100 in a manner that is dependent on the phosphorylation sites in the middle of the protein, while Prp3 and Prp4 interact with the nuclear decay complex independent of Prp31. Together our results suggest recruitment of the nuclear decay machinery to the spliceosome to ensure production of properly spliced mRNA.","corpus_id":15566719,"score":2},{"doc_id":"22402490","title":"Air2p is critical for the assembly and RNA-binding of the TRAMP complex and the KOW domain of Mtr4p is crucial for exosome activation.","abstract":"Trf4/5p-Air1/2p-Mtr4p polyadenylation complex (TRAMP) is an essential component of nuclear RNA surveillance in yeast. It recognizes a variety of nuclear transcripts produced by all three RNA polymerases, adds short poly(A) tails to aberrant or unstable RNAs and activates the exosome for their degradation. Despite the advances in understanding the structural features of the isolated complex subunits or their fragments, the details of complex assembly, RNA recognition and exosome activation remain poorly understood. Here we provide the first understanding of the RNA binding mode of the complex. We show that Air2p is an RNA-binding subunit of TRAMP. We identify the zinc knuckles (ZnK) 2, 3 and 4 as the RNA-binding domains, and reveal the essentiality of ZnK4 for TRAMP4 polyadenylation activity. Furthermore, we identify Air2p as the key component of TRAMP4 assembly providing bridging between Mtr4p and Trf4p. The former is bound via the N-terminus of Air2p, while the latter is bound via ZnK5, the linker between ZnK4 and 5 and the C-terminus of the protein. Finally, we uncover the RNA binding part of the Mtr4p arch, the KOW domain, as the essential component for TRAMP-mediated exosome activation.","corpus_id":13918453,"score":2},{"doc_id":"22532666","title":"RNA unwinding by the Trf4/Air2/Mtr4 polyadenylation (TRAMP) complex.","abstract":"Many RNA-processing events in the cell nucleus involve the Trf4/Air2/Mtr4 polyadenylation (TRAMP) complex, which contains the poly(A) polymerase Trf4p, the Zn-knuckle protein Air2p, and the RNA helicase Mtr4p. TRAMP polyadenylates RNAs designated for processing by the nuclear exosome. In addition, TRAMP functions as an exosome cofactor during RNA degradation, and it has been speculated that this role involves disruption of RNA secondary structure. However, it is unknown whether TRAMP displays RNA unwinding activity. It is also not clear how unwinding would be coordinated with polyadenylation and the function of the RNA helicase Mtr4p in modulating poly(A) addition. Here, we show that TRAMP robustly unwinds RNA duplexes. The unwinding activity of Mtr4p is significantly stimulated by Trf4p/Air2p, but the stimulation of Mtr4p does not depend on ongoing polyadenylation. Nonetheless, polyadenylation enables TRAMP to unwind RNA substrates that it otherwise cannot separate. Moreover, TRAMP displays optimal unwinding activity on substrates with a minimal Mtr4p binding site comprised of adenylates. Our results suggest a model for coordination between unwinding and polyadenylation activities by TRAMP that reveals remarkable synergy between helicase and poly(A) polymerase.","corpus_id":4679498,"score":2},{"doc_id":"22817747","title":"Comparison of the yeast and human nuclear exosome complexes.","abstract":"Most RNAs in eukaryotic cells are produced as precursors that undergo processing at the 3' and/or 5' end to generate the mature transcript. In addition, many transcripts are degraded not only as part of normal recycling, but also when recognized as aberrant by the RNA surveillance machinery. The exosome, a conserved multiprotein complex containing two nucleases, is involved in both the 3' processing and the turnover of many RNAs in the cell. A series of factors, including the TRAMP (Trf4-Air2-Mtr4 polyadenylation) complex, Mpp6 and Rrp47, help to define the targets to be processed and/or degraded and assist in exosome function. The majority of the data on the exosome and RNA maturation/decay have been derived from work performed in the yeast Saccharomyces cerevisiae. In the present paper, we provide an overview of the exosome and its role in RNA processing/degradation and discuss important new insights into exosome composition and function in human cells.","corpus_id":5368191,"score":2},{"doc_id":"22923767","title":"Air proteins control differential TRAMP substrate specificity for nuclear RNA surveillance.","abstract":"RNA surveillance systems function at critical steps during the formation and function of RNA molecules in all organisms. The RNA exosome plays a central role in RNA surveillance by processing and degrading RNA molecules in the nucleus and cytoplasm of eukaryotic cells. The exosome functions as a complex of proteins composed of a nine-member core and two ribonucleases. The identity of the molecular determinants of exosome RNA substrate specificity remains an important unsolved aspect of RNA surveillance. In the nucleus of Saccharomyces cerevisiae, TRAMP complexes recognize and polyadenylate RNAs, which enhances RNA degradation by the exosome and may contribute to its specificity. TRAMPs contain either of two putative RNA-binding factors called Air proteins. Previous studies suggested that these proteins function interchangeably in targeting the poly(A)-polymerase activity of TRAMPs to RNAs. Experiments reported here show that the Air proteins govern separable functions. Phenotypic analysis and RNA deep-sequencing results from air mutants reveal specific requirements for each Air protein in the regulation of the levels of noncoding and coding RNAs. Loss of these regulatory functions results in specific metabolic and plasmid inheritance defects. These findings reveal differential functions for Air proteins in RNA metabolism and indicate that they control the substrate specificity of the RNA exosome.","corpus_id":23382542,"score":2},{"doc_id":"23417976","title":"Nuclear RNA surveillance: role of TRAMP in controlling exosome specificity.","abstract":"The advent of high-throughput sequencing technologies has revealed that pervasive transcription generates RNAs from nearly all regions of eukaryotic genomes. Normally, these transcripts undergo rapid degradation by a nuclear RNA surveillance system primarily featuring the RNA exosome. This multimeric protein complex plays a critical role in the efficient turnover and processing of a vast array of RNAs in the nucleus. Despite its initial discovery over a decade ago, important questions remain concerning the mechanisms that recruit and activate the nuclear exosome. Specificity and modulation of exosome activity requires additional protein cofactors, including the conserved TRAMP polyadenylation complex. Recent studies suggest that helicase and RNA-binding subunits of TRAMP direct RNA substrates for polyadenylation, which enhances their degradation by Dis3/Rrp44 and Rrp6, the two exosome-associated ribonucleases. These findings indicate that the exosome and TRAMP have evolved highly flexible functions that allow recognition of a wide range of RNA substrates. This flexibility provides the nuclear RNA surveillance system with the ability to regulate the levels of a broad range of coding and noncoding RNAs, which results in profound effects on gene expression, cellular development, gene silencing, and heterochromatin formation. This review summarizes recent findings on the nuclear RNA surveillance complexes, and speculates upon possible mechanisms for TRAMP-mediated substrate recognition and exosome activation.","corpus_id":2740798,"score":2},{"doc_id":"23910895","title":"Threading the barrel of the RNA exosome.","abstract":"In eukaryotes, the exosome complex degrades RNA backbones and plays key roles in RNA processing and surveillance. It was predicted that RNA substrates are threaded through a central channel. This pathway is conserved between eukaryotic and archaeal complexes, even though nuclease activity was lost from the nine-subunit eukaryotic core (EXO-9) and transferred to associated proteins. The exosome cooperates with nuclear and cytoplasmic cofactors, including RNA helicases Mtr4 and Ski2, respectively. Structures of an RNA-bound exosome and both helicases revealed how substrates are channeled through EXO-9 to the associated nuclease Rrp44. Recent high-throughput analyses provided fresh insights relating exosome structure to its diverse in vivo functions. They also revealed surprisingly high degradation rates for newly synthesized RNAs, particularly RNA polymerase III transcripts.","corpus_id":30260906,"score":2},{"doc_id":"23953113","title":"The yeast ski complex: crystal structure and RNA channeling to the exosome complex.","abstract":"The Ski complex is a conserved multiprotein assembly required for the cytoplasmic functions of the exosome, including RNA turnover, surveillance, and interference. Ski2, Ski3, and Ski8 assemble in a tetramer with 1:1:2 stoichiometry. The crystal structure of an S. cerevisiae 370 kDa core complex shows that Ski3 forms an array of 33 TPR motifs organized in N-terminal and C-terminal arms. The C-terminal arm of Ski3 and the two Ski8 subunits position the helicase core of Ski2 centrally within the complex, enhancing RNA binding. The Ski3 N-terminal arm and the Ski2 insertion domain allosterically modulate the ATPase and helicase activities of the complex. Biochemical data suggest that the Ski complex can thread RNAs directly to the exosome, coupling the helicase and the exoribonuclease through a continuous RNA channel. Finally, we identify a Ski8-binding motif common to Ski3 and Spo11, rationalizing the moonlighting properties of Ski8 in mRNA decay and meiosis.","corpus_id":12699297,"score":2},{"doc_id":"24047896","title":"Cotranscriptional recruitment of RNA exosome cofactors Rrp47p and Mpp6p and two distinct Trf-Air-Mtr4 polyadenylation (TRAMP) complexes assists the exonuclease Rrp6p in the targeting and degradation of an aberrant messenger ribonucleoprotein particle (mRNP) in yeast.","abstract":"The cotranscriptional mRNA processing and packaging reactions that lead to the formation of export-competent messenger ribonucleoprotein particles (mRNPs) are under the surveillance of quality control steps. Aberrant mRNPs resulting from faulty events are retained in the nucleus with ensuing elimination of their mRNA component. The molecular mechanisms by which the surveillance system recognizes defective mRNPs and stimulates their destruction by the RNA degradation machinery are still not completely elucidated. Using an experimental approach in which mRNP formation in yeast is disturbed by the action of the bacterial Rho helicase, we have shown previously that the targeting of Rho-induced aberrant mRNPs is mediated by Rrp6p, which is recruited cotranscriptionally in association with Nrd1p following Rho action. Here we investigated the specific involvement in this quality control process of different cofactors associated with the nuclear RNA degradation machinery. We show that, in addition to the main hydrolytic action of the exonuclease Rrp6p, the cofactors Rrp47p, Mpp6p as well as the Trf-Air-Mtr4 polyadenylation (TRAMP) components Trf4p, Trf5p, and Air2p contribute significantly by stimulating the degradation process upon their cotranscriptional recruitment. Trf4p and Trf5p are apparently recruited in two distinct TRAMP complexes that both contain Air2p as component. Surprisingly, Rrp47p appears to play an important role in mutual protein stabilization with Rrp6p, which highlights a close association between the two partners. Together, our results provide an integrated view of how different cofactors of the RNA degradation machinery cooperate to target and eliminate aberrant mRNPs.","corpus_id":25705209,"score":2},{"doc_id":"24097436","title":"Cotranscriptional recruitment of yeast TRAMP complex to intronic sequences promotes optimal pre-mRNA splicing.","abstract":"Most unwanted RNA transcripts in the nucleus of eukaryotic cells, such as splicing-defective pre-mRNAs and spliced-out introns, are rapidly degraded by the nuclear exosome. In budding yeast, a number of these unwanted RNA transcripts, including spliced-out introns, are first recognized by the nuclear exosome cofactor Trf4/5p-Air1/2p-Mtr4p polyadenylation (TRAMP) complex before subsequent nuclear-exosome-mediated degradation. However, it remains unclear when spliced-out introns are recognized by TRAMP, and whether TRAMP may have any potential roles in pre-mRNA splicing. Here, we demonstrated that TRAMP is cotranscriptionally recruited to nascent RNA transcripts, with particular enrichment at intronic sequences. Deletion of TRAMP components led to further accumulation of unspliced pre-mRNAs even in a yeast strain defective in nuclear exosome activity, suggesting a novel stimulatory role of TRAMP in splicing. We also uncovered new genetic and physical interactions between TRAMP and several splicing factors, and further showed that TRAMP is required for optimal recruitment of the splicing factor Msl5p. Our study provided the first evidence that TRAMP facilitates pre-mRNA splicing, and we interpreted this as a fail-safe mechanism to ensure the cotranscriptional recruitment of TRAMP before or during splicing to prepare for the subsequent targeting of spliced-out introns to rapid degradation by the nuclear exosome.","corpus_id":745968,"score":2},{"doc_id":"24189234","title":"Structure determination of an 11-subunit exosome in complex with RNA by molecular replacement.","abstract":"The RNA exosome is an evolutionarily conserved multi-protein complex involved in the 3' degradation of a variety of RNA transcripts. In the nucleus, the exosome participates in the maturation of structured RNAs, in the surveillance of pre-mRNAs and in the decay of a variety of noncoding transcripts. In the cytoplasm, the exosome degrades mRNAs in constitutive and regulated turnover pathways. Several structures of subcomplexes of eukaryotic exosomes or related prokaryotic exosome-like complexes are known, but how the complete assembly is organized to fulfil processive RNA degradation has been unclear. An atomic snapshot of a Saccharomyces cerevisiae 420 kDa exosome complex bound to an RNA substrate in the pre-cleavage state of a hydrolytic reaction has been determined. Here, the crystallographic steps towards the structural elucidation, which was carried out by molecular replacement, are presented.","corpus_id":-1,"score":2},{"doc_id":"25066235","title":"Molecular basis for coordinating transcription termination with noncoding RNA degradation.","abstract":"The Nrd1-Nab3-Sen1 (NNS) complex is essential for controlling pervasive transcription and generating sn/snoRNAs in S. cerevisiae. The NNS complex terminates transcription of noncoding RNA genes and promotes exosome-dependent processing/degradation of the released transcripts. The Trf4-Air2-Mtr4 (TRAMP) complex polyadenylates NNS target RNAs and favors their degradation. NNS-dependent termination and degradation are coupled, but the mechanism underlying this coupling remains enigmatic. Here we provide structural and functional evidence demonstrating that the same domain of Nrd1p interacts with RNA polymerase II and Trf4p in a mutually exclusive manner, thus defining two alternative forms of the NNS complex, one involved in termination and the other in degradation. We show that the Nrd1-Trf4 interaction is required for optimal exosome activity in vivo and for the stimulation of polyadenylation of NNS targets by TRAMP in vitro. We propose that transcription termination and RNA degradation are coordinated by switching between two alternative partners of the NNS complex.","corpus_id":10054242,"score":2},{"doc_id":"25110014","title":"Exosome substrate targeting: the long and short of it.","abstract":"The exosome ribonuclease complex functions in both the limited trimming of the 3'-ends of nuclear substrates during RNA processing events and the complete destruction of nuclear and cytoplasmic RNAs. The two RNases of the eukaryotic exosome, Rrp44 (rRNA-processing protein 44) and Rrp6, are bound at either end of a catalytically inert cylindrical core. RNA substrates are threaded through the internal channel of the core to Rrp44 by RNA helicase components of the nuclear TRAMP complex (Trf4-Air2-Mtr4 polyadenylation complex) or the cytoplasmic Ski (superkiller) complex. Recent studies reveal that Rrp44 can also associate directly with substrates via channel-independent routes. Although the substrates of the exosome are known, it is not clear whether specific substrates are restricted to one or other pathway. Data currently available support the model that processed substrates are targeted directly to the catalytic subunits, whereas at least some substrates that are directed towards discard pathways must be threaded through the exosome core.","corpus_id":25351651,"score":2},{"doc_id":"25144737","title":"The RNA helicases AtMTR4 and HEN2 target specific subsets of nuclear transcripts for degradation by the nuclear exosome in Arabidopsis thaliana.","abstract":"The RNA exosome is the major 3'-5' RNA degradation machine of eukaryotic cells and participates in processing, surveillance and turnover of both nuclear and cytoplasmic RNA. In both yeast and human, all nuclear functions of the exosome require the RNA helicase MTR4. We show that the Arabidopsis core exosome can associate with two related RNA helicases, AtMTR4 and HEN2. Reciprocal co-immunoprecipitation shows that each of the RNA helicases co-purifies with the exosome core complex and with distinct sets of specific proteins. While AtMTR4 is a predominantly nucleolar protein, HEN2 is located in the nucleoplasm and appears to be excluded from nucleoli. We have previously shown that the major role of AtMTR4 is the degradation of rRNA precursors and rRNA maturation by-products. Here, we demonstrate that HEN2 is involved in the degradation of a large number of polyadenylated nuclear exosome substrates such as snoRNA and miRNA precursors, incompletely spliced mRNAs, and spurious transcripts produced from pseudogenes and intergenic regions. Only a weak accumulation of these exosome substrate targets is observed in mtr4 mutants, suggesting that MTR4 can contribute, but plays rather a minor role for the degradation of non-ribosomal RNAs and cryptic transcripts in Arabidopsis. Consistently, transgene post-transcriptional gene silencing (PTGS) is marginally affected in mtr4 mutants, but increased in hen2 mutants, suggesting that it is mostly the nucleoplasmic exosome that degrades aberrant transgene RNAs to limit their entry in the PTGS pathway. Interestingly, HEN2 is conserved throughout green algae, mosses and land plants but absent from metazoans and other eukaryotic lineages. Our data indicate that, in contrast to human and yeast, plants have two functionally specialized RNA helicases that assist the exosome in the degradation of specific nucleolar and nucleoplasmic RNA populations, respectively.","corpus_id":10129090,"score":2},{"doc_id":"25319414","title":"The exosome-binding factors Rrp6 and Rrp47 form a composite surface for recruiting the Mtr4 helicase.","abstract":"The exosome is a conserved multi-subunit ribonuclease complex that functions in 3' end processing, turnover and surveillance of nuclear and cytoplasmic RNAs. In the yeast nucleus, the 10-subunit core complex of the exosome (Exo-10) physically and functionally interacts with the Rrp6 exoribonuclease and its associated cofactor Rrp47, the helicase Mtr4 and Mpp6. Here, we show that binding of Mtr4 to Exo-10 in vitro is dependent upon both Rrp6 and Rrp47, whereas Mpp6 binds directly and independently of other cofactors. Crystallographic analyses reveal that the N-terminal domains of Rrp6 and Rrp47 form a highly intertwined structural unit. Rrp6 and Rrp47 synergize to create a composite and conserved surface groove that binds the N-terminus of Mtr4. Mutation of conserved residues within Rrp6 and Mtr4 at the structural interface disrupts their interaction and inhibits growth of strains expressing a C-terminal GFP fusion of Mtr4. These studies provide detailed structural insight into the interaction between the Rrp6-Rrp47 complex and Mtr4, revealing an important link between Mtr4 and the core exosome.","corpus_id":12902394,"score":2},{"doc_id":"25414331","title":"The Mtr4 ratchet helix and arch domain both function to promote RNA unwinding.","abstract":"Mtr4 is a conserved Ski2-like RNA helicase and a subunit of the TRAMP complex that activates exosome-mediated 3'-5' turnover in nuclear RNA surveillance and processing pathways. Prominent features of the Mtr4 structure include a four-domain ring-like helicase core and a large arch domain that spans the core. The 'ratchet helix' is positioned to interact with RNA substrates as they move through the helicase. However, the contribution of the ratchet helix in Mtr4 activity is poorly understood. Here we show that strict conservation along the ratchet helix is particularly extensive for Ski2-like RNA helicases compared to related helicases. Mutation of residues along the ratchet helix alters in vitro activity in Mtr4 and TRAMP and causes slow growth phenotypes in vivo. We also identify a residue on the ratchet helix that influences Mtr4 affinity for polyadenylated substrates. Previous work indicated that deletion of the arch domain has minimal effect on Mtr4 unwinding activity. We now show that combining the arch deletion with ratchet helix mutations abolishes helicase activity and produces a lethal in vivo phenotype. These studies demonstrate that the ratchet helix modulates helicase activity and suggest that the arch domain plays a previously unrecognized role in unwinding substrates.","corpus_id":14553431,"score":2},{"doc_id":"25589546","title":"Interaction between the RNA-dependent ATPase and poly(A) polymerase subunits of the TRAMP complex is mediated by short peptides and important for snoRNA processing.","abstract":"The RNA exosome is one of the main 3′ to 5′ exoribonucleases in eukaryotic cells. Although it is responsible for degradation or processing of a wide variety of substrate RNAs, it is very specific and distinguishes between substrate and non-substrate RNAs as well as between substrates that need to be 3′ processed and those that need to be completely degraded. This specificity does not appear to be determined by the exosome itself but rather by about a dozen other proteins. Four of these exosome cofactors have enzymatic activity, namely, the nuclear RNA-dependent ATPase Mtr4, its cytoplasmic paralog Ski2 and the nuclear non-canonical poly(A) polymerases, Trf4 and Trf5. Mtr4 and either Trf4 or Trf5 assemble into a TRAMP complex. However, how these enzymes assemble into a TRAMP complex and the functional consequences of TRAMP complex assembly remain unknown. Here, we identify an important interaction site between Mtr4 and Trf5, and show that disrupting the Mtr4/Trf interaction disrupts specific TRAMP and exosome functions, including snoRNA processing.","corpus_id":10169624,"score":2},{"doc_id":"25775092","title":"Nab3 facilitates the function of the TRAMP complex in RNA processing via recruitment of Rrp6 independent of Nrd1.","abstract":"Non-coding RNAs (ncRNAs) play critical roles in gene regulation. In eukaryotic cells, ncRNAs are processed and/or degraded by the nuclear exosome, a ribonuclease complex containing catalytic subunits Dis3 and Rrp6. The TRAMP (Trf4/5-Air1/2-Mtr4 polyadenylation) complex is a critical exosome cofactor in budding yeast that stimulates the exosome to process/degrade ncRNAs and human TRAMP components have recently been identified. Importantly, mutations in exosome and exosome cofactor genes cause neurodegenerative disease. How the TRAMP complex interacts with other exosome cofactors to orchestrate regulation of the exosome is an open question. To identify novel interactions of the TRAMP exosome cofactor, we performed a high copy suppressor screen of a thermosensitive air1/2 TRAMP mutant. Here, we report that the Nab3 RNA-binding protein of the Nrd1-Nab3-Sen1 (NNS) complex is a potent suppressor of TRAMP mutants. Unlike Nab3, Nrd1 and Sen1 do not suppress TRAMP mutants and Nrd1 binding is not required for Nab3-mediated suppression of TRAMP suggesting an independent role for Nab3. Critically, Nab3 decreases ncRNA levels in TRAMP mutants, Nab3-mediated suppression of air1/2 cells requires the nuclear exosome component, Rrp6, and Nab3 directly binds Rrp6. We extend this analysis to identify a human RNA binding protein, RALY, which shares identity with Nab3 and can suppress TRAMP mutants. These results suggest that Nab3 facilitates TRAMP function by recruiting Rrp6 to ncRNAs for processing/degradation independent of Nrd1. The data raise the intriguing possibility that Nab3 and Nrd1 can function independently to recruit Rrp6 to ncRNA targets, providing combinatorial flexibility in RNA processing.","corpus_id":7393748,"score":2},{"doc_id":"26612606","title":"Rrp6: Integrated roles in nuclear RNA metabolism and transcription termination.","abstract":"The yeast RNA exosome is a eukaryotic ribonuclease complex essential for RNA processing, surveillance, and turnover. It is comprised of a barrel-shaped core and cap as well as a 3'-5' ribonuclease known as Dis3 that contains both endo- and exonuclease domains. A second exonuclease, Rrp6, is added in the nucleus. Dis3 and Rrp6 have both shared and distinct roles in RNA metabolism, and this review will focus primarily on Rrp6 and the roles of the RNA exosome in the nucleus. The functions of the nuclear exosome are modulated by cofactors and interacting partners specific to each type of substrate. Generally, the cofactor TRAMP (Trf4/5-Air2/1-Mtr4 polyadenylation) complex helps unwind unstable RNAs, RNAs requiring processing such as rRNAs, tRNAs, or snRNAs or improperly processed RNAs and direct it toward the exosome. In yeast, Rrp6 interacts with Nrd1, the cap-binding complex, and RNA polymerase II to aid in nascent RNA processing, termination, and polyA tail length regulation. Recent studies have shown that proper termination and processing of short, noncoding RNAs by Rrp6 is particularly important for transcription regulation across the genome and has important implications for regulation of diverse processes at the cellular level. Loss of proper Rrp6 and exosome activity may contribute to various pathologies such as autoimmune disease, neurological disorders, and cancer. WIREs RNA 2016, 7:91-104. doi: 10.1002/wrna.1317 For further resources related to this article, please visit the WIREs website.","corpus_id":206553336,"score":2},{"doc_id":"26820724","title":"Mutations in Mtr4 Structural Domains Reveal Their Important Role in Regulating tRNAiMet Turnover in Saccharomyces cerevisiae and Mtr4p Enzymatic Activities In Vitro.","abstract":"RNA processing and turnover play important roles in the maturation, metabolism and quality control of a large variety of RNAs thereby contributing to gene expression and cellular health. The TRAMP complex, composed of Air2p, Trf4p and Mtr4p, stimulates nuclear exosome-dependent RNA processing and degradation in Saccharomyces cerevisiae. The Mtr4 protein structure is composed of a helicase core and a novel so-called arch domain, which protrudes from the core. The helicase core contains highly conserved helicase domains RecA-1 and 2, and two structural domains of unclear functions, winged helix domain (WH) and ratchet domain. How the structural domains (arch, WH and ratchet domain) coordinate with the helicase domains and what roles they are playing in regulating Mtr4p helicase activity are unknown. We created a library of Mtr4p structural domain mutants for the first time and screened for those defective in the turnover of TRAMP and exosome substrate, hypomodified tRNAiMet. We found these domains regulate Mtr4p enzymatic activities differently through characterizing the arch domain mutants K700N and P731S, WH mutant K904N, and ratchet domain mutant R1030G. Arch domain mutants greatly reduced Mtr4p RNA binding, which surprisingly did not lead to significant defects on either in vivo tRNAiMet turnover, or in vitro unwinding activities. WH mutant K904N and Ratchet domain mutant R1030G showed decreased tRNAiMet turnover in vivo, as well as reduced RNA binding, ATPase and unwinding activities of Mtr4p in vitro. Particularly, K904 was found to be very important for steady protein levels in vivo. Overall, we conclude that arch domain plays a role in RNA binding but is largely dispensable for Mtr4p enzymatic activities, however the structural domains in the helicase core significantly contribute to Mtr4p ATPase and unwinding activities.","corpus_id":1065968,"score":2},{"doc_id":"27076633","title":"Exosome Cofactors Connect Transcription Termination to RNA Processing by Guiding Terminated Transcripts to the Appropriate Exonuclease within the Nuclear Exosome.","abstract":"The yeast Nrd1 interacts with the C-terminal domain (CTD) of RNA polymerase II (RNApII) through its CTD-interacting domain (CID) and also associates with the nuclear exosome, thereby acting as both a transcription termination and RNA processing factor. Previously, we found that the Nrd1 CID is required to recruit the nuclear exosome to the Nrd1 complex, but it was not clear which exosome subunits were contacted. Here, we show that two nuclear exosome cofactors, Mpp6 and Trf4, directly and competitively interact with the Nrd1 CID and differentially regulate the association of Nrd1 with two catalytic subunits of the exosome. Importantly, Mpp6 promotes the processing of Nrd1-terminated transcripts preferentially by Dis3, whereas Trf4 leads to Rrp6-dependent processing. This suggests that Mpp6 and Trf4 may play a role in choosing a particular RNA processing route for Nrd1-terminated transcripts within the exosome by guiding the transcripts to the appropriate exonuclease.","corpus_id":2267218,"score":2},{"doc_id":"27166441","title":"TRAMP Stimulation of Exosome.","abstract":"In order to control and/or enhance the specificity and activity of nuclear surveillance and degradation, exosomes cooperate with the polyadenylation complex called TRAMP. Two forms of TRAMP operate in budding yeast, TRAMP4 and TRAMP5. They oligoadenylate defective or precursor forms of RNAs and promote trimming or complete degradation by exosomes. TRAMPs target a wide variety of nuclear transcripts. The known substrates include the noncoding RNAs originating from pervasive transcription from diverse parts of the yeast genome. Although TRAMP and exosomes can be triggered to a subset of their targets via the RNA-binding complex Nrd1, it is still not completely understood how TRAMP recognizes other aberrant RNAs. The existence of TRAMP-like complexes in other organisms indicates the importance of nuclear surveillance for general cell biology. In this chapter, we review the current understanding of TRAMP function and substrate repertoire. We discuss the advances in TRAMP biochemistry with respect to its catalytic activities and RNA recognition. Finally, we speculate about the possible mechanisms by which TRAMP activates exosomes.","corpus_id":33184183,"score":2},{"doc_id":"27174052","title":"CryoEM structure of yeast cytoplasmic exosome complex.","abstract":"The eukaryotic multi-subunit RNA exosome complex plays crucial roles in 3'-to-5' RNA processing and decay. Rrp6 and Ski7 are the major cofactors for the nuclear and cytoplasmic exosomes, respectively. In the cytoplasm, Ski7 helps the exosome to target mRNAs for degradation and turnover via a through-core pathway. However, the interaction between Ski7 and the exosome complex has remained unclear. The transaction of RNA substrates within the exosome is also elusive. In this work, we used single-particle cryo-electron microscopy to solve the structures of the Ski7-exosome complex in RNA-free and RNA-bound forms at resolutions of 4.2 Å and 5.8 Å, respectively. These structures reveal that the N-terminal domain of Ski7 adopts a structural arrangement and interacts with the exosome in a similar fashion to the C-terminal domain of nuclear Rrp6. Further structural analysis of exosomes with RNA substrates harboring 3' overhangs of different length suggests a switch mechanism of RNA-induced exosome activation in the through-core pathway of RNA processing.","corpus_id":32179906,"score":2},{"doc_id":"27345150","title":"Structure of a Cytoplasmic 11-Subunit RNA Exosome Complex.","abstract":"The RNA exosome complex associates with nuclear and cytoplasmic cofactors to mediate the decay, surveillance, or processing of a wide variety of transcripts. In the cytoplasm, the conserved core of the exosome (Exo10) functions together with the conserved Ski complex. The interaction of S. cerevisiae Exo10 and Ski is not direct but requires a bridging cofactor, Ski7. Here, we report the 2.65 Å resolution structure of S. cerevisiae Exo10 bound to the interacting domain of Ski7. Extensive hydrophobic interactions rationalize the high affinity and stability of this complex, pointing to Ski7 as a constitutive component of the cytosolic exosome. Despite the absence of sequence homology, cytoplasmic Ski7 and nuclear Rrp6 bind Exo10 using similar surfaces and recognition motifs. Knowledge of the interacting residues in the yeast complexes allowed us to identify a splice variant of human HBS1-Like as a Ski7-like exosome-binding protein, revealing the evolutionary conservation of this cytoplasmic cofactor.","corpus_id":37833407,"score":2},{"doc_id":"27434818","title":"Interaction properties of human TRAMP-like proteins and their role in pre-rRNA 5'ETS turnover.","abstract":"In yeast, the Trf4/5-Air1/2-Mtr4 polyadenylation (TRAMP) complex acts as a cofactor for the nuclear exosome to promote degradation of various RNAs. However, the corresponding machinery in mammals is less characterized. We analyzed the interactions of the human TRAMP-like proteins, PAPD5, ZCCHC7, and MTR4, with the nuclear exosome. PAPD5 and ZCCHC7 exhibited mutual interactions in presence of the exosome catalytic subunit RRP6, whereas MTR4 was dispensable for their assembly. Furthermore, the human TRAMP-like proteins were involved in the RRP6-catalyzed turnover of pre-rRNA 5'ETS fragments. These results suggest the significant role for RRP6 in the assembly of TRAMP-like proteins during nucleolar RNA surveillance.","corpus_id":38072991,"score":2},{"doc_id":"27474443","title":"A conserved virus-induced cytoplasmic TRAMP-like complex recruits the exosome to target viral RNA for degradation.","abstract":"RNA degradation is tightly regulated to selectively target aberrant RNAs, including viral RNA, but this regulation is incompletely understood. Through RNAi screening in Drosophila cells, we identified the 3'-to-5' RNA exosome and two components of the exosome cofactor TRAMP (Trf4/5-Air1/2-Mtr4 polyadenylation) complex, dMtr4 and dZcchc7, as antiviral against a panel of RNA viruses. We extended our studies to human orthologs and found that the exosome as well as TRAMP components hMTR4 and hZCCHC7 are antiviral. While hMTR4 and hZCCHC7 are normally nuclear, infection by cytoplasmic RNA viruses induces their export, forming a cytoplasmic complex that specifically recognizes and induces degradation of viral mRNAs. Furthermore, the 3' untranslated region (UTR) of bunyaviral mRNA is sufficient to confer virus-induced exosomal degradation. Altogether, our results reveal that signals from viral infection repurpose TRAMP components to a cytoplasmic surveillance role where they selectively engage viral RNAs for degradation to restrict a broad range of viruses.","corpus_id":33869258,"score":2},{"doc_id":"28733371","title":"An Mtr4/ZFC3H1 complex facilitates turnover of unstable nuclear RNAs to prevent their cytoplasmic transport and global translational repression.","abstract":"Many long noncoding RNAs (lncRNAs) are unstable and rapidly degraded in the nucleus by the nuclear exosome. An exosome adaptor complex called NEXT (nuclear exosome targeting) functions to facilitate turnover of some of these lncRNAs. Here we show that knockdown of one NEXT subunit, Mtr4, but neither of the other two subunits, resulted in accumulation of two types of lncRNAs: prematurely terminated RNAs (ptRNAs) and upstream antisense RNAs (uaRNAs). This suggested a NEXT-independent Mtr4 function, and, consistent with this, we isolated a distinct complex containing Mtr4 and the zinc finger protein ZFC3H1. Strikingly, knockdown of either protein not only increased pt/uaRNA levels but also led to their accumulation in the cytoplasm. Furthermore, all pt/uaRNAs examined associated with active ribosomes, but, paradoxically, this correlated with a global reduction in heavy polysomes and overall repression of translation. Our findings highlight a critical role for Mtr4/ZFC3H1 in nuclear surveillance of naturally unstable lncRNAs to prevent their accumulation, transport to the cytoplasm, and resultant disruption of protein synthesis.","corpus_id":20566212,"score":2},{"doc_id":"28742025","title":"Structure and reconstitution of yeast Mpp6-nuclear exosome complexes reveals that Mpp6 stimulates RNA decay and recruits the Mtr4 helicase.","abstract":"Nuclear RNA exosomes catalyze a range of RNA processing and decay activities that are coordinated in part by cofactors, including Mpp6, Rrp47, and the Mtr4 RNA helicase. Mpp6 interacts with the nine-subunit exosome core, while Rrp47 stabilizes the exoribonuclease Rrp6 and recruits Mtr4, but it is less clear if these cofactors work together. Using biochemistry with Saccharomyces cerevisiae proteins, we show that Rrp47 and Mpp6 stimulate exosome-mediated RNA decay, albeit with unique dependencies on elements within the nuclear exosome. Mpp6-exosomes can recruit Mtr4, while Mpp6 and Rrp47 each contribute to Mtr4-dependent RNA decay, with maximal Mtr4-dependent decay observed with both cofactors. The 3.3 Å structure of a twelve-subunit nuclear Mpp6 exosome bound to RNA shows the central region of Mpp6 bound to the exosome core, positioning its Mtr4 recruitment domain next to Rrp6 and the exosome central channel. Genetic analysis reveals interactions that are largely consistent with our model.","corpus_id":261364015,"score":2},{"doc_id":"28877463","title":"Mpp6 Incorporation in the Nuclear Exosome Contributes to RNA Channeling through the Mtr4 Helicase.","abstract":"The RNA-degrading exosome mediates the processing and decay of many cellular transcripts. In the yeast nucleus, the ubiquitous 10-subunit exosome core complex (Exo-9-Rrp44) functions with four conserved cofactors (Rrp6, Rrp47, Mtr4, and Mpp6). Biochemical and structural studies to date have shed insights into the mechanisms of the exosome core and its nuclear cofactors, with the exception of Mpp6. We report the 3.2-Å resolution crystal structure of a S. cerevisiae Exo-9-Mpp6 complex, revealing how linear motifs in the Mpp6 middle domain bind Rrp40 via evolutionary conserved residues. In particular, Mpp6 binds near a tryptophan residue of Rrp40 that is mutated in human patients suffering from pontocerebellar hypoplasia. Using biochemical assays, we show that Mpp6 is required for the ability of Mtr4 to extend the trajectory of an RNA entering the exosome core, suggesting that it promotes the channeling of substrates from the nuclear helicase to the processive RNase.","corpus_id":12726485,"score":2},{"doc_id":"17983848","title":"Intrinsic 5'-deoxyribose-5-phosphate lyase activity in Saccharomyces cerevisiae Trf4 protein with a possible role in base excision DNA repair.","abstract":"In Saccharomyces cerevisiae, the base excision DNA repair (BER) pathway has been thought to involve only a multinucleotide (long-patch) mechanism (LP-BER), in contrast to most known cases that include a major single-nucleotide pathway (SN-BER). The key step in mammalian SN-BER, removal of the 5'-terminal abasic residue generated by AP endonuclease incision, is effected by DNA polymerase beta (Polbeta). Computational analysis indicates that yeast Trf4 protein, with roles in sister chromatin cohesion and RNA quality control, is a new member of the X family of DNA polymerases that includes Polbeta. Previous studies of yeast trf4Delta mutants revealed hypersensitivity to methylmethane sulfonate (MMS) but not UV light, a characteristic of BER mutants in other organisms. We found that, like mammalian Polbeta, Trf4 is able to form a Schiff base intermediate with a 5'-deoxyribose-5-phosphate substrate and to excise the abasic residue through a dRP lyase activity. Also like Polbeta, Trf4 forms stable cross-links in vitro to 5'-incised 2-deoxyribonolactone residues in DNA. We determined the sensitivity to MMS of strains with a trf4Delta mutation in a rad27Delta background, in an AP lyase-deficient background (ogg1 ntg1 ntg2), or in a pol4Delta background. Only a RAD27 genetic interaction was detected: there was higher sensitivity for strains mutated in both TRF4 and RAD27 than either single mutant, and overexpression of Trf4 in a rad27Delta background partially suppressed MMS sensitivity. The data strongly suggest a role for Trf4 in a pathway parallel to the Rad27-dependent LP-BER in yeast. Finally, we demonstrate that Trf5 significantly affects MMS sensitivity and thus probably BER efficiency in cells expressing either wild-type Trf4 or a C-terminus-deleted form.","corpus_id":42872015,"score":1},{"doc_id":"18042682","title":"Crystal structure of an archaeal Ski2p-like protein from Pyrococcus horikoshii OT3.","abstract":"The Ski complex composed of Ski2p, Ski3p, and Ski8p plays an essential role in the 3' to 5' cytoplasmic mRNA degradation pathway in yeast. Ski2p is a putative RNA helicase, belonging in the DExD/H-box protein families and conserved in eukarya as well as in archaea. The gene product (Ph1280p) from the hyperthermophilic archaeon Pyrococcus horikoshii OT3 shows sequence homology with Ski2p, sharing 22.6% identical amino acids with a central region of Ski2p. In order to gain structural information about the Ski2p-like RNA helicase, we overproduced Ph1280p in Escherichia coli cells, and purified it to apparent homogeneity. Ph1280p exhibits DNA/RNA-dependent ATPase activity with an optimal temperature at approximately 90 degrees C. The crystal structure of Ph1280p has been solved at a resolution of 3.5 A using single-wavelength anomalous dispersion (SAD) and selenomethionyl (Se-Met)-substituted protein. Ph1280p comprises four subdomains; the two N-terminal subdomains (N1 and N2) fold into an RecA-like architecture with the conserved helicase motifs, while the two C-terminal subdomains (C1 and C2) fold into alpha-helical structures containing a winged helix (WH)-fold and helix-hairpin-helix (HhH)-fold, respectively. Although the structure of each of the Ph1280p subdomains can be individually superimposed on the corresponding domains in other helicases, such as the Escherichia coli DNA helicase RecQ, the relative orientation of the helicase and C-terminal subdomains in Ph1280p is significantly different from that of other helicases. This structural feature is implicated in substrate specificity for the Ski2-like helicase and would play a critical role in the 3' to 5' cytoplasmic mRNA degradation in the Ski complex.","corpus_id":45433442,"score":1},{"doc_id":"19070634","title":"Identification and characterization of nuclear non-canonical poly(A) polymerases from Trypanosoma brucei.","abstract":"Regulation of nuclear genome expression in Trypanosoma brucei is critical for this protozoan parasite's successful transition between its vertebrate and invertebrate host environments. The canonical eukaryotic circuits such as modulation of transcription initiation, mRNA splicing and polyadenylation appear to be nearly non-existent in T. brucei suggesting that the transcriptome is primarily defined by mRNA turnover. Our previous work has highlighted sequence similarities between terminal RNA uridylyl transferases (TUTases) and non-canonical poly(A) polymerases, which are widely implicated in regulating nuclear, cytoplasmic and organellar RNA decay throughout the eukaryotic lineage. Here, we have continued characterization of TUTase-like proteins in T. brucei and identified two nuclear non-canonical poly(A) polymerases (ncPAPs). The 82kDa TbncPAP1 is essential for viability of procyclic and bloodstream forms of T. brucei. Similar to Trf4/5 proteins from budding yeast, TbncPAP1 requires protein cofactor(s) to exert poly(A) polymerase activity in vitro. The recombinant 54kDa TbncPAP2 showed a PAP activity as an individual polypeptide. Proteomic analysis of the TbncPAP1 interactions demonstrated its association with Mtr4 RNA helicase and several RNA binding proteins, including a potential ortholog of Air1p/2p proteins, which indicates the presence of a stable TRAMP-like complex in trypanosomes. Our findings suggest that TbncPAP1 may be a \"quality control\" nuclear PAP involved in targeting aberrant or anti-sense transcripts for degradation by the 3'-exosome. Such mechanisms are likely to play a major role in alleviating promiscuity of the transcriptional machinery.","corpus_id":19494397,"score":1},{"doc_id":"19327365","title":"Crystal structure of Escherichia coli polynucleotide phosphorylase core bound to RNase E, RNA and manganese: implications for catalytic mechanism and RNA degradosome assembly.","abstract":"Polynucleotide phosphorylase (PNPase) is a processive exoribonuclease that contributes to messenger RNA turnover and quality control of ribosomal RNA precursors in many bacterial species. In Escherichia coli, a proportion of the PNPase is recruited into a multi-enzyme assembly, known as the RNA degradosome, through an interaction with the scaffolding domain of the endoribonuclease RNase E. Here, we report crystal structures of E. coli PNPase complexed with the recognition site from RNase E and with manganese in the presence or in the absence of modified RNA. The homotrimeric PNPase engages RNase E on the periphery of its ring-like architecture through a pseudo-continuous anti-parallel beta-sheet. A similar interaction pattern occurs in the structurally homologous human exosome between the Rrp45 and Rrp46 subunits. At the centre of the PNPase ring is a tapered channel with an adjustable aperture where RNA bases stack on phenylalanine side chains and trigger structural changes that propagate to the active sites. Manganese can substitute for magnesium as an essential co-factor for PNPase catalysis, and our crystal structure of the enzyme in complex with manganese suggests how the metal is positioned to stabilise the transition state. We discuss the implications of these structural observations for the catalytic mechanism of PNPase, its processive mode of action, and its assembly into the RNA degradosome.","corpus_id":23416178,"score":1},{"doc_id":"20711761","title":"1H, 13C, and 15N chemical shift assignments of ZCCHC9.","abstract":"ZCCHC9 is a human nuclear protein with sequence homology to yeast Air1p/Air2p proteins which are RNA-binding subunits of the Trf4/Air2/Mtr4 polyadenylation (TRAMP) complex involved in nuclear RNA quality control and degradation in yeast. The ZCCHC9 protein contains four retroviral-type zinc knuckle motifs. Here, we report the NMR spectral assignment of the zinc knuckle region of ZCCHC9. These data will allow performing NMR structural and RNA-binding studies of ZCCHC9 with the aim to investigate its role in the RNA quality control in human.","corpus_id":11114207,"score":1},{"doc_id":"23166521","title":"Polyadenylation-dependent control of long noncoding RNA expression by the poly(A)-binding protein nuclear 1.","abstract":"The poly(A)-binding protein nuclear 1 (PABPN1) is a ubiquitously expressed protein that is thought to function during mRNA poly(A) tail synthesis in the nucleus. Despite the predicted role of PABPN1 in mRNA polyadenylation, little is known about the impact of PABPN1 deficiency on human gene expression. Specifically, it remains unclear whether PABPN1 is required for general mRNA expression or for the regulation of specific transcripts. Using RNA sequencing (RNA-seq), we show here that the large majority of protein-coding genes express normal levels of mRNA in PABPN1-deficient cells, arguing that PABPN1 may not be required for the bulk of mRNA expression. Unexpectedly, and contrary to the view that PABPN1 functions exclusively at protein-coding genes, we identified a class of PABPN1-sensitive long noncoding RNAs (lncRNAs), the majority of which accumulated in conditions of PABPN1 deficiency. Using the spliced transcript produced from a snoRNA host gene as a model lncRNA, we show that PABPN1 promotes lncRNA turnover via a polyadenylation-dependent mechanism. PABPN1-sensitive lncRNAs are targeted by the exosome and the RNA helicase MTR4/SKIV2L2; yet, the polyadenylation activity of TRF4-2, a putative human TRAMP subunit, appears to be dispensable for PABPN1-dependent regulation. In addition to identifying a novel function for PABPN1 in lncRNA turnover, our results provide new insights into the post-transcriptional regulation of human lncRNAs.","corpus_id":1053760,"score":1},{"doc_id":"21063153","title":"Crystal structure of a PFU-PUL domain pair of Saccharomyces cerevisiae Doa1/Ufd3.","abstract":"Doa1/Ufd3 is involved in ubiquitin (Ub)-dependent cellular processes in Saccharomyces cerevisiae, and consists of WD40, PFU, and PUL domains. Previous studies showed that the PFU and PUL domains interact with Ub and Hse1, and Cdc48, respectively. However, their detailed functional interactions with Doa1 remained elusive. We report the crystal structure of the PFU-PUL domain pair of yeast Doa1 at 1.9 Å resolution. The conserved surface of the PFU domain may be involved in binding to Ub and Hse1. Unexpectedly, the PUL domain consists of an Armadillo (ARM)-like repeat structure. The positively charged concave surface of the PUL domain may bind to the negatively charged C-terminal region of Cdc48. A structural comparison of Doa1 with Ufd2 revealed that they share a similar ARM-like repeat, supporting a model in which Doa1 and Ufd2 compete for Cdc48 binding and may dictate the fate of ubiquitinated proteins in the proteasome pathway.","corpus_id":6528918,"score":0},{"doc_id":"21984415","title":"Molecular architecture of a multifunctional MCM complex.","abstract":"DNA replication is strictly regulated through a sequence of steps that involve many macromolecular protein complexes. One of them is the replicative helicase, which is required for initiation and elongation phases. A MCM helicase found as a prophage in the genome of Bacillus cereus is fused with a primase domain constituting an integrative arrangement of two essential activities for replication. We have isolated this helicase-primase complex (BcMCM) showing that it can bind DNA and displays not only helicase and primase but also DNA polymerase activity. Using single-particle electron microscopy and 3D reconstruction, we obtained structures of BcMCM using ATPγS or ADP in the absence and presence of DNA. The complex depicts the typical hexameric ring shape. The dissection of the unwinding mechanism using site-directed mutagenesis in the Walker A, Walker B, arginine finger and the helicase channels, suggests that the BcMCM complex unwinds DNA following the extrusion model similarly to the E1 helicase from papillomavirus.","corpus_id":3055885,"score":0},{"doc_id":"22813733","title":"Molecular architecture of the yeast monopolin complex.","abstract":"The Saccharomyces cerevisiae monopolin complex directs proper chromosome segregation in meiosis I by mediating co-orientation of sister kinetochores on the meiosis I spindle. The monopolin subunits Csm1 and Lrs4 form a V-shaped complex that may directly crosslink sister kinetochores. We report here biochemical characterization of the monopolin complex subunits Mam1 and Hrr25 and of the complete four-protein monopolin complex. By purifying monopolin subcomplexes with different subunit combinations, we have determined the stoichiometry and overall architecture of the full monopolin complex. We have determined the crystal structure of Csm1 bound to a Mam1 fragment, showing how Mam1 wraps around the Csm1 dimer and alters the stoichiometry of kinetochore-protein binding by Csm1. We further show that the kinase activity of Hrr25 is altered by Mam1 binding, and we identify Hrr25 phosphorylation sites on Mam1 that may affect monopolin complex stability and/or kinetochore binding in meiosis.","corpus_id":6368384,"score":0},{"doc_id":"25849387","title":"A noncanonical PWI domain in the N-terminal helicase-associated region of the spliceosomal Brr2 protein.","abstract":"The spliceosomal RNA helicase Brr2 is required for the assembly of a catalytically active spliceosome on a messenger RNA precursor. Brr2 exhibits an unusual organization with tandem helicase units, each comprising dual RecA-like domains and a Sec63 homology unit, preceded by a more than 400-residue N-terminal helicase-associated region. Whereas recent crystal structures have provided insights into the molecular architecture and regulation of the Brr2 helicase region, little is known about the structural organization and function of its N-terminal part. Here, a near-atomic resolution crystal structure of a PWI-like domain that resides in the N-terminal region of Chaetomium thermophilum Brr2 is presented. CD spectroscopic studies suggested that this domain is conserved in the yeast and human Brr2 orthologues. Although canonical PWI domains act as low-specificity nucleic acid-binding domains, no significant affinity of the unusual PWI domain of Brr2 for a broad spectrum of DNAs and RNAs was detected in band-shift assays. Consistently, the C. thermophilum Brr2 PWI-like domain, in the conformation seen in the present crystal structure, lacks an expanded positively charged surface patch as observed in at least one canonical, nucleic acid-binding PWI domain. Instead, in a comprehensive yeast two-hybrid screen against human spliceosomal proteins, fragments of the N-terminal region of human Brr2 were found to interact with several other spliceosomal proteins. At least one of these interactions, with the Prp19 complex protein SPF27, depended on the presence of the PWI-like domain. The results suggest that the N-terminal region of Brr2 serves as a versatile protein-protein interaction platform in the spliceosome and that some interactions require or are reinforced by the PWI-like domain.","corpus_id":19950529,"score":0},{"doc_id":"25914052","title":"Architecture of the ubiquitylation module of the yeast Ccr4-Not complex.","abstract":"The Ccr4-Not complex regulates eukaryotic gene expression at multiple levels, including mRNA turnover, translational repression, and transcription. We have studied the ubiquitylation module of the yeast Ccr4-Not complex and addressed how E3 ligase binds cognate E2 and how it is tethered to the complex. The 2.8-Å resolution crystal structure of the N-terminal RING domain of Not4 in complex with Ubc4 shows the detailed interactions of this E3-E2 complex. The 3.6-Å resolution crystal structure of the C-terminal domain of the yeast Not4 in complex with the C-terminal domain of Not1 reveals how a largely extended region at the C-terminus of Not4 wraps around a HEAT-repeat region of Not1. This C-terminal region of Not4 is only partly conserved in metazoans, rationalizing its weaker Not1-binding properties. The structural and biochemical data show how Not1 can incorporate both the ubiquitylation module and the Not2-Not3/5 module concomitantly in the Ccr4-Not complex.","corpus_id":12471595,"score":0},{"doc_id":"26124149","title":"Structural basis for the activation of the C. elegans noncanonical cytoplasmic poly(A)-polymerase GLD-2 by GLD-3.","abstract":"The Caenorhabditis elegans germ-line development defective (GLD)-2-GLD-3 complex up-regulates the expression of genes required for meiotic progression. GLD-2-GLD-3 acts by extending the short poly(A) tail of germ-line-specific mRNAs, switching them from a dormant state into a translationally active state. GLD-2 is a cytoplasmic noncanonical poly(A) polymerase that lacks the RNA-binding domain typical of the canonical nuclear poly(A)-polymerase Pap1. The activity of C. elegans GLD-2 in vivo and in vitro depends on its association with the multi-K homology (KH) domain-containing protein, GLD-3, a homolog of Bicaudal-C. We have identified a minimal polyadenylation complex that includes the conserved nucleotidyl-transferase core of GLD-2 and the N-terminal domain of GLD-3, and determined its structure at 2.3-Å resolution. The structure shows that the N-terminal domain of GLD-3 does not fold into the predicted KH domain but wraps around the catalytic domain of GLD-2. The picture that emerges from the structural and biochemical data are that GLD-3 activates GLD-2 both indirectly by stabilizing the enzyme and directly by contributing positively charged residues near the RNA-binding cleft. The RNA-binding cleft of GLD-2 has distinct structural features compared with the poly(A)-polymerases Pap1 and Trf4. Consistently, GLD-2 has distinct biochemical properties: It displays unusual specificity in vitro for single-stranded RNAs with at least one adenosine at the 3' end. GLD-2 thus appears to have evolved specialized nucleotidyl-transferase properties that match the 3' end features of dormant cytoplasmic mRNAs.","corpus_id":31001608,"score":0},{"doc_id":"26637280","title":"The large N-terminal region of the Brr2 RNA helicase guides productive spliceosome activation.","abstract":"The Brr2 helicase provides the key remodeling activity for spliceosome catalytic activation, during which it disrupts the U4/U6 di-snRNP (small nuclear RNA protein), and its activity has to be tightly regulated. Brr2 exhibits an unusual architecture, including an ∼500-residue N-terminal region, whose functions and molecular mechanisms are presently unknown, followed by a tandem array of structurally similar helicase units (cassettes), only the first of which is catalytically active. Here, we show by crystal structure analysis of full-length Brr2 in complex with a regulatory Jab1/MPN domain of the Prp8 protein and by cross-linking/mass spectrometry of isolated Brr2 that the Brr2 N-terminal region encompasses two folded domains and adjacent linear elements that clamp and interconnect the helicase cassettes. Stepwise N-terminal truncations led to yeast growth and splicing defects, reduced Brr2 association with U4/U6•U5 tri-snRNPs, and increased ATP-dependent disruption of the tri-snRNP, yielding U4/U6 di-snRNP and U5 snRNP. Trends in the RNA-binding, ATPase, and helicase activities of the Brr2 truncation variants are fully rationalized by the crystal structure, demonstrating that the N-terminal region autoinhibits Brr2 via substrate competition and conformational clamping. Our results reveal molecular mechanisms that prevent premature and unproductive tri-snRNP disruption and suggest novel principles of Brr2-dependent splicing regulation.","corpus_id":2238955,"score":0},{"doc_id":"28652207","title":"Characterizing the molecular architectures of chromatin-modifying complexes.","abstract":"Eukaryotic cells package their genome in the form of a DNA-protein complex known as chromatin. This organization not only condenses the genome to fit within the confines of the nucleus, but also provides a platform for a cell to regulate accessibility to different gene sequences. The basic packaging element of chromatin is the nucleosome, which consists of 146 base pairs of DNA wrapped around histone proteins. One major means that a cell regulates chromatin structure is by depositing post-translational modifications on nucleosomal histone proteins, and thereby altering internucleosomal interactions and/or binding to different chromatin associated factors. These chromatin modifications are often catalyzed by multi-subunit enzyme complexes, whose large size, sophisticated composition, and inherent conformational flexibility pose significant technical challenges to their biochemical and structural characterization. Multiple structural approaches including nuclear magnetic resonance spectroscopy, X-ray crystallography, single-particle electron microscopy, and crosslinking coupled to mass spectrometry are often used synergistically to probe the overall architecture, subunit organization, and catalytic mechanisms of these macromolecular assemblies. In this review, we highlight several recent chromatin-modifying complexes studies that embodies this multipronged structural approach, and explore common themes amongst them. This article is part of a Special Issue entitled: Biophysics in Canada, edited by Lewis Kay, John Baenziger, Albert Berghuis and Peter Tieleman.","corpus_id":205856271,"score":0}],"string":"[\n {\n \"doc_id\": \"18000032\",\n \"title\": \"Degradation of hypomodified tRNA(iMet) in vivo involves RNA-dependent ATPase activity of the DExH helicase Mtr4p.\",\n \"abstract\": \"Effective turnover of many incorrectly processed RNAs in yeast, including hypomodified tRNA(iMet), requires the TRAMP complex, which appends a short poly(A) tail to RNA designated for decay. The poly(A) tail stimulates degradation by the exosome. The TRAMP complex contains the poly(A) polymerase Trf4p, the RNA-binding protein Air2p, and the DExH RNA helicase Mtr4p. The role of Mtr4p in RNA degradation processes involving the TRAMP complex has been unclear. Here we show through a genetic analysis that MTR4 is required for degradation but not for polyadenylation of hypomodified tRNA(iMet). A suppressor of the trm6-504 mutation in the tRNA m(1)A58 methyltransferase (Trm6p/Trm61p), which causes a reduced level of tRNA(iMet), was mapped to MTR4. This mtr4-20 mutation changed a single amino acid in the conserved helicase motif VI of Mtr4p. The mutation stabilizes hypomodified tRNA(iMet) in vivo but has no effect on TRAMP complex stability or polyadenylation activity in vivo or in vitro. We further show that purified recombinant Mtr4p displays RNA-dependent ATPase activity and unwinds RNA duplexes with a 3'-to-5' polarity in an ATP-dependent fashion. Unwinding and RNA-stimulated ATPase activities are strongly reduced in the recombinant mutant Mtr4-20p, suggesting that these activities of Mtr4p are critical for degradation of polyadenylated hypomodified tRNA(iMet).\",\n \"corpus_id\": 19996245,\n \"score\": 2\n },\n {\n \"doc_id\": \"18025105\",\n \"title\": \"Global role for polyadenylation-assisted nuclear RNA degradation in posttranscriptional gene silencing.\",\n \"abstract\": \"Fission yeast Cid14, a component of the TRAMP (Cid14/Trf4-Air1-Mtr4 polyadenylation) complex, polyadenylates nuclear RNA and stimulates degradation by the exosome for RNA quality control. Here, we analyze patterns of global gene expression in cells lacking the Cid14 or the Dis3/Rpr44 subunit of the nuclear exosome. We found that transcripts from many genes induced during meiosis, including key regulators, accumulated in the absence of Cid14 or Dis3. Moreover, our data suggest that additional substrates include transcripts involved in heterochromatin assembly. Mutant cells lacking Cid14 and/or Dis3 accumulate transcripts corresponding to naturally silenced repeat elements within heterochromatic domains, reflecting defects in centromeric gene silencing and derepression of subtelomeric gene expression. We also uncover roles for Cid14 and Dis3 in maintaining the genomic integrity of ribosomal DNA. Our data indicate that polyadenylation-assisted nuclear RNA turnover functions in eliminating a variety of RNA targets to control diverse processes, such as heterochromatic gene silencing, meiotic differentiation, and maintenance of genomic integrity.\",\n \"corpus_id\": 15469514,\n \"score\": 2\n },\n {\n \"doc_id\": \"18591258\",\n \"title\": \"A yeast exosome cofactor, Mpp6, functions in RNA surveillance and in the degradation of noncoding RNA transcripts.\",\n \"abstract\": \"A genome-wide screen for synthetic lethal (SL) interactions with loss of the nuclear exosome cofactors Rrp47/Lrp1 or Air1 identified 3'-->5' exonucleases, the THO complex required for mRNP assembly, and Ynr024w (Mpp6). SL interactions with mpp6Delta were confirmed for rrp47Delta and nuclear exosome component Rrp6. The results of bioinformatic analyses revealed homology between Mpp6 and a human exosome cofactor, underlining the high conservation of the RNA surveillance system. Mpp6 is an RNA binding protein that physically associates with the exosome and was localized throughout the nucleus. The results of functional analyses demonstrated roles for Mpp6 in the surveillance of both pre-rRNA and pre-mRNAs and in the degradation of \\\"cryptic\\\" noncoding RNAs (ncRNAs) derived from intergenic regions and the ribosomal DNA spacer heterochromatin. Strikingly, these ncRNAs are also targeted by other exosome cofactors, including Rrp47, the TRAMP complex (which includes Air1), and the Nrd1/Nab3 complex, and are degraded by both Rrp6 and the core exosome. Heterochromatic transcripts and other ncRNAs are characterized by very rapid degradation, and we predict that functional redundancy is an important feature of ncRNA metabolism.\",\n \"corpus_id\": 14385449,\n \"score\": 2\n },\n {\n \"doc_id\": \"18765642\",\n \"title\": \"TRF4 is involved in polyadenylation of snRNAs in Drosophila melanogaster.\",\n \"abstract\": \"The Saccharomyces cerevisiae poly(A) polymerases Trf4 and Trf5 are involved in an RNA quality control mechanism, where polyadenylated RNAs are degraded by the nuclear exosome. Although Trf4/5 homologue genes are distributed throughout multicellular organisms, their biological roles remain to be elucidated. We isolated here the two homologues of Trf4/5 in Drosophila melanogaster, named DmTRF4-1 and DmTRF4-2, and investigated their biological function. DmTRF4-1 displayed poly(A) polymerase activity in vitro, whereas DmTRF4-2 did not. Gene knockdown of DmTRF4-1 by RNA interference is lethal in flies, as is the case for the trf4 trf5 double mutants. In contrast, disruption of DmTRF4-2 results in viable flies. Cellular localization analysis suggested that DmTRF4-1 localizes in the nucleolus. Abnormal polyadenylation of snRNAs was observed in transgenic flies overexpressing DmTRF4-1 and was slightly increased by the suppression of DmRrp6, the 3'-5' exonuclease of the nuclear exosome. These results suggest that DmTRF4-1 and DmRrp6 are involved in the polyadenylation-mediated degradation of snRNAs in vivo.\",\n \"corpus_id\": 7961480,\n \"score\": 2\n },\n {\n \"doc_id\": \"19369424\",\n \"title\": \"Regulation of NAB2 mRNA 3'-end formation requires the core exosome and the Trf4p component of the TRAMP complex.\",\n \"abstract\": \"The nuclear exosome functions in a variety of pathways catalyzing formation of mature RNA 3'-ends or the destruction of aberrant RNA transcripts. The RNA 3'-end formation activity of the exosome appeared restricted to small noncoding RNAs. However, the nuclear exosome controls the level of the mRNA encoding the poly(A)-binding protein Nab2p in a manner requiring an A(26) sequence in the mRNA 3' untranslated regions (UTR), and the activities of Nab2p and the exosome-associated exoribonuclease Rrp6p. Here we show that the A(26) sequence inhibits normal 3'-end processing of NAB2 mRNA in vivo and in vitro, and makes formation of the mature 3'-end dependent on trimming of the transcript by the core exosome and the Trf4p component of the TRAMP complex from a downstream site. The detection of mature, polyadenylated transcripts ending at, or within, the A(26) sequence indicates that exosome trimming sometimes gives way to polyadenylation of the mRNA. Alternatively, Rrp6p and the TRAMP-associated Mtr4p degrade these transcripts thereby limiting the amount of Nab2p in the cell. These findings suggest that NAB2 mRNA 3'-end formation requires the exosome and TRAMP complex, and that competition between polyadenylation and Rrp6p-dependent degradation controls the level of this mRNA.\",\n \"corpus_id\": 25961000,\n \"score\": 2\n },\n {\n \"doc_id\": \"19593367\",\n \"title\": \"Distinct roles of non-canonical poly(A) polymerases in RNA metabolism.\",\n \"abstract\": \"Trf4p and Trf5p are non-canonical poly(A) polymerases and are part of the heteromeric protein complexes TRAMP4 and TRAMP5 that promote the degradation of aberrant and short-lived RNA substrates by interacting with the nuclear exosome. To assess the level of functional redundancy between the paralogous Trf4 and Trf5 proteins and to investigate the role of the Trf4-dependent polyadenylation in vivo, we used DNA microarrays to compare gene expression of the wild-type yeast strain of S. cerevisiae with either that of trf4Delta or trf5Delta mutant strains or the trf4Delta mutant expressing the polyadenylation-defective Trf4(DADA) protein. We found little overlap between the sets of transcripts with altered expression in the trf4Delta or the trf5Delta mutants, suggesting that Trf4p and Trf5p target distinct groups of RNAs for degradation. Surprisingly, most RNAs the expression of which was altered by the trf4 deletion were restored to wild-type levels by overexpression of TRF4(DADA), showing that the polyadenylation activity of Trf4p is dispensable in vivo. Apart from previously reported Trf4p and Trf5p target RNAs, this analysis along with in vivo cross-linking and RNA immunopurification-chip experiments revealed that both the TRAMP4 and the TRAMP5 complexes stimulate the degradation of spliced-out introns via a mechanism that is independent of the polyadenylation activity of Trf4p. In addition, we show that disruption of trf4 causes severe shortening of telomeres suggesting that TRF4 functions in the maintenance of telomere length. Finally, our study demonstrates that TRF4, the exosome, and TRF5 participate in antisense RNA-mediated regulation of genes involved in phosphate metabolism. In conclusion, our results suggest that paralogous TRAMP complexes have distinct RNA selectivities with functional implications in RNA surveillance as well as other RNA-related processes. This indicates widespread and integrative functions of TRAMP complexes for the coordination of different gene expression regulatory processes.\",\n \"corpus_id\": 11210046,\n \"score\": 2\n },\n {\n \"doc_id\": \"19707589\",\n \"title\": \"The CCR4-NOT complex physically and functionally interacts with TRAMP and the nuclear exosome.\",\n \"abstract\": \"BACKGROUND: Ccr4-Not is a highly conserved multi-protein complex consisting in yeast of 9 subunits, including Not5 and the major yeast deadenylase Ccr4. It has been connected functionally in the nucleus to transcription by RNA polymerase II and in the cytoplasm to mRNA degradation. However, there has been no evidence so far that this complex is important for RNA degradation in the nucleus. METHODOLOGY/PRINCIPAL FINDINGS: In this work we point to a new role for the Ccr4-Not complex in nuclear RNA metabolism. We determine the importance of the Ccr4-Not complex for the levels of non-coding nuclear RNAs, such as mis-processed and polyadenylated snoRNAs, whose turnover depends upon the nuclear exosome and TRAMP. Consistently, mutation of both the Ccr4-Not complex and the nuclear exosome results in synthetic slow growth phenotypes. We demonstrate physical interactions between the Ccr4-Not complex and the exosome. First, Not5 co-purifies with the exosome. Second, several exosome subunits co-purify with the Ccr4-Not complex. Third, the Ccr4-Not complex is important for the integrity of large exosome-containing complexes. Finally, we reveal a connection between the Ccr4-Not complex and TRAMP through the association of the Mtr4 helicase with the Ccr4-Not complex and the importance of specific subunits of Ccr4-Not for the association of Mtr4 with the nuclear exosome subunit Rrp6. CONCLUSIONS/SIGNIFICANCE: We propose a model in which the Ccr4-Not complex may provide a platform contributing to dynamic interactions between the nuclear exosome and its co-factor TRAMP. Our findings connect for the first time the different players involved in nuclear and cytoplasmic RNA degradation.\",\n \"corpus_id\": 7014268,\n \"score\": 2\n },\n {\n \"doc_id\": \"19955569\",\n \"title\": \"TRAMP complex enhances RNA degradation by the nuclear exosome component Rrp6.\",\n \"abstract\": \"The RNA-processing exosome contains ribonucleases that degrade aberrant RNAs in archael and eukaryotic cells. In Saccharomyces cerevisiae, the nuclear/nucleolar 3'-5' exoribonuclease Rrp6 distinguishes the nuclear exosome from the cytoplasmic exosome. In vivo, the TRAMP complex enhances the ability of the nuclear exosome to destroy some aberrant RNAs. Previous reports showed that purified TRAMP enhanced RNA degradation by the nuclear exosome in vitro. However, the exoribonucleolytic component(s) of the nuclear exosome enhanced by TRAMP remain unidentified. We show that TRAMP does not significantly enhance RNA degradation by purified exosomes lacking Rrp6 in vitro, suggesting that TRAMP activation experiments with nuclear exosome preparations reflect, in part, effects on the activity of Rrp6. Consistent with this, we show that incubation of purified TRAMP with recombinant Rrp6 results in a 10-fold enhancement of the rate of RNA degradation. This increased activity results from enhancement of the hydrolytic activity of Rrp6 because TRAMP cannot enhance the activity of an Rrp6 mutant lacking a key amino acid side chain in its active site. We observed no ATP or polyadenylation dependence for the enhancement of Rrp6 activity by TRAMP, suggesting that neither the poly(A) polymerase activity of Trf4 nor the helicase activity of Mtr4 plays a role in the enhancement. These findings identify TRAMP as an exosome-independent enhancer of Rrp6 activity.\",\n \"corpus_id\": 1313810,\n \"score\": 2\n },\n {\n \"doc_id\": \"20512111\",\n \"title\": \"The crystal structure of Mtr4 reveals a novel arch domain required for rRNA processing.\",\n \"abstract\": \"The essential RNA helicase, Mtr4, performs a critical role in RNA processing and degradation as an activator of the nuclear exosome. The molecular basis for this vital function is not understood and detailed analysis is significantly limited by the lack of structural data. In this study, we present the crystal structure of Mtr4. The structure reveals a new arch-like domain that is specific to Mtr4 and Ski2 (the cytosolic homologue of Mtr4). In vivo and in vitro analyses demonstrate that the Mtr4 arch domain is required for proper 5.8S rRNA processing, and suggest that the arch functions independently of canonical helicase activity. In addition, extensive conservation along the face of the putative RNA exit site highlights a potential interface with the exosome. These studies provide a molecular framework for understanding fundamental aspects of helicase function in exosome activation, and more broadly define the molecular architecture of Ski2-like helicases.\",\n \"corpus_id\": 24491250,\n \"score\": 2\n },\n {\n \"doc_id\": \"20566885\",\n \"title\": \"Structural analysis reveals the characteristic features of Mtr4, a DExH helicase involved in nuclear RNA processing and surveillance.\",\n \"abstract\": \"Mtr4 is a conserved RNA helicase that functions together with the nuclear exosome. It participates in the processing of structured RNAs, including the maturation of 5.8S ribosomal RNA (rRNA). It also interacts with the polyadenylating Trf4-Air2 heterodimer to form the so-called TRAMP (Trf4-Air2-Mtr4 Polyadenylation) complex. TRAMP is involved in exosome-mediated degradation of aberrant RNAs in nuclear surveillance pathways. We report the 2.9-A resolution crystal structure of Saccharomyces cerevisiae Mtr4 in complex with ADP and RNA. The structure shows a central ATPase core similar to that of other DExH helicases. Inserted in the DExH core is a region characteristic of Mtr4 orthologues that folds into an elongated stalk connected to a beta-barrel domain. This domain shows unexpected similarity to the KOW domain of L24, a ribosomal protein that binds 23S rRNA. We find that indeed the KOW domain of Mtr4 is able to bind in vitro transcribed tRNA(iMet), suggesting it might assist in presenting RNA substrates to the helicase core. The interaction of Mtr4 with Trf4-Air2 is mediated not by the stalk/KOW insertion but by the DExH core. We find that in the context of the TRAMP complex, the DExH core functions independently in vitro as an RNA helicase and a protein-binding platform. Mtr4 has thus evolved specific structural and surface features to perform its multiple functions.\",\n \"corpus_id\": 21161196,\n \"score\": 2\n },\n {\n \"doc_id\": \"20634320\",\n \"title\": \"Loss of Topoisomerase I leads to R-loop-mediated transcriptional blocks during ribosomal RNA synthesis.\",\n \"abstract\": \"Pre-rRNA transcription by RNA Polymerase I (Pol I) is very robust on active rDNA repeats. Loss of yeast Topoisomerase I (Top1) generated truncated pre-rRNA fragments, which were stabilized in strains lacking TRAMP (Trf4/Trf5-Air1/Air2-Mtr4 polyadenylation complexes) or exosome degradation activities. Loss of both Top1 and Top2 blocked pre-rRNA synthesis, with pre-rRNAs truncated predominately in the 18S 5' region. Positive supercoils in front of Pol I are predicted to slow elongation, while rDNA opening in its wake might cause R-loop formation. Chromatin immunoprecipitation analysis showed substantial levels of RNA/DNA hybrids in the wild type, particularly over the 18S 5' region. The absence of RNase H1 and H2 in cells depleted of Top1 increased the accumulation of RNA/DNA hybrids and reduced pre-rRNA truncation and pre-rRNA synthesis. Hybrid accumulation over the rDNA was greatly exacerbated when Top1, Top2, and RNase H were all absent. Electron microscopy (EM) analysis revealed Pol I pileups in the wild type, particularly over the 18S. Pileups were longer and more frequent in the absence of Top1, and their frequency was exacerbated when RNase H activity was also lacking. We conclude that the loss of Top1 enhances inherent R-loop formation, particularly over the 5' region of the rDNA, imposing persistent transcription blocks when RNase H is limiting.\",\n \"corpus_id\": 21483556,\n \"score\": 2\n },\n {\n \"doc_id\": \"20696927\",\n \"title\": \"Structure and function of the polymerase core of TRAMP, a RNA surveillance complex.\",\n \"abstract\": \"The Trf4p/Air2p/Mtr4p polyadenylation (TRAMP) complex recognizes aberrant RNAs in Saccharomyces cerevisiae and targets them for degradation. A TRAMP subcomplex consisting of a noncanonical poly(A) RNA polymerase in the Pol ss superfamily of nucleotidyl transferases, Trf4p, and a zinc knuckle protein, Air2p, mediates initial substrate recognition. Trf4p and related eukaryotic poly(A) and poly(U) polymerases differ from other characterized enzymes in the Pol ss superfamily both in sequence and in the lack of recognizable nucleic acid binding motifs. Here we report, at 2.7-A resolution, the structure of Trf4p in complex with a fragment of Air2p comprising two zinc knuckle motifs. Trf4p consists of a catalytic and central domain similar in fold to those of other noncanonical Pol beta RNA polymerases, and the two zinc knuckle motifs of Air2p interact with the Trf4p central domain. The interaction surface on Trf4p is highly conserved across eukaryotes, providing evidence that the Trf4p/Air2p complex is conserved in higher eukaryotes as well as in yeast and that the TRAMP complex may also function in RNA surveillance in higher eukaryotes. We show that Air2p, and in particular sequences encompassing a zinc knuckle motif near its N terminus, modulate Trf4p activity, and we present data supporting a role for this zinc knuckle in RNA binding. Finally, we show that the RNA 3' end plays a role in substrate recognition.\",\n \"corpus_id\": 20249410,\n \"score\": 2\n },\n {\n \"doc_id\": \"21460797\",\n \"title\": \"The nuclear RNA polymerase II surveillance system targets polymerase III transcripts.\",\n \"abstract\": \"A key question in nuclear RNA surveillance is how target RNAs are recognized. To address this, we identified in vivo binding sites for nuclear RNA surveillance factors, Nrd1, Nab3 and the Trf4/5–Air1/2–Mtr4 polyadenylation (TRAMP) complex poly(A) polymerase Trf4, by UV crosslinking. Hit clusters were reproducibly found over known binding sites on small nucleolar RNAs (snoRNAs), pre-mRNAs and cryptic, unstable non-protein-coding RNAs (ncRNAs) ('CUTs'), along with ~642 predicted long anti-sense ncRNAs (asRNAs), ~178 intergenic ncRNAs and, surprisingly, ~1384 mRNAs. Five putative asRNAs tested were confirmed to exist and were stabilized by loss of Nrd1, Nab3 or Trf4. Mapping of micro-deletions and substitutions allowed clear definition of preferred, in vivo Nab3 and Nrd1 binding sites. Nrd1 and Nab3 were believed to be Pol II specific but, unexpectedly, bound many oligoadenylated Pol III transcripts, predominately pre-tRNAs. Depletion of Nrd1 or Nab3 stabilized tested Pol III transcripts and their oligoadenylation was dependent on Nrd1–Nab3 and TRAMP. Surveillance targets were enriched for non-encoded A-rich tails. These were generally very short (1–5 nt), potentially explaining why adenylation destabilizes these RNAs while stabilizing mRNAs with long poly(A) tails.\",\n \"corpus_id\": 14260193,\n \"score\": 2\n },\n {\n \"doc_id\": \"21663793\",\n \"title\": \"The RNA helicase Mtr4p modulates polyadenylation in the TRAMP complex.\",\n \"abstract\": \"Many steps in nuclear RNA processing, surveillance, and degradation require TRAMP, a complex containing the poly(A) polymerase Trf4p, the Zn-knuckle protein Air2p, and the RNA helicase Mtr4p. TRAMP polyadenylates RNAs designated for decay or trimming by the nuclear exosome. It has been unclear how polyadenylation by TRAMP differs from polyadenylation by conventional poly(A) polymerase, which produces poly(A) tails that stabilize RNAs. Using reconstituted S. cerevisiae TRAMP, we show that TRAMP inherently suppresses poly(A) addition after only 3-4 adenosines. This poly(A) tail length restriction is controlled by Mtr4p. The helicase detects the number of 3'-terminal adenosines and, over several adenylation steps, elicits precisely tuned adjustments of ATP affinities and rate constants for adenylation and TRAMP dissociation. Our data establish Mtr4p as a critical regulator of polyadenylation by TRAMP and reveal that an RNA helicase can control the activity of another enzyme in a highly complex fashion and in response to features in RNA.\",\n \"corpus_id\": 17613517,\n \"score\": 2\n },\n {\n \"doc_id\": \"21878619\",\n \"title\": \"Air1 zinc knuckles 4 and 5 and a conserved IWRXY motif are critical for the function and integrity of the Trf4/5-Air1/2-Mtr4 polyadenylation (TRAMP) RNA quality control complex.\",\n \"abstract\": \"In Saccharomyces cerevisiae, non-coding RNAs, including cryptic unstable transcripts (CUTs), are subject to degradation by the exosome. The Trf4/5-Air1/2-Mtr4 polyadenylation (TRAMP) complex in S. cerevisiae is a nuclear exosome cofactor that recruits the exosome to degrade RNAs. Trf4/5 are poly(A) polymerases, Mtr4 is an RNA helicase, and Air1/2 are putative RNA-binding proteins that contain five CCHC zinc knuckles (ZnKs). One central question is how the TRAMP complex, especially the Air1/2 protein, recognizes its RNA substrates. To characterize the function of the Air1/2 protein, we used random mutagenesis of the AIR1/2 gene to identify residues critical for Air protein function. We identified air1-C178R and air2-C167R alleles encoding air1/2 mutant proteins with a substitution in the second cysteine of ZnK5. Mutagenesis of the second cysteine in AIR1/2 ZnK1-5 reveals that Air1/2 ZnK4 and -5 are critical for Air protein function in vivo. In addition, we find that the level of CUT, NEL025c, in air1 ZnK1-5 mutants is stabilized, particularly in air1 ZnK4, suggesting a role for Air1 ZnK4 in the degradation of CUTs. We also find that Air1/2 ZnK4 and -5 are critical for Trf4 interaction and that the Air1-Trf4 interaction and Air1 level are critical for TRAMP complex integrity. We identify a conserved IWRXY motif in the Air1 ZnK4-5 linker that is important for Trf4 interaction. We also find that hZCCHC7, a putative human orthologue of Air1 that contains the IWRXY motif, localizes to the nucleolus in human cells and interacts with both mammalian Trf4 orthologues, PAPD5 and PAPD7 (PAP-associated domain containing 5 and 7), suggesting that hZCCHC7 is the Air component of a human TRAMP complex.\",\n \"corpus_id\": 22629431,\n \"score\": 2\n },\n {\n \"doc_id\": \"22114319\",\n \"title\": \"The crystal structure of S. cerevisiae Ski2, a DExH helicase associated with the cytoplasmic functions of the exosome.\",\n \"abstract\": \"Ski2 is a cytoplasmic RNA helicase that functions together with the exosome in the turnover and quality control of mRNAs. Ski2 is conserved in eukaryotes and is related to the helicase Mtr4, a cofactor of the nuclear exosome involved in the processing and quality control of a variety of structured RNAs. We have determined the 2.4 Å resolution crystal structure of the 113 kDa helicase region of Saccharomyces cerevisiae Ski2. The structure shows that Ski2 has an overall architecture similar to that of Mtr4, with a core DExH region and an extended insertion domain. The insertion is not required for the formation of the Ski2-Ski3-Ski8 complex, but is instead an RNA-binding domain. While this is reminiscent of the Mtr4 insertion, there are specific structural and biochemical differences between the two helicases. The insertion of yeast Mtr4 consists of a β-barrel domain that is flexibly attached to a helical stalk, contains a KOW signature motif, and binds in vitro-transcribed tRNA(i)(Met), but not single-stranded RNA. The β-barrel domain of yeast Ski2 does not contain a KOW motif and is tightly packed against the helical stalk, forming a single structural unit maintained by a zinc-binding site. Biochemically, the Ski2 insertion has broad substrate specificity, binding both single-stranded and double-stranded RNAs. We speculate that the Ski2 and Mtr4 insertion domains have evolved with different properties tailored to the type of transcripts that are the substrates of the cytoplasmic and nuclear exosome.\",\n \"corpus_id\": 22357595,\n \"score\": 2\n },\n {\n \"doc_id\": \"22319136\",\n \"title\": \"The TRAMP complex shows tRNA editing activity in S. cerevisiae.\",\n \"abstract\": \"Transfer RNA (tRNA) editing is a widespread processing phenomenon that alters the sequence of primary transcripts by base substitutions as well as nucleotide deletions and insertions at internal or terminal transcript positions. In the corresponding tRNAs, these events are an important prerequisite for the generation of functional transcripts. Although many editing events are well characterized at the reaction level, it is unclear in most cases from which ancestral activities the modern editing enzymes evolved. Here, we show that in Saccharomyces cerevisiae, the noncanonical poly(A) polymerase Trf4p in the TRAMP complex can be recruited for such an editing reaction at an introduced tRNA transcript. As a distributive polymerase involved in RNA surveillance and quality control, it has a broad substrate spectrum and binds only transiently to the transcripts, limiting the number of added nucleotides at the editing position. These features exactly meet the criteria for an ancestral enzyme of a modern editing activity. Accordingly, our observations are a strong experimental support for the hypothesis that enzymatic promiscuity serves as an evolutionary starting point for the emergence of new functions and activities.\",\n \"corpus_id\": 1502516,\n \"score\": 2\n },\n {\n \"doc_id\": \"22336707\",\n \"title\": \"Tri-snRNP-associated proteins interact with subunits of the TRAMP and nuclear exosome complexes, linking RNA decay and pre-mRNA splicing.\",\n \"abstract\": \"Nuclear RNA decay factors are involved in many different pathways including rRNA processing, snRNA and snoRNA biogenesis, pre-mRNA processing, and the rapid decay of cryptic intergenic transcripts. In contrast to its yeast counterpart, the mammalian nuclear decay machinery is largely uncharacterized. Here we report interactions of several putative components of the human nuclear RNA decay machinery, including the TRAMP complex protein Mtr4 and the nuclear exosome constituents PM/Scl-100 and PM/Scl-75, with components of the U4/U6.U5 tri-snRNP complex required for pre-mRNA splicing. The tri-snRNP component Prp31 interacts indirectly with Mtr4 and PM/Scl-100 in a manner that is dependent on the phosphorylation sites in the middle of the protein, while Prp3 and Prp4 interact with the nuclear decay complex independent of Prp31. Together our results suggest recruitment of the nuclear decay machinery to the spliceosome to ensure production of properly spliced mRNA.\",\n \"corpus_id\": 15566719,\n \"score\": 2\n },\n {\n \"doc_id\": \"22402490\",\n \"title\": \"Air2p is critical for the assembly and RNA-binding of the TRAMP complex and the KOW domain of Mtr4p is crucial for exosome activation.\",\n \"abstract\": \"Trf4/5p-Air1/2p-Mtr4p polyadenylation complex (TRAMP) is an essential component of nuclear RNA surveillance in yeast. It recognizes a variety of nuclear transcripts produced by all three RNA polymerases, adds short poly(A) tails to aberrant or unstable RNAs and activates the exosome for their degradation. Despite the advances in understanding the structural features of the isolated complex subunits or their fragments, the details of complex assembly, RNA recognition and exosome activation remain poorly understood. Here we provide the first understanding of the RNA binding mode of the complex. We show that Air2p is an RNA-binding subunit of TRAMP. We identify the zinc knuckles (ZnK) 2, 3 and 4 as the RNA-binding domains, and reveal the essentiality of ZnK4 for TRAMP4 polyadenylation activity. Furthermore, we identify Air2p as the key component of TRAMP4 assembly providing bridging between Mtr4p and Trf4p. The former is bound via the N-terminus of Air2p, while the latter is bound via ZnK5, the linker between ZnK4 and 5 and the C-terminus of the protein. Finally, we uncover the RNA binding part of the Mtr4p arch, the KOW domain, as the essential component for TRAMP-mediated exosome activation.\",\n \"corpus_id\": 13918453,\n \"score\": 2\n },\n {\n \"doc_id\": \"22532666\",\n \"title\": \"RNA unwinding by the Trf4/Air2/Mtr4 polyadenylation (TRAMP) complex.\",\n \"abstract\": \"Many RNA-processing events in the cell nucleus involve the Trf4/Air2/Mtr4 polyadenylation (TRAMP) complex, which contains the poly(A) polymerase Trf4p, the Zn-knuckle protein Air2p, and the RNA helicase Mtr4p. TRAMP polyadenylates RNAs designated for processing by the nuclear exosome. In addition, TRAMP functions as an exosome cofactor during RNA degradation, and it has been speculated that this role involves disruption of RNA secondary structure. However, it is unknown whether TRAMP displays RNA unwinding activity. It is also not clear how unwinding would be coordinated with polyadenylation and the function of the RNA helicase Mtr4p in modulating poly(A) addition. Here, we show that TRAMP robustly unwinds RNA duplexes. The unwinding activity of Mtr4p is significantly stimulated by Trf4p/Air2p, but the stimulation of Mtr4p does not depend on ongoing polyadenylation. Nonetheless, polyadenylation enables TRAMP to unwind RNA substrates that it otherwise cannot separate. Moreover, TRAMP displays optimal unwinding activity on substrates with a minimal Mtr4p binding site comprised of adenylates. Our results suggest a model for coordination between unwinding and polyadenylation activities by TRAMP that reveals remarkable synergy between helicase and poly(A) polymerase.\",\n \"corpus_id\": 4679498,\n \"score\": 2\n },\n {\n \"doc_id\": \"22817747\",\n \"title\": \"Comparison of the yeast and human nuclear exosome complexes.\",\n \"abstract\": \"Most RNAs in eukaryotic cells are produced as precursors that undergo processing at the 3' and/or 5' end to generate the mature transcript. In addition, many transcripts are degraded not only as part of normal recycling, but also when recognized as aberrant by the RNA surveillance machinery. The exosome, a conserved multiprotein complex containing two nucleases, is involved in both the 3' processing and the turnover of many RNAs in the cell. A series of factors, including the TRAMP (Trf4-Air2-Mtr4 polyadenylation) complex, Mpp6 and Rrp47, help to define the targets to be processed and/or degraded and assist in exosome function. The majority of the data on the exosome and RNA maturation/decay have been derived from work performed in the yeast Saccharomyces cerevisiae. In the present paper, we provide an overview of the exosome and its role in RNA processing/degradation and discuss important new insights into exosome composition and function in human cells.\",\n \"corpus_id\": 5368191,\n \"score\": 2\n },\n {\n \"doc_id\": \"22923767\",\n \"title\": \"Air proteins control differential TRAMP substrate specificity for nuclear RNA surveillance.\",\n \"abstract\": \"RNA surveillance systems function at critical steps during the formation and function of RNA molecules in all organisms. The RNA exosome plays a central role in RNA surveillance by processing and degrading RNA molecules in the nucleus and cytoplasm of eukaryotic cells. The exosome functions as a complex of proteins composed of a nine-member core and two ribonucleases. The identity of the molecular determinants of exosome RNA substrate specificity remains an important unsolved aspect of RNA surveillance. In the nucleus of Saccharomyces cerevisiae, TRAMP complexes recognize and polyadenylate RNAs, which enhances RNA degradation by the exosome and may contribute to its specificity. TRAMPs contain either of two putative RNA-binding factors called Air proteins. Previous studies suggested that these proteins function interchangeably in targeting the poly(A)-polymerase activity of TRAMPs to RNAs. Experiments reported here show that the Air proteins govern separable functions. Phenotypic analysis and RNA deep-sequencing results from air mutants reveal specific requirements for each Air protein in the regulation of the levels of noncoding and coding RNAs. Loss of these regulatory functions results in specific metabolic and plasmid inheritance defects. These findings reveal differential functions for Air proteins in RNA metabolism and indicate that they control the substrate specificity of the RNA exosome.\",\n \"corpus_id\": 23382542,\n \"score\": 2\n },\n {\n \"doc_id\": \"23417976\",\n \"title\": \"Nuclear RNA surveillance: role of TRAMP in controlling exosome specificity.\",\n \"abstract\": \"The advent of high-throughput sequencing technologies has revealed that pervasive transcription generates RNAs from nearly all regions of eukaryotic genomes. Normally, these transcripts undergo rapid degradation by a nuclear RNA surveillance system primarily featuring the RNA exosome. This multimeric protein complex plays a critical role in the efficient turnover and processing of a vast array of RNAs in the nucleus. Despite its initial discovery over a decade ago, important questions remain concerning the mechanisms that recruit and activate the nuclear exosome. Specificity and modulation of exosome activity requires additional protein cofactors, including the conserved TRAMP polyadenylation complex. Recent studies suggest that helicase and RNA-binding subunits of TRAMP direct RNA substrates for polyadenylation, which enhances their degradation by Dis3/Rrp44 and Rrp6, the two exosome-associated ribonucleases. These findings indicate that the exosome and TRAMP have evolved highly flexible functions that allow recognition of a wide range of RNA substrates. This flexibility provides the nuclear RNA surveillance system with the ability to regulate the levels of a broad range of coding and noncoding RNAs, which results in profound effects on gene expression, cellular development, gene silencing, and heterochromatin formation. This review summarizes recent findings on the nuclear RNA surveillance complexes, and speculates upon possible mechanisms for TRAMP-mediated substrate recognition and exosome activation.\",\n \"corpus_id\": 2740798,\n \"score\": 2\n },\n {\n \"doc_id\": \"23910895\",\n \"title\": \"Threading the barrel of the RNA exosome.\",\n \"abstract\": \"In eukaryotes, the exosome complex degrades RNA backbones and plays key roles in RNA processing and surveillance. It was predicted that RNA substrates are threaded through a central channel. This pathway is conserved between eukaryotic and archaeal complexes, even though nuclease activity was lost from the nine-subunit eukaryotic core (EXO-9) and transferred to associated proteins. The exosome cooperates with nuclear and cytoplasmic cofactors, including RNA helicases Mtr4 and Ski2, respectively. Structures of an RNA-bound exosome and both helicases revealed how substrates are channeled through EXO-9 to the associated nuclease Rrp44. Recent high-throughput analyses provided fresh insights relating exosome structure to its diverse in vivo functions. They also revealed surprisingly high degradation rates for newly synthesized RNAs, particularly RNA polymerase III transcripts.\",\n \"corpus_id\": 30260906,\n \"score\": 2\n },\n {\n \"doc_id\": \"23953113\",\n \"title\": \"The yeast ski complex: crystal structure and RNA channeling to the exosome complex.\",\n \"abstract\": \"The Ski complex is a conserved multiprotein assembly required for the cytoplasmic functions of the exosome, including RNA turnover, surveillance, and interference. Ski2, Ski3, and Ski8 assemble in a tetramer with 1:1:2 stoichiometry. The crystal structure of an S. cerevisiae 370 kDa core complex shows that Ski3 forms an array of 33 TPR motifs organized in N-terminal and C-terminal arms. The C-terminal arm of Ski3 and the two Ski8 subunits position the helicase core of Ski2 centrally within the complex, enhancing RNA binding. The Ski3 N-terminal arm and the Ski2 insertion domain allosterically modulate the ATPase and helicase activities of the complex. Biochemical data suggest that the Ski complex can thread RNAs directly to the exosome, coupling the helicase and the exoribonuclease through a continuous RNA channel. Finally, we identify a Ski8-binding motif common to Ski3 and Spo11, rationalizing the moonlighting properties of Ski8 in mRNA decay and meiosis.\",\n \"corpus_id\": 12699297,\n \"score\": 2\n },\n {\n \"doc_id\": \"24047896\",\n \"title\": \"Cotranscriptional recruitment of RNA exosome cofactors Rrp47p and Mpp6p and two distinct Trf-Air-Mtr4 polyadenylation (TRAMP) complexes assists the exonuclease Rrp6p in the targeting and degradation of an aberrant messenger ribonucleoprotein particle (mRNP) in yeast.\",\n \"abstract\": \"The cotranscriptional mRNA processing and packaging reactions that lead to the formation of export-competent messenger ribonucleoprotein particles (mRNPs) are under the surveillance of quality control steps. Aberrant mRNPs resulting from faulty events are retained in the nucleus with ensuing elimination of their mRNA component. The molecular mechanisms by which the surveillance system recognizes defective mRNPs and stimulates their destruction by the RNA degradation machinery are still not completely elucidated. Using an experimental approach in which mRNP formation in yeast is disturbed by the action of the bacterial Rho helicase, we have shown previously that the targeting of Rho-induced aberrant mRNPs is mediated by Rrp6p, which is recruited cotranscriptionally in association with Nrd1p following Rho action. Here we investigated the specific involvement in this quality control process of different cofactors associated with the nuclear RNA degradation machinery. We show that, in addition to the main hydrolytic action of the exonuclease Rrp6p, the cofactors Rrp47p, Mpp6p as well as the Trf-Air-Mtr4 polyadenylation (TRAMP) components Trf4p, Trf5p, and Air2p contribute significantly by stimulating the degradation process upon their cotranscriptional recruitment. Trf4p and Trf5p are apparently recruited in two distinct TRAMP complexes that both contain Air2p as component. Surprisingly, Rrp47p appears to play an important role in mutual protein stabilization with Rrp6p, which highlights a close association between the two partners. Together, our results provide an integrated view of how different cofactors of the RNA degradation machinery cooperate to target and eliminate aberrant mRNPs.\",\n \"corpus_id\": 25705209,\n \"score\": 2\n },\n {\n \"doc_id\": \"24097436\",\n \"title\": \"Cotranscriptional recruitment of yeast TRAMP complex to intronic sequences promotes optimal pre-mRNA splicing.\",\n \"abstract\": \"Most unwanted RNA transcripts in the nucleus of eukaryotic cells, such as splicing-defective pre-mRNAs and spliced-out introns, are rapidly degraded by the nuclear exosome. In budding yeast, a number of these unwanted RNA transcripts, including spliced-out introns, are first recognized by the nuclear exosome cofactor Trf4/5p-Air1/2p-Mtr4p polyadenylation (TRAMP) complex before subsequent nuclear-exosome-mediated degradation. However, it remains unclear when spliced-out introns are recognized by TRAMP, and whether TRAMP may have any potential roles in pre-mRNA splicing. Here, we demonstrated that TRAMP is cotranscriptionally recruited to nascent RNA transcripts, with particular enrichment at intronic sequences. Deletion of TRAMP components led to further accumulation of unspliced pre-mRNAs even in a yeast strain defective in nuclear exosome activity, suggesting a novel stimulatory role of TRAMP in splicing. We also uncovered new genetic and physical interactions between TRAMP and several splicing factors, and further showed that TRAMP is required for optimal recruitment of the splicing factor Msl5p. Our study provided the first evidence that TRAMP facilitates pre-mRNA splicing, and we interpreted this as a fail-safe mechanism to ensure the cotranscriptional recruitment of TRAMP before or during splicing to prepare for the subsequent targeting of spliced-out introns to rapid degradation by the nuclear exosome.\",\n \"corpus_id\": 745968,\n \"score\": 2\n },\n {\n \"doc_id\": \"24189234\",\n \"title\": \"Structure determination of an 11-subunit exosome in complex with RNA by molecular replacement.\",\n \"abstract\": \"The RNA exosome is an evolutionarily conserved multi-protein complex involved in the 3' degradation of a variety of RNA transcripts. In the nucleus, the exosome participates in the maturation of structured RNAs, in the surveillance of pre-mRNAs and in the decay of a variety of noncoding transcripts. In the cytoplasm, the exosome degrades mRNAs in constitutive and regulated turnover pathways. Several structures of subcomplexes of eukaryotic exosomes or related prokaryotic exosome-like complexes are known, but how the complete assembly is organized to fulfil processive RNA degradation has been unclear. An atomic snapshot of a Saccharomyces cerevisiae 420 kDa exosome complex bound to an RNA substrate in the pre-cleavage state of a hydrolytic reaction has been determined. Here, the crystallographic steps towards the structural elucidation, which was carried out by molecular replacement, are presented.\",\n \"corpus_id\": -1,\n \"score\": 2\n },\n {\n \"doc_id\": \"25066235\",\n \"title\": \"Molecular basis for coordinating transcription termination with noncoding RNA degradation.\",\n \"abstract\": \"The Nrd1-Nab3-Sen1 (NNS) complex is essential for controlling pervasive transcription and generating sn/snoRNAs in S. cerevisiae. The NNS complex terminates transcription of noncoding RNA genes and promotes exosome-dependent processing/degradation of the released transcripts. The Trf4-Air2-Mtr4 (TRAMP) complex polyadenylates NNS target RNAs and favors their degradation. NNS-dependent termination and degradation are coupled, but the mechanism underlying this coupling remains enigmatic. Here we provide structural and functional evidence demonstrating that the same domain of Nrd1p interacts with RNA polymerase II and Trf4p in a mutually exclusive manner, thus defining two alternative forms of the NNS complex, one involved in termination and the other in degradation. We show that the Nrd1-Trf4 interaction is required for optimal exosome activity in vivo and for the stimulation of polyadenylation of NNS targets by TRAMP in vitro. We propose that transcription termination and RNA degradation are coordinated by switching between two alternative partners of the NNS complex.\",\n \"corpus_id\": 10054242,\n \"score\": 2\n },\n {\n \"doc_id\": \"25110014\",\n \"title\": \"Exosome substrate targeting: the long and short of it.\",\n \"abstract\": \"The exosome ribonuclease complex functions in both the limited trimming of the 3'-ends of nuclear substrates during RNA processing events and the complete destruction of nuclear and cytoplasmic RNAs. The two RNases of the eukaryotic exosome, Rrp44 (rRNA-processing protein 44) and Rrp6, are bound at either end of a catalytically inert cylindrical core. RNA substrates are threaded through the internal channel of the core to Rrp44 by RNA helicase components of the nuclear TRAMP complex (Trf4-Air2-Mtr4 polyadenylation complex) or the cytoplasmic Ski (superkiller) complex. Recent studies reveal that Rrp44 can also associate directly with substrates via channel-independent routes. Although the substrates of the exosome are known, it is not clear whether specific substrates are restricted to one or other pathway. Data currently available support the model that processed substrates are targeted directly to the catalytic subunits, whereas at least some substrates that are directed towards discard pathways must be threaded through the exosome core.\",\n \"corpus_id\": 25351651,\n \"score\": 2\n },\n {\n \"doc_id\": \"25144737\",\n \"title\": \"The RNA helicases AtMTR4 and HEN2 target specific subsets of nuclear transcripts for degradation by the nuclear exosome in Arabidopsis thaliana.\",\n \"abstract\": \"The RNA exosome is the major 3'-5' RNA degradation machine of eukaryotic cells and participates in processing, surveillance and turnover of both nuclear and cytoplasmic RNA. In both yeast and human, all nuclear functions of the exosome require the RNA helicase MTR4. We show that the Arabidopsis core exosome can associate with two related RNA helicases, AtMTR4 and HEN2. Reciprocal co-immunoprecipitation shows that each of the RNA helicases co-purifies with the exosome core complex and with distinct sets of specific proteins. While AtMTR4 is a predominantly nucleolar protein, HEN2 is located in the nucleoplasm and appears to be excluded from nucleoli. We have previously shown that the major role of AtMTR4 is the degradation of rRNA precursors and rRNA maturation by-products. Here, we demonstrate that HEN2 is involved in the degradation of a large number of polyadenylated nuclear exosome substrates such as snoRNA and miRNA precursors, incompletely spliced mRNAs, and spurious transcripts produced from pseudogenes and intergenic regions. Only a weak accumulation of these exosome substrate targets is observed in mtr4 mutants, suggesting that MTR4 can contribute, but plays rather a minor role for the degradation of non-ribosomal RNAs and cryptic transcripts in Arabidopsis. Consistently, transgene post-transcriptional gene silencing (PTGS) is marginally affected in mtr4 mutants, but increased in hen2 mutants, suggesting that it is mostly the nucleoplasmic exosome that degrades aberrant transgene RNAs to limit their entry in the PTGS pathway. Interestingly, HEN2 is conserved throughout green algae, mosses and land plants but absent from metazoans and other eukaryotic lineages. Our data indicate that, in contrast to human and yeast, plants have two functionally specialized RNA helicases that assist the exosome in the degradation of specific nucleolar and nucleoplasmic RNA populations, respectively.\",\n \"corpus_id\": 10129090,\n \"score\": 2\n },\n {\n \"doc_id\": \"25319414\",\n \"title\": \"The exosome-binding factors Rrp6 and Rrp47 form a composite surface for recruiting the Mtr4 helicase.\",\n \"abstract\": \"The exosome is a conserved multi-subunit ribonuclease complex that functions in 3' end processing, turnover and surveillance of nuclear and cytoplasmic RNAs. In the yeast nucleus, the 10-subunit core complex of the exosome (Exo-10) physically and functionally interacts with the Rrp6 exoribonuclease and its associated cofactor Rrp47, the helicase Mtr4 and Mpp6. Here, we show that binding of Mtr4 to Exo-10 in vitro is dependent upon both Rrp6 and Rrp47, whereas Mpp6 binds directly and independently of other cofactors. Crystallographic analyses reveal that the N-terminal domains of Rrp6 and Rrp47 form a highly intertwined structural unit. Rrp6 and Rrp47 synergize to create a composite and conserved surface groove that binds the N-terminus of Mtr4. Mutation of conserved residues within Rrp6 and Mtr4 at the structural interface disrupts their interaction and inhibits growth of strains expressing a C-terminal GFP fusion of Mtr4. These studies provide detailed structural insight into the interaction between the Rrp6-Rrp47 complex and Mtr4, revealing an important link between Mtr4 and the core exosome.\",\n \"corpus_id\": 12902394,\n \"score\": 2\n },\n {\n \"doc_id\": \"25414331\",\n \"title\": \"The Mtr4 ratchet helix and arch domain both function to promote RNA unwinding.\",\n \"abstract\": \"Mtr4 is a conserved Ski2-like RNA helicase and a subunit of the TRAMP complex that activates exosome-mediated 3'-5' turnover in nuclear RNA surveillance and processing pathways. Prominent features of the Mtr4 structure include a four-domain ring-like helicase core and a large arch domain that spans the core. The 'ratchet helix' is positioned to interact with RNA substrates as they move through the helicase. However, the contribution of the ratchet helix in Mtr4 activity is poorly understood. Here we show that strict conservation along the ratchet helix is particularly extensive for Ski2-like RNA helicases compared to related helicases. Mutation of residues along the ratchet helix alters in vitro activity in Mtr4 and TRAMP and causes slow growth phenotypes in vivo. We also identify a residue on the ratchet helix that influences Mtr4 affinity for polyadenylated substrates. Previous work indicated that deletion of the arch domain has minimal effect on Mtr4 unwinding activity. We now show that combining the arch deletion with ratchet helix mutations abolishes helicase activity and produces a lethal in vivo phenotype. These studies demonstrate that the ratchet helix modulates helicase activity and suggest that the arch domain plays a previously unrecognized role in unwinding substrates.\",\n \"corpus_id\": 14553431,\n \"score\": 2\n },\n {\n \"doc_id\": \"25589546\",\n \"title\": \"Interaction between the RNA-dependent ATPase and poly(A) polymerase subunits of the TRAMP complex is mediated by short peptides and important for snoRNA processing.\",\n \"abstract\": \"The RNA exosome is one of the main 3′ to 5′ exoribonucleases in eukaryotic cells. Although it is responsible for degradation or processing of a wide variety of substrate RNAs, it is very specific and distinguishes between substrate and non-substrate RNAs as well as between substrates that need to be 3′ processed and those that need to be completely degraded. This specificity does not appear to be determined by the exosome itself but rather by about a dozen other proteins. Four of these exosome cofactors have enzymatic activity, namely, the nuclear RNA-dependent ATPase Mtr4, its cytoplasmic paralog Ski2 and the nuclear non-canonical poly(A) polymerases, Trf4 and Trf5. Mtr4 and either Trf4 or Trf5 assemble into a TRAMP complex. However, how these enzymes assemble into a TRAMP complex and the functional consequences of TRAMP complex assembly remain unknown. Here, we identify an important interaction site between Mtr4 and Trf5, and show that disrupting the Mtr4/Trf interaction disrupts specific TRAMP and exosome functions, including snoRNA processing.\",\n \"corpus_id\": 10169624,\n \"score\": 2\n },\n {\n \"doc_id\": \"25775092\",\n \"title\": \"Nab3 facilitates the function of the TRAMP complex in RNA processing via recruitment of Rrp6 independent of Nrd1.\",\n \"abstract\": \"Non-coding RNAs (ncRNAs) play critical roles in gene regulation. In eukaryotic cells, ncRNAs are processed and/or degraded by the nuclear exosome, a ribonuclease complex containing catalytic subunits Dis3 and Rrp6. The TRAMP (Trf4/5-Air1/2-Mtr4 polyadenylation) complex is a critical exosome cofactor in budding yeast that stimulates the exosome to process/degrade ncRNAs and human TRAMP components have recently been identified. Importantly, mutations in exosome and exosome cofactor genes cause neurodegenerative disease. How the TRAMP complex interacts with other exosome cofactors to orchestrate regulation of the exosome is an open question. To identify novel interactions of the TRAMP exosome cofactor, we performed a high copy suppressor screen of a thermosensitive air1/2 TRAMP mutant. Here, we report that the Nab3 RNA-binding protein of the Nrd1-Nab3-Sen1 (NNS) complex is a potent suppressor of TRAMP mutants. Unlike Nab3, Nrd1 and Sen1 do not suppress TRAMP mutants and Nrd1 binding is not required for Nab3-mediated suppression of TRAMP suggesting an independent role for Nab3. Critically, Nab3 decreases ncRNA levels in TRAMP mutants, Nab3-mediated suppression of air1/2 cells requires the nuclear exosome component, Rrp6, and Nab3 directly binds Rrp6. We extend this analysis to identify a human RNA binding protein, RALY, which shares identity with Nab3 and can suppress TRAMP mutants. These results suggest that Nab3 facilitates TRAMP function by recruiting Rrp6 to ncRNAs for processing/degradation independent of Nrd1. The data raise the intriguing possibility that Nab3 and Nrd1 can function independently to recruit Rrp6 to ncRNA targets, providing combinatorial flexibility in RNA processing.\",\n \"corpus_id\": 7393748,\n \"score\": 2\n },\n {\n \"doc_id\": \"26612606\",\n \"title\": \"Rrp6: Integrated roles in nuclear RNA metabolism and transcription termination.\",\n \"abstract\": \"The yeast RNA exosome is a eukaryotic ribonuclease complex essential for RNA processing, surveillance, and turnover. It is comprised of a barrel-shaped core and cap as well as a 3'-5' ribonuclease known as Dis3 that contains both endo- and exonuclease domains. A second exonuclease, Rrp6, is added in the nucleus. Dis3 and Rrp6 have both shared and distinct roles in RNA metabolism, and this review will focus primarily on Rrp6 and the roles of the RNA exosome in the nucleus. The functions of the nuclear exosome are modulated by cofactors and interacting partners specific to each type of substrate. Generally, the cofactor TRAMP (Trf4/5-Air2/1-Mtr4 polyadenylation) complex helps unwind unstable RNAs, RNAs requiring processing such as rRNAs, tRNAs, or snRNAs or improperly processed RNAs and direct it toward the exosome. In yeast, Rrp6 interacts with Nrd1, the cap-binding complex, and RNA polymerase II to aid in nascent RNA processing, termination, and polyA tail length regulation. Recent studies have shown that proper termination and processing of short, noncoding RNAs by Rrp6 is particularly important for transcription regulation across the genome and has important implications for regulation of diverse processes at the cellular level. Loss of proper Rrp6 and exosome activity may contribute to various pathologies such as autoimmune disease, neurological disorders, and cancer. WIREs RNA 2016, 7:91-104. doi: 10.1002/wrna.1317 For further resources related to this article, please visit the WIREs website.\",\n \"corpus_id\": 206553336,\n \"score\": 2\n },\n {\n \"doc_id\": \"26820724\",\n \"title\": \"Mutations in Mtr4 Structural Domains Reveal Their Important Role in Regulating tRNAiMet Turnover in Saccharomyces cerevisiae and Mtr4p Enzymatic Activities In Vitro.\",\n \"abstract\": \"RNA processing and turnover play important roles in the maturation, metabolism and quality control of a large variety of RNAs thereby contributing to gene expression and cellular health. The TRAMP complex, composed of Air2p, Trf4p and Mtr4p, stimulates nuclear exosome-dependent RNA processing and degradation in Saccharomyces cerevisiae. The Mtr4 protein structure is composed of a helicase core and a novel so-called arch domain, which protrudes from the core. The helicase core contains highly conserved helicase domains RecA-1 and 2, and two structural domains of unclear functions, winged helix domain (WH) and ratchet domain. How the structural domains (arch, WH and ratchet domain) coordinate with the helicase domains and what roles they are playing in regulating Mtr4p helicase activity are unknown. We created a library of Mtr4p structural domain mutants for the first time and screened for those defective in the turnover of TRAMP and exosome substrate, hypomodified tRNAiMet. We found these domains regulate Mtr4p enzymatic activities differently through characterizing the arch domain mutants K700N and P731S, WH mutant K904N, and ratchet domain mutant R1030G. Arch domain mutants greatly reduced Mtr4p RNA binding, which surprisingly did not lead to significant defects on either in vivo tRNAiMet turnover, or in vitro unwinding activities. WH mutant K904N and Ratchet domain mutant R1030G showed decreased tRNAiMet turnover in vivo, as well as reduced RNA binding, ATPase and unwinding activities of Mtr4p in vitro. Particularly, K904 was found to be very important for steady protein levels in vivo. Overall, we conclude that arch domain plays a role in RNA binding but is largely dispensable for Mtr4p enzymatic activities, however the structural domains in the helicase core significantly contribute to Mtr4p ATPase and unwinding activities.\",\n \"corpus_id\": 1065968,\n \"score\": 2\n },\n {\n \"doc_id\": \"27076633\",\n \"title\": \"Exosome Cofactors Connect Transcription Termination to RNA Processing by Guiding Terminated Transcripts to the Appropriate Exonuclease within the Nuclear Exosome.\",\n \"abstract\": \"The yeast Nrd1 interacts with the C-terminal domain (CTD) of RNA polymerase II (RNApII) through its CTD-interacting domain (CID) and also associates with the nuclear exosome, thereby acting as both a transcription termination and RNA processing factor. Previously, we found that the Nrd1 CID is required to recruit the nuclear exosome to the Nrd1 complex, but it was not clear which exosome subunits were contacted. Here, we show that two nuclear exosome cofactors, Mpp6 and Trf4, directly and competitively interact with the Nrd1 CID and differentially regulate the association of Nrd1 with two catalytic subunits of the exosome. Importantly, Mpp6 promotes the processing of Nrd1-terminated transcripts preferentially by Dis3, whereas Trf4 leads to Rrp6-dependent processing. This suggests that Mpp6 and Trf4 may play a role in choosing a particular RNA processing route for Nrd1-terminated transcripts within the exosome by guiding the transcripts to the appropriate exonuclease.\",\n \"corpus_id\": 2267218,\n \"score\": 2\n },\n {\n \"doc_id\": \"27166441\",\n \"title\": \"TRAMP Stimulation of Exosome.\",\n \"abstract\": \"In order to control and/or enhance the specificity and activity of nuclear surveillance and degradation, exosomes cooperate with the polyadenylation complex called TRAMP. Two forms of TRAMP operate in budding yeast, TRAMP4 and TRAMP5. They oligoadenylate defective or precursor forms of RNAs and promote trimming or complete degradation by exosomes. TRAMPs target a wide variety of nuclear transcripts. The known substrates include the noncoding RNAs originating from pervasive transcription from diverse parts of the yeast genome. Although TRAMP and exosomes can be triggered to a subset of their targets via the RNA-binding complex Nrd1, it is still not completely understood how TRAMP recognizes other aberrant RNAs. The existence of TRAMP-like complexes in other organisms indicates the importance of nuclear surveillance for general cell biology. In this chapter, we review the current understanding of TRAMP function and substrate repertoire. We discuss the advances in TRAMP biochemistry with respect to its catalytic activities and RNA recognition. Finally, we speculate about the possible mechanisms by which TRAMP activates exosomes.\",\n \"corpus_id\": 33184183,\n \"score\": 2\n },\n {\n \"doc_id\": \"27174052\",\n \"title\": \"CryoEM structure of yeast cytoplasmic exosome complex.\",\n \"abstract\": \"The eukaryotic multi-subunit RNA exosome complex plays crucial roles in 3'-to-5' RNA processing and decay. Rrp6 and Ski7 are the major cofactors for the nuclear and cytoplasmic exosomes, respectively. In the cytoplasm, Ski7 helps the exosome to target mRNAs for degradation and turnover via a through-core pathway. However, the interaction between Ski7 and the exosome complex has remained unclear. The transaction of RNA substrates within the exosome is also elusive. In this work, we used single-particle cryo-electron microscopy to solve the structures of the Ski7-exosome complex in RNA-free and RNA-bound forms at resolutions of 4.2 Å and 5.8 Å, respectively. These structures reveal that the N-terminal domain of Ski7 adopts a structural arrangement and interacts with the exosome in a similar fashion to the C-terminal domain of nuclear Rrp6. Further structural analysis of exosomes with RNA substrates harboring 3' overhangs of different length suggests a switch mechanism of RNA-induced exosome activation in the through-core pathway of RNA processing.\",\n \"corpus_id\": 32179906,\n \"score\": 2\n },\n {\n \"doc_id\": \"27345150\",\n \"title\": \"Structure of a Cytoplasmic 11-Subunit RNA Exosome Complex.\",\n \"abstract\": \"The RNA exosome complex associates with nuclear and cytoplasmic cofactors to mediate the decay, surveillance, or processing of a wide variety of transcripts. In the cytoplasm, the conserved core of the exosome (Exo10) functions together with the conserved Ski complex. The interaction of S. cerevisiae Exo10 and Ski is not direct but requires a bridging cofactor, Ski7. Here, we report the 2.65 Å resolution structure of S. cerevisiae Exo10 bound to the interacting domain of Ski7. Extensive hydrophobic interactions rationalize the high affinity and stability of this complex, pointing to Ski7 as a constitutive component of the cytosolic exosome. Despite the absence of sequence homology, cytoplasmic Ski7 and nuclear Rrp6 bind Exo10 using similar surfaces and recognition motifs. Knowledge of the interacting residues in the yeast complexes allowed us to identify a splice variant of human HBS1-Like as a Ski7-like exosome-binding protein, revealing the evolutionary conservation of this cytoplasmic cofactor.\",\n \"corpus_id\": 37833407,\n \"score\": 2\n },\n {\n \"doc_id\": \"27434818\",\n \"title\": \"Interaction properties of human TRAMP-like proteins and their role in pre-rRNA 5'ETS turnover.\",\n \"abstract\": \"In yeast, the Trf4/5-Air1/2-Mtr4 polyadenylation (TRAMP) complex acts as a cofactor for the nuclear exosome to promote degradation of various RNAs. However, the corresponding machinery in mammals is less characterized. We analyzed the interactions of the human TRAMP-like proteins, PAPD5, ZCCHC7, and MTR4, with the nuclear exosome. PAPD5 and ZCCHC7 exhibited mutual interactions in presence of the exosome catalytic subunit RRP6, whereas MTR4 was dispensable for their assembly. Furthermore, the human TRAMP-like proteins were involved in the RRP6-catalyzed turnover of pre-rRNA 5'ETS fragments. These results suggest the significant role for RRP6 in the assembly of TRAMP-like proteins during nucleolar RNA surveillance.\",\n \"corpus_id\": 38072991,\n \"score\": 2\n },\n {\n \"doc_id\": \"27474443\",\n \"title\": \"A conserved virus-induced cytoplasmic TRAMP-like complex recruits the exosome to target viral RNA for degradation.\",\n \"abstract\": \"RNA degradation is tightly regulated to selectively target aberrant RNAs, including viral RNA, but this regulation is incompletely understood. Through RNAi screening in Drosophila cells, we identified the 3'-to-5' RNA exosome and two components of the exosome cofactor TRAMP (Trf4/5-Air1/2-Mtr4 polyadenylation) complex, dMtr4 and dZcchc7, as antiviral against a panel of RNA viruses. We extended our studies to human orthologs and found that the exosome as well as TRAMP components hMTR4 and hZCCHC7 are antiviral. While hMTR4 and hZCCHC7 are normally nuclear, infection by cytoplasmic RNA viruses induces their export, forming a cytoplasmic complex that specifically recognizes and induces degradation of viral mRNAs. Furthermore, the 3' untranslated region (UTR) of bunyaviral mRNA is sufficient to confer virus-induced exosomal degradation. Altogether, our results reveal that signals from viral infection repurpose TRAMP components to a cytoplasmic surveillance role where they selectively engage viral RNAs for degradation to restrict a broad range of viruses.\",\n \"corpus_id\": 33869258,\n \"score\": 2\n },\n {\n \"doc_id\": \"28733371\",\n \"title\": \"An Mtr4/ZFC3H1 complex facilitates turnover of unstable nuclear RNAs to prevent their cytoplasmic transport and global translational repression.\",\n \"abstract\": \"Many long noncoding RNAs (lncRNAs) are unstable and rapidly degraded in the nucleus by the nuclear exosome. An exosome adaptor complex called NEXT (nuclear exosome targeting) functions to facilitate turnover of some of these lncRNAs. Here we show that knockdown of one NEXT subunit, Mtr4, but neither of the other two subunits, resulted in accumulation of two types of lncRNAs: prematurely terminated RNAs (ptRNAs) and upstream antisense RNAs (uaRNAs). This suggested a NEXT-independent Mtr4 function, and, consistent with this, we isolated a distinct complex containing Mtr4 and the zinc finger protein ZFC3H1. Strikingly, knockdown of either protein not only increased pt/uaRNA levels but also led to their accumulation in the cytoplasm. Furthermore, all pt/uaRNAs examined associated with active ribosomes, but, paradoxically, this correlated with a global reduction in heavy polysomes and overall repression of translation. Our findings highlight a critical role for Mtr4/ZFC3H1 in nuclear surveillance of naturally unstable lncRNAs to prevent their accumulation, transport to the cytoplasm, and resultant disruption of protein synthesis.\",\n \"corpus_id\": 20566212,\n \"score\": 2\n },\n {\n \"doc_id\": \"28742025\",\n \"title\": \"Structure and reconstitution of yeast Mpp6-nuclear exosome complexes reveals that Mpp6 stimulates RNA decay and recruits the Mtr4 helicase.\",\n \"abstract\": \"Nuclear RNA exosomes catalyze a range of RNA processing and decay activities that are coordinated in part by cofactors, including Mpp6, Rrp47, and the Mtr4 RNA helicase. Mpp6 interacts with the nine-subunit exosome core, while Rrp47 stabilizes the exoribonuclease Rrp6 and recruits Mtr4, but it is less clear if these cofactors work together. Using biochemistry with Saccharomyces cerevisiae proteins, we show that Rrp47 and Mpp6 stimulate exosome-mediated RNA decay, albeit with unique dependencies on elements within the nuclear exosome. Mpp6-exosomes can recruit Mtr4, while Mpp6 and Rrp47 each contribute to Mtr4-dependent RNA decay, with maximal Mtr4-dependent decay observed with both cofactors. The 3.3 Å structure of a twelve-subunit nuclear Mpp6 exosome bound to RNA shows the central region of Mpp6 bound to the exosome core, positioning its Mtr4 recruitment domain next to Rrp6 and the exosome central channel. Genetic analysis reveals interactions that are largely consistent with our model.\",\n \"corpus_id\": 261364015,\n \"score\": 2\n },\n {\n \"doc_id\": \"28877463\",\n \"title\": \"Mpp6 Incorporation in the Nuclear Exosome Contributes to RNA Channeling through the Mtr4 Helicase.\",\n \"abstract\": \"The RNA-degrading exosome mediates the processing and decay of many cellular transcripts. In the yeast nucleus, the ubiquitous 10-subunit exosome core complex (Exo-9-Rrp44) functions with four conserved cofactors (Rrp6, Rrp47, Mtr4, and Mpp6). Biochemical and structural studies to date have shed insights into the mechanisms of the exosome core and its nuclear cofactors, with the exception of Mpp6. We report the 3.2-Å resolution crystal structure of a S. cerevisiae Exo-9-Mpp6 complex, revealing how linear motifs in the Mpp6 middle domain bind Rrp40 via evolutionary conserved residues. In particular, Mpp6 binds near a tryptophan residue of Rrp40 that is mutated in human patients suffering from pontocerebellar hypoplasia. Using biochemical assays, we show that Mpp6 is required for the ability of Mtr4 to extend the trajectory of an RNA entering the exosome core, suggesting that it promotes the channeling of substrates from the nuclear helicase to the processive RNase.\",\n \"corpus_id\": 12726485,\n \"score\": 2\n },\n {\n \"doc_id\": \"17983848\",\n \"title\": \"Intrinsic 5'-deoxyribose-5-phosphate lyase activity in Saccharomyces cerevisiae Trf4 protein with a possible role in base excision DNA repair.\",\n \"abstract\": \"In Saccharomyces cerevisiae, the base excision DNA repair (BER) pathway has been thought to involve only a multinucleotide (long-patch) mechanism (LP-BER), in contrast to most known cases that include a major single-nucleotide pathway (SN-BER). The key step in mammalian SN-BER, removal of the 5'-terminal abasic residue generated by AP endonuclease incision, is effected by DNA polymerase beta (Polbeta). Computational analysis indicates that yeast Trf4 protein, with roles in sister chromatin cohesion and RNA quality control, is a new member of the X family of DNA polymerases that includes Polbeta. Previous studies of yeast trf4Delta mutants revealed hypersensitivity to methylmethane sulfonate (MMS) but not UV light, a characteristic of BER mutants in other organisms. We found that, like mammalian Polbeta, Trf4 is able to form a Schiff base intermediate with a 5'-deoxyribose-5-phosphate substrate and to excise the abasic residue through a dRP lyase activity. Also like Polbeta, Trf4 forms stable cross-links in vitro to 5'-incised 2-deoxyribonolactone residues in DNA. We determined the sensitivity to MMS of strains with a trf4Delta mutation in a rad27Delta background, in an AP lyase-deficient background (ogg1 ntg1 ntg2), or in a pol4Delta background. Only a RAD27 genetic interaction was detected: there was higher sensitivity for strains mutated in both TRF4 and RAD27 than either single mutant, and overexpression of Trf4 in a rad27Delta background partially suppressed MMS sensitivity. The data strongly suggest a role for Trf4 in a pathway parallel to the Rad27-dependent LP-BER in yeast. Finally, we demonstrate that Trf5 significantly affects MMS sensitivity and thus probably BER efficiency in cells expressing either wild-type Trf4 or a C-terminus-deleted form.\",\n \"corpus_id\": 42872015,\n \"score\": 1\n },\n {\n \"doc_id\": \"18042682\",\n \"title\": \"Crystal structure of an archaeal Ski2p-like protein from Pyrococcus horikoshii OT3.\",\n \"abstract\": \"The Ski complex composed of Ski2p, Ski3p, and Ski8p plays an essential role in the 3' to 5' cytoplasmic mRNA degradation pathway in yeast. Ski2p is a putative RNA helicase, belonging in the DExD/H-box protein families and conserved in eukarya as well as in archaea. The gene product (Ph1280p) from the hyperthermophilic archaeon Pyrococcus horikoshii OT3 shows sequence homology with Ski2p, sharing 22.6% identical amino acids with a central region of Ski2p. In order to gain structural information about the Ski2p-like RNA helicase, we overproduced Ph1280p in Escherichia coli cells, and purified it to apparent homogeneity. Ph1280p exhibits DNA/RNA-dependent ATPase activity with an optimal temperature at approximately 90 degrees C. The crystal structure of Ph1280p has been solved at a resolution of 3.5 A using single-wavelength anomalous dispersion (SAD) and selenomethionyl (Se-Met)-substituted protein. Ph1280p comprises four subdomains; the two N-terminal subdomains (N1 and N2) fold into an RecA-like architecture with the conserved helicase motifs, while the two C-terminal subdomains (C1 and C2) fold into alpha-helical structures containing a winged helix (WH)-fold and helix-hairpin-helix (HhH)-fold, respectively. Although the structure of each of the Ph1280p subdomains can be individually superimposed on the corresponding domains in other helicases, such as the Escherichia coli DNA helicase RecQ, the relative orientation of the helicase and C-terminal subdomains in Ph1280p is significantly different from that of other helicases. This structural feature is implicated in substrate specificity for the Ski2-like helicase and would play a critical role in the 3' to 5' cytoplasmic mRNA degradation in the Ski complex.\",\n \"corpus_id\": 45433442,\n \"score\": 1\n },\n {\n \"doc_id\": \"19070634\",\n \"title\": \"Identification and characterization of nuclear non-canonical poly(A) polymerases from Trypanosoma brucei.\",\n \"abstract\": \"Regulation of nuclear genome expression in Trypanosoma brucei is critical for this protozoan parasite's successful transition between its vertebrate and invertebrate host environments. The canonical eukaryotic circuits such as modulation of transcription initiation, mRNA splicing and polyadenylation appear to be nearly non-existent in T. brucei suggesting that the transcriptome is primarily defined by mRNA turnover. Our previous work has highlighted sequence similarities between terminal RNA uridylyl transferases (TUTases) and non-canonical poly(A) polymerases, which are widely implicated in regulating nuclear, cytoplasmic and organellar RNA decay throughout the eukaryotic lineage. Here, we have continued characterization of TUTase-like proteins in T. brucei and identified two nuclear non-canonical poly(A) polymerases (ncPAPs). The 82kDa TbncPAP1 is essential for viability of procyclic and bloodstream forms of T. brucei. Similar to Trf4/5 proteins from budding yeast, TbncPAP1 requires protein cofactor(s) to exert poly(A) polymerase activity in vitro. The recombinant 54kDa TbncPAP2 showed a PAP activity as an individual polypeptide. Proteomic analysis of the TbncPAP1 interactions demonstrated its association with Mtr4 RNA helicase and several RNA binding proteins, including a potential ortholog of Air1p/2p proteins, which indicates the presence of a stable TRAMP-like complex in trypanosomes. Our findings suggest that TbncPAP1 may be a \\\"quality control\\\" nuclear PAP involved in targeting aberrant or anti-sense transcripts for degradation by the 3'-exosome. Such mechanisms are likely to play a major role in alleviating promiscuity of the transcriptional machinery.\",\n \"corpus_id\": 19494397,\n \"score\": 1\n },\n {\n \"doc_id\": \"19327365\",\n \"title\": \"Crystal structure of Escherichia coli polynucleotide phosphorylase core bound to RNase E, RNA and manganese: implications for catalytic mechanism and RNA degradosome assembly.\",\n \"abstract\": \"Polynucleotide phosphorylase (PNPase) is a processive exoribonuclease that contributes to messenger RNA turnover and quality control of ribosomal RNA precursors in many bacterial species. In Escherichia coli, a proportion of the PNPase is recruited into a multi-enzyme assembly, known as the RNA degradosome, through an interaction with the scaffolding domain of the endoribonuclease RNase E. Here, we report crystal structures of E. coli PNPase complexed with the recognition site from RNase E and with manganese in the presence or in the absence of modified RNA. The homotrimeric PNPase engages RNase E on the periphery of its ring-like architecture through a pseudo-continuous anti-parallel beta-sheet. A similar interaction pattern occurs in the structurally homologous human exosome between the Rrp45 and Rrp46 subunits. At the centre of the PNPase ring is a tapered channel with an adjustable aperture where RNA bases stack on phenylalanine side chains and trigger structural changes that propagate to the active sites. Manganese can substitute for magnesium as an essential co-factor for PNPase catalysis, and our crystal structure of the enzyme in complex with manganese suggests how the metal is positioned to stabilise the transition state. We discuss the implications of these structural observations for the catalytic mechanism of PNPase, its processive mode of action, and its assembly into the RNA degradosome.\",\n \"corpus_id\": 23416178,\n \"score\": 1\n },\n {\n \"doc_id\": \"20711761\",\n \"title\": \"1H, 13C, and 15N chemical shift assignments of ZCCHC9.\",\n \"abstract\": \"ZCCHC9 is a human nuclear protein with sequence homology to yeast Air1p/Air2p proteins which are RNA-binding subunits of the Trf4/Air2/Mtr4 polyadenylation (TRAMP) complex involved in nuclear RNA quality control and degradation in yeast. The ZCCHC9 protein contains four retroviral-type zinc knuckle motifs. Here, we report the NMR spectral assignment of the zinc knuckle region of ZCCHC9. These data will allow performing NMR structural and RNA-binding studies of ZCCHC9 with the aim to investigate its role in the RNA quality control in human.\",\n \"corpus_id\": 11114207,\n \"score\": 1\n },\n {\n \"doc_id\": \"23166521\",\n \"title\": \"Polyadenylation-dependent control of long noncoding RNA expression by the poly(A)-binding protein nuclear 1.\",\n \"abstract\": \"The poly(A)-binding protein nuclear 1 (PABPN1) is a ubiquitously expressed protein that is thought to function during mRNA poly(A) tail synthesis in the nucleus. Despite the predicted role of PABPN1 in mRNA polyadenylation, little is known about the impact of PABPN1 deficiency on human gene expression. Specifically, it remains unclear whether PABPN1 is required for general mRNA expression or for the regulation of specific transcripts. Using RNA sequencing (RNA-seq), we show here that the large majority of protein-coding genes express normal levels of mRNA in PABPN1-deficient cells, arguing that PABPN1 may not be required for the bulk of mRNA expression. Unexpectedly, and contrary to the view that PABPN1 functions exclusively at protein-coding genes, we identified a class of PABPN1-sensitive long noncoding RNAs (lncRNAs), the majority of which accumulated in conditions of PABPN1 deficiency. Using the spliced transcript produced from a snoRNA host gene as a model lncRNA, we show that PABPN1 promotes lncRNA turnover via a polyadenylation-dependent mechanism. PABPN1-sensitive lncRNAs are targeted by the exosome and the RNA helicase MTR4/SKIV2L2; yet, the polyadenylation activity of TRF4-2, a putative human TRAMP subunit, appears to be dispensable for PABPN1-dependent regulation. In addition to identifying a novel function for PABPN1 in lncRNA turnover, our results provide new insights into the post-transcriptional regulation of human lncRNAs.\",\n \"corpus_id\": 1053760,\n \"score\": 1\n },\n {\n \"doc_id\": \"21063153\",\n \"title\": \"Crystal structure of a PFU-PUL domain pair of Saccharomyces cerevisiae Doa1/Ufd3.\",\n \"abstract\": \"Doa1/Ufd3 is involved in ubiquitin (Ub)-dependent cellular processes in Saccharomyces cerevisiae, and consists of WD40, PFU, and PUL domains. Previous studies showed that the PFU and PUL domains interact with Ub and Hse1, and Cdc48, respectively. However, their detailed functional interactions with Doa1 remained elusive. We report the crystal structure of the PFU-PUL domain pair of yeast Doa1 at 1.9 Å resolution. The conserved surface of the PFU domain may be involved in binding to Ub and Hse1. Unexpectedly, the PUL domain consists of an Armadillo (ARM)-like repeat structure. The positively charged concave surface of the PUL domain may bind to the negatively charged C-terminal region of Cdc48. A structural comparison of Doa1 with Ufd2 revealed that they share a similar ARM-like repeat, supporting a model in which Doa1 and Ufd2 compete for Cdc48 binding and may dictate the fate of ubiquitinated proteins in the proteasome pathway.\",\n \"corpus_id\": 6528918,\n \"score\": 0\n },\n {\n \"doc_id\": \"21984415\",\n \"title\": \"Molecular architecture of a multifunctional MCM complex.\",\n \"abstract\": \"DNA replication is strictly regulated through a sequence of steps that involve many macromolecular protein complexes. One of them is the replicative helicase, which is required for initiation and elongation phases. A MCM helicase found as a prophage in the genome of Bacillus cereus is fused with a primase domain constituting an integrative arrangement of two essential activities for replication. We have isolated this helicase-primase complex (BcMCM) showing that it can bind DNA and displays not only helicase and primase but also DNA polymerase activity. Using single-particle electron microscopy and 3D reconstruction, we obtained structures of BcMCM using ATPγS or ADP in the absence and presence of DNA. The complex depicts the typical hexameric ring shape. The dissection of the unwinding mechanism using site-directed mutagenesis in the Walker A, Walker B, arginine finger and the helicase channels, suggests that the BcMCM complex unwinds DNA following the extrusion model similarly to the E1 helicase from papillomavirus.\",\n \"corpus_id\": 3055885,\n \"score\": 0\n },\n {\n \"doc_id\": \"22813733\",\n \"title\": \"Molecular architecture of the yeast monopolin complex.\",\n \"abstract\": \"The Saccharomyces cerevisiae monopolin complex directs proper chromosome segregation in meiosis I by mediating co-orientation of sister kinetochores on the meiosis I spindle. The monopolin subunits Csm1 and Lrs4 form a V-shaped complex that may directly crosslink sister kinetochores. We report here biochemical characterization of the monopolin complex subunits Mam1 and Hrr25 and of the complete four-protein monopolin complex. By purifying monopolin subcomplexes with different subunit combinations, we have determined the stoichiometry and overall architecture of the full monopolin complex. We have determined the crystal structure of Csm1 bound to a Mam1 fragment, showing how Mam1 wraps around the Csm1 dimer and alters the stoichiometry of kinetochore-protein binding by Csm1. We further show that the kinase activity of Hrr25 is altered by Mam1 binding, and we identify Hrr25 phosphorylation sites on Mam1 that may affect monopolin complex stability and/or kinetochore binding in meiosis.\",\n \"corpus_id\": 6368384,\n \"score\": 0\n },\n {\n \"doc_id\": \"25849387\",\n \"title\": \"A noncanonical PWI domain in the N-terminal helicase-associated region of the spliceosomal Brr2 protein.\",\n \"abstract\": \"The spliceosomal RNA helicase Brr2 is required for the assembly of a catalytically active spliceosome on a messenger RNA precursor. Brr2 exhibits an unusual organization with tandem helicase units, each comprising dual RecA-like domains and a Sec63 homology unit, preceded by a more than 400-residue N-terminal helicase-associated region. Whereas recent crystal structures have provided insights into the molecular architecture and regulation of the Brr2 helicase region, little is known about the structural organization and function of its N-terminal part. Here, a near-atomic resolution crystal structure of a PWI-like domain that resides in the N-terminal region of Chaetomium thermophilum Brr2 is presented. CD spectroscopic studies suggested that this domain is conserved in the yeast and human Brr2 orthologues. Although canonical PWI domains act as low-specificity nucleic acid-binding domains, no significant affinity of the unusual PWI domain of Brr2 for a broad spectrum of DNAs and RNAs was detected in band-shift assays. Consistently, the C. thermophilum Brr2 PWI-like domain, in the conformation seen in the present crystal structure, lacks an expanded positively charged surface patch as observed in at least one canonical, nucleic acid-binding PWI domain. Instead, in a comprehensive yeast two-hybrid screen against human spliceosomal proteins, fragments of the N-terminal region of human Brr2 were found to interact with several other spliceosomal proteins. At least one of these interactions, with the Prp19 complex protein SPF27, depended on the presence of the PWI-like domain. The results suggest that the N-terminal region of Brr2 serves as a versatile protein-protein interaction platform in the spliceosome and that some interactions require or are reinforced by the PWI-like domain.\",\n \"corpus_id\": 19950529,\n \"score\": 0\n },\n {\n \"doc_id\": \"25914052\",\n \"title\": \"Architecture of the ubiquitylation module of the yeast Ccr4-Not complex.\",\n \"abstract\": \"The Ccr4-Not complex regulates eukaryotic gene expression at multiple levels, including mRNA turnover, translational repression, and transcription. We have studied the ubiquitylation module of the yeast Ccr4-Not complex and addressed how E3 ligase binds cognate E2 and how it is tethered to the complex. The 2.8-Å resolution crystal structure of the N-terminal RING domain of Not4 in complex with Ubc4 shows the detailed interactions of this E3-E2 complex. The 3.6-Å resolution crystal structure of the C-terminal domain of the yeast Not4 in complex with the C-terminal domain of Not1 reveals how a largely extended region at the C-terminus of Not4 wraps around a HEAT-repeat region of Not1. This C-terminal region of Not4 is only partly conserved in metazoans, rationalizing its weaker Not1-binding properties. The structural and biochemical data show how Not1 can incorporate both the ubiquitylation module and the Not2-Not3/5 module concomitantly in the Ccr4-Not complex.\",\n \"corpus_id\": 12471595,\n \"score\": 0\n },\n {\n \"doc_id\": \"26124149\",\n \"title\": \"Structural basis for the activation of the C. elegans noncanonical cytoplasmic poly(A)-polymerase GLD-2 by GLD-3.\",\n \"abstract\": \"The Caenorhabditis elegans germ-line development defective (GLD)-2-GLD-3 complex up-regulates the expression of genes required for meiotic progression. GLD-2-GLD-3 acts by extending the short poly(A) tail of germ-line-specific mRNAs, switching them from a dormant state into a translationally active state. GLD-2 is a cytoplasmic noncanonical poly(A) polymerase that lacks the RNA-binding domain typical of the canonical nuclear poly(A)-polymerase Pap1. The activity of C. elegans GLD-2 in vivo and in vitro depends on its association with the multi-K homology (KH) domain-containing protein, GLD-3, a homolog of Bicaudal-C. We have identified a minimal polyadenylation complex that includes the conserved nucleotidyl-transferase core of GLD-2 and the N-terminal domain of GLD-3, and determined its structure at 2.3-Å resolution. The structure shows that the N-terminal domain of GLD-3 does not fold into the predicted KH domain but wraps around the catalytic domain of GLD-2. The picture that emerges from the structural and biochemical data are that GLD-3 activates GLD-2 both indirectly by stabilizing the enzyme and directly by contributing positively charged residues near the RNA-binding cleft. The RNA-binding cleft of GLD-2 has distinct structural features compared with the poly(A)-polymerases Pap1 and Trf4. Consistently, GLD-2 has distinct biochemical properties: It displays unusual specificity in vitro for single-stranded RNAs with at least one adenosine at the 3' end. GLD-2 thus appears to have evolved specialized nucleotidyl-transferase properties that match the 3' end features of dormant cytoplasmic mRNAs.\",\n \"corpus_id\": 31001608,\n \"score\": 0\n },\n {\n \"doc_id\": \"26637280\",\n \"title\": \"The large N-terminal region of the Brr2 RNA helicase guides productive spliceosome activation.\",\n \"abstract\": \"The Brr2 helicase provides the key remodeling activity for spliceosome catalytic activation, during which it disrupts the U4/U6 di-snRNP (small nuclear RNA protein), and its activity has to be tightly regulated. Brr2 exhibits an unusual architecture, including an ∼500-residue N-terminal region, whose functions and molecular mechanisms are presently unknown, followed by a tandem array of structurally similar helicase units (cassettes), only the first of which is catalytically active. Here, we show by crystal structure analysis of full-length Brr2 in complex with a regulatory Jab1/MPN domain of the Prp8 protein and by cross-linking/mass spectrometry of isolated Brr2 that the Brr2 N-terminal region encompasses two folded domains and adjacent linear elements that clamp and interconnect the helicase cassettes. Stepwise N-terminal truncations led to yeast growth and splicing defects, reduced Brr2 association with U4/U6•U5 tri-snRNPs, and increased ATP-dependent disruption of the tri-snRNP, yielding U4/U6 di-snRNP and U5 snRNP. Trends in the RNA-binding, ATPase, and helicase activities of the Brr2 truncation variants are fully rationalized by the crystal structure, demonstrating that the N-terminal region autoinhibits Brr2 via substrate competition and conformational clamping. Our results reveal molecular mechanisms that prevent premature and unproductive tri-snRNP disruption and suggest novel principles of Brr2-dependent splicing regulation.\",\n \"corpus_id\": 2238955,\n \"score\": 0\n },\n {\n \"doc_id\": \"28652207\",\n \"title\": \"Characterizing the molecular architectures of chromatin-modifying complexes.\",\n \"abstract\": \"Eukaryotic cells package their genome in the form of a DNA-protein complex known as chromatin. This organization not only condenses the genome to fit within the confines of the nucleus, but also provides a platform for a cell to regulate accessibility to different gene sequences. The basic packaging element of chromatin is the nucleosome, which consists of 146 base pairs of DNA wrapped around histone proteins. One major means that a cell regulates chromatin structure is by depositing post-translational modifications on nucleosomal histone proteins, and thereby altering internucleosomal interactions and/or binding to different chromatin associated factors. These chromatin modifications are often catalyzed by multi-subunit enzyme complexes, whose large size, sophisticated composition, and inherent conformational flexibility pose significant technical challenges to their biochemical and structural characterization. Multiple structural approaches including nuclear magnetic resonance spectroscopy, X-ray crystallography, single-particle electron microscopy, and crosslinking coupled to mass spectrometry are often used synergistically to probe the overall architecture, subunit organization, and catalytic mechanisms of these macromolecular assemblies. In this review, we highlight several recent chromatin-modifying complexes studies that embodies this multipronged structural approach, and explore common themes amongst them. This article is part of a Special Issue entitled: Biophysics in Canada, edited by Lewis Kay, John Baenziger, Albert Berghuis and Peter Tieleman.\",\n \"corpus_id\": 205856271,\n \"score\": 0\n }\n]","isConversational":false}}},{"rowIdx":52,"cells":{"query":{"kind":"string","value":"{\n \"doc_id\": \"25372670\",\n \"title\": \"Covering complete proteomes with X-ray structures: a current snapshot.\",\n \"abstract\": \"Structural genomics programs have developed and applied structure-determination pipelines to a wide range of protein targets, facilitating the visualization of macromolecular interactions and the understanding of their molecular and biochemical functions. The fundamental question of whether three-dimensional structures of all proteins and all functional annotations can be determined using X-ray crystallography is investigated. A first-of-its-kind large-scale analysis of crystallization propensity for all proteins encoded in 1953 fully sequenced genomes was performed. It is shown that current X-ray crystallographic knowhow combined with homology modeling can provide structures for 25% of modeling families (protein clusters for which structural models can be obtained through homology modeling), with at least one structural model produced for each Gene Ontology functional annotation. The coverage varies between superkingdoms, with 19% for eukaryotes, 35% for bacteria and 49% for archaea, and with those of viruses following the coverage values of their hosts. It is shown that the crystallization propensities of proteomes from the taxonomic superkingdoms are distinct. The use of knowledge-based target selection is shown to substantially increase the ability to produce X-ray structures. It is demonstrated that the human proteome has one of the highest attainable coverage values among eukaryotes, and GPCR membrane proteins suitable for X-ray structure determination were determined.\",\n \"corpus_id\": 1327886\n}"},"candidates":{"kind":"list like","value":[{"doc_id":"18542855","title":"A general target selection method for crystallographic proteomics.","abstract":"Increasing the success in obtaining structures and maximizing the value of the structures determined are the two major goals of target selection in structural proteomics. This chapter presents an efficient and flexible target selection procedure supplemented with a Web-based resource that is suitable for small- to large-scale structural genomics projects that use crystallography as the major means of structure determination. Based on three criteria, biological significance, structural novelty, and \"crystallizability,\" the approach first removes (filters) targets that do not meet minimal criteria and then ranks the remaining targets based on their \"crystallizability\" estimates. This novel procedure was designed to maximize selection efficiency, and its prevailing criteria categories make it suitable for a broad range of structural proteomics projects.","corpus_id":14432449,"score":2},{"doc_id":"18542882","title":"NMR screening for rapid protein characterization in structural proteomics.","abstract":"In the age of structural proteomics when protein structures are targeted on a genome-wide scale, the identification of proteins that are amenable to analysis using x-ray crystallography or NMR spectroscopy is the key to high throughput structure determination. NMR screening is a beneficial part of a structural proteomics pipeline because of its ability to provide detailed biophysical information about the protein targets under investigation at an early stage of the structure determination process. This chapter describes efficient methods for the production of uniformly (15)N-labeled proteins for NMR screening using both conventional IPTG induction and autoinduction approaches in E. coli. Details of sample preparation for NMR and the acquisition of 1D (1)H NMR and 2D (1)H-(15)N HSQC spectra to assess the structural characteristics and suitability of proteins for further structural studies are also provided.","corpus_id":40931011,"score":2},{"doc_id":"18563369","title":"Protein structure determination by x-ray crystallography.","abstract":"X-ray biocrystallography is the most powerful method to obtain a macromolecular structure. The improvement of computational technologies in recent years and the development of new and powerful computer programs together with the enormous increment in the number of protein structures deposited in the Protein Data Bank, render the resolution of new structures easier than in the past. The aim of this chapter is to provide practical procedures useful for solving a new structure. It is impossible to give more than a flavor of what the x-ray crystallographic technique entails in one brief chapter; therefore, this chapter focuses its attention on the Molecular Replacement method. Whenever applicable, this method allows the resolution of macromolecular structures starting from a single data set and a search model downloaded from the PDB, with the aid only of computer work.","corpus_id":36064476,"score":2},{"doc_id":"18761469","title":"Structural proteomics by NMR spectroscopy.","abstract":"Structural proteomics is one of the powerful research areas in the postgenomic era, elucidating structure-function relationships of uncharacterized gene products based on the 3D protein structure. It proposes biochemical and cellular functions of unannotated proteins and thereby identifies potential drug design and protein engineering targets. Recently, a number of pioneering groups in structural proteomics research have achieved proof of structural proteomic theory by predicting the 3D structures of hypothetical proteins that successfully identified the biological functions of those proteins. The pioneering groups made use of a number of techniques, including NMR spectroscopy, which has been applied successfully to structural proteomics studies over the past 10 years. In addition, advances in hardware design, data acquisition methods, sample preparation and automation of data analysis have been developed and successfully applied to high-throughput structure determination techniques. These efforts ensure that NMR spectroscopy will become an important methodology for performing structural proteomics research on a genomic scale. NMR-based structural proteomics together with x-ray crystallography will provide a comprehensive structural database to predict the basic biological functions of hypothetical proteins identified by the genome projects.","corpus_id":207200996,"score":2},{"doc_id":"19465771","title":"Generalized X-ray and neutron crystallographic analysis: more accurate and complete structures for biological macromolecules.","abstract":"X-ray and neutron crystallographic techniques provide complementary information on the structure and function of biological macromolecules. X-ray and neutron (XN) crystallographic data have been combined in a joint structure-refinement procedure that has been developed using recent advances in modern computational methodologies, including cross-validated maximum-likelihood target functions with gradient-based optimization and simulated annealing. The XN approach for complete (including hydrogen) macromolecular structure analysis provides more accurate and complete structures, as demonstrated for diisopropyl fluorophosphatase, photoactive yellow protein and human aldose reductase. Furthermore, this method has several practical advantages, including the easier determination of the orientation of water molecules, hydroxyl groups and some amino-acid side chains.","corpus_id":17111309,"score":2},{"doc_id":"19523904","title":"PSI-2: structural genomics to cover protein domain family space.","abstract":"One major objective of structural genomics efforts, including the NIH-funded Protein Structure Initiative (PSI), has been to increase the structural coverage of protein sequence space. Here, we present the target selection strategy used during the second phase of PSI (PSI-2). This strategy, jointly devised by the bioinformatics groups associated with the PSI-2 large-scale production centers, targets representatives from large, structurally uncharacterized protein domain families, and from structurally uncharacterized subfamilies in very large and diverse families with incomplete structural coverage. These very large families are extremely diverse both structurally and functionally, and are highly overrepresented in known proteomes. On the basis of several metrics, we then discuss to what extent PSI-2, during its first 3 years, has increased the structural coverage of genomes, and contributed structural and functional novelty. Together, the results presented here suggest that PSI-2 is successfully meeting its objectives and provides useful insights into structural and functional space.","corpus_id":20208185,"score":2},{"doc_id":"19765976","title":"High-throughput crystallography for structural genomics.","abstract":"Protein X-ray crystallography recently celebrated its 50th anniversary. The structures of myoglobin and hemoglobin determined by Kendrew and Perutz provided the first glimpses into the complex protein architecture and chemistry. Since then, the field of structural molecular biology has experienced extraordinary progress and now more than 55000 protein structures have been deposited into the Protein Data Bank. In the past decade many advances in macromolecular crystallography have been driven by world-wide structural genomics efforts. This was made possible because of third-generation synchrotron sources, structure phasing approaches using anomalous signal, and cryo-crystallography. Complementary progress in molecular biology, proteomics, hardware and software for crystallographic data collection, structure determination and refinement, computer science, databases, robotics and automation improved and accelerated many processes. These advancements provide the robust foundation for structural molecular biology and assure strong contribution to science in the future. In this report we focus mainly on reviewing structural genomics high-throughput X-ray crystallography technologies and their impact.","corpus_id":22065223,"score":2},{"doc_id":"20443165","title":"Homology modeling of G-protein-coupled receptors with X-ray structures on the rise.","abstract":"GPCRs are key components of signal transduction pathways and are important drug targets. Recently determined GPCR structures provide opportunities for advancements in GPCR modeling. This review focuses on the choice of experimental templates, the treatment of extracellular loops and the description of ligand-binding sites in GPCR modeling. Four important conclusions are reached in this review: (i) multi-template models may produce better structures than single-template models, although inferior models may also be generated by multi-template approaches, warranting the development and application of improved model assessment methods; (ii) cautious incorporation of knowledge-based constraints can improve the quality of models and docking; (iii) molecular dynamics simulations account for structural features not observed in X-ray structures and may refine docking poses; and (iv) while progress in de novo methods for long loop prediction is ongoing, loopless models provide a practical alternative for docking and virtual screening applications.","corpus_id":11837650,"score":2},{"doc_id":"21833866","title":"X-ray crystallography.","abstract":"X-ray crystallography has been particularly important in the study of the enzyme nitrogenase, providing researchers with high-resolution structural models that have been essential to studying the enzyme's unique metal clusters and nucleotide-binding modes and protein interactions. While several important nitrogenase structures have already been determined using X-ray crystallography, the technique still holds great potential for future significant discoveries involving reaction intermediates and redox states of the enzyme's metal clusters. Thus, it is important to inform future nitrogenase researchers about the procedures for obtaining crystals of nitrogenase component proteins and their complexes and determining their structures. While nitrogenase component proteins from several bacteria have been crystallized, the majority of structures and those of highest resolution are of the nitrogenase proteins from the bacteria Azotobacter vinelandii. Therefore, the bulk of this chapter will focus on methods for crystallization and structure determination of nitrogenase component proteins from A. vinelandii.","corpus_id":104916134,"score":2},{"doc_id":"22354707","title":"Target selection for structural genomics based on combining fold recognition and crystallisation prediction methods: application to the human proteome.","abstract":"The objective of this study is to automatically identify regions of the human proteome that are suitable for 3D structure determination by X-ray crystallography and to annotate them according to their likelihood to produce diffraction quality crystals. The results provide a powerful tool for structural genomics laboratories who wish to select human proteins based on the statistical likelihood of crystallisation success. Combining fold recognition and crystallisation prediction algorithms enables the efficient calculation of the crystallisability of the entire human proteome. This novel study estimates that there are approximately 40,000 crystallisable regions in the human proteome. Currently, only 15% of these regions (approx. 6,000 sequences) have been solved to at least 95% sequence identity. The remaining unsolved regions have been categorised into 5 crystallisation classes and an integral membrane protein (IMP) class, based on established structure prediction, crystallisation prediction and transmembrane (TM) helix prediction algorithms. Approximately 750 unsolved regions (2% of the proteome) have been identified as having a PDB fold representative (template) and an 'optimal' likelihood of crystallisation. At the other end of the spectrum, more than 10,500 non-IMP regions with a PDB template are classified as 'very difficult' to crystallise (26%) and almost 2,500 regions (6%) were predicted to contain at least 3 TM helices. The 3D-SPECS (3D Structural Proteomics Explorer with Crystallisation Scores) website contains crystallisation predictions for the entire human proteome and can be found at http://www.bioinformaticsplus.org/3dspecs.","corpus_id":13282350,"score":2},{"doc_id":"23132076","title":"Determination of soluble and membrane protein structures by X-ray crystallography.","abstract":"X-ray crystallography is a technique used to determine the atomic-detail structure of a biological macromolecule. The method relies on the ability to generate a three-dimensional crystal of a highly purified protein or nucleic acid for diffraction by X-rays. The extent of scattering of X-rays by the crystal determines the accuracy of the resulting structural model. Unlike electrons, X-rays cannot be refocused after they have been scattered by their target. Thus, calculations are needed to reconstruct the image of the macromolecule that builds the crystal lattice. Tremendous advances over the past 60 years in recombinant expression and purification, crystal growth methods and equipment, X-ray sources, computer processing power, programs, and graphics have taken X-ray crystallography from a highly specialized field to one increasingly accessible to researchers in the biomedical sciences. In this chapter, we review the major concepts of macromolecular X-ray crystallography, focusing mainly on techniques for crystallizing soluble and membrane proteins, and provide a protocol for the crystallization of lysozyme as a model for the crystallization of other proteins.","corpus_id":29230067,"score":2},{"doc_id":"23232152","title":"Utilization of protein intrinsic disorder knowledge in structural proteomics.","abstract":"Intrinsically disordered proteins (IDPs) and proteins with long disordered regions are highly abundant in various proteomes. Despite their lack of well-defined ordered structure, these proteins and regions are frequently involved in crucial biological processes. Although in recent years these proteins have attracted the attention of many researchers, IDPs represent a significant challenge for structural characterization since these proteins can impact many of the processes in the structure determination pipeline. Here we investigate the effects of IDPs on the structure determination process and the utility of disorder prediction in selecting and improving proteins for structural characterization. Examination of the extent of intrinsic disorder in existing crystal structures found that relatively few protein crystal structures contain extensive regions of intrinsic disorder. Although intrinsic disorder is not the only cause of crystallization failures and many structured proteins cannot be crystallized, filtering out highly disordered proteins from structure-determination target lists is still likely to be cost effective. Therefore it is desirable to avoid highly disordered proteins from structure-determination target lists and we show that disorder prediction can be applied effectively to enrich structure determination pipelines with proteins more likely to yield crystal structures. For structural investigation of specific proteins, disorder prediction can be used to improve targets for structure determination. Finally, a framework for considering intrinsic disorder in the structure determination pipeline is proposed.","corpus_id":22301019,"score":2},{"doc_id":"23737050","title":"X-ray crystallography of viruses.","abstract":"For about 30 years X-ray crystallography has been by far the most powerful approach for determining virus structures at close to atomic resolutions. Information provided by these studies has deeply and extensively enriched and shaped our vision of the virus world. In turn, the ever increasing complexity and size of the virus structures being investigated have constituted a major driving force for methodological and conceptual developments in X-ray macromolecular crystallography. Landmarks of new virus structures determinations, such as the ones from the first animal viruses or from the first membrane-containing viruses, have often been associated to methodological breakthroughs in X-ray crystallography. In this chapter we present the common ground of proteins and virus crystallography with an emphasis in the peculiarities of virus studies. For example, the solution of the phase problem, a central issue in X-ray diffraction, has benefited enormously from the presence of non-crystallographic symmetry in virus crystals.","corpus_id":24255211,"score":2},{"doc_id":"24648090","title":"Protein structure validation and analysis with X-ray crystallography.","abstract":"X-ray crystallography is the main technique for the determination of protein structures. About 85 % of all protein structures known to date have been elucidated using X-ray crystallography. Knowledge of the three-dimensional structure of proteins can be used in various applications in biotechnology, biomedicine, drug design, and basic research and as a validation tool for protein modifications, ligand binding, and structural authenticity. Moreover, the requirement for pure, homogeneous, and stable protein solutions in crystallizations makes X-ray crystallography beneficial in other fields of protein research as well. Here, we describe the technique of X-ray protein crystallography and the steps involved for a successful three-dimensional crystal structure determination.","corpus_id":10634886,"score":2},{"doc_id":"25416941","title":"A glimpse of structural biology through X-ray crystallography.","abstract":"Since determination of the myoglobin structure in 1957, X-ray crystallography, as the anchoring tool of structural biology, has played an instrumental role in deciphering the secrets of life. Knowledge gained through X-ray crystallography has fundamentally advanced our views on cellular processes and greatly facilitated development of modern medicine. In this brief narrative, I describe my personal understanding of the evolution of structural biology through X-ray crystallography-using as examples mechanistic understanding of protein kinases and integral membrane proteins-and comment on the impact of technological development and outlook of X-ray crystallography.","corpus_id":28185107,"score":2},{"doc_id":"25604506","title":"X-ray crystallography and its impact on understanding bacterial cell wall remodeling processes.","abstract":"The molecular structure of matter defines its properties and function. This is especially true for biological macromolecules such as proteins, which participate in virtually all biochemical processes. A three dimensional structural model of a protein is thus essential for the detailed understanding of its physiological function and the characterization of essential properties such as ligand binding and reaction mechanism. X-ray crystallography is a well-established technique that has been used for many years, but it is still by far the most widely used method for structure determination. A particular strength of this technique is the elucidation of atomic details of molecular interactions, thus providing an invaluable tool for a multitude of scientific projects ranging from the structural classification of macromolecules over the validation of enzymatic mechanisms or the understanding of host-pathogen interactions to structure-guided drug design. In the first part of this review, we describe essential methodological and practical aspects of X-ray crystallography. We provide some pointers that should allow researchers without a background in structural biology to assess the overall quality and reliability of a crystal structure. To highlight its potential, we then survey the impact X-ray crystallography has had on advancing an understanding of a class of enzymes that modify the bacterial cell wall. A substantial number of different bacterial amidase structures have been solved, mostly by X-ray crystallography. Comparison of these structures highlights conserved as well as divergent features. In combination with functional analyses, structural information on these enzymes has therefore proven to be a valuable template not only for understanding their mechanism of catalysis, but also for targeted interference with substrate binding.","corpus_id":205290612,"score":2},{"doc_id":"26177814","title":"X-ray crystallography over the past decade for novel drug discovery - where are we heading next?","abstract":"INTRODUCTION: Macromolecular X-ray crystallography has been the primary methodology for determining the three-dimensional structures of proteins, nucleic acids and viruses. Structural information has paved the way for structure-guided drug discovery and laid the foundations for structural bioinformatics. However, X-ray crystallography still has a few fundamental limitations, some of which may be overcome and complemented using emerging methods and technologies in other areas of structural biology. AREAS COVERED: This review describes how structural knowledge gained from X-ray crystallography has been used to advance other biophysical methods for structure determination (and vice versa). This article also covers current practices for integrating data generated by other biochemical and biophysical methods with those obtained from X-ray crystallography. Finally, the authors articulate their vision about how a combination of structural and biochemical/biophysical methods may improve our understanding of biological processes and interactions. EXPERT OPINION: X-ray crystallography has been, and will continue to serve as, the central source of experimental structural biology data used in the discovery of new drugs. However, other structural biology techniques are useful not only to overcome the major limitation of X-ray crystallography, but also to provide complementary structural data that is useful in drug discovery. The use of recent advancements in biochemical, spectroscopy and bioinformatics methods may revolutionize drug discovery, albeit only when these data are combined and analyzed with effective data management systems. Accurate and complete data management is crucial for developing experimental procedures that are robust and reproducible.","corpus_id":35716775,"score":2},{"doc_id":"26935210","title":"The impact of structural genomics: the first quindecennial.","abstract":"The period 2000-2015 brought the advent of high-throughput approaches to protein structure determination. With the overall funding on the order of $2 billion (in 2010 dollars), the structural genomics (SG) consortia established worldwide have developed pipelines for target selection, protein production, sample preparation, crystallization, and structure determination by X-ray crystallography and NMR. These efforts resulted in the determination of over 13,500 protein structures, mostly from unique protein families, and increased the structural coverage of the expanding protein universe. SG programs contributed over 4400 publications to the scientific literature. The NIH-funded Protein Structure Initiatives alone have produced over 2000 scientific publications, which to date have attracted more than 93,000 citations. Software and database developments that were necessary to handle high-throughput structure determination workflows have led to structures of better quality and improved integrity of the associated data. Organized and accessible data have a positive impact on the reproducibility of scientific experiments. Most of the experimental data generated by the SG centers are freely available to the community and has been utilized by scientists in various fields of research. SG projects have created, improved, streamlined, and validated many protocols for protein production and crystallization, data collection, and functional analysis, significantly benefiting biological and biomedical research.","corpus_id":2688876,"score":2},{"doc_id":"27154589","title":"NMR in structural genomics to increase structural coverage of the protein universe: Delivered by Prof. Kurt Wüthrich on 7 July 2013 at the 38th FEBS Congress in St. Petersburg, Russia.","abstract":"For more than a decade, the Joint Center for Structural Genomics (JCSG; www.jcsg.org) worked toward increased three-dimensional structure coverage of the protein universe. This coordinated quest was one of the main goals of the four high-throughput (HT) structure determination centers of the Protein Structure Initiative (PSI; www.nigms.nih.gov/Research/specificareas/PSI). To achieve the goals of the PSI, the JCSG made use of the complementarity of structure determination by X-ray crystallography and nuclear magnetic resonance (NMR) spectroscopy to increase and diversify the range of targets entering the HT structure determination pipeline. The overall strategy, for both techniques, was to determine atomic resolution structures for representatives of large protein families, as defined by the Pfam database, which had no structural coverage and could make significant contributions to biological and biomedical research. Furthermore, the experimental structures could be leveraged by homology modeling to further expand the structural coverage of the protein universe and increase biological insights. Here, we describe what could be achieved by this structural genomics approach, using as an illustration the contributions from 20 NMR structure determinations out of a total of 98 JCSG NMR structures, which were selected because they are the first three-dimensional structure representations of the respective Pfam protein families. The information from this small sample is representative for the overall results from crystal and NMR structure determination in the JCSG. There are five new folds, which were classified as domains of unknown functions (DUF), three of the proteins could be functionally annotated based on three-dimensional structure similarity with previously characterized proteins, and 12 proteins showed only limited similarity with previous deposits in the Protein Data Bank (PDB) and were classified as DUFs.","corpus_id":30172260,"score":2},{"doc_id":"27924015","title":"TSTMP: target selection for structural genomics of human transmembrane proteins.","abstract":"The TSTMP database is designed to help the target selection of human transmembrane proteins for structural genomics projects and structure modeling studies. Currently, there are only 60 known 3D structures among the polytopic human transmembrane proteins and about a further 600 could be modeled using existing structures. Although there are a great number of human transmembrane protein structures left to be determined, surprisingly only a small fraction of these proteins have 'selected' (or above) status according to the current version the TargetDB/TargetTrack database. This figure is even worse regarding those transmembrane proteins that would contribute the most to the structural coverage of the human transmembrane proteome. The database was built by sorting out proteins from the human transmembrane proteome with known structure and searching for suitable model structures for the remaining proteins by combining the results of a state-of-the-art transmembrane specific fold recognition algorithm and a sequence similarity search algorithm. Proteins were searched for homologues among the human transmembrane proteins in order to select targets whose successful structure determination would lead to the best structural coverage of the human transmembrane proteome. The pipeline constructed for creating the TSTMP database guarantees to keep the database up-to-date. The database is available at http://tstmp.enzim.ttk.mta.hu.","corpus_id":11511784,"score":2},{"doc_id":"28843631","title":"Structural Coverage of the Proteome for Pharmaceutical Applications.","abstract":"Structure-based computational drug discovery efforts have traditionally focused on the structure of a single, well-known drug target. Important applications, such as target deconvolution and the analysis of polypharmacology, require proteome-scale molecular docking and have been inaccessible to structure-based in silico approaches. One important reason for this inaccessibility was that the structure of most proteins was not known. Lately, this 'structure gap' has been closing rapidly, and proteome-scale molecular docking seems within reach. Here, we survey the current state of structural coverage of the human genome and find that coverage is truly proteome-wide, both overall and in most pharmaceutically relevant categories of proteins. The time is right for structure-based approaches to target deconvolution and polypharmacology.","corpus_id":46294778,"score":2},{"doc_id":"29079755","title":"A proteome view of structural, functional, and taxonomic characteristics of major protein domain clusters.","abstract":"Proteome-scale bioinformatics research is increasingly conducted as the number of completely sequenced genomes increases, but analysis of protein domains (PDs) usually relies on similarity in their amino acid sequences and/or three-dimensional structures. Here, we present results from a bi-clustering analysis on presence/absence data for 6,580 unique PDs in 2,134 species with a sequenced genome, thus covering a complete set of proteins, for the three superkingdoms of life, Bacteria, Archaea, and Eukarya. Our analysis revealed eight distinctive PD clusters, which, following an analysis of enrichment of Gene Ontology functions and CATH classification of protein structures, were shown to exhibit structural and functional properties that are taxa-characteristic. For examples, the largest cluster is ubiquitous in all three superkingdoms, constituting a set of 1,472 persistent domains created early in evolution and retained in living organisms and characterized by basic cellular functions and ancient structural architectures, while an Archaea and Eukarya bi-superkingdom cluster suggests its PDs may have existed in the ancestor of the two superkingdoms, and others are single superkingdom- or taxa (e.g. Fungi)-specific. These results contribute to increase our appreciation of PD diversity and our knowledge of how PDs are used in species, yielding implications on species evolution.","corpus_id":3315660,"score":2},{"doc_id":"29295714","title":"fDETECT webserver: fast predictor of propensity for protein production, purification, and crystallization.","abstract":"BACKGROUND: Development of predictors of propensity of protein sequences for successful crystallization has been actively pursued for over a decade. A few novel methods that expanded the scope of these predictions to address additional steps of protein production and structure determination pipelines were released in recent years. The predictive performance of the current methods is modest. This is because the only input that they use is the protein sequence and since the experimental annotations of these data might be inconsistent given that they were collected across many laboratories and centers. However, even these modest levels of predictive quality are still practical compared to the reported low success rates of crystallization, which are below 10%. We focus on another important aspect related to a high computational cost of running the predictors that offer the expanded scope. RESULTS: We introduce a novel fDETECT webserver that provides very fast and modestly accurate predictions of the success of protein production, purification, crystallization, and structure determination. Empirical tests on two datasets demonstrate that fDETECT is more accurate than the only other similarly fast method, and similarly accurate and three orders of magnitude faster than the currently most accurate predictors. Our method predicts a single protein in about 120 milliseconds and needs less than an hour to generate the four predictions for an entire human proteome. Moreover, we empirically show that fDETECT secures similar levels of predictive performance when compared with four representative methods that only predict success of crystallization, while it also provides the other three predictions. A webserver that implements fDETECT is available at http://biomine.cs.vcu.edu/servers/fDETECT/ . CONCLUSIONS: fDETECT is a computational tool that supports target selection for protein production and X-ray crystallography-based structure determination. It offers predictive quality that matches or exceeds other state-of-the-art tools and is especially suitable for the analysis of large protein sets.","corpus_id":23971370,"score":2},{"doc_id":"18311631","title":"Internet resources in GPCR modelling.","abstract":"G-Protein coupled receptors (GPCRs), one of the most important families of drug targets, belong to the super family of integral membrane proteins characterized by seven transmembrane helices. Because they are difficult to crystallize, the three dimensional structure of these receptors have not yet been determined by X-ray crystallography, except one. In the absence of a 3-D structure, in-silico approaches for solving the structure of this class of proteins are widely used and provide valuable information for structure based drug design. There are several web servers and computer programs available that automate the modelling process of GPCRs. Some of these include Modeller, Swiss-Model server, Homer, etc. Using these tools reliable homology models of human histamine H1 receptor (HRH1) and thrombin receptor (PAR-1) have been generated which explain the binding mode of the standard antagonists of these receptors and may be useful in designing their novel antagonists.","corpus_id":43909951,"score":1},{"doc_id":"18542859","title":"Prediction of protein disorder.","abstract":"The recent advance in our understanding of the relation of protein structure and function cautions that many proteins, or regions of proteins, exist and function without a well-defined three-dimensional structure. These intrinsically disordered/unstructured proteins (IDP/IUP) are frequent in proteomes and carry out essential functions, but their lack of stable structures hampers efforts of solving structures at high resolution by x-ray crystallography and/or NMR. Thus, filtering such proteins/regions out of high-throughput structural genomics pipelines would be of significant benefit in terms of cost and success rate. This chapter outlines the theoretical background of structural disorder, and provides practical advice on the application of advanced bioinformatic predictors to this end, that is to recognize fully/mostly disordered proteins or regions, which are incompatible with structure determination. An emphasis is also given to a somewhat different approach, in which ordered/disordered regions are explicitly delineated to the end of making constructs amenable for structure determination even when disordered regions are present.","corpus_id":28242106,"score":1},{"doc_id":"18592171","title":"Plant proteomics.","abstract":"An understanding of gene function requires a complementation of gene and gene expression analysis by the systematic analysis of proteins. Progress in plant proteomics has been lagging behind animal and microbial proteomics due to the lack of plant genome data and the problems involved in successful protein extraction from plant material. With the sequencing of more and more plant genomes, this slow progress will soon be overcome. The moss Physcomitrella patens is a model organism in the field of plant functional genomics. P. patens is the first seedless plant for which the complete genome was sequenced. Genome annotation is currently in progress. While identification of proteins requires knowledge of all coding genes of the organism under study, gene annotation and functional characterization benefit greatly from the findings of proteome analysis. The proteome of P. patens is accessible and approaches are under way to increase the spectrum of proteomic methods applied to this plant. Here we provide a protocol for the extraction of proteins from P. patens and describe the basic and still most important method of proteome analysis, two-dimensional polyacrylamide electrophoresis of proteins. As this technique (not entirely unjustifiably) has the reputation of being unpredictably complicated, we provide a detailed protocol intended to reduce the reluctance that many scientists may have in using this technique.","corpus_id":32604142,"score":1},{"doc_id":"19061901","title":"Selecting optimum eukaryotic integral membrane proteins for structure determination by rapid expression and solubilization screening.","abstract":"A medium-throughput approach is used to rapidly identify membrane proteins from a eukaryotic organism that are most amenable to expression in amounts and quality adequate to support structure determination. The goal was to expand knowledge of new membrane protein structures based on proteome-wide coverage. In the first phase, membrane proteins from the budding yeast Saccharomyces cerevisiae were selected for homologous expression in S. cerevisiae, a system that can be adapted to expression of membrane proteins from other eukaryotes. We performed medium-scale expression and solubilization tests on 351 rationally selected membrane proteins from S. cerevisiae. These targets are inclusive of all annotated and unannotated membrane protein families within the organism's membrane proteome. Two hundred seventy-two targets were expressed, and of these, 234 solubilized in the detergent n-dodecyl-beta-D-maltopyranoside. Furthermore, we report the identity of a subset of targets that were purified to homogeneity to facilitate structure determinations. The extensibility of this approach is demonstrated with the expression of 10 human integral membrane proteins from the solute carrier superfamily. This discovery-oriented pipeline provides an efficient way to select proteins from particular membrane protein classes, families, or organisms that may be more suited to structure analysis than others.","corpus_id":5108816,"score":1},{"doc_id":"19303027","title":"X-ray crystallography of chemical compounds.","abstract":"AIMS: Accurate knowledge of molecular structure is a prerequisite for rational drug design. This review examines the role of X-ray crystallography in providing the required structural information and advances in the field of X-ray crystallography that enhance or expand its role. MAIN METHODS: X-ray crystallography of new drugs candidates and intermediates can provide valuable information of new syntheses and parameters for quantitative structure activity relationships (QSAR). KEY FINDINGS: Crystallographic studies play a vital role in many disciplines including materials science, chemistry, pharmacology, and molecular biology. X-ray crystallography is the most comprehensive technique available to determine molecular structure. A requirement for the high accuracy of crystallographic structures is that a 'good crystal' must be found, and this is often the rate-limiting step. In the past three decades developments in detectors, increases in computer power, and powerful graphics capabilities have contributed to a dramatic increase in the number of materials characterized by X-ray crystallography. More recently the advent of high-throughput crystallization techniques has enhanced our ability to produce that one good crystal required for crystallographic analysis. SIGNIFICANCE: Continuing advances in all phases of a crystallographic study have expanded the ranges of samples which can be analyzes by X-ray crystallography to include larger molecules, smaller or weakly diffracting crystals, and twinned crystals.","corpus_id":206727089,"score":1},{"doc_id":"20739007","title":"Unlocking the eukaryotic membrane protein structural proteome.","abstract":"Most of the 231 unique membrane protein structures (as of 3/2010) are of bacterial membrane proteins (MPs) expressed in bacteria, or eukaryotic MPs from natural sources. However eukaryotic membrane proteins, especially those with more than three membrane crossings rarely succumb to any suitable expression in bacterial cells. They typically require expression in eukaryotic cells that can provide appropriate endoplasmic reticulum, chaperones, targeting and post-translational processing. In evidence, only approximately 20 eukaryotic MP structures have resulted from heterologous expression. This is required for a general approach to target particular human or pathogen membrane proteins of importance to human health. The first of these appeared in 2005. Our review addresses the special issues that pertain to the expression of eukaryotic and human membrane proteins, and recent advances in the tool kit for crystallization and structure determination.","corpus_id":9786205,"score":1},{"doc_id":"21253444","title":"Modeling G Protein-Coupled Receptors: a Concrete Possibility.","abstract":"G protein-coupled receptors (GPCRs) are a large superfamily of membrane bound signaling proteins that are involved in the regulation of a wide range of physiological functions and constitute the most common target for therapeutic intervention. Due to the paucity of crystal structures, homology modeling has become a widespread technique for the construction of GPCR models, which have been applied to the study of their structure-function relationships and to the identification of lead ligands through virtual screening. Rhodopsin has been for years the only available template. However, recent breakthroughs in GPCR crystallography have led to the solution of the structures of a few additional receptors. In light of these newly elucidated crystal structures, we have been able to produce a substantial amount of data to demonstrate that accurate models of GPCRs in complex with their ligands can be constructed through homology modeling followed by fully flexible molecular docking. These results have been confirmed by our success in the first blind assessment of GPCR modeling and docking, organized in coordination with the solution of the X-ray structure of the adenosine A(2A) receptor. Taken together, these data indicate that: a) the transmembrane helical bundle can be modeled with considerable accuracy; b) predicting the binding mode of a ligand, although doable, is challenging; c) modeling of the extracellular and intracellular loops is still problematic.","corpus_id":22758210,"score":1},{"doc_id":"21415888","title":"The impact of structural proteomics on biotechnology.","abstract":"Structural proteomics (SP) projects are capable of producing thousands of protein structures per year by employing semi-automated technologies. It is too early to assess and evaluate the scientific impact of these protein structures, although SP initiatives have substantially changed the traditional way of protein characterization. Many of the methodologies and technologies developed by SP have been adapted by structural biology laboratories and pharmaceutical companies to lower the costs, increase the speed and productivity of structure determination pipelines and to enhance drug discovery programs. The advent of genomic and proteomic technologies have facilitated rapid advances in our understanding of the molecular details of cellular function. The purpose of this review is to consider the impact of these technologies on protein structure analysis and to illustrate how it's directing the focus of research relevant to biotechnology.","corpus_id":5748358,"score":1},{"doc_id":"21824995","title":"The Proteome Folding Project: proteome-scale prediction of structure and function.","abstract":"The incompleteness of proteome structure and function annotation is a critical problem for biologists and, in particular, severely limits interpretation of high-throughput and next-generation experiments. We have developed a proteome annotation pipeline based on structure prediction, where function and structure annotations are generated using an integration of sequence comparison, fold recognition, and grid-computing-enabled de novo structure prediction. We predict protein domain boundaries and three-dimensional (3D) structures for protein domains from 94 genomes (including human, Arabidopsis, rice, mouse, fly, yeast, Escherichia coli, and worm). De novo structure predictions were distributed on a grid of more than 1.5 million CPUs worldwide (World Community Grid). We generated significant numbers of new confident fold annotations (9% of domains that are otherwise unannotated in these genomes). We demonstrate that predicted structures can be combined with annotations from the Gene Ontology database to predict new and more specific molecular functions.","corpus_id":43308922,"score":1},{"doc_id":"22073123","title":"Structural annotation of Mycobacterium tuberculosis proteome.","abstract":"Of the ∼4000 ORFs identified through the genome sequence of Mycobacterium tuberculosis (TB) H37Rv, experimentally determined structures are available for 312. Since knowledge of protein structures is essential to obtain a high-resolution understanding of the underlying biology, we seek to obtain a structural annotation for the genome, using computational methods. Structural models were obtained and validated for ∼2877 ORFs, covering ∼70% of the genome. Functional annotation of each protein was based on fold-based functional assignments and a novel binding site based ligand association. New algorithms for binding site detection and genome scale binding site comparison at the structural level, recently reported from the laboratory, were utilized. Besides these, the annotation covers detection of various sequence and sub-structural motifs and quaternary structure predictions based on the corresponding templates. The study provides an opportunity to obtain a global perspective of the fold distribution in the genome. The annotation indicates that cellular metabolism can be achieved with only 219 folds. New insights about the folds that predominate in the genome, as well as the fold-combinations that make up multi-domain proteins are also obtained. 1728 binding pockets have been associated with ligands through binding site identification and sub-structure similarity analyses. The resource (http://proline.physics.iisc.ernet.in/Tbstructuralannotation), being one of the first to be based on structure-derived functional annotations at a genome scale, is expected to be useful for better understanding of TB and for application in drug discovery. The reported annotation pipeline is fairly generic and can be applied to other genomes as well.","corpus_id":25133690,"score":1},{"doc_id":"23023127","title":"Structure-based prediction of protein-protein interactions on a genome-wide scale.","abstract":"The genome-wide identification of pairs of interacting proteins is an important step in the elucidation of cell regulatory mechanisms. Much of our present knowledge derives from high-throughput techniques such as the yeast two-hybrid assay and affinity purification, as well as from manual curation of experiments on individual systems. A variety of computational approaches based, for example, on sequence homology, gene co-expression and phylogenetic profiles, have also been developed for the genome-wide inference of protein-protein interactions (PPIs). Yet comparative studies suggest that the development of accurate and complete repertoires of PPIs is still in its early stages. Here we show that three-dimensional structural information can be used to predict PPIs with an accuracy and coverage that are superior to predictions based on non-structural evidence. Moreover, an algorithm, termed PrePPI, which combines structural information with other functional clues, is comparable in accuracy to high-throughput experiments, yielding over 30,000 high-confidence interactions for yeast and over 300,000 for human. Experimental tests of a number of predictions demonstrate the ability of the PrePPI algorithm to identify unexpected PPIs of considerable biological interest. The surprising effectiveness of three-dimensional structural information can be attributed to the use of homology models combined with the exploitation of both close and remote geometric relationships between proteins.","corpus_id":3147406,"score":1},{"doc_id":"23445222","title":"G-protein-coupled receptor structure, ligand binding and activation as studied by solid-state NMR spectroscopy.","abstract":"GPCRs (G-protein-coupled receptors) are versatile signalling molecules at the cell surface and make up the largest and most diverse family of membrane receptors in the human genome. They convert a large variety of extracellular stimuli into intracellular responses through the activation of heterotrimeric G-proteins, which make them key regulatory elements in a broad range of normal and pathological processes, and are therefore one of the most important targets for pharmaceutical drug discovery. Knowledge of a GPCR structure enables us to gain a mechanistic insight into its function and dynamics, and further aid rational drug design. Despite intensive research carried out over the last three decades, resolving the structural basis of GPCR function is still a major activity. The crystal structures obtained in the last 5 years provide the first opportunity to understand how protein structure dictates the unique functional properties of these complex signalling molecules. However, owing to the intrinsic hydrophobicity, flexibility and instability of membrane proteins, it is still a challenge to crystallize GPCRs, and, when this is possible, it is no longer in its native membrane environment and no longer without modification. Furthermore, the conformational change of the transmembrane α-helices associated with the structure activation increases the difficulty of capturing the activation state of a GPCR to a higher resolution by X-ray crystallography. On the other hand, solid-state NMR may offer a unique opportunity to study membrane protein structure, ligand binding and activation at atomic resolution in the native membrane environment, as well as described functionally significant dynamics. In the present review, we discuss some recent achievements of solid-state NMR for understanding GPCRs, the largest mammalian proteome at ~1% of the total expressed proteins. Structural information, details of determination, details of ligand conformations and the consequences of ligand binding to initiate activation can all be explored with solid-state NMR.","corpus_id":19311202,"score":1},{"doc_id":"23537065","title":"X-ray structural information of GPCRs in drug design: what are the limitations and where do we go?","abstract":"INTRODUCTION: In 2007, the X-ray structural determination of non-rhodopsin G-Protein coupled receptors (GPCRs), considered the most extensively targeted protein class for marketed drugs, commenced. With the relatively rapid availability of additional structures, an assessment of the progression made is needed in addition to the assessment of the understandings gleaned, deployment successes and forthcoming prospects. AREAS COVERED: The author reviews the approaches and tools that have made it possible to determine the three dimensional structures of GPCRs using X-ray crystallography. Furthermore, the author describes the methods suited for crystallization of membrane bound GPCR proteins including the lipidic cubic phase and various protein modification approaches. The author also provides highlights, from the literature, of the structures determined to date including targets solved, the nature of the content provided (such as selectivity, activating vs. inactivating determinants) and how these structural features relate to drug design strategies. EXPERT OPINION: The GPCR X-ray structures that have been so far determined have yielded significant information. This has presented dramatic evidence concerning their ability to impact the discovery of compounds through their action as traditional, orthosteric modulators. It is, however, noted that more challenging design strategies, such as identifying biased agonists and the use of sites remote from the orthosteric site for allosteric modulation, are still in their infancy.","corpus_id":5394525,"score":1},{"doc_id":"23663289","title":"Discovering putative prion sequences in complete proteomes using probabilistic representations of Q/N-rich domains.","abstract":"BACKGROUND: Prion proteins conform a special class among amyloids due to their ability to transmit aggregative folds. Prions are known to act as infectious agents in neurodegenerative diseases in animals, or as key elements in transcription and translation processes in yeast. It has been suggested that prions contain specific sequential domains with distinctive amino acid composition and physicochemical properties that allow them to control the switch between soluble and β-sheet aggregated states. Those prion-forming domains are low complexity segments enriched in glutamine/asparagine and depleted in charged residues and prolines. Different predictive methods have been developed to discover novel prions by either assessing the compositional bias of these stretches or estimating the propensity of protein sequences to form amyloid aggregates. However, the available algorithms hitherto lack a thorough statistical calibration against large sequence databases, which makes them unable to accurately predict prions without retrieving a large number of false positives. RESULTS: Here we present a computational strategy to predict putative prion-forming proteins in complete proteomes using probabilistic representations of prionogenic glutamine/asparagine rich regions. After benchmarking our predictive model against large sets of non-prionic sequences, we were able to filter out known prions with high precision and accuracy, generating prediction sets with few false positives. The algorithm was used to scan all the proteomes annotated in public databases for the presence of putative prion proteins. We analyzed the presence of putative prion proteins in all taxa, from viruses and archaea to plants and higher eukaryotes, and found that most organisms encode evolutionarily unrelated proteins with susceptibility to behave as prions. CONCLUSIONS: To our knowledge, this is the first wide-ranging study aiming to predict prion domains in complete proteomes. Approaches of this kind could be of great importance to identify potential targets for further experimental testing and to try to reach a deeper understanding of prions' functional and regulatory mechanisms.","corpus_id":3103149,"score":1},{"doc_id":"24474570","title":"Structural genomics studies of human caries pathogen Streptococcus mutans.","abstract":"Gram-positive bacterium Streptococcus mutans is the primary causative agent of human dental caries. To better understand this pathogen at the atomic structure level and to establish potential drug and vaccine targets, we have carried out structural genomics research since 2005. To achieve the goal, we have developed various in-house automation systems including novel high-throughput crystallization equipment and methods, based on which a large-scale, high-efficiency and low-cost platform has been establish in our laboratory. From a total of 1,963 annotated open reading frames, 1,391 non-membrane targets were selected prioritized by protein sequence similarities to unknown structures, and clustered by restriction sites to allow for cost-effective high-throughput conventional cloning. Selected proteins were over-expressed in different strains of Escherichia coli. Clones expressed soluble proteins were selected, expanded, and expressed proteins were purified and subjected to crystallization trials. Finally, protein crystals were subjected to X-ray analysis and structures were determined by crystallographic methods. Using the previously established procedures, we have so far obtained more than 200 kinds of protein crystals and 100 kinds of crystal structures involved in different biological pathways. In this paper we demonstrate and review a possibility of performing structural genomics studies at moderate laboratory scale. Furthermore, the techniques and methods developed in our study can be widely applied to conventional structural biology research practice.","corpus_id":952566,"score":1},{"doc_id":"25950968","title":"Antibody fragments for stabilization and crystallization of G protein-coupled receptors and their signaling complexes.","abstract":"G protein-coupled receptors (GPCRs) are one of the key players in extracellular signal recognition and their subsequent communications with cellular signaling machinery. Crystallization and high-resolution structure determination of GPCRs has been one of the major advances in the area of GPCR biology over the last 7-8 years. There have primarily been three approaches to GPCR crystallization till date. These are fusion protein strategy, thermostabilization, and antibody fragment-mediated crystallization. Of these, antibody fragment-mediated crystallization has not only provided the first breakthrough in structure determination of a non-rhodopsin GPCR but it has also assisted in obtaining structures of fully active conformations of GPCRs. Antibody fragment approach has also been crucial in obtaining structural information on GPCR signaling complexes. Here, we highlight the specific examples of GPCR crystal structures that have utilized antibody fragments for promoting crystallogenesis and structure solution. We also discuss emerging powerful technologies such as the nanobody technology and the synthetic phage display libraries in the context of GPCR crystallization and underline how these tools are likely to propel key GPCR structural studies in future.","corpus_id":19440620,"score":1},{"doc_id":"26105824","title":"Structural Annotation of the Mycobacterium tuberculosis Proteome.","abstract":"Efforts from the TB Structural Genomics Consortium together with those of tuberculosis structural biologists worldwide have led to the determination of about 350 structures, making up nearly a tenth of the pathogen's proteome. Given that knowledge of protein structures is essential to obtaining a high-resolution understanding of the underlying biology, it is desirable to have a structural view of the entire proteome. Indeed, structure prediction methods have advanced sufficiently to allow structural models of many more proteins to be built based on homology modeling and fold recognition strategies. By means of these approaches, structural models for about 2,877 proteins, making up nearly 70% of the Mycobacterium tuberculosis proteome, are available. Knowledge from bioinformatics has made significant inroads into an improved annotation of the M. tuberculosis genome and in the prediction of key protein players that interact in vital pathways, some of which are unique to the organism. Functional inferences have been made for a large number of proteins based on fold-function associations. More importantly, ligand-binding pockets of the proteins are identified and scanned against a large database, leading to binding site-based ligand associations and hence structure-based function annotation. Near proteome-wide structural models provide a global perspective of the fold distribution in the genome. New insights about the folds that predominate in the genome, as well as the fold combinations that make up multidomain proteins, are also obtained. This chapter describes the structural proteome, functional inferences drawn from it, and its applications in drug discovery.","corpus_id":25842598,"score":1},{"doc_id":"26152196","title":"A Molecular Pharmacologist's Guide to G Protein-Coupled Receptor Crystallography.","abstract":"G protein-coupled receptor (GPCR) structural biology has progressed dramatically in the last decade. There are now over 120 GPCR crystal structures deposited in the Protein Data Bank of 32 different receptors from families scattered across the phylogenetic tree, including class B, C, and Frizzled GPCRs. These structures have been obtained in combination with a wide variety of ligands and captured in a range of conformational states. This surge in structural knowledge has enlightened research into the molecular recognition of biologically active molecules, the mechanisms of receptor activation, the dynamics of functional selectivity, and fueled structure-based drug design efforts for GPCRs. Here we summarize the innovations in both protein engineering/molecular biology and crystallography techniques that have led to these advances in GPCR structural biology and discuss how they may influence the resulting structural models. We also provide a brief molecular pharmacologist's guide to GPCR X-ray crystallography, outlining some key aspects in the process of structure determination, with the goal to encourage noncrystallographers to interrogate structures at the molecular level. Finally, we show how chemogenomics approaches can be used to marry the wealth of existing receptor pharmacology data with the expanding repertoire of structures, providing a deeper understanding of the mechanistic details of GPCR function.","corpus_id":33806112,"score":1},{"doc_id":"26578815","title":"Unexpected features of the dark proteome.","abstract":"We surveyed the \"dark\" proteome-that is, regions of proteins never observed by experimental structure determination and inaccessible to homology modeling. For 546,000 Swiss-Prot proteins, we found that 44-54% of the proteome in eukaryotes and viruses was dark, compared with only ∼14% in archaea and bacteria. Surprisingly, most of the dark proteome could not be accounted for by conventional explanations, such as intrinsic disorder or transmembrane regions. Nearly half of the dark proteome comprised dark proteins, in which the entire sequence lacked similarity to any known structure. Dark proteins fulfill a wide variety of functions, but a subset showed distinct and largely unexpected features, such as association with secretion, specific tissues, the endoplasmic reticulum, disulfide bonding, and proteolytic cleavage. Dark proteins also had short sequence length, low evolutionary reuse, and few known interactions with other proteins. These results suggest new research directions in structural and computational biology.","corpus_id":7544524,"score":1},{"doc_id":"27115630","title":"Data Mining of Macromolecular Structures.","abstract":"The use of macromolecular structures is widespread for a variety of applications, from teaching protein structure principles all the way to ligand optimization in drug development. Applying data mining techniques on these experimentally determined structures requires a highly uniform, standardized structural data source. The Protein Data Bank (PDB) has evolved over the years toward becoming the standard resource for macromolecular structures. However, the process selecting the data most suitable for specific applications is still very much based on personal preferences and understanding of the experimental techniques used to obtain these models. In this chapter, we will first explain the challenges with data standardization, annotation, and uniformity in the PDB entries determined by X-ray crystallography. We then discuss the specific effect that crystallographic data quality and model optimization methods have on structural models and how validation tools can be used to make informed choices. We also discuss specific advantages of using the PDB_REDO databank as a resource for structural data. Finally, we will provide guidelines on how to select the most suitable protein structure models for detailed analysis and how to select a set of structure models suitable for data mining.","corpus_id":21804481,"score":1},{"doc_id":"27363390","title":"A De-Novo Genome Analysis Pipeline (DeNoGAP) for large-scale comparative prokaryotic genomics studies.","abstract":"BACKGROUND: Comparative analysis of whole genome sequence data from closely related prokaryotic species or strains is becoming an increasingly important and accessible approach for addressing both fundamental and applied biological questions. While there are number of excellent tools developed for performing this task, most scale poorly when faced with hundreds of genome sequences, and many require extensive manual curation. RESULTS: We have developed a de-novo genome analysis pipeline (DeNoGAP) for the automated, iterative and high-throughput analysis of data from comparative genomics projects involving hundreds of whole genome sequences. The pipeline is designed to perform reference-assisted and de novo gene prediction, homolog protein family assignment, ortholog prediction, functional annotation, and pan-genome analysis using a range of proven tools and databases. While most existing methods scale quadratically with the number of genomes since they rely on pairwise comparisons among predicted protein sequences, DeNoGAP scales linearly since the homology assignment is based on iteratively refined hidden Markov models. This iterative clustering strategy enables DeNoGAP to handle a very large number of genomes using minimal computational resources. Moreover, the modular structure of the pipeline permits easy updates as new analysis programs become available. CONCLUSION: DeNoGAP integrates bioinformatics tools and databases for comparative analysis of a large number of genomes. The pipeline offers tools and algorithms for annotation and analysis of completed and draft genome sequences. The pipeline is developed using Perl, BioPerl and SQLite on Ubuntu Linux version 12.04 LTS. Currently, the software package accompanies script for automated installation of necessary external programs on Ubuntu Linux; however, the pipeline should be also compatible with other Linux and Unix systems after necessary external programs are installed. DeNoGAP is freely available at https://sourceforge.net/projects/denogap/ .","corpus_id":7434744,"score":1},{"doc_id":"29175107","title":"Viruses of archaea: Structural, functional, environmental and evolutionary genomics.","abstract":"Viruses of archaea represent one of the most enigmatic parts of the virosphere. Most of the characterized archaeal viruses infect extremophilic hosts and display remarkable diversity of virion morphotypes, many of which have never been observed among viruses of bacteria or eukaryotes. The uniqueness of the virion morphologies is matched by the distinctiveness of the genomes of these viruses, with ∼75% of genes encoding unique proteins, refractory to functional annotation based on sequence analyses. In this review, we summarize the state-of-the-art knowledge on various aspects of archaeal virus genomics. First, we outline how structural and functional genomics efforts provided valuable insights into the functions of viral proteins and revealed intricate details of the archaeal virus-host interactions. We then highlight recent metagenomics studies, which provided a glimpse at the diversity of uncultivated viruses associated with the ubiquitous archaea in the oceans, including Thaumarchaeota, Marine Group II Euryarchaeota, and others. These findings, combined with the recent discovery that archaeal viruses mediate a rapid turnover of thaumarchaea in the deep sea ecosystems, illuminate the prominent role of these viruses in the biosphere. Finally, we discuss the origins and evolution of archaeal viruses and emphasize the evolutionary relationships between viruses and non-viral mobile genetic elements. Further exploration of the archaeal virus diversity as well as functional studies on diverse virus-host systems are bound to uncover novel, unexpected facets of the archaeal virome.","corpus_id":46841377,"score":1},{"doc_id":"19514836","title":"Human P450s involved in drug metabolism and the use of structural modelling for understanding substrate selectivity and binding affinity.","abstract":"The human cytochrome P450 enzymes and their substrates are reviewed, together with current knowledge on the three-dimensional structures of P450s obtained from X-ray crystallographic studies and from homology modelling based on mammalian P450 template crystal structures. There is a particular focus on human Phase 1 drug metabolism mediated by P450s, and a rationalization of their substrate selectivities and binding strengths in terms of lipophilicity and active site interactions. The combination of molecular modelling and quantitative structure-activity relationship (QSAR) studies facilitates understanding of the factors which determine substrate selectivity and binding to the human drug-metabolizing P450s.","corpus_id":29239172,"score":0},{"doc_id":"19756152","title":"Comparative sequence and structural analyses of G-protein-coupled receptor crystal structures and implications for molecular models.","abstract":"BACKGROUND: Up until recently the only available experimental (high resolution) structure of a G-protein-coupled receptor (GPCR) was that of bovine rhodopsin. In the past few years the determination of GPCR structures has accelerated with three new receptors, as well as squid rhodopsin, being successfully crystallized. All share a common molecular architecture of seven transmembrane helices and can therefore serve as templates for building molecular models of homologous GPCRs. However, despite the common general architecture of these structures key differences do exist between them. The choice of which experimental GPCR structure(s) to use for building a comparative model of a particular GPCR is unclear and without detailed structural and sequence analyses, could be arbitrary. The aim of this study is therefore to perform a systematic and detailed analysis of sequence-structure relationships of known GPCR structures. METHODOLOGY: We analyzed in detail conserved and unique sequence motifs and structural features in experimentally-determined GPCR structures. Deeper insight into specific and important structural features of GPCRs as well as valuable information for template selection has been gained. Using key features a workflow has been formulated for identifying the most appropriate template(s) for building homology models of GPCRs of unknown structure. This workflow was applied to a set of 14 human family A GPCRs suggesting for each the most appropriate template(s) for building a comparative molecular model. CONCLUSIONS: The available crystal structures represent only a subset of all possible structural variation in family A GPCRs. Some GPCRs have structural features that are distributed over different crystal structures or which are not present in the templates suggesting that homology models should be built using multiple templates. This study provides a systematic analysis of GPCR crystal structures and a consistent method for identifying suitable templates for GPCR homology modelling that will help to produce more reliable three-dimensional models.","corpus_id":12095116,"score":0},{"doc_id":"21036924","title":"Parallel proteomics to improve coverage and confidence in the partially annotated Oryctolagus cuniculus mitochondrial proteome.","abstract":"The ability to decipher the dynamic protein component of any system is determined by the inherent limitations of the technologies used, the complexity of the sample, and the existence of an annotated genome. In the absence of an annotated genome, large-scale proteomic investigations can be technically difficult. Yet the functional and biological species differences across animal models can lead to selection of partially or nonannotated organisms over those with an annotated genome. The outweighing of biology over technology leads us to investigate the degree to which a parallel approach can facilitate proteome coverage in the absence of complete genome annotation. When studying species without complete genome annotation, a particular challenge is how to ensure high proteome coverage while meeting the bioinformatic stringencies of high-throughput proteomics. A protein inventory of Oryctolagus cuniculus mitochondria was created by overlapping \"protein-centric\" and \"peptide-centric\" one-dimensional and two-dimensional liquid chromatography strategies; with additional partitioning into membrane-enriched and soluble fractions. With the use of these five parallel approaches, 2934 unique peptides were identified, corresponding to 558 nonredundant protein groups. 230 of these proteins (41%) were identified by only a single technical approach, confirming the need for parallel techniques to improve annotation. To determine the extent of coverage, a side-by-side comparison with human and mouse cardiomyocyte mitochondrial studies was performed. A nonredundant list of 995 discrete proteins was compiled, of which 244 (25%) were common across species. The current investigation identified 142 unique protein groups, the majority of which were detected here by only one technical approach, in particular peptide- and protein-centric two-dimensional liquid chromatography. Although no single approach achieved more than 40% coverage, the combination of three approaches (protein- and peptide-centric two-dimensional liquid chromatography and subfractionation) contributed 96% of all identifications. Parallel techniques ensured minimal false discovery, and reduced single peptide-based identifications while maximizing sequence coverage in the absence of the annotated rabbit proteome.","corpus_id":22633207,"score":0},{"doc_id":"21521153","title":"Comparative modeling: the state of the art and protein drug target structure prediction.","abstract":"The goal of computational protein structure prediction is to provide three-dimensional (3D) structures with resolution comparable to experimental results. Comparative modeling, which predicts the 3D structure of a protein based on its sequence similarity to homologous structures, is the most accurate computational method for structure prediction. In the last two decades, significant progress has been made on comparative modeling methods. Using the large number of protein structures deposited in the Protein Data Bank (~65,000), automatic prediction pipelines are generating a tremendous number of models (~1.9 million) for sequences whose structures have not been experimentally determined. Accurate models are suitable for a wide range of applications, such as prediction of protein binding sites, prediction of the effect of protein mutations, and structure-guided virtual screening. In particular, comparative modeling has enabled structure-based drug design against protein targets with unknown structures. In this review, we describe the theoretical basis of comparative modeling, the available automatic methods and databases, and the algorithms to evaluate the accuracy of predicted structures. Finally, we discuss relevant applications in the prediction of important drug target proteins, focusing on the G protein-coupled receptor (GPCR) and protein kinase families.","corpus_id":25286842,"score":0},{"doc_id":"21605354","title":"GPCR-SSFE: a comprehensive database of G-protein-coupled receptor template predictions and homology models.","abstract":"BACKGROUND: G protein-coupled receptors (GPCRs) transduce a wide variety of extracellular signals to within the cell and therefore have a key role in regulating cell activity and physiological function. GPCR malfunction is responsible for a wide range of diseases including cancer, diabetes and hyperthyroidism and a large proportion of drugs on the market target these receptors. The three dimensional structure of GPCRs is important for elucidating the molecular mechanisms underlying these diseases and for performing structure-based drug design. Although structural data are restricted to only a handful of GPCRs, homology models can be used as a proxy for those receptors not having crystal structures. However, many researchers working on GPCRs are not experienced homology modellers and are therefore unable to benefit from the information that can be gleaned from such three-dimensional models. Here, we present a comprehensive database called the GPCR-SSFE, which provides initial homology models of the transmembrane helices for a large variety of family A GPCRs. DESCRIPTION: Extending on our previous theoretical work, we have developed an automated pipeline for GPCR homology modelling and applied it to a large set of family A GPCR sequences. Our pipeline is a fragment-based approach that exploits available family A crystal structures. The GPCR-SSFE database stores the template predictions, sequence alignments, identified sequence and structure motifs and homology models for 5025 family A GPCRs. Users are able to browse the GPCR dataset according to their pharmacological classification or search for results using a UniProt entry name. It is also possible for a user to submit a GPCR sequence that is not contained in the database for analysis and homology model building. The models can be viewed using a Jmol applet and are also available for download along with the alignments. CONCLUSIONS: The data provided by GPCR-SSFE are useful for investigating general and detailed sequence-structure-function relationships of GPCRs, performing structure-based drug design and for better understanding the molecular mechanisms underlying disease-associated mutations in GPCRs. The effectiveness of our multiple template and fragment approach is demonstrated by the accuracy of our predicted homology models compared to recently published crystal structures.","corpus_id":18225548,"score":0},{"doc_id":"21730144","title":"Reductive evolution of proteomes and protein structures.","abstract":"The lengths of orthologous protein families in Eukarya are almost double the lengths found in Bacteria and Archaea. Here we examine protein structures in 745 genomes and show that protein length differences between superkingdoms arise as much shorter prokaryotic nondomain linker sequences. Eukaryotic, bacterial, and archaeal linkers are 250, 86, and 73 aa residues in length, respectively, whereas folded domain sequences are 281, 280, and 256 residues, respectively. Cryptic domains match linkers (P < 0.0001) with probabilities ranging between 0.022 and 0.042; accordingly, they do not affect length estimates significantly. Linker sequences support intermolecular binding within proteomes and they are probably enriched in intrinsically disordered regions as well. Reductively evolved linker sequence lengths in growth rate maximized cells should be proportional to proteome diversity. By using total in-frame coding capacity of a genome [i.e., coding sequence (CDS)] as a reliable measure of proteome diversity, we find linker lengths of prokaryotes clearly evolve in proportion to CDS values, whereas those of eukaryotes are more randomly larger than expected. Domain lengths scarcely change over the entire range of CDS values. Thus, the protein linkers of prokaryotes evolve reductively whereas those of eukaryotes do not.","corpus_id":35349764,"score":0},{"doc_id":"21903279","title":"GPCR agonist binding revealed by modeling and crystallography.","abstract":"Despite recent progress in structural coverage of the G-protein-coupled receptor (GPCR) family, high plasticity of these membrane proteins poses additional challenges for crystallographic studies of their complexes with different classes of ligands, especially agonists. The ability to predict computationally the binding of natural and clinically relevant agonists and corresponding changes in the receptor pocket, starting from inactive GPCR structures, is therefore of great interest for understanding GPCR biology and drug action. Comparison of computational models published in 2009 and 2010 with recently determined agonist-bound structures of β-adrenergic and adenosine A(2A) receptors reveals high accuracy of the predicted agonist binding poses (0.8 Å and 1.7 Å respectively) and receptor interactions. In the case of the β(2)AR, energy-based models with limited backbone flexibility have also allowed characterization of side-chain rotations and a finite backbone shift in the pocket region as determinants of full, partial or inverse agonism. Development of accurate models of agonist binding for other GPCRs will be instrumental for functional and pharmacological studies, complementing biochemical and crystallographic techniques.","corpus_id":23835678,"score":0},{"doc_id":"22266727","title":"Structure and activation of rhodopsin.","abstract":"Rhodopsin is the first G-protein-coupled receptor (GPCR) with its three-dimensional structure solved by X-ray crystallography. The crystal structure of rhodopsin has revealed the molecular mechanism of photoreception and signal transduction in the visual system. Although several other GPCR crystal structures have been reported over the past few years, the rhodopsin structure remains an important model for understanding the structural and functional characteristics of other GPCRs. This review summarizes the structural features, the photoactivation, and the G protein signal transduction of rhodopsin.","corpus_id":2427513,"score":0},{"doc_id":"22871550","title":"Structural basis for protein synthesis: snapshots of the ribosome in motion.","abstract":"The ribosome undergoes numerous large-scale conformational changes during protein synthesis, but the molecular basis for these changes have been unclear. Recent cryo-electron microscopic and X-ray crystallographic structures of both the bacterial and eukaryotic ribosome now provide snapshots of the wide range of motions that occur within the ribosome. X-ray crystallographic structures of the ribosome have also pinpointed local deformations in ribosomal RNA that occur when the two ribosomal subunits rotate with respect to each other. These structural results establish the foundation for unraveling the mechanics of the ribosome that are universal, and those that differ in bacteria and eukaryotes.","corpus_id":20161470,"score":0},{"doc_id":"23356326","title":"Genomics and biology of Rudiviruses, a model for the study of virus-host interactions in Archaea.","abstract":"Archaeal viruses, especially viruses that infect hyperthermophilic archaea of the phylum Crenarchaeota, constitute one of the least understood parts of the virosphere. However, owing to recent substantial research efforts by several groups, archaeal viruses are starting to gradually reveal their secrets. In the present review, we summarize the current knowledge on one of the emerging model systems for studies on crenarchaeal viruses, the Rudiviridae. We discuss the recent advances towards understanding the function and structure of the proteins encoded by the rudivirus genomes, their role in the virus life cycle, and outline the directions for further research on this model system. In addition, a revised genome annotation of SIRV2 (Sulfolobus islandicus rod-shaped virus 2) is presented. Future studies on archaeal viruses, combined with the knowledge on viruses of bacteria and eukaryotes, should lead to a better global understanding of the diversity and evolution of virus-host interactions in the viral world.","corpus_id":4852943,"score":0},{"doc_id":"24710297","title":"Annotation of Protein Domains Reveals Remarkable Conservation in the Functional Make up of Proteomes Across Superkingdoms.","abstract":"The functional repertoire of a cell is largely embodied in its proteome, the collection of proteins encoded in the genome of an organism. The molecular functions of proteins are the direct consequence of their structure and structure can be inferred from sequence using hidden Markov models of structural recognition. Here we analyze the functional annotation of protein domain structures in almost a thousand sequenced genomes, exploring the functional and structural diversity of proteomes. We find there is a remarkable conservation in the distribution of domains with respect to the molecular functions they perform in the three superkingdoms of life. In general, most of the protein repertoire is spent in functions related to metabolic processes but there are significant differences in the usage of domains for regulatory and extra-cellular processes both within and between superkingdoms. Our results support the hypotheses that the proteomes of superkingdom Eukarya evolved via genome expansion mechanisms that were directed towards innovating new domain architectures for regulatory and extra/intracellular process functions needed for example to maintain the integrity of multicellular structure or to interact with environmental biotic and abiotic factors (e.g., cell signaling and adhesion, immune responses, and toxin production). Proteomes of microbial superkingdoms Archaea and Bacteria retained fewer numbers of domains and maintained simple and smaller protein repertoires. Viruses appear to play an important role in the evolution of superkingdoms. We finally identify few genomic outliers that deviate significantly from the conserved functional design. These include Nanoarchaeum equitans, proteobacterial symbionts of insects with extremely reduced genomes, Tenericutes and Guillardia theta. These organisms spend most of their domains on information functions, including translation and transcription, rather than on metabolism and harbor a domain repertoire characteristic of parasitic organisms. In contrast, the functional repertoire of the proteomes of the Planctomycetes-Verrucomicrobia-Chlamydiae superphylum was no different than the rest of bacteria, failing to support claims of them representing a separate superkingdom. In turn, Protista and Bacteria shared similar functional distribution patterns suggesting an ancestral evolutionary link between these groups.","corpus_id":144996,"score":0},{"doc_id":"25037487","title":"Computational reconstruction of proteome-wide protein interaction networks between HTLV retroviruses and Homo sapiens.","abstract":"BACKGROUND: Human T-cell leukemia viruses (HTLV) tend to induce some fatal human diseases like Adult T-cell Leukemia (ATL) by targeting human T lymphocytes. To indentify the protein-protein interactions (PPI) between HTLV viruses and Homo sapiens is one of the significant approaches to reveal the underlying mechanism of HTLV infection and host defence. At present, as biological experiments are labor-intensive and expensive, the identified part of the HTLV-human PPI networks is rather small. Although recent years have witnessed much progress in computational modeling for reconstructing pathogen-host PPI networks, data scarcity and data unavailability are two major challenges to be effectively addressed. To our knowledge, no computational method for proteome-wide HTLV-human PPI networks reconstruction has been reported. RESULTS: In this work we develop Multi-instance Adaboost method to conduct homolog knowledge transfer for computationally reconstructing proteome-wide HTLV-human PPI networks. In this method, the homolog knowledge in the form of gene ontology (GO) is treated as auxiliary homolog instance to address the problems of data scarcity and data unavailability, while the potential negative knowledge transfer is automatically attenuated by AdaBoost instance reweighting. The cross validation experiments show that the homolog knowledge transfer in the form of independent homolog instances can effectively enrich the feature information and substitute for the missing GO information. Moreover, the independent tests show that the method can validate 70.3% of the recently curated interactions, significantly exceeding the 2.1% recognition rate by the HT-Y2H experiment. We have used the method to reconstruct the proteome-wide HTLV-human PPI networks and further conducted gene ontology based clustering of the predicted networks for further biomedical research. The gene ontology based clustering analysis of the predictions provides much biological insight into the pathogenesis of HTLV retroviruses. CONCLUSIONS: The Multi-instance AdaBoost method can effectively address the problems of data scarcity and data unavailability for the proteome-wide HTLV-human PPI interaction networks reconstruction. The gene ontology based clustering analysis of the predictions reveals some important signaling pathways and biological modules that HTLV retroviruses are likely to target.","corpus_id":8263652,"score":0},{"doc_id":"25911153","title":"ProtoBug: functional families from the complete proteomes of insects.","abstract":"ProtoBug (http://www.protobug.cs.huji.ac.il) is a database and resource of protein families in Arthropod genomes. ProtoBug platform presents the relatedness of complete proteomes from 17 insects as well as a proteome of the crustacean, Daphnia pulex. The represented proteomes from insects include louse, bee, beetle, ants, flies and mosquitoes. Based on an unsupervised clustering method, protein sequences were clustered into a hierarchical tree, called ProtoBug. ProtoBug covers about 300,000 sequences that are partitioned to families. At the default setting, all sequences are partitioned to ∼20,000 families (excluding singletons). From the species perspective, each of the 18 analysed proteomes is composed of 5000-8000 families. In the regime of the advanced operational mode, the ProtoBug provides rich navigation capabilities for touring the hierarchy of the families at any selected resolution. A proteome viewer shows the composition of sequences from any of the 18 analysed proteomes. Using functional annotation from an expert system (Pfam) we assigned domains, families and repeats by 4400 keywords that cover 73% of the sequences. A strict inference protocol is applied for expanding the functional knowledge. Consequently, secured annotations were associated with 81% of the proteins, and with 70% of the families (≥10 proteins each). ProtoBug is a database and webtool with rich visualization and navigation tools. The properties of each family in relation to other families in the ProtoBug tree, and in view of the taxonomy composition are reported. Furthermore, the user can paste its own sequences to find relatedness to any of the ProtoBug families. The database and the navigation tools are the basis for functional discoveries that span 350 million years of evolution of Arthropods. ProtoBug is available with no restriction at: www.protobug.cs.huji.ac.il. Database URL: www.protobug.cs.huji.ac.il","corpus_id":17100459,"score":0},{"doc_id":"28699533","title":"Class A GPCRs: Structure, Function, Modeling and Structure-based Ligand Design.","abstract":"G protein-coupled receptors (GPCRs), especially the class A, are the most heavily investigated drug targets in the pharmaceutical industry. Tremendous efforts have been made by both industry and academia to understand the molecular structure and function of this large family of transmembrane proteins. Our understanding in GPCR activation has evolved from the classical inactive-active two-state model to a complex view of GPCR conformational ensemble associated with multiple interacting partners such as ligands, allosteric modulators, ions and downstream signaling proteins. New drug targets and ligand design strategies are unveiled. Meanwhile, breakthroughs in X-ray crystallography have resulted in high-resolution structures of over 30 GPCRs, providing structural basis for drug design and functional studies. These enabled wide applications of computational approaches in GPCR research have led to several groundbreaking studies in the last few years. While a large fraction of human GPCRs has yet to be crystallized, homology modeling plays a pivotal role in the simulation of these GPCRs. Here, we review the recent updates on class A GPCR structure and function, with a focus on the applications and perspectives of molecular modeling in GPCR ligand design.","corpus_id":22069155,"score":0},{"doc_id":"29163404","title":"Do Viruses Exchange Genes across Superkingdoms of Life?","abstract":"Viruses can be classified into archaeoviruses, bacterioviruses, and eukaryoviruses according to the taxonomy of the infected host. The host-constrained perception of viruses implies preference of genetic exchange between viruses and cellular organisms of their host superkingdoms and viral origins from host cells either via escape or reduction. However, viruses frequently establish non-lytic interactions with organisms and endogenize into the genomes of bacterial endosymbionts that reside in eukaryotic cells. Such interactions create opportunities for genetic exchange between viruses and organisms of non-host superkingdoms. Here, we take an atypical approach to revisit virus-cell interactions by first identifying protein fold structures in the proteomes of archaeoviruses, bacterioviruses, and eukaryoviruses and second by tracing their spread in the proteomes of superkingdoms Archaea, Bacteria, and Eukarya. The exercise quantified protein structural homologies between viruses and organisms of their host and non-host superkingdoms and revealed likely candidates for virus-to-cell and cell-to-virus gene transfers. Unexpected lifestyle-driven genetic affiliations between bacterioviruses and Eukarya and eukaryoviruses and Bacteria were also predicted in addition to a large cohort of protein folds that were universally shared by viral and cellular proteomes and virus-specific protein folds not detected in cellular proteomes. These protein folds provide unique insights into viral origins and evolution that are generally difficult to recover with traditional sequence alignment-dependent evolutionary analyses owing to the fast mutation rates of viral gene sequences.","corpus_id":7589025,"score":0}],"string":"[\n {\n \"doc_id\": \"18542855\",\n \"title\": \"A general target selection method for crystallographic proteomics.\",\n \"abstract\": \"Increasing the success in obtaining structures and maximizing the value of the structures determined are the two major goals of target selection in structural proteomics. This chapter presents an efficient and flexible target selection procedure supplemented with a Web-based resource that is suitable for small- to large-scale structural genomics projects that use crystallography as the major means of structure determination. Based on three criteria, biological significance, structural novelty, and \\\"crystallizability,\\\" the approach first removes (filters) targets that do not meet minimal criteria and then ranks the remaining targets based on their \\\"crystallizability\\\" estimates. This novel procedure was designed to maximize selection efficiency, and its prevailing criteria categories make it suitable for a broad range of structural proteomics projects.\",\n \"corpus_id\": 14432449,\n \"score\": 2\n },\n {\n \"doc_id\": \"18542882\",\n \"title\": \"NMR screening for rapid protein characterization in structural proteomics.\",\n \"abstract\": \"In the age of structural proteomics when protein structures are targeted on a genome-wide scale, the identification of proteins that are amenable to analysis using x-ray crystallography or NMR spectroscopy is the key to high throughput structure determination. NMR screening is a beneficial part of a structural proteomics pipeline because of its ability to provide detailed biophysical information about the protein targets under investigation at an early stage of the structure determination process. This chapter describes efficient methods for the production of uniformly (15)N-labeled proteins for NMR screening using both conventional IPTG induction and autoinduction approaches in E. coli. Details of sample preparation for NMR and the acquisition of 1D (1)H NMR and 2D (1)H-(15)N HSQC spectra to assess the structural characteristics and suitability of proteins for further structural studies are also provided.\",\n \"corpus_id\": 40931011,\n \"score\": 2\n },\n {\n \"doc_id\": \"18563369\",\n \"title\": \"Protein structure determination by x-ray crystallography.\",\n \"abstract\": \"X-ray biocrystallography is the most powerful method to obtain a macromolecular structure. The improvement of computational technologies in recent years and the development of new and powerful computer programs together with the enormous increment in the number of protein structures deposited in the Protein Data Bank, render the resolution of new structures easier than in the past. The aim of this chapter is to provide practical procedures useful for solving a new structure. It is impossible to give more than a flavor of what the x-ray crystallographic technique entails in one brief chapter; therefore, this chapter focuses its attention on the Molecular Replacement method. Whenever applicable, this method allows the resolution of macromolecular structures starting from a single data set and a search model downloaded from the PDB, with the aid only of computer work.\",\n \"corpus_id\": 36064476,\n \"score\": 2\n },\n {\n \"doc_id\": \"18761469\",\n \"title\": \"Structural proteomics by NMR spectroscopy.\",\n \"abstract\": \"Structural proteomics is one of the powerful research areas in the postgenomic era, elucidating structure-function relationships of uncharacterized gene products based on the 3D protein structure. It proposes biochemical and cellular functions of unannotated proteins and thereby identifies potential drug design and protein engineering targets. Recently, a number of pioneering groups in structural proteomics research have achieved proof of structural proteomic theory by predicting the 3D structures of hypothetical proteins that successfully identified the biological functions of those proteins. The pioneering groups made use of a number of techniques, including NMR spectroscopy, which has been applied successfully to structural proteomics studies over the past 10 years. In addition, advances in hardware design, data acquisition methods, sample preparation and automation of data analysis have been developed and successfully applied to high-throughput structure determination techniques. These efforts ensure that NMR spectroscopy will become an important methodology for performing structural proteomics research on a genomic scale. NMR-based structural proteomics together with x-ray crystallography will provide a comprehensive structural database to predict the basic biological functions of hypothetical proteins identified by the genome projects.\",\n \"corpus_id\": 207200996,\n \"score\": 2\n },\n {\n \"doc_id\": \"19465771\",\n \"title\": \"Generalized X-ray and neutron crystallographic analysis: more accurate and complete structures for biological macromolecules.\",\n \"abstract\": \"X-ray and neutron crystallographic techniques provide complementary information on the structure and function of biological macromolecules. X-ray and neutron (XN) crystallographic data have been combined in a joint structure-refinement procedure that has been developed using recent advances in modern computational methodologies, including cross-validated maximum-likelihood target functions with gradient-based optimization and simulated annealing. The XN approach for complete (including hydrogen) macromolecular structure analysis provides more accurate and complete structures, as demonstrated for diisopropyl fluorophosphatase, photoactive yellow protein and human aldose reductase. Furthermore, this method has several practical advantages, including the easier determination of the orientation of water molecules, hydroxyl groups and some amino-acid side chains.\",\n \"corpus_id\": 17111309,\n \"score\": 2\n },\n {\n \"doc_id\": \"19523904\",\n \"title\": \"PSI-2: structural genomics to cover protein domain family space.\",\n \"abstract\": \"One major objective of structural genomics efforts, including the NIH-funded Protein Structure Initiative (PSI), has been to increase the structural coverage of protein sequence space. Here, we present the target selection strategy used during the second phase of PSI (PSI-2). This strategy, jointly devised by the bioinformatics groups associated with the PSI-2 large-scale production centers, targets representatives from large, structurally uncharacterized protein domain families, and from structurally uncharacterized subfamilies in very large and diverse families with incomplete structural coverage. These very large families are extremely diverse both structurally and functionally, and are highly overrepresented in known proteomes. On the basis of several metrics, we then discuss to what extent PSI-2, during its first 3 years, has increased the structural coverage of genomes, and contributed structural and functional novelty. Together, the results presented here suggest that PSI-2 is successfully meeting its objectives and provides useful insights into structural and functional space.\",\n \"corpus_id\": 20208185,\n \"score\": 2\n },\n {\n \"doc_id\": \"19765976\",\n \"title\": \"High-throughput crystallography for structural genomics.\",\n \"abstract\": \"Protein X-ray crystallography recently celebrated its 50th anniversary. The structures of myoglobin and hemoglobin determined by Kendrew and Perutz provided the first glimpses into the complex protein architecture and chemistry. Since then, the field of structural molecular biology has experienced extraordinary progress and now more than 55000 protein structures have been deposited into the Protein Data Bank. In the past decade many advances in macromolecular crystallography have been driven by world-wide structural genomics efforts. This was made possible because of third-generation synchrotron sources, structure phasing approaches using anomalous signal, and cryo-crystallography. Complementary progress in molecular biology, proteomics, hardware and software for crystallographic data collection, structure determination and refinement, computer science, databases, robotics and automation improved and accelerated many processes. These advancements provide the robust foundation for structural molecular biology and assure strong contribution to science in the future. In this report we focus mainly on reviewing structural genomics high-throughput X-ray crystallography technologies and their impact.\",\n \"corpus_id\": 22065223,\n \"score\": 2\n },\n {\n \"doc_id\": \"20443165\",\n \"title\": \"Homology modeling of G-protein-coupled receptors with X-ray structures on the rise.\",\n \"abstract\": \"GPCRs are key components of signal transduction pathways and are important drug targets. Recently determined GPCR structures provide opportunities for advancements in GPCR modeling. This review focuses on the choice of experimental templates, the treatment of extracellular loops and the description of ligand-binding sites in GPCR modeling. Four important conclusions are reached in this review: (i) multi-template models may produce better structures than single-template models, although inferior models may also be generated by multi-template approaches, warranting the development and application of improved model assessment methods; (ii) cautious incorporation of knowledge-based constraints can improve the quality of models and docking; (iii) molecular dynamics simulations account for structural features not observed in X-ray structures and may refine docking poses; and (iv) while progress in de novo methods for long loop prediction is ongoing, loopless models provide a practical alternative for docking and virtual screening applications.\",\n \"corpus_id\": 11837650,\n \"score\": 2\n },\n {\n \"doc_id\": \"21833866\",\n \"title\": \"X-ray crystallography.\",\n \"abstract\": \"X-ray crystallography has been particularly important in the study of the enzyme nitrogenase, providing researchers with high-resolution structural models that have been essential to studying the enzyme's unique metal clusters and nucleotide-binding modes and protein interactions. While several important nitrogenase structures have already been determined using X-ray crystallography, the technique still holds great potential for future significant discoveries involving reaction intermediates and redox states of the enzyme's metal clusters. Thus, it is important to inform future nitrogenase researchers about the procedures for obtaining crystals of nitrogenase component proteins and their complexes and determining their structures. While nitrogenase component proteins from several bacteria have been crystallized, the majority of structures and those of highest resolution are of the nitrogenase proteins from the bacteria Azotobacter vinelandii. Therefore, the bulk of this chapter will focus on methods for crystallization and structure determination of nitrogenase component proteins from A. vinelandii.\",\n \"corpus_id\": 104916134,\n \"score\": 2\n },\n {\n \"doc_id\": \"22354707\",\n \"title\": \"Target selection for structural genomics based on combining fold recognition and crystallisation prediction methods: application to the human proteome.\",\n \"abstract\": \"The objective of this study is to automatically identify regions of the human proteome that are suitable for 3D structure determination by X-ray crystallography and to annotate them according to their likelihood to produce diffraction quality crystals. The results provide a powerful tool for structural genomics laboratories who wish to select human proteins based on the statistical likelihood of crystallisation success. Combining fold recognition and crystallisation prediction algorithms enables the efficient calculation of the crystallisability of the entire human proteome. This novel study estimates that there are approximately 40,000 crystallisable regions in the human proteome. Currently, only 15% of these regions (approx. 6,000 sequences) have been solved to at least 95% sequence identity. The remaining unsolved regions have been categorised into 5 crystallisation classes and an integral membrane protein (IMP) class, based on established structure prediction, crystallisation prediction and transmembrane (TM) helix prediction algorithms. Approximately 750 unsolved regions (2% of the proteome) have been identified as having a PDB fold representative (template) and an 'optimal' likelihood of crystallisation. At the other end of the spectrum, more than 10,500 non-IMP regions with a PDB template are classified as 'very difficult' to crystallise (26%) and almost 2,500 regions (6%) were predicted to contain at least 3 TM helices. The 3D-SPECS (3D Structural Proteomics Explorer with Crystallisation Scores) website contains crystallisation predictions for the entire human proteome and can be found at http://www.bioinformaticsplus.org/3dspecs.\",\n \"corpus_id\": 13282350,\n \"score\": 2\n },\n {\n \"doc_id\": \"23132076\",\n \"title\": \"Determination of soluble and membrane protein structures by X-ray crystallography.\",\n \"abstract\": \"X-ray crystallography is a technique used to determine the atomic-detail structure of a biological macromolecule. The method relies on the ability to generate a three-dimensional crystal of a highly purified protein or nucleic acid for diffraction by X-rays. The extent of scattering of X-rays by the crystal determines the accuracy of the resulting structural model. Unlike electrons, X-rays cannot be refocused after they have been scattered by their target. Thus, calculations are needed to reconstruct the image of the macromolecule that builds the crystal lattice. Tremendous advances over the past 60 years in recombinant expression and purification, crystal growth methods and equipment, X-ray sources, computer processing power, programs, and graphics have taken X-ray crystallography from a highly specialized field to one increasingly accessible to researchers in the biomedical sciences. In this chapter, we review the major concepts of macromolecular X-ray crystallography, focusing mainly on techniques for crystallizing soluble and membrane proteins, and provide a protocol for the crystallization of lysozyme as a model for the crystallization of other proteins.\",\n \"corpus_id\": 29230067,\n \"score\": 2\n },\n {\n \"doc_id\": \"23232152\",\n \"title\": \"Utilization of protein intrinsic disorder knowledge in structural proteomics.\",\n \"abstract\": \"Intrinsically disordered proteins (IDPs) and proteins with long disordered regions are highly abundant in various proteomes. Despite their lack of well-defined ordered structure, these proteins and regions are frequently involved in crucial biological processes. Although in recent years these proteins have attracted the attention of many researchers, IDPs represent a significant challenge for structural characterization since these proteins can impact many of the processes in the structure determination pipeline. Here we investigate the effects of IDPs on the structure determination process and the utility of disorder prediction in selecting and improving proteins for structural characterization. Examination of the extent of intrinsic disorder in existing crystal structures found that relatively few protein crystal structures contain extensive regions of intrinsic disorder. Although intrinsic disorder is not the only cause of crystallization failures and many structured proteins cannot be crystallized, filtering out highly disordered proteins from structure-determination target lists is still likely to be cost effective. Therefore it is desirable to avoid highly disordered proteins from structure-determination target lists and we show that disorder prediction can be applied effectively to enrich structure determination pipelines with proteins more likely to yield crystal structures. For structural investigation of specific proteins, disorder prediction can be used to improve targets for structure determination. Finally, a framework for considering intrinsic disorder in the structure determination pipeline is proposed.\",\n \"corpus_id\": 22301019,\n \"score\": 2\n },\n {\n \"doc_id\": \"23737050\",\n \"title\": \"X-ray crystallography of viruses.\",\n \"abstract\": \"For about 30 years X-ray crystallography has been by far the most powerful approach for determining virus structures at close to atomic resolutions. Information provided by these studies has deeply and extensively enriched and shaped our vision of the virus world. In turn, the ever increasing complexity and size of the virus structures being investigated have constituted a major driving force for methodological and conceptual developments in X-ray macromolecular crystallography. Landmarks of new virus structures determinations, such as the ones from the first animal viruses or from the first membrane-containing viruses, have often been associated to methodological breakthroughs in X-ray crystallography. In this chapter we present the common ground of proteins and virus crystallography with an emphasis in the peculiarities of virus studies. For example, the solution of the phase problem, a central issue in X-ray diffraction, has benefited enormously from the presence of non-crystallographic symmetry in virus crystals.\",\n \"corpus_id\": 24255211,\n \"score\": 2\n },\n {\n \"doc_id\": \"24648090\",\n \"title\": \"Protein structure validation and analysis with X-ray crystallography.\",\n \"abstract\": \"X-ray crystallography is the main technique for the determination of protein structures. About 85 % of all protein structures known to date have been elucidated using X-ray crystallography. Knowledge of the three-dimensional structure of proteins can be used in various applications in biotechnology, biomedicine, drug design, and basic research and as a validation tool for protein modifications, ligand binding, and structural authenticity. Moreover, the requirement for pure, homogeneous, and stable protein solutions in crystallizations makes X-ray crystallography beneficial in other fields of protein research as well. Here, we describe the technique of X-ray protein crystallography and the steps involved for a successful three-dimensional crystal structure determination.\",\n \"corpus_id\": 10634886,\n \"score\": 2\n },\n {\n \"doc_id\": \"25416941\",\n \"title\": \"A glimpse of structural biology through X-ray crystallography.\",\n \"abstract\": \"Since determination of the myoglobin structure in 1957, X-ray crystallography, as the anchoring tool of structural biology, has played an instrumental role in deciphering the secrets of life. Knowledge gained through X-ray crystallography has fundamentally advanced our views on cellular processes and greatly facilitated development of modern medicine. In this brief narrative, I describe my personal understanding of the evolution of structural biology through X-ray crystallography-using as examples mechanistic understanding of protein kinases and integral membrane proteins-and comment on the impact of technological development and outlook of X-ray crystallography.\",\n \"corpus_id\": 28185107,\n \"score\": 2\n },\n {\n \"doc_id\": \"25604506\",\n \"title\": \"X-ray crystallography and its impact on understanding bacterial cell wall remodeling processes.\",\n \"abstract\": \"The molecular structure of matter defines its properties and function. This is especially true for biological macromolecules such as proteins, which participate in virtually all biochemical processes. A three dimensional structural model of a protein is thus essential for the detailed understanding of its physiological function and the characterization of essential properties such as ligand binding and reaction mechanism. X-ray crystallography is a well-established technique that has been used for many years, but it is still by far the most widely used method for structure determination. A particular strength of this technique is the elucidation of atomic details of molecular interactions, thus providing an invaluable tool for a multitude of scientific projects ranging from the structural classification of macromolecules over the validation of enzymatic mechanisms or the understanding of host-pathogen interactions to structure-guided drug design. In the first part of this review, we describe essential methodological and practical aspects of X-ray crystallography. We provide some pointers that should allow researchers without a background in structural biology to assess the overall quality and reliability of a crystal structure. To highlight its potential, we then survey the impact X-ray crystallography has had on advancing an understanding of a class of enzymes that modify the bacterial cell wall. A substantial number of different bacterial amidase structures have been solved, mostly by X-ray crystallography. Comparison of these structures highlights conserved as well as divergent features. In combination with functional analyses, structural information on these enzymes has therefore proven to be a valuable template not only for understanding their mechanism of catalysis, but also for targeted interference with substrate binding.\",\n \"corpus_id\": 205290612,\n \"score\": 2\n },\n {\n \"doc_id\": \"26177814\",\n \"title\": \"X-ray crystallography over the past decade for novel drug discovery - where are we heading next?\",\n \"abstract\": \"INTRODUCTION: Macromolecular X-ray crystallography has been the primary methodology for determining the three-dimensional structures of proteins, nucleic acids and viruses. Structural information has paved the way for structure-guided drug discovery and laid the foundations for structural bioinformatics. However, X-ray crystallography still has a few fundamental limitations, some of which may be overcome and complemented using emerging methods and technologies in other areas of structural biology. AREAS COVERED: This review describes how structural knowledge gained from X-ray crystallography has been used to advance other biophysical methods for structure determination (and vice versa). This article also covers current practices for integrating data generated by other biochemical and biophysical methods with those obtained from X-ray crystallography. Finally, the authors articulate their vision about how a combination of structural and biochemical/biophysical methods may improve our understanding of biological processes and interactions. EXPERT OPINION: X-ray crystallography has been, and will continue to serve as, the central source of experimental structural biology data used in the discovery of new drugs. However, other structural biology techniques are useful not only to overcome the major limitation of X-ray crystallography, but also to provide complementary structural data that is useful in drug discovery. The use of recent advancements in biochemical, spectroscopy and bioinformatics methods may revolutionize drug discovery, albeit only when these data are combined and analyzed with effective data management systems. Accurate and complete data management is crucial for developing experimental procedures that are robust and reproducible.\",\n \"corpus_id\": 35716775,\n \"score\": 2\n },\n {\n \"doc_id\": \"26935210\",\n \"title\": \"The impact of structural genomics: the first quindecennial.\",\n \"abstract\": \"The period 2000-2015 brought the advent of high-throughput approaches to protein structure determination. With the overall funding on the order of $2 billion (in 2010 dollars), the structural genomics (SG) consortia established worldwide have developed pipelines for target selection, protein production, sample preparation, crystallization, and structure determination by X-ray crystallography and NMR. These efforts resulted in the determination of over 13,500 protein structures, mostly from unique protein families, and increased the structural coverage of the expanding protein universe. SG programs contributed over 4400 publications to the scientific literature. The NIH-funded Protein Structure Initiatives alone have produced over 2000 scientific publications, which to date have attracted more than 93,000 citations. Software and database developments that were necessary to handle high-throughput structure determination workflows have led to structures of better quality and improved integrity of the associated data. Organized and accessible data have a positive impact on the reproducibility of scientific experiments. Most of the experimental data generated by the SG centers are freely available to the community and has been utilized by scientists in various fields of research. SG projects have created, improved, streamlined, and validated many protocols for protein production and crystallization, data collection, and functional analysis, significantly benefiting biological and biomedical research.\",\n \"corpus_id\": 2688876,\n \"score\": 2\n },\n {\n \"doc_id\": \"27154589\",\n \"title\": \"NMR in structural genomics to increase structural coverage of the protein universe: Delivered by Prof. Kurt Wüthrich on 7 July 2013 at the 38th FEBS Congress in St. Petersburg, Russia.\",\n \"abstract\": \"For more than a decade, the Joint Center for Structural Genomics (JCSG; www.jcsg.org) worked toward increased three-dimensional structure coverage of the protein universe. This coordinated quest was one of the main goals of the four high-throughput (HT) structure determination centers of the Protein Structure Initiative (PSI; www.nigms.nih.gov/Research/specificareas/PSI). To achieve the goals of the PSI, the JCSG made use of the complementarity of structure determination by X-ray crystallography and nuclear magnetic resonance (NMR) spectroscopy to increase and diversify the range of targets entering the HT structure determination pipeline. The overall strategy, for both techniques, was to determine atomic resolution structures for representatives of large protein families, as defined by the Pfam database, which had no structural coverage and could make significant contributions to biological and biomedical research. Furthermore, the experimental structures could be leveraged by homology modeling to further expand the structural coverage of the protein universe and increase biological insights. Here, we describe what could be achieved by this structural genomics approach, using as an illustration the contributions from 20 NMR structure determinations out of a total of 98 JCSG NMR structures, which were selected because they are the first three-dimensional structure representations of the respective Pfam protein families. The information from this small sample is representative for the overall results from crystal and NMR structure determination in the JCSG. There are five new folds, which were classified as domains of unknown functions (DUF), three of the proteins could be functionally annotated based on three-dimensional structure similarity with previously characterized proteins, and 12 proteins showed only limited similarity with previous deposits in the Protein Data Bank (PDB) and were classified as DUFs.\",\n \"corpus_id\": 30172260,\n \"score\": 2\n },\n {\n \"doc_id\": \"27924015\",\n \"title\": \"TSTMP: target selection for structural genomics of human transmembrane proteins.\",\n \"abstract\": \"The TSTMP database is designed to help the target selection of human transmembrane proteins for structural genomics projects and structure modeling studies. Currently, there are only 60 known 3D structures among the polytopic human transmembrane proteins and about a further 600 could be modeled using existing structures. Although there are a great number of human transmembrane protein structures left to be determined, surprisingly only a small fraction of these proteins have 'selected' (or above) status according to the current version the TargetDB/TargetTrack database. This figure is even worse regarding those transmembrane proteins that would contribute the most to the structural coverage of the human transmembrane proteome. The database was built by sorting out proteins from the human transmembrane proteome with known structure and searching for suitable model structures for the remaining proteins by combining the results of a state-of-the-art transmembrane specific fold recognition algorithm and a sequence similarity search algorithm. Proteins were searched for homologues among the human transmembrane proteins in order to select targets whose successful structure determination would lead to the best structural coverage of the human transmembrane proteome. The pipeline constructed for creating the TSTMP database guarantees to keep the database up-to-date. The database is available at http://tstmp.enzim.ttk.mta.hu.\",\n \"corpus_id\": 11511784,\n \"score\": 2\n },\n {\n \"doc_id\": \"28843631\",\n \"title\": \"Structural Coverage of the Proteome for Pharmaceutical Applications.\",\n \"abstract\": \"Structure-based computational drug discovery efforts have traditionally focused on the structure of a single, well-known drug target. Important applications, such as target deconvolution and the analysis of polypharmacology, require proteome-scale molecular docking and have been inaccessible to structure-based in silico approaches. One important reason for this inaccessibility was that the structure of most proteins was not known. Lately, this 'structure gap' has been closing rapidly, and proteome-scale molecular docking seems within reach. Here, we survey the current state of structural coverage of the human genome and find that coverage is truly proteome-wide, both overall and in most pharmaceutically relevant categories of proteins. The time is right for structure-based approaches to target deconvolution and polypharmacology.\",\n \"corpus_id\": 46294778,\n \"score\": 2\n },\n {\n \"doc_id\": \"29079755\",\n \"title\": \"A proteome view of structural, functional, and taxonomic characteristics of major protein domain clusters.\",\n \"abstract\": \"Proteome-scale bioinformatics research is increasingly conducted as the number of completely sequenced genomes increases, but analysis of protein domains (PDs) usually relies on similarity in their amino acid sequences and/or three-dimensional structures. Here, we present results from a bi-clustering analysis on presence/absence data for 6,580 unique PDs in 2,134 species with a sequenced genome, thus covering a complete set of proteins, for the three superkingdoms of life, Bacteria, Archaea, and Eukarya. Our analysis revealed eight distinctive PD clusters, which, following an analysis of enrichment of Gene Ontology functions and CATH classification of protein structures, were shown to exhibit structural and functional properties that are taxa-characteristic. For examples, the largest cluster is ubiquitous in all three superkingdoms, constituting a set of 1,472 persistent domains created early in evolution and retained in living organisms and characterized by basic cellular functions and ancient structural architectures, while an Archaea and Eukarya bi-superkingdom cluster suggests its PDs may have existed in the ancestor of the two superkingdoms, and others are single superkingdom- or taxa (e.g. Fungi)-specific. These results contribute to increase our appreciation of PD diversity and our knowledge of how PDs are used in species, yielding implications on species evolution.\",\n \"corpus_id\": 3315660,\n \"score\": 2\n },\n {\n \"doc_id\": \"29295714\",\n \"title\": \"fDETECT webserver: fast predictor of propensity for protein production, purification, and crystallization.\",\n \"abstract\": \"BACKGROUND: Development of predictors of propensity of protein sequences for successful crystallization has been actively pursued for over a decade. A few novel methods that expanded the scope of these predictions to address additional steps of protein production and structure determination pipelines were released in recent years. The predictive performance of the current methods is modest. This is because the only input that they use is the protein sequence and since the experimental annotations of these data might be inconsistent given that they were collected across many laboratories and centers. However, even these modest levels of predictive quality are still practical compared to the reported low success rates of crystallization, which are below 10%. We focus on another important aspect related to a high computational cost of running the predictors that offer the expanded scope. RESULTS: We introduce a novel fDETECT webserver that provides very fast and modestly accurate predictions of the success of protein production, purification, crystallization, and structure determination. Empirical tests on two datasets demonstrate that fDETECT is more accurate than the only other similarly fast method, and similarly accurate and three orders of magnitude faster than the currently most accurate predictors. Our method predicts a single protein in about 120 milliseconds and needs less than an hour to generate the four predictions for an entire human proteome. Moreover, we empirically show that fDETECT secures similar levels of predictive performance when compared with four representative methods that only predict success of crystallization, while it also provides the other three predictions. A webserver that implements fDETECT is available at http://biomine.cs.vcu.edu/servers/fDETECT/ . CONCLUSIONS: fDETECT is a computational tool that supports target selection for protein production and X-ray crystallography-based structure determination. It offers predictive quality that matches or exceeds other state-of-the-art tools and is especially suitable for the analysis of large protein sets.\",\n \"corpus_id\": 23971370,\n \"score\": 2\n },\n {\n \"doc_id\": \"18311631\",\n \"title\": \"Internet resources in GPCR modelling.\",\n \"abstract\": \"G-Protein coupled receptors (GPCRs), one of the most important families of drug targets, belong to the super family of integral membrane proteins characterized by seven transmembrane helices. Because they are difficult to crystallize, the three dimensional structure of these receptors have not yet been determined by X-ray crystallography, except one. In the absence of a 3-D structure, in-silico approaches for solving the structure of this class of proteins are widely used and provide valuable information for structure based drug design. There are several web servers and computer programs available that automate the modelling process of GPCRs. Some of these include Modeller, Swiss-Model server, Homer, etc. Using these tools reliable homology models of human histamine H1 receptor (HRH1) and thrombin receptor (PAR-1) have been generated which explain the binding mode of the standard antagonists of these receptors and may be useful in designing their novel antagonists.\",\n \"corpus_id\": 43909951,\n \"score\": 1\n },\n {\n \"doc_id\": \"18542859\",\n \"title\": \"Prediction of protein disorder.\",\n \"abstract\": \"The recent advance in our understanding of the relation of protein structure and function cautions that many proteins, or regions of proteins, exist and function without a well-defined three-dimensional structure. These intrinsically disordered/unstructured proteins (IDP/IUP) are frequent in proteomes and carry out essential functions, but their lack of stable structures hampers efforts of solving structures at high resolution by x-ray crystallography and/or NMR. Thus, filtering such proteins/regions out of high-throughput structural genomics pipelines would be of significant benefit in terms of cost and success rate. This chapter outlines the theoretical background of structural disorder, and provides practical advice on the application of advanced bioinformatic predictors to this end, that is to recognize fully/mostly disordered proteins or regions, which are incompatible with structure determination. An emphasis is also given to a somewhat different approach, in which ordered/disordered regions are explicitly delineated to the end of making constructs amenable for structure determination even when disordered regions are present.\",\n \"corpus_id\": 28242106,\n \"score\": 1\n },\n {\n \"doc_id\": \"18592171\",\n \"title\": \"Plant proteomics.\",\n \"abstract\": \"An understanding of gene function requires a complementation of gene and gene expression analysis by the systematic analysis of proteins. Progress in plant proteomics has been lagging behind animal and microbial proteomics due to the lack of plant genome data and the problems involved in successful protein extraction from plant material. With the sequencing of more and more plant genomes, this slow progress will soon be overcome. The moss Physcomitrella patens is a model organism in the field of plant functional genomics. P. patens is the first seedless plant for which the complete genome was sequenced. Genome annotation is currently in progress. While identification of proteins requires knowledge of all coding genes of the organism under study, gene annotation and functional characterization benefit greatly from the findings of proteome analysis. The proteome of P. patens is accessible and approaches are under way to increase the spectrum of proteomic methods applied to this plant. Here we provide a protocol for the extraction of proteins from P. patens and describe the basic and still most important method of proteome analysis, two-dimensional polyacrylamide electrophoresis of proteins. As this technique (not entirely unjustifiably) has the reputation of being unpredictably complicated, we provide a detailed protocol intended to reduce the reluctance that many scientists may have in using this technique.\",\n \"corpus_id\": 32604142,\n \"score\": 1\n },\n {\n \"doc_id\": \"19061901\",\n \"title\": \"Selecting optimum eukaryotic integral membrane proteins for structure determination by rapid expression and solubilization screening.\",\n \"abstract\": \"A medium-throughput approach is used to rapidly identify membrane proteins from a eukaryotic organism that are most amenable to expression in amounts and quality adequate to support structure determination. The goal was to expand knowledge of new membrane protein structures based on proteome-wide coverage. In the first phase, membrane proteins from the budding yeast Saccharomyces cerevisiae were selected for homologous expression in S. cerevisiae, a system that can be adapted to expression of membrane proteins from other eukaryotes. We performed medium-scale expression and solubilization tests on 351 rationally selected membrane proteins from S. cerevisiae. These targets are inclusive of all annotated and unannotated membrane protein families within the organism's membrane proteome. Two hundred seventy-two targets were expressed, and of these, 234 solubilized in the detergent n-dodecyl-beta-D-maltopyranoside. Furthermore, we report the identity of a subset of targets that were purified to homogeneity to facilitate structure determinations. The extensibility of this approach is demonstrated with the expression of 10 human integral membrane proteins from the solute carrier superfamily. This discovery-oriented pipeline provides an efficient way to select proteins from particular membrane protein classes, families, or organisms that may be more suited to structure analysis than others.\",\n \"corpus_id\": 5108816,\n \"score\": 1\n },\n {\n \"doc_id\": \"19303027\",\n \"title\": \"X-ray crystallography of chemical compounds.\",\n \"abstract\": \"AIMS: Accurate knowledge of molecular structure is a prerequisite for rational drug design. This review examines the role of X-ray crystallography in providing the required structural information and advances in the field of X-ray crystallography that enhance or expand its role. MAIN METHODS: X-ray crystallography of new drugs candidates and intermediates can provide valuable information of new syntheses and parameters for quantitative structure activity relationships (QSAR). KEY FINDINGS: Crystallographic studies play a vital role in many disciplines including materials science, chemistry, pharmacology, and molecular biology. X-ray crystallography is the most comprehensive technique available to determine molecular structure. A requirement for the high accuracy of crystallographic structures is that a 'good crystal' must be found, and this is often the rate-limiting step. In the past three decades developments in detectors, increases in computer power, and powerful graphics capabilities have contributed to a dramatic increase in the number of materials characterized by X-ray crystallography. More recently the advent of high-throughput crystallization techniques has enhanced our ability to produce that one good crystal required for crystallographic analysis. SIGNIFICANCE: Continuing advances in all phases of a crystallographic study have expanded the ranges of samples which can be analyzes by X-ray crystallography to include larger molecules, smaller or weakly diffracting crystals, and twinned crystals.\",\n \"corpus_id\": 206727089,\n \"score\": 1\n },\n {\n \"doc_id\": \"20739007\",\n \"title\": \"Unlocking the eukaryotic membrane protein structural proteome.\",\n \"abstract\": \"Most of the 231 unique membrane protein structures (as of 3/2010) are of bacterial membrane proteins (MPs) expressed in bacteria, or eukaryotic MPs from natural sources. However eukaryotic membrane proteins, especially those with more than three membrane crossings rarely succumb to any suitable expression in bacterial cells. They typically require expression in eukaryotic cells that can provide appropriate endoplasmic reticulum, chaperones, targeting and post-translational processing. In evidence, only approximately 20 eukaryotic MP structures have resulted from heterologous expression. This is required for a general approach to target particular human or pathogen membrane proteins of importance to human health. The first of these appeared in 2005. Our review addresses the special issues that pertain to the expression of eukaryotic and human membrane proteins, and recent advances in the tool kit for crystallization and structure determination.\",\n \"corpus_id\": 9786205,\n \"score\": 1\n },\n {\n \"doc_id\": \"21253444\",\n \"title\": \"Modeling G Protein-Coupled Receptors: a Concrete Possibility.\",\n \"abstract\": \"G protein-coupled receptors (GPCRs) are a large superfamily of membrane bound signaling proteins that are involved in the regulation of a wide range of physiological functions and constitute the most common target for therapeutic intervention. Due to the paucity of crystal structures, homology modeling has become a widespread technique for the construction of GPCR models, which have been applied to the study of their structure-function relationships and to the identification of lead ligands through virtual screening. Rhodopsin has been for years the only available template. However, recent breakthroughs in GPCR crystallography have led to the solution of the structures of a few additional receptors. In light of these newly elucidated crystal structures, we have been able to produce a substantial amount of data to demonstrate that accurate models of GPCRs in complex with their ligands can be constructed through homology modeling followed by fully flexible molecular docking. These results have been confirmed by our success in the first blind assessment of GPCR modeling and docking, organized in coordination with the solution of the X-ray structure of the adenosine A(2A) receptor. Taken together, these data indicate that: a) the transmembrane helical bundle can be modeled with considerable accuracy; b) predicting the binding mode of a ligand, although doable, is challenging; c) modeling of the extracellular and intracellular loops is still problematic.\",\n \"corpus_id\": 22758210,\n \"score\": 1\n },\n {\n \"doc_id\": \"21415888\",\n \"title\": \"The impact of structural proteomics on biotechnology.\",\n \"abstract\": \"Structural proteomics (SP) projects are capable of producing thousands of protein structures per year by employing semi-automated technologies. It is too early to assess and evaluate the scientific impact of these protein structures, although SP initiatives have substantially changed the traditional way of protein characterization. Many of the methodologies and technologies developed by SP have been adapted by structural biology laboratories and pharmaceutical companies to lower the costs, increase the speed and productivity of structure determination pipelines and to enhance drug discovery programs. The advent of genomic and proteomic technologies have facilitated rapid advances in our understanding of the molecular details of cellular function. The purpose of this review is to consider the impact of these technologies on protein structure analysis and to illustrate how it's directing the focus of research relevant to biotechnology.\",\n \"corpus_id\": 5748358,\n \"score\": 1\n },\n {\n \"doc_id\": \"21824995\",\n \"title\": \"The Proteome Folding Project: proteome-scale prediction of structure and function.\",\n \"abstract\": \"The incompleteness of proteome structure and function annotation is a critical problem for biologists and, in particular, severely limits interpretation of high-throughput and next-generation experiments. We have developed a proteome annotation pipeline based on structure prediction, where function and structure annotations are generated using an integration of sequence comparison, fold recognition, and grid-computing-enabled de novo structure prediction. We predict protein domain boundaries and three-dimensional (3D) structures for protein domains from 94 genomes (including human, Arabidopsis, rice, mouse, fly, yeast, Escherichia coli, and worm). De novo structure predictions were distributed on a grid of more than 1.5 million CPUs worldwide (World Community Grid). We generated significant numbers of new confident fold annotations (9% of domains that are otherwise unannotated in these genomes). We demonstrate that predicted structures can be combined with annotations from the Gene Ontology database to predict new and more specific molecular functions.\",\n \"corpus_id\": 43308922,\n \"score\": 1\n },\n {\n \"doc_id\": \"22073123\",\n \"title\": \"Structural annotation of Mycobacterium tuberculosis proteome.\",\n \"abstract\": \"Of the ∼4000 ORFs identified through the genome sequence of Mycobacterium tuberculosis (TB) H37Rv, experimentally determined structures are available for 312. Since knowledge of protein structures is essential to obtain a high-resolution understanding of the underlying biology, we seek to obtain a structural annotation for the genome, using computational methods. Structural models were obtained and validated for ∼2877 ORFs, covering ∼70% of the genome. Functional annotation of each protein was based on fold-based functional assignments and a novel binding site based ligand association. New algorithms for binding site detection and genome scale binding site comparison at the structural level, recently reported from the laboratory, were utilized. Besides these, the annotation covers detection of various sequence and sub-structural motifs and quaternary structure predictions based on the corresponding templates. The study provides an opportunity to obtain a global perspective of the fold distribution in the genome. The annotation indicates that cellular metabolism can be achieved with only 219 folds. New insights about the folds that predominate in the genome, as well as the fold-combinations that make up multi-domain proteins are also obtained. 1728 binding pockets have been associated with ligands through binding site identification and sub-structure similarity analyses. The resource (http://proline.physics.iisc.ernet.in/Tbstructuralannotation), being one of the first to be based on structure-derived functional annotations at a genome scale, is expected to be useful for better understanding of TB and for application in drug discovery. The reported annotation pipeline is fairly generic and can be applied to other genomes as well.\",\n \"corpus_id\": 25133690,\n \"score\": 1\n },\n {\n \"doc_id\": \"23023127\",\n \"title\": \"Structure-based prediction of protein-protein interactions on a genome-wide scale.\",\n \"abstract\": \"The genome-wide identification of pairs of interacting proteins is an important step in the elucidation of cell regulatory mechanisms. Much of our present knowledge derives from high-throughput techniques such as the yeast two-hybrid assay and affinity purification, as well as from manual curation of experiments on individual systems. A variety of computational approaches based, for example, on sequence homology, gene co-expression and phylogenetic profiles, have also been developed for the genome-wide inference of protein-protein interactions (PPIs). Yet comparative studies suggest that the development of accurate and complete repertoires of PPIs is still in its early stages. Here we show that three-dimensional structural information can be used to predict PPIs with an accuracy and coverage that are superior to predictions based on non-structural evidence. Moreover, an algorithm, termed PrePPI, which combines structural information with other functional clues, is comparable in accuracy to high-throughput experiments, yielding over 30,000 high-confidence interactions for yeast and over 300,000 for human. Experimental tests of a number of predictions demonstrate the ability of the PrePPI algorithm to identify unexpected PPIs of considerable biological interest. The surprising effectiveness of three-dimensional structural information can be attributed to the use of homology models combined with the exploitation of both close and remote geometric relationships between proteins.\",\n \"corpus_id\": 3147406,\n \"score\": 1\n },\n {\n \"doc_id\": \"23445222\",\n \"title\": \"G-protein-coupled receptor structure, ligand binding and activation as studied by solid-state NMR spectroscopy.\",\n \"abstract\": \"GPCRs (G-protein-coupled receptors) are versatile signalling molecules at the cell surface and make up the largest and most diverse family of membrane receptors in the human genome. They convert a large variety of extracellular stimuli into intracellular responses through the activation of heterotrimeric G-proteins, which make them key regulatory elements in a broad range of normal and pathological processes, and are therefore one of the most important targets for pharmaceutical drug discovery. Knowledge of a GPCR structure enables us to gain a mechanistic insight into its function and dynamics, and further aid rational drug design. Despite intensive research carried out over the last three decades, resolving the structural basis of GPCR function is still a major activity. The crystal structures obtained in the last 5 years provide the first opportunity to understand how protein structure dictates the unique functional properties of these complex signalling molecules. However, owing to the intrinsic hydrophobicity, flexibility and instability of membrane proteins, it is still a challenge to crystallize GPCRs, and, when this is possible, it is no longer in its native membrane environment and no longer without modification. Furthermore, the conformational change of the transmembrane α-helices associated with the structure activation increases the difficulty of capturing the activation state of a GPCR to a higher resolution by X-ray crystallography. On the other hand, solid-state NMR may offer a unique opportunity to study membrane protein structure, ligand binding and activation at atomic resolution in the native membrane environment, as well as described functionally significant dynamics. In the present review, we discuss some recent achievements of solid-state NMR for understanding GPCRs, the largest mammalian proteome at ~1% of the total expressed proteins. Structural information, details of determination, details of ligand conformations and the consequences of ligand binding to initiate activation can all be explored with solid-state NMR.\",\n \"corpus_id\": 19311202,\n \"score\": 1\n },\n {\n \"doc_id\": \"23537065\",\n \"title\": \"X-ray structural information of GPCRs in drug design: what are the limitations and where do we go?\",\n \"abstract\": \"INTRODUCTION: In 2007, the X-ray structural determination of non-rhodopsin G-Protein coupled receptors (GPCRs), considered the most extensively targeted protein class for marketed drugs, commenced. With the relatively rapid availability of additional structures, an assessment of the progression made is needed in addition to the assessment of the understandings gleaned, deployment successes and forthcoming prospects. AREAS COVERED: The author reviews the approaches and tools that have made it possible to determine the three dimensional structures of GPCRs using X-ray crystallography. Furthermore, the author describes the methods suited for crystallization of membrane bound GPCR proteins including the lipidic cubic phase and various protein modification approaches. The author also provides highlights, from the literature, of the structures determined to date including targets solved, the nature of the content provided (such as selectivity, activating vs. inactivating determinants) and how these structural features relate to drug design strategies. EXPERT OPINION: The GPCR X-ray structures that have been so far determined have yielded significant information. This has presented dramatic evidence concerning their ability to impact the discovery of compounds through their action as traditional, orthosteric modulators. It is, however, noted that more challenging design strategies, such as identifying biased agonists and the use of sites remote from the orthosteric site for allosteric modulation, are still in their infancy.\",\n \"corpus_id\": 5394525,\n \"score\": 1\n },\n {\n \"doc_id\": \"23663289\",\n \"title\": \"Discovering putative prion sequences in complete proteomes using probabilistic representations of Q/N-rich domains.\",\n \"abstract\": \"BACKGROUND: Prion proteins conform a special class among amyloids due to their ability to transmit aggregative folds. Prions are known to act as infectious agents in neurodegenerative diseases in animals, or as key elements in transcription and translation processes in yeast. It has been suggested that prions contain specific sequential domains with distinctive amino acid composition and physicochemical properties that allow them to control the switch between soluble and β-sheet aggregated states. Those prion-forming domains are low complexity segments enriched in glutamine/asparagine and depleted in charged residues and prolines. Different predictive methods have been developed to discover novel prions by either assessing the compositional bias of these stretches or estimating the propensity of protein sequences to form amyloid aggregates. However, the available algorithms hitherto lack a thorough statistical calibration against large sequence databases, which makes them unable to accurately predict prions without retrieving a large number of false positives. RESULTS: Here we present a computational strategy to predict putative prion-forming proteins in complete proteomes using probabilistic representations of prionogenic glutamine/asparagine rich regions. After benchmarking our predictive model against large sets of non-prionic sequences, we were able to filter out known prions with high precision and accuracy, generating prediction sets with few false positives. The algorithm was used to scan all the proteomes annotated in public databases for the presence of putative prion proteins. We analyzed the presence of putative prion proteins in all taxa, from viruses and archaea to plants and higher eukaryotes, and found that most organisms encode evolutionarily unrelated proteins with susceptibility to behave as prions. CONCLUSIONS: To our knowledge, this is the first wide-ranging study aiming to predict prion domains in complete proteomes. Approaches of this kind could be of great importance to identify potential targets for further experimental testing and to try to reach a deeper understanding of prions' functional and regulatory mechanisms.\",\n \"corpus_id\": 3103149,\n \"score\": 1\n },\n {\n \"doc_id\": \"24474570\",\n \"title\": \"Structural genomics studies of human caries pathogen Streptococcus mutans.\",\n \"abstract\": \"Gram-positive bacterium Streptococcus mutans is the primary causative agent of human dental caries. To better understand this pathogen at the atomic structure level and to establish potential drug and vaccine targets, we have carried out structural genomics research since 2005. To achieve the goal, we have developed various in-house automation systems including novel high-throughput crystallization equipment and methods, based on which a large-scale, high-efficiency and low-cost platform has been establish in our laboratory. From a total of 1,963 annotated open reading frames, 1,391 non-membrane targets were selected prioritized by protein sequence similarities to unknown structures, and clustered by restriction sites to allow for cost-effective high-throughput conventional cloning. Selected proteins were over-expressed in different strains of Escherichia coli. Clones expressed soluble proteins were selected, expanded, and expressed proteins were purified and subjected to crystallization trials. Finally, protein crystals were subjected to X-ray analysis and structures were determined by crystallographic methods. Using the previously established procedures, we have so far obtained more than 200 kinds of protein crystals and 100 kinds of crystal structures involved in different biological pathways. In this paper we demonstrate and review a possibility of performing structural genomics studies at moderate laboratory scale. Furthermore, the techniques and methods developed in our study can be widely applied to conventional structural biology research practice.\",\n \"corpus_id\": 952566,\n \"score\": 1\n },\n {\n \"doc_id\": \"25950968\",\n \"title\": \"Antibody fragments for stabilization and crystallization of G protein-coupled receptors and their signaling complexes.\",\n \"abstract\": \"G protein-coupled receptors (GPCRs) are one of the key players in extracellular signal recognition and their subsequent communications with cellular signaling machinery. Crystallization and high-resolution structure determination of GPCRs has been one of the major advances in the area of GPCR biology over the last 7-8 years. There have primarily been three approaches to GPCR crystallization till date. These are fusion protein strategy, thermostabilization, and antibody fragment-mediated crystallization. Of these, antibody fragment-mediated crystallization has not only provided the first breakthrough in structure determination of a non-rhodopsin GPCR but it has also assisted in obtaining structures of fully active conformations of GPCRs. Antibody fragment approach has also been crucial in obtaining structural information on GPCR signaling complexes. Here, we highlight the specific examples of GPCR crystal structures that have utilized antibody fragments for promoting crystallogenesis and structure solution. We also discuss emerging powerful technologies such as the nanobody technology and the synthetic phage display libraries in the context of GPCR crystallization and underline how these tools are likely to propel key GPCR structural studies in future.\",\n \"corpus_id\": 19440620,\n \"score\": 1\n },\n {\n \"doc_id\": \"26105824\",\n \"title\": \"Structural Annotation of the Mycobacterium tuberculosis Proteome.\",\n \"abstract\": \"Efforts from the TB Structural Genomics Consortium together with those of tuberculosis structural biologists worldwide have led to the determination of about 350 structures, making up nearly a tenth of the pathogen's proteome. Given that knowledge of protein structures is essential to obtaining a high-resolution understanding of the underlying biology, it is desirable to have a structural view of the entire proteome. Indeed, structure prediction methods have advanced sufficiently to allow structural models of many more proteins to be built based on homology modeling and fold recognition strategies. By means of these approaches, structural models for about 2,877 proteins, making up nearly 70% of the Mycobacterium tuberculosis proteome, are available. Knowledge from bioinformatics has made significant inroads into an improved annotation of the M. tuberculosis genome and in the prediction of key protein players that interact in vital pathways, some of which are unique to the organism. Functional inferences have been made for a large number of proteins based on fold-function associations. More importantly, ligand-binding pockets of the proteins are identified and scanned against a large database, leading to binding site-based ligand associations and hence structure-based function annotation. Near proteome-wide structural models provide a global perspective of the fold distribution in the genome. New insights about the folds that predominate in the genome, as well as the fold combinations that make up multidomain proteins, are also obtained. This chapter describes the structural proteome, functional inferences drawn from it, and its applications in drug discovery.\",\n \"corpus_id\": 25842598,\n \"score\": 1\n },\n {\n \"doc_id\": \"26152196\",\n \"title\": \"A Molecular Pharmacologist's Guide to G Protein-Coupled Receptor Crystallography.\",\n \"abstract\": \"G protein-coupled receptor (GPCR) structural biology has progressed dramatically in the last decade. There are now over 120 GPCR crystal structures deposited in the Protein Data Bank of 32 different receptors from families scattered across the phylogenetic tree, including class B, C, and Frizzled GPCRs. These structures have been obtained in combination with a wide variety of ligands and captured in a range of conformational states. This surge in structural knowledge has enlightened research into the molecular recognition of biologically active molecules, the mechanisms of receptor activation, the dynamics of functional selectivity, and fueled structure-based drug design efforts for GPCRs. Here we summarize the innovations in both protein engineering/molecular biology and crystallography techniques that have led to these advances in GPCR structural biology and discuss how they may influence the resulting structural models. We also provide a brief molecular pharmacologist's guide to GPCR X-ray crystallography, outlining some key aspects in the process of structure determination, with the goal to encourage noncrystallographers to interrogate structures at the molecular level. Finally, we show how chemogenomics approaches can be used to marry the wealth of existing receptor pharmacology data with the expanding repertoire of structures, providing a deeper understanding of the mechanistic details of GPCR function.\",\n \"corpus_id\": 33806112,\n \"score\": 1\n },\n {\n \"doc_id\": \"26578815\",\n \"title\": \"Unexpected features of the dark proteome.\",\n \"abstract\": \"We surveyed the \\\"dark\\\" proteome-that is, regions of proteins never observed by experimental structure determination and inaccessible to homology modeling. For 546,000 Swiss-Prot proteins, we found that 44-54% of the proteome in eukaryotes and viruses was dark, compared with only ∼14% in archaea and bacteria. Surprisingly, most of the dark proteome could not be accounted for by conventional explanations, such as intrinsic disorder or transmembrane regions. Nearly half of the dark proteome comprised dark proteins, in which the entire sequence lacked similarity to any known structure. Dark proteins fulfill a wide variety of functions, but a subset showed distinct and largely unexpected features, such as association with secretion, specific tissues, the endoplasmic reticulum, disulfide bonding, and proteolytic cleavage. Dark proteins also had short sequence length, low evolutionary reuse, and few known interactions with other proteins. These results suggest new research directions in structural and computational biology.\",\n \"corpus_id\": 7544524,\n \"score\": 1\n },\n {\n \"doc_id\": \"27115630\",\n \"title\": \"Data Mining of Macromolecular Structures.\",\n \"abstract\": \"The use of macromolecular structures is widespread for a variety of applications, from teaching protein structure principles all the way to ligand optimization in drug development. Applying data mining techniques on these experimentally determined structures requires a highly uniform, standardized structural data source. The Protein Data Bank (PDB) has evolved over the years toward becoming the standard resource for macromolecular structures. However, the process selecting the data most suitable for specific applications is still very much based on personal preferences and understanding of the experimental techniques used to obtain these models. In this chapter, we will first explain the challenges with data standardization, annotation, and uniformity in the PDB entries determined by X-ray crystallography. We then discuss the specific effect that crystallographic data quality and model optimization methods have on structural models and how validation tools can be used to make informed choices. We also discuss specific advantages of using the PDB_REDO databank as a resource for structural data. Finally, we will provide guidelines on how to select the most suitable protein structure models for detailed analysis and how to select a set of structure models suitable for data mining.\",\n \"corpus_id\": 21804481,\n \"score\": 1\n },\n {\n \"doc_id\": \"27363390\",\n \"title\": \"A De-Novo Genome Analysis Pipeline (DeNoGAP) for large-scale comparative prokaryotic genomics studies.\",\n \"abstract\": \"BACKGROUND: Comparative analysis of whole genome sequence data from closely related prokaryotic species or strains is becoming an increasingly important and accessible approach for addressing both fundamental and applied biological questions. While there are number of excellent tools developed for performing this task, most scale poorly when faced with hundreds of genome sequences, and many require extensive manual curation. RESULTS: We have developed a de-novo genome analysis pipeline (DeNoGAP) for the automated, iterative and high-throughput analysis of data from comparative genomics projects involving hundreds of whole genome sequences. The pipeline is designed to perform reference-assisted and de novo gene prediction, homolog protein family assignment, ortholog prediction, functional annotation, and pan-genome analysis using a range of proven tools and databases. While most existing methods scale quadratically with the number of genomes since they rely on pairwise comparisons among predicted protein sequences, DeNoGAP scales linearly since the homology assignment is based on iteratively refined hidden Markov models. This iterative clustering strategy enables DeNoGAP to handle a very large number of genomes using minimal computational resources. Moreover, the modular structure of the pipeline permits easy updates as new analysis programs become available. CONCLUSION: DeNoGAP integrates bioinformatics tools and databases for comparative analysis of a large number of genomes. The pipeline offers tools and algorithms for annotation and analysis of completed and draft genome sequences. The pipeline is developed using Perl, BioPerl and SQLite on Ubuntu Linux version 12.04 LTS. Currently, the software package accompanies script for automated installation of necessary external programs on Ubuntu Linux; however, the pipeline should be also compatible with other Linux and Unix systems after necessary external programs are installed. DeNoGAP is freely available at https://sourceforge.net/projects/denogap/ .\",\n \"corpus_id\": 7434744,\n \"score\": 1\n },\n {\n \"doc_id\": \"29175107\",\n \"title\": \"Viruses of archaea: Structural, functional, environmental and evolutionary genomics.\",\n \"abstract\": \"Viruses of archaea represent one of the most enigmatic parts of the virosphere. Most of the characterized archaeal viruses infect extremophilic hosts and display remarkable diversity of virion morphotypes, many of which have never been observed among viruses of bacteria or eukaryotes. The uniqueness of the virion morphologies is matched by the distinctiveness of the genomes of these viruses, with ∼75% of genes encoding unique proteins, refractory to functional annotation based on sequence analyses. In this review, we summarize the state-of-the-art knowledge on various aspects of archaeal virus genomics. First, we outline how structural and functional genomics efforts provided valuable insights into the functions of viral proteins and revealed intricate details of the archaeal virus-host interactions. We then highlight recent metagenomics studies, which provided a glimpse at the diversity of uncultivated viruses associated with the ubiquitous archaea in the oceans, including Thaumarchaeota, Marine Group II Euryarchaeota, and others. These findings, combined with the recent discovery that archaeal viruses mediate a rapid turnover of thaumarchaea in the deep sea ecosystems, illuminate the prominent role of these viruses in the biosphere. Finally, we discuss the origins and evolution of archaeal viruses and emphasize the evolutionary relationships between viruses and non-viral mobile genetic elements. Further exploration of the archaeal virus diversity as well as functional studies on diverse virus-host systems are bound to uncover novel, unexpected facets of the archaeal virome.\",\n \"corpus_id\": 46841377,\n \"score\": 1\n },\n {\n \"doc_id\": \"19514836\",\n \"title\": \"Human P450s involved in drug metabolism and the use of structural modelling for understanding substrate selectivity and binding affinity.\",\n \"abstract\": \"The human cytochrome P450 enzymes and their substrates are reviewed, together with current knowledge on the three-dimensional structures of P450s obtained from X-ray crystallographic studies and from homology modelling based on mammalian P450 template crystal structures. There is a particular focus on human Phase 1 drug metabolism mediated by P450s, and a rationalization of their substrate selectivities and binding strengths in terms of lipophilicity and active site interactions. The combination of molecular modelling and quantitative structure-activity relationship (QSAR) studies facilitates understanding of the factors which determine substrate selectivity and binding to the human drug-metabolizing P450s.\",\n \"corpus_id\": 29239172,\n \"score\": 0\n },\n {\n \"doc_id\": \"19756152\",\n \"title\": \"Comparative sequence and structural analyses of G-protein-coupled receptor crystal structures and implications for molecular models.\",\n \"abstract\": \"BACKGROUND: Up until recently the only available experimental (high resolution) structure of a G-protein-coupled receptor (GPCR) was that of bovine rhodopsin. In the past few years the determination of GPCR structures has accelerated with three new receptors, as well as squid rhodopsin, being successfully crystallized. All share a common molecular architecture of seven transmembrane helices and can therefore serve as templates for building molecular models of homologous GPCRs. However, despite the common general architecture of these structures key differences do exist between them. The choice of which experimental GPCR structure(s) to use for building a comparative model of a particular GPCR is unclear and without detailed structural and sequence analyses, could be arbitrary. The aim of this study is therefore to perform a systematic and detailed analysis of sequence-structure relationships of known GPCR structures. METHODOLOGY: We analyzed in detail conserved and unique sequence motifs and structural features in experimentally-determined GPCR structures. Deeper insight into specific and important structural features of GPCRs as well as valuable information for template selection has been gained. Using key features a workflow has been formulated for identifying the most appropriate template(s) for building homology models of GPCRs of unknown structure. This workflow was applied to a set of 14 human family A GPCRs suggesting for each the most appropriate template(s) for building a comparative molecular model. CONCLUSIONS: The available crystal structures represent only a subset of all possible structural variation in family A GPCRs. Some GPCRs have structural features that are distributed over different crystal structures or which are not present in the templates suggesting that homology models should be built using multiple templates. This study provides a systematic analysis of GPCR crystal structures and a consistent method for identifying suitable templates for GPCR homology modelling that will help to produce more reliable three-dimensional models.\",\n \"corpus_id\": 12095116,\n \"score\": 0\n },\n {\n \"doc_id\": \"21036924\",\n \"title\": \"Parallel proteomics to improve coverage and confidence in the partially annotated Oryctolagus cuniculus mitochondrial proteome.\",\n \"abstract\": \"The ability to decipher the dynamic protein component of any system is determined by the inherent limitations of the technologies used, the complexity of the sample, and the existence of an annotated genome. In the absence of an annotated genome, large-scale proteomic investigations can be technically difficult. Yet the functional and biological species differences across animal models can lead to selection of partially or nonannotated organisms over those with an annotated genome. The outweighing of biology over technology leads us to investigate the degree to which a parallel approach can facilitate proteome coverage in the absence of complete genome annotation. When studying species without complete genome annotation, a particular challenge is how to ensure high proteome coverage while meeting the bioinformatic stringencies of high-throughput proteomics. A protein inventory of Oryctolagus cuniculus mitochondria was created by overlapping \\\"protein-centric\\\" and \\\"peptide-centric\\\" one-dimensional and two-dimensional liquid chromatography strategies; with additional partitioning into membrane-enriched and soluble fractions. With the use of these five parallel approaches, 2934 unique peptides were identified, corresponding to 558 nonredundant protein groups. 230 of these proteins (41%) were identified by only a single technical approach, confirming the need for parallel techniques to improve annotation. To determine the extent of coverage, a side-by-side comparison with human and mouse cardiomyocyte mitochondrial studies was performed. A nonredundant list of 995 discrete proteins was compiled, of which 244 (25%) were common across species. The current investigation identified 142 unique protein groups, the majority of which were detected here by only one technical approach, in particular peptide- and protein-centric two-dimensional liquid chromatography. Although no single approach achieved more than 40% coverage, the combination of three approaches (protein- and peptide-centric two-dimensional liquid chromatography and subfractionation) contributed 96% of all identifications. Parallel techniques ensured minimal false discovery, and reduced single peptide-based identifications while maximizing sequence coverage in the absence of the annotated rabbit proteome.\",\n \"corpus_id\": 22633207,\n \"score\": 0\n },\n {\n \"doc_id\": \"21521153\",\n \"title\": \"Comparative modeling: the state of the art and protein drug target structure prediction.\",\n \"abstract\": \"The goal of computational protein structure prediction is to provide three-dimensional (3D) structures with resolution comparable to experimental results. Comparative modeling, which predicts the 3D structure of a protein based on its sequence similarity to homologous structures, is the most accurate computational method for structure prediction. In the last two decades, significant progress has been made on comparative modeling methods. Using the large number of protein structures deposited in the Protein Data Bank (~65,000), automatic prediction pipelines are generating a tremendous number of models (~1.9 million) for sequences whose structures have not been experimentally determined. Accurate models are suitable for a wide range of applications, such as prediction of protein binding sites, prediction of the effect of protein mutations, and structure-guided virtual screening. In particular, comparative modeling has enabled structure-based drug design against protein targets with unknown structures. In this review, we describe the theoretical basis of comparative modeling, the available automatic methods and databases, and the algorithms to evaluate the accuracy of predicted structures. Finally, we discuss relevant applications in the prediction of important drug target proteins, focusing on the G protein-coupled receptor (GPCR) and protein kinase families.\",\n \"corpus_id\": 25286842,\n \"score\": 0\n },\n {\n \"doc_id\": \"21605354\",\n \"title\": \"GPCR-SSFE: a comprehensive database of G-protein-coupled receptor template predictions and homology models.\",\n \"abstract\": \"BACKGROUND: G protein-coupled receptors (GPCRs) transduce a wide variety of extracellular signals to within the cell and therefore have a key role in regulating cell activity and physiological function. GPCR malfunction is responsible for a wide range of diseases including cancer, diabetes and hyperthyroidism and a large proportion of drugs on the market target these receptors. The three dimensional structure of GPCRs is important for elucidating the molecular mechanisms underlying these diseases and for performing structure-based drug design. Although structural data are restricted to only a handful of GPCRs, homology models can be used as a proxy for those receptors not having crystal structures. However, many researchers working on GPCRs are not experienced homology modellers and are therefore unable to benefit from the information that can be gleaned from such three-dimensional models. Here, we present a comprehensive database called the GPCR-SSFE, which provides initial homology models of the transmembrane helices for a large variety of family A GPCRs. DESCRIPTION: Extending on our previous theoretical work, we have developed an automated pipeline for GPCR homology modelling and applied it to a large set of family A GPCR sequences. Our pipeline is a fragment-based approach that exploits available family A crystal structures. The GPCR-SSFE database stores the template predictions, sequence alignments, identified sequence and structure motifs and homology models for 5025 family A GPCRs. Users are able to browse the GPCR dataset according to their pharmacological classification or search for results using a UniProt entry name. It is also possible for a user to submit a GPCR sequence that is not contained in the database for analysis and homology model building. The models can be viewed using a Jmol applet and are also available for download along with the alignments. CONCLUSIONS: The data provided by GPCR-SSFE are useful for investigating general and detailed sequence-structure-function relationships of GPCRs, performing structure-based drug design and for better understanding the molecular mechanisms underlying disease-associated mutations in GPCRs. The effectiveness of our multiple template and fragment approach is demonstrated by the accuracy of our predicted homology models compared to recently published crystal structures.\",\n \"corpus_id\": 18225548,\n \"score\": 0\n },\n {\n \"doc_id\": \"21730144\",\n \"title\": \"Reductive evolution of proteomes and protein structures.\",\n \"abstract\": \"The lengths of orthologous protein families in Eukarya are almost double the lengths found in Bacteria and Archaea. Here we examine protein structures in 745 genomes and show that protein length differences between superkingdoms arise as much shorter prokaryotic nondomain linker sequences. Eukaryotic, bacterial, and archaeal linkers are 250, 86, and 73 aa residues in length, respectively, whereas folded domain sequences are 281, 280, and 256 residues, respectively. Cryptic domains match linkers (P < 0.0001) with probabilities ranging between 0.022 and 0.042; accordingly, they do not affect length estimates significantly. Linker sequences support intermolecular binding within proteomes and they are probably enriched in intrinsically disordered regions as well. Reductively evolved linker sequence lengths in growth rate maximized cells should be proportional to proteome diversity. By using total in-frame coding capacity of a genome [i.e., coding sequence (CDS)] as a reliable measure of proteome diversity, we find linker lengths of prokaryotes clearly evolve in proportion to CDS values, whereas those of eukaryotes are more randomly larger than expected. Domain lengths scarcely change over the entire range of CDS values. Thus, the protein linkers of prokaryotes evolve reductively whereas those of eukaryotes do not.\",\n \"corpus_id\": 35349764,\n \"score\": 0\n },\n {\n \"doc_id\": \"21903279\",\n \"title\": \"GPCR agonist binding revealed by modeling and crystallography.\",\n \"abstract\": \"Despite recent progress in structural coverage of the G-protein-coupled receptor (GPCR) family, high plasticity of these membrane proteins poses additional challenges for crystallographic studies of their complexes with different classes of ligands, especially agonists. The ability to predict computationally the binding of natural and clinically relevant agonists and corresponding changes in the receptor pocket, starting from inactive GPCR structures, is therefore of great interest for understanding GPCR biology and drug action. Comparison of computational models published in 2009 and 2010 with recently determined agonist-bound structures of β-adrenergic and adenosine A(2A) receptors reveals high accuracy of the predicted agonist binding poses (0.8 Å and 1.7 Å respectively) and receptor interactions. In the case of the β(2)AR, energy-based models with limited backbone flexibility have also allowed characterization of side-chain rotations and a finite backbone shift in the pocket region as determinants of full, partial or inverse agonism. Development of accurate models of agonist binding for other GPCRs will be instrumental for functional and pharmacological studies, complementing biochemical and crystallographic techniques.\",\n \"corpus_id\": 23835678,\n \"score\": 0\n },\n {\n \"doc_id\": \"22266727\",\n \"title\": \"Structure and activation of rhodopsin.\",\n \"abstract\": \"Rhodopsin is the first G-protein-coupled receptor (GPCR) with its three-dimensional structure solved by X-ray crystallography. The crystal structure of rhodopsin has revealed the molecular mechanism of photoreception and signal transduction in the visual system. Although several other GPCR crystal structures have been reported over the past few years, the rhodopsin structure remains an important model for understanding the structural and functional characteristics of other GPCRs. This review summarizes the structural features, the photoactivation, and the G protein signal transduction of rhodopsin.\",\n \"corpus_id\": 2427513,\n \"score\": 0\n },\n {\n \"doc_id\": \"22871550\",\n \"title\": \"Structural basis for protein synthesis: snapshots of the ribosome in motion.\",\n \"abstract\": \"The ribosome undergoes numerous large-scale conformational changes during protein synthesis, but the molecular basis for these changes have been unclear. Recent cryo-electron microscopic and X-ray crystallographic structures of both the bacterial and eukaryotic ribosome now provide snapshots of the wide range of motions that occur within the ribosome. X-ray crystallographic structures of the ribosome have also pinpointed local deformations in ribosomal RNA that occur when the two ribosomal subunits rotate with respect to each other. These structural results establish the foundation for unraveling the mechanics of the ribosome that are universal, and those that differ in bacteria and eukaryotes.\",\n \"corpus_id\": 20161470,\n \"score\": 0\n },\n {\n \"doc_id\": \"23356326\",\n \"title\": \"Genomics and biology of Rudiviruses, a model for the study of virus-host interactions in Archaea.\",\n \"abstract\": \"Archaeal viruses, especially viruses that infect hyperthermophilic archaea of the phylum Crenarchaeota, constitute one of the least understood parts of the virosphere. However, owing to recent substantial research efforts by several groups, archaeal viruses are starting to gradually reveal their secrets. In the present review, we summarize the current knowledge on one of the emerging model systems for studies on crenarchaeal viruses, the Rudiviridae. We discuss the recent advances towards understanding the function and structure of the proteins encoded by the rudivirus genomes, their role in the virus life cycle, and outline the directions for further research on this model system. In addition, a revised genome annotation of SIRV2 (Sulfolobus islandicus rod-shaped virus 2) is presented. Future studies on archaeal viruses, combined with the knowledge on viruses of bacteria and eukaryotes, should lead to a better global understanding of the diversity and evolution of virus-host interactions in the viral world.\",\n \"corpus_id\": 4852943,\n \"score\": 0\n },\n {\n \"doc_id\": \"24710297\",\n \"title\": \"Annotation of Protein Domains Reveals Remarkable Conservation in the Functional Make up of Proteomes Across Superkingdoms.\",\n \"abstract\": \"The functional repertoire of a cell is largely embodied in its proteome, the collection of proteins encoded in the genome of an organism. The molecular functions of proteins are the direct consequence of their structure and structure can be inferred from sequence using hidden Markov models of structural recognition. Here we analyze the functional annotation of protein domain structures in almost a thousand sequenced genomes, exploring the functional and structural diversity of proteomes. We find there is a remarkable conservation in the distribution of domains with respect to the molecular functions they perform in the three superkingdoms of life. In general, most of the protein repertoire is spent in functions related to metabolic processes but there are significant differences in the usage of domains for regulatory and extra-cellular processes both within and between superkingdoms. Our results support the hypotheses that the proteomes of superkingdom Eukarya evolved via genome expansion mechanisms that were directed towards innovating new domain architectures for regulatory and extra/intracellular process functions needed for example to maintain the integrity of multicellular structure or to interact with environmental biotic and abiotic factors (e.g., cell signaling and adhesion, immune responses, and toxin production). Proteomes of microbial superkingdoms Archaea and Bacteria retained fewer numbers of domains and maintained simple and smaller protein repertoires. Viruses appear to play an important role in the evolution of superkingdoms. We finally identify few genomic outliers that deviate significantly from the conserved functional design. These include Nanoarchaeum equitans, proteobacterial symbionts of insects with extremely reduced genomes, Tenericutes and Guillardia theta. These organisms spend most of their domains on information functions, including translation and transcription, rather than on metabolism and harbor a domain repertoire characteristic of parasitic organisms. In contrast, the functional repertoire of the proteomes of the Planctomycetes-Verrucomicrobia-Chlamydiae superphylum was no different than the rest of bacteria, failing to support claims of them representing a separate superkingdom. In turn, Protista and Bacteria shared similar functional distribution patterns suggesting an ancestral evolutionary link between these groups.\",\n \"corpus_id\": 144996,\n \"score\": 0\n },\n {\n \"doc_id\": \"25037487\",\n \"title\": \"Computational reconstruction of proteome-wide protein interaction networks between HTLV retroviruses and Homo sapiens.\",\n \"abstract\": \"BACKGROUND: Human T-cell leukemia viruses (HTLV) tend to induce some fatal human diseases like Adult T-cell Leukemia (ATL) by targeting human T lymphocytes. To indentify the protein-protein interactions (PPI) between HTLV viruses and Homo sapiens is one of the significant approaches to reveal the underlying mechanism of HTLV infection and host defence. At present, as biological experiments are labor-intensive and expensive, the identified part of the HTLV-human PPI networks is rather small. Although recent years have witnessed much progress in computational modeling for reconstructing pathogen-host PPI networks, data scarcity and data unavailability are two major challenges to be effectively addressed. To our knowledge, no computational method for proteome-wide HTLV-human PPI networks reconstruction has been reported. RESULTS: In this work we develop Multi-instance Adaboost method to conduct homolog knowledge transfer for computationally reconstructing proteome-wide HTLV-human PPI networks. In this method, the homolog knowledge in the form of gene ontology (GO) is treated as auxiliary homolog instance to address the problems of data scarcity and data unavailability, while the potential negative knowledge transfer is automatically attenuated by AdaBoost instance reweighting. The cross validation experiments show that the homolog knowledge transfer in the form of independent homolog instances can effectively enrich the feature information and substitute for the missing GO information. Moreover, the independent tests show that the method can validate 70.3% of the recently curated interactions, significantly exceeding the 2.1% recognition rate by the HT-Y2H experiment. We have used the method to reconstruct the proteome-wide HTLV-human PPI networks and further conducted gene ontology based clustering of the predicted networks for further biomedical research. The gene ontology based clustering analysis of the predictions provides much biological insight into the pathogenesis of HTLV retroviruses. CONCLUSIONS: The Multi-instance AdaBoost method can effectively address the problems of data scarcity and data unavailability for the proteome-wide HTLV-human PPI interaction networks reconstruction. The gene ontology based clustering analysis of the predictions reveals some important signaling pathways and biological modules that HTLV retroviruses are likely to target.\",\n \"corpus_id\": 8263652,\n \"score\": 0\n },\n {\n \"doc_id\": \"25911153\",\n \"title\": \"ProtoBug: functional families from the complete proteomes of insects.\",\n \"abstract\": \"ProtoBug (http://www.protobug.cs.huji.ac.il) is a database and resource of protein families in Arthropod genomes. ProtoBug platform presents the relatedness of complete proteomes from 17 insects as well as a proteome of the crustacean, Daphnia pulex. The represented proteomes from insects include louse, bee, beetle, ants, flies and mosquitoes. Based on an unsupervised clustering method, protein sequences were clustered into a hierarchical tree, called ProtoBug. ProtoBug covers about 300,000 sequences that are partitioned to families. At the default setting, all sequences are partitioned to ∼20,000 families (excluding singletons). From the species perspective, each of the 18 analysed proteomes is composed of 5000-8000 families. In the regime of the advanced operational mode, the ProtoBug provides rich navigation capabilities for touring the hierarchy of the families at any selected resolution. A proteome viewer shows the composition of sequences from any of the 18 analysed proteomes. Using functional annotation from an expert system (Pfam) we assigned domains, families and repeats by 4400 keywords that cover 73% of the sequences. A strict inference protocol is applied for expanding the functional knowledge. Consequently, secured annotations were associated with 81% of the proteins, and with 70% of the families (≥10 proteins each). ProtoBug is a database and webtool with rich visualization and navigation tools. The properties of each family in relation to other families in the ProtoBug tree, and in view of the taxonomy composition are reported. Furthermore, the user can paste its own sequences to find relatedness to any of the ProtoBug families. The database and the navigation tools are the basis for functional discoveries that span 350 million years of evolution of Arthropods. ProtoBug is available with no restriction at: www.protobug.cs.huji.ac.il. Database URL: www.protobug.cs.huji.ac.il\",\n \"corpus_id\": 17100459,\n \"score\": 0\n },\n {\n \"doc_id\": \"28699533\",\n \"title\": \"Class A GPCRs: Structure, Function, Modeling and Structure-based Ligand Design.\",\n \"abstract\": \"G protein-coupled receptors (GPCRs), especially the class A, are the most heavily investigated drug targets in the pharmaceutical industry. Tremendous efforts have been made by both industry and academia to understand the molecular structure and function of this large family of transmembrane proteins. Our understanding in GPCR activation has evolved from the classical inactive-active two-state model to a complex view of GPCR conformational ensemble associated with multiple interacting partners such as ligands, allosteric modulators, ions and downstream signaling proteins. New drug targets and ligand design strategies are unveiled. Meanwhile, breakthroughs in X-ray crystallography have resulted in high-resolution structures of over 30 GPCRs, providing structural basis for drug design and functional studies. These enabled wide applications of computational approaches in GPCR research have led to several groundbreaking studies in the last few years. While a large fraction of human GPCRs has yet to be crystallized, homology modeling plays a pivotal role in the simulation of these GPCRs. Here, we review the recent updates on class A GPCR structure and function, with a focus on the applications and perspectives of molecular modeling in GPCR ligand design.\",\n \"corpus_id\": 22069155,\n \"score\": 0\n },\n {\n \"doc_id\": \"29163404\",\n \"title\": \"Do Viruses Exchange Genes across Superkingdoms of Life?\",\n \"abstract\": \"Viruses can be classified into archaeoviruses, bacterioviruses, and eukaryoviruses according to the taxonomy of the infected host. The host-constrained perception of viruses implies preference of genetic exchange between viruses and cellular organisms of their host superkingdoms and viral origins from host cells either via escape or reduction. However, viruses frequently establish non-lytic interactions with organisms and endogenize into the genomes of bacterial endosymbionts that reside in eukaryotic cells. Such interactions create opportunities for genetic exchange between viruses and organisms of non-host superkingdoms. Here, we take an atypical approach to revisit virus-cell interactions by first identifying protein fold structures in the proteomes of archaeoviruses, bacterioviruses, and eukaryoviruses and second by tracing their spread in the proteomes of superkingdoms Archaea, Bacteria, and Eukarya. The exercise quantified protein structural homologies between viruses and organisms of their host and non-host superkingdoms and revealed likely candidates for virus-to-cell and cell-to-virus gene transfers. Unexpected lifestyle-driven genetic affiliations between bacterioviruses and Eukarya and eukaryoviruses and Bacteria were also predicted in addition to a large cohort of protein folds that were universally shared by viral and cellular proteomes and virus-specific protein folds not detected in cellular proteomes. These protein folds provide unique insights into viral origins and evolution that are generally difficult to recover with traditional sequence alignment-dependent evolutionary analyses owing to the fast mutation rates of viral gene sequences.\",\n \"corpus_id\": 7589025,\n \"score\": 0\n }\n]","isConversational":false}}},{"rowIdx":53,"cells":{"query":{"kind":"string","value":"{\n \"doc_id\": \"20018841\",\n \"title\": \"The C terminus of the Alb3 membrane insertase recruits cpSRP43 to the thylakoid membrane.\",\n \"abstract\": \"The YidC/Oxa1/Alb3 family of membrane proteins controls the insertion and assembly of membrane proteins in bacteria, mitochondria, and chloroplasts. Here we describe the molecular mechanisms underlying the interaction of Alb3 with the chloroplast signal recognition particle (cpSRP). The Alb3 C-terminal domain (A3CT) is intrinsically disordered and recruits cpSRP to the thylakoid membrane by a coupled binding and folding mechanism. Two conserved, positively charged motifs reminiscent of chromodomain interaction motifs in histone tails are identified in A3CT that are essential for the Alb3-cpSRP43 interaction. They are absent in the C-terminal domain of Alb4, which therefore does not interact with cpSRP43. Chromodomain 2 in cpSRP43 appears as a central binding platform that can interact simultaneously with A3CT and cpSRP54. The observed negative cooperativity of the two binding events provides the first insights into cargo release at the thylakoid membrane. Taken together, our data show how Alb3 participates in cpSRP-dependent membrane targeting, and our data provide a molecular explanation why Alb4 cannot compensate for the loss of Alb3. Oxa1 and YidC utilize their positively charged, C-terminal domains for ribosome interaction in co-translational targeting. Alb3 is adapted for the chloroplast-specific Alb3-cpSRP43 interaction in post-translational targeting by extending the spectrum of chromodomain interactions.\",\n \"corpus_id\": 46230486\n}"},"candidates":{"kind":"list like","value":[{"doc_id":"18234665","title":"The crystal structure of the periplasmic domain of the Escherichia coli membrane protein insertase YidC contains a substrate binding cleft.","abstract":"In bacteria the biogenesis of inner membrane proteins requires targeting and insertion factors such as the signal recognition particle and the Sec translocon. YidC is an essential membrane protein involved in the insertion of inner membrane proteins together with the Sec translocon, but also as a separate entity. YidC of Escherichia coli is a member of the conserved YidC (in bacteria)/Oxa1 (in mitochondria)/Alb3 (in chloroplasts) protein family and contains six transmembrane segments and a large periplasmic domain (P1). We determined the crystal structure of the periplasmic domain of YidC from E. coli (P1D) at 1.8 A resolution. The structure of P1D shows the conserved beta-supersandwich fold of carbohydrate-binding proteins and an alpha-helical linker region at the C terminus that packs against the beta-supersandwich by a highly conserved interface. P1D exhibits an elongated cleft of similar architecture as found in the structural homologs. However, the electrostatic properties and molecular details of the cleft make it unlikely to interact with carbohydrate substrates. The cleft in P1D is occupied by a polyethylene glycol molecule suggesting an elongated peptide or acyl chain as a natural ligand. The region of P1D previously reported to interact with SecF maps to a surface area in the vicinity of the cleft. The conserved C-terminal region of the P1 domain was reported to be essential for the membrane insertase function of YidC. The analysis of this region suggests a role in membrane interaction and/or in the regulation of YidC interaction with binding partners.","corpus_id":22545719,"score":2},{"doc_id":"18586266","title":"Assembly of chloroplast signal recognition particle involves structural rearrangement in cpSRP43.","abstract":"Signal recognition particle in chloroplasts (cpSRP) exhibits the unusual ability to bind and target full-length proteins to the thylakoid membrane. Unlike cytosolic SRPs in prokaryotes and eukaryotes, cpSRP lacks an RNA moiety and functions as a heterodimer composed of a conserved 54-kDa guanosine triphosphatase (cpSRP54) and a unique 43-kDa subunit (cpSRP43). Assembly of the cpSRP heterodimer is a prerequisite for post-translational targeting activities and takes place through interactions between chromatin modifier domain 2 (CD2) of cpSRP43 and a unique 10-amino-acid region in cpSRP54 (cpSRP54(pep)). We have used multidimensional NMR spectroscopy and other biophysical methods to examine the assembly and structure of the cpSRP43-cpSRP54 interface. Our data show that CD2 of cpSRP43 binds to cpSRP54(pep) in a 1:1 stoichiometry with an apparent K(d) of approximately 1.06 muM. Steady-state fluorescence and far-UV circular dichroism data suggest that the CD2-cpSRP54(pep) interaction causes significant conformational changes in both CD2 and the peptide. Comparison of the three-dimensional solution structures of CD2 alone and in complex with cpSRP54(pep) shows that significant structural changes are induced in CD2 in order to establish a binding interface contributed mostly by residues in the N-terminal segment of CD2 (Phe5-Val10) and an arginine doublet (Arg536 and Arg537) in the cpSRP54 peptide. Taken together, our results provide new insights into the mechanism of cpSRP assembly and the structural forces that stabilize the functionally critical cpSRP43-cpSRP54 interaction.","corpus_id":10283219,"score":2},{"doc_id":"18621669","title":"Structural basis for specific substrate recognition by the chloroplast signal recognition particle protein cpSRP43.","abstract":"Secretory and membrane proteins carry amino-terminal signal sequences that, in cotranslational targeting, are recognized by the signal recognition particle protein SRP54 without sequence specificity. The most abundant membrane proteins on Earth are the light-harvesting chlorophyll a/b binding proteins (LHCPs). They are synthesized in the cytoplasm, imported into the chloroplast, and posttranslationally targeted to the thylakoid membrane by cpSRP, a heterodimer formed by cpSRP54 and cpSRP43. We present the 1.5 angstrom crystal structure of cpSRP43 characterized by a unique arrangement of chromodomains and ankyrin repeats. The overall shape and charge distribution of cpSRP43 resembles the SRP RNA, which is absent in chloroplasts. The complex with the internal signal sequence of LHCPs reveals that cpSRP43 specifically recognizes a DPLG peptide motif. We describe how cpSPR43 adapts the universally conserved SRP system to posttranslational targeting and insertion of the LHCP family of membrane proteins.","corpus_id":206513119,"score":2},{"doc_id":"18633119","title":"Quantitative proteomics of a chloroplast SRP54 sorting mutant and its genetic interactions with CLPC1 in Arabidopsis.","abstract":"cpSRP54 (for chloroplast SIGNAL RECOGNITION PARTICLE54) is involved in cotranslational and posttranslational sorting of thylakoid proteins. The Arabidopsis (Arabidopsis thaliana) cpSRP54 null mutant, ffc1-2, is pale green with delayed development. Western-blot analysis of individual leaves showed that the SRP sorting pathway, but not the SecY/E translocon, was strongly down-regulated with progressive leaf development in both wild-type and ffc1-2 plants. To further understand the impact of cpSRP54 deletion, a quantitative comparison of ffc2-1 was carried out for total leaf proteomes of young seedlings and for chloroplast proteomes of fully developed leaves using stable isotope labeling (isobaric stable isotope labeling and isotope-coded affinity tags) and two-dimensional gels. This showed that cpSRP54 deletion led to a change in light-harvesting complex composition, an increase of PsbS, and a decreased photosystem I/II ratio. Moreover, the cpSRP54 deletion led in young leaves to up-regulation of thylakoid proteases and stromal chaperones, including ClpC. In contrast, the stromal protein homeostasis machinery returned to wild-type levels in mature leaves, consistent with the developmental down-regulation of the SRP pathway. A differential response between young and mature leaves was also found in carbon metabolism, with an up-regulation of the Calvin cycle and the photorespiratory pathway in peroxisomes and mitochondria in young leaves but not in old leaves. The Calvin cycle was down-regulated in mature leaves to adjust to the reduced capacity of the light reaction, while reactive oxygen species defense proteins were up-regulated. The significance of ClpC up-regulation was confirmed through the generation of an ffc2-1 clpc1 double mutant. This mutant was seedling lethal under autotrophic conditions but could be partially rescued under heterotrophic conditions.","corpus_id":42791587,"score":2},{"doc_id":"18755190","title":"Evolutionary substitution of two amino acids in chloroplast SRP54 of higher plants cause its inability to bind SRP RNA.","abstract":"The chloroplast signal recognition particle (cpSRP) consists of a conserved 54 kDa subunit (cpSRP54) and a unique 43 kDa subunit (cpSRP43) but lacks SRP-RNA, an essential and universally conserved component of cytosolic SRPs. High sequence similarity exists between cpSRP54 and bacterial SRP54 except for a plant-specific C-terminal extension containing the cpSRP43-binding motif. We found that cpSRP54 of higher plants lacks the ability to bind SRP-RNA because of two amino acid substitutions within a region corresponding to the RNA binding domain of cytosolic SRP54, whereas the C-terminal extension does not affect RNA binding. Phylogenetic analysis revealed that these mutations occur in the cpSRP54 homologues of higher plants but not in most algae.","corpus_id":1569836,"score":2},{"doc_id":"18764927","title":"Non-identical contributions of two membrane-bound cpSRP components, cpFtsY and Alb3, to thylakoid biogenesis.","abstract":"The insertion of light-harvesting chlorophyll proteins (LHCPs) into the thylakoid membrane of the chloroplast is cpSRP-dependent, and requires the stromal components cpSRP54 and cpSRP43, the membrane-bound SRP receptor cpFtsY and the integral membrane protein Alb3. Previous studies demonstrated that the Arabidopsis mutant lacking both cpSRP54 and cpSRP43 had pale yellow leaves, but was viable, whereas the mutants lacking Alb3 exhibit an albino phenotype that is more severe and seedling lethality. We previously showed that a maize mutant lacking cpFtsY had a pale yellow-green phenotype and was seedling lethal. To compare the in vivo requirements of cpFtsY and Alb3 in thylakoid biogenesis in greater detail, we isolated Arabidopsis null mutants of cpftsY, and performed biochemical comparisons with the Arabidopsis alb3 mutant. Both cpftsY and alb3 null mutants were seedling lethal on a synthetic medium lacking sucrose, whereas on a medium supplemented with sucrose, they were able to grow to later developmental stages, but were mostly infertile. cpftsY mutant plants had yellow leaves in which the levels of LHCPs were reduced to 10-33% compared with wild type. In contrast, alb3 had yellowish white leaves, and the LHCP levels were less than or equal to 10% of those of wild type. Intriguingly, whereas accumulation of the Sec and Tat machineries were normal in both mutants, the Sec pathway substrate Cyt f was more severely decreased in the cpftsY mutant than in alb3, which may indicate a functional link between cpFtsY and Sec translocation machinery. These results suggest that cpFtsY and Alb3 have essentially similar, but slightly distinct, contributions to thylakoid biogenesis.","corpus_id":28676639,"score":2},{"doc_id":"19293157","title":"The membrane-binding motif of the chloroplast signal recognition particle receptor (cpFtsY) regulates GTPase activity.","abstract":"The chloroplast signal recognition particle (cpSRP) and its receptor (cpFtsY) function in thylakoid biogenesis to target integral membrane proteins to thylakoids. Unlike cytosolic SRP receptors in eukaryotes, cpFtsY partitions between thylakoid membranes and the soluble stroma. Based on sequence alignments, a membrane-binding motif identified in Escherichia coli FtsY appears to be conserved in cpFtsY, yet whether the proposed motif is responsible for the membrane-binding function of cpFtsY has yet to be shown experimentally. Our studies show that a small N-terminal region in cpFtsY stabilizes a membrane interaction critical to cpFtsY function in cpSRP-dependent protein targeting. This membrane-binding motif is both necessary and sufficient to direct cpFtsY and fused passenger proteins to thylakoids. Our results demonstrate that the cpFtsY membrane-binding motif may be functionally replaced by the corresponding region from E. coli, confirming that the membrane-binding motif is conserved among organellar and prokaryotic homologs. Furthermore, the capacity of cpFtsY for lipid binding correlates with liposome-induced GTP hydrolysis stimulation. Mutations that debilitate the membrane-binding motif in cpFtsY result in higher rates of GTP hydrolysis, suggesting that negative regulation is provided by the intact membrane-binding region in the absence of a bilayer. Furthermore, NMR and CD structural studies of the N-terminal region and the analogous region in the E. coli SRP receptor revealed a conformational change in secondary structure that takes place upon lipid binding. These studies suggest that the cpFtsY membrane-binding motif plays a critical role in the intramolecular communication that regulates cpSRP receptor functions at the membrane.","corpus_id":39255863,"score":2},{"doc_id":"19366667","title":"Independent gene duplications of the YidC/Oxa/Alb3 family enabled a specialized cotranslational function.","abstract":"YidC/Oxa/Alb3 family proteins catalyze the insertion of integral membrane proteins in bacteria, mitochondria, and chloroplasts, respectively. Unlike gram-negative organisms, gram-positive bacteria express 2 paralogs of this family, YidC1/SpoIIIJ and YidC2/YgjG. In Streptococcus mutans, deletion of yidC2 results in a stress-sensitive phenotype similar to that of mutants lacking the signal recognition particle (SRP) protein translocation pathway, while deletion of yidC1 has a less severe phenotype. In contrast to eukaryotes and gram-negative bacteria, SRP-deficient mutants are viable in S. mutans; however, double SRP-yidC2 mutants are severely compromised. Thus, YidC2 may enable loss of the SRP by playing an independent but overlapping role in cotranslational protein insertion into the membrane. This is reminiscent of the situation in mitochondria that lack an SRP pathway and where Oxa1 facilitates cotranslational membrane protein insertion by binding directly to translation-active ribosomes. Here, we show that OXA1 complements a lack of yidC2 in S. mutans. YidC2 also functions reciprocally in oxa1-deficient Saccharomyces cerevisiae mutants and mediates the cotranslational insertion of mitochondrial translation products into the inner membrane. YidC2, like Oxa1, contains a positively charged C-terminal extension and associates with translating ribosomes. Our results are consistent with a gene-duplication event in gram-positive bacteria that enabled the specialization of a YidC isoform that mediates cotranslational activity independent of an SRP pathway.","corpus_id":23829375,"score":2},{"doc_id":"19534824","title":"The evolution of YidC/Oxa/Alb3 family in the three domains of life: a phylogenomic analysis.","abstract":"BACKGROUND: YidC/Oxa/Alb3 family includes a group of conserved translocases that are essential for protein insertion into inner membranes of bacteria and mitochondria, and thylakoid membranes of chloroplasts. Because mitochondria and chloroplasts are of bacterial origin, Oxa and Alb3, like many other mitochondrial/chloroplastic proteins, are hypothetically derived from the pre-existing protein (YidC) of bacterial endosymbionts. Here, we test this hypothesis and investigate the evolutionary history of the whole YidC/Oxa/Alb3 family in the three domains of life. RESULTS: Our comprehensive analyses of the phylogenetic distribution and phylogeny of the YidC/Oxa/Alb3 family lead to the following findings: 1) In archaea, YidC homologs are only sporadically distributed in Euryarchaeota; 2) Most bacteria contain only one YidC gene copy; some species in a few taxa (Bacillus, Lactobacillales, Actinobacteria and Clostridia) have two gene copies; 3) Eukaryotic Oxa and Alb3 have two separate prokaryotic origins, but they might not arise directly from the YidC of proteobacteria and cyanobacteria through the endosymbiosis origins of mitochondrium and chloroplast, respectively; 4) An ancient duplication occurred on both Oxa and Alb3 immediately after their origins, and thus most eukaryotes generally bear two Oxa and two Alb3. However, secondary loss, duplication or acquisition of new domain also occurred on the two genes in some lineages, especially in protists, resulting in a rich diversity or adaptive differentiation of the two translocases in these lineages. CONCLUSION: YidC is distributed in bacteria and some Euryarchaeota. Although mitochondrial Oxa and chloroplastic Alb3 are derived from the prokaryotic YidC, their origin might be not related to the endosymbiosis events of the two organelles. In some eukaryotic lineages, especially in protists, Oxa and Alb3 have diverse evolutionary histories. Finally, a model for the evolutionary history of the entire YidC/Oxa/Alb3 family in the three domains of life is proposed.","corpus_id":-1,"score":2},{"doc_id":"19995738","title":"Alb4 of Arabidopsis promotes assembly and stabilization of a non chlorophyll-binding photosynthetic complex, the CF1CF0-ATP synthase.","abstract":"All members of the YidC/Oxa1/Alb3 protein family are evolutionarily conserved and appear to function in membrane protein integration and protein complex stabilization. Here, we report on a second thylakoidal isoform of Alb3, named Alb4. Analysis of Arabidopsis knockout mutant lines shows that Alb4 is required in assembly and/or stability of the CF1CF0-ATP synthase (ATPase). alb4 mutant lines not only have reduced steady-state levels of ATPase subunits, but also their assembly into high-molecular-mass complexes is altered, leading to a reduction of ATP synthesis in the mutants. Moreover, we show that Alb4 but not Alb3 physically interacts with the subunits CF1beta and CF0II. Summarizing, the data indicate that Alb4 functions to stabilize or promote assembly of CF1 during its attachment to the membrane-embedded CF0 part.","corpus_id":281657,"score":2},{"doc_id":"20498370","title":"cpSRP43 is a novel chaperone specific for light-harvesting chlorophyll a,b-binding proteins.","abstract":"The biosynthesis of most membrane proteins is directly coupled to membrane insertion, and therefore, molecular chaperones are not required. The light-harvesting chlorophyll a,b-binding proteins (LHCPs) present a prominent exception as they are synthesized in the cytoplasm, and after import into the chloroplast, they are targeted and inserted into the thylakoid membrane. Upon arrival in the stroma, LHCPs form a soluble transit complex with the chloroplast signal recognition particle (cpSRP) consisting of an SRP54 homolog and the unique cpSRP43 composed of three chromodomains and four ankyrin repeats. Here we describe that cpSRP43 alone prevents aggregation of LHCP by formation of a complex with nanomolar affinity, whereas cpSRP54 is not required for this chaperone activity. Other stromal chaperones like trigger factor cannot replace cpSRP43, which implies that LHCPs require a specific chaperone. Although cpSRP43 does not have an ATPase activity, it can dissolve aggregates of LHCPs similar to chaperones of the Hsp104/ClpB family. We show that the LHCP-cpSRP43 interaction is predominantly hydrophobic but strictly depends on an intact DPLG motif between the second and third transmembrane region. The cpSRP43 ankyrin repeats that provide the binding site for the DPLG motif are sufficient for the chaperone function, whereas the chromodomains are dispensable. Taken together, we define cpSRP43 as a highly specific chaperone for LHCPs in addition to its established function as a targeting factor for this family of membrane proteins.","corpus_id":12037009,"score":2},{"doc_id":"20709425","title":"Component interactions, regulation and mechanisms of chloroplast signal recognition particle-dependent protein transport.","abstract":"The chloroplast proteome comprises nuclear- and plastome-encoded proteins. In order to function correctly these proteins must be transported, either cotranslationally or posttranslationally, to their final destination in the chloroplast. Here the chloroplast signal recognition particle (cpSRP) which is present in two different stromal pools plays an essential role. On the one hand, the conserved 54kDa subunit (cpSRP54) is associated with 70S ribosomes to function in the cotranslational transport of the plastid-encoded thylakoid membrane protein D1. On the other hand, the cpSRP consists of cpSRP54 and a unique 43kDa subunit (cpSRP43) and facilitates the transport of nuclear-encoded light-harvesting chlorophyll-binding proteins (LHCPs), the most abundant membrane proteins of the thylakoids. In addition to cpSRP, the cpSRP receptor cpFtsY and the thylakoid membrane protein Alb3 are required for posttranslational LHCP integration in a GTP-dependent manner. In contrast to the universally conserved cytosolic SRP, the chloroplast SRP of higher plants lacks an SRP-RNA component. Interestingly, cpSRP-RNA genes have been identified in the plastome of lower plants, indicating that their cpSRP structure resembles the cytosolic SRP.","corpus_id":40931935,"score":2},{"doc_id":"20729200","title":"A dynamic cpSRP43-Albino3 interaction mediates translocase regulation of chloroplast signal recognition particle (cpSRP)-targeting components.","abstract":"The chloroplast signal recognition particle (cpSRP) and its receptor, chloroplast FtsY (cpFtsY), form an essential complex with the translocase Albino3 (Alb3) during post-translational targeting of light-harvesting chlorophyll-binding proteins (LHCPs). Here, we describe a combination of studies that explore the binding interface and functional role of a previously identified cpSRP43-Alb3 interaction. Using recombinant proteins corresponding to the C terminus of Alb3 (Alb3-Cterm) and various domains of cpSRP43, we identify the ankyrin repeat region of cpSRP43 as the domain primarily responsible for the interaction with Alb3-Cterm. Furthermore, we show Alb3-Cterm dissociates a cpSRP·LHCP targeting complex in vitro and stimulates GTP hydrolysis by cpSRP54 and cpFtsY in a strictly cpSRP43-dependent manner. These results support a model in which interactions between the ankyrin region of cpSRP43 and the C terminus of Alb3 promote distinct membrane-localized events, including LHCP release from cpSRP and release of targeting components from Alb3.","corpus_id":35780521,"score":2},{"doc_id":"20800571","title":"Inserting membrane proteins: the YidC/Oxa1/Alb3 machinery in bacteria, mitochondria, and chloroplasts.","abstract":"The evolutionarily conserved YidC/Oxa1p/Alb3 family of proteins plays important roles in the membrane biogenesis in bacteria, mitochondria, and chloroplasts. The members in this family function as novel membrane protein insertases, chaperones, and assembly factors for transmembrane proteins, including energy transduction complexes localized in the bacterial and mitochondrial inner membrane, and in the chloroplast thylakoid membrane. In this review, we will present recent progress with this class of proteins in membrane protein biogenesis and discuss the structure/function relationships. This article is part of a Special Issue entitled Protein translocation across or insertion into membranes.","corpus_id":41093923,"score":2},{"doc_id":"20828566","title":"Interplay between the cpSRP pathway components, the substrate LHCP and the translocase Alb3: an in vivo and in vitro study.","abstract":"The chloroplast signal recognition particle (cpSRP) and its receptor, cpFtsY, posttranslationally target the nuclear-encoded light-harvesting chlorophyll-binding proteins (LHCPs) to the translocase Alb3 in the thylakoid membrane. In this study, we analyzed the interplay between the cpSRP pathway components, the substrate protein LHCP and the translocase Alb3 by using in vivo and in vitro techniques. We propose that cpSRP43 is crucial for the binding of LHCP-loaded cpSRP and cpFtsY to Alb3. In addition, our data suggest that a direct interaction between Alb3 and LHCP contributes to the formation of this complex.","corpus_id":37536189,"score":2},{"doc_id":"21194367","title":"Evolution of YidC/Oxa1/Alb3 insertases: three independent gene duplications followed by functional specialization in bacteria, mitochondria and chloroplasts.","abstract":"Members of the YidC/Oxa1/Alb3 protein family facilitate the insertion, folding and assembly of proteins of the inner membranes of bacteria and mitochondria and the thylakoid membrane of plastids. All homologs share a conserved hydrophobic core region comprising five transmembrane domains. On the basis of phylogenetic analyses, six subgroups of the family can be distinguished which presumably arose from three independent gene duplications followed by functional specialization. During evolution of bacteria, mitochondria and chloroplasts, subgroup-specific regions were added to the core domain to facilitate the association with ribosomes or other components contributing to the substrate spectrum of YidC/Oxa1/Alb3 proteins.","corpus_id":2813617,"score":2},{"doc_id":"21466505","title":"Binding of chloroplast signal recognition particle to a thylakoid membrane protein substrate in aqueous solution and delineation of the cpSRP43-substrate interaction domain.","abstract":"A cpSRP [chloroplast SRP (signal recognition particle)] comprising cpSRP54 and cpSRP43 subunits mediates the insertion of light-harvesting proteins into the thylakoid membrane. We dissected its interaction with a full-length membrane protein substrate in aqueous solution by insertion of site-specific photo-activatable cross-linkers into in vitro-synthesized Lhcb1 (major light-harvesting chlorophyll-binding protein of photosystem II). We show that Lhcb1 residues 166-176 cross-link specifically to the cpSRP43 subunit. Some cross-link positions within Lhcb1 are in the 'L18' peptide required for targeting of cpSRP substrates, whereas other cross-linking positions define a new targeting signal in the third transmembrane span. Lhcb1 was not found to cross-link to cpSRP54 at any position, and cross-linking to cpSRP43 is unaffected by the absence of cpSRP54. cpSRP43 thus effectively binds substrates autonomously, and its ability to independently bind an extended 20+-residue substrate region highlights a major difference with other SRP types where the SRP54 subunit binds to hydrophobic target sequences. The results also show that cpSRP43 can bind to a hydrophobic, three-membrane span, substrate in aqueous solution, presumably reflecting a role for cpSRP in the chloroplast stroma. This mode of action, and the specificity of the cpSRP43-substrate interaction, may be associated with cpSRP's unique post-translational mode of action.","corpus_id":10105595,"score":2},{"doc_id":"21832051","title":"Interaction studies between the chloroplast signal recognition particle subunit cpSRP43 and the full-length translocase Alb3 reveal a membrane-embedded binding region in Alb3 protein.","abstract":"Posttranslational targeting of the light-harvesting chlorophyll a,b-binding proteins depends on the function of the chloroplast signal recognition particle, its receptor cpFtsY, and the translocase Alb3. The thylakoid membrane protein Alb3 of Arabidopsis chloroplasts belongs to the evolutionarily conserved YidC/Oxa1/Alb3 protein family; the members of this family facilitate the insertion, folding, and assembly of membrane proteins in bacteria, mitochondria, and chloroplasts. Here, we analyzed the interaction sites of full-length Alb3 with the cpSRP pathway component cpSRP43 by using in vitro and in vivo studies. Bimolecular fluorescence complementation and Alb3 proteoliposome studies showed that the interaction of cpSRP43 is dependent on a binding domain in the C terminus of Alb3 as well as an additional membrane-embedded binding site in the fifth transmembrane domain (TMD5) of Alb3. The C-terminal binding domain was mapped to residues 374-388, and the binding domain within TMD5 was mapped to residues 314-318 located close to the luminal end of TMD5. A direct binding between cpSRP43 and these binding motifs was shown by pepspot analysis. Further studies using blue-native gel electrophoresis revealed that full-length Alb3 is able to form dimers. This finding and the identification of a membrane-embedded cpSRP43 binding site in Alb3 support a model in which cpSRP43 inserts into a dimeric Alb3 translocation pore during cpSRP-dependent delivery of light-harvesting chlorophyll a,b-binding proteins.","corpus_id":24720011,"score":2},{"doc_id":"22231402","title":"Chromodomains read the arginine code of post-translational targeting.","abstract":"Chromodomains typically recruit protein complexes to chromatin and read the epigenetic histone code by recognizing lysine methylation in histone tails. We report the crystal structure of the chloroplast signal recognition particle (cpSRP) core from Arabidopsis thaliana, with the cpSRP54 tail comprising an arginine-rich motif bound to the second chromodomain of cpSRP43. A twinned aromatic cage reads out two neighboring nonmethylated arginines and adapts chromodomains to a non-nuclear function in post-translational targeting.","corpus_id":22901035,"score":2},{"doc_id":"23111630","title":"The YidC/Oxa1/Alb3 protein family: common principles and distinct features.","abstract":"The members of the YidC/Oxa1/Alb3 protein family are evolutionary conserved in all three domains of life. They facilitate the insertion of membrane proteins into bacterial, mitochondrial, and thylakoid membranes and have been implicated in membrane protein folding and complex formation. The major classes of substrates are small hydrophobic subunits of large energy-transducing complexes involved in respiration and light capturing. All YidC-like proteins share a conserved membrane region, whereas the N- and C-terminal regions are diverse and fulfill accessory functions in protein targeting.","corpus_id":23982847,"score":2},{"doc_id":"23933010","title":"Elucidating the native architecture of the YidC: ribosome complex.","abstract":"Membrane protein biogenesis in bacteria occurs via dedicated molecular systems SecYEG and YidC that function independently and in cooperation. YidC belongs to the universally conserved Oxa1/Alb3/YidC family of membrane insertases and is believed to associate with translating ribosomes at the membrane surface. Here, we have examined the architecture of the YidC:ribosome complex formed upon YidC-mediated membrane protein insertion. Fluorescence correlation spectroscopy was employed to investigate the complex assembly under physiological conditions. A slightly acidic environment stimulates binding of detergent-solubilized YidC to ribosomes due to electrostatic interactions, while YidC acquires specificity for translating ribosomes at pH-neutral conditions. The nanodisc reconstitution of the YidC to embed it into a native phospholipid membrane environment strongly enhances the YidC:ribosome complex formation. A single copy of YidC suffices for the binding of translating ribosome both in detergent and at the lipid membrane interface, thus being the minimal functional unit. Data reveal molecular details on the insertase functioning and interactions and suggest a new structural model for the YidC:ribosome complex.","corpus_id":20454463,"score":2},{"doc_id":"24418623","title":"The membrane insertase YidC.","abstract":"The membrane insertases YidC-Oxa1-Alb3 provide a simple cellular system that catalyzes the transmembrane topology of newly synthesized membrane proteins. The insertases are composed of a single protein with 5 to 6 transmembrane (TM) helices that contact hydrophobic segments of the substrate proteins. Since YidC also cooperates with the Sec translocase it is widely involved in the assembly of many different membrane proteins including proteins that obtain complex membrane topologies. Homologues found in mitochondria (Oxa1) and thylakoids (Alb3) point to a common evolutionary origin and also demonstrate the general importance of this cellular process. This article is part of a Special Issue entitled: Protein trafficking and secretion in bacteria. Guest Editors: Anastassios Economou and Ross Dalbey.","corpus_id":6255282,"score":2},{"doc_id":"24612058","title":"The Arabidopsis Tellurite resistance C protein together with ALB3 is involved in photosystem II protein synthesis.","abstract":"Assembly of photosystem II (PSII) occurs sequentially and requires several auxiliary proteins, such as ALB3 (ALBINO3). Here, we describe the role of the Arabidopsis thaliana thylakoid membrane protein Tellurite resistance C (AtTerC) in this process. Knockout of AtTerC was previously shown to be seedling-lethal. This phenotype was rescued by expressing TerC fused C-terminally to GFP in the terc-1 background, and the resulting terc-1TerC- GFP line and an artificial miRNA-based knockdown allele (amiR-TerC) were used to analyze the TerC function. The alterations in chlorophyll fluorescence and thylakoid ultrastructure observed in amiR-TerC plants and terc-1TerC- GFP were attributed to defects in PSII. We show that this phenotype resulted from a reduction in the rate of de novo synthesis of PSII core proteins, but later steps in PSII biogenesis appeared to be less affected. Yeast two-hybrid assays showed that TerC interacts with PSII proteins. In particular, its interaction with the PSII assembly factor ALB3 has been demonstrated by co-immunoprecipitation. ALB3 is thought to assist in incorporation of CP43 into PSII via interaction with Low PSII Accumulation2 (LPA2) Low PSII Accumulation3 (LPA3). Homozygous lpa2 mutants expressing amiR-TerC displayed markedly exacerbated phenotypes, leading to seedling lethality, indicating an additive effect. We propose a model in which TerC, together with ALB3, facilitates de novo synthesis of thylakoid membrane proteins, for instance CP43, at the membrane insertion step.","corpus_id":20573960,"score":2},{"doc_id":"24739968","title":"Structural basis of Sec-independent membrane protein insertion by YidC.","abstract":"Newly synthesized membrane proteins must be accurately inserted into the membrane, folded and assembled for proper functioning. The protein YidC inserts its substrates into the membrane, thereby facilitating membrane protein assembly in bacteria; the homologous proteins Oxa1 and Alb3 have the same function in mitochondria and chloroplasts, respectively. In the bacterial cytoplasmic membrane, YidC functions as an independent insertase and a membrane chaperone in cooperation with the translocon SecYEG. Here we present the crystal structure of YidC from Bacillus halodurans, at 2.4 Å resolution. The structure reveals a novel fold, in which five conserved transmembrane helices form a positively charged hydrophilic groove that is open towards both the lipid bilayer and the cytoplasm but closed on the extracellular side. Structure-based in vivo analyses reveal that a conserved arginine residue in the groove is important for the insertion of membrane proteins by YidC. We propose an insertion mechanism for single-spanning membrane proteins, in which the hydrophilic environment generated by the groove recruits the extracellular regions of substrates into the low-dielectric environment of the membrane.","corpus_id":4451969,"score":2},{"doc_id":"25012291","title":"A structural model of the active ribosome-bound membrane protein insertase YidC.","abstract":"The integration of most membrane proteins into the cytoplasmic membrane of bacteria occurs co-translationally. The universally conserved YidC protein mediates this process either individually as a membrane protein insertase, or in concert with the SecY complex. Here, we present a structural model of YidC based on evolutionary co-variation analysis, lipid-versus-protein-exposure and molecular dynamics simulations. The model suggests a distinctive arrangement of the conserved five transmembrane domains and a helical hairpin between transmembrane segment 2 (TM2) and TM3 on the cytoplasmic membrane surface. The model was used for docking into a cryo-electron microscopy reconstruction of a translating YidC-ribosome complex carrying the YidC substrate FOc. This structure reveals how a single copy of YidC interacts with the ribosome at the ribosomal tunnel exit and identifies a site for membrane protein insertion at the YidC protein-lipid interface. Together, these data suggest a mechanism for the co-translational mode of YidC-mediated membrane protein insertion.","corpus_id":8125594,"score":2},{"doc_id":"25833951","title":"Chloroplast SRP54 Was Recruited for Posttranslational Protein Transport via Complex Formation with Chloroplast SRP43 during Land Plant Evolution.","abstract":"In bacteria, membrane proteins are targeted cotranslationally via a signal recognition particle (SRP). During the evolution of higher plant chloroplasts from cyanobacteria, the SRP pathway underwent striking adaptations that enable the posttranslational transport of the abundant light-harvesting chlorophyll-a/b-binding proteins (LHCPs). The conserved 54-kDa SRP subunit in higher plant chloroplasts (cpSRP54) is not bound to an SRP RNA, an essential SRP component in bacteria, but forms a stable heterodimer with the chloroplast-specific cpSRP43. This heterodimeric cpSRP recognizes LHCP and delivers it to the thylakoid membrane whereby cpSRP43 plays a central role. This study shows that the cpSRP system in the green alga Chlamydomonas reinhardtii differs significantly from that of higher plants as cpSRP43 is not complexed to cpSRP54 in Chlamydomonas and cpSRP54 is not involved in LHCP recognition. This divergence is attributed to altered residues within the cpSRP54 tail and the second chromodomain of cpSRP43 that are crucial for the formation of the binding interface in Arabidopsis. These changes are highly conserved among chlorophytes, whereas all land plants contain cpSRP proteins with typical interaction motifs. These data demonstrate that the coevolution of LHCPs and cpSRP43 occurred independently of complex formation with cpSRP54 and that the interaction between cpSRP54 and cpSRP43 evolved later during the transition from chlorophytes to land plants. Furthermore, our data show that in higher plants a heterodimeric form of cpSRP is required for the formation of a low molecular weight transit complex with LHCP.","corpus_id":205345422,"score":2},{"doc_id":"25918165","title":"Regulation of Structural Dynamics within a Signal Recognition Particle Promotes Binding of Protein Targeting Substrates.","abstract":"Protein targeting is critical in all living organisms and involves a signal recognition particle (SRP), an SRP receptor, and a translocase. In co-translational targeting, interactions among these proteins are mediated by the ribosome. In chloroplasts, the light-harvesting chlorophyll-binding protein (LHCP) in the thylakoid membrane is targeted post-translationally without a ribosome. A multidomain chloroplast-specific subunit of the SRP, cpSRP43, is proposed to take on the role of coordinating the sequence of targeting events. Here, we demonstrate that cpSRP43 exhibits significant interdomain dynamics that are reduced upon binding its SRP binding partner, cpSRP54. We showed that the affinity of cpSRP43 for the binding motif of LHCP (L18) increases when cpSRP43 is complexed to the binding motif of cpSRP54 (cpSRP54pep). These results support the conclusion that substrate binding to the chloroplast SRP is modulated by protein structural dynamics in which a major role of cpSRP54 is to improve substrate binding efficiency to the cpSRP.","corpus_id":10593109,"score":2},{"doc_id":"25947384","title":"YidC/Alb3/Oxa1 Family of Insertases.","abstract":"The YidC/Alb3/Oxa1 family functions in the insertion and folding of proteins in the bacterial cytoplasmic membrane, the chloroplast thylakoid membrane, and the mitochondrial inner membrane. All members share a conserved region composed of five transmembrane regions. These proteins mediate membrane insertion of an assorted group of proteins, ranging from respiratory subunits in the mitochondria and light-harvesting chlorophyll-binding proteins in chloroplasts to ATP synthase subunits in bacteria. This review discusses the YidC/Alb3/Oxa1 protein family as well as their function in membrane insertion and two new structures of the bacterial YidC, which suggest a mechanism for membrane insertion by this family of insertases.","corpus_id":205380419,"score":2},{"doc_id":"26105652","title":"The extreme Albino3 (Alb3) C terminus is required for Alb3 stability and function in Arabidopsis thaliana.","abstract":"MAIN CONCLUSION: The extreme Alb3 C terminus is important for Alb3 stability in a light dependent manner, but is dispensable for LHCP insertion or D1 synthesis. YidC/Oxa1/Alb3 dependent insertion of membrane proteins is evolutionary conserved among bacteria, mitochondria and chloroplasts. Chloroplasts are challenged by the need to coordinate membrane integration of nuclear encoded, post-translationally targeted proteins into the thylakoids as well as of proteins translated on plastid ribosomes. The pathway facilitating post-translational targeting of the light-harvesting chlorophyll a/b binding proteins involves the chloroplast signal recognition particle, cpSRP54 and cpSRP43, as well as its membrane receptor FtsY and the translocase Alb3. Interaction of cpSRP43 with Alb3 is mediated by the positively charged, stromal exposed C terminus of Alb3. In this study, we utilized an Alb3 T-DNA insertion mutant in Arabidopsis thaliana lacking the last 75 amino acids to elucidate the function of this domain (alb3∆C). However, the truncated Alb3 protein (Alb3∆C) proved to be unstable under standard growth conditions, resulting in a reduction of Alb3∆C to 20 % of wild-type levels. In contrast, accumulation of Alb3∆C was comparable to wild type under low light growth conditions. Alb3∆C mutants grown under low light conditions were only slightly paler than wild type, accumulated almost wild-type levels of light harvesting proteins and were not affected in D1 synthesis, therefore showing that the extreme Alb3 C terminus is dispensable for both, co- and post-translational, protein insertion into the thylakoid membrane. However, reduction of Alb3∆C levels as observed under standard growth conditions resulted not only in a severely diminished accumulation of all thylakoid complexes but also in a strong defect in D1 synthesis and membrane insertion.","corpus_id":1546146,"score":2},{"doc_id":"26265777","title":"Genetic and Physical Interaction Studies Reveal Functional Similarities between ALBINO3 and ALBINO4 in Arabidopsis.","abstract":"ALBINO3 (ALB3) is a well-known component of a thylakoid protein-targeting complex that interacts with the chloroplast signal recognition particle (cpSRP) and the cpSRP receptor, chloroplast filamentous temperature-sensitive Y (cpFtsY). Its protein-inserting function has been established mainly for light-harvesting complex proteins, which first interact with the unique chloroplast cpSRP43 component and then are delivered to the ALB3 integrase by a GTP-dependent cpSRP-cpFtsY interaction. In Arabidopsis (Arabidopsis thaliana), a subsequently discovered ALB3 homolog, ALB4, has been proposed to be involved not in light-harvesting complex protein targeting, but instead in the stabilization of the ATP synthase complex. Here, however, we show that ALB3 and ALB4 share significant functional overlap, and that both proteins are required for the efficient insertion of cytochrome f and potentially other subunits of pigment-bearing protein complexes. Genetic and physical interactions between ALB4 and ALB3, and physical interactions between ALB4 and cpSRP, suggest that the two ALB proteins may engage similar sets of interactors for their specific functions. We propose that ALB4 optimizes the insertion of thylakoid proteins by participating in the ALB3-cpSRP pathway for certain substrates (e.g. cytochrome f and the Rieske protein). Although ALB4 has clearly diverged from ALB3 in relation to the partner-recruiting C-terminal domain, our analysis suggests that one putative cpSRP-binding motif has not been entirely lost.","corpus_id":44622706,"score":2},{"doc_id":"26568381","title":"Structural basis for cpSRP43 chromodomain selectivity and dynamics in Alb3 insertase interaction.","abstract":"Canonical membrane protein biogenesis requires co-translational delivery of ribosome-associated proteins to the Sec translocase and depends on the signal recognition particle (SRP) and its receptor (SR). In contrast, high-throughput delivery of abundant light-harvesting chlorophyll a,b-binding proteins (LHCPs) in chloroplasts to the Alb3 insertase occurs post-translationally via a soluble transit complex including the cpSRP43/cpSRP54 heterodimer (cpSRP). Here we describe the molecular mechanisms of tethering cpSRP to the Alb3 insertase by specific interaction of cpSRP43 chromodomain 3 with a linear motif in the Alb3 C-terminal tail. Combining NMR spectroscopy, X-ray crystallography and biochemical analyses, we dissect the structural basis for selectivity of chromodomains 2 and 3 for their respective ligands cpSRP54 and Alb3, respectively. Negative cooperativity in ligand binding can be explained by dynamics in the chromodomain interface. Our study provides a model for membrane recruitment of the transit complex and may serve as a prototype for a functional gain by the tandem arrangement of chromodomains.","corpus_id":18904763,"score":2},{"doc_id":"26951662","title":"Conformational dynamics of a membrane protein chaperone enables spatially regulated substrate capture and release.","abstract":"Membrane protein biogenesis poses enormous challenges to cellular protein homeostasis and requires effective molecular chaperones. Compared with chaperones that promote soluble protein folding, membrane protein chaperones require tight spatiotemporal coordination of their substrate binding and release cycles. Here we define the chaperone cycle for cpSRP43, which protects the largest family of membrane proteins, the light harvesting chlorophyll a/b-binding proteins (LHCPs), during their delivery. Biochemical and NMR analyses demonstrate that cpSRP43 samples three distinct conformations. The stromal factor cpSRP54 drives cpSRP43 to the active state, allowing it to tightly bind substrate in the aqueous compartment. Bidentate interactions with the Alb3 translocase drive cpSRP43 to a partially inactive state, triggering selective release of LHCP's transmembrane domains in a productive unloading complex at the membrane. Our work demonstrates how the intrinsic conformational dynamics of a chaperone enables spatially coordinated substrate capture and release, which may be general to other ATP-independent chaperone systems.","corpus_id":20516816,"score":2},{"doc_id":"27653474","title":"Domain Organization in the 54-kDa Subunit of the Chloroplast Signal Recognition Particle.","abstract":"Chloroplast signal recognition particle (cpSRP) is a heterodimer composed of an evolutionarily conserved 54-kDa GTPase (cpSRP54) and a unique 43-kDa subunit (cpSRP43) responsible for delivering light-harvesting chlorophyll binding protein to the thylakoid membrane. While a nearly complete three-dimensional structure of cpSRP43 has been determined, no high-resolution structure is yet available for cpSRP54. In this study, we developed and examined an in silico three-dimensional model of the structure of cpSRP54 by homology modeling using cytosolic homologs. Model selection was guided by single-molecule Förster resonance energy transfer experiments, which revealed the presence of at least two distinct conformations. Small angle x-ray scattering showed that the linking region among the GTPase (G-domain) and methionine-rich (M-domain) domains, an M-domain loop, and the cpSRP43 binding C-terminal extension of cpSRP54 are predominantly disordered. Interestingly, the linker and loop segments were observed to play an important role in organizing the domain arrangement of cpSRP54. Further, deletion of the finger loop abolished loading of the cpSRP cargo, light-harvesting chlorophyll binding protein. These data highlight important structural dynamics relevant to cpSRP54's role in the post- and cotranslational signaling processes.","corpus_id":206304100,"score":2},{"doc_id":"27698412","title":"ALB3 Insertase Mediates Cytochrome b6 Co-translational Import into the Thylakoid Membrane.","abstract":"The cytochrome b6 f complex occupies an electrochemically central position in the electron-transport chain bridging the photosynthetic reaction center of PS I and PS II. In plants, the subunits of these thylakoid membrane protein complexes are both chloroplast and nuclear encoded. How the chloroplast-encoded subunits of multi-spanning cytochrome b6 are targeted and inserted into the thylakoid membrane is not fully understood. Experimental approaches to evaluate the cytochrome b6 import mechanism in vivo have been limited to bacterial membranes and were not a part of the chloroplast environment. To evaluate the mechanism governing cytochrome b6 integration in vivo, we performed a comparative analysis of both native and synthetic cytochrome b6 insertion into purified thylakoids. Using biophysical and biochemical methods, we show that cytochrome b6 insertion into the thylakoid membrane is a non-spontaneous co-translational process that involves ALB3 insertase. Furthermore, we provided evidence that CSP41 (chloroplast stem-loop-binding protein of 41 kDa) interacts with RNC-cytochrome b6 complexes, and may be involved in cytochrome b6 (petB) transcript stabilization or processing.","corpus_id":16173499,"score":2},{"doc_id":"27861610","title":"The Chloroplast SRP Systems of Chaetosphaeridium globosum and Physcomitrella patens as Intermediates in the Evolution of SRP-Dependent Protein Transport in Higher Plants.","abstract":"The bacterial signal recognition particle (SRP) mediates the cotranslational targeting of membrane proteins and is a high affinity complex consisting of a SRP54 protein subunit (Ffh) and an SRP RNA. The chloroplast SRP (cpSRP) pathway has adapted throughout evolution to enable the posttranslational targeting of the light harvesting chlorophyll a/b binding proteins (LHCPs) to the thylakoid membrane. In spermatophytes (seed plants), the cpSRP lacks the SRP RNA and is instead formed by a high affinity interaction of the conserved 54-kD subunit (cpSRP54) with the chloroplast-specific cpSRP43 protein. This heterodimeric cpSRP recognizes LHCP and delivers it to the thylakoid membrane. However, in contrast to spermatophytes, plastid SRP RNAs were identified within all streptophyte lineages and in all chlorophyte branches. Furthermore, it was shown that cpSRP43 does not interact with cpSRP54 in chlorophytes (e.g., Chlamydomonas reinhardtii). In this study, we biochemically characterized the cpSRP system of the charophyte Chaetosphaeridium globosum and the bryophyte Physcomitrella patens. Interaction studies demonstrate low affinity binding of cpSRP54 to cpSRP43 (Kd ~10 μM) in Chaetosphaeridium globosum and Physcomitrella patens as well as relatively low affinity binding of cpSRP54 to cpSRP RNA (Kd ~1 μM) in Physcomitrella patens. CpSRP54/cpSRP43 complex formation in charophytes is supported by the finding that specific alterations in the second chromodomain of cpSRP43, that are conserved within charophytes and absent in land plants, do not interfere with cpSRP54 binding. Furthermore, our data show that the elongated apical loop structure of the Physcomitrella patens cpSRP RNA contributes to the low binding affinity between cpSRP54 and the cpSRP RNA.","corpus_id":12969329,"score":2},{"doc_id":"27895118","title":"Co-evolution of Two GTPases Enables Efficient Protein Targeting in an RNA-less Chloroplast Signal Recognition Particle Pathway.","abstract":"The signal recognition particle (SRP) is an essential ribonucleoprotein particle that mediates the co-translational targeting of newly synthesized proteins to cellular membranes. The SRP RNA is a universally conserved component of SRP that mediates key interactions between two GTPases in SRP and its receptor, thus enabling rapid delivery of cargo to the target membrane. Notably, this essential RNA is bypassed in the chloroplast (cp) SRP of green plants. Previously, we showed that the cpSRP and cpSRP receptor GTPases (cpSRP54 and cpFtsY, respectively) interact efficiently by themselves without the SRP RNA. Here, we explore the molecular mechanism by which this is accomplished. Fluorescence analyses showed that, in the absence of SRP RNA, the M-domain of cpSRP54 both accelerates and stabilizes complex assembly between cpSRP54 and cpFtsY. Cross-linking coupled with mass spectrometry and mutational analyses identified a new interaction between complementarily charged residues on the cpFtsY G-domain and the vicinity of the cpSRP54 M-domain. These residues are specifically conserved in plastids, and their evolution coincides with the loss of SRP RNA in green plants. These results provide an example of how proteins replace the functions of RNA during evolution.","corpus_id":30894142,"score":2},{"doc_id":"27895124","title":"Anionic Phospholipids and the Albino3 Translocase Activate Signal Recognition Particle-Receptor Interaction during Light-harvesting Chlorophyll a/b-binding Protein Targeting.","abstract":"The universally conserved signal recognition particle (SRP) co-translationally delivers newly synthesized membrane and secretory proteins to the target cellular membrane. The only exception is found in the chloroplast of green plants, where the chloroplast SRP (cpSRP) post-translationally targets light-harvesting chlorophyll a/b-binding proteins (LHCP) to the thylakoid membrane. The mechanism and regulation of this post-translational mode of targeting by cpSRP remain unclear. Using biochemical and biophysical methods, here we show that anionic phospholipids activate the cpSRP receptor cpFtsY to promote rapid and stable cpSRP54·cpFtsY complex assembly. Furthermore, the stromal domain of the Alb3 translocase binds with high affinity to and regulates GTP hydrolysis in the cpSRP54·cpFtsY complex, suggesting that cpFtsY is primarily responsible for initial recruitment of the targeting complex to Alb3. These results suggest a new model for the sequential recruitment, remodeling, and unloading of the targeting complex at membrane translocase sites in the post-translational cpSRP pathway.","corpus_id":22441687,"score":2},{"doc_id":"28684427","title":"Suppressors of the Chloroplast Protein Import Mutant tic40 Reveal a Genetic Link between Protein Import and Thylakoid Biogenesis.","abstract":"To extend our understanding of chloroplast protein import and the role played by the import machinery component Tic40, we performed a genetic screen for suppressors of chlorotic tic40 knockout mutant Arabidopsis thaliana plants. As a result, two suppressor of tic40 loci, stic1 and stic2, were identified and characterized. The stic1 locus corresponds to the gene ALBINO4 (ALB4), which encodes a paralog of the well-known thylakoid protein targeting factor ALB3. The stic2 locus identified a previously unknown stromal protein that interacts physically with both ALB4 and ALB3. Genetic studies showed that ALB4 and STIC2 act together in a common pathway that also involves cpSRP54 and cpFtsY. Thus, we conclude that ALB4 and STIC2 both participate in thylakoid protein targeting, potentially for a specific subset of thylakoidal proteins, and that this targeting pathway becomes disadvantageous to the plant in the absence of Tic40. As the stic1 and stic2 mutants both suppressed tic40 specifically (other TIC-related mutants were not suppressed), we hypothesize that Tic40 is a multifunctional protein that, in addition to its originally described role in protein import, is able to influence downstream processes leading to thylakoid biogenesis.","corpus_id":3855270,"score":2},{"doc_id":"28844594","title":"YidC Insertase of Escherichia coli: Water Accessibility and Membrane Shaping.","abstract":"The YidC/Oxa1/Alb3 family of membrane proteins function to insert proteins into membranes in bacteria, mitochondria, and chloroplasts. Recent X-ray structures of YidC from Bacillus halodurans and Escherichia coli revealed a hydrophilic groove that is accessible from the lipid bilayer and the cytoplasm. Here, we explore the water accessibility within the conserved core region of the E. coli YidC using in vivo cysteine alkylation scanning and molecular dynamics (MD) simulations of YidC in POPE/POPG membranes. As expected from the structure, YidC possesses an aqueous membrane cavity localized to the membrane inner leaflet. Both the scanning data and the MD simulations show that the lipid-exposed transmembrane helices 3, 4, and 5 are short, leading to membrane thinning around YidC. Close examination of the MD data reveals previously unrecognized structural features that are likely important for protein stability and function.","corpus_id":205263772,"score":2},{"doc_id":"29162052","title":"Chloroplast PetD protein: evidence for SRP/Alb3-dependent insertion into the thylakoid membrane.","abstract":"BACKGROUND: In thylakoid membrane, each monomer of the dimeric complex of cytochrome b 6 f is comprised of eight subunits that are both nucleus- and plastid-encoded. Proper cytochrome b 6 f complex integration into the thylakoid membrane requires numerous regulatory factors for coordinated transport, insertion and assembly of the subunits. Although, the chloroplast-encoded cytochrome b 6 f subunit IV (PetD) consists of three transmembrane helices, the signal and the mechanism of protein integration into the thylakoid membrane have not been identified. RESULTS: Here, we demonstrate that the native PetD subunit cannot incorporate into the thylakoid membranes spontaneously, but that proper integration occurs through the post-translational signal recognition particle (SRP) pathway. Furthermore, we show that PetD insertion into thylakoid membrane involves the coordinated action of cpFTSY, cpSRP54 and ALB3 insertase. CONCLUSIONS: PetD subunit integration into the thylakoid membrane is a post-translational and an SRP-dependent process that requires the formation of the cpSRP-cpFtsY-ALB3-PetD complex. This data provides a new insight into the molecular mechanisms by which membrane proteins integration into the thylakoid membrane is accomplished and is not limited to PetD.","corpus_id":12969189,"score":2},{"doc_id":"29281821","title":"Identification of Oxa1 Homologs Operating in the Eukaryotic Endoplasmic Reticulum.","abstract":"Members of the evolutionarily conserved Oxa1/Alb3/YidC family mediate membrane protein biogenesis at the mitochondrial inner membrane, chloroplast thylakoid membrane, and bacterial plasma membrane, respectively. Despite their broad phylogenetic distribution, no Oxa1/Alb3/YidC homologs are known to operate in eukaryotic cells outside the endosymbiotic organelles. Here, we present bioinformatic evidence that the tail-anchored protein insertion factor WRB/Get1, the \"endoplasmic reticulum (ER) membrane complex\" subunit EMC3, and TMCO1 are ER-resident homologs of the Oxa1/Alb3/YidC family. Topology mapping and co-evolution-based modeling demonstrate that Get1, EMC3, and TMCO1 share a conserved Oxa1-like architecture. Biochemical analysis of human TMCO1, the only homolog not previously linked to membrane protein biogenesis, shows that it associates with the Sec translocon and ribosomes. These findings suggest a specific biochemical function for TMCO1 and define a superfamily of proteins-the \"Oxa1 superfamily\"-whose shared function is to facilitate membrane protein biogenesis.","corpus_id":4321058,"score":2},{"doc_id":"19307606","title":"Translocation and assembly of mitochondrially coded Saccharomyces cerevisiae cytochrome c oxidase subunit Cox2 by Oxa1 and Yme1 in the absence of Cox18.","abstract":"Members of the Oxa1/YidC/Alb3 family of protein translocases are essential for assembly of energy-transducing membrane complexes. In Saccharomyces cerevisiae, Oxa1 and its paralog, Cox18, are required for assembly of Cox2, a mitochondrially encoded subunit of cytochrome c oxidase. Oxa1 is known to be required for cotranslational export of the Cox2 N-terminal domain across the inner mitochondrial membrane, while Cox18 is known to be required for post-translational export of the Cox2 C-tail domain. We find that overexpression of Oxa1 does not compensate for the absence of Cox18 at the level of respiratory growth. However, it does promote some translocation of the Cox2 C-tail domain across the inner membrane and causes increased accumulation of Cox2, which remains unassembled. This result suggests that Cox18 not only translocates the C-tail, but also must deliver it in a distinct state competent for cytochrome oxidase assembly. We identified respiring mutants from a cox18Delta strain overexpressing OXA1, whose respiratory growth requires overexpression of OXA1. The recessive nuclear mutations allow some assembly of Cox2 into cytochrome c oxidase. After failing to identify these mutations by methods based on transformation, we successfully located them to MGR1 and MGR3 by comparative hybridization to whole-genome tiling arrays and microarray-assisted bulk segregant analysis followed by linkage mapping. While Mgr1 and Mgr3 are known to associate with the Yme1 mitochondrial inner membrane i-AAA protease and to participate in membrane protein degradation, their absence does not appear to stabilize Cox2 under these conditions. Instead, Yme1 probably chaperones the folding and/or assembly of Oxa1-exported Cox2 in the absence of Mrg1 or Mgr3, since respiratory growth and cytochrome c oxidase assembly in a cox18 mgr3 double-mutant strain overexpressing OXA1 is YME1 dependent.","corpus_id":18698603,"score":1},{"doc_id":"19361278","title":"From the Sec complex to the membrane insertase YidC.","abstract":"The key enzymes that catalyze the insertion of proteins into membranes are the Sec translocase and the YidC membrane insertase. Recent insights into the structure and functional intermediates of these enzymes have provided a first molecular glimpse of how they help the newly synthesized proteins to enter the membrane bilayer. In this process, the new proteins undergo a number of specific interactions in the cytoplasm and at the membrane surface before they insert into the bilayer and translocate their external domains across the membrane. The components involved in this pathway recognize each other at the molecular level, forming a route the membrane protein can move along.","corpus_id":38220412,"score":1},{"doc_id":"19450532","title":"YidC and Oxa1 form dimeric insertion pores on the translating ribosome.","abstract":"The YidC/Oxa1/Alb3 family of membrane proteins facilitates the insertion and assembly of membrane proteins in bacteria, mitochondria, and chloroplasts. Here we present the structures of both Escherichia coli YidC and Saccharomyces cerevisiae Oxa1 bound to E. coli ribosome nascent chain complexes determined by cryo-electron microscopy. Dimers of YidC and Oxa1 are localized above the exit of the ribosomal tunnel. Crosslinking experiments show that the ribosome specifically stabilizes the dimeric state. Functionally important and conserved transmembrane helices of YidC and Oxa1 were localized at the dimer interface by cysteine crosslinking. Both Oxa1 and YidC dimers contact the ribosome at ribosomal protein L23 and conserved rRNA helices 59 and 24, similarly to what was observed for the nonhomologous SecYEG translocon. We suggest that dimers of the YidC and Oxa1 proteins form insertion pores and share a common overall architecture with the SecY monomer.","corpus_id":32266828,"score":1},{"doc_id":"22108384","title":"Unbalanced charge distribution as a determinant for dependence of a subset of Escherichia coli membrane proteins on the membrane insertase YidC.","abstract":"UNLABELLED: Membrane proteins are involved in numerous essential cell processes, including transport, gene regulation, motility, and metabolism. To function properly, they must be inserted into the membrane and folded correctly. YidC, an essential protein in Escherichia coli with homologues in other bacteria, Archaea, mitochondria, and chloroplasts, functions by incompletely understood mechanisms in the insertion and folding of certain membrane proteins. Using a genome-scale approach, we identified 69 E. coli membrane proteins that, in the absence of YidC, exhibited aberrant localization by microscopy. Further examination of a subset revealed biochemical defects in membrane insertion in the absence of YidC, indicating their dependence on YidC for proper membrane insertion or folding. Membrane proteins possessing an unfavorable distribution of positively charged residues were significantly more likely to depend on YidC for membrane insertion. Correcting the charge distribution of a charge-unbalanced YidC-dependent membrane protein abrogated its requirement for YidC, while perturbing the charge distribution of a charge-balanced YidC-independent membrane protein rendered it YidC dependent, demonstrating that charge distribution can be a necessary and sufficient determinant of YidC dependence. These findings provide insights into a mechanism by which YidC promotes proper membrane protein biogenesis and suggest a critical function of YidC in all organisms and organelles that express it. IMPORTANCE: Biological membranes are fundamental components of cells, providing barriers that enclose the cell and separate compartments. Proteins inserted into biological membranes serve critical functions in molecular transport, molecular partitioning, and other essential cell processes. The mechanisms involved in the insertion of proteins into membranes, however, are incompletely understood. The YidC protein is critical for the insertion of a subset of proteins into membranes across an evolutionarily wide group of organisms. Here we identify a large group of proteins that depend on YidC for membrane insertion in Escherichia coli, and we identify unfavorable distribution of charge as an important determinant of YidC dependence for proper membrane insertion.","corpus_id":7343309,"score":1},{"doc_id":"23179441","title":"Arabidopsis thaliana Oxa proteins locate to mitochondria and fulfill essential roles during embryo development.","abstract":"Members of the Alb3/Oxa1/YidC protein family function as insertases in chloroplasts, mitochondria, and bacteria. Due to independent gene duplications, all organisms possess two isoforms, Oxa1 and Oxa2 except gram-negative bacteria, which encode only for one YidC-like protein. The genome of Arabidopsis thaliana however, encodes for eight different isoforms. The localization of three of these isoforms has been identified earlier: Alb3 and Alb4 located in thylakoid membranes of chloroplasts while AtOxa1 was found in the inner membrane of mitochondria. Here, we show that the second Oxa1 protein, Oxa1b as well as two Oxa2 proteins are also localized in mitochondria. The last two isoforms most likely encode truncated versions of Oxa-like proteins, which might be inoperable pseudogenes. Homozygous mutant lines were only obtained for Oxa1b, which did not reveal any significant phenotypes, while T-DNA insertion lines of Oxa1a, Oxa2a and Oxa2b resulted only in heterozygous plants indicating that these genes are indispensable for plant development. Phenotyping heterozygous lines showed that embryos are either retarded in growth, display an albino phenotype or embryo formation was entirely abolished suggesting that Oxa1a and both Oxa2 proteins function in embryo formation although at different developmental stages as indicated by the various phenotypes observed.","corpus_id":7778849,"score":1},{"doc_id":"23198851","title":"Partial suppression of Oxa1 mutants by mitochondria-targeted signal recognition particle provides insights into the evolution of the cotranslational insertion systems.","abstract":"The biogenesis of hydrophobic membrane proteins involves their cotranslational membrane integration in order to prevent their unproductive aggregation. In the cytosol of bacteria and eukaryotes, membrane targeting of ribosomes that synthesize membrane proteins is achieved by signal recognition particles (SRPs) and their cognate membrane-bound receptors. As is evident from the genomes of fully sequenced eukaryotes, mitochondria generally lack an SRP system. Instead, mitochondrial ribosomes are physically associated with the protein insertion machinery in the inner membrane. Accordingly, deletion of ribosome-binding sites on the Oxa1 insertase and the Mba1 ribosome receptor in yeast leads to severe defects in cotranslational protein insertion and results in respiration-deficient mutants. In this study, we expressed mitochondria-targeted versions of the bacterial SRP protein Ffh and its receptor FtsY in these yeast mutants. Interestingly, Ffh was found to bind to the large subunit of mitochondrial ribosomes, and could relieve, to some degree, the defect of these insertion mutants. Although FtsY could also bind to mitochondrial membranes, it did not improve membrane protein biogenesis in this strain, presumably because of its inability to interact with Ffh. Hence, mitochondrial ribosomes are still able to interact physically and functionally with the bacterial SRP system. Our observations are consistent with a model according to which the protein insertion system in mitochondria evolved in three steps. The loss of genes for hydrophilic polypeptides (step 1) allowed the development of ribosome-binding sites on membrane proteins (step 2), which finally made the existence of an SRP-mediated system dispensable (step 3).","corpus_id":205132734,"score":1},{"doc_id":"23935050","title":"Interaction of Streptococcus mutans YidC1 and YidC2 with translating and nontranslating ribosomes.","abstract":"The YidC/OxaI/Alb3 family of membrane proteins is involved in the biogenesis of integral membrane proteins in bacteria, mitochondria, and chloroplasts. Gram-positive bacteria often contain multiple YidC paralogs that can be subdivided into two major classes, namely, YidC1 and YidC2. The Streptococcus mutans YidC1 and YidC2 proteins possess C-terminal tails that differ in charges (+9 and + 14) and lengths (33 and 61 amino acids). The longer YidC2 C terminus bears a resemblance to the C-terminal ribosome-binding domain of the mitochondrial OxaI protein and, in contrast to the shorter YidC1 C terminus, can mediate the interaction with mitochondrial ribosomes. These observations have led to the suggestion that YidC1 and YidC2 differ in their abilities to interact with ribosomes. However, the interaction with bacterial translating ribosomes has never been addressed. Here we demonstrate that Escherichia coli ribosomes are able to interact with both YidC1 and YidC2. The interaction is stimulated by the presence of a nascent membrane protein substrate and abolished upon deletion of the C-terminal tail, which also abrogates the YidC-dependent membrane insertion of subunit c of the F1F0-ATPase into the membrane. It is concluded that both YidC1 and YidC2 interact with ribosomes, suggesting that the modes of membrane insertion by these membrane insertases are similar.","corpus_id":26095938,"score":1},{"doc_id":"24013010","title":"The chloroplast signal recognition particle (CpSRP) pathway as a tool to minimize chlorophyll antenna size and maximize photosynthetic productivity.","abstract":"The concept of the Truncated Light-harvesting chlorophyll Antenna (TLA) size, as a tool by which to maximize sunlight utilization and photosynthetic productivity in microalgal mass cultures or high-density plant canopies, is discussed. TLA technology is known to improve sunlight-to-product energy conversion efficiencies and is hereby exemplified by photosynthetic productivity estimates of wild type and a TLA strain under simulated mass culture conditions. Recent advances in the generation of TLA-type mutants by targeting genes of the chloroplast signal-recognition particle (CpSRP) pathway, affecting the thylakoid membrane assembly of light-harvesting proteins, are also summarized. Two distinct CpSRP assembly pathways are recognized, one entailing post-translational, the other a co-translational mechanism. Differences between the post-translational and co-translational integration mechanisms are outlined, as these pertain to the CpSRP-mediated assembly of thylakoid membrane protein complexes in higher plants and green microalgae. The applicability of the CpSRP pathway genes in efforts to generate TLA-type strains with enhanced solar energy conversion efficiency in photosynthesis is evaluated.","corpus_id":35681793,"score":1},{"doc_id":"25466392","title":"Crystal structure of Escherichia coli YidC, a membrane protein chaperone and insertase.","abstract":"Bacterial YidC, an evolutionally conserved membrane protein, functions as a membrane protein chaperone in cooperation with the Sec translocon and as an independent insertase for membrane proteins. In Gram-negative bacteria, the transmembrane and periplasmic regions of YidC interact with the Sec proteins, forming a multi-protein complex for Sec-dependent membrane protein integration. Here, we report the crystal structure of full-length Escherichia coli YidC. The structure reveals that a hydrophilic groove, formed by five transmembrane helices, is a conserved structural feature of YidC, as compared to the previous YidC structure from Bacillus halodurans, which lacks a periplasmic domain. Structural mapping of the substrate- or Sec protein-contact sites suggested the importance of the groove for the YidC functions as a chaperone and an insertase, and provided structural insight into the multi-protein complex.","corpus_id":6499559,"score":1},{"doc_id":"25666136","title":"The Escherichia coli membrane protein insertase YidC assists in the biogenesis of penicillin binding proteins.","abstract":"UNLABELLED: Membrane proteins need to be properly inserted and folded in the membrane in order to perform a range of activities that are essential for the survival of bacteria. The Sec translocon and the YidC insertase are responsible for the insertion of the majority of proteins into the cytoplasmic membrane. YidC can act in combination with the Sec translocon in the insertion and folding of membrane proteins. However, YidC also functions as an insertase independently of the Sec translocon for so-called YidC-only substrates. In addition, YidC can act as a foldase and promote the proper assembly of membrane protein complexes. Here, we investigate the effect of Escherichia coli YidC depletion on the assembly of penicillin binding proteins (PBPs), which are involved in cell wall synthesis. YidC depletion does not affect the total amount of the specific cell division PBP3 (FtsI) in the membrane, but the amount of active PBP3, as assessed by substrate binding, is reduced 2-fold. A similar reduction in the amount of active PBP2 was observed, while the levels of active PBP1A/1B and PBP5 were essentially similar. PBP1B and PBP3 disappeared from higher-Mw bands upon YidC depletion, indicating that YidC might play a role in PBP complex formation. Taken together, our results suggest that the foldase activity of YidC can extend to the periplasmic domains of membrane proteins. IMPORTANCE: This study addresses the role of the membrane protein insertase YidC in the biogenesis of penicillin binding proteins (PBPs). PBPs are proteins containing one transmembrane segment and a large periplasmic or extracellular domain, which are involved in peptidoglycan synthesis. We observe that in the absence of YidC, two critical PBPs are not correctly folded even though the total amount of protein in the membrane is not affected. Our findings extend the function of YidC as a foldase for membrane protein (complexes) to periplasmic domains of membrane proteins.","corpus_id":23286715,"score":1},{"doc_id":"26023232","title":"Role of the Cytosolic Loop C2 and the C Terminus of YidC in Ribosome Binding and Insertion Activity.","abstract":"Members of the YidC/Oxa1/Alb3 protein family mediate membrane protein insertion, and this process is initiated by the assembly of YidC·ribosome nascent chain complexes at the inner leaflet of the lipid bilayer. The positively charged C terminus of Escherichia coli YidC plays a significant role in ribosome binding but is not the sole determinant because deletion does not completely abrogate ribosome binding. The positively charged cytosolic loops C1 and C2 of YidC may provide additional docking sites. We performed systematic sequential deletions within these cytosolic domains and studied their effect on the YidC insertase activity and interaction with translation-stalled (programmed) ribosome. Deletions within loop C1 strongly affected the activity of YidC in vivo but did not influence ribosome binding or substrate insertion, whereas loop C2 appeared to be involved in ribosome binding. Combining the latter deletion with the removal of the C terminus of YidC abolished YidC-mediated insertion. We propose that these two regions play an crucial role in the formation and stabilization of an active YidC·ribosome nascent chain complex, allowing for co-translational membrane insertion, whereas loop C1 may be involved in the downstream chaperone activity of YidC or in other protein-protein interactions.","corpus_id":205351012,"score":1},{"doc_id":"26256539","title":"A YidC-like Protein in the Archaeal Plasma Membrane.","abstract":"Cells possess specialized machinery to direct the insertion of membrane proteins into the lipid bilayer. In bacteria, the essential protein YidC inserts certain proteins into the plasma membrane, and eukaryotic orthologs are present in the mitochondrial inner membrane and the chloroplast thylakoid membrane. The existence of homologous insertases in archaea has been proposed based on phylogenetic analysis. However, limited sequence identity, distinct architecture, and the absence of experimental data have made this assignment ambiguous. Here we describe the 3.5-Å crystal structure of an archaeal DUF106 protein from Methanocaldococcus jannaschii (Mj0480), revealing a lipid-exposed hydrophilic surface presented by a conserved YidC-like fold. Functional analysis reveals selective binding of Mj0480 to ribosomes displaying a stalled YidC substrate, and a direct interaction between the buried hydrophilic surface of Mj0480 and the nascent chain. These data provide direct experimental evidence that the archaeal DUF106 proteins are YidC/Oxa1/Alb3-like insertases of the archaeal plasma membrane.","corpus_id":1363419,"score":1},{"doc_id":"26331454","title":"Membrane Insertases Are Present in All Three Domains of Life.","abstract":"In this issue of Structure, Borowska et al. (2015) report the crystal structure and provide experimental evidence on an archaeal membrane insertase, the DUF106 protein from Methanocaldococcus jannaschii, demonstrating that YidC/Oxa1/Alb3-like insertases exist in the archaeal plasma membrane.","corpus_id":4966598,"score":1},{"doc_id":"28454841","title":"Assisted and Unassisted Protein Insertion into Liposomes.","abstract":"The insertion of newly synthesized membrane proteins is a well-regulated and fascinating process occurring in every living cell. Several translocases and insertases have been found in prokaryotic and eukaryotic cells, the Sec61 complex and the Get complex in the endoplasmic reticulum and the SecYEG complex and YidC in bacteria and archaea. In mitochondria, TOM and TIM complexes transport nuclear-encoded proteins, whereas the Oxa1 is required for the insertion of mitochondria-encoded membrane proteins. Related to the bacterial YidC and the mitochondrial Oxa1 are the Alb3 and Alb4 proteins in chloroplasts. These membrane insertases are comparably simple and can be studied in vitro, after their biochemical purification and reconstitution in artificial lipid bilayers such as liposomes or nanodiscs. Here, we describe the recent progress to study the molecular mechanism of YidC-dependent and unassisted membrane insertion at the single molecule level.","corpus_id":8591349,"score":1},{"doc_id":"29330366","title":"Each protomer of a dimeric YidC functions as a single membrane insertase.","abstract":"The membrane insertase YidC catalyzes the entrance of newly synthesized proteins into the lipid bilayer. As an integral membrane protein itself, YidC can be found as a monomer, a dimer or also as a member of the holotranslocase SecYEGDF-YajC-YidC. To investigate whether the dimeric YidC is functional and whether two copies cooperate to insert a single substrate, we constructed a fusion protein where two copies of YidC are connected by a short linker peptide. The 120 kDa protein is stable and functional as it supports the membrane insertion of the M13 procoat protein, the C-tailed protein SciP and the fusion protein Pf3-Lep. Mutations that inhibit either protomer do not inactivate the insertase and rather keep it functional. When both protomers are defective, the substrate proteins accumulate in the cytoplasm. This suggests that the dimeric YidC operates as two insertases. Consistent with this, we show that the dimeric YidC can bind two substrate proteins simultaneously, suggesting that YidC indeed functions as a monomer.","corpus_id":5227038,"score":1},{"doc_id":"29330529","title":"The interaction network of the YidC insertase with the SecYEG translocon, SRP and the SRP receptor FtsY.","abstract":"YidC/Oxa1/Alb3 are essential proteins that operate independently or cooperatively with the Sec machinery during membrane protein insertion in bacteria, archaea and eukaryotic organelles. Although the interaction between the bacterial SecYEG translocon and YidC has been observed in multiple studies, it is still unknown which domains of YidC are in contact with the SecYEG translocon. By in vivo and in vitro site-directed and para-formaldehyde cross-linking we identified the auxiliary transmembrane domain 1 of E. coli YidC as a major contact site for SecY and SecG. Additional SecY contacts were observed for the tightly packed globular domain and the C1 loop of YidC, which reveals that the hydrophilic cavity of YidC faces the lateral gate of SecY. Surprisingly, YidC-SecYEG contacts were only observed when YidC and SecYEG were present at about stoichiometric concentrations, suggesting that the YidC-SecYEG contact in vivo is either very transient or only observed for a very small SecYEG sub-population. This is different for the YidC-SRP and YidC-FtsY interaction, which involves the C1 loop of YidC and is efficiently observed even at sub-stoichiometric concentrations of SRP/FtsY. In summary, our data provide a first detailed view on how YidC interacts with the SecYEG translocon and the SRP-targeting machinery.","corpus_id":28986778,"score":1},{"doc_id":"18259071","title":"Purification, crystallization and preliminary structural characterization of the periplasmic domain P1 of the Escherichia coli membrane-protein insertase YidC.","abstract":"In Escherichia coli, the biogenesis of inner membrane proteins (IMPs) requires targeting and insertion factors such as the signal recognition particle (SRP) and the Sec translocon. Recent studies have identified YidC as a novel and essential component involved in membrane insertion of IMPs both in conjunction with the Sec translocon and as a separate entity. E. coli YidC is a member of the YidC (in bacteria)/Oxa1 (in mitochondria)/Alb3 (in chloroplasts) protein family and contains six transmembrane segments and a very large periplasmic domain P1. The overproduction, purification, crystallization and preliminary crystallographic studies of the native and selenomethionine-labelled P1 domain are reported here as a first step towards the elucidation of the molecular mechanism of YidC as a membrane-protein insertase.","corpus_id":19450572,"score":0},{"doc_id":"22040291","title":"The SCO2 protein disulphide isomerase is required for thylakoid biogenesis and interacts with LHCB1 chlorophyll a/b binding proteins which affects chlorophyll biosynthesis in Arabidopsis seedlings.","abstract":"The process of chloroplast biogenesis requires a multitude of pathways and processes to establish chloroplast function. In cotyledons of seedlings, chloroplasts develop either directly from proplastids (also named eoplasts) or, if germinated in the dark, via etioplasts, whereas in leaves chloroplasts derive from proplastids in the apical meristem and are then multiplied by division. The snowy cotyledon 2, sco2, mutations specifically disrupt chloroplast biogenesis in cotyledons. SCO2 encodes a chloroplast-localized protein disulphide isomerase, hypothesized to be involved in protein folding. Analysis of co-expressed genes with SCO2 revealed that genes with similar expression patterns encode chloroplast proteins involved in protein translation and in chlorophyll biosynthesis. Indeed, sco2-1 accumulates increased levels of the chlorophyll precursor, protochlorophyllide, in both dark grown cotyledons and leaves. Yeast two-hybrid analyses demonstrated that SCO2 directly interacts with the chlorophyll-binding LHCB1 proteins, being confirmed in planta using bimolecular fluorescence complementation (BIFC). Furthermore, ultrastructural analysis of sco2-1 chloroplasts revealed that formation and movement of transport vesicles from the inner envelope to the thylakoids is perturbed. SCO2 does not interact with the signal recognition particle proteins SRP54 and FtsY, which were shown to be involved in targeting of LHCB1 to the thylakoids. We hypothesize that SCO2 provides an alternative targeting pathway for light-harvesting chlorophyll binding (LHCB) proteins to the thylakoids via transport vesicles predominantly in cotyledons, with the signal recognition particle (SRP) pathway predominant in rosette leaves. Therefore, we propose that SCO2 is involved in the integration of LHCB1 proteins into the thylakoids that feeds back on the regulation of the tetrapyrrole biosynthetic pathway and nuclear gene expression.","corpus_id":3333983,"score":0},{"doc_id":"25084381","title":"Crystallization and preliminary X-ray diffraction analysis of YidC, a membrane-protein chaperone and insertase from Bacillus halodurans.","abstract":"YidC, a member of the YidC/Oxa1/Alb3 family, inserts proteins into the membrane and facilitates membrane-protein folding in bacteria. YidC plays key roles in both Sec-mediated integration and Sec-independent insertion of membrane proteins. Here, Bacillus halodurans YidC2, which has five transmembrane helices conserved among the other family members, was identified as a target protein for structure determination by a fluorescent size-exclusion chromatography analysis. The protein was overexpressed, purified and crystallized in the lipidic cubic phase. The crystals diffracted X-rays to 2.4 Å resolution and belonged to space group P21, with unit-cell parameters a = 43.9, b = 60.6, c = 58.9 Å, β = 100.3°. The experimental phases were determined by the multiwavelength anomalous diffraction method using a mercury-derivatized crystal.","corpus_id":-1,"score":0}],"string":"[\n {\n \"doc_id\": \"18234665\",\n \"title\": \"The crystal structure of the periplasmic domain of the Escherichia coli membrane protein insertase YidC contains a substrate binding cleft.\",\n \"abstract\": \"In bacteria the biogenesis of inner membrane proteins requires targeting and insertion factors such as the signal recognition particle and the Sec translocon. YidC is an essential membrane protein involved in the insertion of inner membrane proteins together with the Sec translocon, but also as a separate entity. YidC of Escherichia coli is a member of the conserved YidC (in bacteria)/Oxa1 (in mitochondria)/Alb3 (in chloroplasts) protein family and contains six transmembrane segments and a large periplasmic domain (P1). We determined the crystal structure of the periplasmic domain of YidC from E. coli (P1D) at 1.8 A resolution. The structure of P1D shows the conserved beta-supersandwich fold of carbohydrate-binding proteins and an alpha-helical linker region at the C terminus that packs against the beta-supersandwich by a highly conserved interface. P1D exhibits an elongated cleft of similar architecture as found in the structural homologs. However, the electrostatic properties and molecular details of the cleft make it unlikely to interact with carbohydrate substrates. The cleft in P1D is occupied by a polyethylene glycol molecule suggesting an elongated peptide or acyl chain as a natural ligand. The region of P1D previously reported to interact with SecF maps to a surface area in the vicinity of the cleft. The conserved C-terminal region of the P1 domain was reported to be essential for the membrane insertase function of YidC. The analysis of this region suggests a role in membrane interaction and/or in the regulation of YidC interaction with binding partners.\",\n \"corpus_id\": 22545719,\n \"score\": 2\n },\n {\n \"doc_id\": \"18586266\",\n \"title\": \"Assembly of chloroplast signal recognition particle involves structural rearrangement in cpSRP43.\",\n \"abstract\": \"Signal recognition particle in chloroplasts (cpSRP) exhibits the unusual ability to bind and target full-length proteins to the thylakoid membrane. Unlike cytosolic SRPs in prokaryotes and eukaryotes, cpSRP lacks an RNA moiety and functions as a heterodimer composed of a conserved 54-kDa guanosine triphosphatase (cpSRP54) and a unique 43-kDa subunit (cpSRP43). Assembly of the cpSRP heterodimer is a prerequisite for post-translational targeting activities and takes place through interactions between chromatin modifier domain 2 (CD2) of cpSRP43 and a unique 10-amino-acid region in cpSRP54 (cpSRP54(pep)). We have used multidimensional NMR spectroscopy and other biophysical methods to examine the assembly and structure of the cpSRP43-cpSRP54 interface. Our data show that CD2 of cpSRP43 binds to cpSRP54(pep) in a 1:1 stoichiometry with an apparent K(d) of approximately 1.06 muM. Steady-state fluorescence and far-UV circular dichroism data suggest that the CD2-cpSRP54(pep) interaction causes significant conformational changes in both CD2 and the peptide. Comparison of the three-dimensional solution structures of CD2 alone and in complex with cpSRP54(pep) shows that significant structural changes are induced in CD2 in order to establish a binding interface contributed mostly by residues in the N-terminal segment of CD2 (Phe5-Val10) and an arginine doublet (Arg536 and Arg537) in the cpSRP54 peptide. Taken together, our results provide new insights into the mechanism of cpSRP assembly and the structural forces that stabilize the functionally critical cpSRP43-cpSRP54 interaction.\",\n \"corpus_id\": 10283219,\n \"score\": 2\n },\n {\n \"doc_id\": \"18621669\",\n \"title\": \"Structural basis for specific substrate recognition by the chloroplast signal recognition particle protein cpSRP43.\",\n \"abstract\": \"Secretory and membrane proteins carry amino-terminal signal sequences that, in cotranslational targeting, are recognized by the signal recognition particle protein SRP54 without sequence specificity. The most abundant membrane proteins on Earth are the light-harvesting chlorophyll a/b binding proteins (LHCPs). They are synthesized in the cytoplasm, imported into the chloroplast, and posttranslationally targeted to the thylakoid membrane by cpSRP, a heterodimer formed by cpSRP54 and cpSRP43. We present the 1.5 angstrom crystal structure of cpSRP43 characterized by a unique arrangement of chromodomains and ankyrin repeats. The overall shape and charge distribution of cpSRP43 resembles the SRP RNA, which is absent in chloroplasts. The complex with the internal signal sequence of LHCPs reveals that cpSRP43 specifically recognizes a DPLG peptide motif. We describe how cpSPR43 adapts the universally conserved SRP system to posttranslational targeting and insertion of the LHCP family of membrane proteins.\",\n \"corpus_id\": 206513119,\n \"score\": 2\n },\n {\n \"doc_id\": \"18633119\",\n \"title\": \"Quantitative proteomics of a chloroplast SRP54 sorting mutant and its genetic interactions with CLPC1 in Arabidopsis.\",\n \"abstract\": \"cpSRP54 (for chloroplast SIGNAL RECOGNITION PARTICLE54) is involved in cotranslational and posttranslational sorting of thylakoid proteins. The Arabidopsis (Arabidopsis thaliana) cpSRP54 null mutant, ffc1-2, is pale green with delayed development. Western-blot analysis of individual leaves showed that the SRP sorting pathway, but not the SecY/E translocon, was strongly down-regulated with progressive leaf development in both wild-type and ffc1-2 plants. To further understand the impact of cpSRP54 deletion, a quantitative comparison of ffc2-1 was carried out for total leaf proteomes of young seedlings and for chloroplast proteomes of fully developed leaves using stable isotope labeling (isobaric stable isotope labeling and isotope-coded affinity tags) and two-dimensional gels. This showed that cpSRP54 deletion led to a change in light-harvesting complex composition, an increase of PsbS, and a decreased photosystem I/II ratio. Moreover, the cpSRP54 deletion led in young leaves to up-regulation of thylakoid proteases and stromal chaperones, including ClpC. In contrast, the stromal protein homeostasis machinery returned to wild-type levels in mature leaves, consistent with the developmental down-regulation of the SRP pathway. A differential response between young and mature leaves was also found in carbon metabolism, with an up-regulation of the Calvin cycle and the photorespiratory pathway in peroxisomes and mitochondria in young leaves but not in old leaves. The Calvin cycle was down-regulated in mature leaves to adjust to the reduced capacity of the light reaction, while reactive oxygen species defense proteins were up-regulated. The significance of ClpC up-regulation was confirmed through the generation of an ffc2-1 clpc1 double mutant. This mutant was seedling lethal under autotrophic conditions but could be partially rescued under heterotrophic conditions.\",\n \"corpus_id\": 42791587,\n \"score\": 2\n },\n {\n \"doc_id\": \"18755190\",\n \"title\": \"Evolutionary substitution of two amino acids in chloroplast SRP54 of higher plants cause its inability to bind SRP RNA.\",\n \"abstract\": \"The chloroplast signal recognition particle (cpSRP) consists of a conserved 54 kDa subunit (cpSRP54) and a unique 43 kDa subunit (cpSRP43) but lacks SRP-RNA, an essential and universally conserved component of cytosolic SRPs. High sequence similarity exists between cpSRP54 and bacterial SRP54 except for a plant-specific C-terminal extension containing the cpSRP43-binding motif. We found that cpSRP54 of higher plants lacks the ability to bind SRP-RNA because of two amino acid substitutions within a region corresponding to the RNA binding domain of cytosolic SRP54, whereas the C-terminal extension does not affect RNA binding. Phylogenetic analysis revealed that these mutations occur in the cpSRP54 homologues of higher plants but not in most algae.\",\n \"corpus_id\": 1569836,\n \"score\": 2\n },\n {\n \"doc_id\": \"18764927\",\n \"title\": \"Non-identical contributions of two membrane-bound cpSRP components, cpFtsY and Alb3, to thylakoid biogenesis.\",\n \"abstract\": \"The insertion of light-harvesting chlorophyll proteins (LHCPs) into the thylakoid membrane of the chloroplast is cpSRP-dependent, and requires the stromal components cpSRP54 and cpSRP43, the membrane-bound SRP receptor cpFtsY and the integral membrane protein Alb3. Previous studies demonstrated that the Arabidopsis mutant lacking both cpSRP54 and cpSRP43 had pale yellow leaves, but was viable, whereas the mutants lacking Alb3 exhibit an albino phenotype that is more severe and seedling lethality. We previously showed that a maize mutant lacking cpFtsY had a pale yellow-green phenotype and was seedling lethal. To compare the in vivo requirements of cpFtsY and Alb3 in thylakoid biogenesis in greater detail, we isolated Arabidopsis null mutants of cpftsY, and performed biochemical comparisons with the Arabidopsis alb3 mutant. Both cpftsY and alb3 null mutants were seedling lethal on a synthetic medium lacking sucrose, whereas on a medium supplemented with sucrose, they were able to grow to later developmental stages, but were mostly infertile. cpftsY mutant plants had yellow leaves in which the levels of LHCPs were reduced to 10-33% compared with wild type. In contrast, alb3 had yellowish white leaves, and the LHCP levels were less than or equal to 10% of those of wild type. Intriguingly, whereas accumulation of the Sec and Tat machineries were normal in both mutants, the Sec pathway substrate Cyt f was more severely decreased in the cpftsY mutant than in alb3, which may indicate a functional link between cpFtsY and Sec translocation machinery. These results suggest that cpFtsY and Alb3 have essentially similar, but slightly distinct, contributions to thylakoid biogenesis.\",\n \"corpus_id\": 28676639,\n \"score\": 2\n },\n {\n \"doc_id\": \"19293157\",\n \"title\": \"The membrane-binding motif of the chloroplast signal recognition particle receptor (cpFtsY) regulates GTPase activity.\",\n \"abstract\": \"The chloroplast signal recognition particle (cpSRP) and its receptor (cpFtsY) function in thylakoid biogenesis to target integral membrane proteins to thylakoids. Unlike cytosolic SRP receptors in eukaryotes, cpFtsY partitions between thylakoid membranes and the soluble stroma. Based on sequence alignments, a membrane-binding motif identified in Escherichia coli FtsY appears to be conserved in cpFtsY, yet whether the proposed motif is responsible for the membrane-binding function of cpFtsY has yet to be shown experimentally. Our studies show that a small N-terminal region in cpFtsY stabilizes a membrane interaction critical to cpFtsY function in cpSRP-dependent protein targeting. This membrane-binding motif is both necessary and sufficient to direct cpFtsY and fused passenger proteins to thylakoids. Our results demonstrate that the cpFtsY membrane-binding motif may be functionally replaced by the corresponding region from E. coli, confirming that the membrane-binding motif is conserved among organellar and prokaryotic homologs. Furthermore, the capacity of cpFtsY for lipid binding correlates with liposome-induced GTP hydrolysis stimulation. Mutations that debilitate the membrane-binding motif in cpFtsY result in higher rates of GTP hydrolysis, suggesting that negative regulation is provided by the intact membrane-binding region in the absence of a bilayer. Furthermore, NMR and CD structural studies of the N-terminal region and the analogous region in the E. coli SRP receptor revealed a conformational change in secondary structure that takes place upon lipid binding. These studies suggest that the cpFtsY membrane-binding motif plays a critical role in the intramolecular communication that regulates cpSRP receptor functions at the membrane.\",\n \"corpus_id\": 39255863,\n \"score\": 2\n },\n {\n \"doc_id\": \"19366667\",\n \"title\": \"Independent gene duplications of the YidC/Oxa/Alb3 family enabled a specialized cotranslational function.\",\n \"abstract\": \"YidC/Oxa/Alb3 family proteins catalyze the insertion of integral membrane proteins in bacteria, mitochondria, and chloroplasts, respectively. Unlike gram-negative organisms, gram-positive bacteria express 2 paralogs of this family, YidC1/SpoIIIJ and YidC2/YgjG. In Streptococcus mutans, deletion of yidC2 results in a stress-sensitive phenotype similar to that of mutants lacking the signal recognition particle (SRP) protein translocation pathway, while deletion of yidC1 has a less severe phenotype. In contrast to eukaryotes and gram-negative bacteria, SRP-deficient mutants are viable in S. mutans; however, double SRP-yidC2 mutants are severely compromised. Thus, YidC2 may enable loss of the SRP by playing an independent but overlapping role in cotranslational protein insertion into the membrane. This is reminiscent of the situation in mitochondria that lack an SRP pathway and where Oxa1 facilitates cotranslational membrane protein insertion by binding directly to translation-active ribosomes. Here, we show that OXA1 complements a lack of yidC2 in S. mutans. YidC2 also functions reciprocally in oxa1-deficient Saccharomyces cerevisiae mutants and mediates the cotranslational insertion of mitochondrial translation products into the inner membrane. YidC2, like Oxa1, contains a positively charged C-terminal extension and associates with translating ribosomes. Our results are consistent with a gene-duplication event in gram-positive bacteria that enabled the specialization of a YidC isoform that mediates cotranslational activity independent of an SRP pathway.\",\n \"corpus_id\": 23829375,\n \"score\": 2\n },\n {\n \"doc_id\": \"19534824\",\n \"title\": \"The evolution of YidC/Oxa/Alb3 family in the three domains of life: a phylogenomic analysis.\",\n \"abstract\": \"BACKGROUND: YidC/Oxa/Alb3 family includes a group of conserved translocases that are essential for protein insertion into inner membranes of bacteria and mitochondria, and thylakoid membranes of chloroplasts. Because mitochondria and chloroplasts are of bacterial origin, Oxa and Alb3, like many other mitochondrial/chloroplastic proteins, are hypothetically derived from the pre-existing protein (YidC) of bacterial endosymbionts. Here, we test this hypothesis and investigate the evolutionary history of the whole YidC/Oxa/Alb3 family in the three domains of life. RESULTS: Our comprehensive analyses of the phylogenetic distribution and phylogeny of the YidC/Oxa/Alb3 family lead to the following findings: 1) In archaea, YidC homologs are only sporadically distributed in Euryarchaeota; 2) Most bacteria contain only one YidC gene copy; some species in a few taxa (Bacillus, Lactobacillales, Actinobacteria and Clostridia) have two gene copies; 3) Eukaryotic Oxa and Alb3 have two separate prokaryotic origins, but they might not arise directly from the YidC of proteobacteria and cyanobacteria through the endosymbiosis origins of mitochondrium and chloroplast, respectively; 4) An ancient duplication occurred on both Oxa and Alb3 immediately after their origins, and thus most eukaryotes generally bear two Oxa and two Alb3. However, secondary loss, duplication or acquisition of new domain also occurred on the two genes in some lineages, especially in protists, resulting in a rich diversity or adaptive differentiation of the two translocases in these lineages. CONCLUSION: YidC is distributed in bacteria and some Euryarchaeota. Although mitochondrial Oxa and chloroplastic Alb3 are derived from the prokaryotic YidC, their origin might be not related to the endosymbiosis events of the two organelles. In some eukaryotic lineages, especially in protists, Oxa and Alb3 have diverse evolutionary histories. Finally, a model for the evolutionary history of the entire YidC/Oxa/Alb3 family in the three domains of life is proposed.\",\n \"corpus_id\": -1,\n \"score\": 2\n },\n {\n \"doc_id\": \"19995738\",\n \"title\": \"Alb4 of Arabidopsis promotes assembly and stabilization of a non chlorophyll-binding photosynthetic complex, the CF1CF0-ATP synthase.\",\n \"abstract\": \"All members of the YidC/Oxa1/Alb3 protein family are evolutionarily conserved and appear to function in membrane protein integration and protein complex stabilization. Here, we report on a second thylakoidal isoform of Alb3, named Alb4. Analysis of Arabidopsis knockout mutant lines shows that Alb4 is required in assembly and/or stability of the CF1CF0-ATP synthase (ATPase). alb4 mutant lines not only have reduced steady-state levels of ATPase subunits, but also their assembly into high-molecular-mass complexes is altered, leading to a reduction of ATP synthesis in the mutants. Moreover, we show that Alb4 but not Alb3 physically interacts with the subunits CF1beta and CF0II. Summarizing, the data indicate that Alb4 functions to stabilize or promote assembly of CF1 during its attachment to the membrane-embedded CF0 part.\",\n \"corpus_id\": 281657,\n \"score\": 2\n },\n {\n \"doc_id\": \"20498370\",\n \"title\": \"cpSRP43 is a novel chaperone specific for light-harvesting chlorophyll a,b-binding proteins.\",\n \"abstract\": \"The biosynthesis of most membrane proteins is directly coupled to membrane insertion, and therefore, molecular chaperones are not required. The light-harvesting chlorophyll a,b-binding proteins (LHCPs) present a prominent exception as they are synthesized in the cytoplasm, and after import into the chloroplast, they are targeted and inserted into the thylakoid membrane. Upon arrival in the stroma, LHCPs form a soluble transit complex with the chloroplast signal recognition particle (cpSRP) consisting of an SRP54 homolog and the unique cpSRP43 composed of three chromodomains and four ankyrin repeats. Here we describe that cpSRP43 alone prevents aggregation of LHCP by formation of a complex with nanomolar affinity, whereas cpSRP54 is not required for this chaperone activity. Other stromal chaperones like trigger factor cannot replace cpSRP43, which implies that LHCPs require a specific chaperone. Although cpSRP43 does not have an ATPase activity, it can dissolve aggregates of LHCPs similar to chaperones of the Hsp104/ClpB family. We show that the LHCP-cpSRP43 interaction is predominantly hydrophobic but strictly depends on an intact DPLG motif between the second and third transmembrane region. The cpSRP43 ankyrin repeats that provide the binding site for the DPLG motif are sufficient for the chaperone function, whereas the chromodomains are dispensable. Taken together, we define cpSRP43 as a highly specific chaperone for LHCPs in addition to its established function as a targeting factor for this family of membrane proteins.\",\n \"corpus_id\": 12037009,\n \"score\": 2\n },\n {\n \"doc_id\": \"20709425\",\n \"title\": \"Component interactions, regulation and mechanisms of chloroplast signal recognition particle-dependent protein transport.\",\n \"abstract\": \"The chloroplast proteome comprises nuclear- and plastome-encoded proteins. In order to function correctly these proteins must be transported, either cotranslationally or posttranslationally, to their final destination in the chloroplast. Here the chloroplast signal recognition particle (cpSRP) which is present in two different stromal pools plays an essential role. On the one hand, the conserved 54kDa subunit (cpSRP54) is associated with 70S ribosomes to function in the cotranslational transport of the plastid-encoded thylakoid membrane protein D1. On the other hand, the cpSRP consists of cpSRP54 and a unique 43kDa subunit (cpSRP43) and facilitates the transport of nuclear-encoded light-harvesting chlorophyll-binding proteins (LHCPs), the most abundant membrane proteins of the thylakoids. In addition to cpSRP, the cpSRP receptor cpFtsY and the thylakoid membrane protein Alb3 are required for posttranslational LHCP integration in a GTP-dependent manner. In contrast to the universally conserved cytosolic SRP, the chloroplast SRP of higher plants lacks an SRP-RNA component. Interestingly, cpSRP-RNA genes have been identified in the plastome of lower plants, indicating that their cpSRP structure resembles the cytosolic SRP.\",\n \"corpus_id\": 40931935,\n \"score\": 2\n },\n {\n \"doc_id\": \"20729200\",\n \"title\": \"A dynamic cpSRP43-Albino3 interaction mediates translocase regulation of chloroplast signal recognition particle (cpSRP)-targeting components.\",\n \"abstract\": \"The chloroplast signal recognition particle (cpSRP) and its receptor, chloroplast FtsY (cpFtsY), form an essential complex with the translocase Albino3 (Alb3) during post-translational targeting of light-harvesting chlorophyll-binding proteins (LHCPs). Here, we describe a combination of studies that explore the binding interface and functional role of a previously identified cpSRP43-Alb3 interaction. Using recombinant proteins corresponding to the C terminus of Alb3 (Alb3-Cterm) and various domains of cpSRP43, we identify the ankyrin repeat region of cpSRP43 as the domain primarily responsible for the interaction with Alb3-Cterm. Furthermore, we show Alb3-Cterm dissociates a cpSRP·LHCP targeting complex in vitro and stimulates GTP hydrolysis by cpSRP54 and cpFtsY in a strictly cpSRP43-dependent manner. These results support a model in which interactions between the ankyrin region of cpSRP43 and the C terminus of Alb3 promote distinct membrane-localized events, including LHCP release from cpSRP and release of targeting components from Alb3.\",\n \"corpus_id\": 35780521,\n \"score\": 2\n },\n {\n \"doc_id\": \"20800571\",\n \"title\": \"Inserting membrane proteins: the YidC/Oxa1/Alb3 machinery in bacteria, mitochondria, and chloroplasts.\",\n \"abstract\": \"The evolutionarily conserved YidC/Oxa1p/Alb3 family of proteins plays important roles in the membrane biogenesis in bacteria, mitochondria, and chloroplasts. The members in this family function as novel membrane protein insertases, chaperones, and assembly factors for transmembrane proteins, including energy transduction complexes localized in the bacterial and mitochondrial inner membrane, and in the chloroplast thylakoid membrane. In this review, we will present recent progress with this class of proteins in membrane protein biogenesis and discuss the structure/function relationships. This article is part of a Special Issue entitled Protein translocation across or insertion into membranes.\",\n \"corpus_id\": 41093923,\n \"score\": 2\n },\n {\n \"doc_id\": \"20828566\",\n \"title\": \"Interplay between the cpSRP pathway components, the substrate LHCP and the translocase Alb3: an in vivo and in vitro study.\",\n \"abstract\": \"The chloroplast signal recognition particle (cpSRP) and its receptor, cpFtsY, posttranslationally target the nuclear-encoded light-harvesting chlorophyll-binding proteins (LHCPs) to the translocase Alb3 in the thylakoid membrane. In this study, we analyzed the interplay between the cpSRP pathway components, the substrate protein LHCP and the translocase Alb3 by using in vivo and in vitro techniques. We propose that cpSRP43 is crucial for the binding of LHCP-loaded cpSRP and cpFtsY to Alb3. In addition, our data suggest that a direct interaction between Alb3 and LHCP contributes to the formation of this complex.\",\n \"corpus_id\": 37536189,\n \"score\": 2\n },\n {\n \"doc_id\": \"21194367\",\n \"title\": \"Evolution of YidC/Oxa1/Alb3 insertases: three independent gene duplications followed by functional specialization in bacteria, mitochondria and chloroplasts.\",\n \"abstract\": \"Members of the YidC/Oxa1/Alb3 protein family facilitate the insertion, folding and assembly of proteins of the inner membranes of bacteria and mitochondria and the thylakoid membrane of plastids. All homologs share a conserved hydrophobic core region comprising five transmembrane domains. On the basis of phylogenetic analyses, six subgroups of the family can be distinguished which presumably arose from three independent gene duplications followed by functional specialization. During evolution of bacteria, mitochondria and chloroplasts, subgroup-specific regions were added to the core domain to facilitate the association with ribosomes or other components contributing to the substrate spectrum of YidC/Oxa1/Alb3 proteins.\",\n \"corpus_id\": 2813617,\n \"score\": 2\n },\n {\n \"doc_id\": \"21466505\",\n \"title\": \"Binding of chloroplast signal recognition particle to a thylakoid membrane protein substrate in aqueous solution and delineation of the cpSRP43-substrate interaction domain.\",\n \"abstract\": \"A cpSRP [chloroplast SRP (signal recognition particle)] comprising cpSRP54 and cpSRP43 subunits mediates the insertion of light-harvesting proteins into the thylakoid membrane. We dissected its interaction with a full-length membrane protein substrate in aqueous solution by insertion of site-specific photo-activatable cross-linkers into in vitro-synthesized Lhcb1 (major light-harvesting chlorophyll-binding protein of photosystem II). We show that Lhcb1 residues 166-176 cross-link specifically to the cpSRP43 subunit. Some cross-link positions within Lhcb1 are in the 'L18' peptide required for targeting of cpSRP substrates, whereas other cross-linking positions define a new targeting signal in the third transmembrane span. Lhcb1 was not found to cross-link to cpSRP54 at any position, and cross-linking to cpSRP43 is unaffected by the absence of cpSRP54. cpSRP43 thus effectively binds substrates autonomously, and its ability to independently bind an extended 20+-residue substrate region highlights a major difference with other SRP types where the SRP54 subunit binds to hydrophobic target sequences. The results also show that cpSRP43 can bind to a hydrophobic, three-membrane span, substrate in aqueous solution, presumably reflecting a role for cpSRP in the chloroplast stroma. This mode of action, and the specificity of the cpSRP43-substrate interaction, may be associated with cpSRP's unique post-translational mode of action.\",\n \"corpus_id\": 10105595,\n \"score\": 2\n },\n {\n \"doc_id\": \"21832051\",\n \"title\": \"Interaction studies between the chloroplast signal recognition particle subunit cpSRP43 and the full-length translocase Alb3 reveal a membrane-embedded binding region in Alb3 protein.\",\n \"abstract\": \"Posttranslational targeting of the light-harvesting chlorophyll a,b-binding proteins depends on the function of the chloroplast signal recognition particle, its receptor cpFtsY, and the translocase Alb3. The thylakoid membrane protein Alb3 of Arabidopsis chloroplasts belongs to the evolutionarily conserved YidC/Oxa1/Alb3 protein family; the members of this family facilitate the insertion, folding, and assembly of membrane proteins in bacteria, mitochondria, and chloroplasts. Here, we analyzed the interaction sites of full-length Alb3 with the cpSRP pathway component cpSRP43 by using in vitro and in vivo studies. Bimolecular fluorescence complementation and Alb3 proteoliposome studies showed that the interaction of cpSRP43 is dependent on a binding domain in the C terminus of Alb3 as well as an additional membrane-embedded binding site in the fifth transmembrane domain (TMD5) of Alb3. The C-terminal binding domain was mapped to residues 374-388, and the binding domain within TMD5 was mapped to residues 314-318 located close to the luminal end of TMD5. A direct binding between cpSRP43 and these binding motifs was shown by pepspot analysis. Further studies using blue-native gel electrophoresis revealed that full-length Alb3 is able to form dimers. This finding and the identification of a membrane-embedded cpSRP43 binding site in Alb3 support a model in which cpSRP43 inserts into a dimeric Alb3 translocation pore during cpSRP-dependent delivery of light-harvesting chlorophyll a,b-binding proteins.\",\n \"corpus_id\": 24720011,\n \"score\": 2\n },\n {\n \"doc_id\": \"22231402\",\n \"title\": \"Chromodomains read the arginine code of post-translational targeting.\",\n \"abstract\": \"Chromodomains typically recruit protein complexes to chromatin and read the epigenetic histone code by recognizing lysine methylation in histone tails. We report the crystal structure of the chloroplast signal recognition particle (cpSRP) core from Arabidopsis thaliana, with the cpSRP54 tail comprising an arginine-rich motif bound to the second chromodomain of cpSRP43. A twinned aromatic cage reads out two neighboring nonmethylated arginines and adapts chromodomains to a non-nuclear function in post-translational targeting.\",\n \"corpus_id\": 22901035,\n \"score\": 2\n },\n {\n \"doc_id\": \"23111630\",\n \"title\": \"The YidC/Oxa1/Alb3 protein family: common principles and distinct features.\",\n \"abstract\": \"The members of the YidC/Oxa1/Alb3 protein family are evolutionary conserved in all three domains of life. They facilitate the insertion of membrane proteins into bacterial, mitochondrial, and thylakoid membranes and have been implicated in membrane protein folding and complex formation. The major classes of substrates are small hydrophobic subunits of large energy-transducing complexes involved in respiration and light capturing. All YidC-like proteins share a conserved membrane region, whereas the N- and C-terminal regions are diverse and fulfill accessory functions in protein targeting.\",\n \"corpus_id\": 23982847,\n \"score\": 2\n },\n {\n \"doc_id\": \"23933010\",\n \"title\": \"Elucidating the native architecture of the YidC: ribosome complex.\",\n \"abstract\": \"Membrane protein biogenesis in bacteria occurs via dedicated molecular systems SecYEG and YidC that function independently and in cooperation. YidC belongs to the universally conserved Oxa1/Alb3/YidC family of membrane insertases and is believed to associate with translating ribosomes at the membrane surface. Here, we have examined the architecture of the YidC:ribosome complex formed upon YidC-mediated membrane protein insertion. Fluorescence correlation spectroscopy was employed to investigate the complex assembly under physiological conditions. A slightly acidic environment stimulates binding of detergent-solubilized YidC to ribosomes due to electrostatic interactions, while YidC acquires specificity for translating ribosomes at pH-neutral conditions. The nanodisc reconstitution of the YidC to embed it into a native phospholipid membrane environment strongly enhances the YidC:ribosome complex formation. A single copy of YidC suffices for the binding of translating ribosome both in detergent and at the lipid membrane interface, thus being the minimal functional unit. Data reveal molecular details on the insertase functioning and interactions and suggest a new structural model for the YidC:ribosome complex.\",\n \"corpus_id\": 20454463,\n \"score\": 2\n },\n {\n \"doc_id\": \"24418623\",\n \"title\": \"The membrane insertase YidC.\",\n \"abstract\": \"The membrane insertases YidC-Oxa1-Alb3 provide a simple cellular system that catalyzes the transmembrane topology of newly synthesized membrane proteins. The insertases are composed of a single protein with 5 to 6 transmembrane (TM) helices that contact hydrophobic segments of the substrate proteins. Since YidC also cooperates with the Sec translocase it is widely involved in the assembly of many different membrane proteins including proteins that obtain complex membrane topologies. Homologues found in mitochondria (Oxa1) and thylakoids (Alb3) point to a common evolutionary origin and also demonstrate the general importance of this cellular process. This article is part of a Special Issue entitled: Protein trafficking and secretion in bacteria. Guest Editors: Anastassios Economou and Ross Dalbey.\",\n \"corpus_id\": 6255282,\n \"score\": 2\n },\n {\n \"doc_id\": \"24612058\",\n \"title\": \"The Arabidopsis Tellurite resistance C protein together with ALB3 is involved in photosystem II protein synthesis.\",\n \"abstract\": \"Assembly of photosystem II (PSII) occurs sequentially and requires several auxiliary proteins, such as ALB3 (ALBINO3). Here, we describe the role of the Arabidopsis thaliana thylakoid membrane protein Tellurite resistance C (AtTerC) in this process. Knockout of AtTerC was previously shown to be seedling-lethal. This phenotype was rescued by expressing TerC fused C-terminally to GFP in the terc-1 background, and the resulting terc-1TerC- GFP line and an artificial miRNA-based knockdown allele (amiR-TerC) were used to analyze the TerC function. The alterations in chlorophyll fluorescence and thylakoid ultrastructure observed in amiR-TerC plants and terc-1TerC- GFP were attributed to defects in PSII. We show that this phenotype resulted from a reduction in the rate of de novo synthesis of PSII core proteins, but later steps in PSII biogenesis appeared to be less affected. Yeast two-hybrid assays showed that TerC interacts with PSII proteins. In particular, its interaction with the PSII assembly factor ALB3 has been demonstrated by co-immunoprecipitation. ALB3 is thought to assist in incorporation of CP43 into PSII via interaction with Low PSII Accumulation2 (LPA2) Low PSII Accumulation3 (LPA3). Homozygous lpa2 mutants expressing amiR-TerC displayed markedly exacerbated phenotypes, leading to seedling lethality, indicating an additive effect. We propose a model in which TerC, together with ALB3, facilitates de novo synthesis of thylakoid membrane proteins, for instance CP43, at the membrane insertion step.\",\n \"corpus_id\": 20573960,\n \"score\": 2\n },\n {\n \"doc_id\": \"24739968\",\n \"title\": \"Structural basis of Sec-independent membrane protein insertion by YidC.\",\n \"abstract\": \"Newly synthesized membrane proteins must be accurately inserted into the membrane, folded and assembled for proper functioning. The protein YidC inserts its substrates into the membrane, thereby facilitating membrane protein assembly in bacteria; the homologous proteins Oxa1 and Alb3 have the same function in mitochondria and chloroplasts, respectively. In the bacterial cytoplasmic membrane, YidC functions as an independent insertase and a membrane chaperone in cooperation with the translocon SecYEG. Here we present the crystal structure of YidC from Bacillus halodurans, at 2.4 Å resolution. The structure reveals a novel fold, in which five conserved transmembrane helices form a positively charged hydrophilic groove that is open towards both the lipid bilayer and the cytoplasm but closed on the extracellular side. Structure-based in vivo analyses reveal that a conserved arginine residue in the groove is important for the insertion of membrane proteins by YidC. We propose an insertion mechanism for single-spanning membrane proteins, in which the hydrophilic environment generated by the groove recruits the extracellular regions of substrates into the low-dielectric environment of the membrane.\",\n \"corpus_id\": 4451969,\n \"score\": 2\n },\n {\n \"doc_id\": \"25012291\",\n \"title\": \"A structural model of the active ribosome-bound membrane protein insertase YidC.\",\n \"abstract\": \"The integration of most membrane proteins into the cytoplasmic membrane of bacteria occurs co-translationally. The universally conserved YidC protein mediates this process either individually as a membrane protein insertase, or in concert with the SecY complex. Here, we present a structural model of YidC based on evolutionary co-variation analysis, lipid-versus-protein-exposure and molecular dynamics simulations. The model suggests a distinctive arrangement of the conserved five transmembrane domains and a helical hairpin between transmembrane segment 2 (TM2) and TM3 on the cytoplasmic membrane surface. The model was used for docking into a cryo-electron microscopy reconstruction of a translating YidC-ribosome complex carrying the YidC substrate FOc. This structure reveals how a single copy of YidC interacts with the ribosome at the ribosomal tunnel exit and identifies a site for membrane protein insertion at the YidC protein-lipid interface. Together, these data suggest a mechanism for the co-translational mode of YidC-mediated membrane protein insertion.\",\n \"corpus_id\": 8125594,\n \"score\": 2\n },\n {\n \"doc_id\": \"25833951\",\n \"title\": \"Chloroplast SRP54 Was Recruited for Posttranslational Protein Transport via Complex Formation with Chloroplast SRP43 during Land Plant Evolution.\",\n \"abstract\": \"In bacteria, membrane proteins are targeted cotranslationally via a signal recognition particle (SRP). During the evolution of higher plant chloroplasts from cyanobacteria, the SRP pathway underwent striking adaptations that enable the posttranslational transport of the abundant light-harvesting chlorophyll-a/b-binding proteins (LHCPs). The conserved 54-kDa SRP subunit in higher plant chloroplasts (cpSRP54) is not bound to an SRP RNA, an essential SRP component in bacteria, but forms a stable heterodimer with the chloroplast-specific cpSRP43. This heterodimeric cpSRP recognizes LHCP and delivers it to the thylakoid membrane whereby cpSRP43 plays a central role. This study shows that the cpSRP system in the green alga Chlamydomonas reinhardtii differs significantly from that of higher plants as cpSRP43 is not complexed to cpSRP54 in Chlamydomonas and cpSRP54 is not involved in LHCP recognition. This divergence is attributed to altered residues within the cpSRP54 tail and the second chromodomain of cpSRP43 that are crucial for the formation of the binding interface in Arabidopsis. These changes are highly conserved among chlorophytes, whereas all land plants contain cpSRP proteins with typical interaction motifs. These data demonstrate that the coevolution of LHCPs and cpSRP43 occurred independently of complex formation with cpSRP54 and that the interaction between cpSRP54 and cpSRP43 evolved later during the transition from chlorophytes to land plants. Furthermore, our data show that in higher plants a heterodimeric form of cpSRP is required for the formation of a low molecular weight transit complex with LHCP.\",\n \"corpus_id\": 205345422,\n \"score\": 2\n },\n {\n \"doc_id\": \"25918165\",\n \"title\": \"Regulation of Structural Dynamics within a Signal Recognition Particle Promotes Binding of Protein Targeting Substrates.\",\n \"abstract\": \"Protein targeting is critical in all living organisms and involves a signal recognition particle (SRP), an SRP receptor, and a translocase. In co-translational targeting, interactions among these proteins are mediated by the ribosome. In chloroplasts, the light-harvesting chlorophyll-binding protein (LHCP) in the thylakoid membrane is targeted post-translationally without a ribosome. A multidomain chloroplast-specific subunit of the SRP, cpSRP43, is proposed to take on the role of coordinating the sequence of targeting events. Here, we demonstrate that cpSRP43 exhibits significant interdomain dynamics that are reduced upon binding its SRP binding partner, cpSRP54. We showed that the affinity of cpSRP43 for the binding motif of LHCP (L18) increases when cpSRP43 is complexed to the binding motif of cpSRP54 (cpSRP54pep). These results support the conclusion that substrate binding to the chloroplast SRP is modulated by protein structural dynamics in which a major role of cpSRP54 is to improve substrate binding efficiency to the cpSRP.\",\n \"corpus_id\": 10593109,\n \"score\": 2\n },\n {\n \"doc_id\": \"25947384\",\n \"title\": \"YidC/Alb3/Oxa1 Family of Insertases.\",\n \"abstract\": \"The YidC/Alb3/Oxa1 family functions in the insertion and folding of proteins in the bacterial cytoplasmic membrane, the chloroplast thylakoid membrane, and the mitochondrial inner membrane. All members share a conserved region composed of five transmembrane regions. These proteins mediate membrane insertion of an assorted group of proteins, ranging from respiratory subunits in the mitochondria and light-harvesting chlorophyll-binding proteins in chloroplasts to ATP synthase subunits in bacteria. This review discusses the YidC/Alb3/Oxa1 protein family as well as their function in membrane insertion and two new structures of the bacterial YidC, which suggest a mechanism for membrane insertion by this family of insertases.\",\n \"corpus_id\": 205380419,\n \"score\": 2\n },\n {\n \"doc_id\": \"26105652\",\n \"title\": \"The extreme Albino3 (Alb3) C terminus is required for Alb3 stability and function in Arabidopsis thaliana.\",\n \"abstract\": \"MAIN CONCLUSION: The extreme Alb3 C terminus is important for Alb3 stability in a light dependent manner, but is dispensable for LHCP insertion or D1 synthesis. YidC/Oxa1/Alb3 dependent insertion of membrane proteins is evolutionary conserved among bacteria, mitochondria and chloroplasts. Chloroplasts are challenged by the need to coordinate membrane integration of nuclear encoded, post-translationally targeted proteins into the thylakoids as well as of proteins translated on plastid ribosomes. The pathway facilitating post-translational targeting of the light-harvesting chlorophyll a/b binding proteins involves the chloroplast signal recognition particle, cpSRP54 and cpSRP43, as well as its membrane receptor FtsY and the translocase Alb3. Interaction of cpSRP43 with Alb3 is mediated by the positively charged, stromal exposed C terminus of Alb3. In this study, we utilized an Alb3 T-DNA insertion mutant in Arabidopsis thaliana lacking the last 75 amino acids to elucidate the function of this domain (alb3∆C). However, the truncated Alb3 protein (Alb3∆C) proved to be unstable under standard growth conditions, resulting in a reduction of Alb3∆C to 20 % of wild-type levels. In contrast, accumulation of Alb3∆C was comparable to wild type under low light growth conditions. Alb3∆C mutants grown under low light conditions were only slightly paler than wild type, accumulated almost wild-type levels of light harvesting proteins and were not affected in D1 synthesis, therefore showing that the extreme Alb3 C terminus is dispensable for both, co- and post-translational, protein insertion into the thylakoid membrane. However, reduction of Alb3∆C levels as observed under standard growth conditions resulted not only in a severely diminished accumulation of all thylakoid complexes but also in a strong defect in D1 synthesis and membrane insertion.\",\n \"corpus_id\": 1546146,\n \"score\": 2\n },\n {\n \"doc_id\": \"26265777\",\n \"title\": \"Genetic and Physical Interaction Studies Reveal Functional Similarities between ALBINO3 and ALBINO4 in Arabidopsis.\",\n \"abstract\": \"ALBINO3 (ALB3) is a well-known component of a thylakoid protein-targeting complex that interacts with the chloroplast signal recognition particle (cpSRP) and the cpSRP receptor, chloroplast filamentous temperature-sensitive Y (cpFtsY). Its protein-inserting function has been established mainly for light-harvesting complex proteins, which first interact with the unique chloroplast cpSRP43 component and then are delivered to the ALB3 integrase by a GTP-dependent cpSRP-cpFtsY interaction. In Arabidopsis (Arabidopsis thaliana), a subsequently discovered ALB3 homolog, ALB4, has been proposed to be involved not in light-harvesting complex protein targeting, but instead in the stabilization of the ATP synthase complex. Here, however, we show that ALB3 and ALB4 share significant functional overlap, and that both proteins are required for the efficient insertion of cytochrome f and potentially other subunits of pigment-bearing protein complexes. Genetic and physical interactions between ALB4 and ALB3, and physical interactions between ALB4 and cpSRP, suggest that the two ALB proteins may engage similar sets of interactors for their specific functions. We propose that ALB4 optimizes the insertion of thylakoid proteins by participating in the ALB3-cpSRP pathway for certain substrates (e.g. cytochrome f and the Rieske protein). Although ALB4 has clearly diverged from ALB3 in relation to the partner-recruiting C-terminal domain, our analysis suggests that one putative cpSRP-binding motif has not been entirely lost.\",\n \"corpus_id\": 44622706,\n \"score\": 2\n },\n {\n \"doc_id\": \"26568381\",\n \"title\": \"Structural basis for cpSRP43 chromodomain selectivity and dynamics in Alb3 insertase interaction.\",\n \"abstract\": \"Canonical membrane protein biogenesis requires co-translational delivery of ribosome-associated proteins to the Sec translocase and depends on the signal recognition particle (SRP) and its receptor (SR). In contrast, high-throughput delivery of abundant light-harvesting chlorophyll a,b-binding proteins (LHCPs) in chloroplasts to the Alb3 insertase occurs post-translationally via a soluble transit complex including the cpSRP43/cpSRP54 heterodimer (cpSRP). Here we describe the molecular mechanisms of tethering cpSRP to the Alb3 insertase by specific interaction of cpSRP43 chromodomain 3 with a linear motif in the Alb3 C-terminal tail. Combining NMR spectroscopy, X-ray crystallography and biochemical analyses, we dissect the structural basis for selectivity of chromodomains 2 and 3 for their respective ligands cpSRP54 and Alb3, respectively. Negative cooperativity in ligand binding can be explained by dynamics in the chromodomain interface. Our study provides a model for membrane recruitment of the transit complex and may serve as a prototype for a functional gain by the tandem arrangement of chromodomains.\",\n \"corpus_id\": 18904763,\n \"score\": 2\n },\n {\n \"doc_id\": \"26951662\",\n \"title\": \"Conformational dynamics of a membrane protein chaperone enables spatially regulated substrate capture and release.\",\n \"abstract\": \"Membrane protein biogenesis poses enormous challenges to cellular protein homeostasis and requires effective molecular chaperones. Compared with chaperones that promote soluble protein folding, membrane protein chaperones require tight spatiotemporal coordination of their substrate binding and release cycles. Here we define the chaperone cycle for cpSRP43, which protects the largest family of membrane proteins, the light harvesting chlorophyll a/b-binding proteins (LHCPs), during their delivery. Biochemical and NMR analyses demonstrate that cpSRP43 samples three distinct conformations. The stromal factor cpSRP54 drives cpSRP43 to the active state, allowing it to tightly bind substrate in the aqueous compartment. Bidentate interactions with the Alb3 translocase drive cpSRP43 to a partially inactive state, triggering selective release of LHCP's transmembrane domains in a productive unloading complex at the membrane. Our work demonstrates how the intrinsic conformational dynamics of a chaperone enables spatially coordinated substrate capture and release, which may be general to other ATP-independent chaperone systems.\",\n \"corpus_id\": 20516816,\n \"score\": 2\n },\n {\n \"doc_id\": \"27653474\",\n \"title\": \"Domain Organization in the 54-kDa Subunit of the Chloroplast Signal Recognition Particle.\",\n \"abstract\": \"Chloroplast signal recognition particle (cpSRP) is a heterodimer composed of an evolutionarily conserved 54-kDa GTPase (cpSRP54) and a unique 43-kDa subunit (cpSRP43) responsible for delivering light-harvesting chlorophyll binding protein to the thylakoid membrane. While a nearly complete three-dimensional structure of cpSRP43 has been determined, no high-resolution structure is yet available for cpSRP54. In this study, we developed and examined an in silico three-dimensional model of the structure of cpSRP54 by homology modeling using cytosolic homologs. Model selection was guided by single-molecule Förster resonance energy transfer experiments, which revealed the presence of at least two distinct conformations. Small angle x-ray scattering showed that the linking region among the GTPase (G-domain) and methionine-rich (M-domain) domains, an M-domain loop, and the cpSRP43 binding C-terminal extension of cpSRP54 are predominantly disordered. Interestingly, the linker and loop segments were observed to play an important role in organizing the domain arrangement of cpSRP54. Further, deletion of the finger loop abolished loading of the cpSRP cargo, light-harvesting chlorophyll binding protein. These data highlight important structural dynamics relevant to cpSRP54's role in the post- and cotranslational signaling processes.\",\n \"corpus_id\": 206304100,\n \"score\": 2\n },\n {\n \"doc_id\": \"27698412\",\n \"title\": \"ALB3 Insertase Mediates Cytochrome b6 Co-translational Import into the Thylakoid Membrane.\",\n \"abstract\": \"The cytochrome b6 f complex occupies an electrochemically central position in the electron-transport chain bridging the photosynthetic reaction center of PS I and PS II. In plants, the subunits of these thylakoid membrane protein complexes are both chloroplast and nuclear encoded. How the chloroplast-encoded subunits of multi-spanning cytochrome b6 are targeted and inserted into the thylakoid membrane is not fully understood. Experimental approaches to evaluate the cytochrome b6 import mechanism in vivo have been limited to bacterial membranes and were not a part of the chloroplast environment. To evaluate the mechanism governing cytochrome b6 integration in vivo, we performed a comparative analysis of both native and synthetic cytochrome b6 insertion into purified thylakoids. Using biophysical and biochemical methods, we show that cytochrome b6 insertion into the thylakoid membrane is a non-spontaneous co-translational process that involves ALB3 insertase. Furthermore, we provided evidence that CSP41 (chloroplast stem-loop-binding protein of 41 kDa) interacts with RNC-cytochrome b6 complexes, and may be involved in cytochrome b6 (petB) transcript stabilization or processing.\",\n \"corpus_id\": 16173499,\n \"score\": 2\n },\n {\n \"doc_id\": \"27861610\",\n \"title\": \"The Chloroplast SRP Systems of Chaetosphaeridium globosum and Physcomitrella patens as Intermediates in the Evolution of SRP-Dependent Protein Transport in Higher Plants.\",\n \"abstract\": \"The bacterial signal recognition particle (SRP) mediates the cotranslational targeting of membrane proteins and is a high affinity complex consisting of a SRP54 protein subunit (Ffh) and an SRP RNA. The chloroplast SRP (cpSRP) pathway has adapted throughout evolution to enable the posttranslational targeting of the light harvesting chlorophyll a/b binding proteins (LHCPs) to the thylakoid membrane. In spermatophytes (seed plants), the cpSRP lacks the SRP RNA and is instead formed by a high affinity interaction of the conserved 54-kD subunit (cpSRP54) with the chloroplast-specific cpSRP43 protein. This heterodimeric cpSRP recognizes LHCP and delivers it to the thylakoid membrane. However, in contrast to spermatophytes, plastid SRP RNAs were identified within all streptophyte lineages and in all chlorophyte branches. Furthermore, it was shown that cpSRP43 does not interact with cpSRP54 in chlorophytes (e.g., Chlamydomonas reinhardtii). In this study, we biochemically characterized the cpSRP system of the charophyte Chaetosphaeridium globosum and the bryophyte Physcomitrella patens. Interaction studies demonstrate low affinity binding of cpSRP54 to cpSRP43 (Kd ~10 μM) in Chaetosphaeridium globosum and Physcomitrella patens as well as relatively low affinity binding of cpSRP54 to cpSRP RNA (Kd ~1 μM) in Physcomitrella patens. CpSRP54/cpSRP43 complex formation in charophytes is supported by the finding that specific alterations in the second chromodomain of cpSRP43, that are conserved within charophytes and absent in land plants, do not interfere with cpSRP54 binding. Furthermore, our data show that the elongated apical loop structure of the Physcomitrella patens cpSRP RNA contributes to the low binding affinity between cpSRP54 and the cpSRP RNA.\",\n \"corpus_id\": 12969329,\n \"score\": 2\n },\n {\n \"doc_id\": \"27895118\",\n \"title\": \"Co-evolution of Two GTPases Enables Efficient Protein Targeting in an RNA-less Chloroplast Signal Recognition Particle Pathway.\",\n \"abstract\": \"The signal recognition particle (SRP) is an essential ribonucleoprotein particle that mediates the co-translational targeting of newly synthesized proteins to cellular membranes. The SRP RNA is a universally conserved component of SRP that mediates key interactions between two GTPases in SRP and its receptor, thus enabling rapid delivery of cargo to the target membrane. Notably, this essential RNA is bypassed in the chloroplast (cp) SRP of green plants. Previously, we showed that the cpSRP and cpSRP receptor GTPases (cpSRP54 and cpFtsY, respectively) interact efficiently by themselves without the SRP RNA. Here, we explore the molecular mechanism by which this is accomplished. Fluorescence analyses showed that, in the absence of SRP RNA, the M-domain of cpSRP54 both accelerates and stabilizes complex assembly between cpSRP54 and cpFtsY. Cross-linking coupled with mass spectrometry and mutational analyses identified a new interaction between complementarily charged residues on the cpFtsY G-domain and the vicinity of the cpSRP54 M-domain. These residues are specifically conserved in plastids, and their evolution coincides with the loss of SRP RNA in green plants. These results provide an example of how proteins replace the functions of RNA during evolution.\",\n \"corpus_id\": 30894142,\n \"score\": 2\n },\n {\n \"doc_id\": \"27895124\",\n \"title\": \"Anionic Phospholipids and the Albino3 Translocase Activate Signal Recognition Particle-Receptor Interaction during Light-harvesting Chlorophyll a/b-binding Protein Targeting.\",\n \"abstract\": \"The universally conserved signal recognition particle (SRP) co-translationally delivers newly synthesized membrane and secretory proteins to the target cellular membrane. The only exception is found in the chloroplast of green plants, where the chloroplast SRP (cpSRP) post-translationally targets light-harvesting chlorophyll a/b-binding proteins (LHCP) to the thylakoid membrane. The mechanism and regulation of this post-translational mode of targeting by cpSRP remain unclear. Using biochemical and biophysical methods, here we show that anionic phospholipids activate the cpSRP receptor cpFtsY to promote rapid and stable cpSRP54·cpFtsY complex assembly. Furthermore, the stromal domain of the Alb3 translocase binds with high affinity to and regulates GTP hydrolysis in the cpSRP54·cpFtsY complex, suggesting that cpFtsY is primarily responsible for initial recruitment of the targeting complex to Alb3. These results suggest a new model for the sequential recruitment, remodeling, and unloading of the targeting complex at membrane translocase sites in the post-translational cpSRP pathway.\",\n \"corpus_id\": 22441687,\n \"score\": 2\n },\n {\n \"doc_id\": \"28684427\",\n \"title\": \"Suppressors of the Chloroplast Protein Import Mutant tic40 Reveal a Genetic Link between Protein Import and Thylakoid Biogenesis.\",\n \"abstract\": \"To extend our understanding of chloroplast protein import and the role played by the import machinery component Tic40, we performed a genetic screen for suppressors of chlorotic tic40 knockout mutant Arabidopsis thaliana plants. As a result, two suppressor of tic40 loci, stic1 and stic2, were identified and characterized. The stic1 locus corresponds to the gene ALBINO4 (ALB4), which encodes a paralog of the well-known thylakoid protein targeting factor ALB3. The stic2 locus identified a previously unknown stromal protein that interacts physically with both ALB4 and ALB3. Genetic studies showed that ALB4 and STIC2 act together in a common pathway that also involves cpSRP54 and cpFtsY. Thus, we conclude that ALB4 and STIC2 both participate in thylakoid protein targeting, potentially for a specific subset of thylakoidal proteins, and that this targeting pathway becomes disadvantageous to the plant in the absence of Tic40. As the stic1 and stic2 mutants both suppressed tic40 specifically (other TIC-related mutants were not suppressed), we hypothesize that Tic40 is a multifunctional protein that, in addition to its originally described role in protein import, is able to influence downstream processes leading to thylakoid biogenesis.\",\n \"corpus_id\": 3855270,\n \"score\": 2\n },\n {\n \"doc_id\": \"28844594\",\n \"title\": \"YidC Insertase of Escherichia coli: Water Accessibility and Membrane Shaping.\",\n \"abstract\": \"The YidC/Oxa1/Alb3 family of membrane proteins function to insert proteins into membranes in bacteria, mitochondria, and chloroplasts. Recent X-ray structures of YidC from Bacillus halodurans and Escherichia coli revealed a hydrophilic groove that is accessible from the lipid bilayer and the cytoplasm. Here, we explore the water accessibility within the conserved core region of the E. coli YidC using in vivo cysteine alkylation scanning and molecular dynamics (MD) simulations of YidC in POPE/POPG membranes. As expected from the structure, YidC possesses an aqueous membrane cavity localized to the membrane inner leaflet. Both the scanning data and the MD simulations show that the lipid-exposed transmembrane helices 3, 4, and 5 are short, leading to membrane thinning around YidC. Close examination of the MD data reveals previously unrecognized structural features that are likely important for protein stability and function.\",\n \"corpus_id\": 205263772,\n \"score\": 2\n },\n {\n \"doc_id\": \"29162052\",\n \"title\": \"Chloroplast PetD protein: evidence for SRP/Alb3-dependent insertion into the thylakoid membrane.\",\n \"abstract\": \"BACKGROUND: In thylakoid membrane, each monomer of the dimeric complex of cytochrome b 6 f is comprised of eight subunits that are both nucleus- and plastid-encoded. Proper cytochrome b 6 f complex integration into the thylakoid membrane requires numerous regulatory factors for coordinated transport, insertion and assembly of the subunits. Although, the chloroplast-encoded cytochrome b 6 f subunit IV (PetD) consists of three transmembrane helices, the signal and the mechanism of protein integration into the thylakoid membrane have not been identified. RESULTS: Here, we demonstrate that the native PetD subunit cannot incorporate into the thylakoid membranes spontaneously, but that proper integration occurs through the post-translational signal recognition particle (SRP) pathway. Furthermore, we show that PetD insertion into thylakoid membrane involves the coordinated action of cpFTSY, cpSRP54 and ALB3 insertase. CONCLUSIONS: PetD subunit integration into the thylakoid membrane is a post-translational and an SRP-dependent process that requires the formation of the cpSRP-cpFtsY-ALB3-PetD complex. This data provides a new insight into the molecular mechanisms by which membrane proteins integration into the thylakoid membrane is accomplished and is not limited to PetD.\",\n \"corpus_id\": 12969189,\n \"score\": 2\n },\n {\n \"doc_id\": \"29281821\",\n \"title\": \"Identification of Oxa1 Homologs Operating in the Eukaryotic Endoplasmic Reticulum.\",\n \"abstract\": \"Members of the evolutionarily conserved Oxa1/Alb3/YidC family mediate membrane protein biogenesis at the mitochondrial inner membrane, chloroplast thylakoid membrane, and bacterial plasma membrane, respectively. Despite their broad phylogenetic distribution, no Oxa1/Alb3/YidC homologs are known to operate in eukaryotic cells outside the endosymbiotic organelles. Here, we present bioinformatic evidence that the tail-anchored protein insertion factor WRB/Get1, the \\\"endoplasmic reticulum (ER) membrane complex\\\" subunit EMC3, and TMCO1 are ER-resident homologs of the Oxa1/Alb3/YidC family. Topology mapping and co-evolution-based modeling demonstrate that Get1, EMC3, and TMCO1 share a conserved Oxa1-like architecture. Biochemical analysis of human TMCO1, the only homolog not previously linked to membrane protein biogenesis, shows that it associates with the Sec translocon and ribosomes. These findings suggest a specific biochemical function for TMCO1 and define a superfamily of proteins-the \\\"Oxa1 superfamily\\\"-whose shared function is to facilitate membrane protein biogenesis.\",\n \"corpus_id\": 4321058,\n \"score\": 2\n },\n {\n \"doc_id\": \"19307606\",\n \"title\": \"Translocation and assembly of mitochondrially coded Saccharomyces cerevisiae cytochrome c oxidase subunit Cox2 by Oxa1 and Yme1 in the absence of Cox18.\",\n \"abstract\": \"Members of the Oxa1/YidC/Alb3 family of protein translocases are essential for assembly of energy-transducing membrane complexes. In Saccharomyces cerevisiae, Oxa1 and its paralog, Cox18, are required for assembly of Cox2, a mitochondrially encoded subunit of cytochrome c oxidase. Oxa1 is known to be required for cotranslational export of the Cox2 N-terminal domain across the inner mitochondrial membrane, while Cox18 is known to be required for post-translational export of the Cox2 C-tail domain. We find that overexpression of Oxa1 does not compensate for the absence of Cox18 at the level of respiratory growth. However, it does promote some translocation of the Cox2 C-tail domain across the inner membrane and causes increased accumulation of Cox2, which remains unassembled. This result suggests that Cox18 not only translocates the C-tail, but also must deliver it in a distinct state competent for cytochrome oxidase assembly. We identified respiring mutants from a cox18Delta strain overexpressing OXA1, whose respiratory growth requires overexpression of OXA1. The recessive nuclear mutations allow some assembly of Cox2 into cytochrome c oxidase. After failing to identify these mutations by methods based on transformation, we successfully located them to MGR1 and MGR3 by comparative hybridization to whole-genome tiling arrays and microarray-assisted bulk segregant analysis followed by linkage mapping. While Mgr1 and Mgr3 are known to associate with the Yme1 mitochondrial inner membrane i-AAA protease and to participate in membrane protein degradation, their absence does not appear to stabilize Cox2 under these conditions. Instead, Yme1 probably chaperones the folding and/or assembly of Oxa1-exported Cox2 in the absence of Mrg1 or Mgr3, since respiratory growth and cytochrome c oxidase assembly in a cox18 mgr3 double-mutant strain overexpressing OXA1 is YME1 dependent.\",\n \"corpus_id\": 18698603,\n \"score\": 1\n },\n {\n \"doc_id\": \"19361278\",\n \"title\": \"From the Sec complex to the membrane insertase YidC.\",\n \"abstract\": \"The key enzymes that catalyze the insertion of proteins into membranes are the Sec translocase and the YidC membrane insertase. Recent insights into the structure and functional intermediates of these enzymes have provided a first molecular glimpse of how they help the newly synthesized proteins to enter the membrane bilayer. In this process, the new proteins undergo a number of specific interactions in the cytoplasm and at the membrane surface before they insert into the bilayer and translocate their external domains across the membrane. The components involved in this pathway recognize each other at the molecular level, forming a route the membrane protein can move along.\",\n \"corpus_id\": 38220412,\n \"score\": 1\n },\n {\n \"doc_id\": \"19450532\",\n \"title\": \"YidC and Oxa1 form dimeric insertion pores on the translating ribosome.\",\n \"abstract\": \"The YidC/Oxa1/Alb3 family of membrane proteins facilitates the insertion and assembly of membrane proteins in bacteria, mitochondria, and chloroplasts. Here we present the structures of both Escherichia coli YidC and Saccharomyces cerevisiae Oxa1 bound to E. coli ribosome nascent chain complexes determined by cryo-electron microscopy. Dimers of YidC and Oxa1 are localized above the exit of the ribosomal tunnel. Crosslinking experiments show that the ribosome specifically stabilizes the dimeric state. Functionally important and conserved transmembrane helices of YidC and Oxa1 were localized at the dimer interface by cysteine crosslinking. Both Oxa1 and YidC dimers contact the ribosome at ribosomal protein L23 and conserved rRNA helices 59 and 24, similarly to what was observed for the nonhomologous SecYEG translocon. We suggest that dimers of the YidC and Oxa1 proteins form insertion pores and share a common overall architecture with the SecY monomer.\",\n \"corpus_id\": 32266828,\n \"score\": 1\n },\n {\n \"doc_id\": \"22108384\",\n \"title\": \"Unbalanced charge distribution as a determinant for dependence of a subset of Escherichia coli membrane proteins on the membrane insertase YidC.\",\n \"abstract\": \"UNLABELLED: Membrane proteins are involved in numerous essential cell processes, including transport, gene regulation, motility, and metabolism. To function properly, they must be inserted into the membrane and folded correctly. YidC, an essential protein in Escherichia coli with homologues in other bacteria, Archaea, mitochondria, and chloroplasts, functions by incompletely understood mechanisms in the insertion and folding of certain membrane proteins. Using a genome-scale approach, we identified 69 E. coli membrane proteins that, in the absence of YidC, exhibited aberrant localization by microscopy. Further examination of a subset revealed biochemical defects in membrane insertion in the absence of YidC, indicating their dependence on YidC for proper membrane insertion or folding. Membrane proteins possessing an unfavorable distribution of positively charged residues were significantly more likely to depend on YidC for membrane insertion. Correcting the charge distribution of a charge-unbalanced YidC-dependent membrane protein abrogated its requirement for YidC, while perturbing the charge distribution of a charge-balanced YidC-independent membrane protein rendered it YidC dependent, demonstrating that charge distribution can be a necessary and sufficient determinant of YidC dependence. These findings provide insights into a mechanism by which YidC promotes proper membrane protein biogenesis and suggest a critical function of YidC in all organisms and organelles that express it. IMPORTANCE: Biological membranes are fundamental components of cells, providing barriers that enclose the cell and separate compartments. Proteins inserted into biological membranes serve critical functions in molecular transport, molecular partitioning, and other essential cell processes. The mechanisms involved in the insertion of proteins into membranes, however, are incompletely understood. The YidC protein is critical for the insertion of a subset of proteins into membranes across an evolutionarily wide group of organisms. Here we identify a large group of proteins that depend on YidC for membrane insertion in Escherichia coli, and we identify unfavorable distribution of charge as an important determinant of YidC dependence for proper membrane insertion.\",\n \"corpus_id\": 7343309,\n \"score\": 1\n },\n {\n \"doc_id\": \"23179441\",\n \"title\": \"Arabidopsis thaliana Oxa proteins locate to mitochondria and fulfill essential roles during embryo development.\",\n \"abstract\": \"Members of the Alb3/Oxa1/YidC protein family function as insertases in chloroplasts, mitochondria, and bacteria. Due to independent gene duplications, all organisms possess two isoforms, Oxa1 and Oxa2 except gram-negative bacteria, which encode only for one YidC-like protein. The genome of Arabidopsis thaliana however, encodes for eight different isoforms. The localization of three of these isoforms has been identified earlier: Alb3 and Alb4 located in thylakoid membranes of chloroplasts while AtOxa1 was found in the inner membrane of mitochondria. Here, we show that the second Oxa1 protein, Oxa1b as well as two Oxa2 proteins are also localized in mitochondria. The last two isoforms most likely encode truncated versions of Oxa-like proteins, which might be inoperable pseudogenes. Homozygous mutant lines were only obtained for Oxa1b, which did not reveal any significant phenotypes, while T-DNA insertion lines of Oxa1a, Oxa2a and Oxa2b resulted only in heterozygous plants indicating that these genes are indispensable for plant development. Phenotyping heterozygous lines showed that embryos are either retarded in growth, display an albino phenotype or embryo formation was entirely abolished suggesting that Oxa1a and both Oxa2 proteins function in embryo formation although at different developmental stages as indicated by the various phenotypes observed.\",\n \"corpus_id\": 7778849,\n \"score\": 1\n },\n {\n \"doc_id\": \"23198851\",\n \"title\": \"Partial suppression of Oxa1 mutants by mitochondria-targeted signal recognition particle provides insights into the evolution of the cotranslational insertion systems.\",\n \"abstract\": \"The biogenesis of hydrophobic membrane proteins involves their cotranslational membrane integration in order to prevent their unproductive aggregation. In the cytosol of bacteria and eukaryotes, membrane targeting of ribosomes that synthesize membrane proteins is achieved by signal recognition particles (SRPs) and their cognate membrane-bound receptors. As is evident from the genomes of fully sequenced eukaryotes, mitochondria generally lack an SRP system. Instead, mitochondrial ribosomes are physically associated with the protein insertion machinery in the inner membrane. Accordingly, deletion of ribosome-binding sites on the Oxa1 insertase and the Mba1 ribosome receptor in yeast leads to severe defects in cotranslational protein insertion and results in respiration-deficient mutants. In this study, we expressed mitochondria-targeted versions of the bacterial SRP protein Ffh and its receptor FtsY in these yeast mutants. Interestingly, Ffh was found to bind to the large subunit of mitochondrial ribosomes, and could relieve, to some degree, the defect of these insertion mutants. Although FtsY could also bind to mitochondrial membranes, it did not improve membrane protein biogenesis in this strain, presumably because of its inability to interact with Ffh. Hence, mitochondrial ribosomes are still able to interact physically and functionally with the bacterial SRP system. Our observations are consistent with a model according to which the protein insertion system in mitochondria evolved in three steps. The loss of genes for hydrophilic polypeptides (step 1) allowed the development of ribosome-binding sites on membrane proteins (step 2), which finally made the existence of an SRP-mediated system dispensable (step 3).\",\n \"corpus_id\": 205132734,\n \"score\": 1\n },\n {\n \"doc_id\": \"23935050\",\n \"title\": \"Interaction of Streptococcus mutans YidC1 and YidC2 with translating and nontranslating ribosomes.\",\n \"abstract\": \"The YidC/OxaI/Alb3 family of membrane proteins is involved in the biogenesis of integral membrane proteins in bacteria, mitochondria, and chloroplasts. Gram-positive bacteria often contain multiple YidC paralogs that can be subdivided into two major classes, namely, YidC1 and YidC2. The Streptococcus mutans YidC1 and YidC2 proteins possess C-terminal tails that differ in charges (+9 and + 14) and lengths (33 and 61 amino acids). The longer YidC2 C terminus bears a resemblance to the C-terminal ribosome-binding domain of the mitochondrial OxaI protein and, in contrast to the shorter YidC1 C terminus, can mediate the interaction with mitochondrial ribosomes. These observations have led to the suggestion that YidC1 and YidC2 differ in their abilities to interact with ribosomes. However, the interaction with bacterial translating ribosomes has never been addressed. Here we demonstrate that Escherichia coli ribosomes are able to interact with both YidC1 and YidC2. The interaction is stimulated by the presence of a nascent membrane protein substrate and abolished upon deletion of the C-terminal tail, which also abrogates the YidC-dependent membrane insertion of subunit c of the F1F0-ATPase into the membrane. It is concluded that both YidC1 and YidC2 interact with ribosomes, suggesting that the modes of membrane insertion by these membrane insertases are similar.\",\n \"corpus_id\": 26095938,\n \"score\": 1\n },\n {\n \"doc_id\": \"24013010\",\n \"title\": \"The chloroplast signal recognition particle (CpSRP) pathway as a tool to minimize chlorophyll antenna size and maximize photosynthetic productivity.\",\n \"abstract\": \"The concept of the Truncated Light-harvesting chlorophyll Antenna (TLA) size, as a tool by which to maximize sunlight utilization and photosynthetic productivity in microalgal mass cultures or high-density plant canopies, is discussed. TLA technology is known to improve sunlight-to-product energy conversion efficiencies and is hereby exemplified by photosynthetic productivity estimates of wild type and a TLA strain under simulated mass culture conditions. Recent advances in the generation of TLA-type mutants by targeting genes of the chloroplast signal-recognition particle (CpSRP) pathway, affecting the thylakoid membrane assembly of light-harvesting proteins, are also summarized. Two distinct CpSRP assembly pathways are recognized, one entailing post-translational, the other a co-translational mechanism. Differences between the post-translational and co-translational integration mechanisms are outlined, as these pertain to the CpSRP-mediated assembly of thylakoid membrane protein complexes in higher plants and green microalgae. The applicability of the CpSRP pathway genes in efforts to generate TLA-type strains with enhanced solar energy conversion efficiency in photosynthesis is evaluated.\",\n \"corpus_id\": 35681793,\n \"score\": 1\n },\n {\n \"doc_id\": \"25466392\",\n \"title\": \"Crystal structure of Escherichia coli YidC, a membrane protein chaperone and insertase.\",\n \"abstract\": \"Bacterial YidC, an evolutionally conserved membrane protein, functions as a membrane protein chaperone in cooperation with the Sec translocon and as an independent insertase for membrane proteins. In Gram-negative bacteria, the transmembrane and periplasmic regions of YidC interact with the Sec proteins, forming a multi-protein complex for Sec-dependent membrane protein integration. Here, we report the crystal structure of full-length Escherichia coli YidC. The structure reveals that a hydrophilic groove, formed by five transmembrane helices, is a conserved structural feature of YidC, as compared to the previous YidC structure from Bacillus halodurans, which lacks a periplasmic domain. Structural mapping of the substrate- or Sec protein-contact sites suggested the importance of the groove for the YidC functions as a chaperone and an insertase, and provided structural insight into the multi-protein complex.\",\n \"corpus_id\": 6499559,\n \"score\": 1\n },\n {\n \"doc_id\": \"25666136\",\n \"title\": \"The Escherichia coli membrane protein insertase YidC assists in the biogenesis of penicillin binding proteins.\",\n \"abstract\": \"UNLABELLED: Membrane proteins need to be properly inserted and folded in the membrane in order to perform a range of activities that are essential for the survival of bacteria. The Sec translocon and the YidC insertase are responsible for the insertion of the majority of proteins into the cytoplasmic membrane. YidC can act in combination with the Sec translocon in the insertion and folding of membrane proteins. However, YidC also functions as an insertase independently of the Sec translocon for so-called YidC-only substrates. In addition, YidC can act as a foldase and promote the proper assembly of membrane protein complexes. Here, we investigate the effect of Escherichia coli YidC depletion on the assembly of penicillin binding proteins (PBPs), which are involved in cell wall synthesis. YidC depletion does not affect the total amount of the specific cell division PBP3 (FtsI) in the membrane, but the amount of active PBP3, as assessed by substrate binding, is reduced 2-fold. A similar reduction in the amount of active PBP2 was observed, while the levels of active PBP1A/1B and PBP5 were essentially similar. PBP1B and PBP3 disappeared from higher-Mw bands upon YidC depletion, indicating that YidC might play a role in PBP complex formation. Taken together, our results suggest that the foldase activity of YidC can extend to the periplasmic domains of membrane proteins. IMPORTANCE: This study addresses the role of the membrane protein insertase YidC in the biogenesis of penicillin binding proteins (PBPs). PBPs are proteins containing one transmembrane segment and a large periplasmic or extracellular domain, which are involved in peptidoglycan synthesis. We observe that in the absence of YidC, two critical PBPs are not correctly folded even though the total amount of protein in the membrane is not affected. Our findings extend the function of YidC as a foldase for membrane protein (complexes) to periplasmic domains of membrane proteins.\",\n \"corpus_id\": 23286715,\n \"score\": 1\n },\n {\n \"doc_id\": \"26023232\",\n \"title\": \"Role of the Cytosolic Loop C2 and the C Terminus of YidC in Ribosome Binding and Insertion Activity.\",\n \"abstract\": \"Members of the YidC/Oxa1/Alb3 protein family mediate membrane protein insertion, and this process is initiated by the assembly of YidC·ribosome nascent chain complexes at the inner leaflet of the lipid bilayer. The positively charged C terminus of Escherichia coli YidC plays a significant role in ribosome binding but is not the sole determinant because deletion does not completely abrogate ribosome binding. The positively charged cytosolic loops C1 and C2 of YidC may provide additional docking sites. We performed systematic sequential deletions within these cytosolic domains and studied their effect on the YidC insertase activity and interaction with translation-stalled (programmed) ribosome. Deletions within loop C1 strongly affected the activity of YidC in vivo but did not influence ribosome binding or substrate insertion, whereas loop C2 appeared to be involved in ribosome binding. Combining the latter deletion with the removal of the C terminus of YidC abolished YidC-mediated insertion. We propose that these two regions play an crucial role in the formation and stabilization of an active YidC·ribosome nascent chain complex, allowing for co-translational membrane insertion, whereas loop C1 may be involved in the downstream chaperone activity of YidC or in other protein-protein interactions.\",\n \"corpus_id\": 205351012,\n \"score\": 1\n },\n {\n \"doc_id\": \"26256539\",\n \"title\": \"A YidC-like Protein in the Archaeal Plasma Membrane.\",\n \"abstract\": \"Cells possess specialized machinery to direct the insertion of membrane proteins into the lipid bilayer. In bacteria, the essential protein YidC inserts certain proteins into the plasma membrane, and eukaryotic orthologs are present in the mitochondrial inner membrane and the chloroplast thylakoid membrane. The existence of homologous insertases in archaea has been proposed based on phylogenetic analysis. However, limited sequence identity, distinct architecture, and the absence of experimental data have made this assignment ambiguous. Here we describe the 3.5-Å crystal structure of an archaeal DUF106 protein from Methanocaldococcus jannaschii (Mj0480), revealing a lipid-exposed hydrophilic surface presented by a conserved YidC-like fold. Functional analysis reveals selective binding of Mj0480 to ribosomes displaying a stalled YidC substrate, and a direct interaction between the buried hydrophilic surface of Mj0480 and the nascent chain. These data provide direct experimental evidence that the archaeal DUF106 proteins are YidC/Oxa1/Alb3-like insertases of the archaeal plasma membrane.\",\n \"corpus_id\": 1363419,\n \"score\": 1\n },\n {\n \"doc_id\": \"26331454\",\n \"title\": \"Membrane Insertases Are Present in All Three Domains of Life.\",\n \"abstract\": \"In this issue of Structure, Borowska et al. (2015) report the crystal structure and provide experimental evidence on an archaeal membrane insertase, the DUF106 protein from Methanocaldococcus jannaschii, demonstrating that YidC/Oxa1/Alb3-like insertases exist in the archaeal plasma membrane.\",\n \"corpus_id\": 4966598,\n \"score\": 1\n },\n {\n \"doc_id\": \"28454841\",\n \"title\": \"Assisted and Unassisted Protein Insertion into Liposomes.\",\n \"abstract\": \"The insertion of newly synthesized membrane proteins is a well-regulated and fascinating process occurring in every living cell. Several translocases and insertases have been found in prokaryotic and eukaryotic cells, the Sec61 complex and the Get complex in the endoplasmic reticulum and the SecYEG complex and YidC in bacteria and archaea. In mitochondria, TOM and TIM complexes transport nuclear-encoded proteins, whereas the Oxa1 is required for the insertion of mitochondria-encoded membrane proteins. Related to the bacterial YidC and the mitochondrial Oxa1 are the Alb3 and Alb4 proteins in chloroplasts. These membrane insertases are comparably simple and can be studied in vitro, after their biochemical purification and reconstitution in artificial lipid bilayers such as liposomes or nanodiscs. Here, we describe the recent progress to study the molecular mechanism of YidC-dependent and unassisted membrane insertion at the single molecule level.\",\n \"corpus_id\": 8591349,\n \"score\": 1\n },\n {\n \"doc_id\": \"29330366\",\n \"title\": \"Each protomer of a dimeric YidC functions as a single membrane insertase.\",\n \"abstract\": \"The membrane insertase YidC catalyzes the entrance of newly synthesized proteins into the lipid bilayer. As an integral membrane protein itself, YidC can be found as a monomer, a dimer or also as a member of the holotranslocase SecYEGDF-YajC-YidC. To investigate whether the dimeric YidC is functional and whether two copies cooperate to insert a single substrate, we constructed a fusion protein where two copies of YidC are connected by a short linker peptide. The 120 kDa protein is stable and functional as it supports the membrane insertion of the M13 procoat protein, the C-tailed protein SciP and the fusion protein Pf3-Lep. Mutations that inhibit either protomer do not inactivate the insertase and rather keep it functional. When both protomers are defective, the substrate proteins accumulate in the cytoplasm. This suggests that the dimeric YidC operates as two insertases. Consistent with this, we show that the dimeric YidC can bind two substrate proteins simultaneously, suggesting that YidC indeed functions as a monomer.\",\n \"corpus_id\": 5227038,\n \"score\": 1\n },\n {\n \"doc_id\": \"29330529\",\n \"title\": \"The interaction network of the YidC insertase with the SecYEG translocon, SRP and the SRP receptor FtsY.\",\n \"abstract\": \"YidC/Oxa1/Alb3 are essential proteins that operate independently or cooperatively with the Sec machinery during membrane protein insertion in bacteria, archaea and eukaryotic organelles. Although the interaction between the bacterial SecYEG translocon and YidC has been observed in multiple studies, it is still unknown which domains of YidC are in contact with the SecYEG translocon. By in vivo and in vitro site-directed and para-formaldehyde cross-linking we identified the auxiliary transmembrane domain 1 of E. coli YidC as a major contact site for SecY and SecG. Additional SecY contacts were observed for the tightly packed globular domain and the C1 loop of YidC, which reveals that the hydrophilic cavity of YidC faces the lateral gate of SecY. Surprisingly, YidC-SecYEG contacts were only observed when YidC and SecYEG were present at about stoichiometric concentrations, suggesting that the YidC-SecYEG contact in vivo is either very transient or only observed for a very small SecYEG sub-population. This is different for the YidC-SRP and YidC-FtsY interaction, which involves the C1 loop of YidC and is efficiently observed even at sub-stoichiometric concentrations of SRP/FtsY. In summary, our data provide a first detailed view on how YidC interacts with the SecYEG translocon and the SRP-targeting machinery.\",\n \"corpus_id\": 28986778,\n \"score\": 1\n },\n {\n \"doc_id\": \"18259071\",\n \"title\": \"Purification, crystallization and preliminary structural characterization of the periplasmic domain P1 of the Escherichia coli membrane-protein insertase YidC.\",\n \"abstract\": \"In Escherichia coli, the biogenesis of inner membrane proteins (IMPs) requires targeting and insertion factors such as the signal recognition particle (SRP) and the Sec translocon. Recent studies have identified YidC as a novel and essential component involved in membrane insertion of IMPs both in conjunction with the Sec translocon and as a separate entity. E. coli YidC is a member of the YidC (in bacteria)/Oxa1 (in mitochondria)/Alb3 (in chloroplasts) protein family and contains six transmembrane segments and a very large periplasmic domain P1. The overproduction, purification, crystallization and preliminary crystallographic studies of the native and selenomethionine-labelled P1 domain are reported here as a first step towards the elucidation of the molecular mechanism of YidC as a membrane-protein insertase.\",\n \"corpus_id\": 19450572,\n \"score\": 0\n },\n {\n \"doc_id\": \"22040291\",\n \"title\": \"The SCO2 protein disulphide isomerase is required for thylakoid biogenesis and interacts with LHCB1 chlorophyll a/b binding proteins which affects chlorophyll biosynthesis in Arabidopsis seedlings.\",\n \"abstract\": \"The process of chloroplast biogenesis requires a multitude of pathways and processes to establish chloroplast function. In cotyledons of seedlings, chloroplasts develop either directly from proplastids (also named eoplasts) or, if germinated in the dark, via etioplasts, whereas in leaves chloroplasts derive from proplastids in the apical meristem and are then multiplied by division. The snowy cotyledon 2, sco2, mutations specifically disrupt chloroplast biogenesis in cotyledons. SCO2 encodes a chloroplast-localized protein disulphide isomerase, hypothesized to be involved in protein folding. Analysis of co-expressed genes with SCO2 revealed that genes with similar expression patterns encode chloroplast proteins involved in protein translation and in chlorophyll biosynthesis. Indeed, sco2-1 accumulates increased levels of the chlorophyll precursor, protochlorophyllide, in both dark grown cotyledons and leaves. Yeast two-hybrid analyses demonstrated that SCO2 directly interacts with the chlorophyll-binding LHCB1 proteins, being confirmed in planta using bimolecular fluorescence complementation (BIFC). Furthermore, ultrastructural analysis of sco2-1 chloroplasts revealed that formation and movement of transport vesicles from the inner envelope to the thylakoids is perturbed. SCO2 does not interact with the signal recognition particle proteins SRP54 and FtsY, which were shown to be involved in targeting of LHCB1 to the thylakoids. We hypothesize that SCO2 provides an alternative targeting pathway for light-harvesting chlorophyll binding (LHCB) proteins to the thylakoids via transport vesicles predominantly in cotyledons, with the signal recognition particle (SRP) pathway predominant in rosette leaves. Therefore, we propose that SCO2 is involved in the integration of LHCB1 proteins into the thylakoids that feeds back on the regulation of the tetrapyrrole biosynthetic pathway and nuclear gene expression.\",\n \"corpus_id\": 3333983,\n \"score\": 0\n },\n {\n \"doc_id\": \"25084381\",\n \"title\": \"Crystallization and preliminary X-ray diffraction analysis of YidC, a membrane-protein chaperone and insertase from Bacillus halodurans.\",\n \"abstract\": \"YidC, a member of the YidC/Oxa1/Alb3 family, inserts proteins into the membrane and facilitates membrane-protein folding in bacteria. YidC plays key roles in both Sec-mediated integration and Sec-independent insertion of membrane proteins. Here, Bacillus halodurans YidC2, which has five transmembrane helices conserved among the other family members, was identified as a target protein for structure determination by a fluorescent size-exclusion chromatography analysis. The protein was overexpressed, purified and crystallized in the lipidic cubic phase. The crystals diffracted X-rays to 2.4 Å resolution and belonged to space group P21, with unit-cell parameters a = 43.9, b = 60.6, c = 58.9 Å, β = 100.3°. The experimental phases were determined by the multiwavelength anomalous diffraction method using a mercury-derivatized crystal.\",\n \"corpus_id\": -1,\n \"score\": 0\n }\n]","isConversational":false}}},{"rowIdx":54,"cells":{"query":{"kind":"string","value":"{\n \"doc_id\": \"23999301\",\n \"title\": \"Analysis of the human cofilin 1 structure reveals conformational changes required for actin binding.\",\n \"abstract\": \"The actin cytoskeleton is the chassis that gives a cell its shape and structure, and supplies the power for numerous dynamic processes including motility, endocytosis, intracellular transport and division. To perform these activities, the cytoskeleton undergoes constant remodelling and reorganization. One of the major actin-remodelling families are the cofilin proteins, made up of cofilin 1, cofilin 2 and actin-depolymerizing factor (ADF), which sever aged ADP-associated actin filaments to reduce filament length and provide new potential nucleation sites. Despite the significant interest in cofilin as a central node in actin-cytoskeleton dynamics, to date the only forms of cofilin for which crystal structures have been solved are from the yeast, Chromalveolata and plant kingdoms; none have previously been reported for an animal cofilin protein. Two distinct regions in animal cofilin are significantly larger than in the forms previously crystallized, suggesting that they would be uniquely organized. Therefore, it was sought to determine the structure of human cofilin 1 by X-ray crystallography to elucidate how it could interact with and regulate dynamic actin-cytoskeletal structures. Although wild-type human cofilin 1 proved to be recalcitrant, a C147A point mutant yielded crystals that diffracted to 2.8 Å resolution. These studies revealed how the actin-binding helix undergoes a conformational change that increases the number of potential hydrogen bonds available for substrate binding.\",\n \"corpus_id\": 29534515\n}"},"candidates":{"kind":"list like","value":[{"doc_id":"18065447","title":"Stochastic severing of actin filaments by actin depolymerizing factor/cofilin controls the emergence of a steady dynamical regime.","abstract":"Actin dynamics (i.e., polymerization/depolymerization) powers a large number of cellular processes. However, a great deal remains to be learned to explain the rapid actin filament turnover observed in vivo. Here, we developed a minimal kinetic model that describes key details of actin filament dynamics in the presence of actin depolymerizing factor (ADF)/cofilin. We limited the molecular mechanism to 1), the spontaneous growth of filaments by polymerization of actin monomers, 2), the ageing of actin subunits in filaments, 3), the cooperative binding of ADF/cofilin to actin filament subunits, and 4), filament severing by ADF/cofilin. First, from numerical simulations and mathematical analysis, we found that the average filament length, L, is controlled by the concentration of actin monomers (power law: 5/6) and ADF/cofilin (power law: -2/3). We also showed that the average subunit residence time inside the filament, T, depends on the actin monomer (power law: -1/6) and ADF/cofilin (power law: -2/3) concentrations. In addition, filament length fluctuations are approximately 20% of the average filament length. Moreover, ADF/cofilin fragmentation while modulating filament length keeps filaments in a high molar ratio of ATP- or ADP-P(i) versus ADP-bound subunits. This latter property has a protective effect against a too high severing activity of ADF/cofilin. We propose that the activity of ADF/cofilin in vivo is under the control of an affinity gradient that builds up dynamically along growing actin filaments. Our analysis shows that ADF/cofilin regulation maintains actin filaments in a highly dynamical state compatible with the cytoskeleton dynamics observed in vivo.","corpus_id":8551262,"score":2},{"doc_id":"18625842","title":"Structure of the actin-depolymerizing factor homology domain in complex with actin.","abstract":"Actin dynamics provide the driving force for many cellular processes including motility and endocytosis. Among the central cytoskeletal regulators are actin-depolymerizing factor (ADF)/cofilin, which depolymerizes actin filaments, and twinfilin, which sequesters actin monomers and caps filament barbed ends. Both interact with actin through an ADF homology (ADF-H) domain, which is also found in several other actin-binding proteins. However, in the absence of an atomic structure for the ADF-H domain in complex with actin, the mechanism by which these proteins interact with actin has remained unknown. Here, we present the crystal structure of twinfilin's C-terminal ADF-H domain in complex with an actin monomer. This domain binds between actin subdomains 1 and 3 through an interface that is conserved among ADF-H domain proteins. Based on this structure, we suggest a mechanism by which ADF/cofilin and twinfilin inhibit nucleotide exchange of actin monomers and present a model for how ADF/cofilin induces filament depolymerization by weakening intrafilament interactions.","corpus_id":12130534,"score":2},{"doc_id":"18763747","title":"Actin-binding proteins: how to reveal the conformational changes.","abstract":"Actin is the most abundant protein in eukaryotes. Under physiological conditions, it can polymerize into polarized filaments. At the heart of these processes are actin-binding proteins that stimulate actin assembly. Most of them are composed of multiple domains that perform both regulatory and signaling functions. Many actin-binding proteins, including WASP and formin family proteins, are auto-inhibited through intramolecular interactions that mask the actin-regulating sites of these proteins. The large flexible molecules of formins have so far eluded crystallization, and have been crystallized only partially. The information from the available crystal structures is valuable, but somewhat difficult to interpret without a larger framework on which to pose the actin-binding mechanism. Single-particle electron microscopy and electron tomography could provide such a large framework with the full-length structures of protein complexes. The recent advances in determining the molecular interactions in protein complexes predict that the molecular modeling and molecular dynamics methods could be employed to study conformational changes in molecules.","corpus_id":20755223,"score":2},{"doc_id":"19289059","title":"The effects of ADF/cofilin and profilin on the conformation of the ATP-binding cleft of monomeric actin.","abstract":"Actin depolymerizing factor (ADF)/cofilin and profilin are small actin-binding proteins, which have central roles in cytoskeletal dynamics in all eukaryotes. When bound to an actin monomer, ADF/cofilins inhibit the nucleotide exchange, whereas most profilins accelerate the nucleotide exchange on actin monomers. In this study the effects of ADF/cofilin and profilin on the accessibility of the actin monomer's ATP-binding pocket was investigated by a fluorescence spectroscopic method. The fluorescence of the actin bound epsilon-ATP was quenched with a neutral quencher (acrylamide) in steady-state and time dependent experiments, and the data were analyzed with a complex form of the Stern-Volmer equation. The experiments revealed that in the presence of ADF/cofilin the accessibility of the bound epsilon-ATP decreased, indicating a closed and more compact ATP-binding pocket induced by the binding of ADF/cofilin. In the presence of profilin the accessibility of the bound epsilon-ATP increased, indicating a more open and approachable protein matrix around the ATP-binding pocket. The results of the fluorescence quenching experiments support a structural mechanism regarding the regulation of the nucleotide exchange on actin monomers by ADF/cofilin and profilin.","corpus_id":22561041,"score":2},{"doc_id":"20368459","title":"Actin filament remodeling by actin depolymerization factor/cofilin.","abstract":"We investigate, using molecular dynamics, how the severing protein, actin depolymerization factor (ADF)/cofilin, modulates the structure, conformational dynamics, and mechanical properties of actin filaments. The actin and cofilactin filament bending stiffness and corresponding persistence lengths obtained from all-atom simulations are comparable to values obtained from analysis of thermal fluctuations in filament shape. Filament flexibility is strongly affected by the nucleotide-linked conformation of the actin subdomain 2 DNase-I binding loop and the filament radial mass density distribution. ADF/cofilin binding between subdomains 1 and 3 of a filament subunit triggers reorganization of subdomain 2 of the neighboring subunit such that the DNase-I binding loop (DB-loop) moves radially away from the filament. Repositioning of the neighboring subunit DB-loop significantly weakens subunit interactions along the long-pitch helix and lowers the filament bending rigidity. Lateral filament contacts between the hydrophobic loop and neighboring short-pitch helix monomers in native filaments are also compromised with cofilin binding. These works provide a molecular interpretation of biochemical solution studies documenting the disruption of filament subunit interactions and also reveal the molecular basis of actin filament allostery and its linkage to ADF/cofilin binding.","corpus_id":16078744,"score":2},{"doc_id":"20441753","title":"The kinetics of cooperative cofilin binding reveals two states of the cofilin-actin filament.","abstract":"The interaction of cofilin with actin filaments displays positive cooperativity. The equilibrium binding and associated thermodynamic properties of this interaction are well described by a simple, one-dimensional Ising model with nearest neighbor interactions. Here we evaluate the kinetic contributions to cooperative binding and the ability of this model to account for binding across a wide range of cofilin concentrations. A Monte Carlo-based simulation protocol that allows for nearest-neighbor interactions between adjacent binding sites was used to globally fit time courses of human cofilin binding to human nonmuscle (beta-, gamma-) actin filaments. Several extensions of the one-dimensional Ising model were tested, and a mechanism that includes isomerization of the actin filament was found to best account for time courses of association as well as irreversible dissociation from a saturated filament. This model predicts two equilibrium states of the cofilin-actin, or cofilactin, filament, and the resulting set of binding parameters are in agreement with equilibrium thermodynamic parameters. We conclude that despite its simplicity, this one-dimensional Ising model is a reliable model for analyzing and interpreting the energetics and kinetics of cooperative cofilin-actin filament interactions. The model predicts that severing activity associated with boundaries between bare and decorated segments will not be linear, but display a transient burst at short times on cofilin activation then dissipate due to a kinetic competition between severing activity and cofilin binding. A second peak of severing activity is predicted to arise from irreversible cofilin dissociation on inactivation. These behaviors predict what we believe to be novel mechanisms of cofilin severing and spatial regulation of actin filament turnover in cells. The methods developed for this system are generally applicable to the kinetic analysis of cooperative ligand binding to linear polymers.","corpus_id":10246219,"score":2},{"doc_id":"20627129","title":"Solution structure and dynamics of ADF/cofilin from Leishmania donovani.","abstract":"Leishmania donovani ADF/cofilin (LdCof) is a novel member of ADF/cofilin family. LdCof depolymerizes, but does not co-sediment with, rabbit muscle actin filaments. Its F-actin depolymerizing activity is pH independent. Further, it possesses weak F-actin severing activity. In order to better understand its characteristic properties, we have determined the solution NMR structure of LdCof and have analyzed protein backbone dynamics from (15)N-relaxation measurements. The structure of LdCof possesses a conserved ADF/cofilin fold with a central mixed β-sheet consisting of six β-strands which is surrounded by five α-helices. LdCof structure has conserved G/F-actin binding site which includes the characteristic long kinked α-helix (α3). LdCof binds to rabbit muscle ADP-G-actin with 1:1 stoichiometry (K(d)∼0.2μM). The F-actin binding site is not well formed and analysis of (15)N-relaxation data shows that residues in the β4-β5 loop region and C-terminal are relatively flexible, which seems to be a determinant for the low F-actin severing activity of LdCof.","corpus_id":25062527,"score":2},{"doc_id":"21628589","title":"Minimal requirements for actin filament disassembly revealed by structural analysis of malaria parasite actin-depolymerizing factor 1.","abstract":"Malaria parasite cell motility is a process that is dependent on the dynamic turnover of parasite-derived actin filaments. Despite its central role, actin's polymerization state is controlled by a set of identifiable regulators that is markedly reduced compared with those of other eukaryotic cells. In Plasmodium falciparum, the most virulent species that affects humans, this minimal repertoire includes two members of the actin-depolymerizing factor/cofilin (AC) family of proteins, P. falciparum actin-depolymerizing factor 1 (PfADF1) and P. falciparum actin-depolymerizing factor 2. This essential class of actin regulator is involved in the control of filament dynamics at multiple levels, from monomer binding through to filament depolymerization and severing. Previous biochemical analyses have suggested that PfADF1 sequesters monomeric actin but, unlike most eukaryotic counterparts, has limited potential to bind or depolymerize filaments. The molecular basis for these unusual properties and implications for parasite cell motility have not been established. Here we present the crystal structure of an apicomplexan AC protein, PfADF1. We show that PfADF1 lacks critical residues previously implicated as essential for AC-mediated actin filament binding and disassembly, having a substantially reduced filament-binding loop and C-terminal α4 helix. Despite this divergence in structure, we demonstrate that PfADF1 is capable of efficient actin filament severing. Furthermore, this severing occurs despite PfADF1's low binding affinity for filaments. Comparative structural analysis along with biochemical and microscopy evidence establishes that severing is reliant on the availability of an exposed basic residue in the filament-binding loop, a conserved minimal requirement that defines AC-mediated filament disassembly across eukaryotic cells.","corpus_id":12063246,"score":2},{"doc_id":"21850706","title":"Actin-depolymerizing factor homology domain: a conserved fold performing diverse roles in cytoskeletal dynamics.","abstract":"Actin filaments form contractile and protrusive structures that play central roles in many processes such as cell migration, morphogenesis, endocytosis, and cytokinesis. During these processes, the dynamics of the actin filaments are precisely regulated by a large array of actin-binding proteins. The actin-depolymerizing factor homology (ADF-H) domain is a structurally conserved protein motif, which promotes cytoskeletal dynamics by interacting with monomeric and/or filamentous actin, and with the Arp2/3 complex. Despite their structural homology, the five classes of ADF-H domain proteins display distinct biochemical activities and cellular roles, only parts of which are currently understood. ADF/cofilin promotes disassembly of aged actin filaments, whereas twinfilin inhibits actin filament assembly via sequestering actin monomers and interacting with filament barbed ends. GMF does not interact with actin, but instead binds Arp2/3 complex and promotes dissociation of Arp2/3-mediated filament branches. Abp1 and drebrin are multidomain proteins that interact with actin filaments and regulate the activities of other proteins during various actin-dependent processes. The exact function of coactosin is currently incompletely understood. In this review article, we discuss the biochemical functions, cellular roles, and regulation of the five groups of ADF-H domain proteins.","corpus_id":20804728,"score":2},{"doc_id":"21875597","title":"The interaction of cofilin with the actin filament.","abstract":"Cofilin is a key actin-binding protein that is critical for controlling the assembly of actin within the cell. Here, we present the results of molecular docking and dynamics studies using a muscle actin filament and human cofilin I. Guided by extensive mutagenesis results and other biophysical and structural studies, we arrive at a model for cofilin bound to the actin filament. This predicted structure agrees very well with electron microscopy results for cofilin-decorated filaments, provides molecular insight into how the known F- and G-actin sites on cofilin interact with the filament, and also suggests new interaction sites that may play a role in cofilin binding. The resulting atomic-scale model also helps us understand the molecular function and regulation of cofilin and provides testable data for future experimental and simulation work.","corpus_id":38919864,"score":2},{"doc_id":"22158895","title":"Remodeling of actin filaments by ADF/cofilin proteins.","abstract":"Cofilin/ADF proteins play key roles in the dynamics of actin, one of the most abundant and highly conserved eukaryotic proteins. We used cryoelectron microscopy to generate a 9-Å resolution three-dimensional reconstruction of cofilin-decorated actin filaments, the highest resolution achieved for a complex of F-actin with an actin-binding protein. We show that the cofilin-induced change in the filament twist is due to a unique conformation of the actin molecule unrelated to any previously observed state. The changes between the actin protomer in naked F-actin and in the actin-cofilin filament are greater than the conformational changes between G- and F-actin. Our results show the structural plasticity of actin, suggest that other actin-binding proteins may also induce large but different conformational changes, and show that F-actin cannot be described by a single molecular model.","corpus_id":6304533,"score":2},{"doc_id":"22421043","title":"ADF/cofilin regulates actomyosin assembly through competitive inhibition of myosin II binding to F-actin.","abstract":"The contractile actin cortex is important for diverse fundamental cell processes, but little is known about how the assembly of F-actin and myosin II motors is regulated. We report that depletion of actin depolymerizing factor (ADF)/cofilin proteins in human cells causes increased contractile cortical actomyosin assembly. Remarkably, our data reveal that the major cellular defects resulting from ADF/cofilin depletion, including cortical F-actin accumulation, were largely due to excessive myosin II activity. We identify that ADF/cofilins from unicellular organisms to humans share a conserved activity to inhibit myosin II binding to F-actin, indicating a mechanistic rationale for our cellular results. Our study establishes an essential requirement for ADF/cofilin proteins in the control of normal cortical contractility and in processes such as mitotic karyokinesis. We propose that ADF/cofilin proteins are necessary for controlling actomyosin assembly and intracellular contractile force generation, a function of equal physiological importance to their established roles in mediating F-actin turnover.","corpus_id":34015387,"score":2},{"doc_id":"22623727","title":"Cofilin nuclear-cytoplasmic shuttling affects cofilin-actin rod formation during stress.","abstract":"Cofilin protein is involved in regulating the actin cytoskeleton during typical steady state conditions, as well as during cell stress conditions where cofilin saturates F-actin, forming cofilin-actin rods. Cofilin can enter the nucleus through an active nuclear localization signal (NLS), accumulating in nuclear actin rods during stress. Here, we characterize the active nuclear export of cofilin through a leptomycin-B-sensitive, CRM1-dependent, nuclear export signal (NES). We also redefine the NLS of cofilin as a bipartite NLS, with an additional basic epitope required for nuclear localization. Using fluorescence lifetime imaging microscopy (FLIM) and Förster resonant energy transfer (FRET) between cofilin moieties and actin, as well as automated image analysis in live cells, we have defined subtle mutations in the cofilin NLS that allow cofilin to bind actin in vivo and affect cofilin dynamics during stress. We further define the requirement of cofilin-actin rod formation in a system of cell stress by temporal live-cell imaging. We propose that cofilin nuclear shuttling is critical for the cofilin-actin rod stress response with cofilin dynamically communicating between the nucleus and cytoplasm during cell stress.","corpus_id":13093547,"score":2},{"doc_id":"22728040","title":"Cytochalasin D acts as an inhibitor of the actin-cofilin interaction.","abstract":"Cofilin, a key regulator of actin filament dynamics, binds to G- and F-actin and promotes actin filament turnover by stimulating depolymerization and severance of actin filaments. In this study, cytochalasin D (CytoD), a widely used inhibitor of actin dynamics, was found to act as an inhibitor of the G-actin-cofilin interaction by binding to G-actin. CytoD also inhibited the binding of cofilin to F-actin and decreased the rate of both actin polymerization and depolymerization in living cells. CytoD altered cellular F-actin organization but did not induce net actin polymerization or depolymerization. These results suggest that CytoD inhibits actin filament dynamics in cells via multiple mechanisms, including the well-known barbed-end capping mechanism and as shown in this study, the inhibition of G- and F-actin binding to cofilin.","corpus_id":205922782,"score":2},{"doc_id":"23153585","title":"Signaling mechanisms and functional roles of cofilin phosphorylation and dephosphorylation.","abstract":"Cofilin and actin-depolymerizing factor (ADF) are actin-binding proteins that play an essential role in regulating actin filament dynamics and reorganization by stimulating the severance and depolymerization of actin filaments. Cofilin/ADF are inactivated by phosphorylation at the serine residue at position 3 by LIM-kinases (LIMKs) and testicular protein kinases (TESKs) and are reactivated by dephosphorylation by the slingshot (SSH) family of protein phosphatases and chronophin. This review describes recent advances in our understanding of the signaling mechanisms regulating LIMKs and SSHs and the functional roles of cofilin phospho-regulation in cell migration, tumor invasion, mitosis, neuronal development, and synaptic plasticity. Accumulating evidence demonstrates that the phospho-regulation of cofilin/ADF is a key convergence point of cell signaling networks that link extracellular stimuli to actin cytoskeletal dynamics and that spatiotemporal control of cofilin/ADF activity by LIMKs and SSHs plays a crucial role in a diverse array of cellular and physiological processes. Perturbations in the normal control of cofilin/ADF activity underlie many pathological conditions, including cancer metastasis and neurological and cardiovascular disorders.","corpus_id":32529565,"score":2},{"doc_id":"23665019","title":"Cooperative and non-cooperative conformational changes of F-actin induced by cofilin.","abstract":"Cofilin is an actin-binding protein that promotes F-actin depolymerization. It is well-known that cofilin-coated F-actin is more twisted than naked F-actin, and that the protomer is more tilted. However, the means by which the local changes induced by the binding of individual cofilin proteins proceed to the global conformational changes of the whole F-actin molecule remain unknown. Here we investigated the cofilin-induced changes in several parts of F-actin, through site-directed spin-label electron paramagnetic resonance spectroscopy analyses of recombinant actins containing single reactive cysteines. We found that the global, cooperative conformational changes induced by cofilin-binding, which were detected by the spin-label attached to the Cys374 residue, occurred without the detachment of the D-loop in subdomain 2 from the neighboring protomer. The two processes of local and global changes do not necessarily proceed in sequence.","corpus_id":2948477,"score":2},{"doc_id":"23727096","title":"Actin filament severing by cofilin dismantles actin patches and produces mother filaments for new patches.","abstract":"BACKGROUND: Yeast cells depend on Arp2/3 complex to assemble actin filaments at sites of endocytosis, but the source of the initial filaments required to activate Arp2/3 complex is not known. RESULTS: We tested the proposal that cofilin severs actin filaments during endocytosis in fission yeast cells using a mutant cofilin defective in severing. We used quantitative fluorescence microscopy to track mGFP-tagged proteins, including early endocytic adaptor proteins, activators of Arp2/3 complex, and actin filaments. Consistent with the hypothesis, actin patches disassembled far more slowly in cells depending on severing-deficient cofilin than in wild-type cells. Even more interesting, actin patches assembled slowly in these cofilin mutant cells. Adaptor proteins End4p and Pan1p accumulated and persisted at endocytic sites more than ten times longer than in wild-type cells, followed by slow but persistent recruitment of activators of Arp2/3 complex, including WASP and myosin-I. Mutations revealed that actin filament binding sites on adaptor proteins Pan1p and End4p contribute to initiating actin polymerization in actin patches. CONCLUSIONS: We propose a \"sever, diffuse, and trigger\" model for the nucleation of actin filaments at sites of endocytosis, whereby cofilin generates actin filament fragments that diffuse through the cytoplasm, bind adaptor proteins at nascent sites of endocytosis, and serve as mother filaments to initiate the autocatalytic assembly of the branched actin filament network of each new patch. This hypothesis explains the source of the \"mother filaments\" that are absolutely required for Arp2/3 complex to nucleate actin polymerization.","corpus_id":-1,"score":2},{"doc_id":"23845993","title":"The effect of ADF/cofilin and profilin on the dynamics of monomeric actin.","abstract":"The main goal of the work was to uncover the dynamical changes in actin induced by the binding of cofilin and profilin. The change in the structure and flexibility of the small domain and its function in the thermodynamic stability of the actin monomer were examined with fluorescence spectroscopy and differential scanning calorimetry (DSC). The structure around the C-terminus of actin is slightly affected by the presence of cofilin and profilin. Temperature dependent fluorescence resonance energy transfer measurements indicated that both actin binding proteins decreased the flexibility of the protein matrix between the subdomains 1 and 2. Time resolved anisotropy decay measurements supported the idea that cofilin and profilin changed similarly the dynamics around the fluorescently labeled Cys-374 and Lys-61 residues in subdomains 1 and 2, respectively. DSC experiments indicated that the thermodynamic stability of actin increased by cofilin and decreased in the presence of profilin. Based on the information obtained it is possible to conclude that while the small domain of actin acts uniformly in the presence of cofilin and profilin the overall stability of actin changes differently in the presence of the studied actin binding proteins. The results support the idea that the small domain of actin behaves as a rigid unit during the opening and closing of the nucleotide binding pocket in the presence of profilin and cofilin as well. The structural arrangement of the nucleotide binding cleft mainly influences the global stability of actin while the dynamics of the different segments can change autonomously.","corpus_id":38459615,"score":2},{"doc_id":"24943913","title":"Coordination of the filament stabilizing versus destabilizing activities of cofilin through its secondary binding site on actin.","abstract":"Cofilin is a ubiquitous modulator of actin cytoskeleton dynamics that can both stabilize and destabilize actin filaments depending on its concentration and/or the presence of regulatory co-factors. Three charge-reversal mutants of yeast cofilin, located in cofilin's filament-specific secondary binding site, were characterized in order to understand why disruption of this site leads to enhanced filament disassembly. Crystal structures of the mutants showed that the mutations specifically affect the secondary actin-binding interface, leaving the primary binding site unaltered. The mutant cofilins show enhanced activity compared to wild-type cofilin in severing and disassembling actin filaments. Electron microscopy and image analysis revealed long actin filaments in the presence of wild-type cofilin, while the mutants induced many short filaments, consistent with enhanced severing. Real-time fluorescence microscopy of labeled actin filaments confirmed that the mutants, unlike wild-type cofilin, were functioning as constitutively active severing proteins. In cells, the mutant cofilins delayed endocytosis, which depends on rapid actin turnover. We conclude that mutating cofilin's secondary actin-binding site increases cofilin's ability to sever and de-polymerize actin filaments. We hypothesize that activators of cofilin severing, like Aip1p, may act by disrupting the interface between cofilin's secondary actin-binding site and the actin filament.","corpus_id":5427074,"score":2},{"doc_id":"26028436","title":"Arp2/3 complex and cofilin modulate binding of tropomyosin to branched actin networks.","abstract":"Tropomyosins are coiled-coil proteins that bind actin filaments and regulate multiple cytoskeletal functions, including actin network dynamics near the leading edge of motile cells. Previous work demonstrated that tropomyosins inhibit actin nucleation by the Arp2/3 complex and prevent filament disassembly by cofilin. We find that the Arp2/3 complex and cofilin, in turn, regulate the binding of tropomyosin to actin filaments. Using fluorescence microscopy, we show that tropomyosin (non-muscle Drosophila Tm1A) polymerizes along actin filaments, starting from \"nuclei\" that appear preferentially on ADP-bound regions of the filament, near the pointed end. Tropomyosin fails to bind dendritic actin networks created in vitro by the Arp2/3 complex, in part because the Arp2/3 complex blocks pointed ends. Cofilin promotes phosphate dissociation and severs filaments, generating new pointed ends and rendering Arp2/3-generated networks competent to bind tropomyosin. Tropomyosin's attraction to pointed ends reflects a strong preference for conformations localized to that region of the filament and reveals a basic molecular mechanism by which lamellipodial actin networks are insulated from the effects of tropomyosin.","corpus_id":15675241,"score":2},{"doc_id":"26747606","title":"Actin-interacting Protein 1 Promotes Disassembly of Actin-depolymerizing Factor/Cofilin-bound Actin Filaments in a pH-dependent Manner.","abstract":"Actin-interacting protein 1 (AIP1) is a conserved WD repeat protein that promotes disassembly of actin filaments when actin-depolymerizing factor (ADF)/cofilin is present. Although AIP1 is known to be essential for a number of cellular events involving dynamic rearrangement of the actin cytoskeleton, the regulatory mechanism of the function of AIP1 is unknown. In this study, we report that two AIP1 isoforms from the nematode Caenorhabditis elegans, known as UNC-78 and AIPL-1, are pH-sensitive in enhancement of actin filament disassembly. Both AIP1 isoforms only weakly enhance disassembly of ADF/cofilin-bound actin filaments at an acidic pH but show stronger disassembly activity at neutral and basic pH values. However, a severing-defective mutant of UNC-78 shows pH-insensitive binding to ADF/cofilin-decorated actin filaments, suggesting that the process of filament severing or disassembly, but not filament binding, is pH-dependent. His-60 of AIP1 is located near the predicted binding surface for the ADF/cofilin-actin complex, and an H60K mutation of AIP1 partially impairs its pH sensitivity, suggesting that His-60 is involved in the pH sensor for AIP1. These biochemical results suggest that pH-dependent changes in AIP1 activity might be a novel regulatory mechanism of actin filament dynamics.","corpus_id":3033515,"score":2},{"doc_id":"26842224","title":"Cofilin-induced cooperative conformational changes of actin subunits revealed using cofilin-actin fusion protein.","abstract":"To investigate cooperative conformational changes of actin filaments induced by cofilin binding, we engineered a fusion protein made of Dictyostelium cofilin and actin. The filaments of the fusion protein were functionally similar to actin filaments bound with cofilin in that they did not bind rhodamine-phalloidin, had quenched fluorescence of pyrene attached to Cys374 and showed enhanced susceptibility of the DNase loop to cleavage by subtilisin. Quantitative analyses of copolymers made of different ratios of the fusion protein and control actin further demonstrated that the fusion protein affects the structure of multiple neighboring actin subunits in copolymers. Based on these and other recent related studies, we propose a mechanism by which conformational changes induced by cofilin binding is propagated unidirectionally to the pointed ends of the filaments, and cofilin clusters grow unidirectionally to the pointed ends following this path. Interestingly, the fusion protein was unable to copolymerize with control actin at pH 6.5 and low ionic strength, suggesting that the structural difference between the actin moiety in the fusion protein and control actin is pH-sensitive.","corpus_id":10386282,"score":2},{"doc_id":"28303963","title":"Structural Analysis of Human Cofilin 2/Filamentous Actin Assemblies: Atomic-Resolution Insights from Magic Angle Spinning NMR Spectroscopy.","abstract":"Cellular actin dynamics is an essential element of numerous cellular processes, such as cell motility, cell division and endocytosis. Actin's involvement in these processes is mediated by many actin-binding proteins, among which the cofilin family plays unique and essential role in accelerating actin treadmilling in filamentous actin (F-actin) in a nucleotide-state dependent manner. Cofilin preferentially interacts with older filaments by recognizing time-dependent changes in F-actin structure associated with the hydrolysis of ATP and release of inorganic phosphate (Pi) from the nucleotide cleft of actin. The structure of cofilin on F-actin and the details of the intermolecular interface remain poorly understood at atomic resolution. Here we report atomic-level characterization by magic angle spinning (MAS) NMR of the muscle isoform of human cofilin 2 (CFL2) bound to F-actin. We demonstrate that resonance assignments for the majority of atoms are readily accomplished and we derive the intermolecular interface between CFL2 and F-actin. The MAS NMR approach reported here establishes the foundation for atomic-resolution characterization of a broad range of actin-associated proteins bound to F-actin.","corpus_id":8859310,"score":2},{"doc_id":"28513458","title":"Cofilin - a protein controlling dynamics of actin filaments.","abstract":"Cofilins are evolutionary conserved proteins present in all Eukaryotic cells. Their primary function is dynamic reorganization of actin cytoskeleton. Two cofilin isoforms are known: cofilin 1, present in all studied non-muscle cells and in embryonic muscle cells, and cofilin 2, which dominates in mature skeletal and cardiac muscles. Polypeptide chains of both isoforms fold into a structure homological to a conservative ADF (actin depolymerizing factor) domain, which is characteristic of actin depolymerizing factor. In cofilin molecule two actin-binding sites were found. One site binds monomeric and filamentous actin, the second one interacts only with the filament. Binding of cofilin to actin filament causes a change in the orientation of subunits, which results in filament severing. This increases number of ends which can either elongate or shorten the filament, depending on the conditions. Cofilin interactions with monomeric actin decreases availability of polymerization-competent actin subunits. Cofilin activity is controlled by phosphorylation, binding membrane phospholipids, local pH and oxidative stress. Under conditions of oxidative stress oxidation of cysteine residues leads to formation of dimers, which are able to cross-link actin filaments. Stable actin-cofilin rods save cellular ATP, which is not used during active polymerization process. This facilitates faster cell recovery from the stress. The final cellular reaction on the environmental stimuli is a resultant of cofilin activity and activities of other actin-binding proteins, which function either synergistically or antagonistically. Due to the central role in the regulation of actin filaments dynamics, cofilin is involved in development of cancer, neurodegenerative diseases, congenital myopathies and cardiomyopathies.","corpus_id":43726288,"score":2},{"doc_id":"28625781","title":"ADF/Cofilin Accelerates Actin Dynamics by Severing Filaments and Promoting Their Depolymerization at Both Ends.","abstract":"Actin-depolymerizing factor (ADF)/cofilins contribute to cytoskeletal dynamics by promoting rapid actin filament disassembly. In the classical view, ADF/cofilin sever filaments, and capping proteins block filament barbed ends whereas pointed ends depolymerize, at a rate that is still debated. Here, by monitoring the activity of the three mammalian ADF/cofilin isoforms on individual skeletal muscle and cytoplasmic actin filaments, we directly quantify the reactions underpinning filament severing and depolymerization from both ends. We find that, in the absence of monomeric actin, soluble ADF/cofilin can associate with bare filament barbed ends to accelerate their depolymerization. Compared to bare filaments, ADF/cofilin-saturated filaments depolymerize faster from their pointed ends and slower from their barbed ends, resulting in similar depolymerization rates at both ends. This effect is isoform specific because depolymerization is faster for ADF- than for cofilin-saturated filaments. We also show that, unexpectedly, ADF/cofilin-saturated filaments qualitatively differ from bare filaments: their barbed ends are very difficult to cap or elongate, and consequently undergo depolymerization even in the presence of capping protein and actin monomers. Such depolymerizing ADF/cofilin-decorated barbed ends are produced during 17% of severing events. They are also the dominant fate of filament barbed ends in the presence of capping protein, because capping allows growing ADF/cofilin domains to reach the barbed ends, thereby promoting their uncapping and subsequent depolymerization. Our experiments thus reveal how ADF/cofilin, together with capping protein, control the dynamics of actin filament barbed and pointed ends. Strikingly, our results propose that significant barbed-end depolymerization may take place in cells.","corpus_id":11585075,"score":2},{"doc_id":"28939776","title":"Phosphomimetic S3D cofilin binds but only weakly severs actin filaments.","abstract":"Many biological processes, including cell division, growth, and motility, rely on rapid remodeling of the actin cytoskeleton and on actin filament severing by the regulatory protein cofilin. Phosphorylation of vertebrate cofilin at Ser-3 regulates both actin binding and severing. Substitution of serine with aspartate at position 3 (S3D) is widely used to mimic cofilin phosphorylation in cells and in vitro The S3D substitution weakens cofilin binding to filaments, and it is presumed that subsequent reduction in cofilin occupancy inhibits filament severing, but this hypothesis has remained untested. Here, using time-resolved phosphorescence anisotropy, electron cryomicroscopy, and all-atom molecular dynamics simulations, we show that S3D cofilin indeed binds filaments with lower affinity, but also with a higher cooperativity than wild-type cofilin, and severs actin weakly across a broad range of occupancies. We found that three factors contribute to the severing deficiency of S3D cofilin. First, the high cooperativity of S3D cofilin generates fewer boundaries between bare and decorated actin segments where severing occurs preferentially. Second, S3D cofilin only weakly alters filament bending and twisting dynamics and therefore does not introduce the mechanical discontinuities required for efficient filament severing at boundaries. Third, Ser-3 modification (i.e. substitution with Asp or phosphorylation) \"undocks\" and repositions the cofilin N terminus away from the filament axis, which compromises S3D cofilin's ability to weaken longitudinal filament subunit interactions. Collectively, our results demonstrate that, in addition to inhibiting actin binding, Ser-3 modification favors formation of a cofilin-binding mode that is unable to sufficiently alter filament mechanical properties and promote severing.","corpus_id":4235107,"score":2},{"doc_id":"29056508","title":"Functions of actin-interacting protein 1 (AIP1)/WD repeat protein 1 (WDR1) in actin filament dynamics and cytoskeletal regulation.","abstract":"Actin-depolymerizing factor (ADF)/cofilin and actin-interacting protein 1 (AIP1), also known as WD-repeat protein 1 (WDR1), are conserved among eukaryotes and play critical roles in dynamic reorganization of the actin cytoskeleton. AIP1 preferentially promotes disassembly of ADF/cofilin-decorated actin filaments but exhibits minimal effects on bare actin filaments. Therefore, AIP1 has been often considered to be an ancillary co-factor of ADF/cofilin that merely boosts ADF/cofilin activity level. However, genetic and cell biological studies show that AIP1 deficiency often causes lethality or severe abnormalities in multiple tissues and organs including muscle, epithelia, and blood, suggesting that AIP1 is a major regulator of many biological processes that depend on actin dynamics. This review summarizes recent progress in studies on the biochemical mechanism of actin filament severing by AIP1 and in vivo functions of AIP1 in model organisms and human diseases.","corpus_id":4962345,"score":2},{"doc_id":"29749375","title":"Structural basis for cofilin binding and actin filament disassembly.","abstract":"Actin depolymerizing factor (ADF) and cofilin accelerate actin dynamics by severing and disassembling actin filaments. Here, we present the 3.8 Å resolution cryo-EM structure of cofilactin (cofilin-decorated actin filament). The actin subunit structure of cofilactin (C-form) is distinct from those of F-actin (F-form) and monomeric actin (G-form). During the transition between these three conformations, the inner domain of actin (subdomains 3 and 4) and the majority of subdomain 1 move as two separate rigid bodies. The cofilin-actin interface consists of three distinct parts. Based on the rigid body movements of actin and the three cofilin-actin interfaces, we propose models for the cooperative binding of cofilin to actin, preferential binding of cofilin to ADP-bound actin filaments and cofilin-mediated severing of actin filaments.","corpus_id":13671035,"score":2},{"doc_id":"18037437","title":"Actin hydrophobic loop 262-274 and filament nucleation and elongation.","abstract":"The importance of actin hydrophobic loop 262-274 dynamics to actin polymerization and filament stability has been shown recently with the use of the yeast mutant actin L180C/L269C/C374A, in which the hydrophobic loop could be locked in a \"parked\" conformation by a disulfide bond between C180 and C269. Such a cross-linked globular actin monomer does not form filaments, suggesting nucleation and/or elongation inhibition. To determine the role of loop dynamics in filament nucleation and/or elongation, we studied the polymerization of the cross-linked actin in the presence of cofilin, to assist with actin nucleation, and with phalloidin, to stabilize the elongating filament segments. We demonstrate here that together, but not individually, phalloidin and cofilin co-rescue the polymerization of cross-linked actin. The polymerization was also rescued by filament seeds added together with phalloidin but not with cofilin. Thus, loop immobilization via cross-linking inhibits both filament nucleation and elongation. Nevertheless, the conformational changes needed to catalyze ATP hydrolysis by actin occur in the cross-linked actin. When actin filaments are fully decorated by cofilin, the helical twist of filamentous actin (F-actin) changes by approximately 5 degrees per subunit. Electron microscopic analysis of filaments rescued by cofilin and phalloidin revealed a dense contact between opposite strands in F-actin and a change of twist by approximately 1 degrees per subunit, indicating either partial or disordered attachment of cofilin to F-actin and/or competition between cofilin and phalloidin to alter F-actin symmetry. Our findings show an importance of the hydrophobic loop conformational dynamics in both actin nucleation and elongation and reveal that the inhibition of these two steps in the cross-linked actin can be relieved by appropriate factors.","corpus_id":29856865,"score":1},{"doc_id":"18258262","title":"Mapping the cofilin binding site on yeast G-actin by chemical cross-linking.","abstract":"Cofilin is a major cytoskeletal protein that binds to both monomeric actin (G-actin) and polymeric actin (F-actin) and is involved in microfilament dynamics. Although an atomic structure of the G-actin-cofilin complex does not exist, models of the complex have been built using molecular dynamics simulations, structural homology considerations, and synchrotron radiolytic footprinting data. The hydrophobic cleft between actin subdomains 1 and 3 and, alternatively, the cleft between actin subdomains 1 and 2 have been proposed as possible high-affinity cofilin binding sites. In this study, the proposed binding of cofilin to the subdomain 1/subdomain 3 region on G-actin has been probed using site-directed mutagenesis, fluorescence labeling, and chemical cross-linking, with yeast actin mutants containing single reactive cysteines in the actin hydrophobic cleft and with cofilin mutants carrying reactive cysteines in the regions predicted to bind to G-actin. Mass spectrometry analysis of the cross-linked complex revealed that cysteine 345 in subdomain 1 of mutant G-actin was cross-linked to native cysteine 62 on cofilin. A cofilin mutant that carried a cysteine substitution in the alpha 3-helix (residue 95) formed a cross-link with residue 144 in actin subdomain 3. Distance constraints imposed by these cross-links provide experimental evidence for cofilin binding between actin subdomains 1 and 3 and fit a corresponding docking-based structure of the complex. The cross-linking of the N-terminal region of recombinant yeast cofilin to actin residues 346 and 374 with dithio-bis-maleimidoethane (12.4 A) and via disulfide bond formation was also documented. This set of cross-linking data confirms the important role of the N-terminal segment of cofilin in interactions with G-actin.","corpus_id":20341341,"score":1},{"doc_id":"18809681","title":"Molecular dissection of the mechanisms of substrate recognition and F-actin-mediated activation of cofilin-phosphatase Slingshot-1.","abstract":"Slingshot-1 (SSH1), a member of a dual-specificity protein phosphatase family, regulates actin dynamics by dephosphorylating and reactivating cofilin, an actin-depolymerizing factor. SSH1 has the SSH family-specific, N-terminal, noncatalytic (SSH-N) domain, consisting of the A and B subdomains. SSH1 is activated by binding to actin filaments. In this study, we examined the mechanisms of SSH1 substrate recognition of phospho-cofilin (P-cofilin) and SSH1 activation by F-actin. We found that P-cofilin binds to a phosphatase-inactive mutant, SSH1(CS), in which the catalytic Cys-393 is replaced by Ser. Using a series of deletion mutants, we provided evidence that both the phosphatase (P) domain and the adjacent B domain are indispensable for P-cofilin binding of SSH1(CS) and cofilin-phosphatase activity of SSH1. In contrast, the A domain is required for the F-actin-mediated activation of SSH1, but not for P-cofilin binding or basal cofilin-phosphatase activity. The P domain alone is sufficient for the phosphatase activity toward p-nitrophenyl phosphate (pNPP), indicating that the SSH-N domain is not essential for the basal phosphatase activity of SSH1. Addition of F-actin increased the cofilin-phosphatase activity of SSH1 more than 1200-fold, but the pNPP-phosphatase activity only 2.2-fold, which suggests that F-actin principally affects the cofilin-specific phosphatase activity of SSH1. When expressed in cultured cells, SSH1, but not its mutant deleted of SSH-N, accumulated in the rear of the lamellipodium. Together, these findings suggest that the conserved SSH-N domain plays critical roles in P-cofilin recognition, F-actin-mediated activation, and subcellular localization of SSH1.","corpus_id":24504120,"score":1},{"doc_id":"19209826","title":"Tropomyosin and ADF/cofilin as collaborators and competitors.","abstract":"Dynamics of actin filaments is pivotal to many fundamental cellular processes such as Dcytokinesis, motility, morphology, vesicle and organelle transport, gene transcription and senescence. In vivo kinetics of actin filament dynamics is far from the equilibrium in vitro and these profound differences are attributed to large number of regulatory proteins. In particular, proteins of the ADF/cofilin family greatly increase actin filament dynamics by severing filaments and enhancing depolymerization of ADP-actin monomers from their pointed ends. Cofilin binds cooperatively to a minor conformer of F-actin in which the subunits are slightly under rotated along the filament helical axis. At high stoichiometry of cofilin to actin subunits, cofilin actually stabilizes actin filaments. Many isoforms oftropomyosin appear to compete with ADF/cofilin proteins for binding to actin filaments. Tropomyosin isoforms studied to date prefer binding to the \"untwisted\" conformer of F-actin and through their protection and stabilization of F-actin, recruit myosin II and assemble different actin superstructures from the cofilin-actin filaments. However, some tropomyosin isoforms may synergize with ADF/cofilin to enhance filament dynamics, suggesting that the different isoforms of tropomyosins, many of which show developmental or tissue specific expression profiles, play major roles in the assembly and turnover of actin superstructures. Different actin superstructures can overlap both spatially and temporally within a cell, but can be differentiated from each other based upon their kinetic and kinematic properties. Furthermore, local regulation of ADF/cofilin activity through signal transduction pathways could be one mechanism to alter the dynamic balance in F-actin-binding of certain tropomyosin isoforms in subcellular domains.","corpus_id":44439879,"score":1},{"doc_id":"19459188","title":"Actin-ADF/cofilin rod formation in Caenorhabditis elegans muscle requires a putative F-actin binding site of ADF/cofilin at the C-terminus.","abstract":"Under a number of stress or pathological conditions, actin and actin depolymerizing factor (ADF)/cofilin form rod-like structures that contain abnormal bundles of actin filaments that are heavily decorated with ADF/cofilin. However, the mechanism of actin rod formation and the physiological role of actin rods are not clearly understood. Here, we report that overexpression of green fluorescent protein-fused UNC-60B, a muscle-specific ADF/cofilin isoform, in Caenorhabditis elegans body wall muscle induces formation of rod-like structures. The rods contained GFP-UNC-60B, actin-interacting protein 1 (AIP1), and actin, but not other major actin-associated proteins, thus resembling actin-ADF/cofilin rods found in other organisms. However, depletion or overexpression of AIP1 did not affect formation of the actin-GFP-UNC-60B rods, suggesting that AIP1 does not play a significant role in the rod assembly. Truncation of the C-terminal tail, a putative F-actin binding site, of UNC-60B abolished induction of the rod formation, strongly suggesting that stable association of UNC-60B with F-actin, which is mediated by its C-terminus, is required for inducing actin-ADF/cofilin rods. This study suggests that C. elegans can be a new model to study functions of actin-ADF/cofilin rods.","corpus_id":998820,"score":1},{"doc_id":"20362448","title":"GMF is a cofilin homolog that binds Arp2/3 complex to stimulate filament debranching and inhibit actin nucleation.","abstract":"Cell locomotion and endocytosis are powered by the rapid polymerization and turnover of branched actin filament networks nucleated by Arp2/3 complex. Although a large number of cellular factors have been identified that stimulate Arp2/3 complex-mediated actin nucleation, only a small number of studies so far have addressed which factors promote actin network debranching. Here, we investigated the function of a conserved homolog of ADF/cofilin, glia maturation factor (GMF). We found that S. cerevisiae GMF (also called Aim7) localizes in vivo to cortical actin patches and displays synthetic genetic interactions with ADF/cofilin. However, GMF lacks detectable actin binding or severing activity and instead binds tightly to Arp2/3 complex. Using in vitro evanescent wave microscopy, we demonstrated that GMF potently stimulates debranching of actin filaments produced by Arp2/3 complex. Further, GMF inhibits nucleation of new daughter filaments. Together, these data suggest that GMF binds Arp2/3 complex to both \"prune\" daughter filaments at the branch points and inhibit new actin assembly. These activities and its genetic interaction with ADF/cofilin support a role for GMF in promoting the remodeling and/or disassembly of branched networks. Therefore, ADF/cofilin and GMF, members of the same superfamily, appear to have evolved to interact with actin and actin-related proteins, respectively, and to make mechanistically distinct contributions to the remodeling of cortical actin structures.","corpus_id":11199973,"score":1},{"doc_id":"20471369","title":"Screening of novel dominant negative mutant actins using glycine targeted scanning identifies G146V actin that cooperatively inhibits cofilin binding.","abstract":"A number of studies suggested that the structure of actin filaments changes by interaction with actin-binding proteins such as cofilin and myosin, and that the conformational changes of the actin subunits within a filament are cooperative. To understand the functions of these cooperative conformational changes induced by actin-binding proteins, we sought to obtain dominant negative mutant actins impaired in cooperative conformational changes. A series of mutant actin genes in which glycine residues in actin were systematically substituted by valine residues were constructed, and were expressed individually in yeast cells that carry a wild-type endogenous actin gene. Six dominant negative actin mutations were identified on the basis of growth inhibition. Among them, G146V mutation was chosen for further biochemical analysis because the Gly146 residue is located at the strategic hinge position connecting the large and small domains of an actin molecule. We found that G146V actin filaments hardly bind cofilin, consistent with a previous suggestion that cofilin binding causes conformational changes of actin around Gly146 (Galkin et al. [3]). Notably, copolymer that consists of 1:10 mixture of the mutant and wild-type actin molecules showed significantly reduced affinity for cofilin, suggesting that G146V mutant actin affects the conformation of neighboring wild-type actin within a filament, and inhibits cofilin binding.","corpus_id":6602995,"score":1},{"doc_id":"20483342","title":"ADF/cofilin binds phosphoinositides in a multivalent manner to act as a PIP(2)-density sensor.","abstract":"Actin-depolymerizing-factor (ADF)/cofilins have emerged as key regulators of cytoskeletal dynamics in cell motility, morphogenesis, endocytosis, and cytokinesis. The activities of ADF/cofilins are regulated by membrane phospholipid PI(4,5)P(2) in vitro and in cells, but the mechanism of the ADF/cofilin-PI(4,5)P(2) interaction has remained controversial. Recent studies suggested that ADF/cofilins interact with PI(4,5)P(2) through a specific binding pocket, and that this interaction is dependent on pH. Here, we combined systematic mutagenesis with biochemical and spectroscopic methods to elucidate the phosphoinositide-binding mechanism of ADF/cofilins. Our analysis revealed that cofilin does not harbor a specific PI(4,5)P(2)-binding pocket, but instead interacts with PI(4,5)P(2) through a large, positively charged surface of the molecule. Cofilin interacts simultaneously with multiple PI(4,5)P(2) headgroups in a cooperative manner. Consequently, interactions of cofilin with membranes and actin exhibit sharp sensitivity to PI(4,5)P(2) density. Finally, we show that cofilin binding to PI(4,5)P(2) is not sensitive to changes in the pH at physiological salt concentration, although the PI(4,5)P(2)-clustering activity of cofilin is moderately inhibited at elevated pH. Collectively, our data demonstrate that ADF/cofilins bind PI(4,5)P(2) headgroups through a multivalent, cooperative mechanism, and suggest that the actin filament disassembly activity of ADF/cofilin can be accurately regulated by small changes in the PI(4,5)P(2) density at cellular membranes.","corpus_id":206294935,"score":1},{"doc_id":"20517925","title":"GMF is an evolutionarily developed Adf/cofilin-super family protein involved in the Arp2/3 complex-mediated organization of the actin cytoskeleton.","abstract":"Actin-depolymerizing factor (ADF)/cofilin is widely expressed in eukaryotes and plays a central role in reorganizing the actin cytoskeleton by disassembling actin filaments. The ADF-homologous domain (ADF-H) is conserved in several other actin-modulating proteins such as twinfilin, Abp1/drebrin, and coactosin. Although these proteins interact with actin via ADF-H, their effects on actin are not identical to each other. Here, we report a novel ADF/cofilin-super family protein, Gmf1 (Glia maturation factor-like protein 1), from the fission yeast Schizosaccharomyces pombe. Gmf1 is a component of actin patches, which are located on the cell cortex and required for endocytosis, and may be involved in the control of the disassembly of actin patches since its overexpression diminishes them. We provide evidence that Gmf1 binds weakly if at all to actin, but it associates with actin-related protein (Arp) 2/3 complex and suppresses its functions such as the promotion of actin polymerization and branching filaments. Importantly, Arp2/3 complex-suppressing activity is conserved among GMF-family proteins from other organisms. Given the functional plasticity of ADF-H, GMF-family proteins possibly have changed their target from conventional actin to Arps through molecular evolution.","corpus_id":10026043,"score":1},{"doc_id":"21613547","title":"Turnover of branched actin filament networks by stochastic fragmentation with ADF/cofilin.","abstract":"Cell motility depends on the rapid assembly, aging, severing, and disassembly of actin filaments in spatially distinct zones. How a set of actin regulatory proteins that sustains actin-based force generation during motility work together in space and time remains poorly understood. We present our study of the distribution and dynamics of Arp2/3 complex, capping protein (CP), and actin-depolymerizing factor (ADF)/cofilin in actin \"comet tails,\" using a minimal reconstituted system with nucleation-promoting factor (NPF)-coated beads. The Arp2/3 complex concentrates at nucleation sites near the beads as well as in the first actin shell. CP colocalizes with actin and is homogeneously distributed throughout the comet tail; it serves to constrain the spatial distribution of ATP/ADP-P(i) filament zones to areas near the bead. The association of ADF/cofilin with the actin network is therefore governed by kinetics of actin assembly, actin nucleotide state, and CP binding. A kinetic simulation accurately validates these observations. Following its binding to the actin networks, ADF/cofilin is able to break up the dense actin filament array of a comet tail. Stochastic severing by ADF/cofilin loosens the tight entanglement of actin filaments inside the comet tail and facilitates turnover through the macroscopic release of large portions of the aged actin network.","corpus_id":17434729,"score":1},{"doc_id":"22010035","title":"Arabidopsis actin depolymerizing factor4 modulates the stochastic dynamic behavior of actin filaments in the cortical array of epidermal cells.","abstract":"Actin filament arrays are constantly remodeled as the needs of cells change as well as during responses to biotic and abiotic stimuli. Previous studies demonstrate that many single actin filaments in the cortical array of living Arabidopsis thaliana epidermal cells undergo stochastic dynamics, a combination of rapid growth balanced by disassembly from prolific severing activity. Filament turnover and dynamics are well understood from in vitro biochemical analyses and simple reconstituted systems. However, the identification in living cells of the molecular players involved in controlling actin dynamics awaits the use of model systems, especially ones where the power of genetics can be combined with imaging of individual actin filaments at high spatial and temporal resolution. Here, we test the hypothesis that actin depolymerizing factor (ADF)/cofilin contributes to stochastic filament severing and facilitates actin turnover. A knockout mutant for Arabidopsis ADF4 has longer hypocotyls and epidermal cells when compared with wild-type seedlings. This correlates with a change in actin filament architecture; cytoskeletal arrays in adf4 cells are significantly more bundled and less dense than in wild-type cells. Several parameters of single actin filament turnover are also altered. Notably, adf4 mutant cells have a 2.5-fold reduced severing frequency as well as significantly increased actin filament lengths and lifetimes. Thus, we provide evidence that ADF4 contributes to the stochastic dynamic turnover of actin filaments in plant cells.","corpus_id":2033160,"score":1},{"doc_id":"22123860","title":"Actin filaments function as a tension sensor by tension-dependent binding of cofilin to the filament.","abstract":"Intracellular and extracellular mechanical forces affect the structure and dynamics of the actin cytoskeleton. However, the underlying molecular and biophysical mechanisms, including how mechanical forces are sensed, are largely unknown. Actin-depolymerizing factor/cofilin proteins are actin-modulating proteins that are ubiquitously distributed in eukaryotes, and they are the most likely candidate as proteins to drive stress fiber disassembly in response to changes in tension in the fiber. In this study, we propose a novel hypothesis that tension in an actin filament prevents the filament from being severed by cofilin. To test this, we placed single actin filaments under tension using optical tweezers. When a fiber was tensed, it was severed after the application of cofilin with a significantly larger delay in comparison with control filaments suspended in solution. The binding rate of cofilin to an actin bundle decreased when the bundle was tensed. These results suggest that tension in an actin filament reduces the cofilin binding, resulting in a decrease in its effective severing activity.","corpus_id":1325745,"score":1},{"doc_id":"22492507","title":"Overexpression of S4D mutant of Leishmania donovani ADF/cofilin impairs flagellum assembly by affecting actin dynamics.","abstract":"Leishmania, like other eukaryotes, contains large amounts of actin and a number of actin-related and actin binding proteins. Our earlier studies have shown that deletion of the gene corresponding to Leishmania actin-depolymerizing protein (ADF/cofilin) adversely affects flagellum assembly, intracellular trafficking, and cell division. To further analyze this, we have now created ADF/cofilin site-specific point mutants and then examined (i) the actin-depolymerizing, G-actin binding, and actin-bound nucleotide exchange activities of the mutant proteins and (ii) the effect of overexpression of these proteins in wild-type cells. Here we show that S4D mutant protein failed to depolymerize F-actin but weakly bound G-actin and inhibited the exchange of G-actin-bound nucleotide. We further observed that overexpression of this protein impaired flagellum assembly and consequently cell motility by severely impairing the assembly of the paraflagellar rod, without significantly affecting vesicular trafficking or cell growth. Taken together, these results indicate that dynamic actin is essentially required in assembly of the eukaryotic flagellum.","corpus_id":6416645,"score":1},{"doc_id":"22558315","title":"Immunological responses and actin dynamics in macrophages are controlled by N-cofilin but are independent from ADF.","abstract":"Dynamic changes in the actin cytoskeleton are essential for immune cell function and a number of immune deficiencies have been linked to mutations, which disturb the actin cytoskeleton. In macrophages and dendritic cells, actin remodelling is critical for motility, phagocytosis and antigen presentation, however the actin binding proteins, which control antigen presentation have been poorly characterized. Here we dissect the specific roles of the family of ADF/cofilin F-actin depolymerizing factors in macrophages and in local immune responses. Macrophage migration, cell polarization and antigen presentation to T-cells require n-cofilin mediated F-actin remodelling. Using a conditional mouse model, we show that n-cofilin also controls MHC class II-dependent antigen presentation. Other cellular processes such as phagocytosis and antigen processing were found to be independent of n-cofilin. Our data identify n-cofilin as a novel regulator of antigen presentation, while ADF on the other hand is dispensable for macrophage motility and antigen presentation.","corpus_id":14378951,"score":1},{"doc_id":"22623720","title":"CAS-1, a C. elegans cyclase-associated protein, is required for sarcomeric actin assembly in striated muscle.","abstract":"Assembly of contractile apparatuses in striated muscle requires precisely regulated reorganization of the actin cytoskeletal proteins into sarcomeric organization. Regulation of actin filament dynamics is one of the essential processes of myofibril assembly, but the mechanism of actin regulation in striated muscle is not clearly understood. Actin depolymerizing factor (ADF)/cofilin is a key enhancer of actin filament dynamics in striated muscle in both vertebrates and nematodes. Here, we report that CAS-1, a cyclase-associated protein in Caenorhabditis elegans, promotes ADF/cofilin-dependent actin filament turnover in vitro and is required for sarcomeric actin organization in striated muscle. CAS-1 is predominantly expressed in striated muscle from embryos to adults. In vitro, CAS-1 binds to actin monomers and enhances exchange of actin-bound ATP/ADP even in the presence of UNC-60B, a muscle-specific ADF/cofilin that inhibits the nucleotide exchange. As a result, CAS-1 and UNC-60B cooperatively enhance actin filament turnover. The two proteins also cooperate to shorten actin filaments. A cas-1 mutation is homozygous lethal with defects in sarcomeric actin organization. cas-1-mutant embryos and worms have aggregates of actin in muscle cells, and UNC-60B is mislocalized to the aggregates. These results provide genetic and biochemical evidence that cyclase-associated protein is a critical regulator of sarcomeric actin organization in striated muscle.","corpus_id":6640149,"score":1},{"doc_id":"22637580","title":"G146V mutation at the hinge region of actin reveals a myosin class-specific requirement of actin conformations for motility.","abstract":"The G146V mutation in actin is dominant lethal in yeast. G146V actin filaments bind cofilin only minimally, presumably because cofilin binding requires the large and small actin domains to twist with respect to one another around the hinge region containing Gly-146, and the mutation inhibits that twisting motion. A number of studies have suggested that force generation by myosin also requires actin filaments to undergo conformational changes. This prompted us to examine the effects of the G146V mutation on myosin motility. When compared with wild-type actin filaments, G146V filaments showed a 78% slower gliding velocity and a 70% smaller stall force on surfaces coated with skeletal heavy meromyosin. In contrast, the G146V mutation had no effect on either gliding velocity or stall force on myosin V surfaces. Kinetic analyses of actin-myosin binding and ATPase activity indicated that the weaker affinity of actin filaments for myosin heads carrying ADP, as well as reduced actin-activated ATPase activity, are the cause of the diminished motility seen with skeletal myosin. Interestingly, the G146V mutation disrupted cooperative binding of myosin II heads to actin filaments. These data suggest that myosin-induced conformational changes in the actin filaments, presumably around the hinge region, are involved in mediating the motility of skeletal myosin but not myosin V and that the specific structural requirements for the actin subunits, and thus the mechanism of motility, differ among myosin classes.","corpus_id":2147167,"score":1},{"doc_id":"22790341","title":"Cofilin overexpression affects actin cytoskeleton organization and migration of human colon adenocarcinoma cells.","abstract":"The dynamic reorganization of actin cytoskeleton is regulated by a large number of actin-binding proteins. Among them, the interaction of ADF/cofilin with monomeric and filamentous actin is very important, since it severs actin filaments. It also positively influences actin treadmilling. The activity of ADF/cofilin is reversibly regulated by phosphorylation and dephosphorylation at Ser-3, with the phosphorylated form (P-cofilin) being inactive. Here, we studied the effects of overexpression of cofilin and two cofilin variants in the human colon adenocarcinoma LS180 cell line. We have generated the LS180 cells expressing three different cofilin variants: WT (wild type), Ser 3 Ala (S3A) (constitutively active) or Ser 3 Asp (S3D) (constitutively inactive cofilin). The cells expressing WT cofilin were characterized by abundant cell spreading and colocalization of cofilin with the submembranous F-actin. Similar effects were observed in cells expressing S3A cofilin. In contrast, LS180 cells expressing S3D cofilin remained longitudinal in morphology and cofilin was equally distributed within the cell body. Furthermore, the migration ability of LS180 cells expressing different cofilin mutants was analyzed. In comparison to control cells, we have noticed a significant, approximately fourfold increase in the migration factor value of cells overexpressing WT type cofilin. The overexpression of S3D cofilin resulted in an almost complete inhibition of cell motility. The estimation of actin pool in the cytosol of LS180 cells expressing S3A cofilin has shown a significantly lower level of total actin in reference to control cells. The opposite effect was observed in LS180 cells overexpressing S3D cofilin. In summary, the results of our experiments indicate that phosphorylation \"status\" of cofilin is a factor affecting the actin cytoskeleton organization and migration abilities of colon adenocarcinoma LS180 cells.","corpus_id":17925954,"score":1},{"doc_id":"23212920","title":"Rapid nucleotide exchange renders Asp-11 mutant actins resistant to depolymerizing activity of cofilin, leading to dominant toxicity in vivo.","abstract":"Conserved Asp-11 of actin is a part of the nucleotide binding pocket, and its mutation to Gln is dominant lethal in yeast, whereas the mutation to Asn in human α-actin dominantly causes congenital myopathy. To elucidate the molecular mechanism of those dominant negative effects, we prepared Dictyostelium versions of D11N and D11Q mutant actins and characterized them in vitro. D11N and D11Q actins underwent salt-dependent reversible polymerization, although the resultant polymerization products contained small anomalous structures in addition to filaments of normal appearance. Both monomeric and polymeric D11Q actin released bound nucleotides more rapidly than the wild type, and intriguingly, both monomeric and polymeric D11Q actins hardly bound cofilin. The deficiency in cofilin binding can be explained by rapid exchange of bound nucleotide with ATP in solution, because cofilin does not bind ATP-bound actin. Copolymers of D11Q and wild type actins bound cofilin, but cofilin-induced depolymerization of the copolymers was slower than that of wild type filaments, which may presumably be the primary reason why this mutant actin is dominantly toxic in vivo. Purified D11N actin was unstable, which made its quantitative biochemical characterization difficult. However, monomeric D11N actin released nucleotides even faster than D11Q, and we speculate that D11N actin also exerts its toxic effects in vivo through a defective interaction with cofilin. We have recently found that two other dominant negative actin mutants are also defective in cofilin binding, and we propose that the defective cofilin binder is a major class of dominant negative actin mutants.","corpus_id":22898101,"score":1},{"doc_id":"23352932","title":"Molecular origins of cofilin-linked changes in actin filament mechanics.","abstract":"The actin regulatory protein cofilin plays a central role in actin assembly dynamics by severing filaments and increasing the concentration of ends from which subunits add and dissociate. Cofilin binding modifies the average structure and mechanical properties of actin filaments, thereby promoting fragmentation of partially decorated filaments at boundaries of bare and cofilin-decorated segments. Despite extensive evidence for cofilin-dependent changes in filament structure and mechanics, it is unclear how the two processes are linked at the molecular level. Here, we use molecular dynamics simulations and coarse-grained analyses to evaluate the molecular origins of the changes in filament compliance due to cofilin binding. Filament subunits with bound cofilin are less flat and maintain a significantly more open nucleotide cleft than bare filament subunits. Decorated filament segments are less twisted, thinner (considering only actin), and less connected than their bare counterparts, which lowers the filament bending persistence length and torsional stiffness. Using coarse-graining as an analysis method reveals that cofilin binding increases the average distance between the adjacent long-axis filament subunit, thereby weakening their interaction. In contrast, a fraction of lateral filament subunit contacts are closer and presumably stronger with cofilin binding. A cofilactin interface contact identified by cryo-electron microscopy is unstable during simulations carried out at 310K, suggesting that this particular interaction may be short lived at ambient temperatures. These results reveal the molecular origins of cofilin-dependent changes in actin filament mechanics that may promote filament severing.","corpus_id":8991800,"score":1},{"doc_id":"23729382","title":"ADF/cofilin is not essential but is critically important for actin activities during phagocytosis in Tetrahymena thermophila.","abstract":"ADF/cofilin is a highly conserved actin-modulating protein. Reorganization of the actin cytoskeleton in vivo through severing and depolymerizing of F-actin by this protein is essential for various cellular events, such as endocytosis, phagocytosis, cytokinesis, and cell migration. We show that in the ciliate Tetrahymena thermophila, the ADF/cofilin homologue Adf73p associates with actin on nascent food vacuoles. Overexpression of Adf73p disrupted the proper localization of actin and inhibited the formation of food vacuoles. In vitro, recombinant Adf73p promoted the depolymerization of filaments made of T. thermophila actin (Act1p). Knockout cells lacking the ADF73 gene are viable but grow extremely slowly and have a severely decreased rate of food vacuole formation. Knockout cells have abnormal aggregates of actin in the cytoplasm. Surprisingly, unlike the case in animals and yeasts, in Tetrahymena, ADF/cofilin is not required for cytokinesis. Thus, the Tetrahymena model shows promise for future studies of the role of ADF/cofilin in vivo.","corpus_id":5276176,"score":1},{"doc_id":"23862734","title":"Cofilin-induced changes in F-actin detected via cross-linking with benzophenone-4-maleimide.","abstract":"Cofilin is a member of the actin depolymerizing factor (ADF)/cofilin family of proteins. It plays a key role in actin dynamics by promoting disassembly and assembly of actin filaments. Upon its binding, cofilin has been shown to bridge two adjacent protomers in filamentous actin (F-actin) and promote the displacement and disordering of subdomain 2 of actin. Here, we present evidence for cofilin promoting a new structural change in the actin filament, as detected via a switch in cross-linking sites. Benzophenone-4-maleimide, which normally forms intramolecular cross-linking in F-actin, cross-links F-actin intermolecularly upon cofilin binding. We mapped the cross-linking sites and found that in the absence of cofilin intramolecular cross-linking occurred between residues Cys374 and Asp11. In contrast, cofilin shifts the cross-linking by this reagent to intermolecular, between residue Cys374, located within subdomain 1 of the upper protomer, and Met44, located in subdomain 2 of the lower protomer. The intermolecular cross-linking of F-actin slows the rate of cofilin dissociation from the filaments and decreases the effect of ionic strength on cofilin-actin binding. These results are consistent with a significant role of filament flexibility in cofilin-actin interactions.","corpus_id":30899512,"score":1},{"doc_id":"24371134","title":"A mechanism for actin filament severing by malaria parasite actin depolymerizing factor 1 via a low affinity binding interface.","abstract":"Actin depolymerizing factor (ADF)/cofilins are essential regulators of actin turnover in eukaryotic cells. These multifunctional proteins facilitate both stabilization and severing of filamentous (F)-actin in a concentration-dependent manner. At high concentrations ADF/cofilins bind stably to F-actin longitudinally between two adjacent actin protomers forming what is called a decorative interaction. Low densities of ADF/cofilins, in contrast, result in the optimal severing of the filament. To date, how these two contrasting modalities are achieved by the same protein remains uncertain. Here, we define the proximate amino acids between the actin filament and the malaria parasite ADF/cofilin, PfADF1 from Plasmodium falciparum. PfADF1 is unique among ADF/cofilins in being able to sever F-actin but do so without stable filament binding. Using chemical cross-linking and mass spectrometry (XL-MS) combined with structure reconstruction we describe a previously overlooked binding interface on the actin filament targeted by PfADF1. This site is distinct from the known binding site that defines decoration. Furthermore, total internal reflection fluorescence (TIRF) microscopy imaging of single actin filaments confirms that this novel low affinity site is required for F-actin severing. Exploring beyond malaria parasites, selective blocking of the decoration site with human cofilin (HsCOF1) using cytochalasin D increases its severing rate. HsCOF1 may therefore also use a decoration-independent site for filament severing. Thus our data suggest that a second, low affinity actin-binding site may be universally used by ADF/cofilins for actin filament severing.","corpus_id":12854318,"score":1},{"doc_id":"24770705","title":"ADF/Cofilin Controls Synaptic Actin Dynamics and Regulates Synaptic Vesicle Mobilization and Exocytosis.","abstract":"Actin is a regulator of synaptic vesicle mobilization and exocytosis, but little is known about the mechanisms that regulate actin at presynaptic terminals. Genetic data on LIMK1, a negative regulator of actin-depolymerizing proteins of the ADF/cofilin family, suggest a role for ADF/cofilin in presynaptic function. However, synapse physiology is fully preserved upon genetic ablation of ADF in mice, and n-cofilin mutant mice display defects in postsynaptic plasticity, but not in presynaptic function. One explanation for this phenomenon is overlapping functions of ADF and n-cofilin in presynaptic physiology. Here, we tested this hypothesis and genetically removed ADF together with n-cofilin from synapses. In double mutants for ADF and n-cofilin, synaptic actin dynamics was impaired and more severely affected than in single mutants. The resulting cytoskeletal defects heavily affected the organization, mobilization, and exocytosis of synaptic vesicles in hippocampal CA3-CA1 synapses. Our data for the first time identify overlapping functions for ADF and n-cofilin in presynaptic physiology and vesicle trafficking. We conclude that n-cofilin is a limiting factor in postsynaptic plasticity, a function which cannot be substituted by ADF. On the presynaptic side, the presence of either ADF or n-cofilin is sufficient to control actin remodeling during vesicle release.","corpus_id":31044670,"score":1},{"doc_id":"25228691","title":"Structure and mechanism of mouse cyclase-associated protein (CAP1) in regulating actin dynamics.","abstract":"Srv2/CAP is a conserved actin-binding protein with important roles in driving cellular actin dynamics in diverse animal, fungal, and plant species. However, there have been conflicting reports about whether the activities of Srv2/CAP are conserved, particularly between yeast and mammalian homologs. Yeast Srv2 has two distinct functions in actin turnover: its hexameric N-terminal-half enhances cofilin-mediated severing of filaments, while its C-terminal-half catalyzes dissociation of cofilin from ADP-actin monomers and stimulates nucleotide exchange. Here, we dissected the structure and function of mouse CAP1 to better understand its mechanistic relationship to yeast Srv2. Although CAP1 has a shorter N-terminal oligomerization sequence compared with Srv2, we find that the N-terminal-half of CAP1 (N-CAP1) forms hexameric structures with six protrusions, similar to N-Srv2. Further, N-CAP1 autonomously binds to F-actin and decorates the sides and ends of filaments, altering F-actin structure and enhancing cofilin-mediated severing. These activities depend on conserved surface residues on the helical-folded domain. Moreover, N-CAP1 enhances yeast cofilin-mediated severing, and conversely, yeast N-Srv2 enhances human cofilin-mediated severing, highlighting the mechanistic conservation between yeast and mammals. Further, we demonstrate that the C-terminal actin-binding β-sheet domain of CAP1 is sufficient to catalyze nucleotide-exchange of ADP-actin monomers, while in the presence of cofilin this activity additionally requires the WH2 domain. Thus, the structures, activities, and mechanisms of mouse and yeast Srv2/CAP homologs are remarkably well conserved, suggesting that the same activities and mechanisms underlie many of the diverse actin-based functions ascribed to Srv2/CAP homologs in different organisms.","corpus_id":21579399,"score":1},{"doc_id":"25373779","title":"Cofilin-2 controls actin filament length in muscle sarcomeres.","abstract":"ADF/cofilins drive cytoskeletal dynamics by promoting the disassembly of \"aged\" ADP-actin filaments. Mammals express several ADF/cofilin isoforms, but their specific biochemical activities and cellular functions have not been studied in detail. Here, we demonstrate that the muscle-specific isoform cofilin-2 promotes actin filament disassembly in sarcomeres to control the precise length of thin filaments in the contractile apparatus. In contrast to other isoforms, cofilin-2 efficiently binds and disassembles both ADP- and ATP/ADP-Pi-actin filaments. We mapped surface-exposed cofilin-2-specific residues required for ATP-actin binding and propose that these residues function as an \"actin nucleotide-state sensor\" among ADF/cofilins. The results suggest that cofilin-2 evolved specific biochemical and cellular properties that allow it to control actin dynamics in sarcomeres, where filament pointed ends may contain a mixture of ADP- and ATP/ADP-Pi-actin subunits. Our findings also offer a rationale for why cofilin-2 mutations in humans lead to myopathies.","corpus_id":10814202,"score":1},{"doc_id":"25864508","title":"Roles of cofilin in development and its mechanisms of regulation.","abstract":"Reorganization of the actin cytoskeleton is essential for cellular processes during animal development. Cofilin and actin depolymerizing factor (ADF) are potent actin-binding proteins that sever and depolymerize actin filaments, acting to generate the dynamics of the actin cytoskeleton. The activity of cofilin is spatially and temporally regulated by a variety of intracellular molecular mechanisms. Cofilin is regulated by cofilin binding molecules, is phosphorylated at Ser-3 (inactivation) by LIM-kinases (LIMKs) and testicular protein kinases (TESKs), and is dephosphorylated (reactivation) by slingshot protein phosphatases (SSHs). Although studies of the molecular mechanisms of cofilin-induced reorganization of the actin cytoskeleton have been ongoing for decades, the multicellular functions of cofilin and its regulation in development are just becoming apparent. This review describes the molecular mechanisms of generating actin dynamics by cofilin and the intracellular signaling pathways for regulating cofilin activity. Furthermore, recent findings of the roles of cofilin in the development of several tissues and organs, especially neural tissues and cells, in model animals are described. Recent developmental studies have indicated that cofilin and its regulatory mechanisms are involved in cellular proliferation and migration, the establishment of cellular polarity, and the dynamic regulation of organ morphology.","corpus_id":36262546,"score":1},{"doc_id":"27153537","title":"Structural Basis for Noncanonical Substrate Recognition of Cofilin/ADF Proteins by LIM Kinases.","abstract":"Cofilin/actin-depolymerizing factor (ADF) proteins are critical nodes that relay signals from protein kinase cascades to the actin cytoskeleton, in particular through site-specific phosphorylation at residue Ser3. This is important for regulation of the roles of cofilin in severing and stabilizing actin filaments. Consequently, cofilin/ADF Ser3 phosphorylation is tightly controlled as an almost exclusive substrate for LIM kinases. Here we determine the LIMK1:cofilin-1 co-crystal structure. We find an interface that is distinct from canonical kinase-substrate interactions. We validate this previously unobserved mechanism for high-fidelity kinase-substrate recognition by in vitro kinase assays, examination of cofilin phosphorylation in mammalian cells, and functional analysis in S. cerevisiae. The interface is conserved across all LIM kinases. Remarkably, we also observe both pre- and postphosphotransfer states in the same crystal lattice. This study therefore provides a molecular understanding of how kinase-substrate recognition acts as a gatekeeper to regulate actin cytoskeletal dynamics.","corpus_id":206994772,"score":1},{"doc_id":"27454820","title":"F-actin dismantling through a redox-driven synergy between Mical and cofilin.","abstract":"Numerous cellular functions depend on actin filament (F-actin) disassembly. The best-characterized disassembly proteins, the ADF (actin-depolymerizing factor)/cofilins (encoded by the twinstar gene in Drosophila), sever filaments and recycle monomers to promote actin assembly. Cofilin is also a relatively weak actin disassembler, posing questions about mechanisms of cellular F-actin destabilization. Here we uncover a key link to targeted F-actin disassembly by finding that F-actin is efficiently dismantled through a post-translational-mediated synergism between cofilin and the actin-oxidizing enzyme Mical. We find that Mical-mediated oxidation of actin improves cofilin binding to filaments, where their combined effect dramatically accelerates F-actin disassembly compared with either effector alone. This synergism is also necessary and sufficient for F-actin disassembly in vivo, magnifying the effects of both Mical and cofilin on cellular remodelling, axon guidance and Semaphorin-Plexin repulsion. Mical and cofilin, therefore, form a redox-dependent synergistic pair that promotes F-actin instability by rapidly dismantling F-actin and generating post-translationally modified actin that has altered assembly properties.","corpus_id":38211458,"score":1},{"doc_id":"27762277","title":"Allosteric regulation by cooperative conformational changes of actin filaments drives mutually exclusive binding with cofilin and myosin.","abstract":"Heavy meromyosin (HMM) of myosin II and cofilin each binds to actin filaments cooperatively and forms clusters along the filaments, but it is unknown whether the two cooperative bindings are correlated and what physiological roles they have. Fluorescence microscopy demonstrated that HMM-GFP and cofilin-mCherry each bound cooperatively to different parts of actin filaments when they were added simultaneously in 0.2 μM ATP, indicating that the two cooperative bindings are mutually exclusive. In 0.1 mM ATP, the motor domain of myosin (S1) strongly inhibited the formation of cofilin clusters along actin filaments. Under this condition, most actin protomers were unoccupied by S1 at any given moment, suggesting that transiently bound S1 alters the structure of actin filaments cooperatively and/or persistently to inhibit cofilin binding. Consistently, cosedimentation experiments using copolymers of actin and actin-S1 fusion protein demonstrated that the fusion protein affects the neighboring actin protomers, reducing their affinity for cofilin. In reciprocal experiments, cofilin-actin fusion protein reduced the affinity of neighboring actin protomers for S1. Thus, allosteric regulation by cooperative conformational changes of actin filaments contributes to mutually exclusive cooperative binding of myosin II and cofilin to actin filaments, and presumably to the differential localization of both proteins in cells.","corpus_id":4582454,"score":1},{"doc_id":"28025492","title":"Cofilin-1 and Other ADF/Cofilin Superfamily Members in Human Malignant Cells.","abstract":"Identification of actin-depolymerizing factor homology (ADF-H) domains in the structures of several related proteins led first to the formation of the ADF/cofilin family, which then expanded to the ADF/cofilin superfamily. This superfamily includes the well-studied cofilin-1 (Cfl-1) and about a dozen different human proteins that interact directly or indirectly with the actin cytoskeleton, provide its remodeling, and alter cell motility. According to some data, Cfl-1 is contained in various human malignant cells (HMCs) and is involved in the formation of malignant properties, including invasiveness, metastatic potential, and resistance to chemotherapeutic drugs. The presence of other ADF/cofilin superfamily proteins in HMCs and their involvement in the regulation of cell motility were discovered with the use of various OMICS technologies. In our review, we discuss the results of the study of Cfl-1 and other ADF/cofilin superfamily proteins, which may be of interest for solving different problems of molecular oncology, as well as for the prospects of further investigations of these proteins in HMCs.","corpus_id":15998513,"score":1},{"doc_id":"29463680","title":"The actin filament twist changes abruptly at boundaries between bare and cofilin-decorated segments.","abstract":"Cofilin/ADF proteins are actin-remodeling proteins, essential for actin disassembly in various cellular processes, including cell division, intracellular transport, and motility. Cofilins bind actin filaments cooperatively and sever them preferentially at boundaries between bare and cofilin-decorated (cofilactin) segments. The cooperative binding to actin has been proposed to originate from conformational changes that propagate allosterically from clusters of bound cofilin to bare actin segments. Estimates of the lengths over which these cooperative conformational changes propagate vary dramatically, ranging from 2 to >100 subunits. Here, we present a general, structure-based method for detecting from cryo-EM micrographs small variations in filament geometry (i.e. twist) with single-subunit precision. How these variations correlate with regulatory protein occupancy reveals how far allosteric, conformational changes propagate along filaments. We used this method to determine the effects of cofilin on the actin filament twist. Our results indicate that cofilin-induced changes in filament twist propagate only 1-2 subunits from the boundary into the bare actin segment, independently of the boundary polarity (i.e. irrespective of whether or not the bare actin segment flanks the pointed or barbed-end side of the boundary) and the pyrene fluorophore labeling of actin. These observations indicate that the filament twist changes abruptly at boundaries between bare and cofilin-decorated segments, thereby constraining mechanistic models of cooperative actin filament interactions and severing by cofilin. The methods presented here extend the capability of cryo-EM to analyze biologically relevant deviations from helical symmetry in actin as well as other classes of linear polymers.","corpus_id":3572019,"score":1},{"doc_id":"29709602","title":"Structure, dynamics, and biochemical characterization of ADF/cofilin Twinstar from Drosophilamelanogaster.","abstract":"BACKGROUND: Twinstar is an ADF/cofilin family protein, which is expressed by the tsr gene in Drosophila melanogaster. Twinstar is one of the main regulators of actin cytoskeleton remodelling and is essential for vital cellular processes like cytokinesis and endocytosis. METHODS: We have characterized the structure and dynamics of Twinstar by solution NMR spectroscopy, the interaction of Twinstar with rabbit muscle actin by ITC, and biochemical activities of Twinstar through different biochemical assays using fluorescence spectroscopy and ultra-centrifugation. RESULTS: The solution structure of Twinstar shows characteristic ADF-H fold with well-formed G/F-site and F-site for interaction with actin. The structure possesses an extended F-loop, which is rigid at the base, but flexible towards its apical region. Twinstar shares similar dynamics for the G/F-site with C. elegans homologs, UNC-60A and UNC-60B. However, the dynamics of its F-loop are different from its C. elegans homologs. Twinstar shows strong affinity for ADP-G-Actin and ATP-G-Actin with Kds of ~7.6 nM and ~0.4 μM, respectively. It shows mild F-actin depolymerizing activity and stable interaction with F-actin with a Kd of ~5.0 μM. It inhibits the rate of the nucleotide exchange in a dose dependent manner. CONCLUSION: On the basis of structure, dynamics, and biochemical activity, Twinstar can be taken to execute its biochemical role by facilitating directional growth and maintenance of length of actin filaments. GENERAL SIGNIFICANCE: This study characterizes the structure, backbone dynamics, and biochemical activities of Twinstar of Drosophila, which provides an insight into the regulation of actin dynamics in the member of phylum insecta.","corpus_id":14009390,"score":1}],"string":"[\n {\n \"doc_id\": \"18065447\",\n \"title\": \"Stochastic severing of actin filaments by actin depolymerizing factor/cofilin controls the emergence of a steady dynamical regime.\",\n \"abstract\": \"Actin dynamics (i.e., polymerization/depolymerization) powers a large number of cellular processes. However, a great deal remains to be learned to explain the rapid actin filament turnover observed in vivo. Here, we developed a minimal kinetic model that describes key details of actin filament dynamics in the presence of actin depolymerizing factor (ADF)/cofilin. We limited the molecular mechanism to 1), the spontaneous growth of filaments by polymerization of actin monomers, 2), the ageing of actin subunits in filaments, 3), the cooperative binding of ADF/cofilin to actin filament subunits, and 4), filament severing by ADF/cofilin. First, from numerical simulations and mathematical analysis, we found that the average filament length, L, is controlled by the concentration of actin monomers (power law: 5/6) and ADF/cofilin (power law: -2/3). We also showed that the average subunit residence time inside the filament, T, depends on the actin monomer (power law: -1/6) and ADF/cofilin (power law: -2/3) concentrations. In addition, filament length fluctuations are approximately 20% of the average filament length. Moreover, ADF/cofilin fragmentation while modulating filament length keeps filaments in a high molar ratio of ATP- or ADP-P(i) versus ADP-bound subunits. This latter property has a protective effect against a too high severing activity of ADF/cofilin. We propose that the activity of ADF/cofilin in vivo is under the control of an affinity gradient that builds up dynamically along growing actin filaments. Our analysis shows that ADF/cofilin regulation maintains actin filaments in a highly dynamical state compatible with the cytoskeleton dynamics observed in vivo.\",\n \"corpus_id\": 8551262,\n \"score\": 2\n },\n {\n \"doc_id\": \"18625842\",\n \"title\": \"Structure of the actin-depolymerizing factor homology domain in complex with actin.\",\n \"abstract\": \"Actin dynamics provide the driving force for many cellular processes including motility and endocytosis. Among the central cytoskeletal regulators are actin-depolymerizing factor (ADF)/cofilin, which depolymerizes actin filaments, and twinfilin, which sequesters actin monomers and caps filament barbed ends. Both interact with actin through an ADF homology (ADF-H) domain, which is also found in several other actin-binding proteins. However, in the absence of an atomic structure for the ADF-H domain in complex with actin, the mechanism by which these proteins interact with actin has remained unknown. Here, we present the crystal structure of twinfilin's C-terminal ADF-H domain in complex with an actin monomer. This domain binds between actin subdomains 1 and 3 through an interface that is conserved among ADF-H domain proteins. Based on this structure, we suggest a mechanism by which ADF/cofilin and twinfilin inhibit nucleotide exchange of actin monomers and present a model for how ADF/cofilin induces filament depolymerization by weakening intrafilament interactions.\",\n \"corpus_id\": 12130534,\n \"score\": 2\n },\n {\n \"doc_id\": \"18763747\",\n \"title\": \"Actin-binding proteins: how to reveal the conformational changes.\",\n \"abstract\": \"Actin is the most abundant protein in eukaryotes. Under physiological conditions, it can polymerize into polarized filaments. At the heart of these processes are actin-binding proteins that stimulate actin assembly. Most of them are composed of multiple domains that perform both regulatory and signaling functions. Many actin-binding proteins, including WASP and formin family proteins, are auto-inhibited through intramolecular interactions that mask the actin-regulating sites of these proteins. The large flexible molecules of formins have so far eluded crystallization, and have been crystallized only partially. The information from the available crystal structures is valuable, but somewhat difficult to interpret without a larger framework on which to pose the actin-binding mechanism. Single-particle electron microscopy and electron tomography could provide such a large framework with the full-length structures of protein complexes. The recent advances in determining the molecular interactions in protein complexes predict that the molecular modeling and molecular dynamics methods could be employed to study conformational changes in molecules.\",\n \"corpus_id\": 20755223,\n \"score\": 2\n },\n {\n \"doc_id\": \"19289059\",\n \"title\": \"The effects of ADF/cofilin and profilin on the conformation of the ATP-binding cleft of monomeric actin.\",\n \"abstract\": \"Actin depolymerizing factor (ADF)/cofilin and profilin are small actin-binding proteins, which have central roles in cytoskeletal dynamics in all eukaryotes. When bound to an actin monomer, ADF/cofilins inhibit the nucleotide exchange, whereas most profilins accelerate the nucleotide exchange on actin monomers. In this study the effects of ADF/cofilin and profilin on the accessibility of the actin monomer's ATP-binding pocket was investigated by a fluorescence spectroscopic method. The fluorescence of the actin bound epsilon-ATP was quenched with a neutral quencher (acrylamide) in steady-state and time dependent experiments, and the data were analyzed with a complex form of the Stern-Volmer equation. The experiments revealed that in the presence of ADF/cofilin the accessibility of the bound epsilon-ATP decreased, indicating a closed and more compact ATP-binding pocket induced by the binding of ADF/cofilin. In the presence of profilin the accessibility of the bound epsilon-ATP increased, indicating a more open and approachable protein matrix around the ATP-binding pocket. The results of the fluorescence quenching experiments support a structural mechanism regarding the regulation of the nucleotide exchange on actin monomers by ADF/cofilin and profilin.\",\n \"corpus_id\": 22561041,\n \"score\": 2\n },\n {\n \"doc_id\": \"20368459\",\n \"title\": \"Actin filament remodeling by actin depolymerization factor/cofilin.\",\n \"abstract\": \"We investigate, using molecular dynamics, how the severing protein, actin depolymerization factor (ADF)/cofilin, modulates the structure, conformational dynamics, and mechanical properties of actin filaments. The actin and cofilactin filament bending stiffness and corresponding persistence lengths obtained from all-atom simulations are comparable to values obtained from analysis of thermal fluctuations in filament shape. Filament flexibility is strongly affected by the nucleotide-linked conformation of the actin subdomain 2 DNase-I binding loop and the filament radial mass density distribution. ADF/cofilin binding between subdomains 1 and 3 of a filament subunit triggers reorganization of subdomain 2 of the neighboring subunit such that the DNase-I binding loop (DB-loop) moves radially away from the filament. Repositioning of the neighboring subunit DB-loop significantly weakens subunit interactions along the long-pitch helix and lowers the filament bending rigidity. Lateral filament contacts between the hydrophobic loop and neighboring short-pitch helix monomers in native filaments are also compromised with cofilin binding. These works provide a molecular interpretation of biochemical solution studies documenting the disruption of filament subunit interactions and also reveal the molecular basis of actin filament allostery and its linkage to ADF/cofilin binding.\",\n \"corpus_id\": 16078744,\n \"score\": 2\n },\n {\n \"doc_id\": \"20441753\",\n \"title\": \"The kinetics of cooperative cofilin binding reveals two states of the cofilin-actin filament.\",\n \"abstract\": \"The interaction of cofilin with actin filaments displays positive cooperativity. The equilibrium binding and associated thermodynamic properties of this interaction are well described by a simple, one-dimensional Ising model with nearest neighbor interactions. Here we evaluate the kinetic contributions to cooperative binding and the ability of this model to account for binding across a wide range of cofilin concentrations. A Monte Carlo-based simulation protocol that allows for nearest-neighbor interactions between adjacent binding sites was used to globally fit time courses of human cofilin binding to human nonmuscle (beta-, gamma-) actin filaments. Several extensions of the one-dimensional Ising model were tested, and a mechanism that includes isomerization of the actin filament was found to best account for time courses of association as well as irreversible dissociation from a saturated filament. This model predicts two equilibrium states of the cofilin-actin, or cofilactin, filament, and the resulting set of binding parameters are in agreement with equilibrium thermodynamic parameters. We conclude that despite its simplicity, this one-dimensional Ising model is a reliable model for analyzing and interpreting the energetics and kinetics of cooperative cofilin-actin filament interactions. The model predicts that severing activity associated with boundaries between bare and decorated segments will not be linear, but display a transient burst at short times on cofilin activation then dissipate due to a kinetic competition between severing activity and cofilin binding. A second peak of severing activity is predicted to arise from irreversible cofilin dissociation on inactivation. These behaviors predict what we believe to be novel mechanisms of cofilin severing and spatial regulation of actin filament turnover in cells. The methods developed for this system are generally applicable to the kinetic analysis of cooperative ligand binding to linear polymers.\",\n \"corpus_id\": 10246219,\n \"score\": 2\n },\n {\n \"doc_id\": \"20627129\",\n \"title\": \"Solution structure and dynamics of ADF/cofilin from Leishmania donovani.\",\n \"abstract\": \"Leishmania donovani ADF/cofilin (LdCof) is a novel member of ADF/cofilin family. LdCof depolymerizes, but does not co-sediment with, rabbit muscle actin filaments. Its F-actin depolymerizing activity is pH independent. Further, it possesses weak F-actin severing activity. In order to better understand its characteristic properties, we have determined the solution NMR structure of LdCof and have analyzed protein backbone dynamics from (15)N-relaxation measurements. The structure of LdCof possesses a conserved ADF/cofilin fold with a central mixed β-sheet consisting of six β-strands which is surrounded by five α-helices. LdCof structure has conserved G/F-actin binding site which includes the characteristic long kinked α-helix (α3). LdCof binds to rabbit muscle ADP-G-actin with 1:1 stoichiometry (K(d)∼0.2μM). The F-actin binding site is not well formed and analysis of (15)N-relaxation data shows that residues in the β4-β5 loop region and C-terminal are relatively flexible, which seems to be a determinant for the low F-actin severing activity of LdCof.\",\n \"corpus_id\": 25062527,\n \"score\": 2\n },\n {\n \"doc_id\": \"21628589\",\n \"title\": \"Minimal requirements for actin filament disassembly revealed by structural analysis of malaria parasite actin-depolymerizing factor 1.\",\n \"abstract\": \"Malaria parasite cell motility is a process that is dependent on the dynamic turnover of parasite-derived actin filaments. Despite its central role, actin's polymerization state is controlled by a set of identifiable regulators that is markedly reduced compared with those of other eukaryotic cells. In Plasmodium falciparum, the most virulent species that affects humans, this minimal repertoire includes two members of the actin-depolymerizing factor/cofilin (AC) family of proteins, P. falciparum actin-depolymerizing factor 1 (PfADF1) and P. falciparum actin-depolymerizing factor 2. This essential class of actin regulator is involved in the control of filament dynamics at multiple levels, from monomer binding through to filament depolymerization and severing. Previous biochemical analyses have suggested that PfADF1 sequesters monomeric actin but, unlike most eukaryotic counterparts, has limited potential to bind or depolymerize filaments. The molecular basis for these unusual properties and implications for parasite cell motility have not been established. Here we present the crystal structure of an apicomplexan AC protein, PfADF1. We show that PfADF1 lacks critical residues previously implicated as essential for AC-mediated actin filament binding and disassembly, having a substantially reduced filament-binding loop and C-terminal α4 helix. Despite this divergence in structure, we demonstrate that PfADF1 is capable of efficient actin filament severing. Furthermore, this severing occurs despite PfADF1's low binding affinity for filaments. Comparative structural analysis along with biochemical and microscopy evidence establishes that severing is reliant on the availability of an exposed basic residue in the filament-binding loop, a conserved minimal requirement that defines AC-mediated filament disassembly across eukaryotic cells.\",\n \"corpus_id\": 12063246,\n \"score\": 2\n },\n {\n \"doc_id\": \"21850706\",\n \"title\": \"Actin-depolymerizing factor homology domain: a conserved fold performing diverse roles in cytoskeletal dynamics.\",\n \"abstract\": \"Actin filaments form contractile and protrusive structures that play central roles in many processes such as cell migration, morphogenesis, endocytosis, and cytokinesis. During these processes, the dynamics of the actin filaments are precisely regulated by a large array of actin-binding proteins. The actin-depolymerizing factor homology (ADF-H) domain is a structurally conserved protein motif, which promotes cytoskeletal dynamics by interacting with monomeric and/or filamentous actin, and with the Arp2/3 complex. Despite their structural homology, the five classes of ADF-H domain proteins display distinct biochemical activities and cellular roles, only parts of which are currently understood. ADF/cofilin promotes disassembly of aged actin filaments, whereas twinfilin inhibits actin filament assembly via sequestering actin monomers and interacting with filament barbed ends. GMF does not interact with actin, but instead binds Arp2/3 complex and promotes dissociation of Arp2/3-mediated filament branches. Abp1 and drebrin are multidomain proteins that interact with actin filaments and regulate the activities of other proteins during various actin-dependent processes. The exact function of coactosin is currently incompletely understood. In this review article, we discuss the biochemical functions, cellular roles, and regulation of the five groups of ADF-H domain proteins.\",\n \"corpus_id\": 20804728,\n \"score\": 2\n },\n {\n \"doc_id\": \"21875597\",\n \"title\": \"The interaction of cofilin with the actin filament.\",\n \"abstract\": \"Cofilin is a key actin-binding protein that is critical for controlling the assembly of actin within the cell. Here, we present the results of molecular docking and dynamics studies using a muscle actin filament and human cofilin I. Guided by extensive mutagenesis results and other biophysical and structural studies, we arrive at a model for cofilin bound to the actin filament. This predicted structure agrees very well with electron microscopy results for cofilin-decorated filaments, provides molecular insight into how the known F- and G-actin sites on cofilin interact with the filament, and also suggests new interaction sites that may play a role in cofilin binding. The resulting atomic-scale model also helps us understand the molecular function and regulation of cofilin and provides testable data for future experimental and simulation work.\",\n \"corpus_id\": 38919864,\n \"score\": 2\n },\n {\n \"doc_id\": \"22158895\",\n \"title\": \"Remodeling of actin filaments by ADF/cofilin proteins.\",\n \"abstract\": \"Cofilin/ADF proteins play key roles in the dynamics of actin, one of the most abundant and highly conserved eukaryotic proteins. We used cryoelectron microscopy to generate a 9-Å resolution three-dimensional reconstruction of cofilin-decorated actin filaments, the highest resolution achieved for a complex of F-actin with an actin-binding protein. We show that the cofilin-induced change in the filament twist is due to a unique conformation of the actin molecule unrelated to any previously observed state. The changes between the actin protomer in naked F-actin and in the actin-cofilin filament are greater than the conformational changes between G- and F-actin. Our results show the structural plasticity of actin, suggest that other actin-binding proteins may also induce large but different conformational changes, and show that F-actin cannot be described by a single molecular model.\",\n \"corpus_id\": 6304533,\n \"score\": 2\n },\n {\n \"doc_id\": \"22421043\",\n \"title\": \"ADF/cofilin regulates actomyosin assembly through competitive inhibition of myosin II binding to F-actin.\",\n \"abstract\": \"The contractile actin cortex is important for diverse fundamental cell processes, but little is known about how the assembly of F-actin and myosin II motors is regulated. We report that depletion of actin depolymerizing factor (ADF)/cofilin proteins in human cells causes increased contractile cortical actomyosin assembly. Remarkably, our data reveal that the major cellular defects resulting from ADF/cofilin depletion, including cortical F-actin accumulation, were largely due to excessive myosin II activity. We identify that ADF/cofilins from unicellular organisms to humans share a conserved activity to inhibit myosin II binding to F-actin, indicating a mechanistic rationale for our cellular results. Our study establishes an essential requirement for ADF/cofilin proteins in the control of normal cortical contractility and in processes such as mitotic karyokinesis. We propose that ADF/cofilin proteins are necessary for controlling actomyosin assembly and intracellular contractile force generation, a function of equal physiological importance to their established roles in mediating F-actin turnover.\",\n \"corpus_id\": 34015387,\n \"score\": 2\n },\n {\n \"doc_id\": \"22623727\",\n \"title\": \"Cofilin nuclear-cytoplasmic shuttling affects cofilin-actin rod formation during stress.\",\n \"abstract\": \"Cofilin protein is involved in regulating the actin cytoskeleton during typical steady state conditions, as well as during cell stress conditions where cofilin saturates F-actin, forming cofilin-actin rods. Cofilin can enter the nucleus through an active nuclear localization signal (NLS), accumulating in nuclear actin rods during stress. Here, we characterize the active nuclear export of cofilin through a leptomycin-B-sensitive, CRM1-dependent, nuclear export signal (NES). We also redefine the NLS of cofilin as a bipartite NLS, with an additional basic epitope required for nuclear localization. Using fluorescence lifetime imaging microscopy (FLIM) and Förster resonant energy transfer (FRET) between cofilin moieties and actin, as well as automated image analysis in live cells, we have defined subtle mutations in the cofilin NLS that allow cofilin to bind actin in vivo and affect cofilin dynamics during stress. We further define the requirement of cofilin-actin rod formation in a system of cell stress by temporal live-cell imaging. We propose that cofilin nuclear shuttling is critical for the cofilin-actin rod stress response with cofilin dynamically communicating between the nucleus and cytoplasm during cell stress.\",\n \"corpus_id\": 13093547,\n \"score\": 2\n },\n {\n \"doc_id\": \"22728040\",\n \"title\": \"Cytochalasin D acts as an inhibitor of the actin-cofilin interaction.\",\n \"abstract\": \"Cofilin, a key regulator of actin filament dynamics, binds to G- and F-actin and promotes actin filament turnover by stimulating depolymerization and severance of actin filaments. In this study, cytochalasin D (CytoD), a widely used inhibitor of actin dynamics, was found to act as an inhibitor of the G-actin-cofilin interaction by binding to G-actin. CytoD also inhibited the binding of cofilin to F-actin and decreased the rate of both actin polymerization and depolymerization in living cells. CytoD altered cellular F-actin organization but did not induce net actin polymerization or depolymerization. These results suggest that CytoD inhibits actin filament dynamics in cells via multiple mechanisms, including the well-known barbed-end capping mechanism and as shown in this study, the inhibition of G- and F-actin binding to cofilin.\",\n \"corpus_id\": 205922782,\n \"score\": 2\n },\n {\n \"doc_id\": \"23153585\",\n \"title\": \"Signaling mechanisms and functional roles of cofilin phosphorylation and dephosphorylation.\",\n \"abstract\": \"Cofilin and actin-depolymerizing factor (ADF) are actin-binding proteins that play an essential role in regulating actin filament dynamics and reorganization by stimulating the severance and depolymerization of actin filaments. Cofilin/ADF are inactivated by phosphorylation at the serine residue at position 3 by LIM-kinases (LIMKs) and testicular protein kinases (TESKs) and are reactivated by dephosphorylation by the slingshot (SSH) family of protein phosphatases and chronophin. This review describes recent advances in our understanding of the signaling mechanisms regulating LIMKs and SSHs and the functional roles of cofilin phospho-regulation in cell migration, tumor invasion, mitosis, neuronal development, and synaptic plasticity. Accumulating evidence demonstrates that the phospho-regulation of cofilin/ADF is a key convergence point of cell signaling networks that link extracellular stimuli to actin cytoskeletal dynamics and that spatiotemporal control of cofilin/ADF activity by LIMKs and SSHs plays a crucial role in a diverse array of cellular and physiological processes. Perturbations in the normal control of cofilin/ADF activity underlie many pathological conditions, including cancer metastasis and neurological and cardiovascular disorders.\",\n \"corpus_id\": 32529565,\n \"score\": 2\n },\n {\n \"doc_id\": \"23665019\",\n \"title\": \"Cooperative and non-cooperative conformational changes of F-actin induced by cofilin.\",\n \"abstract\": \"Cofilin is an actin-binding protein that promotes F-actin depolymerization. It is well-known that cofilin-coated F-actin is more twisted than naked F-actin, and that the protomer is more tilted. However, the means by which the local changes induced by the binding of individual cofilin proteins proceed to the global conformational changes of the whole F-actin molecule remain unknown. Here we investigated the cofilin-induced changes in several parts of F-actin, through site-directed spin-label electron paramagnetic resonance spectroscopy analyses of recombinant actins containing single reactive cysteines. We found that the global, cooperative conformational changes induced by cofilin-binding, which were detected by the spin-label attached to the Cys374 residue, occurred without the detachment of the D-loop in subdomain 2 from the neighboring protomer. The two processes of local and global changes do not necessarily proceed in sequence.\",\n \"corpus_id\": 2948477,\n \"score\": 2\n },\n {\n \"doc_id\": \"23727096\",\n \"title\": \"Actin filament severing by cofilin dismantles actin patches and produces mother filaments for new patches.\",\n \"abstract\": \"BACKGROUND: Yeast cells depend on Arp2/3 complex to assemble actin filaments at sites of endocytosis, but the source of the initial filaments required to activate Arp2/3 complex is not known. RESULTS: We tested the proposal that cofilin severs actin filaments during endocytosis in fission yeast cells using a mutant cofilin defective in severing. We used quantitative fluorescence microscopy to track mGFP-tagged proteins, including early endocytic adaptor proteins, activators of Arp2/3 complex, and actin filaments. Consistent with the hypothesis, actin patches disassembled far more slowly in cells depending on severing-deficient cofilin than in wild-type cells. Even more interesting, actin patches assembled slowly in these cofilin mutant cells. Adaptor proteins End4p and Pan1p accumulated and persisted at endocytic sites more than ten times longer than in wild-type cells, followed by slow but persistent recruitment of activators of Arp2/3 complex, including WASP and myosin-I. Mutations revealed that actin filament binding sites on adaptor proteins Pan1p and End4p contribute to initiating actin polymerization in actin patches. CONCLUSIONS: We propose a \\\"sever, diffuse, and trigger\\\" model for the nucleation of actin filaments at sites of endocytosis, whereby cofilin generates actin filament fragments that diffuse through the cytoplasm, bind adaptor proteins at nascent sites of endocytosis, and serve as mother filaments to initiate the autocatalytic assembly of the branched actin filament network of each new patch. This hypothesis explains the source of the \\\"mother filaments\\\" that are absolutely required for Arp2/3 complex to nucleate actin polymerization.\",\n \"corpus_id\": -1,\n \"score\": 2\n },\n {\n \"doc_id\": \"23845993\",\n \"title\": \"The effect of ADF/cofilin and profilin on the dynamics of monomeric actin.\",\n \"abstract\": \"The main goal of the work was to uncover the dynamical changes in actin induced by the binding of cofilin and profilin. The change in the structure and flexibility of the small domain and its function in the thermodynamic stability of the actin monomer were examined with fluorescence spectroscopy and differential scanning calorimetry (DSC). The structure around the C-terminus of actin is slightly affected by the presence of cofilin and profilin. Temperature dependent fluorescence resonance energy transfer measurements indicated that both actin binding proteins decreased the flexibility of the protein matrix between the subdomains 1 and 2. Time resolved anisotropy decay measurements supported the idea that cofilin and profilin changed similarly the dynamics around the fluorescently labeled Cys-374 and Lys-61 residues in subdomains 1 and 2, respectively. DSC experiments indicated that the thermodynamic stability of actin increased by cofilin and decreased in the presence of profilin. Based on the information obtained it is possible to conclude that while the small domain of actin acts uniformly in the presence of cofilin and profilin the overall stability of actin changes differently in the presence of the studied actin binding proteins. The results support the idea that the small domain of actin behaves as a rigid unit during the opening and closing of the nucleotide binding pocket in the presence of profilin and cofilin as well. The structural arrangement of the nucleotide binding cleft mainly influences the global stability of actin while the dynamics of the different segments can change autonomously.\",\n \"corpus_id\": 38459615,\n \"score\": 2\n },\n {\n \"doc_id\": \"24943913\",\n \"title\": \"Coordination of the filament stabilizing versus destabilizing activities of cofilin through its secondary binding site on actin.\",\n \"abstract\": \"Cofilin is a ubiquitous modulator of actin cytoskeleton dynamics that can both stabilize and destabilize actin filaments depending on its concentration and/or the presence of regulatory co-factors. Three charge-reversal mutants of yeast cofilin, located in cofilin's filament-specific secondary binding site, were characterized in order to understand why disruption of this site leads to enhanced filament disassembly. Crystal structures of the mutants showed that the mutations specifically affect the secondary actin-binding interface, leaving the primary binding site unaltered. The mutant cofilins show enhanced activity compared to wild-type cofilin in severing and disassembling actin filaments. Electron microscopy and image analysis revealed long actin filaments in the presence of wild-type cofilin, while the mutants induced many short filaments, consistent with enhanced severing. Real-time fluorescence microscopy of labeled actin filaments confirmed that the mutants, unlike wild-type cofilin, were functioning as constitutively active severing proteins. In cells, the mutant cofilins delayed endocytosis, which depends on rapid actin turnover. We conclude that mutating cofilin's secondary actin-binding site increases cofilin's ability to sever and de-polymerize actin filaments. We hypothesize that activators of cofilin severing, like Aip1p, may act by disrupting the interface between cofilin's secondary actin-binding site and the actin filament.\",\n \"corpus_id\": 5427074,\n \"score\": 2\n },\n {\n \"doc_id\": \"26028436\",\n \"title\": \"Arp2/3 complex and cofilin modulate binding of tropomyosin to branched actin networks.\",\n \"abstract\": \"Tropomyosins are coiled-coil proteins that bind actin filaments and regulate multiple cytoskeletal functions, including actin network dynamics near the leading edge of motile cells. Previous work demonstrated that tropomyosins inhibit actin nucleation by the Arp2/3 complex and prevent filament disassembly by cofilin. We find that the Arp2/3 complex and cofilin, in turn, regulate the binding of tropomyosin to actin filaments. Using fluorescence microscopy, we show that tropomyosin (non-muscle Drosophila Tm1A) polymerizes along actin filaments, starting from \\\"nuclei\\\" that appear preferentially on ADP-bound regions of the filament, near the pointed end. Tropomyosin fails to bind dendritic actin networks created in vitro by the Arp2/3 complex, in part because the Arp2/3 complex blocks pointed ends. Cofilin promotes phosphate dissociation and severs filaments, generating new pointed ends and rendering Arp2/3-generated networks competent to bind tropomyosin. Tropomyosin's attraction to pointed ends reflects a strong preference for conformations localized to that region of the filament and reveals a basic molecular mechanism by which lamellipodial actin networks are insulated from the effects of tropomyosin.\",\n \"corpus_id\": 15675241,\n \"score\": 2\n },\n {\n \"doc_id\": \"26747606\",\n \"title\": \"Actin-interacting Protein 1 Promotes Disassembly of Actin-depolymerizing Factor/Cofilin-bound Actin Filaments in a pH-dependent Manner.\",\n \"abstract\": \"Actin-interacting protein 1 (AIP1) is a conserved WD repeat protein that promotes disassembly of actin filaments when actin-depolymerizing factor (ADF)/cofilin is present. Although AIP1 is known to be essential for a number of cellular events involving dynamic rearrangement of the actin cytoskeleton, the regulatory mechanism of the function of AIP1 is unknown. In this study, we report that two AIP1 isoforms from the nematode Caenorhabditis elegans, known as UNC-78 and AIPL-1, are pH-sensitive in enhancement of actin filament disassembly. Both AIP1 isoforms only weakly enhance disassembly of ADF/cofilin-bound actin filaments at an acidic pH but show stronger disassembly activity at neutral and basic pH values. However, a severing-defective mutant of UNC-78 shows pH-insensitive binding to ADF/cofilin-decorated actin filaments, suggesting that the process of filament severing or disassembly, but not filament binding, is pH-dependent. His-60 of AIP1 is located near the predicted binding surface for the ADF/cofilin-actin complex, and an H60K mutation of AIP1 partially impairs its pH sensitivity, suggesting that His-60 is involved in the pH sensor for AIP1. These biochemical results suggest that pH-dependent changes in AIP1 activity might be a novel regulatory mechanism of actin filament dynamics.\",\n \"corpus_id\": 3033515,\n \"score\": 2\n },\n {\n \"doc_id\": \"26842224\",\n \"title\": \"Cofilin-induced cooperative conformational changes of actin subunits revealed using cofilin-actin fusion protein.\",\n \"abstract\": \"To investigate cooperative conformational changes of actin filaments induced by cofilin binding, we engineered a fusion protein made of Dictyostelium cofilin and actin. The filaments of the fusion protein were functionally similar to actin filaments bound with cofilin in that they did not bind rhodamine-phalloidin, had quenched fluorescence of pyrene attached to Cys374 and showed enhanced susceptibility of the DNase loop to cleavage by subtilisin. Quantitative analyses of copolymers made of different ratios of the fusion protein and control actin further demonstrated that the fusion protein affects the structure of multiple neighboring actin subunits in copolymers. Based on these and other recent related studies, we propose a mechanism by which conformational changes induced by cofilin binding is propagated unidirectionally to the pointed ends of the filaments, and cofilin clusters grow unidirectionally to the pointed ends following this path. Interestingly, the fusion protein was unable to copolymerize with control actin at pH 6.5 and low ionic strength, suggesting that the structural difference between the actin moiety in the fusion protein and control actin is pH-sensitive.\",\n \"corpus_id\": 10386282,\n \"score\": 2\n },\n {\n \"doc_id\": \"28303963\",\n \"title\": \"Structural Analysis of Human Cofilin 2/Filamentous Actin Assemblies: Atomic-Resolution Insights from Magic Angle Spinning NMR Spectroscopy.\",\n \"abstract\": \"Cellular actin dynamics is an essential element of numerous cellular processes, such as cell motility, cell division and endocytosis. Actin's involvement in these processes is mediated by many actin-binding proteins, among which the cofilin family plays unique and essential role in accelerating actin treadmilling in filamentous actin (F-actin) in a nucleotide-state dependent manner. Cofilin preferentially interacts with older filaments by recognizing time-dependent changes in F-actin structure associated with the hydrolysis of ATP and release of inorganic phosphate (Pi) from the nucleotide cleft of actin. The structure of cofilin on F-actin and the details of the intermolecular interface remain poorly understood at atomic resolution. Here we report atomic-level characterization by magic angle spinning (MAS) NMR of the muscle isoform of human cofilin 2 (CFL2) bound to F-actin. We demonstrate that resonance assignments for the majority of atoms are readily accomplished and we derive the intermolecular interface between CFL2 and F-actin. The MAS NMR approach reported here establishes the foundation for atomic-resolution characterization of a broad range of actin-associated proteins bound to F-actin.\",\n \"corpus_id\": 8859310,\n \"score\": 2\n },\n {\n \"doc_id\": \"28513458\",\n \"title\": \"Cofilin - a protein controlling dynamics of actin filaments.\",\n \"abstract\": \"Cofilins are evolutionary conserved proteins present in all Eukaryotic cells. Their primary function is dynamic reorganization of actin cytoskeleton. Two cofilin isoforms are known: cofilin 1, present in all studied non-muscle cells and in embryonic muscle cells, and cofilin 2, which dominates in mature skeletal and cardiac muscles. Polypeptide chains of both isoforms fold into a structure homological to a conservative ADF (actin depolymerizing factor) domain, which is characteristic of actin depolymerizing factor. In cofilin molecule two actin-binding sites were found. One site binds monomeric and filamentous actin, the second one interacts only with the filament. Binding of cofilin to actin filament causes a change in the orientation of subunits, which results in filament severing. This increases number of ends which can either elongate or shorten the filament, depending on the conditions. Cofilin interactions with monomeric actin decreases availability of polymerization-competent actin subunits. Cofilin activity is controlled by phosphorylation, binding membrane phospholipids, local pH and oxidative stress. Under conditions of oxidative stress oxidation of cysteine residues leads to formation of dimers, which are able to cross-link actin filaments. Stable actin-cofilin rods save cellular ATP, which is not used during active polymerization process. This facilitates faster cell recovery from the stress. The final cellular reaction on the environmental stimuli is a resultant of cofilin activity and activities of other actin-binding proteins, which function either synergistically or antagonistically. Due to the central role in the regulation of actin filaments dynamics, cofilin is involved in development of cancer, neurodegenerative diseases, congenital myopathies and cardiomyopathies.\",\n \"corpus_id\": 43726288,\n \"score\": 2\n },\n {\n \"doc_id\": \"28625781\",\n \"title\": \"ADF/Cofilin Accelerates Actin Dynamics by Severing Filaments and Promoting Their Depolymerization at Both Ends.\",\n \"abstract\": \"Actin-depolymerizing factor (ADF)/cofilins contribute to cytoskeletal dynamics by promoting rapid actin filament disassembly. In the classical view, ADF/cofilin sever filaments, and capping proteins block filament barbed ends whereas pointed ends depolymerize, at a rate that is still debated. Here, by monitoring the activity of the three mammalian ADF/cofilin isoforms on individual skeletal muscle and cytoplasmic actin filaments, we directly quantify the reactions underpinning filament severing and depolymerization from both ends. We find that, in the absence of monomeric actin, soluble ADF/cofilin can associate with bare filament barbed ends to accelerate their depolymerization. Compared to bare filaments, ADF/cofilin-saturated filaments depolymerize faster from their pointed ends and slower from their barbed ends, resulting in similar depolymerization rates at both ends. This effect is isoform specific because depolymerization is faster for ADF- than for cofilin-saturated filaments. We also show that, unexpectedly, ADF/cofilin-saturated filaments qualitatively differ from bare filaments: their barbed ends are very difficult to cap or elongate, and consequently undergo depolymerization even in the presence of capping protein and actin monomers. Such depolymerizing ADF/cofilin-decorated barbed ends are produced during 17% of severing events. They are also the dominant fate of filament barbed ends in the presence of capping protein, because capping allows growing ADF/cofilin domains to reach the barbed ends, thereby promoting their uncapping and subsequent depolymerization. Our experiments thus reveal how ADF/cofilin, together with capping protein, control the dynamics of actin filament barbed and pointed ends. Strikingly, our results propose that significant barbed-end depolymerization may take place in cells.\",\n \"corpus_id\": 11585075,\n \"score\": 2\n },\n {\n \"doc_id\": \"28939776\",\n \"title\": \"Phosphomimetic S3D cofilin binds but only weakly severs actin filaments.\",\n \"abstract\": \"Many biological processes, including cell division, growth, and motility, rely on rapid remodeling of the actin cytoskeleton and on actin filament severing by the regulatory protein cofilin. Phosphorylation of vertebrate cofilin at Ser-3 regulates both actin binding and severing. Substitution of serine with aspartate at position 3 (S3D) is widely used to mimic cofilin phosphorylation in cells and in vitro The S3D substitution weakens cofilin binding to filaments, and it is presumed that subsequent reduction in cofilin occupancy inhibits filament severing, but this hypothesis has remained untested. Here, using time-resolved phosphorescence anisotropy, electron cryomicroscopy, and all-atom molecular dynamics simulations, we show that S3D cofilin indeed binds filaments with lower affinity, but also with a higher cooperativity than wild-type cofilin, and severs actin weakly across a broad range of occupancies. We found that three factors contribute to the severing deficiency of S3D cofilin. First, the high cooperativity of S3D cofilin generates fewer boundaries between bare and decorated actin segments where severing occurs preferentially. Second, S3D cofilin only weakly alters filament bending and twisting dynamics and therefore does not introduce the mechanical discontinuities required for efficient filament severing at boundaries. Third, Ser-3 modification (i.e. substitution with Asp or phosphorylation) \\\"undocks\\\" and repositions the cofilin N terminus away from the filament axis, which compromises S3D cofilin's ability to weaken longitudinal filament subunit interactions. Collectively, our results demonstrate that, in addition to inhibiting actin binding, Ser-3 modification favors formation of a cofilin-binding mode that is unable to sufficiently alter filament mechanical properties and promote severing.\",\n \"corpus_id\": 4235107,\n \"score\": 2\n },\n {\n \"doc_id\": \"29056508\",\n \"title\": \"Functions of actin-interacting protein 1 (AIP1)/WD repeat protein 1 (WDR1) in actin filament dynamics and cytoskeletal regulation.\",\n \"abstract\": \"Actin-depolymerizing factor (ADF)/cofilin and actin-interacting protein 1 (AIP1), also known as WD-repeat protein 1 (WDR1), are conserved among eukaryotes and play critical roles in dynamic reorganization of the actin cytoskeleton. AIP1 preferentially promotes disassembly of ADF/cofilin-decorated actin filaments but exhibits minimal effects on bare actin filaments. Therefore, AIP1 has been often considered to be an ancillary co-factor of ADF/cofilin that merely boosts ADF/cofilin activity level. However, genetic and cell biological studies show that AIP1 deficiency often causes lethality or severe abnormalities in multiple tissues and organs including muscle, epithelia, and blood, suggesting that AIP1 is a major regulator of many biological processes that depend on actin dynamics. This review summarizes recent progress in studies on the biochemical mechanism of actin filament severing by AIP1 and in vivo functions of AIP1 in model organisms and human diseases.\",\n \"corpus_id\": 4962345,\n \"score\": 2\n },\n {\n \"doc_id\": \"29749375\",\n \"title\": \"Structural basis for cofilin binding and actin filament disassembly.\",\n \"abstract\": \"Actin depolymerizing factor (ADF) and cofilin accelerate actin dynamics by severing and disassembling actin filaments. Here, we present the 3.8 Å resolution cryo-EM structure of cofilactin (cofilin-decorated actin filament). The actin subunit structure of cofilactin (C-form) is distinct from those of F-actin (F-form) and monomeric actin (G-form). During the transition between these three conformations, the inner domain of actin (subdomains 3 and 4) and the majority of subdomain 1 move as two separate rigid bodies. The cofilin-actin interface consists of three distinct parts. Based on the rigid body movements of actin and the three cofilin-actin interfaces, we propose models for the cooperative binding of cofilin to actin, preferential binding of cofilin to ADP-bound actin filaments and cofilin-mediated severing of actin filaments.\",\n \"corpus_id\": 13671035,\n \"score\": 2\n },\n {\n \"doc_id\": \"18037437\",\n \"title\": \"Actin hydrophobic loop 262-274 and filament nucleation and elongation.\",\n \"abstract\": \"The importance of actin hydrophobic loop 262-274 dynamics to actin polymerization and filament stability has been shown recently with the use of the yeast mutant actin L180C/L269C/C374A, in which the hydrophobic loop could be locked in a \\\"parked\\\" conformation by a disulfide bond between C180 and C269. Such a cross-linked globular actin monomer does not form filaments, suggesting nucleation and/or elongation inhibition. To determine the role of loop dynamics in filament nucleation and/or elongation, we studied the polymerization of the cross-linked actin in the presence of cofilin, to assist with actin nucleation, and with phalloidin, to stabilize the elongating filament segments. We demonstrate here that together, but not individually, phalloidin and cofilin co-rescue the polymerization of cross-linked actin. The polymerization was also rescued by filament seeds added together with phalloidin but not with cofilin. Thus, loop immobilization via cross-linking inhibits both filament nucleation and elongation. Nevertheless, the conformational changes needed to catalyze ATP hydrolysis by actin occur in the cross-linked actin. When actin filaments are fully decorated by cofilin, the helical twist of filamentous actin (F-actin) changes by approximately 5 degrees per subunit. Electron microscopic analysis of filaments rescued by cofilin and phalloidin revealed a dense contact between opposite strands in F-actin and a change of twist by approximately 1 degrees per subunit, indicating either partial or disordered attachment of cofilin to F-actin and/or competition between cofilin and phalloidin to alter F-actin symmetry. Our findings show an importance of the hydrophobic loop conformational dynamics in both actin nucleation and elongation and reveal that the inhibition of these two steps in the cross-linked actin can be relieved by appropriate factors.\",\n \"corpus_id\": 29856865,\n \"score\": 1\n },\n {\n \"doc_id\": \"18258262\",\n \"title\": \"Mapping the cofilin binding site on yeast G-actin by chemical cross-linking.\",\n \"abstract\": \"Cofilin is a major cytoskeletal protein that binds to both monomeric actin (G-actin) and polymeric actin (F-actin) and is involved in microfilament dynamics. Although an atomic structure of the G-actin-cofilin complex does not exist, models of the complex have been built using molecular dynamics simulations, structural homology considerations, and synchrotron radiolytic footprinting data. The hydrophobic cleft between actin subdomains 1 and 3 and, alternatively, the cleft between actin subdomains 1 and 2 have been proposed as possible high-affinity cofilin binding sites. In this study, the proposed binding of cofilin to the subdomain 1/subdomain 3 region on G-actin has been probed using site-directed mutagenesis, fluorescence labeling, and chemical cross-linking, with yeast actin mutants containing single reactive cysteines in the actin hydrophobic cleft and with cofilin mutants carrying reactive cysteines in the regions predicted to bind to G-actin. Mass spectrometry analysis of the cross-linked complex revealed that cysteine 345 in subdomain 1 of mutant G-actin was cross-linked to native cysteine 62 on cofilin. A cofilin mutant that carried a cysteine substitution in the alpha 3-helix (residue 95) formed a cross-link with residue 144 in actin subdomain 3. Distance constraints imposed by these cross-links provide experimental evidence for cofilin binding between actin subdomains 1 and 3 and fit a corresponding docking-based structure of the complex. The cross-linking of the N-terminal region of recombinant yeast cofilin to actin residues 346 and 374 with dithio-bis-maleimidoethane (12.4 A) and via disulfide bond formation was also documented. This set of cross-linking data confirms the important role of the N-terminal segment of cofilin in interactions with G-actin.\",\n \"corpus_id\": 20341341,\n \"score\": 1\n },\n {\n \"doc_id\": \"18809681\",\n \"title\": \"Molecular dissection of the mechanisms of substrate recognition and F-actin-mediated activation of cofilin-phosphatase Slingshot-1.\",\n \"abstract\": \"Slingshot-1 (SSH1), a member of a dual-specificity protein phosphatase family, regulates actin dynamics by dephosphorylating and reactivating cofilin, an actin-depolymerizing factor. SSH1 has the SSH family-specific, N-terminal, noncatalytic (SSH-N) domain, consisting of the A and B subdomains. SSH1 is activated by binding to actin filaments. In this study, we examined the mechanisms of SSH1 substrate recognition of phospho-cofilin (P-cofilin) and SSH1 activation by F-actin. We found that P-cofilin binds to a phosphatase-inactive mutant, SSH1(CS), in which the catalytic Cys-393 is replaced by Ser. Using a series of deletion mutants, we provided evidence that both the phosphatase (P) domain and the adjacent B domain are indispensable for P-cofilin binding of SSH1(CS) and cofilin-phosphatase activity of SSH1. In contrast, the A domain is required for the F-actin-mediated activation of SSH1, but not for P-cofilin binding or basal cofilin-phosphatase activity. The P domain alone is sufficient for the phosphatase activity toward p-nitrophenyl phosphate (pNPP), indicating that the SSH-N domain is not essential for the basal phosphatase activity of SSH1. Addition of F-actin increased the cofilin-phosphatase activity of SSH1 more than 1200-fold, but the pNPP-phosphatase activity only 2.2-fold, which suggests that F-actin principally affects the cofilin-specific phosphatase activity of SSH1. When expressed in cultured cells, SSH1, but not its mutant deleted of SSH-N, accumulated in the rear of the lamellipodium. Together, these findings suggest that the conserved SSH-N domain plays critical roles in P-cofilin recognition, F-actin-mediated activation, and subcellular localization of SSH1.\",\n \"corpus_id\": 24504120,\n \"score\": 1\n },\n {\n \"doc_id\": \"19209826\",\n \"title\": \"Tropomyosin and ADF/cofilin as collaborators and competitors.\",\n \"abstract\": \"Dynamics of actin filaments is pivotal to many fundamental cellular processes such as Dcytokinesis, motility, morphology, vesicle and organelle transport, gene transcription and senescence. In vivo kinetics of actin filament dynamics is far from the equilibrium in vitro and these profound differences are attributed to large number of regulatory proteins. In particular, proteins of the ADF/cofilin family greatly increase actin filament dynamics by severing filaments and enhancing depolymerization of ADP-actin monomers from their pointed ends. Cofilin binds cooperatively to a minor conformer of F-actin in which the subunits are slightly under rotated along the filament helical axis. At high stoichiometry of cofilin to actin subunits, cofilin actually stabilizes actin filaments. Many isoforms oftropomyosin appear to compete with ADF/cofilin proteins for binding to actin filaments. Tropomyosin isoforms studied to date prefer binding to the \\\"untwisted\\\" conformer of F-actin and through their protection and stabilization of F-actin, recruit myosin II and assemble different actin superstructures from the cofilin-actin filaments. However, some tropomyosin isoforms may synergize with ADF/cofilin to enhance filament dynamics, suggesting that the different isoforms of tropomyosins, many of which show developmental or tissue specific expression profiles, play major roles in the assembly and turnover of actin superstructures. Different actin superstructures can overlap both spatially and temporally within a cell, but can be differentiated from each other based upon their kinetic and kinematic properties. Furthermore, local regulation of ADF/cofilin activity through signal transduction pathways could be one mechanism to alter the dynamic balance in F-actin-binding of certain tropomyosin isoforms in subcellular domains.\",\n \"corpus_id\": 44439879,\n \"score\": 1\n },\n {\n \"doc_id\": \"19459188\",\n \"title\": \"Actin-ADF/cofilin rod formation in Caenorhabditis elegans muscle requires a putative F-actin binding site of ADF/cofilin at the C-terminus.\",\n \"abstract\": \"Under a number of stress or pathological conditions, actin and actin depolymerizing factor (ADF)/cofilin form rod-like structures that contain abnormal bundles of actin filaments that are heavily decorated with ADF/cofilin. However, the mechanism of actin rod formation and the physiological role of actin rods are not clearly understood. Here, we report that overexpression of green fluorescent protein-fused UNC-60B, a muscle-specific ADF/cofilin isoform, in Caenorhabditis elegans body wall muscle induces formation of rod-like structures. The rods contained GFP-UNC-60B, actin-interacting protein 1 (AIP1), and actin, but not other major actin-associated proteins, thus resembling actin-ADF/cofilin rods found in other organisms. However, depletion or overexpression of AIP1 did not affect formation of the actin-GFP-UNC-60B rods, suggesting that AIP1 does not play a significant role in the rod assembly. Truncation of the C-terminal tail, a putative F-actin binding site, of UNC-60B abolished induction of the rod formation, strongly suggesting that stable association of UNC-60B with F-actin, which is mediated by its C-terminus, is required for inducing actin-ADF/cofilin rods. This study suggests that C. elegans can be a new model to study functions of actin-ADF/cofilin rods.\",\n \"corpus_id\": 998820,\n \"score\": 1\n },\n {\n \"doc_id\": \"20362448\",\n \"title\": \"GMF is a cofilin homolog that binds Arp2/3 complex to stimulate filament debranching and inhibit actin nucleation.\",\n \"abstract\": \"Cell locomotion and endocytosis are powered by the rapid polymerization and turnover of branched actin filament networks nucleated by Arp2/3 complex. Although a large number of cellular factors have been identified that stimulate Arp2/3 complex-mediated actin nucleation, only a small number of studies so far have addressed which factors promote actin network debranching. Here, we investigated the function of a conserved homolog of ADF/cofilin, glia maturation factor (GMF). We found that S. cerevisiae GMF (also called Aim7) localizes in vivo to cortical actin patches and displays synthetic genetic interactions with ADF/cofilin. However, GMF lacks detectable actin binding or severing activity and instead binds tightly to Arp2/3 complex. Using in vitro evanescent wave microscopy, we demonstrated that GMF potently stimulates debranching of actin filaments produced by Arp2/3 complex. Further, GMF inhibits nucleation of new daughter filaments. Together, these data suggest that GMF binds Arp2/3 complex to both \\\"prune\\\" daughter filaments at the branch points and inhibit new actin assembly. These activities and its genetic interaction with ADF/cofilin support a role for GMF in promoting the remodeling and/or disassembly of branched networks. Therefore, ADF/cofilin and GMF, members of the same superfamily, appear to have evolved to interact with actin and actin-related proteins, respectively, and to make mechanistically distinct contributions to the remodeling of cortical actin structures.\",\n \"corpus_id\": 11199973,\n \"score\": 1\n },\n {\n \"doc_id\": \"20471369\",\n \"title\": \"Screening of novel dominant negative mutant actins using glycine targeted scanning identifies G146V actin that cooperatively inhibits cofilin binding.\",\n \"abstract\": \"A number of studies suggested that the structure of actin filaments changes by interaction with actin-binding proteins such as cofilin and myosin, and that the conformational changes of the actin subunits within a filament are cooperative. To understand the functions of these cooperative conformational changes induced by actin-binding proteins, we sought to obtain dominant negative mutant actins impaired in cooperative conformational changes. A series of mutant actin genes in which glycine residues in actin were systematically substituted by valine residues were constructed, and were expressed individually in yeast cells that carry a wild-type endogenous actin gene. Six dominant negative actin mutations were identified on the basis of growth inhibition. Among them, G146V mutation was chosen for further biochemical analysis because the Gly146 residue is located at the strategic hinge position connecting the large and small domains of an actin molecule. We found that G146V actin filaments hardly bind cofilin, consistent with a previous suggestion that cofilin binding causes conformational changes of actin around Gly146 (Galkin et al. [3]). Notably, copolymer that consists of 1:10 mixture of the mutant and wild-type actin molecules showed significantly reduced affinity for cofilin, suggesting that G146V mutant actin affects the conformation of neighboring wild-type actin within a filament, and inhibits cofilin binding.\",\n \"corpus_id\": 6602995,\n \"score\": 1\n },\n {\n \"doc_id\": \"20483342\",\n \"title\": \"ADF/cofilin binds phosphoinositides in a multivalent manner to act as a PIP(2)-density sensor.\",\n \"abstract\": \"Actin-depolymerizing-factor (ADF)/cofilins have emerged as key regulators of cytoskeletal dynamics in cell motility, morphogenesis, endocytosis, and cytokinesis. The activities of ADF/cofilins are regulated by membrane phospholipid PI(4,5)P(2) in vitro and in cells, but the mechanism of the ADF/cofilin-PI(4,5)P(2) interaction has remained controversial. Recent studies suggested that ADF/cofilins interact with PI(4,5)P(2) through a specific binding pocket, and that this interaction is dependent on pH. Here, we combined systematic mutagenesis with biochemical and spectroscopic methods to elucidate the phosphoinositide-binding mechanism of ADF/cofilins. Our analysis revealed that cofilin does not harbor a specific PI(4,5)P(2)-binding pocket, but instead interacts with PI(4,5)P(2) through a large, positively charged surface of the molecule. Cofilin interacts simultaneously with multiple PI(4,5)P(2) headgroups in a cooperative manner. Consequently, interactions of cofilin with membranes and actin exhibit sharp sensitivity to PI(4,5)P(2) density. Finally, we show that cofilin binding to PI(4,5)P(2) is not sensitive to changes in the pH at physiological salt concentration, although the PI(4,5)P(2)-clustering activity of cofilin is moderately inhibited at elevated pH. Collectively, our data demonstrate that ADF/cofilins bind PI(4,5)P(2) headgroups through a multivalent, cooperative mechanism, and suggest that the actin filament disassembly activity of ADF/cofilin can be accurately regulated by small changes in the PI(4,5)P(2) density at cellular membranes.\",\n \"corpus_id\": 206294935,\n \"score\": 1\n },\n {\n \"doc_id\": \"20517925\",\n \"title\": \"GMF is an evolutionarily developed Adf/cofilin-super family protein involved in the Arp2/3 complex-mediated organization of the actin cytoskeleton.\",\n \"abstract\": \"Actin-depolymerizing factor (ADF)/cofilin is widely expressed in eukaryotes and plays a central role in reorganizing the actin cytoskeleton by disassembling actin filaments. The ADF-homologous domain (ADF-H) is conserved in several other actin-modulating proteins such as twinfilin, Abp1/drebrin, and coactosin. Although these proteins interact with actin via ADF-H, their effects on actin are not identical to each other. Here, we report a novel ADF/cofilin-super family protein, Gmf1 (Glia maturation factor-like protein 1), from the fission yeast Schizosaccharomyces pombe. Gmf1 is a component of actin patches, which are located on the cell cortex and required for endocytosis, and may be involved in the control of the disassembly of actin patches since its overexpression diminishes them. We provide evidence that Gmf1 binds weakly if at all to actin, but it associates with actin-related protein (Arp) 2/3 complex and suppresses its functions such as the promotion of actin polymerization and branching filaments. Importantly, Arp2/3 complex-suppressing activity is conserved among GMF-family proteins from other organisms. Given the functional plasticity of ADF-H, GMF-family proteins possibly have changed their target from conventional actin to Arps through molecular evolution.\",\n \"corpus_id\": 10026043,\n \"score\": 1\n },\n {\n \"doc_id\": \"21613547\",\n \"title\": \"Turnover of branched actin filament networks by stochastic fragmentation with ADF/cofilin.\",\n \"abstract\": \"Cell motility depends on the rapid assembly, aging, severing, and disassembly of actin filaments in spatially distinct zones. How a set of actin regulatory proteins that sustains actin-based force generation during motility work together in space and time remains poorly understood. We present our study of the distribution and dynamics of Arp2/3 complex, capping protein (CP), and actin-depolymerizing factor (ADF)/cofilin in actin \\\"comet tails,\\\" using a minimal reconstituted system with nucleation-promoting factor (NPF)-coated beads. The Arp2/3 complex concentrates at nucleation sites near the beads as well as in the first actin shell. CP colocalizes with actin and is homogeneously distributed throughout the comet tail; it serves to constrain the spatial distribution of ATP/ADP-P(i) filament zones to areas near the bead. The association of ADF/cofilin with the actin network is therefore governed by kinetics of actin assembly, actin nucleotide state, and CP binding. A kinetic simulation accurately validates these observations. Following its binding to the actin networks, ADF/cofilin is able to break up the dense actin filament array of a comet tail. Stochastic severing by ADF/cofilin loosens the tight entanglement of actin filaments inside the comet tail and facilitates turnover through the macroscopic release of large portions of the aged actin network.\",\n \"corpus_id\": 17434729,\n \"score\": 1\n },\n {\n \"doc_id\": \"22010035\",\n \"title\": \"Arabidopsis actin depolymerizing factor4 modulates the stochastic dynamic behavior of actin filaments in the cortical array of epidermal cells.\",\n \"abstract\": \"Actin filament arrays are constantly remodeled as the needs of cells change as well as during responses to biotic and abiotic stimuli. Previous studies demonstrate that many single actin filaments in the cortical array of living Arabidopsis thaliana epidermal cells undergo stochastic dynamics, a combination of rapid growth balanced by disassembly from prolific severing activity. Filament turnover and dynamics are well understood from in vitro biochemical analyses and simple reconstituted systems. However, the identification in living cells of the molecular players involved in controlling actin dynamics awaits the use of model systems, especially ones where the power of genetics can be combined with imaging of individual actin filaments at high spatial and temporal resolution. Here, we test the hypothesis that actin depolymerizing factor (ADF)/cofilin contributes to stochastic filament severing and facilitates actin turnover. A knockout mutant for Arabidopsis ADF4 has longer hypocotyls and epidermal cells when compared with wild-type seedlings. This correlates with a change in actin filament architecture; cytoskeletal arrays in adf4 cells are significantly more bundled and less dense than in wild-type cells. Several parameters of single actin filament turnover are also altered. Notably, adf4 mutant cells have a 2.5-fold reduced severing frequency as well as significantly increased actin filament lengths and lifetimes. Thus, we provide evidence that ADF4 contributes to the stochastic dynamic turnover of actin filaments in plant cells.\",\n \"corpus_id\": 2033160,\n \"score\": 1\n },\n {\n \"doc_id\": \"22123860\",\n \"title\": \"Actin filaments function as a tension sensor by tension-dependent binding of cofilin to the filament.\",\n \"abstract\": \"Intracellular and extracellular mechanical forces affect the structure and dynamics of the actin cytoskeleton. However, the underlying molecular and biophysical mechanisms, including how mechanical forces are sensed, are largely unknown. Actin-depolymerizing factor/cofilin proteins are actin-modulating proteins that are ubiquitously distributed in eukaryotes, and they are the most likely candidate as proteins to drive stress fiber disassembly in response to changes in tension in the fiber. In this study, we propose a novel hypothesis that tension in an actin filament prevents the filament from being severed by cofilin. To test this, we placed single actin filaments under tension using optical tweezers. When a fiber was tensed, it was severed after the application of cofilin with a significantly larger delay in comparison with control filaments suspended in solution. The binding rate of cofilin to an actin bundle decreased when the bundle was tensed. These results suggest that tension in an actin filament reduces the cofilin binding, resulting in a decrease in its effective severing activity.\",\n \"corpus_id\": 1325745,\n \"score\": 1\n },\n {\n \"doc_id\": \"22492507\",\n \"title\": \"Overexpression of S4D mutant of Leishmania donovani ADF/cofilin impairs flagellum assembly by affecting actin dynamics.\",\n \"abstract\": \"Leishmania, like other eukaryotes, contains large amounts of actin and a number of actin-related and actin binding proteins. Our earlier studies have shown that deletion of the gene corresponding to Leishmania actin-depolymerizing protein (ADF/cofilin) adversely affects flagellum assembly, intracellular trafficking, and cell division. To further analyze this, we have now created ADF/cofilin site-specific point mutants and then examined (i) the actin-depolymerizing, G-actin binding, and actin-bound nucleotide exchange activities of the mutant proteins and (ii) the effect of overexpression of these proteins in wild-type cells. Here we show that S4D mutant protein failed to depolymerize F-actin but weakly bound G-actin and inhibited the exchange of G-actin-bound nucleotide. We further observed that overexpression of this protein impaired flagellum assembly and consequently cell motility by severely impairing the assembly of the paraflagellar rod, without significantly affecting vesicular trafficking or cell growth. Taken together, these results indicate that dynamic actin is essentially required in assembly of the eukaryotic flagellum.\",\n \"corpus_id\": 6416645,\n \"score\": 1\n },\n {\n \"doc_id\": \"22558315\",\n \"title\": \"Immunological responses and actin dynamics in macrophages are controlled by N-cofilin but are independent from ADF.\",\n \"abstract\": \"Dynamic changes in the actin cytoskeleton are essential for immune cell function and a number of immune deficiencies have been linked to mutations, which disturb the actin cytoskeleton. In macrophages and dendritic cells, actin remodelling is critical for motility, phagocytosis and antigen presentation, however the actin binding proteins, which control antigen presentation have been poorly characterized. Here we dissect the specific roles of the family of ADF/cofilin F-actin depolymerizing factors in macrophages and in local immune responses. Macrophage migration, cell polarization and antigen presentation to T-cells require n-cofilin mediated F-actin remodelling. Using a conditional mouse model, we show that n-cofilin also controls MHC class II-dependent antigen presentation. Other cellular processes such as phagocytosis and antigen processing were found to be independent of n-cofilin. Our data identify n-cofilin as a novel regulator of antigen presentation, while ADF on the other hand is dispensable for macrophage motility and antigen presentation.\",\n \"corpus_id\": 14378951,\n \"score\": 1\n },\n {\n \"doc_id\": \"22623720\",\n \"title\": \"CAS-1, a C. elegans cyclase-associated protein, is required for sarcomeric actin assembly in striated muscle.\",\n \"abstract\": \"Assembly of contractile apparatuses in striated muscle requires precisely regulated reorganization of the actin cytoskeletal proteins into sarcomeric organization. Regulation of actin filament dynamics is one of the essential processes of myofibril assembly, but the mechanism of actin regulation in striated muscle is not clearly understood. Actin depolymerizing factor (ADF)/cofilin is a key enhancer of actin filament dynamics in striated muscle in both vertebrates and nematodes. Here, we report that CAS-1, a cyclase-associated protein in Caenorhabditis elegans, promotes ADF/cofilin-dependent actin filament turnover in vitro and is required for sarcomeric actin organization in striated muscle. CAS-1 is predominantly expressed in striated muscle from embryos to adults. In vitro, CAS-1 binds to actin monomers and enhances exchange of actin-bound ATP/ADP even in the presence of UNC-60B, a muscle-specific ADF/cofilin that inhibits the nucleotide exchange. As a result, CAS-1 and UNC-60B cooperatively enhance actin filament turnover. The two proteins also cooperate to shorten actin filaments. A cas-1 mutation is homozygous lethal with defects in sarcomeric actin organization. cas-1-mutant embryos and worms have aggregates of actin in muscle cells, and UNC-60B is mislocalized to the aggregates. These results provide genetic and biochemical evidence that cyclase-associated protein is a critical regulator of sarcomeric actin organization in striated muscle.\",\n \"corpus_id\": 6640149,\n \"score\": 1\n },\n {\n \"doc_id\": \"22637580\",\n \"title\": \"G146V mutation at the hinge region of actin reveals a myosin class-specific requirement of actin conformations for motility.\",\n \"abstract\": \"The G146V mutation in actin is dominant lethal in yeast. G146V actin filaments bind cofilin only minimally, presumably because cofilin binding requires the large and small actin domains to twist with respect to one another around the hinge region containing Gly-146, and the mutation inhibits that twisting motion. A number of studies have suggested that force generation by myosin also requires actin filaments to undergo conformational changes. This prompted us to examine the effects of the G146V mutation on myosin motility. When compared with wild-type actin filaments, G146V filaments showed a 78% slower gliding velocity and a 70% smaller stall force on surfaces coated with skeletal heavy meromyosin. In contrast, the G146V mutation had no effect on either gliding velocity or stall force on myosin V surfaces. Kinetic analyses of actin-myosin binding and ATPase activity indicated that the weaker affinity of actin filaments for myosin heads carrying ADP, as well as reduced actin-activated ATPase activity, are the cause of the diminished motility seen with skeletal myosin. Interestingly, the G146V mutation disrupted cooperative binding of myosin II heads to actin filaments. These data suggest that myosin-induced conformational changes in the actin filaments, presumably around the hinge region, are involved in mediating the motility of skeletal myosin but not myosin V and that the specific structural requirements for the actin subunits, and thus the mechanism of motility, differ among myosin classes.\",\n \"corpus_id\": 2147167,\n \"score\": 1\n },\n {\n \"doc_id\": \"22790341\",\n \"title\": \"Cofilin overexpression affects actin cytoskeleton organization and migration of human colon adenocarcinoma cells.\",\n \"abstract\": \"The dynamic reorganization of actin cytoskeleton is regulated by a large number of actin-binding proteins. Among them, the interaction of ADF/cofilin with monomeric and filamentous actin is very important, since it severs actin filaments. It also positively influences actin treadmilling. The activity of ADF/cofilin is reversibly regulated by phosphorylation and dephosphorylation at Ser-3, with the phosphorylated form (P-cofilin) being inactive. Here, we studied the effects of overexpression of cofilin and two cofilin variants in the human colon adenocarcinoma LS180 cell line. We have generated the LS180 cells expressing three different cofilin variants: WT (wild type), Ser 3 Ala (S3A) (constitutively active) or Ser 3 Asp (S3D) (constitutively inactive cofilin). The cells expressing WT cofilin were characterized by abundant cell spreading and colocalization of cofilin with the submembranous F-actin. Similar effects were observed in cells expressing S3A cofilin. In contrast, LS180 cells expressing S3D cofilin remained longitudinal in morphology and cofilin was equally distributed within the cell body. Furthermore, the migration ability of LS180 cells expressing different cofilin mutants was analyzed. In comparison to control cells, we have noticed a significant, approximately fourfold increase in the migration factor value of cells overexpressing WT type cofilin. The overexpression of S3D cofilin resulted in an almost complete inhibition of cell motility. The estimation of actin pool in the cytosol of LS180 cells expressing S3A cofilin has shown a significantly lower level of total actin in reference to control cells. The opposite effect was observed in LS180 cells overexpressing S3D cofilin. In summary, the results of our experiments indicate that phosphorylation \\\"status\\\" of cofilin is a factor affecting the actin cytoskeleton organization and migration abilities of colon adenocarcinoma LS180 cells.\",\n \"corpus_id\": 17925954,\n \"score\": 1\n },\n {\n \"doc_id\": \"23212920\",\n \"title\": \"Rapid nucleotide exchange renders Asp-11 mutant actins resistant to depolymerizing activity of cofilin, leading to dominant toxicity in vivo.\",\n \"abstract\": \"Conserved Asp-11 of actin is a part of the nucleotide binding pocket, and its mutation to Gln is dominant lethal in yeast, whereas the mutation to Asn in human α-actin dominantly causes congenital myopathy. To elucidate the molecular mechanism of those dominant negative effects, we prepared Dictyostelium versions of D11N and D11Q mutant actins and characterized them in vitro. D11N and D11Q actins underwent salt-dependent reversible polymerization, although the resultant polymerization products contained small anomalous structures in addition to filaments of normal appearance. Both monomeric and polymeric D11Q actin released bound nucleotides more rapidly than the wild type, and intriguingly, both monomeric and polymeric D11Q actins hardly bound cofilin. The deficiency in cofilin binding can be explained by rapid exchange of bound nucleotide with ATP in solution, because cofilin does not bind ATP-bound actin. Copolymers of D11Q and wild type actins bound cofilin, but cofilin-induced depolymerization of the copolymers was slower than that of wild type filaments, which may presumably be the primary reason why this mutant actin is dominantly toxic in vivo. Purified D11N actin was unstable, which made its quantitative biochemical characterization difficult. However, monomeric D11N actin released nucleotides even faster than D11Q, and we speculate that D11N actin also exerts its toxic effects in vivo through a defective interaction with cofilin. We have recently found that two other dominant negative actin mutants are also defective in cofilin binding, and we propose that the defective cofilin binder is a major class of dominant negative actin mutants.\",\n \"corpus_id\": 22898101,\n \"score\": 1\n },\n {\n \"doc_id\": \"23352932\",\n \"title\": \"Molecular origins of cofilin-linked changes in actin filament mechanics.\",\n \"abstract\": \"The actin regulatory protein cofilin plays a central role in actin assembly dynamics by severing filaments and increasing the concentration of ends from which subunits add and dissociate. Cofilin binding modifies the average structure and mechanical properties of actin filaments, thereby promoting fragmentation of partially decorated filaments at boundaries of bare and cofilin-decorated segments. Despite extensive evidence for cofilin-dependent changes in filament structure and mechanics, it is unclear how the two processes are linked at the molecular level. Here, we use molecular dynamics simulations and coarse-grained analyses to evaluate the molecular origins of the changes in filament compliance due to cofilin binding. Filament subunits with bound cofilin are less flat and maintain a significantly more open nucleotide cleft than bare filament subunits. Decorated filament segments are less twisted, thinner (considering only actin), and less connected than their bare counterparts, which lowers the filament bending persistence length and torsional stiffness. Using coarse-graining as an analysis method reveals that cofilin binding increases the average distance between the adjacent long-axis filament subunit, thereby weakening their interaction. In contrast, a fraction of lateral filament subunit contacts are closer and presumably stronger with cofilin binding. A cofilactin interface contact identified by cryo-electron microscopy is unstable during simulations carried out at 310K, suggesting that this particular interaction may be short lived at ambient temperatures. These results reveal the molecular origins of cofilin-dependent changes in actin filament mechanics that may promote filament severing.\",\n \"corpus_id\": 8991800,\n \"score\": 1\n },\n {\n \"doc_id\": \"23729382\",\n \"title\": \"ADF/cofilin is not essential but is critically important for actin activities during phagocytosis in Tetrahymena thermophila.\",\n \"abstract\": \"ADF/cofilin is a highly conserved actin-modulating protein. Reorganization of the actin cytoskeleton in vivo through severing and depolymerizing of F-actin by this protein is essential for various cellular events, such as endocytosis, phagocytosis, cytokinesis, and cell migration. We show that in the ciliate Tetrahymena thermophila, the ADF/cofilin homologue Adf73p associates with actin on nascent food vacuoles. Overexpression of Adf73p disrupted the proper localization of actin and inhibited the formation of food vacuoles. In vitro, recombinant Adf73p promoted the depolymerization of filaments made of T. thermophila actin (Act1p). Knockout cells lacking the ADF73 gene are viable but grow extremely slowly and have a severely decreased rate of food vacuole formation. Knockout cells have abnormal aggregates of actin in the cytoplasm. Surprisingly, unlike the case in animals and yeasts, in Tetrahymena, ADF/cofilin is not required for cytokinesis. Thus, the Tetrahymena model shows promise for future studies of the role of ADF/cofilin in vivo.\",\n \"corpus_id\": 5276176,\n \"score\": 1\n },\n {\n \"doc_id\": \"23862734\",\n \"title\": \"Cofilin-induced changes in F-actin detected via cross-linking with benzophenone-4-maleimide.\",\n \"abstract\": \"Cofilin is a member of the actin depolymerizing factor (ADF)/cofilin family of proteins. It plays a key role in actin dynamics by promoting disassembly and assembly of actin filaments. Upon its binding, cofilin has been shown to bridge two adjacent protomers in filamentous actin (F-actin) and promote the displacement and disordering of subdomain 2 of actin. Here, we present evidence for cofilin promoting a new structural change in the actin filament, as detected via a switch in cross-linking sites. Benzophenone-4-maleimide, which normally forms intramolecular cross-linking in F-actin, cross-links F-actin intermolecularly upon cofilin binding. We mapped the cross-linking sites and found that in the absence of cofilin intramolecular cross-linking occurred between residues Cys374 and Asp11. In contrast, cofilin shifts the cross-linking by this reagent to intermolecular, between residue Cys374, located within subdomain 1 of the upper protomer, and Met44, located in subdomain 2 of the lower protomer. The intermolecular cross-linking of F-actin slows the rate of cofilin dissociation from the filaments and decreases the effect of ionic strength on cofilin-actin binding. These results are consistent with a significant role of filament flexibility in cofilin-actin interactions.\",\n \"corpus_id\": 30899512,\n \"score\": 1\n },\n {\n \"doc_id\": \"24371134\",\n \"title\": \"A mechanism for actin filament severing by malaria parasite actin depolymerizing factor 1 via a low affinity binding interface.\",\n \"abstract\": \"Actin depolymerizing factor (ADF)/cofilins are essential regulators of actin turnover in eukaryotic cells. These multifunctional proteins facilitate both stabilization and severing of filamentous (F)-actin in a concentration-dependent manner. At high concentrations ADF/cofilins bind stably to F-actin longitudinally between two adjacent actin protomers forming what is called a decorative interaction. Low densities of ADF/cofilins, in contrast, result in the optimal severing of the filament. To date, how these two contrasting modalities are achieved by the same protein remains uncertain. Here, we define the proximate amino acids between the actin filament and the malaria parasite ADF/cofilin, PfADF1 from Plasmodium falciparum. PfADF1 is unique among ADF/cofilins in being able to sever F-actin but do so without stable filament binding. Using chemical cross-linking and mass spectrometry (XL-MS) combined with structure reconstruction we describe a previously overlooked binding interface on the actin filament targeted by PfADF1. This site is distinct from the known binding site that defines decoration. Furthermore, total internal reflection fluorescence (TIRF) microscopy imaging of single actin filaments confirms that this novel low affinity site is required for F-actin severing. Exploring beyond malaria parasites, selective blocking of the decoration site with human cofilin (HsCOF1) using cytochalasin D increases its severing rate. HsCOF1 may therefore also use a decoration-independent site for filament severing. Thus our data suggest that a second, low affinity actin-binding site may be universally used by ADF/cofilins for actin filament severing.\",\n \"corpus_id\": 12854318,\n \"score\": 1\n },\n {\n \"doc_id\": \"24770705\",\n \"title\": \"ADF/Cofilin Controls Synaptic Actin Dynamics and Regulates Synaptic Vesicle Mobilization and Exocytosis.\",\n \"abstract\": \"Actin is a regulator of synaptic vesicle mobilization and exocytosis, but little is known about the mechanisms that regulate actin at presynaptic terminals. Genetic data on LIMK1, a negative regulator of actin-depolymerizing proteins of the ADF/cofilin family, suggest a role for ADF/cofilin in presynaptic function. However, synapse physiology is fully preserved upon genetic ablation of ADF in mice, and n-cofilin mutant mice display defects in postsynaptic plasticity, but not in presynaptic function. One explanation for this phenomenon is overlapping functions of ADF and n-cofilin in presynaptic physiology. Here, we tested this hypothesis and genetically removed ADF together with n-cofilin from synapses. In double mutants for ADF and n-cofilin, synaptic actin dynamics was impaired and more severely affected than in single mutants. The resulting cytoskeletal defects heavily affected the organization, mobilization, and exocytosis of synaptic vesicles in hippocampal CA3-CA1 synapses. Our data for the first time identify overlapping functions for ADF and n-cofilin in presynaptic physiology and vesicle trafficking. We conclude that n-cofilin is a limiting factor in postsynaptic plasticity, a function which cannot be substituted by ADF. On the presynaptic side, the presence of either ADF or n-cofilin is sufficient to control actin remodeling during vesicle release.\",\n \"corpus_id\": 31044670,\n \"score\": 1\n },\n {\n \"doc_id\": \"25228691\",\n \"title\": \"Structure and mechanism of mouse cyclase-associated protein (CAP1) in regulating actin dynamics.\",\n \"abstract\": \"Srv2/CAP is a conserved actin-binding protein with important roles in driving cellular actin dynamics in diverse animal, fungal, and plant species. However, there have been conflicting reports about whether the activities of Srv2/CAP are conserved, particularly between yeast and mammalian homologs. Yeast Srv2 has two distinct functions in actin turnover: its hexameric N-terminal-half enhances cofilin-mediated severing of filaments, while its C-terminal-half catalyzes dissociation of cofilin from ADP-actin monomers and stimulates nucleotide exchange. Here, we dissected the structure and function of mouse CAP1 to better understand its mechanistic relationship to yeast Srv2. Although CAP1 has a shorter N-terminal oligomerization sequence compared with Srv2, we find that the N-terminal-half of CAP1 (N-CAP1) forms hexameric structures with six protrusions, similar to N-Srv2. Further, N-CAP1 autonomously binds to F-actin and decorates the sides and ends of filaments, altering F-actin structure and enhancing cofilin-mediated severing. These activities depend on conserved surface residues on the helical-folded domain. Moreover, N-CAP1 enhances yeast cofilin-mediated severing, and conversely, yeast N-Srv2 enhances human cofilin-mediated severing, highlighting the mechanistic conservation between yeast and mammals. Further, we demonstrate that the C-terminal actin-binding β-sheet domain of CAP1 is sufficient to catalyze nucleotide-exchange of ADP-actin monomers, while in the presence of cofilin this activity additionally requires the WH2 domain. Thus, the structures, activities, and mechanisms of mouse and yeast Srv2/CAP homologs are remarkably well conserved, suggesting that the same activities and mechanisms underlie many of the diverse actin-based functions ascribed to Srv2/CAP homologs in different organisms.\",\n \"corpus_id\": 21579399,\n \"score\": 1\n },\n {\n \"doc_id\": \"25373779\",\n \"title\": \"Cofilin-2 controls actin filament length in muscle sarcomeres.\",\n \"abstract\": \"ADF/cofilins drive cytoskeletal dynamics by promoting the disassembly of \\\"aged\\\" ADP-actin filaments. Mammals express several ADF/cofilin isoforms, but their specific biochemical activities and cellular functions have not been studied in detail. Here, we demonstrate that the muscle-specific isoform cofilin-2 promotes actin filament disassembly in sarcomeres to control the precise length of thin filaments in the contractile apparatus. In contrast to other isoforms, cofilin-2 efficiently binds and disassembles both ADP- and ATP/ADP-Pi-actin filaments. We mapped surface-exposed cofilin-2-specific residues required for ATP-actin binding and propose that these residues function as an \\\"actin nucleotide-state sensor\\\" among ADF/cofilins. The results suggest that cofilin-2 evolved specific biochemical and cellular properties that allow it to control actin dynamics in sarcomeres, where filament pointed ends may contain a mixture of ADP- and ATP/ADP-Pi-actin subunits. Our findings also offer a rationale for why cofilin-2 mutations in humans lead to myopathies.\",\n \"corpus_id\": 10814202,\n \"score\": 1\n },\n {\n \"doc_id\": \"25864508\",\n \"title\": \"Roles of cofilin in development and its mechanisms of regulation.\",\n \"abstract\": \"Reorganization of the actin cytoskeleton is essential for cellular processes during animal development. Cofilin and actin depolymerizing factor (ADF) are potent actin-binding proteins that sever and depolymerize actin filaments, acting to generate the dynamics of the actin cytoskeleton. The activity of cofilin is spatially and temporally regulated by a variety of intracellular molecular mechanisms. Cofilin is regulated by cofilin binding molecules, is phosphorylated at Ser-3 (inactivation) by LIM-kinases (LIMKs) and testicular protein kinases (TESKs), and is dephosphorylated (reactivation) by slingshot protein phosphatases (SSHs). Although studies of the molecular mechanisms of cofilin-induced reorganization of the actin cytoskeleton have been ongoing for decades, the multicellular functions of cofilin and its regulation in development are just becoming apparent. This review describes the molecular mechanisms of generating actin dynamics by cofilin and the intracellular signaling pathways for regulating cofilin activity. Furthermore, recent findings of the roles of cofilin in the development of several tissues and organs, especially neural tissues and cells, in model animals are described. Recent developmental studies have indicated that cofilin and its regulatory mechanisms are involved in cellular proliferation and migration, the establishment of cellular polarity, and the dynamic regulation of organ morphology.\",\n \"corpus_id\": 36262546,\n \"score\": 1\n },\n {\n \"doc_id\": \"27153537\",\n \"title\": \"Structural Basis for Noncanonical Substrate Recognition of Cofilin/ADF Proteins by LIM Kinases.\",\n \"abstract\": \"Cofilin/actin-depolymerizing factor (ADF) proteins are critical nodes that relay signals from protein kinase cascades to the actin cytoskeleton, in particular through site-specific phosphorylation at residue Ser3. This is important for regulation of the roles of cofilin in severing and stabilizing actin filaments. Consequently, cofilin/ADF Ser3 phosphorylation is tightly controlled as an almost exclusive substrate for LIM kinases. Here we determine the LIMK1:cofilin-1 co-crystal structure. We find an interface that is distinct from canonical kinase-substrate interactions. We validate this previously unobserved mechanism for high-fidelity kinase-substrate recognition by in vitro kinase assays, examination of cofilin phosphorylation in mammalian cells, and functional analysis in S. cerevisiae. The interface is conserved across all LIM kinases. Remarkably, we also observe both pre- and postphosphotransfer states in the same crystal lattice. This study therefore provides a molecular understanding of how kinase-substrate recognition acts as a gatekeeper to regulate actin cytoskeletal dynamics.\",\n \"corpus_id\": 206994772,\n \"score\": 1\n },\n {\n \"doc_id\": \"27454820\",\n \"title\": \"F-actin dismantling through a redox-driven synergy between Mical and cofilin.\",\n \"abstract\": \"Numerous cellular functions depend on actin filament (F-actin) disassembly. The best-characterized disassembly proteins, the ADF (actin-depolymerizing factor)/cofilins (encoded by the twinstar gene in Drosophila), sever filaments and recycle monomers to promote actin assembly. Cofilin is also a relatively weak actin disassembler, posing questions about mechanisms of cellular F-actin destabilization. Here we uncover a key link to targeted F-actin disassembly by finding that F-actin is efficiently dismantled through a post-translational-mediated synergism between cofilin and the actin-oxidizing enzyme Mical. We find that Mical-mediated oxidation of actin improves cofilin binding to filaments, where their combined effect dramatically accelerates F-actin disassembly compared with either effector alone. This synergism is also necessary and sufficient for F-actin disassembly in vivo, magnifying the effects of both Mical and cofilin on cellular remodelling, axon guidance and Semaphorin-Plexin repulsion. Mical and cofilin, therefore, form a redox-dependent synergistic pair that promotes F-actin instability by rapidly dismantling F-actin and generating post-translationally modified actin that has altered assembly properties.\",\n \"corpus_id\": 38211458,\n \"score\": 1\n },\n {\n \"doc_id\": \"27762277\",\n \"title\": \"Allosteric regulation by cooperative conformational changes of actin filaments drives mutually exclusive binding with cofilin and myosin.\",\n \"abstract\": \"Heavy meromyosin (HMM) of myosin II and cofilin each binds to actin filaments cooperatively and forms clusters along the filaments, but it is unknown whether the two cooperative bindings are correlated and what physiological roles they have. Fluorescence microscopy demonstrated that HMM-GFP and cofilin-mCherry each bound cooperatively to different parts of actin filaments when they were added simultaneously in 0.2 μM ATP, indicating that the two cooperative bindings are mutually exclusive. In 0.1 mM ATP, the motor domain of myosin (S1) strongly inhibited the formation of cofilin clusters along actin filaments. Under this condition, most actin protomers were unoccupied by S1 at any given moment, suggesting that transiently bound S1 alters the structure of actin filaments cooperatively and/or persistently to inhibit cofilin binding. Consistently, cosedimentation experiments using copolymers of actin and actin-S1 fusion protein demonstrated that the fusion protein affects the neighboring actin protomers, reducing their affinity for cofilin. In reciprocal experiments, cofilin-actin fusion protein reduced the affinity of neighboring actin protomers for S1. Thus, allosteric regulation by cooperative conformational changes of actin filaments contributes to mutually exclusive cooperative binding of myosin II and cofilin to actin filaments, and presumably to the differential localization of both proteins in cells.\",\n \"corpus_id\": 4582454,\n \"score\": 1\n },\n {\n \"doc_id\": \"28025492\",\n \"title\": \"Cofilin-1 and Other ADF/Cofilin Superfamily Members in Human Malignant Cells.\",\n \"abstract\": \"Identification of actin-depolymerizing factor homology (ADF-H) domains in the structures of several related proteins led first to the formation of the ADF/cofilin family, which then expanded to the ADF/cofilin superfamily. This superfamily includes the well-studied cofilin-1 (Cfl-1) and about a dozen different human proteins that interact directly or indirectly with the actin cytoskeleton, provide its remodeling, and alter cell motility. According to some data, Cfl-1 is contained in various human malignant cells (HMCs) and is involved in the formation of malignant properties, including invasiveness, metastatic potential, and resistance to chemotherapeutic drugs. The presence of other ADF/cofilin superfamily proteins in HMCs and their involvement in the regulation of cell motility were discovered with the use of various OMICS technologies. In our review, we discuss the results of the study of Cfl-1 and other ADF/cofilin superfamily proteins, which may be of interest for solving different problems of molecular oncology, as well as for the prospects of further investigations of these proteins in HMCs.\",\n \"corpus_id\": 15998513,\n \"score\": 1\n },\n {\n \"doc_id\": \"29463680\",\n \"title\": \"The actin filament twist changes abruptly at boundaries between bare and cofilin-decorated segments.\",\n \"abstract\": \"Cofilin/ADF proteins are actin-remodeling proteins, essential for actin disassembly in various cellular processes, including cell division, intracellular transport, and motility. Cofilins bind actin filaments cooperatively and sever them preferentially at boundaries between bare and cofilin-decorated (cofilactin) segments. The cooperative binding to actin has been proposed to originate from conformational changes that propagate allosterically from clusters of bound cofilin to bare actin segments. Estimates of the lengths over which these cooperative conformational changes propagate vary dramatically, ranging from 2 to >100 subunits. Here, we present a general, structure-based method for detecting from cryo-EM micrographs small variations in filament geometry (i.e. twist) with single-subunit precision. How these variations correlate with regulatory protein occupancy reveals how far allosteric, conformational changes propagate along filaments. We used this method to determine the effects of cofilin on the actin filament twist. Our results indicate that cofilin-induced changes in filament twist propagate only 1-2 subunits from the boundary into the bare actin segment, independently of the boundary polarity (i.e. irrespective of whether or not the bare actin segment flanks the pointed or barbed-end side of the boundary) and the pyrene fluorophore labeling of actin. These observations indicate that the filament twist changes abruptly at boundaries between bare and cofilin-decorated segments, thereby constraining mechanistic models of cooperative actin filament interactions and severing by cofilin. The methods presented here extend the capability of cryo-EM to analyze biologically relevant deviations from helical symmetry in actin as well as other classes of linear polymers.\",\n \"corpus_id\": 3572019,\n \"score\": 1\n },\n {\n \"doc_id\": \"29709602\",\n \"title\": \"Structure, dynamics, and biochemical characterization of ADF/cofilin Twinstar from Drosophilamelanogaster.\",\n \"abstract\": \"BACKGROUND: Twinstar is an ADF/cofilin family protein, which is expressed by the tsr gene in Drosophila melanogaster. Twinstar is one of the main regulators of actin cytoskeleton remodelling and is essential for vital cellular processes like cytokinesis and endocytosis. METHODS: We have characterized the structure and dynamics of Twinstar by solution NMR spectroscopy, the interaction of Twinstar with rabbit muscle actin by ITC, and biochemical activities of Twinstar through different biochemical assays using fluorescence spectroscopy and ultra-centrifugation. RESULTS: The solution structure of Twinstar shows characteristic ADF-H fold with well-formed G/F-site and F-site for interaction with actin. The structure possesses an extended F-loop, which is rigid at the base, but flexible towards its apical region. Twinstar shares similar dynamics for the G/F-site with C. elegans homologs, UNC-60A and UNC-60B. However, the dynamics of its F-loop are different from its C. elegans homologs. Twinstar shows strong affinity for ADP-G-Actin and ATP-G-Actin with Kds of ~7.6 nM and ~0.4 μM, respectively. It shows mild F-actin depolymerizing activity and stable interaction with F-actin with a Kd of ~5.0 μM. It inhibits the rate of the nucleotide exchange in a dose dependent manner. CONCLUSION: On the basis of structure, dynamics, and biochemical activity, Twinstar can be taken to execute its biochemical role by facilitating directional growth and maintenance of length of actin filaments. GENERAL SIGNIFICANCE: This study characterizes the structure, backbone dynamics, and biochemical activities of Twinstar of Drosophila, which provides an insight into the regulation of actin dynamics in the member of phylum insecta.\",\n \"corpus_id\": 14009390,\n \"score\": 1\n }\n]","isConversational":false}}},{"rowIdx":55,"cells":{"query":{"kind":"string","value":"{\n \"doc_id\": \"28650318\",\n \"title\": \"Tandem hnRNP A1 RNA recognition motifs act in concert to repress the splicing of survival motor neuron exon 7.\",\n \"abstract\": \"HnRNP A1 regulates many alternative splicing events by the recognition of splicing silencer elements. Here, we provide the solution structures of its two RNA recognition motifs (RRMs) in complex with short RNA. In addition, we show by NMR that both RRMs of hnRNP A1 can bind simultaneously to a single bipartite motif of the human intronic splicing silencer ISS-N1, which controls survival of motor neuron exon 7 splicing. RRM2 binds to the upstream motif and RRM1 to the downstream motif. Combining the insights from the structure with in cell splicing assays we show that the architecture and organization of the two RRMs is essential to hnRNP A1 function. The disruption of the inter-RRM interaction or the loss of RNA binding capacity of either RRM impairs splicing repression by hnRNP A1. Furthermore, both binding sites within the ISS-N1 are important for splicing repression and their contributions are cumulative rather than synergistic.\",\n \"corpus_id\": 3883845\n}"},"candidates":{"kind":"list like","value":[{"doc_id":"18371932","title":"Antisense masking of an hnRNP A1/A2 intronic splicing silencer corrects SMN2 splicing in transgenic mice.","abstract":"Survival of motor neuron 2, centromeric (SMN2) is a gene that modifies the severity of spinal muscular atrophy (SMA), a motor-neuron disease that is the leading genetic cause of infant mortality. Increasing inclusion of SMN2 exon 7, which is predominantly skipped, holds promise to treat or possibly cure SMA; one practical strategy is the disruption of splicing silencers that impair exon 7 recognition. By using an antisense oligonucleotide (ASO)-tiling method, we systematically screened the proximal intronic regions flanking exon 7 and identified two intronic splicing silencers (ISSs): one in intron 6 and a recently described one in intron 7. We analyzed the intron 7 ISS by mutagenesis, coupled with splicing assays, RNA-affinity chromatography, and protein overexpression, and found two tandem hnRNP A1/A2 motifs within the ISS that are responsible for its inhibitory character. Mutations in these two motifs, or ASOs that block them, promote very efficient exon 7 inclusion. We screened 31 ASOs in this region and selected two optimal ones to test in human SMN2 transgenic mice. Both ASOs strongly increased hSMN2 exon 7 inclusion in the liver and kidney of the transgenic animals. Our results show that the high-resolution ASO-tiling approach can identify cis-elements that modulate splicing positively or negatively. Most importantly, our results highlight the therapeutic potential of some of these ASOs in the context of SMA.","corpus_id":269375,"score":2},{"doc_id":"19667073","title":"Cooperative-binding and splicing-repressive properties of hnRNP A1.","abstract":"hnRNP A1 binds to RNA in a cooperative manner. Initial hnRNP A1 binding to an exonic splicing silencer at the 3' end of human immunodeficiency virus type 1 (HIV-1) tat exon 3, which is a high-affinity site, is followed by cooperative spreading in a 3'-to-5' direction. As hnRNP A1 propagates toward the 5' end of the exon, it antagonizes binding of a serine/arginine-rich (SR) protein to an exonic splicing enhancer, thereby inhibiting splicing at that exon's alternative 3' splice site. tat exon 3 and the preceding intron of HIV-1 pre-mRNA can fold into an elaborate RNA secondary structure in solution, which could potentially influence hnRNP A1 binding. We report here that hnRNP A1 binding and splicing repression can occur on an unstructured RNA. Moreover, hnRNP A1 can effectively unwind an RNA hairpin upon binding, displacing a bound protein. We further show that hnRNP A1 can also spread in a 5'-to-3' direction, although when initial binding takes place in the middle of an RNA, spreading preferentially proceeds in a 3'-to-5' direction. Finally, when two distant high-affinity sites are present on the same RNA, they facilitate cooperative spreading of hnRNP A1 between the two sites.","corpus_id":206830155,"score":2},{"doc_id":"20947024","title":"Structural insights into RNA recognition by the alternate-splicing regulator CUG-binding protein 1.","abstract":"CUG-binding protein 1 (CUGBP1) regulates multiple aspects of nuclear and cytoplasmic mRNA processing, with implications for onset of myotonic dystrophy. CUGBP1 harbors three RRM domains and preferentially targets UGU-rich mRNA elements. We describe crystal structures of CUGBP1 RRM1 and tandem RRM1/2 domains bound to RNAs containing tandem UGU(U/G) elements. Both RRM1 in RRM1-RNA and RRM2 in RRM1/2-RNA complexes use similar principles to target UGU(U/G) elements, with recognition mediated by face-to-edge stacking and water-mediated hydrogen-bonding networks. The UG step adopts a left-handed Z-RNA conformation, with the syn guanine recognized through Hoogsteen edge-protein backbone hydrogen-bonding interactions. NMR studies on the RRM1/2-RNA complex establish that both RRM domains target tandem UGUU motifs in solution, whereas filter-binding assays identify a preference for recognition of GU over AU or GC steps. We discuss the implications of CUGBP1-mediated targeting and sequestration of UGU(U/G) elements on pre-mRNA alternative-splicing regulation, translational regulation, and mRNA decay.","corpus_id":30900930,"score":2},{"doc_id":"21120954","title":"SMN2 exon 7 splicing is inhibited by binding of hnRNP A1 to a common ESS motif that spans the 3' splice site.","abstract":"Spinal Muscular Atrophy is caused by homozygous loss of SMN1 with phenotypic modulation by SMN2. SMN2 expresses only limited amounts of full-length transcript due to skipping of exon 7 caused by disruption of an SF2/ASF binding ESE. Additionally, hnRNP A1 has been reported to inhibit inclusion of SMN2 exon 7. We previously reported high similarity between the sequence spanning the 3' ss of SMN1 and SMN2 exon 7 and an hnRNP A1 binding ESS, which regulates MCAD exon 5 splicing. We show here that this 3' ss motif indeed functions as a crucial hnRNP A1 binding ESS, which inhibits inclusion of SMN1/2 exon 7 and is antagonized by the SMN1 ESE, but not by the inactive SMN2 sequence. Pull-down experiments revealed a specific interaction between hnRNP A1 and the 3' ss AG-dinucleotide, which could be disrupted by mutations shown to improve splicing in reporter minigenes. Genomic analyses revealed that in the human genome, 3' ss matching the SMN1/2 ESS motif region are much less abundant than 3' ss with a disrupted ESS motif. This indicates that this ESS may be a general splicing inhibitory motif, which binds hnRNP A1 and inhibits exon inclusion by binding to 3' ss harboring this ESS motif.","corpus_id":39402594,"score":2},{"doc_id":"23247503","title":"Solution structure of the two RNA recognition motifs of hnRNP A1 using segmental isotope labeling: how the relative orientation between RRMs influences the nucleic acid binding topology.","abstract":"Human hnRNP A1 is a multi-functional protein involved in many aspects of nucleic-acid processing such as alternative splicing, micro-RNA biogenesis, nucleo-cytoplasmic mRNA transport and telomere biogenesis and maintenance. The N-terminal region of hnRNP A1, also named unwinding protein 1 (UP1), is composed of two closely related RNA recognition motifs (RRM), and is followed by a C-terminal glycine rich region. Although crystal structures of UP1 revealed inter-domain interactions between RRM1 and RRM2 in both the free and bound form of UP1, these interactions have never been established in solution. Moreover, the relative orientation of hnRNP A1 RRMs is different in the free and bound crystal structures of UP1, raising the question of the biological significance of this domain movement. In the present study, we have used NMR spectroscopy in combination with segmental isotope labeling techniques to carefully analyze the inter-RRM contacts present in solution and subsequently determine the structure of UP1 in solution. Our data unambiguously demonstrate that hnRNP A1 RRMs interact in solution, and surprisingly, the relative orientation of the two RRMs observed in solution is different from the one found in the crystal structure of free UP1 and rather resembles the one observed in the nucleic-acid bound form of the protein. This strongly supports the idea that the two RRMs of hnRNP A1 have a single defined relative orientation which is the conformation previously observed in the bound form and now observed in solution using NMR. It is likely that the conformation in the crystal structure of the free form is a less stable form induced by crystal contacts. Importantly, the relative orientation of the RRMs in proteins containing multiple-RRMs strongly influences the RNA binding topologies that are practically accessible to these proteins. Indeed, RRM domains are asymmetric binding platforms contacting single-stranded nucleic acids in a single defined orientation. Therefore, the path of the nucleic acid molecule on the multiple RRM domains is strongly dependent on whether the RRMs are interacting with each other. The different nucleic acid recognition modes by multiple-RRM domains are briefly reviewed and analyzed on the basis of the current structural information.","corpus_id":1210587,"score":2},{"doc_id":"25081215","title":"RNA recognition and self-association of CPEB4 is mediated by its tandem RRM domains.","abstract":"Cytoplasmic polyadenylation is regulated by the interaction of the cytoplasmic polyadenylation element binding proteins (CPEB) with cytoplasmic polyadenylation element (CPE) containing mRNAs. The CPEB family comprises four paralogs, CPEB1-4, each composed of a variable N-terminal region, two RNA recognition motif (RRM) and a C-terminal ZZ-domain. We have characterized the RRM domains of CPEB4 and their binding properties using a combination of biochemical, biophysical and NMR techniques. Isothermal titration calorimetry, NMR and electrophoretic mobility shift assay experiments demonstrate that both the RRM domains are required for an optimal CPE interaction and the presence of either one or two adenosines in the two most commonly used consensus CPE motifs has little effect on the affinity of the interaction. Both the single RRM1 and the tandem RRM1-RRM2 have the ability to dimerize, although representing a minor population. Self-association does not affect the proteins' ability to interact with RNA as demonstrated by ion mobility-mass spectrometry. Chemical shift effects measured by NMR of the apo forms of the RRM1-RRM2 samples indicate that the two domains are orientated toward each other. NMR titration experiments show that residues on the β-sheet surface on RRM1 and at the C-terminus of RRM2 are affected upon RNA binding. We propose a model of the CPEB4 RRM1-RRM2-CPE complex that illustrates the experimental data.","corpus_id":13890195,"score":2},{"doc_id":"25727246","title":"Splicing regulation in spinal muscular atrophy by an RNA structure formed by long-distance interactions.","abstract":"Humans carry two copies of the survival motor neuron gene: SMN1 and SMN2. Loss of SMN1 coupled with skipping of SMN2 exon 7 causes spinal muscular atrophy (SMA), a leading genetic disease associated with infant mortality. Our discovery of intronic splicing silencer N1 (ISS-N1) is a promising target, currently in a phase III clinical trial, for an antisense oligonucleotide-mediated splicing correction in SMA. We have recently shown that the first residue of ISS-N1 is locked in a unique RNA structure that we term ISTL1 (internal stem through long-distance interaction-1). Complementary strands of ISTL1 are separated from each other by 279 nucleotides. Using site-specific mutations and chemical structure probing, we confirmed the formation and functional significance of ISTL1. Located in the middle of intron 7, the 3' strand of ISTL1 falls within an inhibitory region that we term ISS-N2. We demonstrate that an antisense oligonucleotide-mediated sequestration of ISS-N2 fully corrects SMN2 exon 7 splicing and restores high levels of SMN in SMA patient cells. These results underscore the therapeutic potential of the regulatory information present in a secondary and high-order RNA structure of a human intron.","corpus_id":35598391,"score":2},{"doc_id":"26003924","title":"The First Crystal Structure of the UP1 Domain of hnRNP A1 Bound to RNA Reveals a New Look for an Old RNA Binding Protein.","abstract":"The heterogeneous nuclear ribonucleoprotein (hnRNP) A1 protein is a multifunctional RNA binding protein implicated in a wide range of biological functions. Mechanisms and putative hnRNP A1-RNA interactions have been inferred primarily from the crystal structure of its UP1 domain bound to ssDNA. RNA stem loops represent an important class of known hnRNP A1 targets, yet little is known about the structural basis of hnRNP A1-RNA recognition. Here, we report the first high-resolution structure (1.92Å) of UP1 bound to a 5'-AGU-3' trinucleotide that resembles sequence elements of several native hnRNP A1-RNA stem loop targets. UP1 interacts specifically with the AG dinucleotide sequence via a \"nucleobase pocket\" formed by the β-sheet surface of RRM1 and the inter-RRM linker; RRM2 does not contact the RNA. The inter-RRM linker forms the lid of the nucleobase pocket and we show using structure-guided mutagenesis that the conserved salt-bridge interactions (R75:D155 and R88:D157) on the α-helical side of the RNA binding surface stabilize the linker in a geometry poised to bind RNA. We further investigated the structural basis of UP1 binding HIViSL3(ESS3) by determining a structural model of the complex scored by small-angle X-ray scattering. UP1 docks on the apical loop of SL3(ESS3) using its RRM1 domain and inter-RRM linker only. The biophysical implications of the structural model were tested by measuring kinetic binding parameters, where mutations introduced within the apical loop reduce binding affinities by slowing down the rate of complex formation. Collectively, the data presented here provide the first insights into hnRNP A1-RNA interactions.","corpus_id":206214449,"score":2},{"doc_id":"26607354","title":"Solution Structure of the HIV-1 Intron Splicing Silencer and its Interactions with the UP1 Domain of hnRNP A1.","abstract":"Splicing patterns in HIV-1 are maintained through cis regulatory elements that recruit antagonistic host RNA binding proteins. The activity of the 3 prime acceptor site A7 is tightly regulated through a complex network of an intronic splicing silencer (ISS), a bipartite exonic splicing silencer (ESS3a/b) and an exonic splicing enhancer (ESE3). Since HIV-1 splicing depends on protein-RNA interactions, it is important to know the tertiary structures surrounding the splice sites. Herein, we present the NMR solution structure of the phylogenetically conserved ISS stem loop. ISS adopts a stable structure consisting of conserved UG wobble pairs, a folded 2X2 (GU/UA) internal loop, a UU bulge and a flexible AGUGA apical loop. Calorimetric and biochemical titrations indicate the UP1 domain of hnRNP A1 binds the ISS apical loop site-specifically and with nanomolar affinity. Collectively, this work provides additional insights into how HIV-1 uses a conserved RNA structure to commandeer a host RNA binding protein.","corpus_id":35676693,"score":2},{"doc_id":"27380775","title":"Global identification of hnRNP A1 binding sites for SSO-based splicing modulation.","abstract":"BACKGROUND: Many pathogenic genetic variants have been shown to disrupt mRNA splicing. Besides splice mutations in the well-conserved splice sites, mutations in splicing regulatory elements (SREs) may deregulate splicing and cause disease. A promising therapeutic approach is to compensate for this deregulation by blocking other SREs with splice-switching oligonucleotides (SSOs). However, the location and sequence of most SREs are not well known. RESULTS: Here, we used individual-nucleotide resolution crosslinking immunoprecipitation (iCLIP) to establish an in vivo binding map for the key splicing regulatory factor hnRNP A1 and to generate an hnRNP A1 consensus binding motif. We find that hnRNP A1 binding in proximal introns may be important for repressing exons. We show that inclusion of the alternative cassette exon 3 in SKA2 can be significantly increased by SSO-based treatment which blocks an iCLIP-identified hnRNP A1 binding site immediately downstream of the 5' splice site. Because pseudoexons are well suited as models for constitutive exons which have been inactivated by pathogenic mutations in SREs, we used a pseudoexon in MTRR as a model and showed that an iCLIP-identified hnRNP A1 binding site downstream of the 5' splice site can be blocked by SSOs to activate the exon. CONCLUSIONS: The hnRNP A1 binding map can be used to identify potential targets for SSO-based therapy. Moreover, together with the hnRNP A1 consensus binding motif, the binding map may be used to predict whether disease-associated mutations and SNPs affect hnRNP A1 binding and eventually mRNA splicing.","corpus_id":3638528,"score":2},{"doc_id":"28193894","title":"Rules of RNA specificity of hnRNP A1 revealed by global and quantitative analysis of its affinity distribution.","abstract":"Heterogeneous nuclear ribonucleoprotein A1 (hnRNP A1) is a multipurpose RNA-binding protein (RBP) involved in normal and pathological RNA metabolism. Transcriptome-wide mapping and in vitro evolution identify consensus hnRNP A1 binding motifs; however, such data do not reveal how surrounding RNA sequence and structural context modulate affinity. We determined the affinity of hnRNP A1 for all possible sequence variants (n = 16,384) of the HIV exon splicing silencer 3 (ESS3) 7-nt apical loop. Analysis of the affinity distribution identifies the optimal motif 5'-YAG-3' and shows how its copy number, position in the loop, and loop structure modulate affinity. For a subset of ESS3 variants, we show that specificity is determined by association rate constants and that variants lacking the minimal sequence motif bind competitively with consensus RNA. Thus, the results reveal general rules of specificity of hnRNP A1 and provide a quantitative framework for understanding how it discriminates between alternative competing RNA ligands in vivo.","corpus_id":4702455,"score":2},{"doc_id":"29379020","title":"Molecular basis for the specific and multivariant recognitions of RNA substrates by human hnRNP A2/B1.","abstract":"Human hnRNP A2/B1 is an RNA-binding protein that plays important roles in many biological processes, including maturation, transport, and metabolism of mRNA, and gene regulation of long noncoding RNAs. hnRNP A2/B1 was reported to control the microRNAs sorting to exosomes and promote primary microRNA processing as a potential m6A \"reader.\" hnRNP A2/B1 contains two RNA recognition motifs that provide sequence-specific recognition of RNA substrates. Here, we determine crystal structures of tandem RRM domains of hnRNP A2/B1 in complex with various RNA substrates, elucidating specific recognitions of AGG and UAG motifs by RRM1 and RRM2 domains, respectively. Further structural and biochemical results demonstrate multivariant binding modes for sequence-diversified RNA substrates, supporting a RNA matchmaker mechanism in hnRNP A2/B1 function. Moreover, our studies in combination with bioinformatic analysis suggest that hnRNP A2/B1 may mediate effects of m6A through a \"m6A switch\" mechanism, instead of acting as a direct \"reader\" of m6A modification.","corpus_id":3310175,"score":2},{"doc_id":"29625167","title":"Idiosyncrasies of hnRNP A1-RNA recognition: Can binding mode influence function.","abstract":"The heterogeneous nuclear ribonucleoproteins (hnRNPs) are a diverse family of RNA binding proteins that function in most stages of RNA metabolism. The prototypical member, hnRNP A1, is composed of three major domains; tandem N-terminal RNA Recognition Motifs (RRMs) and a C-terminal mostly intrinsically disordered region. HnRNP A1 is broadly implicated in basic cellular RNA processing events such as splicing, stability, nuclear export and translation. Due to its ubiquity and abundance, hnRNP A1 is also frequently usurped to control viral gene expression. Deregulation of the RNA metabolism functions of hnRNP A1 in neuronal cells contributes to several neurodegenerative disorders. Because of these roles in human pathologies, the study of hnRNP A1 provides opportunities for the development of novel therapeutics, with disruption of its RNA binding capabilities being the most promising target. The functional diversity of hnRNP A1 is reflected in the complex nature by which it interacts with various RNA targets. Indeed, hnRNP A1 binds both structured and unstructured RNAs with binding affinities that span several magnitudes. Available structures of hnRNP A1-RNA complexes also suggest a degree of plasticity in molecular recognition. Given the reinvigoration in hnRNP A1, the goal of this review is to use the available structural biochemical developments as a framework to interpret its wide-range of RNA functions.","corpus_id":4792730,"score":2},{"doc_id":"18703504","title":"TDP-43 overexpression enhances exon 7 inclusion during the survival of motor neuron pre-mRNA splicing.","abstract":"TDP-43 is a highly conserved, 43-kDa RNA-binding protein implicated to play a role in transcription repression, nuclear organization, and alternative splicing. More recently, this factor has been identified as the major disease protein of several neurodegenerative diseases, including frontotemporal lobar degeneration with ubiquitin-positive inclusions and amyotrophic lateral sclerosis. For the splicing activity, the factor has been shown to be mainly an exon-skipping promoter. In this study using the survival of motor neuron (SMN) minigenes as the reporters in transfection assay, we show for the first time that TDP-43 could also act as an exon-inclusion factor. Furthermore, both RNA-recognition motif domains are required for its ability to enhance the SMN2 exon 7 inclusion. Combined protein-immunoprecipitation and RNA-immunoprecipitation experiments also suggested that this exon inclusion activity might be mediated by multimeric complex(es) consisting of this protein interacting with other splicing factors, including Htra2-beta1. Our data further evidence TDP-43 as a multifunctional RNA-binding protein for a diverse set of cellular activities.","corpus_id":25958855,"score":1},{"doc_id":"19926721","title":"hnRNP A1 and hnRNP H can collaborate to modulate 5' splice site selection.","abstract":"The mammalian proteins hnRNP A1 and hnRNP H control many splicing decisions in viral and cellular primary transcripts. To explain some of these activities, we have proposed that self-interactions between bound proteins create an RNA loop that represses internal splice sites while simultaneously activating the external sites that are brought in closer proximity. Here we show that a variety of hnRNP H binding sites can affect 5' splice site selection. The addition of two sets of hnRNP H sites in a model pre-mRNA modulates 5' splice site selection cooperatively, consistent with the looping model. Notably, binding sites for hnRNP A1 and H on the same pre-mRNA can similarly collaborate to modulate 5' splice site selection. The C-terminal portion of hnRNP H that contains the glycine-rich domains (GRD) is essential for splicing activity, and it can be functionally replaced by the GRD of hnRNP A1. Finally, we used the bioluminescence resonance energy transfer (BRET) technology to document the existence of homotypic and heterotypic interactions between hnRNP H and hnRNP A1 in live cells. Overall, our study suggests that interactions between different hnRNP proteins bound to distinct locations on a pre-mRNA can change its conformation to affect splicing decisions.","corpus_id":30321269,"score":1},{"doc_id":"20515750","title":"Splicing regulation of the survival motor neuron genes and implications for treatment of spinal muscular atrophy.","abstract":"Proximal spinal muscular atrophy (SMA) is a neuromuscular disease caused by low levels of the survival motor neuron (SMN) protein. The reduced SMN levels are due to loss of the survival motor neuron-1 (SMN1) gene. Humans carry a nearly identical SMN2 gene that generates a truncated protein, due to a C to T nucleotide alteration in exon 7 that leads to inefficient RNA splicing of exon 7. This exclusion of SMN exon 7 is central to the onset of the SMA disease, however, this offers a unique therapeutic intervention in which corrective splicing of the SMN2 gene would restore SMN function. Exon 7 splicing is regulated by a number of exonic and intronic splicing regulatory sequences and trans-factors that bind them. A better understanding of the way SMN pre-mRNA is spliced has lead to the development of targeted therapies aimed at correcting SMN2 splicing. As therapeutics targeted toward correction of SMN2 splicing continue to be developed available SMA mouse models can be utilized in validating their potential in disease treatment.","corpus_id":24755471,"score":1},{"doc_id":"22132154","title":"hnRNP A1 and hnRNP F modulate the alternative splicing of exon 11 of the insulin receptor gene.","abstract":"Exon 11 of the insulin receptor gene (INSR) is alternatively spliced in a developmentally and tissue-specific manner. Linker scanning mutations in a 5' GA-rich enhancer in intron 10 identified AGGGA sequences that are important for enhancer function. Using RNA-affinity purification and mass spectrometry, we identified hnRNP F and hnRNP A1 binding to these AGGGA sites and also to similar motifs at the 3' end of the intron. The hnRNPs have opposite functional effects with hnRNP F promoting and hnRNP A1 inhibiting exon 11 inclusion, and deletion of the GA-rich elements eliminates both effects. We also observed specific binding of hnRNP A1 to the 5' splice site of intron 11. The SR protein SRSF1 (SF2/ASF) co-purified on the GA-rich enhancer and, interestingly, also competes with hnRNP A1 for binding to the splice site. A point mutation -3U→C decreases hnRNP A1 binding, increases SRSF1 binding and renders the exon constitutive. Lastly, our data point to a functional interaction between hnRNP F and SRSF1 as a mutant that eliminates SRSF1 binding to exon 11, or a SRSF1 knockdown, which prevents the stimulatory effect of hnRNP F over expression.","corpus_id":11656500,"score":1},{"doc_id":"22154809","title":"Solution structure of the HIV-1 exon splicing silencer 3.","abstract":"Alternative splicing of the human immunodeficiency virus type 1 (HIV-1) genomic RNA is necessary to produce the complete viral protein complement, and aberrations in the splicing pattern impair HIV-1 replication. Genome splicing in HIV-1 is tightly regulated by the dynamic assembly/disassembly of trans host factors with cis RNA control elements. The host protein, heterogeneous nuclear ribonucleoprotein (hnRNP) A1, regulates splicing at several highly conserved HIV-1 3' splice sites by binding 5'-UAG-3' elements embedded within regions containing RNA structure. The physical determinants of hnRNP A1 splice site recognition remain poorly defined in HIV-1, thus precluding a detailed understanding of the molecular basis of the splicing pattern. Here, the three-dimensional structure of the exon splicing silencer 3 (ESS3) from HIV-1 has been determined using NMR spectroscopy. ESS3 adopts a 27-nucleotide hairpin with a 10-bp A-form stem that contains a pH-sensitive A(+)C wobble pair. The seven-nucleotide hairpin loop contains the high-affinity hnRNP-A1-responsive 5'-UAGU-3' element and a proximal 5'-GAU-3' motif. The NMR structure shows that the heptaloop adopts a well-organized conformation stabilized primarily by base stacking interactions reminiscent of a U-turn. The apex of the loop is quasi-symmetric with UA dinucleotide steps from the 5'-GAU-3' and 5'-UAGU-3' motifs stacking on opposite sides of the hairpin. As a step towards understanding the binding mechanism, we performed calorimetric and NMR titrations of several hnRNP A1 subdomains into ESS3. The data show that the UP1 domain forms a high-affinity (K(d)=37.8±1.1 nM) complex with ESS3 via site-specific interactions with the loop.","corpus_id":22385574,"score":1},{"doc_id":"22325350","title":"hnRNP A1 proofreads 3' splice site recognition by U2AF.","abstract":"One of the earliest steps in metazoan pre-mRNA splicing involves binding of U2 snRNP auxiliary factor (U2AF) 65 KDa subunit to the polypyrimidine (Py) tract and of the 35 KDa subunit to the invariant AG dinucleotide at the intron 3' end. Here we use in vitro and in vivo depletion, as well as reconstitution assays using purified components, to identify hnRNP A1 as an RNA binding protein that allows U2AF to discriminate between pyrimidine-rich RNA sequences followed or not by a 3' splice site AG. Biochemical and NMR data indicate that hnRNP A1 forms a ternary complex with the U2AF heterodimer on AG-containing/uridine-rich RNAs, while it displaces U2AF from non-AG-containing/uridine-rich RNAs, an activity that requires the glycine-rich domain of hnRNP A1. Consistent with the functional relevance of this activity for splicing, proofreading assays reveal a role for hnRNP A1 in U2AF-mediated recruitment of U2 snRNP to the pre-mRNA.","corpus_id":10951645,"score":1},{"doc_id":"23394998","title":"hnRNP L and hnRNP A1 induce extended U1 snRNA interactions with an exon to repress spliceosome assembly.","abstract":"Pre-mRNA splicing is catalyzed through the activity of the spliceosome, a dynamic enzymatic complex. Forcing aberrant interactions within the spliceosome can reduce splicing efficiency and alter splice site choice; however, it is unknown whether such alterations are naturally exploited mechanisms of splicing regulation. Here, we demonstrate that hnRNP L represses CD45 exon 4 by recruiting hnRNP A1 to a sequence upstream of the 5' splice site. Together, hnRNP L and A1 induce extended contacts between the 5' splice site-bound U1 snRNA and neighboring exonic sequences that, in turn, inhibit stable association of U6 snRNA and subsequent catalysis. Importantly, analysis of several exons regulated by hnRNP L shows a clear relationship between the potential for binding of hnRNP A1 and U1 snRNA and the effect of hnRNP L on splicing. Together, our results demonstrate that conformational perturbations within the spliceosome are a naturally occurring and generalizable mechanism for controlling alternative splicing decisions.","corpus_id":14521439,"score":1},{"doc_id":"23430061","title":"hnRNP A1 contacts exon 5 to promote exon 6 inclusion of apoptotic Fas gene.","abstract":"Fas is a transmembrane cell surface protein recognized by Fas ligand (FasL). When FasL binds to Fas, the target cells undergo apoptosis. A soluble Fas molecule that lacks the transmembrane domain is produced from skipping of exon 6 encoding this region in alternative splicing procedure. The soluble Fas molecule has the opposite function of intact Fas molecule, protecting cells from apoptosis. Here we show that knockdown of hnRNP A1 promotes exon 6 skipping of Fas pre-mRNA, whereas overexpression of hnRNP A1 reduces exon 6 skipping. Based on the bioinformatics approach, we have hypothesized that hnRNP A1 functions through interrupting 5' splice site selection of exon 5 by interacting with its potential binding site close to 5' splice site of exon 5. Consistent with our hypothesis, we demonstrate that mutations of the hnRNP A1 binding site on exon 5 disrupted the effects of hnRNP A1 on exon 6 inclusion. RNA pull-down assay and then western blot analysis with hnRNP A1 antibody prove that hnRNP A1 contacts the potential binding site RNA sequence on exon 5 but not the mutant sequence. In addition, we show that the mutation of 5' splice site on exon 5 to a less conserved sequence destructed the effects of hnRNP A1 on exon 6 inclusion. Therefore we conclude that hnRNP A1 interacts with exon 5 to promote distal exon 6 inclusion of Fas pre-mRNA. Our study reveals a novel alternative splicing mechanism of Fas pre-mRNA.","corpus_id":2289833,"score":1},{"doc_id":"23646903","title":"Minimal functional domains of paralogues hnRNP L and hnRNP LL exhibit mechanistic differences in exonic splicing repression.","abstract":"Understanding functional distinctions between related splicing regulatory proteins is critical to deciphering tissue-specific control of alternative splicing. The hnRNP (heterogeneous nuclear ribonucleoprotein) L and hnRNP LL (hnRNP L-like) proteins are paralogues that have overlapping, but distinct, expression patterns and functional consequences. These two proteins share high sequence similarity in their RRMs (RNA-recognition motifs), but diverge in regions outside of the RRMs. In the present study, we use an MS2-tethering assay to delineate the minimal domains of hnRNP L and hnRNP LL which are required for repressing exon inclusion. We demonstrate that for both proteins, regions outside the RRMs, the N-terminal region, and a linker sequence between RRMs 2 and 3, are necessary for exon repression, but are only sufficient for repression in the case of hnRNP LL. In addition, both proteins require at least one RRM for maximal repression. Notably, we demonstrate that the region encompassing RRMs 1 and 2 of hnRNP LL imparts a second silencing activity not observed for hnRNP L. This additional functional component of hnRNP LL is consistent with the fact that the full-length hnRNP LL has a greater silencing activity than hnRNP L. Thus the results of the present study provide important insight into the functional and mechanistic variations that can exist between two highly related hnRNP proteins.","corpus_id":2877643,"score":1},{"doc_id":"24240615","title":"Molecular basis of UG-rich RNA recognition by the human splicing factor TDP-43.","abstract":"TDP-43 encodes an alternative-splicing regulator with tandem RNA-recognition motifs (RRMs). The protein regulates cystic fibrosis transmembrane regulator (CFTR) exon 9 splicing through binding to long UG-rich RNA sequences and is found in cytoplasmic inclusions of several neurodegenerative diseases. We solved the solution structure of the TDP-43 RRMs in complex with UG-rich RNA. Ten nucleotides are bound by both RRMs, and six are recognized sequence specifically. Among these, a central G interacts with both RRMs and stabilizes a new tandem RRM arrangement. Mutations that eliminate recognition of this key nucleotide or crucial inter-RRM interactions disrupt RNA binding and TDP-43-dependent splicing regulation. In contrast, point mutations that affect base-specific recognition in either RRM have weaker effects. Our findings reveal not only how TDP-43 recognizes UG repeats but also how RNA binding-dependent inter-RRM interactions are crucial for TDP-43 function.","corpus_id":13783277,"score":1},{"doc_id":"24628426","title":"Thermodynamic and phylogenetic insights into hnRNP A1 recognition of the HIV-1 exon splicing silencer 3 element.","abstract":"Complete expression of the HIV-1 genome requires balanced usage of suboptimal splice sites. The 3' acceptor site A7 (ssA7) is negatively regulated in part by an interaction between the host hnRNP A1 protein and a viral splicing silencer (ESS3). Binding of hnRNP A1 to ESS3 and other upstream silencers is sufficient to occlude spliceosome assembly. Efforts to understand the splicing repressive properties of hnRNP A1 on ssA7 have revealed hnRNP A1 binds specific sites within the context of a highly folded RNA structure; however, biochemical models assert hnRNP A1 disrupts RNA structure through cooperative spreading. In an effort to improve our understanding of the ssA7 binding properties of hnRNP A1, herein we have performed a combined phylogenetic and biophysical study of the interaction of its UP1 domain with ESS3. Phylogenetic analyses of group M sequences (x̅ = 2860) taken from the Los Alamos HIV database reveal the ESS3 stem loop (SL3(ESS3)) structure has been conserved throughout HIV-1 evolution, despite variations in primary sequence. Calorimetric titrations with UP1 clearly show the SL3(ESS3) structure is a critical binding determinant because deletion of the base-paired region reduces the affinity by ∼150-fold (Kd values of 27.8 nM and 4.2 μM). Cytosine substitutions of conserved apical loop nucleobases show UP1 preferentially binds purines over pyrimidines, where site-specific interactions were detected via saturation transfer difference nuclear magnetic resonance. Chemical shift mapping of the UP1-SL3(ESS3) interface by (1)H-(15)N heteronuclear single-quantum coherence spectroscopy titrations reveals a broad interaction surface on UP1 that encompasses both RRM domains and the inter-RRM linker. Collectively, our results describe a UP1 binding mechanism that is likely different from current models used to explain the alternative splicing properties of hnRNP A1.","corpus_id":8536035,"score":1},{"doc_id":"24692659","title":"Characterization of the RNA recognition mode of hnRNP G extends its role in SMN2 splicing regulation.","abstract":"Regulation of SMN2 exon 7 splicing is crucial for the production of active SMN protein and the survival of Spinal Muscular Atrophy (SMA) patients. One of the most efficient activators of exon 7 inclusion is hnRNP G, which is recruited to the exon by Tra2-β1. We report that in addition to the C-terminal region of hnRNP G, the RNA Recognition Motif (RRM) and the middle part of the protein containing the Arg-Gly-Gly (RGG) box are important for this function. To better understand the mode of action of hnRNP G in this context we determined the structure of its RRM bound to an SMN2 derived RNA. The RRM interacts with a 5'-AAN-3' motif and specifically recognizes the two consecutive adenines. By testing the effect of mutations in hnRNP G RRM and in its putative binding sites on the splicing of SMN2 exon 7, we show that it specifically binds to exon 7. This interaction is required for hnRNP G splicing activity and we propose its recruitment to a polyA tract located upstream of the Tra2-β1 binding site. Finally, our data suggest that hnRNP G plays a major role in the recruitment of the Tra2-β1/hnRNP G/SRSF9 trimeric complex to SMN2 exon 7.","corpus_id":11994416,"score":1},{"doc_id":"24892836","title":"Absence of an intron splicing silencer in porcine Smn1 intron 7 confers immunity to the exon skipping mutation in human SMN2.","abstract":"Spinal Muscular Atrophy is caused by homozygous loss of SMN1. All patients retain at least one copy of SMN2 which produces an identical protein but at lower levels due to a silent mutation in exon 7 which results in predominant exclusion of the exon. Therapies targeting the splicing of SMN2 exon 7 have been in development for several years, and their efficacy has been measured using either in vitro cellular assays or in vivo small animal models such as mice. In this study we evaluated the potential for constructing a mini-pig animal model by introducing minimal changes in the endogenous porcine Smn1 gene to maintain the native genomic structure and regulation. We found that while a Smn2-like mutation can be introduced in the porcine Smn1 gene and can diminish the function of the ESE, it would not recapitulate the splicing pattern seen in human SMN2 due to absence of a functional ISS immediately downstream of exon 7. We investigated the ISS region and show here that the porcine ISS is inactive due to disruption of a proximal hnRNP A1 binding site, while a distal hnRNP A1 binding site remains functional but is unable to maintain the functionality of the ISS as a whole.","corpus_id":16895730,"score":1},{"doc_id":"26051023","title":"The Signature of the Five-Stranded vRRM Fold Defined by Functional, Structural and Computational Analysis of the hnRNP L Protein.","abstract":"The RNA recognition motif (RRM) is the far most abundant RNA binding domain. In addition to the typical β1α1β2β3α2β4 fold, various sub-structural elements have been described and reportedly contribute to the high functional versatility of RRMs. The heterogeneous nuclear ribonucleoprotein L (hnRNP L) is a highly abundant protein of 64 kDa comprising four RRM domains. Involved in many aspects of RNA metabolism, hnRNP L specifically binds to RNAs containing CA repeats or CA-rich clusters. However, a comprehensive structural description of hnRNP L including its sub-structural elements is missing. Here, we present the structural characterization of the RRM domains of hnRNP L and demonstrate their function in repressing exon 4 of SLC2A2. By comparison of the sub-structural elements between the two highly similar paralog families of hnRNP L and PTB, we defined signatures underlying interacting C-terminal coils (ICCs), the RRM34 domain interaction and RRMs with a C-terminal fifth β-strand, a variation we denoted vRRMs. Furthermore, computational analysis revealed new putative ICC-containing RRM families and allowed us to propose an evolutionary scenario explaining the origins of the ICC and fifth β-strand sub-structural extensions. Our studies provide insights of domain requirements in alternative splicing mediated by hnRNP L and molecular descriptions for the sub-structural elements. In addition, the analysis presented may help to classify other abundant RRM extensions and to predict structure-function relationships.","corpus_id":206214482,"score":1},{"doc_id":"26419278","title":"A rare variant (c.863G>T) in exon 7 of SMN1 disrupts mRNA splicing and is responsible for spinal muscular atrophy.","abstract":"Proximal spinal muscular atrophy (SMA) is an autosomal recessive neuromuscular disorder caused by deletion or mutation of SMN1 (survival motor neuron 1). SMN exon 7 splicing is regulated by a number of exonic and intronic regulatory sequences and the trans-factors that bind them. Variants located in or near these regulated regions should be evaluated to determine their effect on splicing. We identified the rare variant c.863G>T (r.835_*3del, p.Gly279Glufs*5) in exon 7 of SMN1 in three patients affected with type I or type II SMA. Most of the SMN1 transcripts exhibited complete loss of exon 7 in vivo. The ex vivo splicing assay demonstrated that the variant disrupts inclusion of exon 7 (~85%) in the SMN1 mRNA; replacement with various bases yielded a variety of splicing effects in SMN1 and SMN2 pre-mRNA. The c.863G>T (r.835_*3del, p.Gly279Glufs*5) variant is located in a region that includes binding sites for multiple splicing factors including Tra2β1. Thus, the variant disrupts Tra2β1 binding, but does not affect binding of hnRNP A1. These findings demonstrate how rare variants influence pre-mRNA splicing of SMN and reveal the functional influence of c.863G>T (r.835_*3del, p.Gly279Glufs*5) variant in patients with SMA.European Journal of Human Genetics advance online publication, 30 September 2015; doi:10.1038/ejhg.2015.213.","corpus_id":22696110,"score":1},{"doc_id":"27489271","title":"Serine/Arginine-Rich Splicing Factor 3 and Heterogeneous Nuclear Ribonucleoprotein A1 Regulate Alternative RNA Splicing and Gene Expression of Human Papillomavirus 18 through Two Functionally Distinguishable cis Elements.","abstract":"UNLABELLED: Human papillomavirus 18 (HPV18) is the second most common oncogenic HPV type associated with cervical, anogenital, and oropharyngeal cancers. Like other oncogenic HPVs, HPV18 encodes two major (one early and one late) polycistronic pre-mRNAs that are regulated by alternative RNA splicing to produce a repertoire of viral transcripts for the expression of individual viral genes. However, RNA cis-regulatory elements and trans-acting factors contributing to HPV18 alternative RNA splicing remain unknown. In this study, an exonic splicing enhancer (ESE) in the nucleotide (nt) 3520 to 3550 region in the HPV18 genome was identified and characterized for promotion of HPV18 929^3434 splicing and E1^E4 production through interaction with SRSF3, a host oncogenic splicing factor differentially expressed in epithelial cells and keratinocytes. Introduction of point mutations in the SRSF3-binding site or knockdown of SRSF3 expression in cells reduces 929^3434 splicing and E1^E4 production but activates other, minor 929^3465 and 929^3506 splicing. Knockdown of SRSF3 expression also enhances the expression of E2 and L1 mRNAs. An exonic splicing silencer (ESS) in the HPV18 nt 612 to 639 region was identified as being inhibitory to the 233^416 splicing of HPV18 E6E7 pre-mRNAs via binding to hnRNP A1, a well-characterized, abundantly and ubiquitously expressed RNA-binding protein. Introduction of point mutations into the hnRNP A1-binding site or knockdown of hnRNP A1 expression promoted 233^416 splicing and reduced E6 expression. These data provide the first evidence that the alternative RNA splicing of HPV18 pre-mRNAs is subject to regulation by viral RNA cis elements and host trans-acting splicing factors. IMPORTANCE: Expression of HPV18 genes is regulated by alternative RNA splicing of viral polycistronic pre-mRNAs to produce a repertoire of viral early and late transcripts. RNA cis elements and trans-acting factors contributing to HPV18 alternative RNA splicing have been discovered in this study for the first time. The identified ESS at the E7 open reading frame (ORF) prevents HPV18 233^416 splicing in the E6 ORF through interaction with a host splicing factor, hnRNP A1, and regulates E6 and E7 expression of the early E6E7 polycistronic pre-mRNA. The identified ESE at the E1^E4 ORF promotes HPV18 929^3434 splicing of both viral early and late pre-mRNAs and E1^E4 production through interaction with SRSF3. This study provides important observations on how alternative RNA splicing of HPV18 pre-mRNAs is subject to regulation by viral RNA cis elements and host splicing factors and offers potential therapeutic targets to overcome HPV-related cancer.","corpus_id":6745667,"score":1},{"doc_id":"18203745","title":"The third RNA recognition motif of Drosophila ELAV protein has a role in multimerization.","abstract":"ELAV is a neuron-specific RNA-binding protein in Drosophila that is required for development and maintenance of neurons. ELAV regulates alternative splicing of Neuroglian and erect wing (ewg) transcripts, and has been shown to form a multimeric complex on the last ewg intron. The protein has three RNA recognition motifs (RRM1, 2 and 3) with a hinge region between RRM2 and 3. In this study, we used the yeast two-hybrid system to determine the multimerization domain of ELAV. Using deletion constructs, we mapped an interaction activity to a region containing most of RRM3. We found three conserved short sequences in RRM3 that were essential for the interaction, and also sufficient to give the interaction activity to RRM2 when introduced into it. In our in vivo functional assay, a mutation in one of the three sequences showed reduced activity in splicing regulation, underlining the functional importance of multimerization. However, RRM2 with the three RRM3 interaction sequences did not function as RRM3 in vivo, which suggested that multimerization is not the only function of RRM3. Our results are consistent with a model in which RRM3 serves as a bi-functional domain that interacts with both RNA and protein.","corpus_id":7152321,"score":0},{"doc_id":"18500819","title":"Solution structure of the second RNA recognition motif (RRM) domain of murine T cell intracellular antigen-1 (TIA-1) and its RNA recognition mode.","abstract":"T cell intracellular antigen-1 (TIA-1), an apoptosis promoting factor, functions as a splicing regulator for the Fas pre-mRNA. TIA-1 possesses three RNA recognition motifs (RRMs) and a glutamine-rich domain. The second RRM (RRM2) is necessary and sufficient for tight, sequence-specific binding to the uridine-rich sequences buried around the 5' splice sites. In the present study, we solved the solution structure of the murine TIA-1 RRM2 by heteronuclear-nuclear magnetic resonance spectroscopy. The TIA-1 RRM2 adopts the RRM fold (betaalphabetabetaalphabeta) and possesses an extra beta-strand between beta2 and beta3, which forms an additional beta-sheet with the C-terminal part of beta2. We refer to this structure as the beta2-beta2' beta-loop. Interestingly, this characteristic beta-loop structure is conserved among a number of RRMs, including the U2AF65 RRM2 and the Sex-lethal RRM1 and RRM2, which also bind to uridine-rich RNAs. Furthermore, we identified a new sequence motif in the beta2-beta2' beta-loop, the DxxT motif. Chemical shift perturbation analyses of both the main and side chains upon binding to the uridine pentamer RNA revealed that most of the beta-sheet surface, including the beta2-beta2' beta-loop, is involved in the RNA binding. An investigation of the chemical shift perturbation revealed similarity in the RNA recognition modes between the TIA-1 and U2AF65 RRMs.","corpus_id":24538172,"score":0},{"doc_id":"18794368","title":"The RNA binding protein hnRNP Q modulates the utilization of exon 7 in the survival motor neuron 2 (SMN2) gene.","abstract":"Spinal muscular atrophy (SMA) is a recessive neuromuscular disorder caused by the homozygous loss of the SMN1 gene. The human SMN2 gene has a C-to-T transition at position +6 of exon 7 and thus produces exon 7-skipping mRNAs. However, we observed an unexpectedly high level of exon 7-containing SMN2 transcripts as well as SMN protein in testis of smn(-/-) SMN2 transgenic mice. Using affinity chromatography, we identified several SMN RNA-associating proteins in mouse testis and human HeLa cells, including hnRNP Q. The major hnRNP Q isoform, Q1, directly bound SMN exon 7 in the vicinity of nucleotide +6. Overexpression of hnRNP Q1 promoted the inclusion of exon 7 in SMN2, probably by activating the use of its upstream 3' splice site. However, the minor isoforms Q2/Q3 could antagonize the activity of hnRNP Q1 and induced exon 7 exclusion. Intriguingly, enhanced exon 7 inclusion was also observed upon concomitant depletion of three hnRNP Q isoforms. Thus, differential expression of hnRNP Q isoforms may result in intricate control of SMN precursor mRNA splicing. Here, we demonstrate that hnRNP Q is a splicing modulator of SMN, further underscoring the potential of hnRNP Q as a therapeutic target for SMA.","corpus_id":7525641,"score":0},{"doc_id":"18806275","title":"hnRNP H enhances skipping of a nonfunctional exon P3A in CHRNA1 and a mutation disrupting its binding causes congenital myasthenic syndrome.","abstract":"In humans and great apes, CHRNA1 encoding the muscle nicotinic acetylcholine receptor alpha subunit carries an inframe exon P3A, the inclusion of which yields a nonfunctional alpha subunit. In muscle, the P3A(-) and P3A(+) transcripts are generated in a 1:1 ratio but the functional significance and regulation of the alternative splicing remain elusive. An intronic mutation (IVS3-8G>A), identified in a patient with congenital myasthenic syndrome, disrupts an intronic splicing silencer (ISS) and results in exclusive inclusion of the downstream P3A exon. We found that the ISS-binding splicing trans-factor was heterogeneous nuclear ribonucleoprotein (hnRNP) H and the mutation attenuated the affinity of hnRNP for the ISS approximately 100-fold. We next showed that direct placement of hnRNP H to the 3' end of intron 3 silences, and siRNA-mediated downregulation of hnRNP H enhances recognition of exon P3A. Analysis of the human genome suggested that the hnRNPH-binding UGGG motif is overrepresented close to the 3' ends of introns. Pursuing this clue, we showed that alternative exons of GRIP1, FAS, VPS13C and NRCAM are downregulated by hnRNP H. Our findings imply that the presence of the hnRNP H-binding motif close to the 3' end of an intron is an essential but underestimated splicing regulator of the downstream exon.","corpus_id":5898711,"score":0},{"doc_id":"19628962","title":"HnRNP C1/C2 may regulate exon 7 splicing in the spinal muscular atrophy gene SMN1.","abstract":"Spinal muscular atrophy (SMA) is caused by loss of SMN1. A nearly identical gene, SMN2, fails to compensate for the loss of SMN1 because SMN2 produces mainly an exon 7-skipped product. The +6C in SMN1 exon 7 proceeds to include exon 7 into mRNA, while the +6U in SMN2 causes skipping of exon 7. Here, approximately 45kD proteins bound to the SMN exon 7 RNA probe was found, and identified as hnRNP C1/C2. In gel-shift assay, hnRNP C1/C2 had a greater affinity for the RNA probe with +6C than for the RNA probe with +6U. In vitro splicing assay showed that anti-hnRNP C1/C2 antibody hampered splicing of SMN1 exon 7, but did not affect splicing of SMN2 exon 7. In conclusion, we showed the possibility that hnRNP C1/C2 enhanced SMN1 exon 7 splicing specifically.","corpus_id":7451984,"score":0},{"doc_id":"19946215","title":"HnRNP L-mediated regulation of mammalian alternative splicing by interference with splice site recognition.","abstract":"Heterogeneous nuclear ribonucleoprotein (hnRNP) L can regulate alternative mRNA splicing in diverse ways, binding to exonic or intronic sites and acting as either an activator or repressor. To investigate the mechanistic basis of hnRNP L-regulated alternative splicing, we focus here on two specific cases of hnRNP L-dependent splice site recognition. First, in the case of TJP1 our microarray data had suggested that exon 20 inclusion is regulated by hnRNP L as a repressor. Here we demonstrate by mutational analysis that exon skipping is mediated by a short silencer sequence consisting of three hnRNP L high-score binding motifs located upstream of the 3' splice site of the regulated exon. UV crosslinking and immunoprecipitation experiments showed that hnRNP L binding interferes with 3' splice site recognition by U2AF65. Second, SLC2A2 contains a CA-repeat sequence close to the 5' splice site of the regulated exon 4. Using psoralen crosslinking, we demonstrate that hnRNP L represses splicing by preventing 5' splice site recognition of the U1 snRNP. In sum, our data provide new insights into the mechanisms of how hnRNP L-bound to intronic sites-regulates exon recognition.","corpus_id":34378098,"score":0},{"doc_id":"20130820","title":"Combined use of MS2 and PP7 coat fusions shows that TIA-1 dominates hnRNP A1 for K-SAM exon splicing control.","abstract":"Splicing of the FGFR2 K-SAM exon is repressed by hnRNP A1 bound to the exon and activated by TIA-1 bound to the downstream intron. Both proteins are expressed similarly by cells whether they splice the exon or not, so it is important to know which one is dominant. To answer this question, we used bacteriophage PP7 and bacteriophage MS2 coat fusions to tether hnRNP A1 and TIA-1 to distinct sites on the same pre-mRNA molecule. hnRNP A1 fused to one coat protein was tethered to a K-SAM exon containing the corresponding coat protein's binding site. TIA-1 fused to the other coat protein was tethered to the downstream intron containing that coat protein's binding site. This led to efficient K-SAM exon splicing. Our results show that TIA-1 is dominant for K-SAM exon splicing control and validate the combined use of PP7 and MS2 coat proteins for studying posttranscriptional events.","corpus_id":18917709,"score":0},{"doc_id":"21398516","title":"Mechanistic control of carcinoembryonic antigen-related cell adhesion molecule-1 (CEACAM1) splice isoforms by the heterogeneous nuclear ribonuclear proteins hnRNP L, hnRNP A1, and hnRNP M.","abstract":"Carcinoembryonic antigen-related cell adhesion molecule-1 (CEACAM1) is expressed in a variety of cell types and is implicated in carcinogenesis. Alternative splicing of CEACAM1 pre-mRNA generates two cytoplasmic domain splice variants characterized by the inclusion (L-isoform) or exclusion (S-isoform) of exon 7. Here we show that the alternative splicing of CEACAM1 pre-mRNA is regulated by novel cis elements residing in exon 7. We report the presence of three exon regulatory elements that lead to the inclusion or exclusion of exon 7 CEACAM1 mRNA in ZR75 breast cancer cells. Heterologous splicing reporter assays demonstrated that the maintenance of authentic alternative splicing mechanisms were independent of the CEACAM1 intron sequence context. We show that forced expression of these exon regulatory elements could alter CEACAM1 splicing in HEK-293 cells. Using RNA affinity chromatography, three members of the heterogeneous nuclear ribonucleoprotein family (hnRNP L, hnRNP A1, and hnRNP M) were identified. RNA immunoprecipitation of hnRNP L and hnRNP A1 revealed a binding motif located central and 3' to exon 7, respectively. Depletion of hnRNP A1 or L by RNAi in HEK-293 cells promoted exon 7 inclusion, whereas overexpression led to exclusion of the variable exon. By contrast, overexpression of hnRNP M showed exon 7 inclusion and production of CEACAM1-L mRNA. Finally, stress-induced cytoplasmic accumulation of hnRNP A1 in MDA-MB-468 cells dynamically alters the CEACAM1-S:CEACAM1:L ratio in favor of the l-isoform. Thus, we have elucidated the molecular factors that control the mechanism of splice-site recognition in the alternative splicing regulation of CEACAM1.","corpus_id":25342291,"score":0},{"doc_id":"21743084","title":"Sequence determinants for the tandem recognition of UGU and CUG rich RNA elements by the two N--terminal RRMs of CELF1.","abstract":"CUGBP, Elav-like family member 1 (CELF1) is an RNA binding protein with important roles in the regulation of splicing, mRNA decay and translation. CELF1 contains three RNA recognition motifs (RRMs). We used gel retardation, gel filtration, isothermal titration calorimetry and NMR titration studies to investigate the recognition of RNA by the first two RRMs of CELF1. NMR shows that RRM1 is promiscuous in binding to both UGU and CUG repeat sequences with comparable chemical shift perturbations. In contrast, RRM2 shows greater selectivity for UGUU rather than CUG motifs. A construct (T187) containing both binding domains (RRM1 and RRM2) was systematically studied for interaction with tandem UGU RNA binding sites with different length linker sequences UGU(U)(x)UGU where x = 1-7. A single U spacer results in interactions only with RRM1, demonstrating both steric constraints in accommodating both RRMs simultaneously at adjacent sites, and also subtle differences in binding affinities between RRMs. However, high affinity co-operative binding (K(d) ~ 0.4 µM) is evident for RNA sequences with x = 2-4, but longer spacers (x ≥ 5) lead to a 10-fold reduction in affinity. Our analysis rationalizes the high affinity interaction of T187 with the 11mer GRE consensus regulatory sequence UGUUUGUUUGU and has significant consequences for the prediction of CELF1 binding sites.","corpus_id":15897106,"score":0},{"doc_id":"22154808","title":"Three RNA recognition motifs participate in RNA recognition and structural organization by the pro-apoptotic factor TIA-1.","abstract":"T-cell intracellular antigen-1 (TIA-1) regulates developmental and stress-responsive pathways through distinct activities at the levels of alternative pre-mRNA splicing and mRNA translation. The TIA-1 polypeptide contains three RNA recognition motifs (RRMs). The central RRM2 and C-terminal RRM3 associate with cellular mRNAs. The N-terminal RRM1 enhances interactions of a C-terminal Q-rich domain of TIA-1 with the U1-C splicing factor, despite linear separation of the domains in the TIA-1 sequence. Given the expanded functional repertoire of the RRM family, it was unknown whether TIA-1 RRM1 contributes to RNA binding as well as documented protein interactions. To address this question, we used isothermal titration calorimetry and small-angle X-ray scattering to dissect the roles of the TIA-1 RRMs in RNA recognition. Notably, the fas RNA exhibited two binding sites with indistinguishable affinities for TIA-1. Analyses of TIA-1 variants established that RRM1 was dispensable for binding AU-rich fas sites, yet all three RRMs were required to bind a polyU RNA with high affinity. Small-angle X-ray scattering analyses demonstrated a \"V\" shape for a TIA-1 construct comprising the three RRMs and revealed that its dimensions became more compact in the RNA-bound state. The sequence-selective involvement of TIA-1 RRM1 in RNA recognition suggests a possible role for RNA sequences in regulating the distinct functions of TIA-1. Further implications for U1-C recruitment by the adjacent TIA-1 binding sites of the fas pre-mRNA and the bent TIA-1 shape, which organizes the N- and C-termini on the same side of the protein, are discussed.","corpus_id":25245338,"score":0},{"doc_id":"22402488","title":"HnRNP L and L-like cooperate in multiple-exon regulation of CD45 alternative splicing.","abstract":"CD45 encodes a trans-membrane protein-tyrosine phosphatase expressed in diverse cells of the immune system. By combinatorial use of three variable exons 4-6, isoforms are generated that differ in their extracellular domain, thereby modulating phosphatase activity and immune response. Alternative splicing of these CD45 exons involves two heterogeneous ribonucleoproteins, hnRNP L and its cell-type specific paralog hnRNP L-like (LL). To address the complex combinatorial splicing of exons 4-6, we investigated hnRNP L/LL protein expression in human B-cells in relation to CD45 splicing patterns, applying RNA-Seq. In addition, mutational and RNA-binding analyses were carried out in HeLa cells. We conclude that hnRNP LL functions as the major CD45 splicing repressor, with two CA elements in exon 6 as its primary target. In exon 4, one element is targeted by both hnRNP L and LL. In contrast, exon 5 was never repressed on its own and only co-regulated with exons 4 and 6. Stable L/LL interaction requires CD45 RNA, specifically exons 4 and 6. We propose a novel model of combinatorial alternative splicing: HnRNP L and LL cooperate on the CD45 pre-mRNA, bridging exons 4 and 6 and looping out exon 5, thereby achieving full repression of the three variable exons.","corpus_id":9572984,"score":0},{"doc_id":"22684629","title":"Control of alternative splicing by forskolin through hnRNP K during neuronal differentiation.","abstract":"The molecular basis of cell signal-regulated alternative splicing at the 3' splice site remains largely unknown. We isolated a protein kinase A-responsive ribonucleic acid (RNA) element from a 3' splice site of the synaptosomal-associated protein 25 (Snap25) gene for forskolin-inhibited splicing during neuronal differentiation of rat pheochromocytoma PC12 cells. The element binds specifically to heterogeneous nuclear ribonucleo protein (hnRNP) K in a phosphatase-sensitive way, which directly competes with the U2 auxiliary factor U2AF65, an essential component of early spliceosomes. Transcripts with similarly localized hnRNP K target motifs upstream of alternative exons are enriched in genes often associated with neurological diseases. We show that such motifs upstream of the Runx1 exon 6 also bind hnRNP K, and importantly, hnRNP K is required for forskolin-induced repression of the exon. Interestingly, this exon encodes the peptide domain that determines the switch of the transcriptional repressor/activator activity of Runx1, a change known to be critical in specifying neuron lineages. Consistent with an important role of the target genes in neurons, knocking down hnRNP K severely disrupts forskolin-induced neurite growth. Thus, through hnRNP K, the neuronal differentiation stimulus forskolin targets a critical 3' splice site component of the splicing machinery to control alternative splicing of crucial genes. This also provides a regulated direct competitor of U2AF65 for cell signal control of 3' splice site usage.","corpus_id":12926386,"score":0},{"doc_id":"23704325","title":"hnRNP A1 and secondary structure coordinate alternative splicing of Mag.","abstract":"Myelin-associated glycoprotein (MAG) is a major component of myelin in the vertebrate central nervous system. MAG is present in the periaxonal region of the myelin structure, where it interacts with neuronal proteins to inhibit axon outgrowth and protect neurons from degeneration. Two alternatively spliced isoforms of Mag mRNA have been identified. The mRNA encoding the shorter isoform, known as S-MAG, contains a termination codon in exon 12, while the mRNA encoding the longer isoform, known as L-MAG, skips exon 12 and produces a protein with a longer C-terminal region. L-MAG is required in the central nervous system. How inclusion of Mag exon 12 is regulated is not clear. In a previous study, we showed that heteronuclear ribonucleoprotein A1 (hnRNP A1) contributes to Mag exon 12 skipping. Here, we show that hnRNP A1 interacts with an element that overlaps the 5' splice site of Mag exon 12. The element has a reduced ability to interact with the U1 snRNP compared with a mutant that improves the splice site consensus. An evolutionarily conserved secondary structure is present surrounding the element. The structure modulates interaction with both hnRNP A1 and U1. Analysis of splice isoforms produced from a series of reporter constructs demonstrates that the hnRNP A1-binding site and the secondary structure both contribute to exclusion of Mag exon 12.","corpus_id":2384706,"score":0},{"doc_id":"23782695","title":"Crystal structures and RNA-binding properties of the RNA recognition motifs of heterogeneous nuclear ribonucleoprotein L: insights into its roles in alternative splicing regulation.","abstract":"Heterogeneous nuclear ribonucleoprotein L (hnRNP L) is an abundant RNA-binding protein implicated in many bioprocesses, including pre-mRNA processing, mRNA export of intronless genes, internal ribosomal entry site-mediated translation, and chromatin modification. It contains four RNA recognition motifs (RRMs) that bind with CA repeats or CA-rich elements. In this study, surface plasmon resonance spectroscopy assays revealed that all four RRM domains contribute to RNA binding. Furthermore, we elucidated the crystal structures of hnRNP L RRM1 and RRM34 at 2.0 and 1.8 Å, respectively. These RRMs all adopt the typical β1α1β2β3α2β4 topology, except for an unusual fifth β-strand in RRM3. RRM3 and RRM4 interact intimately with each other mainly through helical surfaces, leading the two β-sheets to face opposite directions. Structure-based mutations and surface plasmon resonance assay results suggested that the β-sheets of RRM1 and RRM34 are accessible for RNA binding. FRET-based gel shift assays (FRET-EMSA) and steady-state FRET assays, together with cross-linking and dynamic light scattering assays, demonstrated that hnRNP L RRM34 facilitates RNA looping when binding to two appropriately separated binding sites within the same target pre-mRNA. EMSA and isothermal titration calorimetry binding studies with in vivo target RNA suggested that hnRNP L-mediated RNA looping may occur in vivo. Our study provides a mechanistic explanation for the dual functions of hnRNP L in alternative splicing regulation as an activator or repressor.","corpus_id":30641280,"score":0},{"doc_id":"23863836","title":"HnRNP A1 controls a splicing regulatory circuit promoting mesenchymal-to-epithelial transition.","abstract":"Epithelial-to-mesenchymal transition (EMT) is an embryonic program used by cancer cells to acquire invasive capabilities becoming metastatic. ΔRon, a constitutively active isoform of the Ron tyrosine kinase receptor, arises from skipping of Ron exon 11 and provided the first example of an alternative splicing variant causatively linked to the activation of tumor EMT. Splicing of exon 11 is controlled by two adjacent regulatory elements, a silencer and an enhancer of splicing located in exon 12. The alternative splicing factor and oncoprotein SRSF1 directly binds to the enhancer, induces the production of ΔRon and activates EMT leading to cell locomotion. Interestingly, we now find an important role for hnRNP A1 in controlling the activity of the Ron silencer. HnRNP A1 is able to antagonize the binding of SRSF1 and prevent exon skipping. Notably, hnRNP A1, by inhibiting the production of ΔRon, activates the reversal program, namely the mesenchymal-to-epithelial transition, which instead occurs at the final metastasis sites. Also, hnRNP A1 affects Ron splicing by regulating the expression level of hnRNP A2/B1, which similarly to SRSF1 can promote ΔRon production. These results shed light on how splicing regulation contributes to the tumor progression and provide potential targets to develop anticancer therapies.","corpus_id":6377441,"score":0},{"doc_id":"24121633","title":"HnRNP L and hnRNP LL antagonistically modulate PTB-mediated splicing suppression of CHRNA1 pre-mRNA.","abstract":"CHRNA1 gene, encoding the muscle nicotinic acetylcholine receptor alpha subunit, harbors an inframe exon P3A. Inclusion of exon P3A disables assembly of the acetylcholine receptor subunits. A single nucleotide mutation in exon P3A identified in congenital myasthenic syndrome causes exclusive inclusion of exon P3A. The mutation gains a de novo binding affinity for a splicing enhancing RNA-binding protein, hnRNP LL, and displaces binding of a splicing suppressing RNA-binding protein, hnRNP L. The hnRNP L binds to another splicing repressor PTB through the proline-rich region and promotes PTB binding to the polypyrimidine tract upstream of exon P3A, whereas hnRNP LL lacking the proline-rich region cannot bind to PTB. Interaction of hnRNP L with PTB inhibits association of U2AF(65) and U1 snRNP with the upstream and downstream of P3A, respectively, which causes a defect in exon P3A definition. HnRNP L and hnRNP LL thus antagonistically modulate PTB-mediated splicing suppression of exon P3A.","corpus_id":5562194,"score":0},{"doc_id":"24533984","title":"hnRNP M facilitates exon 7 inclusion of SMN2 pre-mRNA in spinal muscular atrophy by targeting an enhancer on exon 7.","abstract":"Spinal muscular atrophy (SMA) is an autosomal recessive genetic disease, which causes death of motor neurons in the anterior horn of the spinal cord. Genetic cause of SMA is the deletion or mutation of SMN1 gene, which encodes the SMN protein. Although SMA patients include SMN2 gene, a duplicate of SMN1 gene, predominant production of exon 7 skipped isoform from SMN2 pre-mRNA, fails to rescue SMA patients. Here we show that hnRNP M, a member of hnRNP protein family, when knocked down, promotes exon 7 skipping of both SMN2 and SMN1 pre-mRNA. By contrast, overexpression of hnRNP M promotes exon 7 inclusion of both SMN2 and SMN1 pre-mRNA. Significantly, hnRNP M promotes exon 7 inclusion in SMA patient cells. Thus, we conclude that hnRNP M promotes exon 7 inclusion of both SMN1 and SMN2 pre-mRNA. We also demonstrate that hnRNP M contacts an enhancer on exon 7, which was previously shown to provide binding site for tra2β. We present evidence that hnRNP M and tra2β contact overlapped sequence on exon 7 but with slightly different RNA sequence requirements. In addition, hnRNP M promotes U2AF65 recruitment on the flanking intron of exon 7. We conclude that hnRNP M promotes exon 7 inclusion of SMN1 and SMN2 pre-mRNA through targeting an enhancer on exon 7 through recruiting U2AF65. Our results provide a clue that hnRNP M is a potential therapeutic target for SMA.","corpus_id":205820651,"score":0},{"doc_id":"24682828","title":"Structure, dynamics and RNA binding of the multi-domain splicing factor TIA-1.","abstract":"Alternative pre-messenger ribonucleic acid (pre-mRNA) splicing is an essential process in eukaryotic gene regulation. The T-cell intracellular antigen-1 (TIA-1) is an apoptosis-promoting factor that modulates alternative splicing of transcripts, including the pre-mRNA encoding the membrane receptor Fas. TIA-1 is a multi-domain ribonucleic acid (RNA) binding protein that recognizes poly-uridine tract RNA sequences to facilitate 5' splice site recognition by the U1 small nuclear ribonucleoprotein (snRNP). Here, we characterize the RNA interaction and conformational dynamics of TIA-1 by nuclear magnetic resonance (NMR), isothermal titration calorimetry (ITC) and small angle X-ray scattering (SAXS). Our NMR-derived solution structure of TIA-1 RRM2-RRM3 (RRM2,3) reveals that RRM2 adopts a canonical RNA recognition motif (RRM) fold, while RRM3 is preceded by an non-canonical helix α0. NMR and SAXS data show that all three RRMs are largely independent structural modules in the absence of RNA, while RNA binding induces a compact arrangement. RRM2,3 binds to pyrimidine-rich FAS pre-mRNA or poly-uridine (U9) RNA with nanomolar affinities. RRM1 has little intrinsic RNA binding affinity and does not strongly contribute to RNA binding in the context of RRM1,2,3. Our data unravel the role of binding avidity and the contributions of the TIA-1 RRMs for recognition of pyrimidine-rich RNAs.","corpus_id":8496882,"score":0},{"doc_id":"25216038","title":"Structural and mechanistic insights into poly(uridine) tract recognition by the hnRNP C RNA recognition motif.","abstract":"HnRNP C is a ubiquitous RNA regulatory factor and the principal constituent of the nuclear hnRNP core particle. The protein contains one amino-terminal RNA recognition motif (RRM) known to bind uridine (U)-rich sequences. This work provides a molecular and mechanistic understanding of this interaction. We solved the solution structures of the RRM in complex with poly(U) oligomers of five and seven nucleotides. The five binding pockets of RRM recognize uridines with an unusual 5'-to-3' gradient of base selectivity. The target recognition is therefore strongly sensitive to base clustering, explaining the preference for contiguous uridine tracts. Using a novel approach integrating the structurally derived recognition consensus of the RRM with a thermodynamic description of its multi-register binding, we modeled the saturation of cellular uridine tracts by this protein. The binding pattern is remarkably consistent with the experimentally observed transcriptome-wide cross-link distribution of the full-length hnRNP C on short uridine tracts. This result re-establishes the RRM as the primary RNA-binding domain of the hnRNP C tetramer and provides a proof of concept for interpreting high-throughput interaction data using structural approaches.","corpus_id":27530107,"score":0},{"doc_id":"25623890","title":"hnRNP L inhibits CD44 V10 exon splicing through interacting with its upstream intron.","abstract":"CD44 is a complex cell adhesion molecule that mediates communication and adhesion between adjacent cells as well as between cells and the extracellular matrix. CD44 pre-mRNA produces various mRNA isoforms through alternative splicing of 20 exons, among which exons 1-5 (C1-C5) and 16-20 (C6-C10) are constant exons, whereas exons 6-15 (V1-V10) are variant exons. CD44 V10 exon has important roles in breast tumor progression and Hodgkin lymphoma. Here we show that increased expression of hnRNP L inhibits V10 exon splicing of CD44 pre-mRNA, whereas reduced expression of hnRNP L promotes V10 exon splicing. In addition, hnRNP L also promotes V10 splicing of endogenous CD44 pre-mRNA. Through mutation analysis, we demonstrate that the effects of hnRNP L on V10 splicing are abolished when the CA-rich sequence on the upstream intron of V10 exon is disrupted. However, hnRNP L effects are stronger if more CA-repeats are provided. Furthermore, we show that hnRNP L directly contacts the CA-rich sequence. Importantly, we provide evidences that hnRNP L inhibits U2AF65 binding on the upstream Py tract of V10 exon. Our results reveal that hnRNP L is a new regulator for CD44 V10 exon splicing.","corpus_id":5403304,"score":0},{"doc_id":"26101706","title":"HnRNP A1 tethers KSRP to an exon splicing silencer that inhibits an erythroid-specific splicing event in PU.1-induced erythroleukemia.","abstract":"Exon 16 inclusion is a critical splicing event that triggers the production of a functional protein 4.1R in mature normal erythroblasts, and is obviated in PU.1-induced erythroleukemia cells. Exon 16 contains an exonic splicing silencer (ESS16) that interacts with hnRNP A/B in heterologous cell context. We here show that ESS16 promotes the recruitment of a protein complex containing hnRNP A1 and a 79-kDa protein in nuclear extracts from either proliferative erythroleukemia cells or cells induced to terminal differentiation. By using 2D gel fractionation and mass spectrometry, we unambiguously identified KSRP as the 79-kDa component interacting with ESS16. Furthermore, we show that KSRP slightly decreases in erythroleukemia cells induced to terminal erythroid differentiation. Yet, KSRP inducible knockdown, through stable transfection of small hairpin KSRP RNA, did not alter exon 16 splicing, suggesting that KSRP alone does not modulate the splicing event. Interestingly, absence of hnRNP A1 prevented KSRP from binding to ESS16. Reciprocally, KSRP interaction with ESS16 was recovered when hnRNP A1 expression is restored in hnRNP A1-null cells. Collectively, this study establishes that hnRNPA1 is part of a KSRP-containing RNP complex, and emphasizes that, aside from its function in AU-rich element-mediated mRNA decay and its role in microRNA biogenesis, KSRP associates with hnRNP A1 to bind an ESS. These findings further support the role of members of the KH-domain protein family in organizing large RNA-protein complex formation, rather than primarily in modulating specific splicing events.","corpus_id":23325791,"score":0},{"doc_id":"26545814","title":"Biochemical identification of new proteins involved in splicing repression at the Drosophila P-element exonic splicing silencer.","abstract":"Splicing of the Drosophila P-element third intron (IVS3) is repressed in somatic tissues due to the function of an exonic splicing silencer (ESS) complex present on the 5' exon RNA. To comprehensively characterize the mechanisms of this alternative splicing regulation, we used biochemical fractionation and affinity purification to isolate the silencer complex assembled in vitro and identify the constituent proteins by mass spectrometry. Functional assays using splicing reporter minigenes identified the proteins hrp36 and hrp38 and the cytoplasmic poly(A)-binding protein PABPC1 as novel functional components of the splicing silencer. hrp48, PSI, and PABPC1 have high-affinity RNA-binding sites on the P-element IVS3 5' exon, whereas hrp36 and hrp38 proteins bind with low affinity to the P-element silencer RNA. RNA pull-down and immobilized protein assays showed that hrp48 protein binding to the silencer RNA can recruit hrp36 and hrp38. These studies identified additional components that function at the P-element ESS and indicated that proteins with low-affinity RNA-binding sites can be recruited in a functional manner through interactions with a protein bound to RNA at a high-affinity binding site. These studies have implications for the role of heterogeneous nuclear ribonucleoproteins (hnRNPs) in the control of alternative splicing at cis-acting regulatory sites.","corpus_id":13608186,"score":0},{"doc_id":"26919236","title":"Heterogeneous nuclear ribonucleoproteins A1 and A2 modulate expression of Tid1 isoforms and EGFR signaling in non-small cell lung cancer.","abstract":"The Tid1 protein is a DnaJ co-chaperone that has two alternative splicing isoforms: Tid1 long form (Tid1-L) and Tid1 short form (Tid1-S). Recent studies have shown that Tid1-L functions as a tumor suppressor by decreasing EGFR signaling in various cancers, including head and neck cancer and non-small cell lung cancer (NSCLC). However, the molecular mechanism responsible for regulating the alternative splicing of Tid1 is not yet known. Two splicing factors, heterogeneous nuclear ribonucleoproteins (hnRNP) A1 and A2, participate in alternative splicing and are known to be overexpressed in lung cancers. In this work, we examined if hnRNP A1 and A2 could regulate the alternative splicing of Tid1 to modulate tumorigenesis in NSCLC. We report that RNAi-mediated depletion of both hnRNP A1/A2 (but not single depletion of either) increased Tid1-L expression, inhibited cell proliferation and attenuated EGFR signaling. Analyses of the expression levels of hnRNP A1, hnRNP A2, EGFR and Tid1-L in NSCLC tissues revealed that hnRNP A1 and A2 are positively correlated with EGFR, but negatively correlated with Tid1-L. NSCLC patients with high-level expression of hnRNP A1, hnRNP A2 and EGFR combined with low-level expression of Tid1-L were associated with poor overall survival. Taken together, our results suggest that hnRNP A1 or A2 are both capable of facilitating the alternative splicing of exon 11 in the Tid1 pre-mRNA, thereby suppressing the expression of Tid1-L and allowing EGFR-related signaling to facilitate NSCLC tumorigenesis.","corpus_id":27438702,"score":0},{"doc_id":"27437398","title":"Crystal Structure of the N-Terminal RNA Recognition Motif of mRNA Decay Regulator AUF1.","abstract":"AU-rich element binding/degradation factor 1 (AUF1) plays a role in destabilizing mRNAs by forming complexes with AU-rich elements (ARE) in the 3'-untranslated regions. Multiple AUF1-ARE complexes regulate the translation of encoded products related to the cell cycle, apoptosis, and inflammation. AUF1 contains two tandem RNA recognition motifs (RRM) and a Gln- (Q-) rich domain in their C-terminal region. To observe how the two RRMs are involved in recognizing ARE, we obtained the AUF1-p37 protein covering the two RRMs. However, only N-terminal RRM (RRM1) was crystallized and its structure was determined at 1.7 Å resolution. It appears that the RRM1 and RRM2 separated before crystallization. To demonstrate which factors affect the separate RRM1-2, we performed limited proteolysis using trypsin. The results indicated that the intact proteins were cleaved by unknown proteases that were associated with them prior to crystallization. In comparison with each of the monomers, the conformations of the β2-β3 loops were highly variable. Furthermore, a comparison with the RRM1-2 structures of HuR and hnRNP A1 revealed that a dimer of RRM1 could be one of the possible conformations of RRM1-2. Our data may provide a guidance for further structural investigations of AUF1 tandem RRM repeat and its mode of ARE binding.","corpus_id":18607490,"score":0},{"doc_id":"28084329","title":"SPSB1-mediated HnRNP A1 ubiquitylation regulates alternative splicing and cell migration in EGF signaling.","abstract":"Extracellular signals have been shown to impact on alternative pre-mRNA splicing; however, the molecular mechanisms and biological significance of signal-induced splicing regulation remain largely unknown. Here, we report that epidermal growth factor (EGF) induces splicing changes through ubiquitylation of a well-known splicing regulator, hnRNP A1. EGF signaling upregulates an E3 ubiquitin (Ub) ligase adaptor, SPRY domain-containing SOCS box protein 1 (SPSB1), which recruits Elongin B/C-Cullin complexes to conjugate lysine 29-linked polyUb chains onto hnRNP A1. Importantly, SPSB1 and ubiquitylation of hnRNP A1 have a critical role in EGF-driven cell migration. Mechanistically, EGF-induced ubiquitylation of hnRNP A1 together with the activation of SR protein kinases (SRPKs) results in the upregulation of a Rac1 splicing isoform, Rac1b, to promote cell motility. These findings unravel a novel crosstalk between protein ubiquitylation and alternative splicing in EGF/EGF receptor signaling, and identify a new EGF/SPSB1/hnRNP A1/Rac1 axis in modulating cell migration, which may have important implications for cancer treatment.","corpus_id":19109215,"score":0},{"doc_id":"28119102","title":"Suppression of 5' splice-sites through multiple exonic motifs by hnRNP L.","abstract":"Selection of 5' splice-sites (5'SS) in alternative splicing plays an important role in gene regulation. Although regulatory mechanisms of heterogeneous nuclear ribonucleoprotein L (hnRNP L), a well-known splicing regulatory protein, have been studied in a substantial level, its role in 5'SS selection is not thoroughly defined. By using a KLF6 pre-mRNA alternative splicing model, we demonstrate in this report that hnRNP L inhibits proximal 5'SS but promotes two consecutive distal 5'SS splicing, antagonizing SRSF1 roles in KLF6 pre-mRNA splicing. In addition, three consecutive CA-rich sequences in a CA cassette immediately upstream of the proximal 5'SS are all required for hnRNP L functions. Importantly, the CA-cassette locations on the proximal exon do not affect hnRNP L roles. We further show that the proximal 5'SS but not the two distal 5'SSs are essential for hnRNP L activities. Notably, in a Bcl-x pre-mRNA model that contains two alternative 5'SS but includes CA-rich elements at distal exon, we demonstrate that hnRNP L also suppresses nearby 5'SS activation. Taken together, we conclude that hnRNP L suppresses 5'SS selection through multiple exonic motifs.","corpus_id":35617076,"score":0},{"doc_id":"28368279","title":"Crystal structure of the human heterogeneous ribonucleoprotein A18 RNA-recognition motif.","abstract":"The heterogeneous ribonucleoprotein A18 (hnRNP A18) is upregulated in hypoxic regions of various solid tumors and promotes tumor growth via the coordination of mRNA transcripts associated with pro-survival genes. Thus, hnRNP A18 represents an important therapeutic target in tumor cells. Presented here is the first X-ray crystal structure to be reported for the RNA-recognition motif of hnRNP A18. By comparing this structure with those of homologous RNA-binding proteins (i.e. hnRNP A1), three residues on one face of an antiparallel β-sheet (Arg48, Phe50 and Phe52) and one residue in an unstructured loop (Arg41) were identified as likely to be involved in protein-nucleic acid interactions. This structure helps to serve as a foundation for biophysical studies of this RNA-binding protein and structure-based drug-design efforts for targeting hnRNP A18 in cancer, such as malignant melanoma, where hnRNP A18 levels are elevated and contribute to disease progression.","corpus_id":4544901,"score":0},{"doc_id":"28379442","title":"An RRM-ZnF RNA recognition module targets RBM10 to exonic sequences to promote exon exclusion.","abstract":"RBM10 is an RNA-binding protein that plays an essential role in development and is frequently mutated in the context of human disease. RBM10 recognizes a diverse set of RNA motifs in introns and exons and regulates alternative splicing. However, the molecular mechanisms underlying this seemingly relaxed sequence specificity are not understood and functional studies have focused on 3΄ intronic sites only. Here, we dissect the RNA code recognized by RBM10 and relate it to the splicing regulatory function of this protein. We show that a two-domain RRM1-ZnF unit recognizes a GGA-centered motif enriched in RBM10 exonic sites with high affinity and specificity and test that the interaction with these exonic sequences promotes exon skipping. Importantly, a second RRM domain (RRM2) of RBM10 recognizes a C-rich sequence, which explains its known interaction with the intronic 3΄ site of NUMB exon 9 contributing to regulation of the Notch pathway in cancer. Together, these findings explain RBM10's broad RNA specificity and suggest that RBM10 functions as a splicing regulator using two RNA-binding units with different specificities to promote exon skipping.","corpus_id":8729390,"score":0},{"doc_id":"29450990","title":"Splicing Site Recognition by Synergy of Three Domains in Splicing Factor RBM10.","abstract":"Splicing factor RBM10 and its close homologues RBM5 and RBM6 govern the splicing of oncogenes such as Fas, NUMB, and Bcl-X. The molecular architecture of these proteins includes zinc fingers (ZnFs) and RNA recognition motifs (RRMs). Three of these domains in RBM10 that constitute the RNA binding part of this splicing factor were found to individually bind RNAs with micromolar affinities. It was thus of interest to further investigate the structural basis of the well-documented high-affinity RNA recognition by RMB10. Here, we investigated RNA binding by combinations of two or three of these domains and discovered that a polypeptide containing RRM1, ZnF1, and RRM2 connected by their natural linkers recognizes a specific sequence of the Fas exon 6 mRNA with an affinity of 20 nM. Nuclear magnetic resonance structures of the RBM10 domains RRM1 and ZnF1 and the natural V354del isoform of RRM2 further confirmed that the interactions with RNA are driven by canonical RNA recognition elements. The well-known high-fidelity RNA splice site recognition by RBM10, and probably by RBM5 and RBM6, can thus be largely rationalized by a cooperative binding action of RRM and ZnF domains.","corpus_id":3855285,"score":0},{"doc_id":"29518215","title":"Molecular basis of titin exon exclusion by RBM20 and the novel titin splice regulator PTB4.","abstract":"RNA-binding motif protein 20 (RBM20) is a cardiac splice regulator that adapts cardiac filling via its diverse substrates-including the sarcomeric protein titin. The molecular basis and regulation of RBM20-dependent exon exclusion are largely unknown. In tissue culture experiments, we show that the combination of RNA recognition motif (RRM) and C-terminus is necessary and sufficient for RBM20 activity, indicating an important function of the ZnF2 domain in splicing repression. Using splice reporter and in vitro binding assays targeting titin exons 241-243, we identified a minimal genomic segment that is necessary for RBM20-mediated splicing repression of the alternative exon. Here, RBM20 binds the cluster containing most RBM20 binding motifs through its RRM domain and represses the upstream and downstream introns. For subsequent exon exclusion, specific regions upstream, downstream and within the alternative exon 242 are required. Regulation of exon exclusion involves PTB4 as a novel titin splice regulator, which counteracts RBM20 repressor activity in HEK293 cells. Together, these mechanistic insights into the regulation and action of RBM20 and PTB4 provide a basis for the future development of RBM20 modulators that adapt titin elasticity in cardiac disease.","corpus_id":3770163,"score":0},{"doc_id":"29581412","title":"HnRNP L represses cryptic exons.","abstract":"The fidelity of RNA splicing is regulated by a network of splicing enhancers and repressors, although the rules that govern this process are not yet fully understood. One mechanism that contributes to splicing fidelity is the repression of nonconserved cryptic exons by splicing factors that recognize dinucleotide repeats. We previously identified that TDP-43 and PTBP1/PTBP2 are capable of repressing cryptic exons utilizing UG and CU repeats, respectively. Here we demonstrate that hnRNP L (HNRNPL) also represses cryptic exons by utilizing exonic CA repeats, particularly near the 5'SS. We hypothesize that hnRNP L regulates CA repeat repression for both cryptic exon repression and developmental processes such as T cell differentiation.","corpus_id":4349626,"score":0}],"string":"[\n {\n \"doc_id\": \"18371932\",\n \"title\": \"Antisense masking of an hnRNP A1/A2 intronic splicing silencer corrects SMN2 splicing in transgenic mice.\",\n \"abstract\": \"Survival of motor neuron 2, centromeric (SMN2) is a gene that modifies the severity of spinal muscular atrophy (SMA), a motor-neuron disease that is the leading genetic cause of infant mortality. Increasing inclusion of SMN2 exon 7, which is predominantly skipped, holds promise to treat or possibly cure SMA; one practical strategy is the disruption of splicing silencers that impair exon 7 recognition. By using an antisense oligonucleotide (ASO)-tiling method, we systematically screened the proximal intronic regions flanking exon 7 and identified two intronic splicing silencers (ISSs): one in intron 6 and a recently described one in intron 7. We analyzed the intron 7 ISS by mutagenesis, coupled with splicing assays, RNA-affinity chromatography, and protein overexpression, and found two tandem hnRNP A1/A2 motifs within the ISS that are responsible for its inhibitory character. Mutations in these two motifs, or ASOs that block them, promote very efficient exon 7 inclusion. We screened 31 ASOs in this region and selected two optimal ones to test in human SMN2 transgenic mice. Both ASOs strongly increased hSMN2 exon 7 inclusion in the liver and kidney of the transgenic animals. Our results show that the high-resolution ASO-tiling approach can identify cis-elements that modulate splicing positively or negatively. Most importantly, our results highlight the therapeutic potential of some of these ASOs in the context of SMA.\",\n \"corpus_id\": 269375,\n \"score\": 2\n },\n {\n \"doc_id\": \"19667073\",\n \"title\": \"Cooperative-binding and splicing-repressive properties of hnRNP A1.\",\n \"abstract\": \"hnRNP A1 binds to RNA in a cooperative manner. Initial hnRNP A1 binding to an exonic splicing silencer at the 3' end of human immunodeficiency virus type 1 (HIV-1) tat exon 3, which is a high-affinity site, is followed by cooperative spreading in a 3'-to-5' direction. As hnRNP A1 propagates toward the 5' end of the exon, it antagonizes binding of a serine/arginine-rich (SR) protein to an exonic splicing enhancer, thereby inhibiting splicing at that exon's alternative 3' splice site. tat exon 3 and the preceding intron of HIV-1 pre-mRNA can fold into an elaborate RNA secondary structure in solution, which could potentially influence hnRNP A1 binding. We report here that hnRNP A1 binding and splicing repression can occur on an unstructured RNA. Moreover, hnRNP A1 can effectively unwind an RNA hairpin upon binding, displacing a bound protein. We further show that hnRNP A1 can also spread in a 5'-to-3' direction, although when initial binding takes place in the middle of an RNA, spreading preferentially proceeds in a 3'-to-5' direction. Finally, when two distant high-affinity sites are present on the same RNA, they facilitate cooperative spreading of hnRNP A1 between the two sites.\",\n \"corpus_id\": 206830155,\n \"score\": 2\n },\n {\n \"doc_id\": \"20947024\",\n \"title\": \"Structural insights into RNA recognition by the alternate-splicing regulator CUG-binding protein 1.\",\n \"abstract\": \"CUG-binding protein 1 (CUGBP1) regulates multiple aspects of nuclear and cytoplasmic mRNA processing, with implications for onset of myotonic dystrophy. CUGBP1 harbors three RRM domains and preferentially targets UGU-rich mRNA elements. We describe crystal structures of CUGBP1 RRM1 and tandem RRM1/2 domains bound to RNAs containing tandem UGU(U/G) elements. Both RRM1 in RRM1-RNA and RRM2 in RRM1/2-RNA complexes use similar principles to target UGU(U/G) elements, with recognition mediated by face-to-edge stacking and water-mediated hydrogen-bonding networks. The UG step adopts a left-handed Z-RNA conformation, with the syn guanine recognized through Hoogsteen edge-protein backbone hydrogen-bonding interactions. NMR studies on the RRM1/2-RNA complex establish that both RRM domains target tandem UGUU motifs in solution, whereas filter-binding assays identify a preference for recognition of GU over AU or GC steps. We discuss the implications of CUGBP1-mediated targeting and sequestration of UGU(U/G) elements on pre-mRNA alternative-splicing regulation, translational regulation, and mRNA decay.\",\n \"corpus_id\": 30900930,\n \"score\": 2\n },\n {\n \"doc_id\": \"21120954\",\n \"title\": \"SMN2 exon 7 splicing is inhibited by binding of hnRNP A1 to a common ESS motif that spans the 3' splice site.\",\n \"abstract\": \"Spinal Muscular Atrophy is caused by homozygous loss of SMN1 with phenotypic modulation by SMN2. SMN2 expresses only limited amounts of full-length transcript due to skipping of exon 7 caused by disruption of an SF2/ASF binding ESE. Additionally, hnRNP A1 has been reported to inhibit inclusion of SMN2 exon 7. We previously reported high similarity between the sequence spanning the 3' ss of SMN1 and SMN2 exon 7 and an hnRNP A1 binding ESS, which regulates MCAD exon 5 splicing. We show here that this 3' ss motif indeed functions as a crucial hnRNP A1 binding ESS, which inhibits inclusion of SMN1/2 exon 7 and is antagonized by the SMN1 ESE, but not by the inactive SMN2 sequence. Pull-down experiments revealed a specific interaction between hnRNP A1 and the 3' ss AG-dinucleotide, which could be disrupted by mutations shown to improve splicing in reporter minigenes. Genomic analyses revealed that in the human genome, 3' ss matching the SMN1/2 ESS motif region are much less abundant than 3' ss with a disrupted ESS motif. This indicates that this ESS may be a general splicing inhibitory motif, which binds hnRNP A1 and inhibits exon inclusion by binding to 3' ss harboring this ESS motif.\",\n \"corpus_id\": 39402594,\n \"score\": 2\n },\n {\n \"doc_id\": \"23247503\",\n \"title\": \"Solution structure of the two RNA recognition motifs of hnRNP A1 using segmental isotope labeling: how the relative orientation between RRMs influences the nucleic acid binding topology.\",\n \"abstract\": \"Human hnRNP A1 is a multi-functional protein involved in many aspects of nucleic-acid processing such as alternative splicing, micro-RNA biogenesis, nucleo-cytoplasmic mRNA transport and telomere biogenesis and maintenance. The N-terminal region of hnRNP A1, also named unwinding protein 1 (UP1), is composed of two closely related RNA recognition motifs (RRM), and is followed by a C-terminal glycine rich region. Although crystal structures of UP1 revealed inter-domain interactions between RRM1 and RRM2 in both the free and bound form of UP1, these interactions have never been established in solution. Moreover, the relative orientation of hnRNP A1 RRMs is different in the free and bound crystal structures of UP1, raising the question of the biological significance of this domain movement. In the present study, we have used NMR spectroscopy in combination with segmental isotope labeling techniques to carefully analyze the inter-RRM contacts present in solution and subsequently determine the structure of UP1 in solution. Our data unambiguously demonstrate that hnRNP A1 RRMs interact in solution, and surprisingly, the relative orientation of the two RRMs observed in solution is different from the one found in the crystal structure of free UP1 and rather resembles the one observed in the nucleic-acid bound form of the protein. This strongly supports the idea that the two RRMs of hnRNP A1 have a single defined relative orientation which is the conformation previously observed in the bound form and now observed in solution using NMR. It is likely that the conformation in the crystal structure of the free form is a less stable form induced by crystal contacts. Importantly, the relative orientation of the RRMs in proteins containing multiple-RRMs strongly influences the RNA binding topologies that are practically accessible to these proteins. Indeed, RRM domains are asymmetric binding platforms contacting single-stranded nucleic acids in a single defined orientation. Therefore, the path of the nucleic acid molecule on the multiple RRM domains is strongly dependent on whether the RRMs are interacting with each other. The different nucleic acid recognition modes by multiple-RRM domains are briefly reviewed and analyzed on the basis of the current structural information.\",\n \"corpus_id\": 1210587,\n \"score\": 2\n },\n {\n \"doc_id\": \"25081215\",\n \"title\": \"RNA recognition and self-association of CPEB4 is mediated by its tandem RRM domains.\",\n \"abstract\": \"Cytoplasmic polyadenylation is regulated by the interaction of the cytoplasmic polyadenylation element binding proteins (CPEB) with cytoplasmic polyadenylation element (CPE) containing mRNAs. The CPEB family comprises four paralogs, CPEB1-4, each composed of a variable N-terminal region, two RNA recognition motif (RRM) and a C-terminal ZZ-domain. We have characterized the RRM domains of CPEB4 and their binding properties using a combination of biochemical, biophysical and NMR techniques. Isothermal titration calorimetry, NMR and electrophoretic mobility shift assay experiments demonstrate that both the RRM domains are required for an optimal CPE interaction and the presence of either one or two adenosines in the two most commonly used consensus CPE motifs has little effect on the affinity of the interaction. Both the single RRM1 and the tandem RRM1-RRM2 have the ability to dimerize, although representing a minor population. Self-association does not affect the proteins' ability to interact with RNA as demonstrated by ion mobility-mass spectrometry. Chemical shift effects measured by NMR of the apo forms of the RRM1-RRM2 samples indicate that the two domains are orientated toward each other. NMR titration experiments show that residues on the β-sheet surface on RRM1 and at the C-terminus of RRM2 are affected upon RNA binding. We propose a model of the CPEB4 RRM1-RRM2-CPE complex that illustrates the experimental data.\",\n \"corpus_id\": 13890195,\n \"score\": 2\n },\n {\n \"doc_id\": \"25727246\",\n \"title\": \"Splicing regulation in spinal muscular atrophy by an RNA structure formed by long-distance interactions.\",\n \"abstract\": \"Humans carry two copies of the survival motor neuron gene: SMN1 and SMN2. Loss of SMN1 coupled with skipping of SMN2 exon 7 causes spinal muscular atrophy (SMA), a leading genetic disease associated with infant mortality. Our discovery of intronic splicing silencer N1 (ISS-N1) is a promising target, currently in a phase III clinical trial, for an antisense oligonucleotide-mediated splicing correction in SMA. We have recently shown that the first residue of ISS-N1 is locked in a unique RNA structure that we term ISTL1 (internal stem through long-distance interaction-1). Complementary strands of ISTL1 are separated from each other by 279 nucleotides. Using site-specific mutations and chemical structure probing, we confirmed the formation and functional significance of ISTL1. Located in the middle of intron 7, the 3' strand of ISTL1 falls within an inhibitory region that we term ISS-N2. We demonstrate that an antisense oligonucleotide-mediated sequestration of ISS-N2 fully corrects SMN2 exon 7 splicing and restores high levels of SMN in SMA patient cells. These results underscore the therapeutic potential of the regulatory information present in a secondary and high-order RNA structure of a human intron.\",\n \"corpus_id\": 35598391,\n \"score\": 2\n },\n {\n \"doc_id\": \"26003924\",\n \"title\": \"The First Crystal Structure of the UP1 Domain of hnRNP A1 Bound to RNA Reveals a New Look for an Old RNA Binding Protein.\",\n \"abstract\": \"The heterogeneous nuclear ribonucleoprotein (hnRNP) A1 protein is a multifunctional RNA binding protein implicated in a wide range of biological functions. Mechanisms and putative hnRNP A1-RNA interactions have been inferred primarily from the crystal structure of its UP1 domain bound to ssDNA. RNA stem loops represent an important class of known hnRNP A1 targets, yet little is known about the structural basis of hnRNP A1-RNA recognition. Here, we report the first high-resolution structure (1.92Å) of UP1 bound to a 5'-AGU-3' trinucleotide that resembles sequence elements of several native hnRNP A1-RNA stem loop targets. UP1 interacts specifically with the AG dinucleotide sequence via a \\\"nucleobase pocket\\\" formed by the β-sheet surface of RRM1 and the inter-RRM linker; RRM2 does not contact the RNA. The inter-RRM linker forms the lid of the nucleobase pocket and we show using structure-guided mutagenesis that the conserved salt-bridge interactions (R75:D155 and R88:D157) on the α-helical side of the RNA binding surface stabilize the linker in a geometry poised to bind RNA. We further investigated the structural basis of UP1 binding HIViSL3(ESS3) by determining a structural model of the complex scored by small-angle X-ray scattering. UP1 docks on the apical loop of SL3(ESS3) using its RRM1 domain and inter-RRM linker only. The biophysical implications of the structural model were tested by measuring kinetic binding parameters, where mutations introduced within the apical loop reduce binding affinities by slowing down the rate of complex formation. Collectively, the data presented here provide the first insights into hnRNP A1-RNA interactions.\",\n \"corpus_id\": 206214449,\n \"score\": 2\n },\n {\n \"doc_id\": \"26607354\",\n \"title\": \"Solution Structure of the HIV-1 Intron Splicing Silencer and its Interactions with the UP1 Domain of hnRNP A1.\",\n \"abstract\": \"Splicing patterns in HIV-1 are maintained through cis regulatory elements that recruit antagonistic host RNA binding proteins. The activity of the 3 prime acceptor site A7 is tightly regulated through a complex network of an intronic splicing silencer (ISS), a bipartite exonic splicing silencer (ESS3a/b) and an exonic splicing enhancer (ESE3). Since HIV-1 splicing depends on protein-RNA interactions, it is important to know the tertiary structures surrounding the splice sites. Herein, we present the NMR solution structure of the phylogenetically conserved ISS stem loop. ISS adopts a stable structure consisting of conserved UG wobble pairs, a folded 2X2 (GU/UA) internal loop, a UU bulge and a flexible AGUGA apical loop. Calorimetric and biochemical titrations indicate the UP1 domain of hnRNP A1 binds the ISS apical loop site-specifically and with nanomolar affinity. Collectively, this work provides additional insights into how HIV-1 uses a conserved RNA structure to commandeer a host RNA binding protein.\",\n \"corpus_id\": 35676693,\n \"score\": 2\n },\n {\n \"doc_id\": \"27380775\",\n \"title\": \"Global identification of hnRNP A1 binding sites for SSO-based splicing modulation.\",\n \"abstract\": \"BACKGROUND: Many pathogenic genetic variants have been shown to disrupt mRNA splicing. Besides splice mutations in the well-conserved splice sites, mutations in splicing regulatory elements (SREs) may deregulate splicing and cause disease. A promising therapeutic approach is to compensate for this deregulation by blocking other SREs with splice-switching oligonucleotides (SSOs). However, the location and sequence of most SREs are not well known. RESULTS: Here, we used individual-nucleotide resolution crosslinking immunoprecipitation (iCLIP) to establish an in vivo binding map for the key splicing regulatory factor hnRNP A1 and to generate an hnRNP A1 consensus binding motif. We find that hnRNP A1 binding in proximal introns may be important for repressing exons. We show that inclusion of the alternative cassette exon 3 in SKA2 can be significantly increased by SSO-based treatment which blocks an iCLIP-identified hnRNP A1 binding site immediately downstream of the 5' splice site. Because pseudoexons are well suited as models for constitutive exons which have been inactivated by pathogenic mutations in SREs, we used a pseudoexon in MTRR as a model and showed that an iCLIP-identified hnRNP A1 binding site downstream of the 5' splice site can be blocked by SSOs to activate the exon. CONCLUSIONS: The hnRNP A1 binding map can be used to identify potential targets for SSO-based therapy. Moreover, together with the hnRNP A1 consensus binding motif, the binding map may be used to predict whether disease-associated mutations and SNPs affect hnRNP A1 binding and eventually mRNA splicing.\",\n \"corpus_id\": 3638528,\n \"score\": 2\n },\n {\n \"doc_id\": \"28193894\",\n \"title\": \"Rules of RNA specificity of hnRNP A1 revealed by global and quantitative analysis of its affinity distribution.\",\n \"abstract\": \"Heterogeneous nuclear ribonucleoprotein A1 (hnRNP A1) is a multipurpose RNA-binding protein (RBP) involved in normal and pathological RNA metabolism. Transcriptome-wide mapping and in vitro evolution identify consensus hnRNP A1 binding motifs; however, such data do not reveal how surrounding RNA sequence and structural context modulate affinity. We determined the affinity of hnRNP A1 for all possible sequence variants (n = 16,384) of the HIV exon splicing silencer 3 (ESS3) 7-nt apical loop. Analysis of the affinity distribution identifies the optimal motif 5'-YAG-3' and shows how its copy number, position in the loop, and loop structure modulate affinity. For a subset of ESS3 variants, we show that specificity is determined by association rate constants and that variants lacking the minimal sequence motif bind competitively with consensus RNA. Thus, the results reveal general rules of specificity of hnRNP A1 and provide a quantitative framework for understanding how it discriminates between alternative competing RNA ligands in vivo.\",\n \"corpus_id\": 4702455,\n \"score\": 2\n },\n {\n \"doc_id\": \"29379020\",\n \"title\": \"Molecular basis for the specific and multivariant recognitions of RNA substrates by human hnRNP A2/B1.\",\n \"abstract\": \"Human hnRNP A2/B1 is an RNA-binding protein that plays important roles in many biological processes, including maturation, transport, and metabolism of mRNA, and gene regulation of long noncoding RNAs. hnRNP A2/B1 was reported to control the microRNAs sorting to exosomes and promote primary microRNA processing as a potential m6A \\\"reader.\\\" hnRNP A2/B1 contains two RNA recognition motifs that provide sequence-specific recognition of RNA substrates. Here, we determine crystal structures of tandem RRM domains of hnRNP A2/B1 in complex with various RNA substrates, elucidating specific recognitions of AGG and UAG motifs by RRM1 and RRM2 domains, respectively. Further structural and biochemical results demonstrate multivariant binding modes for sequence-diversified RNA substrates, supporting a RNA matchmaker mechanism in hnRNP A2/B1 function. Moreover, our studies in combination with bioinformatic analysis suggest that hnRNP A2/B1 may mediate effects of m6A through a \\\"m6A switch\\\" mechanism, instead of acting as a direct \\\"reader\\\" of m6A modification.\",\n \"corpus_id\": 3310175,\n \"score\": 2\n },\n {\n \"doc_id\": \"29625167\",\n \"title\": \"Idiosyncrasies of hnRNP A1-RNA recognition: Can binding mode influence function.\",\n \"abstract\": \"The heterogeneous nuclear ribonucleoproteins (hnRNPs) are a diverse family of RNA binding proteins that function in most stages of RNA metabolism. The prototypical member, hnRNP A1, is composed of three major domains; tandem N-terminal RNA Recognition Motifs (RRMs) and a C-terminal mostly intrinsically disordered region. HnRNP A1 is broadly implicated in basic cellular RNA processing events such as splicing, stability, nuclear export and translation. Due to its ubiquity and abundance, hnRNP A1 is also frequently usurped to control viral gene expression. Deregulation of the RNA metabolism functions of hnRNP A1 in neuronal cells contributes to several neurodegenerative disorders. Because of these roles in human pathologies, the study of hnRNP A1 provides opportunities for the development of novel therapeutics, with disruption of its RNA binding capabilities being the most promising target. The functional diversity of hnRNP A1 is reflected in the complex nature by which it interacts with various RNA targets. Indeed, hnRNP A1 binds both structured and unstructured RNAs with binding affinities that span several magnitudes. Available structures of hnRNP A1-RNA complexes also suggest a degree of plasticity in molecular recognition. Given the reinvigoration in hnRNP A1, the goal of this review is to use the available structural biochemical developments as a framework to interpret its wide-range of RNA functions.\",\n \"corpus_id\": 4792730,\n \"score\": 2\n },\n {\n \"doc_id\": \"18703504\",\n \"title\": \"TDP-43 overexpression enhances exon 7 inclusion during the survival of motor neuron pre-mRNA splicing.\",\n \"abstract\": \"TDP-43 is a highly conserved, 43-kDa RNA-binding protein implicated to play a role in transcription repression, nuclear organization, and alternative splicing. More recently, this factor has been identified as the major disease protein of several neurodegenerative diseases, including frontotemporal lobar degeneration with ubiquitin-positive inclusions and amyotrophic lateral sclerosis. For the splicing activity, the factor has been shown to be mainly an exon-skipping promoter. In this study using the survival of motor neuron (SMN) minigenes as the reporters in transfection assay, we show for the first time that TDP-43 could also act as an exon-inclusion factor. Furthermore, both RNA-recognition motif domains are required for its ability to enhance the SMN2 exon 7 inclusion. Combined protein-immunoprecipitation and RNA-immunoprecipitation experiments also suggested that this exon inclusion activity might be mediated by multimeric complex(es) consisting of this protein interacting with other splicing factors, including Htra2-beta1. Our data further evidence TDP-43 as a multifunctional RNA-binding protein for a diverse set of cellular activities.\",\n \"corpus_id\": 25958855,\n \"score\": 1\n },\n {\n \"doc_id\": \"19926721\",\n \"title\": \"hnRNP A1 and hnRNP H can collaborate to modulate 5' splice site selection.\",\n \"abstract\": \"The mammalian proteins hnRNP A1 and hnRNP H control many splicing decisions in viral and cellular primary transcripts. To explain some of these activities, we have proposed that self-interactions between bound proteins create an RNA loop that represses internal splice sites while simultaneously activating the external sites that are brought in closer proximity. Here we show that a variety of hnRNP H binding sites can affect 5' splice site selection. The addition of two sets of hnRNP H sites in a model pre-mRNA modulates 5' splice site selection cooperatively, consistent with the looping model. Notably, binding sites for hnRNP A1 and H on the same pre-mRNA can similarly collaborate to modulate 5' splice site selection. The C-terminal portion of hnRNP H that contains the glycine-rich domains (GRD) is essential for splicing activity, and it can be functionally replaced by the GRD of hnRNP A1. Finally, we used the bioluminescence resonance energy transfer (BRET) technology to document the existence of homotypic and heterotypic interactions between hnRNP H and hnRNP A1 in live cells. Overall, our study suggests that interactions between different hnRNP proteins bound to distinct locations on a pre-mRNA can change its conformation to affect splicing decisions.\",\n \"corpus_id\": 30321269,\n \"score\": 1\n },\n {\n \"doc_id\": \"20515750\",\n \"title\": \"Splicing regulation of the survival motor neuron genes and implications for treatment of spinal muscular atrophy.\",\n \"abstract\": \"Proximal spinal muscular atrophy (SMA) is a neuromuscular disease caused by low levels of the survival motor neuron (SMN) protein. The reduced SMN levels are due to loss of the survival motor neuron-1 (SMN1) gene. Humans carry a nearly identical SMN2 gene that generates a truncated protein, due to a C to T nucleotide alteration in exon 7 that leads to inefficient RNA splicing of exon 7. This exclusion of SMN exon 7 is central to the onset of the SMA disease, however, this offers a unique therapeutic intervention in which corrective splicing of the SMN2 gene would restore SMN function. Exon 7 splicing is regulated by a number of exonic and intronic splicing regulatory sequences and trans-factors that bind them. A better understanding of the way SMN pre-mRNA is spliced has lead to the development of targeted therapies aimed at correcting SMN2 splicing. As therapeutics targeted toward correction of SMN2 splicing continue to be developed available SMA mouse models can be utilized in validating their potential in disease treatment.\",\n \"corpus_id\": 24755471,\n \"score\": 1\n },\n {\n \"doc_id\": \"22132154\",\n \"title\": \"hnRNP A1 and hnRNP F modulate the alternative splicing of exon 11 of the insulin receptor gene.\",\n \"abstract\": \"Exon 11 of the insulin receptor gene (INSR) is alternatively spliced in a developmentally and tissue-specific manner. Linker scanning mutations in a 5' GA-rich enhancer in intron 10 identified AGGGA sequences that are important for enhancer function. Using RNA-affinity purification and mass spectrometry, we identified hnRNP F and hnRNP A1 binding to these AGGGA sites and also to similar motifs at the 3' end of the intron. The hnRNPs have opposite functional effects with hnRNP F promoting and hnRNP A1 inhibiting exon 11 inclusion, and deletion of the GA-rich elements eliminates both effects. We also observed specific binding of hnRNP A1 to the 5' splice site of intron 11. The SR protein SRSF1 (SF2/ASF) co-purified on the GA-rich enhancer and, interestingly, also competes with hnRNP A1 for binding to the splice site. A point mutation -3U→C decreases hnRNP A1 binding, increases SRSF1 binding and renders the exon constitutive. Lastly, our data point to a functional interaction between hnRNP F and SRSF1 as a mutant that eliminates SRSF1 binding to exon 11, or a SRSF1 knockdown, which prevents the stimulatory effect of hnRNP F over expression.\",\n \"corpus_id\": 11656500,\n \"score\": 1\n },\n {\n \"doc_id\": \"22154809\",\n \"title\": \"Solution structure of the HIV-1 exon splicing silencer 3.\",\n \"abstract\": \"Alternative splicing of the human immunodeficiency virus type 1 (HIV-1) genomic RNA is necessary to produce the complete viral protein complement, and aberrations in the splicing pattern impair HIV-1 replication. Genome splicing in HIV-1 is tightly regulated by the dynamic assembly/disassembly of trans host factors with cis RNA control elements. The host protein, heterogeneous nuclear ribonucleoprotein (hnRNP) A1, regulates splicing at several highly conserved HIV-1 3' splice sites by binding 5'-UAG-3' elements embedded within regions containing RNA structure. The physical determinants of hnRNP A1 splice site recognition remain poorly defined in HIV-1, thus precluding a detailed understanding of the molecular basis of the splicing pattern. Here, the three-dimensional structure of the exon splicing silencer 3 (ESS3) from HIV-1 has been determined using NMR spectroscopy. ESS3 adopts a 27-nucleotide hairpin with a 10-bp A-form stem that contains a pH-sensitive A(+)C wobble pair. The seven-nucleotide hairpin loop contains the high-affinity hnRNP-A1-responsive 5'-UAGU-3' element and a proximal 5'-GAU-3' motif. The NMR structure shows that the heptaloop adopts a well-organized conformation stabilized primarily by base stacking interactions reminiscent of a U-turn. The apex of the loop is quasi-symmetric with UA dinucleotide steps from the 5'-GAU-3' and 5'-UAGU-3' motifs stacking on opposite sides of the hairpin. As a step towards understanding the binding mechanism, we performed calorimetric and NMR titrations of several hnRNP A1 subdomains into ESS3. The data show that the UP1 domain forms a high-affinity (K(d)=37.8±1.1 nM) complex with ESS3 via site-specific interactions with the loop.\",\n \"corpus_id\": 22385574,\n \"score\": 1\n },\n {\n \"doc_id\": \"22325350\",\n \"title\": \"hnRNP A1 proofreads 3' splice site recognition by U2AF.\",\n \"abstract\": \"One of the earliest steps in metazoan pre-mRNA splicing involves binding of U2 snRNP auxiliary factor (U2AF) 65 KDa subunit to the polypyrimidine (Py) tract and of the 35 KDa subunit to the invariant AG dinucleotide at the intron 3' end. Here we use in vitro and in vivo depletion, as well as reconstitution assays using purified components, to identify hnRNP A1 as an RNA binding protein that allows U2AF to discriminate between pyrimidine-rich RNA sequences followed or not by a 3' splice site AG. Biochemical and NMR data indicate that hnRNP A1 forms a ternary complex with the U2AF heterodimer on AG-containing/uridine-rich RNAs, while it displaces U2AF from non-AG-containing/uridine-rich RNAs, an activity that requires the glycine-rich domain of hnRNP A1. Consistent with the functional relevance of this activity for splicing, proofreading assays reveal a role for hnRNP A1 in U2AF-mediated recruitment of U2 snRNP to the pre-mRNA.\",\n \"corpus_id\": 10951645,\n \"score\": 1\n },\n {\n \"doc_id\": \"23394998\",\n \"title\": \"hnRNP L and hnRNP A1 induce extended U1 snRNA interactions with an exon to repress spliceosome assembly.\",\n \"abstract\": \"Pre-mRNA splicing is catalyzed through the activity of the spliceosome, a dynamic enzymatic complex. Forcing aberrant interactions within the spliceosome can reduce splicing efficiency and alter splice site choice; however, it is unknown whether such alterations are naturally exploited mechanisms of splicing regulation. Here, we demonstrate that hnRNP L represses CD45 exon 4 by recruiting hnRNP A1 to a sequence upstream of the 5' splice site. Together, hnRNP L and A1 induce extended contacts between the 5' splice site-bound U1 snRNA and neighboring exonic sequences that, in turn, inhibit stable association of U6 snRNA and subsequent catalysis. Importantly, analysis of several exons regulated by hnRNP L shows a clear relationship between the potential for binding of hnRNP A1 and U1 snRNA and the effect of hnRNP L on splicing. Together, our results demonstrate that conformational perturbations within the spliceosome are a naturally occurring and generalizable mechanism for controlling alternative splicing decisions.\",\n \"corpus_id\": 14521439,\n \"score\": 1\n },\n {\n \"doc_id\": \"23430061\",\n \"title\": \"hnRNP A1 contacts exon 5 to promote exon 6 inclusion of apoptotic Fas gene.\",\n \"abstract\": \"Fas is a transmembrane cell surface protein recognized by Fas ligand (FasL). When FasL binds to Fas, the target cells undergo apoptosis. A soluble Fas molecule that lacks the transmembrane domain is produced from skipping of exon 6 encoding this region in alternative splicing procedure. The soluble Fas molecule has the opposite function of intact Fas molecule, protecting cells from apoptosis. Here we show that knockdown of hnRNP A1 promotes exon 6 skipping of Fas pre-mRNA, whereas overexpression of hnRNP A1 reduces exon 6 skipping. Based on the bioinformatics approach, we have hypothesized that hnRNP A1 functions through interrupting 5' splice site selection of exon 5 by interacting with its potential binding site close to 5' splice site of exon 5. Consistent with our hypothesis, we demonstrate that mutations of the hnRNP A1 binding site on exon 5 disrupted the effects of hnRNP A1 on exon 6 inclusion. RNA pull-down assay and then western blot analysis with hnRNP A1 antibody prove that hnRNP A1 contacts the potential binding site RNA sequence on exon 5 but not the mutant sequence. In addition, we show that the mutation of 5' splice site on exon 5 to a less conserved sequence destructed the effects of hnRNP A1 on exon 6 inclusion. Therefore we conclude that hnRNP A1 interacts with exon 5 to promote distal exon 6 inclusion of Fas pre-mRNA. Our study reveals a novel alternative splicing mechanism of Fas pre-mRNA.\",\n \"corpus_id\": 2289833,\n \"score\": 1\n },\n {\n \"doc_id\": \"23646903\",\n \"title\": \"Minimal functional domains of paralogues hnRNP L and hnRNP LL exhibit mechanistic differences in exonic splicing repression.\",\n \"abstract\": \"Understanding functional distinctions between related splicing regulatory proteins is critical to deciphering tissue-specific control of alternative splicing. The hnRNP (heterogeneous nuclear ribonucleoprotein) L and hnRNP LL (hnRNP L-like) proteins are paralogues that have overlapping, but distinct, expression patterns and functional consequences. These two proteins share high sequence similarity in their RRMs (RNA-recognition motifs), but diverge in regions outside of the RRMs. In the present study, we use an MS2-tethering assay to delineate the minimal domains of hnRNP L and hnRNP LL which are required for repressing exon inclusion. We demonstrate that for both proteins, regions outside the RRMs, the N-terminal region, and a linker sequence between RRMs 2 and 3, are necessary for exon repression, but are only sufficient for repression in the case of hnRNP LL. In addition, both proteins require at least one RRM for maximal repression. Notably, we demonstrate that the region encompassing RRMs 1 and 2 of hnRNP LL imparts a second silencing activity not observed for hnRNP L. This additional functional component of hnRNP LL is consistent with the fact that the full-length hnRNP LL has a greater silencing activity than hnRNP L. Thus the results of the present study provide important insight into the functional and mechanistic variations that can exist between two highly related hnRNP proteins.\",\n \"corpus_id\": 2877643,\n \"score\": 1\n },\n {\n \"doc_id\": \"24240615\",\n \"title\": \"Molecular basis of UG-rich RNA recognition by the human splicing factor TDP-43.\",\n \"abstract\": \"TDP-43 encodes an alternative-splicing regulator with tandem RNA-recognition motifs (RRMs). The protein regulates cystic fibrosis transmembrane regulator (CFTR) exon 9 splicing through binding to long UG-rich RNA sequences and is found in cytoplasmic inclusions of several neurodegenerative diseases. We solved the solution structure of the TDP-43 RRMs in complex with UG-rich RNA. Ten nucleotides are bound by both RRMs, and six are recognized sequence specifically. Among these, a central G interacts with both RRMs and stabilizes a new tandem RRM arrangement. Mutations that eliminate recognition of this key nucleotide or crucial inter-RRM interactions disrupt RNA binding and TDP-43-dependent splicing regulation. In contrast, point mutations that affect base-specific recognition in either RRM have weaker effects. Our findings reveal not only how TDP-43 recognizes UG repeats but also how RNA binding-dependent inter-RRM interactions are crucial for TDP-43 function.\",\n \"corpus_id\": 13783277,\n \"score\": 1\n },\n {\n \"doc_id\": \"24628426\",\n \"title\": \"Thermodynamic and phylogenetic insights into hnRNP A1 recognition of the HIV-1 exon splicing silencer 3 element.\",\n \"abstract\": \"Complete expression of the HIV-1 genome requires balanced usage of suboptimal splice sites. The 3' acceptor site A7 (ssA7) is negatively regulated in part by an interaction between the host hnRNP A1 protein and a viral splicing silencer (ESS3). Binding of hnRNP A1 to ESS3 and other upstream silencers is sufficient to occlude spliceosome assembly. Efforts to understand the splicing repressive properties of hnRNP A1 on ssA7 have revealed hnRNP A1 binds specific sites within the context of a highly folded RNA structure; however, biochemical models assert hnRNP A1 disrupts RNA structure through cooperative spreading. In an effort to improve our understanding of the ssA7 binding properties of hnRNP A1, herein we have performed a combined phylogenetic and biophysical study of the interaction of its UP1 domain with ESS3. Phylogenetic analyses of group M sequences (x̅ = 2860) taken from the Los Alamos HIV database reveal the ESS3 stem loop (SL3(ESS3)) structure has been conserved throughout HIV-1 evolution, despite variations in primary sequence. Calorimetric titrations with UP1 clearly show the SL3(ESS3) structure is a critical binding determinant because deletion of the base-paired region reduces the affinity by ∼150-fold (Kd values of 27.8 nM and 4.2 μM). Cytosine substitutions of conserved apical loop nucleobases show UP1 preferentially binds purines over pyrimidines, where site-specific interactions were detected via saturation transfer difference nuclear magnetic resonance. Chemical shift mapping of the UP1-SL3(ESS3) interface by (1)H-(15)N heteronuclear single-quantum coherence spectroscopy titrations reveals a broad interaction surface on UP1 that encompasses both RRM domains and the inter-RRM linker. Collectively, our results describe a UP1 binding mechanism that is likely different from current models used to explain the alternative splicing properties of hnRNP A1.\",\n \"corpus_id\": 8536035,\n \"score\": 1\n },\n {\n \"doc_id\": \"24692659\",\n \"title\": \"Characterization of the RNA recognition mode of hnRNP G extends its role in SMN2 splicing regulation.\",\n \"abstract\": \"Regulation of SMN2 exon 7 splicing is crucial for the production of active SMN protein and the survival of Spinal Muscular Atrophy (SMA) patients. One of the most efficient activators of exon 7 inclusion is hnRNP G, which is recruited to the exon by Tra2-β1. We report that in addition to the C-terminal region of hnRNP G, the RNA Recognition Motif (RRM) and the middle part of the protein containing the Arg-Gly-Gly (RGG) box are important for this function. To better understand the mode of action of hnRNP G in this context we determined the structure of its RRM bound to an SMN2 derived RNA. The RRM interacts with a 5'-AAN-3' motif and specifically recognizes the two consecutive adenines. By testing the effect of mutations in hnRNP G RRM and in its putative binding sites on the splicing of SMN2 exon 7, we show that it specifically binds to exon 7. This interaction is required for hnRNP G splicing activity and we propose its recruitment to a polyA tract located upstream of the Tra2-β1 binding site. Finally, our data suggest that hnRNP G plays a major role in the recruitment of the Tra2-β1/hnRNP G/SRSF9 trimeric complex to SMN2 exon 7.\",\n \"corpus_id\": 11994416,\n \"score\": 1\n },\n {\n \"doc_id\": \"24892836\",\n \"title\": \"Absence of an intron splicing silencer in porcine Smn1 intron 7 confers immunity to the exon skipping mutation in human SMN2.\",\n \"abstract\": \"Spinal Muscular Atrophy is caused by homozygous loss of SMN1. All patients retain at least one copy of SMN2 which produces an identical protein but at lower levels due to a silent mutation in exon 7 which results in predominant exclusion of the exon. Therapies targeting the splicing of SMN2 exon 7 have been in development for several years, and their efficacy has been measured using either in vitro cellular assays or in vivo small animal models such as mice. In this study we evaluated the potential for constructing a mini-pig animal model by introducing minimal changes in the endogenous porcine Smn1 gene to maintain the native genomic structure and regulation. We found that while a Smn2-like mutation can be introduced in the porcine Smn1 gene and can diminish the function of the ESE, it would not recapitulate the splicing pattern seen in human SMN2 due to absence of a functional ISS immediately downstream of exon 7. We investigated the ISS region and show here that the porcine ISS is inactive due to disruption of a proximal hnRNP A1 binding site, while a distal hnRNP A1 binding site remains functional but is unable to maintain the functionality of the ISS as a whole.\",\n \"corpus_id\": 16895730,\n \"score\": 1\n },\n {\n \"doc_id\": \"26051023\",\n \"title\": \"The Signature of the Five-Stranded vRRM Fold Defined by Functional, Structural and Computational Analysis of the hnRNP L Protein.\",\n \"abstract\": \"The RNA recognition motif (RRM) is the far most abundant RNA binding domain. In addition to the typical β1α1β2β3α2β4 fold, various sub-structural elements have been described and reportedly contribute to the high functional versatility of RRMs. The heterogeneous nuclear ribonucleoprotein L (hnRNP L) is a highly abundant protein of 64 kDa comprising four RRM domains. Involved in many aspects of RNA metabolism, hnRNP L specifically binds to RNAs containing CA repeats or CA-rich clusters. However, a comprehensive structural description of hnRNP L including its sub-structural elements is missing. Here, we present the structural characterization of the RRM domains of hnRNP L and demonstrate their function in repressing exon 4 of SLC2A2. By comparison of the sub-structural elements between the two highly similar paralog families of hnRNP L and PTB, we defined signatures underlying interacting C-terminal coils (ICCs), the RRM34 domain interaction and RRMs with a C-terminal fifth β-strand, a variation we denoted vRRMs. Furthermore, computational analysis revealed new putative ICC-containing RRM families and allowed us to propose an evolutionary scenario explaining the origins of the ICC and fifth β-strand sub-structural extensions. Our studies provide insights of domain requirements in alternative splicing mediated by hnRNP L and molecular descriptions for the sub-structural elements. In addition, the analysis presented may help to classify other abundant RRM extensions and to predict structure-function relationships.\",\n \"corpus_id\": 206214482,\n \"score\": 1\n },\n {\n \"doc_id\": \"26419278\",\n \"title\": \"A rare variant (c.863G>T) in exon 7 of SMN1 disrupts mRNA splicing and is responsible for spinal muscular atrophy.\",\n \"abstract\": \"Proximal spinal muscular atrophy (SMA) is an autosomal recessive neuromuscular disorder caused by deletion or mutation of SMN1 (survival motor neuron 1). SMN exon 7 splicing is regulated by a number of exonic and intronic regulatory sequences and the trans-factors that bind them. Variants located in or near these regulated regions should be evaluated to determine their effect on splicing. We identified the rare variant c.863G>T (r.835_*3del, p.Gly279Glufs*5) in exon 7 of SMN1 in three patients affected with type I or type II SMA. Most of the SMN1 transcripts exhibited complete loss of exon 7 in vivo. The ex vivo splicing assay demonstrated that the variant disrupts inclusion of exon 7 (~85%) in the SMN1 mRNA; replacement with various bases yielded a variety of splicing effects in SMN1 and SMN2 pre-mRNA. The c.863G>T (r.835_*3del, p.Gly279Glufs*5) variant is located in a region that includes binding sites for multiple splicing factors including Tra2β1. Thus, the variant disrupts Tra2β1 binding, but does not affect binding of hnRNP A1. These findings demonstrate how rare variants influence pre-mRNA splicing of SMN and reveal the functional influence of c.863G>T (r.835_*3del, p.Gly279Glufs*5) variant in patients with SMA.European Journal of Human Genetics advance online publication, 30 September 2015; doi:10.1038/ejhg.2015.213.\",\n \"corpus_id\": 22696110,\n \"score\": 1\n },\n {\n \"doc_id\": \"27489271\",\n \"title\": \"Serine/Arginine-Rich Splicing Factor 3 and Heterogeneous Nuclear Ribonucleoprotein A1 Regulate Alternative RNA Splicing and Gene Expression of Human Papillomavirus 18 through Two Functionally Distinguishable cis Elements.\",\n \"abstract\": \"UNLABELLED: Human papillomavirus 18 (HPV18) is the second most common oncogenic HPV type associated with cervical, anogenital, and oropharyngeal cancers. Like other oncogenic HPVs, HPV18 encodes two major (one early and one late) polycistronic pre-mRNAs that are regulated by alternative RNA splicing to produce a repertoire of viral transcripts for the expression of individual viral genes. However, RNA cis-regulatory elements and trans-acting factors contributing to HPV18 alternative RNA splicing remain unknown. In this study, an exonic splicing enhancer (ESE) in the nucleotide (nt) 3520 to 3550 region in the HPV18 genome was identified and characterized for promotion of HPV18 929^3434 splicing and E1^E4 production through interaction with SRSF3, a host oncogenic splicing factor differentially expressed in epithelial cells and keratinocytes. Introduction of point mutations in the SRSF3-binding site or knockdown of SRSF3 expression in cells reduces 929^3434 splicing and E1^E4 production but activates other, minor 929^3465 and 929^3506 splicing. Knockdown of SRSF3 expression also enhances the expression of E2 and L1 mRNAs. An exonic splicing silencer (ESS) in the HPV18 nt 612 to 639 region was identified as being inhibitory to the 233^416 splicing of HPV18 E6E7 pre-mRNAs via binding to hnRNP A1, a well-characterized, abundantly and ubiquitously expressed RNA-binding protein. Introduction of point mutations into the hnRNP A1-binding site or knockdown of hnRNP A1 expression promoted 233^416 splicing and reduced E6 expression. These data provide the first evidence that the alternative RNA splicing of HPV18 pre-mRNAs is subject to regulation by viral RNA cis elements and host trans-acting splicing factors. IMPORTANCE: Expression of HPV18 genes is regulated by alternative RNA splicing of viral polycistronic pre-mRNAs to produce a repertoire of viral early and late transcripts. RNA cis elements and trans-acting factors contributing to HPV18 alternative RNA splicing have been discovered in this study for the first time. The identified ESS at the E7 open reading frame (ORF) prevents HPV18 233^416 splicing in the E6 ORF through interaction with a host splicing factor, hnRNP A1, and regulates E6 and E7 expression of the early E6E7 polycistronic pre-mRNA. The identified ESE at the E1^E4 ORF promotes HPV18 929^3434 splicing of both viral early and late pre-mRNAs and E1^E4 production through interaction with SRSF3. This study provides important observations on how alternative RNA splicing of HPV18 pre-mRNAs is subject to regulation by viral RNA cis elements and host splicing factors and offers potential therapeutic targets to overcome HPV-related cancer.\",\n \"corpus_id\": 6745667,\n \"score\": 1\n },\n {\n \"doc_id\": \"18203745\",\n \"title\": \"The third RNA recognition motif of Drosophila ELAV protein has a role in multimerization.\",\n \"abstract\": \"ELAV is a neuron-specific RNA-binding protein in Drosophila that is required for development and maintenance of neurons. ELAV regulates alternative splicing of Neuroglian and erect wing (ewg) transcripts, and has been shown to form a multimeric complex on the last ewg intron. The protein has three RNA recognition motifs (RRM1, 2 and 3) with a hinge region between RRM2 and 3. In this study, we used the yeast two-hybrid system to determine the multimerization domain of ELAV. Using deletion constructs, we mapped an interaction activity to a region containing most of RRM3. We found three conserved short sequences in RRM3 that were essential for the interaction, and also sufficient to give the interaction activity to RRM2 when introduced into it. In our in vivo functional assay, a mutation in one of the three sequences showed reduced activity in splicing regulation, underlining the functional importance of multimerization. However, RRM2 with the three RRM3 interaction sequences did not function as RRM3 in vivo, which suggested that multimerization is not the only function of RRM3. Our results are consistent with a model in which RRM3 serves as a bi-functional domain that interacts with both RNA and protein.\",\n \"corpus_id\": 7152321,\n \"score\": 0\n },\n {\n \"doc_id\": \"18500819\",\n \"title\": \"Solution structure of the second RNA recognition motif (RRM) domain of murine T cell intracellular antigen-1 (TIA-1) and its RNA recognition mode.\",\n \"abstract\": \"T cell intracellular antigen-1 (TIA-1), an apoptosis promoting factor, functions as a splicing regulator for the Fas pre-mRNA. TIA-1 possesses three RNA recognition motifs (RRMs) and a glutamine-rich domain. The second RRM (RRM2) is necessary and sufficient for tight, sequence-specific binding to the uridine-rich sequences buried around the 5' splice sites. In the present study, we solved the solution structure of the murine TIA-1 RRM2 by heteronuclear-nuclear magnetic resonance spectroscopy. The TIA-1 RRM2 adopts the RRM fold (betaalphabetabetaalphabeta) and possesses an extra beta-strand between beta2 and beta3, which forms an additional beta-sheet with the C-terminal part of beta2. We refer to this structure as the beta2-beta2' beta-loop. Interestingly, this characteristic beta-loop structure is conserved among a number of RRMs, including the U2AF65 RRM2 and the Sex-lethal RRM1 and RRM2, which also bind to uridine-rich RNAs. Furthermore, we identified a new sequence motif in the beta2-beta2' beta-loop, the DxxT motif. Chemical shift perturbation analyses of both the main and side chains upon binding to the uridine pentamer RNA revealed that most of the beta-sheet surface, including the beta2-beta2' beta-loop, is involved in the RNA binding. An investigation of the chemical shift perturbation revealed similarity in the RNA recognition modes between the TIA-1 and U2AF65 RRMs.\",\n \"corpus_id\": 24538172,\n \"score\": 0\n },\n {\n \"doc_id\": \"18794368\",\n \"title\": \"The RNA binding protein hnRNP Q modulates the utilization of exon 7 in the survival motor neuron 2 (SMN2) gene.\",\n \"abstract\": \"Spinal muscular atrophy (SMA) is a recessive neuromuscular disorder caused by the homozygous loss of the SMN1 gene. The human SMN2 gene has a C-to-T transition at position +6 of exon 7 and thus produces exon 7-skipping mRNAs. However, we observed an unexpectedly high level of exon 7-containing SMN2 transcripts as well as SMN protein in testis of smn(-/-) SMN2 transgenic mice. Using affinity chromatography, we identified several SMN RNA-associating proteins in mouse testis and human HeLa cells, including hnRNP Q. The major hnRNP Q isoform, Q1, directly bound SMN exon 7 in the vicinity of nucleotide +6. Overexpression of hnRNP Q1 promoted the inclusion of exon 7 in SMN2, probably by activating the use of its upstream 3' splice site. However, the minor isoforms Q2/Q3 could antagonize the activity of hnRNP Q1 and induced exon 7 exclusion. Intriguingly, enhanced exon 7 inclusion was also observed upon concomitant depletion of three hnRNP Q isoforms. Thus, differential expression of hnRNP Q isoforms may result in intricate control of SMN precursor mRNA splicing. Here, we demonstrate that hnRNP Q is a splicing modulator of SMN, further underscoring the potential of hnRNP Q as a therapeutic target for SMA.\",\n \"corpus_id\": 7525641,\n \"score\": 0\n },\n {\n \"doc_id\": \"18806275\",\n \"title\": \"hnRNP H enhances skipping of a nonfunctional exon P3A in CHRNA1 and a mutation disrupting its binding causes congenital myasthenic syndrome.\",\n \"abstract\": \"In humans and great apes, CHRNA1 encoding the muscle nicotinic acetylcholine receptor alpha subunit carries an inframe exon P3A, the inclusion of which yields a nonfunctional alpha subunit. In muscle, the P3A(-) and P3A(+) transcripts are generated in a 1:1 ratio but the functional significance and regulation of the alternative splicing remain elusive. An intronic mutation (IVS3-8G>A), identified in a patient with congenital myasthenic syndrome, disrupts an intronic splicing silencer (ISS) and results in exclusive inclusion of the downstream P3A exon. We found that the ISS-binding splicing trans-factor was heterogeneous nuclear ribonucleoprotein (hnRNP) H and the mutation attenuated the affinity of hnRNP for the ISS approximately 100-fold. We next showed that direct placement of hnRNP H to the 3' end of intron 3 silences, and siRNA-mediated downregulation of hnRNP H enhances recognition of exon P3A. Analysis of the human genome suggested that the hnRNPH-binding UGGG motif is overrepresented close to the 3' ends of introns. Pursuing this clue, we showed that alternative exons of GRIP1, FAS, VPS13C and NRCAM are downregulated by hnRNP H. Our findings imply that the presence of the hnRNP H-binding motif close to the 3' end of an intron is an essential but underestimated splicing regulator of the downstream exon.\",\n \"corpus_id\": 5898711,\n \"score\": 0\n },\n {\n \"doc_id\": \"19628962\",\n \"title\": \"HnRNP C1/C2 may regulate exon 7 splicing in the spinal muscular atrophy gene SMN1.\",\n \"abstract\": \"Spinal muscular atrophy (SMA) is caused by loss of SMN1. A nearly identical gene, SMN2, fails to compensate for the loss of SMN1 because SMN2 produces mainly an exon 7-skipped product. The +6C in SMN1 exon 7 proceeds to include exon 7 into mRNA, while the +6U in SMN2 causes skipping of exon 7. Here, approximately 45kD proteins bound to the SMN exon 7 RNA probe was found, and identified as hnRNP C1/C2. In gel-shift assay, hnRNP C1/C2 had a greater affinity for the RNA probe with +6C than for the RNA probe with +6U. In vitro splicing assay showed that anti-hnRNP C1/C2 antibody hampered splicing of SMN1 exon 7, but did not affect splicing of SMN2 exon 7. In conclusion, we showed the possibility that hnRNP C1/C2 enhanced SMN1 exon 7 splicing specifically.\",\n \"corpus_id\": 7451984,\n \"score\": 0\n },\n {\n \"doc_id\": \"19946215\",\n \"title\": \"HnRNP L-mediated regulation of mammalian alternative splicing by interference with splice site recognition.\",\n \"abstract\": \"Heterogeneous nuclear ribonucleoprotein (hnRNP) L can regulate alternative mRNA splicing in diverse ways, binding to exonic or intronic sites and acting as either an activator or repressor. To investigate the mechanistic basis of hnRNP L-regulated alternative splicing, we focus here on two specific cases of hnRNP L-dependent splice site recognition. First, in the case of TJP1 our microarray data had suggested that exon 20 inclusion is regulated by hnRNP L as a repressor. Here we demonstrate by mutational analysis that exon skipping is mediated by a short silencer sequence consisting of three hnRNP L high-score binding motifs located upstream of the 3' splice site of the regulated exon. UV crosslinking and immunoprecipitation experiments showed that hnRNP L binding interferes with 3' splice site recognition by U2AF65. Second, SLC2A2 contains a CA-repeat sequence close to the 5' splice site of the regulated exon 4. Using psoralen crosslinking, we demonstrate that hnRNP L represses splicing by preventing 5' splice site recognition of the U1 snRNP. In sum, our data provide new insights into the mechanisms of how hnRNP L-bound to intronic sites-regulates exon recognition.\",\n \"corpus_id\": 34378098,\n \"score\": 0\n },\n {\n \"doc_id\": \"20130820\",\n \"title\": \"Combined use of MS2 and PP7 coat fusions shows that TIA-1 dominates hnRNP A1 for K-SAM exon splicing control.\",\n \"abstract\": \"Splicing of the FGFR2 K-SAM exon is repressed by hnRNP A1 bound to the exon and activated by TIA-1 bound to the downstream intron. Both proteins are expressed similarly by cells whether they splice the exon or not, so it is important to know which one is dominant. To answer this question, we used bacteriophage PP7 and bacteriophage MS2 coat fusions to tether hnRNP A1 and TIA-1 to distinct sites on the same pre-mRNA molecule. hnRNP A1 fused to one coat protein was tethered to a K-SAM exon containing the corresponding coat protein's binding site. TIA-1 fused to the other coat protein was tethered to the downstream intron containing that coat protein's binding site. This led to efficient K-SAM exon splicing. Our results show that TIA-1 is dominant for K-SAM exon splicing control and validate the combined use of PP7 and MS2 coat proteins for studying posttranscriptional events.\",\n \"corpus_id\": 18917709,\n \"score\": 0\n },\n {\n \"doc_id\": \"21398516\",\n \"title\": \"Mechanistic control of carcinoembryonic antigen-related cell adhesion molecule-1 (CEACAM1) splice isoforms by the heterogeneous nuclear ribonuclear proteins hnRNP L, hnRNP A1, and hnRNP M.\",\n \"abstract\": \"Carcinoembryonic antigen-related cell adhesion molecule-1 (CEACAM1) is expressed in a variety of cell types and is implicated in carcinogenesis. Alternative splicing of CEACAM1 pre-mRNA generates two cytoplasmic domain splice variants characterized by the inclusion (L-isoform) or exclusion (S-isoform) of exon 7. Here we show that the alternative splicing of CEACAM1 pre-mRNA is regulated by novel cis elements residing in exon 7. We report the presence of three exon regulatory elements that lead to the inclusion or exclusion of exon 7 CEACAM1 mRNA in ZR75 breast cancer cells. Heterologous splicing reporter assays demonstrated that the maintenance of authentic alternative splicing mechanisms were independent of the CEACAM1 intron sequence context. We show that forced expression of these exon regulatory elements could alter CEACAM1 splicing in HEK-293 cells. Using RNA affinity chromatography, three members of the heterogeneous nuclear ribonucleoprotein family (hnRNP L, hnRNP A1, and hnRNP M) were identified. RNA immunoprecipitation of hnRNP L and hnRNP A1 revealed a binding motif located central and 3' to exon 7, respectively. Depletion of hnRNP A1 or L by RNAi in HEK-293 cells promoted exon 7 inclusion, whereas overexpression led to exclusion of the variable exon. By contrast, overexpression of hnRNP M showed exon 7 inclusion and production of CEACAM1-L mRNA. Finally, stress-induced cytoplasmic accumulation of hnRNP A1 in MDA-MB-468 cells dynamically alters the CEACAM1-S:CEACAM1:L ratio in favor of the l-isoform. Thus, we have elucidated the molecular factors that control the mechanism of splice-site recognition in the alternative splicing regulation of CEACAM1.\",\n \"corpus_id\": 25342291,\n \"score\": 0\n },\n {\n \"doc_id\": \"21743084\",\n \"title\": \"Sequence determinants for the tandem recognition of UGU and CUG rich RNA elements by the two N--terminal RRMs of CELF1.\",\n \"abstract\": \"CUGBP, Elav-like family member 1 (CELF1) is an RNA binding protein with important roles in the regulation of splicing, mRNA decay and translation. CELF1 contains three RNA recognition motifs (RRMs). We used gel retardation, gel filtration, isothermal titration calorimetry and NMR titration studies to investigate the recognition of RNA by the first two RRMs of CELF1. NMR shows that RRM1 is promiscuous in binding to both UGU and CUG repeat sequences with comparable chemical shift perturbations. In contrast, RRM2 shows greater selectivity for UGUU rather than CUG motifs. A construct (T187) containing both binding domains (RRM1 and RRM2) was systematically studied for interaction with tandem UGU RNA binding sites with different length linker sequences UGU(U)(x)UGU where x = 1-7. A single U spacer results in interactions only with RRM1, demonstrating both steric constraints in accommodating both RRMs simultaneously at adjacent sites, and also subtle differences in binding affinities between RRMs. However, high affinity co-operative binding (K(d) ~ 0.4 µM) is evident for RNA sequences with x = 2-4, but longer spacers (x ≥ 5) lead to a 10-fold reduction in affinity. Our analysis rationalizes the high affinity interaction of T187 with the 11mer GRE consensus regulatory sequence UGUUUGUUUGU and has significant consequences for the prediction of CELF1 binding sites.\",\n \"corpus_id\": 15897106,\n \"score\": 0\n },\n {\n \"doc_id\": \"22154808\",\n \"title\": \"Three RNA recognition motifs participate in RNA recognition and structural organization by the pro-apoptotic factor TIA-1.\",\n \"abstract\": \"T-cell intracellular antigen-1 (TIA-1) regulates developmental and stress-responsive pathways through distinct activities at the levels of alternative pre-mRNA splicing and mRNA translation. The TIA-1 polypeptide contains three RNA recognition motifs (RRMs). The central RRM2 and C-terminal RRM3 associate with cellular mRNAs. The N-terminal RRM1 enhances interactions of a C-terminal Q-rich domain of TIA-1 with the U1-C splicing factor, despite linear separation of the domains in the TIA-1 sequence. Given the expanded functional repertoire of the RRM family, it was unknown whether TIA-1 RRM1 contributes to RNA binding as well as documented protein interactions. To address this question, we used isothermal titration calorimetry and small-angle X-ray scattering to dissect the roles of the TIA-1 RRMs in RNA recognition. Notably, the fas RNA exhibited two binding sites with indistinguishable affinities for TIA-1. Analyses of TIA-1 variants established that RRM1 was dispensable for binding AU-rich fas sites, yet all three RRMs were required to bind a polyU RNA with high affinity. Small-angle X-ray scattering analyses demonstrated a \\\"V\\\" shape for a TIA-1 construct comprising the three RRMs and revealed that its dimensions became more compact in the RNA-bound state. The sequence-selective involvement of TIA-1 RRM1 in RNA recognition suggests a possible role for RNA sequences in regulating the distinct functions of TIA-1. Further implications for U1-C recruitment by the adjacent TIA-1 binding sites of the fas pre-mRNA and the bent TIA-1 shape, which organizes the N- and C-termini on the same side of the protein, are discussed.\",\n \"corpus_id\": 25245338,\n \"score\": 0\n },\n {\n \"doc_id\": \"22402488\",\n \"title\": \"HnRNP L and L-like cooperate in multiple-exon regulation of CD45 alternative splicing.\",\n \"abstract\": \"CD45 encodes a trans-membrane protein-tyrosine phosphatase expressed in diverse cells of the immune system. By combinatorial use of three variable exons 4-6, isoforms are generated that differ in their extracellular domain, thereby modulating phosphatase activity and immune response. Alternative splicing of these CD45 exons involves two heterogeneous ribonucleoproteins, hnRNP L and its cell-type specific paralog hnRNP L-like (LL). To address the complex combinatorial splicing of exons 4-6, we investigated hnRNP L/LL protein expression in human B-cells in relation to CD45 splicing patterns, applying RNA-Seq. In addition, mutational and RNA-binding analyses were carried out in HeLa cells. We conclude that hnRNP LL functions as the major CD45 splicing repressor, with two CA elements in exon 6 as its primary target. In exon 4, one element is targeted by both hnRNP L and LL. In contrast, exon 5 was never repressed on its own and only co-regulated with exons 4 and 6. Stable L/LL interaction requires CD45 RNA, specifically exons 4 and 6. We propose a novel model of combinatorial alternative splicing: HnRNP L and LL cooperate on the CD45 pre-mRNA, bridging exons 4 and 6 and looping out exon 5, thereby achieving full repression of the three variable exons.\",\n \"corpus_id\": 9572984,\n \"score\": 0\n },\n {\n \"doc_id\": \"22684629\",\n \"title\": \"Control of alternative splicing by forskolin through hnRNP K during neuronal differentiation.\",\n \"abstract\": \"The molecular basis of cell signal-regulated alternative splicing at the 3' splice site remains largely unknown. We isolated a protein kinase A-responsive ribonucleic acid (RNA) element from a 3' splice site of the synaptosomal-associated protein 25 (Snap25) gene for forskolin-inhibited splicing during neuronal differentiation of rat pheochromocytoma PC12 cells. The element binds specifically to heterogeneous nuclear ribonucleo protein (hnRNP) K in a phosphatase-sensitive way, which directly competes with the U2 auxiliary factor U2AF65, an essential component of early spliceosomes. Transcripts with similarly localized hnRNP K target motifs upstream of alternative exons are enriched in genes often associated with neurological diseases. We show that such motifs upstream of the Runx1 exon 6 also bind hnRNP K, and importantly, hnRNP K is required for forskolin-induced repression of the exon. Interestingly, this exon encodes the peptide domain that determines the switch of the transcriptional repressor/activator activity of Runx1, a change known to be critical in specifying neuron lineages. Consistent with an important role of the target genes in neurons, knocking down hnRNP K severely disrupts forskolin-induced neurite growth. Thus, through hnRNP K, the neuronal differentiation stimulus forskolin targets a critical 3' splice site component of the splicing machinery to control alternative splicing of crucial genes. This also provides a regulated direct competitor of U2AF65 for cell signal control of 3' splice site usage.\",\n \"corpus_id\": 12926386,\n \"score\": 0\n },\n {\n \"doc_id\": \"23704325\",\n \"title\": \"hnRNP A1 and secondary structure coordinate alternative splicing of Mag.\",\n \"abstract\": \"Myelin-associated glycoprotein (MAG) is a major component of myelin in the vertebrate central nervous system. MAG is present in the periaxonal region of the myelin structure, where it interacts with neuronal proteins to inhibit axon outgrowth and protect neurons from degeneration. Two alternatively spliced isoforms of Mag mRNA have been identified. The mRNA encoding the shorter isoform, known as S-MAG, contains a termination codon in exon 12, while the mRNA encoding the longer isoform, known as L-MAG, skips exon 12 and produces a protein with a longer C-terminal region. L-MAG is required in the central nervous system. How inclusion of Mag exon 12 is regulated is not clear. In a previous study, we showed that heteronuclear ribonucleoprotein A1 (hnRNP A1) contributes to Mag exon 12 skipping. Here, we show that hnRNP A1 interacts with an element that overlaps the 5' splice site of Mag exon 12. The element has a reduced ability to interact with the U1 snRNP compared with a mutant that improves the splice site consensus. An evolutionarily conserved secondary structure is present surrounding the element. The structure modulates interaction with both hnRNP A1 and U1. Analysis of splice isoforms produced from a series of reporter constructs demonstrates that the hnRNP A1-binding site and the secondary structure both contribute to exclusion of Mag exon 12.\",\n \"corpus_id\": 2384706,\n \"score\": 0\n },\n {\n \"doc_id\": \"23782695\",\n \"title\": \"Crystal structures and RNA-binding properties of the RNA recognition motifs of heterogeneous nuclear ribonucleoprotein L: insights into its roles in alternative splicing regulation.\",\n \"abstract\": \"Heterogeneous nuclear ribonucleoprotein L (hnRNP L) is an abundant RNA-binding protein implicated in many bioprocesses, including pre-mRNA processing, mRNA export of intronless genes, internal ribosomal entry site-mediated translation, and chromatin modification. It contains four RNA recognition motifs (RRMs) that bind with CA repeats or CA-rich elements. In this study, surface plasmon resonance spectroscopy assays revealed that all four RRM domains contribute to RNA binding. Furthermore, we elucidated the crystal structures of hnRNP L RRM1 and RRM34 at 2.0 and 1.8 Å, respectively. These RRMs all adopt the typical β1α1β2β3α2β4 topology, except for an unusual fifth β-strand in RRM3. RRM3 and RRM4 interact intimately with each other mainly through helical surfaces, leading the two β-sheets to face opposite directions. Structure-based mutations and surface plasmon resonance assay results suggested that the β-sheets of RRM1 and RRM34 are accessible for RNA binding. FRET-based gel shift assays (FRET-EMSA) and steady-state FRET assays, together with cross-linking and dynamic light scattering assays, demonstrated that hnRNP L RRM34 facilitates RNA looping when binding to two appropriately separated binding sites within the same target pre-mRNA. EMSA and isothermal titration calorimetry binding studies with in vivo target RNA suggested that hnRNP L-mediated RNA looping may occur in vivo. Our study provides a mechanistic explanation for the dual functions of hnRNP L in alternative splicing regulation as an activator or repressor.\",\n \"corpus_id\": 30641280,\n \"score\": 0\n },\n {\n \"doc_id\": \"23863836\",\n \"title\": \"HnRNP A1 controls a splicing regulatory circuit promoting mesenchymal-to-epithelial transition.\",\n \"abstract\": \"Epithelial-to-mesenchymal transition (EMT) is an embryonic program used by cancer cells to acquire invasive capabilities becoming metastatic. ΔRon, a constitutively active isoform of the Ron tyrosine kinase receptor, arises from skipping of Ron exon 11 and provided the first example of an alternative splicing variant causatively linked to the activation of tumor EMT. Splicing of exon 11 is controlled by two adjacent regulatory elements, a silencer and an enhancer of splicing located in exon 12. The alternative splicing factor and oncoprotein SRSF1 directly binds to the enhancer, induces the production of ΔRon and activates EMT leading to cell locomotion. Interestingly, we now find an important role for hnRNP A1 in controlling the activity of the Ron silencer. HnRNP A1 is able to antagonize the binding of SRSF1 and prevent exon skipping. Notably, hnRNP A1, by inhibiting the production of ΔRon, activates the reversal program, namely the mesenchymal-to-epithelial transition, which instead occurs at the final metastasis sites. Also, hnRNP A1 affects Ron splicing by regulating the expression level of hnRNP A2/B1, which similarly to SRSF1 can promote ΔRon production. These results shed light on how splicing regulation contributes to the tumor progression and provide potential targets to develop anticancer therapies.\",\n \"corpus_id\": 6377441,\n \"score\": 0\n },\n {\n \"doc_id\": \"24121633\",\n \"title\": \"HnRNP L and hnRNP LL antagonistically modulate PTB-mediated splicing suppression of CHRNA1 pre-mRNA.\",\n \"abstract\": \"CHRNA1 gene, encoding the muscle nicotinic acetylcholine receptor alpha subunit, harbors an inframe exon P3A. Inclusion of exon P3A disables assembly of the acetylcholine receptor subunits. A single nucleotide mutation in exon P3A identified in congenital myasthenic syndrome causes exclusive inclusion of exon P3A. The mutation gains a de novo binding affinity for a splicing enhancing RNA-binding protein, hnRNP LL, and displaces binding of a splicing suppressing RNA-binding protein, hnRNP L. The hnRNP L binds to another splicing repressor PTB through the proline-rich region and promotes PTB binding to the polypyrimidine tract upstream of exon P3A, whereas hnRNP LL lacking the proline-rich region cannot bind to PTB. Interaction of hnRNP L with PTB inhibits association of U2AF(65) and U1 snRNP with the upstream and downstream of P3A, respectively, which causes a defect in exon P3A definition. HnRNP L and hnRNP LL thus antagonistically modulate PTB-mediated splicing suppression of exon P3A.\",\n \"corpus_id\": 5562194,\n \"score\": 0\n },\n {\n \"doc_id\": \"24533984\",\n \"title\": \"hnRNP M facilitates exon 7 inclusion of SMN2 pre-mRNA in spinal muscular atrophy by targeting an enhancer on exon 7.\",\n \"abstract\": \"Spinal muscular atrophy (SMA) is an autosomal recessive genetic disease, which causes death of motor neurons in the anterior horn of the spinal cord. Genetic cause of SMA is the deletion or mutation of SMN1 gene, which encodes the SMN protein. Although SMA patients include SMN2 gene, a duplicate of SMN1 gene, predominant production of exon 7 skipped isoform from SMN2 pre-mRNA, fails to rescue SMA patients. Here we show that hnRNP M, a member of hnRNP protein family, when knocked down, promotes exon 7 skipping of both SMN2 and SMN1 pre-mRNA. By contrast, overexpression of hnRNP M promotes exon 7 inclusion of both SMN2 and SMN1 pre-mRNA. Significantly, hnRNP M promotes exon 7 inclusion in SMA patient cells. Thus, we conclude that hnRNP M promotes exon 7 inclusion of both SMN1 and SMN2 pre-mRNA. We also demonstrate that hnRNP M contacts an enhancer on exon 7, which was previously shown to provide binding site for tra2β. We present evidence that hnRNP M and tra2β contact overlapped sequence on exon 7 but with slightly different RNA sequence requirements. In addition, hnRNP M promotes U2AF65 recruitment on the flanking intron of exon 7. We conclude that hnRNP M promotes exon 7 inclusion of SMN1 and SMN2 pre-mRNA through targeting an enhancer on exon 7 through recruiting U2AF65. Our results provide a clue that hnRNP M is a potential therapeutic target for SMA.\",\n \"corpus_id\": 205820651,\n \"score\": 0\n },\n {\n \"doc_id\": \"24682828\",\n \"title\": \"Structure, dynamics and RNA binding of the multi-domain splicing factor TIA-1.\",\n \"abstract\": \"Alternative pre-messenger ribonucleic acid (pre-mRNA) splicing is an essential process in eukaryotic gene regulation. The T-cell intracellular antigen-1 (TIA-1) is an apoptosis-promoting factor that modulates alternative splicing of transcripts, including the pre-mRNA encoding the membrane receptor Fas. TIA-1 is a multi-domain ribonucleic acid (RNA) binding protein that recognizes poly-uridine tract RNA sequences to facilitate 5' splice site recognition by the U1 small nuclear ribonucleoprotein (snRNP). Here, we characterize the RNA interaction and conformational dynamics of TIA-1 by nuclear magnetic resonance (NMR), isothermal titration calorimetry (ITC) and small angle X-ray scattering (SAXS). Our NMR-derived solution structure of TIA-1 RRM2-RRM3 (RRM2,3) reveals that RRM2 adopts a canonical RNA recognition motif (RRM) fold, while RRM3 is preceded by an non-canonical helix α0. NMR and SAXS data show that all three RRMs are largely independent structural modules in the absence of RNA, while RNA binding induces a compact arrangement. RRM2,3 binds to pyrimidine-rich FAS pre-mRNA or poly-uridine (U9) RNA with nanomolar affinities. RRM1 has little intrinsic RNA binding affinity and does not strongly contribute to RNA binding in the context of RRM1,2,3. Our data unravel the role of binding avidity and the contributions of the TIA-1 RRMs for recognition of pyrimidine-rich RNAs.\",\n \"corpus_id\": 8496882,\n \"score\": 0\n },\n {\n \"doc_id\": \"25216038\",\n \"title\": \"Structural and mechanistic insights into poly(uridine) tract recognition by the hnRNP C RNA recognition motif.\",\n \"abstract\": \"HnRNP C is a ubiquitous RNA regulatory factor and the principal constituent of the nuclear hnRNP core particle. The protein contains one amino-terminal RNA recognition motif (RRM) known to bind uridine (U)-rich sequences. This work provides a molecular and mechanistic understanding of this interaction. We solved the solution structures of the RRM in complex with poly(U) oligomers of five and seven nucleotides. The five binding pockets of RRM recognize uridines with an unusual 5'-to-3' gradient of base selectivity. The target recognition is therefore strongly sensitive to base clustering, explaining the preference for contiguous uridine tracts. Using a novel approach integrating the structurally derived recognition consensus of the RRM with a thermodynamic description of its multi-register binding, we modeled the saturation of cellular uridine tracts by this protein. The binding pattern is remarkably consistent with the experimentally observed transcriptome-wide cross-link distribution of the full-length hnRNP C on short uridine tracts. This result re-establishes the RRM as the primary RNA-binding domain of the hnRNP C tetramer and provides a proof of concept for interpreting high-throughput interaction data using structural approaches.\",\n \"corpus_id\": 27530107,\n \"score\": 0\n },\n {\n \"doc_id\": \"25623890\",\n \"title\": \"hnRNP L inhibits CD44 V10 exon splicing through interacting with its upstream intron.\",\n \"abstract\": \"CD44 is a complex cell adhesion molecule that mediates communication and adhesion between adjacent cells as well as between cells and the extracellular matrix. CD44 pre-mRNA produces various mRNA isoforms through alternative splicing of 20 exons, among which exons 1-5 (C1-C5) and 16-20 (C6-C10) are constant exons, whereas exons 6-15 (V1-V10) are variant exons. CD44 V10 exon has important roles in breast tumor progression and Hodgkin lymphoma. Here we show that increased expression of hnRNP L inhibits V10 exon splicing of CD44 pre-mRNA, whereas reduced expression of hnRNP L promotes V10 exon splicing. In addition, hnRNP L also promotes V10 splicing of endogenous CD44 pre-mRNA. Through mutation analysis, we demonstrate that the effects of hnRNP L on V10 splicing are abolished when the CA-rich sequence on the upstream intron of V10 exon is disrupted. However, hnRNP L effects are stronger if more CA-repeats are provided. Furthermore, we show that hnRNP L directly contacts the CA-rich sequence. Importantly, we provide evidences that hnRNP L inhibits U2AF65 binding on the upstream Py tract of V10 exon. Our results reveal that hnRNP L is a new regulator for CD44 V10 exon splicing.\",\n \"corpus_id\": 5403304,\n \"score\": 0\n },\n {\n \"doc_id\": \"26101706\",\n \"title\": \"HnRNP A1 tethers KSRP to an exon splicing silencer that inhibits an erythroid-specific splicing event in PU.1-induced erythroleukemia.\",\n \"abstract\": \"Exon 16 inclusion is a critical splicing event that triggers the production of a functional protein 4.1R in mature normal erythroblasts, and is obviated in PU.1-induced erythroleukemia cells. Exon 16 contains an exonic splicing silencer (ESS16) that interacts with hnRNP A/B in heterologous cell context. We here show that ESS16 promotes the recruitment of a protein complex containing hnRNP A1 and a 79-kDa protein in nuclear extracts from either proliferative erythroleukemia cells or cells induced to terminal differentiation. By using 2D gel fractionation and mass spectrometry, we unambiguously identified KSRP as the 79-kDa component interacting with ESS16. Furthermore, we show that KSRP slightly decreases in erythroleukemia cells induced to terminal erythroid differentiation. Yet, KSRP inducible knockdown, through stable transfection of small hairpin KSRP RNA, did not alter exon 16 splicing, suggesting that KSRP alone does not modulate the splicing event. Interestingly, absence of hnRNP A1 prevented KSRP from binding to ESS16. Reciprocally, KSRP interaction with ESS16 was recovered when hnRNP A1 expression is restored in hnRNP A1-null cells. Collectively, this study establishes that hnRNPA1 is part of a KSRP-containing RNP complex, and emphasizes that, aside from its function in AU-rich element-mediated mRNA decay and its role in microRNA biogenesis, KSRP associates with hnRNP A1 to bind an ESS. These findings further support the role of members of the KH-domain protein family in organizing large RNA-protein complex formation, rather than primarily in modulating specific splicing events.\",\n \"corpus_id\": 23325791,\n \"score\": 0\n },\n {\n \"doc_id\": \"26545814\",\n \"title\": \"Biochemical identification of new proteins involved in splicing repression at the Drosophila P-element exonic splicing silencer.\",\n \"abstract\": \"Splicing of the Drosophila P-element third intron (IVS3) is repressed in somatic tissues due to the function of an exonic splicing silencer (ESS) complex present on the 5' exon RNA. To comprehensively characterize the mechanisms of this alternative splicing regulation, we used biochemical fractionation and affinity purification to isolate the silencer complex assembled in vitro and identify the constituent proteins by mass spectrometry. Functional assays using splicing reporter minigenes identified the proteins hrp36 and hrp38 and the cytoplasmic poly(A)-binding protein PABPC1 as novel functional components of the splicing silencer. hrp48, PSI, and PABPC1 have high-affinity RNA-binding sites on the P-element IVS3 5' exon, whereas hrp36 and hrp38 proteins bind with low affinity to the P-element silencer RNA. RNA pull-down and immobilized protein assays showed that hrp48 protein binding to the silencer RNA can recruit hrp36 and hrp38. These studies identified additional components that function at the P-element ESS and indicated that proteins with low-affinity RNA-binding sites can be recruited in a functional manner through interactions with a protein bound to RNA at a high-affinity binding site. These studies have implications for the role of heterogeneous nuclear ribonucleoproteins (hnRNPs) in the control of alternative splicing at cis-acting regulatory sites.\",\n \"corpus_id\": 13608186,\n \"score\": 0\n },\n {\n \"doc_id\": \"26919236\",\n \"title\": \"Heterogeneous nuclear ribonucleoproteins A1 and A2 modulate expression of Tid1 isoforms and EGFR signaling in non-small cell lung cancer.\",\n \"abstract\": \"The Tid1 protein is a DnaJ co-chaperone that has two alternative splicing isoforms: Tid1 long form (Tid1-L) and Tid1 short form (Tid1-S). Recent studies have shown that Tid1-L functions as a tumor suppressor by decreasing EGFR signaling in various cancers, including head and neck cancer and non-small cell lung cancer (NSCLC). However, the molecular mechanism responsible for regulating the alternative splicing of Tid1 is not yet known. Two splicing factors, heterogeneous nuclear ribonucleoproteins (hnRNP) A1 and A2, participate in alternative splicing and are known to be overexpressed in lung cancers. In this work, we examined if hnRNP A1 and A2 could regulate the alternative splicing of Tid1 to modulate tumorigenesis in NSCLC. We report that RNAi-mediated depletion of both hnRNP A1/A2 (but not single depletion of either) increased Tid1-L expression, inhibited cell proliferation and attenuated EGFR signaling. Analyses of the expression levels of hnRNP A1, hnRNP A2, EGFR and Tid1-L in NSCLC tissues revealed that hnRNP A1 and A2 are positively correlated with EGFR, but negatively correlated with Tid1-L. NSCLC patients with high-level expression of hnRNP A1, hnRNP A2 and EGFR combined with low-level expression of Tid1-L were associated with poor overall survival. Taken together, our results suggest that hnRNP A1 or A2 are both capable of facilitating the alternative splicing of exon 11 in the Tid1 pre-mRNA, thereby suppressing the expression of Tid1-L and allowing EGFR-related signaling to facilitate NSCLC tumorigenesis.\",\n \"corpus_id\": 27438702,\n \"score\": 0\n },\n {\n \"doc_id\": \"27437398\",\n \"title\": \"Crystal Structure of the N-Terminal RNA Recognition Motif of mRNA Decay Regulator AUF1.\",\n \"abstract\": \"AU-rich element binding/degradation factor 1 (AUF1) plays a role in destabilizing mRNAs by forming complexes with AU-rich elements (ARE) in the 3'-untranslated regions. Multiple AUF1-ARE complexes regulate the translation of encoded products related to the cell cycle, apoptosis, and inflammation. AUF1 contains two tandem RNA recognition motifs (RRM) and a Gln- (Q-) rich domain in their C-terminal region. To observe how the two RRMs are involved in recognizing ARE, we obtained the AUF1-p37 protein covering the two RRMs. However, only N-terminal RRM (RRM1) was crystallized and its structure was determined at 1.7 Å resolution. It appears that the RRM1 and RRM2 separated before crystallization. To demonstrate which factors affect the separate RRM1-2, we performed limited proteolysis using trypsin. The results indicated that the intact proteins were cleaved by unknown proteases that were associated with them prior to crystallization. In comparison with each of the monomers, the conformations of the β2-β3 loops were highly variable. Furthermore, a comparison with the RRM1-2 structures of HuR and hnRNP A1 revealed that a dimer of RRM1 could be one of the possible conformations of RRM1-2. Our data may provide a guidance for further structural investigations of AUF1 tandem RRM repeat and its mode of ARE binding.\",\n \"corpus_id\": 18607490,\n \"score\": 0\n },\n {\n \"doc_id\": \"28084329\",\n \"title\": \"SPSB1-mediated HnRNP A1 ubiquitylation regulates alternative splicing and cell migration in EGF signaling.\",\n \"abstract\": \"Extracellular signals have been shown to impact on alternative pre-mRNA splicing; however, the molecular mechanisms and biological significance of signal-induced splicing regulation remain largely unknown. Here, we report that epidermal growth factor (EGF) induces splicing changes through ubiquitylation of a well-known splicing regulator, hnRNP A1. EGF signaling upregulates an E3 ubiquitin (Ub) ligase adaptor, SPRY domain-containing SOCS box protein 1 (SPSB1), which recruits Elongin B/C-Cullin complexes to conjugate lysine 29-linked polyUb chains onto hnRNP A1. Importantly, SPSB1 and ubiquitylation of hnRNP A1 have a critical role in EGF-driven cell migration. Mechanistically, EGF-induced ubiquitylation of hnRNP A1 together with the activation of SR protein kinases (SRPKs) results in the upregulation of a Rac1 splicing isoform, Rac1b, to promote cell motility. These findings unravel a novel crosstalk between protein ubiquitylation and alternative splicing in EGF/EGF receptor signaling, and identify a new EGF/SPSB1/hnRNP A1/Rac1 axis in modulating cell migration, which may have important implications for cancer treatment.\",\n \"corpus_id\": 19109215,\n \"score\": 0\n },\n {\n \"doc_id\": \"28119102\",\n \"title\": \"Suppression of 5' splice-sites through multiple exonic motifs by hnRNP L.\",\n \"abstract\": \"Selection of 5' splice-sites (5'SS) in alternative splicing plays an important role in gene regulation. Although regulatory mechanisms of heterogeneous nuclear ribonucleoprotein L (hnRNP L), a well-known splicing regulatory protein, have been studied in a substantial level, its role in 5'SS selection is not thoroughly defined. By using a KLF6 pre-mRNA alternative splicing model, we demonstrate in this report that hnRNP L inhibits proximal 5'SS but promotes two consecutive distal 5'SS splicing, antagonizing SRSF1 roles in KLF6 pre-mRNA splicing. In addition, three consecutive CA-rich sequences in a CA cassette immediately upstream of the proximal 5'SS are all required for hnRNP L functions. Importantly, the CA-cassette locations on the proximal exon do not affect hnRNP L roles. We further show that the proximal 5'SS but not the two distal 5'SSs are essential for hnRNP L activities. Notably, in a Bcl-x pre-mRNA model that contains two alternative 5'SS but includes CA-rich elements at distal exon, we demonstrate that hnRNP L also suppresses nearby 5'SS activation. Taken together, we conclude that hnRNP L suppresses 5'SS selection through multiple exonic motifs.\",\n \"corpus_id\": 35617076,\n \"score\": 0\n },\n {\n \"doc_id\": \"28368279\",\n \"title\": \"Crystal structure of the human heterogeneous ribonucleoprotein A18 RNA-recognition motif.\",\n \"abstract\": \"The heterogeneous ribonucleoprotein A18 (hnRNP A18) is upregulated in hypoxic regions of various solid tumors and promotes tumor growth via the coordination of mRNA transcripts associated with pro-survival genes. Thus, hnRNP A18 represents an important therapeutic target in tumor cells. Presented here is the first X-ray crystal structure to be reported for the RNA-recognition motif of hnRNP A18. By comparing this structure with those of homologous RNA-binding proteins (i.e. hnRNP A1), three residues on one face of an antiparallel β-sheet (Arg48, Phe50 and Phe52) and one residue in an unstructured loop (Arg41) were identified as likely to be involved in protein-nucleic acid interactions. This structure helps to serve as a foundation for biophysical studies of this RNA-binding protein and structure-based drug-design efforts for targeting hnRNP A18 in cancer, such as malignant melanoma, where hnRNP A18 levels are elevated and contribute to disease progression.\",\n \"corpus_id\": 4544901,\n \"score\": 0\n },\n {\n \"doc_id\": \"28379442\",\n \"title\": \"An RRM-ZnF RNA recognition module targets RBM10 to exonic sequences to promote exon exclusion.\",\n \"abstract\": \"RBM10 is an RNA-binding protein that plays an essential role in development and is frequently mutated in the context of human disease. RBM10 recognizes a diverse set of RNA motifs in introns and exons and regulates alternative splicing. However, the molecular mechanisms underlying this seemingly relaxed sequence specificity are not understood and functional studies have focused on 3΄ intronic sites only. Here, we dissect the RNA code recognized by RBM10 and relate it to the splicing regulatory function of this protein. We show that a two-domain RRM1-ZnF unit recognizes a GGA-centered motif enriched in RBM10 exonic sites with high affinity and specificity and test that the interaction with these exonic sequences promotes exon skipping. Importantly, a second RRM domain (RRM2) of RBM10 recognizes a C-rich sequence, which explains its known interaction with the intronic 3΄ site of NUMB exon 9 contributing to regulation of the Notch pathway in cancer. Together, these findings explain RBM10's broad RNA specificity and suggest that RBM10 functions as a splicing regulator using two RNA-binding units with different specificities to promote exon skipping.\",\n \"corpus_id\": 8729390,\n \"score\": 0\n },\n {\n \"doc_id\": \"29450990\",\n \"title\": \"Splicing Site Recognition by Synergy of Three Domains in Splicing Factor RBM10.\",\n \"abstract\": \"Splicing factor RBM10 and its close homologues RBM5 and RBM6 govern the splicing of oncogenes such as Fas, NUMB, and Bcl-X. The molecular architecture of these proteins includes zinc fingers (ZnFs) and RNA recognition motifs (RRMs). Three of these domains in RBM10 that constitute the RNA binding part of this splicing factor were found to individually bind RNAs with micromolar affinities. It was thus of interest to further investigate the structural basis of the well-documented high-affinity RNA recognition by RMB10. Here, we investigated RNA binding by combinations of two or three of these domains and discovered that a polypeptide containing RRM1, ZnF1, and RRM2 connected by their natural linkers recognizes a specific sequence of the Fas exon 6 mRNA with an affinity of 20 nM. Nuclear magnetic resonance structures of the RBM10 domains RRM1 and ZnF1 and the natural V354del isoform of RRM2 further confirmed that the interactions with RNA are driven by canonical RNA recognition elements. The well-known high-fidelity RNA splice site recognition by RBM10, and probably by RBM5 and RBM6, can thus be largely rationalized by a cooperative binding action of RRM and ZnF domains.\",\n \"corpus_id\": 3855285,\n \"score\": 0\n },\n {\n \"doc_id\": \"29518215\",\n \"title\": \"Molecular basis of titin exon exclusion by RBM20 and the novel titin splice regulator PTB4.\",\n \"abstract\": \"RNA-binding motif protein 20 (RBM20) is a cardiac splice regulator that adapts cardiac filling via its diverse substrates-including the sarcomeric protein titin. The molecular basis and regulation of RBM20-dependent exon exclusion are largely unknown. In tissue culture experiments, we show that the combination of RNA recognition motif (RRM) and C-terminus is necessary and sufficient for RBM20 activity, indicating an important function of the ZnF2 domain in splicing repression. Using splice reporter and in vitro binding assays targeting titin exons 241-243, we identified a minimal genomic segment that is necessary for RBM20-mediated splicing repression of the alternative exon. Here, RBM20 binds the cluster containing most RBM20 binding motifs through its RRM domain and represses the upstream and downstream introns. For subsequent exon exclusion, specific regions upstream, downstream and within the alternative exon 242 are required. Regulation of exon exclusion involves PTB4 as a novel titin splice regulator, which counteracts RBM20 repressor activity in HEK293 cells. Together, these mechanistic insights into the regulation and action of RBM20 and PTB4 provide a basis for the future development of RBM20 modulators that adapt titin elasticity in cardiac disease.\",\n \"corpus_id\": 3770163,\n \"score\": 0\n },\n {\n \"doc_id\": \"29581412\",\n \"title\": \"HnRNP L represses cryptic exons.\",\n \"abstract\": \"The fidelity of RNA splicing is regulated by a network of splicing enhancers and repressors, although the rules that govern this process are not yet fully understood. One mechanism that contributes to splicing fidelity is the repression of nonconserved cryptic exons by splicing factors that recognize dinucleotide repeats. We previously identified that TDP-43 and PTBP1/PTBP2 are capable of repressing cryptic exons utilizing UG and CU repeats, respectively. Here we demonstrate that hnRNP L (HNRNPL) also represses cryptic exons by utilizing exonic CA repeats, particularly near the 5'SS. We hypothesize that hnRNP L regulates CA repeat repression for both cryptic exon repression and developmental processes such as T cell differentiation.\",\n \"corpus_id\": 4349626,\n \"score\": 0\n }\n]","isConversational":false}}},{"rowIdx":56,"cells":{"query":{"kind":"string","value":"{\n \"doc_id\": \"24753571\",\n \"title\": \"A bimodular nuclear localization signal assembled via an extended double-stranded RNA-binding domain acts as an RNA-sensing signal for transportin 1.\",\n \"abstract\": \"The human RNA-editing enzyme adenosine deaminase acting on RNA (ADAR1) carries a unique nuclear localization signal (NLS) that overlaps one of its double-stranded RNA-binding domains (dsRBDs). This dsRBD-NLS is recognized by the nuclear import receptor transportin 1 (Trn1; also called karyopherin-β2) in an RNA-sensitive manner. Most Trn1 cargos bear a well-characterized proline-tyrosine-NLS, which is missing from the dsRBD-NLS. Here, we report the structure of the dsRBD-NLS, which reveals an unusual dsRBD fold extended by an additional N-terminal α-helix that brings the N- and C-terminal flanking regions in close proximity. We demonstrate experimentally that the atypical ADAR1-NLS is bimodular and is formed by the combination of the two flexible fragments flanking the folded domain. The intervening dsRBD acts only as an RNA-sensing scaffold, allowing the two NLS modules to be properly positioned for interacting with Trn1. We also provide a structural model showing how Trn1 can recognize the dsRBD-NLS and how dsRNA binding can interfere with Trn1 binding.\",\n \"corpus_id\": 259098\n}"},"candidates":{"kind":"list like","value":[{"doc_id":"18343812","title":"A PY-NLS nuclear targeting signal is required for nuclear localization and function of the Saccharomyces cerevisiae mRNA-binding protein Hrp1.","abstract":"Proteins destined for import into the nucleus contain nuclear localization signals (NLSs) that are recognized by import receptors termed karyopherins or importins. Until recently, the only nuclear import sequence that had been well defined and characterized was the classical NLS (cNLS), which is recognized by importin alpha. However, Chook and coworkers (Lee, B. J., Cansizoglu, A. E., Süel, K. E., Louis, T. H., Zhang, Z., and Chook, Y. M. (2006) Cell 126, 543-558) have provided new insight into nuclear targeting with their identification of a novel NLS, termed the PY-NLS, that is recognized by the human karyopherin beta2/transportin (Kapbeta2) receptor. Here, we demonstrate that the PY-NLS is conserved in Saccharomyces cerevisiae and show for the first time that the PY-NLS is a functional nuclear targeting sequence in vivo. The apparent ortholog of Kapbeta2 in yeast, Kap104, has two known cargos, the mRNA-binding proteins Hrp1 and Nab2, which both contain putative PY-NLS-like sequences. We find that the PY-NLS-like sequence within Hrp1, which closely matches the PY-NLS consensus, is both necessary and sufficient for nuclear import and is also required for receptor binding and protein function. In contrast, the PY-NLS-like sequences in Nab2, which vary from the PY-NLS consensus, are not required for proper import or protein function, suggesting that Kap104 may interact with different cargos using multiple mechanisms. Dissection of the PY-NLS consensus reveals that the minimal PY-NLS in yeast consists of the C-terminal portion of the human consensus, R/H/KX(2-5)PY, with upstream basic or hydrophobic residues enhancing the targeting function. Finally, we apply this analysis to a bioinformatic search of the yeast proteome as a preliminary search for new potential Kap104 cargos.","corpus_id":28660584,"score":2},{"doc_id":"19124606","title":"RNA-regulated interaction of transportin-1 and exportin-5 with the double-stranded RNA-binding domain regulates nucleocytoplasmic shuttling of ADAR1.","abstract":"Double-stranded RNA (dsRNA)-binding proteins interact with substrate RNAs via dsRNA-binding domains (dsRBDs). Several proteins harboring these domains exhibit nucleocytoplasmic shuttling and possibly remain associated with their substrate RNAs bound in the nucleus during nuclear export. In the human RNA-editing enzyme ADAR1-c, the nuclear localization signal overlaps the third dsRBD, while the corresponding import factor is unknown. The protein also lacks a clear nuclear export signal but shuttles between the nucleus and the cytoplasm. Here we identify transportin-1 as the import receptor for ADAR1. Interestingly, dsRNA binding interferes with transportin-1 binding. At the same time, each of the dsRBDs in ADAR1 interacts with the export factor exportin-5. RNA binding stimulates this interaction but is not a prerequisite. Thus, our data demonstrate a role for some dsRBDs as RNA-sensitive nucleocytoplasmic transport signals. dsRBD3 in ADAR1 can mediate nuclear import, while interaction of all dsRBDs might control nuclear export. This finding may have implications for other proteins containing dsRBDs and suggests a selective nuclear export mechanism for substrates interacting with these proteins.","corpus_id":19334062,"score":2},{"doc_id":"19617375","title":"Identification of a selective nuclear import signal in adenosine deaminases acting on RNA.","abstract":"The adenosine deaminases acting on RNA (ADARs) comprise a family of RNA editing enzymes that selectively modify single codons within RNA primary transcripts with often profound impact on protein function. Little is known about the mechanisms that regulate nuclear RNA editing activity. Editing levels show cell-type specific and developmental modulation that does not strictly coincide with observed expression levels of ADARs. Here, we provide evidence for a molecular mechanism that might control nuclear import of specific ADARs and, in turn, nuclear RNA editing. We identify an in vivo ADAR3 interaction partner, importin alpha 1 (KPNA2) that specifically recognizes an arginine-rich ADAR3 sequence motif and show that it acts as a functional nuclear localization sequence. Furthermore, whereas KPNA2, but not KPNA1 or KNPA3, recognizes the ADAR3 NLS, we observe the converse binding specificity with ADAR2. Interestingly, alternative splicing of ADAR2 pre-mRNA introduces an ADAR3-like NLS that alters the interaction profile with the importins. Thus, in vivo RNA editing might be regulated, in part, through controlled subcellular localization of ADARs, which in turn is governed by the coordinated local expression of importin alpha proteins and ADAR protein variants.","corpus_id":7301226,"score":2},{"doc_id":"20308327","title":"A glycine-rich domain of hnRNP H/F promotes nucleocytoplasmic shuttling and nuclear import through an interaction with transportin 1.","abstract":"Heterogeneous nuclear ribonucleoprotein (hnRNP) H and F are members of a closely related subfamily of hnRNP proteins that are implicated in many aspects of RNA processing. hnRNP H and F are alternative splicing factors for numerous U2- and U12-dependent introns. The proteins have three RNA binding domains and two glycine-rich domains and localize to both the nucleus and cytoplasm, but little is known about which domains govern subcellular localization or splicing activity. We show here that the central glycine-tyrosine-arginine-rich (GYR) domain is responsible for nuclear localization, and a nonclassical nuclear localization signal (NLS) was mapped to a short, highly conserved sequence whose activity was compromised by point mutations. Glutathione S-transferase (GST) pulldown assays demonstrated that the hnRNP H NLS interacts with the import receptor transportin 1. Finally, we show that hnRNP H/F are transcription-dependent shuttling proteins. Collectively, the results suggest that hnRNP H and F are GYR domain-dependent shuttling proteins whose posttranslational modifications may alter nuclear localization and hence function.","corpus_id":3148086,"score":2},{"doc_id":"21728134","title":"ADAR proteins: double-stranded RNA and Z-DNA binding domains.","abstract":"Adenosine deaminases acting on RNA (ADAR) catalyze adenosine to inosine editing within double-stranded RNA (dsRNA) substrates. Inosine is read as a guanine by most cellular processes and therefore these changes create codons for a different amino acid, stop codons or even a new splice-site allowing protein diversity generated from a single gene. We review here the current structural and molecular knowledge on RNA editing by the ADAR family of protein. We focus especially on two types of nucleic acid binding domains present in ADARs, namely the dsRNA and Z-DNA binding domains.","corpus_id":206650423,"score":2},{"doc_id":"22105828","title":"Molecular dynamics simulation of conformational heterogeneity in transportin 1.","abstract":"Transportin 1 (Trn1), as a typical transport receptor of the karyopherin-β family, mediates numerous RNA binding proteins into the nucleus by recognizing proline-tyrosine nuclear localization signals (PY-NLSs). Such process is regulated by RanGTP through its nucleotide cycle, which is associated with ligand dissociation. Yet a proper description including dynamic properties of Trn1 and its response on ligand/Ran binding has not been accessible so far. Here, we use molecular dynamics simulations to probe the conformational dynamics of the apo-Trn1 and Trn1 in complex with ligand and Ran. The results reveal a strikingly intrinsic flexibility and conformational heterogeneity of Trn1, identified as generally segmental architecture. The segments rotate relative to each other about a flexible hinge and thereby force Trn1 to adopt a conformation compatible with the binding of Ran or substrates. Such binding significantly suppresses the flexibility and conformational heterogeneity of Trn1 and results in a disorder-to-order transition of HR8 loop, which facilitates this loop to allosterically communicate with the C-terminal arch of Trn1. These results give insights into the disassembly and recycling of the Trn1, which has important implications for the regulation of the nuclear transport cycle and for the ligand selectivity.","corpus_id":206406236,"score":2},{"doc_id":"22210494","title":"Solution structure of the N-terminal dsRBD of Drosophila ADAR and interaction studies with RNA.","abstract":"Adenosine deaminases that act on RNA (ADAR) catalyze adenosine to inosine (A-to-I) editing in double-stranded RNA (dsRNA) substrates. Inosine is read as guanosine by the translation machinery; therefore A-to-I editing events in coding sequences may result in recoding genetic information. Whereas vertebrates have two catalytically active enzymes, namely ADAR1 and ADAR2, Drosophila has a single ADAR protein (dADAR) related to ADAR2. The structural determinants controlling substrate recognition and editing of a specific adenosine within dsRNA substrates are only partially understood. Here, we report the solution structure of the N-terminal dsRNA binding domain (dsRBD) of dADAR and use NMR chemical shift perturbations to identify the protein surface involved in RNA binding. Additionally, we show that Drosophila ADAR edits the R/G site in the mammalian GluR-2 pre-mRNA which is naturally modified by both ADAR1 and ADAR2. We then constructed a model showing how dADAR dsRBD1 binds to the GluR-2 R/G stem-loop. This model revealed that most side chains interacting with the RNA sugar-phosphate backbone need only small displacement to adapt for dsRNA binding and are thus ready to bind to their dsRNA target. It also predicts that dADAR dsRBD1 would bind to dsRNA with less sequence specificity than dsRBDs of ADAR2. Altogether, this study gives new insights into dsRNA substrate recognition by Drosophila ADAR.","corpus_id":30989248,"score":2},{"doc_id":"22778397","title":"Structural and energetic basis of ALS-causing mutations in the atypical proline-tyrosine nuclear localization signal of the Fused in Sarcoma protein (FUS).","abstract":"Mutations in the proline/tyrosine-nuclear localization signal (PY-NLS) of the Fused in Sarcoma protein (FUS) cause amyotrophic lateral sclerosis (ALS). Here we report the crystal structure of the FUS PY-NLS bound to its nuclear import receptor Karyopherinβ2 (Kapβ2; also known as Transportin). The FUS PY-NLS occupies the structurally invariant C-terminal arch of Kapβ2, tracing a path similar to that of other characterized PY-NLSs. Unlike other PY-NLSs, which generally bind Kapβ2 in fully extended conformations, the FUS peptide is atypical as its central portion forms a 2.5-turn α-helix. The Kapβ2-binding epitopes of the FUS PY-NLS consist of an N-terminal PGKM hydrophobic motif, a central arginine-rich α-helix, and a C-terminal PY motif. ALS mutations are found almost exclusively within these epitopes. Each ALS mutation site makes multiple contacts with Kapβ2 and mutations of these residues decrease binding affinities for Kapβ2 (K(D) for wild-type FUS PY-NLS is 9.5 nM) up to ninefold. Thermodynamic analyses of ALS mutations in the FUS PY-NLS show that the weakening of FUS-Kapβ2 binding affinity, the degree of cytoplasmic mislocalization, and ALS disease severity are correlated.","corpus_id":31306170,"score":2},{"doc_id":"22918483","title":"RNA recognition by double-stranded RNA binding domains: a matter of shape and sequence.","abstract":"The double-stranded RNA binding domain (dsRBD) is a small protein domain of 65-70 amino acids adopting an αβββα fold, whose central property is to bind to double-stranded RNA (dsRNA). This domain is present in proteins implicated in many aspects of cellular life, including antiviral response, RNA editing, RNA processing, RNA transport and, last but not least, RNA silencing. Even though proteins containing dsRBDs can bind to very specific dsRNA targets in vivo, the binding of dsRBDs to dsRNA is commonly believed to be shape-dependent rather than sequence-specific. Interestingly, recent structural information on dsRNA recognition by dsRBDs opens the possibility that this domain performs a direct readout of RNA sequence in the minor groove, allowing a global reconsideration of the principles describing dsRNA recognition by dsRBDs. We review in this article the current structural and molecular knowledge on dsRBDs, emphasizing the intricate relationship between the amino acid sequence, the structure of the domain and its RNA recognition capacity. We especially focus on the molecular determinants of dsRNA recognition and describe how sequence discrimination can be achieved by this type of domain.","corpus_id":1949699,"score":2},{"doc_id":"23056579","title":"FUS-NLS/Transportin 1 complex structure provides insights into the nuclear targeting mechanism of FUS and the implications in ALS.","abstract":"The C-terminal nuclear localization sequence of FUsed in Sarcoma (FUS-NLS) is critical for its nuclear import mediated by transportin (Trn1). Familial amyotrophic lateral sclerosis (ALS) related mutations are clustered in FUS-NLS. We report here the structural, biochemical and cell biological characterization of the FUS-NLS and its clinical implications. The crystal structure of the FUS-NLS/Trn1 complex shows extensive contacts between the two proteins and a unique α-helical structure in the FUS-NLS. The binding affinity between Trn1 and FUS-NLS (wide-type and 12 ALS-associated mutants) was determined. As compared to the wide-type FUS-NLS (K(D) = 1.7 nM), each ALS-associated mutation caused a decreased affinity and the range of this reduction varied widely from 1.4-fold over 700-fold. The affinity of the mutants correlated with the extent of impaired nuclear localization, and more importantly, with the duration of disease progression in ALS patients. This study provides a comprehensive understanding of the nuclear targeting mechanism of FUS and illustrates the significance of FUS-NLS in ALS.","corpus_id":3912886,"score":2},{"doc_id":"23535894","title":"Crystal structure of human Karyopherin β2 bound to the PY-NLS of Saccharomyces cerevisiae Nab2.","abstract":"Import-Karyopherin or Importin proteins bind nuclear localization signals (NLSs) to mediate the import of proteins into the cell nucleus. Karyopherin β2 or Kapβ2, also known as Transportin, is a member of this transporter family responsible for the import of numerous RNA binding proteins. Kapβ2 recognizes a targeting signal termed the PY-NLS that lies within its cargos to target them through the nuclear pore complex. The recognition of PY-NLS by Kapβ2 is conserved throughout eukaryotes. Kap104, the Kapβ2 homolog in Saccharomyces cerevisiae, recognizes PY-NLSs in cargos Nab2, Hrp1, and Tfg2. We have determined the crystal structure of Kapβ2 bound to the PY-NLS of the mRNA processing protein Nab2 at 3.05-Å resolution. A seven-residue segment of the PY-NLS of Nab2 is observed to bind Kapβ2 in an extended conformation and occupies the same PY-NLS binding site observed in other Kapβ2·PY-NLS structures.","corpus_id":1563489,"score":2},{"doc_id":"23882114","title":"The double-stranded RNA binding domain of human Dicer functions as a nuclear localization signal.","abstract":"Dicer is a key player in microRNA (miRNA) and RNA interference (RNAi) pathways, processing miRNA precursors and double-stranded RNA into ∼21-nt-long products ultimately triggering sequence-dependent gene silencing. Although processing of substrates in vertebrate cells occurs in the cytoplasm, there is growing evidence suggesting Dicer is also present and functional in the nucleus. To address this possibility, we searched for a nuclear localization signal (NLS) in human Dicer and identified its C-terminal double-stranded RNA binding domain (dsRBD) as harboring NLS activity. We show that the dsRBD-NLS can mediate nuclear import of a reporter protein via interaction with importins β, 7, and 8. In the context of full-length Dicer, the dsRBD-NLS is masked. However, duplication of the dsRBD localizes the full-length protein to the nucleus. Furthermore, deletion of the N-terminal helicase domain results in partial accumulation of Dicer in the nucleus upon leptomycin B treatment, indicating that CRM1 contributes to nuclear export of Dicer. Finally, we demonstrate that human Dicer has the ability to shuttle between the nucleus and the cytoplasm. We conclude that Dicer is a shuttling protein whose steady-state localization is cytoplasmic.","corpus_id":207217413,"score":2},{"doc_id":"24449914","title":"Structural basis for nuclear import of splicing factors by human Transportin 3.","abstract":"Transportin 3 (Tnpo3, Transportin-SR2) is implicated in nuclear import of splicing factors and HIV-1 replication. Herein, we show that the majority of cellular Tnpo3 binding partners contain arginine-serine (RS) repeat domains and present crystal structures of human Tnpo3 in its free as well as GTPase Ran- and alternative splicing factor/splicing factor 2 (ASF/SF2)-bound forms. The flexible β-karyopherin fold of Tnpo3 embraces the RNA recognition motif and RS domains of the cargo. A constellation of charged residues on and around the arginine-rich helix of Tnpo3 HEAT repeat 15 engage the phosphorylated RS domain and are critical for the recognition and nuclear import of ASF/SF2. Mutations in the same region of Tnpo3 impair its interaction with the cleavage and polyadenylation specificity factor 6 (CPSF6) and its ability to support HIV-1 replication. Steric incompatibility of the RS domain and RanGTP engagement by Tnpo3 provides the mechanism for cargo release in the nucleus. Our results elucidate the structural bases for nuclear import of splicing factors and the Tnpo3-CPSF6 nexus in HIV-1 biology.","corpus_id":22578720,"score":2},{"doc_id":"24780099","title":"Transportin-1 and Transportin-2: protein nuclear import and beyond.","abstract":"Nearly 20 years after its identification as a new β-karyopherin mediating the nuclear import of the RNA-binding protein hnRNP A1, Transportin-1 is still commonly overlooked in comparison with its best known cousin, Importin-β. Transportin-1 is nonetheless a considerable player in nucleo-cytoplasmic transport. Over the past few years, significant progress has been made in the characterization of the nuclear localization signals (NLSs) that Transportin-1 recognizes, thereby providing the molecular basis of its diversified repertoire of cargoes. The recent discovery that mutations in the Transportin-dependent NLS of FUS cause mislocalization of this protein and result in amyotrophic lateral sclerosis illustrates the importance of Transportin-dependent import for human health. Besides, new functions of Transportin-1 are emerging in processes other than nuclear import. Here, we summarize what is known about Transportin-1 and the related β-karyopherin Transportin-2.","corpus_id":26022824,"score":2},{"doc_id":"24801449","title":"Substrate recognition and specificity of double-stranded RNA binding proteins.","abstract":"Recognition of double-stranded (ds) RNA is an important part of many cellular pathways, including RNA silencing, viral recognition, RNA editing, processing, and transport. dsRNA recognition is often achieved by dsRNA binding domains (dsRBDs). We use atomistic molecular dynamics simulations to examine the binding interface of the transactivation response RNA binding protein (TRBP) dsRBDs to dsRNA substrates. Our results explain the exclusive selectivity of dsRBDs toward dsRNA and against DNA-RNA hybrid and dsDNA duplexes. We also provide corresponding experimental evidence. The dsRNA duplex is recognized by dsRBDs through the A-form of three duplex grooves and by the chemical properties of RNA bases, which have 2'-hydroxyl groups on their sugar rings. Our simulations show that TRBP dsRBD discriminates dsRNA- from DNA-containing duplexes primarily through interactions at two duplex grooves. The simulations also reveal that the conformation of the DNA-RNA duplex can be altered by dsRBD proteins, resulting in a weak binding of dsRBDs to DNA-RNA hybrids. Our study reveals the structural and molecular basis of protein-RNA interaction that gives rise to the observed substrate specificity of dsRNA binding proteins.","corpus_id":18192088,"score":2},{"doc_id":"24905200","title":"An RNA editor, adenosine deaminase acting on double-stranded RNA (ADAR1).","abstract":"Adenosine deaminase acting on RNA1 (ADAR1) catalyzes the C6 deamination of adenosine (A) to produce inosine (I) in regions of RNA with double-stranded (ds) character. This process is known as A-to-I RNA editing. Alternative promoters drive the expression of the Adar1 gene and alternative splicing gives rise to transcripts that encode 2 ADAR1 protein size isoforms. ADAR1 p150 is an interferon (IFN)-inducible dsRNA adenosine deaminase found in the cytoplasm and nucleus, whereas ADAR1 p110 is constitutively expressed and nuclear in localization. Dependent on the duplex structure of the dsRNA substrate, deamination of adenosine by ADAR can be either highly site-selective or nonspecific. A-to-I editing can alter the stability of RNA structures and the coding of RNA as I is read as G instead of A by ribosomes during mRNA translation and by polymerases during RNA replication. A-to-I editing is of broad physiologic significance. Both the production and the action of IFNs, and hence the subsequent interaction of viruses with their hosts, are among the processes affected by A-to-I editing.","corpus_id":22858275,"score":2},{"doc_id":"24954387","title":"'Black sheep' that don't leave the double-stranded RNA-binding domain fold.","abstract":"The canonical double-stranded RNA (dsRNA)-binding domain (dsRBD) is composed of an α1-β1-β2-β3-α2 secondary structure that folds in three dimensions to recognize dsRNA. Recently, structural and functional studies of divergent dsRBDs revealed adaptations that include intra- and/or intermolecular protein interactions, sometimes in the absence of detectable dsRNA-binding ability. We describe here how discrete dsRBD components can accommodate pronounced amino-acid sequence changes while maintaining the core fold. We exemplify the growing importance of divergent dsRBDs in mRNA decay by discussing Dicer, Staufen (STAU)1 and 2, trans-activation responsive RNA-binding protein (TARBP)2, protein activator of protein kinase RNA-activated (PKR) (PACT), DiGeorge syndrome critical region (DGCR)8, DEAH box helicase proteins (DHX) 9 and 30, and dsRBD-like fold-containing proteins that have ribosome-related functions. We also elaborate on the computational limitations to discovering yet-to-be-identified divergent dsRBDs.","corpus_id":33816117,"score":2},{"doc_id":"25584639","title":"Functions of double-stranded RNA-binding domains in nucleocytoplasmic transport.","abstract":"The double-stranded RNA-binding domain (dsRBD) is a small protein domain found in eukaryotic, prokaryotic and viral proteins, whose central property is to bind to double-stranded RNA (dsRNA). Aside from this major function, recent examples of dsRBDs involved in the regulation of the sub-cellular localization of proteins, suggest that the participation of dsRBDs in nucleocytoplasmic trafficking is likely to represent a widespread auxiliary function of this type of RNA-binding domain. Overall, dsRBDs from proteins involved in many different biological processes have been reported to be implicated in nuclear import and export, as well as cytoplasmic, nuclear and nucleolar retention. Interestingly, the function of dsRBDs in nucleocytoplasmic trafficking is often regulated by their dsRNA-binding capacity, which can either enhance or impair the transport from one compartment to another. Here, we present and discuss the emerging function of dsRBDs in nucleocytoplasmic transport.","corpus_id":7795593,"score":2},{"doc_id":"26173234","title":"Nuclear localization signals for four distinct karyopherin-β nuclear import systems.","abstract":"The Karyopherin-β family of proteins mediates nuclear transport of macromolecules. Nuclear versus cytoplasmic localization of proteins is often suggested by the presence of NLSs (nuclear localization signals) or NESs (nuclear export signals). Import-Karyopherin-βs or Importins bind to NLSs in their protein cargos to transport them through nuclear pore complexes into the nucleus. Until recently, only two classes of NLS had been biochemically and structurally characterized: the classical NLS, which is recognized by the Importin-α/β heterodimer and the PY-NLS (proline-tyrosine NLS), which is recognized by Karyopherin-β2 or Transportin-1. Structures of two other Karyopherin-βs, Kap121 and Transportin-SR2, in complex with their respective cargos were reported for the first time recently, revealing two new distinct classes of NLSs. The present paper briefly describes the classical NLS, reviews recent literature on the PY-NLS and provides in-depth reviews of the two newly discovered classes of NLSs that bind Kap121p and Transportin-SR respectively.","corpus_id":21558738,"score":2},{"doc_id":"27618664","title":"Karyopherin-β2 Recognition of a PY-NLS Variant that Lacks the Proline-Tyrosine Motif.","abstract":"Karyopherin-β2 or Transportin-1 binds proline-tyrosine nuclear localization signals (PY-NLSs) in its cargos. PY-NLSs are described by structural disorder, overall positive charge, and binding epitopes composed of an N-terminal hydrophobic or basic motif and a C-terminal R-X2-5P-Y motif. The N-terminal tail of histone H3 binds Kapβ2 with high affinity but does not contain a recognizable PY-NLS. The crystal structure of the Kapβ2-H3 tail shows residues 11-27 of H3 binding to the PY-NLS site of Kapβ2. H3 residues (11)TGGKAPRK(18) bind the site for PY-NLS Epitope 1 (N-terminal hydrophobic/basic motif), which is most important for Kapβ2-binding. H3 residue Arg26 occupies the PY-NLS Epitope 2 position (usually arginine of R-X2-5P-Y) but PY-NLS Epitope 3 (proline-tyrosine motif) is missing in the H3 tail. Histone H3 thus provides an example of a PY-NLS variant with no proline-tyrosine or homologous proline-hydrophobic motif. The H3 tail uses a very strong Epitope 1 to compensate for loss of the often-conserved proline-tyrosine epitope.","corpus_id":205263282,"score":2},{"doc_id":"29449323","title":"Structural basis of siRNA recognition by TRBP double-stranded RNA binding domains.","abstract":"The accurate cleavage of pre-micro(mi)RNAs by Dicer and mi/siRNA guide strand selection are important steps in forming the RNA-induced silencing complex (RISC). The role of Dicer binding partner TRBP in these processes remains poorly understood. Here, we solved the solution structure of the two N-terminal dsRNA binding domains (dsRBDs) of TRBP in complex with a functionally asymmetric siRNA using NMR, EPR, and single-molecule spectroscopy. We find that siRNA recognition by the dsRBDs is not sequence-specific but rather depends on the RNA shape. The two dsRBDs can swap their binding sites, giving rise to two equally populated, pseudo-symmetrical complexes, showing that TRBP is not a primary sensor of siRNA asymmetry. Using our structure to model a Dicer-TRBP-siRNA ternary complex, we show that TRBP's dsRBDs and Dicer's RNase III domains bind a canonical 19 base pair siRNA on opposite sides, supporting a mechanism whereby TRBP influences Dicer-mediated cleavage accuracy by binding the dsRNA region of the pre-miRNA during Dicer cleavage.","corpus_id":3996101,"score":2},{"doc_id":"29677513","title":"Nuclear Import Receptor Inhibits Phase Separation of FUS through Binding to Multiple Sites.","abstract":"Liquid-liquid phase separation (LLPS) is believed to underlie formation of biomolecular condensates, cellular compartments that concentrate macromolecules without surrounding membranes. Physical mechanisms that control condensate formation/dissolution are poorly understood. The RNA-binding protein fused in sarcoma (FUS) undergoes LLPS in vitro and associates with condensates in cells. We show that the importin karyopherin-β2/transportin-1 inhibits LLPS of FUS. This activity depends on tight binding of karyopherin-β2 to the C-terminal proline-tyrosine nuclear localization signal (PY-NLS) of FUS. Nuclear magnetic resonance (NMR) analyses reveal weak interactions of karyopherin-β2 with sequence elements and structural domains distributed throughout the entirety of FUS. Biochemical analyses demonstrate that most of these same regions also contribute to LLPS of FUS. The data lead to a model where high-affinity binding of karyopherin-β2 to the FUS PY-NLS tethers the proteins together, allowing multiple, distributed weak intermolecular contacts to disrupt FUS self-association, blocking LLPS. Karyopherin-β2 may act analogously to control condensates in diverse cellular contexts.","corpus_id":5011616,"score":2},{"doc_id":"19390115","title":"An extra double-stranded RNA binding domain confers high activity to a squid RNA editing enzyme.","abstract":"RNA editing by adenosine deamination is particularly prevalent in the squid nervous system. We hypothesized that the squid editing enzyme might contain structural differences that help explain this phenomenon. As a first step, a squid adenosine deaminase that acts on RNA (sqADAR2a) cDNA and the gene that encodes it were cloned from the giant axon system. PCR and RNase protection assays showed that a splice variant of this clone (sqADAR2b) was also expressed in this tissue. Both versions are homologous to the vertebrate ADAR2 family. sqADAR2b encodes a conventional ADAR2 family member with an evolutionarily conserved deaminase domain and two double-stranded RNA binding domains (dsRBD). sqADAR2a differs from sqADAR2b by containing an optional exon that encodes an \"extra\" dsRBD. Both splice variants are expressed at comparable levels and are extensively edited, each in a unique pattern. Recombinant sqADAR2a and sqADAR2b, produced in Pichia pastoris, are both active on duplex RNA. Using a standard 48-h protein induction, both sqADAR2a and sqADAR2b exhibit promiscuous self-editing; however, this activity is particularly robust for sqADAR2a. By decreasing the induction time to 16 h, self-editing was mostly eliminated. We next tested the ability of sqADAR2a and sqADAR2b to edit two K+ channel mRNAs in vitro. Both substrates are known to be edited in squid. For each mRNA, sqADAR2a edited many more sites than sqADAR2b. These data suggest that the \"extra\" dsRBD confers high activity on sqADAR2a.","corpus_id":10303487,"score":1},{"doc_id":"19651874","title":"Editing of HIV-1 RNA by the double-stranded RNA deaminase ADAR1 stimulates viral infection.","abstract":"Adenosine deaminases that act on dsRNA (ADARs) are enzymes that target double-stranded regions of RNA converting adenosines into inosines (A-to-I editing) thus contributing to genome complexity and fine regulation of gene expression. It has been described that a member of the ADAR family, ADAR1, can target viruses and affect their replication process. Here we report evidence showing that ADAR1 stimulates human immuno deficiency virus type 1 (HIV-1) replication by using both editing-dependent and editing-independent mechanisms. We show that over-expression of ADAR1 in HIV-1 producer cells increases viral protein accumulation in an editing-independent manner. Moreover, HIV-1 virions generated in the presence of over-expressed ADAR1 but not an editing-inactive ADAR1 mutant are released more efficiently and display enhanced infectivity, as demonstrated by challenge assays performed with T cell lines and primary CD4(+) T lymphocytes. Finally, we report that ADAR1 associates with HIV-1 RNAs and edits adenosines in the 5' untranslated region (UTR) and the Rev and Tat coding sequence. Overall these results suggest that HIV-1 has evolved mechanisms to take advantage of specific RNA editing activity of the host cell and disclose a stimulatory function of ADAR1 in the spread of HIV-1.","corpus_id":12314845,"score":1},{"doc_id":"20106953","title":"Structure of the Arabidopsis thaliana DCL4 DUF283 domain reveals a noncanonical double-stranded RNA-binding fold for protein-protein interaction.","abstract":"Dicer or Dicer-like (DCL) protein is a catalytic component involved in microRNA (miRNA) or small interference RNA (siRNA) processing pathway, whose fragment structures have been partially solved. However, the structure and function of the unique DUF283 domain within dicer is largely unknown. Here we report the first structure of the DUF283 domain from the Arabidopsis thaliana DCL4. The DUF283 domain adopts an alpha-beta-beta-beta-alpha topology and resembles the structural similarity to the double-stranded RNA-binding domain. Notably, the N-terminal alpha helix of DUF283 runs cross over the C-terminal alpha helix orthogonally, therefore, N- and C-termini of DUF283 are in close proximity. Biochemical analysis shows that the DUF283 domain of DCL4 displays weak dsRNA binding affinity and specifically binds to double-stranded RNA-binding domain 1 (dsRBD1) of Arabidopsis DRB4, whereas the DUF283 domain of DCL1 specifically binds to dsRBD2 of Arabidopsis HYL1. These data suggest a potential functional role of the Arabidopsis DUF283 domain in target selection in small RNA processing.","corpus_id":23053213,"score":1},{"doc_id":"21080422","title":"Structures of the first and second double-stranded RNA-binding domains of human TAR RNA-binding protein.","abstract":"The TAR RNA-binding Protein (TRBP) is a double-stranded RNA (dsRNA)-binding protein, which binds to Dicer and is required for the RNA interference pathway. TRBP consists of three dsRNA-binding domains (dsRBDs). The first and second dsRBDs (dsRBD1 and dsRBD2, respectively) have affinities for dsRNA, whereas the third dsRBD (dsRBD3) binds to Dicer. In this study, we prepared the single domain fragments of human TRBP corresponding to dsRBD1 and dsRBD2 and solved the crystal structure of dsRBD1 and the solution structure of dsRBD2. The two structures contain an α-β-β-β-α fold, which is common to the dsRBDs. The overall structures of dsRBD1 and dsRBD2 are similar to each other, except for a slight shift of the first α helix. The residues involved in dsRNA binding are conserved. We examined the small interfering RNA (siRNA)-binding properties of these dsRBDs by isothermal titration colorimetry measurements. The dsRBD1 and dsRBD2 fragments both bound to siRNA, with dissociation constants of 220 and 113 nM, respectively. In contrast, the full-length TRBP and its fragment with dsRBD1 and dsRBD2 exhibited much smaller dissociation constants (0.24 and 0.25 nM, respectively), indicating that the tandem dsRBDs bind simultaneously to one siRNA molecule. On the other hand, the loop between the first α helix and the first β strand of dsRBD2, but not dsRBD1, has a Trp residue, which forms hydrophobic and cation-π interactions with the surrounding residues. A circular dichroism analysis revealed that the thermal stability of dsRBD2 is higher than that of dsRBD1 and depends on the Trp residue.","corpus_id":23896039,"score":1},{"doc_id":"21182352","title":"Adenosine deaminases acting on RNA, RNA editing, and interferon action.","abstract":"Adenosine deaminases acting on RNA (ADARs) catalyze adenosine (A) to inosine (I) editing of RNA that possesses double-stranded (ds) structure. A-to-I RNA editing results in nucleotide substitution, because I is recognized as G instead of A both by ribosomes and by RNA polymerases. A-to-I substitution can also cause dsRNA destabilization, as I:U mismatch base pairs are less stable than A:U base pairs. Three mammalian ADAR genes are known, of which two encode active deaminases (ADAR1 and ADAR2). Alternative promoters together with alternative splicing give rise to two protein size forms of ADAR1: an interferon-inducible ADAR1-p150 deaminase that binds dsRNA and Z-DNA, and a constitutively expressed ADAR1-p110 deaminase. ADAR2, like ADAR1-p110, is constitutively expressed and binds dsRNA. A-to-I editing occurs with both viral and cellular RNAs, and affects a broad range of biological processes. These include virus growth and persistence, apoptosis and embryogenesis, neurotransmitter receptor and ion channel function, pancreatic cell function, and post-transcriptional gene regulation by microRNAs. Biochemical processes that provide a framework for understanding the physiologic changes following ADAR-catalyzed A-to-I ( = G) editing events include mRNA translation by changing codons and hence the amino acid sequence of proteins; pre-mRNA splicing by altering splice site recognition sequences; RNA stability by changing sequences involved in nuclease recognition; genetic stability in the case of RNA virus genomes by changing sequences during viral RNA replication; and RNA-structure-dependent activities such as microRNA production or targeting or protein-RNA interactions.","corpus_id":34002988,"score":1},{"doc_id":"21587236","title":"Predicting sites of ADAR editing in double-stranded RNA.","abstract":"ADAR (adenosine deaminase that acts on RNA) editing enzymes target coding and noncoding double-stranded RNA (dsRNA) and are essential for neuronal function. Early studies showed that ADARs preferentially target adenosines with certain 5' and 3' neighbours. Here we use current Sanger sequencing protocols to perform a more accurate and quantitative analysis. We quantified editing sites in an ∼800-bp dsRNA after reaction with human ADAR1 or ADAR2, or their catalytic domains alone. These large data sets revealed that neighbour preferences are mostly dictated by the catalytic domain, but ADAR2's dsRNA-binding motifs contribute to 3' neighbour preferences. For all proteins, the 5' nearest neighbour was most influential, but adjacent bases also affected editing site choice. We developed algorithms to predict editing sites in dsRNA of any sequence, and provide a web-based application. The predictive power of the algorithm on fully base-paired dsRNA, compared with biological substrates containing mismatches, bulges and loops, elucidates structural contributions to editing specificity.","corpus_id":466712,"score":1},{"doc_id":"23012356","title":"Identification of a karyopherin β1/β2 proline-tyrosine nuclear localization signal in huntingtin protein.","abstract":"Among the known pathways of protein nuclear import, the karyopherin β2/transportin pathway is only the second to have a defined nuclear localization signal (NLS) consensus. Huntingtin, a 350-kDa protein, has defined roles in the nucleus, as well as a CRM1/exportin-dependent nuclear export signal; however, the NLS and exact pathway of import have remained elusive. Here, using a live cell assay and affinity chromatography, we show that huntingtin has a karyopherin β2-dependent proline-tyrosine (PY)-NLS in the amino terminus of the protein. This NLS comprises three consensus components: a basic charged sequence, a downstream conserved arginine, and a PY sequence. Unlike the classic PY-NLS, which has an unstructured intervening sequence between the consensus components, we show that a β sheet structured region separating the consensus elements is critical for huntingtin NLS function. The huntingtin PY-NLS is also capable of import through the importin/karyopherin β1 pathway but was not functional in all cell types tested. We propose that this huntingtin PY-NLS may comprise a new class of multiple import factor-dependent NLSs with an internal structural component that may regulate NLS activity.","corpus_id":19925966,"score":1},{"doc_id":"23194006","title":"Second double-stranded RNA binding domain of dicer-like ribonuclease 1: structural and biochemical characterization.","abstract":"Dicer-like ribonuclease III enzymes are involved in different paths related to RNA silencing in plants. Little is known about the structural aspects of these processes. Here we present a structural characterization of the second double-stranded RNA binding domain (dsRBD) of DCL1, which is presumed to participate in pri-micro-RNA recognition and subcellular localization of this protein. We determined the solution structure and found that it has a canonical fold but bears some variation with respect to other homologous domains. We also found that this domain binds both double-stranded RNA and double-stranded DNA, in contrast to most dsRBDs. Our characterization shows that this domain likely has functions other than substrate recognition and binding.","corpus_id":12632746,"score":1},{"doc_id":"23279110","title":"A proline-tyrosine nuclear localization signal (PY-NLS) is required for the nuclear import of fission yeast PAB2, but not of human PABPN1.","abstract":"Nuclear poly(A)-binding proteins (PABPs) are evolutionarily conserved proteins that play key roles in eukaryotic gene expression. In the fission yeast Schizosaccharomyces pombe, the major nuclear PABP, Pab2, functions in the maturation of small nucleolar RNAs as well as in nuclear RNA decay. Despite knowledge about its nuclear functions, nothing is known about how Pab2 is imported into the nucleus. Here, we show that Pab2 contains a proline-tyrosine nuclear localization signal (PY-NLS) that is necessary and sufficient for its nuclear localization and function. Consistent with the role of karyopherin β2 (Kapβ2)-type receptors in the import of PY-NLS cargoes, we show that the fission yeast ortholog of human Kapβ2, Kap104, binds to recombinant Pab2 and is required for Pab2 nuclear localization. The absence of arginine methylation in a basic region N-terminal to the PY-core motif of Pab2 did not affect its nuclear localization. However, in the context of a sub-optimal PY-NLS, we found that Pab2 was more efficiently targeted to the nucleus in the absence of arginine methylation, suggesting that this modification can affect the import kinetics of a PY-NLS cargo. Although a sequence resembling a PY-NLS motif can be found in the human Pab2 ortholog, PABPN1, our results indicate that neither a functional PY-NLS nor Kapβ2 activity are required to promote entry of PABPN1 into the nucleus of human cells. Our findings describe the mechanism by which Pab2 is imported into the nucleus, providing the first example of a PY-NLS import system in fission yeast. In addition, this study suggests the existence of alternative or redundant nuclear import pathways for human PABPN1.","corpus_id":19781449,"score":1},{"doc_id":"23886622","title":"Complementation of HYPONASTIC LEAVES1 by double-strand RNA-binding domains of DICER-LIKE1 in nuclear dicing bodies.","abstract":"MicroRNAs (miRNAs) are a class of small regulatory RNAs that are found in almost all of the eukaryotes. Arabidopsis (Arabidopsis thaliana) miRNAs are processed from primary miRNAs (pri-miRNAs), mainly by the ribonuclease III-like enzyme DICER-LIKE1 (DCL1) and its specific partner, HYPONASTIC LEAVES1 (HYL1), a double-strand RNA-binding protein, both of which contain two double-strand RNA-binding domains (dsRBDs). These dsRBDs are essential for miRNA processing, but the functions of them are not clear. Here, we report that the two dsRBDs of DCL1 (DCL1-D1D2), and to some extent the second dsRBD (DCL1-D2), complement the hyl1 mutant, but not the first dsRBD of DCL1 (DCL1-D1). DCL1-D1 is diffusely distributed throughout the nucleoplasm, whereas DCL1-D2 and DCL1-D1D2 concentrate in nuclear dicing bodies in which DCL1 and HYL1 colocalize. We show further that protein-protein interaction is mainly mediated by DCL1-D2, while DCL1-D1 plays a major role in binding of pri-miRNAs. These results suggest parallel roles between C-terminal dsRBDs of DCL1 and N-terminal dsRBDs of HYL1 and support a model in which Arabidopsis pri-miRNAs are recruited to dicing bodies through functionally divergent dsRBDs of microprocessor for accurate processing of plant pri-miRNAs.","corpus_id":45315406,"score":1},{"doc_id":"25564529","title":"Recognition of duplex RNA by the deaminase domain of the RNA editing enzyme ADAR2.","abstract":"Adenosine deaminases acting on RNA (ADARs) hydrolytically deaminate adenosines (A) in a wide variety of duplex RNAs and misregulation of editing is correlated with human disease. However, our understanding of reaction selectivity is limited. ADARs are modular enzymes with multiple double-stranded RNA binding domains (dsRBDs) and a catalytic domain. While dsRBD binding is understood, little is known about ADAR catalytic domain/RNA interactions. Here we use a recently discovered RNA substrate that is rapidly deaminated by the isolated human ADAR2 deaminase domain (hADAR2-D) to probe these interactions. We introduced the nucleoside analog 8-azanebularine (8-azaN) into this RNA (and derived constructs) to mechanistically trap the protein-RNA complex without catalytic turnover for EMSA and ribonuclease footprinting analyses. EMSA showed that hADAR2-D requires duplex RNA and is sensitive to 2'-deoxy substitution at nucleotides opposite the editing site, the local sequence and 8-azaN nucleotide positioning on the duplex. Ribonuclease V1 footprinting shows that hADAR2-D protects ∼ 23 nt on the edited strand around the editing site in an asymmetric fashion (∼ 18 nt on the 5' side and ∼ 5 nt on the 3' side). These studies provide a deeper understanding of the ADAR catalytic domain-RNA interaction and new tools for biophysical analysis of ADAR-RNA complexes.","corpus_id":4713151,"score":1},{"doc_id":"26184879","title":"Dynamic profiling of double-stranded RNA binding proteins.","abstract":"Double-stranded (ds) RNA is a key player in numerous biological activities in cells, including RNA interference, anti-viral immunity and mRNA transport. The class of proteins responsible for recognizing dsRNA is termed double-stranded RNA binding proteins (dsRBP). However, little is known about the molecular mechanisms underlying the interaction between dsRBPs and dsRNA. Here we examined four human dsRBPs, ADAD2, TRBP, Staufen 1 and ADAR1 on six dsRNA substrates that vary in length and secondary structure. We combined single molecule pull-down (SiMPull), single molecule protein-induced fluorescence enhancement (smPIFE) and molecular dynamics (MD) simulations to investigate the dsRNA-dsRBP interactions. Our results demonstrate that despite the highly conserved dsRNA binding domains, the dsRBPs exhibit diverse substrate specificities and dynamic properties when in contact with different RNA substrates. While TRBP and ADAR1 have a preference for binding simple duplex RNA, ADAD2 and Staufen1 display higher affinity to highly structured RNA substrates. Upon interaction with RNA substrates, TRBP and Staufen1 exhibit dynamic sliding whereas two deaminases ADAR1 and ADAD2 mostly remain immobile when bound. MD simulations provide a detailed atomic interaction map that is largely consistent with the affinity differences observed experimentally. Collectively, our study highlights the diverse nature of substrate specificity and mobility exhibited by dsRBPs that may be critical for their cellular function.","corpus_id":2876634,"score":1},{"doc_id":"26252972","title":"Effect of mismatch on binding of ADAR2/GluR-2 pre-mRNA complex.","abstract":"RNA editing plays an important role in realizing the full potential of a given genome. Different from RNA splicing, RNA editing fine-tunes the sequence of RNA by changing only one or two nucleotides. A-I editing [deamination of adenosine (A) to create inosine (I)] is best characterized in mammals and occurs in the regions of double-stranded RNA (dsRNA). Adenosine deaminases acting on RNA (ADARs) are members of a family of enzymes involved in A-I deamination editing in numerous mRNA and pre-mRNA transcripts. Experimental study shows that ADAR2 selectively edits the R/G site, while ADAR1 edits more promiscuously at several other adenosines. How ADAR2 selects specific sites for deamination is poorly understood. Mismatches have been suggested to be important factors that allow the ADAR2 to achieve specific deamination. Using molecular dynamic simulation, we studied the effect of mismatch on binding stability of the dsRNA/ADAR2 complex. By comparison of two binding domains of ADAR2, we found that ADAR2 dsRBM2 (second binding domain of ADAR2) does not bind well with mismatch reversed GluR-2 RNA. When mismatch is reversed, dsRBM2 of ADAR2 slides along the RNA duplex in the simulation. Detailed structural analysis indicates that the minor groove width of dsRNA and global shape of RNA may play an important role in the specific reading mechanism of ADAR2.","corpus_id":3395726,"score":1},{"doc_id":"26275108","title":"RNA editing by ADAR1 prevents MDA5 sensing of endogenous dsRNA as nonself.","abstract":"Adenosine-to-inosine (A-to-I) editing is a highly prevalent posttranscriptional modification of RNA, mediated by ADAR (adenosine deaminase acting on RNA) enzymes. In addition to RNA editing, additional functions have been proposed for ADAR1. To determine the specific role of RNA editing by ADAR1, we generated mice with an editing-deficient knock-in mutation (Adar1(E861A), where E861A denotes Glu(861)→Ala(861)). Adar1(E861A/E861A) embryos died at ~E13.5 (embryonic day 13.5), with activated interferon and double-stranded RNA (dsRNA)-sensing pathways. Genome-wide analysis of the in vivo substrates of ADAR1 identified clustered hyperediting within long dsRNA stem loops within 3' untranslated regions of endogenous transcripts. Finally, embryonic death and phenotypes of Adar1(E861A/E861A) were rescued by concurrent deletion of the cytosolic sensor of dsRNA, MDA5. A-to-I editing of endogenous dsRNA is the essential function of ADAR1, preventing the activation of the cytosolic dsRNA response by endogenous transcripts.","corpus_id":206640044,"score":1},{"doc_id":"26987516","title":"dsRNA-protein interactions studied by molecular dynamics techniques. Unravelling dsRNA recognition by DCL1.","abstract":"Double stranded RNA (dsRNA) participates in several biological processes, where RNA molecules acquire secondary structure inside the cell through base complementarity. The double stranded RNA binding domain (dsRBD) is one of the main protein folds that is able to recognize and bind to dsRNA regions. The N-terminal dsRBD of DCL1 in Arabidopsis thaliana (DCL1-1), in contrast to other studied dsRBDs, lacks a stable structure, behaving as an intrinsically disordered protein. DCL1-1 does however recognize dsRNA by acquiring a canonical fold in the presence of its substrate. Here we present a detailed modeling and molecular dynamics study of dsRNA recognition by DCL1-1. We found that DCL1-1 forms stable complexes with different RNAs and we characterized the residues involved in binding. Although the domain shows a binding loop substantially shorter than other homologs, it can still interact with the dsRNA and results in bending of the dsRNA A-type helix. Furthermore, we found that R8, a non-conserved residue located in the first dsRNA binding region, recognizes preferentially mismatched base pairs. We discuss our findings in the context of the function of DCL1-1 within the microRNA processing complex.","corpus_id":46756551,"score":1},{"doc_id":"18485366","title":"Classical NLS proteins from Saccharomyces cerevisiae.","abstract":"Proteins can enter the nucleus through various receptor-mediated import pathways. One class of import cargos carries a classical nuclear localization signal (cNLS) containing a short cluster of basic residues. This pathway involves importin alpha (Impalpha), which possesses the cNLS binding site, and importin beta (Impbeta), which translocates the import complex through the nuclear pore complex. The defining criteria for a cNLS protein from Saccharomyces cerevisiae are an in vivo import defect in Impalpha and Impbeta mutants, direct binding to purified Impalpha, and stimulation of this binding by Impbeta. We show for the first time that endogenous S. cerevisiae proteins Prp20, Cdc6, Swi5, Cdc45, and Clb2 fulfill all of these criteria identifying them as authentic yeast cNLS cargos. Furthermore, we found that the targeting signal of Prp20 is a bipartite cNLS and that of Cdc6 is a monopartite cNLS. Basic residues present within these motifs are of different significance for the interaction with Impalpha. We determined the binding constants for import complexes containing the five cNLS proteins by surface plasmon resonance spectrometry. The dissociation constants for cNLS/alpha/beta complexes differ considerably, ranging from 1 nM for Cdc6 to 112 nM for Swi5, suggesting that the nuclear import kinetics is determined by the strength of cNLS/Impalpha binding. Impbeta enhances the affinity of Impalpha for cNLSs approximately 100-fold. This stimulation of cNLS binding to Impalpha results from a faster association in the presence of Impbeta, whereas the dissociation rate is unaffected by Impbeta. This implies that, after entry into the nucleus, the release of Impbeta by the Ran guanosine triphosphatase (Ran GTPase) from the import complex is not sufficient to dissociate the cNLS/Impalpha subcomplex. Our observation that the nucleoporin Nup2, which had been previously shown to release the cNLS from Impalpha in vitro, is required for efficient import of all the genuine cNLS cargos supports a general role of Nup2 in import termination.","corpus_id":37755065,"score":0},{"doc_id":"19208642","title":"The regulatory domain of the RIG-I family ATPase LGP2 senses double-stranded RNA.","abstract":"RIG-I and MDA5 sense cytoplasmic viral RNA and set-off a signal transduction cascade, leading to antiviral innate immune response. The third RIG-I-like receptor, LGP2, differentially regulates RIG-I- and MDA5-dependent RNA sensing in an unknown manner. All three receptors possess a C-terminal regulatory domain (RD), which in the case of RIG-I senses the viral pattern 5'-triphosphate RNA and activates ATP-dependent signaling by RIG-I. Here we report the 2.6 A crystal structure of LGP2 RD along with in vitro and in vivo functional analyses and a homology model of MDA5 RD. Although LGP2 RD is structurally related to RIG-I RD, we find it rather binds double-stranded RNA (dsRNA) and this binding is independent of 5'-triphosphates. We identify conserved and receptor-specific parts of the RNA binding site. Latter are required for specific dsRNA binding by LGP2 RD and could confer pattern selectivity between RIG-I-like receptors. Our data furthermore suggest that LGP2 RD modulates RIG-I-dependent signaling via competition for dsRNA, another pattern sensed by RIG-I, while a fully functional LGP2 is required to augment MDA5-dependent signaling.","corpus_id":10376776,"score":0},{"doc_id":"20064523","title":"Functional interaction of the Ras effector RASSF5 with the tyrosine kinase Lck: critical role in nucleocytoplasmic transport and cell cycle regulation.","abstract":"RASSF5 is a member of the Ras association domain family, which is known to be involved in cell growth regulation. Expression of RASSF5 is extinguished selectively by epigenetic mechanism(s) in different cancers and cell lines, and reexpression usually suppresses cell proliferation and tumorigenicity. To date, the mechanism regulating RASSF5 nuclear transport and its role in cell growth regulation remains unclear. Using heterokaryon assay, we have demonstrated that RASSF5 shuttles between the nucleus and the cytoplasm, and its export from the nucleus is sensitive to leptomycin B, suggesting that RASSF5 is exported from the nucleus by a CRM-1-dependent export pathway. We further demonstrate that RASSF5 contains a hydrophobic-rich nuclear export signal (NES) towards the C-terminus and two nuclear localization signals-one each at the N-terminus and the C-terminus. Combination of mutational and immunofluorescence analyses suggests that the functional NES residing between amino acids 260 and 300 in the C-terminus is necessary for the efficient export of RASSF5 from the nucleus. In addition, substitution of conserved hydrophobic residues within the minimal NES impaired RASSF5 export from the nucleus. Furthermore, exchange of proline residues within the putative Src homology 3 binding motifs altered the export of RASSF5 from the nucleus despite the presence of functional NES, suggesting that multiple domains independently modulate the nucleocytoplasmic transport of RASSF5. Interestingly, the present investigation provided evidence that RASSF5 interacts with the tyrosine kinase Lck through its C-terminal Src homology 2 binding motif and showed that Lck-mediated phosphorylation is critical for the efficient translocation of RASSF5 into the nuclear compartment. Interestingly, our data demonstrate that wild type and nuclear export defective (DeltaNES) mutant of RASSF5 but not the import defective mutant of accumulate the cells at G1/S phase and induce apoptosis. Furthermore, the Lck-interaction-defective mutant of RASSF5 induces apoptosis without altering cell cycle progression, suggesting that RASSF5 induces apoptosis independent of cell cycle arrest. Together, our data demonstrate that interaction with Lck is critical for RASSF5 phosphorylation, which in turn regulates the cell growth control activity of RASSF5. Finally, we have shown that RASSF5 encodes four splice variants and is translocated to the nucleus by the classical nuclear import pathway. One of the splice variants, RASSF5C, was found to be localized in the cytoplasm and translocated into the nucleus upon leptomycin B treatment despite the absence of N-terminal nuclear localization signal, suggesting that distribution of RASSF5 variants in different cellular compartments may be critical for Ras-dependent cell growth regulation. Collectively, the present investigation provided evidence that Lck-mediated phosphorylation regulates the nucleocytoplasmic shuttling and cell growth control activities of RASSF5.","corpus_id":20594790,"score":0},{"doc_id":"20226070","title":"Solution structure of the Drosha double-stranded RNA-binding domain.","abstract":"BACKGROUND: Drosha is a nuclear RNase III enzyme that initiates processing of regulatory microRNA. Together with partner protein DiGeorge syndrome critical region 8 (DGCR8), it forms the Microprocessor complex, which cleaves precursor transcripts called primary microRNA to produce hairpin precursor microRNA. In addition to two RNase III catalytic domains, Drosha contains a C-terminal double-stranded RNA-binding domain (dsRBD). To gain insight into the function of this domain, we determined the nuclear magnetic resonance (NMR) solution structure. RESULTS: We report here the solution structure of the dsRBD from Drosha (Drosha-dsRBD). The alphabetabetabetaalpha fold is similar to other dsRBD structures. A unique extended loop distinguishes this domain from other dsRBDs of known structure. CONCLUSIONS: Despite uncertainties about RNA-binding properties of the Drosha-dsRBD, its structure suggests it retains RNA-binding features. We propose that this domain may contribute to substrate recognition in the Drosha-DGCR8 Microprocessor complex.","corpus_id":63614,"score":0},{"doc_id":"20512930","title":"Characterization of an Importin alpha/beta-recognized nuclear localization signal in beta-dystroglycan.","abstract":"Beta-dystroglycan (beta-DG) is a widely expressed transmembrane protein that plays important roles in connecting the extracellular matrix to the cytoskeleton, and thereby contributing to plasma membrane integrity and signal transduction. We previously observed nuclear localization of beta-DG in cultured cell lines, implying the existence of a nuclear targeting mechanism that directs it to the nucleus instead of the plasma membrane. In this study, we delineate the nuclear import pathway of beta-DG, characterizing a functional nuclear localization signal (NLS) in the beta-DG cytoplasmic domain, within amino acids 776-782. The NLS either alone or in the context of the whole beta-DG protein was able to target the heterologous GFP protein to the nucleus, with site-directed mutagenesis indicating that amino acids R(779) and K(780) are critical for NLS functionality. The nuclear transport molecules Importin (Imp)alpha and Impbeta bound with high affinity to the NLS of beta-DG and were found to be essential for NLS-dependent nuclear import in an in vitro reconstituted nuclear transport assay; cotransfection experiments confirmed the dependence on Ran for nuclear accumulation. Intriguingly, experiments suggested that tyrosine phosphorylation of beta-DG may result in cytoplasmic retention, with Y(892) playing a key role. beta-DG thus follows a conventional Impalpha/beta-dependent nuclear import pathway, with important implications for its potential function in the nucleus.","corpus_id":13269928,"score":0},{"doc_id":"20818336","title":"An actin-regulated importin α/β-dependent extended bipartite NLS directs nuclear import of MRTF-A.","abstract":"Myocardin-related transcription factors (MRTFs) are actin-regulated transcriptional coactivators, which bind G-actin through their N-terminal RPEL domains. In response to signal-induced actin polymerisation and concomitant G-actin depletion, MRTFs accumulate in the nucleus and activate target gene transcription through their partner protein SRF. Nuclear accumulation of MRTFs in response to signal is inhibited by increased G-actin level. Here, we study the mechanism by which MRTF-A enters the nucleus. We show that MRTF-A contains an unusually long bipartite nuclear localisation signal (NLS), comprising two basic elements separated by 30 residues, embedded within the RPEL domain. Using siRNA-mediated protein depletion in vivo, and nuclear import assays in vitro, we show that the MRTF-A extended bipartite NLS uses the importin (Imp)α/β-dependent import pathway, and that import is inhibited by G-actin. Interaction of the NLS with the Impα-Impβ heterodimer requires both NLS basic elements, and is dependent on the Impα major and minor binding pockets. Binding of the Impα-Impβ heterodimer to the intact MRTF-A RPEL domain occurs competitively with G-actin. Thus, MRTF-A contains an actin-sensitive nuclear import signal.","corpus_id":9839642,"score":0},{"doc_id":"20977914","title":"Molecular basis for specificity of nuclear import and prediction of nuclear localization.","abstract":"Although proteins are translated on cytoplasmic ribosomes, many of these proteins play essential roles in the nucleus, mediating key cellular processes including but not limited to DNA replication and repair as well as transcription and RNA processing. Thus, understanding how these critical nuclear proteins are accurately targeted to the nucleus is of paramount importance in biology. Interaction and structural studies in the recent years have jointly revealed some general rules on the specificity determinants of the recognition of nuclear targeting signals by their specific receptors, at least for two nuclear import pathways: (i) the classical pathway, which involves the classical nuclear localization sequences (cNLSs) and the receptors importin-α/karyopherin-α and importin-β/karyopherin-β1; and (ii) the karyopherin-β2 pathway, which employs the proline-tyrosine (PY)-NLSs and the receptor transportin-1/karyopherin-β2. The understanding of specificity rules allows the prediction of protein nuclear localization. We review the current understanding of the molecular determinants of the specificity of nuclear import, focusing on the importin-α•cargo recognition, as well as the currently available databases and predictive tools relevant to nuclear localization. This article is part of a Special Issue entitled: Regulation of Signaling and Cellular Fate through Modulation of Nuclear Protein Import.","corpus_id":5130899,"score":0},{"doc_id":"21029753","title":"The importin β binding domain as a master regulator of nucleocytoplasmic transport.","abstract":"Specific and efficient recognition of import cargoes is essential to ensure nucleocytoplasmic transport. To this end, the prototypical karyopherin importin β associates with import cargoes directly or, more commonly, through import adaptors, such as importin α and snurportin. Adaptor proteins bind the nuclear localization sequence (NLS) of import cargoes while recruiting importin β via an N-terminal importin β binding (IBB) domain. The use of adaptors greatly expands and amplifies the repertoire of cellular cargoes that importin β can efficiently import into the cell nucleus and allows for fine regulation of nuclear import. Accordingly, the IBB domain is a dedicated NLS, unique to adaptor proteins that functions as a molecular liaison between importin β and import cargoes. This review provides an overview of the molecular role played by the IBB domain in orchestrating nucleocytoplasmic transport. Recent work has determined that the IBB domain has specialized functions at every step of the import and export pathway. Unexpectedly, this stretch of ~40 amino acids plays an essential role in regulating processes such as formation of the import complex, docking and translocation through the nuclear pore complex (NPC), release of import cargoes into the cell nucleus and finally recycling of import adaptors and importin β into the cytoplasm. Thus, the IBB domain is a master regulator of nucleocytoplasmic transport, whose complex molecular function is only recently beginning to emerge. This article is part of a Special Issue entitled: Regulation of Signaling and Cellular Fate through Modulation of Nuclear Protein Import.","corpus_id":205831150,"score":0},{"doc_id":"21401918","title":"Intermolecular masking of the HIV-1 Rev NLS by the cellular protein HIC: novel insights into the regulation of Rev nuclear import.","abstract":"BACKGROUND: The HIV-1 regulatory protein Rev, which is essential for viral replication, mediates the nuclear export of unspliced viral transcripts. Rev nuclear function requires active nucleocytoplasmic shuttling, and Rev nuclear import is mediated by the recognition of its Nuclear Localisation Signal (NLS) by multiple import factors, which include transportin and importin β. However, it remains unclear which nuclear import pathway(s) predominate in vivo, and the cellular environment that modulates Rev nucleocytoplasmic shuttling remains to be characterised. RESULTS: In our study, we have identified the cellular protein HIC (Human I-mfa domain-Containing protein) as a novel interactor of HIV-1 Rev. We demonstrate that HIC selectively interferes with Rev NLS interaction with importin β and impedes its nuclear import and function, but does not affect Rev nuclear import mediated by transportin. Hence, the molecular determinants mediating Rev-NLS recognition by importin β and transportin appear to be distinct. Furthermore, we have employed HIC and M9 M, a peptide specifically designed to inhibit the transportin-mediated nuclear import pathway, to characterise Rev nuclear import pathways within different cellular environments. Remarkably, we could show that in 293T, HeLa, COS7, Jurkat, U937, THP-1 and CEM cells, Rev nuclear import is cell type specific and alternatively mediated by transportin or importin β, in a mutually exclusive fashion. CONCLUSIONS: Rev cytoplasmic sequestration by HIC may represent a novel mechanism for the control of Rev function. These studies highlight that the multivalent nature of the Rev NLS for different import receptors enables Rev to adapt its nuclear trafficking strategy.","corpus_id":6402228,"score":0},{"doc_id":"21559489","title":"Conservation of complex nuclear localization signals utilizing classical and non-classical nuclear import pathways in LANA homologs of KSHV and RFHV.","abstract":"ORF73 latency-associated nuclear antigen (LANA) of the Kaposi's sarcoma-associated herpesvirus (KSHV) is targeted to the nucleus of infected cells where it binds to chromatin and mediates viral episome persistence, interacts with cellular proteins and plays a role in latency and tumorigenesis. A structurally related LANA homolog has been identified in the retroperitoneal fibromatosis herpesvirus (RFHV), the macaque homolog of KSHV. Here, we report the evolutionary and functional conservation of a novel bi-functional nuclear localization signal (NLS) in KSHV and RFHV LANA. N-terminal peptides from both proteins were fused to EGFP or double EGFP fusions to examine their ability to induce nuclear transport of a heterologous protein. In addition, GST-pull down experiments were used to analyze the ability of LANA peptides to interact with members of the karyopherin family of nuclear transport receptors. Our studies revealed that both LANA proteins contain an N-terminal arginine/glycine (RG)-rich domain spanning a conserved chromatin-binding motif, which binds directly to importin β1 in a RanGTP-sensitive manner and serves as an NLS in the importin β1-mediated non-classical nuclear import pathway. Embedded within this domain is a conserved lysine/arginine-(KR)-rich bipartite motif that binds directly to multiple members of the importin α family of nuclear import adaptors in a RanGTP-insensitive manner and serves as an NLS in the classical importin α/β-mediated nuclear import pathway. The positioning of a classical bipartite kr-NLS embedded within a non-classical rg-NLS is a unique arrangement in these viral proteins, whose nuclear localization is critical to their functionality and to the virus life cycle. The ability to interact with multiple import receptors provides alternate pathways for nuclear localization of LANA. Since different import receptors can import cargo to distinct subnuclear compartments, a multifunctional NLS may provide LANA with an increased ability to interact with different nuclear components in its multifunctional role to maintain viral latency.","corpus_id":2678202,"score":0},{"doc_id":"21965294","title":"Evolutionary development of redundant nuclear localization signals in the mRNA export factor NXF1.","abstract":"In human cells, the mRNA export factor NXF1 resides in the nucleoplasm and at nuclear pore complexes. Karyopherin β2 or transportin recognizes a proline-tyrosine nuclear localization signal (PY-NLS) in the N-terminal tail of NXF1 and imports it into the nucleus. Here biochemical and cellular studies to understand the energetic organization of the NXF1 PY-NLS reveal unexpected redundancy in the nuclear import pathways used by NXF1. Human NXF1 can be imported via importin β, karyopherin β2, importin 4, importin 11, and importin α. Two NLS epitopes within the N-terminal tail, an N-terminal basic segment and a C-terminal R-X(2-5)-P-Y motif, provide the majority of binding energy for all five karyopherins. Mutation of both NLS epitopes abolishes binding to the karyopherins, mislocalized NXF1 to the cytoplasm, and significantly compromised its mRNA export function. The understanding of how different karyopherins recognize human NXF1, the examination of NXF1 sequences from divergent eukaryotes, and the interactions of NXF1 homologues with various karyopherins reveals the evolutionary development of redundant NLSs in NXF1 of higher eukaryotes. Redundancy of nuclear import pathways for NXF1 increases progressively from fungi to nematodes and insects to chordates, potentially paralleling the increasing complexity in mRNA export regulation and the evolution of new nuclear functions for NXF1.","corpus_id":6333447,"score":0},{"doc_id":"22028839","title":"Pigment epithelium-derived factor (PEDF) interacts with transportin SR2, and active nuclear import is facilitated by a novel nuclear localization motif.","abstract":"PEDF (Pigment epithelium-derived factor) is a non-inhibitory member of the serpin gene family (serpinF1) that displays neurotrophic and anti-angiogenic properties. PEDF contains a secretion signal sequence, but although originally regarded as a secreted extracellular protein, endogenous PEDF is found in the cytoplasm and nucleus of several mammalian cell types. In this study we employed a yeast two-hybrid interaction trap screen to identify transportin-SR2, a member of the importin-β family of nuclear transport karyopherins, as a putative PEDF binding partner. The interaction was supported in vitro by GST-pulldown and co-immunoprecipitation. Following transfection of HEK293 cells with GFP-tagged PEDF the protein was predominantly localised to the nucleus, suggesting that active import of PEDF occurs. A motif (YxxYRVRS) shared by PEDF and the unrelated transportin-SR2 substrate, RNA binding motif protein 4b, was identified and we investigated its potential as a nuclear localization signal (NLS) sequence. Site-directed mutagenesis of this helix A motif in PEDF resulted in a GFP-tagged mutant protein being excluded from the nucleus, and mutation of two arginine residues (R67, R69) was sufficient to abolish nuclear import and PEDF interaction with transportin-SR2. These results suggest a novel NLS and mechanism for serpinF1 nuclear import, which may be critical for anti-angiogenic and neurotrophic function.","corpus_id":14637106,"score":0},{"doc_id":"22454253","title":"Solution structures of the double-stranded RNA-binding domains from RNA helicase A.","abstract":"RNA helicase A (RHA) is a highly conserved protein with multifaceted functions in the gene expression of cellular and viral mRNAs. RHA recognizes highly structured nucleotides and catalytically rearranges the various interactions between RNA, DNA, and protein molecules to provide a platform for the ribonucleoprotein complex. We present the first solution structures of the double-stranded RNA-binding domains (dsRBDs), dsRBD1 and dsRBD2, from mouse RHA. We discuss the binding mode of the dsRBDs of RHA, in comparison with the known dsRBD structures in their complexes. Our structural data provide important information for the elucidation of the molecular reassembly mediated by RHA.","corpus_id":39641797,"score":0},{"doc_id":"22457361","title":"Extra double-stranded RNA binding domain (dsRBD) in a squid RNA editing enzyme confers resistance to high salt environment.","abstract":"A-to-I RNA editing is particularly common in coding regions of squid mRNAs. Previously, we isolated a squid editing enzyme (sqADAR2) that shows a unique structural feature when compared with other ADAR2 family members: an additional double-stranded RNA (dsRNA) binding domain (dsRBD). Alternative splicing includes or excludes this motif, generating a novel or a conventional variant termed sqADAR2a and sqADAR2b, respectively. The extra dsRBD of sqADAR2a increases its editing activity in vitro. We hypothesized that the high activity is due to an increase in the affinity of the enzyme for dsRNA. This may be important because protein-RNA interactions can be influenced by physical factors. We became particularly interested in analyzing the effects of salt on interactions between sqADAR2 and RNA because squid cells have a ∼3-fold higher ionic strength and proportionally more Cl(-) than vertebrate cells. To date, in vitro biochemical analyses of adenosine deamination have been conducted using vertebrate-like ionic strength buffers containing chloride as the major anion, although the vast majority of cellular anions are known to be organic. We found that squid-like salt conditions severely impair the binding affinity of conventional ADAR2s for dsRNA, leading to a decrease in nonspecific and site-specific editing activity. Inhibition of editing was mostly due to high Cl(-) levels and not to the high concentrations of K(+), Na(+), and organic anions like glutamate. Interestingly, the extra dsRBD in sqADAR2a conferred resistance to the high Cl(-) levels found in squid neurons. It does so by increasing the affinity of sqADAR2 for dsRNA by 30- or 100-fold in vertebrate-like or squid-like conditions, respectively. Site-directed mutagenesis of squid ADAR2a showed that its increased affinity and editing activity are directly attributable to the RNA binding activity of the extra dsRBD.","corpus_id":42250771,"score":0},{"doc_id":"22752847","title":"Backbone ¹HN, ¹³C, and ¹⁵N resonance assignments of the tandem RNA-binding domains of human DGCR8.","abstract":"Double-stranded RNA binding domain (dsRBD) containing proteins are critical components of the microRNA (miRNA) pathway, with key roles in small RNA biogenesis, modification, and regulation. DiGeorge Critical Region 8 (DGCR8) is a 773 amino acid, dsRBD-containing protein that was originally identified in humans as a protein encoded in the region of chromosome 22 that is deleted in patients with DiGeorge syndrome. Now, it is realized that DGCR8 complements the nuclear RNase III Drosha to initiate miRNA biogenesis by promoting efficient recognition and cleavage of primary miRNAs (pri-miRNA). A pair of C-terminal tandem dsRBDs separated by a flexible linker are required for pri-miRNA substrate binding and recognition. The crystal structure of the DGCR8 core region comprising residues 493-720 revealed that each dsRBD adopts the canonical αβββα fold. However, several residues located in important flexible regions including the β1-β2-loop implicated in canonical dsRNA recognition are absent in the crystal structure and no RNA-bound structure of DGCR8 has been reported. Here we report the (1)H(N), (13)C, and (15)N backbone resonance assignments of the 24 kDa, 214 amino acid human DGCR8(core) (residues 493-706) by heteronuclear NMR spectroscopy. Our assignments lay the foundation for a detailed solution state characterization of the dynamical and RNA-binding properties of this protein in solution.","corpus_id":207390110,"score":0},{"doc_id":"23856623","title":"Nuclear Respiratory Factor 2β (NRF-2β) recruits NRF-2α to the nucleus by binding to importin-α:β via an unusual monopartite-type nuclear localization signal.","abstract":"Nuclear respiratory factor 2 (NRF-2) is a mammalian transcription factor composed of two distinct and unrelated proteins: NRF-2α, which binds to DNA through its Ets domain, and NRF-2β, which contains the transcription activation domain. The activity of NRF-2 in neurons is regulated by nuclear localization; however, the mechanism by which NRF-2 is imported into the nucleus remains unknown. By using in vitro nuclear import assays and immuno-cytofluorescence, we dissect the nuclear import pathways of NRF-2. We show that both NRF-2α and NRF-2β contain intrinsic nuclear localization signals (NLSs): the Ets domain within NRF-2α and the NLS within NRF-2β (amino acids 311/321: EEPPAKRQCIE) that is recognized by importin-α:β. When NRF-2α and NRF-2β form a complex, the nuclear import of NRF-2αβ becomes strictly dependent on the NLS within NRF-2β. Therefore, the nuclear import mechanism of NRF-2 is unique among Ets factors. The NRF-2β NLS contains only two lysine/arginine residues, unlike other known importin-α:β-dependent NLSs. Using ELISA-based binding assays, we show that it is bound by importin-α in almost the same manner and with similar affinity to that of the classical monopartite NLSs, such as c-myc and SV40 T-antigen NLSs. However, the part of the tryptophan array of importin-α that is essential for the recognition of classical monopartite NLSs by generating apolar pockets for the P3 and the P5 lysine/arginine side chains is not required for the recognition of the NRF-2β NLS. We conclude that the NRF-2β NLS is an unusual but is, nevertheless, a bona fide monopartite-type NLS.","corpus_id":35274670,"score":0},{"doc_id":"24347303","title":"The HBM domain: introducing bimodularity to bacterial sensing.","abstract":"We have recently reported the three dimensional structure of the McpS chemoreceptor sensor domain in complex with its cognate ligands. The domain was characterized by a bimodular architecture, where ligand binding to each module caused a chemotactic response. This is a novel small molecule binding domain, which, however, is un-annotated in relevant databases. We report here the domain signature of the family of McpS-like sensor domains, which was termed helical bimodular (HBM) domain. The HBM domain was identified in Bacteria and Archaea and forms part of chemoreceptors and histidine kinases. The conservation of amino acids in the ligand binding sites of both modules suggests that HBM family members recognize similar ligands.","corpus_id":206391627,"score":0},{"doc_id":"24478460","title":"Transportin acts to regulate mitotic assembly events by target binding rather than Ran sequestration.","abstract":"The nuclear import receptors importin β and transportin play a different role in mitosis: both act phenotypically as spatial regulators to ensure that mitotic spindle, nuclear membrane, and nuclear pore assembly occur exclusively around chromatin. Importin β is known to act by repressing assembly factors in regions distant from chromatin, whereas RanGTP produced on chromatin frees factors from importin β for localized assembly. The mechanism of transportin regulation was unknown. Diametrically opposed models for transportin action are as follows: 1) indirect action by RanGTP sequestration, thus down-regulating release of assembly factors from importin β, and 2) direct action by transportin binding and inhibiting assembly factors. Experiments in Xenopus assembly extracts with M9M, a superaffinity nuclear localization sequence that displaces cargoes bound by transportin, or TLB, a mutant transportin that can bind cargo and RanGTP simultaneously, support direct inhibition. Consistently, simple addition of M9M to mitotic cytosol induces microtubule aster assembly. ELYS and the nucleoporin 107-160 complex, components of mitotic kinetochores and nuclear pores, are blocked from binding to kinetochores in vitro by transportin, a block reversible by M9M. In vivo, 30% of M9M-transfected cells have spindle/cytokinesis defects. We conclude that the cell contains importin β and transportin \"global positioning system\"or \"GPS\" pathways that are mechanistically parallel.","corpus_id":17512874,"score":0},{"doc_id":"25851436","title":"Deformability in the cleavage site of primary microRNA is not sensed by the double-stranded RNA binding domains in the microprocessor component DGCR8.","abstract":"The prevalence of double-stranded RNA (dsRNA) in eukaryotic cells has only recently been appreciated. Of interest here, RNA silencing begins with dsRNA substrates that are bound by the dsRNA-binding domains (dsRBDs) of their processing proteins. Specifically, processing of microRNA (miRNA) in the nucleus minimally requires the enzyme Drosha and its dsRBD-containing cofactor protein, DGCR8. The smallest recombinant construct of DGCR8 that is sufficient for in vitro dsRNA binding, referred to as DGCR8-Core, consists of its two dsRBDs and a C-terminal tail. As dsRBDs rarely recognize the nucleotide sequence of dsRNA, it is reasonable to hypothesize that DGCR8 function is dependent on the recognition of specific structural features in the miRNA precursor. Previously, we demonstrated that noncanonical structural elements that promote RNA flexibility within the stem of miRNA precursors are necessary for efficient in vitro cleavage by reconstituted Microprocessor complexes. Here, we combine gel shift assays with in vitro processing assays to demonstrate that neither the N-terminal dsRBD of DGCR8 in isolation nor the DGCR8-Core construct is sensitive to the presence of noncanonical structural elements within the stem of miRNA precursors, or to single-stranded segments flanking the stem. Extending DGCR8-Core to include an N-terminal heme-binding region does not change our conclusions. Thus, our data suggest that although the DGCR8-Core region is necessary for dsRNA binding and recruitment to the Microprocessor, it is not sufficient to establish the previously observed connection between RNA flexibility and processing efficiency.","corpus_id":20692760,"score":0},{"doc_id":"25960296","title":"Identification and characterization of a nuclear localization signal of TRIM28 that overlaps with the HP1 box.","abstract":"Tripartite motif-containing 28 (TRIM28) is a transcription regulator, which forms a repressor complex containing heterochromatin protein 1 (HP1). Here, we report identification of a nuclear localization signal (NLS) within the 462-494 amino acid region of TRIM28 that overlaps with its HP1 binding site, HP1 box. GST-pulldown experiments revealed the interaction of the arginine-rich TRIM28 NLS with various importin α subtypes (α1, α2 and α4). In vitro transport assay demonstrated that nuclear localization of GFP-TRIM28 NLS is mediated by importin αs, in conjunction with importin β1 and Ran. Further, we demonstrated that HP1 and importin αs compete for binding to TRIM28. Together, our findings suggest that importin α has an essential role in the nuclear delivery and preferential HP1 interaction of TRIM28.","corpus_id":20772132,"score":0},{"doc_id":"27332119","title":"Binding by TRBP-dsRBD2 Does Not Induce Bending of Double-Stranded RNA.","abstract":"Protein-nucleic acid interactions are central to a variety of biological processes, many of which involve large-scale conformational changes that lead to bending of the nucleic acid helix. Here, we focus on the nonsequence-specific protein TRBP, whose double-stranded RNA-binding domains (dsRBDs) interact with the A-form geometry of double-stranded RNA (dsRNA). Crystal structures of dsRBD-dsRNA interactions suggest that the dsRNA helix must bend in such a way that its major groove expands to conform to the dsRBD's binding surface. We show through isothermal titration calorimetry experiments that dsRBD2 of TRBP binds dsRNA with a temperature-independent observed binding affinity (KD ∼500 nM). Furthermore, a near-zero observed heat capacity change (ΔCp = 70 ± 40 cal·mol(-1)·K(-1)) suggests that large-scale conformational changes do not occur upon binding. This result is bolstered by molecular-dynamics simulations in which dsRBD-dsRNA interactions generate only modest bending of the RNA along its helical axis. Overall, these results suggest that this particular dsRBD-dsRNA interaction produces little to no change in the A-form geometry of dsRNA in solution. These results further support our previous hypothesis, based on extensive gel-shift assays, that TRBP preferentially binds to sites of nearly ideal A-form structure while being excluded from sites of local deformation in the RNA helical structure. The implications of this mechanism for efficient micro-RNA processing will be discussed.","corpus_id":29963528,"score":0},{"doc_id":"28792523","title":"Engineering double-stranded RNA binding activity into the Drosha double-stranded RNA binding domain results in a loss of microRNA processing function.","abstract":"Canonical processing of miRNA begins in the nucleus with the Microprocessor complex, which is minimally composed of the RNase III enzyme Drosha and two copies of its cofactor protein DGCR8. In structural analogy to most RNase III enzymes, Drosha possesses a modular domain with the double-stranded RNA binding domain (dsRBD) fold. Unlike the dsRBDs found in most members of the RNase III family, the Drosha-dsRBD does not display double-stranded RNA binding activity; perhaps related to this, the Drosha-dsRBD amino acid sequence does not conform well to the canonical patterns expected for a dsRBD. In this article, we investigate the impact on miRNA processing of engineering double-stranded RNA binding activity into Drosha's non-canonical dsRBD. Our findings corroborate previous studies that have demonstrated the Drosha-dsRBD is necessary for miRNA processing and suggest that the amino acid composition in the second α-helix of the domain is critical to support its evolved function.","corpus_id":37626108,"score":0},{"doc_id":"29036638","title":"The basic tilted helix bundle domain of the prolyl isomerase FKBP25 is a novel double-stranded RNA binding module.","abstract":"Prolyl isomerases are defined by a catalytic domain that facilitates the cis-trans interconversion of proline residues. In most cases, additional domains in these enzymes add important biological function, including recruitment to a set of protein substrates. Here, we report that the N-terminal basic tilted helix bundle (BTHB) domain of the human prolyl isomerase FKBP25 confers specific binding to double-stranded RNA (dsRNA). This binding is selective over DNA as well as single-stranded oligonucleotides. We find that FKBP25 RNA-association is required for its nucleolar localization and for the vast majority of its protein interactions, including those with 60S pre-ribosome and early ribosome biogenesis factors. An independent mobility of the BTHB and FKBP catalytic domains supports a model by which the N-terminus of FKBP25 is anchored to regions of dsRNA, whereas the FKBP domain is free to interact with neighboring proteins. Apart from the identification of the BTHB as a new dsRNA-binding module, this domain adds to the growing list of auxiliary functions used by prolyl isomerases to define their primary cellular targets.","corpus_id":33563066,"score":0}],"string":"[\n {\n \"doc_id\": \"18343812\",\n \"title\": \"A PY-NLS nuclear targeting signal is required for nuclear localization and function of the Saccharomyces cerevisiae mRNA-binding protein Hrp1.\",\n \"abstract\": \"Proteins destined for import into the nucleus contain nuclear localization signals (NLSs) that are recognized by import receptors termed karyopherins or importins. Until recently, the only nuclear import sequence that had been well defined and characterized was the classical NLS (cNLS), which is recognized by importin alpha. However, Chook and coworkers (Lee, B. J., Cansizoglu, A. E., Süel, K. E., Louis, T. H., Zhang, Z., and Chook, Y. M. (2006) Cell 126, 543-558) have provided new insight into nuclear targeting with their identification of a novel NLS, termed the PY-NLS, that is recognized by the human karyopherin beta2/transportin (Kapbeta2) receptor. Here, we demonstrate that the PY-NLS is conserved in Saccharomyces cerevisiae and show for the first time that the PY-NLS is a functional nuclear targeting sequence in vivo. The apparent ortholog of Kapbeta2 in yeast, Kap104, has two known cargos, the mRNA-binding proteins Hrp1 and Nab2, which both contain putative PY-NLS-like sequences. We find that the PY-NLS-like sequence within Hrp1, which closely matches the PY-NLS consensus, is both necessary and sufficient for nuclear import and is also required for receptor binding and protein function. In contrast, the PY-NLS-like sequences in Nab2, which vary from the PY-NLS consensus, are not required for proper import or protein function, suggesting that Kap104 may interact with different cargos using multiple mechanisms. Dissection of the PY-NLS consensus reveals that the minimal PY-NLS in yeast consists of the C-terminal portion of the human consensus, R/H/KX(2-5)PY, with upstream basic or hydrophobic residues enhancing the targeting function. Finally, we apply this analysis to a bioinformatic search of the yeast proteome as a preliminary search for new potential Kap104 cargos.\",\n \"corpus_id\": 28660584,\n \"score\": 2\n },\n {\n \"doc_id\": \"19124606\",\n \"title\": \"RNA-regulated interaction of transportin-1 and exportin-5 with the double-stranded RNA-binding domain regulates nucleocytoplasmic shuttling of ADAR1.\",\n \"abstract\": \"Double-stranded RNA (dsRNA)-binding proteins interact with substrate RNAs via dsRNA-binding domains (dsRBDs). Several proteins harboring these domains exhibit nucleocytoplasmic shuttling and possibly remain associated with their substrate RNAs bound in the nucleus during nuclear export. In the human RNA-editing enzyme ADAR1-c, the nuclear localization signal overlaps the third dsRBD, while the corresponding import factor is unknown. The protein also lacks a clear nuclear export signal but shuttles between the nucleus and the cytoplasm. Here we identify transportin-1 as the import receptor for ADAR1. Interestingly, dsRNA binding interferes with transportin-1 binding. At the same time, each of the dsRBDs in ADAR1 interacts with the export factor exportin-5. RNA binding stimulates this interaction but is not a prerequisite. Thus, our data demonstrate a role for some dsRBDs as RNA-sensitive nucleocytoplasmic transport signals. dsRBD3 in ADAR1 can mediate nuclear import, while interaction of all dsRBDs might control nuclear export. This finding may have implications for other proteins containing dsRBDs and suggests a selective nuclear export mechanism for substrates interacting with these proteins.\",\n \"corpus_id\": 19334062,\n \"score\": 2\n },\n {\n \"doc_id\": \"19617375\",\n \"title\": \"Identification of a selective nuclear import signal in adenosine deaminases acting on RNA.\",\n \"abstract\": \"The adenosine deaminases acting on RNA (ADARs) comprise a family of RNA editing enzymes that selectively modify single codons within RNA primary transcripts with often profound impact on protein function. Little is known about the mechanisms that regulate nuclear RNA editing activity. Editing levels show cell-type specific and developmental modulation that does not strictly coincide with observed expression levels of ADARs. Here, we provide evidence for a molecular mechanism that might control nuclear import of specific ADARs and, in turn, nuclear RNA editing. We identify an in vivo ADAR3 interaction partner, importin alpha 1 (KPNA2) that specifically recognizes an arginine-rich ADAR3 sequence motif and show that it acts as a functional nuclear localization sequence. Furthermore, whereas KPNA2, but not KPNA1 or KNPA3, recognizes the ADAR3 NLS, we observe the converse binding specificity with ADAR2. Interestingly, alternative splicing of ADAR2 pre-mRNA introduces an ADAR3-like NLS that alters the interaction profile with the importins. Thus, in vivo RNA editing might be regulated, in part, through controlled subcellular localization of ADARs, which in turn is governed by the coordinated local expression of importin alpha proteins and ADAR protein variants.\",\n \"corpus_id\": 7301226,\n \"score\": 2\n },\n {\n \"doc_id\": \"20308327\",\n \"title\": \"A glycine-rich domain of hnRNP H/F promotes nucleocytoplasmic shuttling and nuclear import through an interaction with transportin 1.\",\n \"abstract\": \"Heterogeneous nuclear ribonucleoprotein (hnRNP) H and F are members of a closely related subfamily of hnRNP proteins that are implicated in many aspects of RNA processing. hnRNP H and F are alternative splicing factors for numerous U2- and U12-dependent introns. The proteins have three RNA binding domains and two glycine-rich domains and localize to both the nucleus and cytoplasm, but little is known about which domains govern subcellular localization or splicing activity. We show here that the central glycine-tyrosine-arginine-rich (GYR) domain is responsible for nuclear localization, and a nonclassical nuclear localization signal (NLS) was mapped to a short, highly conserved sequence whose activity was compromised by point mutations. Glutathione S-transferase (GST) pulldown assays demonstrated that the hnRNP H NLS interacts with the import receptor transportin 1. Finally, we show that hnRNP H/F are transcription-dependent shuttling proteins. Collectively, the results suggest that hnRNP H and F are GYR domain-dependent shuttling proteins whose posttranslational modifications may alter nuclear localization and hence function.\",\n \"corpus_id\": 3148086,\n \"score\": 2\n },\n {\n \"doc_id\": \"21728134\",\n \"title\": \"ADAR proteins: double-stranded RNA and Z-DNA binding domains.\",\n \"abstract\": \"Adenosine deaminases acting on RNA (ADAR) catalyze adenosine to inosine editing within double-stranded RNA (dsRNA) substrates. Inosine is read as a guanine by most cellular processes and therefore these changes create codons for a different amino acid, stop codons or even a new splice-site allowing protein diversity generated from a single gene. We review here the current structural and molecular knowledge on RNA editing by the ADAR family of protein. We focus especially on two types of nucleic acid binding domains present in ADARs, namely the dsRNA and Z-DNA binding domains.\",\n \"corpus_id\": 206650423,\n \"score\": 2\n },\n {\n \"doc_id\": \"22105828\",\n \"title\": \"Molecular dynamics simulation of conformational heterogeneity in transportin 1.\",\n \"abstract\": \"Transportin 1 (Trn1), as a typical transport receptor of the karyopherin-β family, mediates numerous RNA binding proteins into the nucleus by recognizing proline-tyrosine nuclear localization signals (PY-NLSs). Such process is regulated by RanGTP through its nucleotide cycle, which is associated with ligand dissociation. Yet a proper description including dynamic properties of Trn1 and its response on ligand/Ran binding has not been accessible so far. Here, we use molecular dynamics simulations to probe the conformational dynamics of the apo-Trn1 and Trn1 in complex with ligand and Ran. The results reveal a strikingly intrinsic flexibility and conformational heterogeneity of Trn1, identified as generally segmental architecture. The segments rotate relative to each other about a flexible hinge and thereby force Trn1 to adopt a conformation compatible with the binding of Ran or substrates. Such binding significantly suppresses the flexibility and conformational heterogeneity of Trn1 and results in a disorder-to-order transition of HR8 loop, which facilitates this loop to allosterically communicate with the C-terminal arch of Trn1. These results give insights into the disassembly and recycling of the Trn1, which has important implications for the regulation of the nuclear transport cycle and for the ligand selectivity.\",\n \"corpus_id\": 206406236,\n \"score\": 2\n },\n {\n \"doc_id\": \"22210494\",\n \"title\": \"Solution structure of the N-terminal dsRBD of Drosophila ADAR and interaction studies with RNA.\",\n \"abstract\": \"Adenosine deaminases that act on RNA (ADAR) catalyze adenosine to inosine (A-to-I) editing in double-stranded RNA (dsRNA) substrates. Inosine is read as guanosine by the translation machinery; therefore A-to-I editing events in coding sequences may result in recoding genetic information. Whereas vertebrates have two catalytically active enzymes, namely ADAR1 and ADAR2, Drosophila has a single ADAR protein (dADAR) related to ADAR2. The structural determinants controlling substrate recognition and editing of a specific adenosine within dsRNA substrates are only partially understood. Here, we report the solution structure of the N-terminal dsRNA binding domain (dsRBD) of dADAR and use NMR chemical shift perturbations to identify the protein surface involved in RNA binding. Additionally, we show that Drosophila ADAR edits the R/G site in the mammalian GluR-2 pre-mRNA which is naturally modified by both ADAR1 and ADAR2. We then constructed a model showing how dADAR dsRBD1 binds to the GluR-2 R/G stem-loop. This model revealed that most side chains interacting with the RNA sugar-phosphate backbone need only small displacement to adapt for dsRNA binding and are thus ready to bind to their dsRNA target. It also predicts that dADAR dsRBD1 would bind to dsRNA with less sequence specificity than dsRBDs of ADAR2. Altogether, this study gives new insights into dsRNA substrate recognition by Drosophila ADAR.\",\n \"corpus_id\": 30989248,\n \"score\": 2\n },\n {\n \"doc_id\": \"22778397\",\n \"title\": \"Structural and energetic basis of ALS-causing mutations in the atypical proline-tyrosine nuclear localization signal of the Fused in Sarcoma protein (FUS).\",\n \"abstract\": \"Mutations in the proline/tyrosine-nuclear localization signal (PY-NLS) of the Fused in Sarcoma protein (FUS) cause amyotrophic lateral sclerosis (ALS). Here we report the crystal structure of the FUS PY-NLS bound to its nuclear import receptor Karyopherinβ2 (Kapβ2; also known as Transportin). The FUS PY-NLS occupies the structurally invariant C-terminal arch of Kapβ2, tracing a path similar to that of other characterized PY-NLSs. Unlike other PY-NLSs, which generally bind Kapβ2 in fully extended conformations, the FUS peptide is atypical as its central portion forms a 2.5-turn α-helix. The Kapβ2-binding epitopes of the FUS PY-NLS consist of an N-terminal PGKM hydrophobic motif, a central arginine-rich α-helix, and a C-terminal PY motif. ALS mutations are found almost exclusively within these epitopes. Each ALS mutation site makes multiple contacts with Kapβ2 and mutations of these residues decrease binding affinities for Kapβ2 (K(D) for wild-type FUS PY-NLS is 9.5 nM) up to ninefold. Thermodynamic analyses of ALS mutations in the FUS PY-NLS show that the weakening of FUS-Kapβ2 binding affinity, the degree of cytoplasmic mislocalization, and ALS disease severity are correlated.\",\n \"corpus_id\": 31306170,\n \"score\": 2\n },\n {\n \"doc_id\": \"22918483\",\n \"title\": \"RNA recognition by double-stranded RNA binding domains: a matter of shape and sequence.\",\n \"abstract\": \"The double-stranded RNA binding domain (dsRBD) is a small protein domain of 65-70 amino acids adopting an αβββα fold, whose central property is to bind to double-stranded RNA (dsRNA). This domain is present in proteins implicated in many aspects of cellular life, including antiviral response, RNA editing, RNA processing, RNA transport and, last but not least, RNA silencing. Even though proteins containing dsRBDs can bind to very specific dsRNA targets in vivo, the binding of dsRBDs to dsRNA is commonly believed to be shape-dependent rather than sequence-specific. Interestingly, recent structural information on dsRNA recognition by dsRBDs opens the possibility that this domain performs a direct readout of RNA sequence in the minor groove, allowing a global reconsideration of the principles describing dsRNA recognition by dsRBDs. We review in this article the current structural and molecular knowledge on dsRBDs, emphasizing the intricate relationship between the amino acid sequence, the structure of the domain and its RNA recognition capacity. We especially focus on the molecular determinants of dsRNA recognition and describe how sequence discrimination can be achieved by this type of domain.\",\n \"corpus_id\": 1949699,\n \"score\": 2\n },\n {\n \"doc_id\": \"23056579\",\n \"title\": \"FUS-NLS/Transportin 1 complex structure provides insights into the nuclear targeting mechanism of FUS and the implications in ALS.\",\n \"abstract\": \"The C-terminal nuclear localization sequence of FUsed in Sarcoma (FUS-NLS) is critical for its nuclear import mediated by transportin (Trn1). Familial amyotrophic lateral sclerosis (ALS) related mutations are clustered in FUS-NLS. We report here the structural, biochemical and cell biological characterization of the FUS-NLS and its clinical implications. The crystal structure of the FUS-NLS/Trn1 complex shows extensive contacts between the two proteins and a unique α-helical structure in the FUS-NLS. The binding affinity between Trn1 and FUS-NLS (wide-type and 12 ALS-associated mutants) was determined. As compared to the wide-type FUS-NLS (K(D) = 1.7 nM), each ALS-associated mutation caused a decreased affinity and the range of this reduction varied widely from 1.4-fold over 700-fold. The affinity of the mutants correlated with the extent of impaired nuclear localization, and more importantly, with the duration of disease progression in ALS patients. This study provides a comprehensive understanding of the nuclear targeting mechanism of FUS and illustrates the significance of FUS-NLS in ALS.\",\n \"corpus_id\": 3912886,\n \"score\": 2\n },\n {\n \"doc_id\": \"23535894\",\n \"title\": \"Crystal structure of human Karyopherin β2 bound to the PY-NLS of Saccharomyces cerevisiae Nab2.\",\n \"abstract\": \"Import-Karyopherin or Importin proteins bind nuclear localization signals (NLSs) to mediate the import of proteins into the cell nucleus. Karyopherin β2 or Kapβ2, also known as Transportin, is a member of this transporter family responsible for the import of numerous RNA binding proteins. Kapβ2 recognizes a targeting signal termed the PY-NLS that lies within its cargos to target them through the nuclear pore complex. The recognition of PY-NLS by Kapβ2 is conserved throughout eukaryotes. Kap104, the Kapβ2 homolog in Saccharomyces cerevisiae, recognizes PY-NLSs in cargos Nab2, Hrp1, and Tfg2. We have determined the crystal structure of Kapβ2 bound to the PY-NLS of the mRNA processing protein Nab2 at 3.05-Å resolution. A seven-residue segment of the PY-NLS of Nab2 is observed to bind Kapβ2 in an extended conformation and occupies the same PY-NLS binding site observed in other Kapβ2·PY-NLS structures.\",\n \"corpus_id\": 1563489,\n \"score\": 2\n },\n {\n \"doc_id\": \"23882114\",\n \"title\": \"The double-stranded RNA binding domain of human Dicer functions as a nuclear localization signal.\",\n \"abstract\": \"Dicer is a key player in microRNA (miRNA) and RNA interference (RNAi) pathways, processing miRNA precursors and double-stranded RNA into ∼21-nt-long products ultimately triggering sequence-dependent gene silencing. Although processing of substrates in vertebrate cells occurs in the cytoplasm, there is growing evidence suggesting Dicer is also present and functional in the nucleus. To address this possibility, we searched for a nuclear localization signal (NLS) in human Dicer and identified its C-terminal double-stranded RNA binding domain (dsRBD) as harboring NLS activity. We show that the dsRBD-NLS can mediate nuclear import of a reporter protein via interaction with importins β, 7, and 8. In the context of full-length Dicer, the dsRBD-NLS is masked. However, duplication of the dsRBD localizes the full-length protein to the nucleus. Furthermore, deletion of the N-terminal helicase domain results in partial accumulation of Dicer in the nucleus upon leptomycin B treatment, indicating that CRM1 contributes to nuclear export of Dicer. Finally, we demonstrate that human Dicer has the ability to shuttle between the nucleus and the cytoplasm. We conclude that Dicer is a shuttling protein whose steady-state localization is cytoplasmic.\",\n \"corpus_id\": 207217413,\n \"score\": 2\n },\n {\n \"doc_id\": \"24449914\",\n \"title\": \"Structural basis for nuclear import of splicing factors by human Transportin 3.\",\n \"abstract\": \"Transportin 3 (Tnpo3, Transportin-SR2) is implicated in nuclear import of splicing factors and HIV-1 replication. Herein, we show that the majority of cellular Tnpo3 binding partners contain arginine-serine (RS) repeat domains and present crystal structures of human Tnpo3 in its free as well as GTPase Ran- and alternative splicing factor/splicing factor 2 (ASF/SF2)-bound forms. The flexible β-karyopherin fold of Tnpo3 embraces the RNA recognition motif and RS domains of the cargo. A constellation of charged residues on and around the arginine-rich helix of Tnpo3 HEAT repeat 15 engage the phosphorylated RS domain and are critical for the recognition and nuclear import of ASF/SF2. Mutations in the same region of Tnpo3 impair its interaction with the cleavage and polyadenylation specificity factor 6 (CPSF6) and its ability to support HIV-1 replication. Steric incompatibility of the RS domain and RanGTP engagement by Tnpo3 provides the mechanism for cargo release in the nucleus. Our results elucidate the structural bases for nuclear import of splicing factors and the Tnpo3-CPSF6 nexus in HIV-1 biology.\",\n \"corpus_id\": 22578720,\n \"score\": 2\n },\n {\n \"doc_id\": \"24780099\",\n \"title\": \"Transportin-1 and Transportin-2: protein nuclear import and beyond.\",\n \"abstract\": \"Nearly 20 years after its identification as a new β-karyopherin mediating the nuclear import of the RNA-binding protein hnRNP A1, Transportin-1 is still commonly overlooked in comparison with its best known cousin, Importin-β. Transportin-1 is nonetheless a considerable player in nucleo-cytoplasmic transport. Over the past few years, significant progress has been made in the characterization of the nuclear localization signals (NLSs) that Transportin-1 recognizes, thereby providing the molecular basis of its diversified repertoire of cargoes. The recent discovery that mutations in the Transportin-dependent NLS of FUS cause mislocalization of this protein and result in amyotrophic lateral sclerosis illustrates the importance of Transportin-dependent import for human health. Besides, new functions of Transportin-1 are emerging in processes other than nuclear import. Here, we summarize what is known about Transportin-1 and the related β-karyopherin Transportin-2.\",\n \"corpus_id\": 26022824,\n \"score\": 2\n },\n {\n \"doc_id\": \"24801449\",\n \"title\": \"Substrate recognition and specificity of double-stranded RNA binding proteins.\",\n \"abstract\": \"Recognition of double-stranded (ds) RNA is an important part of many cellular pathways, including RNA silencing, viral recognition, RNA editing, processing, and transport. dsRNA recognition is often achieved by dsRNA binding domains (dsRBDs). We use atomistic molecular dynamics simulations to examine the binding interface of the transactivation response RNA binding protein (TRBP) dsRBDs to dsRNA substrates. Our results explain the exclusive selectivity of dsRBDs toward dsRNA and against DNA-RNA hybrid and dsDNA duplexes. We also provide corresponding experimental evidence. The dsRNA duplex is recognized by dsRBDs through the A-form of three duplex grooves and by the chemical properties of RNA bases, which have 2'-hydroxyl groups on their sugar rings. Our simulations show that TRBP dsRBD discriminates dsRNA- from DNA-containing duplexes primarily through interactions at two duplex grooves. The simulations also reveal that the conformation of the DNA-RNA duplex can be altered by dsRBD proteins, resulting in a weak binding of dsRBDs to DNA-RNA hybrids. Our study reveals the structural and molecular basis of protein-RNA interaction that gives rise to the observed substrate specificity of dsRNA binding proteins.\",\n \"corpus_id\": 18192088,\n \"score\": 2\n },\n {\n \"doc_id\": \"24905200\",\n \"title\": \"An RNA editor, adenosine deaminase acting on double-stranded RNA (ADAR1).\",\n \"abstract\": \"Adenosine deaminase acting on RNA1 (ADAR1) catalyzes the C6 deamination of adenosine (A) to produce inosine (I) in regions of RNA with double-stranded (ds) character. This process is known as A-to-I RNA editing. Alternative promoters drive the expression of the Adar1 gene and alternative splicing gives rise to transcripts that encode 2 ADAR1 protein size isoforms. ADAR1 p150 is an interferon (IFN)-inducible dsRNA adenosine deaminase found in the cytoplasm and nucleus, whereas ADAR1 p110 is constitutively expressed and nuclear in localization. Dependent on the duplex structure of the dsRNA substrate, deamination of adenosine by ADAR can be either highly site-selective or nonspecific. A-to-I editing can alter the stability of RNA structures and the coding of RNA as I is read as G instead of A by ribosomes during mRNA translation and by polymerases during RNA replication. A-to-I editing is of broad physiologic significance. Both the production and the action of IFNs, and hence the subsequent interaction of viruses with their hosts, are among the processes affected by A-to-I editing.\",\n \"corpus_id\": 22858275,\n \"score\": 2\n },\n {\n \"doc_id\": \"24954387\",\n \"title\": \"'Black sheep' that don't leave the double-stranded RNA-binding domain fold.\",\n \"abstract\": \"The canonical double-stranded RNA (dsRNA)-binding domain (dsRBD) is composed of an α1-β1-β2-β3-α2 secondary structure that folds in three dimensions to recognize dsRNA. Recently, structural and functional studies of divergent dsRBDs revealed adaptations that include intra- and/or intermolecular protein interactions, sometimes in the absence of detectable dsRNA-binding ability. We describe here how discrete dsRBD components can accommodate pronounced amino-acid sequence changes while maintaining the core fold. We exemplify the growing importance of divergent dsRBDs in mRNA decay by discussing Dicer, Staufen (STAU)1 and 2, trans-activation responsive RNA-binding protein (TARBP)2, protein activator of protein kinase RNA-activated (PKR) (PACT), DiGeorge syndrome critical region (DGCR)8, DEAH box helicase proteins (DHX) 9 and 30, and dsRBD-like fold-containing proteins that have ribosome-related functions. We also elaborate on the computational limitations to discovering yet-to-be-identified divergent dsRBDs.\",\n \"corpus_id\": 33816117,\n \"score\": 2\n },\n {\n \"doc_id\": \"25584639\",\n \"title\": \"Functions of double-stranded RNA-binding domains in nucleocytoplasmic transport.\",\n \"abstract\": \"The double-stranded RNA-binding domain (dsRBD) is a small protein domain found in eukaryotic, prokaryotic and viral proteins, whose central property is to bind to double-stranded RNA (dsRNA). Aside from this major function, recent examples of dsRBDs involved in the regulation of the sub-cellular localization of proteins, suggest that the participation of dsRBDs in nucleocytoplasmic trafficking is likely to represent a widespread auxiliary function of this type of RNA-binding domain. Overall, dsRBDs from proteins involved in many different biological processes have been reported to be implicated in nuclear import and export, as well as cytoplasmic, nuclear and nucleolar retention. Interestingly, the function of dsRBDs in nucleocytoplasmic trafficking is often regulated by their dsRNA-binding capacity, which can either enhance or impair the transport from one compartment to another. Here, we present and discuss the emerging function of dsRBDs in nucleocytoplasmic transport.\",\n \"corpus_id\": 7795593,\n \"score\": 2\n },\n {\n \"doc_id\": \"26173234\",\n \"title\": \"Nuclear localization signals for four distinct karyopherin-β nuclear import systems.\",\n \"abstract\": \"The Karyopherin-β family of proteins mediates nuclear transport of macromolecules. Nuclear versus cytoplasmic localization of proteins is often suggested by the presence of NLSs (nuclear localization signals) or NESs (nuclear export signals). Import-Karyopherin-βs or Importins bind to NLSs in their protein cargos to transport them through nuclear pore complexes into the nucleus. Until recently, only two classes of NLS had been biochemically and structurally characterized: the classical NLS, which is recognized by the Importin-α/β heterodimer and the PY-NLS (proline-tyrosine NLS), which is recognized by Karyopherin-β2 or Transportin-1. Structures of two other Karyopherin-βs, Kap121 and Transportin-SR2, in complex with their respective cargos were reported for the first time recently, revealing two new distinct classes of NLSs. The present paper briefly describes the classical NLS, reviews recent literature on the PY-NLS and provides in-depth reviews of the two newly discovered classes of NLSs that bind Kap121p and Transportin-SR respectively.\",\n \"corpus_id\": 21558738,\n \"score\": 2\n },\n {\n \"doc_id\": \"27618664\",\n \"title\": \"Karyopherin-β2 Recognition of a PY-NLS Variant that Lacks the Proline-Tyrosine Motif.\",\n \"abstract\": \"Karyopherin-β2 or Transportin-1 binds proline-tyrosine nuclear localization signals (PY-NLSs) in its cargos. PY-NLSs are described by structural disorder, overall positive charge, and binding epitopes composed of an N-terminal hydrophobic or basic motif and a C-terminal R-X2-5P-Y motif. The N-terminal tail of histone H3 binds Kapβ2 with high affinity but does not contain a recognizable PY-NLS. The crystal structure of the Kapβ2-H3 tail shows residues 11-27 of H3 binding to the PY-NLS site of Kapβ2. H3 residues (11)TGGKAPRK(18) bind the site for PY-NLS Epitope 1 (N-terminal hydrophobic/basic motif), which is most important for Kapβ2-binding. H3 residue Arg26 occupies the PY-NLS Epitope 2 position (usually arginine of R-X2-5P-Y) but PY-NLS Epitope 3 (proline-tyrosine motif) is missing in the H3 tail. Histone H3 thus provides an example of a PY-NLS variant with no proline-tyrosine or homologous proline-hydrophobic motif. The H3 tail uses a very strong Epitope 1 to compensate for loss of the often-conserved proline-tyrosine epitope.\",\n \"corpus_id\": 205263282,\n \"score\": 2\n },\n {\n \"doc_id\": \"29449323\",\n \"title\": \"Structural basis of siRNA recognition by TRBP double-stranded RNA binding domains.\",\n \"abstract\": \"The accurate cleavage of pre-micro(mi)RNAs by Dicer and mi/siRNA guide strand selection are important steps in forming the RNA-induced silencing complex (RISC). The role of Dicer binding partner TRBP in these processes remains poorly understood. Here, we solved the solution structure of the two N-terminal dsRNA binding domains (dsRBDs) of TRBP in complex with a functionally asymmetric siRNA using NMR, EPR, and single-molecule spectroscopy. We find that siRNA recognition by the dsRBDs is not sequence-specific but rather depends on the RNA shape. The two dsRBDs can swap their binding sites, giving rise to two equally populated, pseudo-symmetrical complexes, showing that TRBP is not a primary sensor of siRNA asymmetry. Using our structure to model a Dicer-TRBP-siRNA ternary complex, we show that TRBP's dsRBDs and Dicer's RNase III domains bind a canonical 19 base pair siRNA on opposite sides, supporting a mechanism whereby TRBP influences Dicer-mediated cleavage accuracy by binding the dsRNA region of the pre-miRNA during Dicer cleavage.\",\n \"corpus_id\": 3996101,\n \"score\": 2\n },\n {\n \"doc_id\": \"29677513\",\n \"title\": \"Nuclear Import Receptor Inhibits Phase Separation of FUS through Binding to Multiple Sites.\",\n \"abstract\": \"Liquid-liquid phase separation (LLPS) is believed to underlie formation of biomolecular condensates, cellular compartments that concentrate macromolecules without surrounding membranes. Physical mechanisms that control condensate formation/dissolution are poorly understood. The RNA-binding protein fused in sarcoma (FUS) undergoes LLPS in vitro and associates with condensates in cells. We show that the importin karyopherin-β2/transportin-1 inhibits LLPS of FUS. This activity depends on tight binding of karyopherin-β2 to the C-terminal proline-tyrosine nuclear localization signal (PY-NLS) of FUS. Nuclear magnetic resonance (NMR) analyses reveal weak interactions of karyopherin-β2 with sequence elements and structural domains distributed throughout the entirety of FUS. Biochemical analyses demonstrate that most of these same regions also contribute to LLPS of FUS. The data lead to a model where high-affinity binding of karyopherin-β2 to the FUS PY-NLS tethers the proteins together, allowing multiple, distributed weak intermolecular contacts to disrupt FUS self-association, blocking LLPS. Karyopherin-β2 may act analogously to control condensates in diverse cellular contexts.\",\n \"corpus_id\": 5011616,\n \"score\": 2\n },\n {\n \"doc_id\": \"19390115\",\n \"title\": \"An extra double-stranded RNA binding domain confers high activity to a squid RNA editing enzyme.\",\n \"abstract\": \"RNA editing by adenosine deamination is particularly prevalent in the squid nervous system. We hypothesized that the squid editing enzyme might contain structural differences that help explain this phenomenon. As a first step, a squid adenosine deaminase that acts on RNA (sqADAR2a) cDNA and the gene that encodes it were cloned from the giant axon system. PCR and RNase protection assays showed that a splice variant of this clone (sqADAR2b) was also expressed in this tissue. Both versions are homologous to the vertebrate ADAR2 family. sqADAR2b encodes a conventional ADAR2 family member with an evolutionarily conserved deaminase domain and two double-stranded RNA binding domains (dsRBD). sqADAR2a differs from sqADAR2b by containing an optional exon that encodes an \\\"extra\\\" dsRBD. Both splice variants are expressed at comparable levels and are extensively edited, each in a unique pattern. Recombinant sqADAR2a and sqADAR2b, produced in Pichia pastoris, are both active on duplex RNA. Using a standard 48-h protein induction, both sqADAR2a and sqADAR2b exhibit promiscuous self-editing; however, this activity is particularly robust for sqADAR2a. By decreasing the induction time to 16 h, self-editing was mostly eliminated. We next tested the ability of sqADAR2a and sqADAR2b to edit two K+ channel mRNAs in vitro. Both substrates are known to be edited in squid. For each mRNA, sqADAR2a edited many more sites than sqADAR2b. These data suggest that the \\\"extra\\\" dsRBD confers high activity on sqADAR2a.\",\n \"corpus_id\": 10303487,\n \"score\": 1\n },\n {\n \"doc_id\": \"19651874\",\n \"title\": \"Editing of HIV-1 RNA by the double-stranded RNA deaminase ADAR1 stimulates viral infection.\",\n \"abstract\": \"Adenosine deaminases that act on dsRNA (ADARs) are enzymes that target double-stranded regions of RNA converting adenosines into inosines (A-to-I editing) thus contributing to genome complexity and fine regulation of gene expression. It has been described that a member of the ADAR family, ADAR1, can target viruses and affect their replication process. Here we report evidence showing that ADAR1 stimulates human immuno deficiency virus type 1 (HIV-1) replication by using both editing-dependent and editing-independent mechanisms. We show that over-expression of ADAR1 in HIV-1 producer cells increases viral protein accumulation in an editing-independent manner. Moreover, HIV-1 virions generated in the presence of over-expressed ADAR1 but not an editing-inactive ADAR1 mutant are released more efficiently and display enhanced infectivity, as demonstrated by challenge assays performed with T cell lines and primary CD4(+) T lymphocytes. Finally, we report that ADAR1 associates with HIV-1 RNAs and edits adenosines in the 5' untranslated region (UTR) and the Rev and Tat coding sequence. Overall these results suggest that HIV-1 has evolved mechanisms to take advantage of specific RNA editing activity of the host cell and disclose a stimulatory function of ADAR1 in the spread of HIV-1.\",\n \"corpus_id\": 12314845,\n \"score\": 1\n },\n {\n \"doc_id\": \"20106953\",\n \"title\": \"Structure of the Arabidopsis thaliana DCL4 DUF283 domain reveals a noncanonical double-stranded RNA-binding fold for protein-protein interaction.\",\n \"abstract\": \"Dicer or Dicer-like (DCL) protein is a catalytic component involved in microRNA (miRNA) or small interference RNA (siRNA) processing pathway, whose fragment structures have been partially solved. However, the structure and function of the unique DUF283 domain within dicer is largely unknown. Here we report the first structure of the DUF283 domain from the Arabidopsis thaliana DCL4. The DUF283 domain adopts an alpha-beta-beta-beta-alpha topology and resembles the structural similarity to the double-stranded RNA-binding domain. Notably, the N-terminal alpha helix of DUF283 runs cross over the C-terminal alpha helix orthogonally, therefore, N- and C-termini of DUF283 are in close proximity. Biochemical analysis shows that the DUF283 domain of DCL4 displays weak dsRNA binding affinity and specifically binds to double-stranded RNA-binding domain 1 (dsRBD1) of Arabidopsis DRB4, whereas the DUF283 domain of DCL1 specifically binds to dsRBD2 of Arabidopsis HYL1. These data suggest a potential functional role of the Arabidopsis DUF283 domain in target selection in small RNA processing.\",\n \"corpus_id\": 23053213,\n \"score\": 1\n },\n {\n \"doc_id\": \"21080422\",\n \"title\": \"Structures of the first and second double-stranded RNA-binding domains of human TAR RNA-binding protein.\",\n \"abstract\": \"The TAR RNA-binding Protein (TRBP) is a double-stranded RNA (dsRNA)-binding protein, which binds to Dicer and is required for the RNA interference pathway. TRBP consists of three dsRNA-binding domains (dsRBDs). The first and second dsRBDs (dsRBD1 and dsRBD2, respectively) have affinities for dsRNA, whereas the third dsRBD (dsRBD3) binds to Dicer. In this study, we prepared the single domain fragments of human TRBP corresponding to dsRBD1 and dsRBD2 and solved the crystal structure of dsRBD1 and the solution structure of dsRBD2. The two structures contain an α-β-β-β-α fold, which is common to the dsRBDs. The overall structures of dsRBD1 and dsRBD2 are similar to each other, except for a slight shift of the first α helix. The residues involved in dsRNA binding are conserved. We examined the small interfering RNA (siRNA)-binding properties of these dsRBDs by isothermal titration colorimetry measurements. The dsRBD1 and dsRBD2 fragments both bound to siRNA, with dissociation constants of 220 and 113 nM, respectively. In contrast, the full-length TRBP and its fragment with dsRBD1 and dsRBD2 exhibited much smaller dissociation constants (0.24 and 0.25 nM, respectively), indicating that the tandem dsRBDs bind simultaneously to one siRNA molecule. On the other hand, the loop between the first α helix and the first β strand of dsRBD2, but not dsRBD1, has a Trp residue, which forms hydrophobic and cation-π interactions with the surrounding residues. A circular dichroism analysis revealed that the thermal stability of dsRBD2 is higher than that of dsRBD1 and depends on the Trp residue.\",\n \"corpus_id\": 23896039,\n \"score\": 1\n },\n {\n \"doc_id\": \"21182352\",\n \"title\": \"Adenosine deaminases acting on RNA, RNA editing, and interferon action.\",\n \"abstract\": \"Adenosine deaminases acting on RNA (ADARs) catalyze adenosine (A) to inosine (I) editing of RNA that possesses double-stranded (ds) structure. A-to-I RNA editing results in nucleotide substitution, because I is recognized as G instead of A both by ribosomes and by RNA polymerases. A-to-I substitution can also cause dsRNA destabilization, as I:U mismatch base pairs are less stable than A:U base pairs. Three mammalian ADAR genes are known, of which two encode active deaminases (ADAR1 and ADAR2). Alternative promoters together with alternative splicing give rise to two protein size forms of ADAR1: an interferon-inducible ADAR1-p150 deaminase that binds dsRNA and Z-DNA, and a constitutively expressed ADAR1-p110 deaminase. ADAR2, like ADAR1-p110, is constitutively expressed and binds dsRNA. A-to-I editing occurs with both viral and cellular RNAs, and affects a broad range of biological processes. These include virus growth and persistence, apoptosis and embryogenesis, neurotransmitter receptor and ion channel function, pancreatic cell function, and post-transcriptional gene regulation by microRNAs. Biochemical processes that provide a framework for understanding the physiologic changes following ADAR-catalyzed A-to-I ( = G) editing events include mRNA translation by changing codons and hence the amino acid sequence of proteins; pre-mRNA splicing by altering splice site recognition sequences; RNA stability by changing sequences involved in nuclease recognition; genetic stability in the case of RNA virus genomes by changing sequences during viral RNA replication; and RNA-structure-dependent activities such as microRNA production or targeting or protein-RNA interactions.\",\n \"corpus_id\": 34002988,\n \"score\": 1\n },\n {\n \"doc_id\": \"21587236\",\n \"title\": \"Predicting sites of ADAR editing in double-stranded RNA.\",\n \"abstract\": \"ADAR (adenosine deaminase that acts on RNA) editing enzymes target coding and noncoding double-stranded RNA (dsRNA) and are essential for neuronal function. Early studies showed that ADARs preferentially target adenosines with certain 5' and 3' neighbours. Here we use current Sanger sequencing protocols to perform a more accurate and quantitative analysis. We quantified editing sites in an ∼800-bp dsRNA after reaction with human ADAR1 or ADAR2, or their catalytic domains alone. These large data sets revealed that neighbour preferences are mostly dictated by the catalytic domain, but ADAR2's dsRNA-binding motifs contribute to 3' neighbour preferences. For all proteins, the 5' nearest neighbour was most influential, but adjacent bases also affected editing site choice. We developed algorithms to predict editing sites in dsRNA of any sequence, and provide a web-based application. The predictive power of the algorithm on fully base-paired dsRNA, compared with biological substrates containing mismatches, bulges and loops, elucidates structural contributions to editing specificity.\",\n \"corpus_id\": 466712,\n \"score\": 1\n },\n {\n \"doc_id\": \"23012356\",\n \"title\": \"Identification of a karyopherin β1/β2 proline-tyrosine nuclear localization signal in huntingtin protein.\",\n \"abstract\": \"Among the known pathways of protein nuclear import, the karyopherin β2/transportin pathway is only the second to have a defined nuclear localization signal (NLS) consensus. Huntingtin, a 350-kDa protein, has defined roles in the nucleus, as well as a CRM1/exportin-dependent nuclear export signal; however, the NLS and exact pathway of import have remained elusive. Here, using a live cell assay and affinity chromatography, we show that huntingtin has a karyopherin β2-dependent proline-tyrosine (PY)-NLS in the amino terminus of the protein. This NLS comprises three consensus components: a basic charged sequence, a downstream conserved arginine, and a PY sequence. Unlike the classic PY-NLS, which has an unstructured intervening sequence between the consensus components, we show that a β sheet structured region separating the consensus elements is critical for huntingtin NLS function. The huntingtin PY-NLS is also capable of import through the importin/karyopherin β1 pathway but was not functional in all cell types tested. We propose that this huntingtin PY-NLS may comprise a new class of multiple import factor-dependent NLSs with an internal structural component that may regulate NLS activity.\",\n \"corpus_id\": 19925966,\n \"score\": 1\n },\n {\n \"doc_id\": \"23194006\",\n \"title\": \"Second double-stranded RNA binding domain of dicer-like ribonuclease 1: structural and biochemical characterization.\",\n \"abstract\": \"Dicer-like ribonuclease III enzymes are involved in different paths related to RNA silencing in plants. Little is known about the structural aspects of these processes. Here we present a structural characterization of the second double-stranded RNA binding domain (dsRBD) of DCL1, which is presumed to participate in pri-micro-RNA recognition and subcellular localization of this protein. We determined the solution structure and found that it has a canonical fold but bears some variation with respect to other homologous domains. We also found that this domain binds both double-stranded RNA and double-stranded DNA, in contrast to most dsRBDs. Our characterization shows that this domain likely has functions other than substrate recognition and binding.\",\n \"corpus_id\": 12632746,\n \"score\": 1\n },\n {\n \"doc_id\": \"23279110\",\n \"title\": \"A proline-tyrosine nuclear localization signal (PY-NLS) is required for the nuclear import of fission yeast PAB2, but not of human PABPN1.\",\n \"abstract\": \"Nuclear poly(A)-binding proteins (PABPs) are evolutionarily conserved proteins that play key roles in eukaryotic gene expression. In the fission yeast Schizosaccharomyces pombe, the major nuclear PABP, Pab2, functions in the maturation of small nucleolar RNAs as well as in nuclear RNA decay. Despite knowledge about its nuclear functions, nothing is known about how Pab2 is imported into the nucleus. Here, we show that Pab2 contains a proline-tyrosine nuclear localization signal (PY-NLS) that is necessary and sufficient for its nuclear localization and function. Consistent with the role of karyopherin β2 (Kapβ2)-type receptors in the import of PY-NLS cargoes, we show that the fission yeast ortholog of human Kapβ2, Kap104, binds to recombinant Pab2 and is required for Pab2 nuclear localization. The absence of arginine methylation in a basic region N-terminal to the PY-core motif of Pab2 did not affect its nuclear localization. However, in the context of a sub-optimal PY-NLS, we found that Pab2 was more efficiently targeted to the nucleus in the absence of arginine methylation, suggesting that this modification can affect the import kinetics of a PY-NLS cargo. Although a sequence resembling a PY-NLS motif can be found in the human Pab2 ortholog, PABPN1, our results indicate that neither a functional PY-NLS nor Kapβ2 activity are required to promote entry of PABPN1 into the nucleus of human cells. Our findings describe the mechanism by which Pab2 is imported into the nucleus, providing the first example of a PY-NLS import system in fission yeast. In addition, this study suggests the existence of alternative or redundant nuclear import pathways for human PABPN1.\",\n \"corpus_id\": 19781449,\n \"score\": 1\n },\n {\n \"doc_id\": \"23886622\",\n \"title\": \"Complementation of HYPONASTIC LEAVES1 by double-strand RNA-binding domains of DICER-LIKE1 in nuclear dicing bodies.\",\n \"abstract\": \"MicroRNAs (miRNAs) are a class of small regulatory RNAs that are found in almost all of the eukaryotes. Arabidopsis (Arabidopsis thaliana) miRNAs are processed from primary miRNAs (pri-miRNAs), mainly by the ribonuclease III-like enzyme DICER-LIKE1 (DCL1) and its specific partner, HYPONASTIC LEAVES1 (HYL1), a double-strand RNA-binding protein, both of which contain two double-strand RNA-binding domains (dsRBDs). These dsRBDs are essential for miRNA processing, but the functions of them are not clear. Here, we report that the two dsRBDs of DCL1 (DCL1-D1D2), and to some extent the second dsRBD (DCL1-D2), complement the hyl1 mutant, but not the first dsRBD of DCL1 (DCL1-D1). DCL1-D1 is diffusely distributed throughout the nucleoplasm, whereas DCL1-D2 and DCL1-D1D2 concentrate in nuclear dicing bodies in which DCL1 and HYL1 colocalize. We show further that protein-protein interaction is mainly mediated by DCL1-D2, while DCL1-D1 plays a major role in binding of pri-miRNAs. These results suggest parallel roles between C-terminal dsRBDs of DCL1 and N-terminal dsRBDs of HYL1 and support a model in which Arabidopsis pri-miRNAs are recruited to dicing bodies through functionally divergent dsRBDs of microprocessor for accurate processing of plant pri-miRNAs.\",\n \"corpus_id\": 45315406,\n \"score\": 1\n },\n {\n \"doc_id\": \"25564529\",\n \"title\": \"Recognition of duplex RNA by the deaminase domain of the RNA editing enzyme ADAR2.\",\n \"abstract\": \"Adenosine deaminases acting on RNA (ADARs) hydrolytically deaminate adenosines (A) in a wide variety of duplex RNAs and misregulation of editing is correlated with human disease. However, our understanding of reaction selectivity is limited. ADARs are modular enzymes with multiple double-stranded RNA binding domains (dsRBDs) and a catalytic domain. While dsRBD binding is understood, little is known about ADAR catalytic domain/RNA interactions. Here we use a recently discovered RNA substrate that is rapidly deaminated by the isolated human ADAR2 deaminase domain (hADAR2-D) to probe these interactions. We introduced the nucleoside analog 8-azanebularine (8-azaN) into this RNA (and derived constructs) to mechanistically trap the protein-RNA complex without catalytic turnover for EMSA and ribonuclease footprinting analyses. EMSA showed that hADAR2-D requires duplex RNA and is sensitive to 2'-deoxy substitution at nucleotides opposite the editing site, the local sequence and 8-azaN nucleotide positioning on the duplex. Ribonuclease V1 footprinting shows that hADAR2-D protects ∼ 23 nt on the edited strand around the editing site in an asymmetric fashion (∼ 18 nt on the 5' side and ∼ 5 nt on the 3' side). These studies provide a deeper understanding of the ADAR catalytic domain-RNA interaction and new tools for biophysical analysis of ADAR-RNA complexes.\",\n \"corpus_id\": 4713151,\n \"score\": 1\n },\n {\n \"doc_id\": \"26184879\",\n \"title\": \"Dynamic profiling of double-stranded RNA binding proteins.\",\n \"abstract\": \"Double-stranded (ds) RNA is a key player in numerous biological activities in cells, including RNA interference, anti-viral immunity and mRNA transport. The class of proteins responsible for recognizing dsRNA is termed double-stranded RNA binding proteins (dsRBP). However, little is known about the molecular mechanisms underlying the interaction between dsRBPs and dsRNA. Here we examined four human dsRBPs, ADAD2, TRBP, Staufen 1 and ADAR1 on six dsRNA substrates that vary in length and secondary structure. We combined single molecule pull-down (SiMPull), single molecule protein-induced fluorescence enhancement (smPIFE) and molecular dynamics (MD) simulations to investigate the dsRNA-dsRBP interactions. Our results demonstrate that despite the highly conserved dsRNA binding domains, the dsRBPs exhibit diverse substrate specificities and dynamic properties when in contact with different RNA substrates. While TRBP and ADAR1 have a preference for binding simple duplex RNA, ADAD2 and Staufen1 display higher affinity to highly structured RNA substrates. Upon interaction with RNA substrates, TRBP and Staufen1 exhibit dynamic sliding whereas two deaminases ADAR1 and ADAD2 mostly remain immobile when bound. MD simulations provide a detailed atomic interaction map that is largely consistent with the affinity differences observed experimentally. Collectively, our study highlights the diverse nature of substrate specificity and mobility exhibited by dsRBPs that may be critical for their cellular function.\",\n \"corpus_id\": 2876634,\n \"score\": 1\n },\n {\n \"doc_id\": \"26252972\",\n \"title\": \"Effect of mismatch on binding of ADAR2/GluR-2 pre-mRNA complex.\",\n \"abstract\": \"RNA editing plays an important role in realizing the full potential of a given genome. Different from RNA splicing, RNA editing fine-tunes the sequence of RNA by changing only one or two nucleotides. A-I editing [deamination of adenosine (A) to create inosine (I)] is best characterized in mammals and occurs in the regions of double-stranded RNA (dsRNA). Adenosine deaminases acting on RNA (ADARs) are members of a family of enzymes involved in A-I deamination editing in numerous mRNA and pre-mRNA transcripts. Experimental study shows that ADAR2 selectively edits the R/G site, while ADAR1 edits more promiscuously at several other adenosines. How ADAR2 selects specific sites for deamination is poorly understood. Mismatches have been suggested to be important factors that allow the ADAR2 to achieve specific deamination. Using molecular dynamic simulation, we studied the effect of mismatch on binding stability of the dsRNA/ADAR2 complex. By comparison of two binding domains of ADAR2, we found that ADAR2 dsRBM2 (second binding domain of ADAR2) does not bind well with mismatch reversed GluR-2 RNA. When mismatch is reversed, dsRBM2 of ADAR2 slides along the RNA duplex in the simulation. Detailed structural analysis indicates that the minor groove width of dsRNA and global shape of RNA may play an important role in the specific reading mechanism of ADAR2.\",\n \"corpus_id\": 3395726,\n \"score\": 1\n },\n {\n \"doc_id\": \"26275108\",\n \"title\": \"RNA editing by ADAR1 prevents MDA5 sensing of endogenous dsRNA as nonself.\",\n \"abstract\": \"Adenosine-to-inosine (A-to-I) editing is a highly prevalent posttranscriptional modification of RNA, mediated by ADAR (adenosine deaminase acting on RNA) enzymes. In addition to RNA editing, additional functions have been proposed for ADAR1. To determine the specific role of RNA editing by ADAR1, we generated mice with an editing-deficient knock-in mutation (Adar1(E861A), where E861A denotes Glu(861)→Ala(861)). Adar1(E861A/E861A) embryos died at ~E13.5 (embryonic day 13.5), with activated interferon and double-stranded RNA (dsRNA)-sensing pathways. Genome-wide analysis of the in vivo substrates of ADAR1 identified clustered hyperediting within long dsRNA stem loops within 3' untranslated regions of endogenous transcripts. Finally, embryonic death and phenotypes of Adar1(E861A/E861A) were rescued by concurrent deletion of the cytosolic sensor of dsRNA, MDA5. A-to-I editing of endogenous dsRNA is the essential function of ADAR1, preventing the activation of the cytosolic dsRNA response by endogenous transcripts.\",\n \"corpus_id\": 206640044,\n \"score\": 1\n },\n {\n \"doc_id\": \"26987516\",\n \"title\": \"dsRNA-protein interactions studied by molecular dynamics techniques. Unravelling dsRNA recognition by DCL1.\",\n \"abstract\": \"Double stranded RNA (dsRNA) participates in several biological processes, where RNA molecules acquire secondary structure inside the cell through base complementarity. The double stranded RNA binding domain (dsRBD) is one of the main protein folds that is able to recognize and bind to dsRNA regions. The N-terminal dsRBD of DCL1 in Arabidopsis thaliana (DCL1-1), in contrast to other studied dsRBDs, lacks a stable structure, behaving as an intrinsically disordered protein. DCL1-1 does however recognize dsRNA by acquiring a canonical fold in the presence of its substrate. Here we present a detailed modeling and molecular dynamics study of dsRNA recognition by DCL1-1. We found that DCL1-1 forms stable complexes with different RNAs and we characterized the residues involved in binding. Although the domain shows a binding loop substantially shorter than other homologs, it can still interact with the dsRNA and results in bending of the dsRNA A-type helix. Furthermore, we found that R8, a non-conserved residue located in the first dsRNA binding region, recognizes preferentially mismatched base pairs. We discuss our findings in the context of the function of DCL1-1 within the microRNA processing complex.\",\n \"corpus_id\": 46756551,\n \"score\": 1\n },\n {\n \"doc_id\": \"18485366\",\n \"title\": \"Classical NLS proteins from Saccharomyces cerevisiae.\",\n \"abstract\": \"Proteins can enter the nucleus through various receptor-mediated import pathways. One class of import cargos carries a classical nuclear localization signal (cNLS) containing a short cluster of basic residues. This pathway involves importin alpha (Impalpha), which possesses the cNLS binding site, and importin beta (Impbeta), which translocates the import complex through the nuclear pore complex. The defining criteria for a cNLS protein from Saccharomyces cerevisiae are an in vivo import defect in Impalpha and Impbeta mutants, direct binding to purified Impalpha, and stimulation of this binding by Impbeta. We show for the first time that endogenous S. cerevisiae proteins Prp20, Cdc6, Swi5, Cdc45, and Clb2 fulfill all of these criteria identifying them as authentic yeast cNLS cargos. Furthermore, we found that the targeting signal of Prp20 is a bipartite cNLS and that of Cdc6 is a monopartite cNLS. Basic residues present within these motifs are of different significance for the interaction with Impalpha. We determined the binding constants for import complexes containing the five cNLS proteins by surface plasmon resonance spectrometry. The dissociation constants for cNLS/alpha/beta complexes differ considerably, ranging from 1 nM for Cdc6 to 112 nM for Swi5, suggesting that the nuclear import kinetics is determined by the strength of cNLS/Impalpha binding. Impbeta enhances the affinity of Impalpha for cNLSs approximately 100-fold. This stimulation of cNLS binding to Impalpha results from a faster association in the presence of Impbeta, whereas the dissociation rate is unaffected by Impbeta. This implies that, after entry into the nucleus, the release of Impbeta by the Ran guanosine triphosphatase (Ran GTPase) from the import complex is not sufficient to dissociate the cNLS/Impalpha subcomplex. Our observation that the nucleoporin Nup2, which had been previously shown to release the cNLS from Impalpha in vitro, is required for efficient import of all the genuine cNLS cargos supports a general role of Nup2 in import termination.\",\n \"corpus_id\": 37755065,\n \"score\": 0\n },\n {\n \"doc_id\": \"19208642\",\n \"title\": \"The regulatory domain of the RIG-I family ATPase LGP2 senses double-stranded RNA.\",\n \"abstract\": \"RIG-I and MDA5 sense cytoplasmic viral RNA and set-off a signal transduction cascade, leading to antiviral innate immune response. The third RIG-I-like receptor, LGP2, differentially regulates RIG-I- and MDA5-dependent RNA sensing in an unknown manner. All three receptors possess a C-terminal regulatory domain (RD), which in the case of RIG-I senses the viral pattern 5'-triphosphate RNA and activates ATP-dependent signaling by RIG-I. Here we report the 2.6 A crystal structure of LGP2 RD along with in vitro and in vivo functional analyses and a homology model of MDA5 RD. Although LGP2 RD is structurally related to RIG-I RD, we find it rather binds double-stranded RNA (dsRNA) and this binding is independent of 5'-triphosphates. We identify conserved and receptor-specific parts of the RNA binding site. Latter are required for specific dsRNA binding by LGP2 RD and could confer pattern selectivity between RIG-I-like receptors. Our data furthermore suggest that LGP2 RD modulates RIG-I-dependent signaling via competition for dsRNA, another pattern sensed by RIG-I, while a fully functional LGP2 is required to augment MDA5-dependent signaling.\",\n \"corpus_id\": 10376776,\n \"score\": 0\n },\n {\n \"doc_id\": \"20064523\",\n \"title\": \"Functional interaction of the Ras effector RASSF5 with the tyrosine kinase Lck: critical role in nucleocytoplasmic transport and cell cycle regulation.\",\n \"abstract\": \"RASSF5 is a member of the Ras association domain family, which is known to be involved in cell growth regulation. Expression of RASSF5 is extinguished selectively by epigenetic mechanism(s) in different cancers and cell lines, and reexpression usually suppresses cell proliferation and tumorigenicity. To date, the mechanism regulating RASSF5 nuclear transport and its role in cell growth regulation remains unclear. Using heterokaryon assay, we have demonstrated that RASSF5 shuttles between the nucleus and the cytoplasm, and its export from the nucleus is sensitive to leptomycin B, suggesting that RASSF5 is exported from the nucleus by a CRM-1-dependent export pathway. We further demonstrate that RASSF5 contains a hydrophobic-rich nuclear export signal (NES) towards the C-terminus and two nuclear localization signals-one each at the N-terminus and the C-terminus. Combination of mutational and immunofluorescence analyses suggests that the functional NES residing between amino acids 260 and 300 in the C-terminus is necessary for the efficient export of RASSF5 from the nucleus. In addition, substitution of conserved hydrophobic residues within the minimal NES impaired RASSF5 export from the nucleus. Furthermore, exchange of proline residues within the putative Src homology 3 binding motifs altered the export of RASSF5 from the nucleus despite the presence of functional NES, suggesting that multiple domains independently modulate the nucleocytoplasmic transport of RASSF5. Interestingly, the present investigation provided evidence that RASSF5 interacts with the tyrosine kinase Lck through its C-terminal Src homology 2 binding motif and showed that Lck-mediated phosphorylation is critical for the efficient translocation of RASSF5 into the nuclear compartment. Interestingly, our data demonstrate that wild type and nuclear export defective (DeltaNES) mutant of RASSF5 but not the import defective mutant of accumulate the cells at G1/S phase and induce apoptosis. Furthermore, the Lck-interaction-defective mutant of RASSF5 induces apoptosis without altering cell cycle progression, suggesting that RASSF5 induces apoptosis independent of cell cycle arrest. Together, our data demonstrate that interaction with Lck is critical for RASSF5 phosphorylation, which in turn regulates the cell growth control activity of RASSF5. Finally, we have shown that RASSF5 encodes four splice variants and is translocated to the nucleus by the classical nuclear import pathway. One of the splice variants, RASSF5C, was found to be localized in the cytoplasm and translocated into the nucleus upon leptomycin B treatment despite the absence of N-terminal nuclear localization signal, suggesting that distribution of RASSF5 variants in different cellular compartments may be critical for Ras-dependent cell growth regulation. Collectively, the present investigation provided evidence that Lck-mediated phosphorylation regulates the nucleocytoplasmic shuttling and cell growth control activities of RASSF5.\",\n \"corpus_id\": 20594790,\n \"score\": 0\n },\n {\n \"doc_id\": \"20226070\",\n \"title\": \"Solution structure of the Drosha double-stranded RNA-binding domain.\",\n \"abstract\": \"BACKGROUND: Drosha is a nuclear RNase III enzyme that initiates processing of regulatory microRNA. Together with partner protein DiGeorge syndrome critical region 8 (DGCR8), it forms the Microprocessor complex, which cleaves precursor transcripts called primary microRNA to produce hairpin precursor microRNA. In addition to two RNase III catalytic domains, Drosha contains a C-terminal double-stranded RNA-binding domain (dsRBD). To gain insight into the function of this domain, we determined the nuclear magnetic resonance (NMR) solution structure. RESULTS: We report here the solution structure of the dsRBD from Drosha (Drosha-dsRBD). The alphabetabetabetaalpha fold is similar to other dsRBD structures. A unique extended loop distinguishes this domain from other dsRBDs of known structure. CONCLUSIONS: Despite uncertainties about RNA-binding properties of the Drosha-dsRBD, its structure suggests it retains RNA-binding features. We propose that this domain may contribute to substrate recognition in the Drosha-DGCR8 Microprocessor complex.\",\n \"corpus_id\": 63614,\n \"score\": 0\n },\n {\n \"doc_id\": \"20512930\",\n \"title\": \"Characterization of an Importin alpha/beta-recognized nuclear localization signal in beta-dystroglycan.\",\n \"abstract\": \"Beta-dystroglycan (beta-DG) is a widely expressed transmembrane protein that plays important roles in connecting the extracellular matrix to the cytoskeleton, and thereby contributing to plasma membrane integrity and signal transduction. We previously observed nuclear localization of beta-DG in cultured cell lines, implying the existence of a nuclear targeting mechanism that directs it to the nucleus instead of the plasma membrane. In this study, we delineate the nuclear import pathway of beta-DG, characterizing a functional nuclear localization signal (NLS) in the beta-DG cytoplasmic domain, within amino acids 776-782. The NLS either alone or in the context of the whole beta-DG protein was able to target the heterologous GFP protein to the nucleus, with site-directed mutagenesis indicating that amino acids R(779) and K(780) are critical for NLS functionality. The nuclear transport molecules Importin (Imp)alpha and Impbeta bound with high affinity to the NLS of beta-DG and were found to be essential for NLS-dependent nuclear import in an in vitro reconstituted nuclear transport assay; cotransfection experiments confirmed the dependence on Ran for nuclear accumulation. Intriguingly, experiments suggested that tyrosine phosphorylation of beta-DG may result in cytoplasmic retention, with Y(892) playing a key role. beta-DG thus follows a conventional Impalpha/beta-dependent nuclear import pathway, with important implications for its potential function in the nucleus.\",\n \"corpus_id\": 13269928,\n \"score\": 0\n },\n {\n \"doc_id\": \"20818336\",\n \"title\": \"An actin-regulated importin α/β-dependent extended bipartite NLS directs nuclear import of MRTF-A.\",\n \"abstract\": \"Myocardin-related transcription factors (MRTFs) are actin-regulated transcriptional coactivators, which bind G-actin through their N-terminal RPEL domains. In response to signal-induced actin polymerisation and concomitant G-actin depletion, MRTFs accumulate in the nucleus and activate target gene transcription through their partner protein SRF. Nuclear accumulation of MRTFs in response to signal is inhibited by increased G-actin level. Here, we study the mechanism by which MRTF-A enters the nucleus. We show that MRTF-A contains an unusually long bipartite nuclear localisation signal (NLS), comprising two basic elements separated by 30 residues, embedded within the RPEL domain. Using siRNA-mediated protein depletion in vivo, and nuclear import assays in vitro, we show that the MRTF-A extended bipartite NLS uses the importin (Imp)α/β-dependent import pathway, and that import is inhibited by G-actin. Interaction of the NLS with the Impα-Impβ heterodimer requires both NLS basic elements, and is dependent on the Impα major and minor binding pockets. Binding of the Impα-Impβ heterodimer to the intact MRTF-A RPEL domain occurs competitively with G-actin. Thus, MRTF-A contains an actin-sensitive nuclear import signal.\",\n \"corpus_id\": 9839642,\n \"score\": 0\n },\n {\n \"doc_id\": \"20977914\",\n \"title\": \"Molecular basis for specificity of nuclear import and prediction of nuclear localization.\",\n \"abstract\": \"Although proteins are translated on cytoplasmic ribosomes, many of these proteins play essential roles in the nucleus, mediating key cellular processes including but not limited to DNA replication and repair as well as transcription and RNA processing. Thus, understanding how these critical nuclear proteins are accurately targeted to the nucleus is of paramount importance in biology. Interaction and structural studies in the recent years have jointly revealed some general rules on the specificity determinants of the recognition of nuclear targeting signals by their specific receptors, at least for two nuclear import pathways: (i) the classical pathway, which involves the classical nuclear localization sequences (cNLSs) and the receptors importin-α/karyopherin-α and importin-β/karyopherin-β1; and (ii) the karyopherin-β2 pathway, which employs the proline-tyrosine (PY)-NLSs and the receptor transportin-1/karyopherin-β2. The understanding of specificity rules allows the prediction of protein nuclear localization. We review the current understanding of the molecular determinants of the specificity of nuclear import, focusing on the importin-α•cargo recognition, as well as the currently available databases and predictive tools relevant to nuclear localization. This article is part of a Special Issue entitled: Regulation of Signaling and Cellular Fate through Modulation of Nuclear Protein Import.\",\n \"corpus_id\": 5130899,\n \"score\": 0\n },\n {\n \"doc_id\": \"21029753\",\n \"title\": \"The importin β binding domain as a master regulator of nucleocytoplasmic transport.\",\n \"abstract\": \"Specific and efficient recognition of import cargoes is essential to ensure nucleocytoplasmic transport. To this end, the prototypical karyopherin importin β associates with import cargoes directly or, more commonly, through import adaptors, such as importin α and snurportin. Adaptor proteins bind the nuclear localization sequence (NLS) of import cargoes while recruiting importin β via an N-terminal importin β binding (IBB) domain. The use of adaptors greatly expands and amplifies the repertoire of cellular cargoes that importin β can efficiently import into the cell nucleus and allows for fine regulation of nuclear import. Accordingly, the IBB domain is a dedicated NLS, unique to adaptor proteins that functions as a molecular liaison between importin β and import cargoes. This review provides an overview of the molecular role played by the IBB domain in orchestrating nucleocytoplasmic transport. Recent work has determined that the IBB domain has specialized functions at every step of the import and export pathway. Unexpectedly, this stretch of ~40 amino acids plays an essential role in regulating processes such as formation of the import complex, docking and translocation through the nuclear pore complex (NPC), release of import cargoes into the cell nucleus and finally recycling of import adaptors and importin β into the cytoplasm. Thus, the IBB domain is a master regulator of nucleocytoplasmic transport, whose complex molecular function is only recently beginning to emerge. This article is part of a Special Issue entitled: Regulation of Signaling and Cellular Fate through Modulation of Nuclear Protein Import.\",\n \"corpus_id\": 205831150,\n \"score\": 0\n },\n {\n \"doc_id\": \"21401918\",\n \"title\": \"Intermolecular masking of the HIV-1 Rev NLS by the cellular protein HIC: novel insights into the regulation of Rev nuclear import.\",\n \"abstract\": \"BACKGROUND: The HIV-1 regulatory protein Rev, which is essential for viral replication, mediates the nuclear export of unspliced viral transcripts. Rev nuclear function requires active nucleocytoplasmic shuttling, and Rev nuclear import is mediated by the recognition of its Nuclear Localisation Signal (NLS) by multiple import factors, which include transportin and importin β. However, it remains unclear which nuclear import pathway(s) predominate in vivo, and the cellular environment that modulates Rev nucleocytoplasmic shuttling remains to be characterised. RESULTS: In our study, we have identified the cellular protein HIC (Human I-mfa domain-Containing protein) as a novel interactor of HIV-1 Rev. We demonstrate that HIC selectively interferes with Rev NLS interaction with importin β and impedes its nuclear import and function, but does not affect Rev nuclear import mediated by transportin. Hence, the molecular determinants mediating Rev-NLS recognition by importin β and transportin appear to be distinct. Furthermore, we have employed HIC and M9 M, a peptide specifically designed to inhibit the transportin-mediated nuclear import pathway, to characterise Rev nuclear import pathways within different cellular environments. Remarkably, we could show that in 293T, HeLa, COS7, Jurkat, U937, THP-1 and CEM cells, Rev nuclear import is cell type specific and alternatively mediated by transportin or importin β, in a mutually exclusive fashion. CONCLUSIONS: Rev cytoplasmic sequestration by HIC may represent a novel mechanism for the control of Rev function. These studies highlight that the multivalent nature of the Rev NLS for different import receptors enables Rev to adapt its nuclear trafficking strategy.\",\n \"corpus_id\": 6402228,\n \"score\": 0\n },\n {\n \"doc_id\": \"21559489\",\n \"title\": \"Conservation of complex nuclear localization signals utilizing classical and non-classical nuclear import pathways in LANA homologs of KSHV and RFHV.\",\n \"abstract\": \"ORF73 latency-associated nuclear antigen (LANA) of the Kaposi's sarcoma-associated herpesvirus (KSHV) is targeted to the nucleus of infected cells where it binds to chromatin and mediates viral episome persistence, interacts with cellular proteins and plays a role in latency and tumorigenesis. A structurally related LANA homolog has been identified in the retroperitoneal fibromatosis herpesvirus (RFHV), the macaque homolog of KSHV. Here, we report the evolutionary and functional conservation of a novel bi-functional nuclear localization signal (NLS) in KSHV and RFHV LANA. N-terminal peptides from both proteins were fused to EGFP or double EGFP fusions to examine their ability to induce nuclear transport of a heterologous protein. In addition, GST-pull down experiments were used to analyze the ability of LANA peptides to interact with members of the karyopherin family of nuclear transport receptors. Our studies revealed that both LANA proteins contain an N-terminal arginine/glycine (RG)-rich domain spanning a conserved chromatin-binding motif, which binds directly to importin β1 in a RanGTP-sensitive manner and serves as an NLS in the importin β1-mediated non-classical nuclear import pathway. Embedded within this domain is a conserved lysine/arginine-(KR)-rich bipartite motif that binds directly to multiple members of the importin α family of nuclear import adaptors in a RanGTP-insensitive manner and serves as an NLS in the classical importin α/β-mediated nuclear import pathway. The positioning of a classical bipartite kr-NLS embedded within a non-classical rg-NLS is a unique arrangement in these viral proteins, whose nuclear localization is critical to their functionality and to the virus life cycle. The ability to interact with multiple import receptors provides alternate pathways for nuclear localization of LANA. Since different import receptors can import cargo to distinct subnuclear compartments, a multifunctional NLS may provide LANA with an increased ability to interact with different nuclear components in its multifunctional role to maintain viral latency.\",\n \"corpus_id\": 2678202,\n \"score\": 0\n },\n {\n \"doc_id\": \"21965294\",\n \"title\": \"Evolutionary development of redundant nuclear localization signals in the mRNA export factor NXF1.\",\n \"abstract\": \"In human cells, the mRNA export factor NXF1 resides in the nucleoplasm and at nuclear pore complexes. Karyopherin β2 or transportin recognizes a proline-tyrosine nuclear localization signal (PY-NLS) in the N-terminal tail of NXF1 and imports it into the nucleus. Here biochemical and cellular studies to understand the energetic organization of the NXF1 PY-NLS reveal unexpected redundancy in the nuclear import pathways used by NXF1. Human NXF1 can be imported via importin β, karyopherin β2, importin 4, importin 11, and importin α. Two NLS epitopes within the N-terminal tail, an N-terminal basic segment and a C-terminal R-X(2-5)-P-Y motif, provide the majority of binding energy for all five karyopherins. Mutation of both NLS epitopes abolishes binding to the karyopherins, mislocalized NXF1 to the cytoplasm, and significantly compromised its mRNA export function. The understanding of how different karyopherins recognize human NXF1, the examination of NXF1 sequences from divergent eukaryotes, and the interactions of NXF1 homologues with various karyopherins reveals the evolutionary development of redundant NLSs in NXF1 of higher eukaryotes. Redundancy of nuclear import pathways for NXF1 increases progressively from fungi to nematodes and insects to chordates, potentially paralleling the increasing complexity in mRNA export regulation and the evolution of new nuclear functions for NXF1.\",\n \"corpus_id\": 6333447,\n \"score\": 0\n },\n {\n \"doc_id\": \"22028839\",\n \"title\": \"Pigment epithelium-derived factor (PEDF) interacts with transportin SR2, and active nuclear import is facilitated by a novel nuclear localization motif.\",\n \"abstract\": \"PEDF (Pigment epithelium-derived factor) is a non-inhibitory member of the serpin gene family (serpinF1) that displays neurotrophic and anti-angiogenic properties. PEDF contains a secretion signal sequence, but although originally regarded as a secreted extracellular protein, endogenous PEDF is found in the cytoplasm and nucleus of several mammalian cell types. In this study we employed a yeast two-hybrid interaction trap screen to identify transportin-SR2, a member of the importin-β family of nuclear transport karyopherins, as a putative PEDF binding partner. The interaction was supported in vitro by GST-pulldown and co-immunoprecipitation. Following transfection of HEK293 cells with GFP-tagged PEDF the protein was predominantly localised to the nucleus, suggesting that active import of PEDF occurs. A motif (YxxYRVRS) shared by PEDF and the unrelated transportin-SR2 substrate, RNA binding motif protein 4b, was identified and we investigated its potential as a nuclear localization signal (NLS) sequence. Site-directed mutagenesis of this helix A motif in PEDF resulted in a GFP-tagged mutant protein being excluded from the nucleus, and mutation of two arginine residues (R67, R69) was sufficient to abolish nuclear import and PEDF interaction with transportin-SR2. These results suggest a novel NLS and mechanism for serpinF1 nuclear import, which may be critical for anti-angiogenic and neurotrophic function.\",\n \"corpus_id\": 14637106,\n \"score\": 0\n },\n {\n \"doc_id\": \"22454253\",\n \"title\": \"Solution structures of the double-stranded RNA-binding domains from RNA helicase A.\",\n \"abstract\": \"RNA helicase A (RHA) is a highly conserved protein with multifaceted functions in the gene expression of cellular and viral mRNAs. RHA recognizes highly structured nucleotides and catalytically rearranges the various interactions between RNA, DNA, and protein molecules to provide a platform for the ribonucleoprotein complex. We present the first solution structures of the double-stranded RNA-binding domains (dsRBDs), dsRBD1 and dsRBD2, from mouse RHA. We discuss the binding mode of the dsRBDs of RHA, in comparison with the known dsRBD structures in their complexes. Our structural data provide important information for the elucidation of the molecular reassembly mediated by RHA.\",\n \"corpus_id\": 39641797,\n \"score\": 0\n },\n {\n \"doc_id\": \"22457361\",\n \"title\": \"Extra double-stranded RNA binding domain (dsRBD) in a squid RNA editing enzyme confers resistance to high salt environment.\",\n \"abstract\": \"A-to-I RNA editing is particularly common in coding regions of squid mRNAs. Previously, we isolated a squid editing enzyme (sqADAR2) that shows a unique structural feature when compared with other ADAR2 family members: an additional double-stranded RNA (dsRNA) binding domain (dsRBD). Alternative splicing includes or excludes this motif, generating a novel or a conventional variant termed sqADAR2a and sqADAR2b, respectively. The extra dsRBD of sqADAR2a increases its editing activity in vitro. We hypothesized that the high activity is due to an increase in the affinity of the enzyme for dsRNA. This may be important because protein-RNA interactions can be influenced by physical factors. We became particularly interested in analyzing the effects of salt on interactions between sqADAR2 and RNA because squid cells have a ∼3-fold higher ionic strength and proportionally more Cl(-) than vertebrate cells. To date, in vitro biochemical analyses of adenosine deamination have been conducted using vertebrate-like ionic strength buffers containing chloride as the major anion, although the vast majority of cellular anions are known to be organic. We found that squid-like salt conditions severely impair the binding affinity of conventional ADAR2s for dsRNA, leading to a decrease in nonspecific and site-specific editing activity. Inhibition of editing was mostly due to high Cl(-) levels and not to the high concentrations of K(+), Na(+), and organic anions like glutamate. Interestingly, the extra dsRBD in sqADAR2a conferred resistance to the high Cl(-) levels found in squid neurons. It does so by increasing the affinity of sqADAR2 for dsRNA by 30- or 100-fold in vertebrate-like or squid-like conditions, respectively. Site-directed mutagenesis of squid ADAR2a showed that its increased affinity and editing activity are directly attributable to the RNA binding activity of the extra dsRBD.\",\n \"corpus_id\": 42250771,\n \"score\": 0\n },\n {\n \"doc_id\": \"22752847\",\n \"title\": \"Backbone ¹HN, ¹³C, and ¹⁵N resonance assignments of the tandem RNA-binding domains of human DGCR8.\",\n \"abstract\": \"Double-stranded RNA binding domain (dsRBD) containing proteins are critical components of the microRNA (miRNA) pathway, with key roles in small RNA biogenesis, modification, and regulation. DiGeorge Critical Region 8 (DGCR8) is a 773 amino acid, dsRBD-containing protein that was originally identified in humans as a protein encoded in the region of chromosome 22 that is deleted in patients with DiGeorge syndrome. Now, it is realized that DGCR8 complements the nuclear RNase III Drosha to initiate miRNA biogenesis by promoting efficient recognition and cleavage of primary miRNAs (pri-miRNA). A pair of C-terminal tandem dsRBDs separated by a flexible linker are required for pri-miRNA substrate binding and recognition. The crystal structure of the DGCR8 core region comprising residues 493-720 revealed that each dsRBD adopts the canonical αβββα fold. However, several residues located in important flexible regions including the β1-β2-loop implicated in canonical dsRNA recognition are absent in the crystal structure and no RNA-bound structure of DGCR8 has been reported. Here we report the (1)H(N), (13)C, and (15)N backbone resonance assignments of the 24 kDa, 214 amino acid human DGCR8(core) (residues 493-706) by heteronuclear NMR spectroscopy. Our assignments lay the foundation for a detailed solution state characterization of the dynamical and RNA-binding properties of this protein in solution.\",\n \"corpus_id\": 207390110,\n \"score\": 0\n },\n {\n \"doc_id\": \"23856623\",\n \"title\": \"Nuclear Respiratory Factor 2β (NRF-2β) recruits NRF-2α to the nucleus by binding to importin-α:β via an unusual monopartite-type nuclear localization signal.\",\n \"abstract\": \"Nuclear respiratory factor 2 (NRF-2) is a mammalian transcription factor composed of two distinct and unrelated proteins: NRF-2α, which binds to DNA through its Ets domain, and NRF-2β, which contains the transcription activation domain. The activity of NRF-2 in neurons is regulated by nuclear localization; however, the mechanism by which NRF-2 is imported into the nucleus remains unknown. By using in vitro nuclear import assays and immuno-cytofluorescence, we dissect the nuclear import pathways of NRF-2. We show that both NRF-2α and NRF-2β contain intrinsic nuclear localization signals (NLSs): the Ets domain within NRF-2α and the NLS within NRF-2β (amino acids 311/321: EEPPAKRQCIE) that is recognized by importin-α:β. When NRF-2α and NRF-2β form a complex, the nuclear import of NRF-2αβ becomes strictly dependent on the NLS within NRF-2β. Therefore, the nuclear import mechanism of NRF-2 is unique among Ets factors. The NRF-2β NLS contains only two lysine/arginine residues, unlike other known importin-α:β-dependent NLSs. Using ELISA-based binding assays, we show that it is bound by importin-α in almost the same manner and with similar affinity to that of the classical monopartite NLSs, such as c-myc and SV40 T-antigen NLSs. However, the part of the tryptophan array of importin-α that is essential for the recognition of classical monopartite NLSs by generating apolar pockets for the P3 and the P5 lysine/arginine side chains is not required for the recognition of the NRF-2β NLS. We conclude that the NRF-2β NLS is an unusual but is, nevertheless, a bona fide monopartite-type NLS.\",\n \"corpus_id\": 35274670,\n \"score\": 0\n },\n {\n \"doc_id\": \"24347303\",\n \"title\": \"The HBM domain: introducing bimodularity to bacterial sensing.\",\n \"abstract\": \"We have recently reported the three dimensional structure of the McpS chemoreceptor sensor domain in complex with its cognate ligands. The domain was characterized by a bimodular architecture, where ligand binding to each module caused a chemotactic response. This is a novel small molecule binding domain, which, however, is un-annotated in relevant databases. We report here the domain signature of the family of McpS-like sensor domains, which was termed helical bimodular (HBM) domain. The HBM domain was identified in Bacteria and Archaea and forms part of chemoreceptors and histidine kinases. The conservation of amino acids in the ligand binding sites of both modules suggests that HBM family members recognize similar ligands.\",\n \"corpus_id\": 206391627,\n \"score\": 0\n },\n {\n \"doc_id\": \"24478460\",\n \"title\": \"Transportin acts to regulate mitotic assembly events by target binding rather than Ran sequestration.\",\n \"abstract\": \"The nuclear import receptors importin β and transportin play a different role in mitosis: both act phenotypically as spatial regulators to ensure that mitotic spindle, nuclear membrane, and nuclear pore assembly occur exclusively around chromatin. Importin β is known to act by repressing assembly factors in regions distant from chromatin, whereas RanGTP produced on chromatin frees factors from importin β for localized assembly. The mechanism of transportin regulation was unknown. Diametrically opposed models for transportin action are as follows: 1) indirect action by RanGTP sequestration, thus down-regulating release of assembly factors from importin β, and 2) direct action by transportin binding and inhibiting assembly factors. Experiments in Xenopus assembly extracts with M9M, a superaffinity nuclear localization sequence that displaces cargoes bound by transportin, or TLB, a mutant transportin that can bind cargo and RanGTP simultaneously, support direct inhibition. Consistently, simple addition of M9M to mitotic cytosol induces microtubule aster assembly. ELYS and the nucleoporin 107-160 complex, components of mitotic kinetochores and nuclear pores, are blocked from binding to kinetochores in vitro by transportin, a block reversible by M9M. In vivo, 30% of M9M-transfected cells have spindle/cytokinesis defects. We conclude that the cell contains importin β and transportin \\\"global positioning system\\\"or \\\"GPS\\\" pathways that are mechanistically parallel.\",\n \"corpus_id\": 17512874,\n \"score\": 0\n },\n {\n \"doc_id\": \"25851436\",\n \"title\": \"Deformability in the cleavage site of primary microRNA is not sensed by the double-stranded RNA binding domains in the microprocessor component DGCR8.\",\n \"abstract\": \"The prevalence of double-stranded RNA (dsRNA) in eukaryotic cells has only recently been appreciated. Of interest here, RNA silencing begins with dsRNA substrates that are bound by the dsRNA-binding domains (dsRBDs) of their processing proteins. Specifically, processing of microRNA (miRNA) in the nucleus minimally requires the enzyme Drosha and its dsRBD-containing cofactor protein, DGCR8. The smallest recombinant construct of DGCR8 that is sufficient for in vitro dsRNA binding, referred to as DGCR8-Core, consists of its two dsRBDs and a C-terminal tail. As dsRBDs rarely recognize the nucleotide sequence of dsRNA, it is reasonable to hypothesize that DGCR8 function is dependent on the recognition of specific structural features in the miRNA precursor. Previously, we demonstrated that noncanonical structural elements that promote RNA flexibility within the stem of miRNA precursors are necessary for efficient in vitro cleavage by reconstituted Microprocessor complexes. Here, we combine gel shift assays with in vitro processing assays to demonstrate that neither the N-terminal dsRBD of DGCR8 in isolation nor the DGCR8-Core construct is sensitive to the presence of noncanonical structural elements within the stem of miRNA precursors, or to single-stranded segments flanking the stem. Extending DGCR8-Core to include an N-terminal heme-binding region does not change our conclusions. Thus, our data suggest that although the DGCR8-Core region is necessary for dsRNA binding and recruitment to the Microprocessor, it is not sufficient to establish the previously observed connection between RNA flexibility and processing efficiency.\",\n \"corpus_id\": 20692760,\n \"score\": 0\n },\n {\n \"doc_id\": \"25960296\",\n \"title\": \"Identification and characterization of a nuclear localization signal of TRIM28 that overlaps with the HP1 box.\",\n \"abstract\": \"Tripartite motif-containing 28 (TRIM28) is a transcription regulator, which forms a repressor complex containing heterochromatin protein 1 (HP1). Here, we report identification of a nuclear localization signal (NLS) within the 462-494 amino acid region of TRIM28 that overlaps with its HP1 binding site, HP1 box. GST-pulldown experiments revealed the interaction of the arginine-rich TRIM28 NLS with various importin α subtypes (α1, α2 and α4). In vitro transport assay demonstrated that nuclear localization of GFP-TRIM28 NLS is mediated by importin αs, in conjunction with importin β1 and Ran. Further, we demonstrated that HP1 and importin αs compete for binding to TRIM28. Together, our findings suggest that importin α has an essential role in the nuclear delivery and preferential HP1 interaction of TRIM28.\",\n \"corpus_id\": 20772132,\n \"score\": 0\n },\n {\n \"doc_id\": \"27332119\",\n \"title\": \"Binding by TRBP-dsRBD2 Does Not Induce Bending of Double-Stranded RNA.\",\n \"abstract\": \"Protein-nucleic acid interactions are central to a variety of biological processes, many of which involve large-scale conformational changes that lead to bending of the nucleic acid helix. Here, we focus on the nonsequence-specific protein TRBP, whose double-stranded RNA-binding domains (dsRBDs) interact with the A-form geometry of double-stranded RNA (dsRNA). Crystal structures of dsRBD-dsRNA interactions suggest that the dsRNA helix must bend in such a way that its major groove expands to conform to the dsRBD's binding surface. We show through isothermal titration calorimetry experiments that dsRBD2 of TRBP binds dsRNA with a temperature-independent observed binding affinity (KD ∼500 nM). Furthermore, a near-zero observed heat capacity change (ΔCp = 70 ± 40 cal·mol(-1)·K(-1)) suggests that large-scale conformational changes do not occur upon binding. This result is bolstered by molecular-dynamics simulations in which dsRBD-dsRNA interactions generate only modest bending of the RNA along its helical axis. Overall, these results suggest that this particular dsRBD-dsRNA interaction produces little to no change in the A-form geometry of dsRNA in solution. These results further support our previous hypothesis, based on extensive gel-shift assays, that TRBP preferentially binds to sites of nearly ideal A-form structure while being excluded from sites of local deformation in the RNA helical structure. The implications of this mechanism for efficient micro-RNA processing will be discussed.\",\n \"corpus_id\": 29963528,\n \"score\": 0\n },\n {\n \"doc_id\": \"28792523\",\n \"title\": \"Engineering double-stranded RNA binding activity into the Drosha double-stranded RNA binding domain results in a loss of microRNA processing function.\",\n \"abstract\": \"Canonical processing of miRNA begins in the nucleus with the Microprocessor complex, which is minimally composed of the RNase III enzyme Drosha and two copies of its cofactor protein DGCR8. In structural analogy to most RNase III enzymes, Drosha possesses a modular domain with the double-stranded RNA binding domain (dsRBD) fold. Unlike the dsRBDs found in most members of the RNase III family, the Drosha-dsRBD does not display double-stranded RNA binding activity; perhaps related to this, the Drosha-dsRBD amino acid sequence does not conform well to the canonical patterns expected for a dsRBD. In this article, we investigate the impact on miRNA processing of engineering double-stranded RNA binding activity into Drosha's non-canonical dsRBD. Our findings corroborate previous studies that have demonstrated the Drosha-dsRBD is necessary for miRNA processing and suggest that the amino acid composition in the second α-helix of the domain is critical to support its evolved function.\",\n \"corpus_id\": 37626108,\n \"score\": 0\n },\n {\n \"doc_id\": \"29036638\",\n \"title\": \"The basic tilted helix bundle domain of the prolyl isomerase FKBP25 is a novel double-stranded RNA binding module.\",\n \"abstract\": \"Prolyl isomerases are defined by a catalytic domain that facilitates the cis-trans interconversion of proline residues. In most cases, additional domains in these enzymes add important biological function, including recruitment to a set of protein substrates. Here, we report that the N-terminal basic tilted helix bundle (BTHB) domain of the human prolyl isomerase FKBP25 confers specific binding to double-stranded RNA (dsRNA). This binding is selective over DNA as well as single-stranded oligonucleotides. We find that FKBP25 RNA-association is required for its nucleolar localization and for the vast majority of its protein interactions, including those with 60S pre-ribosome and early ribosome biogenesis factors. An independent mobility of the BTHB and FKBP catalytic domains supports a model by which the N-terminus of FKBP25 is anchored to regions of dsRNA, whereas the FKBP domain is free to interact with neighboring proteins. Apart from the identification of the BTHB as a new dsRNA-binding module, this domain adds to the growing list of auxiliary functions used by prolyl isomerases to define their primary cellular targets.\",\n \"corpus_id\": 33563066,\n \"score\": 0\n }\n]","isConversational":false}}},{"rowIdx":57,"cells":{"query":{"kind":"string","value":"{\n \"doc_id\": \"24878921\",\n \"title\": \"Unique subunit packing in mycobacterial nanoRNase leads to alternate substrate recognitions in DHH phosphodiesterases.\",\n \"abstract\": \"DHH superfamily includes RecJ, nanoRNases (NrnA), cyclic nucleotide phosphodiesterases and pyrophosphatases. In this study, we have carried out in vitro and in vivo investigations on the bifunctional NrnA-homolog from Mycobacterium smegmatis, MSMEG_2630. The crystal structure of MSMEG_2630 was determined to 2.2-Å resolution and reveals a dimer consisting of two identical subunits with each subunit folding into an N-terminal DHH domain and a C-terminal DHHA1 domain. The overall structure and fold of the individual domains is similar to other members of DHH superfamily. However, MSMEG_2630 exhibits a distinct quaternary structure in contrast to other DHH phosphodiesterases. This novel mode of subunit packing and variations in the linker region that enlarge the domain interface are responsible for alternate recognitions of substrates in the bifunctional nanoRNases. MSMEG_2630 exhibits bifunctional 3'-5' exonuclease [on both deoxyribonucleic acid (DNA) and ribonucleic acid (RNA) substrates] as well as CysQ-like phosphatase activity (on pAp) in vitro with a preference for nanoRNA substrates over single-stranded DNA of equivalent lengths. A transposon disruption of MSMEG_2630 in M. smegmatis causes growth impairment in the presence of various DNA-damaging agents. Further phylogenetic analysis and genome organization reveals clustering of bacterial nanoRNases into two distinct subfamilies with possible role in transcriptional and translational events during stress.\",\n \"corpus_id\": 8448797\n}"},"candidates":{"kind":"list like","value":[{"doc_id":"19553197","title":"Degradation of nanoRNA is performed by multiple redundant RNases in Bacillus subtilis.","abstract":"Escherichia coli possesses only one essential oligoribonuclease (Orn), an enzyme that can degrade oligoribonucleotides of five residues and shorter in length (nanoRNA). Firmicutes including Bacillus subtilis do not have an Orn homolog. We had previously identified YtqI (NrnA) as functional analog of Orn in B. subtilis. Screening a genomic library from B. subtilis for genes that can complement a conditional orn mutant, we identify here YngD (NrnB) as a second nanoRNase in B. subtilis. Like NrnA, NrnB is a member of the DHH/DHHA1 protein family of phosphoesterases. NrnB degrades nanoRNA 5-mers in vitro similarily to Orn. Low expression levels of NrnB are sufficient for orn complementation. YhaM, a known RNase present in B. subtilis, degrades nanoRNA efficiently in vitro but requires high levels of expression for only partial complementation of the orn(-) strain. A triple mutant (nrnA(-), nrnB(-), yhaM(-)) in B. subtilis is viable and shows almost no impairment in growth. Lastly, RNase J1 seems also to have some 5'-to-3' exoribonuclease activity on nanoRNA and thus can potentially finish degradation of RNA. We conclude that, unlike in E. coli, degradation of nanoRNA is performed in a redundant fashion in B. subtilis.","corpus_id":3011249,"score":2},{"doc_id":"19901023","title":"YybT is a signaling protein that contains a cyclic dinucleotide phosphodiesterase domain and a GGDEF domain with ATPase activity.","abstract":"The cyclic dinucleotide c-di-AMP [corrected] synthesized by the diadenylate cyclase domain was discovered recently [corrected] as a messenger molecule for signaling DNA breaks in Bacillus subtilis. By searching bacterial genomes, we identified a family of DHH/DHHA1 domain proteins (COG3387) that co-occur with a subset of the diadenylate cyclase domain proteins. Here we report that the B. subtilis protein YybT, a member of the COG3387 family proteins, exhibits phosphodiesterase activity toward cyclic dinucleotides. The DHH/DHHA1 domain hydrolyzes c-di-AMP and c-di-GMP to generate the linear dinucleotides 5'-pApA and 5'-pGpG. The data suggest that c-di-AMP could be the physiological substrate for YybT given the physiologically relevant Michaelis-Menten constant (K(m)) and the presence of YybT family proteins in the bacteria lacking c-di-GMP signaling network. The bacterial regulator ppGpp was found to be a strong competitive inhibitor of the DHH/DHHA1 domain, suggesting that YybT is under tight control during stringent response. In addition, the atypical GGDEF domain of YybT exhibits unexpected ATPase activity, distinct from the common diguanylate cyclase activity for GGDEF domains. We further demonstrate the participation of YybT in DNA damage and acid resistance by characterizing the phenotypes of the DeltayybT mutant. The novel enzymatic activity and stress resistance together point toward a role for YybT in stress signaling and response.","corpus_id":23848463,"score":2},{"doc_id":"20129927","title":"Structure of RecJ exonuclease defines its specificity for single-stranded DNA.","abstract":"RecJ is a single-stranded DNA (ssDNA)-specific 5'-3' exonuclease that plays an important role in DNA repair and recombination. To elucidate how RecJ achieves its high specificity for ssDNA, we determined the entire structures of RecJ both in a ligand-free form and in a complex with Mn(2+) or Mg(2+) by x-ray crystallography. The entire RecJ consists of four domains that form a molecule with an O-like structure. One of two newly identified domains had structural similarities to an oligonucleotide/oligosaccharide-binding (OB) fold. The OB fold domain alone could bind to DNA, indicating that this domain is a novel member of the OB fold superfamily. The truncated RecJ containing only the core domain exhibited much lower affinity for the ssDNA substrate compared with intact RecJ. These results support the hypothesis that these structural features allow specific binding of RecJ to ssDNA. In addition, the structure of the RecJ-Mn(2+) complex suggests that the hydrolysis reaction catalyzed by RecJ proceeds through a two-metal ion mechanism.","corpus_id":41263393,"score":2},{"doc_id":"21087930","title":"Role of RecJ-like protein with 5'-3' exonuclease activity in oligo(deoxy)nucleotide degradation.","abstract":"RecJ-like proteins belonging to the DHH family have been proposed to function as oligoribonucleases and 3'-phosphoadenosine 5'-phosphate (pAp) phosphatases in bacteria and archaea, which do not have Orn (oligoribonuclease) and CysQ (pAp phosphatase) homologs. In this study, we analyzed the biochemical and physiological characterization of the RecJ-like protein TTHA0118 from Thermus thermophilus HB8. TTHA0118 had high enzymatic activity as an oligodeoxyribonucleotide- and oligoribonucleotide-specific exonuclease and as pAp phosphatase. The polarity of degradation was 5' to 3', in contrast to previous reports about Bacillus subtilis NrnA, a RecJ-like protein. TTHA0118 preferentially hydrolyzed short oligodeoxyribonucleotides and oligoribonucleotides, whereas the RecJ exonuclease from T. thermophilus HB8 showed no such length dependence on oligodeoxyribonucleotide substrates. An insertion mutation of the ttha0118 gene led to growth reduction in minimum essential medium. Added 5'-mononucleotides, nucleosides, and cysteine increased growth of the ttha0118 mutant in minimum essential medium. The RecJ-like protein Mpn140 from Mycoplasma pneumoniae M129, which cannot synthesize nucleic acid precursors de novo, showed similar biochemical features to TTHA0118. Furthermore, B. subtilis NrnA also hydrolyzed oligo(deoxy)ribonucleotides in a 5'-3' direction. These results suggested that these RecJ-like proteins act in recycling short oligonucleotides to mononucleotides and in controlling pAp concentrations in vivo.","corpus_id":205304044,"score":2},{"doc_id":"22114320","title":"Characterization of NrnA homologs from Mycobacterium tuberculosis and Mycoplasma pneumoniae.","abstract":"Processive RNases are unable to degrade efficiently very short oligonucleotides, and they are complemented by specific enzymes, nanoRNases, that assist in this process. We previously identified NrnA (YtqI) from Bacillus subtilis as a bifunctional protein with the ability to degrade nanoRNA (RNA oligos ≤5 nucleotides) and to dephosphorylate 3'-phosphoadenosine 5'-phosphate (pAp) to AMP. While the former activity is analogous to that of oligoribonuclease (Orn) from Escherichia coli, the latter corresponds to CysQ. NrnA homologs are widely present in bacterial and archaeal genomes. They are found preferably in genomes that lack Orn or CysQ homologs. Here, we characterize NrnA homologs from important human pathogens, Mpn140 from Mycoplasma pneumoniae, and Rv2837c from Mycobacterium tuberculosis. Like NrnA, these enzymes degrade nanoRNA and dephosphorylate pAp in vitro. However, they show dissimilar preferences for specific nanoRNA substrate lengths. Whereas NrnA prefers RNA 3-mers with a 10-fold higher specific activity compared to 5-mers, Rv2837c shows a preference for nanoRNA of a different length, namely, 2-mers. Mpn140 degrades Cy5-labeled nanoRNA substrates in vitro with activities varying within one order of magnitude as follows: 5-mer>4-mer>3-mer>2-mer. In agreement with these in vitro activities, both Rv2837c and Mpn140 can complement the lack of their functional counterparts in E. coli: CysQ and Orn. The NrnA homolog from Streptococcus mutans, SMU.1297, was previously shown to hydrolyze pAp and to complement an E. coli cysQ mutant. Here, we show that SMU.1297 can complement an E. coli orn(-) mutant, suggesting that having both pAp-phosphatase and nanoRNase activity is a common feature of NrnA homologs.","corpus_id":207216898,"score":2},{"doc_id":"22262096","title":"Identification of a novel nanoRNase in Bartonella.","abstract":"In Escherichia coli, only one essential oligoribonuclease (Orn) can degrade oligoribonucleotides of five residues and shorter in length (nanoRNA). In Bacillus subtilis, NrnA and NrnB, which do not show any sequence similarity to Orn, have been identified as functional analogues of Orn. Sequence comparisons did not identify orn, nrnA or nrnB homologues in the genomes of the Chlamydia/Cyanobacteria and Alphaproteobacteria family members. Screening a genomic library from Bartonella birtlesii, a member of the Alphaproteobacteria, for genes that can complement a conditional orn mutant in E. coli, we identified BA0969 (NrnC) as a functional analogue of Orn. NrnC is highly conserved (more than 80 % identity) in the Bartonella genomes sequenced to date. Biochemical characterization showed that this protein exhibits oligo RNA degradation activity (nanoRNase activity). Like Orn from E. coli, NrnC is inhibited by micromolar amounts of 3'-phosphoadenosine 5'-phosphate in vitro. NrnC homologues are widely present in genomes of Alphaproteobacteria. Knock down of nrnC decreases the growth ability of Bartonella henselae, demonstrating the importance of nanoRNase activity in this bacterium.","corpus_id":32163321,"score":2},{"doc_id":"23851074","title":"Crystal structure of the ligand-binding form of nanoRNase from Bacteroides fragilis, a member of the DHH/DHHA1 phosphoesterase family of proteins.","abstract":"NanoRNase (Nrn) specifically degrades nucleoside 3',5'-bisphosphate and the very short RNA, nanoRNA, during the final step of mRNA degradation. The crystal structure of Nrn in complex with a reaction product GMP was determined. The overall structure consists of two domains that are interconnected by a flexible loop and form a cleft. Two Mn²⁺ ions are coordinated by conserved residues in the DHH motif of the N-terminal domain. GMP binds near the DHHA1 motif region in the C-terminal domain. Our structure enables us to predict the substrate-bound form of Nrn as well as other DHH/DHHA1 phosphoesterase family proteins.","corpus_id":5312659,"score":2},{"doc_id":"26078723","title":"Functional Analysis of a c-di-AMP-specific Phosphodiesterase MsPDE from Mycobacterium smegmatis.","abstract":"Cyclic di‑AMP (c-di-AMP) is a second signaling molecule involved in the regulation of bacterial physiological processes and interaction between pathogen and host. However, the regulatory network mediated by c-di-AMP in Mycobacterium remains obscure. In M. smegmatis, a diadenylate cyclase (DAC) was reported recently, but there is still no investigation on c-di-AMP phosphodiesterase (PDE). Here, we provide a systematic study on signaling mechanism of c-di-AMP PDE in M. smegmatis. Based on our enzymatic analysis, MsPDE (MSMEG_2630), which contained a DHH-DHHA1 domain, displayed a 200-fold higher hydrolytic efficiency (kcat /Km ) to c-di-AMP than to c-di-GMP. MsPDE was capable of converting c-di-AMP to pApA and AMP, and hydrolyzing pApA to AMP. Site-directed mutations in DHH and DHHA1 revealed that DHH domain was critical for the phosphodiesterase activity. To explore the regulatory role of c-di-AMP in vivo, we constructed the mspde mutant (Δmspde) and found that deficiency of MsPDE significantly enhanced intracellular C12-C20 fatty acid accumulation. Deficiency of DAC in many bacteria results in cell death. However, we acquired the M. smegmatis strain with DAC gene disrupted (ΔmsdisA) by homologous recombination approach. Deletion of msdisA reduced bacterial C12-C20 fatty acids production but scarcely affected bacterial survival. We also provided evidences that superfluous c-di-AMP in M. smegmatis could lead to abnormal colonial morphology. Collectively, our results indicate that MsPDE is a functional c-di-AMP-specific phosphodiesterase both in vitro and in vivo. Our study also expands the regulatory network mediated by c-di-AMP in M. smegmatis.","corpus_id":10487511,"score":2},{"doc_id":"26668313","title":"Structural and Biochemical Insight into the Mechanism of Rv2837c from Mycobacterium tuberculosis as a C-di-NMP Phosphodiesterase.","abstract":"The intracellular infections of Mycobacterium tuberculosis which is the causative agent of Tuberculosis (TB) are regulated by many cyclic di-nucleotide (c-di-NMP) signalling. Rv2837c from M. tuberculosis is a soluble, stand-alone DHH-DHHA1 domain phosphodiesterase that down-regulates c-di-AMP through catalytic degradation and plays an important role in M. tuberculosis infections. Here, we report the crystal structure of Rv2837c (2.0 Å), and its complex with hydrolysis intermediate 5'-pApA (2.35 Å). Our structures indicate both DHH and DHHA1 domains are essential for c-di-AMP degradation. Further structural analysis shows that Rv2837c does not distinguish adenine from guanine, which explains why Rv2837c hydrolyzes all linear di-nucleotides with almost the same efficiency. We observed that Rv2837c degraded other c-di-NMPs at a lower rate than it did on c-di-AMP. Nevertheless, our data also showed that Rv2837c significantly decreases concentrations of both c-di-AMP and c-di-GMP in vivo. Our results suggest that beside its major role in c-di-AMP degradation Rv2837c could also regulate c-di-GMP signaling pathways in bacterial cell.","corpus_id":-1,"score":2},{"doc_id":"28894100","title":"Structural Basis for the Bidirectional Activity of Bacillus nanoRNase NrnA.","abstract":"NanoRNAs are RNA fragments 2 to 5 nucleotides in length that are generated as byproducts of RNA degradation and abortive transcription initiation. Cells have specialized enzymes to degrade nanoRNAs, such as the DHH phosphoesterase family member NanoRNase A (NrnA). This enzyme was originally identified as a 3' → 5' exonuclease, but we show here that NrnA is bidirectional, degrading 2-5 nucleotide long RNA oligomers from the 3' end, and longer RNA substrates from the 5' end. The crystal structure of Bacillus subtilis NrnA reveals a dynamic bi-lobal architecture, with the catalytic N-terminal DHH domain linked to the substrate binding C-terminal DHHA1 domain via an extended linker. Whereas this arrangement is similar to the structure of RecJ, a 5' → 3' DHH family DNase and other DHH family nanoRNases, Bacillus NrnA has gained an extended substrate-binding patch that we posit is responsible for its 3' → 5' activity.","corpus_id":19302627,"score":2},{"doc_id":"29107484","title":"Structural and Biophysical Analysis of the Soluble DHH/DHHA1-Type Phosphodiesterase TM1595 from Thermotoga maritima.","abstract":"The concentration of messenger molecules in bacterial cells needs to be tightly regulated. This can be achieved by either controlling the synthesis rate, degradation, or export by specific transporters, respectively. The regulation of the essential second messenger c-di-AMP is achieved by modulation of the diadenylate cyclase activity as well as by specific phosphodiesterases that hydrolyze c-di-AMP in the cell. We provide here structural and biochemical data on the DHH-type phosphodiesterase TmPDE (TM1595) from Thermotoga maritima. Our analysis shows that TmPDE is preferentially degrading linear dinucleotides, such as 5'-pApA, 5'-pGpG, and 5'-pApG, compared with cyclic dinucleotide substrates. The high-resolution structural data provided here describe all steps of the PDE reaction: the ligand-free enzyme, two substrate-bound states, and three post-reaction states. We can furthermore show that Pde2 from Streptococcus pneumoniae shares both structural features and substrate specificity based on small-angle X-ray scattering data and biochemical assays.","corpus_id":34360580,"score":2},{"doc_id":"29203646","title":"Structural and biochemical characterization of the catalytic domains of GdpP reveals a unified hydrolysis mechanism for the DHH/DHHA1 phosphodiesterase.","abstract":"The Asp-His-His and Asp-His-His-associated (DHH/DHHA1) domain-containing phosphodiesterases (PDEs) that catalyze degradation of cyclic di-adenosine monophosphate (c-di-AMP) could be subdivided into two subfamilies based on the final product [5'-phosphadenylyl-adenosine (5'-pApA) or AMP]. In a previous study, we revealed that Rv2837c, a stand-alone DHH/DHHA1 PDE, employs a 5'-pApA internal flipping mechanism to produce AMPs. However, why the membrane-bound DHH/DHHA1 PDE can only degrade c-di-AMP to 5'-pApA remains obscure. Here, we report the crystal structure of the DHH/DHHA1 domain of GdpP (GdpP-C), and structures in complex with c-di-AMP, cyclic di-guanosine monophosphate (c-di-GMP), and 5'-pApA. Structural analysis reveals that GdpP-C binds nucleotide substrates quite differently from how Rv2837c does in terms of substrate-binding position. Accordingly, the nucleotide-binding site of the DHH/DHHA1 PDEs is organized into three (C, G, and R) subsites. For GdpP-C, in the C and G sites c-di-AMP binds and degrades into 5'-pApA, and its G site determines nucleotide specificity. To further degrade into AMPs, 5'-pApA must slide into the C and R sites for flipping and hydrolysis as in Rv2837c. Subsequent mutagenesis and enzymatic studies of GdpP-C and Rv2837c uncover the complete flipping process and reveal a unified catalytic mechanism for members of both DHH/DHHA1 PDE subfamilies.","corpus_id":44924419,"score":2},{"doc_id":"29458847","title":"The special existences: nanoRNA and nanoRNase.","abstract":"To adapt to a wide range of nutritional and environmental changes, cells must adjust their gene expression profiles. This process is completed by the frequent transcription and rapid degradation of mRNA. mRNA decay is initiated by a series of endo- and exoribonucleases. These enzymes leave behind 2- to 5-nt-long oligoribonucleotides termed \"nanoRNAs\" that are degraded by specific nanoRNases; the degradation of nanoRNA is essential because nanoRNA can mediate the priming of transcription initiation that is harmful for the cell via an unknown mechanism. Identified nanoRNases include Orn in E. coli, NrnA and NrnB in B. subtilis, and NrnC in Bartonella. Even though these nanoRNases can degrade nanoRNA specifically into mononucleotides, the biochemical features, structural features and functional mechanisms of these enzymes are different. Sequence analysis has identified homologs of these nanoRNases in different bacteria, including Gammaproteobacteria, Betaproteobacteria, Alphaproteobacteria, Firmicutes and Cyanobacteria. However, there are several bacteria, such as those belonging to the class Thermolithobacteria, that do not have homologs of these nanoRNases. In this paper, the source of nanoRNA, the features of different kinds of nanoRNases and the distribution of these enzymes in prokaryotes are described in detail.","corpus_id":3428188,"score":2},{"doc_id":"29609115","title":"NanoRNase from Aeropyrum pernix shows nuclease activity on ssDNA and ssRNA.","abstract":"In cells, degrading DNA and RNA by various nucleases is very important. These processes are strictly controlled and regulated to maintain DNA integrity and to mature or recycle various RNAs. NanoRNase (Nrn) is a 3'-exonuclease that specifically degrades nanoRNAs shorter than 5 nucleotides. Several Nrns have been identified and characterized in bacteria, mainly in Firmicutes. Archaea often grow in extreme environments and might be subjected to more damage to DNA/RNA, so DNA repair and recycling of damaged RNA are very important in archaea. There is no report on the identification and characterization of Nrn in archaea. Aeropyrum pernix encodes three potential Nrns: NrnA (Ape1437), NrnB (Ape0124), and an Nrn-like protein Ape2190. Biochemical characterization showed that only Ape0124 could degrade ssDNA and ssRNA from the 3'-end in the presence of Mn2+. Interestingly, unlike bacterial Nrns, Ape0124 prefers ssDNA, including short nanoDNA, and degrades nanoRNA with lower efficiency. The 3'-DNA backbone was found to be required for efficiently hydrolyzing the phosphodiester bonds. In addition, Ape0124 also degrads the 3'-overhang of double-stranded DNA. Interestingly, Ape0124 could hydrolyze pAp into AMP, which is a feature of bacterial NrnA, not NrnB. Our results indicate that Ape0124 is a novel Nrn with a combined substrate profile of bacterial NrnA and NrnB.","corpus_id":5047026,"score":2},{"doc_id":"19094995","title":"Orchestration of Haemophilus influenzae RecJ exonuclease by interaction with single-stranded DNA-binding protein.","abstract":"RecJ exonuclease plays crucial roles in several DNA repair and recombination pathways, and its ubiquity in bacterial species points to its ancient origin and vital cellular function. RecJ exonuclease from Haemophilus influenzae is a 575-amino-acid protein that harbors the characteristic motifs conserved among RecJ homologs. The purified protein exhibits a processive 5'-3' single-stranded-DNA-specific exonuclease activity. The exonuclease activity of H. influenzae RecJ (HiRecJ) was supported by Mg(2+) or Mn(2+) and inhibited by Cd(2+), suggesting a different mode of metal binding in HiRecJ as compared to Escherichia coli RecJ (EcoRecJ). Site-directed mutagenesis of highly conserved residues in HiRecJ abolished enzymatic activity. Interestingly, substitution of alanine for aspartate 77 resulted in a catalytically inactive enzyme that bound to DNA with a significantly higher affinity as compared to the wild-type enzyme. Noticeably, steady-state kinetic studies showed that H. influenzae single-stranded DNA-binding protein (HiSSB) increased the affinity of HiRecJ for single-stranded DNA and stimulated its exonuclease activity. HiSSB, whose C-terminal tail had been deleted, failed to enhance RecJ exonuclease activity. More importantly, HiRecJ was found to directly associate with its cognate single-stranded DNA-binding protein (SSB), as demonstrated by various in vitro assays. Interaction studies carried out with the truncated variants of HiRecJ and HiSSB revealed that the two proteins interact via the C-terminus of SSB protein and the core-catalytic domain of RecJ. Taken together, these results emphasize direct interaction between RecJ and SSB, which confers functional cooperativity to these two proteins. In addition, these results implicate SSB as being involved in the recruitment of RecJ to DNA and provide insights into the interplay between these proteins in repair and recombination pathways.","corpus_id":11311767,"score":1},{"doc_id":"19801656","title":"A mycobacterial cyclic AMP phosphodiesterase that moonlights as a modifier of cell wall permeability.","abstract":"Mycobacterium tuberculosis utilizes many mechanisms to establish itself within the macrophage, and bacterially derived cAMP is important in modulating the host cellular response. Although the genome of M. tuberculosis is endowed with a number of mammalian-like adenylyl cyclases, only a single cAMP phosphodiesterase has been identified that can decrease levels of cAMP produced by the bacterium. We present the crystal structure of the full-length and sole cAMP phosphodiesterase, Rv0805, found in M. tuberculosis, whose orthologs are present only in the genomes of slow growing and pathogenic mycobacteria. The dimeric core catalytic domain of Rv0805 adopts a metallophosphoesterase-fold, and the C-terminal region builds the active site and contributes to multiple substrate utilization. Localization of Rv0805 to the cell wall is dependent on its C terminus, and expression of either wild type or mutationally inactivated Rv0805 in M. smegmatis alters cell permeability to hydrophobic cytotoxic compounds. Rv0805 may therefore play a key role in the pathogenicity of mycobacteria, not only by hydrolyzing bacterial cAMP, but also by moonlighting as a protein that can alter cell wall functioning.","corpus_id":12891246,"score":1},{"doc_id":"22055185","title":"The structural basis for substrate recognition by mammalian polynucleotide kinase 3' phosphatase.","abstract":"Mammalian polynucleotide kinase 3' phosphatase (PNK) plays a key role in the repair of DNA damage, functioning as part of both the nonhomologous end-joining (NHEJ) and base excision repair (BER) pathways. Through its two catalytic activities, PNK ensures that DNA termini are compatible with extension and ligation by either removing 3'-phosphates from, or by phosphorylating 5'-hydroxyl groups on, the ribose sugar of the DNA backbone. We have now determined crystal structures of murine PNK with DNA molecules bound to both of its active sites. The structure of ssDNA engaged with the 3'-phosphatase domain suggests a mechanism of substrate interaction that assists DNA end seeking. The structure of dsDNA bound to the 5'-kinase domain reveals a mechanism of DNA bending that facilitates recognition of DNA ends in the context of single-strand and double-strand breaks and suggests a close functional cooperation in substrate recognition between the kinase and phosphatase active sites.","corpus_id":3002202,"score":1},{"doc_id":"22147708","title":"Structural and functional insights into the DNA replication factor Cdc45 reveal an evolutionary relationship to the DHH family of phosphoesterases.","abstract":"Cdc45 is an essential protein conserved in all eukaryotes and is involved both in the initiation of DNA replication and the progression of the replication fork. With GINS, Cdc45 is an essential cofactor of the Mcm2-7 replicative helicase complex. Despite its importance, no detailed information is available on either the structure or the biochemistry of the protein. Intriguingly, whereas homologues of both GINS and Mcm proteins have been described in Archaea, no counterpart for Cdc45 is known. Herein we report a bioinformatic analysis that shows a weak but significant relationship among eukaryotic Cdc45 proteins and a large family of phosphoesterases that has been described as the DHH family, including inorganic pyrophosphatases and RecJ ssDNA exonucleases. These enzymes catalyze the hydrolysis of phosphodiester bonds via a mechanism involving two Mn(2+) ions. Only a subset of the amino acids that coordinates Mn(2+) is conserved in Cdc45. We report biochemical and structural data on the recombinant human Cdc45 protein, consistent with the proposed DHH family affiliation. Like the RecJ exonucleases, the human Cdc45 protein is able to bind single-stranded, but not double-stranded DNA. Small angle x-ray scattering data are consistent with a model compatible with the crystallographic structure of the RecJ/DHH family members.","corpus_id":13938433,"score":1},{"doc_id":"24261692","title":"Site-directed mutagenesis maps interactions that enhance cognate and limit promiscuous catalysis by an alkaline phosphatase superfamily phosphodiesterase.","abstract":"Catalytic promiscuity, an evolutionary concept, also provides a powerful tool for gaining mechanistic insights into enzymatic reactions. Members of the alkaline phosphatase (AP) superfamily are highly amenable to such investigation, with several members having been shown to exhibit promiscuous activity for the cognate reactions of other superfamily members. Previous work has shown that nucleotide pyrophosphatase/phosphodiesterase (NPP) exhibits a >10⁶-fold preference for the hydrolysis of phosphate diesters over phosphate monoesters, and that the reaction specificity is reduced 10³-fold when the size of the substituent on the transferred phosphoryl group of phosphate diester substrates is reduced to a methyl group. Here we show additional specificity contributions from the binding pocket for this substituent (herein termed the R' substituent) that account for an additional ~250-fold differential specificity with the minimal methyl substituent. Removal of four hydrophobic side chains suggested on the basis of structural inspection to interact favorably with R' substituents decreases phosphate diester reactivity 10⁴-fold with an optimal diester substrate (R' = 5'-deoxythymidine) and 50-fold with a minimal diester substrate (R' = CH₃). These mutations also enhance the enzyme's promiscuous phosphate monoesterase activity by nearly an order of magnitude, an effect that is traced by mutation to the reduction of unfavorable interactions with the two residues closest to the nonbridging phosphoryl oxygen atoms. The quadruple R' pocket mutant exhibits the same activity toward phosphate diester and phosphate monoester substrates that have identical leaving groups, with substantial rate enhancements of ~10¹¹-fold. This observation suggests that the Zn²⁺ bimetallo core of AP superfamily enzymes, which is equipotent in phosphate monoester and diester catalysis, has the potential to become specialized for the hydrolysis of each class of phosphate esters via addition of side chains that interact with the substrate atoms and substituents that project away from the Zn²⁺ bimetallo core.","corpus_id":7543687,"score":1},{"doc_id":"26138487","title":"Structural basis for substrate recognition and processive cleavage mechanisms of the trimeric exonuclease PhoExo I.","abstract":"Nucleases play important roles in nucleic acid processes, such as replication, repair and recombination. Recently, we identified a novel single-strand specific 3'-5' exonuclease, PfuExo I, from the hyperthermophilic archaeon Pyrococcus furiosus, which may be involved in the Thermococcales-specific DNA repair system. PfuExo I forms a trimer and cleaves single-stranded DNA at every two nucleotides. Here, we report the structural basis for the cleavage mechanism of this novel exonuclease family. A structural analysis of PhoExo I, the homologous enzyme from P. horikoshii OT3, showed that PhoExo I utilizes an RNase H-like active site and possesses a 3'-OH recognition site ∼9 Å away from the active site, which enables cleavage at every two nucleotides. Analyses of the heterotrimeric and monomeric PhoExo I activities showed that trimerization is indispensable for its processive cleavage mechanism, but only one active site of the trimer is required.","corpus_id":8052172,"score":1},{"doc_id":"26648913","title":"A Novel C-Terminal Domain of RecJ is Critical for Interaction with HerA in Deinococcus radiodurans.","abstract":"Homologous recombination (HR) generates error-free repair products, which plays an important role in double strand break repair and replication fork rescue processes. DNA end resection, the critical step in HR, is usually performed by a series of nuclease/helicase. RecJ was identified as a 5'-3' exonuclease involved in bacterial DNA end resection. Typical RecJ possesses a conserved DHH domain, a DHHA1 domain, and an oligonucleotide/oligosaccharide-binding (OB) fold. However, RecJs from Deinococcus-Thermus phylum, such as Deinococcus radiodurans RecJ (DrRecJ), possess an extra C-terminal domain (CTD), of which the function has not been characterized. Here, we showed that a CTD-deletion of DrRecJ (DrRecJΔC) could not restore drrecJ mutant growth and mitomycin C (MMC)-sensitive phenotypes, indicating that this domain is essential for DrRecJ in vivo. DrRecJΔC displayed reduced DNA nuclease activity and DNA binding ability. Direct interaction was identified between DrRecJ-CTD and DrHerA, which stimulates DrRecJ nuclease activity by enhancing its DNA binding affinity. Moreover, DrNurA nuclease, another partner of DrHerA, inhibited the stimulation of DrHerA on DrRecJ nuclease activity by interaction with DrHerA. Opposing growth and MMC-resistance phenotypes between the recJ and nurA mutants were observed. A novel modulation mechanism among DrRecJ, DrHerA, and DrNurA was also suggested.","corpus_id":217284,"score":1},{"doc_id":"27058167","title":"Structural basis for DNA 5´-end resection by RecJ.","abstract":"The resection of DNA strand with a 5´ end at double-strand breaks is an essential step in recombinational DNA repair. RecJ, a member of DHH family proteins, is the only 5´ nuclease involved in the RecF recombination pathway. Here, we report the crystal structures of Deinococcus radiodurans RecJ in complex with deoxythymidine monophosphate (dTMP), ssDNA, the C-terminal region of single-stranded DNA-binding protein (SSB-Ct) and a mechanistic insight into the RecF pathway. A terminal 5´-phosphate-binding pocket above the active site determines the 5´-3´ polarity of the deoxy-exonuclease of RecJ; a helical gateway at the entrance to the active site admits ssDNA only; and the continuous stacking interactions between protein and nine nucleotides ensure the processive end resection. The active site of RecJ in the N-terminal domain contains two divalent cations that coordinate the nucleophilic water. The ssDNA makes a 180° turn at the scissile phosphate. The C-terminal domain of RecJ binds the SSB-Ct, which explains how RecJ and SSB work together to efficiently process broken DNA ends for homologous recombination.","corpus_id":-1,"score":1},{"doc_id":"28837073","title":"Two Archaeal RecJ Nucleases from Methanocaldococcus jannaschii Show Reverse Hydrolysis Polarity: Implication to Their Unique Function in Archaea.","abstract":"Bacterial nuclease RecJ, which exists in almost all bacterial species, specifically degrades single-stranded (ss) DNA in the 5' to 3' direction. Some archaeal phyla, except Crenarchaea, also encode RecJ homologs. Compared with bacterial RecJ, archaeal RecJ exhibits a largely different amino acid sequence and domain organization. Archaeal RecJs from Thermococcus kodakarensis and Pyrococcus furiosus show 5'→3' exonuclease activity on ssDNA. Interestingly, more than one RecJ exists in some Euryarchaeota classes, such as Methanomicrobia, Methanococci, Methanomicrobia, Methanobacteria, and Archaeoglobi. Here we report the biochemical characterization of two RecJs from Methanocaldococcus jannaschii, the long RecJ1 (MJ0977) and short RecJ2 (MJ0831) to understand their enzymatic properties. RecJ1 is a 5'→3' exonuclease with a preference to ssDNA; however, RecJ2 is a 3'→5' exonuclease with a preference to ssRNA. The 5' terminal phosphate promotes RecJ1 activity, but the 3' terminal phosphate inhibits RecJ2 nuclease. Go-Ichi-Ni-San (GINS) complex does not interact with two RecJs and does not promote their nuclease activities. Finally, we discuss the diversity, function, and molecular evolution of RecJ in archaeal taxonomy. Our analyses provide insight into the function and evolution of conserved archaeal RecJ/eukaryotic Cdc45 protein.","corpus_id":11782396,"score":1},{"doc_id":"18374646","title":"Structure of the active subunit of the yeast exosome core, Rrp44: diverse modes of substrate recruitment in the RNase II nuclease family.","abstract":"The eukaryotic exosome is a macromolecular complex essential for RNA processing and decay. It has recently been shown that the RNase activity of the yeast exosome core can be mapped to a single subunit, Rrp44, which processively degrades single-stranded RNAs as well as RNAs containing secondary structures. Here we present the 2.3 A resolution crystal structure of S. cerevisiae Rrp44 in complex with single-stranded RNA. Although Rrp44 has a linear domain organization similar to bacterial RNase II, in three dimensions the domains have a different arrangement. The three domains of the classical nucleic-acid-binding OB fold are positioned on the catalytic domain such that the RNA-binding path observed in RNase II is occluded. Instead, RNA is threaded to the catalytic site via an alternative route suggesting a mechanism for RNA-duplex unwinding. The structure provides a molecular rationale for the observed biochemical properties of the RNase R family of nucleases.","corpus_id":25938454,"score":0},{"doc_id":"19828435","title":"Mechanism for the allosteric regulation of phosphodiesterase 2A deduced from the X-ray structure of a near full-length construct.","abstract":"We report the X-ray crystal structure of a phosphodiesterase (PDE) that includes both catalytic and regulatory domains. PDE2A (215-900) crystallized as a dimer in which each subunit had an extended organization of regulatory GAF-A and GAF-B and catalytic domains connected by long alpha-helices. The subunits cross at the GAF-B/catalytic domain linker, and each side of the dimer contains in series the GAF-A and GAF-B of one subunit and the catalytic domain of the other subunit. A dimer interface extends over the entire length of the molecule. The substrate binding pocket of each catalytic domain is occluded by the H-loop. We deduced from comparisons with structures of isolated, ligand-bound catalytic subunits that the H-loop swings out to allow substrate access. However, in dimeric PDE2A (215-900), the H-loops of the two catalytic subunits pack against each other at the dimer interface, necessitating movement of the catalytic subunits to allow for H-loop movement. Comparison of the unliganded GAF-B of PDE2A (215-900) with previous structures of isolated, cGMP-bound GAF domains indicates that cGMP binding induces a significant shift in the GAF-B/catalytic domain linker. We propose that cGMP binding to GAF-B causes movement, through this linker region, of the catalytic domains, such that the H-loops no longer pack at the dimer interface and are, instead, free to swing out to allow substrate access. This increase in substrate access is proposed as the basis for PDE2A activation by cGMP and may be a general mechanism for regulation of all PDEs.","corpus_id":22927729,"score":0},{"doc_id":"19836403","title":"Crystal Structures of the histidine acid phosphatase from Francisella tularensis provide insight into substrate recognition.","abstract":"Histidine acid phosphatases catalyze the transfer of a phosphoryl group from phosphomonoesters to water at acidic pH using an active-site histidine. The histidine acid phosphatase from the category A pathogen Francisella tularensis (FtHAP) has been implicated in intramacrophage survival and virulence, motivating interest in understanding the structure and mechanism of this enzyme. Here, we report a structure-based study of ligand recognition by FtHAP. The 1.70-A-resolution structure of FtHAP complexed with the competitive inhibitor l(+)-tartrate was solved using single-wavelength anomalous diffraction phasing. Structures of the ligand-free enzyme and the complex with inorganic phosphate were determined at resolutions of 1.85 and 1.70 A, respectively. The structure of the Asp261Ala mutant enzyme complexed with the substrate 3'-AMP was determined at 1.50 A resolution to gain insight into substrate recognition. FtHAP exhibits a two-domain fold similar to that of human prostatic acid phosphatase, consisting of an alpha/beta core domain and a smaller domain that caps the core domain. The structures show that the core domain supplies the phosphoryl binding site, catalytic histidine (His17), and an aspartic acid residue (Asp261) that protonates the leaving group, while the cap domain contributes residues that enforce substrate preference. FtHAP and human prostatic acid phosphatase differ in the orientation of the crucial first helix of the cap domain, implying differences in the substrate preferences of the two enzymes. 3'-AMP binds in one end of a 15-A-long tunnel, with the adenine clamped between Phe23 and Tyr135, and the ribose 2'-hydroxyl interacting with Gln132. The importance of the clamp is confirmed with site-directed mutagenesis; mutation of Phe23 and Tyr135 individually to Ala increases K(m) by factors of 7 and 10, respectively. The structural data are consistent with a role for FtHAP in scavenging phosphate from small molecules present in host macrophage cells.","corpus_id":10190381,"score":0},{"doc_id":"20050614","title":"Structural determinants of substrate recognition in the HAD superfamily member D-glycero-D-manno-heptose-1,7-bisphosphate phosphatase (GmhB) .","abstract":"The haloalkanoic acid dehalogenase (HAD) enzyme superfamily is the largest family of phosphohydrolases. In HAD members, the structural elements that provide the binding interactions that support substrate specificity are separated from those that orchestrate catalysis. For most HAD phosphatases, a cap domain functions in substrate recognition. However, for the HAD phosphatases that lack a cap domain, an alternate strategy for substrate selection must be operative. One such HAD phosphatase, GmhB of the HisB subfamily, was selected for structure-function analysis. Herein, the X-ray crystallographic structures of Escherichia coli GmhB in the apo form (1.6 A resolution), in a complex with Mg(2+) and orthophosphate (1.8 A resolution), and in a complex with Mg(2+) and d-glycero-d-manno-heptose 1beta,7-bisphosphate (2.2 A resolution) were determined, in addition to the structure of Bordetella bronchiseptica GmhB bound to Mg(2+) and orthophosphate (1.7 A resolution). The structures show that in place of a cap domain, the GmhB catalytic site is elaborated by three peptide inserts or loops that pack to form a concave, semicircular surface around the substrate leaving group. Structure-guided kinetic analysis of site-directed mutants was conducted in parallel with a bioinformatics study of sequence diversification within the HisB subfamily to identify loop residues that serve as substrate recognition elements and that distinguish GmhB from its subfamily counterpart, the histidinol-phosphate phosphatase domain of HisB. We show that GmhB and the histidinol-phosphate phosphatase domain use the same design of three substrate recognition loops inserted into the cap domain yet, through selective residue usage on the loops, have achieved unique substrate specificity and thus novel biochemical function.","corpus_id":5126557,"score":0},{"doc_id":"20363939","title":"Structural and functional characterization of an RNase HI domain from the bifunctional protein Rv2228c from Mycobacterium tuberculosis.","abstract":"The open reading frame Rv2228c from Mycobacterium tuberculosis is predicted to encode a protein composed of two domains, each with individual functions, annotated through sequence similarity searches. The N-terminal domain is homologous with prokaryotic and eukaryotic RNase H domains and the C-terminal domain with alpha-ribazole phosphatase (CobC). The N-terminal domain of Rv2228c (Rv2228c/N) and the full-length protein were expressed as fusions with maltose binding protein (MBP). Rv2228c/N was shown to have RNase H activity with a hybrid RNA/DNA substrate as well as double-stranded RNase activity. The full-length protein was shown to have additional CobC activity. The crystal structure of the MBP-Rv2228c/N fusion protein was solved by molecular replacement and refined at 2.25-A resolution (R = 0.182; R(free) = 0.238). The protein is monomeric in solution but associates in the crystal to form a dimer. The Rv2228c/N domain has the classic RNase H fold and catalytic machinery but lacks several surface features that play important roles in the cleavage of RNA/DNA hybrids by other RNases H. The absence of either the basic protrusion of some RNases H or the hybrid binding domain of others appears to be compensated by the C-terminal CobC domain in full-length Rv2228c. The double-stranded-RNase activity of Rv2228c/N contrasts with classical RNases H and is attributed to the absence in Rv2228c/N of a key phosphate binding pocket.","corpus_id":22429245,"score":0},{"doc_id":"20637039","title":"Mycobacterium tuberculosis Rv1302 and Mycobacterium smegmatis MSMEG_4947 have WecA function and MSMEG_4947 is required for the growth of M. smegmatis.","abstract":"The disaccharide d-N-acetylglucosamine-l-rhamnose plays an important role in the mycobacterial cell wall as a linker connecting arabinogalactan and peptidoglycan via a phosphodiester linkage. The first step of the disaccharide linker is the formation of decaprenyl phosphate-GlcNAc, which is catalyzed by GlcNAc-1-phosphate transferase. In Gram-negative bacteria, the wecA gene specifies the UDP-GlcNAc: undecaprenyl phosphate GlcNAc-1-phosphate transferase (WecA), which catalyzes the first step in the biosynthesis of lipopolysaccharide O-antigen. Mycobacterium tuberculosis Rv1302 and Mycobacterium smegmatis MSMEG_4947 show homology to Escherichia coli WecA protein. We cloned Rv1302 and MSMEG_4947 and introduced plasmids pYJ-1 (carrying Rv1302) and pYJ-2 (carrying MSMEG_4947) into a wecA-defective strain of E. coli MV501, respectively. Lipopolysaccharide analysis demonstrated that lipopolysaccharide synthesis in MV501 (pYJ-1) and MV501 (pYJ-2) was restored upon complementation with Rv1302 and MSMEG_4947, respectively. This provides the first evidence that Rv1302 and MSMEG_4947 have the same function as E. coli WecA. We also generated an M. smegmatis MSMEG_4947 knockout mutant using a homologous recombination strategy. The disruption of MSMEG_4947 in the M. smegmatis genome resulted in the loss of viability at a nonpermissive temperature. Scanning electron microscopy and transmission electron microscopy results showed that the lack of the MSMEG_4947 protein causes drastic morphological changes in M. smegmatis.","corpus_id":30888646,"score":0},{"doc_id":"20673833","title":"Structure of the RNA binding domain of a DEAD-box helicase bound to its ribosomal RNA target reveals a novel mode of recognition by an RNA recognition motif.","abstract":"DEAD-box RNA helicases of the bacterial DbpA subfamily are localized to their biological substrate when a carboxy-terminal RNA recognition motif domain binds tightly and specifically to a segment of 23S ribosomal RNA (rRNA) that includes hairpin 92 of the peptidyl transferase center. A complex between a fragment of 23S rRNA and the RNA binding domain (RBD) of the Bacillus subtilis DbpA protein YxiN was crystallized and its structure was determined to 2.9 A resolution, revealing an RNA recognition mode that differs from those observed with other RNA recognition motifs. The RBD is bound between two RNA strands at a three-way junction. Multiple phosphates of the RNA backbone interact with an electropositive band generated by lysines of the RBD. Nucleotides of the single-stranded loop of hairpin 92 interact with the RBD, including the guanosine base of G2553, which forms three hydrogen bonds with the peptide backbone. A G2553U mutation reduces the RNA binding affinity by 2 orders of magnitude, confirming that G2553 is a sequence specificity determinant in RNA binding. Binding of the RBD to 23S rRNA in the late stages of ribosome subunit maturation would position the ATP-binding duplex destabilization fragment of the protein for interaction with rRNA in the peptidyl transferase cleft of the subunit, allowing it to \"melt out\" unstable secondary structures and allow proper folding.","corpus_id":23325038,"score":0},{"doc_id":"21036780","title":"The PIN-domain ribonucleases and the prokaryotic VapBC toxin-antitoxin array.","abstract":"The PIN-domains are small proteins of ~130 amino acids that are found in bacteria, archaea and eukaryotes and are defined by a group of three strictly conserved acidic amino acids. The conserved three-dimensional structures of the PIN-domains cluster these acidic residues in an enzymatic active site. PIN-domains cleave single-stranded RNA in a sequence-specific, Mg²+- or Mn²+-dependent manner. These ribonucleases are toxic to the cells which express them and to offset this toxicity, they are co-expressed with tight binding protein inhibitors. The genes encoding these two proteins are adjacent in the genome of all prokaryotic organisms where they are found. This sequential arrangement of inhibitor-RNAse genes conforms to that of the so-called toxin-antitoxin (TA) modules and the PIN-domain TAs have been named VapBC TAs (virulence associated proteins, VapB is the inhibitor which contains a transcription factor domain and VapC is the PIN-domain ribonuclease). The presence of large numbers of vapBC loci in disparate prokaryotes has motivated many researchers to investigate their biochemical and biological functions. For example, the devastating human pathogen Mycobacterium tuberculosis has 45 vapBC loci encoded in its genome whereas its non-pathogenic relative, Mycobacterium smegmatis has just one vapBC operon. On another branch of the prokaryotic tree, the nitrogen-fixing symbiont of legumes, Sinorhizobium meliloti has 21 vapBC loci and at least one of these loci have been implicated in the regulation of growth in the plant nodule. A range of biological functions has been suggested for these operons and this review sets out to survey the PIN-domains and summarise the current knowledge about the vapBC TA systems and their roles in diverse bacteria.","corpus_id":27952561,"score":0},{"doc_id":"21575707","title":"The effect of MSMEG_6402 gene disruption on the cell wall structure of Mycobacterium smegmatis.","abstract":"Arabinogalactan (AG) of mycobacterial cell wall consists of arabinan region, galactan region and disaccharide linker. The arabinan is composed of D-arabinofuranose residues, and decaprenyphosphoryl-D-arabinose (DPA) is the donor of the D-arabinofuranose residues. DPA is formed from phosphoribose diphosphate (PRPP) in a four-step process catalyzed by transferase, phosphatase and epimerase, respectively. Mycobacterium tuberculosis Rv3806c has been identified as PRPP: decaprenyl-phosphate 5-phosphoribosyltransferase, and heteromeric Rv3790/Rv3791 has epimerase activity. Rv3807c is putative phospholipid phosphatase. However, there is no direct biochemical evidence since expression of Rv3807c has been unsuccessful. Mycobacterium smegmatis MSMEG_6402 is ortholog of Rv3807c. To investigate the function of MSMEG_6402 on AG biosynthesis, a conditional MSMEG_6402 gene knock out (M. sm-ΔM_6402) strain was constructed through homologous recombination technique. The morphological and compositional changes of cell wall were examined in the M. sm-ΔM_6402 strain. The M. sm-ΔM_6402 strain grew at non-permissive temperature slower than that at permissive temperature, indicating that MSMEG_6402 is non-essential for growth of M. smegmatis. The change of cell shape and detectable bulging on the cell surface of M. sm-ΔM_6402 strain were observed by scanning electron microscopy, and curled as well as deformed cell wall of M. sm-ΔM_6402 strain was revealed by transmission electron microscopy. Analysis of sugar composition in the cell wall by HPLC indicated that the ratio of arabinofuran to galactofuran in M. sm-ΔM_6402 strain was changed to 1.7:1 comparing with 2:1 in the wild type. It demonstrates that the lacking MSMEG_6402 interferes the biosynthesis of arabinan. Analyzing 5' P-DPR and DPR from both M. sm-ΔM_6402 strain and wild type M. smegmatis is undergoing in this lab.","corpus_id":21075993,"score":0},{"doc_id":"21887349","title":"Diversity in the architecture of ATLs, a family of plant ubiquitin-ligases, leads to recognition and targeting of substrates in different cellular environments.","abstract":"Ubiquitin-ligases or E3s are components of the ubiquitin proteasome system (UPS) that coordinate the transfer of ubiquitin to the target protein. A major class of ubiquitin-ligases consists of RING-finger domain proteins that include the substrate recognition sequences in the same polypeptide; these are known as single-subunit RING finger E3s. We are studying a particular family of RING finger E3s, named ATL, that contain a transmembrane domain and the RING-H2 finger domain; none of the member of the family contains any other previously described domain. Although the study of a few members in A. thaliana and O. sativa has been reported, the role of this family in the life cycle of a plant is still vague. To provide tools to advance on the functional analysis of this family we have undertaken a phylogenetic analysis of ATLs in twenty-four plant genomes. ATLs were found in all the 24 plant species analyzed, in numbers ranging from 20-28 in two basal species to 162 in soybean. Analysis of ATLs arrayed in tandem indicates that sets of genes are expanding in a species-specific manner. To get insights into the domain architecture of ATLs we generated 75 pHMM LOGOs from 1815 ATLs, and unraveled potential protein-protein interaction regions by means of yeast two-hybrid assays. Several ATLs were found to interact with DSK2a/ubiquilin through a region at the amino-terminal end, suggesting that this is a widespread interaction that may assist in the mode of action of ATLs; the region was traced to a distinct sequence LOGO. Our analysis provides significant observations on the evolution and expansion of the ATL family in addition to information on the domain structure of this class of ubiquitin-ligases that may be involved in plant adaptation to environmental stress.","corpus_id":848860,"score":0},{"doc_id":"22118811","title":"Unpairing and gating: sequence-independent substrate recognition by FEN superfamily nucleases.","abstract":"Structure-specific 5'-nucleases form a superfamily of evolutionarily conserved phosphodiesterases that catalyse a precise incision of a diverse range of DNA and RNA substrates in a sequence-independent manner. Superfamily members, such as flap endonucleases, exonuclease 1, DNA repair protein XPG, endonuclease GEN1 and the 5'-3'-exoribonucleases, play key roles in many cellular processes such as DNA replication and repair, recombination, transcription, RNA turnover and RNA interference. In this review, we discuss recent results that highlight the conserved architectures and active sites of the structure-specific 5'-nucleases. Despite substrate diversity, a common gating mechanism for sequence-independent substrate recognition and incision emerges, whereby double nucleotide unpairing of substrates is required to access the active site.","corpus_id":615647,"score":0},{"doc_id":"22136875","title":"Structural basis for promoter-10 element recognition by the bacterial RNA polymerase σ subunit.","abstract":"The key step in bacterial promoter opening is recognition of the -10 promoter element (T(-12)A(-11)T(-10)A(-9)A(-8)T(-7) consensus sequence) by the RNA polymerase σ subunit. We determined crystal structures of σ domain 2 bound to single-stranded DNA bearing-10 element sequences. Extensive interactions occur between the protein and the DNA backbone of every -10 element nucleotide. Base-specific interactions occur primarily with A(-11) and T(-7), which are flipped out of the single-stranded DNA base stack and buried deep in protein pockets. The structures, along with biochemical data, support a model where the recognition of the -10 element sequence drives initial promoter opening as the bases of the nontemplate strand are extruded from the DNA double-helix and captured by σ. These results provide a detailed structural basis for the critical roles of A(-11) and T(-7) in promoter melting and reveal important insights into the initiation of transcription bubble formation.","corpus_id":2328156,"score":0},{"doc_id":"22329974","title":"The CMG (CDC45/RecJ, MCM, GINS) complex is a conserved component of the DNA replication system in all archaea and eukaryotes.","abstract":"BACKGROUND: In eukaryotes, the CMG (CDC45, MCM, GINS) complex containing the replicative helicase MCM is a key player in DNA replication. Archaeal homologs of the eukaryotic MCM and GINS proteins have been identified but until recently no homolog of the CDC45 protein was known. Two recent developments, namely the discovery of archaeal GINS-associated nuclease (GAN) that belongs to the RecJ family of the DHH hydrolase superfamily and the demonstration of homology between the DHH domains of CDC45 and RecJ, show that at least some Archaea possess a full complement of homologs of the CMG complex subunits. Here we present the results of in-depth phylogenomic analysis of RecJ homologs in archaea. RESULTS: We confirm and extend the recent hypothesis that CDC45 is the eukaryotic ortholog of the bacterial and archaeal RecJ family nucleases. At least one RecJ homolog was identified in all sequenced archaeal genomes, with the single exception of Caldivirga maquilingensis. These proteins include previously unnoticed remote RecJ homologs with inactivated DHH domain in Thermoproteales. Combined with phylogenetic tree reconstruction of diverse eukaryotic, archaeal and bacterial DHH subfamilies, this analysis yields a complex scenario of RecJ family evolution in Archaea which includes independent inactivation of the nuclease domain in Crenarchaeota and Halobacteria, and loss of this domain in Methanococcales. CONCLUSIONS: The archaeal complex of a CDC45/RecJ homolog, MCM and GINS is homologous and most likely functionally analogous to the eukaryotic CMG complex, and appears to be a key component of the DNA replication machinery in all Archaea. It is inferred that the last common archaeo-eukaryotic ancestor encoded a CMG complex that contained an active nuclease of the RecJ family. The inactivated RecJ homologs in several archaeal lineages most likely are dedicated structural components of replication complexes.","corpus_id":343399,"score":0},{"doc_id":"22393399","title":"Myelin 2',3'-cyclic nucleotide 3'-phosphodiesterase: active-site ligand binding and molecular conformation.","abstract":"The 2',3'-cyclic nucleotide 3'-phosphodiesterase (CNPase) is a highly abundant membrane-associated enzyme in the myelin sheath of the vertebrate nervous system. CNPase is a member of the 2H phosphoesterase family and catalyzes the formation of 2'-nucleotide products from 2',3'-cyclic substrates; however, its physiological substrate and function remain unknown. It is likely that CNPase participates in RNA metabolism in the myelinating cell. We solved crystal structures of the phosphodiesterase domain of mouse CNPase, showing the binding mode of nucleotide ligands in the active site. The binding mode of the product 2'-AMP provides a detailed view of the reaction mechanism. Comparisons of CNPase crystal structures highlight flexible loops, which could play roles in substrate recognition; large differences in the active-site vicinity are observed when comparing more distant members of the 2H family. We also studied the full-length CNPase, showing its N-terminal domain is involved in RNA binding and dimerization. Our results provide a detailed picture of the CNPase active site during its catalytic cycle, and suggest a specific function for the previously uncharacterized N-terminal domain.","corpus_id":18014531,"score":0},{"doc_id":"22506030","title":"Functional characterization of EngA(MS), a P-loop GTPase of Mycobacterium smegmatis.","abstract":"Bacterial P-loop GTPases belong to a family of proteins that selectively hydrolyze a small molecule guanosine tri-phosphate (GTP) to guanosine di-phosphate (GDP) and inorganic phosphate, and regulate several essential cellular activities such as cell division, chromosomal segregation and ribosomal assembly. A comparative genome sequence analysis of different mycobacterial species indicates the presence of multiple P-loop GTPases that exhibit highly conserved motifs. However, an exact function of most of these GTPases in mycobacteria remains elusive. In the present study we characterized the function of a P-loop GTPase in mycobacteria by employing an EngA homologue from Mycobacterium smegmatis, encoded by an open reading frame, designated as MSMEG_3738. Amino acid sequence alignment and phylogenetic analysis suggest that MSMEG_3738 (termed as EngA(MS)) is highly conserved in mycobacteria. Homology modeling of EngA(MS) reveals a cloverleaf structure comprising of α/β fold typical to EngA family of GTPases. Recombinant EngA(MS) purified from E. coli exhibits a GTP hydrolysis activity which is inhibited by the presence of GDP. Interestingly, the EngA(MS) protein is co-eluted with 16S and 23S ribosomal RNA during purification and exhibits association with 30S, 50S and 70S ribosomal subunits. Further studies demonstrate that GTP is essential for interaction of EngA(MS) with 50S subunit of ribosome and specifically C-terminal domains of EngA(MS) are required to facilitate this interaction. Moreover, EngA(MS) devoid of N-terminal region interacts well with 50S even in the absence of GTP, indicating a regulatory role of the N-terminal domain in EngA(MS)-50S interaction.","corpus_id":10831390,"score":0},{"doc_id":"22590585","title":"MSMEG_2731, an uncharacterized nucleic acid binding protein from Mycobacterium smegmatis, physically interacts with RPS1.","abstract":"While the M. smegmatis genome has been sequenced, only a small portion of the genes have been characterized experimentally. Here, we purify and characterize MSMEG_2731, a conserved hypothetical alanine and arginine rich M. smegmatis protein. Using ultracentrifugation, we show that MSMEG_2731 is a monomer in vitro. MSMEG_2731 exists at a steady level throughout the M. smegmatis life-cycle. Combining results from pull-down techniques and LS-MS/MS, we show that MSMEG_2731 interacts with ribosomal protein S1. The existence of this interaction was confirmed by co-immunoprecipitation. We also show that MSMEG_2731 can bind ssDNA, dsDNA and RNA in vitro. Based on the interactions of MSMEG_2731 with RPS1 and RNA, we propose that MSMEG_2731 is involved in the transcription-translation process in vivo.","corpus_id":16929529,"score":0},{"doc_id":"22641846","title":"Mycobacterium smegmatis SftH exemplifies a distinctive clade of superfamily II DNA-dependent ATPases with 3' to 5' translocase and helicase activities.","abstract":"Bacterial DNA helicases are nucleic acid-dependent NTPases that play important roles in DNA replication, recombination and repair. We are interested in the DNA helicases of Mycobacteria, a genus of the phylum Actinobacteria, which includes the human pathogen Mycobacterium tuberculosis and its avirulent relative Mycobacterium smegmatis. Here, we identify and characterize M. smegmatis SftH, a superfamily II helicase with a distinctive domain structure, comprising an N-terminal NTPase domain and a C-terminal DUF1998 domain (containing a putative tetracysteine metal-binding motif). We show that SftH is a monomeric DNA-dependent ATPase/dATPase that translocates 3' to 5' on single-stranded DNA and has 3' to 5' helicase activity. SftH homologs are found in bacteria representing 12 different phyla, being especially prevalent in Actinobacteria (including M. tuberculosis). SftH homologs are evident in more than 30 genera of Archaea. Among eukarya, SftH homologs are present in plants and fungi.","corpus_id":1065928,"score":0},{"doc_id":"23549043","title":"Mycobacterium smegmatis Lhr Is a DNA-dependent ATPase and a 3'-to-5' DNA translocase and helicase that prefers to unwind 3'-tailed RNA:DNA hybrids.","abstract":"We are interested in the distinctive roster of helicases of Mycobacterium, a genus of the phylum Actinobacteria that includes the human pathogen Mycobacterium tuberculosis and its avirulent relative Mycobacterium smegmatis. Here, we identify and characterize M. smegmatis Lhr as the exemplar of a novel clade of superfamily II helicases, by virtue of its biochemical specificities and signature domain organization. Lhr is a 1507-amino acid monomeric nucleic acid-dependent ATPase that uses the energy of ATP hydrolysis to drive unidirectional 3'-to-5' translocation along single strand DNA and to unwind duplexes en route. The ATPase is more active in the presence of calcium than magnesium. ATP hydrolysis is triggered by either single strand DNA or single strand RNA, yet the apparent affinity for a DNA activator is 11-fold higher than for an RNA strand of identical size and nucleobase sequence. Lhr is 8-fold better at unwinding an RNA:DNA hybrid than it is at displacing a DNA:DNA duplex of identical nucleobase sequence. The truncated derivative Lhr-(1-856) is an autonomous ATPase, 3'-to-5' translocase, and RNA:DNA helicase. Lhr-(1-856) is 100-fold better RNA:DNA helicase than DNA:DNA helicase. Lhr homologs are found in bacteria representing eight different phyla, being especially prevalent in Actinobacteria (including M. tuberculosis) and Proteobacteria (including Escherichia coli).","corpus_id":27294611,"score":0},{"doc_id":"24115125","title":"Crystal structure of Mycobacterium tuberculosis CarD, an essential RNA polymerase binding protein, reveals a quasidomain-swapped dimeric structural architecture.","abstract":"Mycobacterium tuberculosis (Mtb) CarD is an essential transcriptional regulator that binds RNA polymerase and plays an important role in reprogramming transcription machinery under diverse stress conditions. Here, we report the crystal structure of CarD at 2.3 Å resolution, that represents the first structural description of CarD/CdnL-Like family of proteins. CarD adopts an overall bi-lobed structural architecture where N-terminal domain resembles 'tudor-like' domain and C-terminal domain adopts a novel five helical fold that lacks the predicted leucine zipper structural motif. The structure reveals dimeric state of CarD resulting from β-strand swapping between the N-terminal domains of each individual subunits. The structure provides crucial insights into the possible mode(s) of CarD/RNAP interactions.","corpus_id":40484432,"score":0},{"doc_id":"24479855","title":"Structural and kinetic studies on adenylosuccinate lyase from Mycobacterium smegmatis and Mycobacterium tuberculosis provide new insights on the catalytic residues of the enzyme.","abstract":"UNLABELLED: Adenylosuccinate lyase (ASL), an enzyme involved in purine biosynthesis, has been recognized as a drug target against microbial infections. In the present study, ASL from Mycobacterium smegmatis (MsASL) and Mycobacterium tuberculosis (MtbASL) were cloned, purified and crystallized. The X-ray crystal structure of MsASL was determined at a resolution of 2.16 Å. It is the first report of an apo-ASL structure with a partially ordered active site C3 loop. Diffracting crystals of MtbASL could not be obtained and a model for its structure was derived using MsASL as a template. These structures suggest that His149 and either Lys285 or Ser279 of MsASL are the residues most likely to function as the catalytic acid and base, respectively. Most of the active site residues were found to be conserved, with the exception of Ser148 and Gly319 of MsASL. Ser148 is structurally equivalent to a threonine in most other ASLs. Gly319 is replaced by an arginine residue in most ASLs. The two enzymes were catalytically much less active compared to ASLs from other organisms. Arg319Gly substitution and reduced flexibility of the C3 loop might account for the low catalytic activity of mycobacterial ASLs. The low activity is consistent with the slow growth rate of Mycobacteria and their high GC containing genomes, as well as their dependence on other salvage pathways for the supply of purine nucleotides. STRUCTURED DIGITAL ABSTRACT: purB and purB bind by x-ray crystallography (View interaction).","corpus_id":22778918,"score":0},{"doc_id":"24652708","title":"Functional analysis of serine acetyltransferase from Mycobacterium smegmatis.","abstract":"Serine acetyltransferase (CysE) is involved in L-cysteine biosynthesis in Mycobacterium, and it is important for the self-defense mechanism of the bacteria. Mycobacterium tuberculosis CysE (Rv2335) has been identified as a serine acetyltransferase, and it is orthologous to Mycobacterium smegmatis MSMEG_5947. In this study, the MSMEG_5947 gene was cloned, expressed, and identified as a serine acetyltransferase. To investigate the function of M. smegmatis CysE, a MSMEG_5947 knockout mutant strain (M. sm-ΔM_5947) was generated through homologous recombination. The growth and morphological characteristics of this strain were studied using growth curves and electron microscopy, respectively. M. sm-ΔM_5947 grew slower than M. smegmatis mc(2) 155. Electron microscopy revealed that the lack of the M. smegmatis CysE protein caused drastic morphological changes. Therefore, deletion of the serine acetyltransferase retards the growth of the Mycobacterium, but serine acetyltransferase expression is not essential for the survival of the bacteria.","corpus_id":3417383,"score":0},{"doc_id":"24813541","title":"Exploring protein domain organization by recognition of secondary structure packing interfaces.","abstract":"MOTIVATION: Protein domains are fundamental units of protein structure, function and evolution; thus, it is critical to gain a deep understanding of protein domain organization. Previous works have attempted to identify key residues involved in organization of domain architecture. Because one of the most important characteristics of domain architecture is the arrangement of secondary structure elements (SSEs), here we present a picture of domain organization through an integrated consideration of SSE arrangements and residue contact networks. RESULTS: In this work, by representing SSEs as main-chain scaffolds and side-chain interfaces and through construction of residue contact networks, we have identified the SSE interfaces well packed within protein domains as SSE packing clusters. In total, 17 334 SSE packing clusters were recognized from 9015 Structural Classification of Proteins domains of <40% sequence identity. The similar SSE packing clusters were observed not only among domains of the same folds, but also among domains of different folds, indicating their roles as common scaffolds for organization of protein domains. Further analysis of 14 small single-domain proteins reveals a high correlation between the SSE packing clusters and the folding nuclei. Consistent with their important roles in domain organization, SSE packing clusters were found to be more conserved than other regions within the same proteins. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.","corpus_id":17292430,"score":0},{"doc_id":"24825023","title":"Phylogenetic relationships and classification of thiolases and thiolase-like proteins of Mycobacterium tuberculosis and Mycobacterium smegmatis.","abstract":"Thiolases are enzymes involved in lipid metabolism. Thiolases remove the acetyl-CoA moiety from 3-ketoacyl-CoAs in the degradative reaction. They can also catalyze the reverse Claisen condensation reaction, which is the first step of biosynthetic processes such as the biosynthesis of sterols and ketone bodies. In human, six distinct thiolases have been identified. Each of these thiolases is different from the other with respect to sequence, oligomeric state, substrate specificity and subcellular localization. Four sequence fingerprints, identifying catalytic loops of thiolases, have been described. In this study genome searches of two mycobacterial species (Mycobacterium tuberculosis and Mycobacterium smegmatis), were carried out, using the six human thiolase sequences as queries. Eight and thirteen different thiolase sequences were identified in M. tuberculosis and M. smegmatis, respectively. In addition, thiolase-like proteins (one encoded in the Mtb and two in the Msm genome) were found. The purpose of this study is to classify these mostly uncharacterized thiolases and thiolase-like proteins. Several other sequences obtained by searches of genome databases of bacteria, mammals and the parasitic protist family of the Trypanosomatidae were included in the analysis. Thiolase-like proteins were also found in the trypanosomatid genomes, but not in those of mammals. In order to study the phylogenetic relationships at a high confidence level, additional thiolase sequences were included such that a total of 130 thiolases and thiolase-like protein sequences were used for the multiple sequence alignment. The resulting phylogenetic tree identifies 12 classes of sequences, each possessing a characteristic set of sequence fingerprints for the catalytic loops. From this analysis it is now possible to assign the mycobacterial thiolases to corresponding homologues in other kingdoms of life. The results of this bioinformatics analysis also show interesting differences between the distributions of M. tuberculosis and M. smegmatis thiolases over the 12 different classes.","corpus_id":19059427,"score":0},{"doc_id":"24970891","title":"The non-catalytic \"cap domain\" of a mycobacterial metallophosphoesterase regulates its expression and localization in the cell.","abstract":"Despite highly conserved core catalytic domains, members of the metallophosphoesterase (MPE) superfamily perform diverse and crucial functions ranging from nucleotide and nucleic acid metabolism to phospholipid hydrolysis. Unique structural elements outside of the catalytic core called \"cap domains\" are thought to provide specialization to these enzymes; however, no directed study has been performed to substantiate this. The cap domain of Rv0805, an MPE from Mycobacterium tuberculosis, is located C-terminal to its catalytic domain and is dispensable for the catalytic activity of this enzyme in vitro. We show here that this C-terminal extension (CTE) mediates in vivo localization of the protein to the cell membrane and cell wall as well as modulates expression levels of Rv0805 in mycobacteria. We also demonstrate that Rv0805 interacts with the cell wall of mycobacteria, possibly with the mycolyl-arabinogalactan-peptidoglycan complex, by virtue of its C terminus, a hitherto unknown property of this MPE. Using a panel of mutant proteins, we identify interactions between active site residues of Rv0805 and the CTE that determine its association with the cell wall. Finally, we show that Rv0805 and a truncated mutant devoid of the CTE produce different phenotypic effects when expressed in mycobacteria. Our study thus provides a detailed dissection of the functions of the cap domain of an MPE and suggests that the repertoire of cellular functions of MPEs cannot be understood without exploring the modulatory effects of these subdomains.","corpus_id":5224611,"score":0},{"doc_id":"25223716","title":"Functional identification of MSMEG_6402 protein from Mycobacterium smegmatis in decaprenylphosphoryl-D-arabinose biosynthesis.","abstract":"The arabinogalactan (AG) of the mycobacterial cell wall consists of an arabinan region, a galactan region and a disaccharide linker. Decaprenylphosphoryl-D-arabinose (DPA) is the donor for arabinofuran residues, which are formed from phosphoribose diphosphate (PRPP) and decaprenyl phosphate (DP). DP is sequentially catalyzed by a three-step process that involves a transferase, a phosphatase and an epimerase. Rv3807c is a putative phospholipid phosphatase that might generate the intermediate product of decaprenyl-phosphoryl-ribose (DPR) in DPA biosynthesis. Mycobacterium smegmatis MSMEG_6402 is a homolog gene of Mycobacterium tuberculosis Rv3807c and was substituted for the functional identification of Rv3807c. Previously, we generated a conditional MSMEG_6402 gene knockout strain (M. sm-ΔM_6402) that exhibited significantly affected cell wall structure. To understand the function of MSMEG_6402 in DPA biosynthesis, this gene was amplified and expressed, and the resulting protein was identified and purified using a His-tagged approach. A MSMEG_6402 enzymatic reaction system with PRPP and DP as substrates was utilized, and the reaction products were separated using thin layer chromatography (TLC). The results revealed a specific lipid-linked sugar band that appeared in the reaction with the addition of MSMEG_6402. Furthermore, ESI-MS detection was utilized in this study, and the results revealed that the enzymatic reaction products involving MSMEG_6402 included DPPR and a sodium ion adduct of DPR. Additionally, the phosphatase activity of MSMEG_6402 was also determined through phosphate group detection using the colorimetric method. Based on our results together with the results of previous studies, including the functional identification and bioinformatics analysis of M. tuberculosis Rv3807c, we propose that MSMEG_6402, as a phosphatase, has an intimate relationship with DPA biosynthesis.","corpus_id":21603495,"score":0},{"doc_id":"25434596","title":"Paralogous cAMP receptor proteins in Mycobacterium smegmatis show biochemical and functional divergence.","abstract":"The cyclic AMP receptor protein (CRP) family of transcription factors consists of global regulators of bacterial gene expression. Here, we identify two paralogous CRPs in the genome of Mycobacterium smegmatis that have 78% identical sequences and characterize them biochemically and functionally. The two proteins (MSMEG_0539 and MSMEG_6189) show differences in cAMP binding affinity, trypsin sensitivity, and binding to a CRP site that we have identified upstream of the msmeg_3781 gene. MSMEG_6189 binds to the CRP site readily in the absence of cAMP, while MSMEG_0539 binds in the presence of cAMP, albeit weakly. msmeg_6189 appears to be an essential gene, while the Δmsmeg_0539 strain was readily obtained. Using promoter-reporter constructs, we show that msmeg_3781 is regulated by CRP binding, and its transcription is repressed by MSMEG_6189. Our results are the first to characterize two paralogous and functional CRPs in a single bacterial genome. This gene duplication event has subsequently led to the evolution of two proteins whose biochemical differences translate to differential gene regulation, thus catering to the specific needs of the organism.","corpus_id":10233471,"score":0},{"doc_id":"25748880","title":"Critical determinants for substrate recognition and catalysis in the M. tuberculosis class II AP-endonuclease/3'-5' exonuclease III.","abstract":"The Mycobacterium tuberculosis AP-endonuclease/3'-5' exodeoxyribonuclease (MtbXthA) is an important player in DNA base excision repair (BER). We demonstrate that the enzyme has robust apurinic/apyrimidinic (AP) endonuclease activity, 3'-5' exonuclease, phosphatase, and phosphodiesterase activities. The enzyme functions as an AP-endonuclease at high ionic environments, while the 3'-5'-exonuclease activity is predominant at low ionic environments. Our molecular modelling and mutational experiments show that E57 and D251 are critical for catalysis. Although nicked DNA and gapped DNA are fair substrates of MtbXthA, the gap-size did not affect the excision activity and furthermore, a substrate with a recessed 3'-end is preferred. To understand the determinants of abasic-site recognition, we examined the possible roles of (i) the base opposite the abasic site, (ii) the abasic ribose ring itself, (iii) local distortions in the AP-site, and (iv) conserved residues located near the active site. Our experiments demonstrate that the first three determinants do not play a role in MtbXthA, and in fact the enzyme exhibits robust endonucleolytic activity against single-stranded AP DNA also. Regarding the fourth determinant, it is known that the catalytic-site of AP endonucleases is surrounded by conserved aromatic residues and intriguingly, the exact residues that are directly involved in abasic site recognition vary with the individual proteins. We therefore, used a combination of mutational analysis, kinetic assays, and structure-based modelling, to identify that Y237, supported by Y137, mediates the formation of the MtbXthA-AP-DNA complex and AP-site incision.","corpus_id":23265291,"score":0},{"doc_id":"25752134","title":"[A hemerythrin-like protein MSMEG_3312 influences erythromycin resistance in mycobacteria].","abstract":"OBJECTIVE: Reactive oxygen species are natural products of metabolism in aerobic organisms, which lead to oxidative damage, such as DNA mutation, protein inactivation and drug resistance. MSMEG_3312 was predicted as a hemerythrin-like protein, which can carry oxygen and reversibly bind to oxygen, thus it might play important roles in the process of oxygen metabolism. In this study, we explored the role of MSMEG_3312 in drug resistance. METHODS: On the basis of bioinformatics, we identified the conserved sequence of HHE domain in MSMEG_3312 and it was predicted to have typical α-helix at secondary structure. To explore potential functions of MSMEG_3312, we constructed the msmeg_3312 knockout strain and compare the susceptibility to various drugs to its parent strain, mc2155. In addition, we also measured the promoter response when treatment of erythromycin. RESULTS: Genetic results showed that MSMEG_3312 is not necessary for M. smegmatis growth at 7H9 rich medium. The msmeg_3312 knockout strain showed increased erythromycin resistance. Moreover, the drug resistance is only limited to erythromycin which its mechanism of action is by binding to the 50S subunit of the bacteria ribosomal complex and then inhibit protein synthesis. However, there were no different MICs of other antibiotics, targets for protein synthesis inhibition, but not 50S subunit, such as tetracyclines, aminoglycosides and chloramphenicol. Moreover, we also showed that the promoter of msmeg_3312 responses to erythromycin. CONCLUSIONS: Hemerythin-like protein MSMEG_3312 is involved in erythromycin resistance.","corpus_id":13587396,"score":0},{"doc_id":"25754266","title":"A new dehydratase conferring innate resistance to thiacetazone and intra-amoebal survival of Mycobacterium smegmatis.","abstract":"Nontuberculous mycobacteria are innately resistant to most antibiotics, although the mechanisms responsible for their drug resistance remain poorly understood. They are particularly refractory to thiacetazone (TAC), a second-line antitubercular drug. Herein, we identified MSMEG_6754 as essential for the innate resistance of Mycobacterium smegmatis to TAC. Transposon-mediated and targeted disruption of MSMEG_6754 resulted in hypersusceptibility to TAC. Conversely, introduction of MSMEG_6754 into Mycobacterium tuberculosis increased resistance 100-fold. Resolution of the crystal structure of MSMEG_6754 revealed a homodimer in which each monomer comprises two hot-dog domains characteristic of dehydratase-like proteins and very similar to the HadAB complex involved in mycolic acid biosynthesis. Gene inactivation of the essential hadB dehydratase could be achieved in M. smegmatis and M. tuberculosis only when the strains carried an integrated copy of MSMEG_6754, supporting the idea that MSMEG_6754 and HadB share redundant dehydratase activity. Using M. smegmatis-Acanthamoeba co-cultures, we found that intra-amoebal growth of the MSMEG_6754 deleted strain was significantly reduced compared with the parental strain. This in vivo growth defect was fully restored upon complementation with catalytically active MSMEG_6754 or HadABC, indicating that MSMEG_6754 plays a critical role in the survival of M. smegmatis within the environmental host.","corpus_id":39134990,"score":0},{"doc_id":"25986906","title":"Biochemical Characterization of Mycobacterium smegmatis RnhC (MSMEG_4305), a Bifunctional Enzyme Composed of Autonomous N-Terminal Type I RNase H and C-Terminal Acid Phosphatase Domains.","abstract":"UNLABELLED: Mycobacterium smegmatis encodes several DNA repair polymerases that are adept at incorporating ribonucleotides, which raises questions about how ribonucleotides in DNA are sensed and removed. RNase H enzymes, of which M. smegmatis encodes four, are strong candidates for a surveillance role. Here, we interrogate the biochemical activity and nucleic acid substrate specificity of M. smegmatis RnhC, a bifunctional RNase H and acid phosphatase. We report that (i) the RnhC nuclease is stringently specific for RNA:DNA hybrid duplexes; (ii) RnhC does not selectively recognize and cleave DNA-RNA or RNA-DNA junctions in duplex nucleic acid; (iii) RnhC cannot incise an embedded monoribonucleotide or diribonucleotide in duplex DNA; (iv) RnhC can incise tracts of 4 or more ribonucleotides embedded in duplex DNA, leaving two or more residual ribonucleotides at the cleaved 3'-OH end and at least one or two ribonucleotides on the 5'-PO4 end; (v) the RNase H activity is inherent in an autonomous 140-amino-acid (aa) N-terminal domain of RnhC; and (vi) the C-terminal 211-aa domain of RnhC is an autonomous acid phosphatase. The cleavage specificity of RnhC is clearly distinct from that of Escherichia coli RNase H2, which selectively incises at an RNA-DNA junction. Thus, we classify RnhC as a type I RNase H. The properties of RnhC are consistent with a role in Okazaki fragment RNA primer removal or in surveillance of oligoribonucleotide tracts embedded in DNA but not in excision repair of single misincorporated ribonucleotides. IMPORTANCE: RNase H enzymes help cleanse the genome of ribonucleotides that are present either as ribotracts (e.g., RNA primers) or as single ribonucleotides embedded in duplex DNA. Mycobacterium smegmatis encodes four RNase H proteins, including RnhC, which is characterized in this study. The nucleic acid substrate and cleavage site specificities of RnhC are consistent with a role in initiating the removal of ribotracts but not in single-ribonucleotide surveillance. RnhC has a C-terminal acid phosphatase domain that is functionally autonomous of its N-terminal RNase H catalytic domain. RnhC homologs are prevalent in Actinobacteria.","corpus_id":5174722,"score":0},{"doc_id":"25999286","title":"The mycobacterial PhoH2 proteins are type II toxin antitoxins coupled to RNA helicase domains.","abstract":"PhoH2 proteins are found in a diverse range of organisms that span the bacterial tree and little is known about this large protein family. PhoH2 proteins have two domains: An N-terminal PIN domain fused to a C-terminal PhoH domain. The genome of Mycobacterium tuberculosis encodes 48 PIN domains and 47 of these constitute the VapC components of the 47 VapBC toxin-antitoxins. The 48th member of the M. tuberculosis PIN domain array is found in the single PhoH2 protein encoded in the genome. All characterized PIN domain proteins are RNases and the PhoH domains are predicted ATPases. This fusion of a PIN domain with an ATPase reflects a much wider association between PIN domains and PhoH domains across many prokaryote genomes. Here, we examine PhoH2 proteins from M. tuberculosis, Mycobacterium smegmatis and a thermophilic homologue from Thermobispora bispora and we show that PhoH2 is a sequence-specific RNA helicase and RNAse. In addition, phoH2 from M. tuberculosis and M. smegmatis is part of a longer mRNA transcript which includes a small, unannotated open reading frame (ORF) upstream of the phoH2 gene. This small gene overlaps with the beginning of the phoH2 gene in a manner similar to the PIN domain toxin-antitoxin operons. We have annotated the upstream gene as phoAT and its putative promoter elements satisfy previously characterized consensus sequences at the -10 site. Conditional growth experiments carried out in M. smegmatis revealed a negative effect on growth by the expression of M. tuberculosis PhoH2 that was alleviated by co-expression of the PhoAT peptide. Thus in M. tuberculosis, PhoH2 represents a new variation on a type II PIN domain toxin-antitoxin systems such that the toxin-antitoxin is now coupled to an RNA helicase whose predicted biological function is to unwind and cleave RNA in a sequence specific manner.","corpus_id":10014412,"score":0},{"doc_id":"26375486","title":"Functional Characterization of Sirtuin-like Protein in Mycobacterium smegmatis.","abstract":"Nicotinamide adenine dinucleotide (NAD)-dependent deacetylases (sirtuins) are well conserved from prokaryotes to eukaryotes. Functions and regulations of mammalian sirtuins have been extensively studied and indicate that sirtuins play an important role in regulation of biological processes, whereas functions of mycobacterial sirtuins were less explored. To examine functions of the sirtuin-like protein in mycobacteria, a Mycobacterium smegmatis sirtuin, MSMEG_5175, was overexpressed in a M. smegmatis strain mc(2)155 to generate an MSMEG_5175-overexpression strain (mc(2)155-MS5175) in the present study. The physiological aspects of mc(2)155-MS5175 strain were characterized showing that they had a lower intracellular NAD level and a higher resistance to isoniazid (INH) as compared to mc(2)155 containing empty pMV261 plasmid (mc(2)155-pMV261). Quantitative proteomic analysis was carried out to determine differentially expressed proteins between mc(2)155-pMV261 and mc(2)155-MS5175. Among 3032 identified proteins, overexpression of MSMEG_5175 results in up-regulation of 34 proteins and down-regulation of 72 proteins, which involve in diverse cellular processes including metabolic activation, transcription and translation, antioxidant, and DNA repair. Down-regulation of catalase peroxidase (KatG) expression in both mRNA and protein levels were observed in mc(2)155-MS5175 strain, suggesting that a decrease in cellular NAD content and down-regulation of KatG expression contribute to the higher resistance to INH in mc(2)155-MS5175. Using a combination of immunoprecipitation and proteomic analysis, we found that acetylation in 27 proteins was decreased in mc(2)155-MS5175 as compared to those in mc(2)155-pMV261, suggesting that these proteins including the beta prime subunit of RNA polymerase (rpoC), ribosomal proteins, and metabolic enzymes were substrates of MSMEG_5175. Acetylation changes in rpoC may affect its function and cause changes in global gene transcription. Taken together, these results suggest that MSMEG_5175 regulates diverse cellular processes resulting in an increase in INH resistance in mycobacteria, and provide a useful resource to further biological exploration into functions of protein acetylation in mycobacteria.","corpus_id":30856459,"score":0},{"doc_id":"26627655","title":"Structural characterization of a mitochondrial 3-ketoacyl-CoA (T1)-like thiolase from Mycobacterium smegmatis.","abstract":"Thiolases catalyze the degradation and synthesis of 3-ketoacyl-CoA molecules. Here, the crystal structures of a T1-like thiolase (MSM-13 thiolase) from Mycobacterium smegmatis in apo and liganded forms are described. Systematic comparisons of six crystallographically independent unliganded MSM-13 thiolase tetramers (dimers of tight dimers) from three different crystal forms revealed that the two tight dimers are connected to a rigid tetramerization domain via flexible hinge regions, generating an asymmetric tetramer. In the liganded structure, CoA is bound to those subunits that are rotated towards the tip of the tetramerization loop of the opposing dimer, suggesting that this loop is important for substrate binding. The hinge regions responsible for this rotation occur near Val123 and Arg149. The Lα1-covering loop-Lα2 region, together with the Nβ2-Nα2 loop of the adjacent subunit, defines a specificity pocket that is larger and more polar than those of other tetrameric thiolases, suggesting that MSM-13 thiolase has a distinct substrate specificity. Consistent with this finding, only residual activity was detected with acetoacetyl-CoA as the substrate in the degradative direction. No activity was observed with acetyl-CoA in the synthetic direction. Structural comparisons with other well characterized thiolases suggest that MSM-13 thiolase is probably a degradative thiolase that is specific for 3-ketoacyl-CoA molecules with polar, bulky acyl chains.","corpus_id":44777818,"score":0},{"doc_id":"26685303","title":"A SIRT4-like auto ADP-ribosyltransferase is essential for the environmental growth of Mycobacterium smegmatis.","abstract":"SIRT family proteins are highly conserved both in the structure and function among all the organisms, and are involved in gene silencing, DNA damage repair, cell growth and metabolism. Here, a SIRT4 homologue MSMEG_4620 was identified and characterized in Mycobacterium smegmatis. MSMEG_4620 exhibits deacetylase activity that can be activated by fatty acids. Interestingly, MSMEG_4620 also possesses auto ADP-ribosylation activity. MSMEG_4620 is modified on arginine residues as revealed by a chemical stability assay. Moreover, the auto ADP-ribosylation activity of MSMEG_4620 was found to be enhanced by ferric ion. Notably, the SIRT4 homologues are widely distributed in the genomes of environmental mycobacterial species instead of pathogenic mycobacterial species. When MSMEG_4620 was deleted in M. smegmatis, the mutant strain showed a growth defect in 7H9 minimal medium compared with the parental strain. Taken together, these results provided the characteristics of a SIRT4 homologue in prokaryotes and implicated its critical roles in the growth of environmental mycobacterial species.","corpus_id":33813572,"score":0},{"doc_id":"26896801","title":"Substrate recognition and cleavage-site selection by a single-subunit protein-only RNase P.","abstract":"RNase P is the enzyme that removes 5' extensions from tRNA precursors. With its diversity of enzyme forms-either protein- or RNA-based, ranging from single polypeptides to multi-subunit ribonucleoproteins-the RNase P enzyme family represents a unique model system to compare the evolution of enzymatic mechanisms. Here we present a comprehensive study of substrate recognition and cleavage-site selection by the nuclear single-subunit proteinaceous RNase P PRORP3 from Arabidopsis thaliana. Compared to bacterial RNase P, the best-characterized RNA-based enzyme form, PRORP3 requires a larger part of intact tRNA structure, but little to no determinants at the cleavage site or interactions with the 5' or 3' extensions of the tRNA. The cleavage site depends on the combined dimensions of acceptor stem and T domain, but also requires the leader to be single-stranded. Overall, the single-subunit PRORP appears mechanistically more similar to the complex nuclear ribonucleoprotein enzymes than to the simpler bacterial RNase P. Mechanistic similarity or dissimilarity among different forms of RNase P thus apparently do not necessarily reflect molecular composition or evolutionary relationship.","corpus_id":18571153,"score":0},{"doc_id":"27653474","title":"Domain Organization in the 54-kDa Subunit of the Chloroplast Signal Recognition Particle.","abstract":"Chloroplast signal recognition particle (cpSRP) is a heterodimer composed of an evolutionarily conserved 54-kDa GTPase (cpSRP54) and a unique 43-kDa subunit (cpSRP43) responsible for delivering light-harvesting chlorophyll binding protein to the thylakoid membrane. While a nearly complete three-dimensional structure of cpSRP43 has been determined, no high-resolution structure is yet available for cpSRP54. In this study, we developed and examined an in silico three-dimensional model of the structure of cpSRP54 by homology modeling using cytosolic homologs. Model selection was guided by single-molecule Förster resonance energy transfer experiments, which revealed the presence of at least two distinct conformations. Small angle x-ray scattering showed that the linking region among the GTPase (G-domain) and methionine-rich (M-domain) domains, an M-domain loop, and the cpSRP43 binding C-terminal extension of cpSRP54 are predominantly disordered. Interestingly, the linker and loop segments were observed to play an important role in organizing the domain arrangement of cpSRP54. Further, deletion of the finger loop abolished loading of the cpSRP cargo, light-harvesting chlorophyll binding protein. These data highlight important structural dynamics relevant to cpSRP54's role in the post- and cotranslational signaling processes.","corpus_id":206304100,"score":0},{"doc_id":"28495884","title":"The uniqueness of subunit α of mycobacterial F-ATP synthases: An evolutionary variant for niche adaptation.","abstract":"The F1F0 -ATP (F-ATP) synthase is essential for growth of Mycobacterium tuberculosis, the causative agent of tuberculosis (TB). In addition to their synthase function most F-ATP synthases possess an ATP-hydrolase activity, which is coupled to proton-pumping activity. However, the mycobacterial enzyme lacks this reverse activity, but the reason for this deficiency is unclear. Here, we report that a Mycobacterium-specific, 36-amino acid long C-terminal domain in the nucleotide-binding subunit α (Mtα) of F-ATP synthase suppresses its ATPase activity and determined the mechanism of suppression. First, we employed vesicles to show that in intact membrane-embedded mycobacterial F-ATP synthases deletion of the C-terminal domain enabled ATPase and proton-pumping activity. We then generated a heterologous F-ATP synthase model system, which demonstrated that transfer of the mycobacterial C-terminal domain to a standard F-ATP synthase α subunit suppresses ATPase activity. Single-molecule rotation assays indicated that the introduction of this Mycobacterium-specific domain decreased the angular velocity of the power-stroke after ATP binding. Solution X-ray scattering data and NMR results revealed the solution shape of Mtα and the 3D structure of the subunit α C-terminal peptide (521)PDEHVEALDEDKLAKEAVKV(540) of M. tubercolosis (Mtα(521-540)), respectively. Together with cross-linking studies, the solution structural data lead to a model, in which Mtα(521-540) comes in close proximity with subunit γ residues 104-109, whose interaction may influence the rotation of the camshaft-like subunit γ. Finally, we propose that the unique segment Mtα(514-549), which is accessible at the C terminus of mycobacterial subunit α, is a promising drug epitope.","corpus_id":205365199,"score":0}],"string":"[\n {\n \"doc_id\": \"19553197\",\n \"title\": \"Degradation of nanoRNA is performed by multiple redundant RNases in Bacillus subtilis.\",\n \"abstract\": \"Escherichia coli possesses only one essential oligoribonuclease (Orn), an enzyme that can degrade oligoribonucleotides of five residues and shorter in length (nanoRNA). Firmicutes including Bacillus subtilis do not have an Orn homolog. We had previously identified YtqI (NrnA) as functional analog of Orn in B. subtilis. Screening a genomic library from B. subtilis for genes that can complement a conditional orn mutant, we identify here YngD (NrnB) as a second nanoRNase in B. subtilis. Like NrnA, NrnB is a member of the DHH/DHHA1 protein family of phosphoesterases. NrnB degrades nanoRNA 5-mers in vitro similarily to Orn. Low expression levels of NrnB are sufficient for orn complementation. YhaM, a known RNase present in B. subtilis, degrades nanoRNA efficiently in vitro but requires high levels of expression for only partial complementation of the orn(-) strain. A triple mutant (nrnA(-), nrnB(-), yhaM(-)) in B. subtilis is viable and shows almost no impairment in growth. Lastly, RNase J1 seems also to have some 5'-to-3' exoribonuclease activity on nanoRNA and thus can potentially finish degradation of RNA. We conclude that, unlike in E. coli, degradation of nanoRNA is performed in a redundant fashion in B. subtilis.\",\n \"corpus_id\": 3011249,\n \"score\": 2\n },\n {\n \"doc_id\": \"19901023\",\n \"title\": \"YybT is a signaling protein that contains a cyclic dinucleotide phosphodiesterase domain and a GGDEF domain with ATPase activity.\",\n \"abstract\": \"The cyclic dinucleotide c-di-AMP [corrected] synthesized by the diadenylate cyclase domain was discovered recently [corrected] as a messenger molecule for signaling DNA breaks in Bacillus subtilis. By searching bacterial genomes, we identified a family of DHH/DHHA1 domain proteins (COG3387) that co-occur with a subset of the diadenylate cyclase domain proteins. Here we report that the B. subtilis protein YybT, a member of the COG3387 family proteins, exhibits phosphodiesterase activity toward cyclic dinucleotides. The DHH/DHHA1 domain hydrolyzes c-di-AMP and c-di-GMP to generate the linear dinucleotides 5'-pApA and 5'-pGpG. The data suggest that c-di-AMP could be the physiological substrate for YybT given the physiologically relevant Michaelis-Menten constant (K(m)) and the presence of YybT family proteins in the bacteria lacking c-di-GMP signaling network. The bacterial regulator ppGpp was found to be a strong competitive inhibitor of the DHH/DHHA1 domain, suggesting that YybT is under tight control during stringent response. In addition, the atypical GGDEF domain of YybT exhibits unexpected ATPase activity, distinct from the common diguanylate cyclase activity for GGDEF domains. We further demonstrate the participation of YybT in DNA damage and acid resistance by characterizing the phenotypes of the DeltayybT mutant. The novel enzymatic activity and stress resistance together point toward a role for YybT in stress signaling and response.\",\n \"corpus_id\": 23848463,\n \"score\": 2\n },\n {\n \"doc_id\": \"20129927\",\n \"title\": \"Structure of RecJ exonuclease defines its specificity for single-stranded DNA.\",\n \"abstract\": \"RecJ is a single-stranded DNA (ssDNA)-specific 5'-3' exonuclease that plays an important role in DNA repair and recombination. To elucidate how RecJ achieves its high specificity for ssDNA, we determined the entire structures of RecJ both in a ligand-free form and in a complex with Mn(2+) or Mg(2+) by x-ray crystallography. The entire RecJ consists of four domains that form a molecule with an O-like structure. One of two newly identified domains had structural similarities to an oligonucleotide/oligosaccharide-binding (OB) fold. The OB fold domain alone could bind to DNA, indicating that this domain is a novel member of the OB fold superfamily. The truncated RecJ containing only the core domain exhibited much lower affinity for the ssDNA substrate compared with intact RecJ. These results support the hypothesis that these structural features allow specific binding of RecJ to ssDNA. In addition, the structure of the RecJ-Mn(2+) complex suggests that the hydrolysis reaction catalyzed by RecJ proceeds through a two-metal ion mechanism.\",\n \"corpus_id\": 41263393,\n \"score\": 2\n },\n {\n \"doc_id\": \"21087930\",\n \"title\": \"Role of RecJ-like protein with 5'-3' exonuclease activity in oligo(deoxy)nucleotide degradation.\",\n \"abstract\": \"RecJ-like proteins belonging to the DHH family have been proposed to function as oligoribonucleases and 3'-phosphoadenosine 5'-phosphate (pAp) phosphatases in bacteria and archaea, which do not have Orn (oligoribonuclease) and CysQ (pAp phosphatase) homologs. In this study, we analyzed the biochemical and physiological characterization of the RecJ-like protein TTHA0118 from Thermus thermophilus HB8. TTHA0118 had high enzymatic activity as an oligodeoxyribonucleotide- and oligoribonucleotide-specific exonuclease and as pAp phosphatase. The polarity of degradation was 5' to 3', in contrast to previous reports about Bacillus subtilis NrnA, a RecJ-like protein. TTHA0118 preferentially hydrolyzed short oligodeoxyribonucleotides and oligoribonucleotides, whereas the RecJ exonuclease from T. thermophilus HB8 showed no such length dependence on oligodeoxyribonucleotide substrates. An insertion mutation of the ttha0118 gene led to growth reduction in minimum essential medium. Added 5'-mononucleotides, nucleosides, and cysteine increased growth of the ttha0118 mutant in minimum essential medium. The RecJ-like protein Mpn140 from Mycoplasma pneumoniae M129, which cannot synthesize nucleic acid precursors de novo, showed similar biochemical features to TTHA0118. Furthermore, B. subtilis NrnA also hydrolyzed oligo(deoxy)ribonucleotides in a 5'-3' direction. These results suggested that these RecJ-like proteins act in recycling short oligonucleotides to mononucleotides and in controlling pAp concentrations in vivo.\",\n \"corpus_id\": 205304044,\n \"score\": 2\n },\n {\n \"doc_id\": \"22114320\",\n \"title\": \"Characterization of NrnA homologs from Mycobacterium tuberculosis and Mycoplasma pneumoniae.\",\n \"abstract\": \"Processive RNases are unable to degrade efficiently very short oligonucleotides, and they are complemented by specific enzymes, nanoRNases, that assist in this process. We previously identified NrnA (YtqI) from Bacillus subtilis as a bifunctional protein with the ability to degrade nanoRNA (RNA oligos ≤5 nucleotides) and to dephosphorylate 3'-phosphoadenosine 5'-phosphate (pAp) to AMP. While the former activity is analogous to that of oligoribonuclease (Orn) from Escherichia coli, the latter corresponds to CysQ. NrnA homologs are widely present in bacterial and archaeal genomes. They are found preferably in genomes that lack Orn or CysQ homologs. Here, we characterize NrnA homologs from important human pathogens, Mpn140 from Mycoplasma pneumoniae, and Rv2837c from Mycobacterium tuberculosis. Like NrnA, these enzymes degrade nanoRNA and dephosphorylate pAp in vitro. However, they show dissimilar preferences for specific nanoRNA substrate lengths. Whereas NrnA prefers RNA 3-mers with a 10-fold higher specific activity compared to 5-mers, Rv2837c shows a preference for nanoRNA of a different length, namely, 2-mers. Mpn140 degrades Cy5-labeled nanoRNA substrates in vitro with activities varying within one order of magnitude as follows: 5-mer>4-mer>3-mer>2-mer. In agreement with these in vitro activities, both Rv2837c and Mpn140 can complement the lack of their functional counterparts in E. coli: CysQ and Orn. The NrnA homolog from Streptococcus mutans, SMU.1297, was previously shown to hydrolyze pAp and to complement an E. coli cysQ mutant. Here, we show that SMU.1297 can complement an E. coli orn(-) mutant, suggesting that having both pAp-phosphatase and nanoRNase activity is a common feature of NrnA homologs.\",\n \"corpus_id\": 207216898,\n \"score\": 2\n },\n {\n \"doc_id\": \"22262096\",\n \"title\": \"Identification of a novel nanoRNase in Bartonella.\",\n \"abstract\": \"In Escherichia coli, only one essential oligoribonuclease (Orn) can degrade oligoribonucleotides of five residues and shorter in length (nanoRNA). In Bacillus subtilis, NrnA and NrnB, which do not show any sequence similarity to Orn, have been identified as functional analogues of Orn. Sequence comparisons did not identify orn, nrnA or nrnB homologues in the genomes of the Chlamydia/Cyanobacteria and Alphaproteobacteria family members. Screening a genomic library from Bartonella birtlesii, a member of the Alphaproteobacteria, for genes that can complement a conditional orn mutant in E. coli, we identified BA0969 (NrnC) as a functional analogue of Orn. NrnC is highly conserved (more than 80 % identity) in the Bartonella genomes sequenced to date. Biochemical characterization showed that this protein exhibits oligo RNA degradation activity (nanoRNase activity). Like Orn from E. coli, NrnC is inhibited by micromolar amounts of 3'-phosphoadenosine 5'-phosphate in vitro. NrnC homologues are widely present in genomes of Alphaproteobacteria. Knock down of nrnC decreases the growth ability of Bartonella henselae, demonstrating the importance of nanoRNase activity in this bacterium.\",\n \"corpus_id\": 32163321,\n \"score\": 2\n },\n {\n \"doc_id\": \"23851074\",\n \"title\": \"Crystal structure of the ligand-binding form of nanoRNase from Bacteroides fragilis, a member of the DHH/DHHA1 phosphoesterase family of proteins.\",\n \"abstract\": \"NanoRNase (Nrn) specifically degrades nucleoside 3',5'-bisphosphate and the very short RNA, nanoRNA, during the final step of mRNA degradation. The crystal structure of Nrn in complex with a reaction product GMP was determined. The overall structure consists of two domains that are interconnected by a flexible loop and form a cleft. Two Mn²⁺ ions are coordinated by conserved residues in the DHH motif of the N-terminal domain. GMP binds near the DHHA1 motif region in the C-terminal domain. Our structure enables us to predict the substrate-bound form of Nrn as well as other DHH/DHHA1 phosphoesterase family proteins.\",\n \"corpus_id\": 5312659,\n \"score\": 2\n },\n {\n \"doc_id\": \"26078723\",\n \"title\": \"Functional Analysis of a c-di-AMP-specific Phosphodiesterase MsPDE from Mycobacterium smegmatis.\",\n \"abstract\": \"Cyclic di‑AMP (c-di-AMP) is a second signaling molecule involved in the regulation of bacterial physiological processes and interaction between pathogen and host. However, the regulatory network mediated by c-di-AMP in Mycobacterium remains obscure. In M. smegmatis, a diadenylate cyclase (DAC) was reported recently, but there is still no investigation on c-di-AMP phosphodiesterase (PDE). Here, we provide a systematic study on signaling mechanism of c-di-AMP PDE in M. smegmatis. Based on our enzymatic analysis, MsPDE (MSMEG_2630), which contained a DHH-DHHA1 domain, displayed a 200-fold higher hydrolytic efficiency (kcat /Km ) to c-di-AMP than to c-di-GMP. MsPDE was capable of converting c-di-AMP to pApA and AMP, and hydrolyzing pApA to AMP. Site-directed mutations in DHH and DHHA1 revealed that DHH domain was critical for the phosphodiesterase activity. To explore the regulatory role of c-di-AMP in vivo, we constructed the mspde mutant (Δmspde) and found that deficiency of MsPDE significantly enhanced intracellular C12-C20 fatty acid accumulation. Deficiency of DAC in many bacteria results in cell death. However, we acquired the M. smegmatis strain with DAC gene disrupted (ΔmsdisA) by homologous recombination approach. Deletion of msdisA reduced bacterial C12-C20 fatty acids production but scarcely affected bacterial survival. We also provided evidences that superfluous c-di-AMP in M. smegmatis could lead to abnormal colonial morphology. Collectively, our results indicate that MsPDE is a functional c-di-AMP-specific phosphodiesterase both in vitro and in vivo. Our study also expands the regulatory network mediated by c-di-AMP in M. smegmatis.\",\n \"corpus_id\": 10487511,\n \"score\": 2\n },\n {\n \"doc_id\": \"26668313\",\n \"title\": \"Structural and Biochemical Insight into the Mechanism of Rv2837c from Mycobacterium tuberculosis as a C-di-NMP Phosphodiesterase.\",\n \"abstract\": \"The intracellular infections of Mycobacterium tuberculosis which is the causative agent of Tuberculosis (TB) are regulated by many cyclic di-nucleotide (c-di-NMP) signalling. Rv2837c from M. tuberculosis is a soluble, stand-alone DHH-DHHA1 domain phosphodiesterase that down-regulates c-di-AMP through catalytic degradation and plays an important role in M. tuberculosis infections. Here, we report the crystal structure of Rv2837c (2.0 Å), and its complex with hydrolysis intermediate 5'-pApA (2.35 Å). Our structures indicate both DHH and DHHA1 domains are essential for c-di-AMP degradation. Further structural analysis shows that Rv2837c does not distinguish adenine from guanine, which explains why Rv2837c hydrolyzes all linear di-nucleotides with almost the same efficiency. We observed that Rv2837c degraded other c-di-NMPs at a lower rate than it did on c-di-AMP. Nevertheless, our data also showed that Rv2837c significantly decreases concentrations of both c-di-AMP and c-di-GMP in vivo. Our results suggest that beside its major role in c-di-AMP degradation Rv2837c could also regulate c-di-GMP signaling pathways in bacterial cell.\",\n \"corpus_id\": -1,\n \"score\": 2\n },\n {\n \"doc_id\": \"28894100\",\n \"title\": \"Structural Basis for the Bidirectional Activity of Bacillus nanoRNase NrnA.\",\n \"abstract\": \"NanoRNAs are RNA fragments 2 to 5 nucleotides in length that are generated as byproducts of RNA degradation and abortive transcription initiation. Cells have specialized enzymes to degrade nanoRNAs, such as the DHH phosphoesterase family member NanoRNase A (NrnA). This enzyme was originally identified as a 3' → 5' exonuclease, but we show here that NrnA is bidirectional, degrading 2-5 nucleotide long RNA oligomers from the 3' end, and longer RNA substrates from the 5' end. The crystal structure of Bacillus subtilis NrnA reveals a dynamic bi-lobal architecture, with the catalytic N-terminal DHH domain linked to the substrate binding C-terminal DHHA1 domain via an extended linker. Whereas this arrangement is similar to the structure of RecJ, a 5' → 3' DHH family DNase and other DHH family nanoRNases, Bacillus NrnA has gained an extended substrate-binding patch that we posit is responsible for its 3' → 5' activity.\",\n \"corpus_id\": 19302627,\n \"score\": 2\n },\n {\n \"doc_id\": \"29107484\",\n \"title\": \"Structural and Biophysical Analysis of the Soluble DHH/DHHA1-Type Phosphodiesterase TM1595 from Thermotoga maritima.\",\n \"abstract\": \"The concentration of messenger molecules in bacterial cells needs to be tightly regulated. This can be achieved by either controlling the synthesis rate, degradation, or export by specific transporters, respectively. The regulation of the essential second messenger c-di-AMP is achieved by modulation of the diadenylate cyclase activity as well as by specific phosphodiesterases that hydrolyze c-di-AMP in the cell. We provide here structural and biochemical data on the DHH-type phosphodiesterase TmPDE (TM1595) from Thermotoga maritima. Our analysis shows that TmPDE is preferentially degrading linear dinucleotides, such as 5'-pApA, 5'-pGpG, and 5'-pApG, compared with cyclic dinucleotide substrates. The high-resolution structural data provided here describe all steps of the PDE reaction: the ligand-free enzyme, two substrate-bound states, and three post-reaction states. We can furthermore show that Pde2 from Streptococcus pneumoniae shares both structural features and substrate specificity based on small-angle X-ray scattering data and biochemical assays.\",\n \"corpus_id\": 34360580,\n \"score\": 2\n },\n {\n \"doc_id\": \"29203646\",\n \"title\": \"Structural and biochemical characterization of the catalytic domains of GdpP reveals a unified hydrolysis mechanism for the DHH/DHHA1 phosphodiesterase.\",\n \"abstract\": \"The Asp-His-His and Asp-His-His-associated (DHH/DHHA1) domain-containing phosphodiesterases (PDEs) that catalyze degradation of cyclic di-adenosine monophosphate (c-di-AMP) could be subdivided into two subfamilies based on the final product [5'-phosphadenylyl-adenosine (5'-pApA) or AMP]. In a previous study, we revealed that Rv2837c, a stand-alone DHH/DHHA1 PDE, employs a 5'-pApA internal flipping mechanism to produce AMPs. However, why the membrane-bound DHH/DHHA1 PDE can only degrade c-di-AMP to 5'-pApA remains obscure. Here, we report the crystal structure of the DHH/DHHA1 domain of GdpP (GdpP-C), and structures in complex with c-di-AMP, cyclic di-guanosine monophosphate (c-di-GMP), and 5'-pApA. Structural analysis reveals that GdpP-C binds nucleotide substrates quite differently from how Rv2837c does in terms of substrate-binding position. Accordingly, the nucleotide-binding site of the DHH/DHHA1 PDEs is organized into three (C, G, and R) subsites. For GdpP-C, in the C and G sites c-di-AMP binds and degrades into 5'-pApA, and its G site determines nucleotide specificity. To further degrade into AMPs, 5'-pApA must slide into the C and R sites for flipping and hydrolysis as in Rv2837c. Subsequent mutagenesis and enzymatic studies of GdpP-C and Rv2837c uncover the complete flipping process and reveal a unified catalytic mechanism for members of both DHH/DHHA1 PDE subfamilies.\",\n \"corpus_id\": 44924419,\n \"score\": 2\n },\n {\n \"doc_id\": \"29458847\",\n \"title\": \"The special existences: nanoRNA and nanoRNase.\",\n \"abstract\": \"To adapt to a wide range of nutritional and environmental changes, cells must adjust their gene expression profiles. This process is completed by the frequent transcription and rapid degradation of mRNA. mRNA decay is initiated by a series of endo- and exoribonucleases. These enzymes leave behind 2- to 5-nt-long oligoribonucleotides termed \\\"nanoRNAs\\\" that are degraded by specific nanoRNases; the degradation of nanoRNA is essential because nanoRNA can mediate the priming of transcription initiation that is harmful for the cell via an unknown mechanism. Identified nanoRNases include Orn in E. coli, NrnA and NrnB in B. subtilis, and NrnC in Bartonella. Even though these nanoRNases can degrade nanoRNA specifically into mononucleotides, the biochemical features, structural features and functional mechanisms of these enzymes are different. Sequence analysis has identified homologs of these nanoRNases in different bacteria, including Gammaproteobacteria, Betaproteobacteria, Alphaproteobacteria, Firmicutes and Cyanobacteria. However, there are several bacteria, such as those belonging to the class Thermolithobacteria, that do not have homologs of these nanoRNases. In this paper, the source of nanoRNA, the features of different kinds of nanoRNases and the distribution of these enzymes in prokaryotes are described in detail.\",\n \"corpus_id\": 3428188,\n \"score\": 2\n },\n {\n \"doc_id\": \"29609115\",\n \"title\": \"NanoRNase from Aeropyrum pernix shows nuclease activity on ssDNA and ssRNA.\",\n \"abstract\": \"In cells, degrading DNA and RNA by various nucleases is very important. These processes are strictly controlled and regulated to maintain DNA integrity and to mature or recycle various RNAs. NanoRNase (Nrn) is a 3'-exonuclease that specifically degrades nanoRNAs shorter than 5 nucleotides. Several Nrns have been identified and characterized in bacteria, mainly in Firmicutes. Archaea often grow in extreme environments and might be subjected to more damage to DNA/RNA, so DNA repair and recycling of damaged RNA are very important in archaea. There is no report on the identification and characterization of Nrn in archaea. Aeropyrum pernix encodes three potential Nrns: NrnA (Ape1437), NrnB (Ape0124), and an Nrn-like protein Ape2190. Biochemical characterization showed that only Ape0124 could degrade ssDNA and ssRNA from the 3'-end in the presence of Mn2+. Interestingly, unlike bacterial Nrns, Ape0124 prefers ssDNA, including short nanoDNA, and degrades nanoRNA with lower efficiency. The 3'-DNA backbone was found to be required for efficiently hydrolyzing the phosphodiester bonds. In addition, Ape0124 also degrads the 3'-overhang of double-stranded DNA. Interestingly, Ape0124 could hydrolyze pAp into AMP, which is a feature of bacterial NrnA, not NrnB. Our results indicate that Ape0124 is a novel Nrn with a combined substrate profile of bacterial NrnA and NrnB.\",\n \"corpus_id\": 5047026,\n \"score\": 2\n },\n {\n \"doc_id\": \"19094995\",\n \"title\": \"Orchestration of Haemophilus influenzae RecJ exonuclease by interaction with single-stranded DNA-binding protein.\",\n \"abstract\": \"RecJ exonuclease plays crucial roles in several DNA repair and recombination pathways, and its ubiquity in bacterial species points to its ancient origin and vital cellular function. RecJ exonuclease from Haemophilus influenzae is a 575-amino-acid protein that harbors the characteristic motifs conserved among RecJ homologs. The purified protein exhibits a processive 5'-3' single-stranded-DNA-specific exonuclease activity. The exonuclease activity of H. influenzae RecJ (HiRecJ) was supported by Mg(2+) or Mn(2+) and inhibited by Cd(2+), suggesting a different mode of metal binding in HiRecJ as compared to Escherichia coli RecJ (EcoRecJ). Site-directed mutagenesis of highly conserved residues in HiRecJ abolished enzymatic activity. Interestingly, substitution of alanine for aspartate 77 resulted in a catalytically inactive enzyme that bound to DNA with a significantly higher affinity as compared to the wild-type enzyme. Noticeably, steady-state kinetic studies showed that H. influenzae single-stranded DNA-binding protein (HiSSB) increased the affinity of HiRecJ for single-stranded DNA and stimulated its exonuclease activity. HiSSB, whose C-terminal tail had been deleted, failed to enhance RecJ exonuclease activity. More importantly, HiRecJ was found to directly associate with its cognate single-stranded DNA-binding protein (SSB), as demonstrated by various in vitro assays. Interaction studies carried out with the truncated variants of HiRecJ and HiSSB revealed that the two proteins interact via the C-terminus of SSB protein and the core-catalytic domain of RecJ. Taken together, these results emphasize direct interaction between RecJ and SSB, which confers functional cooperativity to these two proteins. In addition, these results implicate SSB as being involved in the recruitment of RecJ to DNA and provide insights into the interplay between these proteins in repair and recombination pathways.\",\n \"corpus_id\": 11311767,\n \"score\": 1\n },\n {\n \"doc_id\": \"19801656\",\n \"title\": \"A mycobacterial cyclic AMP phosphodiesterase that moonlights as a modifier of cell wall permeability.\",\n \"abstract\": \"Mycobacterium tuberculosis utilizes many mechanisms to establish itself within the macrophage, and bacterially derived cAMP is important in modulating the host cellular response. Although the genome of M. tuberculosis is endowed with a number of mammalian-like adenylyl cyclases, only a single cAMP phosphodiesterase has been identified that can decrease levels of cAMP produced by the bacterium. We present the crystal structure of the full-length and sole cAMP phosphodiesterase, Rv0805, found in M. tuberculosis, whose orthologs are present only in the genomes of slow growing and pathogenic mycobacteria. The dimeric core catalytic domain of Rv0805 adopts a metallophosphoesterase-fold, and the C-terminal region builds the active site and contributes to multiple substrate utilization. Localization of Rv0805 to the cell wall is dependent on its C terminus, and expression of either wild type or mutationally inactivated Rv0805 in M. smegmatis alters cell permeability to hydrophobic cytotoxic compounds. Rv0805 may therefore play a key role in the pathogenicity of mycobacteria, not only by hydrolyzing bacterial cAMP, but also by moonlighting as a protein that can alter cell wall functioning.\",\n \"corpus_id\": 12891246,\n \"score\": 1\n },\n {\n \"doc_id\": \"22055185\",\n \"title\": \"The structural basis for substrate recognition by mammalian polynucleotide kinase 3' phosphatase.\",\n \"abstract\": \"Mammalian polynucleotide kinase 3' phosphatase (PNK) plays a key role in the repair of DNA damage, functioning as part of both the nonhomologous end-joining (NHEJ) and base excision repair (BER) pathways. Through its two catalytic activities, PNK ensures that DNA termini are compatible with extension and ligation by either removing 3'-phosphates from, or by phosphorylating 5'-hydroxyl groups on, the ribose sugar of the DNA backbone. We have now determined crystal structures of murine PNK with DNA molecules bound to both of its active sites. The structure of ssDNA engaged with the 3'-phosphatase domain suggests a mechanism of substrate interaction that assists DNA end seeking. The structure of dsDNA bound to the 5'-kinase domain reveals a mechanism of DNA bending that facilitates recognition of DNA ends in the context of single-strand and double-strand breaks and suggests a close functional cooperation in substrate recognition between the kinase and phosphatase active sites.\",\n \"corpus_id\": 3002202,\n \"score\": 1\n },\n {\n \"doc_id\": \"22147708\",\n \"title\": \"Structural and functional insights into the DNA replication factor Cdc45 reveal an evolutionary relationship to the DHH family of phosphoesterases.\",\n \"abstract\": \"Cdc45 is an essential protein conserved in all eukaryotes and is involved both in the initiation of DNA replication and the progression of the replication fork. With GINS, Cdc45 is an essential cofactor of the Mcm2-7 replicative helicase complex. Despite its importance, no detailed information is available on either the structure or the biochemistry of the protein. Intriguingly, whereas homologues of both GINS and Mcm proteins have been described in Archaea, no counterpart for Cdc45 is known. Herein we report a bioinformatic analysis that shows a weak but significant relationship among eukaryotic Cdc45 proteins and a large family of phosphoesterases that has been described as the DHH family, including inorganic pyrophosphatases and RecJ ssDNA exonucleases. These enzymes catalyze the hydrolysis of phosphodiester bonds via a mechanism involving two Mn(2+) ions. Only a subset of the amino acids that coordinates Mn(2+) is conserved in Cdc45. We report biochemical and structural data on the recombinant human Cdc45 protein, consistent with the proposed DHH family affiliation. Like the RecJ exonucleases, the human Cdc45 protein is able to bind single-stranded, but not double-stranded DNA. Small angle x-ray scattering data are consistent with a model compatible with the crystallographic structure of the RecJ/DHH family members.\",\n \"corpus_id\": 13938433,\n \"score\": 1\n },\n {\n \"doc_id\": \"24261692\",\n \"title\": \"Site-directed mutagenesis maps interactions that enhance cognate and limit promiscuous catalysis by an alkaline phosphatase superfamily phosphodiesterase.\",\n \"abstract\": \"Catalytic promiscuity, an evolutionary concept, also provides a powerful tool for gaining mechanistic insights into enzymatic reactions. Members of the alkaline phosphatase (AP) superfamily are highly amenable to such investigation, with several members having been shown to exhibit promiscuous activity for the cognate reactions of other superfamily members. Previous work has shown that nucleotide pyrophosphatase/phosphodiesterase (NPP) exhibits a >10⁶-fold preference for the hydrolysis of phosphate diesters over phosphate monoesters, and that the reaction specificity is reduced 10³-fold when the size of the substituent on the transferred phosphoryl group of phosphate diester substrates is reduced to a methyl group. Here we show additional specificity contributions from the binding pocket for this substituent (herein termed the R' substituent) that account for an additional ~250-fold differential specificity with the minimal methyl substituent. Removal of four hydrophobic side chains suggested on the basis of structural inspection to interact favorably with R' substituents decreases phosphate diester reactivity 10⁴-fold with an optimal diester substrate (R' = 5'-deoxythymidine) and 50-fold with a minimal diester substrate (R' = CH₃). These mutations also enhance the enzyme's promiscuous phosphate monoesterase activity by nearly an order of magnitude, an effect that is traced by mutation to the reduction of unfavorable interactions with the two residues closest to the nonbridging phosphoryl oxygen atoms. The quadruple R' pocket mutant exhibits the same activity toward phosphate diester and phosphate monoester substrates that have identical leaving groups, with substantial rate enhancements of ~10¹¹-fold. This observation suggests that the Zn²⁺ bimetallo core of AP superfamily enzymes, which is equipotent in phosphate monoester and diester catalysis, has the potential to become specialized for the hydrolysis of each class of phosphate esters via addition of side chains that interact with the substrate atoms and substituents that project away from the Zn²⁺ bimetallo core.\",\n \"corpus_id\": 7543687,\n \"score\": 1\n },\n {\n \"doc_id\": \"26138487\",\n \"title\": \"Structural basis for substrate recognition and processive cleavage mechanisms of the trimeric exonuclease PhoExo I.\",\n \"abstract\": \"Nucleases play important roles in nucleic acid processes, such as replication, repair and recombination. Recently, we identified a novel single-strand specific 3'-5' exonuclease, PfuExo I, from the hyperthermophilic archaeon Pyrococcus furiosus, which may be involved in the Thermococcales-specific DNA repair system. PfuExo I forms a trimer and cleaves single-stranded DNA at every two nucleotides. Here, we report the structural basis for the cleavage mechanism of this novel exonuclease family. A structural analysis of PhoExo I, the homologous enzyme from P. horikoshii OT3, showed that PhoExo I utilizes an RNase H-like active site and possesses a 3'-OH recognition site ∼9 Å away from the active site, which enables cleavage at every two nucleotides. Analyses of the heterotrimeric and monomeric PhoExo I activities showed that trimerization is indispensable for its processive cleavage mechanism, but only one active site of the trimer is required.\",\n \"corpus_id\": 8052172,\n \"score\": 1\n },\n {\n \"doc_id\": \"26648913\",\n \"title\": \"A Novel C-Terminal Domain of RecJ is Critical for Interaction with HerA in Deinococcus radiodurans.\",\n \"abstract\": \"Homologous recombination (HR) generates error-free repair products, which plays an important role in double strand break repair and replication fork rescue processes. DNA end resection, the critical step in HR, is usually performed by a series of nuclease/helicase. RecJ was identified as a 5'-3' exonuclease involved in bacterial DNA end resection. Typical RecJ possesses a conserved DHH domain, a DHHA1 domain, and an oligonucleotide/oligosaccharide-binding (OB) fold. However, RecJs from Deinococcus-Thermus phylum, such as Deinococcus radiodurans RecJ (DrRecJ), possess an extra C-terminal domain (CTD), of which the function has not been characterized. Here, we showed that a CTD-deletion of DrRecJ (DrRecJΔC) could not restore drrecJ mutant growth and mitomycin C (MMC)-sensitive phenotypes, indicating that this domain is essential for DrRecJ in vivo. DrRecJΔC displayed reduced DNA nuclease activity and DNA binding ability. Direct interaction was identified between DrRecJ-CTD and DrHerA, which stimulates DrRecJ nuclease activity by enhancing its DNA binding affinity. Moreover, DrNurA nuclease, another partner of DrHerA, inhibited the stimulation of DrHerA on DrRecJ nuclease activity by interaction with DrHerA. Opposing growth and MMC-resistance phenotypes between the recJ and nurA mutants were observed. A novel modulation mechanism among DrRecJ, DrHerA, and DrNurA was also suggested.\",\n \"corpus_id\": 217284,\n \"score\": 1\n },\n {\n \"doc_id\": \"27058167\",\n \"title\": \"Structural basis for DNA 5´-end resection by RecJ.\",\n \"abstract\": \"The resection of DNA strand with a 5´ end at double-strand breaks is an essential step in recombinational DNA repair. RecJ, a member of DHH family proteins, is the only 5´ nuclease involved in the RecF recombination pathway. Here, we report the crystal structures of Deinococcus radiodurans RecJ in complex with deoxythymidine monophosphate (dTMP), ssDNA, the C-terminal region of single-stranded DNA-binding protein (SSB-Ct) and a mechanistic insight into the RecF pathway. A terminal 5´-phosphate-binding pocket above the active site determines the 5´-3´ polarity of the deoxy-exonuclease of RecJ; a helical gateway at the entrance to the active site admits ssDNA only; and the continuous stacking interactions between protein and nine nucleotides ensure the processive end resection. The active site of RecJ in the N-terminal domain contains two divalent cations that coordinate the nucleophilic water. The ssDNA makes a 180° turn at the scissile phosphate. The C-terminal domain of RecJ binds the SSB-Ct, which explains how RecJ and SSB work together to efficiently process broken DNA ends for homologous recombination.\",\n \"corpus_id\": -1,\n \"score\": 1\n },\n {\n \"doc_id\": \"28837073\",\n \"title\": \"Two Archaeal RecJ Nucleases from Methanocaldococcus jannaschii Show Reverse Hydrolysis Polarity: Implication to Their Unique Function in Archaea.\",\n \"abstract\": \"Bacterial nuclease RecJ, which exists in almost all bacterial species, specifically degrades single-stranded (ss) DNA in the 5' to 3' direction. Some archaeal phyla, except Crenarchaea, also encode RecJ homologs. Compared with bacterial RecJ, archaeal RecJ exhibits a largely different amino acid sequence and domain organization. Archaeal RecJs from Thermococcus kodakarensis and Pyrococcus furiosus show 5'→3' exonuclease activity on ssDNA. Interestingly, more than one RecJ exists in some Euryarchaeota classes, such as Methanomicrobia, Methanococci, Methanomicrobia, Methanobacteria, and Archaeoglobi. Here we report the biochemical characterization of two RecJs from Methanocaldococcus jannaschii, the long RecJ1 (MJ0977) and short RecJ2 (MJ0831) to understand their enzymatic properties. RecJ1 is a 5'→3' exonuclease with a preference to ssDNA; however, RecJ2 is a 3'→5' exonuclease with a preference to ssRNA. The 5' terminal phosphate promotes RecJ1 activity, but the 3' terminal phosphate inhibits RecJ2 nuclease. Go-Ichi-Ni-San (GINS) complex does not interact with two RecJs and does not promote their nuclease activities. Finally, we discuss the diversity, function, and molecular evolution of RecJ in archaeal taxonomy. Our analyses provide insight into the function and evolution of conserved archaeal RecJ/eukaryotic Cdc45 protein.\",\n \"corpus_id\": 11782396,\n \"score\": 1\n },\n {\n \"doc_id\": \"18374646\",\n \"title\": \"Structure of the active subunit of the yeast exosome core, Rrp44: diverse modes of substrate recruitment in the RNase II nuclease family.\",\n \"abstract\": \"The eukaryotic exosome is a macromolecular complex essential for RNA processing and decay. It has recently been shown that the RNase activity of the yeast exosome core can be mapped to a single subunit, Rrp44, which processively degrades single-stranded RNAs as well as RNAs containing secondary structures. Here we present the 2.3 A resolution crystal structure of S. cerevisiae Rrp44 in complex with single-stranded RNA. Although Rrp44 has a linear domain organization similar to bacterial RNase II, in three dimensions the domains have a different arrangement. The three domains of the classical nucleic-acid-binding OB fold are positioned on the catalytic domain such that the RNA-binding path observed in RNase II is occluded. Instead, RNA is threaded to the catalytic site via an alternative route suggesting a mechanism for RNA-duplex unwinding. The structure provides a molecular rationale for the observed biochemical properties of the RNase R family of nucleases.\",\n \"corpus_id\": 25938454,\n \"score\": 0\n },\n {\n \"doc_id\": \"19828435\",\n \"title\": \"Mechanism for the allosteric regulation of phosphodiesterase 2A deduced from the X-ray structure of a near full-length construct.\",\n \"abstract\": \"We report the X-ray crystal structure of a phosphodiesterase (PDE) that includes both catalytic and regulatory domains. PDE2A (215-900) crystallized as a dimer in which each subunit had an extended organization of regulatory GAF-A and GAF-B and catalytic domains connected by long alpha-helices. The subunits cross at the GAF-B/catalytic domain linker, and each side of the dimer contains in series the GAF-A and GAF-B of one subunit and the catalytic domain of the other subunit. A dimer interface extends over the entire length of the molecule. The substrate binding pocket of each catalytic domain is occluded by the H-loop. We deduced from comparisons with structures of isolated, ligand-bound catalytic subunits that the H-loop swings out to allow substrate access. However, in dimeric PDE2A (215-900), the H-loops of the two catalytic subunits pack against each other at the dimer interface, necessitating movement of the catalytic subunits to allow for H-loop movement. Comparison of the unliganded GAF-B of PDE2A (215-900) with previous structures of isolated, cGMP-bound GAF domains indicates that cGMP binding induces a significant shift in the GAF-B/catalytic domain linker. We propose that cGMP binding to GAF-B causes movement, through this linker region, of the catalytic domains, such that the H-loops no longer pack at the dimer interface and are, instead, free to swing out to allow substrate access. This increase in substrate access is proposed as the basis for PDE2A activation by cGMP and may be a general mechanism for regulation of all PDEs.\",\n \"corpus_id\": 22927729,\n \"score\": 0\n },\n {\n \"doc_id\": \"19836403\",\n \"title\": \"Crystal Structures of the histidine acid phosphatase from Francisella tularensis provide insight into substrate recognition.\",\n \"abstract\": \"Histidine acid phosphatases catalyze the transfer of a phosphoryl group from phosphomonoesters to water at acidic pH using an active-site histidine. The histidine acid phosphatase from the category A pathogen Francisella tularensis (FtHAP) has been implicated in intramacrophage survival and virulence, motivating interest in understanding the structure and mechanism of this enzyme. Here, we report a structure-based study of ligand recognition by FtHAP. The 1.70-A-resolution structure of FtHAP complexed with the competitive inhibitor l(+)-tartrate was solved using single-wavelength anomalous diffraction phasing. Structures of the ligand-free enzyme and the complex with inorganic phosphate were determined at resolutions of 1.85 and 1.70 A, respectively. The structure of the Asp261Ala mutant enzyme complexed with the substrate 3'-AMP was determined at 1.50 A resolution to gain insight into substrate recognition. FtHAP exhibits a two-domain fold similar to that of human prostatic acid phosphatase, consisting of an alpha/beta core domain and a smaller domain that caps the core domain. The structures show that the core domain supplies the phosphoryl binding site, catalytic histidine (His17), and an aspartic acid residue (Asp261) that protonates the leaving group, while the cap domain contributes residues that enforce substrate preference. FtHAP and human prostatic acid phosphatase differ in the orientation of the crucial first helix of the cap domain, implying differences in the substrate preferences of the two enzymes. 3'-AMP binds in one end of a 15-A-long tunnel, with the adenine clamped between Phe23 and Tyr135, and the ribose 2'-hydroxyl interacting with Gln132. The importance of the clamp is confirmed with site-directed mutagenesis; mutation of Phe23 and Tyr135 individually to Ala increases K(m) by factors of 7 and 10, respectively. The structural data are consistent with a role for FtHAP in scavenging phosphate from small molecules present in host macrophage cells.\",\n \"corpus_id\": 10190381,\n \"score\": 0\n },\n {\n \"doc_id\": \"20050614\",\n \"title\": \"Structural determinants of substrate recognition in the HAD superfamily member D-glycero-D-manno-heptose-1,7-bisphosphate phosphatase (GmhB) .\",\n \"abstract\": \"The haloalkanoic acid dehalogenase (HAD) enzyme superfamily is the largest family of phosphohydrolases. In HAD members, the structural elements that provide the binding interactions that support substrate specificity are separated from those that orchestrate catalysis. For most HAD phosphatases, a cap domain functions in substrate recognition. However, for the HAD phosphatases that lack a cap domain, an alternate strategy for substrate selection must be operative. One such HAD phosphatase, GmhB of the HisB subfamily, was selected for structure-function analysis. Herein, the X-ray crystallographic structures of Escherichia coli GmhB in the apo form (1.6 A resolution), in a complex with Mg(2+) and orthophosphate (1.8 A resolution), and in a complex with Mg(2+) and d-glycero-d-manno-heptose 1beta,7-bisphosphate (2.2 A resolution) were determined, in addition to the structure of Bordetella bronchiseptica GmhB bound to Mg(2+) and orthophosphate (1.7 A resolution). The structures show that in place of a cap domain, the GmhB catalytic site is elaborated by three peptide inserts or loops that pack to form a concave, semicircular surface around the substrate leaving group. Structure-guided kinetic analysis of site-directed mutants was conducted in parallel with a bioinformatics study of sequence diversification within the HisB subfamily to identify loop residues that serve as substrate recognition elements and that distinguish GmhB from its subfamily counterpart, the histidinol-phosphate phosphatase domain of HisB. We show that GmhB and the histidinol-phosphate phosphatase domain use the same design of three substrate recognition loops inserted into the cap domain yet, through selective residue usage on the loops, have achieved unique substrate specificity and thus novel biochemical function.\",\n \"corpus_id\": 5126557,\n \"score\": 0\n },\n {\n \"doc_id\": \"20363939\",\n \"title\": \"Structural and functional characterization of an RNase HI domain from the bifunctional protein Rv2228c from Mycobacterium tuberculosis.\",\n \"abstract\": \"The open reading frame Rv2228c from Mycobacterium tuberculosis is predicted to encode a protein composed of two domains, each with individual functions, annotated through sequence similarity searches. The N-terminal domain is homologous with prokaryotic and eukaryotic RNase H domains and the C-terminal domain with alpha-ribazole phosphatase (CobC). The N-terminal domain of Rv2228c (Rv2228c/N) and the full-length protein were expressed as fusions with maltose binding protein (MBP). Rv2228c/N was shown to have RNase H activity with a hybrid RNA/DNA substrate as well as double-stranded RNase activity. The full-length protein was shown to have additional CobC activity. The crystal structure of the MBP-Rv2228c/N fusion protein was solved by molecular replacement and refined at 2.25-A resolution (R = 0.182; R(free) = 0.238). The protein is monomeric in solution but associates in the crystal to form a dimer. The Rv2228c/N domain has the classic RNase H fold and catalytic machinery but lacks several surface features that play important roles in the cleavage of RNA/DNA hybrids by other RNases H. The absence of either the basic protrusion of some RNases H or the hybrid binding domain of others appears to be compensated by the C-terminal CobC domain in full-length Rv2228c. The double-stranded-RNase activity of Rv2228c/N contrasts with classical RNases H and is attributed to the absence in Rv2228c/N of a key phosphate binding pocket.\",\n \"corpus_id\": 22429245,\n \"score\": 0\n },\n {\n \"doc_id\": \"20637039\",\n \"title\": \"Mycobacterium tuberculosis Rv1302 and Mycobacterium smegmatis MSMEG_4947 have WecA function and MSMEG_4947 is required for the growth of M. smegmatis.\",\n \"abstract\": \"The disaccharide d-N-acetylglucosamine-l-rhamnose plays an important role in the mycobacterial cell wall as a linker connecting arabinogalactan and peptidoglycan via a phosphodiester linkage. The first step of the disaccharide linker is the formation of decaprenyl phosphate-GlcNAc, which is catalyzed by GlcNAc-1-phosphate transferase. In Gram-negative bacteria, the wecA gene specifies the UDP-GlcNAc: undecaprenyl phosphate GlcNAc-1-phosphate transferase (WecA), which catalyzes the first step in the biosynthesis of lipopolysaccharide O-antigen. Mycobacterium tuberculosis Rv1302 and Mycobacterium smegmatis MSMEG_4947 show homology to Escherichia coli WecA protein. We cloned Rv1302 and MSMEG_4947 and introduced plasmids pYJ-1 (carrying Rv1302) and pYJ-2 (carrying MSMEG_4947) into a wecA-defective strain of E. coli MV501, respectively. Lipopolysaccharide analysis demonstrated that lipopolysaccharide synthesis in MV501 (pYJ-1) and MV501 (pYJ-2) was restored upon complementation with Rv1302 and MSMEG_4947, respectively. This provides the first evidence that Rv1302 and MSMEG_4947 have the same function as E. coli WecA. We also generated an M. smegmatis MSMEG_4947 knockout mutant using a homologous recombination strategy. The disruption of MSMEG_4947 in the M. smegmatis genome resulted in the loss of viability at a nonpermissive temperature. Scanning electron microscopy and transmission electron microscopy results showed that the lack of the MSMEG_4947 protein causes drastic morphological changes in M. smegmatis.\",\n \"corpus_id\": 30888646,\n \"score\": 0\n },\n {\n \"doc_id\": \"20673833\",\n \"title\": \"Structure of the RNA binding domain of a DEAD-box helicase bound to its ribosomal RNA target reveals a novel mode of recognition by an RNA recognition motif.\",\n \"abstract\": \"DEAD-box RNA helicases of the bacterial DbpA subfamily are localized to their biological substrate when a carboxy-terminal RNA recognition motif domain binds tightly and specifically to a segment of 23S ribosomal RNA (rRNA) that includes hairpin 92 of the peptidyl transferase center. A complex between a fragment of 23S rRNA and the RNA binding domain (RBD) of the Bacillus subtilis DbpA protein YxiN was crystallized and its structure was determined to 2.9 A resolution, revealing an RNA recognition mode that differs from those observed with other RNA recognition motifs. The RBD is bound between two RNA strands at a three-way junction. Multiple phosphates of the RNA backbone interact with an electropositive band generated by lysines of the RBD. Nucleotides of the single-stranded loop of hairpin 92 interact with the RBD, including the guanosine base of G2553, which forms three hydrogen bonds with the peptide backbone. A G2553U mutation reduces the RNA binding affinity by 2 orders of magnitude, confirming that G2553 is a sequence specificity determinant in RNA binding. Binding of the RBD to 23S rRNA in the late stages of ribosome subunit maturation would position the ATP-binding duplex destabilization fragment of the protein for interaction with rRNA in the peptidyl transferase cleft of the subunit, allowing it to \\\"melt out\\\" unstable secondary structures and allow proper folding.\",\n \"corpus_id\": 23325038,\n \"score\": 0\n },\n {\n \"doc_id\": \"21036780\",\n \"title\": \"The PIN-domain ribonucleases and the prokaryotic VapBC toxin-antitoxin array.\",\n \"abstract\": \"The PIN-domains are small proteins of ~130 amino acids that are found in bacteria, archaea and eukaryotes and are defined by a group of three strictly conserved acidic amino acids. The conserved three-dimensional structures of the PIN-domains cluster these acidic residues in an enzymatic active site. PIN-domains cleave single-stranded RNA in a sequence-specific, Mg²+- or Mn²+-dependent manner. These ribonucleases are toxic to the cells which express them and to offset this toxicity, they are co-expressed with tight binding protein inhibitors. The genes encoding these two proteins are adjacent in the genome of all prokaryotic organisms where they are found. This sequential arrangement of inhibitor-RNAse genes conforms to that of the so-called toxin-antitoxin (TA) modules and the PIN-domain TAs have been named VapBC TAs (virulence associated proteins, VapB is the inhibitor which contains a transcription factor domain and VapC is the PIN-domain ribonuclease). The presence of large numbers of vapBC loci in disparate prokaryotes has motivated many researchers to investigate their biochemical and biological functions. For example, the devastating human pathogen Mycobacterium tuberculosis has 45 vapBC loci encoded in its genome whereas its non-pathogenic relative, Mycobacterium smegmatis has just one vapBC operon. On another branch of the prokaryotic tree, the nitrogen-fixing symbiont of legumes, Sinorhizobium meliloti has 21 vapBC loci and at least one of these loci have been implicated in the regulation of growth in the plant nodule. A range of biological functions has been suggested for these operons and this review sets out to survey the PIN-domains and summarise the current knowledge about the vapBC TA systems and their roles in diverse bacteria.\",\n \"corpus_id\": 27952561,\n \"score\": 0\n },\n {\n \"doc_id\": \"21575707\",\n \"title\": \"The effect of MSMEG_6402 gene disruption on the cell wall structure of Mycobacterium smegmatis.\",\n \"abstract\": \"Arabinogalactan (AG) of mycobacterial cell wall consists of arabinan region, galactan region and disaccharide linker. The arabinan is composed of D-arabinofuranose residues, and decaprenyphosphoryl-D-arabinose (DPA) is the donor of the D-arabinofuranose residues. DPA is formed from phosphoribose diphosphate (PRPP) in a four-step process catalyzed by transferase, phosphatase and epimerase, respectively. Mycobacterium tuberculosis Rv3806c has been identified as PRPP: decaprenyl-phosphate 5-phosphoribosyltransferase, and heteromeric Rv3790/Rv3791 has epimerase activity. Rv3807c is putative phospholipid phosphatase. However, there is no direct biochemical evidence since expression of Rv3807c has been unsuccessful. Mycobacterium smegmatis MSMEG_6402 is ortholog of Rv3807c. To investigate the function of MSMEG_6402 on AG biosynthesis, a conditional MSMEG_6402 gene knock out (M. sm-ΔM_6402) strain was constructed through homologous recombination technique. The morphological and compositional changes of cell wall were examined in the M. sm-ΔM_6402 strain. The M. sm-ΔM_6402 strain grew at non-permissive temperature slower than that at permissive temperature, indicating that MSMEG_6402 is non-essential for growth of M. smegmatis. The change of cell shape and detectable bulging on the cell surface of M. sm-ΔM_6402 strain were observed by scanning electron microscopy, and curled as well as deformed cell wall of M. sm-ΔM_6402 strain was revealed by transmission electron microscopy. Analysis of sugar composition in the cell wall by HPLC indicated that the ratio of arabinofuran to galactofuran in M. sm-ΔM_6402 strain was changed to 1.7:1 comparing with 2:1 in the wild type. It demonstrates that the lacking MSMEG_6402 interferes the biosynthesis of arabinan. Analyzing 5' P-DPR and DPR from both M. sm-ΔM_6402 strain and wild type M. smegmatis is undergoing in this lab.\",\n \"corpus_id\": 21075993,\n \"score\": 0\n },\n {\n \"doc_id\": \"21887349\",\n \"title\": \"Diversity in the architecture of ATLs, a family of plant ubiquitin-ligases, leads to recognition and targeting of substrates in different cellular environments.\",\n \"abstract\": \"Ubiquitin-ligases or E3s are components of the ubiquitin proteasome system (UPS) that coordinate the transfer of ubiquitin to the target protein. A major class of ubiquitin-ligases consists of RING-finger domain proteins that include the substrate recognition sequences in the same polypeptide; these are known as single-subunit RING finger E3s. We are studying a particular family of RING finger E3s, named ATL, that contain a transmembrane domain and the RING-H2 finger domain; none of the member of the family contains any other previously described domain. Although the study of a few members in A. thaliana and O. sativa has been reported, the role of this family in the life cycle of a plant is still vague. To provide tools to advance on the functional analysis of this family we have undertaken a phylogenetic analysis of ATLs in twenty-four plant genomes. ATLs were found in all the 24 plant species analyzed, in numbers ranging from 20-28 in two basal species to 162 in soybean. Analysis of ATLs arrayed in tandem indicates that sets of genes are expanding in a species-specific manner. To get insights into the domain architecture of ATLs we generated 75 pHMM LOGOs from 1815 ATLs, and unraveled potential protein-protein interaction regions by means of yeast two-hybrid assays. Several ATLs were found to interact with DSK2a/ubiquilin through a region at the amino-terminal end, suggesting that this is a widespread interaction that may assist in the mode of action of ATLs; the region was traced to a distinct sequence LOGO. Our analysis provides significant observations on the evolution and expansion of the ATL family in addition to information on the domain structure of this class of ubiquitin-ligases that may be involved in plant adaptation to environmental stress.\",\n \"corpus_id\": 848860,\n \"score\": 0\n },\n {\n \"doc_id\": \"22118811\",\n \"title\": \"Unpairing and gating: sequence-independent substrate recognition by FEN superfamily nucleases.\",\n \"abstract\": \"Structure-specific 5'-nucleases form a superfamily of evolutionarily conserved phosphodiesterases that catalyse a precise incision of a diverse range of DNA and RNA substrates in a sequence-independent manner. Superfamily members, such as flap endonucleases, exonuclease 1, DNA repair protein XPG, endonuclease GEN1 and the 5'-3'-exoribonucleases, play key roles in many cellular processes such as DNA replication and repair, recombination, transcription, RNA turnover and RNA interference. In this review, we discuss recent results that highlight the conserved architectures and active sites of the structure-specific 5'-nucleases. Despite substrate diversity, a common gating mechanism for sequence-independent substrate recognition and incision emerges, whereby double nucleotide unpairing of substrates is required to access the active site.\",\n \"corpus_id\": 615647,\n \"score\": 0\n },\n {\n \"doc_id\": \"22136875\",\n \"title\": \"Structural basis for promoter-10 element recognition by the bacterial RNA polymerase σ subunit.\",\n \"abstract\": \"The key step in bacterial promoter opening is recognition of the -10 promoter element (T(-12)A(-11)T(-10)A(-9)A(-8)T(-7) consensus sequence) by the RNA polymerase σ subunit. We determined crystal structures of σ domain 2 bound to single-stranded DNA bearing-10 element sequences. Extensive interactions occur between the protein and the DNA backbone of every -10 element nucleotide. Base-specific interactions occur primarily with A(-11) and T(-7), which are flipped out of the single-stranded DNA base stack and buried deep in protein pockets. The structures, along with biochemical data, support a model where the recognition of the -10 element sequence drives initial promoter opening as the bases of the nontemplate strand are extruded from the DNA double-helix and captured by σ. These results provide a detailed structural basis for the critical roles of A(-11) and T(-7) in promoter melting and reveal important insights into the initiation of transcription bubble formation.\",\n \"corpus_id\": 2328156,\n \"score\": 0\n },\n {\n \"doc_id\": \"22329974\",\n \"title\": \"The CMG (CDC45/RecJ, MCM, GINS) complex is a conserved component of the DNA replication system in all archaea and eukaryotes.\",\n \"abstract\": \"BACKGROUND: In eukaryotes, the CMG (CDC45, MCM, GINS) complex containing the replicative helicase MCM is a key player in DNA replication. Archaeal homologs of the eukaryotic MCM and GINS proteins have been identified but until recently no homolog of the CDC45 protein was known. Two recent developments, namely the discovery of archaeal GINS-associated nuclease (GAN) that belongs to the RecJ family of the DHH hydrolase superfamily and the demonstration of homology between the DHH domains of CDC45 and RecJ, show that at least some Archaea possess a full complement of homologs of the CMG complex subunits. Here we present the results of in-depth phylogenomic analysis of RecJ homologs in archaea. RESULTS: We confirm and extend the recent hypothesis that CDC45 is the eukaryotic ortholog of the bacterial and archaeal RecJ family nucleases. At least one RecJ homolog was identified in all sequenced archaeal genomes, with the single exception of Caldivirga maquilingensis. These proteins include previously unnoticed remote RecJ homologs with inactivated DHH domain in Thermoproteales. Combined with phylogenetic tree reconstruction of diverse eukaryotic, archaeal and bacterial DHH subfamilies, this analysis yields a complex scenario of RecJ family evolution in Archaea which includes independent inactivation of the nuclease domain in Crenarchaeota and Halobacteria, and loss of this domain in Methanococcales. CONCLUSIONS: The archaeal complex of a CDC45/RecJ homolog, MCM and GINS is homologous and most likely functionally analogous to the eukaryotic CMG complex, and appears to be a key component of the DNA replication machinery in all Archaea. It is inferred that the last common archaeo-eukaryotic ancestor encoded a CMG complex that contained an active nuclease of the RecJ family. The inactivated RecJ homologs in several archaeal lineages most likely are dedicated structural components of replication complexes.\",\n \"corpus_id\": 343399,\n \"score\": 0\n },\n {\n \"doc_id\": \"22393399\",\n \"title\": \"Myelin 2',3'-cyclic nucleotide 3'-phosphodiesterase: active-site ligand binding and molecular conformation.\",\n \"abstract\": \"The 2',3'-cyclic nucleotide 3'-phosphodiesterase (CNPase) is a highly abundant membrane-associated enzyme in the myelin sheath of the vertebrate nervous system. CNPase is a member of the 2H phosphoesterase family and catalyzes the formation of 2'-nucleotide products from 2',3'-cyclic substrates; however, its physiological substrate and function remain unknown. It is likely that CNPase participates in RNA metabolism in the myelinating cell. We solved crystal structures of the phosphodiesterase domain of mouse CNPase, showing the binding mode of nucleotide ligands in the active site. The binding mode of the product 2'-AMP provides a detailed view of the reaction mechanism. Comparisons of CNPase crystal structures highlight flexible loops, which could play roles in substrate recognition; large differences in the active-site vicinity are observed when comparing more distant members of the 2H family. We also studied the full-length CNPase, showing its N-terminal domain is involved in RNA binding and dimerization. Our results provide a detailed picture of the CNPase active site during its catalytic cycle, and suggest a specific function for the previously uncharacterized N-terminal domain.\",\n \"corpus_id\": 18014531,\n \"score\": 0\n },\n {\n \"doc_id\": \"22506030\",\n \"title\": \"Functional characterization of EngA(MS), a P-loop GTPase of Mycobacterium smegmatis.\",\n \"abstract\": \"Bacterial P-loop GTPases belong to a family of proteins that selectively hydrolyze a small molecule guanosine tri-phosphate (GTP) to guanosine di-phosphate (GDP) and inorganic phosphate, and regulate several essential cellular activities such as cell division, chromosomal segregation and ribosomal assembly. A comparative genome sequence analysis of different mycobacterial species indicates the presence of multiple P-loop GTPases that exhibit highly conserved motifs. However, an exact function of most of these GTPases in mycobacteria remains elusive. In the present study we characterized the function of a P-loop GTPase in mycobacteria by employing an EngA homologue from Mycobacterium smegmatis, encoded by an open reading frame, designated as MSMEG_3738. Amino acid sequence alignment and phylogenetic analysis suggest that MSMEG_3738 (termed as EngA(MS)) is highly conserved in mycobacteria. Homology modeling of EngA(MS) reveals a cloverleaf structure comprising of α/β fold typical to EngA family of GTPases. Recombinant EngA(MS) purified from E. coli exhibits a GTP hydrolysis activity which is inhibited by the presence of GDP. Interestingly, the EngA(MS) protein is co-eluted with 16S and 23S ribosomal RNA during purification and exhibits association with 30S, 50S and 70S ribosomal subunits. Further studies demonstrate that GTP is essential for interaction of EngA(MS) with 50S subunit of ribosome and specifically C-terminal domains of EngA(MS) are required to facilitate this interaction. Moreover, EngA(MS) devoid of N-terminal region interacts well with 50S even in the absence of GTP, indicating a regulatory role of the N-terminal domain in EngA(MS)-50S interaction.\",\n \"corpus_id\": 10831390,\n \"score\": 0\n },\n {\n \"doc_id\": \"22590585\",\n \"title\": \"MSMEG_2731, an uncharacterized nucleic acid binding protein from Mycobacterium smegmatis, physically interacts with RPS1.\",\n \"abstract\": \"While the M. smegmatis genome has been sequenced, only a small portion of the genes have been characterized experimentally. Here, we purify and characterize MSMEG_2731, a conserved hypothetical alanine and arginine rich M. smegmatis protein. Using ultracentrifugation, we show that MSMEG_2731 is a monomer in vitro. MSMEG_2731 exists at a steady level throughout the M. smegmatis life-cycle. Combining results from pull-down techniques and LS-MS/MS, we show that MSMEG_2731 interacts with ribosomal protein S1. The existence of this interaction was confirmed by co-immunoprecipitation. We also show that MSMEG_2731 can bind ssDNA, dsDNA and RNA in vitro. Based on the interactions of MSMEG_2731 with RPS1 and RNA, we propose that MSMEG_2731 is involved in the transcription-translation process in vivo.\",\n \"corpus_id\": 16929529,\n \"score\": 0\n },\n {\n \"doc_id\": \"22641846\",\n \"title\": \"Mycobacterium smegmatis SftH exemplifies a distinctive clade of superfamily II DNA-dependent ATPases with 3' to 5' translocase and helicase activities.\",\n \"abstract\": \"Bacterial DNA helicases are nucleic acid-dependent NTPases that play important roles in DNA replication, recombination and repair. We are interested in the DNA helicases of Mycobacteria, a genus of the phylum Actinobacteria, which includes the human pathogen Mycobacterium tuberculosis and its avirulent relative Mycobacterium smegmatis. Here, we identify and characterize M. smegmatis SftH, a superfamily II helicase with a distinctive domain structure, comprising an N-terminal NTPase domain and a C-terminal DUF1998 domain (containing a putative tetracysteine metal-binding motif). We show that SftH is a monomeric DNA-dependent ATPase/dATPase that translocates 3' to 5' on single-stranded DNA and has 3' to 5' helicase activity. SftH homologs are found in bacteria representing 12 different phyla, being especially prevalent in Actinobacteria (including M. tuberculosis). SftH homologs are evident in more than 30 genera of Archaea. Among eukarya, SftH homologs are present in plants and fungi.\",\n \"corpus_id\": 1065928,\n \"score\": 0\n },\n {\n \"doc_id\": \"23549043\",\n \"title\": \"Mycobacterium smegmatis Lhr Is a DNA-dependent ATPase and a 3'-to-5' DNA translocase and helicase that prefers to unwind 3'-tailed RNA:DNA hybrids.\",\n \"abstract\": \"We are interested in the distinctive roster of helicases of Mycobacterium, a genus of the phylum Actinobacteria that includes the human pathogen Mycobacterium tuberculosis and its avirulent relative Mycobacterium smegmatis. Here, we identify and characterize M. smegmatis Lhr as the exemplar of a novel clade of superfamily II helicases, by virtue of its biochemical specificities and signature domain organization. Lhr is a 1507-amino acid monomeric nucleic acid-dependent ATPase that uses the energy of ATP hydrolysis to drive unidirectional 3'-to-5' translocation along single strand DNA and to unwind duplexes en route. The ATPase is more active in the presence of calcium than magnesium. ATP hydrolysis is triggered by either single strand DNA or single strand RNA, yet the apparent affinity for a DNA activator is 11-fold higher than for an RNA strand of identical size and nucleobase sequence. Lhr is 8-fold better at unwinding an RNA:DNA hybrid than it is at displacing a DNA:DNA duplex of identical nucleobase sequence. The truncated derivative Lhr-(1-856) is an autonomous ATPase, 3'-to-5' translocase, and RNA:DNA helicase. Lhr-(1-856) is 100-fold better RNA:DNA helicase than DNA:DNA helicase. Lhr homologs are found in bacteria representing eight different phyla, being especially prevalent in Actinobacteria (including M. tuberculosis) and Proteobacteria (including Escherichia coli).\",\n \"corpus_id\": 27294611,\n \"score\": 0\n },\n {\n \"doc_id\": \"24115125\",\n \"title\": \"Crystal structure of Mycobacterium tuberculosis CarD, an essential RNA polymerase binding protein, reveals a quasidomain-swapped dimeric structural architecture.\",\n \"abstract\": \"Mycobacterium tuberculosis (Mtb) CarD is an essential transcriptional regulator that binds RNA polymerase and plays an important role in reprogramming transcription machinery under diverse stress conditions. Here, we report the crystal structure of CarD at 2.3 Å resolution, that represents the first structural description of CarD/CdnL-Like family of proteins. CarD adopts an overall bi-lobed structural architecture where N-terminal domain resembles 'tudor-like' domain and C-terminal domain adopts a novel five helical fold that lacks the predicted leucine zipper structural motif. The structure reveals dimeric state of CarD resulting from β-strand swapping between the N-terminal domains of each individual subunits. The structure provides crucial insights into the possible mode(s) of CarD/RNAP interactions.\",\n \"corpus_id\": 40484432,\n \"score\": 0\n },\n {\n \"doc_id\": \"24479855\",\n \"title\": \"Structural and kinetic studies on adenylosuccinate lyase from Mycobacterium smegmatis and Mycobacterium tuberculosis provide new insights on the catalytic residues of the enzyme.\",\n \"abstract\": \"UNLABELLED: Adenylosuccinate lyase (ASL), an enzyme involved in purine biosynthesis, has been recognized as a drug target against microbial infections. In the present study, ASL from Mycobacterium smegmatis (MsASL) and Mycobacterium tuberculosis (MtbASL) were cloned, purified and crystallized. The X-ray crystal structure of MsASL was determined at a resolution of 2.16 Å. It is the first report of an apo-ASL structure with a partially ordered active site C3 loop. Diffracting crystals of MtbASL could not be obtained and a model for its structure was derived using MsASL as a template. These structures suggest that His149 and either Lys285 or Ser279 of MsASL are the residues most likely to function as the catalytic acid and base, respectively. Most of the active site residues were found to be conserved, with the exception of Ser148 and Gly319 of MsASL. Ser148 is structurally equivalent to a threonine in most other ASLs. Gly319 is replaced by an arginine residue in most ASLs. The two enzymes were catalytically much less active compared to ASLs from other organisms. Arg319Gly substitution and reduced flexibility of the C3 loop might account for the low catalytic activity of mycobacterial ASLs. The low activity is consistent with the slow growth rate of Mycobacteria and their high GC containing genomes, as well as their dependence on other salvage pathways for the supply of purine nucleotides. STRUCTURED DIGITAL ABSTRACT: purB and purB bind by x-ray crystallography (View interaction).\",\n \"corpus_id\": 22778918,\n \"score\": 0\n },\n {\n \"doc_id\": \"24652708\",\n \"title\": \"Functional analysis of serine acetyltransferase from Mycobacterium smegmatis.\",\n \"abstract\": \"Serine acetyltransferase (CysE) is involved in L-cysteine biosynthesis in Mycobacterium, and it is important for the self-defense mechanism of the bacteria. Mycobacterium tuberculosis CysE (Rv2335) has been identified as a serine acetyltransferase, and it is orthologous to Mycobacterium smegmatis MSMEG_5947. In this study, the MSMEG_5947 gene was cloned, expressed, and identified as a serine acetyltransferase. To investigate the function of M. smegmatis CysE, a MSMEG_5947 knockout mutant strain (M. sm-ΔM_5947) was generated through homologous recombination. The growth and morphological characteristics of this strain were studied using growth curves and electron microscopy, respectively. M. sm-ΔM_5947 grew slower than M. smegmatis mc(2) 155. Electron microscopy revealed that the lack of the M. smegmatis CysE protein caused drastic morphological changes. Therefore, deletion of the serine acetyltransferase retards the growth of the Mycobacterium, but serine acetyltransferase expression is not essential for the survival of the bacteria.\",\n \"corpus_id\": 3417383,\n \"score\": 0\n },\n {\n \"doc_id\": \"24813541\",\n \"title\": \"Exploring protein domain organization by recognition of secondary structure packing interfaces.\",\n \"abstract\": \"MOTIVATION: Protein domains are fundamental units of protein structure, function and evolution; thus, it is critical to gain a deep understanding of protein domain organization. Previous works have attempted to identify key residues involved in organization of domain architecture. Because one of the most important characteristics of domain architecture is the arrangement of secondary structure elements (SSEs), here we present a picture of domain organization through an integrated consideration of SSE arrangements and residue contact networks. RESULTS: In this work, by representing SSEs as main-chain scaffolds and side-chain interfaces and through construction of residue contact networks, we have identified the SSE interfaces well packed within protein domains as SSE packing clusters. In total, 17 334 SSE packing clusters were recognized from 9015 Structural Classification of Proteins domains of <40% sequence identity. The similar SSE packing clusters were observed not only among domains of the same folds, but also among domains of different folds, indicating their roles as common scaffolds for organization of protein domains. Further analysis of 14 small single-domain proteins reveals a high correlation between the SSE packing clusters and the folding nuclei. Consistent with their important roles in domain organization, SSE packing clusters were found to be more conserved than other regions within the same proteins. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.\",\n \"corpus_id\": 17292430,\n \"score\": 0\n },\n {\n \"doc_id\": \"24825023\",\n \"title\": \"Phylogenetic relationships and classification of thiolases and thiolase-like proteins of Mycobacterium tuberculosis and Mycobacterium smegmatis.\",\n \"abstract\": \"Thiolases are enzymes involved in lipid metabolism. Thiolases remove the acetyl-CoA moiety from 3-ketoacyl-CoAs in the degradative reaction. They can also catalyze the reverse Claisen condensation reaction, which is the first step of biosynthetic processes such as the biosynthesis of sterols and ketone bodies. In human, six distinct thiolases have been identified. Each of these thiolases is different from the other with respect to sequence, oligomeric state, substrate specificity and subcellular localization. Four sequence fingerprints, identifying catalytic loops of thiolases, have been described. In this study genome searches of two mycobacterial species (Mycobacterium tuberculosis and Mycobacterium smegmatis), were carried out, using the six human thiolase sequences as queries. Eight and thirteen different thiolase sequences were identified in M. tuberculosis and M. smegmatis, respectively. In addition, thiolase-like proteins (one encoded in the Mtb and two in the Msm genome) were found. The purpose of this study is to classify these mostly uncharacterized thiolases and thiolase-like proteins. Several other sequences obtained by searches of genome databases of bacteria, mammals and the parasitic protist family of the Trypanosomatidae were included in the analysis. Thiolase-like proteins were also found in the trypanosomatid genomes, but not in those of mammals. In order to study the phylogenetic relationships at a high confidence level, additional thiolase sequences were included such that a total of 130 thiolases and thiolase-like protein sequences were used for the multiple sequence alignment. The resulting phylogenetic tree identifies 12 classes of sequences, each possessing a characteristic set of sequence fingerprints for the catalytic loops. From this analysis it is now possible to assign the mycobacterial thiolases to corresponding homologues in other kingdoms of life. The results of this bioinformatics analysis also show interesting differences between the distributions of M. tuberculosis and M. smegmatis thiolases over the 12 different classes.\",\n \"corpus_id\": 19059427,\n \"score\": 0\n },\n {\n \"doc_id\": \"24970891\",\n \"title\": \"The non-catalytic \\\"cap domain\\\" of a mycobacterial metallophosphoesterase regulates its expression and localization in the cell.\",\n \"abstract\": \"Despite highly conserved core catalytic domains, members of the metallophosphoesterase (MPE) superfamily perform diverse and crucial functions ranging from nucleotide and nucleic acid metabolism to phospholipid hydrolysis. Unique structural elements outside of the catalytic core called \\\"cap domains\\\" are thought to provide specialization to these enzymes; however, no directed study has been performed to substantiate this. The cap domain of Rv0805, an MPE from Mycobacterium tuberculosis, is located C-terminal to its catalytic domain and is dispensable for the catalytic activity of this enzyme in vitro. We show here that this C-terminal extension (CTE) mediates in vivo localization of the protein to the cell membrane and cell wall as well as modulates expression levels of Rv0805 in mycobacteria. We also demonstrate that Rv0805 interacts with the cell wall of mycobacteria, possibly with the mycolyl-arabinogalactan-peptidoglycan complex, by virtue of its C terminus, a hitherto unknown property of this MPE. Using a panel of mutant proteins, we identify interactions between active site residues of Rv0805 and the CTE that determine its association with the cell wall. Finally, we show that Rv0805 and a truncated mutant devoid of the CTE produce different phenotypic effects when expressed in mycobacteria. Our study thus provides a detailed dissection of the functions of the cap domain of an MPE and suggests that the repertoire of cellular functions of MPEs cannot be understood without exploring the modulatory effects of these subdomains.\",\n \"corpus_id\": 5224611,\n \"score\": 0\n },\n {\n \"doc_id\": \"25223716\",\n \"title\": \"Functional identification of MSMEG_6402 protein from Mycobacterium smegmatis in decaprenylphosphoryl-D-arabinose biosynthesis.\",\n \"abstract\": \"The arabinogalactan (AG) of the mycobacterial cell wall consists of an arabinan region, a galactan region and a disaccharide linker. Decaprenylphosphoryl-D-arabinose (DPA) is the donor for arabinofuran residues, which are formed from phosphoribose diphosphate (PRPP) and decaprenyl phosphate (DP). DP is sequentially catalyzed by a three-step process that involves a transferase, a phosphatase and an epimerase. Rv3807c is a putative phospholipid phosphatase that might generate the intermediate product of decaprenyl-phosphoryl-ribose (DPR) in DPA biosynthesis. Mycobacterium smegmatis MSMEG_6402 is a homolog gene of Mycobacterium tuberculosis Rv3807c and was substituted for the functional identification of Rv3807c. Previously, we generated a conditional MSMEG_6402 gene knockout strain (M. sm-ΔM_6402) that exhibited significantly affected cell wall structure. To understand the function of MSMEG_6402 in DPA biosynthesis, this gene was amplified and expressed, and the resulting protein was identified and purified using a His-tagged approach. A MSMEG_6402 enzymatic reaction system with PRPP and DP as substrates was utilized, and the reaction products were separated using thin layer chromatography (TLC). The results revealed a specific lipid-linked sugar band that appeared in the reaction with the addition of MSMEG_6402. Furthermore, ESI-MS detection was utilized in this study, and the results revealed that the enzymatic reaction products involving MSMEG_6402 included DPPR and a sodium ion adduct of DPR. Additionally, the phosphatase activity of MSMEG_6402 was also determined through phosphate group detection using the colorimetric method. Based on our results together with the results of previous studies, including the functional identification and bioinformatics analysis of M. tuberculosis Rv3807c, we propose that MSMEG_6402, as a phosphatase, has an intimate relationship with DPA biosynthesis.\",\n \"corpus_id\": 21603495,\n \"score\": 0\n },\n {\n \"doc_id\": \"25434596\",\n \"title\": \"Paralogous cAMP receptor proteins in Mycobacterium smegmatis show biochemical and functional divergence.\",\n \"abstract\": \"The cyclic AMP receptor protein (CRP) family of transcription factors consists of global regulators of bacterial gene expression. Here, we identify two paralogous CRPs in the genome of Mycobacterium smegmatis that have 78% identical sequences and characterize them biochemically and functionally. The two proteins (MSMEG_0539 and MSMEG_6189) show differences in cAMP binding affinity, trypsin sensitivity, and binding to a CRP site that we have identified upstream of the msmeg_3781 gene. MSMEG_6189 binds to the CRP site readily in the absence of cAMP, while MSMEG_0539 binds in the presence of cAMP, albeit weakly. msmeg_6189 appears to be an essential gene, while the Δmsmeg_0539 strain was readily obtained. Using promoter-reporter constructs, we show that msmeg_3781 is regulated by CRP binding, and its transcription is repressed by MSMEG_6189. Our results are the first to characterize two paralogous and functional CRPs in a single bacterial genome. This gene duplication event has subsequently led to the evolution of two proteins whose biochemical differences translate to differential gene regulation, thus catering to the specific needs of the organism.\",\n \"corpus_id\": 10233471,\n \"score\": 0\n },\n {\n \"doc_id\": \"25748880\",\n \"title\": \"Critical determinants for substrate recognition and catalysis in the M. tuberculosis class II AP-endonuclease/3'-5' exonuclease III.\",\n \"abstract\": \"The Mycobacterium tuberculosis AP-endonuclease/3'-5' exodeoxyribonuclease (MtbXthA) is an important player in DNA base excision repair (BER). We demonstrate that the enzyme has robust apurinic/apyrimidinic (AP) endonuclease activity, 3'-5' exonuclease, phosphatase, and phosphodiesterase activities. The enzyme functions as an AP-endonuclease at high ionic environments, while the 3'-5'-exonuclease activity is predominant at low ionic environments. Our molecular modelling and mutational experiments show that E57 and D251 are critical for catalysis. Although nicked DNA and gapped DNA are fair substrates of MtbXthA, the gap-size did not affect the excision activity and furthermore, a substrate with a recessed 3'-end is preferred. To understand the determinants of abasic-site recognition, we examined the possible roles of (i) the base opposite the abasic site, (ii) the abasic ribose ring itself, (iii) local distortions in the AP-site, and (iv) conserved residues located near the active site. Our experiments demonstrate that the first three determinants do not play a role in MtbXthA, and in fact the enzyme exhibits robust endonucleolytic activity against single-stranded AP DNA also. Regarding the fourth determinant, it is known that the catalytic-site of AP endonucleases is surrounded by conserved aromatic residues and intriguingly, the exact residues that are directly involved in abasic site recognition vary with the individual proteins. We therefore, used a combination of mutational analysis, kinetic assays, and structure-based modelling, to identify that Y237, supported by Y137, mediates the formation of the MtbXthA-AP-DNA complex and AP-site incision.\",\n \"corpus_id\": 23265291,\n \"score\": 0\n },\n {\n \"doc_id\": \"25752134\",\n \"title\": \"[A hemerythrin-like protein MSMEG_3312 influences erythromycin resistance in mycobacteria].\",\n \"abstract\": \"OBJECTIVE: Reactive oxygen species are natural products of metabolism in aerobic organisms, which lead to oxidative damage, such as DNA mutation, protein inactivation and drug resistance. MSMEG_3312 was predicted as a hemerythrin-like protein, which can carry oxygen and reversibly bind to oxygen, thus it might play important roles in the process of oxygen metabolism. In this study, we explored the role of MSMEG_3312 in drug resistance. METHODS: On the basis of bioinformatics, we identified the conserved sequence of HHE domain in MSMEG_3312 and it was predicted to have typical α-helix at secondary structure. To explore potential functions of MSMEG_3312, we constructed the msmeg_3312 knockout strain and compare the susceptibility to various drugs to its parent strain, mc2155. In addition, we also measured the promoter response when treatment of erythromycin. RESULTS: Genetic results showed that MSMEG_3312 is not necessary for M. smegmatis growth at 7H9 rich medium. The msmeg_3312 knockout strain showed increased erythromycin resistance. Moreover, the drug resistance is only limited to erythromycin which its mechanism of action is by binding to the 50S subunit of the bacteria ribosomal complex and then inhibit protein synthesis. However, there were no different MICs of other antibiotics, targets for protein synthesis inhibition, but not 50S subunit, such as tetracyclines, aminoglycosides and chloramphenicol. Moreover, we also showed that the promoter of msmeg_3312 responses to erythromycin. CONCLUSIONS: Hemerythin-like protein MSMEG_3312 is involved in erythromycin resistance.\",\n \"corpus_id\": 13587396,\n \"score\": 0\n },\n {\n \"doc_id\": \"25754266\",\n \"title\": \"A new dehydratase conferring innate resistance to thiacetazone and intra-amoebal survival of Mycobacterium smegmatis.\",\n \"abstract\": \"Nontuberculous mycobacteria are innately resistant to most antibiotics, although the mechanisms responsible for their drug resistance remain poorly understood. They are particularly refractory to thiacetazone (TAC), a second-line antitubercular drug. Herein, we identified MSMEG_6754 as essential for the innate resistance of Mycobacterium smegmatis to TAC. Transposon-mediated and targeted disruption of MSMEG_6754 resulted in hypersusceptibility to TAC. Conversely, introduction of MSMEG_6754 into Mycobacterium tuberculosis increased resistance 100-fold. Resolution of the crystal structure of MSMEG_6754 revealed a homodimer in which each monomer comprises two hot-dog domains characteristic of dehydratase-like proteins and very similar to the HadAB complex involved in mycolic acid biosynthesis. Gene inactivation of the essential hadB dehydratase could be achieved in M. smegmatis and M. tuberculosis only when the strains carried an integrated copy of MSMEG_6754, supporting the idea that MSMEG_6754 and HadB share redundant dehydratase activity. Using M. smegmatis-Acanthamoeba co-cultures, we found that intra-amoebal growth of the MSMEG_6754 deleted strain was significantly reduced compared with the parental strain. This in vivo growth defect was fully restored upon complementation with catalytically active MSMEG_6754 or HadABC, indicating that MSMEG_6754 plays a critical role in the survival of M. smegmatis within the environmental host.\",\n \"corpus_id\": 39134990,\n \"score\": 0\n },\n {\n \"doc_id\": \"25986906\",\n \"title\": \"Biochemical Characterization of Mycobacterium smegmatis RnhC (MSMEG_4305), a Bifunctional Enzyme Composed of Autonomous N-Terminal Type I RNase H and C-Terminal Acid Phosphatase Domains.\",\n \"abstract\": \"UNLABELLED: Mycobacterium smegmatis encodes several DNA repair polymerases that are adept at incorporating ribonucleotides, which raises questions about how ribonucleotides in DNA are sensed and removed. RNase H enzymes, of which M. smegmatis encodes four, are strong candidates for a surveillance role. Here, we interrogate the biochemical activity and nucleic acid substrate specificity of M. smegmatis RnhC, a bifunctional RNase H and acid phosphatase. We report that (i) the RnhC nuclease is stringently specific for RNA:DNA hybrid duplexes; (ii) RnhC does not selectively recognize and cleave DNA-RNA or RNA-DNA junctions in duplex nucleic acid; (iii) RnhC cannot incise an embedded monoribonucleotide or diribonucleotide in duplex DNA; (iv) RnhC can incise tracts of 4 or more ribonucleotides embedded in duplex DNA, leaving two or more residual ribonucleotides at the cleaved 3'-OH end and at least one or two ribonucleotides on the 5'-PO4 end; (v) the RNase H activity is inherent in an autonomous 140-amino-acid (aa) N-terminal domain of RnhC; and (vi) the C-terminal 211-aa domain of RnhC is an autonomous acid phosphatase. The cleavage specificity of RnhC is clearly distinct from that of Escherichia coli RNase H2, which selectively incises at an RNA-DNA junction. Thus, we classify RnhC as a type I RNase H. The properties of RnhC are consistent with a role in Okazaki fragment RNA primer removal or in surveillance of oligoribonucleotide tracts embedded in DNA but not in excision repair of single misincorporated ribonucleotides. IMPORTANCE: RNase H enzymes help cleanse the genome of ribonucleotides that are present either as ribotracts (e.g., RNA primers) or as single ribonucleotides embedded in duplex DNA. Mycobacterium smegmatis encodes four RNase H proteins, including RnhC, which is characterized in this study. The nucleic acid substrate and cleavage site specificities of RnhC are consistent with a role in initiating the removal of ribotracts but not in single-ribonucleotide surveillance. RnhC has a C-terminal acid phosphatase domain that is functionally autonomous of its N-terminal RNase H catalytic domain. RnhC homologs are prevalent in Actinobacteria.\",\n \"corpus_id\": 5174722,\n \"score\": 0\n },\n {\n \"doc_id\": \"25999286\",\n \"title\": \"The mycobacterial PhoH2 proteins are type II toxin antitoxins coupled to RNA helicase domains.\",\n \"abstract\": \"PhoH2 proteins are found in a diverse range of organisms that span the bacterial tree and little is known about this large protein family. PhoH2 proteins have two domains: An N-terminal PIN domain fused to a C-terminal PhoH domain. The genome of Mycobacterium tuberculosis encodes 48 PIN domains and 47 of these constitute the VapC components of the 47 VapBC toxin-antitoxins. The 48th member of the M. tuberculosis PIN domain array is found in the single PhoH2 protein encoded in the genome. All characterized PIN domain proteins are RNases and the PhoH domains are predicted ATPases. This fusion of a PIN domain with an ATPase reflects a much wider association between PIN domains and PhoH domains across many prokaryote genomes. Here, we examine PhoH2 proteins from M. tuberculosis, Mycobacterium smegmatis and a thermophilic homologue from Thermobispora bispora and we show that PhoH2 is a sequence-specific RNA helicase and RNAse. In addition, phoH2 from M. tuberculosis and M. smegmatis is part of a longer mRNA transcript which includes a small, unannotated open reading frame (ORF) upstream of the phoH2 gene. This small gene overlaps with the beginning of the phoH2 gene in a manner similar to the PIN domain toxin-antitoxin operons. We have annotated the upstream gene as phoAT and its putative promoter elements satisfy previously characterized consensus sequences at the -10 site. Conditional growth experiments carried out in M. smegmatis revealed a negative effect on growth by the expression of M. tuberculosis PhoH2 that was alleviated by co-expression of the PhoAT peptide. Thus in M. tuberculosis, PhoH2 represents a new variation on a type II PIN domain toxin-antitoxin systems such that the toxin-antitoxin is now coupled to an RNA helicase whose predicted biological function is to unwind and cleave RNA in a sequence specific manner.\",\n \"corpus_id\": 10014412,\n \"score\": 0\n },\n {\n \"doc_id\": \"26375486\",\n \"title\": \"Functional Characterization of Sirtuin-like Protein in Mycobacterium smegmatis.\",\n \"abstract\": \"Nicotinamide adenine dinucleotide (NAD)-dependent deacetylases (sirtuins) are well conserved from prokaryotes to eukaryotes. Functions and regulations of mammalian sirtuins have been extensively studied and indicate that sirtuins play an important role in regulation of biological processes, whereas functions of mycobacterial sirtuins were less explored. To examine functions of the sirtuin-like protein in mycobacteria, a Mycobacterium smegmatis sirtuin, MSMEG_5175, was overexpressed in a M. smegmatis strain mc(2)155 to generate an MSMEG_5175-overexpression strain (mc(2)155-MS5175) in the present study. The physiological aspects of mc(2)155-MS5175 strain were characterized showing that they had a lower intracellular NAD level and a higher resistance to isoniazid (INH) as compared to mc(2)155 containing empty pMV261 plasmid (mc(2)155-pMV261). Quantitative proteomic analysis was carried out to determine differentially expressed proteins between mc(2)155-pMV261 and mc(2)155-MS5175. Among 3032 identified proteins, overexpression of MSMEG_5175 results in up-regulation of 34 proteins and down-regulation of 72 proteins, which involve in diverse cellular processes including metabolic activation, transcription and translation, antioxidant, and DNA repair. Down-regulation of catalase peroxidase (KatG) expression in both mRNA and protein levels were observed in mc(2)155-MS5175 strain, suggesting that a decrease in cellular NAD content and down-regulation of KatG expression contribute to the higher resistance to INH in mc(2)155-MS5175. Using a combination of immunoprecipitation and proteomic analysis, we found that acetylation in 27 proteins was decreased in mc(2)155-MS5175 as compared to those in mc(2)155-pMV261, suggesting that these proteins including the beta prime subunit of RNA polymerase (rpoC), ribosomal proteins, and metabolic enzymes were substrates of MSMEG_5175. Acetylation changes in rpoC may affect its function and cause changes in global gene transcription. Taken together, these results suggest that MSMEG_5175 regulates diverse cellular processes resulting in an increase in INH resistance in mycobacteria, and provide a useful resource to further biological exploration into functions of protein acetylation in mycobacteria.\",\n \"corpus_id\": 30856459,\n \"score\": 0\n },\n {\n \"doc_id\": \"26627655\",\n \"title\": \"Structural characterization of a mitochondrial 3-ketoacyl-CoA (T1)-like thiolase from Mycobacterium smegmatis.\",\n \"abstract\": \"Thiolases catalyze the degradation and synthesis of 3-ketoacyl-CoA molecules. Here, the crystal structures of a T1-like thiolase (MSM-13 thiolase) from Mycobacterium smegmatis in apo and liganded forms are described. Systematic comparisons of six crystallographically independent unliganded MSM-13 thiolase tetramers (dimers of tight dimers) from three different crystal forms revealed that the two tight dimers are connected to a rigid tetramerization domain via flexible hinge regions, generating an asymmetric tetramer. In the liganded structure, CoA is bound to those subunits that are rotated towards the tip of the tetramerization loop of the opposing dimer, suggesting that this loop is important for substrate binding. The hinge regions responsible for this rotation occur near Val123 and Arg149. The Lα1-covering loop-Lα2 region, together with the Nβ2-Nα2 loop of the adjacent subunit, defines a specificity pocket that is larger and more polar than those of other tetrameric thiolases, suggesting that MSM-13 thiolase has a distinct substrate specificity. Consistent with this finding, only residual activity was detected with acetoacetyl-CoA as the substrate in the degradative direction. No activity was observed with acetyl-CoA in the synthetic direction. Structural comparisons with other well characterized thiolases suggest that MSM-13 thiolase is probably a degradative thiolase that is specific for 3-ketoacyl-CoA molecules with polar, bulky acyl chains.\",\n \"corpus_id\": 44777818,\n \"score\": 0\n },\n {\n \"doc_id\": \"26685303\",\n \"title\": \"A SIRT4-like auto ADP-ribosyltransferase is essential for the environmental growth of Mycobacterium smegmatis.\",\n \"abstract\": \"SIRT family proteins are highly conserved both in the structure and function among all the organisms, and are involved in gene silencing, DNA damage repair, cell growth and metabolism. Here, a SIRT4 homologue MSMEG_4620 was identified and characterized in Mycobacterium smegmatis. MSMEG_4620 exhibits deacetylase activity that can be activated by fatty acids. Interestingly, MSMEG_4620 also possesses auto ADP-ribosylation activity. MSMEG_4620 is modified on arginine residues as revealed by a chemical stability assay. Moreover, the auto ADP-ribosylation activity of MSMEG_4620 was found to be enhanced by ferric ion. Notably, the SIRT4 homologues are widely distributed in the genomes of environmental mycobacterial species instead of pathogenic mycobacterial species. When MSMEG_4620 was deleted in M. smegmatis, the mutant strain showed a growth defect in 7H9 minimal medium compared with the parental strain. Taken together, these results provided the characteristics of a SIRT4 homologue in prokaryotes and implicated its critical roles in the growth of environmental mycobacterial species.\",\n \"corpus_id\": 33813572,\n \"score\": 0\n },\n {\n \"doc_id\": \"26896801\",\n \"title\": \"Substrate recognition and cleavage-site selection by a single-subunit protein-only RNase P.\",\n \"abstract\": \"RNase P is the enzyme that removes 5' extensions from tRNA precursors. With its diversity of enzyme forms-either protein- or RNA-based, ranging from single polypeptides to multi-subunit ribonucleoproteins-the RNase P enzyme family represents a unique model system to compare the evolution of enzymatic mechanisms. Here we present a comprehensive study of substrate recognition and cleavage-site selection by the nuclear single-subunit proteinaceous RNase P PRORP3 from Arabidopsis thaliana. Compared to bacterial RNase P, the best-characterized RNA-based enzyme form, PRORP3 requires a larger part of intact tRNA structure, but little to no determinants at the cleavage site or interactions with the 5' or 3' extensions of the tRNA. The cleavage site depends on the combined dimensions of acceptor stem and T domain, but also requires the leader to be single-stranded. Overall, the single-subunit PRORP appears mechanistically more similar to the complex nuclear ribonucleoprotein enzymes than to the simpler bacterial RNase P. Mechanistic similarity or dissimilarity among different forms of RNase P thus apparently do not necessarily reflect molecular composition or evolutionary relationship.\",\n \"corpus_id\": 18571153,\n \"score\": 0\n },\n {\n \"doc_id\": \"27653474\",\n \"title\": \"Domain Organization in the 54-kDa Subunit of the Chloroplast Signal Recognition Particle.\",\n \"abstract\": \"Chloroplast signal recognition particle (cpSRP) is a heterodimer composed of an evolutionarily conserved 54-kDa GTPase (cpSRP54) and a unique 43-kDa subunit (cpSRP43) responsible for delivering light-harvesting chlorophyll binding protein to the thylakoid membrane. While a nearly complete three-dimensional structure of cpSRP43 has been determined, no high-resolution structure is yet available for cpSRP54. In this study, we developed and examined an in silico three-dimensional model of the structure of cpSRP54 by homology modeling using cytosolic homologs. Model selection was guided by single-molecule Förster resonance energy transfer experiments, which revealed the presence of at least two distinct conformations. Small angle x-ray scattering showed that the linking region among the GTPase (G-domain) and methionine-rich (M-domain) domains, an M-domain loop, and the cpSRP43 binding C-terminal extension of cpSRP54 are predominantly disordered. Interestingly, the linker and loop segments were observed to play an important role in organizing the domain arrangement of cpSRP54. Further, deletion of the finger loop abolished loading of the cpSRP cargo, light-harvesting chlorophyll binding protein. These data highlight important structural dynamics relevant to cpSRP54's role in the post- and cotranslational signaling processes.\",\n \"corpus_id\": 206304100,\n \"score\": 0\n },\n {\n \"doc_id\": \"28495884\",\n \"title\": \"The uniqueness of subunit α of mycobacterial F-ATP synthases: An evolutionary variant for niche adaptation.\",\n \"abstract\": \"The F1F0 -ATP (F-ATP) synthase is essential for growth of Mycobacterium tuberculosis, the causative agent of tuberculosis (TB). In addition to their synthase function most F-ATP synthases possess an ATP-hydrolase activity, which is coupled to proton-pumping activity. However, the mycobacterial enzyme lacks this reverse activity, but the reason for this deficiency is unclear. Here, we report that a Mycobacterium-specific, 36-amino acid long C-terminal domain in the nucleotide-binding subunit α (Mtα) of F-ATP synthase suppresses its ATPase activity and determined the mechanism of suppression. First, we employed vesicles to show that in intact membrane-embedded mycobacterial F-ATP synthases deletion of the C-terminal domain enabled ATPase and proton-pumping activity. We then generated a heterologous F-ATP synthase model system, which demonstrated that transfer of the mycobacterial C-terminal domain to a standard F-ATP synthase α subunit suppresses ATPase activity. Single-molecule rotation assays indicated that the introduction of this Mycobacterium-specific domain decreased the angular velocity of the power-stroke after ATP binding. Solution X-ray scattering data and NMR results revealed the solution shape of Mtα and the 3D structure of the subunit α C-terminal peptide (521)PDEHVEALDEDKLAKEAVKV(540) of M. tubercolosis (Mtα(521-540)), respectively. Together with cross-linking studies, the solution structural data lead to a model, in which Mtα(521-540) comes in close proximity with subunit γ residues 104-109, whose interaction may influence the rotation of the camshaft-like subunit γ. Finally, we propose that the unique segment Mtα(514-549), which is accessible at the C terminus of mycobacterial subunit α, is a promising drug epitope.\",\n \"corpus_id\": 205365199,\n \"score\": 0\n }\n]","isConversational":false}}},{"rowIdx":58,"cells":{"query":{"kind":"string","value":"{\n \"doc_id\": \"27230667\",\n \"title\": \"Characterisation of assembly and ubiquitylation by the RBCC motif of Trim5α.\",\n \"abstract\": \"The post-entry restriction factor Trim5α blocks infection of retroviral pathogens shortly after the virus gains entry to the cell, preventing reverse transcription and integration into the host genome. Central to the mechanism of restriction is recognition of the lattice of capsid protein that forms the inner-shell of the retrovirus. To recognise this lattice, Trim5α has been shown to assemble into a large hexagonal array, complementary to the capsid lattice. Structures of the Trim5α coiled-coil region reveal an elongated anti-parallel dimer consistent with the edges of this array placing the Bbox domain at each end of the coiled-coil to facilitate assembly. To investigate the nature of this assembly we have designed and characterised a monomeric version of the TRIM RBCC motif with a truncated coiled-coil. Biophysical characterisation by SEC-MALLS, AUC, and SAXS demonstrate that this construct forms compact folded domain that assembles into a trimer that would support the formation of a hexagonal lattice. Furthermore, the RING domain and elements of the coiled-coil region are shown to contribute to assembly. Ubiquitylation assays demonstrate that this assembly increases ubiquitylation activity providing a link from recognition of the capsid lattice and assembly to the activation of innate immune signalling and restriction.\",\n \"corpus_id\": 4405032\n}"},"candidates":{"kind":"list like","value":[{"doc_id":"18799578","title":"The TRIM5alpha B-box 2 domain promotes cooperative binding to the retroviral capsid by mediating higher-order self-association.","abstract":"The retroviral restriction factor, TRIM5alpha, blocks infection of a spectrum of retroviruses soon after virus entry into the cell. TRIM5alpha consists of RING, B-box 2, coiled-coil, and B30.2(SPRY) domains. The B-box 2 domain is essential for retrovirus restriction by TRIM5alpha, but its specific function is unknown. We show here that the B-box 2 domain mediates higher-order self-association of TRIM5alpha(rh) oligomers. This self-association increases the efficiency of TRIM5alpha binding to the retroviral capsid, thus potentiating restriction of retroviral infection. The contribution of the B-box 2 domain to cooperative TRIM5alpha association with the retroviral capsid explains the conditional nature of the restriction phenotype exhibited by some B-box 2 TRIM5alpha mutants; the potentiation of capsid binding that results from B-box 2-mediated self-association is essential for restriction when B30.2(SPRY) domain-mediated interactions with the retroviral capsid are weak. Thus, B-box 2-dependent higher-order self-association and B30.2(SPRY)-dependent capsid binding represent complementary mechanisms whereby sufficiently dense arrays of capsid-bound TRIM5alpha proteins can be achieved.","corpus_id":22203532,"score":2},{"doc_id":"19656869","title":"A B-box 2 surface patch important for TRIM5alpha self-association, capsid binding avidity, and retrovirus restriction.","abstract":"TRIM5alpha is a tripartite motif (TRIM) protein that consists of RING, B-box 2, coiled-coil, and B30.2(SPRY) domains. The TRIM5alpha(rh) protein from rhesus monkeys recognizes the human immunodeficiency virus type 1 (HIV-1) capsid as it enters the host cell and blocks virus infection prior to reverse transcription. HIV-1-restricting ability can be eliminated by disruption of the B-box 2 domain. Changes in the TRIM5alpha(rh) B-box 2 domain have been associated with alterations in TRIM5alpha(rh) turnover, the formation of cytoplasmic bodies and higher-order oligomerization. We present here the nuclear magnetic resonance structure of the TRIM5 B-box 2 domain and identify an unusual hydrophobic patch (cluster 1) on the domain surface. Alteration of cluster 1 or the flanking arginine 121 resulted in various degrees of inactivation of HIV-1 restriction, in some cases depending on compensatory changes in other nearby charged residues. For this panel of TRIM5alpha(rh) B-box 2 mutants, inhibition of HIV-1 infection was strongly correlated with higher-order self-association and binding affinity for capsid complexes but not with TRIM5alpha(rh) half-life or the formation of cytoplasmic bodies. Thus, promoting cooperative TRIM5alpha(rh) interactions with the HIV-1 capsid represents a major mechanism whereby the B-box 2 domain potentiates HIV-1 restriction.","corpus_id":29220668,"score":2},{"doc_id":"20012523","title":"TRIM5alpha.","abstract":"TRIM5alpha protein blocks retroviral replication at early postentry stage reducing the accumulation of reverse transcriptase products. TRIM5alpha proteins of Old World primates restrict HIV-1 infection whereas TRIM5alpha proteins of most New World monkeys restrict SIV(mac) infection. TRIM5alpha protein has a RING domain, B-box 2 domain, coiled-coil domain, and PRYSPRY domain. The PRYSPRY domain of TRIM5alpha determines viral specificity and restriction potency by mediating recognition of the retroviral capsid. The coiled-coil domain is essential for TRIM5alpha oligomerization, which contributes to binding avidity for the viral capsid. The RING domain and B-box 2 domain are required for efficient restriction activity of TRIM5alpha protein but the mechanisms remain to be defined.","corpus_id":263604735,"score":2},{"doc_id":"21187419","title":"Hexagonal assembly of a restricting TRIM5alpha protein.","abstract":"TRIM5α proteins are restriction factors that protect mammalian cells from retroviral infections by binding incoming viral capsids, accelerating their dissociation, and preventing reverse transcription of the viral genome. Individual TRIM5 isoforms can often protect cells against a broad range of retroviruses, as exemplified by rhesus monkey TRIM5α and its variant, TRIM5-21R, which recognize HIV-1 as well as several distantly related retroviruses. Although capsid recognition is not yet fully understood, previous work has shown that the C-terminal SPRY/B30.2 domain of dimeric TRIM5α binds directly to viral capsids, and that higher-order TRIM5α oligomerization appears to contribute to the efficiency of capsid recognition. Here, we report that recombinant TRIM5-21R spontaneously assembled into two-dimensional paracrystalline hexagonal lattices comprising open, six-sided rings. TRIM5-21R assembly did not require the C-terminal SPRY domain, but did require both protein dimerization and a B-box 2 residue (Arg121) previously implicated in TRIM5α restriction and higher-order assembly. Furthermore, TRIM5-21R assembly was promoted by binding to hexagonal arrays of the HIV-1 CA protein that mimic the surface of the viral capsid. We therefore propose that TRIM5α proteins have evolved to restrict a range of different retroviruses by assembling a deformable hexagonal scaffold that positions the capsid-binding domains to match the symmetry and spacing of the capsid surface lattice. Capsid recognition therefore involves a synergistic combination of direct binding interactions, avidity effects, templated assembly, and lattice complementarity.","corpus_id":101883,"score":2},{"doc_id":"21455494","title":"Rhesus TRIM5α disrupts the HIV-1 capsid at the inter-hexamer interfaces.","abstract":"TRIM proteins play important roles in the innate immune defense against retroviral infection, including human immunodeficiency virus type-1 (HIV-1). Rhesus macaque TRIM5α (TRIM5α(rh)) targets the HIV-1 capsid and blocks infection at an early post-entry stage, prior to reverse transcription. Studies have shown that binding of TRIM5α to the assembled capsid is essential for restriction and requires the coiled-coil and B30.2/SPRY domains, but the molecular mechanism of restriction is not fully understood. In this study, we investigated, by cryoEM combined with mutagenesis and chemical cross-linking, the direct interactions between HIV-1 capsid protein (CA) assemblies and purified TRIM5α(rh) containing coiled-coil and SPRY domains (CC-SPRY(rh)). Concentration-dependent binding of CC-SPRY(rh) to CA assemblies was observed, while under equivalent conditions the human protein did not bind. Importantly, CC-SPRY(rh), but not its human counterpart, disrupted CA tubes in a non-random fashion, releasing fragments of protofilaments consisting of CA hexamers without dissociation into monomers. Furthermore, such structural destruction was prevented by inter-hexamer crosslinking using P207C/T216C mutant CA with disulfide bonds at the CTD-CTD trimer interface of capsid assemblies, but not by intra-hexamer crosslinking via A14C/E45C at the NTD-NTD interface. The same disruption effect by TRIM5α(rh) on the inter-hexamer interfaces also occurred with purified intact HIV-1 cores. These results provide insights concerning how TRIM5α disrupts the virion core and demonstrate that structural damage of the viral capsid by TRIM5α is likely one of the important components of the mechanism of TRIM5α-mediated HIV-1 restriction.","corpus_id":10472091,"score":2},{"doc_id":"21512573","title":"TRIM5 is an innate immune sensor for the retrovirus capsid lattice.","abstract":"TRIM5 is a RING domain-E3 ubiquitin ligase that restricts infection by human immunodeficiency virus (HIV)-1 and other retroviruses immediately following virus invasion of the target cell cytoplasm. Antiviral potency correlates with TRIM5 avidity for the retrovirion capsid lattice and several reports indicate that TRIM5 has a role in signal transduction, but the precise mechanism of restriction is unknown. Here we demonstrate that TRIM5 promotes innate immune signalling and that this activity is amplified by retroviral infection and interaction with the capsid lattice. Acting with the heterodimeric, ubiquitin-conjugating enzyme UBC13-UEV1A (also known as UBE2N-UBE2V1), TRIM5 catalyses the synthesis of unattached K63-linked ubiquitin chains that activate the TAK1 (also known as MAP3K7) kinase complex and stimulate AP-1 and NFκB signalling. Interaction with the HIV-1 capsid lattice greatly enhances the UBC13-UEV1A-dependent E3 activity of TRIM5 and challenge with retroviruses induces the transcription of AP-1 and NF-κB-dependent factors with a magnitude that tracks with TRIM5 avidity for the invading capsid. Finally, TAK1 and UBC13-UEV1A contribute to capsid-specific restriction by TRIM5. Thus, the retroviral restriction factor TRIM5 has two additional activities that are linked to restriction: it constitutively promotes innate immune signalling and it acts as a pattern recognition receptor specific for the retrovirus capsid lattice.","corpus_id":4339114,"score":2},{"doc_id":"21680743","title":"Determinants of the higher order association of the restriction factor TRIM5alpha and other tripartite motif (TRIM) proteins.","abstract":"Many tripartite motif (TRIM) proteins self-associate, forming dimers and higher order complexes. For example, dimers of TRIM5α, a host factor that restricts retrovirus infection, assemble into higher order arrays on the surface of the viral capsid, resulting in an increase in avidity. Here we show that the higher order association of different TRIM proteins exhibits a wide range of efficiencies. Homologous association (self-association) was more efficient than the heterologous association of different TRIM proteins, indicating that specificity determinants of higher order self-association exist. To investigate the structural determinants of higher order self-association, we studied TRIM mutants and chimeras. These studies revealed the following: 1) the RING domain contributes to the efficiency of higher order self-association, which enhances the binding of TRIM5α to the human immunodeficiency virus (HIV-1) capsid; 2) the RING and B-box 2 domains work together as a homologous unit to promote higher order association of dimers; 3) dimerization is probably required for efficient higher order self-association; 4) the Linker 2 region contributes to higher order self-association, independently of effects of Linker 2 changes on TRIM dimerization; and 5) for efficiently self-associating TRIM proteins, the B30.2(SPRY) domain is not required for higher order self-association. These results support a model in which both ends of the core TRIM dimer (RING-B-box 2 at one end and Linker 2 at the other) contribute to the formation of higher order arrays.","corpus_id":11327163,"score":2},{"doc_id":"21734049","title":"Contribution of E3-ubiquitin ligase activity to HIV-1 restriction by TRIM5alpha(rh): structure of the RING domain of TRIM5alpha.","abstract":"TRIM5α(rh) is a cytosolic protein that potently restricts HIV-1 before reverse transcription. TRIM5α(rh) is composed of four different domains: RING, B-box 2, coiled coil, and B30.2(SPRY). The contribution of each of these domains to restriction has been extensively studied, with the exception of the RING domain. The RING domain of TRIM5α exhibits E3-ubiquitin ligase activity, but the contribution of this activity to the restriction of HIV-1 is not known. To test the hypothesis that the E3-ubiquitin ligase activity of the RING domain modulates TRIM5α(rh) restriction of HIV-1, we correlated the E3-ubiquitin ligase activity of a panel of TRIM5α(rh) RING domain variants with the ability of these mutant proteins to restrict HIV-1. For this purpose, we first solved the nuclear magnetic resonance structure of the RING domain of TRIM5α and defined potential functional regions of the RING domain by homology to other RING domains. With this structural information, we performed a systematic mutagenesis of the RING domain regions and tested the TRIM5α RING domain variants for the ability to undergo self-ubiquitylation. Several residues, particularly the ones on the E2-binding region of the RING domain, were defective in their self-ubiquitylation ability. To correlate HIV-1 restriction to self-ubiquitylation, we used RING domain mutant proteins that were defective in self-ubiquitylation but preserve important properties required for potent restriction by TRIM5α(rh), such as capsid binding and higher-order self-association. From these investigations, we found a set of residues that when mutated results in TRIM5α molecules that lost both the ability to potently restrict HIV-1 and their self-ubiquitylation activity. Remarkably, all of these changes were in residues located in the E2-binding region of the RING domain. Overall, these results demonstrate a role for TRIM5α self-ubiquitylation in the ability of TRIM5α to restrict HIV-1.","corpus_id":6973193,"score":2},{"doc_id":"21994740","title":"Caging the beast: TRIM5α binding to the HIV-1 core.","abstract":"The potent HIV-1 inhibitor TRIM5α blocks HIV-1 infection by accelerating the uncoating of HIV-1. TRIM5α is known to form higher-order self-association complexes that contribute to the avidity of TRIM5α for the HIV-1 capsid, and are essential to inhibit infection; these higher-order self-association complexes are dependent upon an intact B-box 2 domain. Even though the ability to form higher-order self-association complexes resembles the clathrin triskelion that forms a protein array, or cage, around the endocytic vesicle, evidence for the ability of TRIM5α to assemble a similar type of structure surrounding the HIV-1 core has been lacking. Recent work by Ganser-Pornillos, Chandrasekaran and colleagues has now demonstrated the ability of the restriction factor TRIM5α to \"cage\" or \"net\" the HIV-1 core by forming an hexagonal array on the surface of the viral capsid. This hexagonal array is strikingly similar in design to the array formed by the clathrin triskelion on the surface of the clathrin-coated endocytic vesicle. This remarkable finding represents an important advance on our understanding of the restriction factor TRIM5α, and suggests that TRIM5α cages the HIV-1 core in order to terminate infection. The present note discusses the implications of this discovery.","corpus_id":7806137,"score":2},{"doc_id":"22114335","title":"RING domain mutations uncouple TRIM5α restriction of HIV-1 from inhibition of reverse transcription and acceleration of uncoating.","abstract":"Rhesus TRIM5α (TRIM5α(rh)) is a cytosolic protein that potently restricts HIV-1 at an early postentry stage, prior to reverse transcription. The ability of TRIM5α(rh) to block HIV-1 infection has been correlated with a decrease of pelletable HIV-1 capsid during infection. To genetically dissect the ability of TRIM5α to block reverse transcription, we studied a set of TRIM5α(rh) RING domain mutants that potently restrict HIV-1 but allow the occurrence of reverse transcription. These TRIM5α(rh) RING variants blocked HIV-1 infection after reverse transcription but prior to integration, as suggested by the routing of nuclear viral DNA to circularization in the form of 2-long terminal repeat (2-LTR) circles. The folding of RING domain variants was similar to that of the wild type, as evaluated by nuclear magnetic resonance. RING domain changes that allowed the occurrence of reverse transcription were impaired in their ability to decrease the amount of pelletable capsid compared with wild-type TRIM5α. Similar effects of this particular group of mutations were observed with human TRIM5α inhibition of N-tropic murine leukemia virus (N-MLV). Interestingly, TRIM5α(rh) RING domain variants also prevented the degradation of TRIM5α(rh) that occurs following cell entry of HIV-1. These data correlated the block of reverse transcription with the ability of TRIM5α to accelerate uncoating. Collectively, these results suggest that TRIM5α(rh) blocks HIV-1 reverse transcription by inducing premature viral uncoating in target cells.","corpus_id":24403782,"score":2},{"doc_id":"22482711","title":"TRIM5 structure, HIV-1 capsid recognition, and innate immune signaling.","abstract":"TRIM5 is a restriction factor that blocks retrovirus infection soon after the virion core enters the cell cytoplasm. Restriction activity is targeted to the virion core via recognition of the capsid protein lattice that encases the viral genomic RNA. In common with all of the many TRIM family members, TRIM5 has RING, B-box, and coiled-coil domains. As an E3 ubiquitin ligase TRIM5 cooperates with the heterodimeric E2, UBC13/UEV1A, to activate the TAK1 (MAP3K7) kinase, NF-κB and AP-1 signaling, and the transcription of inflammatory cytokines and chemokines. TAK1, UBC13, and UEV1A all contribute to TRIM5-mediated retrovirus restriction activity. Interaction of the carboxy-terminal PRYSPRY or cyclophilin domains of TRIM5 with the retroviral capsid lattice stimulates the formation of a complementary lattice by TRIM5, with greatly increased TRIM5 E3 activity, and host cell signal transduction. Structural and biochemical studies on TRIM5 have opened a much needed window on how the innate immune system detects the distinct molecular features of HIV-1 and other retroviruses.","corpus_id":22704306,"score":2},{"doc_id":"23091002","title":"Structural insight into HIV-1 capsid recognition by rhesus TRIM5α.","abstract":"Tripartite motif protein isoform 5 alpha (TRIM5α) is a potent antiviral protein that restricts infection by HIV-1 and other retroviruses. TRIM5α recognizes the lattice of the retrovirus capsid through its B30.2 (PRY/SPRY) domain in a species-specific manner. Upon binding, TRIM5α induces premature disassembly of the viral capsid and activates the downstream innate immune response. We have determined the crystal structure of the rhesus TRIM5α PRY/SPRY domain that reveals essential features for capsid binding. Combined cryo-electron microscopy and biochemical data show that the monomeric rhesus TRIM5α PRY/SPRY, but not the human TRIM5α PRY/SPRY, can bind to HIV-1 capsid protein assemblies without causing disruption of the capsid. This suggests that the PRY/SPRY domain alone constitutes an important pattern-sensing component of TRIM5α that is capable of interacting with viral capsids of different curvatures. Our results provide molecular insights into the mechanisms of TRIM5α-mediated retroviral restriction.","corpus_id":26633942,"score":2},{"doc_id":"23637418","title":"Virus-specific effects of TRIM5α(rh) RING domain functions on restriction of retroviruses.","abstract":"The tripartite motif protein TRIM5α restricts particular retrovirus infections by binding to the incoming capsid and inhibiting the early stage of virus infection. The TRIM5α RING domain exhibits E3 ubiquitin ligase activity and assists the higher-order association of TRIM5α dimers, which promotes capsid binding. We characterized a panel of RING domain mutants of the rhesus monkey TRIM5α (TRIM5α(rh)) protein. The RING domain function that significantly contributed to retroviral restriction depended upon the restricted virus. The E3 ubiquitin ligase activity of the RING domain contributes to the potency of HIV-1 restriction. Nonetheless, TRIM5α(rh) mutants without detectable E3 ubiquitin ligase activity still blocked reverse transcription and inhibited HIV-1 infection at a moderate level. When TRIM5α(rh) capsid binding was weakened by substitution with a less efficient B30.2/SPRY domain, the promotion of higher-order association by the RING domain was more important to HIV-1 restriction than its E3 ubiquitin ligase activity. For the restriction of N-tropic murine leukemia virus (N-MLV) and equine infectious anemia virus (EIAV) infection, promotion of higher-order association represented the major contribution of the RING domain. Thus, both identity of the target virus and the B30.2/SPRY domain-mediated affinity for the viral capsid determine the relative contribution of the two known RING domain functions to TRIM5α restriction of retrovirus infection.","corpus_id":16531158,"score":2},{"doc_id":"24158810","title":"CryoEM analysis of capsid assembly and structural changes upon interactions with a host restriction factor, TRIM5α.","abstract":"After virus fusion with a target cell, the viral core is released into the host cell cytoplasm and undergoes a controlled disassembly process, termed uncoating, before or as reverse transcription takes place. The cellular protein TRIM5α is a host cell restriction factor that blocks HIV-1 infection in rhesus macaque cells by targeting the viral capsid and inducing premature uncoating. The molecular mechanism of the interaction between capsid and TRIM5α remains unclear. Here, we describe an approach that utilizes cryo-electron microscopy (cryoEM) to examine the structural changes exerted on HIV-1 capsid (CA) assembly by TRIM5α binding. The TRIM5α interaction sites on CA assembly were further dissected by combining cryoEM with pair-wise cysteine mutations that crosslink CA either within a CA hexamer or between CA hexamers. Based on the structural information from cryoEM and crosslinking results from in vitro CA assemblies and purified intact HIV-1 cores, we demonstrate that direct binding of TRIM5α CC-SPRY domains to the viral capsid results in disruption and fragmentation of the surface lattice of HIV-1 capsid, specifically at inter-hexamer interfaces. The method described here can be easily adopted to study other important interactions in multi-protein complexes.","corpus_id":20581636,"score":2},{"doc_id":"24550273","title":"The tripartite motif coiled-coil is an elongated antiparallel hairpin dimer.","abstract":"Tripartite motif (TRIM) proteins make up a large family of coiled-coil-containing RING E3 ligases that function in many cellular processes, particularly innate antiviral response pathways. Both dimerization and higher-order assembly are important elements of TRIM protein function, but the atomic details of TRIM tertiary and quaternary structure have not been fully understood. Here, we present crystallographic and biochemical analyses of the TRIM coiled-coil and show that TRIM proteins dimerize by forming interdigitating antiparallel helical hairpins that position the N-terminal catalytic RING domains at opposite ends of the dimer and the C-terminal substrate-binding domains at the center. The dimer core comprises an antiparallel coiled-coil with a distinctive, symmetric pattern of flanking heptad and central hendecad repeats that appear to be conserved across the entire TRIM family. Our studies reveal how the coiled-coil organizes TRIM25 to polyubiquitylate the RIG-I/viral RNA recognition complex and how dimers of the TRIM5α protein are arranged within hexagonal arrays that recognize the HIV-1 capsid lattice and restrict retroviral replication.","corpus_id":2015949,"score":2},{"doc_id":"24872590","title":"Restriction of HIV-1 by rhesus TRIM5α is governed by alpha helices in the Linker2 region.","abstract":"UNLABELLED: TRIM5α proteins are a potent barrier to the cross-species transmission of retroviruses. TRIM5α proteins exhibit an ability to self-associate at many levels, ultimately leading to the formation of protein assemblies with hexagonal symmetry in vitro and cytoplasmic assemblies when expressed in cells. However, the role of these assemblies in restriction, the determinants that mediate their formation, and the organization of TRIM5α molecules within these assemblies have remained unclear. Here we show that α-helical elements within the Linker2 region of rhesus macaque TRIM5α govern the ability to form cytoplasmic assemblies in cells and restrict HIV-1 infection. Mutations that reduce α-helix formation by the Linker2 region disrupt assembly and restriction. More importantly, mutations that enhance the α-helical content of the Linker2 region, relative to the wild-type protein, also exhibit an increased ability to form cytoplasmic assemblies and restrict HIV-1 infection. Molecular modeling of the TRIM5α dimer suggests a model in which α-helical elements within the Linker2 region dock to α-helices of the coiled-coil domain, likely establishing proper orientation and spacing of protein domains necessary for assembly and restriction. Collectively, these studies provide critical insight into the determinants governing TRIM5α assembly and restriction and demonstrate that the antiviral potency of TRIM5α proteins can be significantly increased without altering the affinity of SPRY/capsid binding. IMPORTANCE: Many members of the tripartite motif (TRIM) family of proteins act as restriction factors that directly inhibit viral infection and activate innate immune signaling pathways. Another common feature of TRIM proteins is the ability to form protein assemblies in the nucleus or the cytoplasm. However, the determinants in TRIM proteins required for assembly and the degree to which assembly affects TRIM protein function have been poorly understood. Here we show that alpha helices in the Linker2 (L2) region of rhesus TRIM5α govern assembly and restriction of HIV-1 infection. Helix-disrupting mutations disrupt the assembly and restriction of HIV-1, while helix-stabilizing mutations enhance assembly and restriction relative to the wild-type protein. Circular dichroism analysis suggests that that the formation of this helical structure is supported by intermolecular interactions with the coiled-coil (CC) domain in the CCL2 dimer. These studies reveal a novel mechanism by which the antiviral activity of TRIM5α proteins can be regulated and provide detailed insight into the assembly determinants of TRIM family proteins.","corpus_id":994073,"score":2},{"doc_id":"24979782","title":"Structural studies of postentry restriction factors reveal antiparallel dimers that enable avid binding to the HIV-1 capsid lattice.","abstract":"Restriction factors (RFs) form important components of host defenses to retroviral infection. The Fv1, Trim5α, and TrimCyp RFs contain N-terminal dimerization and C-terminal specificity domains that target assembled retroviral capsid (CA) proteins enclosing the viral core. However, the molecular detail of the interaction between RFs and their CA targets is unknown. Therefore, we have determined the crystal structure of the B-box and coiled-coil (BCC) region from Trim5α and used small-angle X-ray scattering to examine the solution structure of Trim5α BCC, the dimerization domain of Fv1 (Fv1Ntd), and the hybrid restriction factor Fv1Cyp comprising Fv1NtD fused to the HIV-1 binding protein Cyclophilin A (CypA). These data reveal that coiled-coil regions of Fv1 and Trim5α form extended antiparallel dimers. In Fv1Cyp, two CypA moieties are located at opposing ends, creating a molecule with a dumbbell appearance. In Trim5α, the B-boxes are located at either end of the coiled-coil, held in place by interactions with a helical motif from the L2 region of the opposing monomer. A comparative analysis of Fv1Cyp and CypA binding to a preformed HIV-1 CA lattice reveals how RF dimerization enhances the affinity of interaction through avidity effects. We conclude that the antiparallel organization of the NtD regions of Fv1 and Trim5α dimers correctly positions C-terminal specificity and N-terminal effector domains and facilitates stable binding to adjacent CA hexamers in viral cores.","corpus_id":205267902,"score":2},{"doc_id":"26043233","title":"Crystal structure of TRIM20 C-terminal coiled-coil/B30.2 fragment: implications for the recognition of higher order oligomers.","abstract":"Many tripartite motif-containing (TRIM) proteins, comprising RING-finger, B-Box, and coiled-coil domains, carry additional B30.2 domains on the C-terminus of the TRIM motif and are considered to be pattern recognition receptors involved in the detection of higher order oligomers (e.g. viral capsid proteins). To investigate the spatial architecture of domains in TRIM proteins we determined the crystal structure of the TRIM20Δ413 fragment at 2.4 Å resolution. This structure comprises the central helical scaffold (CHS) and C-terminal B30.2 domains and reveals an anti-parallel arrangement of CHS domains placing the B-box domains 170 Å apart from each other. Small-angle X-ray scattering confirmed that the linker between CHS and B30.2 domains is flexible in solution. The crystal structure suggests an interaction between the B30.2 domain and an extended stretch in the CHS domain, which involves residues that are mutated in the inherited disease Familial Mediterranean Fever. Dimerization of B30.2 domains by means of the CHS domain is crucial for TRIM20 to bind pro-IL-1β in vitro. To exemplify how TRIM proteins could be involved in binding higher order oligomers we discuss three possible models for the TRIM5α/HIV-1 capsid interaction assuming different conformations of B30.2 domains.","corpus_id":18642941,"score":2},{"doc_id":"26101372","title":"TRIM5α requires Ube2W to anchor Lys63-linked ubiquitin chains and restrict reverse transcription.","abstract":"TRIM5α is an antiviral, cytoplasmic, E3 ubiquitin (Ub) ligase that assembles on incoming retroviral capsids and induces their premature dissociation. It inhibits reverse transcription of the viral genome and can also synthesize unanchored polyubiquitin (polyUb) chains to stimulate innate immune responses. Here, we show that TRIM5α employs the E2 Ub-conjugating enzyme Ube2W to anchor the Lys63-linked polyUb chains in a process of TRIM5α auto-ubiquitination. Chain anchoring is initiated, in cells and in vitro, through Ube2W-catalyzed monoubiquitination of TRIM5α. This modification serves as a substrate for the elongation of anchored Lys63-linked polyUb chains, catalyzed by the heterodimeric E2 enzyme Ube2N/Ube2V2. Ube2W targets multiple TRIM5α internal lysines with Ub especially lysines 45 and 50, rather than modifying the N-terminal amino group, which is instead αN-acetylated in cells. E2 depletion or Ub mutation inhibits TRIM5α ubiquitination in cells and restores restricted viral reverse transcription, but not infection. Our data indicate that the stepwise formation of anchored Lys63-linked polyUb is a critical early step in the TRIM5α restriction mechanism and identify the E2 Ub-conjugating cofactors involved.","corpus_id":449065,"score":2},{"doc_id":"26212332","title":"RING Dimerization Links Higher-Order Assembly of TRIM5α to Synthesis of K63-Linked Polyubiquitin.","abstract":"Members of the tripartite motif (TRIM) protein family of RING E3 ubiquitin (Ub) ligases promote innate immune responses by catalyzing synthesis of polyubiquitin chains linked through lysine 63 (K63). Here, we investigate the mechanism by which the TRIM5α retroviral restriction factor activates Ubc13, the K63-linkage-specific E2. Structural, biochemical, and functional characterization of the TRIM5α:Ubc13-Ub interactions reveals that activation of the Ubc13-Ub conjugate requires dimerization of the TRIM5α RING domain. Our data explain how higher-order oligomerization of TRIM5α, which is promoted by the interaction with the retroviral capsid, enhances the E3 Ub ligase activity of TRIM5α and contributes to its antiretroviral function. This E3 mechanism, in which RING dimerization is transient and depends on the interaction of the TRIM protein with the ligand, is likely to be conserved in many members of the TRIM family and may have evolved to facilitate recognition of repetitive epitope patterns associated with infection.","corpus_id":19763051,"score":2},{"doc_id":"26468522","title":"TRIM5 Retroviral Restriction Activity Correlates with the Ability To Induce Innate Immune Signaling.","abstract":"UNLABELLED: Host restriction factor TRIM5 inhibits retroviral transduction in a species-specific manner by binding to and destabilizing the retroviral capsid lattice before reverse transcription is completed. However, the restriction mechanism may not be that simple since TRIM5 E3 ubiquitin ligase activity, the proteasome, autophagy, and TAK1-dependent AP-1 signaling have been suggested to contribute to restriction. Here, we show that, among a panel of seven primate and Carnivora TRIM5 orthologues, each of which has potential for potent retroviral restriction activity, all activated AP-1 signaling. In contrast, TRIM family paralogues most closely related to TRIM5 did not. While each primate species has a single TRIM5 gene, mice have at least seven TRIM5 homologues that cluster into two groups, Trim12a, -b, and -c and Trim30a, -b, -c, and -d. The three Trim12 proteins activated innate immune signaling, while the Trim30 proteins did not, though none of the murine Trim5 homologues restricted any of a panel of cloned retroviruses. To determine if any mouse TRIM5 homologues had potential for restriction activity, each was fused to the human immunodeficiency virus type 1 (HIV-1) CA binding protein cyclophilin A (CypA). The three Trim12-CypA fusions all activated AP-1 and restricted HIV-1 transduction, whereas the Trim30-CypA fusions did neither. AP-1 activation and HIV-1 restriction by the Trim12-CypA fusions were inhibited by disruption of TAK1. Overall then, these experiments demonstrate that there is a strong correlation between TRIM5 retroviral restriction activity and the ability to activate TAK1-dependent innate immune signaling. IMPORTANCE: The importance of retroviruses for the evolution of susceptible host organisms cannot be overestimated. Eight percent of the human genome is retrovirus sequence, fixed in the germ line during past infection. Understanding how metazoa protect their genomes from mutagenic retrovirus infection is therefore of fundamental importance to biology. TRIM5 is a cellular protein that protects host genome integrity by disrupting the retroviral capsid as it transports viral nucleic acid to the host cell nucleus. Previous data suggest that innate immune signaling contributes to TRIM5-mediated restriction. Here, we show that activation of innate immune signaling is conserved among primate and carnivore TRIM5 orthologues and among 3 of the 7 mouse Trim5 homologues and that such activity is required for TRIM5-mediated restriction activity.","corpus_id":12769922,"score":2},{"doc_id":"26676782","title":"TRIM5alpha-mediated ubiquitin chain conjugation is required for inhibition of HIV-1 reverse transcription and capsid destabilization.","abstract":"Rhesus macaque TRIM5α (rhTRIM5α) is a retroviral restriction factor, which inhibits HIV-1 infection. Previous studies have revealed that TRIM5α restriction occurs via a two-step process. The first step is restriction factor binding, which is sufficient to inhibit infection. The second step, which is sensitive to proteasome inhibition, prevents the accumulation of reverse transcription products in the target cell. However, because of the pleotropic effects of proteasome inhibitors, the molecular mechanisms underlying the individual steps in the restriction process have remained poorly understood. In this study, we have fused the small catalytic domain of Herpes Simplex Virus UL36 Deubiquitinase (DUb) to the N-terminal RING domain of rhTRIM5α, which results in a ubiquitination resistant protein. Cell lines stably expressing this fusion protein inhibited HIV-1 infection to the same degree as a control fusion to a catalytically inactive DUb. However, reverse transcription products were substantially increased in the DUb-TRIM5α fusion relative to the catalytically inactive control or the wild type TRIM5α. Similarly, expression of DUb-rhTRIM5α resulted in the accumulation of viral cores in target cells following infection, while the catalytically inactive control and wt rhTRIM5α induced the abortive disassembly of viral cores, indicating a role for ubiquitin conjugation in rhTRIM5α-mediated destabilization of HIV-1 cores. Finally, DUb-rhTRIM5α failed to activate NF-kB signaling pathways, when compared to controls, demonstrating that this ubiquination dependent activity is separable from the ability to restrict retroviral infection. IMPORTANCE: These studies provide direct evidence that ubiquitin conjugation to rhTRIM5α-containing complexes is required for the second step of HIV-1 restriction. They also provide a novel tool by which the biological activities of TRIM family proteins might be dissected to better understand their function and underlying mechanisms of action.","corpus_id":3836930,"score":2},{"doc_id":"26764007","title":"TRIM5α Degradation via Autophagy Is Not Required for Retroviral Restriction.","abstract":"UNLABELLED: TRIM5α is an interferon-inducible retroviral restriction factor that prevents infection by inducing the abortive disassembly of capsid cores recognized by its C-terminal PRY/SPRY domain. The mechanism by which TRIM5α mediates the disassembly of viral cores is poorly understood. Previous studies demonstrated that proteasome inhibitors abrogate the ability of TRIM5α to induce premature core disassembly and prevent reverse transcription; however, viral infection is still inhibited, indicating that the proteasome is partially involved in the restriction process. Alternatively, we and others have observed that TRIM5α associates with proteins involved in autophagic degradation pathways, and one recent study found that autophagic degradation is required for the restriction of retroviruses by TRIM5α. Here, we show that TRIM5α is basally degraded via autophagy in the absence of restriction-sensitive virus. We observe that the autophagy markers LC3b and lysosome-associated membrane protein 2A (LAMP2A) localize to a subset of TRIM5α cytoplasmic bodies, and inhibition of lysosomal degradation with bafilomycin A1 increases this association. To test the requirement for macroautophagy in restriction, we examined the ability of TRIM5α to restrict retroviral infection in cells depleted of the autophagic mediators ATG5, Beclin1, and p62. In all cases, restriction of retroviruses by human TRIM5α, rhesus macaque TRIM5α, and owl monkey TRIM-Cyp remained potent in cells depleted of these autophagic effectors by small interfering RNA (siRNA) knockdown or clustered regularly interspaced short palindromic repeat (CRISPR)-Cas9 genome editing. Collectively, these results are consistent with observations that the turnover of TRIM5α proteins is sensitive to autophagy inhibition; however, the data presented here do not support observations that the inhibition of autophagy abrogates retroviral restriction by TRIM5 proteins. IMPORTANCE: Restriction factors are a class of proteins that inhibit viral replication. Following fusion of a retrovirus with a host cell membrane, the retroviral capsid is released into the cytoplasm of the target cell. TRIM5α inhibits retroviral infection by promoting the abortive disassembly of incoming retroviral capsid cores; as a result, the retroviral genome is unable to traffic to the nucleus, and the viral life cycle is extinguished. In the process of restriction, TRIM5α itself is degraded by the proteasome. However, in the present study, we have shown that in the absence of a restriction-sensitive virus, TRIM5α is degraded by both proteasomal and autophagic degradation pathways. Notably, we observed that restriction of retroviruses by TRIM5α does not require autophagic machinery. These data indicate that the effector functions of TRIM5α can be separated from its degradation and may have further implications for understanding the mechanisms of other TRIM family members.","corpus_id":22248080,"score":2},{"doc_id":"27253059","title":"Mechanism of B-box 2 domain-mediated higher-order assembly of the retroviral restriction factor TRIM5α.","abstract":"Restriction factors and pattern recognition receptors are important components of intrinsic cellular defenses against viral infection. Mammalian TRIM5α proteins are restriction factors and receptors that target the capsid cores of retroviruses and activate ubiquitin-dependent antiviral responses upon capsid recognition. Here, we report crystallographic and functional studies of the TRIM5α B-box 2 domain, which mediates higher-order assembly of TRIM5 proteins. The B-box can form both dimers and trimers, and the trimers can link multiple TRIM5α proteins into a hexagonal net that matches the lattice arrangement of capsid subunits and enables avid capsid binding. Two modes of conformational flexibility allow TRIM5α to accommodate the variable curvature of retroviral capsids. B-box mediated interactions also modulate TRIM5α's E3 ubiquitin ligase activity, by stereochemically restricting how the N-terminal RING domain can dimerize. Overall, these studies define important molecular details of cellular recognition of retroviruses, and how recognition links to downstream processes to disable the virus.","corpus_id":2670083,"score":2},{"doc_id":"27253068","title":"Primate TRIM5 proteins form hexagonal nets on HIV-1 capsids.","abstract":"TRIM5 proteins are restriction factors that block retroviral infections by binding viral capsids and preventing reverse transcription. Capsid recognition is mediated by C-terminal domains on TRIM5α (SPRY) or TRIMCyp (cyclophilin A), which interact weakly with capsids. Efficient capsid recognition also requires the conserved N-terminal tripartite motifs (TRIM), which mediate oligomerization and create avidity effects. To characterize how TRIM5 proteins recognize viral capsids, we developed methods for isolating native recombinant TRIM5 proteins and purifying stable HIV-1 capsids. Biochemical and EM analyses revealed that TRIM5 proteins assembled into hexagonal nets, both alone and on capsid surfaces. These nets comprised open hexameric rings, with the SPRY domains centered on the edges and the B-box and RING domains at the vertices. Thus, the principles of hexagonal TRIM5 assembly and capsid pattern recognition are conserved across primates, allowing TRIM5 assemblies to maintain the conformational plasticity necessary to recognize divergent and pleomorphic retroviral capsids.","corpus_id":22091893,"score":2},{"doc_id":"27402535","title":"Crystal structure of the Trim5α Bbox2 domain from rhesus macaques describes a plastic oligomerisation interface.","abstract":"Retroviral pathogens have been an evolutionary pressure for many primate species, driving the development of an intrinsic cellular response to retroviruses and antiretroviral proteins. One such antiretroviral protein is the restriction factor Trim5α, that blocks HIV-1 infection in rhesus macaques at an early post-entry stage in the retroviral lifecycle. Trim5α self-assembles into a large hexagonal array, complimentary to the retroviral capsid. Assembly is mediated by the conserved N-terminal architecture comprising a RING domain, a Bbox domain, and a coiled coil. Recently we have shown that the Bbox domain and elements of the coiled coil form a trimer in solution, and that the Bbox domain drives assembly. During crystallisation experiments using the trimer forming construct, we determined the structure of a dimeric Bbox domain to a resolution of 1.8Å. Interface analysis reveals that residues previously shown to be required for assembly and restriction, Glu120 and Arg121, are central to the interface. Comparison to a mutant Trim5α dimer interface shows a translation of the Bbox dimerisation interface removing interactions important in the wildtype protein.","corpus_id":3928870,"score":2},{"doc_id":"27821283","title":"Dynamic conformational changes in the rhesus TRIM5α dimer dictate the potency of HIV-1 restriction.","abstract":"The TRIM5α protein from rhesus macaques (rhTRIM5α) mediates a potent inhibition of HIV-1 infection via a mechanism that involves the abortive disassembly of the viral core. We have demonstrated that alpha-helical elements within the Linker 2 (L2) region, which lies between the SPRY domain and the Coiled-Coil domain, influence the potency of restriction. Here, we utilize single-molecule FRET analysis to reveal that the L2 region of the TRIM5α dimer undergoes dynamic conformational changes, which results in the displacement of L2 regions by 25 angstroms relative to each other. Analysis of restriction enhancing or abrogating mutations in the L2 region reveal that restriction defective mutants are unable to undergo dynamic conformational changes and do not assume compact, alpha-helical conformations in the L2 region. These data suggest a model in which conformational changes in the L2 region mediate displacement of CA bound SPRY domains to induce the destabilization of assembled capsid during restriction.","corpus_id":9884527,"score":2},{"doc_id":"29040325","title":"TRIM5α SPRY/coiled-coil interactions optimize avid retroviral capsid recognition.","abstract":"Restriction factors are important components of intrinsic cellular defense mechanisms against viral pathogens. TRIM5α is a restriction factor that intercepts the incoming capsid cores of retroviruses such as HIV and provides an effective species-specific barrier to retroviral infection. The TRIM5α SPRY domain directly binds the capsid with only very weak, millimolar-level affinity, and productive capsid recognition therefore requires both TRIM5α dimerization and assembly of the dimers into a multivalent hexagonal lattice to promote avid binding. Here, we explore the important unresolved question of whether the SPRY domains are flexibly linked to the TRIM lattice or more precisely positioned to maximize avidity. Biochemical and biophysical experiments indicate that the linker segment connecting the SPRY domain to the coiled-coil domain adopts an α-helical fold, and that this helical portion mediates interactions between the two domains. Targeted mutations were generated to disrupt the putative packing interface without affecting dimerization or higher-order assembly, and we identified mutant proteins that were nevertheless deficient in capsid binding in vitro and restriction activity in cells. Our studies therefore support a model wherein substantial avidity gains during assembly-mediated capsid recognition by TRIM5α come in part from tailored spacing of tethered recognition domains.","corpus_id":24085982,"score":2},{"doc_id":"29187540","title":"General Model for Retroviral Capsid Pattern Recognition by TRIM5 Proteins.","abstract":"Restriction factors are intrinsic cellular defense proteins that have evolved to block microbial infections. Retroviruses such as HIV-1 are restricted by TRIM5 proteins, which recognize the viral capsid shell that surrounds, organizes, and protects the viral genome. TRIM5α uses a SPRY domain to bind capsids with low intrinsic affinity (KD of >1 mM) and therefore requires higher-order assembly into a hexagonal lattice to generate sufficient avidity for productive capsid recognition. TRIMCyp, on the other hand, binds HIV-1 capsids through a cyclophilin A domain, which has a well-defined binding site and higher affinity (KD of ∼10 μM) for isolated capsid subunits. Therefore, it has been argued that TRIMCyp proteins have dispensed with the need for higher-order assembly to function as antiviral factors. Here, we show that, consistent with its high degree of sequence similarity with TRIM5α, the TRIMCyp B-box 2 domain shares the same ability to self-associate and facilitate assembly of a TRIMCyp hexagonal lattice that can wrap about the HIV-1 capsid. We also show that under stringent experimental conditions, TRIMCyp-mediated restriction of HIV-1 is indeed dependent on higher-order assembly. Both forms of TRIM5 therefore use the same mechanism of avidity-driven capsid pattern recognition. IMPORTANCE Rhesus macaques and owl monkeys are highly resistant to HIV-1 infection due to the activity of TRIM5 restriction factors. The rhesus macaque TRIM5α protein blocks HIV-1 through a mechanism that requires self-assembly of a hexagonal TRIM5α lattice around the invading viral core. Lattice assembly amplifies very weak interactions between the TRIM5α SPRY domain and the HIV-1 capsid. Assembly also promotes dimerization of the TRIM5α RING E3 ligase domain, resulting in synthesis of polyubiquitin chains that mediate downstream steps of restriction. In contrast to rhesus TRIM5α, the owl monkey TRIM5 homolog, TRIMCyp, binds isolated HIV-1 CA subunits much more tightly through its cyclophilin A domain and therefore was thought to act independently of higher-order assembly. Here, we show that TRIMCyp shares the assembly properties of TRIM5α and that both forms of TRIM5 use the same mechanism of hexagonal lattice formation to promote viral recognition and restriction.","corpus_id":4961124,"score":2},{"doc_id":"19153241","title":"An invariant surface patch on the TRIM5alpha PRYSPRY domain is required for retroviral restriction but dispensable for capsid binding.","abstract":"TRIM5alpha is a retrovirus restriction factor in the host cell cytoplasm that blocks infection before provirus establishment. Restriction activity requires capsid (CA)-specific recognition by the PRYSPRY domain of TRIM5alpha. To better understand the restriction mechanism, nine charge-cluster-to-triple-alanine mutants in the TRIM5alpha PRYSPRY domain were assessed for CA-specific restriction activity. Five mutants distributed along the TRIM5alpha PRYSPRY primary sequence disrupted restriction activity against N-tropic murine leukemia virus and equine infectious anemia virus. Modeling of the TRIM5alpha PRYSPRY domain based on the crystal structures of PRYSPRY-19q13.4.1, GUSTAVUS, and TRIM21 identified a surface patch where disruptive mutants clustered. All mutants in this patch retained CA-binding activity, a reticular distribution in the cytoplasm, and steady-state protein levels comparable to those of the wild type. Residues in the essential patch are conserved in TRIM5alpha orthologues and in closely related paralogues. The same surface patch in the TRIM18 and TRIM20 PRYSPRY domains is the site of mutants causing Opitz syndrome and familial Mediterranean fever. These results indicate that, in addition to CA-specific binding, the PRYSPRY domain possesses a second function, possibly binding of a cofactor, that is essential for retroviral restriction activity by TRIM5alpha.","corpus_id":12109250,"score":1},{"doc_id":"20110098","title":"Contribution of RING domain to retrovirus restriction by TRIM5alpha depends on combination of host and virus.","abstract":"The anti-retroviral restriction factor TRIM5alpha contains the RING domain, which is frequently observed in E3 ubiquitin ligases. It was previously proposed that TRIM5alpha restricts human immunodeficiency virus type 1 (HIV-1) via proteasome-dependent and -independent pathways. Here we examined the effects of RING domain mutations on retrovirus restriction by TRIM5alpha in various combinations of virus and host species. Simian immunodeficiency virus isolated from macaque (SIVmac) successfully avoided attacks by RING mutants of African green monkey (AGM)-TRIM5alpha that could still restrict HIV-1. Addition of proteasome inhibitor did not affect the anti-HIV-1 activity of AGM-TRIM5alpha, whereas it disrupted at least partly its anti-SIVmac activity. In the case of mutant human TRIM5alpha carrying proline at the position 332, however, both HIV-1 and SIVmac restrictions were eliminated as a result of RING domain mutations. These results suggested that the mechanisms of retrovirus restriction by TRIM5alpha vary depending on the combination of host and virus.","corpus_id":34391584,"score":1},{"doc_id":"21205312","title":"Characterization of a core fragment of the rhesus monkey TRIM5α protein.","abstract":"BACKGROUND: Like all tripartite motif (TRIM) proteins, the retroviral restriction factor TRIM5α consists of RING, B-box 2 and coiled-coil domains, with a C-terminal B30.2(SPRY) domain. Although structures have been determined for some individual TRIM domains, the structure of an intact TRIM protein is unknown. RESULTS: Here, we express and characterize a protease-resistant 29-kD core fragment containing the B-box 2, coiled coil and adjacent linker (L2) region of TRIM5α. This BCCL2 protein formed dimers and higher-order oligomers in solution. Approximately 40% of the BCCL2 secondary structure consisted of alpha helices. Partial loss of alpha-helical content and dissociation of dimers occurred at 42°C, with the residual alpha helices remaining stable up to 80°C. CONCLUSIONS: These results indicate that the B-box 2, coiled-coil and linker 2 regions of TRIM5α form a core dimerization motif that exhibits a high level of alpha-helical content.","corpus_id":16955118,"score":1},{"doc_id":"21490953","title":"SUMO-interacting motifs of human TRIM5α are important for antiviral activity.","abstract":"Human TRIM5α potently restricts particular strains of murine leukemia viruses (the so-called N-tropic strains) but not others (the B- or NB-tropic strains) during early stages of infection. We show that overexpression of SUMO-1 in human 293T cells, but not in mouse MDTF cells, profoundly blocks N-MLV infection. This block is dependent on the tropism of the incoming virus, as neither B-, NB-, nor the mutant R110E of N-MLV CA (a B-tropic switch) are affected by SUMO-1 overexpression. The block occurred prior to reverse transcription and could be abrogated by large amounts of restricted virus. Knockdown of TRIM5α in 293T SUMO-1-overexpressing cells resulted in ablation of the SUMO-1 antiviral effects, and this loss of restriction could be restored by expression of a human TRIM5α shRNA-resistant plasmid. Amino acid sequence analysis of human TRIM5α revealed a consensus SUMO conjugation site at the N-terminus and three putative SUMO interacting motifs (SIMs) in the B30.2 domain. Mutations of the TRIM5α consensus SUMO conjugation site did not affect the antiviral activity of TRIM5α in any of the cell types tested. Mutation of the SIM consensus sequences, however, abolished TRIM5α antiviral activity against N-MLV. Mutation of lysines at a potential site of SUMOylation in the CA region of the Gag gene reduced the SUMO-1 block and the TRIM5α restriction of N-MLV. Our data suggest a novel aspect of TRIM5α-mediated restriction, in which the presence of intact SIMs in TRIM5α, and also the SUMO conjugation of CA, are required for restriction. We propose that at least a portion of the antiviral activity of TRIM5α is mediated through the binding of its SIMs to SUMO-conjugated CA.","corpus_id":5948075,"score":1},{"doc_id":"21568899","title":"Retroviral restriction factors TRIM5α: therapeutic strategy to inhibit HIV-1 replication.","abstract":"Tripartite motif protein 5-alpha (TRIM5α) is a cytoplasmic protein that efficiently recognizes the incoming capsid (CA) protein of retroviruses and potently inhibits virus infection in a species-specific manner. Through directly recognizing and interacting with HIV CA, TRIM5α is capable of disrupting the ordered process of viral uncoating, eventually interfering with HIV-1 reverse transcription and virus replication. TRIM5α protein contains four domains: RING domain, B-box 2 domain, coiled-coil domain, and B30.2 domain (SPRY) domain. All of the domains are necessary for efficient retrovirus restriction and the B30.2 domain has been shown to be the determinant of the specificity of restriction. Species-specific innate resistance against viral infections offers novel avenues for antiviral therapeutics. Various mutants of TRIM5α have been described which differently affect the HIV-1 reverse transcription process. This makes the establishment of new and improved models for HIV replication and AIDS pathogenesis by monitoring endogenous TRIM5α an attractive approach. TRIM5α-mediated restriction is modulated by the host protein Cyclophilin A (Cyp A) which could effectively interact with the CA of HIV-1. Here we will review the structure and roles of TRIM5α protein, the interaction between Cyp A and TRIM5α, as well as gene therapy strategies associated with TRIM5α to inhibit HIV-1 infection.","corpus_id":12366103,"score":1},{"doc_id":"21680520","title":"Role of TRIM5α RING domain E3 ubiquitin ligase activity in capsid disassembly, reverse transcription blockade, and restriction of simian immunodeficiency virus.","abstract":"The mammalian tripartite motif protein, TRIM5α, recognizes retroviral capsids entering the cytoplasm and blocks virus infection. Depending on the particular TRIM5α protein and retrovirus, complete disruption of the TRIM5α RING domain decreases virus-restricting activity to various degrees. TRIM5α exhibits RING domain-dependent E3 ubiquitin ligase activity, but the specific role of this activity in viral restriction is unknown. We created a panel of African green monkey TRIM5α (TRIM5α(AGM)) mutants, many of which are specifically altered in RING domain E3 ubiquitin ligase function, and characterized the phenotypes of these mutants with respect to restriction of simian and human immunodeficiency viruses (SIV(mac) and HIV-1, respectively). TRIM5α(AGM) ubiquitin ligase activity was essential for both the accelerated disassembly of SIV(mac) capsids and the disruption of reverse transcription. The levels of SIV(mac) particulate capsids in the cytosol of target cells expressing the TRIM5α variants strongly correlated with the levels of viral late reverse transcripts. RING-mediated ubiquitylation and B30.2(SPRY) domain-determined capsid binding independently contributed to the potency of SIV(mac) restriction by TRIM5α(AGM). In contrast, TRIM5α proteins attenuated in RING ubiquitin ligase function still accelerated HIV-1 capsid disassembly, inhibited reverse transcription, and blocked infection. Replacement of the helix-4/5 loop in the SIV(mac) capsid with the corresponding region of the HIV-1 capsid diminished the dependence of restriction on TRIM5α RING function. Thus, ubiquitylation mediated by the RING domain of TRIM5α(AGM) is essential for blocking SIV(mac) infection at the stage of capsid uncoating.","corpus_id":25158696,"score":1},{"doc_id":"21866272","title":"TRIM5 acts as more than a retroviral restriction factor.","abstract":"The retrovirus restriction factor TRIM5α blocks post-entry infection of retroviruses in a species-specific manner. As a cellular E3 ubiquitin ligase, TRIM5α binds to the retroviral capsid lattice in the cytoplasm of an infected cell and accelerates the uncoating process of retroviral capsid, thus providing a potent restriction to HIV-1 and other retrovirus infections. The precise mechanism by which this restriction is imposed remains under scrutiny, and evidence is lacking to link the E3 ubiquitin ligase activity of TRIM5α to its ability to restrict retrovirus infection. In a recent study, Pertel and colleagues have uncovered the link between the two, providing compelling evidence to suggest that following the interaction with the retroviral capsid, TRIM5 triggers an antiviral innate immune response by functioning as a pattern recognition receptor. This unique function of TRIM5 is dependent on its association with the E2 ubiquitin-conjugating enzyme complex UBC13-UEV1A and subsequent activation of the TAK1 kinase complex and downstream genes involved in innate immune responses. These findings have defined a novel function for TRIM5 as a pattern recognition receptor in innate immune recognition and provided valuable mechanistic insight into its role as a retroviral restriction factor. Here we discuss the significance of these new findings in understanding TRIM5-mediated HIV restriction.","corpus_id":5565058,"score":1},{"doc_id":"21911161","title":"Reduction of N-tropic mutant porcine endogenous retrovirus infectivity by human tripartite motif-containing 5-isoform alpha.","abstract":"In cases of retroviral infection, the host cell deploys antiviral proteins as a type of innate immunity. Tripartite motif-containing 5-isoform alpha (TRIM5α) is a potent antiviral protein. TRIM5α has been reported to restrict human immunodeficiency virus (HIV) 1 infection in rhesus monkey cells by targeting the incoming viral capsid at the postentry or preintegration stage of the viral life cycle. As a consequence, virus replication and reverse transcription are interrupted. TRIM5α of human origin has also been shown to inhibit N-tropic murine leukemia virus infection. To investigate the inhibitory effect of TRIM5α on porcine endogenous retrovirus (PERV) infection in humans, we constructed a 293T cell line stably expressing human TRIM5α (293T-huTRIM5α) and tested the infectivity of vesicular stomatitis virus glycoprotein envelope pseudotyped viruses (wild-type PERV [wt-PERV], N-tropic mutant PERV, N-tropic murine leukemia virus, and MoMLV). Infectivity of N-tropic mutant PERV was reduced by 43.3% in 293T-huTRIM5α cells, a decrease in efficiency that was more than 3-fold greater than that of wt-PERV in 293T-huTRIM5α cells. Human TRIM5α exhibited inhibitory activity against N-tropic MLV and N-tropic mutant PERV, but showed no antiviral activity against Moloney murine leukemia virus or wt-PERV.","corpus_id":27428098,"score":1},{"doc_id":"22193888","title":"The cell biology of TRIM5α.","abstract":"The tripartite motif (TRIM)-containing proteins are involved in many cellular functions such as cell signaling, apoptosis, cell differentiation, and immune modulation. TRIM5 proteins, including TRIM5α and TRIM-Cyp, are known to possess antiretroviral activity against many different retroviruses. Besides being retroviral restriction factors, TRIM5 proteins participate in other cellular functions that have recently emerged in the study of TRIM5α. In this review, we discuss properties of TRIM5α such as cytoplasmic body formation, protein turnover, and trafficking. Also, we discuss recent insights into innate immune modulation mediated by TRIM5α, highlighting the various functions TRIM5α has in cellular processes.","corpus_id":43893067,"score":1},{"doc_id":"22291694","title":"TRIM5α and Species Tropism of HIV/SIV.","abstract":"Human immunodeficiency virus type 1 (HIV-1) infects humans and chimpanzees but not old world monkeys (OWMs) such as the rhesus monkey (Rh) and cynomolgus monkey (CM). HIV-1 efficiently enters cells of OWMs but encounters a block before reverse transcription. This narrow host range is attributed to a barrier in the host cell. In 2004, the screening of a Rh cDNA library identified tripartite motif 5α (TRIM5α) as a cellular antiviral factor. TRIM5α is one of splicing variants produced by TRIM5 gene and TRIM5 proteins are members of the TRIM family containing RING, B-box 2, and coiled-coil domains. The RING domain is frequently found in E3 ubiquitin ligase and TRIM5α is degraded via the ubiquitin-proteasome-dependent pathway. Among TRIM5 splicing variants, TRIM5α alone has an additional C-terminal PRYSPRY (B30.2) domain. Previous studies have shown that sequence variation in variable regions of the PRYSPRY domain among different monkey species affects species-specific retrovirus infection, while amino acid sequence differences in the viral capsid protein determine viral sensitivity to restriction. TRIM5α recognizes the multimerized capsid proteins (viral core) of an incoming virus by its PRYSPRY domain and is thus believed to control retroviral infection. There are significant intraspecies variations in the Rh-TRIM5 gene. It has also been reported that some Rh and CM individuals have retrotransposed cyclophilin A open reading frame in the TRIM5 gene, which produces TRIM5-cyclophilin A fusion protein (TRIMCyp). TRIMCyp, which was originally identified as an anti-HIV-1 factor of New World owl monkeys, is an interesting example of the gain of a new function by retrotransposition. As different TRIM5 genotypes of Rh showed different levels of simian immunodeficiency virus replication in vivo, the TRIM5 genotyping is thought to be important in acquired immunodeficiency syndrome monkey models.","corpus_id":6438419,"score":1},{"doc_id":"22435067","title":"Role of Human TRIM5α in Intrinsic Immunity.","abstract":"Human immunodeficiency virus (HIV) has a very narrow host range. HIV type 1 (HIV-1) does not infect Old World monkeys, such as the rhesus monkey (Rh). Rh TRIM5α was identified as a factor that confers resistance, intrinsic immunity, to HIV-1 infection. Unfortunately, human TRIM5α is almost powerless to restrict HIV-1. However, human TRIM5α potently restricts N-tropic murine leukemia viruses (MLV) but not B-tropic MLV, indicating that human TRIM5α represents the restriction factor previously designated as Ref1. African green monkey TRIM5α represents another restriction factor previously designated as Lv1, which restricts both HIV-1 and simian immunodeficiency virus isolated from macaque (SIVmac) infection. TRIM5 is a member of the tripartite motif family containing RING, B-box2, and coiled-coil domains. The RING domain is frequently found in E3 ubiquitin ligase, and TRIM5α is thought to degrade viral core via ubiquitin-proteasome-dependent and -independent pathways. The alpha isoform of TRIM5 has an additional C-terminal PRYSPRY domain, which is a determinant of species-specific retrovirus restriction by TRIM5α. On the other hand, the target regions of viral capsid protein (CA) are scattered on the surface of core. A single amino acid difference in the surface-exposed loop between α-helices 6 and 7 (L6/7) of HIV type 2 (HIV-2) CA affects viral sensitivity to human TRIM5α and was also shown to be associated with viral load in West African HIV-2 patients, indicating that human TRIM5α is a critical modulator of HIV-2 replication in vivo. Interestingly, L6/7 of CA corresponds to the MLV determinant of sensitivity to mouse factor Fv1, which potently restricts N-tropic MLV. In addition, human genetic polymorphisms also affect antiviral activity of human TRIM5α. Recently, human TRIM5α was shown to activate signaling pathways that lead to activation of NF-κB and AP-1 by interacting with TAK1 complex. TRIM5α is thus involved in control of viral infection in multiple ways.","corpus_id":2912377,"score":1},{"doc_id":"22847415","title":"Structure of the rhesus monkey TRIM5α PRYSPRY domain, the HIV capsid recognition module.","abstract":"Tripartite motif protein TRIM5α blocks retroviral replication after cell entry, and species-specific differences in its activity are determined by sequence variations within the C-terminal B30.2/PRYSPRY domain. Here we report a high-resolution structure of a TRIM5α PRYSPRY domain, the PRYSPRY of the rhesus monkey TRIM5α that potently restricts HIV infection, and identify features involved in its interaction with the HIV capsid. The extensive capsid-binding interface maps on the structurally divergent face of the protein formed by hypervariable loop segments, confirming that TRIM5α evolution is largely determined by its binding specificity. Interactions with the capsid are mediated by flexible variable loops via a mechanism that parallels antigen recognition by IgM antibodies, a similarity that may help explain some of the unusual functional properties of TRIM5α. Distinctive features of this pathogen-recognition interface, such as structural plasticity conferred by the mobile v1 segment and interaction with multiple epitopes, may allow restriction of divergent retroviruses and increase resistance to capsid mutations.","corpus_id":18506201,"score":1},{"doc_id":"23084420","title":"Contribution of SUMO-interacting motifs and SUMOylation to the antiretroviral properties of TRIM5α.","abstract":"Recent findings suggested that the SUMO-interacting motifs (SIMs) present in the human TRIM5α (TRIM5α(hu)) protein play an important role in the ability of TRIM5α(hu) to restrict N-MLV. Here we explored the role of SIMs in the ability of rhesus TRIM5α (TRIM5α(rh)) to restrict HIV-1, and found that TRIM5α(rh) SIM mutants IL376KK (SIM1mut) and VI405KK (SIM2mut) completely lost their ability to block HIV-1 infection. Interestingly, these mutants also lost the recently described property of TRIM5α(rh) to shuttle into the nucleus. Analysis of these variants revealed that they are unable to interact with the HIV-1 core, which might explain the reason that these variants are not active against HIV-1. Furthermore, NMR titration experiments to assay the binding between the PRYSPRY domain of TRIM5α(rh) and the small ubiquitin-like modifier 1(SUMO-1) revealed no interaction. In addition, we examined the role of SUMOylation in restriction, and find out that inhibition of SUMOylation by the adenoviral protein Gam1 did not alter the retroviral restriction ability of TRIM5α. Overall, our results do not support a role for SIMs or SUMOylation in the antiviral properties of TRIM5α.","corpus_id":39621283,"score":1},{"doc_id":"23320071","title":"Delaying reverse transcription does not increase sensitivity of HIV-1 to human TRIM5α.","abstract":"BACKGROUND: Because uncoating of the capsid is linked to reverse transcription, modifications that delay this process lead to the persistence in the cytoplasm of capsids susceptible to recognition by the human restriction factor TRIM5α (hTRIM5α). It is unknown, however, if increasing the time available for capsid-hTRIM5α interactions would actually render viruses more sensitive to hTRIM5α. RESULTS: Viral sensitivity to hTRIM5α was evaluated by comparing their replication in human U373-X4 cells in which hTRIM5α activity had or had not been inhibited by overexpression of human TRIM5γ. No differences were observed comparing wild-type HIV-1 and variants carrying mutations in reverse transcriptase or the central polypurine tract that delayed the completion of reverse transcription. In addition, the effect of delaying the onset of reverse transcription for several hours by treating target cells with nevirapine was evaluated using viral isolates with different sensitivities to hTRIM5α. Delaying reverse transcription led to a time-dependent loss in viral infectivity that was increased by inhibiting capsid-cyclophilin A interactions, but did not result in increased viral sensitivity to hTRIM5α, regardless of their intrinsic sensitivity to this restriction factor. CONCLUSIONS: Consistent with prior studies, the HIV-1 capsid can be targeted for destruction by hTRIM5α, but different strains display considerable variability in their sensitivity to this restriction factor. Capsids can also be lost more slowly through a TRIM5α-independent process that is accelerated when capsid-cyclophilin A interactions are inhibited, an effect that may reflect changes in the intrinsic stability of the capsid. Blocking the onset or delaying reverse transcription does not, however, increase viral sensitivity to hTRIM5α, indicating that the recognition of the capsids by hTRIM5α is completed rapidly following entry into the cytoplasm, as previously observed for the simian restriction factors TRIM-Cyp and rhesus TRIM5α.","corpus_id":16613455,"score":1},{"doc_id":"23548691","title":"Viral attachment induces rapid recruitment of an innate immune sensor (TRIM5α) to the plasma membrane.","abstract":"TRIM5α (tripartite motif 5α) acts as a pattern recognition receptor specific for the retrovirus capsid lattice and blocks infection by HIV-1 immediately after entry. However, the precise mechanisms underlying this rapid recognition of viral components remain elusive. Here, we analyzed the influence of viral exposure on TRIM5α. Total internal reflection fluorescence microscopy and lipid flotation assays revealed rapid recruitment of a TRIM5α subpopulation to the plasma membrane (PM) upon exposure to vesicular stomatitis virus-G-pseudotyped HIV-1 viral-like particles (VLPs), but not to envelope (Env)-less HIV-1 VLPs. TRIM5α signals were frequently colocalized with those of HIV-1 capsid at the PM. Exposure to HIV-1 Env-pseudotyped HIV-1 vectors also triggered translocation of endogenous TRIM5α to lipid microdomains within human T cells. Similarly, clustering of lipid microdomains by a glycosphingolipid stereoisomer resulted in rapid TRIM5α recruitment to the PM. Of note, recruitment of endogenous rhesus TRIM5α to the PM prior to HIV-1 infection significantly increased the potency of viral restriction. Our data therefore suggest the importance of TRIM5α recruitment to the PM for TRIM5α-mediated innate immune sensing and restriction of retroviral infection.","corpus_id":32856651,"score":1},{"doc_id":"24554657","title":"Contribution of PDZD8 to stabilization of the human immunodeficiency virus type 1 capsid.","abstract":"UNLABELLED: Following human immunodeficiency virus type 1 (HIV-1) entry into the host cell, the viral capsid gradually disassembles in a process called uncoating. A proper rate of uncoating is important for reverse transcription of the HIV-1 genome. Host restriction factors such as TRIM5α and TRIMCyp bind retroviral capsids and cause premature disassembly, leading to blocks in reverse transcription. Other host factors, such as cyclophilin A, stabilize the HIV-1 capsid and are required for efficient infection in some cell types. Here, we show that a heat-labile factor greater than 100 kDa in the cytoplasm of cells from multiple vertebrate species slows the spontaneous disassembly of HIV-1 capsid-nucleocapsid (CA-NC) complexes in vitro. We identified the PDZ domain-containing protein 8 (PDZD8) as a critical component of the capsid-stabilizing activity in the cytoplasmic extracts. PDZD8 has been previously reported to bind the HIV-1 Gag polyprotein and to make a positive contribution to the efficiency of HIV-1 infection (M. S. Henning, S. G. Morham, S. P. Goff, and M. H. Naghavi, J. Virol. 84:: 8990-8995, 2010, doi:10.1128/JVI.00843-10). PDZD8 knockdown accelerated the disassembly of HIV-1 capsids in infected cells, resulting in decreased reverse transcription. The PDZD8 coiled-coil domain is sufficient for HIV-1 capsid binding, but other parts of the protein, including the PDZ domain, are apparently required for stabilizing the capsid and supporting HIV-1 infection. In summary, PDZD8 interacts with and stabilizes the HIV-1 capsid and thus represents a potentially targetable host cofactor for HIV-1 infection. IMPORTANCE: After human immunodeficiency virus type 1 (HIV-1) gains access to the interior of the target cell, host cell factors can influence virus infection in either a positive or negative way. HIV-1 depends upon certain host cell factors to assist processes that are required for virus replication. One example of such a host factor is PDZD8. This work shows that PDZD8 helps to stabilize the HIV-1 capsid, a huge complex of the viral RNA, enzymes, and protein. When PDZD8 is prevented from interacting with the HIV-1 capsid, the capsid becomes unstable and HIV-1 infection is inhibited. These results show that PDZD8 regulates the uncoating of the HIV-1 capsid. Interfering with the interaction of PDZD8 and capsid could prove to be a useful strategy for intervening in HIV-1 infection and transmission.","corpus_id":31806380,"score":1},{"doc_id":"24583231","title":"The conserved sumoylation consensus site in TRIM5α modulates its immune activation functions.","abstract":"TRIM5α is a type I interferon-stimulated anti-retroviral restriction factor expressed in most primates and homologous proteins are expressed in other mammals. Through its C-terminal PRYSPRY (B30.2) domain, TRIM5α binds to incoming and intact post-fusion retroviral cores in the cytoplasm. Following this direct interaction, the retroviral capsid core is destabilized and progression of the virus life cycle is interrupted. Specific recognition of its viral target by TRIM5α also triggers the induction of an antiviral state involving the activation of transcription factors NF-κB- and AP-1. In addition to PRYSPRY, several other TRIM5α domains are important for anti-retroviral function, including a RING zinc-binding motif. This domain has \"E3\" ubiquitin ligase activity and is involved in both the direct inhibition of incoming retroviruses and innate immune activation. A highly conserved sumoylation consensus site is present between the RING motif and the N-terminal extremity of TRIM5α. No clear role in restriction has been mapped to this sumoylation site, and no sumoylated forms of TRIM5α have been observed. Here we confirm that mutating the putatively sumoylated lysine (K10) of the Rhesus macaque TRIM5α (TRIM5αRh) to an arginine has only a small effect on restriction. However, we show that the mutation significantly decreases the TRIM5α-induced generation of free K63-linked ubiquitin chains, an intermediate in the activation of innate immunity pathways. Accordingly, K10R decreases TRIM5α-mediated activation of both NF-κB and AP-1. Concomitantly, we find that K10R causes a large increase in the levels of ubiquitylated TRIM5α. Finally, treatment with the nuclear export inhibitor leptomycin B shows that K10R enhances the nuclear localization of TRIM5αRh, while at the same time reducing its level of association with nuclear SUMO bodies. In conclusion, the TRIM5α sumoylation site appears to modulate the E3 ubiquitin ligase activities of the adjacent RING domain, promoting K63-linked ubiquitin chains at the expense of auto-ubiquitylation which is probably K48-linked. Consistently, we find this sumoylation site to be important for innate immune activation by TRIM5α. In addition, lysine 10 regulates TRIM5α nuclear shuttling and nuclear localization, which may also be related to its role in innate immunity activation.","corpus_id":13309522,"score":1},{"doc_id":"25880753","title":"TRIM5α is a SUMO substrate.","abstract":"BACKGROUND: The TRIM5α restriction factor interferes with retroviral infections by inhibiting an early step of viral replication. TRIM5α activity was recently proposed to be regulated by the SUMO machinery and one SUMO consensus conjugation site as well as three putative SUMO interacting motifs (SIMs) were identified within TRIM5α sequence. Whereas mutation of the SIM sequences was found to abolish TRIM5α antiviral activity, mutation of the consensus SUMO conjugation site did not affect its restriction capacity, although this putative site has never been shown to be actually a SUMO substrate. FINDINGS: Here we further demonstrate that TRIM5α relies on the SUMO machinery to promote restriction, since SUMO1 overexpression enhances TRIM5α-mediated retroviral inhibition whereas knockdown of SUMO1 or E2 SUMO conjugating enzyme Ubc9 prevents restriction. Furthermore, we show for the first time that TRIM5α is SUMOylated both in vitro and in cellulo and that Lysine 10 is the main SUMOylation site. Mutation of the consensus SUMO conjugation motif in position 10 abrogated SUMOylation at this position, but did not disrupt TRIM5α antiviral activity. CONCLUSIONS: Altogether, our results confirm that the SUMO machinery is involved in TRIM5α-mediated retroviral restriction, and demonstrate that TRIM5α is a SUMO 1 and SUMO 2 substrate. The inability to abrogate TRIM5α antiviral activity by mutating its main SUMO conjugation motif supports the notion that non-covalent interaction with SUMO or SUMOylated proteins rather than TRIM5α direct SUMOylation is required.","corpus_id":1333081,"score":1},{"doc_id":"26372380","title":"Impact of TRIM5α in vivo.","abstract":"HIV type 1 (HIV-1) has a very narrow host range that is limited to humans and chimpanzees. HIV-1 cannot replicate well in Old World monkey cells such as rhesus and cynomolgus monkeys. Tripartite motif (TRIM)5α is a key molecule that confers potent resistance against HIV-1 infection and is composed of really interesting new gene, B-box2, coiled-coil and PRYSPRY domains. Interaction between TRIM5α PRYSPRY domains and HIV-1 capsid core triggers the anti-HIV-1 activity of TRIM5α. Analysis of natural HIV variants and extensive mutational experiments has revealed the presence of critical amino acid residues in both the PRYSPRY domain and HIV capsid for potent HIV suppression by TRIM5α. Genetic manipulation of the human TRIM5 gene could establish human cells totally resistant to HIV-1, which may lead to a cure for HIV-1 infection in the future.","corpus_id":7060927,"score":1},{"doc_id":"29196608","title":"Rhesus monkey TRIM5α protein SPRY domain contributes to AP-1 activation.","abstract":"TRIM5α is an important host restriction factor that could potently block retrovirus infection. The SPRY domain of TRIM5α mediates post-entry restriction by recognition of and binding to the retroviral capsid. Human TRIM5α also functions as an innate immune sensor to activate AP-1 and NF-κB signaling, which subsequently restrict virus replication. Previous studies have shown that the AP-1 and NF-κB signaling activation relies on the RING motif of TRIM5α. In this study, we have demonstrated that the SPRY domain is essential for rhesus macaque TRIM5α to activate AP-1 but not NF-κB signaling. The AP-1 activation mainly depends on all of the β-sheet barrel on SPRY structure of TRIM5α. Furthermore, the SPRY-mediated auto-ubiquitination of TRIM5α is required for AP-1 activation. This study reports that rhesus macaque TRIM5α mainly undergoes Lys27-linked and Met1-linked auto-polyubiquitination. Finally, we found that the TRIM5α signaling function was positively correlated with its retroviral restriction activity. This study discovered an important role of the SPRY domain in immune signaling and antiviral activity and further expanded our knowledge of the antiviral mechanism of TRIM5α.","corpus_id":3648191,"score":1},{"doc_id":"29237846","title":"The Three-Fold Axis of the HIV-1 Capsid Lattice Is the Species-Specific Binding Interface for TRIM5α.","abstract":"Rhesus TRIM5α (rhTRIM5α) potently restricts replication of human immunodeficiency virus type 1 (HIV-1). Restriction is mediated through direct binding of the C-terminal B30.2 domain of TRIM5α to the assembled HIV-1 capsid core. This host-pathogen interaction involves multiple capsid molecules within the hexagonal HIV-1 capsid lattice. However, the molecular details of this interaction and the precise site at which the B30.2 domain binds remain largely unknown. The human orthologue of TRIM5α (hsTRIM5α) fails to block infection by HIV-1 both in vivo and in vitro This is thought to be due to differences in binding to the capsid lattice. To map the species-specific binding surface on the HIV-1 capsid lattice, we used microscale thermophoresis and dual-focus fluorescence correlation spectroscopy to measure binding affinity of rhesus and human TRIM5α B30.2 domains to a series of HIV-1 capsid variants that mimic distinct capsid arrangements at each of the symmetry axes of the HIV-1 capsid lattice. These surrogates include previously characterized capsid oligomers, as well as a novel chemically cross-linked capsid trimer that contains cysteine substitutions near the 3-fold axis of symmetry. The results demonstrate that TRIM5α binding involves multiple capsid molecules along the 2-fold and 3-fold interfaces between hexamers and indicate that the binding interface at the 3-fold axis contributes to the well-established differences in restriction potency between TRIM5α orthologues. IMPORTANCE TRIM5α is a cellular protein that fends off infection by retroviruses through binding to the viruses' protein shell surrounding its genetic material. This shell is composed of several hundred capsid proteins arranged in a honeycomb-like hexagonal pattern that is conserved across retroviruses. By binding to the complex lattice formed by multiple capsid proteins, rather than to a single capsid monomer, TRIM5α restriction activity persists despite the high mutation rate in retroviruses such as HIV-1. In rhesus monkeys, but not in humans, TRIM5α confers resistance to HIV-1. By measuring the binding of human and rhesus TRIM5α to a series of engineered HIV-1 capsid mimics of distinct capsid lattice interfaces, we reveal the HIV-1 capsid surface critical for species-specific binding by TRIM5α.","corpus_id":3590121,"score":1},{"doc_id":"18799572","title":"Biochemical and biophysical characterization of a chimeric TRIM21-TRIM5alpha protein.","abstract":"The tripartite motif (TRIM) protein, TRIM5alpha, is an endogenous factor in primates that recognizes the capsids of certain retroviruses after virus entry into the host cell. TRIM5alpha promotes premature uncoating of the capsid, thus blocking virus infection. Low levels of expression and tendencies to aggregate have hindered the biochemical, biophysical, and structural characterization of TRIM proteins. Here, a chimeric TRIM5alpha protein (TRIM5(Rh)-21R) with a RING domain derived from TRIM21 was expressed in baculovirus-infected insect cells and purified. Although a fraction of the TRIM5(Rh)-21R protein formed large aggregates, soluble fractions of the protein formed oligomers (mainly dimers), exhibited a protease-resistant core, and contained a high percentage of helical secondary structure. Cross-linking followed by negative staining and electron microscopy suggested a globular structure. The purified TRIM5(Rh)-21R protein displayed E3-ligase activity in vitro and also self-ubiquitylated in the presence of ubiquitin-activating and -conjugating enzymes. The purified TRIM5(Rh)-21R protein specifically associated with human immunodeficiency virus type 1 capsid-like complexes; a deletion within the V1 variable region of the B30.2(SPRY) domain decreased capsid binding. Thus, the TRIM5(Rh)-21R restriction factor can directly recognize retroviral capsid-like complexes in the absence of other mammalian proteins.","corpus_id":22489148,"score":0},{"doc_id":"19951947","title":"Determinants for the rhesus monkey TRIM5alpha-mediated block of the late phase of HIV-1 replication.","abstract":"Rhesus monkey TRIM5alpha (TRIM5alpharh) includes RING, B-box, coiled-coil, and B30.2(PRYSPRY) domains and blocks HIV-1 infection by targeting HIV-1 core through a B30.2(PRYSPRY) domain. Previously, we reported that TRIM5alpharh also blocks HIV-1 production in a B30.2(PRYSPRY)-independent manner. Efficient encapsidation of TRIM5alpharh, but not human TRIM5alpha (TRIM5alphahu), in HIV-1 virus-like particles suggests the interaction between Gag and TRIM5alpharh during viral assembly. Here, we determined responsible regions for late restriction activity of TRIM5alpharh. The RING disruption, but not the replacement with human TRIM21 RING, ablated the efficient encapsidation and the late restriction, suggesting that a RING structure was essential for the late restriction and efficient interaction with HIV-1 Gag. The prominent cytoplasmic body formation of TRIM5alpharh, which depended on the coiled-coil domain and the ensuing linker 2 region, was not required for the encapsidation. Intriguingly, TRIM5alpharh coiled-coil domain mutants (M133T and/or T146A) showed impaired late restriction activity, despite the efficient encapsidation and cytoplasmic body formation. Our results suggest that the TRIM5alpharh-mediated late restriction involves at least two distinct activities as follows: (i) interaction with HIV-1 Gag polyprotein through the N-terminal, RING, and B-box 2 regions of a TRIM5alpharh monomer, and (ii) an effector function(s) that depends upon the coiled-coil and linker 2 domains of TRIM5alpharh. We speculate that the TRIM5alpharh coiled-coil region recruits additional factor(s), such as other TRIM family proteins or a cellular protease, during the late restriction. RBCC domains of TRIM family proteins may play a role in sensing newly synthesized viral proteins as a part of innate immunity against viral infection.","corpus_id":42539395,"score":0},{"doc_id":"20929586","title":"A novel envelope mediated post entry restriction of murine leukaemia virus in human cells is Ref1/TRIM5α independent.","abstract":"BACKGROUND: 'Intrinsic' resistance to retroviral infection was first recognised with the Friend virus susceptibility gene (Fv1), which determines susceptibility to murine leukaemia virus (MLV) infection in different murine species. Similarly, the tripartite motif (TRIM) family of proteins determine lentiviral restriction in a primate host-species specific manner. For example rhesus TRIM5α (rhTRIM5α) can potently restrict HIV-1 infection while human TRIM5α (huTRIM5α) only has a mild effect on SIVmac and HIV-1 infectivity (Lv1). Human TRIM5α is able to restrict MLV-N virus replication, but is ineffective against MLV-B or MLV-NB virus infection. Lv2 restriction of some HIV-2 viruses is seen in human cells. Like Lv1, Lv2 is a post-entry restriction factor, whose viral determinants have been mapped to the viral capsid (CA). Unlike Lv1, however, Lv2 is determined by envelope (Env) in addition to CA. Here we present evidence of a novel Env determined post entry restriction to infection in human cells of pseudotyped MLV-B and MLV-NB cores. RESULTS: We generated retroviral vectors pseudotyped with various gamma and lentiviral Envs on MLV-B and -NB CAs containing a green fluorescent protein (GFP) reporter. Flow cytometry was used to determine transduction efficiencies in NP2/CD4/CXCR4 (glioma cell line stably transduced with the HIV receptors) and HeLa/CD4 cell lines. The HeLa/CD4 cell line restricted both MLV CAs in an Env dependent manner, compared to NP2/CD4/CXCR4 cells. Quantitative polymerase chain reaction (QT-PCR) analysis of reverse transcription (RT) transcripts demonstrates that this restriction occurs at a post entry and RT level. siRNA knockdown of huTRIM5α ruled out a direct role for this cellular component in mediating this restriction. We describe a previously unobserved Env determined restriction of MLV-B and MLV-NB CAs in HeLa/CD4 cells when pseudotyped with HIV-2 and RD114 Envs, but not gibbon ape leukaemia virus (GALV), HIV-1 or Amphotrophic (Ampho) Envs. CONCLUSIONS: Our data further demonstrate the variability of Env and CA mediated susceptibility to post entry host cell restriction. We discuss the relevance of these findings in light of the growing evidence supporting the complexities involved in innate host immunity to retroviral infection.","corpus_id":6951798,"score":0},{"doc_id":"21247355","title":"Recent insights into the mechanism and consequences of TRIM5α retroviral restriction.","abstract":"The cellular factor TRIM5α inhibits infection by numerous retroviruses in a species-specific manner. The TRIM5α protein from rhesus macaques (rhTRIM5α) restricts infection by HIV-1 while human TRIM5α (huTRIM5α) restricts infection by murine leukemia virus (MLV). In owl monkeys a related protein TRIM-Cyp restricts HIV-1 infection. Several models have been proposed for retroviral restriction by TRIM5 proteins (TRIM5α and TRIM-Cyp). These models collectively suggest that TRIM5 proteins mediate restriction by directly binding to specific determinants in the viral capsid. Through their ability to self-associate TRIM5 proteins compartmentalize the viral capsid core and mediate its abortive disassembly via a poorly understood mechanism that is sensitive to proteasome inhibitors. In this review, we discuss TRIM5-mediated restriction in detail. We also discuss how polymorphisms within human and rhesus macaque populations have been demonstrated to affect disease progression of immunodeficiency viruses in these species.","corpus_id":34016773,"score":0},{"doc_id":"21264255","title":"The antiviral spectra of TRIM5α orthologues and human TRIM family proteins against lentiviral production.","abstract":"BACKGROUND: Rhesus monkey TRIM5α (TRIM5αrh) recognizes the incoming HIV-1 core through its C-terminal B30.2(PRYSPRY) domain and promotes its premature disassembly or degradation before reverse transcription. Previously, we have shown that TRIM5αrh blocks HIV-1 production through the N-terminal RBCC domain by the recognition of Gag polyproteins. Although all TRIM family proteins have RBCC domains, it remains elusive whether they possess similar late-restriction activities. METHODOLOGY/PRINCIPAL FINDINGS: We examined the antiviral spectra of TRIM5α orthologues and human TRIM family members which have a genetic locus proximal to human TRIM5α (TRIM5αhu), against primate lentiviral production. When HIV-1 virus-like particles (VLPs) were generated in the presence of TRIM5α proteins, rhesus, African green and cynomolgus monkey TRIM5α (TRIM5αag and TRIM5αcy), but not TRIM5αhu, were efficiently incorporated into VLPs, suggesting an interaction between HIV-1 Gag and TRIM5α proteins. TRIM5αrh potently restricted the viral production of HIV-1 groups M and O and HIV-2, but not simian lentiviruses including SIV(MAC)1A11, SIV(AGM)Tan-1 or SIV(AGM)SAB-1. TRIM5αhu did not show notable late restriction activities against these lentiviruses. TRIM5αag and TRIM5αcy showed intermediate restriction phenotypes against HIV-1 and HIV-2, but showed no restriction activity against SIV production. A series of chimeric TRIM5α constructs indicated that the N-terminal region of TRIM5αag and TRIM5αcy are essential for the late restriction activity, while the C-terminal region of TRIM5αcy negatively regulates the late restriction activity against HIV-1. When select human TRIM family proteins were examined, TRIM21 and 22 were efficiently incorporated into HIV-1 VLPs, while only TRIM22 reduced HIV-1 titers up to 5-fold. The antiviral activities and encapsidation efficiencies did not correlate with their relative expression levels in the producer cells. CONCLUSIONS/SIGNIFICANCE: Our results demonstrated the variations in the late restriction activities among closely related TRIM5α orthologues and a subset of human TRIM family proteins, providing further insights into the late restriction activities of TRIM proteins.","corpus_id":9065725,"score":0},{"doc_id":"21483490","title":"Novel escape mutants suggest an extensive TRIM5α binding site spanning the entire outer surface of the murine leukemia virus capsid protein.","abstract":"After entry into target cells, retroviruses encounter the host restriction factors such as Fv1 and TRIM5α. While it is clear that these factors target retrovirus capsid proteins (CA), recognition remains poorly defined in the absence of structural information. To better understand the binding interaction between TRIM5α and CA, we selected a panel of novel N-tropic murine leukaemia virus (N-MLV) escape mutants by a serial passage of replication competent N-MLV in rhesus macaque TRIM5α (rhTRIM5α)-positive cells using a small percentage of unrestricted cells to allow multiple rounds of virus replication. The newly identified mutations, many of which involve changes in charge, are distributed over the outer 'top' surface of N-MLV CA, including the N-terminal β-hairpin, and map up to 29 A(o) apart. Biological characterisation with a number of restriction factors revealed that only one of the new mutations affects restriction by human TRIM5α, indicating significant differences in the binding interaction between N-MLV and the two TRIM5αs, whereas three of the mutations result in dual sensitivity to Fv1(n) and Fv1(b). Structural studies of two mutants show that no major changes in the overall CA conformation are associated with escape from restriction. We conclude that interactions involving much, if not all, of the surface of CA are vital for TRIM5α binding.","corpus_id":7191281,"score":0},{"doc_id":"21575157","title":"Trafficking of some old world primate TRIM5α proteins through the nucleus.","abstract":"BACKGROUND: TRIM5α and TRIMCyp are cytoplasmic proteins that bind incoming retroviral capsids and mediate early blocks to viral infection. TRIM5 proteins form cytoplasmic bodies, which are highly dynamic structures. So far, TRIM5 proteins have been found only in the cytoplasm of cells. Interestingly, other proteins from the TRIM family localize to the nucleus. Therefore, we tested the possibility that TRIM5 proteins traffic to the nucleus and the impact of this trafficking on retroviral restriction. RESULTS: Here we report that the TRIM5α proteins of two Old World primates, humans and rhesus monkeys, are transported into the nucleus and are shuttled back to the cytoplasm by a leptomycin B-sensitive mechanism. In leptomycin B-treated cells, these TRIM5α proteins formed nuclear bodies that also contained TRIM19 (PML). Deletion of the amino terminus, including the linker 1 (L1) region, resulted in TRIM5α proteins that accumulated in nuclear bodies. Leptomycin B treatment of TRIM5α-expressing target cells only minimally affected the restriction of retrovirus infection. CONCLUSIONS: We discovered the ability of human and rhesus TRIM5α to shuttle into and out of the nucleus. This novel trafficking ability of TRIM5α proteins could be important for an as-yet-unknown function of TRIM5α.","corpus_id":6357793,"score":0},{"doc_id":"23369348","title":"Role of SUMO-1 and SUMO interacting motifs in rhesus TRIM5α-mediated restriction.","abstract":"BACKGROUND: TRIM5α is a member of the tripartite motif family of proteins that restricts retroviral infection in a species-specific manner. The restriction requires an interaction between the viral capsid lattice and the B30.2/SPRY domain of TRIM5α. Previously, we determined that two SUMO interacting motifs (SIMs) present in the B30.2/SPRY domain of human TRIM5α (huTRIM5α) were important for the restriction of N-tropic Murine Leukemia Virus. Here, we examined whether SUMO expression and the SIM1 and SIM2 motifs in rhesus monkey TRIM5α (rhTRIM5α) are similarly important for Human Immunodeficiency Type 1 (HIV-) restriction. RESULTS: We found that mutation of SIM1 and SIM2 of rhTRIM5α abolished the restriction of HIV-1 virus. Further, knockdown of SUMO-1 in rhTRIM5α expressing cells abolished restriction of HIV-1. These results may be due, in part, to the ability of SUMO-1 to stabilize rhTRIM5α protein expression, as SUMO-1 knockdown increased rhTRIM5α turnover and the mutations in SIM1 and SIM2 led to more rapid degradation than the wild type protein. The NF-κB signaling ability of rhTRIM5α was also attenuated by SUMO-1 knockdown. Finally, upon inhibition of CRM1-dependent nuclear export with Leptomycin B (LMB), wild type rhTRIM5α localized to SUMO-1 bodies in the nucleus, while the SIM1 and SIM2 mutants did not localize to SUMO-1. CONCLUSIONS: Our results suggest that the rhTRIM5α B30.2/SPRY domain is not only important for the recognition of the HIV-1 CA, but it is also important for its association with SUMO-1 or SUMO-1 modified proteins. These interactions help to maintain TRIM5α protein levels and its nuclear localization into specific nuclear bodies.","corpus_id":6416723,"score":0},{"doc_id":"24599998","title":"Higher-order structure of the Rous sarcoma virus SP assembly domain.","abstract":"UNLABELLED: Purified retroviral Gag proteins can assemble in vitro to form immature virus-like particles (VLPs). By cryoelectron tomography, Rous sarcoma virus VLPs show an organized hexameric lattice consisting chiefly of the capsid (CA) domain, with periodic stalk-like densities below the lattice. We hypothesize that the structure represented by these densities is formed by amino acid residues immediately downstream of the folded CA, namely, the short spacer peptide SP, along with a dozen flanking residues. These 24 residues comprise the SP assembly (SPA) domain, and we propose that neighboring SPA units in a Gag hexamer coalesce to form a six-helix bundle. Using in vitro assembly, alanine scanning mutagenesis, and biophysical analyses, we have further characterized the structure and function of SPA. Most of the amino acid residues in SPA could not be mutated individually without abrogating assembly, with the exception of a few residues near the N and C termini, as well as three hydrophilic residues within SPA. We interpret these results to mean that the amino acids that do not tolerate mutations contribute to higher-order structures in VLPs. Hydrogen-deuterium exchange analyses of unassembled Gag compared that of assembled VLPs showed strong protection at the SPA region, consistent with a higher-order structure. Circular dichroism revealed that a 29mer SPA peptide shifts from a random coil to a helix in a concentration-dependent manner. Analytical ultracentrifugation showed concentration-dependent self-association of the peptide into a hexamer. Taken together, these results provide strong evidence for the formation of a critical six-helix bundle in Gag assembly. IMPORTANCE: The structure of a retrovirus like HIV is created by several thousand molecules of the viral Gag protein, which assemble to form the known hexagonal protein lattice in the virus particle. How the Gag proteins pack together in the lattice is incompletely understood. A short segment of Gag known to be critical for proper assembly has been hypothesized to form a six-helix bundle, which may be the nucleating event that leads to lattice formation. The experiments reported here, using the avian Rous sarcoma virus as a model system, further define the nature of this segment of Gag, show that it is in a higher-order structure in the virus particle, and provide the first direct evidence that it forms a six-helix bundle in retrovirus assembly. Such knowledge may provide underpinnings for the development of antiretroviral drugs that interfere with virus assembly.","corpus_id":30771997,"score":0},{"doc_id":"28767697","title":"Cyclophilin A potentiates TRIM5α inhibition of HIV-1 nuclear import without promoting TRIM5α binding to the viral capsid.","abstract":"The host immunophilin cyclophilin A (CypA) binds to the capsid protein (CA) of HIV-1 and regulates its infectivity. Depending on the target cell type, CypA can either promote or inhibit HIV-1 infection. The ability of CypA to promote HIV-1 infection has been extensively studied and linked to several steps in early replication including uncoating, reverse transcription and nuclear import. By contrast, the mechanism by which CypA inhibits infection is less well understood. We investigated the mechanism by which CypA potentiates restriction of HIV-1 by the tripartite motif-containing protein 5 (TRIM5α). Depletion of TRIM5α in the African green monkey cell line Vero, resulted in a loss of inhibition of infection by CypA, demonstrating that inhibition by CypA is mediated by TRIM5α. Complementary genetic and biochemical assays failed to demonstrate an ability of CypA to promote binding of TRIM5α to the viral capsid. TRIM5α inhibits HIV-1 reverse transcription in a proteasome-dependent manner; however, we observed that inhibition of proteasome activity did not reduce the ability of CypA to inhibit infection, suggesting that CypA acts at a step after reverse transcription. Accordingly, we observed a CypA-dependent reduction in the accumulation of nuclear HIV-1 DNA, indicating that CypA specifically promotes TRIM5α inhibition of HIV-1 nuclear import. We also observed that the ability of CypA to inhibit HIV-1 infection is abolished by amino acid substitutions within the conserved CPSF6-binding surface in CA. Our results indicate that CypA inhibits HIV-1 infection in Vero cells not by promoting TRIM5α binding to the capsid but by blocking nuclear import of the HIV-1 preintegration complex.","corpus_id":40789255,"score":0}],"string":"[\n {\n \"doc_id\": \"18799578\",\n \"title\": \"The TRIM5alpha B-box 2 domain promotes cooperative binding to the retroviral capsid by mediating higher-order self-association.\",\n \"abstract\": \"The retroviral restriction factor, TRIM5alpha, blocks infection of a spectrum of retroviruses soon after virus entry into the cell. TRIM5alpha consists of RING, B-box 2, coiled-coil, and B30.2(SPRY) domains. The B-box 2 domain is essential for retrovirus restriction by TRIM5alpha, but its specific function is unknown. We show here that the B-box 2 domain mediates higher-order self-association of TRIM5alpha(rh) oligomers. This self-association increases the efficiency of TRIM5alpha binding to the retroviral capsid, thus potentiating restriction of retroviral infection. The contribution of the B-box 2 domain to cooperative TRIM5alpha association with the retroviral capsid explains the conditional nature of the restriction phenotype exhibited by some B-box 2 TRIM5alpha mutants; the potentiation of capsid binding that results from B-box 2-mediated self-association is essential for restriction when B30.2(SPRY) domain-mediated interactions with the retroviral capsid are weak. Thus, B-box 2-dependent higher-order self-association and B30.2(SPRY)-dependent capsid binding represent complementary mechanisms whereby sufficiently dense arrays of capsid-bound TRIM5alpha proteins can be achieved.\",\n \"corpus_id\": 22203532,\n \"score\": 2\n },\n {\n \"doc_id\": \"19656869\",\n \"title\": \"A B-box 2 surface patch important for TRIM5alpha self-association, capsid binding avidity, and retrovirus restriction.\",\n \"abstract\": \"TRIM5alpha is a tripartite motif (TRIM) protein that consists of RING, B-box 2, coiled-coil, and B30.2(SPRY) domains. The TRIM5alpha(rh) protein from rhesus monkeys recognizes the human immunodeficiency virus type 1 (HIV-1) capsid as it enters the host cell and blocks virus infection prior to reverse transcription. HIV-1-restricting ability can be eliminated by disruption of the B-box 2 domain. Changes in the TRIM5alpha(rh) B-box 2 domain have been associated with alterations in TRIM5alpha(rh) turnover, the formation of cytoplasmic bodies and higher-order oligomerization. We present here the nuclear magnetic resonance structure of the TRIM5 B-box 2 domain and identify an unusual hydrophobic patch (cluster 1) on the domain surface. Alteration of cluster 1 or the flanking arginine 121 resulted in various degrees of inactivation of HIV-1 restriction, in some cases depending on compensatory changes in other nearby charged residues. For this panel of TRIM5alpha(rh) B-box 2 mutants, inhibition of HIV-1 infection was strongly correlated with higher-order self-association and binding affinity for capsid complexes but not with TRIM5alpha(rh) half-life or the formation of cytoplasmic bodies. Thus, promoting cooperative TRIM5alpha(rh) interactions with the HIV-1 capsid represents a major mechanism whereby the B-box 2 domain potentiates HIV-1 restriction.\",\n \"corpus_id\": 29220668,\n \"score\": 2\n },\n {\n \"doc_id\": \"20012523\",\n \"title\": \"TRIM5alpha.\",\n \"abstract\": \"TRIM5alpha protein blocks retroviral replication at early postentry stage reducing the accumulation of reverse transcriptase products. TRIM5alpha proteins of Old World primates restrict HIV-1 infection whereas TRIM5alpha proteins of most New World monkeys restrict SIV(mac) infection. TRIM5alpha protein has a RING domain, B-box 2 domain, coiled-coil domain, and PRYSPRY domain. The PRYSPRY domain of TRIM5alpha determines viral specificity and restriction potency by mediating recognition of the retroviral capsid. The coiled-coil domain is essential for TRIM5alpha oligomerization, which contributes to binding avidity for the viral capsid. The RING domain and B-box 2 domain are required for efficient restriction activity of TRIM5alpha protein but the mechanisms remain to be defined.\",\n \"corpus_id\": 263604735,\n \"score\": 2\n },\n {\n \"doc_id\": \"21187419\",\n \"title\": \"Hexagonal assembly of a restricting TRIM5alpha protein.\",\n \"abstract\": \"TRIM5α proteins are restriction factors that protect mammalian cells from retroviral infections by binding incoming viral capsids, accelerating their dissociation, and preventing reverse transcription of the viral genome. Individual TRIM5 isoforms can often protect cells against a broad range of retroviruses, as exemplified by rhesus monkey TRIM5α and its variant, TRIM5-21R, which recognize HIV-1 as well as several distantly related retroviruses. Although capsid recognition is not yet fully understood, previous work has shown that the C-terminal SPRY/B30.2 domain of dimeric TRIM5α binds directly to viral capsids, and that higher-order TRIM5α oligomerization appears to contribute to the efficiency of capsid recognition. Here, we report that recombinant TRIM5-21R spontaneously assembled into two-dimensional paracrystalline hexagonal lattices comprising open, six-sided rings. TRIM5-21R assembly did not require the C-terminal SPRY domain, but did require both protein dimerization and a B-box 2 residue (Arg121) previously implicated in TRIM5α restriction and higher-order assembly. Furthermore, TRIM5-21R assembly was promoted by binding to hexagonal arrays of the HIV-1 CA protein that mimic the surface of the viral capsid. We therefore propose that TRIM5α proteins have evolved to restrict a range of different retroviruses by assembling a deformable hexagonal scaffold that positions the capsid-binding domains to match the symmetry and spacing of the capsid surface lattice. Capsid recognition therefore involves a synergistic combination of direct binding interactions, avidity effects, templated assembly, and lattice complementarity.\",\n \"corpus_id\": 101883,\n \"score\": 2\n },\n {\n \"doc_id\": \"21455494\",\n \"title\": \"Rhesus TRIM5α disrupts the HIV-1 capsid at the inter-hexamer interfaces.\",\n \"abstract\": \"TRIM proteins play important roles in the innate immune defense against retroviral infection, including human immunodeficiency virus type-1 (HIV-1). Rhesus macaque TRIM5α (TRIM5α(rh)) targets the HIV-1 capsid and blocks infection at an early post-entry stage, prior to reverse transcription. Studies have shown that binding of TRIM5α to the assembled capsid is essential for restriction and requires the coiled-coil and B30.2/SPRY domains, but the molecular mechanism of restriction is not fully understood. In this study, we investigated, by cryoEM combined with mutagenesis and chemical cross-linking, the direct interactions between HIV-1 capsid protein (CA) assemblies and purified TRIM5α(rh) containing coiled-coil and SPRY domains (CC-SPRY(rh)). Concentration-dependent binding of CC-SPRY(rh) to CA assemblies was observed, while under equivalent conditions the human protein did not bind. Importantly, CC-SPRY(rh), but not its human counterpart, disrupted CA tubes in a non-random fashion, releasing fragments of protofilaments consisting of CA hexamers without dissociation into monomers. Furthermore, such structural destruction was prevented by inter-hexamer crosslinking using P207C/T216C mutant CA with disulfide bonds at the CTD-CTD trimer interface of capsid assemblies, but not by intra-hexamer crosslinking via A14C/E45C at the NTD-NTD interface. The same disruption effect by TRIM5α(rh) on the inter-hexamer interfaces also occurred with purified intact HIV-1 cores. These results provide insights concerning how TRIM5α disrupts the virion core and demonstrate that structural damage of the viral capsid by TRIM5α is likely one of the important components of the mechanism of TRIM5α-mediated HIV-1 restriction.\",\n \"corpus_id\": 10472091,\n \"score\": 2\n },\n {\n \"doc_id\": \"21512573\",\n \"title\": \"TRIM5 is an innate immune sensor for the retrovirus capsid lattice.\",\n \"abstract\": \"TRIM5 is a RING domain-E3 ubiquitin ligase that restricts infection by human immunodeficiency virus (HIV)-1 and other retroviruses immediately following virus invasion of the target cell cytoplasm. Antiviral potency correlates with TRIM5 avidity for the retrovirion capsid lattice and several reports indicate that TRIM5 has a role in signal transduction, but the precise mechanism of restriction is unknown. Here we demonstrate that TRIM5 promotes innate immune signalling and that this activity is amplified by retroviral infection and interaction with the capsid lattice. Acting with the heterodimeric, ubiquitin-conjugating enzyme UBC13-UEV1A (also known as UBE2N-UBE2V1), TRIM5 catalyses the synthesis of unattached K63-linked ubiquitin chains that activate the TAK1 (also known as MAP3K7) kinase complex and stimulate AP-1 and NFκB signalling. Interaction with the HIV-1 capsid lattice greatly enhances the UBC13-UEV1A-dependent E3 activity of TRIM5 and challenge with retroviruses induces the transcription of AP-1 and NF-κB-dependent factors with a magnitude that tracks with TRIM5 avidity for the invading capsid. Finally, TAK1 and UBC13-UEV1A contribute to capsid-specific restriction by TRIM5. Thus, the retroviral restriction factor TRIM5 has two additional activities that are linked to restriction: it constitutively promotes innate immune signalling and it acts as a pattern recognition receptor specific for the retrovirus capsid lattice.\",\n \"corpus_id\": 4339114,\n \"score\": 2\n },\n {\n \"doc_id\": \"21680743\",\n \"title\": \"Determinants of the higher order association of the restriction factor TRIM5alpha and other tripartite motif (TRIM) proteins.\",\n \"abstract\": \"Many tripartite motif (TRIM) proteins self-associate, forming dimers and higher order complexes. For example, dimers of TRIM5α, a host factor that restricts retrovirus infection, assemble into higher order arrays on the surface of the viral capsid, resulting in an increase in avidity. Here we show that the higher order association of different TRIM proteins exhibits a wide range of efficiencies. Homologous association (self-association) was more efficient than the heterologous association of different TRIM proteins, indicating that specificity determinants of higher order self-association exist. To investigate the structural determinants of higher order self-association, we studied TRIM mutants and chimeras. These studies revealed the following: 1) the RING domain contributes to the efficiency of higher order self-association, which enhances the binding of TRIM5α to the human immunodeficiency virus (HIV-1) capsid; 2) the RING and B-box 2 domains work together as a homologous unit to promote higher order association of dimers; 3) dimerization is probably required for efficient higher order self-association; 4) the Linker 2 region contributes to higher order self-association, independently of effects of Linker 2 changes on TRIM dimerization; and 5) for efficiently self-associating TRIM proteins, the B30.2(SPRY) domain is not required for higher order self-association. These results support a model in which both ends of the core TRIM dimer (RING-B-box 2 at one end and Linker 2 at the other) contribute to the formation of higher order arrays.\",\n \"corpus_id\": 11327163,\n \"score\": 2\n },\n {\n \"doc_id\": \"21734049\",\n \"title\": \"Contribution of E3-ubiquitin ligase activity to HIV-1 restriction by TRIM5alpha(rh): structure of the RING domain of TRIM5alpha.\",\n \"abstract\": \"TRIM5α(rh) is a cytosolic protein that potently restricts HIV-1 before reverse transcription. TRIM5α(rh) is composed of four different domains: RING, B-box 2, coiled coil, and B30.2(SPRY). The contribution of each of these domains to restriction has been extensively studied, with the exception of the RING domain. The RING domain of TRIM5α exhibits E3-ubiquitin ligase activity, but the contribution of this activity to the restriction of HIV-1 is not known. To test the hypothesis that the E3-ubiquitin ligase activity of the RING domain modulates TRIM5α(rh) restriction of HIV-1, we correlated the E3-ubiquitin ligase activity of a panel of TRIM5α(rh) RING domain variants with the ability of these mutant proteins to restrict HIV-1. For this purpose, we first solved the nuclear magnetic resonance structure of the RING domain of TRIM5α and defined potential functional regions of the RING domain by homology to other RING domains. With this structural information, we performed a systematic mutagenesis of the RING domain regions and tested the TRIM5α RING domain variants for the ability to undergo self-ubiquitylation. Several residues, particularly the ones on the E2-binding region of the RING domain, were defective in their self-ubiquitylation ability. To correlate HIV-1 restriction to self-ubiquitylation, we used RING domain mutant proteins that were defective in self-ubiquitylation but preserve important properties required for potent restriction by TRIM5α(rh), such as capsid binding and higher-order self-association. From these investigations, we found a set of residues that when mutated results in TRIM5α molecules that lost both the ability to potently restrict HIV-1 and their self-ubiquitylation activity. Remarkably, all of these changes were in residues located in the E2-binding region of the RING domain. Overall, these results demonstrate a role for TRIM5α self-ubiquitylation in the ability of TRIM5α to restrict HIV-1.\",\n \"corpus_id\": 6973193,\n \"score\": 2\n },\n {\n \"doc_id\": \"21994740\",\n \"title\": \"Caging the beast: TRIM5α binding to the HIV-1 core.\",\n \"abstract\": \"The potent HIV-1 inhibitor TRIM5α blocks HIV-1 infection by accelerating the uncoating of HIV-1. TRIM5α is known to form higher-order self-association complexes that contribute to the avidity of TRIM5α for the HIV-1 capsid, and are essential to inhibit infection; these higher-order self-association complexes are dependent upon an intact B-box 2 domain. Even though the ability to form higher-order self-association complexes resembles the clathrin triskelion that forms a protein array, or cage, around the endocytic vesicle, evidence for the ability of TRIM5α to assemble a similar type of structure surrounding the HIV-1 core has been lacking. Recent work by Ganser-Pornillos, Chandrasekaran and colleagues has now demonstrated the ability of the restriction factor TRIM5α to \\\"cage\\\" or \\\"net\\\" the HIV-1 core by forming an hexagonal array on the surface of the viral capsid. This hexagonal array is strikingly similar in design to the array formed by the clathrin triskelion on the surface of the clathrin-coated endocytic vesicle. This remarkable finding represents an important advance on our understanding of the restriction factor TRIM5α, and suggests that TRIM5α cages the HIV-1 core in order to terminate infection. The present note discusses the implications of this discovery.\",\n \"corpus_id\": 7806137,\n \"score\": 2\n },\n {\n \"doc_id\": \"22114335\",\n \"title\": \"RING domain mutations uncouple TRIM5α restriction of HIV-1 from inhibition of reverse transcription and acceleration of uncoating.\",\n \"abstract\": \"Rhesus TRIM5α (TRIM5α(rh)) is a cytosolic protein that potently restricts HIV-1 at an early postentry stage, prior to reverse transcription. The ability of TRIM5α(rh) to block HIV-1 infection has been correlated with a decrease of pelletable HIV-1 capsid during infection. To genetically dissect the ability of TRIM5α to block reverse transcription, we studied a set of TRIM5α(rh) RING domain mutants that potently restrict HIV-1 but allow the occurrence of reverse transcription. These TRIM5α(rh) RING variants blocked HIV-1 infection after reverse transcription but prior to integration, as suggested by the routing of nuclear viral DNA to circularization in the form of 2-long terminal repeat (2-LTR) circles. The folding of RING domain variants was similar to that of the wild type, as evaluated by nuclear magnetic resonance. RING domain changes that allowed the occurrence of reverse transcription were impaired in their ability to decrease the amount of pelletable capsid compared with wild-type TRIM5α. Similar effects of this particular group of mutations were observed with human TRIM5α inhibition of N-tropic murine leukemia virus (N-MLV). Interestingly, TRIM5α(rh) RING domain variants also prevented the degradation of TRIM5α(rh) that occurs following cell entry of HIV-1. These data correlated the block of reverse transcription with the ability of TRIM5α to accelerate uncoating. Collectively, these results suggest that TRIM5α(rh) blocks HIV-1 reverse transcription by inducing premature viral uncoating in target cells.\",\n \"corpus_id\": 24403782,\n \"score\": 2\n },\n {\n \"doc_id\": \"22482711\",\n \"title\": \"TRIM5 structure, HIV-1 capsid recognition, and innate immune signaling.\",\n \"abstract\": \"TRIM5 is a restriction factor that blocks retrovirus infection soon after the virion core enters the cell cytoplasm. Restriction activity is targeted to the virion core via recognition of the capsid protein lattice that encases the viral genomic RNA. In common with all of the many TRIM family members, TRIM5 has RING, B-box, and coiled-coil domains. As an E3 ubiquitin ligase TRIM5 cooperates with the heterodimeric E2, UBC13/UEV1A, to activate the TAK1 (MAP3K7) kinase, NF-κB and AP-1 signaling, and the transcription of inflammatory cytokines and chemokines. TAK1, UBC13, and UEV1A all contribute to TRIM5-mediated retrovirus restriction activity. Interaction of the carboxy-terminal PRYSPRY or cyclophilin domains of TRIM5 with the retroviral capsid lattice stimulates the formation of a complementary lattice by TRIM5, with greatly increased TRIM5 E3 activity, and host cell signal transduction. Structural and biochemical studies on TRIM5 have opened a much needed window on how the innate immune system detects the distinct molecular features of HIV-1 and other retroviruses.\",\n \"corpus_id\": 22704306,\n \"score\": 2\n },\n {\n \"doc_id\": \"23091002\",\n \"title\": \"Structural insight into HIV-1 capsid recognition by rhesus TRIM5α.\",\n \"abstract\": \"Tripartite motif protein isoform 5 alpha (TRIM5α) is a potent antiviral protein that restricts infection by HIV-1 and other retroviruses. TRIM5α recognizes the lattice of the retrovirus capsid through its B30.2 (PRY/SPRY) domain in a species-specific manner. Upon binding, TRIM5α induces premature disassembly of the viral capsid and activates the downstream innate immune response. We have determined the crystal structure of the rhesus TRIM5α PRY/SPRY domain that reveals essential features for capsid binding. Combined cryo-electron microscopy and biochemical data show that the monomeric rhesus TRIM5α PRY/SPRY, but not the human TRIM5α PRY/SPRY, can bind to HIV-1 capsid protein assemblies without causing disruption of the capsid. This suggests that the PRY/SPRY domain alone constitutes an important pattern-sensing component of TRIM5α that is capable of interacting with viral capsids of different curvatures. Our results provide molecular insights into the mechanisms of TRIM5α-mediated retroviral restriction.\",\n \"corpus_id\": 26633942,\n \"score\": 2\n },\n {\n \"doc_id\": \"23637418\",\n \"title\": \"Virus-specific effects of TRIM5α(rh) RING domain functions on restriction of retroviruses.\",\n \"abstract\": \"The tripartite motif protein TRIM5α restricts particular retrovirus infections by binding to the incoming capsid and inhibiting the early stage of virus infection. The TRIM5α RING domain exhibits E3 ubiquitin ligase activity and assists the higher-order association of TRIM5α dimers, which promotes capsid binding. We characterized a panel of RING domain mutants of the rhesus monkey TRIM5α (TRIM5α(rh)) protein. The RING domain function that significantly contributed to retroviral restriction depended upon the restricted virus. The E3 ubiquitin ligase activity of the RING domain contributes to the potency of HIV-1 restriction. Nonetheless, TRIM5α(rh) mutants without detectable E3 ubiquitin ligase activity still blocked reverse transcription and inhibited HIV-1 infection at a moderate level. When TRIM5α(rh) capsid binding was weakened by substitution with a less efficient B30.2/SPRY domain, the promotion of higher-order association by the RING domain was more important to HIV-1 restriction than its E3 ubiquitin ligase activity. For the restriction of N-tropic murine leukemia virus (N-MLV) and equine infectious anemia virus (EIAV) infection, promotion of higher-order association represented the major contribution of the RING domain. Thus, both identity of the target virus and the B30.2/SPRY domain-mediated affinity for the viral capsid determine the relative contribution of the two known RING domain functions to TRIM5α restriction of retrovirus infection.\",\n \"corpus_id\": 16531158,\n \"score\": 2\n },\n {\n \"doc_id\": \"24158810\",\n \"title\": \"CryoEM analysis of capsid assembly and structural changes upon interactions with a host restriction factor, TRIM5α.\",\n \"abstract\": \"After virus fusion with a target cell, the viral core is released into the host cell cytoplasm and undergoes a controlled disassembly process, termed uncoating, before or as reverse transcription takes place. The cellular protein TRIM5α is a host cell restriction factor that blocks HIV-1 infection in rhesus macaque cells by targeting the viral capsid and inducing premature uncoating. The molecular mechanism of the interaction between capsid and TRIM5α remains unclear. Here, we describe an approach that utilizes cryo-electron microscopy (cryoEM) to examine the structural changes exerted on HIV-1 capsid (CA) assembly by TRIM5α binding. The TRIM5α interaction sites on CA assembly were further dissected by combining cryoEM with pair-wise cysteine mutations that crosslink CA either within a CA hexamer or between CA hexamers. Based on the structural information from cryoEM and crosslinking results from in vitro CA assemblies and purified intact HIV-1 cores, we demonstrate that direct binding of TRIM5α CC-SPRY domains to the viral capsid results in disruption and fragmentation of the surface lattice of HIV-1 capsid, specifically at inter-hexamer interfaces. The method described here can be easily adopted to study other important interactions in multi-protein complexes.\",\n \"corpus_id\": 20581636,\n \"score\": 2\n },\n {\n \"doc_id\": \"24550273\",\n \"title\": \"The tripartite motif coiled-coil is an elongated antiparallel hairpin dimer.\",\n \"abstract\": \"Tripartite motif (TRIM) proteins make up a large family of coiled-coil-containing RING E3 ligases that function in many cellular processes, particularly innate antiviral response pathways. Both dimerization and higher-order assembly are important elements of TRIM protein function, but the atomic details of TRIM tertiary and quaternary structure have not been fully understood. Here, we present crystallographic and biochemical analyses of the TRIM coiled-coil and show that TRIM proteins dimerize by forming interdigitating antiparallel helical hairpins that position the N-terminal catalytic RING domains at opposite ends of the dimer and the C-terminal substrate-binding domains at the center. The dimer core comprises an antiparallel coiled-coil with a distinctive, symmetric pattern of flanking heptad and central hendecad repeats that appear to be conserved across the entire TRIM family. Our studies reveal how the coiled-coil organizes TRIM25 to polyubiquitylate the RIG-I/viral RNA recognition complex and how dimers of the TRIM5α protein are arranged within hexagonal arrays that recognize the HIV-1 capsid lattice and restrict retroviral replication.\",\n \"corpus_id\": 2015949,\n \"score\": 2\n },\n {\n \"doc_id\": \"24872590\",\n \"title\": \"Restriction of HIV-1 by rhesus TRIM5α is governed by alpha helices in the Linker2 region.\",\n \"abstract\": \"UNLABELLED: TRIM5α proteins are a potent barrier to the cross-species transmission of retroviruses. TRIM5α proteins exhibit an ability to self-associate at many levels, ultimately leading to the formation of protein assemblies with hexagonal symmetry in vitro and cytoplasmic assemblies when expressed in cells. However, the role of these assemblies in restriction, the determinants that mediate their formation, and the organization of TRIM5α molecules within these assemblies have remained unclear. Here we show that α-helical elements within the Linker2 region of rhesus macaque TRIM5α govern the ability to form cytoplasmic assemblies in cells and restrict HIV-1 infection. Mutations that reduce α-helix formation by the Linker2 region disrupt assembly and restriction. More importantly, mutations that enhance the α-helical content of the Linker2 region, relative to the wild-type protein, also exhibit an increased ability to form cytoplasmic assemblies and restrict HIV-1 infection. Molecular modeling of the TRIM5α dimer suggests a model in which α-helical elements within the Linker2 region dock to α-helices of the coiled-coil domain, likely establishing proper orientation and spacing of protein domains necessary for assembly and restriction. Collectively, these studies provide critical insight into the determinants governing TRIM5α assembly and restriction and demonstrate that the antiviral potency of TRIM5α proteins can be significantly increased without altering the affinity of SPRY/capsid binding. IMPORTANCE: Many members of the tripartite motif (TRIM) family of proteins act as restriction factors that directly inhibit viral infection and activate innate immune signaling pathways. Another common feature of TRIM proteins is the ability to form protein assemblies in the nucleus or the cytoplasm. However, the determinants in TRIM proteins required for assembly and the degree to which assembly affects TRIM protein function have been poorly understood. Here we show that alpha helices in the Linker2 (L2) region of rhesus TRIM5α govern assembly and restriction of HIV-1 infection. Helix-disrupting mutations disrupt the assembly and restriction of HIV-1, while helix-stabilizing mutations enhance assembly and restriction relative to the wild-type protein. Circular dichroism analysis suggests that that the formation of this helical structure is supported by intermolecular interactions with the coiled-coil (CC) domain in the CCL2 dimer. These studies reveal a novel mechanism by which the antiviral activity of TRIM5α proteins can be regulated and provide detailed insight into the assembly determinants of TRIM family proteins.\",\n \"corpus_id\": 994073,\n \"score\": 2\n },\n {\n \"doc_id\": \"24979782\",\n \"title\": \"Structural studies of postentry restriction factors reveal antiparallel dimers that enable avid binding to the HIV-1 capsid lattice.\",\n \"abstract\": \"Restriction factors (RFs) form important components of host defenses to retroviral infection. The Fv1, Trim5α, and TrimCyp RFs contain N-terminal dimerization and C-terminal specificity domains that target assembled retroviral capsid (CA) proteins enclosing the viral core. However, the molecular detail of the interaction between RFs and their CA targets is unknown. Therefore, we have determined the crystal structure of the B-box and coiled-coil (BCC) region from Trim5α and used small-angle X-ray scattering to examine the solution structure of Trim5α BCC, the dimerization domain of Fv1 (Fv1Ntd), and the hybrid restriction factor Fv1Cyp comprising Fv1NtD fused to the HIV-1 binding protein Cyclophilin A (CypA). These data reveal that coiled-coil regions of Fv1 and Trim5α form extended antiparallel dimers. In Fv1Cyp, two CypA moieties are located at opposing ends, creating a molecule with a dumbbell appearance. In Trim5α, the B-boxes are located at either end of the coiled-coil, held in place by interactions with a helical motif from the L2 region of the opposing monomer. A comparative analysis of Fv1Cyp and CypA binding to a preformed HIV-1 CA lattice reveals how RF dimerization enhances the affinity of interaction through avidity effects. We conclude that the antiparallel organization of the NtD regions of Fv1 and Trim5α dimers correctly positions C-terminal specificity and N-terminal effector domains and facilitates stable binding to adjacent CA hexamers in viral cores.\",\n \"corpus_id\": 205267902,\n \"score\": 2\n },\n {\n \"doc_id\": \"26043233\",\n \"title\": \"Crystal structure of TRIM20 C-terminal coiled-coil/B30.2 fragment: implications for the recognition of higher order oligomers.\",\n \"abstract\": \"Many tripartite motif-containing (TRIM) proteins, comprising RING-finger, B-Box, and coiled-coil domains, carry additional B30.2 domains on the C-terminus of the TRIM motif and are considered to be pattern recognition receptors involved in the detection of higher order oligomers (e.g. viral capsid proteins). To investigate the spatial architecture of domains in TRIM proteins we determined the crystal structure of the TRIM20Δ413 fragment at 2.4 Å resolution. This structure comprises the central helical scaffold (CHS) and C-terminal B30.2 domains and reveals an anti-parallel arrangement of CHS domains placing the B-box domains 170 Å apart from each other. Small-angle X-ray scattering confirmed that the linker between CHS and B30.2 domains is flexible in solution. The crystal structure suggests an interaction between the B30.2 domain and an extended stretch in the CHS domain, which involves residues that are mutated in the inherited disease Familial Mediterranean Fever. Dimerization of B30.2 domains by means of the CHS domain is crucial for TRIM20 to bind pro-IL-1β in vitro. To exemplify how TRIM proteins could be involved in binding higher order oligomers we discuss three possible models for the TRIM5α/HIV-1 capsid interaction assuming different conformations of B30.2 domains.\",\n \"corpus_id\": 18642941,\n \"score\": 2\n },\n {\n \"doc_id\": \"26101372\",\n \"title\": \"TRIM5α requires Ube2W to anchor Lys63-linked ubiquitin chains and restrict reverse transcription.\",\n \"abstract\": \"TRIM5α is an antiviral, cytoplasmic, E3 ubiquitin (Ub) ligase that assembles on incoming retroviral capsids and induces their premature dissociation. It inhibits reverse transcription of the viral genome and can also synthesize unanchored polyubiquitin (polyUb) chains to stimulate innate immune responses. Here, we show that TRIM5α employs the E2 Ub-conjugating enzyme Ube2W to anchor the Lys63-linked polyUb chains in a process of TRIM5α auto-ubiquitination. Chain anchoring is initiated, in cells and in vitro, through Ube2W-catalyzed monoubiquitination of TRIM5α. This modification serves as a substrate for the elongation of anchored Lys63-linked polyUb chains, catalyzed by the heterodimeric E2 enzyme Ube2N/Ube2V2. Ube2W targets multiple TRIM5α internal lysines with Ub especially lysines 45 and 50, rather than modifying the N-terminal amino group, which is instead αN-acetylated in cells. E2 depletion or Ub mutation inhibits TRIM5α ubiquitination in cells and restores restricted viral reverse transcription, but not infection. Our data indicate that the stepwise formation of anchored Lys63-linked polyUb is a critical early step in the TRIM5α restriction mechanism and identify the E2 Ub-conjugating cofactors involved.\",\n \"corpus_id\": 449065,\n \"score\": 2\n },\n {\n \"doc_id\": \"26212332\",\n \"title\": \"RING Dimerization Links Higher-Order Assembly of TRIM5α to Synthesis of K63-Linked Polyubiquitin.\",\n \"abstract\": \"Members of the tripartite motif (TRIM) protein family of RING E3 ubiquitin (Ub) ligases promote innate immune responses by catalyzing synthesis of polyubiquitin chains linked through lysine 63 (K63). Here, we investigate the mechanism by which the TRIM5α retroviral restriction factor activates Ubc13, the K63-linkage-specific E2. Structural, biochemical, and functional characterization of the TRIM5α:Ubc13-Ub interactions reveals that activation of the Ubc13-Ub conjugate requires dimerization of the TRIM5α RING domain. Our data explain how higher-order oligomerization of TRIM5α, which is promoted by the interaction with the retroviral capsid, enhances the E3 Ub ligase activity of TRIM5α and contributes to its antiretroviral function. This E3 mechanism, in which RING dimerization is transient and depends on the interaction of the TRIM protein with the ligand, is likely to be conserved in many members of the TRIM family and may have evolved to facilitate recognition of repetitive epitope patterns associated with infection.\",\n \"corpus_id\": 19763051,\n \"score\": 2\n },\n {\n \"doc_id\": \"26468522\",\n \"title\": \"TRIM5 Retroviral Restriction Activity Correlates with the Ability To Induce Innate Immune Signaling.\",\n \"abstract\": \"UNLABELLED: Host restriction factor TRIM5 inhibits retroviral transduction in a species-specific manner by binding to and destabilizing the retroviral capsid lattice before reverse transcription is completed. However, the restriction mechanism may not be that simple since TRIM5 E3 ubiquitin ligase activity, the proteasome, autophagy, and TAK1-dependent AP-1 signaling have been suggested to contribute to restriction. Here, we show that, among a panel of seven primate and Carnivora TRIM5 orthologues, each of which has potential for potent retroviral restriction activity, all activated AP-1 signaling. In contrast, TRIM family paralogues most closely related to TRIM5 did not. While each primate species has a single TRIM5 gene, mice have at least seven TRIM5 homologues that cluster into two groups, Trim12a, -b, and -c and Trim30a, -b, -c, and -d. The three Trim12 proteins activated innate immune signaling, while the Trim30 proteins did not, though none of the murine Trim5 homologues restricted any of a panel of cloned retroviruses. To determine if any mouse TRIM5 homologues had potential for restriction activity, each was fused to the human immunodeficiency virus type 1 (HIV-1) CA binding protein cyclophilin A (CypA). The three Trim12-CypA fusions all activated AP-1 and restricted HIV-1 transduction, whereas the Trim30-CypA fusions did neither. AP-1 activation and HIV-1 restriction by the Trim12-CypA fusions were inhibited by disruption of TAK1. Overall then, these experiments demonstrate that there is a strong correlation between TRIM5 retroviral restriction activity and the ability to activate TAK1-dependent innate immune signaling. IMPORTANCE: The importance of retroviruses for the evolution of susceptible host organisms cannot be overestimated. Eight percent of the human genome is retrovirus sequence, fixed in the germ line during past infection. Understanding how metazoa protect their genomes from mutagenic retrovirus infection is therefore of fundamental importance to biology. TRIM5 is a cellular protein that protects host genome integrity by disrupting the retroviral capsid as it transports viral nucleic acid to the host cell nucleus. Previous data suggest that innate immune signaling contributes to TRIM5-mediated restriction. Here, we show that activation of innate immune signaling is conserved among primate and carnivore TRIM5 orthologues and among 3 of the 7 mouse Trim5 homologues and that such activity is required for TRIM5-mediated restriction activity.\",\n \"corpus_id\": 12769922,\n \"score\": 2\n },\n {\n \"doc_id\": \"26676782\",\n \"title\": \"TRIM5alpha-mediated ubiquitin chain conjugation is required for inhibition of HIV-1 reverse transcription and capsid destabilization.\",\n \"abstract\": \"Rhesus macaque TRIM5α (rhTRIM5α) is a retroviral restriction factor, which inhibits HIV-1 infection. Previous studies have revealed that TRIM5α restriction occurs via a two-step process. The first step is restriction factor binding, which is sufficient to inhibit infection. The second step, which is sensitive to proteasome inhibition, prevents the accumulation of reverse transcription products in the target cell. However, because of the pleotropic effects of proteasome inhibitors, the molecular mechanisms underlying the individual steps in the restriction process have remained poorly understood. In this study, we have fused the small catalytic domain of Herpes Simplex Virus UL36 Deubiquitinase (DUb) to the N-terminal RING domain of rhTRIM5α, which results in a ubiquitination resistant protein. Cell lines stably expressing this fusion protein inhibited HIV-1 infection to the same degree as a control fusion to a catalytically inactive DUb. However, reverse transcription products were substantially increased in the DUb-TRIM5α fusion relative to the catalytically inactive control or the wild type TRIM5α. Similarly, expression of DUb-rhTRIM5α resulted in the accumulation of viral cores in target cells following infection, while the catalytically inactive control and wt rhTRIM5α induced the abortive disassembly of viral cores, indicating a role for ubiquitin conjugation in rhTRIM5α-mediated destabilization of HIV-1 cores. Finally, DUb-rhTRIM5α failed to activate NF-kB signaling pathways, when compared to controls, demonstrating that this ubiquination dependent activity is separable from the ability to restrict retroviral infection. IMPORTANCE: These studies provide direct evidence that ubiquitin conjugation to rhTRIM5α-containing complexes is required for the second step of HIV-1 restriction. They also provide a novel tool by which the biological activities of TRIM family proteins might be dissected to better understand their function and underlying mechanisms of action.\",\n \"corpus_id\": 3836930,\n \"score\": 2\n },\n {\n \"doc_id\": \"26764007\",\n \"title\": \"TRIM5α Degradation via Autophagy Is Not Required for Retroviral Restriction.\",\n \"abstract\": \"UNLABELLED: TRIM5α is an interferon-inducible retroviral restriction factor that prevents infection by inducing the abortive disassembly of capsid cores recognized by its C-terminal PRY/SPRY domain. The mechanism by which TRIM5α mediates the disassembly of viral cores is poorly understood. Previous studies demonstrated that proteasome inhibitors abrogate the ability of TRIM5α to induce premature core disassembly and prevent reverse transcription; however, viral infection is still inhibited, indicating that the proteasome is partially involved in the restriction process. Alternatively, we and others have observed that TRIM5α associates with proteins involved in autophagic degradation pathways, and one recent study found that autophagic degradation is required for the restriction of retroviruses by TRIM5α. Here, we show that TRIM5α is basally degraded via autophagy in the absence of restriction-sensitive virus. We observe that the autophagy markers LC3b and lysosome-associated membrane protein 2A (LAMP2A) localize to a subset of TRIM5α cytoplasmic bodies, and inhibition of lysosomal degradation with bafilomycin A1 increases this association. To test the requirement for macroautophagy in restriction, we examined the ability of TRIM5α to restrict retroviral infection in cells depleted of the autophagic mediators ATG5, Beclin1, and p62. In all cases, restriction of retroviruses by human TRIM5α, rhesus macaque TRIM5α, and owl monkey TRIM-Cyp remained potent in cells depleted of these autophagic effectors by small interfering RNA (siRNA) knockdown or clustered regularly interspaced short palindromic repeat (CRISPR)-Cas9 genome editing. Collectively, these results are consistent with observations that the turnover of TRIM5α proteins is sensitive to autophagy inhibition; however, the data presented here do not support observations that the inhibition of autophagy abrogates retroviral restriction by TRIM5 proteins. IMPORTANCE: Restriction factors are a class of proteins that inhibit viral replication. Following fusion of a retrovirus with a host cell membrane, the retroviral capsid is released into the cytoplasm of the target cell. TRIM5α inhibits retroviral infection by promoting the abortive disassembly of incoming retroviral capsid cores; as a result, the retroviral genome is unable to traffic to the nucleus, and the viral life cycle is extinguished. In the process of restriction, TRIM5α itself is degraded by the proteasome. However, in the present study, we have shown that in the absence of a restriction-sensitive virus, TRIM5α is degraded by both proteasomal and autophagic degradation pathways. Notably, we observed that restriction of retroviruses by TRIM5α does not require autophagic machinery. These data indicate that the effector functions of TRIM5α can be separated from its degradation and may have further implications for understanding the mechanisms of other TRIM family members.\",\n \"corpus_id\": 22248080,\n \"score\": 2\n },\n {\n \"doc_id\": \"27253059\",\n \"title\": \"Mechanism of B-box 2 domain-mediated higher-order assembly of the retroviral restriction factor TRIM5α.\",\n \"abstract\": \"Restriction factors and pattern recognition receptors are important components of intrinsic cellular defenses against viral infection. Mammalian TRIM5α proteins are restriction factors and receptors that target the capsid cores of retroviruses and activate ubiquitin-dependent antiviral responses upon capsid recognition. Here, we report crystallographic and functional studies of the TRIM5α B-box 2 domain, which mediates higher-order assembly of TRIM5 proteins. The B-box can form both dimers and trimers, and the trimers can link multiple TRIM5α proteins into a hexagonal net that matches the lattice arrangement of capsid subunits and enables avid capsid binding. Two modes of conformational flexibility allow TRIM5α to accommodate the variable curvature of retroviral capsids. B-box mediated interactions also modulate TRIM5α's E3 ubiquitin ligase activity, by stereochemically restricting how the N-terminal RING domain can dimerize. Overall, these studies define important molecular details of cellular recognition of retroviruses, and how recognition links to downstream processes to disable the virus.\",\n \"corpus_id\": 2670083,\n \"score\": 2\n },\n {\n \"doc_id\": \"27253068\",\n \"title\": \"Primate TRIM5 proteins form hexagonal nets on HIV-1 capsids.\",\n \"abstract\": \"TRIM5 proteins are restriction factors that block retroviral infections by binding viral capsids and preventing reverse transcription. Capsid recognition is mediated by C-terminal domains on TRIM5α (SPRY) or TRIMCyp (cyclophilin A), which interact weakly with capsids. Efficient capsid recognition also requires the conserved N-terminal tripartite motifs (TRIM), which mediate oligomerization and create avidity effects. To characterize how TRIM5 proteins recognize viral capsids, we developed methods for isolating native recombinant TRIM5 proteins and purifying stable HIV-1 capsids. Biochemical and EM analyses revealed that TRIM5 proteins assembled into hexagonal nets, both alone and on capsid surfaces. These nets comprised open hexameric rings, with the SPRY domains centered on the edges and the B-box and RING domains at the vertices. Thus, the principles of hexagonal TRIM5 assembly and capsid pattern recognition are conserved across primates, allowing TRIM5 assemblies to maintain the conformational plasticity necessary to recognize divergent and pleomorphic retroviral capsids.\",\n \"corpus_id\": 22091893,\n \"score\": 2\n },\n {\n \"doc_id\": \"27402535\",\n \"title\": \"Crystal structure of the Trim5α Bbox2 domain from rhesus macaques describes a plastic oligomerisation interface.\",\n \"abstract\": \"Retroviral pathogens have been an evolutionary pressure for many primate species, driving the development of an intrinsic cellular response to retroviruses and antiretroviral proteins. One such antiretroviral protein is the restriction factor Trim5α, that blocks HIV-1 infection in rhesus macaques at an early post-entry stage in the retroviral lifecycle. Trim5α self-assembles into a large hexagonal array, complimentary to the retroviral capsid. Assembly is mediated by the conserved N-terminal architecture comprising a RING domain, a Bbox domain, and a coiled coil. Recently we have shown that the Bbox domain and elements of the coiled coil form a trimer in solution, and that the Bbox domain drives assembly. During crystallisation experiments using the trimer forming construct, we determined the structure of a dimeric Bbox domain to a resolution of 1.8Å. Interface analysis reveals that residues previously shown to be required for assembly and restriction, Glu120 and Arg121, are central to the interface. Comparison to a mutant Trim5α dimer interface shows a translation of the Bbox dimerisation interface removing interactions important in the wildtype protein.\",\n \"corpus_id\": 3928870,\n \"score\": 2\n },\n {\n \"doc_id\": \"27821283\",\n \"title\": \"Dynamic conformational changes in the rhesus TRIM5α dimer dictate the potency of HIV-1 restriction.\",\n \"abstract\": \"The TRIM5α protein from rhesus macaques (rhTRIM5α) mediates a potent inhibition of HIV-1 infection via a mechanism that involves the abortive disassembly of the viral core. We have demonstrated that alpha-helical elements within the Linker 2 (L2) region, which lies between the SPRY domain and the Coiled-Coil domain, influence the potency of restriction. Here, we utilize single-molecule FRET analysis to reveal that the L2 region of the TRIM5α dimer undergoes dynamic conformational changes, which results in the displacement of L2 regions by 25 angstroms relative to each other. Analysis of restriction enhancing or abrogating mutations in the L2 region reveal that restriction defective mutants are unable to undergo dynamic conformational changes and do not assume compact, alpha-helical conformations in the L2 region. These data suggest a model in which conformational changes in the L2 region mediate displacement of CA bound SPRY domains to induce the destabilization of assembled capsid during restriction.\",\n \"corpus_id\": 9884527,\n \"score\": 2\n },\n {\n \"doc_id\": \"29040325\",\n \"title\": \"TRIM5α SPRY/coiled-coil interactions optimize avid retroviral capsid recognition.\",\n \"abstract\": \"Restriction factors are important components of intrinsic cellular defense mechanisms against viral pathogens. TRIM5α is a restriction factor that intercepts the incoming capsid cores of retroviruses such as HIV and provides an effective species-specific barrier to retroviral infection. The TRIM5α SPRY domain directly binds the capsid with only very weak, millimolar-level affinity, and productive capsid recognition therefore requires both TRIM5α dimerization and assembly of the dimers into a multivalent hexagonal lattice to promote avid binding. Here, we explore the important unresolved question of whether the SPRY domains are flexibly linked to the TRIM lattice or more precisely positioned to maximize avidity. Biochemical and biophysical experiments indicate that the linker segment connecting the SPRY domain to the coiled-coil domain adopts an α-helical fold, and that this helical portion mediates interactions between the two domains. Targeted mutations were generated to disrupt the putative packing interface without affecting dimerization or higher-order assembly, and we identified mutant proteins that were nevertheless deficient in capsid binding in vitro and restriction activity in cells. Our studies therefore support a model wherein substantial avidity gains during assembly-mediated capsid recognition by TRIM5α come in part from tailored spacing of tethered recognition domains.\",\n \"corpus_id\": 24085982,\n \"score\": 2\n },\n {\n \"doc_id\": \"29187540\",\n \"title\": \"General Model for Retroviral Capsid Pattern Recognition by TRIM5 Proteins.\",\n \"abstract\": \"Restriction factors are intrinsic cellular defense proteins that have evolved to block microbial infections. Retroviruses such as HIV-1 are restricted by TRIM5 proteins, which recognize the viral capsid shell that surrounds, organizes, and protects the viral genome. TRIM5α uses a SPRY domain to bind capsids with low intrinsic affinity (KD of >1 mM) and therefore requires higher-order assembly into a hexagonal lattice to generate sufficient avidity for productive capsid recognition. TRIMCyp, on the other hand, binds HIV-1 capsids through a cyclophilin A domain, which has a well-defined binding site and higher affinity (KD of ∼10 μM) for isolated capsid subunits. Therefore, it has been argued that TRIMCyp proteins have dispensed with the need for higher-order assembly to function as antiviral factors. Here, we show that, consistent with its high degree of sequence similarity with TRIM5α, the TRIMCyp B-box 2 domain shares the same ability to self-associate and facilitate assembly of a TRIMCyp hexagonal lattice that can wrap about the HIV-1 capsid. We also show that under stringent experimental conditions, TRIMCyp-mediated restriction of HIV-1 is indeed dependent on higher-order assembly. Both forms of TRIM5 therefore use the same mechanism of avidity-driven capsid pattern recognition. IMPORTANCE Rhesus macaques and owl monkeys are highly resistant to HIV-1 infection due to the activity of TRIM5 restriction factors. The rhesus macaque TRIM5α protein blocks HIV-1 through a mechanism that requires self-assembly of a hexagonal TRIM5α lattice around the invading viral core. Lattice assembly amplifies very weak interactions between the TRIM5α SPRY domain and the HIV-1 capsid. Assembly also promotes dimerization of the TRIM5α RING E3 ligase domain, resulting in synthesis of polyubiquitin chains that mediate downstream steps of restriction. In contrast to rhesus TRIM5α, the owl monkey TRIM5 homolog, TRIMCyp, binds isolated HIV-1 CA subunits much more tightly through its cyclophilin A domain and therefore was thought to act independently of higher-order assembly. Here, we show that TRIMCyp shares the assembly properties of TRIM5α and that both forms of TRIM5 use the same mechanism of hexagonal lattice formation to promote viral recognition and restriction.\",\n \"corpus_id\": 4961124,\n \"score\": 2\n },\n {\n \"doc_id\": \"19153241\",\n \"title\": \"An invariant surface patch on the TRIM5alpha PRYSPRY domain is required for retroviral restriction but dispensable for capsid binding.\",\n \"abstract\": \"TRIM5alpha is a retrovirus restriction factor in the host cell cytoplasm that blocks infection before provirus establishment. Restriction activity requires capsid (CA)-specific recognition by the PRYSPRY domain of TRIM5alpha. To better understand the restriction mechanism, nine charge-cluster-to-triple-alanine mutants in the TRIM5alpha PRYSPRY domain were assessed for CA-specific restriction activity. Five mutants distributed along the TRIM5alpha PRYSPRY primary sequence disrupted restriction activity against N-tropic murine leukemia virus and equine infectious anemia virus. Modeling of the TRIM5alpha PRYSPRY domain based on the crystal structures of PRYSPRY-19q13.4.1, GUSTAVUS, and TRIM21 identified a surface patch where disruptive mutants clustered. All mutants in this patch retained CA-binding activity, a reticular distribution in the cytoplasm, and steady-state protein levels comparable to those of the wild type. Residues in the essential patch are conserved in TRIM5alpha orthologues and in closely related paralogues. The same surface patch in the TRIM18 and TRIM20 PRYSPRY domains is the site of mutants causing Opitz syndrome and familial Mediterranean fever. These results indicate that, in addition to CA-specific binding, the PRYSPRY domain possesses a second function, possibly binding of a cofactor, that is essential for retroviral restriction activity by TRIM5alpha.\",\n \"corpus_id\": 12109250,\n \"score\": 1\n },\n {\n \"doc_id\": \"20110098\",\n \"title\": \"Contribution of RING domain to retrovirus restriction by TRIM5alpha depends on combination of host and virus.\",\n \"abstract\": \"The anti-retroviral restriction factor TRIM5alpha contains the RING domain, which is frequently observed in E3 ubiquitin ligases. It was previously proposed that TRIM5alpha restricts human immunodeficiency virus type 1 (HIV-1) via proteasome-dependent and -independent pathways. Here we examined the effects of RING domain mutations on retrovirus restriction by TRIM5alpha in various combinations of virus and host species. Simian immunodeficiency virus isolated from macaque (SIVmac) successfully avoided attacks by RING mutants of African green monkey (AGM)-TRIM5alpha that could still restrict HIV-1. Addition of proteasome inhibitor did not affect the anti-HIV-1 activity of AGM-TRIM5alpha, whereas it disrupted at least partly its anti-SIVmac activity. In the case of mutant human TRIM5alpha carrying proline at the position 332, however, both HIV-1 and SIVmac restrictions were eliminated as a result of RING domain mutations. These results suggested that the mechanisms of retrovirus restriction by TRIM5alpha vary depending on the combination of host and virus.\",\n \"corpus_id\": 34391584,\n \"score\": 1\n },\n {\n \"doc_id\": \"21205312\",\n \"title\": \"Characterization of a core fragment of the rhesus monkey TRIM5α protein.\",\n \"abstract\": \"BACKGROUND: Like all tripartite motif (TRIM) proteins, the retroviral restriction factor TRIM5α consists of RING, B-box 2 and coiled-coil domains, with a C-terminal B30.2(SPRY) domain. Although structures have been determined for some individual TRIM domains, the structure of an intact TRIM protein is unknown. RESULTS: Here, we express and characterize a protease-resistant 29-kD core fragment containing the B-box 2, coiled coil and adjacent linker (L2) region of TRIM5α. This BCCL2 protein formed dimers and higher-order oligomers in solution. Approximately 40% of the BCCL2 secondary structure consisted of alpha helices. Partial loss of alpha-helical content and dissociation of dimers occurred at 42°C, with the residual alpha helices remaining stable up to 80°C. CONCLUSIONS: These results indicate that the B-box 2, coiled-coil and linker 2 regions of TRIM5α form a core dimerization motif that exhibits a high level of alpha-helical content.\",\n \"corpus_id\": 16955118,\n \"score\": 1\n },\n {\n \"doc_id\": \"21490953\",\n \"title\": \"SUMO-interacting motifs of human TRIM5α are important for antiviral activity.\",\n \"abstract\": \"Human TRIM5α potently restricts particular strains of murine leukemia viruses (the so-called N-tropic strains) but not others (the B- or NB-tropic strains) during early stages of infection. We show that overexpression of SUMO-1 in human 293T cells, but not in mouse MDTF cells, profoundly blocks N-MLV infection. This block is dependent on the tropism of the incoming virus, as neither B-, NB-, nor the mutant R110E of N-MLV CA (a B-tropic switch) are affected by SUMO-1 overexpression. The block occurred prior to reverse transcription and could be abrogated by large amounts of restricted virus. Knockdown of TRIM5α in 293T SUMO-1-overexpressing cells resulted in ablation of the SUMO-1 antiviral effects, and this loss of restriction could be restored by expression of a human TRIM5α shRNA-resistant plasmid. Amino acid sequence analysis of human TRIM5α revealed a consensus SUMO conjugation site at the N-terminus and three putative SUMO interacting motifs (SIMs) in the B30.2 domain. Mutations of the TRIM5α consensus SUMO conjugation site did not affect the antiviral activity of TRIM5α in any of the cell types tested. Mutation of the SIM consensus sequences, however, abolished TRIM5α antiviral activity against N-MLV. Mutation of lysines at a potential site of SUMOylation in the CA region of the Gag gene reduced the SUMO-1 block and the TRIM5α restriction of N-MLV. Our data suggest a novel aspect of TRIM5α-mediated restriction, in which the presence of intact SIMs in TRIM5α, and also the SUMO conjugation of CA, are required for restriction. We propose that at least a portion of the antiviral activity of TRIM5α is mediated through the binding of its SIMs to SUMO-conjugated CA.\",\n \"corpus_id\": 5948075,\n \"score\": 1\n },\n {\n \"doc_id\": \"21568899\",\n \"title\": \"Retroviral restriction factors TRIM5α: therapeutic strategy to inhibit HIV-1 replication.\",\n \"abstract\": \"Tripartite motif protein 5-alpha (TRIM5α) is a cytoplasmic protein that efficiently recognizes the incoming capsid (CA) protein of retroviruses and potently inhibits virus infection in a species-specific manner. Through directly recognizing and interacting with HIV CA, TRIM5α is capable of disrupting the ordered process of viral uncoating, eventually interfering with HIV-1 reverse transcription and virus replication. TRIM5α protein contains four domains: RING domain, B-box 2 domain, coiled-coil domain, and B30.2 domain (SPRY) domain. All of the domains are necessary for efficient retrovirus restriction and the B30.2 domain has been shown to be the determinant of the specificity of restriction. Species-specific innate resistance against viral infections offers novel avenues for antiviral therapeutics. Various mutants of TRIM5α have been described which differently affect the HIV-1 reverse transcription process. This makes the establishment of new and improved models for HIV replication and AIDS pathogenesis by monitoring endogenous TRIM5α an attractive approach. TRIM5α-mediated restriction is modulated by the host protein Cyclophilin A (Cyp A) which could effectively interact with the CA of HIV-1. Here we will review the structure and roles of TRIM5α protein, the interaction between Cyp A and TRIM5α, as well as gene therapy strategies associated with TRIM5α to inhibit HIV-1 infection.\",\n \"corpus_id\": 12366103,\n \"score\": 1\n },\n {\n \"doc_id\": \"21680520\",\n \"title\": \"Role of TRIM5α RING domain E3 ubiquitin ligase activity in capsid disassembly, reverse transcription blockade, and restriction of simian immunodeficiency virus.\",\n \"abstract\": \"The mammalian tripartite motif protein, TRIM5α, recognizes retroviral capsids entering the cytoplasm and blocks virus infection. Depending on the particular TRIM5α protein and retrovirus, complete disruption of the TRIM5α RING domain decreases virus-restricting activity to various degrees. TRIM5α exhibits RING domain-dependent E3 ubiquitin ligase activity, but the specific role of this activity in viral restriction is unknown. We created a panel of African green monkey TRIM5α (TRIM5α(AGM)) mutants, many of which are specifically altered in RING domain E3 ubiquitin ligase function, and characterized the phenotypes of these mutants with respect to restriction of simian and human immunodeficiency viruses (SIV(mac) and HIV-1, respectively). TRIM5α(AGM) ubiquitin ligase activity was essential for both the accelerated disassembly of SIV(mac) capsids and the disruption of reverse transcription. The levels of SIV(mac) particulate capsids in the cytosol of target cells expressing the TRIM5α variants strongly correlated with the levels of viral late reverse transcripts. RING-mediated ubiquitylation and B30.2(SPRY) domain-determined capsid binding independently contributed to the potency of SIV(mac) restriction by TRIM5α(AGM). In contrast, TRIM5α proteins attenuated in RING ubiquitin ligase function still accelerated HIV-1 capsid disassembly, inhibited reverse transcription, and blocked infection. Replacement of the helix-4/5 loop in the SIV(mac) capsid with the corresponding region of the HIV-1 capsid diminished the dependence of restriction on TRIM5α RING function. Thus, ubiquitylation mediated by the RING domain of TRIM5α(AGM) is essential for blocking SIV(mac) infection at the stage of capsid uncoating.\",\n \"corpus_id\": 25158696,\n \"score\": 1\n },\n {\n \"doc_id\": \"21866272\",\n \"title\": \"TRIM5 acts as more than a retroviral restriction factor.\",\n \"abstract\": \"The retrovirus restriction factor TRIM5α blocks post-entry infection of retroviruses in a species-specific manner. As a cellular E3 ubiquitin ligase, TRIM5α binds to the retroviral capsid lattice in the cytoplasm of an infected cell and accelerates the uncoating process of retroviral capsid, thus providing a potent restriction to HIV-1 and other retrovirus infections. The precise mechanism by which this restriction is imposed remains under scrutiny, and evidence is lacking to link the E3 ubiquitin ligase activity of TRIM5α to its ability to restrict retrovirus infection. In a recent study, Pertel and colleagues have uncovered the link between the two, providing compelling evidence to suggest that following the interaction with the retroviral capsid, TRIM5 triggers an antiviral innate immune response by functioning as a pattern recognition receptor. This unique function of TRIM5 is dependent on its association with the E2 ubiquitin-conjugating enzyme complex UBC13-UEV1A and subsequent activation of the TAK1 kinase complex and downstream genes involved in innate immune responses. These findings have defined a novel function for TRIM5 as a pattern recognition receptor in innate immune recognition and provided valuable mechanistic insight into its role as a retroviral restriction factor. Here we discuss the significance of these new findings in understanding TRIM5-mediated HIV restriction.\",\n \"corpus_id\": 5565058,\n \"score\": 1\n },\n {\n \"doc_id\": \"21911161\",\n \"title\": \"Reduction of N-tropic mutant porcine endogenous retrovirus infectivity by human tripartite motif-containing 5-isoform alpha.\",\n \"abstract\": \"In cases of retroviral infection, the host cell deploys antiviral proteins as a type of innate immunity. Tripartite motif-containing 5-isoform alpha (TRIM5α) is a potent antiviral protein. TRIM5α has been reported to restrict human immunodeficiency virus (HIV) 1 infection in rhesus monkey cells by targeting the incoming viral capsid at the postentry or preintegration stage of the viral life cycle. As a consequence, virus replication and reverse transcription are interrupted. TRIM5α of human origin has also been shown to inhibit N-tropic murine leukemia virus infection. To investigate the inhibitory effect of TRIM5α on porcine endogenous retrovirus (PERV) infection in humans, we constructed a 293T cell line stably expressing human TRIM5α (293T-huTRIM5α) and tested the infectivity of vesicular stomatitis virus glycoprotein envelope pseudotyped viruses (wild-type PERV [wt-PERV], N-tropic mutant PERV, N-tropic murine leukemia virus, and MoMLV). Infectivity of N-tropic mutant PERV was reduced by 43.3% in 293T-huTRIM5α cells, a decrease in efficiency that was more than 3-fold greater than that of wt-PERV in 293T-huTRIM5α cells. Human TRIM5α exhibited inhibitory activity against N-tropic MLV and N-tropic mutant PERV, but showed no antiviral activity against Moloney murine leukemia virus or wt-PERV.\",\n \"corpus_id\": 27428098,\n \"score\": 1\n },\n {\n \"doc_id\": \"22193888\",\n \"title\": \"The cell biology of TRIM5α.\",\n \"abstract\": \"The tripartite motif (TRIM)-containing proteins are involved in many cellular functions such as cell signaling, apoptosis, cell differentiation, and immune modulation. TRIM5 proteins, including TRIM5α and TRIM-Cyp, are known to possess antiretroviral activity against many different retroviruses. Besides being retroviral restriction factors, TRIM5 proteins participate in other cellular functions that have recently emerged in the study of TRIM5α. In this review, we discuss properties of TRIM5α such as cytoplasmic body formation, protein turnover, and trafficking. Also, we discuss recent insights into innate immune modulation mediated by TRIM5α, highlighting the various functions TRIM5α has in cellular processes.\",\n \"corpus_id\": 43893067,\n \"score\": 1\n },\n {\n \"doc_id\": \"22291694\",\n \"title\": \"TRIM5α and Species Tropism of HIV/SIV.\",\n \"abstract\": \"Human immunodeficiency virus type 1 (HIV-1) infects humans and chimpanzees but not old world monkeys (OWMs) such as the rhesus monkey (Rh) and cynomolgus monkey (CM). HIV-1 efficiently enters cells of OWMs but encounters a block before reverse transcription. This narrow host range is attributed to a barrier in the host cell. In 2004, the screening of a Rh cDNA library identified tripartite motif 5α (TRIM5α) as a cellular antiviral factor. TRIM5α is one of splicing variants produced by TRIM5 gene and TRIM5 proteins are members of the TRIM family containing RING, B-box 2, and coiled-coil domains. The RING domain is frequently found in E3 ubiquitin ligase and TRIM5α is degraded via the ubiquitin-proteasome-dependent pathway. Among TRIM5 splicing variants, TRIM5α alone has an additional C-terminal PRYSPRY (B30.2) domain. Previous studies have shown that sequence variation in variable regions of the PRYSPRY domain among different monkey species affects species-specific retrovirus infection, while amino acid sequence differences in the viral capsid protein determine viral sensitivity to restriction. TRIM5α recognizes the multimerized capsid proteins (viral core) of an incoming virus by its PRYSPRY domain and is thus believed to control retroviral infection. There are significant intraspecies variations in the Rh-TRIM5 gene. It has also been reported that some Rh and CM individuals have retrotransposed cyclophilin A open reading frame in the TRIM5 gene, which produces TRIM5-cyclophilin A fusion protein (TRIMCyp). TRIMCyp, which was originally identified as an anti-HIV-1 factor of New World owl monkeys, is an interesting example of the gain of a new function by retrotransposition. As different TRIM5 genotypes of Rh showed different levels of simian immunodeficiency virus replication in vivo, the TRIM5 genotyping is thought to be important in acquired immunodeficiency syndrome monkey models.\",\n \"corpus_id\": 6438419,\n \"score\": 1\n },\n {\n \"doc_id\": \"22435067\",\n \"title\": \"Role of Human TRIM5α in Intrinsic Immunity.\",\n \"abstract\": \"Human immunodeficiency virus (HIV) has a very narrow host range. HIV type 1 (HIV-1) does not infect Old World monkeys, such as the rhesus monkey (Rh). Rh TRIM5α was identified as a factor that confers resistance, intrinsic immunity, to HIV-1 infection. Unfortunately, human TRIM5α is almost powerless to restrict HIV-1. However, human TRIM5α potently restricts N-tropic murine leukemia viruses (MLV) but not B-tropic MLV, indicating that human TRIM5α represents the restriction factor previously designated as Ref1. African green monkey TRIM5α represents another restriction factor previously designated as Lv1, which restricts both HIV-1 and simian immunodeficiency virus isolated from macaque (SIVmac) infection. TRIM5 is a member of the tripartite motif family containing RING, B-box2, and coiled-coil domains. The RING domain is frequently found in E3 ubiquitin ligase, and TRIM5α is thought to degrade viral core via ubiquitin-proteasome-dependent and -independent pathways. The alpha isoform of TRIM5 has an additional C-terminal PRYSPRY domain, which is a determinant of species-specific retrovirus restriction by TRIM5α. On the other hand, the target regions of viral capsid protein (CA) are scattered on the surface of core. A single amino acid difference in the surface-exposed loop between α-helices 6 and 7 (L6/7) of HIV type 2 (HIV-2) CA affects viral sensitivity to human TRIM5α and was also shown to be associated with viral load in West African HIV-2 patients, indicating that human TRIM5α is a critical modulator of HIV-2 replication in vivo. Interestingly, L6/7 of CA corresponds to the MLV determinant of sensitivity to mouse factor Fv1, which potently restricts N-tropic MLV. In addition, human genetic polymorphisms also affect antiviral activity of human TRIM5α. Recently, human TRIM5α was shown to activate signaling pathways that lead to activation of NF-κB and AP-1 by interacting with TAK1 complex. TRIM5α is thus involved in control of viral infection in multiple ways.\",\n \"corpus_id\": 2912377,\n \"score\": 1\n },\n {\n \"doc_id\": \"22847415\",\n \"title\": \"Structure of the rhesus monkey TRIM5α PRYSPRY domain, the HIV capsid recognition module.\",\n \"abstract\": \"Tripartite motif protein TRIM5α blocks retroviral replication after cell entry, and species-specific differences in its activity are determined by sequence variations within the C-terminal B30.2/PRYSPRY domain. Here we report a high-resolution structure of a TRIM5α PRYSPRY domain, the PRYSPRY of the rhesus monkey TRIM5α that potently restricts HIV infection, and identify features involved in its interaction with the HIV capsid. The extensive capsid-binding interface maps on the structurally divergent face of the protein formed by hypervariable loop segments, confirming that TRIM5α evolution is largely determined by its binding specificity. Interactions with the capsid are mediated by flexible variable loops via a mechanism that parallels antigen recognition by IgM antibodies, a similarity that may help explain some of the unusual functional properties of TRIM5α. Distinctive features of this pathogen-recognition interface, such as structural plasticity conferred by the mobile v1 segment and interaction with multiple epitopes, may allow restriction of divergent retroviruses and increase resistance to capsid mutations.\",\n \"corpus_id\": 18506201,\n \"score\": 1\n },\n {\n \"doc_id\": \"23084420\",\n \"title\": \"Contribution of SUMO-interacting motifs and SUMOylation to the antiretroviral properties of TRIM5α.\",\n \"abstract\": \"Recent findings suggested that the SUMO-interacting motifs (SIMs) present in the human TRIM5α (TRIM5α(hu)) protein play an important role in the ability of TRIM5α(hu) to restrict N-MLV. Here we explored the role of SIMs in the ability of rhesus TRIM5α (TRIM5α(rh)) to restrict HIV-1, and found that TRIM5α(rh) SIM mutants IL376KK (SIM1mut) and VI405KK (SIM2mut) completely lost their ability to block HIV-1 infection. Interestingly, these mutants also lost the recently described property of TRIM5α(rh) to shuttle into the nucleus. Analysis of these variants revealed that they are unable to interact with the HIV-1 core, which might explain the reason that these variants are not active against HIV-1. Furthermore, NMR titration experiments to assay the binding between the PRYSPRY domain of TRIM5α(rh) and the small ubiquitin-like modifier 1(SUMO-1) revealed no interaction. In addition, we examined the role of SUMOylation in restriction, and find out that inhibition of SUMOylation by the adenoviral protein Gam1 did not alter the retroviral restriction ability of TRIM5α. Overall, our results do not support a role for SIMs or SUMOylation in the antiviral properties of TRIM5α.\",\n \"corpus_id\": 39621283,\n \"score\": 1\n },\n {\n \"doc_id\": \"23320071\",\n \"title\": \"Delaying reverse transcription does not increase sensitivity of HIV-1 to human TRIM5α.\",\n \"abstract\": \"BACKGROUND: Because uncoating of the capsid is linked to reverse transcription, modifications that delay this process lead to the persistence in the cytoplasm of capsids susceptible to recognition by the human restriction factor TRIM5α (hTRIM5α). It is unknown, however, if increasing the time available for capsid-hTRIM5α interactions would actually render viruses more sensitive to hTRIM5α. RESULTS: Viral sensitivity to hTRIM5α was evaluated by comparing their replication in human U373-X4 cells in which hTRIM5α activity had or had not been inhibited by overexpression of human TRIM5γ. No differences were observed comparing wild-type HIV-1 and variants carrying mutations in reverse transcriptase or the central polypurine tract that delayed the completion of reverse transcription. In addition, the effect of delaying the onset of reverse transcription for several hours by treating target cells with nevirapine was evaluated using viral isolates with different sensitivities to hTRIM5α. Delaying reverse transcription led to a time-dependent loss in viral infectivity that was increased by inhibiting capsid-cyclophilin A interactions, but did not result in increased viral sensitivity to hTRIM5α, regardless of their intrinsic sensitivity to this restriction factor. CONCLUSIONS: Consistent with prior studies, the HIV-1 capsid can be targeted for destruction by hTRIM5α, but different strains display considerable variability in their sensitivity to this restriction factor. Capsids can also be lost more slowly through a TRIM5α-independent process that is accelerated when capsid-cyclophilin A interactions are inhibited, an effect that may reflect changes in the intrinsic stability of the capsid. Blocking the onset or delaying reverse transcription does not, however, increase viral sensitivity to hTRIM5α, indicating that the recognition of the capsids by hTRIM5α is completed rapidly following entry into the cytoplasm, as previously observed for the simian restriction factors TRIM-Cyp and rhesus TRIM5α.\",\n \"corpus_id\": 16613455,\n \"score\": 1\n },\n {\n \"doc_id\": \"23548691\",\n \"title\": \"Viral attachment induces rapid recruitment of an innate immune sensor (TRIM5α) to the plasma membrane.\",\n \"abstract\": \"TRIM5α (tripartite motif 5α) acts as a pattern recognition receptor specific for the retrovirus capsid lattice and blocks infection by HIV-1 immediately after entry. However, the precise mechanisms underlying this rapid recognition of viral components remain elusive. Here, we analyzed the influence of viral exposure on TRIM5α. Total internal reflection fluorescence microscopy and lipid flotation assays revealed rapid recruitment of a TRIM5α subpopulation to the plasma membrane (PM) upon exposure to vesicular stomatitis virus-G-pseudotyped HIV-1 viral-like particles (VLPs), but not to envelope (Env)-less HIV-1 VLPs. TRIM5α signals were frequently colocalized with those of HIV-1 capsid at the PM. Exposure to HIV-1 Env-pseudotyped HIV-1 vectors also triggered translocation of endogenous TRIM5α to lipid microdomains within human T cells. Similarly, clustering of lipid microdomains by a glycosphingolipid stereoisomer resulted in rapid TRIM5α recruitment to the PM. Of note, recruitment of endogenous rhesus TRIM5α to the PM prior to HIV-1 infection significantly increased the potency of viral restriction. Our data therefore suggest the importance of TRIM5α recruitment to the PM for TRIM5α-mediated innate immune sensing and restriction of retroviral infection.\",\n \"corpus_id\": 32856651,\n \"score\": 1\n },\n {\n \"doc_id\": \"24554657\",\n \"title\": \"Contribution of PDZD8 to stabilization of the human immunodeficiency virus type 1 capsid.\",\n \"abstract\": \"UNLABELLED: Following human immunodeficiency virus type 1 (HIV-1) entry into the host cell, the viral capsid gradually disassembles in a process called uncoating. A proper rate of uncoating is important for reverse transcription of the HIV-1 genome. Host restriction factors such as TRIM5α and TRIMCyp bind retroviral capsids and cause premature disassembly, leading to blocks in reverse transcription. Other host factors, such as cyclophilin A, stabilize the HIV-1 capsid and are required for efficient infection in some cell types. Here, we show that a heat-labile factor greater than 100 kDa in the cytoplasm of cells from multiple vertebrate species slows the spontaneous disassembly of HIV-1 capsid-nucleocapsid (CA-NC) complexes in vitro. We identified the PDZ domain-containing protein 8 (PDZD8) as a critical component of the capsid-stabilizing activity in the cytoplasmic extracts. PDZD8 has been previously reported to bind the HIV-1 Gag polyprotein and to make a positive contribution to the efficiency of HIV-1 infection (M. S. Henning, S. G. Morham, S. P. Goff, and M. H. Naghavi, J. Virol. 84:: 8990-8995, 2010, doi:10.1128/JVI.00843-10). PDZD8 knockdown accelerated the disassembly of HIV-1 capsids in infected cells, resulting in decreased reverse transcription. The PDZD8 coiled-coil domain is sufficient for HIV-1 capsid binding, but other parts of the protein, including the PDZ domain, are apparently required for stabilizing the capsid and supporting HIV-1 infection. In summary, PDZD8 interacts with and stabilizes the HIV-1 capsid and thus represents a potentially targetable host cofactor for HIV-1 infection. IMPORTANCE: After human immunodeficiency virus type 1 (HIV-1) gains access to the interior of the target cell, host cell factors can influence virus infection in either a positive or negative way. HIV-1 depends upon certain host cell factors to assist processes that are required for virus replication. One example of such a host factor is PDZD8. This work shows that PDZD8 helps to stabilize the HIV-1 capsid, a huge complex of the viral RNA, enzymes, and protein. When PDZD8 is prevented from interacting with the HIV-1 capsid, the capsid becomes unstable and HIV-1 infection is inhibited. These results show that PDZD8 regulates the uncoating of the HIV-1 capsid. Interfering with the interaction of PDZD8 and capsid could prove to be a useful strategy for intervening in HIV-1 infection and transmission.\",\n \"corpus_id\": 31806380,\n \"score\": 1\n },\n {\n \"doc_id\": \"24583231\",\n \"title\": \"The conserved sumoylation consensus site in TRIM5α modulates its immune activation functions.\",\n \"abstract\": \"TRIM5α is a type I interferon-stimulated anti-retroviral restriction factor expressed in most primates and homologous proteins are expressed in other mammals. Through its C-terminal PRYSPRY (B30.2) domain, TRIM5α binds to incoming and intact post-fusion retroviral cores in the cytoplasm. Following this direct interaction, the retroviral capsid core is destabilized and progression of the virus life cycle is interrupted. Specific recognition of its viral target by TRIM5α also triggers the induction of an antiviral state involving the activation of transcription factors NF-κB- and AP-1. In addition to PRYSPRY, several other TRIM5α domains are important for anti-retroviral function, including a RING zinc-binding motif. This domain has \\\"E3\\\" ubiquitin ligase activity and is involved in both the direct inhibition of incoming retroviruses and innate immune activation. A highly conserved sumoylation consensus site is present between the RING motif and the N-terminal extremity of TRIM5α. No clear role in restriction has been mapped to this sumoylation site, and no sumoylated forms of TRIM5α have been observed. Here we confirm that mutating the putatively sumoylated lysine (K10) of the Rhesus macaque TRIM5α (TRIM5αRh) to an arginine has only a small effect on restriction. However, we show that the mutation significantly decreases the TRIM5α-induced generation of free K63-linked ubiquitin chains, an intermediate in the activation of innate immunity pathways. Accordingly, K10R decreases TRIM5α-mediated activation of both NF-κB and AP-1. Concomitantly, we find that K10R causes a large increase in the levels of ubiquitylated TRIM5α. Finally, treatment with the nuclear export inhibitor leptomycin B shows that K10R enhances the nuclear localization of TRIM5αRh, while at the same time reducing its level of association with nuclear SUMO bodies. In conclusion, the TRIM5α sumoylation site appears to modulate the E3 ubiquitin ligase activities of the adjacent RING domain, promoting K63-linked ubiquitin chains at the expense of auto-ubiquitylation which is probably K48-linked. Consistently, we find this sumoylation site to be important for innate immune activation by TRIM5α. In addition, lysine 10 regulates TRIM5α nuclear shuttling and nuclear localization, which may also be related to its role in innate immunity activation.\",\n \"corpus_id\": 13309522,\n \"score\": 1\n },\n {\n \"doc_id\": \"25880753\",\n \"title\": \"TRIM5α is a SUMO substrate.\",\n \"abstract\": \"BACKGROUND: The TRIM5α restriction factor interferes with retroviral infections by inhibiting an early step of viral replication. TRIM5α activity was recently proposed to be regulated by the SUMO machinery and one SUMO consensus conjugation site as well as three putative SUMO interacting motifs (SIMs) were identified within TRIM5α sequence. Whereas mutation of the SIM sequences was found to abolish TRIM5α antiviral activity, mutation of the consensus SUMO conjugation site did not affect its restriction capacity, although this putative site has never been shown to be actually a SUMO substrate. FINDINGS: Here we further demonstrate that TRIM5α relies on the SUMO machinery to promote restriction, since SUMO1 overexpression enhances TRIM5α-mediated retroviral inhibition whereas knockdown of SUMO1 or E2 SUMO conjugating enzyme Ubc9 prevents restriction. Furthermore, we show for the first time that TRIM5α is SUMOylated both in vitro and in cellulo and that Lysine 10 is the main SUMOylation site. Mutation of the consensus SUMO conjugation motif in position 10 abrogated SUMOylation at this position, but did not disrupt TRIM5α antiviral activity. CONCLUSIONS: Altogether, our results confirm that the SUMO machinery is involved in TRIM5α-mediated retroviral restriction, and demonstrate that TRIM5α is a SUMO 1 and SUMO 2 substrate. The inability to abrogate TRIM5α antiviral activity by mutating its main SUMO conjugation motif supports the notion that non-covalent interaction with SUMO or SUMOylated proteins rather than TRIM5α direct SUMOylation is required.\",\n \"corpus_id\": 1333081,\n \"score\": 1\n },\n {\n \"doc_id\": \"26372380\",\n \"title\": \"Impact of TRIM5α in vivo.\",\n \"abstract\": \"HIV type 1 (HIV-1) has a very narrow host range that is limited to humans and chimpanzees. HIV-1 cannot replicate well in Old World monkey cells such as rhesus and cynomolgus monkeys. Tripartite motif (TRIM)5α is a key molecule that confers potent resistance against HIV-1 infection and is composed of really interesting new gene, B-box2, coiled-coil and PRYSPRY domains. Interaction between TRIM5α PRYSPRY domains and HIV-1 capsid core triggers the anti-HIV-1 activity of TRIM5α. Analysis of natural HIV variants and extensive mutational experiments has revealed the presence of critical amino acid residues in both the PRYSPRY domain and HIV capsid for potent HIV suppression by TRIM5α. Genetic manipulation of the human TRIM5 gene could establish human cells totally resistant to HIV-1, which may lead to a cure for HIV-1 infection in the future.\",\n \"corpus_id\": 7060927,\n \"score\": 1\n },\n {\n \"doc_id\": \"29196608\",\n \"title\": \"Rhesus monkey TRIM5α protein SPRY domain contributes to AP-1 activation.\",\n \"abstract\": \"TRIM5α is an important host restriction factor that could potently block retrovirus infection. The SPRY domain of TRIM5α mediates post-entry restriction by recognition of and binding to the retroviral capsid. Human TRIM5α also functions as an innate immune sensor to activate AP-1 and NF-κB signaling, which subsequently restrict virus replication. Previous studies have shown that the AP-1 and NF-κB signaling activation relies on the RING motif of TRIM5α. In this study, we have demonstrated that the SPRY domain is essential for rhesus macaque TRIM5α to activate AP-1 but not NF-κB signaling. The AP-1 activation mainly depends on all of the β-sheet barrel on SPRY structure of TRIM5α. Furthermore, the SPRY-mediated auto-ubiquitination of TRIM5α is required for AP-1 activation. This study reports that rhesus macaque TRIM5α mainly undergoes Lys27-linked and Met1-linked auto-polyubiquitination. Finally, we found that the TRIM5α signaling function was positively correlated with its retroviral restriction activity. This study discovered an important role of the SPRY domain in immune signaling and antiviral activity and further expanded our knowledge of the antiviral mechanism of TRIM5α.\",\n \"corpus_id\": 3648191,\n \"score\": 1\n },\n {\n \"doc_id\": \"29237846\",\n \"title\": \"The Three-Fold Axis of the HIV-1 Capsid Lattice Is the Species-Specific Binding Interface for TRIM5α.\",\n \"abstract\": \"Rhesus TRIM5α (rhTRIM5α) potently restricts replication of human immunodeficiency virus type 1 (HIV-1). Restriction is mediated through direct binding of the C-terminal B30.2 domain of TRIM5α to the assembled HIV-1 capsid core. This host-pathogen interaction involves multiple capsid molecules within the hexagonal HIV-1 capsid lattice. However, the molecular details of this interaction and the precise site at which the B30.2 domain binds remain largely unknown. The human orthologue of TRIM5α (hsTRIM5α) fails to block infection by HIV-1 both in vivo and in vitro This is thought to be due to differences in binding to the capsid lattice. To map the species-specific binding surface on the HIV-1 capsid lattice, we used microscale thermophoresis and dual-focus fluorescence correlation spectroscopy to measure binding affinity of rhesus and human TRIM5α B30.2 domains to a series of HIV-1 capsid variants that mimic distinct capsid arrangements at each of the symmetry axes of the HIV-1 capsid lattice. These surrogates include previously characterized capsid oligomers, as well as a novel chemically cross-linked capsid trimer that contains cysteine substitutions near the 3-fold axis of symmetry. The results demonstrate that TRIM5α binding involves multiple capsid molecules along the 2-fold and 3-fold interfaces between hexamers and indicate that the binding interface at the 3-fold axis contributes to the well-established differences in restriction potency between TRIM5α orthologues. IMPORTANCE TRIM5α is a cellular protein that fends off infection by retroviruses through binding to the viruses' protein shell surrounding its genetic material. This shell is composed of several hundred capsid proteins arranged in a honeycomb-like hexagonal pattern that is conserved across retroviruses. By binding to the complex lattice formed by multiple capsid proteins, rather than to a single capsid monomer, TRIM5α restriction activity persists despite the high mutation rate in retroviruses such as HIV-1. In rhesus monkeys, but not in humans, TRIM5α confers resistance to HIV-1. By measuring the binding of human and rhesus TRIM5α to a series of engineered HIV-1 capsid mimics of distinct capsid lattice interfaces, we reveal the HIV-1 capsid surface critical for species-specific binding by TRIM5α.\",\n \"corpus_id\": 3590121,\n \"score\": 1\n },\n {\n \"doc_id\": \"18799572\",\n \"title\": \"Biochemical and biophysical characterization of a chimeric TRIM21-TRIM5alpha protein.\",\n \"abstract\": \"The tripartite motif (TRIM) protein, TRIM5alpha, is an endogenous factor in primates that recognizes the capsids of certain retroviruses after virus entry into the host cell. TRIM5alpha promotes premature uncoating of the capsid, thus blocking virus infection. Low levels of expression and tendencies to aggregate have hindered the biochemical, biophysical, and structural characterization of TRIM proteins. Here, a chimeric TRIM5alpha protein (TRIM5(Rh)-21R) with a RING domain derived from TRIM21 was expressed in baculovirus-infected insect cells and purified. Although a fraction of the TRIM5(Rh)-21R protein formed large aggregates, soluble fractions of the protein formed oligomers (mainly dimers), exhibited a protease-resistant core, and contained a high percentage of helical secondary structure. Cross-linking followed by negative staining and electron microscopy suggested a globular structure. The purified TRIM5(Rh)-21R protein displayed E3-ligase activity in vitro and also self-ubiquitylated in the presence of ubiquitin-activating and -conjugating enzymes. The purified TRIM5(Rh)-21R protein specifically associated with human immunodeficiency virus type 1 capsid-like complexes; a deletion within the V1 variable region of the B30.2(SPRY) domain decreased capsid binding. Thus, the TRIM5(Rh)-21R restriction factor can directly recognize retroviral capsid-like complexes in the absence of other mammalian proteins.\",\n \"corpus_id\": 22489148,\n \"score\": 0\n },\n {\n \"doc_id\": \"19951947\",\n \"title\": \"Determinants for the rhesus monkey TRIM5alpha-mediated block of the late phase of HIV-1 replication.\",\n \"abstract\": \"Rhesus monkey TRIM5alpha (TRIM5alpharh) includes RING, B-box, coiled-coil, and B30.2(PRYSPRY) domains and blocks HIV-1 infection by targeting HIV-1 core through a B30.2(PRYSPRY) domain. Previously, we reported that TRIM5alpharh also blocks HIV-1 production in a B30.2(PRYSPRY)-independent manner. Efficient encapsidation of TRIM5alpharh, but not human TRIM5alpha (TRIM5alphahu), in HIV-1 virus-like particles suggests the interaction between Gag and TRIM5alpharh during viral assembly. Here, we determined responsible regions for late restriction activity of TRIM5alpharh. The RING disruption, but not the replacement with human TRIM21 RING, ablated the efficient encapsidation and the late restriction, suggesting that a RING structure was essential for the late restriction and efficient interaction with HIV-1 Gag. The prominent cytoplasmic body formation of TRIM5alpharh, which depended on the coiled-coil domain and the ensuing linker 2 region, was not required for the encapsidation. Intriguingly, TRIM5alpharh coiled-coil domain mutants (M133T and/or T146A) showed impaired late restriction activity, despite the efficient encapsidation and cytoplasmic body formation. Our results suggest that the TRIM5alpharh-mediated late restriction involves at least two distinct activities as follows: (i) interaction with HIV-1 Gag polyprotein through the N-terminal, RING, and B-box 2 regions of a TRIM5alpharh monomer, and (ii) an effector function(s) that depends upon the coiled-coil and linker 2 domains of TRIM5alpharh. We speculate that the TRIM5alpharh coiled-coil region recruits additional factor(s), such as other TRIM family proteins or a cellular protease, during the late restriction. RBCC domains of TRIM family proteins may play a role in sensing newly synthesized viral proteins as a part of innate immunity against viral infection.\",\n \"corpus_id\": 42539395,\n \"score\": 0\n },\n {\n \"doc_id\": \"20929586\",\n \"title\": \"A novel envelope mediated post entry restriction of murine leukaemia virus in human cells is Ref1/TRIM5α independent.\",\n \"abstract\": \"BACKGROUND: 'Intrinsic' resistance to retroviral infection was first recognised with the Friend virus susceptibility gene (Fv1), which determines susceptibility to murine leukaemia virus (MLV) infection in different murine species. Similarly, the tripartite motif (TRIM) family of proteins determine lentiviral restriction in a primate host-species specific manner. For example rhesus TRIM5α (rhTRIM5α) can potently restrict HIV-1 infection while human TRIM5α (huTRIM5α) only has a mild effect on SIVmac and HIV-1 infectivity (Lv1). Human TRIM5α is able to restrict MLV-N virus replication, but is ineffective against MLV-B or MLV-NB virus infection. Lv2 restriction of some HIV-2 viruses is seen in human cells. Like Lv1, Lv2 is a post-entry restriction factor, whose viral determinants have been mapped to the viral capsid (CA). Unlike Lv1, however, Lv2 is determined by envelope (Env) in addition to CA. Here we present evidence of a novel Env determined post entry restriction to infection in human cells of pseudotyped MLV-B and MLV-NB cores. RESULTS: We generated retroviral vectors pseudotyped with various gamma and lentiviral Envs on MLV-B and -NB CAs containing a green fluorescent protein (GFP) reporter. Flow cytometry was used to determine transduction efficiencies in NP2/CD4/CXCR4 (glioma cell line stably transduced with the HIV receptors) and HeLa/CD4 cell lines. The HeLa/CD4 cell line restricted both MLV CAs in an Env dependent manner, compared to NP2/CD4/CXCR4 cells. Quantitative polymerase chain reaction (QT-PCR) analysis of reverse transcription (RT) transcripts demonstrates that this restriction occurs at a post entry and RT level. siRNA knockdown of huTRIM5α ruled out a direct role for this cellular component in mediating this restriction. We describe a previously unobserved Env determined restriction of MLV-B and MLV-NB CAs in HeLa/CD4 cells when pseudotyped with HIV-2 and RD114 Envs, but not gibbon ape leukaemia virus (GALV), HIV-1 or Amphotrophic (Ampho) Envs. CONCLUSIONS: Our data further demonstrate the variability of Env and CA mediated susceptibility to post entry host cell restriction. We discuss the relevance of these findings in light of the growing evidence supporting the complexities involved in innate host immunity to retroviral infection.\",\n \"corpus_id\": 6951798,\n \"score\": 0\n },\n {\n \"doc_id\": \"21247355\",\n \"title\": \"Recent insights into the mechanism and consequences of TRIM5α retroviral restriction.\",\n \"abstract\": \"The cellular factor TRIM5α inhibits infection by numerous retroviruses in a species-specific manner. The TRIM5α protein from rhesus macaques (rhTRIM5α) restricts infection by HIV-1 while human TRIM5α (huTRIM5α) restricts infection by murine leukemia virus (MLV). In owl monkeys a related protein TRIM-Cyp restricts HIV-1 infection. Several models have been proposed for retroviral restriction by TRIM5 proteins (TRIM5α and TRIM-Cyp). These models collectively suggest that TRIM5 proteins mediate restriction by directly binding to specific determinants in the viral capsid. Through their ability to self-associate TRIM5 proteins compartmentalize the viral capsid core and mediate its abortive disassembly via a poorly understood mechanism that is sensitive to proteasome inhibitors. In this review, we discuss TRIM5-mediated restriction in detail. We also discuss how polymorphisms within human and rhesus macaque populations have been demonstrated to affect disease progression of immunodeficiency viruses in these species.\",\n \"corpus_id\": 34016773,\n \"score\": 0\n },\n {\n \"doc_id\": \"21264255\",\n \"title\": \"The antiviral spectra of TRIM5α orthologues and human TRIM family proteins against lentiviral production.\",\n \"abstract\": \"BACKGROUND: Rhesus monkey TRIM5α (TRIM5αrh) recognizes the incoming HIV-1 core through its C-terminal B30.2(PRYSPRY) domain and promotes its premature disassembly or degradation before reverse transcription. Previously, we have shown that TRIM5αrh blocks HIV-1 production through the N-terminal RBCC domain by the recognition of Gag polyproteins. Although all TRIM family proteins have RBCC domains, it remains elusive whether they possess similar late-restriction activities. METHODOLOGY/PRINCIPAL FINDINGS: We examined the antiviral spectra of TRIM5α orthologues and human TRIM family members which have a genetic locus proximal to human TRIM5α (TRIM5αhu), against primate lentiviral production. When HIV-1 virus-like particles (VLPs) were generated in the presence of TRIM5α proteins, rhesus, African green and cynomolgus monkey TRIM5α (TRIM5αag and TRIM5αcy), but not TRIM5αhu, were efficiently incorporated into VLPs, suggesting an interaction between HIV-1 Gag and TRIM5α proteins. TRIM5αrh potently restricted the viral production of HIV-1 groups M and O and HIV-2, but not simian lentiviruses including SIV(MAC)1A11, SIV(AGM)Tan-1 or SIV(AGM)SAB-1. TRIM5αhu did not show notable late restriction activities against these lentiviruses. TRIM5αag and TRIM5αcy showed intermediate restriction phenotypes against HIV-1 and HIV-2, but showed no restriction activity against SIV production. A series of chimeric TRIM5α constructs indicated that the N-terminal region of TRIM5αag and TRIM5αcy are essential for the late restriction activity, while the C-terminal region of TRIM5αcy negatively regulates the late restriction activity against HIV-1. When select human TRIM family proteins were examined, TRIM21 and 22 were efficiently incorporated into HIV-1 VLPs, while only TRIM22 reduced HIV-1 titers up to 5-fold. The antiviral activities and encapsidation efficiencies did not correlate with their relative expression levels in the producer cells. CONCLUSIONS/SIGNIFICANCE: Our results demonstrated the variations in the late restriction activities among closely related TRIM5α orthologues and a subset of human TRIM family proteins, providing further insights into the late restriction activities of TRIM proteins.\",\n \"corpus_id\": 9065725,\n \"score\": 0\n },\n {\n \"doc_id\": \"21483490\",\n \"title\": \"Novel escape mutants suggest an extensive TRIM5α binding site spanning the entire outer surface of the murine leukemia virus capsid protein.\",\n \"abstract\": \"After entry into target cells, retroviruses encounter the host restriction factors such as Fv1 and TRIM5α. While it is clear that these factors target retrovirus capsid proteins (CA), recognition remains poorly defined in the absence of structural information. To better understand the binding interaction between TRIM5α and CA, we selected a panel of novel N-tropic murine leukaemia virus (N-MLV) escape mutants by a serial passage of replication competent N-MLV in rhesus macaque TRIM5α (rhTRIM5α)-positive cells using a small percentage of unrestricted cells to allow multiple rounds of virus replication. The newly identified mutations, many of which involve changes in charge, are distributed over the outer 'top' surface of N-MLV CA, including the N-terminal β-hairpin, and map up to 29 A(o) apart. Biological characterisation with a number of restriction factors revealed that only one of the new mutations affects restriction by human TRIM5α, indicating significant differences in the binding interaction between N-MLV and the two TRIM5αs, whereas three of the mutations result in dual sensitivity to Fv1(n) and Fv1(b). Structural studies of two mutants show that no major changes in the overall CA conformation are associated with escape from restriction. We conclude that interactions involving much, if not all, of the surface of CA are vital for TRIM5α binding.\",\n \"corpus_id\": 7191281,\n \"score\": 0\n },\n {\n \"doc_id\": \"21575157\",\n \"title\": \"Trafficking of some old world primate TRIM5α proteins through the nucleus.\",\n \"abstract\": \"BACKGROUND: TRIM5α and TRIMCyp are cytoplasmic proteins that bind incoming retroviral capsids and mediate early blocks to viral infection. TRIM5 proteins form cytoplasmic bodies, which are highly dynamic structures. So far, TRIM5 proteins have been found only in the cytoplasm of cells. Interestingly, other proteins from the TRIM family localize to the nucleus. Therefore, we tested the possibility that TRIM5 proteins traffic to the nucleus and the impact of this trafficking on retroviral restriction. RESULTS: Here we report that the TRIM5α proteins of two Old World primates, humans and rhesus monkeys, are transported into the nucleus and are shuttled back to the cytoplasm by a leptomycin B-sensitive mechanism. In leptomycin B-treated cells, these TRIM5α proteins formed nuclear bodies that also contained TRIM19 (PML). Deletion of the amino terminus, including the linker 1 (L1) region, resulted in TRIM5α proteins that accumulated in nuclear bodies. Leptomycin B treatment of TRIM5α-expressing target cells only minimally affected the restriction of retrovirus infection. CONCLUSIONS: We discovered the ability of human and rhesus TRIM5α to shuttle into and out of the nucleus. This novel trafficking ability of TRIM5α proteins could be important for an as-yet-unknown function of TRIM5α.\",\n \"corpus_id\": 6357793,\n \"score\": 0\n },\n {\n \"doc_id\": \"23369348\",\n \"title\": \"Role of SUMO-1 and SUMO interacting motifs in rhesus TRIM5α-mediated restriction.\",\n \"abstract\": \"BACKGROUND: TRIM5α is a member of the tripartite motif family of proteins that restricts retroviral infection in a species-specific manner. The restriction requires an interaction between the viral capsid lattice and the B30.2/SPRY domain of TRIM5α. Previously, we determined that two SUMO interacting motifs (SIMs) present in the B30.2/SPRY domain of human TRIM5α (huTRIM5α) were important for the restriction of N-tropic Murine Leukemia Virus. Here, we examined whether SUMO expression and the SIM1 and SIM2 motifs in rhesus monkey TRIM5α (rhTRIM5α) are similarly important for Human Immunodeficiency Type 1 (HIV-) restriction. RESULTS: We found that mutation of SIM1 and SIM2 of rhTRIM5α abolished the restriction of HIV-1 virus. Further, knockdown of SUMO-1 in rhTRIM5α expressing cells abolished restriction of HIV-1. These results may be due, in part, to the ability of SUMO-1 to stabilize rhTRIM5α protein expression, as SUMO-1 knockdown increased rhTRIM5α turnover and the mutations in SIM1 and SIM2 led to more rapid degradation than the wild type protein. The NF-κB signaling ability of rhTRIM5α was also attenuated by SUMO-1 knockdown. Finally, upon inhibition of CRM1-dependent nuclear export with Leptomycin B (LMB), wild type rhTRIM5α localized to SUMO-1 bodies in the nucleus, while the SIM1 and SIM2 mutants did not localize to SUMO-1. CONCLUSIONS: Our results suggest that the rhTRIM5α B30.2/SPRY domain is not only important for the recognition of the HIV-1 CA, but it is also important for its association with SUMO-1 or SUMO-1 modified proteins. These interactions help to maintain TRIM5α protein levels and its nuclear localization into specific nuclear bodies.\",\n \"corpus_id\": 6416723,\n \"score\": 0\n },\n {\n \"doc_id\": \"24599998\",\n \"title\": \"Higher-order structure of the Rous sarcoma virus SP assembly domain.\",\n \"abstract\": \"UNLABELLED: Purified retroviral Gag proteins can assemble in vitro to form immature virus-like particles (VLPs). By cryoelectron tomography, Rous sarcoma virus VLPs show an organized hexameric lattice consisting chiefly of the capsid (CA) domain, with periodic stalk-like densities below the lattice. We hypothesize that the structure represented by these densities is formed by amino acid residues immediately downstream of the folded CA, namely, the short spacer peptide SP, along with a dozen flanking residues. These 24 residues comprise the SP assembly (SPA) domain, and we propose that neighboring SPA units in a Gag hexamer coalesce to form a six-helix bundle. Using in vitro assembly, alanine scanning mutagenesis, and biophysical analyses, we have further characterized the structure and function of SPA. Most of the amino acid residues in SPA could not be mutated individually without abrogating assembly, with the exception of a few residues near the N and C termini, as well as three hydrophilic residues within SPA. We interpret these results to mean that the amino acids that do not tolerate mutations contribute to higher-order structures in VLPs. Hydrogen-deuterium exchange analyses of unassembled Gag compared that of assembled VLPs showed strong protection at the SPA region, consistent with a higher-order structure. Circular dichroism revealed that a 29mer SPA peptide shifts from a random coil to a helix in a concentration-dependent manner. Analytical ultracentrifugation showed concentration-dependent self-association of the peptide into a hexamer. Taken together, these results provide strong evidence for the formation of a critical six-helix bundle in Gag assembly. IMPORTANCE: The structure of a retrovirus like HIV is created by several thousand molecules of the viral Gag protein, which assemble to form the known hexagonal protein lattice in the virus particle. How the Gag proteins pack together in the lattice is incompletely understood. A short segment of Gag known to be critical for proper assembly has been hypothesized to form a six-helix bundle, which may be the nucleating event that leads to lattice formation. The experiments reported here, using the avian Rous sarcoma virus as a model system, further define the nature of this segment of Gag, show that it is in a higher-order structure in the virus particle, and provide the first direct evidence that it forms a six-helix bundle in retrovirus assembly. Such knowledge may provide underpinnings for the development of antiretroviral drugs that interfere with virus assembly.\",\n \"corpus_id\": 30771997,\n \"score\": 0\n },\n {\n \"doc_id\": \"28767697\",\n \"title\": \"Cyclophilin A potentiates TRIM5α inhibition of HIV-1 nuclear import without promoting TRIM5α binding to the viral capsid.\",\n \"abstract\": \"The host immunophilin cyclophilin A (CypA) binds to the capsid protein (CA) of HIV-1 and regulates its infectivity. Depending on the target cell type, CypA can either promote or inhibit HIV-1 infection. The ability of CypA to promote HIV-1 infection has been extensively studied and linked to several steps in early replication including uncoating, reverse transcription and nuclear import. By contrast, the mechanism by which CypA inhibits infection is less well understood. We investigated the mechanism by which CypA potentiates restriction of HIV-1 by the tripartite motif-containing protein 5 (TRIM5α). Depletion of TRIM5α in the African green monkey cell line Vero, resulted in a loss of inhibition of infection by CypA, demonstrating that inhibition by CypA is mediated by TRIM5α. Complementary genetic and biochemical assays failed to demonstrate an ability of CypA to promote binding of TRIM5α to the viral capsid. TRIM5α inhibits HIV-1 reverse transcription in a proteasome-dependent manner; however, we observed that inhibition of proteasome activity did not reduce the ability of CypA to inhibit infection, suggesting that CypA acts at a step after reverse transcription. Accordingly, we observed a CypA-dependent reduction in the accumulation of nuclear HIV-1 DNA, indicating that CypA specifically promotes TRIM5α inhibition of HIV-1 nuclear import. We also observed that the ability of CypA to inhibit HIV-1 infection is abolished by amino acid substitutions within the conserved CPSF6-binding surface in CA. Our results indicate that CypA inhibits HIV-1 infection in Vero cells not by promoting TRIM5α binding to the capsid but by blocking nuclear import of the HIV-1 preintegration complex.\",\n \"corpus_id\": 40789255,\n \"score\": 0\n }\n]","isConversational":false}}},{"rowIdx":59,"cells":{"query":{"kind":"string","value":"{\n \"doc_id\": \"27180300\",\n \"title\": \"Cloning, expression and characterization of a mucin-binding GAPDH from Lactobacillus acidophilus.\",\n \"abstract\": \"Glyceraldehyde-3-phosphate dehydrogenase (GAPDH) is a ubiquitous enzyme involved in glycolysis. It is also referred to as a moonlighting protein as it has many diverse functions like regulation of apoptosis, iron homeostasis, cell-matrix interactions, adherence to human colon etc. apart from its principal role in glycolysis. Lactobacilli are lactic acid bacteria which colonize the human gut and confer various health benefits to humans. In the present study, we have cloned, expressed and purified the GAPDH from Lactobacillus acidophilus to get a recombinant product (r-LaGAPDH) and characterized it. Size exclusion chromatography shows that r-LaGAPDH exists as a tetramer in solution and have a mucin binding and hemagglutination activity indicating carbohydrate like binding adhesion mechanism. Fluorescence spectroscopy studies showed an interaction of r-LaGAPDH with mannose, galactose, N-acetylgalactosamine and N-acetylglucosamine with a Kd of 3.6±0.7×10(-3)M, 4.34±0.09×10(-3)M, 4±0.87×10(-3)M and 3.7±0.28×10(-3)M respectively. We hope that this preliminary data will generate more interest in further elucidation of the roles of GAPDH in the adhesion processes of the bacteria.\",\n \"corpus_id\": 41216604\n}"},"candidates":{"kind":"list like","value":[{"doc_id":"18194256","title":"Cell surface Lactobacillus plantarum LA 318 glyceraldehyde-3-phosphate dehydrogenase (GAPDH) adheres to human colonic mucin.","abstract":"AIMS: To characterize the adhesion molecule of Lactobacillus plantarum LA 318 that shows high adhesion to human colonic mucin (HCM). METHODS AND RESULTS: The adhesion test used the BIACORE assay where PBS-washed bacterial cells showed a significant decrease in adherence to HCM than distilled water-washed cells. A component in the PBS wash fraction adhered to the HCM and a main protein was detected as a c. 40-kDa band using SDS-PAGE. Using homology comparisons of the N-terminal amino acid sequences compared with sequence databases, this protein was identified as glyceraldehyde-3-phosphate dehydrogenase (GAPDH). The DNA sequence of LA 318 GAPDH was 100% identical to the GAPDH (gapB) of L. plantarum WCFS1. The purified GAPDH adhered to HCM. CONCLUSIONS: We found the adhesin of L. plantarum LA 318 to HCM in its culture PBS wash fraction. The molecule was identified as GAPDH. Because LA 318 possesses the same adhesin as many pathogens, the lactobacilli GAPDH may compete with pathogens infecting the intestine. SIGNIFICANCE AND IMPACT OF THE STUDY: This is the first report showing GAPDH expressed on the cell surface of lactobacilli adheres to mucin suggesting L. plantarum LA 318 adheres to HCM using GAPDH binding activity to colonize the human intestinal mucosa.","corpus_id":22346488,"score":2},{"doc_id":"18790050","title":"Cell surface glyceraldehyde-3-phosphate dehydrogenase (GAPDH) of Lactobacillus plantarum LA 318 recognizes human A and B blood group antigens.","abstract":"Lactobacillus plantarum LA 318 is a potential probiotic strain isolated from normal human intestinal tissue that shows high adhesion to human colonic mucin mediated by the bacterial cell surface glyceraldehyde-3-phosphate dehydrogenase (GAPDH). We report the adhesion mechanism of the lactobacilli is in part due to GAPDH binding to human ABO-type blood group antigens expressed on human colonic mucin (HCM). After periodate oxidation of HCM, adhesion of L. plantarum LA 318 bacterial cells significantly decreased compared to normal HCM. A BIACORE binding assay of GAPDH to blood group antigens was then performed. High binding was observed to A and B group antigens, while binding to H group antigen was lower (P<0.01). No interaction was observed between GAPDH and various monosaccharides. Furthermore, GAPDH binding to the B-trisaccharide biotinyl polymer (BP)-probe [Galalpha1-3 (Fucalpha1-2) Gal-] was significantly higher as compared to B-disaccharide, Lewis D-trisaccharide, 3-fucosyl-N-acetylglucosamine and alpha-N-acetylneuraminic acid BP-probes. The data suggests the trisaccharide structure is important in binding to the blood group antigens. The binding of GAPDH to HCM significantly decreased after incubation with NAD+. This suggests that the NAD binding domain on GAPDH may be related to binding to HCM.","corpus_id":21794166,"score":2},{"doc_id":"19220903","title":"Surface displaced alfa-enolase of Lactobacillus plantarum is a fibronectin binding protein.","abstract":"BACKGROUND: Lactic acid bacteria of the genus Lactobacillus and Bifidobacterium are one of the most important health promoting groups of the human intestinal microbiota. Their protective role within the gut consists in out competing invading pathogens for ecological niches and metabolic substrates. Among the features necessary to provide health benefits, commensal microorganisms must have the ability to adhere to human intestinal cells and consequently to colonize the gut. Studies on mechanisms mediating adhesion of lactobacilli to human intestinal cells showed that factors involved in the interaction vary mostly among different species and strains, mainly regarding interaction between bacterial adhesins and extracellular matrix or mucus proteins. We have investigated the adhesive properties of Lactobacillus plantarum, a member of the human microbiota of healthy individuals. RESULTS: We show the identification of a Lactobacillus plantarum LM3 cell surface protein (48 kDa), which specifically binds to human fibronectin (Fn), an extracellular matrix protein. By means of mass spectrometric analysis this protein was identified as the product of the L. plantarum enoA1 gene, coding the EnoA1 alfa-enolase. Surface localization of EnoA1 was proved by immune electron microscopy. In the mutant strain LM3-CC1, carrying the enoA1 null mutation, the 48 kDa adhesin was not anymore detectable neither by anti-enolase Western blot nor by Fn-overlay immunoblotting assay. Moreover, by an adhesion assay we show that LM3-CC1 cells bind to fibronectin-coated surfaces less efficiently than wild type cells, thus demonstrating the significance of the surface displaced EnoA1 protein for the L. plantarum LM3 adhesion to fibronectin. CONCLUSION: Adhesion to host tissues represents a crucial early step in the colonization process of either pathogens or commensal bacteria. We demonstrated the involvement of the L. plantarum Eno A1 alfa-enolase in Fn-binding, by studying LM3 and LM3-CC1 surface proteins. Isolation of LM3-CC1 strain was possible for the presence of expressed enoA2 gene in the L. plantarum genome, giving the possibility, for the first time to our knowledge, to quantitatively compare adhesion of wild type and mutant strain, and to assess doubtless the role of L. plantarum Eno A1 as a fibronectin binding protein.","corpus_id":-1,"score":2},{"doc_id":"19672048","title":"Identification of novel proteins secreted by Lactobacillus plantarum that bind to mucin and fibronectin.","abstract":"Lactobacillus plantarum is a lactic acid bacterium that can be isolated from a high variety of fermented foods, including dairy products. In the present work, eight novel proteins secreted by three L. plantarum strains have been identified by tandem mass spectrometry. Seven of them were predicted as extracellular proteins containing putative signal peptides. The sixth, identified as glyceraldehyde 3-phosphate dehydrogenase (GAPDH), is a cytoplasmic protein that has been detected on the surface of several microorganisms. Muramidase and GAPDH were secreted only by the L. plantarum BMCM12 strain. Two other bands present in this strain were not identified, in spite of their yielding good tryptic profiles, suggesting an absence of homolog sequences in the molecular databases. Four of these proteins, including GAPDH, bound to mucin and fibronectin. These proteins might play important roles in the physiology and ecology of this bacterium, notably in the interaction with the human host.","corpus_id":45227396,"score":2},{"doc_id":"19737900","title":"Identification of the binding domain of Streptococcus oralis glyceraldehyde-3-phosphate dehydrogenase for Porphyromonas gingivalis major fimbriae.","abstract":"Porphyromonas gingivalis forms communities with antecedent oral biofilm constituent streptococci. P. gingivalis major fimbriae bind to glyceraldehyde-3-phosphate dehydrogenase (GAPDH) present on the streptococcal surface, and this interaction plays an important role in P. gingivalis colonization. This study identified the binding domain of Streptococcus oralis GAPDH for P. gingivalis fimbriae. S. oralis recombinant GAPDH (rGAPDH) was digested with lysyl endopeptidase. Cleaved fragments of rGAPDH were applied to a reverse-phase high-pressure liquid chromatograph equipped with a C18 column. Each peak was collected; the binding activity toward P. gingivalis recombinant fimbrillin (rFimA) was analyzed with a biomolecular interaction analysis system. The fragment displaying the strongest binding activity was further digested with various proteinases, after which the binding activity of each fragment was measured. The amino acid sequence of each fragment was determined by direct sequencing, mass spectrometric analysis, and amino acid analysis. Amino acid residues 166 to 183 of S. oralis GAPDH exhibited the strongest binding activity toward rFimA; confocal laser scanning microscopy revealed that the synthetic peptide corresponding to amino acid residues 166 to 183 of S. oralis GAPDH (pep166-183, DNFGVVEGLMTTIHAYTG) inhibits S. oralis-P. gingivalis biofilm formation in a dose-dependent manner. Moreover, pep166-183 inhibited interbacterial biofilm formation by several oral streptococci and P. gingivalis strains with different types of FimA. These results indicate that the binding domain of S. oralis GAPDH for P. gingivalis fimbriae exists within the region encompassing amino acid residues 166 to 183 of GAPDH and that pep166-183 may be a potent inhibitor of P. gingivalis colonization in the oral cavity.","corpus_id":30954518,"score":2},{"doc_id":"20054117","title":"Structure of glyceraldehyde-3-phosphate dehydrogenase from the archaeal hyperthermophile Methanocaldococcus jannaschii.","abstract":"The X-ray crystal structure of glyceraldehyde-3-phosphate dehydrogenase (GAPDH) from the hyperthermophilic archaeon Methanocaldococcus jannaschii (Mj-GAPDH) was determined to 1.81 A resolution. The crystal belonged to space group C222(1), with unit-cell parameters a = 83.4, b = 152.0, c = 118.6 A. The structure was solved by molecular replacement and was refined to a final R factor of 17.1% (R(free) = 19.8%). The final structure included the cofactor NADP(+) at the nucleotide-binding site and featured unoccupied inorganic and substrate phosphate-binding sites. A comparison with GAPDH structures from mesophilic sources suggested that Mj-GAPDH is stabilized by extensive electrostatic interactions between the C-terminal alpha-helices and various distal loop regions, which are likely to contribute to thermal stability. The key phosphate-binding residues in the active site of Mj-GAPDH are conserved in other archaeal GAPDH proteins. These residues undergo a conformational shift in response to occupancy of the inorganic phosphate site.","corpus_id":40110104,"score":2},{"doc_id":"20562289","title":"Functional roles of aggregation-promoting-like factor in stress tolerance and adherence of Lactobacillus acidophilus NCFM.","abstract":"Aggregation-promoting factors (Apf) are secreted proteins that have been associated with a diverse number of functional roles in lactobacilli, including self-aggregation, the bridging of conjugal pairs, coaggregation with other commensal or pathogenic bacteria, and maintenance of cell shape. In silico genome analysis of Lactobacillus acidophilus NCFM identified LBA0493 as a 696-bp apf gene that encodes a putative 21-kDa Apf protein. Transcriptional studies of NCFM during growth in milk showed apf to be one of the most highly upregulated genes in the genome. In the present study, reverse transcriptase-quantitative PCR (RT-QPCR) analysis revealed that the apf gene was highly induced during the stationary phase compared to that during the logarithmic phase. To investigate the functional role of Apf in NCFM, an Delta apf deletion mutant was constructed. The resulting Delta apf mutant, NCK2033, did not show a significant difference in cell morphology or growth compared to that of the NCFMDelta upp reference strain, NCK1909. The autoaggregation phenotype of NCK2033 in planktonic culture was unaffected. Additional phenotypic assays revealed that NCK2033 was more susceptible to treatments with oxgall bile and sodium dodecyl sulfate (SDS). Survival rates of NCK2033 decreased when stationary-phase cells were exposed to simulated small-intestinal and gastric juices. Furthermore, NCK2033 in the stationary phase showed a reduction of in vitro adherence to Caco-2 intestinal epithelial cells, mucin glycoproteins, and fibronectin. The data suggest that the Apf-like proteins may contribute to the survival of L. acidophilus during transit through the digestive tract and, potentially, participate in the interactions with the host intestinal mucosa.","corpus_id":206716041,"score":2},{"doc_id":"21138769","title":"Expression, purification and kinetic characterization of His-tagged glyceraldehyde-3-phosphate dehydrogenase from Trypanosoma cruzi.","abstract":"Trypanosomes are flagellated protozoa responsible for serious parasitic diseases that have been classified by the World Health Organization as tropical sicknesses of major importance. One important drug target receiving considerable attention is the enzyme glyceraldehyde-3-phosphate dehydrogenase from the protozoan parasite Trypanosoma cruzi, the causative agent of Chagas disease (T. cruzi Glyceraldehyde-3-phosphate dehydrogenase (TcGAPDH); EC 1.2.1.12). TcGAPDH is a key enzyme in the glycolytic pathway of T. cruzi and catalyzes the oxidative phosphorylation of D-glyceraldehyde-3-phosphate (G3P) to 1,3-bisphosphoglycerate (1,3-BPG) coupled to the reduction of oxidized nicotinamide adenine dinucleotide, (NAD(+)) to NADH, the reduced form. Herein, we describe the cloning of the T. cruzi gene for TcGAPDH into the pET-28a(+) vector, its expression as a tagged protein in Escherichia coli, purification and kinetic characterization. The His(6)-tagged TcGAPDH was purified by affinity chromatography. Enzyme activity assays for the recombinant His(6)-TcGAPDH were carried out spectrophotometrically to determine the kinetic parameters. The apparent Michaelis-Menten constant (K(M)(app)) determined for D-glyceraldehyde-3-phosphate and NAD(+) were 352±21 and 272±25 μM, respectively, which were consistent with the values for the untagged enzyme reported in the literature. We have demonstrated by the use of Isothermal Titration Calorimetry (ITC) that this vector modification resulted in activity preserved for a higher period. We also report here the use of response surface methodology (RSM) to determine the region of optimal conditions for enzyme activity. A quadratic model was developed by RSM to describe the enzyme activity in terms of pH and temperature as independent variables. According to the RMS contour plots and variance analysis, the maximum enzyme activity was at 29.1°C and pH 8.6. Above 37°C, the enzyme activity starts to fall, which may be related to previous reports that the quaternary structure begins a process of disassembly.","corpus_id":23550288,"score":2},{"doc_id":"21205411","title":"Cloning, expression and characterization of NAD+-dependent glyceraldehyde-3-phosphate dehydrogenase of adult Haemonchus contortus.","abstract":"Glyceraldehyde-3-phosphate dehydrogenase (GAPDH) regulates a wide range of biological processes, including pathogen evasion. In the present research, the GAPDH gene of Haemonchus contortus (HcGAPDH) was cloned and characterized. Specific primers for the rapid amplification of cDNA ends (RACE) were designed based on the expressed sequence tag (EST, AW670737) to amplify the 3' and 5' ends of HcGAPDH. The full length of cDNA from this gene was obtained by overlapping the sequences of 3' and 5' extremities and amplification by reverse transcription polymerase chain reaction (RT-PCR). The biochemical activities of the recombinant protein HcGAPDH, which was expressed in prokaryotic cells and purified by affinity chromatography, were analysed by assays of enzymatic activity, thermal stability and pH. The results showed that the cloned full-length cDNA comprised 1303 bp and encoded a peptide with 341 amino acid residues which showed sequence similarity to several known GAPDHs. The biochemical assay showed that the protein encoded by the HcGAPDH exhibited enzymatic activity with NAD+ as a cofactor. HcGAPDH was stable between pH 5 and 9 and maintained activity at high temperatures of up to 75°C. The natural GAPDH of Haemonchus contortus detected by immunoblot assay was approximately 38 kDa in size, and the recombinant HcGAPDH was recognized strongly by serum from naturally infected goats.","corpus_id":206231862,"score":2},{"doc_id":"21546586","title":"Role of Mycoplasma pneumoniae glyceraldehyde-3-phosphate dehydrogenase (GAPDH) in mediating interactions with the human extracellular matrix.","abstract":"In different, phylogenetically unrelated micro-organisms, glycolytic enzymes play a dual role. In the cytosol they are involved in metabolic reactions whereas the surface-localized fraction of the enzymes contributes to adhesion and virulence. Glyceraldehyde-3-phosphate dehydrogenase (GAPDH) is a typical member of this group of multifunctional proteins. In this study, we characterized the GAPDH of Mycoplasma pneumoniae, a common pathogen of the human respiratory mucosa. Full-length GAPDH of M. pneumoniae was successfully expressed and used to produce a polyclonal antiserum. By immunofluorescence, colony blot and ELISA experiments with different fractions of the M. pneumoniae proteins, GAPDH was demonstrated to be present in the cytosol and at even higher concentrations at the surface of mycoplasmas. Nevertheless, antibodies against recombinant GAPDH were not detected in sera of immunized animals or of patients with confirmed M. pneumoniae infection. Recombinant GAPDH bound to different human cell lines in a concentration-dependent manner, and binding was inhibited by specific anti-GAPDH serum. In contrast, this antiserum did not significantly influence the adherence of M. pneumoniae to HeLa cells. When different human extracellular matrix proteins were tested in Western blot assays, GAPDH bound to fibrinogen. The results showed that the GAPDH of M. pneumoniae is a member of the family of cytosol-localized glycolytic enzymes, which also occur at the surface of the bacterium, and mediates interactions with the extracellular matrix proteins of the human host. Thus, the surface-exposed fraction of GAPDH may be a factor that contributes to the successful colonization of the human respiratory tract by M. pneumoniae.","corpus_id":31168591,"score":2},{"doc_id":"21622872","title":"Protein-carbohydrate interactions between Lactobacillus salivarius and pig mucins.","abstract":"Adherence to the gastrointestinal tract is a key element desirable for many of the proposed beneficial health effects of probiotic bacteria. The aims of this study were to determine the amounts of adhesion of 3 Lactobacillus salivarius strains (Lb6, Lb9, and Lb10) to porcine small intestinal mucins and to determine whether adhesion is a function of lectin-like activities. Dot and Western blot assays were performed to investigate bacterial adhesion. Several carbohydrates and glycoproteins were evaluated to determine whether they interfered with adhesion of the Lactobacillus strains to intestinal mucins and to determine whether they had lectin-like activities. The Lb9 and Lb10 strains had greater association with piglet mucins than did those from 22- to 24-wk-old finishing pigs (P = 0.021 and 0.037, respectively), whereas the Lb6 strain adhered to both (P = 0.138). Western blot assays showed that bacterial adhesion detected piglet mucosa from the duodenum, jejunum, and ileum. In finishing pigs, the adhesion was variable throughout the gastrointestinal tract. Galactose and mannose diminished the interaction of the Lb9 and Lb10 strains in intestinal mucosa (P = 0.028 and 0.026, respectively), whereas pig gastric mucin reduced the adhesion of the Lb6 strain (P = 0.013). Adhesion of the Lb9 and Lb10 strains to intestinal mucosa was less after protease treatment (P = 0.023 and 0.018, respectively), which indicates that proteins are needed for the Lb9 and Lb10 strains to recognize mucin. The Lb6 strain also demonstrated diminished adhesion after periodate treatment (P = 0.038). From these results, we suggest that the nature of the bacterial lectin-like substance is a surface protein that loosely binds to the bacterial cell surface. All the tested strains adhered to specific targets in the small intestinal mucosa of piglets, and the bacteria had lectin-like proteins involved in this adhesion.","corpus_id":30876729,"score":2},{"doc_id":"21895736","title":"GAPDH: a common enzyme with uncommon functions.","abstract":"Glyceraldehyde-3-phosphate dehydrogenase (GAPDH) has long been recognized as an important enzyme for energy metabolism and the production of ATP and pyruvate through anaerobic glycolysis in the cytoplasm. Recent studies have shown that GAPDH has multiple functions independent of its role in energy metabolism. Although increased GAPDH gene expression and enzymatic function is associated with cell proliferation and tumourigenesis, conditions such as oxidative stress impair GAPDH catalytic activity and lead to cellular aging and apoptosis. The mechanism(s) underlying the effects of GAPDH on cellular proliferation remains unclear, yet much evidence has been accrued that demonstrates a variety of interacting partners for GAPDH, including proteins, various RNA species and telomeric DNA. The present mini review summarizes recent findings relating to the extraglycolytic functions of GAPDH and highlights the significant role this enzyme plays in regulating both cell survival and apoptotic death.","corpus_id":23499684,"score":2},{"doc_id":"22224921","title":"Characterization of the adherence properties of human Lactobacilli strains to be used as vaginal probiotics.","abstract":"In the present work, the adhesion of 43 human lactobacilli isolates to mucin has been studied. The most adherent strains were selected, and their capacities to adhere to three epithelial cell lines were studied. All intestinal strains and one vaginal isolate adhered to HT-29 cells. The latter was the most adherent to Caco-2 cells, although two of the intestinal isolates were also highly adherent. Moreover, five of the eight strains strongly adhered to HeLa cells. The binding of an Actinomyces neuii clinical isolate to HeLa cells was enhanced by two of the lactobacilli and by their secreted proteins, while those of another two strains almost abolished it. None of the strains were able to interfere with the adhesion of Candida albicans to HeLa cells. The components of the extracellular proteome of all strains were identified by MALDI-TOF/MS. Among them, a collagen-binding A precursor and aggregation-promoting factor-like proteins are suggested to participate on adhesion to Caco-2 and HeLa cells, respectively. In this way, several proteins with LysM domains might explain the ability of some bacterial supernatants to block A. neuii adhesion to HeLa cell cultures. Finally, glyceraldehyde 3-phosphate dehydrogenase (GAPDH) could explain the good adhesion of some strains to mucin.","corpus_id":17812155,"score":2},{"doc_id":"22292499","title":"The multifunctional glycolytic protein glyceraldehyde-3-phosphate dehydrogenase (GAPDH) is a novel macrophage lactoferrin receptor.","abstract":"Several proteins with limited cell type distribution have been shown to bind lactoferrin. However, except in the case of hepatic and intestinal cells, these have not been definitively identified and characterized. Here we report that the multifunctional glycolytic protein glyceraldehyde-3-phosphate dehydrogenase (GAPDH) functions as a novel receptor for lactoferrin (Lf) in macrophages. GAPDH is a well-known moonlighting protein, and previous work from our laboratory has indicated its localization on macrophage cell surfaces, wherein it functions as a transferrin (Tf) receptor. The K(D) value for GAPDH-lactoferrin interaction was determined to be 43.8 nmol/L. Utilizing co-immunoprecipitation, immunoflorescence, and immunogold labelling electron microscopy we could demonstrate the trafficking of lactoferrin to the endosomal compartment along with GAPDH. We also found that upon iron depletion the binding of lactoferrin to macrophage cell surface is enhanced. This correlated with an increased expression of surface GAPDH, while other known lactoferrin receptors CD14 and lipoprotein receptor-related protein (LRP) were found to remain unaltered in expression levels. This suggests that upon iron depletion, cells prefer to use GAPDH to acquire lactoferrin. As GAPDH is an ubiquitously expressed molecule, its function as a receptor for lactoferrin may not be limited to macrophages.","corpus_id":41523959,"score":2},{"doc_id":"22389474","title":"Glutamine synthetase and glucose-6-phosphate isomerase are adhesive moonlighting proteins of Lactobacillus crispatus released by epithelial cathelicidin LL-37.","abstract":"Glutamine synthetase (GS) and glucose-6-phosphate isomerase (GPI) were identified as novel adhesive moonlighting proteins of Lactobacillus crispatus ST1. Both proteins were bound onto the bacterial surface at acidic pHs, whereas a suspension of the cells to pH 8 caused their release into the buffer, a pattern previously observed with surface-bound enolase and glyceraldehyde-3-phosphate dehydrogenase (GAPDH) of L. crispatus. The pH shift was associated with a rapid and transient increase in cell wall permeability, as measured by cell staining with propidium iodide. A gradual increase in the release of the four moonlighting proteins was also observed after the treatment of L. crispatus ST1 cells with increasing concentrations of the antimicrobial cationic peptide LL-37, which kills bacteria by disturbing membrane integrity and was here observed to increase the cell wall permeability of L. crispatus ST1. At pH 4, the fusion proteins His(6)-GS, His(6)-GPI, His(6)-enolase, and His(6)-GAPDH showed localized binding to cell division septa and poles of L. crispatus ST1 cells, whereas no binding to Lactobacillus rhamnosus GG was detected. Strain ST1 showed a pH-dependent adherence to the basement membrane preparation Matrigel. Purified His(6)-GS and His(6)-GPI proteins bound to type I collagen, and His(6)-GS also bound to laminin, and their level of binding was higher at pH 5.5 than at pH 6.5. His(6)-GS also expressed a plasminogen receptor function. The results show the strain-dependent surface association of moonlighting proteins in lactobacilli and that these proteins are released from the L. crispatus surface after cell trauma, under conditions of alkaline stress, or in the presence of the antimicrobial peptide LL-37 produced by human cells.","corpus_id":26905372,"score":2},{"doc_id":"22869137","title":"Preliminary crystallographic analysis of glyceraldehyde-3-phosphate dehydrogenase 3 from Saccharomyces cerevisiae.","abstract":"Glyceraldehyde-3-phosphate dehydrogenase (GAPDH) is an important enzyme in the glycolytic pathway. In addition to its conventional metabolic role, GAPDH has been identified to possess diverse cellular functions. In this study, glyceraldehyde-3-phosphate dehydrogenase 3, the third isoform of GAPDH from Saccharomyces cerevisiae, was cloned, expressed, purified and crystallized. The crystals belonged to space group I4(1)22, with unit-cell parameters a = b = 116.13, c = 119.21 Å. X-ray diffraction data were collected to a resolution of 2.6 Å. The structure was solved by molecular replacement and refinement is in progress.","corpus_id":12460695,"score":2},{"doc_id":"23264054","title":"Identification and characterization of Porphyromonas gingivalis client proteins that bind to Streptococcus oralis glyceraldehyde-3-phosphate dehydrogenase.","abstract":"Coaggregation of Porphyromonas gingivalis and oral streptococci is thought to play an important role in P. gingivalis colonization. Previously, we reported that P. gingivalis major fimbriae interacted with Streptococcus oralis glyceraldehyde-3-phosphate dehydrogenase (GAPDH), and that amino acid residues 166 to 183 of GAPDH exhibited strong binding activity toward P. gingivalis fimbriae (H. Nagata, M. Iwasaki, K. Maeda, M. Kuboniwa, E. Hashino, M. Toe, N. Minamino, H. Kuwahara, and S. Shizukuishi, Infect. Immun. 77:5130-5138, 2009). The present study aimed to identify and characterize P. gingivalis components other than fimbriae that interact with S. oralis GAPDH. A pulldown assay was performed to detect potential interactions between P. gingivalis client proteins and S. oralis recombinant GAPDH with amino acid residues 166 to 183 deleted by site-directed mutagenesis. Seven proteins, namely, tonB-dependent receptor protein (RagA4), arginine-specific proteinase B, 4-hydroxybutyryl-coenzyme A dehydratase (AbfD), lysine-specific proteinase, GAPDH, NAD-dependent glutamate dehydrogenase (GDH), and malate dehydrogenase (MDH), were identified by two-dimensional gel electrophoresis followed by proteomic analysis using tandem mass spectrometry. Interactions between these client proteins and S. oralis GAPDH were analyzed with a biomolecular interaction analysis system. S. oralis GAPDH showed high affinity for five of the seven client proteins (RagA4, AbfD, GAPDH, GDH, and MDH). Interactions between P. gingivalis and S. oralis were measured by a turbidimetric method and fluorescence microscopy. RagA4, AbfD, and GDH enhanced coaggregation, whereas GAPDH and MDH inhibited coaggregation. Furthermore, the expression of luxS in P. gingivalis was upregulated by RagA4, AbfD, and GDH but was downregulated by MDH. These results indicate that the five P. gingivalis client proteins function as regulators in P. gingivalis biofilm formation with oral streptococci.","corpus_id":-1,"score":2},{"doc_id":"23872606","title":"The Roles of Moonlighting Proteins in Bacteria.","abstract":"Moonlighting proteins, characterized by their multiple autonomous functions, have been detected in bacteria. Surprisingly, many of these proteins are conserved and involved in metabolic pathway or the cell stress response. They localise to the bacterial surface to take on additional activities, which have been hypothesised to contribute to bacterial virulence or bacterial benefit. In this review, we compare the functions of moonlighting proteins in bacteria, describe the structural basis of moonlighting functions, and summarise the regulation of secretion and localisation of moonlighting proteins.","corpus_id":10530383,"score":2},{"doc_id":"24566472","title":"Biochemical characterisation of glyceraldehyde 3-phosphate dehydrogenase (GAPDH) from the liver fluke, Fasciola hepatica.","abstract":"Glyceraldehyde 3-phosphate dehydrogenase (GAPDH) catalyses one of the two steps in glycolysis which generate the reduced coenzyme NADH. This reaction precedes the two ATP generating steps. Thus, inhibition of GAPDH will lead to substantially reduced energy generation. Consequently, there has been considerable interest in developing GAPDH inhibitors as anti-cancer and anti-parasitic agents. Here, we describe the biochemical characterisation of GAPDH from the common liver fluke Fasciola hepatica (FhGAPDH). The primary sequence of FhGAPDH is similar to that from other trematodes and the predicted structure shows high similarity to those from other animals including the mammalian hosts. FhGAPDH lacks a binding pocket which has been exploited in the design of novel antitrypanosomal compounds. The protein can be expressed in, and purified from Escherichia coli; the recombinant protein was active and showed no cooperativity towards glyceraldehyde 3-phosphate as a substrate. In the absence of ligands, FhGAPDH was a mixture of homodimers and tetramers, as judged by protein-protein crosslinking and analytical gel filtration. The addition of either NAD⁺ or glyceraldehyde 3-phosphate shifted this equilibrium towards a compact dimer. Thermal scanning fluorimetry demonstrated that this form was considerably more stable than the unliganded one. These responses to ligand binding differ from those seen in mammalian enzymes. These differences could be exploited in the discovery of reagents which selectively disrupt the function of FhGAPDH.","corpus_id":11247617,"score":2},{"doc_id":"25005093","title":"Cloning, expression, purification, crystallization and preliminary X-ray diffraction analysis of glyceraldehyde-3-phosphate dehydrogenase from Streptococcus agalactiae NEM316.","abstract":"Glyceraldehyde-3-phosphate dehydrogenase (GAPDH) is an essential enzyme involved in glycolysis. Despite lacking the secretory signal sequence, this cytosolic enzyme has been found localized at the surface of several bacteria and fungi. As a surface protein, GAPDH exhibits various adhesive functions, thereby facilitating colonization and invasion of host tissues. Streptococcus agalactiae, also known as group B streptococcus (GBS), binds onto the host using its surface adhesins and causes sepsis and pneumonia in neonates. GAPDH is one of the surface adhesins of GBS binding to human plasminogen and is a virulent factor associated with host colonization. Although the surface-associated GAPDH has been shown to bind to a variety of host extracellular matrix (ECM) molecules in various bacteria, the molecular mechanism underlying their interaction is not fully understood. To investigate this, structural studies on GAPDH of S. agalactiae were initiated. The gapC gene of S. agalactiae NEM316 encoding GAPDH protein was cloned into pET-28a vector, overexpressed in Escherichia coli BL21(DE3) cells and purified to homogeneity. The purified protein was crystallized using the hanging-drop vapour-diffusion method. The GAPDH crystals obtained in two different crystallization conditions diffracted to 2.8 and 2.6 Å resolution, belonging to two different space groups P2₁ and P2₁2₁2₁, respectively. The structure was solved by molecular replacement and structure refinement is now in progress.","corpus_id":8146533,"score":2},{"doc_id":"25183032","title":"A homolog of glyceraldehyde-3-phosphate dehydrogenase from Riemerella anatipestifer is an extracellular protein and exhibits biological activity.","abstract":"Riemerella anatipestifer is the causative agent of septicemia anserum exsudativa in ducks. Its pathogenesis and virulence factors are still unclear. The glycolytic enzyme, glyceraldehyde-3-phosphate dehydrogenase (GAPDH), an anchorless and multifunctional protein on the surface of several pathogenic microorganisms, is involved in virulence and adhesion. Whether homologs of GAPDH exist, and display similar characteristics in R. anatipestifer (RaGAPDH) has not been determined. In our research, the RaGAPDH activity from various R. anatipestifer isolates was confirmed. Twenty-two gapdh genes from genomic DNA of R. anatipestifer isolates were cloned and sequenced for phylogenetic analysis. The distribution of RaGAPDH in R. anatipestifer CZ2 strain was confirmed by antisera to recombinant RaGAPDH. The ability of purified RaGAPDH to bind host proteins was analyzed by solid-phase ligand-binding assay. Results revealed that all R. anatipestifer isolates showed different levels of GAPDH activity except four strains, which contained a gapdh-like gene. The gapdh of R. anatipestifer, which is located phylogenetically in the same branch as enterohemorrhagic Escherichia coli (EHEC), belonged to class I GAPDH, and encoded a 36.7-kDa protein. All RaGAPDH-encoding gene sequences from field isolates of R. anatipestifer displayed 100% homology. The RaGAPDH localized on the extracellular membrane of several R. anatipestifer strains. Further, it was released into the culture medium, and exhibited GAPDH enzyme activity. We also confirmed the binding of RaGAPDH to plasminogen and fibrinogen. These results demonstrated that GAPDH was present in R. anatipestifer, although not in all strains, and that RaGAPDH might contribute to the microorganism's virulence.","corpus_id":6888725,"score":2},{"doc_id":"25614994","title":"\"Moonlighting\" GAPDH Protein Localizes with AMPA Receptor GluA2 and L1 Axonal Cell Adhesion Molecule at Fiber Cell Borders in the Lens.","abstract":"PURPOSE: The canonical role of glyceraldehyde phosphate dehydrogenase (GAPDH) is as an enzyme in glycolysis. GAPDH is also a principal \"moonlighting\" protein with additional roles at diverse sites in a variety of cells. Surface GAPDH on mammalian, yeast, and bacterial cells acts as a receptor and also mediates cell contacts. In neurons, extracellular GAPDH localizes at synapses. Two GAPDH binding partners at synapses are α-Amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid glutamate receptor (AMPA) GluA2 subunit at dendritic spines and L1 cell adhesion molecule at pre-synaptic membranes, and both proteins are also expressed in lenses. Fiber cell membrane protrusions and dendritic spines have similar size, shape, and spacing, contain F-actin, and express clathrin/AP-2 Adaptor at their surfaces linked with Tyr-phosphatase STEP-regulated endocytosis of AMPA/GluA2 receptors. AMPA receptors work with NMDA (N-methyl-d-aspartate) and GABA (γ-aminobutyric acid) receptors, calcium calmodulin kinase II (CaMKIIα), channel proteins, STEP, and ephrin receptors, which are also expressed in lenses. In neurons, coordinate AMPA/GluA2 receptor endocytosis with GAPDH is linked with disease. GAPDH was previously characterized as a fiber cell membrane protein and shown to decrease substantially in interior fiber cells in human age-related cataract. Here, we examined GAPDH spatial expression in healthy lenses in two vertebrate species. METHODS: In situ methods were used to examine GAPDH expression in lenses of healthy young adult rabbits and chickens. Immunoblots were used to detect L1 in lenses. RESULTS: The present study demonstrated that GAPDH is present at fiber cell borders in adult rabbit and chicken lenses with evidence of focal concentrations along the fiber cell perimeter, and overlapped with detection of p-Tyr-GluA2, L1, STEP, actin and clathrin. We observed that L1-140 kDa was the prominent form in lens. CONCLUSIONS: Our findings indicate investigations into GAPDH \"moonlighting\" activities similar to its role in cell-cell interactions at neuron surfaces are warranted in the lens.","corpus_id":207451998,"score":2},{"doc_id":"25870284","title":"Glycolytic flux controls D-serine synthesis through glyceraldehyde-3-phosphate dehydrogenase in astrocytes.","abstract":"D-Serine is an essential coagonist with glutamate for stimulation of N-methyl-D-aspartate (NMDA) glutamate receptors. Although astrocytic metabolic processes are known to regulate synaptic glutamate levels, mechanisms that control D-serine levels are not well defined. Here we show that d-serine production in astrocytes is modulated by the interaction between the D-serine synthetic enzyme serine racemase (SRR) and a glycolytic enzyme, glyceraldehyde 3-phosphate dehydrogenase (GAPDH). In primary cultured astrocytes, glycolysis activity was negatively correlated with D-serine level. We show that SRR interacts directly with GAPDH, and that activation of glycolysis augments this interaction. Biochemical assays using mutant forms of GAPDH with either reduced activity or reduced affinity to SRR revealed that GAPDH suppresses SRR activity by direct binding to GAPDH and through NADH, a product of GAPDH. NADH allosterically inhibits the activity of SRR by promoting the disassociation of ATP from SRR. Thus, astrocytic production of D-serine is modulated by glycolytic activity via interactions between GAPDH and SRR. We found that SRR is expressed in astrocytes in the subiculum of the human hippocampus, where neurons are known to be particularly vulnerable to loss of energy. Collectively, our findings suggest that astrocytic energy metabolism controls D-serine production, thereby influencing glutamatergic neurotransmission in the hippocampus.","corpus_id":24884128,"score":2},{"doc_id":"26781495","title":"Identification of Surface Proteins from Lactobacillus casei BL23 Able to Bind Fibronectin and Collagen.","abstract":"Strains of lactobacilli show the capacity to attach to extracellular matrix proteins. Cell-wall fractions of Lactobacillus casei BL23 enriched in fibronectin, and collagen-binding proteins were isolated. Mass spectrometry analysis of their protein content revealed the presence of stress-related proteins (GroEL, ClpL), translational elongation factors (EF-Tu, EF-G), oligopeptide solute-binding proteins, and the glycolytic enzymes enolase and glyceraldehyde-3-phosphate dehydrogenase (GAPDH). The latter two enzymes were expressed in Escherichia coli and purified as glutathione-S-transferase (GST) fusion proteins, and their in vitro binding activity to fibronectin and collagen was confirmed. These results reinforce the idea that lactobacilli display on their surfaces a variety of moonlighting proteins that can be important in their adaptation to survive at intestinal mucosal sites and in the interaction with host cells.","corpus_id":21781645,"score":2},{"doc_id":"26946538","title":"Lactobacillus acidophilus binds to MUC3 component of cultured intestinal epithelial cells with highest affinity.","abstract":"Lactobacillus strains have been shown to adhere to the mucosal components of intestinal epithelial cells. However, established in vitro adhesion assays have several drawbacks in assessing the adhesion of new Lactobacillus strains. The present study aimed to compare the adhesion of four different Lactobacillus strains and select the most adherent microbe, based on in silico approach supported by in vitro results. The mucus-binding proteins in Lactobacillus acidophilus, L. plantarum, L. brevis and L. fermentum were identified and their capacities to interact with intestinal mucin were compared by molecular docking analysis. Lactobacillus acidophilus had the maximal affinity of binding to mucin with predicted free energy of -6.066 kcal mol(-1) Further, in vitro experimental assay of adhesion was performed to validate the in silico results. The adhesion of L. acidophilus to mucous secreting colon epithelial HT-29 MTX cells was highest at 12%, and it formed biofilm with maximum depth (Z = 84 μm). Lactobacillus acidophilus was determined to be the most adherent strain in the study. All the Lactobacillus strains tested in this study, displayed maximum affinity of binding to MUC3 component of mucus as compared to other gastrointestinal mucins. These findings may have importance in the design of probiotics and health care management.","corpus_id":30542391,"score":2},{"doc_id":"27350617","title":"Carbohydrate-binding specificities of potential probiotic Lactobacillus strains in porcine jejunal (IPEC-J2) cells and porcine mucin.","abstract":"Bacterial lectins are carbohydrate-binding adhesins that recognize glycoreceptors in the gut mucus and epithelium of hosts. In this study, the contribution of lectin-like activities to adhesion of Lactobacillus mucosae LM1 and Lactobacillus johnsonii PF01, which were isolated from swine intestine, were compared to those of the commercial probiotic Lactobacillus rhamnosus GG. Both LM1 and PF01 strains have been reported to have good adhesion ability to crude intestinal mucus of pigs. To confirm this, we quantified their adhesion to porcine gastric mucin and intestinal porcine enterocytes isolated from the jejunum of piglets (IPEC-J2). In addition, we examined their carbohydrate-binding specificities by suspending bacterial cells in carbohydrate solutions prior to adhesion assays. We found that the selected carbohydrates affected the adherences of LM1 to IPEC-J2 cells and of LGG to mucin. In addition, compared to adhesion to IPEC-J2 cells, adhesion to mucin by both LM1 and LGG was characterized by enhanced specific recognition of glycoreceptor components such as galactose, mannose, and N-acetylglucosamine. Hydrophobic interactions might make a greater contribution to adhesion of PF01. A similar adhesin profile between a probiotic and a pathogen, suggest a correlation between shared pathogen-probiotic glycoreceptor recognition and the ability to exclude enteropathogens such as Escherichia coli K88 and Salmonella Typhimurium KCCM 40253. These findings extend our understanding of the mechanisms of the intestinal adhesion and pathogen-inhibition abilities of probiotic Lactobacillus strains.","corpus_id":14451370,"score":2},{"doc_id":"28533178","title":"Mucin- and carbohydrate-stimulated adhesion and subproteome changes of the probiotic bacterium Lactobacillus acidophilus NCFM.","abstract":"Adhesion to intestinal mucosa is a crucial property for probiotic bacteria. Adhesion is thought to increase host-bacterial interactions, thus potentially enabling health benefits to the host. Molecular events connected with adhesion and surface proteome changes were investigated for the probiotic Lactobacillus acidophilus NCFM cultured with established or emerging prebiotic carbohydrates as carbon source and in the presence of mucin, the glycoprotein of the epithelial mucus layer. Variation in adhesion to HT29-cells and mucin was associated with carbon source and mucin-induced subproteome abundancy differences. Specifically, while growth on fructooligosaccharides (FOS) only stimulated adhesion to intestinal HT-29 cells, cellobiose and polydextrose in addition increased adhesion to mucin. Adhesion to HT-29 cells increased by about 2-fold for bacteria grown on mucin-supplemented glucose. Comparative 2DE-MS surface proteome analysis showed different proteins in energy metabolism appearing on the surface, suggesting they exert moonlighting functions. Mucin-supplemented bacteria had relative abundance of pyruvate kinase and fructose-bisphosphate aldolase increased by about 2-fold while six spots with 3.2-2.1 fold reduced relative abundance comprised elongation factor G, phosphoglycerate kinase, BipAEFTU family GTP-binding protein, ribonucleoside triphosphate reductase, adenylosuccinate synthetase, 30S ribosomal protein S1, and manganese-dependent inorganic pyrophosphatase. Surface proteome of cellobiose- compared to glucose-grown L. acidophilus NCFM had phosphate starvation inducible protein stress-related, thermostable pullulanase, and elongation factor G increasing 4.4-2.4 fold, while GAPDH, elongation factor Ts, and pyruvate kinase were reduced by 2.0-1.5 fold in relative abundance. Addition of recombinant L. acidophilus NCFM elongation factor G and pyruvate kinase to a coated mucin layer significantly suppressed subsequent adhesion of the bacterium. BIOLOGICAL SIGNIFICANCE: Human diet is important for intestinal health and food components, especially non-digestible carbohydrates can beneficially modify the microbiota. In the present study, effects of emerging and established prebiotic carbohydrates on the probiotic potential of Lactobacillus acidophilus NCFM were investigated by testing adhesion to a mucin layer and intestinal cells, and comparing this with changes in abundancy of surface proteins thought to be important for host interactions. Increased adhesion was observed following culturing of the bacterium with fructooligosaccharides, cellobiose or polydextrose, as well as mucin-supplemented glucose as carbon source. Enhanced adhesion ability can prolong bacterial residence in GIT yielding positive health effects. Higher relative abundance of certain surface proteins under various conditions (i.e. grown on cellobiose or mucin-supplemented glucose) suggested involvement of these proteins in adhesion, as confirmed by competition in case of two recombinantly produced moonlighting proteins. Combination of Lactobacillus acidophilus NCFM with different carbohydrates revealed potential bacterial determinants of synbiotic interactions, including stimulation of adhesion.","corpus_id":4016941,"score":2},{"doc_id":"28861445","title":"Data regarding the growth of Lactobacillus acidophilus NCFM on different carbohydrates and recombinant production of elongation factor G and pyruvate kinase.","abstract":"The present study describes the growth of the very well-known probiotic bacterium Lactobacillus acidophilus NCFM on different carbohydrates. Furthermore, recombinant production of putative moonlighting proteins elongation factor G and pyruvate kinase from this bacterium is described. For further and detailed interpretation of the data presented here, please see the research article \"Mucin- and carbohydrate-stimulated adhesion and subproteome changes of the probiotic bacterium Lactobacillus acidophilus NCFM\" (Celebioglu et al., 2017) [1].","corpus_id":8363423,"score":2},{"doc_id":"29061520","title":"Understanding the adhesion mechanism of a mucin binding domain from Lactobacillus fermentum and its role in enteropathogen exclusion.","abstract":"Lactobacillus species possesses surface exposed Mucin Binding Protein (MucBP) which plays a role in adhesion to gastrointestinal mucin. MucBP contains one or more mucin binding domain (MBD), the functionality of which has yet not been characterized thoroughly. Here, we have characterized a 93-amino acid MBD (MBD93) of MucBP (LAF_0673) from Lactobacillus fermentum. Multiple sequence alignment of L. fermentum MBD93 exhibited ∼60% sequence homology with MBDs from other Lactobacillus species. Further, we cloned, expressed and purified MBD93 from Escherichia coli as N-terminal histidine-tagged protein (6X His-MBD93). The purified MBD93 was able to bind to mucin and showed strong affinity towards the terminally expressed mucin glycans viz. N-acetylgalactosamine (GalNAc), N-acetylglucosamine (GlcNAc), Galactose (Gal), and Sialic acid (N-acetylneuraminic acid; Neu5Ac). In silico experiments further confirmed the interaction between homology modeled MBD93 to mucin glycans through hydrogen-bonding with its surface amino acid residues Ser57, Pro58, Ile60, Tyr63 and Ala65. We also have demonstrated that MBD93 was able to inhibit the adhesion of enteric pathogens, including E. coli, Salmonella Paratyphi A, Shigella sonnei and Proteus vulgaris to mucin. Our results suggested that L. fermentum MBD93 is a functionally sufficient unit to act as an adhesin and to protect from invading enteric pathogens.","corpus_id":3992929,"score":2},{"doc_id":"29229289","title":"Expression of fibronectin-binding protein of L. acidophilus NCFM and in vitro refolding to adhesion capable native-like protein from inclusion bodies.","abstract":"The ability of Lactobacilli to adhere to host epithelial surface and intestinal tracts is important for colonization and persistence of bacteria in the host gut. Extracellular matrix components like fibronectin, mucin, collagen and other adhesion molecules serve as substratum for attachment of bacteria. However, the precise structure, function and mechanism of binding of microbial surface adhesion proteins such as Fibronectin-binding protein (FBP) with host molecules remains unclear. This is primarily due to limitations in high expression of these proteins in biologically active form. To study adhesion of its FBP (64 kDa), the fbp gene of L. acidophilus NCFM was cloned and expressed in E. coli. However, the fibronectin-binding protein expressed in soluble form could not be purified by Ni-NTA affinity chromatography possibly because of partially buried Histidine tag in the recombinant fusion protein. Therefore, the protein was expressed as inclusion bodies (IBs) at 37 °C and solubilized in urea followed by purification in denatured form by Ni-NTA affinity chromatography. The purified denatured protein was refolded in vitro to structurally stable and biologically active form. The conformational properties of the refolded protein were studied by circular dichroism, which showed prominence of α+ β structural element. The refolded FBP also showed significant binding to human intestinal tissue sections. Our optimized refolding protocol from IBs of this recombinant probiotic FBP led into high amounts of biologically active protein. Our results help in increasing understanding of structure-function relation of surface adhesion proteins and host-microbial interactions.","corpus_id":3435700,"score":2},{"doc_id":"29412508","title":"Proteomics Analysis of the Adhesion Activity of Lactobacillus acidophilus ATCC 4356 Upon Growth in an Intestine-Like pH Environment.","abstract":"Many health effects of Lactobacillus acidophilus are desirable among these the adhesion ability is vital to enhance the possibility of colonization and stabilization associated with the gut mucosal barrier. In this study, the growth characteristics and the adhesion activity of L. acidophilus in the intestine-like pH environment (pH 7.5) are identified. The number of bacteria adhering to the HT-29 cells is found with a gradual increase trend (pH 5.5-7.5). This also leads to the morphological changes of L. acidophilus after exposure to different pH environments. Furthermore, with the help of the isobaric tags for relative and absolute quantification (iTRAQ) proteomic analysis, 207 proteins are detected differentially expressed at pH of 7.5. The use of GO analysis and KEGG analysis indicates three essential pathways related to the cell envelope peptide-glycan biosynthesis, carbohydrate metabolism, and amino acid metabolism are obviously changed. Adhesion related surface protein fmtB and PrtP are upregulated in pH 7.5 group. While the moonlight proteins like pyruvate kinase, which binds specifically to the mucin layer and inhibits the adhesive activity of L. acidophilus, is found downregulated. These results could be useful to understand the adhesion mechanism of L. acidophilus adapting for the gut mucosal barrier in the intestinal environment.","corpus_id":4327304,"score":2},{"doc_id":"18388461","title":"Molecular cloning and characterization of a bile salt hydrolase from Lactobacillus acidophilus PF01.","abstract":"Phenotypic screening for bile salt hydrolase (BSH) activity was performed on Lactobacillus acidophilus PF01 isolated from piglet feces. A gene encoding BSH was identified and cloned from the genomic library of L. acidophilus PF01. The bsh gene and surrounding regions were characterized by nucleotide sequence analysis and were found to contain a single open reading frame (ORF) of 951 nucleotides encoding a 316 amino acid protein. The potential bsh promoter region was located upstream of the start codon. The protein deduced from the complete ORF had high similarity with other BSHs, and four amino acid motifs located around the active site, FGRNXD, AGLNF, VLTNXP, and GXGXGXXGXPGD, were highly conserved. The bsh gene was cloned into the pET21b expression vector and expressed in Escherichia coli BLR(DE3) by induction with 0.1mM of isopropylthiogalactopyranoside. The BSH enzyme was purified with apparent homogeneity using a Ni2+-NTA agarose column and characterized. The overexpressed recombinant BSH enzyme of L. acidophilus PF01 exhibited hydrolase activity against tauroconjugated bile salts, but not glycoconjugated bile salts. It showed the highest activity against taurocholic acid. The maximum BSH activity occurred at approximately 40oC. The enzyme maintained approximately 70% of its maximum activity even at 60 degrees , whereas its activity rapidly decreased at below 37 degrees . The optimum pH was 6, and BSH activity was rapidly inactivated below pH 5 and above pH 7.","corpus_id":22000866,"score":1},{"doc_id":"19233780","title":"Temporal gene expression and probiotic attributes of Lactobacillus acidophilus during growth in milk.","abstract":"Lactic acid bacteria have been used as starter strains in the production of fermented dairy products for centuries. Lactobacillus acidophilus is a widely recognized probiotic bacteria commonly added to yogurt and used in dietary supplements. In this study, a whole genome microarray was employed to monitor gene expression of L. acidophilus NCFM cells propagated in 11% skim milk during early, mid and late logarithmic phase, and stationary phase. Approximately 21% of 1,864 open reading frames were differentially expressed at least in one time point. Genes differentially expressed in skim milk included several members of the proteolytic enzyme system. Expression of prtP (proteinase precursor) and prtM (maturase) increased over time as well as several peptidases and transport systems. Expression of Opp1 (oligopeptide transport system 1) was highest at 4 h, whereas gene expression of Opp2 increased over time reaching its highest level at 12 h, suggesting that the 2 systems have different specificities. Expression of a 2-component regulatory system, previously shown to regulate acid tolerance and proteolytic activity, also increased during the early log and early stationary phases of growth. Expression of the genes involved in lactose utilization increased immediately (5 min) upon exposure to milk. The acidification activity, survival under storage conditions, and adhesion to mucin and Caco-2 tissue culture cells of selected mutants containing insertionally inactivated genes differentially expressed in the wild-type strain during growth in milk were examined for any potential links between probiotic properties and bacterial growth and survival in milk. Some of the most interesting genes found to be expressed in milk were correlated with signaling (autoinducer-2) and adherence to mucin and intestinal epithelial cells, in vitro.","corpus_id":39378929,"score":1},{"doc_id":"19346347","title":"Characterization of Rhamnosidases from Lactobacillus plantarum and Lactobacillus acidophilus.","abstract":"Lactobacilli are known to use plant materials as a food source. Many such materials are rich in rhamnose-containing polyphenols, and thus it can be anticipated that lactobacilli will contain rhamnosidases. Therefore, genome sequences of food-grade lactobacilli were screened for putative rhamnosidases. In the genome of Lactobacillus plantarum, two putative rhamnosidase genes (ram1(Lp) and ram2(Lp)) were identified, while in Lactobacillus acidophilus, one rhamnosidase gene was found (ramA(La)). Gene products from all three genes were produced after introduction into Escherichia coli and were then tested for their enzymatic properties. Ram1(Lp), Ram2(Lp), and RamA(La) were able to efficiently hydrolyze rutin and other rutinosides, while RamA(La) was, in addition, able to cleave naringin, a neohesperidoside. Subsequently, the potential application of Lactobacillus rhamnosidases in food processing was investigated using a single matrix, tomato pulp. Recombinant Ram1(Lp) and RamA(La) enzymes were shown to remove the rhamnose from rutinosides in this material, but efficient conversion required adjustment of the tomato pulp to pH 6. The potential of Ram1(Lp) for fermentation of plant flavonoids was further investigated by expression in the food-grade bacterium Lactococcus lactis. This system was used for fermentation of tomato pulp, with the aim of improving the bioavailability of flavonoids in processed tomato products. While import of flavonoids into L. lactis appeared to be a limiting factor, rhamnose removal was confirmed, indicating that rhamnosidase-producing bacteria may find commercial application, depending on the technological properties of the strains and enzymes.","corpus_id":25742385,"score":1},{"doc_id":"20033357","title":"Cloning, expression, purification, and characterization of a novel esterase from Lactobacillus plantarum.","abstract":"Lactobacillus plantarum is an important lactic acid bacterium, usually found as natural inhabitant of food, such as fermented vegetables and meat products. However, little information about lactic acid bacteria, especially concerning L. plantarum, as a source of useful enzymes has been reported. The aim of this study was to clone, express in Escherichia coli, purify, and characterize an esterase from L. plantarum ATCC 8014. The esterase gene (1014 bp) was amplified and cloned in pET14b expression vector to express a His(6)-tagged protein in E. coli. Recombinant L. plantarum esterase was purified by Ni-NTA resin, presenting an apparent molecular mass of about 38 kDa. It presented highest activity at pH 6.0 and 40 degrees C. Also, it presented preference for p-nitrophenyl butyrate, but hydrolyzed more efficiently p-nitrophenyl acetate. Besides, this study shows, for the first time, CD data about secondary structure of an esterase from L. plantarum.","corpus_id":33110116,"score":1},{"doc_id":"20392597","title":"Association of Lactobacillus acidophilus with mice Peyer's patches.","abstract":"OBJECTIVE: To clarify the adhesion mechanism of Lactobacillus acidophilus to Peyer's patches. METHODS: Adhesion of L. acidophilus FN001 to mice Peyer's patches was studied in vitro using a fluorescent quantization method. The nature of adhesion mediator was studied by the differing effects of physical, chemical, and enzymatic pre-treatments of the bacteria and the inhibitory effects of sugars on the adhesion. The presence of lectin-like proteins on the cell surface was determined by hemagglutination assay. The effect of L. acidophilus FN001 on the inhibition of adhesion of pathogens to Peyer's patches was also studied. RESULTS: The adhesion of L. acidophilus FN001 was strongly inhibited in the presence of D-mannose and methyl-α-D-mannoside. Pretreatment of L. acidophilus FN001 with pepsin and trypsin decreased the adhesive capacity indicating that some cell surface proteins might be involved in the adhesion. L. acidophilus FN001 showed agglutinating activity toward the rabbit red cells in a mannose specific manner, which was decreased after protease pretreatment, suggesting possible occurrence of mannose specific lectin(s) on the L. acidophilus FN001 surface. In adhesion inhibition assay, L. acidophilus NF001, when applied to Peyer's patches first or at the same time with pathogen, significantly inhibited adhesion of Escherichia coli ATCC25922 to Peyer's patches. CONCLUSION: L. acidophilus FN001 contains some mannose-specific protein(s) on its surface that mediates its adhesion to the Peyer's patches. FN001 inhibits the adhesion of E. coli, which also contains mannose specific lectin.","corpus_id":5674555,"score":1},{"doc_id":"20828617","title":"Recombinant human sperm-specific glyceraldehyde-3-phosphate dehydrogenase (GAPDHS) is expressed at high yield as an active homotetramer in baculovirus-infected insect cells.","abstract":"The sperm-specific glyceraldehyde-3-phosphate dehydrogenase (GAPDHS) isoform is a promising contraceptive target because it is specific to male germ cells, essential for sperm motility and male fertility, and well suited to pharmacological inhibition. However, GAPDHS is difficult to isolate from native sources and recombinant expression frequently results in high production of insoluble enzyme. We chose to use the Bac-to-Bac baculovirus-insect cell system to express a His-tagged form of human GAPDHS (Hu his-GAPDHS) lacking the proline-rich N-terminal sequence. This recombinant Hu his-GAPDHS was successfully produced in Spodoptera frugiperda 9 (Sf9) cells by infection with recombinant virus as a soluble, enzymatically active form in high yield, >35 mg/L culture. Biochemical characterization of the purified enzyme by mass spectrometry and size exclusion chromatography confirmed the presence of the tetrameric form. Further characterization by peptide ion matching mass spectrometry and Edman sequencing showed that unlike the mixed tetramer forms produced in bacterial expression systems, human his-GAPDHS expressed in baculovirus-infected insect cells is homotetrameric. The ability to express and purify active human GAPDHS as homotetramers in high amounts will greatly aid in drug discovery efforts targeting this enzyme for discovery of novel contraceptives and three compounds were identified as inhibitors of Hu his-GAPDHS from a pilot screen of 1120 FDA-approved compounds.","corpus_id":7697867,"score":1},{"doc_id":"21131525","title":"Lactobacillus plantarum extracellular chitin-binding protein and its role in the interaction between chitin, Caco-2 cells, and mucin.","abstract":"In the present work, we describe the adhesion capabilities of a recombinant Lactococcus lactis strain producing an extracellular protein from Lactobacillus plantarum. Our results show that this protein may offer the bacterium a mechanism to bind to N-acetylglucosamine-containing polymers, such as human mucins, present in different environments.","corpus_id":12226545,"score":1},{"doc_id":"21622166","title":"Identification of the Lactobacillus SLP domain that binds gastric mucin.","abstract":"Surface layer proteins (SLPs) of lactobacillus bacteria have some structural regions responsible for adhesion to the intestinal epithelium. To identify the SLP and the smallest domain within the protein that is responsible for the adhesion of the bacterium to the intestinal epithelium, L. plantarum strain CGMCC1258 was investigated in this study. Using bioinformatics and molecular techniques, we first identified and purified a novel protein, integral membrane protein-2 (IMP-2, 33-45 kDa) responsible for adhesion to gastric mucin. Truncated forms of IMP-2 were then constructed and expressed, and the amino acids from 515 to 575 (designated micro IMP, MIMP) was identified as the smallest domain responsible for adhesion to gastric mucin. Competing assay was performed, which further confirmed the ability of MIMP to compete with enteroinvasive E. coli and enteropathogenic E. coli to adhere to cells of a normal colon cell line, NCM460. Furthermore, MIMP could maturate dendritic cells. These findings set a foundation for further investigation on the role of MIMP in the treatment and prevention of inflammation-related diseases of the intestine.","corpus_id":22794855,"score":1},{"doc_id":"24282406","title":"Plant cytoplasmic GAPDH: redox post-translational modifications and moonlighting properties.","abstract":"Glyceraldehyde-3-phosphate dehydrogenase (GAPDH) is a ubiquitous enzyme involved in glycolysis and shown, particularly in animal cells, to play additional roles in several unrelated non-metabolic processes such as control of gene expression and apoptosis. This functional versatility is regulated, in part at least, by redox post-translational modifications that alter GAPDH catalytic activity and influence the subcellular localization of the enzyme. In spite of the well established moonlighting (multifunctional) properties of animal GAPDH, little is known about non-metabolic roles of GAPDH in plants. Plant cells contain several GAPDH isoforms with different catalytic and regulatory properties, located both in the cytoplasm and in plastids, and participating in glycolysis and the Calvin-Benson cycle. A general feature of all GAPDH proteins is the presence of an acidic catalytic cysteine in the active site that is overly sensitive to oxidative modifications, including glutathionylation and S-nitrosylation. In Arabidopsis, oxidatively modified cytoplasmic GAPDH has been successfully used as a tool to investigate the role of reduced glutathione, thioredoxins and glutaredoxins in the control of different types of redox post-translational modifications. Oxidative modifications inhibit GAPDH activity, but might enable additional functions in plant cells. Mounting evidence support the concept that plant cytoplasmic GAPDH may fulfill alternative, non-metabolic functions that are triggered by redox post-translational modifications of the protein under stress conditions. The aim of this review is to detail the molecular mechanisms underlying the redox regulation of plant cytoplasmic GAPDH in the light of its crystal structure, and to provide a brief inventory of the well known redox-dependent multi-facetted properties of animal GAPDH, together with the emerging roles of oxidatively modified GAPDH in stress signaling pathways in plants.","corpus_id":1666747,"score":1},{"doc_id":"25074810","title":"Moonlighting cell-surface GAPDH recruits apotransferrin to effect iron egress from mammalian cells.","abstract":"Iron (Fe(2+), Fe(3+)) homeostasis is a tightly regulated process, involving precise control of iron influx and egress from cells. Although the mechanisms of its import into cells by iron carrier molecules are well characterized, iron export remains poorly understood. The current paradigm envisages unique functions associated with specialized macromolecules for its cellular import (transferrin receptors) or export (ferroportin, also known as SLC40A1). Previous studies have revealed that iron-depleted cells recruit glyceraldehyde-3-phosphate dehydrogenase (GAPDH), a multitasking, 'moonlighting' protein, to their surface for internalization of the iron carrier holotransferrin. Here, we report that under the converse condition of intracellular iron excess, cells switch the isoform of GAPDH on their surface to one that now recruits iron-free apotransferrin in close association with ferroportin to facilitate the efflux of iron. Increased expression of surface GAPDH correlated with increased apotransferrin binding and enhanced iron export from cells, a capability lost in GAPDH-knockdown cells. These findings were confirmed in vivo utilizing a rodent model of iron overload. Besides identifying for the first time an apotransferrin receptor, our work uncovers the two-way switching of multifunctional molecules to manage cellular micronutrient requirements.","corpus_id":9917899,"score":1},{"doc_id":"25246025","title":"Glyceraldehyde-3-phosphate dehydrogenase (GAPDH) and Alzheimer's disease.","abstract":"Glyceraldehyde-3-phosphate dehydrogenase (GAPDH) is a ubiquitous enzyme that catalyzes the sixth step of glycolysis and thus, serves to break down glucose for energy production. Beyond the traditional aerobic metabolism of glucose, recent studies have highlighted additional roles played by GAPDH in non-metabolic processes, such as control of gene expression and redox post-translational modifications. Neuroproteomics have revealed high affinity interactions between GAPDH and Alzheimer's disease-associated proteins, including the β-amyloid, β-amyloid precursor protein and tau. This neuronal protein interaction may lead to impairment of the GAPDH glycolytic function in Alzheimer's disease and may be a forerunner of its participation in apoptosis. The present review examines the crucial implication of GAPDH in neurodegenerative processes and clarifies its role in apoptotic cell death.","corpus_id":19312008,"score":1},{"doc_id":"25721875","title":"Identification and characterization of enolase as a collagen-binding protein in Lactobacillus plantarum.","abstract":"Collagen is a target of pathogens for adhesion, colonization, and invasion of host tissue. Probiotic bacteria can mimic the same mechanism as used by the pathogens in the colonization process, expressing cell surface proteins that specifically interact with extracellular matrix component proteins. The capability to bind collagen is expressed by several Lactobacillus isolates, including some Lactobacillus plantarum strains. In this study we report the involvement of the L. plantarum EnoA1 alfa-enolase in type I collagen (CnI) binding. By adhesion assays, we show that the mutant strain LM3-CC1, carrying a null mutation in the enoA1 gene, binds to immobilized collagen less efficiently than wild type strain. CnI overlay assay and Elisa tests, performed on the purified EnoA1, show that this protein can bind collagen both under denaturing and native conditions. By using truncated recombinant enolase proteins, we also show that the region spanning from 73rd to the 140th amino acid residues is involved in CnI binding.","corpus_id":45253710,"score":1},{"doc_id":"26378175","title":"Dengue Virus NS1 Protein Modulates Cellular Energy Metabolism by Increasing Glyceraldehyde-3-Phosphate Dehydrogenase Activity.","abstract":"UNLABELLED: Dengue is one of the main public health concerns worldwide. Recent estimates indicate that over 390 million people are infected annually with the dengue virus (DENV), resulting in thousands of deaths. Among the DENV nonstructural proteins, the NS1 protein is the only one whose function during replication is still unknown. NS1 is a 46- to 55-kDa glycoprotein commonly found as both a membrane-associated homodimer and a soluble hexameric barrel-shaped lipoprotein. Despite its role in the pathogenic process, NS1 is essential for proper RNA accumulation and virus production. In the present study, we identified that glyceraldehyde-3-phosphate dehydrogenase (GAPDH) interacts with intracellular NS1. Molecular docking revealed that this interaction occurs through the hydrophobic protrusion of NS1 and the hydrophobic residues located at the opposite side of the catalytic site. Moreover, addition of purified recombinant NS1 enhanced the glycolytic activity of GAPDH in vitro. Interestingly, we observed that DENV infection promoted the relocalization of GAPDH to the perinuclear region, where NS1 is commonly found. Both DENV infection and expression of NS1 itself resulted in increased GAPDH activity. Our findings indicate that the NS1 protein acts to increase glycolytic flux and, consequently, energy production, which is consistent with the recent finding that DENV induces and requires glycolysis for proper replication. This is the first report to propose that NS1 is an important modulator of cellular energy metabolism. The data presented here provide new insights that may be useful for further drug design and the development of alternative antiviral therapies against DENV. IMPORTANCE: Dengue represents a serious public health problem worldwide and is caused by infection with dengue virus (DENV). Estimates indicate that half of the global population is at risk of infection, with almost 400 million cases occurring per year. The NS1 glycoprotein is found in both the intracellular and the extracellular milieus. Despite the fact that NS1 has been commonly associated with DENV pathogenesis, it plays a pivotal but unknown role in the replication process. In an effort to understand the role of intracellular NS1, we demonstrate that glyceraldehyde-3-phosphate dehydrogenase (GAPDH) interacts with NS1. Our results indicate that NS1 increases the glycolytic activity of GAPDH in vitro. Interestingly, the GAPDH activity was increased during DENV infection, and NS1 expression alone was sufficient to enhance intracellular GAPDH activity in BHK-21 cells. Overall, our findings suggest that NS1 is an important modulator of cellular energy metabolism by increasing glycolytic flux.","corpus_id":3086859,"score":1},{"doc_id":"28864008","title":"Temporal and spatial expression of glyceraldehyde 3-phosphate dehydrogenase (Gapdh) in the mouse placenta.","abstract":"Glucose metabolism in trophoblast cells is essential to provide the required energy for the development and function of the placenta. Glyceraldehyde 3-phosphate dehydrogenase (Gapdh), a key enzyme in the glycolysis pathway has been considered ubiquitously expressed in cells. There is, however, a growing body of evidence suggesting that Gapdh has many functions in pathways unrelated to glucose metabolism. In the present study, we show that GAPDH expression and sub-cellular localization changes through gestation in the mouse placenta. Our findings raise the possibility that GAPDH has multiple functions in trophoblast cells and the developing placenta, while also cautioning against its use as an endogenous reference or standard for gene expression in the placenta.","corpus_id":26825081,"score":1},{"doc_id":"29205785","title":"Plant Polyphenols Stimulate Adhesion to Intestinal Mucosa and Induce Proteome Changes in the Probiotic Lactobacillus acidophilus NCFM.","abstract":"SCOPE: Plant phenolics, known to exert beneficial effects on human health, were supplemented to cultures of the probiotic bacterium Lactobacillus acidophilus NCFM (NCFM) to assess their effect on its adhesive capacity and the abundancy of individual proteins. METHODS AND RESULTS: The presence of resveratrol and ferulic acid during bacterial growth stimulated adhesion of NCFM to mucin and human intestinal HT-29 cells, while tannic acid improved adhesion only to HT-29 cells and caffeic acid had very modest effect overall. Some dosage dependence was found for the four phenolics supplemented at 100, 250, and 500 μg mL-1 to the cultures. Notably, 500 μg mL-1 ferulic acid only stimulated adhesion to mucin. Analyses of differential whole-cell as well as surface proteomes revealed relative abundancy changes for a total of 27 and 22 NCFM proteins, respectively. These changes include enzymes acting in metabolic pathways, such as glycolysis, nucleotide metabolism, and stress response, as well as known moonlighting or surface-associated proteins. CONCLUSION: The five plant phenolics found in various foods stimulate the adhesive capacity of NCFM in diverse ways and elicit relative abundancy changes of specific proteins, providing molecular level insight into the mechanism of the putative beneficial effects of the polyphenols.","corpus_id":3422937,"score":1},{"doc_id":"29574117","title":"GAPDH as a model non-canonical AU-rich RNA binding protein.","abstract":"Glyceraldehyde-3-phosphate dehydrogenase (GAPDH) plays a key role in glycolysis but is also known for its involvement in a myriad of extra-glycolytic functions. While GAPDH is not the only enzyme with established moonlighting roles, it shows great diversity in terms of its functions, cellular localizations, protein partners, and post-translational modifications. This review focuses on GAPDH's role as a non-canonical RNA binding protein to regulate the stability and translation of cellular mRNAs. Despite the clear involvement of GAPDH in gene expression regulation, how and where GAPDH binds to its RNA targets is still unknown. In addition, the mechanism by which GAPDH switches among its various cellular functions is also unknown. This review will summarize our current understanding of GAPDH-mediated regulation of RNA function.","corpus_id":22951427,"score":1},{"doc_id":"18298409","title":"Regulation of plant cytosolic glyceraldehyde 3-phosphate dehydrogenase isoforms by thiol modifications.","abstract":"Cytosolic NAD-dependent glyceraldehyde 3-P dehydrogenase (GAPDH; GapC; EC 1.2.1.12) catalyzes the oxidation of triose phosphates during glycolysis in all organisms, but additional functions of the protein has been put forward. Because of its reactive cysteine residue in the active site, it is susceptible to protein modification and oxidation. The addition of GSSG, and much more efficiently of S-nitrosoglutathione, was shown to inactivate the enzymes from Arabidopsis thaliana (isoforms GapC1 and 2), spinach, yeast and rabbit muscle. Inactivation was fully or at least partially reversible upon addition of DTT. The incorporation of glutathione upon formation of a mixed disulfide could be shown using biotinylated glutathione ethyl ester. Furthermore, using the biotin-switch assay, nitrosylated thiol groups could be shown to occur after treatment with nitric oxide donors. Using mass spectrometry and mutant proteins with one cysteine lacking, both cysteines (Cys-155 and Cys-159) were found to occur as glutathionylated and as nitrosylated forms. In preliminary experiments, it was shown that both GapC1 and GapC2 can bind to a partial gene sequence of the NADP-dependent malate dehydrogenase (EC 1.2.1.37; At5g58330). Transiently expressed GapC-green fluorescent protein fusion proteins were localized to the nucleus in A. thaliana protoplasts. As nuclear localization and DNA binding of GAPDH had been shown in numerous systems to occur upon stress, we assume that such mechanism might be part of the signaling pathway to induce increased malate-valve capacity and possibly other protective systems upon overreduction and initial formation of reactive oxygen and nitrogen species as well as to decrease and protect metabolism at the same time by modification of essential cysteine residues.","corpus_id":25470362,"score":0},{"doc_id":"19160814","title":"[Cloning, expression and characterization of a heterodimeric beta-galactosidase from Lactobacillus acidophilus ATCC 4356].","abstract":"UNLABELLED: Heterodimeric beta-galactosidase of Lactobacillus acidophilus belongs to glycoside hydrolase family 2, encoded by two overlapping and translational coupling genes, lacL and lacM. The lacL and lacM genes of the sequenced strain L. acidophilus NCFM encode polypeptides with calculated molecular masses of 73,253 and 35,817 Da, respectively. OBJECTIVE: To clone, overexpress and characterize the enzyme in Escherichia coli. METHODS: We cloned the fragment (2834 bp) containing ribose-binding site (RBS) and coding regions of the lacLM genes from L. acidophilus ATCC 4356 into expression vector pQE31. RBS and HIS-Tag of pQE31 were substituted by inserted fragment. Recombinant plasmid was electrotransformed into E. coli JM109. Expression product was purified by ammonium sulphate fractionation, anion-exchange, affinity chromatography and gel permeation. Native molecular mass of homogenous enzyme was measured by gel permeation, and beta-galactosidase activity was determined by using o-nitrophenyl-beta-D-galactopyranoside (ONPG) as the substrate. RESULTS: Overexpression of the soluble enzyme in E. coli was achieved. Amino acid residue 512 of recombinant LacL was different from that of L. acidophilus NCFM. Homogenous enzyme was obtained by purification. The homogenous enzyme had a specific activity of 226 U/mg protein, a native molecular mass of 96.3+/-4.6 kDa, an optimum temperature at 49 degrees C and an optimum pH of 7. The Km and Vmax values of the enzyme were 2.18+/-0.12 mmol/L, 273+/-5 U/mg protein respectively.","corpus_id":7280802,"score":0},{"doc_id":"20030066","title":"[Expression profile analysis of intestinal Caco-2 cells treated with Lactobacillus acidophilus NCFM].","abstract":"OBJECTIVE: Lactobacillus acidophilus NCFM is a probiotic strain that promotes human health. We evaluated the influence of Lactobacillus acidophilus NCFM on the genetic expression patterns in the Caco-2 cells. METHODS: Caco-2 cells were treated with Lactobacillus acidophilus NCFM for 2h. The total RNA of cells was extracted. Hybridization with Human Genome U133 Plus 2.0 Array was performed. The image scanning and data analysis were performed subsequently. Genes with significant expression changes were selected and analyzed. To support the microarray data, three striking difference genes were studied using Real-time RT PCR. RESULTS: Microarrays analysis showed that the expression levels of 508 genes were altered as compared with the control 473 of them were up-regulated, and 35 were down-regulated. It was supposed that many genes in Caco-2 cell were induced, so that Lactobacillus acidophilus NCFM could play a part in immune system process, antioxidant activity, biological adhesion, cholesterol absorption and so on. Three striking difference genes CCL2, PTX3 and TNFRSF9 which involved immune system process were validated by Real-time RT PCR. And the results of Real-time RT PCR showed the same expression trend as in microarray. CONCLUSION: Based on the results of gene expression alterations, the beneficial function of Lactobacillus acidophilus NCFM could be more greatly and deeply understood than ever before, and the mechanism of lactic acid bacteria would be revealed.","corpus_id":25294185,"score":0},{"doc_id":"22847419","title":"Glyceraldehyde-3-phosphate dehydrogenase (GAPDH) induces cancer cell senescence by interacting with telomerase RNA component.","abstract":"Oxidative stress regulates telomere homeostasis and cellular aging by unclear mechanisms. Glyceraldehyde 3-phosphate dehydrogenase (GAPDH) is a key mediator of many oxidative stress responses, involving GAPDH nuclear translocation and induction of cell death. We report here that GAPDH interacts with the telomerase RNA component (TERC), inhibits telomerase activity, and induces telomere shortening and breast cancer cell senescence. The Rossmann fold containing NAD(+) binding region on GAPDH is responsible for the interaction with TERC, whereas a lysine residue in the GAPDH catalytic domain is required for inhibiting telomerase activity and disrupting telomere maintenance. Furthermore, the GAPDH substrate glyceraldehyde-3-phosphate (G3P) and the nitric oxide donor S-nitrosoglutathione (GSNO) both negatively regulate GAPDH inhibition of telomerase activity. Thus, we demonstrate that GAPDH is regulated to target the telomerase complex, resulting in an arrest of telomere maintenance and cancer cell proliferation.","corpus_id":26847560,"score":0},{"doc_id":"23401169","title":"Activities of free and encapsulated Lactobacillus acidophilus LA5 or Lactobacillus casei 01 in processed longan juices on exposure to simulated gastrointestinal tract.","abstract":"BACKGROUND: Fruit drinks containing probiotics are gaining interest in the global marketplace. For example, longan juice, containing carbohydrate and various bioactive components, is a potentially health-promoting beverage as well as probiotic carrier for human consumption. In this study, high-pressure and thermal processes were applied to eliminate competitive micro-organisms in longan juice prior to the addition of Lactobacillus acidophilus LA5 or Lactobacillus casei 01. The activities of these probiotics in a simulated gastrointestinal tract were also investigated. RESULTS: Encapsulated probiotics could survive in the acidic environment of the stomach and small intestine, while the free cells were completely eliminated. In the colon experiment, the influence of encapsulated L. casei 01 on colon lactobacilli was significantly greater than that of encapsulated L. acidophilus LA5. Both encapsulated probiotics suspended in processed longan juices led to extensive increases in the formation of lactic acid and short-chain fatty acids (SCFA). Acetate was the major SCFA produced by colon bacteria, followed by propionate and butyrate. The discernible clear zone suggested that L. casei 01 provided greater antibacterial activity than L. acidophilus LA5. CONCLUSION: Both encapsulated probiotics along with processed longan juice led to significant increases in colon lactobacilli, lactic acid and SCFA formation.","corpus_id":13046861,"score":0},{"doc_id":"25425319","title":"The domestication of the probiotic bacterium Lactobacillus acidophilus.","abstract":"Lactobacillus acidophilus is a Gram-positive lactic acid bacterium that has had widespread historical use in the dairy industry and more recently as a probiotic. Although L. acidophilus has been designated as safe for human consumption, increasing commercial regulation and clinical demands for probiotic validation has resulted in a need to understand its genetic diversity. By drawing on large, well-characterised collections of lactic acid bacteria, we examined L. acidophilus isolates spanning 92 years and including multiple strains in current commercial use. Analysis of the whole genome sequence data set (34 isolate genomes) demonstrated L. acidophilus was a low diversity, monophyletic species with commercial isolates essentially identical at the sequence level. Our results indicate that commercial use has domesticated L. acidophilus with genetically stable, invariant strains being consumed globally by the human population.","corpus_id":1238128,"score":0},{"doc_id":"25635270","title":"Effect of iron on the probiotic properties of the vaginal isolate Lactobacillus jensenii CECT 4306.","abstract":"The vaginal microbiota of healthy, fertile women is dominated by lactobacilli. As a defence mechanism, these bacteria produce H₂O₂ to discourage colonization of the vagina by undesirable micro-organisms. In particular, Lactobacillus jensenii CECT 4306 is a strong producer of H₂O₂ and has been found to protect itself from the bactericidal effects of this compound through the activity of extracellular peroxidases. However, this peroxidase activity is dependent on the presence of Fe(3+), which is found in elevated concentrations in the vaginal mucosa as a consequence of the menstrual discharge. The aim of the present work was to evaluate whether Fe(3+) is able to modulate other potential probiotic properties of strain 4306. We found that Fe(3+) enhances the adhesion of L. jensenii CECT 4306 to mucin and to HT-29 and HT-29 MTX cells, and, in addition, improves the anti-inflammatory profile, as judged by an increase in the ratio of IL-10/IL-12p70 that were secreted by macrophages. A comparison of total, secreted and surface proteins produced in the presence and absence of Fe(3+) revealed significant differences in the concentration of the moonlighting protein glyceraldehyde-3-phosphate dehydrogenase (GAPDH). In conclusion, Fe(3+) seems to improve the probiotic characteristics of L. jensenii CECT 4306, and future research of the interactions of this strain with its vaginal environment may reveal further information about different aspects of its probiotic potential.","corpus_id":23056969,"score":0},{"doc_id":"26544973","title":"Lactobacillus acidophilus-Rutin Interplay Investigated by Proteomics.","abstract":"Dietary polyphenols are bioactive molecules that beneficially affect human health, due to their anti-oxidant, anti-inflammatory, cardio-protective and chemopreventive properties. They are absorbed in a very low percentage in the small intestine and reach intact the colon, where they are metabolized by the gut microbiota. Although it is well documented a key role of microbial metabolism in the absorption of polyphenols and modulation of their biological activity, molecular mechanisms at the basis of the bacteria-polyphenols interplay are still poorly understood. In this context, differential proteomics was applied to reveal adaptive response mechanisms that enabled a potential probiotic Lactobacillus acidophilus strain to survive in the presence of the dietary polyphenol rutin. The response to rutin mainly modulated the expression level of proteins involved in general stress response mechanisms and, in particular, induced the activation of protein quality control systems, and affected carbohydrate and amino acid metabolism, protein synthesis and cell wall integrity. Moreover, rutin triggered the expression of proteins involved in oxidation-reduction processes. This study provides a first general view of the impact of dietary polyphenols on metabolic and biological processes of L. acidophilus.","corpus_id":11226590,"score":0},{"doc_id":"26582368","title":"The E3 ubiquitin-ligase SEVEN IN ABSENTIA like 7 mono-ubiquitinates glyceraldehyde-3-phosphate dehydrogenase 1 isoform in vitro and is required for its nuclear localization in Arabidopsis thaliana.","abstract":"The E3 ubiquitin-protein ligases are associated to various processes such as cell cycle control and diverse developmental pathways. Arabidopsis thaliana SEVEN IN ABSENTIA like 7, which has ubiquitin ligase activity, is located in the nucleus and cytosol and is expressed at several stages in almost all plant tissues suggesting an important role in plant functions. However, the mechanism underlying the regulation of this protein is unknown. Since we found that the SEVEN IN ABSENTIA like 7 gene expression is altered in plants with impaired mitochondria, and in plants deficient in the glycolytic enzyme glyceraldehyde-3-phosphate dehydrogenase 1, we decided to study the possible interactions between both proteins as potential partners in plant signaling functions. We found that SEVEN IN ABSENTIA like 7 is able to interact in vitro with glyceraldehyde-3-phosphate dehydrogenase and that the Lys231 residue of the last is essential for this function. Following the interaction, a concomitant increase in the glyceraldehyde-3-phosphate dehydrogenase catalytic activity was observed. However, when SEVEN IN ABSENTIA like 7 was supplemented with E1 and E2 proteins to form a complete E1-E2-E3 modifier complex, we observed the mono-ubiquitination of glyceraldehyde-3-phosphate dehydrogenase 1 at the Lys76 residue and a dramatic decrease of its catalytic activity. Moreover, we found that localization of glyceraldehyde-3-phosphate dehydrogenase 1 in the nucleus is dependent on the expression SEVEN IN ABSENTIA like 7. These observations suggest that the association of both proteins might result in different biological consequences in plants either through affecting the glycolytic flux or via cytoplasm-nucleus relocation.","corpus_id":205992188,"score":0},{"doc_id":"28411221","title":"An Extracellular Cell-Attached Pullulanase Confers Branched α-Glucan Utilization in Human Gut Lactobacillus acidophilus.","abstract":"Of the few predicted extracellular glycan-active enzymes, glycoside hydrolase family 13 subfamily 14 (GH13_14) pullulanases are the most common in human gut lactobacilli. These enzymes share a unique modular organization, not observed in other bacteria, featuring a catalytic module, two starch binding modules, a domain of unknown function, and a C-terminal surface layer association protein (SLAP) domain. Here, we explore the specificity of a representative of this group of pullulanases, Lactobacillus acidophilus Pul13_14 (LaPul13_14), and its role in branched α-glucan metabolism in the well-characterized Lactobacillus acidophilus NCFM, which is widely used as a probiotic. Growth experiments with L. acidophilus NCFM on starch-derived branched substrates revealed a preference for α-glucans with short branches of about two to three glucosyl moieties over amylopectin with longer branches. Cell-attached debranching activity was measurable in the presence of α-glucans but was repressed by glucose. The debranching activity is conferred exclusively by LaPul13_14 and is abolished in a mutant strain lacking a functional LaPul13_14 gene. Hydrolysis kinetics of recombinant LaPul13_14 confirmed the preference for short-branched α-glucan oligomers consistent with the growth data. Curiously, this enzyme displayed the highest catalytic efficiency and the lowest Km reported for a pullulanase. Inhibition kinetics revealed mixed inhibition by β-cyclodextrin, suggesting the presence of additional glucan binding sites besides the active site of the enzyme, which may contribute to the unprecedented substrate affinity. The enzyme also displays high thermostability and higher activity in the acidic pH range, reflecting adaptation to the physiologically challenging conditions in the human gut. IMPORTANCE Starch is one of the most abundant glycans in the human diet. Branched α-1,6-glucans in dietary starch and glycogen are nondegradable by human enzymes and constitute a metabolic resource for the gut microbiota. The role of health-beneficial lactobacilli prevalent in the human small intestine in starch metabolism remains unexplored in contrast to colonic bacterial residents. This study highlights the pivotal role of debranching enzymes in the breakdown of starchy branched α-glucan oligomers (α-limit dextrins) by human gut lactobacilli exemplified by Lactobacillus acidophilus NCFM, which is one of the best-characterized strains used as probiotics. Our data bring novel insight into the metabolic preference of L. acidophilus for α-glucans with short α-1,6-branches. The unprecedented affinity of the debranching enzyme that confers growth on these substrates reflects its adaptation to the nutrient-competitive gut ecological niche and constitutes a potential advantage in cross-feeding from human and bacterial dietary starch metabolism.","corpus_id":41564431,"score":0},{"doc_id":"28539286","title":"[Expression, purification and activity analysis of GGDEF and EAL domain-containing proteins from Lactobacillus acidophilus].","abstract":"OBJECTIVE: To identify the functions of the proteins containing the GGDEF or EAL domain in Lactobacillus acidophilus for investigation of the regulatory mechanism of c-di-GMP in this strain. METHODS: The DNA fragments of NH13_07045-GGDEF, NH13_07050 and NH13_07055 from Lactobacillus acidophilus ATCC4356 were amplified by PCR and cloned into the expression vector pMAL-His-c2. After sequencing, the recombinant plasmids were transformed into competent Escherichia coli cells, which were induced by IPTG to express the recombinant proteins fused with maltose binding protein (MBP). The fusion proteins were purified using amylose resin column for diguanylate cyclase (DGC) or phosphodiesterase (PDE) activity assays in vitro followed by analysis with high-performance liquid chromatography (HPLC). RESULTS: The target DNA fragments were obtained by PCR, and their sequences were all identical to that in GenBank. The purified and concentrated fusion proteins, which were identified by SDS-PAGE and Western blotting, had relative molecular masses of 59 kD, 67 kD and 72 kD. HPLC analysis showed no DGC activity in NH13_07045-GGDEF, while PDE activity was found in NH13_07050 but not in NH13_07055. CONCLUSION: We obtained the protein encoded by NH13_07050 that possesses PDE activity in vitro. This protein may facilitate the evaluation of the regulatory function of c-di-GMP in Lactobacillus acidophilus.","corpus_id":25041923,"score":0},{"doc_id":"28992252","title":"Uromodulin-SlpA binding dictates Lactobacillus acidophilus uptake by intestinal epithelial M cells.","abstract":"Bacterial access to the gut immune system is a crucial process to promote host immune responses. The probiotic L-92 strain of Lactobacillus acidophilus exerts anti-allergic immunomodulatory effects upon oral administration in mice. Here, we show that microfold cells (M cells) are responsible for L-92 internalization for evoking L-92-mediated immune responses. L-92 specifically bound to uromodulin, a glycosylphosphatidylinositol-anchored protein expressed exclusively on M cells among intestinal epithelial cells. Internalization of L-92 into M cells was significantly reduced in uromodulin-deficient (Umod-/-) mice compared to Umod+/+ mice. Furthermore, the binding of L-92 to uromodulin was significantly decreased after removal of surface layer protein A (SlpA) from the bacteria. Our study thus revealed a crucial role of uromodulin on the M-cell surface for the uptake of SlpA-positive lactic acid bacteria into M cells, possibly leading to subsequent delivery of the bacteria to dendritic cells closely associated with M cells for immunomodulation. Our study also shed light on the possibility that SlpA and uromodulin could be used as vehicle and target, respectively, for efficient mucosal vaccine delivery.","corpus_id":37781861,"score":0},{"doc_id":"29747062","title":"Biochemical characterization of a recombinant Lactobacillus acidophilus strain expressing exogenous FomA protein.","abstract":"In previous research, to combine the immunogenicity of Fusobacterium nucleatum (F. nucleatum) and the probiotic properties of Lactobacillus acidophilus (L. acidophilus), we constructed a FomA-expressing L. acidophilus strain and assessed its immunogenicity. Our findings indicated that oral administration of the recombinant L. acidophilus strain reduced the risk of periodontal infection by Porphyromonas gingivalis (P. gingivalis) and F. nucleatum. However, because the exogenous FomA is an heterologous protein for the original bacterium, in this study, we assessed whether the biochemical characteristics of the recombinant L. acidophilus strain change due to the expression of the exogenous FomA protein. OBJECTIVES: To test the biochemical characteristics of a recombinant L. acidophilus strain expressing exogenous FomA and assess its antibiotic sensitivity. DESIGNS: We assessed the colony morphology, growth, acid production, and carbohydrate fermentation abilities of the recombinant L. acidophilus strain. In addition, we tested the adhesive ability and antimicrobial activity of the recombinant and assessed its antibiotic sensitivity through a drug susceptibility test. RESULTS: The experimental results showed that the colony and microscopic morphology of the recombinant L. acidophilus strain was consistent with the original strain, and the recombinant strain grew well when cultured under aerobic or anaerobic conditions, exhibiting a growth rate that was identical to that of the standard strain. Similarly, the supernatants of the recombinant L. acidophilus can inhibit the growth of E. coli and P. gingivalis at different concentrations, and the recombinant strain displayed essentially the same drug sensitivity profile as the original L. acidophilus. However, to our surprise, the recombinant strains exhibited a greater adhesion ability than the reference strain. CONCLUSIONS: Our study demonstrated that, in addition to an increased adhesion ability, the recombinant L. acidophilus strain maintained the basic characteristics of the standard strain ATCC 4356, including antibiotic sensitivity. Thus, the recombinant strains have great potential to be utilized as a safe and effective periodontitis vaccine in the future.","corpus_id":13690298,"score":0}],"string":"[\n {\n \"doc_id\": \"18194256\",\n \"title\": \"Cell surface Lactobacillus plantarum LA 318 glyceraldehyde-3-phosphate dehydrogenase (GAPDH) adheres to human colonic mucin.\",\n \"abstract\": \"AIMS: To characterize the adhesion molecule of Lactobacillus plantarum LA 318 that shows high adhesion to human colonic mucin (HCM). METHODS AND RESULTS: The adhesion test used the BIACORE assay where PBS-washed bacterial cells showed a significant decrease in adherence to HCM than distilled water-washed cells. A component in the PBS wash fraction adhered to the HCM and a main protein was detected as a c. 40-kDa band using SDS-PAGE. Using homology comparisons of the N-terminal amino acid sequences compared with sequence databases, this protein was identified as glyceraldehyde-3-phosphate dehydrogenase (GAPDH). The DNA sequence of LA 318 GAPDH was 100% identical to the GAPDH (gapB) of L. plantarum WCFS1. The purified GAPDH adhered to HCM. CONCLUSIONS: We found the adhesin of L. plantarum LA 318 to HCM in its culture PBS wash fraction. The molecule was identified as GAPDH. Because LA 318 possesses the same adhesin as many pathogens, the lactobacilli GAPDH may compete with pathogens infecting the intestine. SIGNIFICANCE AND IMPACT OF THE STUDY: This is the first report showing GAPDH expressed on the cell surface of lactobacilli adheres to mucin suggesting L. plantarum LA 318 adheres to HCM using GAPDH binding activity to colonize the human intestinal mucosa.\",\n \"corpus_id\": 22346488,\n \"score\": 2\n },\n {\n \"doc_id\": \"18790050\",\n \"title\": \"Cell surface glyceraldehyde-3-phosphate dehydrogenase (GAPDH) of Lactobacillus plantarum LA 318 recognizes human A and B blood group antigens.\",\n \"abstract\": \"Lactobacillus plantarum LA 318 is a potential probiotic strain isolated from normal human intestinal tissue that shows high adhesion to human colonic mucin mediated by the bacterial cell surface glyceraldehyde-3-phosphate dehydrogenase (GAPDH). We report the adhesion mechanism of the lactobacilli is in part due to GAPDH binding to human ABO-type blood group antigens expressed on human colonic mucin (HCM). After periodate oxidation of HCM, adhesion of L. plantarum LA 318 bacterial cells significantly decreased compared to normal HCM. A BIACORE binding assay of GAPDH to blood group antigens was then performed. High binding was observed to A and B group antigens, while binding to H group antigen was lower (P<0.01). No interaction was observed between GAPDH and various monosaccharides. Furthermore, GAPDH binding to the B-trisaccharide biotinyl polymer (BP)-probe [Galalpha1-3 (Fucalpha1-2) Gal-] was significantly higher as compared to B-disaccharide, Lewis D-trisaccharide, 3-fucosyl-N-acetylglucosamine and alpha-N-acetylneuraminic acid BP-probes. The data suggests the trisaccharide structure is important in binding to the blood group antigens. The binding of GAPDH to HCM significantly decreased after incubation with NAD+. This suggests that the NAD binding domain on GAPDH may be related to binding to HCM.\",\n \"corpus_id\": 21794166,\n \"score\": 2\n },\n {\n \"doc_id\": \"19220903\",\n \"title\": \"Surface displaced alfa-enolase of Lactobacillus plantarum is a fibronectin binding protein.\",\n \"abstract\": \"BACKGROUND: Lactic acid bacteria of the genus Lactobacillus and Bifidobacterium are one of the most important health promoting groups of the human intestinal microbiota. Their protective role within the gut consists in out competing invading pathogens for ecological niches and metabolic substrates. Among the features necessary to provide health benefits, commensal microorganisms must have the ability to adhere to human intestinal cells and consequently to colonize the gut. Studies on mechanisms mediating adhesion of lactobacilli to human intestinal cells showed that factors involved in the interaction vary mostly among different species and strains, mainly regarding interaction between bacterial adhesins and extracellular matrix or mucus proteins. We have investigated the adhesive properties of Lactobacillus plantarum, a member of the human microbiota of healthy individuals. RESULTS: We show the identification of a Lactobacillus plantarum LM3 cell surface protein (48 kDa), which specifically binds to human fibronectin (Fn), an extracellular matrix protein. By means of mass spectrometric analysis this protein was identified as the product of the L. plantarum enoA1 gene, coding the EnoA1 alfa-enolase. Surface localization of EnoA1 was proved by immune electron microscopy. In the mutant strain LM3-CC1, carrying the enoA1 null mutation, the 48 kDa adhesin was not anymore detectable neither by anti-enolase Western blot nor by Fn-overlay immunoblotting assay. Moreover, by an adhesion assay we show that LM3-CC1 cells bind to fibronectin-coated surfaces less efficiently than wild type cells, thus demonstrating the significance of the surface displaced EnoA1 protein for the L. plantarum LM3 adhesion to fibronectin. CONCLUSION: Adhesion to host tissues represents a crucial early step in the colonization process of either pathogens or commensal bacteria. We demonstrated the involvement of the L. plantarum Eno A1 alfa-enolase in Fn-binding, by studying LM3 and LM3-CC1 surface proteins. Isolation of LM3-CC1 strain was possible for the presence of expressed enoA2 gene in the L. plantarum genome, giving the possibility, for the first time to our knowledge, to quantitatively compare adhesion of wild type and mutant strain, and to assess doubtless the role of L. plantarum Eno A1 as a fibronectin binding protein.\",\n \"corpus_id\": -1,\n \"score\": 2\n },\n {\n \"doc_id\": \"19672048\",\n \"title\": \"Identification of novel proteins secreted by Lactobacillus plantarum that bind to mucin and fibronectin.\",\n \"abstract\": \"Lactobacillus plantarum is a lactic acid bacterium that can be isolated from a high variety of fermented foods, including dairy products. In the present work, eight novel proteins secreted by three L. plantarum strains have been identified by tandem mass spectrometry. Seven of them were predicted as extracellular proteins containing putative signal peptides. The sixth, identified as glyceraldehyde 3-phosphate dehydrogenase (GAPDH), is a cytoplasmic protein that has been detected on the surface of several microorganisms. Muramidase and GAPDH were secreted only by the L. plantarum BMCM12 strain. Two other bands present in this strain were not identified, in spite of their yielding good tryptic profiles, suggesting an absence of homolog sequences in the molecular databases. Four of these proteins, including GAPDH, bound to mucin and fibronectin. These proteins might play important roles in the physiology and ecology of this bacterium, notably in the interaction with the human host.\",\n \"corpus_id\": 45227396,\n \"score\": 2\n },\n {\n \"doc_id\": \"19737900\",\n \"title\": \"Identification of the binding domain of Streptococcus oralis glyceraldehyde-3-phosphate dehydrogenase for Porphyromonas gingivalis major fimbriae.\",\n \"abstract\": \"Porphyromonas gingivalis forms communities with antecedent oral biofilm constituent streptococci. P. gingivalis major fimbriae bind to glyceraldehyde-3-phosphate dehydrogenase (GAPDH) present on the streptococcal surface, and this interaction plays an important role in P. gingivalis colonization. This study identified the binding domain of Streptococcus oralis GAPDH for P. gingivalis fimbriae. S. oralis recombinant GAPDH (rGAPDH) was digested with lysyl endopeptidase. Cleaved fragments of rGAPDH were applied to a reverse-phase high-pressure liquid chromatograph equipped with a C18 column. Each peak was collected; the binding activity toward P. gingivalis recombinant fimbrillin (rFimA) was analyzed with a biomolecular interaction analysis system. The fragment displaying the strongest binding activity was further digested with various proteinases, after which the binding activity of each fragment was measured. The amino acid sequence of each fragment was determined by direct sequencing, mass spectrometric analysis, and amino acid analysis. Amino acid residues 166 to 183 of S. oralis GAPDH exhibited the strongest binding activity toward rFimA; confocal laser scanning microscopy revealed that the synthetic peptide corresponding to amino acid residues 166 to 183 of S. oralis GAPDH (pep166-183, DNFGVVEGLMTTIHAYTG) inhibits S. oralis-P. gingivalis biofilm formation in a dose-dependent manner. Moreover, pep166-183 inhibited interbacterial biofilm formation by several oral streptococci and P. gingivalis strains with different types of FimA. These results indicate that the binding domain of S. oralis GAPDH for P. gingivalis fimbriae exists within the region encompassing amino acid residues 166 to 183 of GAPDH and that pep166-183 may be a potent inhibitor of P. gingivalis colonization in the oral cavity.\",\n \"corpus_id\": 30954518,\n \"score\": 2\n },\n {\n \"doc_id\": \"20054117\",\n \"title\": \"Structure of glyceraldehyde-3-phosphate dehydrogenase from the archaeal hyperthermophile Methanocaldococcus jannaschii.\",\n \"abstract\": \"The X-ray crystal structure of glyceraldehyde-3-phosphate dehydrogenase (GAPDH) from the hyperthermophilic archaeon Methanocaldococcus jannaschii (Mj-GAPDH) was determined to 1.81 A resolution. The crystal belonged to space group C222(1), with unit-cell parameters a = 83.4, b = 152.0, c = 118.6 A. The structure was solved by molecular replacement and was refined to a final R factor of 17.1% (R(free) = 19.8%). The final structure included the cofactor NADP(+) at the nucleotide-binding site and featured unoccupied inorganic and substrate phosphate-binding sites. A comparison with GAPDH structures from mesophilic sources suggested that Mj-GAPDH is stabilized by extensive electrostatic interactions between the C-terminal alpha-helices and various distal loop regions, which are likely to contribute to thermal stability. The key phosphate-binding residues in the active site of Mj-GAPDH are conserved in other archaeal GAPDH proteins. These residues undergo a conformational shift in response to occupancy of the inorganic phosphate site.\",\n \"corpus_id\": 40110104,\n \"score\": 2\n },\n {\n \"doc_id\": \"20562289\",\n \"title\": \"Functional roles of aggregation-promoting-like factor in stress tolerance and adherence of Lactobacillus acidophilus NCFM.\",\n \"abstract\": \"Aggregation-promoting factors (Apf) are secreted proteins that have been associated with a diverse number of functional roles in lactobacilli, including self-aggregation, the bridging of conjugal pairs, coaggregation with other commensal or pathogenic bacteria, and maintenance of cell shape. In silico genome analysis of Lactobacillus acidophilus NCFM identified LBA0493 as a 696-bp apf gene that encodes a putative 21-kDa Apf protein. Transcriptional studies of NCFM during growth in milk showed apf to be one of the most highly upregulated genes in the genome. In the present study, reverse transcriptase-quantitative PCR (RT-QPCR) analysis revealed that the apf gene was highly induced during the stationary phase compared to that during the logarithmic phase. To investigate the functional role of Apf in NCFM, an Delta apf deletion mutant was constructed. The resulting Delta apf mutant, NCK2033, did not show a significant difference in cell morphology or growth compared to that of the NCFMDelta upp reference strain, NCK1909. The autoaggregation phenotype of NCK2033 in planktonic culture was unaffected. Additional phenotypic assays revealed that NCK2033 was more susceptible to treatments with oxgall bile and sodium dodecyl sulfate (SDS). Survival rates of NCK2033 decreased when stationary-phase cells were exposed to simulated small-intestinal and gastric juices. Furthermore, NCK2033 in the stationary phase showed a reduction of in vitro adherence to Caco-2 intestinal epithelial cells, mucin glycoproteins, and fibronectin. The data suggest that the Apf-like proteins may contribute to the survival of L. acidophilus during transit through the digestive tract and, potentially, participate in the interactions with the host intestinal mucosa.\",\n \"corpus_id\": 206716041,\n \"score\": 2\n },\n {\n \"doc_id\": \"21138769\",\n \"title\": \"Expression, purification and kinetic characterization of His-tagged glyceraldehyde-3-phosphate dehydrogenase from Trypanosoma cruzi.\",\n \"abstract\": \"Trypanosomes are flagellated protozoa responsible for serious parasitic diseases that have been classified by the World Health Organization as tropical sicknesses of major importance. One important drug target receiving considerable attention is the enzyme glyceraldehyde-3-phosphate dehydrogenase from the protozoan parasite Trypanosoma cruzi, the causative agent of Chagas disease (T. cruzi Glyceraldehyde-3-phosphate dehydrogenase (TcGAPDH); EC 1.2.1.12). TcGAPDH is a key enzyme in the glycolytic pathway of T. cruzi and catalyzes the oxidative phosphorylation of D-glyceraldehyde-3-phosphate (G3P) to 1,3-bisphosphoglycerate (1,3-BPG) coupled to the reduction of oxidized nicotinamide adenine dinucleotide, (NAD(+)) to NADH, the reduced form. Herein, we describe the cloning of the T. cruzi gene for TcGAPDH into the pET-28a(+) vector, its expression as a tagged protein in Escherichia coli, purification and kinetic characterization. The His(6)-tagged TcGAPDH was purified by affinity chromatography. Enzyme activity assays for the recombinant His(6)-TcGAPDH were carried out spectrophotometrically to determine the kinetic parameters. The apparent Michaelis-Menten constant (K(M)(app)) determined for D-glyceraldehyde-3-phosphate and NAD(+) were 352±21 and 272±25 μM, respectively, which were consistent with the values for the untagged enzyme reported in the literature. We have demonstrated by the use of Isothermal Titration Calorimetry (ITC) that this vector modification resulted in activity preserved for a higher period. We also report here the use of response surface methodology (RSM) to determine the region of optimal conditions for enzyme activity. A quadratic model was developed by RSM to describe the enzyme activity in terms of pH and temperature as independent variables. According to the RMS contour plots and variance analysis, the maximum enzyme activity was at 29.1°C and pH 8.6. Above 37°C, the enzyme activity starts to fall, which may be related to previous reports that the quaternary structure begins a process of disassembly.\",\n \"corpus_id\": 23550288,\n \"score\": 2\n },\n {\n \"doc_id\": \"21205411\",\n \"title\": \"Cloning, expression and characterization of NAD+-dependent glyceraldehyde-3-phosphate dehydrogenase of adult Haemonchus contortus.\",\n \"abstract\": \"Glyceraldehyde-3-phosphate dehydrogenase (GAPDH) regulates a wide range of biological processes, including pathogen evasion. In the present research, the GAPDH gene of Haemonchus contortus (HcGAPDH) was cloned and characterized. Specific primers for the rapid amplification of cDNA ends (RACE) were designed based on the expressed sequence tag (EST, AW670737) to amplify the 3' and 5' ends of HcGAPDH. The full length of cDNA from this gene was obtained by overlapping the sequences of 3' and 5' extremities and amplification by reverse transcription polymerase chain reaction (RT-PCR). The biochemical activities of the recombinant protein HcGAPDH, which was expressed in prokaryotic cells and purified by affinity chromatography, were analysed by assays of enzymatic activity, thermal stability and pH. The results showed that the cloned full-length cDNA comprised 1303 bp and encoded a peptide with 341 amino acid residues which showed sequence similarity to several known GAPDHs. The biochemical assay showed that the protein encoded by the HcGAPDH exhibited enzymatic activity with NAD+ as a cofactor. HcGAPDH was stable between pH 5 and 9 and maintained activity at high temperatures of up to 75°C. The natural GAPDH of Haemonchus contortus detected by immunoblot assay was approximately 38 kDa in size, and the recombinant HcGAPDH was recognized strongly by serum from naturally infected goats.\",\n \"corpus_id\": 206231862,\n \"score\": 2\n },\n {\n \"doc_id\": \"21546586\",\n \"title\": \"Role of Mycoplasma pneumoniae glyceraldehyde-3-phosphate dehydrogenase (GAPDH) in mediating interactions with the human extracellular matrix.\",\n \"abstract\": \"In different, phylogenetically unrelated micro-organisms, glycolytic enzymes play a dual role. In the cytosol they are involved in metabolic reactions whereas the surface-localized fraction of the enzymes contributes to adhesion and virulence. Glyceraldehyde-3-phosphate dehydrogenase (GAPDH) is a typical member of this group of multifunctional proteins. In this study, we characterized the GAPDH of Mycoplasma pneumoniae, a common pathogen of the human respiratory mucosa. Full-length GAPDH of M. pneumoniae was successfully expressed and used to produce a polyclonal antiserum. By immunofluorescence, colony blot and ELISA experiments with different fractions of the M. pneumoniae proteins, GAPDH was demonstrated to be present in the cytosol and at even higher concentrations at the surface of mycoplasmas. Nevertheless, antibodies against recombinant GAPDH were not detected in sera of immunized animals or of patients with confirmed M. pneumoniae infection. Recombinant GAPDH bound to different human cell lines in a concentration-dependent manner, and binding was inhibited by specific anti-GAPDH serum. In contrast, this antiserum did not significantly influence the adherence of M. pneumoniae to HeLa cells. When different human extracellular matrix proteins were tested in Western blot assays, GAPDH bound to fibrinogen. The results showed that the GAPDH of M. pneumoniae is a member of the family of cytosol-localized glycolytic enzymes, which also occur at the surface of the bacterium, and mediates interactions with the extracellular matrix proteins of the human host. Thus, the surface-exposed fraction of GAPDH may be a factor that contributes to the successful colonization of the human respiratory tract by M. pneumoniae.\",\n \"corpus_id\": 31168591,\n \"score\": 2\n },\n {\n \"doc_id\": \"21622872\",\n \"title\": \"Protein-carbohydrate interactions between Lactobacillus salivarius and pig mucins.\",\n \"abstract\": \"Adherence to the gastrointestinal tract is a key element desirable for many of the proposed beneficial health effects of probiotic bacteria. The aims of this study were to determine the amounts of adhesion of 3 Lactobacillus salivarius strains (Lb6, Lb9, and Lb10) to porcine small intestinal mucins and to determine whether adhesion is a function of lectin-like activities. Dot and Western blot assays were performed to investigate bacterial adhesion. Several carbohydrates and glycoproteins were evaluated to determine whether they interfered with adhesion of the Lactobacillus strains to intestinal mucins and to determine whether they had lectin-like activities. The Lb9 and Lb10 strains had greater association with piglet mucins than did those from 22- to 24-wk-old finishing pigs (P = 0.021 and 0.037, respectively), whereas the Lb6 strain adhered to both (P = 0.138). Western blot assays showed that bacterial adhesion detected piglet mucosa from the duodenum, jejunum, and ileum. In finishing pigs, the adhesion was variable throughout the gastrointestinal tract. Galactose and mannose diminished the interaction of the Lb9 and Lb10 strains in intestinal mucosa (P = 0.028 and 0.026, respectively), whereas pig gastric mucin reduced the adhesion of the Lb6 strain (P = 0.013). Adhesion of the Lb9 and Lb10 strains to intestinal mucosa was less after protease treatment (P = 0.023 and 0.018, respectively), which indicates that proteins are needed for the Lb9 and Lb10 strains to recognize mucin. The Lb6 strain also demonstrated diminished adhesion after periodate treatment (P = 0.038). From these results, we suggest that the nature of the bacterial lectin-like substance is a surface protein that loosely binds to the bacterial cell surface. All the tested strains adhered to specific targets in the small intestinal mucosa of piglets, and the bacteria had lectin-like proteins involved in this adhesion.\",\n \"corpus_id\": 30876729,\n \"score\": 2\n },\n {\n \"doc_id\": \"21895736\",\n \"title\": \"GAPDH: a common enzyme with uncommon functions.\",\n \"abstract\": \"Glyceraldehyde-3-phosphate dehydrogenase (GAPDH) has long been recognized as an important enzyme for energy metabolism and the production of ATP and pyruvate through anaerobic glycolysis in the cytoplasm. Recent studies have shown that GAPDH has multiple functions independent of its role in energy metabolism. Although increased GAPDH gene expression and enzymatic function is associated with cell proliferation and tumourigenesis, conditions such as oxidative stress impair GAPDH catalytic activity and lead to cellular aging and apoptosis. The mechanism(s) underlying the effects of GAPDH on cellular proliferation remains unclear, yet much evidence has been accrued that demonstrates a variety of interacting partners for GAPDH, including proteins, various RNA species and telomeric DNA. The present mini review summarizes recent findings relating to the extraglycolytic functions of GAPDH and highlights the significant role this enzyme plays in regulating both cell survival and apoptotic death.\",\n \"corpus_id\": 23499684,\n \"score\": 2\n },\n {\n \"doc_id\": \"22224921\",\n \"title\": \"Characterization of the adherence properties of human Lactobacilli strains to be used as vaginal probiotics.\",\n \"abstract\": \"In the present work, the adhesion of 43 human lactobacilli isolates to mucin has been studied. The most adherent strains were selected, and their capacities to adhere to three epithelial cell lines were studied. All intestinal strains and one vaginal isolate adhered to HT-29 cells. The latter was the most adherent to Caco-2 cells, although two of the intestinal isolates were also highly adherent. Moreover, five of the eight strains strongly adhered to HeLa cells. The binding of an Actinomyces neuii clinical isolate to HeLa cells was enhanced by two of the lactobacilli and by their secreted proteins, while those of another two strains almost abolished it. None of the strains were able to interfere with the adhesion of Candida albicans to HeLa cells. The components of the extracellular proteome of all strains were identified by MALDI-TOF/MS. Among them, a collagen-binding A precursor and aggregation-promoting factor-like proteins are suggested to participate on adhesion to Caco-2 and HeLa cells, respectively. In this way, several proteins with LysM domains might explain the ability of some bacterial supernatants to block A. neuii adhesion to HeLa cell cultures. Finally, glyceraldehyde 3-phosphate dehydrogenase (GAPDH) could explain the good adhesion of some strains to mucin.\",\n \"corpus_id\": 17812155,\n \"score\": 2\n },\n {\n \"doc_id\": \"22292499\",\n \"title\": \"The multifunctional glycolytic protein glyceraldehyde-3-phosphate dehydrogenase (GAPDH) is a novel macrophage lactoferrin receptor.\",\n \"abstract\": \"Several proteins with limited cell type distribution have been shown to bind lactoferrin. However, except in the case of hepatic and intestinal cells, these have not been definitively identified and characterized. Here we report that the multifunctional glycolytic protein glyceraldehyde-3-phosphate dehydrogenase (GAPDH) functions as a novel receptor for lactoferrin (Lf) in macrophages. GAPDH is a well-known moonlighting protein, and previous work from our laboratory has indicated its localization on macrophage cell surfaces, wherein it functions as a transferrin (Tf) receptor. The K(D) value for GAPDH-lactoferrin interaction was determined to be 43.8 nmol/L. Utilizing co-immunoprecipitation, immunoflorescence, and immunogold labelling electron microscopy we could demonstrate the trafficking of lactoferrin to the endosomal compartment along with GAPDH. We also found that upon iron depletion the binding of lactoferrin to macrophage cell surface is enhanced. This correlated with an increased expression of surface GAPDH, while other known lactoferrin receptors CD14 and lipoprotein receptor-related protein (LRP) were found to remain unaltered in expression levels. This suggests that upon iron depletion, cells prefer to use GAPDH to acquire lactoferrin. As GAPDH is an ubiquitously expressed molecule, its function as a receptor for lactoferrin may not be limited to macrophages.\",\n \"corpus_id\": 41523959,\n \"score\": 2\n },\n {\n \"doc_id\": \"22389474\",\n \"title\": \"Glutamine synthetase and glucose-6-phosphate isomerase are adhesive moonlighting proteins of Lactobacillus crispatus released by epithelial cathelicidin LL-37.\",\n \"abstract\": \"Glutamine synthetase (GS) and glucose-6-phosphate isomerase (GPI) were identified as novel adhesive moonlighting proteins of Lactobacillus crispatus ST1. Both proteins were bound onto the bacterial surface at acidic pHs, whereas a suspension of the cells to pH 8 caused their release into the buffer, a pattern previously observed with surface-bound enolase and glyceraldehyde-3-phosphate dehydrogenase (GAPDH) of L. crispatus. The pH shift was associated with a rapid and transient increase in cell wall permeability, as measured by cell staining with propidium iodide. A gradual increase in the release of the four moonlighting proteins was also observed after the treatment of L. crispatus ST1 cells with increasing concentrations of the antimicrobial cationic peptide LL-37, which kills bacteria by disturbing membrane integrity and was here observed to increase the cell wall permeability of L. crispatus ST1. At pH 4, the fusion proteins His(6)-GS, His(6)-GPI, His(6)-enolase, and His(6)-GAPDH showed localized binding to cell division septa and poles of L. crispatus ST1 cells, whereas no binding to Lactobacillus rhamnosus GG was detected. Strain ST1 showed a pH-dependent adherence to the basement membrane preparation Matrigel. Purified His(6)-GS and His(6)-GPI proteins bound to type I collagen, and His(6)-GS also bound to laminin, and their level of binding was higher at pH 5.5 than at pH 6.5. His(6)-GS also expressed a plasminogen receptor function. The results show the strain-dependent surface association of moonlighting proteins in lactobacilli and that these proteins are released from the L. crispatus surface after cell trauma, under conditions of alkaline stress, or in the presence of the antimicrobial peptide LL-37 produced by human cells.\",\n \"corpus_id\": 26905372,\n \"score\": 2\n },\n {\n \"doc_id\": \"22869137\",\n \"title\": \"Preliminary crystallographic analysis of glyceraldehyde-3-phosphate dehydrogenase 3 from Saccharomyces cerevisiae.\",\n \"abstract\": \"Glyceraldehyde-3-phosphate dehydrogenase (GAPDH) is an important enzyme in the glycolytic pathway. In addition to its conventional metabolic role, GAPDH has been identified to possess diverse cellular functions. In this study, glyceraldehyde-3-phosphate dehydrogenase 3, the third isoform of GAPDH from Saccharomyces cerevisiae, was cloned, expressed, purified and crystallized. The crystals belonged to space group I4(1)22, with unit-cell parameters a = b = 116.13, c = 119.21 Å. X-ray diffraction data were collected to a resolution of 2.6 Å. The structure was solved by molecular replacement and refinement is in progress.\",\n \"corpus_id\": 12460695,\n \"score\": 2\n },\n {\n \"doc_id\": \"23264054\",\n \"title\": \"Identification and characterization of Porphyromonas gingivalis client proteins that bind to Streptococcus oralis glyceraldehyde-3-phosphate dehydrogenase.\",\n \"abstract\": \"Coaggregation of Porphyromonas gingivalis and oral streptococci is thought to play an important role in P. gingivalis colonization. Previously, we reported that P. gingivalis major fimbriae interacted with Streptococcus oralis glyceraldehyde-3-phosphate dehydrogenase (GAPDH), and that amino acid residues 166 to 183 of GAPDH exhibited strong binding activity toward P. gingivalis fimbriae (H. Nagata, M. Iwasaki, K. Maeda, M. Kuboniwa, E. Hashino, M. Toe, N. Minamino, H. Kuwahara, and S. Shizukuishi, Infect. Immun. 77:5130-5138, 2009). The present study aimed to identify and characterize P. gingivalis components other than fimbriae that interact with S. oralis GAPDH. A pulldown assay was performed to detect potential interactions between P. gingivalis client proteins and S. oralis recombinant GAPDH with amino acid residues 166 to 183 deleted by site-directed mutagenesis. Seven proteins, namely, tonB-dependent receptor protein (RagA4), arginine-specific proteinase B, 4-hydroxybutyryl-coenzyme A dehydratase (AbfD), lysine-specific proteinase, GAPDH, NAD-dependent glutamate dehydrogenase (GDH), and malate dehydrogenase (MDH), were identified by two-dimensional gel electrophoresis followed by proteomic analysis using tandem mass spectrometry. Interactions between these client proteins and S. oralis GAPDH were analyzed with a biomolecular interaction analysis system. S. oralis GAPDH showed high affinity for five of the seven client proteins (RagA4, AbfD, GAPDH, GDH, and MDH). Interactions between P. gingivalis and S. oralis were measured by a turbidimetric method and fluorescence microscopy. RagA4, AbfD, and GDH enhanced coaggregation, whereas GAPDH and MDH inhibited coaggregation. Furthermore, the expression of luxS in P. gingivalis was upregulated by RagA4, AbfD, and GDH but was downregulated by MDH. These results indicate that the five P. gingivalis client proteins function as regulators in P. gingivalis biofilm formation with oral streptococci.\",\n \"corpus_id\": -1,\n \"score\": 2\n },\n {\n \"doc_id\": \"23872606\",\n \"title\": \"The Roles of Moonlighting Proteins in Bacteria.\",\n \"abstract\": \"Moonlighting proteins, characterized by their multiple autonomous functions, have been detected in bacteria. Surprisingly, many of these proteins are conserved and involved in metabolic pathway or the cell stress response. They localise to the bacterial surface to take on additional activities, which have been hypothesised to contribute to bacterial virulence or bacterial benefit. In this review, we compare the functions of moonlighting proteins in bacteria, describe the structural basis of moonlighting functions, and summarise the regulation of secretion and localisation of moonlighting proteins.\",\n \"corpus_id\": 10530383,\n \"score\": 2\n },\n {\n \"doc_id\": \"24566472\",\n \"title\": \"Biochemical characterisation of glyceraldehyde 3-phosphate dehydrogenase (GAPDH) from the liver fluke, Fasciola hepatica.\",\n \"abstract\": \"Glyceraldehyde 3-phosphate dehydrogenase (GAPDH) catalyses one of the two steps in glycolysis which generate the reduced coenzyme NADH. This reaction precedes the two ATP generating steps. Thus, inhibition of GAPDH will lead to substantially reduced energy generation. Consequently, there has been considerable interest in developing GAPDH inhibitors as anti-cancer and anti-parasitic agents. Here, we describe the biochemical characterisation of GAPDH from the common liver fluke Fasciola hepatica (FhGAPDH). The primary sequence of FhGAPDH is similar to that from other trematodes and the predicted structure shows high similarity to those from other animals including the mammalian hosts. FhGAPDH lacks a binding pocket which has been exploited in the design of novel antitrypanosomal compounds. The protein can be expressed in, and purified from Escherichia coli; the recombinant protein was active and showed no cooperativity towards glyceraldehyde 3-phosphate as a substrate. In the absence of ligands, FhGAPDH was a mixture of homodimers and tetramers, as judged by protein-protein crosslinking and analytical gel filtration. The addition of either NAD⁺ or glyceraldehyde 3-phosphate shifted this equilibrium towards a compact dimer. Thermal scanning fluorimetry demonstrated that this form was considerably more stable than the unliganded one. These responses to ligand binding differ from those seen in mammalian enzymes. These differences could be exploited in the discovery of reagents which selectively disrupt the function of FhGAPDH.\",\n \"corpus_id\": 11247617,\n \"score\": 2\n },\n {\n \"doc_id\": \"25005093\",\n \"title\": \"Cloning, expression, purification, crystallization and preliminary X-ray diffraction analysis of glyceraldehyde-3-phosphate dehydrogenase from Streptococcus agalactiae NEM316.\",\n \"abstract\": \"Glyceraldehyde-3-phosphate dehydrogenase (GAPDH) is an essential enzyme involved in glycolysis. Despite lacking the secretory signal sequence, this cytosolic enzyme has been found localized at the surface of several bacteria and fungi. As a surface protein, GAPDH exhibits various adhesive functions, thereby facilitating colonization and invasion of host tissues. Streptococcus agalactiae, also known as group B streptococcus (GBS), binds onto the host using its surface adhesins and causes sepsis and pneumonia in neonates. GAPDH is one of the surface adhesins of GBS binding to human plasminogen and is a virulent factor associated with host colonization. Although the surface-associated GAPDH has been shown to bind to a variety of host extracellular matrix (ECM) molecules in various bacteria, the molecular mechanism underlying their interaction is not fully understood. To investigate this, structural studies on GAPDH of S. agalactiae were initiated. The gapC gene of S. agalactiae NEM316 encoding GAPDH protein was cloned into pET-28a vector, overexpressed in Escherichia coli BL21(DE3) cells and purified to homogeneity. The purified protein was crystallized using the hanging-drop vapour-diffusion method. The GAPDH crystals obtained in two different crystallization conditions diffracted to 2.8 and 2.6 Å resolution, belonging to two different space groups P2₁ and P2₁2₁2₁, respectively. The structure was solved by molecular replacement and structure refinement is now in progress.\",\n \"corpus_id\": 8146533,\n \"score\": 2\n },\n {\n \"doc_id\": \"25183032\",\n \"title\": \"A homolog of glyceraldehyde-3-phosphate dehydrogenase from Riemerella anatipestifer is an extracellular protein and exhibits biological activity.\",\n \"abstract\": \"Riemerella anatipestifer is the causative agent of septicemia anserum exsudativa in ducks. Its pathogenesis and virulence factors are still unclear. The glycolytic enzyme, glyceraldehyde-3-phosphate dehydrogenase (GAPDH), an anchorless and multifunctional protein on the surface of several pathogenic microorganisms, is involved in virulence and adhesion. Whether homologs of GAPDH exist, and display similar characteristics in R. anatipestifer (RaGAPDH) has not been determined. In our research, the RaGAPDH activity from various R. anatipestifer isolates was confirmed. Twenty-two gapdh genes from genomic DNA of R. anatipestifer isolates were cloned and sequenced for phylogenetic analysis. The distribution of RaGAPDH in R. anatipestifer CZ2 strain was confirmed by antisera to recombinant RaGAPDH. The ability of purified RaGAPDH to bind host proteins was analyzed by solid-phase ligand-binding assay. Results revealed that all R. anatipestifer isolates showed different levels of GAPDH activity except four strains, which contained a gapdh-like gene. The gapdh of R. anatipestifer, which is located phylogenetically in the same branch as enterohemorrhagic Escherichia coli (EHEC), belonged to class I GAPDH, and encoded a 36.7-kDa protein. All RaGAPDH-encoding gene sequences from field isolates of R. anatipestifer displayed 100% homology. The RaGAPDH localized on the extracellular membrane of several R. anatipestifer strains. Further, it was released into the culture medium, and exhibited GAPDH enzyme activity. We also confirmed the binding of RaGAPDH to plasminogen and fibrinogen. These results demonstrated that GAPDH was present in R. anatipestifer, although not in all strains, and that RaGAPDH might contribute to the microorganism's virulence.\",\n \"corpus_id\": 6888725,\n \"score\": 2\n },\n {\n \"doc_id\": \"25614994\",\n \"title\": \"\\\"Moonlighting\\\" GAPDH Protein Localizes with AMPA Receptor GluA2 and L1 Axonal Cell Adhesion Molecule at Fiber Cell Borders in the Lens.\",\n \"abstract\": \"PURPOSE: The canonical role of glyceraldehyde phosphate dehydrogenase (GAPDH) is as an enzyme in glycolysis. GAPDH is also a principal \\\"moonlighting\\\" protein with additional roles at diverse sites in a variety of cells. Surface GAPDH on mammalian, yeast, and bacterial cells acts as a receptor and also mediates cell contacts. In neurons, extracellular GAPDH localizes at synapses. Two GAPDH binding partners at synapses are α-Amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid glutamate receptor (AMPA) GluA2 subunit at dendritic spines and L1 cell adhesion molecule at pre-synaptic membranes, and both proteins are also expressed in lenses. Fiber cell membrane protrusions and dendritic spines have similar size, shape, and spacing, contain F-actin, and express clathrin/AP-2 Adaptor at their surfaces linked with Tyr-phosphatase STEP-regulated endocytosis of AMPA/GluA2 receptors. AMPA receptors work with NMDA (N-methyl-d-aspartate) and GABA (γ-aminobutyric acid) receptors, calcium calmodulin kinase II (CaMKIIα), channel proteins, STEP, and ephrin receptors, which are also expressed in lenses. In neurons, coordinate AMPA/GluA2 receptor endocytosis with GAPDH is linked with disease. GAPDH was previously characterized as a fiber cell membrane protein and shown to decrease substantially in interior fiber cells in human age-related cataract. Here, we examined GAPDH spatial expression in healthy lenses in two vertebrate species. METHODS: In situ methods were used to examine GAPDH expression in lenses of healthy young adult rabbits and chickens. Immunoblots were used to detect L1 in lenses. RESULTS: The present study demonstrated that GAPDH is present at fiber cell borders in adult rabbit and chicken lenses with evidence of focal concentrations along the fiber cell perimeter, and overlapped with detection of p-Tyr-GluA2, L1, STEP, actin and clathrin. We observed that L1-140 kDa was the prominent form in lens. CONCLUSIONS: Our findings indicate investigations into GAPDH \\\"moonlighting\\\" activities similar to its role in cell-cell interactions at neuron surfaces are warranted in the lens.\",\n \"corpus_id\": 207451998,\n \"score\": 2\n },\n {\n \"doc_id\": \"25870284\",\n \"title\": \"Glycolytic flux controls D-serine synthesis through glyceraldehyde-3-phosphate dehydrogenase in astrocytes.\",\n \"abstract\": \"D-Serine is an essential coagonist with glutamate for stimulation of N-methyl-D-aspartate (NMDA) glutamate receptors. Although astrocytic metabolic processes are known to regulate synaptic glutamate levels, mechanisms that control D-serine levels are not well defined. Here we show that d-serine production in astrocytes is modulated by the interaction between the D-serine synthetic enzyme serine racemase (SRR) and a glycolytic enzyme, glyceraldehyde 3-phosphate dehydrogenase (GAPDH). In primary cultured astrocytes, glycolysis activity was negatively correlated with D-serine level. We show that SRR interacts directly with GAPDH, and that activation of glycolysis augments this interaction. Biochemical assays using mutant forms of GAPDH with either reduced activity or reduced affinity to SRR revealed that GAPDH suppresses SRR activity by direct binding to GAPDH and through NADH, a product of GAPDH. NADH allosterically inhibits the activity of SRR by promoting the disassociation of ATP from SRR. Thus, astrocytic production of D-serine is modulated by glycolytic activity via interactions between GAPDH and SRR. We found that SRR is expressed in astrocytes in the subiculum of the human hippocampus, where neurons are known to be particularly vulnerable to loss of energy. Collectively, our findings suggest that astrocytic energy metabolism controls D-serine production, thereby influencing glutamatergic neurotransmission in the hippocampus.\",\n \"corpus_id\": 24884128,\n \"score\": 2\n },\n {\n \"doc_id\": \"26781495\",\n \"title\": \"Identification of Surface Proteins from Lactobacillus casei BL23 Able to Bind Fibronectin and Collagen.\",\n \"abstract\": \"Strains of lactobacilli show the capacity to attach to extracellular matrix proteins. Cell-wall fractions of Lactobacillus casei BL23 enriched in fibronectin, and collagen-binding proteins were isolated. Mass spectrometry analysis of their protein content revealed the presence of stress-related proteins (GroEL, ClpL), translational elongation factors (EF-Tu, EF-G), oligopeptide solute-binding proteins, and the glycolytic enzymes enolase and glyceraldehyde-3-phosphate dehydrogenase (GAPDH). The latter two enzymes were expressed in Escherichia coli and purified as glutathione-S-transferase (GST) fusion proteins, and their in vitro binding activity to fibronectin and collagen was confirmed. These results reinforce the idea that lactobacilli display on their surfaces a variety of moonlighting proteins that can be important in their adaptation to survive at intestinal mucosal sites and in the interaction with host cells.\",\n \"corpus_id\": 21781645,\n \"score\": 2\n },\n {\n \"doc_id\": \"26946538\",\n \"title\": \"Lactobacillus acidophilus binds to MUC3 component of cultured intestinal epithelial cells with highest affinity.\",\n \"abstract\": \"Lactobacillus strains have been shown to adhere to the mucosal components of intestinal epithelial cells. However, established in vitro adhesion assays have several drawbacks in assessing the adhesion of new Lactobacillus strains. The present study aimed to compare the adhesion of four different Lactobacillus strains and select the most adherent microbe, based on in silico approach supported by in vitro results. The mucus-binding proteins in Lactobacillus acidophilus, L. plantarum, L. brevis and L. fermentum were identified and their capacities to interact with intestinal mucin were compared by molecular docking analysis. Lactobacillus acidophilus had the maximal affinity of binding to mucin with predicted free energy of -6.066 kcal mol(-1) Further, in vitro experimental assay of adhesion was performed to validate the in silico results. The adhesion of L. acidophilus to mucous secreting colon epithelial HT-29 MTX cells was highest at 12%, and it formed biofilm with maximum depth (Z = 84 μm). Lactobacillus acidophilus was determined to be the most adherent strain in the study. All the Lactobacillus strains tested in this study, displayed maximum affinity of binding to MUC3 component of mucus as compared to other gastrointestinal mucins. These findings may have importance in the design of probiotics and health care management.\",\n \"corpus_id\": 30542391,\n \"score\": 2\n },\n {\n \"doc_id\": \"27350617\",\n \"title\": \"Carbohydrate-binding specificities of potential probiotic Lactobacillus strains in porcine jejunal (IPEC-J2) cells and porcine mucin.\",\n \"abstract\": \"Bacterial lectins are carbohydrate-binding adhesins that recognize glycoreceptors in the gut mucus and epithelium of hosts. In this study, the contribution of lectin-like activities to adhesion of Lactobacillus mucosae LM1 and Lactobacillus johnsonii PF01, which were isolated from swine intestine, were compared to those of the commercial probiotic Lactobacillus rhamnosus GG. Both LM1 and PF01 strains have been reported to have good adhesion ability to crude intestinal mucus of pigs. To confirm this, we quantified their adhesion to porcine gastric mucin and intestinal porcine enterocytes isolated from the jejunum of piglets (IPEC-J2). In addition, we examined their carbohydrate-binding specificities by suspending bacterial cells in carbohydrate solutions prior to adhesion assays. We found that the selected carbohydrates affected the adherences of LM1 to IPEC-J2 cells and of LGG to mucin. In addition, compared to adhesion to IPEC-J2 cells, adhesion to mucin by both LM1 and LGG was characterized by enhanced specific recognition of glycoreceptor components such as galactose, mannose, and N-acetylglucosamine. Hydrophobic interactions might make a greater contribution to adhesion of PF01. A similar adhesin profile between a probiotic and a pathogen, suggest a correlation between shared pathogen-probiotic glycoreceptor recognition and the ability to exclude enteropathogens such as Escherichia coli K88 and Salmonella Typhimurium KCCM 40253. These findings extend our understanding of the mechanisms of the intestinal adhesion and pathogen-inhibition abilities of probiotic Lactobacillus strains.\",\n \"corpus_id\": 14451370,\n \"score\": 2\n },\n {\n \"doc_id\": \"28533178\",\n \"title\": \"Mucin- and carbohydrate-stimulated adhesion and subproteome changes of the probiotic bacterium Lactobacillus acidophilus NCFM.\",\n \"abstract\": \"Adhesion to intestinal mucosa is a crucial property for probiotic bacteria. Adhesion is thought to increase host-bacterial interactions, thus potentially enabling health benefits to the host. Molecular events connected with adhesion and surface proteome changes were investigated for the probiotic Lactobacillus acidophilus NCFM cultured with established or emerging prebiotic carbohydrates as carbon source and in the presence of mucin, the glycoprotein of the epithelial mucus layer. Variation in adhesion to HT29-cells and mucin was associated with carbon source and mucin-induced subproteome abundancy differences. Specifically, while growth on fructooligosaccharides (FOS) only stimulated adhesion to intestinal HT-29 cells, cellobiose and polydextrose in addition increased adhesion to mucin. Adhesion to HT-29 cells increased by about 2-fold for bacteria grown on mucin-supplemented glucose. Comparative 2DE-MS surface proteome analysis showed different proteins in energy metabolism appearing on the surface, suggesting they exert moonlighting functions. Mucin-supplemented bacteria had relative abundance of pyruvate kinase and fructose-bisphosphate aldolase increased by about 2-fold while six spots with 3.2-2.1 fold reduced relative abundance comprised elongation factor G, phosphoglycerate kinase, BipAEFTU family GTP-binding protein, ribonucleoside triphosphate reductase, adenylosuccinate synthetase, 30S ribosomal protein S1, and manganese-dependent inorganic pyrophosphatase. Surface proteome of cellobiose- compared to glucose-grown L. acidophilus NCFM had phosphate starvation inducible protein stress-related, thermostable pullulanase, and elongation factor G increasing 4.4-2.4 fold, while GAPDH, elongation factor Ts, and pyruvate kinase were reduced by 2.0-1.5 fold in relative abundance. Addition of recombinant L. acidophilus NCFM elongation factor G and pyruvate kinase to a coated mucin layer significantly suppressed subsequent adhesion of the bacterium. BIOLOGICAL SIGNIFICANCE: Human diet is important for intestinal health and food components, especially non-digestible carbohydrates can beneficially modify the microbiota. In the present study, effects of emerging and established prebiotic carbohydrates on the probiotic potential of Lactobacillus acidophilus NCFM were investigated by testing adhesion to a mucin layer and intestinal cells, and comparing this with changes in abundancy of surface proteins thought to be important for host interactions. Increased adhesion was observed following culturing of the bacterium with fructooligosaccharides, cellobiose or polydextrose, as well as mucin-supplemented glucose as carbon source. Enhanced adhesion ability can prolong bacterial residence in GIT yielding positive health effects. Higher relative abundance of certain surface proteins under various conditions (i.e. grown on cellobiose or mucin-supplemented glucose) suggested involvement of these proteins in adhesion, as confirmed by competition in case of two recombinantly produced moonlighting proteins. Combination of Lactobacillus acidophilus NCFM with different carbohydrates revealed potential bacterial determinants of synbiotic interactions, including stimulation of adhesion.\",\n \"corpus_id\": 4016941,\n \"score\": 2\n },\n {\n \"doc_id\": \"28861445\",\n \"title\": \"Data regarding the growth of Lactobacillus acidophilus NCFM on different carbohydrates and recombinant production of elongation factor G and pyruvate kinase.\",\n \"abstract\": \"The present study describes the growth of the very well-known probiotic bacterium Lactobacillus acidophilus NCFM on different carbohydrates. Furthermore, recombinant production of putative moonlighting proteins elongation factor G and pyruvate kinase from this bacterium is described. For further and detailed interpretation of the data presented here, please see the research article \\\"Mucin- and carbohydrate-stimulated adhesion and subproteome changes of the probiotic bacterium Lactobacillus acidophilus NCFM\\\" (Celebioglu et al., 2017) [1].\",\n \"corpus_id\": 8363423,\n \"score\": 2\n },\n {\n \"doc_id\": \"29061520\",\n \"title\": \"Understanding the adhesion mechanism of a mucin binding domain from Lactobacillus fermentum and its role in enteropathogen exclusion.\",\n \"abstract\": \"Lactobacillus species possesses surface exposed Mucin Binding Protein (MucBP) which plays a role in adhesion to gastrointestinal mucin. MucBP contains one or more mucin binding domain (MBD), the functionality of which has yet not been characterized thoroughly. Here, we have characterized a 93-amino acid MBD (MBD93) of MucBP (LAF_0673) from Lactobacillus fermentum. Multiple sequence alignment of L. fermentum MBD93 exhibited ∼60% sequence homology with MBDs from other Lactobacillus species. Further, we cloned, expressed and purified MBD93 from Escherichia coli as N-terminal histidine-tagged protein (6X His-MBD93). The purified MBD93 was able to bind to mucin and showed strong affinity towards the terminally expressed mucin glycans viz. N-acetylgalactosamine (GalNAc), N-acetylglucosamine (GlcNAc), Galactose (Gal), and Sialic acid (N-acetylneuraminic acid; Neu5Ac). In silico experiments further confirmed the interaction between homology modeled MBD93 to mucin glycans through hydrogen-bonding with its surface amino acid residues Ser57, Pro58, Ile60, Tyr63 and Ala65. We also have demonstrated that MBD93 was able to inhibit the adhesion of enteric pathogens, including E. coli, Salmonella Paratyphi A, Shigella sonnei and Proteus vulgaris to mucin. Our results suggested that L. fermentum MBD93 is a functionally sufficient unit to act as an adhesin and to protect from invading enteric pathogens.\",\n \"corpus_id\": 3992929,\n \"score\": 2\n },\n {\n \"doc_id\": \"29229289\",\n \"title\": \"Expression of fibronectin-binding protein of L. acidophilus NCFM and in vitro refolding to adhesion capable native-like protein from inclusion bodies.\",\n \"abstract\": \"The ability of Lactobacilli to adhere to host epithelial surface and intestinal tracts is important for colonization and persistence of bacteria in the host gut. Extracellular matrix components like fibronectin, mucin, collagen and other adhesion molecules serve as substratum for attachment of bacteria. However, the precise structure, function and mechanism of binding of microbial surface adhesion proteins such as Fibronectin-binding protein (FBP) with host molecules remains unclear. This is primarily due to limitations in high expression of these proteins in biologically active form. To study adhesion of its FBP (64 kDa), the fbp gene of L. acidophilus NCFM was cloned and expressed in E. coli. However, the fibronectin-binding protein expressed in soluble form could not be purified by Ni-NTA affinity chromatography possibly because of partially buried Histidine tag in the recombinant fusion protein. Therefore, the protein was expressed as inclusion bodies (IBs) at 37 °C and solubilized in urea followed by purification in denatured form by Ni-NTA affinity chromatography. The purified denatured protein was refolded in vitro to structurally stable and biologically active form. The conformational properties of the refolded protein were studied by circular dichroism, which showed prominence of α+ β structural element. The refolded FBP also showed significant binding to human intestinal tissue sections. Our optimized refolding protocol from IBs of this recombinant probiotic FBP led into high amounts of biologically active protein. Our results help in increasing understanding of structure-function relation of surface adhesion proteins and host-microbial interactions.\",\n \"corpus_id\": 3435700,\n \"score\": 2\n },\n {\n \"doc_id\": \"29412508\",\n \"title\": \"Proteomics Analysis of the Adhesion Activity of Lactobacillus acidophilus ATCC 4356 Upon Growth in an Intestine-Like pH Environment.\",\n \"abstract\": \"Many health effects of Lactobacillus acidophilus are desirable among these the adhesion ability is vital to enhance the possibility of colonization and stabilization associated with the gut mucosal barrier. In this study, the growth characteristics and the adhesion activity of L. acidophilus in the intestine-like pH environment (pH 7.5) are identified. The number of bacteria adhering to the HT-29 cells is found with a gradual increase trend (pH 5.5-7.5). This also leads to the morphological changes of L. acidophilus after exposure to different pH environments. Furthermore, with the help of the isobaric tags for relative and absolute quantification (iTRAQ) proteomic analysis, 207 proteins are detected differentially expressed at pH of 7.5. The use of GO analysis and KEGG analysis indicates three essential pathways related to the cell envelope peptide-glycan biosynthesis, carbohydrate metabolism, and amino acid metabolism are obviously changed. Adhesion related surface protein fmtB and PrtP are upregulated in pH 7.5 group. While the moonlight proteins like pyruvate kinase, which binds specifically to the mucin layer and inhibits the adhesive activity of L. acidophilus, is found downregulated. These results could be useful to understand the adhesion mechanism of L. acidophilus adapting for the gut mucosal barrier in the intestinal environment.\",\n \"corpus_id\": 4327304,\n \"score\": 2\n },\n {\n \"doc_id\": \"18388461\",\n \"title\": \"Molecular cloning and characterization of a bile salt hydrolase from Lactobacillus acidophilus PF01.\",\n \"abstract\": \"Phenotypic screening for bile salt hydrolase (BSH) activity was performed on Lactobacillus acidophilus PF01 isolated from piglet feces. A gene encoding BSH was identified and cloned from the genomic library of L. acidophilus PF01. The bsh gene and surrounding regions were characterized by nucleotide sequence analysis and were found to contain a single open reading frame (ORF) of 951 nucleotides encoding a 316 amino acid protein. The potential bsh promoter region was located upstream of the start codon. The protein deduced from the complete ORF had high similarity with other BSHs, and four amino acid motifs located around the active site, FGRNXD, AGLNF, VLTNXP, and GXGXGXXGXPGD, were highly conserved. The bsh gene was cloned into the pET21b expression vector and expressed in Escherichia coli BLR(DE3) by induction with 0.1mM of isopropylthiogalactopyranoside. The BSH enzyme was purified with apparent homogeneity using a Ni2+-NTA agarose column and characterized. The overexpressed recombinant BSH enzyme of L. acidophilus PF01 exhibited hydrolase activity against tauroconjugated bile salts, but not glycoconjugated bile salts. It showed the highest activity against taurocholic acid. The maximum BSH activity occurred at approximately 40oC. The enzyme maintained approximately 70% of its maximum activity even at 60 degrees , whereas its activity rapidly decreased at below 37 degrees . The optimum pH was 6, and BSH activity was rapidly inactivated below pH 5 and above pH 7.\",\n \"corpus_id\": 22000866,\n \"score\": 1\n },\n {\n \"doc_id\": \"19233780\",\n \"title\": \"Temporal gene expression and probiotic attributes of Lactobacillus acidophilus during growth in milk.\",\n \"abstract\": \"Lactic acid bacteria have been used as starter strains in the production of fermented dairy products for centuries. Lactobacillus acidophilus is a widely recognized probiotic bacteria commonly added to yogurt and used in dietary supplements. In this study, a whole genome microarray was employed to monitor gene expression of L. acidophilus NCFM cells propagated in 11% skim milk during early, mid and late logarithmic phase, and stationary phase. Approximately 21% of 1,864 open reading frames were differentially expressed at least in one time point. Genes differentially expressed in skim milk included several members of the proteolytic enzyme system. Expression of prtP (proteinase precursor) and prtM (maturase) increased over time as well as several peptidases and transport systems. Expression of Opp1 (oligopeptide transport system 1) was highest at 4 h, whereas gene expression of Opp2 increased over time reaching its highest level at 12 h, suggesting that the 2 systems have different specificities. Expression of a 2-component regulatory system, previously shown to regulate acid tolerance and proteolytic activity, also increased during the early log and early stationary phases of growth. Expression of the genes involved in lactose utilization increased immediately (5 min) upon exposure to milk. The acidification activity, survival under storage conditions, and adhesion to mucin and Caco-2 tissue culture cells of selected mutants containing insertionally inactivated genes differentially expressed in the wild-type strain during growth in milk were examined for any potential links between probiotic properties and bacterial growth and survival in milk. Some of the most interesting genes found to be expressed in milk were correlated with signaling (autoinducer-2) and adherence to mucin and intestinal epithelial cells, in vitro.\",\n \"corpus_id\": 39378929,\n \"score\": 1\n },\n {\n \"doc_id\": \"19346347\",\n \"title\": \"Characterization of Rhamnosidases from Lactobacillus plantarum and Lactobacillus acidophilus.\",\n \"abstract\": \"Lactobacilli are known to use plant materials as a food source. Many such materials are rich in rhamnose-containing polyphenols, and thus it can be anticipated that lactobacilli will contain rhamnosidases. Therefore, genome sequences of food-grade lactobacilli were screened for putative rhamnosidases. In the genome of Lactobacillus plantarum, two putative rhamnosidase genes (ram1(Lp) and ram2(Lp)) were identified, while in Lactobacillus acidophilus, one rhamnosidase gene was found (ramA(La)). Gene products from all three genes were produced after introduction into Escherichia coli and were then tested for their enzymatic properties. Ram1(Lp), Ram2(Lp), and RamA(La) were able to efficiently hydrolyze rutin and other rutinosides, while RamA(La) was, in addition, able to cleave naringin, a neohesperidoside. Subsequently, the potential application of Lactobacillus rhamnosidases in food processing was investigated using a single matrix, tomato pulp. Recombinant Ram1(Lp) and RamA(La) enzymes were shown to remove the rhamnose from rutinosides in this material, but efficient conversion required adjustment of the tomato pulp to pH 6. The potential of Ram1(Lp) for fermentation of plant flavonoids was further investigated by expression in the food-grade bacterium Lactococcus lactis. This system was used for fermentation of tomato pulp, with the aim of improving the bioavailability of flavonoids in processed tomato products. While import of flavonoids into L. lactis appeared to be a limiting factor, rhamnose removal was confirmed, indicating that rhamnosidase-producing bacteria may find commercial application, depending on the technological properties of the strains and enzymes.\",\n \"corpus_id\": 25742385,\n \"score\": 1\n },\n {\n \"doc_id\": \"20033357\",\n \"title\": \"Cloning, expression, purification, and characterization of a novel esterase from Lactobacillus plantarum.\",\n \"abstract\": \"Lactobacillus plantarum is an important lactic acid bacterium, usually found as natural inhabitant of food, such as fermented vegetables and meat products. However, little information about lactic acid bacteria, especially concerning L. plantarum, as a source of useful enzymes has been reported. The aim of this study was to clone, express in Escherichia coli, purify, and characterize an esterase from L. plantarum ATCC 8014. The esterase gene (1014 bp) was amplified and cloned in pET14b expression vector to express a His(6)-tagged protein in E. coli. Recombinant L. plantarum esterase was purified by Ni-NTA resin, presenting an apparent molecular mass of about 38 kDa. It presented highest activity at pH 6.0 and 40 degrees C. Also, it presented preference for p-nitrophenyl butyrate, but hydrolyzed more efficiently p-nitrophenyl acetate. Besides, this study shows, for the first time, CD data about secondary structure of an esterase from L. plantarum.\",\n \"corpus_id\": 33110116,\n \"score\": 1\n },\n {\n \"doc_id\": \"20392597\",\n \"title\": \"Association of Lactobacillus acidophilus with mice Peyer's patches.\",\n \"abstract\": \"OBJECTIVE: To clarify the adhesion mechanism of Lactobacillus acidophilus to Peyer's patches. METHODS: Adhesion of L. acidophilus FN001 to mice Peyer's patches was studied in vitro using a fluorescent quantization method. The nature of adhesion mediator was studied by the differing effects of physical, chemical, and enzymatic pre-treatments of the bacteria and the inhibitory effects of sugars on the adhesion. The presence of lectin-like proteins on the cell surface was determined by hemagglutination assay. The effect of L. acidophilus FN001 on the inhibition of adhesion of pathogens to Peyer's patches was also studied. RESULTS: The adhesion of L. acidophilus FN001 was strongly inhibited in the presence of D-mannose and methyl-α-D-mannoside. Pretreatment of L. acidophilus FN001 with pepsin and trypsin decreased the adhesive capacity indicating that some cell surface proteins might be involved in the adhesion. L. acidophilus FN001 showed agglutinating activity toward the rabbit red cells in a mannose specific manner, which was decreased after protease pretreatment, suggesting possible occurrence of mannose specific lectin(s) on the L. acidophilus FN001 surface. In adhesion inhibition assay, L. acidophilus NF001, when applied to Peyer's patches first or at the same time with pathogen, significantly inhibited adhesion of Escherichia coli ATCC25922 to Peyer's patches. CONCLUSION: L. acidophilus FN001 contains some mannose-specific protein(s) on its surface that mediates its adhesion to the Peyer's patches. FN001 inhibits the adhesion of E. coli, which also contains mannose specific lectin.\",\n \"corpus_id\": 5674555,\n \"score\": 1\n },\n {\n \"doc_id\": \"20828617\",\n \"title\": \"Recombinant human sperm-specific glyceraldehyde-3-phosphate dehydrogenase (GAPDHS) is expressed at high yield as an active homotetramer in baculovirus-infected insect cells.\",\n \"abstract\": \"The sperm-specific glyceraldehyde-3-phosphate dehydrogenase (GAPDHS) isoform is a promising contraceptive target because it is specific to male germ cells, essential for sperm motility and male fertility, and well suited to pharmacological inhibition. However, GAPDHS is difficult to isolate from native sources and recombinant expression frequently results in high production of insoluble enzyme. We chose to use the Bac-to-Bac baculovirus-insect cell system to express a His-tagged form of human GAPDHS (Hu his-GAPDHS) lacking the proline-rich N-terminal sequence. This recombinant Hu his-GAPDHS was successfully produced in Spodoptera frugiperda 9 (Sf9) cells by infection with recombinant virus as a soluble, enzymatically active form in high yield, >35 mg/L culture. Biochemical characterization of the purified enzyme by mass spectrometry and size exclusion chromatography confirmed the presence of the tetrameric form. Further characterization by peptide ion matching mass spectrometry and Edman sequencing showed that unlike the mixed tetramer forms produced in bacterial expression systems, human his-GAPDHS expressed in baculovirus-infected insect cells is homotetrameric. The ability to express and purify active human GAPDHS as homotetramers in high amounts will greatly aid in drug discovery efforts targeting this enzyme for discovery of novel contraceptives and three compounds were identified as inhibitors of Hu his-GAPDHS from a pilot screen of 1120 FDA-approved compounds.\",\n \"corpus_id\": 7697867,\n \"score\": 1\n },\n {\n \"doc_id\": \"21131525\",\n \"title\": \"Lactobacillus plantarum extracellular chitin-binding protein and its role in the interaction between chitin, Caco-2 cells, and mucin.\",\n \"abstract\": \"In the present work, we describe the adhesion capabilities of a recombinant Lactococcus lactis strain producing an extracellular protein from Lactobacillus plantarum. Our results show that this protein may offer the bacterium a mechanism to bind to N-acetylglucosamine-containing polymers, such as human mucins, present in different environments.\",\n \"corpus_id\": 12226545,\n \"score\": 1\n },\n {\n \"doc_id\": \"21622166\",\n \"title\": \"Identification of the Lactobacillus SLP domain that binds gastric mucin.\",\n \"abstract\": \"Surface layer proteins (SLPs) of lactobacillus bacteria have some structural regions responsible for adhesion to the intestinal epithelium. To identify the SLP and the smallest domain within the protein that is responsible for the adhesion of the bacterium to the intestinal epithelium, L. plantarum strain CGMCC1258 was investigated in this study. Using bioinformatics and molecular techniques, we first identified and purified a novel protein, integral membrane protein-2 (IMP-2, 33-45 kDa) responsible for adhesion to gastric mucin. Truncated forms of IMP-2 were then constructed and expressed, and the amino acids from 515 to 575 (designated micro IMP, MIMP) was identified as the smallest domain responsible for adhesion to gastric mucin. Competing assay was performed, which further confirmed the ability of MIMP to compete with enteroinvasive E. coli and enteropathogenic E. coli to adhere to cells of a normal colon cell line, NCM460. Furthermore, MIMP could maturate dendritic cells. These findings set a foundation for further investigation on the role of MIMP in the treatment and prevention of inflammation-related diseases of the intestine.\",\n \"corpus_id\": 22794855,\n \"score\": 1\n },\n {\n \"doc_id\": \"24282406\",\n \"title\": \"Plant cytoplasmic GAPDH: redox post-translational modifications and moonlighting properties.\",\n \"abstract\": \"Glyceraldehyde-3-phosphate dehydrogenase (GAPDH) is a ubiquitous enzyme involved in glycolysis and shown, particularly in animal cells, to play additional roles in several unrelated non-metabolic processes such as control of gene expression and apoptosis. This functional versatility is regulated, in part at least, by redox post-translational modifications that alter GAPDH catalytic activity and influence the subcellular localization of the enzyme. In spite of the well established moonlighting (multifunctional) properties of animal GAPDH, little is known about non-metabolic roles of GAPDH in plants. Plant cells contain several GAPDH isoforms with different catalytic and regulatory properties, located both in the cytoplasm and in plastids, and participating in glycolysis and the Calvin-Benson cycle. A general feature of all GAPDH proteins is the presence of an acidic catalytic cysteine in the active site that is overly sensitive to oxidative modifications, including glutathionylation and S-nitrosylation. In Arabidopsis, oxidatively modified cytoplasmic GAPDH has been successfully used as a tool to investigate the role of reduced glutathione, thioredoxins and glutaredoxins in the control of different types of redox post-translational modifications. Oxidative modifications inhibit GAPDH activity, but might enable additional functions in plant cells. Mounting evidence support the concept that plant cytoplasmic GAPDH may fulfill alternative, non-metabolic functions that are triggered by redox post-translational modifications of the protein under stress conditions. The aim of this review is to detail the molecular mechanisms underlying the redox regulation of plant cytoplasmic GAPDH in the light of its crystal structure, and to provide a brief inventory of the well known redox-dependent multi-facetted properties of animal GAPDH, together with the emerging roles of oxidatively modified GAPDH in stress signaling pathways in plants.\",\n \"corpus_id\": 1666747,\n \"score\": 1\n },\n {\n \"doc_id\": \"25074810\",\n \"title\": \"Moonlighting cell-surface GAPDH recruits apotransferrin to effect iron egress from mammalian cells.\",\n \"abstract\": \"Iron (Fe(2+), Fe(3+)) homeostasis is a tightly regulated process, involving precise control of iron influx and egress from cells. Although the mechanisms of its import into cells by iron carrier molecules are well characterized, iron export remains poorly understood. The current paradigm envisages unique functions associated with specialized macromolecules for its cellular import (transferrin receptors) or export (ferroportin, also known as SLC40A1). Previous studies have revealed that iron-depleted cells recruit glyceraldehyde-3-phosphate dehydrogenase (GAPDH), a multitasking, 'moonlighting' protein, to their surface for internalization of the iron carrier holotransferrin. Here, we report that under the converse condition of intracellular iron excess, cells switch the isoform of GAPDH on their surface to one that now recruits iron-free apotransferrin in close association with ferroportin to facilitate the efflux of iron. Increased expression of surface GAPDH correlated with increased apotransferrin binding and enhanced iron export from cells, a capability lost in GAPDH-knockdown cells. These findings were confirmed in vivo utilizing a rodent model of iron overload. Besides identifying for the first time an apotransferrin receptor, our work uncovers the two-way switching of multifunctional molecules to manage cellular micronutrient requirements.\",\n \"corpus_id\": 9917899,\n \"score\": 1\n },\n {\n \"doc_id\": \"25246025\",\n \"title\": \"Glyceraldehyde-3-phosphate dehydrogenase (GAPDH) and Alzheimer's disease.\",\n \"abstract\": \"Glyceraldehyde-3-phosphate dehydrogenase (GAPDH) is a ubiquitous enzyme that catalyzes the sixth step of glycolysis and thus, serves to break down glucose for energy production. Beyond the traditional aerobic metabolism of glucose, recent studies have highlighted additional roles played by GAPDH in non-metabolic processes, such as control of gene expression and redox post-translational modifications. Neuroproteomics have revealed high affinity interactions between GAPDH and Alzheimer's disease-associated proteins, including the β-amyloid, β-amyloid precursor protein and tau. This neuronal protein interaction may lead to impairment of the GAPDH glycolytic function in Alzheimer's disease and may be a forerunner of its participation in apoptosis. The present review examines the crucial implication of GAPDH in neurodegenerative processes and clarifies its role in apoptotic cell death.\",\n \"corpus_id\": 19312008,\n \"score\": 1\n },\n {\n \"doc_id\": \"25721875\",\n \"title\": \"Identification and characterization of enolase as a collagen-binding protein in Lactobacillus plantarum.\",\n \"abstract\": \"Collagen is a target of pathogens for adhesion, colonization, and invasion of host tissue. Probiotic bacteria can mimic the same mechanism as used by the pathogens in the colonization process, expressing cell surface proteins that specifically interact with extracellular matrix component proteins. The capability to bind collagen is expressed by several Lactobacillus isolates, including some Lactobacillus plantarum strains. In this study we report the involvement of the L. plantarum EnoA1 alfa-enolase in type I collagen (CnI) binding. By adhesion assays, we show that the mutant strain LM3-CC1, carrying a null mutation in the enoA1 gene, binds to immobilized collagen less efficiently than wild type strain. CnI overlay assay and Elisa tests, performed on the purified EnoA1, show that this protein can bind collagen both under denaturing and native conditions. By using truncated recombinant enolase proteins, we also show that the region spanning from 73rd to the 140th amino acid residues is involved in CnI binding.\",\n \"corpus_id\": 45253710,\n \"score\": 1\n },\n {\n \"doc_id\": \"26378175\",\n \"title\": \"Dengue Virus NS1 Protein Modulates Cellular Energy Metabolism by Increasing Glyceraldehyde-3-Phosphate Dehydrogenase Activity.\",\n \"abstract\": \"UNLABELLED: Dengue is one of the main public health concerns worldwide. Recent estimates indicate that over 390 million people are infected annually with the dengue virus (DENV), resulting in thousands of deaths. Among the DENV nonstructural proteins, the NS1 protein is the only one whose function during replication is still unknown. NS1 is a 46- to 55-kDa glycoprotein commonly found as both a membrane-associated homodimer and a soluble hexameric barrel-shaped lipoprotein. Despite its role in the pathogenic process, NS1 is essential for proper RNA accumulation and virus production. In the present study, we identified that glyceraldehyde-3-phosphate dehydrogenase (GAPDH) interacts with intracellular NS1. Molecular docking revealed that this interaction occurs through the hydrophobic protrusion of NS1 and the hydrophobic residues located at the opposite side of the catalytic site. Moreover, addition of purified recombinant NS1 enhanced the glycolytic activity of GAPDH in vitro. Interestingly, we observed that DENV infection promoted the relocalization of GAPDH to the perinuclear region, where NS1 is commonly found. Both DENV infection and expression of NS1 itself resulted in increased GAPDH activity. Our findings indicate that the NS1 protein acts to increase glycolytic flux and, consequently, energy production, which is consistent with the recent finding that DENV induces and requires glycolysis for proper replication. This is the first report to propose that NS1 is an important modulator of cellular energy metabolism. The data presented here provide new insights that may be useful for further drug design and the development of alternative antiviral therapies against DENV. IMPORTANCE: Dengue represents a serious public health problem worldwide and is caused by infection with dengue virus (DENV). Estimates indicate that half of the global population is at risk of infection, with almost 400 million cases occurring per year. The NS1 glycoprotein is found in both the intracellular and the extracellular milieus. Despite the fact that NS1 has been commonly associated with DENV pathogenesis, it plays a pivotal but unknown role in the replication process. In an effort to understand the role of intracellular NS1, we demonstrate that glyceraldehyde-3-phosphate dehydrogenase (GAPDH) interacts with NS1. Our results indicate that NS1 increases the glycolytic activity of GAPDH in vitro. Interestingly, the GAPDH activity was increased during DENV infection, and NS1 expression alone was sufficient to enhance intracellular GAPDH activity in BHK-21 cells. Overall, our findings suggest that NS1 is an important modulator of cellular energy metabolism by increasing glycolytic flux.\",\n \"corpus_id\": 3086859,\n \"score\": 1\n },\n {\n \"doc_id\": \"28864008\",\n \"title\": \"Temporal and spatial expression of glyceraldehyde 3-phosphate dehydrogenase (Gapdh) in the mouse placenta.\",\n \"abstract\": \"Glucose metabolism in trophoblast cells is essential to provide the required energy for the development and function of the placenta. Glyceraldehyde 3-phosphate dehydrogenase (Gapdh), a key enzyme in the glycolysis pathway has been considered ubiquitously expressed in cells. There is, however, a growing body of evidence suggesting that Gapdh has many functions in pathways unrelated to glucose metabolism. In the present study, we show that GAPDH expression and sub-cellular localization changes through gestation in the mouse placenta. Our findings raise the possibility that GAPDH has multiple functions in trophoblast cells and the developing placenta, while also cautioning against its use as an endogenous reference or standard for gene expression in the placenta.\",\n \"corpus_id\": 26825081,\n \"score\": 1\n },\n {\n \"doc_id\": \"29205785\",\n \"title\": \"Plant Polyphenols Stimulate Adhesion to Intestinal Mucosa and Induce Proteome Changes in the Probiotic Lactobacillus acidophilus NCFM.\",\n \"abstract\": \"SCOPE: Plant phenolics, known to exert beneficial effects on human health, were supplemented to cultures of the probiotic bacterium Lactobacillus acidophilus NCFM (NCFM) to assess their effect on its adhesive capacity and the abundancy of individual proteins. METHODS AND RESULTS: The presence of resveratrol and ferulic acid during bacterial growth stimulated adhesion of NCFM to mucin and human intestinal HT-29 cells, while tannic acid improved adhesion only to HT-29 cells and caffeic acid had very modest effect overall. Some dosage dependence was found for the four phenolics supplemented at 100, 250, and 500 μg mL-1 to the cultures. Notably, 500 μg mL-1 ferulic acid only stimulated adhesion to mucin. Analyses of differential whole-cell as well as surface proteomes revealed relative abundancy changes for a total of 27 and 22 NCFM proteins, respectively. These changes include enzymes acting in metabolic pathways, such as glycolysis, nucleotide metabolism, and stress response, as well as known moonlighting or surface-associated proteins. CONCLUSION: The five plant phenolics found in various foods stimulate the adhesive capacity of NCFM in diverse ways and elicit relative abundancy changes of specific proteins, providing molecular level insight into the mechanism of the putative beneficial effects of the polyphenols.\",\n \"corpus_id\": 3422937,\n \"score\": 1\n },\n {\n \"doc_id\": \"29574117\",\n \"title\": \"GAPDH as a model non-canonical AU-rich RNA binding protein.\",\n \"abstract\": \"Glyceraldehyde-3-phosphate dehydrogenase (GAPDH) plays a key role in glycolysis but is also known for its involvement in a myriad of extra-glycolytic functions. While GAPDH is not the only enzyme with established moonlighting roles, it shows great diversity in terms of its functions, cellular localizations, protein partners, and post-translational modifications. This review focuses on GAPDH's role as a non-canonical RNA binding protein to regulate the stability and translation of cellular mRNAs. Despite the clear involvement of GAPDH in gene expression regulation, how and where GAPDH binds to its RNA targets is still unknown. In addition, the mechanism by which GAPDH switches among its various cellular functions is also unknown. This review will summarize our current understanding of GAPDH-mediated regulation of RNA function.\",\n \"corpus_id\": 22951427,\n \"score\": 1\n },\n {\n \"doc_id\": \"18298409\",\n \"title\": \"Regulation of plant cytosolic glyceraldehyde 3-phosphate dehydrogenase isoforms by thiol modifications.\",\n \"abstract\": \"Cytosolic NAD-dependent glyceraldehyde 3-P dehydrogenase (GAPDH; GapC; EC 1.2.1.12) catalyzes the oxidation of triose phosphates during glycolysis in all organisms, but additional functions of the protein has been put forward. Because of its reactive cysteine residue in the active site, it is susceptible to protein modification and oxidation. The addition of GSSG, and much more efficiently of S-nitrosoglutathione, was shown to inactivate the enzymes from Arabidopsis thaliana (isoforms GapC1 and 2), spinach, yeast and rabbit muscle. Inactivation was fully or at least partially reversible upon addition of DTT. The incorporation of glutathione upon formation of a mixed disulfide could be shown using biotinylated glutathione ethyl ester. Furthermore, using the biotin-switch assay, nitrosylated thiol groups could be shown to occur after treatment with nitric oxide donors. Using mass spectrometry and mutant proteins with one cysteine lacking, both cysteines (Cys-155 and Cys-159) were found to occur as glutathionylated and as nitrosylated forms. In preliminary experiments, it was shown that both GapC1 and GapC2 can bind to a partial gene sequence of the NADP-dependent malate dehydrogenase (EC 1.2.1.37; At5g58330). Transiently expressed GapC-green fluorescent protein fusion proteins were localized to the nucleus in A. thaliana protoplasts. As nuclear localization and DNA binding of GAPDH had been shown in numerous systems to occur upon stress, we assume that such mechanism might be part of the signaling pathway to induce increased malate-valve capacity and possibly other protective systems upon overreduction and initial formation of reactive oxygen and nitrogen species as well as to decrease and protect metabolism at the same time by modification of essential cysteine residues.\",\n \"corpus_id\": 25470362,\n \"score\": 0\n },\n {\n \"doc_id\": \"19160814\",\n \"title\": \"[Cloning, expression and characterization of a heterodimeric beta-galactosidase from Lactobacillus acidophilus ATCC 4356].\",\n \"abstract\": \"UNLABELLED: Heterodimeric beta-galactosidase of Lactobacillus acidophilus belongs to glycoside hydrolase family 2, encoded by two overlapping and translational coupling genes, lacL and lacM. The lacL and lacM genes of the sequenced strain L. acidophilus NCFM encode polypeptides with calculated molecular masses of 73,253 and 35,817 Da, respectively. OBJECTIVE: To clone, overexpress and characterize the enzyme in Escherichia coli. METHODS: We cloned the fragment (2834 bp) containing ribose-binding site (RBS) and coding regions of the lacLM genes from L. acidophilus ATCC 4356 into expression vector pQE31. RBS and HIS-Tag of pQE31 were substituted by inserted fragment. Recombinant plasmid was electrotransformed into E. coli JM109. Expression product was purified by ammonium sulphate fractionation, anion-exchange, affinity chromatography and gel permeation. Native molecular mass of homogenous enzyme was measured by gel permeation, and beta-galactosidase activity was determined by using o-nitrophenyl-beta-D-galactopyranoside (ONPG) as the substrate. RESULTS: Overexpression of the soluble enzyme in E. coli was achieved. Amino acid residue 512 of recombinant LacL was different from that of L. acidophilus NCFM. Homogenous enzyme was obtained by purification. The homogenous enzyme had a specific activity of 226 U/mg protein, a native molecular mass of 96.3+/-4.6 kDa, an optimum temperature at 49 degrees C and an optimum pH of 7. The Km and Vmax values of the enzyme were 2.18+/-0.12 mmol/L, 273+/-5 U/mg protein respectively.\",\n \"corpus_id\": 7280802,\n \"score\": 0\n },\n {\n \"doc_id\": \"20030066\",\n \"title\": \"[Expression profile analysis of intestinal Caco-2 cells treated with Lactobacillus acidophilus NCFM].\",\n \"abstract\": \"OBJECTIVE: Lactobacillus acidophilus NCFM is a probiotic strain that promotes human health. We evaluated the influence of Lactobacillus acidophilus NCFM on the genetic expression patterns in the Caco-2 cells. METHODS: Caco-2 cells were treated with Lactobacillus acidophilus NCFM for 2h. The total RNA of cells was extracted. Hybridization with Human Genome U133 Plus 2.0 Array was performed. The image scanning and data analysis were performed subsequently. Genes with significant expression changes were selected and analyzed. To support the microarray data, three striking difference genes were studied using Real-time RT PCR. RESULTS: Microarrays analysis showed that the expression levels of 508 genes were altered as compared with the control 473 of them were up-regulated, and 35 were down-regulated. It was supposed that many genes in Caco-2 cell were induced, so that Lactobacillus acidophilus NCFM could play a part in immune system process, antioxidant activity, biological adhesion, cholesterol absorption and so on. Three striking difference genes CCL2, PTX3 and TNFRSF9 which involved immune system process were validated by Real-time RT PCR. And the results of Real-time RT PCR showed the same expression trend as in microarray. CONCLUSION: Based on the results of gene expression alterations, the beneficial function of Lactobacillus acidophilus NCFM could be more greatly and deeply understood than ever before, and the mechanism of lactic acid bacteria would be revealed.\",\n \"corpus_id\": 25294185,\n \"score\": 0\n },\n {\n \"doc_id\": \"22847419\",\n \"title\": \"Glyceraldehyde-3-phosphate dehydrogenase (GAPDH) induces cancer cell senescence by interacting with telomerase RNA component.\",\n \"abstract\": \"Oxidative stress regulates telomere homeostasis and cellular aging by unclear mechanisms. Glyceraldehyde 3-phosphate dehydrogenase (GAPDH) is a key mediator of many oxidative stress responses, involving GAPDH nuclear translocation and induction of cell death. We report here that GAPDH interacts with the telomerase RNA component (TERC), inhibits telomerase activity, and induces telomere shortening and breast cancer cell senescence. The Rossmann fold containing NAD(+) binding region on GAPDH is responsible for the interaction with TERC, whereas a lysine residue in the GAPDH catalytic domain is required for inhibiting telomerase activity and disrupting telomere maintenance. Furthermore, the GAPDH substrate glyceraldehyde-3-phosphate (G3P) and the nitric oxide donor S-nitrosoglutathione (GSNO) both negatively regulate GAPDH inhibition of telomerase activity. Thus, we demonstrate that GAPDH is regulated to target the telomerase complex, resulting in an arrest of telomere maintenance and cancer cell proliferation.\",\n \"corpus_id\": 26847560,\n \"score\": 0\n },\n {\n \"doc_id\": \"23401169\",\n \"title\": \"Activities of free and encapsulated Lactobacillus acidophilus LA5 or Lactobacillus casei 01 in processed longan juices on exposure to simulated gastrointestinal tract.\",\n \"abstract\": \"BACKGROUND: Fruit drinks containing probiotics are gaining interest in the global marketplace. For example, longan juice, containing carbohydrate and various bioactive components, is a potentially health-promoting beverage as well as probiotic carrier for human consumption. In this study, high-pressure and thermal processes were applied to eliminate competitive micro-organisms in longan juice prior to the addition of Lactobacillus acidophilus LA5 or Lactobacillus casei 01. The activities of these probiotics in a simulated gastrointestinal tract were also investigated. RESULTS: Encapsulated probiotics could survive in the acidic environment of the stomach and small intestine, while the free cells were completely eliminated. In the colon experiment, the influence of encapsulated L. casei 01 on colon lactobacilli was significantly greater than that of encapsulated L. acidophilus LA5. Both encapsulated probiotics suspended in processed longan juices led to extensive increases in the formation of lactic acid and short-chain fatty acids (SCFA). Acetate was the major SCFA produced by colon bacteria, followed by propionate and butyrate. The discernible clear zone suggested that L. casei 01 provided greater antibacterial activity than L. acidophilus LA5. CONCLUSION: Both encapsulated probiotics along with processed longan juice led to significant increases in colon lactobacilli, lactic acid and SCFA formation.\",\n \"corpus_id\": 13046861,\n \"score\": 0\n },\n {\n \"doc_id\": \"25425319\",\n \"title\": \"The domestication of the probiotic bacterium Lactobacillus acidophilus.\",\n \"abstract\": \"Lactobacillus acidophilus is a Gram-positive lactic acid bacterium that has had widespread historical use in the dairy industry and more recently as a probiotic. Although L. acidophilus has been designated as safe for human consumption, increasing commercial regulation and clinical demands for probiotic validation has resulted in a need to understand its genetic diversity. By drawing on large, well-characterised collections of lactic acid bacteria, we examined L. acidophilus isolates spanning 92 years and including multiple strains in current commercial use. Analysis of the whole genome sequence data set (34 isolate genomes) demonstrated L. acidophilus was a low diversity, monophyletic species with commercial isolates essentially identical at the sequence level. Our results indicate that commercial use has domesticated L. acidophilus with genetically stable, invariant strains being consumed globally by the human population.\",\n \"corpus_id\": 1238128,\n \"score\": 0\n },\n {\n \"doc_id\": \"25635270\",\n \"title\": \"Effect of iron on the probiotic properties of the vaginal isolate Lactobacillus jensenii CECT 4306.\",\n \"abstract\": \"The vaginal microbiota of healthy, fertile women is dominated by lactobacilli. As a defence mechanism, these bacteria produce H₂O₂ to discourage colonization of the vagina by undesirable micro-organisms. In particular, Lactobacillus jensenii CECT 4306 is a strong producer of H₂O₂ and has been found to protect itself from the bactericidal effects of this compound through the activity of extracellular peroxidases. However, this peroxidase activity is dependent on the presence of Fe(3+), which is found in elevated concentrations in the vaginal mucosa as a consequence of the menstrual discharge. The aim of the present work was to evaluate whether Fe(3+) is able to modulate other potential probiotic properties of strain 4306. We found that Fe(3+) enhances the adhesion of L. jensenii CECT 4306 to mucin and to HT-29 and HT-29 MTX cells, and, in addition, improves the anti-inflammatory profile, as judged by an increase in the ratio of IL-10/IL-12p70 that were secreted by macrophages. A comparison of total, secreted and surface proteins produced in the presence and absence of Fe(3+) revealed significant differences in the concentration of the moonlighting protein glyceraldehyde-3-phosphate dehydrogenase (GAPDH). In conclusion, Fe(3+) seems to improve the probiotic characteristics of L. jensenii CECT 4306, and future research of the interactions of this strain with its vaginal environment may reveal further information about different aspects of its probiotic potential.\",\n \"corpus_id\": 23056969,\n \"score\": 0\n },\n {\n \"doc_id\": \"26544973\",\n \"title\": \"Lactobacillus acidophilus-Rutin Interplay Investigated by Proteomics.\",\n \"abstract\": \"Dietary polyphenols are bioactive molecules that beneficially affect human health, due to their anti-oxidant, anti-inflammatory, cardio-protective and chemopreventive properties. They are absorbed in a very low percentage in the small intestine and reach intact the colon, where they are metabolized by the gut microbiota. Although it is well documented a key role of microbial metabolism in the absorption of polyphenols and modulation of their biological activity, molecular mechanisms at the basis of the bacteria-polyphenols interplay are still poorly understood. In this context, differential proteomics was applied to reveal adaptive response mechanisms that enabled a potential probiotic Lactobacillus acidophilus strain to survive in the presence of the dietary polyphenol rutin. The response to rutin mainly modulated the expression level of proteins involved in general stress response mechanisms and, in particular, induced the activation of protein quality control systems, and affected carbohydrate and amino acid metabolism, protein synthesis and cell wall integrity. Moreover, rutin triggered the expression of proteins involved in oxidation-reduction processes. This study provides a first general view of the impact of dietary polyphenols on metabolic and biological processes of L. acidophilus.\",\n \"corpus_id\": 11226590,\n \"score\": 0\n },\n {\n \"doc_id\": \"26582368\",\n \"title\": \"The E3 ubiquitin-ligase SEVEN IN ABSENTIA like 7 mono-ubiquitinates glyceraldehyde-3-phosphate dehydrogenase 1 isoform in vitro and is required for its nuclear localization in Arabidopsis thaliana.\",\n \"abstract\": \"The E3 ubiquitin-protein ligases are associated to various processes such as cell cycle control and diverse developmental pathways. Arabidopsis thaliana SEVEN IN ABSENTIA like 7, which has ubiquitin ligase activity, is located in the nucleus and cytosol and is expressed at several stages in almost all plant tissues suggesting an important role in plant functions. However, the mechanism underlying the regulation of this protein is unknown. Since we found that the SEVEN IN ABSENTIA like 7 gene expression is altered in plants with impaired mitochondria, and in plants deficient in the glycolytic enzyme glyceraldehyde-3-phosphate dehydrogenase 1, we decided to study the possible interactions between both proteins as potential partners in plant signaling functions. We found that SEVEN IN ABSENTIA like 7 is able to interact in vitro with glyceraldehyde-3-phosphate dehydrogenase and that the Lys231 residue of the last is essential for this function. Following the interaction, a concomitant increase in the glyceraldehyde-3-phosphate dehydrogenase catalytic activity was observed. However, when SEVEN IN ABSENTIA like 7 was supplemented with E1 and E2 proteins to form a complete E1-E2-E3 modifier complex, we observed the mono-ubiquitination of glyceraldehyde-3-phosphate dehydrogenase 1 at the Lys76 residue and a dramatic decrease of its catalytic activity. Moreover, we found that localization of glyceraldehyde-3-phosphate dehydrogenase 1 in the nucleus is dependent on the expression SEVEN IN ABSENTIA like 7. These observations suggest that the association of both proteins might result in different biological consequences in plants either through affecting the glycolytic flux or via cytoplasm-nucleus relocation.\",\n \"corpus_id\": 205992188,\n \"score\": 0\n },\n {\n \"doc_id\": \"28411221\",\n \"title\": \"An Extracellular Cell-Attached Pullulanase Confers Branched α-Glucan Utilization in Human Gut Lactobacillus acidophilus.\",\n \"abstract\": \"Of the few predicted extracellular glycan-active enzymes, glycoside hydrolase family 13 subfamily 14 (GH13_14) pullulanases are the most common in human gut lactobacilli. These enzymes share a unique modular organization, not observed in other bacteria, featuring a catalytic module, two starch binding modules, a domain of unknown function, and a C-terminal surface layer association protein (SLAP) domain. Here, we explore the specificity of a representative of this group of pullulanases, Lactobacillus acidophilus Pul13_14 (LaPul13_14), and its role in branched α-glucan metabolism in the well-characterized Lactobacillus acidophilus NCFM, which is widely used as a probiotic. Growth experiments with L. acidophilus NCFM on starch-derived branched substrates revealed a preference for α-glucans with short branches of about two to three glucosyl moieties over amylopectin with longer branches. Cell-attached debranching activity was measurable in the presence of α-glucans but was repressed by glucose. The debranching activity is conferred exclusively by LaPul13_14 and is abolished in a mutant strain lacking a functional LaPul13_14 gene. Hydrolysis kinetics of recombinant LaPul13_14 confirmed the preference for short-branched α-glucan oligomers consistent with the growth data. Curiously, this enzyme displayed the highest catalytic efficiency and the lowest Km reported for a pullulanase. Inhibition kinetics revealed mixed inhibition by β-cyclodextrin, suggesting the presence of additional glucan binding sites besides the active site of the enzyme, which may contribute to the unprecedented substrate affinity. The enzyme also displays high thermostability and higher activity in the acidic pH range, reflecting adaptation to the physiologically challenging conditions in the human gut. IMPORTANCE Starch is one of the most abundant glycans in the human diet. Branched α-1,6-glucans in dietary starch and glycogen are nondegradable by human enzymes and constitute a metabolic resource for the gut microbiota. The role of health-beneficial lactobacilli prevalent in the human small intestine in starch metabolism remains unexplored in contrast to colonic bacterial residents. This study highlights the pivotal role of debranching enzymes in the breakdown of starchy branched α-glucan oligomers (α-limit dextrins) by human gut lactobacilli exemplified by Lactobacillus acidophilus NCFM, which is one of the best-characterized strains used as probiotics. Our data bring novel insight into the metabolic preference of L. acidophilus for α-glucans with short α-1,6-branches. The unprecedented affinity of the debranching enzyme that confers growth on these substrates reflects its adaptation to the nutrient-competitive gut ecological niche and constitutes a potential advantage in cross-feeding from human and bacterial dietary starch metabolism.\",\n \"corpus_id\": 41564431,\n \"score\": 0\n },\n {\n \"doc_id\": \"28539286\",\n \"title\": \"[Expression, purification and activity analysis of GGDEF and EAL domain-containing proteins from Lactobacillus acidophilus].\",\n \"abstract\": \"OBJECTIVE: To identify the functions of the proteins containing the GGDEF or EAL domain in Lactobacillus acidophilus for investigation of the regulatory mechanism of c-di-GMP in this strain. METHODS: The DNA fragments of NH13_07045-GGDEF, NH13_07050 and NH13_07055 from Lactobacillus acidophilus ATCC4356 were amplified by PCR and cloned into the expression vector pMAL-His-c2. After sequencing, the recombinant plasmids were transformed into competent Escherichia coli cells, which were induced by IPTG to express the recombinant proteins fused with maltose binding protein (MBP). The fusion proteins were purified using amylose resin column for diguanylate cyclase (DGC) or phosphodiesterase (PDE) activity assays in vitro followed by analysis with high-performance liquid chromatography (HPLC). RESULTS: The target DNA fragments were obtained by PCR, and their sequences were all identical to that in GenBank. The purified and concentrated fusion proteins, which were identified by SDS-PAGE and Western blotting, had relative molecular masses of 59 kD, 67 kD and 72 kD. HPLC analysis showed no DGC activity in NH13_07045-GGDEF, while PDE activity was found in NH13_07050 but not in NH13_07055. CONCLUSION: We obtained the protein encoded by NH13_07050 that possesses PDE activity in vitro. This protein may facilitate the evaluation of the regulatory function of c-di-GMP in Lactobacillus acidophilus.\",\n \"corpus_id\": 25041923,\n \"score\": 0\n },\n {\n \"doc_id\": \"28992252\",\n \"title\": \"Uromodulin-SlpA binding dictates Lactobacillus acidophilus uptake by intestinal epithelial M cells.\",\n \"abstract\": \"Bacterial access to the gut immune system is a crucial process to promote host immune responses. The probiotic L-92 strain of Lactobacillus acidophilus exerts anti-allergic immunomodulatory effects upon oral administration in mice. Here, we show that microfold cells (M cells) are responsible for L-92 internalization for evoking L-92-mediated immune responses. L-92 specifically bound to uromodulin, a glycosylphosphatidylinositol-anchored protein expressed exclusively on M cells among intestinal epithelial cells. Internalization of L-92 into M cells was significantly reduced in uromodulin-deficient (Umod-/-) mice compared to Umod+/+ mice. Furthermore, the binding of L-92 to uromodulin was significantly decreased after removal of surface layer protein A (SlpA) from the bacteria. Our study thus revealed a crucial role of uromodulin on the M-cell surface for the uptake of SlpA-positive lactic acid bacteria into M cells, possibly leading to subsequent delivery of the bacteria to dendritic cells closely associated with M cells for immunomodulation. Our study also shed light on the possibility that SlpA and uromodulin could be used as vehicle and target, respectively, for efficient mucosal vaccine delivery.\",\n \"corpus_id\": 37781861,\n \"score\": 0\n },\n {\n \"doc_id\": \"29747062\",\n \"title\": \"Biochemical characterization of a recombinant Lactobacillus acidophilus strain expressing exogenous FomA protein.\",\n \"abstract\": \"In previous research, to combine the immunogenicity of Fusobacterium nucleatum (F. nucleatum) and the probiotic properties of Lactobacillus acidophilus (L. acidophilus), we constructed a FomA-expressing L. acidophilus strain and assessed its immunogenicity. Our findings indicated that oral administration of the recombinant L. acidophilus strain reduced the risk of periodontal infection by Porphyromonas gingivalis (P. gingivalis) and F. nucleatum. However, because the exogenous FomA is an heterologous protein for the original bacterium, in this study, we assessed whether the biochemical characteristics of the recombinant L. acidophilus strain change due to the expression of the exogenous FomA protein. OBJECTIVES: To test the biochemical characteristics of a recombinant L. acidophilus strain expressing exogenous FomA and assess its antibiotic sensitivity. DESIGNS: We assessed the colony morphology, growth, acid production, and carbohydrate fermentation abilities of the recombinant L. acidophilus strain. In addition, we tested the adhesive ability and antimicrobial activity of the recombinant and assessed its antibiotic sensitivity through a drug susceptibility test. RESULTS: The experimental results showed that the colony and microscopic morphology of the recombinant L. acidophilus strain was consistent with the original strain, and the recombinant strain grew well when cultured under aerobic or anaerobic conditions, exhibiting a growth rate that was identical to that of the standard strain. Similarly, the supernatants of the recombinant L. acidophilus can inhibit the growth of E. coli and P. gingivalis at different concentrations, and the recombinant strain displayed essentially the same drug sensitivity profile as the original L. acidophilus. However, to our surprise, the recombinant strains exhibited a greater adhesion ability than the reference strain. CONCLUSIONS: Our study demonstrated that, in addition to an increased adhesion ability, the recombinant L. acidophilus strain maintained the basic characteristics of the standard strain ATCC 4356, including antibiotic sensitivity. Thus, the recombinant strains have great potential to be utilized as a safe and effective periodontitis vaccine in the future.\",\n \"corpus_id\": 13690298,\n \"score\": 0\n }\n]","isConversational":false}}},{"rowIdx":60,"cells":{"query":{"kind":"string","value":"{\n \"doc_id\": \"24029071\",\n \"title\": \"Bacteriophage T5 encodes a homolog of the eukaryotic transcription coactivator PC4 implicated in recombination-dependent DNA replication.\",\n \"abstract\": \"The RNA polymerase II cofactor PC4 globally regulates transcription of protein-encoding genes through interactions with unwinding DNA, the basal transcription machinery and transcription activators. Here, we report the surprising identification of PC4 homologs in all sequenced representatives of the T5 family of bacteriophages, as well as in an archaeon and seven phyla of eubacteria. We have solved the crystal structure of the full-length T5 protein at 1.9Å, revealing a striking resemblance to the characteristic single-stranded DNA (ssDNA)-binding core domain of PC4. Intriguing novel structural features include a potential regulatory region at the N-terminus and a C-terminal extension of the homodimerisation interface. The genome organisation of T5-related bacteriophages points at involvement of the PC4 homolog in recombination-dependent DNA replication, strongly suggesting that the protein corresponds to the hitherto elusive replicative ssDNA-binding protein of the T5 family. Our findings imply that PC4-like factors intervene in multiple unwinding-related processes by acting as versatile modifiers of nucleic acid conformation and raise the possibility that the eukaryotic transcription coactivator derives from ancestral DNA replication, recombination and repair factors.\",\n \"corpus_id\": 9828419\n}"},"candidates":{"kind":"list like","value":[{"doc_id":"18275380","title":"Mechanism of eukaryotic homologous recombination.","abstract":"Homologous recombination (HR) serves to eliminate deleterious lesions, such as double-stranded breaks and interstrand crosslinks, from chromosomes. HR is also critical for the preservation of replication forks, for telomere maintenance, and chromosome segregation in meiosis I. As such, HR is indispensable for the maintenance of genome integrity and the avoidance of cancers in humans. The HR reaction is mediated by a conserved class of enzymes termed recombinases. Two recombinases, Rad51 and Dmc1, catalyze the pairing and shuffling of homologous DNA sequences in eukaryotic cells via a filamentous intermediate on ssDNA called the presynaptic filament. The assembly of the presynaptic filament is a rate-limiting process that is enhanced by recombination mediators, such as the breast tumor suppressor BRCA2. HR accessory factors that facilitate other stages of the Rad51- and Dmc1-catalyzed homologous DNA pairing and strand exchange reaction have also been identified. Recent progress on elucidating the mechanisms of action of Rad51 and Dmc1 and their cohorts of ancillary factors is reviewed here.","corpus_id":30295291,"score":2},{"doc_id":"18831760","title":"The Mycoplasma pneumoniae MPN229 gene encodes a protein that selectively binds single-stranded DNA and stimulates Recombinase A-mediated DNA strand exchange.","abstract":"BACKGROUND: Mycoplasma pneumoniae has previously been characterized as a micro-organism that is genetically highly stable. In spite of this genetic stability, homologous DNA recombination has been hypothesized to lie at the basis of antigenic variation of the major surface protein, P1, of M. pneumoniae. In order to identify the proteins that may be involved in homologous DNA recombination in M. pneumoniae, we set out to characterize the MPN229 open reading frame (ORF), which bears sequence similarity to the gene encoding the single-stranded DNA-binding (SSB) protein of other micro-organisms. RESULTS: The MPN229 ORF has the capacity to encode a 166-amino acid protein with a calculated molecular mass of 18.4 kDa. The amino acid sequence of this protein (Mpn SSB) is most closely related to that of the protein predicted to be encoded by the MG091 gene from Mycoplasma genitalium (61% identity). The MPN229 ORF was cloned, and different versions of Mpn SSB were expressed in E. coli and purified to > 95% homogeneity. The purified protein was found to exist primarily as a homo-tetramer in solution, and to strongly and selectively bind single-stranded DNA (ssDNA) in a divalent cation- and DNA substrate sequence-independent manner. Mpn SSB was found to bind with a higher affinity to ssDNA substrates larger than 20 nucleotides than to smaller substrates. In addition, the protein strongly stimulated E. coli Recombinase A (RecA)-promoted DNA strand exchange, which indicated that Mpn SSB may play an important role in DNA recombination processes in M. pneumoniae. CONCLUSION: The M. pneumoniae MPN229 gene encodes a protein, Mpn SSB, which selectively and efficiently binds ssDNA, and stimulates E. coli RecA-promoted homologous DNA recombination. Consequently, the Mpn SSB protein may play a crucial role in DNA recombinatorial pathways in M. pneumoniae. The results from this study will pave the way for unraveling these pathways and assess their role in antigenic variation of M. pneumoniae.","corpus_id":8615785,"score":2},{"doc_id":"19038270","title":"Human transcriptional coactivator PC4 stimulates DNA end joining and activates DSB repair activity.","abstract":"Human transcriptional coactivator PC4 is a highly abundant nuclear protein that is involved in diverse cellular processes ranging from transcription to chromatin organization. Earlier, we have shown that PC4, a positive activator of p53, overexpresses upon genotoxic insult in a p53-dependent manner. In the present study, we show that PC4 stimulates ligase-mediated DNA end joining irrespective of the source of DNA ligase. Pull-down assays reveal that PC4 helps in the association of DNA ends through its C-terminal domain. In vitro nonhomologous end-joining assays with cell-free extracts show that PC4 enhances the joining of noncomplementary DNA ends. Interestingly, we found that PC4 activates double-strand break (DSB) repair activity through stimulation of DSB rejoining in vivo. Together, these findings demonstrate PC4 as an activator of nonhomologous end joining and DSB repair activity.","corpus_id":43300497,"score":2},{"doc_id":"19047459","title":"Recruitment of RNA polymerase II cofactor PC4 to DNA damage sites.","abstract":"The multifunctional nuclear protein positive cofactor 4 (PC4) is involved in various cellular processes including transcription, replication, and chromatin organization. Recently, PC4 has been identified as a suppressor of oxidative mutagenesis in Escherichia coli and Saccharomyces cerevisiae. To investigate a potential role of PC4 in mammalian DNA repair, we used a combination of live cell microscopy, microirradiation, and fluorescence recovery after photobleaching analysis. We found a clear accumulation of endogenous PC4 at DNA damage sites introduced by either chemical agents or laser microirradiation. Using fluorescent fusion proteins and specific mutants, we demonstrated that the rapid recruitment of PC4 to laser-induced DNA damage sites is independent of poly(ADP-ribosyl)ation and gammaH2AX but depends on its single strand binding capacity. Furthermore, PC4 showed a high turnover at DNA damages sites compared with the repair factors replication protein A and proliferating cell nuclear antigen. We propose that PC4 plays a role in the early response to DNA damage by recognizing single-stranded DNA and may thus initiate or facilitate the subsequent steps of DNA repair.","corpus_id":5573494,"score":2},{"doc_id":"19139058","title":"Transcription-associated recombination in eukaryotes: link between transcription, replication and recombination.","abstract":"Homologous recombination (HR) is an important DNA repair pathway and is essential for cellular survival. It plays a major role in repairing replication-associated lesions and is functionally connected to replication. Transcription is another cellular process, which has emerged to have a connection with HR. Transcription enhances HR, which is a ubiquitous phenomenon referred to as transcription-associated recombination (TAR). Recent evidence suggests that TAR plays a role in inducing genetic instability, for example in the THO mutants (Tho2, Hpr1, Mft1 and Thp2) in yeast or during the development of the immune system leading to genetic diversity in mammals. On the other hand, evidence also suggests that TAR may play a role in preventing genetic instability in many different ways, one of which is by rescuing replication during transcription. Hence, TAR is a double-edged sword and plays a role in both preventing and inducing genetic instability. In spite of the interesting nature of TAR, the mechanism behind TAR has remained elusive. Recent advances in the area, however, suggest a link between TAR and replication and show specific genetic requirements for TAR that differ from regular HR. In this review, we aim to present the available evidence for TAR in both lower and higher eukaryotes and discuss its possible mechanisms, with emphasis on its connection with replication.","corpus_id":42121615,"score":2},{"doc_id":"19525231","title":"Interaction between the transactivation domain of p53 and PC4 exemplifies acidic activation domains as single-stranded DNA mimics.","abstract":"The tumor suppressor p53 regulates cell cycle arrest and apoptosis by transactivating several genes that are critical for these processes. The transcriptional activity of p53 is often regulated by post-translational modifications and its interactions with various transcriptional coactivators. Here we report a physical interaction between the N-terminal transactivation domain (TAD) of p53 and the C-terminal DNA-binding domain of positive cofactor 4 (PC4(CTD)). Using NMR spectroscopy, we showed that residues 35-57 (TAD2) interact with PC4. (15)N,(1)H HSQC and fluorescence competition experiments indicated that TAD binds to the DNA-binding site of PC4. Hepta-phosphorylation of the TAD peptide increased its binding affinity. Computer modeling of the p53N-PC4 complex revealed several important interactions that are reminiscent of those in the single-stranded DNA-PC4 complex. The ubiquitous nature of the acidic transactivation domain of p53 in mediating interactions with several transcription cofactors is also manifested as a DNA mimetic.","corpus_id":28468533,"score":2},{"doc_id":"20305379","title":"Sub1/PC4 a chromatin associated protein with multiple functions in transcription.","abstract":"Yeast Sub1 and its human ortholog PC4 display multiple cellular functions in vivo. Sub1/PC4 contains a unique conserved non-specific DNA-binding domain and is involved in distinct DNA-dependent processes including replication, DNA repair and transcription. Sub1/PC4 is a non-histone chromatin-associated protein initially described as a co-activator for RNA polymerase (Pol) II transcription in vitro. Recently, biochemical and genomic studies showed that Sub1 is not restricted to Pol II transcription but is also involved in Pol III transcription revealing a more general role in transcription than anticipated. Sub1/PC4 appears to play a dual (positive and negative) complex role in gene expression and has multiple effects in distinct steps of the transcription cycle, consisting of initiation, elongation, termination and reinitiation. Here, the multiple transcriptional functions of Sub1/PC4 will be reviewed and the recent findings and their possible implications in the understanding of Sub1/PC4 function in transcription will be discussed.","corpus_id":10796722,"score":2},{"doc_id":"20690856","title":"Regulation of homologous recombination in eukaryotes.","abstract":"Homologous recombination (HR) is required for accurate chromosome segregation during the first meiotic division and constitutes a key repair and tolerance pathway for complex DNA damage, including DNA double-strand breaks, interstrand crosslinks, and DNA gaps. In addition, recombination and replication are inextricably linked, as recombination recovers stalled and broken replication forks, enabling the evolution of larger genomes/replicons. Defects in recombination lead to genomic instability and elevated cancer predisposition, demonstrating a clear cellular need for recombination. However, recombination can also lead to genome rearrangements. Unrestrained recombination causes undesired endpoints (translocation, deletion, inversion) and the accumulation of toxic recombination intermediates. Evidently, HR must be carefully regulated to match specific cellular needs. Here, we review the factors and mechanistic stages of recombination that are subject to regulation and suggest that recombination achieves flexibility and robustness by proceeding through metastable, reversible intermediates.","corpus_id":7874976,"score":2},{"doc_id":"21129204","title":"Structural analysis of bacteriophage T4 DNA replication: a review in the Virology Journal series on bacteriophage T4 and its relatives.","abstract":"The bacteriophage T4 encodes 10 proteins, known collectively as the replisome, that are responsible for the replication of the phage genome. The replisomal proteins can be subdivided into three activities; the replicase, responsible for duplicating DNA, the primosomal proteins, responsible for unwinding and Okazaki fragment initiation, and the Okazaki repair proteins. The replicase includes the gp43 DNA polymerase, the gp45 processivity clamp, the gp44/62 clamp loader complex, and the gp32 single-stranded DNA binding protein. The primosomal proteins include the gp41 hexameric helicase, the gp61 primase, and the gp59 helicase loading protein. The RNaseH, a 5' to 3' exonuclease and T4 DNA ligase comprise the activities necessary for Okazaki repair. The T4 provides a model system for DNA replication. As a consequence, significant effort has been put forth to solve the crystallographic structures of these replisomal proteins. In this review, we discuss the structures that are available and provide comparison to related proteins when the T4 structures are unavailable. Three of the ten full-length T4 replisomal proteins have been determined; the gp59 helicase loading protein, the RNase H, and the gp45 processivity clamp. The core of T4 gp32 and two proteins from the T4 related phage RB69, the gp43 polymerase and the gp45 clamp are also solved. The T4 gp44/62 clamp loader has not been crystallized but a comparison to the E. coli gamma complex is provided. The structures of T4 gp41 helicase, gp61 primase, and T4 DNA ligase are unknown, structures from bacteriophage T7 proteins are discussed instead. To better understand the functionality of T4 DNA replication, in depth structural analysis will require complexes between proteins and DNA substrates. A DNA primer template bound by gp43 polymerase, a fork DNA substrate bound by RNase H, gp43 polymerase bound to gp32 protein, and RNase H bound to gp32 have been crystallographically determined. The preparation and crystallization of complexes is a significant challenge. We discuss alternate approaches, such as small angle X-ray and neutron scattering to generate molecular envelopes for modeling macromolecular assemblies.","corpus_id":9996923,"score":2},{"doc_id":"21193408","title":"Coactivator function of positive cofactor 4 (PC4) in Sp1-directed luteinizing hormone receptor (LHR) gene transcription.","abstract":"The LHR has an essential role in sexual development and reproductive function, and its transcription is subjected to several modes of regulation. In this study, we investigated PC4 coactivator function in the control of LHR transcription. Knockdown of PC4 by siRNA inhibited the LHR basal promoter activity and trichostatin A (TSA)-induced gene transcriptional activation and expression in MCF-7 cells. While overexpression of PC4 alone had no effect on the LHR gene, it significantly enhanced Sp1- but not Sp3-mediated LHR transcriptional activity. PC4 directly interacts with Sp1 at the LHR promoter, and this interaction is negatively regulated by PC4 phosphorylation. The coactivator domain (22-91 aa) of PC4 and DNA binding domain of Sp1 are essential for PC4/Sp1 interaction. ChIP assay revealed significant occupancy of PC4 at the LHR promoter that increased upon TSA treatment. Disruption of PC4 expression significantly reduced TSA-induced recruitment of TFIIB and RNAP II, at the promoter. PC4 functions are beyond TSA-induced phosphatase release, PI3K-mediated Sp1 phosphorylation, and HDAC1/2/mSin3A co-repressor release indicating its role as linker coactivator of Sp1 and the transcriptional machinery. These findings demonstrated a critical aspect of LHR modulation whereby PC4 acts as a coactivator of Sp1 to contribute to the human of LHR transcription.","corpus_id":5470766,"score":2},{"doc_id":"21599536","title":"Presynaptic filament dynamics in homologous recombination and DNA repair.","abstract":"Homologous recombination (HR) is an essential genome stability mechanism used for high-fidelity repair of DNA double-strand breaks and for the recovery of stalled or collapsed DNA replication forks. The crucial homology search and DNA strand exchange steps of HR are catalyzed by presynaptic filaments-helical filaments of a recombinase enzyme bound to single-stranded DNA (ssDNA). Presynaptic filaments are fundamentally dynamic structures, the assembly, catalytic turnover, and disassembly of which must be closely coordinated with other elements of the DNA recombination, repair, and replication machinery in order for genome maintenance functions to be effective. Here, we reviewed the major dynamic elements controlling the assembly, activity, and disassembly of presynaptic filaments; some intrinsic such as recombinase ATP-binding and hydrolytic activities, others extrinsic such as ssDNA-binding proteins, mediator proteins, and DNA motor proteins. We examined dynamic behavior on multiple levels, including atomic- and filament-level structural changes associated with ATP binding and hydrolysis as evidenced in crystal structures, as well as subunit binding and dissociation events driven by intrinsic and extrinsic factors. We examined the biochemical properties of recombination proteins from four model systems (T4 phage, Escherichia coli, Saccharomyces cerevisiae, and Homo sapiens), demonstrating how their properties are tailored for the context-specific requirements in these diverse species. We proposed that the presynaptic filament has evolved to rely on multiple external factors for increased multilevel regulation of HR processes in genomes with greater structural and sequence complexity.","corpus_id":30926436,"score":2},{"doc_id":"22055186","title":"Sub1 and RPA associate with RNA polymerase II at different stages of transcription.","abstract":"Single-stranded DNA-binding proteins play many roles in nucleic acid metabolism, but their importance during transcription remains unclear. Quantitative proteomic analysis of RNA polymerase II (RNApII) preinitiation complexes (PICs) identified Sub1 and the replication protein A complex (RPA), both of which bind single-stranded DNA (ssDNA). Sub1, homolog of mammalian coactivator PC4, exhibits strong genetic interactions with factors necessary for promoter melting. Sub1 localizes near the transcription bubble in vitro and binds to promoters in vivo dependent upon PIC assembly. In contrast, RPA localizes to transcribed regions of active genes, strongly correlated with transcribing RNApII but independently of replication. RFA1 interacts genetically with transcription elongation factor genes. Interestingly, RPA levels increase at active promoters in cells carrying a Sub1 deletion or ssDNA-binding mutant, suggesting competition for a common binding site. We propose that Sub1 and RPA interact with the nontemplate strand of RNApII complexes during initiation and elongation, respectively.","corpus_id":11830059,"score":2},{"doc_id":"22207204","title":"The interface of transcription and DNA replication in the mitochondria.","abstract":"DNA replication of the mitochondrial genome is unique in that replication is not primed by RNA derived from dedicated primases, but instead by extension of processed RNA transcripts laid down by the mitochondrial RNA polymerase. Thus, the RNA polymerase serves not only to generate the transcripts but also the primers needed for mitochondrial DNA replication. The interface between this transcription and DNA replication is not well understood but must be highly regulated and coordinated to carry out both mitochondrial DNA replication and transcription. This review focuses on the extension of RNA primers for DNA replication by the replication machinery and summarizes the current models of DNA replication in mitochondria as well as the proteins involved in mitochondrial DNA replication, namely, the DNA polymerase γ and its accessory subunit, the mitochondrial DNA helicase, the single-stranded DNA binding protein, topoisomerase I and IIIα and RNaseH1. This article is part of a Special Issue entitled: Mitochondrial Gene Expression.","corpus_id":24587140,"score":2},{"doc_id":"22427673","title":"Mutational analysis of the T4 gp59 helicase loader reveals its sites for interaction with helicase, single-stranded binding protein, and DNA.","abstract":"Efficient DNA replication involves coordinated interactions among DNA polymerase, multiple factors, and the DNA. From bacteriophage T4 to eukaryotes, these factors include a helicase to unwind the DNA ahead of the replication fork, a single-stranded binding protein (SSB) to bind to the ssDNA on the lagging strand, and a helicase loader that associates with the fork, helicase, and SSB. The previously reported structure of the helicase loader in the T4 system, gene product (gp)59, has revealed an N-terminal domain, which shares structural homology with the high mobility group (HMG) proteins from eukaryotic organisms. Modeling of this structure with fork DNA has suggested that the HMG-like domain could bind to the duplex DNA ahead of the fork, whereas the C-terminal portion of gp59 would provide the docking sites for helicase (T4 gp41), SSB (T4 gp32), and the ssDNA fork arms. To test this model, we have used random and targeted mutagenesis to generate mutations throughout gp59. We have assayed the ability of the mutant proteins to bind to fork, primed fork, and ssDNAs, to interact with SSB, to stimulate helicase activity, and to function in leading and lagging strand DNA synthesis. Our results provide strong biochemical support for the role of the N-terminal gp59 HMG motif in fork binding and the interaction of the C-terminal portion of gp59 with helicase and SSB. Our results also suggest that processive replication may involve the switching of gp59 between its interactions with helicase and SSB.","corpus_id":26548293,"score":2},{"doc_id":"22948907","title":"Structural features of the single-stranded DNA-binding protein MoSub1 from Magnaporthe oryzae.","abstract":"The well studied general transcription cofactor Sub1/PC4 has multiple functions in transcription. It plays both a negative and a positive role in transcription initiation and is involved in elongation and downstream transcription processes and as a transcription reinitiation factor. MoSub1, a Sub1/PC4 orthologue from rice blast fungus, binds the single-stranded DNA dT(12) tightly with an affinity of 186 nM. The crystal structure of MoSub1 has been solved to 1.79 Å resolution. The structure of the protein shows high similiarity to the structure of PC4 and it has a similar dimer interface and DNA-binding region to PC4, indicating that MoSub1 could bind DNA using the same motif as other proteins of the Sub1/PC4 family. There are two novel features in the MoSub1 structure: a region N-terminal to the DNA-binding domain and a C-terminal extension. The region N-terminal to the DNA-binding domain of MoSub1 turns back towards the DNA-binding site and may interact directly with DNA or the DNA-binding site. The C-terminal extension region, which is absent in PC4, may not be capable of interacting with DNA and is one possible reason for the differences between Sub1 and PC4.","corpus_id":20917803,"score":2},{"doc_id":"22976174","title":"Functions of single-strand DNA-binding proteins in DNA replication, recombination, and repair.","abstract":"Double-stranded (ds) DNA contains all of the necessary genetic information, although practical use of this information requires unwinding of the duplex DNA. DNA unwinding creates single-stranded (ss) DNA intermediates that serve as templates for myriad cellular functions. Exposure of ssDNA presents several problems to the cell. First, ssDNA is thermodynamically less stable than dsDNA, which leads to spontaneous formation of duplex secondary structures that impede genome maintenance processes. Second, relative to dsDNA, ssDNA is hypersensitive to chemical and nucleolytic attacks that can cause damage to the genome. Cells deal with these potential problems by encoding specialized ssDNA-binding proteins (SSBs) that bind to and stabilize ssDNA structures required for essential genomic processes. SSBs are essential proteins found in all domains of life. SSBs bind ssDNA with high affinity and in a sequence-independent manner and, in doing so, SSBs help to form the central nucleoprotein complex substrate for DNA replication, recombination, and repair processes. While SSBs are found in every organism, the proteins themselves share surprisingly little sequence similarity, subunit composition, and oligomerization states. All SSB proteins contain at least one DNA-binding oligonucleotide/oligosaccharide binding (OB) fold, which consists minimally of a five stranded beta-sheet arranged as a beta barrel capped by a single alpha helix. The OB fold is responsible for both ssDNA binding and oligomerization (for SSBs that operate as oligomers). The overall organization of OB folds varies between bacteria, eukaryotes, and archaea. As part of SSB/ssDNA cellular structures, SSBs play direct roles in the DNA replication, recombination, and repair. In many cases, SSBs have been found to form specific complexes with diverse genome maintenance proteins, often helping to recruit SSB/ssDNA-processing enzymes to the proper cellular sites of action. This clustering of genome maintenance factors can help to stimulate and coordinate the activities of individual enzymes and is also important for dislodging SSB from ssDNA. These features support a model in which DNA metabolic processes have evolved to work on ssDNA/SSB nucleoprotein filaments rather than on naked ssDNA. In this volume, methods are described to interrogate SSB-DNA and SSB-protein binding functions along with approaches that aim to understand the cellular functions of SSB. This introductory chapter offers a general overview of SSBs that focuses on their structures, DNA-binding mechanisms, and protein-binding partners.","corpus_id":20789227,"score":2},{"doc_id":"23303792","title":"Structures of apo- and ssDNA-bound YdbC from Lactococcus lactis uncover the function of protein domain family DUF2128 and expand the single-stranded DNA-binding domain proteome.","abstract":"Single-stranded DNA (ssDNA) binding proteins are important in basal metabolic pathways for gene transcription, recombination, DNA repair and replication in all domains of life. Their main cellular role is to stabilize melted duplex DNA and protect genomic DNA from degradation. We have uncovered the molecular function of protein domain family domain of unknown function DUF2128 (PF09901) as a novel ssDNA binding domain. This bacterial domain strongly associates into a dimer and presents a highly positively charged surface that is consistent with its function in non-specific ssDNA binding. Lactococcus lactis YdbC is a representative of DUF2128. The solution NMR structures of the 20 kDa apo-YdbC dimer and YdbC:dT(19)G(1) complex were determined. The ssDNA-binding energetics to YdbC were characterized by isothermal titration calorimetry. YdbC shows comparable nanomolar affinities for pyrimidine and mixed oligonucleotides, and the affinity is sufficiently strong to disrupt duplex DNA. In addition, YdbC binds with lower affinity to ssRNA, making it a versatile nucleic acid-binding domain. The DUF2128 family is related to the eukaryotic nuclear protein positive cofactor 4 (PC4) family and to the PUR family both by fold similarity and molecular function.","corpus_id":17595961,"score":2},{"doc_id":"23435232","title":"Characterization of an unusual bipolar helicase encoded by bacteriophage T5.","abstract":"Bacteriophage T5 has a 120 kb double-stranded linear DNA genome encoding most of the genes required for its own replication. This lytic bacteriophage has a burst size of ∼500 new phage particles per infected cell, demonstrating that it is able to turn each infected bacterium into a highly efficient DNA manufacturing machine. To begin to understand DNA replication in this prodigious bacteriophage, we have characterized a putative helicase encoded by gene D2. We show that bacteriophage T5 D2 protein is the first viral helicase to be described with bipolar DNA unwinding activities that require the same core catalytic residues for unwinding in either direction. However, unwinding of partially single- and double-stranded DNA test substrates in the 3'-5' direction is more robust and can be distinguished from the 5'-3' activity by a number of features including helicase complex stability, salt sensitivity and the length of single-stranded DNA overhang required for initiation of helicase action. The presence of D2 in an early gene cluster, the identification of a putative helix-turn-helix DNA-binding motif outside the helicase core and homology with known eukaryotic and prokaryotic replication initiators suggest an involvement for this unusual helicase in DNA replication initiation.","corpus_id":18931209,"score":2},{"doc_id":"23732982","title":"Interaction of T4 UvsW helicase and single-stranded DNA binding protein gp32 through its carboxy-terminal acidic tail.","abstract":"Bacteriophage T4 UvsW helicase contains both unwinding and annealing activities and displays some functional similarities to bacterial RecG and RecQ helicases. UvsW is involved in several DNA repair pathways, playing important roles in recombination-dependent DNA repair and the reorganization of stalled replication forks. The T4 single-stranded DNA (ssDNA) binding protein gp32 is a central player in nearly all DNA replication and repair processes and is thought to facilitate their coordination by recruiting and regulating the various proteins involved. Here, we show that the activities of the UvsW protein are modulated by gp32. UvsW-catalyzed unwinding of recombination intermediates such as D-loops and static X-DNA (Holliday junction mimic) to ssDNA products is enhanced by the gp32 protein. The enhancement requires the presence of the protein interaction domain of gp32 (the acidic carboxy-terminus), suggesting that a specific interaction between UvsW and gp32 is required. In the absence of this interaction, the ssDNA annealing and ATP-dependent translocation activities of UvsW are severely inhibited when gp32 coats the ssDNA lattice. However, when UvsW and gp32 do interact, UvsW is able to efficiently displace the gp32 protein from the ssDNA. This ability of UvsW to remove gp32 from ssDNA may explain its ability to enhance the strand invasion activity of the T4 recombinase (UvsX) and suggests a possible new role for UvsW in gp32-mediated DNA transactions.","corpus_id":33374945,"score":2},{"doc_id":"23881942","title":"Archaeology of eukaryotic DNA replication.","abstract":"Recent advances in the characterization of the archaeal DNA replication system together with comparative genomic analysis have led to the identification of several previously uncharacterized archaeal proteins involved in replication and currently reveal a nearly complete correspondence between the components of the archaeal and eukaryotic replication machineries. It can be inferred that the archaeal ancestor of eukaryotes and even the last common ancestor of all extant archaea possessed replication machineries that were comparable in complexity to the eukaryotic replication system. The eukaryotic replication system encompasses multiple paralogs of ancestral components such that heteromeric complexes in eukaryotes replace archaeal homomeric complexes, apparently along with subfunctionalization of the eukaryotic complex subunits. In the archaea, parallel, lineage-specific duplications of many genes encoding replication machinery components are detectable as well; most of these archaeal paralogs remain to be functionally characterized. The archaeal replication system shows remarkable plasticity whereby even some essential components such as DNA polymerase and single-stranded DNA-binding protein are displaced by unrelated proteins with analogous activities in some lineages.","corpus_id":22434475,"score":2},{"doc_id":"24482743","title":"Identification of the ssDNA-binding protein of bacteriophage T5: Implications for T5 replication.","abstract":"In a recent study, we identified and characterized the long-elusive replicative single-stranded DNA-binding protein of bacteriophage T5, which we showed is related to the eukaryotic transcription coactivator PC4. Here, we provide an extended discussion of these data, report several additional observations and consider implications for the recombination-dependent replication mechanism of the T5 genus, which is still poorly understood.","corpus_id":9442522,"score":2},{"doc_id":"25083707","title":"Phage ORF family recombinases: conservation of activities and involvement of the central channel in DNA binding.","abstract":"Genetic and biochemical evidence suggests that λ Orf is a recombination mediator, promoting nucleation of either bacterial RecA or phage Redβ recombinases onto single-stranded DNA (ssDNA) bound by SSB protein. We have identified a diverse family of Orf proteins that includes representatives implicated in DNA base flipping and those fused to an HNH endonuclease domain. To confirm a functional relationship with the Orf family, a distantly-related homolog, YbcN, from Escherichia coli cryptic prophage DLP12 was purified and characterized. As with its λ relative, YbcN showed a preference for binding ssDNA over duplex. Neither Orf nor YbcN displayed a significant preference for duplex DNA containing mismatches or 1-3 nucleotide bulges. YbcN also bound E. coli SSB, although unlike Orf, it failed to associate with an SSB mutant lacking the flexible C-terminal tail involved in coordinating heterologous protein-protein interactions. Residues conserved in the Orf family that flank the central cavity in the λ Orf crystal structure were targeted for mutagenesis to help determine the mode of DNA binding. Several of these mutant proteins showed significant defects in DNA binding consistent with the central aperture being important for substrate recognition. The widespread conservation of Orf-like proteins highlights the importance of targeting SSB coated ssDNA during lambdoid phage recombination.","corpus_id":9546534,"score":2},{"doc_id":"25481875","title":"Regulation of the bacteriophage T4 Dda helicase by Gp32 single-stranded DNA-binding protein.","abstract":"Dda, one of three helicases encoded by bacteriophage T4, has been well-characterized biochemically but its biological role remains unclear. It is thought to be involved in origin dependent DNA replication, recombination-dependent replication, anti-recombination, and recombination repair. The Gp32 protein of bacteriophage T4 plays critical roles in DNA replication, recombination, and repair by coordinating protein components of the replication fork and by stabilizing ssDNA. Previous work demonstrated that stimulation of DNA synthesis by Dda helicase appears to require direct Gp32-Dda protein-protein interactions and that Gp32 and Dda form a tight complex in the absence of ssDNA. Here we characterize the effects of Gp32-Dda physical and functional interactions through changes in the duplex DNA unwinding and ATPase activities of Dda helicase in the presence of different variants of Gp32 and different DNA repair and replication intermediate structures. Results show that Gp32-Dda interactions can be enhancing or inhibitory, depending on the Gp32 domain seen by Dda. Protein-protein interactions with Gp32 stimulate the unwinding activity of Dda, an effect associated with increased turnover of ATP, suggesting a higher rate of ATPase-driven translocation. Dda-Gp32 interactions also promote the unwinding of DNA substrates at higher salt concentrations and in the presence of substrate-bound DNA polymerase. Conversely, the formation of Gp32 clusters on ssDNA can inhibit unwinding, suggesting that Gp32-ssDNA formation sterically regulates which portions of replication and recombination intermediates are accessible for processing by Dda helicase. The data suggest a mechanism of replication fork restart in which Gp32 promotes Dda activity in template switching while preventing premature fork progression.","corpus_id":10770482,"score":2},{"doc_id":"25646379","title":"DNA-pairing and annealing processes in homologous recombination and homology-directed repair.","abstract":"The formation of heteroduplex DNA is a central step in the exchange of DNA sequences via homologous recombination, and in the accurate repair of broken chromosomes via homology-directed repair pathways. In cells, heteroduplex DNA largely arises through the activities of recombination proteins that promote DNA-pairing and annealing reactions. Classes of proteins involved in pairing and annealing include RecA-family DNA-pairing proteins, single-stranded DNA (ssDNA)-binding proteins, recombination mediator proteins, annealing proteins, and nucleases. This review explores the properties of these pairing and annealing proteins, and highlights their roles in complex recombination processes including the double Holliday junction (DhJ) formation, synthesis-dependent strand annealing, and single-strand annealing pathways--DNA transactions that are critical both for genome stability in individual organisms and for the evolution of species.","corpus_id":2479895,"score":2},{"doc_id":"25739870","title":"Substitution of tryptophan 89 with tyrosine switches the DNA binding mode of PC4.","abstract":"PC4, a well-known general transcription cofactor, has multiple functions in transcription and DNA repair. Residue W89, is engaged in stacking interactions with DNA in PC4, but substituted by tyrosine in some PC4 orthologous proteins. In order to understand the consequences and reveal the molecular details of this substitution we have determined the crystal structures of the PC4 orthologue MoSub1 and a PC4 W89Y mutant in complex with DNA. In the structure of MoSub1-DNA complex, Y74 interacts directly with a single nucleotide of oligo DNA. By comparison, the equivalent residue, W89 in wild type PC4 interacts with two nucleotides and the base of the second nucleotide has distinct orientation relative to that of the first one. A hydrophobic patch around W89 that favours interaction with two nucleotides is not formed in the PC4 W89Y mutant. Therefore, the change of the surface hydrophobicity around residue 89 results in a difference between the modes of DNA interaction. These results indicate that the conserved Y74 in MoSub1 or W89 in PC4, are not only key residues in making specific interactions with DNA but also required to determine the DNA binding mode of PC4 proteins.","corpus_id":14934233,"score":2},{"doc_id":"25961912","title":"PC4 promotes genome stability and DNA repair through binding of ssDNA at DNA damage sites.","abstract":"The transcriptional cofactor PC4 is an ancient single-strand DNA (ssDNA)-binding protein that has a homologue in bacteriophage T5 where it is likely the elusive replicative ssDNA-binding protein. We hypothesize that human PC4 has retained functions in ssDNA binding to stabilize replication forks and prevent genome instability in mammalian cells. Here we demonstrate that PC4 is recruited to hydroxyurea (HU)-stalled replication forks, which is dependent on active transcription and its ssDNA-binding ability. Interestingly, we demonstrate that ssDNA binding by PC4 is critical to suppress spontaneous DNA damage and promote cellular survival. PC4 accumulation co-localizes with replication protein A (RPA) at stalled forks and is increased upon RPA depletion, demonstrating compensatory functions in ssDNA binding. Depletion of PC4 not only results in defective resolution of HU-induced DNA damage but also significantly reduces homologous recombination repair efficiency. Altogether, our results indicate that PC4 has similar functions to RPA in binding ssDNA to promote genome stability, especially at sites of replication-transcription collisions. Oncogene advance online publication, 11 May 2015; doi:10.1038/onc.2015.135.","corpus_id":27942986,"score":2},{"doc_id":"25972894","title":"Replication and transcription on a collision course: eukaryotic regulation mechanisms and implications for DNA stability.","abstract":"DNA replication and transcription are vital cellular processes during which the genetic information is copied into complementary DNA and RNA molecules. Highly complex machineries required for DNA and RNA synthesis compete for the same DNA template, therefore being on a collision course. Unscheduled replication-transcription clashes alter the gene transcription program and generate replication stress, reducing fork speed. Molecular pathways and mechanisms that minimize the conflict between replication and transcription have been extensively characterized in prokaryotic cells and recently identified also in eukaryotes. A pathological outcome of replication-transcription collisions is the formation of stable RNA:DNA hybrids in molecular structures called R-loops. Growing evidence suggests that R-loop accumulation promotes both genetic and epigenetic instability, thus severely affecting genome functionality. In the present review, we summarize the current knowledge related to replication and transcription conflicts in eukaryotes, their consequences on genome stability and the pathways involved in their resolution. These findings are relevant to clarify the molecular basis of cancer and neurodegenerative diseases.","corpus_id":17350826,"score":2},{"doc_id":"28009009","title":"Bacteriophage T5 gene D10 encodes a branch-migration protein.","abstract":"Helicases catalyze the unwinding of double-stranded nucleic acids where structure and phosphate backbone contacts, rather than nucleobase sequence, usually determines substrate specificity. We have expressed and purified a putative helicase encoded by the D10 gene of bacteriophage T5. Here we report that this hitherto uncharacterized protein possesses branch migration and DNA unwinding activity. The initiation of substrate unwinding showed some sequence dependency, while DNA binding and DNA-dependent ATPase activity did not. DNA footprinting and purine-base interference assays demonstrated that D10 engages these substrates with a defined polarity that may be established by protein-nucleobase contacts. Bioinformatic analysis of the nucleotide databases revealed genes predicted to encode proteins related to D10 in archaebacteria, bacteriophages and in viruses known to infect a range of eukaryotic organisms.","corpus_id":15888543,"score":2},{"doc_id":"28416612","title":"A biochemical and biophysical model of G-quadruplex DNA recognition by positive coactivator of transcription 4.","abstract":"DNA sequences that are guanine-rich have received considerable attention because of their potential to fold into a secondary, four-stranded DNA structure termed G-quadruplex (G4), which has been implicated in genomic instability and some human diseases. We have previously identified positive coactivator of transcription (PC4), a single-stranded DNA (ssDNA)-binding protein, as a novel G4 interactor. Here, to expand on these previous observations, we biochemically and biophysically characterized the interaction between PC4 and G4DNA. PC4 can bind alternative G4DNA topologies with a low nanomolar Kd value of ∼2 nm, similar to that observed for ssDNA. In consideration of the different structural features between G4DNA and ssDNA, these binding data indicated that PC4 can interact with G4DNA in a manner distinct from ssDNA. The stoichiometry of the PC4-G4 complex was 1:1 for PC4 dimer:G4 substrate. PC4 did not enhance the rate of folding of G4DNA, and formation of the PC4-G4DNA complex did not result in unfolding of the G4DNA structure. We assembled a G4DNA structure flanked by duplex DNA. We find that PC4 can interact with this G4DNA, as well as the complementary C-rich strand. Molecular docking simulations and DNA footprinting experiments suggest a model where a PC4 dimer accommodates the DNA with one monomer on the G4 strand and the second monomer bound to the C-rich strand. Collectively, these data provide a novel mode of PC4 binding to a DNA secondary structure that remains within the framework of the model for binding to ssDNA. Additionally, consideration of the PC4-G4DNA interaction could provide insight into the biological functions of PC4, which remain incompletely understood.","corpus_id":205364196,"score":2},{"doc_id":"29588157","title":"Gp2.5, the multifunctional bacteriophage T7 single-stranded DNA binding protein.","abstract":"The essential bacteriophage T7-encoded single-stranded DNA binding protein is the nexus of T7 DNA metabolism. Multiple layers of macromolecular interactions mediate its function in replication, recombination, repair, and the maturation of viral genomes. In addition to binding ssDNA, the protein binds to DNA polymerase and DNA helicase, regulating their activities. The protein displays potent homologous DNA annealing activity, underscoring its role in recombination.","corpus_id":4410095,"score":2},{"doc_id":"18184592","title":"Structure and DNA binding of the human Rtf1 Plus3 domain.","abstract":"The yeast Paf1 complex consists of Paf1, Rtf1, Cdc73, Ctr9, and Leo1 and regulates histone H2B ubiquitination, histone H3 methylation, RNA polymerase II carboxy-terminal domain (CTD) Ser2 phosphorylation, and RNA 3' end processing. We provide structural insight into the Paf1 complex with the NMR structure of the conserved and functionally important Plus3 domain of human Rtf1. A predominantly beta-stranded subdomain displays structural similarity to Dicer/Argonaute PAZ domains and to Tudor domains. We further demonstrate that the highly basic Rtf1 Plus3 domain can interact in vitro with single-stranded DNA via residues on the rim of the beta sheet, reminiscent of siRNA binding by PAZ domains, but did not detect binding to double-stranded DNA or RNA. We discuss the potential role of Rtf1 Plus3 ssDNA binding during transcription elongation.","corpus_id":38494347,"score":1},{"doc_id":"18321528","title":"Crystal structure and RNA binding of the Tex protein from Pseudomonas aeruginosa.","abstract":"Tex is a highly conserved bacterial protein that likely functions in a variety of transcriptional processes. Here, we describe two crystal structures of the 86-kDa Tex protein from Pseudomonas aeruginosa at 2.3 and 2.5 A resolution, respectively. These structures reveal a relatively flat and elongated protein, with several potential nucleic acid binding motifs clustered at one end, including an S1 domain near the C-terminus that displays considerable structural flexibility. Tex binds nucleic acids, with a preference for single-stranded RNA, and the Tex S1 domain is required for this binding activity. Point mutants further demonstrate that the primary nucleic acid binding site corresponds to a surface of the S1 domain. Sequence alignment and modeling indicate that the eukaryotic Spt6 transcription factor adopts a similar core structure. Structural analysis further suggests that the RNA polymerase and nucleosome interacting regions of Spt6 flank opposite sides of the Tex-like scaffold. Therefore, the Tex structure may represent a conserved scaffold that binds single-stranded RNA to regulate transcription in both eukaryotic and prokaryotic organisms.","corpus_id":6130388,"score":1},{"doc_id":"18656357","title":"Functional and structural basis for a bacteriophage homolog of human RAD52.","abstract":"In eukaryotes, homologous recombination proteins such as RAD51 and RAD52 play crucial roles in DNA repair and genome stability. Human RAD52 is a member of a large single-strand annealing protein (SSAP) family [1] and stimulates Rad51-dependent recombination [2, 3]. In prokaryotes and phages, it has been difficult to establish the presence of RAD52 homologs with conserved sequences. Putative SSAPs were recently found in several phages that infect strains of Lactococcus lactis[4]. One of these SSAPs was identified as Sak and was found in the virulent L. lactis phage ul36, which belongs to the Siphoviridae family [4, 5]. In this study, we show that Sak is homologous to the N terminus of human RAD52. Purified Sak binds single-stranded DNA (ssDNA) preferentially over double-stranded DNA (dsDNA) and promotes the renaturation of long complementary ssDNAs. Sak also binds RecA and stimulates homologous recombination reactions. Mutations shown to modulate RAD52 DNA binding [6] affect Sak similarly. Remarkably, electron-microscopic reconstruction of Sak reveals an undecameric (11) subunit ring, similar to the crystal structure of the N-terminal fragment of human RAD52 [7, 8]. For the first time, we propose a viral homolog of RAD52 at the amino acid, phylogenic, functional, and structural levels.","corpus_id":15024131,"score":1},{"doc_id":"19074952","title":"The crystal structure of a replicative hexameric helicase DnaC and its complex with single-stranded DNA.","abstract":"DNA helicases are motor proteins that play essential roles in DNA replication, repair and recombination. In the replicative hexameric helicase, the fundamental reaction is the unwinding of duplex DNA; however, our understanding of this function remains vague due to insufficient structural information. Here, we report two crystal structures of the DnaB-family replicative helicase from Geobacillus kaustophilus HTA426 (GkDnaC) in the apo-form and bound to single-stranded DNA (ssDNA). The GkDnaC-ssDNA complex structure reveals that three symmetrical basic grooves on the interior surface of the hexamer individually encircle ssDNA. The ssDNA-binding pockets in this structure are directed toward the N-terminal domain collar of the hexameric ring, thus orienting the ssDNA toward the DnaG primase to facilitate the synthesis of short RNA primers. These findings provide insight into the mechanism of ssDNA binding and provide a working model to establish a novel mechanism for DNA translocation at the replication fork.","corpus_id":10859265,"score":1},{"doc_id":"19285993","title":"Single-stranded DNA-binding protein complex from Helicobacter pylori suggests an ssDNA-binding surface.","abstract":"Single-stranded DNA (ssDNA)-binding protein (SSB) plays an important role in DNA replication, recombination, and repair. SSB consists of an N-terminal ssDNA-binding domain with an oligonucleotide/oligosaccharide binding fold and a flexible C-terminal tail involved in protein-protein interactions. SSB from Helicobacter pylori (HpSSB) was isolated, and the ssDNA-binding characteristics of HpSSB were analyzed by fluorescence titration and electrophoretic mobility shift assay. Tryptophan fluorescence quenching was measured as 61%, and the calculated cooperative affinity was 5.4x10(7) M(-1) with an ssDNA-binding length of 25-30 nt. The crystal structure of the C-terminally truncated protein (HpSSBc) in complex with 35-mer ssDNA [HpSSBc-(dT)(35)] was determined at a resolution of 2.3 A. The HpSSBc monomer folds as an oligonucleotide/oligosaccharide binding fold with a Y-shaped conformation. The ssDNA wrapped around the HpSSBc tetramer through a continuous binding path comprising five essential aromatic residues and a positively charged surface formed by numerous basic residues.","corpus_id":33474012,"score":1},{"doc_id":"19338667","title":"The N-terminal domain of Escherichia coli RecA have multiple functions in promoting homologous recombination.","abstract":"Escherichia coli RecA mediates homologous recombination, a process essential to maintaining genome integrity. In the presence of ATP, RecA proteins bind a single-stranded DNA (ssDNA) to form a RecA-ssDNA presynaptic nucleoprotein filament that captures donor double-stranded DNA (dsDNA), searches for homology, and then catalyzes the strand exchange between ssDNA and dsDNA to produce a new heteroduplex DNA. Based upon a recently reported crystal structure of the RecA-ssDNA nucleoprotein filament, we carried out structural and functional studies of the N-terminal domain (NTD) of the RecA protein. The RecA NTD was thought to be required for monomer-monomer interaction. Here we report that it has two other distinct roles in promoting homologous recombination. It first facilitates the formation of a RecA-ssDNA presynaptic nucleoprotein filament by converting ATP to an ADP-Pi intermediate. Then, once the RecA-ssDNA presynaptic nucleoprotein filament is stably assembled in the presence of ATPgammaS, the NTD is required to capture donor dsDNA. Our results also suggest that the second function of NTD may be similar to that of Arg243 and Lys245, which were implicated earlier as binding sites of donor dsDNA. A two-step model is proposed to explain how a RecA-ssDNA presynaptic nucleoprotein filament interacts with donor dsDNA.","corpus_id":2586706,"score":1},{"doc_id":"19445949","title":"Dynamic regulatory interactions of rad51, rad52, and replication protein-a in recombination intermediates.","abstract":"Rad51, Rad52, and replication protein-A (RPA) play crucial roles in the repair of DNA double-strand breaks in Saccharomyces cerevisiae. Rad51 mediates DNA strand exchange, a key reaction in DNA recombination. Rad52 recruits Rad51 into single-stranded DNAs (ssDNAs) that are saturated with RPA. Rad52 also promotes annealing of ssDNA strands that are complexed with RPA. Specific protein-protein interactions are involved in these reactions. Here we report new biochemical characteristics of these protein interactions. First, Rad52-RPA interaction requires multiple molecules of RPA to be associated with ssDNA, suggesting that multiple contacts between the Rad52 ring and RPA-ssDNA filament are needed for stable binding. Second, RPA-t11, which is a recombination-deficient mutant of RPA, displays a defect in interacting with Rad52 in the presence of salt above 50 mM, explaining the defect in Rad52-mediated ssDNA annealing in the presence of this mutation. Third, ssDNA annealing promoted by Rad52 is preceded by aggregation of multiple RPA-ssDNA complexes with Rad52, and Rad51 inhibits this aggregation. These results suggest a regulatory role for Rad51 that suppresses ssDNA annealing and facilitates DNA strand invasion. Finally, the Rad51-double-stranded DNA complex disrupts Rad52-RPA interaction in ssDNA and titrates Rad52 from RPA. This suggests an additional regulatory role for Rad51 following DNA strand invasion, where Rad51-double-stranded DNA may inhibit illegitimate second-end capture to ensure the error-free repair of a DNA double-strand break.","corpus_id":206205013,"score":1},{"doc_id":"20404922","title":"Shared active site architecture between the large subunit of eukaryotic primase and DNA photolyase.","abstract":"BACKGROUND: DNA synthesis during replication relies on RNA primers synthesised by the primase, a specialised DNA-dependent RNA polymerase that can initiate nucleic acid synthesis de novo. In archaeal and eukaryotic organisms, the primase is a heterodimeric enzyme resulting from the constitutive association of a small (PriS) and large (PriL) subunit. The ability of the primase to initiate synthesis of an RNA primer depends on a conserved Fe-S domain at the C-terminus of PriL (PriL-CTD). However, the critical role of the PriL-CTD in the catalytic mechanism of initiation is not understood. METHODOLOGY/PRINCIPAL FINDINGS: Here we report the crystal structure of the yeast PriL-CTD at 1.55 A resolution. The structure reveals that the PriL-CTD folds in two largely independent alpha-helical domains joined at their interface by a [4Fe-4S] cluster. The larger N-terminal domain represents the most conserved portion of the PriL-CTD, whereas the smaller C-terminal domain is largely absent in archaeal PriL. Unexpectedly, the N-terminal domain reveals a striking structural similarity with the active site region of the DNA photolyase/cryptochrome family of flavoproteins. The region of similarity includes PriL-CTD residues that are known to be essential for initiation of RNA primer synthesis by the primase. CONCLUSION/SIGNIFICANCE: Our study reports the first crystallographic model of the conserved Fe-S domain of the archaeal/eukaryotic primase. The structural comparison with a cryptochrome protein bound to flavin adenine dinucleotide and single-stranded DNA provides important insight into the mechanism of RNA primer synthesis by the primase.","corpus_id":3766603,"score":1},{"doc_id":"21195035","title":"Physical interaction between archaeal DNA repair helicase Hel308 and Replication Protein A (RPA).","abstract":"Hel308 is a super-family 2 helicase in archaea with homologues in higher eukaryotes (HelQ and PolQ) that contribute to repair of DNA strand crosslinks (ICLs). However, the contribution of Hel308 to repair processes in archaea is far from clear, including how it co-operates with other proteins of DNA replication, repair and recombination. In this study we identified a physical interaction of Hel308 with RPA. Hel308 did not interact with SSB, and interaction with RPA required a conserved amino acid motif at the Hel308 C-terminus. We propose that in archaea RPA acts as a platform for loading of Hel308 onto aberrant single-stranded DNA (ssDNA) that arises at blocked replication forks. In line with data from a human Hel308 homologue, the helicase activity of archaeal Hel308 was only modestly stimulated (1.5-2 fold) by RPA under some conditions, and much less so than for other known interactions between helicases and single strand DNA (ssDNA) binding proteins. This supports a model for RPA localising Hel308 to DNA damage sites in archaea, rather than it directly stimulating the mechanism of helicase unwinding.","corpus_id":5223600,"score":1},{"doc_id":"21265762","title":"Structure and function of a novel endonuclease acting on branched DNA substrates.","abstract":"Branched DNA structures that occur during DNA repair and recombination must be efficiently processed by structure-specific endonucleases in order to avoid cell death. In the present paper, we summarize our screen for new interaction partners for the archaeal replication clamp that led to the functional characterization of a novel endonuclease family, dubbed NucS. Structural analyses of Pyrococcus abyssi NucS revealed an unexpected binding site for ssDNA (single-stranded DNA) that directs, together with the replication clamp, the nuclease activity of this protein towards ssDNA-dsDNA (double-stranded DNA) junctions. Our studies suggest that understanding the detailed architecture and dynamic behaviour of the NucS (nuclease specific for ssDNA)-PCNA (proliferating-cell nuclear antigen) complex with DNA will be crucial for identification of its physiologically relevant activities.","corpus_id":13314147,"score":1},{"doc_id":"21804533","title":"Tyrosine phosphorylation enhances RAD52-mediated annealing by modulating its DNA binding.","abstract":"RAD52 protein has an important role in homology-directed DNA repair by mediating RAD51 nucleoprotein filament formation on single-stranded DNA (ssDNA) protected by replication protein-A (RPA) and annealing of RPA-coated ssDNA. In human, cellular response to DNA damage includes phosphorylation of RAD52 by c-ABL kinase at tyrosine 104. To address how this phosphorylation modulates RAD52 function, we used an amber suppressor technology to substitute tyrosine 104 with chemically stable phosphotyrosine analogue (p-Carboxymethyl-L-phenylalanine, pCMF). The RAD52(Y104pCMF) retained ssDNA-binding activity characteristic of unmodified RAD52 but showed lower affinity for double-stranded DNA (dsDNA) binding. Single-molecule analyses revealed that RAD52(Y104pCMF) specifically targets and wraps ssDNA. While RAD52(Y104pCMF) is confined to ssDNA region, unmodified RAD52 readily diffuses into dsDNA region. The Y104pCMF substitution also increased the ssDNA annealing rate and allowed overcoming the inhibitory effect of dsDNA. We propose that phosphorylation at Y104 enhances ssDNA annealing activity of RAD52 by attenuating dsDNA binding. Implications of phosphorylation-mediated activation of RAD52 annealing activity are discussed.","corpus_id":13330473,"score":1},{"doc_id":"22549990","title":"MALDI-MS detection of noncovalent interactions of single stranded DNA with Escherichia coli single-stranded DNA-binding protein.","abstract":"The Escherichia coli single-stranded DNA binding protein (SSB) selectively binds single-stranded (ss) DNA and participates in the process of DNA replication, recombination and repair. Different binding modes have previously been observed in SSB•ssDNA complexes, due to the four potential binding sites of SSB. Here, chemical cross-linking, combined with high-mass matrix-assisted laser desorption/ionization (MALDI) mass spectrometry (MS), is used to determine the stoichiometry of the SSB•ssDNA complex. SSB forms a stable homotetramer in solution, but only the monomeric species (m/z 19,100) can be detected with standard MALDI-MS. With chemical cross-linking, the quaternary structure of SSB is conserved, and the tetramer (m/z 79,500) was observed. We found that ssDNA also functions as a stabilizer to conserve the quaternary structure of SSB, as evidenced by the detection of a SSB•ssDNA complex at m/z 94,200 even in the absence of chemical cross-linking. The stability of the SSB•ssDNA complex with MALDI strongly depends on the length and strand of oligonucleotides and the stoichiometry of the SSB•ssDNA complex, which could be attributed to electrostatic interactions that are enhanced in the gas phase. The key factor affecting the stoichiometry of the SSB•ssDNA complex is how ssDNA binds to SSB, rather than the protein-to-DNA ratio. This further suggests that detection of the complex by MALDI is a result of specific binding, and not due to non-specific aggregation in the MALDI plume.","corpus_id":5594670,"score":1},{"doc_id":"22698072","title":"Thermodynamic analysis of DNA binding by a Bacillus single stranded DNA binding protein.","abstract":"BACKGROUND: Single-stranded DNA binding proteins (SSB) are essential for DNA replication, repair, and recombination in all organisms. SSB works in concert with a variety of DNA metabolizing enzymes such as DNA polymerase. RESULTS: We have cloned and purified SSB from Bacillus anthracis (SSB(BA)). In the absence of DNA, at concentrations ≤100 μg/ml, SSB(BA) did not form a stable tetramer and appeared to resemble bacteriophage T4 gene 32 protein. Fluorescence anisotropy studies demonstrated that SSB(BA) bound ssDNA with high affinity comparable to other prokaryotic SSBs. Thermodynamic analysis indicated both hydrophobic and ionic contributions to ssDNA binding. FRET analysis of oligo(dT)(70) binding suggested that SSB(BA) forms a tetrameric assembly upon ssDNA binding. This report provides evidence of a bacterial SSB that utilizes a novel mechanism for DNA binding through the formation of a transient tetrameric structure. CONCLUSIONS: Unlike other prokaryotic SSB proteins, SSB(BA) from Bacillus anthracis appeared to be monomeric at concentrations ≤100 μg/ml as determined by SE-HPLC. SSB(BA) retained its ability to bind ssDNA with very high affinity, comparable to SSB proteins which are tetrameric. In the presence of a long ssDNA template, SSB(BA) appears to form a transient tetrameric structure. Its unique structure appears to be due to the cumulative effect of multiple key amino acid changes in its sequence during evolution, leading to perturbation of stable dimer and tetramer formation. The structural features of SSB(BA) could promote facile assembly and disassembly of the protein-DNA complex required in processes such as DNA replication.","corpus_id":15966117,"score":1},{"doc_id":"22749146","title":"Homologous recombination in eukaryotes.","abstract":"Homologous recombination (HR) is a mechanistically conserved pathway that ensures maintenance of genomic integrity. During meiosis, HR results in DNA crossover events between homologous chromosomes that produce the genetic diversity inherent in germ cells. The physical connection established between homologs during the crossover event is essential to facilitate correct chromosome segregation. HR is also involved in maintenance of somatic cell genomic stability by restoring replication after a stalled replication fork has encountered a DNA lesion or strand break, as well as following exogenous stresses such as ionizing radiation that induce DNA double-strand breaks. The importance of HR can be gauged by the conservation of HR genes and functions from bacteria to man. Here we review the players and mechanics of eukaryotic HR.","corpus_id":36235967,"score":1},{"doc_id":"23584157","title":"DNA replication and homologous recombination factors: acting together to maintain genome stability.","abstract":"Genome duplication requires the coordinated action of multiple proteins to ensure a fast replication with high fidelity. These factors form a complex called the Replisome, which is assembled onto the DNA duplex to promote its unwinding and to catalyze the polymerization of two new strands. Key constituents of the Replisome are the Cdc45-Mcm2-7-GINS helicase and the And1-Claspin-Tipin-Tim1 complex, which coordinate DNA unwinding with polymerase alpha-, delta-, and epsilon- dependent DNA polymerization. These factors encounter numerous obstacles, such as endogenous DNA lesions leading to template breakage and complex structures arising from intrinsic features of specific DNA sequences. To overcome these roadblocks, homologous recombination DNA repair factors, such as Rad51 and the Mre11-Rad50-Nbs1 complex, are required to ensure complete and faithful replication. Consistent with this notion, many of the genes involved in this process result in lethal phenotypes when inactivated in organisms with complex and large genomes. Here, we summarize the architectural and functional properties of the Replisome and propose a unified view of DNA replication and repair processes.","corpus_id":18778307,"score":1},{"doc_id":"24338568","title":"Control of helicase loading in the coupled DNA replication and recombination systems of bacteriophage T4.","abstract":"The Gp59 protein of bacteriophage T4 promotes DNA replication by loading the replicative helicase, Gp41, onto replication forks and recombination intermediates. Gp59 also blocks DNA synthesis by Gp43 polymerase until Gp41 is loaded, ensuring that synthesis is tightly coupled to unwinding. The distinct polymerase blocking and helicase loading activities of Gp59 likely involve different binding interactions with DNA and protein partners. Here, we investigate how interactions of Gp59 with DNA and Gp32, the T4 single-stranded DNA (ssDNA)-binding protein, are related to these activities. A previously characterized mutant, Gp59-I87A, exhibits markedly reduced affinity for ssDNA and pseudo-fork DNA substrates. We demonstrate that on Gp32-covered ssDNA, the DNA binding defect of Gp59-I87A is not detrimental to helicase loading and translocation. In contrast, on pseudo-fork DNA the I87A mutation is detrimental to helicase loading and unwinding in the presence or absence of Gp32. Other results indicate that Gp32 binding to lagging strand ssDNA relieves the blockage of Gp43 polymerase activity by Gp59, whereas the inhibition of Gp43 exonuclease activity is maintained. Our findings suggest that Gp59-Gp32 and Gp59-DNA interactions perform separate but complementary roles in T4 DNA metabolism; Gp59-Gp32 interactions are needed to load Gp41 onto D-loops, and other nucleoprotein structures containing clusters of Gp32. Gp59-DNA interactions are needed to load Gp41 onto nascent or collapsed replication forks lacking clusters of Gp32 and to coordinate bidirectional replication from T4 origins. The dual functionalities of Gp59 allow it to promote the initiation or re-start of DNA replication from a wide variety of recombination and replication intermediates.","corpus_id":34570636,"score":1},{"doc_id":"24970156","title":"Homologous recombination as a replication fork escort: fork-protection and recovery.","abstract":"Homologous recombination is a universal mechanism that allows DNA repair and ensures the efficiency of DNA replication. The substrate initiating the process of homologous recombination is a single-stranded DNA that promotes a strand exchange reaction resulting in a genetic exchange that promotes genetic diversity and DNA repair. The molecular mechanisms by which homologous recombination repairs a double-strand break have been extensively studied and are now well characterized. However, the mechanisms by which homologous recombination contribute to DNA replication in eukaryotes remains poorly understood. Studies in bacteria have identified multiple roles for the machinery of homologous recombination at replication forks. Here, we review our understanding of the molecular pathways involving the homologous recombination machinery to support the robustness of DNA replication. In addition to its role in fork-recovery and in rebuilding a functional replication fork apparatus, homologous recombination may also act as a fork-protection mechanism. We discuss that some of the fork-escort functions of homologous recombination might be achieved by loading of the recombination machinery at inactivated forks without a need for a strand exchange step; as well as the consequence of such a model for the stability of eukaryotic genomes.","corpus_id":7453721,"score":1},{"doc_id":"25101062","title":"Evolution of replicative DNA polymerases in archaea and their contributions to the eukaryotic replication machinery.","abstract":"The elaborate eukaryotic DNA replication machinery evolved from the archaeal ancestors that themselves show considerable complexity. Here we discuss the comparative genomic and phylogenetic analysis of the core replication enzymes, the DNA polymerases, in archaea and their relationships with the eukaryotic polymerases. In archaea, there are three groups of family B DNA polymerases, historically known as PolB1, PolB2 and PolB3. All three groups appear to descend from the last common ancestors of the extant archaea but their subsequent evolutionary trajectories seem to have been widely different. Although PolB3 is present in all archaea, with the exception of Thaumarchaeota, and appears to be directly involved in lagging strand replication, the evolution of this gene does not follow the archaeal phylogeny, conceivably due to multiple horizontal transfers and/or dramatic differences in evolutionary rates. In contrast, PolB1 is missing in Euryarchaeota but otherwise seems to have evolved vertically. The third archaeal group of family B polymerases, PolB2, includes primarily proteins in which the catalytic centers of the polymerase and exonuclease domains are disrupted and accordingly the enzymes appear to be inactivated. The members of the PolB2 group are scattered across archaea and might be involved in repair or regulation of replication along with inactivated members of the RadA family ATPases and an additional, uncharacterized protein that are encoded within the same predicted operon. In addition to the family B polymerases, all archaea, with the exception of the Crenarchaeota, encode enzymes of a distinct family D the origin of which is unclear. We examine multiple considerations that appear compatible with the possibility that family D polymerases are highly derived homologs of family B. The eukaryotic DNA polymerases show a highly complex relationship with their archaeal ancestors including contributions of proteins and domains from both the family B and the family D archaeal polymerases.","corpus_id":12728106,"score":1},{"doc_id":"25202305","title":"Structural insights into eukaryotic DNA replication.","abstract":"THREE DNA POLYMERASES OF THE B FAMILY FUNCTION AT THE REPLICATION FORK IN EUKARYOTIC CELLS: DNA polymerases α, δ, and ε. DNA polymerase α, an heterotetramer composed of two primase subunits and two polymerase subunits, initiates replication. DNA polymerases δ and ε elongate the primers generated by pol α. The DNA polymerase from bacteriophage RB69 has served as a model for eukaryotic B family polymerases for some time. The recent crystal structures of pol δ, α, and ε revealed similarities but also a number of unexpected differences between the eukaryotic polymerases and their bacteriophage counterpart, and also among the three yeast polymerases. This review will focus on their shared structural elements as well as the features that are unique to each of these polymerases.","corpus_id":6070858,"score":1},{"doc_id":"25498946","title":"Leishmania braziliensis replication protein A subunit 1: molecular modelling, protein expression and analysis of its affinity for both DNA and RNA.","abstract":"BACKGROUND: Replication factor A (RPA) is a single-strand DNA binding protein involved in DNA replication, recombination and repair processes. It is composed by the subunits RPA-1, RPA-2 and RPA-3; the major DNA-binding activity resides in the subunit 1 of the heterotrimeric RPA complex. In yeast and higher eukaryotes, besides the three basic structural DNA-binding domains, the RPA-1 subunit contains an N-terminal region involved in protein-protein interactions with a fourth DNA-binding domain. Remarkably, the N-terminal extension is absent in the RPA-1 of the pathogenic protozoan Leishmania (Leishmania) amazonensis; however, the protein maintains its ability to bind ssDNA. In a recent work, we identify Leishmania (Viannia) braziliensis RPA-1 by its specific binding to the untranslated regions of the HSP70 mRNAs, suggesting that this protein might be also an RNA-binding protein. METHODS: Both rLbRPA-1 purified by His-tag affinity chromatography as well as the in vitro transcribed L. braziliensis 3' HSP70-II UTR were used to perform pull down assays to asses nucleic acid binding properties. Also, homology modeling was carried out to construct the LbRPA-1 tridimensional structure to search relevant amino acid residues to bind nucleic acids. RESULTS: In this work, after obtaining the recombinant L. braziliensis RPA-1 protein under native conditions, competitive and non-competitive pull-down assays confirmed the single-stranded DNA binding activity of this protein and demonstrated its interaction with the 3' UTR from the HSP70-II mRNA. As expected, this protein exhibits a high affinity for ssDNA, but we have found that RPA-1 interacts also with RNA. Additionally, we carried out a structural analysis of L. braziliensis RPA-1 protein using the X-ray diffraction structure of Ustilago maydis homologous protein as a template. Our results indicate that, in spite of the evolutionary divergence between both organisms, the structure of these two RPA-1 proteins seems to be highly conserved. CONCLUSION: The LbRPA-1 protein is a ssDNA binding protein, but also it shows affinity in vitro for the HSP70 mRNA; this finding supports a possible in vivo role in the HSP70 mRNA metabolism. On the other hand, the three dimensional model of Leishmania RPA-1 serves as a starting point for both functional analysis and its exploration as a chemotherapeutic target to combat leishmaniasis.","corpus_id":9475795,"score":1},{"doc_id":"25831490","title":"Human RECQ1 helicase-driven DNA unwinding, annealing, and branch migration: insights from DNA complex structures.","abstract":"RecQ helicases are a widely conserved family of ATP-dependent motors with diverse roles in nearly every aspect of bacterial and eukaryotic genome maintenance. However, the physical mechanisms by which RecQ helicases recognize and process specific DNA replication and repair intermediates are largely unknown. Here, we solved crystal structures of the human RECQ1 helicase in complexes with tailed-duplex DNA and ssDNA. The structures map the interactions of the ssDNA tail and the branch point along the helicase and Zn-binding domains, which, together with reported structures of other helicases, define the catalytic stages of helicase action. We also identify a strand-separating pin, which (uniquely in RECQ1) is buttressed by the protein dimer interface. A duplex DNA-binding surface on the C-terminal domain is shown to play a role in DNA unwinding, strand annealing, and Holliday junction (HJ) branch migration. We have combined EM and analytical ultracentrifugation approaches to show that RECQ1 can form what appears to be a flat, homotetrameric complex and propose that RECQ1 tetramers are involved in HJ recognition. This tetrameric arrangement suggests a platform for coordinated activity at the advancing and receding duplexes of an HJ during branch migration.","corpus_id":6945343,"score":1},{"doc_id":"26744780","title":"Structural basis of nucleic-acid recognition and double-strand unwinding by the essential neuronal protein Pur-alpha.","abstract":"The neuronal DNA-/RNA-binding protein Pur-alpha is a transcription regulator and core factor for mRNA localization. Pur-alpha-deficient mice die after birth with pleiotropic neuronal defects. Here, we report the crystal structure of the DNA-/RNA-binding domain of Pur-alpha in complex with ssDNA. It reveals base-specific recognition and offers a molecular explanation for the effect of point mutations in the 5q31.3 microdeletion syndrome. Consistent with the crystal structure, biochemical and NMR data indicate that Pur-alpha binds DNA and RNA in the same way, suggesting binding modes for tri- and hexanucleotide-repeat RNAs in two neurodegenerative RNAopathies. Additionally, structure-based in vitro experiments resolved the molecular mechanism of Pur-alpha's unwindase activity. Complementing in vivo analyses in Drosophila demonstrated the importance of a highly conserved phenylalanine for Pur-alpha's unwinding and neuroprotective function. By uncovering the molecular mechanisms of nucleic-acid binding, this study contributes to understanding the cellular role of Pur-alpha and its implications in neurodegenerative diseases.","corpus_id":261268337,"score":1},{"doc_id":"27893960","title":"Eukaryotic DNA Polymerases in Homologous Recombination.","abstract":"Homologous recombination (HR) is a central process to ensure genomic stability in somatic cells and during meiosis. HR-associated DNA synthesis determines in large part the fidelity of the process. A number of recent studies have demonstrated that DNA synthesis during HR is conservative, less processive, and more mutagenic than replicative DNA synthesis. In this review, we describe mechanistic features of DNA synthesis during different types of HR-mediated DNA repair, including synthesis-dependent strand annealing, break-induced replication, and meiotic recombination. We highlight recent findings from diverse eukaryotic organisms, including humans, that suggest both replicative and translesion DNA polymerases are involved in HR-associated DNA synthesis. Our focus is to integrate the emerging literature about DNA polymerase involvement during HR with the unique aspects of these repair mechanisms, including mutagenesis and template switching.","corpus_id":2412487,"score":1},{"doc_id":"28383499","title":"Eukaryotic Replicative Helicase Subunit Interaction with DNA and Its Role in DNA Replication.","abstract":"The replicative helicase unwinds parental double-stranded DNA at a replication fork to provide single-stranded DNA templates for the replicative polymerases. In eukaryotes, the replicative helicase is composed of the Cdc45 protein, the heterohexameric ring-shaped Mcm2-7 complex, and the tetrameric GINS complex (CMG). The CMG proteins bind directly to DNA, as demonstrated by experiments with purified proteins. The mechanism and function of these DNA-protein interactions are presently being investigated, and a number of important discoveries relating to how the helicase proteins interact with DNA have been reported recently. While some of the protein-DNA interactions directly relate to the unwinding function of the enzyme complex, other protein-DNA interactions may be important for minichromosome maintenance (MCM) loading, origin melting or replication stress. This review describes our current understanding of how the eukaryotic replicative helicase subunits interact with DNA structures in vitro, and proposed models for the in vivo functions of replicative helicase-DNA interactions are also described.","corpus_id":8127478,"score":1},{"doc_id":"28468824","title":"The DEAD-box protein DDX43 (HAGE) is a dual RNA-DNA helicase and has a K-homology domain required for full nucleic acid unwinding activity.","abstract":"The K-homology (KH) domain is a nucleic acid-binding domain present in many proteins but has not been reported in helicases. DDX43, also known as HAGE (helicase antigen gene), is a member of the DEAD-box protein family. It contains a helicase core domain in its C terminus and a potential KH domain in its N terminus. DDX43 is highly expressed in many tumors and is, therefore, considered a potential target for immunotherapy. Despite its potential as a therapeutic target, little is known about its activities. Here, we purified recombinant DDX43 protein to near homogeneity and found that it exists as a monomer in solution. Biochemical assays demonstrated that it is an ATP-dependent RNA and DNA helicase. Although DDX43 was active on duplex RNA regardless of the orientation of the single-stranded RNA tail, it preferred a 5' to 3' polarity on RNA and a 3' to 5' direction on DNA. Truncation mutations and site-directed mutagenesis confirmed that the KH domain in DDX43 is responsible for nucleic acid binding. Compared with the activity of the full-length protein, the C-terminal helicase domain had no unwinding activity on RNA substrates and had significantly reduced unwinding activity on DNA. Moreover, the full-length DDX43 protein, with single amino acid change in the KH domain, had reduced unwinding and binding activates on RNA and DNA substrates. Our results demonstrate that DDX43 is a dual helicase and the KH domain is required for its full unwinding activity.","corpus_id":21471882,"score":1},{"doc_id":"29138440","title":"Structural Basis for DNA Recognition of a Single-stranded DNA-binding Protein from Enterobacter Phage Enc34.","abstract":"Modern DNA sequencing capabilities have led to the discovery of a large number of new bacteriophage genomes, which are a rich source of novel proteins with an unidentified biological role. The genome of Enterobacter cancerogenus bacteriophage Enc34 contains several proteins of unknown function that are nevertheless conserved among distantly related phages. Here, we report the crystal structure of a conserved Enc34 replication protein ORF6 which contains a domain of unknown function DUF2815. Despite the low (~15%) sequence identity, the Enc34 ORF6 structurally resembles the gene 2.5 protein from bacteriophage T7, and likewise is a single-stranded DNA (ssDNA)-binding protein (SSB) that consists of a variation of the oligosaccharide/oligonucleotide-binding (OB)-fold and an unstructured C-terminal segment. We further report the crystal structure of a C-terminally truncated ORF6 in complex with an ssDNA oligonucleotide that reveals a DNA-binding mode involving two aromatic stacks and multiple electrostatic interactions, with implications for a common ssDNA recognition mechanism for all T7-type SSBs.","corpus_id":2034399,"score":1},{"doc_id":"29444826","title":"Polymerase θ-helicase efficiently unwinds DNA and RNA-DNA hybrids.","abstract":"POLQ is a unique multifunctional replication and repair gene that encodes for a N-terminal superfamily 2 helicase and a C-terminal A-family polymerase. Although the function of the polymerase domain has been investigated, little is understood regarding the helicase domain. Multiple studies have reported that polymerase θ-helicase (Polθ-helicase) is unable to unwind DNA. However, it exhibits ATPase activity that is stimulated by single-stranded DNA, which presents a biochemical conundrum. In contrast to previous reports, we demonstrate that Polθ-helicase (residues 1-894) efficiently unwinds DNA with 3'-5' polarity, including DNA with 3' or 5' overhangs, blunt-ended DNA, and replication forks. Polθ-helicase also efficiently unwinds RNA-DNA hybrids and exhibits a preference for unwinding the lagging strand at replication forks, similar to related HELQ helicase. Finally, we find that Polθ-helicase can facilitate strand displacement synthesis by Polθ-polymerase, suggesting a plausible function for the helicase domain. Taken together, these findings indicate nucleic acid unwinding as a relevant activity for Polθ in replication repair.","corpus_id":4872770,"score":1},{"doc_id":"18848568","title":"Bacteriophage T5 DNA ejection under pressure.","abstract":"The transfer of the bacteriophage genome from the capsid into the host cell is a key step of the infectious process. In bacteriophage T5, DNA ejection can be triggered in vitro by simple binding of the phage to its purified Escherichia coli receptor FhuA. Using electrophoresis and cryo-electron microscopy, we measure the extent of DNA ejection as a function of the external osmotic pressure. In the high pressure range (7-16 atm), the amount of DNA ejected decreases with increasing pressure, as theoretically predicted and observed for lambda and SPP1 bacteriophages. In the low and moderate pressure range (2-7 atm), T5 exhibits an unexpected behavior. Instead of a unique ejected length, multiple populations coexist. Some phages eject their complete genome, whereas others stop at some nonrandom states that do not depend on the applied pressure. We show that contrarily to what is observed for the phages SPP1 and lambda, T5 ejection cannot be explained as resulting from a simple pressure equilibrium between the inside and outside of the capsid. Kinetics parameters and/or structural characteristics of the ejection machinery could play a determinant role in T5 DNA ejection.","corpus_id":27898318,"score":0},{"doc_id":"21419780","title":"Crystal structures of the S. cerevisiae Spt6 core and C-terminal tandem SH2 domain.","abstract":"The conserved and essential eukaryotic protein Spt6 functions in transcription elongation, chromatin maintenance, and RNA processing. Spt6 has three characterized functions. It is a histone chaperone capable of reassembling nucleosomes, a central component of transcription elongation complexes, and is required for recruitment of RNA processing factors to elongating RNA polymerase II (RNAPII). Here, we report multiple crystal structures of the 168-kDa Spt6 protein from Saccharomyces cerevisiae that together represent essentially all of the ordered sequence. Our two structures of the ∼900-residue core region reveal a series of putative nucleic acid and protein-protein interaction domains that fold into an elongated form that resembles the bacterial protein Tex. The similarity to a bacterial transcription factor suggests that the core domain performs nucleosome-independent activities, and as with Tex, we find that Spt6 binds DNA. Unlike Tex, however, the Spt6 S1 domain does not contribute to this activity. Crystal structures of the Spt6 C-terminal region reveal a tandem SH2 domain structure composed of two closely associated SH2 folds. One of these SH2 folds is cryptic, while the other shares striking structural similarity with metazoan SH2 domains and possesses structural features associated with the ability to bind phosphorylated substrates including phosphotyrosine. Binding studies with phosphopeptides that mimic the RNAPII C-terminal domain revealed affinities typical of other RNAPII C-terminal domain-binding proteins but did not indicate a specific interaction. Overall, these findings provide a structural foundation for understanding how Spt6 encodes several distinct functions within a single polypeptide chain.","corpus_id":17833160,"score":0}],"string":"[\n {\n \"doc_id\": \"18275380\",\n \"title\": \"Mechanism of eukaryotic homologous recombination.\",\n \"abstract\": \"Homologous recombination (HR) serves to eliminate deleterious lesions, such as double-stranded breaks and interstrand crosslinks, from chromosomes. HR is also critical for the preservation of replication forks, for telomere maintenance, and chromosome segregation in meiosis I. As such, HR is indispensable for the maintenance of genome integrity and the avoidance of cancers in humans. The HR reaction is mediated by a conserved class of enzymes termed recombinases. Two recombinases, Rad51 and Dmc1, catalyze the pairing and shuffling of homologous DNA sequences in eukaryotic cells via a filamentous intermediate on ssDNA called the presynaptic filament. The assembly of the presynaptic filament is a rate-limiting process that is enhanced by recombination mediators, such as the breast tumor suppressor BRCA2. HR accessory factors that facilitate other stages of the Rad51- and Dmc1-catalyzed homologous DNA pairing and strand exchange reaction have also been identified. Recent progress on elucidating the mechanisms of action of Rad51 and Dmc1 and their cohorts of ancillary factors is reviewed here.\",\n \"corpus_id\": 30295291,\n \"score\": 2\n },\n {\n \"doc_id\": \"18831760\",\n \"title\": \"The Mycoplasma pneumoniae MPN229 gene encodes a protein that selectively binds single-stranded DNA and stimulates Recombinase A-mediated DNA strand exchange.\",\n \"abstract\": \"BACKGROUND: Mycoplasma pneumoniae has previously been characterized as a micro-organism that is genetically highly stable. In spite of this genetic stability, homologous DNA recombination has been hypothesized to lie at the basis of antigenic variation of the major surface protein, P1, of M. pneumoniae. In order to identify the proteins that may be involved in homologous DNA recombination in M. pneumoniae, we set out to characterize the MPN229 open reading frame (ORF), which bears sequence similarity to the gene encoding the single-stranded DNA-binding (SSB) protein of other micro-organisms. RESULTS: The MPN229 ORF has the capacity to encode a 166-amino acid protein with a calculated molecular mass of 18.4 kDa. The amino acid sequence of this protein (Mpn SSB) is most closely related to that of the protein predicted to be encoded by the MG091 gene from Mycoplasma genitalium (61% identity). The MPN229 ORF was cloned, and different versions of Mpn SSB were expressed in E. coli and purified to > 95% homogeneity. The purified protein was found to exist primarily as a homo-tetramer in solution, and to strongly and selectively bind single-stranded DNA (ssDNA) in a divalent cation- and DNA substrate sequence-independent manner. Mpn SSB was found to bind with a higher affinity to ssDNA substrates larger than 20 nucleotides than to smaller substrates. In addition, the protein strongly stimulated E. coli Recombinase A (RecA)-promoted DNA strand exchange, which indicated that Mpn SSB may play an important role in DNA recombination processes in M. pneumoniae. CONCLUSION: The M. pneumoniae MPN229 gene encodes a protein, Mpn SSB, which selectively and efficiently binds ssDNA, and stimulates E. coli RecA-promoted homologous DNA recombination. Consequently, the Mpn SSB protein may play a crucial role in DNA recombinatorial pathways in M. pneumoniae. The results from this study will pave the way for unraveling these pathways and assess their role in antigenic variation of M. pneumoniae.\",\n \"corpus_id\": 8615785,\n \"score\": 2\n },\n {\n \"doc_id\": \"19038270\",\n \"title\": \"Human transcriptional coactivator PC4 stimulates DNA end joining and activates DSB repair activity.\",\n \"abstract\": \"Human transcriptional coactivator PC4 is a highly abundant nuclear protein that is involved in diverse cellular processes ranging from transcription to chromatin organization. Earlier, we have shown that PC4, a positive activator of p53, overexpresses upon genotoxic insult in a p53-dependent manner. In the present study, we show that PC4 stimulates ligase-mediated DNA end joining irrespective of the source of DNA ligase. Pull-down assays reveal that PC4 helps in the association of DNA ends through its C-terminal domain. In vitro nonhomologous end-joining assays with cell-free extracts show that PC4 enhances the joining of noncomplementary DNA ends. Interestingly, we found that PC4 activates double-strand break (DSB) repair activity through stimulation of DSB rejoining in vivo. Together, these findings demonstrate PC4 as an activator of nonhomologous end joining and DSB repair activity.\",\n \"corpus_id\": 43300497,\n \"score\": 2\n },\n {\n \"doc_id\": \"19047459\",\n \"title\": \"Recruitment of RNA polymerase II cofactor PC4 to DNA damage sites.\",\n \"abstract\": \"The multifunctional nuclear protein positive cofactor 4 (PC4) is involved in various cellular processes including transcription, replication, and chromatin organization. Recently, PC4 has been identified as a suppressor of oxidative mutagenesis in Escherichia coli and Saccharomyces cerevisiae. To investigate a potential role of PC4 in mammalian DNA repair, we used a combination of live cell microscopy, microirradiation, and fluorescence recovery after photobleaching analysis. We found a clear accumulation of endogenous PC4 at DNA damage sites introduced by either chemical agents or laser microirradiation. Using fluorescent fusion proteins and specific mutants, we demonstrated that the rapid recruitment of PC4 to laser-induced DNA damage sites is independent of poly(ADP-ribosyl)ation and gammaH2AX but depends on its single strand binding capacity. Furthermore, PC4 showed a high turnover at DNA damages sites compared with the repair factors replication protein A and proliferating cell nuclear antigen. We propose that PC4 plays a role in the early response to DNA damage by recognizing single-stranded DNA and may thus initiate or facilitate the subsequent steps of DNA repair.\",\n \"corpus_id\": 5573494,\n \"score\": 2\n },\n {\n \"doc_id\": \"19139058\",\n \"title\": \"Transcription-associated recombination in eukaryotes: link between transcription, replication and recombination.\",\n \"abstract\": \"Homologous recombination (HR) is an important DNA repair pathway and is essential for cellular survival. It plays a major role in repairing replication-associated lesions and is functionally connected to replication. Transcription is another cellular process, which has emerged to have a connection with HR. Transcription enhances HR, which is a ubiquitous phenomenon referred to as transcription-associated recombination (TAR). Recent evidence suggests that TAR plays a role in inducing genetic instability, for example in the THO mutants (Tho2, Hpr1, Mft1 and Thp2) in yeast or during the development of the immune system leading to genetic diversity in mammals. On the other hand, evidence also suggests that TAR may play a role in preventing genetic instability in many different ways, one of which is by rescuing replication during transcription. Hence, TAR is a double-edged sword and plays a role in both preventing and inducing genetic instability. In spite of the interesting nature of TAR, the mechanism behind TAR has remained elusive. Recent advances in the area, however, suggest a link between TAR and replication and show specific genetic requirements for TAR that differ from regular HR. In this review, we aim to present the available evidence for TAR in both lower and higher eukaryotes and discuss its possible mechanisms, with emphasis on its connection with replication.\",\n \"corpus_id\": 42121615,\n \"score\": 2\n },\n {\n \"doc_id\": \"19525231\",\n \"title\": \"Interaction between the transactivation domain of p53 and PC4 exemplifies acidic activation domains as single-stranded DNA mimics.\",\n \"abstract\": \"The tumor suppressor p53 regulates cell cycle arrest and apoptosis by transactivating several genes that are critical for these processes. The transcriptional activity of p53 is often regulated by post-translational modifications and its interactions with various transcriptional coactivators. Here we report a physical interaction between the N-terminal transactivation domain (TAD) of p53 and the C-terminal DNA-binding domain of positive cofactor 4 (PC4(CTD)). Using NMR spectroscopy, we showed that residues 35-57 (TAD2) interact with PC4. (15)N,(1)H HSQC and fluorescence competition experiments indicated that TAD binds to the DNA-binding site of PC4. Hepta-phosphorylation of the TAD peptide increased its binding affinity. Computer modeling of the p53N-PC4 complex revealed several important interactions that are reminiscent of those in the single-stranded DNA-PC4 complex. The ubiquitous nature of the acidic transactivation domain of p53 in mediating interactions with several transcription cofactors is also manifested as a DNA mimetic.\",\n \"corpus_id\": 28468533,\n \"score\": 2\n },\n {\n \"doc_id\": \"20305379\",\n \"title\": \"Sub1/PC4 a chromatin associated protein with multiple functions in transcription.\",\n \"abstract\": \"Yeast Sub1 and its human ortholog PC4 display multiple cellular functions in vivo. Sub1/PC4 contains a unique conserved non-specific DNA-binding domain and is involved in distinct DNA-dependent processes including replication, DNA repair and transcription. Sub1/PC4 is a non-histone chromatin-associated protein initially described as a co-activator for RNA polymerase (Pol) II transcription in vitro. Recently, biochemical and genomic studies showed that Sub1 is not restricted to Pol II transcription but is also involved in Pol III transcription revealing a more general role in transcription than anticipated. Sub1/PC4 appears to play a dual (positive and negative) complex role in gene expression and has multiple effects in distinct steps of the transcription cycle, consisting of initiation, elongation, termination and reinitiation. Here, the multiple transcriptional functions of Sub1/PC4 will be reviewed and the recent findings and their possible implications in the understanding of Sub1/PC4 function in transcription will be discussed.\",\n \"corpus_id\": 10796722,\n \"score\": 2\n },\n {\n \"doc_id\": \"20690856\",\n \"title\": \"Regulation of homologous recombination in eukaryotes.\",\n \"abstract\": \"Homologous recombination (HR) is required for accurate chromosome segregation during the first meiotic division and constitutes a key repair and tolerance pathway for complex DNA damage, including DNA double-strand breaks, interstrand crosslinks, and DNA gaps. In addition, recombination and replication are inextricably linked, as recombination recovers stalled and broken replication forks, enabling the evolution of larger genomes/replicons. Defects in recombination lead to genomic instability and elevated cancer predisposition, demonstrating a clear cellular need for recombination. However, recombination can also lead to genome rearrangements. Unrestrained recombination causes undesired endpoints (translocation, deletion, inversion) and the accumulation of toxic recombination intermediates. Evidently, HR must be carefully regulated to match specific cellular needs. Here, we review the factors and mechanistic stages of recombination that are subject to regulation and suggest that recombination achieves flexibility and robustness by proceeding through metastable, reversible intermediates.\",\n \"corpus_id\": 7874976,\n \"score\": 2\n },\n {\n \"doc_id\": \"21129204\",\n \"title\": \"Structural analysis of bacteriophage T4 DNA replication: a review in the Virology Journal series on bacteriophage T4 and its relatives.\",\n \"abstract\": \"The bacteriophage T4 encodes 10 proteins, known collectively as the replisome, that are responsible for the replication of the phage genome. The replisomal proteins can be subdivided into three activities; the replicase, responsible for duplicating DNA, the primosomal proteins, responsible for unwinding and Okazaki fragment initiation, and the Okazaki repair proteins. The replicase includes the gp43 DNA polymerase, the gp45 processivity clamp, the gp44/62 clamp loader complex, and the gp32 single-stranded DNA binding protein. The primosomal proteins include the gp41 hexameric helicase, the gp61 primase, and the gp59 helicase loading protein. The RNaseH, a 5' to 3' exonuclease and T4 DNA ligase comprise the activities necessary for Okazaki repair. The T4 provides a model system for DNA replication. As a consequence, significant effort has been put forth to solve the crystallographic structures of these replisomal proteins. In this review, we discuss the structures that are available and provide comparison to related proteins when the T4 structures are unavailable. Three of the ten full-length T4 replisomal proteins have been determined; the gp59 helicase loading protein, the RNase H, and the gp45 processivity clamp. The core of T4 gp32 and two proteins from the T4 related phage RB69, the gp43 polymerase and the gp45 clamp are also solved. The T4 gp44/62 clamp loader has not been crystallized but a comparison to the E. coli gamma complex is provided. The structures of T4 gp41 helicase, gp61 primase, and T4 DNA ligase are unknown, structures from bacteriophage T7 proteins are discussed instead. To better understand the functionality of T4 DNA replication, in depth structural analysis will require complexes between proteins and DNA substrates. A DNA primer template bound by gp43 polymerase, a fork DNA substrate bound by RNase H, gp43 polymerase bound to gp32 protein, and RNase H bound to gp32 have been crystallographically determined. The preparation and crystallization of complexes is a significant challenge. We discuss alternate approaches, such as small angle X-ray and neutron scattering to generate molecular envelopes for modeling macromolecular assemblies.\",\n \"corpus_id\": 9996923,\n \"score\": 2\n },\n {\n \"doc_id\": \"21193408\",\n \"title\": \"Coactivator function of positive cofactor 4 (PC4) in Sp1-directed luteinizing hormone receptor (LHR) gene transcription.\",\n \"abstract\": \"The LHR has an essential role in sexual development and reproductive function, and its transcription is subjected to several modes of regulation. In this study, we investigated PC4 coactivator function in the control of LHR transcription. Knockdown of PC4 by siRNA inhibited the LHR basal promoter activity and trichostatin A (TSA)-induced gene transcriptional activation and expression in MCF-7 cells. While overexpression of PC4 alone had no effect on the LHR gene, it significantly enhanced Sp1- but not Sp3-mediated LHR transcriptional activity. PC4 directly interacts with Sp1 at the LHR promoter, and this interaction is negatively regulated by PC4 phosphorylation. The coactivator domain (22-91 aa) of PC4 and DNA binding domain of Sp1 are essential for PC4/Sp1 interaction. ChIP assay revealed significant occupancy of PC4 at the LHR promoter that increased upon TSA treatment. Disruption of PC4 expression significantly reduced TSA-induced recruitment of TFIIB and RNAP II, at the promoter. PC4 functions are beyond TSA-induced phosphatase release, PI3K-mediated Sp1 phosphorylation, and HDAC1/2/mSin3A co-repressor release indicating its role as linker coactivator of Sp1 and the transcriptional machinery. These findings demonstrated a critical aspect of LHR modulation whereby PC4 acts as a coactivator of Sp1 to contribute to the human of LHR transcription.\",\n \"corpus_id\": 5470766,\n \"score\": 2\n },\n {\n \"doc_id\": \"21599536\",\n \"title\": \"Presynaptic filament dynamics in homologous recombination and DNA repair.\",\n \"abstract\": \"Homologous recombination (HR) is an essential genome stability mechanism used for high-fidelity repair of DNA double-strand breaks and for the recovery of stalled or collapsed DNA replication forks. The crucial homology search and DNA strand exchange steps of HR are catalyzed by presynaptic filaments-helical filaments of a recombinase enzyme bound to single-stranded DNA (ssDNA). Presynaptic filaments are fundamentally dynamic structures, the assembly, catalytic turnover, and disassembly of which must be closely coordinated with other elements of the DNA recombination, repair, and replication machinery in order for genome maintenance functions to be effective. Here, we reviewed the major dynamic elements controlling the assembly, activity, and disassembly of presynaptic filaments; some intrinsic such as recombinase ATP-binding and hydrolytic activities, others extrinsic such as ssDNA-binding proteins, mediator proteins, and DNA motor proteins. We examined dynamic behavior on multiple levels, including atomic- and filament-level structural changes associated with ATP binding and hydrolysis as evidenced in crystal structures, as well as subunit binding and dissociation events driven by intrinsic and extrinsic factors. We examined the biochemical properties of recombination proteins from four model systems (T4 phage, Escherichia coli, Saccharomyces cerevisiae, and Homo sapiens), demonstrating how their properties are tailored for the context-specific requirements in these diverse species. We proposed that the presynaptic filament has evolved to rely on multiple external factors for increased multilevel regulation of HR processes in genomes with greater structural and sequence complexity.\",\n \"corpus_id\": 30926436,\n \"score\": 2\n },\n {\n \"doc_id\": \"22055186\",\n \"title\": \"Sub1 and RPA associate with RNA polymerase II at different stages of transcription.\",\n \"abstract\": \"Single-stranded DNA-binding proteins play many roles in nucleic acid metabolism, but their importance during transcription remains unclear. Quantitative proteomic analysis of RNA polymerase II (RNApII) preinitiation complexes (PICs) identified Sub1 and the replication protein A complex (RPA), both of which bind single-stranded DNA (ssDNA). Sub1, homolog of mammalian coactivator PC4, exhibits strong genetic interactions with factors necessary for promoter melting. Sub1 localizes near the transcription bubble in vitro and binds to promoters in vivo dependent upon PIC assembly. In contrast, RPA localizes to transcribed regions of active genes, strongly correlated with transcribing RNApII but independently of replication. RFA1 interacts genetically with transcription elongation factor genes. Interestingly, RPA levels increase at active promoters in cells carrying a Sub1 deletion or ssDNA-binding mutant, suggesting competition for a common binding site. We propose that Sub1 and RPA interact with the nontemplate strand of RNApII complexes during initiation and elongation, respectively.\",\n \"corpus_id\": 11830059,\n \"score\": 2\n },\n {\n \"doc_id\": \"22207204\",\n \"title\": \"The interface of transcription and DNA replication in the mitochondria.\",\n \"abstract\": \"DNA replication of the mitochondrial genome is unique in that replication is not primed by RNA derived from dedicated primases, but instead by extension of processed RNA transcripts laid down by the mitochondrial RNA polymerase. Thus, the RNA polymerase serves not only to generate the transcripts but also the primers needed for mitochondrial DNA replication. The interface between this transcription and DNA replication is not well understood but must be highly regulated and coordinated to carry out both mitochondrial DNA replication and transcription. This review focuses on the extension of RNA primers for DNA replication by the replication machinery and summarizes the current models of DNA replication in mitochondria as well as the proteins involved in mitochondrial DNA replication, namely, the DNA polymerase γ and its accessory subunit, the mitochondrial DNA helicase, the single-stranded DNA binding protein, topoisomerase I and IIIα and RNaseH1. This article is part of a Special Issue entitled: Mitochondrial Gene Expression.\",\n \"corpus_id\": 24587140,\n \"score\": 2\n },\n {\n \"doc_id\": \"22427673\",\n \"title\": \"Mutational analysis of the T4 gp59 helicase loader reveals its sites for interaction with helicase, single-stranded binding protein, and DNA.\",\n \"abstract\": \"Efficient DNA replication involves coordinated interactions among DNA polymerase, multiple factors, and the DNA. From bacteriophage T4 to eukaryotes, these factors include a helicase to unwind the DNA ahead of the replication fork, a single-stranded binding protein (SSB) to bind to the ssDNA on the lagging strand, and a helicase loader that associates with the fork, helicase, and SSB. The previously reported structure of the helicase loader in the T4 system, gene product (gp)59, has revealed an N-terminal domain, which shares structural homology with the high mobility group (HMG) proteins from eukaryotic organisms. Modeling of this structure with fork DNA has suggested that the HMG-like domain could bind to the duplex DNA ahead of the fork, whereas the C-terminal portion of gp59 would provide the docking sites for helicase (T4 gp41), SSB (T4 gp32), and the ssDNA fork arms. To test this model, we have used random and targeted mutagenesis to generate mutations throughout gp59. We have assayed the ability of the mutant proteins to bind to fork, primed fork, and ssDNAs, to interact with SSB, to stimulate helicase activity, and to function in leading and lagging strand DNA synthesis. Our results provide strong biochemical support for the role of the N-terminal gp59 HMG motif in fork binding and the interaction of the C-terminal portion of gp59 with helicase and SSB. Our results also suggest that processive replication may involve the switching of gp59 between its interactions with helicase and SSB.\",\n \"corpus_id\": 26548293,\n \"score\": 2\n },\n {\n \"doc_id\": \"22948907\",\n \"title\": \"Structural features of the single-stranded DNA-binding protein MoSub1 from Magnaporthe oryzae.\",\n \"abstract\": \"The well studied general transcription cofactor Sub1/PC4 has multiple functions in transcription. It plays both a negative and a positive role in transcription initiation and is involved in elongation and downstream transcription processes and as a transcription reinitiation factor. MoSub1, a Sub1/PC4 orthologue from rice blast fungus, binds the single-stranded DNA dT(12) tightly with an affinity of 186 nM. The crystal structure of MoSub1 has been solved to 1.79 Å resolution. The structure of the protein shows high similiarity to the structure of PC4 and it has a similar dimer interface and DNA-binding region to PC4, indicating that MoSub1 could bind DNA using the same motif as other proteins of the Sub1/PC4 family. There are two novel features in the MoSub1 structure: a region N-terminal to the DNA-binding domain and a C-terminal extension. The region N-terminal to the DNA-binding domain of MoSub1 turns back towards the DNA-binding site and may interact directly with DNA or the DNA-binding site. The C-terminal extension region, which is absent in PC4, may not be capable of interacting with DNA and is one possible reason for the differences between Sub1 and PC4.\",\n \"corpus_id\": 20917803,\n \"score\": 2\n },\n {\n \"doc_id\": \"22976174\",\n \"title\": \"Functions of single-strand DNA-binding proteins in DNA replication, recombination, and repair.\",\n \"abstract\": \"Double-stranded (ds) DNA contains all of the necessary genetic information, although practical use of this information requires unwinding of the duplex DNA. DNA unwinding creates single-stranded (ss) DNA intermediates that serve as templates for myriad cellular functions. Exposure of ssDNA presents several problems to the cell. First, ssDNA is thermodynamically less stable than dsDNA, which leads to spontaneous formation of duplex secondary structures that impede genome maintenance processes. Second, relative to dsDNA, ssDNA is hypersensitive to chemical and nucleolytic attacks that can cause damage to the genome. Cells deal with these potential problems by encoding specialized ssDNA-binding proteins (SSBs) that bind to and stabilize ssDNA structures required for essential genomic processes. SSBs are essential proteins found in all domains of life. SSBs bind ssDNA with high affinity and in a sequence-independent manner and, in doing so, SSBs help to form the central nucleoprotein complex substrate for DNA replication, recombination, and repair processes. While SSBs are found in every organism, the proteins themselves share surprisingly little sequence similarity, subunit composition, and oligomerization states. All SSB proteins contain at least one DNA-binding oligonucleotide/oligosaccharide binding (OB) fold, which consists minimally of a five stranded beta-sheet arranged as a beta barrel capped by a single alpha helix. The OB fold is responsible for both ssDNA binding and oligomerization (for SSBs that operate as oligomers). The overall organization of OB folds varies between bacteria, eukaryotes, and archaea. As part of SSB/ssDNA cellular structures, SSBs play direct roles in the DNA replication, recombination, and repair. In many cases, SSBs have been found to form specific complexes with diverse genome maintenance proteins, often helping to recruit SSB/ssDNA-processing enzymes to the proper cellular sites of action. This clustering of genome maintenance factors can help to stimulate and coordinate the activities of individual enzymes and is also important for dislodging SSB from ssDNA. These features support a model in which DNA metabolic processes have evolved to work on ssDNA/SSB nucleoprotein filaments rather than on naked ssDNA. In this volume, methods are described to interrogate SSB-DNA and SSB-protein binding functions along with approaches that aim to understand the cellular functions of SSB. This introductory chapter offers a general overview of SSBs that focuses on their structures, DNA-binding mechanisms, and protein-binding partners.\",\n \"corpus_id\": 20789227,\n \"score\": 2\n },\n {\n \"doc_id\": \"23303792\",\n \"title\": \"Structures of apo- and ssDNA-bound YdbC from Lactococcus lactis uncover the function of protein domain family DUF2128 and expand the single-stranded DNA-binding domain proteome.\",\n \"abstract\": \"Single-stranded DNA (ssDNA) binding proteins are important in basal metabolic pathways for gene transcription, recombination, DNA repair and replication in all domains of life. Their main cellular role is to stabilize melted duplex DNA and protect genomic DNA from degradation. We have uncovered the molecular function of protein domain family domain of unknown function DUF2128 (PF09901) as a novel ssDNA binding domain. This bacterial domain strongly associates into a dimer and presents a highly positively charged surface that is consistent with its function in non-specific ssDNA binding. Lactococcus lactis YdbC is a representative of DUF2128. The solution NMR structures of the 20 kDa apo-YdbC dimer and YdbC:dT(19)G(1) complex were determined. The ssDNA-binding energetics to YdbC were characterized by isothermal titration calorimetry. YdbC shows comparable nanomolar affinities for pyrimidine and mixed oligonucleotides, and the affinity is sufficiently strong to disrupt duplex DNA. In addition, YdbC binds with lower affinity to ssRNA, making it a versatile nucleic acid-binding domain. The DUF2128 family is related to the eukaryotic nuclear protein positive cofactor 4 (PC4) family and to the PUR family both by fold similarity and molecular function.\",\n \"corpus_id\": 17595961,\n \"score\": 2\n },\n {\n \"doc_id\": \"23435232\",\n \"title\": \"Characterization of an unusual bipolar helicase encoded by bacteriophage T5.\",\n \"abstract\": \"Bacteriophage T5 has a 120 kb double-stranded linear DNA genome encoding most of the genes required for its own replication. This lytic bacteriophage has a burst size of ∼500 new phage particles per infected cell, demonstrating that it is able to turn each infected bacterium into a highly efficient DNA manufacturing machine. To begin to understand DNA replication in this prodigious bacteriophage, we have characterized a putative helicase encoded by gene D2. We show that bacteriophage T5 D2 protein is the first viral helicase to be described with bipolar DNA unwinding activities that require the same core catalytic residues for unwinding in either direction. However, unwinding of partially single- and double-stranded DNA test substrates in the 3'-5' direction is more robust and can be distinguished from the 5'-3' activity by a number of features including helicase complex stability, salt sensitivity and the length of single-stranded DNA overhang required for initiation of helicase action. The presence of D2 in an early gene cluster, the identification of a putative helix-turn-helix DNA-binding motif outside the helicase core and homology with known eukaryotic and prokaryotic replication initiators suggest an involvement for this unusual helicase in DNA replication initiation.\",\n \"corpus_id\": 18931209,\n \"score\": 2\n },\n {\n \"doc_id\": \"23732982\",\n \"title\": \"Interaction of T4 UvsW helicase and single-stranded DNA binding protein gp32 through its carboxy-terminal acidic tail.\",\n \"abstract\": \"Bacteriophage T4 UvsW helicase contains both unwinding and annealing activities and displays some functional similarities to bacterial RecG and RecQ helicases. UvsW is involved in several DNA repair pathways, playing important roles in recombination-dependent DNA repair and the reorganization of stalled replication forks. The T4 single-stranded DNA (ssDNA) binding protein gp32 is a central player in nearly all DNA replication and repair processes and is thought to facilitate their coordination by recruiting and regulating the various proteins involved. Here, we show that the activities of the UvsW protein are modulated by gp32. UvsW-catalyzed unwinding of recombination intermediates such as D-loops and static X-DNA (Holliday junction mimic) to ssDNA products is enhanced by the gp32 protein. The enhancement requires the presence of the protein interaction domain of gp32 (the acidic carboxy-terminus), suggesting that a specific interaction between UvsW and gp32 is required. In the absence of this interaction, the ssDNA annealing and ATP-dependent translocation activities of UvsW are severely inhibited when gp32 coats the ssDNA lattice. However, when UvsW and gp32 do interact, UvsW is able to efficiently displace the gp32 protein from the ssDNA. This ability of UvsW to remove gp32 from ssDNA may explain its ability to enhance the strand invasion activity of the T4 recombinase (UvsX) and suggests a possible new role for UvsW in gp32-mediated DNA transactions.\",\n \"corpus_id\": 33374945,\n \"score\": 2\n },\n {\n \"doc_id\": \"23881942\",\n \"title\": \"Archaeology of eukaryotic DNA replication.\",\n \"abstract\": \"Recent advances in the characterization of the archaeal DNA replication system together with comparative genomic analysis have led to the identification of several previously uncharacterized archaeal proteins involved in replication and currently reveal a nearly complete correspondence between the components of the archaeal and eukaryotic replication machineries. It can be inferred that the archaeal ancestor of eukaryotes and even the last common ancestor of all extant archaea possessed replication machineries that were comparable in complexity to the eukaryotic replication system. The eukaryotic replication system encompasses multiple paralogs of ancestral components such that heteromeric complexes in eukaryotes replace archaeal homomeric complexes, apparently along with subfunctionalization of the eukaryotic complex subunits. In the archaea, parallel, lineage-specific duplications of many genes encoding replication machinery components are detectable as well; most of these archaeal paralogs remain to be functionally characterized. The archaeal replication system shows remarkable plasticity whereby even some essential components such as DNA polymerase and single-stranded DNA-binding protein are displaced by unrelated proteins with analogous activities in some lineages.\",\n \"corpus_id\": 22434475,\n \"score\": 2\n },\n {\n \"doc_id\": \"24482743\",\n \"title\": \"Identification of the ssDNA-binding protein of bacteriophage T5: Implications for T5 replication.\",\n \"abstract\": \"In a recent study, we identified and characterized the long-elusive replicative single-stranded DNA-binding protein of bacteriophage T5, which we showed is related to the eukaryotic transcription coactivator PC4. Here, we provide an extended discussion of these data, report several additional observations and consider implications for the recombination-dependent replication mechanism of the T5 genus, which is still poorly understood.\",\n \"corpus_id\": 9442522,\n \"score\": 2\n },\n {\n \"doc_id\": \"25083707\",\n \"title\": \"Phage ORF family recombinases: conservation of activities and involvement of the central channel in DNA binding.\",\n \"abstract\": \"Genetic and biochemical evidence suggests that λ Orf is a recombination mediator, promoting nucleation of either bacterial RecA or phage Redβ recombinases onto single-stranded DNA (ssDNA) bound by SSB protein. We have identified a diverse family of Orf proteins that includes representatives implicated in DNA base flipping and those fused to an HNH endonuclease domain. To confirm a functional relationship with the Orf family, a distantly-related homolog, YbcN, from Escherichia coli cryptic prophage DLP12 was purified and characterized. As with its λ relative, YbcN showed a preference for binding ssDNA over duplex. Neither Orf nor YbcN displayed a significant preference for duplex DNA containing mismatches or 1-3 nucleotide bulges. YbcN also bound E. coli SSB, although unlike Orf, it failed to associate with an SSB mutant lacking the flexible C-terminal tail involved in coordinating heterologous protein-protein interactions. Residues conserved in the Orf family that flank the central cavity in the λ Orf crystal structure were targeted for mutagenesis to help determine the mode of DNA binding. Several of these mutant proteins showed significant defects in DNA binding consistent with the central aperture being important for substrate recognition. The widespread conservation of Orf-like proteins highlights the importance of targeting SSB coated ssDNA during lambdoid phage recombination.\",\n \"corpus_id\": 9546534,\n \"score\": 2\n },\n {\n \"doc_id\": \"25481875\",\n \"title\": \"Regulation of the bacteriophage T4 Dda helicase by Gp32 single-stranded DNA-binding protein.\",\n \"abstract\": \"Dda, one of three helicases encoded by bacteriophage T4, has been well-characterized biochemically but its biological role remains unclear. It is thought to be involved in origin dependent DNA replication, recombination-dependent replication, anti-recombination, and recombination repair. The Gp32 protein of bacteriophage T4 plays critical roles in DNA replication, recombination, and repair by coordinating protein components of the replication fork and by stabilizing ssDNA. Previous work demonstrated that stimulation of DNA synthesis by Dda helicase appears to require direct Gp32-Dda protein-protein interactions and that Gp32 and Dda form a tight complex in the absence of ssDNA. Here we characterize the effects of Gp32-Dda physical and functional interactions through changes in the duplex DNA unwinding and ATPase activities of Dda helicase in the presence of different variants of Gp32 and different DNA repair and replication intermediate structures. Results show that Gp32-Dda interactions can be enhancing or inhibitory, depending on the Gp32 domain seen by Dda. Protein-protein interactions with Gp32 stimulate the unwinding activity of Dda, an effect associated with increased turnover of ATP, suggesting a higher rate of ATPase-driven translocation. Dda-Gp32 interactions also promote the unwinding of DNA substrates at higher salt concentrations and in the presence of substrate-bound DNA polymerase. Conversely, the formation of Gp32 clusters on ssDNA can inhibit unwinding, suggesting that Gp32-ssDNA formation sterically regulates which portions of replication and recombination intermediates are accessible for processing by Dda helicase. The data suggest a mechanism of replication fork restart in which Gp32 promotes Dda activity in template switching while preventing premature fork progression.\",\n \"corpus_id\": 10770482,\n \"score\": 2\n },\n {\n \"doc_id\": \"25646379\",\n \"title\": \"DNA-pairing and annealing processes in homologous recombination and homology-directed repair.\",\n \"abstract\": \"The formation of heteroduplex DNA is a central step in the exchange of DNA sequences via homologous recombination, and in the accurate repair of broken chromosomes via homology-directed repair pathways. In cells, heteroduplex DNA largely arises through the activities of recombination proteins that promote DNA-pairing and annealing reactions. Classes of proteins involved in pairing and annealing include RecA-family DNA-pairing proteins, single-stranded DNA (ssDNA)-binding proteins, recombination mediator proteins, annealing proteins, and nucleases. This review explores the properties of these pairing and annealing proteins, and highlights their roles in complex recombination processes including the double Holliday junction (DhJ) formation, synthesis-dependent strand annealing, and single-strand annealing pathways--DNA transactions that are critical both for genome stability in individual organisms and for the evolution of species.\",\n \"corpus_id\": 2479895,\n \"score\": 2\n },\n {\n \"doc_id\": \"25739870\",\n \"title\": \"Substitution of tryptophan 89 with tyrosine switches the DNA binding mode of PC4.\",\n \"abstract\": \"PC4, a well-known general transcription cofactor, has multiple functions in transcription and DNA repair. Residue W89, is engaged in stacking interactions with DNA in PC4, but substituted by tyrosine in some PC4 orthologous proteins. In order to understand the consequences and reveal the molecular details of this substitution we have determined the crystal structures of the PC4 orthologue MoSub1 and a PC4 W89Y mutant in complex with DNA. In the structure of MoSub1-DNA complex, Y74 interacts directly with a single nucleotide of oligo DNA. By comparison, the equivalent residue, W89 in wild type PC4 interacts with two nucleotides and the base of the second nucleotide has distinct orientation relative to that of the first one. A hydrophobic patch around W89 that favours interaction with two nucleotides is not formed in the PC4 W89Y mutant. Therefore, the change of the surface hydrophobicity around residue 89 results in a difference between the modes of DNA interaction. These results indicate that the conserved Y74 in MoSub1 or W89 in PC4, are not only key residues in making specific interactions with DNA but also required to determine the DNA binding mode of PC4 proteins.\",\n \"corpus_id\": 14934233,\n \"score\": 2\n },\n {\n \"doc_id\": \"25961912\",\n \"title\": \"PC4 promotes genome stability and DNA repair through binding of ssDNA at DNA damage sites.\",\n \"abstract\": \"The transcriptional cofactor PC4 is an ancient single-strand DNA (ssDNA)-binding protein that has a homologue in bacteriophage T5 where it is likely the elusive replicative ssDNA-binding protein. We hypothesize that human PC4 has retained functions in ssDNA binding to stabilize replication forks and prevent genome instability in mammalian cells. Here we demonstrate that PC4 is recruited to hydroxyurea (HU)-stalled replication forks, which is dependent on active transcription and its ssDNA-binding ability. Interestingly, we demonstrate that ssDNA binding by PC4 is critical to suppress spontaneous DNA damage and promote cellular survival. PC4 accumulation co-localizes with replication protein A (RPA) at stalled forks and is increased upon RPA depletion, demonstrating compensatory functions in ssDNA binding. Depletion of PC4 not only results in defective resolution of HU-induced DNA damage but also significantly reduces homologous recombination repair efficiency. Altogether, our results indicate that PC4 has similar functions to RPA in binding ssDNA to promote genome stability, especially at sites of replication-transcription collisions. Oncogene advance online publication, 11 May 2015; doi:10.1038/onc.2015.135.\",\n \"corpus_id\": 27942986,\n \"score\": 2\n },\n {\n \"doc_id\": \"25972894\",\n \"title\": \"Replication and transcription on a collision course: eukaryotic regulation mechanisms and implications for DNA stability.\",\n \"abstract\": \"DNA replication and transcription are vital cellular processes during which the genetic information is copied into complementary DNA and RNA molecules. Highly complex machineries required for DNA and RNA synthesis compete for the same DNA template, therefore being on a collision course. Unscheduled replication-transcription clashes alter the gene transcription program and generate replication stress, reducing fork speed. Molecular pathways and mechanisms that minimize the conflict between replication and transcription have been extensively characterized in prokaryotic cells and recently identified also in eukaryotes. A pathological outcome of replication-transcription collisions is the formation of stable RNA:DNA hybrids in molecular structures called R-loops. Growing evidence suggests that R-loop accumulation promotes both genetic and epigenetic instability, thus severely affecting genome functionality. In the present review, we summarize the current knowledge related to replication and transcription conflicts in eukaryotes, their consequences on genome stability and the pathways involved in their resolution. These findings are relevant to clarify the molecular basis of cancer and neurodegenerative diseases.\",\n \"corpus_id\": 17350826,\n \"score\": 2\n },\n {\n \"doc_id\": \"28009009\",\n \"title\": \"Bacteriophage T5 gene D10 encodes a branch-migration protein.\",\n \"abstract\": \"Helicases catalyze the unwinding of double-stranded nucleic acids where structure and phosphate backbone contacts, rather than nucleobase sequence, usually determines substrate specificity. We have expressed and purified a putative helicase encoded by the D10 gene of bacteriophage T5. Here we report that this hitherto uncharacterized protein possesses branch migration and DNA unwinding activity. The initiation of substrate unwinding showed some sequence dependency, while DNA binding and DNA-dependent ATPase activity did not. DNA footprinting and purine-base interference assays demonstrated that D10 engages these substrates with a defined polarity that may be established by protein-nucleobase contacts. Bioinformatic analysis of the nucleotide databases revealed genes predicted to encode proteins related to D10 in archaebacteria, bacteriophages and in viruses known to infect a range of eukaryotic organisms.\",\n \"corpus_id\": 15888543,\n \"score\": 2\n },\n {\n \"doc_id\": \"28416612\",\n \"title\": \"A biochemical and biophysical model of G-quadruplex DNA recognition by positive coactivator of transcription 4.\",\n \"abstract\": \"DNA sequences that are guanine-rich have received considerable attention because of their potential to fold into a secondary, four-stranded DNA structure termed G-quadruplex (G4), which has been implicated in genomic instability and some human diseases. We have previously identified positive coactivator of transcription (PC4), a single-stranded DNA (ssDNA)-binding protein, as a novel G4 interactor. Here, to expand on these previous observations, we biochemically and biophysically characterized the interaction between PC4 and G4DNA. PC4 can bind alternative G4DNA topologies with a low nanomolar Kd value of ∼2 nm, similar to that observed for ssDNA. In consideration of the different structural features between G4DNA and ssDNA, these binding data indicated that PC4 can interact with G4DNA in a manner distinct from ssDNA. The stoichiometry of the PC4-G4 complex was 1:1 for PC4 dimer:G4 substrate. PC4 did not enhance the rate of folding of G4DNA, and formation of the PC4-G4DNA complex did not result in unfolding of the G4DNA structure. We assembled a G4DNA structure flanked by duplex DNA. We find that PC4 can interact with this G4DNA, as well as the complementary C-rich strand. Molecular docking simulations and DNA footprinting experiments suggest a model where a PC4 dimer accommodates the DNA with one monomer on the G4 strand and the second monomer bound to the C-rich strand. Collectively, these data provide a novel mode of PC4 binding to a DNA secondary structure that remains within the framework of the model for binding to ssDNA. Additionally, consideration of the PC4-G4DNA interaction could provide insight into the biological functions of PC4, which remain incompletely understood.\",\n \"corpus_id\": 205364196,\n \"score\": 2\n },\n {\n \"doc_id\": \"29588157\",\n \"title\": \"Gp2.5, the multifunctional bacteriophage T7 single-stranded DNA binding protein.\",\n \"abstract\": \"The essential bacteriophage T7-encoded single-stranded DNA binding protein is the nexus of T7 DNA metabolism. Multiple layers of macromolecular interactions mediate its function in replication, recombination, repair, and the maturation of viral genomes. In addition to binding ssDNA, the protein binds to DNA polymerase and DNA helicase, regulating their activities. The protein displays potent homologous DNA annealing activity, underscoring its role in recombination.\",\n \"corpus_id\": 4410095,\n \"score\": 2\n },\n {\n \"doc_id\": \"18184592\",\n \"title\": \"Structure and DNA binding of the human Rtf1 Plus3 domain.\",\n \"abstract\": \"The yeast Paf1 complex consists of Paf1, Rtf1, Cdc73, Ctr9, and Leo1 and regulates histone H2B ubiquitination, histone H3 methylation, RNA polymerase II carboxy-terminal domain (CTD) Ser2 phosphorylation, and RNA 3' end processing. We provide structural insight into the Paf1 complex with the NMR structure of the conserved and functionally important Plus3 domain of human Rtf1. A predominantly beta-stranded subdomain displays structural similarity to Dicer/Argonaute PAZ domains and to Tudor domains. We further demonstrate that the highly basic Rtf1 Plus3 domain can interact in vitro with single-stranded DNA via residues on the rim of the beta sheet, reminiscent of siRNA binding by PAZ domains, but did not detect binding to double-stranded DNA or RNA. We discuss the potential role of Rtf1 Plus3 ssDNA binding during transcription elongation.\",\n \"corpus_id\": 38494347,\n \"score\": 1\n },\n {\n \"doc_id\": \"18321528\",\n \"title\": \"Crystal structure and RNA binding of the Tex protein from Pseudomonas aeruginosa.\",\n \"abstract\": \"Tex is a highly conserved bacterial protein that likely functions in a variety of transcriptional processes. Here, we describe two crystal structures of the 86-kDa Tex protein from Pseudomonas aeruginosa at 2.3 and 2.5 A resolution, respectively. These structures reveal a relatively flat and elongated protein, with several potential nucleic acid binding motifs clustered at one end, including an S1 domain near the C-terminus that displays considerable structural flexibility. Tex binds nucleic acids, with a preference for single-stranded RNA, and the Tex S1 domain is required for this binding activity. Point mutants further demonstrate that the primary nucleic acid binding site corresponds to a surface of the S1 domain. Sequence alignment and modeling indicate that the eukaryotic Spt6 transcription factor adopts a similar core structure. Structural analysis further suggests that the RNA polymerase and nucleosome interacting regions of Spt6 flank opposite sides of the Tex-like scaffold. Therefore, the Tex structure may represent a conserved scaffold that binds single-stranded RNA to regulate transcription in both eukaryotic and prokaryotic organisms.\",\n \"corpus_id\": 6130388,\n \"score\": 1\n },\n {\n \"doc_id\": \"18656357\",\n \"title\": \"Functional and structural basis for a bacteriophage homolog of human RAD52.\",\n \"abstract\": \"In eukaryotes, homologous recombination proteins such as RAD51 and RAD52 play crucial roles in DNA repair and genome stability. Human RAD52 is a member of a large single-strand annealing protein (SSAP) family [1] and stimulates Rad51-dependent recombination [2, 3]. In prokaryotes and phages, it has been difficult to establish the presence of RAD52 homologs with conserved sequences. Putative SSAPs were recently found in several phages that infect strains of Lactococcus lactis[4]. One of these SSAPs was identified as Sak and was found in the virulent L. lactis phage ul36, which belongs to the Siphoviridae family [4, 5]. In this study, we show that Sak is homologous to the N terminus of human RAD52. Purified Sak binds single-stranded DNA (ssDNA) preferentially over double-stranded DNA (dsDNA) and promotes the renaturation of long complementary ssDNAs. Sak also binds RecA and stimulates homologous recombination reactions. Mutations shown to modulate RAD52 DNA binding [6] affect Sak similarly. Remarkably, electron-microscopic reconstruction of Sak reveals an undecameric (11) subunit ring, similar to the crystal structure of the N-terminal fragment of human RAD52 [7, 8]. For the first time, we propose a viral homolog of RAD52 at the amino acid, phylogenic, functional, and structural levels.\",\n \"corpus_id\": 15024131,\n \"score\": 1\n },\n {\n \"doc_id\": \"19074952\",\n \"title\": \"The crystal structure of a replicative hexameric helicase DnaC and its complex with single-stranded DNA.\",\n \"abstract\": \"DNA helicases are motor proteins that play essential roles in DNA replication, repair and recombination. In the replicative hexameric helicase, the fundamental reaction is the unwinding of duplex DNA; however, our understanding of this function remains vague due to insufficient structural information. Here, we report two crystal structures of the DnaB-family replicative helicase from Geobacillus kaustophilus HTA426 (GkDnaC) in the apo-form and bound to single-stranded DNA (ssDNA). The GkDnaC-ssDNA complex structure reveals that three symmetrical basic grooves on the interior surface of the hexamer individually encircle ssDNA. The ssDNA-binding pockets in this structure are directed toward the N-terminal domain collar of the hexameric ring, thus orienting the ssDNA toward the DnaG primase to facilitate the synthesis of short RNA primers. These findings provide insight into the mechanism of ssDNA binding and provide a working model to establish a novel mechanism for DNA translocation at the replication fork.\",\n \"corpus_id\": 10859265,\n \"score\": 1\n },\n {\n \"doc_id\": \"19285993\",\n \"title\": \"Single-stranded DNA-binding protein complex from Helicobacter pylori suggests an ssDNA-binding surface.\",\n \"abstract\": \"Single-stranded DNA (ssDNA)-binding protein (SSB) plays an important role in DNA replication, recombination, and repair. SSB consists of an N-terminal ssDNA-binding domain with an oligonucleotide/oligosaccharide binding fold and a flexible C-terminal tail involved in protein-protein interactions. SSB from Helicobacter pylori (HpSSB) was isolated, and the ssDNA-binding characteristics of HpSSB were analyzed by fluorescence titration and electrophoretic mobility shift assay. Tryptophan fluorescence quenching was measured as 61%, and the calculated cooperative affinity was 5.4x10(7) M(-1) with an ssDNA-binding length of 25-30 nt. The crystal structure of the C-terminally truncated protein (HpSSBc) in complex with 35-mer ssDNA [HpSSBc-(dT)(35)] was determined at a resolution of 2.3 A. The HpSSBc monomer folds as an oligonucleotide/oligosaccharide binding fold with a Y-shaped conformation. The ssDNA wrapped around the HpSSBc tetramer through a continuous binding path comprising five essential aromatic residues and a positively charged surface formed by numerous basic residues.\",\n \"corpus_id\": 33474012,\n \"score\": 1\n },\n {\n \"doc_id\": \"19338667\",\n \"title\": \"The N-terminal domain of Escherichia coli RecA have multiple functions in promoting homologous recombination.\",\n \"abstract\": \"Escherichia coli RecA mediates homologous recombination, a process essential to maintaining genome integrity. In the presence of ATP, RecA proteins bind a single-stranded DNA (ssDNA) to form a RecA-ssDNA presynaptic nucleoprotein filament that captures donor double-stranded DNA (dsDNA), searches for homology, and then catalyzes the strand exchange between ssDNA and dsDNA to produce a new heteroduplex DNA. Based upon a recently reported crystal structure of the RecA-ssDNA nucleoprotein filament, we carried out structural and functional studies of the N-terminal domain (NTD) of the RecA protein. The RecA NTD was thought to be required for monomer-monomer interaction. Here we report that it has two other distinct roles in promoting homologous recombination. It first facilitates the formation of a RecA-ssDNA presynaptic nucleoprotein filament by converting ATP to an ADP-Pi intermediate. Then, once the RecA-ssDNA presynaptic nucleoprotein filament is stably assembled in the presence of ATPgammaS, the NTD is required to capture donor dsDNA. Our results also suggest that the second function of NTD may be similar to that of Arg243 and Lys245, which were implicated earlier as binding sites of donor dsDNA. A two-step model is proposed to explain how a RecA-ssDNA presynaptic nucleoprotein filament interacts with donor dsDNA.\",\n \"corpus_id\": 2586706,\n \"score\": 1\n },\n {\n \"doc_id\": \"19445949\",\n \"title\": \"Dynamic regulatory interactions of rad51, rad52, and replication protein-a in recombination intermediates.\",\n \"abstract\": \"Rad51, Rad52, and replication protein-A (RPA) play crucial roles in the repair of DNA double-strand breaks in Saccharomyces cerevisiae. Rad51 mediates DNA strand exchange, a key reaction in DNA recombination. Rad52 recruits Rad51 into single-stranded DNAs (ssDNAs) that are saturated with RPA. Rad52 also promotes annealing of ssDNA strands that are complexed with RPA. Specific protein-protein interactions are involved in these reactions. Here we report new biochemical characteristics of these protein interactions. First, Rad52-RPA interaction requires multiple molecules of RPA to be associated with ssDNA, suggesting that multiple contacts between the Rad52 ring and RPA-ssDNA filament are needed for stable binding. Second, RPA-t11, which is a recombination-deficient mutant of RPA, displays a defect in interacting with Rad52 in the presence of salt above 50 mM, explaining the defect in Rad52-mediated ssDNA annealing in the presence of this mutation. Third, ssDNA annealing promoted by Rad52 is preceded by aggregation of multiple RPA-ssDNA complexes with Rad52, and Rad51 inhibits this aggregation. These results suggest a regulatory role for Rad51 that suppresses ssDNA annealing and facilitates DNA strand invasion. Finally, the Rad51-double-stranded DNA complex disrupts Rad52-RPA interaction in ssDNA and titrates Rad52 from RPA. This suggests an additional regulatory role for Rad51 following DNA strand invasion, where Rad51-double-stranded DNA may inhibit illegitimate second-end capture to ensure the error-free repair of a DNA double-strand break.\",\n \"corpus_id\": 206205013,\n \"score\": 1\n },\n {\n \"doc_id\": \"20404922\",\n \"title\": \"Shared active site architecture between the large subunit of eukaryotic primase and DNA photolyase.\",\n \"abstract\": \"BACKGROUND: DNA synthesis during replication relies on RNA primers synthesised by the primase, a specialised DNA-dependent RNA polymerase that can initiate nucleic acid synthesis de novo. In archaeal and eukaryotic organisms, the primase is a heterodimeric enzyme resulting from the constitutive association of a small (PriS) and large (PriL) subunit. The ability of the primase to initiate synthesis of an RNA primer depends on a conserved Fe-S domain at the C-terminus of PriL (PriL-CTD). However, the critical role of the PriL-CTD in the catalytic mechanism of initiation is not understood. METHODOLOGY/PRINCIPAL FINDINGS: Here we report the crystal structure of the yeast PriL-CTD at 1.55 A resolution. The structure reveals that the PriL-CTD folds in two largely independent alpha-helical domains joined at their interface by a [4Fe-4S] cluster. The larger N-terminal domain represents the most conserved portion of the PriL-CTD, whereas the smaller C-terminal domain is largely absent in archaeal PriL. Unexpectedly, the N-terminal domain reveals a striking structural similarity with the active site region of the DNA photolyase/cryptochrome family of flavoproteins. The region of similarity includes PriL-CTD residues that are known to be essential for initiation of RNA primer synthesis by the primase. CONCLUSION/SIGNIFICANCE: Our study reports the first crystallographic model of the conserved Fe-S domain of the archaeal/eukaryotic primase. The structural comparison with a cryptochrome protein bound to flavin adenine dinucleotide and single-stranded DNA provides important insight into the mechanism of RNA primer synthesis by the primase.\",\n \"corpus_id\": 3766603,\n \"score\": 1\n },\n {\n \"doc_id\": \"21195035\",\n \"title\": \"Physical interaction between archaeal DNA repair helicase Hel308 and Replication Protein A (RPA).\",\n \"abstract\": \"Hel308 is a super-family 2 helicase in archaea with homologues in higher eukaryotes (HelQ and PolQ) that contribute to repair of DNA strand crosslinks (ICLs). However, the contribution of Hel308 to repair processes in archaea is far from clear, including how it co-operates with other proteins of DNA replication, repair and recombination. In this study we identified a physical interaction of Hel308 with RPA. Hel308 did not interact with SSB, and interaction with RPA required a conserved amino acid motif at the Hel308 C-terminus. We propose that in archaea RPA acts as a platform for loading of Hel308 onto aberrant single-stranded DNA (ssDNA) that arises at blocked replication forks. In line with data from a human Hel308 homologue, the helicase activity of archaeal Hel308 was only modestly stimulated (1.5-2 fold) by RPA under some conditions, and much less so than for other known interactions between helicases and single strand DNA (ssDNA) binding proteins. This supports a model for RPA localising Hel308 to DNA damage sites in archaea, rather than it directly stimulating the mechanism of helicase unwinding.\",\n \"corpus_id\": 5223600,\n \"score\": 1\n },\n {\n \"doc_id\": \"21265762\",\n \"title\": \"Structure and function of a novel endonuclease acting on branched DNA substrates.\",\n \"abstract\": \"Branched DNA structures that occur during DNA repair and recombination must be efficiently processed by structure-specific endonucleases in order to avoid cell death. In the present paper, we summarize our screen for new interaction partners for the archaeal replication clamp that led to the functional characterization of a novel endonuclease family, dubbed NucS. Structural analyses of Pyrococcus abyssi NucS revealed an unexpected binding site for ssDNA (single-stranded DNA) that directs, together with the replication clamp, the nuclease activity of this protein towards ssDNA-dsDNA (double-stranded DNA) junctions. Our studies suggest that understanding the detailed architecture and dynamic behaviour of the NucS (nuclease specific for ssDNA)-PCNA (proliferating-cell nuclear antigen) complex with DNA will be crucial for identification of its physiologically relevant activities.\",\n \"corpus_id\": 13314147,\n \"score\": 1\n },\n {\n \"doc_id\": \"21804533\",\n \"title\": \"Tyrosine phosphorylation enhances RAD52-mediated annealing by modulating its DNA binding.\",\n \"abstract\": \"RAD52 protein has an important role in homology-directed DNA repair by mediating RAD51 nucleoprotein filament formation on single-stranded DNA (ssDNA) protected by replication protein-A (RPA) and annealing of RPA-coated ssDNA. In human, cellular response to DNA damage includes phosphorylation of RAD52 by c-ABL kinase at tyrosine 104. To address how this phosphorylation modulates RAD52 function, we used an amber suppressor technology to substitute tyrosine 104 with chemically stable phosphotyrosine analogue (p-Carboxymethyl-L-phenylalanine, pCMF). The RAD52(Y104pCMF) retained ssDNA-binding activity characteristic of unmodified RAD52 but showed lower affinity for double-stranded DNA (dsDNA) binding. Single-molecule analyses revealed that RAD52(Y104pCMF) specifically targets and wraps ssDNA. While RAD52(Y104pCMF) is confined to ssDNA region, unmodified RAD52 readily diffuses into dsDNA region. The Y104pCMF substitution also increased the ssDNA annealing rate and allowed overcoming the inhibitory effect of dsDNA. We propose that phosphorylation at Y104 enhances ssDNA annealing activity of RAD52 by attenuating dsDNA binding. Implications of phosphorylation-mediated activation of RAD52 annealing activity are discussed.\",\n \"corpus_id\": 13330473,\n \"score\": 1\n },\n {\n \"doc_id\": \"22549990\",\n \"title\": \"MALDI-MS detection of noncovalent interactions of single stranded DNA with Escherichia coli single-stranded DNA-binding protein.\",\n \"abstract\": \"The Escherichia coli single-stranded DNA binding protein (SSB) selectively binds single-stranded (ss) DNA and participates in the process of DNA replication, recombination and repair. Different binding modes have previously been observed in SSB•ssDNA complexes, due to the four potential binding sites of SSB. Here, chemical cross-linking, combined with high-mass matrix-assisted laser desorption/ionization (MALDI) mass spectrometry (MS), is used to determine the stoichiometry of the SSB•ssDNA complex. SSB forms a stable homotetramer in solution, but only the monomeric species (m/z 19,100) can be detected with standard MALDI-MS. With chemical cross-linking, the quaternary structure of SSB is conserved, and the tetramer (m/z 79,500) was observed. We found that ssDNA also functions as a stabilizer to conserve the quaternary structure of SSB, as evidenced by the detection of a SSB•ssDNA complex at m/z 94,200 even in the absence of chemical cross-linking. The stability of the SSB•ssDNA complex with MALDI strongly depends on the length and strand of oligonucleotides and the stoichiometry of the SSB•ssDNA complex, which could be attributed to electrostatic interactions that are enhanced in the gas phase. The key factor affecting the stoichiometry of the SSB•ssDNA complex is how ssDNA binds to SSB, rather than the protein-to-DNA ratio. This further suggests that detection of the complex by MALDI is a result of specific binding, and not due to non-specific aggregation in the MALDI plume.\",\n \"corpus_id\": 5594670,\n \"score\": 1\n },\n {\n \"doc_id\": \"22698072\",\n \"title\": \"Thermodynamic analysis of DNA binding by a Bacillus single stranded DNA binding protein.\",\n \"abstract\": \"BACKGROUND: Single-stranded DNA binding proteins (SSB) are essential for DNA replication, repair, and recombination in all organisms. SSB works in concert with a variety of DNA metabolizing enzymes such as DNA polymerase. RESULTS: We have cloned and purified SSB from Bacillus anthracis (SSB(BA)). In the absence of DNA, at concentrations ≤100 μg/ml, SSB(BA) did not form a stable tetramer and appeared to resemble bacteriophage T4 gene 32 protein. Fluorescence anisotropy studies demonstrated that SSB(BA) bound ssDNA with high affinity comparable to other prokaryotic SSBs. Thermodynamic analysis indicated both hydrophobic and ionic contributions to ssDNA binding. FRET analysis of oligo(dT)(70) binding suggested that SSB(BA) forms a tetrameric assembly upon ssDNA binding. This report provides evidence of a bacterial SSB that utilizes a novel mechanism for DNA binding through the formation of a transient tetrameric structure. CONCLUSIONS: Unlike other prokaryotic SSB proteins, SSB(BA) from Bacillus anthracis appeared to be monomeric at concentrations ≤100 μg/ml as determined by SE-HPLC. SSB(BA) retained its ability to bind ssDNA with very high affinity, comparable to SSB proteins which are tetrameric. In the presence of a long ssDNA template, SSB(BA) appears to form a transient tetrameric structure. Its unique structure appears to be due to the cumulative effect of multiple key amino acid changes in its sequence during evolution, leading to perturbation of stable dimer and tetramer formation. The structural features of SSB(BA) could promote facile assembly and disassembly of the protein-DNA complex required in processes such as DNA replication.\",\n \"corpus_id\": 15966117,\n \"score\": 1\n },\n {\n \"doc_id\": \"22749146\",\n \"title\": \"Homologous recombination in eukaryotes.\",\n \"abstract\": \"Homologous recombination (HR) is a mechanistically conserved pathway that ensures maintenance of genomic integrity. During meiosis, HR results in DNA crossover events between homologous chromosomes that produce the genetic diversity inherent in germ cells. The physical connection established between homologs during the crossover event is essential to facilitate correct chromosome segregation. HR is also involved in maintenance of somatic cell genomic stability by restoring replication after a stalled replication fork has encountered a DNA lesion or strand break, as well as following exogenous stresses such as ionizing radiation that induce DNA double-strand breaks. The importance of HR can be gauged by the conservation of HR genes and functions from bacteria to man. Here we review the players and mechanics of eukaryotic HR.\",\n \"corpus_id\": 36235967,\n \"score\": 1\n },\n {\n \"doc_id\": \"23584157\",\n \"title\": \"DNA replication and homologous recombination factors: acting together to maintain genome stability.\",\n \"abstract\": \"Genome duplication requires the coordinated action of multiple proteins to ensure a fast replication with high fidelity. These factors form a complex called the Replisome, which is assembled onto the DNA duplex to promote its unwinding and to catalyze the polymerization of two new strands. Key constituents of the Replisome are the Cdc45-Mcm2-7-GINS helicase and the And1-Claspin-Tipin-Tim1 complex, which coordinate DNA unwinding with polymerase alpha-, delta-, and epsilon- dependent DNA polymerization. These factors encounter numerous obstacles, such as endogenous DNA lesions leading to template breakage and complex structures arising from intrinsic features of specific DNA sequences. To overcome these roadblocks, homologous recombination DNA repair factors, such as Rad51 and the Mre11-Rad50-Nbs1 complex, are required to ensure complete and faithful replication. Consistent with this notion, many of the genes involved in this process result in lethal phenotypes when inactivated in organisms with complex and large genomes. Here, we summarize the architectural and functional properties of the Replisome and propose a unified view of DNA replication and repair processes.\",\n \"corpus_id\": 18778307,\n \"score\": 1\n },\n {\n \"doc_id\": \"24338568\",\n \"title\": \"Control of helicase loading in the coupled DNA replication and recombination systems of bacteriophage T4.\",\n \"abstract\": \"The Gp59 protein of bacteriophage T4 promotes DNA replication by loading the replicative helicase, Gp41, onto replication forks and recombination intermediates. Gp59 also blocks DNA synthesis by Gp43 polymerase until Gp41 is loaded, ensuring that synthesis is tightly coupled to unwinding. The distinct polymerase blocking and helicase loading activities of Gp59 likely involve different binding interactions with DNA and protein partners. Here, we investigate how interactions of Gp59 with DNA and Gp32, the T4 single-stranded DNA (ssDNA)-binding protein, are related to these activities. A previously characterized mutant, Gp59-I87A, exhibits markedly reduced affinity for ssDNA and pseudo-fork DNA substrates. We demonstrate that on Gp32-covered ssDNA, the DNA binding defect of Gp59-I87A is not detrimental to helicase loading and translocation. In contrast, on pseudo-fork DNA the I87A mutation is detrimental to helicase loading and unwinding in the presence or absence of Gp32. Other results indicate that Gp32 binding to lagging strand ssDNA relieves the blockage of Gp43 polymerase activity by Gp59, whereas the inhibition of Gp43 exonuclease activity is maintained. Our findings suggest that Gp59-Gp32 and Gp59-DNA interactions perform separate but complementary roles in T4 DNA metabolism; Gp59-Gp32 interactions are needed to load Gp41 onto D-loops, and other nucleoprotein structures containing clusters of Gp32. Gp59-DNA interactions are needed to load Gp41 onto nascent or collapsed replication forks lacking clusters of Gp32 and to coordinate bidirectional replication from T4 origins. The dual functionalities of Gp59 allow it to promote the initiation or re-start of DNA replication from a wide variety of recombination and replication intermediates.\",\n \"corpus_id\": 34570636,\n \"score\": 1\n },\n {\n \"doc_id\": \"24970156\",\n \"title\": \"Homologous recombination as a replication fork escort: fork-protection and recovery.\",\n \"abstract\": \"Homologous recombination is a universal mechanism that allows DNA repair and ensures the efficiency of DNA replication. The substrate initiating the process of homologous recombination is a single-stranded DNA that promotes a strand exchange reaction resulting in a genetic exchange that promotes genetic diversity and DNA repair. The molecular mechanisms by which homologous recombination repairs a double-strand break have been extensively studied and are now well characterized. However, the mechanisms by which homologous recombination contribute to DNA replication in eukaryotes remains poorly understood. Studies in bacteria have identified multiple roles for the machinery of homologous recombination at replication forks. Here, we review our understanding of the molecular pathways involving the homologous recombination machinery to support the robustness of DNA replication. In addition to its role in fork-recovery and in rebuilding a functional replication fork apparatus, homologous recombination may also act as a fork-protection mechanism. We discuss that some of the fork-escort functions of homologous recombination might be achieved by loading of the recombination machinery at inactivated forks without a need for a strand exchange step; as well as the consequence of such a model for the stability of eukaryotic genomes.\",\n \"corpus_id\": 7453721,\n \"score\": 1\n },\n {\n \"doc_id\": \"25101062\",\n \"title\": \"Evolution of replicative DNA polymerases in archaea and their contributions to the eukaryotic replication machinery.\",\n \"abstract\": \"The elaborate eukaryotic DNA replication machinery evolved from the archaeal ancestors that themselves show considerable complexity. Here we discuss the comparative genomic and phylogenetic analysis of the core replication enzymes, the DNA polymerases, in archaea and their relationships with the eukaryotic polymerases. In archaea, there are three groups of family B DNA polymerases, historically known as PolB1, PolB2 and PolB3. All three groups appear to descend from the last common ancestors of the extant archaea but their subsequent evolutionary trajectories seem to have been widely different. Although PolB3 is present in all archaea, with the exception of Thaumarchaeota, and appears to be directly involved in lagging strand replication, the evolution of this gene does not follow the archaeal phylogeny, conceivably due to multiple horizontal transfers and/or dramatic differences in evolutionary rates. In contrast, PolB1 is missing in Euryarchaeota but otherwise seems to have evolved vertically. The third archaeal group of family B polymerases, PolB2, includes primarily proteins in which the catalytic centers of the polymerase and exonuclease domains are disrupted and accordingly the enzymes appear to be inactivated. The members of the PolB2 group are scattered across archaea and might be involved in repair or regulation of replication along with inactivated members of the RadA family ATPases and an additional, uncharacterized protein that are encoded within the same predicted operon. In addition to the family B polymerases, all archaea, with the exception of the Crenarchaeota, encode enzymes of a distinct family D the origin of which is unclear. We examine multiple considerations that appear compatible with the possibility that family D polymerases are highly derived homologs of family B. The eukaryotic DNA polymerases show a highly complex relationship with their archaeal ancestors including contributions of proteins and domains from both the family B and the family D archaeal polymerases.\",\n \"corpus_id\": 12728106,\n \"score\": 1\n },\n {\n \"doc_id\": \"25202305\",\n \"title\": \"Structural insights into eukaryotic DNA replication.\",\n \"abstract\": \"THREE DNA POLYMERASES OF THE B FAMILY FUNCTION AT THE REPLICATION FORK IN EUKARYOTIC CELLS: DNA polymerases α, δ, and ε. DNA polymerase α, an heterotetramer composed of two primase subunits and two polymerase subunits, initiates replication. DNA polymerases δ and ε elongate the primers generated by pol α. The DNA polymerase from bacteriophage RB69 has served as a model for eukaryotic B family polymerases for some time. The recent crystal structures of pol δ, α, and ε revealed similarities but also a number of unexpected differences between the eukaryotic polymerases and their bacteriophage counterpart, and also among the three yeast polymerases. This review will focus on their shared structural elements as well as the features that are unique to each of these polymerases.\",\n \"corpus_id\": 6070858,\n \"score\": 1\n },\n {\n \"doc_id\": \"25498946\",\n \"title\": \"Leishmania braziliensis replication protein A subunit 1: molecular modelling, protein expression and analysis of its affinity for both DNA and RNA.\",\n \"abstract\": \"BACKGROUND: Replication factor A (RPA) is a single-strand DNA binding protein involved in DNA replication, recombination and repair processes. It is composed by the subunits RPA-1, RPA-2 and RPA-3; the major DNA-binding activity resides in the subunit 1 of the heterotrimeric RPA complex. In yeast and higher eukaryotes, besides the three basic structural DNA-binding domains, the RPA-1 subunit contains an N-terminal region involved in protein-protein interactions with a fourth DNA-binding domain. Remarkably, the N-terminal extension is absent in the RPA-1 of the pathogenic protozoan Leishmania (Leishmania) amazonensis; however, the protein maintains its ability to bind ssDNA. In a recent work, we identify Leishmania (Viannia) braziliensis RPA-1 by its specific binding to the untranslated regions of the HSP70 mRNAs, suggesting that this protein might be also an RNA-binding protein. METHODS: Both rLbRPA-1 purified by His-tag affinity chromatography as well as the in vitro transcribed L. braziliensis 3' HSP70-II UTR were used to perform pull down assays to asses nucleic acid binding properties. Also, homology modeling was carried out to construct the LbRPA-1 tridimensional structure to search relevant amino acid residues to bind nucleic acids. RESULTS: In this work, after obtaining the recombinant L. braziliensis RPA-1 protein under native conditions, competitive and non-competitive pull-down assays confirmed the single-stranded DNA binding activity of this protein and demonstrated its interaction with the 3' UTR from the HSP70-II mRNA. As expected, this protein exhibits a high affinity for ssDNA, but we have found that RPA-1 interacts also with RNA. Additionally, we carried out a structural analysis of L. braziliensis RPA-1 protein using the X-ray diffraction structure of Ustilago maydis homologous protein as a template. Our results indicate that, in spite of the evolutionary divergence between both organisms, the structure of these two RPA-1 proteins seems to be highly conserved. CONCLUSION: The LbRPA-1 protein is a ssDNA binding protein, but also it shows affinity in vitro for the HSP70 mRNA; this finding supports a possible in vivo role in the HSP70 mRNA metabolism. On the other hand, the three dimensional model of Leishmania RPA-1 serves as a starting point for both functional analysis and its exploration as a chemotherapeutic target to combat leishmaniasis.\",\n \"corpus_id\": 9475795,\n \"score\": 1\n },\n {\n \"doc_id\": \"25831490\",\n \"title\": \"Human RECQ1 helicase-driven DNA unwinding, annealing, and branch migration: insights from DNA complex structures.\",\n \"abstract\": \"RecQ helicases are a widely conserved family of ATP-dependent motors with diverse roles in nearly every aspect of bacterial and eukaryotic genome maintenance. However, the physical mechanisms by which RecQ helicases recognize and process specific DNA replication and repair intermediates are largely unknown. Here, we solved crystal structures of the human RECQ1 helicase in complexes with tailed-duplex DNA and ssDNA. The structures map the interactions of the ssDNA tail and the branch point along the helicase and Zn-binding domains, which, together with reported structures of other helicases, define the catalytic stages of helicase action. We also identify a strand-separating pin, which (uniquely in RECQ1) is buttressed by the protein dimer interface. A duplex DNA-binding surface on the C-terminal domain is shown to play a role in DNA unwinding, strand annealing, and Holliday junction (HJ) branch migration. We have combined EM and analytical ultracentrifugation approaches to show that RECQ1 can form what appears to be a flat, homotetrameric complex and propose that RECQ1 tetramers are involved in HJ recognition. This tetrameric arrangement suggests a platform for coordinated activity at the advancing and receding duplexes of an HJ during branch migration.\",\n \"corpus_id\": 6945343,\n \"score\": 1\n },\n {\n \"doc_id\": \"26744780\",\n \"title\": \"Structural basis of nucleic-acid recognition and double-strand unwinding by the essential neuronal protein Pur-alpha.\",\n \"abstract\": \"The neuronal DNA-/RNA-binding protein Pur-alpha is a transcription regulator and core factor for mRNA localization. Pur-alpha-deficient mice die after birth with pleiotropic neuronal defects. Here, we report the crystal structure of the DNA-/RNA-binding domain of Pur-alpha in complex with ssDNA. It reveals base-specific recognition and offers a molecular explanation for the effect of point mutations in the 5q31.3 microdeletion syndrome. Consistent with the crystal structure, biochemical and NMR data indicate that Pur-alpha binds DNA and RNA in the same way, suggesting binding modes for tri- and hexanucleotide-repeat RNAs in two neurodegenerative RNAopathies. Additionally, structure-based in vitro experiments resolved the molecular mechanism of Pur-alpha's unwindase activity. Complementing in vivo analyses in Drosophila demonstrated the importance of a highly conserved phenylalanine for Pur-alpha's unwinding and neuroprotective function. By uncovering the molecular mechanisms of nucleic-acid binding, this study contributes to understanding the cellular role of Pur-alpha and its implications in neurodegenerative diseases.\",\n \"corpus_id\": 261268337,\n \"score\": 1\n },\n {\n \"doc_id\": \"27893960\",\n \"title\": \"Eukaryotic DNA Polymerases in Homologous Recombination.\",\n \"abstract\": \"Homologous recombination (HR) is a central process to ensure genomic stability in somatic cells and during meiosis. HR-associated DNA synthesis determines in large part the fidelity of the process. A number of recent studies have demonstrated that DNA synthesis during HR is conservative, less processive, and more mutagenic than replicative DNA synthesis. In this review, we describe mechanistic features of DNA synthesis during different types of HR-mediated DNA repair, including synthesis-dependent strand annealing, break-induced replication, and meiotic recombination. We highlight recent findings from diverse eukaryotic organisms, including humans, that suggest both replicative and translesion DNA polymerases are involved in HR-associated DNA synthesis. Our focus is to integrate the emerging literature about DNA polymerase involvement during HR with the unique aspects of these repair mechanisms, including mutagenesis and template switching.\",\n \"corpus_id\": 2412487,\n \"score\": 1\n },\n {\n \"doc_id\": \"28383499\",\n \"title\": \"Eukaryotic Replicative Helicase Subunit Interaction with DNA and Its Role in DNA Replication.\",\n \"abstract\": \"The replicative helicase unwinds parental double-stranded DNA at a replication fork to provide single-stranded DNA templates for the replicative polymerases. In eukaryotes, the replicative helicase is composed of the Cdc45 protein, the heterohexameric ring-shaped Mcm2-7 complex, and the tetrameric GINS complex (CMG). The CMG proteins bind directly to DNA, as demonstrated by experiments with purified proteins. The mechanism and function of these DNA-protein interactions are presently being investigated, and a number of important discoveries relating to how the helicase proteins interact with DNA have been reported recently. While some of the protein-DNA interactions directly relate to the unwinding function of the enzyme complex, other protein-DNA interactions may be important for minichromosome maintenance (MCM) loading, origin melting or replication stress. This review describes our current understanding of how the eukaryotic replicative helicase subunits interact with DNA structures in vitro, and proposed models for the in vivo functions of replicative helicase-DNA interactions are also described.\",\n \"corpus_id\": 8127478,\n \"score\": 1\n },\n {\n \"doc_id\": \"28468824\",\n \"title\": \"The DEAD-box protein DDX43 (HAGE) is a dual RNA-DNA helicase and has a K-homology domain required for full nucleic acid unwinding activity.\",\n \"abstract\": \"The K-homology (KH) domain is a nucleic acid-binding domain present in many proteins but has not been reported in helicases. DDX43, also known as HAGE (helicase antigen gene), is a member of the DEAD-box protein family. It contains a helicase core domain in its C terminus and a potential KH domain in its N terminus. DDX43 is highly expressed in many tumors and is, therefore, considered a potential target for immunotherapy. Despite its potential as a therapeutic target, little is known about its activities. Here, we purified recombinant DDX43 protein to near homogeneity and found that it exists as a monomer in solution. Biochemical assays demonstrated that it is an ATP-dependent RNA and DNA helicase. Although DDX43 was active on duplex RNA regardless of the orientation of the single-stranded RNA tail, it preferred a 5' to 3' polarity on RNA and a 3' to 5' direction on DNA. Truncation mutations and site-directed mutagenesis confirmed that the KH domain in DDX43 is responsible for nucleic acid binding. Compared with the activity of the full-length protein, the C-terminal helicase domain had no unwinding activity on RNA substrates and had significantly reduced unwinding activity on DNA. Moreover, the full-length DDX43 protein, with single amino acid change in the KH domain, had reduced unwinding and binding activates on RNA and DNA substrates. Our results demonstrate that DDX43 is a dual helicase and the KH domain is required for its full unwinding activity.\",\n \"corpus_id\": 21471882,\n \"score\": 1\n },\n {\n \"doc_id\": \"29138440\",\n \"title\": \"Structural Basis for DNA Recognition of a Single-stranded DNA-binding Protein from Enterobacter Phage Enc34.\",\n \"abstract\": \"Modern DNA sequencing capabilities have led to the discovery of a large number of new bacteriophage genomes, which are a rich source of novel proteins with an unidentified biological role. The genome of Enterobacter cancerogenus bacteriophage Enc34 contains several proteins of unknown function that are nevertheless conserved among distantly related phages. Here, we report the crystal structure of a conserved Enc34 replication protein ORF6 which contains a domain of unknown function DUF2815. Despite the low (~15%) sequence identity, the Enc34 ORF6 structurally resembles the gene 2.5 protein from bacteriophage T7, and likewise is a single-stranded DNA (ssDNA)-binding protein (SSB) that consists of a variation of the oligosaccharide/oligonucleotide-binding (OB)-fold and an unstructured C-terminal segment. We further report the crystal structure of a C-terminally truncated ORF6 in complex with an ssDNA oligonucleotide that reveals a DNA-binding mode involving two aromatic stacks and multiple electrostatic interactions, with implications for a common ssDNA recognition mechanism for all T7-type SSBs.\",\n \"corpus_id\": 2034399,\n \"score\": 1\n },\n {\n \"doc_id\": \"29444826\",\n \"title\": \"Polymerase θ-helicase efficiently unwinds DNA and RNA-DNA hybrids.\",\n \"abstract\": \"POLQ is a unique multifunctional replication and repair gene that encodes for a N-terminal superfamily 2 helicase and a C-terminal A-family polymerase. Although the function of the polymerase domain has been investigated, little is understood regarding the helicase domain. Multiple studies have reported that polymerase θ-helicase (Polθ-helicase) is unable to unwind DNA. However, it exhibits ATPase activity that is stimulated by single-stranded DNA, which presents a biochemical conundrum. In contrast to previous reports, we demonstrate that Polθ-helicase (residues 1-894) efficiently unwinds DNA with 3'-5' polarity, including DNA with 3' or 5' overhangs, blunt-ended DNA, and replication forks. Polθ-helicase also efficiently unwinds RNA-DNA hybrids and exhibits a preference for unwinding the lagging strand at replication forks, similar to related HELQ helicase. Finally, we find that Polθ-helicase can facilitate strand displacement synthesis by Polθ-polymerase, suggesting a plausible function for the helicase domain. Taken together, these findings indicate nucleic acid unwinding as a relevant activity for Polθ in replication repair.\",\n \"corpus_id\": 4872770,\n \"score\": 1\n },\n {\n \"doc_id\": \"18848568\",\n \"title\": \"Bacteriophage T5 DNA ejection under pressure.\",\n \"abstract\": \"The transfer of the bacteriophage genome from the capsid into the host cell is a key step of the infectious process. In bacteriophage T5, DNA ejection can be triggered in vitro by simple binding of the phage to its purified Escherichia coli receptor FhuA. Using electrophoresis and cryo-electron microscopy, we measure the extent of DNA ejection as a function of the external osmotic pressure. In the high pressure range (7-16 atm), the amount of DNA ejected decreases with increasing pressure, as theoretically predicted and observed for lambda and SPP1 bacteriophages. In the low and moderate pressure range (2-7 atm), T5 exhibits an unexpected behavior. Instead of a unique ejected length, multiple populations coexist. Some phages eject their complete genome, whereas others stop at some nonrandom states that do not depend on the applied pressure. We show that contrarily to what is observed for the phages SPP1 and lambda, T5 ejection cannot be explained as resulting from a simple pressure equilibrium between the inside and outside of the capsid. Kinetics parameters and/or structural characteristics of the ejection machinery could play a determinant role in T5 DNA ejection.\",\n \"corpus_id\": 27898318,\n \"score\": 0\n },\n {\n \"doc_id\": \"21419780\",\n \"title\": \"Crystal structures of the S. cerevisiae Spt6 core and C-terminal tandem SH2 domain.\",\n \"abstract\": \"The conserved and essential eukaryotic protein Spt6 functions in transcription elongation, chromatin maintenance, and RNA processing. Spt6 has three characterized functions. It is a histone chaperone capable of reassembling nucleosomes, a central component of transcription elongation complexes, and is required for recruitment of RNA processing factors to elongating RNA polymerase II (RNAPII). Here, we report multiple crystal structures of the 168-kDa Spt6 protein from Saccharomyces cerevisiae that together represent essentially all of the ordered sequence. Our two structures of the ∼900-residue core region reveal a series of putative nucleic acid and protein-protein interaction domains that fold into an elongated form that resembles the bacterial protein Tex. The similarity to a bacterial transcription factor suggests that the core domain performs nucleosome-independent activities, and as with Tex, we find that Spt6 binds DNA. Unlike Tex, however, the Spt6 S1 domain does not contribute to this activity. Crystal structures of the Spt6 C-terminal region reveal a tandem SH2 domain structure composed of two closely associated SH2 folds. One of these SH2 folds is cryptic, while the other shares striking structural similarity with metazoan SH2 domains and possesses structural features associated with the ability to bind phosphorylated substrates including phosphotyrosine. Binding studies with phosphopeptides that mimic the RNAPII C-terminal domain revealed affinities typical of other RNAPII C-terminal domain-binding proteins but did not indicate a specific interaction. Overall, these findings provide a structural foundation for understanding how Spt6 encodes several distinct functions within a single polypeptide chain.\",\n \"corpus_id\": 17833160,\n \"score\": 0\n }\n]","isConversational":false}}},{"rowIdx":61,"cells":{"query":{"kind":"string","value":"{\n \"doc_id\": \"24482743\",\n \"title\": \"Identification of the ssDNA-binding protein of bacteriophage T5: Implications for T5 replication.\",\n \"abstract\": \"In a recent study, we identified and characterized the long-elusive replicative single-stranded DNA-binding protein of bacteriophage T5, which we showed is related to the eukaryotic transcription coactivator PC4. Here, we provide an extended discussion of these data, report several additional observations and consider implications for the recombination-dependent replication mechanism of the T5 genus, which is still poorly understood.\",\n \"corpus_id\": 9442522\n}"},"candidates":{"kind":"list like","value":[{"doc_id":"18238893","title":"Acidic C-terminal tail of the ssDNA-binding protein of bacteriophage T7 and ssDNA compete for the same binding surface.","abstract":"ssDNA-binding proteins are key components of the machinery that mediates replication, recombination, and repair. Prokaryotic ssDNA-binding proteins share a conserved DNA-binding fold and an acidic C-terminal tail. It has been proposed that in the absence of ssDNA, the C-terminal tail contacts the ssDNA-binding cleft, therefore predicting that the binding of ssDNA and the C-terminal tail is mutually exclusive. Using chemical cross-linking, competition studies, and NMR chemical-shift mapping, we demonstrate that: (i) the C-terminal peptide of the gene 2.5 protein cross-links to the core of the protein only in the absence of ssDNA, (ii) the cross-linked species fails to bind to ssDNA, and (iii) a C-terminal peptide and ssDNA bind to the same overall surface of the protein. We propose that the protection of the DNA-binding cleft by the electrostatic shield of the C-terminal tail observed in prokaryotic ssDNA-binding proteins, ribosomal proteins, and high-mobility group proteins is an evolutionarily conserved mechanism. This mechanism prevents random binding of charged molecules to the nucleic acid-binding pocket and coordinates nucleic acid-protein and protein-protein interactions.","corpus_id":1217841,"score":2},{"doc_id":"19571366","title":"Interaction of bacteriophage T4 and T7 single-stranded DNA-binding proteins with DNA.","abstract":"Bacteriophages T4 and T7 are well-studied model replication systems, which have allowed researchers to determine the roles of many proteins central to DNA replication, recombination and repair. Here we summarize and discuss the results from two recently developed single-molecule methods to determine the salt-dependent DNA-binding kinetics and thermodynamics of the single-stranded DNA (ssDNA)-binding proteins (SSBs) from these systems. We use these methods to characterize both the equilibrium double-stranded DNA (dsDNA) and ssDNA binding of the SSBs T4 gene 32 protein (gp32) and T7 gene 2.5 protein (gp2.5). Despite the overall two-orders-of-magnitude weaker binding of gp2.5 to both forms of DNA, we find that both proteins exhibit four-orders-of-magnitude preferential binding to ssDNA relative to dsDNA. This strong preferential ssDNA binding as well as the weak dsDNA binding is essential for the ability of both proteins to search dsDNA in one dimension to find available ssDNA-binding sites at the replication fork.","corpus_id":21083142,"score":2},{"doc_id":"20951652","title":"On the mutagenicity of homologous recombination and double-strand break repair in bacteriophage.","abstract":"The double-strand break (DSB) repair via homologous recombination is generally construed as a high-fidelity process. However, some molecular genetic observations show that the recombination and the recombinational DSB repair may be mutagenic and even highly mutagenic. Here we developed an effective and precise method for studying the fidelity of DSB repair in vivo by combining DSBs produced site-specifically by the SegC endonuclease with the famous advantages of the recombination analysis of bacteriophage T4 rII mutants. The method is based on the comparison of the rate of reversion of rII mutation in the presence and in the absence of a DSB repair event initiated in the proximity of the mutation. We observed that DSB repair may moderately (up to 6-fold) increase the apparent reversion frequency, the effect of being dependent on the mutation structure. We also studied the effect of the T4 recombinase deficiency (amber mutation in the uvsX gene) on the fidelity of DSB repair. We observed that DSBs are still repaired via homologous recombination in the uvsX mutants, and the apparent fidelity of this repair is higher than that seen in the wild-type background. The mutator effect of the DSB repair may look unexpected given that most of the normal DNA synthesis in bacteriophage T4 is performed via a recombination-dependent replication (RDR) pathway, which is thought to be indistinguishable from DSB repair. There are three possible explanations for the observed mutagenicity of DSB repair: (1) the origin-dependent (early) DNA replication may be more accurate than the RDR; (2) the step of replication initiation may be more mutagenic than the process of elongation; and (3) the apparent mutagenicity may just reflect some non-randomness in the pool of replicating DNA, i.e., preferential replication of the sequences already involved in replication. We discuss the DSB repair pathway in the absence of UvsX recombinase.","corpus_id":207147290,"score":2},{"doc_id":"21129203","title":"Initiation of bacteriophage T4 DNA replication and replication fork dynamics: a review in the Virology Journal series on bacteriophage T4 and its relatives.","abstract":"Bacteriophage T4 initiates DNA replication from specialized structures that form in its genome. Immediately after infection, RNA-DNA hybrids (R-loops) occur on (at least some) replication origins, with the annealed RNA serving as a primer for leading-strand synthesis in one direction. As the infection progresses, replication initiation becomes dependent on recombination proteins in a process called recombination-dependent replication (RDR). RDR occurs when the replication machinery is assembled onto D-loop recombination intermediates, and in this case, the invading 3' DNA end is used as a primer for leading strand synthesis. Over the last 15 years, these two modes of T4 DNA replication initiation have been studied in vivo using a variety of approaches, including replication of plasmids with segments of the T4 genome, analysis of replication intermediates by two-dimensional gel electrophoresis, and genomic approaches that measure DNA copy number as the infection progresses. In addition, biochemical approaches have reconstituted replication from origin R-loop structures and have clarified some detailed roles of both replication and recombination proteins in the process of RDR and related pathways. We will also discuss the parallels between T4 DNA replication modes and similar events in cellular and eukaryotic organelle DNA replication, and close with some current questions of interest concerning the mechanisms of replication, recombination and repair in phage T4.","corpus_id":14822419,"score":2},{"doc_id":"22500043","title":"Assembly and dynamics of Gp59-Gp32-single-stranded DNA (ssDNA), a DNA helicase loading complex required for recombination-dependent replication in bacteriophage T4.","abstract":"The Gp59 protein of bacteriophage T4 plays critical roles in recombination-dependent DNA replication and repair by correctly loading the replicative helicase, Gp41, onto recombination intermediates. Previous work demonstrated that Gp59 is required to load helicase onto single-stranded DNA that is saturated with Gp32, the T4 single-stranded DNA (ssDNA)-binding protein. Gp59 and Gp32 bind simultaneously to ssDNA, forming a Gp59-Gp32-ssDNA complex that is a key intermediate in helicase loading. Here we characterize the assembly and dynamics of this helicase loading complex (HLC) through changes in the fluorescent states of Gp32F, a fluorescein-Gp32 conjugate. Results show that HLC formation requires a minimum Gp32-ssDNA cluster size and that Gp59 co-localizes with Gp32-ssDNA clusters in the presence of excess free ssDNA. These and other results indicate that Gp59 targets helicase assembly onto Gp32-ssDNA clusters that form on the displaced strand of D-loops, which suggests a mechanism for the rapid initiation of recombination-dependent DNA replication. Helicase loading at the HLC requires ATP binding (not hydrolysis) by Gp41 and results in local remodeling of Gp32 within the HLC. Subsequent ATPase-driven translocation of Gp41 progressively disrupts Gp32-ssDNA interactions. Evidence suggests that Gp59 from the HLC is recycled to promote multiple rounds of helicase assembly on Gp32-ssDNA, a capability that could be important for the restart of stalled replication forks.","corpus_id":25923293,"score":2},{"doc_id":"22976174","title":"Functions of single-strand DNA-binding proteins in DNA replication, recombination, and repair.","abstract":"Double-stranded (ds) DNA contains all of the necessary genetic information, although practical use of this information requires unwinding of the duplex DNA. DNA unwinding creates single-stranded (ss) DNA intermediates that serve as templates for myriad cellular functions. Exposure of ssDNA presents several problems to the cell. First, ssDNA is thermodynamically less stable than dsDNA, which leads to spontaneous formation of duplex secondary structures that impede genome maintenance processes. Second, relative to dsDNA, ssDNA is hypersensitive to chemical and nucleolytic attacks that can cause damage to the genome. Cells deal with these potential problems by encoding specialized ssDNA-binding proteins (SSBs) that bind to and stabilize ssDNA structures required for essential genomic processes. SSBs are essential proteins found in all domains of life. SSBs bind ssDNA with high affinity and in a sequence-independent manner and, in doing so, SSBs help to form the central nucleoprotein complex substrate for DNA replication, recombination, and repair processes. While SSBs are found in every organism, the proteins themselves share surprisingly little sequence similarity, subunit composition, and oligomerization states. All SSB proteins contain at least one DNA-binding oligonucleotide/oligosaccharide binding (OB) fold, which consists minimally of a five stranded beta-sheet arranged as a beta barrel capped by a single alpha helix. The OB fold is responsible for both ssDNA binding and oligomerization (for SSBs that operate as oligomers). The overall organization of OB folds varies between bacteria, eukaryotes, and archaea. As part of SSB/ssDNA cellular structures, SSBs play direct roles in the DNA replication, recombination, and repair. In many cases, SSBs have been found to form specific complexes with diverse genome maintenance proteins, often helping to recruit SSB/ssDNA-processing enzymes to the proper cellular sites of action. This clustering of genome maintenance factors can help to stimulate and coordinate the activities of individual enzymes and is also important for dislodging SSB from ssDNA. These features support a model in which DNA metabolic processes have evolved to work on ssDNA/SSB nucleoprotein filaments rather than on naked ssDNA. In this volume, methods are described to interrogate SSB-DNA and SSB-protein binding functions along with approaches that aim to understand the cellular functions of SSB. This introductory chapter offers a general overview of SSBs that focuses on their structures, DNA-binding mechanisms, and protein-binding partners.","corpus_id":20789227,"score":2},{"doc_id":"23119018","title":"Characterization of the Holliday junction resolving enzyme encoded by the Bacillus subtilis bacteriophage SPP1.","abstract":"Recombination-dependent DNA replication, which is a central component of viral replication restart, is poorly understood in Firmicutes bacteriophages. Phage SPP1 initiates unidirectional theta DNA replication from a discrete replication origin (oriL), and when replication progresses, the fork might stall by the binding of the origin binding protein G38P to the late replication origin (oriR). Replication restart is dependent on viral recombination proteins to synthesize a linear head-to-tail concatemer, which is the substrate for viral DNA packaging. To identify new functions involved in this process, uncharacterized genes from phage SPP1 were analyzed. Immediately after infection, SPP1 transcribes a number of genes involved in recombination and replication from P(E2) and P(E3) promoters. Resequencing the region corresponding to the last two hypothetical genes transcribed from the P(E2) operon (genes 44 and 45) showed that they are in fact a single gene, re-annotated here as gene 44, that encodes a single polypeptide, named gene 44 product (G44P, 27.5 kDa). G44P shares a low but significant degree of identity in its C-terminal region with virus-encoded RusA-like resolvases. The data presented here demonstrate that G44P, which is a dimer in solution, binds with high affinity but without sequence specificity to several double-stranded DNA recombination intermediates. G44P preferentially cleaves Holliday junctions, but also, with lower efficiency, replicated D-loops. It also partially complemented the loss of RecU resolvase activity in B. subtilis cells. These in vitro and in vivo data suggest a role for G44P in replication restart during the transition to concatemeric viral replication.","corpus_id":8779781,"score":2},{"doc_id":"23435232","title":"Characterization of an unusual bipolar helicase encoded by bacteriophage T5.","abstract":"Bacteriophage T5 has a 120 kb double-stranded linear DNA genome encoding most of the genes required for its own replication. This lytic bacteriophage has a burst size of ∼500 new phage particles per infected cell, demonstrating that it is able to turn each infected bacterium into a highly efficient DNA manufacturing machine. To begin to understand DNA replication in this prodigious bacteriophage, we have characterized a putative helicase encoded by gene D2. We show that bacteriophage T5 D2 protein is the first viral helicase to be described with bipolar DNA unwinding activities that require the same core catalytic residues for unwinding in either direction. However, unwinding of partially single- and double-stranded DNA test substrates in the 3'-5' direction is more robust and can be distinguished from the 5'-3' activity by a number of features including helicase complex stability, salt sensitivity and the length of single-stranded DNA overhang required for initiation of helicase action. The presence of D2 in an early gene cluster, the identification of a putative helix-turn-helix DNA-binding motif outside the helicase core and homology with known eukaryotic and prokaryotic replication initiators suggest an involvement for this unusual helicase in DNA replication initiation.","corpus_id":18931209,"score":2},{"doc_id":"23732982","title":"Interaction of T4 UvsW helicase and single-stranded DNA binding protein gp32 through its carboxy-terminal acidic tail.","abstract":"Bacteriophage T4 UvsW helicase contains both unwinding and annealing activities and displays some functional similarities to bacterial RecG and RecQ helicases. UvsW is involved in several DNA repair pathways, playing important roles in recombination-dependent DNA repair and the reorganization of stalled replication forks. The T4 single-stranded DNA (ssDNA) binding protein gp32 is a central player in nearly all DNA replication and repair processes and is thought to facilitate their coordination by recruiting and regulating the various proteins involved. Here, we show that the activities of the UvsW protein are modulated by gp32. UvsW-catalyzed unwinding of recombination intermediates such as D-loops and static X-DNA (Holliday junction mimic) to ssDNA products is enhanced by the gp32 protein. The enhancement requires the presence of the protein interaction domain of gp32 (the acidic carboxy-terminus), suggesting that a specific interaction between UvsW and gp32 is required. In the absence of this interaction, the ssDNA annealing and ATP-dependent translocation activities of UvsW are severely inhibited when gp32 coats the ssDNA lattice. However, when UvsW and gp32 do interact, UvsW is able to efficiently displace the gp32 protein from the ssDNA. This ability of UvsW to remove gp32 from ssDNA may explain its ability to enhance the strand invasion activity of the T4 recombinase (UvsX) and suggests a possible new role for UvsW in gp32-mediated DNA transactions.","corpus_id":33374945,"score":2},{"doc_id":"24029071","title":"Bacteriophage T5 encodes a homolog of the eukaryotic transcription coactivator PC4 implicated in recombination-dependent DNA replication.","abstract":"The RNA polymerase II cofactor PC4 globally regulates transcription of protein-encoding genes through interactions with unwinding DNA, the basal transcription machinery and transcription activators. Here, we report the surprising identification of PC4 homologs in all sequenced representatives of the T5 family of bacteriophages, as well as in an archaeon and seven phyla of eubacteria. We have solved the crystal structure of the full-length T5 protein at 1.9Å, revealing a striking resemblance to the characteristic single-stranded DNA (ssDNA)-binding core domain of PC4. Intriguing novel structural features include a potential regulatory region at the N-terminus and a C-terminal extension of the homodimerisation interface. The genome organisation of T5-related bacteriophages points at involvement of the PC4 homolog in recombination-dependent DNA replication, strongly suggesting that the protein corresponds to the hitherto elusive replicative ssDNA-binding protein of the T5 family. Our findings imply that PC4-like factors intervene in multiple unwinding-related processes by acting as versatile modifiers of nucleic acid conformation and raise the possibility that the eukaryotic transcription coactivator derives from ancestral DNA replication, recombination and repair factors.","corpus_id":9828419,"score":2},{"doc_id":"24124995","title":"Kinetics of presynaptic filament assembly in the presence of single-stranded DNA binding protein and recombination mediator protein.","abstract":"Enzymes of the RecA/Rad51 family catalyze DNA strand exchange reactions that are important for homologous recombination and for the accurate repair of DNA double-strand breaks. RecA/Rad51 recombinases are activated by their assembly into presynaptic filaments on single-stranded DNA (ssDNA), a process that is regulated by ssDNA binding protein (SSB) and mediator proteins. Mediator proteins stimulate strand exchange by accelerating the rate-limiting displacement of SSB from ssDNA by the incoming recombinase. The use of mediators is a highly conserved strategy in recombination, but the precise mechanism of mediator activity is unknown. In this study, the well-defined bacteriophage T4 recombination system (UvsX recombinase, Gp32 SSB, and UvsY mediator) is used to examine the kinetics of presynaptic filament assembly on native ssDNA in vitro. Results indicate that the ATP-dependent assembly of UvsX presynaptic filaments on Gp32-covered ssDNA is limited by a salt-sensitive nucleation step in the absence of mediator. Filament nucleation is selectively enhanced and rendered salt-resistant by mediator protein UvsY, which appears to stabilize a prenucleation complex. This mechanism potentially explains how UvsY promotes presynaptic filament assembly at physiologically relevant ionic strengths and Gp32 concentrations. Other data suggest that presynaptic filament assembly involves multiple nucleation events, resulting in many short UvsX-ssDNA filaments or clusters, which may be the relevant form for recombination in vivo. Together, these findings provide the first detailed kinetic model for presynaptic filament assembly involving all three major protein components (recombinase, mediator, and SSB) on native ssDNA.","corpus_id":7908663,"score":2},{"doc_id":"24338568","title":"Control of helicase loading in the coupled DNA replication and recombination systems of bacteriophage T4.","abstract":"The Gp59 protein of bacteriophage T4 promotes DNA replication by loading the replicative helicase, Gp41, onto replication forks and recombination intermediates. Gp59 also blocks DNA synthesis by Gp43 polymerase until Gp41 is loaded, ensuring that synthesis is tightly coupled to unwinding. The distinct polymerase blocking and helicase loading activities of Gp59 likely involve different binding interactions with DNA and protein partners. Here, we investigate how interactions of Gp59 with DNA and Gp32, the T4 single-stranded DNA (ssDNA)-binding protein, are related to these activities. A previously characterized mutant, Gp59-I87A, exhibits markedly reduced affinity for ssDNA and pseudo-fork DNA substrates. We demonstrate that on Gp32-covered ssDNA, the DNA binding defect of Gp59-I87A is not detrimental to helicase loading and translocation. In contrast, on pseudo-fork DNA the I87A mutation is detrimental to helicase loading and unwinding in the presence or absence of Gp32. Other results indicate that Gp32 binding to lagging strand ssDNA relieves the blockage of Gp43 polymerase activity by Gp59, whereas the inhibition of Gp43 exonuclease activity is maintained. Our findings suggest that Gp59-Gp32 and Gp59-DNA interactions perform separate but complementary roles in T4 DNA metabolism; Gp59-Gp32 interactions are needed to load Gp41 onto D-loops, and other nucleoprotein structures containing clusters of Gp32. Gp59-DNA interactions are needed to load Gp41 onto nascent or collapsed replication forks lacking clusters of Gp32 and to coordinate bidirectional replication from T4 origins. The dual functionalities of Gp59 allow it to promote the initiation or re-start of DNA replication from a wide variety of recombination and replication intermediates.","corpus_id":34570636,"score":2},{"doc_id":"24591606","title":"Single-molecule studies of polymerase dynamics and stoichiometry at the bacteriophage T7 replication machinery.","abstract":"Replication of DNA plays a central role in transmitting hereditary information from cell to cell. To achieve reliable DNA replication, multiple proteins form a stable complex, known as the replisome, enabling them to act together in a highly coordinated fashion. Over the past decade, the roles of the various proteins within the replisome have been determined. Although many of their interactions have been characterized, it remains poorly understood how replication proteins enter and leave the replisome. In this study, we visualize fluorescently labeled bacteriophage T7 DNA polymerases within the replisome while we simultaneously observe the kinetics of the replication process. This combination of observables allows us to monitor both the activity and dynamics of individual polymerases during coordinated leading- and lagging-strand synthesis. Our data suggest that lagging-strand polymerases are exchanged at a frequency similar to that of Okazaki fragment synthesis and that two or more polymerases are present in the replisome during DNA replication. Our studies imply a highly dynamic picture of the replisome with lagging-strand DNA polymerases residing at the fork for the synthesis of only a few Okazaki fragments. Further, new lagging-strand polymerases are readily recruited from a pool of polymerases that are proximally bound to the replisome and continuously replenished from solution.","corpus_id":205267763,"score":2},{"doc_id":"24970156","title":"Homologous recombination as a replication fork escort: fork-protection and recovery.","abstract":"Homologous recombination is a universal mechanism that allows DNA repair and ensures the efficiency of DNA replication. The substrate initiating the process of homologous recombination is a single-stranded DNA that promotes a strand exchange reaction resulting in a genetic exchange that promotes genetic diversity and DNA repair. The molecular mechanisms by which homologous recombination repairs a double-strand break have been extensively studied and are now well characterized. However, the mechanisms by which homologous recombination contribute to DNA replication in eukaryotes remains poorly understood. Studies in bacteria have identified multiple roles for the machinery of homologous recombination at replication forks. Here, we review our understanding of the molecular pathways involving the homologous recombination machinery to support the robustness of DNA replication. In addition to its role in fork-recovery and in rebuilding a functional replication fork apparatus, homologous recombination may also act as a fork-protection mechanism. We discuss that some of the fork-escort functions of homologous recombination might be achieved by loading of the recombination machinery at inactivated forks without a need for a strand exchange step; as well as the consequence of such a model for the stability of eukaryotic genomes.","corpus_id":7453721,"score":2},{"doc_id":"25481875","title":"Regulation of the bacteriophage T4 Dda helicase by Gp32 single-stranded DNA-binding protein.","abstract":"Dda, one of three helicases encoded by bacteriophage T4, has been well-characterized biochemically but its biological role remains unclear. It is thought to be involved in origin dependent DNA replication, recombination-dependent replication, anti-recombination, and recombination repair. The Gp32 protein of bacteriophage T4 plays critical roles in DNA replication, recombination, and repair by coordinating protein components of the replication fork and by stabilizing ssDNA. Previous work demonstrated that stimulation of DNA synthesis by Dda helicase appears to require direct Gp32-Dda protein-protein interactions and that Gp32 and Dda form a tight complex in the absence of ssDNA. Here we characterize the effects of Gp32-Dda physical and functional interactions through changes in the duplex DNA unwinding and ATPase activities of Dda helicase in the presence of different variants of Gp32 and different DNA repair and replication intermediate structures. Results show that Gp32-Dda interactions can be enhancing or inhibitory, depending on the Gp32 domain seen by Dda. Protein-protein interactions with Gp32 stimulate the unwinding activity of Dda, an effect associated with increased turnover of ATP, suggesting a higher rate of ATPase-driven translocation. Dda-Gp32 interactions also promote the unwinding of DNA substrates at higher salt concentrations and in the presence of substrate-bound DNA polymerase. Conversely, the formation of Gp32 clusters on ssDNA can inhibit unwinding, suggesting that Gp32-ssDNA formation sterically regulates which portions of replication and recombination intermediates are accessible for processing by Dda helicase. The data suggest a mechanism of replication fork restart in which Gp32 promotes Dda activity in template switching while preventing premature fork progression.","corpus_id":10770482,"score":2},{"doc_id":"25961912","title":"PC4 promotes genome stability and DNA repair through binding of ssDNA at DNA damage sites.","abstract":"The transcriptional cofactor PC4 is an ancient single-strand DNA (ssDNA)-binding protein that has a homologue in bacteriophage T5 where it is likely the elusive replicative ssDNA-binding protein. We hypothesize that human PC4 has retained functions in ssDNA binding to stabilize replication forks and prevent genome instability in mammalian cells. Here we demonstrate that PC4 is recruited to hydroxyurea (HU)-stalled replication forks, which is dependent on active transcription and its ssDNA-binding ability. Interestingly, we demonstrate that ssDNA binding by PC4 is critical to suppress spontaneous DNA damage and promote cellular survival. PC4 accumulation co-localizes with replication protein A (RPA) at stalled forks and is increased upon RPA depletion, demonstrating compensatory functions in ssDNA binding. Depletion of PC4 not only results in defective resolution of HU-induced DNA damage but also significantly reduces homologous recombination repair efficiency. Altogether, our results indicate that PC4 has similar functions to RPA in binding ssDNA to promote genome stability, especially at sites of replication-transcription collisions. Oncogene advance online publication, 11 May 2015; doi:10.1038/onc.2015.135.","corpus_id":27942986,"score":2},{"doc_id":"27241928","title":"The Replication System of Bacteriophage T7.","abstract":"The replication system of bacteriophage T7 is remarkable in that the 40,000 nucleotide genome is replicated over 100-fold in a matter of minutes. In order to accomplish this feat T7 has evolved an efficient and economical process for the replication of its DNA. The T7 replisome provides a model system to study DNA replication. Four proteins are sufficient for reconstitution of the functional replication complex, yet the assembled replisome recapitulates all the key features of more complex prokaryotic and eukaryotic systems. In this review, we describe chemical mechanisms employed by individual proteins at the replication fork. Integration of structural, biochemical, and single-molecule data reveals a compelling view on how a nearly 1-MDa molecular machine acts as a unit to synthetize the two antiparallel DNA strands in a coordinated fashion.","corpus_id":9271394,"score":2},{"doc_id":"27241929","title":"Protein-Primed Replication of Bacteriophage Φ29 DNA.","abstract":"The requirement of DNA polymerases for a 3'-hydroxyl (3'-OH) group to prime DNA synthesis raised the question about how the ends of linear chromosomes could be replicated. Among the strategies that have evolved to handle the end replication problem, a group of linear phages and eukaryotic and archaeal viruses, among others, make use of a protein (terminal protein, TP) that primes DNA synthesis from the end of their genomes. The replicative DNA polymerase recognizes the OH group of a specific residue in the TP to initiate replication that is guided by an internal 3' nucleotide of the template strand. By a sliding-back mechanism or variants of it the terminal nucleotide(s) is(are) recovered and the TP becomes covalently attached to the genome ends. Bacillus subtilis phage ϕ29 is the organism in which such a mechanism has been studied more extensively, having allowed to lay the foundations of the so-called protein-primed replication mechanism. Here we focus on the main biochemical and structural features of the two main proteins responsible for the protein-primed initiation step: the DNA polymerase and the TP. Thus, we will discuss the structural determinants of the DNA polymerase responsible for its ability to use sequentially a TP and a DNA as primers, as well as for its inherent capacity to couple high processive synthesis to strand displacement. On the other hand, we will review how TP primes initiation followed by a transition step for further DNA-primed replication by the same polymerase molecule. Finally, we will review how replication is compartmentalized in vivo.","corpus_id":39975788,"score":2},{"doc_id":"27547754","title":"DNA-Binding Proteins Essential for Protein-Primed Bacteriophage Φ29 DNA Replication.","abstract":"Bacillus subtilis phage Φ29 has a linear, double-stranded DNA 19 kb long with an inverted terminal repeat of 6 nucleotides and a protein covalently linked to the 5' ends of the DNA. This protein, called terminal protein (TP), is the primer for the initiation of replication, a reaction catalyzed by the viral DNA polymerase at the two DNA ends. The DNA polymerase further elongates the nascent DNA chain in a processive manner, coupling strand displacement with elongation. The viral protein p5 is a single-stranded DNA binding protein (SSB) that binds to the single strands generated by strand displacement during the elongation process. Viral protein p6 is a double-stranded DNA binding protein (DBP) that preferentially binds to the origins of replication at the Φ29 DNA ends and is required for the initiation of replication. Both SSB and DBP are essential for Φ29 DNA amplification. This review focuses on the role of these phage DNA-binding proteins in Φ29 DNA replication both in vitro and in vivo, as well as on the implication of several B. subtilis DNA-binding proteins in different processes of the viral cycle. We will revise the enzymatic activities of the Φ29 DNA polymerase: TP-deoxynucleotidylation, processive DNA polymerization coupled to strand displacement, 3'-5' exonucleolysis and pyrophosphorolysis. The resolution of the Φ29 DNA polymerase structure has shed light on the translocation mechanism and the determinants responsible for processivity and strand displacement. These two properties have made Φ29 DNA polymerase one of the main enzymes used in the current DNA amplification technologies. The determination of the structure of Φ29 TP revealed the existence of three domains: the priming domain, where the primer residue Ser232, as well as Phe230, involved in the determination of the initiating nucleotide, are located, the intermediate domain, involved in DNA polymerase binding, and the N-terminal domain, responsible for DNA binding and localization of the TP at the bacterial nucleoid, where viral DNA replication takes place. The biochemical properties of the Φ29 DBP and SSB and their function in the initiation and elongation of Φ29 DNA replication, respectively, will be described.","corpus_id":2294957,"score":2},{"doc_id":"27694621","title":"Single-molecule FRET studies of the cooperative and non-cooperative binding kinetics of the bacteriophage T4 single-stranded DNA binding protein (gp32) to ssDNA lattices at replication fork junctions.","abstract":"Gene 32 protein (gp32) is the single-stranded (ss) DNA binding protein of the bacteriophage T4. It binds transiently and cooperatively to ssDNA sequences exposed during the DNA replication process and regulates the interactions of the other sub-assemblies of the replication complex during the replication cycle. We here use single-molecule FRET techniques to build on previous thermodynamic studies of gp32 binding to initiate studies of the dynamics of the isolated and cooperative binding of gp32 molecules within the replication complex. DNA primer/template (p/t) constructs are used as models to determine the effects of ssDNA lattice length, gp32 concentration, salt concentration, binding cooperativity and binding polarity at p/t junctions. Hidden Markov models (HMMs) and transition density plots (TDPs) are used to characterize the dynamics of the multi-step assembly pathway of gp32 at p/t junctions of differing polarity, and show that isolated gp32 molecules bind to their ssDNA targets weakly and dissociate quickly, while cooperatively bound dimeric or trimeric clusters of gp32 bind much more tightly, can 'slide' on ssDNA sequences, and exhibit binding dynamics that depend on p/t junction polarities. The potential relationships of these binding dynamics to interactions with other components of the T4 DNA replication complex are discussed.","corpus_id":4409127,"score":2},{"doc_id":"28009009","title":"Bacteriophage T5 gene D10 encodes a branch-migration protein.","abstract":"Helicases catalyze the unwinding of double-stranded nucleic acids where structure and phosphate backbone contacts, rather than nucleobase sequence, usually determines substrate specificity. We have expressed and purified a putative helicase encoded by the D10 gene of bacteriophage T5. Here we report that this hitherto uncharacterized protein possesses branch migration and DNA unwinding activity. The initiation of substrate unwinding showed some sequence dependency, while DNA binding and DNA-dependent ATPase activity did not. DNA footprinting and purine-base interference assays demonstrated that D10 engages these substrates with a defined polarity that may be established by protein-nucleobase contacts. Bioinformatic analysis of the nucleotide databases revealed genes predicted to encode proteins related to D10 in archaebacteria, bacteriophages and in viruses known to infect a range of eukaryotic organisms.","corpus_id":15888543,"score":2},{"doc_id":"28416612","title":"A biochemical and biophysical model of G-quadruplex DNA recognition by positive coactivator of transcription 4.","abstract":"DNA sequences that are guanine-rich have received considerable attention because of their potential to fold into a secondary, four-stranded DNA structure termed G-quadruplex (G4), which has been implicated in genomic instability and some human diseases. We have previously identified positive coactivator of transcription (PC4), a single-stranded DNA (ssDNA)-binding protein, as a novel G4 interactor. Here, to expand on these previous observations, we biochemically and biophysically characterized the interaction between PC4 and G4DNA. PC4 can bind alternative G4DNA topologies with a low nanomolar Kd value of ∼2 nm, similar to that observed for ssDNA. In consideration of the different structural features between G4DNA and ssDNA, these binding data indicated that PC4 can interact with G4DNA in a manner distinct from ssDNA. The stoichiometry of the PC4-G4 complex was 1:1 for PC4 dimer:G4 substrate. PC4 did not enhance the rate of folding of G4DNA, and formation of the PC4-G4DNA complex did not result in unfolding of the G4DNA structure. We assembled a G4DNA structure flanked by duplex DNA. We find that PC4 can interact with this G4DNA, as well as the complementary C-rich strand. Molecular docking simulations and DNA footprinting experiments suggest a model where a PC4 dimer accommodates the DNA with one monomer on the G4 strand and the second monomer bound to the C-rich strand. Collectively, these data provide a novel mode of PC4 binding to a DNA secondary structure that remains within the framework of the model for binding to ssDNA. Additionally, consideration of the PC4-G4DNA interaction could provide insight into the biological functions of PC4, which remain incompletely understood.","corpus_id":205364196,"score":2},{"doc_id":"29588157","title":"Gp2.5, the multifunctional bacteriophage T7 single-stranded DNA binding protein.","abstract":"The essential bacteriophage T7-encoded single-stranded DNA binding protein is the nexus of T7 DNA metabolism. Multiple layers of macromolecular interactions mediate its function in replication, recombination, repair, and the maturation of viral genomes. In addition to binding ssDNA, the protein binds to DNA polymerase and DNA helicase, regulating their activities. The protein displays potent homologous DNA annealing activity, underscoring its role in recombination.","corpus_id":4410095,"score":2},{"doc_id":"29634784","title":"The role of the C-domain of bacteriophage T4 gene 32 protein in ssDNA binding and dsDNA helix-destabilization: Kinetic, single-molecule, and cross-linking studies.","abstract":"The model single-stranded DNA binding protein of bacteriophage T4, gene 32 protein (gp32) has well-established roles in DNA replication, recombination, and repair. gp32 is a single-chain polypeptide consisting of three domains. Based on thermodynamics and kinetics measurements, we have proposed that gp32 can undergo a conformational change where the acidic C-terminal domain binds internally to or near the single-stranded (ss) DNA binding surface in the core (central) domain, blocking ssDNA interaction. To test this model, we have employed a variety of experimental approaches and gp32 variants to characterize this conformational change. Utilizing stopped-flow methods, the association kinetics of wild type and truncated forms of gp32 with ssDNA were measured. When the C-domain is present, the log-log plot of k vs. [NaCl] shows a positive slope, whereas when it is absent (*I protein), there is little rate change with salt concentration, as expected for this model. A gp32 variant lacking residues 292-296 within the C-domain, ΔPR201, displays kinetic properties intermediate between gp32 and *I. The single molecule force-induced DNA helix-destabilizing activitiesas well as the single- and double-stranded DNA affinities of ΔPR201 and gp32 truncated at residue 295 also fall between full-length protein and *I. Finally, chemical cross-linking of recombinant C-domain and gp32 lacking both N- and C-terminal domains is inhibited by increasing concentrations of a short single-stranded oligonucleotide, and the salt dependence of cross-linking mirrors that expected for the model. Taken together, these results provide the first evidence in support of this model that have been obtained through structural probes.","corpus_id":4978868,"score":2},{"doc_id":"17939025","title":"Identification and characterization of a single-stranded DNA-binding protein from thermophilic bacteriophage GVE2.","abstract":"Single-stranded DNA-binding (SSB) proteins are indispensable for survival of almost all known living organisms. Due to their numerous applications in diverse molecular biology and analytical methods, SSB proteins have received increasing research interest. In this investigation, a novel SSB gene was identified from a deep-sea thermophilic bacteriophage Geobacillus virus E2 (GVE2) for the first time. The GVE2 SSB protein shared homologies to known SSB proteins from other species. After recombinant expression in E. coli, the purified SSB protein was used for antibody preparation. The Northern and Western blots showed that the GVE2 SSB gene might be an early viral gene. As revealed by DNA binding assay, the recombinant GVE2 SSB protein had single-stranded DNA binding capacity.","corpus_id":25302239,"score":1},{"doc_id":"18000001","title":"The process of displacing the single-stranded DNA-binding protein from single-stranded DNA by RecO and RecR proteins.","abstract":"The regions of single-stranded (ss) DNA that result from DNA damage are immediately coated by the ssDNA-binding protein (SSB). RecF pathway proteins facilitate the displacement of SSB from ssDNA, allowing the RecA protein to form protein filaments on the ssDNA region, which facilitates the process of recombinational DNA repair. In this study, we examined the mechanism of SSB displacement from ssDNA using purified Thermus thermophilus RecF pathway proteins. To date, RecO and RecR are thought to act as the RecOR complex. However, our results indicate that RecO and RecR have distinct functions. We found that RecR binds both RecF and RecO, and that RecO binds RecR, SSB and ssDNA. The electron microscopic studies indicated that SSB is displaced from ssDNA by RecO. In addition, pull-down assays indicated that the displaced SSB still remains indirectly attached to ssDNA through its interaction with RecO in the RecO-ssDNA complex. In the presence of both SSB and RecO, the ssDNA-dependent ATPase activity of RecA was inhibited, but was restored by the addition of RecR. Interestingly, the interaction of RecR with RecO affected the ssDNA-binding properties of RecO. These results suggest a model of SSB displacement from the ssDNA by RecF pathway proteins.","corpus_id":17497862,"score":1},{"doc_id":"18054234","title":"14-3-3 cruciform-binding proteins as regulators of eukaryotic DNA replication.","abstract":"Cruciforms are secondary DNA structures, serving as recognition signals at or near eukaryotic (yeast and mammalian) origins of DNA replication. The cruciform-binding protein is a member of the 14-3-3 protein family and binds to origins of DNA replication in a cell cycle-dependent manner. Five 14-3-3 protein isoforms (beta, gamma, epsilon, zeta and sigma) have been identified as having cruciform binding activity.","corpus_id":43369439,"score":1},{"doc_id":"19025561","title":"Identification of host receptor and receptor-binding module of a newly sequenced T5-like phage EPS7.","abstract":"The virulent bacteriophage EPS7 active against a number of Salmonella serovar and Escherichia coli strains, isolated from the local sewage in Korea, belongs to the family Siphoviridae. The ESP7 genome constitutes a linear double-stranded DNA of 111 382 bp. DNA sequencing and genomic analysis of EPS7 showed that it belongs to the phage T5 family. We identified the EPS7 genes involved in DNA repair, replication, viral structure and bacterial lysis by comparing the EPS7 genome with that of T5. In contrast, the tail genes encoding for putative host receptor-binding protein and the putative receptor-blocking lipoprotein precursor of EPS7 exhibit high homologies with the corresponding gene products of BF23, another member of the T5-family. BF23 binds to BtuB, a surface receptor in the host and involved in vitamin B12 uptake, but its infection is independent of TonB. By constructing a series of deletion mutants in Salmonella and in E. coli and studying phage infection in the mutant hosts, we showed that BtuB is also the host receptor of the phage EPS7. Whether EPS7 infection depends on TonB needs to be further studied.","corpus_id":21037952,"score":1},{"doc_id":"19597347","title":"DNA ligase I and Nbs1 proteins associate in a complex and colocalize at replication factories.","abstract":"DNA ligase I is the main DNA ligase activity involved in eukaryotic DNA replication acting in the joining of Okazaki fragments. This enzyme is also implicated in nucleotide excision repair and in the long-patch base excision repair while its role in the recombinational repair pathways is poorly understood. DNA ligase I is phosphorylated during cell cycle at several serine and threonine residues that regulate its participation in different DNA transactions by modulating the interaction with different protein partners. Here we use an antibody-based array method to identify novel DNA ligase-interacting partners. We show that DNA ligase I participates in several multiprotein complexes with proteins involved in DNA replication and repair, cell cycle control, and protein modification. In particular we demonstrate that DNA ligase I complexes with Nbs1, a core component of the MRN complex critical for detection, processing and repair of double-stranded DNA breaks. The analysis of epitope tagged DNA ligase I mutants demonstrates that the association is mediated by the catalytic fragment of the enzyme. DNA ligase I and Nbs1 colocalize at replication factories during unperturbed replication and after treatment with DNA damaging agents. Since MRN complex is involved in the repair of double-stranded DNA breaks by homologous recombination at stalled replication forks our data support the notion that DNA ligase I participates in homology dependent pathways that deal with replication-associated lesions generated when replication fork encounters DNA damage.","corpus_id":9101456,"score":1},{"doc_id":"20012581","title":"Eukaryotic single-stranded DNA binding proteins: central factors in genome stability.","abstract":"The single-stranded DNA binding proteins (SSBs) are required to maintain the integrity of the genome in all organisms. Replication protein A (RPA) is a nuclear SSB protein found in all eukaryotes and is required for multiple processes in DNA metabolism such as DNA replication, DNA repair, DNA recombination, telomere maintenance and DNA damage signalling. RPA is a heterotrimeric complex, binds ssDNA with high affinity, and interacts specifically with multiple proteins to fulfil its function in eukaryotes. RPA is phosphorylated in a cell cycle and DNA damage-dependent manner with evidence suggesting that phosphorylation has an important function in modulating the cellular DNA damage response. Considering the DNA-binding properties of RPA a mechanism of \"molecular counting\" to initiate DNA damage-dependent signalling is discussed. Recently a human homologue to the RPA2 subunit, called RPA4, was discovered and RPA4 can substitute for RPA2 in the RPA complex resulting in an \"alternative\" RPA (aRPA), which can bind to ssDNA with similar affinity as canonical RPA. Additional human SSBs, hSSB1 and hSSB2, were recently identified, with hSSB1 being localized in the nucleus and having implications in DNA repair. Mitochondrial SSBs (mtSSBs) have been found in all eukaryotes studied. mtSSBs are related to prokaryotic SSBs and essential to main the genome stability in eukaryotic mitochondria. Recently human mtSSB was identified as a novel binding partner of p53 and that it is able to stimulate the intrinsic exonuclease activity of p53. These findings and recent results associated with mutations in RPA suggest a link of SSBs to cancer.","corpus_id":20597186,"score":1},{"doc_id":"20360609","title":"Regulation of single-stranded DNA binding by the C termini of Escherichia coli single-stranded DNA-binding (SSB) protein.","abstract":"The homotetrameric Escherichia coli single-stranded DNA-binding (SSB) protein plays a central role in DNA replication, repair, and recombination. In addition to its essential activity of binding to transiently formed single-stranded (ss) DNA, SSB also binds an array of partner proteins and recruits them to their sites of action using its four intrinsically disordered C-terminal tails. Here we show that the binding of ssDNA to SSB is inhibited by the SSB C-terminal tails, specifically by the last 8 highly acidic amino acids that comprise the binding site for its multiple partner proteins. We examined the energetics of ssDNA binding to short oligodeoxynucleotides and find that at moderate salt concentration, removal of the acidic C-terminal ends increases the intrinsic affinity for ssDNA and enhances the negative cooperativity between ssDNA binding sites, indicating that the C termini exert an inhibitory effect on ssDNA binding. This inhibitory effect decreases as the salt concentration increases. Binding of ssDNA to approximately half of the SSB subunits relieves the inhibitory effect for all of the subunits. The inhibition by the C termini is due primarily to a less favorable entropy change upon ssDNA binding. These observations explain why ssDNA binding to SSB enhances the affinity of SSB for its partner proteins and suggest that the C termini of SSB may interact, at least transiently, with its ssDNA binding sites. This inhibition and its relief by ssDNA binding suggest a mechanism that enhances the ability of SSB to selectively recruit its partner proteins to sites on DNA.","corpus_id":14508187,"score":1},{"doc_id":"21169364","title":"A mechanism for single-stranded DNA-binding protein (SSB) displacement from single-stranded DNA upon SSB-RecO interaction.","abstract":"Displacement of single-stranded DNA (ssDNA)-binding protein (SSB) from ssDNA is necessary for filament formation of RecA on ssDNA to initiate homologous recombination. The interaction between RecO and SSB is considered to be important for SSB displacement; however, the interaction has not been characterized at the atomic level. In this study, to clarify the mechanism underlying SSB displacement from ssDNA upon RecO binding, we examined the interaction between Thermus thermophilus RecO and cognate SSB by NMR analysis. We found that SSB interacts with the C-terminal positively charged region of RecO. Based on this result, we constructed some RecO mutants. The R127A mutant had considerably decreased binding affinity for SSB and could not anneal SSB-coated ssDNAs. Further, the mutant in the RecOR complex prevented the recovery of ssDNA-dependent ATPase activity of RecA from inhibition by SSB. These results indicated that the region surrounding Arg-127 is the binding site of SSB. We also performed NMR analysis using the C-terminal peptide of SSB and found that the acidic region of SSB is involved in the interaction with RecO, as seen in other protein-SSB interactions. Taken together with the findings of previous studies, we propose a model for SSB displacement from ssDNA where the acidic C-terminal region of SSB weakens the ssDNA binding affinity of SSB when the dynamics of the C-terminal region are suppressed by interactions with other proteins, including RecO.","corpus_id":19851355,"score":1},{"doc_id":"21264493","title":"Identification of a soybean chloroplast DNA replication origin-binding protein.","abstract":"Replication of chloroplast DNA (ctDNA) in several plants and in Chlamydomonas reinhardii has been shown to occur by a double displacement loop (D-loop) mechanism and potentially also by a rolling circle mechanism. D-loop replication origins have been mapped in several species. Minimal replication origin sequences used as probes identified two potential binding proteins by southwestern blot analysis. A 28 kDa (apparent molecular weight by SDS-PAGE analysis) soybean protein has been isolated by origin sequence-specific DNA affinity chromatography from total chloroplast proteins. Mass spectrometry analysis identified this protein as the product of the soybean C6SY33 gene (accession number ACU14156), which is annotated as encoding a putative uncharacterized protein with a molecular weight of 25,897 Da, very near the observed molecular weight of the purified protein based on gel electrophoresis. Western blot analysis using an antibody against a homologous Arabidopsis protein indicates that this soybean protein is localized specifically in chloroplasts. The soybean protein shares some homology within a single-stranded DNA binding (SSB) domain of E. coli SSB and an Arabidopsis thaliana mitochondrial-localized SSB of about 21 kDa (mtSSB). However, the soybean protein induces a specific electrophoretic mobility shift only when incubated with a double-stranded fragment containing the previously mapped ctDNA replication oriA region. This protein has no electrophoretic mobility shift activity when incubated with single-stranded DNA. In contrast, the Arabidopsis mtSSB causes a mobility shift only with single-stranded DNA but not with the oriA fragment or with control dsDNA of unrelated sequence. These results suggest that the 26 kDa soybean protein is a specific origin binding protein that may be involved in initiation of ctDNA replication.","corpus_id":12653285,"score":1},{"doc_id":"22027892","title":"Mgm101 is a Rad52-related protein required for mitochondrial DNA recombination.","abstract":"Homologous recombination is a conserved molecular process that has primarily evolved for the repair of double-stranded DNA breaks and stalled replication forks. However, the recombination machinery in mitochondria is poorly understood. Here, we show that the yeast mitochondrial nucleoid protein, Mgm101, is related to the Rad52-type recombination proteins that are widespread in organisms from bacteriophage to humans. Mgm101 is required for repeat-mediated recombination and suppression of mtDNA fragmentation in vivo. It preferentially binds to single-stranded DNA and catalyzes the annealing of ssDNA precomplexed with the mitochondrial ssDNA-binding protein, Rim1. Transmission electron microscopy showed that Mgm101 forms large oligomeric rings of ∼14-fold symmetry and highly compressed helical filaments. Specific mutations affecting ring formation reduce protein stability in vitro. The data suggest that the ring structure may provide a scaffold for stabilization of Mgm101 by preventing the aggregation of the otherwise unstable monomeric conformation. Upon binding to ssDNA, Mgm101 is remobilized from the rings to form distinct nucleoprotein filaments. These studies reveal a recombination protein of likely bacteriophage origin in mitochondria and support the notion that recombination is indispensable for mtDNA integrity.","corpus_id":25369495,"score":1},{"doc_id":"22116609","title":"Accurate prediction of the binding free energy and analysis of the mechanism of the interaction of replication protein A (RPA) with ssDNA.","abstract":"The eukaryotic replication protein A (RPA) has several pivotal functions in the cell metabolism, such as chromosomal replication, prevention of hairpin formation, DNA repair and recombination, and signaling after DNA damage. Moreover, RPA seems to have a crucial role in organizing the sequential assembly of DNA processing proteins along single stranded DNA (ssDNA). The strong RPA affinity for ssDNA, K(A) between 10(-9)-10(-10) M, is characterized by a low cooperativity with minor variation for changes on the nucleotide sequence. Recently, new data on RPA interactions was reported, including the binding free energy of the complex RPA70AB with dC(8) and dC(5), which has been estimated to be -10 ± 0.4 kcal mol(-1) and -7 ± 1 kcal mol(-1), respectively. In view of these results we performed a study based on molecular dynamics aimed to reproduce the absolute binding free energy of RPA70AB with the dC(5) and dC(8) oligonucleotides. We used several tools to analyze the binding free energy, rigidity, and time evolution of the complex. The results obtained by MM-PBSA method, with the use of ligand free geometry as a reference for the receptor in the separate trajectory approach, are in excellent agreement with the experimental data, with ±4 kcal mol(-1) error. This result shows that the MM-PB(GB)SA methods can provide accurate quantitative estimates of the binding free energy for interacting complexes when appropriate geometries are used for the receptor, ligand and complex. The decomposition of the MM-GBSA energy for each residue in the receptor allowed us to correlate the change of the affinity of the mutated protein with the ΔG(gas+sol) contribution of the residue considered in the mutation. The agreement with experiment is optimal and a strong change in the binding free energy can be considered as the dominant factor in the loss for the binding affinity resulting from mutation.","corpus_id":25221707,"score":1},{"doc_id":"22304461","title":"Specificity of binding of single-stranded DNA-binding protein to its target.","abstract":"Single-stranded DNA-binding proteins (SSBs) bind single-stranded DNA (ssDNA) and participate in all genetic processes involving ssDNA, such as replication, recombination, and repair. Here we applied atomic force microscopy to directly image SSB-DNA complexes under various conditions. We used the hybrid DNA construct methodology in which the ssDNA segment is conjugated to the DNA duplex. The duplex part of the construct plays the role of a marker, allowing unambiguous identification of specific and nonspecific SSB-DNA complexes. We designed hybrid DNA substrates with 5'- and 3'-ssDNA termini to clarify the role of ssDNA polarity on SSB loading. The hybrid substrates, in which two duplexes are connected with ssDNA, were the models for gapped DNA substrates. We demonstrated that Escherichia coli SSB binds to ssDNA ends and internal ssDNA regions with the same efficiency. However, the specific recognition by ssDNA requires the presence of Mg(2+) cations or a high ionic strength. In the absence of Mg(2+) cations and under low-salt conditions, the protein is capable of binding DNA duplexes. In addition, the number of interprotein interactions increases, resulting in the formation of clusters on double-stranded DNA. This finding suggests that the protein adopts different conformations depending on ionic strength, and specific recognition of ssDNA by SSB requires a high ionic strength or the presence of Mg(2+) cations.","corpus_id":22406614,"score":1},{"doc_id":"22549990","title":"MALDI-MS detection of noncovalent interactions of single stranded DNA with Escherichia coli single-stranded DNA-binding protein.","abstract":"The Escherichia coli single-stranded DNA binding protein (SSB) selectively binds single-stranded (ss) DNA and participates in the process of DNA replication, recombination and repair. Different binding modes have previously been observed in SSB•ssDNA complexes, due to the four potential binding sites of SSB. Here, chemical cross-linking, combined with high-mass matrix-assisted laser desorption/ionization (MALDI) mass spectrometry (MS), is used to determine the stoichiometry of the SSB•ssDNA complex. SSB forms a stable homotetramer in solution, but only the monomeric species (m/z 19,100) can be detected with standard MALDI-MS. With chemical cross-linking, the quaternary structure of SSB is conserved, and the tetramer (m/z 79,500) was observed. We found that ssDNA also functions as a stabilizer to conserve the quaternary structure of SSB, as evidenced by the detection of a SSB•ssDNA complex at m/z 94,200 even in the absence of chemical cross-linking. The stability of the SSB•ssDNA complex with MALDI strongly depends on the length and strand of oligonucleotides and the stoichiometry of the SSB•ssDNA complex, which could be attributed to electrostatic interactions that are enhanced in the gas phase. The key factor affecting the stoichiometry of the SSB•ssDNA complex is how ssDNA binds to SSB, rather than the protein-to-DNA ratio. This further suggests that detection of the complex by MALDI is a result of specific binding, and not due to non-specific aggregation in the MALDI plume.","corpus_id":5594670,"score":1},{"doc_id":"22698072","title":"Thermodynamic analysis of DNA binding by a Bacillus single stranded DNA binding protein.","abstract":"BACKGROUND: Single-stranded DNA binding proteins (SSB) are essential for DNA replication, repair, and recombination in all organisms. SSB works in concert with a variety of DNA metabolizing enzymes such as DNA polymerase. RESULTS: We have cloned and purified SSB from Bacillus anthracis (SSB(BA)). In the absence of DNA, at concentrations ≤100 μg/ml, SSB(BA) did not form a stable tetramer and appeared to resemble bacteriophage T4 gene 32 protein. Fluorescence anisotropy studies demonstrated that SSB(BA) bound ssDNA with high affinity comparable to other prokaryotic SSBs. Thermodynamic analysis indicated both hydrophobic and ionic contributions to ssDNA binding. FRET analysis of oligo(dT)(70) binding suggested that SSB(BA) forms a tetrameric assembly upon ssDNA binding. This report provides evidence of a bacterial SSB that utilizes a novel mechanism for DNA binding through the formation of a transient tetrameric structure. CONCLUSIONS: Unlike other prokaryotic SSB proteins, SSB(BA) from Bacillus anthracis appeared to be monomeric at concentrations ≤100 μg/ml as determined by SE-HPLC. SSB(BA) retained its ability to bind ssDNA with very high affinity, comparable to SSB proteins which are tetrameric. In the presence of a long ssDNA template, SSB(BA) appears to form a transient tetrameric structure. Its unique structure appears to be due to the cumulative effect of multiple key amino acid changes in its sequence during evolution, leading to perturbation of stable dimer and tetramer formation. The structural features of SSB(BA) could promote facile assembly and disassembly of the protein-DNA complex required in processes such as DNA replication.","corpus_id":15966117,"score":1},{"doc_id":"22918586","title":"The structure and function of replication protein A in DNA replication.","abstract":"In all organisms from bacteria and archaea to eukarya, single-stranded DNA binding proteins play an essential role in most, if not all, nuclear metabolism involving single-stranded DNA (ssDNA). Replication protein A (RPA), the major eukaryotic ssDNA binding protein, has two important roles in DNA metabolism: (1) in binding ssDNA to protect it and to keep it unfolded, and (2) in coordinating the assembly and disassembly of numerous proteins and protein complexes during processes such as DNA replication. Since its discovery as a vital player in the process of replication, RPAs roles in recombination and DNA repair quickly became evident. This chapter summarizes the current understanding of RPA's roles in replication by reviewing the available structural data, DNA-binding properties, interactions with various replication proteins, and interactions with DNA repair proteins when DNA replication is stalled.","corpus_id":22295425,"score":1},{"doc_id":"23070815","title":"Structure and conformational change of a replication protein A heterotrimer bound to ssDNA.","abstract":"Replication protein A (RPA) is the main eukaryotic ssDNA-binding protein with essential roles in DNA replication, recombination, and repair. RPA maintains the DNA as single-stranded and also interacts with other DNA-processing proteins, coordinating their assembly and disassembly on DNA. RPA binds to ssDNA in two conformational states with opposing affinities for DNA and proteins. The RPA-protein interactions are compatible with a low DNA affinity state that involves DNA-binding domain A (DBD-A) and DBD-B but not with the high DNA affinity state that additionally engages DBD-C and DBD-D. The structure of the high-affinity RPA-ssDNA complex reported here shows a compact quaternary structure held together by a four-way interface between DBD-B, DBD-C, the intervening linker (BC linker), and ssDNA. The BC linker binds into the DNA-binding groove of DBD-B, mimicking DNA. The associated conformational change and partial occlusion of the DBD-A-DBA-B protein-protein interaction site establish a mechanism for the allosteric coupling of RPA-DNA and RPA-protein interactions.","corpus_id":3371729,"score":1},{"doc_id":"23303792","title":"Structures of apo- and ssDNA-bound YdbC from Lactococcus lactis uncover the function of protein domain family DUF2128 and expand the single-stranded DNA-binding domain proteome.","abstract":"Single-stranded DNA (ssDNA) binding proteins are important in basal metabolic pathways for gene transcription, recombination, DNA repair and replication in all domains of life. Their main cellular role is to stabilize melted duplex DNA and protect genomic DNA from degradation. We have uncovered the molecular function of protein domain family domain of unknown function DUF2128 (PF09901) as a novel ssDNA binding domain. This bacterial domain strongly associates into a dimer and presents a highly positively charged surface that is consistent with its function in non-specific ssDNA binding. Lactococcus lactis YdbC is a representative of DUF2128. The solution NMR structures of the 20 kDa apo-YdbC dimer and YdbC:dT(19)G(1) complex were determined. The ssDNA-binding energetics to YdbC were characterized by isothermal titration calorimetry. YdbC shows comparable nanomolar affinities for pyrimidine and mixed oligonucleotides, and the affinity is sufficiently strong to disrupt duplex DNA. In addition, YdbC binds with lower affinity to ssRNA, making it a versatile nucleic acid-binding domain. The DUF2128 family is related to the eukaryotic nuclear protein positive cofactor 4 (PC4) family and to the PUR family both by fold similarity and molecular function.","corpus_id":17595961,"score":1},{"doc_id":"24006472","title":"Mechanism of homologous recombination and implications for aging-related deletions in mitochondrial DNA.","abstract":"Homologous recombination is a universal process, conserved from bacteriophage to human, which is important for the repair of double-strand DNA breaks. Recombination in mitochondrial DNA (mtDNA) was documented more than 4 decades ago, but the underlying molecular mechanism has remained elusive. Recent studies have revealed the presence of a Rad52-type recombination system of bacteriophage origin in mitochondria, which operates by a single-strand annealing mechanism independent of the canonical RecA/Rad51-type recombinases. Increasing evidence supports the notion that, like in bacteriophages, mtDNA inheritance is a coordinated interplay between recombination, repair, and replication. These findings could have profound implications for understanding the mechanism of mtDNA inheritance and the generation of mtDNA deletions in aging cells.","corpus_id":33328160,"score":1},{"doc_id":"24021816","title":"Multiple C-terminal tails within a single E. coli SSB homotetramer coordinate DNA replication and repair.","abstract":"Escherichia coli single-stranded DNA binding protein (SSB) plays essential roles in DNA replication, recombination and repair. SSB functions as a homotetramer with each subunit possessing a DNA binding domain (OB-fold) and an intrinsically disordered C-terminus, of which the last nine amino acids provide the site for interaction with at least a dozen other proteins that function in DNA metabolism. To examine how many C-termini are needed for SSB function, we engineered covalently linked forms of SSB that possess only one or two C-termini within a four-OB-fold \"tetramer\". Whereas E. coli expressing SSB with only two tails can survive, expression of a single-tailed SSB is dominant lethal. E. coli expressing only the two-tailed SSB recovers faster from exposure to DNA damaging agents but accumulates more mutations. A single-tailed SSB shows defects in coupled leading and lagging strand DNA replication and does not support replication restart in vitro. These deficiencies in vitro provide a plausible explanation for the lethality observed in vivo. These results indicate that a single SSB tetramer must interact simultaneously with multiple protein partners during some essential roles in genome maintenance.","corpus_id":497163,"score":1},{"doc_id":"24198424","title":"Insights into bacteriophage T5 structure from analysis of its morphogenesis genes and protein components.","abstract":"Bacteriophage T5 represents a large family of lytic Siphoviridae infecting Gram-negative bacteria. The low-resolution structure of T5 showed the T=13 geometry of the capsid and the unusual trimeric organization of the tail tube, and the assembly pathway of the capsid was established. Although major structural proteins of T5 have been identified in these studies, most of the genes encoding the morphogenesis proteins remained to be identified. Here, we combine a proteomic analysis of T5 particles with a bioinformatic study and electron microscopic immunolocalization to assign function to the genes encoding the structural proteins, the packaging proteins, and other nonstructural components required for T5 assembly. A head maturation protease that likely accounts for the cleavage of the different capsid proteins is identified. Two other proteins involved in capsid maturation add originality to the T5 capsid assembly mechanism: the single head-to-tail joining protein, which closes the T5 capsid after DNA packaging, and the nicking endonuclease responsible for the single-strand interruptions in the T5 genome. We localize most of the tail proteins that were hitherto uncharacterized and provide a detailed description of the tail tip composition. Our findings highlight novel variations of viral assembly strategies and of virion particle architecture. They further recommend T5 for exploring phage structure and assembly and for deciphering conformational rearrangements that accompany DNA transfer from the capsid to the host cytoplasm.","corpus_id":26143905,"score":1},{"doc_id":"24371279","title":"Single molecule analysis of Thermus thermophilus SSB protein dynamics on single-stranded DNA.","abstract":"Single-stranded (ss) DNA binding (SSB) proteins play central roles in DNA replication, recombination and repair in all organisms. We previously showed that Escherichia coli (Eco) SSB, a homotetrameric bacterial SSB, undergoes not only rapid ssDNA-binding mode transitions but also one-dimensional diffusion (or migration) while remaining bound to ssDNA. Whereas the majority of bacterial SSB family members function as homotetramers, dimeric SSB proteins were recently discovered in a distinct bacterial lineage of extremophiles, the Thermus-Deinococcus group. Here we show, using single-molecule fluorescence resonance energy transfer (FRET), that homodimeric bacterial SSB from Thermus thermophilus (Tth) is able to diffuse spontaneously along ssDNA over a wide range of salt concentrations (20-500 mM NaCl), and that TthSSB diffusion can help transiently melt the DNA hairpin structures. Furthermore, we show that two TthSSB molecules undergo transitions among different DNA-binding modes while remaining bound to ssDNA. Our results extend our previous observations on homotetrameric SSBs to homodimeric SSBs, indicating that the dynamic features may be shared among different types of SSB proteins. These dynamic features of SSBs may facilitate SSB redistribution and removal on/from ssDNA, and help recruit other SSB-interacting proteins onto ssDNA for subsequent DNA processing in DNA replication, recombination and repair.","corpus_id":16808196,"score":1},{"doc_id":"24730652","title":"Structural analysis of replication protein A recruitment of the DNA damage response protein SMARCAL1.","abstract":"SWI/SNF-related, matrix-associated, actin-dependent regulator of chromatin, subfamily A-like1 (SMARCAL1) is a recently identified DNA damage response protein involved in remodeling stalled replication forks. The eukaryotic single-strand DNA binding protein replication protein A (RPA) recruits SMARCAL1 to stalled forks in vivo and facilitates regression of forks containing leading strand gaps. Both activities are mediated by a direct interaction between an RPA binding motif (RBM) at the N-terminus of SMARCAL1 and the C-terminal winged-helix domain of the RPA 32 kDa subunit (RPA32C). Here we report a biophysical and structural characterization of the SMARCAL1-RPA interaction. Isothermal titration calorimetry and circular dichroism spectroscopy revealed that RPA32C binds SMARCAL1-RBM with a Kd of 2.5 μM and induces a disorder-to-helix transition. The crystal structure of RPA32C was refined to 1.4 Å resolution, and the SMARCAL1-RBM binding site was mapped on the structure on the basis of nuclear magnetic resonance chemical shift perturbations. Conservation of the interaction surface to other RBM-containing proteins allowed construction of a model for the RPA32C/SMARCAL1-RBM complex. The implications of our results are discussed with respect to the recruitment of SMARCAL1 and other DNA damage response and repair proteins to stalled replication forks.","corpus_id":14046675,"score":1},{"doc_id":"25162017","title":"C-terminal domain swapping of SSB changes the size of the ssDNA binding site.","abstract":"Single-stranded DNA-binding protein (SSB) plays an important role in DNA metabolism, including DNA replication, repair, and recombination, and is therefore essential for cell survival. Bacterial SSB consists of an N-terminal ssDNA-binding/oligomerization domain and a flexible C-terminal protein-protein interaction domain. We characterized the ssDNA-binding properties of Klebsiella pneumoniae SSB (KpSSB), Salmonella enterica Serovar Typhimurium LT2 SSB (StSSB), Pseudomonas aeruginosa PAO1 SSB (PaSSB), and two chimeric KpSSB proteins, namely, KpSSBnStSSBc and KpSSBnPaSSBc. The C-terminal domain of StSSB or PaSSB was exchanged with that of KpSSB through protein chimeragenesis. By using the electrophoretic mobility shift assay, we characterized the stoichiometry of KpSSB, StSSB, PaSSB, KpSSBnStSSBc, and KpSSBnPaSSBc, complexed with a series of ssDNA homopolymers. The binding site sizes were determined to be 26 ± 2, 21 ± 2, 29 ± 2, 21 ± 2, and 29 ± 2 nucleotides (nt), respectively. Comparison of the binding site sizes of KpSSB, KpSSBnStSSBc, and KpSSBnPaSSBc showed that the C-terminal domain swapping of SSB changes the size of the binding site. Our observations suggest that not only the conserved N-terminal domain but also the C-terminal domain of SSB is an important determinant for ssDNA binding.","corpus_id":18626099,"score":1},{"doc_id":"25171654","title":"Replication protein A: single-stranded DNA's first responder: dynamic DNA-interactions allow replication protein A to direct single-strand DNA intermediates into different pathways for synthesis or repair.","abstract":"Replication protein A (RPA), the major single-stranded DNA-binding protein in eukaryotic cells, is required for processing of single-stranded DNA (ssDNA) intermediates found in replication, repair, and recombination. Recent studies have shown that RPA binding to ssDNA is highly dynamic and that more than high-affinity binding is needed for function. Analysis of DNA binding mutants identified forms of RPA with reduced affinity for ssDNA that are fully active, and other mutants with higher affinity that are inactive. Single molecule studies showed that while RPA binds ssDNA with high affinity, the RPA complex can rapidly diffuse along ssDNA and be displaced by other proteins that act on ssDNA. Finally, dynamic DNA binding allows RPA to prevent error-prone repair of double-stranded breaks and promote error-free repair. Together, these findings suggest a new paradigm where RPA acts as a first responder at sites with ssDNA, thereby actively coordinating DNA repair and DNA synthesis.","corpus_id":20212094,"score":1},{"doc_id":"25787788","title":"Mechanochemical regulations of RPA's binding to ssDNA.","abstract":"Replication protein A (RPA) is a ubiquitous eukaryotic single-stranded DNA (ssDNA) binding protein that serves to protect ssDNA from degradation and annealing, and as a template for recruitment of many downstream factors in virtually all DNA transactions in cell. During many of these transactions, DNA is tethered and is likely subject to force. Previous studies of RPA's binding behavior on ssDNA were conducted in the absence of force; therefore the RPA-ssDNA conformations regulated by force remain unclear. Here, using a combination of atomic force microscopy imaging and mechanical manipulation of single ssDNA tethers, we show that force mediates a switch of the RPA bound ssDNA from amorphous aggregation to a much more regular extended conformation. Further, we found an interesting non-monotonic dependence of the binding affinity on monovalent salt concentration in the presence of force. In addition, we discovered that zinc in micromolar concentrations drives ssDNA to a unique, highly stiff and more compact state. These results provide new mechanochemical insights into the influences and the mechanisms of action of RPA on large single ssDNA.","corpus_id":16520668,"score":1},{"doc_id":"26350770","title":"Complete genome sequences of T5-related Escherichia coli bacteriophages DT57C and DT571/2 isolated from horse feces.","abstract":"We report the complete genome sequencing of two Escherichia coli T5-related bacteriophages, DT57C and DT571/2, isolated from the same specimen of horse feces. These two isolates share 96 % nucleotide sequence identity and can thus be considered representatives of the same novel species within the genus T5likevirus. The observed variation in the ltfA gene of these phages, resulting from a recent recombination event, may explain the observed host-range differences, suggesting that a modular mechanism makes a significant contribution to the short-term evolution (or adaptation) of T5-like phage genomes in the intestinal ecosystem. Comparison of our isolates to their closest relative, coliphage T5, revealed high overall synteny of the genomes and high conservation of the sequences of almost all structural proteins as well as of the other proteins with identified functions. At the same time, numerous alterations and non-orthologous replacements of non-structural protein genes (mostly of those with unknown functions) as well as substantial differences in tail fiber locus organization support the conclusion that DT57C and DT571/2 form a species-level group clearly distinct from bacteriophage T5.","corpus_id":19670085,"score":1},{"doc_id":"27131360","title":"The Borrelia burgdorferi telomere resolvase, ResT, anneals ssDNA complexed with its cognate ssDNA-binding protein.","abstract":"Spirochetes of the genus Borrelia possess unusual genomes that consist in a linear chromosome and multiple linear and circular plasmids. The linear replicons are terminated by covalently closed hairpin ends, referred to as hairpin telomeres. The hairpin telomeres represent a simple solution to the end-replication problem. Deoxyribonucleic acid replication initiates internally and proceeds bidirectionally toward the hairpin telomeres. The telomere resolvase, ResT, forms the hairpin telomeres from replicated telomere intermediates in a reaction with similarities to those promoted by type IB topoisomerases and tyrosine recombinases. ResT has also been shown to possess DNA single-strand annealing activity. We report here that ResT promotes single-strand annealing of both free DNA strands and ssDNA complexed with single-stranded DNA binding protein (SSB). The annealing of complementary strands bound by SSB requires a ResT-SSB interaction that is mediated by the conserved amphipathic C-terminal tail of SSB. These properties of ResT are similar to those demonstrated for the recombination mediator protein, RecO, of the RecF pathway. Borrelia burgdorferi is unusual in lacking identifiable homologs of the RecFOR proteins. We propose that ResT may provide missing RecFOR functions.","corpus_id":14989698,"score":1},{"doc_id":"27131385","title":"Dynamic binding of replication protein a is required for DNA repair.","abstract":"Replication protein A (RPA), the major eukaryotic single-stranded DNA (ssDNA) binding protein, is essential for replication, repair and recombination. High-affinity ssDNA-binding by RPA depends on two DNA binding domains in the large subunit of RPA. Mutation of the evolutionarily conserved aromatic residues in these two domains results in a separation-of-function phenotype: aromatic residue mutants support DNA replication but are defective in DNA repair. We used biochemical and single-molecule analyses, and Brownian Dynamics simulations to determine the molecular basis of this phenotype. Our studies demonstrated that RPA binds to ssDNA in at least two modes characterized by different dissociation kinetics. We also showed that the aromatic residues contribute to the formation of the longer-lived state, are required for stable binding to short ssDNA regions and are needed for RPA melting of partially duplex DNA structures. We conclude that stable binding and/or the melting of secondary DNA structures by RPA is required for DNA repair, including RAD51 mediated DNA strand exchange, but is dispensable for DNA replication. It is likely that the binding modes are in equilibrium and reflect dynamics in the RPA-DNA complex. This suggests that dynamic binding of RPA to DNA is necessary for different cellular functions.","corpus_id":6467961,"score":1},{"doc_id":"27151292","title":"Replication protein A and more: single-stranded DNA-binding proteins in eukaryotic cells.","abstract":"Single-stranded DNA-binding proteins (SSBs) play essential roles in DNA replication, recombinational repair, and maintenance of genome stability. In human, the major SSB, replication protein A (RPA), is a stable heterotrimer composed of subunits of RPA1, RPA2, and RPA3, each of which is conserved not only in mammals but also in all other eukaryotic species. In addition to RPA, other SSBs have also been identified in the human genome, including sensor of single-stranded DNA complexes 1 and 2 (SOSS1/2). In this review, we summarize our current understanding of how these SSBs contribute to the maintenance of genome stability.","corpus_id":3052726,"score":1},{"doc_id":"27185951","title":"Chemo-mechanical pushing of proteins along single-stranded DNA.","abstract":"Single-stranded (ss)DNA binding (SSB) proteins bind with high affinity to ssDNA generated during DNA replication, recombination, and repair; however, these SSBs must eventually be displaced from or reorganized along the ssDNA. One potential mechanism for reorganization is for an ssDNA translocase (ATP-dependent motor) to push the SSB along ssDNA. Here we use single molecule total internal reflection fluorescence microscopy to detect such pushing events. When Cy5-labeled Escherichia coli (Ec) SSB is bound to surface-immobilized 3'-Cy3-labeled ssDNA, a fluctuating FRET signal is observed, consistent with random diffusion of SSB along the ssDNA. Addition of Saccharomyces cerevisiae Pif1, a 5' to 3' ssDNA translocase, results in the appearance of isolated, irregularly spaced saw-tooth FRET spikes only in the presence of ATP. These FRET spikes result from translocase-induced directional (5' to 3') pushing of the SSB toward the 3' ssDNA end, followed by displacement of the SSB from the DNA end. Similar ATP-dependent pushing events, but in the opposite (3' to 5') direction, are observed with EcRep and EcUvrD (both 3' to 5' ssDNA translocases). Simulations indicate that these events reflect active pushing by the translocase. The ability of translocases to chemo-mechanically push heterologous SSB proteins along ssDNA provides a potential mechanism for reorganization and clearance of tightly bound SSBs from ssDNA.","corpus_id":1201982,"score":1},{"doc_id":"27624131","title":"Examining a DNA Replication Requirement for Bacteriophage λ Red- and Rac Prophage RecET-Promoted Recombination in Escherichia coli.","abstract":"UNLABELLED: Recombineering, in vivo genetic engineering with bacteriophage homologous recombination systems, is a powerful technique for making genetic modifications in bacteria. Two systems widely used in Escherichia coli are the Red system from phage λ and RecET from the defective Rac prophage. We investigated the in vivo dependence of recombineering on DNA replication of the recombining substrate using plasmid targets. For λ Red recombination, when DNA replication of a circular target plasmid is prevented, recombination with single-stranded DNA oligonucleotides is greatly reduced compared to that under replicating conditions. For RecET recombination, when DNA replication of the targeted plasmid is prevented, the recombination frequency is also reduced, to a level identical to that seen for the Red system in the absence of replication. The very low level of oligonucleotide recombination observed in the absence of any phage recombination functions is the same in the presence or absence of DNA replication. In contrast, both the Red and RecET systems recombine a nonreplicating linear dimer plasmid with high efficiency to yield a circular monomer. Therefore, the DNA replication requirement is substrate dependent. Our data are consistent with recombination by both the Red and RecET systems occurring predominately by single-strand annealing rather than by strand invasion. IMPORTANCE: Bacteriophage homologous recombination systems are widely used for in vivo genetic engineering in bacteria. Single- or double-stranded linear DNA substrates containing short flanking homologies to chromosome targets are used to generate precise and accurate genetic modifications when introduced into bacteria expressing phage recombinases. Understanding the molecular mechanism of these recombination systems will facilitate improvements in the technology. Here, two phage-specific systems are shown to require exposure of complementary single-strand homologous targets for efficient recombination; these single-strand regions may be created during DNA replication or by single-strand exonuclease digestion of linear duplex DNA. Previously, in vitro studies reported that these recombinases promote the single-strand annealing of two complementary DNAs and also strand invasion of a single DNA strand into duplex DNA to create a three-stranded region. Here, in vivo experiments show that recombinase-mediated annealing of complementary single-stranded DNA is the predominant recombination pathway in E. coli.","corpus_id":18971153,"score":1},{"doc_id":"29458770","title":"Single-Molecule Studies of ssDNA-Binding Proteins Exchange.","abstract":"Single-stranded DNA-binding protein (SSB) is important not only for the protection of single-stranded DNA (ssDNA) but also for the recruitment of other proteins for DNA replication, recombination, and repair. The interaction of SSB with ssDNA is highly dynamic as it exists as an intermediate during cellular processes that unwind dsDNA. It has been proposed that SSB redistributes itself among multiple ssDNA segments, but transient intermediates are difficult to observe in bulk experiments. We can use single-molecule FRET microscopy to observe intermediates of the transfer of a single Escherichia coli SSB from one ssDNA strand to another or exchange of one SSB for another on a single ssDNA in real time. This single-molecule approach can be further applicable to understand relative binding affinities and competitive dynamics for other SSBs and variants across various systems.","corpus_id":3440559,"score":1},{"doc_id":"29681468","title":"Discrimination against RNA Backbones by a ssDNA Binding Protein.","abstract":"Pot1 is the shelterin component responsible for the protection of the single-stranded DNA (ssDNA) overhang at telomeres in nearly all eukaryotic organisms. The C-terminal domain of the DNA-binding domain, Pot1pC, exhibits non-specific ssDNA recognition, achieved through thermodynamically equivalent alternative binding conformations. Given this flexibility, it is unclear how specificity for ssDNA over RNA, an activity required for biological function, is achieved. Examination of the ribose-position specificity of Pot1pC shows that ssDNA specificity is additive but not uniformly distributed across the ligand. High-resolution structures of several Pot1pC complexes with RNA-DNA chimeric ligands reveal Pot1pC discriminates against RNA by utilizing non-compensatory binding modes that feature significant rearrangement of the binding interface. These alternative conformations, accessed through both ligand and protein flexibility, recover much, but not all, of the binding energy, leading to the observed reduction in affinities. These findings suggest that intermolecular interfaces are remarkably sophisticated in their tuning of specificity toward flexible ligands.","corpus_id":5066050,"score":1},{"doc_id":"18848568","title":"Bacteriophage T5 DNA ejection under pressure.","abstract":"The transfer of the bacteriophage genome from the capsid into the host cell is a key step of the infectious process. In bacteriophage T5, DNA ejection can be triggered in vitro by simple binding of the phage to its purified Escherichia coli receptor FhuA. Using electrophoresis and cryo-electron microscopy, we measure the extent of DNA ejection as a function of the external osmotic pressure. In the high pressure range (7-16 atm), the amount of DNA ejected decreases with increasing pressure, as theoretically predicted and observed for lambda and SPP1 bacteriophages. In the low and moderate pressure range (2-7 atm), T5 exhibits an unexpected behavior. Instead of a unique ejected length, multiple populations coexist. Some phages eject their complete genome, whereas others stop at some nonrandom states that do not depend on the applied pressure. We show that contrarily to what is observed for the phages SPP1 and lambda, T5 ejection cannot be explained as resulting from a simple pressure equilibrium between the inside and outside of the capsid. Kinetics parameters and/or structural characteristics of the ejection machinery could play a determinant role in T5 DNA ejection.","corpus_id":27898318,"score":0},{"doc_id":"19919545","title":"Identification and characterization of the metal ion-dependent L-alanoyl-D-glutamate peptidase encoded by bacteriophage T5.","abstract":"Although bacteriophage T5 is known to have lytic proteins for cell wall hydrolysis and phage progeny escape, their activities are still unknown. This is the first report on the cloning, expression and biochemical characterization of a bacteriophage T5 lytic hydrolase. The endolysin-encoding lys gene of virulent coliphage T5 was cloned in Escherichia coli cells, and an electrophoretically homogeneous product of this gene was obtained with a high yield (78% of total activity). The protein purified was shown to be an L-alanoyl-D-glutamate peptidase. The enzyme demonstrated maximal activity in diluted buffers (25-50 mM) at pH 8.5. The enzyme was strongly inhibited by EDTA and BAPTA, and fully reactivated by calcium/manganese chlorides. It was found that, along with E. coli peptidoglycan, peptidase of bacteriophage T5 can lyse peptidoglycans of other Gram-negative microorganisms (Pectobacterium carotovorum, Pseudomonas putida, Proteus vulgaris, and Proteus mirabilis). This endolysin is the first example of an L-alanoyl-D-glutamate peptidase in a virulent phage infecting Gram-negative bacteria. There are, however, a great many sequences in databases that are highly similar to that of bacteriophage T5 hydrolase, indicating a wide distribution of endolytic L-alanoyl-D-glutamate peptidases. The article discusses how an enzyme with such substrate specificity could be fixed in the process of evolution.","corpus_id":24741775,"score":0}],"string":"[\n {\n \"doc_id\": \"18238893\",\n \"title\": \"Acidic C-terminal tail of the ssDNA-binding protein of bacteriophage T7 and ssDNA compete for the same binding surface.\",\n \"abstract\": \"ssDNA-binding proteins are key components of the machinery that mediates replication, recombination, and repair. Prokaryotic ssDNA-binding proteins share a conserved DNA-binding fold and an acidic C-terminal tail. It has been proposed that in the absence of ssDNA, the C-terminal tail contacts the ssDNA-binding cleft, therefore predicting that the binding of ssDNA and the C-terminal tail is mutually exclusive. Using chemical cross-linking, competition studies, and NMR chemical-shift mapping, we demonstrate that: (i) the C-terminal peptide of the gene 2.5 protein cross-links to the core of the protein only in the absence of ssDNA, (ii) the cross-linked species fails to bind to ssDNA, and (iii) a C-terminal peptide and ssDNA bind to the same overall surface of the protein. We propose that the protection of the DNA-binding cleft by the electrostatic shield of the C-terminal tail observed in prokaryotic ssDNA-binding proteins, ribosomal proteins, and high-mobility group proteins is an evolutionarily conserved mechanism. This mechanism prevents random binding of charged molecules to the nucleic acid-binding pocket and coordinates nucleic acid-protein and protein-protein interactions.\",\n \"corpus_id\": 1217841,\n \"score\": 2\n },\n {\n \"doc_id\": \"19571366\",\n \"title\": \"Interaction of bacteriophage T4 and T7 single-stranded DNA-binding proteins with DNA.\",\n \"abstract\": \"Bacteriophages T4 and T7 are well-studied model replication systems, which have allowed researchers to determine the roles of many proteins central to DNA replication, recombination and repair. Here we summarize and discuss the results from two recently developed single-molecule methods to determine the salt-dependent DNA-binding kinetics and thermodynamics of the single-stranded DNA (ssDNA)-binding proteins (SSBs) from these systems. We use these methods to characterize both the equilibrium double-stranded DNA (dsDNA) and ssDNA binding of the SSBs T4 gene 32 protein (gp32) and T7 gene 2.5 protein (gp2.5). Despite the overall two-orders-of-magnitude weaker binding of gp2.5 to both forms of DNA, we find that both proteins exhibit four-orders-of-magnitude preferential binding to ssDNA relative to dsDNA. This strong preferential ssDNA binding as well as the weak dsDNA binding is essential for the ability of both proteins to search dsDNA in one dimension to find available ssDNA-binding sites at the replication fork.\",\n \"corpus_id\": 21083142,\n \"score\": 2\n },\n {\n \"doc_id\": \"20951652\",\n \"title\": \"On the mutagenicity of homologous recombination and double-strand break repair in bacteriophage.\",\n \"abstract\": \"The double-strand break (DSB) repair via homologous recombination is generally construed as a high-fidelity process. However, some molecular genetic observations show that the recombination and the recombinational DSB repair may be mutagenic and even highly mutagenic. Here we developed an effective and precise method for studying the fidelity of DSB repair in vivo by combining DSBs produced site-specifically by the SegC endonuclease with the famous advantages of the recombination analysis of bacteriophage T4 rII mutants. The method is based on the comparison of the rate of reversion of rII mutation in the presence and in the absence of a DSB repair event initiated in the proximity of the mutation. We observed that DSB repair may moderately (up to 6-fold) increase the apparent reversion frequency, the effect of being dependent on the mutation structure. We also studied the effect of the T4 recombinase deficiency (amber mutation in the uvsX gene) on the fidelity of DSB repair. We observed that DSBs are still repaired via homologous recombination in the uvsX mutants, and the apparent fidelity of this repair is higher than that seen in the wild-type background. The mutator effect of the DSB repair may look unexpected given that most of the normal DNA synthesis in bacteriophage T4 is performed via a recombination-dependent replication (RDR) pathway, which is thought to be indistinguishable from DSB repair. There are three possible explanations for the observed mutagenicity of DSB repair: (1) the origin-dependent (early) DNA replication may be more accurate than the RDR; (2) the step of replication initiation may be more mutagenic than the process of elongation; and (3) the apparent mutagenicity may just reflect some non-randomness in the pool of replicating DNA, i.e., preferential replication of the sequences already involved in replication. We discuss the DSB repair pathway in the absence of UvsX recombinase.\",\n \"corpus_id\": 207147290,\n \"score\": 2\n },\n {\n \"doc_id\": \"21129203\",\n \"title\": \"Initiation of bacteriophage T4 DNA replication and replication fork dynamics: a review in the Virology Journal series on bacteriophage T4 and its relatives.\",\n \"abstract\": \"Bacteriophage T4 initiates DNA replication from specialized structures that form in its genome. Immediately after infection, RNA-DNA hybrids (R-loops) occur on (at least some) replication origins, with the annealed RNA serving as a primer for leading-strand synthesis in one direction. As the infection progresses, replication initiation becomes dependent on recombination proteins in a process called recombination-dependent replication (RDR). RDR occurs when the replication machinery is assembled onto D-loop recombination intermediates, and in this case, the invading 3' DNA end is used as a primer for leading strand synthesis. Over the last 15 years, these two modes of T4 DNA replication initiation have been studied in vivo using a variety of approaches, including replication of plasmids with segments of the T4 genome, analysis of replication intermediates by two-dimensional gel electrophoresis, and genomic approaches that measure DNA copy number as the infection progresses. In addition, biochemical approaches have reconstituted replication from origin R-loop structures and have clarified some detailed roles of both replication and recombination proteins in the process of RDR and related pathways. We will also discuss the parallels between T4 DNA replication modes and similar events in cellular and eukaryotic organelle DNA replication, and close with some current questions of interest concerning the mechanisms of replication, recombination and repair in phage T4.\",\n \"corpus_id\": 14822419,\n \"score\": 2\n },\n {\n \"doc_id\": \"22500043\",\n \"title\": \"Assembly and dynamics of Gp59-Gp32-single-stranded DNA (ssDNA), a DNA helicase loading complex required for recombination-dependent replication in bacteriophage T4.\",\n \"abstract\": \"The Gp59 protein of bacteriophage T4 plays critical roles in recombination-dependent DNA replication and repair by correctly loading the replicative helicase, Gp41, onto recombination intermediates. Previous work demonstrated that Gp59 is required to load helicase onto single-stranded DNA that is saturated with Gp32, the T4 single-stranded DNA (ssDNA)-binding protein. Gp59 and Gp32 bind simultaneously to ssDNA, forming a Gp59-Gp32-ssDNA complex that is a key intermediate in helicase loading. Here we characterize the assembly and dynamics of this helicase loading complex (HLC) through changes in the fluorescent states of Gp32F, a fluorescein-Gp32 conjugate. Results show that HLC formation requires a minimum Gp32-ssDNA cluster size and that Gp59 co-localizes with Gp32-ssDNA clusters in the presence of excess free ssDNA. These and other results indicate that Gp59 targets helicase assembly onto Gp32-ssDNA clusters that form on the displaced strand of D-loops, which suggests a mechanism for the rapid initiation of recombination-dependent DNA replication. Helicase loading at the HLC requires ATP binding (not hydrolysis) by Gp41 and results in local remodeling of Gp32 within the HLC. Subsequent ATPase-driven translocation of Gp41 progressively disrupts Gp32-ssDNA interactions. Evidence suggests that Gp59 from the HLC is recycled to promote multiple rounds of helicase assembly on Gp32-ssDNA, a capability that could be important for the restart of stalled replication forks.\",\n \"corpus_id\": 25923293,\n \"score\": 2\n },\n {\n \"doc_id\": \"22976174\",\n \"title\": \"Functions of single-strand DNA-binding proteins in DNA replication, recombination, and repair.\",\n \"abstract\": \"Double-stranded (ds) DNA contains all of the necessary genetic information, although practical use of this information requires unwinding of the duplex DNA. DNA unwinding creates single-stranded (ss) DNA intermediates that serve as templates for myriad cellular functions. Exposure of ssDNA presents several problems to the cell. First, ssDNA is thermodynamically less stable than dsDNA, which leads to spontaneous formation of duplex secondary structures that impede genome maintenance processes. Second, relative to dsDNA, ssDNA is hypersensitive to chemical and nucleolytic attacks that can cause damage to the genome. Cells deal with these potential problems by encoding specialized ssDNA-binding proteins (SSBs) that bind to and stabilize ssDNA structures required for essential genomic processes. SSBs are essential proteins found in all domains of life. SSBs bind ssDNA with high affinity and in a sequence-independent manner and, in doing so, SSBs help to form the central nucleoprotein complex substrate for DNA replication, recombination, and repair processes. While SSBs are found in every organism, the proteins themselves share surprisingly little sequence similarity, subunit composition, and oligomerization states. All SSB proteins contain at least one DNA-binding oligonucleotide/oligosaccharide binding (OB) fold, which consists minimally of a five stranded beta-sheet arranged as a beta barrel capped by a single alpha helix. The OB fold is responsible for both ssDNA binding and oligomerization (for SSBs that operate as oligomers). The overall organization of OB folds varies between bacteria, eukaryotes, and archaea. As part of SSB/ssDNA cellular structures, SSBs play direct roles in the DNA replication, recombination, and repair. In many cases, SSBs have been found to form specific complexes with diverse genome maintenance proteins, often helping to recruit SSB/ssDNA-processing enzymes to the proper cellular sites of action. This clustering of genome maintenance factors can help to stimulate and coordinate the activities of individual enzymes and is also important for dislodging SSB from ssDNA. These features support a model in which DNA metabolic processes have evolved to work on ssDNA/SSB nucleoprotein filaments rather than on naked ssDNA. In this volume, methods are described to interrogate SSB-DNA and SSB-protein binding functions along with approaches that aim to understand the cellular functions of SSB. This introductory chapter offers a general overview of SSBs that focuses on their structures, DNA-binding mechanisms, and protein-binding partners.\",\n \"corpus_id\": 20789227,\n \"score\": 2\n },\n {\n \"doc_id\": \"23119018\",\n \"title\": \"Characterization of the Holliday junction resolving enzyme encoded by the Bacillus subtilis bacteriophage SPP1.\",\n \"abstract\": \"Recombination-dependent DNA replication, which is a central component of viral replication restart, is poorly understood in Firmicutes bacteriophages. Phage SPP1 initiates unidirectional theta DNA replication from a discrete replication origin (oriL), and when replication progresses, the fork might stall by the binding of the origin binding protein G38P to the late replication origin (oriR). Replication restart is dependent on viral recombination proteins to synthesize a linear head-to-tail concatemer, which is the substrate for viral DNA packaging. To identify new functions involved in this process, uncharacterized genes from phage SPP1 were analyzed. Immediately after infection, SPP1 transcribes a number of genes involved in recombination and replication from P(E2) and P(E3) promoters. Resequencing the region corresponding to the last two hypothetical genes transcribed from the P(E2) operon (genes 44 and 45) showed that they are in fact a single gene, re-annotated here as gene 44, that encodes a single polypeptide, named gene 44 product (G44P, 27.5 kDa). G44P shares a low but significant degree of identity in its C-terminal region with virus-encoded RusA-like resolvases. The data presented here demonstrate that G44P, which is a dimer in solution, binds with high affinity but without sequence specificity to several double-stranded DNA recombination intermediates. G44P preferentially cleaves Holliday junctions, but also, with lower efficiency, replicated D-loops. It also partially complemented the loss of RecU resolvase activity in B. subtilis cells. These in vitro and in vivo data suggest a role for G44P in replication restart during the transition to concatemeric viral replication.\",\n \"corpus_id\": 8779781,\n \"score\": 2\n },\n {\n \"doc_id\": \"23435232\",\n \"title\": \"Characterization of an unusual bipolar helicase encoded by bacteriophage T5.\",\n \"abstract\": \"Bacteriophage T5 has a 120 kb double-stranded linear DNA genome encoding most of the genes required for its own replication. This lytic bacteriophage has a burst size of ∼500 new phage particles per infected cell, demonstrating that it is able to turn each infected bacterium into a highly efficient DNA manufacturing machine. To begin to understand DNA replication in this prodigious bacteriophage, we have characterized a putative helicase encoded by gene D2. We show that bacteriophage T5 D2 protein is the first viral helicase to be described with bipolar DNA unwinding activities that require the same core catalytic residues for unwinding in either direction. However, unwinding of partially single- and double-stranded DNA test substrates in the 3'-5' direction is more robust and can be distinguished from the 5'-3' activity by a number of features including helicase complex stability, salt sensitivity and the length of single-stranded DNA overhang required for initiation of helicase action. The presence of D2 in an early gene cluster, the identification of a putative helix-turn-helix DNA-binding motif outside the helicase core and homology with known eukaryotic and prokaryotic replication initiators suggest an involvement for this unusual helicase in DNA replication initiation.\",\n \"corpus_id\": 18931209,\n \"score\": 2\n },\n {\n \"doc_id\": \"23732982\",\n \"title\": \"Interaction of T4 UvsW helicase and single-stranded DNA binding protein gp32 through its carboxy-terminal acidic tail.\",\n \"abstract\": \"Bacteriophage T4 UvsW helicase contains both unwinding and annealing activities and displays some functional similarities to bacterial RecG and RecQ helicases. UvsW is involved in several DNA repair pathways, playing important roles in recombination-dependent DNA repair and the reorganization of stalled replication forks. The T4 single-stranded DNA (ssDNA) binding protein gp32 is a central player in nearly all DNA replication and repair processes and is thought to facilitate their coordination by recruiting and regulating the various proteins involved. Here, we show that the activities of the UvsW protein are modulated by gp32. UvsW-catalyzed unwinding of recombination intermediates such as D-loops and static X-DNA (Holliday junction mimic) to ssDNA products is enhanced by the gp32 protein. The enhancement requires the presence of the protein interaction domain of gp32 (the acidic carboxy-terminus), suggesting that a specific interaction between UvsW and gp32 is required. In the absence of this interaction, the ssDNA annealing and ATP-dependent translocation activities of UvsW are severely inhibited when gp32 coats the ssDNA lattice. However, when UvsW and gp32 do interact, UvsW is able to efficiently displace the gp32 protein from the ssDNA. This ability of UvsW to remove gp32 from ssDNA may explain its ability to enhance the strand invasion activity of the T4 recombinase (UvsX) and suggests a possible new role for UvsW in gp32-mediated DNA transactions.\",\n \"corpus_id\": 33374945,\n \"score\": 2\n },\n {\n \"doc_id\": \"24029071\",\n \"title\": \"Bacteriophage T5 encodes a homolog of the eukaryotic transcription coactivator PC4 implicated in recombination-dependent DNA replication.\",\n \"abstract\": \"The RNA polymerase II cofactor PC4 globally regulates transcription of protein-encoding genes through interactions with unwinding DNA, the basal transcription machinery and transcription activators. Here, we report the surprising identification of PC4 homologs in all sequenced representatives of the T5 family of bacteriophages, as well as in an archaeon and seven phyla of eubacteria. We have solved the crystal structure of the full-length T5 protein at 1.9Å, revealing a striking resemblance to the characteristic single-stranded DNA (ssDNA)-binding core domain of PC4. Intriguing novel structural features include a potential regulatory region at the N-terminus and a C-terminal extension of the homodimerisation interface. The genome organisation of T5-related bacteriophages points at involvement of the PC4 homolog in recombination-dependent DNA replication, strongly suggesting that the protein corresponds to the hitherto elusive replicative ssDNA-binding protein of the T5 family. Our findings imply that PC4-like factors intervene in multiple unwinding-related processes by acting as versatile modifiers of nucleic acid conformation and raise the possibility that the eukaryotic transcription coactivator derives from ancestral DNA replication, recombination and repair factors.\",\n \"corpus_id\": 9828419,\n \"score\": 2\n },\n {\n \"doc_id\": \"24124995\",\n \"title\": \"Kinetics of presynaptic filament assembly in the presence of single-stranded DNA binding protein and recombination mediator protein.\",\n \"abstract\": \"Enzymes of the RecA/Rad51 family catalyze DNA strand exchange reactions that are important for homologous recombination and for the accurate repair of DNA double-strand breaks. RecA/Rad51 recombinases are activated by their assembly into presynaptic filaments on single-stranded DNA (ssDNA), a process that is regulated by ssDNA binding protein (SSB) and mediator proteins. Mediator proteins stimulate strand exchange by accelerating the rate-limiting displacement of SSB from ssDNA by the incoming recombinase. The use of mediators is a highly conserved strategy in recombination, but the precise mechanism of mediator activity is unknown. In this study, the well-defined bacteriophage T4 recombination system (UvsX recombinase, Gp32 SSB, and UvsY mediator) is used to examine the kinetics of presynaptic filament assembly on native ssDNA in vitro. Results indicate that the ATP-dependent assembly of UvsX presynaptic filaments on Gp32-covered ssDNA is limited by a salt-sensitive nucleation step in the absence of mediator. Filament nucleation is selectively enhanced and rendered salt-resistant by mediator protein UvsY, which appears to stabilize a prenucleation complex. This mechanism potentially explains how UvsY promotes presynaptic filament assembly at physiologically relevant ionic strengths and Gp32 concentrations. Other data suggest that presynaptic filament assembly involves multiple nucleation events, resulting in many short UvsX-ssDNA filaments or clusters, which may be the relevant form for recombination in vivo. Together, these findings provide the first detailed kinetic model for presynaptic filament assembly involving all three major protein components (recombinase, mediator, and SSB) on native ssDNA.\",\n \"corpus_id\": 7908663,\n \"score\": 2\n },\n {\n \"doc_id\": \"24338568\",\n \"title\": \"Control of helicase loading in the coupled DNA replication and recombination systems of bacteriophage T4.\",\n \"abstract\": \"The Gp59 protein of bacteriophage T4 promotes DNA replication by loading the replicative helicase, Gp41, onto replication forks and recombination intermediates. Gp59 also blocks DNA synthesis by Gp43 polymerase until Gp41 is loaded, ensuring that synthesis is tightly coupled to unwinding. The distinct polymerase blocking and helicase loading activities of Gp59 likely involve different binding interactions with DNA and protein partners. Here, we investigate how interactions of Gp59 with DNA and Gp32, the T4 single-stranded DNA (ssDNA)-binding protein, are related to these activities. A previously characterized mutant, Gp59-I87A, exhibits markedly reduced affinity for ssDNA and pseudo-fork DNA substrates. We demonstrate that on Gp32-covered ssDNA, the DNA binding defect of Gp59-I87A is not detrimental to helicase loading and translocation. In contrast, on pseudo-fork DNA the I87A mutation is detrimental to helicase loading and unwinding in the presence or absence of Gp32. Other results indicate that Gp32 binding to lagging strand ssDNA relieves the blockage of Gp43 polymerase activity by Gp59, whereas the inhibition of Gp43 exonuclease activity is maintained. Our findings suggest that Gp59-Gp32 and Gp59-DNA interactions perform separate but complementary roles in T4 DNA metabolism; Gp59-Gp32 interactions are needed to load Gp41 onto D-loops, and other nucleoprotein structures containing clusters of Gp32. Gp59-DNA interactions are needed to load Gp41 onto nascent or collapsed replication forks lacking clusters of Gp32 and to coordinate bidirectional replication from T4 origins. The dual functionalities of Gp59 allow it to promote the initiation or re-start of DNA replication from a wide variety of recombination and replication intermediates.\",\n \"corpus_id\": 34570636,\n \"score\": 2\n },\n {\n \"doc_id\": \"24591606\",\n \"title\": \"Single-molecule studies of polymerase dynamics and stoichiometry at the bacteriophage T7 replication machinery.\",\n \"abstract\": \"Replication of DNA plays a central role in transmitting hereditary information from cell to cell. To achieve reliable DNA replication, multiple proteins form a stable complex, known as the replisome, enabling them to act together in a highly coordinated fashion. Over the past decade, the roles of the various proteins within the replisome have been determined. Although many of their interactions have been characterized, it remains poorly understood how replication proteins enter and leave the replisome. In this study, we visualize fluorescently labeled bacteriophage T7 DNA polymerases within the replisome while we simultaneously observe the kinetics of the replication process. This combination of observables allows us to monitor both the activity and dynamics of individual polymerases during coordinated leading- and lagging-strand synthesis. Our data suggest that lagging-strand polymerases are exchanged at a frequency similar to that of Okazaki fragment synthesis and that two or more polymerases are present in the replisome during DNA replication. Our studies imply a highly dynamic picture of the replisome with lagging-strand DNA polymerases residing at the fork for the synthesis of only a few Okazaki fragments. Further, new lagging-strand polymerases are readily recruited from a pool of polymerases that are proximally bound to the replisome and continuously replenished from solution.\",\n \"corpus_id\": 205267763,\n \"score\": 2\n },\n {\n \"doc_id\": \"24970156\",\n \"title\": \"Homologous recombination as a replication fork escort: fork-protection and recovery.\",\n \"abstract\": \"Homologous recombination is a universal mechanism that allows DNA repair and ensures the efficiency of DNA replication. The substrate initiating the process of homologous recombination is a single-stranded DNA that promotes a strand exchange reaction resulting in a genetic exchange that promotes genetic diversity and DNA repair. The molecular mechanisms by which homologous recombination repairs a double-strand break have been extensively studied and are now well characterized. However, the mechanisms by which homologous recombination contribute to DNA replication in eukaryotes remains poorly understood. Studies in bacteria have identified multiple roles for the machinery of homologous recombination at replication forks. Here, we review our understanding of the molecular pathways involving the homologous recombination machinery to support the robustness of DNA replication. In addition to its role in fork-recovery and in rebuilding a functional replication fork apparatus, homologous recombination may also act as a fork-protection mechanism. We discuss that some of the fork-escort functions of homologous recombination might be achieved by loading of the recombination machinery at inactivated forks without a need for a strand exchange step; as well as the consequence of such a model for the stability of eukaryotic genomes.\",\n \"corpus_id\": 7453721,\n \"score\": 2\n },\n {\n \"doc_id\": \"25481875\",\n \"title\": \"Regulation of the bacteriophage T4 Dda helicase by Gp32 single-stranded DNA-binding protein.\",\n \"abstract\": \"Dda, one of three helicases encoded by bacteriophage T4, has been well-characterized biochemically but its biological role remains unclear. It is thought to be involved in origin dependent DNA replication, recombination-dependent replication, anti-recombination, and recombination repair. The Gp32 protein of bacteriophage T4 plays critical roles in DNA replication, recombination, and repair by coordinating protein components of the replication fork and by stabilizing ssDNA. Previous work demonstrated that stimulation of DNA synthesis by Dda helicase appears to require direct Gp32-Dda protein-protein interactions and that Gp32 and Dda form a tight complex in the absence of ssDNA. Here we characterize the effects of Gp32-Dda physical and functional interactions through changes in the duplex DNA unwinding and ATPase activities of Dda helicase in the presence of different variants of Gp32 and different DNA repair and replication intermediate structures. Results show that Gp32-Dda interactions can be enhancing or inhibitory, depending on the Gp32 domain seen by Dda. Protein-protein interactions with Gp32 stimulate the unwinding activity of Dda, an effect associated with increased turnover of ATP, suggesting a higher rate of ATPase-driven translocation. Dda-Gp32 interactions also promote the unwinding of DNA substrates at higher salt concentrations and in the presence of substrate-bound DNA polymerase. Conversely, the formation of Gp32 clusters on ssDNA can inhibit unwinding, suggesting that Gp32-ssDNA formation sterically regulates which portions of replication and recombination intermediates are accessible for processing by Dda helicase. The data suggest a mechanism of replication fork restart in which Gp32 promotes Dda activity in template switching while preventing premature fork progression.\",\n \"corpus_id\": 10770482,\n \"score\": 2\n },\n {\n \"doc_id\": \"25961912\",\n \"title\": \"PC4 promotes genome stability and DNA repair through binding of ssDNA at DNA damage sites.\",\n \"abstract\": \"The transcriptional cofactor PC4 is an ancient single-strand DNA (ssDNA)-binding protein that has a homologue in bacteriophage T5 where it is likely the elusive replicative ssDNA-binding protein. We hypothesize that human PC4 has retained functions in ssDNA binding to stabilize replication forks and prevent genome instability in mammalian cells. Here we demonstrate that PC4 is recruited to hydroxyurea (HU)-stalled replication forks, which is dependent on active transcription and its ssDNA-binding ability. Interestingly, we demonstrate that ssDNA binding by PC4 is critical to suppress spontaneous DNA damage and promote cellular survival. PC4 accumulation co-localizes with replication protein A (RPA) at stalled forks and is increased upon RPA depletion, demonstrating compensatory functions in ssDNA binding. Depletion of PC4 not only results in defective resolution of HU-induced DNA damage but also significantly reduces homologous recombination repair efficiency. Altogether, our results indicate that PC4 has similar functions to RPA in binding ssDNA to promote genome stability, especially at sites of replication-transcription collisions. Oncogene advance online publication, 11 May 2015; doi:10.1038/onc.2015.135.\",\n \"corpus_id\": 27942986,\n \"score\": 2\n },\n {\n \"doc_id\": \"27241928\",\n \"title\": \"The Replication System of Bacteriophage T7.\",\n \"abstract\": \"The replication system of bacteriophage T7 is remarkable in that the 40,000 nucleotide genome is replicated over 100-fold in a matter of minutes. In order to accomplish this feat T7 has evolved an efficient and economical process for the replication of its DNA. The T7 replisome provides a model system to study DNA replication. Four proteins are sufficient for reconstitution of the functional replication complex, yet the assembled replisome recapitulates all the key features of more complex prokaryotic and eukaryotic systems. In this review, we describe chemical mechanisms employed by individual proteins at the replication fork. Integration of structural, biochemical, and single-molecule data reveals a compelling view on how a nearly 1-MDa molecular machine acts as a unit to synthetize the two antiparallel DNA strands in a coordinated fashion.\",\n \"corpus_id\": 9271394,\n \"score\": 2\n },\n {\n \"doc_id\": \"27241929\",\n \"title\": \"Protein-Primed Replication of Bacteriophage Φ29 DNA.\",\n \"abstract\": \"The requirement of DNA polymerases for a 3'-hydroxyl (3'-OH) group to prime DNA synthesis raised the question about how the ends of linear chromosomes could be replicated. Among the strategies that have evolved to handle the end replication problem, a group of linear phages and eukaryotic and archaeal viruses, among others, make use of a protein (terminal protein, TP) that primes DNA synthesis from the end of their genomes. The replicative DNA polymerase recognizes the OH group of a specific residue in the TP to initiate replication that is guided by an internal 3' nucleotide of the template strand. By a sliding-back mechanism or variants of it the terminal nucleotide(s) is(are) recovered and the TP becomes covalently attached to the genome ends. Bacillus subtilis phage ϕ29 is the organism in which such a mechanism has been studied more extensively, having allowed to lay the foundations of the so-called protein-primed replication mechanism. Here we focus on the main biochemical and structural features of the two main proteins responsible for the protein-primed initiation step: the DNA polymerase and the TP. Thus, we will discuss the structural determinants of the DNA polymerase responsible for its ability to use sequentially a TP and a DNA as primers, as well as for its inherent capacity to couple high processive synthesis to strand displacement. On the other hand, we will review how TP primes initiation followed by a transition step for further DNA-primed replication by the same polymerase molecule. Finally, we will review how replication is compartmentalized in vivo.\",\n \"corpus_id\": 39975788,\n \"score\": 2\n },\n {\n \"doc_id\": \"27547754\",\n \"title\": \"DNA-Binding Proteins Essential for Protein-Primed Bacteriophage Φ29 DNA Replication.\",\n \"abstract\": \"Bacillus subtilis phage Φ29 has a linear, double-stranded DNA 19 kb long with an inverted terminal repeat of 6 nucleotides and a protein covalently linked to the 5' ends of the DNA. This protein, called terminal protein (TP), is the primer for the initiation of replication, a reaction catalyzed by the viral DNA polymerase at the two DNA ends. The DNA polymerase further elongates the nascent DNA chain in a processive manner, coupling strand displacement with elongation. The viral protein p5 is a single-stranded DNA binding protein (SSB) that binds to the single strands generated by strand displacement during the elongation process. Viral protein p6 is a double-stranded DNA binding protein (DBP) that preferentially binds to the origins of replication at the Φ29 DNA ends and is required for the initiation of replication. Both SSB and DBP are essential for Φ29 DNA amplification. This review focuses on the role of these phage DNA-binding proteins in Φ29 DNA replication both in vitro and in vivo, as well as on the implication of several B. subtilis DNA-binding proteins in different processes of the viral cycle. We will revise the enzymatic activities of the Φ29 DNA polymerase: TP-deoxynucleotidylation, processive DNA polymerization coupled to strand displacement, 3'-5' exonucleolysis and pyrophosphorolysis. The resolution of the Φ29 DNA polymerase structure has shed light on the translocation mechanism and the determinants responsible for processivity and strand displacement. These two properties have made Φ29 DNA polymerase one of the main enzymes used in the current DNA amplification technologies. The determination of the structure of Φ29 TP revealed the existence of three domains: the priming domain, where the primer residue Ser232, as well as Phe230, involved in the determination of the initiating nucleotide, are located, the intermediate domain, involved in DNA polymerase binding, and the N-terminal domain, responsible for DNA binding and localization of the TP at the bacterial nucleoid, where viral DNA replication takes place. The biochemical properties of the Φ29 DBP and SSB and their function in the initiation and elongation of Φ29 DNA replication, respectively, will be described.\",\n \"corpus_id\": 2294957,\n \"score\": 2\n },\n {\n \"doc_id\": \"27694621\",\n \"title\": \"Single-molecule FRET studies of the cooperative and non-cooperative binding kinetics of the bacteriophage T4 single-stranded DNA binding protein (gp32) to ssDNA lattices at replication fork junctions.\",\n \"abstract\": \"Gene 32 protein (gp32) is the single-stranded (ss) DNA binding protein of the bacteriophage T4. It binds transiently and cooperatively to ssDNA sequences exposed during the DNA replication process and regulates the interactions of the other sub-assemblies of the replication complex during the replication cycle. We here use single-molecule FRET techniques to build on previous thermodynamic studies of gp32 binding to initiate studies of the dynamics of the isolated and cooperative binding of gp32 molecules within the replication complex. DNA primer/template (p/t) constructs are used as models to determine the effects of ssDNA lattice length, gp32 concentration, salt concentration, binding cooperativity and binding polarity at p/t junctions. Hidden Markov models (HMMs) and transition density plots (TDPs) are used to characterize the dynamics of the multi-step assembly pathway of gp32 at p/t junctions of differing polarity, and show that isolated gp32 molecules bind to their ssDNA targets weakly and dissociate quickly, while cooperatively bound dimeric or trimeric clusters of gp32 bind much more tightly, can 'slide' on ssDNA sequences, and exhibit binding dynamics that depend on p/t junction polarities. The potential relationships of these binding dynamics to interactions with other components of the T4 DNA replication complex are discussed.\",\n \"corpus_id\": 4409127,\n \"score\": 2\n },\n {\n \"doc_id\": \"28009009\",\n \"title\": \"Bacteriophage T5 gene D10 encodes a branch-migration protein.\",\n \"abstract\": \"Helicases catalyze the unwinding of double-stranded nucleic acids where structure and phosphate backbone contacts, rather than nucleobase sequence, usually determines substrate specificity. We have expressed and purified a putative helicase encoded by the D10 gene of bacteriophage T5. Here we report that this hitherto uncharacterized protein possesses branch migration and DNA unwinding activity. The initiation of substrate unwinding showed some sequence dependency, while DNA binding and DNA-dependent ATPase activity did not. DNA footprinting and purine-base interference assays demonstrated that D10 engages these substrates with a defined polarity that may be established by protein-nucleobase contacts. Bioinformatic analysis of the nucleotide databases revealed genes predicted to encode proteins related to D10 in archaebacteria, bacteriophages and in viruses known to infect a range of eukaryotic organisms.\",\n \"corpus_id\": 15888543,\n \"score\": 2\n },\n {\n \"doc_id\": \"28416612\",\n \"title\": \"A biochemical and biophysical model of G-quadruplex DNA recognition by positive coactivator of transcription 4.\",\n \"abstract\": \"DNA sequences that are guanine-rich have received considerable attention because of their potential to fold into a secondary, four-stranded DNA structure termed G-quadruplex (G4), which has been implicated in genomic instability and some human diseases. We have previously identified positive coactivator of transcription (PC4), a single-stranded DNA (ssDNA)-binding protein, as a novel G4 interactor. Here, to expand on these previous observations, we biochemically and biophysically characterized the interaction between PC4 and G4DNA. PC4 can bind alternative G4DNA topologies with a low nanomolar Kd value of ∼2 nm, similar to that observed for ssDNA. In consideration of the different structural features between G4DNA and ssDNA, these binding data indicated that PC4 can interact with G4DNA in a manner distinct from ssDNA. The stoichiometry of the PC4-G4 complex was 1:1 for PC4 dimer:G4 substrate. PC4 did not enhance the rate of folding of G4DNA, and formation of the PC4-G4DNA complex did not result in unfolding of the G4DNA structure. We assembled a G4DNA structure flanked by duplex DNA. We find that PC4 can interact with this G4DNA, as well as the complementary C-rich strand. Molecular docking simulations and DNA footprinting experiments suggest a model where a PC4 dimer accommodates the DNA with one monomer on the G4 strand and the second monomer bound to the C-rich strand. Collectively, these data provide a novel mode of PC4 binding to a DNA secondary structure that remains within the framework of the model for binding to ssDNA. Additionally, consideration of the PC4-G4DNA interaction could provide insight into the biological functions of PC4, which remain incompletely understood.\",\n \"corpus_id\": 205364196,\n \"score\": 2\n },\n {\n \"doc_id\": \"29588157\",\n \"title\": \"Gp2.5, the multifunctional bacteriophage T7 single-stranded DNA binding protein.\",\n \"abstract\": \"The essential bacteriophage T7-encoded single-stranded DNA binding protein is the nexus of T7 DNA metabolism. Multiple layers of macromolecular interactions mediate its function in replication, recombination, repair, and the maturation of viral genomes. In addition to binding ssDNA, the protein binds to DNA polymerase and DNA helicase, regulating their activities. The protein displays potent homologous DNA annealing activity, underscoring its role in recombination.\",\n \"corpus_id\": 4410095,\n \"score\": 2\n },\n {\n \"doc_id\": \"29634784\",\n \"title\": \"The role of the C-domain of bacteriophage T4 gene 32 protein in ssDNA binding and dsDNA helix-destabilization: Kinetic, single-molecule, and cross-linking studies.\",\n \"abstract\": \"The model single-stranded DNA binding protein of bacteriophage T4, gene 32 protein (gp32) has well-established roles in DNA replication, recombination, and repair. gp32 is a single-chain polypeptide consisting of three domains. Based on thermodynamics and kinetics measurements, we have proposed that gp32 can undergo a conformational change where the acidic C-terminal domain binds internally to or near the single-stranded (ss) DNA binding surface in the core (central) domain, blocking ssDNA interaction. To test this model, we have employed a variety of experimental approaches and gp32 variants to characterize this conformational change. Utilizing stopped-flow methods, the association kinetics of wild type and truncated forms of gp32 with ssDNA were measured. When the C-domain is present, the log-log plot of k vs. [NaCl] shows a positive slope, whereas when it is absent (*I protein), there is little rate change with salt concentration, as expected for this model. A gp32 variant lacking residues 292-296 within the C-domain, ΔPR201, displays kinetic properties intermediate between gp32 and *I. The single molecule force-induced DNA helix-destabilizing activitiesas well as the single- and double-stranded DNA affinities of ΔPR201 and gp32 truncated at residue 295 also fall between full-length protein and *I. Finally, chemical cross-linking of recombinant C-domain and gp32 lacking both N- and C-terminal domains is inhibited by increasing concentrations of a short single-stranded oligonucleotide, and the salt dependence of cross-linking mirrors that expected for the model. Taken together, these results provide the first evidence in support of this model that have been obtained through structural probes.\",\n \"corpus_id\": 4978868,\n \"score\": 2\n },\n {\n \"doc_id\": \"17939025\",\n \"title\": \"Identification and characterization of a single-stranded DNA-binding protein from thermophilic bacteriophage GVE2.\",\n \"abstract\": \"Single-stranded DNA-binding (SSB) proteins are indispensable for survival of almost all known living organisms. Due to their numerous applications in diverse molecular biology and analytical methods, SSB proteins have received increasing research interest. In this investigation, a novel SSB gene was identified from a deep-sea thermophilic bacteriophage Geobacillus virus E2 (GVE2) for the first time. The GVE2 SSB protein shared homologies to known SSB proteins from other species. After recombinant expression in E. coli, the purified SSB protein was used for antibody preparation. The Northern and Western blots showed that the GVE2 SSB gene might be an early viral gene. As revealed by DNA binding assay, the recombinant GVE2 SSB protein had single-stranded DNA binding capacity.\",\n \"corpus_id\": 25302239,\n \"score\": 1\n },\n {\n \"doc_id\": \"18000001\",\n \"title\": \"The process of displacing the single-stranded DNA-binding protein from single-stranded DNA by RecO and RecR proteins.\",\n \"abstract\": \"The regions of single-stranded (ss) DNA that result from DNA damage are immediately coated by the ssDNA-binding protein (SSB). RecF pathway proteins facilitate the displacement of SSB from ssDNA, allowing the RecA protein to form protein filaments on the ssDNA region, which facilitates the process of recombinational DNA repair. In this study, we examined the mechanism of SSB displacement from ssDNA using purified Thermus thermophilus RecF pathway proteins. To date, RecO and RecR are thought to act as the RecOR complex. However, our results indicate that RecO and RecR have distinct functions. We found that RecR binds both RecF and RecO, and that RecO binds RecR, SSB and ssDNA. The electron microscopic studies indicated that SSB is displaced from ssDNA by RecO. In addition, pull-down assays indicated that the displaced SSB still remains indirectly attached to ssDNA through its interaction with RecO in the RecO-ssDNA complex. In the presence of both SSB and RecO, the ssDNA-dependent ATPase activity of RecA was inhibited, but was restored by the addition of RecR. Interestingly, the interaction of RecR with RecO affected the ssDNA-binding properties of RecO. These results suggest a model of SSB displacement from the ssDNA by RecF pathway proteins.\",\n \"corpus_id\": 17497862,\n \"score\": 1\n },\n {\n \"doc_id\": \"18054234\",\n \"title\": \"14-3-3 cruciform-binding proteins as regulators of eukaryotic DNA replication.\",\n \"abstract\": \"Cruciforms are secondary DNA structures, serving as recognition signals at or near eukaryotic (yeast and mammalian) origins of DNA replication. The cruciform-binding protein is a member of the 14-3-3 protein family and binds to origins of DNA replication in a cell cycle-dependent manner. Five 14-3-3 protein isoforms (beta, gamma, epsilon, zeta and sigma) have been identified as having cruciform binding activity.\",\n \"corpus_id\": 43369439,\n \"score\": 1\n },\n {\n \"doc_id\": \"19025561\",\n \"title\": \"Identification of host receptor and receptor-binding module of a newly sequenced T5-like phage EPS7.\",\n \"abstract\": \"The virulent bacteriophage EPS7 active against a number of Salmonella serovar and Escherichia coli strains, isolated from the local sewage in Korea, belongs to the family Siphoviridae. The ESP7 genome constitutes a linear double-stranded DNA of 111 382 bp. DNA sequencing and genomic analysis of EPS7 showed that it belongs to the phage T5 family. We identified the EPS7 genes involved in DNA repair, replication, viral structure and bacterial lysis by comparing the EPS7 genome with that of T5. In contrast, the tail genes encoding for putative host receptor-binding protein and the putative receptor-blocking lipoprotein precursor of EPS7 exhibit high homologies with the corresponding gene products of BF23, another member of the T5-family. BF23 binds to BtuB, a surface receptor in the host and involved in vitamin B12 uptake, but its infection is independent of TonB. By constructing a series of deletion mutants in Salmonella and in E. coli and studying phage infection in the mutant hosts, we showed that BtuB is also the host receptor of the phage EPS7. Whether EPS7 infection depends on TonB needs to be further studied.\",\n \"corpus_id\": 21037952,\n \"score\": 1\n },\n {\n \"doc_id\": \"19597347\",\n \"title\": \"DNA ligase I and Nbs1 proteins associate in a complex and colocalize at replication factories.\",\n \"abstract\": \"DNA ligase I is the main DNA ligase activity involved in eukaryotic DNA replication acting in the joining of Okazaki fragments. This enzyme is also implicated in nucleotide excision repair and in the long-patch base excision repair while its role in the recombinational repair pathways is poorly understood. DNA ligase I is phosphorylated during cell cycle at several serine and threonine residues that regulate its participation in different DNA transactions by modulating the interaction with different protein partners. Here we use an antibody-based array method to identify novel DNA ligase-interacting partners. We show that DNA ligase I participates in several multiprotein complexes with proteins involved in DNA replication and repair, cell cycle control, and protein modification. In particular we demonstrate that DNA ligase I complexes with Nbs1, a core component of the MRN complex critical for detection, processing and repair of double-stranded DNA breaks. The analysis of epitope tagged DNA ligase I mutants demonstrates that the association is mediated by the catalytic fragment of the enzyme. DNA ligase I and Nbs1 colocalize at replication factories during unperturbed replication and after treatment with DNA damaging agents. Since MRN complex is involved in the repair of double-stranded DNA breaks by homologous recombination at stalled replication forks our data support the notion that DNA ligase I participates in homology dependent pathways that deal with replication-associated lesions generated when replication fork encounters DNA damage.\",\n \"corpus_id\": 9101456,\n \"score\": 1\n },\n {\n \"doc_id\": \"20012581\",\n \"title\": \"Eukaryotic single-stranded DNA binding proteins: central factors in genome stability.\",\n \"abstract\": \"The single-stranded DNA binding proteins (SSBs) are required to maintain the integrity of the genome in all organisms. Replication protein A (RPA) is a nuclear SSB protein found in all eukaryotes and is required for multiple processes in DNA metabolism such as DNA replication, DNA repair, DNA recombination, telomere maintenance and DNA damage signalling. RPA is a heterotrimeric complex, binds ssDNA with high affinity, and interacts specifically with multiple proteins to fulfil its function in eukaryotes. RPA is phosphorylated in a cell cycle and DNA damage-dependent manner with evidence suggesting that phosphorylation has an important function in modulating the cellular DNA damage response. Considering the DNA-binding properties of RPA a mechanism of \\\"molecular counting\\\" to initiate DNA damage-dependent signalling is discussed. Recently a human homologue to the RPA2 subunit, called RPA4, was discovered and RPA4 can substitute for RPA2 in the RPA complex resulting in an \\\"alternative\\\" RPA (aRPA), which can bind to ssDNA with similar affinity as canonical RPA. Additional human SSBs, hSSB1 and hSSB2, were recently identified, with hSSB1 being localized in the nucleus and having implications in DNA repair. Mitochondrial SSBs (mtSSBs) have been found in all eukaryotes studied. mtSSBs are related to prokaryotic SSBs and essential to main the genome stability in eukaryotic mitochondria. Recently human mtSSB was identified as a novel binding partner of p53 and that it is able to stimulate the intrinsic exonuclease activity of p53. These findings and recent results associated with mutations in RPA suggest a link of SSBs to cancer.\",\n \"corpus_id\": 20597186,\n \"score\": 1\n },\n {\n \"doc_id\": \"20360609\",\n \"title\": \"Regulation of single-stranded DNA binding by the C termini of Escherichia coli single-stranded DNA-binding (SSB) protein.\",\n \"abstract\": \"The homotetrameric Escherichia coli single-stranded DNA-binding (SSB) protein plays a central role in DNA replication, repair, and recombination. In addition to its essential activity of binding to transiently formed single-stranded (ss) DNA, SSB also binds an array of partner proteins and recruits them to their sites of action using its four intrinsically disordered C-terminal tails. Here we show that the binding of ssDNA to SSB is inhibited by the SSB C-terminal tails, specifically by the last 8 highly acidic amino acids that comprise the binding site for its multiple partner proteins. We examined the energetics of ssDNA binding to short oligodeoxynucleotides and find that at moderate salt concentration, removal of the acidic C-terminal ends increases the intrinsic affinity for ssDNA and enhances the negative cooperativity between ssDNA binding sites, indicating that the C termini exert an inhibitory effect on ssDNA binding. This inhibitory effect decreases as the salt concentration increases. Binding of ssDNA to approximately half of the SSB subunits relieves the inhibitory effect for all of the subunits. The inhibition by the C termini is due primarily to a less favorable entropy change upon ssDNA binding. These observations explain why ssDNA binding to SSB enhances the affinity of SSB for its partner proteins and suggest that the C termini of SSB may interact, at least transiently, with its ssDNA binding sites. This inhibition and its relief by ssDNA binding suggest a mechanism that enhances the ability of SSB to selectively recruit its partner proteins to sites on DNA.\",\n \"corpus_id\": 14508187,\n \"score\": 1\n },\n {\n \"doc_id\": \"21169364\",\n \"title\": \"A mechanism for single-stranded DNA-binding protein (SSB) displacement from single-stranded DNA upon SSB-RecO interaction.\",\n \"abstract\": \"Displacement of single-stranded DNA (ssDNA)-binding protein (SSB) from ssDNA is necessary for filament formation of RecA on ssDNA to initiate homologous recombination. The interaction between RecO and SSB is considered to be important for SSB displacement; however, the interaction has not been characterized at the atomic level. In this study, to clarify the mechanism underlying SSB displacement from ssDNA upon RecO binding, we examined the interaction between Thermus thermophilus RecO and cognate SSB by NMR analysis. We found that SSB interacts with the C-terminal positively charged region of RecO. Based on this result, we constructed some RecO mutants. The R127A mutant had considerably decreased binding affinity for SSB and could not anneal SSB-coated ssDNAs. Further, the mutant in the RecOR complex prevented the recovery of ssDNA-dependent ATPase activity of RecA from inhibition by SSB. These results indicated that the region surrounding Arg-127 is the binding site of SSB. We also performed NMR analysis using the C-terminal peptide of SSB and found that the acidic region of SSB is involved in the interaction with RecO, as seen in other protein-SSB interactions. Taken together with the findings of previous studies, we propose a model for SSB displacement from ssDNA where the acidic C-terminal region of SSB weakens the ssDNA binding affinity of SSB when the dynamics of the C-terminal region are suppressed by interactions with other proteins, including RecO.\",\n \"corpus_id\": 19851355,\n \"score\": 1\n },\n {\n \"doc_id\": \"21264493\",\n \"title\": \"Identification of a soybean chloroplast DNA replication origin-binding protein.\",\n \"abstract\": \"Replication of chloroplast DNA (ctDNA) in several plants and in Chlamydomonas reinhardii has been shown to occur by a double displacement loop (D-loop) mechanism and potentially also by a rolling circle mechanism. D-loop replication origins have been mapped in several species. Minimal replication origin sequences used as probes identified two potential binding proteins by southwestern blot analysis. A 28 kDa (apparent molecular weight by SDS-PAGE analysis) soybean protein has been isolated by origin sequence-specific DNA affinity chromatography from total chloroplast proteins. Mass spectrometry analysis identified this protein as the product of the soybean C6SY33 gene (accession number ACU14156), which is annotated as encoding a putative uncharacterized protein with a molecular weight of 25,897 Da, very near the observed molecular weight of the purified protein based on gel electrophoresis. Western blot analysis using an antibody against a homologous Arabidopsis protein indicates that this soybean protein is localized specifically in chloroplasts. The soybean protein shares some homology within a single-stranded DNA binding (SSB) domain of E. coli SSB and an Arabidopsis thaliana mitochondrial-localized SSB of about 21 kDa (mtSSB). However, the soybean protein induces a specific electrophoretic mobility shift only when incubated with a double-stranded fragment containing the previously mapped ctDNA replication oriA region. This protein has no electrophoretic mobility shift activity when incubated with single-stranded DNA. In contrast, the Arabidopsis mtSSB causes a mobility shift only with single-stranded DNA but not with the oriA fragment or with control dsDNA of unrelated sequence. These results suggest that the 26 kDa soybean protein is a specific origin binding protein that may be involved in initiation of ctDNA replication.\",\n \"corpus_id\": 12653285,\n \"score\": 1\n },\n {\n \"doc_id\": \"22027892\",\n \"title\": \"Mgm101 is a Rad52-related protein required for mitochondrial DNA recombination.\",\n \"abstract\": \"Homologous recombination is a conserved molecular process that has primarily evolved for the repair of double-stranded DNA breaks and stalled replication forks. However, the recombination machinery in mitochondria is poorly understood. Here, we show that the yeast mitochondrial nucleoid protein, Mgm101, is related to the Rad52-type recombination proteins that are widespread in organisms from bacteriophage to humans. Mgm101 is required for repeat-mediated recombination and suppression of mtDNA fragmentation in vivo. It preferentially binds to single-stranded DNA and catalyzes the annealing of ssDNA precomplexed with the mitochondrial ssDNA-binding protein, Rim1. Transmission electron microscopy showed that Mgm101 forms large oligomeric rings of ∼14-fold symmetry and highly compressed helical filaments. Specific mutations affecting ring formation reduce protein stability in vitro. The data suggest that the ring structure may provide a scaffold for stabilization of Mgm101 by preventing the aggregation of the otherwise unstable monomeric conformation. Upon binding to ssDNA, Mgm101 is remobilized from the rings to form distinct nucleoprotein filaments. These studies reveal a recombination protein of likely bacteriophage origin in mitochondria and support the notion that recombination is indispensable for mtDNA integrity.\",\n \"corpus_id\": 25369495,\n \"score\": 1\n },\n {\n \"doc_id\": \"22116609\",\n \"title\": \"Accurate prediction of the binding free energy and analysis of the mechanism of the interaction of replication protein A (RPA) with ssDNA.\",\n \"abstract\": \"The eukaryotic replication protein A (RPA) has several pivotal functions in the cell metabolism, such as chromosomal replication, prevention of hairpin formation, DNA repair and recombination, and signaling after DNA damage. Moreover, RPA seems to have a crucial role in organizing the sequential assembly of DNA processing proteins along single stranded DNA (ssDNA). The strong RPA affinity for ssDNA, K(A) between 10(-9)-10(-10) M, is characterized by a low cooperativity with minor variation for changes on the nucleotide sequence. Recently, new data on RPA interactions was reported, including the binding free energy of the complex RPA70AB with dC(8) and dC(5), which has been estimated to be -10 ± 0.4 kcal mol(-1) and -7 ± 1 kcal mol(-1), respectively. In view of these results we performed a study based on molecular dynamics aimed to reproduce the absolute binding free energy of RPA70AB with the dC(5) and dC(8) oligonucleotides. We used several tools to analyze the binding free energy, rigidity, and time evolution of the complex. The results obtained by MM-PBSA method, with the use of ligand free geometry as a reference for the receptor in the separate trajectory approach, are in excellent agreement with the experimental data, with ±4 kcal mol(-1) error. This result shows that the MM-PB(GB)SA methods can provide accurate quantitative estimates of the binding free energy for interacting complexes when appropriate geometries are used for the receptor, ligand and complex. The decomposition of the MM-GBSA energy for each residue in the receptor allowed us to correlate the change of the affinity of the mutated protein with the ΔG(gas+sol) contribution of the residue considered in the mutation. The agreement with experiment is optimal and a strong change in the binding free energy can be considered as the dominant factor in the loss for the binding affinity resulting from mutation.\",\n \"corpus_id\": 25221707,\n \"score\": 1\n },\n {\n \"doc_id\": \"22304461\",\n \"title\": \"Specificity of binding of single-stranded DNA-binding protein to its target.\",\n \"abstract\": \"Single-stranded DNA-binding proteins (SSBs) bind single-stranded DNA (ssDNA) and participate in all genetic processes involving ssDNA, such as replication, recombination, and repair. Here we applied atomic force microscopy to directly image SSB-DNA complexes under various conditions. We used the hybrid DNA construct methodology in which the ssDNA segment is conjugated to the DNA duplex. The duplex part of the construct plays the role of a marker, allowing unambiguous identification of specific and nonspecific SSB-DNA complexes. We designed hybrid DNA substrates with 5'- and 3'-ssDNA termini to clarify the role of ssDNA polarity on SSB loading. The hybrid substrates, in which two duplexes are connected with ssDNA, were the models for gapped DNA substrates. We demonstrated that Escherichia coli SSB binds to ssDNA ends and internal ssDNA regions with the same efficiency. However, the specific recognition by ssDNA requires the presence of Mg(2+) cations or a high ionic strength. In the absence of Mg(2+) cations and under low-salt conditions, the protein is capable of binding DNA duplexes. In addition, the number of interprotein interactions increases, resulting in the formation of clusters on double-stranded DNA. This finding suggests that the protein adopts different conformations depending on ionic strength, and specific recognition of ssDNA by SSB requires a high ionic strength or the presence of Mg(2+) cations.\",\n \"corpus_id\": 22406614,\n \"score\": 1\n },\n {\n \"doc_id\": \"22549990\",\n \"title\": \"MALDI-MS detection of noncovalent interactions of single stranded DNA with Escherichia coli single-stranded DNA-binding protein.\",\n \"abstract\": \"The Escherichia coli single-stranded DNA binding protein (SSB) selectively binds single-stranded (ss) DNA and participates in the process of DNA replication, recombination and repair. Different binding modes have previously been observed in SSB•ssDNA complexes, due to the four potential binding sites of SSB. Here, chemical cross-linking, combined with high-mass matrix-assisted laser desorption/ionization (MALDI) mass spectrometry (MS), is used to determine the stoichiometry of the SSB•ssDNA complex. SSB forms a stable homotetramer in solution, but only the monomeric species (m/z 19,100) can be detected with standard MALDI-MS. With chemical cross-linking, the quaternary structure of SSB is conserved, and the tetramer (m/z 79,500) was observed. We found that ssDNA also functions as a stabilizer to conserve the quaternary structure of SSB, as evidenced by the detection of a SSB•ssDNA complex at m/z 94,200 even in the absence of chemical cross-linking. The stability of the SSB•ssDNA complex with MALDI strongly depends on the length and strand of oligonucleotides and the stoichiometry of the SSB•ssDNA complex, which could be attributed to electrostatic interactions that are enhanced in the gas phase. The key factor affecting the stoichiometry of the SSB•ssDNA complex is how ssDNA binds to SSB, rather than the protein-to-DNA ratio. This further suggests that detection of the complex by MALDI is a result of specific binding, and not due to non-specific aggregation in the MALDI plume.\",\n \"corpus_id\": 5594670,\n \"score\": 1\n },\n {\n \"doc_id\": \"22698072\",\n \"title\": \"Thermodynamic analysis of DNA binding by a Bacillus single stranded DNA binding protein.\",\n \"abstract\": \"BACKGROUND: Single-stranded DNA binding proteins (SSB) are essential for DNA replication, repair, and recombination in all organisms. SSB works in concert with a variety of DNA metabolizing enzymes such as DNA polymerase. RESULTS: We have cloned and purified SSB from Bacillus anthracis (SSB(BA)). In the absence of DNA, at concentrations ≤100 μg/ml, SSB(BA) did not form a stable tetramer and appeared to resemble bacteriophage T4 gene 32 protein. Fluorescence anisotropy studies demonstrated that SSB(BA) bound ssDNA with high affinity comparable to other prokaryotic SSBs. Thermodynamic analysis indicated both hydrophobic and ionic contributions to ssDNA binding. FRET analysis of oligo(dT)(70) binding suggested that SSB(BA) forms a tetrameric assembly upon ssDNA binding. This report provides evidence of a bacterial SSB that utilizes a novel mechanism for DNA binding through the formation of a transient tetrameric structure. CONCLUSIONS: Unlike other prokaryotic SSB proteins, SSB(BA) from Bacillus anthracis appeared to be monomeric at concentrations ≤100 μg/ml as determined by SE-HPLC. SSB(BA) retained its ability to bind ssDNA with very high affinity, comparable to SSB proteins which are tetrameric. In the presence of a long ssDNA template, SSB(BA) appears to form a transient tetrameric structure. Its unique structure appears to be due to the cumulative effect of multiple key amino acid changes in its sequence during evolution, leading to perturbation of stable dimer and tetramer formation. The structural features of SSB(BA) could promote facile assembly and disassembly of the protein-DNA complex required in processes such as DNA replication.\",\n \"corpus_id\": 15966117,\n \"score\": 1\n },\n {\n \"doc_id\": \"22918586\",\n \"title\": \"The structure and function of replication protein A in DNA replication.\",\n \"abstract\": \"In all organisms from bacteria and archaea to eukarya, single-stranded DNA binding proteins play an essential role in most, if not all, nuclear metabolism involving single-stranded DNA (ssDNA). Replication protein A (RPA), the major eukaryotic ssDNA binding protein, has two important roles in DNA metabolism: (1) in binding ssDNA to protect it and to keep it unfolded, and (2) in coordinating the assembly and disassembly of numerous proteins and protein complexes during processes such as DNA replication. Since its discovery as a vital player in the process of replication, RPAs roles in recombination and DNA repair quickly became evident. This chapter summarizes the current understanding of RPA's roles in replication by reviewing the available structural data, DNA-binding properties, interactions with various replication proteins, and interactions with DNA repair proteins when DNA replication is stalled.\",\n \"corpus_id\": 22295425,\n \"score\": 1\n },\n {\n \"doc_id\": \"23070815\",\n \"title\": \"Structure and conformational change of a replication protein A heterotrimer bound to ssDNA.\",\n \"abstract\": \"Replication protein A (RPA) is the main eukaryotic ssDNA-binding protein with essential roles in DNA replication, recombination, and repair. RPA maintains the DNA as single-stranded and also interacts with other DNA-processing proteins, coordinating their assembly and disassembly on DNA. RPA binds to ssDNA in two conformational states with opposing affinities for DNA and proteins. The RPA-protein interactions are compatible with a low DNA affinity state that involves DNA-binding domain A (DBD-A) and DBD-B but not with the high DNA affinity state that additionally engages DBD-C and DBD-D. The structure of the high-affinity RPA-ssDNA complex reported here shows a compact quaternary structure held together by a four-way interface between DBD-B, DBD-C, the intervening linker (BC linker), and ssDNA. The BC linker binds into the DNA-binding groove of DBD-B, mimicking DNA. The associated conformational change and partial occlusion of the DBD-A-DBA-B protein-protein interaction site establish a mechanism for the allosteric coupling of RPA-DNA and RPA-protein interactions.\",\n \"corpus_id\": 3371729,\n \"score\": 1\n },\n {\n \"doc_id\": \"23303792\",\n \"title\": \"Structures of apo- and ssDNA-bound YdbC from Lactococcus lactis uncover the function of protein domain family DUF2128 and expand the single-stranded DNA-binding domain proteome.\",\n \"abstract\": \"Single-stranded DNA (ssDNA) binding proteins are important in basal metabolic pathways for gene transcription, recombination, DNA repair and replication in all domains of life. Their main cellular role is to stabilize melted duplex DNA and protect genomic DNA from degradation. We have uncovered the molecular function of protein domain family domain of unknown function DUF2128 (PF09901) as a novel ssDNA binding domain. This bacterial domain strongly associates into a dimer and presents a highly positively charged surface that is consistent with its function in non-specific ssDNA binding. Lactococcus lactis YdbC is a representative of DUF2128. The solution NMR structures of the 20 kDa apo-YdbC dimer and YdbC:dT(19)G(1) complex were determined. The ssDNA-binding energetics to YdbC were characterized by isothermal titration calorimetry. YdbC shows comparable nanomolar affinities for pyrimidine and mixed oligonucleotides, and the affinity is sufficiently strong to disrupt duplex DNA. In addition, YdbC binds with lower affinity to ssRNA, making it a versatile nucleic acid-binding domain. The DUF2128 family is related to the eukaryotic nuclear protein positive cofactor 4 (PC4) family and to the PUR family both by fold similarity and molecular function.\",\n \"corpus_id\": 17595961,\n \"score\": 1\n },\n {\n \"doc_id\": \"24006472\",\n \"title\": \"Mechanism of homologous recombination and implications for aging-related deletions in mitochondrial DNA.\",\n \"abstract\": \"Homologous recombination is a universal process, conserved from bacteriophage to human, which is important for the repair of double-strand DNA breaks. Recombination in mitochondrial DNA (mtDNA) was documented more than 4 decades ago, but the underlying molecular mechanism has remained elusive. Recent studies have revealed the presence of a Rad52-type recombination system of bacteriophage origin in mitochondria, which operates by a single-strand annealing mechanism independent of the canonical RecA/Rad51-type recombinases. Increasing evidence supports the notion that, like in bacteriophages, mtDNA inheritance is a coordinated interplay between recombination, repair, and replication. These findings could have profound implications for understanding the mechanism of mtDNA inheritance and the generation of mtDNA deletions in aging cells.\",\n \"corpus_id\": 33328160,\n \"score\": 1\n },\n {\n \"doc_id\": \"24021816\",\n \"title\": \"Multiple C-terminal tails within a single E. coli SSB homotetramer coordinate DNA replication and repair.\",\n \"abstract\": \"Escherichia coli single-stranded DNA binding protein (SSB) plays essential roles in DNA replication, recombination and repair. SSB functions as a homotetramer with each subunit possessing a DNA binding domain (OB-fold) and an intrinsically disordered C-terminus, of which the last nine amino acids provide the site for interaction with at least a dozen other proteins that function in DNA metabolism. To examine how many C-termini are needed for SSB function, we engineered covalently linked forms of SSB that possess only one or two C-termini within a four-OB-fold \\\"tetramer\\\". Whereas E. coli expressing SSB with only two tails can survive, expression of a single-tailed SSB is dominant lethal. E. coli expressing only the two-tailed SSB recovers faster from exposure to DNA damaging agents but accumulates more mutations. A single-tailed SSB shows defects in coupled leading and lagging strand DNA replication and does not support replication restart in vitro. These deficiencies in vitro provide a plausible explanation for the lethality observed in vivo. These results indicate that a single SSB tetramer must interact simultaneously with multiple protein partners during some essential roles in genome maintenance.\",\n \"corpus_id\": 497163,\n \"score\": 1\n },\n {\n \"doc_id\": \"24198424\",\n \"title\": \"Insights into bacteriophage T5 structure from analysis of its morphogenesis genes and protein components.\",\n \"abstract\": \"Bacteriophage T5 represents a large family of lytic Siphoviridae infecting Gram-negative bacteria. The low-resolution structure of T5 showed the T=13 geometry of the capsid and the unusual trimeric organization of the tail tube, and the assembly pathway of the capsid was established. Although major structural proteins of T5 have been identified in these studies, most of the genes encoding the morphogenesis proteins remained to be identified. Here, we combine a proteomic analysis of T5 particles with a bioinformatic study and electron microscopic immunolocalization to assign function to the genes encoding the structural proteins, the packaging proteins, and other nonstructural components required for T5 assembly. A head maturation protease that likely accounts for the cleavage of the different capsid proteins is identified. Two other proteins involved in capsid maturation add originality to the T5 capsid assembly mechanism: the single head-to-tail joining protein, which closes the T5 capsid after DNA packaging, and the nicking endonuclease responsible for the single-strand interruptions in the T5 genome. We localize most of the tail proteins that were hitherto uncharacterized and provide a detailed description of the tail tip composition. Our findings highlight novel variations of viral assembly strategies and of virion particle architecture. They further recommend T5 for exploring phage structure and assembly and for deciphering conformational rearrangements that accompany DNA transfer from the capsid to the host cytoplasm.\",\n \"corpus_id\": 26143905,\n \"score\": 1\n },\n {\n \"doc_id\": \"24371279\",\n \"title\": \"Single molecule analysis of Thermus thermophilus SSB protein dynamics on single-stranded DNA.\",\n \"abstract\": \"Single-stranded (ss) DNA binding (SSB) proteins play central roles in DNA replication, recombination and repair in all organisms. We previously showed that Escherichia coli (Eco) SSB, a homotetrameric bacterial SSB, undergoes not only rapid ssDNA-binding mode transitions but also one-dimensional diffusion (or migration) while remaining bound to ssDNA. Whereas the majority of bacterial SSB family members function as homotetramers, dimeric SSB proteins were recently discovered in a distinct bacterial lineage of extremophiles, the Thermus-Deinococcus group. Here we show, using single-molecule fluorescence resonance energy transfer (FRET), that homodimeric bacterial SSB from Thermus thermophilus (Tth) is able to diffuse spontaneously along ssDNA over a wide range of salt concentrations (20-500 mM NaCl), and that TthSSB diffusion can help transiently melt the DNA hairpin structures. Furthermore, we show that two TthSSB molecules undergo transitions among different DNA-binding modes while remaining bound to ssDNA. Our results extend our previous observations on homotetrameric SSBs to homodimeric SSBs, indicating that the dynamic features may be shared among different types of SSB proteins. These dynamic features of SSBs may facilitate SSB redistribution and removal on/from ssDNA, and help recruit other SSB-interacting proteins onto ssDNA for subsequent DNA processing in DNA replication, recombination and repair.\",\n \"corpus_id\": 16808196,\n \"score\": 1\n },\n {\n \"doc_id\": \"24730652\",\n \"title\": \"Structural analysis of replication protein A recruitment of the DNA damage response protein SMARCAL1.\",\n \"abstract\": \"SWI/SNF-related, matrix-associated, actin-dependent regulator of chromatin, subfamily A-like1 (SMARCAL1) is a recently identified DNA damage response protein involved in remodeling stalled replication forks. The eukaryotic single-strand DNA binding protein replication protein A (RPA) recruits SMARCAL1 to stalled forks in vivo and facilitates regression of forks containing leading strand gaps. Both activities are mediated by a direct interaction between an RPA binding motif (RBM) at the N-terminus of SMARCAL1 and the C-terminal winged-helix domain of the RPA 32 kDa subunit (RPA32C). Here we report a biophysical and structural characterization of the SMARCAL1-RPA interaction. Isothermal titration calorimetry and circular dichroism spectroscopy revealed that RPA32C binds SMARCAL1-RBM with a Kd of 2.5 μM and induces a disorder-to-helix transition. The crystal structure of RPA32C was refined to 1.4 Å resolution, and the SMARCAL1-RBM binding site was mapped on the structure on the basis of nuclear magnetic resonance chemical shift perturbations. Conservation of the interaction surface to other RBM-containing proteins allowed construction of a model for the RPA32C/SMARCAL1-RBM complex. The implications of our results are discussed with respect to the recruitment of SMARCAL1 and other DNA damage response and repair proteins to stalled replication forks.\",\n \"corpus_id\": 14046675,\n \"score\": 1\n },\n {\n \"doc_id\": \"25162017\",\n \"title\": \"C-terminal domain swapping of SSB changes the size of the ssDNA binding site.\",\n \"abstract\": \"Single-stranded DNA-binding protein (SSB) plays an important role in DNA metabolism, including DNA replication, repair, and recombination, and is therefore essential for cell survival. Bacterial SSB consists of an N-terminal ssDNA-binding/oligomerization domain and a flexible C-terminal protein-protein interaction domain. We characterized the ssDNA-binding properties of Klebsiella pneumoniae SSB (KpSSB), Salmonella enterica Serovar Typhimurium LT2 SSB (StSSB), Pseudomonas aeruginosa PAO1 SSB (PaSSB), and two chimeric KpSSB proteins, namely, KpSSBnStSSBc and KpSSBnPaSSBc. The C-terminal domain of StSSB or PaSSB was exchanged with that of KpSSB through protein chimeragenesis. By using the electrophoretic mobility shift assay, we characterized the stoichiometry of KpSSB, StSSB, PaSSB, KpSSBnStSSBc, and KpSSBnPaSSBc, complexed with a series of ssDNA homopolymers. The binding site sizes were determined to be 26 ± 2, 21 ± 2, 29 ± 2, 21 ± 2, and 29 ± 2 nucleotides (nt), respectively. Comparison of the binding site sizes of KpSSB, KpSSBnStSSBc, and KpSSBnPaSSBc showed that the C-terminal domain swapping of SSB changes the size of the binding site. Our observations suggest that not only the conserved N-terminal domain but also the C-terminal domain of SSB is an important determinant for ssDNA binding.\",\n \"corpus_id\": 18626099,\n \"score\": 1\n },\n {\n \"doc_id\": \"25171654\",\n \"title\": \"Replication protein A: single-stranded DNA's first responder: dynamic DNA-interactions allow replication protein A to direct single-strand DNA intermediates into different pathways for synthesis or repair.\",\n \"abstract\": \"Replication protein A (RPA), the major single-stranded DNA-binding protein in eukaryotic cells, is required for processing of single-stranded DNA (ssDNA) intermediates found in replication, repair, and recombination. Recent studies have shown that RPA binding to ssDNA is highly dynamic and that more than high-affinity binding is needed for function. Analysis of DNA binding mutants identified forms of RPA with reduced affinity for ssDNA that are fully active, and other mutants with higher affinity that are inactive. Single molecule studies showed that while RPA binds ssDNA with high affinity, the RPA complex can rapidly diffuse along ssDNA and be displaced by other proteins that act on ssDNA. Finally, dynamic DNA binding allows RPA to prevent error-prone repair of double-stranded breaks and promote error-free repair. Together, these findings suggest a new paradigm where RPA acts as a first responder at sites with ssDNA, thereby actively coordinating DNA repair and DNA synthesis.\",\n \"corpus_id\": 20212094,\n \"score\": 1\n },\n {\n \"doc_id\": \"25787788\",\n \"title\": \"Mechanochemical regulations of RPA's binding to ssDNA.\",\n \"abstract\": \"Replication protein A (RPA) is a ubiquitous eukaryotic single-stranded DNA (ssDNA) binding protein that serves to protect ssDNA from degradation and annealing, and as a template for recruitment of many downstream factors in virtually all DNA transactions in cell. During many of these transactions, DNA is tethered and is likely subject to force. Previous studies of RPA's binding behavior on ssDNA were conducted in the absence of force; therefore the RPA-ssDNA conformations regulated by force remain unclear. Here, using a combination of atomic force microscopy imaging and mechanical manipulation of single ssDNA tethers, we show that force mediates a switch of the RPA bound ssDNA from amorphous aggregation to a much more regular extended conformation. Further, we found an interesting non-monotonic dependence of the binding affinity on monovalent salt concentration in the presence of force. In addition, we discovered that zinc in micromolar concentrations drives ssDNA to a unique, highly stiff and more compact state. These results provide new mechanochemical insights into the influences and the mechanisms of action of RPA on large single ssDNA.\",\n \"corpus_id\": 16520668,\n \"score\": 1\n },\n {\n \"doc_id\": \"26350770\",\n \"title\": \"Complete genome sequences of T5-related Escherichia coli bacteriophages DT57C and DT571/2 isolated from horse feces.\",\n \"abstract\": \"We report the complete genome sequencing of two Escherichia coli T5-related bacteriophages, DT57C and DT571/2, isolated from the same specimen of horse feces. These two isolates share 96 % nucleotide sequence identity and can thus be considered representatives of the same novel species within the genus T5likevirus. The observed variation in the ltfA gene of these phages, resulting from a recent recombination event, may explain the observed host-range differences, suggesting that a modular mechanism makes a significant contribution to the short-term evolution (or adaptation) of T5-like phage genomes in the intestinal ecosystem. Comparison of our isolates to their closest relative, coliphage T5, revealed high overall synteny of the genomes and high conservation of the sequences of almost all structural proteins as well as of the other proteins with identified functions. At the same time, numerous alterations and non-orthologous replacements of non-structural protein genes (mostly of those with unknown functions) as well as substantial differences in tail fiber locus organization support the conclusion that DT57C and DT571/2 form a species-level group clearly distinct from bacteriophage T5.\",\n \"corpus_id\": 19670085,\n \"score\": 1\n },\n {\n \"doc_id\": \"27131360\",\n \"title\": \"The Borrelia burgdorferi telomere resolvase, ResT, anneals ssDNA complexed with its cognate ssDNA-binding protein.\",\n \"abstract\": \"Spirochetes of the genus Borrelia possess unusual genomes that consist in a linear chromosome and multiple linear and circular plasmids. The linear replicons are terminated by covalently closed hairpin ends, referred to as hairpin telomeres. The hairpin telomeres represent a simple solution to the end-replication problem. Deoxyribonucleic acid replication initiates internally and proceeds bidirectionally toward the hairpin telomeres. The telomere resolvase, ResT, forms the hairpin telomeres from replicated telomere intermediates in a reaction with similarities to those promoted by type IB topoisomerases and tyrosine recombinases. ResT has also been shown to possess DNA single-strand annealing activity. We report here that ResT promotes single-strand annealing of both free DNA strands and ssDNA complexed with single-stranded DNA binding protein (SSB). The annealing of complementary strands bound by SSB requires a ResT-SSB interaction that is mediated by the conserved amphipathic C-terminal tail of SSB. These properties of ResT are similar to those demonstrated for the recombination mediator protein, RecO, of the RecF pathway. Borrelia burgdorferi is unusual in lacking identifiable homologs of the RecFOR proteins. We propose that ResT may provide missing RecFOR functions.\",\n \"corpus_id\": 14989698,\n \"score\": 1\n },\n {\n \"doc_id\": \"27131385\",\n \"title\": \"Dynamic binding of replication protein a is required for DNA repair.\",\n \"abstract\": \"Replication protein A (RPA), the major eukaryotic single-stranded DNA (ssDNA) binding protein, is essential for replication, repair and recombination. High-affinity ssDNA-binding by RPA depends on two DNA binding domains in the large subunit of RPA. Mutation of the evolutionarily conserved aromatic residues in these two domains results in a separation-of-function phenotype: aromatic residue mutants support DNA replication but are defective in DNA repair. We used biochemical and single-molecule analyses, and Brownian Dynamics simulations to determine the molecular basis of this phenotype. Our studies demonstrated that RPA binds to ssDNA in at least two modes characterized by different dissociation kinetics. We also showed that the aromatic residues contribute to the formation of the longer-lived state, are required for stable binding to short ssDNA regions and are needed for RPA melting of partially duplex DNA structures. We conclude that stable binding and/or the melting of secondary DNA structures by RPA is required for DNA repair, including RAD51 mediated DNA strand exchange, but is dispensable for DNA replication. It is likely that the binding modes are in equilibrium and reflect dynamics in the RPA-DNA complex. This suggests that dynamic binding of RPA to DNA is necessary for different cellular functions.\",\n \"corpus_id\": 6467961,\n \"score\": 1\n },\n {\n \"doc_id\": \"27151292\",\n \"title\": \"Replication protein A and more: single-stranded DNA-binding proteins in eukaryotic cells.\",\n \"abstract\": \"Single-stranded DNA-binding proteins (SSBs) play essential roles in DNA replication, recombinational repair, and maintenance of genome stability. In human, the major SSB, replication protein A (RPA), is a stable heterotrimer composed of subunits of RPA1, RPA2, and RPA3, each of which is conserved not only in mammals but also in all other eukaryotic species. In addition to RPA, other SSBs have also been identified in the human genome, including sensor of single-stranded DNA complexes 1 and 2 (SOSS1/2). In this review, we summarize our current understanding of how these SSBs contribute to the maintenance of genome stability.\",\n \"corpus_id\": 3052726,\n \"score\": 1\n },\n {\n \"doc_id\": \"27185951\",\n \"title\": \"Chemo-mechanical pushing of proteins along single-stranded DNA.\",\n \"abstract\": \"Single-stranded (ss)DNA binding (SSB) proteins bind with high affinity to ssDNA generated during DNA replication, recombination, and repair; however, these SSBs must eventually be displaced from or reorganized along the ssDNA. One potential mechanism for reorganization is for an ssDNA translocase (ATP-dependent motor) to push the SSB along ssDNA. Here we use single molecule total internal reflection fluorescence microscopy to detect such pushing events. When Cy5-labeled Escherichia coli (Ec) SSB is bound to surface-immobilized 3'-Cy3-labeled ssDNA, a fluctuating FRET signal is observed, consistent with random diffusion of SSB along the ssDNA. Addition of Saccharomyces cerevisiae Pif1, a 5' to 3' ssDNA translocase, results in the appearance of isolated, irregularly spaced saw-tooth FRET spikes only in the presence of ATP. These FRET spikes result from translocase-induced directional (5' to 3') pushing of the SSB toward the 3' ssDNA end, followed by displacement of the SSB from the DNA end. Similar ATP-dependent pushing events, but in the opposite (3' to 5') direction, are observed with EcRep and EcUvrD (both 3' to 5' ssDNA translocases). Simulations indicate that these events reflect active pushing by the translocase. The ability of translocases to chemo-mechanically push heterologous SSB proteins along ssDNA provides a potential mechanism for reorganization and clearance of tightly bound SSBs from ssDNA.\",\n \"corpus_id\": 1201982,\n \"score\": 1\n },\n {\n \"doc_id\": \"27624131\",\n \"title\": \"Examining a DNA Replication Requirement for Bacteriophage λ Red- and Rac Prophage RecET-Promoted Recombination in Escherichia coli.\",\n \"abstract\": \"UNLABELLED: Recombineering, in vivo genetic engineering with bacteriophage homologous recombination systems, is a powerful technique for making genetic modifications in bacteria. Two systems widely used in Escherichia coli are the Red system from phage λ and RecET from the defective Rac prophage. We investigated the in vivo dependence of recombineering on DNA replication of the recombining substrate using plasmid targets. For λ Red recombination, when DNA replication of a circular target plasmid is prevented, recombination with single-stranded DNA oligonucleotides is greatly reduced compared to that under replicating conditions. For RecET recombination, when DNA replication of the targeted plasmid is prevented, the recombination frequency is also reduced, to a level identical to that seen for the Red system in the absence of replication. The very low level of oligonucleotide recombination observed in the absence of any phage recombination functions is the same in the presence or absence of DNA replication. In contrast, both the Red and RecET systems recombine a nonreplicating linear dimer plasmid with high efficiency to yield a circular monomer. Therefore, the DNA replication requirement is substrate dependent. Our data are consistent with recombination by both the Red and RecET systems occurring predominately by single-strand annealing rather than by strand invasion. IMPORTANCE: Bacteriophage homologous recombination systems are widely used for in vivo genetic engineering in bacteria. Single- or double-stranded linear DNA substrates containing short flanking homologies to chromosome targets are used to generate precise and accurate genetic modifications when introduced into bacteria expressing phage recombinases. Understanding the molecular mechanism of these recombination systems will facilitate improvements in the technology. Here, two phage-specific systems are shown to require exposure of complementary single-strand homologous targets for efficient recombination; these single-strand regions may be created during DNA replication or by single-strand exonuclease digestion of linear duplex DNA. Previously, in vitro studies reported that these recombinases promote the single-strand annealing of two complementary DNAs and also strand invasion of a single DNA strand into duplex DNA to create a three-stranded region. Here, in vivo experiments show that recombinase-mediated annealing of complementary single-stranded DNA is the predominant recombination pathway in E. coli.\",\n \"corpus_id\": 18971153,\n \"score\": 1\n },\n {\n \"doc_id\": \"29458770\",\n \"title\": \"Single-Molecule Studies of ssDNA-Binding Proteins Exchange.\",\n \"abstract\": \"Single-stranded DNA-binding protein (SSB) is important not only for the protection of single-stranded DNA (ssDNA) but also for the recruitment of other proteins for DNA replication, recombination, and repair. The interaction of SSB with ssDNA is highly dynamic as it exists as an intermediate during cellular processes that unwind dsDNA. It has been proposed that SSB redistributes itself among multiple ssDNA segments, but transient intermediates are difficult to observe in bulk experiments. We can use single-molecule FRET microscopy to observe intermediates of the transfer of a single Escherichia coli SSB from one ssDNA strand to another or exchange of one SSB for another on a single ssDNA in real time. This single-molecule approach can be further applicable to understand relative binding affinities and competitive dynamics for other SSBs and variants across various systems.\",\n \"corpus_id\": 3440559,\n \"score\": 1\n },\n {\n \"doc_id\": \"29681468\",\n \"title\": \"Discrimination against RNA Backbones by a ssDNA Binding Protein.\",\n \"abstract\": \"Pot1 is the shelterin component responsible for the protection of the single-stranded DNA (ssDNA) overhang at telomeres in nearly all eukaryotic organisms. The C-terminal domain of the DNA-binding domain, Pot1pC, exhibits non-specific ssDNA recognition, achieved through thermodynamically equivalent alternative binding conformations. Given this flexibility, it is unclear how specificity for ssDNA over RNA, an activity required for biological function, is achieved. Examination of the ribose-position specificity of Pot1pC shows that ssDNA specificity is additive but not uniformly distributed across the ligand. High-resolution structures of several Pot1pC complexes with RNA-DNA chimeric ligands reveal Pot1pC discriminates against RNA by utilizing non-compensatory binding modes that feature significant rearrangement of the binding interface. These alternative conformations, accessed through both ligand and protein flexibility, recover much, but not all, of the binding energy, leading to the observed reduction in affinities. These findings suggest that intermolecular interfaces are remarkably sophisticated in their tuning of specificity toward flexible ligands.\",\n \"corpus_id\": 5066050,\n \"score\": 1\n },\n {\n \"doc_id\": \"18848568\",\n \"title\": \"Bacteriophage T5 DNA ejection under pressure.\",\n \"abstract\": \"The transfer of the bacteriophage genome from the capsid into the host cell is a key step of the infectious process. In bacteriophage T5, DNA ejection can be triggered in vitro by simple binding of the phage to its purified Escherichia coli receptor FhuA. Using electrophoresis and cryo-electron microscopy, we measure the extent of DNA ejection as a function of the external osmotic pressure. In the high pressure range (7-16 atm), the amount of DNA ejected decreases with increasing pressure, as theoretically predicted and observed for lambda and SPP1 bacteriophages. In the low and moderate pressure range (2-7 atm), T5 exhibits an unexpected behavior. Instead of a unique ejected length, multiple populations coexist. Some phages eject their complete genome, whereas others stop at some nonrandom states that do not depend on the applied pressure. We show that contrarily to what is observed for the phages SPP1 and lambda, T5 ejection cannot be explained as resulting from a simple pressure equilibrium between the inside and outside of the capsid. Kinetics parameters and/or structural characteristics of the ejection machinery could play a determinant role in T5 DNA ejection.\",\n \"corpus_id\": 27898318,\n \"score\": 0\n },\n {\n \"doc_id\": \"19919545\",\n \"title\": \"Identification and characterization of the metal ion-dependent L-alanoyl-D-glutamate peptidase encoded by bacteriophage T5.\",\n \"abstract\": \"Although bacteriophage T5 is known to have lytic proteins for cell wall hydrolysis and phage progeny escape, their activities are still unknown. This is the first report on the cloning, expression and biochemical characterization of a bacteriophage T5 lytic hydrolase. The endolysin-encoding lys gene of virulent coliphage T5 was cloned in Escherichia coli cells, and an electrophoretically homogeneous product of this gene was obtained with a high yield (78% of total activity). The protein purified was shown to be an L-alanoyl-D-glutamate peptidase. The enzyme demonstrated maximal activity in diluted buffers (25-50 mM) at pH 8.5. The enzyme was strongly inhibited by EDTA and BAPTA, and fully reactivated by calcium/manganese chlorides. It was found that, along with E. coli peptidoglycan, peptidase of bacteriophage T5 can lyse peptidoglycans of other Gram-negative microorganisms (Pectobacterium carotovorum, Pseudomonas putida, Proteus vulgaris, and Proteus mirabilis). This endolysin is the first example of an L-alanoyl-D-glutamate peptidase in a virulent phage infecting Gram-negative bacteria. There are, however, a great many sequences in databases that are highly similar to that of bacteriophage T5 hydrolase, indicating a wide distribution of endolytic L-alanoyl-D-glutamate peptidases. The article discusses how an enzyme with such substrate specificity could be fixed in the process of evolution.\",\n \"corpus_id\": 24741775,\n \"score\": 0\n }\n]","isConversational":false}}},{"rowIdx":62,"cells":{"query":{"kind":"string","value":"{\n \"doc_id\": \"29551714\",\n \"title\": \"Blind estimation of DED camera gain in Electron Microscopy.\",\n \"abstract\": \"The introduction of Direct Electron Detector (DED) videos in the Electron Microscope field has boosted Single Particle Analysis to a point in which it is currently considered to be a key technique in Structural Biology. In this article we introduce an approach to estimate the DED camera gain at each pixel from the movies themselves. This gain is needed to have the set of recorded frames into a coherent gray level range, homogeneous over the whole image. The algorithm does not need any other input than the DED movie itself, being capable of providing an estimate of the camera gain image, helping to identify dead pixels and cases of incorrectly calibrated cameras. We propose the algorithm to be used either to validate the experimentally acquired gain image (for instance, to follow its possible change over time) or to verify that there is no residual gain image after experimentally correcting for the camera gain. We show results for a number of DED camera models currently in use (DE, Falcon II, Falcon 3, and K2).\",\n \"corpus_id\": 4272190\n}"},"candidates":{"kind":"list like","value":[{"doc_id":"18195445","title":"Blind camera fingerprinting and image clustering.","abstract":"Previous studies have shown how to \"fingerprint\" a digital camera given a set of images known to come from the camera. A clustering technique is proposed to construct such fingerprints from a mixed set of images, enabling identification of each image's source camera without any prior knowledge of source.","corpus_id":18523431,"score":2},{"doc_id":"19104544","title":"Robust autonomous detection of the defective pixels in detectors using a probabilistic technique.","abstract":"Detection of defective pixels in solid-state detectors/sensor arrays has received limited research attention. Few approaches currently exist for detecting the defective pixels using real images captured with cameras equipped with such detectors, and they are ad hoc and limited in their applicability. In this paper, we present a probabilistic novel integrated technique for autonomously detecting the defective pixels in image sensor arrays. It can be applied to images containing rich scene information, captured with any digital camera equipped with a solid-state detector, to detect different kinds of defective pixels in the detector. We apply our technique to the detection of various defective pixels in an experimental camera equipped with a charge coupled device (CCD) array and two out of the four HgCdTe detectors of the UKIRT's wide field camera (WFCAM) used for infrared (IR) astronomy [Astron. Astrophys.467, 777-784 (2007)].","corpus_id":8516427,"score":2},{"doc_id":"20057054","title":"A toolkit for the characterization of CCD cameras for transmission electron microscopy.","abstract":"Charge-coupled devices (CCD) are nowadays commonly utilized in transmission electron microscopy (TEM) for applications in life sciences. Direct access to digitized images has revolutionized the use of electron microscopy, sparking developments such as automated collection of tomographic data, focal series, random conical tilt pairs and ultralarge single-particle data sets. Nevertheless, for ultrahigh-resolution work photographic plates are often still preferred. In the ideal case, the quality of the recorded image of a vitrified biological sample would solely be determined by the counting statistics of the limited electron dose the sample can withstand before beam-induced alterations dominate. Unfortunately, the image is degraded by the non-ideal point-spread function of the detector, as a result of a scintillator coupled by fibre optics to a CCD, and the addition of several inherent noise components. Different detector manufacturers provide different types of figures of merit when advertising the quality of their detector. It is hard for most laboratories to verify whether all of the anticipated specifications are met. In this report, a set of algorithms is presented to characterize on-axis slow-scan large-area CCD-based TEM detectors. These tools have been added to a publicly available image-processing toolbox for MATLAB. Three in-house CCD cameras were carefully characterized, yielding, among others, statistics for hot and bad pixels, the modulation transfer function, the conversion factor, the effective gain and the detective quantum efficiency. These statistics will aid data-collection strategy programs and provide prior information for quantitative imaging. The relative performance of the characterized detectors is discussed and a comparison is made with similar detectors that are used in the field of X-ray crystallography.","corpus_id":-1,"score":2},{"doc_id":"20382479","title":"Characterization of a direct detection device imaging camera for transmission electron microscopy.","abstract":"The complete characterization of a novel direct detection device (DDD) camera for transmission electron microscopy is reported, for the first time at primary electron energies of 120 and 200 keV. Unlike a standard charge coupled device (CCD) camera, this device does not require a scintillator. The DDD transfers signal up to 65 lines/mm providing the basis for a high-performance platform for a new generation of wide field-of-view high-resolution cameras. An image of a thin section of virus particles is presented to illustrate the substantially improved performance of this sensor over current indirectly coupled CCD cameras.","corpus_id":19834016,"score":2},{"doc_id":"21524337","title":"Electronic detectors for electron microscopy.","abstract":"Electron microscopy (EM) is an important tool for high-resolution structure determination in applications ranging from condensed matter to biology. Electronic detectors are now used in most applications in EM as they offer convenience and immediate feedback that is not possible with film or image plates. The earliest forms of electronic detector used routinely in transmission electron microscopy (TEM) were charge coupled devices (CCDs) and for many applications these remain perfectly adequate. There are however applications, such as the study of radiation-sensitive biological samples, where film is still used and improved detectors would be of great value. The emphasis in this review is therefore on detectors for use in such applications. Two of the most promising candidates for improved detection are: monolithic active pixel sensors (MAPS) and hybrid pixel detectors (of which Medipix2 was chosen for this study). From the studies described in this review, a back-thinned MAPS detector appears well suited to replace film in for the study of radiation-sensitive samples at 300 keV, while Medipix2 is suited to use at lower energies and especially in situations with very low count rates. The performance of a detector depends on the energy of electrons to be recorded, which in turn is dependent on the application it is being used for; results are described for a wide range of electron energies ranging from 40 to 300 keV. The basic properties of detectors are discussed in terms of their modulation transfer function (MTF) and detective quantum efficiency (DQE) as a function of spatial frequency.","corpus_id":34044951,"score":2},{"doc_id":"21619932","title":"Practical performance evaluation of a 10k × 10k CCD for electron cryo-microscopy.","abstract":"Electron cryo-microscopy (cryo-EM) images are commonly collected using either charge-coupled devices (CCD) or photographic film. Both film and the current generation of 16 megapixel (4k × 4k) CCD cameras have yielded high-resolution structures. Yet, despite the many advantages of CCD cameras, more than two times as many structures of biological macromolecules have been published in recent years using photographic film. The continued preference to film, especially for subnanometer-resolution structures, may be partially influenced by the finer sampling and larger effective specimen imaging area offered by film. Large format digital cameras may finally allow them to overtake film as the preferred detector for cryo-EM. We have evaluated a 111-megapixel (10k × 10k) CCD camera with a 9 μm pixel size. The spectral signal-to-noise ratios of low dose images of carbon film indicate that this detector is capable of providing signal up to at least 2/5 Nyquist frequency potentially retrievable for 3D reconstructions of biological specimens, resulting in more than double the effective specimen imaging area of existing 4k × 4k CCD cameras. We verified our estimates using frozen-hydrated ε15 bacteriophage as a biological test specimen with previously determined structure, yielding a ∼7 Å resolution single particle reconstruction from only 80 CCD frames. Finally, we explored the limits of current CCD technology by comparing the performance of this detector to various CCD cameras used for recording data yielding subnanometer resolution cryo-EM structures submitted to the electron microscopy data bank (http://www.emdatabank.org/).","corpus_id":206492149,"score":2},{"doc_id":"22149850","title":"Technical Note: modification of the standard gain correction algorithm to compensate for the number of used reference flat frames in detector performance studies.","abstract":"PURPOSE: The x-ray performance evaluation of digital x-ray detectors is based on the calculation of the modulation transfer function (MTF), the noise power spectrum (NPS), and the resultant detective quantum efficiency (DQE). The flat images used for the extraction of the NPS should not contain any fixed pattern noise (FPN) to avoid contamination from nonstochastic processes. The \"gold standard\" method used for the reduction of the FPN (i.e., the different gain between pixels) in linear x-ray detectors is based on normalization with an average reference flat-field. However, the noise in the corrected image depends on the number of flat frames used for the average flat image. The aim of this study is to modify the standard gain correction algorithm to make it independent on the used reference flat frames. METHODS: Many publications suggest the use of 10-16 reference flat frames, while other studies use higher numbers (e.g., 48 frames) to reduce the propagated noise from the average flat image. This study quantifies experimentally the effect of the number of used reference flat frames on the NPS and DQE values and appropriately modifies the gain correction algorithm to compensate for this effect. RESULTS: It is shown that using the suggested gain correction algorithm a minimum number of reference flat frames (i.e., down to one frame) can be used to eliminate the FPN from the raw flat image. This saves computer memory and time during the x-ray performance evaluation. CONCLUSIONS: The authors show that the method presented in the study (a) leads to the maximum DQE value that one would have by using the conventional method and very large number of frames and (b) has been compared to an independent gain correction method based on the subtraction of flat-field images, leading to identical DQE values. They believe this provides robust validation of the proposed method.","corpus_id":21340859,"score":2},{"doc_id":"22164102","title":"Range camera self-calibration based on integrated bundle adjustment via joint setup with a 2D digital camera.","abstract":"Time-of-flight cameras, based on photonic mixer device (PMD) technology, are capable of measuring distances to objects at high frame rates, however, the measured ranges and the intensity data contain systematic errors that need to be corrected. In this paper, a new integrated range camera self-calibration method via joint setup with a digital (RGB) camera is presented. This method can simultaneously estimate the systematic range error parameters as well as the interior and external orientation parameters of the camera. The calibration approach is based on photogrammetric bundle adjustment of observation equations originating from collinearity condition and a range errors model. Addition of a digital camera to the calibration process overcomes the limitations of small field of view and low pixel resolution of the range camera. The tests are performed on a dataset captured by a PMD[vision]-O3 camera from a multi-resolution test field of high contrast targets. An average improvement of 83% in RMS of range error and 72% in RMS of coordinate residual, over that achieved with basic calibration, was realized in an independent accuracy assessment. Our proposed calibration method also achieved 25% and 36% improvement on RMS of range error and coordinate residual, respectively, over that obtained by integrated calibration of the single PMD camera.","corpus_id":11319237,"score":2},{"doc_id":"23747527","title":"Ranking TEM cameras by their response to electron shot noise.","abstract":"We demonstrate two ways in which the Fourier transforms of images that consist solely of randomly distributed electrons (shot noise) can be used to compare the relative performance of different electronic cameras. The principle is to determine how closely the Fourier transform of a given image does, or does not, approach that of an image produced by an ideal camera, i.e. one for which single-electron events are modeled as Kronecker delta functions located at the same pixels where the electrons were incident on the camera. Experimentally, the average width of the single-electron response is characterized by fitting a single Lorentzian function to the azimuthally averaged amplitude of the Fourier transform. The reciprocal of the spatial frequency at which the Lorentzian function falls to a value of 0.5 provides an estimate of the number of pixels at which the corresponding line-spread function falls to a value of 1/e. In addition, the excess noise due to stochastic variations in the magnitude of the response of the camera (for single-electron events) is characterized by the amount to which the appropriately normalized power spectrum does, or does not, exceed the total number of electrons in the image. These simple measurements provide an easy way to evaluate the relative performance of different cameras. To illustrate this point we present data for three different types of scintillator-coupled camera plus a silicon-pixel (direct detection) camera.","corpus_id":21295829,"score":2},{"doc_id":"23748163","title":"Noise models and cryo-EM drift correction with a direct-electron camera.","abstract":"Blurring due to specimen-holder drift is a common occurrence in cryo-EM images. Cameras employing active-pixel sensors are capable of high frame rates such that a single low-dose exposure can be acquired as a series of frames. In this paper we consider the possibility of tracking and compensating for overall drift in typical single-particle specimens through the analysis of frame sequences. A problem that arises in tracking through cross-correlation of frames obtained with the DE-12 camera from Direct Electron LLC is the presence of \"hot-pixel noise\". This random pattern of bright pixels is highly correlated among frames. We show how a model of this noise can be employed to greatly reduce its effects. A filter function is derived that optimizes the tracking of image shifts by cross-correlation, and we demonstrate the tracking of specimen drift in typical cryo-EM specimens.","corpus_id":37435159,"score":2},{"doc_id":"24189638","title":"Quantitative characterization of electron detectors for transmission electron microscopy.","abstract":"A new generation of direct electron detectors for transmission electron microscopy (TEM) promises significant improvement over previous detectors in terms of their modulation transfer function (MTF) and detective quantum efficiency (DQE). However, the performance of these new detectors needs to be carefully monitored in order to optimize imaging conditions and check for degradation over time. We have developed an easy-to-use software tool, FindDQE, to measure MTF and DQE of electron detectors using images of a microscope's built-in beam stop. Using this software, we have determined the DQE curves of four direct electron detectors currently available: the Gatan K2 Summit, the FEI Falcon I and II, and the Direct Electron DE-12, under a variety of total dose and dose rate conditions. We have additionally measured the curves for the Gatan US4000 and TVIPS TemCam-F416 scintillator-based cameras. We compare the results from our new method with published curves.","corpus_id":32106926,"score":2},{"doc_id":"25186400","title":"Reduction of ring artifacts in CBCT: detection and correction of pixel gain variations in flat panel detectors.","abstract":"PURPOSE: In using flat panel detectors (FPD) for cone beam computed tomography (CBCT), pixel gain variations may lead to structured nonuniformities in projections and ring artifacts in CBCT images. Such gain variations can be caused by change in detector entrance exposure levels or beam hardening, and they are not accounted by conventional flat field correction methods. In this work, the authors presented a method to identify isolated pixel clusters that exhibit gain variations and proposed a pixel gain correction (PGC) method to suppress both beam hardening and exposure level dependent gain variations. METHODS: To modulate both beam spectrum and entrance exposure, flood field FPD projections were acquired using beam filters with varying thicknesses. \" Ideal\" pixel values were estimated by performing polynomial fits in both raw and flat field corrected projections. Residuals were calculated by taking the difference between measured and ideal pixel values to identify clustered image and FPD artifacts in flat field corrected and raw images, respectively. To correct clustered image artifacts, the ratio of ideal to measured pixel values in filtered images were utilized as pixel-specific gain correction factors, referred as PGC method, and they were tabulated as a function of pixel value in a look-up table. RESULTS: 0.035% of detector pixels lead to clustered image artifacts in flat field corrected projections, where 80% of these pixels were traced back and linked to artifacts in the FPD. The performance of PGC method was tested in variety of imaging conditions and phantoms. The PGC method reduced clustered image artifacts and fixed pattern noise in projections, and ring artifacts in CBCT images. CONCLUSIONS: Clustered projection image artifacts that lead to ring artifacts in CBCT can be better identified with our artifact detection approach. When compared to the conventional flat field correction method, the proposed PGC method enables characterization of nonlinear pixel gain variations as a function of change in x-ray spectrum and intensity. Hence, it can better suppress image artifacts due to beam hardening as well as artifacts that arise from detector entrance exposure variation.","corpus_id":27003539,"score":2},{"doc_id":"25194828","title":"Comparison of optimal performance at 300keV of three direct electron detectors for use in low dose electron microscopy.","abstract":"Low dose electron imaging applications such as electron cryo-microscopy are now benefitting from the improved performance and flexibility of recently introduced electron imaging detectors in which electrons are directly incident on backthinned CMOS sensors. There are currently three commercially available detectors of this type: the Direct Electron DE-20, the FEI Falcon II and the Gatan K2 Summit. These have different characteristics and so it is important to compare their imaging properties carefully with a view to optimise how each is used. Results at 300keV for both the modulation transfer function (MTF) and the detective quantum efficiency (DQE) are presented. Of these, the DQE is the most important in the study of radiation sensitive samples where detector performance is crucial. We find that all three detectors have a better DQE than film. The K2 Summit has the best DQE at low spatial frequencies but with increasing spatial frequency its DQE falls below that of the Falcon II.","corpus_id":8670203,"score":2},{"doc_id":"26431895","title":"FEI's direct electron detector developments: Embarking on a revolution in cryo-TEM.","abstract":"In early 2011 FEI Company launched the \"Falcon\", its first commercial direct electron detector product intended for application in 3-D electron microscopy in the life sciences. In this paper we discuss the principle of direct electron detection and its implementation in Falcon cameras. We describe the signal formation in the sensor and its impact on the detection quantum efficiency (DQE) of the sensor. Insights into the signal formation led us to improved camera designs. Three significant improvements are discussed. ( 1) Back thinning of the sensor. This is implemented in the second-generation Falcon (Falcon 2), where the sensor thickness is reduced to 50μm, and in the latest generation Falcon 3 detector with further back-thinning down to 30μm. ( 2) The introduction of electron counting, a signal processing technology implemented in Falcon 3. ( 3) Dose fractionation mode, which allows the user to access intermediate results during the illumination of the sample.","corpus_id":24692393,"score":2},{"doc_id":"28517660","title":"SU-E-I-103: Detecting Anomalous Pixels and Correlated Artifacts in Digital Detectors from Flat-Field Images.","abstract":"PURPOSE: Anomalous pixels may be defined as those pixels whose exposure response relationship is deviant from the typical, expected or calibrated response. A group of anomalous pixels may Result in visible correlated artifacts. Here we demonstrate an approach to identify anomalous pixels and correlated artifacts using flat-field images. METHODS: Using manufacturer specific calibration geometry, sets of four flat-field images per detector were obtained with varying input air kerma values (0.5 to 160 μGy) from 9 digital detectors at 6 institutions. Images obtained before and after calibration, with both proper and improper gain maps and structured artifacts were additionally acquired with some detectors. Image analysis methodology under consideration by AAPM Task Group 150 was used. After eliminating 10mm borders, images were divided into square regions (100mm2 ). Anomalous pixels were identified as pixels within each region with valuesabove or below ±3 standard deviations (SD) relative to the mean value of the region. If these pixels were identified in all four images comprising a set, then they were reported as anomalous. Line artifacts were identified as rows and columns with cumulative profile values that were above or below ±3 SD with respect to the mean value of neighboring profiles in the set of four flat-field mages. Results were verified with visual inspection of the images. RESULTS: For four sets of images, the algorithm did not identify any anomalous pixels, and none were spotted on visible inspection as well, while for five sets of images the identified anomalous pixels matched visual inspection results. Anomalous pixel detection failed in regions with an unusually large number of defects and structured noise, since those regions exhibited relatively large SD. Line artifacts consistent with visual analysis were identified correctly when present. CONCLUSIONS: A practical approach to identify anomalous pixels and correlated artifacts from flat-field images is demonstrated.","corpus_id":25428110,"score":2},{"doc_id":"18447528","title":"A charge coupled device camera with electron decelerator for intermediate voltage electron microscopy.","abstract":"Electron microscopists are increasingly turning to intermediate voltage electron microscopes (IVEMs) operating at 300-400 kV for a wide range of studies. They are also increasingly taking advantage of slow-scan charge coupled device (CCD) cameras, which have become widely used on electron microscopes. Under some conditions, CCDs provide an improvement in data quality over photographic film, as well as the many advantages of direct digital readout. However, CCD performance is seriously degraded on IVEMs compared to the more conventional 100 kV microscopes. In order to increase the efficiency and quality of data recording on IVEMs, we have developed a CCD camera system in which the electrons are decelerated to below 100 kV before impacting the camera, resulting in greatly improved performance in both signal quality and resolution compared to other CCDs used in electron microscopy. These improvements will allow high-quality image and diffraction data to be collected directly with the CCD, enabling improvements in data collection for applications including high-resolution electron crystallography, single particle reconstruction of protein structures, tomographic studies of cell ultrastructure, and remote microscope operation. This approach will enable us to use even larger format CCD chips that are being developed with smaller pixels.","corpus_id":19557303,"score":1},{"doc_id":"18805922","title":"Analysis of molecular concentration and brightness from fluorescence fluctuation data with an electron multiplied CCD camera.","abstract":"We demonstrate the calculation of particle brightness and concentration from fluorescence-fluctuation photon-counting statistics using an electron-multiplied charge-coupled device (EMCCD) camera. This technique provides a concentration-independent measure of particle brightness in dynamic systems. The high sensitivity and highly parallel detection of EMCCD cameras allow for imaging of dynamic particle brightness, providing the capability to follow aggregation reactions in real time. A critical factor of the EMCCD camera is the presence of nonlinearity at high intensities. These nonlinearities arise due to limited capacity of the CCD well and to the analog-to-digital converter maximum range. However, we show that the specific camera we used (with a 16-bit analog-to-digital converter) has sufficient dynamic range for most microscopy applications. In addition, we explore the importance of camera timing behavior as it is affected by the vertical frame transfer speed of the camera. Although the camera has microsecond exposure time for illumination of a few pixels, the exposure time increased to milliseconds for full-field illumination. Finally, we demonstrate the ability of the technique to follow concentration changes and measure single-molecule brightness in real time in living cells.","corpus_id":42330095,"score":1},{"doc_id":"20378810","title":"Four-dimensional electron microscopy.","abstract":"The discovery of the electron over a century ago and the realization of its dual character have given birth to one of the two most powerful imaging instruments: the electron microscope. The electron microscope's ability to resolve three-dimensional (3D) structures on the atomic scale is continuing to affect different fields, including materials science and biology. In this Review, we highlight recent developments and inventions made by introducing the fourth dimension of time in electron microscopy. Today, ultrafast electron microscopy (4D UEM) enables a resolution that is 10 orders of magnitude better than that of conventional microscopes, which are limited by the video-camera rate of recording. After presenting the central concept involved, that of single-electron stroboscopic imaging, we discuss prototypical applications, which include the visualization of complex structures when unfolding on different length and time scales. The developed UEM variant techniques are several, and here we illucidate convergent-beam and near-field imaging, as well as tomography and scanning-pulse microscopy. We conclude with current explorations in imaging of nanomaterials and biostructures and an outlook on possible future directions in space-time, 4D electron microscopy.","corpus_id":5449372,"score":1},{"doc_id":"23426864","title":"Direct detection pays off for electron cryo-microscopy.","abstract":"Improved electron detectors and image-processing techniques will allow the structures of macromolecules to be determined from tens of thousands of single-particle cryo-EM images, rather than the hundreds of thousands needed previously.","corpus_id":12668402,"score":1},{"doc_id":"23931506","title":"Practical aspects of adjusting digital cameras.","abstract":"This chapter introduces the adjustment of digital camera settings using the tools found within image acquisition software and discusses measuring gray-level information such as (1) the histogram, (2) line scan, and (3) other strategies. The pixel values in an image can be measured within many image capture software programs in two ways. The first is a histogram of pixel gray values and the second is a line-scan plot across a selectable axis of the image. Understanding how to evaluate the information presented by these tools is critical to properly adjusting the camera to maximize the image contrast without losing grayscale information. This chapter discusses the 0-255 grayscale resolution of an 8-bit camera; however, the concepts are the same for cameras of any bit depth. This chapter also describes camera settings, such as exposure time, offset, and gain, and the steps for contrast stretching such as setting the exposure time, adjusting offset and gain, and camera versus image display controls.","corpus_id":28794853,"score":1},{"doc_id":"23931507","title":"Cameras for digital microscopy.","abstract":"This chapter reviews the fundamental characteristics of charge-coupled devices (CCDs) and related detectors, outlines the relevant parameters for their use in microscopy, and considers promising recent developments in the technology of detectors. Electronic imaging with a CCD involves three stages--interaction of a photon with the photosensitive surface, storage of the liberated charge, and readout or measurement of the stored charge. The most demanding applications in fluorescence microscopy may require as much as four orders of greater magnitude sensitivity. The image in the present-day light microscope is usually acquired with a CCD camera. The CCD is composed of a large matrix of photosensitive elements (often referred to as \"pixels\" shorthand for picture elements, which simultaneously capture an image over the entire detector surface. The light-intensity information for each pixel is stored as electronic charge and is converted to an analog voltage by a readout amplifier. This analog voltage is subsequently converted to a numerical value by a digitizer situated on the CCD chip, or very close to it. Several (three to six) amplifiers are required for each pixel, and to date, uniform images with a homogeneous background have been a problem because of the inherent difficulties of balancing the gain in all of the amplifiers. Complementary metal oxide semiconductor sensors also exhibit relatively high noise associated with the requisite high-speed switching. Both of these deficiencies are being addressed, and sensor performance is nearing that required for scientific imaging.","corpus_id":205144142,"score":1},{"doc_id":"23931509","title":"Electronic cameras for low-light microscopy.","abstract":"This chapter introduces to electronic cameras, discusses the various parameters considered for evaluating their performance, and describes some of the key features of different camera formats. The chapter also presents the basic understanding of functioning of the electronic cameras and how these properties can be exploited to optimize image quality under low-light conditions. Although there are many types of cameras available for microscopy, the most reliable type is the charge-coupled device (CCD) camera, which remains preferred for high-performance systems. If time resolution and frame rate are of no concern, slow-scan CCDs certainly offer the best available performance, both in terms of the signal-to-noise ratio and their spatial resolution. Slow-scan cameras are thus the first choice for experiments using fixed specimens such as measurements using immune fluorescence and fluorescence in situ hybridization. However, if video rate imaging is required, one need not evaluate slow-scan CCD cameras. A very basic video CCD may suffice if samples are heavily labeled or are not perturbed by high intensity illumination. When video rate imaging is required for very dim specimens, the electron multiplying CCD camera is probably the most appropriate at this technological stage. Intensified CCDs provide a unique tool for applications in which high-speed gating is required. The variable integration time video cameras are very attractive options if one needs to acquire images at video rate acquisition, as well as with longer integration times for less bright samples. This flexibility can facilitate many diverse applications with highly varied light levels.","corpus_id":29024134,"score":1},{"doc_id":"23968652","title":"Influence of electron dose rate on electron counting images recorded with the K2 camera.","abstract":"A recent technological breakthrough in electron cryomicroscopy (cryoEM) is the development of direct electron detection cameras for data acquisition. By bypassing the traditional phosphor scintillator and fiber optic coupling, these cameras have greatly enhanced sensitivity and detective quantum efficiency (DQE). Of the three currently available commercial cameras, the Gatan K2 Summit was designed specifically for counting individual electron events. Counting further enhances the DQE, allows for practical doubling of detector resolution and eliminates noise arising from the variable deposition of energy by each primary electron. While counting has many advantages, undercounting of electrons happens when more than one electron strikes the same area of the detector within the analog readout period (coincidence loss), which influences image quality. In this work, we characterized the K2 Summit in electron counting mode, and studied the relationship of dose rate and coincidence loss and its influence on the quality of counted images. We found that coincidence loss reduces low frequency amplitudes but has no significant influence on the signal-to-noise ratio of the recorded image. It also has little influence on high frequency signals. Images of frozen hydrated archaeal 20S proteasome (~700 kDa, D7 symmetry) recorded at the optimal dose rate retained both high-resolution signal and low-resolution contrast and enabled calculating a 3.6 Å three-dimensional reconstruction from only 10,000 particles.","corpus_id":263553017,"score":1},{"doc_id":"25528571","title":"Seeing tobacco mosaic virus through direct electron detectors.","abstract":"With the introduction of direct electron detectors (DED) to the field of electron cryo-microscopy, a wave of atomic-resolution structures has become available. As the new detectors still require comparative characterization, we have used tobacco mosaic virus (TMV) as a test specimen to study the quality of 3D image reconstructions from data recorded on the two direct electron detector cameras, K2 Summit and Falcon II. Using DED movie frames, we explored related image-processing aspects and compared the performance of micrograph-based and segment-based motion correction approaches. In addition, we investigated the effect of dose deposition on the atomic-resolution structure of TMV and show that radiation damage affects negative carboxyl chains first in a side-chain specific manner. Finally, using 450,000 asymmetric units and limiting the effects of radiation damage, we determined a high-resolution cryo-EM map at 3.35Å resolution. Here, we provide a comparative case study of highly ordered TMV recorded on different direct electron detectors to establish recording and processing conditions that enable structure determination up to 3.2Å in resolution using cryo-EM.","corpus_id":20499036,"score":1},{"doc_id":"26546989","title":"Single-particle cryo-EM data acquisition by using direct electron detection camera.","abstract":"Recent advances in single-particle electron cryo-microscopy (cryo-EM) were largely facilitated by the application of direct electron detection cameras. These cameras feature not only a significant improvement in detective quantum efficiency but also a high frame rate that enables images to be acquired as 'movies' made of stacks of many frames. In this review, we discuss how the applications of direct electron detection cameras in cryo-EM have changed the way the data are acquired.","corpus_id":24462765,"score":1},{"doc_id":"26750260","title":"High Dynamic Range Pixel Array Detector for Scanning Transmission Electron Microscopy.","abstract":"We describe a hybrid pixel array detector (electron microscope pixel array detector, or EMPAD) adapted for use in electron microscope applications, especially as a universal detector for scanning transmission electron microscopy. The 128×128 pixel detector consists of a 500 µm thick silicon diode array bump-bonded pixel-by-pixel to an application-specific integrated circuit. The in-pixel circuitry provides a 1,000,000:1 dynamic range within a single frame, allowing the direct electron beam to be imaged while still maintaining single electron sensitivity. A 1.1 kHz framing rate enables rapid data collection and minimizes sample drift distortions while scanning. By capturing the entire unsaturated diffraction pattern in scanning mode, one can simultaneously capture bright field, dark field, and phase contrast information, as well as being able to analyze the full scattering distribution, allowing true center of mass imaging. The scattering is recorded on an absolute scale, so that information such as local sample thickness can be directly determined. This paper describes the detector architecture, data acquisition system, and preliminary results from experiments with 80-200 keV electron beams.","corpus_id":5984477,"score":1},{"doc_id":"26950127","title":"Compressive Video Recovery Using Block Match Multi-Frame Motion Estimation Based on Single Pixel Cameras.","abstract":"Compressive sensing (CS) theory has opened up new paths for the development of signal processing applications. Based on this theory, a novel single pixel camera architecture has been introduced to overcome the current limitations and challenges of traditional focal plane arrays. However, video quality based on this method is limited by existing acquisition and recovery methods, and the method also suffers from being time-consuming. In this paper, a multi-frame motion estimation algorithm is proposed in CS video to enhance the video quality. The proposed algorithm uses multiple frames to implement motion estimation. Experimental results show that using multi-frame motion estimation can improve the quality of recovered videos. To further reduce the motion estimation time, a block match algorithm is used to process motion estimation. Experiments demonstrate that using the block match algorithm can reduce motion estimation time by 30%.","corpus_id":702420,"score":1},{"doc_id":"27572725","title":"Processing of Cryo-EM Movie Data.","abstract":"Direct detector device (DDD) cameras dramatically enhance the capabilities of electron cryomicroscopy (cryo-EM) due to their improved detective quantum efficiency (DQE) relative to other detectors. DDDs use semiconductor technology that allows micrographs to be recorded as movies rather than integrated individual exposures. Movies from DDDs improve cryo-EM in another, more surprising, way. DDD movies revealed beam-induced specimen movement as a major source of image degradation and provide a way to partially correct the problem by aligning frames or regions of frames to account for this specimen movement. In this chapter, we use a self-consistent mathematical notation to explain, compare, and contrast several of the most popular existing algorithms for computationally correcting specimen movement in DDD movies. We conclude by discussing future developments in algorithms for processing DDD movies that would extend the capabilities of cryo-EM even further.","corpus_id":3572644,"score":1},{"doc_id":"28372435","title":"A direct electron detector for time-resolved MeV electron microscopy.","abstract":"The introduction of direct electron detectors enabled the structural biology revolution of cryogenic electron microscopy. Direct electron detectors are now expected to have a similarly dramatic impact on time-resolved MeV electron microscopy, particularly by enabling both spatial and temporal jitter correction. Here we report on the commissioning of a direct electron detector for time-resolved MeV electron microscopy. The direct electron detector demonstrated MeV single electron sensitivity and is capable of recording megapixel images at 180 Hz. The detector has a 15-bit dynamic range, better than 30-μm spatial resolution and less than 20 analogue-to-digital converter count RMS pixel noise. The unique capabilities of the direct electron detector and the data analysis required to take advantage of these capabilities are presented. The technical challenges associated with generating and processing large amounts of data are also discussed.","corpus_id":46882296,"score":1},{"doc_id":"28529964","title":"Ultrafast electron microscopy integrated with a direct electron detection camera.","abstract":"In the past decade, we have witnessed the rapid growth of the field of ultrafast electron microscopy (UEM), which provides intuitive means to watch atomic and molecular motions of matter. Yet, because of the limited current of the pulsed electron beam resulting from space-charge effects, observations have been mainly made to periodic motions of the crystalline structure of hundreds of nanometers or higher by stroboscopic imaging at high repetition rates. Here, we develop an advanced UEM with robust capabilities for circumventing the present limitations by integrating a direct electron detection camera for the first time which allows for imaging at low repetition rates. This approach is expected to promote UEM to a more powerful platform to visualize molecular and collective motions and dissect fundamental physical, chemical, and materials phenomena in space and time.","corpus_id":31970282,"score":1},{"doc_id":"29482132","title":"Software electron counting for low-dose scanning transmission electron microscopy.","abstract":"The performance of the detector is of key importance for low-dose imaging in transmission electron microscopy, and counting every single electron can be considered as the ultimate goal. In scanning transmission electron microscopy, low-dose imaging can be realized by very fast scanning, however, this also introduces artifacts and a loss of resolution in the scan direction. We have developed a software approach to correct for artifacts introduced by fast scans, making use of a scintillator and photomultiplier response that extends over several pixels. The parameters for this correction can be directly extracted from the raw image. Finally, the images can be converted into electron counts. This approach enables low-dose imaging in the scanning transmission electron microscope via high scan speeds while retaining the image quality of artifact-free slower scans.","corpus_id":3593705,"score":1},{"doc_id":"21428104","title":"[Radiometric calibration of LCTF-based multispectral area CCD camera].","abstract":"Multispectral area CCD camera based on liquid crystal tunable filter (LCTF) is a new spectral imaging system, which could record image of one wavelength on the area CCD by utilizing electrically controlled birefringence of liquid-crystal and interference principle of polarized light. Because of the special working principle of LCTF and frame transfer area CCD, the existing radiometric calibration method can not meet the precision need of remote sensing application if it is used for LCTF-camera. An improved radiometric calibration method is proposed, in which the camera performance test and calibration experiment are carried out relying on the devices of integrating sphere and standard detector, and the absolute calibration coefficient is calculated via correcting frame transfer smear and improving data process algorithm. Then the validity of the laboratory calibration coefficient is checked by a field validation experiment. Experimental result indicates that the calibration coefficient is valid, and the radiation information on the ground could be accurately inverted from the calibrated image data. With the resolution of radiometric calibration of LCTF-camera and the improvement of calibration precision, the application field of the image data acquired by the camera would be extended effectively.","corpus_id":25211232,"score":0},{"doc_id":"21529037","title":"Omnifocus video camera.","abstract":"The omnifocus video camera takes videos, in which objects at different distances are all in focus in a single video display. The omnifocus video camera consists of an array of color video cameras combined with a unique distance mapping camera called the Divcam. The color video cameras are all aimed at the same scene, but each is focused at a different distance. The Divcam provides real-time distance information for every pixel in the scene. A pixel selection utility uses the distance information to select individual pixels from the multiple video outputs focused at different distances, in order to generate the final single video display that is everywhere in focus. This paper presents principle of operation, design consideration, detailed construction, and over all performance of the omnifocus video camera. The major emphasis of the paper is the proof of concept, but the prototype has been developed enough to demonstrate the superiority of this video camera over a conventional video camera. The resolution of the prototype is high, capturing even fine details such as fingerprints in the image. Just as the movie camera was a significant advance over the still camera, the omnifocus video camera represents a significant advance over all-focus cameras for still images.","corpus_id":20792979,"score":0},{"doc_id":"21779142","title":"Physical Activity Recognition Based on Motion in Images Acquired by a Wearable Camera.","abstract":"A new technique to extract and evaluate physical activity patterns from image sequences captured by a wearable camera is presented in this paper. Unlike standard activity recognition schemes, the video data captured by our device do not include the wearer him/herself. The physical activity of the wearer, such as walking or exercising, is analyzed indirectly through the camera motion extracted from the acquired video frames. Two key tasks, pixel correspondence identification and motion feature extraction, are studied to recognize activity patterns. We utilize a multiscale approach to identify pixel correspondences. When compared with the existing methods such as the Good Features detector and the Speed-up Robust Feature (SURF) detector, our technique is more accurate and computationally efficient. Once the pixel correspondences are determined which define representative motion vectors, we build a set of activity pattern features based on motion statistics in each frame. Finally, the physical activity of the person wearing a camera is determined according to the global motion distribution in the video. Our algorithms are tested using different machine learning techniques such as the K-Nearest Neighbor (KNN), Naive Bayesian and Support Vector Machine (SVM). The results show that many types of physical activities can be recognized from field acquired real-world video. Our results also indicate that, with a design of specific motion features in the input vectors, different classifiers can be used successfully with similar performances.","corpus_id":207102242,"score":0},{"doc_id":"22291543","title":"Sensor for distance measurement using pixel grey-level information.","abstract":"An alternative method for distance measurement is presented, based on a radiometric approach to the image formation process. The proposed methodology uses images from an infrared emitting diode (IRED) to estimate the distance between the camera and the IRED. Camera output grey-level intensities are a function of the accumulated image irradiance, which is also related by inverse distance square law to the distance between the camera and the IRED. Analyzing camera-IRED distance, magnitudes that affected image grey-level intensities, and therefore accumulated image irradiance, were integrated into a differential model which was calibrated and used for distance estimation over a 200 to 600 cm range. In a preliminary model, the camera and the emitter were aligned.","corpus_id":3206542,"score":0},{"doc_id":"22399909","title":"Real time speed estimation of moving vehicles from side view images from an uncalibrated video camera.","abstract":"In order to estimate the speed of a moving vehicle with side view camera images, velocity vectors of a sufficient number of reference points identified on the vehicle must be found using frame images. This procedure involves two main steps. In the first step, a sufficient number of points from the vehicle is selected, and these points must be accurately tracked on at least two successive video frames. In the second step, by using the displacement vectors of the tracked points and passed time, the velocity vectors of those points are computed. Computed velocity vectors are defined in the video image coordinate system and displacement vectors are measured by the means of pixel units. Then the magnitudes of the computed vectors in image space should be transformed to the object space to find the absolute values of these magnitudes. This transformation requires an image to object space information in a mathematical sense that is achieved by means of the calibration and orientation parameters of the video frame images. This paper presents proposed solutions for the problems of using side view camera images mentioned here.","corpus_id":17691028,"score":0},{"doc_id":"22402684","title":"Online tracking of outdoor lighting variations for augmented reality with moving cameras.","abstract":"In augmented reality, one of key tasks to achieve a convincing visual appearance consistency between virtual objects and video scenes is to have a coherent illumination along the whole sequence. As outdoor illumination is largely dependent on the weather, the lighting condition may change from frame to frame. In this paper, we propose a full image-based approach for online tracking of outdoor illumination variations from videos captured with moving cameras. Our key idea is to estimate the relative intensities of sunlight and skylight via a sparse set of planar feature-points extracted from each frame. To address the inevitable feature misalignments, a set of constraints are introduced to select the most reliable ones. Exploiting the spatial and temporal coherence of illumination, the relative intensities of sunlight and skylight are finally estimated by using an optimization process. We validate our technique on a set of real-life videos and show that the results with our estimations are visually coherent along the video sequences.","corpus_id":2602599,"score":0},{"doc_id":"22545028","title":"Image Alignment for Multiple Camera High Dynamic Range Microscopy.","abstract":"This paper investigates the problem of image alignment for multiple camera high dynamic range (HDR) imaging. HDR imaging combines information from images taken with different exposure settings. Combining information from multiple cameras requires an alignment process that is robust to the intensity differences in the images. HDR applications that use a limited number of component images require an alignment technique that is robust to large exposure differences. We evaluate the suitability for HDR alignment of three exposure-robust techniques. We conclude that image alignment based on matching feature descriptors extracted from radiant power images from calibrated cameras yields the most accurate and robust solution. We demonstrate the use of this alignment technique in a high dynamic range video microscope that enables live specimen imaging with a greater level of detail than can be captured with a single camera.","corpus_id":18800763,"score":0},{"doc_id":"22566049","title":"Electron microscopy.","abstract":"Correlative light (LM) and transmission electron microscopic (TEM) analysis is useful, if ultrastructural details of cells need to be related to functional aspects which can only be examined at the LM level. The first protocol presented here introduces a relatively simple way of obtaining TEM images which, on the one hand, reveal ultrastructural details of individual cells and, on the other hand, are large enough to allow a correlation with light micrographs. The second protocol describes a technique for estimating mineral densities of hard tissues using backscattered electron images obtained with a scanning electron microscope. This technique can be used to analyze the mineralization processes which occur throughout tooth formation.","corpus_id":39721085,"score":0},{"doc_id":"22778608","title":"Using the standard deviation of a region of interest in an image to estimate camera to emitter distance.","abstract":"In this study, a camera to infrared diode (IRED) distance estimation problem was analyzed. The main objective was to define an alternative to measures depth only using the information extracted from pixel grey levels of the IRED image to estimate the distance between the camera and the IRED. In this paper, the standard deviation of the pixel grey level in the region of interest containing the IRED image is proposed as an empirical parameter to define a model for estimating camera to emitter distance. This model includes the camera exposure time, IRED radiant intensity and the distance between the camera and the IRED. An expression for the standard deviation model related to these magnitudes was also derived and calibrated using different images taken under different conditions. From this analysis, we determined the optimum parameters to ensure the best accuracy provided by this alternative. Once the model calibration had been carried out, a differential method to estimate the distance between the camera and the IRED was defined and applied, considering that the camera was aligned with the IRED. The results indicate that this method represents a useful alternative for determining the depth information.","corpus_id":6646364,"score":0},{"doc_id":"22967215","title":"4D electron microscopy: principles and applications.","abstract":"The transmission electron microscope (TEM) is a powerful tool enabling the visualization of atoms with length scales smaller than the Bohr radius at a factor of only 20 larger than the relativistic electron wavelength of 2.5 pm at 200 keV. The ability to visualize matter at these scales in a TEM is largely due to the efforts made in correcting for the imperfections in the lens systems which introduce aberrations and ultimately limit the achievable spatial resolution. In addition to the progress made in increasing the spatial resolution, the TEM has become an all-in-one characterization tool. Indeed, most of the properties of a material can be directly mapped in the TEM, including the composition, structure, bonding, morphology, and defects. The scope of applications spans essentially all of the physical sciences and includes biology. Until recently, however, high resolution visualization of structural changes occurring on sub-millisecond time scales was not possible. In order to reach the ultrashort temporal domain within which fundamental atomic motions take place, while simultaneously retaining high spatial resolution, an entirely new approach from that of millisecond-limited TEM cameras had to be conceived. As shown below, the approach is also different from that of nanosecond-limited TEM, whose resolution cannot offer the ultrafast regimes of dynamics. For this reason \"ultrafast electron microscopy\" is reserved for the field which is concerned with femtosecond to picosecond resolution capability of structural dynamics. In conventional TEMs, electrons are produced by heating a source or by applying a strong extraction field. Both methods result in the stochastic emission of electrons, with no control over temporal spacing or relative arrival time at the specimen. The timing issue can be overcome by exploiting the photoelectric effect and using pulsed lasers to generate precisely timed electron packets of ultrashort duration. The spatial and temporal resolutions achievable with short intense pulses containing a large number of electrons, however, are limited to tens of nanometers and nanoseconds, respectively. This is because Coulomb repulsion is significant in such a pulse, and the electrons spread in space and time, thus limiting the beam coherence. It is therefore not possible to image the ultrafast elementary dynamics of complex transformations. The challenge was to retain the high spatial resolution of a conventional TEM while simultaneously enabling the temporal resolution required to visualize atomic-scale motions. In this Account, we discuss the development of four-dimensional ultrafast electron microscopy (4D UEM) and summarize techniques and applications that illustrate the power of the approach. In UEM, images are obtained either stroboscopically with coherent single-electron packets or with a single electron bunch. Coulomb repulsion is absent under the single-electron condition, thus permitting imaging, diffraction, and spectroscopy, all with high spatiotemporal resolution, the atomic scale (sub-nanometer and femtosecond). The time resolution is limited only by the laser pulse duration and energy carried by the electron packets; the CCD camera has no bearing on the temporal resolution. In the regime of single pulses of electrons, the temporal resolution of picoseconds can be attained when hundreds of electrons are in the bunch. The applications given here are selected to highlight phenomena of different length and time scales, from atomic motions during structural dynamics to phase transitions and nanomechanical oscillations. We conclude with a brief discussion of emerging methods, which include scanning ultrafast electron microscopy (S-UEM), scanning transmission ultrafast electron microscopy (ST-UEM) with convergent beams, and time-resolved imaging of biological structures at ambient conditions with environmental cells.","corpus_id":2463705,"score":0},{"doc_id":"23132073","title":"Single particle electron microscopy.","abstract":"Single particle electron microscopy is a versatile technique for the structural analysis of protein complexes in near-native conditions. While tremendous progress has been made during the past few decades in techniques for specimen preparation, imaging, and image analysis, the field is still in development. In the context of this volume on electron crystallography, the following chapter gives practical guidelines on how to begin single particle EM studies, including preparing specimens, selecting imaging conditions, and choosing which of the many approaches to image analysis are appropriate for a specific sample.","corpus_id":38047303,"score":0},{"doc_id":"23797254","title":"Digital multi-focusing from a single photograph taken with an uncalibrated conventional camera.","abstract":"The demand to restore all-in-focus images from defocused images and produce photographs focused at different depths is emerging in more and more cases, such as low-end hand-held cameras and surveillance cameras. In this paper, we manage to solve this challenging multi-focusing problem with a single image taken with an uncalibrated conventional camera. Different from all existing multi-focusing approaches, our method does not need to include a deconvolution process, which is quite time-consuming and will cause ringing artifacts in the focused region and low depth-of-field. This paper proposes a novel systematic approach to realize multi-focusing from a single photograph. First of all, with the optical explanation for the local smooth assumption, we present a new point-to-point defocus model. Next, the blur map of the input image, which reflects the amount of defocus blur at each pixel in the image, is estimated by two steps. 1) With the sharp edge prior, a rough blur map is obtained by estimating the blur amount at the edge regions. 2) The guided image filter is applied to propagate the blur value from the edge regions to the whole image by which a refined blur map is obtained. Thus far, we can restore the all-in-focus photograph from a defocused input. To further produce photographs focused at different depths, the depth map from the blur map must be derived. To eliminate the ambiguity over the focal plane, user interaction is introduced and a binary graph cut algorithm is used. So we introduce user interaction and use a binary graph cut algorithm to eliminate the ambiguity over the focal plane. Coupled with the camera parameters, this approach produces images focused at different depths. The performance of this new multi-focusing algorithm is evaluated both objectively and subjectively by various test images. Both results demonstrate that this algorithm produces high quality depth maps and multi-focusing results, outperforming the previous approaches.","corpus_id":14328265,"score":0},{"doc_id":"24569482","title":"Atomic model of the F420-reducing [NiFe] hydrogenase by electron cryo-microscopy using a direct electron detector.","abstract":"The introduction of direct electron detectors with higher detective quantum efficiency and fast read-out marks the beginning of a new era in electron cryo-microscopy. Using the FEI Falcon II direct electron detector in video mode, we have reconstructed a map at 3.36 Å resolution of the 1.2 MDa F420-reducing hydrogenase (Frh) from methanogenic archaea from only 320,000 asymmetric units. Videos frames were aligned by a combination of image and particle alignment procedures to overcome the effects of beam-induced motion. The reconstructed density map shows all secondary structure as well as clear side chain densities for most residues. The full coordination of all cofactors in the electron transfer chain (a [NiFe] center, four [4Fe4S] clusters and an FAD) is clearly visible along with a well-defined substrate access channel. From the rigidity of the complex we conclude that catalysis is diffusion-limited and does not depend on protein flexibility or conformational changes. DOI: http://dx.doi.org/10.7554/eLife.01963.001.","corpus_id":16176308,"score":0},{"doc_id":"25122622","title":"Beam-induced motion correction for sub-megadalton cryo-EM particles.","abstract":"In electron cryo-microscopy (cryo-EM), the electron beam that is used for imaging also causes the sample to move. This motion blurs the images and limits the resolution attainable by single-particle analysis. In a previous Research article (Bai et al., 2013) we showed that correcting for this motion by processing movies from fast direct-electron detectors allowed structure determination to near-atomic resolution from 35,000 ribosome particles. In this Research advance article, we show that an improved movie processing algorithm is applicable to a much wider range of specimens. The new algorithm estimates straight movement tracks by considering multiple particles that are close to each other in the field of view, and models the fall-off of high-resolution information content by radiation damage in a dose-dependent manner. Application of the new algorithm to four data sets illustrates its potential for significantly improving cryo-EM structures, even for particles that are smaller than 200 kDa.","corpus_id":12574480,"score":0},{"doc_id":"25359822","title":"Fast auto-acquisition tomography tilt series by using HD video camera in ultra-high voltage electron microscope.","abstract":"The ultra-high voltage electron microscope (UHVEM) H-3000 with the world highest acceleration voltage of 3 MV can observe remarkable three dimensional microstructures of microns-thick samples[1]. Acquiring a tilt series of electron tomography is laborious work and thus an automatic technique is highly desired. We proposed the Auto-Focus system using image Sharpness (AFS)[2,3] for UHVEM tomography tilt series acquisition. In the method, five images with different defocus values are firstly acquired and the image sharpness are calculated. The sharpness are then fitted to a quasi-Gaussian function to decide the best focus value[3]. Defocused images acquired by the slow scan CCD (SS-CCD) camera (Hitachi F486BK) are of high quality but one minute is taken for acquisition of five defocused images. In this study, we introduce a high-definition video camera (HD video camera; Hamamatsu Photonics K. K. C9721S) for fast acquisition of images[4]. It is an analog camera but the camera image is captured by a PC and the effective image resolution is 1280×1023 pixels. This resolution is lower than that of the SS-CCD camera of 4096×4096 pixels. However, the HD video camera captures one image for only 1/30 second. In exchange for the faster acquisition the S/N of images are low. To improve the S/N, 22 captured frames are integrated so that each image sharpness is enough to become lower fitting error. As countermeasure against low resolution, we selected a large defocus step, which is typically five times of the manual defocus step, to discriminate different defocused images. By using HD video camera for autofocus process, the time consumption for each autofocus procedure was reduced to about six seconds. It took one second for correction of an image position and the total correction time was seven seconds, which was shorter by one order than that using SS-CCD camera. When we used SS-CCD camera for final image capture, it took 30 seconds to record one tilt image. We can obtain a tilt series of 61 images within 30 minutes. Accuracy and repeatability were good enough to practical use (Figure 1). We successfully reduced the total acquisition time of a tomography tilt series in half than before.jmicro;63/suppl_1/i25/DFU066F1F1DFU066F1Fig. 1.Objective lens current change with a tilt angle during acquisition of tomography series (Sample: a rat hepatocyte, thickness: 2 m, magnification: 4k, acc. voltage: 2 MV). Tilt angle range is ±60 degree with 2 degree step angle. Two series were acquired in the same area. Both data were almost same and the deviation was smaller than the minimum step by manual, so auto-focus worked well. We also developed a computer-aided three dimensional (3D) visualization and analysis software for electron tomography \"HawkC\" which can sectionalize the 3D data semi-automatically[5,6]. If this auto-acquisition system is used with IMOD reconstruction software[7] and HawkC software, we will be able to do on-line UHVEM tomography. The system would help pathology examination in the future. This work was supported by the Ministry of Education, Culture, Sports, Science and Technology (MEXT), Japan, under a Grant-in-Aid for Scientific Research (Grant No. 23560024, 23560786), and SENTAN, Japan Science and Technology Agency, Japan.","corpus_id":29568336,"score":0},{"doc_id":"25576587","title":"Pose Estimation for General Cameras Using Lines.","abstract":"In this paper, we address the problem of pose estimation under the framework of generalized camera models. We propose a solution based on the knowledge of the coordinates of 3-D straight lines (expressed in the world coordinate frame) and their corresponding image pixels. Previous approaches used the knowledge of the coordinates of 3-D points (zero dimensional elements) and their corresponding images (zero dimensional elements). In this paper, pixels belonging to the image of 3-D lines are used. There is no need to establish correspondences between pixels and 3-D points. Correspondences are established between 3-D lines and their images. There is no need to identify individual pixels. The use of correspondences between pixels (that belong to the images of the 3-D lines) and 3-D lines facilitates the correspondence problem when compared to the use of world and image points. This is one of the contributions of this paper. The approach is both evaluated and validated using synthetic data and also real images.","corpus_id":12909267,"score":0},{"doc_id":"25637660","title":"A statistical approach to the initial volume problem in Single Particle Analysis by Electron Microscopy.","abstract":"Cryo Electron Microscopy is a powerful Structural Biology technique, allowing the elucidation of the three-dimensional structure of biological macromolecules. In particular, the structural study of purified macromolecules -often referred as Single Particle Analysis(SPA)- is normally performed through an iterative process that needs a first estimation of the three-dimensional structure that is progressively refined using experimental data. It is well-known the local optimisation nature of this refinement, so that the initial choice of this first structure may substantially change the final result. Computational algorithms aiming to providing this first structure already exist. However, the question is far from settled and more robust algorithms are still needed so that the refinement process can be performed with sufficient guarantees. In this article we present a new algorithm that addresses the initial volume problem in SPA by setting it in a Weighted Least Squares framework and calculating the weights through a statistical approach based on the cumulative density function of different image similarity measures. We show that the new algorithm is significantly more robust than other state-of-the-art algorithms currently in use in the field. The algorithm is available as part of the software suite Xmipp (http://xmipp.cnb.csic.es) and Scipion (http://scipion.cnb.csic.es) under the name \"Significant\".","corpus_id":15342000,"score":0},{"doc_id":"26296328","title":"Alignment of cryo-EM movies of individual particles by optimization of image translations.","abstract":"Direct detector device (DDD) cameras have revolutionized single particle electron cryomicroscopy (cryo-EM). In addition to an improved camera detective quantum efficiency, acquisition of DDD movies allows for correction of movement of the specimen, due to both instabilities in the microscope specimen stage and electron beam-induced movement. Unlike specimen stage drift, beam-induced movement is not always homogeneous within an image. Local correlation in the trajectories of nearby particles suggests that beam-induced motion is due to deformation of the ice layer. Algorithms have already been described that can correct movement for large regions of frames and for >1MDa protein particles. Another algorithm allows individual <1MDa protein particle trajectories to be estimated, but requires rolling averages to be calculated from frames and fits linear trajectories for particles. Here we describe an algorithm that allows for individual <1MDa particle images to be aligned without frame averaging or linear trajectories. The algorithm maximizes the overall correlation of the shifted frames with the sum of the shifted frames. The optimum in this single objective function is found efficiently by making use of analytically calculated derivatives of the function. To smooth estimates of particle trajectories, rapid changes in particle positions between frames are penalized in the objective function and weighted averaging of nearby trajectories ensures local correlation in trajectories. This individual particle motion correction, in combination with weighting of Fourier components to account for increasing radiation damage in later frames, can be used to improve 3-D maps from single particle cryo-EM.","corpus_id":17501197,"score":0},{"doc_id":"26417490","title":"Camera array based light field microscopy.","abstract":"This paper proposes a novel approach for high-resolution light field microscopy imaging by using a camera array. In this approach, we apply a two-stage relay system for expanding the aperture plane of the microscope into the size of an imaging lens array, and utilize a sensor array for acquiring different sub-apertures images formed by corresponding imaging lenses. By combining the rectified and synchronized images from 5 × 5 viewpoints with our prototype system, we successfully recovered color light field videos for various fast-moving microscopic specimens with a spatial resolution of 0.79 megapixels at 30 frames per second, corresponding to an unprecedented data throughput of 562.5 MB/s for light field microscopy. We also demonstrated the use of the reported platform for different applications, including post-capture refocusing, phase reconstruction, 3D imaging, and optical metrology.","corpus_id":23832264,"score":0},{"doc_id":"26500051","title":"Modulated CMOS camera for fluorescence lifetime microscopy.","abstract":"Widefield frequency-domain fluorescence lifetime imaging microscopy (FD-FLIM) is a fast and accurate method to measure the fluorescence lifetime of entire images. However, the complexity and high costs involved in construction of such a system limit the extensive use of this technique. PCO AG recently released the first luminescence lifetime imaging camera based on a high frequency modulated CMOS image sensor, QMFLIM2. Here we tested and provide operational procedures to calibrate the camera and to improve the accuracy using corrections necessary for image analysis. With its flexible input/output options, we are able to use a modulated laser diode or a 20 MHz pulsed white supercontinuum laser as the light source. The output of the camera consists of a stack of modulated images that can be analyzed by the SimFCS software using the phasor approach. The nonuniform system response across the image sensor must be calibrated at the pixel level. This pixel calibration is crucial and needed for every camera settings, e.g. modulation frequency and exposure time. A significant dependency of the modulation signal on the intensity was also observed and hence an additional calibration is needed for each pixel depending on the pixel intensity level. These corrections are important not only for the fundamental frequency, but also for the higher harmonics when using the pulsed supercontinuum laser. With these post data acquisition corrections, the PCO CMOS-FLIM camera can be used for various biomedical applications requiring a large frame and high speed acquisition. Microsc. Res. Tech. 78:1075-1081, 2015. © 2015 Wiley Periodicals, Inc.","corpus_id":25731197,"score":0},{"doc_id":"26685238","title":"Depth Estimation Using a Sliding Camera.","abstract":"Image-based 3D reconstruction technology is widely used in different fields. The conventional algorithms are mainly based on stereo matching between two or more fixed cameras, and high accuracy can only be achieved using a large camera array, which is very expensive and inconvenient in many applications. Another popular choice is utilizing structure-from-motion methods for arbitrarily placed camera(s). However, due to too many degrees of freedom, its computational cost is heavy and its accuracy is rather limited. In this paper, we propose a novel depth estimation algorithm using a sliding camera system. By analyzing the geometric properties of the camera system, we design a camera pose initialization algorithm that can work satisfyingly with only a small number of feature points and is robust to noise. For pixels corresponding to different depths, an adaptive iterative algorithm is proposed to choose optimal frames for stereo matching, which can take advantage of continuously pose-changing imaging and save the time consumption amazingly too. The proposed algorithm can also be easily extended to handle less constrained situations (such as using a camera mounted on a moving robot or vehicle). Experimental results on both synthetic and real-world data have illustrated the effectiveness of the proposed algorithm.","corpus_id":4662274,"score":0},{"doc_id":"26697863","title":"Computation in electron microscopy.","abstract":"Some uses of the computer and computation in high-resolution transmission electron microscopy are reviewed. The theory of image calculation using Bloch wave and multislice methods with and without aberration correction is reviewed and some applications are discussed. The inverse problem of reconstructing the specimen structure from an experimentally measured electron microscope image is discussed. Some future directions of software development are given.","corpus_id":10248349,"score":0},{"doc_id":"27320661","title":"Development of automatic body condition scoring using a low-cost 3-dimensional Kinect camera.","abstract":"Body condition scoring (BCS) is a farm-management tool for estimating dairy cows' energy reserves. Today, BCS is performed manually by experts. This paper presents a 3-dimensional algorithm that provides a topographical understanding of the cow's body to estimate BCS. An automatic BCS system consisting of a Kinect camera (Microsoft Corp., Redmond, WA) triggered by a passive infrared motion detector was designed and implemented. Image processing and regression algorithms were developed and included the following steps: (1) image restoration, the removal of noise; (2) object recognition and separation, identification and separation of the cows; (3) movie and image selection, selection of movies and frames that include the relevant data; (4) image rotation, alignment of the cow parallel to the x-axis; and (5) image cropping and normalization, removal of irrelevant data, setting the image size to 150×200 pixels, and normalizing image values. All steps were performed automatically, including image selection and classification. Fourteen individual features per cow, derived from the cows' topography, were automatically extracted from the movies and from the farm's herd-management records. These features appear to be measurable in a commercial farm. Manual BCS was performed by a trained expert and compared with the output of the training set. A regression model was developed, correlating the features with the manual BCS references. Data were acquired for 4 d, resulting in a database of 422 movies of 101 cows. Movies containing cows' back ends were automatically selected (389 movies). The data were divided into a training set of 81 cows and a test set of 20 cows; both sets included the identical full range of BCS classes. Accuracy tests gave a mean absolute error of 0.26, median absolute error of 0.19, and coefficient of determination of 0.75, with 100% correct classification within 1 step and 91% correct classification within a half step for BCS classes. Results indicated good repeatability, with all standard deviations under 0.33. The algorithm is independent of the background and requires 10 cows for training with approximately 30 movies of 4 s each.","corpus_id":42557141,"score":0},{"doc_id":"27828094","title":"Detection and removal of fence occlusions in an image using a video of the static/dynamic scene.","abstract":"The advent of inexpensive smartphones/tablets/phablets equipped with cameras has resulted in the average person capturing cherished moments as images/videos and sharing them on the internet. However, at several locations, an amateur photographer may be frustrated with the captured images. For example, the object of interest to the photographer might be occluded or fenced. Currently available image de-fencing methods in the literature are limited by non-robust fence detection and can handle only static occluded scenes whose video is captured by constrained camera motion. In this work, we propose an algorithm to obtain a de-fenced image using a few frames from a video of the occluded static or dynamic scene. We also present a new fenced image database captured under challenging scenarios such as clutter, poor lighting, viewpoint distortion, etc. Initially, we propose a supervised learning-based approach to detect fence pixels and validate its performance with qualitative as well as quantitative results. We rely on the idea that freehand panning of the fenced scene is likely to render visible hidden pixels of the reference frame in other frames of the captured video. Our approach necessitates the solution of three problems: (i) detection of spatial locations of fences/occlusions in the frames of the video, (ii) estimation of relative motion between the observations, and (iii) data fusion to fill in occluded pixels in the reference image. We assume the de-fenced image as a Markov random field and obtain its maximum a posteriori estimate by solving the corresponding inverse problem. Several experiments on synthetic and real-world data demonstrate the effectiveness of the proposed approach.","corpus_id":9745398,"score":0},{"doc_id":"28439538","title":"Adaptive foveated single-pixel imaging with dynamic supersampling.","abstract":"In contrast to conventional multipixel cameras, single-pixel cameras capture images using a single detector that measures the correlations between the scene and a set of patterns. However, these systems typically exhibit low frame rates, because to fully sample a scene in this way requires at least the same number of correlation measurements as the number of pixels in the reconstructed image. To mitigate this, a range of compressive sensing techniques have been developed which use a priori knowledge to reconstruct images from an undersampled measurement set. Here, we take a different approach and adopt a strategy inspired by the foveated vision found in the animal kingdom-a framework that exploits the spatiotemporal redundancy of many dynamic scenes. In our system, a high-resolution foveal region tracks motion within the scene, yet unlike a simple zoom, every frame delivers new spatial information from across the entire field of view. This strategy rapidly records the detail of quickly changing features in the scene while simultaneously accumulating detail of more slowly evolving regions over several consecutive frames. This architecture provides video streams in which both the resolution and exposure time spatially vary and adapt dynamically in response to the evolution of the scene. The degree of local frame rate enhancement is scene-dependent, but here, we demonstrate a factor of 4, thereby helping to mitigate one of the main drawbacks of single-pixel imaging techniques. The methods described here complement existing compressive sensing approaches and may be applied to enhance computational imagers that rely on sequential correlation measurements.","corpus_id":5196689,"score":0},{"doc_id":"28862618","title":"The EIGER detector for low-energy electron microscopy and photoemission electron microscopy.","abstract":"EIGER is a single-photon-counting hybrid pixel detector developed at the Paul Scherrer Institut, Switzerland. It is designed for applications at synchrotron light sources with photon energies above 5 keV. Features of EIGER include a small pixel size (75 µm × 75 µm), a high frame rate (up to 23 kHz), a small dead-time between frames (down to 3 µs) and a dynamic range up to 32-bit. In this article, the use of EIGER as a detector for electrons in low-energy electron microscopy (LEEM) and photoemission electron microscopy (PEEM) is reported. It is demonstrated that, with only a minimal modification to the sensitive part of the detector, EIGER is able to detect electrons emitted or reflected by the sample and accelerated to 8-20 keV. The imaging capabilities are shown to be superior to the standard microchannel plate detector for these types of applications. This is due to the much higher signal-to-noise ratio, better homogeneity and improved dynamic range. In addition, the operation of the EIGER detector is not affected by radiation damage from electrons in the present energy range and guarantees more stable performance over time. To benchmark the detector capabilities, LEEM experiments are performed on selected surfaces and the magnetic and electronic properties of individual iron nanoparticles with sizes ranging from 8 to 22 nm are detected using the PEEM endstation at the Surface/Interface Microscopy (SIM) beamline of the Swiss Light Source.","corpus_id":206357833,"score":0},{"doc_id":"28863668","title":"Gain depletion of X-ray framing camera.","abstract":"X-ray imaging is very useful to investigate imploded core plasma in inertial fusion experiments. We can obtain information from X-ray images, such as shape, density, and temperature. An X-ray framing camera (XFC) capable of taking two-dimensional, time-resolved X-ray images is used to capture the images. In previous work, we developed a numerical model of an XFC to analyze its X-ray image. The calculated results agreed qualitatively with experimental results. However, it was not accurate enough to determine the absolute value of the signal. We thought this discrepancy was caused by gain depletion. In high energy laser experiments, high photon flux may cause gain depletion. This is a problem for accurate X-ray measurement. In this paper, we report our new model, including gain depletion. The new model is evaluated by tabletop laser experiments and high energy laser experiments. The results calculated using the new model agree quantitatively with our experimental results. Furthermore, we confirmed that gain depletion occurs in our high energy laser experiments. For quantitatively accurate X-ray intensity measurements, the XFC should be used with limited incident photon flux such that the gain linearity is guaranteed.","corpus_id":24611389,"score":0},{"doc_id":"29324929","title":"Our solution for fusion of simultaneusly acquired whole body scintigrams and optical images, as usesful tool in clinical practice in patients with differentiated thyroid carcinomas after radioiodine therapy. A useful tool in clinical practice.","abstract":"OBJECTIVE: After radioiodine therapy of differentiated thyroid cancer (DTC) patients, whole body scintigraphy (WBS) is standard procedure before releasing the patient from the hospital. A common problem is the precise localization of regions where the iod-avide tissue is located. Sometimes is practically impossible to perform precise topographic localization of such regions. METHOD: In order to face this problem, we have developed a low-cost Vision-Fusion system for web-camera image acquisition simultaneously with routine scintigraphic whole body acquisition including the algorithm for fusion of images given from both cameras. For image acquisition in the gamma part of the spectra we used e.cam dual head gamma camera (Siemens, Erlangen, Germany) in WBS modality, with matrix size of 256×1024 pixels and bed speed of 6cm/min, equipped with high energy collimator. For optical image acquisition in visible part of spectra we have used web-camera model C905 (Logitech, USA) with Carl Zeiss® optics, native resolution 1600×1200 pixels, 34o field of view, 30g weight, with autofocus option turned \"off\" and auto white balance turned \"on\". Web camera is connected to upper head of gamma camera (GC) by a holder of lightweight aluminum rod and a plexiglas adapter. Our own Vision-Fusion software for image acquisition and coregistration was developed using NI LabVIEW programming environment 2015 (National Instruments, Texas, USA) and two additional LabVIEW modules: NI Vision Acquisition Software (VAS) and NI Vision Development Module (VDM). Vision acquisition software enables communication and control between laptop computer and web-camera. Vision development module is image processing library used for image preprocessing and fusion. Software starts the web-camera image acquisition before starting image acquisition on GC and stops it when GC completes the acquisition. Web-camera is in continuous acquisition mode with frame rate f depending on speed of patient bed movement v (f=v/∆cm, where ∆cm is a displacement step that can be changed in Settings option of Vision-Fusion software; by default, ∆cm is set to 1cm corresponding to ∆p=15 pixels). All images captured while patient's bed is moving are processed. Movement of patient's bed is checked using cross-correlation of two successive images. After each image capturing, algorithm extracts the central region of interest (ROI) of the image, with the same width as captured image (1600 pixels) and the height that is equal to the ∆p displacement in pixels. All extracted central ROI are placed next to each other in the overall whole-body image. Stacking of narrow central ROI introduces negligible distortion in the overall whole-body image. The first step for fusion of the scintigram and the optical image was determination of spatial transformation between them. We have made an experiment with two markers (point radioactivity sources of 99mTc pertechnetate 1MBq) visible in both images (WBS and optical) to find transformation of coordinates between images. The distance between point markers is used for spatial coregistration of the gamma and optical images. At the end of coregistration process, gamma image is rescaled in spatial domain and added to the optical image (green or red channel, amplification changeable from user interface). SUBJECTS: We tested our system for 10 patients with DTC who received radioiodine therapy (8 women and two men, with average age of 50.10±12.26 years). Five patients received 5.55Gbq, three 3.70GBq and two 1.85GBq. Whole-body scintigraphy and optical image acquisition were performed 72 hours after application of radioiodine therapy. CONCLUSION: Based on our first results during clinical testing of our system, we can conclude that our system can improve diagnostic possibility of whole body scintigraphy to detect thyroid remnant tissue in patients with DTC after radioiodine therapy.","corpus_id":43376373,"score":0},{"doc_id":"29603952","title":"Joint camera blur and pose estimation from aliased data.","abstract":"A joint-estimation algorithm is presented that enables simultaneous camera blur and pose estimation from a known calibration target in the presence of aliasing. Specifically, a parametric maximum-likelihood (ML) point-spread function estimate is derived for characterizing a camera's optical imperfections through the use of a calibration target in an otherwise loosely controlled environment. The imaging perspective, ambient-light levels, target reflectance, detector gain and offset, quantum efficiency, and read-noise levels are all treated as nuisance parameters. The Cramér-Rao bound is derived, and simulations demonstrate that the proposed estimator achieves near optimal mean squared error performance. The proposed method is applied to experimental data to validate the fidelity of the forward models as well as to establish the utility of the resulting ML estimates for both system identification and subsequent image restoration.","corpus_id":4590504,"score":0}],"string":"[\n {\n \"doc_id\": \"18195445\",\n \"title\": \"Blind camera fingerprinting and image clustering.\",\n \"abstract\": \"Previous studies have shown how to \\\"fingerprint\\\" a digital camera given a set of images known to come from the camera. A clustering technique is proposed to construct such fingerprints from a mixed set of images, enabling identification of each image's source camera without any prior knowledge of source.\",\n \"corpus_id\": 18523431,\n \"score\": 2\n },\n {\n \"doc_id\": \"19104544\",\n \"title\": \"Robust autonomous detection of the defective pixels in detectors using a probabilistic technique.\",\n \"abstract\": \"Detection of defective pixels in solid-state detectors/sensor arrays has received limited research attention. Few approaches currently exist for detecting the defective pixels using real images captured with cameras equipped with such detectors, and they are ad hoc and limited in their applicability. In this paper, we present a probabilistic novel integrated technique for autonomously detecting the defective pixels in image sensor arrays. It can be applied to images containing rich scene information, captured with any digital camera equipped with a solid-state detector, to detect different kinds of defective pixels in the detector. We apply our technique to the detection of various defective pixels in an experimental camera equipped with a charge coupled device (CCD) array and two out of the four HgCdTe detectors of the UKIRT's wide field camera (WFCAM) used for infrared (IR) astronomy [Astron. Astrophys.467, 777-784 (2007)].\",\n \"corpus_id\": 8516427,\n \"score\": 2\n },\n {\n \"doc_id\": \"20057054\",\n \"title\": \"A toolkit for the characterization of CCD cameras for transmission electron microscopy.\",\n \"abstract\": \"Charge-coupled devices (CCD) are nowadays commonly utilized in transmission electron microscopy (TEM) for applications in life sciences. Direct access to digitized images has revolutionized the use of electron microscopy, sparking developments such as automated collection of tomographic data, focal series, random conical tilt pairs and ultralarge single-particle data sets. Nevertheless, for ultrahigh-resolution work photographic plates are often still preferred. In the ideal case, the quality of the recorded image of a vitrified biological sample would solely be determined by the counting statistics of the limited electron dose the sample can withstand before beam-induced alterations dominate. Unfortunately, the image is degraded by the non-ideal point-spread function of the detector, as a result of a scintillator coupled by fibre optics to a CCD, and the addition of several inherent noise components. Different detector manufacturers provide different types of figures of merit when advertising the quality of their detector. It is hard for most laboratories to verify whether all of the anticipated specifications are met. In this report, a set of algorithms is presented to characterize on-axis slow-scan large-area CCD-based TEM detectors. These tools have been added to a publicly available image-processing toolbox for MATLAB. Three in-house CCD cameras were carefully characterized, yielding, among others, statistics for hot and bad pixels, the modulation transfer function, the conversion factor, the effective gain and the detective quantum efficiency. These statistics will aid data-collection strategy programs and provide prior information for quantitative imaging. The relative performance of the characterized detectors is discussed and a comparison is made with similar detectors that are used in the field of X-ray crystallography.\",\n \"corpus_id\": -1,\n \"score\": 2\n },\n {\n \"doc_id\": \"20382479\",\n \"title\": \"Characterization of a direct detection device imaging camera for transmission electron microscopy.\",\n \"abstract\": \"The complete characterization of a novel direct detection device (DDD) camera for transmission electron microscopy is reported, for the first time at primary electron energies of 120 and 200 keV. Unlike a standard charge coupled device (CCD) camera, this device does not require a scintillator. The DDD transfers signal up to 65 lines/mm providing the basis for a high-performance platform for a new generation of wide field-of-view high-resolution cameras. An image of a thin section of virus particles is presented to illustrate the substantially improved performance of this sensor over current indirectly coupled CCD cameras.\",\n \"corpus_id\": 19834016,\n \"score\": 2\n },\n {\n \"doc_id\": \"21524337\",\n \"title\": \"Electronic detectors for electron microscopy.\",\n \"abstract\": \"Electron microscopy (EM) is an important tool for high-resolution structure determination in applications ranging from condensed matter to biology. Electronic detectors are now used in most applications in EM as they offer convenience and immediate feedback that is not possible with film or image plates. The earliest forms of electronic detector used routinely in transmission electron microscopy (TEM) were charge coupled devices (CCDs) and for many applications these remain perfectly adequate. There are however applications, such as the study of radiation-sensitive biological samples, where film is still used and improved detectors would be of great value. The emphasis in this review is therefore on detectors for use in such applications. Two of the most promising candidates for improved detection are: monolithic active pixel sensors (MAPS) and hybrid pixel detectors (of which Medipix2 was chosen for this study). From the studies described in this review, a back-thinned MAPS detector appears well suited to replace film in for the study of radiation-sensitive samples at 300 keV, while Medipix2 is suited to use at lower energies and especially in situations with very low count rates. The performance of a detector depends on the energy of electrons to be recorded, which in turn is dependent on the application it is being used for; results are described for a wide range of electron energies ranging from 40 to 300 keV. The basic properties of detectors are discussed in terms of their modulation transfer function (MTF) and detective quantum efficiency (DQE) as a function of spatial frequency.\",\n \"corpus_id\": 34044951,\n \"score\": 2\n },\n {\n \"doc_id\": \"21619932\",\n \"title\": \"Practical performance evaluation of a 10k × 10k CCD for electron cryo-microscopy.\",\n \"abstract\": \"Electron cryo-microscopy (cryo-EM) images are commonly collected using either charge-coupled devices (CCD) or photographic film. Both film and the current generation of 16 megapixel (4k × 4k) CCD cameras have yielded high-resolution structures. Yet, despite the many advantages of CCD cameras, more than two times as many structures of biological macromolecules have been published in recent years using photographic film. The continued preference to film, especially for subnanometer-resolution structures, may be partially influenced by the finer sampling and larger effective specimen imaging area offered by film. Large format digital cameras may finally allow them to overtake film as the preferred detector for cryo-EM. We have evaluated a 111-megapixel (10k × 10k) CCD camera with a 9 μm pixel size. The spectral signal-to-noise ratios of low dose images of carbon film indicate that this detector is capable of providing signal up to at least 2/5 Nyquist frequency potentially retrievable for 3D reconstructions of biological specimens, resulting in more than double the effective specimen imaging area of existing 4k × 4k CCD cameras. We verified our estimates using frozen-hydrated ε15 bacteriophage as a biological test specimen with previously determined structure, yielding a ∼7 Å resolution single particle reconstruction from only 80 CCD frames. Finally, we explored the limits of current CCD technology by comparing the performance of this detector to various CCD cameras used for recording data yielding subnanometer resolution cryo-EM structures submitted to the electron microscopy data bank (http://www.emdatabank.org/).\",\n \"corpus_id\": 206492149,\n \"score\": 2\n },\n {\n \"doc_id\": \"22149850\",\n \"title\": \"Technical Note: modification of the standard gain correction algorithm to compensate for the number of used reference flat frames in detector performance studies.\",\n \"abstract\": \"PURPOSE: The x-ray performance evaluation of digital x-ray detectors is based on the calculation of the modulation transfer function (MTF), the noise power spectrum (NPS), and the resultant detective quantum efficiency (DQE). The flat images used for the extraction of the NPS should not contain any fixed pattern noise (FPN) to avoid contamination from nonstochastic processes. The \\\"gold standard\\\" method used for the reduction of the FPN (i.e., the different gain between pixels) in linear x-ray detectors is based on normalization with an average reference flat-field. However, the noise in the corrected image depends on the number of flat frames used for the average flat image. The aim of this study is to modify the standard gain correction algorithm to make it independent on the used reference flat frames. METHODS: Many publications suggest the use of 10-16 reference flat frames, while other studies use higher numbers (e.g., 48 frames) to reduce the propagated noise from the average flat image. This study quantifies experimentally the effect of the number of used reference flat frames on the NPS and DQE values and appropriately modifies the gain correction algorithm to compensate for this effect. RESULTS: It is shown that using the suggested gain correction algorithm a minimum number of reference flat frames (i.e., down to one frame) can be used to eliminate the FPN from the raw flat image. This saves computer memory and time during the x-ray performance evaluation. CONCLUSIONS: The authors show that the method presented in the study (a) leads to the maximum DQE value that one would have by using the conventional method and very large number of frames and (b) has been compared to an independent gain correction method based on the subtraction of flat-field images, leading to identical DQE values. They believe this provides robust validation of the proposed method.\",\n \"corpus_id\": 21340859,\n \"score\": 2\n },\n {\n \"doc_id\": \"22164102\",\n \"title\": \"Range camera self-calibration based on integrated bundle adjustment via joint setup with a 2D digital camera.\",\n \"abstract\": \"Time-of-flight cameras, based on photonic mixer device (PMD) technology, are capable of measuring distances to objects at high frame rates, however, the measured ranges and the intensity data contain systematic errors that need to be corrected. In this paper, a new integrated range camera self-calibration method via joint setup with a digital (RGB) camera is presented. This method can simultaneously estimate the systematic range error parameters as well as the interior and external orientation parameters of the camera. The calibration approach is based on photogrammetric bundle adjustment of observation equations originating from collinearity condition and a range errors model. Addition of a digital camera to the calibration process overcomes the limitations of small field of view and low pixel resolution of the range camera. The tests are performed on a dataset captured by a PMD[vision]-O3 camera from a multi-resolution test field of high contrast targets. An average improvement of 83% in RMS of range error and 72% in RMS of coordinate residual, over that achieved with basic calibration, was realized in an independent accuracy assessment. Our proposed calibration method also achieved 25% and 36% improvement on RMS of range error and coordinate residual, respectively, over that obtained by integrated calibration of the single PMD camera.\",\n \"corpus_id\": 11319237,\n \"score\": 2\n },\n {\n \"doc_id\": \"23747527\",\n \"title\": \"Ranking TEM cameras by their response to electron shot noise.\",\n \"abstract\": \"We demonstrate two ways in which the Fourier transforms of images that consist solely of randomly distributed electrons (shot noise) can be used to compare the relative performance of different electronic cameras. The principle is to determine how closely the Fourier transform of a given image does, or does not, approach that of an image produced by an ideal camera, i.e. one for which single-electron events are modeled as Kronecker delta functions located at the same pixels where the electrons were incident on the camera. Experimentally, the average width of the single-electron response is characterized by fitting a single Lorentzian function to the azimuthally averaged amplitude of the Fourier transform. The reciprocal of the spatial frequency at which the Lorentzian function falls to a value of 0.5 provides an estimate of the number of pixels at which the corresponding line-spread function falls to a value of 1/e. In addition, the excess noise due to stochastic variations in the magnitude of the response of the camera (for single-electron events) is characterized by the amount to which the appropriately normalized power spectrum does, or does not, exceed the total number of electrons in the image. These simple measurements provide an easy way to evaluate the relative performance of different cameras. To illustrate this point we present data for three different types of scintillator-coupled camera plus a silicon-pixel (direct detection) camera.\",\n \"corpus_id\": 21295829,\n \"score\": 2\n },\n {\n \"doc_id\": \"23748163\",\n \"title\": \"Noise models and cryo-EM drift correction with a direct-electron camera.\",\n \"abstract\": \"Blurring due to specimen-holder drift is a common occurrence in cryo-EM images. Cameras employing active-pixel sensors are capable of high frame rates such that a single low-dose exposure can be acquired as a series of frames. In this paper we consider the possibility of tracking and compensating for overall drift in typical single-particle specimens through the analysis of frame sequences. A problem that arises in tracking through cross-correlation of frames obtained with the DE-12 camera from Direct Electron LLC is the presence of \\\"hot-pixel noise\\\". This random pattern of bright pixels is highly correlated among frames. We show how a model of this noise can be employed to greatly reduce its effects. A filter function is derived that optimizes the tracking of image shifts by cross-correlation, and we demonstrate the tracking of specimen drift in typical cryo-EM specimens.\",\n \"corpus_id\": 37435159,\n \"score\": 2\n },\n {\n \"doc_id\": \"24189638\",\n \"title\": \"Quantitative characterization of electron detectors for transmission electron microscopy.\",\n \"abstract\": \"A new generation of direct electron detectors for transmission electron microscopy (TEM) promises significant improvement over previous detectors in terms of their modulation transfer function (MTF) and detective quantum efficiency (DQE). However, the performance of these new detectors needs to be carefully monitored in order to optimize imaging conditions and check for degradation over time. We have developed an easy-to-use software tool, FindDQE, to measure MTF and DQE of electron detectors using images of a microscope's built-in beam stop. Using this software, we have determined the DQE curves of four direct electron detectors currently available: the Gatan K2 Summit, the FEI Falcon I and II, and the Direct Electron DE-12, under a variety of total dose and dose rate conditions. We have additionally measured the curves for the Gatan US4000 and TVIPS TemCam-F416 scintillator-based cameras. We compare the results from our new method with published curves.\",\n \"corpus_id\": 32106926,\n \"score\": 2\n },\n {\n \"doc_id\": \"25186400\",\n \"title\": \"Reduction of ring artifacts in CBCT: detection and correction of pixel gain variations in flat panel detectors.\",\n \"abstract\": \"PURPOSE: In using flat panel detectors (FPD) for cone beam computed tomography (CBCT), pixel gain variations may lead to structured nonuniformities in projections and ring artifacts in CBCT images. Such gain variations can be caused by change in detector entrance exposure levels or beam hardening, and they are not accounted by conventional flat field correction methods. In this work, the authors presented a method to identify isolated pixel clusters that exhibit gain variations and proposed a pixel gain correction (PGC) method to suppress both beam hardening and exposure level dependent gain variations. METHODS: To modulate both beam spectrum and entrance exposure, flood field FPD projections were acquired using beam filters with varying thicknesses. \\\" Ideal\\\" pixel values were estimated by performing polynomial fits in both raw and flat field corrected projections. Residuals were calculated by taking the difference between measured and ideal pixel values to identify clustered image and FPD artifacts in flat field corrected and raw images, respectively. To correct clustered image artifacts, the ratio of ideal to measured pixel values in filtered images were utilized as pixel-specific gain correction factors, referred as PGC method, and they were tabulated as a function of pixel value in a look-up table. RESULTS: 0.035% of detector pixels lead to clustered image artifacts in flat field corrected projections, where 80% of these pixels were traced back and linked to artifacts in the FPD. The performance of PGC method was tested in variety of imaging conditions and phantoms. The PGC method reduced clustered image artifacts and fixed pattern noise in projections, and ring artifacts in CBCT images. CONCLUSIONS: Clustered projection image artifacts that lead to ring artifacts in CBCT can be better identified with our artifact detection approach. When compared to the conventional flat field correction method, the proposed PGC method enables characterization of nonlinear pixel gain variations as a function of change in x-ray spectrum and intensity. Hence, it can better suppress image artifacts due to beam hardening as well as artifacts that arise from detector entrance exposure variation.\",\n \"corpus_id\": 27003539,\n \"score\": 2\n },\n {\n \"doc_id\": \"25194828\",\n \"title\": \"Comparison of optimal performance at 300keV of three direct electron detectors for use in low dose electron microscopy.\",\n \"abstract\": \"Low dose electron imaging applications such as electron cryo-microscopy are now benefitting from the improved performance and flexibility of recently introduced electron imaging detectors in which electrons are directly incident on backthinned CMOS sensors. There are currently three commercially available detectors of this type: the Direct Electron DE-20, the FEI Falcon II and the Gatan K2 Summit. These have different characteristics and so it is important to compare their imaging properties carefully with a view to optimise how each is used. Results at 300keV for both the modulation transfer function (MTF) and the detective quantum efficiency (DQE) are presented. Of these, the DQE is the most important in the study of radiation sensitive samples where detector performance is crucial. We find that all three detectors have a better DQE than film. The K2 Summit has the best DQE at low spatial frequencies but with increasing spatial frequency its DQE falls below that of the Falcon II.\",\n \"corpus_id\": 8670203,\n \"score\": 2\n },\n {\n \"doc_id\": \"26431895\",\n \"title\": \"FEI's direct electron detector developments: Embarking on a revolution in cryo-TEM.\",\n \"abstract\": \"In early 2011 FEI Company launched the \\\"Falcon\\\", its first commercial direct electron detector product intended for application in 3-D electron microscopy in the life sciences. In this paper we discuss the principle of direct electron detection and its implementation in Falcon cameras. We describe the signal formation in the sensor and its impact on the detection quantum efficiency (DQE) of the sensor. Insights into the signal formation led us to improved camera designs. Three significant improvements are discussed. ( 1) Back thinning of the sensor. This is implemented in the second-generation Falcon (Falcon 2), where the sensor thickness is reduced to 50μm, and in the latest generation Falcon 3 detector with further back-thinning down to 30μm. ( 2) The introduction of electron counting, a signal processing technology implemented in Falcon 3. ( 3) Dose fractionation mode, which allows the user to access intermediate results during the illumination of the sample.\",\n \"corpus_id\": 24692393,\n \"score\": 2\n },\n {\n \"doc_id\": \"28517660\",\n \"title\": \"SU-E-I-103: Detecting Anomalous Pixels and Correlated Artifacts in Digital Detectors from Flat-Field Images.\",\n \"abstract\": \"PURPOSE: Anomalous pixels may be defined as those pixels whose exposure response relationship is deviant from the typical, expected or calibrated response. A group of anomalous pixels may Result in visible correlated artifacts. Here we demonstrate an approach to identify anomalous pixels and correlated artifacts using flat-field images. METHODS: Using manufacturer specific calibration geometry, sets of four flat-field images per detector were obtained with varying input air kerma values (0.5 to 160 μGy) from 9 digital detectors at 6 institutions. Images obtained before and after calibration, with both proper and improper gain maps and structured artifacts were additionally acquired with some detectors. Image analysis methodology under consideration by AAPM Task Group 150 was used. After eliminating 10mm borders, images were divided into square regions (100mm2 ). Anomalous pixels were identified as pixels within each region with valuesabove or below ±3 standard deviations (SD) relative to the mean value of the region. If these pixels were identified in all four images comprising a set, then they were reported as anomalous. Line artifacts were identified as rows and columns with cumulative profile values that were above or below ±3 SD with respect to the mean value of neighboring profiles in the set of four flat-field mages. Results were verified with visual inspection of the images. RESULTS: For four sets of images, the algorithm did not identify any anomalous pixels, and none were spotted on visible inspection as well, while for five sets of images the identified anomalous pixels matched visual inspection results. Anomalous pixel detection failed in regions with an unusually large number of defects and structured noise, since those regions exhibited relatively large SD. Line artifacts consistent with visual analysis were identified correctly when present. CONCLUSIONS: A practical approach to identify anomalous pixels and correlated artifacts from flat-field images is demonstrated.\",\n \"corpus_id\": 25428110,\n \"score\": 2\n },\n {\n \"doc_id\": \"18447528\",\n \"title\": \"A charge coupled device camera with electron decelerator for intermediate voltage electron microscopy.\",\n \"abstract\": \"Electron microscopists are increasingly turning to intermediate voltage electron microscopes (IVEMs) operating at 300-400 kV for a wide range of studies. They are also increasingly taking advantage of slow-scan charge coupled device (CCD) cameras, which have become widely used on electron microscopes. Under some conditions, CCDs provide an improvement in data quality over photographic film, as well as the many advantages of direct digital readout. However, CCD performance is seriously degraded on IVEMs compared to the more conventional 100 kV microscopes. In order to increase the efficiency and quality of data recording on IVEMs, we have developed a CCD camera system in which the electrons are decelerated to below 100 kV before impacting the camera, resulting in greatly improved performance in both signal quality and resolution compared to other CCDs used in electron microscopy. These improvements will allow high-quality image and diffraction data to be collected directly with the CCD, enabling improvements in data collection for applications including high-resolution electron crystallography, single particle reconstruction of protein structures, tomographic studies of cell ultrastructure, and remote microscope operation. This approach will enable us to use even larger format CCD chips that are being developed with smaller pixels.\",\n \"corpus_id\": 19557303,\n \"score\": 1\n },\n {\n \"doc_id\": \"18805922\",\n \"title\": \"Analysis of molecular concentration and brightness from fluorescence fluctuation data with an electron multiplied CCD camera.\",\n \"abstract\": \"We demonstrate the calculation of particle brightness and concentration from fluorescence-fluctuation photon-counting statistics using an electron-multiplied charge-coupled device (EMCCD) camera. This technique provides a concentration-independent measure of particle brightness in dynamic systems. The high sensitivity and highly parallel detection of EMCCD cameras allow for imaging of dynamic particle brightness, providing the capability to follow aggregation reactions in real time. A critical factor of the EMCCD camera is the presence of nonlinearity at high intensities. These nonlinearities arise due to limited capacity of the CCD well and to the analog-to-digital converter maximum range. However, we show that the specific camera we used (with a 16-bit analog-to-digital converter) has sufficient dynamic range for most microscopy applications. In addition, we explore the importance of camera timing behavior as it is affected by the vertical frame transfer speed of the camera. Although the camera has microsecond exposure time for illumination of a few pixels, the exposure time increased to milliseconds for full-field illumination. Finally, we demonstrate the ability of the technique to follow concentration changes and measure single-molecule brightness in real time in living cells.\",\n \"corpus_id\": 42330095,\n \"score\": 1\n },\n {\n \"doc_id\": \"20378810\",\n \"title\": \"Four-dimensional electron microscopy.\",\n \"abstract\": \"The discovery of the electron over a century ago and the realization of its dual character have given birth to one of the two most powerful imaging instruments: the electron microscope. The electron microscope's ability to resolve three-dimensional (3D) structures on the atomic scale is continuing to affect different fields, including materials science and biology. In this Review, we highlight recent developments and inventions made by introducing the fourth dimension of time in electron microscopy. Today, ultrafast electron microscopy (4D UEM) enables a resolution that is 10 orders of magnitude better than that of conventional microscopes, which are limited by the video-camera rate of recording. After presenting the central concept involved, that of single-electron stroboscopic imaging, we discuss prototypical applications, which include the visualization of complex structures when unfolding on different length and time scales. The developed UEM variant techniques are several, and here we illucidate convergent-beam and near-field imaging, as well as tomography and scanning-pulse microscopy. We conclude with current explorations in imaging of nanomaterials and biostructures and an outlook on possible future directions in space-time, 4D electron microscopy.\",\n \"corpus_id\": 5449372,\n \"score\": 1\n },\n {\n \"doc_id\": \"23426864\",\n \"title\": \"Direct detection pays off for electron cryo-microscopy.\",\n \"abstract\": \"Improved electron detectors and image-processing techniques will allow the structures of macromolecules to be determined from tens of thousands of single-particle cryo-EM images, rather than the hundreds of thousands needed previously.\",\n \"corpus_id\": 12668402,\n \"score\": 1\n },\n {\n \"doc_id\": \"23931506\",\n \"title\": \"Practical aspects of adjusting digital cameras.\",\n \"abstract\": \"This chapter introduces the adjustment of digital camera settings using the tools found within image acquisition software and discusses measuring gray-level information such as (1) the histogram, (2) line scan, and (3) other strategies. The pixel values in an image can be measured within many image capture software programs in two ways. The first is a histogram of pixel gray values and the second is a line-scan plot across a selectable axis of the image. Understanding how to evaluate the information presented by these tools is critical to properly adjusting the camera to maximize the image contrast without losing grayscale information. This chapter discusses the 0-255 grayscale resolution of an 8-bit camera; however, the concepts are the same for cameras of any bit depth. This chapter also describes camera settings, such as exposure time, offset, and gain, and the steps for contrast stretching such as setting the exposure time, adjusting offset and gain, and camera versus image display controls.\",\n \"corpus_id\": 28794853,\n \"score\": 1\n },\n {\n \"doc_id\": \"23931507\",\n \"title\": \"Cameras for digital microscopy.\",\n \"abstract\": \"This chapter reviews the fundamental characteristics of charge-coupled devices (CCDs) and related detectors, outlines the relevant parameters for their use in microscopy, and considers promising recent developments in the technology of detectors. Electronic imaging with a CCD involves three stages--interaction of a photon with the photosensitive surface, storage of the liberated charge, and readout or measurement of the stored charge. The most demanding applications in fluorescence microscopy may require as much as four orders of greater magnitude sensitivity. The image in the present-day light microscope is usually acquired with a CCD camera. The CCD is composed of a large matrix of photosensitive elements (often referred to as \\\"pixels\\\" shorthand for picture elements, which simultaneously capture an image over the entire detector surface. The light-intensity information for each pixel is stored as electronic charge and is converted to an analog voltage by a readout amplifier. This analog voltage is subsequently converted to a numerical value by a digitizer situated on the CCD chip, or very close to it. Several (three to six) amplifiers are required for each pixel, and to date, uniform images with a homogeneous background have been a problem because of the inherent difficulties of balancing the gain in all of the amplifiers. Complementary metal oxide semiconductor sensors also exhibit relatively high noise associated with the requisite high-speed switching. Both of these deficiencies are being addressed, and sensor performance is nearing that required for scientific imaging.\",\n \"corpus_id\": 205144142,\n \"score\": 1\n },\n {\n \"doc_id\": \"23931509\",\n \"title\": \"Electronic cameras for low-light microscopy.\",\n \"abstract\": \"This chapter introduces to electronic cameras, discusses the various parameters considered for evaluating their performance, and describes some of the key features of different camera formats. The chapter also presents the basic understanding of functioning of the electronic cameras and how these properties can be exploited to optimize image quality under low-light conditions. Although there are many types of cameras available for microscopy, the most reliable type is the charge-coupled device (CCD) camera, which remains preferred for high-performance systems. If time resolution and frame rate are of no concern, slow-scan CCDs certainly offer the best available performance, both in terms of the signal-to-noise ratio and their spatial resolution. Slow-scan cameras are thus the first choice for experiments using fixed specimens such as measurements using immune fluorescence and fluorescence in situ hybridization. However, if video rate imaging is required, one need not evaluate slow-scan CCD cameras. A very basic video CCD may suffice if samples are heavily labeled or are not perturbed by high intensity illumination. When video rate imaging is required for very dim specimens, the electron multiplying CCD camera is probably the most appropriate at this technological stage. Intensified CCDs provide a unique tool for applications in which high-speed gating is required. The variable integration time video cameras are very attractive options if one needs to acquire images at video rate acquisition, as well as with longer integration times for less bright samples. This flexibility can facilitate many diverse applications with highly varied light levels.\",\n \"corpus_id\": 29024134,\n \"score\": 1\n },\n {\n \"doc_id\": \"23968652\",\n \"title\": \"Influence of electron dose rate on electron counting images recorded with the K2 camera.\",\n \"abstract\": \"A recent technological breakthrough in electron cryomicroscopy (cryoEM) is the development of direct electron detection cameras for data acquisition. By bypassing the traditional phosphor scintillator and fiber optic coupling, these cameras have greatly enhanced sensitivity and detective quantum efficiency (DQE). Of the three currently available commercial cameras, the Gatan K2 Summit was designed specifically for counting individual electron events. Counting further enhances the DQE, allows for practical doubling of detector resolution and eliminates noise arising from the variable deposition of energy by each primary electron. While counting has many advantages, undercounting of electrons happens when more than one electron strikes the same area of the detector within the analog readout period (coincidence loss), which influences image quality. In this work, we characterized the K2 Summit in electron counting mode, and studied the relationship of dose rate and coincidence loss and its influence on the quality of counted images. We found that coincidence loss reduces low frequency amplitudes but has no significant influence on the signal-to-noise ratio of the recorded image. It also has little influence on high frequency signals. Images of frozen hydrated archaeal 20S proteasome (~700 kDa, D7 symmetry) recorded at the optimal dose rate retained both high-resolution signal and low-resolution contrast and enabled calculating a 3.6 Å three-dimensional reconstruction from only 10,000 particles.\",\n \"corpus_id\": 263553017,\n \"score\": 1\n },\n {\n \"doc_id\": \"25528571\",\n \"title\": \"Seeing tobacco mosaic virus through direct electron detectors.\",\n \"abstract\": \"With the introduction of direct electron detectors (DED) to the field of electron cryo-microscopy, a wave of atomic-resolution structures has become available. As the new detectors still require comparative characterization, we have used tobacco mosaic virus (TMV) as a test specimen to study the quality of 3D image reconstructions from data recorded on the two direct electron detector cameras, K2 Summit and Falcon II. Using DED movie frames, we explored related image-processing aspects and compared the performance of micrograph-based and segment-based motion correction approaches. In addition, we investigated the effect of dose deposition on the atomic-resolution structure of TMV and show that radiation damage affects negative carboxyl chains first in a side-chain specific manner. Finally, using 450,000 asymmetric units and limiting the effects of radiation damage, we determined a high-resolution cryo-EM map at 3.35Å resolution. Here, we provide a comparative case study of highly ordered TMV recorded on different direct electron detectors to establish recording and processing conditions that enable structure determination up to 3.2Å in resolution using cryo-EM.\",\n \"corpus_id\": 20499036,\n \"score\": 1\n },\n {\n \"doc_id\": \"26546989\",\n \"title\": \"Single-particle cryo-EM data acquisition by using direct electron detection camera.\",\n \"abstract\": \"Recent advances in single-particle electron cryo-microscopy (cryo-EM) were largely facilitated by the application of direct electron detection cameras. These cameras feature not only a significant improvement in detective quantum efficiency but also a high frame rate that enables images to be acquired as 'movies' made of stacks of many frames. In this review, we discuss how the applications of direct electron detection cameras in cryo-EM have changed the way the data are acquired.\",\n \"corpus_id\": 24462765,\n \"score\": 1\n },\n {\n \"doc_id\": \"26750260\",\n \"title\": \"High Dynamic Range Pixel Array Detector for Scanning Transmission Electron Microscopy.\",\n \"abstract\": \"We describe a hybrid pixel array detector (electron microscope pixel array detector, or EMPAD) adapted for use in electron microscope applications, especially as a universal detector for scanning transmission electron microscopy. The 128×128 pixel detector consists of a 500 µm thick silicon diode array bump-bonded pixel-by-pixel to an application-specific integrated circuit. The in-pixel circuitry provides a 1,000,000:1 dynamic range within a single frame, allowing the direct electron beam to be imaged while still maintaining single electron sensitivity. A 1.1 kHz framing rate enables rapid data collection and minimizes sample drift distortions while scanning. By capturing the entire unsaturated diffraction pattern in scanning mode, one can simultaneously capture bright field, dark field, and phase contrast information, as well as being able to analyze the full scattering distribution, allowing true center of mass imaging. The scattering is recorded on an absolute scale, so that information such as local sample thickness can be directly determined. This paper describes the detector architecture, data acquisition system, and preliminary results from experiments with 80-200 keV electron beams.\",\n \"corpus_id\": 5984477,\n \"score\": 1\n },\n {\n \"doc_id\": \"26950127\",\n \"title\": \"Compressive Video Recovery Using Block Match Multi-Frame Motion Estimation Based on Single Pixel Cameras.\",\n \"abstract\": \"Compressive sensing (CS) theory has opened up new paths for the development of signal processing applications. Based on this theory, a novel single pixel camera architecture has been introduced to overcome the current limitations and challenges of traditional focal plane arrays. However, video quality based on this method is limited by existing acquisition and recovery methods, and the method also suffers from being time-consuming. In this paper, a multi-frame motion estimation algorithm is proposed in CS video to enhance the video quality. The proposed algorithm uses multiple frames to implement motion estimation. Experimental results show that using multi-frame motion estimation can improve the quality of recovered videos. To further reduce the motion estimation time, a block match algorithm is used to process motion estimation. Experiments demonstrate that using the block match algorithm can reduce motion estimation time by 30%.\",\n \"corpus_id\": 702420,\n \"score\": 1\n },\n {\n \"doc_id\": \"27572725\",\n \"title\": \"Processing of Cryo-EM Movie Data.\",\n \"abstract\": \"Direct detector device (DDD) cameras dramatically enhance the capabilities of electron cryomicroscopy (cryo-EM) due to their improved detective quantum efficiency (DQE) relative to other detectors. DDDs use semiconductor technology that allows micrographs to be recorded as movies rather than integrated individual exposures. Movies from DDDs improve cryo-EM in another, more surprising, way. DDD movies revealed beam-induced specimen movement as a major source of image degradation and provide a way to partially correct the problem by aligning frames or regions of frames to account for this specimen movement. In this chapter, we use a self-consistent mathematical notation to explain, compare, and contrast several of the most popular existing algorithms for computationally correcting specimen movement in DDD movies. We conclude by discussing future developments in algorithms for processing DDD movies that would extend the capabilities of cryo-EM even further.\",\n \"corpus_id\": 3572644,\n \"score\": 1\n },\n {\n \"doc_id\": \"28372435\",\n \"title\": \"A direct electron detector for time-resolved MeV electron microscopy.\",\n \"abstract\": \"The introduction of direct electron detectors enabled the structural biology revolution of cryogenic electron microscopy. Direct electron detectors are now expected to have a similarly dramatic impact on time-resolved MeV electron microscopy, particularly by enabling both spatial and temporal jitter correction. Here we report on the commissioning of a direct electron detector for time-resolved MeV electron microscopy. The direct electron detector demonstrated MeV single electron sensitivity and is capable of recording megapixel images at 180 Hz. The detector has a 15-bit dynamic range, better than 30-μm spatial resolution and less than 20 analogue-to-digital converter count RMS pixel noise. The unique capabilities of the direct electron detector and the data analysis required to take advantage of these capabilities are presented. The technical challenges associated with generating and processing large amounts of data are also discussed.\",\n \"corpus_id\": 46882296,\n \"score\": 1\n },\n {\n \"doc_id\": \"28529964\",\n \"title\": \"Ultrafast electron microscopy integrated with a direct electron detection camera.\",\n \"abstract\": \"In the past decade, we have witnessed the rapid growth of the field of ultrafast electron microscopy (UEM), which provides intuitive means to watch atomic and molecular motions of matter. Yet, because of the limited current of the pulsed electron beam resulting from space-charge effects, observations have been mainly made to periodic motions of the crystalline structure of hundreds of nanometers or higher by stroboscopic imaging at high repetition rates. Here, we develop an advanced UEM with robust capabilities for circumventing the present limitations by integrating a direct electron detection camera for the first time which allows for imaging at low repetition rates. This approach is expected to promote UEM to a more powerful platform to visualize molecular and collective motions and dissect fundamental physical, chemical, and materials phenomena in space and time.\",\n \"corpus_id\": 31970282,\n \"score\": 1\n },\n {\n \"doc_id\": \"29482132\",\n \"title\": \"Software electron counting for low-dose scanning transmission electron microscopy.\",\n \"abstract\": \"The performance of the detector is of key importance for low-dose imaging in transmission electron microscopy, and counting every single electron can be considered as the ultimate goal. In scanning transmission electron microscopy, low-dose imaging can be realized by very fast scanning, however, this also introduces artifacts and a loss of resolution in the scan direction. We have developed a software approach to correct for artifacts introduced by fast scans, making use of a scintillator and photomultiplier response that extends over several pixels. The parameters for this correction can be directly extracted from the raw image. Finally, the images can be converted into electron counts. This approach enables low-dose imaging in the scanning transmission electron microscope via high scan speeds while retaining the image quality of artifact-free slower scans.\",\n \"corpus_id\": 3593705,\n \"score\": 1\n },\n {\n \"doc_id\": \"21428104\",\n \"title\": \"[Radiometric calibration of LCTF-based multispectral area CCD camera].\",\n \"abstract\": \"Multispectral area CCD camera based on liquid crystal tunable filter (LCTF) is a new spectral imaging system, which could record image of one wavelength on the area CCD by utilizing electrically controlled birefringence of liquid-crystal and interference principle of polarized light. Because of the special working principle of LCTF and frame transfer area CCD, the existing radiometric calibration method can not meet the precision need of remote sensing application if it is used for LCTF-camera. An improved radiometric calibration method is proposed, in which the camera performance test and calibration experiment are carried out relying on the devices of integrating sphere and standard detector, and the absolute calibration coefficient is calculated via correcting frame transfer smear and improving data process algorithm. Then the validity of the laboratory calibration coefficient is checked by a field validation experiment. Experimental result indicates that the calibration coefficient is valid, and the radiation information on the ground could be accurately inverted from the calibrated image data. With the resolution of radiometric calibration of LCTF-camera and the improvement of calibration precision, the application field of the image data acquired by the camera would be extended effectively.\",\n \"corpus_id\": 25211232,\n \"score\": 0\n },\n {\n \"doc_id\": \"21529037\",\n \"title\": \"Omnifocus video camera.\",\n \"abstract\": \"The omnifocus video camera takes videos, in which objects at different distances are all in focus in a single video display. The omnifocus video camera consists of an array of color video cameras combined with a unique distance mapping camera called the Divcam. The color video cameras are all aimed at the same scene, but each is focused at a different distance. The Divcam provides real-time distance information for every pixel in the scene. A pixel selection utility uses the distance information to select individual pixels from the multiple video outputs focused at different distances, in order to generate the final single video display that is everywhere in focus. This paper presents principle of operation, design consideration, detailed construction, and over all performance of the omnifocus video camera. The major emphasis of the paper is the proof of concept, but the prototype has been developed enough to demonstrate the superiority of this video camera over a conventional video camera. The resolution of the prototype is high, capturing even fine details such as fingerprints in the image. Just as the movie camera was a significant advance over the still camera, the omnifocus video camera represents a significant advance over all-focus cameras for still images.\",\n \"corpus_id\": 20792979,\n \"score\": 0\n },\n {\n \"doc_id\": \"21779142\",\n \"title\": \"Physical Activity Recognition Based on Motion in Images Acquired by a Wearable Camera.\",\n \"abstract\": \"A new technique to extract and evaluate physical activity patterns from image sequences captured by a wearable camera is presented in this paper. Unlike standard activity recognition schemes, the video data captured by our device do not include the wearer him/herself. The physical activity of the wearer, such as walking or exercising, is analyzed indirectly through the camera motion extracted from the acquired video frames. Two key tasks, pixel correspondence identification and motion feature extraction, are studied to recognize activity patterns. We utilize a multiscale approach to identify pixel correspondences. When compared with the existing methods such as the Good Features detector and the Speed-up Robust Feature (SURF) detector, our technique is more accurate and computationally efficient. Once the pixel correspondences are determined which define representative motion vectors, we build a set of activity pattern features based on motion statistics in each frame. Finally, the physical activity of the person wearing a camera is determined according to the global motion distribution in the video. Our algorithms are tested using different machine learning techniques such as the K-Nearest Neighbor (KNN), Naive Bayesian and Support Vector Machine (SVM). The results show that many types of physical activities can be recognized from field acquired real-world video. Our results also indicate that, with a design of specific motion features in the input vectors, different classifiers can be used successfully with similar performances.\",\n \"corpus_id\": 207102242,\n \"score\": 0\n },\n {\n \"doc_id\": \"22291543\",\n \"title\": \"Sensor for distance measurement using pixel grey-level information.\",\n \"abstract\": \"An alternative method for distance measurement is presented, based on a radiometric approach to the image formation process. The proposed methodology uses images from an infrared emitting diode (IRED) to estimate the distance between the camera and the IRED. Camera output grey-level intensities are a function of the accumulated image irradiance, which is also related by inverse distance square law to the distance between the camera and the IRED. Analyzing camera-IRED distance, magnitudes that affected image grey-level intensities, and therefore accumulated image irradiance, were integrated into a differential model which was calibrated and used for distance estimation over a 200 to 600 cm range. In a preliminary model, the camera and the emitter were aligned.\",\n \"corpus_id\": 3206542,\n \"score\": 0\n },\n {\n \"doc_id\": \"22399909\",\n \"title\": \"Real time speed estimation of moving vehicles from side view images from an uncalibrated video camera.\",\n \"abstract\": \"In order to estimate the speed of a moving vehicle with side view camera images, velocity vectors of a sufficient number of reference points identified on the vehicle must be found using frame images. This procedure involves two main steps. In the first step, a sufficient number of points from the vehicle is selected, and these points must be accurately tracked on at least two successive video frames. In the second step, by using the displacement vectors of the tracked points and passed time, the velocity vectors of those points are computed. Computed velocity vectors are defined in the video image coordinate system and displacement vectors are measured by the means of pixel units. Then the magnitudes of the computed vectors in image space should be transformed to the object space to find the absolute values of these magnitudes. This transformation requires an image to object space information in a mathematical sense that is achieved by means of the calibration and orientation parameters of the video frame images. This paper presents proposed solutions for the problems of using side view camera images mentioned here.\",\n \"corpus_id\": 17691028,\n \"score\": 0\n },\n {\n \"doc_id\": \"22402684\",\n \"title\": \"Online tracking of outdoor lighting variations for augmented reality with moving cameras.\",\n \"abstract\": \"In augmented reality, one of key tasks to achieve a convincing visual appearance consistency between virtual objects and video scenes is to have a coherent illumination along the whole sequence. As outdoor illumination is largely dependent on the weather, the lighting condition may change from frame to frame. In this paper, we propose a full image-based approach for online tracking of outdoor illumination variations from videos captured with moving cameras. Our key idea is to estimate the relative intensities of sunlight and skylight via a sparse set of planar feature-points extracted from each frame. To address the inevitable feature misalignments, a set of constraints are introduced to select the most reliable ones. Exploiting the spatial and temporal coherence of illumination, the relative intensities of sunlight and skylight are finally estimated by using an optimization process. We validate our technique on a set of real-life videos and show that the results with our estimations are visually coherent along the video sequences.\",\n \"corpus_id\": 2602599,\n \"score\": 0\n },\n {\n \"doc_id\": \"22545028\",\n \"title\": \"Image Alignment for Multiple Camera High Dynamic Range Microscopy.\",\n \"abstract\": \"This paper investigates the problem of image alignment for multiple camera high dynamic range (HDR) imaging. HDR imaging combines information from images taken with different exposure settings. Combining information from multiple cameras requires an alignment process that is robust to the intensity differences in the images. HDR applications that use a limited number of component images require an alignment technique that is robust to large exposure differences. We evaluate the suitability for HDR alignment of three exposure-robust techniques. We conclude that image alignment based on matching feature descriptors extracted from radiant power images from calibrated cameras yields the most accurate and robust solution. We demonstrate the use of this alignment technique in a high dynamic range video microscope that enables live specimen imaging with a greater level of detail than can be captured with a single camera.\",\n \"corpus_id\": 18800763,\n \"score\": 0\n },\n {\n \"doc_id\": \"22566049\",\n \"title\": \"Electron microscopy.\",\n \"abstract\": \"Correlative light (LM) and transmission electron microscopic (TEM) analysis is useful, if ultrastructural details of cells need to be related to functional aspects which can only be examined at the LM level. The first protocol presented here introduces a relatively simple way of obtaining TEM images which, on the one hand, reveal ultrastructural details of individual cells and, on the other hand, are large enough to allow a correlation with light micrographs. The second protocol describes a technique for estimating mineral densities of hard tissues using backscattered electron images obtained with a scanning electron microscope. This technique can be used to analyze the mineralization processes which occur throughout tooth formation.\",\n \"corpus_id\": 39721085,\n \"score\": 0\n },\n {\n \"doc_id\": \"22778608\",\n \"title\": \"Using the standard deviation of a region of interest in an image to estimate camera to emitter distance.\",\n \"abstract\": \"In this study, a camera to infrared diode (IRED) distance estimation problem was analyzed. The main objective was to define an alternative to measures depth only using the information extracted from pixel grey levels of the IRED image to estimate the distance between the camera and the IRED. In this paper, the standard deviation of the pixel grey level in the region of interest containing the IRED image is proposed as an empirical parameter to define a model for estimating camera to emitter distance. This model includes the camera exposure time, IRED radiant intensity and the distance between the camera and the IRED. An expression for the standard deviation model related to these magnitudes was also derived and calibrated using different images taken under different conditions. From this analysis, we determined the optimum parameters to ensure the best accuracy provided by this alternative. Once the model calibration had been carried out, a differential method to estimate the distance between the camera and the IRED was defined and applied, considering that the camera was aligned with the IRED. The results indicate that this method represents a useful alternative for determining the depth information.\",\n \"corpus_id\": 6646364,\n \"score\": 0\n },\n {\n \"doc_id\": \"22967215\",\n \"title\": \"4D electron microscopy: principles and applications.\",\n \"abstract\": \"The transmission electron microscope (TEM) is a powerful tool enabling the visualization of atoms with length scales smaller than the Bohr radius at a factor of only 20 larger than the relativistic electron wavelength of 2.5 pm at 200 keV. The ability to visualize matter at these scales in a TEM is largely due to the efforts made in correcting for the imperfections in the lens systems which introduce aberrations and ultimately limit the achievable spatial resolution. In addition to the progress made in increasing the spatial resolution, the TEM has become an all-in-one characterization tool. Indeed, most of the properties of a material can be directly mapped in the TEM, including the composition, structure, bonding, morphology, and defects. The scope of applications spans essentially all of the physical sciences and includes biology. Until recently, however, high resolution visualization of structural changes occurring on sub-millisecond time scales was not possible. In order to reach the ultrashort temporal domain within which fundamental atomic motions take place, while simultaneously retaining high spatial resolution, an entirely new approach from that of millisecond-limited TEM cameras had to be conceived. As shown below, the approach is also different from that of nanosecond-limited TEM, whose resolution cannot offer the ultrafast regimes of dynamics. For this reason \\\"ultrafast electron microscopy\\\" is reserved for the field which is concerned with femtosecond to picosecond resolution capability of structural dynamics. In conventional TEMs, electrons are produced by heating a source or by applying a strong extraction field. Both methods result in the stochastic emission of electrons, with no control over temporal spacing or relative arrival time at the specimen. The timing issue can be overcome by exploiting the photoelectric effect and using pulsed lasers to generate precisely timed electron packets of ultrashort duration. The spatial and temporal resolutions achievable with short intense pulses containing a large number of electrons, however, are limited to tens of nanometers and nanoseconds, respectively. This is because Coulomb repulsion is significant in such a pulse, and the electrons spread in space and time, thus limiting the beam coherence. It is therefore not possible to image the ultrafast elementary dynamics of complex transformations. The challenge was to retain the high spatial resolution of a conventional TEM while simultaneously enabling the temporal resolution required to visualize atomic-scale motions. In this Account, we discuss the development of four-dimensional ultrafast electron microscopy (4D UEM) and summarize techniques and applications that illustrate the power of the approach. In UEM, images are obtained either stroboscopically with coherent single-electron packets or with a single electron bunch. Coulomb repulsion is absent under the single-electron condition, thus permitting imaging, diffraction, and spectroscopy, all with high spatiotemporal resolution, the atomic scale (sub-nanometer and femtosecond). The time resolution is limited only by the laser pulse duration and energy carried by the electron packets; the CCD camera has no bearing on the temporal resolution. In the regime of single pulses of electrons, the temporal resolution of picoseconds can be attained when hundreds of electrons are in the bunch. The applications given here are selected to highlight phenomena of different length and time scales, from atomic motions during structural dynamics to phase transitions and nanomechanical oscillations. We conclude with a brief discussion of emerging methods, which include scanning ultrafast electron microscopy (S-UEM), scanning transmission ultrafast electron microscopy (ST-UEM) with convergent beams, and time-resolved imaging of biological structures at ambient conditions with environmental cells.\",\n \"corpus_id\": 2463705,\n \"score\": 0\n },\n {\n \"doc_id\": \"23132073\",\n \"title\": \"Single particle electron microscopy.\",\n \"abstract\": \"Single particle electron microscopy is a versatile technique for the structural analysis of protein complexes in near-native conditions. While tremendous progress has been made during the past few decades in techniques for specimen preparation, imaging, and image analysis, the field is still in development. In the context of this volume on electron crystallography, the following chapter gives practical guidelines on how to begin single particle EM studies, including preparing specimens, selecting imaging conditions, and choosing which of the many approaches to image analysis are appropriate for a specific sample.\",\n \"corpus_id\": 38047303,\n \"score\": 0\n },\n {\n \"doc_id\": \"23797254\",\n \"title\": \"Digital multi-focusing from a single photograph taken with an uncalibrated conventional camera.\",\n \"abstract\": \"The demand to restore all-in-focus images from defocused images and produce photographs focused at different depths is emerging in more and more cases, such as low-end hand-held cameras and surveillance cameras. In this paper, we manage to solve this challenging multi-focusing problem with a single image taken with an uncalibrated conventional camera. Different from all existing multi-focusing approaches, our method does not need to include a deconvolution process, which is quite time-consuming and will cause ringing artifacts in the focused region and low depth-of-field. This paper proposes a novel systematic approach to realize multi-focusing from a single photograph. First of all, with the optical explanation for the local smooth assumption, we present a new point-to-point defocus model. Next, the blur map of the input image, which reflects the amount of defocus blur at each pixel in the image, is estimated by two steps. 1) With the sharp edge prior, a rough blur map is obtained by estimating the blur amount at the edge regions. 2) The guided image filter is applied to propagate the blur value from the edge regions to the whole image by which a refined blur map is obtained. Thus far, we can restore the all-in-focus photograph from a defocused input. To further produce photographs focused at different depths, the depth map from the blur map must be derived. To eliminate the ambiguity over the focal plane, user interaction is introduced and a binary graph cut algorithm is used. So we introduce user interaction and use a binary graph cut algorithm to eliminate the ambiguity over the focal plane. Coupled with the camera parameters, this approach produces images focused at different depths. The performance of this new multi-focusing algorithm is evaluated both objectively and subjectively by various test images. Both results demonstrate that this algorithm produces high quality depth maps and multi-focusing results, outperforming the previous approaches.\",\n \"corpus_id\": 14328265,\n \"score\": 0\n },\n {\n \"doc_id\": \"24569482\",\n \"title\": \"Atomic model of the F420-reducing [NiFe] hydrogenase by electron cryo-microscopy using a direct electron detector.\",\n \"abstract\": \"The introduction of direct electron detectors with higher detective quantum efficiency and fast read-out marks the beginning of a new era in electron cryo-microscopy. Using the FEI Falcon II direct electron detector in video mode, we have reconstructed a map at 3.36 Å resolution of the 1.2 MDa F420-reducing hydrogenase (Frh) from methanogenic archaea from only 320,000 asymmetric units. Videos frames were aligned by a combination of image and particle alignment procedures to overcome the effects of beam-induced motion. The reconstructed density map shows all secondary structure as well as clear side chain densities for most residues. The full coordination of all cofactors in the electron transfer chain (a [NiFe] center, four [4Fe4S] clusters and an FAD) is clearly visible along with a well-defined substrate access channel. From the rigidity of the complex we conclude that catalysis is diffusion-limited and does not depend on protein flexibility or conformational changes. DOI: http://dx.doi.org/10.7554/eLife.01963.001.\",\n \"corpus_id\": 16176308,\n \"score\": 0\n },\n {\n \"doc_id\": \"25122622\",\n \"title\": \"Beam-induced motion correction for sub-megadalton cryo-EM particles.\",\n \"abstract\": \"In electron cryo-microscopy (cryo-EM), the electron beam that is used for imaging also causes the sample to move. This motion blurs the images and limits the resolution attainable by single-particle analysis. In a previous Research article (Bai et al., 2013) we showed that correcting for this motion by processing movies from fast direct-electron detectors allowed structure determination to near-atomic resolution from 35,000 ribosome particles. In this Research advance article, we show that an improved movie processing algorithm is applicable to a much wider range of specimens. The new algorithm estimates straight movement tracks by considering multiple particles that are close to each other in the field of view, and models the fall-off of high-resolution information content by radiation damage in a dose-dependent manner. Application of the new algorithm to four data sets illustrates its potential for significantly improving cryo-EM structures, even for particles that are smaller than 200 kDa.\",\n \"corpus_id\": 12574480,\n \"score\": 0\n },\n {\n \"doc_id\": \"25359822\",\n \"title\": \"Fast auto-acquisition tomography tilt series by using HD video camera in ultra-high voltage electron microscope.\",\n \"abstract\": \"The ultra-high voltage electron microscope (UHVEM) H-3000 with the world highest acceleration voltage of 3 MV can observe remarkable three dimensional microstructures of microns-thick samples[1]. Acquiring a tilt series of electron tomography is laborious work and thus an automatic technique is highly desired. We proposed the Auto-Focus system using image Sharpness (AFS)[2,3] for UHVEM tomography tilt series acquisition. In the method, five images with different defocus values are firstly acquired and the image sharpness are calculated. The sharpness are then fitted to a quasi-Gaussian function to decide the best focus value[3]. Defocused images acquired by the slow scan CCD (SS-CCD) camera (Hitachi F486BK) are of high quality but one minute is taken for acquisition of five defocused images. In this study, we introduce a high-definition video camera (HD video camera; Hamamatsu Photonics K. K. C9721S) for fast acquisition of images[4]. It is an analog camera but the camera image is captured by a PC and the effective image resolution is 1280×1023 pixels. This resolution is lower than that of the SS-CCD camera of 4096×4096 pixels. However, the HD video camera captures one image for only 1/30 second. In exchange for the faster acquisition the S/N of images are low. To improve the S/N, 22 captured frames are integrated so that each image sharpness is enough to become lower fitting error. As countermeasure against low resolution, we selected a large defocus step, which is typically five times of the manual defocus step, to discriminate different defocused images. By using HD video camera for autofocus process, the time consumption for each autofocus procedure was reduced to about six seconds. It took one second for correction of an image position and the total correction time was seven seconds, which was shorter by one order than that using SS-CCD camera. When we used SS-CCD camera for final image capture, it took 30 seconds to record one tilt image. We can obtain a tilt series of 61 images within 30 minutes. Accuracy and repeatability were good enough to practical use (Figure 1). We successfully reduced the total acquisition time of a tomography tilt series in half than before.jmicro;63/suppl_1/i25/DFU066F1F1DFU066F1Fig. 1.Objective lens current change with a tilt angle during acquisition of tomography series (Sample: a rat hepatocyte, thickness: 2 m, magnification: 4k, acc. voltage: 2 MV). Tilt angle range is ±60 degree with 2 degree step angle. Two series were acquired in the same area. Both data were almost same and the deviation was smaller than the minimum step by manual, so auto-focus worked well. We also developed a computer-aided three dimensional (3D) visualization and analysis software for electron tomography \\\"HawkC\\\" which can sectionalize the 3D data semi-automatically[5,6]. If this auto-acquisition system is used with IMOD reconstruction software[7] and HawkC software, we will be able to do on-line UHVEM tomography. The system would help pathology examination in the future. This work was supported by the Ministry of Education, Culture, Sports, Science and Technology (MEXT), Japan, under a Grant-in-Aid for Scientific Research (Grant No. 23560024, 23560786), and SENTAN, Japan Science and Technology Agency, Japan.\",\n \"corpus_id\": 29568336,\n \"score\": 0\n },\n {\n \"doc_id\": \"25576587\",\n \"title\": \"Pose Estimation for General Cameras Using Lines.\",\n \"abstract\": \"In this paper, we address the problem of pose estimation under the framework of generalized camera models. We propose a solution based on the knowledge of the coordinates of 3-D straight lines (expressed in the world coordinate frame) and their corresponding image pixels. Previous approaches used the knowledge of the coordinates of 3-D points (zero dimensional elements) and their corresponding images (zero dimensional elements). In this paper, pixels belonging to the image of 3-D lines are used. There is no need to establish correspondences between pixels and 3-D points. Correspondences are established between 3-D lines and their images. There is no need to identify individual pixels. The use of correspondences between pixels (that belong to the images of the 3-D lines) and 3-D lines facilitates the correspondence problem when compared to the use of world and image points. This is one of the contributions of this paper. The approach is both evaluated and validated using synthetic data and also real images.\",\n \"corpus_id\": 12909267,\n \"score\": 0\n },\n {\n \"doc_id\": \"25637660\",\n \"title\": \"A statistical approach to the initial volume problem in Single Particle Analysis by Electron Microscopy.\",\n \"abstract\": \"Cryo Electron Microscopy is a powerful Structural Biology technique, allowing the elucidation of the three-dimensional structure of biological macromolecules. In particular, the structural study of purified macromolecules -often referred as Single Particle Analysis(SPA)- is normally performed through an iterative process that needs a first estimation of the three-dimensional structure that is progressively refined using experimental data. It is well-known the local optimisation nature of this refinement, so that the initial choice of this first structure may substantially change the final result. Computational algorithms aiming to providing this first structure already exist. However, the question is far from settled and more robust algorithms are still needed so that the refinement process can be performed with sufficient guarantees. In this article we present a new algorithm that addresses the initial volume problem in SPA by setting it in a Weighted Least Squares framework and calculating the weights through a statistical approach based on the cumulative density function of different image similarity measures. We show that the new algorithm is significantly more robust than other state-of-the-art algorithms currently in use in the field. The algorithm is available as part of the software suite Xmipp (http://xmipp.cnb.csic.es) and Scipion (http://scipion.cnb.csic.es) under the name \\\"Significant\\\".\",\n \"corpus_id\": 15342000,\n \"score\": 0\n },\n {\n \"doc_id\": \"26296328\",\n \"title\": \"Alignment of cryo-EM movies of individual particles by optimization of image translations.\",\n \"abstract\": \"Direct detector device (DDD) cameras have revolutionized single particle electron cryomicroscopy (cryo-EM). In addition to an improved camera detective quantum efficiency, acquisition of DDD movies allows for correction of movement of the specimen, due to both instabilities in the microscope specimen stage and electron beam-induced movement. Unlike specimen stage drift, beam-induced movement is not always homogeneous within an image. Local correlation in the trajectories of nearby particles suggests that beam-induced motion is due to deformation of the ice layer. Algorithms have already been described that can correct movement for large regions of frames and for >1MDa protein particles. Another algorithm allows individual <1MDa protein particle trajectories to be estimated, but requires rolling averages to be calculated from frames and fits linear trajectories for particles. Here we describe an algorithm that allows for individual <1MDa particle images to be aligned without frame averaging or linear trajectories. The algorithm maximizes the overall correlation of the shifted frames with the sum of the shifted frames. The optimum in this single objective function is found efficiently by making use of analytically calculated derivatives of the function. To smooth estimates of particle trajectories, rapid changes in particle positions between frames are penalized in the objective function and weighted averaging of nearby trajectories ensures local correlation in trajectories. This individual particle motion correction, in combination with weighting of Fourier components to account for increasing radiation damage in later frames, can be used to improve 3-D maps from single particle cryo-EM.\",\n \"corpus_id\": 17501197,\n \"score\": 0\n },\n {\n \"doc_id\": \"26417490\",\n \"title\": \"Camera array based light field microscopy.\",\n \"abstract\": \"This paper proposes a novel approach for high-resolution light field microscopy imaging by using a camera array. In this approach, we apply a two-stage relay system for expanding the aperture plane of the microscope into the size of an imaging lens array, and utilize a sensor array for acquiring different sub-apertures images formed by corresponding imaging lenses. By combining the rectified and synchronized images from 5 × 5 viewpoints with our prototype system, we successfully recovered color light field videos for various fast-moving microscopic specimens with a spatial resolution of 0.79 megapixels at 30 frames per second, corresponding to an unprecedented data throughput of 562.5 MB/s for light field microscopy. We also demonstrated the use of the reported platform for different applications, including post-capture refocusing, phase reconstruction, 3D imaging, and optical metrology.\",\n \"corpus_id\": 23832264,\n \"score\": 0\n },\n {\n \"doc_id\": \"26500051\",\n \"title\": \"Modulated CMOS camera for fluorescence lifetime microscopy.\",\n \"abstract\": \"Widefield frequency-domain fluorescence lifetime imaging microscopy (FD-FLIM) is a fast and accurate method to measure the fluorescence lifetime of entire images. However, the complexity and high costs involved in construction of such a system limit the extensive use of this technique. PCO AG recently released the first luminescence lifetime imaging camera based on a high frequency modulated CMOS image sensor, QMFLIM2. Here we tested and provide operational procedures to calibrate the camera and to improve the accuracy using corrections necessary for image analysis. With its flexible input/output options, we are able to use a modulated laser diode or a 20 MHz pulsed white supercontinuum laser as the light source. The output of the camera consists of a stack of modulated images that can be analyzed by the SimFCS software using the phasor approach. The nonuniform system response across the image sensor must be calibrated at the pixel level. This pixel calibration is crucial and needed for every camera settings, e.g. modulation frequency and exposure time. A significant dependency of the modulation signal on the intensity was also observed and hence an additional calibration is needed for each pixel depending on the pixel intensity level. These corrections are important not only for the fundamental frequency, but also for the higher harmonics when using the pulsed supercontinuum laser. With these post data acquisition corrections, the PCO CMOS-FLIM camera can be used for various biomedical applications requiring a large frame and high speed acquisition. Microsc. Res. Tech. 78:1075-1081, 2015. © 2015 Wiley Periodicals, Inc.\",\n \"corpus_id\": 25731197,\n \"score\": 0\n },\n {\n \"doc_id\": \"26685238\",\n \"title\": \"Depth Estimation Using a Sliding Camera.\",\n \"abstract\": \"Image-based 3D reconstruction technology is widely used in different fields. The conventional algorithms are mainly based on stereo matching between two or more fixed cameras, and high accuracy can only be achieved using a large camera array, which is very expensive and inconvenient in many applications. Another popular choice is utilizing structure-from-motion methods for arbitrarily placed camera(s). However, due to too many degrees of freedom, its computational cost is heavy and its accuracy is rather limited. In this paper, we propose a novel depth estimation algorithm using a sliding camera system. By analyzing the geometric properties of the camera system, we design a camera pose initialization algorithm that can work satisfyingly with only a small number of feature points and is robust to noise. For pixels corresponding to different depths, an adaptive iterative algorithm is proposed to choose optimal frames for stereo matching, which can take advantage of continuously pose-changing imaging and save the time consumption amazingly too. The proposed algorithm can also be easily extended to handle less constrained situations (such as using a camera mounted on a moving robot or vehicle). Experimental results on both synthetic and real-world data have illustrated the effectiveness of the proposed algorithm.\",\n \"corpus_id\": 4662274,\n \"score\": 0\n },\n {\n \"doc_id\": \"26697863\",\n \"title\": \"Computation in electron microscopy.\",\n \"abstract\": \"Some uses of the computer and computation in high-resolution transmission electron microscopy are reviewed. The theory of image calculation using Bloch wave and multislice methods with and without aberration correction is reviewed and some applications are discussed. The inverse problem of reconstructing the specimen structure from an experimentally measured electron microscope image is discussed. Some future directions of software development are given.\",\n \"corpus_id\": 10248349,\n \"score\": 0\n },\n {\n \"doc_id\": \"27320661\",\n \"title\": \"Development of automatic body condition scoring using a low-cost 3-dimensional Kinect camera.\",\n \"abstract\": \"Body condition scoring (BCS) is a farm-management tool for estimating dairy cows' energy reserves. Today, BCS is performed manually by experts. This paper presents a 3-dimensional algorithm that provides a topographical understanding of the cow's body to estimate BCS. An automatic BCS system consisting of a Kinect camera (Microsoft Corp., Redmond, WA) triggered by a passive infrared motion detector was designed and implemented. Image processing and regression algorithms were developed and included the following steps: (1) image restoration, the removal of noise; (2) object recognition and separation, identification and separation of the cows; (3) movie and image selection, selection of movies and frames that include the relevant data; (4) image rotation, alignment of the cow parallel to the x-axis; and (5) image cropping and normalization, removal of irrelevant data, setting the image size to 150×200 pixels, and normalizing image values. All steps were performed automatically, including image selection and classification. Fourteen individual features per cow, derived from the cows' topography, were automatically extracted from the movies and from the farm's herd-management records. These features appear to be measurable in a commercial farm. Manual BCS was performed by a trained expert and compared with the output of the training set. A regression model was developed, correlating the features with the manual BCS references. Data were acquired for 4 d, resulting in a database of 422 movies of 101 cows. Movies containing cows' back ends were automatically selected (389 movies). The data were divided into a training set of 81 cows and a test set of 20 cows; both sets included the identical full range of BCS classes. Accuracy tests gave a mean absolute error of 0.26, median absolute error of 0.19, and coefficient of determination of 0.75, with 100% correct classification within 1 step and 91% correct classification within a half step for BCS classes. Results indicated good repeatability, with all standard deviations under 0.33. The algorithm is independent of the background and requires 10 cows for training with approximately 30 movies of 4 s each.\",\n \"corpus_id\": 42557141,\n \"score\": 0\n },\n {\n \"doc_id\": \"27828094\",\n \"title\": \"Detection and removal of fence occlusions in an image using a video of the static/dynamic scene.\",\n \"abstract\": \"The advent of inexpensive smartphones/tablets/phablets equipped with cameras has resulted in the average person capturing cherished moments as images/videos and sharing them on the internet. However, at several locations, an amateur photographer may be frustrated with the captured images. For example, the object of interest to the photographer might be occluded or fenced. Currently available image de-fencing methods in the literature are limited by non-robust fence detection and can handle only static occluded scenes whose video is captured by constrained camera motion. In this work, we propose an algorithm to obtain a de-fenced image using a few frames from a video of the occluded static or dynamic scene. We also present a new fenced image database captured under challenging scenarios such as clutter, poor lighting, viewpoint distortion, etc. Initially, we propose a supervised learning-based approach to detect fence pixels and validate its performance with qualitative as well as quantitative results. We rely on the idea that freehand panning of the fenced scene is likely to render visible hidden pixels of the reference frame in other frames of the captured video. Our approach necessitates the solution of three problems: (i) detection of spatial locations of fences/occlusions in the frames of the video, (ii) estimation of relative motion between the observations, and (iii) data fusion to fill in occluded pixels in the reference image. We assume the de-fenced image as a Markov random field and obtain its maximum a posteriori estimate by solving the corresponding inverse problem. Several experiments on synthetic and real-world data demonstrate the effectiveness of the proposed approach.\",\n \"corpus_id\": 9745398,\n \"score\": 0\n },\n {\n \"doc_id\": \"28439538\",\n \"title\": \"Adaptive foveated single-pixel imaging with dynamic supersampling.\",\n \"abstract\": \"In contrast to conventional multipixel cameras, single-pixel cameras capture images using a single detector that measures the correlations between the scene and a set of patterns. However, these systems typically exhibit low frame rates, because to fully sample a scene in this way requires at least the same number of correlation measurements as the number of pixels in the reconstructed image. To mitigate this, a range of compressive sensing techniques have been developed which use a priori knowledge to reconstruct images from an undersampled measurement set. Here, we take a different approach and adopt a strategy inspired by the foveated vision found in the animal kingdom-a framework that exploits the spatiotemporal redundancy of many dynamic scenes. In our system, a high-resolution foveal region tracks motion within the scene, yet unlike a simple zoom, every frame delivers new spatial information from across the entire field of view. This strategy rapidly records the detail of quickly changing features in the scene while simultaneously accumulating detail of more slowly evolving regions over several consecutive frames. This architecture provides video streams in which both the resolution and exposure time spatially vary and adapt dynamically in response to the evolution of the scene. The degree of local frame rate enhancement is scene-dependent, but here, we demonstrate a factor of 4, thereby helping to mitigate one of the main drawbacks of single-pixel imaging techniques. The methods described here complement existing compressive sensing approaches and may be applied to enhance computational imagers that rely on sequential correlation measurements.\",\n \"corpus_id\": 5196689,\n \"score\": 0\n },\n {\n \"doc_id\": \"28862618\",\n \"title\": \"The EIGER detector for low-energy electron microscopy and photoemission electron microscopy.\",\n \"abstract\": \"EIGER is a single-photon-counting hybrid pixel detector developed at the Paul Scherrer Institut, Switzerland. It is designed for applications at synchrotron light sources with photon energies above 5 keV. Features of EIGER include a small pixel size (75 µm × 75 µm), a high frame rate (up to 23 kHz), a small dead-time between frames (down to 3 µs) and a dynamic range up to 32-bit. In this article, the use of EIGER as a detector for electrons in low-energy electron microscopy (LEEM) and photoemission electron microscopy (PEEM) is reported. It is demonstrated that, with only a minimal modification to the sensitive part of the detector, EIGER is able to detect electrons emitted or reflected by the sample and accelerated to 8-20 keV. The imaging capabilities are shown to be superior to the standard microchannel plate detector for these types of applications. This is due to the much higher signal-to-noise ratio, better homogeneity and improved dynamic range. In addition, the operation of the EIGER detector is not affected by radiation damage from electrons in the present energy range and guarantees more stable performance over time. To benchmark the detector capabilities, LEEM experiments are performed on selected surfaces and the magnetic and electronic properties of individual iron nanoparticles with sizes ranging from 8 to 22 nm are detected using the PEEM endstation at the Surface/Interface Microscopy (SIM) beamline of the Swiss Light Source.\",\n \"corpus_id\": 206357833,\n \"score\": 0\n },\n {\n \"doc_id\": \"28863668\",\n \"title\": \"Gain depletion of X-ray framing camera.\",\n \"abstract\": \"X-ray imaging is very useful to investigate imploded core plasma in inertial fusion experiments. We can obtain information from X-ray images, such as shape, density, and temperature. An X-ray framing camera (XFC) capable of taking two-dimensional, time-resolved X-ray images is used to capture the images. In previous work, we developed a numerical model of an XFC to analyze its X-ray image. The calculated results agreed qualitatively with experimental results. However, it was not accurate enough to determine the absolute value of the signal. We thought this discrepancy was caused by gain depletion. In high energy laser experiments, high photon flux may cause gain depletion. This is a problem for accurate X-ray measurement. In this paper, we report our new model, including gain depletion. The new model is evaluated by tabletop laser experiments and high energy laser experiments. The results calculated using the new model agree quantitatively with our experimental results. Furthermore, we confirmed that gain depletion occurs in our high energy laser experiments. For quantitatively accurate X-ray intensity measurements, the XFC should be used with limited incident photon flux such that the gain linearity is guaranteed.\",\n \"corpus_id\": 24611389,\n \"score\": 0\n },\n {\n \"doc_id\": \"29324929\",\n \"title\": \"Our solution for fusion of simultaneusly acquired whole body scintigrams and optical images, as usesful tool in clinical practice in patients with differentiated thyroid carcinomas after radioiodine therapy. A useful tool in clinical practice.\",\n \"abstract\": \"OBJECTIVE: After radioiodine therapy of differentiated thyroid cancer (DTC) patients, whole body scintigraphy (WBS) is standard procedure before releasing the patient from the hospital. A common problem is the precise localization of regions where the iod-avide tissue is located. Sometimes is practically impossible to perform precise topographic localization of such regions. METHOD: In order to face this problem, we have developed a low-cost Vision-Fusion system for web-camera image acquisition simultaneously with routine scintigraphic whole body acquisition including the algorithm for fusion of images given from both cameras. For image acquisition in the gamma part of the spectra we used e.cam dual head gamma camera (Siemens, Erlangen, Germany) in WBS modality, with matrix size of 256×1024 pixels and bed speed of 6cm/min, equipped with high energy collimator. For optical image acquisition in visible part of spectra we have used web-camera model C905 (Logitech, USA) with Carl Zeiss® optics, native resolution 1600×1200 pixels, 34o field of view, 30g weight, with autofocus option turned \\\"off\\\" and auto white balance turned \\\"on\\\". Web camera is connected to upper head of gamma camera (GC) by a holder of lightweight aluminum rod and a plexiglas adapter. Our own Vision-Fusion software for image acquisition and coregistration was developed using NI LabVIEW programming environment 2015 (National Instruments, Texas, USA) and two additional LabVIEW modules: NI Vision Acquisition Software (VAS) and NI Vision Development Module (VDM). Vision acquisition software enables communication and control between laptop computer and web-camera. Vision development module is image processing library used for image preprocessing and fusion. Software starts the web-camera image acquisition before starting image acquisition on GC and stops it when GC completes the acquisition. Web-camera is in continuous acquisition mode with frame rate f depending on speed of patient bed movement v (f=v/∆cm, where ∆cm is a displacement step that can be changed in Settings option of Vision-Fusion software; by default, ∆cm is set to 1cm corresponding to ∆p=15 pixels). All images captured while patient's bed is moving are processed. Movement of patient's bed is checked using cross-correlation of two successive images. After each image capturing, algorithm extracts the central region of interest (ROI) of the image, with the same width as captured image (1600 pixels) and the height that is equal to the ∆p displacement in pixels. All extracted central ROI are placed next to each other in the overall whole-body image. Stacking of narrow central ROI introduces negligible distortion in the overall whole-body image. The first step for fusion of the scintigram and the optical image was determination of spatial transformation between them. We have made an experiment with two markers (point radioactivity sources of 99mTc pertechnetate 1MBq) visible in both images (WBS and optical) to find transformation of coordinates between images. The distance between point markers is used for spatial coregistration of the gamma and optical images. At the end of coregistration process, gamma image is rescaled in spatial domain and added to the optical image (green or red channel, amplification changeable from user interface). SUBJECTS: We tested our system for 10 patients with DTC who received radioiodine therapy (8 women and two men, with average age of 50.10±12.26 years). Five patients received 5.55Gbq, three 3.70GBq and two 1.85GBq. Whole-body scintigraphy and optical image acquisition were performed 72 hours after application of radioiodine therapy. CONCLUSION: Based on our first results during clinical testing of our system, we can conclude that our system can improve diagnostic possibility of whole body scintigraphy to detect thyroid remnant tissue in patients with DTC after radioiodine therapy.\",\n \"corpus_id\": 43376373,\n \"score\": 0\n },\n {\n \"doc_id\": \"29603952\",\n \"title\": \"Joint camera blur and pose estimation from aliased data.\",\n \"abstract\": \"A joint-estimation algorithm is presented that enables simultaneous camera blur and pose estimation from a known calibration target in the presence of aliasing. Specifically, a parametric maximum-likelihood (ML) point-spread function estimate is derived for characterizing a camera's optical imperfections through the use of a calibration target in an otherwise loosely controlled environment. The imaging perspective, ambient-light levels, target reflectance, detector gain and offset, quantum efficiency, and read-noise levels are all treated as nuisance parameters. The Cramér-Rao bound is derived, and simulations demonstrate that the proposed estimator achieves near optimal mean squared error performance. The proposed method is applied to experimental data to validate the fidelity of the forward models as well as to establish the utility of the resulting ML estimates for both system identification and subsequent image restoration.\",\n \"corpus_id\": 4590504,\n \"score\": 0\n }\n]","isConversational":false}}},{"rowIdx":63,"cells":{"query":{"kind":"string","value":"{\n \"doc_id\": \"29395788\",\n \"title\": \"MonoRes: Automatic and Accurate Estimation of Local Resolution for Electron Microscopy Maps.\",\n \"abstract\": \"Since the beginning of electron microscopy, resolution has been a critical parameter. In this article, we propose a fully automatic, accurate method for determining the local resolution of a 3D map (MonoRes). The foundation of this algorithm is an extension of the concept of analytic signal, termed monogenic signal. The map is filtered at different frequencies and the amplitude of the monogenic signal is calculated, after which a criterion is applied to determine the resolution at each voxel. MonoRes is fully automatic without compulsory user parameters, with great accuracy in all tests, and is computationally more rapid than existing methods in the field. In addition, MonoRes offers the option of local filtering of the original map based on the calculated local resolution.\",\n \"corpus_id\": 46822743\n}"},"candidates":{"kind":"list like","value":[{"doc_id":"20888958","title":"Resolution measures in molecular electron microscopy.","abstract":"Resolution measures in molecular electron microscopy provide means to evaluate quality of macromolecular structures computed from sets of their two-dimensional (2D) line projections. When the amount of detail in the computed density map is low there are no external standards by which the resolution of the result can be judged. Instead, resolution measures in molecular electron microscopy evaluate consistency of the results in reciprocal space and present it as a one-dimensional (1D) function of the modulus of spatial frequency. Here we provide description of standard resolution measures commonly used in electron microscopy. We point out that the organizing principle is the relationship between these measures and the spectral signal-to-noise ratio (SSNR) of the computed density map. Within this framework it becomes straightforward to describe the connection between the outcome of resolution evaluations and the quality of electron microscopy maps, in particular, the optimum filtration, in the Wiener sense, of the computed map. We also provide a discussion of practical difficulties of evaluation of resolution in electron microscopy, particularly in terms of its sensitivity to data processing operations used during structure determination process in single particle analysis and in electron tomography (ET).","corpus_id":23444182,"score":2},{"doc_id":"23006110","title":"Estimation theoretic measure of resolution for stochastic localization microscopy.","abstract":"One approach to super-resolution fluorescence microscopy, termed stochastic localization microscopy, relies on the nanometer scale spatial localization of individual fluorescent emitters that stochastically label specific features of the specimen. The precision of emitter localization is an important determinant of the resulting image resolution but is insufficient to specify how well the derived images capture the structure of the specimen. We address this deficiency by considering the inference of specimen structure based on the estimated emitter locations. By using estimation theory, we develop a measure of spatial resolution that jointly depends on the density of the emitter labels, the precision of emitter localization, and prior information regarding the spatial frequency content of the labeled object. The Nyquist criterion does not set the scaling of this measure with emitter number. Given prior information and a fixed emitter labeling density, our resolution measure asymptotes to a finite value as the precision of emitter localization improves. By considering the present experimental capabilities, this asymptotic behavior implies that further resolution improvements require increases in labeling density above typical current values. Our treatment also yields algorithms to enhance reliable image features. Overall, our formalism facilitates the rigorous statistical interpretation of the data produced by stochastic localization imaging techniques.","corpus_id":7413132,"score":2},{"doc_id":"23954653","title":"One number does not fit all: mapping local variations in resolution in cryo-EM reconstructions.","abstract":"The resolution of density maps from single particle analysis is usually measured in terms of the highest spatial frequency to which consistent information has been obtained. This calculation represents an average over the entire reconstructed volume. In practice, however, substantial local variations in resolution may occur, either from intrinsic properties of the specimen or for technical reasons such as a non-isotropic distribution of viewing orientations. To address this issue, we propose the use of a space-frequency representation, the short-space Fourier transform, to assess the quality of a density map, voxel-by-voxel, i.e. by local resolution mapping. In this approach, the experimental volume is divided into small subvolumes and the resolution determined for each of them. It is illustrated in applications both to model data and to experimental density maps. Regions with lower-than-average resolution may be mobile components or ones with incomplete occupancy or result from multiple conformational states. To improve the interpretability of reconstructions, we propose an adaptive filtering approach that reconciles the resolution to which individual features are calculated with the results of the local resolution map.","corpus_id":5441800,"score":2},{"doc_id":"24213166","title":"Quantifying the local resolution of cryo-EM density maps.","abstract":"We propose a definition of local resolution for three-dimensional electron cryo-microscopy (cryo-EM) density maps that uses local sinusoidal features. Our algorithm has no free parameters and is applicable to other imaging modalities, including tomography. By evaluating the local resolution of single-particle reconstructions and subtomogram averages for four example data sets, we report variable resolution across a 4- to 40-Å range.","corpus_id":13250075,"score":2},{"doc_id":"27666962","title":"A review of resolution measures and related aspects in 3D Electron Microscopy.","abstract":"Fourier Shell Correlation, Spectral Signal-to-Noise Ratio, Fourier Neighbour Correlation, and Differential Phase Residual are different measures that have been proposed over time to determine the spatial resolution achieved by a certain 3D reconstruction. Estimates of B-factors to describe the reduction in signal-to-noise ratio with increasing resolution is also a useful parameter. All these concepts are interrelated and different thresholds have been given for each one of them. However, the problem of resolution assessment in 3DEM is still far from settled and preferences are normally adopted in order to choose the \"correct\" threshold. In this paper we review the different concepts, their theoretical foundations and the derivation of their statistical distributions (the basis for establishing sensible thresholds). We provide theoretical justifications for some common practices in the field for which a formal justification was missing. We also analyze the relationship between SSNR and B-factors, the electron dose needed for achieving a given contrast and resolution, the number of images required, etc. Finally, we review the consequences for the number of particles needed to achieve a certain resolution and how to analyze the Signal-to-Noise Ratio for a sequence of imaging operations.","corpus_id":25932382,"score":2},{"doc_id":"29274623","title":"Automatic estimation of a scale resolution in forensic images.","abstract":"This paper proposes a new method for an automatic detection of a resolution of a scale or a ruler with graduation marks in the shoeprint images. The method creates a vector of the correlations estimated from the co-occurrence matrices for every row in a shoeprint image. The scale resolution is estimated from maxima in Fourier spectrum of the correlations' vectors. The proposed method is evaluated on over 500 images taken at crime scenes and in a forensics laboratory. The experimental results indicate the possibility of applying the proposed method to automatically estimate the scale resolution in forensic images. The automatic detection of a scale resolution could be used to automatically rescale a forensic image before the printing this image in \"one-to-one\" scale. Furthermore, the proposed method could be used to automatically rescale images to an equal scale thus allowing to compare the images digitally.","corpus_id":4576484,"score":2},{"doc_id":"18285628","title":"Minimally resolution biased electron-density maps.","abstract":"Electron-density maps are calculated by Fourier syntheses with coefficients based on structure factors. Diffraction experiments provide intensities up to a limited resolution; as a consequence, the Fourier syntheses always show series-termination errors. The worse the resolution, the less accurate is the Fourier representation of the electron density. In general, each atomic peak is shifted from the correct position, shows a deformed (with respect to the true distribution of the electrons in the atomic domain) profile, and is surrounded by a series of negative and positive ripples of gradually decreasing amplitude. An algorithm is described which is able to reduce the resolution bias by relocating the peaks in more correct positions and by modifying the peak profile to better fit the real atomic electron densities. Some experimental tests are performed showing the usefulness of the procedure.","corpus_id":22247257,"score":1},{"doc_id":"21244844","title":"Accurate flexible fitting of high-resolution protein structures into cryo-electron microscopy maps using coarse-grained pseudo-energy minimization.","abstract":"Cryo-electron microscopy (cryo-EM) has been widely used to explore conformational states of large biomolecular assemblies. The detailed interpretation of cryo-EM data requires the flexible fitting of a known high-resolution protein structure into a low-resolution cryo-EM map. To this end, we have developed what we believe is a new method based on a two-bead-per-residue protein representation, and a modified form of the elastic network model that allows large-scale conformational changes while maintaining pseudobonds and secondary structures. Our method minimizes a pseudo-energy which linearly combines various terms of the modified elastic network model energy with a cryo-EM-fitting score and a collision energy that penalizes steric collisions. Unlike previous flexible fitting efforts using the lowest few normal modes, our method effectively utilizes all normal modes so that both global and local structural changes can be fully modeled. We have validated our method for a diverse set of 10 pairs of protein structures using simulated cryo-EM maps with a range of resolutions and in the absence/presence of random noise. We have shown that our method is both accurate and efficient compared with alternative techniques, and its performance is robust to the addition of random noise. Our method is also shown to be useful for the flexible fitting of three experimental cryo-EM maps.","corpus_id":13957824,"score":1},{"doc_id":"23215134","title":"Unified resolution bounds for conventional and stochastic localization fluorescence microscopy.","abstract":"Superresolution microscopy enables imaging in the optical far field with ~20 nm-scale resolution. However, classical concepts of resolution using point-spread and modulation-transfer functions fail to describe the physical limits of superresolution techniques based on stochastic localization of single emitters. Prior treatments of stochastic localization microscopy have defined how accurately a single emitter's position can be determined, but these bounds are restricted to sparse emitters, do not describe conventional microscopy, and fail to provide unified concepts of resolution for all optical methods. Here we introduce a measure of resolution, the information transfer function (ITF), that gives physical limits for conventional and stochastic localization techniques. The ITF bounds the accuracy of image determination as a function of spatial frequency and for conventional microscopy is proportional to the square of the modulation-transfer function. We use the ITF to describe how emitter density and photon counts affect imaging performance across the continuum from conventional to superresolution microscopy, without assuming emitters are sparse. This unified physical description of resolution facilitates experimental choices and designs of image reconstruction algorithms.","corpus_id":12132490,"score":1},{"doc_id":"23261401","title":"FASTDEF: fast defocus and astigmatism estimation for high-throughput transmission electron microscopy.","abstract":"In this work we present a fast and automated algorithm for estimating the contrast transfer function (CTF) of a transmission electron microscope. The approach is very suitable for High Throughput work because: (a) it does not require any initial defocus estimation, (b) it is almost an order of magnitude faster than existing approaches, (c) it opens the way to well-defined extensions to the estimation of higher order aberrations, at the same time that provides defocus and astigmatism estimations comparable in accuracy to well established methods, such as Xmipp and CTFFIND3 approaches. The new algorithm is based on obtaining the wrapped modulating phase of the power spectra density pattern by the use of a quadrature filter. This phase is further unwrapped in order to obtain the continuous and smooth absolute phase map; then a Zernike polynomial fitting is performed and the defocus and astigmatism parameters are determined. While the method does not require an initial estimation of the defocus parameters or any non-linear optimization procedure, these approaches can be used if further refinement is desired. Results of the CTF estimation method are presented for standard negative stained images, cryo-electron microscopy images in the absence of carbon support, as well as micrographs with only ice. Additionally, we have also tested the proposed method with micrographs acquired from tilted and untilted samples, obtaining good results. The algorithm is freely available as a part of the Xmipp package [http://xmipp.cnb.csic.es].","corpus_id":9415778,"score":1},{"doc_id":"23872039","title":"High-resolution noise substitution to measure overfitting and validate resolution in 3D structure determination by single particle electron cryomicroscopy.","abstract":"Three-dimensional (3D) structure determination by single particle electron cryomicroscopy (cryoEM) involves the calculation of an initial 3D model, followed by extensive iterative improvement of the orientation determination of the individual particle images and the resulting 3D map. Because there is much more noise than signal at high resolution in the images, this creates the possibility of noise reinforcement in the 3D map, which can give a false impression of the resolution attained. The balance between signal and noise in the final map at its limiting resolution depends on the image processing procedure and is not easily predicted. There is a growing awareness in the cryoEM community of how to avoid such over-fitting and over-estimation of resolution. Equally, there has been a reluctance to use the two principal methods of avoidance because they give lower resolution estimates, which some people believe are too pessimistic. Here we describe a simple test that is compatible with any image processing protocol. The test allows measurement of the amount of signal and the amount of noise from overfitting that is present in the final 3D map. We have applied the method to two different sets of cryoEM images of the enzyme beta-galactosidase using several image processing packages. Our procedure involves substituting the Fourier components of the initial particle image stack beyond a chosen resolution by either the Fourier components from an adjacent area of background, or by simple randomisation of the phases of the particle structure factors. This substituted noise thus has the same spectral power distribution as the original data. Comparison of the Fourier Shell Correlation (FSC) plots from the 3D map obtained using the experimental data with that from the same data with high-resolution noise (HR-noise) substituted allows an unambiguous measurement of the amount of overfitting and an accompanying resolution assessment. A simple formula can be used to calculate an unbiased FSC from the two curves, even when a substantial amount of overfitting is present. The approach is software independent. The user is therefore completely free to use any established method or novel combination of methods, provided the HR-noise test is carried out in parallel. Applying this procedure to cryoEM images of beta-galactosidase shows how overfitting varies greatly depending on the procedure, but in the best case shows no overfitting and a resolution of ~6 Å. (382 words).","corpus_id":25196434,"score":1},{"doc_id":"26278980","title":"CTFFIND4: Fast and accurate defocus estimation from electron micrographs.","abstract":"CTFFIND is a widely-used program for the estimation of objective lens defocus parameters from transmission electron micrographs. Defocus parameters are estimated by fitting a model of the microscope's contrast transfer function (CTF) to an image's amplitude spectrum. Here we describe modifications to the algorithm which make it significantly faster and more suitable for use with images collected using modern technologies such as dose fractionation and phase plates. We show that this new version preserves the accuracy of the original algorithm while allowing for higher throughput. We also describe a measure of the quality of the fit as a function of spatial frequency and suggest this can be used to define the highest resolution at which CTF oscillations were successfully modeled.","corpus_id":1121396,"score":1},{"doc_id":"26509596","title":"Resolution limits of ultrafast ultrasound localization microscopy.","abstract":"As in other imaging methods based on waves, the resolution of ultrasound imaging is limited by the wavelength. However, the diffraction-limit can be overcome by super-localizing single events from isolated sources. In recent years, we developed plane-wave ultrasound allowing frame rates up to 20 000 fps. Ultrafast processes such as rapid movement or disruption of ultrasound contrast agents (UCA) can thus be monitored, providing us with distinct punctual sources that could be localized beyond the diffraction limit. We previously showed experimentally that resolutions beyond λ/10 can be reached in ultrafast ultrasound localization microscopy (uULM) using a 128 transducer matrix in reception. Higher resolutions are theoretically achievable and the aim of this study is to predict the maximum resolution in uULM with respect to acquisition parameters (frequency, transducer geometry, sampling electronics). The accuracy of uULM is the error on the localization of a bubble, considered a point-source in a homogeneous medium. The proposed model consists in two steps: determining the timing accuracy of the microbubble echo in radiofrequency data, then transferring this time accuracy into spatial accuracy. The simplified model predicts a maximum resolution of 40 μm for a 1.75 MHz transducer matrix composed of two rows of 64 elements. Experimental confirmation of the model was performed by flowing microbubbles within a 60 μm microfluidic channel and localizing their blinking under ultrafast imaging (500 Hz frame rate). The experimental resolution, determined as the standard deviation in the positioning of the microbubbles, was predicted within 6 μm (13%) of the theoretical values and followed the analytical relationship with respect to the number of elements and depth. Understanding the underlying physical principles determining the resolution of superlocalization will allow the optimization of the imaging setup for each organ. Ultimately, accuracies better than the size of capillaries are achievable at several centimeter depths.","corpus_id":27380330,"score":1},{"doc_id":"26605834","title":"Validating maps from single particle electron cryomicroscopy.","abstract":"Progress in single particle cryo-EM, most recently due to the introduction of direct detector devices, has made the high-resolution structure determination of biological assemblies smaller than 500kDa more routine, but has also increased attention on the need for tools to demonstrate the validity of single particle maps. Although map validation is a continuing subject of research, some consensus has been reached on procedures that reduce model bias and over-fitting during map refinement as well as specific tests that demonstrate map validity. Tilt-pair analysis may be used as a method for demonstrating the consistency at low resolution of a map with image data. For higher-resolution maps, new procedures for more robust resolution assessment and for validating the refinement of atomic coordinate models into single particle maps have been developed.","corpus_id":29976510,"score":1},{"doc_id":"17855124","title":"Markov random field based automatic image alignment for electron tomography.","abstract":"We present a method for automatic full-precision alignment of the images in a tomographic tilt series. Full-precision automatic alignment of cryo electron microscopy images has remained a difficult challenge to date, due to the limited electron dose and low image contrast. These facts lead to poor signal to noise ratio (SNR) in the images, which causes automatic feature trackers to generate errors, even with high contrast gold particles as fiducial features. To enable fully automatic alignment for full-precision reconstructions, we frame the problem probabilistically as finding the most likely particle tracks given a set of noisy images, using contextual information to make the solution more robust to the noise in each image. To solve this maximum likelihood problem, we use Markov Random Fields (MRF) to establish the correspondence of features in alignment and robust optimization for projection model estimation. The resulting algorithm, called Robust Alignment and Projection Estimation for Tomographic Reconstruction, or RAPTOR, has not needed any manual intervention for the difficult datasets we have tried, and has provided sub-pixel alignment that is as good as the manual approach by an expert user. We are able to automatically map complete and partial marker trajectories and thus obtain highly accurate image alignment. Our method has been applied to challenging cryo electron tomographic datasets with low SNR from intact bacterial cells, as well as several plastic section and X-ray datasets.","corpus_id":18525199,"score":0},{"doc_id":"18503678","title":"A 3D Hough transform for indexing EBSD and Kossel patterns.","abstract":"A three-dimensional Hough transform is designed for the detection of conic curves (hyperbolae and ellipses) formed by the gnomonic projection of diffraction Kossel cones. This new procedure is applied to a high-angular-accuracy analysis of electron backscatter diffraction (EBSD) patterns and to a fully automatic indexing of X-ray Kossel patterns in the SEM. The high-accuracy analysis of EBSD patterns allows for the determination of local elastic strains, without any reference pattern, and with a spatial resolution of a few tens of nanometres. An accuracy of 2 x 10(-4) is achieved on geometrically calculated diagrams. This paper presents also the first fully automatic indexing of Kossel patterns. This automatic indexing procedure can be applied to local texture analysis, as well as to local elastic strain measurements. Although the spatial resolution of Kossel is about 1 microm, the accuracy of strain measurement is in this case much higher than that presently obtained on EBSD.","corpus_id":25389633,"score":0},{"doc_id":"18708469","title":"Multiple subunit fitting into a low-resolution density map of a macromolecular complex using a gaussian mixture model.","abstract":"Recently, electron microscopy measurement of single particles has enabled us to reconstruct a low-resolution 3D density map of large biomolecular complexes. If structures of the complex subunits can be solved by x-ray crystallography at atomic resolution, fitting these models into the 3D density map can generate an atomic resolution model of the entire large complex. The fitting of multiple subunits, however, generally requires large computational costs; therefore, development of an efficient algorithm is required. We developed a fast fitting program, \"gmfit\", which employs a Gaussian mixture model (GMM) to represent approximated shapes of the 3D density map and the atomic models. A GMM is a distribution function composed by adding together several 3D Gaussian density functions. Because our model analytically provides an integral of a product of two distribution functions, it enables us to quickly calculate the fitness of the density map and the atomic models. Using the integral, two types of potential energy function are introduced: the attraction potential energy between a 3D density map and each subunit, and the repulsion potential energy between subunits. The restraint energy for symmetry is also employed to build symmetrical origomeric complexes. To find the optimal configuration of subunits, we randomly generated initial configurations of subunit models, and performed a steepest-descent method using forces and torques of the three potential energies. Comparison between an original density map and its GMM showed that the required number of Gaussian distribution functions for a given accuracy depended on both resolution and molecular size. We then performed test fitting calculations for simulated low-resolution density maps of atomic models of homodimer, trimer, and hexamer, using different search parameters. The results indicated that our method was able to rebuild atomic models of a complex even for maps of 30 A resolution if sufficient numbers (eight or more) of Gaussian distribution functions were employed for each subunit, and the symmetric restraints were assigned for complexes with more than three subunits. As a more realistic test, we tried to build an atomic model of the GroEL/ES complex by fitting 21-subunit atomic models into the 3D density map obtained by cryoelectron microscopy using the C7 symmetric restraints. A model with low root mean-square deviations (14.7 A) was obtained as the lowest-energy model, showing that our fitting method was reasonably accurate. Inclusion of other restraints from biological and biochemical experiments could further enhance the accuracy.","corpus_id":14849875,"score":0},{"doc_id":"18989044","title":"Computational approaches for automatic structural analysis of large biomolecular complexes.","abstract":"We present computational solutions to two problems of macromolecular structure interpretation from reconstructed three-dimensional electron microscopy (3D-EM) maps of large bio-molecular complexes at intermediate resolution (5A-15 A). The two problems addressed are: 1) 3D structural alignment (matching) between identified and segmented 3D maps of structure units (e.g. trimeric configuration of proteins), and 2) the secondary structure identification of a segmented protein 3D map (i.e.locations of alpha-helices, beta-sheets). For problem 1, we present an efficient algorithm to correlate spatially (and structurally) two 3D maps of structure units. Besides providing a similarity score between structure units, the algorithm yields an effective technique for resolution refinement of repeated structure units, by 3D alignment and averaging. For problem 2, we present an efficient algorithm to compute eigenvalues and link eigenvectors of a Gaussian convoluted structure tensor derived from the protein 3D Map, thereby identifying and locating secondary structural motifs of proteins. The efficiency and performance of our approach is demonstrated on several experimentally reconstructed 3D maps of virus capsid shells from single-particle cryo-electron microscopy (cryo-EM), as well as computationally simulated protein structure density 3D maps generated from protein model entries in the Protein Data Bank.","corpus_id":1636056,"score":0},{"doc_id":"19434159","title":"Experimental characterization of 3D localization techniques for particle-tracking and super-resolution microscopy.","abstract":"Three-dimensional (3D) particle localization at the nanometer scale plays a central role in 3D particle tracking and 3D localization-based super-resolution microscopy. Here we introduce a localization algorithm that is independent of theoretical models and therefore generally applicable to a large number of experimental realizations. Applying this algorithm and a convertible experimental setup we compare the performance of the two major 3D techniques based on astigmatic distortions and on multiplane detection. In both methods we obtain experimental 3D localization accuracies in agreement with theoretical predictions and characterize the depth dependence of the localization accuracy in detail.","corpus_id":30824985,"score":0},{"doc_id":"20109465","title":"Building and refining protein models within cryo-electron microscopy density maps based on homology modeling and multiscale structure refinement.","abstract":"Automatic modeling methods using cryoelectron microscopy (cryoEM) density maps as constraints are promising approaches to building atomic models of individual proteins or protein domains. However, their application to large macromolecular assemblies has not been possible largely due to computational limitations inherent to such unsupervised methods. Here we describe a new method, EM-IMO (electron microscopy-iterative modular optimization), for building, modifying and refining local structures of protein models using cryoEM maps as a constraint. As a supervised refinement method, EM-IMO allows users to specify parameters derived from inspections so as to guide, and as a consequence, significantly speed up the refinement. An EM-IMO-based refinement protocol is first benchmarked on a data set of 50 homology models using simulated density maps. A multiscale refinement strategy that combines EM-IMO-based and molecular dynamics-based refinement is then applied to build backbone models for the seven conformers of the five capsid proteins in our near-atomic-resolution cryoEM map of the grass carp reovirus virion, a member of the Aquareovirus genus of the Reoviridae family. The refined models allow us to reconstruct a backbone model of the entire grass carp reovirus capsid and provide valuable functional insights that are described in the accompanying publication [Cheng, L., Zhu, J., Hui, W. H., Zhang, X., Honig, B., Fang, Q. & Zhou, Z. H. (2010). Backbone model of an aquareovirus virion by cryo-electron microscopy and bioinformatics. J. Mol. Biol. ( this issue). doi:10.1016/j.jmb.2009.12.027.]. Our study demonstrates that the integrated use of homology modeling and a multiscale refinement protocol that combines supervised and automated structure refinement offers a practical strategy for building atomic models based on medium- to high-resolution cryoEM density maps.","corpus_id":42992578,"score":0},{"doc_id":"20713087","title":"Automatic mosaicking and volume assembly for high-throughput serial-section transmission electron microscopy.","abstract":"We describe a computationally efficient and robust, fully-automatic method for large-scale electron microscopy image registration. The proposed method is able to construct large image mosaics from thousands of smaller, overlapping tiles with unknown or uncertain positions, and to align sections from a serial section capture into a common coordinate system. The method also accounts for nonlinear deformations both in constructing sections and in aligning sections to each other. The underlying algorithms are based on the Fourier shift property which allows for a computationally efficient and robust method. We demonstrate results on two electron microscopy datasets. We also quantify the accuracy of the algorithm through a simulated image capture experiment. The publicly available software tools include the algorithms and a Graphical User Interface for easy access to the algorithms.","corpus_id":27997186,"score":0},{"doc_id":"21844593","title":"Electron microscopy at a sub-50 pm resolution.","abstract":"An aberration-corrected electron microscope developed in CREST project has been applied for imaging atoms and clusters buried inside crystals. The resolution of the microscope in scanning transmission electron microscopy (STEM) has experimentally proved to be better than 47 pm by use of a cold-field emission gun at 300 kV. The high resolution has given an advantage for imaging light elements such as lithium atoms discriminating one by one. Moreover, a three-dimensional structure imaging has been demonstrated for dopant clusters by a sub-50 pm STEM, using its high depth resolution.","corpus_id":21567355,"score":0},{"doc_id":"21860371","title":"Structure of HIV-1 capsid assemblies by cryo-electron microscopy and iterative helical real-space reconstruction.","abstract":"Cryo-electron microscopy (cryo-EM), combined with image processing, is an increasingly powerful tool for structure determination of macromolecular protein complexes and assemblies. In fact, single particle electron microscopy and two-dimensional (2D) electron crystallography have become relatively routine methodologies and a large number of structures have been solved using these methods. At the same time, image processing and three-dimensional (3D) reconstruction of helical objects has rapidly developed, especially, the iterative helical real-space reconstruction (IHRSR) method, which uses single particle analysis tools in conjunction with helical symmetry. Many biological entities function in filamentous or helical forms, including actin filaments, microtubules, amyloid fibers, tobacco mosaic viruses, and bacteria flagella, and, because a 3D density map of a helical entity can be attained from a single projection image, compared to the many images required for 3D reconstruction of a non-helical object, with the IHRSR method, structural analysis of such flexible and disordered helical assemblies is now attainable. In this video article, we provide detailed protocols for obtaining a 3D density map of a helical protein assembly (HIV-1 capsid is our example), including protocols for cryo-EM specimen preparation, low dose data collection by cryo-EM, indexing of helical diffraction patterns, and image processing and 3D reconstruction using IHRSR. Compared to other techniques, cryo-EM offers optimal specimen preservation under near native conditions. Samples are embedded in a thin layer of vitreous ice, by rapid freezing, and imaged in electron microscopes at liquid nitrogen temperature, under low dose conditions to minimize the radiation damage. Sample images are obtained under near native conditions at the expense of low signal and low contrast in the recorded micrographs. Fortunately, the process of helical reconstruction has largely been automated, with the exception of indexing the helical diffraction pattern. Here, we describe an approach to index helical structure and determine helical symmetries (helical parameters) from digitized micrographs, an essential step for 3D helical reconstruction. Briefly, we obtain an initial 3D density map by applying the IHRSR method. This initial map is then iteratively refined by introducing constraints for the alignment parameters of each segment, thus controlling their degrees of freedom. Further improvement is achieved by correcting for the contrast transfer function (CTF) of the electron microscope (amplitude and phase correction) and by optimizing the helical symmetry of the assembly.","corpus_id":8398013,"score":0},{"doc_id":"22088388","title":"An accurate multislice method for low-energy transmission electron microscopy.","abstract":"The conventional multislice method (CMS), originally proposed by Cowley and Moodie (1957), is an important algorithm for image and electron diffraction calculations in transmission electron microscopy. Nevertheless, this method is based on the so-called high-energy approximation, which neglects the second differential term ∂(2)φ(r)/∂z(2) to greatly simplify the calculation without severe loss of accuracy. In the current study, we show that for low-energy transmission electron microscopy (LE-TEM) (<100 kV), the high-energy approximation error becomes large and the accurate multislice method, proposed by Chen and Van Dyck (1997), can be used as an alternative method to obtain more accurate calculations. The accurate multislice method, called the revised real space method (RRS) in this paper, can be realized by treating the propagation and scattering as an entirety in real space. A detailed comparison of the numerical results of the RRS and CMS at different accelerating voltages, Debye-Waller factors, and beam tilts is performed. Results show that for image and diffraction simulations in LE-TEM, CMS is no longer sufficiently accurate and the RRS procedure can be used as an alternative method with reasonable computing time.","corpus_id":3076886,"score":0},{"doc_id":"22320813","title":"Quantitative accuracy of MAP reconstruction for dynamic PET imaging in small animals.","abstract":"PURPOSE: Iterative reconstruction algorithms are becoming more commonly employed in positron emission tomography (PET) imaging; however, the quantitative accuracy of the reconstructed images still requires validation for various levels of contrast and counting statistics. METHODS: The authors present an evaluation of the quantitative accuracy of the 3D maximum a posteriori (3D-MAP) image reconstruction algorithm for dynamic PET imaging with comparisons to two of the most widely used reconstruction algorithms: the 2D filtered-backprojection (2D-FBP) and 2D-ordered subsets expectation maximization (2D-OSEM) on the Siemens microPET scanners. The study was performed for various levels of count density encountered in typical dynamic scanning as well as the imaging of cardiac activity concentration in small animal studies on the Focus 120. Specially designed phantoms were used for evaluation of the spatial resolution, image quality, and quantitative accuracy. A normal mouse was employed to evaluate the accuracy of the blood time activity concentration extracted from left ventricle regions of interest (ROIs) within the images as compared to the actual blood activity concentration measured from arterial blood sampling. RESULTS: For MAP reconstructions, the spatial resolution and contrast have been found to reach a stable value after 20 iterations independent of the β values (i.e., hyper parameter which controls the weight of the penalty term) and count density within the frame. The spatial resolution obtained with 3D-MAP reaches values of ∼1.0 mm with a β of 0.01 while the 2D-FBP has value of 1.8 mm and 2D-OSEM has a value of 1.6 mm. It has been observed that the lower the hyper parameter β used in MAP, more iterations are needed to reach the stable noise level (i.e., image roughness). The spatial resolution is improved by using a lower β value at the expense of higher image noise. However, with similar noise level the spatial resolution achieved by 3D-MAP was observed to be better than that by 2D-FBP or 2D-OSEM. Using an image quality phantom containing hot spheres, the estimated activity concentration in the largest sphere has the expected concentration relative to the background area for all the MAP images. The obtained recovery coefficients have been also shown to be almost independent of the count density. 2D-FBP and 2D-OSEM do not perform as well, yielding recovery coefficients lower than those observed with 3D-MAP (approximately 33% lower for the smallest sphere). However, a small positive bias was observed in MAP reconstructed images for frames of very low count density. This bias is present in the uniform area for count density of less than 0.05 × 10(6) counts/ml. For the dynamic mouse study, it was observed that 3D-MAP (even gated at diastole) cannot predict accurately the blood activity concentration due to residual spill-over activity from the myocardium into the left ventricle (approximately 15%). However, 3D-MAP predicts blood activity concentration closer to blood sampling than 2D-FBP. CONCLUSIONS: The authors observed that 3D-MAP produces more accurate activity concentration estimates than 2D-FBP or 2D-OSEM at all practical levels of statistics and contrasts due to improved spatial resolution leading to lesser partial volume effect.","corpus_id":2867190,"score":0},{"doc_id":"22457262","title":"Automatic off-resonance correction in spiral imaging with piecewise linear autofocus.","abstract":"Off-resonance generates blurring artifacts in spiral images. Applications that often utilize spiral trajectories, such as fine-resolution imaging and rapid scanning, typically preclude the measurement of accurate field maps needed for effective off-resonance correction. Automatic deblurring, or autofocus, algorithms have been developed to estimate the field map directly from the corrupted data prior to off-resonance correction, eliminating the need for field map measurements. These algorithms rely in whole or in part on optimizing an objective function, and suffer from problems related to the accurate minimization and utility of the function. Here, a new method is presented to correct off-resonance blurring automatically without an objective function using a piecewise linear framework. Local linear field maps are estimated with a combination of k-space spectral analysis and mapdrift, an image feature-based correlation technique, for subsequent piecewise linear deblurring. This approach enables field map estimation without optimization, provides accurate off-resonance correction, is suitable for low signal-to-noise ratio and fine-resolution applications, and does not require access to the raw data. Deblurred images from fine-resolution spiral scans of a phantom and healthy volunteers at 3T show that the proposed method can be superior to conventional autofocus and comparable to field map-based correction.","corpus_id":21826795,"score":0},{"doc_id":"22696408","title":"Nhs: network-based hierarchical segmentation for cryo-electron microscopy density maps.","abstract":"Cryo-electron microscopy (cryo-EM) experiments yield low-resolution (3-30 Å) 3D-density maps of macromolecules. These density maps are segmented to identify structurally distinct proteins, protein domains, and subunits. Such partitioning aids the inference of protein motions and guides fitting of high-resolution atomistic structures. Cryo-EM density map segmentation has traditionally required tedious and subjective manual partitioning or semisupervised computational methods, whereas validation of resulting segmentations has remained an open problem in this field. We introduce a network-based hierarchical segmentation (Nhs) method, that provides a multi-scale partitioning, reflecting local and global clustering, while requiring no user input. This approach models each map as a graph, where map voxels constitute nodes and weighted edges connect neighboring voxels. Nhs initiates Markov diffusion (or random walk) on the weighted graph. As Markov probabilities homogenize through diffusion, an intrinsic segmentation emerges. We validate the segmentations with ground-truth maps based on atomistic models. When implemented on density maps in the 2010 Cryo-EM Modeling Challenge, Nhs efficiently and objectively partitions macromolecules into structurally and functionally relevant subregions at multiple scales.","corpus_id":2375325,"score":0},{"doc_id":"22869601","title":"Virtual nanoscopy: generation of ultra-large high resolution electron microscopy maps.","abstract":"A key obstacle in uncovering the orchestration between molecular and cellular events is the vastly different length scales on which they occur. We describe here a methodology for ultrastructurally mapping regions of cells and tissue as large as 1 mm(2) at nanometer resolution. Our approach employs standard transmission electron microscopy, rapid automated data collection, and stitching to create large virtual slides. It greatly facilitates correlative light-electron microscopy studies to relate structure and function and provides a genuine representation of ultrastructural events. The method is scalable as illustrated by slides up to 281 gigapixels in size. Here, we applied virtual nanoscopy in a correlative light-electron microscopy study to address the role of the endothelial glycocalyx in protein leakage over the glomerular filtration barrier, in an immunogold labeling study of internalization of oncolytic reovirus in human dendritic cells, in a cryo-electron microscopy study of intact vitrified mouse embryonic cells, and in an ultrastructural mapping of a complete zebrafish embryo slice.","corpus_id":7365300,"score":0},{"doc_id":"23251611","title":"Accurate construction of photoactivated localization microscopy (PALM) images for quantitative measurements.","abstract":"Localization-based superresolution microscopy techniques such as Photoactivated Localization Microscopy (PALM) and Stochastic Optical Reconstruction Microscopy (STORM) have allowed investigations of cellular structures with unprecedented optical resolutions. One major obstacle to interpreting superresolution images, however, is the overcounting of molecule numbers caused by fluorophore photoblinking. Using both experimental and simulated images, we determined the effects of photoblinking on the accurate reconstruction of superresolution images and on quantitative measurements of structural dimension and molecule density made from those images. We found that structural dimension and relative density measurements can be made reliably from images that contain photoblinking-related overcounting, but accurate absolute density measurements, and consequently faithful representations of molecule counts and positions in cellular structures, require the application of a clustering algorithm to group localizations that originate from the same molecule. We analyzed how applying a simple algorithm with different clustering thresholds (t(Thresh) and d(Thresh)) affects the accuracy of reconstructed images, and developed an easy method to select optimal thresholds. We also identified an empirical criterion to evaluate whether an imaging condition is appropriate for accurate superresolution image reconstruction with the clustering algorithm. Both the threshold selection method and imaging condition criterion are easy to implement within existing PALM clustering algorithms and experimental conditions. The main advantage of our method is that it generates a superresolution image and molecule position list that faithfully represents molecule counts and positions within a cellular structure, rather than only summarizing structural properties into ensemble parameters. This feature makes it particularly useful for cellular structures of heterogeneous densities and irregular geometries, and allows a variety of quantitative measurements tailored to specific needs of different biological systems.","corpus_id":4843137,"score":0},{"doc_id":"23333657","title":"TMaCS: a hybrid template matching and classification system for partially-automated particle selection.","abstract":"Selection of particle images from electron micrographs presents a bottleneck in determining the structures of macromolecular assemblies by single particle electron cryomicroscopy (cryo-EM). The problem is particularly important when an experimentalist wants to improve the resolution of a 3D map by increasing by tens or hundreds of thousands of images the size of the dataset used for calculating the map. Although several existing methods for automatic particle image selection work well for large protein complexes that produce high-contrast images, it is well known in the cryo-EM community that small complexes that give low-contrast images are often refractory to existing automated particle image selection schemes. Here we develop a method for partially-automated particle image selection when an initial 3D map of the protein under investigation is already available. Candidate particle images are selected from micrographs by template matching with template images derived from projections of the existing 3D map. The candidate particle images are then used to train a support vector machine, which classifies the candidates as particle images or non-particle images. In a final step in the analysis, the selected particle images are subjected to projection matching against the initial 3D map, with the correlation coefficient between the particle image and the best matching map projection used to assess the reliability of the particle image. We show that this approach is able to rapidly select particle images from micrographs of a rotary ATPase, a type of membrane protein complex involved in many aspects of biology.","corpus_id":25508463,"score":0},{"doc_id":"23646160","title":"Real-time analysis and visualization for single-molecule based super-resolution microscopy.","abstract":"Accurate multidimensional localization of isolated fluorescent emitters is a time consuming process in single-molecule based super-resolution microscopy. We demonstrate a functional method for real-time reconstruction with automatic feedback control, without compromising the localization accuracy. Compatible with high frame rates of EM-CCD cameras, it relies on a wavelet segmentation algorithm, together with a mix of CPU/GPU implementation. A combination with Gaussian fitting allows direct access to 3D localization. Automatic feedback control ensures optimal molecule density throughout the acquisition process. With this method, we significantly improve the efficiency and feasibility of localization-based super-resolution microscopy.","corpus_id":17235975,"score":0},{"doc_id":"23796504","title":"Computational methods for constructing protein structure models from 3D electron microscopy maps.","abstract":"Protein structure determination by cryo-electron microscopy (EM) has made significant progress in the past decades. Resolutions of EM maps have been improving as evidenced by recently reported structures that are solved at high resolutions close to 3Å. Computational methods play a key role in interpreting EM data. Among many computational procedures applied to an EM map to obtain protein structure information, in this article we focus on reviewing computational methods that model protein three-dimensional (3D) structures from a 3D EM density map that is constructed from two-dimensional (2D) maps. The computational methods we discuss range from de novo methods, which identify structural elements in an EM map, to structure fitting methods, where known high resolution structures are fit into a low-resolution EM map. A list of available computational tools is also provided.","corpus_id":18201425,"score":0},{"doc_id":"23831940","title":"Method for local temperature measurement in a nanoreactor for in situ high-resolution electron microscopy.","abstract":"In situ high-resolution transmission electron microscopy (TEM) of solids under reactive gas conditions can be facilitated by microelectromechanical system devices called nanoreactors. These nanoreactors are windowed cells containing nanoliter volumes of gas at ambient pressures and elevated temperatures. However, due to the high spatial confinement of the reaction environment, traditional methods for measuring process parameters, such as the local temperature, are difficult to apply. To address this issue, we devise an electron energy loss spectroscopy (EELS) method that probes the local temperature of the reaction volume under inspection by the electron beam. The local gas density, as measured using quantitative EELS, is combined with the inherent relation between gas density and temperature, as described by the ideal gas law, to obtain the local temperature. Using this method we determined the temperature gradient in a nanoreactor in situ, while the average, global temperature was monitored by a traditional measurement of the electrical resistivity of the heater. The local gas temperatures had a maximum of 56 °C deviation from the global heater values under the applied conditions. The local temperatures, obtained with the proposed method, are in good agreement with predictions from an analytical model.","corpus_id":46460360,"score":0},{"doc_id":"24113625","title":"Quantitative magnetic susceptibility mapping without phase unwrapping using WASSR.","abstract":"The magnetic susceptibility of tissue within and around an image voxel affects the magnetic field and thus the local frequency in that voxel. Recently, it has been shown that spatial maps of frequency can be used to quantify local susceptibility if the contributions of surrounding tissue can be deconvolved. Currently, such quantitative susceptibility mapping (QSM) methods employ gradient recalled echo (GRE) imaging to measure spatial differences in the signal phase evolution as a function of echo time, from which frequencies can be deduced. Analysis of these phase images, however, is complicated by phase wraps, despite the availability and usage of various phase unwrapping algorithms. In addition, lengthy high-resolution GRE scanning often heats the magnet bore, causing the magnetic field to drift over several Hertz, which is on the order of the frequency differences between tissues. Here, we explore the feasibility of applying the WAter Saturation Shift Referencing (WASSR) method for 3D whole brain susceptibility imaging. WASSR uses direct saturation of water protons as a function of frequency irradiation offset to generate frequency maps without phase wraps, which can be combined with any image or spectroscopy acquisition. By utilizing a series of fast short-echo-time direct saturation images with multiple radiofrequency offsets, a frequency correction for field drift can be applied based on the individual image phases. Regions of interest were delineated with an automated atlas-based method, and the average magnetic susceptibilities calculated from frequency maps obtained from WASSR correlated well with those from the phase-based multi-echo GRE approach at 3T.","corpus_id":6833271,"score":0},{"doc_id":"24387516","title":"Adaptive nonlocal means filtering based on local noise level for CT denoising.","abstract":"PURPOSE: To develop and evaluate an image-domain noise reduction method based on a modified nonlocal means (NLM) algorithm that is adaptive to local noise level of CT images and to implement this method in a time frame consistent with clinical workflow. METHODS: A computationally efficient technique for local noise estimation directly from CT images was developed. A forward projection, based on a 2D fan-beam approximation, was used to generate the projection data, with a noise model incorporating the effects of the bowtie filter and automatic exposure control. The noise propagation from projection data to images was analytically derived. The analytical noise map was validated using repeated scans of a phantom. A 3D NLM denoising algorithm was modified to adapt its denoising strength locally based on this noise map. The performance of this adaptive NLM filter was evaluated in phantom studies in terms of in-plane and cross-plane high-contrast spatial resolution, noise power spectrum (NPS), subjective low-contrast spatial resolution using the American College of Radiology (ACR) accreditation phantom, and objective low-contrast spatial resolution using a channelized Hotelling model observer (CHO). Graphical processing units (GPU) implementation of this noise map calculation and the adaptive NLM filtering were developed to meet demands of clinical workflow. Adaptive NLM was piloted on lower dose scans in clinical practice. RESULTS: The local noise level estimation matches the noise distribution determined from multiple repetitive scans of a phantom, demonstrated by small variations in the ratio map between the analytical noise map and the one calculated from repeated scans. The phantom studies demonstrated that the adaptive NLM filter can reduce noise substantially without degrading the high-contrast spatial resolution, as illustrated by modulation transfer function and slice sensitivity profile results. The NPS results show that adaptive NLM denoising preserves the shape and peak frequency of the noise power spectrum better than commercial smoothing kernels, and indicate that the spatial resolution at low contrast levels is not significantly degraded. Both the subjective evaluation using the ACR phantom and the objective evaluation on a low-contrast detection task using a CHO model observer demonstrate an improvement on low-contrast performance. The GPU implementation can process and transfer 300 slice images within 5 min. On patient data, the adaptive NLM algorithm provides more effective denoising of CT data throughout a volume than standard NLM, and may allow significant lowering of radiation dose. After a two week pilot study of lower dose CT urography and CT enterography exams, both GI and GU radiology groups elected to proceed with permanent implementation of adaptive NLM in their GI and GU CT practices. CONCLUSIONS: This work describes and validates a computationally efficient technique for noise map estimation directly from CT images, and an adaptive NLM filtering based on this noise map, on phantom and patient data. Both the noise map calculation and the adaptive NLM filtering can be performed in times that allow integration with clinical workflow. The adaptive NLM algorithm provides effective denoising of CT data throughout a volume, and may allow significant lowering of radiation dose.","corpus_id":35353066,"score":0},{"doc_id":"24466491","title":"Improved localization accuracy in stochastic super-resolution fluorescence microscopy by K-factor image deshadowing.","abstract":"Localization of a single fluorescent particle with sub-diffraction-limit accuracy is a key merit in localization microscopy. Existing methods such as photoactivated localization microscopy (PALM) and stochastic optical reconstruction microscopy (STORM) achieve localization accuracies of single emitters that can reach an order of magnitude lower than the conventional resolving capabilities of optical microscopy. However, these techniques require a sparse distribution of simultaneously activated fluorophores in the field of view, resulting in larger time needed for the construction of the full image. In this paper we present the use of a nonlinear image decomposition algorithm termed K-factor, which reduces an image into a nonlinear set of contrast-ordered decompositions whose joint product reassembles the original image. The K-factor technique, when implemented on raw data prior to localization, can improve the localization accuracy of standard existing methods, and also enable the localization of overlapping particles, allowing the use of increased fluorophore activation density, and thereby increased data collection speed. Numerical simulations of fluorescence data with random probe positions, and especially at high densities of activated fluorophores, demonstrate an improvement of up to 85% in the localization precision compared to single fitting techniques. Implementing the proposed concept on experimental data of cellular structures yielded a 37% improvement in resolution for the same super-resolution image acquisition time, and a decrease of 42% in the collection time of super-resolution data with the same resolution.","corpus_id":263472317,"score":0},{"doc_id":"24491638","title":"A modular hierarchical approach to 3D electron microscopy image segmentation.","abstract":"The study of neural circuit reconstruction, i.e., connectomics, is a challenging problem in neuroscience. Automated and semi-automated electron microscopy (EM) image analysis can be tremendously helpful for connectomics research. In this paper, we propose a fully automatic approach for intra-section segmentation and inter-section reconstruction of neurons using EM images. A hierarchical merge tree structure is built to represent multiple region hypotheses and supervised classification techniques are used to evaluate their potentials, based on which we resolve the merge tree with consistency constraints to acquire final intra-section segmentation. Then, we use a supervised learning based linking procedure for the inter-section neuron reconstruction. Also, we develop a semi-automatic method that utilizes the intermediate outputs of our automatic algorithm and achieves intra-segmentation with minimal user intervention. The experimental results show that our automatic method can achieve close-to-human intra-segmentation accuracy and state-of-the-art inter-section reconstruction accuracy. We also show that our semi-automatic method can further improve the intra-segmentation accuracy.","corpus_id":1213873,"score":0},{"doc_id":"24577277","title":"Fluorophore localization algorithms for super-resolution microscopy.","abstract":"Super-resolution localization microscopy methods provide powerful new capabilities for probing biology at the nanometer scale via fluorescence. These methods rely on two key innovations: switchable fluorophores (which blink on and off and can be sequentially imaged) and powerful localization algorithms (which estimate the positions of the fluorophores in the images). These techniques have spurred a flurry of innovation in algorithm development over the last several years. In this Review, we survey the fundamental issues for single-fluorophore fitting routines, localization algorithms based on principles other than fitting, three-dimensional imaging, dipole imaging and techniques for estimating fluorophore positions from images of multiple activated fluorophores. We offer practical advice for users and adopters of algorithms, and we identify areas for further development.","corpus_id":35570325,"score":0},{"doc_id":"24974203","title":"Efficient initial volume determination from electron microscopy images of single particles.","abstract":"MOTIVATION: Structural information of macromolecular complexes provides key insights into the way they carry out their biological functions. The reconstruction process leading to the final 3D map requires an approximate initial model. Generation of an initial model is still an open and challenging problem in single-particle analysis. RESULTS: We present a fast and efficient approach to obtain a reliable, low-resolution estimation of the 3D structure of a macromolecule, without any a priori knowledge, addressing the well-known issue of initial volume estimation in the field of single-particle analysis. The input of the algorithm is a set of class average images obtained from individual projections of a biological object at random and unknown orientations by transmission electron microscopy micrographs. The proposed method is based on an initial non-lineal dimensionality reduction approach, which allows to automatically selecting representative small sets of class average images capturing the most of the structural information of the particle under study. These reduced sets are then used to generate volumes from random orientation assignments. The best volume is determined from these guesses using a random sample consensus (RANSAC) approach. We have tested our proposed algorithm, which we will term 3D-RANSAC, with simulated and experimental data, obtaining satisfactory results under the low signal-to-noise conditions typical of cryo-electron microscopy. AVAILABILITY: The algorithm is freely available as part of the Xmipp 3.1 package [http://xmipp.cnb.csic.es]. CONTACT: jvargas@cnb.csic.es SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.","corpus_id":8183036,"score":0},{"doc_id":"25497718","title":"Simultaneous orientation and thickness mapping in transmission electron microscopy.","abstract":"In this paper we introduce an approach for simultaneous thickness and orientation mapping of crystalline samples by means of transmission electron microscopy. We show that local thickness and orientation values can be extracted from experimental dark-field (DF) image data acquired at different specimen tilts. The method has been implemented to automatically acquire the necessary data and then map thickness and crystal orientation for a given region of interest. We have applied this technique to a specimen prepared from a commercial semiconductor device, containing multiple 22 nm technology transistor structures. The performance and limitations of our method are discussed and compared to those of other techniques available.","corpus_id":4881934,"score":0},{"doc_id":"25980777","title":"A fully automatic reference deconvolution strategy to increase the accuracy of in vivo lipid signal quantification.","abstract":"PURPOSE: Lipid signals measured by (1) H MR spectroscopy cannot be adequately quantified by common fitting routines like VARPRO or AMARES, if lipid spectra are distorted by irregular spatial and temporal inhomogeneities of the static magnetic field during readout. A fully automatic reference deconvolution algorithm is presented that eliminates these distortions before application of fitting routines. METHODS: The measured signal of the dominant methyl resonance is isolated with aid of a spectral estimator (estimation of parameters via rotational invariance techniques) and used as reference signal for estimation of distortions. A Wiener filter is applied to deconvolve those distortions in the lipid spectrum. Performance of the algorithm is assessed for different bandwidths and shapes of distortions, using artificially distorted as well as measured data. RESULTS: Application of the fully automatic reference deconvolution algorithm on simulated spectra yields a distinct increase in quantification accuracy. Deconvolved in vivo spectra of subcutaneous fat indicate reduced spectral overlap after application of the proposed strategy. CONCLUSION: The proposed method is helpful for in vivo magnetic resonance spectroscopy of adipose tissue to correct for effects of field inhomogeneities within the voxel and for inevitable eddy current effects. Quantification accuracy is improved by eliminating distortions before application of fitting routines. Magn Reson Med, 2015. © 2015 Wiley Periodicals, Inc.","corpus_id":30036972,"score":0},{"doc_id":"26025554","title":"Navigating 3D electron microscopy maps with EM-SURFER.","abstract":"BACKGROUND: The Electron Microscopy DataBank (EMDB) is growing rapidly, accumulating biological structural data obtained mainly by electron microscopy and tomography, which are emerging techniques for determining large biomolecular complex and subcellular structures. Together with the Protein Data Bank (PDB), EMDB is becoming a fundamental resource of the tertiary structures of biological macromolecules. To take full advantage of this indispensable resource, the ability to search the database by structural similarity is essential. However, unlike high-resolution structures stored in PDB, methods for comparing low-resolution electron microscopy (EM) density maps in EMDB are not well established. RESULTS: We developed a computational method for efficiently searching low-resolution EM maps. The method uses a compact fingerprint representation of EM maps based on the 3D Zernike descriptor, which is derived from a mathematical series expansion for EM maps that are considered as 3D functions. The method is implemented in a web server named EM-SURFER, which allows users to search against the entire EMDB in real-time. EM-SURFER compares the global shapes of EM maps. Examples of search results from different types of query structures are discussed. CONCLUSIONS: We developed EM-SURFER, which retrieves structurally relevant matches for query EM maps from EMDB within seconds. The unique capability of EM-SURFER to detect 3D shape similarity of low-resolution EM maps should prove invaluable in structural biology.","corpus_id":5835864,"score":0},{"doc_id":"26098742","title":"SNSMIL, a real-time single molecule identification and localization algorithm for super-resolution fluorescence microscopy.","abstract":"Single molecule localization based super-resolution fluorescence microscopy offers significantly higher spatial resolution than predicted by Abbe's resolution limit for far field optical microscopy. Such super-resolution images are reconstructed from wide-field or total internal reflection single molecule fluorescence recordings. Discrimination between emission of single fluorescent molecules and background noise fluctuations remains a great challenge in current data analysis. Here we present a real-time, and robust single molecule identification and localization algorithm, SNSMIL (Shot Noise based Single Molecule Identification and Localization). This algorithm is based on the intrinsic nature of noise, i.e., its Poisson or shot noise characteristics and a new identification criterion, QSNSMIL, is defined. SNSMIL improves the identification accuracy of single fluorescent molecules in experimental or simulated datasets with high and inhomogeneous background. The implementation of SNSMIL relies on a graphics processing unit (GPU), making real-time analysis feasible as shown for real experimental and simulated datasets.","corpus_id":6299069,"score":0},{"doc_id":"26475830","title":"Fast clustering using adaptive density peak detection.","abstract":"Common limitations of clustering methods include the slow algorithm convergence, the instability of the pre-specification on a number of intrinsic parameters, and the lack of robustness to outliers. A recent clustering approach proposed a fast search algorithm of cluster centers based on their local densities. However, the selection of the key intrinsic parameters in the algorithm was not systematically investigated. It is relatively difficult to estimate the \"optimal\" parameters since the original definition of the local density in the algorithm is based on a truncated counting measure. In this paper, we propose a clustering procedure with adaptive density peak detection, where the local density is estimated through the nonparametric multivariate kernel estimation. The model parameter is then able to be calculated from the equations with statistical theoretical justification. We also develop an automatic cluster centroid selection method through maximizing an average silhouette index. The advantage and flexibility of the proposed method are demonstrated through simulation studies and the analysis of a few benchmark gene expression data sets. The method only needs to perform in one single step without any iteration and thus is fast and has a great potential to apply on big data analysis. A user-friendly R package ADPclust is developed for public use.","corpus_id":7670906,"score":0},{"doc_id":"26745932","title":"Improved accuracy of quantitative parameter estimates in dynamic contrast-enhanced CT study with low temporal resolution.","abstract":"PURPOSE: A previously proposed method to reduce radiation dose to patient in dynamic contrast-enhanced (DCE) CT is enhanced by principal component analysis (PCA) filtering which improves the signal-to-noise ratio (SNR) of time-concentration curves in the DCE-CT study. The efficacy of the combined method to maintain the accuracy of kinetic parameter estimates at low temporal resolution is investigated with pixel-by-pixel kinetic analysis of DCE-CT data. METHODS: The method is based on DCE-CT scanning performed with low temporal resolution to reduce the radiation dose to the patient. The arterial input function (AIF) with high temporal resolution can be generated with a coarsely sampled AIF through a previously published method of AIF estimation. To increase the SNR of time-concentration curves (tissue curves), first, a region-of-interest is segmented into squares composed of 3 × 3 pixels in size. Subsequently, the PCA filtering combined with a fraction of residual information criterion is applied to all the segmented squares for further improvement of their SNRs. The proposed method was applied to each DCE-CT data set of a cohort of 14 patients at varying levels of down-sampling. The kinetic analyses using the modified Tofts' model and singular value decomposition method, then, were carried out for each of the down-sampling schemes between the intervals from 2 to 15 s. The results were compared with analyses done with the measured data in high temporal resolution (i.e., original scanning frequency) as the reference. RESULTS: The patients' AIFs were estimated to high accuracy based on the 11 orthonormal bases of arterial impulse responses established in the previous paper. In addition, noise in the images was effectively reduced by using five principal components of the tissue curves for filtering. Kinetic analyses using the proposed method showed superior results compared to those with down-sampling alone; they were able to maintain the accuracy in the quantitative histogram parameters of volume transfer constant [standard deviation (SD), 98th percentile, and range], rate constant (SD), blood volume fraction (mean, SD, 98th percentile, and range), and blood flow (mean, SD, median, 98th percentile, and range) for sampling intervals between 10 and 15 s. CONCLUSIONS: The proposed method of PCA filtering combined with the AIF estimation technique allows low frequency scanning for DCE-CT study to reduce patient radiation dose. The results indicate that the method is useful in pixel-by-pixel kinetic analysis of DCE-CT data for patients with cervical cancer.","corpus_id":25669508,"score":0},{"doc_id":"26851711","title":"A new gradient shimming method based on undistorted field map of B0 inhomogeneity.","abstract":"Most existing gradient shimming methods for NMR spectrometers estimate field maps that resolve B0 inhomogeneity spatially from dual gradient-echo (GRE) images acquired at different echo times. However, the distortions induced by B0 inhomogeneity that always exists in the GRE images can result in estimated field maps that are distorted in both geometry and intensity, leading to inaccurate shimming. This work proposes a new gradient shimming method based on undistorted field map of B0 inhomogeneity obtained by a more accurate field map estimation technique. Compared to the traditional field map estimation method, this new method exploits both the positive and negative polarities of the frequency encoded gradients to eliminate the distortions caused by B0 inhomogeneity in the field map. Next, the corresponding automatic post-data procedure is introduced to obtain undistorted B0 field map based on knowledge of the invariant characteristics of the B0 inhomogeneity and the variant polarity of the encoded gradient. The experimental results on both simulated and real gradient shimming tests demonstrate the high performance of this new method.","corpus_id":42431239,"score":0},{"doc_id":"26894674","title":"Fitmunk: improving protein structures by accurate, automatic modeling of side-chain conformations.","abstract":"Improvements in crystallographic hardware and software have allowed automated structure-solution pipelines to approach a near-`one-click' experience for the initial determination of macromolecular structures. However, in many cases the resulting initial model requires a laborious, iterative process of refinement and validation. A new method has been developed for the automatic modeling of side-chain conformations that takes advantage of rotamer-prediction methods in a crystallographic context. The algorithm, which is based on deterministic dead-end elimination (DEE) theory, uses new dense conformer libraries and a hybrid energy function derived from experimental data and prior information about rotamer frequencies to find the optimal conformation of each side chain. In contrast to existing methods, which incorporate the electron-density term into protein-modeling frameworks, the proposed algorithm is designed to take advantage of the highly discriminatory nature of electron-density maps. This method has been implemented in the program Fitmunk, which uses extensive conformational sampling. This improves the accuracy of the modeling and makes it a versatile tool for crystallographic model building, refinement and validation. Fitmunk was extensively tested on over 115 new structures, as well as a subset of 1100 structures from the PDB. It is demonstrated that the ability of Fitmunk to model more than 95% of side chains accurately is beneficial for improving the quality of crystallographic protein models, especially at medium and low resolutions. Fitmunk can be used for model validation of existing structures and as a tool to assess whether side chains are modeled optimally or could be better fitted into electron density. Fitmunk is available as a web service at http://kniahini.med.virginia.edu/fitmunk/server/ or at http://fitmunk.bitbucket.org/.","corpus_id":263091334,"score":0},{"doc_id":"27102900","title":"Local analysis of strains and rotations for macromolecular electron microscopy maps.","abstract":"Macromolecular complexes perform their physiological functions by local rearrangements of their constituents and biochemically interacting with their reaction partners. These rearrangements may involve local rotations and the induction of local strains causing different mechanical efforts and stretches at the different areas of the protein. The analysis of these local deformations may reveal important insight into the way proteins perform their tasks. In this paper we introduce a method to perform this kind of local analysis using Electron Microscopy volumes in a fully objective and automatic manner. For doing so, we exploit the continuous nature of the result of an elastic image registration using B-splines as its basis functions. We show that the results obtained by the new automatic method are consistent with previous observations on these macromolecules.","corpus_id":3931111,"score":0},{"doc_id":"27170866","title":"Accurate and Fully Automatic Hippocampus Segmentation Using Subject-Specific 3D Optimal Local Maps Into a Hybrid Active Contour Model.","abstract":"Assessing the structural integrity of the hippocampus (HC) is an essential step toward prevention, diagnosis, and follow-up of various brain disorders due to the implication of the structural changes of the HC in those disorders. In this respect, the development of automatic segmentation methods that can accurately, reliably, and reproducibly segment the HC has attracted considerable attention over the past decades. This paper presents an innovative 3-D fully automatic method to be used on top of the multiatlas concept for the HC segmentation. The method is based on a subject-specific set of 3-D optimal local maps (OLMs) that locally control the influence of each energy term of a hybrid active contour model (ACM). The complete set of the OLMs for a set of training images is defined simultaneously via an optimization scheme. At the same time, the optimal ACM parameters are also calculated. Therefore, heuristic parameter fine-tuning is not required. Training OLMs are subsequently combined, by applying an extended multiatlas concept, to produce the OLMs that are anatomically more suitable to the test image. The proposed algorithm was tested on three different and publicly available data sets. Its accuracy was compared with that of state-of-the-art methods demonstrating the efficacy and robustness of the proposed method.","corpus_id":206418115,"score":0},{"doc_id":"27374400","title":"VirusMapper: open-source nanoscale mapping of viral architecture through super-resolution microscopy.","abstract":"The nanoscale molecular assembly of mammalian viruses during their infectious life cycle remains poorly understood. Their small dimensions, generally bellow the 300nm diffraction limit of light microscopes, has limited most imaging studies to electron microscopy. The recent development of super-resolution (SR) light microscopy now allows the visualisation of viral structures at resolutions of tens of nanometers. In addition, these techniques provide the added benefit of molecular specific labelling and the capacity to investigate viral structural dynamics using live-cell microscopy. However, there is a lack of robust analytical tools that allow for precise mapping of viral structure within the setting of infection. Here we present an open-source analytical framework that combines super-resolution imaging and naïve single-particle analysis to generate unbiased molecular models. This tool, VirusMapper, is a high-throughput, user-friendly, ImageJ-based software package allowing for automatic statistical mapping of conserved multi-molecular structures, such as viral substructures or intact viruses. We demonstrate the usability of VirusMapper by applying it to SIM and STED images of vaccinia virus in isolation and when engaged with host cells. VirusMapper allows for the generation of accurate, high-content, molecular specific virion models and detection of nanoscale changes in viral architecture.","corpus_id":19081301,"score":0},{"doc_id":"27657649","title":"StatSTEM: An efficient approach for accurate and precise model-based quantification of atomic resolution electron microscopy images.","abstract":"An efficient model-based estimation algorithm is introduced to quantify the atomic column positions and intensities from atomic resolution (scanning) transmission electron microscopy ((S)TEM) images. This algorithm uses the least squares estimator on image segments containing individual columns fully accounting for overlap between neighbouring columns, enabling the analysis of a large field of view. For this algorithm, the accuracy and precision with which measurements for the atomic column positions and scattering cross-sections from annular dark field (ADF) STEM images can be estimated, has been investigated. The highest attainable precision is reached even for low dose images. Furthermore, the advantages of the model-based approach taking into account overlap between neighbouring columns are highlighted. This is done for the estimation of the distance between two neighbouring columns as a function of their distance and for the estimation of the scattering cross-section which is compared to the integrated intensity from a Voronoi cell. To provide end-users this well-established quantification method, a user friendly program, StatSTEM, is developed which is freely available under a GNU public license.","corpus_id":8829069,"score":0},{"doc_id":"27825346","title":"A vessel segmentation method for multi-modality angiographic images based on multi-scale filtering and statistical models.","abstract":"BACKGROUND: Accurate segmentation of blood vessels plays an important role in the computer-aided diagnosis and interventional treatment of vascular diseases. The statistical method is an important component of effective vessel segmentation; however, several limitations discourage the segmentation effect, i.e., dependence of the image modality, uneven contrast media, bias field, and overlapping intensity distribution of the object and background. In addition, the mixture models of the statistical methods are constructed relaying on the characteristics of the image histograms. Thus, it is a challenging issue for the traditional methods to be available in vessel segmentation from multi-modality angiographic images. METHODS: To overcome these limitations, a flexible segmentation method with a fixed mixture model has been proposed for various angiography modalities. Our method mainly consists of three parts. Firstly, multi-scale filtering algorithm was used on the original images to enhance vessels and suppress noises. As a result, the filtered data achieved a new statistical characteristic. Secondly, a mixture model formed by three probabilistic distributions (two Exponential distributions and one Gaussian distribution) was built to fit the histogram curve of the filtered data, where the expectation maximization (EM) algorithm was used for parameters estimation. Finally, three-dimensional (3D) Markov random field (MRF) were employed to improve the accuracy of pixel-wise classification and posterior probability estimation. To quantitatively evaluate the performance of the proposed method, two phantoms simulating blood vessels with different tubular structures and noises have been devised. Meanwhile, four clinical angiographic data sets from different human organs have been used to qualitatively validate the method. To further test the performance, comparison tests between the proposed method and the traditional ones have been conducted on two different brain magnetic resonance angiography (MRA) data sets. RESULTS: The results of the phantoms were satisfying, e.g., the noise was greatly suppressed, the percentages of the misclassified voxels, i.e., the segmentation error ratios, were no more than 0.3%, and the Dice similarity coefficients (DSCs) were above 94%. According to the opinions of clinical vascular specialists, the vessels in various data sets were extracted with high accuracy since complete vessel trees were extracted while lesser non-vessels and background were falsely classified as vessel. In the comparison experiments, the proposed method showed its superiority in accuracy and robustness for extracting vascular structures from multi-modality angiographic images with complicated background noises. CONCLUSIONS: The experimental results demonstrated that our proposed method was available for various angiographic data. The main reason was that the constructed mixture probability model could unitarily classify vessel object from the multi-scale filtered data of various angiography images. The advantages of the proposed method lie in the following aspects: firstly, it can extract the vessels with poor angiography quality, since the multi-scale filtering algorithm can improve the vessel intensity in the circumstance such as uneven contrast media and bias field; secondly, it performed well for extracting the vessels in multi-modality angiographic images despite various signal-noises; and thirdly, it was implemented with better accuracy, and robustness than the traditional methods. Generally, these traits declare that the proposed method would have significant clinical application.","corpus_id":2808081,"score":0},{"doc_id":"28132494","title":"Introduction to high-resolution cryo-electron microscopy.","abstract":"Wprowadzenie do wysokorozdzielczej kriogenicznej mikroskopii elektronowej. For many years two techniques have dominated structural biology - X-ray crystallography and NMR spectroscopy. Traditional cryo-electron microscopy of biological macromolecules produced macromolecular reconstructions at resolution limited to 6-10 Å. Recent development of transmission electron microscopes, in particular the development of direct electron detectors, and continuous improvements in the available software, have led to the \"resolution revolution\" in cryo-EM. It is now possible to routinely obtain near-atomic-resolution 3D maps of intact biological macromolecules as small as ~100 kDa. Thus, cryo-EM is now becoming the method of choice for structural analysis of many complex assemblies that are unsuitable for structure determination by other methods.","corpus_id":1205060,"score":0},{"doc_id":"28269606","title":"Automatic segmentation of multimodal brain tumor images based on classification of super-voxels.","abstract":"Despite the rapid growth in brain tumor segmentation approaches, there are still many challenges in this field. Automatic segmentation of brain images has a critical role in decreasing the burden of manual labeling and increasing robustness of brain tumor diagnosis. We consider segmentation of glioma tumors, which have a wide variation in size, shape and appearance properties. In this paper images are enhanced and normalized to same scale in a preprocessing step. The enhanced images are then segmented based on their intensities using 3D super-voxels. Usually in images a tumor region can be regarded as a salient object. Inspired by this observation, we propose a new feature which uses a saliency detection algorithm. An edge-aware filtering technique is employed to align edges of the original image to the saliency map which enhances the boundaries of the tumor. Then, for classification of tumors in brain images, a set of robust texture features are extracted from super-voxels. Experimental results indicate that our proposed method outperforms a comparable state-of-the-art algorithm in term of dice score.","corpus_id":54569036,"score":0},{"doc_id":"28373678","title":"Analyzing Single Molecule Localization Microscopy Data Using Cubic Splines.","abstract":"The resolution of super-resolution microscopy based on single molecule localization is in part determined by the accuracy of the localization algorithm. In most published approaches to date this localization is done by fitting an analytical function that approximates the point spread function (PSF) of the microscope. However, particularly for localization in 3D, analytical functions such as a Gaussian, which are computationally inexpensive, may not accurately capture the PSF shape leading to reduced fitting accuracy. On the other hand, analytical functions that can accurately capture the PSF shape, such as those based on pupil functions, can be computationally expensive. Here we investigate the use of cubic splines as an alternative fitting approach. We demonstrate that cubic splines can capture the shape of any PSF with high accuracy and that they can be used for fitting the PSF with only a 2-3x increase in computation time as compared to Gaussian fitting. We provide an open-source software package that measures the PSF of any microscope and uses the measured PSF to perform 3D single molecule localization microscopy analysis with reasonable accuracy and speed.","corpus_id":4521653,"score":0},{"doc_id":"28519516","title":"SU-E-I-19: Local Search Clustering Algorithm for DCE-MRI Analysis.","abstract":"PURPOSE: To develop a local search clustering algorithm for analyzing the dynamic contrasted enhanced (DCE)-MRI data for determining the vascular permeability. The clustered signal will have better contrast-to-noise ratio (CNR) and thus can improve the analysis. METHODS: In DCE-MRI, data often suffer from low CNR. The CNR is particularly poor in central nervous system and could lead to spurious results. We propose a local search clustering algorithm that groups proximal voxels with similar uptake curves and T1 values. The algorithm starts with a seed voxel, and then grows outward to recruit new voxels into a cluster. Once a cluster is formed, all members of the current cluster form a 'seed collection' and the seed point of the cluster becomes the seed collection. The expansions and updates continue with the seed point/collection until the stopping criterion is met. To investigate the effectiveness of our clustering algorithm, we used a 64×64 2D Shepp-Logan phantom. Variations on the T1 values and permeability parameters were applied on different regions in the phantom. The time resolution was set to 30sec and 82 post-contrast data were created. After the DCE-MRI data were generated, Gaussian noise was applied to the images to investigate the effect of noise on the clustering algorithm. DCE analysis was performed on the clustered data and the results were compared against the Result obtained from voxel-by-voxel analysis. RESULTS: The addition of noise degraded the results of DCE estimation. The clustering algorithm on average reduced the errors of the permeability parameters by more than 50% compared to the voxel-by-voxel analysis. CONCLUSIONS: We developed a local search clustering algorithm to segment the concentration time curves of the DCE-MRI data. The proposed clustering algorithm enhances the apparent CNR within the clustered data and reduces the errors of the permeability parameters.","corpus_id":642910,"score":0},{"doc_id":"28572576","title":"EMBuilder: A Template Matching-based Automatic Model-building Program for High-resolution Cryo-Electron Microscopy Maps.","abstract":"The resolution of electron-potential maps in single-particle cryo-electron microscopy (cryoEM) is approaching atomic or near- atomic resolution. However, no program currently exists for de novo cryoEM model building at resolutions exceeding beyond 3.5 Å. Here, we present a program, EMBuilder, based on template matching, to generate cryoEM models at high resolution. The program identifies features in both secondary-structure and Cα stages. In the secondary structure stage, helices and strands are identified with pre-computed templates, and the voxel size of the entire map is then refined to account for microscopic magnification errors. The identified secondary structures are then extended from both ends in the Cα stage via a log-likelihood (LLK) target function, and if possible, the side chains are also assigned. This program can build models of large proteins (~1 MDa) in a reasonable amount of time (~1 day) and thus has the potential to greatly decrease the manual workload required for model building of high-resolution cryoEM maps.","corpus_id":3273894,"score":0},{"doc_id":"28593507","title":"A stochastic algorithm for automatic hand pose and motion estimation.","abstract":"In this paper, a novel, robust, and simple method for automatically estimating the hand pose is proposed and validated. The method uses a multi-camera optoelectronic system and a model-based stochastic algorithm. The approach is marker-based and relies on an Unscented Kalman Filter. A hand kinematic model is introduced for constraining relative marker's positions and improving the algorithm robustness with respect to outliers and possible occlusions. The algorithm outputs are 3D coordinate measures of markers and hand joint angle values. To validate the proposed algorithm, a comparison with ground truths for angular and 3D coordinate measures is carried out. The comparative analysis shows the advantages of using the model-based stochastic algorithm with respect to standard processing software of optoelectronic cameras in terms of implementation simplicity, time consumption, and user effort. The accuracy is remarkable, with a difference of maximum 0.035r a d and 4m m with respect to angular and 3D Cartesian coordinates ground truths, respectively.","corpus_id":207291610,"score":0},{"doc_id":"28774465","title":"A new preprocessing parameter estimation based on geodesic active contour model for automatic vestibular neuritis diagnosis.","abstract":"The diagnostic of the vestibular neuritis (VN) presents many difficulties to traditional assessment methods This paper deals with a fully automatic VN diagnostic system based on nystagmus parameter estimation using a pupil detection algorithm. A geodesic active contour model is implemented to find an accurate segmentation region of the pupil. Hence, the novelty of the proposed algorithm is to speed up the standard segmentation by using a specific mask located on the region of interest. This allows a drastically computing time reduction and a great performance and accuracy of the obtained results. After using this fast segmentation algorithm, the obtained estimated parameters are represented in temporal and frequency settings. A useful principal component analysis (PCA) selection procedure is then applied to obtain a reduced number of estimated parameters which are used to train a multi neural network (MNN). Experimental results on 90 eye movement videos show the effectiveness and the accuracy of the proposed estimation algorithm versus previous work.","corpus_id":4224138,"score":0},{"doc_id":"29388866","title":"Diagnostic Electron Microscopy of Retina.","abstract":"The electron microscopy techniques were used in various fields as an analytical technique under in vitro conditions, which provides the sufficient resolution for better visualization and interpretation. This review gives a brief overview of the analytical application of transmission electron microscopy (TEM) and scanning electron microscopy (SEM) techniques and critical findings in different retinal pathologies. This review article aims to improvise understanding of retinal microstructures for clinicians which will help to improve the interpretation of the current advanced imaging techniques.","corpus_id":3452963,"score":0}],"string":"[\n {\n \"doc_id\": \"20888958\",\n \"title\": \"Resolution measures in molecular electron microscopy.\",\n \"abstract\": \"Resolution measures in molecular electron microscopy provide means to evaluate quality of macromolecular structures computed from sets of their two-dimensional (2D) line projections. When the amount of detail in the computed density map is low there are no external standards by which the resolution of the result can be judged. Instead, resolution measures in molecular electron microscopy evaluate consistency of the results in reciprocal space and present it as a one-dimensional (1D) function of the modulus of spatial frequency. Here we provide description of standard resolution measures commonly used in electron microscopy. We point out that the organizing principle is the relationship between these measures and the spectral signal-to-noise ratio (SSNR) of the computed density map. Within this framework it becomes straightforward to describe the connection between the outcome of resolution evaluations and the quality of electron microscopy maps, in particular, the optimum filtration, in the Wiener sense, of the computed map. We also provide a discussion of practical difficulties of evaluation of resolution in electron microscopy, particularly in terms of its sensitivity to data processing operations used during structure determination process in single particle analysis and in electron tomography (ET).\",\n \"corpus_id\": 23444182,\n \"score\": 2\n },\n {\n \"doc_id\": \"23006110\",\n \"title\": \"Estimation theoretic measure of resolution for stochastic localization microscopy.\",\n \"abstract\": \"One approach to super-resolution fluorescence microscopy, termed stochastic localization microscopy, relies on the nanometer scale spatial localization of individual fluorescent emitters that stochastically label specific features of the specimen. The precision of emitter localization is an important determinant of the resulting image resolution but is insufficient to specify how well the derived images capture the structure of the specimen. We address this deficiency by considering the inference of specimen structure based on the estimated emitter locations. By using estimation theory, we develop a measure of spatial resolution that jointly depends on the density of the emitter labels, the precision of emitter localization, and prior information regarding the spatial frequency content of the labeled object. The Nyquist criterion does not set the scaling of this measure with emitter number. Given prior information and a fixed emitter labeling density, our resolution measure asymptotes to a finite value as the precision of emitter localization improves. By considering the present experimental capabilities, this asymptotic behavior implies that further resolution improvements require increases in labeling density above typical current values. Our treatment also yields algorithms to enhance reliable image features. Overall, our formalism facilitates the rigorous statistical interpretation of the data produced by stochastic localization imaging techniques.\",\n \"corpus_id\": 7413132,\n \"score\": 2\n },\n {\n \"doc_id\": \"23954653\",\n \"title\": \"One number does not fit all: mapping local variations in resolution in cryo-EM reconstructions.\",\n \"abstract\": \"The resolution of density maps from single particle analysis is usually measured in terms of the highest spatial frequency to which consistent information has been obtained. This calculation represents an average over the entire reconstructed volume. In practice, however, substantial local variations in resolution may occur, either from intrinsic properties of the specimen or for technical reasons such as a non-isotropic distribution of viewing orientations. To address this issue, we propose the use of a space-frequency representation, the short-space Fourier transform, to assess the quality of a density map, voxel-by-voxel, i.e. by local resolution mapping. In this approach, the experimental volume is divided into small subvolumes and the resolution determined for each of them. It is illustrated in applications both to model data and to experimental density maps. Regions with lower-than-average resolution may be mobile components or ones with incomplete occupancy or result from multiple conformational states. To improve the interpretability of reconstructions, we propose an adaptive filtering approach that reconciles the resolution to which individual features are calculated with the results of the local resolution map.\",\n \"corpus_id\": 5441800,\n \"score\": 2\n },\n {\n \"doc_id\": \"24213166\",\n \"title\": \"Quantifying the local resolution of cryo-EM density maps.\",\n \"abstract\": \"We propose a definition of local resolution for three-dimensional electron cryo-microscopy (cryo-EM) density maps that uses local sinusoidal features. Our algorithm has no free parameters and is applicable to other imaging modalities, including tomography. By evaluating the local resolution of single-particle reconstructions and subtomogram averages for four example data sets, we report variable resolution across a 4- to 40-Å range.\",\n \"corpus_id\": 13250075,\n \"score\": 2\n },\n {\n \"doc_id\": \"27666962\",\n \"title\": \"A review of resolution measures and related aspects in 3D Electron Microscopy.\",\n \"abstract\": \"Fourier Shell Correlation, Spectral Signal-to-Noise Ratio, Fourier Neighbour Correlation, and Differential Phase Residual are different measures that have been proposed over time to determine the spatial resolution achieved by a certain 3D reconstruction. Estimates of B-factors to describe the reduction in signal-to-noise ratio with increasing resolution is also a useful parameter. All these concepts are interrelated and different thresholds have been given for each one of them. However, the problem of resolution assessment in 3DEM is still far from settled and preferences are normally adopted in order to choose the \\\"correct\\\" threshold. In this paper we review the different concepts, their theoretical foundations and the derivation of their statistical distributions (the basis for establishing sensible thresholds). We provide theoretical justifications for some common practices in the field for which a formal justification was missing. We also analyze the relationship between SSNR and B-factors, the electron dose needed for achieving a given contrast and resolution, the number of images required, etc. Finally, we review the consequences for the number of particles needed to achieve a certain resolution and how to analyze the Signal-to-Noise Ratio for a sequence of imaging operations.\",\n \"corpus_id\": 25932382,\n \"score\": 2\n },\n {\n \"doc_id\": \"29274623\",\n \"title\": \"Automatic estimation of a scale resolution in forensic images.\",\n \"abstract\": \"This paper proposes a new method for an automatic detection of a resolution of a scale or a ruler with graduation marks in the shoeprint images. The method creates a vector of the correlations estimated from the co-occurrence matrices for every row in a shoeprint image. The scale resolution is estimated from maxima in Fourier spectrum of the correlations' vectors. The proposed method is evaluated on over 500 images taken at crime scenes and in a forensics laboratory. The experimental results indicate the possibility of applying the proposed method to automatically estimate the scale resolution in forensic images. The automatic detection of a scale resolution could be used to automatically rescale a forensic image before the printing this image in \\\"one-to-one\\\" scale. Furthermore, the proposed method could be used to automatically rescale images to an equal scale thus allowing to compare the images digitally.\",\n \"corpus_id\": 4576484,\n \"score\": 2\n },\n {\n \"doc_id\": \"18285628\",\n \"title\": \"Minimally resolution biased electron-density maps.\",\n \"abstract\": \"Electron-density maps are calculated by Fourier syntheses with coefficients based on structure factors. Diffraction experiments provide intensities up to a limited resolution; as a consequence, the Fourier syntheses always show series-termination errors. The worse the resolution, the less accurate is the Fourier representation of the electron density. In general, each atomic peak is shifted from the correct position, shows a deformed (with respect to the true distribution of the electrons in the atomic domain) profile, and is surrounded by a series of negative and positive ripples of gradually decreasing amplitude. An algorithm is described which is able to reduce the resolution bias by relocating the peaks in more correct positions and by modifying the peak profile to better fit the real atomic electron densities. Some experimental tests are performed showing the usefulness of the procedure.\",\n \"corpus_id\": 22247257,\n \"score\": 1\n },\n {\n \"doc_id\": \"21244844\",\n \"title\": \"Accurate flexible fitting of high-resolution protein structures into cryo-electron microscopy maps using coarse-grained pseudo-energy minimization.\",\n \"abstract\": \"Cryo-electron microscopy (cryo-EM) has been widely used to explore conformational states of large biomolecular assemblies. The detailed interpretation of cryo-EM data requires the flexible fitting of a known high-resolution protein structure into a low-resolution cryo-EM map. To this end, we have developed what we believe is a new method based on a two-bead-per-residue protein representation, and a modified form of the elastic network model that allows large-scale conformational changes while maintaining pseudobonds and secondary structures. Our method minimizes a pseudo-energy which linearly combines various terms of the modified elastic network model energy with a cryo-EM-fitting score and a collision energy that penalizes steric collisions. Unlike previous flexible fitting efforts using the lowest few normal modes, our method effectively utilizes all normal modes so that both global and local structural changes can be fully modeled. We have validated our method for a diverse set of 10 pairs of protein structures using simulated cryo-EM maps with a range of resolutions and in the absence/presence of random noise. We have shown that our method is both accurate and efficient compared with alternative techniques, and its performance is robust to the addition of random noise. Our method is also shown to be useful for the flexible fitting of three experimental cryo-EM maps.\",\n \"corpus_id\": 13957824,\n \"score\": 1\n },\n {\n \"doc_id\": \"23215134\",\n \"title\": \"Unified resolution bounds for conventional and stochastic localization fluorescence microscopy.\",\n \"abstract\": \"Superresolution microscopy enables imaging in the optical far field with ~20 nm-scale resolution. However, classical concepts of resolution using point-spread and modulation-transfer functions fail to describe the physical limits of superresolution techniques based on stochastic localization of single emitters. Prior treatments of stochastic localization microscopy have defined how accurately a single emitter's position can be determined, but these bounds are restricted to sparse emitters, do not describe conventional microscopy, and fail to provide unified concepts of resolution for all optical methods. Here we introduce a measure of resolution, the information transfer function (ITF), that gives physical limits for conventional and stochastic localization techniques. The ITF bounds the accuracy of image determination as a function of spatial frequency and for conventional microscopy is proportional to the square of the modulation-transfer function. We use the ITF to describe how emitter density and photon counts affect imaging performance across the continuum from conventional to superresolution microscopy, without assuming emitters are sparse. This unified physical description of resolution facilitates experimental choices and designs of image reconstruction algorithms.\",\n \"corpus_id\": 12132490,\n \"score\": 1\n },\n {\n \"doc_id\": \"23261401\",\n \"title\": \"FASTDEF: fast defocus and astigmatism estimation for high-throughput transmission electron microscopy.\",\n \"abstract\": \"In this work we present a fast and automated algorithm for estimating the contrast transfer function (CTF) of a transmission electron microscope. The approach is very suitable for High Throughput work because: (a) it does not require any initial defocus estimation, (b) it is almost an order of magnitude faster than existing approaches, (c) it opens the way to well-defined extensions to the estimation of higher order aberrations, at the same time that provides defocus and astigmatism estimations comparable in accuracy to well established methods, such as Xmipp and CTFFIND3 approaches. The new algorithm is based on obtaining the wrapped modulating phase of the power spectra density pattern by the use of a quadrature filter. This phase is further unwrapped in order to obtain the continuous and smooth absolute phase map; then a Zernike polynomial fitting is performed and the defocus and astigmatism parameters are determined. While the method does not require an initial estimation of the defocus parameters or any non-linear optimization procedure, these approaches can be used if further refinement is desired. Results of the CTF estimation method are presented for standard negative stained images, cryo-electron microscopy images in the absence of carbon support, as well as micrographs with only ice. Additionally, we have also tested the proposed method with micrographs acquired from tilted and untilted samples, obtaining good results. The algorithm is freely available as a part of the Xmipp package [http://xmipp.cnb.csic.es].\",\n \"corpus_id\": 9415778,\n \"score\": 1\n },\n {\n \"doc_id\": \"23872039\",\n \"title\": \"High-resolution noise substitution to measure overfitting and validate resolution in 3D structure determination by single particle electron cryomicroscopy.\",\n \"abstract\": \"Three-dimensional (3D) structure determination by single particle electron cryomicroscopy (cryoEM) involves the calculation of an initial 3D model, followed by extensive iterative improvement of the orientation determination of the individual particle images and the resulting 3D map. Because there is much more noise than signal at high resolution in the images, this creates the possibility of noise reinforcement in the 3D map, which can give a false impression of the resolution attained. The balance between signal and noise in the final map at its limiting resolution depends on the image processing procedure and is not easily predicted. There is a growing awareness in the cryoEM community of how to avoid such over-fitting and over-estimation of resolution. Equally, there has been a reluctance to use the two principal methods of avoidance because they give lower resolution estimates, which some people believe are too pessimistic. Here we describe a simple test that is compatible with any image processing protocol. The test allows measurement of the amount of signal and the amount of noise from overfitting that is present in the final 3D map. We have applied the method to two different sets of cryoEM images of the enzyme beta-galactosidase using several image processing packages. Our procedure involves substituting the Fourier components of the initial particle image stack beyond a chosen resolution by either the Fourier components from an adjacent area of background, or by simple randomisation of the phases of the particle structure factors. This substituted noise thus has the same spectral power distribution as the original data. Comparison of the Fourier Shell Correlation (FSC) plots from the 3D map obtained using the experimental data with that from the same data with high-resolution noise (HR-noise) substituted allows an unambiguous measurement of the amount of overfitting and an accompanying resolution assessment. A simple formula can be used to calculate an unbiased FSC from the two curves, even when a substantial amount of overfitting is present. The approach is software independent. The user is therefore completely free to use any established method or novel combination of methods, provided the HR-noise test is carried out in parallel. Applying this procedure to cryoEM images of beta-galactosidase shows how overfitting varies greatly depending on the procedure, but in the best case shows no overfitting and a resolution of ~6 Å. (382 words).\",\n \"corpus_id\": 25196434,\n \"score\": 1\n },\n {\n \"doc_id\": \"26278980\",\n \"title\": \"CTFFIND4: Fast and accurate defocus estimation from electron micrographs.\",\n \"abstract\": \"CTFFIND is a widely-used program for the estimation of objective lens defocus parameters from transmission electron micrographs. Defocus parameters are estimated by fitting a model of the microscope's contrast transfer function (CTF) to an image's amplitude spectrum. Here we describe modifications to the algorithm which make it significantly faster and more suitable for use with images collected using modern technologies such as dose fractionation and phase plates. We show that this new version preserves the accuracy of the original algorithm while allowing for higher throughput. We also describe a measure of the quality of the fit as a function of spatial frequency and suggest this can be used to define the highest resolution at which CTF oscillations were successfully modeled.\",\n \"corpus_id\": 1121396,\n \"score\": 1\n },\n {\n \"doc_id\": \"26509596\",\n \"title\": \"Resolution limits of ultrafast ultrasound localization microscopy.\",\n \"abstract\": \"As in other imaging methods based on waves, the resolution of ultrasound imaging is limited by the wavelength. However, the diffraction-limit can be overcome by super-localizing single events from isolated sources. In recent years, we developed plane-wave ultrasound allowing frame rates up to 20 000 fps. Ultrafast processes such as rapid movement or disruption of ultrasound contrast agents (UCA) can thus be monitored, providing us with distinct punctual sources that could be localized beyond the diffraction limit. We previously showed experimentally that resolutions beyond λ/10 can be reached in ultrafast ultrasound localization microscopy (uULM) using a 128 transducer matrix in reception. Higher resolutions are theoretically achievable and the aim of this study is to predict the maximum resolution in uULM with respect to acquisition parameters (frequency, transducer geometry, sampling electronics). The accuracy of uULM is the error on the localization of a bubble, considered a point-source in a homogeneous medium. The proposed model consists in two steps: determining the timing accuracy of the microbubble echo in radiofrequency data, then transferring this time accuracy into spatial accuracy. The simplified model predicts a maximum resolution of 40 μm for a 1.75 MHz transducer matrix composed of two rows of 64 elements. Experimental confirmation of the model was performed by flowing microbubbles within a 60 μm microfluidic channel and localizing their blinking under ultrafast imaging (500 Hz frame rate). The experimental resolution, determined as the standard deviation in the positioning of the microbubbles, was predicted within 6 μm (13%) of the theoretical values and followed the analytical relationship with respect to the number of elements and depth. Understanding the underlying physical principles determining the resolution of superlocalization will allow the optimization of the imaging setup for each organ. Ultimately, accuracies better than the size of capillaries are achievable at several centimeter depths.\",\n \"corpus_id\": 27380330,\n \"score\": 1\n },\n {\n \"doc_id\": \"26605834\",\n \"title\": \"Validating maps from single particle electron cryomicroscopy.\",\n \"abstract\": \"Progress in single particle cryo-EM, most recently due to the introduction of direct detector devices, has made the high-resolution structure determination of biological assemblies smaller than 500kDa more routine, but has also increased attention on the need for tools to demonstrate the validity of single particle maps. Although map validation is a continuing subject of research, some consensus has been reached on procedures that reduce model bias and over-fitting during map refinement as well as specific tests that demonstrate map validity. Tilt-pair analysis may be used as a method for demonstrating the consistency at low resolution of a map with image data. For higher-resolution maps, new procedures for more robust resolution assessment and for validating the refinement of atomic coordinate models into single particle maps have been developed.\",\n \"corpus_id\": 29976510,\n \"score\": 1\n },\n {\n \"doc_id\": \"17855124\",\n \"title\": \"Markov random field based automatic image alignment for electron tomography.\",\n \"abstract\": \"We present a method for automatic full-precision alignment of the images in a tomographic tilt series. Full-precision automatic alignment of cryo electron microscopy images has remained a difficult challenge to date, due to the limited electron dose and low image contrast. These facts lead to poor signal to noise ratio (SNR) in the images, which causes automatic feature trackers to generate errors, even with high contrast gold particles as fiducial features. To enable fully automatic alignment for full-precision reconstructions, we frame the problem probabilistically as finding the most likely particle tracks given a set of noisy images, using contextual information to make the solution more robust to the noise in each image. To solve this maximum likelihood problem, we use Markov Random Fields (MRF) to establish the correspondence of features in alignment and robust optimization for projection model estimation. The resulting algorithm, called Robust Alignment and Projection Estimation for Tomographic Reconstruction, or RAPTOR, has not needed any manual intervention for the difficult datasets we have tried, and has provided sub-pixel alignment that is as good as the manual approach by an expert user. We are able to automatically map complete and partial marker trajectories and thus obtain highly accurate image alignment. Our method has been applied to challenging cryo electron tomographic datasets with low SNR from intact bacterial cells, as well as several plastic section and X-ray datasets.\",\n \"corpus_id\": 18525199,\n \"score\": 0\n },\n {\n \"doc_id\": \"18503678\",\n \"title\": \"A 3D Hough transform for indexing EBSD and Kossel patterns.\",\n \"abstract\": \"A three-dimensional Hough transform is designed for the detection of conic curves (hyperbolae and ellipses) formed by the gnomonic projection of diffraction Kossel cones. This new procedure is applied to a high-angular-accuracy analysis of electron backscatter diffraction (EBSD) patterns and to a fully automatic indexing of X-ray Kossel patterns in the SEM. The high-accuracy analysis of EBSD patterns allows for the determination of local elastic strains, without any reference pattern, and with a spatial resolution of a few tens of nanometres. An accuracy of 2 x 10(-4) is achieved on geometrically calculated diagrams. This paper presents also the first fully automatic indexing of Kossel patterns. This automatic indexing procedure can be applied to local texture analysis, as well as to local elastic strain measurements. Although the spatial resolution of Kossel is about 1 microm, the accuracy of strain measurement is in this case much higher than that presently obtained on EBSD.\",\n \"corpus_id\": 25389633,\n \"score\": 0\n },\n {\n \"doc_id\": \"18708469\",\n \"title\": \"Multiple subunit fitting into a low-resolution density map of a macromolecular complex using a gaussian mixture model.\",\n \"abstract\": \"Recently, electron microscopy measurement of single particles has enabled us to reconstruct a low-resolution 3D density map of large biomolecular complexes. If structures of the complex subunits can be solved by x-ray crystallography at atomic resolution, fitting these models into the 3D density map can generate an atomic resolution model of the entire large complex. The fitting of multiple subunits, however, generally requires large computational costs; therefore, development of an efficient algorithm is required. We developed a fast fitting program, \\\"gmfit\\\", which employs a Gaussian mixture model (GMM) to represent approximated shapes of the 3D density map and the atomic models. A GMM is a distribution function composed by adding together several 3D Gaussian density functions. Because our model analytically provides an integral of a product of two distribution functions, it enables us to quickly calculate the fitness of the density map and the atomic models. Using the integral, two types of potential energy function are introduced: the attraction potential energy between a 3D density map and each subunit, and the repulsion potential energy between subunits. The restraint energy for symmetry is also employed to build symmetrical origomeric complexes. To find the optimal configuration of subunits, we randomly generated initial configurations of subunit models, and performed a steepest-descent method using forces and torques of the three potential energies. Comparison between an original density map and its GMM showed that the required number of Gaussian distribution functions for a given accuracy depended on both resolution and molecular size. We then performed test fitting calculations for simulated low-resolution density maps of atomic models of homodimer, trimer, and hexamer, using different search parameters. The results indicated that our method was able to rebuild atomic models of a complex even for maps of 30 A resolution if sufficient numbers (eight or more) of Gaussian distribution functions were employed for each subunit, and the symmetric restraints were assigned for complexes with more than three subunits. As a more realistic test, we tried to build an atomic model of the GroEL/ES complex by fitting 21-subunit atomic models into the 3D density map obtained by cryoelectron microscopy using the C7 symmetric restraints. A model with low root mean-square deviations (14.7 A) was obtained as the lowest-energy model, showing that our fitting method was reasonably accurate. Inclusion of other restraints from biological and biochemical experiments could further enhance the accuracy.\",\n \"corpus_id\": 14849875,\n \"score\": 0\n },\n {\n \"doc_id\": \"18989044\",\n \"title\": \"Computational approaches for automatic structural analysis of large biomolecular complexes.\",\n \"abstract\": \"We present computational solutions to two problems of macromolecular structure interpretation from reconstructed three-dimensional electron microscopy (3D-EM) maps of large bio-molecular complexes at intermediate resolution (5A-15 A). The two problems addressed are: 1) 3D structural alignment (matching) between identified and segmented 3D maps of structure units (e.g. trimeric configuration of proteins), and 2) the secondary structure identification of a segmented protein 3D map (i.e.locations of alpha-helices, beta-sheets). For problem 1, we present an efficient algorithm to correlate spatially (and structurally) two 3D maps of structure units. Besides providing a similarity score between structure units, the algorithm yields an effective technique for resolution refinement of repeated structure units, by 3D alignment and averaging. For problem 2, we present an efficient algorithm to compute eigenvalues and link eigenvectors of a Gaussian convoluted structure tensor derived from the protein 3D Map, thereby identifying and locating secondary structural motifs of proteins. The efficiency and performance of our approach is demonstrated on several experimentally reconstructed 3D maps of virus capsid shells from single-particle cryo-electron microscopy (cryo-EM), as well as computationally simulated protein structure density 3D maps generated from protein model entries in the Protein Data Bank.\",\n \"corpus_id\": 1636056,\n \"score\": 0\n },\n {\n \"doc_id\": \"19434159\",\n \"title\": \"Experimental characterization of 3D localization techniques for particle-tracking and super-resolution microscopy.\",\n \"abstract\": \"Three-dimensional (3D) particle localization at the nanometer scale plays a central role in 3D particle tracking and 3D localization-based super-resolution microscopy. Here we introduce a localization algorithm that is independent of theoretical models and therefore generally applicable to a large number of experimental realizations. Applying this algorithm and a convertible experimental setup we compare the performance of the two major 3D techniques based on astigmatic distortions and on multiplane detection. In both methods we obtain experimental 3D localization accuracies in agreement with theoretical predictions and characterize the depth dependence of the localization accuracy in detail.\",\n \"corpus_id\": 30824985,\n \"score\": 0\n },\n {\n \"doc_id\": \"20109465\",\n \"title\": \"Building and refining protein models within cryo-electron microscopy density maps based on homology modeling and multiscale structure refinement.\",\n \"abstract\": \"Automatic modeling methods using cryoelectron microscopy (cryoEM) density maps as constraints are promising approaches to building atomic models of individual proteins or protein domains. However, their application to large macromolecular assemblies has not been possible largely due to computational limitations inherent to such unsupervised methods. Here we describe a new method, EM-IMO (electron microscopy-iterative modular optimization), for building, modifying and refining local structures of protein models using cryoEM maps as a constraint. As a supervised refinement method, EM-IMO allows users to specify parameters derived from inspections so as to guide, and as a consequence, significantly speed up the refinement. An EM-IMO-based refinement protocol is first benchmarked on a data set of 50 homology models using simulated density maps. A multiscale refinement strategy that combines EM-IMO-based and molecular dynamics-based refinement is then applied to build backbone models for the seven conformers of the five capsid proteins in our near-atomic-resolution cryoEM map of the grass carp reovirus virion, a member of the Aquareovirus genus of the Reoviridae family. The refined models allow us to reconstruct a backbone model of the entire grass carp reovirus capsid and provide valuable functional insights that are described in the accompanying publication [Cheng, L., Zhu, J., Hui, W. H., Zhang, X., Honig, B., Fang, Q. & Zhou, Z. H. (2010). Backbone model of an aquareovirus virion by cryo-electron microscopy and bioinformatics. J. Mol. Biol. ( this issue). doi:10.1016/j.jmb.2009.12.027.]. Our study demonstrates that the integrated use of homology modeling and a multiscale refinement protocol that combines supervised and automated structure refinement offers a practical strategy for building atomic models based on medium- to high-resolution cryoEM density maps.\",\n \"corpus_id\": 42992578,\n \"score\": 0\n },\n {\n \"doc_id\": \"20713087\",\n \"title\": \"Automatic mosaicking and volume assembly for high-throughput serial-section transmission electron microscopy.\",\n \"abstract\": \"We describe a computationally efficient and robust, fully-automatic method for large-scale electron microscopy image registration. The proposed method is able to construct large image mosaics from thousands of smaller, overlapping tiles with unknown or uncertain positions, and to align sections from a serial section capture into a common coordinate system. The method also accounts for nonlinear deformations both in constructing sections and in aligning sections to each other. The underlying algorithms are based on the Fourier shift property which allows for a computationally efficient and robust method. We demonstrate results on two electron microscopy datasets. We also quantify the accuracy of the algorithm through a simulated image capture experiment. The publicly available software tools include the algorithms and a Graphical User Interface for easy access to the algorithms.\",\n \"corpus_id\": 27997186,\n \"score\": 0\n },\n {\n \"doc_id\": \"21844593\",\n \"title\": \"Electron microscopy at a sub-50 pm resolution.\",\n \"abstract\": \"An aberration-corrected electron microscope developed in CREST project has been applied for imaging atoms and clusters buried inside crystals. The resolution of the microscope in scanning transmission electron microscopy (STEM) has experimentally proved to be better than 47 pm by use of a cold-field emission gun at 300 kV. The high resolution has given an advantage for imaging light elements such as lithium atoms discriminating one by one. Moreover, a three-dimensional structure imaging has been demonstrated for dopant clusters by a sub-50 pm STEM, using its high depth resolution.\",\n \"corpus_id\": 21567355,\n \"score\": 0\n },\n {\n \"doc_id\": \"21860371\",\n \"title\": \"Structure of HIV-1 capsid assemblies by cryo-electron microscopy and iterative helical real-space reconstruction.\",\n \"abstract\": \"Cryo-electron microscopy (cryo-EM), combined with image processing, is an increasingly powerful tool for structure determination of macromolecular protein complexes and assemblies. In fact, single particle electron microscopy and two-dimensional (2D) electron crystallography have become relatively routine methodologies and a large number of structures have been solved using these methods. At the same time, image processing and three-dimensional (3D) reconstruction of helical objects has rapidly developed, especially, the iterative helical real-space reconstruction (IHRSR) method, which uses single particle analysis tools in conjunction with helical symmetry. Many biological entities function in filamentous or helical forms, including actin filaments, microtubules, amyloid fibers, tobacco mosaic viruses, and bacteria flagella, and, because a 3D density map of a helical entity can be attained from a single projection image, compared to the many images required for 3D reconstruction of a non-helical object, with the IHRSR method, structural analysis of such flexible and disordered helical assemblies is now attainable. In this video article, we provide detailed protocols for obtaining a 3D density map of a helical protein assembly (HIV-1 capsid is our example), including protocols for cryo-EM specimen preparation, low dose data collection by cryo-EM, indexing of helical diffraction patterns, and image processing and 3D reconstruction using IHRSR. Compared to other techniques, cryo-EM offers optimal specimen preservation under near native conditions. Samples are embedded in a thin layer of vitreous ice, by rapid freezing, and imaged in electron microscopes at liquid nitrogen temperature, under low dose conditions to minimize the radiation damage. Sample images are obtained under near native conditions at the expense of low signal and low contrast in the recorded micrographs. Fortunately, the process of helical reconstruction has largely been automated, with the exception of indexing the helical diffraction pattern. Here, we describe an approach to index helical structure and determine helical symmetries (helical parameters) from digitized micrographs, an essential step for 3D helical reconstruction. Briefly, we obtain an initial 3D density map by applying the IHRSR method. This initial map is then iteratively refined by introducing constraints for the alignment parameters of each segment, thus controlling their degrees of freedom. Further improvement is achieved by correcting for the contrast transfer function (CTF) of the electron microscope (amplitude and phase correction) and by optimizing the helical symmetry of the assembly.\",\n \"corpus_id\": 8398013,\n \"score\": 0\n },\n {\n \"doc_id\": \"22088388\",\n \"title\": \"An accurate multislice method for low-energy transmission electron microscopy.\",\n \"abstract\": \"The conventional multislice method (CMS), originally proposed by Cowley and Moodie (1957), is an important algorithm for image and electron diffraction calculations in transmission electron microscopy. Nevertheless, this method is based on the so-called high-energy approximation, which neglects the second differential term ∂(2)φ(r)/∂z(2) to greatly simplify the calculation without severe loss of accuracy. In the current study, we show that for low-energy transmission electron microscopy (LE-TEM) (<100 kV), the high-energy approximation error becomes large and the accurate multislice method, proposed by Chen and Van Dyck (1997), can be used as an alternative method to obtain more accurate calculations. The accurate multislice method, called the revised real space method (RRS) in this paper, can be realized by treating the propagation and scattering as an entirety in real space. A detailed comparison of the numerical results of the RRS and CMS at different accelerating voltages, Debye-Waller factors, and beam tilts is performed. Results show that for image and diffraction simulations in LE-TEM, CMS is no longer sufficiently accurate and the RRS procedure can be used as an alternative method with reasonable computing time.\",\n \"corpus_id\": 3076886,\n \"score\": 0\n },\n {\n \"doc_id\": \"22320813\",\n \"title\": \"Quantitative accuracy of MAP reconstruction for dynamic PET imaging in small animals.\",\n \"abstract\": \"PURPOSE: Iterative reconstruction algorithms are becoming more commonly employed in positron emission tomography (PET) imaging; however, the quantitative accuracy of the reconstructed images still requires validation for various levels of contrast and counting statistics. METHODS: The authors present an evaluation of the quantitative accuracy of the 3D maximum a posteriori (3D-MAP) image reconstruction algorithm for dynamic PET imaging with comparisons to two of the most widely used reconstruction algorithms: the 2D filtered-backprojection (2D-FBP) and 2D-ordered subsets expectation maximization (2D-OSEM) on the Siemens microPET scanners. The study was performed for various levels of count density encountered in typical dynamic scanning as well as the imaging of cardiac activity concentration in small animal studies on the Focus 120. Specially designed phantoms were used for evaluation of the spatial resolution, image quality, and quantitative accuracy. A normal mouse was employed to evaluate the accuracy of the blood time activity concentration extracted from left ventricle regions of interest (ROIs) within the images as compared to the actual blood activity concentration measured from arterial blood sampling. RESULTS: For MAP reconstructions, the spatial resolution and contrast have been found to reach a stable value after 20 iterations independent of the β values (i.e., hyper parameter which controls the weight of the penalty term) and count density within the frame. The spatial resolution obtained with 3D-MAP reaches values of ∼1.0 mm with a β of 0.01 while the 2D-FBP has value of 1.8 mm and 2D-OSEM has a value of 1.6 mm. It has been observed that the lower the hyper parameter β used in MAP, more iterations are needed to reach the stable noise level (i.e., image roughness). The spatial resolution is improved by using a lower β value at the expense of higher image noise. However, with similar noise level the spatial resolution achieved by 3D-MAP was observed to be better than that by 2D-FBP or 2D-OSEM. Using an image quality phantom containing hot spheres, the estimated activity concentration in the largest sphere has the expected concentration relative to the background area for all the MAP images. The obtained recovery coefficients have been also shown to be almost independent of the count density. 2D-FBP and 2D-OSEM do not perform as well, yielding recovery coefficients lower than those observed with 3D-MAP (approximately 33% lower for the smallest sphere). However, a small positive bias was observed in MAP reconstructed images for frames of very low count density. This bias is present in the uniform area for count density of less than 0.05 × 10(6) counts/ml. For the dynamic mouse study, it was observed that 3D-MAP (even gated at diastole) cannot predict accurately the blood activity concentration due to residual spill-over activity from the myocardium into the left ventricle (approximately 15%). However, 3D-MAP predicts blood activity concentration closer to blood sampling than 2D-FBP. CONCLUSIONS: The authors observed that 3D-MAP produces more accurate activity concentration estimates than 2D-FBP or 2D-OSEM at all practical levels of statistics and contrasts due to improved spatial resolution leading to lesser partial volume effect.\",\n \"corpus_id\": 2867190,\n \"score\": 0\n },\n {\n \"doc_id\": \"22457262\",\n \"title\": \"Automatic off-resonance correction in spiral imaging with piecewise linear autofocus.\",\n \"abstract\": \"Off-resonance generates blurring artifacts in spiral images. Applications that often utilize spiral trajectories, such as fine-resolution imaging and rapid scanning, typically preclude the measurement of accurate field maps needed for effective off-resonance correction. Automatic deblurring, or autofocus, algorithms have been developed to estimate the field map directly from the corrupted data prior to off-resonance correction, eliminating the need for field map measurements. These algorithms rely in whole or in part on optimizing an objective function, and suffer from problems related to the accurate minimization and utility of the function. Here, a new method is presented to correct off-resonance blurring automatically without an objective function using a piecewise linear framework. Local linear field maps are estimated with a combination of k-space spectral analysis and mapdrift, an image feature-based correlation technique, for subsequent piecewise linear deblurring. This approach enables field map estimation without optimization, provides accurate off-resonance correction, is suitable for low signal-to-noise ratio and fine-resolution applications, and does not require access to the raw data. Deblurred images from fine-resolution spiral scans of a phantom and healthy volunteers at 3T show that the proposed method can be superior to conventional autofocus and comparable to field map-based correction.\",\n \"corpus_id\": 21826795,\n \"score\": 0\n },\n {\n \"doc_id\": \"22696408\",\n \"title\": \"Nhs: network-based hierarchical segmentation for cryo-electron microscopy density maps.\",\n \"abstract\": \"Cryo-electron microscopy (cryo-EM) experiments yield low-resolution (3-30 Å) 3D-density maps of macromolecules. These density maps are segmented to identify structurally distinct proteins, protein domains, and subunits. Such partitioning aids the inference of protein motions and guides fitting of high-resolution atomistic structures. Cryo-EM density map segmentation has traditionally required tedious and subjective manual partitioning or semisupervised computational methods, whereas validation of resulting segmentations has remained an open problem in this field. We introduce a network-based hierarchical segmentation (Nhs) method, that provides a multi-scale partitioning, reflecting local and global clustering, while requiring no user input. This approach models each map as a graph, where map voxels constitute nodes and weighted edges connect neighboring voxels. Nhs initiates Markov diffusion (or random walk) on the weighted graph. As Markov probabilities homogenize through diffusion, an intrinsic segmentation emerges. We validate the segmentations with ground-truth maps based on atomistic models. When implemented on density maps in the 2010 Cryo-EM Modeling Challenge, Nhs efficiently and objectively partitions macromolecules into structurally and functionally relevant subregions at multiple scales.\",\n \"corpus_id\": 2375325,\n \"score\": 0\n },\n {\n \"doc_id\": \"22869601\",\n \"title\": \"Virtual nanoscopy: generation of ultra-large high resolution electron microscopy maps.\",\n \"abstract\": \"A key obstacle in uncovering the orchestration between molecular and cellular events is the vastly different length scales on which they occur. We describe here a methodology for ultrastructurally mapping regions of cells and tissue as large as 1 mm(2) at nanometer resolution. Our approach employs standard transmission electron microscopy, rapid automated data collection, and stitching to create large virtual slides. It greatly facilitates correlative light-electron microscopy studies to relate structure and function and provides a genuine representation of ultrastructural events. The method is scalable as illustrated by slides up to 281 gigapixels in size. Here, we applied virtual nanoscopy in a correlative light-electron microscopy study to address the role of the endothelial glycocalyx in protein leakage over the glomerular filtration barrier, in an immunogold labeling study of internalization of oncolytic reovirus in human dendritic cells, in a cryo-electron microscopy study of intact vitrified mouse embryonic cells, and in an ultrastructural mapping of a complete zebrafish embryo slice.\",\n \"corpus_id\": 7365300,\n \"score\": 0\n },\n {\n \"doc_id\": \"23251611\",\n \"title\": \"Accurate construction of photoactivated localization microscopy (PALM) images for quantitative measurements.\",\n \"abstract\": \"Localization-based superresolution microscopy techniques such as Photoactivated Localization Microscopy (PALM) and Stochastic Optical Reconstruction Microscopy (STORM) have allowed investigations of cellular structures with unprecedented optical resolutions. One major obstacle to interpreting superresolution images, however, is the overcounting of molecule numbers caused by fluorophore photoblinking. Using both experimental and simulated images, we determined the effects of photoblinking on the accurate reconstruction of superresolution images and on quantitative measurements of structural dimension and molecule density made from those images. We found that structural dimension and relative density measurements can be made reliably from images that contain photoblinking-related overcounting, but accurate absolute density measurements, and consequently faithful representations of molecule counts and positions in cellular structures, require the application of a clustering algorithm to group localizations that originate from the same molecule. We analyzed how applying a simple algorithm with different clustering thresholds (t(Thresh) and d(Thresh)) affects the accuracy of reconstructed images, and developed an easy method to select optimal thresholds. We also identified an empirical criterion to evaluate whether an imaging condition is appropriate for accurate superresolution image reconstruction with the clustering algorithm. Both the threshold selection method and imaging condition criterion are easy to implement within existing PALM clustering algorithms and experimental conditions. The main advantage of our method is that it generates a superresolution image and molecule position list that faithfully represents molecule counts and positions within a cellular structure, rather than only summarizing structural properties into ensemble parameters. This feature makes it particularly useful for cellular structures of heterogeneous densities and irregular geometries, and allows a variety of quantitative measurements tailored to specific needs of different biological systems.\",\n \"corpus_id\": 4843137,\n \"score\": 0\n },\n {\n \"doc_id\": \"23333657\",\n \"title\": \"TMaCS: a hybrid template matching and classification system for partially-automated particle selection.\",\n \"abstract\": \"Selection of particle images from electron micrographs presents a bottleneck in determining the structures of macromolecular assemblies by single particle electron cryomicroscopy (cryo-EM). The problem is particularly important when an experimentalist wants to improve the resolution of a 3D map by increasing by tens or hundreds of thousands of images the size of the dataset used for calculating the map. Although several existing methods for automatic particle image selection work well for large protein complexes that produce high-contrast images, it is well known in the cryo-EM community that small complexes that give low-contrast images are often refractory to existing automated particle image selection schemes. Here we develop a method for partially-automated particle image selection when an initial 3D map of the protein under investigation is already available. Candidate particle images are selected from micrographs by template matching with template images derived from projections of the existing 3D map. The candidate particle images are then used to train a support vector machine, which classifies the candidates as particle images or non-particle images. In a final step in the analysis, the selected particle images are subjected to projection matching against the initial 3D map, with the correlation coefficient between the particle image and the best matching map projection used to assess the reliability of the particle image. We show that this approach is able to rapidly select particle images from micrographs of a rotary ATPase, a type of membrane protein complex involved in many aspects of biology.\",\n \"corpus_id\": 25508463,\n \"score\": 0\n },\n {\n \"doc_id\": \"23646160\",\n \"title\": \"Real-time analysis and visualization for single-molecule based super-resolution microscopy.\",\n \"abstract\": \"Accurate multidimensional localization of isolated fluorescent emitters is a time consuming process in single-molecule based super-resolution microscopy. We demonstrate a functional method for real-time reconstruction with automatic feedback control, without compromising the localization accuracy. Compatible with high frame rates of EM-CCD cameras, it relies on a wavelet segmentation algorithm, together with a mix of CPU/GPU implementation. A combination with Gaussian fitting allows direct access to 3D localization. Automatic feedback control ensures optimal molecule density throughout the acquisition process. With this method, we significantly improve the efficiency and feasibility of localization-based super-resolution microscopy.\",\n \"corpus_id\": 17235975,\n \"score\": 0\n },\n {\n \"doc_id\": \"23796504\",\n \"title\": \"Computational methods for constructing protein structure models from 3D electron microscopy maps.\",\n \"abstract\": \"Protein structure determination by cryo-electron microscopy (EM) has made significant progress in the past decades. Resolutions of EM maps have been improving as evidenced by recently reported structures that are solved at high resolutions close to 3Å. Computational methods play a key role in interpreting EM data. Among many computational procedures applied to an EM map to obtain protein structure information, in this article we focus on reviewing computational methods that model protein three-dimensional (3D) structures from a 3D EM density map that is constructed from two-dimensional (2D) maps. The computational methods we discuss range from de novo methods, which identify structural elements in an EM map, to structure fitting methods, where known high resolution structures are fit into a low-resolution EM map. A list of available computational tools is also provided.\",\n \"corpus_id\": 18201425,\n \"score\": 0\n },\n {\n \"doc_id\": \"23831940\",\n \"title\": \"Method for local temperature measurement in a nanoreactor for in situ high-resolution electron microscopy.\",\n \"abstract\": \"In situ high-resolution transmission electron microscopy (TEM) of solids under reactive gas conditions can be facilitated by microelectromechanical system devices called nanoreactors. These nanoreactors are windowed cells containing nanoliter volumes of gas at ambient pressures and elevated temperatures. However, due to the high spatial confinement of the reaction environment, traditional methods for measuring process parameters, such as the local temperature, are difficult to apply. To address this issue, we devise an electron energy loss spectroscopy (EELS) method that probes the local temperature of the reaction volume under inspection by the electron beam. The local gas density, as measured using quantitative EELS, is combined with the inherent relation between gas density and temperature, as described by the ideal gas law, to obtain the local temperature. Using this method we determined the temperature gradient in a nanoreactor in situ, while the average, global temperature was monitored by a traditional measurement of the electrical resistivity of the heater. The local gas temperatures had a maximum of 56 °C deviation from the global heater values under the applied conditions. The local temperatures, obtained with the proposed method, are in good agreement with predictions from an analytical model.\",\n \"corpus_id\": 46460360,\n \"score\": 0\n },\n {\n \"doc_id\": \"24113625\",\n \"title\": \"Quantitative magnetic susceptibility mapping without phase unwrapping using WASSR.\",\n \"abstract\": \"The magnetic susceptibility of tissue within and around an image voxel affects the magnetic field and thus the local frequency in that voxel. Recently, it has been shown that spatial maps of frequency can be used to quantify local susceptibility if the contributions of surrounding tissue can be deconvolved. Currently, such quantitative susceptibility mapping (QSM) methods employ gradient recalled echo (GRE) imaging to measure spatial differences in the signal phase evolution as a function of echo time, from which frequencies can be deduced. Analysis of these phase images, however, is complicated by phase wraps, despite the availability and usage of various phase unwrapping algorithms. In addition, lengthy high-resolution GRE scanning often heats the magnet bore, causing the magnetic field to drift over several Hertz, which is on the order of the frequency differences between tissues. Here, we explore the feasibility of applying the WAter Saturation Shift Referencing (WASSR) method for 3D whole brain susceptibility imaging. WASSR uses direct saturation of water protons as a function of frequency irradiation offset to generate frequency maps without phase wraps, which can be combined with any image or spectroscopy acquisition. By utilizing a series of fast short-echo-time direct saturation images with multiple radiofrequency offsets, a frequency correction for field drift can be applied based on the individual image phases. Regions of interest were delineated with an automated atlas-based method, and the average magnetic susceptibilities calculated from frequency maps obtained from WASSR correlated well with those from the phase-based multi-echo GRE approach at 3T.\",\n \"corpus_id\": 6833271,\n \"score\": 0\n },\n {\n \"doc_id\": \"24387516\",\n \"title\": \"Adaptive nonlocal means filtering based on local noise level for CT denoising.\",\n \"abstract\": \"PURPOSE: To develop and evaluate an image-domain noise reduction method based on a modified nonlocal means (NLM) algorithm that is adaptive to local noise level of CT images and to implement this method in a time frame consistent with clinical workflow. METHODS: A computationally efficient technique for local noise estimation directly from CT images was developed. A forward projection, based on a 2D fan-beam approximation, was used to generate the projection data, with a noise model incorporating the effects of the bowtie filter and automatic exposure control. The noise propagation from projection data to images was analytically derived. The analytical noise map was validated using repeated scans of a phantom. A 3D NLM denoising algorithm was modified to adapt its denoising strength locally based on this noise map. The performance of this adaptive NLM filter was evaluated in phantom studies in terms of in-plane and cross-plane high-contrast spatial resolution, noise power spectrum (NPS), subjective low-contrast spatial resolution using the American College of Radiology (ACR) accreditation phantom, and objective low-contrast spatial resolution using a channelized Hotelling model observer (CHO). Graphical processing units (GPU) implementation of this noise map calculation and the adaptive NLM filtering were developed to meet demands of clinical workflow. Adaptive NLM was piloted on lower dose scans in clinical practice. RESULTS: The local noise level estimation matches the noise distribution determined from multiple repetitive scans of a phantom, demonstrated by small variations in the ratio map between the analytical noise map and the one calculated from repeated scans. The phantom studies demonstrated that the adaptive NLM filter can reduce noise substantially without degrading the high-contrast spatial resolution, as illustrated by modulation transfer function and slice sensitivity profile results. The NPS results show that adaptive NLM denoising preserves the shape and peak frequency of the noise power spectrum better than commercial smoothing kernels, and indicate that the spatial resolution at low contrast levels is not significantly degraded. Both the subjective evaluation using the ACR phantom and the objective evaluation on a low-contrast detection task using a CHO model observer demonstrate an improvement on low-contrast performance. The GPU implementation can process and transfer 300 slice images within 5 min. On patient data, the adaptive NLM algorithm provides more effective denoising of CT data throughout a volume than standard NLM, and may allow significant lowering of radiation dose. After a two week pilot study of lower dose CT urography and CT enterography exams, both GI and GU radiology groups elected to proceed with permanent implementation of adaptive NLM in their GI and GU CT practices. CONCLUSIONS: This work describes and validates a computationally efficient technique for noise map estimation directly from CT images, and an adaptive NLM filtering based on this noise map, on phantom and patient data. Both the noise map calculation and the adaptive NLM filtering can be performed in times that allow integration with clinical workflow. The adaptive NLM algorithm provides effective denoising of CT data throughout a volume, and may allow significant lowering of radiation dose.\",\n \"corpus_id\": 35353066,\n \"score\": 0\n },\n {\n \"doc_id\": \"24466491\",\n \"title\": \"Improved localization accuracy in stochastic super-resolution fluorescence microscopy by K-factor image deshadowing.\",\n \"abstract\": \"Localization of a single fluorescent particle with sub-diffraction-limit accuracy is a key merit in localization microscopy. Existing methods such as photoactivated localization microscopy (PALM) and stochastic optical reconstruction microscopy (STORM) achieve localization accuracies of single emitters that can reach an order of magnitude lower than the conventional resolving capabilities of optical microscopy. However, these techniques require a sparse distribution of simultaneously activated fluorophores in the field of view, resulting in larger time needed for the construction of the full image. In this paper we present the use of a nonlinear image decomposition algorithm termed K-factor, which reduces an image into a nonlinear set of contrast-ordered decompositions whose joint product reassembles the original image. The K-factor technique, when implemented on raw data prior to localization, can improve the localization accuracy of standard existing methods, and also enable the localization of overlapping particles, allowing the use of increased fluorophore activation density, and thereby increased data collection speed. Numerical simulations of fluorescence data with random probe positions, and especially at high densities of activated fluorophores, demonstrate an improvement of up to 85% in the localization precision compared to single fitting techniques. Implementing the proposed concept on experimental data of cellular structures yielded a 37% improvement in resolution for the same super-resolution image acquisition time, and a decrease of 42% in the collection time of super-resolution data with the same resolution.\",\n \"corpus_id\": 263472317,\n \"score\": 0\n },\n {\n \"doc_id\": \"24491638\",\n \"title\": \"A modular hierarchical approach to 3D electron microscopy image segmentation.\",\n \"abstract\": \"The study of neural circuit reconstruction, i.e., connectomics, is a challenging problem in neuroscience. Automated and semi-automated electron microscopy (EM) image analysis can be tremendously helpful for connectomics research. In this paper, we propose a fully automatic approach for intra-section segmentation and inter-section reconstruction of neurons using EM images. A hierarchical merge tree structure is built to represent multiple region hypotheses and supervised classification techniques are used to evaluate their potentials, based on which we resolve the merge tree with consistency constraints to acquire final intra-section segmentation. Then, we use a supervised learning based linking procedure for the inter-section neuron reconstruction. Also, we develop a semi-automatic method that utilizes the intermediate outputs of our automatic algorithm and achieves intra-segmentation with minimal user intervention. The experimental results show that our automatic method can achieve close-to-human intra-segmentation accuracy and state-of-the-art inter-section reconstruction accuracy. We also show that our semi-automatic method can further improve the intra-segmentation accuracy.\",\n \"corpus_id\": 1213873,\n \"score\": 0\n },\n {\n \"doc_id\": \"24577277\",\n \"title\": \"Fluorophore localization algorithms for super-resolution microscopy.\",\n \"abstract\": \"Super-resolution localization microscopy methods provide powerful new capabilities for probing biology at the nanometer scale via fluorescence. These methods rely on two key innovations: switchable fluorophores (which blink on and off and can be sequentially imaged) and powerful localization algorithms (which estimate the positions of the fluorophores in the images). These techniques have spurred a flurry of innovation in algorithm development over the last several years. In this Review, we survey the fundamental issues for single-fluorophore fitting routines, localization algorithms based on principles other than fitting, three-dimensional imaging, dipole imaging and techniques for estimating fluorophore positions from images of multiple activated fluorophores. We offer practical advice for users and adopters of algorithms, and we identify areas for further development.\",\n \"corpus_id\": 35570325,\n \"score\": 0\n },\n {\n \"doc_id\": \"24974203\",\n \"title\": \"Efficient initial volume determination from electron microscopy images of single particles.\",\n \"abstract\": \"MOTIVATION: Structural information of macromolecular complexes provides key insights into the way they carry out their biological functions. The reconstruction process leading to the final 3D map requires an approximate initial model. Generation of an initial model is still an open and challenging problem in single-particle analysis. RESULTS: We present a fast and efficient approach to obtain a reliable, low-resolution estimation of the 3D structure of a macromolecule, without any a priori knowledge, addressing the well-known issue of initial volume estimation in the field of single-particle analysis. The input of the algorithm is a set of class average images obtained from individual projections of a biological object at random and unknown orientations by transmission electron microscopy micrographs. The proposed method is based on an initial non-lineal dimensionality reduction approach, which allows to automatically selecting representative small sets of class average images capturing the most of the structural information of the particle under study. These reduced sets are then used to generate volumes from random orientation assignments. The best volume is determined from these guesses using a random sample consensus (RANSAC) approach. We have tested our proposed algorithm, which we will term 3D-RANSAC, with simulated and experimental data, obtaining satisfactory results under the low signal-to-noise conditions typical of cryo-electron microscopy. AVAILABILITY: The algorithm is freely available as part of the Xmipp 3.1 package [http://xmipp.cnb.csic.es]. CONTACT: jvargas@cnb.csic.es SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.\",\n \"corpus_id\": 8183036,\n \"score\": 0\n },\n {\n \"doc_id\": \"25497718\",\n \"title\": \"Simultaneous orientation and thickness mapping in transmission electron microscopy.\",\n \"abstract\": \"In this paper we introduce an approach for simultaneous thickness and orientation mapping of crystalline samples by means of transmission electron microscopy. We show that local thickness and orientation values can be extracted from experimental dark-field (DF) image data acquired at different specimen tilts. The method has been implemented to automatically acquire the necessary data and then map thickness and crystal orientation for a given region of interest. We have applied this technique to a specimen prepared from a commercial semiconductor device, containing multiple 22 nm technology transistor structures. The performance and limitations of our method are discussed and compared to those of other techniques available.\",\n \"corpus_id\": 4881934,\n \"score\": 0\n },\n {\n \"doc_id\": \"25980777\",\n \"title\": \"A fully automatic reference deconvolution strategy to increase the accuracy of in vivo lipid signal quantification.\",\n \"abstract\": \"PURPOSE: Lipid signals measured by (1) H MR spectroscopy cannot be adequately quantified by common fitting routines like VARPRO or AMARES, if lipid spectra are distorted by irregular spatial and temporal inhomogeneities of the static magnetic field during readout. A fully automatic reference deconvolution algorithm is presented that eliminates these distortions before application of fitting routines. METHODS: The measured signal of the dominant methyl resonance is isolated with aid of a spectral estimator (estimation of parameters via rotational invariance techniques) and used as reference signal for estimation of distortions. A Wiener filter is applied to deconvolve those distortions in the lipid spectrum. Performance of the algorithm is assessed for different bandwidths and shapes of distortions, using artificially distorted as well as measured data. RESULTS: Application of the fully automatic reference deconvolution algorithm on simulated spectra yields a distinct increase in quantification accuracy. Deconvolved in vivo spectra of subcutaneous fat indicate reduced spectral overlap after application of the proposed strategy. CONCLUSION: The proposed method is helpful for in vivo magnetic resonance spectroscopy of adipose tissue to correct for effects of field inhomogeneities within the voxel and for inevitable eddy current effects. Quantification accuracy is improved by eliminating distortions before application of fitting routines. Magn Reson Med, 2015. © 2015 Wiley Periodicals, Inc.\",\n \"corpus_id\": 30036972,\n \"score\": 0\n },\n {\n \"doc_id\": \"26025554\",\n \"title\": \"Navigating 3D electron microscopy maps with EM-SURFER.\",\n \"abstract\": \"BACKGROUND: The Electron Microscopy DataBank (EMDB) is growing rapidly, accumulating biological structural data obtained mainly by electron microscopy and tomography, which are emerging techniques for determining large biomolecular complex and subcellular structures. Together with the Protein Data Bank (PDB), EMDB is becoming a fundamental resource of the tertiary structures of biological macromolecules. To take full advantage of this indispensable resource, the ability to search the database by structural similarity is essential. However, unlike high-resolution structures stored in PDB, methods for comparing low-resolution electron microscopy (EM) density maps in EMDB are not well established. RESULTS: We developed a computational method for efficiently searching low-resolution EM maps. The method uses a compact fingerprint representation of EM maps based on the 3D Zernike descriptor, which is derived from a mathematical series expansion for EM maps that are considered as 3D functions. The method is implemented in a web server named EM-SURFER, which allows users to search against the entire EMDB in real-time. EM-SURFER compares the global shapes of EM maps. Examples of search results from different types of query structures are discussed. CONCLUSIONS: We developed EM-SURFER, which retrieves structurally relevant matches for query EM maps from EMDB within seconds. The unique capability of EM-SURFER to detect 3D shape similarity of low-resolution EM maps should prove invaluable in structural biology.\",\n \"corpus_id\": 5835864,\n \"score\": 0\n },\n {\n \"doc_id\": \"26098742\",\n \"title\": \"SNSMIL, a real-time single molecule identification and localization algorithm for super-resolution fluorescence microscopy.\",\n \"abstract\": \"Single molecule localization based super-resolution fluorescence microscopy offers significantly higher spatial resolution than predicted by Abbe's resolution limit for far field optical microscopy. Such super-resolution images are reconstructed from wide-field or total internal reflection single molecule fluorescence recordings. Discrimination between emission of single fluorescent molecules and background noise fluctuations remains a great challenge in current data analysis. Here we present a real-time, and robust single molecule identification and localization algorithm, SNSMIL (Shot Noise based Single Molecule Identification and Localization). This algorithm is based on the intrinsic nature of noise, i.e., its Poisson or shot noise characteristics and a new identification criterion, QSNSMIL, is defined. SNSMIL improves the identification accuracy of single fluorescent molecules in experimental or simulated datasets with high and inhomogeneous background. The implementation of SNSMIL relies on a graphics processing unit (GPU), making real-time analysis feasible as shown for real experimental and simulated datasets.\",\n \"corpus_id\": 6299069,\n \"score\": 0\n },\n {\n \"doc_id\": \"26475830\",\n \"title\": \"Fast clustering using adaptive density peak detection.\",\n \"abstract\": \"Common limitations of clustering methods include the slow algorithm convergence, the instability of the pre-specification on a number of intrinsic parameters, and the lack of robustness to outliers. A recent clustering approach proposed a fast search algorithm of cluster centers based on their local densities. However, the selection of the key intrinsic parameters in the algorithm was not systematically investigated. It is relatively difficult to estimate the \\\"optimal\\\" parameters since the original definition of the local density in the algorithm is based on a truncated counting measure. In this paper, we propose a clustering procedure with adaptive density peak detection, where the local density is estimated through the nonparametric multivariate kernel estimation. The model parameter is then able to be calculated from the equations with statistical theoretical justification. We also develop an automatic cluster centroid selection method through maximizing an average silhouette index. The advantage and flexibility of the proposed method are demonstrated through simulation studies and the analysis of a few benchmark gene expression data sets. The method only needs to perform in one single step without any iteration and thus is fast and has a great potential to apply on big data analysis. A user-friendly R package ADPclust is developed for public use.\",\n \"corpus_id\": 7670906,\n \"score\": 0\n },\n {\n \"doc_id\": \"26745932\",\n \"title\": \"Improved accuracy of quantitative parameter estimates in dynamic contrast-enhanced CT study with low temporal resolution.\",\n \"abstract\": \"PURPOSE: A previously proposed method to reduce radiation dose to patient in dynamic contrast-enhanced (DCE) CT is enhanced by principal component analysis (PCA) filtering which improves the signal-to-noise ratio (SNR) of time-concentration curves in the DCE-CT study. The efficacy of the combined method to maintain the accuracy of kinetic parameter estimates at low temporal resolution is investigated with pixel-by-pixel kinetic analysis of DCE-CT data. METHODS: The method is based on DCE-CT scanning performed with low temporal resolution to reduce the radiation dose to the patient. The arterial input function (AIF) with high temporal resolution can be generated with a coarsely sampled AIF through a previously published method of AIF estimation. To increase the SNR of time-concentration curves (tissue curves), first, a region-of-interest is segmented into squares composed of 3 × 3 pixels in size. Subsequently, the PCA filtering combined with a fraction of residual information criterion is applied to all the segmented squares for further improvement of their SNRs. The proposed method was applied to each DCE-CT data set of a cohort of 14 patients at varying levels of down-sampling. The kinetic analyses using the modified Tofts' model and singular value decomposition method, then, were carried out for each of the down-sampling schemes between the intervals from 2 to 15 s. The results were compared with analyses done with the measured data in high temporal resolution (i.e., original scanning frequency) as the reference. RESULTS: The patients' AIFs were estimated to high accuracy based on the 11 orthonormal bases of arterial impulse responses established in the previous paper. In addition, noise in the images was effectively reduced by using five principal components of the tissue curves for filtering. Kinetic analyses using the proposed method showed superior results compared to those with down-sampling alone; they were able to maintain the accuracy in the quantitative histogram parameters of volume transfer constant [standard deviation (SD), 98th percentile, and range], rate constant (SD), blood volume fraction (mean, SD, 98th percentile, and range), and blood flow (mean, SD, median, 98th percentile, and range) for sampling intervals between 10 and 15 s. CONCLUSIONS: The proposed method of PCA filtering combined with the AIF estimation technique allows low frequency scanning for DCE-CT study to reduce patient radiation dose. The results indicate that the method is useful in pixel-by-pixel kinetic analysis of DCE-CT data for patients with cervical cancer.\",\n \"corpus_id\": 25669508,\n \"score\": 0\n },\n {\n \"doc_id\": \"26851711\",\n \"title\": \"A new gradient shimming method based on undistorted field map of B0 inhomogeneity.\",\n \"abstract\": \"Most existing gradient shimming methods for NMR spectrometers estimate field maps that resolve B0 inhomogeneity spatially from dual gradient-echo (GRE) images acquired at different echo times. However, the distortions induced by B0 inhomogeneity that always exists in the GRE images can result in estimated field maps that are distorted in both geometry and intensity, leading to inaccurate shimming. This work proposes a new gradient shimming method based on undistorted field map of B0 inhomogeneity obtained by a more accurate field map estimation technique. Compared to the traditional field map estimation method, this new method exploits both the positive and negative polarities of the frequency encoded gradients to eliminate the distortions caused by B0 inhomogeneity in the field map. Next, the corresponding automatic post-data procedure is introduced to obtain undistorted B0 field map based on knowledge of the invariant characteristics of the B0 inhomogeneity and the variant polarity of the encoded gradient. The experimental results on both simulated and real gradient shimming tests demonstrate the high performance of this new method.\",\n \"corpus_id\": 42431239,\n \"score\": 0\n },\n {\n \"doc_id\": \"26894674\",\n \"title\": \"Fitmunk: improving protein structures by accurate, automatic modeling of side-chain conformations.\",\n \"abstract\": \"Improvements in crystallographic hardware and software have allowed automated structure-solution pipelines to approach a near-`one-click' experience for the initial determination of macromolecular structures. However, in many cases the resulting initial model requires a laborious, iterative process of refinement and validation. A new method has been developed for the automatic modeling of side-chain conformations that takes advantage of rotamer-prediction methods in a crystallographic context. The algorithm, which is based on deterministic dead-end elimination (DEE) theory, uses new dense conformer libraries and a hybrid energy function derived from experimental data and prior information about rotamer frequencies to find the optimal conformation of each side chain. In contrast to existing methods, which incorporate the electron-density term into protein-modeling frameworks, the proposed algorithm is designed to take advantage of the highly discriminatory nature of electron-density maps. This method has been implemented in the program Fitmunk, which uses extensive conformational sampling. This improves the accuracy of the modeling and makes it a versatile tool for crystallographic model building, refinement and validation. Fitmunk was extensively tested on over 115 new structures, as well as a subset of 1100 structures from the PDB. It is demonstrated that the ability of Fitmunk to model more than 95% of side chains accurately is beneficial for improving the quality of crystallographic protein models, especially at medium and low resolutions. Fitmunk can be used for model validation of existing structures and as a tool to assess whether side chains are modeled optimally or could be better fitted into electron density. Fitmunk is available as a web service at http://kniahini.med.virginia.edu/fitmunk/server/ or at http://fitmunk.bitbucket.org/.\",\n \"corpus_id\": 263091334,\n \"score\": 0\n },\n {\n \"doc_id\": \"27102900\",\n \"title\": \"Local analysis of strains and rotations for macromolecular electron microscopy maps.\",\n \"abstract\": \"Macromolecular complexes perform their physiological functions by local rearrangements of their constituents and biochemically interacting with their reaction partners. These rearrangements may involve local rotations and the induction of local strains causing different mechanical efforts and stretches at the different areas of the protein. The analysis of these local deformations may reveal important insight into the way proteins perform their tasks. In this paper we introduce a method to perform this kind of local analysis using Electron Microscopy volumes in a fully objective and automatic manner. For doing so, we exploit the continuous nature of the result of an elastic image registration using B-splines as its basis functions. We show that the results obtained by the new automatic method are consistent with previous observations on these macromolecules.\",\n \"corpus_id\": 3931111,\n \"score\": 0\n },\n {\n \"doc_id\": \"27170866\",\n \"title\": \"Accurate and Fully Automatic Hippocampus Segmentation Using Subject-Specific 3D Optimal Local Maps Into a Hybrid Active Contour Model.\",\n \"abstract\": \"Assessing the structural integrity of the hippocampus (HC) is an essential step toward prevention, diagnosis, and follow-up of various brain disorders due to the implication of the structural changes of the HC in those disorders. In this respect, the development of automatic segmentation methods that can accurately, reliably, and reproducibly segment the HC has attracted considerable attention over the past decades. This paper presents an innovative 3-D fully automatic method to be used on top of the multiatlas concept for the HC segmentation. The method is based on a subject-specific set of 3-D optimal local maps (OLMs) that locally control the influence of each energy term of a hybrid active contour model (ACM). The complete set of the OLMs for a set of training images is defined simultaneously via an optimization scheme. At the same time, the optimal ACM parameters are also calculated. Therefore, heuristic parameter fine-tuning is not required. Training OLMs are subsequently combined, by applying an extended multiatlas concept, to produce the OLMs that are anatomically more suitable to the test image. The proposed algorithm was tested on three different and publicly available data sets. Its accuracy was compared with that of state-of-the-art methods demonstrating the efficacy and robustness of the proposed method.\",\n \"corpus_id\": 206418115,\n \"score\": 0\n },\n {\n \"doc_id\": \"27374400\",\n \"title\": \"VirusMapper: open-source nanoscale mapping of viral architecture through super-resolution microscopy.\",\n \"abstract\": \"The nanoscale molecular assembly of mammalian viruses during their infectious life cycle remains poorly understood. Their small dimensions, generally bellow the 300nm diffraction limit of light microscopes, has limited most imaging studies to electron microscopy. The recent development of super-resolution (SR) light microscopy now allows the visualisation of viral structures at resolutions of tens of nanometers. In addition, these techniques provide the added benefit of molecular specific labelling and the capacity to investigate viral structural dynamics using live-cell microscopy. However, there is a lack of robust analytical tools that allow for precise mapping of viral structure within the setting of infection. Here we present an open-source analytical framework that combines super-resolution imaging and naïve single-particle analysis to generate unbiased molecular models. This tool, VirusMapper, is a high-throughput, user-friendly, ImageJ-based software package allowing for automatic statistical mapping of conserved multi-molecular structures, such as viral substructures or intact viruses. We demonstrate the usability of VirusMapper by applying it to SIM and STED images of vaccinia virus in isolation and when engaged with host cells. VirusMapper allows for the generation of accurate, high-content, molecular specific virion models and detection of nanoscale changes in viral architecture.\",\n \"corpus_id\": 19081301,\n \"score\": 0\n },\n {\n \"doc_id\": \"27657649\",\n \"title\": \"StatSTEM: An efficient approach for accurate and precise model-based quantification of atomic resolution electron microscopy images.\",\n \"abstract\": \"An efficient model-based estimation algorithm is introduced to quantify the atomic column positions and intensities from atomic resolution (scanning) transmission electron microscopy ((S)TEM) images. This algorithm uses the least squares estimator on image segments containing individual columns fully accounting for overlap between neighbouring columns, enabling the analysis of a large field of view. For this algorithm, the accuracy and precision with which measurements for the atomic column positions and scattering cross-sections from annular dark field (ADF) STEM images can be estimated, has been investigated. The highest attainable precision is reached even for low dose images. Furthermore, the advantages of the model-based approach taking into account overlap between neighbouring columns are highlighted. This is done for the estimation of the distance between two neighbouring columns as a function of their distance and for the estimation of the scattering cross-section which is compared to the integrated intensity from a Voronoi cell. To provide end-users this well-established quantification method, a user friendly program, StatSTEM, is developed which is freely available under a GNU public license.\",\n \"corpus_id\": 8829069,\n \"score\": 0\n },\n {\n \"doc_id\": \"27825346\",\n \"title\": \"A vessel segmentation method for multi-modality angiographic images based on multi-scale filtering and statistical models.\",\n \"abstract\": \"BACKGROUND: Accurate segmentation of blood vessels plays an important role in the computer-aided diagnosis and interventional treatment of vascular diseases. The statistical method is an important component of effective vessel segmentation; however, several limitations discourage the segmentation effect, i.e., dependence of the image modality, uneven contrast media, bias field, and overlapping intensity distribution of the object and background. In addition, the mixture models of the statistical methods are constructed relaying on the characteristics of the image histograms. Thus, it is a challenging issue for the traditional methods to be available in vessel segmentation from multi-modality angiographic images. METHODS: To overcome these limitations, a flexible segmentation method with a fixed mixture model has been proposed for various angiography modalities. Our method mainly consists of three parts. Firstly, multi-scale filtering algorithm was used on the original images to enhance vessels and suppress noises. As a result, the filtered data achieved a new statistical characteristic. Secondly, a mixture model formed by three probabilistic distributions (two Exponential distributions and one Gaussian distribution) was built to fit the histogram curve of the filtered data, where the expectation maximization (EM) algorithm was used for parameters estimation. Finally, three-dimensional (3D) Markov random field (MRF) were employed to improve the accuracy of pixel-wise classification and posterior probability estimation. To quantitatively evaluate the performance of the proposed method, two phantoms simulating blood vessels with different tubular structures and noises have been devised. Meanwhile, four clinical angiographic data sets from different human organs have been used to qualitatively validate the method. To further test the performance, comparison tests between the proposed method and the traditional ones have been conducted on two different brain magnetic resonance angiography (MRA) data sets. RESULTS: The results of the phantoms were satisfying, e.g., the noise was greatly suppressed, the percentages of the misclassified voxels, i.e., the segmentation error ratios, were no more than 0.3%, and the Dice similarity coefficients (DSCs) were above 94%. According to the opinions of clinical vascular specialists, the vessels in various data sets were extracted with high accuracy since complete vessel trees were extracted while lesser non-vessels and background were falsely classified as vessel. In the comparison experiments, the proposed method showed its superiority in accuracy and robustness for extracting vascular structures from multi-modality angiographic images with complicated background noises. CONCLUSIONS: The experimental results demonstrated that our proposed method was available for various angiographic data. The main reason was that the constructed mixture probability model could unitarily classify vessel object from the multi-scale filtered data of various angiography images. The advantages of the proposed method lie in the following aspects: firstly, it can extract the vessels with poor angiography quality, since the multi-scale filtering algorithm can improve the vessel intensity in the circumstance such as uneven contrast media and bias field; secondly, it performed well for extracting the vessels in multi-modality angiographic images despite various signal-noises; and thirdly, it was implemented with better accuracy, and robustness than the traditional methods. Generally, these traits declare that the proposed method would have significant clinical application.\",\n \"corpus_id\": 2808081,\n \"score\": 0\n },\n {\n \"doc_id\": \"28132494\",\n \"title\": \"Introduction to high-resolution cryo-electron microscopy.\",\n \"abstract\": \"Wprowadzenie do wysokorozdzielczej kriogenicznej mikroskopii elektronowej. For many years two techniques have dominated structural biology - X-ray crystallography and NMR spectroscopy. Traditional cryo-electron microscopy of biological macromolecules produced macromolecular reconstructions at resolution limited to 6-10 Å. Recent development of transmission electron microscopes, in particular the development of direct electron detectors, and continuous improvements in the available software, have led to the \\\"resolution revolution\\\" in cryo-EM. It is now possible to routinely obtain near-atomic-resolution 3D maps of intact biological macromolecules as small as ~100 kDa. Thus, cryo-EM is now becoming the method of choice for structural analysis of many complex assemblies that are unsuitable for structure determination by other methods.\",\n \"corpus_id\": 1205060,\n \"score\": 0\n },\n {\n \"doc_id\": \"28269606\",\n \"title\": \"Automatic segmentation of multimodal brain tumor images based on classification of super-voxels.\",\n \"abstract\": \"Despite the rapid growth in brain tumor segmentation approaches, there are still many challenges in this field. Automatic segmentation of brain images has a critical role in decreasing the burden of manual labeling and increasing robustness of brain tumor diagnosis. We consider segmentation of glioma tumors, which have a wide variation in size, shape and appearance properties. In this paper images are enhanced and normalized to same scale in a preprocessing step. The enhanced images are then segmented based on their intensities using 3D super-voxels. Usually in images a tumor region can be regarded as a salient object. Inspired by this observation, we propose a new feature which uses a saliency detection algorithm. An edge-aware filtering technique is employed to align edges of the original image to the saliency map which enhances the boundaries of the tumor. Then, for classification of tumors in brain images, a set of robust texture features are extracted from super-voxels. Experimental results indicate that our proposed method outperforms a comparable state-of-the-art algorithm in term of dice score.\",\n \"corpus_id\": 54569036,\n \"score\": 0\n },\n {\n \"doc_id\": \"28373678\",\n \"title\": \"Analyzing Single Molecule Localization Microscopy Data Using Cubic Splines.\",\n \"abstract\": \"The resolution of super-resolution microscopy based on single molecule localization is in part determined by the accuracy of the localization algorithm. In most published approaches to date this localization is done by fitting an analytical function that approximates the point spread function (PSF) of the microscope. However, particularly for localization in 3D, analytical functions such as a Gaussian, which are computationally inexpensive, may not accurately capture the PSF shape leading to reduced fitting accuracy. On the other hand, analytical functions that can accurately capture the PSF shape, such as those based on pupil functions, can be computationally expensive. Here we investigate the use of cubic splines as an alternative fitting approach. We demonstrate that cubic splines can capture the shape of any PSF with high accuracy and that they can be used for fitting the PSF with only a 2-3x increase in computation time as compared to Gaussian fitting. We provide an open-source software package that measures the PSF of any microscope and uses the measured PSF to perform 3D single molecule localization microscopy analysis with reasonable accuracy and speed.\",\n \"corpus_id\": 4521653,\n \"score\": 0\n },\n {\n \"doc_id\": \"28519516\",\n \"title\": \"SU-E-I-19: Local Search Clustering Algorithm for DCE-MRI Analysis.\",\n \"abstract\": \"PURPOSE: To develop a local search clustering algorithm for analyzing the dynamic contrasted enhanced (DCE)-MRI data for determining the vascular permeability. The clustered signal will have better contrast-to-noise ratio (CNR) and thus can improve the analysis. METHODS: In DCE-MRI, data often suffer from low CNR. The CNR is particularly poor in central nervous system and could lead to spurious results. We propose a local search clustering algorithm that groups proximal voxels with similar uptake curves and T1 values. The algorithm starts with a seed voxel, and then grows outward to recruit new voxels into a cluster. Once a cluster is formed, all members of the current cluster form a 'seed collection' and the seed point of the cluster becomes the seed collection. The expansions and updates continue with the seed point/collection until the stopping criterion is met. To investigate the effectiveness of our clustering algorithm, we used a 64×64 2D Shepp-Logan phantom. Variations on the T1 values and permeability parameters were applied on different regions in the phantom. The time resolution was set to 30sec and 82 post-contrast data were created. After the DCE-MRI data were generated, Gaussian noise was applied to the images to investigate the effect of noise on the clustering algorithm. DCE analysis was performed on the clustered data and the results were compared against the Result obtained from voxel-by-voxel analysis. RESULTS: The addition of noise degraded the results of DCE estimation. The clustering algorithm on average reduced the errors of the permeability parameters by more than 50% compared to the voxel-by-voxel analysis. CONCLUSIONS: We developed a local search clustering algorithm to segment the concentration time curves of the DCE-MRI data. The proposed clustering algorithm enhances the apparent CNR within the clustered data and reduces the errors of the permeability parameters.\",\n \"corpus_id\": 642910,\n \"score\": 0\n },\n {\n \"doc_id\": \"28572576\",\n \"title\": \"EMBuilder: A Template Matching-based Automatic Model-building Program for High-resolution Cryo-Electron Microscopy Maps.\",\n \"abstract\": \"The resolution of electron-potential maps in single-particle cryo-electron microscopy (cryoEM) is approaching atomic or near- atomic resolution. However, no program currently exists for de novo cryoEM model building at resolutions exceeding beyond 3.5 Å. Here, we present a program, EMBuilder, based on template matching, to generate cryoEM models at high resolution. The program identifies features in both secondary-structure and Cα stages. In the secondary structure stage, helices and strands are identified with pre-computed templates, and the voxel size of the entire map is then refined to account for microscopic magnification errors. The identified secondary structures are then extended from both ends in the Cα stage via a log-likelihood (LLK) target function, and if possible, the side chains are also assigned. This program can build models of large proteins (~1 MDa) in a reasonable amount of time (~1 day) and thus has the potential to greatly decrease the manual workload required for model building of high-resolution cryoEM maps.\",\n \"corpus_id\": 3273894,\n \"score\": 0\n },\n {\n \"doc_id\": \"28593507\",\n \"title\": \"A stochastic algorithm for automatic hand pose and motion estimation.\",\n \"abstract\": \"In this paper, a novel, robust, and simple method for automatically estimating the hand pose is proposed and validated. The method uses a multi-camera optoelectronic system and a model-based stochastic algorithm. The approach is marker-based and relies on an Unscented Kalman Filter. A hand kinematic model is introduced for constraining relative marker's positions and improving the algorithm robustness with respect to outliers and possible occlusions. The algorithm outputs are 3D coordinate measures of markers and hand joint angle values. To validate the proposed algorithm, a comparison with ground truths for angular and 3D coordinate measures is carried out. The comparative analysis shows the advantages of using the model-based stochastic algorithm with respect to standard processing software of optoelectronic cameras in terms of implementation simplicity, time consumption, and user effort. The accuracy is remarkable, with a difference of maximum 0.035r a d and 4m m with respect to angular and 3D Cartesian coordinates ground truths, respectively.\",\n \"corpus_id\": 207291610,\n \"score\": 0\n },\n {\n \"doc_id\": \"28774465\",\n \"title\": \"A new preprocessing parameter estimation based on geodesic active contour model for automatic vestibular neuritis diagnosis.\",\n \"abstract\": \"The diagnostic of the vestibular neuritis (VN) presents many difficulties to traditional assessment methods This paper deals with a fully automatic VN diagnostic system based on nystagmus parameter estimation using a pupil detection algorithm. A geodesic active contour model is implemented to find an accurate segmentation region of the pupil. Hence, the novelty of the proposed algorithm is to speed up the standard segmentation by using a specific mask located on the region of interest. This allows a drastically computing time reduction and a great performance and accuracy of the obtained results. After using this fast segmentation algorithm, the obtained estimated parameters are represented in temporal and frequency settings. A useful principal component analysis (PCA) selection procedure is then applied to obtain a reduced number of estimated parameters which are used to train a multi neural network (MNN). Experimental results on 90 eye movement videos show the effectiveness and the accuracy of the proposed estimation algorithm versus previous work.\",\n \"corpus_id\": 4224138,\n \"score\": 0\n },\n {\n \"doc_id\": \"29388866\",\n \"title\": \"Diagnostic Electron Microscopy of Retina.\",\n \"abstract\": \"The electron microscopy techniques were used in various fields as an analytical technique under in vitro conditions, which provides the sufficient resolution for better visualization and interpretation. This review gives a brief overview of the analytical application of transmission electron microscopy (TEM) and scanning electron microscopy (SEM) techniques and critical findings in different retinal pathologies. This review article aims to improvise understanding of retinal microstructures for clinicians which will help to improve the interpretation of the current advanced imaging techniques.\",\n \"corpus_id\": 3452963,\n \"score\": 0\n }\n]","isConversational":false}}},{"rowIdx":64,"cells":{"query":{"kind":"string","value":"{\n \"doc_id\": \"29312997\",\n \"title\": \"A Survey of the Use of Iterative Reconstruction Algorithms in Electron Microscopy.\",\n \"abstract\": \"One of the key steps in Electron Microscopy is the tomographic reconstruction of a three-dimensional (3D) map of the specimen being studied from a set of two-dimensional (2D) projections acquired at the microscope. This tomographic reconstruction may be performed with different reconstruction algorithms that can be grouped into several large families: direct Fourier inversion methods, back-projection methods, Radon methods, or iterative algorithms. In this review, we focus on the latter family of algorithms, explaining the mathematical rationale behind the different algorithms in this family as they have been introduced in the field of Electron Microscopy. We cover their use in Single Particle Analysis (SPA) as well as in Electron Tomography (ET).\",\n \"corpus_id\": 26646474\n}"},"candidates":{"kind":"list like","value":[{"doc_id":"18353677","title":"Fast projection matching for cryo-electron microscopy image reconstruction.","abstract":"A new FFT-accelerated projection matching method is presented and tested. The electron microscopy images are represented by their Fourier-Bessel transforms and the 3D model by its expansion in spherical harmonics, or more specifically in terms of symmetry-adapted functions. The rotational and translational properties of these representations are used to quickly access all the possible 2D projections of the 3D model, which allow an exhaustive inspection of the whole five-dimensional domain of parameters associated to each particle.","corpus_id":2011492,"score":2},{"doc_id":"19398410","title":"Electronic noise modeling in statistical iterative reconstruction.","abstract":"We consider electronic noise modeling in tomographic image reconstruction when the measured signal is the sum of a Gaussian distributed electronic noise component and another random variable whose log-likelihood function satisfies a certain linearity condition. Examples of such likelihood functions include the Poisson distribution and an exponential dispersion (ED) model that can approximate the signal statistics in integration mode X-ray detectors. We formulate the image reconstruction problem as a maximum-likelihood estimation problem. Using an expectation-maximization approach, we demonstrate that a reconstruction algorithm can be obtained following a simple substitution rule from the one previously derived without electronic noise considerations. To illustrate the applicability of the substitution rule, we present examples of a fully iterative reconstruction algorithm and a sinogram smoothing algorithm both in transmission CT reconstruction when the measured signal contains additive electronic noise. Our simulation studies show the potential usefulness of accurate electronic noise modeling in low-dose CT applications.","corpus_id":16528431,"score":2},{"doc_id":"19850372","title":"On the efficiency of iterative ordered subset reconstruction algorithms for acceleration on GPUs.","abstract":"Expectation Maximization (EM) and the Simultaneous Iterative Reconstruction Technique (SIRT) are two iterative computed tomography reconstruction algorithms often used when the data contain a high amount of statistical noise, have been acquired from a limited angular range, or have a limited number of views. A popular mechanism to increase the rate of convergence of these types of algorithms has been to perform the correctional updates within subsets of the projection data. This has given rise to the method of Ordered Subsets EM (OS-EM) and the Simultaneous Algebraic Reconstruction Technique (SART). Commodity graphics hardware (GPUs) has shown great promise to combat the high computational demands incurred by iterative reconstruction algorithms. However, we find that the special architecture and programming model of GPUs add extra constraints on the real-time performance of ordered subsets algorithms, counteracting the speedup benefits of smaller subsets observed on CPUs. This gives rise to new relationships governing the optimal number of subsets as well as relaxation factor settings for obtaining the smallest wall-clock time for reconstruction-a factor that is likely application-dependent. In this paper we study the generalization of SIRT into Ordered Subsets SIRT and show that this allows one to optimize the computational performance of GPU-accelerated iterative algebraic reconstruction methods.","corpus_id":262235127,"score":2},{"doc_id":"20051344","title":"Development and optimization of regularized tomographic reconstruction algorithms utilizing equally-sloped tomography.","abstract":"We develop two new algorithms for tomographic reconstruction which incorporate the technique of equally-sloped tomography (EST) and allow for the optimized and flexible implementation of regularization schemes, such as total variation constraints, and the incorporation of arbitrary physical constraints. The founding structure of the developed algorithms is EST, a technique of tomographic acquisition and reconstruction first proposed by Miao in 2005 for performing tomographic image reconstructions from a limited number of noisy projections in an accurate manner by avoiding direct interpolations. EST has recently been successfully applied to coherent diffraction microscopy, electron microscopy, and computed tomography for image enhancement and radiation dose reduction. However, the bottleneck of EST lies in its slow speed due to its higher computation requirements. In this paper, we formulate the EST approach as a constrained problem and subsequently transform it into a series of linear problems, which can be accurately solved by the operator splitting method. Based on these mathematical formulations, we develop two iterative algorithms for tomographic image reconstructions through EST, which incorporate Bregman and continuative regularization. Our numerical experiment results indicate that the new tomographic image reconstruction algorithms not only significantly reduce the computational time, but also improve the image quality. We anticipate that EST coupled with the novel iterative algorithms will find broad applications in X-ray tomography, electron microscopy, coherent diffraction microscopy, and other tomography fields.","corpus_id":8240156,"score":2},{"doc_id":"20622984","title":"Parallelism of iterative CT reconstruction based on local reconstruction algorithm.","abstract":"An iterative algorithm is suited to reconstruct CT images from noisy or truncated projection data. However, as a disadvantage, the algorithm requires significant computational time. Although a parallel technique can be used to reduce the computational time, a large amount of communication overhead becomes an obstacle to its performance (Li et al. in J. X-Ray Sci. Technol. 13:1-10, 2005). To overcome this problem, we proposed an innovative parallel method based on the local iterative CT reconstruction algorithm (Wang et al. in Scanning 18:582-588, 1996 and IEEE Trans. Med. Imaging 15(5):657-664, 1996). The object to be reconstructed is partitioned into a number of subregions and assigned to different processing elements (PEs). Within each PE, local iterative reconstruction is performed to recover the subregion. Several numerical experiments were conducted on a high performance computing cluster. And the FORBILD head phantom (Lauritsch and Bruder http://www.imp.uni-erlangen.de/phantoms/head/head.html) was used as benchmark to measure the parallel performance. The experimental results showed that the proposed parallel algorithm significantly reduces the reconstruction time, hence achieving a high speedup and efficiency.","corpus_id":765945,"score":2},{"doc_id":"20888956","title":"Fundamentals of three-dimensional reconstruction from projections.","abstract":"Three-dimensional (3D) reconstruction of an object mass density from the set of its 2D line projections lies at a core of both single-particle reconstruction technique and electron tomography. Both techniques utilize electron microscope to collect a set of projections of either multiple objects representing in principle the same macromolecular complex in an isolated form, or a subcellular structure isolated in situ. Therefore, the goal of macromolecular electron microscopy is to invert the projection transformation to recover the distribution of the mass density of the original object. The problem is interesting in that in its discrete form it is ill-posed and not invertible. Various algorithms have been proposed to cope with the practical difficulties of this inversion problem and their differ widely in terms of their robustness with respect to noise in the data, completeness of the collected projection dataset, errors in projections orientation parameters, abilities to efficiently handle large datasets, and other obstacles typically encountered in molecular electron microscopy. Here, we review the theoretical foundations of 3D reconstruction from line projections followed by an overview of reconstruction algorithms routinely used in practice of electron microscopy.","corpus_id":23406418,"score":2},{"doc_id":"21333489","title":"Iterative reconstruction algorithms with α-divergence for PET imaging.","abstract":"This paper presents a class of image reconstruction algorithms based on Amari's α-divergence for position emission tomography. The α-divergence is actually a family of divergences indexed by α∈(-∞, +∞) that can measure discrepancy between two distributions. We consider it to model the discrepancy between projections and their estimates. By iteratively minimizing the α-divergence, a multiplicative updating algorithm is derived using an auxiliary function. The well-known ML-EM algorithm and the SA-WLS algorithm suggested by Zhu et al. arise as two special cases of our method. We prove the monotonic convergence of the algorithm, which Zhu et al. has not provided. The experiments were performed on both simulated and clinical data to study the interesting and useful behavior of the algorithm in cases where different parameters (α) were used. The results showed that some chosen algorithms exhibited much better performance than the prevalent ones.","corpus_id":9859828,"score":2},{"doc_id":"21741915","title":"A distributed multi-GPU system for high speed electron microscopic tomographic reconstruction.","abstract":"Full resolution electron microscopic tomographic (EMT) reconstruction of large-scale tilt series requires significant computing power. The desire to perform multiple cycles of iterative reconstruction and realignment dramatically increases the pressing need to improve reconstruction performance. This has motivated us to develop a distributed multi-GPU (graphics processing unit) system to provide the required computing power for rapid constrained, iterative reconstructions of very large three-dimensional (3D) volumes. The participating GPUs reconstruct segments of the volume in parallel, and subsequently, the segments are assembled to form the complete 3D volume. Owing to its power and versatility, the CUDA (NVIDIA, USA) platform was selected for GPU implementation of the EMT reconstruction. For a system containing 10 GPUs provided by 5 GTX295 cards, 10 cycles of SIRT reconstruction for a tomogram of 4096(2) × 512 voxels from an input tilt series containing 122 projection images of 4096(2) pixels (single precision float) takes a total of 1845 s of which 1032 s are for computation with the remainder being the system overhead. The same system takes only 39 s total to reconstruct 1024(2) × 256 voxels from 122 1024(2) pixel projections. While the system overhead is non-trivial, performance analysis indicates that adding extra GPUs to the system would lead to steadily enhanced overall performance. Therefore, this system can be easily expanded to generate superior computing power for very large tomographic reconstructions and especially to empower iterative cycles of reconstruction and realignment.","corpus_id":17305025,"score":2},{"doc_id":"21864687","title":"Single-particle reconstruction using L(2)-gradient flow.","abstract":"In this paper, we present an iterative algorithm for reconstructing a three-dimensional density function from a set of two dimensional electron microscopy images. By minimizing an energy functional consisting of a fidelity term and a regularization term, an L(2)-gradient flow is derived. The flow is integrated by a finite element method in the spatial direction and an explicit Euler scheme in the temporal direction. Our method compares favorably with those of the weighted back projection, Fourier method, algebraic reconstruction technique and simultaneous iterative reconstruction technique.","corpus_id":263434046,"score":2},{"doc_id":"22536462","title":"FAST WAVELET-BASED SINGLE-PARTICLE RECONSTRUCTION IN CRYO-EM.","abstract":"This paper presents a novel algorithm for the 3D tomographic inversion problem that arises in single-particle electron cryo-microscopy (Cryo-EM). It is based on two key components: 1) a variational formulation that promotes sparsity in the wavelet domain and 2) the Toeplitz structure of the combined projection/back-projection operator. The first idea has proven to be very effective for the recovery of piecewise-smooth signals, which is confirmed by our numerical experiments. The second idea allows for a computationally efficient implementation of the reconstruction procedure, using only one circulant convolution per iteration.","corpus_id":8925374,"score":2},{"doc_id":"22951262","title":"Advanced reconstruction algorithms for electron tomography: from comparison to combination.","abstract":"In this work, the simultaneous iterative reconstruction technique (SIRT), the total variation minimization (TVM) reconstruction technique and the discrete algebraic reconstruction technique (DART) for electron tomography are compared and the advantages and disadvantages are discussed. Furthermore, we describe how the result of a three dimensional (3D) reconstruction based on TVM can provide objective information that is needed as the input for a DART reconstruction. This approach results in a tomographic reconstruction of which the segmentation is carried out in an objective manner.","corpus_id":12478769,"score":2},{"doc_id":"23464329","title":"Radiation dose reduction in medical x-ray CT via Fourier-based iterative reconstruction.","abstract":"PURPOSE: A Fourier-based iterative reconstruction technique, termed Equally Sloped Tomography (EST), is developed in conjunction with advanced mathematical regularization to investigate radiation dose reduction in x-ray CT. The method is experimentally implemented on fan-beam CT and evaluated as a function of imaging dose on a series of image quality phantoms and anonymous pediatric patient data sets. Numerical simulation experiments are also performed to explore the extension of EST to helical cone-beam geometry. METHODS: EST is a Fourier based iterative algorithm, which iterates back and forth between real and Fourier space utilizing the algebraically exact pseudopolar fast Fourier transform (PPFFT). In each iteration, physical constraints and mathematical regularization are applied in real space, while the measured data are enforced in Fourier space. The algorithm is automatically terminated when a proposed termination criterion is met. Experimentally, fan-beam projections were acquired by the Siemens z-flying focal spot technology, and subsequently interleaved and rebinned to a pseudopolar grid. Image quality phantoms were scanned at systematically varied mAs settings, reconstructed by EST and conventional reconstruction methods such as filtered back projection (FBP), and quantified using metrics including resolution, signal-to-noise ratios (SNRs), and contrast-to-noise ratios (CNRs). Pediatric data sets were reconstructed at their original acquisition settings and additionally simulated to lower dose settings for comparison and evaluation of the potential for radiation dose reduction. Numerical experiments were conducted to quantify EST and other iterative methods in terms of image quality and computation time. The extension of EST to helical cone-beam CT was implemented by using the advanced single-slice rebinning (ASSR) method. RESULTS: Based on the phantom and pediatric patient fan-beam CT data, it is demonstrated that EST reconstructions with the lowest scanner flux setting of 39 mAs produce comparable image quality, resolution, and contrast relative to FBP with the 140 mAs flux setting. Compared to the algebraic reconstruction technique and the expectation maximization statistical reconstruction algorithm, a significant reduction in computation time is achieved with EST. Finally, numerical experiments on helical cone-beam CT data suggest that the combination of EST and ASSR produces reconstructions with higher image quality and lower noise than the Feldkamp Davis and Kress (FDK) method and the conventional ASSR approach. CONCLUSIONS: A Fourier-based iterative method has been applied to the reconstruction of fan-bean CT data with reduced x-ray fluence. This method incorporates advantageous features in both real and Fourier space iterative schemes: using a fast and algebraically exact method to calculate forward projection, enforcing the measured data in Fourier space, and applying physical constraints and flexible regularization in real space. Our results suggest that EST can be utilized for radiation dose reduction in x-ray CT via the readily implementable technique of lowering mAs settings. Numerical experiments further indicate that EST requires less computation time than several other iterative algorithms and can, in principle, be extended to helical cone-beam geometry in combination with the ASSR method.","corpus_id":13455029,"score":2},{"doc_id":"23706690","title":"Expectation maximization (EM) algorithms using polar symmetries for computed tomography (CT) image reconstruction.","abstract":"We suggest a symmetric-polar pixellation scheme which makes possible a reduction of the computational cost for expectation maximization (EM) iterative algorithms. The proposed symmetric-polar pixellation allows us to deal with 3D images as a whole problem without dividing the 3D problem into 2D slices approach. Performance evaluation of each approach in terms of stability and image quality is presented. Exhaustive comparisons between all approaches were conducted in a 2D based image reconstruction model. From these 2D approaches, that showing the best performances were finally implemented and evaluated in a 3D based image reconstruction model. Comparison to 3D images reconstructed with FBP is also presented. Although the algorithm is presented in the context of computed tomography (CT) image reconstruction, it can be applied to any other tomographic technique as well, due to the fact that the only requirement is a scanning geometry involving measurements of an object under different projection angles. Real data have been acquired with a small animal (CT) scanner to verify the proposed mathematical description of the CT system.","corpus_id":8143656,"score":2},{"doc_id":"23955748","title":"A model based iterative reconstruction algorithm for high angle annular dark field-scanning transmission electron microscope (HAADF-STEM) tomography.","abstract":"High angle annular dark field (HAADF)-scanning transmission electron microscope (STEM) data is increasingly being used in the physical sciences to research materials in 3D because it reduces the effects of Bragg diffraction seen in bright field TEM data. Typically, tomographic reconstructions are performed by directly applying either filtered back projection (FBP) or the simultaneous iterative reconstruction technique (SIRT) to the data. Since HAADF-STEM tomography is a limited angle tomography modality with low signal to noise ratio, these methods can result in significant artifacts in the reconstructed volume. In this paper, we develop a model based iterative reconstruction algorithm for HAADF-STEM tomography. We combine a model for image formation in HAADF-STEM tomography along with a prior model to formulate the tomographic reconstruction as a maximum a posteriori probability (MAP) estimation problem. Our formulation also accounts for certain missing measurements by treating them as nuisance parameters in the MAP estimation framework. We adapt the iterative coordinate descent algorithm to develop an efficient method to minimize the corresponding MAP cost function. Reconstructions of simulated as well as experimental data sets show results that are superior to FBP and SIRT reconstructions, significantly suppressing artifacts and enhancing contrast.","corpus_id":8192264,"score":2},{"doc_id":"24008024","title":"Weighted simultaneous iterative reconstruction technique for single-axis tomography.","abstract":"Tomographic techniques play a crucial role in imaging methods such as transmission electron microscopy (TEM) due to their unique capabilities to reconstruct three-dimensional object information. However, the accuracy of the two standard tomographic reconstruction techniques, the weighted back-projection (W-BP) and the simultaneous iterative reconstruction technique (SIRT) is reduced under common experimental restrictions, such as limited tilt range or noise. We demonstrate that the combination of W-BP and SIRT leads to an improved tomographic reconstruction technique: the weighted SIRT. Convergence, resolution and reconstruction error of the W-SIRT are analyzed by a detailed analytical, numerical, and experimental comparison with established methods. Our reconstruction technique is not restricted to TEM tomography but can be applied to all problems sharing single axis imaging geometry.","corpus_id":33934794,"score":2},{"doc_id":"24326216","title":"Iterative reconstruction of cryo-electron tomograms using nonuniform fast Fourier transforms.","abstract":"Algorithms for three-dimensional (3D) reconstruction of objects based on their projections are essential in various biological and medical imaging modalities. In cryo-electron tomography (CET) a major challenge for reconstruction is the limited range of projection angles, which manifests itself as a \"missing wedge\" of data in Fourier space making the reconstruction problem ill-posed. Here, we apply an iterative reconstruction method that makes use of nonuniform fast Fourier transform (NUFFT) to the reconstruction of cryo-electron tomograms. According to several measures the reconstructions are superior to those obtained using conventional methods, most notably weighted backprojection. Most importantly, we show that it is possible to fill in partially the unsampled region in Fourier space with meaningful information without making assumptions about the data or applying prior knowledge. As a consequence, particles of known structure can be localized with higher confidence in cryotomograms and subtomogram averaging yields higher resolution densities.","corpus_id":5514970,"score":2},{"doc_id":"25048191","title":"Comparing five different iterative reconstruction algorithms for computed tomography in an ROC study.","abstract":"OBJECTIVES: The purpose of this study was to evaluate lesion conspicuity achieved with five different iterative reconstruction techniques from four CT vendors at three different dose levels. Comparisons were made of iterative algorithm and filtered back projection (FBP) among and within systems. METHODS: An anthropomorphic liver phantom was examined with four CT systems, each from a different vendor. CTDIvol levels of 5 mGy, 10 mGy and 15 mGy were chosen. Images were reconstructed with FBP and the iterative algorithm on the system. Images were interpreted independently by four observers, and the areas under the ROC curve (AUCs) were calculated. Noise and contrast-to-noise ratios (CNR) were measured. RESULTS: One iterative algorithm increased AUC (0.79, 0.95, and 0.97) compared to FBP (0.70, 0.86, and 0.93) at all dose levels (p < 0.001 and p = 0.047). Another algorithm increased AUC from 0.78 with FBP to 0.84 (p = 0.007) at 5 mGy. Differences at 10 and 15 mGy were not significant (p-values: 0.084-0.883). Three algorithms showed no difference in AUC compared to FBP (p-values: 0.008-1.000). All of the algorithms decreased noise (10-71%) and improved CNR. CONCLUSIONS: Only two algorithms improved lesion detection, even though noise reduction was shown with all algorithms. KEY POINTS: Iterative reconstruction algorithms affected lesion detection differently at different dose levels. One iterative algorithm improved lesion detectability compared to filtered back projection. Three algorithms did not significantly improve lesion detectability. One algorithm improved lesion detectability at the lowest dose level.","corpus_id":24858397,"score":2},{"doc_id":"25304701","title":"Iterative reconstruction: how it works, how to apply it.","abstract":"Computed tomography acquires X-ray projection data from multiple angles though an object to generate a tomographic rendition of its attenuation characteristics. Filtered back projection is a fast, closed analytical solution to the reconstruction process, whereby all projections are equally weighted, but is prone to deliver inadequate image quality when the dose levels are reduced. Iterative reconstruction is an algorithmic method that uses statistical and geometric models to variably weight the image data in a process that can be solved iteratively to independently reduce noise and preserve resolution and image quality. Applications of this technology in a clinical setting can result in lower dose on the order of 20-40% compared to a standard filtered back projection reconstruction for most exams. A carefully planned implementation strategy and methodological approach is necessary to achieve the goals of lower dose with uncompromised image quality.","corpus_id":22095801,"score":2},{"doc_id":"25436931","title":"Atomic resolution tomography reconstruction of tilt series based on a GPU accelerated hybrid input-output algorithm using polar Fourier transform.","abstract":"Advances in diffraction and transmission electron microscopy (TEM) have greatly improved the prospect of three-dimensional (3D) structure reconstruction from two-dimensional (2D) images or diffraction patterns recorded in a tilt series at atomic resolution. Here, we report a new graphics processing unit (GPU) accelerated iterative transformation algorithm (ITA) based on polar fast Fourier transform for reconstructing 3D structure from 2D diffraction patterns. The algorithm also applies to image tilt series by calculating diffraction patterns from the recorded images using the projection-slice theorem. A gold icosahedral nanoparticle of 309 atoms is used as the model to test the feasibility, performance and robustness of the developed algorithm using simulations. Atomic resolution in 3D is achieved for the 309 atoms Au nanoparticle using 75 diffraction patterns covering 150° rotation. The capability demonstrated here provides an opportunity to uncover the 3D structure of small objects of nanometers in size by electron diffraction.","corpus_id":10994340,"score":2},{"doc_id":"25659894","title":"Progressive Stochastic Reconstruction Technique (PSRT) for cryo electron tomography.","abstract":"Cryo Electron Tomography (cryoET) plays an essential role in Structural Biology, as it is the only technique that allows to study the structure of large macromolecular complexes in their close to native environment in situ. The reconstruction methods currently in use, such as Weighted Back Projection (WBP) or Simultaneous Iterative Reconstruction Technique (SIRT), deliver noisy and low-contrast reconstructions, which complicates the application of high-resolution protocols, such as Subtomogram Averaging (SA). We propose a Progressive Stochastic Reconstruction Technique (PSRT) - a novel iterative approach to tomographic reconstruction in cryoET based on Monte Carlo random walks guided by Metropolis-Hastings sampling strategy. We design a progressive reconstruction scheme to suit the conditions present in cryoET and apply it successfully to reconstructions of macromolecular complexes from both synthetic and experimental datasets. We show how to integrate PSRT into SA, where it provides an elegant solution to the region-of-interest problem and delivers high-contrast reconstructions that significantly improve template-based localization without any loss of high-resolution structural information. Furthermore, the locality of SA is exploited to design an importance sampling scheme which significantly speeds up the otherwise slow Monte Carlo approach. Finally, we design a new memory efficient solution for the specimen-level interior problem of cryoET, removing all associated artifacts.","corpus_id":206494153,"score":2},{"doc_id":"25680211","title":"BSIRT: a block-iterative SIRT parallel algorithm using curvilinear projection model.","abstract":"Large-field high-resolution electron tomography enables visualizing detailed mechanisms under global structure. As field enlarges, the distortions of reconstruction and processing time become more critical. Using the curvilinear projection model can improve the quality of large-field ET reconstruction, but its computational complexity further exacerbates the processing time. Moreover, there is no parallel strategy on GPU for iterative reconstruction method with curvilinear projection. Here we propose a new Block-iterative SIRT parallel algorithm with the curvilinear projection model (BSIRT) for large-field ET reconstruction, to improve the quality of reconstruction and accelerate the reconstruction process. We also develop some key techniques, including block-iterative method with the curvilinear projection, a scope-based data decomposition method and a page-based data transfer scheme to implement the parallelization of BSIRT on GPU platform. Experimental results show that BSIRT can improve the reconstruction quality as well as the speed of the reconstruction process.","corpus_id":23818719,"score":2},{"doc_id":"26008761","title":"Three-dimensional reconstruction methods in Single Particle Analysis from transmission electron microscopy data.","abstract":"The Transmission Electron Microscope provides two-dimensional (2D) images of the specimens under study. However, the architecture of these specimens is defined in a three-dimensional (3D) coordinate space, in volumetric terms, making the direct microscope output somehow \"short\" in terms of dimensionality. This situation has prompted the development of methods to quantitatively estimate 3D volumes from sets of 2D images, which are usually referred to as \"three-dimensional reconstruction methods\". These 3D reconstruction methods build on four considerations: (1) The relationship between the 2D images and the 3D volume must be of a particularly simple type, (2) many 2D images are needed to gain 3D volumetric information, (3) the 2D images and the 3D volume have to be in the same coordinate reference frame and (4), in practical terms, the reconstructed 3D volume will only be an approximation to the original 3D volume which gave raise to the 2D projections. In this work we will adopt a quite general view, trying to address a large community of interested readers, although some sections will be particularly devoted to the 3D analysis of isolated macromolecular complexes in the application area normally referred to as Single Particle Analysis (SPA).","corpus_id":2983500,"score":2},{"doc_id":"26046398","title":"Matched Backprojection Operator for Combined Scanning Transmission Electron Microscopy Tilt- and Focal Series.","abstract":"Combined tilt- and focal series scanning transmission electron microscopy is a recently developed method to obtain nanoscale three-dimensional (3D) information of thin specimens. In this study, we formulate the forward projection in this acquisition scheme as a linear operator and prove that it is a generalization of the Ray transform for parallel illumination. We analytically derive the corresponding backprojection operator as the adjoint of the forward projection. We further demonstrate that the matched backprojection operator drastically improves the convergence rate of iterative 3D reconstruction compared to the case where a backprojection based on heuristic weighting is used. In addition, we show that the 3D reconstruction is of better quality.","corpus_id":22162282,"score":2},{"doc_id":"26094203","title":"A fast iterative convolution weighting approach for gridding-based direct Fourier three-dimensional reconstruction with correction for the contrast transfer function.","abstract":"We describe a fast and accurate method for the reconstruction of macromolecular complexes from a set of projections. Direct Fourier inversion (in which the Fourier Slice Theorem plays a central role) is a solution for dealing with this inverse problem. Unfortunately, the set of projections provides a non-equidistantly sampled version of the macromolecule Fourier transform in the single particle field (and, therefore, a direct Fourier inversion) may not be an optimal solution. In this paper, we introduce a gridding-based direct Fourier method for the three-dimensional reconstruction approach that uses a weighting technique to compute a uniform sampled Fourier transform. Moreover, the contrast transfer function of the microscope, which is a limiting factor in pursuing a high resolution reconstruction, is corrected by the algorithm. Parallelization of this algorithm, both on threads and on multiple CPU's, makes the process of three-dimensional reconstruction even faster. The experimental results show that our proposed gridding-based direct Fourier reconstruction is slightly more accurate than similar existing methods and presents a lower computational complexity both in terms of time and memory, thereby allowing its use on larger volumes. The algorithm is fully implemented in the open-source Xmipp package and is downloadable from http://xmipp.cnb.csic.es.","corpus_id":205524467,"score":2},{"doc_id":"26405903","title":"FASART: An iterative reconstruction algorithm with inter-iteration adaptive NAD filter.","abstract":"Electron tomography (ET) is an essential imaging technique for studying structures of large biological specimens. These structures are reconstructed from a set of projections obtained at different sample orientations by tilting the specimen. However, most of existing reconstruction methods are not appropriate when the data are extremely noisy and incomplete. A new iterative method has been proposed: adaptive simultaneous algebraic reconstruction with inter-iteration adaptive non-linear anisotropic diffusion (NAD) filter (FASART). We also adopted an adaptive parameter and discussed the step for the filter in this reconstruction method. Experimental results show that FASART can restrain the noise generated in the process of iterative reconstruction and still preserve the more details of the structure edges.","corpus_id":33402313,"score":2},{"doc_id":"26418739","title":"A Novel Iterative CT Reconstruction Approach Based on FBP Algorithm.","abstract":"The Filtered Back-Projection (FBP) algorithm and its modified versions are the most important techniques for CT (Computerized tomography) reconstruction, however, it may produce aliasing degradation in the reconstructed images due to projection discretization. The general iterative reconstruction (IR) algorithms suffer from their heavy calculation burden and other drawbacks. In this paper, an iterative FBP approach is proposed to reduce the aliasing degradation. In the approach, the image reconstructed by FBP algorithm is treated as the intermediate image and projected along the original projection directions to produce the reprojection data. The difference between the original and reprojection data is filtered by a special digital filter, and then is reconstructed by FBP to produce a correction term. The correction term is added to the intermediate image to update it. This procedure can be performed iteratively to improve the reconstruction performance gradually until certain stopping criterion is satisfied. Some simulations and tests on real data show the proposed approach is better than FBP algorithm or some IR algorithms in term of some general image criteria. The calculation burden is several times that of FBP, which is much less than that of general IR algorithms and acceptable in the most situations. Therefore, the proposed algorithm has the potential applications in practical CT systems.","corpus_id":17630373,"score":2},{"doc_id":"26459139","title":"Total Variation-Based Reduction of Streak Artifacts, Ring Artifacts and Noise in 3D Reconstruction from Optical Projection Tomography.","abstract":"Optical projection tomography (OPT) is a computed tomography technique at optical frequencies for samples of 0.5-15 mm in size, which fills an important \"imaging gap\" between confocal microscopy (for smaller samples) and large-sample methods such as fluorescence molecular tomography or micro magnetic resonance imaging. OPT operates in either fluorescence or transmission mode. Two-dimensional (2D) projections are taken over 360° with a fixed rotational increment around the vertical axis. Standard 3D reconstruction from 2D OPT uses the filtered backprojection (FBP) algorithm based on the Radon transform. FBP approximates the inverse Radon transform using a ramp filter that spreads reconstructed pixels to neighbor pixels thus producing streak and other types of artifacts, as well as noise. Artifacts increase the variation of grayscale values in the reconstructed images. We present an algorithm that improves the quality of reconstruction even for a low number of projections by simultaneously minimizing the sum of absolute brightness changes in the reconstructed volume (the total variation) and the error between measured and reconstructed data. We demonstrate the efficiency of the method on real biological data acquired on a dedicated OPT device.","corpus_id":9662152,"score":2},{"doc_id":"26916079","title":"On geometric artifacts in cryo electron tomography.","abstract":"Single-tilt scheme is nowadays the prevalent acquisition geometry in electron tomography and subtomogram averaging experiments. Being an incomplete scheme that induces ill-posedness in the sense of the X-ray or Radon transform inverse problem, it introduces a number of artifacts that directly influence the quality of tomographic reconstructions. Though individually described by different authors before, a systematic study of these acquisition geometry-related artifacts in one place and across representative set of reconstruction methods has not been, to our knowledge, performed before. Moreover, the effects of these artifacts on the reconstructed density are sometimes misinterpreted, attributing them to the wrong cause, especially if their effects accumulate. In this work, we systematically study the major artifacts of single-tilt geometry known as the missing wedge (incomplete projection set problem), the missing information and the specimen-level interior problem (long-object problem). First, we illustratively describe, using a unified terminology, how and why these artifacts arise and when they can be avoided. Next, we describe the effects of these artifacts on the reconstructions across all major classes of reconstruction methods, including newly-appeared methods like the Iterative Nonuniform fast Fourier transform based Reconstruction method (INFR) and the Progressive Stochastic Reconstruction Technique (PSRT). Finally, we draw conclusions and recommendations on numerous points, especially regarding the mutual influence of the geometric artifacts, ability of different reconstruction methods to suppress them as well as implications to the interpretation of both electron tomography and subtomogram averaging experiments.","corpus_id":20770177,"score":2},{"doc_id":"28874736","title":"GENFIRE: A generalized Fourier iterative reconstruction algorithm for high-resolution 3D imaging.","abstract":"Tomography has made a radical impact on diverse fields ranging from the study of 3D atomic arrangements in matter to the study of human health in medicine. Despite its very diverse applications, the core of tomography remains the same, that is, a mathematical method must be implemented to reconstruct the 3D structure of an object from a number of 2D projections. Here, we present the mathematical implementation of a tomographic algorithm, termed GENeralized Fourier Iterative REconstruction (GENFIRE), for high-resolution 3D reconstruction from a limited number of 2D projections. GENFIRE first assembles a 3D Fourier grid with oversampling and then iterates between real and reciprocal space to search for a global solution that is concurrently consistent with the measured data and general physical constraints. The algorithm requires minimal human intervention and also incorporates angular refinement to reduce the tilt angle error. We demonstrate that GENFIRE can produce superior results relative to several other popular tomographic reconstruction techniques through numerical simulations and by experimentally reconstructing the 3D structure of a porous material and a frozen-hydrated marine cyanobacterium. Equipped with a graphical user interface, GENFIRE is freely available from our website and is expected to find broad applications across different disciplines.","corpus_id":19700086,"score":2},{"doc_id":"19131666","title":"Fast 3D iterative image reconstruction for SPECT with rotating slat collimators.","abstract":"As an alternative to the use of traditional parallel hole collimators, SPECT imaging can be performed using rotating slat collimators. While maintaining the spatial resolution, a gain in image quality could be expected from the higher photon collection efficiency of this type of collimator. However, the use of iterative methods to do fully three-dimensional (3D) reconstruction is computationally much more expensive and furthermore involves slow convergence compared to a classical SPECT reconstruction. It has been proposed to do 3D reconstruction by splitting the system matrix into two separate matrices, forcing the reconstruction to first estimate the sinograms from the rotating slat SPECT data before estimating the image. While alleviating the computational load by one order of magnitude, this split matrix approach would result in fast computation of the projections in an iterative algorithm, but does not solve the problem of slow convergence. There is thus a need for an algorithm which speeds up convergence while maintaining image quality for rotating slat collimated SPECT cameras. Therefore, we developed a reconstruction algorithm based on the split matrix approach which allows both a fast calculation of the forward and backward projection and a fast convergence. In this work, an algorithm of the maximum likelihood expectation maximization (MLEM) type, obtained from a split system matrix MLEM reconstruction, is proposed as a reconstruction method for rotating slat collimated SPECT data. Here, we compare this new algorithm to the conventional split system matrix MLEM method and to a gold standard fully 3D MLEM reconstruction algorithm on the basis of computational load, convergence and contrast-to-noise. Furthermore, ordered subsets expectation maximization (OSEM) implementations of these three algorithms are compared. Calculation of computational load and convergence for the different algorithms shows a speedup for the new method of 38 and 426 compared to the split matrix MLEM approach and the fully 3D MLEM respectively and a speedup of 16 and 21 compared to the split matrix OSEM and the fully 3D OSEM respectively. A contrast-to-noise study based on simulated data shows that our new approach has comparable accuracy as the fully 3D reconstruction method. The algorithm developed in this study allows iterative image reconstruction of rotating slat collimated SPECT data with equal image quality in a comparable amount of computation time as a classical SPECT reconstruction.","corpus_id":41250680,"score":1},{"doc_id":"19792279","title":"Reconstruction algorithm for single-particle diffraction imaging experiments.","abstract":"We introduce the EMC algorithm for reconstructing a particle's three-dimensional (3D) diffraction intensity from very many photon shot-noise limited two-dimensional measurements, when the particle orientation in each measurement is unknown. The algorithm combines a maximization step (M) of the intensity's likelihood function, with expansion (E) and compression (C) steps that map the 3D intensity model to a redundant tomographic representation and back again. After a few iterations of the EMC update rule, the reconstructed intensity is given to the difference-map algorithm for reconstruction of the particle contrast. We demonstrate reconstructions with simulated data and investigate the effects of particle complexity, number of measurements, and the number of photons per measurement. The relatively transparent scaling behavior of our algorithm provides an estimate of the data processing resources required for future single-particle imaging experiments.","corpus_id":8132982,"score":1},{"doc_id":"21361216","title":"Reconstruction of brachytherapy seed positions and orientations from cone-beam CT x-ray projections via a novel iterative forward projection matching method.","abstract":"PURPOSE: To generalize and experimentally validate a novel algorithm for reconstructing the 3D pose (position and orientation) of implanted brachytherapy seeds from a set of a few measured 2D cone-beam CT (CBCT) x-ray projections. METHODS: The iterative forward projection matching (IFPM) algorithm was generalized to reconstruct the 3D pose, as well as the centroid, of brachytherapy seeds from three to ten measured 2D projections. The gIFPM algorithm finds the set of seed poses that minimizes the sum-of-squared-difference of the pixel-by-pixel intensities between computed and measured autosegmented radiographic projections of the implant. Numerical simulations of clinically realistic brachytherapy seed configurations were performed to demonstrate the proof of principle. An in-house machined brachytherapy phantom, which supports precise specification of seed position and orientation at known values for simulated implant geometries, was used to experimentally validate this algorithm. The phantom was scanned on an ACUITY CBCT digital simulator over a full 660 sinogram projections. Three to ten x-ray images were selected from the full set of CBCT sinogram projections and postprocessed to create binary seed-only images. RESULTS: In the numerical simulations, seed reconstruction position and orientation errors were approximately 0.6 mm and 5 degrees, respectively. The physical phantom measurements demonstrated an absolute positional accuracy of (0.78 +/- 0.57) mm or less. The theta and phi angle errors were found to be (5.7 +/- 4.9) degrees and (6.0 +/- 4.1) degrees, respectively, or less when using three projections; with six projections, results were slightly better. The mean registration error was better than 1 mm/6 degrees compared to the measured seed projections. Each test trial converged in 10-20 iterations with computation time of 12-18 min/iteration on a 1 GHz processor. CONCLUSIONS: This work describes a novel, accurate, and completely automatic method for reconstructing seed orientations, as well as centroids, from a small number of radiographic projections, in support of intraoperative planning and adaptive replanning. Unlike standard back-projection methods, gIFPM avoids the need to match corresponding seed images on the projections. This algorithm also successfully reconstructs overlapping clustered and highly migrated seeds in the implant. The accuracy of better than 1 mm and 6 degrees demonstrates that gIFPM has the potential to support 2D Task Group 43 calculations in clinical practice.","corpus_id":21908970,"score":1},{"doc_id":"21490573","title":"Single particle electron microscopy reconstruction of the exosome complex using the random conical tilt method.","abstract":"Single particle electron microscopy (EM) reconstruction has recently become a popular tool to get the three-dimensional (3D) structure of large macromolecular complexes. Compared to X-ray crystallography, it has some unique advantages. First, single particle EM reconstruction does not need to crystallize the protein sample, which is the bottleneck in X-ray crystallography, especially for large macromolecular complexes. Secondly, it does not need large amounts of protein samples. Compared with milligrams of proteins necessary for crystallization, single particle EM reconstruction only needs several micro-liters of protein solution at nano-molar concentrations, using the negative staining EM method. However, despite a few macromolecular assemblies with high symmetry, single particle EM is limited at relatively low resolution (lower than 1 nm resolution) for many specimens especially those without symmetry. This technique is also limited by the size of the molecules under study, i.e. 100 kDa for negatively stained specimens and 300 kDa for frozen-hydrated specimens in general. For a new sample of unknown structure, we generally use a heavy metal solution to embed the molecules by negative staining. The specimen is then examined in a transmission electron microscope to take two-dimensional (2D) micrographs of the molecules. Ideally, the protein molecules have a homogeneous 3D structure but exhibit different orientations in the micrographs. These micrographs are digitized and processed in computers as \"single particles\". Using two-dimensional alignment and classification techniques, homogenous molecules in the same views are clustered into classes. Their averages enhance the signal of the molecule's 2D shapes. After we assign the particles with the proper relative orientation (Euler angles), we will be able to reconstruct the 2D particle images into a 3D virtual volume. In single particle 3D reconstruction, an essential step is to correctly assign the proper orientation of each single particle. There are several methods to assign the view for each particle, including the angular reconstitution(1) and random conical tilt (RCT) method(2). In this protocol, we describe our practice in getting the 3D reconstruction of yeast exosome complex using negative staining EM and RCT. It should be noted that our protocol of electron microscopy and image processing follows the basic principle of RCT but is not the only way to perform the method. We first describe how to embed the protein sample into a layer of Uranyl-Formate with a thickness comparable to the protein size, using a holey carbon grid covered with a layer of continuous thin carbon film. Then the specimen is inserted into a transmission electron microscope to collect untilted (0-degree) and tilted (55-degree) pairs of micrographs that will be used later for processing and obtaining an initial 3D model of the yeast exosome. To this end, we perform RCT and then refine the initial 3D model by using the projection matching refinement method(3).","corpus_id":45189809,"score":1},{"doc_id":"21860371","title":"Structure of HIV-1 capsid assemblies by cryo-electron microscopy and iterative helical real-space reconstruction.","abstract":"Cryo-electron microscopy (cryo-EM), combined with image processing, is an increasingly powerful tool for structure determination of macromolecular protein complexes and assemblies. In fact, single particle electron microscopy and two-dimensional (2D) electron crystallography have become relatively routine methodologies and a large number of structures have been solved using these methods. At the same time, image processing and three-dimensional (3D) reconstruction of helical objects has rapidly developed, especially, the iterative helical real-space reconstruction (IHRSR) method, which uses single particle analysis tools in conjunction with helical symmetry. Many biological entities function in filamentous or helical forms, including actin filaments, microtubules, amyloid fibers, tobacco mosaic viruses, and bacteria flagella, and, because a 3D density map of a helical entity can be attained from a single projection image, compared to the many images required for 3D reconstruction of a non-helical object, with the IHRSR method, structural analysis of such flexible and disordered helical assemblies is now attainable. In this video article, we provide detailed protocols for obtaining a 3D density map of a helical protein assembly (HIV-1 capsid is our example), including protocols for cryo-EM specimen preparation, low dose data collection by cryo-EM, indexing of helical diffraction patterns, and image processing and 3D reconstruction using IHRSR. Compared to other techniques, cryo-EM offers optimal specimen preservation under near native conditions. Samples are embedded in a thin layer of vitreous ice, by rapid freezing, and imaged in electron microscopes at liquid nitrogen temperature, under low dose conditions to minimize the radiation damage. Sample images are obtained under near native conditions at the expense of low signal and low contrast in the recorded micrographs. Fortunately, the process of helical reconstruction has largely been automated, with the exception of indexing the helical diffraction pattern. Here, we describe an approach to index helical structure and determine helical symmetries (helical parameters) from digitized micrographs, an essential step for 3D helical reconstruction. Briefly, we obtain an initial 3D density map by applying the IHRSR method. This initial map is then iteratively refined by introducing constraints for the alignment parameters of each segment, thus controlling their degrees of freedom. Further improvement is achieved by correcting for the contrast transfer function (CTF) of the electron microscope (amplitude and phase correction) and by optimizing the helical symmetry of the assembly.","corpus_id":8398013,"score":1},{"doc_id":"22565698","title":"Investigation of discrete imaging models and iterative image reconstruction in differential X-ray phase-contrast tomography.","abstract":"Differential X-ray phase-contrast tomography (DPCT) refers to a class of promising methods for reconstructing the X-ray refractive index distribution of materials that present weak X-ray absorption contrast. The tomographic projection data in DPCT, from which an estimate of the refractive index distribution is reconstructed, correspond to one-dimensional (1D) derivatives of the two-dimensional (2D) Radon transform of the refractive index distribution. There is an important need for the development of iterative image reconstruction methods for DPCT that can yield useful images from few-view projection data, thereby mitigating the long data-acquisition times and large radiation doses associated with use of analytic reconstruction methods. In this work, we analyze the numerical and statistical properties of two classes of discrete imaging models that form the basis for iterative image reconstruction in DPCT. We also investigate the use of one of the models with a modern image reconstruction algorithm for performing few-view image reconstruction of a tissue specimen.","corpus_id":110280,"score":1},{"doc_id":"22897395","title":"Recent advances in the application of electron tomography to materials chemistry.","abstract":"Nowadays, tomography plays a central role in pureand applied science, in medicine, and in many branches of engineering and technology. It entails reconstructing the three-dimensional (3D) structure of an object from a tilt series of two-dimensional (2D) images. Its origin goes back to 1917, when Radon showed mathematically how a series of 2D projection images could be converted to the 3D structural one. Tomographic X-ray and positron scanning for 3D medical imaging, with a resolution of ∼1 mm, is now ubiquitous in major hospitals. Electron tomography, a relatively new chemical tool, with a resolution of ∼1 nm, has been recently adopted by materials chemists as an invaluable aid for the 3D study of the morphologies, spatially-discriminating chemical compositions, and defect properties of nanostructured materials. In this Account, we review the advances that have been made in facilitating the recording of the required series of 2D electron microscopic images and the subsequent process of 3D reconstruction of specimens that are vulnerable, to a greater or lesser degree, to electron beam damage. We describe how high-fidelity 3D tomograms may be obtained from relatively few 2D images by incorporating prior structural knowledge into the reconstruction process. In particular, we highlight the vital role of compressed sensing, a recently developed procedure well-known to information theorists that exploits ideas of image compression and \"sparsity\" (that the important image information can be captured in a reduced data set). We also touch upon another promising approach, \"discrete\" tomography, which builds into the reconstruction process a prior assumption that the object can be described in discrete terms, such as the number of constituent materials and their expected densities. Other advances made recently that we outline, such as the availability of aberration-corrected electron microscopes, electron wavelength monochromators, and sophisticated specimen goniometers, have all contributed significantly to the further development of quantitative 3D studies of nanostructured materials, including nanoparticle-heterogeneous catalysts, fuel-cell components, and drug-delivery systems, as well as photovoltaic and plasmonic devices, and are likely to enhance our knowledge of many other facets of materials chemistry, such as organic-inorganic composites, solar-energy devices, bionanotechnology, biomineralization, and energy-storage systems composed of high-permittivity metal oxides.","corpus_id":5409733,"score":1},{"doc_id":"24132427","title":"Reconstructing plant cells in 3D by serial section electron tomography.","abstract":"In micrographs acquired with a transmission electron microscope, 3-dimensional (3D) objects are superimposed onto a 2D screen. This reduction in dimension necessarily leads to a degradation of image resolution. To overcome this problem, 3D microscopy techniques, such as tomography and single particle analysis, have been developed. Tomography has been used to visualize cells in 3D, and single particle analysis has been used to investigate macromolecules and viral particles. In this chapter we will describe how we have collected tilting series micrographs from plant cells and how we have reconstructed the cellular volumes using dual axis electron tomography.","corpus_id":45191325,"score":1},{"doc_id":"24161732","title":"Optimod--an automated approach for constructing and optimizing initial models for single-particle electron microscopy.","abstract":"Single-particle cryo-electron microscopy is now well established as a technique for the structural characterization of large macromolecules and macromolecular complexes. The raw data is very noisy and consists of two-dimensional projections, from which the 3D biological object must be reconstructed. The 3D object depends upon knowledge of proper angular orientations assigned to the 2D projection images. Numerous algorithms have been developed for determining relative angular orientations between 2D images, but the transition from 2D to 3D remains challenging and can result in erroneous and conflicting results. Here we describe a general, automated procedure, called OptiMod, for reconstructing and optimizing 3D models using common-lines methodologies. OptiMod approximates orientation angles and reconstructs independent maps from 2D class averages. It then iterates the procedure, while considering each map as a raw solution that needs to be compared with other possible outcomes. We incorporate procedures for 3D alignment, clustering, and refinement to optimize each map, as well as standard scoring metrics to facilitate the selection of the optimal model. We also show that small angle tilt-pair data can be included as one of the scoring metrics to improve the selection of the optimal initial model, and also to provide a validation check. The overall approach is demonstrated using two experimental cryo-EM data sets--the 80S ribosome that represents a relatively straightforward case for ab initio reconstruction, and the Tf-TfR complex that represents a challenging case in that it has previously been shown to provide multiple equally plausible solutions to the initial model problem.","corpus_id":36681249,"score":1},{"doc_id":"24275806","title":"Quantitative analysis of emphysema and airway measurements according to iterative reconstruction algorithms: comparison of filtered back projection, adaptive statistical iterative reconstruction and model-based iterative reconstruction.","abstract":"OBJECTIVES: To evaluate filtered back projection (FBP) and two iterative reconstruction (IR) algorithms and their effects on the quantitative analysis of lung parenchyma and airway measurements on computed tomography (CT) images. METHODS: Low-dose chest CT obtained in 281 adult patients were reconstructed using three algorithms: FBP, adaptive statistical IR (ASIR) and model-based IR (MBIR). Measurements of each dataset were compared: total lung volume, emphysema index (EI), airway measurements of the lumen and wall area as well as average wall thickness. Accuracy of airway measurements of each algorithm was also evaluated using an airway phantom. RESULTS: EI using a threshold of -950 HU was significantly different among the three algorithms in decreasing order of FBP (2.30 %), ASIR (1.49 %) and MBIR (1.20 %) (P < 0.01). Wall thickness was also significantly different among the three algorithms with FBP (2.09 mm) demonstrating thicker walls than ASIR (2.00 mm) and MBIR (1.88 mm) (P < 0.01). Airway phantom analysis revealed that MBIR showed the most accurate value for airway measurements. CONCLUSION: The three algorithms presented different EIs and wall thicknesses, decreasing in the order of FBP, ASIR and MBIR. Thus, care should be taken in selecting the appropriate IR algorithm on quantitative analysis of the lung. KEY POINTS: • Computed tomography is increasingly used to provide objective measurements of intra-thoracic structures. • Iterative reconstruction algorithms can affect quantitative measurements of lung and airways. • Care should be taken in selecting reconstruction algorithms in longitudinal analysis. • Model-based iterative reconstruction seems to provide the most accurate airway measurements.","corpus_id":22157737,"score":1},{"doc_id":"25359850","title":"3D structure determination of protein using TEM single particle analysis.","abstract":"Proteins play important roles in cell functions such as enzymes, cell trafficking, neurotransmission, muscle contraction and hormone secretion. However, some proteins are very difficult to be crystallized and their structures are undetermined. Several techniques have been developed to elucidate the structure of macromolecules; X-ray or electron crystallography, nuclear magnetic resonance spectroscopy, and high-resolution electron microscopy. Among them, electron microscopy based single particle reconstruction (SPA) technique is a computer-aided structure determination method. This method reconstructs the 3D structure from projection images of dispersed protein. A large number of two-dimensional particle images are picked up from EM films, aligned and classified to generate 2D averages, and used to reconstruct the 3D structure by assigning the Euler angle of each 2D average. Due to the necessity of elaborate collaboration between the classical biology and the innovative information technology including parallel computing, scientists needed to break unseen barriers to get a start of this analysis. However, recent progresses in electron microscopes, mathematical algorithms, and computational abilities greatly reduced the height of barriers and expanded targets that are considered to be primarily addressable using single particle analysis. Membrane proteins are one of these targets to which the single particle analysis is successfully applied for the understanding of their 3D structures. For this purpose, we have developed various SPA methods [1-5] and applied them to different proteins [6-8].Here, we introduce reconstructed proteins, and discuss the availability of this technique. The intramembrane-cleaving proteases (I-CLiPs) that sever the transmembrane domains of their substrates have been identified in a range of organisms and play a variety of roles in biological conditions. I-CLiPs have been classified into three groups: serine-, aspartyl- and metalloprotease-type. Signal peptide peptidase (SPP) is an atypical aspartic protease that hydrolyzes peptide bonds within the transmembrane domain of substrates and is implicated in several biological and pathological functions. The structure of human SPP was determined by SPA at a resolution of 22 Å [8]. SPP forms a slender, bullet-shaped homotetramer with dimensions of 85 x 85 x 130 Å. The SPP complex has four concaves on the rhombus-like sides, connected to a large chamber inside the molecule. For the tetrameric assembly, the N-terminal region of SPP was found to be sufficient. Moreover, when N-terminal region was overexpressed, the formation of the endogenous SPP tetramer was inhibited, which suppressed the proteolytic activity within cells. From these data, the N-terminal region is considered to work as the structural scaffold. Transmembrane (TM) translocation of newly synthesized secretion proteins and membrane proteins are carried out by a Sec translocon protein complex. The polypeptide-conducting pore is formed by the SecYEG-SecA complex in bacteria, and the membrane protein SecDF is necessary for the efficient transport of proteins. However the molecular mechanism how SecDF realized efficient transport is not clear. A previous X-ray structural study of the whole protein and subdomain suggest that SecDF has at least two conformational variants, which could reflect molecular dynamics of this protein. To confirm this hypothesis, we analyzed the 3D structure of SecDF using dark field STEM electron tomography and single particle reconstruction. We determined two different whole SecDF protein structures which well explains the X-ray data. From these data, we would like to propose the possible molecular mechanism of SecDF during polypeptide translocation.","corpus_id":29044380,"score":1},{"doc_id":"26258639","title":"A software tool for tomographic axial superresolution in STED microscopy.","abstract":"A method for generating three-dimensional tomograms from multiple three-dimensional axial projections in STimulated Emission Depletion (STED) superresolution microscopy is introduced. Our STED< method, based on the use of a micromirror placed on top of a standard microscopic sample, is used to record a three-dimensional projection at an oblique angle in relation to the main optical axis. Combining the STED< projection with the regular STED image into a single view by tomographic reconstruction, is shown to result in a tomogram with three-to-four-fold improved apparent axial resolution. Registration of the different projections is based on the use of a mutual-information histogram similarity metric. Fusion of the projections into a single view is based on Richardson-Lucy iterative deconvolution algorithm, modified to work with multiple projections. Our tomographic reconstruction method is demonstrated to work with real biological STED superresolution images, including a data set with a limited signal-to-noise ratio (SNR); the reconstruction software (SuperTomo) and its source code will be released under BSD open-source license.","corpus_id":44396491,"score":1},{"doc_id":"26393699","title":"Tomographic reconstruction in soft x-ray microscopy using focus-stack back-projection.","abstract":"Tomographic reconstruction in soft x-ray microscopy is a powerful technique for obtaining high-resolution 3D images of biological samples. However, the depth of focus of such zone-plate-based microscopes is typically shorter than the thickness of many relevant biological objects, challenging the validity of the projection assumption used in conventional reconstruction algorithms. In order to make full use of the soft x-ray microscopes' high resolution, the tomographic reconstruction needs to take the depth of focus into account. Here we present a method to achieve high resolution in the full sample when the depth of focus is short compared to the sample thickness. The method relies on the back-projection of focus-stacked image data from x-ray microscopy. We demonstrate the method on theoretical and experimental data.","corpus_id":2023724,"score":1},{"doc_id":"27646194","title":"Biological application of Compressed Sensing Tomography in the Scanning Electron Microscope.","abstract":"The three-dimensional tomographic reconstruction of a biological sample, namely collagen fibrils in human dermal tissue, was obtained from a set of projection-images acquired in the Scanning Electron Microscope. A tailored strategy for the transmission imaging mode was implemented in the microscope and proved effective in acquiring the projections needed for the tomographic reconstruction. Suitable projection alignment and Compressed Sensing formulation were used to overcome the limitations arising from the experimental acquisition strategy and to improve the reconstruction of the sample. The undetermined problem of structure reconstruction from a set of projections, limited in number and angular range, was indeed supported by exploiting the sparsity of the object projected in the electron microscopy images. In particular, the proposed system was able to preserve the reconstruction accuracy even in presence of a significant reduction of experimental projections.","corpus_id":15380257,"score":1},{"doc_id":"28463289","title":"Comparative study of fully three-dimensional reconstruction algorithms for lens-free microscopy.","abstract":"We propose a three-dimensional (3D) imaging platform based on lens-free microscopy to perform multiangle acquisitions on 3D cell cultures embedded in extracellular matrices. Lens-free microscopy acquisitions present some inherent issues such as the lack of phase information on the sensor plane and a limited angular coverage. We developed and compared three different algorithms based on the Fourier diffraction theorem to obtain fully 3D reconstructions. These algorithms present an increasing complexity associated with a better reconstruction quality. Two of them are based on a regularized inverse problem approach. To compare the reconstruction methods in terms of artefact reduction, signal-to-noise ratio, and computation time, we tested them on two experimental datasets: an endothelial cell culture and a prostate cell culture grown in a 3D extracellular matrix with large reconstructed volumes up to ∼5 mm<sup>3</sup> with a resolution sufficient to resolve isolated single cells. The lens-free reconstructions compare well with standard microscopy.","corpus_id":46771637,"score":1},{"doc_id":"28689080","title":"3D reconstruction of the magnetic vector potential using model based iterative reconstruction.","abstract":"Lorentz transmission electron microscopy (TEM) observations of magnetic nanoparticles contain information on the magnetic and electrostatic potentials. Vector field electron tomography (VFET) can be used to reconstruct electromagnetic potentials of the nanoparticles from their corresponding LTEM images. The VFET approach is based on the conventional filtered back projection approach to tomographic reconstructions and the availability of an incomplete set of measurements due to experimental limitations means that the reconstructed vector fields exhibit significant artifacts. In this paper, we outline a model-based iterative reconstruction (MBIR) algorithm to reconstruct the magnetic vector potential of magnetic nanoparticles. We combine a forward model for image formation in TEM experiments with a prior model to formulate the tomographic problem as a maximum a-posteriori probability estimation problem (MAP). The MAP cost function is minimized iteratively to determine the vector potential. A comparative reconstruction study of simulated as well as experimental data sets show that the MBIR approach yields quantifiably better reconstructions than the VFET approach.","corpus_id":30968793,"score":1},{"doc_id":"28893337","title":"Optimization of Three-Dimensional (3D) Chemical Imaging by Soft X-Ray Spectro-Tomography Using a Compressed Sensing Algorithm.","abstract":"Soft X-ray spectro-tomography provides three-dimensional (3D) chemical mapping based on natural X-ray absorption properties. Since radiation damage is intrinsic to X-ray absorption, it is important to find ways to maximize signal within a given dose. For tomography, using the smallest number of tilt series images that gives a faithful reconstruction is one such method. Compressed sensing (CS) methods have relatively recently been applied to tomographic reconstruction algorithms, providing faithful 3D reconstructions with a much smaller number of projection images than when conventional reconstruction methods are used. Here, CS is applied in the context of scanning transmission X-ray microscopy tomography. Reconstructions by weighted back-projection, the simultaneous iterative reconstruction technique, and CS are compared. The effects of varying tilt angle increment and angular range for the tomographic reconstructions are examined. Optimization of the regularization parameter in the CS reconstruction is explored and discussed. The comparisons show that CS can provide improved reconstruction fidelity relative to weighted back-projection and simultaneous iterative reconstruction techniques, with increasingly pronounced advantages as the angular sampling is reduced. In particular, missing wedge artifacts are significantly reduced and there is enhanced recovery of sharp edges. Examples of using CS for low-dose scanning transmission X-ray microscopy spectroscopic tomography are presented.","corpus_id":1969431,"score":1},{"doc_id":"19001695","title":"Non-iterative conductivity reconstruction algorithm using projected current density in MREIT.","abstract":"Magnetic resonance electrical impedance tomography (MREIT) is to visualize the current density and the conductivity distribution in an electrical object Omega using the measured magnetic flux data by an MRI scanner. MREIT uses only one component B(z) of the magnetic flux density B = (B(x), B(y), B(z)) generated by an injected electrical current into the object. In this paper, we propose a fast and direct non-iterative algorithm to reconstruct the internal conductivity distribution in Omega with the measured B(z) data. To develop the algorithm, we investigate the relation between the projected current density J(P), a uniquely determined component of J by the map from current J to measured B(z) data and the isotropic conductivity. Three-dimensional numerical simulations and phantom experiments are studied to show the feasibility of the proposed method by comparing with those using the conventional iterative harmonic B(z) algorithm.","corpus_id":33943794,"score":0},{"doc_id":"20302885","title":"Single particle reconstruction of membrane proteins: a tool for understanding the 3D structure of disease-related macromolecules.","abstract":"Membrane proteins play important roles in cell functions such as neurotransmission, muscle contraction, and hormone secretion, but their structures are mostly undetermined. Several techniques have been developed to elucidate the structure of macromolecules; X-ray or electron crystallography, nuclear magnetic resonance spectroscopy, and high-resolution electron microscopy. Electron microscopy-based single particle reconstruction, a computer-aided structure determination method, reconstructs a three-dimensional (3D) structure from projections of monodispersed protein. A large number of particle images are picked up from EM films, aligned and classified to generate two-dimensional (2D) averages, and, using the Euler angle of each 2D average, reconstructed into a 3D structure. This method is challenging due to the necessity for close collaboration between classical biochemistry and innovative information technology, including parallel computing. However, recent progress in electron microscopy, mathematical algorithms, and computational ability has greatly increased the subjects that are considered to be primarily addressable using single particle reconstruction. Membrane proteins are one of these targets to which the single particle reconstruction is successfully applied for understanding of their structures. In this paper, we will introduce recently reconstructed channel-related proteins and discuss the applicability of this technique in understanding molecular structures and their roles in pathology.","corpus_id":11433876,"score":0},{"doc_id":"20378810","title":"Four-dimensional electron microscopy.","abstract":"The discovery of the electron over a century ago and the realization of its dual character have given birth to one of the two most powerful imaging instruments: the electron microscope. The electron microscope's ability to resolve three-dimensional (3D) structures on the atomic scale is continuing to affect different fields, including materials science and biology. In this Review, we highlight recent developments and inventions made by introducing the fourth dimension of time in electron microscopy. Today, ultrafast electron microscopy (4D UEM) enables a resolution that is 10 orders of magnitude better than that of conventional microscopes, which are limited by the video-camera rate of recording. After presenting the central concept involved, that of single-electron stroboscopic imaging, we discuss prototypical applications, which include the visualization of complex structures when unfolding on different length and time scales. The developed UEM variant techniques are several, and here we illucidate convergent-beam and near-field imaging, as well as tomography and scanning-pulse microscopy. We conclude with current explorations in imaging of nanomaterials and biostructures and an outlook on possible future directions in space-time, 4D electron microscopy.","corpus_id":5449372,"score":0},{"doc_id":"21089788","title":"Iterative reconstruction of Fourier-rebinned PET data using sinogram blurring function estimated from point source scans.","abstract":"PURPOSE: The accuracy of the system model that governs the transformation from the image space to the projection space in positron emission tomography (PET) greatly affects the quality of reconstructed images. For efficient computation in iterative reconstructions, the system model in PET can be factored into a product of geometric projection and sinogram blurring function. To further speed up reconstruction, fully 3D PET data can be rebinned into a stack of 2D sinograms and then be reconstructed using 2D iterative algorithms. The purpose of this work is to develop a method to estimate the sinogram blurring function to be used in reconstruction of Fourier-rebinned data. METHODS: In a previous work, the authors developed an approach to estimating the sinogram blurring function of nonrebinned PET data from experimental scans of point sources. In this study, the authors extend this method to the estimation of sinogram blurring function for Fourier-rebinned PET data. A point source was scanned at a set of sampled positions in the microPET II scanner. The sinogram blurring function is considered to be separable between the transaxial and axial directions. A radially and angularly variant 2D blurring function is estimated from Fourier-rebinned point source scans to model the transaxial blurring with consideration of the detector block structure of the scanner; a space-variant 1D blurring kernel along the axial direction is estimated separately to model the correlation between neighboring planes due to detector intrinsic blurring and Fourier rebinning. The estimated sinogram blurring function is incorporated in a 2D maximum a posteriori (MAP) reconstruction algorithm for image reconstruction. RESULTS: Physical phantom experiments were performed on the microPET II scanner to validate the proposed method. The authors compared the proposed method to 2D MAP reconstruction without sinogram blurring model and 2D MAP reconstruction with a Monte Carlo based blurring model. The results show that the proposed method produces images with improved contrast and spatial resolution. The reconstruction time is unaffected by the new method since the blurring component takes a relatively negligible part of the overall reconstruction time. CONCLUSIONS: The proposed method can estimate sinogram blurring matrix for Fourier-rebinned PET data and can be used to improve contrast and spatial resolution of reconstructed images. The method can be applied to other human and animal scanners.","corpus_id":20398743,"score":0},{"doc_id":"21752659","title":"The use of trehalose in the preparation of specimens for molecular electron microscopy.","abstract":"Biological specimens have to be prepared for imaging in the electron microscope in a way that preserves their native structure. Two-dimensional (2D) protein crystals to be analyzed by electron crystallography are best preserved by sugar embedding. One of the sugars often used to embed 2D crystals is trehalose, a disaccharide used by many organisms for protection against stress conditions. Sugars such as trehalose can also be added to negative staining solutions used to prepare proteins and macromolecular complexes for structural studies by single-particle electron microscopy (EM). In this review, we describe trehalose and its characteristics that make it so well suited for preparation of EM specimens and we review specimen preparation methods with a focus on the use of trehalose.","corpus_id":11326090,"score":0},{"doc_id":"23026379","title":"Electron tomography of HEK293T cells using scanning electron microscope-based scanning transmission electron microscopy.","abstract":"Based on a scanning electron microscope operated at 30 kV with a homemade specimen holder and a multiangle solid-state detector behind the sample, low-kV scanning transmission electron microscopy (STEM) is presented with subsequent electron tomography for three-dimensional (3D) volume structure. Because of the low acceleration voltage, the stronger electron-atom scattering leads to a stronger contrast in the resulting image than standard TEM, especially for light elements. Furthermore, the low-kV STEM yields less radiation damage to the specimen, hence the structure can be preserved. In this work, two-dimensional STEM images of a 1-μm-thick cell section with projection angles between ±50° were collected, and the 3D volume structure was reconstructed using the simultaneous iterative reconstructive technique algorithm with the TomoJ plugin for ImageJ, which are both public domain software. Furthermore, the cross-sectional structure was obtained with the Volume Viewer plugin in ImageJ. Although the tilting angle is constrained and limits the resulting structural resolution, slicing the reconstructed volume generated the depth profile of the thick specimen with sufficient resolution to examine cellular uptake of Au nanoparticles, and the final position of these nanoparticles inside the cell was imaged.","corpus_id":41862161,"score":0},{"doc_id":"24357373","title":"Biological applications of phase-contrast electron microscopy.","abstract":"Here, I review the principles and applications of phase-contrast electron microscopy using phase plates. First, I develop the principle of phase contrast based on a minimal model of microscopy, introducing a double Fourier-transform process to mathematically formulate the image formation. Next, I explain four phase-contrast (PC) schemes, defocus PC, Zernike PC, Hilbert differential contrast, and schlieren optics, as image-filtering processes in the context of the minimal model, with particular emphases on the Zernike PC and corresponding Zernike phase plates. Finally, I review applications of Zernike PC cryo-electron microscopy to biological systems such as protein molecules, virus particles, and cells, including single-particle analysis to delineate three-dimensional (3D) structures of protein and virus particles and cryo-electron tomography to reconstruct 3D images of complex protein systems and cells.","corpus_id":44908094,"score":0},{"doc_id":"25010640","title":"Ultra-low peak voltage CT colonography: effect of iterative reconstruction algorithms on performance of radiologists who use anthropomorphic colonic phantoms.","abstract":"PURPOSE: To analyze the effect of a decrease in computed tomographic (CT) colonographic voltage, from 100 and 120 kVp to 80 kVp and reconstructed with filtered back projection ( FBP filtered back projection ), on radiation dose, image noise, and diagnostic performance in anthropomorphic phantoms and to assess the effect of iterative reconstruction ( IR iterative reconstruction ) algorithms on radiologists' performance for 80-kVp CT colonography. MATERIALS AND METHODS: Seven colon phantoms with 68 simulated polyps (≥6 mm) were scanned at three peak voltage settings (80, 100, 120 kVp) and 10 mAs. Images were reconstructed by using FBP filtered back projection , hybrid statistic-based IR iterative reconstruction , and knowledge-based IR iterative reconstruction algorithms. Effective radiation dose, image noise, and per-polyp sensitivity were recorded and compared by two reviewers with Friedman test, repeated measures analysis of variance, and McNemar test. RESULTS: Median size-specific dose estimate and effective radiation dose of 80-kVp CT colonography was 0.231 mGy and 0.167 mSv, respectively, which was lower than with 100- and 120-kVp CT colonography, with significant difference between 80 and 120 kVp (P = .0005). Image noise (202.0 HU) at 80-kVp FBP filtered back projection CT colonography was significantly higher than at 100-kVp FBP filtered back projection (139.1 HU) and 120-kVp FBP filtered back projection (120.4 HU) (P < .0001). Per-polyp sensitivity (reviewer 1, 14.7% [10 of 68]; reviewer 2, 7.4% [five of 68]) at 80-kVp FBP filtered back projection was significantly lower than at 100-kVp FBP filtered back projection (reviewer 1, 57.4% [39 of 68]; reviewer 2, 39.7% [27 of 68]) and 120-kVp FBP filtered back projection (reviewer 1, 85.3% [58 of 68]; reviewer 2, 83.8% [57 of 68]) (P < .0001). With statistic-based IR iterative reconstruction , image noise at 80 kVp decreased significantly (52.8% [106.7 HU of 202.0 HU]) compared with that at 80-kVp FBP filtered back projection (P < .0001), but per-polyp sensitivity (reviewer 1, 79.4% [54 of 68]; reviewer 2, 66.2% [45 of 68]) at 80-kVp statistic-based IR iterative reconstruction remained significantly lower than at 100-kVp statistic-based IR iterative reconstruction (reviewer 1, 95.6% [65 of 68]; reviewer 2, 86.8% [59 of 68]) (P = .001) and 120-kVp statistic-based IR iterative reconstruction (reviewer 1, 98.5% [67 of 68]; reviewer 2, 89.7% [61 of 68]) (P < .001). For knowledge-based IR iterative reconstruction , per-polyp sensitivity at 80 kVp was improved to 98.5% (67 of 68) and 94.1% (64 of 68), not significantly different from that at 100 kVp (reviewer 1, 100% [68 of 68]; reviewer 2, 95.6% [65 of 68]) and 120 kVp (reviewer 1, 100% [68 of 68]; reviewer 2, 95.6% [65 of 68]) (P > .999). CONCLUSION: A decrease in tube voltage to 80 kVp caused reduction in radiation dose (0.166 mSv) with deterioration in image noise and per-polyp sensitivity. By using a knowledge-based IR iterative reconstruction algorithm, radiologists' performance of 80-kVp CT colonography was acceptable and on par with that at 100- or 120-kVp CT colonography.","corpus_id":33987840,"score":0},{"doc_id":"25136491","title":"High resolution three-dimensional photoacoutic tomography with CCD-camera based ultrasound detection.","abstract":"A photoacoustic tomograph based on optical ultrasound detection is demonstrated, which is capable of high resolution real-time projection imaging and fast three-dimensional (3D) imaging. Snapshots of the pressure field outside the imaged object are taken at defined delay times after photoacoustic excitation by use of a charge coupled device (CCD) camera in combination with an optical phase contrast method. From the obtained wave patterns photoacoustic projection images are reconstructed using a back propagation Fourier domain reconstruction algorithm. Applying the inverse Radon transform to a set of projections recorded over a half rotation of the sample provides 3D photoacoustic tomography images in less than one minute with a resolution below 100 µm. The sensitivity of the device was experimentally determined to be 5.1 kPa over a projection length of 1 mm. In vivo images of the vasculature of a mouse demonstrate the potential of the developed method for biomedical applications.","corpus_id":15037430,"score":0},{"doc_id":"25528453","title":"Iterative reconstruction of magnetic induction using Lorentz transmission electron tomography.","abstract":"Intense ongoing research on complex nanomagnetic structures requires a fundamental understanding of the 3D magnetization and the stray fields around the nano-objects. 3D visualization of such fields offers the best way to achieve this. Lorentz transmission electron microscopy provides a suitable combination of high resolution and ability to quantitatively visualize the magnetization vectors using phase retrieval methods. In this paper, we present a formalism to represent the magnetic phase shift of electrons as a Radon transform of the magnetic induction of the sample. Using this formalism, we then present the application of common tomographic methods particularly the iterative methods, to reconstruct the 3D components of the vector field. We present an analysis of the effect of missing wedge and the limited angular sampling as well as reconstruction of complex 3D magnetization in a nanowire using simulations.","corpus_id":7367666,"score":0},{"doc_id":"26179326","title":"Single-Particle Cryo-EM and 3D Reconstruction of Hybrid Nanoparticles with Electron-Dense Components.","abstract":"Single-particle cryo-electron microscopy (cryo-EM), accompanied with 3D reconstruction, is a broadly applicable tool for the structural characterization of macromolecules and nanoparticles. Recently, the cryo-EM field has pushed the limits of this technique to higher resolutions and samples of smaller molecular mass, however, some samples still present hurdles to this technique. Hybrid particles with electron-dense components, which have been studied using single-particle cryo-EM yet with limited success in 3D reconstruction due to the interference caused by electron-dense elements, constitute one group of such challenging samples. To process such hybrid particles, a masking method is developed in this work to adaptively remove pixels arising from electron-dense portions in individual projection images while maintaining maximal biomass signals for subsequent 2D alignment, 3D reconstruction, and iterative refinements. As demonstrated by the success in 3D reconstruction of an octahedron DNA/gold hybrid particle, which has been previously published without a 3D reconstruction, the devised strategy that combines adaptive masking and standard single-particle 3D reconstruction approach has overcome the hurdle of electron-dense elements interference, and is generally applicable to cryo-EM structural characterization of most, if not all, hybrid nanomaterials with electron-dense components.","corpus_id":206498175,"score":0},{"doc_id":"26697863","title":"Computation in electron microscopy.","abstract":"Some uses of the computer and computation in high-resolution transmission electron microscopy are reviewed. The theory of image calculation using Bloch wave and multislice methods with and without aberration correction is reviewed and some applications are discussed. The inverse problem of reconstructing the specimen structure from an experimentally measured electron microscope image is discussed. Some future directions of software development are given.","corpus_id":10248349,"score":0},{"doc_id":"27339510","title":"Cryo-electron microscopy and cryo-electron tomography of nanoparticles.","abstract":"Cryo-transmission electron microscopy (cryo-TEM or cryo-EM) and cryo-electron tomography (cryo-ET) offer robust and powerful ways to visualize nanoparticles. These techniques involve imaging of the sample in a frozen-hydrated state, allowing visualization of nanoparticles essentially as they exist in solution. Cryo-TEM grid preparation can be performed with the sample in aqueous solvents or in various organic and ionic solvents. Two-dimensional (2D) cryo-TEM provides a direct way to visualize the polydispersity within a nanoparticle preparation. Fourier transforms of cryo-TEM images can confirm the structural periodicity within a sample. While measurement of specimen parameters can be performed with 2D TEM images, determination of a three-dimensional (3D) structure often facilitates more spatially accurate quantization. 3D structures can be determined in one of two ways. If the nanoparticle has a homogeneous structure, then 2D projection images of different particles can be averaged using a computational process referred to as single particle reconstruction. Alternatively, if the nanoparticle has a heterogeneous structure, then a structure can be generated by cryo-ET. This involves collecting a tilt-series of 2D projection images for a defined region of the grid, which can be used to generate a 3D tomogram. Occasionally it is advantageous to calculate both a single particle reconstruction, to reveal the regular portions of a nanoparticle structure, and a cryo-electron tomogram, to reveal the irregular features. A sampling of 2D cryo-TEM images and 3D structures are presented for protein based, DNA based, lipid based, and polymer based nanoparticles. WIREs Nanomed Nanobiotechnol 2017, 9:e1417. doi: 10.1002/wnan.1417 For further resources related to this article, please visit the WIREs website.","corpus_id":25926091,"score":0},{"doc_id":"28416035","title":"Measuring the Autocorrelation Function of Nanoscale Three-Dimensional Density Distribution in Individual Cells Using Scanning Transmission Electron Microscopy, Atomic Force Microscopy, and a New Deconvolution Algorithm.","abstract":"Essentially all biological processes are highly dependent on the nanoscale architecture of the cellular components where these processes take place. Statistical measures, such as the autocorrelation function (ACF) of the three-dimensional (3D) mass-density distribution, are widely used to characterize cellular nanostructure. However, conventional methods of reconstruction of the deterministic 3D mass-density distribution, from which these statistical measures can be calculated, have been inadequate for thick biological structures, such as whole cells, due to the conflict between the need for nanoscale resolution and its inverse relationship with thickness after conventional tomographic reconstruction. To tackle the problem, we have developed a robust method to calculate the ACF of the 3D mass-density distribution without tomography. Assuming the biological mass distribution is isotropic, our method allows for accurate statistical characterization of the 3D mass-density distribution by ACF with two data sets: a single projection image by scanning transmission electron microscopy and a thickness map by atomic force microscopy. Here we present validation of the ACF reconstruction algorithm, as well as its application to calculate the statistics of the 3D distribution of mass-density in a region containing the nucleus of an entire mammalian cell. This method may provide important insights into architectural changes that accompany cellular processes.","corpus_id":27830361,"score":0}],"string":"[\n {\n \"doc_id\": \"18353677\",\n \"title\": \"Fast projection matching for cryo-electron microscopy image reconstruction.\",\n \"abstract\": \"A new FFT-accelerated projection matching method is presented and tested. The electron microscopy images are represented by their Fourier-Bessel transforms and the 3D model by its expansion in spherical harmonics, or more specifically in terms of symmetry-adapted functions. The rotational and translational properties of these representations are used to quickly access all the possible 2D projections of the 3D model, which allow an exhaustive inspection of the whole five-dimensional domain of parameters associated to each particle.\",\n \"corpus_id\": 2011492,\n \"score\": 2\n },\n {\n \"doc_id\": \"19398410\",\n \"title\": \"Electronic noise modeling in statistical iterative reconstruction.\",\n \"abstract\": \"We consider electronic noise modeling in tomographic image reconstruction when the measured signal is the sum of a Gaussian distributed electronic noise component and another random variable whose log-likelihood function satisfies a certain linearity condition. Examples of such likelihood functions include the Poisson distribution and an exponential dispersion (ED) model that can approximate the signal statistics in integration mode X-ray detectors. We formulate the image reconstruction problem as a maximum-likelihood estimation problem. Using an expectation-maximization approach, we demonstrate that a reconstruction algorithm can be obtained following a simple substitution rule from the one previously derived without electronic noise considerations. To illustrate the applicability of the substitution rule, we present examples of a fully iterative reconstruction algorithm and a sinogram smoothing algorithm both in transmission CT reconstruction when the measured signal contains additive electronic noise. Our simulation studies show the potential usefulness of accurate electronic noise modeling in low-dose CT applications.\",\n \"corpus_id\": 16528431,\n \"score\": 2\n },\n {\n \"doc_id\": \"19850372\",\n \"title\": \"On the efficiency of iterative ordered subset reconstruction algorithms for acceleration on GPUs.\",\n \"abstract\": \"Expectation Maximization (EM) and the Simultaneous Iterative Reconstruction Technique (SIRT) are two iterative computed tomography reconstruction algorithms often used when the data contain a high amount of statistical noise, have been acquired from a limited angular range, or have a limited number of views. A popular mechanism to increase the rate of convergence of these types of algorithms has been to perform the correctional updates within subsets of the projection data. This has given rise to the method of Ordered Subsets EM (OS-EM) and the Simultaneous Algebraic Reconstruction Technique (SART). Commodity graphics hardware (GPUs) has shown great promise to combat the high computational demands incurred by iterative reconstruction algorithms. However, we find that the special architecture and programming model of GPUs add extra constraints on the real-time performance of ordered subsets algorithms, counteracting the speedup benefits of smaller subsets observed on CPUs. This gives rise to new relationships governing the optimal number of subsets as well as relaxation factor settings for obtaining the smallest wall-clock time for reconstruction-a factor that is likely application-dependent. In this paper we study the generalization of SIRT into Ordered Subsets SIRT and show that this allows one to optimize the computational performance of GPU-accelerated iterative algebraic reconstruction methods.\",\n \"corpus_id\": 262235127,\n \"score\": 2\n },\n {\n \"doc_id\": \"20051344\",\n \"title\": \"Development and optimization of regularized tomographic reconstruction algorithms utilizing equally-sloped tomography.\",\n \"abstract\": \"We develop two new algorithms for tomographic reconstruction which incorporate the technique of equally-sloped tomography (EST) and allow for the optimized and flexible implementation of regularization schemes, such as total variation constraints, and the incorporation of arbitrary physical constraints. The founding structure of the developed algorithms is EST, a technique of tomographic acquisition and reconstruction first proposed by Miao in 2005 for performing tomographic image reconstructions from a limited number of noisy projections in an accurate manner by avoiding direct interpolations. EST has recently been successfully applied to coherent diffraction microscopy, electron microscopy, and computed tomography for image enhancement and radiation dose reduction. However, the bottleneck of EST lies in its slow speed due to its higher computation requirements. In this paper, we formulate the EST approach as a constrained problem and subsequently transform it into a series of linear problems, which can be accurately solved by the operator splitting method. Based on these mathematical formulations, we develop two iterative algorithms for tomographic image reconstructions through EST, which incorporate Bregman and continuative regularization. Our numerical experiment results indicate that the new tomographic image reconstruction algorithms not only significantly reduce the computational time, but also improve the image quality. We anticipate that EST coupled with the novel iterative algorithms will find broad applications in X-ray tomography, electron microscopy, coherent diffraction microscopy, and other tomography fields.\",\n \"corpus_id\": 8240156,\n \"score\": 2\n },\n {\n \"doc_id\": \"20622984\",\n \"title\": \"Parallelism of iterative CT reconstruction based on local reconstruction algorithm.\",\n \"abstract\": \"An iterative algorithm is suited to reconstruct CT images from noisy or truncated projection data. However, as a disadvantage, the algorithm requires significant computational time. Although a parallel technique can be used to reduce the computational time, a large amount of communication overhead becomes an obstacle to its performance (Li et al. in J. X-Ray Sci. Technol. 13:1-10, 2005). To overcome this problem, we proposed an innovative parallel method based on the local iterative CT reconstruction algorithm (Wang et al. in Scanning 18:582-588, 1996 and IEEE Trans. Med. Imaging 15(5):657-664, 1996). The object to be reconstructed is partitioned into a number of subregions and assigned to different processing elements (PEs). Within each PE, local iterative reconstruction is performed to recover the subregion. Several numerical experiments were conducted on a high performance computing cluster. And the FORBILD head phantom (Lauritsch and Bruder http://www.imp.uni-erlangen.de/phantoms/head/head.html) was used as benchmark to measure the parallel performance. The experimental results showed that the proposed parallel algorithm significantly reduces the reconstruction time, hence achieving a high speedup and efficiency.\",\n \"corpus_id\": 765945,\n \"score\": 2\n },\n {\n \"doc_id\": \"20888956\",\n \"title\": \"Fundamentals of three-dimensional reconstruction from projections.\",\n \"abstract\": \"Three-dimensional (3D) reconstruction of an object mass density from the set of its 2D line projections lies at a core of both single-particle reconstruction technique and electron tomography. Both techniques utilize electron microscope to collect a set of projections of either multiple objects representing in principle the same macromolecular complex in an isolated form, or a subcellular structure isolated in situ. Therefore, the goal of macromolecular electron microscopy is to invert the projection transformation to recover the distribution of the mass density of the original object. The problem is interesting in that in its discrete form it is ill-posed and not invertible. Various algorithms have been proposed to cope with the practical difficulties of this inversion problem and their differ widely in terms of their robustness with respect to noise in the data, completeness of the collected projection dataset, errors in projections orientation parameters, abilities to efficiently handle large datasets, and other obstacles typically encountered in molecular electron microscopy. Here, we review the theoretical foundations of 3D reconstruction from line projections followed by an overview of reconstruction algorithms routinely used in practice of electron microscopy.\",\n \"corpus_id\": 23406418,\n \"score\": 2\n },\n {\n \"doc_id\": \"21333489\",\n \"title\": \"Iterative reconstruction algorithms with α-divergence for PET imaging.\",\n \"abstract\": \"This paper presents a class of image reconstruction algorithms based on Amari's α-divergence for position emission tomography. The α-divergence is actually a family of divergences indexed by α∈(-∞, +∞) that can measure discrepancy between two distributions. We consider it to model the discrepancy between projections and their estimates. By iteratively minimizing the α-divergence, a multiplicative updating algorithm is derived using an auxiliary function. The well-known ML-EM algorithm and the SA-WLS algorithm suggested by Zhu et al. arise as two special cases of our method. We prove the monotonic convergence of the algorithm, which Zhu et al. has not provided. The experiments were performed on both simulated and clinical data to study the interesting and useful behavior of the algorithm in cases where different parameters (α) were used. The results showed that some chosen algorithms exhibited much better performance than the prevalent ones.\",\n \"corpus_id\": 9859828,\n \"score\": 2\n },\n {\n \"doc_id\": \"21741915\",\n \"title\": \"A distributed multi-GPU system for high speed electron microscopic tomographic reconstruction.\",\n \"abstract\": \"Full resolution electron microscopic tomographic (EMT) reconstruction of large-scale tilt series requires significant computing power. The desire to perform multiple cycles of iterative reconstruction and realignment dramatically increases the pressing need to improve reconstruction performance. This has motivated us to develop a distributed multi-GPU (graphics processing unit) system to provide the required computing power for rapid constrained, iterative reconstructions of very large three-dimensional (3D) volumes. The participating GPUs reconstruct segments of the volume in parallel, and subsequently, the segments are assembled to form the complete 3D volume. Owing to its power and versatility, the CUDA (NVIDIA, USA) platform was selected for GPU implementation of the EMT reconstruction. For a system containing 10 GPUs provided by 5 GTX295 cards, 10 cycles of SIRT reconstruction for a tomogram of 4096(2) × 512 voxels from an input tilt series containing 122 projection images of 4096(2) pixels (single precision float) takes a total of 1845 s of which 1032 s are for computation with the remainder being the system overhead. The same system takes only 39 s total to reconstruct 1024(2) × 256 voxels from 122 1024(2) pixel projections. While the system overhead is non-trivial, performance analysis indicates that adding extra GPUs to the system would lead to steadily enhanced overall performance. Therefore, this system can be easily expanded to generate superior computing power for very large tomographic reconstructions and especially to empower iterative cycles of reconstruction and realignment.\",\n \"corpus_id\": 17305025,\n \"score\": 2\n },\n {\n \"doc_id\": \"21864687\",\n \"title\": \"Single-particle reconstruction using L(2)-gradient flow.\",\n \"abstract\": \"In this paper, we present an iterative algorithm for reconstructing a three-dimensional density function from a set of two dimensional electron microscopy images. By minimizing an energy functional consisting of a fidelity term and a regularization term, an L(2)-gradient flow is derived. The flow is integrated by a finite element method in the spatial direction and an explicit Euler scheme in the temporal direction. Our method compares favorably with those of the weighted back projection, Fourier method, algebraic reconstruction technique and simultaneous iterative reconstruction technique.\",\n \"corpus_id\": 263434046,\n \"score\": 2\n },\n {\n \"doc_id\": \"22536462\",\n \"title\": \"FAST WAVELET-BASED SINGLE-PARTICLE RECONSTRUCTION IN CRYO-EM.\",\n \"abstract\": \"This paper presents a novel algorithm for the 3D tomographic inversion problem that arises in single-particle electron cryo-microscopy (Cryo-EM). It is based on two key components: 1) a variational formulation that promotes sparsity in the wavelet domain and 2) the Toeplitz structure of the combined projection/back-projection operator. The first idea has proven to be very effective for the recovery of piecewise-smooth signals, which is confirmed by our numerical experiments. The second idea allows for a computationally efficient implementation of the reconstruction procedure, using only one circulant convolution per iteration.\",\n \"corpus_id\": 8925374,\n \"score\": 2\n },\n {\n \"doc_id\": \"22951262\",\n \"title\": \"Advanced reconstruction algorithms for electron tomography: from comparison to combination.\",\n \"abstract\": \"In this work, the simultaneous iterative reconstruction technique (SIRT), the total variation minimization (TVM) reconstruction technique and the discrete algebraic reconstruction technique (DART) for electron tomography are compared and the advantages and disadvantages are discussed. Furthermore, we describe how the result of a three dimensional (3D) reconstruction based on TVM can provide objective information that is needed as the input for a DART reconstruction. This approach results in a tomographic reconstruction of which the segmentation is carried out in an objective manner.\",\n \"corpus_id\": 12478769,\n \"score\": 2\n },\n {\n \"doc_id\": \"23464329\",\n \"title\": \"Radiation dose reduction in medical x-ray CT via Fourier-based iterative reconstruction.\",\n \"abstract\": \"PURPOSE: A Fourier-based iterative reconstruction technique, termed Equally Sloped Tomography (EST), is developed in conjunction with advanced mathematical regularization to investigate radiation dose reduction in x-ray CT. The method is experimentally implemented on fan-beam CT and evaluated as a function of imaging dose on a series of image quality phantoms and anonymous pediatric patient data sets. Numerical simulation experiments are also performed to explore the extension of EST to helical cone-beam geometry. METHODS: EST is a Fourier based iterative algorithm, which iterates back and forth between real and Fourier space utilizing the algebraically exact pseudopolar fast Fourier transform (PPFFT). In each iteration, physical constraints and mathematical regularization are applied in real space, while the measured data are enforced in Fourier space. The algorithm is automatically terminated when a proposed termination criterion is met. Experimentally, fan-beam projections were acquired by the Siemens z-flying focal spot technology, and subsequently interleaved and rebinned to a pseudopolar grid. Image quality phantoms were scanned at systematically varied mAs settings, reconstructed by EST and conventional reconstruction methods such as filtered back projection (FBP), and quantified using metrics including resolution, signal-to-noise ratios (SNRs), and contrast-to-noise ratios (CNRs). Pediatric data sets were reconstructed at their original acquisition settings and additionally simulated to lower dose settings for comparison and evaluation of the potential for radiation dose reduction. Numerical experiments were conducted to quantify EST and other iterative methods in terms of image quality and computation time. The extension of EST to helical cone-beam CT was implemented by using the advanced single-slice rebinning (ASSR) method. RESULTS: Based on the phantom and pediatric patient fan-beam CT data, it is demonstrated that EST reconstructions with the lowest scanner flux setting of 39 mAs produce comparable image quality, resolution, and contrast relative to FBP with the 140 mAs flux setting. Compared to the algebraic reconstruction technique and the expectation maximization statistical reconstruction algorithm, a significant reduction in computation time is achieved with EST. Finally, numerical experiments on helical cone-beam CT data suggest that the combination of EST and ASSR produces reconstructions with higher image quality and lower noise than the Feldkamp Davis and Kress (FDK) method and the conventional ASSR approach. CONCLUSIONS: A Fourier-based iterative method has been applied to the reconstruction of fan-bean CT data with reduced x-ray fluence. This method incorporates advantageous features in both real and Fourier space iterative schemes: using a fast and algebraically exact method to calculate forward projection, enforcing the measured data in Fourier space, and applying physical constraints and flexible regularization in real space. Our results suggest that EST can be utilized for radiation dose reduction in x-ray CT via the readily implementable technique of lowering mAs settings. Numerical experiments further indicate that EST requires less computation time than several other iterative algorithms and can, in principle, be extended to helical cone-beam geometry in combination with the ASSR method.\",\n \"corpus_id\": 13455029,\n \"score\": 2\n },\n {\n \"doc_id\": \"23706690\",\n \"title\": \"Expectation maximization (EM) algorithms using polar symmetries for computed tomography (CT) image reconstruction.\",\n \"abstract\": \"We suggest a symmetric-polar pixellation scheme which makes possible a reduction of the computational cost for expectation maximization (EM) iterative algorithms. The proposed symmetric-polar pixellation allows us to deal with 3D images as a whole problem without dividing the 3D problem into 2D slices approach. Performance evaluation of each approach in terms of stability and image quality is presented. Exhaustive comparisons between all approaches were conducted in a 2D based image reconstruction model. From these 2D approaches, that showing the best performances were finally implemented and evaluated in a 3D based image reconstruction model. Comparison to 3D images reconstructed with FBP is also presented. Although the algorithm is presented in the context of computed tomography (CT) image reconstruction, it can be applied to any other tomographic technique as well, due to the fact that the only requirement is a scanning geometry involving measurements of an object under different projection angles. Real data have been acquired with a small animal (CT) scanner to verify the proposed mathematical description of the CT system.\",\n \"corpus_id\": 8143656,\n \"score\": 2\n },\n {\n \"doc_id\": \"23955748\",\n \"title\": \"A model based iterative reconstruction algorithm for high angle annular dark field-scanning transmission electron microscope (HAADF-STEM) tomography.\",\n \"abstract\": \"High angle annular dark field (HAADF)-scanning transmission electron microscope (STEM) data is increasingly being used in the physical sciences to research materials in 3D because it reduces the effects of Bragg diffraction seen in bright field TEM data. Typically, tomographic reconstructions are performed by directly applying either filtered back projection (FBP) or the simultaneous iterative reconstruction technique (SIRT) to the data. Since HAADF-STEM tomography is a limited angle tomography modality with low signal to noise ratio, these methods can result in significant artifacts in the reconstructed volume. In this paper, we develop a model based iterative reconstruction algorithm for HAADF-STEM tomography. We combine a model for image formation in HAADF-STEM tomography along with a prior model to formulate the tomographic reconstruction as a maximum a posteriori probability (MAP) estimation problem. Our formulation also accounts for certain missing measurements by treating them as nuisance parameters in the MAP estimation framework. We adapt the iterative coordinate descent algorithm to develop an efficient method to minimize the corresponding MAP cost function. Reconstructions of simulated as well as experimental data sets show results that are superior to FBP and SIRT reconstructions, significantly suppressing artifacts and enhancing contrast.\",\n \"corpus_id\": 8192264,\n \"score\": 2\n },\n {\n \"doc_id\": \"24008024\",\n \"title\": \"Weighted simultaneous iterative reconstruction technique for single-axis tomography.\",\n \"abstract\": \"Tomographic techniques play a crucial role in imaging methods such as transmission electron microscopy (TEM) due to their unique capabilities to reconstruct three-dimensional object information. However, the accuracy of the two standard tomographic reconstruction techniques, the weighted back-projection (W-BP) and the simultaneous iterative reconstruction technique (SIRT) is reduced under common experimental restrictions, such as limited tilt range or noise. We demonstrate that the combination of W-BP and SIRT leads to an improved tomographic reconstruction technique: the weighted SIRT. Convergence, resolution and reconstruction error of the W-SIRT are analyzed by a detailed analytical, numerical, and experimental comparison with established methods. Our reconstruction technique is not restricted to TEM tomography but can be applied to all problems sharing single axis imaging geometry.\",\n \"corpus_id\": 33934794,\n \"score\": 2\n },\n {\n \"doc_id\": \"24326216\",\n \"title\": \"Iterative reconstruction of cryo-electron tomograms using nonuniform fast Fourier transforms.\",\n \"abstract\": \"Algorithms for three-dimensional (3D) reconstruction of objects based on their projections are essential in various biological and medical imaging modalities. In cryo-electron tomography (CET) a major challenge for reconstruction is the limited range of projection angles, which manifests itself as a \\\"missing wedge\\\" of data in Fourier space making the reconstruction problem ill-posed. Here, we apply an iterative reconstruction method that makes use of nonuniform fast Fourier transform (NUFFT) to the reconstruction of cryo-electron tomograms. According to several measures the reconstructions are superior to those obtained using conventional methods, most notably weighted backprojection. Most importantly, we show that it is possible to fill in partially the unsampled region in Fourier space with meaningful information without making assumptions about the data or applying prior knowledge. As a consequence, particles of known structure can be localized with higher confidence in cryotomograms and subtomogram averaging yields higher resolution densities.\",\n \"corpus_id\": 5514970,\n \"score\": 2\n },\n {\n \"doc_id\": \"25048191\",\n \"title\": \"Comparing five different iterative reconstruction algorithms for computed tomography in an ROC study.\",\n \"abstract\": \"OBJECTIVES: The purpose of this study was to evaluate lesion conspicuity achieved with five different iterative reconstruction techniques from four CT vendors at three different dose levels. Comparisons were made of iterative algorithm and filtered back projection (FBP) among and within systems. METHODS: An anthropomorphic liver phantom was examined with four CT systems, each from a different vendor. CTDIvol levels of 5 mGy, 10 mGy and 15 mGy were chosen. Images were reconstructed with FBP and the iterative algorithm on the system. Images were interpreted independently by four observers, and the areas under the ROC curve (AUCs) were calculated. Noise and contrast-to-noise ratios (CNR) were measured. RESULTS: One iterative algorithm increased AUC (0.79, 0.95, and 0.97) compared to FBP (0.70, 0.86, and 0.93) at all dose levels (p < 0.001 and p = 0.047). Another algorithm increased AUC from 0.78 with FBP to 0.84 (p = 0.007) at 5 mGy. Differences at 10 and 15 mGy were not significant (p-values: 0.084-0.883). Three algorithms showed no difference in AUC compared to FBP (p-values: 0.008-1.000). All of the algorithms decreased noise (10-71%) and improved CNR. CONCLUSIONS: Only two algorithms improved lesion detection, even though noise reduction was shown with all algorithms. KEY POINTS: Iterative reconstruction algorithms affected lesion detection differently at different dose levels. One iterative algorithm improved lesion detectability compared to filtered back projection. Three algorithms did not significantly improve lesion detectability. One algorithm improved lesion detectability at the lowest dose level.\",\n \"corpus_id\": 24858397,\n \"score\": 2\n },\n {\n \"doc_id\": \"25304701\",\n \"title\": \"Iterative reconstruction: how it works, how to apply it.\",\n \"abstract\": \"Computed tomography acquires X-ray projection data from multiple angles though an object to generate a tomographic rendition of its attenuation characteristics. Filtered back projection is a fast, closed analytical solution to the reconstruction process, whereby all projections are equally weighted, but is prone to deliver inadequate image quality when the dose levels are reduced. Iterative reconstruction is an algorithmic method that uses statistical and geometric models to variably weight the image data in a process that can be solved iteratively to independently reduce noise and preserve resolution and image quality. Applications of this technology in a clinical setting can result in lower dose on the order of 20-40% compared to a standard filtered back projection reconstruction for most exams. A carefully planned implementation strategy and methodological approach is necessary to achieve the goals of lower dose with uncompromised image quality.\",\n \"corpus_id\": 22095801,\n \"score\": 2\n },\n {\n \"doc_id\": \"25436931\",\n \"title\": \"Atomic resolution tomography reconstruction of tilt series based on a GPU accelerated hybrid input-output algorithm using polar Fourier transform.\",\n \"abstract\": \"Advances in diffraction and transmission electron microscopy (TEM) have greatly improved the prospect of three-dimensional (3D) structure reconstruction from two-dimensional (2D) images or diffraction patterns recorded in a tilt series at atomic resolution. Here, we report a new graphics processing unit (GPU) accelerated iterative transformation algorithm (ITA) based on polar fast Fourier transform for reconstructing 3D structure from 2D diffraction patterns. The algorithm also applies to image tilt series by calculating diffraction patterns from the recorded images using the projection-slice theorem. A gold icosahedral nanoparticle of 309 atoms is used as the model to test the feasibility, performance and robustness of the developed algorithm using simulations. Atomic resolution in 3D is achieved for the 309 atoms Au nanoparticle using 75 diffraction patterns covering 150° rotation. The capability demonstrated here provides an opportunity to uncover the 3D structure of small objects of nanometers in size by electron diffraction.\",\n \"corpus_id\": 10994340,\n \"score\": 2\n },\n {\n \"doc_id\": \"25659894\",\n \"title\": \"Progressive Stochastic Reconstruction Technique (PSRT) for cryo electron tomography.\",\n \"abstract\": \"Cryo Electron Tomography (cryoET) plays an essential role in Structural Biology, as it is the only technique that allows to study the structure of large macromolecular complexes in their close to native environment in situ. The reconstruction methods currently in use, such as Weighted Back Projection (WBP) or Simultaneous Iterative Reconstruction Technique (SIRT), deliver noisy and low-contrast reconstructions, which complicates the application of high-resolution protocols, such as Subtomogram Averaging (SA). We propose a Progressive Stochastic Reconstruction Technique (PSRT) - a novel iterative approach to tomographic reconstruction in cryoET based on Monte Carlo random walks guided by Metropolis-Hastings sampling strategy. We design a progressive reconstruction scheme to suit the conditions present in cryoET and apply it successfully to reconstructions of macromolecular complexes from both synthetic and experimental datasets. We show how to integrate PSRT into SA, where it provides an elegant solution to the region-of-interest problem and delivers high-contrast reconstructions that significantly improve template-based localization without any loss of high-resolution structural information. Furthermore, the locality of SA is exploited to design an importance sampling scheme which significantly speeds up the otherwise slow Monte Carlo approach. Finally, we design a new memory efficient solution for the specimen-level interior problem of cryoET, removing all associated artifacts.\",\n \"corpus_id\": 206494153,\n \"score\": 2\n },\n {\n \"doc_id\": \"25680211\",\n \"title\": \"BSIRT: a block-iterative SIRT parallel algorithm using curvilinear projection model.\",\n \"abstract\": \"Large-field high-resolution electron tomography enables visualizing detailed mechanisms under global structure. As field enlarges, the distortions of reconstruction and processing time become more critical. Using the curvilinear projection model can improve the quality of large-field ET reconstruction, but its computational complexity further exacerbates the processing time. Moreover, there is no parallel strategy on GPU for iterative reconstruction method with curvilinear projection. Here we propose a new Block-iterative SIRT parallel algorithm with the curvilinear projection model (BSIRT) for large-field ET reconstruction, to improve the quality of reconstruction and accelerate the reconstruction process. We also develop some key techniques, including block-iterative method with the curvilinear projection, a scope-based data decomposition method and a page-based data transfer scheme to implement the parallelization of BSIRT on GPU platform. Experimental results show that BSIRT can improve the reconstruction quality as well as the speed of the reconstruction process.\",\n \"corpus_id\": 23818719,\n \"score\": 2\n },\n {\n \"doc_id\": \"26008761\",\n \"title\": \"Three-dimensional reconstruction methods in Single Particle Analysis from transmission electron microscopy data.\",\n \"abstract\": \"The Transmission Electron Microscope provides two-dimensional (2D) images of the specimens under study. However, the architecture of these specimens is defined in a three-dimensional (3D) coordinate space, in volumetric terms, making the direct microscope output somehow \\\"short\\\" in terms of dimensionality. This situation has prompted the development of methods to quantitatively estimate 3D volumes from sets of 2D images, which are usually referred to as \\\"three-dimensional reconstruction methods\\\". These 3D reconstruction methods build on four considerations: (1) The relationship between the 2D images and the 3D volume must be of a particularly simple type, (2) many 2D images are needed to gain 3D volumetric information, (3) the 2D images and the 3D volume have to be in the same coordinate reference frame and (4), in practical terms, the reconstructed 3D volume will only be an approximation to the original 3D volume which gave raise to the 2D projections. In this work we will adopt a quite general view, trying to address a large community of interested readers, although some sections will be particularly devoted to the 3D analysis of isolated macromolecular complexes in the application area normally referred to as Single Particle Analysis (SPA).\",\n \"corpus_id\": 2983500,\n \"score\": 2\n },\n {\n \"doc_id\": \"26046398\",\n \"title\": \"Matched Backprojection Operator for Combined Scanning Transmission Electron Microscopy Tilt- and Focal Series.\",\n \"abstract\": \"Combined tilt- and focal series scanning transmission electron microscopy is a recently developed method to obtain nanoscale three-dimensional (3D) information of thin specimens. In this study, we formulate the forward projection in this acquisition scheme as a linear operator and prove that it is a generalization of the Ray transform for parallel illumination. We analytically derive the corresponding backprojection operator as the adjoint of the forward projection. We further demonstrate that the matched backprojection operator drastically improves the convergence rate of iterative 3D reconstruction compared to the case where a backprojection based on heuristic weighting is used. In addition, we show that the 3D reconstruction is of better quality.\",\n \"corpus_id\": 22162282,\n \"score\": 2\n },\n {\n \"doc_id\": \"26094203\",\n \"title\": \"A fast iterative convolution weighting approach for gridding-based direct Fourier three-dimensional reconstruction with correction for the contrast transfer function.\",\n \"abstract\": \"We describe a fast and accurate method for the reconstruction of macromolecular complexes from a set of projections. Direct Fourier inversion (in which the Fourier Slice Theorem plays a central role) is a solution for dealing with this inverse problem. Unfortunately, the set of projections provides a non-equidistantly sampled version of the macromolecule Fourier transform in the single particle field (and, therefore, a direct Fourier inversion) may not be an optimal solution. In this paper, we introduce a gridding-based direct Fourier method for the three-dimensional reconstruction approach that uses a weighting technique to compute a uniform sampled Fourier transform. Moreover, the contrast transfer function of the microscope, which is a limiting factor in pursuing a high resolution reconstruction, is corrected by the algorithm. Parallelization of this algorithm, both on threads and on multiple CPU's, makes the process of three-dimensional reconstruction even faster. The experimental results show that our proposed gridding-based direct Fourier reconstruction is slightly more accurate than similar existing methods and presents a lower computational complexity both in terms of time and memory, thereby allowing its use on larger volumes. The algorithm is fully implemented in the open-source Xmipp package and is downloadable from http://xmipp.cnb.csic.es.\",\n \"corpus_id\": 205524467,\n \"score\": 2\n },\n {\n \"doc_id\": \"26405903\",\n \"title\": \"FASART: An iterative reconstruction algorithm with inter-iteration adaptive NAD filter.\",\n \"abstract\": \"Electron tomography (ET) is an essential imaging technique for studying structures of large biological specimens. These structures are reconstructed from a set of projections obtained at different sample orientations by tilting the specimen. However, most of existing reconstruction methods are not appropriate when the data are extremely noisy and incomplete. A new iterative method has been proposed: adaptive simultaneous algebraic reconstruction with inter-iteration adaptive non-linear anisotropic diffusion (NAD) filter (FASART). We also adopted an adaptive parameter and discussed the step for the filter in this reconstruction method. Experimental results show that FASART can restrain the noise generated in the process of iterative reconstruction and still preserve the more details of the structure edges.\",\n \"corpus_id\": 33402313,\n \"score\": 2\n },\n {\n \"doc_id\": \"26418739\",\n \"title\": \"A Novel Iterative CT Reconstruction Approach Based on FBP Algorithm.\",\n \"abstract\": \"The Filtered Back-Projection (FBP) algorithm and its modified versions are the most important techniques for CT (Computerized tomography) reconstruction, however, it may produce aliasing degradation in the reconstructed images due to projection discretization. The general iterative reconstruction (IR) algorithms suffer from their heavy calculation burden and other drawbacks. In this paper, an iterative FBP approach is proposed to reduce the aliasing degradation. In the approach, the image reconstructed by FBP algorithm is treated as the intermediate image and projected along the original projection directions to produce the reprojection data. The difference between the original and reprojection data is filtered by a special digital filter, and then is reconstructed by FBP to produce a correction term. The correction term is added to the intermediate image to update it. This procedure can be performed iteratively to improve the reconstruction performance gradually until certain stopping criterion is satisfied. Some simulations and tests on real data show the proposed approach is better than FBP algorithm or some IR algorithms in term of some general image criteria. The calculation burden is several times that of FBP, which is much less than that of general IR algorithms and acceptable in the most situations. Therefore, the proposed algorithm has the potential applications in practical CT systems.\",\n \"corpus_id\": 17630373,\n \"score\": 2\n },\n {\n \"doc_id\": \"26459139\",\n \"title\": \"Total Variation-Based Reduction of Streak Artifacts, Ring Artifacts and Noise in 3D Reconstruction from Optical Projection Tomography.\",\n \"abstract\": \"Optical projection tomography (OPT) is a computed tomography technique at optical frequencies for samples of 0.5-15 mm in size, which fills an important \\\"imaging gap\\\" between confocal microscopy (for smaller samples) and large-sample methods such as fluorescence molecular tomography or micro magnetic resonance imaging. OPT operates in either fluorescence or transmission mode. Two-dimensional (2D) projections are taken over 360° with a fixed rotational increment around the vertical axis. Standard 3D reconstruction from 2D OPT uses the filtered backprojection (FBP) algorithm based on the Radon transform. FBP approximates the inverse Radon transform using a ramp filter that spreads reconstructed pixels to neighbor pixels thus producing streak and other types of artifacts, as well as noise. Artifacts increase the variation of grayscale values in the reconstructed images. We present an algorithm that improves the quality of reconstruction even for a low number of projections by simultaneously minimizing the sum of absolute brightness changes in the reconstructed volume (the total variation) and the error between measured and reconstructed data. We demonstrate the efficiency of the method on real biological data acquired on a dedicated OPT device.\",\n \"corpus_id\": 9662152,\n \"score\": 2\n },\n {\n \"doc_id\": \"26916079\",\n \"title\": \"On geometric artifacts in cryo electron tomography.\",\n \"abstract\": \"Single-tilt scheme is nowadays the prevalent acquisition geometry in electron tomography and subtomogram averaging experiments. Being an incomplete scheme that induces ill-posedness in the sense of the X-ray or Radon transform inverse problem, it introduces a number of artifacts that directly influence the quality of tomographic reconstructions. Though individually described by different authors before, a systematic study of these acquisition geometry-related artifacts in one place and across representative set of reconstruction methods has not been, to our knowledge, performed before. Moreover, the effects of these artifacts on the reconstructed density are sometimes misinterpreted, attributing them to the wrong cause, especially if their effects accumulate. In this work, we systematically study the major artifacts of single-tilt geometry known as the missing wedge (incomplete projection set problem), the missing information and the specimen-level interior problem (long-object problem). First, we illustratively describe, using a unified terminology, how and why these artifacts arise and when they can be avoided. Next, we describe the effects of these artifacts on the reconstructions across all major classes of reconstruction methods, including newly-appeared methods like the Iterative Nonuniform fast Fourier transform based Reconstruction method (INFR) and the Progressive Stochastic Reconstruction Technique (PSRT). Finally, we draw conclusions and recommendations on numerous points, especially regarding the mutual influence of the geometric artifacts, ability of different reconstruction methods to suppress them as well as implications to the interpretation of both electron tomography and subtomogram averaging experiments.\",\n \"corpus_id\": 20770177,\n \"score\": 2\n },\n {\n \"doc_id\": \"28874736\",\n \"title\": \"GENFIRE: A generalized Fourier iterative reconstruction algorithm for high-resolution 3D imaging.\",\n \"abstract\": \"Tomography has made a radical impact on diverse fields ranging from the study of 3D atomic arrangements in matter to the study of human health in medicine. Despite its very diverse applications, the core of tomography remains the same, that is, a mathematical method must be implemented to reconstruct the 3D structure of an object from a number of 2D projections. Here, we present the mathematical implementation of a tomographic algorithm, termed GENeralized Fourier Iterative REconstruction (GENFIRE), for high-resolution 3D reconstruction from a limited number of 2D projections. GENFIRE first assembles a 3D Fourier grid with oversampling and then iterates between real and reciprocal space to search for a global solution that is concurrently consistent with the measured data and general physical constraints. The algorithm requires minimal human intervention and also incorporates angular refinement to reduce the tilt angle error. We demonstrate that GENFIRE can produce superior results relative to several other popular tomographic reconstruction techniques through numerical simulations and by experimentally reconstructing the 3D structure of a porous material and a frozen-hydrated marine cyanobacterium. Equipped with a graphical user interface, GENFIRE is freely available from our website and is expected to find broad applications across different disciplines.\",\n \"corpus_id\": 19700086,\n \"score\": 2\n },\n {\n \"doc_id\": \"19131666\",\n \"title\": \"Fast 3D iterative image reconstruction for SPECT with rotating slat collimators.\",\n \"abstract\": \"As an alternative to the use of traditional parallel hole collimators, SPECT imaging can be performed using rotating slat collimators. While maintaining the spatial resolution, a gain in image quality could be expected from the higher photon collection efficiency of this type of collimator. However, the use of iterative methods to do fully three-dimensional (3D) reconstruction is computationally much more expensive and furthermore involves slow convergence compared to a classical SPECT reconstruction. It has been proposed to do 3D reconstruction by splitting the system matrix into two separate matrices, forcing the reconstruction to first estimate the sinograms from the rotating slat SPECT data before estimating the image. While alleviating the computational load by one order of magnitude, this split matrix approach would result in fast computation of the projections in an iterative algorithm, but does not solve the problem of slow convergence. There is thus a need for an algorithm which speeds up convergence while maintaining image quality for rotating slat collimated SPECT cameras. Therefore, we developed a reconstruction algorithm based on the split matrix approach which allows both a fast calculation of the forward and backward projection and a fast convergence. In this work, an algorithm of the maximum likelihood expectation maximization (MLEM) type, obtained from a split system matrix MLEM reconstruction, is proposed as a reconstruction method for rotating slat collimated SPECT data. Here, we compare this new algorithm to the conventional split system matrix MLEM method and to a gold standard fully 3D MLEM reconstruction algorithm on the basis of computational load, convergence and contrast-to-noise. Furthermore, ordered subsets expectation maximization (OSEM) implementations of these three algorithms are compared. Calculation of computational load and convergence for the different algorithms shows a speedup for the new method of 38 and 426 compared to the split matrix MLEM approach and the fully 3D MLEM respectively and a speedup of 16 and 21 compared to the split matrix OSEM and the fully 3D OSEM respectively. A contrast-to-noise study based on simulated data shows that our new approach has comparable accuracy as the fully 3D reconstruction method. The algorithm developed in this study allows iterative image reconstruction of rotating slat collimated SPECT data with equal image quality in a comparable amount of computation time as a classical SPECT reconstruction.\",\n \"corpus_id\": 41250680,\n \"score\": 1\n },\n {\n \"doc_id\": \"19792279\",\n \"title\": \"Reconstruction algorithm for single-particle diffraction imaging experiments.\",\n \"abstract\": \"We introduce the EMC algorithm for reconstructing a particle's three-dimensional (3D) diffraction intensity from very many photon shot-noise limited two-dimensional measurements, when the particle orientation in each measurement is unknown. The algorithm combines a maximization step (M) of the intensity's likelihood function, with expansion (E) and compression (C) steps that map the 3D intensity model to a redundant tomographic representation and back again. After a few iterations of the EMC update rule, the reconstructed intensity is given to the difference-map algorithm for reconstruction of the particle contrast. We demonstrate reconstructions with simulated data and investigate the effects of particle complexity, number of measurements, and the number of photons per measurement. The relatively transparent scaling behavior of our algorithm provides an estimate of the data processing resources required for future single-particle imaging experiments.\",\n \"corpus_id\": 8132982,\n \"score\": 1\n },\n {\n \"doc_id\": \"21361216\",\n \"title\": \"Reconstruction of brachytherapy seed positions and orientations from cone-beam CT x-ray projections via a novel iterative forward projection matching method.\",\n \"abstract\": \"PURPOSE: To generalize and experimentally validate a novel algorithm for reconstructing the 3D pose (position and orientation) of implanted brachytherapy seeds from a set of a few measured 2D cone-beam CT (CBCT) x-ray projections. METHODS: The iterative forward projection matching (IFPM) algorithm was generalized to reconstruct the 3D pose, as well as the centroid, of brachytherapy seeds from three to ten measured 2D projections. The gIFPM algorithm finds the set of seed poses that minimizes the sum-of-squared-difference of the pixel-by-pixel intensities between computed and measured autosegmented radiographic projections of the implant. Numerical simulations of clinically realistic brachytherapy seed configurations were performed to demonstrate the proof of principle. An in-house machined brachytherapy phantom, which supports precise specification of seed position and orientation at known values for simulated implant geometries, was used to experimentally validate this algorithm. The phantom was scanned on an ACUITY CBCT digital simulator over a full 660 sinogram projections. Three to ten x-ray images were selected from the full set of CBCT sinogram projections and postprocessed to create binary seed-only images. RESULTS: In the numerical simulations, seed reconstruction position and orientation errors were approximately 0.6 mm and 5 degrees, respectively. The physical phantom measurements demonstrated an absolute positional accuracy of (0.78 +/- 0.57) mm or less. The theta and phi angle errors were found to be (5.7 +/- 4.9) degrees and (6.0 +/- 4.1) degrees, respectively, or less when using three projections; with six projections, results were slightly better. The mean registration error was better than 1 mm/6 degrees compared to the measured seed projections. Each test trial converged in 10-20 iterations with computation time of 12-18 min/iteration on a 1 GHz processor. CONCLUSIONS: This work describes a novel, accurate, and completely automatic method for reconstructing seed orientations, as well as centroids, from a small number of radiographic projections, in support of intraoperative planning and adaptive replanning. Unlike standard back-projection methods, gIFPM avoids the need to match corresponding seed images on the projections. This algorithm also successfully reconstructs overlapping clustered and highly migrated seeds in the implant. The accuracy of better than 1 mm and 6 degrees demonstrates that gIFPM has the potential to support 2D Task Group 43 calculations in clinical practice.\",\n \"corpus_id\": 21908970,\n \"score\": 1\n },\n {\n \"doc_id\": \"21490573\",\n \"title\": \"Single particle electron microscopy reconstruction of the exosome complex using the random conical tilt method.\",\n \"abstract\": \"Single particle electron microscopy (EM) reconstruction has recently become a popular tool to get the three-dimensional (3D) structure of large macromolecular complexes. Compared to X-ray crystallography, it has some unique advantages. First, single particle EM reconstruction does not need to crystallize the protein sample, which is the bottleneck in X-ray crystallography, especially for large macromolecular complexes. Secondly, it does not need large amounts of protein samples. Compared with milligrams of proteins necessary for crystallization, single particle EM reconstruction only needs several micro-liters of protein solution at nano-molar concentrations, using the negative staining EM method. However, despite a few macromolecular assemblies with high symmetry, single particle EM is limited at relatively low resolution (lower than 1 nm resolution) for many specimens especially those without symmetry. This technique is also limited by the size of the molecules under study, i.e. 100 kDa for negatively stained specimens and 300 kDa for frozen-hydrated specimens in general. For a new sample of unknown structure, we generally use a heavy metal solution to embed the molecules by negative staining. The specimen is then examined in a transmission electron microscope to take two-dimensional (2D) micrographs of the molecules. Ideally, the protein molecules have a homogeneous 3D structure but exhibit different orientations in the micrographs. These micrographs are digitized and processed in computers as \\\"single particles\\\". Using two-dimensional alignment and classification techniques, homogenous molecules in the same views are clustered into classes. Their averages enhance the signal of the molecule's 2D shapes. After we assign the particles with the proper relative orientation (Euler angles), we will be able to reconstruct the 2D particle images into a 3D virtual volume. In single particle 3D reconstruction, an essential step is to correctly assign the proper orientation of each single particle. There are several methods to assign the view for each particle, including the angular reconstitution(1) and random conical tilt (RCT) method(2). In this protocol, we describe our practice in getting the 3D reconstruction of yeast exosome complex using negative staining EM and RCT. It should be noted that our protocol of electron microscopy and image processing follows the basic principle of RCT but is not the only way to perform the method. We first describe how to embed the protein sample into a layer of Uranyl-Formate with a thickness comparable to the protein size, using a holey carbon grid covered with a layer of continuous thin carbon film. Then the specimen is inserted into a transmission electron microscope to collect untilted (0-degree) and tilted (55-degree) pairs of micrographs that will be used later for processing and obtaining an initial 3D model of the yeast exosome. To this end, we perform RCT and then refine the initial 3D model by using the projection matching refinement method(3).\",\n \"corpus_id\": 45189809,\n \"score\": 1\n },\n {\n \"doc_id\": \"21860371\",\n \"title\": \"Structure of HIV-1 capsid assemblies by cryo-electron microscopy and iterative helical real-space reconstruction.\",\n \"abstract\": \"Cryo-electron microscopy (cryo-EM), combined with image processing, is an increasingly powerful tool for structure determination of macromolecular protein complexes and assemblies. In fact, single particle electron microscopy and two-dimensional (2D) electron crystallography have become relatively routine methodologies and a large number of structures have been solved using these methods. At the same time, image processing and three-dimensional (3D) reconstruction of helical objects has rapidly developed, especially, the iterative helical real-space reconstruction (IHRSR) method, which uses single particle analysis tools in conjunction with helical symmetry. Many biological entities function in filamentous or helical forms, including actin filaments, microtubules, amyloid fibers, tobacco mosaic viruses, and bacteria flagella, and, because a 3D density map of a helical entity can be attained from a single projection image, compared to the many images required for 3D reconstruction of a non-helical object, with the IHRSR method, structural analysis of such flexible and disordered helical assemblies is now attainable. In this video article, we provide detailed protocols for obtaining a 3D density map of a helical protein assembly (HIV-1 capsid is our example), including protocols for cryo-EM specimen preparation, low dose data collection by cryo-EM, indexing of helical diffraction patterns, and image processing and 3D reconstruction using IHRSR. Compared to other techniques, cryo-EM offers optimal specimen preservation under near native conditions. Samples are embedded in a thin layer of vitreous ice, by rapid freezing, and imaged in electron microscopes at liquid nitrogen temperature, under low dose conditions to minimize the radiation damage. Sample images are obtained under near native conditions at the expense of low signal and low contrast in the recorded micrographs. Fortunately, the process of helical reconstruction has largely been automated, with the exception of indexing the helical diffraction pattern. Here, we describe an approach to index helical structure and determine helical symmetries (helical parameters) from digitized micrographs, an essential step for 3D helical reconstruction. Briefly, we obtain an initial 3D density map by applying the IHRSR method. This initial map is then iteratively refined by introducing constraints for the alignment parameters of each segment, thus controlling their degrees of freedom. Further improvement is achieved by correcting for the contrast transfer function (CTF) of the electron microscope (amplitude and phase correction) and by optimizing the helical symmetry of the assembly.\",\n \"corpus_id\": 8398013,\n \"score\": 1\n },\n {\n \"doc_id\": \"22565698\",\n \"title\": \"Investigation of discrete imaging models and iterative image reconstruction in differential X-ray phase-contrast tomography.\",\n \"abstract\": \"Differential X-ray phase-contrast tomography (DPCT) refers to a class of promising methods for reconstructing the X-ray refractive index distribution of materials that present weak X-ray absorption contrast. The tomographic projection data in DPCT, from which an estimate of the refractive index distribution is reconstructed, correspond to one-dimensional (1D) derivatives of the two-dimensional (2D) Radon transform of the refractive index distribution. There is an important need for the development of iterative image reconstruction methods for DPCT that can yield useful images from few-view projection data, thereby mitigating the long data-acquisition times and large radiation doses associated with use of analytic reconstruction methods. In this work, we analyze the numerical and statistical properties of two classes of discrete imaging models that form the basis for iterative image reconstruction in DPCT. We also investigate the use of one of the models with a modern image reconstruction algorithm for performing few-view image reconstruction of a tissue specimen.\",\n \"corpus_id\": 110280,\n \"score\": 1\n },\n {\n \"doc_id\": \"22897395\",\n \"title\": \"Recent advances in the application of electron tomography to materials chemistry.\",\n \"abstract\": \"Nowadays, tomography plays a central role in pureand applied science, in medicine, and in many branches of engineering and technology. It entails reconstructing the three-dimensional (3D) structure of an object from a tilt series of two-dimensional (2D) images. Its origin goes back to 1917, when Radon showed mathematically how a series of 2D projection images could be converted to the 3D structural one. Tomographic X-ray and positron scanning for 3D medical imaging, with a resolution of ∼1 mm, is now ubiquitous in major hospitals. Electron tomography, a relatively new chemical tool, with a resolution of ∼1 nm, has been recently adopted by materials chemists as an invaluable aid for the 3D study of the morphologies, spatially-discriminating chemical compositions, and defect properties of nanostructured materials. In this Account, we review the advances that have been made in facilitating the recording of the required series of 2D electron microscopic images and the subsequent process of 3D reconstruction of specimens that are vulnerable, to a greater or lesser degree, to electron beam damage. We describe how high-fidelity 3D tomograms may be obtained from relatively few 2D images by incorporating prior structural knowledge into the reconstruction process. In particular, we highlight the vital role of compressed sensing, a recently developed procedure well-known to information theorists that exploits ideas of image compression and \\\"sparsity\\\" (that the important image information can be captured in a reduced data set). We also touch upon another promising approach, \\\"discrete\\\" tomography, which builds into the reconstruction process a prior assumption that the object can be described in discrete terms, such as the number of constituent materials and their expected densities. Other advances made recently that we outline, such as the availability of aberration-corrected electron microscopes, electron wavelength monochromators, and sophisticated specimen goniometers, have all contributed significantly to the further development of quantitative 3D studies of nanostructured materials, including nanoparticle-heterogeneous catalysts, fuel-cell components, and drug-delivery systems, as well as photovoltaic and plasmonic devices, and are likely to enhance our knowledge of many other facets of materials chemistry, such as organic-inorganic composites, solar-energy devices, bionanotechnology, biomineralization, and energy-storage systems composed of high-permittivity metal oxides.\",\n \"corpus_id\": 5409733,\n \"score\": 1\n },\n {\n \"doc_id\": \"24132427\",\n \"title\": \"Reconstructing plant cells in 3D by serial section electron tomography.\",\n \"abstract\": \"In micrographs acquired with a transmission electron microscope, 3-dimensional (3D) objects are superimposed onto a 2D screen. This reduction in dimension necessarily leads to a degradation of image resolution. To overcome this problem, 3D microscopy techniques, such as tomography and single particle analysis, have been developed. Tomography has been used to visualize cells in 3D, and single particle analysis has been used to investigate macromolecules and viral particles. In this chapter we will describe how we have collected tilting series micrographs from plant cells and how we have reconstructed the cellular volumes using dual axis electron tomography.\",\n \"corpus_id\": 45191325,\n \"score\": 1\n },\n {\n \"doc_id\": \"24161732\",\n \"title\": \"Optimod--an automated approach for constructing and optimizing initial models for single-particle electron microscopy.\",\n \"abstract\": \"Single-particle cryo-electron microscopy is now well established as a technique for the structural characterization of large macromolecules and macromolecular complexes. The raw data is very noisy and consists of two-dimensional projections, from which the 3D biological object must be reconstructed. The 3D object depends upon knowledge of proper angular orientations assigned to the 2D projection images. Numerous algorithms have been developed for determining relative angular orientations between 2D images, but the transition from 2D to 3D remains challenging and can result in erroneous and conflicting results. Here we describe a general, automated procedure, called OptiMod, for reconstructing and optimizing 3D models using common-lines methodologies. OptiMod approximates orientation angles and reconstructs independent maps from 2D class averages. It then iterates the procedure, while considering each map as a raw solution that needs to be compared with other possible outcomes. We incorporate procedures for 3D alignment, clustering, and refinement to optimize each map, as well as standard scoring metrics to facilitate the selection of the optimal model. We also show that small angle tilt-pair data can be included as one of the scoring metrics to improve the selection of the optimal initial model, and also to provide a validation check. The overall approach is demonstrated using two experimental cryo-EM data sets--the 80S ribosome that represents a relatively straightforward case for ab initio reconstruction, and the Tf-TfR complex that represents a challenging case in that it has previously been shown to provide multiple equally plausible solutions to the initial model problem.\",\n \"corpus_id\": 36681249,\n \"score\": 1\n },\n {\n \"doc_id\": \"24275806\",\n \"title\": \"Quantitative analysis of emphysema and airway measurements according to iterative reconstruction algorithms: comparison of filtered back projection, adaptive statistical iterative reconstruction and model-based iterative reconstruction.\",\n \"abstract\": \"OBJECTIVES: To evaluate filtered back projection (FBP) and two iterative reconstruction (IR) algorithms and their effects on the quantitative analysis of lung parenchyma and airway measurements on computed tomography (CT) images. METHODS: Low-dose chest CT obtained in 281 adult patients were reconstructed using three algorithms: FBP, adaptive statistical IR (ASIR) and model-based IR (MBIR). Measurements of each dataset were compared: total lung volume, emphysema index (EI), airway measurements of the lumen and wall area as well as average wall thickness. Accuracy of airway measurements of each algorithm was also evaluated using an airway phantom. RESULTS: EI using a threshold of -950 HU was significantly different among the three algorithms in decreasing order of FBP (2.30 %), ASIR (1.49 %) and MBIR (1.20 %) (P < 0.01). Wall thickness was also significantly different among the three algorithms with FBP (2.09 mm) demonstrating thicker walls than ASIR (2.00 mm) and MBIR (1.88 mm) (P < 0.01). Airway phantom analysis revealed that MBIR showed the most accurate value for airway measurements. CONCLUSION: The three algorithms presented different EIs and wall thicknesses, decreasing in the order of FBP, ASIR and MBIR. Thus, care should be taken in selecting the appropriate IR algorithm on quantitative analysis of the lung. KEY POINTS: • Computed tomography is increasingly used to provide objective measurements of intra-thoracic structures. • Iterative reconstruction algorithms can affect quantitative measurements of lung and airways. • Care should be taken in selecting reconstruction algorithms in longitudinal analysis. • Model-based iterative reconstruction seems to provide the most accurate airway measurements.\",\n \"corpus_id\": 22157737,\n \"score\": 1\n },\n {\n \"doc_id\": \"25359850\",\n \"title\": \"3D structure determination of protein using TEM single particle analysis.\",\n \"abstract\": \"Proteins play important roles in cell functions such as enzymes, cell trafficking, neurotransmission, muscle contraction and hormone secretion. However, some proteins are very difficult to be crystallized and their structures are undetermined. Several techniques have been developed to elucidate the structure of macromolecules; X-ray or electron crystallography, nuclear magnetic resonance spectroscopy, and high-resolution electron microscopy. Among them, electron microscopy based single particle reconstruction (SPA) technique is a computer-aided structure determination method. This method reconstructs the 3D structure from projection images of dispersed protein. A large number of two-dimensional particle images are picked up from EM films, aligned and classified to generate 2D averages, and used to reconstruct the 3D structure by assigning the Euler angle of each 2D average. Due to the necessity of elaborate collaboration between the classical biology and the innovative information technology including parallel computing, scientists needed to break unseen barriers to get a start of this analysis. However, recent progresses in electron microscopes, mathematical algorithms, and computational abilities greatly reduced the height of barriers and expanded targets that are considered to be primarily addressable using single particle analysis. Membrane proteins are one of these targets to which the single particle analysis is successfully applied for the understanding of their 3D structures. For this purpose, we have developed various SPA methods [1-5] and applied them to different proteins [6-8].Here, we introduce reconstructed proteins, and discuss the availability of this technique. The intramembrane-cleaving proteases (I-CLiPs) that sever the transmembrane domains of their substrates have been identified in a range of organisms and play a variety of roles in biological conditions. I-CLiPs have been classified into three groups: serine-, aspartyl- and metalloprotease-type. Signal peptide peptidase (SPP) is an atypical aspartic protease that hydrolyzes peptide bonds within the transmembrane domain of substrates and is implicated in several biological and pathological functions. The structure of human SPP was determined by SPA at a resolution of 22 Å [8]. SPP forms a slender, bullet-shaped homotetramer with dimensions of 85 x 85 x 130 Å. The SPP complex has four concaves on the rhombus-like sides, connected to a large chamber inside the molecule. For the tetrameric assembly, the N-terminal region of SPP was found to be sufficient. Moreover, when N-terminal region was overexpressed, the formation of the endogenous SPP tetramer was inhibited, which suppressed the proteolytic activity within cells. From these data, the N-terminal region is considered to work as the structural scaffold. Transmembrane (TM) translocation of newly synthesized secretion proteins and membrane proteins are carried out by a Sec translocon protein complex. The polypeptide-conducting pore is formed by the SecYEG-SecA complex in bacteria, and the membrane protein SecDF is necessary for the efficient transport of proteins. However the molecular mechanism how SecDF realized efficient transport is not clear. A previous X-ray structural study of the whole protein and subdomain suggest that SecDF has at least two conformational variants, which could reflect molecular dynamics of this protein. To confirm this hypothesis, we analyzed the 3D structure of SecDF using dark field STEM electron tomography and single particle reconstruction. We determined two different whole SecDF protein structures which well explains the X-ray data. From these data, we would like to propose the possible molecular mechanism of SecDF during polypeptide translocation.\",\n \"corpus_id\": 29044380,\n \"score\": 1\n },\n {\n \"doc_id\": \"26258639\",\n \"title\": \"A software tool for tomographic axial superresolution in STED microscopy.\",\n \"abstract\": \"A method for generating three-dimensional tomograms from multiple three-dimensional axial projections in STimulated Emission Depletion (STED) superresolution microscopy is introduced. Our STED< method, based on the use of a micromirror placed on top of a standard microscopic sample, is used to record a three-dimensional projection at an oblique angle in relation to the main optical axis. Combining the STED< projection with the regular STED image into a single view by tomographic reconstruction, is shown to result in a tomogram with three-to-four-fold improved apparent axial resolution. Registration of the different projections is based on the use of a mutual-information histogram similarity metric. Fusion of the projections into a single view is based on Richardson-Lucy iterative deconvolution algorithm, modified to work with multiple projections. Our tomographic reconstruction method is demonstrated to work with real biological STED superresolution images, including a data set with a limited signal-to-noise ratio (SNR); the reconstruction software (SuperTomo) and its source code will be released under BSD open-source license.\",\n \"corpus_id\": 44396491,\n \"score\": 1\n },\n {\n \"doc_id\": \"26393699\",\n \"title\": \"Tomographic reconstruction in soft x-ray microscopy using focus-stack back-projection.\",\n \"abstract\": \"Tomographic reconstruction in soft x-ray microscopy is a powerful technique for obtaining high-resolution 3D images of biological samples. However, the depth of focus of such zone-plate-based microscopes is typically shorter than the thickness of many relevant biological objects, challenging the validity of the projection assumption used in conventional reconstruction algorithms. In order to make full use of the soft x-ray microscopes' high resolution, the tomographic reconstruction needs to take the depth of focus into account. Here we present a method to achieve high resolution in the full sample when the depth of focus is short compared to the sample thickness. The method relies on the back-projection of focus-stacked image data from x-ray microscopy. We demonstrate the method on theoretical and experimental data.\",\n \"corpus_id\": 2023724,\n \"score\": 1\n },\n {\n \"doc_id\": \"27646194\",\n \"title\": \"Biological application of Compressed Sensing Tomography in the Scanning Electron Microscope.\",\n \"abstract\": \"The three-dimensional tomographic reconstruction of a biological sample, namely collagen fibrils in human dermal tissue, was obtained from a set of projection-images acquired in the Scanning Electron Microscope. A tailored strategy for the transmission imaging mode was implemented in the microscope and proved effective in acquiring the projections needed for the tomographic reconstruction. Suitable projection alignment and Compressed Sensing formulation were used to overcome the limitations arising from the experimental acquisition strategy and to improve the reconstruction of the sample. The undetermined problem of structure reconstruction from a set of projections, limited in number and angular range, was indeed supported by exploiting the sparsity of the object projected in the electron microscopy images. In particular, the proposed system was able to preserve the reconstruction accuracy even in presence of a significant reduction of experimental projections.\",\n \"corpus_id\": 15380257,\n \"score\": 1\n },\n {\n \"doc_id\": \"28463289\",\n \"title\": \"Comparative study of fully three-dimensional reconstruction algorithms for lens-free microscopy.\",\n \"abstract\": \"We propose a three-dimensional (3D) imaging platform based on lens-free microscopy to perform multiangle acquisitions on 3D cell cultures embedded in extracellular matrices. Lens-free microscopy acquisitions present some inherent issues such as the lack of phase information on the sensor plane and a limited angular coverage. We developed and compared three different algorithms based on the Fourier diffraction theorem to obtain fully 3D reconstructions. These algorithms present an increasing complexity associated with a better reconstruction quality. Two of them are based on a regularized inverse problem approach. To compare the reconstruction methods in terms of artefact reduction, signal-to-noise ratio, and computation time, we tested them on two experimental datasets: an endothelial cell culture and a prostate cell culture grown in a 3D extracellular matrix with large reconstructed volumes up to ∼5 mm<sup>3</sup> with a resolution sufficient to resolve isolated single cells. The lens-free reconstructions compare well with standard microscopy.\",\n \"corpus_id\": 46771637,\n \"score\": 1\n },\n {\n \"doc_id\": \"28689080\",\n \"title\": \"3D reconstruction of the magnetic vector potential using model based iterative reconstruction.\",\n \"abstract\": \"Lorentz transmission electron microscopy (TEM) observations of magnetic nanoparticles contain information on the magnetic and electrostatic potentials. Vector field electron tomography (VFET) can be used to reconstruct electromagnetic potentials of the nanoparticles from their corresponding LTEM images. The VFET approach is based on the conventional filtered back projection approach to tomographic reconstructions and the availability of an incomplete set of measurements due to experimental limitations means that the reconstructed vector fields exhibit significant artifacts. In this paper, we outline a model-based iterative reconstruction (MBIR) algorithm to reconstruct the magnetic vector potential of magnetic nanoparticles. We combine a forward model for image formation in TEM experiments with a prior model to formulate the tomographic problem as a maximum a-posteriori probability estimation problem (MAP). The MAP cost function is minimized iteratively to determine the vector potential. A comparative reconstruction study of simulated as well as experimental data sets show that the MBIR approach yields quantifiably better reconstructions than the VFET approach.\",\n \"corpus_id\": 30968793,\n \"score\": 1\n },\n {\n \"doc_id\": \"28893337\",\n \"title\": \"Optimization of Three-Dimensional (3D) Chemical Imaging by Soft X-Ray Spectro-Tomography Using a Compressed Sensing Algorithm.\",\n \"abstract\": \"Soft X-ray spectro-tomography provides three-dimensional (3D) chemical mapping based on natural X-ray absorption properties. Since radiation damage is intrinsic to X-ray absorption, it is important to find ways to maximize signal within a given dose. For tomography, using the smallest number of tilt series images that gives a faithful reconstruction is one such method. Compressed sensing (CS) methods have relatively recently been applied to tomographic reconstruction algorithms, providing faithful 3D reconstructions with a much smaller number of projection images than when conventional reconstruction methods are used. Here, CS is applied in the context of scanning transmission X-ray microscopy tomography. Reconstructions by weighted back-projection, the simultaneous iterative reconstruction technique, and CS are compared. The effects of varying tilt angle increment and angular range for the tomographic reconstructions are examined. Optimization of the regularization parameter in the CS reconstruction is explored and discussed. The comparisons show that CS can provide improved reconstruction fidelity relative to weighted back-projection and simultaneous iterative reconstruction techniques, with increasingly pronounced advantages as the angular sampling is reduced. In particular, missing wedge artifacts are significantly reduced and there is enhanced recovery of sharp edges. Examples of using CS for low-dose scanning transmission X-ray microscopy spectroscopic tomography are presented.\",\n \"corpus_id\": 1969431,\n \"score\": 1\n },\n {\n \"doc_id\": \"19001695\",\n \"title\": \"Non-iterative conductivity reconstruction algorithm using projected current density in MREIT.\",\n \"abstract\": \"Magnetic resonance electrical impedance tomography (MREIT) is to visualize the current density and the conductivity distribution in an electrical object Omega using the measured magnetic flux data by an MRI scanner. MREIT uses only one component B(z) of the magnetic flux density B = (B(x), B(y), B(z)) generated by an injected electrical current into the object. In this paper, we propose a fast and direct non-iterative algorithm to reconstruct the internal conductivity distribution in Omega with the measured B(z) data. To develop the algorithm, we investigate the relation between the projected current density J(P), a uniquely determined component of J by the map from current J to measured B(z) data and the isotropic conductivity. Three-dimensional numerical simulations and phantom experiments are studied to show the feasibility of the proposed method by comparing with those using the conventional iterative harmonic B(z) algorithm.\",\n \"corpus_id\": 33943794,\n \"score\": 0\n },\n {\n \"doc_id\": \"20302885\",\n \"title\": \"Single particle reconstruction of membrane proteins: a tool for understanding the 3D structure of disease-related macromolecules.\",\n \"abstract\": \"Membrane proteins play important roles in cell functions such as neurotransmission, muscle contraction, and hormone secretion, but their structures are mostly undetermined. Several techniques have been developed to elucidate the structure of macromolecules; X-ray or electron crystallography, nuclear magnetic resonance spectroscopy, and high-resolution electron microscopy. Electron microscopy-based single particle reconstruction, a computer-aided structure determination method, reconstructs a three-dimensional (3D) structure from projections of monodispersed protein. A large number of particle images are picked up from EM films, aligned and classified to generate two-dimensional (2D) averages, and, using the Euler angle of each 2D average, reconstructed into a 3D structure. This method is challenging due to the necessity for close collaboration between classical biochemistry and innovative information technology, including parallel computing. However, recent progress in electron microscopy, mathematical algorithms, and computational ability has greatly increased the subjects that are considered to be primarily addressable using single particle reconstruction. Membrane proteins are one of these targets to which the single particle reconstruction is successfully applied for understanding of their structures. In this paper, we will introduce recently reconstructed channel-related proteins and discuss the applicability of this technique in understanding molecular structures and their roles in pathology.\",\n \"corpus_id\": 11433876,\n \"score\": 0\n },\n {\n \"doc_id\": \"20378810\",\n \"title\": \"Four-dimensional electron microscopy.\",\n \"abstract\": \"The discovery of the electron over a century ago and the realization of its dual character have given birth to one of the two most powerful imaging instruments: the electron microscope. The electron microscope's ability to resolve three-dimensional (3D) structures on the atomic scale is continuing to affect different fields, including materials science and biology. In this Review, we highlight recent developments and inventions made by introducing the fourth dimension of time in electron microscopy. Today, ultrafast electron microscopy (4D UEM) enables a resolution that is 10 orders of magnitude better than that of conventional microscopes, which are limited by the video-camera rate of recording. After presenting the central concept involved, that of single-electron stroboscopic imaging, we discuss prototypical applications, which include the visualization of complex structures when unfolding on different length and time scales. The developed UEM variant techniques are several, and here we illucidate convergent-beam and near-field imaging, as well as tomography and scanning-pulse microscopy. We conclude with current explorations in imaging of nanomaterials and biostructures and an outlook on possible future directions in space-time, 4D electron microscopy.\",\n \"corpus_id\": 5449372,\n \"score\": 0\n },\n {\n \"doc_id\": \"21089788\",\n \"title\": \"Iterative reconstruction of Fourier-rebinned PET data using sinogram blurring function estimated from point source scans.\",\n \"abstract\": \"PURPOSE: The accuracy of the system model that governs the transformation from the image space to the projection space in positron emission tomography (PET) greatly affects the quality of reconstructed images. For efficient computation in iterative reconstructions, the system model in PET can be factored into a product of geometric projection and sinogram blurring function. To further speed up reconstruction, fully 3D PET data can be rebinned into a stack of 2D sinograms and then be reconstructed using 2D iterative algorithms. The purpose of this work is to develop a method to estimate the sinogram blurring function to be used in reconstruction of Fourier-rebinned data. METHODS: In a previous work, the authors developed an approach to estimating the sinogram blurring function of nonrebinned PET data from experimental scans of point sources. In this study, the authors extend this method to the estimation of sinogram blurring function for Fourier-rebinned PET data. A point source was scanned at a set of sampled positions in the microPET II scanner. The sinogram blurring function is considered to be separable between the transaxial and axial directions. A radially and angularly variant 2D blurring function is estimated from Fourier-rebinned point source scans to model the transaxial blurring with consideration of the detector block structure of the scanner; a space-variant 1D blurring kernel along the axial direction is estimated separately to model the correlation between neighboring planes due to detector intrinsic blurring and Fourier rebinning. The estimated sinogram blurring function is incorporated in a 2D maximum a posteriori (MAP) reconstruction algorithm for image reconstruction. RESULTS: Physical phantom experiments were performed on the microPET II scanner to validate the proposed method. The authors compared the proposed method to 2D MAP reconstruction without sinogram blurring model and 2D MAP reconstruction with a Monte Carlo based blurring model. The results show that the proposed method produces images with improved contrast and spatial resolution. The reconstruction time is unaffected by the new method since the blurring component takes a relatively negligible part of the overall reconstruction time. CONCLUSIONS: The proposed method can estimate sinogram blurring matrix for Fourier-rebinned PET data and can be used to improve contrast and spatial resolution of reconstructed images. The method can be applied to other human and animal scanners.\",\n \"corpus_id\": 20398743,\n \"score\": 0\n },\n {\n \"doc_id\": \"21752659\",\n \"title\": \"The use of trehalose in the preparation of specimens for molecular electron microscopy.\",\n \"abstract\": \"Biological specimens have to be prepared for imaging in the electron microscope in a way that preserves their native structure. Two-dimensional (2D) protein crystals to be analyzed by electron crystallography are best preserved by sugar embedding. One of the sugars often used to embed 2D crystals is trehalose, a disaccharide used by many organisms for protection against stress conditions. Sugars such as trehalose can also be added to negative staining solutions used to prepare proteins and macromolecular complexes for structural studies by single-particle electron microscopy (EM). In this review, we describe trehalose and its characteristics that make it so well suited for preparation of EM specimens and we review specimen preparation methods with a focus on the use of trehalose.\",\n \"corpus_id\": 11326090,\n \"score\": 0\n },\n {\n \"doc_id\": \"23026379\",\n \"title\": \"Electron tomography of HEK293T cells using scanning electron microscope-based scanning transmission electron microscopy.\",\n \"abstract\": \"Based on a scanning electron microscope operated at 30 kV with a homemade specimen holder and a multiangle solid-state detector behind the sample, low-kV scanning transmission electron microscopy (STEM) is presented with subsequent electron tomography for three-dimensional (3D) volume structure. Because of the low acceleration voltage, the stronger electron-atom scattering leads to a stronger contrast in the resulting image than standard TEM, especially for light elements. Furthermore, the low-kV STEM yields less radiation damage to the specimen, hence the structure can be preserved. In this work, two-dimensional STEM images of a 1-μm-thick cell section with projection angles between ±50° were collected, and the 3D volume structure was reconstructed using the simultaneous iterative reconstructive technique algorithm with the TomoJ plugin for ImageJ, which are both public domain software. Furthermore, the cross-sectional structure was obtained with the Volume Viewer plugin in ImageJ. Although the tilting angle is constrained and limits the resulting structural resolution, slicing the reconstructed volume generated the depth profile of the thick specimen with sufficient resolution to examine cellular uptake of Au nanoparticles, and the final position of these nanoparticles inside the cell was imaged.\",\n \"corpus_id\": 41862161,\n \"score\": 0\n },\n {\n \"doc_id\": \"24357373\",\n \"title\": \"Biological applications of phase-contrast electron microscopy.\",\n \"abstract\": \"Here, I review the principles and applications of phase-contrast electron microscopy using phase plates. First, I develop the principle of phase contrast based on a minimal model of microscopy, introducing a double Fourier-transform process to mathematically formulate the image formation. Next, I explain four phase-contrast (PC) schemes, defocus PC, Zernike PC, Hilbert differential contrast, and schlieren optics, as image-filtering processes in the context of the minimal model, with particular emphases on the Zernike PC and corresponding Zernike phase plates. Finally, I review applications of Zernike PC cryo-electron microscopy to biological systems such as protein molecules, virus particles, and cells, including single-particle analysis to delineate three-dimensional (3D) structures of protein and virus particles and cryo-electron tomography to reconstruct 3D images of complex protein systems and cells.\",\n \"corpus_id\": 44908094,\n \"score\": 0\n },\n {\n \"doc_id\": \"25010640\",\n \"title\": \"Ultra-low peak voltage CT colonography: effect of iterative reconstruction algorithms on performance of radiologists who use anthropomorphic colonic phantoms.\",\n \"abstract\": \"PURPOSE: To analyze the effect of a decrease in computed tomographic (CT) colonographic voltage, from 100 and 120 kVp to 80 kVp and reconstructed with filtered back projection ( FBP filtered back projection ), on radiation dose, image noise, and diagnostic performance in anthropomorphic phantoms and to assess the effect of iterative reconstruction ( IR iterative reconstruction ) algorithms on radiologists' performance for 80-kVp CT colonography. MATERIALS AND METHODS: Seven colon phantoms with 68 simulated polyps (≥6 mm) were scanned at three peak voltage settings (80, 100, 120 kVp) and 10 mAs. Images were reconstructed by using FBP filtered back projection , hybrid statistic-based IR iterative reconstruction , and knowledge-based IR iterative reconstruction algorithms. Effective radiation dose, image noise, and per-polyp sensitivity were recorded and compared by two reviewers with Friedman test, repeated measures analysis of variance, and McNemar test. RESULTS: Median size-specific dose estimate and effective radiation dose of 80-kVp CT colonography was 0.231 mGy and 0.167 mSv, respectively, which was lower than with 100- and 120-kVp CT colonography, with significant difference between 80 and 120 kVp (P = .0005). Image noise (202.0 HU) at 80-kVp FBP filtered back projection CT colonography was significantly higher than at 100-kVp FBP filtered back projection (139.1 HU) and 120-kVp FBP filtered back projection (120.4 HU) (P < .0001). Per-polyp sensitivity (reviewer 1, 14.7% [10 of 68]; reviewer 2, 7.4% [five of 68]) at 80-kVp FBP filtered back projection was significantly lower than at 100-kVp FBP filtered back projection (reviewer 1, 57.4% [39 of 68]; reviewer 2, 39.7% [27 of 68]) and 120-kVp FBP filtered back projection (reviewer 1, 85.3% [58 of 68]; reviewer 2, 83.8% [57 of 68]) (P < .0001). With statistic-based IR iterative reconstruction , image noise at 80 kVp decreased significantly (52.8% [106.7 HU of 202.0 HU]) compared with that at 80-kVp FBP filtered back projection (P < .0001), but per-polyp sensitivity (reviewer 1, 79.4% [54 of 68]; reviewer 2, 66.2% [45 of 68]) at 80-kVp statistic-based IR iterative reconstruction remained significantly lower than at 100-kVp statistic-based IR iterative reconstruction (reviewer 1, 95.6% [65 of 68]; reviewer 2, 86.8% [59 of 68]) (P = .001) and 120-kVp statistic-based IR iterative reconstruction (reviewer 1, 98.5% [67 of 68]; reviewer 2, 89.7% [61 of 68]) (P < .001). For knowledge-based IR iterative reconstruction , per-polyp sensitivity at 80 kVp was improved to 98.5% (67 of 68) and 94.1% (64 of 68), not significantly different from that at 100 kVp (reviewer 1, 100% [68 of 68]; reviewer 2, 95.6% [65 of 68]) and 120 kVp (reviewer 1, 100% [68 of 68]; reviewer 2, 95.6% [65 of 68]) (P > .999). CONCLUSION: A decrease in tube voltage to 80 kVp caused reduction in radiation dose (0.166 mSv) with deterioration in image noise and per-polyp sensitivity. By using a knowledge-based IR iterative reconstruction algorithm, radiologists' performance of 80-kVp CT colonography was acceptable and on par with that at 100- or 120-kVp CT colonography.\",\n \"corpus_id\": 33987840,\n \"score\": 0\n },\n {\n \"doc_id\": \"25136491\",\n \"title\": \"High resolution three-dimensional photoacoutic tomography with CCD-camera based ultrasound detection.\",\n \"abstract\": \"A photoacoustic tomograph based on optical ultrasound detection is demonstrated, which is capable of high resolution real-time projection imaging and fast three-dimensional (3D) imaging. Snapshots of the pressure field outside the imaged object are taken at defined delay times after photoacoustic excitation by use of a charge coupled device (CCD) camera in combination with an optical phase contrast method. From the obtained wave patterns photoacoustic projection images are reconstructed using a back propagation Fourier domain reconstruction algorithm. Applying the inverse Radon transform to a set of projections recorded over a half rotation of the sample provides 3D photoacoustic tomography images in less than one minute with a resolution below 100 µm. The sensitivity of the device was experimentally determined to be 5.1 kPa over a projection length of 1 mm. In vivo images of the vasculature of a mouse demonstrate the potential of the developed method for biomedical applications.\",\n \"corpus_id\": 15037430,\n \"score\": 0\n },\n {\n \"doc_id\": \"25528453\",\n \"title\": \"Iterative reconstruction of magnetic induction using Lorentz transmission electron tomography.\",\n \"abstract\": \"Intense ongoing research on complex nanomagnetic structures requires a fundamental understanding of the 3D magnetization and the stray fields around the nano-objects. 3D visualization of such fields offers the best way to achieve this. Lorentz transmission electron microscopy provides a suitable combination of high resolution and ability to quantitatively visualize the magnetization vectors using phase retrieval methods. In this paper, we present a formalism to represent the magnetic phase shift of electrons as a Radon transform of the magnetic induction of the sample. Using this formalism, we then present the application of common tomographic methods particularly the iterative methods, to reconstruct the 3D components of the vector field. We present an analysis of the effect of missing wedge and the limited angular sampling as well as reconstruction of complex 3D magnetization in a nanowire using simulations.\",\n \"corpus_id\": 7367666,\n \"score\": 0\n },\n {\n \"doc_id\": \"26179326\",\n \"title\": \"Single-Particle Cryo-EM and 3D Reconstruction of Hybrid Nanoparticles with Electron-Dense Components.\",\n \"abstract\": \"Single-particle cryo-electron microscopy (cryo-EM), accompanied with 3D reconstruction, is a broadly applicable tool for the structural characterization of macromolecules and nanoparticles. Recently, the cryo-EM field has pushed the limits of this technique to higher resolutions and samples of smaller molecular mass, however, some samples still present hurdles to this technique. Hybrid particles with electron-dense components, which have been studied using single-particle cryo-EM yet with limited success in 3D reconstruction due to the interference caused by electron-dense elements, constitute one group of such challenging samples. To process such hybrid particles, a masking method is developed in this work to adaptively remove pixels arising from electron-dense portions in individual projection images while maintaining maximal biomass signals for subsequent 2D alignment, 3D reconstruction, and iterative refinements. As demonstrated by the success in 3D reconstruction of an octahedron DNA/gold hybrid particle, which has been previously published without a 3D reconstruction, the devised strategy that combines adaptive masking and standard single-particle 3D reconstruction approach has overcome the hurdle of electron-dense elements interference, and is generally applicable to cryo-EM structural characterization of most, if not all, hybrid nanomaterials with electron-dense components.\",\n \"corpus_id\": 206498175,\n \"score\": 0\n },\n {\n \"doc_id\": \"26697863\",\n \"title\": \"Computation in electron microscopy.\",\n \"abstract\": \"Some uses of the computer and computation in high-resolution transmission electron microscopy are reviewed. The theory of image calculation using Bloch wave and multislice methods with and without aberration correction is reviewed and some applications are discussed. The inverse problem of reconstructing the specimen structure from an experimentally measured electron microscope image is discussed. Some future directions of software development are given.\",\n \"corpus_id\": 10248349,\n \"score\": 0\n },\n {\n \"doc_id\": \"27339510\",\n \"title\": \"Cryo-electron microscopy and cryo-electron tomography of nanoparticles.\",\n \"abstract\": \"Cryo-transmission electron microscopy (cryo-TEM or cryo-EM) and cryo-electron tomography (cryo-ET) offer robust and powerful ways to visualize nanoparticles. These techniques involve imaging of the sample in a frozen-hydrated state, allowing visualization of nanoparticles essentially as they exist in solution. Cryo-TEM grid preparation can be performed with the sample in aqueous solvents or in various organic and ionic solvents. Two-dimensional (2D) cryo-TEM provides a direct way to visualize the polydispersity within a nanoparticle preparation. Fourier transforms of cryo-TEM images can confirm the structural periodicity within a sample. While measurement of specimen parameters can be performed with 2D TEM images, determination of a three-dimensional (3D) structure often facilitates more spatially accurate quantization. 3D structures can be determined in one of two ways. If the nanoparticle has a homogeneous structure, then 2D projection images of different particles can be averaged using a computational process referred to as single particle reconstruction. Alternatively, if the nanoparticle has a heterogeneous structure, then a structure can be generated by cryo-ET. This involves collecting a tilt-series of 2D projection images for a defined region of the grid, which can be used to generate a 3D tomogram. Occasionally it is advantageous to calculate both a single particle reconstruction, to reveal the regular portions of a nanoparticle structure, and a cryo-electron tomogram, to reveal the irregular features. A sampling of 2D cryo-TEM images and 3D structures are presented for protein based, DNA based, lipid based, and polymer based nanoparticles. WIREs Nanomed Nanobiotechnol 2017, 9:e1417. doi: 10.1002/wnan.1417 For further resources related to this article, please visit the WIREs website.\",\n \"corpus_id\": 25926091,\n \"score\": 0\n },\n {\n \"doc_id\": \"28416035\",\n \"title\": \"Measuring the Autocorrelation Function of Nanoscale Three-Dimensional Density Distribution in Individual Cells Using Scanning Transmission Electron Microscopy, Atomic Force Microscopy, and a New Deconvolution Algorithm.\",\n \"abstract\": \"Essentially all biological processes are highly dependent on the nanoscale architecture of the cellular components where these processes take place. Statistical measures, such as the autocorrelation function (ACF) of the three-dimensional (3D) mass-density distribution, are widely used to characterize cellular nanostructure. However, conventional methods of reconstruction of the deterministic 3D mass-density distribution, from which these statistical measures can be calculated, have been inadequate for thick biological structures, such as whole cells, due to the conflict between the need for nanoscale resolution and its inverse relationship with thickness after conventional tomographic reconstruction. To tackle the problem, we have developed a robust method to calculate the ACF of the 3D mass-density distribution without tomography. Assuming the biological mass distribution is isotropic, our method allows for accurate statistical characterization of the 3D mass-density distribution by ACF with two data sets: a single projection image by scanning transmission electron microscopy and a thickness map by atomic force microscopy. Here we present validation of the ACF reconstruction algorithm, as well as its application to calculate the statistics of the 3D distribution of mass-density in a region containing the nucleus of an entire mammalian cell. This method may provide important insights into architectural changes that accompany cellular processes.\",\n \"corpus_id\": 27830361,\n \"score\": 0\n }\n]","isConversational":false}}},{"rowIdx":65,"cells":{"query":{"kind":"string","value":"{\n \"doc_id\": \"27769763\",\n \"title\": \"Fast and automatic identification of particle tilt pairs based on Delaunay triangulation.\",\n \"abstract\": \"Random conical tilt (RCT) and orthogonal tilt reconstruction (OTR) are two remarkable methods for reconstructing the three-dimensional structure of macromolecules at low resolution. These techniques use two images at two different sample tilts. One of the most demanding steps in these methods at the image processing level is to identify corresponding particles on both micrographs, and manual or semiautomatic matching methods are usually used. Here we present an approach to solve this bottleneck with a fully automatic method for assigning particle tilt pairs. This new algorithm behaves correctly with a variety of samples, covering the range from small to large macromolecules and from sparse to densely populated fields of view. It is also more rapid than previous approaches. The roots of the method lie in a Delaunay triangulation of the set of independently picked coordinates on both the untilted and tilted micrographs. These triangulations are then used to search an affine transformation between the untilted and tilted triangles. The affine transformation that maximizes the number of correspondences between the two micrographs defines the coordinate matching.\",\n \"corpus_id\": 3919789\n}"},"candidates":{"kind":"list like","value":[{"doc_id":"18272396","title":"Angle determination for side views in single particle electron microscopy.","abstract":"In order to build a first model in single particle electron microscopy the relative angular orientation of each image of a protein complex must be determined. These orientations can be described by three Eulerian angles. Images of complexes that present the same view can be aligned in two-dimensions and averaged in order to increase their signal-to-noise ratio. Based on these averaged images, several standard approaches exist for determining Euler angles for randomly oriented projection images. The common lines and angular reconstitution methods work well for particles with symmetry while the random conical tilting and related orthogonal tilt reconstruction methods work in most cases but require the acquisition of tilt pairs of images. For the situation where views of particles can be identified that are rotations about a single axis parallel to the grid, an alternative algorithm to determine the orientations of class averages without the need to acquire tilt pairs can be applied. This type of view of a complex is usually called a side view. This paper describes the detailed workings and characterization of an algorithm, named rotational analysis, which uses real-space fiducial markers derived from the averages themselves to determine the Euler angles for side views. We demonstrate how this algorithm works in practice by applying it to a data set of images of affinity-purified bovine mitochondrial ATP synthase.","corpus_id":25712277,"score":2},{"doc_id":"20888964","title":"The orthogonal tilt reconstruction method.","abstract":"Generating reliable initial models for novel asymmetric molecules, particularly heterogeneous ones, remains a major challenge in cryo-electron microscopy. Geometric reconstruction methods, relying on the ability to tilt the microscope stage to obtain two or more views of each molecule, are arguably the most robust for these types of samples as they generate independent reconstructions for each characteristic view obtained. Random Conical Tilt (RCT) is the classic geometric reconstruction method. Pairs of images are collected at high tilt (around 50°) and 0°. The latter are used to sort the data into characteristic views of the molecule and the former are used for their reconstruction. RCT's greatest strength is its ability to generate structures regardless of the number of orientations adopted by the sample on the support. Its major drawback stems from the limited tilt of the microscope stage; this results in an incomplete sampling of the structure in Fourier space and artifacts in its real space representation. Orthogonal Tilt Reconstruction (OTR), a modification of this data collection strategy, results in fully sampled structures. It relies on collecting data at -45° and +45° and treating the tilt pairs as equivalent to the ideal 0°/90° that cannot be collected directly in the microscope. OTR requires a sample that adopts a large number of orientations on the support. Here, the RCT and OTR methods are reviewed and their performances with a biological test sample are compared. The steps required to apply OTR are also discussed.","corpus_id":25782305,"score":2},{"doc_id":"21536134","title":"Validation of the orthogonal tilt reconstruction method with a biological test sample.","abstract":"Electron microscopy of frozen-hydrated samples (cryo-EM) can yield high resolution structures of macromolecular complexes by accurately determining the orientation of large numbers of experimental views of the sample relative to an existing 3D model. The \"initial model problem\", the challenge of obtaining these orientations ab initio, remains a major bottleneck in determining the structure of novel macromolecules, chiefly those lacking internal symmetry. We previously proposed a method for the generation of initial models--orthogonal tilt reconstruction (OTR)--that bypasses limitations inherent to the other two existing methods, random conical tilt (RCT) and angular reconstitution (AR). Here we present a validation of OTR with a biological test sample whose structure was previously solved by RCT: the complex between the yeast exosome and the subunit Rrp44. We show that, as originally demonstrated with synthetic data, OTR generates initial models that do not exhibit the \"missing cone\" artifacts associated with RCT and show an isotropic distribution of information when compared with the known structure. This eliminates the need for further user intervention to solve these artifacts and makes OTR ideal for automation and the analysis of heterogeneous samples. With the former in mind, we propose a set of simple quantitative criteria that can be used, in combination, to select from a large set of initial reconstructions a subset that can be used as reliable references for refinement to higher resolution.","corpus_id":24370377,"score":2},{"doc_id":"21939668","title":"Tilt-pair analysis of images from a range of different specimens in single-particle electron cryomicroscopy.","abstract":"The comparison of a pair of electron microscope images recorded at different specimen tilt angles provides a powerful approach for evaluating the quality of images, image-processing procedures, or three-dimensional structures. Here, we analyze tilt-pair images recorded from a range of specimens with different symmetries and molecular masses and show how the analysis can produce valuable information not easily obtained otherwise. We show that the accuracy of orientation determination of individual single particles depends on molecular mass, as expected theoretically since the information in each particle image increases with molecular mass. The angular uncertainty is less than 1° for particles of high molecular mass (~50 MDa), several degrees for particles in the range 1-5 MDa, and tens of degrees for particles below 1 MDa. Orientational uncertainty may be the major contributor to the effective temperature factor (B-factor) describing contrast loss and therefore the maximum resolution of a structure determination. We also made two unexpected observations. Single particles that are known to be flexible showed a wider spread in orientation accuracy, and the orientations of the largest particles examined changed by several degrees during typical low-dose exposures. Smaller particles presumably also reorient during the exposure; hence, specimen movement is a second major factor that limits resolution. Tilt pairs thus enable assessment of orientation accuracy, map quality, specimen motion, and conformational heterogeneity. A convincing tilt-pair parameter plot, where 60% of the particles show a single cluster around the expected tilt axis and tilt angle, provides confidence in a structure determined using electron cryomicroscopy.","corpus_id":25176486,"score":2},{"doc_id":"23142631","title":"Automated correlation of single particle tilt pairs for Random Conical Tilt and Orthogonal Tilt Reconstructions.","abstract":"One of the major methodological challenges in single particle electron microscopy is obtaining initial reconstructions which represent the structural heterogeneity of the dataset. Random Conical Tilt and Orthogonal Tilt Reconstruction techniques in combination with 3D alignment and classification can be used to obtain initial low-resolution reconstructions which represent the full range of structural heterogeneity of the dataset. In order to achieve statistical significance, however, a large number of 3D reconstructions, and, in turn, a large number of tilted image pairs are required. The extraction of single particle tilted image pairs from micrographs can be tedious and time-consuming, as it requires intensive user input even for semi-automated approaches. To overcome the bottleneck of manual selection of a large number of tilt pairs, we developed an algorithm for the correlation of single particle images from tilted image pairs in a fully automated and user-independent manner. The algorithm reliably correlates correct pairs even from noisy micrographs. We further demonstrate the applicability of the algorithm by using it to obtain initial references both from negative stain and unstained cryo datasets.","corpus_id":32528253,"score":2},{"doc_id":"24582855","title":"Web server for tilt-pair validation of single particle maps from electron cryomicroscopy.","abstract":"Three-dimensional structures of biological assemblies may be calculated from images of single particles obtained by electron cryomicroscopy. A key step is the correct determination of the orientation of the particle in individual image projections. A useful tool for validation of the quality of a 3D map and its consistency with images is tilt-pair analysis. In a successful tilt-pair test, the relative angle between orientations assigned to each image of a tilt-pair agrees with the known relative rotation angle of the microscope specimen holder during the experiment. To make the procedure easy to apply to the increasing number of single particle maps, we have developed software and a web server for tilt-pair analysis. The tilt-pair analysis program reports the overall agreement of the assigned orientations with the known tilt angle and axis of the experiment and the distribution of tilt transformations for individual particles recorded in a single image field. We illustrate application of the validation tool to several single particle specimens and describe how to interpret the scores.","corpus_id":30520891,"score":2},{"doc_id":"24694675","title":"Automated particle correspondence and accurate tilt-axis detection in tilted-image pairs.","abstract":"Tilted electron microscope images are routinely collected for an ab initio structure reconstruction as a part of the Random Conical Tilt (RCT) or Orthogonal Tilt Reconstruction (OTR) methods, as well as for various applications using the \"free-hand\" procedure. These procedures all require identification of particle pairs in two corresponding images as well as accurate estimation of the tilt-axis used to rotate the electron microscope (EM) grid. Here we present a computational approach, PCT (particle correspondence from tilted pairs), based on tilt-invariant context and projection matching that addresses both problems. The method benefits from treating the two problems as a single optimization task. It automatically finds corresponding particle pairs and accurately computes tilt-axis direction even in the cases when EM grid is not perfectly planar.","corpus_id":8635565,"score":2},{"doc_id":"24734998","title":"Extending particle tracking capability with Delaunay triangulation.","abstract":"Particle tracking, the analysis of individual moving elements in time series of microscopic images, enables burgeoning new applications, but there is need to better resolve conformation and dynamics. Here we describe the advantages of Delaunay triangulation to extend the capabilities of particle tracking in three areas: (1) discriminating irregularly shaped objects, which allows one to track items other than point features; (2) combining time and space to better connect missing frames in trajectories; and (3) identifying shape backbone. To demonstrate the method, specific examples are given, involving analyzing the time-dependent molecular conformations of actin filaments and λ-DNA. The main limitation of this method, shared by all other clustering techniques, is the difficulty to separate objects when they are very close. This can be mitigated by inspecting locally to remove edges that are longer than their neighbors and also edges that link two objects, using methods described here, so that the combination of Delaunay triangulation with edge removal can be robustly applied to processing large data sets. As common software packages, both commercial and open source, can construct Delaunay triangulation on command, the methods described in this paper are both computationally efficient and easy to implement.","corpus_id":13335348,"score":2},{"doc_id":"24815505","title":"Alternative automatic alignment method for specimen tilt-series images based on back-projected volume data cross-correlations.","abstract":"We devised a new automatic image alignment method for a specimen tilt series; this method is based on the volume data cross-correlation among 3-D cross-sections reconstructed from different sets of projection images (including a single image) for tilt-series alignment or tilt-axis search purposes. This method requires neither markers nor image feature points traceable through the tilt series, and it was examined through simulations and applied to biological thin sections. The method automatically aligned tilt series centred at the correctly detected tilt axis with a precision sufficient for practical applications.","corpus_id":5516936,"score":2},{"doc_id":"25016098","title":"Robust evaluation of 3D electron cryomicroscopy data using tilt-pairs.","abstract":"Determining the structure of a protein complex using electron microscopy requires the calculation of a 3D density map from 2D images of single particles. Since the individual images are taken at low electron dose to avoid radiation damage, they are noisy and difficult to align with each other. This can result in incorrect maps, making validation essential. Pairs of electron micrographs taken at known angles to each other (tilt-pairs) can be used to measure the accuracy of assigned projection orientations and verify the soundness of calculated maps. Here we establish a statistical framework for evaluating images and density maps using tilt-pairs. The directional distribution of such angular data is modelled using a Fisher distribution on the unit sphere. This provides a simple, quantitative and easily comparable metric, the concentration parameter κ, for evaluating the quality of datasets and density maps that is independent of the data collection and analysis methods. A large κ is indicative of good agreement between the particle images and the 3D density map. For structure validation, we recommend κ>10 and a p-value <0.01. The statistical framework herein allows one to objectively answer the question: Is a reconstructed density map correct within a particular confidence interval?","corpus_id":9196955,"score":2},{"doc_id":"25654984","title":"A tilt-pair based method for assigning the projection directions of randomly oriented single-particle molecules.","abstract":"In this article, we describe an improved method to assign the projection angle for averaged images using tilt-pair images for three-dimensional reconstructions from randomly oriented single-particle molecular images. Our study addressed the so-called 'initial volume problem' in the single-particle reconstruction, which involves estimation of projection angles of the particle images. The projected images of the particles in different tilt observations were mixed and averaged for the characteristic views. After the ranking of these group average images in terms of reliable tilt angle information, mutual tilt angles between images are assigned from the constituent tilt-pair information. Then, multiples of the conical tilt series are made and merged to construct a network graph of the particle images in terms of projection angles, which are optimized for the three-dimensional reconstruction. We developed the method with images of a synthetic object and applied it to a single-particle image data set of the purified deacetylase from archaea. With the introduction of low-angle tilt observations to minimize unfavorable imaging conditions due to tilting, the results demonstrated reasonable reconstruction models without imposing symmetry to the structure. This method also guides its users to discriminate particle images of different conformational state of the molecule.","corpus_id":22112573,"score":2},{"doc_id":"26390853","title":"Cryo-EM and the elucidation of new macromolecular structures: Random Conical Tilt revisited.","abstract":"Cryo-Electron Microscopy (cryo-EM) of macromolecular complexes is a fundamental structural biology technique which is expanding at a very fast pace. Key to its success in elucidating the three-dimensional structure of a macromolecular complex, especially of small and non-symmetric ones, is the ability to start from a low resolution map, which is subsequently refined with the actual images collected at the microscope. There are several methods to produce this first structure. Among them, Random Conical Tilt (RCT) plays a prominent role due to its unbiased nature (it can create an initial model based on experimental measurements). In this article, we revise the fundamental mathematical expressions supporting RCT, providing new expressions handling all key geometrical parameters without the need of intermediate operations, leading to improved automation and overall reliability, essential for the success of cryo-EM when analyzing new complexes. We show that the here proposed RCT workflow based on the new formulation performs very well in practical cases, requiring very few image pairs (as low as 13 image pairs in one of our examples) to obtain relevant 3D maps.","corpus_id":13916472,"score":2},{"doc_id":"26433028","title":"A novel fully automatic scheme for fiducial marker-based alignment in electron tomography.","abstract":"Although the topic of fiducial marker-based alignment in electron tomography (ET) has been widely discussed for decades, alignment without human intervention remains a difficult problem. Specifically, the emergence of subtomogram averaging has increased the demand for batch processing during tomographic reconstruction; fully automatic fiducial marker-based alignment is the main technique in this process. However, the lack of an accurate method for detecting and tracking fiducial markers precludes fully automatic alignment. In this paper, we present a novel, fully automatic alignment scheme for ET. Our scheme has two main contributions: First, we present a series of algorithms to ensure a high recognition rate and precise localization during the detection of fiducial markers. Our proposed solution reduces fiducial marker detection to a sampling and classification problem and further introduces an algorithm to solve the parameter dependence of marker diameter and marker number. Second, we propose a novel algorithm to solve the tracking of fiducial markers by reducing the tracking problem to an incomplete point set registration problem. Because a global optimization of a point set registration occurs, the result of our tracking is independent of the initial image position in the tilt series, allowing for the robust tracking of fiducial markers without pre-alignment. The experimental results indicate that our method can achieve an accurate tracking, almost identical to the current best one in IMOD with half automatic scheme. Furthermore, our scheme is fully automatic, depends on fewer parameters (only requires a gross value of the marker diameter) and does not require any manual interaction, providing the possibility of automatic batch processing of electron tomographic reconstruction.","corpus_id":3986209,"score":2},{"doc_id":"17855124","title":"Markov random field based automatic image alignment for electron tomography.","abstract":"We present a method for automatic full-precision alignment of the images in a tomographic tilt series. Full-precision automatic alignment of cryo electron microscopy images has remained a difficult challenge to date, due to the limited electron dose and low image contrast. These facts lead to poor signal to noise ratio (SNR) in the images, which causes automatic feature trackers to generate errors, even with high contrast gold particles as fiducial features. To enable fully automatic alignment for full-precision reconstructions, we frame the problem probabilistically as finding the most likely particle tracks given a set of noisy images, using contextual information to make the solution more robust to the noise in each image. To solve this maximum likelihood problem, we use Markov Random Fields (MRF) to establish the correspondence of features in alignment and robust optimization for projection model estimation. The resulting algorithm, called Robust Alignment and Projection Estimation for Tomographic Reconstruction, or RAPTOR, has not needed any manual intervention for the difficult datasets we have tried, and has provided sub-pixel alignment that is as good as the manual approach by an expert user. We are able to automatically map complete and partial marker trajectories and thus obtain highly accurate image alignment. Our method has been applied to challenging cryo electron tomographic datasets with low SNR from intact bacterial cells, as well as several plastic section and X-ray datasets.","corpus_id":18525199,"score":1},{"doc_id":"18023735","title":"Delaunay-Object-Dynamics: cell mechanics with a 3D kinetic and dynamic weighted Delaunay-triangulation.","abstract":"Mathematical methods in Biology are of increasing relevance for understanding the control and the dynamics of biological systems with medical relevance. In particular, agent-based methods turn more and more important because of fast increasing computational power which makes even large systems accessible. An overview of different mathematical methods used in Theoretical Biology is provided and a novel agent-based method for cell mechanics based on Delaunay-triangulations and Voronoi-tessellations is explained in more detail: The Delaunay-Object-Dynamics method. It is claimed that the model combines physically realistic cell mechanics with a reasonable computational load. The power of the approach is illustrated with two examples, avascular tumor growth and genesis of lymphoid tissue in a cell-flow equilibrium.","corpus_id":35441203,"score":1},{"doc_id":"19555764","title":"Automatic particle selection from electron micrographs using machine learning techniques.","abstract":"The 3D reconstruction of biological specimens using Electron Microscopy is currently capable of achieving subnanometer resolution. Unfortunately, this goal requires gathering tens of thousands of projection images that are frequently selected manually from micrographs. In this paper we introduce a new automatic particle selection that learns from the user which particles are of interest. The training phase is semi-supervised so that the user can correct the algorithm during picking and specifically identify incorrectly picked particles. By treating such errors specially, the algorithm attempts to minimize the number of false positives. We show that our algorithm is able to produce datasets with fewer wrongly selected particles than previously reported methods. Another advantage is that we avoid the need for an initial reference volume from which to generate picking projections by instead learning which particles to pick from the user. This package has been made publicly available in the open-source package Xmipp.","corpus_id":11037812,"score":1},{"doc_id":"23144522","title":"Quality Tetrahedral Mesh Smoothing via Boundary-Optimized Delaunay Triangulation.","abstract":"Despite its great success in improving the quality of a tetrahedral mesh, the original optimal Delaunay triangulation (ODT) is designed to move only inner vertices and thus cannot handle input meshes containing \"bad\" triangles on boundaries. In the current work, we present an integrated approach called boundary-optimized Delaunay triangulation (B-ODT) to smooth (improve) a tetrahedral mesh. In our method, both inner and boundary vertices are repositioned by analytically minimizing the error between a paraboloid function and its piecewise linear interpolation over the neighborhood of each vertex. In addition to the guaranteed volume-preserving property, the proposed algorithm can be readily adapted to preserve sharp features in the original mesh. A number of experiments are included to demonstrate the performance of our method.","corpus_id":1888384,"score":1},{"doc_id":"23454482","title":"Automatic post-picking using MAPPOS improves particle image detection from cryo-EM micrographs.","abstract":"Cryo-electron microscopy (cryo-EM) studies using single particle reconstruction are extensively used to reveal structural information on macromolecular complexes. Aiming at the highest achievable resolution, state of the art electron microscopes automatically acquire thousands of high-quality micrographs. Particles are detected on and boxed out from each micrograph using fully- or semi-automated approaches. However, the obtained particles still require laborious manual post-picking classification, which is one major bottleneck for single particle analysis of large datasets. We introduce MAPPOS, a supervised post-picking strategy for the classification of boxed particle images, as additional strategy adding to the already efficient automated particle picking routines. MAPPOS employs machine learning techniques to train a robust classifier from a small number of characteristic image features. In order to accurately quantify the performance of MAPPOS we used simulated particle and non-particle images. In addition, we verified our method by applying it to an experimental cryo-EM dataset and comparing the results to the manual classification of the same dataset. Comparisons between MAPPOS and manual post-picking classification by several human experts demonstrated that merely a few hundred sample images are sufficient for MAPPOS to classify an entire dataset with a human-like performance. MAPPOS was shown to greatly accelerate the throughput of large datasets by reducing the manual workload by orders of magnitude while maintaining a reliable identification of non-particle images.","corpus_id":9789870,"score":1},{"doc_id":"23483043","title":"Blocking Delaunay triangulations.","abstract":"Given a set B of n black points in general position, we say that a set of white points W blocks B if in the Delaunay triangulation of [Formula: see text] there is no edge connecting two black points. We give the following bounds for the size of the smallest set W blocking B: (i) [Formula: see text] white points are always sufficient to block a set of n black points, (ii) if B is in convex position, [Formula: see text] white points are always sufficient to block it, and (iii) at least [Formula: see text] white points are always necessary to block a set of n black points.","corpus_id":263586149,"score":1},{"doc_id":"23492377","title":"Computing 2D constrained delaunay triangulation using the GPU.","abstract":"We propose the first graphics processing unit (GPU) solution to compute the 2D constrained Delaunay triangulation (CDT) of a planar straight line graph (PSLG) consisting of points and edges. There are many existing CPU algorithms to solve the CDT problem in computational geometry, yet there has been no prior approach to solve this problem efficiently using the parallel computing power of the GPU. For the special case of the CDT problem where the PSLG consists of just points, which is simply the normal Delaunay triangulation (DT) problem, a hybrid approach using the GPU together with the CPU to partially speed up the computation has already been presented in the literature. Our work, on the other hand, accelerates the entire computation on the GPU. Our implementation using the CUDA programming model on NVIDIA GPUs is numerically robust, and runs up to an order of magnitude faster than the best sequential implementations on the CPU. This result is reflected in our experiment with both randomly generated PSLGs and real-world GIS data having millions of points and edges.","corpus_id":6289286,"score":1},{"doc_id":"23857566","title":"Automatic particle detection in microscopy using temporal correlations.","abstract":"One of the fundamental problems in the analysis of single particle tracking data is the detection of individual particle positions from microscopy images. Distinguishing true particles from noise with a minimum of false positives and false negatives is an important step that will have substantial impact on all further analysis of the data. A common approach is to obtain a plausible set of particles from a larger set of candidate particles by filtering using manually selected threshold values for intensity, size, shape, and other parameters describing a particle. This introduces subjectivity into the analysis and hinders reproducibility. In this paper, we introduce a method for automatic selection of these threshold values based on maximizing temporal correlations in particle count time series. We use Markov Chain Monte Carlo to find the threshold values corresponding to the maximum correlation, and we study several experimental data sets to assess the performance of the method in practice by comparing manually selected threshold values from several independent experts with automatically selected threshold values. We conclude that the method produces useful results, reducing subjectivity and the need for manual intervention, a great benefit being its easy integratability into many already existing particle detection algorithms.","corpus_id":34973618,"score":1},{"doc_id":"23958728","title":"A pattern matching approach to the automatic selection of particles from low-contrast electron micrographs.","abstract":"MOTIVATION: Structural information of macromolecular complexes provides key insights into the way they carry out their biological functions. Achieving high-resolution structural details with electron microscopy requires the identification of a large number (up to hundreds of thousands) of single particles from electron micrographs, which is a laborious task if it has to be manually done and constitutes a hurdle towards high-throughput. Automatic particle selection in micrographs is far from being settled and new and more robust algorithms are required to reduce the number of false positives and false negatives. RESULTS: In this article, we introduce an automatic particle picker that learns from the user the kind of particles he is interested in. Particle candidates are quickly and robustly classified as particles or non-particles. A number of new discriminative shape-related features as well as some statistical description of the image grey intensities are used to train two support vector machine classifiers. Experimental results demonstrate that the proposed method: (i) has a considerably low computational complexity and (ii) provides results better or comparable with previously reported methods at a fraction of their computing time. AVAILABILITY: The algorithm is fully implemented in the open-source Xmipp package and downloadable from http://xmipp.cnb.csic.es.","corpus_id":11199882,"score":1},{"doc_id":"24974203","title":"Efficient initial volume determination from electron microscopy images of single particles.","abstract":"MOTIVATION: Structural information of macromolecular complexes provides key insights into the way they carry out their biological functions. The reconstruction process leading to the final 3D map requires an approximate initial model. Generation of an initial model is still an open and challenging problem in single-particle analysis. RESULTS: We present a fast and efficient approach to obtain a reliable, low-resolution estimation of the 3D structure of a macromolecule, without any a priori knowledge, addressing the well-known issue of initial volume estimation in the field of single-particle analysis. The input of the algorithm is a set of class average images obtained from individual projections of a biological object at random and unknown orientations by transmission electron microscopy micrographs. The proposed method is based on an initial non-lineal dimensionality reduction approach, which allows to automatically selecting representative small sets of class average images capturing the most of the structural information of the particle under study. These reduced sets are then used to generate volumes from random orientation assignments. The best volume is determined from these guesses using a random sample consensus (RANSAC) approach. We have tested our proposed algorithm, which we will term 3D-RANSAC, with simulated and experimental data, obtaining satisfactory results under the low signal-to-noise conditions typical of cryo-electron microscopy. AVAILABILITY: The algorithm is freely available as part of the Xmipp 3.1 package [http://xmipp.cnb.csic.es]. CONTACT: jvargas@cnb.csic.es SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.","corpus_id":8183036,"score":1},{"doc_id":"26193484","title":"A Bayesian approach for suppression of limited angular sampling artifacts in single particle 3D reconstruction.","abstract":"In the single particle reconstruction, the initial 3D structure often suffers from the limited angular sampling artifact. Selecting 2D class averages of particle images generally improves the accuracy and efficiency of the reference-free 3D angle estimation, but causes an insufficient angular sampling to fill the information of the target object in the 3D frequency space. Similarly, the initial 3D structure by the random-conical tilt reconstruction has the well-known \"missing cone\" artifact. Here, we attempted to solve the limited angular sampling problem by sequentially applying maximum a posteriori estimate with expectation maximization algorithm (sMAP-EM). Using both simulated and experimental cryo-electron microscope images, the sMAP-EM was compared to the direct Fourier method on the basis of reconstruction error and resolution. To establish selection criteria of the final regularization weight for the sMAP-EM, the effects of noise level and sampling sparseness on the reconstructions were examined with evenly distributed sampling simulations. The frequency information filled in the missing cone of the conical tilt sampling simulations was assessed by developing new quantitative measurements. All the results of visual and numerical evaluations showed the sMAP-EM performed better than the direct Fourier method, regardless of the sampling method, noise level, and sampling sparseness. Furthermore, the frequency domain analysis demonstrated that the sMAP-EM can fill the meaningful information in the unmeasured angular space without detailed a priori knowledge of the objects. The current research demonstrated that the sMAP-EM has a high potential to facilitate the determination of 3D protein structures at near atomic-resolution.","corpus_id":23990990,"score":1},{"doc_id":"26433027","title":"Simultaneous determination of sample thickness, tilt, and electron mean free path using tomographic tilt images based on Beer-Lambert law.","abstract":"Cryo-electron tomography (cryo-ET) is an emerging technique that can elucidate the architecture of macromolecular complexes and cellular ultrastructure in a near-native state. Some important sample parameters, such as thickness and tilt, are needed for 3-D reconstruction. However, these parameters can currently only be determined using trial 3-D reconstructions. Accurate electron mean free path plays a significant role in modeling image formation process essential for simulation of electron microscopy images and model-based iterative 3-D reconstruction methods; however, their values are voltage and sample dependent and have only been experimentally measured for a limited number of sample conditions. Here, we report a computational method, tomoThickness, based on the Beer-Lambert law, to simultaneously determine the sample thickness, tilt and electron inelastic mean free path by solving an overdetermined nonlinear least square optimization problem utilizing the strong constraints of tilt relationships. The method has been extensively tested with both stained and cryo datasets. The fitted electron mean free paths are consistent with reported experimental measurements. The accurate thickness estimation eliminates the need for a generous assignment of Z-dimension size of the tomogram. Interestingly, we have also found that nearly all samples are a few degrees tilted relative to the electron beam. Compensation of the intrinsic sample tilt can result in horizontal structure and reduced Z-dimension of tomograms. Our fast, pre-reconstruction method can thus provide important sample parameters that can help improve performance of tomographic reconstruction of a wide range of samples.","corpus_id":39148235,"score":1},{"doc_id":"26931650","title":"High resolution single particle refinement in EMAN2.1.","abstract":"EMAN2.1 is a complete image processing suite for quantitative analysis of grayscale images, with a primary focus on transmission electron microscopy, with complete workflows for performing high resolution single particle reconstruction, 2-D and 3-D heterogeneity analysis, random conical tilt reconstruction and subtomogram averaging, among other tasks. In this manuscript we provide the first detailed description of the high resolution single particle analysis pipeline and the philosophy behind its approach to the reconstruction problem. High resolution refinement is a fully automated process, and involves an advanced set of heuristics to select optimal algorithms for each specific refinement task. A gold standard FSC is produced automatically as part of refinement, providing a robust resolution estimate for the final map, and this is used to optimally filter the final CTF phase and amplitude corrected structure. Additional methods are in-place to reduce model bias during refinement, and to permit cross-validation using other computational methods.","corpus_id":3553550,"score":1},{"doc_id":"27313000","title":"Implementation of a cryo-electron tomography tilt-scheme optimized for high resolution subtomogram averaging.","abstract":"Cryo-electron tomography (cryoET) allows 3D structural information to be obtained from cells and other biological samples in their close-to-native state. In combination with subtomogram averaging, detailed structures of repeating features can be resolved. CryoET data is collected as a series of images of the sample from different tilt angles; this is performed by physically rotating the sample in the microscope between each image. The angles at which the images are collected, and the order in which they are collected, together are called the tilt-scheme. Here we describe a \"dose-symmetric tilt-scheme\" that begins at low tilt and then alternates between increasingly positive and negative tilts. This tilt-scheme maximizes the amount of high-resolution information maintained in the tomogram for subsequent subtomogram averaging, and may also be advantageous for other applications. We describe implementation of the tilt-scheme in combination with further data-collection refinements including setting thresholds on acceptable drift and improving focus accuracy. Requirements for microscope set-up are introduced, and a macro is provided which automates the application of the tilt-scheme within SerialEM.","corpus_id":3910770,"score":1},{"doc_id":"18784030","title":"Noniterative interpolation-based super-resolution minimizing aliasing in the reconstructed image.","abstract":"Super-resolution (SR) techniques produce a high-resolution image from a set of low-resolution undersampled images. In this paper, we propose a new method for super-resolution that uses sampling theory concepts to derive a noniterative SR algorithm. We first raise the issue of the validity of the data model usually assumed in SR, pointing out that it imposes a band-limited reconstructed image plus a certain type of noise. We propose a sampling theory framework with a prefiltering step that allows us to work with more general data models and also a specific new method for SR that uses Delaunay triangulation and B-splines to build the super-resolved image. The proposed method is noniterative and well posed. We prove its effectiveness against traditional iterative and noniterative SR methods on synthetic and real data. Additionally, we also prove that we can first solve the interpolation problem and then make the deblurring not only when the motion is translational but also when there are rotations and shifts and the imaging system Point Spread Function (PSF) is rotationally symmetric.","corpus_id":14215955,"score":0},{"doc_id":"18817555","title":"Abbreviation definition identification based on automatic precision estimates.","abstract":"BACKGROUND: The rapid growth of biomedical literature presents challenges for automatic text processing, and one of the challenges is abbreviation identification. The presence of unrecognized abbreviations in text hinders indexing algorithms and adversely affects information retrieval and extraction. Automatic abbreviation definition identification can help resolve these issues. However, abbreviations and their definitions identified by an automatic process are of uncertain validity. Due to the size of databases such as MEDLINE only a small fraction of abbreviation-definition pairs can be examined manually. An automatic way to estimate the accuracy of abbreviation-definition pairs extracted from text is needed. In this paper we propose an abbreviation definition identification algorithm that employs a variety of strategies to identify the most probable abbreviation definition. In addition our algorithm produces an accuracy estimate, pseudo-precision, for each strategy without using a human-judged gold standard. The pseudo-precisions determine the order in which the algorithm applies the strategies in seeking to identify the definition of an abbreviation. RESULTS: On the Medstract corpus our algorithm produced 97% precision and 85% recall which is higher than previously reported results. We also annotated 1250 randomly selected MEDLINE records as a gold standard. On this set we achieved 96.5% precision and 83.2% recall. This compares favourably with the well known Schwartz and Hearst algorithm. CONCLUSION: We developed an algorithm for abbreviation identification that uses a variety of strategies to identify the most probable definition for an abbreviation and also produces an estimated accuracy of the result. This process is purely automatic.","corpus_id":4401810,"score":0},{"doc_id":"19163065","title":"Automatic chromosome pairing using mutual information.","abstract":"Cytogenetics is a key tool in the detection of acquired chromosomal abnormalities and in the diagnosis of genetic diseases such as leukemia. The karyotyping is a set of procedures, in the scope of the cytogenetics, that produces a visual representation of the 46 chromosomes (called karyogram), paired and arranged in decreasing order of size. The pairing procedure aims to identify all pairs of homologous chromosomes. The pairing criterion is based on dimensional, morphological,and textural features similarity. This process is time consuming when performed manually, and demanding from a technical point of view. An automatic pairing algorithm would thus bring benefits, but it remains an open problem to date. In this paper a new strategy for automatic pairing of homologous chromosomes is proposed. Besides the traditional features described in the literature, the Mutual Information (MI) is used to discriminate chromosome textural differences. A supervised non-linear classifier is trained by using manual classifications provided by expert technicians, combining the different features computed from each pair. Simulations using 836 real chromosome images, obtained with a Leica Optical Microscope DM 2500, in a leave-one-out cross validation fashion, were performed for training and testing the algorithm. Promising and relevant results were found, despite the poor quality of the original chromosome images, contrasting with state-of the-art algorithms and datasets found in the literature.","corpus_id":2447074,"score":0},{"doc_id":"19493107","title":"Three-dimensional reconstruction of biological macromolecular complexes from in-lens scanning electron micrographs.","abstract":"Two helical samples: F-actin and the bacteriophage T4 tail sheath were reconstructed in three dimensions from contrast enhanced (rotational shadowing and negatively stained) in-lens cryo-field emission scanning electron micrographs, using the iterative real-space helical reconstruction method. The F-actin--and bacteriophage T4 reconstructions compare favourably to an atomic model refined against fibre diffraction data and a cryo-electron microscopy reconstruction, respectively. These results show that single-particle methods, developed for macromolecules imaged in the transmission electron microscope can be applied to cryo-field emission scanning electron micrographs data with appropriate symmetry.","corpus_id":35005,"score":0},{"doc_id":"19526263","title":"Automatic identification and truncation of boundary outlets in complex imaging-derived biomedical geometries.","abstract":"Efficient and accurate reconstruction of imaging-derived geometries and subsequent quality mesh generation are enabling technologies for both clinical and research simulations. A challenging part of this process is the introduction of computable, orthogonal boundary patches, namely, the outlets, into treed structures, such as vasculature, arterial or airway trees. We present efficient and robust algorithms for automatically identifying and truncating the outlets for complex geometries. Our approach is based on a conceptual decomposition of objects into tips, segments, and branches, where the tips determine the outlets. We define the tips by introducing a novel concept called the average interior center of curvature and identify the tips that are stable and noise resistant. We compute well-defined orthogonal planes, which truncate the tips into outlets. The rims of the outlets are connected into curves, and the outlets are then closed using Delaunay triangulation. We illustrate the effectiveness and robustness of our approach with a variety of complex lung and coronary artery geometries.","corpus_id":18529580,"score":0},{"doc_id":"20363682","title":"Face transformation with harmonic models by the finite-volume method with delaunay triangulation.","abstract":"To carry out face transformation, this paper presents new numerical algorithms, which consist of two parts, namely, the harmonic models for changes of face characteristics and the splitting techniques for grayness transition. The main method in this paper is a combination of the finite-volume method (FVM) with Delaunay triangulation to solve the Laplace equations in the harmonic transformation of face images. The advantages of the FVM with Delaunay triangulation are given as follows: 1) easy to formulate the linear algebraic equations; 2) good in retaining the pertinent geometric and physical need; and 3) less central processing unit time needed. Numerical and graphical experiments have been conducted for the face transformation from a female (woman) to a male (man), and vice versa. The computed sequential errors are O(N⁻³/²), where N² is the division number of a pixel into subpixels. These computed errors coincide with the analysis on the splitting-shooting method (SSM) with piecewise constant interpolation in the previous paper of Li and Bai. In computation, the average absolute errors of restored pixel grayness can be smaller than 2 out of 256 grayness levels. The FVM is as simple as the finite-difference method (FDM) and as flexible as the finite-element method (FEM). Hence, the FVM is particularly useful when dealing with large face images with a huge number of pixels in shape distortion. The numerical transformation of face images in this paper can be used not only in pattern recognition but also in resampling, image morphing, and computer animation.","corpus_id":12959692,"score":0},{"doc_id":"21089695","title":"[A review of automatic particle recognition in Cryo-EM images].","abstract":"Advances in cryo-electron microscopy (Cryo-EM) and single-particle reconstruction have led to increasingly high resolutions of macromolecular three-dimensional reconstruction. However, for keeping up the continuing improvements in resolution, it is necessary to increase the number of particles included in performing reconstructions. Manual selection of particles, even assisted by computer, is a bottleneck of single-particle reconstruction. Cryo-EM image has low signal-to-noise ratio and low contrast, which leads to difficulty in particle picking. Various approaches have been developed to address the problem of automatic particle. This paper describes the application of template-based method, edge based method, feature-based method, neural network, DoG-based and simulated annealing approach in particle picking. The characteristics of various approaches are discussed, and the future development is presented.","corpus_id":38932072,"score":0},{"doc_id":"21490573","title":"Single particle electron microscopy reconstruction of the exosome complex using the random conical tilt method.","abstract":"Single particle electron microscopy (EM) reconstruction has recently become a popular tool to get the three-dimensional (3D) structure of large macromolecular complexes. Compared to X-ray crystallography, it has some unique advantages. First, single particle EM reconstruction does not need to crystallize the protein sample, which is the bottleneck in X-ray crystallography, especially for large macromolecular complexes. Secondly, it does not need large amounts of protein samples. Compared with milligrams of proteins necessary for crystallization, single particle EM reconstruction only needs several micro-liters of protein solution at nano-molar concentrations, using the negative staining EM method. However, despite a few macromolecular assemblies with high symmetry, single particle EM is limited at relatively low resolution (lower than 1 nm resolution) for many specimens especially those without symmetry. This technique is also limited by the size of the molecules under study, i.e. 100 kDa for negatively stained specimens and 300 kDa for frozen-hydrated specimens in general. For a new sample of unknown structure, we generally use a heavy metal solution to embed the molecules by negative staining. The specimen is then examined in a transmission electron microscope to take two-dimensional (2D) micrographs of the molecules. Ideally, the protein molecules have a homogeneous 3D structure but exhibit different orientations in the micrographs. These micrographs are digitized and processed in computers as \"single particles\". Using two-dimensional alignment and classification techniques, homogenous molecules in the same views are clustered into classes. Their averages enhance the signal of the molecule's 2D shapes. After we assign the particles with the proper relative orientation (Euler angles), we will be able to reconstruct the 2D particle images into a 3D virtual volume. In single particle 3D reconstruction, an essential step is to correctly assign the proper orientation of each single particle. There are several methods to assign the view for each particle, including the angular reconstitution(1) and random conical tilt (RCT) method(2). In this protocol, we describe our practice in getting the 3D reconstruction of yeast exosome complex using negative staining EM and RCT. It should be noted that our protocol of electron microscopy and image processing follows the basic principle of RCT but is not the only way to perform the method. We first describe how to embed the protein sample into a layer of Uranyl-Formate with a thickness comparable to the protein size, using a holey carbon grid covered with a layer of continuous thin carbon film. Then the specimen is inserted into a transmission electron microscope to collect untilted (0-degree) and tilted (55-degree) pairs of micrographs that will be used later for processing and obtaining an initial 3D model of the yeast exosome. To this end, we perform RCT and then refine the initial 3D model by using the projection matching refinement method(3).","corpus_id":45189809,"score":0},{"doc_id":"21947520","title":"Automatic construction of parts+geometry models for initializing groupwise registration.","abstract":"Groupwise nonrigid image registration is a powerful tool to automatically establish correspondences across sets of images. Such correspondences are widely used for constructing statistical models of shape and appearance. As existing techniques usually treat registration as an optimization problem, a good initialization is required. Although the standard initialization-affine transformation-generally works well, it is often inadequate when registering images of complex structures. In this paper we present a more sophisticated method that uses the sparse matches of a parts+geometry model as the initialization. We show that both the model and its matches can be automatically obtained, and that the matches are able to effectively initialize a groupwise nonrigid registration algorithm, leading to accurate dense correspondences. We also show that the dense mesh models constructed during the groupwise registration process can be used to accurately annotate new images. We demonstrate the efficacy of the approach on three datasets of increasing difficulty, and report on a detailed quantitative evaluation of its performance.","corpus_id":31358433,"score":0},{"doc_id":"22027381","title":"Super-resolution without dense flow.","abstract":"Super-resolution is a widely applied technique that improves the resolution of input images by software methods. Most conventional reconstruction-based super-resolution algorithms assume accurate dense optical flow fields between the input frames, and their performance degrades rapidly when the motion estimation result is not accurate enough. However, optical flow estimation is usually difficult, particularly when complicated motion is presented in real-world videos. In this paper, we explore a new way to solve this problem by using sparse feature point correspondences between the input images. The feature point correspondences, which are obtained by matching a set of feature points, are usually precise and much more robust than dense optical flow fields. This is because the feature points represent well-selected significant locations in the image, and performing matching on the feature point set is usually very accurate. In order to utilize the sparse correspondences in conventional super-resolution, we extract an adaptive support region with a reliable local flow field from each corresponding feature point pair. The normalized prior is also proposed to increase the visual consistency of the reconstructed result. Extensive experiments on real data were carried out, and results show that the proposed algorithm produces high-resolution images with better quality, particularly in the presence of large-scale or complicated motion fields.","corpus_id":18031777,"score":0},{"doc_id":"22291925","title":"IPET and FETR: experimental approach for studying molecular structure dynamics by cryo-electron tomography of a single-molecule structure.","abstract":"The dynamic personalities and structural heterogeneity of proteins are essential for proper functioning. Structural determination of dynamic/heterogeneous proteins is limited by conventional approaches of X-ray and electron microscopy (EM) of single-particle reconstruction that require an average from thousands to millions different molecules. Cryo-electron tomography (cryoET) is an approach to determine three-dimensional (3D) reconstruction of a single and unique biological object such as bacteria and cells, by imaging the object from a series of tilting angles. However, cconventional reconstruction methods use large-size whole-micrographs that are limited by reconstruction resolution (lower than 20 Å), especially for small and low-symmetric molecule (<400 kDa). In this study, we demonstrated the adverse effects from image distortion and the measuring tilt-errors (including tilt-axis and tilt-angle errors) both play a major role in limiting the reconstruction resolution. Therefore, we developed a \"focused electron tomography reconstruction\" (FETR) algorithm to improve the resolution by decreasing the reconstructing image size so that it contains only a single-instance protein. FETR can tolerate certain levels of image-distortion and measuring tilt-errors, and can also precisely determine the translational parameters via an iterative refinement process that contains a series of automatically generated dynamic filters and masks. To describe this method, a set of simulated cryoET images was employed; to validate this approach, the real experimental images from negative-staining and cryoET were used. Since this approach can obtain the structure of a single-instance molecule/particle, we named it individual-particle electron tomography (IPET) as a new robust strategy/approach that does not require a pre-given initial model, class averaging of multiple molecules or an extended ordered lattice, but can tolerate small tilt-errors for high-resolution single \"snapshot\" molecule structure determination. Thus, FETR/IPET provides a completely new opportunity for a single-molecule structure determination, and could be used to study the dynamic character and equilibrium fluctuation of macromolecules.","corpus_id":4807732,"score":0},{"doc_id":"22325257","title":"Delaunay triangulation-based pit density estimation for the classification of polyps in high-magnification chromo-colonoscopy.","abstract":"In this work we propose a method to extract shape-based features from endoscopic images for an automated classification of colonic polyps. This method is based on the density of pits as used in the pit pattern classification scheme which is commonly used for the classification of colonic polyps. For the detection of pits we employ a noise-robust variant of the LBP operator. To be able to be robust against local texture variations we extend this operator by an adaptive thresholding. Based on the detected pit candidates we compute a Delaunay triangulation and use the edge lengths of the resulting triangles to construct histograms. These are then used in conjunction with the k-NN classifier to classify images. We show that, compared to a previously developed method, we are not only able to almost always get higher classification results in our application scenario, but that the proposed method is also able to significantly outperform the previously developed method in terms of the computational demand.","corpus_id":1632357,"score":0},{"doc_id":"23113939","title":"A rule-based algorithm for automatic bond type perception.","abstract":"Assigning bond orders is a necessary and essential step for characterizing a chemical structure correctly in force field based simulations. Several methods have been developed to do this. They all have advantages but with limitations too. Here, an automatic algorithm for assigning chemical connectivity and bond order regardless of hydrogen for organic molecules is provided, and only three dimensional coordinates and element identities are needed for our algorithm. The algorithm uses hard rules, length rules and conjugation rules to fix the structures. The hard rules determine bond orders based on the basic chemical rules; the length rules determine bond order by the length between two atoms based on a set of predefined values for different bond types; the conjugation rules determine bond orders by using the length information derived from the previous rule, the bond angles and some small structural patterns. The algorithm is extensively evaluated in three datasets, and achieves good accuracy of predictions for all the datasets. Finally, the limitation and future improvement of the algorithm are discussed.","corpus_id":16697891,"score":0},{"doc_id":"23193202","title":"Alpha shape and Delaunay triangulation in studies of protein-related interactions.","abstract":"In recent years, more 3D protein structures have become available, which has made the analysis of large molecular structures much easier. There is a strong demand for geometric models for the study of protein-related interactions. Alpha shape and Delaunay triangulation are powerful tools to represent protein structures and have advantages in characterizing the surface curvature and atom contacts. This review presents state-of-the-art applications of alpha shape and Delaunay triangulation in the studies on protein-DNA, protein-protein, protein-ligand interactions and protein structure analysis.","corpus_id":14520590,"score":0},{"doc_id":"23333657","title":"TMaCS: a hybrid template matching and classification system for partially-automated particle selection.","abstract":"Selection of particle images from electron micrographs presents a bottleneck in determining the structures of macromolecular assemblies by single particle electron cryomicroscopy (cryo-EM). The problem is particularly important when an experimentalist wants to improve the resolution of a 3D map by increasing by tens or hundreds of thousands of images the size of the dataset used for calculating the map. Although several existing methods for automatic particle image selection work well for large protein complexes that produce high-contrast images, it is well known in the cryo-EM community that small complexes that give low-contrast images are often refractory to existing automated particle image selection schemes. Here we develop a method for partially-automated particle image selection when an initial 3D map of the protein under investigation is already available. Candidate particle images are selected from micrographs by template matching with template images derived from projections of the existing 3D map. The candidate particle images are then used to train a support vector machine, which classifies the candidates as particle images or non-particle images. In a final step in the analysis, the selected particle images are subjected to projection matching against the initial 3D map, with the correlation coefficient between the particle image and the best matching map projection used to assess the reliability of the particle image. We show that this approach is able to rapidly select particle images from micrographs of a rotary ATPase, a type of membrane protein complex involved in many aspects of biology.","corpus_id":25508463,"score":0},{"doc_id":"23933392","title":"Particle quality assessment and sorting for automatic and semiautomatic particle-picking techniques.","abstract":"Three-dimensional reconstruction of biological specimens using electron microscopy by single particle methodologies requires the identification and extraction of the imaged particles from the acquired micrographs. Automatic and semiautomatic particle selection approaches can localize these particles, minimizing the user interaction, but at the cost of selecting a non-negligible number of incorrect particles, which can corrupt the final three-dimensional reconstruction. In this work, we present a novel particle quality assessment and sorting method that can separate most erroneously picked particles from correct ones. The proposed method is based on multivariate statistical analysis of a particle set that has been picked previously using any automatic or manual approach. The new method uses different sets of particle descriptors, which are morphology-based, histogram-based and signal to noise analysis based. We have tested our proposed algorithm with experimental data obtaining very satisfactory results. The algorithm is freely available as a part of the Xmipp 3.0 package [http://xmipp.cnb.csic.es].","corpus_id":7094288,"score":0},{"doc_id":"24051799","title":"Selecting the aspect ratio of a scatter plot based on its delaunay triangulation.","abstract":"Scatter plots are diagrams that visualize two-dimensional data as sets of points in the plane. They allow users to detect correlations and clusters in the data. Whether or not a user can accomplish these tasks highly depends on the aspect ratio selected for the plot, i.e., the ratio between the horizontal and the vertical extent of the diagram. We argue that an aspect ratio is good if the Delaunay triangulation of the scatter plot at this aspect ratio has some nice geometric property, e.g., a large minimum angle or a small total edge length. More precisely, we consider the following optimization problem. Given a set Q of points in the plane, find a scale factor s such that scaling the x-coordinates of the points in Q by s and the y-coordinates by 1=s yields a point set P(s) that optimizes a property of the Delaunay triangulation of P(s), over all choices of s. We present an algorithm that solves this problem efficiently and demonstrate its usefulness on real-world instances. Moreover, we discuss an empirical test in which we asked 64 participants to choose the aspect ratios of 18 scatter plots. We tested six different quality measures that our algorithm can optimize. In conclusion, minimizing the total edge length and minimizing what we call the 'uncompactness' of the triangles of the Delaunay triangulation yielded the aspect ratios that were most similar to those chosen by the participants in the test.","corpus_id":1322188,"score":0},{"doc_id":"24144335","title":"gEMpicker: a highly parallel GPU-accelerated particle picking tool for cryo-electron microscopy.","abstract":"BACKGROUND: Picking images of particles in cryo-electron micrographs is an important step in solving the 3D structures of large macromolecular assemblies. However, in order to achieve sub-nanometre resolution it is often necessary to capture and process many thousands or even several millions of 2D particle images. Thus, a computational bottleneck in reaching high resolution is the accurate and automatic picking of particles from raw cryo-electron micrographs. RESULTS: We have developed \"gEMpicker\", a highly parallel correlation-based particle picking tool. To our knowledge, gEMpicker is the first particle picking program to use multiple graphics processor units (GPUs) to accelerate the calculation. When tested on the publicly available keyhole limpet hemocyanin dataset, we find that gEMpicker gives similar results to the FindEM program. However, compared to calculating correlations on one core of a contemporary central processor unit (CPU), running gEMpicker on a modern GPU gives a speed-up of about 27 ×. To achieve even higher processing speeds, the basic correlation calculations are accelerated considerably by using a hierarchy of parallel programming techniques to distribute the calculation over multiple GPUs and CPU cores attached to multiple nodes of a computer cluster. By using a theoretically optimal reduction algorithm to collect and combine the cluster calculation results, the speed of the overall calculation scales almost linearly with the number of cluster nodes available. CONCLUSIONS: The very high picking throughput that is now possible using GPU-powered workstations or computer clusters will help experimentalists to achieve higher resolution 3D reconstructions more rapidly than before.","corpus_id":10430036,"score":0},{"doc_id":"24390311","title":"High-resolution cryo-electron microscopy on macromolecular complexes and cell organelles.","abstract":"Cryo-electron microscopy techniques and computational 3-D reconstruction of macromolecular assemblies are tightly linked tools in modern structural biology. This symbiosis has produced vast amounts of detailed information on the structure and function of biological macromolecules. Typically, one of two fundamentally different strategies is used depending on the specimens and their environment. A: 3-D reconstruction based on repetitive and structurally identical unit cells that allow for averaging, and B: tomographic 3-D reconstructions where tilt-series between approximately ± 60 and ± 70° at small angular increments are collected from highly complex and flexible structures that are beyond averaging procedures, at least during the first round of 3-D reconstruction. Strategies of group A are averaging-based procedures and collect large number of 2-D projections at different angles that are computationally aligned, averaged together, and back-projected in 3-D space to reach a most complete 3-D dataset with high resolution, today often down to atomic detail. Evidently, success relies on structurally repetitive particles and an aligning procedure that unambiguously determines the angular relationship of all 2-D projections with respect to each other. The alignment procedure of small particles may rely on their packing into a regular array such as a 2-D crystal, an icosahedral (viral) particle, or a helical assembly. Critically important for cryo-methods, each particle will only be exposed once to the electron beam, making these procedures optimal for highest-resolution studies where beam-induced damage is a significant concern. In contrast, tomographic 3-D reconstruction procedures (group B) do not rely on averaging, but collect an entire dataset from the very same structure of interest. Data acquisition requires collecting a large series of tilted projections at angular increments of 1-2° or less and a tilt range of ± 60° or more. Accordingly, tomographic data collection exposes its specimens to a large electron dose, which is particularly problematic for frozen-hydrated samples. Currently, cryo-electron tomography is a rapidly emerging technology, on one end driven by the newest developments of hardware such as super-stabile microscopy stages as well as the latest generation of direct electron detectors and cameras. On the other end, success also strongly depends on new software developments on all kinds of fronts such as tilt-series alignment and back-projection procedures that are all adapted to the very low-dose and therefore very noisy primary data. Here, we will review the status quo of cryo-electron microscopy and discuss the future of cellular cryo-electron tomography from data collection to data analysis, CTF-correction of tilt-series, post-tomographic sub-volume averaging, and 3-D particle classification. We will also discuss the pros and cons of plunge freezing of cellular specimens to vitrified sectioning procedures and their suitability for post-tomographic volume averaging despite multiple artifacts that may distort specimens to some degree.","corpus_id":13894885,"score":0},{"doc_id":"24607413","title":"Automated particle picking for low-contrast macromolecules in cryo-electron microscopy.","abstract":"Cryo-electron microscopy is an increasingly popular tool for studying the structure and dynamics of biological macromolecules at high resolution. A crucial step in automating single-particle reconstruction of a biological sample is the selection of particle images from a micrograph. We present a novel algorithm for selecting particle images in low-contrast conditions; it proves more effective than the human eye on close-to-focus micrographs, yielding improved or comparable resolution in reconstructions of two macromolecular complexes.","corpus_id":10473929,"score":0},{"doc_id":"24613762","title":"Single particle analysis integrated with microscopy: a high-throughput approach for reconstructing icosahedral particles.","abstract":"In cryo-electron microscopy and single particle analysis, data acquisition and image processing are generally carried out in sequential steps and computation of a three-dimensional reconstruction only begins once all the micrographs have been acquired. We are developing an integrated system for processing images of icosahedral particles during microscopy to provide reconstructed density maps in real-time at the highest possible resolution. The system is designed as a combination of pipelines to run in parallel on a computer cluster and analyzes micrographs as they are acquired, handling automatically all the processing steps from defocus estimation and particle picking to origin/orientation determination. An ab initio model is determined independently from the first micrographs collected, and new models are generated as more particles become available. As a proof of concept, we simulated data acquisition sessions using three sets of micrographs of good to excellent quality that were previously recorded from different icosahedral viruses. Results show that the processing of single micrographs can keep pace with an acquisition rate of about two images per minute. The reconstructed density map improves steadily during the image acquisition phase and its quality at the end of data collection is only moderately inferior to that obtained by expert users who processed semi-automatically all the micrographs after the acquisition. The current prototype demonstrates the advantages of integrating three-dimensional image processing with microscopy, which include an ability to monitor acquisition in terms of the final structure and to predict how much data and microscope resources are needed to achieve a desired resolution.","corpus_id":1625897,"score":0},{"doc_id":"25544475","title":"How cryo-EM is revolutionizing structural biology.","abstract":"For many years, structure determination of biological macromolecules by cryo-electron microscopy (cryo-EM) was limited to large complexes or low-resolution models. With recent advances in electron detection and image processing, the resolution by cryo-EM is now beginning to rival X-ray crystallography. A new generation of electron detectors record images with unprecedented quality, while new image-processing tools correct for sample movements and classify images according to different structural states. Combined, these advances yield density maps with sufficient detail to deduce the atomic structure for a range of specimens. Here, we review the recent advances and illustrate the exciting new opportunities that they offer to structural biology research.","corpus_id":19727349,"score":0},{"doc_id":"25839831","title":"SubspaceEM: A fast maximum-a-posteriori algorithm for cryo-EM single particle reconstruction.","abstract":"Single particle reconstruction methods based on the maximum-likelihood principle and the expectation-maximization (E-M) algorithm are popular because of their ability to produce high resolution structures. However, these algorithms are computationally very expensive, requiring a network of computational servers. To overcome this computational bottleneck, we propose a new mathematical framework for accelerating maximum-likelihood reconstructions. The speedup is by orders of magnitude and the proposed algorithm produces similar quality reconstructions compared to the standard maximum-likelihood formulation. Our approach uses subspace approximations of the cryo-electron microscopy (cryo-EM) data and projection images, greatly reducing the number of image transformations and comparisons that are computed. Experiments using simulated and actual cryo-EM data show that speedup in overall execution time compared to traditional maximum-likelihood reconstruction reaches factors of over 300.","corpus_id":17850477,"score":0},{"doc_id":"26094203","title":"A fast iterative convolution weighting approach for gridding-based direct Fourier three-dimensional reconstruction with correction for the contrast transfer function.","abstract":"We describe a fast and accurate method for the reconstruction of macromolecular complexes from a set of projections. Direct Fourier inversion (in which the Fourier Slice Theorem plays a central role) is a solution for dealing with this inverse problem. Unfortunately, the set of projections provides a non-equidistantly sampled version of the macromolecule Fourier transform in the single particle field (and, therefore, a direct Fourier inversion) may not be an optimal solution. In this paper, we introduce a gridding-based direct Fourier method for the three-dimensional reconstruction approach that uses a weighting technique to compute a uniform sampled Fourier transform. Moreover, the contrast transfer function of the microscope, which is a limiting factor in pursuing a high resolution reconstruction, is corrected by the algorithm. Parallelization of this algorithm, both on threads and on multiple CPU's, makes the process of three-dimensional reconstruction even faster. The experimental results show that our proposed gridding-based direct Fourier reconstruction is slightly more accurate than similar existing methods and presents a lower computational complexity both in terms of time and memory, thereby allowing its use on larger volumes. The algorithm is fully implemented in the open-source Xmipp package and is downloadable from http://xmipp.cnb.csic.es.","corpus_id":205524467,"score":0},{"doc_id":"26705325","title":"Principles of cryo-EM single-particle image processing.","abstract":"Single-particle reconstruction is the process by which 3D density maps are obtained from a set of low-dose cryo-EM images of individual macromolecules. This review considers the fundamental principles of this process and the steps in the overall workflow for single-particle image processing. Also considered are the limits that image signal-to-noise ratio places on resolution and the distinguishing of heterogeneous particle populations.","corpus_id":21949411,"score":0},{"doc_id":"27215953","title":"Skin lesion image segmentation using Delaunay Triangulation for melanoma detection.","abstract":"Developing automatic diagnostic tools for the early detection of skin cancer lesions in dermoscopic images can help to reduce melanoma-induced mortality. Image segmentation is a key step in the automated skin lesion diagnosis pipeline. In this paper, a fast and fully-automatic algorithm for skin lesion segmentation in dermoscopic images is presented. Delaunay Triangulation is used to extract a binary mask of the lesion region, without the need of any training stage. A quantitative experimental evaluation has been conducted on a publicly available database, by taking into account six well-known state-of-the-art segmentation methods for comparison. The results of the experimental analysis demonstrate that the proposed approach is highly accurate when dealing with benign lesions, while the segmentation accuracy significantly decreases when melanoma images are processed. This behavior led us to consider geometrical and color features extracted from the binary masks generated by our algorithm for classification, achieving promising results for melanoma detection.","corpus_id":4861162,"score":0},{"doc_id":"27353419","title":"A new approach for categorizing pig lying behaviour based on a Delaunay triangulation method.","abstract":"Machine vision-based monitoring of pig lying behaviour is a fast and non-intrusive approach that could be used to improve animal health and welfare. Four pens with 22 pigs in each were selected at a commercial pig farm and monitored for 15 days using top view cameras. Three thermal categories were selected relative to room setpoint temperature. An image processing technique based on Delaunay triangulation (DT) was utilized. Different lying patterns (close, normal and far) were defined regarding the perimeter of each DT triangle and the percentages of each lying pattern were obtained in each thermal category. A method using a multilayer perceptron (MLP) neural network, to automatically classify group lying behaviour of pigs into three thermal categories, was developed and tested for its feasibility. The DT features (mean value of perimeters, maximum and minimum length of sides of triangles) were calculated as inputs for the MLP classifier. The network was trained, validated and tested and the results revealed that MLP could classify lying features into the three thermal categories with high overall accuracy (95.6%). The technique indicates that a combination of image processing, MLP classification and mathematical modelling can be used as a precise method for quantifying pig lying behaviour in welfare investigations.","corpus_id":52833710,"score":0},{"doc_id":"27424268","title":"DeepPicker: A deep learning approach for fully automated particle picking in cryo-EM.","abstract":"Particle picking is a time-consuming step in single-particle analysis and often requires significant interventions from users, which has become a bottleneck for future automated electron cryo-microscopy (cryo-EM). Here we report a deep learning framework, called DeepPicker, to address this problem and fill the current gaps toward a fully automated cryo-EM pipeline. DeepPicker employs a novel cross-molecule training strategy to capture common features of particles from previously-analyzed micrographs, and thus does not require any human intervention during particle picking. Tests on the recently-published cryo-EM data of three complexes have demonstrated that our deep learning based scheme can successfully accomplish the human-level particle picking process and identify a sufficient number of particles that are comparable to those picked manually by human experts. These results indicate that DeepPicker can provide a practically useful tool to significantly reduce the time and manual effort spent in single-particle analysis and thus greatly facilitate high-resolution cryo-EM structure determination. DeepPicker is released as an open-source program, which can be downloaded from https://github.com/nejyeah/DeepPicker-python.","corpus_id":3908505,"score":0},{"doc_id":"27716029","title":"Simulating cryo electron tomograms of crowded cell cytoplasm for assessment of automated particle picking.","abstract":"BACKGROUND: Cryo-electron tomography is an important tool to study structures of macromolecular complexes in close to native states. A whole cell cryo electron tomogram contains structural information of all its macromolecular complexes. However, extracting this information remains challenging, and relies on sophisticated image processing, in particular for template-free particle extraction, classification and averaging. To develop these methods it is crucial to realistically simulate tomograms of crowded cellular environments, which can then serve as ground truth models for assessing and optimizing methods for detection of complexes in cell tomograms. RESULTS: We present a framework to generate crowded mixtures of macromolecular complexes for realistically simulating cryo electron tomograms including noise and image distortions due to the missing-wedge effects. Simulated tomograms are then used for assessing the template-free Difference-of-Gaussian (DoG) particle-picking method to detect complexes of different shapes and sizes under various crowding and noise levels. We identified DoG parameter settings that maximize precision and recall for detecting particles over a wide range of sizes and shapes. We observed that medium sized DoG scaling factors showed the overall best performance. To further improve performance, we propose a combination strategy for integrating results from multiple parameter settings. With increasing macromolecular crowding levels, the precision of particle picking remained relatively high, while the recall was dramatically reduced, which limits the detection of sufficient copy numbers of complexes in a crowded environment. Over a wide range of increasing noise levels, the DoG particle picking performance remained stable, but dramatically reduced beyond a specific noise threshold. CONCLUSIONS: Automatic and reference-free particle picking is an important first step in a visual proteomics analysis of cell tomograms. However, cell cytoplasm is highly crowded, which makes particle detection challenging. It is therefore important to test particle-picking methods in a realistic crowded setting. Here, we present a framework for simulating tomograms of cellular environments at high crowding levels and assess the DoG particle picking method. We determined optimal parameter settings to maximize the performance of the DoG particle-picking method.","corpus_id":704700,"score":0},{"doc_id":"28343096","title":"SD-SEM: sparse-dense correspondence for 3D reconstruction of microscopic samples.","abstract":"Scanning electron microscopy (SEM) imaging has been a principal component of many studies in biomedical, mechanical, and materials sciences since its emergence. Despite the high resolution of captured images, they remain two-dimensional (2D). In this work, a novel framework using sparse-dense correspondence is introduced and investigated for 3D reconstruction of stereo SEM images. SEM micrographs from microscopic samples are captured by tilting the specimen stage by a known angle. The pair of SEM micrographs is then rectified using sparse scale invariant feature transform (SIFT) features/descriptors and a contrario RANSAC for matching outlier removal to ensure a gross horizontal displacement between corresponding points. This is followed by dense correspondence estimation using dense SIFT descriptors and employing a factor graph representation of the energy minimization functional and loopy belief propagation (LBP) as means of optimization. Given the pixel-by-pixel correspondence and the tilt angle of the specimen stage during the acquisition of micrographs, depth can be recovered. Extensive tests reveal the strength of the proposed method for high-quality reconstruction of microscopic samples.","corpus_id":31788671,"score":0},{"doc_id":"28368809","title":"A Two-Phase Improved Correlation Method for Automatic Particle Selection in Cryo-EM.","abstract":"Particle selection from cryo-electron microscopy (Cryo-EM) images is very important for high-resolution reconstruction of macromolecular structure. The methods of particle selection can be roughly grouped into two classes, template-matching methods and feature-based methods. In general, template-matching methods usually generate better results than feature-based methods. However, the accuracy of template-matching methods is restricted by the noise and low contrast of Cryo-EM images. Moreover, the processing speed of template-matching methods, restricted by the random orientation of particles, further limits their practical applications. In this paper, combining the advantages of feature-based methods and template-matching methods, we present a two-phase improved correlation method for automatic, fast particle selection. In Phase I, we generate a preliminary particle set using rotation-invariant features of particles. In Phase II, we filter the preliminary particle set using a correlation method to reduce the interference of the high noise background and improve the precision of particle selection. We apply several optimization strategies, including a modified adaboost algorithm, Divide and Conquer technique, cascade strategy and graphics processing unit parallel technique, to improve feature recognition ability and reduce processing time. In addition, we developed two correlation score functions for different correlation situations. Experimental results on the benchmark of Cryo-EM images show that our method can improve the accuracy and processing speed of particle selection significantly.","corpus_id":9195465,"score":0},{"doc_id":"28732461","title":"A deep convolutional neural network approach to single-particle recognition in cryo-electron microscopy.","abstract":"BACKGROUND: Single-particle cryo-electron microscopy (cryo-EM) has become a mainstream tool for the structural determination of biological macromolecular complexes. However, high-resolution cryo-EM reconstruction often requires hundreds of thousands of single-particle images. Particle extraction from experimental micrographs thus can be laborious and presents a major practical bottleneck in cryo-EM structural determination. Existing computational methods for particle picking often use low-resolution templates for particle matching, making them susceptible to reference-dependent bias. It is critical to develop a highly efficient template-free method for the automatic recognition of particle images from cryo-EM micrographs. RESULTS: We developed a deep learning-based algorithmic framework, DeepEM, for single-particle recognition from noisy cryo-EM micrographs, enabling automated particle picking, selection and verification in an integrated fashion. The kernel of DeepEM is built upon a convolutional neural network (CNN) composed of eight layers, which can be recursively trained to be highly \"knowledgeable\". Our approach exhibits an improved performance and accuracy when tested on the standard KLH dataset. Application of DeepEM to several challenging experimental cryo-EM datasets demonstrated its ability to avoid the selection of un-wanted particles and non-particles even when true particles contain fewer features. CONCLUSIONS: The DeepEM methodology, derived from a deep CNN, allows automated particle extraction from raw cryo-EM micrographs in the absence of a template. It demonstrates an improved performance, objectivity and accuracy. Application of this novel method is expected to free the labor involved in single-particle verification, significantly improving the efficiency of cryo-EM data processing.","corpus_id":9763578,"score":0},{"doc_id":"29486249","title":"Exploring applications of crowdsourcing to cryo-EM.","abstract":"Extraction of particles from cryo-electron microscopy (cryo-EM) micrographs is a crucial step in processing single-particle datasets. Although algorithms have been developed for automatic particle picking, these algorithms generally rely on two-dimensional templates for particle identification, which may exhibit biases that can propagate artifacts through the reconstruction pipeline. Manual picking is viewed as a gold-standard solution for particle selection, but it is too time-consuming to perform on data sets of thousands of images. In recent years, crowdsourcing has proven effective at leveraging the open web to manually curate datasets. In particular, citizen science projects such as Galaxy Zoo have shown the power of appealing to users' scientific interests to process enormous amounts of data. To this end, we explored the possible applications of crowdsourcing in cryo-EM particle picking, presenting a variety of novel experiments including the production of a fully annotated particle set from untrained citizen scientists. We show the possibilities and limitations of crowdsourcing particle selection tasks, and explore further options for crowdsourcing cryo-EM data processing.","corpus_id":3749368,"score":0}],"string":"[\n {\n \"doc_id\": \"18272396\",\n \"title\": \"Angle determination for side views in single particle electron microscopy.\",\n \"abstract\": \"In order to build a first model in single particle electron microscopy the relative angular orientation of each image of a protein complex must be determined. These orientations can be described by three Eulerian angles. Images of complexes that present the same view can be aligned in two-dimensions and averaged in order to increase their signal-to-noise ratio. Based on these averaged images, several standard approaches exist for determining Euler angles for randomly oriented projection images. The common lines and angular reconstitution methods work well for particles with symmetry while the random conical tilting and related orthogonal tilt reconstruction methods work in most cases but require the acquisition of tilt pairs of images. For the situation where views of particles can be identified that are rotations about a single axis parallel to the grid, an alternative algorithm to determine the orientations of class averages without the need to acquire tilt pairs can be applied. This type of view of a complex is usually called a side view. This paper describes the detailed workings and characterization of an algorithm, named rotational analysis, which uses real-space fiducial markers derived from the averages themselves to determine the Euler angles for side views. We demonstrate how this algorithm works in practice by applying it to a data set of images of affinity-purified bovine mitochondrial ATP synthase.\",\n \"corpus_id\": 25712277,\n \"score\": 2\n },\n {\n \"doc_id\": \"20888964\",\n \"title\": \"The orthogonal tilt reconstruction method.\",\n \"abstract\": \"Generating reliable initial models for novel asymmetric molecules, particularly heterogeneous ones, remains a major challenge in cryo-electron microscopy. Geometric reconstruction methods, relying on the ability to tilt the microscope stage to obtain two or more views of each molecule, are arguably the most robust for these types of samples as they generate independent reconstructions for each characteristic view obtained. Random Conical Tilt (RCT) is the classic geometric reconstruction method. Pairs of images are collected at high tilt (around 50°) and 0°. The latter are used to sort the data into characteristic views of the molecule and the former are used for their reconstruction. RCT's greatest strength is its ability to generate structures regardless of the number of orientations adopted by the sample on the support. Its major drawback stems from the limited tilt of the microscope stage; this results in an incomplete sampling of the structure in Fourier space and artifacts in its real space representation. Orthogonal Tilt Reconstruction (OTR), a modification of this data collection strategy, results in fully sampled structures. It relies on collecting data at -45° and +45° and treating the tilt pairs as equivalent to the ideal 0°/90° that cannot be collected directly in the microscope. OTR requires a sample that adopts a large number of orientations on the support. Here, the RCT and OTR methods are reviewed and their performances with a biological test sample are compared. The steps required to apply OTR are also discussed.\",\n \"corpus_id\": 25782305,\n \"score\": 2\n },\n {\n \"doc_id\": \"21536134\",\n \"title\": \"Validation of the orthogonal tilt reconstruction method with a biological test sample.\",\n \"abstract\": \"Electron microscopy of frozen-hydrated samples (cryo-EM) can yield high resolution structures of macromolecular complexes by accurately determining the orientation of large numbers of experimental views of the sample relative to an existing 3D model. The \\\"initial model problem\\\", the challenge of obtaining these orientations ab initio, remains a major bottleneck in determining the structure of novel macromolecules, chiefly those lacking internal symmetry. We previously proposed a method for the generation of initial models--orthogonal tilt reconstruction (OTR)--that bypasses limitations inherent to the other two existing methods, random conical tilt (RCT) and angular reconstitution (AR). Here we present a validation of OTR with a biological test sample whose structure was previously solved by RCT: the complex between the yeast exosome and the subunit Rrp44. We show that, as originally demonstrated with synthetic data, OTR generates initial models that do not exhibit the \\\"missing cone\\\" artifacts associated with RCT and show an isotropic distribution of information when compared with the known structure. This eliminates the need for further user intervention to solve these artifacts and makes OTR ideal for automation and the analysis of heterogeneous samples. With the former in mind, we propose a set of simple quantitative criteria that can be used, in combination, to select from a large set of initial reconstructions a subset that can be used as reliable references for refinement to higher resolution.\",\n \"corpus_id\": 24370377,\n \"score\": 2\n },\n {\n \"doc_id\": \"21939668\",\n \"title\": \"Tilt-pair analysis of images from a range of different specimens in single-particle electron cryomicroscopy.\",\n \"abstract\": \"The comparison of a pair of electron microscope images recorded at different specimen tilt angles provides a powerful approach for evaluating the quality of images, image-processing procedures, or three-dimensional structures. Here, we analyze tilt-pair images recorded from a range of specimens with different symmetries and molecular masses and show how the analysis can produce valuable information not easily obtained otherwise. We show that the accuracy of orientation determination of individual single particles depends on molecular mass, as expected theoretically since the information in each particle image increases with molecular mass. The angular uncertainty is less than 1° for particles of high molecular mass (~50 MDa), several degrees for particles in the range 1-5 MDa, and tens of degrees for particles below 1 MDa. Orientational uncertainty may be the major contributor to the effective temperature factor (B-factor) describing contrast loss and therefore the maximum resolution of a structure determination. We also made two unexpected observations. Single particles that are known to be flexible showed a wider spread in orientation accuracy, and the orientations of the largest particles examined changed by several degrees during typical low-dose exposures. Smaller particles presumably also reorient during the exposure; hence, specimen movement is a second major factor that limits resolution. Tilt pairs thus enable assessment of orientation accuracy, map quality, specimen motion, and conformational heterogeneity. A convincing tilt-pair parameter plot, where 60% of the particles show a single cluster around the expected tilt axis and tilt angle, provides confidence in a structure determined using electron cryomicroscopy.\",\n \"corpus_id\": 25176486,\n \"score\": 2\n },\n {\n \"doc_id\": \"23142631\",\n \"title\": \"Automated correlation of single particle tilt pairs for Random Conical Tilt and Orthogonal Tilt Reconstructions.\",\n \"abstract\": \"One of the major methodological challenges in single particle electron microscopy is obtaining initial reconstructions which represent the structural heterogeneity of the dataset. Random Conical Tilt and Orthogonal Tilt Reconstruction techniques in combination with 3D alignment and classification can be used to obtain initial low-resolution reconstructions which represent the full range of structural heterogeneity of the dataset. In order to achieve statistical significance, however, a large number of 3D reconstructions, and, in turn, a large number of tilted image pairs are required. The extraction of single particle tilted image pairs from micrographs can be tedious and time-consuming, as it requires intensive user input even for semi-automated approaches. To overcome the bottleneck of manual selection of a large number of tilt pairs, we developed an algorithm for the correlation of single particle images from tilted image pairs in a fully automated and user-independent manner. The algorithm reliably correlates correct pairs even from noisy micrographs. We further demonstrate the applicability of the algorithm by using it to obtain initial references both from negative stain and unstained cryo datasets.\",\n \"corpus_id\": 32528253,\n \"score\": 2\n },\n {\n \"doc_id\": \"24582855\",\n \"title\": \"Web server for tilt-pair validation of single particle maps from electron cryomicroscopy.\",\n \"abstract\": \"Three-dimensional structures of biological assemblies may be calculated from images of single particles obtained by electron cryomicroscopy. A key step is the correct determination of the orientation of the particle in individual image projections. A useful tool for validation of the quality of a 3D map and its consistency with images is tilt-pair analysis. In a successful tilt-pair test, the relative angle between orientations assigned to each image of a tilt-pair agrees with the known relative rotation angle of the microscope specimen holder during the experiment. To make the procedure easy to apply to the increasing number of single particle maps, we have developed software and a web server for tilt-pair analysis. The tilt-pair analysis program reports the overall agreement of the assigned orientations with the known tilt angle and axis of the experiment and the distribution of tilt transformations for individual particles recorded in a single image field. We illustrate application of the validation tool to several single particle specimens and describe how to interpret the scores.\",\n \"corpus_id\": 30520891,\n \"score\": 2\n },\n {\n \"doc_id\": \"24694675\",\n \"title\": \"Automated particle correspondence and accurate tilt-axis detection in tilted-image pairs.\",\n \"abstract\": \"Tilted electron microscope images are routinely collected for an ab initio structure reconstruction as a part of the Random Conical Tilt (RCT) or Orthogonal Tilt Reconstruction (OTR) methods, as well as for various applications using the \\\"free-hand\\\" procedure. These procedures all require identification of particle pairs in two corresponding images as well as accurate estimation of the tilt-axis used to rotate the electron microscope (EM) grid. Here we present a computational approach, PCT (particle correspondence from tilted pairs), based on tilt-invariant context and projection matching that addresses both problems. The method benefits from treating the two problems as a single optimization task. It automatically finds corresponding particle pairs and accurately computes tilt-axis direction even in the cases when EM grid is not perfectly planar.\",\n \"corpus_id\": 8635565,\n \"score\": 2\n },\n {\n \"doc_id\": \"24734998\",\n \"title\": \"Extending particle tracking capability with Delaunay triangulation.\",\n \"abstract\": \"Particle tracking, the analysis of individual moving elements in time series of microscopic images, enables burgeoning new applications, but there is need to better resolve conformation and dynamics. Here we describe the advantages of Delaunay triangulation to extend the capabilities of particle tracking in three areas: (1) discriminating irregularly shaped objects, which allows one to track items other than point features; (2) combining time and space to better connect missing frames in trajectories; and (3) identifying shape backbone. To demonstrate the method, specific examples are given, involving analyzing the time-dependent molecular conformations of actin filaments and λ-DNA. The main limitation of this method, shared by all other clustering techniques, is the difficulty to separate objects when they are very close. This can be mitigated by inspecting locally to remove edges that are longer than their neighbors and also edges that link two objects, using methods described here, so that the combination of Delaunay triangulation with edge removal can be robustly applied to processing large data sets. As common software packages, both commercial and open source, can construct Delaunay triangulation on command, the methods described in this paper are both computationally efficient and easy to implement.\",\n \"corpus_id\": 13335348,\n \"score\": 2\n },\n {\n \"doc_id\": \"24815505\",\n \"title\": \"Alternative automatic alignment method for specimen tilt-series images based on back-projected volume data cross-correlations.\",\n \"abstract\": \"We devised a new automatic image alignment method for a specimen tilt series; this method is based on the volume data cross-correlation among 3-D cross-sections reconstructed from different sets of projection images (including a single image) for tilt-series alignment or tilt-axis search purposes. This method requires neither markers nor image feature points traceable through the tilt series, and it was examined through simulations and applied to biological thin sections. The method automatically aligned tilt series centred at the correctly detected tilt axis with a precision sufficient for practical applications.\",\n \"corpus_id\": 5516936,\n \"score\": 2\n },\n {\n \"doc_id\": \"25016098\",\n \"title\": \"Robust evaluation of 3D electron cryomicroscopy data using tilt-pairs.\",\n \"abstract\": \"Determining the structure of a protein complex using electron microscopy requires the calculation of a 3D density map from 2D images of single particles. Since the individual images are taken at low electron dose to avoid radiation damage, they are noisy and difficult to align with each other. This can result in incorrect maps, making validation essential. Pairs of electron micrographs taken at known angles to each other (tilt-pairs) can be used to measure the accuracy of assigned projection orientations and verify the soundness of calculated maps. Here we establish a statistical framework for evaluating images and density maps using tilt-pairs. The directional distribution of such angular data is modelled using a Fisher distribution on the unit sphere. This provides a simple, quantitative and easily comparable metric, the concentration parameter κ, for evaluating the quality of datasets and density maps that is independent of the data collection and analysis methods. A large κ is indicative of good agreement between the particle images and the 3D density map. For structure validation, we recommend κ>10 and a p-value <0.01. The statistical framework herein allows one to objectively answer the question: Is a reconstructed density map correct within a particular confidence interval?\",\n \"corpus_id\": 9196955,\n \"score\": 2\n },\n {\n \"doc_id\": \"25654984\",\n \"title\": \"A tilt-pair based method for assigning the projection directions of randomly oriented single-particle molecules.\",\n \"abstract\": \"In this article, we describe an improved method to assign the projection angle for averaged images using tilt-pair images for three-dimensional reconstructions from randomly oriented single-particle molecular images. Our study addressed the so-called 'initial volume problem' in the single-particle reconstruction, which involves estimation of projection angles of the particle images. The projected images of the particles in different tilt observations were mixed and averaged for the characteristic views. After the ranking of these group average images in terms of reliable tilt angle information, mutual tilt angles between images are assigned from the constituent tilt-pair information. Then, multiples of the conical tilt series are made and merged to construct a network graph of the particle images in terms of projection angles, which are optimized for the three-dimensional reconstruction. We developed the method with images of a synthetic object and applied it to a single-particle image data set of the purified deacetylase from archaea. With the introduction of low-angle tilt observations to minimize unfavorable imaging conditions due to tilting, the results demonstrated reasonable reconstruction models without imposing symmetry to the structure. This method also guides its users to discriminate particle images of different conformational state of the molecule.\",\n \"corpus_id\": 22112573,\n \"score\": 2\n },\n {\n \"doc_id\": \"26390853\",\n \"title\": \"Cryo-EM and the elucidation of new macromolecular structures: Random Conical Tilt revisited.\",\n \"abstract\": \"Cryo-Electron Microscopy (cryo-EM) of macromolecular complexes is a fundamental structural biology technique which is expanding at a very fast pace. Key to its success in elucidating the three-dimensional structure of a macromolecular complex, especially of small and non-symmetric ones, is the ability to start from a low resolution map, which is subsequently refined with the actual images collected at the microscope. There are several methods to produce this first structure. Among them, Random Conical Tilt (RCT) plays a prominent role due to its unbiased nature (it can create an initial model based on experimental measurements). In this article, we revise the fundamental mathematical expressions supporting RCT, providing new expressions handling all key geometrical parameters without the need of intermediate operations, leading to improved automation and overall reliability, essential for the success of cryo-EM when analyzing new complexes. We show that the here proposed RCT workflow based on the new formulation performs very well in practical cases, requiring very few image pairs (as low as 13 image pairs in one of our examples) to obtain relevant 3D maps.\",\n \"corpus_id\": 13916472,\n \"score\": 2\n },\n {\n \"doc_id\": \"26433028\",\n \"title\": \"A novel fully automatic scheme for fiducial marker-based alignment in electron tomography.\",\n \"abstract\": \"Although the topic of fiducial marker-based alignment in electron tomography (ET) has been widely discussed for decades, alignment without human intervention remains a difficult problem. Specifically, the emergence of subtomogram averaging has increased the demand for batch processing during tomographic reconstruction; fully automatic fiducial marker-based alignment is the main technique in this process. However, the lack of an accurate method for detecting and tracking fiducial markers precludes fully automatic alignment. In this paper, we present a novel, fully automatic alignment scheme for ET. Our scheme has two main contributions: First, we present a series of algorithms to ensure a high recognition rate and precise localization during the detection of fiducial markers. Our proposed solution reduces fiducial marker detection to a sampling and classification problem and further introduces an algorithm to solve the parameter dependence of marker diameter and marker number. Second, we propose a novel algorithm to solve the tracking of fiducial markers by reducing the tracking problem to an incomplete point set registration problem. Because a global optimization of a point set registration occurs, the result of our tracking is independent of the initial image position in the tilt series, allowing for the robust tracking of fiducial markers without pre-alignment. The experimental results indicate that our method can achieve an accurate tracking, almost identical to the current best one in IMOD with half automatic scheme. Furthermore, our scheme is fully automatic, depends on fewer parameters (only requires a gross value of the marker diameter) and does not require any manual interaction, providing the possibility of automatic batch processing of electron tomographic reconstruction.\",\n \"corpus_id\": 3986209,\n \"score\": 2\n },\n {\n \"doc_id\": \"17855124\",\n \"title\": \"Markov random field based automatic image alignment for electron tomography.\",\n \"abstract\": \"We present a method for automatic full-precision alignment of the images in a tomographic tilt series. Full-precision automatic alignment of cryo electron microscopy images has remained a difficult challenge to date, due to the limited electron dose and low image contrast. These facts lead to poor signal to noise ratio (SNR) in the images, which causes automatic feature trackers to generate errors, even with high contrast gold particles as fiducial features. To enable fully automatic alignment for full-precision reconstructions, we frame the problem probabilistically as finding the most likely particle tracks given a set of noisy images, using contextual information to make the solution more robust to the noise in each image. To solve this maximum likelihood problem, we use Markov Random Fields (MRF) to establish the correspondence of features in alignment and robust optimization for projection model estimation. The resulting algorithm, called Robust Alignment and Projection Estimation for Tomographic Reconstruction, or RAPTOR, has not needed any manual intervention for the difficult datasets we have tried, and has provided sub-pixel alignment that is as good as the manual approach by an expert user. We are able to automatically map complete and partial marker trajectories and thus obtain highly accurate image alignment. Our method has been applied to challenging cryo electron tomographic datasets with low SNR from intact bacterial cells, as well as several plastic section and X-ray datasets.\",\n \"corpus_id\": 18525199,\n \"score\": 1\n },\n {\n \"doc_id\": \"18023735\",\n \"title\": \"Delaunay-Object-Dynamics: cell mechanics with a 3D kinetic and dynamic weighted Delaunay-triangulation.\",\n \"abstract\": \"Mathematical methods in Biology are of increasing relevance for understanding the control and the dynamics of biological systems with medical relevance. In particular, agent-based methods turn more and more important because of fast increasing computational power which makes even large systems accessible. An overview of different mathematical methods used in Theoretical Biology is provided and a novel agent-based method for cell mechanics based on Delaunay-triangulations and Voronoi-tessellations is explained in more detail: The Delaunay-Object-Dynamics method. It is claimed that the model combines physically realistic cell mechanics with a reasonable computational load. The power of the approach is illustrated with two examples, avascular tumor growth and genesis of lymphoid tissue in a cell-flow equilibrium.\",\n \"corpus_id\": 35441203,\n \"score\": 1\n },\n {\n \"doc_id\": \"19555764\",\n \"title\": \"Automatic particle selection from electron micrographs using machine learning techniques.\",\n \"abstract\": \"The 3D reconstruction of biological specimens using Electron Microscopy is currently capable of achieving subnanometer resolution. Unfortunately, this goal requires gathering tens of thousands of projection images that are frequently selected manually from micrographs. In this paper we introduce a new automatic particle selection that learns from the user which particles are of interest. The training phase is semi-supervised so that the user can correct the algorithm during picking and specifically identify incorrectly picked particles. By treating such errors specially, the algorithm attempts to minimize the number of false positives. We show that our algorithm is able to produce datasets with fewer wrongly selected particles than previously reported methods. Another advantage is that we avoid the need for an initial reference volume from which to generate picking projections by instead learning which particles to pick from the user. This package has been made publicly available in the open-source package Xmipp.\",\n \"corpus_id\": 11037812,\n \"score\": 1\n },\n {\n \"doc_id\": \"23144522\",\n \"title\": \"Quality Tetrahedral Mesh Smoothing via Boundary-Optimized Delaunay Triangulation.\",\n \"abstract\": \"Despite its great success in improving the quality of a tetrahedral mesh, the original optimal Delaunay triangulation (ODT) is designed to move only inner vertices and thus cannot handle input meshes containing \\\"bad\\\" triangles on boundaries. In the current work, we present an integrated approach called boundary-optimized Delaunay triangulation (B-ODT) to smooth (improve) a tetrahedral mesh. In our method, both inner and boundary vertices are repositioned by analytically minimizing the error between a paraboloid function and its piecewise linear interpolation over the neighborhood of each vertex. In addition to the guaranteed volume-preserving property, the proposed algorithm can be readily adapted to preserve sharp features in the original mesh. A number of experiments are included to demonstrate the performance of our method.\",\n \"corpus_id\": 1888384,\n \"score\": 1\n },\n {\n \"doc_id\": \"23454482\",\n \"title\": \"Automatic post-picking using MAPPOS improves particle image detection from cryo-EM micrographs.\",\n \"abstract\": \"Cryo-electron microscopy (cryo-EM) studies using single particle reconstruction are extensively used to reveal structural information on macromolecular complexes. Aiming at the highest achievable resolution, state of the art electron microscopes automatically acquire thousands of high-quality micrographs. Particles are detected on and boxed out from each micrograph using fully- or semi-automated approaches. However, the obtained particles still require laborious manual post-picking classification, which is one major bottleneck for single particle analysis of large datasets. We introduce MAPPOS, a supervised post-picking strategy for the classification of boxed particle images, as additional strategy adding to the already efficient automated particle picking routines. MAPPOS employs machine learning techniques to train a robust classifier from a small number of characteristic image features. In order to accurately quantify the performance of MAPPOS we used simulated particle and non-particle images. In addition, we verified our method by applying it to an experimental cryo-EM dataset and comparing the results to the manual classification of the same dataset. Comparisons between MAPPOS and manual post-picking classification by several human experts demonstrated that merely a few hundred sample images are sufficient for MAPPOS to classify an entire dataset with a human-like performance. MAPPOS was shown to greatly accelerate the throughput of large datasets by reducing the manual workload by orders of magnitude while maintaining a reliable identification of non-particle images.\",\n \"corpus_id\": 9789870,\n \"score\": 1\n },\n {\n \"doc_id\": \"23483043\",\n \"title\": \"Blocking Delaunay triangulations.\",\n \"abstract\": \"Given a set B of n black points in general position, we say that a set of white points W blocks B if in the Delaunay triangulation of [Formula: see text] there is no edge connecting two black points. We give the following bounds for the size of the smallest set W blocking B: (i) [Formula: see text] white points are always sufficient to block a set of n black points, (ii) if B is in convex position, [Formula: see text] white points are always sufficient to block it, and (iii) at least [Formula: see text] white points are always necessary to block a set of n black points.\",\n \"corpus_id\": 263586149,\n \"score\": 1\n },\n {\n \"doc_id\": \"23492377\",\n \"title\": \"Computing 2D constrained delaunay triangulation using the GPU.\",\n \"abstract\": \"We propose the first graphics processing unit (GPU) solution to compute the 2D constrained Delaunay triangulation (CDT) of a planar straight line graph (PSLG) consisting of points and edges. There are many existing CPU algorithms to solve the CDT problem in computational geometry, yet there has been no prior approach to solve this problem efficiently using the parallel computing power of the GPU. For the special case of the CDT problem where the PSLG consists of just points, which is simply the normal Delaunay triangulation (DT) problem, a hybrid approach using the GPU together with the CPU to partially speed up the computation has already been presented in the literature. Our work, on the other hand, accelerates the entire computation on the GPU. Our implementation using the CUDA programming model on NVIDIA GPUs is numerically robust, and runs up to an order of magnitude faster than the best sequential implementations on the CPU. This result is reflected in our experiment with both randomly generated PSLGs and real-world GIS data having millions of points and edges.\",\n \"corpus_id\": 6289286,\n \"score\": 1\n },\n {\n \"doc_id\": \"23857566\",\n \"title\": \"Automatic particle detection in microscopy using temporal correlations.\",\n \"abstract\": \"One of the fundamental problems in the analysis of single particle tracking data is the detection of individual particle positions from microscopy images. Distinguishing true particles from noise with a minimum of false positives and false negatives is an important step that will have substantial impact on all further analysis of the data. A common approach is to obtain a plausible set of particles from a larger set of candidate particles by filtering using manually selected threshold values for intensity, size, shape, and other parameters describing a particle. This introduces subjectivity into the analysis and hinders reproducibility. In this paper, we introduce a method for automatic selection of these threshold values based on maximizing temporal correlations in particle count time series. We use Markov Chain Monte Carlo to find the threshold values corresponding to the maximum correlation, and we study several experimental data sets to assess the performance of the method in practice by comparing manually selected threshold values from several independent experts with automatically selected threshold values. We conclude that the method produces useful results, reducing subjectivity and the need for manual intervention, a great benefit being its easy integratability into many already existing particle detection algorithms.\",\n \"corpus_id\": 34973618,\n \"score\": 1\n },\n {\n \"doc_id\": \"23958728\",\n \"title\": \"A pattern matching approach to the automatic selection of particles from low-contrast electron micrographs.\",\n \"abstract\": \"MOTIVATION: Structural information of macromolecular complexes provides key insights into the way they carry out their biological functions. Achieving high-resolution structural details with electron microscopy requires the identification of a large number (up to hundreds of thousands) of single particles from electron micrographs, which is a laborious task if it has to be manually done and constitutes a hurdle towards high-throughput. Automatic particle selection in micrographs is far from being settled and new and more robust algorithms are required to reduce the number of false positives and false negatives. RESULTS: In this article, we introduce an automatic particle picker that learns from the user the kind of particles he is interested in. Particle candidates are quickly and robustly classified as particles or non-particles. A number of new discriminative shape-related features as well as some statistical description of the image grey intensities are used to train two support vector machine classifiers. Experimental results demonstrate that the proposed method: (i) has a considerably low computational complexity and (ii) provides results better or comparable with previously reported methods at a fraction of their computing time. AVAILABILITY: The algorithm is fully implemented in the open-source Xmipp package and downloadable from http://xmipp.cnb.csic.es.\",\n \"corpus_id\": 11199882,\n \"score\": 1\n },\n {\n \"doc_id\": \"24974203\",\n \"title\": \"Efficient initial volume determination from electron microscopy images of single particles.\",\n \"abstract\": \"MOTIVATION: Structural information of macromolecular complexes provides key insights into the way they carry out their biological functions. The reconstruction process leading to the final 3D map requires an approximate initial model. Generation of an initial model is still an open and challenging problem in single-particle analysis. RESULTS: We present a fast and efficient approach to obtain a reliable, low-resolution estimation of the 3D structure of a macromolecule, without any a priori knowledge, addressing the well-known issue of initial volume estimation in the field of single-particle analysis. The input of the algorithm is a set of class average images obtained from individual projections of a biological object at random and unknown orientations by transmission electron microscopy micrographs. The proposed method is based on an initial non-lineal dimensionality reduction approach, which allows to automatically selecting representative small sets of class average images capturing the most of the structural information of the particle under study. These reduced sets are then used to generate volumes from random orientation assignments. The best volume is determined from these guesses using a random sample consensus (RANSAC) approach. We have tested our proposed algorithm, which we will term 3D-RANSAC, with simulated and experimental data, obtaining satisfactory results under the low signal-to-noise conditions typical of cryo-electron microscopy. AVAILABILITY: The algorithm is freely available as part of the Xmipp 3.1 package [http://xmipp.cnb.csic.es]. CONTACT: jvargas@cnb.csic.es SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.\",\n \"corpus_id\": 8183036,\n \"score\": 1\n },\n {\n \"doc_id\": \"26193484\",\n \"title\": \"A Bayesian approach for suppression of limited angular sampling artifacts in single particle 3D reconstruction.\",\n \"abstract\": \"In the single particle reconstruction, the initial 3D structure often suffers from the limited angular sampling artifact. Selecting 2D class averages of particle images generally improves the accuracy and efficiency of the reference-free 3D angle estimation, but causes an insufficient angular sampling to fill the information of the target object in the 3D frequency space. Similarly, the initial 3D structure by the random-conical tilt reconstruction has the well-known \\\"missing cone\\\" artifact. Here, we attempted to solve the limited angular sampling problem by sequentially applying maximum a posteriori estimate with expectation maximization algorithm (sMAP-EM). Using both simulated and experimental cryo-electron microscope images, the sMAP-EM was compared to the direct Fourier method on the basis of reconstruction error and resolution. To establish selection criteria of the final regularization weight for the sMAP-EM, the effects of noise level and sampling sparseness on the reconstructions were examined with evenly distributed sampling simulations. The frequency information filled in the missing cone of the conical tilt sampling simulations was assessed by developing new quantitative measurements. All the results of visual and numerical evaluations showed the sMAP-EM performed better than the direct Fourier method, regardless of the sampling method, noise level, and sampling sparseness. Furthermore, the frequency domain analysis demonstrated that the sMAP-EM can fill the meaningful information in the unmeasured angular space without detailed a priori knowledge of the objects. The current research demonstrated that the sMAP-EM has a high potential to facilitate the determination of 3D protein structures at near atomic-resolution.\",\n \"corpus_id\": 23990990,\n \"score\": 1\n },\n {\n \"doc_id\": \"26433027\",\n \"title\": \"Simultaneous determination of sample thickness, tilt, and electron mean free path using tomographic tilt images based on Beer-Lambert law.\",\n \"abstract\": \"Cryo-electron tomography (cryo-ET) is an emerging technique that can elucidate the architecture of macromolecular complexes and cellular ultrastructure in a near-native state. Some important sample parameters, such as thickness and tilt, are needed for 3-D reconstruction. However, these parameters can currently only be determined using trial 3-D reconstructions. Accurate electron mean free path plays a significant role in modeling image formation process essential for simulation of electron microscopy images and model-based iterative 3-D reconstruction methods; however, their values are voltage and sample dependent and have only been experimentally measured for a limited number of sample conditions. Here, we report a computational method, tomoThickness, based on the Beer-Lambert law, to simultaneously determine the sample thickness, tilt and electron inelastic mean free path by solving an overdetermined nonlinear least square optimization problem utilizing the strong constraints of tilt relationships. The method has been extensively tested with both stained and cryo datasets. The fitted electron mean free paths are consistent with reported experimental measurements. The accurate thickness estimation eliminates the need for a generous assignment of Z-dimension size of the tomogram. Interestingly, we have also found that nearly all samples are a few degrees tilted relative to the electron beam. Compensation of the intrinsic sample tilt can result in horizontal structure and reduced Z-dimension of tomograms. Our fast, pre-reconstruction method can thus provide important sample parameters that can help improve performance of tomographic reconstruction of a wide range of samples.\",\n \"corpus_id\": 39148235,\n \"score\": 1\n },\n {\n \"doc_id\": \"26931650\",\n \"title\": \"High resolution single particle refinement in EMAN2.1.\",\n \"abstract\": \"EMAN2.1 is a complete image processing suite for quantitative analysis of grayscale images, with a primary focus on transmission electron microscopy, with complete workflows for performing high resolution single particle reconstruction, 2-D and 3-D heterogeneity analysis, random conical tilt reconstruction and subtomogram averaging, among other tasks. In this manuscript we provide the first detailed description of the high resolution single particle analysis pipeline and the philosophy behind its approach to the reconstruction problem. High resolution refinement is a fully automated process, and involves an advanced set of heuristics to select optimal algorithms for each specific refinement task. A gold standard FSC is produced automatically as part of refinement, providing a robust resolution estimate for the final map, and this is used to optimally filter the final CTF phase and amplitude corrected structure. Additional methods are in-place to reduce model bias during refinement, and to permit cross-validation using other computational methods.\",\n \"corpus_id\": 3553550,\n \"score\": 1\n },\n {\n \"doc_id\": \"27313000\",\n \"title\": \"Implementation of a cryo-electron tomography tilt-scheme optimized for high resolution subtomogram averaging.\",\n \"abstract\": \"Cryo-electron tomography (cryoET) allows 3D structural information to be obtained from cells and other biological samples in their close-to-native state. In combination with subtomogram averaging, detailed structures of repeating features can be resolved. CryoET data is collected as a series of images of the sample from different tilt angles; this is performed by physically rotating the sample in the microscope between each image. The angles at which the images are collected, and the order in which they are collected, together are called the tilt-scheme. Here we describe a \\\"dose-symmetric tilt-scheme\\\" that begins at low tilt and then alternates between increasingly positive and negative tilts. This tilt-scheme maximizes the amount of high-resolution information maintained in the tomogram for subsequent subtomogram averaging, and may also be advantageous for other applications. We describe implementation of the tilt-scheme in combination with further data-collection refinements including setting thresholds on acceptable drift and improving focus accuracy. Requirements for microscope set-up are introduced, and a macro is provided which automates the application of the tilt-scheme within SerialEM.\",\n \"corpus_id\": 3910770,\n \"score\": 1\n },\n {\n \"doc_id\": \"18784030\",\n \"title\": \"Noniterative interpolation-based super-resolution minimizing aliasing in the reconstructed image.\",\n \"abstract\": \"Super-resolution (SR) techniques produce a high-resolution image from a set of low-resolution undersampled images. In this paper, we propose a new method for super-resolution that uses sampling theory concepts to derive a noniterative SR algorithm. We first raise the issue of the validity of the data model usually assumed in SR, pointing out that it imposes a band-limited reconstructed image plus a certain type of noise. We propose a sampling theory framework with a prefiltering step that allows us to work with more general data models and also a specific new method for SR that uses Delaunay triangulation and B-splines to build the super-resolved image. The proposed method is noniterative and well posed. We prove its effectiveness against traditional iterative and noniterative SR methods on synthetic and real data. Additionally, we also prove that we can first solve the interpolation problem and then make the deblurring not only when the motion is translational but also when there are rotations and shifts and the imaging system Point Spread Function (PSF) is rotationally symmetric.\",\n \"corpus_id\": 14215955,\n \"score\": 0\n },\n {\n \"doc_id\": \"18817555\",\n \"title\": \"Abbreviation definition identification based on automatic precision estimates.\",\n \"abstract\": \"BACKGROUND: The rapid growth of biomedical literature presents challenges for automatic text processing, and one of the challenges is abbreviation identification. The presence of unrecognized abbreviations in text hinders indexing algorithms and adversely affects information retrieval and extraction. Automatic abbreviation definition identification can help resolve these issues. However, abbreviations and their definitions identified by an automatic process are of uncertain validity. Due to the size of databases such as MEDLINE only a small fraction of abbreviation-definition pairs can be examined manually. An automatic way to estimate the accuracy of abbreviation-definition pairs extracted from text is needed. In this paper we propose an abbreviation definition identification algorithm that employs a variety of strategies to identify the most probable abbreviation definition. In addition our algorithm produces an accuracy estimate, pseudo-precision, for each strategy without using a human-judged gold standard. The pseudo-precisions determine the order in which the algorithm applies the strategies in seeking to identify the definition of an abbreviation. RESULTS: On the Medstract corpus our algorithm produced 97% precision and 85% recall which is higher than previously reported results. We also annotated 1250 randomly selected MEDLINE records as a gold standard. On this set we achieved 96.5% precision and 83.2% recall. This compares favourably with the well known Schwartz and Hearst algorithm. CONCLUSION: We developed an algorithm for abbreviation identification that uses a variety of strategies to identify the most probable definition for an abbreviation and also produces an estimated accuracy of the result. This process is purely automatic.\",\n \"corpus_id\": 4401810,\n \"score\": 0\n },\n {\n \"doc_id\": \"19163065\",\n \"title\": \"Automatic chromosome pairing using mutual information.\",\n \"abstract\": \"Cytogenetics is a key tool in the detection of acquired chromosomal abnormalities and in the diagnosis of genetic diseases such as leukemia. The karyotyping is a set of procedures, in the scope of the cytogenetics, that produces a visual representation of the 46 chromosomes (called karyogram), paired and arranged in decreasing order of size. The pairing procedure aims to identify all pairs of homologous chromosomes. The pairing criterion is based on dimensional, morphological,and textural features similarity. This process is time consuming when performed manually, and demanding from a technical point of view. An automatic pairing algorithm would thus bring benefits, but it remains an open problem to date. In this paper a new strategy for automatic pairing of homologous chromosomes is proposed. Besides the traditional features described in the literature, the Mutual Information (MI) is used to discriminate chromosome textural differences. A supervised non-linear classifier is trained by using manual classifications provided by expert technicians, combining the different features computed from each pair. Simulations using 836 real chromosome images, obtained with a Leica Optical Microscope DM 2500, in a leave-one-out cross validation fashion, were performed for training and testing the algorithm. Promising and relevant results were found, despite the poor quality of the original chromosome images, contrasting with state-of the-art algorithms and datasets found in the literature.\",\n \"corpus_id\": 2447074,\n \"score\": 0\n },\n {\n \"doc_id\": \"19493107\",\n \"title\": \"Three-dimensional reconstruction of biological macromolecular complexes from in-lens scanning electron micrographs.\",\n \"abstract\": \"Two helical samples: F-actin and the bacteriophage T4 tail sheath were reconstructed in three dimensions from contrast enhanced (rotational shadowing and negatively stained) in-lens cryo-field emission scanning electron micrographs, using the iterative real-space helical reconstruction method. The F-actin--and bacteriophage T4 reconstructions compare favourably to an atomic model refined against fibre diffraction data and a cryo-electron microscopy reconstruction, respectively. These results show that single-particle methods, developed for macromolecules imaged in the transmission electron microscope can be applied to cryo-field emission scanning electron micrographs data with appropriate symmetry.\",\n \"corpus_id\": 35005,\n \"score\": 0\n },\n {\n \"doc_id\": \"19526263\",\n \"title\": \"Automatic identification and truncation of boundary outlets in complex imaging-derived biomedical geometries.\",\n \"abstract\": \"Efficient and accurate reconstruction of imaging-derived geometries and subsequent quality mesh generation are enabling technologies for both clinical and research simulations. A challenging part of this process is the introduction of computable, orthogonal boundary patches, namely, the outlets, into treed structures, such as vasculature, arterial or airway trees. We present efficient and robust algorithms for automatically identifying and truncating the outlets for complex geometries. Our approach is based on a conceptual decomposition of objects into tips, segments, and branches, where the tips determine the outlets. We define the tips by introducing a novel concept called the average interior center of curvature and identify the tips that are stable and noise resistant. We compute well-defined orthogonal planes, which truncate the tips into outlets. The rims of the outlets are connected into curves, and the outlets are then closed using Delaunay triangulation. We illustrate the effectiveness and robustness of our approach with a variety of complex lung and coronary artery geometries.\",\n \"corpus_id\": 18529580,\n \"score\": 0\n },\n {\n \"doc_id\": \"20363682\",\n \"title\": \"Face transformation with harmonic models by the finite-volume method with delaunay triangulation.\",\n \"abstract\": \"To carry out face transformation, this paper presents new numerical algorithms, which consist of two parts, namely, the harmonic models for changes of face characteristics and the splitting techniques for grayness transition. The main method in this paper is a combination of the finite-volume method (FVM) with Delaunay triangulation to solve the Laplace equations in the harmonic transformation of face images. The advantages of the FVM with Delaunay triangulation are given as follows: 1) easy to formulate the linear algebraic equations; 2) good in retaining the pertinent geometric and physical need; and 3) less central processing unit time needed. Numerical and graphical experiments have been conducted for the face transformation from a female (woman) to a male (man), and vice versa. The computed sequential errors are O(N⁻³/²), where N² is the division number of a pixel into subpixels. These computed errors coincide with the analysis on the splitting-shooting method (SSM) with piecewise constant interpolation in the previous paper of Li and Bai. In computation, the average absolute errors of restored pixel grayness can be smaller than 2 out of 256 grayness levels. The FVM is as simple as the finite-difference method (FDM) and as flexible as the finite-element method (FEM). Hence, the FVM is particularly useful when dealing with large face images with a huge number of pixels in shape distortion. The numerical transformation of face images in this paper can be used not only in pattern recognition but also in resampling, image morphing, and computer animation.\",\n \"corpus_id\": 12959692,\n \"score\": 0\n },\n {\n \"doc_id\": \"21089695\",\n \"title\": \"[A review of automatic particle recognition in Cryo-EM images].\",\n \"abstract\": \"Advances in cryo-electron microscopy (Cryo-EM) and single-particle reconstruction have led to increasingly high resolutions of macromolecular three-dimensional reconstruction. However, for keeping up the continuing improvements in resolution, it is necessary to increase the number of particles included in performing reconstructions. Manual selection of particles, even assisted by computer, is a bottleneck of single-particle reconstruction. Cryo-EM image has low signal-to-noise ratio and low contrast, which leads to difficulty in particle picking. Various approaches have been developed to address the problem of automatic particle. This paper describes the application of template-based method, edge based method, feature-based method, neural network, DoG-based and simulated annealing approach in particle picking. The characteristics of various approaches are discussed, and the future development is presented.\",\n \"corpus_id\": 38932072,\n \"score\": 0\n },\n {\n \"doc_id\": \"21490573\",\n \"title\": \"Single particle electron microscopy reconstruction of the exosome complex using the random conical tilt method.\",\n \"abstract\": \"Single particle electron microscopy (EM) reconstruction has recently become a popular tool to get the three-dimensional (3D) structure of large macromolecular complexes. Compared to X-ray crystallography, it has some unique advantages. First, single particle EM reconstruction does not need to crystallize the protein sample, which is the bottleneck in X-ray crystallography, especially for large macromolecular complexes. Secondly, it does not need large amounts of protein samples. Compared with milligrams of proteins necessary for crystallization, single particle EM reconstruction only needs several micro-liters of protein solution at nano-molar concentrations, using the negative staining EM method. However, despite a few macromolecular assemblies with high symmetry, single particle EM is limited at relatively low resolution (lower than 1 nm resolution) for many specimens especially those without symmetry. This technique is also limited by the size of the molecules under study, i.e. 100 kDa for negatively stained specimens and 300 kDa for frozen-hydrated specimens in general. For a new sample of unknown structure, we generally use a heavy metal solution to embed the molecules by negative staining. The specimen is then examined in a transmission electron microscope to take two-dimensional (2D) micrographs of the molecules. Ideally, the protein molecules have a homogeneous 3D structure but exhibit different orientations in the micrographs. These micrographs are digitized and processed in computers as \\\"single particles\\\". Using two-dimensional alignment and classification techniques, homogenous molecules in the same views are clustered into classes. Their averages enhance the signal of the molecule's 2D shapes. After we assign the particles with the proper relative orientation (Euler angles), we will be able to reconstruct the 2D particle images into a 3D virtual volume. In single particle 3D reconstruction, an essential step is to correctly assign the proper orientation of each single particle. There are several methods to assign the view for each particle, including the angular reconstitution(1) and random conical tilt (RCT) method(2). In this protocol, we describe our practice in getting the 3D reconstruction of yeast exosome complex using negative staining EM and RCT. It should be noted that our protocol of electron microscopy and image processing follows the basic principle of RCT but is not the only way to perform the method. We first describe how to embed the protein sample into a layer of Uranyl-Formate with a thickness comparable to the protein size, using a holey carbon grid covered with a layer of continuous thin carbon film. Then the specimen is inserted into a transmission electron microscope to collect untilted (0-degree) and tilted (55-degree) pairs of micrographs that will be used later for processing and obtaining an initial 3D model of the yeast exosome. To this end, we perform RCT and then refine the initial 3D model by using the projection matching refinement method(3).\",\n \"corpus_id\": 45189809,\n \"score\": 0\n },\n {\n \"doc_id\": \"21947520\",\n \"title\": \"Automatic construction of parts+geometry models for initializing groupwise registration.\",\n \"abstract\": \"Groupwise nonrigid image registration is a powerful tool to automatically establish correspondences across sets of images. Such correspondences are widely used for constructing statistical models of shape and appearance. As existing techniques usually treat registration as an optimization problem, a good initialization is required. Although the standard initialization-affine transformation-generally works well, it is often inadequate when registering images of complex structures. In this paper we present a more sophisticated method that uses the sparse matches of a parts+geometry model as the initialization. We show that both the model and its matches can be automatically obtained, and that the matches are able to effectively initialize a groupwise nonrigid registration algorithm, leading to accurate dense correspondences. We also show that the dense mesh models constructed during the groupwise registration process can be used to accurately annotate new images. We demonstrate the efficacy of the approach on three datasets of increasing difficulty, and report on a detailed quantitative evaluation of its performance.\",\n \"corpus_id\": 31358433,\n \"score\": 0\n },\n {\n \"doc_id\": \"22027381\",\n \"title\": \"Super-resolution without dense flow.\",\n \"abstract\": \"Super-resolution is a widely applied technique that improves the resolution of input images by software methods. Most conventional reconstruction-based super-resolution algorithms assume accurate dense optical flow fields between the input frames, and their performance degrades rapidly when the motion estimation result is not accurate enough. However, optical flow estimation is usually difficult, particularly when complicated motion is presented in real-world videos. In this paper, we explore a new way to solve this problem by using sparse feature point correspondences between the input images. The feature point correspondences, which are obtained by matching a set of feature points, are usually precise and much more robust than dense optical flow fields. This is because the feature points represent well-selected significant locations in the image, and performing matching on the feature point set is usually very accurate. In order to utilize the sparse correspondences in conventional super-resolution, we extract an adaptive support region with a reliable local flow field from each corresponding feature point pair. The normalized prior is also proposed to increase the visual consistency of the reconstructed result. Extensive experiments on real data were carried out, and results show that the proposed algorithm produces high-resolution images with better quality, particularly in the presence of large-scale or complicated motion fields.\",\n \"corpus_id\": 18031777,\n \"score\": 0\n },\n {\n \"doc_id\": \"22291925\",\n \"title\": \"IPET and FETR: experimental approach for studying molecular structure dynamics by cryo-electron tomography of a single-molecule structure.\",\n \"abstract\": \"The dynamic personalities and structural heterogeneity of proteins are essential for proper functioning. Structural determination of dynamic/heterogeneous proteins is limited by conventional approaches of X-ray and electron microscopy (EM) of single-particle reconstruction that require an average from thousands to millions different molecules. Cryo-electron tomography (cryoET) is an approach to determine three-dimensional (3D) reconstruction of a single and unique biological object such as bacteria and cells, by imaging the object from a series of tilting angles. However, cconventional reconstruction methods use large-size whole-micrographs that are limited by reconstruction resolution (lower than 20 Å), especially for small and low-symmetric molecule (<400 kDa). In this study, we demonstrated the adverse effects from image distortion and the measuring tilt-errors (including tilt-axis and tilt-angle errors) both play a major role in limiting the reconstruction resolution. Therefore, we developed a \\\"focused electron tomography reconstruction\\\" (FETR) algorithm to improve the resolution by decreasing the reconstructing image size so that it contains only a single-instance protein. FETR can tolerate certain levels of image-distortion and measuring tilt-errors, and can also precisely determine the translational parameters via an iterative refinement process that contains a series of automatically generated dynamic filters and masks. To describe this method, a set of simulated cryoET images was employed; to validate this approach, the real experimental images from negative-staining and cryoET were used. Since this approach can obtain the structure of a single-instance molecule/particle, we named it individual-particle electron tomography (IPET) as a new robust strategy/approach that does not require a pre-given initial model, class averaging of multiple molecules or an extended ordered lattice, but can tolerate small tilt-errors for high-resolution single \\\"snapshot\\\" molecule structure determination. Thus, FETR/IPET provides a completely new opportunity for a single-molecule structure determination, and could be used to study the dynamic character and equilibrium fluctuation of macromolecules.\",\n \"corpus_id\": 4807732,\n \"score\": 0\n },\n {\n \"doc_id\": \"22325257\",\n \"title\": \"Delaunay triangulation-based pit density estimation for the classification of polyps in high-magnification chromo-colonoscopy.\",\n \"abstract\": \"In this work we propose a method to extract shape-based features from endoscopic images for an automated classification of colonic polyps. This method is based on the density of pits as used in the pit pattern classification scheme which is commonly used for the classification of colonic polyps. For the detection of pits we employ a noise-robust variant of the LBP operator. To be able to be robust against local texture variations we extend this operator by an adaptive thresholding. Based on the detected pit candidates we compute a Delaunay triangulation and use the edge lengths of the resulting triangles to construct histograms. These are then used in conjunction with the k-NN classifier to classify images. We show that, compared to a previously developed method, we are not only able to almost always get higher classification results in our application scenario, but that the proposed method is also able to significantly outperform the previously developed method in terms of the computational demand.\",\n \"corpus_id\": 1632357,\n \"score\": 0\n },\n {\n \"doc_id\": \"23113939\",\n \"title\": \"A rule-based algorithm for automatic bond type perception.\",\n \"abstract\": \"Assigning bond orders is a necessary and essential step for characterizing a chemical structure correctly in force field based simulations. Several methods have been developed to do this. They all have advantages but with limitations too. Here, an automatic algorithm for assigning chemical connectivity and bond order regardless of hydrogen for organic molecules is provided, and only three dimensional coordinates and element identities are needed for our algorithm. The algorithm uses hard rules, length rules and conjugation rules to fix the structures. The hard rules determine bond orders based on the basic chemical rules; the length rules determine bond order by the length between two atoms based on a set of predefined values for different bond types; the conjugation rules determine bond orders by using the length information derived from the previous rule, the bond angles and some small structural patterns. The algorithm is extensively evaluated in three datasets, and achieves good accuracy of predictions for all the datasets. Finally, the limitation and future improvement of the algorithm are discussed.\",\n \"corpus_id\": 16697891,\n \"score\": 0\n },\n {\n \"doc_id\": \"23193202\",\n \"title\": \"Alpha shape and Delaunay triangulation in studies of protein-related interactions.\",\n \"abstract\": \"In recent years, more 3D protein structures have become available, which has made the analysis of large molecular structures much easier. There is a strong demand for geometric models for the study of protein-related interactions. Alpha shape and Delaunay triangulation are powerful tools to represent protein structures and have advantages in characterizing the surface curvature and atom contacts. This review presents state-of-the-art applications of alpha shape and Delaunay triangulation in the studies on protein-DNA, protein-protein, protein-ligand interactions and protein structure analysis.\",\n \"corpus_id\": 14520590,\n \"score\": 0\n },\n {\n \"doc_id\": \"23333657\",\n \"title\": \"TMaCS: a hybrid template matching and classification system for partially-automated particle selection.\",\n \"abstract\": \"Selection of particle images from electron micrographs presents a bottleneck in determining the structures of macromolecular assemblies by single particle electron cryomicroscopy (cryo-EM). The problem is particularly important when an experimentalist wants to improve the resolution of a 3D map by increasing by tens or hundreds of thousands of images the size of the dataset used for calculating the map. Although several existing methods for automatic particle image selection work well for large protein complexes that produce high-contrast images, it is well known in the cryo-EM community that small complexes that give low-contrast images are often refractory to existing automated particle image selection schemes. Here we develop a method for partially-automated particle image selection when an initial 3D map of the protein under investigation is already available. Candidate particle images are selected from micrographs by template matching with template images derived from projections of the existing 3D map. The candidate particle images are then used to train a support vector machine, which classifies the candidates as particle images or non-particle images. In a final step in the analysis, the selected particle images are subjected to projection matching against the initial 3D map, with the correlation coefficient between the particle image and the best matching map projection used to assess the reliability of the particle image. We show that this approach is able to rapidly select particle images from micrographs of a rotary ATPase, a type of membrane protein complex involved in many aspects of biology.\",\n \"corpus_id\": 25508463,\n \"score\": 0\n },\n {\n \"doc_id\": \"23933392\",\n \"title\": \"Particle quality assessment and sorting for automatic and semiautomatic particle-picking techniques.\",\n \"abstract\": \"Three-dimensional reconstruction of biological specimens using electron microscopy by single particle methodologies requires the identification and extraction of the imaged particles from the acquired micrographs. Automatic and semiautomatic particle selection approaches can localize these particles, minimizing the user interaction, but at the cost of selecting a non-negligible number of incorrect particles, which can corrupt the final three-dimensional reconstruction. In this work, we present a novel particle quality assessment and sorting method that can separate most erroneously picked particles from correct ones. The proposed method is based on multivariate statistical analysis of a particle set that has been picked previously using any automatic or manual approach. The new method uses different sets of particle descriptors, which are morphology-based, histogram-based and signal to noise analysis based. We have tested our proposed algorithm with experimental data obtaining very satisfactory results. The algorithm is freely available as a part of the Xmipp 3.0 package [http://xmipp.cnb.csic.es].\",\n \"corpus_id\": 7094288,\n \"score\": 0\n },\n {\n \"doc_id\": \"24051799\",\n \"title\": \"Selecting the aspect ratio of a scatter plot based on its delaunay triangulation.\",\n \"abstract\": \"Scatter plots are diagrams that visualize two-dimensional data as sets of points in the plane. They allow users to detect correlations and clusters in the data. Whether or not a user can accomplish these tasks highly depends on the aspect ratio selected for the plot, i.e., the ratio between the horizontal and the vertical extent of the diagram. We argue that an aspect ratio is good if the Delaunay triangulation of the scatter plot at this aspect ratio has some nice geometric property, e.g., a large minimum angle or a small total edge length. More precisely, we consider the following optimization problem. Given a set Q of points in the plane, find a scale factor s such that scaling the x-coordinates of the points in Q by s and the y-coordinates by 1=s yields a point set P(s) that optimizes a property of the Delaunay triangulation of P(s), over all choices of s. We present an algorithm that solves this problem efficiently and demonstrate its usefulness on real-world instances. Moreover, we discuss an empirical test in which we asked 64 participants to choose the aspect ratios of 18 scatter plots. We tested six different quality measures that our algorithm can optimize. In conclusion, minimizing the total edge length and minimizing what we call the 'uncompactness' of the triangles of the Delaunay triangulation yielded the aspect ratios that were most similar to those chosen by the participants in the test.\",\n \"corpus_id\": 1322188,\n \"score\": 0\n },\n {\n \"doc_id\": \"24144335\",\n \"title\": \"gEMpicker: a highly parallel GPU-accelerated particle picking tool for cryo-electron microscopy.\",\n \"abstract\": \"BACKGROUND: Picking images of particles in cryo-electron micrographs is an important step in solving the 3D structures of large macromolecular assemblies. However, in order to achieve sub-nanometre resolution it is often necessary to capture and process many thousands or even several millions of 2D particle images. Thus, a computational bottleneck in reaching high resolution is the accurate and automatic picking of particles from raw cryo-electron micrographs. RESULTS: We have developed \\\"gEMpicker\\\", a highly parallel correlation-based particle picking tool. To our knowledge, gEMpicker is the first particle picking program to use multiple graphics processor units (GPUs) to accelerate the calculation. When tested on the publicly available keyhole limpet hemocyanin dataset, we find that gEMpicker gives similar results to the FindEM program. However, compared to calculating correlations on one core of a contemporary central processor unit (CPU), running gEMpicker on a modern GPU gives a speed-up of about 27 ×. To achieve even higher processing speeds, the basic correlation calculations are accelerated considerably by using a hierarchy of parallel programming techniques to distribute the calculation over multiple GPUs and CPU cores attached to multiple nodes of a computer cluster. By using a theoretically optimal reduction algorithm to collect and combine the cluster calculation results, the speed of the overall calculation scales almost linearly with the number of cluster nodes available. CONCLUSIONS: The very high picking throughput that is now possible using GPU-powered workstations or computer clusters will help experimentalists to achieve higher resolution 3D reconstructions more rapidly than before.\",\n \"corpus_id\": 10430036,\n \"score\": 0\n },\n {\n \"doc_id\": \"24390311\",\n \"title\": \"High-resolution cryo-electron microscopy on macromolecular complexes and cell organelles.\",\n \"abstract\": \"Cryo-electron microscopy techniques and computational 3-D reconstruction of macromolecular assemblies are tightly linked tools in modern structural biology. This symbiosis has produced vast amounts of detailed information on the structure and function of biological macromolecules. Typically, one of two fundamentally different strategies is used depending on the specimens and their environment. A: 3-D reconstruction based on repetitive and structurally identical unit cells that allow for averaging, and B: tomographic 3-D reconstructions where tilt-series between approximately ± 60 and ± 70° at small angular increments are collected from highly complex and flexible structures that are beyond averaging procedures, at least during the first round of 3-D reconstruction. Strategies of group A are averaging-based procedures and collect large number of 2-D projections at different angles that are computationally aligned, averaged together, and back-projected in 3-D space to reach a most complete 3-D dataset with high resolution, today often down to atomic detail. Evidently, success relies on structurally repetitive particles and an aligning procedure that unambiguously determines the angular relationship of all 2-D projections with respect to each other. The alignment procedure of small particles may rely on their packing into a regular array such as a 2-D crystal, an icosahedral (viral) particle, or a helical assembly. Critically important for cryo-methods, each particle will only be exposed once to the electron beam, making these procedures optimal for highest-resolution studies where beam-induced damage is a significant concern. In contrast, tomographic 3-D reconstruction procedures (group B) do not rely on averaging, but collect an entire dataset from the very same structure of interest. Data acquisition requires collecting a large series of tilted projections at angular increments of 1-2° or less and a tilt range of ± 60° or more. Accordingly, tomographic data collection exposes its specimens to a large electron dose, which is particularly problematic for frozen-hydrated samples. Currently, cryo-electron tomography is a rapidly emerging technology, on one end driven by the newest developments of hardware such as super-stabile microscopy stages as well as the latest generation of direct electron detectors and cameras. On the other end, success also strongly depends on new software developments on all kinds of fronts such as tilt-series alignment and back-projection procedures that are all adapted to the very low-dose and therefore very noisy primary data. Here, we will review the status quo of cryo-electron microscopy and discuss the future of cellular cryo-electron tomography from data collection to data analysis, CTF-correction of tilt-series, post-tomographic sub-volume averaging, and 3-D particle classification. We will also discuss the pros and cons of plunge freezing of cellular specimens to vitrified sectioning procedures and their suitability for post-tomographic volume averaging despite multiple artifacts that may distort specimens to some degree.\",\n \"corpus_id\": 13894885,\n \"score\": 0\n },\n {\n \"doc_id\": \"24607413\",\n \"title\": \"Automated particle picking for low-contrast macromolecules in cryo-electron microscopy.\",\n \"abstract\": \"Cryo-electron microscopy is an increasingly popular tool for studying the structure and dynamics of biological macromolecules at high resolution. A crucial step in automating single-particle reconstruction of a biological sample is the selection of particle images from a micrograph. We present a novel algorithm for selecting particle images in low-contrast conditions; it proves more effective than the human eye on close-to-focus micrographs, yielding improved or comparable resolution in reconstructions of two macromolecular complexes.\",\n \"corpus_id\": 10473929,\n \"score\": 0\n },\n {\n \"doc_id\": \"24613762\",\n \"title\": \"Single particle analysis integrated with microscopy: a high-throughput approach for reconstructing icosahedral particles.\",\n \"abstract\": \"In cryo-electron microscopy and single particle analysis, data acquisition and image processing are generally carried out in sequential steps and computation of a three-dimensional reconstruction only begins once all the micrographs have been acquired. We are developing an integrated system for processing images of icosahedral particles during microscopy to provide reconstructed density maps in real-time at the highest possible resolution. The system is designed as a combination of pipelines to run in parallel on a computer cluster and analyzes micrographs as they are acquired, handling automatically all the processing steps from defocus estimation and particle picking to origin/orientation determination. An ab initio model is determined independently from the first micrographs collected, and new models are generated as more particles become available. As a proof of concept, we simulated data acquisition sessions using three sets of micrographs of good to excellent quality that were previously recorded from different icosahedral viruses. Results show that the processing of single micrographs can keep pace with an acquisition rate of about two images per minute. The reconstructed density map improves steadily during the image acquisition phase and its quality at the end of data collection is only moderately inferior to that obtained by expert users who processed semi-automatically all the micrographs after the acquisition. The current prototype demonstrates the advantages of integrating three-dimensional image processing with microscopy, which include an ability to monitor acquisition in terms of the final structure and to predict how much data and microscope resources are needed to achieve a desired resolution.\",\n \"corpus_id\": 1625897,\n \"score\": 0\n },\n {\n \"doc_id\": \"25544475\",\n \"title\": \"How cryo-EM is revolutionizing structural biology.\",\n \"abstract\": \"For many years, structure determination of biological macromolecules by cryo-electron microscopy (cryo-EM) was limited to large complexes or low-resolution models. With recent advances in electron detection and image processing, the resolution by cryo-EM is now beginning to rival X-ray crystallography. A new generation of electron detectors record images with unprecedented quality, while new image-processing tools correct for sample movements and classify images according to different structural states. Combined, these advances yield density maps with sufficient detail to deduce the atomic structure for a range of specimens. Here, we review the recent advances and illustrate the exciting new opportunities that they offer to structural biology research.\",\n \"corpus_id\": 19727349,\n \"score\": 0\n },\n {\n \"doc_id\": \"25839831\",\n \"title\": \"SubspaceEM: A fast maximum-a-posteriori algorithm for cryo-EM single particle reconstruction.\",\n \"abstract\": \"Single particle reconstruction methods based on the maximum-likelihood principle and the expectation-maximization (E-M) algorithm are popular because of their ability to produce high resolution structures. However, these algorithms are computationally very expensive, requiring a network of computational servers. To overcome this computational bottleneck, we propose a new mathematical framework for accelerating maximum-likelihood reconstructions. The speedup is by orders of magnitude and the proposed algorithm produces similar quality reconstructions compared to the standard maximum-likelihood formulation. Our approach uses subspace approximations of the cryo-electron microscopy (cryo-EM) data and projection images, greatly reducing the number of image transformations and comparisons that are computed. Experiments using simulated and actual cryo-EM data show that speedup in overall execution time compared to traditional maximum-likelihood reconstruction reaches factors of over 300.\",\n \"corpus_id\": 17850477,\n \"score\": 0\n },\n {\n \"doc_id\": \"26094203\",\n \"title\": \"A fast iterative convolution weighting approach for gridding-based direct Fourier three-dimensional reconstruction with correction for the contrast transfer function.\",\n \"abstract\": \"We describe a fast and accurate method for the reconstruction of macromolecular complexes from a set of projections. Direct Fourier inversion (in which the Fourier Slice Theorem plays a central role) is a solution for dealing with this inverse problem. Unfortunately, the set of projections provides a non-equidistantly sampled version of the macromolecule Fourier transform in the single particle field (and, therefore, a direct Fourier inversion) may not be an optimal solution. In this paper, we introduce a gridding-based direct Fourier method for the three-dimensional reconstruction approach that uses a weighting technique to compute a uniform sampled Fourier transform. Moreover, the contrast transfer function of the microscope, which is a limiting factor in pursuing a high resolution reconstruction, is corrected by the algorithm. Parallelization of this algorithm, both on threads and on multiple CPU's, makes the process of three-dimensional reconstruction even faster. The experimental results show that our proposed gridding-based direct Fourier reconstruction is slightly more accurate than similar existing methods and presents a lower computational complexity both in terms of time and memory, thereby allowing its use on larger volumes. The algorithm is fully implemented in the open-source Xmipp package and is downloadable from http://xmipp.cnb.csic.es.\",\n \"corpus_id\": 205524467,\n \"score\": 0\n },\n {\n \"doc_id\": \"26705325\",\n \"title\": \"Principles of cryo-EM single-particle image processing.\",\n \"abstract\": \"Single-particle reconstruction is the process by which 3D density maps are obtained from a set of low-dose cryo-EM images of individual macromolecules. This review considers the fundamental principles of this process and the steps in the overall workflow for single-particle image processing. Also considered are the limits that image signal-to-noise ratio places on resolution and the distinguishing of heterogeneous particle populations.\",\n \"corpus_id\": 21949411,\n \"score\": 0\n },\n {\n \"doc_id\": \"27215953\",\n \"title\": \"Skin lesion image segmentation using Delaunay Triangulation for melanoma detection.\",\n \"abstract\": \"Developing automatic diagnostic tools for the early detection of skin cancer lesions in dermoscopic images can help to reduce melanoma-induced mortality. Image segmentation is a key step in the automated skin lesion diagnosis pipeline. In this paper, a fast and fully-automatic algorithm for skin lesion segmentation in dermoscopic images is presented. Delaunay Triangulation is used to extract a binary mask of the lesion region, without the need of any training stage. A quantitative experimental evaluation has been conducted on a publicly available database, by taking into account six well-known state-of-the-art segmentation methods for comparison. The results of the experimental analysis demonstrate that the proposed approach is highly accurate when dealing with benign lesions, while the segmentation accuracy significantly decreases when melanoma images are processed. This behavior led us to consider geometrical and color features extracted from the binary masks generated by our algorithm for classification, achieving promising results for melanoma detection.\",\n \"corpus_id\": 4861162,\n \"score\": 0\n },\n {\n \"doc_id\": \"27353419\",\n \"title\": \"A new approach for categorizing pig lying behaviour based on a Delaunay triangulation method.\",\n \"abstract\": \"Machine vision-based monitoring of pig lying behaviour is a fast and non-intrusive approach that could be used to improve animal health and welfare. Four pens with 22 pigs in each were selected at a commercial pig farm and monitored for 15 days using top view cameras. Three thermal categories were selected relative to room setpoint temperature. An image processing technique based on Delaunay triangulation (DT) was utilized. Different lying patterns (close, normal and far) were defined regarding the perimeter of each DT triangle and the percentages of each lying pattern were obtained in each thermal category. A method using a multilayer perceptron (MLP) neural network, to automatically classify group lying behaviour of pigs into three thermal categories, was developed and tested for its feasibility. The DT features (mean value of perimeters, maximum and minimum length of sides of triangles) were calculated as inputs for the MLP classifier. The network was trained, validated and tested and the results revealed that MLP could classify lying features into the three thermal categories with high overall accuracy (95.6%). The technique indicates that a combination of image processing, MLP classification and mathematical modelling can be used as a precise method for quantifying pig lying behaviour in welfare investigations.\",\n \"corpus_id\": 52833710,\n \"score\": 0\n },\n {\n \"doc_id\": \"27424268\",\n \"title\": \"DeepPicker: A deep learning approach for fully automated particle picking in cryo-EM.\",\n \"abstract\": \"Particle picking is a time-consuming step in single-particle analysis and often requires significant interventions from users, which has become a bottleneck for future automated electron cryo-microscopy (cryo-EM). Here we report a deep learning framework, called DeepPicker, to address this problem and fill the current gaps toward a fully automated cryo-EM pipeline. DeepPicker employs a novel cross-molecule training strategy to capture common features of particles from previously-analyzed micrographs, and thus does not require any human intervention during particle picking. Tests on the recently-published cryo-EM data of three complexes have demonstrated that our deep learning based scheme can successfully accomplish the human-level particle picking process and identify a sufficient number of particles that are comparable to those picked manually by human experts. These results indicate that DeepPicker can provide a practically useful tool to significantly reduce the time and manual effort spent in single-particle analysis and thus greatly facilitate high-resolution cryo-EM structure determination. DeepPicker is released as an open-source program, which can be downloaded from https://github.com/nejyeah/DeepPicker-python.\",\n \"corpus_id\": 3908505,\n \"score\": 0\n },\n {\n \"doc_id\": \"27716029\",\n \"title\": \"Simulating cryo electron tomograms of crowded cell cytoplasm for assessment of automated particle picking.\",\n \"abstract\": \"BACKGROUND: Cryo-electron tomography is an important tool to study structures of macromolecular complexes in close to native states. A whole cell cryo electron tomogram contains structural information of all its macromolecular complexes. However, extracting this information remains challenging, and relies on sophisticated image processing, in particular for template-free particle extraction, classification and averaging. To develop these methods it is crucial to realistically simulate tomograms of crowded cellular environments, which can then serve as ground truth models for assessing and optimizing methods for detection of complexes in cell tomograms. RESULTS: We present a framework to generate crowded mixtures of macromolecular complexes for realistically simulating cryo electron tomograms including noise and image distortions due to the missing-wedge effects. Simulated tomograms are then used for assessing the template-free Difference-of-Gaussian (DoG) particle-picking method to detect complexes of different shapes and sizes under various crowding and noise levels. We identified DoG parameter settings that maximize precision and recall for detecting particles over a wide range of sizes and shapes. We observed that medium sized DoG scaling factors showed the overall best performance. To further improve performance, we propose a combination strategy for integrating results from multiple parameter settings. With increasing macromolecular crowding levels, the precision of particle picking remained relatively high, while the recall was dramatically reduced, which limits the detection of sufficient copy numbers of complexes in a crowded environment. Over a wide range of increasing noise levels, the DoG particle picking performance remained stable, but dramatically reduced beyond a specific noise threshold. CONCLUSIONS: Automatic and reference-free particle picking is an important first step in a visual proteomics analysis of cell tomograms. However, cell cytoplasm is highly crowded, which makes particle detection challenging. It is therefore important to test particle-picking methods in a realistic crowded setting. Here, we present a framework for simulating tomograms of cellular environments at high crowding levels and assess the DoG particle picking method. We determined optimal parameter settings to maximize the performance of the DoG particle-picking method.\",\n \"corpus_id\": 704700,\n \"score\": 0\n },\n {\n \"doc_id\": \"28343096\",\n \"title\": \"SD-SEM: sparse-dense correspondence for 3D reconstruction of microscopic samples.\",\n \"abstract\": \"Scanning electron microscopy (SEM) imaging has been a principal component of many studies in biomedical, mechanical, and materials sciences since its emergence. Despite the high resolution of captured images, they remain two-dimensional (2D). In this work, a novel framework using sparse-dense correspondence is introduced and investigated for 3D reconstruction of stereo SEM images. SEM micrographs from microscopic samples are captured by tilting the specimen stage by a known angle. The pair of SEM micrographs is then rectified using sparse scale invariant feature transform (SIFT) features/descriptors and a contrario RANSAC for matching outlier removal to ensure a gross horizontal displacement between corresponding points. This is followed by dense correspondence estimation using dense SIFT descriptors and employing a factor graph representation of the energy minimization functional and loopy belief propagation (LBP) as means of optimization. Given the pixel-by-pixel correspondence and the tilt angle of the specimen stage during the acquisition of micrographs, depth can be recovered. Extensive tests reveal the strength of the proposed method for high-quality reconstruction of microscopic samples.\",\n \"corpus_id\": 31788671,\n \"score\": 0\n },\n {\n \"doc_id\": \"28368809\",\n \"title\": \"A Two-Phase Improved Correlation Method for Automatic Particle Selection in Cryo-EM.\",\n \"abstract\": \"Particle selection from cryo-electron microscopy (Cryo-EM) images is very important for high-resolution reconstruction of macromolecular structure. The methods of particle selection can be roughly grouped into two classes, template-matching methods and feature-based methods. In general, template-matching methods usually generate better results than feature-based methods. However, the accuracy of template-matching methods is restricted by the noise and low contrast of Cryo-EM images. Moreover, the processing speed of template-matching methods, restricted by the random orientation of particles, further limits their practical applications. In this paper, combining the advantages of feature-based methods and template-matching methods, we present a two-phase improved correlation method for automatic, fast particle selection. In Phase I, we generate a preliminary particle set using rotation-invariant features of particles. In Phase II, we filter the preliminary particle set using a correlation method to reduce the interference of the high noise background and improve the precision of particle selection. We apply several optimization strategies, including a modified adaboost algorithm, Divide and Conquer technique, cascade strategy and graphics processing unit parallel technique, to improve feature recognition ability and reduce processing time. In addition, we developed two correlation score functions for different correlation situations. Experimental results on the benchmark of Cryo-EM images show that our method can improve the accuracy and processing speed of particle selection significantly.\",\n \"corpus_id\": 9195465,\n \"score\": 0\n },\n {\n \"doc_id\": \"28732461\",\n \"title\": \"A deep convolutional neural network approach to single-particle recognition in cryo-electron microscopy.\",\n \"abstract\": \"BACKGROUND: Single-particle cryo-electron microscopy (cryo-EM) has become a mainstream tool for the structural determination of biological macromolecular complexes. However, high-resolution cryo-EM reconstruction often requires hundreds of thousands of single-particle images. Particle extraction from experimental micrographs thus can be laborious and presents a major practical bottleneck in cryo-EM structural determination. Existing computational methods for particle picking often use low-resolution templates for particle matching, making them susceptible to reference-dependent bias. It is critical to develop a highly efficient template-free method for the automatic recognition of particle images from cryo-EM micrographs. RESULTS: We developed a deep learning-based algorithmic framework, DeepEM, for single-particle recognition from noisy cryo-EM micrographs, enabling automated particle picking, selection and verification in an integrated fashion. The kernel of DeepEM is built upon a convolutional neural network (CNN) composed of eight layers, which can be recursively trained to be highly \\\"knowledgeable\\\". Our approach exhibits an improved performance and accuracy when tested on the standard KLH dataset. Application of DeepEM to several challenging experimental cryo-EM datasets demonstrated its ability to avoid the selection of un-wanted particles and non-particles even when true particles contain fewer features. CONCLUSIONS: The DeepEM methodology, derived from a deep CNN, allows automated particle extraction from raw cryo-EM micrographs in the absence of a template. It demonstrates an improved performance, objectivity and accuracy. Application of this novel method is expected to free the labor involved in single-particle verification, significantly improving the efficiency of cryo-EM data processing.\",\n \"corpus_id\": 9763578,\n \"score\": 0\n },\n {\n \"doc_id\": \"29486249\",\n \"title\": \"Exploring applications of crowdsourcing to cryo-EM.\",\n \"abstract\": \"Extraction of particles from cryo-electron microscopy (cryo-EM) micrographs is a crucial step in processing single-particle datasets. Although algorithms have been developed for automatic particle picking, these algorithms generally rely on two-dimensional templates for particle identification, which may exhibit biases that can propagate artifacts through the reconstruction pipeline. Manual picking is viewed as a gold-standard solution for particle selection, but it is too time-consuming to perform on data sets of thousands of images. In recent years, crowdsourcing has proven effective at leveraging the open web to manually curate datasets. In particular, citizen science projects such as Galaxy Zoo have shown the power of appealing to users' scientific interests to process enormous amounts of data. To this end, we explored the possible applications of crowdsourcing in cryo-EM particle picking, presenting a variety of novel experiments including the production of a fully annotated particle set from untrained citizen scientists. We show the possibilities and limitations of crowdsourcing particle selection tasks, and explore further options for crowdsourcing cryo-EM data processing.\",\n \"corpus_id\": 3749368,\n \"score\": 0\n }\n]","isConversational":false}}},{"rowIdx":66,"cells":{"query":{"kind":"string","value":"{\n \"doc_id\": \"27666962\",\n \"title\": \"A review of resolution measures and related aspects in 3D Electron Microscopy.\",\n \"abstract\": \"Fourier Shell Correlation, Spectral Signal-to-Noise Ratio, Fourier Neighbour Correlation, and Differential Phase Residual are different measures that have been proposed over time to determine the spatial resolution achieved by a certain 3D reconstruction. Estimates of B-factors to describe the reduction in signal-to-noise ratio with increasing resolution is also a useful parameter. All these concepts are interrelated and different thresholds have been given for each one of them. However, the problem of resolution assessment in 3DEM is still far from settled and preferences are normally adopted in order to choose the \\\"correct\\\" threshold. In this paper we review the different concepts, their theoretical foundations and the derivation of their statistical distributions (the basis for establishing sensible thresholds). We provide theoretical justifications for some common practices in the field for which a formal justification was missing. We also analyze the relationship between SSNR and B-factors, the electron dose needed for achieving a given contrast and resolution, the number of images required, etc. Finally, we review the consequences for the number of particles needed to achieve a certain resolution and how to analyze the Signal-to-Noise Ratio for a sequence of imaging operations.\",\n \"corpus_id\": 25932382\n}"},"candidates":{"kind":"list like","value":[{"doc_id":"20161040","title":"A resolution measure for three-dimensional microscopy.","abstract":"A three-dimensional (3D) resolution measure for the conventional optical microscope is introduced which overcomes the drawbacks of the classical 3D (axial) resolution limit. Formulated within the context of a parameter estimation problem and based on the Cramer-Rao lower bound, this 3D resolution measure indicates the accuracy with which a given distance between two objects in 3D space can be determined from the acquired image. It predicts that, given enough photons from the objects of interest, arbitrarily small distances of separation can be estimated with prespecified accuracy. Using simulated images of point source pairs, we show that the maximum likelihood estimator is capable of attaining the accuracy predicted by the resolution measure. We also demonstrate how different factors, such as extraneous noise sources and the spatial orientation of the imaged object pair, can affect the accuracy with which a given distance of separation can be determined.","corpus_id":17715714,"score":2},{"doc_id":"20888958","title":"Resolution measures in molecular electron microscopy.","abstract":"Resolution measures in molecular electron microscopy provide means to evaluate quality of macromolecular structures computed from sets of their two-dimensional (2D) line projections. When the amount of detail in the computed density map is low there are no external standards by which the resolution of the result can be judged. Instead, resolution measures in molecular electron microscopy evaluate consistency of the results in reciprocal space and present it as a one-dimensional (1D) function of the modulus of spatial frequency. Here we provide description of standard resolution measures commonly used in electron microscopy. We point out that the organizing principle is the relationship between these measures and the spectral signal-to-noise ratio (SSNR) of the computed density map. Within this framework it becomes straightforward to describe the connection between the outcome of resolution evaluations and the quality of electron microscopy maps, in particular, the optimum filtration, in the Wiener sense, of the computed map. We also provide a discussion of practical difficulties of evaluation of resolution in electron microscopy, particularly in terms of its sensitivity to data processing operations used during structure determination process in single particle analysis and in electron tomography (ET).","corpus_id":23444182,"score":2},{"doc_id":"21627992","title":"Limiting factors in atomic resolution cryo electron microscopy: no simple tricks.","abstract":"To bring cryo electron microscopy (cryoEM) of large biological complexes to atomic resolution, several factors--in both cryoEM image acquisition and 3D reconstruction--that may be neglected at low resolution become significantly limiting. Here we present thorough analyses of four limiting factors: (a) electron-beam tilt, (b) inaccurate determination of defocus values, (c) focus gradient through particles, and (d) particularly for large particles, dynamic (multiple) scattering of electrons. We also propose strategies to cope with these factors: (a) the divergence and direction tilt components of electron-beam tilt could be reduced by maintaining parallel illumination and by using a coma-free alignment procedure, respectively. Moreover, the effect of all beam tilt components, including spiral tilt, could be eliminated by use of a spherical aberration corrector. ( b) More accurate measurement of defocus value could be obtained by imaging areas adjacent to the target area at high electron dose and by measuring the image shift induced by tilting the electron beam. ( c) Each known Fourier coefficient in the Fourier transform of a cryoEM image is the sum of two Fourier coefficients of the 3D structure, one on each of two curved 'characteristic surfaces' in 3D Fourier space. We describe a simple model-based iterative method that could recover these two Fourier coefficients on the two characteristic surfaces. ( d) The effect of dynamic scattering could be corrected by deconvolution of a transfer function. These analyses and our proposed strategies offer useful guidance for future experimental designs targeting atomic resolution cryoEM reconstruction.","corpus_id":8742056,"score":2},{"doc_id":"23872039","title":"High-resolution noise substitution to measure overfitting and validate resolution in 3D structure determination by single particle electron cryomicroscopy.","abstract":"Three-dimensional (3D) structure determination by single particle electron cryomicroscopy (cryoEM) involves the calculation of an initial 3D model, followed by extensive iterative improvement of the orientation determination of the individual particle images and the resulting 3D map. Because there is much more noise than signal at high resolution in the images, this creates the possibility of noise reinforcement in the 3D map, which can give a false impression of the resolution attained. The balance between signal and noise in the final map at its limiting resolution depends on the image processing procedure and is not easily predicted. There is a growing awareness in the cryoEM community of how to avoid such over-fitting and over-estimation of resolution. Equally, there has been a reluctance to use the two principal methods of avoidance because they give lower resolution estimates, which some people believe are too pessimistic. Here we describe a simple test that is compatible with any image processing protocol. The test allows measurement of the amount of signal and the amount of noise from overfitting that is present in the final 3D map. We have applied the method to two different sets of cryoEM images of the enzyme beta-galactosidase using several image processing packages. Our procedure involves substituting the Fourier components of the initial particle image stack beyond a chosen resolution by either the Fourier components from an adjacent area of background, or by simple randomisation of the phases of the particle structure factors. This substituted noise thus has the same spectral power distribution as the original data. Comparison of the Fourier Shell Correlation (FSC) plots from the 3D map obtained using the experimental data with that from the same data with high-resolution noise (HR-noise) substituted allows an unambiguous measurement of the amount of overfitting and an accompanying resolution assessment. A simple formula can be used to calculate an unbiased FSC from the two curves, even when a substantial amount of overfitting is present. The approach is software independent. The user is therefore completely free to use any established method or novel combination of methods, provided the HR-noise test is carried out in parallel. Applying this procedure to cryoEM images of beta-galactosidase shows how overfitting varies greatly depending on the procedure, but in the best case shows no overfitting and a resolution of ~6 Å. (382 words).","corpus_id":25196434,"score":2},{"doc_id":"24384117","title":"ResLog plots as an empirical metric of the quality of cryo-EM reconstructions.","abstract":"Compared to the field of X-ray crystallography, the field of single particle three-dimensional electron microscopy has few reliable metrics for assessing the quality of 3D reconstructions. New metrics are needed that can determine whether a given 3D reconstruction accurately reflects the structure of the particles from which it was derived or instead depicts a plausible though incorrect structure due to coarse misalignment of particles. Here an empirical procedure is presented for differentiating between a reconstruction with well-aligned particles and a reconstruction with grossly misclassified particles. For a given dataset, 3D reconstructions are computed from subsets of particles with decreasing numbers of particles contributing to the reconstruction. A plot of inverse resolution vs. the logarithm of the number of particles (a \"ResLog\" plot) provides metrics for the reliability of the reconstruction and the overall quality of the dataset and processing. Specifically, the y-intercept of a regression line provides a measure of the relative accuracy of the particle alignment and classification, and the slope is an indicator of the overall data quality including the imaging conditions and processing steps. ResLog plots can also be used to optimize conditions for data collection and reconstruction parameters. Although resolution estimates can vary by method of calculation, ResLog-derived parameters are consistent whether calculated by Fourier shell correlation or Fourier neighbor correlation, or a new coordinate-based metric that serves as a yardstick for structures where atomic coordinates are available. ResLog plots could become part of a standard set of parameters to be included in 3D reconstruction reports.","corpus_id":5394651,"score":2},{"doc_id":"24566042","title":"Electron dose dependence of signal-to-noise ratio, atom contrast and resolution in transmission electron microscope images.","abstract":"In order to achieve the highest resolution in aberration-corrected (AC) high-resolution transmission electron microscopy (HRTEM) images, high electron doses are required which only a few samples can withstand. In this paper we perform dose-dependent AC-HRTEM image calculations, and study the dependence of the signal-to-noise ratio, atom contrast and resolution on electron dose and sampling. We introduce dose-dependent contrast, which can be used to evaluate the visibility of objects under different dose conditions. Based on our calculations, we determine optimum samplings for high and low electron dose imaging conditions.","corpus_id":12131201,"score":2},{"doc_id":"25836194","title":"Young's double-slit experiment: noise-resolution duality.","abstract":"Statistical aspects of Young's double-slit diffraction experiment are analysed quantitatively. It is shown that the signal-to-noise ratio and the spatial resolution in the detected diffraction pattern satisfy a duality relationship which implies that both of them cannot be improved simultaneously beyond a certain limit if the total number of particles forming the image is fixed. As a consequence of this duality, it is possible to estimate the minimal number of particles that have to be detected in order for two slits separated by a given distance to be resolved with a confidence level corresponding to a pre-defined signal-to-noise ratio, e.g. according to the Rose criterion. These results are related to the recently introduced imaging system quality characteristic which combines the spatial resolution and the noise sensitivity, and allows one to estimate the efficiency with which imaging quanta are utilised in a system to deliver maximal amount of information about the imaged object. The presented results can be useful for applications where the imaging quanta are at a premium or where minimization of the radiation dose is important.","corpus_id":35880581,"score":2},{"doc_id":"29395788","title":"MonoRes: Automatic and Accurate Estimation of Local Resolution for Electron Microscopy Maps.","abstract":"Since the beginning of electron microscopy, resolution has been a critical parameter. In this article, we propose a fully automatic, accurate method for determining the local resolution of a 3D map (MonoRes). The foundation of this algorithm is an extension of the concept of analytic signal, termed monogenic signal. The map is filtered at different frequencies and the amplitude of the monogenic signal is calculated, after which a criterion is applied to determine the resolution at each voxel. MonoRes is fully automatic without compulsory user parameters, with great accuracy in all tests, and is computationally more rapid than existing methods in the field. In addition, MonoRes offers the option of local filtering of the original map based on the calculated local resolution.","corpus_id":46822743,"score":2},{"doc_id":"18171501","title":"Spatial resolution and information transfer in scanning transmission electron microscopy.","abstract":"The relation between image resolution and information transfer is explored. It is shown that the existence of higher frequency transfer in the image is just a necessary but not sufficient condition for the achievement of higher resolution. Adopting a two-point resolution criterion, we suggest that a 10% contrast level between two features in an image should be used as a practical definition of resolution. In the context of scanning transmission electron microscopy, it is shown that the channeling effect does not have a direct connection with image resolution because sharp channeling peaks do not move with the scanning probe. Through a quantitative comparison between experimental image and simulation, a Fourier-space approach is proposed to estimate defocus and sample thickness. The effective atom size in Z-contrast imaging depends on the annular detector's inner angle. Therefore, an optimum angle exists for the highest resolution as a trade-off between reduced atom size and reduced signal with limited information transfer due to noise.","corpus_id":29968171,"score":1},{"doc_id":"20126419","title":"A 3D Resolution Measure for Optical Microscopy.","abstract":"An information-theoretic three-dimensional (3D) resolution measure for the optical microscope is introduced. Based on the Cramer-Rao inequality, this resolution measure specifies a lower bound on the accuracy with which a given distance separating two objects in 3D space can be estimated from the acquired image. Useful in many applications, accurate determination of the distance of separation can, for example, help to characterize the interaction that occurs between two closely spaced biomolecules in a biological cell. In addition to presenting the underlying theory, we show that the resolution measure predicts that, by detecting a sufficient number of photons from an object pair, arbitrarily small distances of separation can be estimated with prespecified accuracy. Furthermore, we illustrate its dependence on properties such as the object pair's 3D spatial orientation. With estimations on simulated images, we show that the maximum likelihood estimator is capable of attaining the accuracy predicted by the resolution measure.","corpus_id":6004128,"score":1},{"doc_id":"20198116","title":"3D RESOLUTION MEASURE FOR MULTIFOCAL PLANE MICROSCOPY.","abstract":"The distance separating two biomolecules in close proximity is an important determinant of the nature of their interaction. While much focus has been given to resolving distances in 2D, the 3D cell in which biological interactions occur necessitates the evaluation of resolution in 3D. Recently, we introduced an information-theoretic 3D resolution measure which predicts that the resolution of an optical microscope is unlimited, and that it improves as more photons are detected from the imaged molecules. Here, we investigate the 3D resolution measure for a multifocal plane microscope. Used for the simultaneous imaging of distinct focal planes within a specimen, multifocal plane microscopy has important applications in the tracking of microscopic objects in 3D. By comparing their 3D resolution measures, we determine the circumstances under which a two-plane microscope setup offers better resolvability than a comparable conventional microscope.","corpus_id":15044035,"score":1},{"doc_id":"20888956","title":"Fundamentals of three-dimensional reconstruction from projections.","abstract":"Three-dimensional (3D) reconstruction of an object mass density from the set of its 2D line projections lies at a core of both single-particle reconstruction technique and electron tomography. Both techniques utilize electron microscope to collect a set of projections of either multiple objects representing in principle the same macromolecular complex in an isolated form, or a subcellular structure isolated in situ. Therefore, the goal of macromolecular electron microscopy is to invert the projection transformation to recover the distribution of the mass density of the original object. The problem is interesting in that in its discrete form it is ill-posed and not invertible. Various algorithms have been proposed to cope with the practical difficulties of this inversion problem and their differ widely in terms of their robustness with respect to noise in the data, completeness of the collected projection dataset, errors in projections orientation parameters, abilities to efficiently handle large datasets, and other obstacles typically encountered in molecular electron microscopy. Here, we review the theoretical foundations of 3D reconstruction from line projections followed by an overview of reconstruction algorithms routinely used in practice of electron microscopy.","corpus_id":23406418,"score":1},{"doc_id":"21757012","title":"An adaptation of the Wiener filter suitable for analyzing images of isolated single particles.","abstract":"The Wiener filter is a standard means of optimizing the signal in sums of aligned, noisy images obtained by electron cryo-microscopy (cryo-EM). However, estimation of the resolution-dependent (\"spectral\") signal-to-noise ratio (SSNR) from the input data has remained problematic, and error reduction due to specific application of the SSNR term within a Wiener filter has not been reported. Here we describe an adjustment to the Wiener filter for optimal summation of images of isolated particles surrounded by large regions of featureless background, as is typically the case in single-particle cryo-EM applications. We show that the density within the particle area can be optimized, in the least-squares sense, by scaling the SSNR term found in the conventional Wiener filter by a factor that reflects the fraction of the image field occupied by the particle. We also give related expressions that allow the SSNR to be computed for application in this new filter, by incorporating a masking step into a Fourier Ring Correlation (FRC), a standard resolution measure. Furthermore, we show that this masked FRC estimation scheme substantially improves on the accuracy of conventional SSNR estimation methods. We demonstrate the validity of our new approach in numeric tests with simulated data corresponding to realistic cryo-EM imaging conditions. This variation of the Wiener filter and accompanying derivation should prove useful for a variety of single-particle cryo-EM applications, including 3D reconstruction.","corpus_id":1605889,"score":1},{"doc_id":"22613568","title":"Optimal noise reduction in 3D reconstructions of single particles using a volume-normalized filter.","abstract":"The high noise level found in single-particle electron cryo-microscopy (cryo-EM) image data presents a special challenge for three-dimensional (3D) reconstruction of the imaged molecules. The spectral signal-to-noise ratio (SSNR) and related Fourier shell correlation (FSC) functions are commonly used to assess and mitigate the noise-generated error in the reconstruction. Calculation of the SSNR and FSC usually includes the noise in the solvent region surrounding the particle and therefore does not accurately reflect the signal in the particle density itself. Here we show that the SSNR in a reconstructed 3D particle map is linearly proportional to the fractional volume occupied by the particle. Using this relationship, we devise a novel filter (the \"single-particle Wiener filter\") to minimize the error in a reconstructed particle map, if the particle volume is known. Moreover, we show how to approximate this filter even when the volume of the particle is not known, by optimizing the signal within a representative interior region of the particle. We show that the new filter improves on previously proposed error-reduction schemes, including the conventional Wiener filter as well as figure-of-merit weighting, and quantify the relationship between all of these methods by theoretical analysis as well as numeric evaluation of both simulated and experimentally collected data. The single-particle Wiener filter is applicable across a broad range of existing 3D reconstruction techniques, but is particularly well suited to the Fourier inversion method, leading to an efficient and accurate implementation.","corpus_id":22228232,"score":1},{"doc_id":"24830764","title":"Macromolecular 3D SEM reconstruction strategies: signal to noise ratio and resolution.","abstract":"Three-dimensional scanning electron microscopy generates quantitative volumetric structural data from SEM images of macromolecules. This technique provides a quick and easy way to define the quaternary structure and handedness of protein complexes. Here, we apply a variety of preparation and imaging methods to filamentous actin in order to explore the relationship between resolution, signal-to-noise ratio, structural preservation and dataset size. This information can be used to define successful imaging strategies for different applications.","corpus_id":205523843,"score":1},{"doc_id":"24989387","title":"Assessment of volumetric noise and resolution performance for linear and nonlinear CT reconstruction methods.","abstract":"PURPOSE: For nonlinear iterative image reconstructions (IR), the computed tomography (CT) noise and resolution properties can depend on the specific imaging conditions, such as lesion contrast and image noise level. Therefore, it is imperative to develop a reliable method to measure the noise and resolution properties under clinically relevant conditions. This study aimed to develop a robust methodology to measure the three-dimensional CT noise and resolution properties under such conditions and to provide guidelines to achieve desirable levels of accuracy and precision. METHODS: The methodology was developed based on a previously reported CT image quality phantom. In this methodology, CT noise properties are measured in the uniform region of the phantom in terms of a task-based 3D noise-power spectrum (NPStask). The in-plane resolution properties are measured in terms of the task transfer function (TTF) by applying a radial edge technique to the rod inserts in the phantom. The z-direction resolution properties are measured from a supplemental phantom, also in terms of the TTF. To account for the possible nonlinearity of IR, the NPStask is measured with respect to the noise magnitude, and the TTF with respect to noise magnitude and edge contrast. To determine the accuracy and precision of the methodology, images of known noise and resolution properties were simulated. The NPStask and TTF were measured on the simulated images and compared to the truth, with criteria established to achieve NPStask and TTF measurements with <10% error. To demonstrate the utility of this methodology, measurements were performed on a commercial CT system using five dose levels, two slice thicknesses, and three reconstruction algorithms (filtered backprojection, FBP; iterative reconstruction in imaging space, IRIS; and sinogram affirmed iterative reconstruction with strengths of 5, SAFIRE5). RESULTS: To achieve NPStask measurements with <10% error, the number of regions of interest needed to be greater than 65. To achieve TTF measurements with <10% error, the contrast-to-noise ratio of the edge needed to be ≥15, achievable by averaging multiple slices across the same edge. The NPStask measured on a commercial CT system showed IR's reduced noise (IRIS, 30% and SAFIRE5, 55%) and \"waxier\" texture (peak frequencies: FBP, 0.25 mm(-1); IRIS, 0.23 mm(-1); and SAFIRE5, 0.16 mm(-1)). The TTF measured within the axial plane showed improved in-plane resolution with SAFIRE5 at the TTF 50% frequency, f50 (FBP, 0.36-0.41 mm(-1); SAFIRE5, 0.37-0.46 mm(-1)). The TTF measured along the axial direction showed improved z-direction resolution with thinner slice thickness (f50: 0.6 mm, 0.35-0.79 mm(-1); 1.5 mm, 0.22-0.3 mm(-1)) and with SAFIRE5 (f50: FBP, 0.35-0.52 mm(-1); SAFIRE5, 0.42-0.79 mm(-1)). Both in-plane and z-direction resolution of SAFIRE5 showed strong dependency on contrast, reflecting SAFIRE5's nonlinearity. CONCLUSIONS: A methodology was developed to measure three-dimensional CT noise and resolution properties for iterative reconstruction, especially at challenging measurement conditions with low contrast and high image noise. The methodology also demonstrated its utility for evaluating commercial CT systems.","corpus_id":1509974,"score":1},{"doc_id":"27139648","title":"3D spatial resolution and spectral resolution of interferometric 3D imaging spectrometry.","abstract":"Recently developed interferometric 3D imaging spectrometry (J. Opt. Soc. Am A18, 765 [2001]1084-7529JOAOD610.1364/JOSAA.18.000765) enables obtainment of the spectral information and 3D spatial information for incoherently illuminated or self-luminous object simultaneously. Using this method, we can obtain multispectral components of complex holograms, which correspond directly to the phase distribution of the wavefronts propagated from the polychromatic object. This paper focuses on the analysis of spectral resolution and 3D spatial resolution in interferometric 3D imaging spectrometry. Our analysis is based on a novel analytical impulse response function defined over four-dimensional space. We found that the experimental results agree well with the theoretical prediction. This work also suggests a new criterion and estimate method regarding 3D spatial resolution of digital holography.","corpus_id":33755490,"score":1},{"doc_id":"17574340","title":"Classification of heterogeneous electron microscopic projections into homogeneous subsets.","abstract":"The co-existence of different states of a macromolecular complex in samples used by three-dimensional electron microscopy (3D-EM) constitutes a serious challenge. The single particle method applied directly to such heterogeneous sets is unable to provide useful information about the encountered conformational diversity and produces reconstructions with severely reduced resolution. One approach to solving this problem is to partition heterogeneous projection set into homogeneous components and apply existing reconstruction techniques to each of them. Due to the nature of the projection images and the high noise level present in them, this classification task is difficult. A method is presented to achieve the desired classification by using a novel image similarity measure and solving the corresponding optimization problem. Unlike the majority of competing approaches, the presented method employs unsupervised classification (it does not require any prior knowledge about the objects being classified) and does not involve a 3D reconstruction procedure. We demonstrate a fast implementation of this method, capable of classifying projection sets that originate from 3D-EM. The method's performance is evaluated on synthetically generated data sets produced by projecting 3D objects that resemble biological structures.","corpus_id":31337515,"score":0},{"doc_id":"18054169","title":"Progress and perspectives for atomic-resolution electron microscopy.","abstract":"The transmission electron microscope (TEM) has evolved into a highly sophisticated instrument that is ideally suited to the characterization of advanced materials. Atomic-level information is routinely accessible using both fixed-beam and scanning TEMs. This report briefly considers developments in the field of atomic-resolution electron microscopy. Recent activities include renewed attention to on-line microscope control ('autotuning'), and assessment and correction of aberrations. Aberration-corrected electron microscopy has developed rapidly in several forms although more work needs to be done to identify standard imaging conditions and to explore novel operating modes. Preparation of samples and image interpretation have also become more demanding. Ongoing problems include discrepancies between measured and simulated image contrast, concerns about radiation damage, and inversion of electron scattering.","corpus_id":2772378,"score":0},{"doc_id":"18445875","title":"Interactively variable isotropic resolution in computed tomography.","abstract":"An individual balancing between spatial resolution and image noise is necessary to fulfil the diagnostic requirements in medical CT imaging. In order to change influencing parameters, such as reconstruction kernel or effective slice thickness, additional raw-data-dependent image reconstructions have to be performed. Therefore, the noise versus resolution trade-off is time consuming and not interactively applicable. Furthermore, isotropic resolution, expressed by an equivalent point spread function (PSF) in every spatial direction, is important for the undistorted visualization and quantitative evaluation of small structures independent of the viewing plane. Theoretically, isotropic resolution can be obtained by matching the in-plane and through-plane resolution with the aforementioned parameters. Practically, however, the user is not assisted in doing so by current reconstruction systems and therefore isotropic resolution is not commonly achieved, in particular not at the desired resolution level. In this paper, an integrated approach is presented for equalizing the in-plane and through-plane spatial resolution by image filtering. The required filter kernels are calculated from previously measured PSFs in x/y- and z-direction. The concepts derived are combined with a variable resolution filtering technique. Both approaches are independent of CT raw data and operate only on reconstructed images which allows for their application in real time. Thereby, the aim of interactively variable, isotropic resolution is achieved. Results were evaluated quantitatively by measuring PSFs and image noise, and qualitatively by comparing the images to direct reconstructions regarded as the gold standard. Filtered images matched direct reconstructions with arbitrary reconstruction kernels with standard deviations in difference images of typically between 1 and 17 HU. Isotropic resolution was achieved within 5% of the selected resolution level. Processing times of 20-100 ms per frame allow for interactive use.","corpus_id":13491816,"score":0},{"doc_id":"18545426","title":"Three-dimensional scheme for time-domain fluorescence molecular tomography based on Laplace transforms with noise-robust factors.","abstract":"As a visualizing and quantitative method, Fluorescence Molecular Tomography (FMT) has many potential applications in biomedical field and its three-dimensional (3D) implementation is needed in both theory and practice. In this paper, we propose a 3D scheme for time-domain FMT within the normalized Born-ratio formulation. A finite element method solution to the Laplace transformed time-domain coupled diffusion equations is employed as the forward model, and the resultant linear inversions at two distinct transform-factors are solved with an algebraic reconstruction technique to separate fluorescent yield and lifetime images. The algorithm is validated using simulated data for 3D cylinder phantoms, and the spatial resolution and quantitativeness of the reconstruction assessed. We demonstrate that the proposed approach can accurately retrieve the positions and shapes of the targets with high spatial resolution and quantitative accuracy, and tolerate a signal-to-noise ratio down to 25dB by appropriately choosing the transform factors.","corpus_id":28159899,"score":0},{"doc_id":"19410651","title":"High-resolution single-particle orientation refinement based on spectrally self-adapting common lines.","abstract":"Three-dimensional (3D) structure determination from electron microscopic images of single molecules can be difficult for particles with low or no internal symmetry, and for images with low signal-to-noise ratio (SNR), due to the existence of false maxima in the scoring function used for orientation search. In attempt to improve robustness of orientation parameter refinement towards noise and poor starting reconstruction quality, we have developed a method for common lines-based orientation search in Fourier space. The Fourier-space formulation enables inclusion of resolution (spatial frequency of the low-pass limit) as a variable that is adjusted in a particle-dependent, self-adaptive manner. The method allows for the underlying 3D structure to be estimated to high resolution, and requires only a crude, low-resolution reconstruction as starting-point for refinement. Benchmarking of the method is performed on experimental and synthetic data.","corpus_id":22833827,"score":0},{"doc_id":"19766422","title":"3D sensitivity encoded ellipsoidal MR spectroscopic imaging of gliomas at 3T.","abstract":"PURPOSE: The goal of this study was to implement time efficient data acquisition and reconstruction methods for 3D magnetic resonance spectroscopic imaging (MRSI) of gliomas at a field strength of 3T using parallel imaging techniques. METHODS: The point spread functions, signal to noise ratio (SNR), spatial resolution, metabolite intensity distributions and Cho:NAA ratio of 3D ellipsoidal, 3D sensitivity encoding (SENSE) and 3D combined ellipsoidal and SENSE (e-SENSE) k-space sampling schemes were compared with conventional k-space data acquisition methods. RESULTS: The 3D SENSE and e-SENSE methods resulted in similar spectral patterns as the conventional MRSI methods. The Cho:NAA ratios were highly correlated (P<.05 for SENSE and P<.001 for e-SENSE) with the ellipsoidal method and all methods exhibited significantly different spectral patterns in tumor regions compared to normal appearing white matter. The geometry factors ranged between 1.2 and 1.3 for both the SENSE and e-SENSE spectra. When corrected for these factors and for differences in data acquisition times, the empirical SNRs were similar to values expected based upon theoretical grounds. The effective spatial resolution of the SENSE spectra was estimated to be same as the corresponding fully sampled k-space data, while the spectra acquired with ellipsoidal and e-SENSE k-space samplings were estimated to have a 2.36-2.47-fold loss in spatial resolution due to the differences in their point spread functions. CONCLUSION: The 3D SENSE method retained the same spatial resolution as full k-space sampling but with a 4-fold reduction in scan time and an acquisition time of 9.28 min. The 3D e-SENSE method had a similar spatial resolution as the corresponding ellipsoidal sampling with a scan time of 4:36 min. Both parallel imaging methods provided clinically interpretable spectra with volumetric coverage and adequate SNR for evaluating Cho, Cr and NAA.","corpus_id":16799720,"score":0},{"doc_id":"19915208","title":"High-resolution low-dose scanning transmission electron microscopy.","abstract":"During the past two decades instrumentation in scanning transmission electron microscopy (STEM) has pushed toward higher intensity electron probes to increase the signal-to-noise ratio of recorded images. While this is suitable for robust specimens, biological specimens require a much reduced electron dose for high-resolution imaging. We describe here protocols for low-dose STEM image recording with a conventional field-emission gun STEM, while maintaining the high-resolution capability of the instrument. Our findings show that a combination of reduced pixel dwell time and reduced gun current can achieve radiation doses comparable to low-dose TEM.","corpus_id":26161322,"score":0},{"doc_id":"20107244","title":"Simultaneous measurement of noise and spatial resolution in PET phantom images.","abstract":"As an aid to evaluating image reconstruction and correction algorithms in positron emission tomography, a phantom procedure has been developed that simultaneously measures image noise and spatial resolution. A commercially available (68)Ge cylinder phantom (20 cm diameter) was positioned in the center of the field-of-view and two identical emission scans were sequentially performed. Image noise was measured by determining the difference between corresponding pixels in the two images and by calculating the standard deviation of these difference data. Spatial resolution was analyzed using a Fourier technique to measure the extent of the blurring at the edge of the phantom images. This paper addresses the noise aspects of the technique as the spatial resolution measurement has been described elsewhere. The noise measurement was validated by comparison with data obtained from multiple replicate images over a range of noise levels. In addition, we illustrate how simultaneous measurement of noise and resolution can be used to evaluate two different corrections for random coincidence events: delayed event subtraction and singles-based randoms correction. For a fixed number of iterations of the maximum-likelihood expectation-maximization algorithm, the singles-based correction gave rise to higher noise than delayed event subtraction. However, when noise and resolution were measured simultaneously it was shown that singles-based randoms correction gave rise to lower noise than delayed event subtraction for a fixed spatial resolution. The proposed method of simultaneously measuring image noise and spatial resolution is useful for evaluating reconstruction algorithms and may aid standardization of data collection between centers.","corpus_id":8822070,"score":0},{"doc_id":"20887850","title":"3D reconstruction from electron micrographs a personal account of its development.","abstract":"Prior to the development of 3D reconstruction, images were interpreted in terms of models made from simple units like ping-pong balls. Generally, people eye-balled the images and with other knowledge about its structure, such as the number of subunits, proposed models to account for the images. How was one to know if the models were correct and to what degree they faithfully represented the true structure? The analysis of electron micrographs of negatively stained viral structures led to the answers and 3D reconstruction.","corpus_id":42559140,"score":0},{"doc_id":"20888959","title":"3D reconstruction from 2D crystal image and diffraction data.","abstract":"Electron crystallography of 2D protein crystals can determine the structure of membrane embedded proteins at high resolution. Images or electron diffraction patterns are recorded with the electron microscope of the frozen hydrated samples, and the 3D structure of the proteins is then determined by computer data processing. Here we introduce the image-processing algorithms for crystallographic Fourier space based methods using the Medical Research Council (MRC) programs, and illustrate the usage of the software packages 2dx, XDP, and IPLT.","corpus_id":18113338,"score":0},{"doc_id":"20888960","title":"Fourier-Bessel reconstruction of helical assemblies.","abstract":"Helical symmetry is commonly used for building macromolecular assemblies. Helical symmetry is naturally present in viruses and cytoskeletal filaments and also occurs during crystallization of isolated proteins, such as Ca-ATPase and the nicotinic acetyl choline receptor. Structure determination of helical assemblies by electron microscopy has a long history dating back to the original work on three-dimensional (3D) reconstruction. A helix offers distinct advantages for structure determination. Not only can one improve resolution by averaging across the constituent subunits, but each helical assembly provides multiple views of these subunits and thus provides a complete 3D data set. This review focuses on Fourier methods of helical reconstruction, covering the theoretical background, a step-by-step guide to the process, and a practical example based on previous work with Ca-ATPase. Given recent results from helical reconstructions at atomic resolution and the development of graphical user interfaces to aid in the process, these methods are likely to continue to make an important contribution to the field of structural biology.","corpus_id":13183416,"score":0},{"doc_id":"21501817","title":"Atomic resolution cryo electron microscopy of macromolecular complexes.","abstract":"Single-particle cryo electron microscopy (cryoEM) is a technique for determining three-dimensional (3D) structures from projection images of molecular complexes preserved in their \"native,\" noncrystalline state. Recently, atomic or near-atomic resolution structures of several viruses and protein assemblies have been determined by single-particle cryoEM, allowing ab initio atomic model building by following the amino acid side chains or nucleic acid bases identifiable in their cryoEM density maps. In particular, these cryoEM structures have revealed extended arms contributing to molecular interactions that are otherwise not resolved by the conventional structural method of X-ray crystallography at similar resolutions. High-resolution cryoEM requires careful consideration of a number of factors, including proper sample preparation to ensure structural homogeneity, optimal configuration of electron imaging conditions to record high-resolution cryoEM images, accurate determination of image parameters to correct image distortions, efficient refinement and computation to reconstruct a 3D density map, and finally appropriate choice of modeling tools to construct atomic models for functional interpretation. This progress illustrates the power of cryoEM and ushers it into the arsenal of structural biology, alongside conventional techniques of X-ray crystallography and NMR, as a major tool (and sometimes the preferred one) for the studies of molecular interactions in supramolecular assemblies or machines.","corpus_id":24267496,"score":0},{"doc_id":"21536524","title":"Spatially regularized compressed sensing for high angular resolution diffusion imaging.","abstract":"Despite the relative recency of its inception, the theory of compressive sampling (aka compressed sensing) (CS) has already revolutionized multiple areas of applied sciences, a particularly important instance of which is medical imaging. Specifically, the theory has provided a different perspective on the important problem of optimal sampling in magnetic resonance imaging (MRI), with an ever-increasing body of works reporting stable and accurate reconstruction of MRI scans from the number of spectral measurements which would have been deemed unacceptably small as recently as five years ago. In this paper, the theory of CS is employed to palliate the problem of long acquisition times, which is known to be a major impediment to the clinical application of high angular resolution diffusion imaging (HARDI). Specifically, we demonstrate that a substantial reduction in data acquisition times is possible through minimization of the number of diffusion encoding gradients required for reliable reconstruction of HARDI scans. The success of such a minimization is primarily due to the availability of spherical ridgelet transformation, which excels in sparsifying HARDI signals. What makes the resulting reconstruction procedure even more accurate is a combination of the sparsity constraints in the diffusion domain with additional constraints imposed on the estimated diffusion field in the spatial domain. Accordingly, the present paper describes an original way to combine the diffusion- and spatial-domain constraints to achieve a maximal reduction in the number of diffusion measurements, while sacrificing little in terms of reconstruction accuracy. Finally, details are provided on an efficient numerical scheme which can be used to solve the aforementioned reconstruction problem by means of standard and readily available estimation tools. The paper is concluded with experimental results which support the practical value of the proposed reconstruction methodology.","corpus_id":3209874,"score":0},{"doc_id":"21761448","title":"A 3D wavelet fusion approach for the reconstruction of isotropic-resolution MR images from orthogonal anisotropic-resolution scans.","abstract":"Hardware constraints, scanning time limitations, patient movement, and signal-to-noise ratio (SNR) considerations, restrict the slice-selection and the in-plane resolutions of MRI differently, generally resulting in anisotropic voxels. This nonuniform sampling can be problematic, especially in image segmentation and clinical examination. To alleviate this, the acquisition is divided into (two or) three separate scans, with higher in-plane resolutions and thick slices, yet orthogonal slice-selection directions. In this work, a noniterative wavelet-based approach for combining the three orthogonal scans is adopted, and its advantages compared with other existing methods, such as Fourier techniques, are discussed, including the consideration of the actual pulse response of the MRI scanner, and its lower computational complexity. Experimental results are shown on simulated and real 7 T MRI data.","corpus_id":17437903,"score":0},{"doc_id":"21844593","title":"Electron microscopy at a sub-50 pm resolution.","abstract":"An aberration-corrected electron microscope developed in CREST project has been applied for imaging atoms and clusters buried inside crystals. The resolution of the microscope in scanning transmission electron microscopy (STEM) has experimentally proved to be better than 47 pm by use of a cold-field emission gun at 300 kV. The high resolution has given an advantage for imaging light elements such as lithium atoms discriminating one by one. Moreover, a three-dimensional structure imaging has been demonstrated for dopant clusters by a sub-50 pm STEM, using its high depth resolution.","corpus_id":21567355,"score":0},{"doc_id":"21934862","title":"Sample drift correction in 3D fluorescence photoactivation localization microscopy.","abstract":"The recent development of diffraction-unlimited far-field fluorescence microscopy has overcome the classical resolution limit of ~250 nm of conventional light microscopy by about a factor of ten. The improved resolution, however, reveals not only biological structures at an unprecedented resolution, but is also susceptible to sample drift on a much finer scale than previously relevant. Without correction, sample drift leads to smeared images with decreased resolution, and in the worst case to misinterpretation of the imaged structures. This poses a problem especially for techniques such as Fluorescence Photoactivation Localization Microscopy (FPALM/PALM) or Stochastic Optical Reconstruction Microscopy (STORM), which often require minutes recording time. Here we discuss an approach that corrects for three-dimensional (3D) drift in images of fixed samples without the requirement for fiduciary markers or instrument modifications. Drift is determined by calculating the spatial cross-correlation function between subsets of localized particles imaged at different times. Correction down to ~5 nm precision is achieved despite the fact that different molecules are imaged in each frame. We demonstrate the performance of our drift correction algorithm with different simulated structures and analyze its dependence on particle density and localization precision. By imaging mitochondria with Biplane FPALM we show our algorithm's feasibility in a practical application.","corpus_id":263364997,"score":0},{"doc_id":"22437612","title":"Electron tomography at 2.4-ångström resolution.","abstract":"Transmission electron microscopy is a powerful imaging tool that has found broad application in materials science, nanoscience and biology. With the introduction of aberration-corrected electron lenses, both the spatial resolution and the image quality in transmission electron microscopy have been significantly improved and resolution below 0.5 ångströms has been demonstrated. To reveal the three-dimensional (3D) structure of thin samples, electron tomography is the method of choice, with cubic-nanometre resolution currently achievable. Discrete tomography has recently been used to generate a 3D atomic reconstruction of a silver nanoparticle two to three nanometres in diameter, but this statistical method assumes prior knowledge of the particle's lattice structure and requires that the atoms fit rigidly on that lattice. Here we report the experimental demonstration of a general electron tomography method that achieves atomic-scale resolution without initial assumptions about the sample structure. By combining a novel projection alignment and tomographic reconstruction method with scanning transmission electron microscopy, we have determined the 3D structure of an approximately ten-nanometre gold nanoparticle at 2.4-ångström resolution. Although we cannot definitively locate all of the atoms inside the nanoparticle, individual atoms are observed in some regions of the particle and several grains are identified in three dimensions. The 3D surface morphology and internal lattice structure revealed are consistent with a distorted icosahedral multiply twinned particle. We anticipate that this general method can be applied not only to determine the 3D structure of nanomaterials at atomic-scale resolution, but also to improve the spatial resolution and image quality in other tomography fields.","corpus_id":1600103,"score":0},{"doc_id":"23086876","title":"Semiautomatic, high-throughput, high-resolution protocol for three-dimensional reconstruction of single particles in electron microscopy.","abstract":"In this chapter we describe the steps needed for reconstructing the three-dimensional structure of a macromolecular complex starting from its projections collected in electron micrographs. The concepts are shown through the use of Xmipp 3.0, a software suite specifically designed for the image processing of biological structures imaged with electron or X-ray microscopy. We illustrate the image processing workflow by applying it to the images of Bovine Papilloma virus published in Wolf et al. (Proc Natl Acad Sci USA 107:6298-6303, 2010). We show that in the case of high-quality, homogeneous datasets with a priori knowledge about the initial volume, we can have a high-resolution 3D reconstruction in less than 1 day using a computer cluster with only 32 processors.","corpus_id":8005001,"score":0},{"doc_id":"23221063","title":"3D PET image reconstruction including both motion correction and registration directly into an MR or stereotaxic spatial atlas.","abstract":"This work explores the feasibility and impact of including both the motion correction and the image registration transformation parameters from positron emission tomography (PET) image space to magnetic resonance (MR), or stereotaxic, image space within the system matrix of PET image reconstruction. This approach is motivated by the fields of neuroscience and psychiatry, where PET is used to investigate differences in activation patterns between different groups of participants, requiring all images to be registered to a common spatial atlas. Currently, image registration is performed after image reconstruction which introduces interpolation effects into the final image. Furthermore, motion correction (also requiring registration) introduces a further level of interpolation, and the overall result of these operations can lead to resolution degradation and possibly artifacts. It is important to note that performing such operations on a post-reconstruction basis means, strictly speaking, that the final images are not ones which maximize the desired objective function (e.g. maximum likelihood (ML), or maximum a posteriori reconstruction (MAP)). To correctly seek parameter estimates in the desired spatial atlas which are in accordance with the chosen reconstruction objective function, it is necessary to include the transformation parameters for both motion correction and registration within the system modeling stage of image reconstruction. Such an approach not only respects the statistically chosen objective function (e.g. ML or MAP), but furthermore should serve to reduce the interpolation effects. To evaluate the proposed method, this work investigates registration (including motion correction) using 2D and 3D simulations based on the high resolution research tomograph (HRRT) PET scanner geometry, with and without resolution modeling, using the ML expectation maximization (MLEM) reconstruction algorithm. The quality of reconstruction was assessed using bias-variance and root mean squared error analyses, comparing the proposed method to conventional post-reconstruction registration methods. An overall reduction in bias (for a cold region: from 41% down to 31% (2D) and 97% down to 65% (3D), and for a hot region: from 11% down to 8% (2D) and from 16% down to 14% (3D)) and in root mean squared error analyses (for a cold region: from 43% to 37% (2D) and from 97% to 65% (3D), and for a hot region: from 11% to 9% (2D) and from 16% down to 14% (3D)) in reconstructed regional mean activities (full regions of interest; all with statistical significance: p < 5 × 10(-10)) is found when including the motion correction and registration in the system matrix of the MLEM reconstruction, with resolution modeling. However, this improvement in performance comes with an extra computational cost of about 40 min. In this context, this work constitutes an important step toward the goal of estimating parameters of interest directly from the raw Poisson-distributed PET data, and hence toward the complete elimination of post-processing steps.","corpus_id":35253278,"score":0},{"doc_id":"23410725","title":"Projection-based volume alignment.","abstract":"When heterogeneous samples of macromolecular assemblies are being examined by 3D electron microscopy (3DEM), often multiple reconstructions are obtained. For example, subtomograms of individual particles can be acquired from tomography, or volumes of multiple 2D classes can be obtained by random conical tilt reconstruction. Of these, similar volumes can be averaged to achieve higher resolution. Volume alignment is an essential step before 3D classification and averaging. Here we present a projection-based volume alignment (PBVA) algorithm. We select a set of projections to represent the reference volume and align them to a second volume. Projection alignment is achieved by maximizing the cross-correlation function with respect to rotation and translation parameters. If data are missing, the cross-correlation functions are normalized accordingly. Accurate alignments are obtained by averaging and quadratic interpolation of the cross-correlation maximum. Comparisons of the computation time between PBVA and traditional 3D cross-correlation methods demonstrate that PBVA outperforms the traditional methods. Performance tests were carried out with different signal-to-noise ratios using modeled noise and with different percentages of missing data using a cryo-EM dataset. All tests show that the algorithm is robust and highly accurate. PBVA was applied to align the reconstructions of a subcomplex of the NADH: ubiquinone oxidoreductase (Complex I) from the yeast Yarrowia lipolytica, followed by classification and averaging.","corpus_id":6689254,"score":0},{"doc_id":"23456116","title":"Structured-light-based highly dense and robust 3D reconstruction.","abstract":"In this paper, a structured-light-based highly dense and robust 3D reconstruction method is proposed by combining a Gray code and region-shifting pattern. The region-shifting pattern is transformed to the trapezoidal and triangle wave shifting pattern by combining all frames of the region-shifting pattern, and then the boundary of the trapezoidal wave shifting pattern and the peak and phase of the triangle wave shifting pattern are estimated. Through this technique, the spatial resolution is increased about three times. Consequently, the 3D points are reconstructed with a resolution much higher than a camera image resolution. Moreover, as the proposed method measures the boundary and the peak with all frames, it increases the signal-to-noise ratio and is more robust than the conventional methods that use only one or two frames to detect them.","corpus_id":9262693,"score":0},{"doc_id":"24106307","title":"High-resolution restoration of 3D structures from widefield images with extreme low signal-to-noise-ratio.","abstract":"Four-dimensional fluorescence microscopy--which records 3D image information as a function of time--provides an unbiased way of tracking dynamic behavior of subcellular components in living samples and capturing key events in complex macromolecular processes. Unfortunately, the combination of phototoxicity and photobleaching can severely limit the density or duration of sampling, thereby limiting the biological information that can be obtained. Although widefield microscopy provides a very light-efficient way of imaging, obtaining high-quality reconstructions requires deconvolution to remove optical aberrations. Unfortunately, most deconvolution methods perform very poorly at low signal-to-noise ratios, thereby requiring moderate photon doses to obtain acceptable resolution. We present a unique deconvolution method that combines an entropy-based regularization function with kernels that can exploit general spatial characteristics of the fluorescence image to push the required dose to extreme low levels, resulting in an enabling technology for high-resolution in vivo biological imaging.","corpus_id":15332429,"score":0},{"doc_id":"24651662","title":"Ophthalmic magnetic resonance imaging at 7 T using a 6-channel transceiver radiofrequency coil array in healthy subjects and patients with intraocular masses.","abstract":"OBJECTIVES: This study was designed to examine the feasibility of ophthalmic magnetic resonance imaging (MRI) at 7 T using a local 6-channel transmit/receive radiofrequency (RF) coil array in healthy volunteers and patients with intraocular masses. MATERIALS AND METHODS: A novel 6-element transceiver RF coil array that makes uses of loop elements and that is customized for eye imaging at 7 T is proposed. Considerations influencing the RF coil design and the characteristics of the proposed RF coil array are presented. Numerical electromagnetic field simulations were conducted to enhance the RF coil characteristics. Specific absorption rate simulations and a thorough assessment of RF power deposition were performed to meet the safety requirements. Phantom experiments were carried out to validate the electromagnetic field simulations and to assess the real performance of the proposed transceiver array. Certified approval for clinical studies was provided by a local notified body before the in vivo studies. The suitability of the RF coil to image the human eye, optical nerve, and orbit was examined in an in vivo feasibility study including (a) 3-dimensional (3D) gradient echo (GRE) imaging, (b) inversion recovery 3D GRE imaging, and (c) 2D T2-weighted fast spin-echo imaging. For this purpose, healthy adult volunteers (n = 17; mean age, 34 ± 11 years) and patients with intraocular masses (uveal melanoma, n = 5; mean age, 57 ± 6 years) were investigated. RESULTS: All subjects tolerated all examinations well with no relevant adverse events. The 6-channel coil array supports high-resolution 3D GRE imaging with a spatial resolution as good as 0.2 × 0.2 × 1.0 mm, which facilitates the depiction of anatomical details of the eye. Rather, uniform signal intensity across the eye was found. A mean signal-to-noise ratio of approximately 35 was found for the lens, whereas the vitreous humor showed a signal-to-noise ratio of approximately 30. The lens-vitreous humor contrast-to-noise ratio was 8, which allows good differentiation between the lens and the vitreous compartment. Inversion recovery prepared 3D GRE imaging using a spatial resolution of 0.4 × 0.4 × 1.0 mm was found to be feasible. T2-weighted 2D fast spin-echo imaging with the proposed RF coil afforded a spatial resolution of 0.25 × 0.25 × 0.7 mm. CONCLUSIONS: This work provides valuable information on the feasibility of ophthalmic MRI at 7 T using a dedicated 6-channel transceiver coil array that supports the acquisition of high-contrast, high-spatial resolution images in healthy volunteers and patients with intraocular masses. The results underscore the challenges of ocular imaging at 7 T and demonstrate that these issues can be offset by using tailored RF coil hardware. The benefits of such improvements would be in positive alignment with explorations that are designed to examine the potential of MRI for the assessment of spatial arrangements of the eye segments and their masses with the ultimate goal to provide imaging means for guiding treatment decisions in ophthalmological diseases.","corpus_id":38810130,"score":0},{"doc_id":"24663755","title":"A phase demodulation method with high spatial resolution for two-dimensional single-shot X-ray Talbot interferometry.","abstract":"A new phase demodulation approach is proposed that uses windowed Fourier transforms to achieve high spatial resolution in fringe pattern analysis with a high signal-to-noise ratio for single-shot X-ray grating-based interferometry. Conventionally, Fourier transforms have been used to demodulate single-fringe patterns, but this requires a fringe pattern with a long period to obtain an acceptable signal-to-noise ratio among the demodulated parameters. However, by controlling the signal-to-noise ratio, the spatial resolution of demodulated parameters is degraded below that obtained from the phase-stepping method, which requires several images to obtain these parameters. In this paper, we introduce the use of a windowed Fourier transform with a process for analyzing the objective spectrum in isolation from other spectra on the Fourier space to overcome the limitations of the Fourier transform method. It is proved that with suitable assumptions the objective spectrum is isolated theoretically, and the spatial resolution is improved by practically accepting the limitations from the assumptions. We demonstrate the validity of the proposed method by comparing the modulation transfer function of a synthetic phantom with the conventional FT method. The proposed method is also valid on practical data obtained by an experimental setup, by which it is demonstrated that a high spatial resolution with high signal-to-noise ratio can be achieved by our proposed method.","corpus_id":207328613,"score":0},{"doc_id":"24718236","title":"Enhanced 3D spatial resolution in quantitative phase microscopy using spatially incoherent illumination.","abstract":"We describe the use of spatially incoherent illumination to make quantitative phase imaging of a semi-transparent sample, even out of the paraxial approximation. The image volume electromagnetic field is collected by scanning the image planes with a quadriwave lateral shearing interferometer, while the sample is spatially incoherently illuminated. In comparison to coherent quantitative phase measurements, incoherent illumination enriches the 3D collected spatial frequencies leading to 3D resolution increase (up to a factor 2). The image contrast loss introduced by the incoherent illumination is simulated and used to compensate the measurements. This restores the quantitative value of phase and intensity. Experimental contrast loss compensation and 3D resolution increase is presented using polystyrene and TiO(2) micro-beads. Our approach will be useful to make diffraction tomography reconstruction with a simplified setup.","corpus_id":13561105,"score":0},{"doc_id":"24784388","title":"Combined iterative reconstruction and image-domain decomposition for dual energy CT using total-variation regularization.","abstract":"PURPOSE: Dual-energy CT (DECT) is being increasingly used for its capability of material decomposition and energy-selective imaging. A generic problem of DECT, however, is that the decomposition process is unstable in the sense that the relative magnitude of decomposed signals is reduced due to signal cancellation while the image noise is accumulating from the two CT images of independent scans. Direct image decomposition, therefore, leads to severe degradation of signal-to-noise ratio on the resultant images. Existing noise suppression techniques are typically implemented in DECT with the procedures of reconstruction and decomposition performed independently, which do not explore the statistical properties of decomposed images during the reconstruction for noise reduction. In this work, the authors propose an iterative approach that combines the reconstruction and the signal decomposition procedures to minimize the DECT image noise without noticeable loss of resolution. METHODS: The proposed algorithm is formulated as an optimization problem, which balances the data fidelity and total variation of decomposed images in one framework, and the decomposition step is carried out iteratively together with reconstruction. The noise in the CT images from the proposed algorithm becomes well correlated even though the noise of the raw projections is independent on the two CT scans. Due to this feature, the proposed algorithm avoids noise accumulation during the decomposition process. The authors evaluate the method performance on noise suppression and spatial resolution using phantom studies and compare the algorithm with conventional denoising approaches as well as combined iterative reconstruction methods with different forms of regularization. RESULTS: On the Catphan©600 phantom, the proposed method outperforms the existing denoising methods on preserving spatial resolution at the same level of noise suppression, i.e., a reduction of noise standard deviation by one order of magnitude. This improvement is mainly attributed to the high noise correlation in the CT images reconstructed by the proposed algorithm. Iterative reconstruction using different regularization, including quadratic orq-generalized Gaussian Markov random field regularization, achieves similar noise suppression from high noise correlation. However, the proposed TV regularization obtains a better edge preserving performance. Studies of electron density measurement also show that our method reduces the average estimation error from 9.5% to 7.1%. On the anthropomorphic head phantom, the proposed method suppresses the noise standard deviation of the decomposed images by a factor of ∼14 without blurring the fine structures in the sinus area. CONCLUSIONS: The authors propose a practical method for DECT imaging reconstruction, which combines the image reconstruction and material decomposition into one optimization framework. Compared to the existing approaches, our method achieves a superior performance on DECT imaging with respect to decomposition accuracy, noise reduction, and spatial resolution.","corpus_id":29606734,"score":0},{"doc_id":"25735299","title":"3D high spectral and spatial resolution imaging of ex vivo mouse brain.","abstract":"PURPOSE: Widely used MRI methods show brain morphology both in vivo and ex vivo at very high resolution. Many of these methods (e.g., T2*-weighted imaging, phase-sensitive imaging, or susceptibility-weighted imaging) are sensitive to local magnetic susceptibility gradients produced by subtle variations in tissue composition. However, the spectral resolution of commonly used methods is limited to maintain reasonable run-time combined with very high spatial resolution. Here, the authors report on data acquisition at increased spectral resolution, with 3-dimensional high spectral and spatial resolution MRI, in order to analyze subtle variations in water proton resonance frequency and lineshape that reflect local anatomy. The resulting information compliments previous studies based on T2* and resonance frequency. METHODS: The proton free induction decay was sampled at high resolution and Fourier transformed to produce a high-resolution water spectrum for each image voxel in a 3D volume. Data were acquired using a multigradient echo pulse sequence (i.e., echo-planar spectroscopic imaging) with a spatial resolution of 50 × 50 × 70 μm(3) and spectral resolution of 3.5 Hz. Data were analyzed in the spectral domain, and images were produced from the various Fourier components of the water resonance. This allowed precise measurement of local variations in water resonance frequency and lineshape, at the expense of significantly increased run time (16-24 h). RESULTS: High contrast T2*-weighted images were produced from the peak of the water resonance (peak height image), revealing a high degree of anatomical detail, specifically in the hippocampus and cerebellum. In images produced from Fourier components of the water resonance at -7.0 Hz from the peak, the contrast between deep white matter tracts and the surrounding tissue is the reverse of the contrast in water peak height images. This indicates the presence of a shoulder in the water resonance that is not present at +7.0 Hz and may be specific to white matter anatomy. Moreover, a frequency shift of 6.76 ± 0.55 Hz was measured between the molecular and granular layers of the cerebellum. This shift is demonstrated in corresponding spectra; water peaks from voxels in the molecular and granular layers are consistently 2 bins apart (7.0 Hz, as dictated by the spectral resolution) from one another. CONCLUSIONS: High spectral and spatial resolution MR imaging has the potential to accurately measure the changes in the water resonance in small voxels. This information can guide optimization and interpretation of more commonly used, more rapid imaging methods that depend on image contrast produced by local susceptibility gradients. In addition, with improved sampling methods, high spectral and spatial resolution data could be acquired in reasonable run times, and used for in vivo scans to increase sensitivity to variations in local susceptibility.","corpus_id":36772517,"score":0},{"doc_id":"25824643","title":"Feasibility and evaluation of dual-source transmit 3D imaging of the orbits: Comparison to high-resolution conventional MRI at 3T.","abstract":"PURPOSE: To prospectively compare the image quality and diagnostic performance of orbital MR images obtained by using a dual-source parallel transmission (pTX) 3D sequence (Sampling Perfection with Application optimized Contrasts using different flip angle Evolution, SPACE) with the image quality of conventional high-resolution standard protocol for clinical use in patients at 3T. MATERIALS AND METHODS: After obtaining institutional review board approval and patient consent, 32 patients with clinical indication for orbital MRI were examined using a high-resolution conventional sequences and 3D pTX SPACE sequences. Quantitative measurements, image quality of the healthy orbit, incidence of artifacts, and the subjective diagnostic performance to establish diagnosis was rated. Statistical significance was calculated by using a Student's t-test and nonparametric Wilcoxon signed rank test. RESULTS: Length measurements were comparable in the two techniques, 3D pTX SPACE resulted in significant faster image acquisition with higher spatial resolution and less motion artifacts as well as better delineation of the optic nerve sheath. However, estimated contrast-to-noise and signal-to-noise and overall image quality as well as subjective scores of the conventional TSE imaging were rated significantly higher. The conventional MR sequences were the preferred techniques by the readers. CONCLUSION: This study demonstrates the feasibility of 3D pTX SPACE of the orbit resulting in a rapid acquisition of isotropic high-resolution images. Although no pathology was missed in 3D pTX SPACE, conventional MRI techniques showed the higher diagnostic confidence in our study, presumably due to the higher signal-to-noise and contrast-to-noise ratios. We observed high-resolution TSE imaging to be the preferred technique, 3D pTX SPACE cannot replace conventional MRI so far.","corpus_id":24155065,"score":0},{"doc_id":"26149628","title":"Positive contrast high-resolution 3D-cine imaging of the cardiovascular system in small animals using a UTE sequence and iron nanoparticles at 4.7, 7 and 9.4 T.","abstract":"BACKGROUND: To show that 3D sequences with ultra-short echo times (UTEs) can generate a positive contrast whatever the magnetic field (4.7, 7 or 9.4 T) and whatever Ultra Small Particles of Iron Oxide (USPIO) concentration injected and to use it for 3D time-resolved imaging of the murine cardiovascular system with high spatial and temporal resolutions. METHODS: Three different concentrations (50, 200 and 500 μmol Fe/kg) of USPIO were injected in mice and static images of the middle part of the animals were acquired at 4.7, 7 and 9.4 T pre and post-contrast with UTE (TE/TR = 0.05/4.5 ms) sequences. Signal-to-Noise Ratio (SNR) and Contrast-to-Noise Ratio (CNR) of blood and static tissus were evaluated before and after contrast agent injection. 3D-cine images (TE/TR = 0.05/3.5 ms, scan time < 12 min) at 156 μm isotropic resolution of the mouse cardiopulmonary system were acquired prospectively with the UTE sequence for the three magnetic fields and with an USPIO dose of 200 μmol Fe/kg. SNR, CNR and signal homogeneity of blood were measured. High spatial (104 μm) or temporal (3.5 ms) resolution 3D-cine imaging (scan time < 35 min) isotropic resolution were also performed at 7 T with a new sequence encoding scheme. RESULTS: UTE imaging generated positive contrast and higher SNR and CNR whatever the magnetic field and the USPIO concentration used compared to pre-contrast images. Time-resolved 3D acquisition enables high blood SNR (66.6 ± 4.5 at 7 T) and CNR (33.2 ± 4.2 at 7 T) without flow or motion artefact. Coronary arteries and aortic valve were visible on images acquired at 104 μm resolution. CONCLUSIONS: We have demonstrated that by combining the injection of iron nanoparticles with 3D-cine UTE sequences, it was possible to generate a strong positive contrast between blood and surrounding tissues. These properties were exploited to produce images of the cardiovascular system in small animals at high magnetic fields with a high spatial and temporal resolution. This approach might be useful to measure the functional cardiac parameters or to assess anatomical modifications to the blood vessels in cardio-vascular disease models.","corpus_id":15280150,"score":0},{"doc_id":"26172829","title":"High-resolution variable-density 3D cones coronary MRA.","abstract":"PURPOSE: To improve the spatial/temporal resolution of whole-heart coronary MR angiography by developing a variable-density (VD) 3D cones acquisition suitable for image reconstruction with parallel imaging and compressed sensing techniques. METHODS: A VD 3D cones trajectory design incorporates both radial and spiral trajectory undersampling techniques to achieve higher resolution. This design is used to generate a VD 3D cones trajectory with 0.8 mm/66 ms isotropic spatial/temporal resolution, using a similar number of readouts as our previous fully sampled cones trajectory (1.2 mm/100 ms). Scans of volunteers and patients are performed to evaluate the performance of the VD trajectory, using non-Cartesian L1 -ESPIRiT for high-resolution image reconstruction. RESULTS: With gridding reconstruction, the high-resolution scans experience an expected drop in signal-to-noise and contrast-to-noise ratios, but with L1 -ESPIRiT, the apparent noise is substantially reduced. Compared with 1.2 mm images, in each volunteer, the L1 -ESPIRiT 0.8 mm images exhibit higher vessel sharpness values in the right and left anterior descending arteries. CONCLUSION: Coronary MR angiography with isotropic submillimeter spatial resolution and high temporal resolution can be performed with VD 3D cones to improve the depiction of coronary arteries.","corpus_id":36807567,"score":0},{"doc_id":"26193484","title":"A Bayesian approach for suppression of limited angular sampling artifacts in single particle 3D reconstruction.","abstract":"In the single particle reconstruction, the initial 3D structure often suffers from the limited angular sampling artifact. Selecting 2D class averages of particle images generally improves the accuracy and efficiency of the reference-free 3D angle estimation, but causes an insufficient angular sampling to fill the information of the target object in the 3D frequency space. Similarly, the initial 3D structure by the random-conical tilt reconstruction has the well-known \"missing cone\" artifact. Here, we attempted to solve the limited angular sampling problem by sequentially applying maximum a posteriori estimate with expectation maximization algorithm (sMAP-EM). Using both simulated and experimental cryo-electron microscope images, the sMAP-EM was compared to the direct Fourier method on the basis of reconstruction error and resolution. To establish selection criteria of the final regularization weight for the sMAP-EM, the effects of noise level and sampling sparseness on the reconstructions were examined with evenly distributed sampling simulations. The frequency information filled in the missing cone of the conical tilt sampling simulations was assessed by developing new quantitative measurements. All the results of visual and numerical evaluations showed the sMAP-EM performed better than the direct Fourier method, regardless of the sampling method, noise level, and sampling sparseness. Furthermore, the frequency domain analysis demonstrated that the sMAP-EM can fill the meaningful information in the unmeasured angular space without detailed a priori knowledge of the objects. The current research demonstrated that the sMAP-EM has a high potential to facilitate the determination of 3D protein structures at near atomic-resolution.","corpus_id":23990990,"score":0},{"doc_id":"26366744","title":"Correction of image drift and distortion in a scanning electron microscopy.","abstract":"Continuous research on small-scale mechanical structures and systems has attracted strong demand for ultrafine deformation and strain measurements. Conventional optical microscope cannot meet such requirements owing to its lower spatial resolution. Therefore, high-resolution scanning electron microscope has become the preferred system for high spatial resolution imaging and measurements. However, scanning electron microscope usually is contaminated by distortion and drift aberrations which cause serious errors to precise imaging and measurements of tiny structures. This paper develops a new method to correct drift and distortion aberrations of scanning electron microscope images, and evaluates the effect of correction by comparing corrected images with scanning electron microscope image of a standard sample. The drift correction is based on the interpolation scheme, where a series of images are captured at one location of the sample and perform image correlation between the first image and the consequent images to interpolate the drift-time relationship of scanning electron microscope images. The distortion correction employs the axial symmetry model of charged particle imaging theory to two images sharing with the same location of one object under different imaging fields of view. The difference apart from rigid displacement between the mentioned two images will give distortion parameters. Three-order precision is considered in the model and experiment shows that one pixel maximum correction is obtained for the employed high-resolution electron microscopic system.","corpus_id":25886524,"score":0},{"doc_id":"26469938","title":"PF2fit: Polar Fast Fourier Matched Alignment of Atomistic Structures with 3D Electron Microscopy Maps.","abstract":"There continue to be increasing occurrences of both atomistic structure models in the PDB (possibly reconstructed from X-ray diffraction or NMR data), and 3D reconstructed cryo-electron microscopy (3D EM) maps (albeit at coarser resolution) of the same or homologous molecule or molecular assembly, deposited in the EMDB. To obtain the best possible structural model of the molecule at the best achievable resolution, and without any missing gaps, one typically aligns (match and fits) the atomistic structure model with the 3D EM map. We discuss a new algorithm and generalized framework, named PF(2) fit (Polar Fast Fourier Fitting) for the best possible structural alignment of atomistic structures with 3D EM. While PF(2) fit enables only a rigid, six dimensional (6D) alignment method, it augments prior work on 6D X-ray structure and 3D EM alignment in multiple ways: Scoring. PF(2) fit includes a new scoring scheme that, in addition to rewarding overlaps between the volumes occupied by the atomistic structure and 3D EM map, rewards overlaps between the volumes complementary to them. We quantitatively demonstrate how this new complementary scoring scheme improves upon existing approaches. PF(2) fit also includes two scoring functions, the non-uniform exterior penalty and the skeleton-secondary structure score, and implements the scattering potential score as an alternative to traditional Gaussian blurring. Search. PF(2) fit utilizes a fast polar Fourier search scheme, whose main advantage is the ability to search over uniformly and adaptively sampled subsets of the space of rigid-body motions. PF(2) fit also implements a new reranking search and scoring methodology that considerably improves alignment metrics in results obtained from the initial search.","corpus_id":6348089,"score":0},{"doc_id":"26551126","title":"Electron Microscopy of Probability Currents at Atomic Resolution.","abstract":"Atomic resolution transmission electron microscopy records the spatially resolved scattered electron density to infer positions, density, and species of atoms. These data are indispensable for studying the relation between structure and properties in solids. Here, we show how this signal can be augmented by the lateral probability current of the scattered electrons in the object plane at similar resolutions and fields of view. The currents are reconstructed from a series of three atomic resolution TEM images recorded under a slight difference of perpendicular line foci. The technique does not rely on the coherence of the electron beam and can be used to reveal electric, magnetic, and strain fields with incoherent electron beams as well as correlations in inelastic transitions, such as electron magnetic chiral dichroism.","corpus_id":206263685,"score":0},{"doc_id":"26594081","title":"Thermodynamic Limits of Spatial Resolution in Active Thermography.","abstract":"Thermal waves are caused by pure diffusion: their amplitude is decreased by more than a factor of 500 within a propagation distance of one wavelength. The diffusion equation, which describes the temperature as a function of space and time, is linear. For every linear equation the superposition principle is valid, which is known as Huygens principle for optical or mechanical wave fields. This limits the spatial resolution, like the Abbe diffraction limit in optics. The resolution is the minimal size of a structure which can be detected at a certain depth. If an embedded structure at a certain depth in a sample is suddenly heated, e.g., by eddy current or absorbed light, an image of the structure can be reconstructed from the measured temperature at the sample surface. To get the resolution the image reconstruction can be considered as the time reversal of the thermal wave. This inverse problem is ill-conditioned and therefore regularization methods have to be used taking additional assumptions like smoothness of the solutions into account. In the present work for the first time, methods of non-equilibrium statistical physics are used to solve this inverse problem without the need of such additional assumptions and without the necessity to choose a regularization parameter. For reconstructing such an embedded structure by thermal waves the resolution turns out to be proportional to the depth and inversely proportional to the natural logarithm of the signal-to-noise ratio. This result could be derived from the diffusion equation by using a delta-source at a certain depth and setting the entropy production caused by thermal diffusion equal to the information loss. No specific model about the stochastic process of the fluctuations and about the distribution densities around the mean values was necessary to get this result.","corpus_id":2600206,"score":0},{"doc_id":"26697863","title":"Computation in electron microscopy.","abstract":"Some uses of the computer and computation in high-resolution transmission electron microscopy are reviewed. The theory of image calculation using Bloch wave and multislice methods with and without aberration correction is reviewed and some applications are discussed. The inverse problem of reconstructing the specimen structure from an experimentally measured electron microscope image is discussed. Some future directions of software development are given.","corpus_id":10248349,"score":0},{"doc_id":"26705325","title":"Principles of cryo-EM single-particle image processing.","abstract":"Single-particle reconstruction is the process by which 3D density maps are obtained from a set of low-dose cryo-EM images of individual macromolecules. This review considers the fundamental principles of this process and the steps in the overall workflow for single-particle image processing. Also considered are the limits that image signal-to-noise ratio places on resolution and the distinguishing of heterogeneous particle populations.","corpus_id":21949411,"score":0},{"doc_id":"27292544","title":"Hollow Cone Electron Imaging for Single Particle 3D Reconstruction of Proteins.","abstract":"The main bottlenecks for high-resolution biological imaging in electron microscopy are radiation sensitivity and low contrast. The phase contrast at low spatial frequencies can be enhanced by using a large defocus but this strongly reduces the resolution. Recently, phase plates have been developed to enhance the contrast at small defocus but electrical charging remains a problem. Single particle cryo-electron microscopy is mostly used to minimize the radiation damage and to enhance the resolution of the 3D reconstructions but it requires averaging images of a massive number of individual particles. Here we present a new route to achieve the same goals by hollow cone dark field imaging using thermal diffuse scattered electrons giving about a 4 times contrast increase as compared to bright field imaging. We demonstrate the 3D reconstruction of a stained GroEL particle can yield about 13.5 Å resolution but using a strongly reduced number of images.","corpus_id":4579340,"score":0},{"doc_id":"27867705","title":"3D differential phase contrast microscopy.","abstract":"We demonstrate 3D phase and absorption recovery from partially coherent intensity images captured with a programmable LED array source. Images are captured through-focus with four different illumination patterns. Using first Born and weak object approximations (WOA), a linear 3D differential phase contrast (DPC) model is derived. The partially coherent transfer functions relate the sample's complex refractive index distribution to intensity measurements at varying defocus. Volumetric reconstruction is achieved by a global FFT-based method, without an intermediate 2D phase retrieval step. Because the illumination is spatially partially coherent, the transverse resolution of the reconstructed field achieves twice the NA of coherent systems and improved axial resolution.","corpus_id":34080890,"score":0},{"doc_id":"28008874","title":"Ultra-high resolution electron microscopy.","abstract":"The last two decades have seen dramatic advances in the resolution of the electron microscope brought about by the successful correction of lens aberrations that previously limited resolution for most of its history. We briefly review these advances, the achievement of sub-Ångstrom resolution and the ability to identify individual atoms, their bonding configurations and even their dynamics and diffusion pathways. We then present a review of the basic physics of electron scattering, lens aberrations and their correction, and an approximate imaging theory for thin crystals which provides physical insight into the various different imaging modes. Then we proceed to describe a more exact imaging theory starting from Yoshioka's formulation and covering full image simulation methods using Bloch waves, the multislice formulation and the frozen phonon/quantum excitation of phonons models. Delocalization of inelastic scattering has become an important limiting factor at atomic resolution. We therefore discuss this issue extensively, showing how the full-width-half-maximum is the appropriate measure for predicting image contrast, but the diameter containing 50% of the excitation is an important measure of the range of the interaction. These two measures can differ by a factor of 5, are not a simple function of binding energy, and full image simulations are required to match to experiment. The Z-dependence of annular dark field images is also discussed extensively, both for single atoms and for crystals, and we show that temporal incoherence must be included accurately if atomic species are to be identified through matching experimental intensities to simulations. Finally we mention a few promising directions for future investigation.","corpus_id":206095047,"score":0},{"doc_id":"28463301","title":"Self-interference compressive digital holography with improved axial resolution and signal-to-noise ratio.","abstract":"Fresnel incoherent correlation holography (FINCH) was proposed to break the barrier of spatial incoherent digital holographic imaging and show the potential of super-resolution imaging preferences. We developed FINCH as a compressive sensing modality and reconstruction procedure as an inverse problem in order to realize 3D tomographic imaging. Improved axial resolution is obtained via compressive reconstruction. Reconstruction guarantees and accuracy of the proposed method are discussed. Compared with the real-valued signal operation, the signal-to-noise ratio of the results is increased when reconstructing from the complex-valued hologram obtained from the FINCH system.","corpus_id":46851950,"score":0},{"doc_id":"29043666","title":"3D Electron Microscopy of the ER.","abstract":"The endoplasmic reticulum (ER) forms an extensive network in plant cells. In leaf cells and vacuolated root cells it is mainly restricted to the cortex whereas in the root meristem the cortical and cytoplasmic ER takes up a large volume throughout the entire cell. Only 3D electron microscopy provides sufficient resolution to understand the spatial organization of the ER in the root. However, high contrast staining and optimally ER specific staining is essential. Here we describe a protocol for selective ER staining that allows automated or semiautomated segmentation of the organelle in 3D datasets obtained from serial sections, Array Tomography, Serial Block Face Scanning Electron Microscopy (SBFSEM), or Focused Ion Beam (FIB) SEM.","corpus_id":44922058,"score":0},{"doc_id":"29727286","title":"Reconstruction From Multiple Particles for 3D Isotropic Resolution in Fluorescence Microscopy.","abstract":"The imaging of proteins within macromolecular complexes has been limited by the low axial resolution of optical microscopes. To overcome this problem, we propose a novel computational reconstruction method that yields isotropic resolution in fluorescence imaging. The guiding principle is to reconstruct a single volume from the observations of multiple rotated particles. Our new operational framework detects particles, estimates their orientation, and reconstructs the final volume. The main challenge comes from the absence of initial template and a priori knowledge about the orientations. We formulate the estimation as a blind inverse problem, and propose a block-coordinate stochastic approach to solve the associated non-convex optimization problem. The reconstruction is performed jointly in multiple channels. We demonstrate that our method is able to reconstruct volumes with 3D isotropic resolution on simulated data. We also perform isotropic reconstructions from real experimental data of doubly labeled purified human centrioles. Our approach revealed the precise localization of the centriolar protein Cep63 around the centriole microtubule barrel. Overall, our method offers new perspectives for applications in biology that require the isotropic mapping of proteins within macromolecular assemblies.","corpus_id":3328607,"score":0}],"string":"[\n {\n \"doc_id\": \"20161040\",\n \"title\": \"A resolution measure for three-dimensional microscopy.\",\n \"abstract\": \"A three-dimensional (3D) resolution measure for the conventional optical microscope is introduced which overcomes the drawbacks of the classical 3D (axial) resolution limit. Formulated within the context of a parameter estimation problem and based on the Cramer-Rao lower bound, this 3D resolution measure indicates the accuracy with which a given distance between two objects in 3D space can be determined from the acquired image. It predicts that, given enough photons from the objects of interest, arbitrarily small distances of separation can be estimated with prespecified accuracy. Using simulated images of point source pairs, we show that the maximum likelihood estimator is capable of attaining the accuracy predicted by the resolution measure. We also demonstrate how different factors, such as extraneous noise sources and the spatial orientation of the imaged object pair, can affect the accuracy with which a given distance of separation can be determined.\",\n \"corpus_id\": 17715714,\n \"score\": 2\n },\n {\n \"doc_id\": \"20888958\",\n \"title\": \"Resolution measures in molecular electron microscopy.\",\n \"abstract\": \"Resolution measures in molecular electron microscopy provide means to evaluate quality of macromolecular structures computed from sets of their two-dimensional (2D) line projections. When the amount of detail in the computed density map is low there are no external standards by which the resolution of the result can be judged. Instead, resolution measures in molecular electron microscopy evaluate consistency of the results in reciprocal space and present it as a one-dimensional (1D) function of the modulus of spatial frequency. Here we provide description of standard resolution measures commonly used in electron microscopy. We point out that the organizing principle is the relationship between these measures and the spectral signal-to-noise ratio (SSNR) of the computed density map. Within this framework it becomes straightforward to describe the connection between the outcome of resolution evaluations and the quality of electron microscopy maps, in particular, the optimum filtration, in the Wiener sense, of the computed map. We also provide a discussion of practical difficulties of evaluation of resolution in electron microscopy, particularly in terms of its sensitivity to data processing operations used during structure determination process in single particle analysis and in electron tomography (ET).\",\n \"corpus_id\": 23444182,\n \"score\": 2\n },\n {\n \"doc_id\": \"21627992\",\n \"title\": \"Limiting factors in atomic resolution cryo electron microscopy: no simple tricks.\",\n \"abstract\": \"To bring cryo electron microscopy (cryoEM) of large biological complexes to atomic resolution, several factors--in both cryoEM image acquisition and 3D reconstruction--that may be neglected at low resolution become significantly limiting. Here we present thorough analyses of four limiting factors: (a) electron-beam tilt, (b) inaccurate determination of defocus values, (c) focus gradient through particles, and (d) particularly for large particles, dynamic (multiple) scattering of electrons. We also propose strategies to cope with these factors: (a) the divergence and direction tilt components of electron-beam tilt could be reduced by maintaining parallel illumination and by using a coma-free alignment procedure, respectively. Moreover, the effect of all beam tilt components, including spiral tilt, could be eliminated by use of a spherical aberration corrector. ( b) More accurate measurement of defocus value could be obtained by imaging areas adjacent to the target area at high electron dose and by measuring the image shift induced by tilting the electron beam. ( c) Each known Fourier coefficient in the Fourier transform of a cryoEM image is the sum of two Fourier coefficients of the 3D structure, one on each of two curved 'characteristic surfaces' in 3D Fourier space. We describe a simple model-based iterative method that could recover these two Fourier coefficients on the two characteristic surfaces. ( d) The effect of dynamic scattering could be corrected by deconvolution of a transfer function. These analyses and our proposed strategies offer useful guidance for future experimental designs targeting atomic resolution cryoEM reconstruction.\",\n \"corpus_id\": 8742056,\n \"score\": 2\n },\n {\n \"doc_id\": \"23872039\",\n \"title\": \"High-resolution noise substitution to measure overfitting and validate resolution in 3D structure determination by single particle electron cryomicroscopy.\",\n \"abstract\": \"Three-dimensional (3D) structure determination by single particle electron cryomicroscopy (cryoEM) involves the calculation of an initial 3D model, followed by extensive iterative improvement of the orientation determination of the individual particle images and the resulting 3D map. Because there is much more noise than signal at high resolution in the images, this creates the possibility of noise reinforcement in the 3D map, which can give a false impression of the resolution attained. The balance between signal and noise in the final map at its limiting resolution depends on the image processing procedure and is not easily predicted. There is a growing awareness in the cryoEM community of how to avoid such over-fitting and over-estimation of resolution. Equally, there has been a reluctance to use the two principal methods of avoidance because they give lower resolution estimates, which some people believe are too pessimistic. Here we describe a simple test that is compatible with any image processing protocol. The test allows measurement of the amount of signal and the amount of noise from overfitting that is present in the final 3D map. We have applied the method to two different sets of cryoEM images of the enzyme beta-galactosidase using several image processing packages. Our procedure involves substituting the Fourier components of the initial particle image stack beyond a chosen resolution by either the Fourier components from an adjacent area of background, or by simple randomisation of the phases of the particle structure factors. This substituted noise thus has the same spectral power distribution as the original data. Comparison of the Fourier Shell Correlation (FSC) plots from the 3D map obtained using the experimental data with that from the same data with high-resolution noise (HR-noise) substituted allows an unambiguous measurement of the amount of overfitting and an accompanying resolution assessment. A simple formula can be used to calculate an unbiased FSC from the two curves, even when a substantial amount of overfitting is present. The approach is software independent. The user is therefore completely free to use any established method or novel combination of methods, provided the HR-noise test is carried out in parallel. Applying this procedure to cryoEM images of beta-galactosidase shows how overfitting varies greatly depending on the procedure, but in the best case shows no overfitting and a resolution of ~6 Å. (382 words).\",\n \"corpus_id\": 25196434,\n \"score\": 2\n },\n {\n \"doc_id\": \"24384117\",\n \"title\": \"ResLog plots as an empirical metric of the quality of cryo-EM reconstructions.\",\n \"abstract\": \"Compared to the field of X-ray crystallography, the field of single particle three-dimensional electron microscopy has few reliable metrics for assessing the quality of 3D reconstructions. New metrics are needed that can determine whether a given 3D reconstruction accurately reflects the structure of the particles from which it was derived or instead depicts a plausible though incorrect structure due to coarse misalignment of particles. Here an empirical procedure is presented for differentiating between a reconstruction with well-aligned particles and a reconstruction with grossly misclassified particles. For a given dataset, 3D reconstructions are computed from subsets of particles with decreasing numbers of particles contributing to the reconstruction. A plot of inverse resolution vs. the logarithm of the number of particles (a \\\"ResLog\\\" plot) provides metrics for the reliability of the reconstruction and the overall quality of the dataset and processing. Specifically, the y-intercept of a regression line provides a measure of the relative accuracy of the particle alignment and classification, and the slope is an indicator of the overall data quality including the imaging conditions and processing steps. ResLog plots can also be used to optimize conditions for data collection and reconstruction parameters. Although resolution estimates can vary by method of calculation, ResLog-derived parameters are consistent whether calculated by Fourier shell correlation or Fourier neighbor correlation, or a new coordinate-based metric that serves as a yardstick for structures where atomic coordinates are available. ResLog plots could become part of a standard set of parameters to be included in 3D reconstruction reports.\",\n \"corpus_id\": 5394651,\n \"score\": 2\n },\n {\n \"doc_id\": \"24566042\",\n \"title\": \"Electron dose dependence of signal-to-noise ratio, atom contrast and resolution in transmission electron microscope images.\",\n \"abstract\": \"In order to achieve the highest resolution in aberration-corrected (AC) high-resolution transmission electron microscopy (HRTEM) images, high electron doses are required which only a few samples can withstand. In this paper we perform dose-dependent AC-HRTEM image calculations, and study the dependence of the signal-to-noise ratio, atom contrast and resolution on electron dose and sampling. We introduce dose-dependent contrast, which can be used to evaluate the visibility of objects under different dose conditions. Based on our calculations, we determine optimum samplings for high and low electron dose imaging conditions.\",\n \"corpus_id\": 12131201,\n \"score\": 2\n },\n {\n \"doc_id\": \"25836194\",\n \"title\": \"Young's double-slit experiment: noise-resolution duality.\",\n \"abstract\": \"Statistical aspects of Young's double-slit diffraction experiment are analysed quantitatively. It is shown that the signal-to-noise ratio and the spatial resolution in the detected diffraction pattern satisfy a duality relationship which implies that both of them cannot be improved simultaneously beyond a certain limit if the total number of particles forming the image is fixed. As a consequence of this duality, it is possible to estimate the minimal number of particles that have to be detected in order for two slits separated by a given distance to be resolved with a confidence level corresponding to a pre-defined signal-to-noise ratio, e.g. according to the Rose criterion. These results are related to the recently introduced imaging system quality characteristic which combines the spatial resolution and the noise sensitivity, and allows one to estimate the efficiency with which imaging quanta are utilised in a system to deliver maximal amount of information about the imaged object. The presented results can be useful for applications where the imaging quanta are at a premium or where minimization of the radiation dose is important.\",\n \"corpus_id\": 35880581,\n \"score\": 2\n },\n {\n \"doc_id\": \"29395788\",\n \"title\": \"MonoRes: Automatic and Accurate Estimation of Local Resolution for Electron Microscopy Maps.\",\n \"abstract\": \"Since the beginning of electron microscopy, resolution has been a critical parameter. In this article, we propose a fully automatic, accurate method for determining the local resolution of a 3D map (MonoRes). The foundation of this algorithm is an extension of the concept of analytic signal, termed monogenic signal. The map is filtered at different frequencies and the amplitude of the monogenic signal is calculated, after which a criterion is applied to determine the resolution at each voxel. MonoRes is fully automatic without compulsory user parameters, with great accuracy in all tests, and is computationally more rapid than existing methods in the field. In addition, MonoRes offers the option of local filtering of the original map based on the calculated local resolution.\",\n \"corpus_id\": 46822743,\n \"score\": 2\n },\n {\n \"doc_id\": \"18171501\",\n \"title\": \"Spatial resolution and information transfer in scanning transmission electron microscopy.\",\n \"abstract\": \"The relation between image resolution and information transfer is explored. It is shown that the existence of higher frequency transfer in the image is just a necessary but not sufficient condition for the achievement of higher resolution. Adopting a two-point resolution criterion, we suggest that a 10% contrast level between two features in an image should be used as a practical definition of resolution. In the context of scanning transmission electron microscopy, it is shown that the channeling effect does not have a direct connection with image resolution because sharp channeling peaks do not move with the scanning probe. Through a quantitative comparison between experimental image and simulation, a Fourier-space approach is proposed to estimate defocus and sample thickness. The effective atom size in Z-contrast imaging depends on the annular detector's inner angle. Therefore, an optimum angle exists for the highest resolution as a trade-off between reduced atom size and reduced signal with limited information transfer due to noise.\",\n \"corpus_id\": 29968171,\n \"score\": 1\n },\n {\n \"doc_id\": \"20126419\",\n \"title\": \"A 3D Resolution Measure for Optical Microscopy.\",\n \"abstract\": \"An information-theoretic three-dimensional (3D) resolution measure for the optical microscope is introduced. Based on the Cramer-Rao inequality, this resolution measure specifies a lower bound on the accuracy with which a given distance separating two objects in 3D space can be estimated from the acquired image. Useful in many applications, accurate determination of the distance of separation can, for example, help to characterize the interaction that occurs between two closely spaced biomolecules in a biological cell. In addition to presenting the underlying theory, we show that the resolution measure predicts that, by detecting a sufficient number of photons from an object pair, arbitrarily small distances of separation can be estimated with prespecified accuracy. Furthermore, we illustrate its dependence on properties such as the object pair's 3D spatial orientation. With estimations on simulated images, we show that the maximum likelihood estimator is capable of attaining the accuracy predicted by the resolution measure.\",\n \"corpus_id\": 6004128,\n \"score\": 1\n },\n {\n \"doc_id\": \"20198116\",\n \"title\": \"3D RESOLUTION MEASURE FOR MULTIFOCAL PLANE MICROSCOPY.\",\n \"abstract\": \"The distance separating two biomolecules in close proximity is an important determinant of the nature of their interaction. While much focus has been given to resolving distances in 2D, the 3D cell in which biological interactions occur necessitates the evaluation of resolution in 3D. Recently, we introduced an information-theoretic 3D resolution measure which predicts that the resolution of an optical microscope is unlimited, and that it improves as more photons are detected from the imaged molecules. Here, we investigate the 3D resolution measure for a multifocal plane microscope. Used for the simultaneous imaging of distinct focal planes within a specimen, multifocal plane microscopy has important applications in the tracking of microscopic objects in 3D. By comparing their 3D resolution measures, we determine the circumstances under which a two-plane microscope setup offers better resolvability than a comparable conventional microscope.\",\n \"corpus_id\": 15044035,\n \"score\": 1\n },\n {\n \"doc_id\": \"20888956\",\n \"title\": \"Fundamentals of three-dimensional reconstruction from projections.\",\n \"abstract\": \"Three-dimensional (3D) reconstruction of an object mass density from the set of its 2D line projections lies at a core of both single-particle reconstruction technique and electron tomography. Both techniques utilize electron microscope to collect a set of projections of either multiple objects representing in principle the same macromolecular complex in an isolated form, or a subcellular structure isolated in situ. Therefore, the goal of macromolecular electron microscopy is to invert the projection transformation to recover the distribution of the mass density of the original object. The problem is interesting in that in its discrete form it is ill-posed and not invertible. Various algorithms have been proposed to cope with the practical difficulties of this inversion problem and their differ widely in terms of their robustness with respect to noise in the data, completeness of the collected projection dataset, errors in projections orientation parameters, abilities to efficiently handle large datasets, and other obstacles typically encountered in molecular electron microscopy. Here, we review the theoretical foundations of 3D reconstruction from line projections followed by an overview of reconstruction algorithms routinely used in practice of electron microscopy.\",\n \"corpus_id\": 23406418,\n \"score\": 1\n },\n {\n \"doc_id\": \"21757012\",\n \"title\": \"An adaptation of the Wiener filter suitable for analyzing images of isolated single particles.\",\n \"abstract\": \"The Wiener filter is a standard means of optimizing the signal in sums of aligned, noisy images obtained by electron cryo-microscopy (cryo-EM). However, estimation of the resolution-dependent (\\\"spectral\\\") signal-to-noise ratio (SSNR) from the input data has remained problematic, and error reduction due to specific application of the SSNR term within a Wiener filter has not been reported. Here we describe an adjustment to the Wiener filter for optimal summation of images of isolated particles surrounded by large regions of featureless background, as is typically the case in single-particle cryo-EM applications. We show that the density within the particle area can be optimized, in the least-squares sense, by scaling the SSNR term found in the conventional Wiener filter by a factor that reflects the fraction of the image field occupied by the particle. We also give related expressions that allow the SSNR to be computed for application in this new filter, by incorporating a masking step into a Fourier Ring Correlation (FRC), a standard resolution measure. Furthermore, we show that this masked FRC estimation scheme substantially improves on the accuracy of conventional SSNR estimation methods. We demonstrate the validity of our new approach in numeric tests with simulated data corresponding to realistic cryo-EM imaging conditions. This variation of the Wiener filter and accompanying derivation should prove useful for a variety of single-particle cryo-EM applications, including 3D reconstruction.\",\n \"corpus_id\": 1605889,\n \"score\": 1\n },\n {\n \"doc_id\": \"22613568\",\n \"title\": \"Optimal noise reduction in 3D reconstructions of single particles using a volume-normalized filter.\",\n \"abstract\": \"The high noise level found in single-particle electron cryo-microscopy (cryo-EM) image data presents a special challenge for three-dimensional (3D) reconstruction of the imaged molecules. The spectral signal-to-noise ratio (SSNR) and related Fourier shell correlation (FSC) functions are commonly used to assess and mitigate the noise-generated error in the reconstruction. Calculation of the SSNR and FSC usually includes the noise in the solvent region surrounding the particle and therefore does not accurately reflect the signal in the particle density itself. Here we show that the SSNR in a reconstructed 3D particle map is linearly proportional to the fractional volume occupied by the particle. Using this relationship, we devise a novel filter (the \\\"single-particle Wiener filter\\\") to minimize the error in a reconstructed particle map, if the particle volume is known. Moreover, we show how to approximate this filter even when the volume of the particle is not known, by optimizing the signal within a representative interior region of the particle. We show that the new filter improves on previously proposed error-reduction schemes, including the conventional Wiener filter as well as figure-of-merit weighting, and quantify the relationship between all of these methods by theoretical analysis as well as numeric evaluation of both simulated and experimentally collected data. The single-particle Wiener filter is applicable across a broad range of existing 3D reconstruction techniques, but is particularly well suited to the Fourier inversion method, leading to an efficient and accurate implementation.\",\n \"corpus_id\": 22228232,\n \"score\": 1\n },\n {\n \"doc_id\": \"24830764\",\n \"title\": \"Macromolecular 3D SEM reconstruction strategies: signal to noise ratio and resolution.\",\n \"abstract\": \"Three-dimensional scanning electron microscopy generates quantitative volumetric structural data from SEM images of macromolecules. This technique provides a quick and easy way to define the quaternary structure and handedness of protein complexes. Here, we apply a variety of preparation and imaging methods to filamentous actin in order to explore the relationship between resolution, signal-to-noise ratio, structural preservation and dataset size. This information can be used to define successful imaging strategies for different applications.\",\n \"corpus_id\": 205523843,\n \"score\": 1\n },\n {\n \"doc_id\": \"24989387\",\n \"title\": \"Assessment of volumetric noise and resolution performance for linear and nonlinear CT reconstruction methods.\",\n \"abstract\": \"PURPOSE: For nonlinear iterative image reconstructions (IR), the computed tomography (CT) noise and resolution properties can depend on the specific imaging conditions, such as lesion contrast and image noise level. Therefore, it is imperative to develop a reliable method to measure the noise and resolution properties under clinically relevant conditions. This study aimed to develop a robust methodology to measure the three-dimensional CT noise and resolution properties under such conditions and to provide guidelines to achieve desirable levels of accuracy and precision. METHODS: The methodology was developed based on a previously reported CT image quality phantom. In this methodology, CT noise properties are measured in the uniform region of the phantom in terms of a task-based 3D noise-power spectrum (NPStask). The in-plane resolution properties are measured in terms of the task transfer function (TTF) by applying a radial edge technique to the rod inserts in the phantom. The z-direction resolution properties are measured from a supplemental phantom, also in terms of the TTF. To account for the possible nonlinearity of IR, the NPStask is measured with respect to the noise magnitude, and the TTF with respect to noise magnitude and edge contrast. To determine the accuracy and precision of the methodology, images of known noise and resolution properties were simulated. The NPStask and TTF were measured on the simulated images and compared to the truth, with criteria established to achieve NPStask and TTF measurements with <10% error. To demonstrate the utility of this methodology, measurements were performed on a commercial CT system using five dose levels, two slice thicknesses, and three reconstruction algorithms (filtered backprojection, FBP; iterative reconstruction in imaging space, IRIS; and sinogram affirmed iterative reconstruction with strengths of 5, SAFIRE5). RESULTS: To achieve NPStask measurements with <10% error, the number of regions of interest needed to be greater than 65. To achieve TTF measurements with <10% error, the contrast-to-noise ratio of the edge needed to be ≥15, achievable by averaging multiple slices across the same edge. The NPStask measured on a commercial CT system showed IR's reduced noise (IRIS, 30% and SAFIRE5, 55%) and \\\"waxier\\\" texture (peak frequencies: FBP, 0.25 mm(-1); IRIS, 0.23 mm(-1); and SAFIRE5, 0.16 mm(-1)). The TTF measured within the axial plane showed improved in-plane resolution with SAFIRE5 at the TTF 50% frequency, f50 (FBP, 0.36-0.41 mm(-1); SAFIRE5, 0.37-0.46 mm(-1)). The TTF measured along the axial direction showed improved z-direction resolution with thinner slice thickness (f50: 0.6 mm, 0.35-0.79 mm(-1); 1.5 mm, 0.22-0.3 mm(-1)) and with SAFIRE5 (f50: FBP, 0.35-0.52 mm(-1); SAFIRE5, 0.42-0.79 mm(-1)). Both in-plane and z-direction resolution of SAFIRE5 showed strong dependency on contrast, reflecting SAFIRE5's nonlinearity. CONCLUSIONS: A methodology was developed to measure three-dimensional CT noise and resolution properties for iterative reconstruction, especially at challenging measurement conditions with low contrast and high image noise. The methodology also demonstrated its utility for evaluating commercial CT systems.\",\n \"corpus_id\": 1509974,\n \"score\": 1\n },\n {\n \"doc_id\": \"27139648\",\n \"title\": \"3D spatial resolution and spectral resolution of interferometric 3D imaging spectrometry.\",\n \"abstract\": \"Recently developed interferometric 3D imaging spectrometry (J. Opt. Soc. Am A18, 765 [2001]1084-7529JOAOD610.1364/JOSAA.18.000765) enables obtainment of the spectral information and 3D spatial information for incoherently illuminated or self-luminous object simultaneously. Using this method, we can obtain multispectral components of complex holograms, which correspond directly to the phase distribution of the wavefronts propagated from the polychromatic object. This paper focuses on the analysis of spectral resolution and 3D spatial resolution in interferometric 3D imaging spectrometry. Our analysis is based on a novel analytical impulse response function defined over four-dimensional space. We found that the experimental results agree well with the theoretical prediction. This work also suggests a new criterion and estimate method regarding 3D spatial resolution of digital holography.\",\n \"corpus_id\": 33755490,\n \"score\": 1\n },\n {\n \"doc_id\": \"17574340\",\n \"title\": \"Classification of heterogeneous electron microscopic projections into homogeneous subsets.\",\n \"abstract\": \"The co-existence of different states of a macromolecular complex in samples used by three-dimensional electron microscopy (3D-EM) constitutes a serious challenge. The single particle method applied directly to such heterogeneous sets is unable to provide useful information about the encountered conformational diversity and produces reconstructions with severely reduced resolution. One approach to solving this problem is to partition heterogeneous projection set into homogeneous components and apply existing reconstruction techniques to each of them. Due to the nature of the projection images and the high noise level present in them, this classification task is difficult. A method is presented to achieve the desired classification by using a novel image similarity measure and solving the corresponding optimization problem. Unlike the majority of competing approaches, the presented method employs unsupervised classification (it does not require any prior knowledge about the objects being classified) and does not involve a 3D reconstruction procedure. We demonstrate a fast implementation of this method, capable of classifying projection sets that originate from 3D-EM. The method's performance is evaluated on synthetically generated data sets produced by projecting 3D objects that resemble biological structures.\",\n \"corpus_id\": 31337515,\n \"score\": 0\n },\n {\n \"doc_id\": \"18054169\",\n \"title\": \"Progress and perspectives for atomic-resolution electron microscopy.\",\n \"abstract\": \"The transmission electron microscope (TEM) has evolved into a highly sophisticated instrument that is ideally suited to the characterization of advanced materials. Atomic-level information is routinely accessible using both fixed-beam and scanning TEMs. This report briefly considers developments in the field of atomic-resolution electron microscopy. Recent activities include renewed attention to on-line microscope control ('autotuning'), and assessment and correction of aberrations. Aberration-corrected electron microscopy has developed rapidly in several forms although more work needs to be done to identify standard imaging conditions and to explore novel operating modes. Preparation of samples and image interpretation have also become more demanding. Ongoing problems include discrepancies between measured and simulated image contrast, concerns about radiation damage, and inversion of electron scattering.\",\n \"corpus_id\": 2772378,\n \"score\": 0\n },\n {\n \"doc_id\": \"18445875\",\n \"title\": \"Interactively variable isotropic resolution in computed tomography.\",\n \"abstract\": \"An individual balancing between spatial resolution and image noise is necessary to fulfil the diagnostic requirements in medical CT imaging. In order to change influencing parameters, such as reconstruction kernel or effective slice thickness, additional raw-data-dependent image reconstructions have to be performed. Therefore, the noise versus resolution trade-off is time consuming and not interactively applicable. Furthermore, isotropic resolution, expressed by an equivalent point spread function (PSF) in every spatial direction, is important for the undistorted visualization and quantitative evaluation of small structures independent of the viewing plane. Theoretically, isotropic resolution can be obtained by matching the in-plane and through-plane resolution with the aforementioned parameters. Practically, however, the user is not assisted in doing so by current reconstruction systems and therefore isotropic resolution is not commonly achieved, in particular not at the desired resolution level. In this paper, an integrated approach is presented for equalizing the in-plane and through-plane spatial resolution by image filtering. The required filter kernels are calculated from previously measured PSFs in x/y- and z-direction. The concepts derived are combined with a variable resolution filtering technique. Both approaches are independent of CT raw data and operate only on reconstructed images which allows for their application in real time. Thereby, the aim of interactively variable, isotropic resolution is achieved. Results were evaluated quantitatively by measuring PSFs and image noise, and qualitatively by comparing the images to direct reconstructions regarded as the gold standard. Filtered images matched direct reconstructions with arbitrary reconstruction kernels with standard deviations in difference images of typically between 1 and 17 HU. Isotropic resolution was achieved within 5% of the selected resolution level. Processing times of 20-100 ms per frame allow for interactive use.\",\n \"corpus_id\": 13491816,\n \"score\": 0\n },\n {\n \"doc_id\": \"18545426\",\n \"title\": \"Three-dimensional scheme for time-domain fluorescence molecular tomography based on Laplace transforms with noise-robust factors.\",\n \"abstract\": \"As a visualizing and quantitative method, Fluorescence Molecular Tomography (FMT) has many potential applications in biomedical field and its three-dimensional (3D) implementation is needed in both theory and practice. In this paper, we propose a 3D scheme for time-domain FMT within the normalized Born-ratio formulation. A finite element method solution to the Laplace transformed time-domain coupled diffusion equations is employed as the forward model, and the resultant linear inversions at two distinct transform-factors are solved with an algebraic reconstruction technique to separate fluorescent yield and lifetime images. The algorithm is validated using simulated data for 3D cylinder phantoms, and the spatial resolution and quantitativeness of the reconstruction assessed. We demonstrate that the proposed approach can accurately retrieve the positions and shapes of the targets with high spatial resolution and quantitative accuracy, and tolerate a signal-to-noise ratio down to 25dB by appropriately choosing the transform factors.\",\n \"corpus_id\": 28159899,\n \"score\": 0\n },\n {\n \"doc_id\": \"19410651\",\n \"title\": \"High-resolution single-particle orientation refinement based on spectrally self-adapting common lines.\",\n \"abstract\": \"Three-dimensional (3D) structure determination from electron microscopic images of single molecules can be difficult for particles with low or no internal symmetry, and for images with low signal-to-noise ratio (SNR), due to the existence of false maxima in the scoring function used for orientation search. In attempt to improve robustness of orientation parameter refinement towards noise and poor starting reconstruction quality, we have developed a method for common lines-based orientation search in Fourier space. The Fourier-space formulation enables inclusion of resolution (spatial frequency of the low-pass limit) as a variable that is adjusted in a particle-dependent, self-adaptive manner. The method allows for the underlying 3D structure to be estimated to high resolution, and requires only a crude, low-resolution reconstruction as starting-point for refinement. Benchmarking of the method is performed on experimental and synthetic data.\",\n \"corpus_id\": 22833827,\n \"score\": 0\n },\n {\n \"doc_id\": \"19766422\",\n \"title\": \"3D sensitivity encoded ellipsoidal MR spectroscopic imaging of gliomas at 3T.\",\n \"abstract\": \"PURPOSE: The goal of this study was to implement time efficient data acquisition and reconstruction methods for 3D magnetic resonance spectroscopic imaging (MRSI) of gliomas at a field strength of 3T using parallel imaging techniques. METHODS: The point spread functions, signal to noise ratio (SNR), spatial resolution, metabolite intensity distributions and Cho:NAA ratio of 3D ellipsoidal, 3D sensitivity encoding (SENSE) and 3D combined ellipsoidal and SENSE (e-SENSE) k-space sampling schemes were compared with conventional k-space data acquisition methods. RESULTS: The 3D SENSE and e-SENSE methods resulted in similar spectral patterns as the conventional MRSI methods. The Cho:NAA ratios were highly correlated (P<.05 for SENSE and P<.001 for e-SENSE) with the ellipsoidal method and all methods exhibited significantly different spectral patterns in tumor regions compared to normal appearing white matter. The geometry factors ranged between 1.2 and 1.3 for both the SENSE and e-SENSE spectra. When corrected for these factors and for differences in data acquisition times, the empirical SNRs were similar to values expected based upon theoretical grounds. The effective spatial resolution of the SENSE spectra was estimated to be same as the corresponding fully sampled k-space data, while the spectra acquired with ellipsoidal and e-SENSE k-space samplings were estimated to have a 2.36-2.47-fold loss in spatial resolution due to the differences in their point spread functions. CONCLUSION: The 3D SENSE method retained the same spatial resolution as full k-space sampling but with a 4-fold reduction in scan time and an acquisition time of 9.28 min. The 3D e-SENSE method had a similar spatial resolution as the corresponding ellipsoidal sampling with a scan time of 4:36 min. Both parallel imaging methods provided clinically interpretable spectra with volumetric coverage and adequate SNR for evaluating Cho, Cr and NAA.\",\n \"corpus_id\": 16799720,\n \"score\": 0\n },\n {\n \"doc_id\": \"19915208\",\n \"title\": \"High-resolution low-dose scanning transmission electron microscopy.\",\n \"abstract\": \"During the past two decades instrumentation in scanning transmission electron microscopy (STEM) has pushed toward higher intensity electron probes to increase the signal-to-noise ratio of recorded images. While this is suitable for robust specimens, biological specimens require a much reduced electron dose for high-resolution imaging. We describe here protocols for low-dose STEM image recording with a conventional field-emission gun STEM, while maintaining the high-resolution capability of the instrument. Our findings show that a combination of reduced pixel dwell time and reduced gun current can achieve radiation doses comparable to low-dose TEM.\",\n \"corpus_id\": 26161322,\n \"score\": 0\n },\n {\n \"doc_id\": \"20107244\",\n \"title\": \"Simultaneous measurement of noise and spatial resolution in PET phantom images.\",\n \"abstract\": \"As an aid to evaluating image reconstruction and correction algorithms in positron emission tomography, a phantom procedure has been developed that simultaneously measures image noise and spatial resolution. A commercially available (68)Ge cylinder phantom (20 cm diameter) was positioned in the center of the field-of-view and two identical emission scans were sequentially performed. Image noise was measured by determining the difference between corresponding pixels in the two images and by calculating the standard deviation of these difference data. Spatial resolution was analyzed using a Fourier technique to measure the extent of the blurring at the edge of the phantom images. This paper addresses the noise aspects of the technique as the spatial resolution measurement has been described elsewhere. The noise measurement was validated by comparison with data obtained from multiple replicate images over a range of noise levels. In addition, we illustrate how simultaneous measurement of noise and resolution can be used to evaluate two different corrections for random coincidence events: delayed event subtraction and singles-based randoms correction. For a fixed number of iterations of the maximum-likelihood expectation-maximization algorithm, the singles-based correction gave rise to higher noise than delayed event subtraction. However, when noise and resolution were measured simultaneously it was shown that singles-based randoms correction gave rise to lower noise than delayed event subtraction for a fixed spatial resolution. The proposed method of simultaneously measuring image noise and spatial resolution is useful for evaluating reconstruction algorithms and may aid standardization of data collection between centers.\",\n \"corpus_id\": 8822070,\n \"score\": 0\n },\n {\n \"doc_id\": \"20887850\",\n \"title\": \"3D reconstruction from electron micrographs a personal account of its development.\",\n \"abstract\": \"Prior to the development of 3D reconstruction, images were interpreted in terms of models made from simple units like ping-pong balls. Generally, people eye-balled the images and with other knowledge about its structure, such as the number of subunits, proposed models to account for the images. How was one to know if the models were correct and to what degree they faithfully represented the true structure? The analysis of electron micrographs of negatively stained viral structures led to the answers and 3D reconstruction.\",\n \"corpus_id\": 42559140,\n \"score\": 0\n },\n {\n \"doc_id\": \"20888959\",\n \"title\": \"3D reconstruction from 2D crystal image and diffraction data.\",\n \"abstract\": \"Electron crystallography of 2D protein crystals can determine the structure of membrane embedded proteins at high resolution. Images or electron diffraction patterns are recorded with the electron microscope of the frozen hydrated samples, and the 3D structure of the proteins is then determined by computer data processing. Here we introduce the image-processing algorithms for crystallographic Fourier space based methods using the Medical Research Council (MRC) programs, and illustrate the usage of the software packages 2dx, XDP, and IPLT.\",\n \"corpus_id\": 18113338,\n \"score\": 0\n },\n {\n \"doc_id\": \"20888960\",\n \"title\": \"Fourier-Bessel reconstruction of helical assemblies.\",\n \"abstract\": \"Helical symmetry is commonly used for building macromolecular assemblies. Helical symmetry is naturally present in viruses and cytoskeletal filaments and also occurs during crystallization of isolated proteins, such as Ca-ATPase and the nicotinic acetyl choline receptor. Structure determination of helical assemblies by electron microscopy has a long history dating back to the original work on three-dimensional (3D) reconstruction. A helix offers distinct advantages for structure determination. Not only can one improve resolution by averaging across the constituent subunits, but each helical assembly provides multiple views of these subunits and thus provides a complete 3D data set. This review focuses on Fourier methods of helical reconstruction, covering the theoretical background, a step-by-step guide to the process, and a practical example based on previous work with Ca-ATPase. Given recent results from helical reconstructions at atomic resolution and the development of graphical user interfaces to aid in the process, these methods are likely to continue to make an important contribution to the field of structural biology.\",\n \"corpus_id\": 13183416,\n \"score\": 0\n },\n {\n \"doc_id\": \"21501817\",\n \"title\": \"Atomic resolution cryo electron microscopy of macromolecular complexes.\",\n \"abstract\": \"Single-particle cryo electron microscopy (cryoEM) is a technique for determining three-dimensional (3D) structures from projection images of molecular complexes preserved in their \\\"native,\\\" noncrystalline state. Recently, atomic or near-atomic resolution structures of several viruses and protein assemblies have been determined by single-particle cryoEM, allowing ab initio atomic model building by following the amino acid side chains or nucleic acid bases identifiable in their cryoEM density maps. In particular, these cryoEM structures have revealed extended arms contributing to molecular interactions that are otherwise not resolved by the conventional structural method of X-ray crystallography at similar resolutions. High-resolution cryoEM requires careful consideration of a number of factors, including proper sample preparation to ensure structural homogeneity, optimal configuration of electron imaging conditions to record high-resolution cryoEM images, accurate determination of image parameters to correct image distortions, efficient refinement and computation to reconstruct a 3D density map, and finally appropriate choice of modeling tools to construct atomic models for functional interpretation. This progress illustrates the power of cryoEM and ushers it into the arsenal of structural biology, alongside conventional techniques of X-ray crystallography and NMR, as a major tool (and sometimes the preferred one) for the studies of molecular interactions in supramolecular assemblies or machines.\",\n \"corpus_id\": 24267496,\n \"score\": 0\n },\n {\n \"doc_id\": \"21536524\",\n \"title\": \"Spatially regularized compressed sensing for high angular resolution diffusion imaging.\",\n \"abstract\": \"Despite the relative recency of its inception, the theory of compressive sampling (aka compressed sensing) (CS) has already revolutionized multiple areas of applied sciences, a particularly important instance of which is medical imaging. Specifically, the theory has provided a different perspective on the important problem of optimal sampling in magnetic resonance imaging (MRI), with an ever-increasing body of works reporting stable and accurate reconstruction of MRI scans from the number of spectral measurements which would have been deemed unacceptably small as recently as five years ago. In this paper, the theory of CS is employed to palliate the problem of long acquisition times, which is known to be a major impediment to the clinical application of high angular resolution diffusion imaging (HARDI). Specifically, we demonstrate that a substantial reduction in data acquisition times is possible through minimization of the number of diffusion encoding gradients required for reliable reconstruction of HARDI scans. The success of such a minimization is primarily due to the availability of spherical ridgelet transformation, which excels in sparsifying HARDI signals. What makes the resulting reconstruction procedure even more accurate is a combination of the sparsity constraints in the diffusion domain with additional constraints imposed on the estimated diffusion field in the spatial domain. Accordingly, the present paper describes an original way to combine the diffusion- and spatial-domain constraints to achieve a maximal reduction in the number of diffusion measurements, while sacrificing little in terms of reconstruction accuracy. Finally, details are provided on an efficient numerical scheme which can be used to solve the aforementioned reconstruction problem by means of standard and readily available estimation tools. The paper is concluded with experimental results which support the practical value of the proposed reconstruction methodology.\",\n \"corpus_id\": 3209874,\n \"score\": 0\n },\n {\n \"doc_id\": \"21761448\",\n \"title\": \"A 3D wavelet fusion approach for the reconstruction of isotropic-resolution MR images from orthogonal anisotropic-resolution scans.\",\n \"abstract\": \"Hardware constraints, scanning time limitations, patient movement, and signal-to-noise ratio (SNR) considerations, restrict the slice-selection and the in-plane resolutions of MRI differently, generally resulting in anisotropic voxels. This nonuniform sampling can be problematic, especially in image segmentation and clinical examination. To alleviate this, the acquisition is divided into (two or) three separate scans, with higher in-plane resolutions and thick slices, yet orthogonal slice-selection directions. In this work, a noniterative wavelet-based approach for combining the three orthogonal scans is adopted, and its advantages compared with other existing methods, such as Fourier techniques, are discussed, including the consideration of the actual pulse response of the MRI scanner, and its lower computational complexity. Experimental results are shown on simulated and real 7 T MRI data.\",\n \"corpus_id\": 17437903,\n \"score\": 0\n },\n {\n \"doc_id\": \"21844593\",\n \"title\": \"Electron microscopy at a sub-50 pm resolution.\",\n \"abstract\": \"An aberration-corrected electron microscope developed in CREST project has been applied for imaging atoms and clusters buried inside crystals. The resolution of the microscope in scanning transmission electron microscopy (STEM) has experimentally proved to be better than 47 pm by use of a cold-field emission gun at 300 kV. The high resolution has given an advantage for imaging light elements such as lithium atoms discriminating one by one. Moreover, a three-dimensional structure imaging has been demonstrated for dopant clusters by a sub-50 pm STEM, using its high depth resolution.\",\n \"corpus_id\": 21567355,\n \"score\": 0\n },\n {\n \"doc_id\": \"21934862\",\n \"title\": \"Sample drift correction in 3D fluorescence photoactivation localization microscopy.\",\n \"abstract\": \"The recent development of diffraction-unlimited far-field fluorescence microscopy has overcome the classical resolution limit of ~250 nm of conventional light microscopy by about a factor of ten. The improved resolution, however, reveals not only biological structures at an unprecedented resolution, but is also susceptible to sample drift on a much finer scale than previously relevant. Without correction, sample drift leads to smeared images with decreased resolution, and in the worst case to misinterpretation of the imaged structures. This poses a problem especially for techniques such as Fluorescence Photoactivation Localization Microscopy (FPALM/PALM) or Stochastic Optical Reconstruction Microscopy (STORM), which often require minutes recording time. Here we discuss an approach that corrects for three-dimensional (3D) drift in images of fixed samples without the requirement for fiduciary markers or instrument modifications. Drift is determined by calculating the spatial cross-correlation function between subsets of localized particles imaged at different times. Correction down to ~5 nm precision is achieved despite the fact that different molecules are imaged in each frame. We demonstrate the performance of our drift correction algorithm with different simulated structures and analyze its dependence on particle density and localization precision. By imaging mitochondria with Biplane FPALM we show our algorithm's feasibility in a practical application.\",\n \"corpus_id\": 263364997,\n \"score\": 0\n },\n {\n \"doc_id\": \"22437612\",\n \"title\": \"Electron tomography at 2.4-ångström resolution.\",\n \"abstract\": \"Transmission electron microscopy is a powerful imaging tool that has found broad application in materials science, nanoscience and biology. With the introduction of aberration-corrected electron lenses, both the spatial resolution and the image quality in transmission electron microscopy have been significantly improved and resolution below 0.5 ångströms has been demonstrated. To reveal the three-dimensional (3D) structure of thin samples, electron tomography is the method of choice, with cubic-nanometre resolution currently achievable. Discrete tomography has recently been used to generate a 3D atomic reconstruction of a silver nanoparticle two to three nanometres in diameter, but this statistical method assumes prior knowledge of the particle's lattice structure and requires that the atoms fit rigidly on that lattice. Here we report the experimental demonstration of a general electron tomography method that achieves atomic-scale resolution without initial assumptions about the sample structure. By combining a novel projection alignment and tomographic reconstruction method with scanning transmission electron microscopy, we have determined the 3D structure of an approximately ten-nanometre gold nanoparticle at 2.4-ångström resolution. Although we cannot definitively locate all of the atoms inside the nanoparticle, individual atoms are observed in some regions of the particle and several grains are identified in three dimensions. The 3D surface morphology and internal lattice structure revealed are consistent with a distorted icosahedral multiply twinned particle. We anticipate that this general method can be applied not only to determine the 3D structure of nanomaterials at atomic-scale resolution, but also to improve the spatial resolution and image quality in other tomography fields.\",\n \"corpus_id\": 1600103,\n \"score\": 0\n },\n {\n \"doc_id\": \"23086876\",\n \"title\": \"Semiautomatic, high-throughput, high-resolution protocol for three-dimensional reconstruction of single particles in electron microscopy.\",\n \"abstract\": \"In this chapter we describe the steps needed for reconstructing the three-dimensional structure of a macromolecular complex starting from its projections collected in electron micrographs. The concepts are shown through the use of Xmipp 3.0, a software suite specifically designed for the image processing of biological structures imaged with electron or X-ray microscopy. We illustrate the image processing workflow by applying it to the images of Bovine Papilloma virus published in Wolf et al. (Proc Natl Acad Sci USA 107:6298-6303, 2010). We show that in the case of high-quality, homogeneous datasets with a priori knowledge about the initial volume, we can have a high-resolution 3D reconstruction in less than 1 day using a computer cluster with only 32 processors.\",\n \"corpus_id\": 8005001,\n \"score\": 0\n },\n {\n \"doc_id\": \"23221063\",\n \"title\": \"3D PET image reconstruction including both motion correction and registration directly into an MR or stereotaxic spatial atlas.\",\n \"abstract\": \"This work explores the feasibility and impact of including both the motion correction and the image registration transformation parameters from positron emission tomography (PET) image space to magnetic resonance (MR), or stereotaxic, image space within the system matrix of PET image reconstruction. This approach is motivated by the fields of neuroscience and psychiatry, where PET is used to investigate differences in activation patterns between different groups of participants, requiring all images to be registered to a common spatial atlas. Currently, image registration is performed after image reconstruction which introduces interpolation effects into the final image. Furthermore, motion correction (also requiring registration) introduces a further level of interpolation, and the overall result of these operations can lead to resolution degradation and possibly artifacts. It is important to note that performing such operations on a post-reconstruction basis means, strictly speaking, that the final images are not ones which maximize the desired objective function (e.g. maximum likelihood (ML), or maximum a posteriori reconstruction (MAP)). To correctly seek parameter estimates in the desired spatial atlas which are in accordance with the chosen reconstruction objective function, it is necessary to include the transformation parameters for both motion correction and registration within the system modeling stage of image reconstruction. Such an approach not only respects the statistically chosen objective function (e.g. ML or MAP), but furthermore should serve to reduce the interpolation effects. To evaluate the proposed method, this work investigates registration (including motion correction) using 2D and 3D simulations based on the high resolution research tomograph (HRRT) PET scanner geometry, with and without resolution modeling, using the ML expectation maximization (MLEM) reconstruction algorithm. The quality of reconstruction was assessed using bias-variance and root mean squared error analyses, comparing the proposed method to conventional post-reconstruction registration methods. An overall reduction in bias (for a cold region: from 41% down to 31% (2D) and 97% down to 65% (3D), and for a hot region: from 11% down to 8% (2D) and from 16% down to 14% (3D)) and in root mean squared error analyses (for a cold region: from 43% to 37% (2D) and from 97% to 65% (3D), and for a hot region: from 11% to 9% (2D) and from 16% down to 14% (3D)) in reconstructed regional mean activities (full regions of interest; all with statistical significance: p < 5 × 10(-10)) is found when including the motion correction and registration in the system matrix of the MLEM reconstruction, with resolution modeling. However, this improvement in performance comes with an extra computational cost of about 40 min. In this context, this work constitutes an important step toward the goal of estimating parameters of interest directly from the raw Poisson-distributed PET data, and hence toward the complete elimination of post-processing steps.\",\n \"corpus_id\": 35253278,\n \"score\": 0\n },\n {\n \"doc_id\": \"23410725\",\n \"title\": \"Projection-based volume alignment.\",\n \"abstract\": \"When heterogeneous samples of macromolecular assemblies are being examined by 3D electron microscopy (3DEM), often multiple reconstructions are obtained. For example, subtomograms of individual particles can be acquired from tomography, or volumes of multiple 2D classes can be obtained by random conical tilt reconstruction. Of these, similar volumes can be averaged to achieve higher resolution. Volume alignment is an essential step before 3D classification and averaging. Here we present a projection-based volume alignment (PBVA) algorithm. We select a set of projections to represent the reference volume and align them to a second volume. Projection alignment is achieved by maximizing the cross-correlation function with respect to rotation and translation parameters. If data are missing, the cross-correlation functions are normalized accordingly. Accurate alignments are obtained by averaging and quadratic interpolation of the cross-correlation maximum. Comparisons of the computation time between PBVA and traditional 3D cross-correlation methods demonstrate that PBVA outperforms the traditional methods. Performance tests were carried out with different signal-to-noise ratios using modeled noise and with different percentages of missing data using a cryo-EM dataset. All tests show that the algorithm is robust and highly accurate. PBVA was applied to align the reconstructions of a subcomplex of the NADH: ubiquinone oxidoreductase (Complex I) from the yeast Yarrowia lipolytica, followed by classification and averaging.\",\n \"corpus_id\": 6689254,\n \"score\": 0\n },\n {\n \"doc_id\": \"23456116\",\n \"title\": \"Structured-light-based highly dense and robust 3D reconstruction.\",\n \"abstract\": \"In this paper, a structured-light-based highly dense and robust 3D reconstruction method is proposed by combining a Gray code and region-shifting pattern. The region-shifting pattern is transformed to the trapezoidal and triangle wave shifting pattern by combining all frames of the region-shifting pattern, and then the boundary of the trapezoidal wave shifting pattern and the peak and phase of the triangle wave shifting pattern are estimated. Through this technique, the spatial resolution is increased about three times. Consequently, the 3D points are reconstructed with a resolution much higher than a camera image resolution. Moreover, as the proposed method measures the boundary and the peak with all frames, it increases the signal-to-noise ratio and is more robust than the conventional methods that use only one or two frames to detect them.\",\n \"corpus_id\": 9262693,\n \"score\": 0\n },\n {\n \"doc_id\": \"24106307\",\n \"title\": \"High-resolution restoration of 3D structures from widefield images with extreme low signal-to-noise-ratio.\",\n \"abstract\": \"Four-dimensional fluorescence microscopy--which records 3D image information as a function of time--provides an unbiased way of tracking dynamic behavior of subcellular components in living samples and capturing key events in complex macromolecular processes. Unfortunately, the combination of phototoxicity and photobleaching can severely limit the density or duration of sampling, thereby limiting the biological information that can be obtained. Although widefield microscopy provides a very light-efficient way of imaging, obtaining high-quality reconstructions requires deconvolution to remove optical aberrations. Unfortunately, most deconvolution methods perform very poorly at low signal-to-noise ratios, thereby requiring moderate photon doses to obtain acceptable resolution. We present a unique deconvolution method that combines an entropy-based regularization function with kernels that can exploit general spatial characteristics of the fluorescence image to push the required dose to extreme low levels, resulting in an enabling technology for high-resolution in vivo biological imaging.\",\n \"corpus_id\": 15332429,\n \"score\": 0\n },\n {\n \"doc_id\": \"24651662\",\n \"title\": \"Ophthalmic magnetic resonance imaging at 7 T using a 6-channel transceiver radiofrequency coil array in healthy subjects and patients with intraocular masses.\",\n \"abstract\": \"OBJECTIVES: This study was designed to examine the feasibility of ophthalmic magnetic resonance imaging (MRI) at 7 T using a local 6-channel transmit/receive radiofrequency (RF) coil array in healthy volunteers and patients with intraocular masses. MATERIALS AND METHODS: A novel 6-element transceiver RF coil array that makes uses of loop elements and that is customized for eye imaging at 7 T is proposed. Considerations influencing the RF coil design and the characteristics of the proposed RF coil array are presented. Numerical electromagnetic field simulations were conducted to enhance the RF coil characteristics. Specific absorption rate simulations and a thorough assessment of RF power deposition were performed to meet the safety requirements. Phantom experiments were carried out to validate the electromagnetic field simulations and to assess the real performance of the proposed transceiver array. Certified approval for clinical studies was provided by a local notified body before the in vivo studies. The suitability of the RF coil to image the human eye, optical nerve, and orbit was examined in an in vivo feasibility study including (a) 3-dimensional (3D) gradient echo (GRE) imaging, (b) inversion recovery 3D GRE imaging, and (c) 2D T2-weighted fast spin-echo imaging. For this purpose, healthy adult volunteers (n = 17; mean age, 34 ± 11 years) and patients with intraocular masses (uveal melanoma, n = 5; mean age, 57 ± 6 years) were investigated. RESULTS: All subjects tolerated all examinations well with no relevant adverse events. The 6-channel coil array supports high-resolution 3D GRE imaging with a spatial resolution as good as 0.2 × 0.2 × 1.0 mm, which facilitates the depiction of anatomical details of the eye. Rather, uniform signal intensity across the eye was found. A mean signal-to-noise ratio of approximately 35 was found for the lens, whereas the vitreous humor showed a signal-to-noise ratio of approximately 30. The lens-vitreous humor contrast-to-noise ratio was 8, which allows good differentiation between the lens and the vitreous compartment. Inversion recovery prepared 3D GRE imaging using a spatial resolution of 0.4 × 0.4 × 1.0 mm was found to be feasible. T2-weighted 2D fast spin-echo imaging with the proposed RF coil afforded a spatial resolution of 0.25 × 0.25 × 0.7 mm. CONCLUSIONS: This work provides valuable information on the feasibility of ophthalmic MRI at 7 T using a dedicated 6-channel transceiver coil array that supports the acquisition of high-contrast, high-spatial resolution images in healthy volunteers and patients with intraocular masses. The results underscore the challenges of ocular imaging at 7 T and demonstrate that these issues can be offset by using tailored RF coil hardware. The benefits of such improvements would be in positive alignment with explorations that are designed to examine the potential of MRI for the assessment of spatial arrangements of the eye segments and their masses with the ultimate goal to provide imaging means for guiding treatment decisions in ophthalmological diseases.\",\n \"corpus_id\": 38810130,\n \"score\": 0\n },\n {\n \"doc_id\": \"24663755\",\n \"title\": \"A phase demodulation method with high spatial resolution for two-dimensional single-shot X-ray Talbot interferometry.\",\n \"abstract\": \"A new phase demodulation approach is proposed that uses windowed Fourier transforms to achieve high spatial resolution in fringe pattern analysis with a high signal-to-noise ratio for single-shot X-ray grating-based interferometry. Conventionally, Fourier transforms have been used to demodulate single-fringe patterns, but this requires a fringe pattern with a long period to obtain an acceptable signal-to-noise ratio among the demodulated parameters. However, by controlling the signal-to-noise ratio, the spatial resolution of demodulated parameters is degraded below that obtained from the phase-stepping method, which requires several images to obtain these parameters. In this paper, we introduce the use of a windowed Fourier transform with a process for analyzing the objective spectrum in isolation from other spectra on the Fourier space to overcome the limitations of the Fourier transform method. It is proved that with suitable assumptions the objective spectrum is isolated theoretically, and the spatial resolution is improved by practically accepting the limitations from the assumptions. We demonstrate the validity of the proposed method by comparing the modulation transfer function of a synthetic phantom with the conventional FT method. The proposed method is also valid on practical data obtained by an experimental setup, by which it is demonstrated that a high spatial resolution with high signal-to-noise ratio can be achieved by our proposed method.\",\n \"corpus_id\": 207328613,\n \"score\": 0\n },\n {\n \"doc_id\": \"24718236\",\n \"title\": \"Enhanced 3D spatial resolution in quantitative phase microscopy using spatially incoherent illumination.\",\n \"abstract\": \"We describe the use of spatially incoherent illumination to make quantitative phase imaging of a semi-transparent sample, even out of the paraxial approximation. The image volume electromagnetic field is collected by scanning the image planes with a quadriwave lateral shearing interferometer, while the sample is spatially incoherently illuminated. In comparison to coherent quantitative phase measurements, incoherent illumination enriches the 3D collected spatial frequencies leading to 3D resolution increase (up to a factor 2). The image contrast loss introduced by the incoherent illumination is simulated and used to compensate the measurements. This restores the quantitative value of phase and intensity. Experimental contrast loss compensation and 3D resolution increase is presented using polystyrene and TiO(2) micro-beads. Our approach will be useful to make diffraction tomography reconstruction with a simplified setup.\",\n \"corpus_id\": 13561105,\n \"score\": 0\n },\n {\n \"doc_id\": \"24784388\",\n \"title\": \"Combined iterative reconstruction and image-domain decomposition for dual energy CT using total-variation regularization.\",\n \"abstract\": \"PURPOSE: Dual-energy CT (DECT) is being increasingly used for its capability of material decomposition and energy-selective imaging. A generic problem of DECT, however, is that the decomposition process is unstable in the sense that the relative magnitude of decomposed signals is reduced due to signal cancellation while the image noise is accumulating from the two CT images of independent scans. Direct image decomposition, therefore, leads to severe degradation of signal-to-noise ratio on the resultant images. Existing noise suppression techniques are typically implemented in DECT with the procedures of reconstruction and decomposition performed independently, which do not explore the statistical properties of decomposed images during the reconstruction for noise reduction. In this work, the authors propose an iterative approach that combines the reconstruction and the signal decomposition procedures to minimize the DECT image noise without noticeable loss of resolution. METHODS: The proposed algorithm is formulated as an optimization problem, which balances the data fidelity and total variation of decomposed images in one framework, and the decomposition step is carried out iteratively together with reconstruction. The noise in the CT images from the proposed algorithm becomes well correlated even though the noise of the raw projections is independent on the two CT scans. Due to this feature, the proposed algorithm avoids noise accumulation during the decomposition process. The authors evaluate the method performance on noise suppression and spatial resolution using phantom studies and compare the algorithm with conventional denoising approaches as well as combined iterative reconstruction methods with different forms of regularization. RESULTS: On the Catphan©600 phantom, the proposed method outperforms the existing denoising methods on preserving spatial resolution at the same level of noise suppression, i.e., a reduction of noise standard deviation by one order of magnitude. This improvement is mainly attributed to the high noise correlation in the CT images reconstructed by the proposed algorithm. Iterative reconstruction using different regularization, including quadratic orq-generalized Gaussian Markov random field regularization, achieves similar noise suppression from high noise correlation. However, the proposed TV regularization obtains a better edge preserving performance. Studies of electron density measurement also show that our method reduces the average estimation error from 9.5% to 7.1%. On the anthropomorphic head phantom, the proposed method suppresses the noise standard deviation of the decomposed images by a factor of ∼14 without blurring the fine structures in the sinus area. CONCLUSIONS: The authors propose a practical method for DECT imaging reconstruction, which combines the image reconstruction and material decomposition into one optimization framework. Compared to the existing approaches, our method achieves a superior performance on DECT imaging with respect to decomposition accuracy, noise reduction, and spatial resolution.\",\n \"corpus_id\": 29606734,\n \"score\": 0\n },\n {\n \"doc_id\": \"25735299\",\n \"title\": \"3D high spectral and spatial resolution imaging of ex vivo mouse brain.\",\n \"abstract\": \"PURPOSE: Widely used MRI methods show brain morphology both in vivo and ex vivo at very high resolution. Many of these methods (e.g., T2*-weighted imaging, phase-sensitive imaging, or susceptibility-weighted imaging) are sensitive to local magnetic susceptibility gradients produced by subtle variations in tissue composition. However, the spectral resolution of commonly used methods is limited to maintain reasonable run-time combined with very high spatial resolution. Here, the authors report on data acquisition at increased spectral resolution, with 3-dimensional high spectral and spatial resolution MRI, in order to analyze subtle variations in water proton resonance frequency and lineshape that reflect local anatomy. The resulting information compliments previous studies based on T2* and resonance frequency. METHODS: The proton free induction decay was sampled at high resolution and Fourier transformed to produce a high-resolution water spectrum for each image voxel in a 3D volume. Data were acquired using a multigradient echo pulse sequence (i.e., echo-planar spectroscopic imaging) with a spatial resolution of 50 × 50 × 70 μm(3) and spectral resolution of 3.5 Hz. Data were analyzed in the spectral domain, and images were produced from the various Fourier components of the water resonance. This allowed precise measurement of local variations in water resonance frequency and lineshape, at the expense of significantly increased run time (16-24 h). RESULTS: High contrast T2*-weighted images were produced from the peak of the water resonance (peak height image), revealing a high degree of anatomical detail, specifically in the hippocampus and cerebellum. In images produced from Fourier components of the water resonance at -7.0 Hz from the peak, the contrast between deep white matter tracts and the surrounding tissue is the reverse of the contrast in water peak height images. This indicates the presence of a shoulder in the water resonance that is not present at +7.0 Hz and may be specific to white matter anatomy. Moreover, a frequency shift of 6.76 ± 0.55 Hz was measured between the molecular and granular layers of the cerebellum. This shift is demonstrated in corresponding spectra; water peaks from voxels in the molecular and granular layers are consistently 2 bins apart (7.0 Hz, as dictated by the spectral resolution) from one another. CONCLUSIONS: High spectral and spatial resolution MR imaging has the potential to accurately measure the changes in the water resonance in small voxels. This information can guide optimization and interpretation of more commonly used, more rapid imaging methods that depend on image contrast produced by local susceptibility gradients. In addition, with improved sampling methods, high spectral and spatial resolution data could be acquired in reasonable run times, and used for in vivo scans to increase sensitivity to variations in local susceptibility.\",\n \"corpus_id\": 36772517,\n \"score\": 0\n },\n {\n \"doc_id\": \"25824643\",\n \"title\": \"Feasibility and evaluation of dual-source transmit 3D imaging of the orbits: Comparison to high-resolution conventional MRI at 3T.\",\n \"abstract\": \"PURPOSE: To prospectively compare the image quality and diagnostic performance of orbital MR images obtained by using a dual-source parallel transmission (pTX) 3D sequence (Sampling Perfection with Application optimized Contrasts using different flip angle Evolution, SPACE) with the image quality of conventional high-resolution standard protocol for clinical use in patients at 3T. MATERIALS AND METHODS: After obtaining institutional review board approval and patient consent, 32 patients with clinical indication for orbital MRI were examined using a high-resolution conventional sequences and 3D pTX SPACE sequences. Quantitative measurements, image quality of the healthy orbit, incidence of artifacts, and the subjective diagnostic performance to establish diagnosis was rated. Statistical significance was calculated by using a Student's t-test and nonparametric Wilcoxon signed rank test. RESULTS: Length measurements were comparable in the two techniques, 3D pTX SPACE resulted in significant faster image acquisition with higher spatial resolution and less motion artifacts as well as better delineation of the optic nerve sheath. However, estimated contrast-to-noise and signal-to-noise and overall image quality as well as subjective scores of the conventional TSE imaging were rated significantly higher. The conventional MR sequences were the preferred techniques by the readers. CONCLUSION: This study demonstrates the feasibility of 3D pTX SPACE of the orbit resulting in a rapid acquisition of isotropic high-resolution images. Although no pathology was missed in 3D pTX SPACE, conventional MRI techniques showed the higher diagnostic confidence in our study, presumably due to the higher signal-to-noise and contrast-to-noise ratios. We observed high-resolution TSE imaging to be the preferred technique, 3D pTX SPACE cannot replace conventional MRI so far.\",\n \"corpus_id\": 24155065,\n \"score\": 0\n },\n {\n \"doc_id\": \"26149628\",\n \"title\": \"Positive contrast high-resolution 3D-cine imaging of the cardiovascular system in small animals using a UTE sequence and iron nanoparticles at 4.7, 7 and 9.4 T.\",\n \"abstract\": \"BACKGROUND: To show that 3D sequences with ultra-short echo times (UTEs) can generate a positive contrast whatever the magnetic field (4.7, 7 or 9.4 T) and whatever Ultra Small Particles of Iron Oxide (USPIO) concentration injected and to use it for 3D time-resolved imaging of the murine cardiovascular system with high spatial and temporal resolutions. METHODS: Three different concentrations (50, 200 and 500 μmol Fe/kg) of USPIO were injected in mice and static images of the middle part of the animals were acquired at 4.7, 7 and 9.4 T pre and post-contrast with UTE (TE/TR = 0.05/4.5 ms) sequences. Signal-to-Noise Ratio (SNR) and Contrast-to-Noise Ratio (CNR) of blood and static tissus were evaluated before and after contrast agent injection. 3D-cine images (TE/TR = 0.05/3.5 ms, scan time < 12 min) at 156 μm isotropic resolution of the mouse cardiopulmonary system were acquired prospectively with the UTE sequence for the three magnetic fields and with an USPIO dose of 200 μmol Fe/kg. SNR, CNR and signal homogeneity of blood were measured. High spatial (104 μm) or temporal (3.5 ms) resolution 3D-cine imaging (scan time < 35 min) isotropic resolution were also performed at 7 T with a new sequence encoding scheme. RESULTS: UTE imaging generated positive contrast and higher SNR and CNR whatever the magnetic field and the USPIO concentration used compared to pre-contrast images. Time-resolved 3D acquisition enables high blood SNR (66.6 ± 4.5 at 7 T) and CNR (33.2 ± 4.2 at 7 T) without flow or motion artefact. Coronary arteries and aortic valve were visible on images acquired at 104 μm resolution. CONCLUSIONS: We have demonstrated that by combining the injection of iron nanoparticles with 3D-cine UTE sequences, it was possible to generate a strong positive contrast between blood and surrounding tissues. These properties were exploited to produce images of the cardiovascular system in small animals at high magnetic fields with a high spatial and temporal resolution. This approach might be useful to measure the functional cardiac parameters or to assess anatomical modifications to the blood vessels in cardio-vascular disease models.\",\n \"corpus_id\": 15280150,\n \"score\": 0\n },\n {\n \"doc_id\": \"26172829\",\n \"title\": \"High-resolution variable-density 3D cones coronary MRA.\",\n \"abstract\": \"PURPOSE: To improve the spatial/temporal resolution of whole-heart coronary MR angiography by developing a variable-density (VD) 3D cones acquisition suitable for image reconstruction with parallel imaging and compressed sensing techniques. METHODS: A VD 3D cones trajectory design incorporates both radial and spiral trajectory undersampling techniques to achieve higher resolution. This design is used to generate a VD 3D cones trajectory with 0.8 mm/66 ms isotropic spatial/temporal resolution, using a similar number of readouts as our previous fully sampled cones trajectory (1.2 mm/100 ms). Scans of volunteers and patients are performed to evaluate the performance of the VD trajectory, using non-Cartesian L1 -ESPIRiT for high-resolution image reconstruction. RESULTS: With gridding reconstruction, the high-resolution scans experience an expected drop in signal-to-noise and contrast-to-noise ratios, but with L1 -ESPIRiT, the apparent noise is substantially reduced. Compared with 1.2 mm images, in each volunteer, the L1 -ESPIRiT 0.8 mm images exhibit higher vessel sharpness values in the right and left anterior descending arteries. CONCLUSION: Coronary MR angiography with isotropic submillimeter spatial resolution and high temporal resolution can be performed with VD 3D cones to improve the depiction of coronary arteries.\",\n \"corpus_id\": 36807567,\n \"score\": 0\n },\n {\n \"doc_id\": \"26193484\",\n \"title\": \"A Bayesian approach for suppression of limited angular sampling artifacts in single particle 3D reconstruction.\",\n \"abstract\": \"In the single particle reconstruction, the initial 3D structure often suffers from the limited angular sampling artifact. Selecting 2D class averages of particle images generally improves the accuracy and efficiency of the reference-free 3D angle estimation, but causes an insufficient angular sampling to fill the information of the target object in the 3D frequency space. Similarly, the initial 3D structure by the random-conical tilt reconstruction has the well-known \\\"missing cone\\\" artifact. Here, we attempted to solve the limited angular sampling problem by sequentially applying maximum a posteriori estimate with expectation maximization algorithm (sMAP-EM). Using both simulated and experimental cryo-electron microscope images, the sMAP-EM was compared to the direct Fourier method on the basis of reconstruction error and resolution. To establish selection criteria of the final regularization weight for the sMAP-EM, the effects of noise level and sampling sparseness on the reconstructions were examined with evenly distributed sampling simulations. The frequency information filled in the missing cone of the conical tilt sampling simulations was assessed by developing new quantitative measurements. All the results of visual and numerical evaluations showed the sMAP-EM performed better than the direct Fourier method, regardless of the sampling method, noise level, and sampling sparseness. Furthermore, the frequency domain analysis demonstrated that the sMAP-EM can fill the meaningful information in the unmeasured angular space without detailed a priori knowledge of the objects. The current research demonstrated that the sMAP-EM has a high potential to facilitate the determination of 3D protein structures at near atomic-resolution.\",\n \"corpus_id\": 23990990,\n \"score\": 0\n },\n {\n \"doc_id\": \"26366744\",\n \"title\": \"Correction of image drift and distortion in a scanning electron microscopy.\",\n \"abstract\": \"Continuous research on small-scale mechanical structures and systems has attracted strong demand for ultrafine deformation and strain measurements. Conventional optical microscope cannot meet such requirements owing to its lower spatial resolution. Therefore, high-resolution scanning electron microscope has become the preferred system for high spatial resolution imaging and measurements. However, scanning electron microscope usually is contaminated by distortion and drift aberrations which cause serious errors to precise imaging and measurements of tiny structures. This paper develops a new method to correct drift and distortion aberrations of scanning electron microscope images, and evaluates the effect of correction by comparing corrected images with scanning electron microscope image of a standard sample. The drift correction is based on the interpolation scheme, where a series of images are captured at one location of the sample and perform image correlation between the first image and the consequent images to interpolate the drift-time relationship of scanning electron microscope images. The distortion correction employs the axial symmetry model of charged particle imaging theory to two images sharing with the same location of one object under different imaging fields of view. The difference apart from rigid displacement between the mentioned two images will give distortion parameters. Three-order precision is considered in the model and experiment shows that one pixel maximum correction is obtained for the employed high-resolution electron microscopic system.\",\n \"corpus_id\": 25886524,\n \"score\": 0\n },\n {\n \"doc_id\": \"26469938\",\n \"title\": \"PF2fit: Polar Fast Fourier Matched Alignment of Atomistic Structures with 3D Electron Microscopy Maps.\",\n \"abstract\": \"There continue to be increasing occurrences of both atomistic structure models in the PDB (possibly reconstructed from X-ray diffraction or NMR data), and 3D reconstructed cryo-electron microscopy (3D EM) maps (albeit at coarser resolution) of the same or homologous molecule or molecular assembly, deposited in the EMDB. To obtain the best possible structural model of the molecule at the best achievable resolution, and without any missing gaps, one typically aligns (match and fits) the atomistic structure model with the 3D EM map. We discuss a new algorithm and generalized framework, named PF(2) fit (Polar Fast Fourier Fitting) for the best possible structural alignment of atomistic structures with 3D EM. While PF(2) fit enables only a rigid, six dimensional (6D) alignment method, it augments prior work on 6D X-ray structure and 3D EM alignment in multiple ways: Scoring. PF(2) fit includes a new scoring scheme that, in addition to rewarding overlaps between the volumes occupied by the atomistic structure and 3D EM map, rewards overlaps between the volumes complementary to them. We quantitatively demonstrate how this new complementary scoring scheme improves upon existing approaches. PF(2) fit also includes two scoring functions, the non-uniform exterior penalty and the skeleton-secondary structure score, and implements the scattering potential score as an alternative to traditional Gaussian blurring. Search. PF(2) fit utilizes a fast polar Fourier search scheme, whose main advantage is the ability to search over uniformly and adaptively sampled subsets of the space of rigid-body motions. PF(2) fit also implements a new reranking search and scoring methodology that considerably improves alignment metrics in results obtained from the initial search.\",\n \"corpus_id\": 6348089,\n \"score\": 0\n },\n {\n \"doc_id\": \"26551126\",\n \"title\": \"Electron Microscopy of Probability Currents at Atomic Resolution.\",\n \"abstract\": \"Atomic resolution transmission electron microscopy records the spatially resolved scattered electron density to infer positions, density, and species of atoms. These data are indispensable for studying the relation between structure and properties in solids. Here, we show how this signal can be augmented by the lateral probability current of the scattered electrons in the object plane at similar resolutions and fields of view. The currents are reconstructed from a series of three atomic resolution TEM images recorded under a slight difference of perpendicular line foci. The technique does not rely on the coherence of the electron beam and can be used to reveal electric, magnetic, and strain fields with incoherent electron beams as well as correlations in inelastic transitions, such as electron magnetic chiral dichroism.\",\n \"corpus_id\": 206263685,\n \"score\": 0\n },\n {\n \"doc_id\": \"26594081\",\n \"title\": \"Thermodynamic Limits of Spatial Resolution in Active Thermography.\",\n \"abstract\": \"Thermal waves are caused by pure diffusion: their amplitude is decreased by more than a factor of 500 within a propagation distance of one wavelength. The diffusion equation, which describes the temperature as a function of space and time, is linear. For every linear equation the superposition principle is valid, which is known as Huygens principle for optical or mechanical wave fields. This limits the spatial resolution, like the Abbe diffraction limit in optics. The resolution is the minimal size of a structure which can be detected at a certain depth. If an embedded structure at a certain depth in a sample is suddenly heated, e.g., by eddy current or absorbed light, an image of the structure can be reconstructed from the measured temperature at the sample surface. To get the resolution the image reconstruction can be considered as the time reversal of the thermal wave. This inverse problem is ill-conditioned and therefore regularization methods have to be used taking additional assumptions like smoothness of the solutions into account. In the present work for the first time, methods of non-equilibrium statistical physics are used to solve this inverse problem without the need of such additional assumptions and without the necessity to choose a regularization parameter. For reconstructing such an embedded structure by thermal waves the resolution turns out to be proportional to the depth and inversely proportional to the natural logarithm of the signal-to-noise ratio. This result could be derived from the diffusion equation by using a delta-source at a certain depth and setting the entropy production caused by thermal diffusion equal to the information loss. No specific model about the stochastic process of the fluctuations and about the distribution densities around the mean values was necessary to get this result.\",\n \"corpus_id\": 2600206,\n \"score\": 0\n },\n {\n \"doc_id\": \"26697863\",\n \"title\": \"Computation in electron microscopy.\",\n \"abstract\": \"Some uses of the computer and computation in high-resolution transmission electron microscopy are reviewed. The theory of image calculation using Bloch wave and multislice methods with and without aberration correction is reviewed and some applications are discussed. The inverse problem of reconstructing the specimen structure from an experimentally measured electron microscope image is discussed. Some future directions of software development are given.\",\n \"corpus_id\": 10248349,\n \"score\": 0\n },\n {\n \"doc_id\": \"26705325\",\n \"title\": \"Principles of cryo-EM single-particle image processing.\",\n \"abstract\": \"Single-particle reconstruction is the process by which 3D density maps are obtained from a set of low-dose cryo-EM images of individual macromolecules. This review considers the fundamental principles of this process and the steps in the overall workflow for single-particle image processing. Also considered are the limits that image signal-to-noise ratio places on resolution and the distinguishing of heterogeneous particle populations.\",\n \"corpus_id\": 21949411,\n \"score\": 0\n },\n {\n \"doc_id\": \"27292544\",\n \"title\": \"Hollow Cone Electron Imaging for Single Particle 3D Reconstruction of Proteins.\",\n \"abstract\": \"The main bottlenecks for high-resolution biological imaging in electron microscopy are radiation sensitivity and low contrast. The phase contrast at low spatial frequencies can be enhanced by using a large defocus but this strongly reduces the resolution. Recently, phase plates have been developed to enhance the contrast at small defocus but electrical charging remains a problem. Single particle cryo-electron microscopy is mostly used to minimize the radiation damage and to enhance the resolution of the 3D reconstructions but it requires averaging images of a massive number of individual particles. Here we present a new route to achieve the same goals by hollow cone dark field imaging using thermal diffuse scattered electrons giving about a 4 times contrast increase as compared to bright field imaging. We demonstrate the 3D reconstruction of a stained GroEL particle can yield about 13.5 Å resolution but using a strongly reduced number of images.\",\n \"corpus_id\": 4579340,\n \"score\": 0\n },\n {\n \"doc_id\": \"27867705\",\n \"title\": \"3D differential phase contrast microscopy.\",\n \"abstract\": \"We demonstrate 3D phase and absorption recovery from partially coherent intensity images captured with a programmable LED array source. Images are captured through-focus with four different illumination patterns. Using first Born and weak object approximations (WOA), a linear 3D differential phase contrast (DPC) model is derived. The partially coherent transfer functions relate the sample's complex refractive index distribution to intensity measurements at varying defocus. Volumetric reconstruction is achieved by a global FFT-based method, without an intermediate 2D phase retrieval step. Because the illumination is spatially partially coherent, the transverse resolution of the reconstructed field achieves twice the NA of coherent systems and improved axial resolution.\",\n \"corpus_id\": 34080890,\n \"score\": 0\n },\n {\n \"doc_id\": \"28008874\",\n \"title\": \"Ultra-high resolution electron microscopy.\",\n \"abstract\": \"The last two decades have seen dramatic advances in the resolution of the electron microscope brought about by the successful correction of lens aberrations that previously limited resolution for most of its history. We briefly review these advances, the achievement of sub-Ångstrom resolution and the ability to identify individual atoms, their bonding configurations and even their dynamics and diffusion pathways. We then present a review of the basic physics of electron scattering, lens aberrations and their correction, and an approximate imaging theory for thin crystals which provides physical insight into the various different imaging modes. Then we proceed to describe a more exact imaging theory starting from Yoshioka's formulation and covering full image simulation methods using Bloch waves, the multislice formulation and the frozen phonon/quantum excitation of phonons models. Delocalization of inelastic scattering has become an important limiting factor at atomic resolution. We therefore discuss this issue extensively, showing how the full-width-half-maximum is the appropriate measure for predicting image contrast, but the diameter containing 50% of the excitation is an important measure of the range of the interaction. These two measures can differ by a factor of 5, are not a simple function of binding energy, and full image simulations are required to match to experiment. The Z-dependence of annular dark field images is also discussed extensively, both for single atoms and for crystals, and we show that temporal incoherence must be included accurately if atomic species are to be identified through matching experimental intensities to simulations. Finally we mention a few promising directions for future investigation.\",\n \"corpus_id\": 206095047,\n \"score\": 0\n },\n {\n \"doc_id\": \"28463301\",\n \"title\": \"Self-interference compressive digital holography with improved axial resolution and signal-to-noise ratio.\",\n \"abstract\": \"Fresnel incoherent correlation holography (FINCH) was proposed to break the barrier of spatial incoherent digital holographic imaging and show the potential of super-resolution imaging preferences. We developed FINCH as a compressive sensing modality and reconstruction procedure as an inverse problem in order to realize 3D tomographic imaging. Improved axial resolution is obtained via compressive reconstruction. Reconstruction guarantees and accuracy of the proposed method are discussed. Compared with the real-valued signal operation, the signal-to-noise ratio of the results is increased when reconstructing from the complex-valued hologram obtained from the FINCH system.\",\n \"corpus_id\": 46851950,\n \"score\": 0\n },\n {\n \"doc_id\": \"29043666\",\n \"title\": \"3D Electron Microscopy of the ER.\",\n \"abstract\": \"The endoplasmic reticulum (ER) forms an extensive network in plant cells. In leaf cells and vacuolated root cells it is mainly restricted to the cortex whereas in the root meristem the cortical and cytoplasmic ER takes up a large volume throughout the entire cell. Only 3D electron microscopy provides sufficient resolution to understand the spatial organization of the ER in the root. However, high contrast staining and optimally ER specific staining is essential. Here we describe a protocol for selective ER staining that allows automated or semiautomated segmentation of the organelle in 3D datasets obtained from serial sections, Array Tomography, Serial Block Face Scanning Electron Microscopy (SBFSEM), or Focused Ion Beam (FIB) SEM.\",\n \"corpus_id\": 44922058,\n \"score\": 0\n },\n {\n \"doc_id\": \"29727286\",\n \"title\": \"Reconstruction From Multiple Particles for 3D Isotropic Resolution in Fluorescence Microscopy.\",\n \"abstract\": \"The imaging of proteins within macromolecular complexes has been limited by the low axial resolution of optical microscopes. To overcome this problem, we propose a novel computational reconstruction method that yields isotropic resolution in fluorescence imaging. The guiding principle is to reconstruct a single volume from the observations of multiple rotated particles. Our new operational framework detects particles, estimates their orientation, and reconstructs the final volume. The main challenge comes from the absence of initial template and a priori knowledge about the orientations. We formulate the estimation as a blind inverse problem, and propose a block-coordinate stochastic approach to solve the associated non-convex optimization problem. The reconstruction is performed jointly in multiple channels. We demonstrate that our method is able to reconstruct volumes with 3D isotropic resolution on simulated data. We also perform isotropic reconstructions from real experimental data of doubly labeled purified human centrioles. Our approach revealed the precise localization of the centriolar protein Cep63 around the centriole microtubule barrel. Overall, our method offers new perspectives for applications in biology that require the isotropic mapping of proteins within macromolecular assemblies.\",\n \"corpus_id\": 3328607,\n \"score\": 0\n }\n]","isConversational":false}}},{"rowIdx":67,"cells":{"query":{"kind":"string","value":"{\n \"doc_id\": \"27102900\",\n \"title\": \"Local analysis of strains and rotations for macromolecular electron microscopy maps.\",\n \"abstract\": \"Macromolecular complexes perform their physiological functions by local rearrangements of their constituents and biochemically interacting with their reaction partners. These rearrangements may involve local rotations and the induction of local strains causing different mechanical efforts and stretches at the different areas of the protein. The analysis of these local deformations may reveal important insight into the way proteins perform their tasks. In this paper we introduce a method to perform this kind of local analysis using Electron Microscopy volumes in a fully objective and automatic manner. For doing so, we exploit the continuous nature of the result of an elastic image registration using B-splines as its basis functions. We show that the results obtained by the new automatic method are consistent with previous observations on these macromolecules.\",\n \"corpus_id\": 3931111\n}"},"candidates":{"kind":"list like","value":[{"doc_id":"19166941","title":"A method for the alignment of heterogeneous macromolecules from electron microscopy.","abstract":"We propose a feature-based image alignment method for single-particle electron microscopy that is able to accommodate various similarity scoring functions while efficiently sampling the two-dimensional transformational space. We use this image alignment method to evaluate the performance of a scoring function that is based on the Mutual Information (MI) of two images rather than one that is based on the cross-correlation function. We show that alignment using MI for the scoring function has far less model-dependent bias than is found with cross-correlation based alignment. We also demonstrate that MI improves the alignment of some types of heterogeneous data, provided that the signal-to-noise ratio is relatively high. These results indicate, therefore, that use of MI as the scoring function is well suited for the alignment of class-averages computed from single-particle images. Our method is tested on data from three model structures and one real dataset.","corpus_id":7807423,"score":2},{"doc_id":"22323229","title":"Macromolecular assembly structures by comparative modeling and electron microscopy.","abstract":"Advances in electron microscopy allow for structure determination of large biological machines at increasingly higher resolutions. A key step in this process is fitting component structures into the electron microscopy-derived density map of their assembly. Comparative modeling can contribute by providing atomic models of the components, via fold assignment, sequence-structure alignment, model building, and model assessment. All four stages of comparative modeling can also benefit from consideration of the density map. In this chapter, we describe numerous types of modeling problems restrained by a density map and available protocols for finding solutions. In particular, we provide detailed instructions for density map-guided modeling using the Integrative Modeling Platform (IMP), MODELLER, and UCSF Chimera.","corpus_id":38263891,"score":2},{"doc_id":"23671335","title":"3DEM Loupe: Analysis of macromolecular dynamics using structures from electron microscopy.","abstract":"Electron microscopy (EM) provides access to structural information of macromolecular complexes in the 3-20 Å resolution range. Normal mode analysis has been extensively used with atomic resolution structures and successfully applied to EM structures. The major application of normal modes is the identification of possible conformational changes in proteins. The analysis can throw light on the mechanism following ligand binding, protein-protein interactions, channel opening and other functional macromolecular movements. In this article, we present a new web server, 3DEM Loupe, which allows normal mode analysis of any uploaded EM volume using a user-friendly interface and an intuitive workflow. Results can be fully explored in 3D through animations and movies generated by the server. The application is freely available at http://3demloupe.cnb.csic.es.","corpus_id":16433573,"score":2},{"doc_id":"24508340","title":"Iterative elastic 3D-to-2D alignment method using normal modes for studying structural dynamics of large macromolecular complexes.","abstract":"This article presents a method to study large-scale conformational changes by combining electron microscopy (EM) single-particle image analysis and normal mode analysis (NMA). It is referred to as HEMNMA, which stands for hybrid electron microscopy normal mode analysis. NMA of a reference structure (atomic-resolution structure or EM volume) is used to predict possible motions that are then confronted with EM images within an automatic iterative elastic 3D-to-2D alignment procedure to identify actual motions in the imaged samples. HEMNMA can be used to extensively analyze the conformational changes and may be used in combination with classic discrete procedures. The identified conformations allow modeling of deformation pathways compatible with the experimental data. HEMNMA was tested with synthetic and experimental data sets of E. coli 70S ribosome, DNA polymerase Pol α and B subunit complex of the eukaryotic primosome, and tomato bushy stunt virus.","corpus_id":14951001,"score":2},{"doc_id":"24565374","title":"Structure, assembly and dynamics of macromolecular complexes by single particle cryo-electron microscopy.","abstract":"BACKGROUND: Proteins in their majority act rarely as single entities. Multisubunit macromolecular complexes are the actors in most of the cellular processes. These nanomachines are hold together by weak protein-protein interactions and undergo functionally important conformational changes. TFIID is such a multiprotein complex acting in eukaryotic transcription initiation. This complex is first to be recruited to the promoter of the genes and triggers the formation of the transcription preinitiation complex involving RNA polymerase II which leads to gene transcription. The exact role of TFIID in this process is not yet understood. METHODS: Last generation electron microscopes, improved data collection and new image analysis tools made it possible to obtain structural information of biological molecules at atomic resolution. Cryo-electron microscopy of vitrified samples visualizes proteins in a fully hydrated, close to native state. Molecular images are recorded at liquid nitrogen temperature in low electron dose conditions to reduce radiation damage. Digital image analysis of these noisy images aims at improving the signal-to-noise ratio, at separating distinct molecular views and at reconstructing a three-dimensional model of the biological particle. RESULTS: Using these methods we showed the early events of an activated transcription initiation process. We explored the interaction of the TFIID coactivator with the yeast Rap1 activator, the transcription factor TFIIA and the promoter DNA. We demonstrated that TFIID serves as an assembly platform for transient protein-protein interactions, which are essential for transcription initiation. CONCLUSIONS: Recent developments in electron microscopy have provided new insights into the structural organization and the dynamic reorganization of large macromolecular complexes. Examples of near-atomic resolutions exist but the molecular flexibility of macromolecular complexes remains the limiting factor in most case. Electron microscopy has the potential to provide both structural and dynamic information of biological assemblies in order to understand the molecular mechanisms of their functions.","corpus_id":15254399,"score":2},{"doc_id":"24914167","title":"Conformations of macromolecules and their complexes from heterogeneous datasets.","abstract":"We describe a new generation of algorithms capable of mapping the structure and conformations of macromolecules and their complexes from large ensembles of heterogeneous snapshots, and demonstrate the feasibility of determining both discrete and continuous macromolecular conformational spectra. These algorithms naturally incorporate conformational heterogeneity without resort to sorting and classification, or prior knowledge of the type of heterogeneity present. They are applicable to single-particle diffraction and image datasets produced by X-ray lasers and cryo-electron microscopy, respectively, and particularly suitable for systems not easily amenable to purification or crystallization.","corpus_id":278146,"score":2},{"doc_id":"25268657","title":"Hybrid Electron Microscopy Normal Mode Analysis graphical interface and protocol.","abstract":"This article presents an integral graphical interface to the Hybrid Electron Microscopy Normal Mode Analysis (HEMNMA) approach that was developed for capturing continuous motions of large macromolecular complexes from single-particle EM images. HEMNMA was shown to be a good approach to analyze multiple conformations of a macromolecular complex but it could not be widely used in the EM field due to a lack of an integral interface. In particular, its use required switching among different software sources as well as selecting modes for image analysis was difficult without the graphical interface. The graphical interface was thus developed to simplify the practical use of HEMNMA. It is implemented in the open-source software package Xmipp 3.1 (http://xmipp.cnb.csic.es) and only a small part of it relies on MATLAB that is accessible through the main interface. Such integration provides the user with an easy way to perform the analysis of macromolecular dynamics and forms a direct connection to the single-particle reconstruction process. A step-by-step HEMNMA protocol with the graphical interface is given in full details in Supplementary material. The graphical interface will be useful to experimentalists who are interested in studies of continuous conformational changes of macromolecular complexes beyond the modeling of continuous heterogeneity in single particle reconstruction.","corpus_id":13918346,"score":2},{"doc_id":"27119636","title":"StructMap: Elastic Distance Analysis of Electron Microscopy Maps for Studying Conformational Changes.","abstract":"Single-particle electron microscopy (EM) has been shown to be very powerful for studying structures and associated conformational changes of macromolecular complexes. In the context of analyzing conformational changes of complexes, distinct EM density maps obtained by image analysis and three-dimensional (3D) reconstruction are usually analyzed in 3D for interpretation of structural differences. However, graphic visualization of these differences based on a quantitative analysis of elastic transformations (deformations) among density maps has not been done yet due to a lack of appropriate methods. Here, we present an approach that allows such visualization. This approach is based on statistical analysis of distances among elastically aligned pairs of EM maps (one map is deformed to fit the other map), and results in visualizing EM maps as points in a lower-dimensional distance space. The distances among points in the new space can be analyzed in terms of clusters or trajectories of points related to potential conformational changes. The results of the method are shown with synthetic and experimental EM maps at different resolutions.","corpus_id":34220297,"score":2},{"doc_id":"27800126","title":"Cryo-electron Microscopy Analysis of Structurally Heterogeneous Macromolecular Complexes.","abstract":"Cryo-electron microscopy (cryo-EM) has for a long time been a technique of choice for determining structure of large and flexible macromolecular complexes that were difficult to study by other experimental techniques such as X-ray crystallography or nuclear magnetic resonance. However, a fast development of instruments and software for cryo-EM in the last decade has allowed that a large range of complexes can be studied by cryo-EM, and that their structures can be obtained at near-atomic resolution, including the structures of small complexes (e.g., membrane proteins) whose size was earlier an obstacle to cryo-EM. Image analysis to identify multiple coexisting structures in the same specimen (multiconformation reconstruction) is now routinely done both to solve structures at near-atomic resolution and to study conformational dynamics. Methods for multiconformation reconstruction and latest examples of their applications are the focus of this review.","corpus_id":15780788,"score":2},{"doc_id":"28088125","title":"Computational methods for analyzing conformational variability of macromolecular complexes from cryo-electron microscopy images.","abstract":"Thanks to latest technical advances in cryo-electron microscopy (cryo-EM), structures of macromolecular complexes (viruses, ribosomes, etc.) are now often obtained at near-atomic resolution. Also, studies of conformational changes of complexes, in connection with their function, are gaining ground. Conformational variability analysis is usually done by classifying images in a number of discrete classes supposedly representing all conformational states present in the specimen. However, discrete classes cannot be meaningfully defined when the conformational change is continuous (the specimen contains a continuum of states instead of a few discrete states). For such cases, first image analysis methods that explicitly consider continuous conformational changes were recently developed. The latest developments in cryo-EM image analysis methods for conformational variability analysis are the focus of this review.","corpus_id":3535220,"score":2},{"doc_id":"28097146","title":"Versatility of Approximating Single-Particle Electron Microscopy Density Maps Using Pseudoatoms and Approximation-Accuracy Control.","abstract":"Three-dimensional Gaussian functions have been shown useful in representing electron microscopy (EM) density maps for studying macromolecular structure and dynamics. Methods that require setting a desired number of Gaussian functions or a maximum number of iterations may result in suboptimal representations of the structure. An alternative is to set a desired error of approximation of the given EM map and then optimize the number of Gaussian functions to achieve this approximation error. In this article, we review different applications of such an approach that uses spherical Gaussian functions of fixed standard deviation, referred to as pseudoatoms. Some of these applications use EM-map normal mode analysis (NMA) with elastic network model (ENM) (applications such as predicting conformational changes of macromolecular complexes or exploring actual conformational changes by normal-mode-based analysis of experimental data) while some other do not use NMA (denoising of EM density maps). In applications based on NMA and ENM, the advantage of using pseudoatoms in EM-map coarse-grain models is that the ENM springs are easily assigned among neighboring grains thanks to their spherical shape and uniformed size. EM-map denoising based on the map coarse-graining was so far only shown using pseudoatoms as grains.","corpus_id":16586832,"score":2},{"doc_id":"18989044","title":"Computational approaches for automatic structural analysis of large biomolecular complexes.","abstract":"We present computational solutions to two problems of macromolecular structure interpretation from reconstructed three-dimensional electron microscopy (3D-EM) maps of large bio-molecular complexes at intermediate resolution (5A-15 A). The two problems addressed are: 1) 3D structural alignment (matching) between identified and segmented 3D maps of structure units (e.g. trimeric configuration of proteins), and 2) the secondary structure identification of a segmented protein 3D map (i.e.locations of alpha-helices, beta-sheets). For problem 1, we present an efficient algorithm to correlate spatially (and structurally) two 3D maps of structure units. Besides providing a similarity score between structure units, the algorithm yields an effective technique for resolution refinement of repeated structure units, by 3D alignment and averaging. For problem 2, we present an efficient algorithm to compute eigenvalues and link eigenvectors of a Gaussian convoluted structure tensor derived from the protein 3D Map, thereby identifying and locating secondary structural motifs of proteins. The efficiency and performance of our approach is demonstrated on several experimentally reconstructed 3D maps of virus capsid shells from single-particle cryo-electron microscopy (cryo-EM), as well as computationally simulated protein structure density 3D maps generated from protein model entries in the Protein Data Bank.","corpus_id":1636056,"score":1},{"doc_id":"20025794","title":"Single-particle reconstruction of biological macromolecules in electron microscopy--30 years.","abstract":"This essay gives the autho's personal account on the development of concepts underlying single-particle reconstruction, a technique in electron microscopy of macromolecular assemblies with a remarkable record of achievements as of late. The ribosome proved to be an ideal testing ground for the development of specimen preparation methods, cryo-EM techniques, and algorithms, with discoveries along the way as a rich reward. Increasingly, cryo-EM and single-particle reconstruction, in combination with classification techniques, is revealing dynamic information on functional molecular machines uninhibited by molecular contacts.","corpus_id":12465805,"score":1},{"doc_id":"20085819","title":"Automated multi-model reconstruction from single-particle electron microscopy data.","abstract":"Biological macromolecules can adopt multiple conformational and compositional states due to structural flexibility and alternative subunit assemblies. This structural heterogeneity poses a major challenge in the study of macromolecular structure using single-particle electron microscopy. We propose a fully automated, unsupervised method for the three-dimensional reconstruction of multiple structural models from heterogeneous data. As a starting reference, our method employs an initial structure that does not account for any heterogeneity. Then, a multi-stage clustering is used to create multiple models representative of the heterogeneity within the sample. The multi-stage clustering combines an existing approach based on Multivariate Statistical Analysis to perform clustering within individual Euler angles, and a newly developed approach to sort out class averages from individual Euler angles into homogeneous groups. Structural models are computed from individual clusters. The whole data classification is further refined using an iterative multi-model projection-matching approach. We tested our method on one synthetic and three distinct experimental datasets. The tests include the cases where a macromolecular complex exhibits structural flexibility and cases where a molecule is found in ligand-bound and unbound states. We propose the use of our approach as an efficient way to reconstruct distinct multiple models from heterogeneous data.","corpus_id":7132823,"score":1},{"doc_id":"20835797","title":"3-D structures of macromolecules using single-particle analysis in EMAN.","abstract":"Single-particle reconstruction is a methodology whereby transmission electron microscopy (TEM) is used to record images of individual monodisperse molecules or macromolecular assemblies, then sets of images of individual particles are computationally combined to produce a 3-D volumetric reconstruction. Ideally the TEM specimen will be prepared in vitreous ice (electron cryomicroscopy), but negative stain preparations may be used for lower resolution work. This technique has been demonstrated to produce structures at resolutions as high as ∼ 4 A, though this is not yet typical. The reconstruction process is quite computationally intensive, and several software packages are available for this task. EMAN is one of the easier to master software suites for single-particle analysis. This protocol explains how to perform an initial low-resolution reconstruction using EMAN.","corpus_id":27244417,"score":1},{"doc_id":"21444766","title":"Macromolecular structural dynamics visualized by pulsed dose control in 4D electron microscopy.","abstract":"Macromolecular conformation dynamics, which span a wide range of time scales, are fundamental to the understanding of properties and functions of their structures. Here, we report direct imaging of structural dynamics of helical macromolecules over the time scales of conformational dynamics (ns to subsecond) by means of four-dimensional (4D) electron microscopy in the single-pulse and stroboscopic modes. With temporally controlled electron dosage, both diffraction and real-space images are obtained without irreversible radiation damage. In this way, the order-disorder transition is revealed for the organic chain polymer. Through a series of equilibrium-temperature and temperature-jump dependencies, it is shown that the metastable structures and entropy of conformations can be mapped in the nonequilibrium region of a \"funnel-like\" free-energy landscape. The T-jump is introduced through a substrate (a \"hot plate\" type arrangement) because only the substrate is made to absorb the pulsed energy. These results illustrate the promise of ultrafast 4D imaging for other applications in the study of polymer physics as well as in the visualization of biological phenomena.","corpus_id":1127528,"score":1},{"doc_id":"23131460","title":"FOLD-EM: automated fold recognition in medium- and low-resolution (4-15 Å) electron density maps.","abstract":"MOTIVATION: Owing to the size and complexity of large multi-component biological assemblies, the most tractable approach to determining their atomic structure is often to fit high-resolution radiographic or nuclear magnetic resonance structures of isolated components into lower resolution electron density maps of the larger assembly obtained using cryo-electron microscopy (cryo-EM). This hybrid approach to structure determination requires that an atomic resolution structure of each component, or a suitable homolog, is available. If neither is available, then the amount of structural information regarding that component is limited by the resolution of the cryo-EM map. However, even if a suitable homolog cannot be identified using sequence analysis, a search for structural homologs should still be performed because structural homology often persists throughout evolution even when sequence homology is undetectable, As macromolecules can often be described as a collection of independently folded domains, one way of searching for structural homologs would be to systematically fit representative domain structures from a protein domain database into the medium/low resolution cryo-EM map and return the best fits. Taken together, the best fitting non-overlapping structures would constitute a 'mosaic' backbone model of the assembly that could aid map interpretation and illuminate biological function. RESULT: Using the computational principles of the Scale-Invariant Feature Transform (SIFT), we have developed FOLD-EM-a computational tool that can identify folded macromolecular domains in medium to low resolution (4-15 Å) electron density maps and return a model of the constituent polypeptides in a fully automated fashion. As a by-product, FOLD-EM can also do flexible multi-domain fitting that may provide insight into conformational changes that occur in macromolecular assemblies.","corpus_id":6876031,"score":1},{"doc_id":"23625506","title":"Novel convergence-oriented approach for evaluation and optimization of workflow in single-particle two-dimensional averaging of electron microscope images.","abstract":"Three-dimensional (3D) protein structures facilitate the understanding of their biological functions and provide valuable information for developing medicines. Single-particle analysis (SPA) from electron microscopy (EM) is a structure determination method suitable for macromolecules. To achieve a high resolution using combinations of several SPA software packages, 'workflow' optimization and comparative evaluation by scoring results are essential. Two-dimensional (2D) averaging is a key step for 3D reconstruction. The integrated convergence-evaluation oriented system (IC-EOS) proposed here provides an effective tool for customizing 2D averaging. This assesses the behavior and characteristics of workflows and evaluates the convergence of iteration steps without human intervention. We chose five base measurements for quantifying convergence: resolution, variance, similarity, shift-distance and rotation-angle. Curve fitting to history graphs scored their stability. We call this score 'fluctuation'. The number of particle images discarded from the library and the number of classification groups were examined to see their effects on optimization levels and fluctuation of measurements, allowing the IC-EOS to select the most appropriate workflow for the target. A case study using a bacterial sodium channel and a simulation study using GroEL showed that resolution of 2D averaging improved with relatively stricter particle selection. With fewer groups, resolutions of class averages improved, but similarities between class-averages and their constituent particle images degraded. Fluctuation was useful for selecting adequate conditions, even when achieved values alone were not conclusive. The vote method, using fluctuation, was robust against noise and enabled a decision without exhaustive search trials. Thus, the IC-EOS is a step toward full automation of SPA.","corpus_id":33894902,"score":1},{"doc_id":"23793721","title":"Intensity-based hierarchical elastic registration using approximating splines.","abstract":"PURPOSE: We introduce a new hierarchical approach for elastic medical image registration using approximating splines. In order to obtain the dense deformation field, we employ Gaussian elastic body splines (GEBS) that incorporate anisotropic landmark errors and rotation information. Since the GEBS approach is based on a physical model in form of analytical solutions of the Navier equation, it can very well cope with the local as well as global deformations present in the images by varying the standard deviation of the Gaussian forces. METHODS: The proposed GEBS approximating model is integrated into the elastic hierarchical image registration framework, which decomposes a nonrigid registration problem into numerous local rigid transformations. The approximating GEBS registration scheme incorporates anisotropic landmark errors as well as rotation information. The anisotropic landmark localization uncertainties can be estimated directly from the image data, and in this case, they represent the minimal stochastic localization error, i.e., the Cramér-Rao bound. The rotation information of each landmark obtained from the hierarchical procedure is transposed in an additional angular landmark, doubling the number of landmarks in the GEBS model. RESULTS: The modified hierarchical registration using the approximating GEBS model is applied to register 161 image pairs from a digital mammogram database. The obtained results are very encouraging, and the proposed approach significantly improved all registrations comparing the mean-square error in relation to approximating TPS with the rotation information. On artificially deformed breast images, the newly proposed method performed better than the state-of-the-art registration algorithm introduced by Rueckert et al. (IEEE Trans Med Imaging 18:712-721, 1999). The average error per breast tissue pixel was less than 2.23 pixels compared to 2.46 pixels for Rueckert's method. CONCLUSION: The proposed hierarchical elastic image registration approach incorporates the GEBS approximation scheme extended with anisotropic landmark localization uncertainties as well as rotation information. Our experimental results show that the proposed scheme improved the registration result significantly.","corpus_id":2656824,"score":1},{"doc_id":"24232828","title":"Interactive multigrid refinement for deformable image registration.","abstract":"Deformable image registration is the spatial mapping of corresponding locations between images and can be used for important applications in radiotherapy. Although numerous methods have attempted to register deformable medical images automatically, such as salient-feature-based registration (SFBR), free-form deformation (FFD), and demons, no automatic method for registration is perfect, and no generic automatic algorithm has shown to work properly for clinical applications due to the fact that the deformation field is often complex and cannot be estimated well by current automatic deformable registration methods. This paper focuses on how to revise registration results interactively for deformable image registration. We can manually revise the transformed image locally in a hierarchical multigrid manner to make the transformed image register well with the reference image. The proposed method is based on multilevel B-spline to interactively revise the deformable transformation in the overlapping region between the reference image and the transformed image. The resulting deformation controls the shape of the transformed image and produces a nice registration or improves the registration results of other registration methods. Experimental results in clinical medical images for adaptive radiotherapy demonstrated the effectiveness of the proposed method.","corpus_id":18196005,"score":1},{"doc_id":"26534841","title":"Localized reconstruction of subunits from electron cryomicroscopy images of macromolecular complexes.","abstract":"Electron cryomicroscopy can yield near-atomic resolution structures of highly ordered macromolecular complexes. Often however some subunits bind in a flexible manner, have different symmetry from the rest of the complex, or are present in sub-stoichiometric amounts, limiting the attainable resolution. Here we report a general method for the localized three-dimensional reconstruction of such subunits. After determining the particle orientations, local areas corresponding to the subunits can be extracted and treated as single particles. We demonstrate the method using three examples including a flexible assembly and complexes harbouring subunits with either partial occupancy or mismatched symmetry. Most notably, the method allows accurate fitting of the monomeric RNA-dependent RNA polymerase bound at the threefold axis of symmetry inside a viral capsid, revealing for the first time its exact orientation and interactions with the capsid proteins. Localized reconstruction is expected to provide novel biological insights in a range of challenging biological systems.","corpus_id":25224478,"score":1},{"doc_id":"26678751","title":"A local-optimization refinement algorithm in single particle analysis for macromolecular complex with multiple rigid modules.","abstract":"Single particle analysis, which can be regarded as an average of signals from thousands or even millions of particle projections, is an efficient method to study the three-dimensional structures of biological macromolecules. An intrinsic assumption in single particle analysis is that all the analyzed particles must have identical composition and conformation. Thus specimen heterogeneity in either composition or conformation has raised great challenges for high-resolution analysis. For particles with multiple conformations, inaccurate alignments and orientation parameters will yield an averaged map with diminished resolution and smeared density. Besides extensive classification approaches, here based on the assumption that the macromolecular complex is made up of multiple rigid modules whose relative orientations and positions are in slight fluctuation around equilibriums, we propose a new method called as local optimization refinement to address this conformational heterogeneity for an improved resolution. The key idea is to optimize the orientation and shift parameters of each rigid module and then reconstruct their three-dimensional structures individually. Using simulated data of 80S/70S ribosomes with relative fluctuations between the large (60S/50S) and the small (40S/30S) subunits, we tested this algorithm and found that the resolutions of both subunits are significantly improved. Our method provides a proof-of-principle solution for high-resolution single particle analysis of macromolecular complexes with dynamic conformations.","corpus_id":14678415,"score":1},{"doc_id":"28368275","title":"Cryo-electron microscopy and X-ray crystallography: complementary approaches to structural biology and drug discovery.","abstract":"The invention of the electron microscope has greatly enhanced the view scientists have of small structural details. Since its implementation, this technology has undergone considerable evolution and the resolution that can be obtained for biological objects has been extended. In addition, the latest generation of cryo-electron microscopes equipped with direct electron detectors and software for the automated collection of images, in combination with the use of advanced image-analysis methods, has dramatically improved the performance of this technique in terms of resolution. While calculating a sub-10 Å resolution structure was an accomplishment less than a decade ago, it is now common to generate structures at sub-5 Å resolution and even better. It is becoming possible to relatively quickly obtain high-resolution structures of biological molecules, in particular large ones (>500 kDa) which, in some cases, have resisted more conventional methods such as X-ray crystallography or nuclear magnetic resonance (NMR). Such newly resolved structures may, for the first time, shed light on the precise mechanisms that are essential for cellular physiological processes. The ability to attain atomic resolution may support the development of new drugs that target these proteins, allowing medicinal chemists to understand the intimacy of the relationship between their molecules and targets. In addition, recent developments in cryo-electron microscopy combined with image analysis can provide unique information on the conformational variability of macromolecular complexes. Conformational flexibility of macromolecular complexes can be investigated using cryo-electron microscopy and multiconformation reconstruction methods. However, the biochemical quality of the sample remains the major bottleneck to routine cryo-electron microscopy-based determination of structures at very high resolution.","corpus_id":2588079,"score":1},{"doc_id":"18334219","title":"De novo backbone trace of GroEL from single particle electron cryomicroscopy.","abstract":"In this work, we employ single-particle electron cryo-microscopy (cryo-EM) to reconstruct GroEL to approximately 4 A resolution with both D7 and C7 symmetry. Using a newly developed skeletonization algorithm and secondary structure element identification in combination with sequence-based secondary structure prediction, we demonstrate that it is possible to achieve a de novo Calpha trace directly from a cryo-EM reconstruction. The topology of our backbone trace is completely accurate, though subtle alterations illustrate significant differences from existing crystal structures. In the map with C7 symmetry, the seven monomers in each ring are identical; however, the subunits have a subtly different structure in each ring, particularly in the equatorial domain. These differences include an asymmetric salt bridge, density in the nucleotide-binding pocket of only one ring, and small shifts in alpha helix positions. This asymmetric conformation is different from previous asymmetric structures, including GroES-bound GroEL, and may represent a \"primed state\" in the chaperonin pathway.","corpus_id":24474229,"score":0},{"doc_id":"18518137","title":"Direct mapping of strain in a strained silicon transistor by high-resolution electron microscopy.","abstract":"Aberration-corrected high-resolution transmission electron microscopy (HRTEM) is used to measure strain in a strained-silicon metal-oxide-semiconductor field-effect transistor. Strain components parallel and perpendicular to the gate are determined directly from the HRTEM image by geometric phase analysis. Si80Ge20 source and drain stressors lead to uniaxial compressive strain in the Si channel, reaching a maximum value of -1.3% just below the gate oxide, equivalent to 2.2 GPa. Strain maps obtained by linear elasticity theory, modeled with the finite-element method, agree with the experimental results to within 0.1%.","corpus_id":42476637,"score":0},{"doc_id":"18575880","title":"Bridging fluorescence microscopy and electron microscopy.","abstract":"Development of new fluorescent probes and fluorescence microscopes has led to new ways to study cell biology. With the emergence of specialized microscopy units at most universities and research centers, the use of these techniques is well within reach for a broad research community. A major breakthrough in fluorescence microscopy in biology is the ability to follow specific targets on or in living cells, revealing dynamic localization and/or function of target molecules. One of the inherent limitations of fluorescence microscopy is the resolution. Several efforts are undertaken to overcome this limit. The traditional and most well-known way to achieve higher resolution imaging is by electron microscopy. Moreover, electron microscopy reveals organelles, membranes, macromolecules, and thus aids in the understanding of cellular complexity and localization of molecules of interest in relation to other structures. With the new probe development, a solid bridge between fluorescence microscopy and electron microscopy is being built, even leading to correlative imaging. This connection provides several benefits, both scientifically as well as practically. Here, I summarize recent developments in bridging microscopy.","corpus_id":24393,"score":0},{"doc_id":"19185480","title":"Probing the macromolecular organization of cells by electron tomography.","abstract":"A major goal in cell biology is to understand the functional organization of macromolecular complexes in vivo. Electron microscopy is helping cell biologists to achieve this goal, thanks to its ability to resolve structural details in the nanometer range. While issues related to specimen preparation, imaging, and image interpretation make this approach to cell architecture difficult, recent improvements in methods, equipment, and software have facilitated the study of both important macromolecular complexes and comparatively large volumes from cellular specimens. Here, we describe recent progress in electron microscopy of cells and the ways in which the relevant methodologies are helping to elucidate cell architecture.","corpus_id":11130652,"score":0},{"doc_id":"19201364","title":"Interactive deformation registration of endorectal prostate MRI using ITK thin plate splines.","abstract":"RATIONALE AND OBJECTIVES: Magnetic resonance imaging with an endorectal coil allows high-resolution imaging of prostate cancer and the surrounding normal organs. These anatomic details can be used to direct radiotherapy. However, organ deformation introduced by the endorectal coil makes it difficult to register magnetic resonance images for treatment planning. In this study, plug-ins for the volume visualization software VolView were implemented on the basis of algorithms from the National Library of Medicine's Insight Segmentation and Registration Toolkit (ITK). MATERIALS AND METHODS: Magnetic resonance images of a phantom simulating human pelvic structures were obtained with and without the endorectal coil balloon inflated. The prostate not deformed by the endorectal balloon was registered to the deformed prostate using an ITK thin plate spline (TPS). This plug-in allows the use of crop planes to limit the deformable registration in the region of interest around the prostate. These crop planes restricted the support of the TPS to the area around the prostate, where most of the deformation occurred. The region outside the crop planes was anchored by grid points. RESULTS: The TPS was more accurate in registering the local deformation of the prostate compared with a TPS variant, the elastic body spline. The TPS was also applied to register an in vivo T(2)-weighted endorectal magnetic resonance image. The intraprostatic tumor was accurately registered. This could potentially guide the boosting of intraprostatic targets. The source and target landmarks were placed graphically. This TPS plug-in allows the registration to be undone. The landmarks could be added, removed, and adjusted in real time and in three dimensions between repeated registrations. CONCLUSION: This interactive TPS plug-in allows a user to obtain a high level of accuracy satisfactory to a specific application efficiently. Because it is open-source software, the imaging community will be able to validate and improve the algorithm.","corpus_id":20777730,"score":0},{"doc_id":"19211241","title":"Structural mapping of spliceosomes by electron microscopy.","abstract":"Eukaryotic genes are transcribed as pre-mRNAs which are interrupted by noncoding introns. Selection and accurate removal of introns is an essential step in gene expression that is performed by a large and highly dynamic macromolecular machine, called spliceosome. A major challenge for structural studies of the spliceosome is represented by its large size as well as its dynamic nature. Electron microscopy is an important technique to study the overall shape and architecture of spliceosomes and their components, and to locate subunits and RNA parts. Recent advances in sample preparation of spliceosomes, technical improvements in EM instrumentation, powerful computer hardware, and new image analysis software will be instrumental to push structural studies of spliceosomes to a higher level of resolution.","corpus_id":32472062,"score":0},{"doc_id":"19499142","title":"Geometric alignment of 2D gel electrophoresis images.","abstract":"OBJECTIVES: 2D gel electrophoresis (2-DE) is the method of choice for analyzing protein expression in the field of proteomics, for example, comparing a reference with a test population. However, due to complex physical and chemical processes the locations of proteins generally vary in different 2-DE images. To cope with these variations, accurate geometric alignment of 2-DE images is important. METHODS: We introduce a new elastic registration approach for 2-DE images, which is based on an analytic solution of the Navier equation using Gaussian elastic body splines (GEBS). With this approach cross-effects in elastic deformations can be handled, which is important for the registration of 2-DE images. In addition, landmark correspondences can be included to aid the registration in regions which are difficult to register using intensity information alone. RESULTS: We have successfully applied our approach to register 2-DE gel images of different levels of complexity. In each case, gel images from a reference group are compared with a test group. To analyze the performance of our approach, we have carried out a quantitative evaluation of the registration results. Moreover, we have performed an experimental comparison with a previous elastic registration scheme. CONCLUSIONS: From the results we found that our approach is well-suited for the registration of 2-DE gel images of different levels of complexity and it turned out that the approach is superior to a previous hybrid scheme. Moreover, our approach is well-suited in a fully automatic setting and the performance can further be improved when landmark correspondences are available.","corpus_id":674636,"score":0},{"doc_id":"19564681","title":"The Max-Inf2/Lorentz Center workshop on New algorithms in macromolecular crystallography and electron microscopy.","abstract":"The resolution gap between macromolecular crystallography and electron microscopy continues to decrease. Recent advances in specimen preparation, instrumentation and computational power have allowed accurate structure determination of larger macromolecular complexes by crystallography and/or by electron microscopy on cryovitrified samples. New possibilities in structural biology have opened up and new challenges are faced to further reduce the resolution gap. A workshop at the Lorentz Center, Leiden, The Netherlands, which took place in May 2008, was organized to push further the limits of both complementary techniques through improved computational methods.","corpus_id":287483,"score":0},{"doc_id":"20512149","title":"Precise mapping of subunits in multiprotein complexes by a versatile electron microscopy label.","abstract":"Positional knowledge of subunits within multiprotein assemblies is crucial for understanding their function. The topological analysis of protein complexes by electron microscopy has undergone impressive development, but analysis of the exact positioning of single subunits has lagged behind. Here we have developed a clonable approximately 80-residue tag that, upon attachment to a target protein, can recruit a structurally prominent electron microscopy label in vitro. This tag is readily visible on single particles and becomes exceptionally distinct after image processing and classification. Thus, our method is applicable for the exact topological mapping of subunits in macromolecular complexes.","corpus_id":12508676,"score":0},{"doc_id":"20530635","title":"Merging molecular electron microscopy and mass spectrometry by carbon film-assisted endoproteinase digestion.","abstract":"Many fundamental processes in the cell are performed by complex macromolecular assemblies that comprise a large number of proteins. Numerous macromolecular assemblies are structurally rather fragile and may suffer during purification, resulting in the partial dissociation of the complexes. These limitations can be overcome by chemical fixation of the assemblies, and recently introduced protocols such as gradient fixation during ultracentrifugation (GraFix) offer advantages for the analysis of fragile macromolecular assemblies. The irreversible fixation, however, is thought to render macromolecular samples useless for studying their protein composition. We therefore developed a novel approach that possesses the advantages of fixation for structure determination by single particle electron microscopy while still allowing a correlative compositional analysis by mass spectrometry. In this method, which we call \"electron microscopy carbon film-assisted digestion\", macromolecular assemblies are chemically fixed and then adsorbed onto electron microscopical carbon films. Parallel, identically prepared specimens are then subjected to structural investigation by electron microscopy and proteomics analysis by mass spectrometry of the digested sample. As identical sample preparation protocols are used for electron microscopy and mass spectrometry, the results of both methods can directly be correlated. In addition, we demonstrate improved sensitivity and reproducibility of electron microscopy carbon film-assisted digestion as compared with standard protocols. We show that sample amounts of as low as 50 fmol are sufficient to obtain a comprehensive protein composition of two model complexes. We suggest our approach to be an optimization technique for the compositional analysis of macromolecules by mass spectrometry in general.","corpus_id":34269447,"score":0},{"doc_id":"20869518","title":"Analysis of the ultrastructure of archaea by electron microscopy.","abstract":"The ultrastructural characterization of archaeal cells is done with both types of electron microscopy, transmission electron microscopy, and scanning electron microscopy. Depending on the scientific question, different preparation methods have to be employed and need to be optimized, according to the special cultivation conditions of these-in many cases extreme-microorganisms. Recent results using various electron microscopy techniques show that archaeal cells have a variety of cell appendages, used for motility as well as for establishing cell-cell and cell-surface contacts. Cryo-preparation methods, in particular high-pressure freezing and freeze-substitution, are crucial for obtaining results: (1) showing the cells in ultrathin sections in a good structural preservation, often with unusual shapes and subcellular complexity, and (2) enabling us to perform immunolocalization studies. This is an important tool to make a link between biochemical and ultrastructural studies.","corpus_id":5264737,"score":0},{"doc_id":"21864783","title":"Measurement of residual elastic strain and lattice rotations with high resolution electron backscatter diffraction.","abstract":"A set of dynamically simulated electron backscatter patterns (EBSPs) for α-Ti crystals progressively rotated by 1° steps were analysed using cross-correlation to determine image shifts from which strains and rotations were calculated. At larger rotations the cross-correlation fails in certain regions of the EBSP where large shifts are generated. These incorrect shifts prevent standard least square error procedures from obtaining a valid solution for the strain and rotation, where the applied rotation exceeds ∼ 8°. Using a robust iterative fitting routine reliable strains and rotations can be obtained for applied rotations of up to and including ∼ 11° even though some image shifts are measured incorrectly. Finally, high resolution electron backscatter diffraction has been used to analyse the residual elastic strain, lattice rotations and density of stored geometrically necessary dislocations in a sample of copper deformed to 10% total strain. The robust iterative fitting analysis allows reliable analysis of a larger proportion of the map, the difference being most obviously beneficial in regions where significant lattice rotations have been generated.","corpus_id":31226838,"score":0},{"doc_id":"22092443","title":"Digital correction of motion artefacts in microscopy image sequences collected from living animals using rigid and nonrigid registration.","abstract":"Digital image analysis is a fundamental component of quantitative microscopy. However, intravital microscopy presents many challenges for digital image analysis. In general, microscopy volumes are inherently anisotropic, suffer from decreasing contrast with tissue depth, lack object edge detail and characteristically have low signal levels. Intravital microscopy introduces the additional problem of motion artefacts, resulting from respiratory motion and heartbeat from specimens imaged in vivo. This paper describes an image registration technique for use with sequences of intravital microscopy images collected in time-series or in 3D volumes. Our registration method involves both rigid and nonrigid components. The rigid registration component corrects global image translations, whereas the nonrigid component manipulates a uniform grid of control points defined by B-splines. Each control point is optimized by minimizing a cost function consisting of two parts: a term to define image similarity, and a term to ensure deformation grid smoothness. Experimental results indicate that this approach is promising based on the analysis of several image volumes collected from the kidney, lung and salivary gland of living rodents.","corpus_id":205343497,"score":0},{"doc_id":"22095783","title":"Cryo-electron microscopy of ribosomal complexes in cotranslational folding, targeting, and translocation.","abstract":"Single-particle cryo-electron microscopy (cryo-EM) became a well-established method to study the structure and function of large macromolecular assemblies in a close to physiological environment. Cryo-EM reconstructions of ribosomal complexes trapped at different stages during translation, cotranslational targeting, and translocation provide new insights on a molecular level into these processes, which are vital for the correct localization and folding of all proteins in the cell. The EM structures in combination with biochemical experiments and available high-resolution crystal or nuclear magnetic resonance (NMR) structures of individual factors and of the ribosome allow for interpretation in quasi-atomic detail of the molecular mechanism of ribosomal complexes, their conformational changes and dynamic interactions with factors like the signal recognition particle, SRP receptor, the translocon, and the chaperone trigger factor. The snapshots obtained by single-particle EM reconstructions enable us to follow the path of a nascent protein from the peptidyl-transferase center, through the ribosomal tunnel, to and across the translocon in the membrane. With new developments in image processing techniques it is possible to sort a biological homogenous sample into different conformational states and to reach subnanometer resolution such that folding of the nascent chain into secondary structure elements can be directly visualized. With improved cryo-electron tomography and correlative light microscopy and EM, it will be possible to visualize ribosomal complexes in their cellular context.","corpus_id":39572148,"score":0},{"doc_id":"22386621","title":"Visualizing macromolecular complexes with in situ liquid scanning transmission electron microscopy.","abstract":"A central focus of biological research is understanding the structure/function relationship of macromolecular protein complexes. Yet conventional transmission electron microscopy techniques are limited to static observations. Here we present the first direct images of purified macromolecular protein complexes using in situ liquid scanning transmission electron microscopy. Our results establish the capability of this technique for visualizing the interface between biology and nanotechnology with high fidelity while also probing the interactions of biomolecules within solution. This method represents an important advancement towards allowing future high-resolution observations of biological processes and conformational dynamics in real-time.","corpus_id":39857094,"score":0},{"doc_id":"22420849","title":"Bacteriophage electron microscopy.","abstract":"Since the advent of the electron microscope approximately 70 years ago, bacterial viruses and electron microscopy are inextricably linked. Electron microscopy proved that bacteriophages are particulate and viral in nature, are complex in size and shape, and have intracellular development cycles and assembly pathways. The principal contribution of electron microscopy to bacteriophage research is the technique of negative staining. Over 5500 bacterial viruses have so far been characterized by electron microscopy, making bacteriophages, at least on paper, the largest viral group in existence. Other notable contributions are cryoelectron microcopy and three-dimensional image reconstruction, particle counting, and immunoelectron microscopy. Scanning electron microscopy has had relatively little impact. Transmission electron microscopy has provided the basis for the recognition and establishment of bacteriophage families and is one of the essential criteria to classify novel viruses into families. It allows for instant diagnosis and is thus the fastest diagnostic technique in virology. The most recent major contribution of electron microscopy is the demonstration that the capsid of tailed phages is monophyletic in origin and that structural links exist between some bacteriophages and viruses of vertebrates and archaea. DNA sequencing cannot replace electron microscopy and vice versa.","corpus_id":19887164,"score":0},{"doc_id":"22445172","title":"ATP-triggered conformational changes delineate substrate-binding and -folding mechanics of the GroEL chaperonin.","abstract":"The chaperonin GroEL assists the folding of nascent or stress-denatured polypeptides by actions of binding and encapsulation. ATP binding initiates a series of conformational changes triggering the association of the cochaperonin GroES, followed by further large movements that eject the substrate polypeptide from hydrophobic binding sites into a GroES-capped, hydrophilic folding chamber. We used cryo-electron microscopy, statistical analysis, and flexible fitting to resolve a set of distinct GroEL-ATP conformations that can be ordered into a trajectory of domain rotation and elevation. The initial conformations are likely to be the ones that capture polypeptide substrate. Then the binding domains extend radially to separate from each other but maintain their binding surfaces facing the cavity, potentially exerting mechanical force upon kinetically trapped, misfolded substrates. The extended conformation also provides a potential docking site for GroES, to trigger the final, 100° domain rotation constituting the \"power stroke\" that ejects substrate into the folding chamber.","corpus_id":8815470,"score":0},{"doc_id":"22566049","title":"Electron microscopy.","abstract":"Correlative light (LM) and transmission electron microscopic (TEM) analysis is useful, if ultrastructural details of cells need to be related to functional aspects which can only be examined at the LM level. The first protocol presented here introduces a relatively simple way of obtaining TEM images which, on the one hand, reveal ultrastructural details of individual cells and, on the other hand, are large enough to allow a correlation with light micrographs. The second protocol describes a technique for estimating mineral densities of hard tissues using backscattered electron images obtained with a scanning electron microscope. This technique can be used to analyze the mineralization processes which occur throughout tooth formation.","corpus_id":39721085,"score":0},{"doc_id":"22704292","title":"Evaluation of the registration of temporal series of contrast-enhanced perfusion magnetic resonance 3D images of the liver.","abstract":"The registration of 2D and 3D images is one of the key tasks in medical image processing and analysis. Accurate registration is a crucial preprocessing step for many tasks; consequently, the evaluation of its accuracy becomes necessary. Unfortunately, this is a difficult task, especially when no golden pattern (true result) is available and when the signal values may have changed between successive images to be registered. This is the case this paper deals with: we have a series of 3D images, magnetic resonance images (MRI) of the liver and adjacent areas that have to be registered. They have been taken while a contrast is diffused through the liver tissue, so intensity of each observed point changes for two reasons: contrast diffusion/perfusion and deformation of the liver (due to body movement and breathing). In this paper, we introduce a new method to automatically compare two or more registration algorithms applied to the same case of a perfusion magnetic resonance dynamic image so that the best of them can be chosen when no ground truth is available. This is done by modeling the function that gives the intensity at a given point as a functional datum, and using statistical techniques to assess its change in comparison with other functions. An example of the application is shown by comparing two parametrizations of a B-spline based registration algorithm. The main result of the proposed method is a suggestive evidence to guide the physician in the process of selecting a registration algorithm, that recommends the algorithm of minimal complexity but still suitable for the case to be analyzed.","corpus_id":7334154,"score":0},{"doc_id":"23152943","title":"Super elastic strain limit in metallic glass films.","abstract":"On monolithic Ni-Nb metallic glass films, we experimentally revealed 6.6% elastic strain limit by in-situ transmission electron microscopy observations. The origin of high elastic strain limit may link with high free volume in the film, causing the rearrangement of loosely bonded atomic clusters (or atoms) upon elastic deformation. This high elastic limit of metallic glass films will shed light on new application fields for metallic glasses, and also trigger more studies for deformation mechanism of amorphous materials in general.","corpus_id":13043780,"score":0},{"doc_id":"23877967","title":"ATP-driven molecular chaperone machines.","abstract":"This review is focused on the mechanisms by which ATP binding and hydrolysis drive chaperone machines assisting protein folding and unfolding. A survey of the key, general chaperone systems Hsp70 and Hsp90, and the unfoldase Hsp100 is followed by a focus on the Hsp60 chaperonin machine which is understood in most detail. Cryo-electron microscopy analysis of the E. coli Hsp60 GroEL reveals intermediate conformations in the ATPase cycle and in substrate folding. These structures suggest a mechanism by which GroEL can forcefully unfold and then encapsulate substrates for subsequent folding in isolation from all other binding surfaces.","corpus_id":7822974,"score":0},{"doc_id":"23958728","title":"A pattern matching approach to the automatic selection of particles from low-contrast electron micrographs.","abstract":"MOTIVATION: Structural information of macromolecular complexes provides key insights into the way they carry out their biological functions. Achieving high-resolution structural details with electron microscopy requires the identification of a large number (up to hundreds of thousands) of single particles from electron micrographs, which is a laborious task if it has to be manually done and constitutes a hurdle towards high-throughput. Automatic particle selection in micrographs is far from being settled and new and more robust algorithms are required to reduce the number of false positives and false negatives. RESULTS: In this article, we introduce an automatic particle picker that learns from the user the kind of particles he is interested in. Particle candidates are quickly and robustly classified as particles or non-particles. A number of new discriminative shape-related features as well as some statistical description of the image grey intensities are used to train two support vector machine classifiers. Experimental results demonstrate that the proposed method: (i) has a considerably low computational complexity and (ii) provides results better or comparable with previously reported methods at a fraction of their computing time. AVAILABILITY: The algorithm is fully implemented in the open-source Xmipp package and downloadable from http://xmipp.cnb.csic.es.","corpus_id":11199882,"score":0},{"doc_id":"24161732","title":"Optimod--an automated approach for constructing and optimizing initial models for single-particle electron microscopy.","abstract":"Single-particle cryo-electron microscopy is now well established as a technique for the structural characterization of large macromolecules and macromolecular complexes. The raw data is very noisy and consists of two-dimensional projections, from which the 3D biological object must be reconstructed. The 3D object depends upon knowledge of proper angular orientations assigned to the 2D projection images. Numerous algorithms have been developed for determining relative angular orientations between 2D images, but the transition from 2D to 3D remains challenging and can result in erroneous and conflicting results. Here we describe a general, automated procedure, called OptiMod, for reconstructing and optimizing 3D models using common-lines methodologies. OptiMod approximates orientation angles and reconstructs independent maps from 2D class averages. It then iterates the procedure, while considering each map as a raw solution that needs to be compared with other possible outcomes. We incorporate procedures for 3D alignment, clustering, and refinement to optimize each map, as well as standard scoring metrics to facilitate the selection of the optimal model. We also show that small angle tilt-pair data can be included as one of the scoring metrics to improve the selection of the optimal initial model, and also to provide a validation check. The overall approach is demonstrated using two experimental cryo-EM data sets--the 80S ribosome that represents a relatively straightforward case for ab initio reconstruction, and the Tf-TfR complex that represents a challenging case in that it has previously been shown to provide multiple equally plausible solutions to the initial model problem.","corpus_id":36681249,"score":0},{"doc_id":"24387943","title":"Multi-modal registration for correlative microscopy using image analogies.","abstract":"Correlative microscopy is a methodology combining the functionality of light microscopy with the high resolution of electron microscopy and other microscopy technologies for the same biological specimen. In this paper, we propose an image registration method for correlative microscopy, which is challenging due to the distinct appearance of biological structures when imaged with different modalities. Our method is based on image analogies and allows to transform images of a given modality into the appearance-space of another modality. Hence, the registration between two different types of microscopy images can be transformed to a mono-modality image registration. We use a sparse representation model to obtain image analogies. The method makes use of corresponding image training patches of two different imaging modalities to learn a dictionary capturing appearance relations. We test our approach on backscattered electron (BSE) scanning electron microscopy (SEM)/confocal and transmission electron microscopy (TEM)/confocal images. We perform rigid, affine, and deformable registration via B-splines and show improvements over direct registration using both mutual information and sum of squared differences similarity measures to account for differences in image appearance.","corpus_id":7173975,"score":0},{"doc_id":"24563543","title":"Evaluation of the stability of an SR398/GroES chaperonin complex.","abstract":"The stability of an SR398/GroES chaperonin complex was examined. As was expected, based on the finding of previous studies, the SR398/GroES complex was extremely stable in the presence of an excess amount of free adenosine 5'-[γ-thio]triphosphate (ATPγS) or adenosine 5'-(β,γ-imido)triphosphate (AMPPNP). However, the complex was not stable in the absence of nucleotides. These results indicate that ATPγS and AMPPNP repeatedly associated to and dissociated from the complex in a non-cooperative manner. This nucleotide exchange did not induce the dissociation of GroES and substrate from SR398, suggesting the importance of the cooperative dissociation of nucleotides from the cis-ring to release GroES and substrate proteins in the GroEL/GroES reaction cycle.","corpus_id":11651875,"score":0},{"doc_id":"24974203","title":"Efficient initial volume determination from electron microscopy images of single particles.","abstract":"MOTIVATION: Structural information of macromolecular complexes provides key insights into the way they carry out their biological functions. The reconstruction process leading to the final 3D map requires an approximate initial model. Generation of an initial model is still an open and challenging problem in single-particle analysis. RESULTS: We present a fast and efficient approach to obtain a reliable, low-resolution estimation of the 3D structure of a macromolecule, without any a priori knowledge, addressing the well-known issue of initial volume estimation in the field of single-particle analysis. The input of the algorithm is a set of class average images obtained from individual projections of a biological object at random and unknown orientations by transmission electron microscopy micrographs. The proposed method is based on an initial non-lineal dimensionality reduction approach, which allows to automatically selecting representative small sets of class average images capturing the most of the structural information of the particle under study. These reduced sets are then used to generate volumes from random orientation assignments. The best volume is determined from these guesses using a random sample consensus (RANSAC) approach. We have tested our proposed algorithm, which we will term 3D-RANSAC, with simulated and experimental data, obtaining satisfactory results under the low signal-to-noise conditions typical of cryo-electron microscopy. AVAILABILITY: The algorithm is freely available as part of the Xmipp 3.1 package [http://xmipp.cnb.csic.es]. CONTACT: jvargas@cnb.csic.es SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.","corpus_id":8183036,"score":0},{"doc_id":"25497718","title":"Simultaneous orientation and thickness mapping in transmission electron microscopy.","abstract":"In this paper we introduce an approach for simultaneous thickness and orientation mapping of crystalline samples by means of transmission electron microscopy. We show that local thickness and orientation values can be extracted from experimental dark-field (DF) image data acquired at different specimen tilts. The method has been implemented to automatically acquire the necessary data and then map thickness and crystal orientation for a given region of interest. We have applied this technique to a specimen prepared from a commercial semiconductor device, containing multiple 22 nm technology transistor structures. The performance and limitations of our method are discussed and compared to those of other techniques available.","corpus_id":4881934,"score":0},{"doc_id":"25637660","title":"A statistical approach to the initial volume problem in Single Particle Analysis by Electron Microscopy.","abstract":"Cryo Electron Microscopy is a powerful Structural Biology technique, allowing the elucidation of the three-dimensional structure of biological macromolecules. In particular, the structural study of purified macromolecules -often referred as Single Particle Analysis(SPA)- is normally performed through an iterative process that needs a first estimation of the three-dimensional structure that is progressively refined using experimental data. It is well-known the local optimisation nature of this refinement, so that the initial choice of this first structure may substantially change the final result. Computational algorithms aiming to providing this first structure already exist. However, the question is far from settled and more robust algorithms are still needed so that the refinement process can be performed with sufficient guarantees. In this article we present a new algorithm that addresses the initial volume problem in SPA by setting it in a Weighted Least Squares framework and calculating the weights through a statistical approach based on the cumulative density function of different image similarity measures. We show that the new algorithm is significantly more robust than other state-of-the-art algorithms currently in use in the field. The algorithm is available as part of the software suite Xmipp (http://xmipp.cnb.csic.es) and Scipion (http://scipion.cnb.csic.es) under the name \"Significant\".","corpus_id":15342000,"score":0},{"doc_id":"26441413","title":"Improving the accuracy of registration-based biomechanical analysis: a finite element approach to lung regional strain quantification.","abstract":"Tissue deformation plays an important role in lung physiology, as lung parenchyma largely deforms during spontaneous ventilation. However, excessive regional deformation may lead to lung injury, as observed in patients undergoing mechanical ventilation. Thus, the accurate estimation of regional strain has recently received great attention in the intensive care community. In this work, we assess the accuracy of regional strain maps computed from direct differentiation of B-Spline (BS) interpolations, a popular technique employed in non-rigid registration of lung computed tomography (CT) images. We show that, while BS-based registration methods give excellent results for the deformation transformation, the strain field directly computed from BS derivatives results in predictions that largely oscillate, thus introducing important errors that can even revert the sign of strain. To alleviate such spurious behavior, we present a novel finite-element (FE) method for the regional strain analysis of lung CT images. The method follows from a variational strain recovery formulation, and delivers a continuous approximation to the strain field in arbitrary domains. From analytical benchmarks, we show that the FE method results in errors that are a fraction of those found for the BS method, both in an average and pointwise sense. The application of the proposed FE method to human lung CT images results in 3D strain maps are heterogeneous and smooth, showing high consistency with specific ventilation maps reported in the literature. We envision that the proposed FE method will considerably improve the accuracy of image-based biomechanical analysis, making it reliable enough for routine medical applications.","corpus_id":34306611,"score":0},{"doc_id":"26611544","title":"Single-particle cryo-electron microscopy of macromolecular complexes.","abstract":"Recent technological breakthroughs in image acquisition have enabled single-particle cryo-electron microscopy (cryo-EM) to achieve near-atomic resolution structural information for biological complexes. The improvements in image quality coupled with powerful computational methods for sorting distinct particle populations now also allow the determination of compositional and conformational ensembles, thereby providing key insights into macromolecular function. However, the inherent instability and dynamic nature of biological assemblies remain a tremendous challenge that often requires tailored approaches for successful implementation of the methodology. Here, we briefly describe the fundamentals of single-particle cryo-EM with an emphasis on covering the breadth of techniques and approaches, including low- and high-resolution methods, aiming to illustrate specific steps that are crucial for obtaining structural information by this method.","corpus_id":4928921,"score":0},{"doc_id":"26694391","title":"Multidirectional Image Sensing for Microscopy Based on a Rotatable Robot.","abstract":"Image sensing at a small scale is essentially important in many fields, including microsample observation, defect inspection, material characterization and so on. However, nowadays, multi-directional micro object imaging is still very challenging due to the limited field of view (FOV) of microscopes. This paper reports a novel approach for multi-directional image sensing in microscopes by developing a rotatable robot. First, a robot with endless rotation ability is designed and integrated with the microscope. Then, the micro object is aligned to the rotation axis of the robot automatically based on the proposed forward-backward alignment strategy. After that, multi-directional images of the sample can be obtained by rotating the robot within one revolution under the microscope. To demonstrate the versatility of this approach, we view various types of micro samples from multiple directions in both optical microscopy and scanning electron microscopy, and panoramic images of the samples are processed as well. The proposed method paves a new way for the microscopy image sensing, and we believe it could have significant impact in many fields, especially for sample detection, manipulation and characterization at a small scale.","corpus_id":8602844,"score":0},{"doc_id":"28951123","title":"Quantitative multiphoton microscopy of murine urinary bladder morphology during in situ uniaxial loading.","abstract":"Urodynamic tests are the gold standard for the diagnosis of bladder dysfunction, and the mechanical compliance of the bladder is an important parameter in these tests. The bladder wall has a layered structure, differentially affected by pathology, so knowledge of the contribution and role of these layers and their constituents to overall bladder compliance will enhance interpretation of these clinical tests. In this study we document the functional morphology of the detrusor and lamina propria of the murine bladder wall using a custom in-situ tensile loading system under multiphoton microscopy (MPM) observation in unloaded state and under incremental uniaxial stretch. Features in the stress-stretch curves of bladder samples were then directly related to corresponding MPM images. Collagen organisation across wall depth was quantified using image analysis techniques. The hypothesis that the lamina propria deformed at low strain by unfolding of the rugae and rearranging collagen fibrils was confirmed. A novel 'pocket' feature in the detrusor was observed along with extensive rearrangement of fibrils in two families at different depths, providing higher stiffness at high stretches in the detrusor. The very different deformations of detrusor and lamina propria were accommodated by the highly coiled structure of collagen in the lamina propria. Imaging and mechanical studies presented here allow gross mechanical response to be attributed to specific components of the bladder wall and further, may be used to investigate the impact of microstructural changes due to pathology or aging, and how they impair tissue functionality. STATEMENT OF SIGNIFICANCE: This article reports the first in-situ multiphoton microscopy observations of microstructural deformation under uniaxial tensile loading of ex vivo bladder. We describe collagen rearrangement through the tissue thickness and relate this directly to the stress-stretch behaviour. We confirm for the first time the unfolding of rugae and realignment of fibrils in the lamina propria during extension and the rapid stiffening as two fibril families in the detrusor are engaged. This technique provides new insight into microstructure function and will enhance understanding of the impact of changes due to pathology or aging.","corpus_id":3462014,"score":0},{"doc_id":"29116053","title":"Elastic strain and twist analysis of protein structural data and allostery of the transmembrane channel KcsA.","abstract":"The abundance of available static protein structural data makes the more effective analysis and interpretation of this data a valuable tool to supplement the experimental study of protein mechanics. Structural displacements can be difficult to analyze and interpret. Previously, we showed that strains provide a more natural and interpretable representation of protein deformations, revealing mechanical coupling between spatially distinct sites of allosteric proteins. Here, we demonstrate that other transformations of displacements yield additional insights. We calculate the divergence and curl of deformations of the transmembrane channel KcsA. Additionally, we introduce quantities analogous to bend, splay, and twist deformation energies of nematic liquid crystals. These transformations enable the decomposition of displacements into different modes of deformation, helping to characterize the type of deformation a protein undergoes. We apply these calculations to study the filter and gating regions of KcsA. We observe a continuous path of rotational deformations physically coupling these two regions, and, we propose, underlying the allosteric interaction between these regions. Bend, splay, and twist distinguish KcsA gate opening, filter opening, and filter-gate coupling, respectively. In general, physically meaningful representations of deformations (like strain, curl, bend, splay, and twist) can make testable predictions and yield insights into protein mechanics, augmenting experimental methods and more fully exploiting available structural data.","corpus_id":3624758,"score":0},{"doc_id":"29293469","title":"Improving oncoplastic breast tumor bed localization for radiotherapy planning using image registration algorithms.","abstract":"Knowledge about tumor bed localization and its shape analysis is a crucial factor for preventing irradiation of healthy tissues during supportive radiotherapy and as a result, cancer recurrence. The localization process is especially hard for tumors placed nearby soft tissues, which undergo complex, nonrigid deformations. Among them, breast cancer can be considered as the most representative example. A natural approach to improving tumor bed localization is the use of image registration algorithms. However, this involves two unusual aspects which are not common in typical medical image registration: the real deformation field is discontinuous, and there is no direct correspondence between the cancer and its bed in the source and the target 3D images respectively. The tumor no longer exists during radiotherapy planning. Therefore, a traditional evaluation approach based on known, smooth deformations and target registration error are not directly applicable. In this work, we propose alternative artificial deformations which model the tumor bed creation process. We perform a comprehensive evaluation of the most commonly used deformable registration algorithms: B-Splines free form deformations (B-Splines FFD), different variants of the Demons and TV-L1 optical flow. The evaluation procedure includes quantitative assessment of the dedicated artificial deformations, target registration error calculation, 3D contour propagation and medical experts visual judgment. The results demonstrate that the currently, practically applied image registration (rigid registration and B-Splines FFD) are not able to correctly reconstruct discontinuous deformation fields. We show that the symmetric Demons provide the most accurate soft tissues alignment in terms of the ability to reconstruct the deformation field, target registration error and relative tumor volume change, while B-Splines FFD and TV-L1 optical flow are not an appropriate choice for the breast tumor bed localization problem, even though the visual alignment seems to be better than for the Demons algorithm. However, no algorithm could recover the deformation field with sufficient accuracy in terms of vector length and rotation angle differences.","corpus_id":46781403,"score":0},{"doc_id":"29395788","title":"MonoRes: Automatic and Accurate Estimation of Local Resolution for Electron Microscopy Maps.","abstract":"Since the beginning of electron microscopy, resolution has been a critical parameter. In this article, we propose a fully automatic, accurate method for determining the local resolution of a 3D map (MonoRes). The foundation of this algorithm is an extension of the concept of analytic signal, termed monogenic signal. The map is filtered at different frequencies and the amplitude of the monogenic signal is calculated, after which a criterion is applied to determine the resolution at each voxel. MonoRes is fully automatic without compulsory user parameters, with great accuracy in all tests, and is computationally more rapid than existing methods in the field. In addition, MonoRes offers the option of local filtering of the original map based on the calculated local resolution.","corpus_id":46822743,"score":0},{"doc_id":"29399437","title":"A non-rigid registration method for the analysis of local deformations in the wood cell wall.","abstract":"This paper concerns the problem of wood cellular structure image registration. Given the large variability of wood geometry and the important changes in the cellular organization due to moisture sorption, an affine-based image registration technique is not exhaustive to describe the overall hygro-mechanical behaviour of wood at micrometre scales. Additionally, free tools currently available for non-rigid image registration are not suitable for quantifying the structural deformations of complex hierarchical materials such as wood, leading to errors due to misalignment. In this paper, we adapt an existing non-rigid registration model based on B-spline functions to our case study. The so-modified algorithm combines the concept of feature recognition within specific regions locally distributed in the material with an optimization problem. Results show that the method is able to quantify local deformations induced by moisture changes in tomographic images of wood cell wall with high accuracy. The local deformations provide new important insights in characterizing the swelling behaviour of wood at the cell wall level.","corpus_id":26860137,"score":0},{"doc_id":"29413406","title":"2D strain mapping using scanning transmission electron microscopy Moiré interferometry and geometrical phase analysis.","abstract":"A strain characterization technique based on Moiré interferometry in a scanning transmission electron microscope (STEM) and geometrical phase analysis (GPA) method is demonstrated. The deformation field is first captured in a single STEM Moiré hologram composed of multiple sets of periodic fringes (Moiré patterns) generated from the interference between the periodic scanning grating, fixing the positions of the electron probe on the sample, and the crystal structure. Applying basic principles from sampling theory, the Moiré patterns arrangement is then simulated using a STEM electron micrograph reference to convert the experimental STEM Moiré hologram into information related to the crystal lattice periodicities. The GPA method is finally applied to extract the 2D relative strain and rotation fields. The STEM Moiré interferometry enables the local information to be de-magnified to a large length scale, comparable to what can be achieved in dark-field electron holography. The STEM Moiré GPA method thus extends the conventional high-resolution STEM GPA capabilities by providing comparable quantitative 2D strain mapping with a larger field of view (up to a few microns).","corpus_id":3750233,"score":0}],"string":"[\n {\n \"doc_id\": \"19166941\",\n \"title\": \"A method for the alignment of heterogeneous macromolecules from electron microscopy.\",\n \"abstract\": \"We propose a feature-based image alignment method for single-particle electron microscopy that is able to accommodate various similarity scoring functions while efficiently sampling the two-dimensional transformational space. We use this image alignment method to evaluate the performance of a scoring function that is based on the Mutual Information (MI) of two images rather than one that is based on the cross-correlation function. We show that alignment using MI for the scoring function has far less model-dependent bias than is found with cross-correlation based alignment. We also demonstrate that MI improves the alignment of some types of heterogeneous data, provided that the signal-to-noise ratio is relatively high. These results indicate, therefore, that use of MI as the scoring function is well suited for the alignment of class-averages computed from single-particle images. Our method is tested on data from three model structures and one real dataset.\",\n \"corpus_id\": 7807423,\n \"score\": 2\n },\n {\n \"doc_id\": \"22323229\",\n \"title\": \"Macromolecular assembly structures by comparative modeling and electron microscopy.\",\n \"abstract\": \"Advances in electron microscopy allow for structure determination of large biological machines at increasingly higher resolutions. A key step in this process is fitting component structures into the electron microscopy-derived density map of their assembly. Comparative modeling can contribute by providing atomic models of the components, via fold assignment, sequence-structure alignment, model building, and model assessment. All four stages of comparative modeling can also benefit from consideration of the density map. In this chapter, we describe numerous types of modeling problems restrained by a density map and available protocols for finding solutions. In particular, we provide detailed instructions for density map-guided modeling using the Integrative Modeling Platform (IMP), MODELLER, and UCSF Chimera.\",\n \"corpus_id\": 38263891,\n \"score\": 2\n },\n {\n \"doc_id\": \"23671335\",\n \"title\": \"3DEM Loupe: Analysis of macromolecular dynamics using structures from electron microscopy.\",\n \"abstract\": \"Electron microscopy (EM) provides access to structural information of macromolecular complexes in the 3-20 Å resolution range. Normal mode analysis has been extensively used with atomic resolution structures and successfully applied to EM structures. The major application of normal modes is the identification of possible conformational changes in proteins. The analysis can throw light on the mechanism following ligand binding, protein-protein interactions, channel opening and other functional macromolecular movements. In this article, we present a new web server, 3DEM Loupe, which allows normal mode analysis of any uploaded EM volume using a user-friendly interface and an intuitive workflow. Results can be fully explored in 3D through animations and movies generated by the server. The application is freely available at http://3demloupe.cnb.csic.es.\",\n \"corpus_id\": 16433573,\n \"score\": 2\n },\n {\n \"doc_id\": \"24508340\",\n \"title\": \"Iterative elastic 3D-to-2D alignment method using normal modes for studying structural dynamics of large macromolecular complexes.\",\n \"abstract\": \"This article presents a method to study large-scale conformational changes by combining electron microscopy (EM) single-particle image analysis and normal mode analysis (NMA). It is referred to as HEMNMA, which stands for hybrid electron microscopy normal mode analysis. NMA of a reference structure (atomic-resolution structure or EM volume) is used to predict possible motions that are then confronted with EM images within an automatic iterative elastic 3D-to-2D alignment procedure to identify actual motions in the imaged samples. HEMNMA can be used to extensively analyze the conformational changes and may be used in combination with classic discrete procedures. The identified conformations allow modeling of deformation pathways compatible with the experimental data. HEMNMA was tested with synthetic and experimental data sets of E. coli 70S ribosome, DNA polymerase Pol α and B subunit complex of the eukaryotic primosome, and tomato bushy stunt virus.\",\n \"corpus_id\": 14951001,\n \"score\": 2\n },\n {\n \"doc_id\": \"24565374\",\n \"title\": \"Structure, assembly and dynamics of macromolecular complexes by single particle cryo-electron microscopy.\",\n \"abstract\": \"BACKGROUND: Proteins in their majority act rarely as single entities. Multisubunit macromolecular complexes are the actors in most of the cellular processes. These nanomachines are hold together by weak protein-protein interactions and undergo functionally important conformational changes. TFIID is such a multiprotein complex acting in eukaryotic transcription initiation. This complex is first to be recruited to the promoter of the genes and triggers the formation of the transcription preinitiation complex involving RNA polymerase II which leads to gene transcription. The exact role of TFIID in this process is not yet understood. METHODS: Last generation electron microscopes, improved data collection and new image analysis tools made it possible to obtain structural information of biological molecules at atomic resolution. Cryo-electron microscopy of vitrified samples visualizes proteins in a fully hydrated, close to native state. Molecular images are recorded at liquid nitrogen temperature in low electron dose conditions to reduce radiation damage. Digital image analysis of these noisy images aims at improving the signal-to-noise ratio, at separating distinct molecular views and at reconstructing a three-dimensional model of the biological particle. RESULTS: Using these methods we showed the early events of an activated transcription initiation process. We explored the interaction of the TFIID coactivator with the yeast Rap1 activator, the transcription factor TFIIA and the promoter DNA. We demonstrated that TFIID serves as an assembly platform for transient protein-protein interactions, which are essential for transcription initiation. CONCLUSIONS: Recent developments in electron microscopy have provided new insights into the structural organization and the dynamic reorganization of large macromolecular complexes. Examples of near-atomic resolutions exist but the molecular flexibility of macromolecular complexes remains the limiting factor in most case. Electron microscopy has the potential to provide both structural and dynamic information of biological assemblies in order to understand the molecular mechanisms of their functions.\",\n \"corpus_id\": 15254399,\n \"score\": 2\n },\n {\n \"doc_id\": \"24914167\",\n \"title\": \"Conformations of macromolecules and their complexes from heterogeneous datasets.\",\n \"abstract\": \"We describe a new generation of algorithms capable of mapping the structure and conformations of macromolecules and their complexes from large ensembles of heterogeneous snapshots, and demonstrate the feasibility of determining both discrete and continuous macromolecular conformational spectra. These algorithms naturally incorporate conformational heterogeneity without resort to sorting and classification, or prior knowledge of the type of heterogeneity present. They are applicable to single-particle diffraction and image datasets produced by X-ray lasers and cryo-electron microscopy, respectively, and particularly suitable for systems not easily amenable to purification or crystallization.\",\n \"corpus_id\": 278146,\n \"score\": 2\n },\n {\n \"doc_id\": \"25268657\",\n \"title\": \"Hybrid Electron Microscopy Normal Mode Analysis graphical interface and protocol.\",\n \"abstract\": \"This article presents an integral graphical interface to the Hybrid Electron Microscopy Normal Mode Analysis (HEMNMA) approach that was developed for capturing continuous motions of large macromolecular complexes from single-particle EM images. HEMNMA was shown to be a good approach to analyze multiple conformations of a macromolecular complex but it could not be widely used in the EM field due to a lack of an integral interface. In particular, its use required switching among different software sources as well as selecting modes for image analysis was difficult without the graphical interface. The graphical interface was thus developed to simplify the practical use of HEMNMA. It is implemented in the open-source software package Xmipp 3.1 (http://xmipp.cnb.csic.es) and only a small part of it relies on MATLAB that is accessible through the main interface. Such integration provides the user with an easy way to perform the analysis of macromolecular dynamics and forms a direct connection to the single-particle reconstruction process. A step-by-step HEMNMA protocol with the graphical interface is given in full details in Supplementary material. The graphical interface will be useful to experimentalists who are interested in studies of continuous conformational changes of macromolecular complexes beyond the modeling of continuous heterogeneity in single particle reconstruction.\",\n \"corpus_id\": 13918346,\n \"score\": 2\n },\n {\n \"doc_id\": \"27119636\",\n \"title\": \"StructMap: Elastic Distance Analysis of Electron Microscopy Maps for Studying Conformational Changes.\",\n \"abstract\": \"Single-particle electron microscopy (EM) has been shown to be very powerful for studying structures and associated conformational changes of macromolecular complexes. In the context of analyzing conformational changes of complexes, distinct EM density maps obtained by image analysis and three-dimensional (3D) reconstruction are usually analyzed in 3D for interpretation of structural differences. However, graphic visualization of these differences based on a quantitative analysis of elastic transformations (deformations) among density maps has not been done yet due to a lack of appropriate methods. Here, we present an approach that allows such visualization. This approach is based on statistical analysis of distances among elastically aligned pairs of EM maps (one map is deformed to fit the other map), and results in visualizing EM maps as points in a lower-dimensional distance space. The distances among points in the new space can be analyzed in terms of clusters or trajectories of points related to potential conformational changes. The results of the method are shown with synthetic and experimental EM maps at different resolutions.\",\n \"corpus_id\": 34220297,\n \"score\": 2\n },\n {\n \"doc_id\": \"27800126\",\n \"title\": \"Cryo-electron Microscopy Analysis of Structurally Heterogeneous Macromolecular Complexes.\",\n \"abstract\": \"Cryo-electron microscopy (cryo-EM) has for a long time been a technique of choice for determining structure of large and flexible macromolecular complexes that were difficult to study by other experimental techniques such as X-ray crystallography or nuclear magnetic resonance. However, a fast development of instruments and software for cryo-EM in the last decade has allowed that a large range of complexes can be studied by cryo-EM, and that their structures can be obtained at near-atomic resolution, including the structures of small complexes (e.g., membrane proteins) whose size was earlier an obstacle to cryo-EM. Image analysis to identify multiple coexisting structures in the same specimen (multiconformation reconstruction) is now routinely done both to solve structures at near-atomic resolution and to study conformational dynamics. Methods for multiconformation reconstruction and latest examples of their applications are the focus of this review.\",\n \"corpus_id\": 15780788,\n \"score\": 2\n },\n {\n \"doc_id\": \"28088125\",\n \"title\": \"Computational methods for analyzing conformational variability of macromolecular complexes from cryo-electron microscopy images.\",\n \"abstract\": \"Thanks to latest technical advances in cryo-electron microscopy (cryo-EM), structures of macromolecular complexes (viruses, ribosomes, etc.) are now often obtained at near-atomic resolution. Also, studies of conformational changes of complexes, in connection with their function, are gaining ground. Conformational variability analysis is usually done by classifying images in a number of discrete classes supposedly representing all conformational states present in the specimen. However, discrete classes cannot be meaningfully defined when the conformational change is continuous (the specimen contains a continuum of states instead of a few discrete states). For such cases, first image analysis methods that explicitly consider continuous conformational changes were recently developed. The latest developments in cryo-EM image analysis methods for conformational variability analysis are the focus of this review.\",\n \"corpus_id\": 3535220,\n \"score\": 2\n },\n {\n \"doc_id\": \"28097146\",\n \"title\": \"Versatility of Approximating Single-Particle Electron Microscopy Density Maps Using Pseudoatoms and Approximation-Accuracy Control.\",\n \"abstract\": \"Three-dimensional Gaussian functions have been shown useful in representing electron microscopy (EM) density maps for studying macromolecular structure and dynamics. Methods that require setting a desired number of Gaussian functions or a maximum number of iterations may result in suboptimal representations of the structure. An alternative is to set a desired error of approximation of the given EM map and then optimize the number of Gaussian functions to achieve this approximation error. In this article, we review different applications of such an approach that uses spherical Gaussian functions of fixed standard deviation, referred to as pseudoatoms. Some of these applications use EM-map normal mode analysis (NMA) with elastic network model (ENM) (applications such as predicting conformational changes of macromolecular complexes or exploring actual conformational changes by normal-mode-based analysis of experimental data) while some other do not use NMA (denoising of EM density maps). In applications based on NMA and ENM, the advantage of using pseudoatoms in EM-map coarse-grain models is that the ENM springs are easily assigned among neighboring grains thanks to their spherical shape and uniformed size. EM-map denoising based on the map coarse-graining was so far only shown using pseudoatoms as grains.\",\n \"corpus_id\": 16586832,\n \"score\": 2\n },\n {\n \"doc_id\": \"18989044\",\n \"title\": \"Computational approaches for automatic structural analysis of large biomolecular complexes.\",\n \"abstract\": \"We present computational solutions to two problems of macromolecular structure interpretation from reconstructed three-dimensional electron microscopy (3D-EM) maps of large bio-molecular complexes at intermediate resolution (5A-15 A). The two problems addressed are: 1) 3D structural alignment (matching) between identified and segmented 3D maps of structure units (e.g. trimeric configuration of proteins), and 2) the secondary structure identification of a segmented protein 3D map (i.e.locations of alpha-helices, beta-sheets). For problem 1, we present an efficient algorithm to correlate spatially (and structurally) two 3D maps of structure units. Besides providing a similarity score between structure units, the algorithm yields an effective technique for resolution refinement of repeated structure units, by 3D alignment and averaging. For problem 2, we present an efficient algorithm to compute eigenvalues and link eigenvectors of a Gaussian convoluted structure tensor derived from the protein 3D Map, thereby identifying and locating secondary structural motifs of proteins. The efficiency and performance of our approach is demonstrated on several experimentally reconstructed 3D maps of virus capsid shells from single-particle cryo-electron microscopy (cryo-EM), as well as computationally simulated protein structure density 3D maps generated from protein model entries in the Protein Data Bank.\",\n \"corpus_id\": 1636056,\n \"score\": 1\n },\n {\n \"doc_id\": \"20025794\",\n \"title\": \"Single-particle reconstruction of biological macromolecules in electron microscopy--30 years.\",\n \"abstract\": \"This essay gives the autho's personal account on the development of concepts underlying single-particle reconstruction, a technique in electron microscopy of macromolecular assemblies with a remarkable record of achievements as of late. The ribosome proved to be an ideal testing ground for the development of specimen preparation methods, cryo-EM techniques, and algorithms, with discoveries along the way as a rich reward. Increasingly, cryo-EM and single-particle reconstruction, in combination with classification techniques, is revealing dynamic information on functional molecular machines uninhibited by molecular contacts.\",\n \"corpus_id\": 12465805,\n \"score\": 1\n },\n {\n \"doc_id\": \"20085819\",\n \"title\": \"Automated multi-model reconstruction from single-particle electron microscopy data.\",\n \"abstract\": \"Biological macromolecules can adopt multiple conformational and compositional states due to structural flexibility and alternative subunit assemblies. This structural heterogeneity poses a major challenge in the study of macromolecular structure using single-particle electron microscopy. We propose a fully automated, unsupervised method for the three-dimensional reconstruction of multiple structural models from heterogeneous data. As a starting reference, our method employs an initial structure that does not account for any heterogeneity. Then, a multi-stage clustering is used to create multiple models representative of the heterogeneity within the sample. The multi-stage clustering combines an existing approach based on Multivariate Statistical Analysis to perform clustering within individual Euler angles, and a newly developed approach to sort out class averages from individual Euler angles into homogeneous groups. Structural models are computed from individual clusters. The whole data classification is further refined using an iterative multi-model projection-matching approach. We tested our method on one synthetic and three distinct experimental datasets. The tests include the cases where a macromolecular complex exhibits structural flexibility and cases where a molecule is found in ligand-bound and unbound states. We propose the use of our approach as an efficient way to reconstruct distinct multiple models from heterogeneous data.\",\n \"corpus_id\": 7132823,\n \"score\": 1\n },\n {\n \"doc_id\": \"20835797\",\n \"title\": \"3-D structures of macromolecules using single-particle analysis in EMAN.\",\n \"abstract\": \"Single-particle reconstruction is a methodology whereby transmission electron microscopy (TEM) is used to record images of individual monodisperse molecules or macromolecular assemblies, then sets of images of individual particles are computationally combined to produce a 3-D volumetric reconstruction. Ideally the TEM specimen will be prepared in vitreous ice (electron cryomicroscopy), but negative stain preparations may be used for lower resolution work. This technique has been demonstrated to produce structures at resolutions as high as ∼ 4 A, though this is not yet typical. The reconstruction process is quite computationally intensive, and several software packages are available for this task. EMAN is one of the easier to master software suites for single-particle analysis. This protocol explains how to perform an initial low-resolution reconstruction using EMAN.\",\n \"corpus_id\": 27244417,\n \"score\": 1\n },\n {\n \"doc_id\": \"21444766\",\n \"title\": \"Macromolecular structural dynamics visualized by pulsed dose control in 4D electron microscopy.\",\n \"abstract\": \"Macromolecular conformation dynamics, which span a wide range of time scales, are fundamental to the understanding of properties and functions of their structures. Here, we report direct imaging of structural dynamics of helical macromolecules over the time scales of conformational dynamics (ns to subsecond) by means of four-dimensional (4D) electron microscopy in the single-pulse and stroboscopic modes. With temporally controlled electron dosage, both diffraction and real-space images are obtained without irreversible radiation damage. In this way, the order-disorder transition is revealed for the organic chain polymer. Through a series of equilibrium-temperature and temperature-jump dependencies, it is shown that the metastable structures and entropy of conformations can be mapped in the nonequilibrium region of a \\\"funnel-like\\\" free-energy landscape. The T-jump is introduced through a substrate (a \\\"hot plate\\\" type arrangement) because only the substrate is made to absorb the pulsed energy. These results illustrate the promise of ultrafast 4D imaging for other applications in the study of polymer physics as well as in the visualization of biological phenomena.\",\n \"corpus_id\": 1127528,\n \"score\": 1\n },\n {\n \"doc_id\": \"23131460\",\n \"title\": \"FOLD-EM: automated fold recognition in medium- and low-resolution (4-15 Å) electron density maps.\",\n \"abstract\": \"MOTIVATION: Owing to the size and complexity of large multi-component biological assemblies, the most tractable approach to determining their atomic structure is often to fit high-resolution radiographic or nuclear magnetic resonance structures of isolated components into lower resolution electron density maps of the larger assembly obtained using cryo-electron microscopy (cryo-EM). This hybrid approach to structure determination requires that an atomic resolution structure of each component, or a suitable homolog, is available. If neither is available, then the amount of structural information regarding that component is limited by the resolution of the cryo-EM map. However, even if a suitable homolog cannot be identified using sequence analysis, a search for structural homologs should still be performed because structural homology often persists throughout evolution even when sequence homology is undetectable, As macromolecules can often be described as a collection of independently folded domains, one way of searching for structural homologs would be to systematically fit representative domain structures from a protein domain database into the medium/low resolution cryo-EM map and return the best fits. Taken together, the best fitting non-overlapping structures would constitute a 'mosaic' backbone model of the assembly that could aid map interpretation and illuminate biological function. RESULT: Using the computational principles of the Scale-Invariant Feature Transform (SIFT), we have developed FOLD-EM-a computational tool that can identify folded macromolecular domains in medium to low resolution (4-15 Å) electron density maps and return a model of the constituent polypeptides in a fully automated fashion. As a by-product, FOLD-EM can also do flexible multi-domain fitting that may provide insight into conformational changes that occur in macromolecular assemblies.\",\n \"corpus_id\": 6876031,\n \"score\": 1\n },\n {\n \"doc_id\": \"23625506\",\n \"title\": \"Novel convergence-oriented approach for evaluation and optimization of workflow in single-particle two-dimensional averaging of electron microscope images.\",\n \"abstract\": \"Three-dimensional (3D) protein structures facilitate the understanding of their biological functions and provide valuable information for developing medicines. Single-particle analysis (SPA) from electron microscopy (EM) is a structure determination method suitable for macromolecules. To achieve a high resolution using combinations of several SPA software packages, 'workflow' optimization and comparative evaluation by scoring results are essential. Two-dimensional (2D) averaging is a key step for 3D reconstruction. The integrated convergence-evaluation oriented system (IC-EOS) proposed here provides an effective tool for customizing 2D averaging. This assesses the behavior and characteristics of workflows and evaluates the convergence of iteration steps without human intervention. We chose five base measurements for quantifying convergence: resolution, variance, similarity, shift-distance and rotation-angle. Curve fitting to history graphs scored their stability. We call this score 'fluctuation'. The number of particle images discarded from the library and the number of classification groups were examined to see their effects on optimization levels and fluctuation of measurements, allowing the IC-EOS to select the most appropriate workflow for the target. A case study using a bacterial sodium channel and a simulation study using GroEL showed that resolution of 2D averaging improved with relatively stricter particle selection. With fewer groups, resolutions of class averages improved, but similarities between class-averages and their constituent particle images degraded. Fluctuation was useful for selecting adequate conditions, even when achieved values alone were not conclusive. The vote method, using fluctuation, was robust against noise and enabled a decision without exhaustive search trials. Thus, the IC-EOS is a step toward full automation of SPA.\",\n \"corpus_id\": 33894902,\n \"score\": 1\n },\n {\n \"doc_id\": \"23793721\",\n \"title\": \"Intensity-based hierarchical elastic registration using approximating splines.\",\n \"abstract\": \"PURPOSE: We introduce a new hierarchical approach for elastic medical image registration using approximating splines. In order to obtain the dense deformation field, we employ Gaussian elastic body splines (GEBS) that incorporate anisotropic landmark errors and rotation information. Since the GEBS approach is based on a physical model in form of analytical solutions of the Navier equation, it can very well cope with the local as well as global deformations present in the images by varying the standard deviation of the Gaussian forces. METHODS: The proposed GEBS approximating model is integrated into the elastic hierarchical image registration framework, which decomposes a nonrigid registration problem into numerous local rigid transformations. The approximating GEBS registration scheme incorporates anisotropic landmark errors as well as rotation information. The anisotropic landmark localization uncertainties can be estimated directly from the image data, and in this case, they represent the minimal stochastic localization error, i.e., the Cramér-Rao bound. The rotation information of each landmark obtained from the hierarchical procedure is transposed in an additional angular landmark, doubling the number of landmarks in the GEBS model. RESULTS: The modified hierarchical registration using the approximating GEBS model is applied to register 161 image pairs from a digital mammogram database. The obtained results are very encouraging, and the proposed approach significantly improved all registrations comparing the mean-square error in relation to approximating TPS with the rotation information. On artificially deformed breast images, the newly proposed method performed better than the state-of-the-art registration algorithm introduced by Rueckert et al. (IEEE Trans Med Imaging 18:712-721, 1999). The average error per breast tissue pixel was less than 2.23 pixels compared to 2.46 pixels for Rueckert's method. CONCLUSION: The proposed hierarchical elastic image registration approach incorporates the GEBS approximation scheme extended with anisotropic landmark localization uncertainties as well as rotation information. Our experimental results show that the proposed scheme improved the registration result significantly.\",\n \"corpus_id\": 2656824,\n \"score\": 1\n },\n {\n \"doc_id\": \"24232828\",\n \"title\": \"Interactive multigrid refinement for deformable image registration.\",\n \"abstract\": \"Deformable image registration is the spatial mapping of corresponding locations between images and can be used for important applications in radiotherapy. Although numerous methods have attempted to register deformable medical images automatically, such as salient-feature-based registration (SFBR), free-form deformation (FFD), and demons, no automatic method for registration is perfect, and no generic automatic algorithm has shown to work properly for clinical applications due to the fact that the deformation field is often complex and cannot be estimated well by current automatic deformable registration methods. This paper focuses on how to revise registration results interactively for deformable image registration. We can manually revise the transformed image locally in a hierarchical multigrid manner to make the transformed image register well with the reference image. The proposed method is based on multilevel B-spline to interactively revise the deformable transformation in the overlapping region between the reference image and the transformed image. The resulting deformation controls the shape of the transformed image and produces a nice registration or improves the registration results of other registration methods. Experimental results in clinical medical images for adaptive radiotherapy demonstrated the effectiveness of the proposed method.\",\n \"corpus_id\": 18196005,\n \"score\": 1\n },\n {\n \"doc_id\": \"26534841\",\n \"title\": \"Localized reconstruction of subunits from electron cryomicroscopy images of macromolecular complexes.\",\n \"abstract\": \"Electron cryomicroscopy can yield near-atomic resolution structures of highly ordered macromolecular complexes. Often however some subunits bind in a flexible manner, have different symmetry from the rest of the complex, or are present in sub-stoichiometric amounts, limiting the attainable resolution. Here we report a general method for the localized three-dimensional reconstruction of such subunits. After determining the particle orientations, local areas corresponding to the subunits can be extracted and treated as single particles. We demonstrate the method using three examples including a flexible assembly and complexes harbouring subunits with either partial occupancy or mismatched symmetry. Most notably, the method allows accurate fitting of the monomeric RNA-dependent RNA polymerase bound at the threefold axis of symmetry inside a viral capsid, revealing for the first time its exact orientation and interactions with the capsid proteins. Localized reconstruction is expected to provide novel biological insights in a range of challenging biological systems.\",\n \"corpus_id\": 25224478,\n \"score\": 1\n },\n {\n \"doc_id\": \"26678751\",\n \"title\": \"A local-optimization refinement algorithm in single particle analysis for macromolecular complex with multiple rigid modules.\",\n \"abstract\": \"Single particle analysis, which can be regarded as an average of signals from thousands or even millions of particle projections, is an efficient method to study the three-dimensional structures of biological macromolecules. An intrinsic assumption in single particle analysis is that all the analyzed particles must have identical composition and conformation. Thus specimen heterogeneity in either composition or conformation has raised great challenges for high-resolution analysis. For particles with multiple conformations, inaccurate alignments and orientation parameters will yield an averaged map with diminished resolution and smeared density. Besides extensive classification approaches, here based on the assumption that the macromolecular complex is made up of multiple rigid modules whose relative orientations and positions are in slight fluctuation around equilibriums, we propose a new method called as local optimization refinement to address this conformational heterogeneity for an improved resolution. The key idea is to optimize the orientation and shift parameters of each rigid module and then reconstruct their three-dimensional structures individually. Using simulated data of 80S/70S ribosomes with relative fluctuations between the large (60S/50S) and the small (40S/30S) subunits, we tested this algorithm and found that the resolutions of both subunits are significantly improved. Our method provides a proof-of-principle solution for high-resolution single particle analysis of macromolecular complexes with dynamic conformations.\",\n \"corpus_id\": 14678415,\n \"score\": 1\n },\n {\n \"doc_id\": \"28368275\",\n \"title\": \"Cryo-electron microscopy and X-ray crystallography: complementary approaches to structural biology and drug discovery.\",\n \"abstract\": \"The invention of the electron microscope has greatly enhanced the view scientists have of small structural details. Since its implementation, this technology has undergone considerable evolution and the resolution that can be obtained for biological objects has been extended. In addition, the latest generation of cryo-electron microscopes equipped with direct electron detectors and software for the automated collection of images, in combination with the use of advanced image-analysis methods, has dramatically improved the performance of this technique in terms of resolution. While calculating a sub-10 Å resolution structure was an accomplishment less than a decade ago, it is now common to generate structures at sub-5 Å resolution and even better. It is becoming possible to relatively quickly obtain high-resolution structures of biological molecules, in particular large ones (>500 kDa) which, in some cases, have resisted more conventional methods such as X-ray crystallography or nuclear magnetic resonance (NMR). Such newly resolved structures may, for the first time, shed light on the precise mechanisms that are essential for cellular physiological processes. The ability to attain atomic resolution may support the development of new drugs that target these proteins, allowing medicinal chemists to understand the intimacy of the relationship between their molecules and targets. In addition, recent developments in cryo-electron microscopy combined with image analysis can provide unique information on the conformational variability of macromolecular complexes. Conformational flexibility of macromolecular complexes can be investigated using cryo-electron microscopy and multiconformation reconstruction methods. However, the biochemical quality of the sample remains the major bottleneck to routine cryo-electron microscopy-based determination of structures at very high resolution.\",\n \"corpus_id\": 2588079,\n \"score\": 1\n },\n {\n \"doc_id\": \"18334219\",\n \"title\": \"De novo backbone trace of GroEL from single particle electron cryomicroscopy.\",\n \"abstract\": \"In this work, we employ single-particle electron cryo-microscopy (cryo-EM) to reconstruct GroEL to approximately 4 A resolution with both D7 and C7 symmetry. Using a newly developed skeletonization algorithm and secondary structure element identification in combination with sequence-based secondary structure prediction, we demonstrate that it is possible to achieve a de novo Calpha trace directly from a cryo-EM reconstruction. The topology of our backbone trace is completely accurate, though subtle alterations illustrate significant differences from existing crystal structures. In the map with C7 symmetry, the seven monomers in each ring are identical; however, the subunits have a subtly different structure in each ring, particularly in the equatorial domain. These differences include an asymmetric salt bridge, density in the nucleotide-binding pocket of only one ring, and small shifts in alpha helix positions. This asymmetric conformation is different from previous asymmetric structures, including GroES-bound GroEL, and may represent a \\\"primed state\\\" in the chaperonin pathway.\",\n \"corpus_id\": 24474229,\n \"score\": 0\n },\n {\n \"doc_id\": \"18518137\",\n \"title\": \"Direct mapping of strain in a strained silicon transistor by high-resolution electron microscopy.\",\n \"abstract\": \"Aberration-corrected high-resolution transmission electron microscopy (HRTEM) is used to measure strain in a strained-silicon metal-oxide-semiconductor field-effect transistor. Strain components parallel and perpendicular to the gate are determined directly from the HRTEM image by geometric phase analysis. Si80Ge20 source and drain stressors lead to uniaxial compressive strain in the Si channel, reaching a maximum value of -1.3% just below the gate oxide, equivalent to 2.2 GPa. Strain maps obtained by linear elasticity theory, modeled with the finite-element method, agree with the experimental results to within 0.1%.\",\n \"corpus_id\": 42476637,\n \"score\": 0\n },\n {\n \"doc_id\": \"18575880\",\n \"title\": \"Bridging fluorescence microscopy and electron microscopy.\",\n \"abstract\": \"Development of new fluorescent probes and fluorescence microscopes has led to new ways to study cell biology. With the emergence of specialized microscopy units at most universities and research centers, the use of these techniques is well within reach for a broad research community. A major breakthrough in fluorescence microscopy in biology is the ability to follow specific targets on or in living cells, revealing dynamic localization and/or function of target molecules. One of the inherent limitations of fluorescence microscopy is the resolution. Several efforts are undertaken to overcome this limit. The traditional and most well-known way to achieve higher resolution imaging is by electron microscopy. Moreover, electron microscopy reveals organelles, membranes, macromolecules, and thus aids in the understanding of cellular complexity and localization of molecules of interest in relation to other structures. With the new probe development, a solid bridge between fluorescence microscopy and electron microscopy is being built, even leading to correlative imaging. This connection provides several benefits, both scientifically as well as practically. Here, I summarize recent developments in bridging microscopy.\",\n \"corpus_id\": 24393,\n \"score\": 0\n },\n {\n \"doc_id\": \"19185480\",\n \"title\": \"Probing the macromolecular organization of cells by electron tomography.\",\n \"abstract\": \"A major goal in cell biology is to understand the functional organization of macromolecular complexes in vivo. Electron microscopy is helping cell biologists to achieve this goal, thanks to its ability to resolve structural details in the nanometer range. While issues related to specimen preparation, imaging, and image interpretation make this approach to cell architecture difficult, recent improvements in methods, equipment, and software have facilitated the study of both important macromolecular complexes and comparatively large volumes from cellular specimens. Here, we describe recent progress in electron microscopy of cells and the ways in which the relevant methodologies are helping to elucidate cell architecture.\",\n \"corpus_id\": 11130652,\n \"score\": 0\n },\n {\n \"doc_id\": \"19201364\",\n \"title\": \"Interactive deformation registration of endorectal prostate MRI using ITK thin plate splines.\",\n \"abstract\": \"RATIONALE AND OBJECTIVES: Magnetic resonance imaging with an endorectal coil allows high-resolution imaging of prostate cancer and the surrounding normal organs. These anatomic details can be used to direct radiotherapy. However, organ deformation introduced by the endorectal coil makes it difficult to register magnetic resonance images for treatment planning. In this study, plug-ins for the volume visualization software VolView were implemented on the basis of algorithms from the National Library of Medicine's Insight Segmentation and Registration Toolkit (ITK). MATERIALS AND METHODS: Magnetic resonance images of a phantom simulating human pelvic structures were obtained with and without the endorectal coil balloon inflated. The prostate not deformed by the endorectal balloon was registered to the deformed prostate using an ITK thin plate spline (TPS). This plug-in allows the use of crop planes to limit the deformable registration in the region of interest around the prostate. These crop planes restricted the support of the TPS to the area around the prostate, where most of the deformation occurred. The region outside the crop planes was anchored by grid points. RESULTS: The TPS was more accurate in registering the local deformation of the prostate compared with a TPS variant, the elastic body spline. The TPS was also applied to register an in vivo T(2)-weighted endorectal magnetic resonance image. The intraprostatic tumor was accurately registered. This could potentially guide the boosting of intraprostatic targets. The source and target landmarks were placed graphically. This TPS plug-in allows the registration to be undone. The landmarks could be added, removed, and adjusted in real time and in three dimensions between repeated registrations. CONCLUSION: This interactive TPS plug-in allows a user to obtain a high level of accuracy satisfactory to a specific application efficiently. Because it is open-source software, the imaging community will be able to validate and improve the algorithm.\",\n \"corpus_id\": 20777730,\n \"score\": 0\n },\n {\n \"doc_id\": \"19211241\",\n \"title\": \"Structural mapping of spliceosomes by electron microscopy.\",\n \"abstract\": \"Eukaryotic genes are transcribed as pre-mRNAs which are interrupted by noncoding introns. Selection and accurate removal of introns is an essential step in gene expression that is performed by a large and highly dynamic macromolecular machine, called spliceosome. A major challenge for structural studies of the spliceosome is represented by its large size as well as its dynamic nature. Electron microscopy is an important technique to study the overall shape and architecture of spliceosomes and their components, and to locate subunits and RNA parts. Recent advances in sample preparation of spliceosomes, technical improvements in EM instrumentation, powerful computer hardware, and new image analysis software will be instrumental to push structural studies of spliceosomes to a higher level of resolution.\",\n \"corpus_id\": 32472062,\n \"score\": 0\n },\n {\n \"doc_id\": \"19499142\",\n \"title\": \"Geometric alignment of 2D gel electrophoresis images.\",\n \"abstract\": \"OBJECTIVES: 2D gel electrophoresis (2-DE) is the method of choice for analyzing protein expression in the field of proteomics, for example, comparing a reference with a test population. However, due to complex physical and chemical processes the locations of proteins generally vary in different 2-DE images. To cope with these variations, accurate geometric alignment of 2-DE images is important. METHODS: We introduce a new elastic registration approach for 2-DE images, which is based on an analytic solution of the Navier equation using Gaussian elastic body splines (GEBS). With this approach cross-effects in elastic deformations can be handled, which is important for the registration of 2-DE images. In addition, landmark correspondences can be included to aid the registration in regions which are difficult to register using intensity information alone. RESULTS: We have successfully applied our approach to register 2-DE gel images of different levels of complexity. In each case, gel images from a reference group are compared with a test group. To analyze the performance of our approach, we have carried out a quantitative evaluation of the registration results. Moreover, we have performed an experimental comparison with a previous elastic registration scheme. CONCLUSIONS: From the results we found that our approach is well-suited for the registration of 2-DE gel images of different levels of complexity and it turned out that the approach is superior to a previous hybrid scheme. Moreover, our approach is well-suited in a fully automatic setting and the performance can further be improved when landmark correspondences are available.\",\n \"corpus_id\": 674636,\n \"score\": 0\n },\n {\n \"doc_id\": \"19564681\",\n \"title\": \"The Max-Inf2/Lorentz Center workshop on New algorithms in macromolecular crystallography and electron microscopy.\",\n \"abstract\": \"The resolution gap between macromolecular crystallography and electron microscopy continues to decrease. Recent advances in specimen preparation, instrumentation and computational power have allowed accurate structure determination of larger macromolecular complexes by crystallography and/or by electron microscopy on cryovitrified samples. New possibilities in structural biology have opened up and new challenges are faced to further reduce the resolution gap. A workshop at the Lorentz Center, Leiden, The Netherlands, which took place in May 2008, was organized to push further the limits of both complementary techniques through improved computational methods.\",\n \"corpus_id\": 287483,\n \"score\": 0\n },\n {\n \"doc_id\": \"20512149\",\n \"title\": \"Precise mapping of subunits in multiprotein complexes by a versatile electron microscopy label.\",\n \"abstract\": \"Positional knowledge of subunits within multiprotein assemblies is crucial for understanding their function. The topological analysis of protein complexes by electron microscopy has undergone impressive development, but analysis of the exact positioning of single subunits has lagged behind. Here we have developed a clonable approximately 80-residue tag that, upon attachment to a target protein, can recruit a structurally prominent electron microscopy label in vitro. This tag is readily visible on single particles and becomes exceptionally distinct after image processing and classification. Thus, our method is applicable for the exact topological mapping of subunits in macromolecular complexes.\",\n \"corpus_id\": 12508676,\n \"score\": 0\n },\n {\n \"doc_id\": \"20530635\",\n \"title\": \"Merging molecular electron microscopy and mass spectrometry by carbon film-assisted endoproteinase digestion.\",\n \"abstract\": \"Many fundamental processes in the cell are performed by complex macromolecular assemblies that comprise a large number of proteins. Numerous macromolecular assemblies are structurally rather fragile and may suffer during purification, resulting in the partial dissociation of the complexes. These limitations can be overcome by chemical fixation of the assemblies, and recently introduced protocols such as gradient fixation during ultracentrifugation (GraFix) offer advantages for the analysis of fragile macromolecular assemblies. The irreversible fixation, however, is thought to render macromolecular samples useless for studying their protein composition. We therefore developed a novel approach that possesses the advantages of fixation for structure determination by single particle electron microscopy while still allowing a correlative compositional analysis by mass spectrometry. In this method, which we call \\\"electron microscopy carbon film-assisted digestion\\\", macromolecular assemblies are chemically fixed and then adsorbed onto electron microscopical carbon films. Parallel, identically prepared specimens are then subjected to structural investigation by electron microscopy and proteomics analysis by mass spectrometry of the digested sample. As identical sample preparation protocols are used for electron microscopy and mass spectrometry, the results of both methods can directly be correlated. In addition, we demonstrate improved sensitivity and reproducibility of electron microscopy carbon film-assisted digestion as compared with standard protocols. We show that sample amounts of as low as 50 fmol are sufficient to obtain a comprehensive protein composition of two model complexes. We suggest our approach to be an optimization technique for the compositional analysis of macromolecules by mass spectrometry in general.\",\n \"corpus_id\": 34269447,\n \"score\": 0\n },\n {\n \"doc_id\": \"20869518\",\n \"title\": \"Analysis of the ultrastructure of archaea by electron microscopy.\",\n \"abstract\": \"The ultrastructural characterization of archaeal cells is done with both types of electron microscopy, transmission electron microscopy, and scanning electron microscopy. Depending on the scientific question, different preparation methods have to be employed and need to be optimized, according to the special cultivation conditions of these-in many cases extreme-microorganisms. Recent results using various electron microscopy techniques show that archaeal cells have a variety of cell appendages, used for motility as well as for establishing cell-cell and cell-surface contacts. Cryo-preparation methods, in particular high-pressure freezing and freeze-substitution, are crucial for obtaining results: (1) showing the cells in ultrathin sections in a good structural preservation, often with unusual shapes and subcellular complexity, and (2) enabling us to perform immunolocalization studies. This is an important tool to make a link between biochemical and ultrastructural studies.\",\n \"corpus_id\": 5264737,\n \"score\": 0\n },\n {\n \"doc_id\": \"21864783\",\n \"title\": \"Measurement of residual elastic strain and lattice rotations with high resolution electron backscatter diffraction.\",\n \"abstract\": \"A set of dynamically simulated electron backscatter patterns (EBSPs) for α-Ti crystals progressively rotated by 1° steps were analysed using cross-correlation to determine image shifts from which strains and rotations were calculated. At larger rotations the cross-correlation fails in certain regions of the EBSP where large shifts are generated. These incorrect shifts prevent standard least square error procedures from obtaining a valid solution for the strain and rotation, where the applied rotation exceeds ∼ 8°. Using a robust iterative fitting routine reliable strains and rotations can be obtained for applied rotations of up to and including ∼ 11° even though some image shifts are measured incorrectly. Finally, high resolution electron backscatter diffraction has been used to analyse the residual elastic strain, lattice rotations and density of stored geometrically necessary dislocations in a sample of copper deformed to 10% total strain. The robust iterative fitting analysis allows reliable analysis of a larger proportion of the map, the difference being most obviously beneficial in regions where significant lattice rotations have been generated.\",\n \"corpus_id\": 31226838,\n \"score\": 0\n },\n {\n \"doc_id\": \"22092443\",\n \"title\": \"Digital correction of motion artefacts in microscopy image sequences collected from living animals using rigid and nonrigid registration.\",\n \"abstract\": \"Digital image analysis is a fundamental component of quantitative microscopy. However, intravital microscopy presents many challenges for digital image analysis. In general, microscopy volumes are inherently anisotropic, suffer from decreasing contrast with tissue depth, lack object edge detail and characteristically have low signal levels. Intravital microscopy introduces the additional problem of motion artefacts, resulting from respiratory motion and heartbeat from specimens imaged in vivo. This paper describes an image registration technique for use with sequences of intravital microscopy images collected in time-series or in 3D volumes. Our registration method involves both rigid and nonrigid components. The rigid registration component corrects global image translations, whereas the nonrigid component manipulates a uniform grid of control points defined by B-splines. Each control point is optimized by minimizing a cost function consisting of two parts: a term to define image similarity, and a term to ensure deformation grid smoothness. Experimental results indicate that this approach is promising based on the analysis of several image volumes collected from the kidney, lung and salivary gland of living rodents.\",\n \"corpus_id\": 205343497,\n \"score\": 0\n },\n {\n \"doc_id\": \"22095783\",\n \"title\": \"Cryo-electron microscopy of ribosomal complexes in cotranslational folding, targeting, and translocation.\",\n \"abstract\": \"Single-particle cryo-electron microscopy (cryo-EM) became a well-established method to study the structure and function of large macromolecular assemblies in a close to physiological environment. Cryo-EM reconstructions of ribosomal complexes trapped at different stages during translation, cotranslational targeting, and translocation provide new insights on a molecular level into these processes, which are vital for the correct localization and folding of all proteins in the cell. The EM structures in combination with biochemical experiments and available high-resolution crystal or nuclear magnetic resonance (NMR) structures of individual factors and of the ribosome allow for interpretation in quasi-atomic detail of the molecular mechanism of ribosomal complexes, their conformational changes and dynamic interactions with factors like the signal recognition particle, SRP receptor, the translocon, and the chaperone trigger factor. The snapshots obtained by single-particle EM reconstructions enable us to follow the path of a nascent protein from the peptidyl-transferase center, through the ribosomal tunnel, to and across the translocon in the membrane. With new developments in image processing techniques it is possible to sort a biological homogenous sample into different conformational states and to reach subnanometer resolution such that folding of the nascent chain into secondary structure elements can be directly visualized. With improved cryo-electron tomography and correlative light microscopy and EM, it will be possible to visualize ribosomal complexes in their cellular context.\",\n \"corpus_id\": 39572148,\n \"score\": 0\n },\n {\n \"doc_id\": \"22386621\",\n \"title\": \"Visualizing macromolecular complexes with in situ liquid scanning transmission electron microscopy.\",\n \"abstract\": \"A central focus of biological research is understanding the structure/function relationship of macromolecular protein complexes. Yet conventional transmission electron microscopy techniques are limited to static observations. Here we present the first direct images of purified macromolecular protein complexes using in situ liquid scanning transmission electron microscopy. Our results establish the capability of this technique for visualizing the interface between biology and nanotechnology with high fidelity while also probing the interactions of biomolecules within solution. This method represents an important advancement towards allowing future high-resolution observations of biological processes and conformational dynamics in real-time.\",\n \"corpus_id\": 39857094,\n \"score\": 0\n },\n {\n \"doc_id\": \"22420849\",\n \"title\": \"Bacteriophage electron microscopy.\",\n \"abstract\": \"Since the advent of the electron microscope approximately 70 years ago, bacterial viruses and electron microscopy are inextricably linked. Electron microscopy proved that bacteriophages are particulate and viral in nature, are complex in size and shape, and have intracellular development cycles and assembly pathways. The principal contribution of electron microscopy to bacteriophage research is the technique of negative staining. Over 5500 bacterial viruses have so far been characterized by electron microscopy, making bacteriophages, at least on paper, the largest viral group in existence. Other notable contributions are cryoelectron microcopy and three-dimensional image reconstruction, particle counting, and immunoelectron microscopy. Scanning electron microscopy has had relatively little impact. Transmission electron microscopy has provided the basis for the recognition and establishment of bacteriophage families and is one of the essential criteria to classify novel viruses into families. It allows for instant diagnosis and is thus the fastest diagnostic technique in virology. The most recent major contribution of electron microscopy is the demonstration that the capsid of tailed phages is monophyletic in origin and that structural links exist between some bacteriophages and viruses of vertebrates and archaea. DNA sequencing cannot replace electron microscopy and vice versa.\",\n \"corpus_id\": 19887164,\n \"score\": 0\n },\n {\n \"doc_id\": \"22445172\",\n \"title\": \"ATP-triggered conformational changes delineate substrate-binding and -folding mechanics of the GroEL chaperonin.\",\n \"abstract\": \"The chaperonin GroEL assists the folding of nascent or stress-denatured polypeptides by actions of binding and encapsulation. ATP binding initiates a series of conformational changes triggering the association of the cochaperonin GroES, followed by further large movements that eject the substrate polypeptide from hydrophobic binding sites into a GroES-capped, hydrophilic folding chamber. We used cryo-electron microscopy, statistical analysis, and flexible fitting to resolve a set of distinct GroEL-ATP conformations that can be ordered into a trajectory of domain rotation and elevation. The initial conformations are likely to be the ones that capture polypeptide substrate. Then the binding domains extend radially to separate from each other but maintain their binding surfaces facing the cavity, potentially exerting mechanical force upon kinetically trapped, misfolded substrates. The extended conformation also provides a potential docking site for GroES, to trigger the final, 100° domain rotation constituting the \\\"power stroke\\\" that ejects substrate into the folding chamber.\",\n \"corpus_id\": 8815470,\n \"score\": 0\n },\n {\n \"doc_id\": \"22566049\",\n \"title\": \"Electron microscopy.\",\n \"abstract\": \"Correlative light (LM) and transmission electron microscopic (TEM) analysis is useful, if ultrastructural details of cells need to be related to functional aspects which can only be examined at the LM level. The first protocol presented here introduces a relatively simple way of obtaining TEM images which, on the one hand, reveal ultrastructural details of individual cells and, on the other hand, are large enough to allow a correlation with light micrographs. The second protocol describes a technique for estimating mineral densities of hard tissues using backscattered electron images obtained with a scanning electron microscope. This technique can be used to analyze the mineralization processes which occur throughout tooth formation.\",\n \"corpus_id\": 39721085,\n \"score\": 0\n },\n {\n \"doc_id\": \"22704292\",\n \"title\": \"Evaluation of the registration of temporal series of contrast-enhanced perfusion magnetic resonance 3D images of the liver.\",\n \"abstract\": \"The registration of 2D and 3D images is one of the key tasks in medical image processing and analysis. Accurate registration is a crucial preprocessing step for many tasks; consequently, the evaluation of its accuracy becomes necessary. Unfortunately, this is a difficult task, especially when no golden pattern (true result) is available and when the signal values may have changed between successive images to be registered. This is the case this paper deals with: we have a series of 3D images, magnetic resonance images (MRI) of the liver and adjacent areas that have to be registered. They have been taken while a contrast is diffused through the liver tissue, so intensity of each observed point changes for two reasons: contrast diffusion/perfusion and deformation of the liver (due to body movement and breathing). In this paper, we introduce a new method to automatically compare two or more registration algorithms applied to the same case of a perfusion magnetic resonance dynamic image so that the best of them can be chosen when no ground truth is available. This is done by modeling the function that gives the intensity at a given point as a functional datum, and using statistical techniques to assess its change in comparison with other functions. An example of the application is shown by comparing two parametrizations of a B-spline based registration algorithm. The main result of the proposed method is a suggestive evidence to guide the physician in the process of selecting a registration algorithm, that recommends the algorithm of minimal complexity but still suitable for the case to be analyzed.\",\n \"corpus_id\": 7334154,\n \"score\": 0\n },\n {\n \"doc_id\": \"23152943\",\n \"title\": \"Super elastic strain limit in metallic glass films.\",\n \"abstract\": \"On monolithic Ni-Nb metallic glass films, we experimentally revealed 6.6% elastic strain limit by in-situ transmission electron microscopy observations. The origin of high elastic strain limit may link with high free volume in the film, causing the rearrangement of loosely bonded atomic clusters (or atoms) upon elastic deformation. This high elastic limit of metallic glass films will shed light on new application fields for metallic glasses, and also trigger more studies for deformation mechanism of amorphous materials in general.\",\n \"corpus_id\": 13043780,\n \"score\": 0\n },\n {\n \"doc_id\": \"23877967\",\n \"title\": \"ATP-driven molecular chaperone machines.\",\n \"abstract\": \"This review is focused on the mechanisms by which ATP binding and hydrolysis drive chaperone machines assisting protein folding and unfolding. A survey of the key, general chaperone systems Hsp70 and Hsp90, and the unfoldase Hsp100 is followed by a focus on the Hsp60 chaperonin machine which is understood in most detail. Cryo-electron microscopy analysis of the E. coli Hsp60 GroEL reveals intermediate conformations in the ATPase cycle and in substrate folding. These structures suggest a mechanism by which GroEL can forcefully unfold and then encapsulate substrates for subsequent folding in isolation from all other binding surfaces.\",\n \"corpus_id\": 7822974,\n \"score\": 0\n },\n {\n \"doc_id\": \"23958728\",\n \"title\": \"A pattern matching approach to the automatic selection of particles from low-contrast electron micrographs.\",\n \"abstract\": \"MOTIVATION: Structural information of macromolecular complexes provides key insights into the way they carry out their biological functions. Achieving high-resolution structural details with electron microscopy requires the identification of a large number (up to hundreds of thousands) of single particles from electron micrographs, which is a laborious task if it has to be manually done and constitutes a hurdle towards high-throughput. Automatic particle selection in micrographs is far from being settled and new and more robust algorithms are required to reduce the number of false positives and false negatives. RESULTS: In this article, we introduce an automatic particle picker that learns from the user the kind of particles he is interested in. Particle candidates are quickly and robustly classified as particles or non-particles. A number of new discriminative shape-related features as well as some statistical description of the image grey intensities are used to train two support vector machine classifiers. Experimental results demonstrate that the proposed method: (i) has a considerably low computational complexity and (ii) provides results better or comparable with previously reported methods at a fraction of their computing time. AVAILABILITY: The algorithm is fully implemented in the open-source Xmipp package and downloadable from http://xmipp.cnb.csic.es.\",\n \"corpus_id\": 11199882,\n \"score\": 0\n },\n {\n \"doc_id\": \"24161732\",\n \"title\": \"Optimod--an automated approach for constructing and optimizing initial models for single-particle electron microscopy.\",\n \"abstract\": \"Single-particle cryo-electron microscopy is now well established as a technique for the structural characterization of large macromolecules and macromolecular complexes. The raw data is very noisy and consists of two-dimensional projections, from which the 3D biological object must be reconstructed. The 3D object depends upon knowledge of proper angular orientations assigned to the 2D projection images. Numerous algorithms have been developed for determining relative angular orientations between 2D images, but the transition from 2D to 3D remains challenging and can result in erroneous and conflicting results. Here we describe a general, automated procedure, called OptiMod, for reconstructing and optimizing 3D models using common-lines methodologies. OptiMod approximates orientation angles and reconstructs independent maps from 2D class averages. It then iterates the procedure, while considering each map as a raw solution that needs to be compared with other possible outcomes. We incorporate procedures for 3D alignment, clustering, and refinement to optimize each map, as well as standard scoring metrics to facilitate the selection of the optimal model. We also show that small angle tilt-pair data can be included as one of the scoring metrics to improve the selection of the optimal initial model, and also to provide a validation check. The overall approach is demonstrated using two experimental cryo-EM data sets--the 80S ribosome that represents a relatively straightforward case for ab initio reconstruction, and the Tf-TfR complex that represents a challenging case in that it has previously been shown to provide multiple equally plausible solutions to the initial model problem.\",\n \"corpus_id\": 36681249,\n \"score\": 0\n },\n {\n \"doc_id\": \"24387943\",\n \"title\": \"Multi-modal registration for correlative microscopy using image analogies.\",\n \"abstract\": \"Correlative microscopy is a methodology combining the functionality of light microscopy with the high resolution of electron microscopy and other microscopy technologies for the same biological specimen. In this paper, we propose an image registration method for correlative microscopy, which is challenging due to the distinct appearance of biological structures when imaged with different modalities. Our method is based on image analogies and allows to transform images of a given modality into the appearance-space of another modality. Hence, the registration between two different types of microscopy images can be transformed to a mono-modality image registration. We use a sparse representation model to obtain image analogies. The method makes use of corresponding image training patches of two different imaging modalities to learn a dictionary capturing appearance relations. We test our approach on backscattered electron (BSE) scanning electron microscopy (SEM)/confocal and transmission electron microscopy (TEM)/confocal images. We perform rigid, affine, and deformable registration via B-splines and show improvements over direct registration using both mutual information and sum of squared differences similarity measures to account for differences in image appearance.\",\n \"corpus_id\": 7173975,\n \"score\": 0\n },\n {\n \"doc_id\": \"24563543\",\n \"title\": \"Evaluation of the stability of an SR398/GroES chaperonin complex.\",\n \"abstract\": \"The stability of an SR398/GroES chaperonin complex was examined. As was expected, based on the finding of previous studies, the SR398/GroES complex was extremely stable in the presence of an excess amount of free adenosine 5'-[γ-thio]triphosphate (ATPγS) or adenosine 5'-(β,γ-imido)triphosphate (AMPPNP). However, the complex was not stable in the absence of nucleotides. These results indicate that ATPγS and AMPPNP repeatedly associated to and dissociated from the complex in a non-cooperative manner. This nucleotide exchange did not induce the dissociation of GroES and substrate from SR398, suggesting the importance of the cooperative dissociation of nucleotides from the cis-ring to release GroES and substrate proteins in the GroEL/GroES reaction cycle.\",\n \"corpus_id\": 11651875,\n \"score\": 0\n },\n {\n \"doc_id\": \"24974203\",\n \"title\": \"Efficient initial volume determination from electron microscopy images of single particles.\",\n \"abstract\": \"MOTIVATION: Structural information of macromolecular complexes provides key insights into the way they carry out their biological functions. The reconstruction process leading to the final 3D map requires an approximate initial model. Generation of an initial model is still an open and challenging problem in single-particle analysis. RESULTS: We present a fast and efficient approach to obtain a reliable, low-resolution estimation of the 3D structure of a macromolecule, without any a priori knowledge, addressing the well-known issue of initial volume estimation in the field of single-particle analysis. The input of the algorithm is a set of class average images obtained from individual projections of a biological object at random and unknown orientations by transmission electron microscopy micrographs. The proposed method is based on an initial non-lineal dimensionality reduction approach, which allows to automatically selecting representative small sets of class average images capturing the most of the structural information of the particle under study. These reduced sets are then used to generate volumes from random orientation assignments. The best volume is determined from these guesses using a random sample consensus (RANSAC) approach. We have tested our proposed algorithm, which we will term 3D-RANSAC, with simulated and experimental data, obtaining satisfactory results under the low signal-to-noise conditions typical of cryo-electron microscopy. AVAILABILITY: The algorithm is freely available as part of the Xmipp 3.1 package [http://xmipp.cnb.csic.es]. CONTACT: jvargas@cnb.csic.es SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.\",\n \"corpus_id\": 8183036,\n \"score\": 0\n },\n {\n \"doc_id\": \"25497718\",\n \"title\": \"Simultaneous orientation and thickness mapping in transmission electron microscopy.\",\n \"abstract\": \"In this paper we introduce an approach for simultaneous thickness and orientation mapping of crystalline samples by means of transmission electron microscopy. We show that local thickness and orientation values can be extracted from experimental dark-field (DF) image data acquired at different specimen tilts. The method has been implemented to automatically acquire the necessary data and then map thickness and crystal orientation for a given region of interest. We have applied this technique to a specimen prepared from a commercial semiconductor device, containing multiple 22 nm technology transistor structures. The performance and limitations of our method are discussed and compared to those of other techniques available.\",\n \"corpus_id\": 4881934,\n \"score\": 0\n },\n {\n \"doc_id\": \"25637660\",\n \"title\": \"A statistical approach to the initial volume problem in Single Particle Analysis by Electron Microscopy.\",\n \"abstract\": \"Cryo Electron Microscopy is a powerful Structural Biology technique, allowing the elucidation of the three-dimensional structure of biological macromolecules. In particular, the structural study of purified macromolecules -often referred as Single Particle Analysis(SPA)- is normally performed through an iterative process that needs a first estimation of the three-dimensional structure that is progressively refined using experimental data. It is well-known the local optimisation nature of this refinement, so that the initial choice of this first structure may substantially change the final result. Computational algorithms aiming to providing this first structure already exist. However, the question is far from settled and more robust algorithms are still needed so that the refinement process can be performed with sufficient guarantees. In this article we present a new algorithm that addresses the initial volume problem in SPA by setting it in a Weighted Least Squares framework and calculating the weights through a statistical approach based on the cumulative density function of different image similarity measures. We show that the new algorithm is significantly more robust than other state-of-the-art algorithms currently in use in the field. The algorithm is available as part of the software suite Xmipp (http://xmipp.cnb.csic.es) and Scipion (http://scipion.cnb.csic.es) under the name \\\"Significant\\\".\",\n \"corpus_id\": 15342000,\n \"score\": 0\n },\n {\n \"doc_id\": \"26441413\",\n \"title\": \"Improving the accuracy of registration-based biomechanical analysis: a finite element approach to lung regional strain quantification.\",\n \"abstract\": \"Tissue deformation plays an important role in lung physiology, as lung parenchyma largely deforms during spontaneous ventilation. However, excessive regional deformation may lead to lung injury, as observed in patients undergoing mechanical ventilation. Thus, the accurate estimation of regional strain has recently received great attention in the intensive care community. In this work, we assess the accuracy of regional strain maps computed from direct differentiation of B-Spline (BS) interpolations, a popular technique employed in non-rigid registration of lung computed tomography (CT) images. We show that, while BS-based registration methods give excellent results for the deformation transformation, the strain field directly computed from BS derivatives results in predictions that largely oscillate, thus introducing important errors that can even revert the sign of strain. To alleviate such spurious behavior, we present a novel finite-element (FE) method for the regional strain analysis of lung CT images. The method follows from a variational strain recovery formulation, and delivers a continuous approximation to the strain field in arbitrary domains. From analytical benchmarks, we show that the FE method results in errors that are a fraction of those found for the BS method, both in an average and pointwise sense. The application of the proposed FE method to human lung CT images results in 3D strain maps are heterogeneous and smooth, showing high consistency with specific ventilation maps reported in the literature. We envision that the proposed FE method will considerably improve the accuracy of image-based biomechanical analysis, making it reliable enough for routine medical applications.\",\n \"corpus_id\": 34306611,\n \"score\": 0\n },\n {\n \"doc_id\": \"26611544\",\n \"title\": \"Single-particle cryo-electron microscopy of macromolecular complexes.\",\n \"abstract\": \"Recent technological breakthroughs in image acquisition have enabled single-particle cryo-electron microscopy (cryo-EM) to achieve near-atomic resolution structural information for biological complexes. The improvements in image quality coupled with powerful computational methods for sorting distinct particle populations now also allow the determination of compositional and conformational ensembles, thereby providing key insights into macromolecular function. However, the inherent instability and dynamic nature of biological assemblies remain a tremendous challenge that often requires tailored approaches for successful implementation of the methodology. Here, we briefly describe the fundamentals of single-particle cryo-EM with an emphasis on covering the breadth of techniques and approaches, including low- and high-resolution methods, aiming to illustrate specific steps that are crucial for obtaining structural information by this method.\",\n \"corpus_id\": 4928921,\n \"score\": 0\n },\n {\n \"doc_id\": \"26694391\",\n \"title\": \"Multidirectional Image Sensing for Microscopy Based on a Rotatable Robot.\",\n \"abstract\": \"Image sensing at a small scale is essentially important in many fields, including microsample observation, defect inspection, material characterization and so on. However, nowadays, multi-directional micro object imaging is still very challenging due to the limited field of view (FOV) of microscopes. This paper reports a novel approach for multi-directional image sensing in microscopes by developing a rotatable robot. First, a robot with endless rotation ability is designed and integrated with the microscope. Then, the micro object is aligned to the rotation axis of the robot automatically based on the proposed forward-backward alignment strategy. After that, multi-directional images of the sample can be obtained by rotating the robot within one revolution under the microscope. To demonstrate the versatility of this approach, we view various types of micro samples from multiple directions in both optical microscopy and scanning electron microscopy, and panoramic images of the samples are processed as well. The proposed method paves a new way for the microscopy image sensing, and we believe it could have significant impact in many fields, especially for sample detection, manipulation and characterization at a small scale.\",\n \"corpus_id\": 8602844,\n \"score\": 0\n },\n {\n \"doc_id\": \"28951123\",\n \"title\": \"Quantitative multiphoton microscopy of murine urinary bladder morphology during in situ uniaxial loading.\",\n \"abstract\": \"Urodynamic tests are the gold standard for the diagnosis of bladder dysfunction, and the mechanical compliance of the bladder is an important parameter in these tests. The bladder wall has a layered structure, differentially affected by pathology, so knowledge of the contribution and role of these layers and their constituents to overall bladder compliance will enhance interpretation of these clinical tests. In this study we document the functional morphology of the detrusor and lamina propria of the murine bladder wall using a custom in-situ tensile loading system under multiphoton microscopy (MPM) observation in unloaded state and under incremental uniaxial stretch. Features in the stress-stretch curves of bladder samples were then directly related to corresponding MPM images. Collagen organisation across wall depth was quantified using image analysis techniques. The hypothesis that the lamina propria deformed at low strain by unfolding of the rugae and rearranging collagen fibrils was confirmed. A novel 'pocket' feature in the detrusor was observed along with extensive rearrangement of fibrils in two families at different depths, providing higher stiffness at high stretches in the detrusor. The very different deformations of detrusor and lamina propria were accommodated by the highly coiled structure of collagen in the lamina propria. Imaging and mechanical studies presented here allow gross mechanical response to be attributed to specific components of the bladder wall and further, may be used to investigate the impact of microstructural changes due to pathology or aging, and how they impair tissue functionality. STATEMENT OF SIGNIFICANCE: This article reports the first in-situ multiphoton microscopy observations of microstructural deformation under uniaxial tensile loading of ex vivo bladder. We describe collagen rearrangement through the tissue thickness and relate this directly to the stress-stretch behaviour. We confirm for the first time the unfolding of rugae and realignment of fibrils in the lamina propria during extension and the rapid stiffening as two fibril families in the detrusor are engaged. This technique provides new insight into microstructure function and will enhance understanding of the impact of changes due to pathology or aging.\",\n \"corpus_id\": 3462014,\n \"score\": 0\n },\n {\n \"doc_id\": \"29116053\",\n \"title\": \"Elastic strain and twist analysis of protein structural data and allostery of the transmembrane channel KcsA.\",\n \"abstract\": \"The abundance of available static protein structural data makes the more effective analysis and interpretation of this data a valuable tool to supplement the experimental study of protein mechanics. Structural displacements can be difficult to analyze and interpret. Previously, we showed that strains provide a more natural and interpretable representation of protein deformations, revealing mechanical coupling between spatially distinct sites of allosteric proteins. Here, we demonstrate that other transformations of displacements yield additional insights. We calculate the divergence and curl of deformations of the transmembrane channel KcsA. Additionally, we introduce quantities analogous to bend, splay, and twist deformation energies of nematic liquid crystals. These transformations enable the decomposition of displacements into different modes of deformation, helping to characterize the type of deformation a protein undergoes. We apply these calculations to study the filter and gating regions of KcsA. We observe a continuous path of rotational deformations physically coupling these two regions, and, we propose, underlying the allosteric interaction between these regions. Bend, splay, and twist distinguish KcsA gate opening, filter opening, and filter-gate coupling, respectively. In general, physically meaningful representations of deformations (like strain, curl, bend, splay, and twist) can make testable predictions and yield insights into protein mechanics, augmenting experimental methods and more fully exploiting available structural data.\",\n \"corpus_id\": 3624758,\n \"score\": 0\n },\n {\n \"doc_id\": \"29293469\",\n \"title\": \"Improving oncoplastic breast tumor bed localization for radiotherapy planning using image registration algorithms.\",\n \"abstract\": \"Knowledge about tumor bed localization and its shape analysis is a crucial factor for preventing irradiation of healthy tissues during supportive radiotherapy and as a result, cancer recurrence. The localization process is especially hard for tumors placed nearby soft tissues, which undergo complex, nonrigid deformations. Among them, breast cancer can be considered as the most representative example. A natural approach to improving tumor bed localization is the use of image registration algorithms. However, this involves two unusual aspects which are not common in typical medical image registration: the real deformation field is discontinuous, and there is no direct correspondence between the cancer and its bed in the source and the target 3D images respectively. The tumor no longer exists during radiotherapy planning. Therefore, a traditional evaluation approach based on known, smooth deformations and target registration error are not directly applicable. In this work, we propose alternative artificial deformations which model the tumor bed creation process. We perform a comprehensive evaluation of the most commonly used deformable registration algorithms: B-Splines free form deformations (B-Splines FFD), different variants of the Demons and TV-L1 optical flow. The evaluation procedure includes quantitative assessment of the dedicated artificial deformations, target registration error calculation, 3D contour propagation and medical experts visual judgment. The results demonstrate that the currently, practically applied image registration (rigid registration and B-Splines FFD) are not able to correctly reconstruct discontinuous deformation fields. We show that the symmetric Demons provide the most accurate soft tissues alignment in terms of the ability to reconstruct the deformation field, target registration error and relative tumor volume change, while B-Splines FFD and TV-L1 optical flow are not an appropriate choice for the breast tumor bed localization problem, even though the visual alignment seems to be better than for the Demons algorithm. However, no algorithm could recover the deformation field with sufficient accuracy in terms of vector length and rotation angle differences.\",\n \"corpus_id\": 46781403,\n \"score\": 0\n },\n {\n \"doc_id\": \"29395788\",\n \"title\": \"MonoRes: Automatic and Accurate Estimation of Local Resolution for Electron Microscopy Maps.\",\n \"abstract\": \"Since the beginning of electron microscopy, resolution has been a critical parameter. In this article, we propose a fully automatic, accurate method for determining the local resolution of a 3D map (MonoRes). The foundation of this algorithm is an extension of the concept of analytic signal, termed monogenic signal. The map is filtered at different frequencies and the amplitude of the monogenic signal is calculated, after which a criterion is applied to determine the resolution at each voxel. MonoRes is fully automatic without compulsory user parameters, with great accuracy in all tests, and is computationally more rapid than existing methods in the field. In addition, MonoRes offers the option of local filtering of the original map based on the calculated local resolution.\",\n \"corpus_id\": 46822743,\n \"score\": 0\n },\n {\n \"doc_id\": \"29399437\",\n \"title\": \"A non-rigid registration method for the analysis of local deformations in the wood cell wall.\",\n \"abstract\": \"This paper concerns the problem of wood cellular structure image registration. Given the large variability of wood geometry and the important changes in the cellular organization due to moisture sorption, an affine-based image registration technique is not exhaustive to describe the overall hygro-mechanical behaviour of wood at micrometre scales. Additionally, free tools currently available for non-rigid image registration are not suitable for quantifying the structural deformations of complex hierarchical materials such as wood, leading to errors due to misalignment. In this paper, we adapt an existing non-rigid registration model based on B-spline functions to our case study. The so-modified algorithm combines the concept of feature recognition within specific regions locally distributed in the material with an optimization problem. Results show that the method is able to quantify local deformations induced by moisture changes in tomographic images of wood cell wall with high accuracy. The local deformations provide new important insights in characterizing the swelling behaviour of wood at the cell wall level.\",\n \"corpus_id\": 26860137,\n \"score\": 0\n },\n {\n \"doc_id\": \"29413406\",\n \"title\": \"2D strain mapping using scanning transmission electron microscopy Moiré interferometry and geometrical phase analysis.\",\n \"abstract\": \"A strain characterization technique based on Moiré interferometry in a scanning transmission electron microscope (STEM) and geometrical phase analysis (GPA) method is demonstrated. The deformation field is first captured in a single STEM Moiré hologram composed of multiple sets of periodic fringes (Moiré patterns) generated from the interference between the periodic scanning grating, fixing the positions of the electron probe on the sample, and the crystal structure. Applying basic principles from sampling theory, the Moiré patterns arrangement is then simulated using a STEM electron micrograph reference to convert the experimental STEM Moiré hologram into information related to the crystal lattice periodicities. The GPA method is finally applied to extract the 2D relative strain and rotation fields. The STEM Moiré interferometry enables the local information to be de-magnified to a large length scale, comparable to what can be achieved in dark-field electron holography. The STEM Moiré GPA method thus extends the conventional high-resolution STEM GPA capabilities by providing comparable quantitative 2D strain mapping with a larger field of view (up to a few microns).\",\n \"corpus_id\": 3750233,\n \"score\": 0\n }\n]","isConversational":false}}},{"rowIdx":68,"cells":{"query":{"kind":"string","value":"{\n \"doc_id\": \"26575957\",\n \"title\": \"Hierarchical Mesoporous Zinc-Nickel-Cobalt Ternary Oxide Nanowire Arrays on Nickel Foam as High-Performance Electrodes for Supercapacitors.\",\n \"abstract\": \"Nickel foam supported hierarchical mesoporous Zn-Ni-Co ternary oxide (ZNCO) nanowire arrays are synthesized by a simple two-step approach including a hydrothermal method and subsequent calcination process and directly utilized for supercapacitive investigation for the first time. The nickel foam supported hierarchical mesoporous ZNCO nanowire arrays possess an ultrahigh specific capacitance value of 2481.8 F g(-1) at 1 A g(-1) and excellent rate capability of about 91.9% capacitance retention at 5 A g(-1). More importantly, an asymmetric supercapacitor with a high energy density (35.6 Wh kg(-1)) and remarkable cycle stability performance (94% capacitance retention over 3000 cycles) is assembled successfully by employing the ZNCO electrode as positive electrode and activated carbon as negative electrode. The remarkable electrochemical behaviors demonstrate that the nickel foam supported hierarchical mesoporous ZNCO nanowire array electrodes are highly desirable for application as advanced supercapacitor electrodes.\",\n \"corpus_id\": 206403340\n}"},"candidates":{"kind":"list like","value":[{"doc_id":"23076678","title":"Enhancing electrochemical reaction sites in nickel-cobalt layered double hydroxides on zinc tin oxide nanowires: a hybrid material for an asymmetric supercapacitor device.","abstract":"Conducting nanowires are of particular interest in energy-related research on devices such as supercapacitors, batteries, water splitting electrodes and solar cells. Their direct electrode/current collector contact and highly conductive 1D structure enable conducting nanowires to provide ultrafast charge transportation. In this paper, we report the facile synthesis of nickel cobalt layered double hydroxides (LDHs) on conducting Zn(2)SnO(4) (ZTO) and the application of this material to a supercapacitor. This study also presents the first report of an enhancement of the active faradic reaction sites (electroactive sites) resulting from the heterostructure. This novel material demonstrates outstanding electrochemical performance with a high specific capacitance of 1805 F g(-1) at 0.5 A g(-1), and an excellent rate performance of 1275 F g(-1) can be achieved at 100 A g(-1). Furthermore, an asymmetric supercapacitor was successfully fabricated using active carbon as a negative electrode. This asymmetric device exhibits a high energy density of 23.7 W h kg(-1) at a power density of 284.2 W kg(-1). Meanwhile, a high power density of 5817.2 W kg(-1) can be achieved at an energy density of 9.7 W h kg(-1). More importantly, this device exhibits long-term cycling stability, with 92.7% capacity retention after 5000 cycles.","corpus_id":205828027,"score":2},{"doc_id":"23169236","title":"Hierarchical NiCo2O4@MnO2 core-shell heterostructured nanowire arrays on Ni foam as high-performance supercapacitor electrodes.","abstract":"An advanced integrated electrode for high-performance supercapacitors has been designed by growing hierarchical NiCo(2)O(4)@MnO(2) core-shell heterostructured nanowire arrays on nickel foam. Such unique array nanoarchitectures exhibit remarkable electrochemical performance with high capacitance and desirable cycle life at high rates.","corpus_id":20114703,"score":2},{"doc_id":"23570565","title":"Construction of high-capacitance 3D CoO@polypyrrole nanowire array electrode for aqueous asymmetric supercapacitor.","abstract":"We have developed a supercapacitor electrode composed of well-aligned CoO nanowire array grown on 3D nickel foam with polypyrrole (PPy) uniformly immobilized onto or firmly anchored to each nanowire surface to boost the pseudocapacitive performance. The electrode architecture takes advantage of the high electrochemical activity from both the CoO and PPy, the high electronic conductivity of PPy, and the short ion diffusion pathway in ordered mesoporous nanowires. These merits together with the elegant synergy between CoO and PPy lead to a high specific capacitance of 2223 F g(-1) approaching the theoretical value, good rate capability, and cycling stability (99.8% capacitance retention after 2000 cycles). An aqueous asymmetric supercapacitor device with a maximum voltage of 1.8 V fabricated by using our hybrid array as the positive electrode and activated carbon film as the negative electrode has demonstrated high energy density (~43.5 Wh kg(-1)), high power density (~5500 W kg(-1) at 11.8 Wh kg(-1)) and outstanding cycleability (~20,000 times). After charging for only ~10 s, two such 4 cm(2) asymmetric supercapacitors connected in series can efficiently power 5 mm diameter red, yellow, and green round LED indicators (lasting for 1 h for red LED) and drive a mini 130 rotation-motor robustly.","corpus_id":5100836,"score":2},{"doc_id":"23650047","title":"Intertwined nanocarbon and manganese oxide hybrid foam for high-energy supercapacitors.","abstract":"Rapid charging and discharging supercapacitors are promising alternative energy storage systems for applications such as portable electronics and electric vehicles. Integration of pseudocapacitive metal oxides with single-structured materials has received a lot of attention recently due to their superior electrochemical performance. In order to realize high energy-density supercapacitors, a simple and scalable method is developed to fabricate a graphene/MWNT/MnO2 nanowire (GMM) hybrid nanostructured foam, via a two-step process. The 3D few-layer graphene/MWNT (GM) architecture is grown on foamed metal foils (nickel foam) via ambient pressure chemical vapor deposition. Hydrothermally synthesized α-MnO2 nanowires are conformally coated onto the GM foam by a simple bath deposition. The as-prepared hierarchical GMM foam yields a monographical graphene foam conformally covered with an intertwined, densely packed CNT/MnO2 nanowire nanocomposite network. Symmetrical electrochemical capacitors (ECs) based on GMM foam electrodes show an extended operational voltage window of 1.6 V in aqueous electrolyte. A superior energy density of 391.7 Wh kg(-1) is obtained for the supercapacitor based on the GMM foam, which is much higher than ECs based on GM foam only (39.72 Wh kg(-1) ). A high specific capacitance (1108.79 F g(-1) ) and power density (799.84 kW kg(-1) ) are also achieved. Moreover, the great capacitance retention (97.94%) after 13 000 charge-discharge cycles and high current handability demonstrate the high stability of the electrodes of the supercapacitor. These excellent performances enable the innovative 3D hierarchical GMM foam to serve as EC electrodes, resulting in energy-storage devices with high stability and power density in neutral aqueous electrolyte.","corpus_id":25684899,"score":2},{"doc_id":"23864110","title":"High energy density asymmetric supercapacitors with a nickel oxide nanoflake cathode and a 3D reduced graphene oxide anode.","abstract":"Here we demonstrate a high energy density asymmetric supercapacitor with nickel oxide nanoflake arrays as the cathode and reduced graphene oxide as the anode. Nickel oxide nanoflake arrays were synthesized on a flexible carbon cloth substrate using a seed-mediated hydrothermal method. The reduced graphene oxide sheets were deposited on three-dimensional (3D) nickel foam by hydrothermal treatment of nickel foam in graphene oxide solution. The nanostructured electrodes provide a large effective surface area. The asymmetric supercapacitor device operates with a voltage of 1.7 V and achieved a remarkable areal capacitance of 248 mF cm(-2) (specific capacitance of 50 F g(-1)) at a charge/discharge current density of 1 mA cm(-2) and a maximum energy density of 39.9 W h kg(-1) (based on the total mass of active materials of 5.0 mg). Furthermore, the device showed an excellent charge/discharge cycling performance in 1.0 M KOH electrolyte at a current density of 5 mA cm(-2), with a capacitance retention of 95% after 3000 cycles.","corpus_id":30627013,"score":2},{"doc_id":"23969779","title":"High-performance supercapacitor and lithium-ion battery based on 3D hierarchical NH4F-induced nickel cobaltate nanosheet-nanowire cluster arrays as self-supported electrodes.","abstract":"A facile hydrothermal method is developed for large-scale production of three-dimensional (3D) hierarchical porous nickel cobaltate nanowire cluster arrays derived from nanosheet arrays with robust adhesion on Ni foam. Based on the morphology evolution upon reaction time, a possible formation process is proposed. The role of NH4F in formation of the structure has also been investigated based on different NH4F amounts. This unique structure significantly enhances the electroactive surface areas of the NiCo2O4 arrays, leading to better interfacial/chemical distributions at the nanoscale, fast ion and electron transfer and good strain accommodation. Thus, when it is used for supercapacitor testing, a specific capacitance of 1069 F g(-1) at a very high current density of 100 A g(-1) was obtained. Even after more than 10,000 cycles at various large current densities, a capacitance of 2000 F g(-1) at 10 A g(-1) with 93.8% retention can be achieved. It also exhibits a high-power density (26.1 kW kg(-1)) at a discharge current density of 80 A g(-1). When used as an anode material for lithium-ion batteries (LIBs), it presents a high reversible capacity of 976 mA h g(-1) at a rate of 200 mA g(-1) with good cycling stability and rate capability. This array material is rarely used as an anode material. Our results show that this unique 3D hierarchical porous nickel cobaltite is promising for electrochemical energy applications.","corpus_id":205869504,"score":2},{"doc_id":"24050440","title":"New energy storage option: toward ZnCo2O4 nanorods/nickel foam architectures for high-performance supercapacitors.","abstract":"Hierarchical ZnCo2O4/nickel foam architectures were first fabricated from a simple scalable solution approach, exhibiting outstanding electrochemical performance in supercapacitors with high specific capacitance (∼1400 F g(-1) at 1 A g(-1)), excellent rate capability (72.5% capacity retention at 20 A g(-1)), and good cycling stability (only 3% loss after 1000 cycles at 6 A g(-1)). All-solid-state supercapacitors were also fabricated by assembling two pieces of the ZnCo2O4-based electrodes, showing superior performance in terms of high specific capacitance and long cycling stability. Our work confirms that the as-prepared architectures can not only be applied in high energy density fields, but also be used in high power density applications, such as electric vehicles, flexible electronics, and energy storage devices.","corpus_id":206784362,"score":2},{"doc_id":"24429842","title":"Superior asymmetric supercapacitor based on Ni-Co oxide nanosheets and carbon nanorods.","abstract":"Nickel and cobalt (Ni-Co) binary oxide nanosheets with mesoporous structure are prepared by a facile approach based on the formation and disassociation of nickel/cobalt-citrate complex, and they show an ultra-high Faradaic capacitance up to 1846 F g(-1) and excellent rate capability. On this basic, advanced aqueous asymmetric supercapacitors (AASs) are successfully built by using the Ni-Co oxide as the positive electrode and three kinds of activated carbons respectively as the negative electrode. As-made AASs are able to work reversibly in a full operated voltage region of 0-1.6 V and exhibit outstanding electrochemical performance. Among them, activated polyaniline-derived carbon (APDC)//Ni-Co oxide AASs shows the highest specific capacitance of 202 F g(-1), the maximum energy density of 71.7 Wh kg(-1), and superior combination of high energy and power density (a energy density of 41.6 Wh kg(-1) at a high power density of 16 kW kg(-1)).","corpus_id":451102,"score":2},{"doc_id":"24562602","title":"Surfactant dependent self-organization of Co3O4 nanowires on Ni foam for high performance supercapacitors: from nanowire microspheres to nanowire paddy fields.","abstract":"Different surfactants were used in a typical hydrothermal process for controlling the morphology of the Co3O4 nanowire superstructure on Ni foam. It is easy for the Co3O4 nanowires to self-organize into nanowire microspheres on Ni foam in the absence of surfactants. And the nanowire microspheres gradually unfold into nanowire paddy fields with the addition of nonionic, cationic and anionic surfactants, respectively. The results of BET and electrochemical measurements show that the specific surface area and capacitance first decrease and then increase with the change in the Co3O4 superstructure morphology. Among these electrodes, the Co3O4 electrode with paddy like nanowires shows an outstanding specific capacitance of 1217.4 F g(-1) and areal specific capacitance as high as 6087 mF cm(-2) at 0.7 A g(-1) with high mass loading (5 mg cm(-2)), good power capability (showing a high specific capacitance of 835.1 F g(-1) (4176 mF cm(-2)) at 5 A g(-1)), excellent cycling stability and high columbic efficiency (∼100%). This exceptional performance is benefited from the almost monodispersed nanowire morphology and high specific surface area (121.4 m(2) g(-1)). At the same time, the asymmetric supercapacitor, employing the Co3O4 electrode with paddy-like nanowires as the positive electrode and the activated carbon electrode as the negative electrode, was successfully assembled. It shows a high specific energy and good long-term electrochemical stability. All these impressive results demonstrate that the Co3O4 electrode with paddy-like nanowires is promising for practical applications in supercapacitors.","corpus_id":6453350,"score":2},{"doc_id":"24643977","title":"3D carbon/cobalt-nickel mixed-oxide hybrid nanostructured arrays for asymmetric supercapacitors.","abstract":"The electrochemical performance of supercapacitors relies not only on the exploitation of high-capacity active materials, but also on the rational design of superior electrode architectures. Herein, a novel supercapacitor electrode comprising 3D hierarchical mixed-oxide nanostructured arrays (NAs) of C/CoNi3 O4 is reported. The network-like C/CoNi3 O4 NAs exhibit a relatively high specific surface area; it is fabricated from ultra-robust Co-Ni hydroxide carbonate precursors through glucose-coating and calcination processes. Thanks to their interconnected three-dimensionally arrayed architecture and mesoporous nature, the C/CoNi3 O4 NA electrode exhibits a large specific capacitance of 1299 F/g and a superior rate performance, demonstrating 78% capacity retention even when the discharge current jumps by 100 times. An optimized asymmetric supercapacitor with the C/CoNi3 O4 NAs as the positive electrode is fabricated. This asymmetric supercapacitor can reversibly cycle at a high potential of 1.8 V, showing excellent cycling durability and also enabling a remarkable power density of ∼13 kW/kg with a high energy density of ∼19.2 W·h/kg. Two such supercapacitors linked in series can simultaneously power four distinct light-emitting diode indicators; they can also drive the motor of remote-controlled model planes. This work not only presents the potential of C/CoNi3 O4 NAs in thin-film supercapacitor applications, but it also demonstrates the superiority of electrodes with such a 3D hierarchical architecture.","corpus_id":11914388,"score":2},{"doc_id":"24661431","title":"Hierarchical mesoporous nickel cobaltite nanoneedle/carbon cloth arrays as superior flexible electrodes for supercapacitors.","abstract":"Hierarchical mesoporous NiCo2O4 nanoneedle arrays on carbon cloth have been fabricated by a simple hydrothermal approach combined with a post-annealing treatment. Such unique array nanoarchitectures exhibit remarkable electrochemical performance with high capacitance and desirable cycle life at high rates. When evaluated as an electrode material for supercapacitors, the NiCo2O4 nanoneedle arrays supported on carbon cloth was able to deliver high specific capacitance of 660 F g-1 at current densities of 2 A g-1 in 2 M KOH aqueous solution. In addition, the composite electrode shows excellent mechanical behavior and long-term cyclic stability (91.8% capacitance retention after 3,000 cycles). The fabrication method presented here is facile, cost-effective, and scalable, which may open a new pathway for real device applications.","corpus_id":18948582,"score":2},{"doc_id":"24771534","title":"Hierarchically porous nickel oxide nanosheets grown on nickel foam prepared by one-step in situ anodization for high-performance supercapacitors.","abstract":"Porous NiO nanosheets are successfully grown on nickel foam substrate through an in situ anodization by using molten KOH as the electrolyte. High-purity NiO is directly obtained by this one-step method without any subsequent treatment. The obtained NiO supported on nickel foam is used as a binder-free electrode for a supercapacitor and its pseudocapacitive behavior has been investigated by cyclic voltammetry and galvanostatic charge-discharge tests in a 6 M aqueous solution of KOH. Electrochemical data demonstrates that this binder-free electrode possesses ultrahigh capacitance (4.74 F cm(-2) at 4 mA cm(-2)), excellent rate capability, and cycling stability. After 1000 cycles, the areal capacitance value is 9.4 % lower than the initial value and maintains 85.4 % of the maximum capacitance value.","corpus_id":7857480,"score":2},{"doc_id":"25110896","title":"Fabrication of nickel-foam-supported layered zinc-cobalt hydroxide nanoflakes for high electrochemical performance in supercapacitors.","abstract":"Nickel foam supported Zn-Co hydroxide nanoflakes were fabricated by a facile solvothermal method. Benefited from the unique structure of Zn-Co hydroxide nanoflakes on a nickel foam substrate, the as prepared materials exhibited an excellent specific capacitance of 901 F g(-1) at 5 A g(-1) and remarkable cycling stability as electrode materials in supercapacitors.","corpus_id":8818190,"score":2},{"doc_id":"25247606","title":"Spinel manganese-nickel-cobalt ternary oxide nanowire array for high-performance electrochemical capacitor applications.","abstract":"Aligned spinel Mn-Ni-Co ternary oxide (MNCO) nanowires are synthesized by a facile hydrothermal method. As an electrode of supercapacitors, the MNCO nanowire array on nickel foam shows an outstanding specific capacitance of 638 F g(-1) at 1 A g(-1) and excellent cycling stability. This exceptional performance benefits from its nanowire architecture, which can provide large reaction surface area, fast ion and electron transfer, and good structural stability. Furthermore, an asymmetric supercapacitor (ASC) with high energy density is assembled successfully by employing the MNCO nanowire array as positive electrode and carbon black as negative electrode. The excellent electrochemical performances indicate the promising potential application of the ASC device in the energy storage field.","corpus_id":20839409,"score":2},{"doc_id":"25258611","title":"High-performance binder-free supercapacitor electrode by direct growth of cobalt-manganese composite oxide nansostructures on nickel foam.","abstract":"A facile approach composed of hydrothermal process and annealing treatment is proposed to directly grow cobalt-manganese composite oxide ((Co,Mn)3O4) nanostructures on three-dimensional (3D) conductive nickel (Ni) foam for a supercapacitor electrode. The as-fabricated porous electrode exhibits excellent rate capability and high specific capacitance of 840.2 F g(-1) at the current density of 10 A g(-1), and the electrode also shows excellent cycling performance, which retains 102% of its initial discharge capacitance after 7,000 cycles. The fabricated binder-free hierarchical composite electrode with superior electrochemical performance is a promising candidate for high-performance supercapacitors.","corpus_id":14987088,"score":2},{"doc_id":"26063601","title":"Mesoporous ZnCo2O4 nanoflakes grown on nickel foam as electrodes for high performance supercapacitors.","abstract":"ZnCo2O4 nanoflakes, as electrodes for supercapacitors, are grown on a cellular nickel foam using a cost-effective hydrothermal procedure. The mesoporous ZnCo2O4 nanoflakes have large electroactive surface areas with strong adhesion to the Ni foam, allowing fast ion and electron transport. The nanoarchitecture electrodes deliver an excellent specific capacitance of 1220 F g(-1) at a current density of 2 A g(-1) in a 2 M KOH aqueous solution and a long-term cyclic stability of 94.2% capacitance retention after 5000 cycles. The fabrication strategy is facile, cost-effective, and can offer great promise for large-scale supercapacitor applications.","corpus_id":19385816,"score":2},{"doc_id":"26372533","title":"Three-Dimensional NiCo2O4@Polypyrrole Coaxial Nanowire Arrays on Carbon Textiles for High-Performance Flexible Asymmetric Solid-State Supercapacitor.","abstract":"In this article, we report a novel electrode of NiCo2O4 nanowire arrays (NWAs) on carbon textiles with a polypyrrole (PPy) nanosphere shell layer to enhance the pseudocapacitive performance. The merits of highly conductive PPy and short ion transport channels in ordered NiCo2O4 mesoporous nanowire arrays together with the synergistic effect between NiCo2O4 and PPy result in a high specific capacitance of 2244 F g(-1), excellent rate capability, and cycling stability in NiCo2O4/PPy electrode. Moreover, a lightweight and flexible asymmetric supercapacitor (ASC) device is successfully assembled using the hybrid NiCo2O4@PPy NWAs and activated carbon (AC) as electrodes, achieving high energy density (58.8 W h kg(-1) at 365 W kg(-1)), outstanding power density (10.2 kW kg(-1) at 28.4 W h kg(-1)) and excellent cycling stability (∼89.2% retention after 5000 cycles), as well as high flexibility. The three-dimensional coaxial architecture design opens up new opportunities to fabricate a high-performance flexible supercapacitor for future portable and wearable electronic devices.","corpus_id":206399613,"score":2},{"doc_id":"26465975","title":"Rational Synthesis of Branched CoMoO4@CoNiO2 Core/Shell Nanowire Arrays for All-Solid-State Supercapacitors with Improved Performance.","abstract":"Effectively composite materials with optimized structures exhibited promising potential in continuing improving the electrochemical performances of supercapacitors in the past few years. Here, we proposed a rational design of branched CoMoO4@CoNiO2 core/shell nanowire arrays on Ni foam by two steps of hydrothermal processing. Owing to the high activity of the scaffold-like CoMoO4 nanowires and the well-defined CoNiO2 nanoneedles, the three-dimensional (3D) electrode architectures achieved remarkable electrochemical performances with high areal specific capacitance (5.31 F/cm(2) at 5 mA/cm(2)) and superior cycling stability(159% of the original specific capacitance, i.e., 95.7% of the maximum retained after 5000 cycles at 30 mA/cm(2)). The all-solid-state asymmetric supercapacitors composed of such electrode and activated carbon (AC) exhibited an areal specific capacitance of 1.54 F/cm(2) at 10 mA/cm(2) and a rate capability (59.75 Wh/kg at a 1464 W/kg) comparable with Li-ion batteries. It also showed an excellent cycling stability with no capacitance attenuation after 50000 cycles at 100 mA/cm(2). After rapid charging (1 s), such supercapacitors in series could lighten a red LED for a long time and drive a mini motor effectively, demonstrating advances in energy storage, scalable integrated applications, and promising commercial potential.","corpus_id":206403319,"score":2},{"doc_id":"26608410","title":"Hierarchical structures composed of MnCo2O4@MnO2 core-shell nanowire arrays with enhanced supercapacitor properties.","abstract":"In this paper, hierarchical MnCo2O4@MnO2 core-shell nanowire arrays (MnCo2O4@MnO2 NWAs) with mesoporous and large surface area are synthesized on 3D nickel foam via a facile, two-step hydrothermal approach without any adscititious surfactant and binder. The electrode architecture takes advantage of the synergistic effects contributed from both the porous MnCo2O4 nanowire core and the MnO2 shell layer. The fabricated MnCo2O4@MnO2 NWA electrode for supercapacitors in aqueous electrolyte exhibits a significantly enhanced specific capacitance (858 F g(-1) at 1 A g(-1)), high energy density (36.0 Wh kg(-1) at 252 W kg(-1)) and long-life cycling stability (retaining 88% of the initial capacitance after 5000 cycles). Then, a symmetrical supercapacitor is fabricated by assembling two MnCo2O4@MnO2 NWA-based electrodes, which shows a high specific capacitance of 678 F g(-1) at 1 A g(-1) and a high energy density of 135.6 Wh kg(-1) at 513 W kg(-1). Thereby, the hierarchical core-shell MnCo2O4@MnO2 NWAs are very promising as next generation high-performance long-life cycling supercapacitors.","corpus_id":43058294,"score":2},{"doc_id":"26742692","title":"Nickel Cobalt Hydroxide @Reduced Graphene Oxide Hybrid Nanolayers for High Performance Asymmetric Supercapacitors with Remarkable Cycling Stability.","abstract":"Nanolayered structures present significantly enhanced electrochemical performance by facilitating the surface-dependent electrochemical reaction processes for supercapacitors, which, however, causes capacitance fade upon cycling due to their poor chemical stability. In this work, we report a simple and effective approach to develop a stable, high performance electrode material by integrating 2D transition metal hydroxide and reduced graphene oxide sheets at nanometer scale. Specifically, a hybrid nanolayer of Ni-Co hydroxide @reduced graphene oxide (Ni,Co-OH/rGO) with an average thickness of 1.37 nm is synthesized through an easy one-pot hydrothermal method. Benefiting from the face to face contact model between Ni-Co hydroxide and rGO sheets, such unique structure presents superior specific capacitance and cycling performance as compared to the pure Ni-Co hydroxide nanolayers. An asymmetric supercapacitor based on Ni,Co-OH/rGO and three-dimensional (3D) hierarchical porous carbon is developed, exhibiting a high energy density of 56.1 Wh kg(-1) along with remarkable cycling stability (80% retention after 17 000 cycles), which holds great promise for practical applications in energy storage devices.","corpus_id":206409199,"score":2},{"doc_id":"27253880","title":"Activated Microporous Carbon Derived from Almond Shells for High Energy Density Asymmetric Supercapacitors.","abstract":"Via the activation treatment of carbonized almond shells with HNO3 and KOH, activated microporous carbon (AMC-3 and AMC-2) was successfully synthesized. These two AMC electrodes demonstrate remarkable electrochemical behaviors such as high rate capability, high specific capacitance, and excellent cycle stability when serving as electrodes for supercapacitors. More importantly, through the use of a Zn-Ni-Co ternary oxide (ZNCO) positive electrode and the AMC negative electrode, asymmetric supercapacitors (ASC) were assembled that deliver superior energy density (53.3 Wh kg(-1) at a power density of 1126.1 W kg(-1) for ASC-2 and 53.6 Wh kg(-1) at a power density of 1124.5 W kg(-1) for ASC-3) and excellent stability (82.7% and 83.4% specific capacitance retention for ZNCO//AMC ASC-2 and ZNCO//AMC ASC-3, respectively, after 5000 cycles). Through these two methods, low-cost, renewable, and environmentally friendly electrode materials can be provided for high energy density supercapacitors.","corpus_id":206421165,"score":2},{"doc_id":"27336591","title":"Wall-like hierarchical metal oxide nanosheet arrays grown on carbon cloth for excellent supercapacitor electrodes.","abstract":"Recently, considerable efforts have been made to satisfy the future requirements of electrochemical energy storage using novel functional electrode materials. Binary transition metal oxides (BTMOs) possess multiple oxidation states that enable multiple redox reactions, showing higher supercapacitive properties than single component metal oxides. In this work, a facile hydrothermal method is provided for the synthesis of wall-like hierarchical metal oxide MMoO4 (M = Ni, Co) nanosheet arrays, which are directly grown on flexible carbon cloth for use as advanced binder-free electrodes for supercapacitors. By virtue of their intriguing structure, the resulted active material nanosheets with a high specific surface area can provide a large electroactive region, which could facilitate easy accession of electrolyte ions and fast charge transport, resulting in an enhanced electrochemical performance. Separately, the as-synthesized MMoO4 (M = Ni, Co) samples have exhibited superior specific capacitances (1483 F g(-1) of NiMoO4 and 452 F g(-1) of CoMoO4 at a current density of 2 A g(-1)), as well as excellent cycling stability (93.1% capacitance retention of NiMoO4 and 95.9% capacitance retention of CoMoO4 after 2000 cycles). The results show that the binder-free electrodes constructed by deposition of MMoO4 (M = Ni, Co) nanosheets on carbon cloth are promising candidates for the application of supercapacitors.","corpus_id":206042461,"score":2},{"doc_id":"27430868","title":"High-Performance Supercapacitor Electrode Based on Cobalt Oxide-Manganese Dioxide-Nickel Oxide Ternary 1D Hybrid Nanotubes.","abstract":"We report a facile method to design Co3O4-MnO2-NiO ternary hybrid 1D nanotube arrays for their application as active material for high-performance supercapacitor electrodes. This as-prepared novel supercapacitor electrode can store charge as high as ∼2020 C/g (equivalent specific capacitance ∼2525 F/g) for a potential window of 0.8 V and has long cycle stability (nearly 80% specific capacitance retains after successive 5700 charge/discharge cycles), significantly high Coulombic efficiency, and fast response time (∼0.17s). The remarkable electrochemical performance of this unique electrode material is the outcome of its enormous reaction platform provided by its special nanostructure morphology and conglomeration of the electrochemical properties of three highly redox active materials in a single unit.","corpus_id":206427693,"score":2},{"doc_id":"27451782","title":"Hierarchical NiO Nanoflake Arrays on Nickel Foam as a Supercapacitor Electrode with High Capacitance and High Rate Capability.","abstract":"In this paper, we report a simple and cost-effective method for fabricating hierarchical NiO nanoflake arrays on nickel foam. X-ray diffraction, scanning electron microscope and transmission electron microscope are employed to study the morphology and structure of the as-synthesized NiO materials. Galvanostatic charge/discharge measurements demonstrate that the hierarchical NiO nanocomposite displays excellent capacitive behavior between the potential range of -0.1-0.5 V, and a maximum specific capacitance as high as 823 F g-1 can be achieved at a charge/discharge current density of 4 A g-1, and it only decreases by 20% when the current density increases to 12 A g-1. The remarkable electrochemical performance of this hierarchical NiO nanocomposite indicates the areat application potential in supercapacitors.","corpus_id":23475280,"score":2},{"doc_id":"27714086","title":"1D Ni-Co oxide and sulfide nanoarray/carbon aerogel hybrid nanostructures for asymmetric supercapacitors with high energy density and excellent cycling stability.","abstract":"The fabrication of supercapacitor electrodes with high energy density and excellent cycling stability is still a great challenge. A carbon aerogel, possessing a hierarchical porous structure, high specific surface area and electrical conductivity, is an ideal backbone to support transition metal oxides and bring hope to prepare electrodes with high energy density and excellent cycling stability. Therefore, NiCo2S4 nanotube array/carbon aerogel and NiCo2O4 nanoneedle array/carbon aerogel hybrid supercapacitor electrode materials were synthesized by assembling Ni-Co precursor needle arrays on the surface of the channel walls of hierarchical porous carbon aerogels derived from chitosan in this study. The 1D nanostructures grow on the channel surface of the carbon aerogel vertically and tightly, contributing to the enhanced electrochemical performance with ultrahigh energy density. The energy density of NiCo2S4 nanotube array/carbon aerogel and NiCo2O4 nanoneedle array/carbon aerogel hybrid asymmetric supercapacitors can reach up to 55.3 Wh kg(-1) and 47.5 Wh kg(-1) at a power density of 400 W kg(-1), respectively. These asymmetric devices also displayed excellent cycling stability with a capacitance retention of about 96.6% and 92% over 5000 cycles.","corpus_id":5837498,"score":2},{"doc_id":"27885371","title":"Hierarchical ternary Ni-Co-Se nanowires for high-performance supercapacitor device design.","abstract":"Large-scale uniform Ni-Co-Se bimetallic ternary nanowires have been successfully synthesized through a successive cation exchange. First, NiSe nanowires in situ grown on nickel foam (NF) were prepared by a facile solvothermal route. Next, a series of ternary materials possessing different proportions of Ni and Co were fabricated by a Co-exchange method using the Ni@NiSe material as a template, which effectively achieved morphological inheritance from the parent material. To explore the electrochemical performance, all synthetic materials were assembled into asymmetric supercapacitor devices. Among asymmetric supercapacitor devices, the Ni@Ni0.8Co0.2Se//active carbon (AC) device exhibited a high specific capacitance of 86 F g(-1) at a current density of 1 A g(-1) and excellent cycling stability with virtually no decrease in capacitance after 2000 continuous charge-discharge cycles. This device still delivered an energy density of 17 Wh kg(-1) even at a high power density of 1526.8 W kg(-1). These superior electrochemical properties of Ni@Ni0.8Co0.2Se as an electrode material for supercapacitor devices confirmed the synergistic effect between Co and Ni ions, suggesting their potential application in the field of energy storage.","corpus_id":29464815,"score":2},{"doc_id":"27991753","title":"Three-Dimensional Hierarchical NixCo1-xO/NiyCo2-yP@C Hybrids on Nickel Foam for Excellent Supercapacitors.","abstract":"Active materials and special structures of the electrode have decisive influence on the electrochemical properties of supercapacitors. Herein, three-dimensional (3D) hierarchical NixCo1-xO/NiyCo2-yP@C (denoted as NiCoOP@C) hybrids have been successfully prepared by a phosphorization treatment of hierarchical NixCo1-xO@C grown on nickel foam. The resulting NiCoOP@C hybrids exhibit an outstanding specific capacitance and cycle performance because they couple the merits of the superior cycling stability of NixCo1-xO, the high specific capacitance of NiyCo2-yP, the mechanical stability of carbon layer, and the 3D hierarchical structure. The specific capacitance of 2638 F g(-1) can be obtained at the current density of 1 A g(-1), and even at the current density of 20 A g(-1), the NiCoOP@C electrode still possesses a specific capacitance of 1144 F g(-1). After 3000 cycles at 10 A g(-1), 84% of the initial specific capacitance is still remained. In addition, an asymmetric ultracapacitor (ASC) is assembled through using NiCoOP@C hybrids as anode and activated carbon as cathode. The as-prepared ASC obtains a maximum energy density of 39.4 Wh kg(-1) at a power density of 394 W kg(-1) and still holds 21 Wh kg(-1) at 7500 W kg(-1).","corpus_id":206434634,"score":2},{"doc_id":"28075058","title":"MOF-Derived Hollow Cage Nix Co3-x O4 and Their Synergy with Graphene for Outstanding Supercapacitors.","abstract":"Highly optimized nickel cobalt mixed oxide has been derived from zeolite imidazole frameworks. While the pure cobalt oxide gives only 178.7 F g(-1) as the specific capacitance at a current density of 1 A g(-1) , the optimized Ni:Co 1:1 has given an extremely high and unprecedented specific capacitance of 1931 F g(-1) at a current density of 1 A g(-1) , with a capacitance retention of 69.5% after 5000 cycles in a three electrode test. This optimized Ni:Co 1:1 mixed oxide is further used to make a composite of nickel cobalt mixed oxide/graphene 3D hydrogel for enhancing the electrochemical performance by virtue of a continuous and porous graphene conductive network. The electrode made from GNi:Co 1:1 successfully achieves an even higher specific capacitance of 2870.8 F g(-1) at 1 A g(-1) and also shows a significant improvement in the cyclic stability with 81% capacitance retention after 5000 cycles. An asymmetric supercapacitor is also assembled using a pure graphene 3D hydrogel as the negative electrode and the GNi:Co 1:1 as the positive electrode. With a potential window of 1.5 V and binder free electrodes, the capacitor gives a high specific energy density of 50.2 Wh kg(-1) at a high power density of 750 W kg(-1) .","corpus_id":8944291,"score":2},{"doc_id":"28094497","title":"An Approach To Fabricate PDMS Encapsulated All-Solid-State Advanced Asymmetric Supercapacitor Device with Vertically Aligned Hierarchical Zn-Fe-Co Ternary Oxide Nanowire and Nitrogen Doped Graphene Nanosheet for High Power Device Applications.","abstract":"We highlight the design and fabrication of a polydimethylsiloxane (PDMS) encapsulated advanced all-solid-state asymmetric supercapacitor (ASC) device consisting of hierarchical mesoporous zinc-iron-cobalt ternary oxide (ZICO) nanowire coated nickel (Ni) foam (ZICO@Ni foam) as a promising positive electrode and nitrogen doped graphene coated Ni foam (N-G@Ni foam) as negative electrode in the presence of PVA-KOH gel electrolyte. Owing to outstanding electrochemical behavior and ultrahigh specific capacitance of ZICO (≈ 2587.4 F/g at 1 A/g) and N-G (550 F/g at 1 A/g) along with their mutual synergistic outputs, the assembled all-solid-state ASC device exhibits an outstanding energy density of ≈40.5 Wh/kg accompanied by a remarkable long-term cycle stability with ≈95% specific capacitance retention even after 5000 charge-discharge cycles. The exclusive hierarchical ZICO nanowires were synthesized by a facile two-step process comprising of a hydrothermal protocol followed by an annealing treatment on a quartz substrate. While Zn(2+) gives the stability of the oxide system, Fe and Co ions provide better electronic conductivity and capacitive response under vigorous cyclic condition. The extraordinary performance of as-fabricated ASC device resembles its suitability for the construction of advanced energy storage devices in modern electronic industries.","corpus_id":206435371,"score":2},{"doc_id":"28102378","title":"A high-performance supercapacitor electrode based on tremella-like NiC2O4@NiO core/shell hierarchical nanostructures on nickel foam.","abstract":"Tremella-like nickel oxalate@nickel oxide (NiC2O4@NiO) core/shell hierarchical nanostructures have been successfully synthesized on nickel foam, using Ni foam as a current collector, a Ni source and a three-dimensional (3D) substrate, through a facile hydrothermal method followed by an electrochemical activation process. The prepared samples can be directly used as binder-free electrodes for supercapacitors. The tremella-like morphology, together with the NiC2O4 nanoblocks on 3D Ni foam, significantly increases the amount of active sites for redox reactions and the conductivity of the electrode material, shortens the diffusion pathway for ions, facilitates the effective penetration of the electrolyte, and lowers the intrinsic equivalent series resistance, demonstrating good potential for energy storage application. This material has a high specific capacitance of 2287.09 F g(-1) at 1 A g(-1), a good cycling stability (remaining 95% after 10 000 cycles) and a good rate capability (83.2% retention upon increasing the current density by 10 times).","corpus_id":-1,"score":2},{"doc_id":"28158923","title":"Ultrathin Mesoporous RuCo2 O4 Nanoflakes: An Advanced Electrode for High-Performance Asymmetric Supercapacitors.","abstract":"A new ruthenium cobalt oxide (RuCo2 O4 ) with a unique marigold-like nanostructure and excellent performance as an advanced electrode material has been successfully prepared by a simple electrodeposition (potentiodynamic mode) method. The RuCo2 O4 marigolds consist of numerous clusters of ultrathin mesoporous nanoflakes, leaving a large interspace between them to provide numerous electrochemically active sites. Strikingly, this unique marigold-like nanostructure provided excellent electrochemical performance in terms of high energy-storage capacitance (1469 F g(-1) at 6 A g(-1) ) with excellent rate proficiency and long-lasting operating cycling stability (ca. 91.3 % capacitance retention after 3000 cycles), confirming that the mesoporous nanoflakes participate in the ultrafast electrochemical reactions. Furthermore, an asymmetric supercapacitor was assembled using RuCo2 O4 (positive electrode) and activated carbon (negative electrode) with aqueous KOH electrolyte. The asymmetric design allowed an upgraded potential range of 1.4 V, which further provided a good energy density of 32.6 Wh kg(-1) (1.1 mWh cm(-3) ). More importantly, the cell delivered an energy density of 12.4 Wh kg(-1) even at a maximum power density of 3.2 kW kg(-1) , which is noticeably superior to carbon-based symmetric systems.","corpus_id":41248285,"score":2},{"doc_id":"28463481","title":"Three-Dimensional Cobalt Phosphide Nanowire Arrays as Negative Electrode Material for Flexible Solid-State Asymmetric Supercapacitors.","abstract":"Despite the great progress that has been accomplished in supercapacitors, the imbalance of the development of positive and negative electrode materials still remains a critical issue to achieve high energy density; therefore, exploring high-performance negative electrode materials is highly desirable. In this article, three-dimensional cobalt phosphide (CoP) nanowire arrays were synthesized on a carbon cloth and were utilized as a binder-free supercapacitor negative electrode. The as-synthesized CoP nanowire arrays presented a high capacitance of 571.3 mF/cm(2) at a current density of 1 mA/cm(2). By using CoP nanowire arrays as the negative electrode and MnO2 nanowire arrays as the positive electrode, a flexible solid-state asymmetric supercapacitor has been fabricated and has exhibited excellent electrochemical performance, such as a high energy density of 0.69 mWh/cm(3) and a high power density of 114.2 mW/cm(3). In addition, the solid-state asymmetric supercapacitor shows high cycle stability with 82% capacitance retention after 5000 charge/discharge cycles. This work demonstrates that CoP is a promising negative electrode material for high-performance supercapacitor applications.","corpus_id":206444459,"score":2},{"doc_id":"28521098","title":"Hybrid Reduced Graphene Oxide Nanosheet Supported Mn-Ni-Co Ternary Oxides for Aqueous Asymmetric Supercapacitors.","abstract":"Hybrid reduced graphene oxide (RGO) nanosheet supported Mn-Ni-Co ternary oxides (MNCO) are prepared through a facile coprecipitation reaction with a subsequent calcination process as electrodes for supercapacitors. Electrochemical measurements prove that RGO can significantly improve the supercapacitive behaviors, compared with the pure MNCO electrode. A high specific capacity of 646.1 C g(-1) at 1 A g(-1) can be achieved and about 89.6% of the capacity can be remained at 30 A g(-1) relative to that of the low-current capacity, indicating attractive rate capability of the RGO-MNCO electrode. Moreover, an asymmetric supercapacitor (ASC) device is fabricated with nitrogen-enriched RGO as the negative electrode and the synthesized RGO-MNCO as the positive electrode. Electrochemical performances investigated at different potential range reveal that the ASC device presents excellent capacitive behavior and reversibility. A maximum energy density of 35.6 Wh kg(-1) at power density of 699.9 W kg(-1) can be delivered. Furthermore, stable cycle capability with 100% Coulombic efficiency and 77.2% the capacitance retention is also achieved after 10000 cycles. The achieved outstanding electrochemical properties indicate that the obtained RGO-MNCO electrode materials are fairly ideal for progressive supercapacitors.","corpus_id":206450220,"score":2},{"doc_id":"28561089","title":"Hierarchical core-shell CoMn2O4@MnO2 nanoneedle arrays for high-performance supercapacitors.","abstract":"Hierarchical mesoporous core-shell CoMn2O4@MnO2 nanoneedle arrays on nickel foam have been manufactured via a two-step hydrothermal process. Electrochemical performances of the CoMn2O4@MnO2 nanomaterials have been tested for supercapacitors and demonstrated outstanding properties. The CoMn2O4@MnO2 electrode delivers a specific capacitance of 2126 F g(-1) at a current density of 1 A g(-1) in 2 M KOH aqueous solution and also shows an excellent cycling stability, which retains 94.4% of the initial capacitance after 5000 charge/discharge cycles at a current density of 4 A g(-1). The result confirms the superiority of the CoMn2O4@MnO2 electrode compared with the CoMn2O4 electrode and demonstrates the potential application of the CoMn2O4@MnO2 nanoneedle array electrode for high-performance energy storage device applications.","corpus_id":3381806,"score":2},{"doc_id":"28678249","title":"Interconnected hierarchical NiCo2O4 microspheres as high-performance electrode materials for supercapacitors.","abstract":"Herein, interconnected hierarchical NiCo2O4 microspheres (IH-NiCo2O4) were prepared via a solvothermal method followed by an annealing treatment. IH-NiCo2O4 possesses large tunnels and abundant mesopores, which are in favor of their applications in energy storage field. When employed as an electrode material for supercapacitors, IH-NiCo2O4 exhibits a high specific capacitance of 1822.3 F g(-1) at a current density of 2 A g(-1), an excellent rate property of 68.6% capacity retention at 20 A g(-1), and an 87.6% specific capacitance retention of its initial value after 7000 cycles at a high current density of 10 A g(-1), superior to those of IH-Co3O4. Furthermore, an optimal asymmetric supercapacitor (ASC) was also constructed with IH-NiCo2O4 as the positive electrode and graphene as the negative electrode. The ASC delivers a high energy density of 39.4 Wh kg(-1) at a power density of 800 W kg(-1). Even at a high power density of 8000 W kg(-1), the energy density still reaches 27.2 Wh kg(-1). Moreover, the ASC shows a good cycling stability with 80.1% specific capacitance retention after 5000 cycles at 6 A g(-1). The excellent electrochemical performance of IH-NiCo2O4 makes it a promising electrode material in energy storage field.","corpus_id":3382025,"score":2},{"doc_id":"28772727","title":"Electrodeposited Porous Mn1.5Co1.5O₄/Ni Composite Electrodes for High-Voltage Asymmetric Supercapacitors.","abstract":"Mesoporous Mn1.5Co1.5O₄ (MCO) spinel films were prepared directly on a conductive nickel (Ni) foam substrate via electrodeposition and an annealing treatment as supercapacitor electrodes. The electrodeposition time markedly influenced the surface morphological, textural, and supercapacitive properties of MCO/Ni electrodes. The (MCO/Ni)-15 min electrode (electrodeposition time: 15 min) exhibited the highest capacitance among three electrodes (electrodeposition times of 7.5, 15, and 30 min, respectively). Further, an asymmetric supercapacitor that utilizes (MCO/Ni)-15 min as a positive electrode, a plasma-treated activated carbon (PAC)/Ni electrode as a negative electrode, and carboxymethyl cellulose-lithium nitrate (LiNO₃) gel electrolyte (denoted as (PAC/Ni)//(MCO/Ni)-15 min) was fabricated. In a stable operation window of 2.0 V, the device exhibited an energy density of 27.6 Wh·kg(-1) and a power density of 1.01 kW·kg(-1) at 1 A·g(-1). After 5000 cycles, the specific energy density retention and power density retention were 96% and 92%, respectively, demonstrating exceptional cycling stability. The good supercapacitive performance and excellent stability of the (PAC/Ni)//(MCO/Ni)-15 min device can be ascribed to the hierarchical structure and high surface area of the (MCO/Ni)-15 min electrode, which facilitate lithium ion intercalation and deintercalation at the electrode/electrolyte interface and mitigate volume change during long-term charge/discharge cycling.","corpus_id":1422364,"score":2},{"doc_id":"28914819","title":"Construction of Hierarchical CuO/Cu₂O@NiCo₂S₄ Nanowire Arrays on Copper Foam for High Performance Supercapacitor Electrodes.","abstract":"Hierarchical copper oxide @ ternary nickel cobalt sulfide (CuO/Cu₂O@NiCo₂S₄) core-shell nanowire arrays on Cu foam have been successfully constructed by a facile two-step strategy. Vertically aligned CuO/Cu₂O nanowire arrays are firstly grown on Cu foam by one-step thermal oxidation of Cu foam, followed by electrodeposition of NiCo₂S₄ nanosheets on the surface of CuO/Cu₂O nanowires to form the CuO/Cu₂O@NiCo₂S₄ core-shell nanostructures. Structural and morphological characterizations indicate that the average thickness of the NiCo₂S₄ nanosheets is ~20 nm and the diameter of CuO/Cu₂O core is ~50 nm. Electrochemical properties of the hierarchical composites as integrated binder-free electrodes for supercapacitor were evaluated by various electrochemical methods. The hierarchical composite electrodes could achieve ultrahigh specific capacitance of 3.186 F cm-2 at 10 mA cm-2, good rate capability (82.06% capacitance retention at the current density from 2 to 50 mA cm-2) and excellent cycling stability, with capacitance retention of 96.73% after 2000 cycles at 10 mA cm-2. These results demonstrate the significance of optimized design and fabrication of electrode materials with more sufficient electrolyte-electrode interface, robust structural integrity and fast ion/electron transfer.","corpus_id":10505325,"score":2},{"doc_id":"28948775","title":"Construction of Hierarchical CNT/rGO-Supported MnMoO4 Nanosheets on Ni Foam for High-Performance Aqueous Hybrid Supercapacitors.","abstract":"Rationally designed conductive hierarchical nanostructures are highly desirable for supporting pseudocapacitive materials to achieve high-performance electrodes for supercapacitors. Herein, manganese molybdate nanosheets were hydrothermally grown with graphene oxide (GO) on three-dimensional nickel foam-supported carbon nanotube structures. Under the optimal graphene oxide concentration, the obtained carbon nanotubes/reduced graphene oxide/MnMoO4 composites (CNT/rGO/MnMoO4) as binder-free supercapacitor cathodes perform with a high specific capacitance of 2374.9 F g-1 at the scan rate of 2 mV s-1 and good long-term stability (97.1% of the initial specific capacitance can be maintained after 3000 charge/discharge cycles). The asymmetric device with CNT/rGO/MnMoO4 as the cathode electrode and the carbon nanotubes/activated carbon on nickel foam (CNT-AC) as the anode electrode can deliver an energy density of 59.4 Wh kg-1 at the power density of 1367.9 W kg-1. These superior performances can be attributed to the synergistic effects from each component of the composite electrodes: highly pseudocapacitive MnMoO4 nanosheets and three-dimensional conductive Ni foam/CNTs/rGO networks. These results suggest that the fabricated asymmetric supercapacitor can be a promising candidate for energy storage devices.","corpus_id":206461320,"score":2},{"doc_id":"29111747","title":"Constructing Ultrahigh-Capacity Zinc-Nickel-Cobalt Oxide@Ni(OH)2 Core-Shell Nanowire Arrays for High-Performance Coaxial Fiber-Shaped Asymmetric Supercapacitors.","abstract":"Increased efforts have recently been devoted to developing high-energy-density flexible supercapacitors for their practical applications in portable and wearable electronics. Although high operating voltages have been achieved in fiber-shaped asymmetric supercapacitors (FASCs), low specific capacitance still restricts the further enhancement of their energy density. This article specifies a facile and cost-effective method to directly grow three-dimensionally well-aligned zinc-nickel-cobalt oxide (ZNCO)@Ni(OH)2 nanowire arrays (NWAs) on a carbon nanotube fiber (CNTF) with an ultrahigh specific capacitance of 2847.5 F/cm3 (10.678 F/cm2) at a current density of 1 mA/cm2, These levels are approximately five times higher than those of ZNCO NWAs/CNTF electrodes (2.10 F/cm2) and four times higher than Ni(OH)2/CNTF electrodes (2.55 F/cm2). Benefiting from their unique features, we successfully fabricated a prototype coaxial FASC (CFASC) with a maximum operating voltage of 1.6 V, which was assembled by adopting ZNCO@Ni(OH)2 NWAs/CNTF as the core electrode and a thin layer of carbon coated vanadium nitride (VN@C) NWAs on a carbon nanotube strip (CNTS) as the outer electrode with KOH poly(vinyl alcohol) (PVA) as the gel electrolyte. A high specific capacitance of 94.67 F/cm3 (573.75 mF/cm2) and an exceptional energy density of 33.66 mWh/cm3 (204.02 μWh/cm2) were achieved for our CFASC device, which represent the highest levels of fiber-shaped supercapacitors to date. More importantly, the fiber-shaped ZnO-based photodetector is powered by the integrated CFASC, and it demonstrates excellent sensitivity in detecting UV light. Thus, this work paves the way to the construction of ultrahigh-capacity electrode materials for next-generation wearable energy-storage devices.","corpus_id":206743922,"score":2},{"doc_id":"29211442","title":"Atomic Layer Deposition of Nickel on ZnO Nanowire Arrays for High-Performance Supercapacitors.","abstract":"A novel hybrid core-shell structure of ZnO nanowires (NWs)/Ni as a pseudocapacitor electrode was successfully fabricated by atomic layer deposition of a nickel shell, and its capacitive performance was systemically investigated. Transmission electron microscopy and X-ray photoelectron spectroscopy results indicated that the NiO was formed at the interface between ZnO and Ni where the Ni was oxidized by ZnO during the ALD of the Ni layer. Electrochemical measurement results revealed that the Ti/ZnO NWs/Ni (1500 cycles) electrode with a 30 nm thick Ni-NiO shell layer had the best supercapacitor properties including ultrahigh specific capacitance (∼2440 F g-1), good rate capability (80.5%) under high current charge-discharge conditions, and a relatively better cycling stability (86.7% of the initial value remained after 750 cycles at 10 A g-1). These attractive capacitive behaviors are mainly attributed to the unique core-shell structure and the combined effect of ZnO NW arrays as short charge transfer pathways for ion diffusion and electron transfer as well as conductive Ni serving as channel for the fast electron transport to Ti substrate. This high-performance Ti/ZnO NWs/Ni hybrid structure is expected to be one of a promising electrodes for high-performance supercapacitor applications.","corpus_id":206469562,"score":2},{"doc_id":"29313663","title":"Construction of Core-Shell NiMoO4@Ni-Co-S Nanorods as Advanced Electrodes for High-Performance Asymmetric Supercapacitors.","abstract":"In this work, hierarchical core-shell NiMoO4@Ni-Co-S nanorods were first successfully grown on nickel foam by a facile two-step method to fabricate a bind-free electrode. The well-aligned electrode wrapped by Ni-Co-S nanosheets displays excellent nanostructural properties and outstanding electrochemical performance, owing to the synergistic effects of both nickel molybdenum oxides and nickel cobalt sulfides. The prepared core-shell nanorods in a three-electrode cell yielded a high specific capacitance of 2.27 F cm-2 (1892 F g-1) at a current density of 5 mA cm-2 and retained 91.7% of the specific capacitance even after 6000 cycles. Their electrochemical performance was further investigated for their use as positive electrode for asymmetric supercapacitors. Notably, the energy density of the asymmetric supercapacitor device reached 2.45 mWh cm-3 at a power density of 0.131 W cm-3, and still retained a remarkable 80.3% of the specific capacitance after 3500 cycles. There is great potential for the electrode composed of the core-shell NiMoO4@Ni-Co-S nanorods for use in an all-solid-state asymmetric supercapacitor device.","corpus_id":206475287,"score":2},{"doc_id":"29363699","title":"Hierarchical 3D NiFe2O4@MnO2 core-shell nanosheet arrays on Ni foam for high-performance asymmetric supercapacitors.","abstract":"Hierarchical NiFe2O4@MnO2 core-shell nanosheet arrays (NSAs) were synthesized on Ni foam as an integrated electrode for supercapacitors, using a facile two-step hydrothermal method followed by calcination treatment. The NiFe2O4 nanosheets were designed as the core and ultrathin MnO2 nanoflakes as the shell, creating a unique three-dimensional (3D) hierarchical electrode on Ni foam. The composite electrode exhibited remarkable electrochemical performance with a high specific capacitance of 1391 F g-1 at a current density of 2 mA cm-2 and long cycling stability at a high current density of 10 mA cm-2 (only 11.4% loss after 3000 cycles). Additionally, an asymmetric supercapacitor (ASC) device was fabricated with a NiFe2O4@MnO2 composite as the positive electrode material and activated carbon (AC) as the negative one. The ASC device exhibited a high energy density (45.2 W h kg-1) at a power density of 174 W kg-1, and an excellent cycling stability over 3000 cycles with 92.5% capacitance retention. The remarkable electrochemical performance demonstrated its great potential as a promising candidate for high-performance supercapacitors.","corpus_id":4228098,"score":2},{"doc_id":"29465411","title":"Three-dimensional cotton-like nickel nanowire@Ni-Co hydroxide nanosheet arrays as binder-free electrode for high-performance asymmetric supercapacitor.","abstract":"Three-dimensional (3D) cotton-like Ni-Co layered double hydroxide nanosheet arrays/nickel nanowires (3D Ni-Co LDH/NiNw) were successfully fabricated through a facile chemical bath deposition method. The 3D nickel nanowires are used as a conductive substrate with robust adhesion for high-pseudocapacitance Ni-Co LDH. The 3D Ni-Co LDH/NiNw electrode shows a high areal specific capacitance of 14 F cm-2 at 5 mA cm-2 and quality specific capacitance of 466.6 F g-1 at 0.125 A g-1 with respect to the whole quality of the electrode. The fabricated asymmetric supercapacitor exhibits a remarkable energy density of 0.387 mWh cm-2 using Ni-Co LDH/NiNw as the negative electrode. This high-performance composite electrode presents a new and affordable general approach for supercapacitors.","corpus_id":3923906,"score":2},{"doc_id":"29675973","title":"A Zinc Cobalt Sulfide Nanosheet Array Derived from a 2D Bimetallic Metal-Organic Frameworks for High-Performance Supercapacitors.","abstract":"Porous ternary metal sulfide integrated electrode materials with abundant electroactive sites and redox reactions are very promising for supercapacitors. Herein, a porous zinc cobalt sulfide nanosheet array on Ni foam (Zn-Co-S/NF) was constructed by facile growth of 2D bimetallic zinc/cobalt-based metal-organic framework (Zn/Co-MOF) nanosheets with leaf-like morphology on NF, followed by additional sulfurization. The Zn-Co-S/NF nanosheet array acted directly as a supercapacitor electrode showing much better electrochemical performance (2354.3 F g-1 and 88.6 % retention over 1000 cycles) when compared with zinc cobalt sulfide powder (355.3 F g-1 and 75.8 % retention over 1000 cycles), which originates from good electrical conductivity and mechanical stability, abundant electroactive sites, and facilitated transportation of electrons and electrolyte ions due to the unique nanosheet array structure. An asymmetric supercapacitor (ASC) device assembled from Zn-Co-S/NF and activated carbon electrodes can deliver a highest energy density of 31.9 Wh kg-1 and a maximum power density of 8.5 kW kg-1 . Most importantly, this ASC also shows good cycling stability (71.0 % retention over 10000 cycles). Furthermore, a red LED can be powered by two connected ASCs, and thus as-synthesized Zn-Co-S/NF has great potential for practical applications.","corpus_id":5012559,"score":2},{"doc_id":"29714380","title":"Phosphorization boosts the capacitance of mixed metal nanosheet arrays for high performance supercapacitor electrodes.","abstract":"Binary transition metal phosphides hold immense potential as innovative electrode materials for constructing high-performance energy storage devices. Herein, porous binary nickel-cobalt phosphide (NiCoP) nanosheet arrays anchored on nickel foam (NF) were rationally designed as self-supported binder-free electrodes with high supercapacitance performance. Taking the combined advantages of compositional features and array architectures, the nickel foam supported NiCoP nanosheet array (NiCoP@NF) electrode possesses superior electrochemical performance in comparison with Ni-Co LDH@NF and NiCoO2@NF electrodes. The NiCoP@NF electrode shows an ultrahigh specific capacitance of 2143 F g-1 at 1 A g-1 and retained 1615 F g-1 even at 20 A g-1, showing excellent rate performance. Furthermore, a binder-free all-solid-state asymmetric supercapacitor device is designed, which exhibits a high energy density of 27 W h kg-1 at a power density of 647 W kg-1. The hierarchical binary nickel-cobalt phosphide nanosheet arrays hold great promise as advanced electrode materials for supercapacitors with high electrochemical performance.","corpus_id":14045608,"score":2},{"doc_id":"22435881","title":"3D graphene-cobalt oxide electrode for high-performance supercapacitor and enzymeless glucose detection.","abstract":"Using a simple hydrothermal procedure, cobalt oxide (Co(3)O(4)) nanowires were in situ synthesized on three-dimensional (3D) graphene foam grown by chemical vapor deposition. The structure and morphology of the resulting 3D graphene/Co(3)O(4) composites were characterized by scanning electron microscopy, transmission electron microscopy, X-ray diffraction, and Raman spectroscopy. The 3D graphene/Co(3)O(4) composite was used as the monolithic free-standing electrode for supercapacitor application and for enzymeless electrochemical detection of glucose. We demonstrate that it is capable of delivering high specific capacitance of ∼1100 F g(-1) at a current density of 10 A g(-1) with excellent cycling stability, and it can detect glucose with a ultrahigh sensitivity of 3.39 mA mM(-1) cm(-2) and a remarkable lower detection limit of <25 nM (S/N = 8.5).","corpus_id":207731399,"score":1},{"doc_id":"24488182","title":"High-performance supercapacitor electrodes based on hierarchical Ti@MnO(2) nanowire arrays.","abstract":"Ti nanowire arrays (NAs) prepared by a facile and template-free hydrothermal method were used as three-dimensional (3D) current collectors for the electrodeposition of MnO2. The resulting Ti@MnO2 NAs exhibit remarkable electrochemical behavior with high specific capacitance, good rate performance and desired cycling stability.","corpus_id":262646037,"score":1},{"doc_id":"25133989","title":"One-step electrodeposited nickel cobalt sulfide nanosheet arrays for high-performance asymmetric supercapacitors.","abstract":"A facile one-step electrodeposition method is developed to prepare ternary nickel cobalt sulfide interconnected nanosheet arrays on conductive carbon substrates as electrodes for supercapacitors, resulting in exceptional energy storage performance. Taking advantages of the highly conductive, mesoporous nature of the nanosheets and open framework of the three-dimensional nanoarchitectures, the ternary sulfide electrodes exhibit high specific capacitance (1418 F g(-1) at 5 A g(-1) and 1285 F g(-1) at 100 A g(-1)) with excellent rate capability. An asymmetric supercapacitor fabricated by the ternary sulfide nanosheet arrays as positive electrode and porous graphene film as negative electrode demonstrates outstanding electrochemical performance for practical energy storage applications. Our asymmetric supercapacitors show a high energy density of 60 Wh kg(-1) at a power density of 1.8 kW kg(-1). Even when charging the cell within 4.5 s, the energy density is still as high as 33 Wh kg(-1) at an outstanding power density of 28.8 kW kg(-1) with robust long-term cycling stability up to 50,000 cycles.","corpus_id":28373700,"score":1},{"doc_id":"25322454","title":"CoNi(2)S(4) nanosheet arrays supported on nickel foams with ultrahigh capacitance for aqueous asymmetric supercapacitor applications.","abstract":"We report that CoNi2S4 nanosheet arrays exhibit ultrahigh specific capacitance of 2906 F g(-1) and areal capacitance of 6.39 F cm(-2) at a current density of 5 mA cm(-2), as well as good rate capability and cycling stability, and superior electrochemical performances with an energy density of 33.9 Wh kg(-1) at a power density of 409 W kg(-1) have been achieved in an assembled aqueous asymmetric supercapacitor. The CoNi2S4 nanosheet arrays were in situ grown on nickel foams by a facile two-step hydrothermal method. The formation mechanism of the CoNi2S4 nanosheet arrays was based on an anion-exchange reaction involving the pseudo Kirkendall effect. The two aqueous asymmetric supercapacitors in series using the CoNi2S4 nanosheet arrays as the positive electrodes can power four 3-mm-diameter red-light-emitting diodes. The outstanding supercapacitive performance of CoNi2S4 nanosheet arrays can be attributed to ravine-like nanosheet architectures with good mechanical and electrical contact, low crystallinity and good wettability without an annealing process, rich redox reactions, as well as high conductivity and transport rate for both electrolyte ions and electrons. Our results demonstrate that CoNi2S4 nanosheet arrays are promising electrode materials for supercapacitor applications.","corpus_id":206806124,"score":1},{"doc_id":"25539030","title":"Hydrothermal growth of hierarchical Ni3S2 and Co3S4 on a reduced graphene oxide hydrogel@Ni foam: a high-energy-density aqueous asymmetric supercapacitor.","abstract":"Ni foam@reduced graphene oxide (rGO) hydrogel-Ni3S2 and Ni foam@rGO hydrogel-Co3S4 composites have been successfully synthesized with the aid of a two-step hydrothermal protocol, where the rGO hydrogel is sandwiched between the metal sulfide and Ni foam substrate. Sonochemical deposition of exfoliated rGO on Ni foam with subsequent hydrothermal treatment results in the formation of a rGO-hydrogel-coated Ni foam. Then second-time hydrothermal treatment of the dried Ni@rGO substrate with corresponding metal nitrate and sodium sulfide results in individual uniform growth of porous Ni3S2 nanorods and a Co3S4 self-assembled nanosheet on a Ni@rGO substrate. Both Ni@rGO-Ni3S2 and Ni@rGO-Co3S4 have been electrochemically characterized in a 6 M KOH electrolyte, exhibiting high specific capacitance values of 987.8 and 1369 F/g, respectively, at 1.5 A/g accompanied by the respective outstanding cycle stability of 97.9% and 96.6% at 12 A/g over 3000 charge-discharge cycles. An advanced aqueous asymmetric (AAS) supercapacitor has been fabricated by exploiting the as-prepared Ni@rGO-Co3S4 as a positive electrode and Ni@rGO-Ni3S2 as a negative electrode. The as-fabricated AAS has shown promising energy densities of 55.16 and 24.84 Wh/kg at high power densities of 975 and 13000 W/kg, respectively, along with an excellent cycle stability of 96.2% specific capacitance retention over 3000 charge-discharge cycles at 12 A/g. The enhanced specific capacitance, stupendous cycle stability, elevated energy density, and a power density as an AAS of these electrode materials indicate that it could be a potential candidate in the field of supercapacitors.","corpus_id":206809525,"score":1},{"doc_id":"25801647","title":"MnO2 Nanosheets Grown on Nitrogen-Doped Hollow Carbon Shells as a High-Performance Electrode for Asymmetric Supercapacitors.","abstract":"A hierarchical hollow hybrid composite, namely, MnO2 nanosheets grown on nitrogen-doped hollow carbon shells (NHCSs@MnO2 ), was synthesized by a facile in situ growth process followed by calcination. The composite has a high surface area (251 m(2) g(-1) ) and mesopores (4.5 nm in diameter), which can efficiently facilitate transport during electrochemical cycling. Owing to the synergistic effect of NHCSs and MnO2 , the composite shows a high specific capacitance of 306 F g(-1) , good rate capability, and an excellent cycling stability of 95.2 % after 5000 cycles at a high current density of 8 A g(-1) . More importantly, an asymmetric supercapacitor (ASC) assembled by using NHCSs@MnO2 and activated carbon as the positive and negative electrodes exhibits high specific capacitance (105.5 F g(-1) at 0.5 A g(-1) and 78.5 F g(-1) at 10 A g(-1) ) with excellent rate capability, achieves a maximum energy density of 43.9 Wh kg(-1) at a power density of 408 W kg(-1) , and has high stability, whereby the ASC retains 81.4 % of its initial capacitance at a current density of 5 A g(-1) after 4000 cycles. Therefore, the NHCSs@MnO2 electrode material is a promising candidate for future energy-storage systems.","corpus_id":8943716,"score":1},{"doc_id":"26935179","title":"Hierarchical CuCo2S4 hollow nanoneedle arrays as novel binder-free electrodes for high-performance asymmetric supercapacitors.","abstract":"Hierarchical CuCo2S4 hollow nanoneedle arrays have been firstly synthesized on a Ni foam using a facile template-free hydrothermal method and applied as novel binder-free electrodes for high-performance asymmetric supercapacitors with ultrahigh specific capacitance, high energy density, excellent rate capability and outstanding long-term cycling stability.","corpus_id":31915775,"score":1},{"doc_id":"27551941","title":"Construction of a Hierarchical NiCo2S4@PPy Core-Shell Heterostructure Nanotube Array on Ni Foam for a High-Performance Asymmetric Supercapacitor.","abstract":"In this paper, a hierarchical NiCo2S4@polypyrrole core-shell heterostructure nanotube array on Ni foam (NiCo2S4@PPy/NF) was successfully developed as a bind-free electrode for supercapacitors. NiCo2S4@PPy-50/NF obtained under 50 s PPy electrodeposition shows a low charge-transfer resistance (0.31 Ω) and a high area specific capacitance of 9.781 F/cm(2) at a current density of 5 mA/cm(2), which is two times higher than that of pristine NiCo2S4/NF (4.255 F/cm(2)). Furthermore, an asymmetric supercapacitor was assembled using NiCo2S4@PPy-50/NF as positive electrode and activated carbon (AC) as negative electrode. The resulting NiCo2S4@PPy-50/NF//AC device exhibits a high energy density of 34.62 Wh/kg at a power density of 120.19 W/kg with good cycling performance (80.64% of the initial capacitance retention at 50 mA/cm(2) over 2500 cycles). The superior electrochemical performance can be attributed to the combined contribution of both component and unique core-shell heterostructure. The results demonstrate that the NiCo2S4@PPy-50 core-shell heterostructure nanotube array is promising as electrode material for supercapacitors in energy storage.","corpus_id":21894828,"score":1},{"doc_id":"28485575","title":"Ni0.85Se@MoSe2 Nanosheet Arrays as the Electrode for High-Performance Supercapacitors.","abstract":"In this study, we report novel Ni0.85Se@MoSe2 nanosheet arrays prepared by a facile one-step hydrothermal method through nickel (Ni) foam as Ni precursor and the framework of MoSe2. Owing to the unique interconnection and hierarchical porous nanosheet array architecture, the Ni0.85Se@MoSe2 nanosheet arrays exhibit a high specific capacitance of 774 F g(-1) at the current density of 1 A g(-1), which is almost 2 times higher than that (401 F g(-1)) of the Ni0.85Se matrix and about 7 times greater than that (113 F g(-1)) of the MoSe2 nanoparticles. Moreover, we report an asymmetric supercapacitor (ASC), which is fabricated by using the Ni0.85Se@MoSe2 nanosheet arrays as the positive electrode and the graphene nanosheets (GNS) as the negative electrode, with aqueous KOH as the electrolyte. The Ni0.85Se@MoSe2//GNS ASC possesses an output voltage of 1.6 V, an energy density of 25.5 Wh kg(-1) at a power density of 420 W kg(-1), and a cycling stability of 88% capacitance retention after 5000 cycles. These results indicate that the Ni0.85Se@MoSe2 nanosheet arrays are a good electrode for supercapacitors.","corpus_id":46218126,"score":1},{"doc_id":"28731092","title":"A Ni-P@NiCo LDH core-shell nanorod-decorated nickel foam with enhanced areal specific capacitance for high-performance supercapacitors.","abstract":"Recently, transition metal-based nanomaterials have played a key role in the applications of supercapacitors. In this study, nickel phosphide (Ni-P) was simply combined with NiCo LDH via facile phosphorization of Ni foam and subsequent electrodeposition to form core-shell nanorod arrays on the Ni foam; the Ni-P@NiCo LDH was then directly used for a pseudocapacitive electrode. Owing to the splendid synergistic effect between Ni-P and NiCo LDH nanosheets as well as the hierarchical structure of 1D nanorods, 2D nanosheets, and 3D Ni foam, the hybrid electrode exhibited significantly enhanced electrochemical performances. The Ni-P@NiCo LDH electrode showed a high specific capacitance of 12.9 F cm(-2) at 5 mA cm(-2) (3470.5 F g(-1) at a current density of 1.3 A g(-1)) that remained as high as 6.4 F cm(-2) at a high current density of 100 mA cm(-2) (1700 F g(-1) at 27 A g(-1)) and excellent cycling stability (96% capacity retention after 10 000 cycles at 40 mA cm(-2)). Furthermore, the asymmetric supercapacitors (ASCs) were assembled using Ni-P@NiCo LDH as a positive electrode and activated carbon (AC) as a negative electrode. The obtained ASCs delivered remarkable energy density and power density as well as good cycling performance. The enhanced electrochemical activities open a new avenue for the development of supercapacitors.","corpus_id":20729210,"score":1},{"doc_id":"28749370","title":"Hierarchical nanosheet-based Ni3S2 microspheres grown on Ni foam for high-performance all-solid-state asymmetric supercapacitors.","abstract":"The hierarchical nanosheet-based Ni3S2 microspheres directly grew on Ni foam using a two-step hydrothermal method. The microsphere with a diameter of ~1 microns and a rough surface was well connected with each other without any binders to provide a larger specific surface area, shorter ion/electron diffusion paths, richer electroactive sites as a supercapacitor electrode. As a three-electrode supercapacitor, it delivers the high specific capacity of 981.8 F g-1 at 2 A g-1, excellent rate capability of 436.4 F g-1 at 12 A g-1, and good cycling stability of 950.9 F g-1 with 96.9% retention after 1000 cycles at 2 A g-1. Furthermore, asymmetric supercapacitor based on Ni3S2-microsphere as a positive electrode and active carbon as a negative electrode shows the high energy density of 29.4 Wh kg-1 at 324.5 W kg-1 and high power density of 3197.6 W kg-1 at 15.1 Wh kg-1. This work demonstrates that nanosheet-based Ni3S2 microspheres coated Ni foam can be an effective electrode for a real supercapacitor.","corpus_id":206086182,"score":1},{"doc_id":"28857459","title":"Cobalt Doping To Boost the Electrochemical Properties of Ni@Ni3 S2 Nanowire Films for High-Performance Supercapacitors.","abstract":"Metal sulfides have aroused great interest for energy storage. However, their low specific capacities and inferior rate capabilities hinder their practical applications. In this work, a facile cobalt-doping process is used to boost the electrochemical performance of Ni@Ni3 S2 core-sheath nanowire film electrodes for high-performance electrochemical energy storage. Co ions are doped successfully and uniformly into Ni3 S2 nanosheets through a facile ion-exchange process. The electrochemical properties of film electrodes are improved greatly, and an ultrahigh volumetric capacity (increased from 105 to 730 C cm-3 at 0.25 A cm-3 ) and excellent rate capability are obtained after Co is doped into Ni@Ni3 S2 core-sheath nanowires. A hybrid asymmetric supercapacitor with Co-doped Ni@Ni3 S2 as the positive electrode and graphene-carbon nanotubes as the negative electrode is assembled and exhibits an ultrahigh volumetric capacitance of 142 F cm-3 (based on the total volume of both electrodes) at 0.5 A cm-3 and excellent cycling stability (only 3 % capacitance decrease after 5000 cycles). Moreover, the volumetric energy density can reach 44.5 mWh cm-3 , which is much larger than those of thin-film lithium batteries (1-10 mWh cm-3 ). These results may provide useful insights for the fabrication of high-performance film electrodes for energy-storage applications.","corpus_id":25925177,"score":1},{"doc_id":"29408138","title":"Microwave synthesis of three-dimensional nickel cobalt sulfide nanosheets grown on nickel foam for high-performance asymmetric supercapacitors.","abstract":"A facile and cost-effective microwave method is developed to prepare ternary nickel cobalt sulfide (NiCo2S4) interconnected nanosheet arrays on nickel foam (NF). When acting as an electrochemical supercapacitor electrode material, the as-prepared NiCo2S4/NF shows a high specific capacitance of 1502 F g-1 at a current density of 1 A g-1, and outstanding cycling stability of 91% capacitance retention after 8000 cycles. In addition, a asymmetric supercapacitor (ASC) is composed of NiCo2S4/NF as positive electrode and activated carbon as negative electrode, which exhibits a high energy density of 34.7 W h kg-1 at a power density of 750 W kg-1 and long-term cyclic stability (83.7% capacity retention after 8000 cycles). Even at a high power density of 15 kW kg-1, it still remains an energy density of 17.9 W h kg-1, which is able to light up a light-emitting diode. These findings provide a new and facile approach to fabricate high-performance electrode for supercapacitors.","corpus_id":3547848,"score":1},{"doc_id":"29431782","title":"A metal-organic framework derived hierarchical nickel-cobalt sulfide nanosheet array on Ni foam with enhanced electrochemical performance for supercapacitors.","abstract":"Metal-organic frameworks (MOFs) have emerged as a new platform for the construction of various functional materials for energy related applications. Here, a facile MOF templating method is developed to fabricate a hierarchical nickel-cobalt sulfide nanosheet array on conductive Ni foam (Ni-Co-S/NF) as a binder-free electrode for supercapacitors. A uniform 2D Co-MOF nanowall array is first grown in situ on Ni foam in aqueous solution at room temperature, and then the Co-MOF nanowalls are converted into hierarchical Ni-Co-S nanoarchitectures via an etching and ion-exchange reaction with Ni(NO3)2, and a subsequent solvothermal sulfurization. Taking advantage of the compositional and structural merits of the hierarchical Ni-Co-S nanosheet array and conductive Ni foam, such as fast electron transportation, short ion diffusion path, abundant active sites and rich redox reactions, the obtained Ni-Co-S/NF electrode exhibits excellent electrochemical capacitive performance (1406.9 F g-1 at 0.5 A g-1, 53.9% retention at 10 A g-1 and 88.6% retention over 1000 cycles), which is superior to control CoS/NF. An asymmetric supercapacitor (ASC) assembled by using the as-fabricated Ni-Co-S/NF as the positive electrode and activated carbon (AC) as the negative electrode delivers a high energy density of 24.8 W h kg-1 at a high power density of 849.5 W kg-1. Even when the power density is as high as 8.5 kW kg-1, the ASC still exhibits a high energy density of 12.5 W h kg-1. This facile synthetic strategy can also be extended to fabricate other hierarchical integrated electrodes for high-efficiency electrochemical energy conversion and storage devices.","corpus_id":4229922,"score":1},{"doc_id":"29745016","title":"Fabrication of a 3D Hierarchical Sandwich Co9 S8 /α-MnS@N-C@MoS2 Nanowire Architectures as Advanced Electrode Material for High Performance Hybrid Supercapacitors.","abstract":"Supercapacitors suffer from lack of energy density and impulse the energy density limit, so a new class of hybrid electrode materials with promising architectures is strongly desirable. Here, the rational design of a 3D hierarchical sandwich Co9 S8 /α-MnS@N-C@MoS2 nanowire architecture is achieved during the hydrothermal sulphurization reaction by the conversion of binary mesoporous metal oxide core to corresponding individual metal sulphides core along with the formation of outer metal sulphide shell at the same time. Benefiting from the 3D hierarchical sandwich architecture, Co9 S8 /α-MnS@N-C@MoS2 electrode exhibits enhanced electrochemical performance with high specific capacity/capacitance of 306 mA h g-1 /1938 F g-1 at 1 A g-1 , and excellent cycling stability with a specific capacity retention of 86.9% after 10 000 cycles at 10 A g-1 . Moreover, the fabricated asymmetric supercapacitor device using Co9 S8 /α-MnS@N-C@MoS2 as the positive electrode and nitrogen doped graphene as the negative electrode demonstrates high energy density of 64.2 Wh kg-1 at 729.2 W kg-1 , and a promising energy density of 23.5 Wh kg-1 is still attained at a high power density of 11 300 W kg-1 . The hybrid electrode with 3D hierarchical sandwich architecture promotes enhanced energy density with excellent cyclic stability for energy storage.","corpus_id":13699361,"score":1}],"string":"[\n {\n \"doc_id\": \"23076678\",\n \"title\": \"Enhancing electrochemical reaction sites in nickel-cobalt layered double hydroxides on zinc tin oxide nanowires: a hybrid material for an asymmetric supercapacitor device.\",\n \"abstract\": \"Conducting nanowires are of particular interest in energy-related research on devices such as supercapacitors, batteries, water splitting electrodes and solar cells. Their direct electrode/current collector contact and highly conductive 1D structure enable conducting nanowires to provide ultrafast charge transportation. In this paper, we report the facile synthesis of nickel cobalt layered double hydroxides (LDHs) on conducting Zn(2)SnO(4) (ZTO) and the application of this material to a supercapacitor. This study also presents the first report of an enhancement of the active faradic reaction sites (electroactive sites) resulting from the heterostructure. This novel material demonstrates outstanding electrochemical performance with a high specific capacitance of 1805 F g(-1) at 0.5 A g(-1), and an excellent rate performance of 1275 F g(-1) can be achieved at 100 A g(-1). Furthermore, an asymmetric supercapacitor was successfully fabricated using active carbon as a negative electrode. This asymmetric device exhibits a high energy density of 23.7 W h kg(-1) at a power density of 284.2 W kg(-1). Meanwhile, a high power density of 5817.2 W kg(-1) can be achieved at an energy density of 9.7 W h kg(-1). More importantly, this device exhibits long-term cycling stability, with 92.7% capacity retention after 5000 cycles.\",\n \"corpus_id\": 205828027,\n \"score\": 2\n },\n {\n \"doc_id\": \"23169236\",\n \"title\": \"Hierarchical NiCo2O4@MnO2 core-shell heterostructured nanowire arrays on Ni foam as high-performance supercapacitor electrodes.\",\n \"abstract\": \"An advanced integrated electrode for high-performance supercapacitors has been designed by growing hierarchical NiCo(2)O(4)@MnO(2) core-shell heterostructured nanowire arrays on nickel foam. Such unique array nanoarchitectures exhibit remarkable electrochemical performance with high capacitance and desirable cycle life at high rates.\",\n \"corpus_id\": 20114703,\n \"score\": 2\n },\n {\n \"doc_id\": \"23570565\",\n \"title\": \"Construction of high-capacitance 3D CoO@polypyrrole nanowire array electrode for aqueous asymmetric supercapacitor.\",\n \"abstract\": \"We have developed a supercapacitor electrode composed of well-aligned CoO nanowire array grown on 3D nickel foam with polypyrrole (PPy) uniformly immobilized onto or firmly anchored to each nanowire surface to boost the pseudocapacitive performance. The electrode architecture takes advantage of the high electrochemical activity from both the CoO and PPy, the high electronic conductivity of PPy, and the short ion diffusion pathway in ordered mesoporous nanowires. These merits together with the elegant synergy between CoO and PPy lead to a high specific capacitance of 2223 F g(-1) approaching the theoretical value, good rate capability, and cycling stability (99.8% capacitance retention after 2000 cycles). An aqueous asymmetric supercapacitor device with a maximum voltage of 1.8 V fabricated by using our hybrid array as the positive electrode and activated carbon film as the negative electrode has demonstrated high energy density (~43.5 Wh kg(-1)), high power density (~5500 W kg(-1) at 11.8 Wh kg(-1)) and outstanding cycleability (~20,000 times). After charging for only ~10 s, two such 4 cm(2) asymmetric supercapacitors connected in series can efficiently power 5 mm diameter red, yellow, and green round LED indicators (lasting for 1 h for red LED) and drive a mini 130 rotation-motor robustly.\",\n \"corpus_id\": 5100836,\n \"score\": 2\n },\n {\n \"doc_id\": \"23650047\",\n \"title\": \"Intertwined nanocarbon and manganese oxide hybrid foam for high-energy supercapacitors.\",\n \"abstract\": \"Rapid charging and discharging supercapacitors are promising alternative energy storage systems for applications such as portable electronics and electric vehicles. Integration of pseudocapacitive metal oxides with single-structured materials has received a lot of attention recently due to their superior electrochemical performance. In order to realize high energy-density supercapacitors, a simple and scalable method is developed to fabricate a graphene/MWNT/MnO2 nanowire (GMM) hybrid nanostructured foam, via a two-step process. The 3D few-layer graphene/MWNT (GM) architecture is grown on foamed metal foils (nickel foam) via ambient pressure chemical vapor deposition. Hydrothermally synthesized α-MnO2 nanowires are conformally coated onto the GM foam by a simple bath deposition. The as-prepared hierarchical GMM foam yields a monographical graphene foam conformally covered with an intertwined, densely packed CNT/MnO2 nanowire nanocomposite network. Symmetrical electrochemical capacitors (ECs) based on GMM foam electrodes show an extended operational voltage window of 1.6 V in aqueous electrolyte. A superior energy density of 391.7 Wh kg(-1) is obtained for the supercapacitor based on the GMM foam, which is much higher than ECs based on GM foam only (39.72 Wh kg(-1) ). A high specific capacitance (1108.79 F g(-1) ) and power density (799.84 kW kg(-1) ) are also achieved. Moreover, the great capacitance retention (97.94%) after 13 000 charge-discharge cycles and high current handability demonstrate the high stability of the electrodes of the supercapacitor. These excellent performances enable the innovative 3D hierarchical GMM foam to serve as EC electrodes, resulting in energy-storage devices with high stability and power density in neutral aqueous electrolyte.\",\n \"corpus_id\": 25684899,\n \"score\": 2\n },\n {\n \"doc_id\": \"23864110\",\n \"title\": \"High energy density asymmetric supercapacitors with a nickel oxide nanoflake cathode and a 3D reduced graphene oxide anode.\",\n \"abstract\": \"Here we demonstrate a high energy density asymmetric supercapacitor with nickel oxide nanoflake arrays as the cathode and reduced graphene oxide as the anode. Nickel oxide nanoflake arrays were synthesized on a flexible carbon cloth substrate using a seed-mediated hydrothermal method. The reduced graphene oxide sheets were deposited on three-dimensional (3D) nickel foam by hydrothermal treatment of nickel foam in graphene oxide solution. The nanostructured electrodes provide a large effective surface area. The asymmetric supercapacitor device operates with a voltage of 1.7 V and achieved a remarkable areal capacitance of 248 mF cm(-2) (specific capacitance of 50 F g(-1)) at a charge/discharge current density of 1 mA cm(-2) and a maximum energy density of 39.9 W h kg(-1) (based on the total mass of active materials of 5.0 mg). Furthermore, the device showed an excellent charge/discharge cycling performance in 1.0 M KOH electrolyte at a current density of 5 mA cm(-2), with a capacitance retention of 95% after 3000 cycles.\",\n \"corpus_id\": 30627013,\n \"score\": 2\n },\n {\n \"doc_id\": \"23969779\",\n \"title\": \"High-performance supercapacitor and lithium-ion battery based on 3D hierarchical NH4F-induced nickel cobaltate nanosheet-nanowire cluster arrays as self-supported electrodes.\",\n \"abstract\": \"A facile hydrothermal method is developed for large-scale production of three-dimensional (3D) hierarchical porous nickel cobaltate nanowire cluster arrays derived from nanosheet arrays with robust adhesion on Ni foam. Based on the morphology evolution upon reaction time, a possible formation process is proposed. The role of NH4F in formation of the structure has also been investigated based on different NH4F amounts. This unique structure significantly enhances the electroactive surface areas of the NiCo2O4 arrays, leading to better interfacial/chemical distributions at the nanoscale, fast ion and electron transfer and good strain accommodation. Thus, when it is used for supercapacitor testing, a specific capacitance of 1069 F g(-1) at a very high current density of 100 A g(-1) was obtained. Even after more than 10,000 cycles at various large current densities, a capacitance of 2000 F g(-1) at 10 A g(-1) with 93.8% retention can be achieved. It also exhibits a high-power density (26.1 kW kg(-1)) at a discharge current density of 80 A g(-1). When used as an anode material for lithium-ion batteries (LIBs), it presents a high reversible capacity of 976 mA h g(-1) at a rate of 200 mA g(-1) with good cycling stability and rate capability. This array material is rarely used as an anode material. Our results show that this unique 3D hierarchical porous nickel cobaltite is promising for electrochemical energy applications.\",\n \"corpus_id\": 205869504,\n \"score\": 2\n },\n {\n \"doc_id\": \"24050440\",\n \"title\": \"New energy storage option: toward ZnCo2O4 nanorods/nickel foam architectures for high-performance supercapacitors.\",\n \"abstract\": \"Hierarchical ZnCo2O4/nickel foam architectures were first fabricated from a simple scalable solution approach, exhibiting outstanding electrochemical performance in supercapacitors with high specific capacitance (∼1400 F g(-1) at 1 A g(-1)), excellent rate capability (72.5% capacity retention at 20 A g(-1)), and good cycling stability (only 3% loss after 1000 cycles at 6 A g(-1)). All-solid-state supercapacitors were also fabricated by assembling two pieces of the ZnCo2O4-based electrodes, showing superior performance in terms of high specific capacitance and long cycling stability. Our work confirms that the as-prepared architectures can not only be applied in high energy density fields, but also be used in high power density applications, such as electric vehicles, flexible electronics, and energy storage devices.\",\n \"corpus_id\": 206784362,\n \"score\": 2\n },\n {\n \"doc_id\": \"24429842\",\n \"title\": \"Superior asymmetric supercapacitor based on Ni-Co oxide nanosheets and carbon nanorods.\",\n \"abstract\": \"Nickel and cobalt (Ni-Co) binary oxide nanosheets with mesoporous structure are prepared by a facile approach based on the formation and disassociation of nickel/cobalt-citrate complex, and they show an ultra-high Faradaic capacitance up to 1846 F g(-1) and excellent rate capability. On this basic, advanced aqueous asymmetric supercapacitors (AASs) are successfully built by using the Ni-Co oxide as the positive electrode and three kinds of activated carbons respectively as the negative electrode. As-made AASs are able to work reversibly in a full operated voltage region of 0-1.6 V and exhibit outstanding electrochemical performance. Among them, activated polyaniline-derived carbon (APDC)//Ni-Co oxide AASs shows the highest specific capacitance of 202 F g(-1), the maximum energy density of 71.7 Wh kg(-1), and superior combination of high energy and power density (a energy density of 41.6 Wh kg(-1) at a high power density of 16 kW kg(-1)).\",\n \"corpus_id\": 451102,\n \"score\": 2\n },\n {\n \"doc_id\": \"24562602\",\n \"title\": \"Surfactant dependent self-organization of Co3O4 nanowires on Ni foam for high performance supercapacitors: from nanowire microspheres to nanowire paddy fields.\",\n \"abstract\": \"Different surfactants were used in a typical hydrothermal process for controlling the morphology of the Co3O4 nanowire superstructure on Ni foam. It is easy for the Co3O4 nanowires to self-organize into nanowire microspheres on Ni foam in the absence of surfactants. And the nanowire microspheres gradually unfold into nanowire paddy fields with the addition of nonionic, cationic and anionic surfactants, respectively. The results of BET and electrochemical measurements show that the specific surface area and capacitance first decrease and then increase with the change in the Co3O4 superstructure morphology. Among these electrodes, the Co3O4 electrode with paddy like nanowires shows an outstanding specific capacitance of 1217.4 F g(-1) and areal specific capacitance as high as 6087 mF cm(-2) at 0.7 A g(-1) with high mass loading (5 mg cm(-2)), good power capability (showing a high specific capacitance of 835.1 F g(-1) (4176 mF cm(-2)) at 5 A g(-1)), excellent cycling stability and high columbic efficiency (∼100%). This exceptional performance is benefited from the almost monodispersed nanowire morphology and high specific surface area (121.4 m(2) g(-1)). At the same time, the asymmetric supercapacitor, employing the Co3O4 electrode with paddy-like nanowires as the positive electrode and the activated carbon electrode as the negative electrode, was successfully assembled. It shows a high specific energy and good long-term electrochemical stability. All these impressive results demonstrate that the Co3O4 electrode with paddy-like nanowires is promising for practical applications in supercapacitors.\",\n \"corpus_id\": 6453350,\n \"score\": 2\n },\n {\n \"doc_id\": \"24643977\",\n \"title\": \"3D carbon/cobalt-nickel mixed-oxide hybrid nanostructured arrays for asymmetric supercapacitors.\",\n \"abstract\": \"The electrochemical performance of supercapacitors relies not only on the exploitation of high-capacity active materials, but also on the rational design of superior electrode architectures. Herein, a novel supercapacitor electrode comprising 3D hierarchical mixed-oxide nanostructured arrays (NAs) of C/CoNi3 O4 is reported. The network-like C/CoNi3 O4 NAs exhibit a relatively high specific surface area; it is fabricated from ultra-robust Co-Ni hydroxide carbonate precursors through glucose-coating and calcination processes. Thanks to their interconnected three-dimensionally arrayed architecture and mesoporous nature, the C/CoNi3 O4 NA electrode exhibits a large specific capacitance of 1299 F/g and a superior rate performance, demonstrating 78% capacity retention even when the discharge current jumps by 100 times. An optimized asymmetric supercapacitor with the C/CoNi3 O4 NAs as the positive electrode is fabricated. This asymmetric supercapacitor can reversibly cycle at a high potential of 1.8 V, showing excellent cycling durability and also enabling a remarkable power density of ∼13 kW/kg with a high energy density of ∼19.2 W·h/kg. Two such supercapacitors linked in series can simultaneously power four distinct light-emitting diode indicators; they can also drive the motor of remote-controlled model planes. This work not only presents the potential of C/CoNi3 O4 NAs in thin-film supercapacitor applications, but it also demonstrates the superiority of electrodes with such a 3D hierarchical architecture.\",\n \"corpus_id\": 11914388,\n \"score\": 2\n },\n {\n \"doc_id\": \"24661431\",\n \"title\": \"Hierarchical mesoporous nickel cobaltite nanoneedle/carbon cloth arrays as superior flexible electrodes for supercapacitors.\",\n \"abstract\": \"Hierarchical mesoporous NiCo2O4 nanoneedle arrays on carbon cloth have been fabricated by a simple hydrothermal approach combined with a post-annealing treatment. Such unique array nanoarchitectures exhibit remarkable electrochemical performance with high capacitance and desirable cycle life at high rates. When evaluated as an electrode material for supercapacitors, the NiCo2O4 nanoneedle arrays supported on carbon cloth was able to deliver high specific capacitance of 660 F g-1 at current densities of 2 A g-1 in 2 M KOH aqueous solution. In addition, the composite electrode shows excellent mechanical behavior and long-term cyclic stability (91.8% capacitance retention after 3,000 cycles). The fabrication method presented here is facile, cost-effective, and scalable, which may open a new pathway for real device applications.\",\n \"corpus_id\": 18948582,\n \"score\": 2\n },\n {\n \"doc_id\": \"24771534\",\n \"title\": \"Hierarchically porous nickel oxide nanosheets grown on nickel foam prepared by one-step in situ anodization for high-performance supercapacitors.\",\n \"abstract\": \"Porous NiO nanosheets are successfully grown on nickel foam substrate through an in situ anodization by using molten KOH as the electrolyte. High-purity NiO is directly obtained by this one-step method without any subsequent treatment. The obtained NiO supported on nickel foam is used as a binder-free electrode for a supercapacitor and its pseudocapacitive behavior has been investigated by cyclic voltammetry and galvanostatic charge-discharge tests in a 6 M aqueous solution of KOH. Electrochemical data demonstrates that this binder-free electrode possesses ultrahigh capacitance (4.74 F cm(-2) at 4 mA cm(-2)), excellent rate capability, and cycling stability. After 1000 cycles, the areal capacitance value is 9.4 % lower than the initial value and maintains 85.4 % of the maximum capacitance value.\",\n \"corpus_id\": 7857480,\n \"score\": 2\n },\n {\n \"doc_id\": \"25110896\",\n \"title\": \"Fabrication of nickel-foam-supported layered zinc-cobalt hydroxide nanoflakes for high electrochemical performance in supercapacitors.\",\n \"abstract\": \"Nickel foam supported Zn-Co hydroxide nanoflakes were fabricated by a facile solvothermal method. Benefited from the unique structure of Zn-Co hydroxide nanoflakes on a nickel foam substrate, the as prepared materials exhibited an excellent specific capacitance of 901 F g(-1) at 5 A g(-1) and remarkable cycling stability as electrode materials in supercapacitors.\",\n \"corpus_id\": 8818190,\n \"score\": 2\n },\n {\n \"doc_id\": \"25247606\",\n \"title\": \"Spinel manganese-nickel-cobalt ternary oxide nanowire array for high-performance electrochemical capacitor applications.\",\n \"abstract\": \"Aligned spinel Mn-Ni-Co ternary oxide (MNCO) nanowires are synthesized by a facile hydrothermal method. As an electrode of supercapacitors, the MNCO nanowire array on nickel foam shows an outstanding specific capacitance of 638 F g(-1) at 1 A g(-1) and excellent cycling stability. This exceptional performance benefits from its nanowire architecture, which can provide large reaction surface area, fast ion and electron transfer, and good structural stability. Furthermore, an asymmetric supercapacitor (ASC) with high energy density is assembled successfully by employing the MNCO nanowire array as positive electrode and carbon black as negative electrode. The excellent electrochemical performances indicate the promising potential application of the ASC device in the energy storage field.\",\n \"corpus_id\": 20839409,\n \"score\": 2\n },\n {\n \"doc_id\": \"25258611\",\n \"title\": \"High-performance binder-free supercapacitor electrode by direct growth of cobalt-manganese composite oxide nansostructures on nickel foam.\",\n \"abstract\": \"A facile approach composed of hydrothermal process and annealing treatment is proposed to directly grow cobalt-manganese composite oxide ((Co,Mn)3O4) nanostructures on three-dimensional (3D) conductive nickel (Ni) foam for a supercapacitor electrode. The as-fabricated porous electrode exhibits excellent rate capability and high specific capacitance of 840.2 F g(-1) at the current density of 10 A g(-1), and the electrode also shows excellent cycling performance, which retains 102% of its initial discharge capacitance after 7,000 cycles. The fabricated binder-free hierarchical composite electrode with superior electrochemical performance is a promising candidate for high-performance supercapacitors.\",\n \"corpus_id\": 14987088,\n \"score\": 2\n },\n {\n \"doc_id\": \"26063601\",\n \"title\": \"Mesoporous ZnCo2O4 nanoflakes grown on nickel foam as electrodes for high performance supercapacitors.\",\n \"abstract\": \"ZnCo2O4 nanoflakes, as electrodes for supercapacitors, are grown on a cellular nickel foam using a cost-effective hydrothermal procedure. The mesoporous ZnCo2O4 nanoflakes have large electroactive surface areas with strong adhesion to the Ni foam, allowing fast ion and electron transport. The nanoarchitecture electrodes deliver an excellent specific capacitance of 1220 F g(-1) at a current density of 2 A g(-1) in a 2 M KOH aqueous solution and a long-term cyclic stability of 94.2% capacitance retention after 5000 cycles. The fabrication strategy is facile, cost-effective, and can offer great promise for large-scale supercapacitor applications.\",\n \"corpus_id\": 19385816,\n \"score\": 2\n },\n {\n \"doc_id\": \"26372533\",\n \"title\": \"Three-Dimensional NiCo2O4@Polypyrrole Coaxial Nanowire Arrays on Carbon Textiles for High-Performance Flexible Asymmetric Solid-State Supercapacitor.\",\n \"abstract\": \"In this article, we report a novel electrode of NiCo2O4 nanowire arrays (NWAs) on carbon textiles with a polypyrrole (PPy) nanosphere shell layer to enhance the pseudocapacitive performance. The merits of highly conductive PPy and short ion transport channels in ordered NiCo2O4 mesoporous nanowire arrays together with the synergistic effect between NiCo2O4 and PPy result in a high specific capacitance of 2244 F g(-1), excellent rate capability, and cycling stability in NiCo2O4/PPy electrode. Moreover, a lightweight and flexible asymmetric supercapacitor (ASC) device is successfully assembled using the hybrid NiCo2O4@PPy NWAs and activated carbon (AC) as electrodes, achieving high energy density (58.8 W h kg(-1) at 365 W kg(-1)), outstanding power density (10.2 kW kg(-1) at 28.4 W h kg(-1)) and excellent cycling stability (∼89.2% retention after 5000 cycles), as well as high flexibility. The three-dimensional coaxial architecture design opens up new opportunities to fabricate a high-performance flexible supercapacitor for future portable and wearable electronic devices.\",\n \"corpus_id\": 206399613,\n \"score\": 2\n },\n {\n \"doc_id\": \"26465975\",\n \"title\": \"Rational Synthesis of Branched CoMoO4@CoNiO2 Core/Shell Nanowire Arrays for All-Solid-State Supercapacitors with Improved Performance.\",\n \"abstract\": \"Effectively composite materials with optimized structures exhibited promising potential in continuing improving the electrochemical performances of supercapacitors in the past few years. Here, we proposed a rational design of branched CoMoO4@CoNiO2 core/shell nanowire arrays on Ni foam by two steps of hydrothermal processing. Owing to the high activity of the scaffold-like CoMoO4 nanowires and the well-defined CoNiO2 nanoneedles, the three-dimensional (3D) electrode architectures achieved remarkable electrochemical performances with high areal specific capacitance (5.31 F/cm(2) at 5 mA/cm(2)) and superior cycling stability(159% of the original specific capacitance, i.e., 95.7% of the maximum retained after 5000 cycles at 30 mA/cm(2)). The all-solid-state asymmetric supercapacitors composed of such electrode and activated carbon (AC) exhibited an areal specific capacitance of 1.54 F/cm(2) at 10 mA/cm(2) and a rate capability (59.75 Wh/kg at a 1464 W/kg) comparable with Li-ion batteries. It also showed an excellent cycling stability with no capacitance attenuation after 50000 cycles at 100 mA/cm(2). After rapid charging (1 s), such supercapacitors in series could lighten a red LED for a long time and drive a mini motor effectively, demonstrating advances in energy storage, scalable integrated applications, and promising commercial potential.\",\n \"corpus_id\": 206403319,\n \"score\": 2\n },\n {\n \"doc_id\": \"26608410\",\n \"title\": \"Hierarchical structures composed of MnCo2O4@MnO2 core-shell nanowire arrays with enhanced supercapacitor properties.\",\n \"abstract\": \"In this paper, hierarchical MnCo2O4@MnO2 core-shell nanowire arrays (MnCo2O4@MnO2 NWAs) with mesoporous and large surface area are synthesized on 3D nickel foam via a facile, two-step hydrothermal approach without any adscititious surfactant and binder. The electrode architecture takes advantage of the synergistic effects contributed from both the porous MnCo2O4 nanowire core and the MnO2 shell layer. The fabricated MnCo2O4@MnO2 NWA electrode for supercapacitors in aqueous electrolyte exhibits a significantly enhanced specific capacitance (858 F g(-1) at 1 A g(-1)), high energy density (36.0 Wh kg(-1) at 252 W kg(-1)) and long-life cycling stability (retaining 88% of the initial capacitance after 5000 cycles). Then, a symmetrical supercapacitor is fabricated by assembling two MnCo2O4@MnO2 NWA-based electrodes, which shows a high specific capacitance of 678 F g(-1) at 1 A g(-1) and a high energy density of 135.6 Wh kg(-1) at 513 W kg(-1). Thereby, the hierarchical core-shell MnCo2O4@MnO2 NWAs are very promising as next generation high-performance long-life cycling supercapacitors.\",\n \"corpus_id\": 43058294,\n \"score\": 2\n },\n {\n \"doc_id\": \"26742692\",\n \"title\": \"Nickel Cobalt Hydroxide @Reduced Graphene Oxide Hybrid Nanolayers for High Performance Asymmetric Supercapacitors with Remarkable Cycling Stability.\",\n \"abstract\": \"Nanolayered structures present significantly enhanced electrochemical performance by facilitating the surface-dependent electrochemical reaction processes for supercapacitors, which, however, causes capacitance fade upon cycling due to their poor chemical stability. In this work, we report a simple and effective approach to develop a stable, high performance electrode material by integrating 2D transition metal hydroxide and reduced graphene oxide sheets at nanometer scale. Specifically, a hybrid nanolayer of Ni-Co hydroxide @reduced graphene oxide (Ni,Co-OH/rGO) with an average thickness of 1.37 nm is synthesized through an easy one-pot hydrothermal method. Benefiting from the face to face contact model between Ni-Co hydroxide and rGO sheets, such unique structure presents superior specific capacitance and cycling performance as compared to the pure Ni-Co hydroxide nanolayers. An asymmetric supercapacitor based on Ni,Co-OH/rGO and three-dimensional (3D) hierarchical porous carbon is developed, exhibiting a high energy density of 56.1 Wh kg(-1) along with remarkable cycling stability (80% retention after 17 000 cycles), which holds great promise for practical applications in energy storage devices.\",\n \"corpus_id\": 206409199,\n \"score\": 2\n },\n {\n \"doc_id\": \"27253880\",\n \"title\": \"Activated Microporous Carbon Derived from Almond Shells for High Energy Density Asymmetric Supercapacitors.\",\n \"abstract\": \"Via the activation treatment of carbonized almond shells with HNO3 and KOH, activated microporous carbon (AMC-3 and AMC-2) was successfully synthesized. These two AMC electrodes demonstrate remarkable electrochemical behaviors such as high rate capability, high specific capacitance, and excellent cycle stability when serving as electrodes for supercapacitors. More importantly, through the use of a Zn-Ni-Co ternary oxide (ZNCO) positive electrode and the AMC negative electrode, asymmetric supercapacitors (ASC) were assembled that deliver superior energy density (53.3 Wh kg(-1) at a power density of 1126.1 W kg(-1) for ASC-2 and 53.6 Wh kg(-1) at a power density of 1124.5 W kg(-1) for ASC-3) and excellent stability (82.7% and 83.4% specific capacitance retention for ZNCO//AMC ASC-2 and ZNCO//AMC ASC-3, respectively, after 5000 cycles). Through these two methods, low-cost, renewable, and environmentally friendly electrode materials can be provided for high energy density supercapacitors.\",\n \"corpus_id\": 206421165,\n \"score\": 2\n },\n {\n \"doc_id\": \"27336591\",\n \"title\": \"Wall-like hierarchical metal oxide nanosheet arrays grown on carbon cloth for excellent supercapacitor electrodes.\",\n \"abstract\": \"Recently, considerable efforts have been made to satisfy the future requirements of electrochemical energy storage using novel functional electrode materials. Binary transition metal oxides (BTMOs) possess multiple oxidation states that enable multiple redox reactions, showing higher supercapacitive properties than single component metal oxides. In this work, a facile hydrothermal method is provided for the synthesis of wall-like hierarchical metal oxide MMoO4 (M = Ni, Co) nanosheet arrays, which are directly grown on flexible carbon cloth for use as advanced binder-free electrodes for supercapacitors. By virtue of their intriguing structure, the resulted active material nanosheets with a high specific surface area can provide a large electroactive region, which could facilitate easy accession of electrolyte ions and fast charge transport, resulting in an enhanced electrochemical performance. Separately, the as-synthesized MMoO4 (M = Ni, Co) samples have exhibited superior specific capacitances (1483 F g(-1) of NiMoO4 and 452 F g(-1) of CoMoO4 at a current density of 2 A g(-1)), as well as excellent cycling stability (93.1% capacitance retention of NiMoO4 and 95.9% capacitance retention of CoMoO4 after 2000 cycles). The results show that the binder-free electrodes constructed by deposition of MMoO4 (M = Ni, Co) nanosheets on carbon cloth are promising candidates for the application of supercapacitors.\",\n \"corpus_id\": 206042461,\n \"score\": 2\n },\n {\n \"doc_id\": \"27430868\",\n \"title\": \"High-Performance Supercapacitor Electrode Based on Cobalt Oxide-Manganese Dioxide-Nickel Oxide Ternary 1D Hybrid Nanotubes.\",\n \"abstract\": \"We report a facile method to design Co3O4-MnO2-NiO ternary hybrid 1D nanotube arrays for their application as active material for high-performance supercapacitor electrodes. This as-prepared novel supercapacitor electrode can store charge as high as ∼2020 C/g (equivalent specific capacitance ∼2525 F/g) for a potential window of 0.8 V and has long cycle stability (nearly 80% specific capacitance retains after successive 5700 charge/discharge cycles), significantly high Coulombic efficiency, and fast response time (∼0.17s). The remarkable electrochemical performance of this unique electrode material is the outcome of its enormous reaction platform provided by its special nanostructure morphology and conglomeration of the electrochemical properties of three highly redox active materials in a single unit.\",\n \"corpus_id\": 206427693,\n \"score\": 2\n },\n {\n \"doc_id\": \"27451782\",\n \"title\": \"Hierarchical NiO Nanoflake Arrays on Nickel Foam as a Supercapacitor Electrode with High Capacitance and High Rate Capability.\",\n \"abstract\": \"In this paper, we report a simple and cost-effective method for fabricating hierarchical NiO nanoflake arrays on nickel foam. X-ray diffraction, scanning electron microscope and transmission electron microscope are employed to study the morphology and structure of the as-synthesized NiO materials. Galvanostatic charge/discharge measurements demonstrate that the hierarchical NiO nanocomposite displays excellent capacitive behavior between the potential range of -0.1-0.5 V, and a maximum specific capacitance as high as 823 F g-1 can be achieved at a charge/discharge current density of 4 A g-1, and it only decreases by 20% when the current density increases to 12 A g-1. The remarkable electrochemical performance of this hierarchical NiO nanocomposite indicates the areat application potential in supercapacitors.\",\n \"corpus_id\": 23475280,\n \"score\": 2\n },\n {\n \"doc_id\": \"27714086\",\n \"title\": \"1D Ni-Co oxide and sulfide nanoarray/carbon aerogel hybrid nanostructures for asymmetric supercapacitors with high energy density and excellent cycling stability.\",\n \"abstract\": \"The fabrication of supercapacitor electrodes with high energy density and excellent cycling stability is still a great challenge. A carbon aerogel, possessing a hierarchical porous structure, high specific surface area and electrical conductivity, is an ideal backbone to support transition metal oxides and bring hope to prepare electrodes with high energy density and excellent cycling stability. Therefore, NiCo2S4 nanotube array/carbon aerogel and NiCo2O4 nanoneedle array/carbon aerogel hybrid supercapacitor electrode materials were synthesized by assembling Ni-Co precursor needle arrays on the surface of the channel walls of hierarchical porous carbon aerogels derived from chitosan in this study. The 1D nanostructures grow on the channel surface of the carbon aerogel vertically and tightly, contributing to the enhanced electrochemical performance with ultrahigh energy density. The energy density of NiCo2S4 nanotube array/carbon aerogel and NiCo2O4 nanoneedle array/carbon aerogel hybrid asymmetric supercapacitors can reach up to 55.3 Wh kg(-1) and 47.5 Wh kg(-1) at a power density of 400 W kg(-1), respectively. These asymmetric devices also displayed excellent cycling stability with a capacitance retention of about 96.6% and 92% over 5000 cycles.\",\n \"corpus_id\": 5837498,\n \"score\": 2\n },\n {\n \"doc_id\": \"27885371\",\n \"title\": \"Hierarchical ternary Ni-Co-Se nanowires for high-performance supercapacitor device design.\",\n \"abstract\": \"Large-scale uniform Ni-Co-Se bimetallic ternary nanowires have been successfully synthesized through a successive cation exchange. First, NiSe nanowires in situ grown on nickel foam (NF) were prepared by a facile solvothermal route. Next, a series of ternary materials possessing different proportions of Ni and Co were fabricated by a Co-exchange method using the Ni@NiSe material as a template, which effectively achieved morphological inheritance from the parent material. To explore the electrochemical performance, all synthetic materials were assembled into asymmetric supercapacitor devices. Among asymmetric supercapacitor devices, the Ni@Ni0.8Co0.2Se//active carbon (AC) device exhibited a high specific capacitance of 86 F g(-1) at a current density of 1 A g(-1) and excellent cycling stability with virtually no decrease in capacitance after 2000 continuous charge-discharge cycles. This device still delivered an energy density of 17 Wh kg(-1) even at a high power density of 1526.8 W kg(-1). These superior electrochemical properties of Ni@Ni0.8Co0.2Se as an electrode material for supercapacitor devices confirmed the synergistic effect between Co and Ni ions, suggesting their potential application in the field of energy storage.\",\n \"corpus_id\": 29464815,\n \"score\": 2\n },\n {\n \"doc_id\": \"27991753\",\n \"title\": \"Three-Dimensional Hierarchical NixCo1-xO/NiyCo2-yP@C Hybrids on Nickel Foam for Excellent Supercapacitors.\",\n \"abstract\": \"Active materials and special structures of the electrode have decisive influence on the electrochemical properties of supercapacitors. Herein, three-dimensional (3D) hierarchical NixCo1-xO/NiyCo2-yP@C (denoted as NiCoOP@C) hybrids have been successfully prepared by a phosphorization treatment of hierarchical NixCo1-xO@C grown on nickel foam. The resulting NiCoOP@C hybrids exhibit an outstanding specific capacitance and cycle performance because they couple the merits of the superior cycling stability of NixCo1-xO, the high specific capacitance of NiyCo2-yP, the mechanical stability of carbon layer, and the 3D hierarchical structure. The specific capacitance of 2638 F g(-1) can be obtained at the current density of 1 A g(-1), and even at the current density of 20 A g(-1), the NiCoOP@C electrode still possesses a specific capacitance of 1144 F g(-1). After 3000 cycles at 10 A g(-1), 84% of the initial specific capacitance is still remained. In addition, an asymmetric ultracapacitor (ASC) is assembled through using NiCoOP@C hybrids as anode and activated carbon as cathode. The as-prepared ASC obtains a maximum energy density of 39.4 Wh kg(-1) at a power density of 394 W kg(-1) and still holds 21 Wh kg(-1) at 7500 W kg(-1).\",\n \"corpus_id\": 206434634,\n \"score\": 2\n },\n {\n \"doc_id\": \"28075058\",\n \"title\": \"MOF-Derived Hollow Cage Nix Co3-x O4 and Their Synergy with Graphene for Outstanding Supercapacitors.\",\n \"abstract\": \"Highly optimized nickel cobalt mixed oxide has been derived from zeolite imidazole frameworks. While the pure cobalt oxide gives only 178.7 F g(-1) as the specific capacitance at a current density of 1 A g(-1) , the optimized Ni:Co 1:1 has given an extremely high and unprecedented specific capacitance of 1931 F g(-1) at a current density of 1 A g(-1) , with a capacitance retention of 69.5% after 5000 cycles in a three electrode test. This optimized Ni:Co 1:1 mixed oxide is further used to make a composite of nickel cobalt mixed oxide/graphene 3D hydrogel for enhancing the electrochemical performance by virtue of a continuous and porous graphene conductive network. The electrode made from GNi:Co 1:1 successfully achieves an even higher specific capacitance of 2870.8 F g(-1) at 1 A g(-1) and also shows a significant improvement in the cyclic stability with 81% capacitance retention after 5000 cycles. An asymmetric supercapacitor is also assembled using a pure graphene 3D hydrogel as the negative electrode and the GNi:Co 1:1 as the positive electrode. With a potential window of 1.5 V and binder free electrodes, the capacitor gives a high specific energy density of 50.2 Wh kg(-1) at a high power density of 750 W kg(-1) .\",\n \"corpus_id\": 8944291,\n \"score\": 2\n },\n {\n \"doc_id\": \"28094497\",\n \"title\": \"An Approach To Fabricate PDMS Encapsulated All-Solid-State Advanced Asymmetric Supercapacitor Device with Vertically Aligned Hierarchical Zn-Fe-Co Ternary Oxide Nanowire and Nitrogen Doped Graphene Nanosheet for High Power Device Applications.\",\n \"abstract\": \"We highlight the design and fabrication of a polydimethylsiloxane (PDMS) encapsulated advanced all-solid-state asymmetric supercapacitor (ASC) device consisting of hierarchical mesoporous zinc-iron-cobalt ternary oxide (ZICO) nanowire coated nickel (Ni) foam (ZICO@Ni foam) as a promising positive electrode and nitrogen doped graphene coated Ni foam (N-G@Ni foam) as negative electrode in the presence of PVA-KOH gel electrolyte. Owing to outstanding electrochemical behavior and ultrahigh specific capacitance of ZICO (≈ 2587.4 F/g at 1 A/g) and N-G (550 F/g at 1 A/g) along with their mutual synergistic outputs, the assembled all-solid-state ASC device exhibits an outstanding energy density of ≈40.5 Wh/kg accompanied by a remarkable long-term cycle stability with ≈95% specific capacitance retention even after 5000 charge-discharge cycles. The exclusive hierarchical ZICO nanowires were synthesized by a facile two-step process comprising of a hydrothermal protocol followed by an annealing treatment on a quartz substrate. While Zn(2+) gives the stability of the oxide system, Fe and Co ions provide better electronic conductivity and capacitive response under vigorous cyclic condition. The extraordinary performance of as-fabricated ASC device resembles its suitability for the construction of advanced energy storage devices in modern electronic industries.\",\n \"corpus_id\": 206435371,\n \"score\": 2\n },\n {\n \"doc_id\": \"28102378\",\n \"title\": \"A high-performance supercapacitor electrode based on tremella-like NiC2O4@NiO core/shell hierarchical nanostructures on nickel foam.\",\n \"abstract\": \"Tremella-like nickel oxalate@nickel oxide (NiC2O4@NiO) core/shell hierarchical nanostructures have been successfully synthesized on nickel foam, using Ni foam as a current collector, a Ni source and a three-dimensional (3D) substrate, through a facile hydrothermal method followed by an electrochemical activation process. The prepared samples can be directly used as binder-free electrodes for supercapacitors. The tremella-like morphology, together with the NiC2O4 nanoblocks on 3D Ni foam, significantly increases the amount of active sites for redox reactions and the conductivity of the electrode material, shortens the diffusion pathway for ions, facilitates the effective penetration of the electrolyte, and lowers the intrinsic equivalent series resistance, demonstrating good potential for energy storage application. This material has a high specific capacitance of 2287.09 F g(-1) at 1 A g(-1), a good cycling stability (remaining 95% after 10 000 cycles) and a good rate capability (83.2% retention upon increasing the current density by 10 times).\",\n \"corpus_id\": -1,\n \"score\": 2\n },\n {\n \"doc_id\": \"28158923\",\n \"title\": \"Ultrathin Mesoporous RuCo2 O4 Nanoflakes: An Advanced Electrode for High-Performance Asymmetric Supercapacitors.\",\n \"abstract\": \"A new ruthenium cobalt oxide (RuCo2 O4 ) with a unique marigold-like nanostructure and excellent performance as an advanced electrode material has been successfully prepared by a simple electrodeposition (potentiodynamic mode) method. The RuCo2 O4 marigolds consist of numerous clusters of ultrathin mesoporous nanoflakes, leaving a large interspace between them to provide numerous electrochemically active sites. Strikingly, this unique marigold-like nanostructure provided excellent electrochemical performance in terms of high energy-storage capacitance (1469 F g(-1) at 6 A g(-1) ) with excellent rate proficiency and long-lasting operating cycling stability (ca. 91.3 % capacitance retention after 3000 cycles), confirming that the mesoporous nanoflakes participate in the ultrafast electrochemical reactions. Furthermore, an asymmetric supercapacitor was assembled using RuCo2 O4 (positive electrode) and activated carbon (negative electrode) with aqueous KOH electrolyte. The asymmetric design allowed an upgraded potential range of 1.4 V, which further provided a good energy density of 32.6 Wh kg(-1) (1.1 mWh cm(-3) ). More importantly, the cell delivered an energy density of 12.4 Wh kg(-1) even at a maximum power density of 3.2 kW kg(-1) , which is noticeably superior to carbon-based symmetric systems.\",\n \"corpus_id\": 41248285,\n \"score\": 2\n },\n {\n \"doc_id\": \"28463481\",\n \"title\": \"Three-Dimensional Cobalt Phosphide Nanowire Arrays as Negative Electrode Material for Flexible Solid-State Asymmetric Supercapacitors.\",\n \"abstract\": \"Despite the great progress that has been accomplished in supercapacitors, the imbalance of the development of positive and negative electrode materials still remains a critical issue to achieve high energy density; therefore, exploring high-performance negative electrode materials is highly desirable. In this article, three-dimensional cobalt phosphide (CoP) nanowire arrays were synthesized on a carbon cloth and were utilized as a binder-free supercapacitor negative electrode. The as-synthesized CoP nanowire arrays presented a high capacitance of 571.3 mF/cm(2) at a current density of 1 mA/cm(2). By using CoP nanowire arrays as the negative electrode and MnO2 nanowire arrays as the positive electrode, a flexible solid-state asymmetric supercapacitor has been fabricated and has exhibited excellent electrochemical performance, such as a high energy density of 0.69 mWh/cm(3) and a high power density of 114.2 mW/cm(3). In addition, the solid-state asymmetric supercapacitor shows high cycle stability with 82% capacitance retention after 5000 charge/discharge cycles. This work demonstrates that CoP is a promising negative electrode material for high-performance supercapacitor applications.\",\n \"corpus_id\": 206444459,\n \"score\": 2\n },\n {\n \"doc_id\": \"28521098\",\n \"title\": \"Hybrid Reduced Graphene Oxide Nanosheet Supported Mn-Ni-Co Ternary Oxides for Aqueous Asymmetric Supercapacitors.\",\n \"abstract\": \"Hybrid reduced graphene oxide (RGO) nanosheet supported Mn-Ni-Co ternary oxides (MNCO) are prepared through a facile coprecipitation reaction with a subsequent calcination process as electrodes for supercapacitors. Electrochemical measurements prove that RGO can significantly improve the supercapacitive behaviors, compared with the pure MNCO electrode. A high specific capacity of 646.1 C g(-1) at 1 A g(-1) can be achieved and about 89.6% of the capacity can be remained at 30 A g(-1) relative to that of the low-current capacity, indicating attractive rate capability of the RGO-MNCO electrode. Moreover, an asymmetric supercapacitor (ASC) device is fabricated with nitrogen-enriched RGO as the negative electrode and the synthesized RGO-MNCO as the positive electrode. Electrochemical performances investigated at different potential range reveal that the ASC device presents excellent capacitive behavior and reversibility. A maximum energy density of 35.6 Wh kg(-1) at power density of 699.9 W kg(-1) can be delivered. Furthermore, stable cycle capability with 100% Coulombic efficiency and 77.2% the capacitance retention is also achieved after 10000 cycles. The achieved outstanding electrochemical properties indicate that the obtained RGO-MNCO electrode materials are fairly ideal for progressive supercapacitors.\",\n \"corpus_id\": 206450220,\n \"score\": 2\n },\n {\n \"doc_id\": \"28561089\",\n \"title\": \"Hierarchical core-shell CoMn2O4@MnO2 nanoneedle arrays for high-performance supercapacitors.\",\n \"abstract\": \"Hierarchical mesoporous core-shell CoMn2O4@MnO2 nanoneedle arrays on nickel foam have been manufactured via a two-step hydrothermal process. Electrochemical performances of the CoMn2O4@MnO2 nanomaterials have been tested for supercapacitors and demonstrated outstanding properties. The CoMn2O4@MnO2 electrode delivers a specific capacitance of 2126 F g(-1) at a current density of 1 A g(-1) in 2 M KOH aqueous solution and also shows an excellent cycling stability, which retains 94.4% of the initial capacitance after 5000 charge/discharge cycles at a current density of 4 A g(-1). The result confirms the superiority of the CoMn2O4@MnO2 electrode compared with the CoMn2O4 electrode and demonstrates the potential application of the CoMn2O4@MnO2 nanoneedle array electrode for high-performance energy storage device applications.\",\n \"corpus_id\": 3381806,\n \"score\": 2\n },\n {\n \"doc_id\": \"28678249\",\n \"title\": \"Interconnected hierarchical NiCo2O4 microspheres as high-performance electrode materials for supercapacitors.\",\n \"abstract\": \"Herein, interconnected hierarchical NiCo2O4 microspheres (IH-NiCo2O4) were prepared via a solvothermal method followed by an annealing treatment. IH-NiCo2O4 possesses large tunnels and abundant mesopores, which are in favor of their applications in energy storage field. When employed as an electrode material for supercapacitors, IH-NiCo2O4 exhibits a high specific capacitance of 1822.3 F g(-1) at a current density of 2 A g(-1), an excellent rate property of 68.6% capacity retention at 20 A g(-1), and an 87.6% specific capacitance retention of its initial value after 7000 cycles at a high current density of 10 A g(-1), superior to those of IH-Co3O4. Furthermore, an optimal asymmetric supercapacitor (ASC) was also constructed with IH-NiCo2O4 as the positive electrode and graphene as the negative electrode. The ASC delivers a high energy density of 39.4 Wh kg(-1) at a power density of 800 W kg(-1). Even at a high power density of 8000 W kg(-1), the energy density still reaches 27.2 Wh kg(-1). Moreover, the ASC shows a good cycling stability with 80.1% specific capacitance retention after 5000 cycles at 6 A g(-1). The excellent electrochemical performance of IH-NiCo2O4 makes it a promising electrode material in energy storage field.\",\n \"corpus_id\": 3382025,\n \"score\": 2\n },\n {\n \"doc_id\": \"28772727\",\n \"title\": \"Electrodeposited Porous Mn1.5Co1.5O₄/Ni Composite Electrodes for High-Voltage Asymmetric Supercapacitors.\",\n \"abstract\": \"Mesoporous Mn1.5Co1.5O₄ (MCO) spinel films were prepared directly on a conductive nickel (Ni) foam substrate via electrodeposition and an annealing treatment as supercapacitor electrodes. The electrodeposition time markedly influenced the surface morphological, textural, and supercapacitive properties of MCO/Ni electrodes. The (MCO/Ni)-15 min electrode (electrodeposition time: 15 min) exhibited the highest capacitance among three electrodes (electrodeposition times of 7.5, 15, and 30 min, respectively). Further, an asymmetric supercapacitor that utilizes (MCO/Ni)-15 min as a positive electrode, a plasma-treated activated carbon (PAC)/Ni electrode as a negative electrode, and carboxymethyl cellulose-lithium nitrate (LiNO₃) gel electrolyte (denoted as (PAC/Ni)//(MCO/Ni)-15 min) was fabricated. In a stable operation window of 2.0 V, the device exhibited an energy density of 27.6 Wh·kg(-1) and a power density of 1.01 kW·kg(-1) at 1 A·g(-1). After 5000 cycles, the specific energy density retention and power density retention were 96% and 92%, respectively, demonstrating exceptional cycling stability. The good supercapacitive performance and excellent stability of the (PAC/Ni)//(MCO/Ni)-15 min device can be ascribed to the hierarchical structure and high surface area of the (MCO/Ni)-15 min electrode, which facilitate lithium ion intercalation and deintercalation at the electrode/electrolyte interface and mitigate volume change during long-term charge/discharge cycling.\",\n \"corpus_id\": 1422364,\n \"score\": 2\n },\n {\n \"doc_id\": \"28914819\",\n \"title\": \"Construction of Hierarchical CuO/Cu₂O@NiCo₂S₄ Nanowire Arrays on Copper Foam for High Performance Supercapacitor Electrodes.\",\n \"abstract\": \"Hierarchical copper oxide @ ternary nickel cobalt sulfide (CuO/Cu₂O@NiCo₂S₄) core-shell nanowire arrays on Cu foam have been successfully constructed by a facile two-step strategy. Vertically aligned CuO/Cu₂O nanowire arrays are firstly grown on Cu foam by one-step thermal oxidation of Cu foam, followed by electrodeposition of NiCo₂S₄ nanosheets on the surface of CuO/Cu₂O nanowires to form the CuO/Cu₂O@NiCo₂S₄ core-shell nanostructures. Structural and morphological characterizations indicate that the average thickness of the NiCo₂S₄ nanosheets is ~20 nm and the diameter of CuO/Cu₂O core is ~50 nm. Electrochemical properties of the hierarchical composites as integrated binder-free electrodes for supercapacitor were evaluated by various electrochemical methods. The hierarchical composite electrodes could achieve ultrahigh specific capacitance of 3.186 F cm-2 at 10 mA cm-2, good rate capability (82.06% capacitance retention at the current density from 2 to 50 mA cm-2) and excellent cycling stability, with capacitance retention of 96.73% after 2000 cycles at 10 mA cm-2. These results demonstrate the significance of optimized design and fabrication of electrode materials with more sufficient electrolyte-electrode interface, robust structural integrity and fast ion/electron transfer.\",\n \"corpus_id\": 10505325,\n \"score\": 2\n },\n {\n \"doc_id\": \"28948775\",\n \"title\": \"Construction of Hierarchical CNT/rGO-Supported MnMoO4 Nanosheets on Ni Foam for High-Performance Aqueous Hybrid Supercapacitors.\",\n \"abstract\": \"Rationally designed conductive hierarchical nanostructures are highly desirable for supporting pseudocapacitive materials to achieve high-performance electrodes for supercapacitors. Herein, manganese molybdate nanosheets were hydrothermally grown with graphene oxide (GO) on three-dimensional nickel foam-supported carbon nanotube structures. Under the optimal graphene oxide concentration, the obtained carbon nanotubes/reduced graphene oxide/MnMoO4 composites (CNT/rGO/MnMoO4) as binder-free supercapacitor cathodes perform with a high specific capacitance of 2374.9 F g-1 at the scan rate of 2 mV s-1 and good long-term stability (97.1% of the initial specific capacitance can be maintained after 3000 charge/discharge cycles). The asymmetric device with CNT/rGO/MnMoO4 as the cathode electrode and the carbon nanotubes/activated carbon on nickel foam (CNT-AC) as the anode electrode can deliver an energy density of 59.4 Wh kg-1 at the power density of 1367.9 W kg-1. These superior performances can be attributed to the synergistic effects from each component of the composite electrodes: highly pseudocapacitive MnMoO4 nanosheets and three-dimensional conductive Ni foam/CNTs/rGO networks. These results suggest that the fabricated asymmetric supercapacitor can be a promising candidate for energy storage devices.\",\n \"corpus_id\": 206461320,\n \"score\": 2\n },\n {\n \"doc_id\": \"29111747\",\n \"title\": \"Constructing Ultrahigh-Capacity Zinc-Nickel-Cobalt Oxide@Ni(OH)2 Core-Shell Nanowire Arrays for High-Performance Coaxial Fiber-Shaped Asymmetric Supercapacitors.\",\n \"abstract\": \"Increased efforts have recently been devoted to developing high-energy-density flexible supercapacitors for their practical applications in portable and wearable electronics. Although high operating voltages have been achieved in fiber-shaped asymmetric supercapacitors (FASCs), low specific capacitance still restricts the further enhancement of their energy density. This article specifies a facile and cost-effective method to directly grow three-dimensionally well-aligned zinc-nickel-cobalt oxide (ZNCO)@Ni(OH)2 nanowire arrays (NWAs) on a carbon nanotube fiber (CNTF) with an ultrahigh specific capacitance of 2847.5 F/cm3 (10.678 F/cm2) at a current density of 1 mA/cm2, These levels are approximately five times higher than those of ZNCO NWAs/CNTF electrodes (2.10 F/cm2) and four times higher than Ni(OH)2/CNTF electrodes (2.55 F/cm2). Benefiting from their unique features, we successfully fabricated a prototype coaxial FASC (CFASC) with a maximum operating voltage of 1.6 V, which was assembled by adopting ZNCO@Ni(OH)2 NWAs/CNTF as the core electrode and a thin layer of carbon coated vanadium nitride (VN@C) NWAs on a carbon nanotube strip (CNTS) as the outer electrode with KOH poly(vinyl alcohol) (PVA) as the gel electrolyte. A high specific capacitance of 94.67 F/cm3 (573.75 mF/cm2) and an exceptional energy density of 33.66 mWh/cm3 (204.02 μWh/cm2) were achieved for our CFASC device, which represent the highest levels of fiber-shaped supercapacitors to date. More importantly, the fiber-shaped ZnO-based photodetector is powered by the integrated CFASC, and it demonstrates excellent sensitivity in detecting UV light. Thus, this work paves the way to the construction of ultrahigh-capacity electrode materials for next-generation wearable energy-storage devices.\",\n \"corpus_id\": 206743922,\n \"score\": 2\n },\n {\n \"doc_id\": \"29211442\",\n \"title\": \"Atomic Layer Deposition of Nickel on ZnO Nanowire Arrays for High-Performance Supercapacitors.\",\n \"abstract\": \"A novel hybrid core-shell structure of ZnO nanowires (NWs)/Ni as a pseudocapacitor electrode was successfully fabricated by atomic layer deposition of a nickel shell, and its capacitive performance was systemically investigated. Transmission electron microscopy and X-ray photoelectron spectroscopy results indicated that the NiO was formed at the interface between ZnO and Ni where the Ni was oxidized by ZnO during the ALD of the Ni layer. Electrochemical measurement results revealed that the Ti/ZnO NWs/Ni (1500 cycles) electrode with a 30 nm thick Ni-NiO shell layer had the best supercapacitor properties including ultrahigh specific capacitance (∼2440 F g-1), good rate capability (80.5%) under high current charge-discharge conditions, and a relatively better cycling stability (86.7% of the initial value remained after 750 cycles at 10 A g-1). These attractive capacitive behaviors are mainly attributed to the unique core-shell structure and the combined effect of ZnO NW arrays as short charge transfer pathways for ion diffusion and electron transfer as well as conductive Ni serving as channel for the fast electron transport to Ti substrate. This high-performance Ti/ZnO NWs/Ni hybrid structure is expected to be one of a promising electrodes for high-performance supercapacitor applications.\",\n \"corpus_id\": 206469562,\n \"score\": 2\n },\n {\n \"doc_id\": \"29313663\",\n \"title\": \"Construction of Core-Shell NiMoO4@Ni-Co-S Nanorods as Advanced Electrodes for High-Performance Asymmetric Supercapacitors.\",\n \"abstract\": \"In this work, hierarchical core-shell NiMoO4@Ni-Co-S nanorods were first successfully grown on nickel foam by a facile two-step method to fabricate a bind-free electrode. The well-aligned electrode wrapped by Ni-Co-S nanosheets displays excellent nanostructural properties and outstanding electrochemical performance, owing to the synergistic effects of both nickel molybdenum oxides and nickel cobalt sulfides. The prepared core-shell nanorods in a three-electrode cell yielded a high specific capacitance of 2.27 F cm-2 (1892 F g-1) at a current density of 5 mA cm-2 and retained 91.7% of the specific capacitance even after 6000 cycles. Their electrochemical performance was further investigated for their use as positive electrode for asymmetric supercapacitors. Notably, the energy density of the asymmetric supercapacitor device reached 2.45 mWh cm-3 at a power density of 0.131 W cm-3, and still retained a remarkable 80.3% of the specific capacitance after 3500 cycles. There is great potential for the electrode composed of the core-shell NiMoO4@Ni-Co-S nanorods for use in an all-solid-state asymmetric supercapacitor device.\",\n \"corpus_id\": 206475287,\n \"score\": 2\n },\n {\n \"doc_id\": \"29363699\",\n \"title\": \"Hierarchical 3D NiFe2O4@MnO2 core-shell nanosheet arrays on Ni foam for high-performance asymmetric supercapacitors.\",\n \"abstract\": \"Hierarchical NiFe2O4@MnO2 core-shell nanosheet arrays (NSAs) were synthesized on Ni foam as an integrated electrode for supercapacitors, using a facile two-step hydrothermal method followed by calcination treatment. The NiFe2O4 nanosheets were designed as the core and ultrathin MnO2 nanoflakes as the shell, creating a unique three-dimensional (3D) hierarchical electrode on Ni foam. The composite electrode exhibited remarkable electrochemical performance with a high specific capacitance of 1391 F g-1 at a current density of 2 mA cm-2 and long cycling stability at a high current density of 10 mA cm-2 (only 11.4% loss after 3000 cycles). Additionally, an asymmetric supercapacitor (ASC) device was fabricated with a NiFe2O4@MnO2 composite as the positive electrode material and activated carbon (AC) as the negative one. The ASC device exhibited a high energy density (45.2 W h kg-1) at a power density of 174 W kg-1, and an excellent cycling stability over 3000 cycles with 92.5% capacitance retention. The remarkable electrochemical performance demonstrated its great potential as a promising candidate for high-performance supercapacitors.\",\n \"corpus_id\": 4228098,\n \"score\": 2\n },\n {\n \"doc_id\": \"29465411\",\n \"title\": \"Three-dimensional cotton-like nickel nanowire@Ni-Co hydroxide nanosheet arrays as binder-free electrode for high-performance asymmetric supercapacitor.\",\n \"abstract\": \"Three-dimensional (3D) cotton-like Ni-Co layered double hydroxide nanosheet arrays/nickel nanowires (3D Ni-Co LDH/NiNw) were successfully fabricated through a facile chemical bath deposition method. The 3D nickel nanowires are used as a conductive substrate with robust adhesion for high-pseudocapacitance Ni-Co LDH. The 3D Ni-Co LDH/NiNw electrode shows a high areal specific capacitance of 14 F cm-2 at 5 mA cm-2 and quality specific capacitance of 466.6 F g-1 at 0.125 A g-1 with respect to the whole quality of the electrode. The fabricated asymmetric supercapacitor exhibits a remarkable energy density of 0.387 mWh cm-2 using Ni-Co LDH/NiNw as the negative electrode. This high-performance composite electrode presents a new and affordable general approach for supercapacitors.\",\n \"corpus_id\": 3923906,\n \"score\": 2\n },\n {\n \"doc_id\": \"29675973\",\n \"title\": \"A Zinc Cobalt Sulfide Nanosheet Array Derived from a 2D Bimetallic Metal-Organic Frameworks for High-Performance Supercapacitors.\",\n \"abstract\": \"Porous ternary metal sulfide integrated electrode materials with abundant electroactive sites and redox reactions are very promising for supercapacitors. Herein, a porous zinc cobalt sulfide nanosheet array on Ni foam (Zn-Co-S/NF) was constructed by facile growth of 2D bimetallic zinc/cobalt-based metal-organic framework (Zn/Co-MOF) nanosheets with leaf-like morphology on NF, followed by additional sulfurization. The Zn-Co-S/NF nanosheet array acted directly as a supercapacitor electrode showing much better electrochemical performance (2354.3 F g-1 and 88.6 % retention over 1000 cycles) when compared with zinc cobalt sulfide powder (355.3 F g-1 and 75.8 % retention over 1000 cycles), which originates from good electrical conductivity and mechanical stability, abundant electroactive sites, and facilitated transportation of electrons and electrolyte ions due to the unique nanosheet array structure. An asymmetric supercapacitor (ASC) device assembled from Zn-Co-S/NF and activated carbon electrodes can deliver a highest energy density of 31.9 Wh kg-1 and a maximum power density of 8.5 kW kg-1 . Most importantly, this ASC also shows good cycling stability (71.0 % retention over 10000 cycles). Furthermore, a red LED can be powered by two connected ASCs, and thus as-synthesized Zn-Co-S/NF has great potential for practical applications.\",\n \"corpus_id\": 5012559,\n \"score\": 2\n },\n {\n \"doc_id\": \"29714380\",\n \"title\": \"Phosphorization boosts the capacitance of mixed metal nanosheet arrays for high performance supercapacitor electrodes.\",\n \"abstract\": \"Binary transition metal phosphides hold immense potential as innovative electrode materials for constructing high-performance energy storage devices. Herein, porous binary nickel-cobalt phosphide (NiCoP) nanosheet arrays anchored on nickel foam (NF) were rationally designed as self-supported binder-free electrodes with high supercapacitance performance. Taking the combined advantages of compositional features and array architectures, the nickel foam supported NiCoP nanosheet array (NiCoP@NF) electrode possesses superior electrochemical performance in comparison with Ni-Co LDH@NF and NiCoO2@NF electrodes. The NiCoP@NF electrode shows an ultrahigh specific capacitance of 2143 F g-1 at 1 A g-1 and retained 1615 F g-1 even at 20 A g-1, showing excellent rate performance. Furthermore, a binder-free all-solid-state asymmetric supercapacitor device is designed, which exhibits a high energy density of 27 W h kg-1 at a power density of 647 W kg-1. The hierarchical binary nickel-cobalt phosphide nanosheet arrays hold great promise as advanced electrode materials for supercapacitors with high electrochemical performance.\",\n \"corpus_id\": 14045608,\n \"score\": 2\n },\n {\n \"doc_id\": \"22435881\",\n \"title\": \"3D graphene-cobalt oxide electrode for high-performance supercapacitor and enzymeless glucose detection.\",\n \"abstract\": \"Using a simple hydrothermal procedure, cobalt oxide (Co(3)O(4)) nanowires were in situ synthesized on three-dimensional (3D) graphene foam grown by chemical vapor deposition. The structure and morphology of the resulting 3D graphene/Co(3)O(4) composites were characterized by scanning electron microscopy, transmission electron microscopy, X-ray diffraction, and Raman spectroscopy. The 3D graphene/Co(3)O(4) composite was used as the monolithic free-standing electrode for supercapacitor application and for enzymeless electrochemical detection of glucose. We demonstrate that it is capable of delivering high specific capacitance of ∼1100 F g(-1) at a current density of 10 A g(-1) with excellent cycling stability, and it can detect glucose with a ultrahigh sensitivity of 3.39 mA mM(-1) cm(-2) and a remarkable lower detection limit of <25 nM (S/N = 8.5).\",\n \"corpus_id\": 207731399,\n \"score\": 1\n },\n {\n \"doc_id\": \"24488182\",\n \"title\": \"High-performance supercapacitor electrodes based on hierarchical Ti@MnO(2) nanowire arrays.\",\n \"abstract\": \"Ti nanowire arrays (NAs) prepared by a facile and template-free hydrothermal method were used as three-dimensional (3D) current collectors for the electrodeposition of MnO2. The resulting Ti@MnO2 NAs exhibit remarkable electrochemical behavior with high specific capacitance, good rate performance and desired cycling stability.\",\n \"corpus_id\": 262646037,\n \"score\": 1\n },\n {\n \"doc_id\": \"25133989\",\n \"title\": \"One-step electrodeposited nickel cobalt sulfide nanosheet arrays for high-performance asymmetric supercapacitors.\",\n \"abstract\": \"A facile one-step electrodeposition method is developed to prepare ternary nickel cobalt sulfide interconnected nanosheet arrays on conductive carbon substrates as electrodes for supercapacitors, resulting in exceptional energy storage performance. Taking advantages of the highly conductive, mesoporous nature of the nanosheets and open framework of the three-dimensional nanoarchitectures, the ternary sulfide electrodes exhibit high specific capacitance (1418 F g(-1) at 5 A g(-1) and 1285 F g(-1) at 100 A g(-1)) with excellent rate capability. An asymmetric supercapacitor fabricated by the ternary sulfide nanosheet arrays as positive electrode and porous graphene film as negative electrode demonstrates outstanding electrochemical performance for practical energy storage applications. Our asymmetric supercapacitors show a high energy density of 60 Wh kg(-1) at a power density of 1.8 kW kg(-1). Even when charging the cell within 4.5 s, the energy density is still as high as 33 Wh kg(-1) at an outstanding power density of 28.8 kW kg(-1) with robust long-term cycling stability up to 50,000 cycles.\",\n \"corpus_id\": 28373700,\n \"score\": 1\n },\n {\n \"doc_id\": \"25322454\",\n \"title\": \"CoNi(2)S(4) nanosheet arrays supported on nickel foams with ultrahigh capacitance for aqueous asymmetric supercapacitor applications.\",\n \"abstract\": \"We report that CoNi2S4 nanosheet arrays exhibit ultrahigh specific capacitance of 2906 F g(-1) and areal capacitance of 6.39 F cm(-2) at a current density of 5 mA cm(-2), as well as good rate capability and cycling stability, and superior electrochemical performances with an energy density of 33.9 Wh kg(-1) at a power density of 409 W kg(-1) have been achieved in an assembled aqueous asymmetric supercapacitor. The CoNi2S4 nanosheet arrays were in situ grown on nickel foams by a facile two-step hydrothermal method. The formation mechanism of the CoNi2S4 nanosheet arrays was based on an anion-exchange reaction involving the pseudo Kirkendall effect. The two aqueous asymmetric supercapacitors in series using the CoNi2S4 nanosheet arrays as the positive electrodes can power four 3-mm-diameter red-light-emitting diodes. The outstanding supercapacitive performance of CoNi2S4 nanosheet arrays can be attributed to ravine-like nanosheet architectures with good mechanical and electrical contact, low crystallinity and good wettability without an annealing process, rich redox reactions, as well as high conductivity and transport rate for both electrolyte ions and electrons. Our results demonstrate that CoNi2S4 nanosheet arrays are promising electrode materials for supercapacitor applications.\",\n \"corpus_id\": 206806124,\n \"score\": 1\n },\n {\n \"doc_id\": \"25539030\",\n \"title\": \"Hydrothermal growth of hierarchical Ni3S2 and Co3S4 on a reduced graphene oxide hydrogel@Ni foam: a high-energy-density aqueous asymmetric supercapacitor.\",\n \"abstract\": \"Ni foam@reduced graphene oxide (rGO) hydrogel-Ni3S2 and Ni foam@rGO hydrogel-Co3S4 composites have been successfully synthesized with the aid of a two-step hydrothermal protocol, where the rGO hydrogel is sandwiched between the metal sulfide and Ni foam substrate. Sonochemical deposition of exfoliated rGO on Ni foam with subsequent hydrothermal treatment results in the formation of a rGO-hydrogel-coated Ni foam. Then second-time hydrothermal treatment of the dried Ni@rGO substrate with corresponding metal nitrate and sodium sulfide results in individual uniform growth of porous Ni3S2 nanorods and a Co3S4 self-assembled nanosheet on a Ni@rGO substrate. Both Ni@rGO-Ni3S2 and Ni@rGO-Co3S4 have been electrochemically characterized in a 6 M KOH electrolyte, exhibiting high specific capacitance values of 987.8 and 1369 F/g, respectively, at 1.5 A/g accompanied by the respective outstanding cycle stability of 97.9% and 96.6% at 12 A/g over 3000 charge-discharge cycles. An advanced aqueous asymmetric (AAS) supercapacitor has been fabricated by exploiting the as-prepared Ni@rGO-Co3S4 as a positive electrode and Ni@rGO-Ni3S2 as a negative electrode. The as-fabricated AAS has shown promising energy densities of 55.16 and 24.84 Wh/kg at high power densities of 975 and 13000 W/kg, respectively, along with an excellent cycle stability of 96.2% specific capacitance retention over 3000 charge-discharge cycles at 12 A/g. The enhanced specific capacitance, stupendous cycle stability, elevated energy density, and a power density as an AAS of these electrode materials indicate that it could be a potential candidate in the field of supercapacitors.\",\n \"corpus_id\": 206809525,\n \"score\": 1\n },\n {\n \"doc_id\": \"25801647\",\n \"title\": \"MnO2 Nanosheets Grown on Nitrogen-Doped Hollow Carbon Shells as a High-Performance Electrode for Asymmetric Supercapacitors.\",\n \"abstract\": \"A hierarchical hollow hybrid composite, namely, MnO2 nanosheets grown on nitrogen-doped hollow carbon shells (NHCSs@MnO2 ), was synthesized by a facile in situ growth process followed by calcination. The composite has a high surface area (251 m(2) g(-1) ) and mesopores (4.5 nm in diameter), which can efficiently facilitate transport during electrochemical cycling. Owing to the synergistic effect of NHCSs and MnO2 , the composite shows a high specific capacitance of 306 F g(-1) , good rate capability, and an excellent cycling stability of 95.2 % after 5000 cycles at a high current density of 8 A g(-1) . More importantly, an asymmetric supercapacitor (ASC) assembled by using NHCSs@MnO2 and activated carbon as the positive and negative electrodes exhibits high specific capacitance (105.5 F g(-1) at 0.5 A g(-1) and 78.5 F g(-1) at 10 A g(-1) ) with excellent rate capability, achieves a maximum energy density of 43.9 Wh kg(-1) at a power density of 408 W kg(-1) , and has high stability, whereby the ASC retains 81.4 % of its initial capacitance at a current density of 5 A g(-1) after 4000 cycles. Therefore, the NHCSs@MnO2 electrode material is a promising candidate for future energy-storage systems.\",\n \"corpus_id\": 8943716,\n \"score\": 1\n },\n {\n \"doc_id\": \"26935179\",\n \"title\": \"Hierarchical CuCo2S4 hollow nanoneedle arrays as novel binder-free electrodes for high-performance asymmetric supercapacitors.\",\n \"abstract\": \"Hierarchical CuCo2S4 hollow nanoneedle arrays have been firstly synthesized on a Ni foam using a facile template-free hydrothermal method and applied as novel binder-free electrodes for high-performance asymmetric supercapacitors with ultrahigh specific capacitance, high energy density, excellent rate capability and outstanding long-term cycling stability.\",\n \"corpus_id\": 31915775,\n \"score\": 1\n },\n {\n \"doc_id\": \"27551941\",\n \"title\": \"Construction of a Hierarchical NiCo2S4@PPy Core-Shell Heterostructure Nanotube Array on Ni Foam for a High-Performance Asymmetric Supercapacitor.\",\n \"abstract\": \"In this paper, a hierarchical NiCo2S4@polypyrrole core-shell heterostructure nanotube array on Ni foam (NiCo2S4@PPy/NF) was successfully developed as a bind-free electrode for supercapacitors. NiCo2S4@PPy-50/NF obtained under 50 s PPy electrodeposition shows a low charge-transfer resistance (0.31 Ω) and a high area specific capacitance of 9.781 F/cm(2) at a current density of 5 mA/cm(2), which is two times higher than that of pristine NiCo2S4/NF (4.255 F/cm(2)). Furthermore, an asymmetric supercapacitor was assembled using NiCo2S4@PPy-50/NF as positive electrode and activated carbon (AC) as negative electrode. The resulting NiCo2S4@PPy-50/NF//AC device exhibits a high energy density of 34.62 Wh/kg at a power density of 120.19 W/kg with good cycling performance (80.64% of the initial capacitance retention at 50 mA/cm(2) over 2500 cycles). The superior electrochemical performance can be attributed to the combined contribution of both component and unique core-shell heterostructure. The results demonstrate that the NiCo2S4@PPy-50 core-shell heterostructure nanotube array is promising as electrode material for supercapacitors in energy storage.\",\n \"corpus_id\": 21894828,\n \"score\": 1\n },\n {\n \"doc_id\": \"28485575\",\n \"title\": \"Ni0.85Se@MoSe2 Nanosheet Arrays as the Electrode for High-Performance Supercapacitors.\",\n \"abstract\": \"In this study, we report novel Ni0.85Se@MoSe2 nanosheet arrays prepared by a facile one-step hydrothermal method through nickel (Ni) foam as Ni precursor and the framework of MoSe2. Owing to the unique interconnection and hierarchical porous nanosheet array architecture, the Ni0.85Se@MoSe2 nanosheet arrays exhibit a high specific capacitance of 774 F g(-1) at the current density of 1 A g(-1), which is almost 2 times higher than that (401 F g(-1)) of the Ni0.85Se matrix and about 7 times greater than that (113 F g(-1)) of the MoSe2 nanoparticles. Moreover, we report an asymmetric supercapacitor (ASC), which is fabricated by using the Ni0.85Se@MoSe2 nanosheet arrays as the positive electrode and the graphene nanosheets (GNS) as the negative electrode, with aqueous KOH as the electrolyte. The Ni0.85Se@MoSe2//GNS ASC possesses an output voltage of 1.6 V, an energy density of 25.5 Wh kg(-1) at a power density of 420 W kg(-1), and a cycling stability of 88% capacitance retention after 5000 cycles. These results indicate that the Ni0.85Se@MoSe2 nanosheet arrays are a good electrode for supercapacitors.\",\n \"corpus_id\": 46218126,\n \"score\": 1\n },\n {\n \"doc_id\": \"28731092\",\n \"title\": \"A Ni-P@NiCo LDH core-shell nanorod-decorated nickel foam with enhanced areal specific capacitance for high-performance supercapacitors.\",\n \"abstract\": \"Recently, transition metal-based nanomaterials have played a key role in the applications of supercapacitors. In this study, nickel phosphide (Ni-P) was simply combined with NiCo LDH via facile phosphorization of Ni foam and subsequent electrodeposition to form core-shell nanorod arrays on the Ni foam; the Ni-P@NiCo LDH was then directly used for a pseudocapacitive electrode. Owing to the splendid synergistic effect between Ni-P and NiCo LDH nanosheets as well as the hierarchical structure of 1D nanorods, 2D nanosheets, and 3D Ni foam, the hybrid electrode exhibited significantly enhanced electrochemical performances. The Ni-P@NiCo LDH electrode showed a high specific capacitance of 12.9 F cm(-2) at 5 mA cm(-2) (3470.5 F g(-1) at a current density of 1.3 A g(-1)) that remained as high as 6.4 F cm(-2) at a high current density of 100 mA cm(-2) (1700 F g(-1) at 27 A g(-1)) and excellent cycling stability (96% capacity retention after 10 000 cycles at 40 mA cm(-2)). Furthermore, the asymmetric supercapacitors (ASCs) were assembled using Ni-P@NiCo LDH as a positive electrode and activated carbon (AC) as a negative electrode. The obtained ASCs delivered remarkable energy density and power density as well as good cycling performance. The enhanced electrochemical activities open a new avenue for the development of supercapacitors.\",\n \"corpus_id\": 20729210,\n \"score\": 1\n },\n {\n \"doc_id\": \"28749370\",\n \"title\": \"Hierarchical nanosheet-based Ni3S2 microspheres grown on Ni foam for high-performance all-solid-state asymmetric supercapacitors.\",\n \"abstract\": \"The hierarchical nanosheet-based Ni3S2 microspheres directly grew on Ni foam using a two-step hydrothermal method. The microsphere with a diameter of ~1 microns and a rough surface was well connected with each other without any binders to provide a larger specific surface area, shorter ion/electron diffusion paths, richer electroactive sites as a supercapacitor electrode. As a three-electrode supercapacitor, it delivers the high specific capacity of 981.8 F g-1 at 2 A g-1, excellent rate capability of 436.4 F g-1 at 12 A g-1, and good cycling stability of 950.9 F g-1 with 96.9% retention after 1000 cycles at 2 A g-1. Furthermore, asymmetric supercapacitor based on Ni3S2-microsphere as a positive electrode and active carbon as a negative electrode shows the high energy density of 29.4 Wh kg-1 at 324.5 W kg-1 and high power density of 3197.6 W kg-1 at 15.1 Wh kg-1. This work demonstrates that nanosheet-based Ni3S2 microspheres coated Ni foam can be an effective electrode for a real supercapacitor.\",\n \"corpus_id\": 206086182,\n \"score\": 1\n },\n {\n \"doc_id\": \"28857459\",\n \"title\": \"Cobalt Doping To Boost the Electrochemical Properties of Ni@Ni3 S2 Nanowire Films for High-Performance Supercapacitors.\",\n \"abstract\": \"Metal sulfides have aroused great interest for energy storage. However, their low specific capacities and inferior rate capabilities hinder their practical applications. In this work, a facile cobalt-doping process is used to boost the electrochemical performance of Ni@Ni3 S2 core-sheath nanowire film electrodes for high-performance electrochemical energy storage. Co ions are doped successfully and uniformly into Ni3 S2 nanosheets through a facile ion-exchange process. The electrochemical properties of film electrodes are improved greatly, and an ultrahigh volumetric capacity (increased from 105 to 730 C cm-3 at 0.25 A cm-3 ) and excellent rate capability are obtained after Co is doped into Ni@Ni3 S2 core-sheath nanowires. A hybrid asymmetric supercapacitor with Co-doped Ni@Ni3 S2 as the positive electrode and graphene-carbon nanotubes as the negative electrode is assembled and exhibits an ultrahigh volumetric capacitance of 142 F cm-3 (based on the total volume of both electrodes) at 0.5 A cm-3 and excellent cycling stability (only 3 % capacitance decrease after 5000 cycles). Moreover, the volumetric energy density can reach 44.5 mWh cm-3 , which is much larger than those of thin-film lithium batteries (1-10 mWh cm-3 ). These results may provide useful insights for the fabrication of high-performance film electrodes for energy-storage applications.\",\n \"corpus_id\": 25925177,\n \"score\": 1\n },\n {\n \"doc_id\": \"29408138\",\n \"title\": \"Microwave synthesis of three-dimensional nickel cobalt sulfide nanosheets grown on nickel foam for high-performance asymmetric supercapacitors.\",\n \"abstract\": \"A facile and cost-effective microwave method is developed to prepare ternary nickel cobalt sulfide (NiCo2S4) interconnected nanosheet arrays on nickel foam (NF). When acting as an electrochemical supercapacitor electrode material, the as-prepared NiCo2S4/NF shows a high specific capacitance of 1502 F g-1 at a current density of 1 A g-1, and outstanding cycling stability of 91% capacitance retention after 8000 cycles. In addition, a asymmetric supercapacitor (ASC) is composed of NiCo2S4/NF as positive electrode and activated carbon as negative electrode, which exhibits a high energy density of 34.7 W h kg-1 at a power density of 750 W kg-1 and long-term cyclic stability (83.7% capacity retention after 8000 cycles). Even at a high power density of 15 kW kg-1, it still remains an energy density of 17.9 W h kg-1, which is able to light up a light-emitting diode. These findings provide a new and facile approach to fabricate high-performance electrode for supercapacitors.\",\n \"corpus_id\": 3547848,\n \"score\": 1\n },\n {\n \"doc_id\": \"29431782\",\n \"title\": \"A metal-organic framework derived hierarchical nickel-cobalt sulfide nanosheet array on Ni foam with enhanced electrochemical performance for supercapacitors.\",\n \"abstract\": \"Metal-organic frameworks (MOFs) have emerged as a new platform for the construction of various functional materials for energy related applications. Here, a facile MOF templating method is developed to fabricate a hierarchical nickel-cobalt sulfide nanosheet array on conductive Ni foam (Ni-Co-S/NF) as a binder-free electrode for supercapacitors. A uniform 2D Co-MOF nanowall array is first grown in situ on Ni foam in aqueous solution at room temperature, and then the Co-MOF nanowalls are converted into hierarchical Ni-Co-S nanoarchitectures via an etching and ion-exchange reaction with Ni(NO3)2, and a subsequent solvothermal sulfurization. Taking advantage of the compositional and structural merits of the hierarchical Ni-Co-S nanosheet array and conductive Ni foam, such as fast electron transportation, short ion diffusion path, abundant active sites and rich redox reactions, the obtained Ni-Co-S/NF electrode exhibits excellent electrochemical capacitive performance (1406.9 F g-1 at 0.5 A g-1, 53.9% retention at 10 A g-1 and 88.6% retention over 1000 cycles), which is superior to control CoS/NF. An asymmetric supercapacitor (ASC) assembled by using the as-fabricated Ni-Co-S/NF as the positive electrode and activated carbon (AC) as the negative electrode delivers a high energy density of 24.8 W h kg-1 at a high power density of 849.5 W kg-1. Even when the power density is as high as 8.5 kW kg-1, the ASC still exhibits a high energy density of 12.5 W h kg-1. This facile synthetic strategy can also be extended to fabricate other hierarchical integrated electrodes for high-efficiency electrochemical energy conversion and storage devices.\",\n \"corpus_id\": 4229922,\n \"score\": 1\n },\n {\n \"doc_id\": \"29745016\",\n \"title\": \"Fabrication of a 3D Hierarchical Sandwich Co9 S8 /α-MnS@N-C@MoS2 Nanowire Architectures as Advanced Electrode Material for High Performance Hybrid Supercapacitors.\",\n \"abstract\": \"Supercapacitors suffer from lack of energy density and impulse the energy density limit, so a new class of hybrid electrode materials with promising architectures is strongly desirable. Here, the rational design of a 3D hierarchical sandwich Co9 S8 /α-MnS@N-C@MoS2 nanowire architecture is achieved during the hydrothermal sulphurization reaction by the conversion of binary mesoporous metal oxide core to corresponding individual metal sulphides core along with the formation of outer metal sulphide shell at the same time. Benefiting from the 3D hierarchical sandwich architecture, Co9 S8 /α-MnS@N-C@MoS2 electrode exhibits enhanced electrochemical performance with high specific capacity/capacitance of 306 mA h g-1 /1938 F g-1 at 1 A g-1 , and excellent cycling stability with a specific capacity retention of 86.9% after 10 000 cycles at 10 A g-1 . Moreover, the fabricated asymmetric supercapacitor device using Co9 S8 /α-MnS@N-C@MoS2 as the positive electrode and nitrogen doped graphene as the negative electrode demonstrates high energy density of 64.2 Wh kg-1 at 729.2 W kg-1 , and a promising energy density of 23.5 Wh kg-1 is still attained at a high power density of 11 300 W kg-1 . The hybrid electrode with 3D hierarchical sandwich architecture promotes enhanced energy density with excellent cyclic stability for energy storage.\",\n \"corpus_id\": 13699361,\n \"score\": 1\n }\n]","isConversational":false}}},{"rowIdx":69,"cells":{"query":{"kind":"string","value":"{\n \"doc_id\": \"28212744\",\n \"title\": \"PARP1 and Sox2: An Unlikely Team of Pioneers to Conquer the Nucleosome.\",\n \"abstract\": \"In this issue of Molecular Cell, Liu and Kraus (2017) demonstrate that the pioneer transcription factor Sox2 requires PARP1 to bind to a subset of its recognition motifs, which are located within nucleosomes across the genome.\",\n \"corpus_id\": 206997198\n}"},"candidates":{"kind":"list like","value":[{"doc_id":"19531481","title":"PARP1 poly(ADP-ribosyl)ates Sox2 to control Sox2 protein levels and FGF4 expression during embryonic stem cell differentiation.","abstract":"Transcription factors Oct4 and Sox2 are key players in maintaining the pluripotent state of embryonic stem cells (ESCs). Small changes in their levels disrupt normal expression of their target genes. However, it remains elusive how protein levels of Oct4 and Sox2 and expression of their target genes are precisely controlled in ESCs. Here we identify PARP1, a DNA-binding protein with an NAD+-dependent enzymatic activity, as a cofactor of Oct4 and Sox2 to regulate expression of their target gene FGF4. We demonstrate for the first time that PARP1 binds the FGF4 enhancer to positively regulate FGF4 expression. Our data show that PARP1 interacts with and poly(ADP-ribosyl)ates Sox2 directly, which may be a step required for dissociation and degradation of inhibitory Sox2 proteins from the FGF4 enhancer. When PARP1 activity is inhibited or absent, poly(ADP-ribosyl)ation of Sox2 decreases and association of Sox2 with FGF4 enhancers increases, accompanied by an elevated level of Sox2 proteins and reduced expression of FGF4. Significantly, specific knockdown of Sox2 expression by RNA interference can considerably abrogate the inhibitory effect of the poly(ADP-ribose) polymerase inhibitor on FGF4 expression. Interestingly, PARP1 deficiency does not affect undifferentiated ESCs but compromises cell survival and/or growth when ESCs are induced into differentiation. Addition of FGF4 can partially rescue the phenotypes caused by PARP1 deficiency during ESC differentiation. Taken together, this study uncovers new mechanisms through which Sox2 protein levels and FGF4 expression are dynamically regulated during ESC differentiation and adds a new member to the family of proteins regulating the properties of ESCs.","corpus_id":5436001,"score":2},{"doc_id":"20371698","title":"Uncoupling of the transactivation and transrepression functions of PARP1 protein.","abstract":"Poly(ADP ribose) polymerase 1 (PARP1) is a nuclear protein that regulates chromatin remodeling and transcription as well as DNA repair and genome stability pathways. Recent studies have revealed a paradoxical dual role of PARP1 protein in transcription. Specifically, although PARP1 controls transcriptional activation of a subset of genes that are heat shock- or hormone-dependent, it also directly inactivates transcription, establishes heterochromatin domains, and silences retrotransposable elements. However, the domains required for these disparate functions are currently unknown. In this paper, we report the discovery of a previously undescribed mutation in the Drosophila Parp locus. We show that the mutants express a deletion mutant of PARP1 protein with an altered DNA binding domain that carries only the second Zn-finger. We demonstrate that this alteration specifically excludes PARP1 protein from heterochromatin and makes PARP1 unable to maintain repression of retrotransposable elements. By characterizing the biological activity of this unique PARP1 mutant protein isoform, we have uncoupled the transactivation and transrepression functions of this protein.","corpus_id":25181289,"score":2},{"doc_id":"22056668","title":"Pioneer transcription factors: establishing competence for gene expression.","abstract":"Transcription factors are adaptor molecules that detect regulatory sequences in the DNA and target the assembly of protein complexes that control gene expression. Yet much of the DNA in the eukaryotic cell is in nucleosomes and thereby occluded by histones, and can be further occluded by higher-order chromatin structures and repressor complexes. Indeed, genome-wide location analyses have revealed that, for all transcription factors tested, the vast majority of potential DNA-binding sites are unoccupied, demonstrating the inaccessibility of most of the nuclear DNA. This raises the question of how target sites at silent genes become bound de novo by transcription factors, thereby initiating regulatory events in chromatin. Binding cooperativity can be sufficient for many kinds of factors to simultaneously engage a target site in chromatin and activate gene expression. However, in cases in which the binding of a series of factors is sequential in time and thus not initially cooperative, special \"pioneer transcription factors\" can be the first to engage target sites in chromatin. Such initial binding can passively enhance transcription by reducing the number of additional factors that are needed to bind the DNA, culminating in activation. In addition, pioneer factor binding can actively open up the local chromatin and directly make it competent for other factors to bind. Passive and active roles for the pioneer factor FoxA occur in embryonic development, steroid hormone induction, and human cancers. Herein we review the field and describe how pioneer factors may enable cellular reprogramming.","corpus_id":7463311,"score":2},{"doc_id":"22362888","title":"SRY (sex determining region Y)-box2 (Sox2)/poly ADP-ribose polymerase 1 (Parp1) complexes regulate pluripotency.","abstract":"To gain insight into mechanisms controlling SRY (sex determining region Y)-box 2 (Sox2) protein activity in mouse embryonic stem cells (ESCs), the endogenous Sox2 gene was tagged with FLAG/Hemagglutinin (HA) sequences by homologous recombination. Sox2 protein complexes were purified from Sox2/FLAG/HA knockin ESCs, and interacting proteins were defined by mass spectrometry. One protein in the complex was poly ADP-ribose polymerase I (Parp1). The results presented below demonstrate that Parp1 regulates Sox2 protein activity. In response to fibroblast growth factor (FGF)/extracellular signal-regulated kinase (ERK) signaling, Parp1 auto-poly ADP-ribosylation enhances Sox2-Parp1 interactions, and this complex inhibits Sox2 binding to octamer-binding transcription factor 4 (Oct4)/Sox2 enhancers. Based on these results, we propose a unique mechanism in which FGF signaling fine-tunes Sox2 activity through posttranslational modification of a critical interacting protein, Parp1, and balances the maintenance of ESC pluripotency and differentiation. In addition, we demonstrate that regulation of Sox2 activity by Parp1 is critical for efficient generation of induced pluripotent stem cells.","corpus_id":34556304,"score":2},{"doc_id":"23657885","title":"DNase-seq predicts regions of rotational nucleosome stability across diverse human cell types.","abstract":"DNase-seq is primarily used to identify nucleosome-depleted DNase I hypersensitive (DHS) sites genome-wide that correspond to active regulatory elements. However, ≈ 40 yr ago it was demonstrated that DNase I also digests with a ≈ 10-bp periodicity around nucleosomes matching the exposure of the DNA minor groove as it wraps around histones. Here, we use DNase-seq data from 49 samples representing diverse cell types to reveal this digestion pattern at individual loci and predict genomic locations where nucleosome rotational positioning, the orientation of DNA with respect to the histone surface, is stably maintained. We call these regions DNase I annotated regions of nucleosome stability (DARNS). Compared to MNase-seq experiments, we show DARNS correspond well to annotated nucleosomes. Interestingly, many DARNS are positioned over only one side of annotated nucleosomes, suggesting that the periodic digestion pattern attenuates over the nucleosome dyad. DARNS reproduce the arrangement of nucleosomes around transcription start sites and are depleted at ubiquitous DHS sites. We also generated DARNS from multiple lymphoblast cell line (LCL) samples. We found that LCL DARNS were enriched at DHS sites present in most of the original 49 samples but absent in LCLs, while multi-cell-type DARNS were enriched at LCL-specific DHS sites. This indicates that variably open DHS sites are often occupied by rotationally stable nucleosomes in cell types where the DHS site is closed. DARNS provide additional information about precise DNA orientation within individual nucleosomes not available from other nucleosome positioning assays and contribute to understanding the role of chromatin in gene regulation.","corpus_id":45663709,"score":2},{"doc_id":"23939864","title":"Artd1/Parp1 regulates reprogramming by transcriptional regulation of Fgf4 via Sox2 ADP-ribosylation.","abstract":"The recently established reprogramming of somatic cells into induced pluripotent stem cells (iPSCs) by Takahashi and Yamanaka represents a valuable tool for future therapeutic applications. To date, the mechanisms underlying this process are still largely unknown. In particular, the mechanisms how the Yamanaka factors (Oct4, Sox2, Klf4, and c-Myc) directly drive reprogramming and which additional components are involved are still not yet understood. In this study, we aimed at analyzing the role of ADP-ribosyltransferase diphtheria toxin-like one (Artd1; formerly called poly(ADP-ribose) polymerase 1 [Parp1]) during reprogramming. We found that poly(ADP-ribosylation) (PARylation) of the reprogramming factor Sox2 by Artd1 plays an important role during the first days upon transduction with the reprogramming factors. A process that happens before Artd1 in conjunction with 10-11 translocation-2 (Tet2) mediates the histone modifications necessary for the establishment of an activated chromatin state at pluripotency loci (e.g., Nanog and Essrb) [Nature 2012;488:652-655]. Wild-type (WT) fibroblasts treated with an Artd1 inhibitor as well as fibroblasts deficient for Artd1 (Artd1-/-) show strongly decreased reprogramming capacity. Our data indicate that Artd1-mediated PARylation of Sox2 favors its binding to the fibroblast growth factor 4 (Fgf4) enhancer, thereby activating Fgf4 expression. The importance of Fgf4 during the first 4 days upon initiation of reprogramming was also highlighted by the observation that exogenous addition of Fgf4 was sufficient to restore the reprogramming capacity of Artd1-/- fibroblast to WT levels. In conclusion, our data clearly show that the interaction between Artd1 and Sox2 is crucial for the first steps of the reprogramming process and that early expression of Fgf4 (day 2 to day 4) is an essential component for the successful generation of iPSCs.","corpus_id":206513034,"score":2},{"doc_id":"25512556","title":"Pioneer transcription factors in cell reprogramming.","abstract":"A subset of eukaryotic transcription factors possesses the remarkable ability to reprogram one type of cell into another. The transcription factors that reprogram cell fate are invariably those that are crucial for the initial cell programming in embryonic development. To elicit cell programming or reprogramming, transcription factors must be able to engage genes that are developmentally silenced and inappropriate for expression in the original cell. Developmentally silenced genes are typically embedded in \"closed\" chromatin that is covered by nucleosomes and not hypersensitive to nuclease probes such as DNase I. Biochemical and genomic studies have shown that transcription factors with the highest reprogramming activity often have the special ability to engage their target sites on nucleosomal DNA, thus behaving as \"pioneer factors\" to initiate events in closed chromatin. Other reprogramming factors appear dependent on pioneer factors for engaging nucleosomes and closed chromatin. However, certain genomic domains in which nucleosomes are occluded by higher-order chromatin structures, such as in heterochromatin, are resistant to pioneer factor binding. Understanding the means by which pioneer factors can engage closed chromatin and how heterochromatin can prevent such binding promises to advance our ability to reprogram cell fates at will and is the topic of this review.","corpus_id":1775111,"score":2},{"doc_id":"25578969","title":"DNA-mediated cooperativity facilitates the co-selection of cryptic enhancer sequences by SOX2 and PAX6 transcription factors.","abstract":"Sox2 and Pax6 are transcription factors that direct cell fate decision during neurogenesis, yet the mechanism behind how they cooperate on enhancer DNA elements and regulate gene expression is unclear. By systematically interrogating Sox2 and Pax6 interaction on minimal enhancer elements, we found that cooperative DNA recognition relies on combinatorial nucleotide switches and precisely spaced, but cryptic composite DNA motifs. Surprisingly, all tested Sox and Pax paralogs have the capacity to cooperate on such enhancer elements. NMR and molecular modeling reveal very few direct protein-protein interactions between Sox2 and Pax6, suggesting that cooperative binding is mediated by allosteric interactions propagating through DNA structure. Furthermore, we detected and validated several novel sites in the human genome targeted cooperatively by Sox2 and Pax6. Collectively, we demonstrate that Sox-Pax partnerships have the potential to substantially alter DNA target specificities and likely enable the pleiotropic and context-specific action of these cell-lineage specifiers.","corpus_id":12404563,"score":2},{"doc_id":"25892221","title":"Pioneer transcription factors target partial DNA motifs on nucleosomes to initiate reprogramming.","abstract":"Pioneer transcription factors (TFs) access silent chromatin and initiate cell-fate changes, using diverse types of DNA binding domains (DBDs). FoxA, the paradigm pioneer TF, has a winged helix DBD that resembles linker histone and thereby binds its target sites on nucleosomes and in compacted chromatin. Herein, we compare the nucleosome and chromatin targeting activities of Oct4 (POU DBD), Sox2 (HMG box DBD), Klf4 (zinc finger DBD), and c-Myc (bHLH DBD), which together reprogram somatic cells to pluripotency. Purified Oct4, Sox2, and Klf4 proteins can bind nucleosomes in vitro, and in vivo they preferentially target silent sites enriched for nucleosomes. Pioneer activity relates simply to the ability of a given DBD to target partial motifs displayed on the nucleosome surface. Such partial motif recognition can occur by coordinate binding between factors. Our findings provide insight into how pioneer factors can target naive chromatin sites.","corpus_id":11011905,"score":2},{"doc_id":"25992972","title":"Differential Nucleosome Occupancies across Oct4-Sox2 Binding Sites in Murine Embryonic Stem Cells.","abstract":"The binding sequence for any transcription factor can be found millions of times within a genome, yet only a small fraction of these sequences encode functional transcription factor binding sites. One of the reasons for this dichotomy is that many other factors, such as nucleosomes, compete for binding. To study how the competition between nucleosomes and transcription factors helps determine a functional transcription factor site from a predicted transcription factor site, we compared experimentally-generated in vitro nucleosome occupancy with in vivo nucleosome occupancy and transcription factor binding in murine embryonic stem cells. Using a solution hybridization enrichment technique, we generated a high-resolution nucleosome map from targeted regions of the genome containing predicted sites and functional sites of Oct4/Sox2 regulation. We found that at Pax6 and Nes, which are bivalently poised in stem cells, functional Oct4 and Sox2 sites show high amounts of in vivo nucleosome displacement compared to in vitro. Oct4 and Sox2, which are active, show no significant displacement of in vivo nucleosomes at functional sites, similar to nonfunctional Oct4/Sox2 binding. This study highlights a complex interplay between Oct4 and Sox2 transcription factors and nucleosomes among different target genes, which may result in distinct patterns of stem cell gene regulation.","corpus_id":16086753,"score":2},{"doc_id":"26826681","title":"Pioneer transcription factors, chromatin dynamics, and cell fate control.","abstract":"Among the diverse transcription factors that are necessary to elicit changes in cell fate, both in embryonic development and in cellular reprogramming, a subset of factors are capable of binding to their target sequences on nucleosomal DNA and initiating regulatory events in silent chromatin. Such 'pioneer transcription factors' initiate cooperative interactions with other regulatory proteins to elicit changes in local chromatin structure. As a consequence of pioneer factor binding, the local chromatin can either become open and competent for activation, closed and repressed, or transcriptionally active. Understanding how pioneer factors initiate chromatin dynamics and how such can be blocked at heterochromatic sites provides insights into controlling cell fate transitions at will.","corpus_id":45121219,"score":2},{"doc_id":"28212747","title":"Catalytic-Independent Functions of PARP-1 Determine Sox2 Pioneer Activity at Intractable Genomic Loci.","abstract":"Pioneer transcription factors (TFs) function as genomic first responders, binding to inaccessible regions of chromatin to promote enhancer formation. The mechanism by which pioneer TFs gain access to chromatin remains an important unanswered question. Here we show that PARP-1, a nucleosome-binding protein, cooperates with intrinsic properties of the pioneer TF Sox2 to facilitate its binding to intractable genomic loci in embryonic stem cells. These actions of PARP-1 occur independently of its poly(ADP-ribosyl) transferase activity. PARP-1-dependent Sox2-binding sites reside in euchromatic regions of the genome with relatively high nucleosome occupancy and low co-occupancy by other transcription factors. PARP-1 stabilizes Sox2 binding to nucleosomes at suboptimal sites through cooperative interactions on DNA. Our results define intrinsic and extrinsic features that determine Sox2 pioneer activity. The conditional pioneer activity observed with Sox2 at a subset of binding sites may be a key feature of other pioneer TFs operating at intractable genomic loci.","corpus_id":23208167,"score":2},{"doc_id":"29452418","title":"PHF20 collaborates with PARP1 to promote stemness and aggressiveness of neuroblastoma cells through activation of SOX2 and OCT4.","abstract":"The differentiation status of neuroblastoma (NB) strongly correlates with its clinical outcomes; however, the molecular mechanisms driving maintenance of stemness and differentiation remain poorly understood. Here, we show that plant homeodomain finger-containing protein 20 (PHF20) functions as a critical epigenetic regulator in sustaining stem cell-like phenotype of NB by using CRISPR/Cas9-based targeted knockout (KO) for high-throughput screening of gene function in NB cell differentiation. The expression of PHF20 in NB was significantly associated with high aggressiveness of the tumor and poor outcomes for NB patients. Deletion of PHF20 inhibited NB cell proliferation, invasive migration, and stem cell-like traits. Mechanistically, PHF20 interacts with poly(ADP-ribose) polymerase 1 (PARP1) and directly binds to promoter regions of octamer-binding transcription factor 4 (OCT4) and sex determining region Y-box 2 (SOX2) to modulate a histone mark associated with active transcription, trimethylation of lysine 4 on histone H3 protein subunit (H3K4me3). Overexpression of OCT4 and SOX2 restored growth and progression of PHF20 KO tumor cells. Consistently, OCT4 and SOX2 protein levels in clinical NB specimens were positively correlated with PHF20 expression. Our results establish PHF20 as a key driver of NB stem cell-like properties and aggressive behaviors, with implications for prognosis and therapy.","corpus_id":3354357,"score":2},{"doc_id":"19339686","title":"Nucleosome-binding affinity as a primary determinant of the nuclear mobility of the pioneer transcription factor FoxA.","abstract":"FoxA proteins are pioneer transcription factors, among the first to bind chromatin domains in development and enable gene activity. The Fox DNA-binding domain structurally resembles linker histone and binds nucleosomes stably. Using fluorescence recovery after photobleaching, we found that FoxA1 and FoxA2 move much more slowly in nuclei than other transcription factor types, including c-Myc, GATA-4, NF-1, and HMGB1. We find that slower nuclear mobility correlates with high nonspecific nucleosome binding, and point mutations that disrupt nonspecific binding markedly increase nuclear mobility. FoxA's distinct nuclear mobility is consistent with its pioneer activity in chromatin.","corpus_id":13257310,"score":1},{"doc_id":"19378173","title":"Nucleosome mapping.","abstract":"The basic repeating unit of chromatin, the nucleosome, is known to play a critical role in regulating the process of gene transcription. The positioning of nucleosomes on a promoter is a significant determinant in its responsiveness to gene-inducing signals. For example, positioning and subsequent mobilization of nucleosomes can regulate the access of various DNA factors to underlying DNA templates. Several mechanisms have been proposed to direct the process of nucleosome displacement such as chemical histone modifications, ATP-dependent remodelling, and the incorporation of histone variants. Thus, rather than being an inert molecular structure, chromatin is highly dynamic in response to the transcription process. In this section, we describe two methodologies that allow the determination of exact nucleosome positioning within specific gene regions.","corpus_id":3173036,"score":1},{"doc_id":"19572828","title":"A non-homogeneous hidden-state model on first order differences for automatic detection of nucleosome positions.","abstract":"The ability to map individual nucleosomes accurately across genomes enables the study of relationships between dynamic changes in nucleosome positioning/occupancy and gene regulation. However, the highly heterogeneous nature of nucleosome densities across genomes and short linker regions pose challenges in mapping nucleosome positions based on high-throughput microarray data of micrococcal nuclease (MNase) digested DNA. Previous works rely on additional detrending and careful visual examination to detect low-signal nucleosomes, which may exist in a subpopulation of cells. We propose a non-homogeneous hidden-state model based on first order differences of experimental data along genomic coordinates that bypasses the need for local detrending and can automatically detect nucleosome positions of various occupancy levels. Our proposed approach is applicable to both low and high resolution MNase-Chip and MNase-Seq (high throughput sequencing) data, and is able to map nucleosome-linker boundaries accurately. This automated algorithm is also computationally efficient and only requires a simple preprocessing step. We provide several examples illustrating the pitfalls of existing methods, the difficulties of detrending the observed hybridization signals and demonstrate the advantages of utilizing first order differences in detecting nucleosome occupancies via simulations and case studies involving MNase-Chip and MNase-Seq data of nucleosome occupancy in yeast S. cerevisiae.","corpus_id":8982077,"score":1},{"doc_id":"20412763","title":"First time, every time: nucleosomes at a promoter can determine the probability of gene activation.","abstract":"Transcription factor binding sites are found in either nucleosome-free or nucleosome-embedded locations, thus in vivo relationships between nucleosome position and gene activation are not fully understood. In this issue of Developmental Cell, Bai et al. show that binding sites located in nucleosome depleted regions guarantee high reliability, not amplitude, of promoter firing.","corpus_id":5275643,"score":1},{"doc_id":"20726797","title":"ChIP-seq and functional analysis of the SOX2 gene in colorectal cancers.","abstract":"SOX2 is an HMG box containing transcription factor that has been implicated in various types of cancer, but its role in colorectal cancers (CRC) has not been studied. Here we show that SOX2 is overexpressed in CRC tissues compared with normal adjacent tissues using immunohistochemical staining and RT-PCR. We also observed an increased SOX2 expression in nucleus of colorectal cancer tissues (46%, 14/30 cases vs. 7%, 2/30 adjacent tissues). Furthermore, knockdown of SOX2 in SW620 colorectal cancer cells decreased their growth rates in vitro cell line, and in vivo in xenograft models. ChIP-Seq analysis of SOX2 revealed a consensus sequence of wwTGywTT. An integrated expression profiling and ChIP-seq analysis show that SOX2 is involved in the BMP signaling pathway, steroid metabolic process, histone modifications, and many receptor-mediated signaling pathways such as IGF1R and ITPR2 (Inositol 1,4,5-triphosphate receptor, type 2).","corpus_id":5861643,"score":1},{"doc_id":"21623366","title":"The nucleosome map of the mammalian liver.","abstract":"Binding to nucleosomal DNA is critical for 'pioneer' transcription factors such as the winged-helix transcription factors Foxa1 and Foxa2 to regulate chromatin structure and gene activation. Here we report the genome-wide map of nucleosome positions in the mouse liver, with emphasis on transcriptional start sites, CpG islands, Foxa2 binding sites and their correlation with gene expression. Despite the heterogeneity of liver tissue, we could clearly discern the nucleosome pattern of the predominant liver cell, the hepatocyte. By analyzing nucleosome occupancy and the distributions of heterochromatin protein 1 (Hp1), CBP (also known as Crebbp) and p300 (Ep300) in Foxa1- and Foxa2-deficient livers, we find that the maintenance of nucleosome position and chromatin structure surrounding Foxa2 binding sites is independent of Foxa1 and Foxa2.","corpus_id":25545264,"score":1},{"doc_id":"21982223","title":"Long live sox2: sox2 lasts a lifetime.","abstract":"Sox2 is a key transcription factor required for the maintenance of pluripotency in embryonic cells and morphogenesis of several epithelia. In this issue of Cell Stem Cell, Arnold et al. (2011) demonstrate that Sox2 marks long-lived adult stem cells to ensure homeostasis in a broad range of adult tissues.","corpus_id":205243399,"score":1},{"doc_id":"22559821","title":"Standardized collection of MNase-seq experiments enables unbiased dataset comparisons.","abstract":"BACKGROUND: The organization of eukaryotic DNA into chromatin has a strong influence on the accessibility and regulation of genetic information. The locations and occupancies of a principle component of chromatin, nucleosomes, are typically assayed through use of enzymatic digestion with micrococcal nuclease (MNase). MNase is an endo-exo nuclease that preferentially digests naked DNA and the DNA in linkers between nucleosomes, thus enriching for nucleosome-associated DNA. To determine nucleosome organization genome-wide, DNA remaining from MNase digestion is sequenced using high-throughput sequencing technologies (MNase-seq). Unfortunately, the results of MNase-seq can vary dramatically due to technical differences and this confounds comparisons between MNase-seq experiments, such as examining condition-dependent chromatin organizations. RESULTS: In this study we use MNase digestion simulations to demonstrate how MNase-seq signals can vary for different nucleosome configuration when experiments are performed with different extents of MNase digestion. Signal variation in these simulations reveals an important DNA sampling bias that results from a neighborhood effect of MNase digestion techniques. The presence of this neighborhood effect ultimately confounds comparisons between different MNase-seq experiments. To address this issue we present a standardized chromatin preparation which controls for technical variance between MNase-based chromatin preparations and enables the collection of similarly sampled (matched) chromatin populations. Standardized preparation of chromatin includes a normalization step for DNA input into MNase digestions and close matching of the extent of digestion between each chromatin preparation using gel densitometry analysis. The protocol also includes directions for successful pairing with multiplex sequencing reactions. CONCLUSIONS: We validated our method by comparing the experiment-to-experiment variation between biological replicates of chromatin preparations from S. cerevisiae. Results from our matched preparation consistently produced MNase-seq datasets that were more closely correlated than other unstandardized approaches. Additionally, we validated the ability of our approach at enabling accurate downstream comparisons of chromatin structures, by comparing the specificity of detecting Tup1-dependent chromatin remodeling events in comparisons between matched and un-matched wild-type and tup1Δ MNase-seq datasets. Our matched MNase-seq datasets demonstrated a significant reduction in non-specific (technical) differences between experiments and were able to maximize the detection of biologically-relevant (Tup1-dependent) changes in chromatin structure.","corpus_id":14105454,"score":1},{"doc_id":"22929772","title":"Genome-wide mapping of nucleosome positions in yeast using high-resolution MNase ChIP-Seq.","abstract":"Eukaryotic DNA is packaged into chromatin where nucleosomes form the basic building unit. Knowing the precise positions of nucleosomes is important because they determine the accessibility of underlying regulatory DNA sequences. Here we describe a detailed method to map on a genomic scale the locations of nucleosomes with very high resolution. Micrococcal nuclease (MNase) digestion followed by chromatin immunoprecipitation and facilitated library construction for deep sequencing provides a simple and accurate map of nucleosome positions.","corpus_id":26494948,"score":1},{"doc_id":"23166509","title":"Controls of nucleosome positioning in the human genome.","abstract":"Nucleosomes are important for gene regulation because their arrangement on the genome can control which proteins bind to DNA. Currently, few human nucleosomes are thought to be consistently positioned across cells; however, this has been difficult to assess due to the limited resolution of existing data. We performed paired-end sequencing of micrococcal nuclease-digested chromatin (MNase-seq) from seven lymphoblastoid cell lines and mapped over 3.6 billion MNase-seq fragments to the human genome to create the highest-resolution map of nucleosome occupancy to date in a human cell type. In contrast to previous results, we find that most nucleosomes have more consistent positioning than expected by chance and a substantial fraction (8.7%) of nucleosomes have moderate to strong positioning. In aggregate, nucleosome sequences have 10 bp periodic patterns in dinucleotide frequency and DNase I sensitivity; and, across cells, nucleosomes frequently have translational offsets that are multiples of 10 bp. We estimate that almost half of the genome contains regularly spaced arrays of nucleosomes, which are enriched in active chromatin domains. Single nucleotide polymorphisms that reduce DNase I sensitivity can disrupt the phasing of nucleosome arrays, which indicates that they often result from positioning against a barrier formed by other proteins. However, nucleosome arrays can also be created by DNA sequence alone. The most striking example is an array of over 400 nucleosomes on chromosome 12 that is created by tandem repetition of sequences with strong positioning properties. In summary, a large fraction of nucleosomes are consistently positioned--in some regions because they adopt favored sequence positions, and in other regions because they are forced into specific arrangements by chromatin remodeling or DNA binding proteins.","corpus_id":4689524,"score":1},{"doc_id":"23169531","title":"Co-motif discovery identifies an Esrrb-Sox2-DNA ternary complex as a mediator of transcriptional differences between mouse embryonic and epiblast stem cells.","abstract":"Transcription factors (TF) often bind in heterodimeric complexes with each TF recognizing a specific neighboring cis element in the regulatory region of the genome. Comprehension of this DNA motif grammar is opaque, yet recent developments have allowed the interrogation of genome-wide TF binding sites. We reasoned that within this data novel motif grammars could be identified that controlled distinct biological programs. For this purpose, we developed a novel motif-discovery tool termed fexcom that systematically interrogates ChIP-seq data to discover spatially constrained TF-TF composite motifs occurring over short DNA distances. We applied this to the extensive ChIP-seq data available from mouse embryonic stem cells (ESCs). In addition to the well-known and most prevalent sox-oct motif, we also discovered a novel constrained spacer motif for Esrrb and Sox2 with a gap of between 2 and 8 bps that Essrb and Sox2 cobind in a selective fashion. Through the use of knockdown experiments, we argue that the Esrrb-Sox2 complex is an arbiter of gene expression differences between ESCs and epiblast stem cells (EpiSC). A number of genes downregulated upon dual Esrrb/Sox2 knockdown (e.g., Klf4, Klf5, Jam2, Pecam1) are similarly downregulated in the ESC to EpiSC transition and contain the esrrb-sox motif. The prototypical Esrrb-Sox2 target gene, containing an esrrb-sox element conserved throughout eutherian and metatherian mammals, is Nr0b1. Through positive regulation of this transcriptional repressor, we argue the Esrrb-Sox2 complex promotes the ESC state through inhibition of the EpiSC transcriptional program and the same trio may also function to maintain trophoblast stem cells.","corpus_id":24689885,"score":1},{"doc_id":"23805837","title":"Contribution of nucleosome binding preferences and co-occurring DNA sequences to transcription factor binding.","abstract":"BACKGROUND: Chromatin plays a critical role in regulating transcription factors (TFs) binding to their canonical transcription factor binding sites (TFBS). Recent studies in vertebrates show that many TFs preferentially bind to genomic regions that are well bound by nucleosomes in vitro. Co-occurring secondary motifs sometimes correlated with functional TFBS. RESULTS: We used a logistic regression to evaluate how well the propensity for nucleosome binding and co-occurrence of a secondary motif identify which canonical motifs are bound in vivo. We used ChIP-seq data for three transcription factors binding to their canonical motifs: c-Jun binding the AP-1 motif (TGA(C)/(G)TCA), GR (glucocorticoid receptor) binding the GR motif (G-ACA---(T)/(C)GT-C), and Hoxa2 (homeobox a2) binding the Pbx (Pre-B-cell leukemia homeobox) motif (TGATTGAT). For all canonical TFBS in the mouse genome, we calculated intrinsic nucleosome occupancy scores (INOS) for its surrounding 150-bps DNA and examined the relationship with in vivo TF binding. In mouse mammary 3134 cells, c-Jun and GR proteins preferentially bound regions calculated to be well-bound by nucleosomes in vitro with the canonical AP-1 and GR motifs themselves contributing to the high INOS. Functional GR motifs are enriched for AP-1 motifs if they are within a nucleosome-sized 150-bps region. GR and Hoxa2 also bind motifs with low INOS, perhaps indicating a different mechanism of action. CONCLUSION: Our analysis quantified the contribution of INOS and co-occurring sequence to the identification of functional canonical motifs in the genome. This analysis revealed an inherent competition between some TFs and nucleosomes for binding canonical TFBS. GR and c-Jun cooperate if they are within 150-bps. Binding of Hoxa2 and a fraction of GR to motifs with low INOS values suggesting they are not in competition with nucleosomes and may function using different mechanisms.","corpus_id":11561522,"score":1},{"doc_id":"25026204","title":"Sox2: masterminding the root of cancer.","abstract":"The transcription factor Sox2 is a master regulator that maintains stemness in embryonic stem cells and neural stem cells. Using elegant lineage tracing strategies and genetic reporter mouse models, two studies (one of which is by Vanner and colleagues in this issue of Cancer Cell) now demonstrate that rare Sox2-expressing cells are the founding cancer stem cell population driving tumor initiation and therapy resistance.","corpus_id":206542422,"score":1},{"doc_id":"25085421","title":"Two distinct promoter architectures centered on dynamic nucleosomes control ribosomal protein gene transcription.","abstract":"In yeast, ribosome production is controlled transcriptionally by tight coregulation of the 138 ribosomal protein genes (RPGs). RPG promoters display limited sequence homology, and the molecular basis for their coregulation remains largely unknown. Here we identify two prevalent RPG promoter types, both characterized by upstream binding of the general transcription factor (TF) Rap1 followed by the RPG-specific Fhl1/Ifh1 pair, with one type also binding the HMG-B protein Hmo1. We show that the regulatory properties of the two promoter types are remarkably similar, suggesting that they are determined to a large extent by Rap1 and the Fhl1/Ifh1 pair. Rapid depletion experiments allowed us to define a hierarchy of TF binding in which Rap1 acts as a pioneer factor required for binding of all other TFs. We also uncovered unexpected features underlying recruitment of Fhl1, whose forkhead DNA-binding domain is not required for binding at most promoters, and Hmo1, whose binding is supported by repeated motifs. Finally, we describe unusually micrococcal nuclease (MNase)-sensitive nucleosomes at all RPG promoters, located between the canonical +1 and -1 nucleosomes, which coincide with sites of Fhl1/Ifh1 and Hmo1 binding. We speculate that these \"fragile\" nucleosomes play an important role in regulating RPG transcriptional output.","corpus_id":10208343,"score":1},{"doc_id":"25380620","title":"Profiling gene promoter occupancy of Sox2 in two phenotypically distinct breast cancer cell subsets using chromatin immunoprecipitation and genome-wide promoter microarrays.","abstract":"INTRODUCTION: Aberrant expression of the embryonic stem cell marker Sox2 has been reported in breast cancer (BC). We previously identified two phenotypically distinct BC cell subsets separated based on their differential response to a Sox2 transcription activity reporter, namely the reporter-unresponsive (RU) and the more tumorigenic reporter-responsive (RR) cells. We hypothesized that Sox2, as a transcription factor, contributes to their phenotypic differences by mediating differential gene expression in these two cell subsets. METHODS: We used chromatin immunoprecipitation and a human genome-wide promoter microarray (ChIP-chip) to determine the promoter occupancies of Sox2 in the MCF7 RU and RR breast cancer cell populations. We validated our findings with conventional chromatin immunoprecipitation, quantitative reverse transcription polymerase chain reaction (qPCR), and western blotting using cell lines, and also performed qPCR using patient RU and RR samples. RESULTS: We found a largely mutually exclusive profile of gene promoters bound by Sox2 between RU and RR cells derived from MCF7 (1830 and 456 genes, respectively, with only 62 overlapping genes). Sox2 was bound to stem cell- and cancer-associated genes in RR cells. Using quantitative RT-PCR, we confirmed that 15 such genes, including PROM1 (CD133), BMI1, GPR49 (LGR5), and MUC15, were expressed significantly higher in RR cells. Using siRNA knockdown or enforced expression of Sox2, we found that Sox2 directly contributes to the higher expression of these genes in RR cells. Mucin-15, a novel Sox2 downstream target in BC, contributes to the mammosphere formation of BC cells. Parallel findings were observed in the RU and RR cells derived from patient samples. CONCLUSIONS: In conclusion, our data supports the model that the Sox2 induces differential gene expression in the two distinct cell subsets in BC, and contributes to their phenotypic differences.","corpus_id":11180637,"score":1},{"doc_id":"25494698","title":"Unbiased chromatin accessibility profiling by RED-seq uncovers unique features of nucleosome variants in vivo.","abstract":"BACKGROUND: Differential accessibility of DNA to nuclear proteins underlies the regulation of numerous cellular processes. Although DNA accessibility is primarily determined by the presence or absence of nucleosomes, differences in nucleosome composition or dynamics may also regulate accessibility. Methods for mapping nucleosome positions and occupancies genome-wide (MNase-seq) have uncovered the nucleosome landscapes of many different cell types and organisms. Conversely, methods specialized for the detection of large nucleosome-free regions of chromatin (DNase-seq, FAIRE-seq) have uncovered numerous gene regulatory elements. However, these methods are less successful in measuring the accessibility of DNA sequences within nucelosome arrays. RESULTS: Here we probe the genome-wide accessibility of multiple cell types in an unbiased manner using restriction endonuclease digestion of chromatin coupled to deep sequencing (RED-seq). Using this method, we identified differences in chromatin accessibility between populations of cells, not only in nucleosome-depleted regions of the genome (e.g., enhancers and promoters), but also within the majority of the genome that is packaged into nucleosome arrays. Furthermore, we identified both large differences in chromatin accessibility in distinct cell lineages and subtle but significant changes during differentiation of mouse embryonic stem cells (ESCs). Most significantly, using RED-seq, we identified differences in accessibility among nucleosomes harboring well-studied histone variants, and show that these differences depend on factors required for their deposition. CONCLUSIONS: Using an unbiased method to probe chromatin accessibility genome-wide, we uncover unique features of chromatin structure that are not observed using more widely-utilized methods. We demonstrate that different types of nucleosomes within mammalian cells exhibit different degrees of accessibility. These findings provide significant insight into the regulation of DNA accessibility.","corpus_id":13054798,"score":1},{"doc_id":"26080409","title":"MPE-seq, a new method for the genome-wide analysis of chromatin structure.","abstract":"The analysis of chromatin structure is essential for the understanding of transcriptional regulation in eukaryotes. Here we describe methidiumpropyl-EDTA sequencing (MPE-seq), a method for the genome-wide characterization of chromatin that involves the digestion of nuclei withMPE-Fe(II) followed by massively parallel sequencing. Like micrococcal nuclease (MNase), MPE-Fe(II) preferentially cleaves the linker DNA between nucleosomes. However, there are differences in the cleavage of nuclear chromatin by MPE-Fe(II) relative to MNase. Most notably, immediately upstream of the transcription start site of active promoters, we frequently observed nucleosome-sized (141-190 bp) and subnucleosome-sized (such as 101-140 bp) peaks of digested chromatin fragments with MPE-seq but not with MNase-seq. These peaks also correlate with the presence of core histones and could thus be due, at least in part, to noncanonical chromatin structures such as labile nucleosome-like particles that have been observed in other contexts. The subnucleosome-sized MPE-seq peaks exhibit a particularly distinct association with active promoters. In addition, unlike MNase, MPE-Fe(II) cleaves nuclear DNA with little sequence bias. In this regard, we found that DNA sequences at RNA splice sites are hypersensitive to digestion by MNase but not by MPE-Fe(II). This phenomenon may have affected the analysis of nucleosome occupancy over exons. These findings collectively indicate that MPE-seq provides a unique and straightforward means for the genome-wide analysis of chromatin structure with minimal DNA sequence bias. In particular, the combined use of MPE-seq and MNase-seq enables the identification of noncanonical chromatin structures that are likely to be important for the regulation of gene expression.","corpus_id":23349334,"score":1},{"doc_id":"26305327","title":"Genome-Wide Profiling of PARP1 Reveals an Interplay with Gene Regulatory Regions and DNA Methylation.","abstract":"Poly (ADP-ribose) polymerase-1 (PARP1) is a nuclear enzyme involved in DNA repair, chromatin remodeling and gene expression. PARP1 interactions with chromatin architectural multi-protein complexes (i.e. nucleosomes) alter chromatin structure resulting in changes in gene expression. Chromatin structure impacts gene regulatory processes including transcription, splicing, DNA repair, replication and recombination. It is important to delineate whether PARP1 randomly associates with nucleosomes or is present at specific nucleosome regions throughout the cell genome. We performed genome-wide association studies in breast cancer cell lines to address these questions. Our studies show that PARP1 associates with epigenetic regulatory elements genome-wide, such as active histone marks, CTCF and DNase hypersensitive sites. Additionally, the binding of PARP1 to chromatin genome-wide is mutually exclusive with DNA methylation pattern suggesting a functional interplay between PARP1 and DNA methylation. Indeed, inhibition of PARylation results in genome-wide changes in DNA methylation patterns. Our results suggest that PARP1 controls the fidelity of gene transcription and marks actively transcribed gene regions by selectively binding to transcriptionally active chromatin. These studies provide a platform for developing our understanding of PARP1's role in gene regulation.","corpus_id":16840041,"score":1},{"doc_id":"26429969","title":"Genome-wide profiling of nucleosome sensitivity and chromatin accessibility in Drosophila melanogaster.","abstract":"Nucleosomal DNA is thought to be generally inaccessible to DNA-binding factors, such as micrococcal nuclease (MNase). Here, we digest Drosophila chromatin with high and low concentrations of MNase to reveal two distinct nucleosome types: MNase-sensitive and MNase-resistant. MNase-resistant nucleosomes assemble on sequences depleted of A/T and enriched in G/C-containing dinucleotides, whereas MNase-sensitive nucleosomes form on A/T-rich sequences found at transcription start and termination sites, enhancers and DNase I hypersensitive sites. Estimates of nucleosome formation energies indicate that MNase-sensitive nucleosomes tend to be less stable than MNase-resistant ones. Strikingly, a decrease in cell growth temperature of about 10°C makes MNase-sensitive nucleosomes less accessible, suggesting that observed variations in MNase sensitivity are related to either thermal fluctuations of chromatin fibers or the activity of enzymatic machinery. In the vicinity of active genes and DNase I hypersensitive sites nucleosomes are organized into periodic arrays, likely due to 'phasing' off potential barriers formed by DNA-bound factors or by nucleosomes anchored to their positions through external interactions. The latter idea is substantiated by our biophysical model of nucleosome positioning and energetics, which predicts that nucleosomes immediately downstream of transcription start sites are anchored and recapitulates nucleosome phasing at active genes significantly better than sequence-dependent models.","corpus_id":17910210,"score":1},{"doc_id":"26764865","title":"Recognition of the nucleosome by chromatin factors and enzymes.","abstract":"Dynamic expression of the genome requires coordinated binding of chromatin factors and enzymes that carry out genome-templated processes. Until recently, the molecular mechanisms governing how these factors and enzymes recognize and act on the fundamental unit of chromatin, the nucleosome core particle, have remained a mystery. A small, yet growing set of structures of the nucleosome in complex with chromatin factors and enzymes highlights the importance of multivalency in defining nucleosome binding and specificity. Many such interactions include an arginine anchor motif, which targets a unique acidic patch on the nucleosome surface. These emerging paradigms for chromatin recognition will be discussed, focusing on several recent structural breakthroughs.","corpus_id":39417690,"score":1},{"doc_id":"26772197","title":"Mapping nucleosome positions using DNase-seq.","abstract":"Although deoxyribonuclease I (DNase I) was used to probe the structure of the nucleosome in the 1960s and 1970s, in the current high-throughput sequencing era, DNase I has mainly been used to study genomic regions devoid of nucleosomes. Here, we reveal for the first time that DNase I can be used to precisely map the (translational) positions of in vivo nucleosomes genome-wide. Specifically, exploiting a distinctive DNase I cleavage profile within nucleosome-associated DNA--including a signature 10.3 base pair oscillation that corresponds to accessibility of the minor groove as DNA winds around the nucleosome--we develop a Bayes-factor-based method that can be used to map nucleosome positions along the genome. Compared to methods that require genetically modified histones, our DNase-based approach is easily applied in any organism, which we demonstrate by producing maps in yeast and human. Compared to micrococcal nuclease (MNase)-based methods that map nucleosomes based on cuts in linker regions, we utilize DNase I cuts both outside and within nucleosomal DNA; the oscillatory nature of the DNase I cleavage profile within nucleosomal DNA enables us to identify translational positioning details not apparent in MNase digestion of linker DNA. Because the oscillatory pattern corresponds to nucleosome rotational positioning, it also reveals the rotational context of transcription factor (TF) binding sites. We show that potential binding sites within nucleosome-associated DNA are often centered preferentially on an exposed major or minor groove. This preferential localization may modulate TF interaction with nucleosome-associated DNA as TFs search for binding sites.","corpus_id":35136751,"score":1},{"doc_id":"26988140","title":"Sox2 in the differentiation of cochlear progenitor cells.","abstract":"HMG domain transcription factor, Sox2, is a critical gene for the development of cochlear hair cells, the receptor cells for hearing, but this has been ascribed to expansion of the progenitors that become hair cells. Here, we show that Sox2 activated Atoh1, a transcription factor important for hair cell differentiation, through an interaction with the 3' enhancer of Atoh1. Binding to consensus sequences in the Atoh1 enhancer was dependent on the level of Sox2, and the extent of enhancer binding correlated to the extent of activation. Atoh1 activation by Sox2 was required for embryonic hair cell development: deletion of Sox2 in an inducible mutant, even after progenitor cells were fully established, halted development of hair cells, and silencing also inhibited postnatal differentiation of hair cells induced by inhibition of γ-secretase. Sox2 is thus required in the cochlea to both expand the progenitor cells and initiate their differentiation to hair cells.","corpus_id":6272016,"score":1},{"doc_id":"27058788","title":"The Pioneer Transcription Factor FoxA Maintains an Accessible Nucleosome Configuration at Enhancers for Tissue-Specific Gene Activation.","abstract":"Nuclear DNA wraps around core histones to form nucleosomes, which restricts the binding of transcription factors to gene regulatory sequences. Pioneer transcription factors can bind DNA sites on nucleosomes and initiate gene regulatory events, often leading to the local opening of chromatin. However, the nucleosomal configuration of open chromatin and the basis for its regulation is unclear. We combined low and high levels of micrococcal nuclease (MNase) digestion along with core histone mapping to assess the nucleosomal configuration at enhancers and promoters in mouse liver. We find that MNase-accessible nucleosomes, bound by transcription factors, are retained more at liver-specific enhancers than at promoters and ubiquitous enhancers. The pioneer factor FoxA displaces linker histone H1, thereby keeping enhancer nucleosomes accessible in chromatin and allowing other liver-specific transcription factors to bind and stimulate transcription. Thus, nucleosomes are not exclusively repressive to gene regulation when they are retained with, and exposed by, pioneer factors.","corpus_id":206994505,"score":1},{"doc_id":"27335664","title":"Nucleosome Positioning.","abstract":"Nucleosome positioning is not only related to genomic DNA compaction but also to other biological functions. After the chromatin is digested by micrococcal nuclease, nucleosomal (nucleosome-bound) DNA fragments can be sequenced and mapped on the genomic DNA sequence. Due to the development of modern DNA sequencing technology, genome-wide nucleosome mapping has been performed in a wide range of eukaryotic species. Comparative analyses of the nucleosome positions have revealed that the nucleosome is more frequently formed in exonic than intronic regions, and that most of transcription start and translation (or transcription) end sites are located in nucleosome linker DNA regions, indicating that nucleosome positioning influences transcription initiation, transcription termination, and gene splicing. In addition, nucleosomal DNA contains guanine and cytosine (G + C)-rich sequences and a high level of cytosine methylation. Thus, the nucleosome positioning system has been conserved during eukaryotic evolution.","corpus_id":17217147,"score":1},{"doc_id":"27458208","title":"Genome-wide analysis reveals positional-nucleosome-oriented binding pattern of pioneer factor FOXA1.","abstract":"The compaction of nucleosomal structures creates a barrier for DNA-binding transcription factors (TFs) to access their cognate cis-regulatory elements. Pioneer factors (PFs) such as FOXA1 are able to directly access these cis-targets within compact chromatin. However, how these PFs interplay with nucleosomes remains to be elucidated, and is critical for us to understand the underlying mechanism of gene regulation. Here, we have conducted a computational analysis on a strand-specific paired-end ChIP-exo (termed as ChIP-ePENS) data of FOXA1 in LNCaP cells by our novel algorithm ePEST. We find that FOXA1 chromatin binding occurs via four distinct border modes (or footprint boundary patterns), with a preferential footprint boundary patterns relative to FOXA1 motif orientation. In addition, from this analysis three fundamental nucleotide positions (oG, oS and oH) emerged as major determinants for blocking exo-digestion and forming these four distinct border modes. By integrating histone MNase-seq data, we found an astonishingly consistent, 'well-positioned' configuration occurs between FOXA1 motifs and dyads of nucleosomes genome-wide. We further performed ChIP-seq of eight chromatin remodelers and found an increased occupancy of these remodelers on FOXA1 motifs for all four border modes (or footprint boundary patterns), indicating the full occupancy of FOXA1 complex on the three blocking sites (oG, oS and oH) likely produces an active regulatory status with well-positioned phasing for protein binding events. Together, our results suggest a positional-nucleosome-oriented accessing model for PFs seeking target motifs, in which FOXA1 can examine each underlying DNA nucleotide and is able to sense all potential motifs regardless of whether they face inward or outward from histone octamers along the DNA helix axis.","corpus_id":18204723,"score":1},{"doc_id":"27502481","title":"Sox2: A multitasking networker.","abstract":"The transcription factor Sox2 is best known as a pluripotency factor in stem and precursor cells and its expression generally correlates with an undifferentiated state. Proposed modes of action include those as classical transcription factor and pre-patterning factor with influence on histone modifications and chromatin structure. Recently, we provided the first detailed analysis of Sox2 expression and function during development of oligodendrocytes, the myelin-forming cells of the CNS. Surprisingly, we found evidence for a role of Sox2 as differentiation factor and found it to act through modulation of microRNA levels. Thus, we add new facets to the functional repertoire of Sox2 and throw light on the networking activity of this multitasking developmental regulator.","corpus_id":5275910,"score":1},{"doc_id":"27889238","title":"Insights into Nucleosome Organization in Mouse Embryonic Stem Cells through Chemical Mapping.","abstract":"Nucleosome organization influences gene activity by controlling DNA accessibility to transcription machinery. Here, we develop a chemical biology approach to determine mammalian nucleosome positions genome-wide. We uncovered surprising features of nucleosome organization in mouse embryonic stem cells. In contrast to the prevailing model, we observe that for nearly all mouse genes, a class of fragile nucleosomes occupies previously designated nucleosome-depleted regions around transcription start sites and transcription termination sites. We show that nucleosomes occupy DNA targets for a subset of DNA-binding proteins, including CCCTC-binding factor (CTCF) and pluripotency factors. Furthermore, we provide evidence that promoter-proximal nucleosomes, with the +1 nucleosome in particular, contribute to the pausing of RNA polymerase II. Lastly, we find a characteristic preference for nucleosomes at exon-intron junctions. Taken together, we establish an accurate method for defining the nucleosome landscape and provide a valuable resource for studying nucleosome-mediated gene regulation in mammalian cells.","corpus_id":5191876,"score":1},{"doc_id":"28301306","title":"Two possible modes of pioneering associated with combinations of H2A.Z and p300/CBP at nucleosome-occupied enhancers.","abstract":"Pioneer transcription factors are defined by their ability to bind nucleosome-occupied regions. Here, we discuss the properties of nucleosomes bound by pioneers at enhancer regions. We describe how select pioneers bind nucleosome-occupied or -depleted enhancer sites. Importantly, by revisiting and expanding existing data sets, we show differential H2A.Z and p300/CBP association at bound enhancers, highlighting two possible pioneering modes.","corpus_id":3554143,"score":1},{"doc_id":"28842672","title":"Downregulation of PARP1 transcription by promoter-associated E2F4-RBL2-HDAC1-BRM complex contributes to repression of pluripotency stem cell factors in human monocytes.","abstract":"Differentiation of certain cell types is followed by a downregulation of PARP1 expression. We show that the reduction in the abundance of PARP1 in hematopoietic progenitor cells and monocytes is tightly controlled by the cell cycle. The differentiation-associated cell cycle exit induces E2F1 replacement with E2F4 at the PARP1 promoter and the assembly of an E2F4-RBL2-HDAC1-BRM(SWI/SNF) repressor complex which deacetylates nucleosomes and compacts chromatin. In G1 arrested cells, PARP1 transcription is reduced by the recruitment of E2F1-RB1-HDAC1-EZH2(PRC2)-BRM/BRG1(SWI/SNF), which additionally trimethylates H3K27 and causes an even higher increase in nucleosome density. The re-establishment of an active chromatin structure by treating post-mitotic monocytes with the HDAC inhibitor and G1 arrested cells with a combination of HDAC and EZH2 inhibitors restores PARP1 expression completely but does not affect the interaction between the components of the repressor complex with chromatin. This suggests that RB1 and RBL2, as well as PRC2, SWI/SNF and HDAC1, do not interfere with the transcription machinery. Interestingly, reinstatement of PARP1 expression by the silencing of RBL2 or by the inhibition of HDACs in monocytes and by transfection with the PARP1 expression vector in differentiated THP-1 cells substantially increased transcription of pluripotency stem cell factors such as POU5F1, SOX2 and NANOG.","corpus_id":46903749,"score":1},{"doc_id":"29027167","title":"Characterization of the Nucleosome Landscape by Micrococcal Nuclease-Sequencing (MNase-seq).","abstract":"MNase-seq allows the genome-wide examination of the nucleosome landscape by determination of nucleosome positioning and occupancy. Typically, native or formaldehyde fixed chromatin is subjected to digestion by micrococcal nuclease (MNase), which degrades linker DNA and yields mainly mono-nucleosomes. The resulting material can be processed directly or can be subjected to an optional chromatin immunoprecipitation step (MNase-ChIP-seq). De-crosslinked and purified DNA is then subjected to next-generation sequencing. The protocol presented here has been tailored for the analysis of nucleosome landscape in the malaria parasite, Plasmodium falciparum, but most steps are directly applicable to other cell types. We also discuss general considerations for experimental design and computational analysis, which are crucial for accurate investigation of the nucleosome landscape.","corpus_id":23351532,"score":1},{"doc_id":"29052192","title":"Profiling Nucleosome Occupancy by MNase-seq: Experimental Protocol and Computational Analysis.","abstract":"Nucleosomes are the basic repeating units of eukaryotic chromatin. They play important roles in chromatin compaction and gene regulation. Therefore, it is important to profile the in vivo locations of nucleosomes in the genome. Here we illustrate how to profile nucleosome occupancy at genome-wide scale using micrococcal nuclease (MNase) digestion combined with high throughput Illumina sequencing (MNase-seq). Nucleosome-associated DNA is relatively insensitive to digestion by micrococcal nuclease (MNase). Upon mild MNase treatment, the undigested nucleosomal DNA can be purified and sequenced allowing a precise localization of in vivo nucleosomes at a genome-wide level.","corpus_id":8706843,"score":1},{"doc_id":"18643465","title":"Nucleosome switches.","abstract":"We present a statistical-mechanical model for the positioning of nucleosomes along genomic DNA molecules as a function of the strength of the binding potential and the chemical potential of the nucleosomes. We show that a significant section of the DNA is composed of two-level nucleosome switching regions where the nucleosome distribution undergoes a localized, first-order transition. The location of the nucleosome switches shows a strong correlation with the location of gene-regulation regions.","corpus_id":16837247,"score":0},{"doc_id":"22737086","title":"In vivo effects of histone H3 depletion on nucleosome occupancy and position in Saccharomyces cerevisiae.","abstract":"Previous studies in Saccharomyces cerevisiae established that depletion of histone H4 results in the genome-wide transcriptional de-repression of hundreds of genes. To probe the mechanism of this transcriptional de-repression, we depleted nucleosomes in vivo by conditional repression of histone H3 transcription. We then measured the resulting changes in transcription by RNA-seq and in chromatin organization by MNase-seq. This experiment also bears on the degree to which trans-acting factors and DNA-encoded elements affect nucleosome position and occupancy in vivo. We identified ∼60,000 nucleosomes genome wide, and we classified ∼2,000 as having preferentially reduced occupancy following H3 depletion and ∼350 as being preferentially retained. We found that the in vivo influence of DNA sequences that favor or disfavor nucleosome occupancy increases following histone H3 depletion, demonstrating that nucleosome density contributes to moderating the influence of DNA sequence on nucleosome formation in vivo. To identify factors important for influencing nucleosome occupancy and position, we compared our data to 40 existing whole-genome data sets. Factors associated with promoters, such as histone acetylation and H2A.z incorporation, were enriched at sites of nucleosome loss. Nucleosome retention was linked to stabilizing marks such as H3K36me2. Notably, the chromatin remodeler Isw2 was uniquely associated with retained occupancy and altered positioning, consistent with Isw2 stabilizing histone-DNA contacts and centering nucleosomes on available DNA in vivo. RNA-seq revealed a greater number of de-repressed genes (∼2,500) than previous studies, and these genes exhibited reduced nucleosome occupancy in their promoters. In summary, we identify factors likely to influence nucleosome stability under normal growth conditions and the specific genomic locations at which they act. We find that DNA-encoded nucleosome stability and chromatin composition dictate which nucleosomes will be lost under conditions of limiting histone protein and that this, in turn, governs which genes are susceptible to a loss of regulatory fidelity.","corpus_id":15417296,"score":0},{"doc_id":"23132853","title":"Activation of the SNF2 family ATPase ALC1 by poly(ADP-ribose) in a stable ALC1·PARP1·nucleosome intermediate.","abstract":"The human ALC1/CHD1L oncogene encodes an SNF2 family ATPase with a macrodomain that binds poly(ADP-ribose) (PAR). We and others previously showed that ALC1 possesses a cryptic ATP-dependent nucleosome remodeling activity that is potently activated in the presence of PARP1 and NAD(+), its substrate for PAR synthesis. In this work, we dissected the mechanism by which PARP1 and NAD(+) activate ALC1 nucleosome remodeling. We demonstrate that ALC1 activation depends on the formation of a stable ALC1·PARylated PARP1·nucleosome intermediate. In addition, by exploiting a novel PAR footprinting assay, we obtained evidence that the ALC1 macrodomain remains stably associated with PAR on autoPARylated PARP1 during the course of nucleosome remodeling reactions. Taken together, our findings are consistent with the model that PAR present on PARylated PARP1 acts as an allosteric effector of ALC1 nucleosome remodeling activity.","corpus_id":6155195,"score":0},{"doc_id":"23910651","title":"Reduced ADP-ribosylation by PARP1 natural polymorphism V762A and by PARP1 inhibitors enhance Hepatitis B virus replication.","abstract":"HepG2 and Huh7 cell lines are frequently used as models to study viral hepatitis and hepatocellular carcinoma. However, they exhibit significantly different capacities in their ability to support hepatitis B virus (HBV) replication. To investigate the basis for this, transcription factor-binding motifs at the HBV core promoter (HBVCP) were tested in luciferase reporter constructs to identify the possible role of host factors. Among the transcription factors screened: PARP1, SP1, HNF4α, HNF3, hB1F and HNF1, deletion of the PARP1 binding motif abrogated transcriptional activity at the HBVCP in HepG2 but not Huh7 cells. Sequencing of the PARP1 gene revealed that HepG2 cells carried an Ala762 allele which has low ADP-ribosylation activity, which was shown to have increased PARP1 binding affinity to its cognate motif thus resulting in higher transcriptional activity. PARP1 inhibitors that are being developed as broad cancer therapeutics also target PARP1 ADP-ribosylation enzymatic function. Four PARP1 inhibitors: PJ-34, ABT888, AZD2281 and AG014699 were tested for their effect on HBV replication. All four small molecules effectively enhanced HBV replication in vitro, confirming the role of PARP1 in HBV replication and that alteration of ADP-ribosylation by mutation or drugs can affect HBV replication. Our data demonstrate that natural polymorphisms in the host affecting proteins such as PARP1 can have a significant effect on HBV replication. Hence, patients who are infected with HBV and are on clinical trials involving PARP1 inhibitors may be at risk from unintended side-effects such as exacerbation of HBV replication.","corpus_id":7327661,"score":0},{"doc_id":"24145797","title":"PARP1 orchestrates variant histone exchange in signal-mediated transcriptional activation.","abstract":"Transcriptional activation is accompanied by multiple molecular events that remodel the local chromatin environment in promoter regions. These molecular events are often orchestrated in response to the activation of signalling pathways, as exemplified by the response of immediate early genes such as FOS to ERK MAP kinase signalling. Here, we demonstrate that inducible NFI recruitment permits PARP1 binding to the FOS promoter by a mutually reinforcing loop. PARP1 and its poly(ADP-ribosyl)ation activity are required for maintaining FOS activation kinetics. We also show that the histone variant H2A.Z associates with the FOS promoter and acts in a transcription-suppressive manner. However, in response to ERK pathway signalling, H2A.Z is replaced by H2A; PARP1 activity is required to promote this exchange. Thus, our work has revealed an additional facet of PARP1 function in promoting dynamic remodelling of promoter-associated nucleosomes to allow transcriptional activation in response to cellular signalling.","corpus_id":14399127,"score":0},{"doc_id":"24256300","title":"Clustered regulatory elements at nucleosome-depleted regions punctuate a constant nucleosomal landscape in Schizosaccharomyces pombe.","abstract":"BACKGROUND: Nucleosomes facilitate the packaging of the eukaryotic genome and modulate the access of regulators to DNA. A detailed description of the nucleosomal organization under different transcriptional programmes is essential to understand their contribution to genomic regulation. RESULTS: To visualize the dynamics of individual nucleosomes under different transcriptional programmes we have generated high-resolution nucleosomal maps in Schizosaccharomyces pombe. We show that 98.5% of the genome remains almost invariable during mitosis and meiosis while remodelling is limited to approximately 1100 nucleosomes in the promoters of a subset of meiotic genes. These inducible nucleosome-depleted regions (NDR) and also those constitutively present in the genome overlap precisely with clusters of binding sites for transcription factors (TF) specific for meiosis and for different functional classes of genes, respectively. Deletion of two TFs affects only a small fraction of all the NDRs to which they bind in vivo, indicating that TFs collectively contribute to NDR maintenance. CONCLUSIONS: Our results show that the nucleosomal profile in S. pombe is largely maintained under different physiological conditions and patterns of gene expression. This relatively constant landscape favours the concentration of regulators in constitutive and inducible NDRs. The combinatorial analysis of binding motifs in this discrete fraction of the genome will facilitate the definition of the transcriptional regulatory networks.","corpus_id":17978747,"score":0},{"doc_id":"24771338","title":"Nucleosome regulatory dynamics in response to TGFβ.","abstract":"Nucleosomes play important roles in a cell beyond their basal functionality in chromatin compaction. Their placement affects all steps in transcriptional regulation, from transcription factor (TF) binding to messenger ribonucleic acid (mRNA) synthesis. Careful profiling of their locations and dynamics in response to stimuli is important to further our understanding of transcriptional regulation by the state of chromatin. We measured nucleosome occupancy in human hepatic cells before and after treatment with transforming growth factor beta 1 (TGFβ1), using massively parallel sequencing. With a newly developed method, SuMMIt, for precise positioning of nucleosomes we inferred dynamics of the nucleosomal landscape. Distinct nucleosome positioning has previously been described at transcription start site and flanking TF binding sites. We found that the average pattern is present at very few sites and, in case of TF binding, the double peak surrounding the sites is just an artifact of averaging over many loci. We systematically searched for depleted nucleosomes in stimulated cells compared to unstimulated cells and identified 24 318 loci. Depending on genomic annotation, 44-78% of them were over-represented in binding motifs for TFs. Changes in binding affinity were verified for HNF4α by qPCR. Strikingly many of these loci were associated with expression changes, as measured by RNA sequencing.","corpus_id":11307141,"score":0},{"doc_id":"25161822","title":"PARP1 enhances inflammatory cytokine expression by alteration of promoter chromatin structure in microglia.","abstract":"BACKGROUND: Poly(ADP-ribose) polymerase 1 (PARP1) is a chromatin-associated enzyme that participates in processes such as transcription and DNA repair through the regulation of chromatin structure. Accumulating evidence suggests an important role for PARP1 enzymatic activity in promoting CNS inflammation by facilitating the expression of inflammatory cytokines in glial cells. However, the molecular mechanisms by which PARP1 enzymatic activity mediates this process are not well understood. In this report we sought to determine the molecular mechanisms by which PARP1 enzymatic activity facilitates the expression of Il1β and TNF in LPS-stimulated BV2 cells. METHODS: PARP1 enzymatic activity and histone ADP-ribosylation were measured in LPS-stimulated BV2 cells by radioactive labelling with (32)P-NAD(+). To assess the effect of histone ADP-ribosylation on nucleosome structure, in vitro nucleosome remodeling, nuclease accessibility and binding assays were performed. These studies were complemented by chromatin immunoprecipitation assays in resting and LPS-stimulated BV2 cells in order to determine the occupancy of PARP1, nucleosomes and the RelA subunit of NF-κB, as well as ADP-ribosylation, at the Il1β and Tnf promoters. Finally, we determined the effect of pharmacological inhibition of PARP1 enzymatic activity on the LPS stimulation-dependent induction of Il1β and Tnf mRNA. RESULTS: Our results indicate that LPS stimulation induces PARP1 enzymatic activity and histone ADP-ribosylation in the chromatin compartment of BV2 cells. In vitro studies show that nucleosome-bound PARP1 disrupts nucleosome structure histone ADP-ribosylation, increasing the accessibility of nucleosomal DNA. Consistent with this PARP1 is constitutively associated with at the Il1β and Tnf promoters in resting BV2 cells. Upon stimulation with LPS, ADP-ribosylation is observed at these promoters, and this is correlated with increased recruitment of the transcription factor NF-κB, resulting in robust transcription of these inflammatory cytokines. Accordingly, pharmacological inhibition of PARP1 enzymatic activity reduces NF-κB recruitment, and Il1β and Tnf expression in LPS-stimulated microglia. CONCLUSIONS: Collectively, our data suggest that PARP1 facilitates inflammatory cytokine expression in microglia by increasing the accessibility of promoter DNA via histone ADP-riboyslation.","corpus_id":13054142,"score":0},{"doc_id":"25555679","title":"RecQ helicases and PARP1 team up in maintaining genome integrity.","abstract":"Genome instability represents a primary hallmark of aging and cancer. RecQL helicases (i.e., RECQL1, WRN, BLM, RECQL4, RECQL5) as well as poly(ADP-ribose) polymerases (PARPs, in particular PARP1) represent two central quality control systems to preserve genome integrity in mammalian cells. Consistently, both enzymatic families have been linked to mechanisms of aging and carcinogenesis in mice and humans. This is in accordance with clinical and epidemiological findings demonstrating that defects in three RecQL helicases, i.e., WRN, BLM, RECQL4, are related to human progeroid and cancer predisposition syndromes, i.e., Werner, Bloom, and Rothmund Thomson syndrome, respectively. Moreover, PARP1 hypomorphy is associated with a higher risk for certain types of cancer. On a molecular level, RecQL helicases and PARP1 are involved in the control of DNA repair, telomere maintenance, and replicative stress. Notably, over the last decade, it became apparent that all five RecQL helicases physically or functionally interact with PARP1 and/or its enzymatic product poly(ADP-ribose) (PAR). Furthermore, a profound body of evidence revealed that the cooperative function of RECQLs and PARP1 represents an important factor for maintaining genome integrity. In this review, we summarize the status quo of this molecular cooperation and discuss open questions that provide a basis for future studies to dissect the cooperative functions of RecQL helicases and PARP1 in aging and carcinogenesis.","corpus_id":29498397,"score":0},{"doc_id":"26269799","title":"Replicating Nucleosomes.","abstract":"Eukaryotic replication disrupts each nucleosome as the fork passes, followed by re-assembly of disrupted nucleosomes and incorporation of newly synthesized histones into nucleosomes in the daughter genomes. In this review, we examine this process of replication-coupled nucleosome assembly to understand how characteristic steady state nucleosome landscapes are attained. Recent studies have begun to elucidate mechanisms involved in histone transfer during replication and maturation of the nucleosome landscape after disruption by replication. A fuller understanding of replication-coupled nucleosome assembly will be needed to explain how epigenetic information is replicated at every cell division.","corpus_id":18044952,"score":0},{"doc_id":"26814966","title":"Genome-wide nucleosome specificity and function of chromatin remodellers in ES cells.","abstract":"ATP-dependent chromatin remodellers allow access to DNA for transcription factors and the general transcription machinery, but whether mammalian chromatin remodellers target specific nucleosomes to regulate transcription is unclear. Here we present genome-wide remodeller-nucleosome interaction profiles for the chromatin remodellers Chd1, Chd2, Chd4, Chd6, Chd8, Chd9, Brg1 and Ep400 in mouse embryonic stem (ES) cells. These remodellers bind one or both full nucleosomes that flank micrococcal nuclease (MNase)-defined nucleosome-free promoter regions (NFRs), where they separate divergent transcription. Surprisingly, large CpG-rich NFRs that extend downstream of annotated transcriptional start sites are nevertheless bound by non-nucleosomal or subnucleosomal histone variants (H3.3 and H2A.Z) and marked by H3K4me3 and H3K27ac modifications. RNA polymerase II therefore navigates hundreds of base pairs of altered chromatin in the sense direction before encountering an MNase-resistant nucleosome at the 3' end of the NFR. Transcriptome analysis after remodeller depletion reveals reciprocal mechanisms of transcriptional regulation by remodellers. Whereas at active genes individual remodellers have either positive or negative roles via altering nucleosome stability, at polycomb-enriched bivalent genes the same remodellers act in an opposite manner. These findings indicate that remodellers target specific nucleosomes at the edge of NFRs, where they regulate ES cell transcriptional programs.","corpus_id":4465573,"score":0},{"doc_id":"26933790","title":"Nucleosome dynamics during chromatin remodeling in vivo.","abstract":"Precise positioning of nucleosomes around regulatory sites is achieved by the action of chromatin remodelers, which use the energy of ATP to slide, evict or change the composition of nucleosomes. Chromatin remodelers act to bind nucleosomes, disrupt histone-DNA interactions and translocate the DNA around the histone core to reposition nucleosomes. Hence, remodeling is expected to involve nucleosomal intermediates with a structural organization that is distinct from intact nucleosomes. We describe the identification of a partially unwrapped nucleosome structure using methods that map histone-DNA contacts genome-wide. This alternative nucleosome structure is likely formed as an intermediate or by-product during nucleosome remodeling by the RSC complex. Identification of the loss of histone-DNA contacts during chromatin remodeling by RSC in vivo has implications for the regulation of transcriptional initiation.","corpus_id":17062908,"score":0},{"doc_id":"26982358","title":"A Pioneer's Tail.","abstract":"In this issue of Immunity, Boller et al. (2016) show that a C-terminal domain of EBF1 is required for chromatin binding and induction of DNase I hypersensitive sites. These properties mark EBF1 as a pioneer factor in B cell development and demonstrate a role for non-DNA binding domains in this process.","corpus_id":12545327,"score":0},{"doc_id":"27462443","title":"Involvement of PARP1 in the regulation of alternative splicing.","abstract":"Specialized chromatin structures such as nucleosomes with specific histone modifications decorate exons in eukaryotic genomes, suggesting a functional connection between chromatin organization and the regulation of pre-mRNA splicing. Through profiling the functional location of Poly (ADP) ribose polymerase, we observed that it is associated with the nucleosomes at exon/intron boundaries of specific genes, suggestive of a role for this enzyme in alternative splicing. Poly (ADP) ribose polymerase has previously been implicated in the PARylation of splicing factors as well as regulation of the histone modification H3K4me3, a mark critical for co-transcriptional splicing. In light of these studies, we hypothesized that interaction of the chromatin-modifying factor, Poly (ADP) ribose polymerase with nucleosomal structures at exon-intron boundaries, might regulate pre-mRNA splicing. Using genome-wide approaches validated by gene-specific assays, we show that depletion of PARP1 or inhibition of its PARylation activity results in changes in alternative splicing of a specific subset of genes. Furthermore, we observed that PARP1 bound to RNA, splicing factors and chromatin, suggesting that Poly (ADP) ribose polymerase serves as a gene regulatory hub to facilitate co-transcriptional splicing. These studies add another function to the multi-functional protein, Poly (ADP) ribose polymerase, and provide a platform for further investigation of this protein's function in organizing chromatin during gene regulatory processes.","corpus_id":37375710,"score":0},{"doc_id":"28991194","title":"PARP1 in Carcinomas and PARP1 Inhibitors as Antineoplastic Drugs.","abstract":"Poly (ADP-ribose) polymerase 1 (PARP1), the best-studied isoform of the nuclear enzyme PARP family, plays a pivotal role in cellular biological processes, such as DNA repair, gene transcription, and so on. PARP1 has been found to be overexpressed in various carcinomas. These all indicate the clinical potential of PARP1 as a therapeutic target of human malignancies. Additionally, multiple preclinical research studies and clinical trials demonstrate that inhibition of PARP1 can repress tumor growth and metastasis. Up until now, PARP1 inhibitors are clinically used not only for monotherapy to suppress various tumors, but also for adjuvant therapy, to maintain or enhance therapeutic effects of mature antineoplastic drugs, as well as protect patients from chemotherapy and surgery-induced injury. To supply a framework for understanding recent research progress of PARP1 in carcinomas, we review the structure, expression, functions, and mechanisms of PARP1, and summarize the clinically mature PARP1-related anticancer agents, to provide some ideas for the development of other promising PARP1 inhibitors in antineoplastic therapy.","corpus_id":22074539,"score":0},{"doc_id":"29563192","title":"Cryo-EM structure of the nucleosome containing the ALB1 enhancer DNA sequence.","abstract":"Pioneer transcription factors specifically target their recognition DNA sequences within nucleosomes. FoxA is the pioneer transcription factor that binds to the ALB1 gene enhancer in liver precursor cells, and is required for liver differentiation in embryos. The ALB1 enhancer DNA sequence is reportedly incorporated into nucleosomes in cells, although the nucleosome structure containing the targeting sites for FoxA has not been clarified yet. In this study, we determined the nucleosome structure containing the ALB1 enhancer (N1) sequence, by cryogenic electron microscopy at 4.0 Å resolution. The nucleosome structure with the ALB1 enhancer DNA is not significantly different from the previously reported nucleosome structure with the Widom 601 DNA. Interestingly, in the nucleosomes, the ALB1 enhancer DNA contains local flexible regions, as compared to the Widom 601 DNA. Consistently, DNaseI treatments revealed that, in the nucleosome, the ALB1 enhancer (N1) DNA is more accessible than the Widom 601 sequence. The histones also associated less strongly with the ALB1 enhancer (N1) DNA than the Widom 601 DNA in the nucleosome. Therefore, the local histone-DNA contacts may be responsible for the enhanced DNA accessibility in the nucleosome with the ALB1 enhancer DNA.","corpus_id":4578710,"score":0}],"string":"[\n {\n \"doc_id\": \"19531481\",\n \"title\": \"PARP1 poly(ADP-ribosyl)ates Sox2 to control Sox2 protein levels and FGF4 expression during embryonic stem cell differentiation.\",\n \"abstract\": \"Transcription factors Oct4 and Sox2 are key players in maintaining the pluripotent state of embryonic stem cells (ESCs). Small changes in their levels disrupt normal expression of their target genes. However, it remains elusive how protein levels of Oct4 and Sox2 and expression of their target genes are precisely controlled in ESCs. Here we identify PARP1, a DNA-binding protein with an NAD+-dependent enzymatic activity, as a cofactor of Oct4 and Sox2 to regulate expression of their target gene FGF4. We demonstrate for the first time that PARP1 binds the FGF4 enhancer to positively regulate FGF4 expression. Our data show that PARP1 interacts with and poly(ADP-ribosyl)ates Sox2 directly, which may be a step required for dissociation and degradation of inhibitory Sox2 proteins from the FGF4 enhancer. When PARP1 activity is inhibited or absent, poly(ADP-ribosyl)ation of Sox2 decreases and association of Sox2 with FGF4 enhancers increases, accompanied by an elevated level of Sox2 proteins and reduced expression of FGF4. Significantly, specific knockdown of Sox2 expression by RNA interference can considerably abrogate the inhibitory effect of the poly(ADP-ribose) polymerase inhibitor on FGF4 expression. Interestingly, PARP1 deficiency does not affect undifferentiated ESCs but compromises cell survival and/or growth when ESCs are induced into differentiation. Addition of FGF4 can partially rescue the phenotypes caused by PARP1 deficiency during ESC differentiation. Taken together, this study uncovers new mechanisms through which Sox2 protein levels and FGF4 expression are dynamically regulated during ESC differentiation and adds a new member to the family of proteins regulating the properties of ESCs.\",\n \"corpus_id\": 5436001,\n \"score\": 2\n },\n {\n \"doc_id\": \"20371698\",\n \"title\": \"Uncoupling of the transactivation and transrepression functions of PARP1 protein.\",\n \"abstract\": \"Poly(ADP ribose) polymerase 1 (PARP1) is a nuclear protein that regulates chromatin remodeling and transcription as well as DNA repair and genome stability pathways. Recent studies have revealed a paradoxical dual role of PARP1 protein in transcription. Specifically, although PARP1 controls transcriptional activation of a subset of genes that are heat shock- or hormone-dependent, it also directly inactivates transcription, establishes heterochromatin domains, and silences retrotransposable elements. However, the domains required for these disparate functions are currently unknown. In this paper, we report the discovery of a previously undescribed mutation in the Drosophila Parp locus. We show that the mutants express a deletion mutant of PARP1 protein with an altered DNA binding domain that carries only the second Zn-finger. We demonstrate that this alteration specifically excludes PARP1 protein from heterochromatin and makes PARP1 unable to maintain repression of retrotransposable elements. By characterizing the biological activity of this unique PARP1 mutant protein isoform, we have uncoupled the transactivation and transrepression functions of this protein.\",\n \"corpus_id\": 25181289,\n \"score\": 2\n },\n {\n \"doc_id\": \"22056668\",\n \"title\": \"Pioneer transcription factors: establishing competence for gene expression.\",\n \"abstract\": \"Transcription factors are adaptor molecules that detect regulatory sequences in the DNA and target the assembly of protein complexes that control gene expression. Yet much of the DNA in the eukaryotic cell is in nucleosomes and thereby occluded by histones, and can be further occluded by higher-order chromatin structures and repressor complexes. Indeed, genome-wide location analyses have revealed that, for all transcription factors tested, the vast majority of potential DNA-binding sites are unoccupied, demonstrating the inaccessibility of most of the nuclear DNA. This raises the question of how target sites at silent genes become bound de novo by transcription factors, thereby initiating regulatory events in chromatin. Binding cooperativity can be sufficient for many kinds of factors to simultaneously engage a target site in chromatin and activate gene expression. However, in cases in which the binding of a series of factors is sequential in time and thus not initially cooperative, special \\\"pioneer transcription factors\\\" can be the first to engage target sites in chromatin. Such initial binding can passively enhance transcription by reducing the number of additional factors that are needed to bind the DNA, culminating in activation. In addition, pioneer factor binding can actively open up the local chromatin and directly make it competent for other factors to bind. Passive and active roles for the pioneer factor FoxA occur in embryonic development, steroid hormone induction, and human cancers. Herein we review the field and describe how pioneer factors may enable cellular reprogramming.\",\n \"corpus_id\": 7463311,\n \"score\": 2\n },\n {\n \"doc_id\": \"22362888\",\n \"title\": \"SRY (sex determining region Y)-box2 (Sox2)/poly ADP-ribose polymerase 1 (Parp1) complexes regulate pluripotency.\",\n \"abstract\": \"To gain insight into mechanisms controlling SRY (sex determining region Y)-box 2 (Sox2) protein activity in mouse embryonic stem cells (ESCs), the endogenous Sox2 gene was tagged with FLAG/Hemagglutinin (HA) sequences by homologous recombination. Sox2 protein complexes were purified from Sox2/FLAG/HA knockin ESCs, and interacting proteins were defined by mass spectrometry. One protein in the complex was poly ADP-ribose polymerase I (Parp1). The results presented below demonstrate that Parp1 regulates Sox2 protein activity. In response to fibroblast growth factor (FGF)/extracellular signal-regulated kinase (ERK) signaling, Parp1 auto-poly ADP-ribosylation enhances Sox2-Parp1 interactions, and this complex inhibits Sox2 binding to octamer-binding transcription factor 4 (Oct4)/Sox2 enhancers. Based on these results, we propose a unique mechanism in which FGF signaling fine-tunes Sox2 activity through posttranslational modification of a critical interacting protein, Parp1, and balances the maintenance of ESC pluripotency and differentiation. In addition, we demonstrate that regulation of Sox2 activity by Parp1 is critical for efficient generation of induced pluripotent stem cells.\",\n \"corpus_id\": 34556304,\n \"score\": 2\n },\n {\n \"doc_id\": \"23657885\",\n \"title\": \"DNase-seq predicts regions of rotational nucleosome stability across diverse human cell types.\",\n \"abstract\": \"DNase-seq is primarily used to identify nucleosome-depleted DNase I hypersensitive (DHS) sites genome-wide that correspond to active regulatory elements. However, ≈ 40 yr ago it was demonstrated that DNase I also digests with a ≈ 10-bp periodicity around nucleosomes matching the exposure of the DNA minor groove as it wraps around histones. Here, we use DNase-seq data from 49 samples representing diverse cell types to reveal this digestion pattern at individual loci and predict genomic locations where nucleosome rotational positioning, the orientation of DNA with respect to the histone surface, is stably maintained. We call these regions DNase I annotated regions of nucleosome stability (DARNS). Compared to MNase-seq experiments, we show DARNS correspond well to annotated nucleosomes. Interestingly, many DARNS are positioned over only one side of annotated nucleosomes, suggesting that the periodic digestion pattern attenuates over the nucleosome dyad. DARNS reproduce the arrangement of nucleosomes around transcription start sites and are depleted at ubiquitous DHS sites. We also generated DARNS from multiple lymphoblast cell line (LCL) samples. We found that LCL DARNS were enriched at DHS sites present in most of the original 49 samples but absent in LCLs, while multi-cell-type DARNS were enriched at LCL-specific DHS sites. This indicates that variably open DHS sites are often occupied by rotationally stable nucleosomes in cell types where the DHS site is closed. DARNS provide additional information about precise DNA orientation within individual nucleosomes not available from other nucleosome positioning assays and contribute to understanding the role of chromatin in gene regulation.\",\n \"corpus_id\": 45663709,\n \"score\": 2\n },\n {\n \"doc_id\": \"23939864\",\n \"title\": \"Artd1/Parp1 regulates reprogramming by transcriptional regulation of Fgf4 via Sox2 ADP-ribosylation.\",\n \"abstract\": \"The recently established reprogramming of somatic cells into induced pluripotent stem cells (iPSCs) by Takahashi and Yamanaka represents a valuable tool for future therapeutic applications. To date, the mechanisms underlying this process are still largely unknown. In particular, the mechanisms how the Yamanaka factors (Oct4, Sox2, Klf4, and c-Myc) directly drive reprogramming and which additional components are involved are still not yet understood. In this study, we aimed at analyzing the role of ADP-ribosyltransferase diphtheria toxin-like one (Artd1; formerly called poly(ADP-ribose) polymerase 1 [Parp1]) during reprogramming. We found that poly(ADP-ribosylation) (PARylation) of the reprogramming factor Sox2 by Artd1 plays an important role during the first days upon transduction with the reprogramming factors. A process that happens before Artd1 in conjunction with 10-11 translocation-2 (Tet2) mediates the histone modifications necessary for the establishment of an activated chromatin state at pluripotency loci (e.g., Nanog and Essrb) [Nature 2012;488:652-655]. Wild-type (WT) fibroblasts treated with an Artd1 inhibitor as well as fibroblasts deficient for Artd1 (Artd1-/-) show strongly decreased reprogramming capacity. Our data indicate that Artd1-mediated PARylation of Sox2 favors its binding to the fibroblast growth factor 4 (Fgf4) enhancer, thereby activating Fgf4 expression. The importance of Fgf4 during the first 4 days upon initiation of reprogramming was also highlighted by the observation that exogenous addition of Fgf4 was sufficient to restore the reprogramming capacity of Artd1-/- fibroblast to WT levels. In conclusion, our data clearly show that the interaction between Artd1 and Sox2 is crucial for the first steps of the reprogramming process and that early expression of Fgf4 (day 2 to day 4) is an essential component for the successful generation of iPSCs.\",\n \"corpus_id\": 206513034,\n \"score\": 2\n },\n {\n \"doc_id\": \"25512556\",\n \"title\": \"Pioneer transcription factors in cell reprogramming.\",\n \"abstract\": \"A subset of eukaryotic transcription factors possesses the remarkable ability to reprogram one type of cell into another. The transcription factors that reprogram cell fate are invariably those that are crucial for the initial cell programming in embryonic development. To elicit cell programming or reprogramming, transcription factors must be able to engage genes that are developmentally silenced and inappropriate for expression in the original cell. Developmentally silenced genes are typically embedded in \\\"closed\\\" chromatin that is covered by nucleosomes and not hypersensitive to nuclease probes such as DNase I. Biochemical and genomic studies have shown that transcription factors with the highest reprogramming activity often have the special ability to engage their target sites on nucleosomal DNA, thus behaving as \\\"pioneer factors\\\" to initiate events in closed chromatin. Other reprogramming factors appear dependent on pioneer factors for engaging nucleosomes and closed chromatin. However, certain genomic domains in which nucleosomes are occluded by higher-order chromatin structures, such as in heterochromatin, are resistant to pioneer factor binding. Understanding the means by which pioneer factors can engage closed chromatin and how heterochromatin can prevent such binding promises to advance our ability to reprogram cell fates at will and is the topic of this review.\",\n \"corpus_id\": 1775111,\n \"score\": 2\n },\n {\n \"doc_id\": \"25578969\",\n \"title\": \"DNA-mediated cooperativity facilitates the co-selection of cryptic enhancer sequences by SOX2 and PAX6 transcription factors.\",\n \"abstract\": \"Sox2 and Pax6 are transcription factors that direct cell fate decision during neurogenesis, yet the mechanism behind how they cooperate on enhancer DNA elements and regulate gene expression is unclear. By systematically interrogating Sox2 and Pax6 interaction on minimal enhancer elements, we found that cooperative DNA recognition relies on combinatorial nucleotide switches and precisely spaced, but cryptic composite DNA motifs. Surprisingly, all tested Sox and Pax paralogs have the capacity to cooperate on such enhancer elements. NMR and molecular modeling reveal very few direct protein-protein interactions between Sox2 and Pax6, suggesting that cooperative binding is mediated by allosteric interactions propagating through DNA structure. Furthermore, we detected and validated several novel sites in the human genome targeted cooperatively by Sox2 and Pax6. Collectively, we demonstrate that Sox-Pax partnerships have the potential to substantially alter DNA target specificities and likely enable the pleiotropic and context-specific action of these cell-lineage specifiers.\",\n \"corpus_id\": 12404563,\n \"score\": 2\n },\n {\n \"doc_id\": \"25892221\",\n \"title\": \"Pioneer transcription factors target partial DNA motifs on nucleosomes to initiate reprogramming.\",\n \"abstract\": \"Pioneer transcription factors (TFs) access silent chromatin and initiate cell-fate changes, using diverse types of DNA binding domains (DBDs). FoxA, the paradigm pioneer TF, has a winged helix DBD that resembles linker histone and thereby binds its target sites on nucleosomes and in compacted chromatin. Herein, we compare the nucleosome and chromatin targeting activities of Oct4 (POU DBD), Sox2 (HMG box DBD), Klf4 (zinc finger DBD), and c-Myc (bHLH DBD), which together reprogram somatic cells to pluripotency. Purified Oct4, Sox2, and Klf4 proteins can bind nucleosomes in vitro, and in vivo they preferentially target silent sites enriched for nucleosomes. Pioneer activity relates simply to the ability of a given DBD to target partial motifs displayed on the nucleosome surface. Such partial motif recognition can occur by coordinate binding between factors. Our findings provide insight into how pioneer factors can target naive chromatin sites.\",\n \"corpus_id\": 11011905,\n \"score\": 2\n },\n {\n \"doc_id\": \"25992972\",\n \"title\": \"Differential Nucleosome Occupancies across Oct4-Sox2 Binding Sites in Murine Embryonic Stem Cells.\",\n \"abstract\": \"The binding sequence for any transcription factor can be found millions of times within a genome, yet only a small fraction of these sequences encode functional transcription factor binding sites. One of the reasons for this dichotomy is that many other factors, such as nucleosomes, compete for binding. To study how the competition between nucleosomes and transcription factors helps determine a functional transcription factor site from a predicted transcription factor site, we compared experimentally-generated in vitro nucleosome occupancy with in vivo nucleosome occupancy and transcription factor binding in murine embryonic stem cells. Using a solution hybridization enrichment technique, we generated a high-resolution nucleosome map from targeted regions of the genome containing predicted sites and functional sites of Oct4/Sox2 regulation. We found that at Pax6 and Nes, which are bivalently poised in stem cells, functional Oct4 and Sox2 sites show high amounts of in vivo nucleosome displacement compared to in vitro. Oct4 and Sox2, which are active, show no significant displacement of in vivo nucleosomes at functional sites, similar to nonfunctional Oct4/Sox2 binding. This study highlights a complex interplay between Oct4 and Sox2 transcription factors and nucleosomes among different target genes, which may result in distinct patterns of stem cell gene regulation.\",\n \"corpus_id\": 16086753,\n \"score\": 2\n },\n {\n \"doc_id\": \"26826681\",\n \"title\": \"Pioneer transcription factors, chromatin dynamics, and cell fate control.\",\n \"abstract\": \"Among the diverse transcription factors that are necessary to elicit changes in cell fate, both in embryonic development and in cellular reprogramming, a subset of factors are capable of binding to their target sequences on nucleosomal DNA and initiating regulatory events in silent chromatin. Such 'pioneer transcription factors' initiate cooperative interactions with other regulatory proteins to elicit changes in local chromatin structure. As a consequence of pioneer factor binding, the local chromatin can either become open and competent for activation, closed and repressed, or transcriptionally active. Understanding how pioneer factors initiate chromatin dynamics and how such can be blocked at heterochromatic sites provides insights into controlling cell fate transitions at will.\",\n \"corpus_id\": 45121219,\n \"score\": 2\n },\n {\n \"doc_id\": \"28212747\",\n \"title\": \"Catalytic-Independent Functions of PARP-1 Determine Sox2 Pioneer Activity at Intractable Genomic Loci.\",\n \"abstract\": \"Pioneer transcription factors (TFs) function as genomic first responders, binding to inaccessible regions of chromatin to promote enhancer formation. The mechanism by which pioneer TFs gain access to chromatin remains an important unanswered question. Here we show that PARP-1, a nucleosome-binding protein, cooperates with intrinsic properties of the pioneer TF Sox2 to facilitate its binding to intractable genomic loci in embryonic stem cells. These actions of PARP-1 occur independently of its poly(ADP-ribosyl) transferase activity. PARP-1-dependent Sox2-binding sites reside in euchromatic regions of the genome with relatively high nucleosome occupancy and low co-occupancy by other transcription factors. PARP-1 stabilizes Sox2 binding to nucleosomes at suboptimal sites through cooperative interactions on DNA. Our results define intrinsic and extrinsic features that determine Sox2 pioneer activity. The conditional pioneer activity observed with Sox2 at a subset of binding sites may be a key feature of other pioneer TFs operating at intractable genomic loci.\",\n \"corpus_id\": 23208167,\n \"score\": 2\n },\n {\n \"doc_id\": \"29452418\",\n \"title\": \"PHF20 collaborates with PARP1 to promote stemness and aggressiveness of neuroblastoma cells through activation of SOX2 and OCT4.\",\n \"abstract\": \"The differentiation status of neuroblastoma (NB) strongly correlates with its clinical outcomes; however, the molecular mechanisms driving maintenance of stemness and differentiation remain poorly understood. Here, we show that plant homeodomain finger-containing protein 20 (PHF20) functions as a critical epigenetic regulator in sustaining stem cell-like phenotype of NB by using CRISPR/Cas9-based targeted knockout (KO) for high-throughput screening of gene function in NB cell differentiation. The expression of PHF20 in NB was significantly associated with high aggressiveness of the tumor and poor outcomes for NB patients. Deletion of PHF20 inhibited NB cell proliferation, invasive migration, and stem cell-like traits. Mechanistically, PHF20 interacts with poly(ADP-ribose) polymerase 1 (PARP1) and directly binds to promoter regions of octamer-binding transcription factor 4 (OCT4) and sex determining region Y-box 2 (SOX2) to modulate a histone mark associated with active transcription, trimethylation of lysine 4 on histone H3 protein subunit (H3K4me3). Overexpression of OCT4 and SOX2 restored growth and progression of PHF20 KO tumor cells. Consistently, OCT4 and SOX2 protein levels in clinical NB specimens were positively correlated with PHF20 expression. Our results establish PHF20 as a key driver of NB stem cell-like properties and aggressive behaviors, with implications for prognosis and therapy.\",\n \"corpus_id\": 3354357,\n \"score\": 2\n },\n {\n \"doc_id\": \"19339686\",\n \"title\": \"Nucleosome-binding affinity as a primary determinant of the nuclear mobility of the pioneer transcription factor FoxA.\",\n \"abstract\": \"FoxA proteins are pioneer transcription factors, among the first to bind chromatin domains in development and enable gene activity. The Fox DNA-binding domain structurally resembles linker histone and binds nucleosomes stably. Using fluorescence recovery after photobleaching, we found that FoxA1 and FoxA2 move much more slowly in nuclei than other transcription factor types, including c-Myc, GATA-4, NF-1, and HMGB1. We find that slower nuclear mobility correlates with high nonspecific nucleosome binding, and point mutations that disrupt nonspecific binding markedly increase nuclear mobility. FoxA's distinct nuclear mobility is consistent with its pioneer activity in chromatin.\",\n \"corpus_id\": 13257310,\n \"score\": 1\n },\n {\n \"doc_id\": \"19378173\",\n \"title\": \"Nucleosome mapping.\",\n \"abstract\": \"The basic repeating unit of chromatin, the nucleosome, is known to play a critical role in regulating the process of gene transcription. The positioning of nucleosomes on a promoter is a significant determinant in its responsiveness to gene-inducing signals. For example, positioning and subsequent mobilization of nucleosomes can regulate the access of various DNA factors to underlying DNA templates. Several mechanisms have been proposed to direct the process of nucleosome displacement such as chemical histone modifications, ATP-dependent remodelling, and the incorporation of histone variants. Thus, rather than being an inert molecular structure, chromatin is highly dynamic in response to the transcription process. In this section, we describe two methodologies that allow the determination of exact nucleosome positioning within specific gene regions.\",\n \"corpus_id\": 3173036,\n \"score\": 1\n },\n {\n \"doc_id\": \"19572828\",\n \"title\": \"A non-homogeneous hidden-state model on first order differences for automatic detection of nucleosome positions.\",\n \"abstract\": \"The ability to map individual nucleosomes accurately across genomes enables the study of relationships between dynamic changes in nucleosome positioning/occupancy and gene regulation. However, the highly heterogeneous nature of nucleosome densities across genomes and short linker regions pose challenges in mapping nucleosome positions based on high-throughput microarray data of micrococcal nuclease (MNase) digested DNA. Previous works rely on additional detrending and careful visual examination to detect low-signal nucleosomes, which may exist in a subpopulation of cells. We propose a non-homogeneous hidden-state model based on first order differences of experimental data along genomic coordinates that bypasses the need for local detrending and can automatically detect nucleosome positions of various occupancy levels. Our proposed approach is applicable to both low and high resolution MNase-Chip and MNase-Seq (high throughput sequencing) data, and is able to map nucleosome-linker boundaries accurately. This automated algorithm is also computationally efficient and only requires a simple preprocessing step. We provide several examples illustrating the pitfalls of existing methods, the difficulties of detrending the observed hybridization signals and demonstrate the advantages of utilizing first order differences in detecting nucleosome occupancies via simulations and case studies involving MNase-Chip and MNase-Seq data of nucleosome occupancy in yeast S. cerevisiae.\",\n \"corpus_id\": 8982077,\n \"score\": 1\n },\n {\n \"doc_id\": \"20412763\",\n \"title\": \"First time, every time: nucleosomes at a promoter can determine the probability of gene activation.\",\n \"abstract\": \"Transcription factor binding sites are found in either nucleosome-free or nucleosome-embedded locations, thus in vivo relationships between nucleosome position and gene activation are not fully understood. In this issue of Developmental Cell, Bai et al. show that binding sites located in nucleosome depleted regions guarantee high reliability, not amplitude, of promoter firing.\",\n \"corpus_id\": 5275643,\n \"score\": 1\n },\n {\n \"doc_id\": \"20726797\",\n \"title\": \"ChIP-seq and functional analysis of the SOX2 gene in colorectal cancers.\",\n \"abstract\": \"SOX2 is an HMG box containing transcription factor that has been implicated in various types of cancer, but its role in colorectal cancers (CRC) has not been studied. Here we show that SOX2 is overexpressed in CRC tissues compared with normal adjacent tissues using immunohistochemical staining and RT-PCR. We also observed an increased SOX2 expression in nucleus of colorectal cancer tissues (46%, 14/30 cases vs. 7%, 2/30 adjacent tissues). Furthermore, knockdown of SOX2 in SW620 colorectal cancer cells decreased their growth rates in vitro cell line, and in vivo in xenograft models. ChIP-Seq analysis of SOX2 revealed a consensus sequence of wwTGywTT. An integrated expression profiling and ChIP-seq analysis show that SOX2 is involved in the BMP signaling pathway, steroid metabolic process, histone modifications, and many receptor-mediated signaling pathways such as IGF1R and ITPR2 (Inositol 1,4,5-triphosphate receptor, type 2).\",\n \"corpus_id\": 5861643,\n \"score\": 1\n },\n {\n \"doc_id\": \"21623366\",\n \"title\": \"The nucleosome map of the mammalian liver.\",\n \"abstract\": \"Binding to nucleosomal DNA is critical for 'pioneer' transcription factors such as the winged-helix transcription factors Foxa1 and Foxa2 to regulate chromatin structure and gene activation. Here we report the genome-wide map of nucleosome positions in the mouse liver, with emphasis on transcriptional start sites, CpG islands, Foxa2 binding sites and their correlation with gene expression. Despite the heterogeneity of liver tissue, we could clearly discern the nucleosome pattern of the predominant liver cell, the hepatocyte. By analyzing nucleosome occupancy and the distributions of heterochromatin protein 1 (Hp1), CBP (also known as Crebbp) and p300 (Ep300) in Foxa1- and Foxa2-deficient livers, we find that the maintenance of nucleosome position and chromatin structure surrounding Foxa2 binding sites is independent of Foxa1 and Foxa2.\",\n \"corpus_id\": 25545264,\n \"score\": 1\n },\n {\n \"doc_id\": \"21982223\",\n \"title\": \"Long live sox2: sox2 lasts a lifetime.\",\n \"abstract\": \"Sox2 is a key transcription factor required for the maintenance of pluripotency in embryonic cells and morphogenesis of several epithelia. In this issue of Cell Stem Cell, Arnold et al. (2011) demonstrate that Sox2 marks long-lived adult stem cells to ensure homeostasis in a broad range of adult tissues.\",\n \"corpus_id\": 205243399,\n \"score\": 1\n },\n {\n \"doc_id\": \"22559821\",\n \"title\": \"Standardized collection of MNase-seq experiments enables unbiased dataset comparisons.\",\n \"abstract\": \"BACKGROUND: The organization of eukaryotic DNA into chromatin has a strong influence on the accessibility and regulation of genetic information. The locations and occupancies of a principle component of chromatin, nucleosomes, are typically assayed through use of enzymatic digestion with micrococcal nuclease (MNase). MNase is an endo-exo nuclease that preferentially digests naked DNA and the DNA in linkers between nucleosomes, thus enriching for nucleosome-associated DNA. To determine nucleosome organization genome-wide, DNA remaining from MNase digestion is sequenced using high-throughput sequencing technologies (MNase-seq). Unfortunately, the results of MNase-seq can vary dramatically due to technical differences and this confounds comparisons between MNase-seq experiments, such as examining condition-dependent chromatin organizations. RESULTS: In this study we use MNase digestion simulations to demonstrate how MNase-seq signals can vary for different nucleosome configuration when experiments are performed with different extents of MNase digestion. Signal variation in these simulations reveals an important DNA sampling bias that results from a neighborhood effect of MNase digestion techniques. The presence of this neighborhood effect ultimately confounds comparisons between different MNase-seq experiments. To address this issue we present a standardized chromatin preparation which controls for technical variance between MNase-based chromatin preparations and enables the collection of similarly sampled (matched) chromatin populations. Standardized preparation of chromatin includes a normalization step for DNA input into MNase digestions and close matching of the extent of digestion between each chromatin preparation using gel densitometry analysis. The protocol also includes directions for successful pairing with multiplex sequencing reactions. CONCLUSIONS: We validated our method by comparing the experiment-to-experiment variation between biological replicates of chromatin preparations from S. cerevisiae. Results from our matched preparation consistently produced MNase-seq datasets that were more closely correlated than other unstandardized approaches. Additionally, we validated the ability of our approach at enabling accurate downstream comparisons of chromatin structures, by comparing the specificity of detecting Tup1-dependent chromatin remodeling events in comparisons between matched and un-matched wild-type and tup1Δ MNase-seq datasets. Our matched MNase-seq datasets demonstrated a significant reduction in non-specific (technical) differences between experiments and were able to maximize the detection of biologically-relevant (Tup1-dependent) changes in chromatin structure.\",\n \"corpus_id\": 14105454,\n \"score\": 1\n },\n {\n \"doc_id\": \"22929772\",\n \"title\": \"Genome-wide mapping of nucleosome positions in yeast using high-resolution MNase ChIP-Seq.\",\n \"abstract\": \"Eukaryotic DNA is packaged into chromatin where nucleosomes form the basic building unit. Knowing the precise positions of nucleosomes is important because they determine the accessibility of underlying regulatory DNA sequences. Here we describe a detailed method to map on a genomic scale the locations of nucleosomes with very high resolution. Micrococcal nuclease (MNase) digestion followed by chromatin immunoprecipitation and facilitated library construction for deep sequencing provides a simple and accurate map of nucleosome positions.\",\n \"corpus_id\": 26494948,\n \"score\": 1\n },\n {\n \"doc_id\": \"23166509\",\n \"title\": \"Controls of nucleosome positioning in the human genome.\",\n \"abstract\": \"Nucleosomes are important for gene regulation because their arrangement on the genome can control which proteins bind to DNA. Currently, few human nucleosomes are thought to be consistently positioned across cells; however, this has been difficult to assess due to the limited resolution of existing data. We performed paired-end sequencing of micrococcal nuclease-digested chromatin (MNase-seq) from seven lymphoblastoid cell lines and mapped over 3.6 billion MNase-seq fragments to the human genome to create the highest-resolution map of nucleosome occupancy to date in a human cell type. In contrast to previous results, we find that most nucleosomes have more consistent positioning than expected by chance and a substantial fraction (8.7%) of nucleosomes have moderate to strong positioning. In aggregate, nucleosome sequences have 10 bp periodic patterns in dinucleotide frequency and DNase I sensitivity; and, across cells, nucleosomes frequently have translational offsets that are multiples of 10 bp. We estimate that almost half of the genome contains regularly spaced arrays of nucleosomes, which are enriched in active chromatin domains. Single nucleotide polymorphisms that reduce DNase I sensitivity can disrupt the phasing of nucleosome arrays, which indicates that they often result from positioning against a barrier formed by other proteins. However, nucleosome arrays can also be created by DNA sequence alone. The most striking example is an array of over 400 nucleosomes on chromosome 12 that is created by tandem repetition of sequences with strong positioning properties. In summary, a large fraction of nucleosomes are consistently positioned--in some regions because they adopt favored sequence positions, and in other regions because they are forced into specific arrangements by chromatin remodeling or DNA binding proteins.\",\n \"corpus_id\": 4689524,\n \"score\": 1\n },\n {\n \"doc_id\": \"23169531\",\n \"title\": \"Co-motif discovery identifies an Esrrb-Sox2-DNA ternary complex as a mediator of transcriptional differences between mouse embryonic and epiblast stem cells.\",\n \"abstract\": \"Transcription factors (TF) often bind in heterodimeric complexes with each TF recognizing a specific neighboring cis element in the regulatory region of the genome. Comprehension of this DNA motif grammar is opaque, yet recent developments have allowed the interrogation of genome-wide TF binding sites. We reasoned that within this data novel motif grammars could be identified that controlled distinct biological programs. For this purpose, we developed a novel motif-discovery tool termed fexcom that systematically interrogates ChIP-seq data to discover spatially constrained TF-TF composite motifs occurring over short DNA distances. We applied this to the extensive ChIP-seq data available from mouse embryonic stem cells (ESCs). In addition to the well-known and most prevalent sox-oct motif, we also discovered a novel constrained spacer motif for Esrrb and Sox2 with a gap of between 2 and 8 bps that Essrb and Sox2 cobind in a selective fashion. Through the use of knockdown experiments, we argue that the Esrrb-Sox2 complex is an arbiter of gene expression differences between ESCs and epiblast stem cells (EpiSC). A number of genes downregulated upon dual Esrrb/Sox2 knockdown (e.g., Klf4, Klf5, Jam2, Pecam1) are similarly downregulated in the ESC to EpiSC transition and contain the esrrb-sox motif. The prototypical Esrrb-Sox2 target gene, containing an esrrb-sox element conserved throughout eutherian and metatherian mammals, is Nr0b1. Through positive regulation of this transcriptional repressor, we argue the Esrrb-Sox2 complex promotes the ESC state through inhibition of the EpiSC transcriptional program and the same trio may also function to maintain trophoblast stem cells.\",\n \"corpus_id\": 24689885,\n \"score\": 1\n },\n {\n \"doc_id\": \"23805837\",\n \"title\": \"Contribution of nucleosome binding preferences and co-occurring DNA sequences to transcription factor binding.\",\n \"abstract\": \"BACKGROUND: Chromatin plays a critical role in regulating transcription factors (TFs) binding to their canonical transcription factor binding sites (TFBS). Recent studies in vertebrates show that many TFs preferentially bind to genomic regions that are well bound by nucleosomes in vitro. Co-occurring secondary motifs sometimes correlated with functional TFBS. RESULTS: We used a logistic regression to evaluate how well the propensity for nucleosome binding and co-occurrence of a secondary motif identify which canonical motifs are bound in vivo. We used ChIP-seq data for three transcription factors binding to their canonical motifs: c-Jun binding the AP-1 motif (TGA(C)/(G)TCA), GR (glucocorticoid receptor) binding the GR motif (G-ACA---(T)/(C)GT-C), and Hoxa2 (homeobox a2) binding the Pbx (Pre-B-cell leukemia homeobox) motif (TGATTGAT). For all canonical TFBS in the mouse genome, we calculated intrinsic nucleosome occupancy scores (INOS) for its surrounding 150-bps DNA and examined the relationship with in vivo TF binding. In mouse mammary 3134 cells, c-Jun and GR proteins preferentially bound regions calculated to be well-bound by nucleosomes in vitro with the canonical AP-1 and GR motifs themselves contributing to the high INOS. Functional GR motifs are enriched for AP-1 motifs if they are within a nucleosome-sized 150-bps region. GR and Hoxa2 also bind motifs with low INOS, perhaps indicating a different mechanism of action. CONCLUSION: Our analysis quantified the contribution of INOS and co-occurring sequence to the identification of functional canonical motifs in the genome. This analysis revealed an inherent competition between some TFs and nucleosomes for binding canonical TFBS. GR and c-Jun cooperate if they are within 150-bps. Binding of Hoxa2 and a fraction of GR to motifs with low INOS values suggesting they are not in competition with nucleosomes and may function using different mechanisms.\",\n \"corpus_id\": 11561522,\n \"score\": 1\n },\n {\n \"doc_id\": \"25026204\",\n \"title\": \"Sox2: masterminding the root of cancer.\",\n \"abstract\": \"The transcription factor Sox2 is a master regulator that maintains stemness in embryonic stem cells and neural stem cells. Using elegant lineage tracing strategies and genetic reporter mouse models, two studies (one of which is by Vanner and colleagues in this issue of Cancer Cell) now demonstrate that rare Sox2-expressing cells are the founding cancer stem cell population driving tumor initiation and therapy resistance.\",\n \"corpus_id\": 206542422,\n \"score\": 1\n },\n {\n \"doc_id\": \"25085421\",\n \"title\": \"Two distinct promoter architectures centered on dynamic nucleosomes control ribosomal protein gene transcription.\",\n \"abstract\": \"In yeast, ribosome production is controlled transcriptionally by tight coregulation of the 138 ribosomal protein genes (RPGs). RPG promoters display limited sequence homology, and the molecular basis for their coregulation remains largely unknown. Here we identify two prevalent RPG promoter types, both characterized by upstream binding of the general transcription factor (TF) Rap1 followed by the RPG-specific Fhl1/Ifh1 pair, with one type also binding the HMG-B protein Hmo1. We show that the regulatory properties of the two promoter types are remarkably similar, suggesting that they are determined to a large extent by Rap1 and the Fhl1/Ifh1 pair. Rapid depletion experiments allowed us to define a hierarchy of TF binding in which Rap1 acts as a pioneer factor required for binding of all other TFs. We also uncovered unexpected features underlying recruitment of Fhl1, whose forkhead DNA-binding domain is not required for binding at most promoters, and Hmo1, whose binding is supported by repeated motifs. Finally, we describe unusually micrococcal nuclease (MNase)-sensitive nucleosomes at all RPG promoters, located between the canonical +1 and -1 nucleosomes, which coincide with sites of Fhl1/Ifh1 and Hmo1 binding. We speculate that these \\\"fragile\\\" nucleosomes play an important role in regulating RPG transcriptional output.\",\n \"corpus_id\": 10208343,\n \"score\": 1\n },\n {\n \"doc_id\": \"25380620\",\n \"title\": \"Profiling gene promoter occupancy of Sox2 in two phenotypically distinct breast cancer cell subsets using chromatin immunoprecipitation and genome-wide promoter microarrays.\",\n \"abstract\": \"INTRODUCTION: Aberrant expression of the embryonic stem cell marker Sox2 has been reported in breast cancer (BC). We previously identified two phenotypically distinct BC cell subsets separated based on their differential response to a Sox2 transcription activity reporter, namely the reporter-unresponsive (RU) and the more tumorigenic reporter-responsive (RR) cells. We hypothesized that Sox2, as a transcription factor, contributes to their phenotypic differences by mediating differential gene expression in these two cell subsets. METHODS: We used chromatin immunoprecipitation and a human genome-wide promoter microarray (ChIP-chip) to determine the promoter occupancies of Sox2 in the MCF7 RU and RR breast cancer cell populations. We validated our findings with conventional chromatin immunoprecipitation, quantitative reverse transcription polymerase chain reaction (qPCR), and western blotting using cell lines, and also performed qPCR using patient RU and RR samples. RESULTS: We found a largely mutually exclusive profile of gene promoters bound by Sox2 between RU and RR cells derived from MCF7 (1830 and 456 genes, respectively, with only 62 overlapping genes). Sox2 was bound to stem cell- and cancer-associated genes in RR cells. Using quantitative RT-PCR, we confirmed that 15 such genes, including PROM1 (CD133), BMI1, GPR49 (LGR5), and MUC15, were expressed significantly higher in RR cells. Using siRNA knockdown or enforced expression of Sox2, we found that Sox2 directly contributes to the higher expression of these genes in RR cells. Mucin-15, a novel Sox2 downstream target in BC, contributes to the mammosphere formation of BC cells. Parallel findings were observed in the RU and RR cells derived from patient samples. CONCLUSIONS: In conclusion, our data supports the model that the Sox2 induces differential gene expression in the two distinct cell subsets in BC, and contributes to their phenotypic differences.\",\n \"corpus_id\": 11180637,\n \"score\": 1\n },\n {\n \"doc_id\": \"25494698\",\n \"title\": \"Unbiased chromatin accessibility profiling by RED-seq uncovers unique features of nucleosome variants in vivo.\",\n \"abstract\": \"BACKGROUND: Differential accessibility of DNA to nuclear proteins underlies the regulation of numerous cellular processes. Although DNA accessibility is primarily determined by the presence or absence of nucleosomes, differences in nucleosome composition or dynamics may also regulate accessibility. Methods for mapping nucleosome positions and occupancies genome-wide (MNase-seq) have uncovered the nucleosome landscapes of many different cell types and organisms. Conversely, methods specialized for the detection of large nucleosome-free regions of chromatin (DNase-seq, FAIRE-seq) have uncovered numerous gene regulatory elements. However, these methods are less successful in measuring the accessibility of DNA sequences within nucelosome arrays. RESULTS: Here we probe the genome-wide accessibility of multiple cell types in an unbiased manner using restriction endonuclease digestion of chromatin coupled to deep sequencing (RED-seq). Using this method, we identified differences in chromatin accessibility between populations of cells, not only in nucleosome-depleted regions of the genome (e.g., enhancers and promoters), but also within the majority of the genome that is packaged into nucleosome arrays. Furthermore, we identified both large differences in chromatin accessibility in distinct cell lineages and subtle but significant changes during differentiation of mouse embryonic stem cells (ESCs). Most significantly, using RED-seq, we identified differences in accessibility among nucleosomes harboring well-studied histone variants, and show that these differences depend on factors required for their deposition. CONCLUSIONS: Using an unbiased method to probe chromatin accessibility genome-wide, we uncover unique features of chromatin structure that are not observed using more widely-utilized methods. We demonstrate that different types of nucleosomes within mammalian cells exhibit different degrees of accessibility. These findings provide significant insight into the regulation of DNA accessibility.\",\n \"corpus_id\": 13054798,\n \"score\": 1\n },\n {\n \"doc_id\": \"26080409\",\n \"title\": \"MPE-seq, a new method for the genome-wide analysis of chromatin structure.\",\n \"abstract\": \"The analysis of chromatin structure is essential for the understanding of transcriptional regulation in eukaryotes. Here we describe methidiumpropyl-EDTA sequencing (MPE-seq), a method for the genome-wide characterization of chromatin that involves the digestion of nuclei withMPE-Fe(II) followed by massively parallel sequencing. Like micrococcal nuclease (MNase), MPE-Fe(II) preferentially cleaves the linker DNA between nucleosomes. However, there are differences in the cleavage of nuclear chromatin by MPE-Fe(II) relative to MNase. Most notably, immediately upstream of the transcription start site of active promoters, we frequently observed nucleosome-sized (141-190 bp) and subnucleosome-sized (such as 101-140 bp) peaks of digested chromatin fragments with MPE-seq but not with MNase-seq. These peaks also correlate with the presence of core histones and could thus be due, at least in part, to noncanonical chromatin structures such as labile nucleosome-like particles that have been observed in other contexts. The subnucleosome-sized MPE-seq peaks exhibit a particularly distinct association with active promoters. In addition, unlike MNase, MPE-Fe(II) cleaves nuclear DNA with little sequence bias. In this regard, we found that DNA sequences at RNA splice sites are hypersensitive to digestion by MNase but not by MPE-Fe(II). This phenomenon may have affected the analysis of nucleosome occupancy over exons. These findings collectively indicate that MPE-seq provides a unique and straightforward means for the genome-wide analysis of chromatin structure with minimal DNA sequence bias. In particular, the combined use of MPE-seq and MNase-seq enables the identification of noncanonical chromatin structures that are likely to be important for the regulation of gene expression.\",\n \"corpus_id\": 23349334,\n \"score\": 1\n },\n {\n \"doc_id\": \"26305327\",\n \"title\": \"Genome-Wide Profiling of PARP1 Reveals an Interplay with Gene Regulatory Regions and DNA Methylation.\",\n \"abstract\": \"Poly (ADP-ribose) polymerase-1 (PARP1) is a nuclear enzyme involved in DNA repair, chromatin remodeling and gene expression. PARP1 interactions with chromatin architectural multi-protein complexes (i.e. nucleosomes) alter chromatin structure resulting in changes in gene expression. Chromatin structure impacts gene regulatory processes including transcription, splicing, DNA repair, replication and recombination. It is important to delineate whether PARP1 randomly associates with nucleosomes or is present at specific nucleosome regions throughout the cell genome. We performed genome-wide association studies in breast cancer cell lines to address these questions. Our studies show that PARP1 associates with epigenetic regulatory elements genome-wide, such as active histone marks, CTCF and DNase hypersensitive sites. Additionally, the binding of PARP1 to chromatin genome-wide is mutually exclusive with DNA methylation pattern suggesting a functional interplay between PARP1 and DNA methylation. Indeed, inhibition of PARylation results in genome-wide changes in DNA methylation patterns. Our results suggest that PARP1 controls the fidelity of gene transcription and marks actively transcribed gene regions by selectively binding to transcriptionally active chromatin. These studies provide a platform for developing our understanding of PARP1's role in gene regulation.\",\n \"corpus_id\": 16840041,\n \"score\": 1\n },\n {\n \"doc_id\": \"26429969\",\n \"title\": \"Genome-wide profiling of nucleosome sensitivity and chromatin accessibility in Drosophila melanogaster.\",\n \"abstract\": \"Nucleosomal DNA is thought to be generally inaccessible to DNA-binding factors, such as micrococcal nuclease (MNase). Here, we digest Drosophila chromatin with high and low concentrations of MNase to reveal two distinct nucleosome types: MNase-sensitive and MNase-resistant. MNase-resistant nucleosomes assemble on sequences depleted of A/T and enriched in G/C-containing dinucleotides, whereas MNase-sensitive nucleosomes form on A/T-rich sequences found at transcription start and termination sites, enhancers and DNase I hypersensitive sites. Estimates of nucleosome formation energies indicate that MNase-sensitive nucleosomes tend to be less stable than MNase-resistant ones. Strikingly, a decrease in cell growth temperature of about 10°C makes MNase-sensitive nucleosomes less accessible, suggesting that observed variations in MNase sensitivity are related to either thermal fluctuations of chromatin fibers or the activity of enzymatic machinery. In the vicinity of active genes and DNase I hypersensitive sites nucleosomes are organized into periodic arrays, likely due to 'phasing' off potential barriers formed by DNA-bound factors or by nucleosomes anchored to their positions through external interactions. The latter idea is substantiated by our biophysical model of nucleosome positioning and energetics, which predicts that nucleosomes immediately downstream of transcription start sites are anchored and recapitulates nucleosome phasing at active genes significantly better than sequence-dependent models.\",\n \"corpus_id\": 17910210,\n \"score\": 1\n },\n {\n \"doc_id\": \"26764865\",\n \"title\": \"Recognition of the nucleosome by chromatin factors and enzymes.\",\n \"abstract\": \"Dynamic expression of the genome requires coordinated binding of chromatin factors and enzymes that carry out genome-templated processes. Until recently, the molecular mechanisms governing how these factors and enzymes recognize and act on the fundamental unit of chromatin, the nucleosome core particle, have remained a mystery. A small, yet growing set of structures of the nucleosome in complex with chromatin factors and enzymes highlights the importance of multivalency in defining nucleosome binding and specificity. Many such interactions include an arginine anchor motif, which targets a unique acidic patch on the nucleosome surface. These emerging paradigms for chromatin recognition will be discussed, focusing on several recent structural breakthroughs.\",\n \"corpus_id\": 39417690,\n \"score\": 1\n },\n {\n \"doc_id\": \"26772197\",\n \"title\": \"Mapping nucleosome positions using DNase-seq.\",\n \"abstract\": \"Although deoxyribonuclease I (DNase I) was used to probe the structure of the nucleosome in the 1960s and 1970s, in the current high-throughput sequencing era, DNase I has mainly been used to study genomic regions devoid of nucleosomes. Here, we reveal for the first time that DNase I can be used to precisely map the (translational) positions of in vivo nucleosomes genome-wide. Specifically, exploiting a distinctive DNase I cleavage profile within nucleosome-associated DNA--including a signature 10.3 base pair oscillation that corresponds to accessibility of the minor groove as DNA winds around the nucleosome--we develop a Bayes-factor-based method that can be used to map nucleosome positions along the genome. Compared to methods that require genetically modified histones, our DNase-based approach is easily applied in any organism, which we demonstrate by producing maps in yeast and human. Compared to micrococcal nuclease (MNase)-based methods that map nucleosomes based on cuts in linker regions, we utilize DNase I cuts both outside and within nucleosomal DNA; the oscillatory nature of the DNase I cleavage profile within nucleosomal DNA enables us to identify translational positioning details not apparent in MNase digestion of linker DNA. Because the oscillatory pattern corresponds to nucleosome rotational positioning, it also reveals the rotational context of transcription factor (TF) binding sites. We show that potential binding sites within nucleosome-associated DNA are often centered preferentially on an exposed major or minor groove. This preferential localization may modulate TF interaction with nucleosome-associated DNA as TFs search for binding sites.\",\n \"corpus_id\": 35136751,\n \"score\": 1\n },\n {\n \"doc_id\": \"26988140\",\n \"title\": \"Sox2 in the differentiation of cochlear progenitor cells.\",\n \"abstract\": \"HMG domain transcription factor, Sox2, is a critical gene for the development of cochlear hair cells, the receptor cells for hearing, but this has been ascribed to expansion of the progenitors that become hair cells. Here, we show that Sox2 activated Atoh1, a transcription factor important for hair cell differentiation, through an interaction with the 3' enhancer of Atoh1. Binding to consensus sequences in the Atoh1 enhancer was dependent on the level of Sox2, and the extent of enhancer binding correlated to the extent of activation. Atoh1 activation by Sox2 was required for embryonic hair cell development: deletion of Sox2 in an inducible mutant, even after progenitor cells were fully established, halted development of hair cells, and silencing also inhibited postnatal differentiation of hair cells induced by inhibition of γ-secretase. Sox2 is thus required in the cochlea to both expand the progenitor cells and initiate their differentiation to hair cells.\",\n \"corpus_id\": 6272016,\n \"score\": 1\n },\n {\n \"doc_id\": \"27058788\",\n \"title\": \"The Pioneer Transcription Factor FoxA Maintains an Accessible Nucleosome Configuration at Enhancers for Tissue-Specific Gene Activation.\",\n \"abstract\": \"Nuclear DNA wraps around core histones to form nucleosomes, which restricts the binding of transcription factors to gene regulatory sequences. Pioneer transcription factors can bind DNA sites on nucleosomes and initiate gene regulatory events, often leading to the local opening of chromatin. However, the nucleosomal configuration of open chromatin and the basis for its regulation is unclear. We combined low and high levels of micrococcal nuclease (MNase) digestion along with core histone mapping to assess the nucleosomal configuration at enhancers and promoters in mouse liver. We find that MNase-accessible nucleosomes, bound by transcription factors, are retained more at liver-specific enhancers than at promoters and ubiquitous enhancers. The pioneer factor FoxA displaces linker histone H1, thereby keeping enhancer nucleosomes accessible in chromatin and allowing other liver-specific transcription factors to bind and stimulate transcription. Thus, nucleosomes are not exclusively repressive to gene regulation when they are retained with, and exposed by, pioneer factors.\",\n \"corpus_id\": 206994505,\n \"score\": 1\n },\n {\n \"doc_id\": \"27335664\",\n \"title\": \"Nucleosome Positioning.\",\n \"abstract\": \"Nucleosome positioning is not only related to genomic DNA compaction but also to other biological functions. After the chromatin is digested by micrococcal nuclease, nucleosomal (nucleosome-bound) DNA fragments can be sequenced and mapped on the genomic DNA sequence. Due to the development of modern DNA sequencing technology, genome-wide nucleosome mapping has been performed in a wide range of eukaryotic species. Comparative analyses of the nucleosome positions have revealed that the nucleosome is more frequently formed in exonic than intronic regions, and that most of transcription start and translation (or transcription) end sites are located in nucleosome linker DNA regions, indicating that nucleosome positioning influences transcription initiation, transcription termination, and gene splicing. In addition, nucleosomal DNA contains guanine and cytosine (G + C)-rich sequences and a high level of cytosine methylation. Thus, the nucleosome positioning system has been conserved during eukaryotic evolution.\",\n \"corpus_id\": 17217147,\n \"score\": 1\n },\n {\n \"doc_id\": \"27458208\",\n \"title\": \"Genome-wide analysis reveals positional-nucleosome-oriented binding pattern of pioneer factor FOXA1.\",\n \"abstract\": \"The compaction of nucleosomal structures creates a barrier for DNA-binding transcription factors (TFs) to access their cognate cis-regulatory elements. Pioneer factors (PFs) such as FOXA1 are able to directly access these cis-targets within compact chromatin. However, how these PFs interplay with nucleosomes remains to be elucidated, and is critical for us to understand the underlying mechanism of gene regulation. Here, we have conducted a computational analysis on a strand-specific paired-end ChIP-exo (termed as ChIP-ePENS) data of FOXA1 in LNCaP cells by our novel algorithm ePEST. We find that FOXA1 chromatin binding occurs via four distinct border modes (or footprint boundary patterns), with a preferential footprint boundary patterns relative to FOXA1 motif orientation. In addition, from this analysis three fundamental nucleotide positions (oG, oS and oH) emerged as major determinants for blocking exo-digestion and forming these four distinct border modes. By integrating histone MNase-seq data, we found an astonishingly consistent, 'well-positioned' configuration occurs between FOXA1 motifs and dyads of nucleosomes genome-wide. We further performed ChIP-seq of eight chromatin remodelers and found an increased occupancy of these remodelers on FOXA1 motifs for all four border modes (or footprint boundary patterns), indicating the full occupancy of FOXA1 complex on the three blocking sites (oG, oS and oH) likely produces an active regulatory status with well-positioned phasing for protein binding events. Together, our results suggest a positional-nucleosome-oriented accessing model for PFs seeking target motifs, in which FOXA1 can examine each underlying DNA nucleotide and is able to sense all potential motifs regardless of whether they face inward or outward from histone octamers along the DNA helix axis.\",\n \"corpus_id\": 18204723,\n \"score\": 1\n },\n {\n \"doc_id\": \"27502481\",\n \"title\": \"Sox2: A multitasking networker.\",\n \"abstract\": \"The transcription factor Sox2 is best known as a pluripotency factor in stem and precursor cells and its expression generally correlates with an undifferentiated state. Proposed modes of action include those as classical transcription factor and pre-patterning factor with influence on histone modifications and chromatin structure. Recently, we provided the first detailed analysis of Sox2 expression and function during development of oligodendrocytes, the myelin-forming cells of the CNS. Surprisingly, we found evidence for a role of Sox2 as differentiation factor and found it to act through modulation of microRNA levels. Thus, we add new facets to the functional repertoire of Sox2 and throw light on the networking activity of this multitasking developmental regulator.\",\n \"corpus_id\": 5275910,\n \"score\": 1\n },\n {\n \"doc_id\": \"27889238\",\n \"title\": \"Insights into Nucleosome Organization in Mouse Embryonic Stem Cells through Chemical Mapping.\",\n \"abstract\": \"Nucleosome organization influences gene activity by controlling DNA accessibility to transcription machinery. Here, we develop a chemical biology approach to determine mammalian nucleosome positions genome-wide. We uncovered surprising features of nucleosome organization in mouse embryonic stem cells. In contrast to the prevailing model, we observe that for nearly all mouse genes, a class of fragile nucleosomes occupies previously designated nucleosome-depleted regions around transcription start sites and transcription termination sites. We show that nucleosomes occupy DNA targets for a subset of DNA-binding proteins, including CCCTC-binding factor (CTCF) and pluripotency factors. Furthermore, we provide evidence that promoter-proximal nucleosomes, with the +1 nucleosome in particular, contribute to the pausing of RNA polymerase II. Lastly, we find a characteristic preference for nucleosomes at exon-intron junctions. Taken together, we establish an accurate method for defining the nucleosome landscape and provide a valuable resource for studying nucleosome-mediated gene regulation in mammalian cells.\",\n \"corpus_id\": 5191876,\n \"score\": 1\n },\n {\n \"doc_id\": \"28301306\",\n \"title\": \"Two possible modes of pioneering associated with combinations of H2A.Z and p300/CBP at nucleosome-occupied enhancers.\",\n \"abstract\": \"Pioneer transcription factors are defined by their ability to bind nucleosome-occupied regions. Here, we discuss the properties of nucleosomes bound by pioneers at enhancer regions. We describe how select pioneers bind nucleosome-occupied or -depleted enhancer sites. Importantly, by revisiting and expanding existing data sets, we show differential H2A.Z and p300/CBP association at bound enhancers, highlighting two possible pioneering modes.\",\n \"corpus_id\": 3554143,\n \"score\": 1\n },\n {\n \"doc_id\": \"28842672\",\n \"title\": \"Downregulation of PARP1 transcription by promoter-associated E2F4-RBL2-HDAC1-BRM complex contributes to repression of pluripotency stem cell factors in human monocytes.\",\n \"abstract\": \"Differentiation of certain cell types is followed by a downregulation of PARP1 expression. We show that the reduction in the abundance of PARP1 in hematopoietic progenitor cells and monocytes is tightly controlled by the cell cycle. The differentiation-associated cell cycle exit induces E2F1 replacement with E2F4 at the PARP1 promoter and the assembly of an E2F4-RBL2-HDAC1-BRM(SWI/SNF) repressor complex which deacetylates nucleosomes and compacts chromatin. In G1 arrested cells, PARP1 transcription is reduced by the recruitment of E2F1-RB1-HDAC1-EZH2(PRC2)-BRM/BRG1(SWI/SNF), which additionally trimethylates H3K27 and causes an even higher increase in nucleosome density. The re-establishment of an active chromatin structure by treating post-mitotic monocytes with the HDAC inhibitor and G1 arrested cells with a combination of HDAC and EZH2 inhibitors restores PARP1 expression completely but does not affect the interaction between the components of the repressor complex with chromatin. This suggests that RB1 and RBL2, as well as PRC2, SWI/SNF and HDAC1, do not interfere with the transcription machinery. Interestingly, reinstatement of PARP1 expression by the silencing of RBL2 or by the inhibition of HDACs in monocytes and by transfection with the PARP1 expression vector in differentiated THP-1 cells substantially increased transcription of pluripotency stem cell factors such as POU5F1, SOX2 and NANOG.\",\n \"corpus_id\": 46903749,\n \"score\": 1\n },\n {\n \"doc_id\": \"29027167\",\n \"title\": \"Characterization of the Nucleosome Landscape by Micrococcal Nuclease-Sequencing (MNase-seq).\",\n \"abstract\": \"MNase-seq allows the genome-wide examination of the nucleosome landscape by determination of nucleosome positioning and occupancy. Typically, native or formaldehyde fixed chromatin is subjected to digestion by micrococcal nuclease (MNase), which degrades linker DNA and yields mainly mono-nucleosomes. The resulting material can be processed directly or can be subjected to an optional chromatin immunoprecipitation step (MNase-ChIP-seq). De-crosslinked and purified DNA is then subjected to next-generation sequencing. The protocol presented here has been tailored for the analysis of nucleosome landscape in the malaria parasite, Plasmodium falciparum, but most steps are directly applicable to other cell types. We also discuss general considerations for experimental design and computational analysis, which are crucial for accurate investigation of the nucleosome landscape.\",\n \"corpus_id\": 23351532,\n \"score\": 1\n },\n {\n \"doc_id\": \"29052192\",\n \"title\": \"Profiling Nucleosome Occupancy by MNase-seq: Experimental Protocol and Computational Analysis.\",\n \"abstract\": \"Nucleosomes are the basic repeating units of eukaryotic chromatin. They play important roles in chromatin compaction and gene regulation. Therefore, it is important to profile the in vivo locations of nucleosomes in the genome. Here we illustrate how to profile nucleosome occupancy at genome-wide scale using micrococcal nuclease (MNase) digestion combined with high throughput Illumina sequencing (MNase-seq). Nucleosome-associated DNA is relatively insensitive to digestion by micrococcal nuclease (MNase). Upon mild MNase treatment, the undigested nucleosomal DNA can be purified and sequenced allowing a precise localization of in vivo nucleosomes at a genome-wide level.\",\n \"corpus_id\": 8706843,\n \"score\": 1\n },\n {\n \"doc_id\": \"18643465\",\n \"title\": \"Nucleosome switches.\",\n \"abstract\": \"We present a statistical-mechanical model for the positioning of nucleosomes along genomic DNA molecules as a function of the strength of the binding potential and the chemical potential of the nucleosomes. We show that a significant section of the DNA is composed of two-level nucleosome switching regions where the nucleosome distribution undergoes a localized, first-order transition. The location of the nucleosome switches shows a strong correlation with the location of gene-regulation regions.\",\n \"corpus_id\": 16837247,\n \"score\": 0\n },\n {\n \"doc_id\": \"22737086\",\n \"title\": \"In vivo effects of histone H3 depletion on nucleosome occupancy and position in Saccharomyces cerevisiae.\",\n \"abstract\": \"Previous studies in Saccharomyces cerevisiae established that depletion of histone H4 results in the genome-wide transcriptional de-repression of hundreds of genes. To probe the mechanism of this transcriptional de-repression, we depleted nucleosomes in vivo by conditional repression of histone H3 transcription. We then measured the resulting changes in transcription by RNA-seq and in chromatin organization by MNase-seq. This experiment also bears on the degree to which trans-acting factors and DNA-encoded elements affect nucleosome position and occupancy in vivo. We identified ∼60,000 nucleosomes genome wide, and we classified ∼2,000 as having preferentially reduced occupancy following H3 depletion and ∼350 as being preferentially retained. We found that the in vivo influence of DNA sequences that favor or disfavor nucleosome occupancy increases following histone H3 depletion, demonstrating that nucleosome density contributes to moderating the influence of DNA sequence on nucleosome formation in vivo. To identify factors important for influencing nucleosome occupancy and position, we compared our data to 40 existing whole-genome data sets. Factors associated with promoters, such as histone acetylation and H2A.z incorporation, were enriched at sites of nucleosome loss. Nucleosome retention was linked to stabilizing marks such as H3K36me2. Notably, the chromatin remodeler Isw2 was uniquely associated with retained occupancy and altered positioning, consistent with Isw2 stabilizing histone-DNA contacts and centering nucleosomes on available DNA in vivo. RNA-seq revealed a greater number of de-repressed genes (∼2,500) than previous studies, and these genes exhibited reduced nucleosome occupancy in their promoters. In summary, we identify factors likely to influence nucleosome stability under normal growth conditions and the specific genomic locations at which they act. We find that DNA-encoded nucleosome stability and chromatin composition dictate which nucleosomes will be lost under conditions of limiting histone protein and that this, in turn, governs which genes are susceptible to a loss of regulatory fidelity.\",\n \"corpus_id\": 15417296,\n \"score\": 0\n },\n {\n \"doc_id\": \"23132853\",\n \"title\": \"Activation of the SNF2 family ATPase ALC1 by poly(ADP-ribose) in a stable ALC1·PARP1·nucleosome intermediate.\",\n \"abstract\": \"The human ALC1/CHD1L oncogene encodes an SNF2 family ATPase with a macrodomain that binds poly(ADP-ribose) (PAR). We and others previously showed that ALC1 possesses a cryptic ATP-dependent nucleosome remodeling activity that is potently activated in the presence of PARP1 and NAD(+), its substrate for PAR synthesis. In this work, we dissected the mechanism by which PARP1 and NAD(+) activate ALC1 nucleosome remodeling. We demonstrate that ALC1 activation depends on the formation of a stable ALC1·PARylated PARP1·nucleosome intermediate. In addition, by exploiting a novel PAR footprinting assay, we obtained evidence that the ALC1 macrodomain remains stably associated with PAR on autoPARylated PARP1 during the course of nucleosome remodeling reactions. Taken together, our findings are consistent with the model that PAR present on PARylated PARP1 acts as an allosteric effector of ALC1 nucleosome remodeling activity.\",\n \"corpus_id\": 6155195,\n \"score\": 0\n },\n {\n \"doc_id\": \"23910651\",\n \"title\": \"Reduced ADP-ribosylation by PARP1 natural polymorphism V762A and by PARP1 inhibitors enhance Hepatitis B virus replication.\",\n \"abstract\": \"HepG2 and Huh7 cell lines are frequently used as models to study viral hepatitis and hepatocellular carcinoma. However, they exhibit significantly different capacities in their ability to support hepatitis B virus (HBV) replication. To investigate the basis for this, transcription factor-binding motifs at the HBV core promoter (HBVCP) were tested in luciferase reporter constructs to identify the possible role of host factors. Among the transcription factors screened: PARP1, SP1, HNF4α, HNF3, hB1F and HNF1, deletion of the PARP1 binding motif abrogated transcriptional activity at the HBVCP in HepG2 but not Huh7 cells. Sequencing of the PARP1 gene revealed that HepG2 cells carried an Ala762 allele which has low ADP-ribosylation activity, which was shown to have increased PARP1 binding affinity to its cognate motif thus resulting in higher transcriptional activity. PARP1 inhibitors that are being developed as broad cancer therapeutics also target PARP1 ADP-ribosylation enzymatic function. Four PARP1 inhibitors: PJ-34, ABT888, AZD2281 and AG014699 were tested for their effect on HBV replication. All four small molecules effectively enhanced HBV replication in vitro, confirming the role of PARP1 in HBV replication and that alteration of ADP-ribosylation by mutation or drugs can affect HBV replication. Our data demonstrate that natural polymorphisms in the host affecting proteins such as PARP1 can have a significant effect on HBV replication. Hence, patients who are infected with HBV and are on clinical trials involving PARP1 inhibitors may be at risk from unintended side-effects such as exacerbation of HBV replication.\",\n \"corpus_id\": 7327661,\n \"score\": 0\n },\n {\n \"doc_id\": \"24145797\",\n \"title\": \"PARP1 orchestrates variant histone exchange in signal-mediated transcriptional activation.\",\n \"abstract\": \"Transcriptional activation is accompanied by multiple molecular events that remodel the local chromatin environment in promoter regions. These molecular events are often orchestrated in response to the activation of signalling pathways, as exemplified by the response of immediate early genes such as FOS to ERK MAP kinase signalling. Here, we demonstrate that inducible NFI recruitment permits PARP1 binding to the FOS promoter by a mutually reinforcing loop. PARP1 and its poly(ADP-ribosyl)ation activity are required for maintaining FOS activation kinetics. We also show that the histone variant H2A.Z associates with the FOS promoter and acts in a transcription-suppressive manner. However, in response to ERK pathway signalling, H2A.Z is replaced by H2A; PARP1 activity is required to promote this exchange. Thus, our work has revealed an additional facet of PARP1 function in promoting dynamic remodelling of promoter-associated nucleosomes to allow transcriptional activation in response to cellular signalling.\",\n \"corpus_id\": 14399127,\n \"score\": 0\n },\n {\n \"doc_id\": \"24256300\",\n \"title\": \"Clustered regulatory elements at nucleosome-depleted regions punctuate a constant nucleosomal landscape in Schizosaccharomyces pombe.\",\n \"abstract\": \"BACKGROUND: Nucleosomes facilitate the packaging of the eukaryotic genome and modulate the access of regulators to DNA. A detailed description of the nucleosomal organization under different transcriptional programmes is essential to understand their contribution to genomic regulation. RESULTS: To visualize the dynamics of individual nucleosomes under different transcriptional programmes we have generated high-resolution nucleosomal maps in Schizosaccharomyces pombe. We show that 98.5% of the genome remains almost invariable during mitosis and meiosis while remodelling is limited to approximately 1100 nucleosomes in the promoters of a subset of meiotic genes. These inducible nucleosome-depleted regions (NDR) and also those constitutively present in the genome overlap precisely with clusters of binding sites for transcription factors (TF) specific for meiosis and for different functional classes of genes, respectively. Deletion of two TFs affects only a small fraction of all the NDRs to which they bind in vivo, indicating that TFs collectively contribute to NDR maintenance. CONCLUSIONS: Our results show that the nucleosomal profile in S. pombe is largely maintained under different physiological conditions and patterns of gene expression. This relatively constant landscape favours the concentration of regulators in constitutive and inducible NDRs. The combinatorial analysis of binding motifs in this discrete fraction of the genome will facilitate the definition of the transcriptional regulatory networks.\",\n \"corpus_id\": 17978747,\n \"score\": 0\n },\n {\n \"doc_id\": \"24771338\",\n \"title\": \"Nucleosome regulatory dynamics in response to TGFβ.\",\n \"abstract\": \"Nucleosomes play important roles in a cell beyond their basal functionality in chromatin compaction. Their placement affects all steps in transcriptional regulation, from transcription factor (TF) binding to messenger ribonucleic acid (mRNA) synthesis. Careful profiling of their locations and dynamics in response to stimuli is important to further our understanding of transcriptional regulation by the state of chromatin. We measured nucleosome occupancy in human hepatic cells before and after treatment with transforming growth factor beta 1 (TGFβ1), using massively parallel sequencing. With a newly developed method, SuMMIt, for precise positioning of nucleosomes we inferred dynamics of the nucleosomal landscape. Distinct nucleosome positioning has previously been described at transcription start site and flanking TF binding sites. We found that the average pattern is present at very few sites and, in case of TF binding, the double peak surrounding the sites is just an artifact of averaging over many loci. We systematically searched for depleted nucleosomes in stimulated cells compared to unstimulated cells and identified 24 318 loci. Depending on genomic annotation, 44-78% of them were over-represented in binding motifs for TFs. Changes in binding affinity were verified for HNF4α by qPCR. Strikingly many of these loci were associated with expression changes, as measured by RNA sequencing.\",\n \"corpus_id\": 11307141,\n \"score\": 0\n },\n {\n \"doc_id\": \"25161822\",\n \"title\": \"PARP1 enhances inflammatory cytokine expression by alteration of promoter chromatin structure in microglia.\",\n \"abstract\": \"BACKGROUND: Poly(ADP-ribose) polymerase 1 (PARP1) is a chromatin-associated enzyme that participates in processes such as transcription and DNA repair through the regulation of chromatin structure. Accumulating evidence suggests an important role for PARP1 enzymatic activity in promoting CNS inflammation by facilitating the expression of inflammatory cytokines in glial cells. However, the molecular mechanisms by which PARP1 enzymatic activity mediates this process are not well understood. In this report we sought to determine the molecular mechanisms by which PARP1 enzymatic activity facilitates the expression of Il1β and TNF in LPS-stimulated BV2 cells. METHODS: PARP1 enzymatic activity and histone ADP-ribosylation were measured in LPS-stimulated BV2 cells by radioactive labelling with (32)P-NAD(+). To assess the effect of histone ADP-ribosylation on nucleosome structure, in vitro nucleosome remodeling, nuclease accessibility and binding assays were performed. These studies were complemented by chromatin immunoprecipitation assays in resting and LPS-stimulated BV2 cells in order to determine the occupancy of PARP1, nucleosomes and the RelA subunit of NF-κB, as well as ADP-ribosylation, at the Il1β and Tnf promoters. Finally, we determined the effect of pharmacological inhibition of PARP1 enzymatic activity on the LPS stimulation-dependent induction of Il1β and Tnf mRNA. RESULTS: Our results indicate that LPS stimulation induces PARP1 enzymatic activity and histone ADP-ribosylation in the chromatin compartment of BV2 cells. In vitro studies show that nucleosome-bound PARP1 disrupts nucleosome structure histone ADP-ribosylation, increasing the accessibility of nucleosomal DNA. Consistent with this PARP1 is constitutively associated with at the Il1β and Tnf promoters in resting BV2 cells. Upon stimulation with LPS, ADP-ribosylation is observed at these promoters, and this is correlated with increased recruitment of the transcription factor NF-κB, resulting in robust transcription of these inflammatory cytokines. Accordingly, pharmacological inhibition of PARP1 enzymatic activity reduces NF-κB recruitment, and Il1β and Tnf expression in LPS-stimulated microglia. CONCLUSIONS: Collectively, our data suggest that PARP1 facilitates inflammatory cytokine expression in microglia by increasing the accessibility of promoter DNA via histone ADP-riboyslation.\",\n \"corpus_id\": 13054142,\n \"score\": 0\n },\n {\n \"doc_id\": \"25555679\",\n \"title\": \"RecQ helicases and PARP1 team up in maintaining genome integrity.\",\n \"abstract\": \"Genome instability represents a primary hallmark of aging and cancer. RecQL helicases (i.e., RECQL1, WRN, BLM, RECQL4, RECQL5) as well as poly(ADP-ribose) polymerases (PARPs, in particular PARP1) represent two central quality control systems to preserve genome integrity in mammalian cells. Consistently, both enzymatic families have been linked to mechanisms of aging and carcinogenesis in mice and humans. This is in accordance with clinical and epidemiological findings demonstrating that defects in three RecQL helicases, i.e., WRN, BLM, RECQL4, are related to human progeroid and cancer predisposition syndromes, i.e., Werner, Bloom, and Rothmund Thomson syndrome, respectively. Moreover, PARP1 hypomorphy is associated with a higher risk for certain types of cancer. On a molecular level, RecQL helicases and PARP1 are involved in the control of DNA repair, telomere maintenance, and replicative stress. Notably, over the last decade, it became apparent that all five RecQL helicases physically or functionally interact with PARP1 and/or its enzymatic product poly(ADP-ribose) (PAR). Furthermore, a profound body of evidence revealed that the cooperative function of RECQLs and PARP1 represents an important factor for maintaining genome integrity. In this review, we summarize the status quo of this molecular cooperation and discuss open questions that provide a basis for future studies to dissect the cooperative functions of RecQL helicases and PARP1 in aging and carcinogenesis.\",\n \"corpus_id\": 29498397,\n \"score\": 0\n },\n {\n \"doc_id\": \"26269799\",\n \"title\": \"Replicating Nucleosomes.\",\n \"abstract\": \"Eukaryotic replication disrupts each nucleosome as the fork passes, followed by re-assembly of disrupted nucleosomes and incorporation of newly synthesized histones into nucleosomes in the daughter genomes. In this review, we examine this process of replication-coupled nucleosome assembly to understand how characteristic steady state nucleosome landscapes are attained. Recent studies have begun to elucidate mechanisms involved in histone transfer during replication and maturation of the nucleosome landscape after disruption by replication. A fuller understanding of replication-coupled nucleosome assembly will be needed to explain how epigenetic information is replicated at every cell division.\",\n \"corpus_id\": 18044952,\n \"score\": 0\n },\n {\n \"doc_id\": \"26814966\",\n \"title\": \"Genome-wide nucleosome specificity and function of chromatin remodellers in ES cells.\",\n \"abstract\": \"ATP-dependent chromatin remodellers allow access to DNA for transcription factors and the general transcription machinery, but whether mammalian chromatin remodellers target specific nucleosomes to regulate transcription is unclear. Here we present genome-wide remodeller-nucleosome interaction profiles for the chromatin remodellers Chd1, Chd2, Chd4, Chd6, Chd8, Chd9, Brg1 and Ep400 in mouse embryonic stem (ES) cells. These remodellers bind one or both full nucleosomes that flank micrococcal nuclease (MNase)-defined nucleosome-free promoter regions (NFRs), where they separate divergent transcription. Surprisingly, large CpG-rich NFRs that extend downstream of annotated transcriptional start sites are nevertheless bound by non-nucleosomal or subnucleosomal histone variants (H3.3 and H2A.Z) and marked by H3K4me3 and H3K27ac modifications. RNA polymerase II therefore navigates hundreds of base pairs of altered chromatin in the sense direction before encountering an MNase-resistant nucleosome at the 3' end of the NFR. Transcriptome analysis after remodeller depletion reveals reciprocal mechanisms of transcriptional regulation by remodellers. Whereas at active genes individual remodellers have either positive or negative roles via altering nucleosome stability, at polycomb-enriched bivalent genes the same remodellers act in an opposite manner. These findings indicate that remodellers target specific nucleosomes at the edge of NFRs, where they regulate ES cell transcriptional programs.\",\n \"corpus_id\": 4465573,\n \"score\": 0\n },\n {\n \"doc_id\": \"26933790\",\n \"title\": \"Nucleosome dynamics during chromatin remodeling in vivo.\",\n \"abstract\": \"Precise positioning of nucleosomes around regulatory sites is achieved by the action of chromatin remodelers, which use the energy of ATP to slide, evict or change the composition of nucleosomes. Chromatin remodelers act to bind nucleosomes, disrupt histone-DNA interactions and translocate the DNA around the histone core to reposition nucleosomes. Hence, remodeling is expected to involve nucleosomal intermediates with a structural organization that is distinct from intact nucleosomes. We describe the identification of a partially unwrapped nucleosome structure using methods that map histone-DNA contacts genome-wide. This alternative nucleosome structure is likely formed as an intermediate or by-product during nucleosome remodeling by the RSC complex. Identification of the loss of histone-DNA contacts during chromatin remodeling by RSC in vivo has implications for the regulation of transcriptional initiation.\",\n \"corpus_id\": 17062908,\n \"score\": 0\n },\n {\n \"doc_id\": \"26982358\",\n \"title\": \"A Pioneer's Tail.\",\n \"abstract\": \"In this issue of Immunity, Boller et al. (2016) show that a C-terminal domain of EBF1 is required for chromatin binding and induction of DNase I hypersensitive sites. These properties mark EBF1 as a pioneer factor in B cell development and demonstrate a role for non-DNA binding domains in this process.\",\n \"corpus_id\": 12545327,\n \"score\": 0\n },\n {\n \"doc_id\": \"27462443\",\n \"title\": \"Involvement of PARP1 in the regulation of alternative splicing.\",\n \"abstract\": \"Specialized chromatin structures such as nucleosomes with specific histone modifications decorate exons in eukaryotic genomes, suggesting a functional connection between chromatin organization and the regulation of pre-mRNA splicing. Through profiling the functional location of Poly (ADP) ribose polymerase, we observed that it is associated with the nucleosomes at exon/intron boundaries of specific genes, suggestive of a role for this enzyme in alternative splicing. Poly (ADP) ribose polymerase has previously been implicated in the PARylation of splicing factors as well as regulation of the histone modification H3K4me3, a mark critical for co-transcriptional splicing. In light of these studies, we hypothesized that interaction of the chromatin-modifying factor, Poly (ADP) ribose polymerase with nucleosomal structures at exon-intron boundaries, might regulate pre-mRNA splicing. Using genome-wide approaches validated by gene-specific assays, we show that depletion of PARP1 or inhibition of its PARylation activity results in changes in alternative splicing of a specific subset of genes. Furthermore, we observed that PARP1 bound to RNA, splicing factors and chromatin, suggesting that Poly (ADP) ribose polymerase serves as a gene regulatory hub to facilitate co-transcriptional splicing. These studies add another function to the multi-functional protein, Poly (ADP) ribose polymerase, and provide a platform for further investigation of this protein's function in organizing chromatin during gene regulatory processes.\",\n \"corpus_id\": 37375710,\n \"score\": 0\n },\n {\n \"doc_id\": \"28991194\",\n \"title\": \"PARP1 in Carcinomas and PARP1 Inhibitors as Antineoplastic Drugs.\",\n \"abstract\": \"Poly (ADP-ribose) polymerase 1 (PARP1), the best-studied isoform of the nuclear enzyme PARP family, plays a pivotal role in cellular biological processes, such as DNA repair, gene transcription, and so on. PARP1 has been found to be overexpressed in various carcinomas. These all indicate the clinical potential of PARP1 as a therapeutic target of human malignancies. Additionally, multiple preclinical research studies and clinical trials demonstrate that inhibition of PARP1 can repress tumor growth and metastasis. Up until now, PARP1 inhibitors are clinically used not only for monotherapy to suppress various tumors, but also for adjuvant therapy, to maintain or enhance therapeutic effects of mature antineoplastic drugs, as well as protect patients from chemotherapy and surgery-induced injury. To supply a framework for understanding recent research progress of PARP1 in carcinomas, we review the structure, expression, functions, and mechanisms of PARP1, and summarize the clinically mature PARP1-related anticancer agents, to provide some ideas for the development of other promising PARP1 inhibitors in antineoplastic therapy.\",\n \"corpus_id\": 22074539,\n \"score\": 0\n },\n {\n \"doc_id\": \"29563192\",\n \"title\": \"Cryo-EM structure of the nucleosome containing the ALB1 enhancer DNA sequence.\",\n \"abstract\": \"Pioneer transcription factors specifically target their recognition DNA sequences within nucleosomes. FoxA is the pioneer transcription factor that binds to the ALB1 gene enhancer in liver precursor cells, and is required for liver differentiation in embryos. The ALB1 enhancer DNA sequence is reportedly incorporated into nucleosomes in cells, although the nucleosome structure containing the targeting sites for FoxA has not been clarified yet. In this study, we determined the nucleosome structure containing the ALB1 enhancer (N1) sequence, by cryogenic electron microscopy at 4.0 Å resolution. The nucleosome structure with the ALB1 enhancer DNA is not significantly different from the previously reported nucleosome structure with the Widom 601 DNA. Interestingly, in the nucleosomes, the ALB1 enhancer DNA contains local flexible regions, as compared to the Widom 601 DNA. Consistently, DNaseI treatments revealed that, in the nucleosome, the ALB1 enhancer (N1) DNA is more accessible than the Widom 601 sequence. The histones also associated less strongly with the ALB1 enhancer (N1) DNA than the Widom 601 DNA in the nucleosome. Therefore, the local histone-DNA contacts may be responsible for the enhanced DNA accessibility in the nucleosome with the ALB1 enhancer DNA.\",\n \"corpus_id\": 4578710,\n \"score\": 0\n }\n]","isConversational":false}}},{"rowIdx":70,"cells":{"query":{"kind":"string","value":"{\n \"doc_id\": \"28985416\",\n \"title\": \"EVLncRNAs: a manually curated database for long non-coding RNAs validated by low-throughput experiments.\",\n \"abstract\": \"Long non-coding RNAs (lncRNAs) play important functional roles in various biological processes. Early databases were utilized to deposit all lncRNA candidates produced by high-throughput experimental and/or computational techniques to facilitate classification, assessment and validation. As more lncRNAs are validated by low-throughput experiments, several databases were established for experimentally validated lncRNAs. However, these databases are small in scale (with a few hundreds of lncRNAs only) and specific in their focuses (plants, diseases or interactions). Thus, it is highly desirable to have a comprehensive dataset for experimentally validated lncRNAs as a central repository for all of their structures, functions and phenotypes. Here, we established EVLncRNAs by curating lncRNAs validated by low-throughput experiments (up to 1 May 2016) and integrating specific databases (lncRNAdb, LncRANDisease, Lnc2Cancer and PLNIncRBase) with additional functional and disease-specific information not covered previously. The current version of EVLncRNAs contains 1543 lncRNAs from 77 species that is 2.9 times larger than the current largest database for experimentally validated lncRNAs. Seventy-four percent lncRNA entries are partially or completely new, comparing to all existing experimentally validated databases. The established database allows users to browse, search and download as well as to submit experimentally validated lncRNAs. The database is available at http://biophy.dzu.edu.cn/EVLncRNAs.\",\n \"corpus_id\": 3298218\n}"},"candidates":{"kind":"list like","value":[{"doc_id":"21112873","title":"lncRNAdb: a reference database for long noncoding RNAs.","abstract":"Large numbers of long RNAs with little or no protein-coding potential [long noncoding RNAs (lncRNAs)] are being identified in eukaryotes. In parallel, increasing data describing the expression profiles, molecular features and functions of individual lncRNAs in a variety of systems are accumulating. To enable the systematic compilation and updating of this information, we have developed a database (lncRNAdb) containing a comprehensive list of lncRNAs that have been shown to have, or to be associated with, biological functions in eukaryotes, as well as messenger RNAs that have regulatory roles. Each entry contains referenced information about the RNA, including sequences, structural information, genomic context, expression, subcellular localization, conservation, functional evidence and other relevant information. lncRNAdb can be searched by querying published RNA names and aliases, sequences, species and associated protein-coding genes, as well as terms contained in the annotations, such as the tissues in which the transcripts are expressed and associated diseases. In addition, lncRNAdb is linked to the UCSC Genome Browser for visualization and Noncoding RNA Expression Database (NRED) for expression information from a variety of sources. lncRNAdb provides a platform for the ongoing collation of the literature pertaining to lncRNAs and their association with other genomic elements. lncRNAdb can be accessed at: http://www.lncrnadb.org/.","corpus_id":2900681,"score":2},{"doc_id":"22135294","title":"NONCODE v3.0: integrative annotation of long noncoding RNAs.","abstract":"Facilitated by the rapid progress of high-throughput sequencing technology, a large number of long noncoding RNAs (lncRNAs) have been identified in mammalian transcriptomes over the past few years. LncRNAs have been shown to play key roles in various biological processes such as imprinting control, circuitry controlling pluripotency and differentiation, immune responses and chromosome dynamics. Notably, a growing number of lncRNAs have been implicated in disease etiology. With the increasing number of published lncRNA studies, the experimental data on lncRNAs (e.g. expression profiles, molecular features and biological functions) have accumulated rapidly. In order to enable a systematic compilation and integration of this information, we have updated the NONCODE database (http://www.noncode.org) to version 3.0 to include the first integrated collection of expression and functional lncRNA data obtained from re-annotated microarray studies in a single database. NONCODE has a user-friendly interface with a variety of search or browse options, a local Genome Browser for visualization and a BLAST server for sequence-alignment search. In addition, NONCODE provides a platform for the ongoing collation of ncRNAs reported in the literature. All data in NONCODE are open to users, and can be downloaded through the website or obtained through the SOAP API and DAS services.","corpus_id":846427,"score":2},{"doc_id":"22336709","title":"Non-coding transcription characterization and annotation: a guide and web resource for non-coding RNA databases.","abstract":"Large-scale transcriptome projects have shown that the number of RNA transcripts not coding for proteins (non-coding RNAs) is much larger than previously recognized. High-throughput technologies, coupled with bioinformatics approaches, have produced increasing amounts of data, highlighting the role of non-coding RNAs (ncRNAs) in biological processes. Data generated by these studies include diverse non-coding RNA classes from organisms of different kingdoms, which were obtained using different experimental and computational assays. This has led to a rapid increase of specialized RNA databases. The fast growth in the number of available databases makes integration of stored information a difficult task. We present here NRDR, a Non-coding RNA Databases Resource for information retrieval on ncRNA databases (www.ncrnadatabases.org). We performed a survey of 102 public databases on ncRNAs and we have introduced four categorizations to classify these databases and to help researchers quickly search and find the information they need: RNA family, information source, information content and available search mechanisms. NRDR is a useful databases searching tool that will facilitate research on ncRNAs.","corpus_id":34157165,"score":2},{"doc_id":"23042674","title":"LNCipedia: a database for annotated human lncRNA transcript sequences and structures.","abstract":"Here, we present LNCipedia (http://www.lncipedia.org), a novel database for human long non-coding RNA (lncRNA) transcripts and genes. LncRNAs constitute a large and diverse class of non-coding RNA genes. Although several lncRNAs have been functionally annotated, the majority remains to be characterized. Different high-throughput methods to identify new lncRNAs (including RNA sequencing and annotation of chromatin-state maps) have been applied in various studies resulting in multiple unrelated lncRNA data sets. LNCipedia offers 21 488 annotated human lncRNA transcripts obtained from different sources. In addition to basic transcript information and gene structure, several statistics are determined for each entry in the database, such as secondary structure information, protein coding potential and microRNA binding sites. Our analyses suggest that, much like microRNAs, many lncRNAs have a significant secondary structure, in-line with their presumed association with proteins or protein complexes. Available literature on specific lncRNAs is linked, and users or authors can submit articles through a web interface. Protein coding potential is assessed by two different prediction algorithms: Coding Potential Calculator and HMMER. In addition, a novel strategy has been integrated for detecting potentially coding lncRNAs by automatically re-analysing the large body of publicly available mass spectrometry data in the PRIDE database. LNCipedia is publicly available and allows users to query and download lncRNA sequences and structures based on different search criteria. The database may serve as a resource to initiate small- and large-scale lncRNA studies. As an example, the LNCipedia content was used to develop a custom microarray for expression profiling of all available lncRNAs.","corpus_id":7002750,"score":2},{"doc_id":"23175614","title":"LncRNADisease: a database for long-non-coding RNA-associated diseases.","abstract":"In this article, we describe a long-non-coding RNA (lncRNA) and disease association database (LncRNADisease), which is publicly accessible at http://cmbi.bjmu.edu.cn/lncrnadisease. In recent years, a large number of lncRNAs have been identified and increasing evidence shows that lncRNAs play critical roles in various biological processes. Therefore, the dysfunctions of lncRNAs are associated with a wide range of diseases. It thus becomes important to understand lncRNAs' roles in diseases and to identify candidate lncRNAs for disease diagnosis, treatment and prognosis. For this purpose, a high-quality lncRNA-disease association database would be extremely beneficial. Here, we describe the LncRNADisease database that collected and curated approximately 480 entries of experimentally supported lncRNA-disease associations, including 166 diseases. LncRNADisease also curated 478 entries of lncRNA interacting partners at various molecular levels, including protein, RNA, miRNA and DNA. Moreover, we annotated lncRNA-disease associations with genomic information, sequences, references and species. We normalized the disease name and the type of lncRNA dysfunction and provided a detailed description for each entry. Finally, we developed a bioinformatic method to predict novel lncRNA-disease associations and integrated the method and the predicted associated diseases of 1564 human lncRNAs into the database.","corpus_id":1969204,"score":2},{"doc_id":"23476021","title":"PLncDB: plant long non-coding RNA database.","abstract":"SUMMARY: Plant long non-coding RNA database (PLncDB) attempts to provide the following functions related to long non-coding RNAs (lncRNAs): (i) Genomic information for a large number of lncRNAs collected from various resources; (ii) an online genome browser for plant lncRNAs based on a platform similar to that of the UCSC Genome Browser; (iii) Integration of transcriptome datasets derived from various samples including different tissues, developmental stages, mutants and stress treatments; and (iv) A list of epigenetic modification datasets and small RNA datasets. Currently, our PLncDB provides a comprehensive genomic view of Arabidopsis lncRNAs for the plant research community. This database will be regularly updated with new plant genome when available so as to greatly facilitate future investigations on plant lncRNAs. AVAILABILITY: PLncDB is freely accessible at http://chualab.rockefeller.edu/gbrowse2/homepage.html and all results can be downloaded for free at the website.","corpus_id":2290617,"score":2},{"doc_id":"24525374","title":"lncRNAMap: a map of putative regulatory functions in the long non-coding transcriptome.","abstract":"BACKGROUND: Recent studies have demonstrated the importance of long non-coding RNAs (lncRNAs) in chromatin remodeling, and in transcriptional and post-transcriptional regulation. However, only a few specific lncRNAs are well understood, whereas others are completely uncharacterized. To address this, there is a need for user-friendly platform to studying the putative regulatory functions of human lncRNAs. DESCRIPTION: lncRNAMap is an integrated and comprehensive database relating to exploration of the putative regulatory functions of human lncRNAs with two mechanisms of regulation, by encoding siRNAs and by acting as miRNA decoys. To investigate lncRNAs producing siRNAs that regulate protein-coding genes, lncRNAMap integrated small RNAs (sRNAs) that were supported by publicly available deep sequencing data from various sRNA libraries and constructed lncRNA-derived siRNA-target interactions. In addition, lncRNAMap demonstrated that lncRNAs can act as targets for miRNAs that would otherwise regulate protein-coding genes. Previously studies indicated that intergenic lncRNAs (lincRNAs) either positive or negative regulated neighboring genes, therefore, lncRNAMap surveyed neighboring genes within a 1Mb distance from the genomic location of specific lncRNAs and provided the expression profiles of lncRNA and its neighboring genes. The gene expression profiles may supply the relationship between lncRNA and its neighboring genes. CONCLUSIONS: lncRNAMap is a powerful user-friendly platform for the investigation of putative regulatory functions of human lncRNAs with producing siRNAs and acting as miRNA decoy. lncRNAMap is freely available on the web at http://lncRNAMap.mbc.nctu.edu.tw/.","corpus_id":7861471,"score":2},{"doc_id":"24813212","title":"lncRNAtor: a comprehensive resource for functional investigation of long non-coding RNAs.","abstract":"MOTIVATION: A number of long non-coding RNAs (lncRNAs) have been identified by deep sequencing methods, but their molecular and cellular functions are known only for a limited number of lncRNAs. Current databases on lncRNAs are mostly for cataloging purpose without providing in-depth information required to infer functions. A comprehensive resource on lncRNA function is an immediate need. RESULTS: We present a database for functional investigation of lncRNAs that encompasses annotation, sequence analysis, gene expression, protein binding and phylogenetic conservation. We have compiled lncRNAs for six species (human, mouse, zebrafish, fruit fly, worm and yeast) from ENSEMBL, HGNC, MGI and lncRNAdb. Each lncRNA was analyzed for coding potential and phylogenetic conservation in different lineages. Gene expression data of 208 RNA-Seq studies (4995 samples), collected from GEO, ENCODE, modENCODE and TCGA databases, were used to provide expression profiles in various tissues, diseases and developmental stages. Importantly, we analyzed RNA-Seq data to identify coexpressed mRNAs that would provide ample insights on lncRNA functions. The resulting gene list can be subject to enrichment analysis such as Gene Ontology or KEGG pathways. Furthermore, we compiled protein-lncRNA interactions by collecting and analyzing publicly available CLIP-seq or PAR-CLIP sequencing data. Finally, we explored evolutionarily conserved lncRNAs with correlated expression between human and six other organisms to identify functional lncRNAs. The whole contents are provided in a user-friendly web interface. AVAILABILITY AND IMPLEMENTATION: lncRNAtor is available at http://lncrnator.ewha.ac.kr/. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.","corpus_id":5133246,"score":2},{"doc_id":"25332392","title":"lncRNASNP: a database of SNPs in lncRNAs and their potential functions in human and mouse.","abstract":"Long non-coding RNAs (lncRNAs) play key roles in various cellular contexts and diseases by diverse mechanisms. With the rapid growth of identified lncRNAs and disease-associated single nucleotide polymorphisms (SNPs), there is a great demand to study SNPs in lncRNAs. Aiming to provide a useful resource about lncRNA SNPs, we systematically identified SNPs in lncRNAs and analyzed their potential impacts on lncRNA structure and function. In total, we identified 495,729 and 777,095 SNPs in more than 30,000 lncRNA transcripts in human and mouse, respectively. A large number of SNPs were predicted with the potential to impact on the miRNA-lncRNA interaction. The experimental evidence and conservation of miRNA-lncRNA interaction, as well as miRNA expressions from TCGA were also integrated to prioritize the miRNA-lncRNA interactions and SNPs on the binding sites. Furthermore, by mapping SNPs to GWAS results, we found that 142 human lncRNA SNPs are GWAS tagSNPs and 197,827 lncRNA SNPs are in the GWAS linkage disequilibrium regions. All these data for human and mouse lncRNAs were imported into lncRNASNP database (http://bioinfo.life.hust.edu.cn/lncRNASNP/), which includes two sub-databases lncRNASNP-human and lncRNASNP-mouse. The lncRNASNP database has a user-friendly interface for searching and browsing through the SNP, lncRNA and miRNA sections.","corpus_id":15612068,"score":2},{"doc_id":"25332394","title":"lncRNAdb v2.0: expanding the reference database for functional long noncoding RNAs.","abstract":"Despite the prevalence of long noncoding RNA (lncRNA) genes in eukaryotic genomes, only a small proportion have been examined for biological function. lncRNAdb, available at http://lncrnadb.org, provides users with a comprehensive, manually curated reference database of 287 eukaryotic lncRNAs that have been described independently in the scientific literature. In addition to capturing a great proportion of the recent literature describing functions for individual lncRNAs, lncRNAdb now offers an improved user interface enabling greater accessibility to sequence information, expression data and the literature. The new features in lncRNAdb include the integration of Illumina Body Atlas expression profiles, nucleotide sequence information, a BLAST search tool and easy export of content via direct download or a REST API. lncRNAdb is now endorsed by RNAcentral and is in compliance with the International Nucleotide Sequence Database Collaboration.","corpus_id":1108199,"score":2},{"doc_id":"25378313","title":"An update on LNCipedia: a database for annotated human lncRNA sequences.","abstract":"The human genome is pervasively transcribed, producing thousands of non-coding RNA transcripts. The majority of these transcripts are long non-coding RNAs (lncRNAs) and novel lncRNA genes are being identified at rapid pace. To streamline these efforts, we created LNCipedia, an online repository of lncRNA transcripts and annotation. Here, we present LNCipedia 3.0 (http://www.lncipedia.org), the latest version of the publicly available human lncRNA database. Compared to the previous version of LNCipedia, the database grew over five times in size, gaining over 90,000 new lncRNA transcripts. Assessment of the protein-coding potential of LNCipedia entries is improved with state-of-the art methods that include large-scale reprocessing of publicly available proteomics data. As a result, a high-confidence set of lncRNA transcripts with low coding potential is defined and made available for download. In addition, a tool to assess lncRNA gene conservation between human, mouse and zebrafish has been implemented.","corpus_id":53306854,"score":2},{"doc_id":"25399417","title":"LncRNAWiki: harnessing community knowledge in collaborative curation of human long non-coding RNAs.","abstract":"Long non-coding RNAs (lncRNAs) perform a diversity of functions in numerous important biological processes and are implicated in many human diseases. In this report we present lncRNAWiki (http://lncrna.big.ac.cn), a wiki-based platform that is open-content and publicly editable and aimed at community-based curation and collection of information on human lncRNAs. Current related databases are dependent primarily on curation by experts, making it laborious to annotate the exponentially accumulated information on lncRNAs, which inevitably requires collective efforts in community-based curation of lncRNAs. Unlike existing databases, lncRNAWiki features comprehensive integration of information on human lncRNAs obtained from multiple different resources and allows not only existing lncRNAs to be edited, updated and curated by different users but also the addition of newly identified lncRNAs by any user. It harnesses community collective knowledge in collecting, editing and annotating human lncRNAs and rewards community-curated efforts by providing explicit authorship based on quantified contributions. LncRNAWiki relies on the underling knowledge of scientific community for collective and collaborative curation of human lncRNAs and thus has the potential to serve as an up-to-date and comprehensive knowledgebase for human lncRNAs.","corpus_id":15128652,"score":2},{"doc_id":"25707511","title":"LncRNA2Function: a comprehensive resource for functional investigation of human lncRNAs based on RNA-seq data.","abstract":"BACKGROUND: The GENCODE project has collected over 10,000 human long non-coding RNA (lncRNA) genes. However, the vast majority of them remain to be functionally characterized. Computational investigation of potential functions of human lncRNA genes is helpful to guide further experimental studies on lncRNAs. RESULTS: In this study, based on expression correlation between lncRNAs and protein-coding genes across 19 human normal tissues, we used the hypergeometric test to functionally annotate a single lncRNA or a set of lncRNAs with significantly enriched functional terms among the protein-coding genes that are significantly co-expressed with the lncRNA(s). The functional terms include all nodes in the Gene Ontology (GO) and 4,380 human biological pathways collected from 12 pathway databases. We successfully mapped 9,625 human lncRNA genes to GO terms and biological pathways, and then developed the first ontology-driven user-friendly web interface named lncRNA2Function, which enables researchers to browse the lncRNAs associated with a specific functional term, the functional terms associated with a specific lncRNA, or to assign functional terms to a set of human lncRNA genes, such as a cluster of co-expressed lncRNAs. The lncRNA2Function is freely available at http://mlg.hit.edu.cn/lncrna2function. CONCLUSIONS: The LncRNA2Function is an important resource for further investigating the functions of a single human lncRNA, or functionally annotating a set of human lncRNAs of interest.","corpus_id":8193629,"score":2},{"doc_id":"25853886","title":"ALDB: a domestic-animal long noncoding RNA database.","abstract":"BACKGROUND: Long noncoding RNAs (lncRNAs) have attracted significant attention in recent years due to their important roles in many biological processes. Domestic animals constitute a unique resource for understanding the genetic basis of phenotypic variation and are ideal models relevant to diverse areas of biomedical research. With improving sequencing technologies, numerous domestic-animal lncRNAs are now available. Thus, there is an immediate need for a database resource that can assist researchers to store, organize, analyze and visualize domestic-animal lncRNAs. RESULTS: The domestic-animal lncRNA database, named ALDB, is the first comprehensive database with a focus on the domestic-animal lncRNAs. It currently archives 12,103 pig intergenic lncRNAs (lincRNAs), 8,923 chicken lincRNAs and 8,250 cow lincRNAs. In addition to the annotations of lincRNAs, it offers related data that is not available yet in existing lncRNA databases (lncRNAdb and NONCODE), such as genome-wide expression profiles and animal quantitative trait loci (QTLs) of domestic animals. Moreover, a collection of interfaces and applications, such as the Basic Local Alignment Search Tool (BLAST), the Generic Genome Browser (GBrowse) and flexible search functionalities, are available to help users effectively explore, analyze and download data related to domestic-animal lncRNAs. CONCLUSIONS: ALDB enables the exploration and comparative analysis of lncRNAs in domestic animals. A user-friendly web interface, integrated information and tools make it valuable to researchers in their studies. ALDB is freely available from http://res.xaut.edu.cn/aldb/index.jsp.","corpus_id":7070813,"score":2},{"doc_id":"26211629","title":"PLNlncRbase: A resource for experimentally identified lncRNAs in plants.","abstract":"Accumulating published reports have confirmed the critical biological role (e.g., cell differentiation, gene regulation, stress response) for plant long non-coding RNAs (lncRNAs). However, a literature-derived database with the aim of lncRNA curation, data deposit and further distribution remains still absent for this particular lncRNA clade. PLNlncRbase has been designed as an easy-to-use resource to provide detailed information for experimentally identified plant lncRNAs. In the current version, PLNlncRbase has manually collected data from nearly 200 published literature, covering a total of 1187 plant lncRNAs in 43 plant species. The user can retrieve plant lncRNA entries from a well-organized interface through a keyword search by using the name of plant species or a lncRNA identifier. Each entry upon a query will be returned with detailed information for a specific plant lncRNA, including the species name, a lncRNA identifier, a brief description of the potential biological role, the lncRNA sequence, the lncRNA classification, an expression pattern of the lncRNA, the tissue/developmental stage/condition for lncRNA expression, the detection method for lncRNA expression, a reference literature, and the potential target gene(s) of the lncRNA extracted from the original reference. This database will be regularly updated to greatly facilitate future investigations of plant lncRNAs pertaining to their biological significance. The PLNlncRbase database is now freely available at http://bioinformatics.ahau.edu.cn/PLNlncRbase.","corpus_id":26682314,"score":2},{"doc_id":"26363021","title":"LncReg: a reference resource for lncRNA-associated regulatory networks.","abstract":"Long non-coding RNAs (lncRNAs) are critical in the regulation of various biological processes. In recent years, plethora of lncRNAs have been identified in mammalian genomes through different approaches, and the researchers are constantly reporting the regulatory roles of these lncRNAs, which leads to complexity of literature about particular lncRNAs. Therefore, for the convenience of the researchers, we collected regulatory relationships of the lncRNAs and built a database called 'LncReg'. This database is developed by collecting 1081 validated lncRNA-associated regulatory entries, including 258 non-redundant lncRNAs and 571 non-redundant genes. With regulatory relationships information, LncReg can provide overall perspectives of regulatory networks of lncRNAs and comprehensive data for bioinformatics research, which is useful for understanding the functional roles of lncRNAs. Database URL: http://bioinformatics.ustc.edu.cn/lncreg/.","corpus_id":17146207,"score":2},{"doc_id":"26481356","title":"Lnc2Cancer: a manually curated database of experimentally supported lncRNAs associated with various human cancers.","abstract":"Lnc2Cancer (http://www.bio-bigdata.net/lnc2cancer) is a manually curated database of cancer-associated long non-coding RNAs (lncRNAs) with experimental support that aims to provide a high-quality and integrated resource for exploring lncRNA deregulation in various human cancers. LncRNAs represent a large category of functional RNA molecules that play a significant role in human cancers. A curated collection and summary of deregulated lncRNAs in cancer is essential to thoroughly understand the mechanisms and functions of lncRNAs. Here, we developed the Lnc2Cancer database, which contains 1057 manually curated associations between 531 lncRNAs and 86 human cancers. Each association includes lncRNA and cancer name, the lncRNA expression pattern, experimental techniques, a brief functional description, the original reference and additional annotation information. Lnc2Cancer provides a user-friendly interface to conveniently browse, retrieve and download data. Lnc2Cancer also offers a submission page for researchers to submit newly validated lncRNA-cancer associations. With the rapidly increasing interest in lncRNAs, Lnc2Cancer will significantly improve our understanding of lncRNA deregulation in cancer and has the potential to be a timely and valuable resource.","corpus_id":16939394,"score":2},{"doc_id":"26578586","title":"GREENC: a Wiki-based database of plant lncRNAs.","abstract":"Long non-coding RNAs (lncRNAs) are functional non-translated molecules greater than 200 nt. Their roles are diverse and they are usually involved in transcriptional regulation. LncRNAs still remain largely uninvestigated in plants with few exceptions. Experimentally validated plant lncRNAs have been shown to regulate important agronomic traits such as phosphate starvation response, flowering time and interaction with symbiotic organisms, making them of great interest in plant biology and in breeding. There is still a lack of lncRNAs in most sequenced plant species, and in those where they have been annotated, different methods have been used, so making the lncRNAs less useful in comparisons within and between species. We developed a pipeline to annotate lncRNAs and applied it to 37 plant species and six algae, resulting in the annotation of more than 120 000 lncRNAs. To facilitate the study of lncRNAs for the plant research community, the information gathered is organised in the Green Non-Coding Database (GreeNC, http://greenc.sciencedesigners.com/).","corpus_id":5166047,"score":2},{"doc_id":"26612864","title":"DIANA-LncBase v2: indexing microRNA targets on non-coding transcripts.","abstract":"microRNAs (miRNAs) are short non-coding RNAs (ncRNAs) that act as post-transcriptional regulators of coding gene expression. Long non-coding RNAs (lncRNAs) have been recently reported to interact with miRNAs. The sponge-like function of lncRNAs introduces an extra layer of complexity in the miRNA interactome. DIANA-LncBase v1 provided a database of experimentally supported and in silico predicted miRNA Recognition Elements (MREs) on lncRNAs. The second version of LncBase (www.microrna.gr/LncBase) presents an extensive collection of miRNA:lncRNA interactions. The significantly enhanced database includes more than 70 000 low and high-throughput, (in)direct miRNA:lncRNA experimentally supported interactions, derived from manually curated publications and the analysis of 153 AGO CLIP-Seq libraries. The new experimental module presents a 14-fold increase compared to the previous release. LncBase v2 hosts in silico predicted miRNA targets on lncRNAs, identified with the DIANA-microT algorithm. The relevant module provides millions of predicted miRNA binding sites, accompanied with detailed metadata and MRE conservation metrics. LncBase v2 caters information regarding cell type specific miRNA:lncRNA regulation and enables users to easily identify interactions in 66 different cell types, spanning 36 tissues for human and mouse. Database entries are also supported by accurate lncRNA expression information, derived from the analysis of more than 6 billion RNA-Seq reads.","corpus_id":16596478,"score":2},{"doc_id":"26657895","title":"CANTATAdb: A Collection of Plant Long Non-Coding RNAs.","abstract":"Long non-coding RNAs (lncRNAs) represent a class of potent regulators of gene expression that are found in a wide array of eukaryotes; however, our knowledge about these molecules in plants is still very limited. In particular, a number of model plant species still lack comprehensive data sets of lncRNAs and their annotations, and very little is known about their biological roles. To meet these shortcomings, we created an online database of lncRNAs in 10 model plant species. The lncRNAs were identified computationally using dozens of publicly available RNA sequencing (RNA-Seq) libraries. Expression values, coding potential, sequence alignments as well as other types of data provide annotation for the identified lncRNAs. In order to better characterize them, we investigated their potential roles in splicing modulation and deregulation of microRNA functions. The data are freely available for searching, browsing and downloading from an online database called CANTATAdb (http://cantata.amu.edu.pl, http://yeti.amu.edu.pl/CANTATA/).","corpus_id":18656798,"score":2},{"doc_id":"26839320","title":"Computational recognition for long non-coding RNA (lncRNA): Software and databases.","abstract":"Since the completion of the Human Genome Project, it has been widely established that most DNA is not transcribed into proteins. These non-protein-coding regions are believed to be moderators within transcriptional and post-transcriptional processes, which play key roles in the onset of diseases. Long non-coding RNAs (lncRNAs) are generally lacking in conserved motifs typically used for detection and thus hard to identify, but nonetheless present certain characteristic features that can be exploited by bioinformatics methods. By combining lncRNA detection with known miRNA, RNA-binding protein and chromatin interaction, current tools are able to recognize and functionally annotate large number of lncRNAs. This review discusses databases and platforms dedicated to cataloging and annotating lncRNAs, as well as tools geared at discovering novel sequences. We emphasize the issues posed by the diversity of lncRNAs and their complex interaction mechanisms, as well as technical issues such as lack of unified nomenclature. We hope that this wide overview of existing platforms and databases might help guide biologists toward the tools they need to analyze their experimental data, while our discussion of limitations and of current lncRNA-related methods may assist in the development of new computational tools.","corpus_id":3911230,"score":2},{"doc_id":"27049585","title":"Long non-coding RNA Databases in Cardiovascular Research.","abstract":"With the rising interest in the regulatory functions of long non-coding RNAs (lncRNAs) in complex human diseases such as cardiovascular diseases, there is an increasing need in public databases offering comprehensive and integrative data for all aspects of these versatile molecules. Recently, a variety of public data repositories that specialized in lncRNAs have been developed, which make use of huge high-throughput data particularly from next-generation sequencing (NGS) approaches. Here, we provide an overview of current lncRNA databases covering basic and functional annotation, lncRNA expression and regulation, interactions with other biomolecules, and genomic variants influencing the structure and function of lncRNAs. The prominent lncRNA antisense noncoding RNA in the INK4 locus (ANRIL), which has been unequivocally associated with coronary artery disease through genome-wide association studies (GWAS), serves as an example to demonstrate the features of each individual database.","corpus_id":3346664,"score":2},{"doc_id":"27087310","title":"NPInter v3.0: an upgraded database of noncoding RNA-associated interactions.","abstract":"Despite the fact that a large quantity of noncoding RNAs (ncRNAs) have been identified, their functions remain unclear. To enable researchers to have a better understanding of ncRNAs' functions, we updated the NPInter database to version 3.0, which contains experimentally verified interactions between ncRNAs (excluding tRNAs and rRNAs), especially long noncoding RNAs (lncRNAs) and other biomolecules (proteins, mRNAs, miRNAs and genomic DNAs). In NPInter v3.0, interactions pertaining to ncRNAs are not only manually curated from scientific literature but also curated from high-throughput technologies. In addition, we also curated lncRNA-miRNA interactions fromin silicopredictions supported by AGO CLIP-seq data. When compared with NPInter v2.0, the interactions are more informative (with additional information on tissues or cell lines, binding sites, conservation, co-expression values and other features) and more organized (with divisions on data sets by data sources, tissues or cell lines, experiments and other criteria). NPInter v3.0 expands the data set to 491,416 interactions in 188 tissues (or cell lines) from 68 kinds of experimental technologies. NPInter v3.0 also improves the user interface and adds new web services, including a local UCSC Genome Browser to visualize binding sites. Additionally, NPInter v3.0 defined a high-confidence set of interactions and predicted the functions of lncRNAs in human and mouse based on the interactions curated in the database. NPInter v3.0 is available athttp://www.bioinfo.org/NPInter/Database URL:http://www.bioinfo.org/NPInter/.","corpus_id":12524699,"score":2},{"doc_id":"27113186","title":"[The beta version of LongMan: a large-scale mammalian lncRNA database orthologous to human lncRNAs].","abstract":"OBJECTIVE: To predict orthologous sequences of the GENCODE-identified 13 562 human long non-coding RNAs (lncRNA) in 16 mammalian genomes and construct a lncRNA database LongMan for lncRNA studies. METHODS: The exon structures of a total of 13 562 human lncRNAs were analyzed using RNAfold, and their orthologous sequences were searched against 16 mammalian genomes using Infernal. The potential orthologous genes, transposons and splicing signals of human lncRNAs were predicted to construct a lncRNA database with a updating mechanism. RESULTS: and CONCLUSION: The lncRNA database LongMan we constructed, which currently contains 133 646 orthologous lncRNAs, provides information of the sequences, alignments, transposons, and species-specific insertions and deletions and allows database search on combinatorial conditions, graphic display and data download. As the first large-scale mammalian orthologous lncRNA database, LongMan has important values in future comparative and functional studies of lncRNAs.","corpus_id":25940287,"score":2},{"doc_id":"27623959","title":"BmncRNAdb: a comprehensive database of non-coding RNAs in the silkworm, Bombyx mori.","abstract":"BACKGROUND: Long non-coding RNAs (lncRNAs) may play critical roles in a wide range of developmental processes of higher organisms. Recently, lncRNAs have been widely identified across eukaryotes and many databases of lncRNAs have been developed for human, mouse, fruit fly, etc. However, there is rare information about them in the only completely domesticated insect, silkworm (Bombyx mori). DESCRIPTION: In this study, we systematically scanned lncRNAs using the available silkworm RNA-seq data and public unigenes. Finally, we identified and collected 6281 lncRNAs in the silkworm. Besides, we also collected 1986 microRNAs (miRNAs) from previous studies. Then, we organized them into a comprehensive and web-based database, BmncRNAdb. This database offers a user-friendly interface for data browse and online analysis as well as the three online tools for users to predict the target genes of lncRNA or miRNA. CONCLUSIONS: We have systematically identified and collected the silkworm lncRNAs and constructed a comprehensive database of the silkworm lncRNAs and miRNAs. This work gives a glimpse into lncRNAs of the silkworm and lays foundations for the ncRNAs study of the silkworm and other insects in the future. The BmncRNAdb is freely available at http://gene.cqu.edu.cn/BmncRNAdb/index.php .","corpus_id":10835608,"score":2},{"doc_id":"27794554","title":"RNAcentral: a comprehensive database of non-coding RNA sequences.","abstract":"RNAcentral is a database of non-coding RNA (ncRNA) sequences that aggregates data from specialised ncRNA resources and provides a single entry point for accessing ncRNA sequences of all ncRNA types from all organisms. Since its launch in 2014, RNAcentral has integrated twelve new resources, taking the total number of collaborating database to 22, and began importing new types of data, such as modified nucleotides from MODOMICS and PDB. We created new species-specific identifiers that refer to unique RNA sequences within a context of single species. The website has been subject to continuous improvements focusing on text and sequence similarity searches as well as genome browsing functionality. All RNAcentral data is provided for free and is available for browsing, bulk downloads, and programmatic access at http://rnacentral.org/.","corpus_id":36012271,"score":2},{"doc_id":"27899613","title":"NSDNA: a manually curated database of experimentally supported ncRNAs associated with nervous system diseases.","abstract":"The Nervous System Disease NcRNAome Atlas (NSDNA) (http://www.bio-bigdata.net/nsdna/) is a manually curated database that provides comprehensive experimentally supported associations about nervous system diseases (NSDs) and noncoding RNAs (ncRNAs). NSDs represent a common group of disorders, some of which are characterized by high morbidity and disabilities. The pathogenesis of NSDs at the molecular level remains poorly understood. ncRNAs are a large family of functionally important RNA molecules. Increasing evidence shows that diverse ncRNAs play a critical role in various NSDs. Mining and summarizing NSD-ncRNA association data can help researchers discover useful information. Hence, we developed an NSDNA database that documents 24 713 associations between 142 NSDs and 8593 ncRNAs in 11 species, curated from more than 1300 articles. This database provides a user-friendly interface for browsing and searching and allows for data downloading flexibility. In addition, NSDNA offers a submission page for researchers to submit novel NSD-ncRNA associations. It represents an extremely useful and valuable resource for researchers who seek to understand the functions and molecular mechanisms of ncRNA involved in NSDs.","corpus_id":16204246,"score":2},{"doc_id":"27924020","title":"LincSNP 2.0: an updated database for linking disease-associated SNPs to human long non-coding RNAs and their TFBSs.","abstract":"We describe LincSNP 2.0 (http://bioinfo.hrbmu.edu.cn/LincSNP), an updated database that is used specifically to store and annotate disease-associated single nucleotide polymorphisms (SNPs) in human long non-coding RNAs (lncRNAs) and their transcription factor binding sites (TFBSs). In LincSNP 2.0, we have updated the database with more data and several new features, including (i) expanding disease-associated SNPs in human lncRNAs; (ii) identifying disease-associated SNPs in lncRNA TFBSs; (iii) updating LD-SNPs from the 1000 Genomes Project; and (iv) collecting more experimentally supported SNP-lncRNA-disease associations. Furthermore, we developed three flexible online tools to retrieve and analyze the data. Linc-Mart is a convenient way for users to customize their own data. Linc-Browse is a tool for all data visualization. Linc-Score predicts the associations between lncRNA and disease. In addition, we provided users a newly designed, user-friendly interface to search and download all the data in LincSNP 2.0 and we also provided an interface to submit novel data into the database. LincSNP 2.0 is a continually updated database and will serve as an important resource for investigating the functions and mechanisms of lncRNAs in human diseases.","corpus_id":14509930,"score":2},{"doc_id":"29069510","title":"Lnc2Meth: a manually curated database of regulatory relationships between long non-coding RNAs and DNA methylation associated with human disease.","abstract":"Lnc2Meth (http://www.bio-bigdata.com/Lnc2Meth/), an interactive resource to identify regulatory relationships between human long non-coding RNAs (lncRNAs) and DNA methylation, is not only a manually curated collection and annotation of experimentally supported lncRNAs-DNA methylation associations but also a platform that effectively integrates tools for calculating and identifying the differentially methylated lncRNAs and protein-coding genes (PCGs) in diverse human diseases. The resource provides: (i) advanced search possibilities, e.g. retrieval of the database by searching the lncRNA symbol of interest, DNA methylation patterns, regulatory mechanisms and disease types; (ii) abundant computationally calculated DNA methylation array profiles for the lncRNAs and PCGs; (iii) the prognostic values for each hit transcript calculated from the patients clinical data; (iv) a genome browser to display the DNA methylation landscape of the lncRNA transcripts for a specific type of disease; (v) tools to re-annotate probes to lncRNA loci and identify the differential methylation patterns for lncRNAs and PCGs with user-supplied external datasets; (vi) an R package (LncDM) to complete the differentially methylated lncRNAs identification and visualization with local computers. Lnc2Meth provides a timely and valuable resource that can be applied to significantly expand our understanding of the regulatory relationships between lncRNAs and DNA methylation in various human diseases.","corpus_id":52801074,"score":2},{"doc_id":"29077939","title":"lncRNASNP2: an updated database of functional SNPs and mutations in human and mouse lncRNAs.","abstract":"Long non-coding RNAs (lncRNAs) are emerging as important regulators in different biological processes through various ways. Because the related data, especially mutations in cancers, increased sharply, we updated the lncRNASNP to version 2 (http://bioinfo.life.hust.edu.cn/lncRNASNP2). lncRNASNP2 provides comprehensive information of SNPs and mutations in lncRNAs, as well as their impacts on lncRNA structure and function. lncRNASNP2 contains 7260238 SNPs on 141353 human lncRNA transcripts and 3921448 SNPs on 117405 mouse lncRNA transcripts. Besides the SNP information in the first version, the following new features were developed to improve the lncRNASNP2. ( i) noncoding variants from COSMIC cancer data (859534) in lncRNAs and their effects on lncRNA structure and function; (ii) TCGA cancer mutations (315234) in lncRNAs and their impacts; (iii) lncRNA expression profiling of 20 cancer types in both tumor and its adjacent samples; (iv) expanded lncRNA-associated diseases; (v) optimized the results about lncRNAs structure change induced by variants; (vi) reduced false positives in miRNA and lncRNA interaction results. Furthermore, we developed online tools for users to analyze new variants in lncRNA. We aim to maintain the lncRNASNP as a useful resource for lncRNAs and their variants.","corpus_id":205234301,"score":2},{"doc_id":"29140524","title":"NONCODEV5: a comprehensive annotation database for long non-coding RNAs.","abstract":"NONCODE (http://www.bioinfo.org/noncode/) is a systematic database that is dedicated to presenting the most complete collection and annotation of non-coding RNAs (ncRNAs), especially long non-coding RNAs (lncRNAs). Since NONCODE 2016 was released two years ago, the amount of novel identified ncRNAs has been enlarged by the reduced cost of next-generation sequencing, which has produced an explosion of newly identified data. The third-generation sequencing revolution has also offered longer and more accurate annotations. Moreover, accumulating evidence confirmed by biological experiments has provided more comprehensive knowledge of lncRNA functions. The ncRNA data set was expanded by collecting newly identified ncRNAs from literature published over the past two years and integration of the latest versions of RefSeq and Ensembl. Additionally, pig was included in the database for the first time, bringing the total number of species to 17. The number of lncRNAs in NONCODEv5 increased from 527 336 to 548 640. NONCODEv5 also introduced three important new features: (i) human lncRNA-disease relationships and single nucleotide polymorphism-lncRNA-disease relationships were constructed; (ii) human exosome lncRNA expression profiles were displayed; (iii) the RNA secondary structures of NONCODE human transcripts were predicted. NONCODEv5 is also accessible through http://www.noncode.org/.","corpus_id":205239047,"score":2},{"doc_id":"29382910","title":"Lnc2Catlas: an atlas of long noncoding RNAs associated with risk of cancers.","abstract":"Lnc2Catlas ( http://lnc2catlas.bioinfotech.org/ ) is an atlas of long noncoding RNAs (lncRNAs) associated with cancer risk. LncRNAs are a class of functional noncoding RNAs with lengths over 200 nt and play a vital role in diverse biological processes. Increasing evidence shows that lncRNA dysfunction is associated with many human cancers/diseases. It is therefore important to understand the underlying relationship between lncRNAs and cancers. To this end, we developed Lnc2Catlas to compile quantitative associations between lncRNAs and cancers using three computational methods, assessing secondary structure disruption, lncRNA-protein interactions, and co-expression networks. Lnc2Catlas was constructed based on 27,670 well-annotated lncRNAs, 31,749,216 SNPs, 1,473 cancer-associated proteins, and 10,539 expression profiles of 33 cancers from The Cancer Genome Atlas (TCGA). Lnc2Catlas contains 247,124 lncRNA-SNP pairs, over two millions lncRNA-protein interactions, and 6,902 co-expression clusters. We deposited Lnc2Catlas on Alibaba Cloud and developed interactive, mobile device-compatible, user-friendly interfaces to help users search and browse Lnc2Catlas with ultra-low latency. Lnc2Catlas can aid in the investigation of associations between lncRNAs and cancers and can provide candidate lncRNAs for further experimental validation. Lnc2Catlas will facilitate an understanding of the associations between lncRNAs and cancer and will help reveal the critical role of lncRNAs in cancer.","corpus_id":19611746,"score":2},{"doc_id":"22976082","title":"An RNA Mapping DataBase for curating RNA structure mapping experiments.","abstract":"SUMMARY: We have established an RNA mapping database (RMDB) to enable structural, thermodynamic and kinetic comparisons across single-nucleotide-resolution RNA structure mapping experiments. The volume of structure mapping data has greatly increased since the development of high-throughput sequencing techniques, accelerated software pipelines and large-scale mutagenesis. For scientists wishing to infer relationships between RNA sequence/structure and these mapping data, there is a need for a database that is curated, tagged with error estimates and interfaced with tools for sharing, visualization, search and meta-analysis. Through its on-line front-end, the RMDB allows users to explore single-nucleotide-resolution mapping data in heat-map, bar-graph and colored secondary structure graphics; to leverage these data to generate secondary structure hypotheses; and to download the data in standardized and computer-friendly files, including the RDAT and community-consensus SNRNASM formats. At the time of writing, the database houses 53 entries, describing more than 2848 experiments of 1098 RNA constructs in several solution conditions and is growing rapidly. AVAILABILITY: Freely available on the web at http://rmdb.stanford.edu. CONTACT: rhiju@stanford.edu. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics Online.","corpus_id":42068269,"score":1},{"doc_id":"23222637","title":"Long non-coding RNAs and p53 regulation.","abstract":"The advent of novel and high-throughput sequencing (next generation) technologies allowed for the sequencing of the genome at an unprecedented depth. The majority of transcribed RNAs have been classified as non-coding RNAs. Among them, long non-coding RNAs (lncRNAs) are emerging as important regulators in many biological processes. Here, we discuss the role of those lncRNAs which are under the control of p53 or that are able to regulate its activity, due to the central role of p53 pathway in many conditions. We also briefly discussed the emerging need of having novel strategies and computational tools to completely unravel the multifaceted roles of lncRNAs and to pave the way to the development of novel diagnostic and therapeutic applications based on these peculiar molecules.","corpus_id":10065501,"score":1},{"doc_id":"23696037","title":"On the classification of long non-coding RNAs.","abstract":"Long non-coding RNAs (lncRNAs) have been found to perform various functions in a wide variety of important biological processes. To make easier interpretation of lncRNA functionality and conduct deep mining on these transcribed sequences, it is convenient to classify lncRNAs into different groups. Here, we summarize classification methods of lncRNAs according to their four major features, namely, genomic location and context, effect exerted on DNA sequences, mechanism of functioning and their targeting mechanism. In combination with the presently available function annotations, we explore potential relationships between different classification categories, and generalize and compare biological features of different lncRNAs within each category. Finally, we present our view on potential further studies. We believe that the classifications of lncRNAs as indicated above are of fundamental importance for lncRNA studies, helpful for further investigation of specific lncRNAs, for formulation of new hypothesis based on different features of lncRNA and for exploration of the underlying lncRNA functional mechanisms.","corpus_id":16088764,"score":1},{"doc_id":"23829531","title":"Identification and function of long non-coding RNAs.","abstract":"It is now clear that eukaryotic cells produce many thousands of non-coding RNAs. The least well-studied of these are longer than 200 nt and are known as lncRNAs (long non-coding RNAs). These loci are of particular interest as their biological relevance remains uncertain. Sequencing projects have identified thousands of these loci in a variety of species, from flies to humans. Genome-wide scans for functionality, such as evolutionary and expression analyses, suggest that many of these molecules have functional roles to play in the cell. Nevertheless, only a handful of lncRNAs have been experimentally investigated, and most of these appear to possess roles in regulating gene expression at a variety of different levels. Several lncRNAs have also been implicated in cancer. This evidence suggests that lncRNAs represent a new class of non-coding gene whose importance should become clearer upon further experimental investigation.","corpus_id":26130066,"score":1},{"doc_id":"24846995","title":"[The emerging landscape of long non-coding RNAs].","abstract":"With the completion of Human Genome Project (HGP), it was revealed that among the 3 billion base pairs in human genome, only 1.5% of them encodes proteins. The remaining 98.5% of the sequence does not encode any protein, and was once regarded as accumulated junk sequences during evolution. However, in the subsequently initiated ENCODE project, it was unexpectedly found that about 75% of the human genome was transcribed into RNAs. Seventy-four percent of them are non-protein-coding RNAs (non-coding RNAs, ncRNAs). In this RNA category, most of the transcripts are longer than 200 nucleotides and thus named as long non-coding RNAs (lncRNAs). ncRNAs regulate gene expression at the transcriptional and post-transcriptional levels, function in fundamental biological processes including cell differentiation and organ development, and are closely associated with many human diseases. In this paper, we review the recent progress in the discovery, classification, expression, and function study of lncRNAs, as well as their roles in the pathogenesis of hu-man diseases.","corpus_id":41118558,"score":1},{"doc_id":"25881700","title":"[Long non-coding RNAs in plants].","abstract":"Long non-coding RNAs (lncRNAs), which are longer than 200 nucleotides in length, widely exist in organisms and function in a variety of biological processes. Currently, most of lncRNAs found in plants are transcribed by RNA polymerase Ⅱ and mediate gene expression through multiple mechanisms, such as target mimicry, transcription interference, histone methylation and DNA methylation, and play important roles in flowering, male sterility, nutrition metabolism, biotic and abiotic stress and other biological processes as regulators in plants. In this review, we summarize the databases, prediction methods, and possible functions of plant lncRNAs discovered in recent years.","corpus_id":7412542,"score":1},{"doc_id":"25936895","title":"Long non-coding RNAs and their biological roles in plants.","abstract":"With the development of genomics and bioinformatics, especially the extensive applications of high-throughput sequencing technology, more transcriptional units with little or no protein-coding potential have been discovered. Such RNA molecules are called non-protein-coding RNAs (npcRNAs or ncRNAs). Among them, long npcRNAs or ncRNAs (lnpcRNAs or lncRNAs) represent diverse classes of transcripts longer than 200 nucleotides. In recent years, the lncRNAs have been considered as important regulators in many essential biological processes. In plants, although a large number of lncRNA transcripts have been predicted and identified in few species, our current knowledge of their biological functions is still limited. Here, we have summarized recent studies on their identification, characteristics, classification, bioinformatics, resources, and current exploration of their biological functions in plants.","corpus_id":14966878,"score":1},{"doc_id":"25986218","title":"Infectious long non-coding RNAs.","abstract":"Long non protein coding RNAs (lncRNAs) constitute a large category of the RNA world, able to regulate different biological processes. In this review we are focusing on infectious lncRNAs, their classification, pathogenesis and impact on the infected organisms. Here they are presented in two separate groups: 'dependent lncRNAs' (comprising satellites RNA, Hepatitis D virus and lncRNAs of viral origin) which need a helper virus and 'independent lncRNAs' (viroids) that can self-replicate. Even though these lncRNA do not encode any protein, their structure and/or sequence comprise all the necessary information to drive specific interactions with host factors and regulate several cellular functions. These new data that have emerged during the last few years concerning lncRNAs modify the way we understand molecular biology's 'central dogma' and give new perspectives for applications and potential therapeutic strategies.","corpus_id":8226183,"score":1},{"doc_id":"26117828","title":"Evolutionary annotation of conserved long non-coding RNAs in major mammalian species.","abstract":"Mammalian genomes contain tens of thousands of long non-coding RNAs (lncRNAs) that have been implicated in diverse biological processes. However, the lncRNA transcriptomes of most mammalian species have not been established, limiting the evolutionary annotation of these novel transcripts. Based on RNA sequencing data from six tissues of nine species, we built comprehensive lncRNA catalogs (4,142-42,558 lncRNAs) covering the major mammalian species. Compared to protein- coding RNAs, expression of lncRNAs exhibits striking lineage specificity. Notably, although 30%-99% human lncRNAs are conserved across different species on DNA locus level, only 20%-27% of these conserved lncRNA loci are detected to transcription, which represents a stark contrast to the proportion of conserved protein-coding genes (48%-80%). This finding provides a valuable resource for experimental scientists to study the mechanisms of lncRNAs. Moreover, we constructed lncRNA expression phylogenetic trees across nine mammals and demonstrated that lncRNA expression profiles can reliably determine phylogenic placement in a manner similar to their coding counterparts. Our data also reveal that the evolutionary rate of lncRNA expression varies among tissues and is significantly higher than those for protein-coding genes. To streamline the processes of browsing lncRNAs and detecting their evolutionary statuses, we integrate all the data produced in this study into a database named PhyloNONCODE (http://www.bioinfo.org/phyloNoncode). Our work starts to place mammalian lncRNAs in an evolutionary context and represent a rich resource for comparative and functional analyses of this critical layer of genome.","corpus_id":15294020,"score":1},{"doc_id":"26183581","title":"A potential signature of eight long non-coding RNAs predicts survival in patients with non-small cell lung cancer.","abstract":"BACKGROUND: Accumulated evidence suggests that dysregulated expression of long non-coding RNAs (lncRNAs) may play a critical role in tumorigenesis and prognosis of cancer, indicating the potential utility of lncRNAs as cancer prognostic or diagnostic markers. However, the power of lncRNA signatures in predicting the survival of patients with non-small cell lung cancer (NSCLC) has not yet been investigated. METHODS: We performed an array-based transcriptional analysis of lncRNAs in large patient cohorts with NSCLC by repurposing microarray probes from the gene expression omnibus database. A risk score model was constructed based on the expression data of these eight lncRNAs in the training dataset of NSCLC patients and was subsequently validated in other two independent NSCLC datasets. The biological implications of prognostic lncRNAs were also analyzed using the functional enrichment analysis. RESULTS: An expression pattern of eight lncRNAs was found to be significantly associated with overall survival (OS) of NSCLC patients in the training dataset. With the eight-lncRNA signature, patients of the training dataset could be classified into high- and low-risk groups with significantly different OS (median survival 1.67 vs. 6.06 years, log-rank test p = 4.33E-09). The prognostic power of eight-lncRNA signature was further validated in other two non-overlapping independent NSCLC cohorts, demonstrating good reproducibility and robustness of this eight-lncRNA signature in predicting OS of NSCLC patients. Multivariate regression and stratified analysis suggested that the prognostic power of the eight-lncRNA signature was independent of clinical and pathological factors. Functional enrichment analyses revealed potential functional roles of the eight prognostic lncRNAs in tumorigenesis. CONCLUSIONS: These findings indicate that the eight-lncRNA signature may be an effective independent prognostic molecular biomarker in the prediction of NSCLC patient survival.","corpus_id":8654442,"score":1},{"doc_id":"26424084","title":"miRSponge: a manually curated database for experimentally supported miRNA sponges and ceRNAs.","abstract":"In this study, we describe miRSponge, a manually curated database, which aims at providing an experimentally supported resource for microRNA (miRNA) sponges. Recent evidence suggests that miRNAs are themselves regulated by competing endogenous RNAs (ceRNAs) or 'miRNA sponges' that contain miRNA binding sites. These competitive molecules can sequester miRNAs to prevent them interacting with their natural targets to play critical roles in various biological and pathological processes. It has become increasingly important to develop a high quality database to record and store ceRNA data to support future studies. To this end, we have established the experimentally supported miRSponge database that contains data on 599 miRNA-sponge interactions and 463 ceRNA relationships from 11 species following manual curating from nearly 1200 published articles. Database classes include endogenously generated molecules including coding genes, pseudogenes, long non-coding RNAs and circular RNAs, along with exogenously introduced molecules including viral RNAs and artificial engineered sponges. Approximately 70% of the interactions were identified experimentally in disease states. miRSponge provides a user-friendly interface for convenient browsing, retrieval and downloading of dataset. A submission page is also included to allow researchers to submit newly validated miRNA sponge data. Database URL: http://www.bio-bigdata.net/miRSponge.","corpus_id":17451032,"score":1},{"doc_id":"26481460","title":"Global identification and analysis of long non-coding RNAs in diploid strawberry Fragaria vesca during flower and fruit development.","abstract":"BACKGROUND: Long non-coding RNAs (lncRNAs) are a new class of regulatory molecules with roles in diverse biological processes. While much effort has been invested in the analysis of lncRNAs from established plant models Arabidopsis, maize, and rice, almost nothing is known about lncRNAs from fruit crops, including those in the Rosaceae family. RESULTS: Here, we present a genome-scale identification and characterization of lncRNAs from a diploid strawberry, Fragaria vesca, based on rich RNA-seq datasets from 35 different flower and fruit tissues. 5,884 Fve-lncRNAs derived from 3,862 loci were identified. These lncRNAs were carefully cataloged based on expression level and whether or not they contain repetitive sequences or generate small RNAs. About one fourth of them are termed high-confidence lncRNAs (hc-lncRNAs) because they are expressed at a level of FPKM higher than 2 and produce neither small RNAs nor contain repetitive sequence. To identify regulatory interactions between lncRNAs and their potential protein-coding (PC) gene targets, pairs of lncRNAs and PC genes with positively or negatively correlated expression trends were identified based on their expression; these pairs may be candidates of cis- or trans-acting lncRNAs and their targets. Finally, blast searches within plant species indicate that lncRNAs are not well conserved. CONCLUSIONS: Our study identifies a large number of tissue-specifically expressed lncRNAs in F. vesca, thereby highlighting their potential contributions to strawberry flower and fruit development and paving the way for future functional studies.","corpus_id":6145679,"score":1},{"doc_id":"26683846","title":"Comprehensive Identification of Long Non-coding RNAs in Purified Cell Types from the Brain Reveals Functional LncRNA in OPC Fate Determination.","abstract":"Long non-coding RNAs (lncRNAs) (> 200 bp) play crucial roles in transcriptional regulation during numerous biological processes. However, it is challenging to comprehensively identify lncRNAs, because they are often expressed at low levels and with more cell-type specificity than are protein-coding genes. In the present study, we performed ab initio transcriptome reconstruction using eight purified cell populations from mouse cortex and detected more than 5000 lncRNAs. Predicting the functions of lncRNAs using cell-type specific data revealed their potential functional roles in Central Nervous System (CNS) development. We performed motif searches in ENCODE DNase I digital footprint data and Mouse ENCODE promoters to infer transcription factor (TF) occupancy. By integrating TF binding and cell-type specific transcriptomic data, we constructed a novel framework that is useful for systematically identifying lncRNAs that are potentially essential for brain cell fate determination. Based on this integrative analysis, we identified lncRNAs that are regulated during Oligodendrocyte Precursor Cell (OPC) differentiation from Neural Stem Cells (NSCs) and that are likely to be involved in oligodendrogenesis. The top candidate, lnc-OPC, shows highly specific expression in OPCs and remarkable sequence conservation among placental mammals. Interestingly, lnc-OPC is significantly up-regulated in glial progenitors from experimental autoimmune encephalomyelitis (EAE) mouse models compared to wild-type mice. OLIG2-binding sites in the upstream regulatory region of lnc-OPC were identified by ChIP (chromatin immunoprecipitation)-Sequencing and validated by luciferase assays. Loss-of-function experiments confirmed that lnc-OPC plays a functional role in OPC genesis. Overall, our results substantiated the role of lncRNA in OPC fate determination and provided an unprecedented data source for future functional investigations in CNS cell types. We present our datasets and analysis results via the interactive genome browser at our laboratory website that is freely accessible to the research community. This is the first lncRNA expression database of collective populations of glia, vascular cells, and neurons. We anticipate that these studies will advance the knowledge of this major class of non-coding genes and their potential roles in neurological development and diseases.","corpus_id":18331444,"score":1},{"doc_id":"26969372","title":"Integrating RNA-seq and ChIP-seq data to characterize long non-coding RNAs in Drosophila melanogaster.","abstract":"BACKGROUND: Recent advances in sequencing technology have opened a new era in RNA studies. Novel types of RNAs such as long non-coding RNAs (lncRNAs) have been discovered by transcriptomic sequencing and some lncRNAs have been found to play essential roles in biological processes. However, only limited information is available for lncRNAs in Drosophila melanogaster, an important model organism. Therefore, the characterization of lncRNAs and identification of new lncRNAs in D. melanogaster is an important area of research. Moreover, there is an increasing interest in the use of ChIP-seq data (H3K4me3, H3K36me3 and Pol II) to detect signatures of active transcription for reported lncRNAs. RESULTS: We have developed a computational approach to identify new lncRNAs from two tissue-specific RNA-seq datasets using the poly(A)-enriched and the ribo-zero method, respectively. In our results, we identified 462 novel lncRNA transcripts, which we combined with 4137 previously published lncRNA transcripts into a curated dataset. We then utilized 61 RNA-seq and 32 ChIP-seq datasets to improve the annotation of the curated lncRNAs with regards to transcriptional direction, exon regions, classification, expression in the brain, possession of a poly(A) tail, and presence of conventional chromatin signatures. Furthermore, we used 30 time-course RNA-seq datasets and 32 ChIP-seq datasets to investigate whether the lncRNAs reported by RNA-seq have active transcription signatures. The results showed that more than half of the reported lncRNAs did not have chromatin signatures related to active transcription. To clarify this issue, we conducted RT-qPCR experiments and found that ~95.24% of the selected lncRNAs were truly transcribed, regardless of whether they were associated with active chromatin signatures or not. CONCLUSIONS: In this study, we discovered a large number of novel lncRNAs, which suggests that many remain to be identified in D. melanogaster. For the lncRNAs that are known, we improved their characterization by integrating a large number of sequencing datasets (93 sets in total) from multiple sources (lncRNAs, RNA-seq and ChIP-seq). The RT-qPCR experiments demonstrated that RNA-seq is a reliable platform to discover lncRNAs. This set of curated lncRNAs with improved annotations can serve as an important resource for investigating the function of lncRNAs in D. melanogaster.","corpus_id":2600022,"score":1},{"doc_id":"27725737","title":"circRNADb: A comprehensive database for human circular RNAs with protein-coding annotations.","abstract":"It has been known that circular RNAs are widely expressed in human tissues and cells, and play important regulatory roles in physiological or pathological processes. However, there is lack of comprehensively annotated human circular RNAs database. In this study we established a circRNA database, named as circRNADb, containing 32,914 human exonic circRNAs carefully selected from diversified sources. The detailed information of the circRNA, including genomic information, exon splicing, genome sequence, internal ribosome entry site (IRES), open reading frame (ORF) and references were provided in circRNADb. In addition, circRNAs were found to be able to encode proteins, which have not been reported in any species. 16328 circRNAs were annotated to have ORF longer than 100 amino acids, of which 7170 have IRES elements. 46 circRNAs from 37 genes were found to have their corresponding proteins expressed according mass spectrometry. The database provides the function of data search, browse, download, submit and feedback for the user to study particular circular RNA of interest and update the database continually. circRNADb will be built to be a biological information platform for circRNA molecules and related biological functions in the future. The database can be freely available through the web server at http://reprod.njmu.edu.cn/circrnadb.","corpus_id":802184,"score":1},{"doc_id":"28751672","title":"The LncRNA Connectivity Map: Using LncRNA Signatures to Connect Small Molecules, LncRNAs, and Diseases.","abstract":"Well characterized the connections among diseases, long non-coding RNAs (lncRNAs) and drugs are important for elucidating the key roles of lncRNAs in biological mechanisms in various biological states. In this study, we constructed a database called LNCmap (LncRNA Connectivity Map), available at http://www.bio-bigdata.com/LNCmap/ , to establish the correlations among diseases, physiological processes, and the action of small molecule therapeutics by attempting to describe all biological states in terms of lncRNA signatures. By reannotating the microarray data from the Connectivity Map database, the LNCmap obtained 237 lncRNA signatures of 5916 instances corresponding to 1262 small molecular drugs. We provided a user-friendly interface for the convenient browsing, retrieval and download of the database, including detailed information and the associations of drugs and corresponding affected lncRNAs. Additionally, we developed two enrichment analysis methods for users to identify candidate drugs for a particular disease by inputting the corresponding lncRNA expression profiles or an associated lncRNA list and then comparing them to the lncRNA signatures in our database. Overall, LNCmap could significantly improve our understanding of the biological roles of lncRNAs and provide a unique resource to reveal the connections among drugs, lncRNAs and diseases.","corpus_id":2974869,"score":1},{"doc_id":"28974472","title":"Stress2TF: a manually curated database of TF regulation in plant response to stress.","abstract":"Considerable studies demonstrate that plant transcription factors (TFs) play key regulatory roles in abiotic/biotic stress conditions, such as drought and pathogen attack. However, there is no effort dedicated to curate experimentally validated stress-TF regulatory relationships from these individual reports into a central database, which put an obstacle in the exploration of stress-TF regulations in plants. To address this issue, we presented a literature-curated database 'Stress2TF' that currently documented 1533 regulatory relationships between 71 abiotic/biotic stresses and 558 TFs in 47 plant species. Each entry in Stress2TF contains detailed information about a stress-TF relationship such as plant name, stress name, TF and brief description of stress-TF relationship. Stress2TF provided a user-friendly interface for entry browse, search and download. In addition, a submission page and several useful tools (e.g., BLAST, network visualization) were integrated. Stress2TF may be a valuable resource for the research of stress-TF regulatory mechanisms in plants. Stress2TF is available at http://csgenomics.ahau.edu.cn/Stress2TF.","corpus_id":34794340,"score":1},{"doc_id":"29053596","title":"Elucidating the Role of Host Long Non-Coding RNA during Viral Infection: Challenges and Paths Forward.","abstract":"Research over the past decade has clearly shown that long non-coding RNAs (lncRNAs) are functional. Many lncRNAs can be related to immunity and the host response to viral infection, but their specific functions remain largely elusive. The vast majority of lncRNAs are annotated with extremely limited knowledge and tend to be expressed at low levels, making ad hoc experimentation difficult. Changes to lncRNA expression during infection can be systematically profiled using deep sequencing; however, this often produces an intractable number of candidate lncRNAs, leaving no clear path forward. For these reasons, it is especially important to prioritize lncRNAs into high-confidence \"hits\" by utilizing multiple methodologies. Large scale perturbation studies may be used to screen lncRNAs involved in phenotypes of interest, such as resistance to viral infection. Single cell transcriptome sequencing quantifies cell-type specific lncRNAs that are less abundant in a mixture. When coupled with iterative experimental validations, new computational strategies for efficiently integrating orthogonal high-throughput data will likely be the driver for elucidating the functional role of lncRNAs during viral infection. This review highlights new high-throughput technologies and discusses the potential for integrative computational analysis to streamline the identification of infection-related lncRNAs and unveil novel targets for antiviral therapeutics.","corpus_id":7715078,"score":1},{"doc_id":"29254923","title":"Progress in long non-coding RNAs in animals.","abstract":"Long non-coding RNAs (lncRNAs) are important transcripts that are more than 200 nucleotides in length, and distribute extensively in animal and plant genomes. Accumulated studies demonstrate that lncRNAs play critical roles in biological processes related to embryogenesis, muscle development, lipid deposition and immune responses. They assist protein complexes in translocating to appropriate locations and participate in regulating gene activation and inactivation. Recently, rapid progress of lncRNA research is emerging, largely due to molecular biological technologies and information developed in the human genome project and the Encyclopedia of DNA Elements (ENCODE) project. For example, a dwarf open reading frame (DWORF) encoded by an annotated lncRNA was reported to activate the SERCA pump. Moreover, small regulatory polypeptide of amino acid response (SPAR) encoded by lncRNA LINC00961 was found to regulate muscle regeneration. These new results have revealed a novel model that lncRNA regulates biological processes using its small peptide product. In this review, we summarize the characteristics, databases, biological functions and molecular regulatory models, as well as research interests of lncRNAs in the future.","corpus_id":3738611,"score":1},{"doc_id":"29485610","title":"High-Throughput Methods to Detect Long Non-Coding RNAs.","abstract":"Increasing evidence suggests that the numbers of long non-coding RNAs (lncRNAs) are more than those of protein-coding genes in various organisms. Although the detection methods for lncRNAs are being increasingly established, there are advantages and disadvantages that exist for each method. In this opinion article, I highlight the differences between microarrays and RNA sequencing (RNA-seq) for the detection of lncRNAs. Compared to RNA-seq, microarrays are limited to the known sequences. However, the detection method as well as data analysis workflow is more established, which makes it easier to analyze the data for bench scientists without extensive knowledge about computer programming. In order to highlight the usage of microarrays over RNA-seq for the detection of lncRNAs, we are organizing a special issue for High-Throughput called \"Microarrays in Non-Coding RNAs Profiling\", which will include the specific usages of microarrays for lncRNAs.","corpus_id":3588102,"score":1},{"doc_id":"29657289","title":"Present Scenario of Long Non-Coding RNAs in Plants.","abstract":"Small non-coding RNAs have been extensively studied in plants over the last decade. In contrast, genome-wide identification of plant long non-coding RNAs (lncRNAs) has recently gained momentum. LncRNAs are now being recognized as important players in gene regulation, and their potent regulatory roles are being studied comprehensively in eukaryotes. LncRNAs were first reported in humans in 1992. Since then, research in animals, particularly in humans, has rapidly progressed, and a vast amount of data has been generated, collected, and organized using computational approaches. Additionally, numerous studies have been conducted to understand the roles of these long RNA species in several diseases. However, the status of lncRNA investigation in plants lags behind that in animals (especially humans). Efforts are being made in this direction using computational tools and high-throughput sequencing technologies, such as the lncRNA microarray technique, RNA-sequencing (RNA-seq), RNA capture sequencing, (RNA CaptureSeq), etc. Given the current scenario, significant amounts of data have been produced regarding plant lncRNAs, and this amount is likely to increase in the subsequent years. In this review we have documented brief information about lncRNAs and their status of research in plants, along with the plant-specific resources/databases for information retrieval on lncRNAs.","corpus_id":4712574,"score":1},{"doc_id":"29670884","title":"Distinct and Modular Organization of Protein Interacting Sites in Long Non-coding RNAs.","abstract":"Background: Long non-coding RNAs (lncRNAs), are being reported to be extensively involved in diverse regulatory roles and have exhibited numerous disease associations. LncRNAs modulate their function through interaction with other biomolecules in the cell including DNA, RNA, and proteins. The availability of genome-scale experimental datasets of RNA binding proteins (RBP) motivated us to understand the role of lncRNAs in terms of its interactions with these proteins. In the current report, we demonstrate a comprehensive study of interactions between RBP and lncRNAs at a transcriptome scale through extensive analysis of the crosslinking and immunoprecipitation (CLIP) experimental datasets available for 70 RNA binding proteins. Results: Our analysis suggests that density of interaction sites for these proteins was significantly higher for specific sub-classes of lncRNAs when compared to protein-coding transcripts. We also observe a positional preference of these RBPs across lncRNA and protein coding transcripts in addition to a significant co-occurrence of RBPs having similar functions, suggesting a modular organization of these elements across lncRNAs. Conclusion: The significant enrichment of RBP sites across some lncRNA classes is suggestive that these interactions might be important in understanding the functional role of lncRNA. We observed a significant enrichment of RBPs which are involved in functional roles such as silencing, splicing, mRNA processing, and transport, indicating the potential participation of lncRNAs in such processes.","corpus_id":4565387,"score":1},{"doc_id":"21504869","title":"Databases and resources for human small non-coding RNAs.","abstract":"Recent advances in high-throughput sequencing have facilitated the genome-wide studies of small non-coding RNAs (sRNAs). Numerous studies have highlighted the role of various classes of sRNAs at different levels of gene regulation and disease. The fast growth of sequence data and the diversity of sRNA species have prompted the need to organise them in annotation databases. There are currently several databases that collect sRNA data. Various tools are provided for access, with special emphasis on the well-characterised family of micro-RNAs. The striking heterogeneity of the new classes of sRNAs and the lack of sufficient functional annotation, however, make integration of these datasets a difficult task. This review describes the currently available databases for human sRNAs that are accessible via the internet, and some of the large datasets for human sRNAs from high-throughput sequencing experiments that are so far only available as supplementary data in publications. Some of the main issues related to the integration and annotation of sRNA datasets are also discussed.","corpus_id":43258,"score":0},{"doc_id":"22833525","title":"RedoxDB--a curated database for experimentally verified protein oxidative modification.","abstract":"SUMMARY: Redox regulation and signaling, which are involved in various cellular processes, have become one of the research focuses in the past decade. Cysteine thiol groups are particularly susceptible to post-translational modification, and their reversible oxidation is of critical role in redox regulation and signaling. With the tremendous improvement of techniques, hundreds of redox proteins along with their redox-sensitive cysteines have been reported, and the number is still fast growing. However, until now there is no database to accommodate the rapid accumulation of information on protein oxidative modification. Here we present RedoxDB-a manually curated database for experimentally validated redox proteins. RedoxDB (version 1.0) consists of two datasets (A and B, for proteins with or without verified modified cysteines, respectively) and includes 2157 redox proteins containing 2203 cysteine residues with oxidative modification. For each modified cysteine, the exact position, modification type and flanking sequence are provided. Additional information, including gene name, organism, sequence, literature references and links to UniProt and PDB, is also supplied. The database supports several functions including data search, blast and browsing. Bulk download of the entire dataset is also available. We expect that RedoxDB will be useful for both experimental studies and computational analyses of protein oxidative modification. AVAILABILITY: The database is freely available at: http://biocomputer.bio.cuhk.edu.hk/RedoxDB. CONTACT: djguo@cuhk.edu.hk SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics Online.","corpus_id":15956955,"score":0},{"doc_id":"24214963","title":"Manually curated database of rice proteins.","abstract":"'Manually Curated Database of Rice Proteins' (MCDRP) available at http://www.genomeindia.org/biocuration is a unique curated database based on published experimental data. Semantic integration of scientific data is essential to gain a higher level of understanding of biological systems. Since the majority of scientific data is available as published literature, text mining is an essential step before the data can be integrated and made available for computer-based search in various databases. However, text mining is a tedious exercise and thus, there is a large gap in the data available in curated databases and published literature. Moreover, data in an experiment can be perceived from several perspectives, which may not reflect in the text-based curation. In order to address such issues, we have demonstrated the feasibility of digitizing the experimental data itself by creating a database on rice proteins based on in-house developed data curation models. Using these models data of individual experiments have been digitized with the help of universal ontologies. Currently, the database has data for over 1800 rice proteins curated from >4000 different experiments of over 400 research articles. Since every aspect of the experiment such as gene name, plant type, tissue and developmental stage has been digitized, experimental data can be rapidly accessed and integrated.","corpus_id":12930216,"score":0},{"doc_id":"25776024","title":"LMPID: a manually curated database of linear motifs mediating protein-protein interactions.","abstract":"Linear motifs (LMs), used by a subset of all protein-protein interactions (PPIs), bind to globular receptors or domains and play an important role in signaling networks. LMPID (Linear Motif mediated Protein Interaction Database) is a manually curated database which provides comprehensive experimentally validated information about the LMs mediating PPIs from all organisms on a single platform. About 2200 entries have been compiled by detailed manual curation of PubMed abstracts, of which about 1000 LM entries were being annotated for the first time, as compared with the Eukaryotic LM resource. The users can submit their query through a user-friendly search page and browse the data in the alphabetical order of the bait gene names and according to the domains interacting with the LM. LMPID is freely accessible at http://bicresources.jcbose. ac.in/ssaha4/lmpid and contains 1750 unique LM instances found within 1181 baits interacting with 552 prey proteins. In summary, LMPID is an attempt to enrich the existing repertoire of resources available for studying the LMs implicated in PPIs and may help in understanding the patterns of LMs binding to a specific domain and develop prediction model to identify novel LMs specific to a domain and further able to predict inhibitors/modulators of PPI of interest.","corpus_id":17433567,"score":0},{"doc_id":"26553799","title":"DASHR: database of small human noncoding RNAs.","abstract":"Small non-coding RNAs (sncRNAs) are highly abundant RNAs, typically <100 nucleotides long, that act as key regulators of diverse cellular processes. Although thousands of sncRNA genes are known to exist in the human genome, no single database provides searchable, unified annotation, and expression information for full sncRNA transcripts and mature RNA products derived from these larger RNAs. Here, we present the Database of small human noncoding RNAs (DASHR). DASHR contains the most comprehensive information to date on human sncRNA genes and mature sncRNA products. DASHR provides a simple user interface for researchers to view sequence and secondary structure, compare expression levels, and evidence of specific processing across all sncRNA genes and mature sncRNA products in various human tissues. DASHR annotation and expression data covers all major classes of sncRNAs including microRNAs (miRNAs), Piwi-interacting (piRNAs), small nuclear, nucleolar, cytoplasmic (sn-, sno-, scRNAs, respectively), transfer (tRNAs), and ribosomal RNAs (rRNAs). Currently, DASHR (v1.0) integrates 187 smRNA high-throughput sequencing (smRNA-seq) datasets with over 2.5 billion reads and annotation data from multiple public sources. DASHR contains annotations for ∼48 000 human sncRNA genes and mature sncRNA products, 82% of which are expressed in one or more of the curated tissues. DASHR is available at http://lisanwanglab.org/DASHR.","corpus_id":2268890,"score":0},{"doc_id":"27374121","title":"HPIDB 2.0: a curated database for host-pathogen interactions.","abstract":"Identification and analysis of host-pathogen interactions (HPI) is essential to study infectious diseases. However, HPI data are sparse in existing molecular interaction databases, especially for agricultural host-pathogen systems. Therefore, resources that annotate, predict and display the HPI that underpin infectious diseases are critical for developing novel intervention strategies. HPIDB 2.0 (http://www.agbase.msstate.edu/hpi/main.html) is a resource for HPI data, and contains 45, 238 manually curated entries in the current release. Since the first description of the database in 2010, multiple enhancements to HPIDB data and interface services were made that are described here. Notably, HPIDB 2.0 now provides targeted biocuration of molecular interaction data. As a member of the International Molecular Exchange consortium, annotations provided by HPIDB 2.0 curators meet community standards to provide detailed contextual experimental information and facilitate data sharing. Moreover, HPIDB 2.0 provides access to rapidly available community annotations that capture minimum molecular interaction information to address immediate researcher needs for HPI network analysis. In addition to curation, HPIDB 2.0 integrates HPI from existing external sources and contains tools to infer additional HPI where annotated data are scarce. Compared to other interaction databases, our data collection approach ensures HPIDB 2.0 users access the most comprehensive HPI data from a wide range of pathogens and their hosts (594 pathogen and 70 host species, as of February 2016). Improvements also include enhanced search capacity, addition of Gene Ontology functional information, and implementation of network visualization. The changes made to HPIDB 2.0 content and interface ensure that users, especially agricultural researchers, are able to easily access and analyse high quality, comprehensive HPI data. All HPIDB 2.0 data are updated regularly, are publically available for direct download, and are disseminated to other molecular interaction resources. Database URL: http://www.agbase.msstate.edu/hpi/main.html.","corpus_id":18761421,"score":0}],"string":"[\n {\n \"doc_id\": \"21112873\",\n \"title\": \"lncRNAdb: a reference database for long noncoding RNAs.\",\n \"abstract\": \"Large numbers of long RNAs with little or no protein-coding potential [long noncoding RNAs (lncRNAs)] are being identified in eukaryotes. In parallel, increasing data describing the expression profiles, molecular features and functions of individual lncRNAs in a variety of systems are accumulating. To enable the systematic compilation and updating of this information, we have developed a database (lncRNAdb) containing a comprehensive list of lncRNAs that have been shown to have, or to be associated with, biological functions in eukaryotes, as well as messenger RNAs that have regulatory roles. Each entry contains referenced information about the RNA, including sequences, structural information, genomic context, expression, subcellular localization, conservation, functional evidence and other relevant information. lncRNAdb can be searched by querying published RNA names and aliases, sequences, species and associated protein-coding genes, as well as terms contained in the annotations, such as the tissues in which the transcripts are expressed and associated diseases. In addition, lncRNAdb is linked to the UCSC Genome Browser for visualization and Noncoding RNA Expression Database (NRED) for expression information from a variety of sources. lncRNAdb provides a platform for the ongoing collation of the literature pertaining to lncRNAs and their association with other genomic elements. lncRNAdb can be accessed at: http://www.lncrnadb.org/.\",\n \"corpus_id\": 2900681,\n \"score\": 2\n },\n {\n \"doc_id\": \"22135294\",\n \"title\": \"NONCODE v3.0: integrative annotation of long noncoding RNAs.\",\n \"abstract\": \"Facilitated by the rapid progress of high-throughput sequencing technology, a large number of long noncoding RNAs (lncRNAs) have been identified in mammalian transcriptomes over the past few years. LncRNAs have been shown to play key roles in various biological processes such as imprinting control, circuitry controlling pluripotency and differentiation, immune responses and chromosome dynamics. Notably, a growing number of lncRNAs have been implicated in disease etiology. With the increasing number of published lncRNA studies, the experimental data on lncRNAs (e.g. expression profiles, molecular features and biological functions) have accumulated rapidly. In order to enable a systematic compilation and integration of this information, we have updated the NONCODE database (http://www.noncode.org) to version 3.0 to include the first integrated collection of expression and functional lncRNA data obtained from re-annotated microarray studies in a single database. NONCODE has a user-friendly interface with a variety of search or browse options, a local Genome Browser for visualization and a BLAST server for sequence-alignment search. In addition, NONCODE provides a platform for the ongoing collation of ncRNAs reported in the literature. All data in NONCODE are open to users, and can be downloaded through the website or obtained through the SOAP API and DAS services.\",\n \"corpus_id\": 846427,\n \"score\": 2\n },\n {\n \"doc_id\": \"22336709\",\n \"title\": \"Non-coding transcription characterization and annotation: a guide and web resource for non-coding RNA databases.\",\n \"abstract\": \"Large-scale transcriptome projects have shown that the number of RNA transcripts not coding for proteins (non-coding RNAs) is much larger than previously recognized. High-throughput technologies, coupled with bioinformatics approaches, have produced increasing amounts of data, highlighting the role of non-coding RNAs (ncRNAs) in biological processes. Data generated by these studies include diverse non-coding RNA classes from organisms of different kingdoms, which were obtained using different experimental and computational assays. This has led to a rapid increase of specialized RNA databases. The fast growth in the number of available databases makes integration of stored information a difficult task. We present here NRDR, a Non-coding RNA Databases Resource for information retrieval on ncRNA databases (www.ncrnadatabases.org). We performed a survey of 102 public databases on ncRNAs and we have introduced four categorizations to classify these databases and to help researchers quickly search and find the information they need: RNA family, information source, information content and available search mechanisms. NRDR is a useful databases searching tool that will facilitate research on ncRNAs.\",\n \"corpus_id\": 34157165,\n \"score\": 2\n },\n {\n \"doc_id\": \"23042674\",\n \"title\": \"LNCipedia: a database for annotated human lncRNA transcript sequences and structures.\",\n \"abstract\": \"Here, we present LNCipedia (http://www.lncipedia.org), a novel database for human long non-coding RNA (lncRNA) transcripts and genes. LncRNAs constitute a large and diverse class of non-coding RNA genes. Although several lncRNAs have been functionally annotated, the majority remains to be characterized. Different high-throughput methods to identify new lncRNAs (including RNA sequencing and annotation of chromatin-state maps) have been applied in various studies resulting in multiple unrelated lncRNA data sets. LNCipedia offers 21 488 annotated human lncRNA transcripts obtained from different sources. In addition to basic transcript information and gene structure, several statistics are determined for each entry in the database, such as secondary structure information, protein coding potential and microRNA binding sites. Our analyses suggest that, much like microRNAs, many lncRNAs have a significant secondary structure, in-line with their presumed association with proteins or protein complexes. Available literature on specific lncRNAs is linked, and users or authors can submit articles through a web interface. Protein coding potential is assessed by two different prediction algorithms: Coding Potential Calculator and HMMER. In addition, a novel strategy has been integrated for detecting potentially coding lncRNAs by automatically re-analysing the large body of publicly available mass spectrometry data in the PRIDE database. LNCipedia is publicly available and allows users to query and download lncRNA sequences and structures based on different search criteria. The database may serve as a resource to initiate small- and large-scale lncRNA studies. As an example, the LNCipedia content was used to develop a custom microarray for expression profiling of all available lncRNAs.\",\n \"corpus_id\": 7002750,\n \"score\": 2\n },\n {\n \"doc_id\": \"23175614\",\n \"title\": \"LncRNADisease: a database for long-non-coding RNA-associated diseases.\",\n \"abstract\": \"In this article, we describe a long-non-coding RNA (lncRNA) and disease association database (LncRNADisease), which is publicly accessible at http://cmbi.bjmu.edu.cn/lncrnadisease. In recent years, a large number of lncRNAs have been identified and increasing evidence shows that lncRNAs play critical roles in various biological processes. Therefore, the dysfunctions of lncRNAs are associated with a wide range of diseases. It thus becomes important to understand lncRNAs' roles in diseases and to identify candidate lncRNAs for disease diagnosis, treatment and prognosis. For this purpose, a high-quality lncRNA-disease association database would be extremely beneficial. Here, we describe the LncRNADisease database that collected and curated approximately 480 entries of experimentally supported lncRNA-disease associations, including 166 diseases. LncRNADisease also curated 478 entries of lncRNA interacting partners at various molecular levels, including protein, RNA, miRNA and DNA. Moreover, we annotated lncRNA-disease associations with genomic information, sequences, references and species. We normalized the disease name and the type of lncRNA dysfunction and provided a detailed description for each entry. Finally, we developed a bioinformatic method to predict novel lncRNA-disease associations and integrated the method and the predicted associated diseases of 1564 human lncRNAs into the database.\",\n \"corpus_id\": 1969204,\n \"score\": 2\n },\n {\n \"doc_id\": \"23476021\",\n \"title\": \"PLncDB: plant long non-coding RNA database.\",\n \"abstract\": \"SUMMARY: Plant long non-coding RNA database (PLncDB) attempts to provide the following functions related to long non-coding RNAs (lncRNAs): (i) Genomic information for a large number of lncRNAs collected from various resources; (ii) an online genome browser for plant lncRNAs based on a platform similar to that of the UCSC Genome Browser; (iii) Integration of transcriptome datasets derived from various samples including different tissues, developmental stages, mutants and stress treatments; and (iv) A list of epigenetic modification datasets and small RNA datasets. Currently, our PLncDB provides a comprehensive genomic view of Arabidopsis lncRNAs for the plant research community. This database will be regularly updated with new plant genome when available so as to greatly facilitate future investigations on plant lncRNAs. AVAILABILITY: PLncDB is freely accessible at http://chualab.rockefeller.edu/gbrowse2/homepage.html and all results can be downloaded for free at the website.\",\n \"corpus_id\": 2290617,\n \"score\": 2\n },\n {\n \"doc_id\": \"24525374\",\n \"title\": \"lncRNAMap: a map of putative regulatory functions in the long non-coding transcriptome.\",\n \"abstract\": \"BACKGROUND: Recent studies have demonstrated the importance of long non-coding RNAs (lncRNAs) in chromatin remodeling, and in transcriptional and post-transcriptional regulation. However, only a few specific lncRNAs are well understood, whereas others are completely uncharacterized. To address this, there is a need for user-friendly platform to studying the putative regulatory functions of human lncRNAs. DESCRIPTION: lncRNAMap is an integrated and comprehensive database relating to exploration of the putative regulatory functions of human lncRNAs with two mechanisms of regulation, by encoding siRNAs and by acting as miRNA decoys. To investigate lncRNAs producing siRNAs that regulate protein-coding genes, lncRNAMap integrated small RNAs (sRNAs) that were supported by publicly available deep sequencing data from various sRNA libraries and constructed lncRNA-derived siRNA-target interactions. In addition, lncRNAMap demonstrated that lncRNAs can act as targets for miRNAs that would otherwise regulate protein-coding genes. Previously studies indicated that intergenic lncRNAs (lincRNAs) either positive or negative regulated neighboring genes, therefore, lncRNAMap surveyed neighboring genes within a 1Mb distance from the genomic location of specific lncRNAs and provided the expression profiles of lncRNA and its neighboring genes. The gene expression profiles may supply the relationship between lncRNA and its neighboring genes. CONCLUSIONS: lncRNAMap is a powerful user-friendly platform for the investigation of putative regulatory functions of human lncRNAs with producing siRNAs and acting as miRNA decoy. lncRNAMap is freely available on the web at http://lncRNAMap.mbc.nctu.edu.tw/.\",\n \"corpus_id\": 7861471,\n \"score\": 2\n },\n {\n \"doc_id\": \"24813212\",\n \"title\": \"lncRNAtor: a comprehensive resource for functional investigation of long non-coding RNAs.\",\n \"abstract\": \"MOTIVATION: A number of long non-coding RNAs (lncRNAs) have been identified by deep sequencing methods, but their molecular and cellular functions are known only for a limited number of lncRNAs. Current databases on lncRNAs are mostly for cataloging purpose without providing in-depth information required to infer functions. A comprehensive resource on lncRNA function is an immediate need. RESULTS: We present a database for functional investigation of lncRNAs that encompasses annotation, sequence analysis, gene expression, protein binding and phylogenetic conservation. We have compiled lncRNAs for six species (human, mouse, zebrafish, fruit fly, worm and yeast) from ENSEMBL, HGNC, MGI and lncRNAdb. Each lncRNA was analyzed for coding potential and phylogenetic conservation in different lineages. Gene expression data of 208 RNA-Seq studies (4995 samples), collected from GEO, ENCODE, modENCODE and TCGA databases, were used to provide expression profiles in various tissues, diseases and developmental stages. Importantly, we analyzed RNA-Seq data to identify coexpressed mRNAs that would provide ample insights on lncRNA functions. The resulting gene list can be subject to enrichment analysis such as Gene Ontology or KEGG pathways. Furthermore, we compiled protein-lncRNA interactions by collecting and analyzing publicly available CLIP-seq or PAR-CLIP sequencing data. Finally, we explored evolutionarily conserved lncRNAs with correlated expression between human and six other organisms to identify functional lncRNAs. The whole contents are provided in a user-friendly web interface. AVAILABILITY AND IMPLEMENTATION: lncRNAtor is available at http://lncrnator.ewha.ac.kr/. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.\",\n \"corpus_id\": 5133246,\n \"score\": 2\n },\n {\n \"doc_id\": \"25332392\",\n \"title\": \"lncRNASNP: a database of SNPs in lncRNAs and their potential functions in human and mouse.\",\n \"abstract\": \"Long non-coding RNAs (lncRNAs) play key roles in various cellular contexts and diseases by diverse mechanisms. With the rapid growth of identified lncRNAs and disease-associated single nucleotide polymorphisms (SNPs), there is a great demand to study SNPs in lncRNAs. Aiming to provide a useful resource about lncRNA SNPs, we systematically identified SNPs in lncRNAs and analyzed their potential impacts on lncRNA structure and function. In total, we identified 495,729 and 777,095 SNPs in more than 30,000 lncRNA transcripts in human and mouse, respectively. A large number of SNPs were predicted with the potential to impact on the miRNA-lncRNA interaction. The experimental evidence and conservation of miRNA-lncRNA interaction, as well as miRNA expressions from TCGA were also integrated to prioritize the miRNA-lncRNA interactions and SNPs on the binding sites. Furthermore, by mapping SNPs to GWAS results, we found that 142 human lncRNA SNPs are GWAS tagSNPs and 197,827 lncRNA SNPs are in the GWAS linkage disequilibrium regions. All these data for human and mouse lncRNAs were imported into lncRNASNP database (http://bioinfo.life.hust.edu.cn/lncRNASNP/), which includes two sub-databases lncRNASNP-human and lncRNASNP-mouse. The lncRNASNP database has a user-friendly interface for searching and browsing through the SNP, lncRNA and miRNA sections.\",\n \"corpus_id\": 15612068,\n \"score\": 2\n },\n {\n \"doc_id\": \"25332394\",\n \"title\": \"lncRNAdb v2.0: expanding the reference database for functional long noncoding RNAs.\",\n \"abstract\": \"Despite the prevalence of long noncoding RNA (lncRNA) genes in eukaryotic genomes, only a small proportion have been examined for biological function. lncRNAdb, available at http://lncrnadb.org, provides users with a comprehensive, manually curated reference database of 287 eukaryotic lncRNAs that have been described independently in the scientific literature. In addition to capturing a great proportion of the recent literature describing functions for individual lncRNAs, lncRNAdb now offers an improved user interface enabling greater accessibility to sequence information, expression data and the literature. The new features in lncRNAdb include the integration of Illumina Body Atlas expression profiles, nucleotide sequence information, a BLAST search tool and easy export of content via direct download or a REST API. lncRNAdb is now endorsed by RNAcentral and is in compliance with the International Nucleotide Sequence Database Collaboration.\",\n \"corpus_id\": 1108199,\n \"score\": 2\n },\n {\n \"doc_id\": \"25378313\",\n \"title\": \"An update on LNCipedia: a database for annotated human lncRNA sequences.\",\n \"abstract\": \"The human genome is pervasively transcribed, producing thousands of non-coding RNA transcripts. The majority of these transcripts are long non-coding RNAs (lncRNAs) and novel lncRNA genes are being identified at rapid pace. To streamline these efforts, we created LNCipedia, an online repository of lncRNA transcripts and annotation. Here, we present LNCipedia 3.0 (http://www.lncipedia.org), the latest version of the publicly available human lncRNA database. Compared to the previous version of LNCipedia, the database grew over five times in size, gaining over 90,000 new lncRNA transcripts. Assessment of the protein-coding potential of LNCipedia entries is improved with state-of-the art methods that include large-scale reprocessing of publicly available proteomics data. As a result, a high-confidence set of lncRNA transcripts with low coding potential is defined and made available for download. In addition, a tool to assess lncRNA gene conservation between human, mouse and zebrafish has been implemented.\",\n \"corpus_id\": 53306854,\n \"score\": 2\n },\n {\n \"doc_id\": \"25399417\",\n \"title\": \"LncRNAWiki: harnessing community knowledge in collaborative curation of human long non-coding RNAs.\",\n \"abstract\": \"Long non-coding RNAs (lncRNAs) perform a diversity of functions in numerous important biological processes and are implicated in many human diseases. In this report we present lncRNAWiki (http://lncrna.big.ac.cn), a wiki-based platform that is open-content and publicly editable and aimed at community-based curation and collection of information on human lncRNAs. Current related databases are dependent primarily on curation by experts, making it laborious to annotate the exponentially accumulated information on lncRNAs, which inevitably requires collective efforts in community-based curation of lncRNAs. Unlike existing databases, lncRNAWiki features comprehensive integration of information on human lncRNAs obtained from multiple different resources and allows not only existing lncRNAs to be edited, updated and curated by different users but also the addition of newly identified lncRNAs by any user. It harnesses community collective knowledge in collecting, editing and annotating human lncRNAs and rewards community-curated efforts by providing explicit authorship based on quantified contributions. LncRNAWiki relies on the underling knowledge of scientific community for collective and collaborative curation of human lncRNAs and thus has the potential to serve as an up-to-date and comprehensive knowledgebase for human lncRNAs.\",\n \"corpus_id\": 15128652,\n \"score\": 2\n },\n {\n \"doc_id\": \"25707511\",\n \"title\": \"LncRNA2Function: a comprehensive resource for functional investigation of human lncRNAs based on RNA-seq data.\",\n \"abstract\": \"BACKGROUND: The GENCODE project has collected over 10,000 human long non-coding RNA (lncRNA) genes. However, the vast majority of them remain to be functionally characterized. Computational investigation of potential functions of human lncRNA genes is helpful to guide further experimental studies on lncRNAs. RESULTS: In this study, based on expression correlation between lncRNAs and protein-coding genes across 19 human normal tissues, we used the hypergeometric test to functionally annotate a single lncRNA or a set of lncRNAs with significantly enriched functional terms among the protein-coding genes that are significantly co-expressed with the lncRNA(s). The functional terms include all nodes in the Gene Ontology (GO) and 4,380 human biological pathways collected from 12 pathway databases. We successfully mapped 9,625 human lncRNA genes to GO terms and biological pathways, and then developed the first ontology-driven user-friendly web interface named lncRNA2Function, which enables researchers to browse the lncRNAs associated with a specific functional term, the functional terms associated with a specific lncRNA, or to assign functional terms to a set of human lncRNA genes, such as a cluster of co-expressed lncRNAs. The lncRNA2Function is freely available at http://mlg.hit.edu.cn/lncrna2function. CONCLUSIONS: The LncRNA2Function is an important resource for further investigating the functions of a single human lncRNA, or functionally annotating a set of human lncRNAs of interest.\",\n \"corpus_id\": 8193629,\n \"score\": 2\n },\n {\n \"doc_id\": \"25853886\",\n \"title\": \"ALDB: a domestic-animal long noncoding RNA database.\",\n \"abstract\": \"BACKGROUND: Long noncoding RNAs (lncRNAs) have attracted significant attention in recent years due to their important roles in many biological processes. Domestic animals constitute a unique resource for understanding the genetic basis of phenotypic variation and are ideal models relevant to diverse areas of biomedical research. With improving sequencing technologies, numerous domestic-animal lncRNAs are now available. Thus, there is an immediate need for a database resource that can assist researchers to store, organize, analyze and visualize domestic-animal lncRNAs. RESULTS: The domestic-animal lncRNA database, named ALDB, is the first comprehensive database with a focus on the domestic-animal lncRNAs. It currently archives 12,103 pig intergenic lncRNAs (lincRNAs), 8,923 chicken lincRNAs and 8,250 cow lincRNAs. In addition to the annotations of lincRNAs, it offers related data that is not available yet in existing lncRNA databases (lncRNAdb and NONCODE), such as genome-wide expression profiles and animal quantitative trait loci (QTLs) of domestic animals. Moreover, a collection of interfaces and applications, such as the Basic Local Alignment Search Tool (BLAST), the Generic Genome Browser (GBrowse) and flexible search functionalities, are available to help users effectively explore, analyze and download data related to domestic-animal lncRNAs. CONCLUSIONS: ALDB enables the exploration and comparative analysis of lncRNAs in domestic animals. A user-friendly web interface, integrated information and tools make it valuable to researchers in their studies. ALDB is freely available from http://res.xaut.edu.cn/aldb/index.jsp.\",\n \"corpus_id\": 7070813,\n \"score\": 2\n },\n {\n \"doc_id\": \"26211629\",\n \"title\": \"PLNlncRbase: A resource for experimentally identified lncRNAs in plants.\",\n \"abstract\": \"Accumulating published reports have confirmed the critical biological role (e.g., cell differentiation, gene regulation, stress response) for plant long non-coding RNAs (lncRNAs). However, a literature-derived database with the aim of lncRNA curation, data deposit and further distribution remains still absent for this particular lncRNA clade. PLNlncRbase has been designed as an easy-to-use resource to provide detailed information for experimentally identified plant lncRNAs. In the current version, PLNlncRbase has manually collected data from nearly 200 published literature, covering a total of 1187 plant lncRNAs in 43 plant species. The user can retrieve plant lncRNA entries from a well-organized interface through a keyword search by using the name of plant species or a lncRNA identifier. Each entry upon a query will be returned with detailed information for a specific plant lncRNA, including the species name, a lncRNA identifier, a brief description of the potential biological role, the lncRNA sequence, the lncRNA classification, an expression pattern of the lncRNA, the tissue/developmental stage/condition for lncRNA expression, the detection method for lncRNA expression, a reference literature, and the potential target gene(s) of the lncRNA extracted from the original reference. This database will be regularly updated to greatly facilitate future investigations of plant lncRNAs pertaining to their biological significance. The PLNlncRbase database is now freely available at http://bioinformatics.ahau.edu.cn/PLNlncRbase.\",\n \"corpus_id\": 26682314,\n \"score\": 2\n },\n {\n \"doc_id\": \"26363021\",\n \"title\": \"LncReg: a reference resource for lncRNA-associated regulatory networks.\",\n \"abstract\": \"Long non-coding RNAs (lncRNAs) are critical in the regulation of various biological processes. In recent years, plethora of lncRNAs have been identified in mammalian genomes through different approaches, and the researchers are constantly reporting the regulatory roles of these lncRNAs, which leads to complexity of literature about particular lncRNAs. Therefore, for the convenience of the researchers, we collected regulatory relationships of the lncRNAs and built a database called 'LncReg'. This database is developed by collecting 1081 validated lncRNA-associated regulatory entries, including 258 non-redundant lncRNAs and 571 non-redundant genes. With regulatory relationships information, LncReg can provide overall perspectives of regulatory networks of lncRNAs and comprehensive data for bioinformatics research, which is useful for understanding the functional roles of lncRNAs. Database URL: http://bioinformatics.ustc.edu.cn/lncreg/.\",\n \"corpus_id\": 17146207,\n \"score\": 2\n },\n {\n \"doc_id\": \"26481356\",\n \"title\": \"Lnc2Cancer: a manually curated database of experimentally supported lncRNAs associated with various human cancers.\",\n \"abstract\": \"Lnc2Cancer (http://www.bio-bigdata.net/lnc2cancer) is a manually curated database of cancer-associated long non-coding RNAs (lncRNAs) with experimental support that aims to provide a high-quality and integrated resource for exploring lncRNA deregulation in various human cancers. LncRNAs represent a large category of functional RNA molecules that play a significant role in human cancers. A curated collection and summary of deregulated lncRNAs in cancer is essential to thoroughly understand the mechanisms and functions of lncRNAs. Here, we developed the Lnc2Cancer database, which contains 1057 manually curated associations between 531 lncRNAs and 86 human cancers. Each association includes lncRNA and cancer name, the lncRNA expression pattern, experimental techniques, a brief functional description, the original reference and additional annotation information. Lnc2Cancer provides a user-friendly interface to conveniently browse, retrieve and download data. Lnc2Cancer also offers a submission page for researchers to submit newly validated lncRNA-cancer associations. With the rapidly increasing interest in lncRNAs, Lnc2Cancer will significantly improve our understanding of lncRNA deregulation in cancer and has the potential to be a timely and valuable resource.\",\n \"corpus_id\": 16939394,\n \"score\": 2\n },\n {\n \"doc_id\": \"26578586\",\n \"title\": \"GREENC: a Wiki-based database of plant lncRNAs.\",\n \"abstract\": \"Long non-coding RNAs (lncRNAs) are functional non-translated molecules greater than 200 nt. Their roles are diverse and they are usually involved in transcriptional regulation. LncRNAs still remain largely uninvestigated in plants with few exceptions. Experimentally validated plant lncRNAs have been shown to regulate important agronomic traits such as phosphate starvation response, flowering time and interaction with symbiotic organisms, making them of great interest in plant biology and in breeding. There is still a lack of lncRNAs in most sequenced plant species, and in those where they have been annotated, different methods have been used, so making the lncRNAs less useful in comparisons within and between species. We developed a pipeline to annotate lncRNAs and applied it to 37 plant species and six algae, resulting in the annotation of more than 120 000 lncRNAs. To facilitate the study of lncRNAs for the plant research community, the information gathered is organised in the Green Non-Coding Database (GreeNC, http://greenc.sciencedesigners.com/).\",\n \"corpus_id\": 5166047,\n \"score\": 2\n },\n {\n \"doc_id\": \"26612864\",\n \"title\": \"DIANA-LncBase v2: indexing microRNA targets on non-coding transcripts.\",\n \"abstract\": \"microRNAs (miRNAs) are short non-coding RNAs (ncRNAs) that act as post-transcriptional regulators of coding gene expression. Long non-coding RNAs (lncRNAs) have been recently reported to interact with miRNAs. The sponge-like function of lncRNAs introduces an extra layer of complexity in the miRNA interactome. DIANA-LncBase v1 provided a database of experimentally supported and in silico predicted miRNA Recognition Elements (MREs) on lncRNAs. The second version of LncBase (www.microrna.gr/LncBase) presents an extensive collection of miRNA:lncRNA interactions. The significantly enhanced database includes more than 70 000 low and high-throughput, (in)direct miRNA:lncRNA experimentally supported interactions, derived from manually curated publications and the analysis of 153 AGO CLIP-Seq libraries. The new experimental module presents a 14-fold increase compared to the previous release. LncBase v2 hosts in silico predicted miRNA targets on lncRNAs, identified with the DIANA-microT algorithm. The relevant module provides millions of predicted miRNA binding sites, accompanied with detailed metadata and MRE conservation metrics. LncBase v2 caters information regarding cell type specific miRNA:lncRNA regulation and enables users to easily identify interactions in 66 different cell types, spanning 36 tissues for human and mouse. Database entries are also supported by accurate lncRNA expression information, derived from the analysis of more than 6 billion RNA-Seq reads.\",\n \"corpus_id\": 16596478,\n \"score\": 2\n },\n {\n \"doc_id\": \"26657895\",\n \"title\": \"CANTATAdb: A Collection of Plant Long Non-Coding RNAs.\",\n \"abstract\": \"Long non-coding RNAs (lncRNAs) represent a class of potent regulators of gene expression that are found in a wide array of eukaryotes; however, our knowledge about these molecules in plants is still very limited. In particular, a number of model plant species still lack comprehensive data sets of lncRNAs and their annotations, and very little is known about their biological roles. To meet these shortcomings, we created an online database of lncRNAs in 10 model plant species. The lncRNAs were identified computationally using dozens of publicly available RNA sequencing (RNA-Seq) libraries. Expression values, coding potential, sequence alignments as well as other types of data provide annotation for the identified lncRNAs. In order to better characterize them, we investigated their potential roles in splicing modulation and deregulation of microRNA functions. The data are freely available for searching, browsing and downloading from an online database called CANTATAdb (http://cantata.amu.edu.pl, http://yeti.amu.edu.pl/CANTATA/).\",\n \"corpus_id\": 18656798,\n \"score\": 2\n },\n {\n \"doc_id\": \"26839320\",\n \"title\": \"Computational recognition for long non-coding RNA (lncRNA): Software and databases.\",\n \"abstract\": \"Since the completion of the Human Genome Project, it has been widely established that most DNA is not transcribed into proteins. These non-protein-coding regions are believed to be moderators within transcriptional and post-transcriptional processes, which play key roles in the onset of diseases. Long non-coding RNAs (lncRNAs) are generally lacking in conserved motifs typically used for detection and thus hard to identify, but nonetheless present certain characteristic features that can be exploited by bioinformatics methods. By combining lncRNA detection with known miRNA, RNA-binding protein and chromatin interaction, current tools are able to recognize and functionally annotate large number of lncRNAs. This review discusses databases and platforms dedicated to cataloging and annotating lncRNAs, as well as tools geared at discovering novel sequences. We emphasize the issues posed by the diversity of lncRNAs and their complex interaction mechanisms, as well as technical issues such as lack of unified nomenclature. We hope that this wide overview of existing platforms and databases might help guide biologists toward the tools they need to analyze their experimental data, while our discussion of limitations and of current lncRNA-related methods may assist in the development of new computational tools.\",\n \"corpus_id\": 3911230,\n \"score\": 2\n },\n {\n \"doc_id\": \"27049585\",\n \"title\": \"Long non-coding RNA Databases in Cardiovascular Research.\",\n \"abstract\": \"With the rising interest in the regulatory functions of long non-coding RNAs (lncRNAs) in complex human diseases such as cardiovascular diseases, there is an increasing need in public databases offering comprehensive and integrative data for all aspects of these versatile molecules. Recently, a variety of public data repositories that specialized in lncRNAs have been developed, which make use of huge high-throughput data particularly from next-generation sequencing (NGS) approaches. Here, we provide an overview of current lncRNA databases covering basic and functional annotation, lncRNA expression and regulation, interactions with other biomolecules, and genomic variants influencing the structure and function of lncRNAs. The prominent lncRNA antisense noncoding RNA in the INK4 locus (ANRIL), which has been unequivocally associated with coronary artery disease through genome-wide association studies (GWAS), serves as an example to demonstrate the features of each individual database.\",\n \"corpus_id\": 3346664,\n \"score\": 2\n },\n {\n \"doc_id\": \"27087310\",\n \"title\": \"NPInter v3.0: an upgraded database of noncoding RNA-associated interactions.\",\n \"abstract\": \"Despite the fact that a large quantity of noncoding RNAs (ncRNAs) have been identified, their functions remain unclear. To enable researchers to have a better understanding of ncRNAs' functions, we updated the NPInter database to version 3.0, which contains experimentally verified interactions between ncRNAs (excluding tRNAs and rRNAs), especially long noncoding RNAs (lncRNAs) and other biomolecules (proteins, mRNAs, miRNAs and genomic DNAs). In NPInter v3.0, interactions pertaining to ncRNAs are not only manually curated from scientific literature but also curated from high-throughput technologies. In addition, we also curated lncRNA-miRNA interactions fromin silicopredictions supported by AGO CLIP-seq data. When compared with NPInter v2.0, the interactions are more informative (with additional information on tissues or cell lines, binding sites, conservation, co-expression values and other features) and more organized (with divisions on data sets by data sources, tissues or cell lines, experiments and other criteria). NPInter v3.0 expands the data set to 491,416 interactions in 188 tissues (or cell lines) from 68 kinds of experimental technologies. NPInter v3.0 also improves the user interface and adds new web services, including a local UCSC Genome Browser to visualize binding sites. Additionally, NPInter v3.0 defined a high-confidence set of interactions and predicted the functions of lncRNAs in human and mouse based on the interactions curated in the database. NPInter v3.0 is available athttp://www.bioinfo.org/NPInter/Database URL:http://www.bioinfo.org/NPInter/.\",\n \"corpus_id\": 12524699,\n \"score\": 2\n },\n {\n \"doc_id\": \"27113186\",\n \"title\": \"[The beta version of LongMan: a large-scale mammalian lncRNA database orthologous to human lncRNAs].\",\n \"abstract\": \"OBJECTIVE: To predict orthologous sequences of the GENCODE-identified 13 562 human long non-coding RNAs (lncRNA) in 16 mammalian genomes and construct a lncRNA database LongMan for lncRNA studies. METHODS: The exon structures of a total of 13 562 human lncRNAs were analyzed using RNAfold, and their orthologous sequences were searched against 16 mammalian genomes using Infernal. The potential orthologous genes, transposons and splicing signals of human lncRNAs were predicted to construct a lncRNA database with a updating mechanism. RESULTS: and CONCLUSION: The lncRNA database LongMan we constructed, which currently contains 133 646 orthologous lncRNAs, provides information of the sequences, alignments, transposons, and species-specific insertions and deletions and allows database search on combinatorial conditions, graphic display and data download. As the first large-scale mammalian orthologous lncRNA database, LongMan has important values in future comparative and functional studies of lncRNAs.\",\n \"corpus_id\": 25940287,\n \"score\": 2\n },\n {\n \"doc_id\": \"27623959\",\n \"title\": \"BmncRNAdb: a comprehensive database of non-coding RNAs in the silkworm, Bombyx mori.\",\n \"abstract\": \"BACKGROUND: Long non-coding RNAs (lncRNAs) may play critical roles in a wide range of developmental processes of higher organisms. Recently, lncRNAs have been widely identified across eukaryotes and many databases of lncRNAs have been developed for human, mouse, fruit fly, etc. However, there is rare information about them in the only completely domesticated insect, silkworm (Bombyx mori). DESCRIPTION: In this study, we systematically scanned lncRNAs using the available silkworm RNA-seq data and public unigenes. Finally, we identified and collected 6281 lncRNAs in the silkworm. Besides, we also collected 1986 microRNAs (miRNAs) from previous studies. Then, we organized them into a comprehensive and web-based database, BmncRNAdb. This database offers a user-friendly interface for data browse and online analysis as well as the three online tools for users to predict the target genes of lncRNA or miRNA. CONCLUSIONS: We have systematically identified and collected the silkworm lncRNAs and constructed a comprehensive database of the silkworm lncRNAs and miRNAs. This work gives a glimpse into lncRNAs of the silkworm and lays foundations for the ncRNAs study of the silkworm and other insects in the future. The BmncRNAdb is freely available at http://gene.cqu.edu.cn/BmncRNAdb/index.php .\",\n \"corpus_id\": 10835608,\n \"score\": 2\n },\n {\n \"doc_id\": \"27794554\",\n \"title\": \"RNAcentral: a comprehensive database of non-coding RNA sequences.\",\n \"abstract\": \"RNAcentral is a database of non-coding RNA (ncRNA) sequences that aggregates data from specialised ncRNA resources and provides a single entry point for accessing ncRNA sequences of all ncRNA types from all organisms. Since its launch in 2014, RNAcentral has integrated twelve new resources, taking the total number of collaborating database to 22, and began importing new types of data, such as modified nucleotides from MODOMICS and PDB. We created new species-specific identifiers that refer to unique RNA sequences within a context of single species. The website has been subject to continuous improvements focusing on text and sequence similarity searches as well as genome browsing functionality. All RNAcentral data is provided for free and is available for browsing, bulk downloads, and programmatic access at http://rnacentral.org/.\",\n \"corpus_id\": 36012271,\n \"score\": 2\n },\n {\n \"doc_id\": \"27899613\",\n \"title\": \"NSDNA: a manually curated database of experimentally supported ncRNAs associated with nervous system diseases.\",\n \"abstract\": \"The Nervous System Disease NcRNAome Atlas (NSDNA) (http://www.bio-bigdata.net/nsdna/) is a manually curated database that provides comprehensive experimentally supported associations about nervous system diseases (NSDs) and noncoding RNAs (ncRNAs). NSDs represent a common group of disorders, some of which are characterized by high morbidity and disabilities. The pathogenesis of NSDs at the molecular level remains poorly understood. ncRNAs are a large family of functionally important RNA molecules. Increasing evidence shows that diverse ncRNAs play a critical role in various NSDs. Mining and summarizing NSD-ncRNA association data can help researchers discover useful information. Hence, we developed an NSDNA database that documents 24 713 associations between 142 NSDs and 8593 ncRNAs in 11 species, curated from more than 1300 articles. This database provides a user-friendly interface for browsing and searching and allows for data downloading flexibility. In addition, NSDNA offers a submission page for researchers to submit novel NSD-ncRNA associations. It represents an extremely useful and valuable resource for researchers who seek to understand the functions and molecular mechanisms of ncRNA involved in NSDs.\",\n \"corpus_id\": 16204246,\n \"score\": 2\n },\n {\n \"doc_id\": \"27924020\",\n \"title\": \"LincSNP 2.0: an updated database for linking disease-associated SNPs to human long non-coding RNAs and their TFBSs.\",\n \"abstract\": \"We describe LincSNP 2.0 (http://bioinfo.hrbmu.edu.cn/LincSNP), an updated database that is used specifically to store and annotate disease-associated single nucleotide polymorphisms (SNPs) in human long non-coding RNAs (lncRNAs) and their transcription factor binding sites (TFBSs). In LincSNP 2.0, we have updated the database with more data and several new features, including (i) expanding disease-associated SNPs in human lncRNAs; (ii) identifying disease-associated SNPs in lncRNA TFBSs; (iii) updating LD-SNPs from the 1000 Genomes Project; and (iv) collecting more experimentally supported SNP-lncRNA-disease associations. Furthermore, we developed three flexible online tools to retrieve and analyze the data. Linc-Mart is a convenient way for users to customize their own data. Linc-Browse is a tool for all data visualization. Linc-Score predicts the associations between lncRNA and disease. In addition, we provided users a newly designed, user-friendly interface to search and download all the data in LincSNP 2.0 and we also provided an interface to submit novel data into the database. LincSNP 2.0 is a continually updated database and will serve as an important resource for investigating the functions and mechanisms of lncRNAs in human diseases.\",\n \"corpus_id\": 14509930,\n \"score\": 2\n },\n {\n \"doc_id\": \"29069510\",\n \"title\": \"Lnc2Meth: a manually curated database of regulatory relationships between long non-coding RNAs and DNA methylation associated with human disease.\",\n \"abstract\": \"Lnc2Meth (http://www.bio-bigdata.com/Lnc2Meth/), an interactive resource to identify regulatory relationships between human long non-coding RNAs (lncRNAs) and DNA methylation, is not only a manually curated collection and annotation of experimentally supported lncRNAs-DNA methylation associations but also a platform that effectively integrates tools for calculating and identifying the differentially methylated lncRNAs and protein-coding genes (PCGs) in diverse human diseases. The resource provides: (i) advanced search possibilities, e.g. retrieval of the database by searching the lncRNA symbol of interest, DNA methylation patterns, regulatory mechanisms and disease types; (ii) abundant computationally calculated DNA methylation array profiles for the lncRNAs and PCGs; (iii) the prognostic values for each hit transcript calculated from the patients clinical data; (iv) a genome browser to display the DNA methylation landscape of the lncRNA transcripts for a specific type of disease; (v) tools to re-annotate probes to lncRNA loci and identify the differential methylation patterns for lncRNAs and PCGs with user-supplied external datasets; (vi) an R package (LncDM) to complete the differentially methylated lncRNAs identification and visualization with local computers. Lnc2Meth provides a timely and valuable resource that can be applied to significantly expand our understanding of the regulatory relationships between lncRNAs and DNA methylation in various human diseases.\",\n \"corpus_id\": 52801074,\n \"score\": 2\n },\n {\n \"doc_id\": \"29077939\",\n \"title\": \"lncRNASNP2: an updated database of functional SNPs and mutations in human and mouse lncRNAs.\",\n \"abstract\": \"Long non-coding RNAs (lncRNAs) are emerging as important regulators in different biological processes through various ways. Because the related data, especially mutations in cancers, increased sharply, we updated the lncRNASNP to version 2 (http://bioinfo.life.hust.edu.cn/lncRNASNP2). lncRNASNP2 provides comprehensive information of SNPs and mutations in lncRNAs, as well as their impacts on lncRNA structure and function. lncRNASNP2 contains 7260238 SNPs on 141353 human lncRNA transcripts and 3921448 SNPs on 117405 mouse lncRNA transcripts. Besides the SNP information in the first version, the following new features were developed to improve the lncRNASNP2. ( i) noncoding variants from COSMIC cancer data (859534) in lncRNAs and their effects on lncRNA structure and function; (ii) TCGA cancer mutations (315234) in lncRNAs and their impacts; (iii) lncRNA expression profiling of 20 cancer types in both tumor and its adjacent samples; (iv) expanded lncRNA-associated diseases; (v) optimized the results about lncRNAs structure change induced by variants; (vi) reduced false positives in miRNA and lncRNA interaction results. Furthermore, we developed online tools for users to analyze new variants in lncRNA. We aim to maintain the lncRNASNP as a useful resource for lncRNAs and their variants.\",\n \"corpus_id\": 205234301,\n \"score\": 2\n },\n {\n \"doc_id\": \"29140524\",\n \"title\": \"NONCODEV5: a comprehensive annotation database for long non-coding RNAs.\",\n \"abstract\": \"NONCODE (http://www.bioinfo.org/noncode/) is a systematic database that is dedicated to presenting the most complete collection and annotation of non-coding RNAs (ncRNAs), especially long non-coding RNAs (lncRNAs). Since NONCODE 2016 was released two years ago, the amount of novel identified ncRNAs has been enlarged by the reduced cost of next-generation sequencing, which has produced an explosion of newly identified data. The third-generation sequencing revolution has also offered longer and more accurate annotations. Moreover, accumulating evidence confirmed by biological experiments has provided more comprehensive knowledge of lncRNA functions. The ncRNA data set was expanded by collecting newly identified ncRNAs from literature published over the past two years and integration of the latest versions of RefSeq and Ensembl. Additionally, pig was included in the database for the first time, bringing the total number of species to 17. The number of lncRNAs in NONCODEv5 increased from 527 336 to 548 640. NONCODEv5 also introduced three important new features: (i) human lncRNA-disease relationships and single nucleotide polymorphism-lncRNA-disease relationships were constructed; (ii) human exosome lncRNA expression profiles were displayed; (iii) the RNA secondary structures of NONCODE human transcripts were predicted. NONCODEv5 is also accessible through http://www.noncode.org/.\",\n \"corpus_id\": 205239047,\n \"score\": 2\n },\n {\n \"doc_id\": \"29382910\",\n \"title\": \"Lnc2Catlas: an atlas of long noncoding RNAs associated with risk of cancers.\",\n \"abstract\": \"Lnc2Catlas ( http://lnc2catlas.bioinfotech.org/ ) is an atlas of long noncoding RNAs (lncRNAs) associated with cancer risk. LncRNAs are a class of functional noncoding RNAs with lengths over 200 nt and play a vital role in diverse biological processes. Increasing evidence shows that lncRNA dysfunction is associated with many human cancers/diseases. It is therefore important to understand the underlying relationship between lncRNAs and cancers. To this end, we developed Lnc2Catlas to compile quantitative associations between lncRNAs and cancers using three computational methods, assessing secondary structure disruption, lncRNA-protein interactions, and co-expression networks. Lnc2Catlas was constructed based on 27,670 well-annotated lncRNAs, 31,749,216 SNPs, 1,473 cancer-associated proteins, and 10,539 expression profiles of 33 cancers from The Cancer Genome Atlas (TCGA). Lnc2Catlas contains 247,124 lncRNA-SNP pairs, over two millions lncRNA-protein interactions, and 6,902 co-expression clusters. We deposited Lnc2Catlas on Alibaba Cloud and developed interactive, mobile device-compatible, user-friendly interfaces to help users search and browse Lnc2Catlas with ultra-low latency. Lnc2Catlas can aid in the investigation of associations between lncRNAs and cancers and can provide candidate lncRNAs for further experimental validation. Lnc2Catlas will facilitate an understanding of the associations between lncRNAs and cancer and will help reveal the critical role of lncRNAs in cancer.\",\n \"corpus_id\": 19611746,\n \"score\": 2\n },\n {\n \"doc_id\": \"22976082\",\n \"title\": \"An RNA Mapping DataBase for curating RNA structure mapping experiments.\",\n \"abstract\": \"SUMMARY: We have established an RNA mapping database (RMDB) to enable structural, thermodynamic and kinetic comparisons across single-nucleotide-resolution RNA structure mapping experiments. The volume of structure mapping data has greatly increased since the development of high-throughput sequencing techniques, accelerated software pipelines and large-scale mutagenesis. For scientists wishing to infer relationships between RNA sequence/structure and these mapping data, there is a need for a database that is curated, tagged with error estimates and interfaced with tools for sharing, visualization, search and meta-analysis. Through its on-line front-end, the RMDB allows users to explore single-nucleotide-resolution mapping data in heat-map, bar-graph and colored secondary structure graphics; to leverage these data to generate secondary structure hypotheses; and to download the data in standardized and computer-friendly files, including the RDAT and community-consensus SNRNASM formats. At the time of writing, the database houses 53 entries, describing more than 2848 experiments of 1098 RNA constructs in several solution conditions and is growing rapidly. AVAILABILITY: Freely available on the web at http://rmdb.stanford.edu. CONTACT: rhiju@stanford.edu. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics Online.\",\n \"corpus_id\": 42068269,\n \"score\": 1\n },\n {\n \"doc_id\": \"23222637\",\n \"title\": \"Long non-coding RNAs and p53 regulation.\",\n \"abstract\": \"The advent of novel and high-throughput sequencing (next generation) technologies allowed for the sequencing of the genome at an unprecedented depth. The majority of transcribed RNAs have been classified as non-coding RNAs. Among them, long non-coding RNAs (lncRNAs) are emerging as important regulators in many biological processes. Here, we discuss the role of those lncRNAs which are under the control of p53 or that are able to regulate its activity, due to the central role of p53 pathway in many conditions. We also briefly discussed the emerging need of having novel strategies and computational tools to completely unravel the multifaceted roles of lncRNAs and to pave the way to the development of novel diagnostic and therapeutic applications based on these peculiar molecules.\",\n \"corpus_id\": 10065501,\n \"score\": 1\n },\n {\n \"doc_id\": \"23696037\",\n \"title\": \"On the classification of long non-coding RNAs.\",\n \"abstract\": \"Long non-coding RNAs (lncRNAs) have been found to perform various functions in a wide variety of important biological processes. To make easier interpretation of lncRNA functionality and conduct deep mining on these transcribed sequences, it is convenient to classify lncRNAs into different groups. Here, we summarize classification methods of lncRNAs according to their four major features, namely, genomic location and context, effect exerted on DNA sequences, mechanism of functioning and their targeting mechanism. In combination with the presently available function annotations, we explore potential relationships between different classification categories, and generalize and compare biological features of different lncRNAs within each category. Finally, we present our view on potential further studies. We believe that the classifications of lncRNAs as indicated above are of fundamental importance for lncRNA studies, helpful for further investigation of specific lncRNAs, for formulation of new hypothesis based on different features of lncRNA and for exploration of the underlying lncRNA functional mechanisms.\",\n \"corpus_id\": 16088764,\n \"score\": 1\n },\n {\n \"doc_id\": \"23829531\",\n \"title\": \"Identification and function of long non-coding RNAs.\",\n \"abstract\": \"It is now clear that eukaryotic cells produce many thousands of non-coding RNAs. The least well-studied of these are longer than 200 nt and are known as lncRNAs (long non-coding RNAs). These loci are of particular interest as their biological relevance remains uncertain. Sequencing projects have identified thousands of these loci in a variety of species, from flies to humans. Genome-wide scans for functionality, such as evolutionary and expression analyses, suggest that many of these molecules have functional roles to play in the cell. Nevertheless, only a handful of lncRNAs have been experimentally investigated, and most of these appear to possess roles in regulating gene expression at a variety of different levels. Several lncRNAs have also been implicated in cancer. This evidence suggests that lncRNAs represent a new class of non-coding gene whose importance should become clearer upon further experimental investigation.\",\n \"corpus_id\": 26130066,\n \"score\": 1\n },\n {\n \"doc_id\": \"24846995\",\n \"title\": \"[The emerging landscape of long non-coding RNAs].\",\n \"abstract\": \"With the completion of Human Genome Project (HGP), it was revealed that among the 3 billion base pairs in human genome, only 1.5% of them encodes proteins. The remaining 98.5% of the sequence does not encode any protein, and was once regarded as accumulated junk sequences during evolution. However, in the subsequently initiated ENCODE project, it was unexpectedly found that about 75% of the human genome was transcribed into RNAs. Seventy-four percent of them are non-protein-coding RNAs (non-coding RNAs, ncRNAs). In this RNA category, most of the transcripts are longer than 200 nucleotides and thus named as long non-coding RNAs (lncRNAs). ncRNAs regulate gene expression at the transcriptional and post-transcriptional levels, function in fundamental biological processes including cell differentiation and organ development, and are closely associated with many human diseases. In this paper, we review the recent progress in the discovery, classification, expression, and function study of lncRNAs, as well as their roles in the pathogenesis of hu-man diseases.\",\n \"corpus_id\": 41118558,\n \"score\": 1\n },\n {\n \"doc_id\": \"25881700\",\n \"title\": \"[Long non-coding RNAs in plants].\",\n \"abstract\": \"Long non-coding RNAs (lncRNAs), which are longer than 200 nucleotides in length, widely exist in organisms and function in a variety of biological processes. Currently, most of lncRNAs found in plants are transcribed by RNA polymerase Ⅱ and mediate gene expression through multiple mechanisms, such as target mimicry, transcription interference, histone methylation and DNA methylation, and play important roles in flowering, male sterility, nutrition metabolism, biotic and abiotic stress and other biological processes as regulators in plants. In this review, we summarize the databases, prediction methods, and possible functions of plant lncRNAs discovered in recent years.\",\n \"corpus_id\": 7412542,\n \"score\": 1\n },\n {\n \"doc_id\": \"25936895\",\n \"title\": \"Long non-coding RNAs and their biological roles in plants.\",\n \"abstract\": \"With the development of genomics and bioinformatics, especially the extensive applications of high-throughput sequencing technology, more transcriptional units with little or no protein-coding potential have been discovered. Such RNA molecules are called non-protein-coding RNAs (npcRNAs or ncRNAs). Among them, long npcRNAs or ncRNAs (lnpcRNAs or lncRNAs) represent diverse classes of transcripts longer than 200 nucleotides. In recent years, the lncRNAs have been considered as important regulators in many essential biological processes. In plants, although a large number of lncRNA transcripts have been predicted and identified in few species, our current knowledge of their biological functions is still limited. Here, we have summarized recent studies on their identification, characteristics, classification, bioinformatics, resources, and current exploration of their biological functions in plants.\",\n \"corpus_id\": 14966878,\n \"score\": 1\n },\n {\n \"doc_id\": \"25986218\",\n \"title\": \"Infectious long non-coding RNAs.\",\n \"abstract\": \"Long non protein coding RNAs (lncRNAs) constitute a large category of the RNA world, able to regulate different biological processes. In this review we are focusing on infectious lncRNAs, their classification, pathogenesis and impact on the infected organisms. Here they are presented in two separate groups: 'dependent lncRNAs' (comprising satellites RNA, Hepatitis D virus and lncRNAs of viral origin) which need a helper virus and 'independent lncRNAs' (viroids) that can self-replicate. Even though these lncRNA do not encode any protein, their structure and/or sequence comprise all the necessary information to drive specific interactions with host factors and regulate several cellular functions. These new data that have emerged during the last few years concerning lncRNAs modify the way we understand molecular biology's 'central dogma' and give new perspectives for applications and potential therapeutic strategies.\",\n \"corpus_id\": 8226183,\n \"score\": 1\n },\n {\n \"doc_id\": \"26117828\",\n \"title\": \"Evolutionary annotation of conserved long non-coding RNAs in major mammalian species.\",\n \"abstract\": \"Mammalian genomes contain tens of thousands of long non-coding RNAs (lncRNAs) that have been implicated in diverse biological processes. However, the lncRNA transcriptomes of most mammalian species have not been established, limiting the evolutionary annotation of these novel transcripts. Based on RNA sequencing data from six tissues of nine species, we built comprehensive lncRNA catalogs (4,142-42,558 lncRNAs) covering the major mammalian species. Compared to protein- coding RNAs, expression of lncRNAs exhibits striking lineage specificity. Notably, although 30%-99% human lncRNAs are conserved across different species on DNA locus level, only 20%-27% of these conserved lncRNA loci are detected to transcription, which represents a stark contrast to the proportion of conserved protein-coding genes (48%-80%). This finding provides a valuable resource for experimental scientists to study the mechanisms of lncRNAs. Moreover, we constructed lncRNA expression phylogenetic trees across nine mammals and demonstrated that lncRNA expression profiles can reliably determine phylogenic placement in a manner similar to their coding counterparts. Our data also reveal that the evolutionary rate of lncRNA expression varies among tissues and is significantly higher than those for protein-coding genes. To streamline the processes of browsing lncRNAs and detecting their evolutionary statuses, we integrate all the data produced in this study into a database named PhyloNONCODE (http://www.bioinfo.org/phyloNoncode). Our work starts to place mammalian lncRNAs in an evolutionary context and represent a rich resource for comparative and functional analyses of this critical layer of genome.\",\n \"corpus_id\": 15294020,\n \"score\": 1\n },\n {\n \"doc_id\": \"26183581\",\n \"title\": \"A potential signature of eight long non-coding RNAs predicts survival in patients with non-small cell lung cancer.\",\n \"abstract\": \"BACKGROUND: Accumulated evidence suggests that dysregulated expression of long non-coding RNAs (lncRNAs) may play a critical role in tumorigenesis and prognosis of cancer, indicating the potential utility of lncRNAs as cancer prognostic or diagnostic markers. However, the power of lncRNA signatures in predicting the survival of patients with non-small cell lung cancer (NSCLC) has not yet been investigated. METHODS: We performed an array-based transcriptional analysis of lncRNAs in large patient cohorts with NSCLC by repurposing microarray probes from the gene expression omnibus database. A risk score model was constructed based on the expression data of these eight lncRNAs in the training dataset of NSCLC patients and was subsequently validated in other two independent NSCLC datasets. The biological implications of prognostic lncRNAs were also analyzed using the functional enrichment analysis. RESULTS: An expression pattern of eight lncRNAs was found to be significantly associated with overall survival (OS) of NSCLC patients in the training dataset. With the eight-lncRNA signature, patients of the training dataset could be classified into high- and low-risk groups with significantly different OS (median survival 1.67 vs. 6.06 years, log-rank test p = 4.33E-09). The prognostic power of eight-lncRNA signature was further validated in other two non-overlapping independent NSCLC cohorts, demonstrating good reproducibility and robustness of this eight-lncRNA signature in predicting OS of NSCLC patients. Multivariate regression and stratified analysis suggested that the prognostic power of the eight-lncRNA signature was independent of clinical and pathological factors. Functional enrichment analyses revealed potential functional roles of the eight prognostic lncRNAs in tumorigenesis. CONCLUSIONS: These findings indicate that the eight-lncRNA signature may be an effective independent prognostic molecular biomarker in the prediction of NSCLC patient survival.\",\n \"corpus_id\": 8654442,\n \"score\": 1\n },\n {\n \"doc_id\": \"26424084\",\n \"title\": \"miRSponge: a manually curated database for experimentally supported miRNA sponges and ceRNAs.\",\n \"abstract\": \"In this study, we describe miRSponge, a manually curated database, which aims at providing an experimentally supported resource for microRNA (miRNA) sponges. Recent evidence suggests that miRNAs are themselves regulated by competing endogenous RNAs (ceRNAs) or 'miRNA sponges' that contain miRNA binding sites. These competitive molecules can sequester miRNAs to prevent them interacting with their natural targets to play critical roles in various biological and pathological processes. It has become increasingly important to develop a high quality database to record and store ceRNA data to support future studies. To this end, we have established the experimentally supported miRSponge database that contains data on 599 miRNA-sponge interactions and 463 ceRNA relationships from 11 species following manual curating from nearly 1200 published articles. Database classes include endogenously generated molecules including coding genes, pseudogenes, long non-coding RNAs and circular RNAs, along with exogenously introduced molecules including viral RNAs and artificial engineered sponges. Approximately 70% of the interactions were identified experimentally in disease states. miRSponge provides a user-friendly interface for convenient browsing, retrieval and downloading of dataset. A submission page is also included to allow researchers to submit newly validated miRNA sponge data. Database URL: http://www.bio-bigdata.net/miRSponge.\",\n \"corpus_id\": 17451032,\n \"score\": 1\n },\n {\n \"doc_id\": \"26481460\",\n \"title\": \"Global identification and analysis of long non-coding RNAs in diploid strawberry Fragaria vesca during flower and fruit development.\",\n \"abstract\": \"BACKGROUND: Long non-coding RNAs (lncRNAs) are a new class of regulatory molecules with roles in diverse biological processes. While much effort has been invested in the analysis of lncRNAs from established plant models Arabidopsis, maize, and rice, almost nothing is known about lncRNAs from fruit crops, including those in the Rosaceae family. RESULTS: Here, we present a genome-scale identification and characterization of lncRNAs from a diploid strawberry, Fragaria vesca, based on rich RNA-seq datasets from 35 different flower and fruit tissues. 5,884 Fve-lncRNAs derived from 3,862 loci were identified. These lncRNAs were carefully cataloged based on expression level and whether or not they contain repetitive sequences or generate small RNAs. About one fourth of them are termed high-confidence lncRNAs (hc-lncRNAs) because they are expressed at a level of FPKM higher than 2 and produce neither small RNAs nor contain repetitive sequence. To identify regulatory interactions between lncRNAs and their potential protein-coding (PC) gene targets, pairs of lncRNAs and PC genes with positively or negatively correlated expression trends were identified based on their expression; these pairs may be candidates of cis- or trans-acting lncRNAs and their targets. Finally, blast searches within plant species indicate that lncRNAs are not well conserved. CONCLUSIONS: Our study identifies a large number of tissue-specifically expressed lncRNAs in F. vesca, thereby highlighting their potential contributions to strawberry flower and fruit development and paving the way for future functional studies.\",\n \"corpus_id\": 6145679,\n \"score\": 1\n },\n {\n \"doc_id\": \"26683846\",\n \"title\": \"Comprehensive Identification of Long Non-coding RNAs in Purified Cell Types from the Brain Reveals Functional LncRNA in OPC Fate Determination.\",\n \"abstract\": \"Long non-coding RNAs (lncRNAs) (> 200 bp) play crucial roles in transcriptional regulation during numerous biological processes. However, it is challenging to comprehensively identify lncRNAs, because they are often expressed at low levels and with more cell-type specificity than are protein-coding genes. In the present study, we performed ab initio transcriptome reconstruction using eight purified cell populations from mouse cortex and detected more than 5000 lncRNAs. Predicting the functions of lncRNAs using cell-type specific data revealed their potential functional roles in Central Nervous System (CNS) development. We performed motif searches in ENCODE DNase I digital footprint data and Mouse ENCODE promoters to infer transcription factor (TF) occupancy. By integrating TF binding and cell-type specific transcriptomic data, we constructed a novel framework that is useful for systematically identifying lncRNAs that are potentially essential for brain cell fate determination. Based on this integrative analysis, we identified lncRNAs that are regulated during Oligodendrocyte Precursor Cell (OPC) differentiation from Neural Stem Cells (NSCs) and that are likely to be involved in oligodendrogenesis. The top candidate, lnc-OPC, shows highly specific expression in OPCs and remarkable sequence conservation among placental mammals. Interestingly, lnc-OPC is significantly up-regulated in glial progenitors from experimental autoimmune encephalomyelitis (EAE) mouse models compared to wild-type mice. OLIG2-binding sites in the upstream regulatory region of lnc-OPC were identified by ChIP (chromatin immunoprecipitation)-Sequencing and validated by luciferase assays. Loss-of-function experiments confirmed that lnc-OPC plays a functional role in OPC genesis. Overall, our results substantiated the role of lncRNA in OPC fate determination and provided an unprecedented data source for future functional investigations in CNS cell types. We present our datasets and analysis results via the interactive genome browser at our laboratory website that is freely accessible to the research community. This is the first lncRNA expression database of collective populations of glia, vascular cells, and neurons. We anticipate that these studies will advance the knowledge of this major class of non-coding genes and their potential roles in neurological development and diseases.\",\n \"corpus_id\": 18331444,\n \"score\": 1\n },\n {\n \"doc_id\": \"26969372\",\n \"title\": \"Integrating RNA-seq and ChIP-seq data to characterize long non-coding RNAs in Drosophila melanogaster.\",\n \"abstract\": \"BACKGROUND: Recent advances in sequencing technology have opened a new era in RNA studies. Novel types of RNAs such as long non-coding RNAs (lncRNAs) have been discovered by transcriptomic sequencing and some lncRNAs have been found to play essential roles in biological processes. However, only limited information is available for lncRNAs in Drosophila melanogaster, an important model organism. Therefore, the characterization of lncRNAs and identification of new lncRNAs in D. melanogaster is an important area of research. Moreover, there is an increasing interest in the use of ChIP-seq data (H3K4me3, H3K36me3 and Pol II) to detect signatures of active transcription for reported lncRNAs. RESULTS: We have developed a computational approach to identify new lncRNAs from two tissue-specific RNA-seq datasets using the poly(A)-enriched and the ribo-zero method, respectively. In our results, we identified 462 novel lncRNA transcripts, which we combined with 4137 previously published lncRNA transcripts into a curated dataset. We then utilized 61 RNA-seq and 32 ChIP-seq datasets to improve the annotation of the curated lncRNAs with regards to transcriptional direction, exon regions, classification, expression in the brain, possession of a poly(A) tail, and presence of conventional chromatin signatures. Furthermore, we used 30 time-course RNA-seq datasets and 32 ChIP-seq datasets to investigate whether the lncRNAs reported by RNA-seq have active transcription signatures. The results showed that more than half of the reported lncRNAs did not have chromatin signatures related to active transcription. To clarify this issue, we conducted RT-qPCR experiments and found that ~95.24% of the selected lncRNAs were truly transcribed, regardless of whether they were associated with active chromatin signatures or not. CONCLUSIONS: In this study, we discovered a large number of novel lncRNAs, which suggests that many remain to be identified in D. melanogaster. For the lncRNAs that are known, we improved their characterization by integrating a large number of sequencing datasets (93 sets in total) from multiple sources (lncRNAs, RNA-seq and ChIP-seq). The RT-qPCR experiments demonstrated that RNA-seq is a reliable platform to discover lncRNAs. This set of curated lncRNAs with improved annotations can serve as an important resource for investigating the function of lncRNAs in D. melanogaster.\",\n \"corpus_id\": 2600022,\n \"score\": 1\n },\n {\n \"doc_id\": \"27725737\",\n \"title\": \"circRNADb: A comprehensive database for human circular RNAs with protein-coding annotations.\",\n \"abstract\": \"It has been known that circular RNAs are widely expressed in human tissues and cells, and play important regulatory roles in physiological or pathological processes. However, there is lack of comprehensively annotated human circular RNAs database. In this study we established a circRNA database, named as circRNADb, containing 32,914 human exonic circRNAs carefully selected from diversified sources. The detailed information of the circRNA, including genomic information, exon splicing, genome sequence, internal ribosome entry site (IRES), open reading frame (ORF) and references were provided in circRNADb. In addition, circRNAs were found to be able to encode proteins, which have not been reported in any species. 16328 circRNAs were annotated to have ORF longer than 100 amino acids, of which 7170 have IRES elements. 46 circRNAs from 37 genes were found to have their corresponding proteins expressed according mass spectrometry. The database provides the function of data search, browse, download, submit and feedback for the user to study particular circular RNA of interest and update the database continually. circRNADb will be built to be a biological information platform for circRNA molecules and related biological functions in the future. The database can be freely available through the web server at http://reprod.njmu.edu.cn/circrnadb.\",\n \"corpus_id\": 802184,\n \"score\": 1\n },\n {\n \"doc_id\": \"28751672\",\n \"title\": \"The LncRNA Connectivity Map: Using LncRNA Signatures to Connect Small Molecules, LncRNAs, and Diseases.\",\n \"abstract\": \"Well characterized the connections among diseases, long non-coding RNAs (lncRNAs) and drugs are important for elucidating the key roles of lncRNAs in biological mechanisms in various biological states. In this study, we constructed a database called LNCmap (LncRNA Connectivity Map), available at http://www.bio-bigdata.com/LNCmap/ , to establish the correlations among diseases, physiological processes, and the action of small molecule therapeutics by attempting to describe all biological states in terms of lncRNA signatures. By reannotating the microarray data from the Connectivity Map database, the LNCmap obtained 237 lncRNA signatures of 5916 instances corresponding to 1262 small molecular drugs. We provided a user-friendly interface for the convenient browsing, retrieval and download of the database, including detailed information and the associations of drugs and corresponding affected lncRNAs. Additionally, we developed two enrichment analysis methods for users to identify candidate drugs for a particular disease by inputting the corresponding lncRNA expression profiles or an associated lncRNA list and then comparing them to the lncRNA signatures in our database. Overall, LNCmap could significantly improve our understanding of the biological roles of lncRNAs and provide a unique resource to reveal the connections among drugs, lncRNAs and diseases.\",\n \"corpus_id\": 2974869,\n \"score\": 1\n },\n {\n \"doc_id\": \"28974472\",\n \"title\": \"Stress2TF: a manually curated database of TF regulation in plant response to stress.\",\n \"abstract\": \"Considerable studies demonstrate that plant transcription factors (TFs) play key regulatory roles in abiotic/biotic stress conditions, such as drought and pathogen attack. However, there is no effort dedicated to curate experimentally validated stress-TF regulatory relationships from these individual reports into a central database, which put an obstacle in the exploration of stress-TF regulations in plants. To address this issue, we presented a literature-curated database 'Stress2TF' that currently documented 1533 regulatory relationships between 71 abiotic/biotic stresses and 558 TFs in 47 plant species. Each entry in Stress2TF contains detailed information about a stress-TF relationship such as plant name, stress name, TF and brief description of stress-TF relationship. Stress2TF provided a user-friendly interface for entry browse, search and download. In addition, a submission page and several useful tools (e.g., BLAST, network visualization) were integrated. Stress2TF may be a valuable resource for the research of stress-TF regulatory mechanisms in plants. Stress2TF is available at http://csgenomics.ahau.edu.cn/Stress2TF.\",\n \"corpus_id\": 34794340,\n \"score\": 1\n },\n {\n \"doc_id\": \"29053596\",\n \"title\": \"Elucidating the Role of Host Long Non-Coding RNA during Viral Infection: Challenges and Paths Forward.\",\n \"abstract\": \"Research over the past decade has clearly shown that long non-coding RNAs (lncRNAs) are functional. Many lncRNAs can be related to immunity and the host response to viral infection, but their specific functions remain largely elusive. The vast majority of lncRNAs are annotated with extremely limited knowledge and tend to be expressed at low levels, making ad hoc experimentation difficult. Changes to lncRNA expression during infection can be systematically profiled using deep sequencing; however, this often produces an intractable number of candidate lncRNAs, leaving no clear path forward. For these reasons, it is especially important to prioritize lncRNAs into high-confidence \\\"hits\\\" by utilizing multiple methodologies. Large scale perturbation studies may be used to screen lncRNAs involved in phenotypes of interest, such as resistance to viral infection. Single cell transcriptome sequencing quantifies cell-type specific lncRNAs that are less abundant in a mixture. When coupled with iterative experimental validations, new computational strategies for efficiently integrating orthogonal high-throughput data will likely be the driver for elucidating the functional role of lncRNAs during viral infection. This review highlights new high-throughput technologies and discusses the potential for integrative computational analysis to streamline the identification of infection-related lncRNAs and unveil novel targets for antiviral therapeutics.\",\n \"corpus_id\": 7715078,\n \"score\": 1\n },\n {\n \"doc_id\": \"29254923\",\n \"title\": \"Progress in long non-coding RNAs in animals.\",\n \"abstract\": \"Long non-coding RNAs (lncRNAs) are important transcripts that are more than 200 nucleotides in length, and distribute extensively in animal and plant genomes. Accumulated studies demonstrate that lncRNAs play critical roles in biological processes related to embryogenesis, muscle development, lipid deposition and immune responses. They assist protein complexes in translocating to appropriate locations and participate in regulating gene activation and inactivation. Recently, rapid progress of lncRNA research is emerging, largely due to molecular biological technologies and information developed in the human genome project and the Encyclopedia of DNA Elements (ENCODE) project. For example, a dwarf open reading frame (DWORF) encoded by an annotated lncRNA was reported to activate the SERCA pump. Moreover, small regulatory polypeptide of amino acid response (SPAR) encoded by lncRNA LINC00961 was found to regulate muscle regeneration. These new results have revealed a novel model that lncRNA regulates biological processes using its small peptide product. In this review, we summarize the characteristics, databases, biological functions and molecular regulatory models, as well as research interests of lncRNAs in the future.\",\n \"corpus_id\": 3738611,\n \"score\": 1\n },\n {\n \"doc_id\": \"29485610\",\n \"title\": \"High-Throughput Methods to Detect Long Non-Coding RNAs.\",\n \"abstract\": \"Increasing evidence suggests that the numbers of long non-coding RNAs (lncRNAs) are more than those of protein-coding genes in various organisms. Although the detection methods for lncRNAs are being increasingly established, there are advantages and disadvantages that exist for each method. In this opinion article, I highlight the differences between microarrays and RNA sequencing (RNA-seq) for the detection of lncRNAs. Compared to RNA-seq, microarrays are limited to the known sequences. However, the detection method as well as data analysis workflow is more established, which makes it easier to analyze the data for bench scientists without extensive knowledge about computer programming. In order to highlight the usage of microarrays over RNA-seq for the detection of lncRNAs, we are organizing a special issue for High-Throughput called \\\"Microarrays in Non-Coding RNAs Profiling\\\", which will include the specific usages of microarrays for lncRNAs.\",\n \"corpus_id\": 3588102,\n \"score\": 1\n },\n {\n \"doc_id\": \"29657289\",\n \"title\": \"Present Scenario of Long Non-Coding RNAs in Plants.\",\n \"abstract\": \"Small non-coding RNAs have been extensively studied in plants over the last decade. In contrast, genome-wide identification of plant long non-coding RNAs (lncRNAs) has recently gained momentum. LncRNAs are now being recognized as important players in gene regulation, and their potent regulatory roles are being studied comprehensively in eukaryotes. LncRNAs were first reported in humans in 1992. Since then, research in animals, particularly in humans, has rapidly progressed, and a vast amount of data has been generated, collected, and organized using computational approaches. Additionally, numerous studies have been conducted to understand the roles of these long RNA species in several diseases. However, the status of lncRNA investigation in plants lags behind that in animals (especially humans). Efforts are being made in this direction using computational tools and high-throughput sequencing technologies, such as the lncRNA microarray technique, RNA-sequencing (RNA-seq), RNA capture sequencing, (RNA CaptureSeq), etc. Given the current scenario, significant amounts of data have been produced regarding plant lncRNAs, and this amount is likely to increase in the subsequent years. In this review we have documented brief information about lncRNAs and their status of research in plants, along with the plant-specific resources/databases for information retrieval on lncRNAs.\",\n \"corpus_id\": 4712574,\n \"score\": 1\n },\n {\n \"doc_id\": \"29670884\",\n \"title\": \"Distinct and Modular Organization of Protein Interacting Sites in Long Non-coding RNAs.\",\n \"abstract\": \"Background: Long non-coding RNAs (lncRNAs), are being reported to be extensively involved in diverse regulatory roles and have exhibited numerous disease associations. LncRNAs modulate their function through interaction with other biomolecules in the cell including DNA, RNA, and proteins. The availability of genome-scale experimental datasets of RNA binding proteins (RBP) motivated us to understand the role of lncRNAs in terms of its interactions with these proteins. In the current report, we demonstrate a comprehensive study of interactions between RBP and lncRNAs at a transcriptome scale through extensive analysis of the crosslinking and immunoprecipitation (CLIP) experimental datasets available for 70 RNA binding proteins. Results: Our analysis suggests that density of interaction sites for these proteins was significantly higher for specific sub-classes of lncRNAs when compared to protein-coding transcripts. We also observe a positional preference of these RBPs across lncRNA and protein coding transcripts in addition to a significant co-occurrence of RBPs having similar functions, suggesting a modular organization of these elements across lncRNAs. Conclusion: The significant enrichment of RBP sites across some lncRNA classes is suggestive that these interactions might be important in understanding the functional role of lncRNA. We observed a significant enrichment of RBPs which are involved in functional roles such as silencing, splicing, mRNA processing, and transport, indicating the potential participation of lncRNAs in such processes.\",\n \"corpus_id\": 4565387,\n \"score\": 1\n },\n {\n \"doc_id\": \"21504869\",\n \"title\": \"Databases and resources for human small non-coding RNAs.\",\n \"abstract\": \"Recent advances in high-throughput sequencing have facilitated the genome-wide studies of small non-coding RNAs (sRNAs). Numerous studies have highlighted the role of various classes of sRNAs at different levels of gene regulation and disease. The fast growth of sequence data and the diversity of sRNA species have prompted the need to organise them in annotation databases. There are currently several databases that collect sRNA data. Various tools are provided for access, with special emphasis on the well-characterised family of micro-RNAs. The striking heterogeneity of the new classes of sRNAs and the lack of sufficient functional annotation, however, make integration of these datasets a difficult task. This review describes the currently available databases for human sRNAs that are accessible via the internet, and some of the large datasets for human sRNAs from high-throughput sequencing experiments that are so far only available as supplementary data in publications. Some of the main issues related to the integration and annotation of sRNA datasets are also discussed.\",\n \"corpus_id\": 43258,\n \"score\": 0\n },\n {\n \"doc_id\": \"22833525\",\n \"title\": \"RedoxDB--a curated database for experimentally verified protein oxidative modification.\",\n \"abstract\": \"SUMMARY: Redox regulation and signaling, which are involved in various cellular processes, have become one of the research focuses in the past decade. Cysteine thiol groups are particularly susceptible to post-translational modification, and their reversible oxidation is of critical role in redox regulation and signaling. With the tremendous improvement of techniques, hundreds of redox proteins along with their redox-sensitive cysteines have been reported, and the number is still fast growing. However, until now there is no database to accommodate the rapid accumulation of information on protein oxidative modification. Here we present RedoxDB-a manually curated database for experimentally validated redox proteins. RedoxDB (version 1.0) consists of two datasets (A and B, for proteins with or without verified modified cysteines, respectively) and includes 2157 redox proteins containing 2203 cysteine residues with oxidative modification. For each modified cysteine, the exact position, modification type and flanking sequence are provided. Additional information, including gene name, organism, sequence, literature references and links to UniProt and PDB, is also supplied. The database supports several functions including data search, blast and browsing. Bulk download of the entire dataset is also available. We expect that RedoxDB will be useful for both experimental studies and computational analyses of protein oxidative modification. AVAILABILITY: The database is freely available at: http://biocomputer.bio.cuhk.edu.hk/RedoxDB. CONTACT: djguo@cuhk.edu.hk SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics Online.\",\n \"corpus_id\": 15956955,\n \"score\": 0\n },\n {\n \"doc_id\": \"24214963\",\n \"title\": \"Manually curated database of rice proteins.\",\n \"abstract\": \"'Manually Curated Database of Rice Proteins' (MCDRP) available at http://www.genomeindia.org/biocuration is a unique curated database based on published experimental data. Semantic integration of scientific data is essential to gain a higher level of understanding of biological systems. Since the majority of scientific data is available as published literature, text mining is an essential step before the data can be integrated and made available for computer-based search in various databases. However, text mining is a tedious exercise and thus, there is a large gap in the data available in curated databases and published literature. Moreover, data in an experiment can be perceived from several perspectives, which may not reflect in the text-based curation. In order to address such issues, we have demonstrated the feasibility of digitizing the experimental data itself by creating a database on rice proteins based on in-house developed data curation models. Using these models data of individual experiments have been digitized with the help of universal ontologies. Currently, the database has data for over 1800 rice proteins curated from >4000 different experiments of over 400 research articles. Since every aspect of the experiment such as gene name, plant type, tissue and developmental stage has been digitized, experimental data can be rapidly accessed and integrated.\",\n \"corpus_id\": 12930216,\n \"score\": 0\n },\n {\n \"doc_id\": \"25776024\",\n \"title\": \"LMPID: a manually curated database of linear motifs mediating protein-protein interactions.\",\n \"abstract\": \"Linear motifs (LMs), used by a subset of all protein-protein interactions (PPIs), bind to globular receptors or domains and play an important role in signaling networks. LMPID (Linear Motif mediated Protein Interaction Database) is a manually curated database which provides comprehensive experimentally validated information about the LMs mediating PPIs from all organisms on a single platform. About 2200 entries have been compiled by detailed manual curation of PubMed abstracts, of which about 1000 LM entries were being annotated for the first time, as compared with the Eukaryotic LM resource. The users can submit their query through a user-friendly search page and browse the data in the alphabetical order of the bait gene names and according to the domains interacting with the LM. LMPID is freely accessible at http://bicresources.jcbose. ac.in/ssaha4/lmpid and contains 1750 unique LM instances found within 1181 baits interacting with 552 prey proteins. In summary, LMPID is an attempt to enrich the existing repertoire of resources available for studying the LMs implicated in PPIs and may help in understanding the patterns of LMs binding to a specific domain and develop prediction model to identify novel LMs specific to a domain and further able to predict inhibitors/modulators of PPI of interest.\",\n \"corpus_id\": 17433567,\n \"score\": 0\n },\n {\n \"doc_id\": \"26553799\",\n \"title\": \"DASHR: database of small human noncoding RNAs.\",\n \"abstract\": \"Small non-coding RNAs (sncRNAs) are highly abundant RNAs, typically <100 nucleotides long, that act as key regulators of diverse cellular processes. Although thousands of sncRNA genes are known to exist in the human genome, no single database provides searchable, unified annotation, and expression information for full sncRNA transcripts and mature RNA products derived from these larger RNAs. Here, we present the Database of small human noncoding RNAs (DASHR). DASHR contains the most comprehensive information to date on human sncRNA genes and mature sncRNA products. DASHR provides a simple user interface for researchers to view sequence and secondary structure, compare expression levels, and evidence of specific processing across all sncRNA genes and mature sncRNA products in various human tissues. DASHR annotation and expression data covers all major classes of sncRNAs including microRNAs (miRNAs), Piwi-interacting (piRNAs), small nuclear, nucleolar, cytoplasmic (sn-, sno-, scRNAs, respectively), transfer (tRNAs), and ribosomal RNAs (rRNAs). Currently, DASHR (v1.0) integrates 187 smRNA high-throughput sequencing (smRNA-seq) datasets with over 2.5 billion reads and annotation data from multiple public sources. DASHR contains annotations for ∼48 000 human sncRNA genes and mature sncRNA products, 82% of which are expressed in one or more of the curated tissues. DASHR is available at http://lisanwanglab.org/DASHR.\",\n \"corpus_id\": 2268890,\n \"score\": 0\n },\n {\n \"doc_id\": \"27374121\",\n \"title\": \"HPIDB 2.0: a curated database for host-pathogen interactions.\",\n \"abstract\": \"Identification and analysis of host-pathogen interactions (HPI) is essential to study infectious diseases. However, HPI data are sparse in existing molecular interaction databases, especially for agricultural host-pathogen systems. Therefore, resources that annotate, predict and display the HPI that underpin infectious diseases are critical for developing novel intervention strategies. HPIDB 2.0 (http://www.agbase.msstate.edu/hpi/main.html) is a resource for HPI data, and contains 45, 238 manually curated entries in the current release. Since the first description of the database in 2010, multiple enhancements to HPIDB data and interface services were made that are described here. Notably, HPIDB 2.0 now provides targeted biocuration of molecular interaction data. As a member of the International Molecular Exchange consortium, annotations provided by HPIDB 2.0 curators meet community standards to provide detailed contextual experimental information and facilitate data sharing. Moreover, HPIDB 2.0 provides access to rapidly available community annotations that capture minimum molecular interaction information to address immediate researcher needs for HPI network analysis. In addition to curation, HPIDB 2.0 integrates HPI from existing external sources and contains tools to infer additional HPI where annotated data are scarce. Compared to other interaction databases, our data collection approach ensures HPIDB 2.0 users access the most comprehensive HPI data from a wide range of pathogens and their hosts (594 pathogen and 70 host species, as of February 2016). Improvements also include enhanced search capacity, addition of Gene Ontology functional information, and implementation of network visualization. The changes made to HPIDB 2.0 content and interface ensure that users, especially agricultural researchers, are able to easily access and analyse high quality, comprehensive HPI data. All HPIDB 2.0 data are updated regularly, are publically available for direct download, and are disseminated to other molecular interaction resources. Database URL: http://www.agbase.msstate.edu/hpi/main.html.\",\n \"corpus_id\": 18761421,\n \"score\": 0\n }\n]","isConversational":false}}},{"rowIdx":71,"cells":{"query":{"kind":"string","value":"{\n \"doc_id\": \"27215190\",\n \"title\": \"A kernel-based clustering method for gene selection with gene expression data.\",\n \"abstract\": \"Gene selection is important for cancer classification based on gene expression data, because of high dimensionality and small sample size. In this paper, we present a new gene selection method based on clustering, in which dissimilarity measures are obtained through kernel functions. It searches for best weights of genes iteratively at the same time to optimize the clustering objective function. Adaptive distance is used in the process, which is suitable to learn the weights of genes during the clustering process, improving the performance of the algorithm. The proposed algorithm is simple and does not require any modification or parameter optimization for each dataset. We tested it on eight publicly available datasets, using two classifiers (support vector machine, k-nearest neighbor), compared with other six competitive feature selectors. The results show that the proposed algorithm is capable of achieving better accuracies and may be an efficient tool for finding possible biomarkers from gene expression data.\",\n \"corpus_id\": 6514989\n}"},"candidates":{"kind":"list like","value":[{"doc_id":"18366602","title":"A comparative study of different machine learning methods on microarray gene expression data.","abstract":"BACKGROUND: Several classification and feature selection methods have been studied for the identification of differentially expressed genes in microarray data. Classification methods such as SVM, RBF Neural Nets, MLP Neural Nets, Bayesian, Decision Tree and Random Forrest methods have been used in recent studies. The accuracy of these methods has been calculated with validation methods such as v-fold validation. However there is lack of comparison between these methods to find a better framework for classification, clustering and analysis of microarray gene expression results. RESULTS: In this study, we compared the efficiency of the classification methods including; SVM, RBF Neural Nets, MLP Neural Nets, Bayesian, Decision Tree and Random Forrest methods. The v-fold cross validation was used to calculate the accuracy of the classifiers. Some of the common clustering methods including K-means, DBC, and EM clustering were applied to the datasets and the efficiency of these methods have been analysed. Further the efficiency of the feature selection methods including support vector machine recursive feature elimination (SVM-RFE), Chi Squared, and CSF were compared. In each case these methods were applied to eight different binary (two class) microarray datasets. We evaluated the class prediction efficiency of each gene list in training and test cross-validation using supervised classifiers. CONCLUSIONS: We presented a study in which we compared some of the common used classification, clustering, and feature selection methods. We applied these methods to eight publicly available datasets, and compared how these methods performed in class prediction of test datasets. We reported that the choice of feature selection methods, the number of genes in the gene list, the number of cases (samples) substantially influence classification success. Based on features chosen by these methods, error rates and accuracy of several classification algorithms were obtained. Results revealed the importance of feature selection in accurately classifying new samples and how an integrated feature selection and classification algorithm is performing and is capable of identifying significant genes.","corpus_id":5422060,"score":2},{"doc_id":"19182978","title":"A two-stage feature selection method for gene expression data.","abstract":"Microarray data referencing gene expression profiles provide valuable answers to a variety of problems, and contributes to advances in clinical medicine. Gene expression data typically has a high dimension and a small sample size. Generally, only relatively small numbers of gene expression data are strongly correlated with a certain phenotype. To analyze gene expression profiles correctly, feature (gene) selection is crucial for classification. Feature (gene) selection has certain advantages, such as effective extraction of genes that influence classification accuracy, elimination of irrelevant genes, and improvement of the classification accuracy calculation. In this paper, we propose a two-stage feature selection method, which uses information gain to implement a gene-ranking process, and combines an improved particle swarm optimization with the K-nearest neighbor method and support vector machine classifiers to calculate the classification accuracy. The experimental results show that the proposed method can effectively select relevant gene subsets, and achieves higher classification accuracy than previous studies.","corpus_id":24680710,"score":2},{"doc_id":"19481202","title":"Simultaneous genes and training samples selection by modified particle swarm optimization for gene expression data classification.","abstract":"Gene expression datasets is a means to classify and predict the diagnostic categories of a patient. Informative genes and representative samples selection are two important aspects for reducing gene expression data. Identifying and pruning redundant genes and samples simultaneously can improve the performance of classification and circumvent the local optima problem. In the present paper, the modified particle swarm optimization was applied to selecting optimal genes and samples simultaneously and support vector machine was used as an objective function to determine the optimum set of genes and samples. To evaluate the performance of the new proposed method, it was applied to three publicly available microarray datasets. It has been demonstrated that the proposed method for gene and sample selection is a useful tool for mining high dimension data.","corpus_id":2761022,"score":2},{"doc_id":"20011240","title":"Feature selection and classification of MAQC-II breast cancer and multiple myeloma microarray gene expression data.","abstract":"Microarray data has a high dimension of variables but available datasets usually have only a small number of samples, thereby making the study of such datasets interesting and challenging. In the task of analyzing microarray data for the purpose of, e.g., predicting gene-disease association, feature selection is very important because it provides a way to handle the high dimensionality by exploiting information redundancy induced by associations among genetic markers. Judicious feature selection in microarray data analysis can result in significant reduction of cost while maintaining or improving the classification or prediction accuracy of learning machines that are employed to sort out the datasets. In this paper, we propose a gene selection method called Recursive Feature Addition (RFA), which combines supervised learning and statistical similarity measures. We compare our method with the following gene selection methods: Support Vector Machine Recursive Feature Elimination (SVMRFE), Leave-One-Out Calculation Sequential Forward Selection (LOOCSFS), Gradient based Leave-one-out Gene Selection (GLGS). To evaluate the performance of these gene selection methods, we employ several popular learning classifiers on the MicroArray Quality Control phase II on predictive modeling (MAQC-II) breast cancer dataset and the MAQC-II multiple myeloma dataset. Experimental results show that gene selection is strictly paired with learning classifier. Overall, our approach outperforms other compared methods. The biological functional analysis based on the MAQC-II breast cancer dataset convinced us to apply our method for phenotype prediction. Additionally, learning classifiers also play important roles in the classification of microarray data and our experimental results indicate that the Nearest Mean Scale Classifier (NMSC) is a good choice due to its prediction reliability and its stability across the three performance measurements: Testing accuracy, MCC values, and AUC errors.","corpus_id":2286996,"score":2},{"doc_id":"20051140","title":"ANMM4CBR: a case-based reasoning method for gene expression data classification.","abstract":"BACKGROUND: Accurate classification of microarray data is critical for successful clinical diagnosis and treatment. The \"curse of dimensionality\" problem and noise in the data, however, undermines the performance of many algorithms. METHOD: In order to obtain a robust classifier, a novel Additive Nonparametric Margin Maximum for Case-Based Reasoning (ANMM4CBR) method is proposed in this article. ANMM4CBR employs a case-based reasoning (CBR) method for classification. CBR is a suitable paradigm for microarray analysis, where the rules that define the domain knowledge are difficult to obtain because usually only a small number of training samples are available. Moreover, in order to select the most informative genes, we propose to perform feature selection via additively optimizing a nonparametric margin maximum criterion, which is defined based on gene pre-selection and sample clustering. Our feature selection method is very robust to noise in the data. RESULTS: The effectiveness of our method is demonstrated on both simulated and real data sets. We show that the ANMM4CBR method performs better than some state-of-the-art methods such as support vector machine (SVM) and k nearest neighbor (kNN), especially when the data contains a high level of noise. AVAILABILITY: The source code is attached as an additional file of this paper.","corpus_id":253190,"score":2},{"doc_id":"21135434","title":"Feature Selection and Kernel Learning for Local Learning-Based Clustering.","abstract":"The performance of the most clustering algorithms highly relies on the representation of data in the input space or the Hilbert space of kernel methods. This paper is to obtain an appropriate data representation through feature selection or kernel learning within the framework of the Local Learning-Based Clustering (LLC) (Wu and Schölkopf 2006) method, which can outperform the global learning-based ones when dealing with the high-dimensional data lying on manifold. Specifically, we associate a weight to each feature or kernel and incorporate it into the built-in regularization of the LLC algorithm to take into account the relevance of each feature or kernel for the clustering. Accordingly, the weights are estimated iteratively in the clustering process. We show that the resulting weighted regularization with an additional constraint on the weights is equivalent to a known sparse-promoting penalty. Hence, the weights of those irrelevant features or kernels can be shrunk toward zero. Extensive experiments show the efficacy of the proposed methods on the benchmark data sets.","corpus_id":18787586,"score":2},{"doc_id":"21241823","title":"An efficient statistical feature selection approach for classification of gene expression data.","abstract":"Classification of gene expression data plays a significant role in prediction and diagnosis of diseases. Gene expression data has a special characteristic that there is a mismatch in gene dimension as opposed to sample dimension. All genes do not contribute for efficient classification of samples. A robust feature selection algorithm is required to identify the important genes which help in classifying the samples efficiently. In order to select informative genes (features) based on relevance and redundancy characteristics, many feature selection algorithms have been introduced in the past. Most of the earlier algorithms require computationally expensive search strategy to find an optimal feature subset. Existing feature selection methods are also sensitive to the evaluation measures. The paper introduces a novel and efficient feature selection approach based on statistically defined effective range of features for every class termed as ERGS (Effective Range based Gene Selection). The basic principle behind ERGS is that higher weight is given to the feature that discriminates the classes clearly. Experimental results on well-known gene expression datasets illustrate the effectiveness of the proposed approach. Two popular classifiers viz. Nave Bayes Classifier (NBC) and Support Vector Machine (SVM) have been used for classification. The proposed feature selection algorithm can be helpful in ranking the genes and also is capable of identifying the most relevant genes responsible for diseases like leukemia, colon tumor, lung cancer, diffuse large B-cell lymphoma (DLBCL), prostate cancer.","corpus_id":42114809,"score":2},{"doc_id":"21376310","title":"A hybrid feature selection method for DNA microarray data.","abstract":"Gene expression profiles, which represent the state of a cell at a molecular level, have great potential as a medical diagnosis tool. In cancer classification, available training data sets are generally of a fairly small sample size compared to the number of genes involved. Along with training data limitations, this constitutes a challenge to certain classification methods. Feature (gene) selection can be used to successfully extract those genes that directly influence classification accuracy and to eliminate genes which have no influence on it. This significantly improves calculation performance and classification accuracy. In this paper, correlation-based feature selection (CFS) and the Taguchi-genetic algorithm (TGA) method were combined into a hybrid method, and the K-nearest neighbor (KNN) with the leave-one-out cross-validation (LOOCV) method served as a classifier for eleven classification profiles to calculate the classification accuracy. Experimental results show that the proposed method reduced redundant features effectively and achieved superior classification accuracy. The classification accuracy obtained by the proposed method was higher in ten out of the eleven gene expression data set test problems when compared to other classification methods from the literature.","corpus_id":13279505,"score":2},{"doc_id":"22369383","title":"Gene selection and classification for cancer microarray data based on machine learning and similarity measures.","abstract":"BACKGROUND: Microarray data have a high dimension of variables and a small sample size. In microarray data analyses, two important issues are how to choose genes, which provide reliable and good prediction for disease status, and how to determine the final gene set that is best for classification. Associations among genetic markers mean one can exploit information redundancy to potentially reduce classification cost in terms of time and money. RESULTS: To deal with redundant information and improve classification, we propose a gene selection method, Recursive Feature Addition, which combines supervised learning and statistical similarity measures. To determine the final optimal gene set for prediction and classification, we propose an algorithm, Lagging Prediction Peephole Optimization. By using six benchmark microarray gene expression data sets, we compared Recursive Feature Addition with recently developed gene selection methods: Support Vector Machine Recursive Feature Elimination, Leave-One-Out Calculation Sequential Forward Selection and several others. CONCLUSIONS: On average, with the use of popular learning machines including Nearest Mean Scaled Classifier, Support Vector Machine, Naive Bayes Classifier and Random Forest, Recursive Feature Addition outperformed other methods. Our studies also showed that Lagging Prediction Peephole Optimization is superior to random strategy; Recursive Feature Addition with Lagging Prediction Peephole Optimization obtained better testing accuracies than the gene selection method varSelRF.","corpus_id":8591392,"score":2},{"doc_id":"23075381","title":"Combining multiple hypothesis testing and affinity propagation clustering leads to accurate, robust and sample size independent classification on gene expression data.","abstract":"BACKGROUND: A feature selection method in microarray gene expression data should be independent of platform, disease and dataset size. Our hypothesis is that among the statistically significant ranked genes in a gene list, there should be clusters of genes that share similar biological functions related to the investigated disease. Thus, instead of keeping N top ranked genes, it would be more appropriate to define and keep a number of gene cluster exemplars. RESULTS: We propose a hybrid FS method (mAP-KL), which combines multiple hypothesis testing and affinity propagation (AP)-clustering algorithm along with the Krzanowski & Lai cluster quality index, to select a small yet informative subset of genes. We applied mAP-KL on real microarray data, as well as on simulated data, and compared its performance against 13 other feature selection approaches. Across a variety of diseases and number of samples, mAP-KL presents competitive classification results, particularly in neuromuscular diseases, where its overall AUC score was 0.91. Furthermore, mAP-KL generates concise yet biologically relevant and informative N-gene expression signatures, which can serve as a valuable tool for diagnostic and prognostic purposes, as well as a source of potential disease biomarkers in a broad range of diseases. CONCLUSIONS: mAP-KL is a data-driven and classifier-independent hybrid feature selection method, which applies to any disease classification problem based on microarray data, regardless of the available samples. Combining multiple hypothesis testing and AP leads to subsets of genes, which classify unknown samples from both, small and large patient cohorts with high accuracy.","corpus_id":15805933,"score":2},{"doc_id":"23148517","title":"Improving accuracy for cancer classification with a new algorithm for genes selection.","abstract":"BACKGROUND: Even though the classification of cancer tissue samples based on gene expression data has advanced considerably in recent years, it faces great challenges to improve accuracy. One of the challenges is to establish an effective method that can select a parsimonious set of relevant genes. So far, most methods for gene selection in literature focus on screening individual or pairs of genes without considering the possible interactions among genes. Here we introduce a new computational method named the Binary Matrix Shuffling Filter (BMSF). It not only overcomes the difficulty associated with the search schemes of traditional wrapper methods and overfitting problem in large dimensional search space but also takes potential gene interactions into account during gene selection. This method, coupled with Support Vector Machine (SVM) for implementation, often selects very small number of genes for easy model interpretability. RESULTS: We applied our method to 9 two-class gene expression datasets involving human cancers. During the gene selection process, the set of genes to be kept in the model was recursively refined and repeatedly updated according to the effect of a given gene on the contributions of other genes in reference to their usefulness in cancer classification. The small number of informative genes selected from each dataset leads to significantly improved leave-one-out (LOOCV) classification accuracy across all 9 datasets for multiple classifiers. Our method also exhibits broad generalization in the genes selected since multiple commonly used classifiers achieved either equivalent or much higher LOOCV accuracy than those reported in literature. CONCLUSIONS: Evaluation of a gene's contribution to binary cancer classification is better to be considered after adjusting for the joint effect of a large number of other genes. A computationally efficient search scheme was provided to perform effective search in the extensive feature space that includes possible interactions of many genes. Performance of the algorithm applied to 9 datasets suggests that it is possible to improve the accuracy of cancer classification by a big margin when joint effects of many genes are considered.","corpus_id":15467622,"score":2},{"doc_id":"25048512","title":"A kernel-based multivariate feature selection method for microarray data classification.","abstract":"High dimensionality and small sample sizes, and their inherent risk of overfitting, pose great challenges for constructing efficient classifiers in microarray data classification. Therefore a feature selection technique should be conducted prior to data classification to enhance prediction performance. In general, filter methods can be considered as principal or auxiliary selection mechanism because of their simplicity, scalability, and low computational complexity. However, a series of trivial examples show that filter methods result in less accurate performance because they ignore the dependencies of features. Although few publications have devoted their attention to reveal the relationship of features by multivariate-based methods, these methods describe relationships among features only by linear methods. While simple linear combination relationship restrict the improvement in performance. In this paper, we used kernel method to discover inherent nonlinear correlations among features as well as between feature and target. Moreover, the number of orthogonal components was determined by kernel Fishers linear discriminant analysis (FLDA) in a self-adaptive manner rather than by manual parameter settings. In order to reveal the effectiveness of our method we performed several experiments and compared the results between our method and other competitive multivariate-based features selectors. In our comparison, we used two classifiers (support vector machine, [Formula: see text]-nearest neighbor) on two group datasets, namely two-class and multi-class datasets. Experimental results demonstrate that the performance of our method is better than others, especially on three hard-classify datasets, namely Wang's Breast Cancer, Gordon's Lung Adenocarcinoma and Pomeroy's Medulloblastoma.","corpus_id":10248536,"score":2},{"doc_id":"25912984","title":"Improving PLS-RFE based gene selection for microarray data classification.","abstract":"Gene selection plays a crucial role in constructing efficient classifiers for microarray data classification, since microarray data is characterized by high dimensionality and small sample sizes and contains irrelevant and redundant genes. In practical use, partial least squares-based gene selection approaches can obtain gene subsets of good qualities, but are considerably time-consuming. In this paper, we propose to integrate partial least squares based recursive feature elimination (PLS-RFE) with two feature elimination schemes: simulated annealing and square root, respectively, to speed up the feature selection process. Inspired from the strategy of annealing schedule, the two proposed approaches eliminate a number of features rather than one least informative feature during each iteration and the number of removed features decreases as the iteration proceeds. To verify the effectiveness and efficiency of the proposed approaches, we perform extensive experiments on six publicly available microarray data with three typical classifiers, including Naïve Bayes, K-Nearest-Neighbor and Support Vector Machine, and compare our approaches with ReliefF, PLS and PLS-RFE feature selectors in terms of classification accuracy and running time. Experimental results demonstrate that the two proposed approaches accelerate the feature selection process impressively without degrading the classification accuracy and obtain more compact feature subsets for both two-category and multi-category problems. Further experimental comparisons in feature subset consistency show that the proposed approach with simulated annealing scheme not only has better time performance, but also obtains slightly better feature subset consistency than the one with square root scheme.","corpus_id":23269611,"score":2},{"doc_id":"25961028","title":"mRMR-ABC: A Hybrid Gene Selection Algorithm for Cancer Classification Using Microarray Gene Expression Profiling.","abstract":"An artificial bee colony (ABC) is a relatively recent swarm intelligence optimization approach. In this paper, we propose the first attempt at applying ABC algorithm in analyzing a microarray gene expression profile. In addition, we propose an innovative feature selection algorithm, minimum redundancy maximum relevance (mRMR), and combine it with an ABC algorithm, mRMR-ABC, to select informative genes from microarray profile. The new approach is based on a support vector machine (SVM) algorithm to measure the classification accuracy for selected genes. We evaluate the performance of the proposed mRMR-ABC algorithm by conducting extensive experiments on six binary and multiclass gene expression microarray datasets. Furthermore, we compare our proposed mRMR-ABC algorithm with previously known techniques. We reimplemented two of these techniques for the sake of a fair comparison using the same parameters. These two techniques are mRMR when combined with a genetic algorithm (mRMR-GA) and mRMR when combined with a particle swarm optimization algorithm (mRMR-PSO). The experimental results prove that the proposed mRMR-ABC algorithm achieves accurate classification performance using small number of predictive genes when tested using both datasets and compared to previously suggested methods. This shows that mRMR-ABC is a promising approach for solving gene selection and cancer classification problems.","corpus_id":14702825,"score":2},{"doc_id":"26159165","title":"Optimal combination of feature selection and classification via local hyperplane based learning strategy.","abstract":"BACKGROUND: Classifying cancers by gene selection is among the most important and challenging procedures in biomedicine. A major challenge is to design an effective method that eliminates irrelevant, redundant, or noisy genes from the classification, while retaining all of the highly discriminative genes. RESULTS: We propose a gene selection method, called local hyperplane-based discriminant analysis (LHDA). LHDA adopts two central ideas. First, it uses a local approximation rather than global measurement; second, it embeds a recently reported classification model, K-Local Hyperplane Distance Nearest Neighbor(HKNN) classifier, into its discriminator. Through classification accuracy-based iterations, LHDA obtains the feature weight vector and finally extracts the optimal feature subset. The performance of the proposed method is evaluated in extensive experiments on synthetic and real microarray benchmark datasets. Eight classical feature selection methods, four classification models and two popular embedded learning schemes, including k-nearest neighbor (KNN), hyperplane k-nearest neighbor (HKNN), Support Vector Machine (SVM) and Random Forest are employed for comparisons. CONCLUSION: The proposed method yielded comparable to or superior performances to seven state-of-the-art models. The nice performance demonstrate the superiority of combining feature weighting with model learning into an unified framework to achieve the two tasks simultaneously.","corpus_id":21786887,"score":2},{"doc_id":"26298581","title":"A Filter Feature Selection Method Based on MFA Score and Redundancy Excluding and It's Application to Tumor Gene Expression Data Analysis.","abstract":"Feature selection techniques have been widely applied to tumor gene expression data analysis in recent years. A filter feature selection method named marginal Fisher analysis score (MFA score) which is based on graph embedding has been proposed, and it has been widely used mainly because it is superior to Fisher score. Considering the heavy redundancy in gene expression data, we proposed a new filter feature selection technique in this paper. It is named MFA score+ and is based on MFA score and redundancy excluding. We applied it to an artificial dataset and eight tumor gene expression datasets to select important features and then used support vector machine as the classifier to classify the samples. Compared with MFA score, t test and Fisher score, it achieved higher classification accuracy.","corpus_id":14706675,"score":2},{"doc_id":"26405958","title":"An effective fuzzy kernel clustering analysis approach for gene expression data.","abstract":"Fuzzy clustering is an important tool for analyzing microarray data. A major problem in applying fuzzy clustering method to microarray gene expression data is the choice of parameters with cluster number and centers. This paper proposes a new approach to fuzzy kernel clustering analysis (FKCA) that identifies desired cluster number and obtains more steady results for gene expression data. First of all, to optimize characteristic differences and estimate optimal cluster number, Gaussian kernel function is introduced to improve spectrum analysis method (SAM). By combining subtractive clustering with max-min distance mean, maximum distance method (MDM) is proposed to determine cluster centers. Then, the corresponding steps of improved SAM (ISAM) and MDM are given respectively, whose superiority and stability are illustrated through performing experimental comparisons on gene expression data. Finally, by introducing ISAM and MDM into FKCA, an effective improved FKCA algorithm is proposed. Experimental results from public gene expression data and UCI database show that the proposed algorithms are feasible for cluster analysis, and the clustering accuracy is higher than the other related clustering algorithms.","corpus_id":28176899,"score":2},{"doc_id":"27056739","title":"A centroid-based gene selection method for microarray data classification.","abstract":"For classification problems based on microarray data, the data typically contains a large number of irrelevant and redundant features. In this paper, a new gene selection method is proposed to choose the best subset of features for microarray data with the irrelevant and redundant features removed. We formulate the selection problem as a L1-regularized optimization problem, based on a newly defined linear discriminant analysis criterion. Instead of calculating the mean of the samples, a kernel-based approach is used to estimate the class centroid to define both the between-class separability and the within-class compactness for the criterion. Theoretical analysis indicates that the global optimal solution of the L1-regularized criterion can be reached with a general condition, on which an efficient algorithm is derived to the feature selection problem in a linear time complexity with respect to the number of features and the number of samples. The experimental results on ten publicly available microarray datasets demonstrate that the proposed method performs effectively and competitively compared with state-of-the-art methods.","corpus_id":8969124,"score":2},{"doc_id":"18023261","title":"Improved binary PSO for feature selection using gene expression data.","abstract":"Gene expression profiles, which represent the state of a cell at a molecular level, have great potential as a medical diagnosis tool. Compared to the number of genes involved, available training data sets generally have a fairly small sample size in cancer type classification. These training data limitations constitute a challenge to certain classification methodologies. A reliable selection method for genes relevant for sample classification is needed in order to speed up the processing rate, decrease the predictive error rate, and to avoid incomprehensibility due to the large number of genes investigated. Improved binary particle swarm optimization (IBPSO) is used in this study to implement feature selection, and the K-nearest neighbor (K-NN) method serves as an evaluator of the IBPSO for gene expression data classification problems. Experimental results show that this method effectively simplifies feature selection and reduces the total number of features needed. The classification accuracy obtained by the proposed method has the highest classification accuracy in nine of the 11 gene expression data test problems, and is comparative to the classification accuracy of the two other test problems, as compared to the best results previously published.","corpus_id":27641839,"score":1},{"doc_id":"18334459","title":"A combination of rough-based feature selection and RBF neural network for classification using gene expression data.","abstract":"This paper presents a novel rough-based feature selection method for gene expression data analysis. It can find the relevant features without requiring the number of clusters to be known a priori and identify the centers that approximate to the correct ones. In this paper, we attempt to introduce a prediction scheme that combines the rough-based feature selection method with radial basis function neural network. For further consider the effect of different feature selection methods and classifiers on this prediction process, we use the NaIve Bayes and linear support vector machine as classifiers, and compare the performance with other feature selection methods, including information gain and principle component analysis. We demonstrate the performance by several published datasets and the results show that our proposed method can achieve high classification accuracy rate.","corpus_id":2076812,"score":1},{"doc_id":"18534831","title":"Medical data mining by fuzzy modeling with selected features.","abstract":"OBJECTIVE: Medical data is often very high dimensional. Depending upon the use, some data dimensions might be more relevant than others. In processing medical data, choosing the optimal subset of features is such important, not only to reduce the processing cost but also to improve the usefulness of the model built from the selected data. This paper presents a data mining study of medical data with fuzzy modeling methods that use feature subsets selected by some indices/methods. METHODS: Specifically, three fuzzy modeling methods including the fuzzy k-nearest neighbor algorithm, a fuzzy clustering-based modeling, and the adaptive network-based fuzzy inference system are employed. For feature selection, a total of 11 indices/methods are used. Medical data mined include the Wisconsin breast cancer dataset and the Pima Indians diabetes dataset. The classification accuracy and computational time are reported. To show how good the best performer is, the globally optimal was also found by carrying out an exhaustive testing of all possible combinations of feature subsets with three features. RESULTS: For the Wisconsin breast cancer dataset, the best accuracy of 97.17% was obtained, which is only 0.25% lower than that was obtained by exhaustive testing. For the Pima Indians diabetes dataset, the best accuracy of 77.65% was obtained, which is only 0.13% lower than that obtained by exhaustive testing. CONCLUSION: This paper has shown that feature selection is important to mining medical data for reducing processing time and for increasing classification accuracy. However, not all combinations of feature selection and modeling methods are equally effective and the best combination is often data-dependent, as supported by the breast cancer and diabetes data analyzed in this paper.","corpus_id":22988546,"score":1},{"doc_id":"19154590","title":"Combining Pareto-optimal clusters using supervised learning for identifying co-expressed genes.","abstract":"BACKGROUND: The landscape of biological and biomedical research is being changed rapidly with the invention of microarrays which enables simultaneous view on the transcription levels of a huge number of genes across different experimental conditions or time points. Using microarray data sets, clustering algorithms have been actively utilized in order to identify groups of co-expressed genes. This article poses the problem of fuzzy clustering in microarray data as a multiobjective optimization problem which simultaneously optimizes two internal fuzzy cluster validity indices to yield a set of Pareto-optimal clustering solutions. Each of these clustering solutions possesses some amount of information regarding the clustering structure of the input data. Motivated by this fact, a novel fuzzy majority voting approach is proposed to combine the clustering information from all the solutions in the resultant Pareto-optimal set. This approach first identifies the genes which are assigned to some particular cluster with high membership degree by most of the Pareto-optimal solutions. Using this set of genes as the training set, the remaining genes are classified by a supervised learning algorithm. In this work, we have used a Support Vector Machine (SVM) classifier for this purpose. RESULTS: The performance of the proposed clustering technique has been demonstrated on five publicly available benchmark microarray data sets, viz., Yeast Sporulation, Yeast Cell Cycle, Arabidopsis Thaliana, Human Fibroblasts Serum and Rat Central Nervous System. Comparative studies of the use of different SVM kernels and several widely used microarray clustering techniques are reported. Moreover, statistical significance tests have been carried out to establish the statistical superiority of the proposed clustering approach. Finally, biological significance tests have been carried out using a web based gene annotation tool to show that the proposed method is able to produce biologically relevant clusters of co-expressed genes. CONCLUSION: The proposed clustering method has been shown to perform better than other well-known clustering algorithms in finding clusters of co-expressed genes efficiently. The clusters of genes produced by the proposed technique are also found to be biologically significant, i.e., consist of genes which belong to the same functional groups. This indicates that the proposed clustering method can be used efficiently to identify co-expressed genes in microarray gene expression data. Supplementary Website The pre-processed and normalized data sets, the matlab code and other related materials are available at http://anirbanmukhopadhyay.50webs.com/mogasvm.html.","corpus_id":1788029,"score":1},{"doc_id":"19426455","title":"A kernel-based approach for detecting outliers of high-dimensional biological data.","abstract":"BACKGROUND: In many cases biomedical data sets contain outliers that make it difficult to achieve reliable knowledge discovery. Data analysis without removing outliers could lead to wrong results and provide misleading information. RESULTS: We propose a new outlier detection method based on Kullback-Leibler (KL) divergence. The original concept of KL divergence was designed as a measure of distance between two distributions. Stemming from that, we extend it to biological sample outlier detection by forming sample sets composed of nearest neighbors. KL divergence is defined between two sample sets with and without the test sample. To handle the non-linearity of sample distribution, original data is mapped into a higher feature space. We address the singularity problem due to small sample size during KL divergence calculation. Kernel functions are applied to avoid direct use of mapping functions. The performance of the proposed method is demonstrated on a synthetic data set, two public microarray data sets, and a mass spectrometry data set for liver cancer study. Comparative studies with Mahalanobis distance based method and one-class support vector machine (SVM) are reported showing that the proposed method performs better in finding outliers. CONCLUSION: Our idea was derived from Markov blanket algorithm that is a feature selection method based on KL divergence. That is, while Markov blanket algorithm removes redundant and irrelevant features, our proposed method detects outliers. Compared to other algorithms, our proposed method shows better or comparable performance for small sample and high-dimensional biological data. This indicates that the proposed method can be used to detect outliers in biological data sets.","corpus_id":10383228,"score":1},{"doc_id":"19525203","title":"A new approach for clustering gene expression time series data.","abstract":"Identifying groups of genes that manifest similar expression patterns is crucial in the analysis of gene expression time series data. Choosing a similarity measure to determine the similarity or distance between profiles is an important task. This paper proposes a suitable dissimilarity measure for gene expression time series data sets. It also presents a graph-based clustering method for finding clusters in gene expression time series data using the new dissimilarity measure. A comparison with other similarity measures used for gene expression data is presented; the new dissimilarity measure is found effective. The clustering method is used in experiments that use real-life datasets and has been found to perform satisfactorily.","corpus_id":8007902,"score":1},{"doc_id":"19594880","title":"Comparison of feature selection and classification for MALDI-MS data.","abstract":"INTRODUCTION: In the classification of Mass Spectrometry (MS) proteomics data, peak detection, feature selection, and learning classifiers are critical to classification accuracy. To better understand which methods are more accurate when classifying data, some publicly available peak detection algorithms for Matrix assisted Laser Desorption Ionization Mass Spectrometry (MALDI-MS) data were recently compared; however, the issue of different feature selection methods and different classification models as they relate to classification performance has not been addressed. With the application of intelligent computing, much progress has been made in the development of feature selection methods and learning classifiers for the analysis of high-throughput biological data. The main objective of this paper is to compare the methods of feature selection and different learning classifiers when applied to MALDI-MS data and to provide a subsequent reference for the analysis of MS proteomics data. RESULTS: We compared a well-known method of feature selection, Support Vector Machine Recursive Feature Elimination (SVMRFE), and a recently developed method, Gradient based Leave-one-out Gene Selection (GLGS) that effectively performs microarray data analysis. We also compared several learning classifiers including K-Nearest Neighbor Classifier (KNNC), Naïve Bayes Classifier (NBC), Nearest Mean Scaled Classifier (NMSC), uncorrelated normal based quadratic Bayes Classifier recorded as UDC, Support Vector Machines, and a distance metric learning for Large Margin Nearest Neighbor classifier (LMNN) based on Mahanalobis distance. To compare, we conducted a comprehensive experimental study using three types of MALDI-MS data. CONCLUSION: Regarding feature selection, SVMRFE outperformed GLGS in classification. As for the learning classifiers, when classification models derived from the best training were compared, SVMs performed the best with respect to the expected testing accuracy. However, the distance metric learning LMNN outperformed SVMs and other classifiers on evaluating the best testing. In such cases, the optimum classification model based on LMNN is worth investigating for future study.","corpus_id":1513386,"score":1},{"doc_id":"21205299","title":"Clustering gene expression data with a penalized graph-based metric.","abstract":"BACKGROUND: The search for cluster structure in microarray datasets is a base problem for the so-called \"-omic sciences\". A difficult problem in clustering is how to handle data with a manifold structure, i.e. data that is not shaped in the form of compact clouds of points, forming arbitrary shapes or paths embedded in a high-dimensional space, as could be the case of some gene expression datasets. RESULTS: In this work we introduce the Penalized k-Nearest-Neighbor-Graph (PKNNG) based metric, a new tool for evaluating distances in such cases. The new metric can be used in combination with most clustering algorithms. The PKNNG metric is based on a two-step procedure: first it constructs the k-Nearest-Neighbor-Graph of the dataset of interest using a low k-value and then it adds edges with a highly penalized weight for connecting the subgraphs produced by the first step. We discuss several possible schemes for connecting the different sub-graphs as well as penalization functions. We show clustering results on several public gene expression datasets and simulated artificial problems to evaluate the behavior of the new metric. CONCLUSIONS: In all cases the PKNNG metric shows promising clustering results. The use of the PKNNG metric can improve the performance of commonly used pairwise-distance based clustering methods, to the level of more advanced algorithms. A great advantage of the new procedure is that researchers do not need to learn a new method, they can simply compute distances with the PKNNG metric and then, for example, use hierarchical clustering to produce an accurate and highly interpretable dendrogram of their high-dimensional data.","corpus_id":10123235,"score":1},{"doc_id":"21493051","title":"A fuzzy-based data transformation for feature extraction to increase classification performance with small medical data sets.","abstract":"OBJECTIVE: Medical data sets are usually small and have very high dimensionality. Too many attributes will make the analysis less efficient and will not necessarily increase accuracy, while too few data will decrease the modeling stability. Consequently, the main objective of this study is to extract the optimal subset of features to increase analytical performance when the data set is small. METHODS: This paper proposes a fuzzy-based non-linear transformation method to extend classification related information from the original data attribute values for a small data set. Based on the new transformed data set, this study applies principal component analysis (PCA) to extract the optimal subset of features. Finally, we use the transformed data with these optimal features as the input data for a learning tool, a support vector machine (SVM). Six medical data sets: Pima Indians' diabetes, Wisconsin diagnostic breast cancer, Parkinson disease, echocardiogram, BUPA liver disorders dataset, and bladder cancer cases in Taiwan, are employed to illustrate the approach presented in this paper. RESULTS: This research uses the t-test to evaluate the classification accuracy for a single data set; and uses the Friedman test to show the proposed method is better than other methods over the multiple data sets. The experiment results indicate that the proposed method has better classification performance than either PCA or kernel principal component analysis (KPCA) when the data set is small, and suggest creating new purpose-related information to improve the analysis performance. CONCLUSION: This paper has shown that feature extraction is important as a function of feature selection for efficient data analysis. When the data set is small, using the fuzzy-based transformation method presented in this work to increase the information available produces better results than the PCA and KPCA approaches.","corpus_id":42526756,"score":1},{"doc_id":"21939564","title":"Top scoring pairs for feature selection in machine learning and applications to cancer outcome prediction.","abstract":"BACKGROUND: The widely used k top scoring pair (k-TSP) algorithm is a simple yet powerful parameter-free classifier. It owes its success in many cancer microarray datasets to an effective feature selection algorithm that is based on relative expression ordering of gene pairs. However, its general robustness does not extend to some difficult datasets, such as those involving cancer outcome prediction, which may be due to the relatively simple voting scheme used by the classifier. We believe that the performance can be enhanced by separating its effective feature selection component and combining it with a powerful classifier such as the support vector machine (SVM). More generally the top scoring pairs generated by the k-TSP ranking algorithm can be used as a dimensionally reduced subspace for other machine learning classifiers. RESULTS: We developed an approach integrating the k-TSP ranking algorithm (TSP) with other machine learning methods, allowing combination of the computationally efficient, multivariate feature ranking of k-TSP with multivariate classifiers such as SVM. We evaluated this hybrid scheme (k-TSP+SVM) in a range of simulated datasets with known data structures. As compared with other feature selection methods, such as a univariate method similar to Fisher's discriminant criterion (Fisher), or a recursive feature elimination embedded in SVM (RFE), TSP is increasingly more effective than the other two methods as the informative genes become progressively more correlated, which is demonstrated both in terms of the classification performance and the ability to recover true informative genes. We also applied this hybrid scheme to four cancer prognosis datasets, in which k-TSP+SVM outperforms k-TSP classifier in all datasets, and achieves either comparable or superior performance to that using SVM alone. In concurrence with what is observed in simulation, TSP appears to be a better feature selector than Fisher and RFE in some of the cancer datasets CONCLUSIONS: The k-TSP ranking algorithm can be used as a computationally efficient, multivariate filter method for feature selection in machine learning. SVM in combination with k-TSP ranking algorithm outperforms k-TSP and SVM alone in simulated datasets and in some cancer prognosis datasets. Simulation studies suggest that as a feature selector, it is better tuned to certain data characteristics, i.e. correlations among informative genes, which is potentially interesting as an alternative feature ranking method in pathway analysis.","corpus_id":17442787,"score":1},{"doc_id":"21982331","title":"Microarray-based cancer prediction using single genes.","abstract":"BACKGROUND: Although numerous methods of using microarray data analysis for cancer classification have been proposed, most utilize many genes to achieve accurate classification. This can hamper interpretability of the models and ease of translation to other assay platforms. We explored the use of single genes to construct classification models. We first identified the genes with the most powerful univariate class discrimination ability and then constructed simple classification rules for class prediction using the single genes. RESULTS: We applied our model development algorithm to eleven cancer gene expression datasets and compared classification accuracy to that for standard methods including Diagonal Linear Discriminant Analysis, k-Nearest Neighbor, Support Vector Machine and Random Forest. The single gene classifiers provided classification accuracy comparable to or better than those obtained by existing methods in most cases. We analyzed the factors that determined when simple single gene classification is effective and when more complex modeling is warranted. CONCLUSIONS: For most of the datasets examined, the single-gene classification methods appear to work as well as more standard methods, suggesting that simple models could perform well in microarray-based cancer prediction.","corpus_id":2914763,"score":1},{"doc_id":"22138042","title":"Robust two-gene classifiers for cancer prediction.","abstract":"Two-gene classifiers have attracted a broad interest for their simplicity and practicality. Most existing two-gene classification algorithms were involved in exhaustive search that led to their low time-efficiencies. In this study, we proposed two new two-gene classification algorithms which used simple univariate gene selection strategy and constructed simple classification rules based on optimal cut-points for two genes selected. We detected the optimal cut-point with the information entropy principle. We applied the two-gene classification models to eleven cancer gene expression datasets and compared their classification performance to that of some established two-gene classification models like the top-scoring pairs model and the greedy pairs model, as well as standard methods including Diagonal Linear Discriminant Analysis, k-Nearest Neighbor, Support Vector Machine and Random Forest. These comparisons indicated that the performance of our two-gene classifiers was comparable to or better than that of compared models.","corpus_id":412865,"score":1},{"doc_id":"22475749","title":"Gene expression data analysis using multiobjective clustering improved with SVM based ensemble.","abstract":"Microarray technology facilitates the monitoring of the expression levels of thousands of genes over different experimental conditions simultaneously. Clustering is a popular data mining tool which can be applied to microarray gene expression data to identify co-expressed genes. Most of the traditional clustering methods optimize a single clustering goodness criterion and thus may not be capable of performing well on all kinds of datasets. Motivated by this, in this article, a multiobjective clustering technique that optimizes cluster compactness and separation simultaneously, has been improved through a novel support vector machine classification based cluster ensemble method. The superiority of MOCSVMEN (MultiObjective Clustering with Support Vector Machine based ENsemble) has been established by comparing its performance with that of several well known existing microarray data clustering algorithms. Two real-life benchmark gene expression datasets have been used for testing the comparative performances of different algorithms. A recently developed metric, called Biological Homogeneity Index (BHI), which computes the clustering goodness with respect to functional annotation, has been used for the comparison purpose.","corpus_id":34523136,"score":1},{"doc_id":"23164195","title":"Clustering gene expression data using a diffraction-inspired framework.","abstract":"BACKGROUND: The recent developments in microarray technology has allowed for the simultaneous measurement of gene expression levels. The large amount of captured data challenges conventional statistical tools for analysing and finding inherent correlations between genes and samples. The unsupervised clustering approach is often used, resulting in the development of a wide variety of algorithms. Typical clustering algorithms require selecting certain parameters to operate, for instance the number of expected clusters, as well as defining a similarity measure to quantify the distance between data points. The diffraction-based clustering algorithm however is designed to overcome this necessity for user-defined parameters, as it is able to automatically search the data for any underlying structure. METHODS: The diffraction-based clustering algorithm presented in this paper is tested using five well-known expression datasets pertaining to cancerous tissue samples. The clustering results are then compared to those results obtained from conventional algorithms such as the k-means, fuzzy c-means, self-organising map, hierarchical clustering algorithm, Gaussian mixture model and density-based spatial clustering of applications with noise (DBSCAN). The performance of each algorithm is measured using an average external criterion and an average validity index. RESULTS: The diffraction-based clustering algorithm is shown to be independent of the number of clusters as the algorithm searches the feature space and requires no form of parameter selection. The results show that the diffraction-based clustering algorithm performs significantly better on the real biological datasets compared to the other existing algorithms. CONCLUSION: The results of the diffraction-based clustering algorithm presented in this paper suggest that the method can provide researchers with a new tool for successfully analysing microarray data.","corpus_id":15141977,"score":1},{"doc_id":"23778014","title":"A classification framework applied to cancer gene expression profiles.","abstract":"Classification of cancer based on gene expression has provided insight into possible treatment strategies. Thus, developing machine learning methods that can successfully distinguish among cancer subtypes or normal versus cancer samples is important. This work discusses supervised learning techniques that have been employed to classify cancers. Furthermore, a two-step feature selection method based on an attribute estimation method (e.g., ReliefF) and a genetic algorithm was employed to find a set of genes that can best differentiate between cancer subtypes or normal versus cancer samples. The application of different classification methods (e.g., decision tree, k-nearest neighbor, support vector machine (SVM), bagging, and random forest) on 5 cancer datasets shows that no classification method universally outperforms all the others. However, k-nearest neighbor and linear SVM generally improve the classification performance over other classifiers. Finally, incorporating diverse types of genomic data (e.g., protein-protein interaction data and gene expression) increase the prediction accuracy as compared to using gene expression alone.","corpus_id":11852825,"score":1},{"doc_id":"24266942","title":"Fuzzy support vector machine: an efficient rule-based classification technique for microarrays.","abstract":"BACKGROUND: The abundance of gene expression microarray data has led to the development of machine learning algorithms applicable for tackling disease diagnosis, disease prognosis, and treatment selection problems. However, these algorithms often produce classifiers with weaknesses in terms of accuracy, robustness, and interpretability. This paper introduces fuzzy support vector machine which is a learning algorithm based on combination of fuzzy classifiers and kernel machines for microarray classification. RESULTS: Experimental results on public leukemia, prostate, and colon cancer datasets show that fuzzy support vector machine applied in combination with filter or wrapper feature selection methods develops a robust model with higher accuracy than the conventional microarray classification models such as support vector machine, artificial neural network, decision trees, k nearest neighbors, and diagonal linear discriminant analysis. Furthermore, the interpretable rule-base inferred from fuzzy support vector machine helps extracting biological knowledge from microarray data. CONCLUSIONS: Fuzzy support vector machine as a new classification model with high generalization power, robustness, and good interpretability seems to be a promising tool for gene expression microarray classification.","corpus_id":5427410,"score":1},{"doc_id":"24625071","title":"Feature weight estimation for gene selection: a local hyperlinear learning approach.","abstract":"BACKGROUND: Modeling high-dimensional data involving thousands of variables is particularly important for gene expression profiling experiments, nevertheless,it remains a challenging task. One of the challenges is to implement an effective method for selecting a small set of relevant genes, buried in high-dimensional irrelevant noises. RELIEF is a popular and widely used approach for feature selection owing to its low computational cost and high accuracy. However, RELIEF based methods suffer from instability, especially in the presence of noisy and/or high-dimensional outliers. RESULTS: We propose an innovative feature weighting algorithm, called LHR, to select informative genes from highly noisy data. LHR is based on RELIEF for feature weighting using classical margin maximization. The key idea of LHR is to estimate the feature weights through local approximation rather than global measurement, which is typically used in existing methods. The weights obtained by our method are very robust in terms of degradation of noisy features, even those with vast dimensions. To demonstrate the performance of our method, extensive experiments involving classification tests have been carried out on both synthetic and real microarray benchmark datasets by combining the proposed technique with standard classifiers, including the support vector machine (SVM), k-nearest neighbor (KNN), hyperplane k-nearest neighbor (HKNN), linear discriminant analysis (LDA) and naive Bayes (NB). CONCLUSION: Experiments on both synthetic and real-world datasets demonstrate the superior performance of the proposed feature selection method combined with supervised learning in three aspects: 1) high classification accuracy, 2) excellent robustness to noise and 3) good stability using to various classification algorithms.","corpus_id":9299356,"score":1},{"doc_id":"24678894","title":"Identification of biomarkers that distinguish chemical contaminants based on gene expression profiles.","abstract":"BACKGROUND: High throughput transcriptomics profiles such as those generated using microarrays have been useful in identifying biomarkers for different classification and toxicity prediction purposes. Here, we investigated the use of microarrays to predict chemical toxicants and their possible mechanisms of action. RESULTS: In this study, in vitro cultures of primary rat hepatocytes were exposed to 105 chemicals and vehicle controls, representing 14 compound classes. We comprehensively compared various normalization of gene expression profiles, feature selection and classification algorithms for the classification of these 105 chemicals into14 compound classes. We found that normalization had little effect on the averaged classification accuracy. Two support vector machine (SVM) methods, LibSVM and sequential minimal optimization, had better classification performance than other methods. SVM recursive feature selection (SVM-RFE) had the highest overfitting rate when an independent dataset was used for a prediction. Therefore, we developed a new feature selection algorithm called gradient method that had a relatively high training classification as well as prediction accuracy with the lowest overfitting rate of the methods tested. Analysis of biomarkers that distinguished the 14 classes of compounds identified a group of genes principally involved in cell cycle function that were significantly downregulated by metal and inflammatory compounds, but were induced by anti-microbial, cancer related drugs, pesticides, and PXR mediators. CONCLUSIONS: Our results indicate that using microarrays and a supervised machine learning approach to predict chemical toxicants, their potential toxicity and mechanisms of action is practical and efficient. Choosing the right feature and classification algorithms for this multiple category classification and prediction is critical.","corpus_id":14684503,"score":1},{"doc_id":"24808006","title":"Multiclass feature selection with kernel Gram-matrix-based criteria.","abstract":"Feature selection has been an important issue in recent decades to determine the most relevant features according to a given classification problem. Numerous methods have emerged that take into account support vector machines (SVMs) in the selection process. Such approaches are powerful but often complex and costly. In this paper, we propose new feature selection methods based on two criteria designed for the optimization of SVM: kernel target alignment and kernel class separability. We demonstrate how these two measures, when fully expressed, can build efficient and simple methods, easily applicable to multiclass problems and iteratively computable with minimal memory requirements. An extensive experimental study is conducted both on artificial and real-world datasets to compare the proposed methods to state-of-the-art feature selection algorithms. The results demonstrate the relevance of the proposed methods both in terms of performance and computational cost.","corpus_id":7834332,"score":1},{"doc_id":"25003163","title":"Multiobjective binary biogeography based optimization for feature selection using gene expression data.","abstract":"Gene expression data play an important role in the development of efficient cancer diagnoses and classification. However, gene expression data are usually redundant and noisy, and only a subset of them present distinct profiles for different classes of samples. Thus, selecting high discriminative genes from gene expression data has become increasingly interesting in the field of bioinformatics. In this paper, a multi-objective biogeography based optimization method is proposed to select the small subset of informative gene relevant to the classification. In the proposed algorithm, firstly, the Fisher-Markov selector is used to choose the 60 top gene expression data. Secondly, to make biogeography based optimization suitable for the discrete problem, binary biogeography based optimization, as called BBBO, is proposed based on a binary migration model and a binary mutation model. Then, multi-objective binary biogeography based optimization, as we called MOBBBO, is proposed by integrating the non-dominated sorting method and the crowding distance method into the BBBO framework. Finally, the MOBBBO method is used for gene selection, and support vector machine is used as the classifier with the leave-one-out cross-validation method (LOOCV). In order to show the effective and efficiency of the algorithm, the proposed algorithm is tested on ten gene expression dataset benchmarks. Experimental results demonstrate that the proposed method is better or at least comparable with previous particle swarm optimization (PSO) algorithm and support vector machine (SVM) from literature when considering the quality of the solutions obtained.","corpus_id":6301202,"score":1},{"doc_id":"25549938","title":"A fast gene selection method for multi-cancer classification using multiple support vector data description.","abstract":"For cancer classification problems based on gene expression, the data usually has only a few dozen sizes but has thousands to tens of thousands of genes which could contain a large number of irrelevant genes. A robust feature selection algorithm is required to remove irrelevant genes and choose the informative ones. Support vector data description (SVDD) has been applied to gene selection for many years. However, SVDD cannot address the problems with multiple classes since it only considers the target class. In addition, it is time-consuming when applying SVDD to gene selection. This paper proposes a novel fast feature selection method based on multiple SVDD and applies it to multi-class microarray data. A recursive feature elimination (RFE) scheme is introduced to iteratively remove irrelevant features, so the proposed method is called multiple SVDD-RFE (MSVDD-RFE). To make full use of all classes for a given task, MSVDD-RFE independently selects a relevant gene subset for each class. The final selected gene subset is the union of these relevant gene subsets. The effectiveness and accuracy of MSVDD-RFE are validated by experiments on five publicly available microarray datasets. Our proposed method is faster and more effective than other methods.","corpus_id":36676816,"score":1},{"doc_id":"26925688","title":"Evaluation of Machine Learning Algorithm Utilization for Lung Cancer Classification Based on Gene Expression Levels.","abstract":"BACKGROUND: Lung cancer remains one of the most common cancers in the world, both in terms of new cases (about 13% of total per year) and deaths (nearly one cancer death in five), because of the high case fatality. Errors in lung cancer type or malignant growth determination lead to degraded treatment efficacy, because anticancer strategy depends on tumor morphology. MATERIALS AND METHODS: We have made an attempt to evaluate effectiveness of machine learning algorithms in the task of lung cancer classification based on gene expression levels. We processed four publicly available data sets. The Dana-Farber Cancer Institute data set contains 203 samples and the task was to classify four cancer types and sound tissue samples. With the University of Michigan data set of 96 samples, the task was to execute a binary classification of adenocarcinoma and non-neoplastic tissues. The University of Toronto data set contains 39 samples and the task was to detect recurrence, while with the Brigham and Women's Hospital data set of 181 samples it was to make a binary classification of malignant pleural mesothelioma and adenocarcinoma. We used the k-nearest neighbor algorithm (k=1, k=5, k=10), naive Bayes classifier with assumption of both a normal distribution of attributes and a distribution through histograms, support vector machine and C4.5 decision tree. Effectiveness of machine learning algorithms was evaluated with the Matthews correlation coefficient. RESULTS: The support vector machine method showed best results among data sets from the Dana-Farber Cancer Institute and Brigham and Women's Hospital. All algorithms with the exception of the C4.5 decision tree showed maximum potential effectiveness in the University of Michigan data set. However, the C4.5 decision tree showed best results for the University of Toronto data set. CONCLUSIONS: Machine learning algorithms can be used for lung cancer morphology classification and similar tasks based on gene expression level evaluation.","corpus_id":28128074,"score":1},{"doc_id":"27081632","title":"A fuzzy based feature selection from independent component subspace for machine learning classification of microarray data.","abstract":"Feature (gene) selection and classification of microarray data are the two most interesting machine learning challenges. In the present work two existing feature selection/extraction algorithms, namely independent component analysis (ICA) and fuzzy backward feature elimination (FBFE) are used which is a new combination of selection/extraction. The main objective of this paper is to select the independent components of the DNA microarray data using FBFE to improve the performance of support vector machine (SVM) and Naïve Bayes (NB) classifier, while making the computational expenses affordable. To show the validity of the proposed method, it is applied to reduce the number of genes for five DNA microarray datasets namely; colon cancer, acute leukemia, prostate cancer, lung cancer II, and high-grade glioma. Now these datasets are then classified using SVM and NB classifiers. Experimental results on these five microarray datasets demonstrate that gene selected by proposed approach, effectively improve the performance of SVM and NB classifiers in terms of classification accuracy. We compare our proposed method with principal component analysis (PCA) as a standard extraction algorithm and find that the proposed method can obtain better classification accuracy, using SVM and NB classifiers with a smaller number of selected genes than the PCA. The curve between the average error rate and number of genes with each dataset represents the selection of required number of genes for the highest accuracy with our proposed method for both the classifiers. ROC shows best subset of genes for both the classifier of different datasets with propose method.","corpus_id":20522236,"score":1},{"doc_id":"27154739","title":"A hybrid gene selection approach for microarray data classification using cellular learning automata and ant colony optimization.","abstract":"This paper proposes an approach for gene selection in microarray data. The proposed approach consists of a primary filter approach using Fisher criterion which reduces the initial genes and hence the search space and time complexity. Then, a wrapper approach which is based on cellular learning automata (CLA) optimized with ant colony method (ACO) is used to find the set of features which improve the classification accuracy. CLA is applied due to its capability to learn and model complicated relationships. The selected features from the last phase are evaluated using ROC curve and the most effective while smallest feature subset is determined. The classifiers which are evaluated in the proposed framework are K-nearest neighbor; support vector machine and naïve Bayes. The proposed approach is evaluated on 4 microarray datasets. The evaluations confirm that the proposed approach can find the smallest subset of genes while approaching the maximum accuracy.","corpus_id":5668832,"score":1},{"doc_id":"27433543","title":"Classification of Microarray Data Using Kernel Fuzzy Inference System.","abstract":"The DNA microarray classification technique has gained more popularity in both research and practice. In real data analysis, such as microarray data, the dataset contains a huge number of insignificant and irrelevant features that tend to lose useful information. Classes with high relevance and feature sets with high significance are generally referred for the selected features, which determine the samples classification into their respective classes. In this paper, kernel fuzzy inference system (K-FIS) algorithm is applied to classify the microarray data (leukemia) using t-test as a feature selection method. Kernel functions are used to map original data points into a higher-dimensional (possibly infinite-dimensional) feature space defined by a (usually nonlinear) function ϕ through a mathematical process called the kernel trick. This paper also presents a comparative study for classification using K-FIS along with support vector machine (SVM) for different set of features (genes). Performance parameters available in the literature such as precision, recall, specificity, F-measure, ROC curve, and accuracy are considered to analyze the efficiency of the classification model. From the proposed approach, it is apparent that K-FIS model obtains similar results when compared with SVM model. This is an indication that the proposed approach relies on kernel function.","corpus_id":16381822,"score":1},{"doc_id":"27879930","title":"Kernel Based Nonlinear Dimensionality Reduction and Classification for Genomic Microarray.","abstract":"Genomic microarrays are powerful research tools in bioinformatics and modern medicinal research because they enable massively-parallel assays and simultaneous monitoring of thousands of gene expression of biological samples. However, a simple microarray experiment often leads to very high-dimensional data and a huge amount of information, the vast amount of data challenges researchers into extracting the important features and reducing the high dimensionality. In this paper, a nonlinear dimensionality reduction kernel method based locally linear embedding(LLE) is proposed, and fuzzy K-nearest neighbors algorithm which denoises datasets will be introduced as a replacement to the classical LLE's KNN algorithm. In addition, kernel method based support vector machine (SVM) will be used to classify genomic microarray data sets in this paper. We demonstrate the application of the techniques to two published DNA microarray data sets. The experimental results confirm the superiority and high success rates of the presented method.","corpus_id":11228877,"score":1},{"doc_id":"28141531","title":"Feature Combination via Clustering.","abstract":"In image classification, feature combination is often used to combine the merits of multiple complementary features and improve the classification accuracy compared with one single feature. Existing feature combination algorithms, e.g., multiple kernel learning, usually determine the weights of features based on the optimization with respect to some classifier-dependent objective function. These algorithms are often computationally expensive, and in some cases are found to perform no better than simple baselines. In this paper, we solve the feature combination problem from a totally different perspective. Our algorithm is based on the simple idea of combining only base kernels suitable to be combined. Since the very aim of feature combination is to obtain the highest possible classification accuracy, we measure the combination suitableness of two base kernels by the maximum possible cross-validation accuracy of their combined kernel. By regarding the pairwise suitableness as the kernel adjacency, we obtain a weighted graph of all base kernels and find that the base kernels suitable to be combined correspond to a cluster in the graph. We then use the dominant sets algorithm to find the cluster and determine the weights of base kernels automatically. In this way, we transform the kernel combination problem into a clustering one. Our algorithm can be implemented in parallel easily and the running time can be adjusted based on available memory to a large extent. In experiments on several data sets, our algorithm generates comparable classification accuracy with the state of the art.","corpus_id":3959381,"score":1},{"doc_id":"28163197","title":"Development of a two-stage gene selection method that incorporates a novel hybrid approach using the cuckoo optimization algorithm and harmony search for cancer classification.","abstract":"For each cancer type, only a few genes are informative. Due to the so-called 'curse of dimensionality' problem, the gene selection task remains a challenge. To overcome this problem, we propose a two-stage gene selection method called MRMR-COA-HS. In the first stage, the minimum redundancy and maximum relevance (MRMR) feature selection is used to select a subset of relevant genes. The selected genes are then fed into a wrapper setup that combines a new algorithm, COA-HS, using the support vector machine as a classifier. The method was applied to four microarray datasets, and the performance was assessed by the leave one out cross-validation method. Comparative performance assessment of the proposed method with other evolutionary algorithms suggested that the proposed algorithm significantly outperforms other methods in selecting a fewer number of genes while maintaining the highest classification accuracy. The functions of the selected genes were further investigated, and it was confirmed that the selected genes are biologically relevant to each cancer type.","corpus_id":3918931,"score":1},{"doc_id":"28182545","title":"A Gene Selection Method for Microarray Data Based on Binary PSO Encoding Gene-to-Class Sensitivity Information.","abstract":"Traditional gene selection methods for microarray data mainly considered the features' relevance by evaluating their utility for achieving accurate predication or exploiting data variance and distribution, and the selected genes were usually poorly explicable. To improve the interpretability of the selected genes as well as prediction accuracy, an improved gene selection method based on binary particle swarm optimization (BPSO) and prior information is proposed in this paper. In the proposed method, BPSO encoding gene-to-class sensitivity (GCS) information is used to perform gene selection. The gene-to-class sensitivity information, extracted from the samples by extreme learning machine (ELM), is encoded into the selection process in four aspects: initializing particles, updating the particles, modifying maximum velocity, and adopting mutation operation adaptively. Constrained by the gene-to-class sensitivity information, the new method can select functional gene subsets which are significantly sensitive to the samples' classes. With the few discriminative genes selected by the proposed method, ELM, K-nearest neighbor and support vector machine classifiers achieve much high prediction accuracy on five public microarray data, which in turn verifies the efficiency and effectiveness of the proposed gene selection method.","corpus_id":3721282,"score":1},{"doc_id":"28184251","title":"A feature selection method based on multiple kernel learning with expression profiles of different types.","abstract":"BACKGROUND: With the development of high-throughput technology, the researchers can acquire large number of expression data with different types from several public databases. Because most of these data have small number of samples and hundreds or thousands features, how to extract informative features from expression data effectively and robustly using feature selection technique is challenging and crucial. So far, a mass of many feature selection approaches have been proposed and applied to analyse expression data of different types. However, most of these methods only are limited to measure the performances on one single type of expression data by accuracy or error rate of classification. RESULTS: In this article, we propose a hybrid feature selection method based on Multiple Kernel Learning (MKL) and evaluate the performance on expression datasets of different types. Firstly, the relevance between features and classifying samples is measured by using the optimizing function of MKL. In this step, an iterative gradient descent process is used to perform the optimization both on the parameters of Support Vector Machine (SVM) and kernel confidence. Then, a set of relevant features is selected by sorting the optimizing function of each feature. Furthermore, we apply an embedded scheme of forward selection to detect the compact feature subsets from the relevant feature set. CONCLUSIONS: We not only compare the classification accuracy with other methods, but also compare the stability, similarity and consistency of different algorithms. The proposed method has a satisfactory capability of feature selection for analysing expression datasets of different types using different performance measurements.","corpus_id":472254,"score":1},{"doc_id":"28541221","title":"Subspace Weighting Co-Clustering of Gene Expression Data.","abstract":"Microarray technology enables the collection of vast amounts of gene expression data from biological experiments. Clustering algorithms have been successfully applied to exploring the gene expression data. Since a set of genes may be possible correlated to a subset of samples, it is useful to use co-clustering to recover co-clusters in the gene expression data. In this paper, we propose a novel algorithm, called Subspace Weighting Co-Clustering (SWCC), for high dimensional gene expression data. In SWCC, a gene subspace weight matrix is introduced to identify the contribution of gene objects in distinguishing different sample clusters. We design a new co-clustering objective function to recover the co-clusters in the gene expression data, in which the subspace weight matrix is employed. An iterative algorithm is developed to solve the objective function, in which the subspace weight matrix is automatically computed during the iterative co-clustering process. Our empirical study shows encouraging results of the proposed algorithm in comparison with six state-of-the-art clustering algorithms on ten gene expression data sets. We also propose to use SWCC for gene clustering and selection. The experimental results show that the selected genes can improve the classification performance of Random Forests.","corpus_id":11075097,"score":1},{"doc_id":"28567418","title":"A Cancer Gene Selection Algorithm Based on the K-S Test and CFS.","abstract":"BACKGROUND: To address the challenging problem of selecting distinguished genes from cancer gene expression datasets, this paper presents a gene subset selection algorithm based on the Kolmogorov-Smirnov (K-S) test and correlation-based feature selection (CFS) principles. The algorithm selects distinguished genes first using the K-S test, and then, it uses CFS to select genes from those selected by the K-S test. RESULTS: We adopted support vector machines (SVM) as the classification tool and used the criteria of accuracy to evaluate the performance of the classifiers on the selected gene subsets. This approach compared the proposed gene subset selection algorithm with the K-S test, CFS, minimum-redundancy maximum-relevancy (mRMR), and ReliefF algorithms. The average experimental results of the aforementioned gene selection algorithms for 5 gene expression datasets demonstrate that, based on accuracy, the performance of the new K-S and CFS-based algorithm is better than those of the K-S test, CFS, mRMR, and ReliefF algorithms. CONCLUSIONS: The experimental results show that the K-S test-CFS gene selection algorithm is a very effective and promising approach compared to the K-S test, CFS, mRMR, and ReliefF algorithms.","corpus_id":3796098,"score":1},{"doc_id":"29535919","title":"Improving Classification of Cancer and Mining Biomarkers from Gene Expression Profiles Using Hybrid Optimization Algorithms and Fuzzy Support Vector Machine.","abstract":"Background: Gene expression data are characteristically high dimensional with a small sample size in contrast to the feature size and variability inherent in biological processes that contribute to difficulties in analysis. Selection of highly discriminative features decreases the computational cost and complexity of the classifier and improves its reliability for prediction of a new class of samples. Methods: The present study used hybrid particle swarm optimization and genetic algorithms for gene selection and a fuzzy support vector machine (SVM) as the classifier. Fuzzy logic is used to infer the importance of each sample in the training phase and decrease the outlier sensitivity of the system to increase the ability to generalize the classifier. A decision-tree algorithm was applied to the most frequent genes to develop a set of rules for each type of cancer. This improved the abilities of the algorithm by finding the best parameters for the classifier during the training phase without the need for trial-and-error by the user. The proposed approach was tested on four benchmark gene expression profiles. Results: Good results have been demonstrated for the proposed algorithm. The classification accuracy for leukemia data is 100%, for colon cancer is 96.67% and for breast cancer is 98%. The results show that the best kernel used in training the SVM classifier is the radial basis function. Conclusions: The experimental results show that the proposed algorithm can decrease the dimensionality of the dataset, determine the most informative gene subset, and improve classification accuracy using the optimal parameters of the classifier with no user interface.","corpus_id":3886504,"score":1},{"doc_id":"18390369","title":"Customizing kernel functions for SVM-based hyperspectral image classification.","abstract":"Previous research applying kernel methods such as support vector machines (SVMs) to hyperspectral image classification has achieved performance competitive with the best available algorithms. However, few efforts have been made to extend SVMs to cover the specific requirements of hyperspectral image classification, for example, by building tailor-made kernels. Observation of real-life spectral imagery from the AVIRIS hyperspectral sensor shows that the useful information for classification is not equally distributed across bands, which provides potential to enhance the SVM's performance through exploring different kernel functions. Spectrally weighted kernels are, therefore, proposed, and a set of particular weights is chosen by either optimizing an estimate of generalization error or evaluating each band's utility level. To assess the effectiveness of the proposed method, experiments are carried out on the publicly available 92AV3C dataset collected from the 220-dimensional AVIRIS hyperspectral sensor. Results indicate that the method is generally effective in improving performance: spectral weighting based on learning weights by gradient descent is found to be slightly better than an alternative method based on estimating \"relevance\" between band information and ground truth.","corpus_id":5799578,"score":0},{"doc_id":"19179252","title":"Constructing ensembles of classifiers by means of weighted instance selection.","abstract":"In this paper, we approach the problem of constructing ensembles of classifiers from the point of view of instance selection. Instance selection is aimed at obtaining a subset of the instances available for training capable of achieving, at least, the same performance as the whole training set. In this way, instance selection algorithms try to keep the performance of the classifiers while reducing the number of instances in the training set. Meanwhile, boosting methods construct an ensemble of classifiers iteratively focusing each new member on the most difficult instances by means of a biased distribution of the training instances. In this work, we show how these two methodologies can be combined advantageously. We can use instance selection algorithms for boosting using as objective to optimize the training error weighted by the biased distribution of the instances given by the boosting method. Our method can be considered as boosting by instance selection. Instance selection has mostly been developed and used for k -nearest neighbor ( k -NN) classifiers. So, as a first step, our methodology is suited to construct ensembles of k -NN classifiers. Constructing ensembles of classifiers by means of instance selection has the important feature of reducing the space complexity of the final ensemble as only a subset of the instances is selected for each classifier. However, the methodology is not restricted to k-NN classifier. Other classifiers, such as decision trees and support vector machines (SVMs), may also benefit from a smaller training set, as they produce simpler classifiers if an instance selection algorithm is performed before training. In the experimental section, we show that the proposed approach is able to produce better and simpler ensembles than random subspace method (RSM) method for k-NN and standard ensemble methods for C4.5 and SVMs.","corpus_id":650561,"score":0},{"doc_id":"21103052","title":"Multi-class clustering of cancer subtypes through SVM based ensemble of pareto-optimal solutions for gene marker identification.","abstract":"With the advancement of microarray technology, it is now possible to study the expression profiles of thousands of genes across different experimental conditions or tissue samples simultaneously. Microarray cancer datasets, organized as samples versus genes fashion, are being used for classification of tissue samples into benign and malignant or their subtypes. They are also useful for identifying potential gene markers for each cancer subtype, which helps in successful diagnosis of particular cancer types. In this article, we have presented an unsupervised cancer classification technique based on multiobjective genetic clustering of the tissue samples. In this regard, a real-coded encoding of the cluster centers is used and cluster compactness and separation are simultaneously optimized. The resultant set of near-Pareto-optimal solutions contains a number of non-dominated solutions. A novel approach to combine the clustering information possessed by the non-dominated solutions through Support Vector Machine (SVM) classifier has been proposed. Final clustering is obtained by consensus among the clusterings yielded by different kernel functions. The performance of the proposed multiobjective clustering method has been compared with that of several other microarray clustering algorithms for three publicly available benchmark cancer datasets. Moreover, statistical significance tests have been conducted to establish the statistical superiority of the proposed clustering method. Furthermore, relevant gene markers have been identified using the clustering result produced by the proposed clustering method and demonstrated visually. Biological relationships among the gene markers are also studied based on gene ontology. The results obtained are found to be promising and can possibly have important impact in the area of unsupervised cancer classification as well as gene marker identification for multiple cancer subtypes.","corpus_id":16715576,"score":0},{"doc_id":"24287336","title":"Direct Kernel Perceptron (DKP): ultra-fast kernel ELM-based classification with non-iterative closed-form weight calculation.","abstract":"The Direct Kernel Perceptron (DKP) (Fernández-Delgado et al., 2010) is a very simple and fast kernel-based classifier, related to the Support Vector Machine (SVM) and to the Extreme Learning Machine (ELM) (Huang, Wang, & Lan, 2011), whose α-coefficients are calculated directly, without any iterative training, using an analytical closed-form expression which involves only the training patterns. The DKP, which is inspired by the Direct Parallel Perceptron, (Auer et al., 2008), uses a Gaussian kernel and a linear classifier (perceptron). The weight vector of this classifier in the feature space minimizes an error measure which combines the training error and the hyperplane margin, without any tunable regularization parameter. This weight vector can be translated, using a variable change, to the α-coefficients, and both are determined without iterative calculations. We calculate solutions using several error functions, achieving the best trade-off between accuracy and efficiency with the linear function. These solutions for the α coefficients can be considered alternatives to the ELM with a new physical meaning in terms of error and margin: in fact, the linear and quadratic DKP are special cases of the two-class ELM when the regularization parameter C takes the values C=0 and C=∞. The linear DKP is extremely efficient and much faster (over a vast collection of 42 benchmark and real-life data sets) than 12 very popular and accurate classifiers including SVM, Multi-Layer Perceptron, Adaboost, Random Forest and Bagging of RPART decision trees, Linear Discriminant Analysis, K-Nearest Neighbors, ELM, Probabilistic Neural Networks, Radial Basis Function neural networks and Generalized ART. Besides, despite its simplicity and extreme efficiency, DKP achieves higher accuracies than 7 out of 12 classifiers, exhibiting small differences with respect to the best ones (SVM, ELM, Adaboost and Random Forest), which are much slower. Thus, the DKP provides an easy and fast way to achieve classification accuracies which are not too far from the best one for a given problem. The C and Matlab code of DKP are freely available.","corpus_id":19260849,"score":0},{"doc_id":"24637294","title":"Vicinal support vector classifier using supervised kernel-based clustering.","abstract":"OBJECTIVE: Support vector machines (SVMs) have drawn considerable attention due to their high generalisation ability and superior classification performance compared to other pattern recognition algorithms. However, the assumption that the learning data is identically generated from unknown probability distributions may limit the application of SVMs for real problems. In this paper, we propose a vicinal support vector classifier (VSVC) which is shown to be able to effectively handle practical applications where the learning data may originate from different probability distributions. METHODS: The proposed VSVC method utilises a set of new vicinal kernel functions which are constructed based on supervised clustering in the kernel-induced feature space. Our proposed approach comprises two steps. In the clustering step, a supervised kernel-based deterministic annealing (SKDA) clustering algorithm is employed to partition the training data into different soft vicinal areas of the feature space in order to construct the vicinal kernel functions. In the training step, the SVM technique is used to minimise the vicinal risk function under the constraints of the vicinal areas defined in the SKDA clustering step. RESULTS: Experimental results on both artificial and real medical datasets show our proposed VSVC achieves better classification accuracy and lower computational time compared to a standard SVM. For an artificial dataset constructed from non-separated data, the classification accuracy of VSVC is between 95.5% and 96.25% (using different cluster numbers) which compares favourably to the 94.5% achieved by SVM. The VSVC training time is between 8.75s and 17.83s (for 2-8 clusters), considerable less than the 65.0s required by SVM. On a real mammography dataset, the best classification accuracy of VSVC is 85.7% and thus clearly outperforms a standard SVM which obtains an accuracy of only 82.1%. A similar performance improvement is confirmed on two further real datasets, a breast cancer dataset (74.01% vs. 72.52%) and a heart dataset (84.77% vs. 83.81%), coupled with a reduction in terms of learning time (32.07s vs. 92.08s and 25.00s vs. 53.31s, respectively). Furthermore, the VSVC results in the number of support vectors being equal to the specified cluster number, and hence in a much sparser solution compared to a standard SVM. CONCLUSION: Incorporating a supervised clustering algorithm into the SVM technique leads to a sparse but effective solution, while making the proposed VSVC adaptive to different probability distributions of the training data.","corpus_id":205694566,"score":0},{"doc_id":"24981891","title":"Semi-supervised weighted kernel clustering based on gravitational search for fault diagnosis.","abstract":"Supervised learning method, like support vector machine (SVM), has been widely applied in diagnosing known faults, however this kind of method fails to work correctly when new or unknown fault occurs. Traditional unsupervised kernel clustering can be used for unknown fault diagnosis, but it could not make use of the historical classification information to improve diagnosis accuracy. In this paper, a semi-supervised kernel clustering model is designed to diagnose known and unknown faults. At first, a novel semi-supervised weighted kernel clustering algorithm based on gravitational search (SWKC-GS) is proposed for clustering of dataset composed of labeled and unlabeled fault samples. The clustering model of SWKC-GS is defined based on wrong classification rate of labeled samples and fuzzy clustering index on the whole dataset. Gravitational search algorithm (GSA) is used to solve the clustering model, while centers of clusters, feature weights and parameter of kernel function are selected as optimization variables. And then, new fault samples are identified and diagnosed by calculating the weighted kernel distance between them and the fault cluster centers. If the fault samples are unknown, they will be added in historical dataset and the SWKC-GS is used to partition the mixed dataset and update the clustering results for diagnosing new fault. In experiments, the proposed method has been applied in fault diagnosis for rotatory bearing, while SWKC-GS has been compared not only with traditional clustering methods, but also with SVM and neural network, for known fault diagnosis. In addition, the proposed method has also been applied in unknown fault diagnosis. The results have shown effectiveness of the proposed method in achieving expected diagnosis accuracy for both known and unknown faults of rotatory bearing.","corpus_id":18958371,"score":0},{"doc_id":"28668006","title":"Hyperspectral sensing data analysis based on quasiconformal mapping-based multiple kernels learning machine.","abstract":"Hyperspectral remote sensing has a strong ability of object information expression, so it provides better support for object classification. Many methods are proposed for the hyperspectral data classification. The spectrum classification is a classical nonlinear problem, and a kernel-based machine is feasible to classify the spectrum data. In the nonlinear kernel-based space, the spectrum data are more discriminative. The kernel functions determine the data distribution in the feature space. In this paper, we propose the quasiconformal multiple kernels-based machine learning for the hyperspectral data classification. In the framework, the structure of hyperspectral data is adaptively adjusted for classification. The multiple kernels extract the multiple features of hyperspectral data for classification. Multiple features-based machine learning exhibits a great potential on the classification of hyperspectral data. Two public datasets, India Pines dataset and Pavia University dataset, are used to test the proposed algorithm. Experimental results demonstrate that the proposed quasiconformal multiple kernels-based hyperspectral data classification method can show competitive performance.","corpus_id":46843724,"score":0},{"doc_id":"29717598","title":"[Cell data clustering method in flow cytometry based on kernel principal component analysis].","abstract":"The process of multi-parametric flow cytometry data analysis is complicate and time-consuming,which requires well-trained professionals to operate on. To overcome this limitation, a method for multi-parameter flow cytometry data processing based on kernel principal component analysis(KPCA) was proposed in this paper. The dimensionality of the data was reduced by nonlinear transform. After the new characteristic variables were obtained,automatical clustering can be achieved using improved K-means algorithm. Experimental data of peripheral blood lymphocyte were processed using the principal component analysis(PCA)-based method and KPCA-based method and then the influence of different feature parameter selections was explored. The results indicate that the KPCA can be successfully applied in the multi-parameter flow cytometry data analysis for efficient and accurate cell clustering, which can improve the efficiency of flow cytometry in clinical diagnosis analysis.","corpus_id":23489249,"score":0}],"string":"[\n {\n \"doc_id\": \"18366602\",\n \"title\": \"A comparative study of different machine learning methods on microarray gene expression data.\",\n \"abstract\": \"BACKGROUND: Several classification and feature selection methods have been studied for the identification of differentially expressed genes in microarray data. Classification methods such as SVM, RBF Neural Nets, MLP Neural Nets, Bayesian, Decision Tree and Random Forrest methods have been used in recent studies. The accuracy of these methods has been calculated with validation methods such as v-fold validation. However there is lack of comparison between these methods to find a better framework for classification, clustering and analysis of microarray gene expression results. RESULTS: In this study, we compared the efficiency of the classification methods including; SVM, RBF Neural Nets, MLP Neural Nets, Bayesian, Decision Tree and Random Forrest methods. The v-fold cross validation was used to calculate the accuracy of the classifiers. Some of the common clustering methods including K-means, DBC, and EM clustering were applied to the datasets and the efficiency of these methods have been analysed. Further the efficiency of the feature selection methods including support vector machine recursive feature elimination (SVM-RFE), Chi Squared, and CSF were compared. In each case these methods were applied to eight different binary (two class) microarray datasets. We evaluated the class prediction efficiency of each gene list in training and test cross-validation using supervised classifiers. CONCLUSIONS: We presented a study in which we compared some of the common used classification, clustering, and feature selection methods. We applied these methods to eight publicly available datasets, and compared how these methods performed in class prediction of test datasets. We reported that the choice of feature selection methods, the number of genes in the gene list, the number of cases (samples) substantially influence classification success. Based on features chosen by these methods, error rates and accuracy of several classification algorithms were obtained. Results revealed the importance of feature selection in accurately classifying new samples and how an integrated feature selection and classification algorithm is performing and is capable of identifying significant genes.\",\n \"corpus_id\": 5422060,\n \"score\": 2\n },\n {\n \"doc_id\": \"19182978\",\n \"title\": \"A two-stage feature selection method for gene expression data.\",\n \"abstract\": \"Microarray data referencing gene expression profiles provide valuable answers to a variety of problems, and contributes to advances in clinical medicine. Gene expression data typically has a high dimension and a small sample size. Generally, only relatively small numbers of gene expression data are strongly correlated with a certain phenotype. To analyze gene expression profiles correctly, feature (gene) selection is crucial for classification. Feature (gene) selection has certain advantages, such as effective extraction of genes that influence classification accuracy, elimination of irrelevant genes, and improvement of the classification accuracy calculation. In this paper, we propose a two-stage feature selection method, which uses information gain to implement a gene-ranking process, and combines an improved particle swarm optimization with the K-nearest neighbor method and support vector machine classifiers to calculate the classification accuracy. The experimental results show that the proposed method can effectively select relevant gene subsets, and achieves higher classification accuracy than previous studies.\",\n \"corpus_id\": 24680710,\n \"score\": 2\n },\n {\n \"doc_id\": \"19481202\",\n \"title\": \"Simultaneous genes and training samples selection by modified particle swarm optimization for gene expression data classification.\",\n \"abstract\": \"Gene expression datasets is a means to classify and predict the diagnostic categories of a patient. Informative genes and representative samples selection are two important aspects for reducing gene expression data. Identifying and pruning redundant genes and samples simultaneously can improve the performance of classification and circumvent the local optima problem. In the present paper, the modified particle swarm optimization was applied to selecting optimal genes and samples simultaneously and support vector machine was used as an objective function to determine the optimum set of genes and samples. To evaluate the performance of the new proposed method, it was applied to three publicly available microarray datasets. It has been demonstrated that the proposed method for gene and sample selection is a useful tool for mining high dimension data.\",\n \"corpus_id\": 2761022,\n \"score\": 2\n },\n {\n \"doc_id\": \"20011240\",\n \"title\": \"Feature selection and classification of MAQC-II breast cancer and multiple myeloma microarray gene expression data.\",\n \"abstract\": \"Microarray data has a high dimension of variables but available datasets usually have only a small number of samples, thereby making the study of such datasets interesting and challenging. In the task of analyzing microarray data for the purpose of, e.g., predicting gene-disease association, feature selection is very important because it provides a way to handle the high dimensionality by exploiting information redundancy induced by associations among genetic markers. Judicious feature selection in microarray data analysis can result in significant reduction of cost while maintaining or improving the classification or prediction accuracy of learning machines that are employed to sort out the datasets. In this paper, we propose a gene selection method called Recursive Feature Addition (RFA), which combines supervised learning and statistical similarity measures. We compare our method with the following gene selection methods: Support Vector Machine Recursive Feature Elimination (SVMRFE), Leave-One-Out Calculation Sequential Forward Selection (LOOCSFS), Gradient based Leave-one-out Gene Selection (GLGS). To evaluate the performance of these gene selection methods, we employ several popular learning classifiers on the MicroArray Quality Control phase II on predictive modeling (MAQC-II) breast cancer dataset and the MAQC-II multiple myeloma dataset. Experimental results show that gene selection is strictly paired with learning classifier. Overall, our approach outperforms other compared methods. The biological functional analysis based on the MAQC-II breast cancer dataset convinced us to apply our method for phenotype prediction. Additionally, learning classifiers also play important roles in the classification of microarray data and our experimental results indicate that the Nearest Mean Scale Classifier (NMSC) is a good choice due to its prediction reliability and its stability across the three performance measurements: Testing accuracy, MCC values, and AUC errors.\",\n \"corpus_id\": 2286996,\n \"score\": 2\n },\n {\n \"doc_id\": \"20051140\",\n \"title\": \"ANMM4CBR: a case-based reasoning method for gene expression data classification.\",\n \"abstract\": \"BACKGROUND: Accurate classification of microarray data is critical for successful clinical diagnosis and treatment. The \\\"curse of dimensionality\\\" problem and noise in the data, however, undermines the performance of many algorithms. METHOD: In order to obtain a robust classifier, a novel Additive Nonparametric Margin Maximum for Case-Based Reasoning (ANMM4CBR) method is proposed in this article. ANMM4CBR employs a case-based reasoning (CBR) method for classification. CBR is a suitable paradigm for microarray analysis, where the rules that define the domain knowledge are difficult to obtain because usually only a small number of training samples are available. Moreover, in order to select the most informative genes, we propose to perform feature selection via additively optimizing a nonparametric margin maximum criterion, which is defined based on gene pre-selection and sample clustering. Our feature selection method is very robust to noise in the data. RESULTS: The effectiveness of our method is demonstrated on both simulated and real data sets. We show that the ANMM4CBR method performs better than some state-of-the-art methods such as support vector machine (SVM) and k nearest neighbor (kNN), especially when the data contains a high level of noise. AVAILABILITY: The source code is attached as an additional file of this paper.\",\n \"corpus_id\": 253190,\n \"score\": 2\n },\n {\n \"doc_id\": \"21135434\",\n \"title\": \"Feature Selection and Kernel Learning for Local Learning-Based Clustering.\",\n \"abstract\": \"The performance of the most clustering algorithms highly relies on the representation of data in the input space or the Hilbert space of kernel methods. This paper is to obtain an appropriate data representation through feature selection or kernel learning within the framework of the Local Learning-Based Clustering (LLC) (Wu and Schölkopf 2006) method, which can outperform the global learning-based ones when dealing with the high-dimensional data lying on manifold. Specifically, we associate a weight to each feature or kernel and incorporate it into the built-in regularization of the LLC algorithm to take into account the relevance of each feature or kernel for the clustering. Accordingly, the weights are estimated iteratively in the clustering process. We show that the resulting weighted regularization with an additional constraint on the weights is equivalent to a known sparse-promoting penalty. Hence, the weights of those irrelevant features or kernels can be shrunk toward zero. Extensive experiments show the efficacy of the proposed methods on the benchmark data sets.\",\n \"corpus_id\": 18787586,\n \"score\": 2\n },\n {\n \"doc_id\": \"21241823\",\n \"title\": \"An efficient statistical feature selection approach for classification of gene expression data.\",\n \"abstract\": \"Classification of gene expression data plays a significant role in prediction and diagnosis of diseases. Gene expression data has a special characteristic that there is a mismatch in gene dimension as opposed to sample dimension. All genes do not contribute for efficient classification of samples. A robust feature selection algorithm is required to identify the important genes which help in classifying the samples efficiently. In order to select informative genes (features) based on relevance and redundancy characteristics, many feature selection algorithms have been introduced in the past. Most of the earlier algorithms require computationally expensive search strategy to find an optimal feature subset. Existing feature selection methods are also sensitive to the evaluation measures. The paper introduces a novel and efficient feature selection approach based on statistically defined effective range of features for every class termed as ERGS (Effective Range based Gene Selection). The basic principle behind ERGS is that higher weight is given to the feature that discriminates the classes clearly. Experimental results on well-known gene expression datasets illustrate the effectiveness of the proposed approach. Two popular classifiers viz. Nave Bayes Classifier (NBC) and Support Vector Machine (SVM) have been used for classification. The proposed feature selection algorithm can be helpful in ranking the genes and also is capable of identifying the most relevant genes responsible for diseases like leukemia, colon tumor, lung cancer, diffuse large B-cell lymphoma (DLBCL), prostate cancer.\",\n \"corpus_id\": 42114809,\n \"score\": 2\n },\n {\n \"doc_id\": \"21376310\",\n \"title\": \"A hybrid feature selection method for DNA microarray data.\",\n \"abstract\": \"Gene expression profiles, which represent the state of a cell at a molecular level, have great potential as a medical diagnosis tool. In cancer classification, available training data sets are generally of a fairly small sample size compared to the number of genes involved. Along with training data limitations, this constitutes a challenge to certain classification methods. Feature (gene) selection can be used to successfully extract those genes that directly influence classification accuracy and to eliminate genes which have no influence on it. This significantly improves calculation performance and classification accuracy. In this paper, correlation-based feature selection (CFS) and the Taguchi-genetic algorithm (TGA) method were combined into a hybrid method, and the K-nearest neighbor (KNN) with the leave-one-out cross-validation (LOOCV) method served as a classifier for eleven classification profiles to calculate the classification accuracy. Experimental results show that the proposed method reduced redundant features effectively and achieved superior classification accuracy. The classification accuracy obtained by the proposed method was higher in ten out of the eleven gene expression data set test problems when compared to other classification methods from the literature.\",\n \"corpus_id\": 13279505,\n \"score\": 2\n },\n {\n \"doc_id\": \"22369383\",\n \"title\": \"Gene selection and classification for cancer microarray data based on machine learning and similarity measures.\",\n \"abstract\": \"BACKGROUND: Microarray data have a high dimension of variables and a small sample size. In microarray data analyses, two important issues are how to choose genes, which provide reliable and good prediction for disease status, and how to determine the final gene set that is best for classification. Associations among genetic markers mean one can exploit information redundancy to potentially reduce classification cost in terms of time and money. RESULTS: To deal with redundant information and improve classification, we propose a gene selection method, Recursive Feature Addition, which combines supervised learning and statistical similarity measures. To determine the final optimal gene set for prediction and classification, we propose an algorithm, Lagging Prediction Peephole Optimization. By using six benchmark microarray gene expression data sets, we compared Recursive Feature Addition with recently developed gene selection methods: Support Vector Machine Recursive Feature Elimination, Leave-One-Out Calculation Sequential Forward Selection and several others. CONCLUSIONS: On average, with the use of popular learning machines including Nearest Mean Scaled Classifier, Support Vector Machine, Naive Bayes Classifier and Random Forest, Recursive Feature Addition outperformed other methods. Our studies also showed that Lagging Prediction Peephole Optimization is superior to random strategy; Recursive Feature Addition with Lagging Prediction Peephole Optimization obtained better testing accuracies than the gene selection method varSelRF.\",\n \"corpus_id\": 8591392,\n \"score\": 2\n },\n {\n \"doc_id\": \"23075381\",\n \"title\": \"Combining multiple hypothesis testing and affinity propagation clustering leads to accurate, robust and sample size independent classification on gene expression data.\",\n \"abstract\": \"BACKGROUND: A feature selection method in microarray gene expression data should be independent of platform, disease and dataset size. Our hypothesis is that among the statistically significant ranked genes in a gene list, there should be clusters of genes that share similar biological functions related to the investigated disease. Thus, instead of keeping N top ranked genes, it would be more appropriate to define and keep a number of gene cluster exemplars. RESULTS: We propose a hybrid FS method (mAP-KL), which combines multiple hypothesis testing and affinity propagation (AP)-clustering algorithm along with the Krzanowski & Lai cluster quality index, to select a small yet informative subset of genes. We applied mAP-KL on real microarray data, as well as on simulated data, and compared its performance against 13 other feature selection approaches. Across a variety of diseases and number of samples, mAP-KL presents competitive classification results, particularly in neuromuscular diseases, where its overall AUC score was 0.91. Furthermore, mAP-KL generates concise yet biologically relevant and informative N-gene expression signatures, which can serve as a valuable tool for diagnostic and prognostic purposes, as well as a source of potential disease biomarkers in a broad range of diseases. CONCLUSIONS: mAP-KL is a data-driven and classifier-independent hybrid feature selection method, which applies to any disease classification problem based on microarray data, regardless of the available samples. Combining multiple hypothesis testing and AP leads to subsets of genes, which classify unknown samples from both, small and large patient cohorts with high accuracy.\",\n \"corpus_id\": 15805933,\n \"score\": 2\n },\n {\n \"doc_id\": \"23148517\",\n \"title\": \"Improving accuracy for cancer classification with a new algorithm for genes selection.\",\n \"abstract\": \"BACKGROUND: Even though the classification of cancer tissue samples based on gene expression data has advanced considerably in recent years, it faces great challenges to improve accuracy. One of the challenges is to establish an effective method that can select a parsimonious set of relevant genes. So far, most methods for gene selection in literature focus on screening individual or pairs of genes without considering the possible interactions among genes. Here we introduce a new computational method named the Binary Matrix Shuffling Filter (BMSF). It not only overcomes the difficulty associated with the search schemes of traditional wrapper methods and overfitting problem in large dimensional search space but also takes potential gene interactions into account during gene selection. This method, coupled with Support Vector Machine (SVM) for implementation, often selects very small number of genes for easy model interpretability. RESULTS: We applied our method to 9 two-class gene expression datasets involving human cancers. During the gene selection process, the set of genes to be kept in the model was recursively refined and repeatedly updated according to the effect of a given gene on the contributions of other genes in reference to their usefulness in cancer classification. The small number of informative genes selected from each dataset leads to significantly improved leave-one-out (LOOCV) classification accuracy across all 9 datasets for multiple classifiers. Our method also exhibits broad generalization in the genes selected since multiple commonly used classifiers achieved either equivalent or much higher LOOCV accuracy than those reported in literature. CONCLUSIONS: Evaluation of a gene's contribution to binary cancer classification is better to be considered after adjusting for the joint effect of a large number of other genes. A computationally efficient search scheme was provided to perform effective search in the extensive feature space that includes possible interactions of many genes. Performance of the algorithm applied to 9 datasets suggests that it is possible to improve the accuracy of cancer classification by a big margin when joint effects of many genes are considered.\",\n \"corpus_id\": 15467622,\n \"score\": 2\n },\n {\n \"doc_id\": \"25048512\",\n \"title\": \"A kernel-based multivariate feature selection method for microarray data classification.\",\n \"abstract\": \"High dimensionality and small sample sizes, and their inherent risk of overfitting, pose great challenges for constructing efficient classifiers in microarray data classification. Therefore a feature selection technique should be conducted prior to data classification to enhance prediction performance. In general, filter methods can be considered as principal or auxiliary selection mechanism because of their simplicity, scalability, and low computational complexity. However, a series of trivial examples show that filter methods result in less accurate performance because they ignore the dependencies of features. Although few publications have devoted their attention to reveal the relationship of features by multivariate-based methods, these methods describe relationships among features only by linear methods. While simple linear combination relationship restrict the improvement in performance. In this paper, we used kernel method to discover inherent nonlinear correlations among features as well as between feature and target. Moreover, the number of orthogonal components was determined by kernel Fishers linear discriminant analysis (FLDA) in a self-adaptive manner rather than by manual parameter settings. In order to reveal the effectiveness of our method we performed several experiments and compared the results between our method and other competitive multivariate-based features selectors. In our comparison, we used two classifiers (support vector machine, [Formula: see text]-nearest neighbor) on two group datasets, namely two-class and multi-class datasets. Experimental results demonstrate that the performance of our method is better than others, especially on three hard-classify datasets, namely Wang's Breast Cancer, Gordon's Lung Adenocarcinoma and Pomeroy's Medulloblastoma.\",\n \"corpus_id\": 10248536,\n \"score\": 2\n },\n {\n \"doc_id\": \"25912984\",\n \"title\": \"Improving PLS-RFE based gene selection for microarray data classification.\",\n \"abstract\": \"Gene selection plays a crucial role in constructing efficient classifiers for microarray data classification, since microarray data is characterized by high dimensionality and small sample sizes and contains irrelevant and redundant genes. In practical use, partial least squares-based gene selection approaches can obtain gene subsets of good qualities, but are considerably time-consuming. In this paper, we propose to integrate partial least squares based recursive feature elimination (PLS-RFE) with two feature elimination schemes: simulated annealing and square root, respectively, to speed up the feature selection process. Inspired from the strategy of annealing schedule, the two proposed approaches eliminate a number of features rather than one least informative feature during each iteration and the number of removed features decreases as the iteration proceeds. To verify the effectiveness and efficiency of the proposed approaches, we perform extensive experiments on six publicly available microarray data with three typical classifiers, including Naïve Bayes, K-Nearest-Neighbor and Support Vector Machine, and compare our approaches with ReliefF, PLS and PLS-RFE feature selectors in terms of classification accuracy and running time. Experimental results demonstrate that the two proposed approaches accelerate the feature selection process impressively without degrading the classification accuracy and obtain more compact feature subsets for both two-category and multi-category problems. Further experimental comparisons in feature subset consistency show that the proposed approach with simulated annealing scheme not only has better time performance, but also obtains slightly better feature subset consistency than the one with square root scheme.\",\n \"corpus_id\": 23269611,\n \"score\": 2\n },\n {\n \"doc_id\": \"25961028\",\n \"title\": \"mRMR-ABC: A Hybrid Gene Selection Algorithm for Cancer Classification Using Microarray Gene Expression Profiling.\",\n \"abstract\": \"An artificial bee colony (ABC) is a relatively recent swarm intelligence optimization approach. In this paper, we propose the first attempt at applying ABC algorithm in analyzing a microarray gene expression profile. In addition, we propose an innovative feature selection algorithm, minimum redundancy maximum relevance (mRMR), and combine it with an ABC algorithm, mRMR-ABC, to select informative genes from microarray profile. The new approach is based on a support vector machine (SVM) algorithm to measure the classification accuracy for selected genes. We evaluate the performance of the proposed mRMR-ABC algorithm by conducting extensive experiments on six binary and multiclass gene expression microarray datasets. Furthermore, we compare our proposed mRMR-ABC algorithm with previously known techniques. We reimplemented two of these techniques for the sake of a fair comparison using the same parameters. These two techniques are mRMR when combined with a genetic algorithm (mRMR-GA) and mRMR when combined with a particle swarm optimization algorithm (mRMR-PSO). The experimental results prove that the proposed mRMR-ABC algorithm achieves accurate classification performance using small number of predictive genes when tested using both datasets and compared to previously suggested methods. This shows that mRMR-ABC is a promising approach for solving gene selection and cancer classification problems.\",\n \"corpus_id\": 14702825,\n \"score\": 2\n },\n {\n \"doc_id\": \"26159165\",\n \"title\": \"Optimal combination of feature selection and classification via local hyperplane based learning strategy.\",\n \"abstract\": \"BACKGROUND: Classifying cancers by gene selection is among the most important and challenging procedures in biomedicine. A major challenge is to design an effective method that eliminates irrelevant, redundant, or noisy genes from the classification, while retaining all of the highly discriminative genes. RESULTS: We propose a gene selection method, called local hyperplane-based discriminant analysis (LHDA). LHDA adopts two central ideas. First, it uses a local approximation rather than global measurement; second, it embeds a recently reported classification model, K-Local Hyperplane Distance Nearest Neighbor(HKNN) classifier, into its discriminator. Through classification accuracy-based iterations, LHDA obtains the feature weight vector and finally extracts the optimal feature subset. The performance of the proposed method is evaluated in extensive experiments on synthetic and real microarray benchmark datasets. Eight classical feature selection methods, four classification models and two popular embedded learning schemes, including k-nearest neighbor (KNN), hyperplane k-nearest neighbor (HKNN), Support Vector Machine (SVM) and Random Forest are employed for comparisons. CONCLUSION: The proposed method yielded comparable to or superior performances to seven state-of-the-art models. The nice performance demonstrate the superiority of combining feature weighting with model learning into an unified framework to achieve the two tasks simultaneously.\",\n \"corpus_id\": 21786887,\n \"score\": 2\n },\n {\n \"doc_id\": \"26298581\",\n \"title\": \"A Filter Feature Selection Method Based on MFA Score and Redundancy Excluding and It's Application to Tumor Gene Expression Data Analysis.\",\n \"abstract\": \"Feature selection techniques have been widely applied to tumor gene expression data analysis in recent years. A filter feature selection method named marginal Fisher analysis score (MFA score) which is based on graph embedding has been proposed, and it has been widely used mainly because it is superior to Fisher score. Considering the heavy redundancy in gene expression data, we proposed a new filter feature selection technique in this paper. It is named MFA score+ and is based on MFA score and redundancy excluding. We applied it to an artificial dataset and eight tumor gene expression datasets to select important features and then used support vector machine as the classifier to classify the samples. Compared with MFA score, t test and Fisher score, it achieved higher classification accuracy.\",\n \"corpus_id\": 14706675,\n \"score\": 2\n },\n {\n \"doc_id\": \"26405958\",\n \"title\": \"An effective fuzzy kernel clustering analysis approach for gene expression data.\",\n \"abstract\": \"Fuzzy clustering is an important tool for analyzing microarray data. A major problem in applying fuzzy clustering method to microarray gene expression data is the choice of parameters with cluster number and centers. This paper proposes a new approach to fuzzy kernel clustering analysis (FKCA) that identifies desired cluster number and obtains more steady results for gene expression data. First of all, to optimize characteristic differences and estimate optimal cluster number, Gaussian kernel function is introduced to improve spectrum analysis method (SAM). By combining subtractive clustering with max-min distance mean, maximum distance method (MDM) is proposed to determine cluster centers. Then, the corresponding steps of improved SAM (ISAM) and MDM are given respectively, whose superiority and stability are illustrated through performing experimental comparisons on gene expression data. Finally, by introducing ISAM and MDM into FKCA, an effective improved FKCA algorithm is proposed. Experimental results from public gene expression data and UCI database show that the proposed algorithms are feasible for cluster analysis, and the clustering accuracy is higher than the other related clustering algorithms.\",\n \"corpus_id\": 28176899,\n \"score\": 2\n },\n {\n \"doc_id\": \"27056739\",\n \"title\": \"A centroid-based gene selection method for microarray data classification.\",\n \"abstract\": \"For classification problems based on microarray data, the data typically contains a large number of irrelevant and redundant features. In this paper, a new gene selection method is proposed to choose the best subset of features for microarray data with the irrelevant and redundant features removed. We formulate the selection problem as a L1-regularized optimization problem, based on a newly defined linear discriminant analysis criterion. Instead of calculating the mean of the samples, a kernel-based approach is used to estimate the class centroid to define both the between-class separability and the within-class compactness for the criterion. Theoretical analysis indicates that the global optimal solution of the L1-regularized criterion can be reached with a general condition, on which an efficient algorithm is derived to the feature selection problem in a linear time complexity with respect to the number of features and the number of samples. The experimental results on ten publicly available microarray datasets demonstrate that the proposed method performs effectively and competitively compared with state-of-the-art methods.\",\n \"corpus_id\": 8969124,\n \"score\": 2\n },\n {\n \"doc_id\": \"18023261\",\n \"title\": \"Improved binary PSO for feature selection using gene expression data.\",\n \"abstract\": \"Gene expression profiles, which represent the state of a cell at a molecular level, have great potential as a medical diagnosis tool. Compared to the number of genes involved, available training data sets generally have a fairly small sample size in cancer type classification. These training data limitations constitute a challenge to certain classification methodologies. A reliable selection method for genes relevant for sample classification is needed in order to speed up the processing rate, decrease the predictive error rate, and to avoid incomprehensibility due to the large number of genes investigated. Improved binary particle swarm optimization (IBPSO) is used in this study to implement feature selection, and the K-nearest neighbor (K-NN) method serves as an evaluator of the IBPSO for gene expression data classification problems. Experimental results show that this method effectively simplifies feature selection and reduces the total number of features needed. The classification accuracy obtained by the proposed method has the highest classification accuracy in nine of the 11 gene expression data test problems, and is comparative to the classification accuracy of the two other test problems, as compared to the best results previously published.\",\n \"corpus_id\": 27641839,\n \"score\": 1\n },\n {\n \"doc_id\": \"18334459\",\n \"title\": \"A combination of rough-based feature selection and RBF neural network for classification using gene expression data.\",\n \"abstract\": \"This paper presents a novel rough-based feature selection method for gene expression data analysis. It can find the relevant features without requiring the number of clusters to be known a priori and identify the centers that approximate to the correct ones. In this paper, we attempt to introduce a prediction scheme that combines the rough-based feature selection method with radial basis function neural network. For further consider the effect of different feature selection methods and classifiers on this prediction process, we use the NaIve Bayes and linear support vector machine as classifiers, and compare the performance with other feature selection methods, including information gain and principle component analysis. We demonstrate the performance by several published datasets and the results show that our proposed method can achieve high classification accuracy rate.\",\n \"corpus_id\": 2076812,\n \"score\": 1\n },\n {\n \"doc_id\": \"18534831\",\n \"title\": \"Medical data mining by fuzzy modeling with selected features.\",\n \"abstract\": \"OBJECTIVE: Medical data is often very high dimensional. Depending upon the use, some data dimensions might be more relevant than others. In processing medical data, choosing the optimal subset of features is such important, not only to reduce the processing cost but also to improve the usefulness of the model built from the selected data. This paper presents a data mining study of medical data with fuzzy modeling methods that use feature subsets selected by some indices/methods. METHODS: Specifically, three fuzzy modeling methods including the fuzzy k-nearest neighbor algorithm, a fuzzy clustering-based modeling, and the adaptive network-based fuzzy inference system are employed. For feature selection, a total of 11 indices/methods are used. Medical data mined include the Wisconsin breast cancer dataset and the Pima Indians diabetes dataset. The classification accuracy and computational time are reported. To show how good the best performer is, the globally optimal was also found by carrying out an exhaustive testing of all possible combinations of feature subsets with three features. RESULTS: For the Wisconsin breast cancer dataset, the best accuracy of 97.17% was obtained, which is only 0.25% lower than that was obtained by exhaustive testing. For the Pima Indians diabetes dataset, the best accuracy of 77.65% was obtained, which is only 0.13% lower than that obtained by exhaustive testing. CONCLUSION: This paper has shown that feature selection is important to mining medical data for reducing processing time and for increasing classification accuracy. However, not all combinations of feature selection and modeling methods are equally effective and the best combination is often data-dependent, as supported by the breast cancer and diabetes data analyzed in this paper.\",\n \"corpus_id\": 22988546,\n \"score\": 1\n },\n {\n \"doc_id\": \"19154590\",\n \"title\": \"Combining Pareto-optimal clusters using supervised learning for identifying co-expressed genes.\",\n \"abstract\": \"BACKGROUND: The landscape of biological and biomedical research is being changed rapidly with the invention of microarrays which enables simultaneous view on the transcription levels of a huge number of genes across different experimental conditions or time points. Using microarray data sets, clustering algorithms have been actively utilized in order to identify groups of co-expressed genes. This article poses the problem of fuzzy clustering in microarray data as a multiobjective optimization problem which simultaneously optimizes two internal fuzzy cluster validity indices to yield a set of Pareto-optimal clustering solutions. Each of these clustering solutions possesses some amount of information regarding the clustering structure of the input data. Motivated by this fact, a novel fuzzy majority voting approach is proposed to combine the clustering information from all the solutions in the resultant Pareto-optimal set. This approach first identifies the genes which are assigned to some particular cluster with high membership degree by most of the Pareto-optimal solutions. Using this set of genes as the training set, the remaining genes are classified by a supervised learning algorithm. In this work, we have used a Support Vector Machine (SVM) classifier for this purpose. RESULTS: The performance of the proposed clustering technique has been demonstrated on five publicly available benchmark microarray data sets, viz., Yeast Sporulation, Yeast Cell Cycle, Arabidopsis Thaliana, Human Fibroblasts Serum and Rat Central Nervous System. Comparative studies of the use of different SVM kernels and several widely used microarray clustering techniques are reported. Moreover, statistical significance tests have been carried out to establish the statistical superiority of the proposed clustering approach. Finally, biological significance tests have been carried out using a web based gene annotation tool to show that the proposed method is able to produce biologically relevant clusters of co-expressed genes. CONCLUSION: The proposed clustering method has been shown to perform better than other well-known clustering algorithms in finding clusters of co-expressed genes efficiently. The clusters of genes produced by the proposed technique are also found to be biologically significant, i.e., consist of genes which belong to the same functional groups. This indicates that the proposed clustering method can be used efficiently to identify co-expressed genes in microarray gene expression data. Supplementary Website The pre-processed and normalized data sets, the matlab code and other related materials are available at http://anirbanmukhopadhyay.50webs.com/mogasvm.html.\",\n \"corpus_id\": 1788029,\n \"score\": 1\n },\n {\n \"doc_id\": \"19426455\",\n \"title\": \"A kernel-based approach for detecting outliers of high-dimensional biological data.\",\n \"abstract\": \"BACKGROUND: In many cases biomedical data sets contain outliers that make it difficult to achieve reliable knowledge discovery. Data analysis without removing outliers could lead to wrong results and provide misleading information. RESULTS: We propose a new outlier detection method based on Kullback-Leibler (KL) divergence. The original concept of KL divergence was designed as a measure of distance between two distributions. Stemming from that, we extend it to biological sample outlier detection by forming sample sets composed of nearest neighbors. KL divergence is defined between two sample sets with and without the test sample. To handle the non-linearity of sample distribution, original data is mapped into a higher feature space. We address the singularity problem due to small sample size during KL divergence calculation. Kernel functions are applied to avoid direct use of mapping functions. The performance of the proposed method is demonstrated on a synthetic data set, two public microarray data sets, and a mass spectrometry data set for liver cancer study. Comparative studies with Mahalanobis distance based method and one-class support vector machine (SVM) are reported showing that the proposed method performs better in finding outliers. CONCLUSION: Our idea was derived from Markov blanket algorithm that is a feature selection method based on KL divergence. That is, while Markov blanket algorithm removes redundant and irrelevant features, our proposed method detects outliers. Compared to other algorithms, our proposed method shows better or comparable performance for small sample and high-dimensional biological data. This indicates that the proposed method can be used to detect outliers in biological data sets.\",\n \"corpus_id\": 10383228,\n \"score\": 1\n },\n {\n \"doc_id\": \"19525203\",\n \"title\": \"A new approach for clustering gene expression time series data.\",\n \"abstract\": \"Identifying groups of genes that manifest similar expression patterns is crucial in the analysis of gene expression time series data. Choosing a similarity measure to determine the similarity or distance between profiles is an important task. This paper proposes a suitable dissimilarity measure for gene expression time series data sets. It also presents a graph-based clustering method for finding clusters in gene expression time series data using the new dissimilarity measure. A comparison with other similarity measures used for gene expression data is presented; the new dissimilarity measure is found effective. The clustering method is used in experiments that use real-life datasets and has been found to perform satisfactorily.\",\n \"corpus_id\": 8007902,\n \"score\": 1\n },\n {\n \"doc_id\": \"19594880\",\n \"title\": \"Comparison of feature selection and classification for MALDI-MS data.\",\n \"abstract\": \"INTRODUCTION: In the classification of Mass Spectrometry (MS) proteomics data, peak detection, feature selection, and learning classifiers are critical to classification accuracy. To better understand which methods are more accurate when classifying data, some publicly available peak detection algorithms for Matrix assisted Laser Desorption Ionization Mass Spectrometry (MALDI-MS) data were recently compared; however, the issue of different feature selection methods and different classification models as they relate to classification performance has not been addressed. With the application of intelligent computing, much progress has been made in the development of feature selection methods and learning classifiers for the analysis of high-throughput biological data. The main objective of this paper is to compare the methods of feature selection and different learning classifiers when applied to MALDI-MS data and to provide a subsequent reference for the analysis of MS proteomics data. RESULTS: We compared a well-known method of feature selection, Support Vector Machine Recursive Feature Elimination (SVMRFE), and a recently developed method, Gradient based Leave-one-out Gene Selection (GLGS) that effectively performs microarray data analysis. We also compared several learning classifiers including K-Nearest Neighbor Classifier (KNNC), Naïve Bayes Classifier (NBC), Nearest Mean Scaled Classifier (NMSC), uncorrelated normal based quadratic Bayes Classifier recorded as UDC, Support Vector Machines, and a distance metric learning for Large Margin Nearest Neighbor classifier (LMNN) based on Mahanalobis distance. To compare, we conducted a comprehensive experimental study using three types of MALDI-MS data. CONCLUSION: Regarding feature selection, SVMRFE outperformed GLGS in classification. As for the learning classifiers, when classification models derived from the best training were compared, SVMs performed the best with respect to the expected testing accuracy. However, the distance metric learning LMNN outperformed SVMs and other classifiers on evaluating the best testing. In such cases, the optimum classification model based on LMNN is worth investigating for future study.\",\n \"corpus_id\": 1513386,\n \"score\": 1\n },\n {\n \"doc_id\": \"21205299\",\n \"title\": \"Clustering gene expression data with a penalized graph-based metric.\",\n \"abstract\": \"BACKGROUND: The search for cluster structure in microarray datasets is a base problem for the so-called \\\"-omic sciences\\\". A difficult problem in clustering is how to handle data with a manifold structure, i.e. data that is not shaped in the form of compact clouds of points, forming arbitrary shapes or paths embedded in a high-dimensional space, as could be the case of some gene expression datasets. RESULTS: In this work we introduce the Penalized k-Nearest-Neighbor-Graph (PKNNG) based metric, a new tool for evaluating distances in such cases. The new metric can be used in combination with most clustering algorithms. The PKNNG metric is based on a two-step procedure: first it constructs the k-Nearest-Neighbor-Graph of the dataset of interest using a low k-value and then it adds edges with a highly penalized weight for connecting the subgraphs produced by the first step. We discuss several possible schemes for connecting the different sub-graphs as well as penalization functions. We show clustering results on several public gene expression datasets and simulated artificial problems to evaluate the behavior of the new metric. CONCLUSIONS: In all cases the PKNNG metric shows promising clustering results. The use of the PKNNG metric can improve the performance of commonly used pairwise-distance based clustering methods, to the level of more advanced algorithms. A great advantage of the new procedure is that researchers do not need to learn a new method, they can simply compute distances with the PKNNG metric and then, for example, use hierarchical clustering to produce an accurate and highly interpretable dendrogram of their high-dimensional data.\",\n \"corpus_id\": 10123235,\n \"score\": 1\n },\n {\n \"doc_id\": \"21493051\",\n \"title\": \"A fuzzy-based data transformation for feature extraction to increase classification performance with small medical data sets.\",\n \"abstract\": \"OBJECTIVE: Medical data sets are usually small and have very high dimensionality. Too many attributes will make the analysis less efficient and will not necessarily increase accuracy, while too few data will decrease the modeling stability. Consequently, the main objective of this study is to extract the optimal subset of features to increase analytical performance when the data set is small. METHODS: This paper proposes a fuzzy-based non-linear transformation method to extend classification related information from the original data attribute values for a small data set. Based on the new transformed data set, this study applies principal component analysis (PCA) to extract the optimal subset of features. Finally, we use the transformed data with these optimal features as the input data for a learning tool, a support vector machine (SVM). Six medical data sets: Pima Indians' diabetes, Wisconsin diagnostic breast cancer, Parkinson disease, echocardiogram, BUPA liver disorders dataset, and bladder cancer cases in Taiwan, are employed to illustrate the approach presented in this paper. RESULTS: This research uses the t-test to evaluate the classification accuracy for a single data set; and uses the Friedman test to show the proposed method is better than other methods over the multiple data sets. The experiment results indicate that the proposed method has better classification performance than either PCA or kernel principal component analysis (KPCA) when the data set is small, and suggest creating new purpose-related information to improve the analysis performance. CONCLUSION: This paper has shown that feature extraction is important as a function of feature selection for efficient data analysis. When the data set is small, using the fuzzy-based transformation method presented in this work to increase the information available produces better results than the PCA and KPCA approaches.\",\n \"corpus_id\": 42526756,\n \"score\": 1\n },\n {\n \"doc_id\": \"21939564\",\n \"title\": \"Top scoring pairs for feature selection in machine learning and applications to cancer outcome prediction.\",\n \"abstract\": \"BACKGROUND: The widely used k top scoring pair (k-TSP) algorithm is a simple yet powerful parameter-free classifier. It owes its success in many cancer microarray datasets to an effective feature selection algorithm that is based on relative expression ordering of gene pairs. However, its general robustness does not extend to some difficult datasets, such as those involving cancer outcome prediction, which may be due to the relatively simple voting scheme used by the classifier. We believe that the performance can be enhanced by separating its effective feature selection component and combining it with a powerful classifier such as the support vector machine (SVM). More generally the top scoring pairs generated by the k-TSP ranking algorithm can be used as a dimensionally reduced subspace for other machine learning classifiers. RESULTS: We developed an approach integrating the k-TSP ranking algorithm (TSP) with other machine learning methods, allowing combination of the computationally efficient, multivariate feature ranking of k-TSP with multivariate classifiers such as SVM. We evaluated this hybrid scheme (k-TSP+SVM) in a range of simulated datasets with known data structures. As compared with other feature selection methods, such as a univariate method similar to Fisher's discriminant criterion (Fisher), or a recursive feature elimination embedded in SVM (RFE), TSP is increasingly more effective than the other two methods as the informative genes become progressively more correlated, which is demonstrated both in terms of the classification performance and the ability to recover true informative genes. We also applied this hybrid scheme to four cancer prognosis datasets, in which k-TSP+SVM outperforms k-TSP classifier in all datasets, and achieves either comparable or superior performance to that using SVM alone. In concurrence with what is observed in simulation, TSP appears to be a better feature selector than Fisher and RFE in some of the cancer datasets CONCLUSIONS: The k-TSP ranking algorithm can be used as a computationally efficient, multivariate filter method for feature selection in machine learning. SVM in combination with k-TSP ranking algorithm outperforms k-TSP and SVM alone in simulated datasets and in some cancer prognosis datasets. Simulation studies suggest that as a feature selector, it is better tuned to certain data characteristics, i.e. correlations among informative genes, which is potentially interesting as an alternative feature ranking method in pathway analysis.\",\n \"corpus_id\": 17442787,\n \"score\": 1\n },\n {\n \"doc_id\": \"21982331\",\n \"title\": \"Microarray-based cancer prediction using single genes.\",\n \"abstract\": \"BACKGROUND: Although numerous methods of using microarray data analysis for cancer classification have been proposed, most utilize many genes to achieve accurate classification. This can hamper interpretability of the models and ease of translation to other assay platforms. We explored the use of single genes to construct classification models. We first identified the genes with the most powerful univariate class discrimination ability and then constructed simple classification rules for class prediction using the single genes. RESULTS: We applied our model development algorithm to eleven cancer gene expression datasets and compared classification accuracy to that for standard methods including Diagonal Linear Discriminant Analysis, k-Nearest Neighbor, Support Vector Machine and Random Forest. The single gene classifiers provided classification accuracy comparable to or better than those obtained by existing methods in most cases. We analyzed the factors that determined when simple single gene classification is effective and when more complex modeling is warranted. CONCLUSIONS: For most of the datasets examined, the single-gene classification methods appear to work as well as more standard methods, suggesting that simple models could perform well in microarray-based cancer prediction.\",\n \"corpus_id\": 2914763,\n \"score\": 1\n },\n {\n \"doc_id\": \"22138042\",\n \"title\": \"Robust two-gene classifiers for cancer prediction.\",\n \"abstract\": \"Two-gene classifiers have attracted a broad interest for their simplicity and practicality. Most existing two-gene classification algorithms were involved in exhaustive search that led to their low time-efficiencies. In this study, we proposed two new two-gene classification algorithms which used simple univariate gene selection strategy and constructed simple classification rules based on optimal cut-points for two genes selected. We detected the optimal cut-point with the information entropy principle. We applied the two-gene classification models to eleven cancer gene expression datasets and compared their classification performance to that of some established two-gene classification models like the top-scoring pairs model and the greedy pairs model, as well as standard methods including Diagonal Linear Discriminant Analysis, k-Nearest Neighbor, Support Vector Machine and Random Forest. These comparisons indicated that the performance of our two-gene classifiers was comparable to or better than that of compared models.\",\n \"corpus_id\": 412865,\n \"score\": 1\n },\n {\n \"doc_id\": \"22475749\",\n \"title\": \"Gene expression data analysis using multiobjective clustering improved with SVM based ensemble.\",\n \"abstract\": \"Microarray technology facilitates the monitoring of the expression levels of thousands of genes over different experimental conditions simultaneously. Clustering is a popular data mining tool which can be applied to microarray gene expression data to identify co-expressed genes. Most of the traditional clustering methods optimize a single clustering goodness criterion and thus may not be capable of performing well on all kinds of datasets. Motivated by this, in this article, a multiobjective clustering technique that optimizes cluster compactness and separation simultaneously, has been improved through a novel support vector machine classification based cluster ensemble method. The superiority of MOCSVMEN (MultiObjective Clustering with Support Vector Machine based ENsemble) has been established by comparing its performance with that of several well known existing microarray data clustering algorithms. Two real-life benchmark gene expression datasets have been used for testing the comparative performances of different algorithms. A recently developed metric, called Biological Homogeneity Index (BHI), which computes the clustering goodness with respect to functional annotation, has been used for the comparison purpose.\",\n \"corpus_id\": 34523136,\n \"score\": 1\n },\n {\n \"doc_id\": \"23164195\",\n \"title\": \"Clustering gene expression data using a diffraction-inspired framework.\",\n \"abstract\": \"BACKGROUND: The recent developments in microarray technology has allowed for the simultaneous measurement of gene expression levels. The large amount of captured data challenges conventional statistical tools for analysing and finding inherent correlations between genes and samples. The unsupervised clustering approach is often used, resulting in the development of a wide variety of algorithms. Typical clustering algorithms require selecting certain parameters to operate, for instance the number of expected clusters, as well as defining a similarity measure to quantify the distance between data points. The diffraction-based clustering algorithm however is designed to overcome this necessity for user-defined parameters, as it is able to automatically search the data for any underlying structure. METHODS: The diffraction-based clustering algorithm presented in this paper is tested using five well-known expression datasets pertaining to cancerous tissue samples. The clustering results are then compared to those results obtained from conventional algorithms such as the k-means, fuzzy c-means, self-organising map, hierarchical clustering algorithm, Gaussian mixture model and density-based spatial clustering of applications with noise (DBSCAN). The performance of each algorithm is measured using an average external criterion and an average validity index. RESULTS: The diffraction-based clustering algorithm is shown to be independent of the number of clusters as the algorithm searches the feature space and requires no form of parameter selection. The results show that the diffraction-based clustering algorithm performs significantly better on the real biological datasets compared to the other existing algorithms. CONCLUSION: The results of the diffraction-based clustering algorithm presented in this paper suggest that the method can provide researchers with a new tool for successfully analysing microarray data.\",\n \"corpus_id\": 15141977,\n \"score\": 1\n },\n {\n \"doc_id\": \"23778014\",\n \"title\": \"A classification framework applied to cancer gene expression profiles.\",\n \"abstract\": \"Classification of cancer based on gene expression has provided insight into possible treatment strategies. Thus, developing machine learning methods that can successfully distinguish among cancer subtypes or normal versus cancer samples is important. This work discusses supervised learning techniques that have been employed to classify cancers. Furthermore, a two-step feature selection method based on an attribute estimation method (e.g., ReliefF) and a genetic algorithm was employed to find a set of genes that can best differentiate between cancer subtypes or normal versus cancer samples. The application of different classification methods (e.g., decision tree, k-nearest neighbor, support vector machine (SVM), bagging, and random forest) on 5 cancer datasets shows that no classification method universally outperforms all the others. However, k-nearest neighbor and linear SVM generally improve the classification performance over other classifiers. Finally, incorporating diverse types of genomic data (e.g., protein-protein interaction data and gene expression) increase the prediction accuracy as compared to using gene expression alone.\",\n \"corpus_id\": 11852825,\n \"score\": 1\n },\n {\n \"doc_id\": \"24266942\",\n \"title\": \"Fuzzy support vector machine: an efficient rule-based classification technique for microarrays.\",\n \"abstract\": \"BACKGROUND: The abundance of gene expression microarray data has led to the development of machine learning algorithms applicable for tackling disease diagnosis, disease prognosis, and treatment selection problems. However, these algorithms often produce classifiers with weaknesses in terms of accuracy, robustness, and interpretability. This paper introduces fuzzy support vector machine which is a learning algorithm based on combination of fuzzy classifiers and kernel machines for microarray classification. RESULTS: Experimental results on public leukemia, prostate, and colon cancer datasets show that fuzzy support vector machine applied in combination with filter or wrapper feature selection methods develops a robust model with higher accuracy than the conventional microarray classification models such as support vector machine, artificial neural network, decision trees, k nearest neighbors, and diagonal linear discriminant analysis. Furthermore, the interpretable rule-base inferred from fuzzy support vector machine helps extracting biological knowledge from microarray data. CONCLUSIONS: Fuzzy support vector machine as a new classification model with high generalization power, robustness, and good interpretability seems to be a promising tool for gene expression microarray classification.\",\n \"corpus_id\": 5427410,\n \"score\": 1\n },\n {\n \"doc_id\": \"24625071\",\n \"title\": \"Feature weight estimation for gene selection: a local hyperlinear learning approach.\",\n \"abstract\": \"BACKGROUND: Modeling high-dimensional data involving thousands of variables is particularly important for gene expression profiling experiments, nevertheless,it remains a challenging task. One of the challenges is to implement an effective method for selecting a small set of relevant genes, buried in high-dimensional irrelevant noises. RELIEF is a popular and widely used approach for feature selection owing to its low computational cost and high accuracy. However, RELIEF based methods suffer from instability, especially in the presence of noisy and/or high-dimensional outliers. RESULTS: We propose an innovative feature weighting algorithm, called LHR, to select informative genes from highly noisy data. LHR is based on RELIEF for feature weighting using classical margin maximization. The key idea of LHR is to estimate the feature weights through local approximation rather than global measurement, which is typically used in existing methods. The weights obtained by our method are very robust in terms of degradation of noisy features, even those with vast dimensions. To demonstrate the performance of our method, extensive experiments involving classification tests have been carried out on both synthetic and real microarray benchmark datasets by combining the proposed technique with standard classifiers, including the support vector machine (SVM), k-nearest neighbor (KNN), hyperplane k-nearest neighbor (HKNN), linear discriminant analysis (LDA) and naive Bayes (NB). CONCLUSION: Experiments on both synthetic and real-world datasets demonstrate the superior performance of the proposed feature selection method combined with supervised learning in three aspects: 1) high classification accuracy, 2) excellent robustness to noise and 3) good stability using to various classification algorithms.\",\n \"corpus_id\": 9299356,\n \"score\": 1\n },\n {\n \"doc_id\": \"24678894\",\n \"title\": \"Identification of biomarkers that distinguish chemical contaminants based on gene expression profiles.\",\n \"abstract\": \"BACKGROUND: High throughput transcriptomics profiles such as those generated using microarrays have been useful in identifying biomarkers for different classification and toxicity prediction purposes. Here, we investigated the use of microarrays to predict chemical toxicants and their possible mechanisms of action. RESULTS: In this study, in vitro cultures of primary rat hepatocytes were exposed to 105 chemicals and vehicle controls, representing 14 compound classes. We comprehensively compared various normalization of gene expression profiles, feature selection and classification algorithms for the classification of these 105 chemicals into14 compound classes. We found that normalization had little effect on the averaged classification accuracy. Two support vector machine (SVM) methods, LibSVM and sequential minimal optimization, had better classification performance than other methods. SVM recursive feature selection (SVM-RFE) had the highest overfitting rate when an independent dataset was used for a prediction. Therefore, we developed a new feature selection algorithm called gradient method that had a relatively high training classification as well as prediction accuracy with the lowest overfitting rate of the methods tested. Analysis of biomarkers that distinguished the 14 classes of compounds identified a group of genes principally involved in cell cycle function that were significantly downregulated by metal and inflammatory compounds, but were induced by anti-microbial, cancer related drugs, pesticides, and PXR mediators. CONCLUSIONS: Our results indicate that using microarrays and a supervised machine learning approach to predict chemical toxicants, their potential toxicity and mechanisms of action is practical and efficient. Choosing the right feature and classification algorithms for this multiple category classification and prediction is critical.\",\n \"corpus_id\": 14684503,\n \"score\": 1\n },\n {\n \"doc_id\": \"24808006\",\n \"title\": \"Multiclass feature selection with kernel Gram-matrix-based criteria.\",\n \"abstract\": \"Feature selection has been an important issue in recent decades to determine the most relevant features according to a given classification problem. Numerous methods have emerged that take into account support vector machines (SVMs) in the selection process. Such approaches are powerful but often complex and costly. In this paper, we propose new feature selection methods based on two criteria designed for the optimization of SVM: kernel target alignment and kernel class separability. We demonstrate how these two measures, when fully expressed, can build efficient and simple methods, easily applicable to multiclass problems and iteratively computable with minimal memory requirements. An extensive experimental study is conducted both on artificial and real-world datasets to compare the proposed methods to state-of-the-art feature selection algorithms. The results demonstrate the relevance of the proposed methods both in terms of performance and computational cost.\",\n \"corpus_id\": 7834332,\n \"score\": 1\n },\n {\n \"doc_id\": \"25003163\",\n \"title\": \"Multiobjective binary biogeography based optimization for feature selection using gene expression data.\",\n \"abstract\": \"Gene expression data play an important role in the development of efficient cancer diagnoses and classification. However, gene expression data are usually redundant and noisy, and only a subset of them present distinct profiles for different classes of samples. Thus, selecting high discriminative genes from gene expression data has become increasingly interesting in the field of bioinformatics. In this paper, a multi-objective biogeography based optimization method is proposed to select the small subset of informative gene relevant to the classification. In the proposed algorithm, firstly, the Fisher-Markov selector is used to choose the 60 top gene expression data. Secondly, to make biogeography based optimization suitable for the discrete problem, binary biogeography based optimization, as called BBBO, is proposed based on a binary migration model and a binary mutation model. Then, multi-objective binary biogeography based optimization, as we called MOBBBO, is proposed by integrating the non-dominated sorting method and the crowding distance method into the BBBO framework. Finally, the MOBBBO method is used for gene selection, and support vector machine is used as the classifier with the leave-one-out cross-validation method (LOOCV). In order to show the effective and efficiency of the algorithm, the proposed algorithm is tested on ten gene expression dataset benchmarks. Experimental results demonstrate that the proposed method is better or at least comparable with previous particle swarm optimization (PSO) algorithm and support vector machine (SVM) from literature when considering the quality of the solutions obtained.\",\n \"corpus_id\": 6301202,\n \"score\": 1\n },\n {\n \"doc_id\": \"25549938\",\n \"title\": \"A fast gene selection method for multi-cancer classification using multiple support vector data description.\",\n \"abstract\": \"For cancer classification problems based on gene expression, the data usually has only a few dozen sizes but has thousands to tens of thousands of genes which could contain a large number of irrelevant genes. A robust feature selection algorithm is required to remove irrelevant genes and choose the informative ones. Support vector data description (SVDD) has been applied to gene selection for many years. However, SVDD cannot address the problems with multiple classes since it only considers the target class. In addition, it is time-consuming when applying SVDD to gene selection. This paper proposes a novel fast feature selection method based on multiple SVDD and applies it to multi-class microarray data. A recursive feature elimination (RFE) scheme is introduced to iteratively remove irrelevant features, so the proposed method is called multiple SVDD-RFE (MSVDD-RFE). To make full use of all classes for a given task, MSVDD-RFE independently selects a relevant gene subset for each class. The final selected gene subset is the union of these relevant gene subsets. The effectiveness and accuracy of MSVDD-RFE are validated by experiments on five publicly available microarray datasets. Our proposed method is faster and more effective than other methods.\",\n \"corpus_id\": 36676816,\n \"score\": 1\n },\n {\n \"doc_id\": \"26925688\",\n \"title\": \"Evaluation of Machine Learning Algorithm Utilization for Lung Cancer Classification Based on Gene Expression Levels.\",\n \"abstract\": \"BACKGROUND: Lung cancer remains one of the most common cancers in the world, both in terms of new cases (about 13% of total per year) and deaths (nearly one cancer death in five), because of the high case fatality. Errors in lung cancer type or malignant growth determination lead to degraded treatment efficacy, because anticancer strategy depends on tumor morphology. MATERIALS AND METHODS: We have made an attempt to evaluate effectiveness of machine learning algorithms in the task of lung cancer classification based on gene expression levels. We processed four publicly available data sets. The Dana-Farber Cancer Institute data set contains 203 samples and the task was to classify four cancer types and sound tissue samples. With the University of Michigan data set of 96 samples, the task was to execute a binary classification of adenocarcinoma and non-neoplastic tissues. The University of Toronto data set contains 39 samples and the task was to detect recurrence, while with the Brigham and Women's Hospital data set of 181 samples it was to make a binary classification of malignant pleural mesothelioma and adenocarcinoma. We used the k-nearest neighbor algorithm (k=1, k=5, k=10), naive Bayes classifier with assumption of both a normal distribution of attributes and a distribution through histograms, support vector machine and C4.5 decision tree. Effectiveness of machine learning algorithms was evaluated with the Matthews correlation coefficient. RESULTS: The support vector machine method showed best results among data sets from the Dana-Farber Cancer Institute and Brigham and Women's Hospital. All algorithms with the exception of the C4.5 decision tree showed maximum potential effectiveness in the University of Michigan data set. However, the C4.5 decision tree showed best results for the University of Toronto data set. CONCLUSIONS: Machine learning algorithms can be used for lung cancer morphology classification and similar tasks based on gene expression level evaluation.\",\n \"corpus_id\": 28128074,\n \"score\": 1\n },\n {\n \"doc_id\": \"27081632\",\n \"title\": \"A fuzzy based feature selection from independent component subspace for machine learning classification of microarray data.\",\n \"abstract\": \"Feature (gene) selection and classification of microarray data are the two most interesting machine learning challenges. In the present work two existing feature selection/extraction algorithms, namely independent component analysis (ICA) and fuzzy backward feature elimination (FBFE) are used which is a new combination of selection/extraction. The main objective of this paper is to select the independent components of the DNA microarray data using FBFE to improve the performance of support vector machine (SVM) and Naïve Bayes (NB) classifier, while making the computational expenses affordable. To show the validity of the proposed method, it is applied to reduce the number of genes for five DNA microarray datasets namely; colon cancer, acute leukemia, prostate cancer, lung cancer II, and high-grade glioma. Now these datasets are then classified using SVM and NB classifiers. Experimental results on these five microarray datasets demonstrate that gene selected by proposed approach, effectively improve the performance of SVM and NB classifiers in terms of classification accuracy. We compare our proposed method with principal component analysis (PCA) as a standard extraction algorithm and find that the proposed method can obtain better classification accuracy, using SVM and NB classifiers with a smaller number of selected genes than the PCA. The curve between the average error rate and number of genes with each dataset represents the selection of required number of genes for the highest accuracy with our proposed method for both the classifiers. ROC shows best subset of genes for both the classifier of different datasets with propose method.\",\n \"corpus_id\": 20522236,\n \"score\": 1\n },\n {\n \"doc_id\": \"27154739\",\n \"title\": \"A hybrid gene selection approach for microarray data classification using cellular learning automata and ant colony optimization.\",\n \"abstract\": \"This paper proposes an approach for gene selection in microarray data. The proposed approach consists of a primary filter approach using Fisher criterion which reduces the initial genes and hence the search space and time complexity. Then, a wrapper approach which is based on cellular learning automata (CLA) optimized with ant colony method (ACO) is used to find the set of features which improve the classification accuracy. CLA is applied due to its capability to learn and model complicated relationships. The selected features from the last phase are evaluated using ROC curve and the most effective while smallest feature subset is determined. The classifiers which are evaluated in the proposed framework are K-nearest neighbor; support vector machine and naïve Bayes. The proposed approach is evaluated on 4 microarray datasets. The evaluations confirm that the proposed approach can find the smallest subset of genes while approaching the maximum accuracy.\",\n \"corpus_id\": 5668832,\n \"score\": 1\n },\n {\n \"doc_id\": \"27433543\",\n \"title\": \"Classification of Microarray Data Using Kernel Fuzzy Inference System.\",\n \"abstract\": \"The DNA microarray classification technique has gained more popularity in both research and practice. In real data analysis, such as microarray data, the dataset contains a huge number of insignificant and irrelevant features that tend to lose useful information. Classes with high relevance and feature sets with high significance are generally referred for the selected features, which determine the samples classification into their respective classes. In this paper, kernel fuzzy inference system (K-FIS) algorithm is applied to classify the microarray data (leukemia) using t-test as a feature selection method. Kernel functions are used to map original data points into a higher-dimensional (possibly infinite-dimensional) feature space defined by a (usually nonlinear) function ϕ through a mathematical process called the kernel trick. This paper also presents a comparative study for classification using K-FIS along with support vector machine (SVM) for different set of features (genes). Performance parameters available in the literature such as precision, recall, specificity, F-measure, ROC curve, and accuracy are considered to analyze the efficiency of the classification model. From the proposed approach, it is apparent that K-FIS model obtains similar results when compared with SVM model. This is an indication that the proposed approach relies on kernel function.\",\n \"corpus_id\": 16381822,\n \"score\": 1\n },\n {\n \"doc_id\": \"27879930\",\n \"title\": \"Kernel Based Nonlinear Dimensionality Reduction and Classification for Genomic Microarray.\",\n \"abstract\": \"Genomic microarrays are powerful research tools in bioinformatics and modern medicinal research because they enable massively-parallel assays and simultaneous monitoring of thousands of gene expression of biological samples. However, a simple microarray experiment often leads to very high-dimensional data and a huge amount of information, the vast amount of data challenges researchers into extracting the important features and reducing the high dimensionality. In this paper, a nonlinear dimensionality reduction kernel method based locally linear embedding(LLE) is proposed, and fuzzy K-nearest neighbors algorithm which denoises datasets will be introduced as a replacement to the classical LLE's KNN algorithm. In addition, kernel method based support vector machine (SVM) will be used to classify genomic microarray data sets in this paper. We demonstrate the application of the techniques to two published DNA microarray data sets. The experimental results confirm the superiority and high success rates of the presented method.\",\n \"corpus_id\": 11228877,\n \"score\": 1\n },\n {\n \"doc_id\": \"28141531\",\n \"title\": \"Feature Combination via Clustering.\",\n \"abstract\": \"In image classification, feature combination is often used to combine the merits of multiple complementary features and improve the classification accuracy compared with one single feature. Existing feature combination algorithms, e.g., multiple kernel learning, usually determine the weights of features based on the optimization with respect to some classifier-dependent objective function. These algorithms are often computationally expensive, and in some cases are found to perform no better than simple baselines. In this paper, we solve the feature combination problem from a totally different perspective. Our algorithm is based on the simple idea of combining only base kernels suitable to be combined. Since the very aim of feature combination is to obtain the highest possible classification accuracy, we measure the combination suitableness of two base kernels by the maximum possible cross-validation accuracy of their combined kernel. By regarding the pairwise suitableness as the kernel adjacency, we obtain a weighted graph of all base kernels and find that the base kernels suitable to be combined correspond to a cluster in the graph. We then use the dominant sets algorithm to find the cluster and determine the weights of base kernels automatically. In this way, we transform the kernel combination problem into a clustering one. Our algorithm can be implemented in parallel easily and the running time can be adjusted based on available memory to a large extent. In experiments on several data sets, our algorithm generates comparable classification accuracy with the state of the art.\",\n \"corpus_id\": 3959381,\n \"score\": 1\n },\n {\n \"doc_id\": \"28163197\",\n \"title\": \"Development of a two-stage gene selection method that incorporates a novel hybrid approach using the cuckoo optimization algorithm and harmony search for cancer classification.\",\n \"abstract\": \"For each cancer type, only a few genes are informative. Due to the so-called 'curse of dimensionality' problem, the gene selection task remains a challenge. To overcome this problem, we propose a two-stage gene selection method called MRMR-COA-HS. In the first stage, the minimum redundancy and maximum relevance (MRMR) feature selection is used to select a subset of relevant genes. The selected genes are then fed into a wrapper setup that combines a new algorithm, COA-HS, using the support vector machine as a classifier. The method was applied to four microarray datasets, and the performance was assessed by the leave one out cross-validation method. Comparative performance assessment of the proposed method with other evolutionary algorithms suggested that the proposed algorithm significantly outperforms other methods in selecting a fewer number of genes while maintaining the highest classification accuracy. The functions of the selected genes were further investigated, and it was confirmed that the selected genes are biologically relevant to each cancer type.\",\n \"corpus_id\": 3918931,\n \"score\": 1\n },\n {\n \"doc_id\": \"28182545\",\n \"title\": \"A Gene Selection Method for Microarray Data Based on Binary PSO Encoding Gene-to-Class Sensitivity Information.\",\n \"abstract\": \"Traditional gene selection methods for microarray data mainly considered the features' relevance by evaluating their utility for achieving accurate predication or exploiting data variance and distribution, and the selected genes were usually poorly explicable. To improve the interpretability of the selected genes as well as prediction accuracy, an improved gene selection method based on binary particle swarm optimization (BPSO) and prior information is proposed in this paper. In the proposed method, BPSO encoding gene-to-class sensitivity (GCS) information is used to perform gene selection. The gene-to-class sensitivity information, extracted from the samples by extreme learning machine (ELM), is encoded into the selection process in four aspects: initializing particles, updating the particles, modifying maximum velocity, and adopting mutation operation adaptively. Constrained by the gene-to-class sensitivity information, the new method can select functional gene subsets which are significantly sensitive to the samples' classes. With the few discriminative genes selected by the proposed method, ELM, K-nearest neighbor and support vector machine classifiers achieve much high prediction accuracy on five public microarray data, which in turn verifies the efficiency and effectiveness of the proposed gene selection method.\",\n \"corpus_id\": 3721282,\n \"score\": 1\n },\n {\n \"doc_id\": \"28184251\",\n \"title\": \"A feature selection method based on multiple kernel learning with expression profiles of different types.\",\n \"abstract\": \"BACKGROUND: With the development of high-throughput technology, the researchers can acquire large number of expression data with different types from several public databases. Because most of these data have small number of samples and hundreds or thousands features, how to extract informative features from expression data effectively and robustly using feature selection technique is challenging and crucial. So far, a mass of many feature selection approaches have been proposed and applied to analyse expression data of different types. However, most of these methods only are limited to measure the performances on one single type of expression data by accuracy or error rate of classification. RESULTS: In this article, we propose a hybrid feature selection method based on Multiple Kernel Learning (MKL) and evaluate the performance on expression datasets of different types. Firstly, the relevance between features and classifying samples is measured by using the optimizing function of MKL. In this step, an iterative gradient descent process is used to perform the optimization both on the parameters of Support Vector Machine (SVM) and kernel confidence. Then, a set of relevant features is selected by sorting the optimizing function of each feature. Furthermore, we apply an embedded scheme of forward selection to detect the compact feature subsets from the relevant feature set. CONCLUSIONS: We not only compare the classification accuracy with other methods, but also compare the stability, similarity and consistency of different algorithms. The proposed method has a satisfactory capability of feature selection for analysing expression datasets of different types using different performance measurements.\",\n \"corpus_id\": 472254,\n \"score\": 1\n },\n {\n \"doc_id\": \"28541221\",\n \"title\": \"Subspace Weighting Co-Clustering of Gene Expression Data.\",\n \"abstract\": \"Microarray technology enables the collection of vast amounts of gene expression data from biological experiments. Clustering algorithms have been successfully applied to exploring the gene expression data. Since a set of genes may be possible correlated to a subset of samples, it is useful to use co-clustering to recover co-clusters in the gene expression data. In this paper, we propose a novel algorithm, called Subspace Weighting Co-Clustering (SWCC), for high dimensional gene expression data. In SWCC, a gene subspace weight matrix is introduced to identify the contribution of gene objects in distinguishing different sample clusters. We design a new co-clustering objective function to recover the co-clusters in the gene expression data, in which the subspace weight matrix is employed. An iterative algorithm is developed to solve the objective function, in which the subspace weight matrix is automatically computed during the iterative co-clustering process. Our empirical study shows encouraging results of the proposed algorithm in comparison with six state-of-the-art clustering algorithms on ten gene expression data sets. We also propose to use SWCC for gene clustering and selection. The experimental results show that the selected genes can improve the classification performance of Random Forests.\",\n \"corpus_id\": 11075097,\n \"score\": 1\n },\n {\n \"doc_id\": \"28567418\",\n \"title\": \"A Cancer Gene Selection Algorithm Based on the K-S Test and CFS.\",\n \"abstract\": \"BACKGROUND: To address the challenging problem of selecting distinguished genes from cancer gene expression datasets, this paper presents a gene subset selection algorithm based on the Kolmogorov-Smirnov (K-S) test and correlation-based feature selection (CFS) principles. The algorithm selects distinguished genes first using the K-S test, and then, it uses CFS to select genes from those selected by the K-S test. RESULTS: We adopted support vector machines (SVM) as the classification tool and used the criteria of accuracy to evaluate the performance of the classifiers on the selected gene subsets. This approach compared the proposed gene subset selection algorithm with the K-S test, CFS, minimum-redundancy maximum-relevancy (mRMR), and ReliefF algorithms. The average experimental results of the aforementioned gene selection algorithms for 5 gene expression datasets demonstrate that, based on accuracy, the performance of the new K-S and CFS-based algorithm is better than those of the K-S test, CFS, mRMR, and ReliefF algorithms. CONCLUSIONS: The experimental results show that the K-S test-CFS gene selection algorithm is a very effective and promising approach compared to the K-S test, CFS, mRMR, and ReliefF algorithms.\",\n \"corpus_id\": 3796098,\n \"score\": 1\n },\n {\n \"doc_id\": \"29535919\",\n \"title\": \"Improving Classification of Cancer and Mining Biomarkers from Gene Expression Profiles Using Hybrid Optimization Algorithms and Fuzzy Support Vector Machine.\",\n \"abstract\": \"Background: Gene expression data are characteristically high dimensional with a small sample size in contrast to the feature size and variability inherent in biological processes that contribute to difficulties in analysis. Selection of highly discriminative features decreases the computational cost and complexity of the classifier and improves its reliability for prediction of a new class of samples. Methods: The present study used hybrid particle swarm optimization and genetic algorithms for gene selection and a fuzzy support vector machine (SVM) as the classifier. Fuzzy logic is used to infer the importance of each sample in the training phase and decrease the outlier sensitivity of the system to increase the ability to generalize the classifier. A decision-tree algorithm was applied to the most frequent genes to develop a set of rules for each type of cancer. This improved the abilities of the algorithm by finding the best parameters for the classifier during the training phase without the need for trial-and-error by the user. The proposed approach was tested on four benchmark gene expression profiles. Results: Good results have been demonstrated for the proposed algorithm. The classification accuracy for leukemia data is 100%, for colon cancer is 96.67% and for breast cancer is 98%. The results show that the best kernel used in training the SVM classifier is the radial basis function. Conclusions: The experimental results show that the proposed algorithm can decrease the dimensionality of the dataset, determine the most informative gene subset, and improve classification accuracy using the optimal parameters of the classifier with no user interface.\",\n \"corpus_id\": 3886504,\n \"score\": 1\n },\n {\n \"doc_id\": \"18390369\",\n \"title\": \"Customizing kernel functions for SVM-based hyperspectral image classification.\",\n \"abstract\": \"Previous research applying kernel methods such as support vector machines (SVMs) to hyperspectral image classification has achieved performance competitive with the best available algorithms. However, few efforts have been made to extend SVMs to cover the specific requirements of hyperspectral image classification, for example, by building tailor-made kernels. Observation of real-life spectral imagery from the AVIRIS hyperspectral sensor shows that the useful information for classification is not equally distributed across bands, which provides potential to enhance the SVM's performance through exploring different kernel functions. Spectrally weighted kernels are, therefore, proposed, and a set of particular weights is chosen by either optimizing an estimate of generalization error or evaluating each band's utility level. To assess the effectiveness of the proposed method, experiments are carried out on the publicly available 92AV3C dataset collected from the 220-dimensional AVIRIS hyperspectral sensor. Results indicate that the method is generally effective in improving performance: spectral weighting based on learning weights by gradient descent is found to be slightly better than an alternative method based on estimating \\\"relevance\\\" between band information and ground truth.\",\n \"corpus_id\": 5799578,\n \"score\": 0\n },\n {\n \"doc_id\": \"19179252\",\n \"title\": \"Constructing ensembles of classifiers by means of weighted instance selection.\",\n \"abstract\": \"In this paper, we approach the problem of constructing ensembles of classifiers from the point of view of instance selection. Instance selection is aimed at obtaining a subset of the instances available for training capable of achieving, at least, the same performance as the whole training set. In this way, instance selection algorithms try to keep the performance of the classifiers while reducing the number of instances in the training set. Meanwhile, boosting methods construct an ensemble of classifiers iteratively focusing each new member on the most difficult instances by means of a biased distribution of the training instances. In this work, we show how these two methodologies can be combined advantageously. We can use instance selection algorithms for boosting using as objective to optimize the training error weighted by the biased distribution of the instances given by the boosting method. Our method can be considered as boosting by instance selection. Instance selection has mostly been developed and used for k -nearest neighbor ( k -NN) classifiers. So, as a first step, our methodology is suited to construct ensembles of k -NN classifiers. Constructing ensembles of classifiers by means of instance selection has the important feature of reducing the space complexity of the final ensemble as only a subset of the instances is selected for each classifier. However, the methodology is not restricted to k-NN classifier. Other classifiers, such as decision trees and support vector machines (SVMs), may also benefit from a smaller training set, as they produce simpler classifiers if an instance selection algorithm is performed before training. In the experimental section, we show that the proposed approach is able to produce better and simpler ensembles than random subspace method (RSM) method for k-NN and standard ensemble methods for C4.5 and SVMs.\",\n \"corpus_id\": 650561,\n \"score\": 0\n },\n {\n \"doc_id\": \"21103052\",\n \"title\": \"Multi-class clustering of cancer subtypes through SVM based ensemble of pareto-optimal solutions for gene marker identification.\",\n \"abstract\": \"With the advancement of microarray technology, it is now possible to study the expression profiles of thousands of genes across different experimental conditions or tissue samples simultaneously. Microarray cancer datasets, organized as samples versus genes fashion, are being used for classification of tissue samples into benign and malignant or their subtypes. They are also useful for identifying potential gene markers for each cancer subtype, which helps in successful diagnosis of particular cancer types. In this article, we have presented an unsupervised cancer classification technique based on multiobjective genetic clustering of the tissue samples. In this regard, a real-coded encoding of the cluster centers is used and cluster compactness and separation are simultaneously optimized. The resultant set of near-Pareto-optimal solutions contains a number of non-dominated solutions. A novel approach to combine the clustering information possessed by the non-dominated solutions through Support Vector Machine (SVM) classifier has been proposed. Final clustering is obtained by consensus among the clusterings yielded by different kernel functions. The performance of the proposed multiobjective clustering method has been compared with that of several other microarray clustering algorithms for three publicly available benchmark cancer datasets. Moreover, statistical significance tests have been conducted to establish the statistical superiority of the proposed clustering method. Furthermore, relevant gene markers have been identified using the clustering result produced by the proposed clustering method and demonstrated visually. Biological relationships among the gene markers are also studied based on gene ontology. The results obtained are found to be promising and can possibly have important impact in the area of unsupervised cancer classification as well as gene marker identification for multiple cancer subtypes.\",\n \"corpus_id\": 16715576,\n \"score\": 0\n },\n {\n \"doc_id\": \"24287336\",\n \"title\": \"Direct Kernel Perceptron (DKP): ultra-fast kernel ELM-based classification with non-iterative closed-form weight calculation.\",\n \"abstract\": \"The Direct Kernel Perceptron (DKP) (Fernández-Delgado et al., 2010) is a very simple and fast kernel-based classifier, related to the Support Vector Machine (SVM) and to the Extreme Learning Machine (ELM) (Huang, Wang, & Lan, 2011), whose α-coefficients are calculated directly, without any iterative training, using an analytical closed-form expression which involves only the training patterns. The DKP, which is inspired by the Direct Parallel Perceptron, (Auer et al., 2008), uses a Gaussian kernel and a linear classifier (perceptron). The weight vector of this classifier in the feature space minimizes an error measure which combines the training error and the hyperplane margin, without any tunable regularization parameter. This weight vector can be translated, using a variable change, to the α-coefficients, and both are determined without iterative calculations. We calculate solutions using several error functions, achieving the best trade-off between accuracy and efficiency with the linear function. These solutions for the α coefficients can be considered alternatives to the ELM with a new physical meaning in terms of error and margin: in fact, the linear and quadratic DKP are special cases of the two-class ELM when the regularization parameter C takes the values C=0 and C=∞. The linear DKP is extremely efficient and much faster (over a vast collection of 42 benchmark and real-life data sets) than 12 very popular and accurate classifiers including SVM, Multi-Layer Perceptron, Adaboost, Random Forest and Bagging of RPART decision trees, Linear Discriminant Analysis, K-Nearest Neighbors, ELM, Probabilistic Neural Networks, Radial Basis Function neural networks and Generalized ART. Besides, despite its simplicity and extreme efficiency, DKP achieves higher accuracies than 7 out of 12 classifiers, exhibiting small differences with respect to the best ones (SVM, ELM, Adaboost and Random Forest), which are much slower. Thus, the DKP provides an easy and fast way to achieve classification accuracies which are not too far from the best one for a given problem. The C and Matlab code of DKP are freely available.\",\n \"corpus_id\": 19260849,\n \"score\": 0\n },\n {\n \"doc_id\": \"24637294\",\n \"title\": \"Vicinal support vector classifier using supervised kernel-based clustering.\",\n \"abstract\": \"OBJECTIVE: Support vector machines (SVMs) have drawn considerable attention due to their high generalisation ability and superior classification performance compared to other pattern recognition algorithms. However, the assumption that the learning data is identically generated from unknown probability distributions may limit the application of SVMs for real problems. In this paper, we propose a vicinal support vector classifier (VSVC) which is shown to be able to effectively handle practical applications where the learning data may originate from different probability distributions. METHODS: The proposed VSVC method utilises a set of new vicinal kernel functions which are constructed based on supervised clustering in the kernel-induced feature space. Our proposed approach comprises two steps. In the clustering step, a supervised kernel-based deterministic annealing (SKDA) clustering algorithm is employed to partition the training data into different soft vicinal areas of the feature space in order to construct the vicinal kernel functions. In the training step, the SVM technique is used to minimise the vicinal risk function under the constraints of the vicinal areas defined in the SKDA clustering step. RESULTS: Experimental results on both artificial and real medical datasets show our proposed VSVC achieves better classification accuracy and lower computational time compared to a standard SVM. For an artificial dataset constructed from non-separated data, the classification accuracy of VSVC is between 95.5% and 96.25% (using different cluster numbers) which compares favourably to the 94.5% achieved by SVM. The VSVC training time is between 8.75s and 17.83s (for 2-8 clusters), considerable less than the 65.0s required by SVM. On a real mammography dataset, the best classification accuracy of VSVC is 85.7% and thus clearly outperforms a standard SVM which obtains an accuracy of only 82.1%. A similar performance improvement is confirmed on two further real datasets, a breast cancer dataset (74.01% vs. 72.52%) and a heart dataset (84.77% vs. 83.81%), coupled with a reduction in terms of learning time (32.07s vs. 92.08s and 25.00s vs. 53.31s, respectively). Furthermore, the VSVC results in the number of support vectors being equal to the specified cluster number, and hence in a much sparser solution compared to a standard SVM. CONCLUSION: Incorporating a supervised clustering algorithm into the SVM technique leads to a sparse but effective solution, while making the proposed VSVC adaptive to different probability distributions of the training data.\",\n \"corpus_id\": 205694566,\n \"score\": 0\n },\n {\n \"doc_id\": \"24981891\",\n \"title\": \"Semi-supervised weighted kernel clustering based on gravitational search for fault diagnosis.\",\n \"abstract\": \"Supervised learning method, like support vector machine (SVM), has been widely applied in diagnosing known faults, however this kind of method fails to work correctly when new or unknown fault occurs. Traditional unsupervised kernel clustering can be used for unknown fault diagnosis, but it could not make use of the historical classification information to improve diagnosis accuracy. In this paper, a semi-supervised kernel clustering model is designed to diagnose known and unknown faults. At first, a novel semi-supervised weighted kernel clustering algorithm based on gravitational search (SWKC-GS) is proposed for clustering of dataset composed of labeled and unlabeled fault samples. The clustering model of SWKC-GS is defined based on wrong classification rate of labeled samples and fuzzy clustering index on the whole dataset. Gravitational search algorithm (GSA) is used to solve the clustering model, while centers of clusters, feature weights and parameter of kernel function are selected as optimization variables. And then, new fault samples are identified and diagnosed by calculating the weighted kernel distance between them and the fault cluster centers. If the fault samples are unknown, they will be added in historical dataset and the SWKC-GS is used to partition the mixed dataset and update the clustering results for diagnosing new fault. In experiments, the proposed method has been applied in fault diagnosis for rotatory bearing, while SWKC-GS has been compared not only with traditional clustering methods, but also with SVM and neural network, for known fault diagnosis. In addition, the proposed method has also been applied in unknown fault diagnosis. The results have shown effectiveness of the proposed method in achieving expected diagnosis accuracy for both known and unknown faults of rotatory bearing.\",\n \"corpus_id\": 18958371,\n \"score\": 0\n },\n {\n \"doc_id\": \"28668006\",\n \"title\": \"Hyperspectral sensing data analysis based on quasiconformal mapping-based multiple kernels learning machine.\",\n \"abstract\": \"Hyperspectral remote sensing has a strong ability of object information expression, so it provides better support for object classification. Many methods are proposed for the hyperspectral data classification. The spectrum classification is a classical nonlinear problem, and a kernel-based machine is feasible to classify the spectrum data. In the nonlinear kernel-based space, the spectrum data are more discriminative. The kernel functions determine the data distribution in the feature space. In this paper, we propose the quasiconformal multiple kernels-based machine learning for the hyperspectral data classification. In the framework, the structure of hyperspectral data is adaptively adjusted for classification. The multiple kernels extract the multiple features of hyperspectral data for classification. Multiple features-based machine learning exhibits a great potential on the classification of hyperspectral data. Two public datasets, India Pines dataset and Pavia University dataset, are used to test the proposed algorithm. Experimental results demonstrate that the proposed quasiconformal multiple kernels-based hyperspectral data classification method can show competitive performance.\",\n \"corpus_id\": 46843724,\n \"score\": 0\n },\n {\n \"doc_id\": \"29717598\",\n \"title\": \"[Cell data clustering method in flow cytometry based on kernel principal component analysis].\",\n \"abstract\": \"The process of multi-parametric flow cytometry data analysis is complicate and time-consuming,which requires well-trained professionals to operate on. To overcome this limitation, a method for multi-parameter flow cytometry data processing based on kernel principal component analysis(KPCA) was proposed in this paper. The dimensionality of the data was reduced by nonlinear transform. After the new characteristic variables were obtained,automatical clustering can be achieved using improved K-means algorithm. Experimental data of peripheral blood lymphocyte were processed using the principal component analysis(PCA)-based method and KPCA-based method and then the influence of different feature parameter selections was explored. The results indicate that the KPCA can be successfully applied in the multi-parameter flow cytometry data analysis for efficient and accurate cell clustering, which can improve the efficiency of flow cytometry in clinical diagnosis analysis.\",\n \"corpus_id\": 23489249,\n \"score\": 0\n }\n]","isConversational":false}}},{"rowIdx":72,"cells":{"query":{"kind":"string","value":"{\n \"doc_id\": \"28448571\",\n \"title\": \"Localization of adenovirus morphogenesis players, together with visualization of assembly intermediates and failed products, favor a model where assembly and packaging occur concurrently at the periphery of the replication center.\",\n \"abstract\": \"Adenovirus (AdV) morphogenesis is a complex process, many aspects of which remain unclear. In particular, it is not settled where in the nucleus assembly and packaging occur, and whether these processes occur in a sequential or a concerted manner. Here we use immunofluorescence and immunoelectron microscopy (immunoEM) to trace packaging factors and structural proteins at late times post infection by either wildtype virus or a delayed packaging mutant. We show that representatives of all assembly factors are present in the previously recognized peripheral replicative zone, which therefore is the AdV assembly factory. Assembly intermediates and abortive products observed in this region favor a concurrent assembly and packaging model comprising two pathways, one for capsid proteins and another one for core components. Only when both pathways are coupled by correct interaction between packaging proteins and the genome is the viral particle produced. Decoupling generates accumulation of empty capsids and unpackaged cores.\",\n \"corpus_id\": 31813727\n}"},"candidates":{"kind":"list like","value":[{"doc_id":"18614642","title":"Presence of the adenovirus IVa2 protein at a single vertex of the mature virion.","abstract":"Assembly of adenovirus particles is thought to be similar to that of bacteriophages, in which the double-stranded DNA genome is inserted into a preformed empty capsid. Previous studies from our and other laboratories have implicated the viral IVa2 protein as a key component of the encapsidation process. IVa2 binds to the packaging sequence on the viral chromosome in a sequence-specific manner, alone and in conjunction with the viral L4 22K protein. In addition, it interacts with the viral L1 52/55-kDa protein, which is required for DNA packaging. Finally, a mutant virus that does not produce IVa2 is unable to produce any capsids. Therefore, it has been proposed that IVa2 nucleates capsid assembly. A prediction of such a model is that the IVa2 protein would be found at a unique vertex of the mature virion. In this study, the location of IVa2 in the virion has been analyzed using immunogold staining and electron microscopy, and the copy number of IVa2 in virions was determined using three independent methods, quantitative mass spectrometry, metabolic labeling, and Western blotting. The results indicate that it resides at a unique vertex and that there are approximately six to eight IVa2 molecules in each particle. These findings support the hypothesis that the IVa2 protein plays multiple roles in the viral assembly process.","corpus_id":206799861,"score":2},{"doc_id":"19458007","title":"Cryo-electron microscopy structure of adenovirus type 2 temperature-sensitive mutant 1 reveals insight into the cell entry defect.","abstract":"The structure of the adenovirus type 2 temperature-sensitive mutant 1 (Ad2ts1) was determined to a resolution of 10 A by cryo-electron microscopy single-particle reconstruction. Ad2ts1 was prepared at a nonpermissive temperature and contains the precursor forms of the capsid proteins IIIa, VI, and VIII; the core proteins VII, X (mu), and terminal protein (TP); and the L1-52K protein. Cell entry studies have shown that although Ad2ts1 can bind the coxsackievirus and Ad receptor and undergo internalization via alphav integrins, this mutant does not escape from the early endosome and is targeted for degradation. Comparison of the Ad2ts1 structure to that of mature Ad indicates that Ad2ts1 has a different core architecture. The Ad2ts1 core is closely associated with the icosahedral capsid, a connection which may be mediated by preproteins IIIa and VI. Density within hexon cavities is assigned to preprotein VI, and membrane disruption assays show that hexon shields the lytic activity of both the mature and precursor forms of protein VI. The internal surface of the penton base in Ad2ts1 appears to be anchored to the core by interactions with preprotein IIIa. Our structural analyses suggest that these connections to the core inhibit the release of the vertex proteins and lead to the cell entry defect of Ad2ts1.","corpus_id":42480890,"score":2},{"doc_id":"21450831","title":"Characterization of Empty adenovirus particles assembled in the absence of a functional adenovirus IVa2 protein.","abstract":"The molecular mechanism for packaging of the adenovirus (Ad) genome into the capsid is likely similar to that of DNA bacteriophages and herpesviruses-the insertion of viral DNA through a portal structure into a preformed prohead driven by an ATP-hydrolyzing molecular machine. It is speculated that the IVa2 protein of adenovirus is the ATPase providing the power stroke of the packaging machinery. Purified IVa2 binds ATP in vitro and, along with a second Ad protein, the L4 22-kilodalton protein (L4-22K), binds specifically to sequences in the Ad genome that are essential for packaging. The efficiency of binding of these proteins in vitro was correlated with the efficiency of packaging in vivo. By utilizing a virus unable to express IVa2, pm8002, it was reported that IVa2 plays a role in assembly of the empty virion. We wanted to address the question of whether the ATP binding, and hence the putative ATPase activity, of IVa2 was required for its role in virus assembly. Our results show that ATPase activity was not required for the assembly of empty virus particles. In addition, we present evidence that particles were assembled in the absence of IVa2 by using two viruses null for IVa2-a deletion mutant virus, ΔIVa2, and the previously described mutant virus, pm8002. Empty virus particles produced by these IVa2 mutant viruses did not contain detectable viral DNA. We conclude that the major role of IVa2 is in viral DNA packaging. A characterization of the empty particles obtained from the IVa2 mutant viruses compared to wild-type empty particles is presented.","corpus_id":2019468,"score":2},{"doc_id":"21470569","title":"Development of a recombinant adenovirus vector production system free of replication-competent adenovirus by utilizing a packaging size limit of the viral genome.","abstract":"In a conventional adenovirus (Ad) vector production method using 293 cells, homologous recombination between Ad vector DNA and 293 cell-derived Ad E1 DNA occurs with low efficiency, resulting in the generation of replication-competent adenovirus (RCA). RCA can induce the spread of replication-incompetent Ad vectors, leading to unexpected tissue damage. In order to overcome this problem, we developed an Ad vector production system free of RCA generation by utilizing the Ad packaging size limit of the viral genome. It is well known that up to approximately 105% (37.7 kb) of the wild-type genome (35.9 kb) can be packaged in the Ad virion. We designed the Ad vector genome by insertion of a transgene expression cassette into the E3 region, such that homologous recombination between the Ad vector DNA and 293 cell-derived Ad E1 DNA would produce an Ad vector genome that exceeds in the size of the packaging limit. In accord with our strategy, no RCA generation was observed during the passages when we used the E1 (3.2kb)-deleted Ad vectors containing a more than 3.0-kb transgene expression cassette in the E3 region. In contrast, the E1 (3.2kb)-deleted Ad vectors, which retain 37.7 kb of the viral genome and have an insertion of a 2.1-kb transgene expression cassette in the E3 region, generated RCA, although RCA derived from this Ad vector exceeded the packaging size limit (105.0%). These results suggest that RCA generation can be avoided when the genome size of RCA is more than 108.3% (38.9 kb) of the wild-type Ad genome. This Ad vector production system generates safe, easy, and efficient Ad vector stock for both basic study as well as clinical research.","corpus_id":20753430,"score":2},{"doc_id":"21611162","title":"Altering the Ad5 packaging domain affects the maturation of the Ad particles.","abstract":"We have previously described a new family of mutant adenoviruses carrying different combinations of attB/attP sequences from bacteriophage PhiC31 flanking the Ad5 packaging domain. These novel helper viruses have a significantly delayed viral life cycle and a severe packaging impairment, regardless of the presence of PhiC31 recombinase. Their infectious viral titers are significantly lower (100-1000 fold) than those of control adenovirus at 36 hours post-infection, but allow for efficient packaging of helper-dependent adenovirus. In the present work, we have analyzed which steps of the adenovirus life cycle are altered in attB-helper adenoviruses and investigated whether these viruses can provide the necessary viral proteins in trans. The entry of attB-adenoviral genomes into the cell nucleus early at early timepoints post-infection was not impaired and viral protein expression levels were found to be similar to those of control adenovirus. However, electron microscopy and capsid protein composition analyses revealed that attB-adenoviruses remain at an intermediate state of maturation 36 hours post-infection in comparison to control adenovirus which were fully mature and infective at this time point. Therefore, an additional 20-24 hours were found to be required for the appearance of mature attB-adenovirus. Interestingly, attB-adenovirus assembly and infectivity was restored by inserting a second packaging signal close to the right-end ITR, thus discarding the possibility that the attB-adenovirus genome was retained in a nuclear compartment deleterious for virus assembly. The present study may have substantive implications for helper-dependent adenovirus technology since helper attB-adenovirus allows for preferential packaging of helper-dependent adenovirus genomes.","corpus_id":12918344,"score":2},{"doc_id":"21632753","title":"Adenovirus structural protein IIIa is involved in the serotype specificity of viral DNA packaging.","abstract":"The packaging of the adenovirus (Ad) genome into a capsid displays serotype specificity. This specificity has been attributed to viral packaging proteins, the IVa2 protein and the L1-52/55K protein. We previously found that the Ad17 L1-52/55K protein was not able to complement the growth of an Ad5 L1-52/55K mutant virus, whereas two other Ad17 packaging proteins, IVa2 and L4-22K, could complement the growth of Ad5 viruses with mutations in the respective genes. In this report, we investigated why the Ad17 L1-52/55K protein was not able to complement the Ad5 L1-52/55K mutant virus. We demonstrate that the Ad17 L1-52/55K protein binds to the Ad5 IVa2 protein in vitro and the Ad5 packaging domain in vivo, activities previously associated with packaging function. The Ad17 L1-52/55K protein also associates with empty Ad5 capsids. Interestingly, we find that the Ad17 L1-52/55K protein is able to complement the growth of an Ad5 L1-52/55K mutant virus in conjunction with the Ad17 structural protein IIIa. The same result was found with the L1-52/55K and IIIa proteins of several other Ad serotypes, including Ad3 and Ad4. The Ad17 IIIa protein associates with empty Ad5 capsids. Consistent with the complementation results, we find that the IIIa protein interacts with the L1-52/55K protein in vitro and associates with the viral packaging domain in vivo. These results underscore the complex nature of virus assembly and genome encapsidation and provide a new model for how the viral genome may tether to the empty capsid during the encapsidation process.","corpus_id":46284009,"score":2},{"doc_id":"21925109","title":"Kinesin-1-mediated capsid disassembly and disruption of the nuclear pore complex promote virus infection.","abstract":"Many viruses deliver their genomes into the host cell nucleus for replication. However, the size restrictions of the nuclear pore complex (NPC), which regulates the passage of proteins, nucleic acids, and solutes through the nuclear envelope, require virus capsid uncoating before viral DNA can access the nucleus. We report a microtubule motor kinesin-1-mediated and NPC-supported mechanism of adenovirus uncoating. The capsid binds to the NPC filament protein Nup214 and kinesin-1 light-chain Klc1/2. The nucleoporin Nup358, which is bound to Nup214/Nup88, interacts with the kinesin-1 heavy-chain Kif5c to indirectly link the capsid to the kinesin motor. Kinesin-1 disrupts capsids docked at Nup214, which compromises the NPC and dislocates nucleoporins and capsid fragments into the cytoplasm. NPC disruption increases nuclear envelope permeability as indicated by the nuclear influx of large cytoplasmic dextran polymers. Thus, kinesin-1 uncoats viral DNA and compromises NPC integrity, allowing viral genomes nuclear access to promote infection.","corpus_id":21936770,"score":2},{"doc_id":"22496236","title":"Replication-uncoupled histone deposition during adenovirus DNA replication.","abstract":"In infected cells, the chromatin structure of the adenovirus genome DNA plays critical roles in its genome functions. Previously, we reported that in early phases of infection, incoming viral DNA is associated with both viral core protein VII and cellular histones. Here we show that in late phases of infection, newly synthesized viral DNA is also associated with histones. We also found that the knockdown of CAF-1, a histone chaperone that functions in the replication-coupled deposition of histones, does not affect the level of histone H3 bound on viral chromatin, although CAF-1 is accumulated at viral DNA replication foci together with PCNA. Chromatin immunoprecipitation assays using epitope-tagged histone H3 demonstrated that histone variant H3.3, which is deposited onto the cellular genome in a replication-independent manner, is selectively associated with both incoming and newly synthesized viral DNAs. Microscopic analyses indicated that histones but not USF1, a transcription factor that regulates viral late gene expression, are excluded from viral DNA replication foci and that this is achieved by the oligomerization of the DNA binding protein (DBP). Taken together, these results suggest that histone deposition onto newly synthesized viral DNA is most likely uncoupled with viral DNA replication, and a possible role of DBP oligomerization in this replication-uncoupled histone deposition is discussed.","corpus_id":1445380,"score":2},{"doc_id":"22754652","title":"Latest insights on adenovirus structure and assembly.","abstract":"Adenovirus (AdV) capsid organization is considerably complex, not only because of its large size (~950 Å) and triangulation number (pseudo T = 25), but also because it contains four types of minor proteins in specialized locations modulating the quasi-equivalent icosahedral interactions. Up until 2009, only its major components (hexon, penton, and fiber) had separately been described in atomic detail. Their relationships within the virion, and the location of minor coat proteins, were inferred from combining the known crystal structures with increasingly more detailed cryo-electron microscopy (cryoEM) maps. There was no structural information on assembly intermediates. Later on that year, two reports described the structural differences between the mature and immature adenoviral particle, starting to shed light on the different stages of viral assembly, and giving further insights into the roles of core and minor coat proteins during morphogenesis [1,2]. Finally, in 2010, two papers describing the atomic resolution structure of the complete virion appeared [3,4]. These reports represent a veritable tour de force for two structural biology techniques: X-ray crystallography and cryoEM, as this is the largest macromolecular complex solved at high resolution by either of them. In particular, the cryoEM analysis provided an unprecedented clear picture of the complex protein networks shaping the icosahedral shell. Here I review these latest developments in the field of AdV structural studies.","corpus_id":15455524,"score":2},{"doc_id":"22811519","title":"The adenovirus L4-22K protein is multifunctional and is an integral component of crucial aspects of infection.","abstract":"A variety of cellular and viral processes are coordinately regulated during adenovirus (Ad) infection to achieve optimal virus production. The Ad late gene product L4-22K has been associated with disparate activities during infection, including the regulation of late gene expression, viral DNA packaging, and infectious virus production. We generated and characterized two L4-22K mutant viruses to further explore L4-22K functions during viral infection. Our results show that L4-22K is indeed important for temporal control of viral gene expression not only because it activates late gene expression but also because it suppresses early gene expression. We also show that the L4-22K protein binds to viral packaging sequences in vivo and is essential to recruit two other packaging proteins, IVa2 and L1-52/55K, to this region. The elimination of L4-22K gave rise to the production of only empty virus capsids and not mature virions, which confirms that the L4-22K protein is required for Ad genome packaging. Finally, L4-22K contributes to adenovirus-induced cell death by regulating the expression of the adenovirus death protein. Thus, the adenovirus L4-22K protein is multifunctional and an integral component of crucial aspects of infection.","corpus_id":31270881,"score":2},{"doc_id":"23388198","title":"Adenoviral E2 IVa2 protein interacts with L4 33K protein and E2 DNA-binding protein.","abstract":"Adenovirus (AdV) is thought to follow a sequential assembly pathway similar to that observed in dsDNA bacteriophages and herpesviruses. First, empty capsids are assembled, and then the genome is packaged through a ring-like structure, referred to as a portal, located at a unique vertex. In human AdV serotype 5 (HAdV5), the IVa2 protein initiates specific recognition of viral genome by associating with the viral packaging domain located between nucleotides 220 and 400 of the genome. IVa2 is located at a unique vertex on mature capsids and plays an essential role during genome packaging, most likely by acting as a DNA packaging ATPase. In this study, we demonstrated interactions among IVa2, 33K and DNA-binding protein (DBP) in virus-infected cells by in vivo cross-linking of HAdV5-infected cells followed by Western blot, and co-immunoprecipitation of IVa2, 33K and DBP from nuclear extracts of HAdV5-infected cells. Confocal microscopy demonstrated co-localization of IVa2, 33K and DBP in virus-infected cells and also in cells transfected with IVa2, 33K and DBP genes. Immunogold electron microscopy of purified HAdV5 showed the presence of IVa2, 33K or DBP at a single site on the virus particles. Our results provide indirect evidence that IVa2, 33K and DBP may form a complex at a unique vertex on viral capsids and cooperate in genome packaging.","corpus_id":12599446,"score":2},{"doc_id":"23552425","title":"The adenovirus L4-33K protein regulates both late gene expression patterns and viral DNA packaging.","abstract":"The adenovirus (Ad) L4-33K protein has been linked to disparate functions during infection. L4-33K is a virus-encoded alternative RNA splicing factor which activates splicing of viral late gene transcripts that contain weak 3' splice sites. Additionally, L4-33K has been indicated to play a role in adenovirus assembly. We generated and characterized an Ad5 L4-33K mutant virus to further explore its function(s) during infection. Infectivity, viral genome replication, and most viral gene expression of the L4-33K mutant virus are comparable to those of the wild-type virus, except for a prominent decrease in the levels of the late proteins IIIa and pVI. The L4-33K mutant virus produces only empty capsids, indicating a defect in viral DNA packaging. We demonstrate that L4-33K does not preferentially bind to viral packaging sequences in vivo, and mutation of L4-33K does not interfere with the binding of the known viral packaging proteins IVa2, L4-22K, L1-52/55K, and IIIa to the packaging sequences in vivo. Collectively, these results demonstrate that the phenotype of an Ad5 L4-33K mutant virus is complex. The L4-33K protein regulates the accumulation of selective Ad late gene mRNAs and is involved in the proper transition of gene expression during the late phase of infection. The L4-33K protein also plays a role in adenovirus morphogenesis by promoting the packaging of the viral genome into the empty capsid. These results demonstrate the multifunctional nature of the L4-33K protein and its involvement in several different and critical aspects of viral infection.","corpus_id":32056891,"score":2},{"doc_id":"23637408","title":"The adenovirus L4-22K protein has distinct functions in the posttranscriptional regulation of gene expression and encapsidation of the viral genome.","abstract":"The adenovirus L4-22K protein is multifunctional and critical for different aspects of viral infection. Packaging of the viral genome into an empty capsid absolutely requires the L4-22K protein to bind to packaging sequences in cooperation with other viral proteins. Additionally, the L4-22K protein is important for the temporal switch from the early to late phase of infection by regulating both early and late gene expression. To better understand the molecular mechanisms of these key functions of the L4-22K protein, we focused our studies on the role of conserved pairs of cysteine and histidine residues in the C-terminal region of L4-22K. We found that mutation of the cysteine residues affected the production of infectious progeny virus but did not interfere with the ability of the L4-22K protein to regulate viral gene expression. These results demonstrate that these two functions of L4-22K may be uncoupled. Mutation of the histidine residues resulted in a mutant with a similar phenotype as a virus deficient in the L4-22K protein, where both viral genome packaging and viral gene expression patterns were disrupted. Interestingly, both mutant L4-22K proteins bound to adenovirus packaging sequences, indicating that the paired cysteine and histidine residues do not function as a zinc finger DNA binding motif. Our results reveal that the L4-22K protein controls viral gene expression at the posttranscriptional level and regulates the accumulation of the L4-33K protein, another critical viral regulator, at the level of alternative pre-mRNA splicing.","corpus_id":19966284,"score":2},{"doc_id":"24227847","title":"Processing of the l1 52/55k protein by the adenovirus protease: a new substrate and new insights into virion maturation.","abstract":"Late in adenovirus assembly, the viral protease (AVP) becomes activated and cleaves multiple copies of three capsid and three core proteins. Proteolytic maturation is an absolute requirement to render the viral particle infectious. We show here that the L1 52/55k protein, which is present in empty capsids but not in mature virions and is required for genome packaging, is the seventh substrate for AVP. A new estimate on its copy number indicates that there are about 50 molecules of the L1 52/55k protein in the immature virus particle. Using a quasi-in vivo situation, i.e., the addition of recombinant AVP to mildly disrupted immature virus particles, we show that cleavage of L1 52/55k is DNA dependent, as is the cleavage of the other viral precursor proteins, and occurs at multiple sites, many not conforming to AVP consensus cleavage sites. Proteolytic processing of L1 52/55k disrupts its interactions with other capsid and core proteins, providing a mechanism for its removal during viral maturation. Our results support a model in which the role of L1 52/55k protein during assembly consists in tethering the viral core to the icosahedral shell and in which maturation proceeds simultaneously with packaging, before the viral particle is sealed.","corpus_id":870372,"score":2},{"doc_id":"24854002","title":"Conserved regions of bovine adenovirus-3 pVIII contain functional domains involved in nuclear localization and packaging in mature infectious virions.","abstract":"Adenoviruses are non-enveloped DNA viruses that replicate in the nucleus of infected cells. One of the core proteins, named pVIII, is a minor capsid protein connecting the core with the inner surface of the capsid. Here, we report the characterization of minor capsid protein pVIII encoded by the L6 region of bovine adenovirus (BAdV)-3. Anti-pVIII serum detected a 24 kDa protein at 12-48 h post-infection and an additional 8 kDa protein at 24-48 h post-infection. While the 24 kDa protein was detected in empty capsids, only the C-terminal-cleaved 8 kDa protein was detected in the mature virion, suggesting that amino acids147-216 of the conserved C-terminus of BAdV-3 pVIII are incorporated in mature virions. Detection of hexon protein associated with both precursor (24 kDa) and cleaved (8 kDa) forms of pVIII suggest that the C-terminus of pVIII interacts with the hexon. The pVIII protein predominantly localizes to the nucleus of BAdV-3-infected cells utilizing the classical importin α/β dependent nuclear import pathway. Analysis of mutant pVIII demonstrated that amino acids 52-72 of the conserved N-terminus bind to importin α-3 with high affinity and are required for the nuclear localization.","corpus_id":46563611,"score":2},{"doc_id":"25421887","title":"Structure, function and dynamics in adenovirus maturation.","abstract":"Here we review the current knowledge on maturation of adenovirus, a non-enveloped icosahedral eukaryotic virus. The adenovirus dsDNA genome fills the capsid in complex with a large amount of histone-like viral proteins, forming the core. Maturation involves proteolytic cleavage of several capsid and core precursor proteins by the viral protease (AVP). AVP uses a peptide cleaved from one of its targets as a \"molecular sled\" to slide on the viral genome and reach its substrates, in a remarkable example of one-dimensional chemistry. Immature adenovirus containing the precursor proteins lacks infectivity because of its inability to uncoat. The immature core is more compact and stable than the mature one, due to the condensing action of unprocessed core polypeptides; shell precursors underpin the vertex region and the connections between capsid and core. Maturation makes the virion metastable, priming it for stepwise uncoating by facilitating vertex release and loosening the condensed genome and its attachment to the icosahedral shell. The packaging scaffold protein L1 52/55k is also a substrate for AVP. Proteolytic processing of L1 52/55k disrupts its interactions with other virion components, providing a mechanism for its removal during maturation. Finally, possible roles for maturation of the terminal protein are discussed.","corpus_id":18742961,"score":2},{"doc_id":"25954255","title":"Adenoviral L4 33K forms ring-like oligomers and stimulates ATPase activity of IVa2: implications in viral genome packaging.","abstract":"The mechanism of genome packaging in adenoviruses (AdVs) is presumed to be similar to that of dsDNA viruses including herpesviruses and dsDNA phages. First, the empty capsids are assembled after which the viral genome is pushed through a unique vertex by a motor which consists of three minimal components: an ATPase, a small terminase and a portal. Various components of this motor exist as ring-like structures forming a central channel through which the DNA travels during packaging. In AdV, the IVa2 protein is believed to function as a packaging ATPase, however, the equivalents of the small terminase and the portal have not been identified in AdVs. IVa2 interacts with another viral protein late region 4 (L4) 33K which is important for genome packaging. Both IVa2 and 33K are expressed at high levels during the late stage of virus infection. The oligomeric state of IVa2 and 33K was analyzed in virus-infected cells, IVa2 and 33K transfected cells, AdV particles, or as recombinant purified proteins. Electron microscopy of the purified proteins showed ring-like oligomers for both proteins which is consistent with their putative roles as a part of the packaging motor. We found that the ATPase activity of IVa2 is stimulated in the presence of 33K and the AdV genome. Our results suggest that the 33K functions analogous to the small terminase proteins and so will be part of the packaging motor complex.","corpus_id":6119398,"score":2},{"doc_id":"26178997","title":"Structures of Adenovirus Incomplete Particles Clarify Capsid Architecture and Show Maturation Changes of Packaging Protein L1 52/55k.","abstract":"UNLABELLED: Adenovirus is one of the most complex icosahedral, nonenveloped viruses. Even after its structure was solved at near-atomic resolution by both cryo-electron microscopy and X-ray crystallography, the location of minor coat proteins is still a subject of debate. The elaborated capsid architecture is the product of a correspondingly complex assembly process, about which many aspects remain unknown. Genome encapsidation involves the concerted action of five virus proteins, and proteolytic processing by the virus protease is needed to prime the virion for sequential uncoating. Protein L1 52/55k is required for packaging, and multiple cleavages by the maturation protease facilitate its release from the nascent virion. Light-density particles are routinely produced in adenovirus infections and are thought to represent assembly intermediates. Here, we present the molecular and structural characterization of two different types of human adenovirus light particles produced by a mutant with delayed packaging. We show that these particles lack core polypeptide V but do not lack the density corresponding to this protein in the X-ray structure, thereby adding support to the adenovirus cryo-electron microscopy model. The two types of light particles present different degrees of proteolytic processing. Their structures provide the first glimpse of the organization of L1 52/55k protein inside the capsid shell and of how this organization changes upon partial maturation. Immature, full-length L1 52/55k is poised beneath the vertices to engage the virus genome. Upon proteolytic processing, L1 52/55k disengages from the capsid shell, facilitating genome release during uncoating. IMPORTANCE: Adenoviruses have been extensively characterized as experimental systems in molecular biology, as human pathogens, and as therapeutic vectors. However, a clear picture of many aspects of their basic biology is still lacking. Two of these aspects are the location of minor coat proteins in the capsid and the molecular details of capsid assembly. Here, we provide evidence supporting one of the two current models for capsid architecture. We also show for the first time the location of the packaging protein L1 52/55k in particles lacking the virus genome and how this location changes during maturation. Our results contribute to clarifying standing questions in adenovirus capsid architecture and provide new details on the role of L1 52/55k protein in assembly.","corpus_id":5903737,"score":2},{"doc_id":"26491163","title":"A Single Maturation Cleavage Site in Adenovirus Impacts Cell Entry and Capsid Assembly.","abstract":"UNLABELLED: Proteolytic maturation drives the conversion of stable, immature virus particles to a mature, metastable state primed for cell infection. In the case of human adenovirus, this proteolytic cleavage is mediated by the virally encoded protease AVP. Protein VI, an internal capsid cement protein and substrate for AVP, is cleaved at two sites, one of which is near the N terminus of the protein. In mature capsids, the 33 residues at the N terminus of protein VI (pVIn) are sequestered inside the cavity formed by peripentonal hexon trimers at the 5-fold vertex. Here, we describe a glycine-to-alanine mutation in the N-terminal cleavage site of protein VI that profoundly impacts proteolytic processing, the generation of infectious particles, and cell entry. The phenotypic effects associated with this mutant provide a mechanistic framework for understanding the multifunctional nature of protein VI. Based on our findings, we propose that the primary function of the pVIn peptide is to mediate interactions between protein VI and hexon during virus replication, driving hexon nuclear accumulation and particle assembly. Once particles are assembled, AVP-mediated cleavage facilitates the release of the membrane lytic region at the amino terminus of mature VI, allowing it to lyse the endosome during cell infection. These findings highlight the importance of a single maturation cleavage site for both infectious particle production and cell entry and emphasize the exquisite spatiotemporal regulation governing adenovirus assembly and disassembly. IMPORTANCE: Postassembly virus maturation is a cornerstone principle in virology. However, a mechanistic understanding of how icosahedral viruses utilize this process to transform immature capsids into infection-competent particles is largely lacking. Adenovirus maturation involves proteolytic processing of seven precursor proteins. There is currently no information for the role of each independent cleavage event in the generation of infectious virions. To address this, we investigated the proteolytic maturation of one adenovirus precursor molecule, protein VI. Structurally, protein VI cements the outer capsid shell and links it to the viral core. Functionally, protein VI is involved in endosome disruption, subcellular trafficking, transcription activation, and virus assembly. Our studies demonstrate that the multifunctional nature of protein VI is largely linked to its maturation. Through mutational analysis, we show that disrupting the N-terminal cleavage of preprotein VI has major deleterious effects on the assembly of infectious virions and their subsequent ability to infect host cells.","corpus_id":3870130,"score":2},{"doc_id":"26764008","title":"Morphological, Biochemical, and Functional Study of Viral Replication Compartments Isolated from Adenovirus-Infected Cells.","abstract":"UNLABELLED: Adenovirus (Ad) replication compartments (RC) are nuclear microenvironments where the viral genome is replicated and a coordinated program of late gene expression is established. These virus-induced nuclear sites seem to behave as central hubs for the regulation of virus-host cell interactions, since proteins that promote efficient viral replication as well as factors that participate in the antiviral response are coopted and concentrated there. To gain further insight into the activities of viral RC, here we report, for the first time, the morphology, composition, and activities of RC isolated from Ad-infected cells. Morphological analyses of isolated RC particles by superresolution microscopy showed that they were indistinguishable from RC within infected cells and that they displayed a dynamic compartmentalization. Furthermore, the RC-containing fractions (RCf) proved to be functional, as they directed de novo synthesis of viral DNA and RNA as well as RNA splicing, activities that are associated with RC in vivo. A detailed analysis of the production of viral late mRNA from RCf at different times postinfection revealed that viral mRNA splicing occurs in RC and that the synthesis, posttranscriptional processing, and release from RC to the nucleoplasm of individual viral late transcripts are spatiotemporally separate events. The results presented here demonstrate that RCf are a powerful system for detailed study into RC structure, composition, and activities and, as a result, the determination of the molecular mechanisms that induce the formation of these viral sites of adenoviruses and other nuclear-replicating viruses. IMPORTANCE: RC may represent molecular hubs where many aspects of virus-host cell interaction are controlled. Here, we show by superresolution microscopy that RCf have morphologies similar to those of RC within Ad-infected cells and that they appear to be compartmentalized, as nucleolin and DBP display different localization in the periphery of these viral sites. RCf proved to be functional, as they direct de novo synthesis of viral DNA and mRNA, allowing the detailed study of the regulation of viral genome replication and expression. Furthermore, we show that the synthesis and splicing of individual viral late mRNA occurs in RC and that they are subject to different temporal patterns of regulation, from their synthesis to their splicing and release from RC to the nucleoplasm. Hence, RCf represent a novel system to study molecular mechanisms that are orchestrated in viral RC to take control of the infected cell and promote an efficient viral replication cycle.","corpus_id":6160153,"score":2},{"doc_id":"27721809","title":"Components of Adenovirus Genome Packaging.","abstract":"Adenoviruses (AdVs) are icosahedral viruses with double-stranded DNA (dsDNA) genomes. Genome packaging in AdV is thought to be similar to that seen in dsDNA containing icosahedral bacteriophages and herpesviruses. Specific recognition of the AdV genome is mediated by a packaging domain located close to the left end of the viral genome and is mediated by the viral packaging machinery. Our understanding of the role of various components of the viral packaging machinery in AdV genome packaging has greatly advanced in recent years. Characterization of empty capsids assembled in the absence of one or more components involved in packaging, identification of the unique vertex, and demonstration of the role of IVa2, the putative packaging ATPase, in genome packaging have provided compelling evidence that AdVs follow a sequential assembly pathway. This review provides a detailed discussion on the functions of the various viral and cellular factors involved in AdV genome packaging. We conclude by briefly discussing the roles of the empty capsids, assembly intermediates, scaffolding proteins, portal vertex and DNA encapsidating enzymes in AdV assembly and packaging.","corpus_id":15315707,"score":2},{"doc_id":"28628648","title":"The adenovirus major core protein VII is dispensable for virion assembly but is essential for lytic infection.","abstract":"The Adenovirus (Ad) genome within the capsid is tightly associated with a virus-encoded, histone-like core protein-protein VII. Two other Ad core proteins, V and X/μ, also are located within the virion and are loosely associated with viral DNA. Core protein VII remains associated with the Ad genome during the early phase of infection. It is not known if naked Ad DNA is packaged into the capsid, as with dsDNA bacteriophage and herpesviruses, followed by the encapsidation of viral core proteins, or if a unique packaging mechanism exists with Ad where a DNA-protein complex is simultaneously packaged into the virion. The latter model would require an entirely new molecular mechanism for packaging compared to known viral packaging motors. We characterized a virus with a conditional knockout of core protein VII. Remarkably, virus particles were assembled efficiently in the absence of protein VII. No changes in protein composition were evident with VII-virus particles, including the abundance of core protein V, but changes in the proteolytic processing of some capsid proteins were evident. Virus particles that lack protein VII enter the cell, but incoming virions did not escape efficiently from endosomes. This greatly diminished all subsequent aspects of the infectious cycle. These results reveal that the Ad major core protein VII is not required to condense viral DNA within the capsid, but rather plays an unexpected role during virus maturation and the early stages of infection. These results establish a new paradigm pertaining to the Ad assembly mechanism and reveal a new and important role of protein VII in early stages of infection.","corpus_id":7448978,"score":2},{"doc_id":"18674782","title":"DNA packaging motor assembly intermediate of bacteriophage phi29.","abstract":"Unraveling the structure and assembly of the DNA packaging ATPases of the tailed double-stranded DNA bacteriophages is integral to understanding the mechanism of DNA translocation. Here, the bacteriophage phi29 packaging ATPase gene product 16 (gp16) was overexpressed in soluble form in Bacillus subtilis (pSAC), purified to near homogeneity, and assembled to the phi29 precursor capsid (prohead) to produce a packaging motor intermediate that was fully active in in vitro DNA packaging. The formation of higher oligomers of the gp16 from monomers was concentration dependent and was characterized by analytical ultracentrifugation, gel filtration, and electron microscopy. The binding of multiple copies of gp16 to the prohead was dependent on the presence of an oligomer of 174- or 120-base prohead RNA (pRNA) fixed to the head-tail connector at the unique portal vertex of the prohead. The use of mutant pRNAs demonstrated that gp16 bound specifically to the A-helix of pRNA, and ribonuclease footprinting of gp16 on pRNA showed that gp16 protected the CC residues of the CCA bulge (residues 18-20) of the A-helix. The binding of gp16 to the prohead/pRNA to constitute the complete and active packaging motor was confirmed by cryo-electron microscopy three-dimensional reconstruction of the prohead/pRNA/gp16 complex. The complex was capable of supercoiling DNA-gp3 as observed previously for gp16 alone; therefore, the binding of gp16 to the prohead, rather than first to DNA-gp3, represents an alternative packaging motor assembly pathway.","corpus_id":20765445,"score":1},{"doc_id":"19196470","title":"Packaging of viral RNAs in virions of adenoviruses.","abstract":"Earlier, we detected viral RNAs packaged in the porcine adenovirus (PAdV) -3 virions. Using Southern blot analysis, we further demonstrated that the viral RNAs were predominantly packaged in CsCl purified mature capsids (containing viral genome) than empty/intermediate capsids. Some of the packaged viral RNAs appear to be polyadenylated. Real-time reverse transcription (RT)-PCR analysis indicated that the copy number of the tested viral mRNAs encoding E1Bsmall and fiber proteins was less than one per full capsid. Moreover, detection of viral RNA packaged in CsCl purified human adenovirus (HAdV) -5 virions indicates that the viral RNA packaging might be a common phenomenon in members of Adenoviridae family. Further quantitative analysis of viral protein, DNA, and RNA in CsCl purified mature and empty/intermediate capsids of recombinant HAdV-5 expressing enhanced green fluorescent protein indicated that the traceable viral RNA detected in empty/intermediate capsids seems associated with the presence of traceable viral genomic DNA. Taken together, our data suggest that the viral RNAs may be passively packaged in adenovirus virion during encapsidation of viral genomic DNA in cell nuclei. Thus, viral RNA packaging may be a characteristic feature of adenoviral genomic DNA encapsidation.","corpus_id":15462435,"score":1},{"doc_id":"19846532","title":"African swine fever virus polyprotein pp62 is essential for viral core development.","abstract":"One of the most characteristic features of African swine fever virus gene expression is its use of two polyproteins, pp220 and pp62, to produce several structural proteins that account for approximately 32% of the total protein virion mass. Equimolecular amounts of these proteins are the major components of the core shell, a thick protein layer that lies beneath the inner envelope, surrounding the viral nucleoid. Polyprotein pp220, which is located immediately underneath the internal envelope, is essential for the encapsidation of the core of the viral particle. In its absence, the infection produces essentially coreless particles. In this study we analyzed, by means of an IPTG (isopropyl-beta-d-thiogalactopyranoside)-inducible virus, the role of polyprotein pp62 in virus assembly. Polyprotein pp62 is indispensable for viral replication. The repression of polyprotein pp62 expression does not alter late gene expression or the proteolytic processing of the polyprotein pp220. However, it has a profound impact on the subcellular localization of polyprotein pp220. Electron microscopy studies revealed that polyprotein pp62 is necessary for the correct assembly and maturation of the core of the viral particle. Its repression leads to the appearance of a significant fraction of empty particles, to an increase in the number of immature-like particles, and to the accumulation of defective particles. Immunoelectron microscopy analysis showed a clear correlation between the amount of polyprotein pp62, the quantity of polyprotein pp220, and the state of development of the core, suggesting that the complete absence of polyprotein pp62 during morphogenesis would produce a homogenous population of empty particles.","corpus_id":206807788,"score":1},{"doc_id":"20060706","title":"Genome packaging in viruses.","abstract":"Genome packaging is a fundamental process in a viral life cycle. Many viruses assemble preformed capsids into which the genomic material is subsequently packaged. These viruses use a packaging motor protein that is driven by the hydrolysis of ATP to condense the nucleic acids into a confined space. How these motor proteins package viral genomes had been poorly understood until recently, when a few X-ray crystal structures and cryo-electron microscopy (cryo-EM) structures became available. Here we discuss various aspects of genome packaging and compare the mechanisms proposed for packaging motors on the basis of structural information.","corpus_id":19551835,"score":1},{"doc_id":"22734445","title":"Influence of loxP insertion upstream of the cis-acting packaging domain on adenovirus packaging efficiency.","abstract":"First-generation AdV enables efficient gene transduction, although its immunogenicity is an important problem in vivo. Helper-dependent AdV (HD-AdV) is one possible solution to this problem. The construction of HD-AdV requires a helper virus, in which the viral packaging domain is flanked by two inserted loxP to hamper its packaging in Cre-expressing 293 cells. Here, we constructed 19L viruses containing loxP at 191 nt from the left end of the genome upstream of the packaging domain, 15L viruses bearing loxP at 143 nt, and a control ΔL virus lacking loxP at these positions. The 19L position is used worldwide, and the 15L position has been reported to result in a lower titer than that of 19L. When the titers were compared for six pairs of 19L and 15L AdV, the 19L AdV produced titers similar to, or sometimes lower than, the 15L and ΔL AdV, unlike the results of previous reports. We next chose one pair of 15L and 19L AdV that produced titers similar to that of ΔL and a competitor AdV lacking loxP for use in a competition assay. When a small amount of the competitor AdV was co-infected, both the 15L and the 19L AdV, but not ΔL, gradually became minority components during subsequent viral passages. Therefore, the loxP insertions at 143 nt and 191 nt decreased the viral packaging efficiency.","corpus_id":24286363,"score":1},{"doc_id":"23737056","title":"Assembly of simple icosahedral viruses.","abstract":"Icosahedral viruses exhibit elegant pathways of capsid assembly and maturation regulated by symmetry principles. Assembly is a dynamic process driven by consecutive and genetically programmed morphogenetic interactions between protein subunits. The non-symmetric capsid subunits are gathered by hydrophobic contacts and non-covalent interactions in assembly intermediates, which serve as blocks to build a symmetric capsid. In some cases, non-symmetric interactions among intermediates are involved in assembly, highlighting the remarkable capacity of capsid proteins to fold into demanding conformations compatible with a closed protein shell. In this chapter, the morphogenesis of structurally simple icosahedral viruses, including representative members of the parvoviruses, picornaviruses or polyomaviruses as paradigms, is described in some detail. Icosahedral virus assembly may occur in different subcellular compartments and involve a panoplia of cellular and viral factors, chaperones, and protein modifications that, in general, are still poorly characterized. Mechanisms of viral genome encapsidation may imply direct interactions between the genome and the assembly intermediates, or active packaging into a preformed empty capsid. High stability of intermediates and proteolytic cleavages during viral maturation usually contribute to the overall irreversible character of the assembly process. These and other simple icosahedral viruses were pioneer models to understand basic principles of virus assembly, continue to be leading subjects of morphogenetic analyses, and have inspired ongoing studies on the assembly of larger viruses and cellular and synthetic macromolecular complexes.","corpus_id":24767972,"score":1},{"doc_id":"24706827","title":"Solving a Levinthal's paradox for virus assembly identifies a unique antiviral strategy.","abstract":"One of the important puzzles in virology is how viruses assemble the protein containers that package their genomes rapidly and efficiently in vivo while avoiding triggering their hosts' antiviral defenses. Viral assembly appears directed toward a relatively small subset of the vast number of all possible assembly intermediates and pathways, akin to Levinthal's paradox for the folding of polypeptide chains. Using an in silico assembly model, we demonstrate that this reduction in complexity can be understood if aspects of in vivo assembly, which have mostly been neglected in in vitro experimental and theoretical modeling assembly studies, are included in the analysis. In particular, we show that the increasing viral coat protein concentration that occurs in infected cells plays unexpected and vital roles in avoiding potential kinetic assembly traps, significantly reducing the number of assembly pathways and assembly initiation sites, and resulting in enhanced assembly efficiency and genome packaging specificity. Because capsid assembly is a vital determinant of the overall fitness of a virus in the infection process, these insights have important consequences for our understanding of how selection impacts on the evolution of viral quasispecies. These results moreover suggest strategies for optimizing the production of protein nanocontainers for drug delivery and of virus-like particles for vaccination. We demonstrate here in silico that drugs targeting the specific RNA-capsid protein contacts can delay assembly, reduce viral load, and lead to an increase of misencapsidation of cellular RNAs, hence opening up unique avenues for antiviral therapy.","corpus_id":7956841,"score":1},{"doc_id":"24784448","title":"Overexpression of Ad5 precursor terminal protein accelerates recombinant adenovirus packaging and amplification in HEK-293 packaging cells.","abstract":"Recombinant adenoviruses are one of the most common vehicles for efficient in vitro and in vivo gene deliveries. Here, we investigate whether exogenous precursor terminal protein (pTP) expression in 293 cells improves the efficiency of adenovirus packaging and amplification. We used a piggyBac transposon-based vector and engineered a stable 293 line that expresses high level of Ad5 pTP, designated as 293pTP. Using the AdBMP6-GLuc that expresses green fluorescent protein (GFP), BMP6 and Gaussia luciferase, we found that the infectivity of AdBMP6-GLuc viral samples packaged in 293pTP cells was titrated up to 19.3 times higher than that packaged in parental 293 cells. AdBMP6-GLuc viral samples packaged in 293pTP cells exhibited significantly higher transduction efficiency in 143B and immortalized mouse embryonic fibroblast (iMEF) cells, as assessed by fluorescence-activated cell sorting analysis of GFP-positive cells, the luciferase activity assay and BMP6-induced osteogenic marker alkaline phosphatase activities in iMEFs. When adenovirus amplification efficiency was analyzed, we found that 293pTP cells infected with AdBMP6-GLuc yielded up to 12.6 times higher titer than that in parental 293 cells, especially at lower multiplicities of infection. These results strongly suggest that exogenous pTP expression may accelerate the packaging and amplification of recombinant adenoviruses. Thus, the engineered 293pTP cells should be a superior packaging line for efficient adenovirus production.","corpus_id":205145088,"score":1},{"doc_id":"27521148","title":"Deletion of pV affects integrity of capsid causing defect in the infectivity of bovine adenovirus-3.","abstract":"Members of the genus Mastadenovirus including bovine adenovirus 3 (BAdV-3) encode a genus-specific unique protein named pV. The pV encoded by BAdV-3 is a protein of 423 aa showing 40.9 % identity to pV of human adenovirus 2. Here, we report the construction and analysis of recombinant BAdV-3 (BAV.dV) containing deletion of pV. The BAV.dV could only be isolated in CRL.pV cells expressing pV, suggesting that pV appears essential for the infection of BAdV-3. Analysis of BAV.dV suggested that despite affecting some late gene expression in virus-infected cells, there was no significant difference in the incorporation of viral proteins in the mature virions. Moreover, analysis of mature virions revealed degraded capsids leading to change in morphology and infectivity of BAV.dV. Furthermore, analysis of the genome sequence of different clones of BAV.dV passaged in different cell lines revealed no mutations in core proteins pVII and pX\\Mu suggesting that the replication defect may not be rescued. Our results suggest that pV is required for proper viral assembly of BAdV-3 as lack of pV produces aberrant capsids. Moreover, altered capsids lead to the production of non-infectious BAV.dV virions.","corpus_id":24839525,"score":1},{"doc_id":"28528442","title":"Herpesvirus Capsid Assembly and DNA Packaging.","abstract":"Herpes simplex virus type I (HSV-1) is the causative agent of several pathologies ranging in severity from the common cold sore to life-threatening encephalitic infection. During productive lytic infection, over 80 viral proteins are expressed in a highly regulated manner, resulting in the replication of viral genomes and assembly of progeny virions. The virion of all herpesviruses consists of an external membrane envelope, a proteinaceous layer called the tegument, and an icosahedral capsid containing the double-stranded linear DNA genome. The capsid shell of HSV-1 is built from four structural proteins: a major capsid protein, VP5, which forms the capsomers (hexons and pentons), the triplex consisting of VP19C and VP23 found between the capsomers, and VP26 which binds to VP5 on hexons but not pentons. In addition, the dodecameric pUL6 portal complex occupies 1 of the 12 capsid vertices, and the capsid vertex specific component (CVSC), a heterotrimer complex of pUL17, pUL25, and pUL36, binds specifically to the triplexes adjacent to each penton. The capsid is assembled in the nucleus where the viral genome is packaged into newly assembled closed capsid shells. Cleavage and packaging of replicated, concatemeric viral DNA requires the seven viral proteins encoded by the UL6, UL15, UL17, UL25, UL28, UL32, and UL33 genes. Considerable advances have been made in understanding the structure of the herpesvirus capsid and the function of several of the DNA packaging proteins by applying biochemical, genetic, and structural techniques. This review is a summary of recent advances with respect to the structure of the HSV-1 virion capsid and what is known about the function of the seven packaging proteins and their interactions with each other and with the capsid shell.","corpus_id":4054191,"score":1},{"doc_id":"29167340","title":"Human Adenovirus Core Protein V Is Targeted by the Host SUMOylation Machinery To Limit Essential Viral Functions.","abstract":"Human adenoviruses (HAdV) are nonenveloped viruses containing a linear, double-stranded DNA genome surrounded by an icosahedral capsid. To allow proper viral replication, the genome is imported through the nuclear pore complex associated with viral core proteins. Until now, the role of these incoming virion proteins during the early phase of infection was poorly understood. The core protein V is speculated to bridge the core and the surrounding capsid. It binds the genome in a sequence-independent manner and localizes in the nucleus of infected cells, accumulating at nucleoli. Here, we show that protein V contains conserved SUMO conjugation motifs (SCMs). Mutation of these consensus motifs resulted in reduced SUMOylation of the protein; thus, protein V represents a novel target of the host SUMOylation machinery. To understand the role of protein V SUMO posttranslational modification during productive HAdV infection, we generated a replication-competent HAdV with SCM mutations within the protein V coding sequence. Phenotypic analyses revealed that these SCM mutations are beneficial for adenoviral replication. Blocking protein V SUMOylation at specific sites shifts the onset of viral DNA replication to earlier time points during infection and promotes viral gene expression. Simultaneously, the altered kinetics within the viral life cycle are accompanied by more efficient proteasomal degradation of host determinants and increased virus progeny production than that observed during wild-type infection. Taken together, our studies show that protein V SUMOylation reduces virus growth; hence, protein V SUMOylation represents an important novel aspect of the host antiviral strategy to limit virus replication and thereby points to potential intervention strategies. IMPORTANCE Many decades of research have revealed that HAdV structural proteins promote viral entry and mainly physical stability of the viral genome in the capsid. Our work over the last years showed that this concept needs expansion as the functions are more diverse. We showed that capsid protein VI regulates the antiviral response by modulation of the transcription factor Daxx during infection. Moreover, core protein VII interacts with SPOC1 restriction factor, which is beneficial for efficient viral gene expression. Here, we were able to show that core protein V also represents a novel substrate of the host SUMOylation machinery and contains several conserved SCMs; mutation of these consensus motifs reduced SUMOylation of the protein. Unexpectedly, we observed that introducing these mutations into HAdV promotes adenoviral replication. In conclusion, we offer novel insights into adenovirus core proteins and provide evidence that SUMOylation of HAdV factors regulates replication efficiency.","corpus_id":4970916,"score":1},{"doc_id":"18077717","title":"The essential human cytomegalovirus gene UL52 is required for cleavage-packaging of the viral genome.","abstract":"Replication of human cytomegalovirus (HCMV) produces large DNA concatemers of head-to-tail-linked viral genomes that upon packaging into capsids are cut into unit-length genomes. The mechanisms underlying cleavage-packaging and the subsequent steps prior to nuclear egress of DNA-filled capsids are incompletely understood. The hitherto uncharacterized product of the essential HCMV UL52 gene was proposed to participate in these processes. To investigate the function of pUL52, we constructed a DeltaUL52 mutant as well as a complementing cell line. We found that replication of viral DNA was not impaired in noncomplementing cells infected with the DeltaUL52 virus, but viral concatemers remained uncleaved. Since the subnuclear localization of the known cleavage-packaging proteins pUL56, pUL89, and pUL104 was unchanged in DeltaUL52-infected fibroblasts, pUL52 does not seem to act via these proteins. Electron microscopy studies revealed only B capsids in the nuclei of DeltaUL52-infected cells, indicating that the mutant virus has a defect in encapsidation of viral DNA. Generation of recombinant HCMV genomes encoding epitope-tagged pUL52 versions showed that only the N-terminally tagged pUL52 supported viral growth, suggesting that the C terminus is crucial for its function. pUL52 was expressed as a 75-kDa protein with true late kinetics. It localized preferentially to the nuclei of infected cells and was found to enclose the replication compartments. Taken together, our results demonstrate an essential role for pUL52 in cleavage-packaging of HCMV DNA. Given its unique subnuclear localization, the function of pUL52 might be distinct from that of other cleavage-packaging proteins.","corpus_id":18247659,"score":0},{"doc_id":"19812148","title":"Effects of major capsid proteins, capsid assembly, and DNA cleavage/packaging on the pUL17/pUL25 complex of herpes simplex virus 1.","abstract":"The U(L)17 and U(L)25 proteins (pU(L)17 and pU(L)25, respectively) of herpes simplex virus 1 are located at the external surface of capsids and are essential for DNA packaging and DNA retention in the capsid, respectively. The current studies were undertaken to determine whether DNA packaging or capsid assembly affected the pU(L)17/pU(L)25 interaction. We found that pU(L)17 and pU(L)25 coimmunoprecipitated from cells infected with wild-type virus, whereas the major capsid protein VP5 (encoded by the U(L)19 gene) did not coimmunoprecipitate with these proteins under stringent conditions. In addition, pU(L)17 (i) coimmunoprecipitated with pU(L)25 in the absence of other viral proteins, (ii) coimmunoprecipitated with pU(L)25 from lysates of infected cells in the presence or absence of VP5, (iii) did not coimmunoprecipitate efficiently with pU(L)25 in the absence of the triplex protein VP23 (encoded by the U(L)18 gene), (iv) required pU(L)25 for proper solubilization and localization within the viral replication compartment, (v) was essential for the sole nuclear localization of pU(L)25, and (vi) required capsid proteins VP5 and VP23 for nuclear localization and normal levels of immunoreactivity in an indirect immunofluorescence assay. Proper localization of pU(L)25 in infected cell nuclei required pU(L)17, pU(L)32, and the major capsid proteins VP5 and VP23, but not the DNA packaging protein pU(L)15. The data suggest that VP23 or triplexes augment the pU(L)17/pU(L)25 interaction and that VP23 and VP5 induce conformational changes in pU(L)17 and pU(L)25, exposing epitopes that are otherwise partially masked in infected cells. These conformational changes can occur in the absence of DNA packaging. The data indicate that the pU(L)17/pU(L)25 complex requires multiple viral proteins and functions for proper localization and biochemical behavior in the infected cell.","corpus_id":7579552,"score":0},{"doc_id":"20181717","title":"Mutational analysis of the herpes simplex virus type 1 UL25 DNA packaging protein reveals regions that are important after the viral DNA has been packaged.","abstract":"The herpes simplex virus type 1 (HSV-1) UL25 gene encodes a minor capsid protein, pUL25, that is essential for packaging the full-length viral genome. Six regions which contain disordered residues have been identified in the high-resolution structure of pUL25. To investigate the significance of these flexible regions, a panel of plasmids was generated encoding mutant proteins, with each member lacking the disordered residues in one of the six regions. In addition, UL25 constructs were produced, which specified proteins that contained missense mutations individually affecting two of the four regions on the surface of pUL25 predicted from evolutionary trace analysis to be important in protein-protein interactions. The impacts of these mutations on viral DNA packaging, virus assembly, and growth were examined. Of the nine mutant proteins analyzed, five failed to complement the growth of a UL25 deletion mutant in Vero cells. These noncomplementing proteins fell into three classes. Proteins in one class did not alter the DNA packaging phenotype of an HSV-1 UL25 deletion mutant, whereas proteins from the other two classes allowed the UL25 null mutant to package full-length viral DNA. Subsequent analysis of the latter classes of mutant proteins demonstrated that one class enabled the null virus to release enveloped virus particles from U2OS cells, whereas the other class prevented egress of mature HSV-1 capsids from the nucleus. These findings reveal a new role for pUL25 in virion assembly, consistent with its flexible structure and location on the capsid.","corpus_id":9107079,"score":0},{"doc_id":"20845949","title":"Trapping of hepatitis B virus capsid assembly intermediates by phenylpropenamide assembly accelerators.","abstract":"Understanding the biological self-assembly process of virus capsids is key to understanding the viral life cycle, as well as serving as a platform for the design of assembly-based antiviral drugs. Here we identify and characterize the phenylpropenamide family of small molecules, known to have antiviral activity in vivo, as assembly effectors of the hepatitis B virus (HBV) capsid. We have found two representative phenylpropenamides to be assembly accelerators, increasing the rate of assembly with only modest increases in the stability of the HBV capsids; these data provide a physical-chemical basis for their antiviral activity. Unlike previously described HBV assembly effectors, the phenylpropenamides do not misdirect assembly; rather, the accelerated reactions proceed on-path to produce morphologically normal capsids. However, capsid assembly in the presence of phenylpropenamides is characterized by kinetic trapping of assembly intermediates. These traps resolve under conditions close to physiological, but we found that trapped intermediates persist under conditions that favor phenylpropenamide binding and strong core protein-protein interactions. The phenylpropenamides serve as chemical probes of the HBV capsid assembly pathway by trapping on-path assembly intermediates, illustrating the governing influence of reaction kinetics on capsid assembly.","corpus_id":106032,"score":0},{"doc_id":"21347350","title":"NS2 protein of hepatitis C virus interacts with structural and non-structural proteins towards virus assembly.","abstract":"Growing experimental evidence indicates that, in addition to the physical virion components, the non-structural proteins of hepatitis C virus (HCV) are intimately involved in orchestrating morphogenesis. Since it is dispensable for HCV RNA replication, the non-structural viral protein NS2 is suggested to play a central role in HCV particle assembly. However, despite genetic evidences, we have almost no understanding about NS2 protein-protein interactions and their role in the production of infectious particles. Here, we used co-immunoprecipitation and/or fluorescence resonance energy transfer with fluorescence lifetime imaging microscopy analyses to study the interactions between NS2 and the viroporin p7 and the HCV glycoprotein E2. In addition, we used alanine scanning insertion mutagenesis as well as other mutations in the context of an infectious virus to investigate the functional role of NS2 in HCV assembly. Finally, the subcellular localization of NS2 and several mutants was analyzed by confocal microscopy. Our data demonstrate molecular interactions between NS2 and p7 and E2. Furthermore, we show that, in the context of an infectious virus, NS2 accumulates over time in endoplasmic reticulum-derived dotted structures and colocalizes with both the envelope glycoproteins and components of the replication complex in close proximity to the HCV core protein and lipid droplets, a location that has been shown to be essential for virus assembly. We show that NS2 transmembrane region is crucial for both E2 interaction and subcellular localization. Moreover, specific mutations in core, envelope proteins, p7 and NS5A reported to abolish viral assembly changed the subcellular localization of NS2 protein. Together, these observations indicate that NS2 protein attracts the envelope proteins at the assembly site and it crosstalks with non-structural proteins for virus assembly.","corpus_id":18422988,"score":0},{"doc_id":"21762796","title":"Visualizing HIV-1 assembly.","abstract":"The assembly of an HIV-1 particle is a complex, multistep process involving several viral and cellular proteins, RNAs and lipids. While many macroscopic and fixed-cell microscopic techniques have provided important insights into the structure of HIV-1 particles and the mechanisms by which they assemble, analysis of individual particles and their assembly in living cells offers the potential of surmounting many of the limitations inherent in other approaches. In this review, we discuss how the recent application of live-cell microscopic imaging techniques has increased our understanding of the process of HIV-1 particle assembly. In particular, we focus on recent studies that have employed total internal reflection fluorescence microscopy and other single-virion imaging techniques in live cells. These approaches have illuminated the dynamics of Gag protein assembly, viral RNA packaging and ESCRT (endosomal sorting complex required for transport) protein recruitment at the level of individual viral particles. Overall, the particular advantages of individual particle imaging in living cells have yielded findings that would have been difficult or impossible to obtain using macroscopic or fixed-cell microscopic techniques.","corpus_id":10910761,"score":0},{"doc_id":"22019738","title":"Stepwise expansion of the bacteriophage ϕ6 procapsid: possible packaging intermediates.","abstract":"The initial assembly product of bacteriophage ϕ6, the procapsid, undergoes major structural transformation during the sequential packaging of its three segments of single-stranded RNA. The procapsid, a compact icosahedrally symmetric particle with deeply recessed vertices, expands to the spherical mature capsid, increasing the volume available to accommodate the genome by 2.5-fold. It has been proposed that expansion and packaging are linked, with each stage in expansion presenting a binding site for a particular RNA segment. To investigate procapsid transformability, we induced expansion by acidification, heating, and elevated salt concentration. Cryo-electron microscopy reconstructions after all three treatments yielded the same partially expanded particle. Analysis by cryo-electron tomography showed that all vertices of a given capsid were either in a compact or an expanded state, indicating a highly cooperative transition. To benchmark the mature capsid, we analyzed filled (in vivo packaged) capsids. When these particles were induced to release their RNA, they reverted to the same intermediate state as expanded procapsids (intermediate 1) or to a second, further expanded state (intermediate 2). This partial reversibility of expansion suggests that the mature spherical capsid conformation is obtained only when sufficient outward pressure is exerted by packaged RNA. The observation of two intermediates is consistent with the proposed three-step packaging process. The model is further supported by the observation that a mutant capable of packaging the second RNA segment without previously packaging the first segment has enhanced susceptibility for switching spontaneously from the procapsid to the first intermediate state.","corpus_id":12492657,"score":0},{"doc_id":"23175377","title":"The human cytomegalovirus UL51 protein is essential for viral genome cleavage-packaging and interacts with the terminase subunits pUL56 and pUL89.","abstract":"Cleavage of human cytomegalovirus (HCMV) genomes as well as their packaging into capsids is an enzymatic process mediated by viral proteins and therefore a promising target for antiviral therapy. The HCMV proteins pUL56 and pUL89 form the terminase and play a central role in cleavage-packaging, but several additional viral proteins, including pUL51, had been suggested to contribute to this process, although they remain largely uncharacterized. To study the function of pUL51 in infected cells, we constructed HCMV mutants encoding epitope-tagged versions of pUL51 and used a conditionally replicating virus (HCMV-UL51-ddFKBP), in which pUL51 levels could be regulated by a synthetic ligand. In cells infected with HCMV-UL51-ddFKBP, viral DNA replication was not affected when pUL51 was knocked down. However, no unit-length genomes and no DNA-filled C capsids were found, indicating that cleavage of concatemeric HCMV DNA and genome packaging into capsids did not occur in the absence of pUL51. pUL51 was expressed mainly with late kinetics and was targeted to nuclear replication compartments, where it colocalized with pUL56 and pUL89. Upon pUL51 knockdown, pUL56 and pUL89 were no longer detectable in replication compartments, suggesting that pUL51 is needed for their correct subnuclear localization. Moreover, pUL51 was found in a complex with the terminase subunits pUL56 and pUL89. Our data provide evidence that pUL51 is crucial for HCMV genome cleavage-packaging and may represent a third component of the viral terminase complex. Interference with the interactions between the terminase subunits by antiviral drugs could be a strategy to disrupt the HCMV replication cycle.","corpus_id":2274085,"score":0},{"doc_id":"23658526","title":"hepatitis c Virus p7 is critical for capsid assembly and envelopment.","abstract":"Hepatitis C virus (HCV) p7 is a membrane-associated ion channel protein crucial for virus production. To analyze how p7 contributes to this process, we dissected HCV morphogenesis into sub-steps including recruitment of HCV core to lipid droplets (LD), virus capsid assembly, unloading of core protein from LDs and subsequent membrane envelopment of capsids. Interestingly, we observed accumulation of slowly sedimenting capsid-like structures lacking the viral envelope in cells transfected with HCV p7 mutant genomes which possess a defect in virion production. Concomitantly, core protein was enriched at the surface of LDs. This indicates a defect in core/capsid unloading from LDs and subsequent membrane envelopment rather than defective trafficking of core to this cellular organelle. Protease and ribonuclease digestion protection assays, rate zonal centrifugation and native, two dimensional gel electrophoresis revealed increased amounts of high-order, non-enveloped core protein complexes unable to protect viral RNA in cells transfected with p7 mutant genomes. These results suggest accumulation of capsid assembly intermediates that had not yet completely incorporated viral RNA in the absence of functional p7. Thus, functional p7 is necessary for the final steps of capsid assembly as well as for capsid envelopment. These results support a model where capsid assembly is linked with membrane envelopment of nascent RNA-containing core protein multimers, a process coordinated by p7. In summary, we provide novel insights into the sequence of HCV assembly events and essential functions of p7.","corpus_id":559775,"score":0},{"doc_id":"24722756","title":"Binding of glutathione to enterovirus capsids is essential for virion morphogenesis.","abstract":"Enteroviruses (family of the Picornaviridae) cover a large group of medically important human pathogens for which no antiviral treatment is approved. Although these viruses have been extensively studied, some aspects of the viral life cycle, in particular morphogenesis, are yet poorly understood. We report the discovery of TP219 as a novel inhibitor of the replication of several enteroviruses, including coxsackievirus and poliovirus. We show that TP219 binds directly glutathione (GSH), thereby rapidly depleting intracellular GSH levels and that this interferes with virus morphogenesis without affecting viral RNA replication. The inhibitory effect on assembly was shown not to depend on an altered reducing environment. Using TP219, we show that GSH is an essential stabilizing cofactor during the transition of protomeric particles into pentameric particles. Sequential passaging of coxsackievirus B3 in the presence of low GSH-levels selected for GSH-independent mutants that harbored a surface-exposed methionine in VP1 at the interface between two protomers. In line with this observation, enteroviruses that already contained this surface-exposed methionine, such as EV71, did not rely on GSH for virus morphogenesis. Biochemical and microscopical analysis provided strong evidence for a direct interaction between GSH and wildtype VP1 and a role for this interaction in localizing assembly intermediates to replication sites. Consistently, the interaction between GSH and mutant VP1 was abolished resulting in a relocalization of the assembly intermediates to replication sites independent from GSH. This study thus reveals GSH as a novel stabilizing host factor essential for the production of infectious enterovirus progeny and provides new insights into the poorly understood process of morphogenesis.","corpus_id":5849001,"score":0},{"doc_id":"25078694","title":"Dynamic and nucleolin-dependent localization of human cytomegalovirus UL84 to the periphery of viral replication compartments and nucleoli.","abstract":"Protein-protein and protein-nucleic acid interactions within subcellular compartments are required for viral genome replication. To understand the localization of the human cytomegalovirus viral replication factor UL84 relative to other proteins involved in viral DNA synthesis and to replicating viral DNA in infected cells, we created a recombinant virus expressing a FLAG-tagged version of UL84 (UL84FLAG) and used this virus in immunofluorescence assays. UL84FLAG localization differed at early and late times of infection, transitioning from diffuse distribution throughout the nucleus to exclusion from the interior of replication compartments, with some concentration at the periphery of replication compartments with newly labeled DNA and the viral DNA polymerase subunit UL44. Early in infection, UL84FLAG colocalized with the viral single-stranded DNA binding protein UL57, but colocalization became less prominent as infection progressed. A portion of UL84FLAG also colocalized with the host nucleolar protein nucleolin at the peripheries of both replication compartments and nucleoli. Small interfering RNA (siRNA)-mediated knockdown of nucleolin resulted in a dramatic elimination of UL84FLAG from replication compartments and other parts of the nucleus and its accumulation in the cytoplasm. Reciprocal coimmunoprecipitation of viral proteins from infected cell lysates revealed association of UL84, UL44, and nucleolin. These results indicate that UL84 localization during infection is dynamic, which is likely relevant to its functions, and suggest that its nuclear and subnuclear localization is highly dependent on direct or indirect interactions with nucleolin. Importance: The protein-protein interactions among viral and cellular proteins required for replication of the human cytomegalovirus (HCMV) DNA genome are poorly understood. We sought to understand how an enigmatic HCMV protein critical for virus replication, UL84, localizes relative to other viral and cellular proteins required for HCMV genome replication and replicating viral DNA. We found that UL84 localizes with viral proteins, viral DNA, and the cellular nucleolar protein nucleolin in the subnuclear replication compartments in which viral DNA replication occurs. Unexpectedly, we also found localization of UL84 with nucleolin in nucleoli and showed that the presence of nucleolin is involved in localization of UL84 to the nucleus. These results add to previous work showing the importance of nucleolin in replication compartment architecture and viral DNA synthesis and are relevant to understanding UL84 function.","corpus_id":44478320,"score":0},{"doc_id":"25428366","title":"Sequential packaging of RNA genomic segments during the assembly of Bluetongue virus.","abstract":"Bluetongue virus (BTV), a member of the Orbivirus genus within the Reoviridae family, has a genome of 10 double-stranded RNA segments, with three distinct size classes. Although the packaging of the viral genome is evidently highly specific such that every virus particle contains a set of 10 RNA segments, the order and mechanism of packaging are not understood. In this study we have combined the use of a cell-free in vitro assembly system with a novel RNA-RNA interaction assay to investigate the mechanism of single-stranded (ss) RNAs packaging during nascent capsid assembly. Exclusion of single or multiple ssRNA segments in the packaging reaction or their addition in different order significantly altered the outcome and suggested a particular role for the smallest segment, S10. Our data suggests that genome packaging probably initiates with the smallest segment which triggers RNA-RNA interaction with other smaller segments forming a complex network. Subsequently, the medium to larger size ssRNAs are recruited until the complete genome is packaging into the capsid. The untranslated regions of the smallest RNA segment, S10, is critical for the instigation of this process. We suggest that the selective packaging observed in BTV may also apply to other members of the Reoviridae family.","corpus_id":10647694,"score":0},{"doc_id":"25635339","title":"Electron microscopic analysis of rotavirus assembly-replication intermediates.","abstract":"Rotaviruses (RVs) replicate their segmented, double-stranded RNA genomes in tandem with early virion assembly. In this study, we sought to gain insight into the ultrastructure of RV assembly-replication intermediates (RIs) using transmission electron microscopy (EM). Specifically, we examined a replicase-competent, subcellular fraction that contains all known RV RIs. Three never-before-seen complexes were visualized in this fraction. Using in vitro reconstitution, we showed that ~15-nm doughnut-shaped proteins in strings were nonstructural protein 2 (NSP2) bound to viral RNA transcripts. Moreover, using immunoaffinity-capture EM, we revealed that ~20-nm pebble-shaped complexes contain the viral RNA polymerase (VP1) and RNA capping enzyme (VP3). Finally, using a gel purification method, we demonstrated that ~30-70-nm electron-dense, particle-shaped complexes represent replicase-competent core RIs, containing VP1, VP3, and NSP2 as well as capsid proteins VP2 and VP6. The results of this study raise new questions about the interactions among viral proteins and RNA during the concerted assembly-replicase process.","corpus_id":9140979,"score":0},{"doc_id":"25717105","title":"Gammaherpesvirus Tegument Protein ORF33 Is Associated With Intranuclear Capsids at an Early Stage of the Tegumentation Process.","abstract":"UNLABELLED: Herpesvirus nascent capsids, after assembly in the nucleus, must acquire a variety of tegument proteins during maturation. However, little is known about the identity of the tegument proteins that are associated with capsids in the nucleus or the molecular mechanisms involved in the nuclear egress of capsids into the cytoplasm, especially for the two human gammaherpesviruses Epstein-Barr virus (EBV) and Kaposi's sarcoma-associated herpesvirus (KSHV), due to a lack of efficient lytic replication systems. Murine gammaherpesvirus 68 (MHV-68) is genetically related to human gammaherpesviruses and serves as an excellent model to study the de novo lytic replication of gammaherpesviruses. We have previously shown that open reading frame 33 (ORF33) of MHV-68 is a tegument protein of mature virions and is essential for virion assembly and egress. However, it remains unclear how ORF33 is incorporated into virions. In this study, we first show that the endogenous ORF33 protein colocalizes with capsid proteins at discrete areas in the nucleus during viral infection. Cosedimentation analysis as well as an immunoprecipitation assay demonstrated that ORF33 is associated with both nuclear and cytoplasmic capsids. An immunogold labeling experiment using an anti-ORF33 monoclonal antibody revealed that ORF33-rich areas in the nucleus are surrounded by immature capsids. Moreover, ORF33 is associated with nucleocapsids prior to primary envelopment as well as with mature virions in the cytoplasm. Finally, we show that ORF33 interacts with two capsid proteins, suggesting that nucleocapsids may interact with ORF33 in a direct manner. In summary, we identified ORF33 to be a tegument protein that is associated with intranuclear capsids prior to primary envelopment, likely through interacting with capsid proteins in a direct manner. IMPORTANCE: Morphogenesis is an essential step in virus propagation that leads to the generation of progeny virions. For herpesviruses, this is a complicated process that starts in the nucleus. Although the process of capsid assembly and genome packaging is relatively well understood, how capsids acquire tegument (the layer between the capsid and the envelope in a herpesvirus virion) and whether the initial tegumentation process takes place in the nucleus remain unclear. We previously showed that ORF33 of MHV-68 is a tegument protein and functions in both the nuclear egress of capsids and final virion maturation in the cytoplasm. In the present study, we show that ORF33 is associated with intranuclear capsids prior to primary envelopment and identify novel interactions between ORF33 and two capsid proteins. Our work provides new insights into the association between tegument proteins and nucleocapsids at an early stage of the virion maturation process for herpesviruses.","corpus_id":46101752,"score":0},{"doc_id":"25863879","title":"The vaccinia virus E6 protein influences virion protein localization during virus assembly.","abstract":"Vaccinia virus mutants in which expression of the virion core protein gene E6R is repressed are defective in virion morphogenesis. E6 deficient infections fail to properly package viroplasm into viral membranes, resulting in an accumulation of empty immature virions and large aggregates of viroplasm. We have used immunogold electron microscopy and immunofluorescence confocal microscopy to assess the intracellular localization of several virion structural proteins and enzymes during E6R mutant infections. We find that during E6R mutant infections virion membrane proteins and virion transcription enzymes maintain a normal localization within viral factories while several major core and lateral body proteins accumulate in aggregated virosomes. The results support a model in which vaccinia virions are assembled from at least three substructures, the membrane, the viroplasm and a \"pre-nucleocapsid\", and that the E6 protein is essential for maintaining proper localization of the seven-protein complex and the viroplasm during assembly.","corpus_id":426850,"score":0},{"doc_id":"25986309","title":"The Role of Packaging Sites in Efficient and Specific Virus Assembly.","abstract":"During the life cycle of many single-stranded RNA viruses, including many human pathogens, a protein shell called the capsid spontaneously assembles around the viral genome. Understanding the mechanisms by which capsid proteins selectively assemble around the viral RNA amidst diverse host RNAs is a key question in virology. In one proposed mechanism, short sequences (packaging sites) within the genomic RNA promote rapid and efficient assembly through specific interactions with the capsid proteins. In this work, we develop a coarse-grained particle-based computational model for capsid proteins and RNA that represents protein-RNA interactions arising both from nonspecific electrostatics and from specific packaging site interactions. Using Brownian dynamics simulations, we explore how the efficiency and specificity of assembly depend on solution conditions (which control protein-protein and nonspecific protein-RNA interactions) and the strength and number of packaging sites. We identify distinct regions in parameter space in which packaging sites lead to highly specific assembly via different mechanisms and others in which packaging sites lead to kinetic traps. We relate these computational predictions to in vitro assays for specificity in which cognate viral RNAs compete against non-cognate RNAs for assembly by capsid proteins.","corpus_id":3591269,"score":0},{"doc_id":"26051211","title":"An alphavirus temperature-sensitive capsid mutant reveals stages of nucleocapsid assembly.","abstract":"Alphaviruses have a nucleocapsid core composed of the RNA genome surrounded by an icosahedral lattice of capsid protein. An insertion after position 186 in the capsid protein produced a strongly temperature-sensitive growth phenotype. Even when the structural proteins were synthesized at the permissive temperature (28°C), subsequent incubation of the cells at the non-permissive temperature (37°C) dramatically decreased mutant capsid protein stability and particle assembly. Electron microscopy confirmed the presence of cytoplasmic nucleocapsids in mutant-infected cells cultured at the permissive temperature, but these nucleocapsids were not stable to sucrose gradient separation. In contrast, nucleocapsids isolated from mutant virus particles had similar stability to that of wildtype virus. Our data support a model in which cytoplasmic nucleocapsids go through a maturation step during packaging into virus particles. The insertion site lies in the interface between capsid proteins in the assembled nucleocapsid, suggesting the region where such a stabilizing transition occurs.","corpus_id":20534693,"score":0},{"doc_id":"26178992","title":"RNA and Nucleocapsid Are Dispensable for Mature HIV-1 Capsid Assembly.","abstract":"UNLABELLED: Human immunodeficiency virus type 1 (HIV-1) is released from infected cells in an immature, noninfectious form in which the structural polyprotein Gag is arranged in a hexameric lattice, forming an incomplete spherical shell. Maturation to the infectious form is mediated by the viral protease, which cleaves Gag at five sites, releasing the CA (capsid) protein, which forms a conical capsid encasing the condensed RNA genome. The pathway of this structural rearrangement is currently not understood, and it is unclear how cone assembly is initiated. RNA represents an integral structural component of retroviruses, and the viral nucleoprotein core has previously been proposed to nucleate mature capsid assembly. We addressed this hypothesis by replacing the RNA-binding NC (nucleocapsid) domain of HIV-1 Gag and the adjacent spacer peptide 2 (SP2) by a leucine zipper (LZ) protein-protein interaction domain [Gag(LZ)] in the viral context. We found that Gag(LZ)-carrying virus [HIV(LZ)] was efficiently released and viral polyproteins were proteolytically processed, though with reduced efficiency. Cryo-electron tomography revealed that the particles lacked a condensed nucleoprotein and contained an increased proportion of aberrant core morphologies caused either by the absence of RNA or by altered Gag processing. Nevertheless, a significant proportion of HIV(LZ) particles contained mature capsids with the wild-type morphology. These results clearly demonstrate that the nucleoprotein complex is dispensable as a nucleator for mature HIV-1 capsid assembly in the viral context. IMPORTANCE: Formation of a closed conical capsid encasing the viral RNA genome is essential for HIV-1 infectivity. It is currently unclear what viral components initiate and regulate the formation of the capsid during virus morphogenesis, but it has been proposed that the ribonucleoprotein complex plays a role. To test this, we prepared virus-like particles lacking the viral nucleocapsid protein and RNA and analyzed their three-dimensional structure by cryo-electron tomography. While most virions displayed an abnormal morphology under these conditions, some particles showed a normal mature morphology with closed conical capsids. These data demonstrate that the presence of RNA and the nucleocapsid protein is not required for the formation of a mature, cone-shaped HIV-1 capsid.","corpus_id":34671999,"score":0},{"doc_id":"26552701","title":"Assembly and Release of Hepatitis B Virus.","abstract":"The hepatitis B virus (HBV) core protein is a dynamic and versatile protein that directs many viral processes. During capsid assembly, core protein allosteric changes ensure efficient formation of a stable capsid that assembles while packaging viral RNA-polymerase complex. Reverse transcription of the RNA genome as well as transport of the capsid to multiple cellular compartments are directed by dynamic phosphorylation and structural changes of core protein. Subsequently, interactions of the capsid with the surface proteins and/or host proteins trigger envelopment and release of the viral capsids or the transport to the nucleus. Held together by many weak protein-protein interactions, the viral capsid is an extraordinary metastable machine that is stable enough to persist in the cellular and extracellular environment but dissociates to allow release of the viral genome at the right time during infection.","corpus_id":41325114,"score":0},{"doc_id":"26657148","title":"Mechanisms of assembly and genome packaging in an RNA virus revealed by high-resolution cryo-EM.","abstract":"Cowpea mosaic virus is a plant-infecting member of the Picornavirales and is of major interest in the development of biotechnology applications. Despite the availability of >100 crystal structures of Picornavirales capsids, relatively little is known about the mechanisms of capsid assembly and genome encapsidation. Here we have determined cryo-electron microscopy reconstructions for the wild-type virus and an empty virus-like particle, to 3.4 Å and 3.0 Å resolution, respectively, and built de novo atomic models of their capsids. These new structures reveal the C-terminal region of the small coat protein subunit, which is essential for virus assembly and which was missing from previously determined crystal structures, as well as residues that bind to the viral genome. These observations allow us to develop a new model for genome encapsidation and capsid assembly.","corpus_id":17500124,"score":0},{"doc_id":"26912613","title":"Nucleic Acid Binding by Mason-Pfizer Monkey Virus CA Promotes Virus Assembly and Genome Packaging.","abstract":"UNLABELLED: The Gag polyprotein of retroviruses drives immature virus assembly by forming hexameric protein lattices. The assembly is primarily mediated by protein-protein interactions between capsid (CA) domains and by interactions between nucleocapsid (NC) domains and RNA. Specific interactions between NC and the viral RNA are required for genome packaging. Previously reported cryoelectron microscopy analysis of immature Mason-Pfizer monkey virus (M-PMV) particles suggested that a basic region (residues RKK) in CA may serve as an additional binding site for nucleic acids. Here, we have introduced mutations into the RKK region in both bacterial and proviral M-PMV vectors and have assessed their impact on M-PMV assembly, structure, RNA binding, budding/release, nuclear trafficking, and infectivity using in vitro and in vivo systems. Our data indicate that the RKK region binds and structures nucleic acid that serves to promote virus particle assembly in the cytoplasm. Moreover, the RKK region appears to be important for recruitment of viral genomic RNA into Gag particles, and this function could be linked to changes in nuclear trafficking. Together these observations suggest that in M-PMV, direct interactions between CA and nucleic acid play important functions in the late stages of the viral life cycle. IMPORTANCE: Assembly of retrovirus particles is driven by the Gag polyprotein, which can self-assemble to form virus particles and interact with RNA to recruit the viral genome into the particles. Generally, the capsid domains of Gag contribute to essential protein-protein interactions during assembly, while the nucleocapsid domain interacts with RNA. The interactions between the nucleocapsid domain and RNA are important both for identifying the genome and for self-assembly of Gag molecules. Here, we show that a region of basic residues in the capsid protein of the betaretrovirus Mason-Pfizer monkey virus (M-PMV) contributes to interaction of Gag with nucleic acid. This interaction appears to provide a critical scaffolding function that promotes assembly of virus particles in the cytoplasm. It is also crucial for packaging the viral genome and thus for infectivity. These data indicate that, surprisingly, interactions between the capsid domain and RNA play an important role in the assembly of M-PMV.","corpus_id":4766834,"score":0},{"doc_id":"27226558","title":"Cellular Casein Kinase 2 and Protein Phosphatase 2A Modulate Replication Site Assembly of Bluetongue Virus.","abstract":"A number of cytoplasmic replicating viruses produce cytoplasmic inclusion bodies or protein aggregates; however, a hallmark of viruses of the Reoviridae family is that they utilize these sites for purposes of replication and capsid assembly, functioning as viral assembly factories. Here we have used bluetongue virus (BTV) as a model system for this broad family of important viruses to understand the mechanisms regulating inclusion body assembly. Newly synthesized viral proteins interact with sequestered viral RNA molecules prior to capsid assembly and double-stranded RNA synthesis within viral inclusion bodies (VIBs). VIBs are predominantly comprised of a BTV-encoded non-structural protein 2 (NS2). Previous in vitro studies indicated that casein kinase 2 (CK2) mediated the phosphorylation of NS2, which regulated the propensity of NS2 to form larger aggregates. Using targeted pharmacological reagents, specific mutation in the viral genome by reverse genetics and confocal microscopy, here we demonstrate that CK2 activity is important for BTV replication. Furthermore, we show that a novel host cell factor, protein phosphatase 2A, is involved in NS2 dephosphorylation and that, together with CK2, it regulates VIB morphology and virus replication. Thus, these two host enzymes influence the dynamic nature of VIB assembly/disassembly, and these concerted activities may be relevant to the assembly and the release of these cores from VIBs.","corpus_id":205358194,"score":0},{"doc_id":"27428992","title":"Coordination of Genomic RNA Packaging with Viral Assembly in HIV-1.","abstract":"The tremendous progress made in unraveling the complexities of human immunodeficiency virus (HIV) replication has resulted in a library of drugs to target key aspects of the replication cycle of the virus. Yet, despite this accumulated wealth of knowledge, we still have much to learn about certain viral processes. One of these is virus assembly, where the viral genome and proteins come together to form infectious progeny. Here we review this topic from the perspective of how the route to production of an infectious virion is orchestrated by the viral genome, and we compare and contrast aspects of the assembly mechanisms employed by HIV-1 with those of other RNA viruses.","corpus_id":1530448,"score":0},{"doc_id":"27881644","title":"Suppression of Adenovirus Replication by Cardiotonic Steroids.","abstract":"The dependence of adenovirus on the host pre-RNA splicing machinery for expression of its complete genome potentially makes it vulnerable to modulators of RNA splicing, such as digoxin and digitoxin. Both drugs reduced the yields of four human adenoviruses (HAdV-A31, -B35, and -C5 and a species D conjunctivitis isolate) by at least 2 to 3 logs by affecting one or more steps needed for genome replication. Immediate early E1A protein levels are unaffected by the drugs, but synthesis of the delayed protein E4orf6 and the major late capsid protein hexon is compromised. Quantitative reverse transcription-PCR (qRT-PCR) analyses revealed that both drugs altered E1A RNA splicing (favoring the production of 13S over 12S RNA) early in infection and partially blocked the transition from 12S and 13S to 9S RNA at late stages of virus replication. Expression of multiple late viral protein mRNAs was lost in the presence of either drug, consistent with the observed block in viral DNA replication. The antiviral effect was dependent on the continued presence of the drug and was rapidly reversible. RIDK34, a derivative of convallotoxin, although having more potent antiviral activity, did not show an improved selectivity index. All three drugs reduced metabolic activity to some degree without evidence of cell death. By blocking adenovirus replication at one or more steps beyond the onset of E1A expression and prior to genome replication, digoxin and digitoxin show potential as antiviral agents for treatment of serious adenovirus infections. Furthermore, understanding the mechanism(s) by which digoxin and digitoxin inhibit adenovirus replication will guide the development of novel antiviral therapies. IMPORTANCE: Despite human adenoviruses being a common and, in some instances, life-threating pathogen in humans, there are few well-tolerated therapies. In this report, we demonstrate that two cardiotonic steroids already in use in humans, digoxin and digitoxin, are potent inhibitors of multiple adenovirus species. A synthetic derivative of the cardiotonic steroid convallotoxin was even more potent than digoxin and digitoxin when tested with HAdV-C5. These drugs alter the cascade of adenovirus gene expression, acting after initiation of early gene expression to block viral DNA replication and synthesis of viral structural proteins. These findings validate a novel approach to treating adenovirus infections through the modulation of host cell processes.","corpus_id":24206090,"score":0},{"doc_id":"28082593","title":"Assembly of a nucleus-like structure during viral replication in bacteria.","abstract":"We observed the assembly of a nucleus-like structure in bacteria during viral infection. Using fluorescence microscopy and cryo-electron tomography, we showed that Pseudomonas chlororaphis phage 201φ2-1 assembled a compartment that separated viral DNA from the cytoplasm. The phage compartment was centered by a bipolar tubulin-based spindle, and it segregated phage and bacterial proteins according to function. Proteins involved in DNA replication and transcription localized inside the compartment, whereas proteins involved in translation and nucleotide synthesis localized outside. Later during infection, viral capsids assembled on the cytoplasmic membrane and moved to the surface of the compartment for DNA packaging. Ultimately, viral particles were released from the compartment and the cell lysed. These results demonstrate that phages have evolved a specialized structure to compartmentalize viral replication.","corpus_id":206654602,"score":0},{"doc_id":"29444942","title":"A Functional Link between RNA Replication and Virion Assembly in the Potyvirus Plum Pox Virus.","abstract":"Accurate assembly of viral particles in the potyvirus Plum pox virus (PPV) has been shown to depend on the contribution of the multifunctional viral protein HCPro. In this study, we show that other viral factors, in addition to the capsid protein (CP) and HCPro, are necessary for the formation of stable PPV virions. The CP produced in Nicotiana benthamiana leaves from a subviral RNA termed LONG, which expresses a truncated polyprotein that lacks P1 and HCPro, together with HCPro supplied in trans, was assembled into virus-like particles and remained stable after in vitro incubation. In contrast, deletions in multiple regions of the LONG coding sequence prevented the CP stabilization mediated by HCPro. In particular, we demonstrated that the first 178 amino acids of P3, but not a specific nucleotide sequence coding for them, are required for CP stability and proper assembly of PPV particles. Using a sequential coagroinfiltration assay, we observed that the subviral LONG RNA replicates and locally spreads in N. benthamiana leaves expressing an RNA silencing suppressor. The analysis of the effect of both point and deletion mutations affecting RNA replication in LONG and full-length PPV demonstrated that this process is essential for the assembly of stable viral particles. Interestingly, in spite of this requirement, the CP produced by a nonreplicating viral RNA can be stably assembled into virions as long as it is coexpressed with a replication-proficient RNA. Altogether, these results highlight the importance of coupling encapsidation to other viral processes to secure a successful infection. IMPORTANCE Viruses of the family Potyviridae are among the most dangerous threats for basically every important crop, and such socioeconomical relevance has made them a subject of many research studies. In spite of this, very little is currently known about proteins and processes controlling viral genome encapsidation by the coat protein. In the case of Plum pox virus (genus Potyvirus), for instance, we have previously shown that the multitasking viral factor HCPro plays a role in the production of stable virions. Here, by using this potyvirus as a model, we move further to show that additional factors are also necessary for the efficient production of potyviral particles. More importantly, a comprehensive screening for such factors led us to the identification of a functional link between virus replication and packaging, unraveling a previously unknown connection of these two key events of the potyviral infection cycle.","corpus_id":4826578,"score":0},{"doc_id":"29558394","title":"Alphavirus Nucleocapsid Packaging and Assembly.","abstract":"Alphavirus nucleocapsids are assembled in the cytoplasm of infected cells from 240 copies of the capsid protein and the approximately 11 kb positive strand genomic RNA. However, the challenge of how the capsid specifically selects its RNA package and assembles around it has remained an elusive one to solve. In this review, we will summarize what is known about the alphavirus capsid protein, the packaging signal, and their roles in the mechanism of packaging and assembly. We will review the discovery of the packaging signal and how there is as much evidence for, as well as against, its requirement to specify packaging of the genomic RNA. Finally, we will compare this model with those of other viral systems including particular reference to a relatively new idea of RNA packaging based on the presence of multiple minimal packaging signals throughout the genome known as the two stage mechanism. This review will provide a basis for further investigating the fundamental ways of how RNA viruses are able to select their own cargo from the relative chaos that is the cytoplasm.","corpus_id":3986519,"score":0}],"string":"[\n {\n \"doc_id\": \"18614642\",\n \"title\": \"Presence of the adenovirus IVa2 protein at a single vertex of the mature virion.\",\n \"abstract\": \"Assembly of adenovirus particles is thought to be similar to that of bacteriophages, in which the double-stranded DNA genome is inserted into a preformed empty capsid. Previous studies from our and other laboratories have implicated the viral IVa2 protein as a key component of the encapsidation process. IVa2 binds to the packaging sequence on the viral chromosome in a sequence-specific manner, alone and in conjunction with the viral L4 22K protein. In addition, it interacts with the viral L1 52/55-kDa protein, which is required for DNA packaging. Finally, a mutant virus that does not produce IVa2 is unable to produce any capsids. Therefore, it has been proposed that IVa2 nucleates capsid assembly. A prediction of such a model is that the IVa2 protein would be found at a unique vertex of the mature virion. In this study, the location of IVa2 in the virion has been analyzed using immunogold staining and electron microscopy, and the copy number of IVa2 in virions was determined using three independent methods, quantitative mass spectrometry, metabolic labeling, and Western blotting. The results indicate that it resides at a unique vertex and that there are approximately six to eight IVa2 molecules in each particle. These findings support the hypothesis that the IVa2 protein plays multiple roles in the viral assembly process.\",\n \"corpus_id\": 206799861,\n \"score\": 2\n },\n {\n \"doc_id\": \"19458007\",\n \"title\": \"Cryo-electron microscopy structure of adenovirus type 2 temperature-sensitive mutant 1 reveals insight into the cell entry defect.\",\n \"abstract\": \"The structure of the adenovirus type 2 temperature-sensitive mutant 1 (Ad2ts1) was determined to a resolution of 10 A by cryo-electron microscopy single-particle reconstruction. Ad2ts1 was prepared at a nonpermissive temperature and contains the precursor forms of the capsid proteins IIIa, VI, and VIII; the core proteins VII, X (mu), and terminal protein (TP); and the L1-52K protein. Cell entry studies have shown that although Ad2ts1 can bind the coxsackievirus and Ad receptor and undergo internalization via alphav integrins, this mutant does not escape from the early endosome and is targeted for degradation. Comparison of the Ad2ts1 structure to that of mature Ad indicates that Ad2ts1 has a different core architecture. The Ad2ts1 core is closely associated with the icosahedral capsid, a connection which may be mediated by preproteins IIIa and VI. Density within hexon cavities is assigned to preprotein VI, and membrane disruption assays show that hexon shields the lytic activity of both the mature and precursor forms of protein VI. The internal surface of the penton base in Ad2ts1 appears to be anchored to the core by interactions with preprotein IIIa. Our structural analyses suggest that these connections to the core inhibit the release of the vertex proteins and lead to the cell entry defect of Ad2ts1.\",\n \"corpus_id\": 42480890,\n \"score\": 2\n },\n {\n \"doc_id\": \"21450831\",\n \"title\": \"Characterization of Empty adenovirus particles assembled in the absence of a functional adenovirus IVa2 protein.\",\n \"abstract\": \"The molecular mechanism for packaging of the adenovirus (Ad) genome into the capsid is likely similar to that of DNA bacteriophages and herpesviruses-the insertion of viral DNA through a portal structure into a preformed prohead driven by an ATP-hydrolyzing molecular machine. It is speculated that the IVa2 protein of adenovirus is the ATPase providing the power stroke of the packaging machinery. Purified IVa2 binds ATP in vitro and, along with a second Ad protein, the L4 22-kilodalton protein (L4-22K), binds specifically to sequences in the Ad genome that are essential for packaging. The efficiency of binding of these proteins in vitro was correlated with the efficiency of packaging in vivo. By utilizing a virus unable to express IVa2, pm8002, it was reported that IVa2 plays a role in assembly of the empty virion. We wanted to address the question of whether the ATP binding, and hence the putative ATPase activity, of IVa2 was required for its role in virus assembly. Our results show that ATPase activity was not required for the assembly of empty virus particles. In addition, we present evidence that particles were assembled in the absence of IVa2 by using two viruses null for IVa2-a deletion mutant virus, ΔIVa2, and the previously described mutant virus, pm8002. Empty virus particles produced by these IVa2 mutant viruses did not contain detectable viral DNA. We conclude that the major role of IVa2 is in viral DNA packaging. A characterization of the empty particles obtained from the IVa2 mutant viruses compared to wild-type empty particles is presented.\",\n \"corpus_id\": 2019468,\n \"score\": 2\n },\n {\n \"doc_id\": \"21470569\",\n \"title\": \"Development of a recombinant adenovirus vector production system free of replication-competent adenovirus by utilizing a packaging size limit of the viral genome.\",\n \"abstract\": \"In a conventional adenovirus (Ad) vector production method using 293 cells, homologous recombination between Ad vector DNA and 293 cell-derived Ad E1 DNA occurs with low efficiency, resulting in the generation of replication-competent adenovirus (RCA). RCA can induce the spread of replication-incompetent Ad vectors, leading to unexpected tissue damage. In order to overcome this problem, we developed an Ad vector production system free of RCA generation by utilizing the Ad packaging size limit of the viral genome. It is well known that up to approximately 105% (37.7 kb) of the wild-type genome (35.9 kb) can be packaged in the Ad virion. We designed the Ad vector genome by insertion of a transgene expression cassette into the E3 region, such that homologous recombination between the Ad vector DNA and 293 cell-derived Ad E1 DNA would produce an Ad vector genome that exceeds in the size of the packaging limit. In accord with our strategy, no RCA generation was observed during the passages when we used the E1 (3.2kb)-deleted Ad vectors containing a more than 3.0-kb transgene expression cassette in the E3 region. In contrast, the E1 (3.2kb)-deleted Ad vectors, which retain 37.7 kb of the viral genome and have an insertion of a 2.1-kb transgene expression cassette in the E3 region, generated RCA, although RCA derived from this Ad vector exceeded the packaging size limit (105.0%). These results suggest that RCA generation can be avoided when the genome size of RCA is more than 108.3% (38.9 kb) of the wild-type Ad genome. This Ad vector production system generates safe, easy, and efficient Ad vector stock for both basic study as well as clinical research.\",\n \"corpus_id\": 20753430,\n \"score\": 2\n },\n {\n \"doc_id\": \"21611162\",\n \"title\": \"Altering the Ad5 packaging domain affects the maturation of the Ad particles.\",\n \"abstract\": \"We have previously described a new family of mutant adenoviruses carrying different combinations of attB/attP sequences from bacteriophage PhiC31 flanking the Ad5 packaging domain. These novel helper viruses have a significantly delayed viral life cycle and a severe packaging impairment, regardless of the presence of PhiC31 recombinase. Their infectious viral titers are significantly lower (100-1000 fold) than those of control adenovirus at 36 hours post-infection, but allow for efficient packaging of helper-dependent adenovirus. In the present work, we have analyzed which steps of the adenovirus life cycle are altered in attB-helper adenoviruses and investigated whether these viruses can provide the necessary viral proteins in trans. The entry of attB-adenoviral genomes into the cell nucleus early at early timepoints post-infection was not impaired and viral protein expression levels were found to be similar to those of control adenovirus. However, electron microscopy and capsid protein composition analyses revealed that attB-adenoviruses remain at an intermediate state of maturation 36 hours post-infection in comparison to control adenovirus which were fully mature and infective at this time point. Therefore, an additional 20-24 hours were found to be required for the appearance of mature attB-adenovirus. Interestingly, attB-adenovirus assembly and infectivity was restored by inserting a second packaging signal close to the right-end ITR, thus discarding the possibility that the attB-adenovirus genome was retained in a nuclear compartment deleterious for virus assembly. The present study may have substantive implications for helper-dependent adenovirus technology since helper attB-adenovirus allows for preferential packaging of helper-dependent adenovirus genomes.\",\n \"corpus_id\": 12918344,\n \"score\": 2\n },\n {\n \"doc_id\": \"21632753\",\n \"title\": \"Adenovirus structural protein IIIa is involved in the serotype specificity of viral DNA packaging.\",\n \"abstract\": \"The packaging of the adenovirus (Ad) genome into a capsid displays serotype specificity. This specificity has been attributed to viral packaging proteins, the IVa2 protein and the L1-52/55K protein. We previously found that the Ad17 L1-52/55K protein was not able to complement the growth of an Ad5 L1-52/55K mutant virus, whereas two other Ad17 packaging proteins, IVa2 and L4-22K, could complement the growth of Ad5 viruses with mutations in the respective genes. In this report, we investigated why the Ad17 L1-52/55K protein was not able to complement the Ad5 L1-52/55K mutant virus. We demonstrate that the Ad17 L1-52/55K protein binds to the Ad5 IVa2 protein in vitro and the Ad5 packaging domain in vivo, activities previously associated with packaging function. The Ad17 L1-52/55K protein also associates with empty Ad5 capsids. Interestingly, we find that the Ad17 L1-52/55K protein is able to complement the growth of an Ad5 L1-52/55K mutant virus in conjunction with the Ad17 structural protein IIIa. The same result was found with the L1-52/55K and IIIa proteins of several other Ad serotypes, including Ad3 and Ad4. The Ad17 IIIa protein associates with empty Ad5 capsids. Consistent with the complementation results, we find that the IIIa protein interacts with the L1-52/55K protein in vitro and associates with the viral packaging domain in vivo. These results underscore the complex nature of virus assembly and genome encapsidation and provide a new model for how the viral genome may tether to the empty capsid during the encapsidation process.\",\n \"corpus_id\": 46284009,\n \"score\": 2\n },\n {\n \"doc_id\": \"21925109\",\n \"title\": \"Kinesin-1-mediated capsid disassembly and disruption of the nuclear pore complex promote virus infection.\",\n \"abstract\": \"Many viruses deliver their genomes into the host cell nucleus for replication. However, the size restrictions of the nuclear pore complex (NPC), which regulates the passage of proteins, nucleic acids, and solutes through the nuclear envelope, require virus capsid uncoating before viral DNA can access the nucleus. We report a microtubule motor kinesin-1-mediated and NPC-supported mechanism of adenovirus uncoating. The capsid binds to the NPC filament protein Nup214 and kinesin-1 light-chain Klc1/2. The nucleoporin Nup358, which is bound to Nup214/Nup88, interacts with the kinesin-1 heavy-chain Kif5c to indirectly link the capsid to the kinesin motor. Kinesin-1 disrupts capsids docked at Nup214, which compromises the NPC and dislocates nucleoporins and capsid fragments into the cytoplasm. NPC disruption increases nuclear envelope permeability as indicated by the nuclear influx of large cytoplasmic dextran polymers. Thus, kinesin-1 uncoats viral DNA and compromises NPC integrity, allowing viral genomes nuclear access to promote infection.\",\n \"corpus_id\": 21936770,\n \"score\": 2\n },\n {\n \"doc_id\": \"22496236\",\n \"title\": \"Replication-uncoupled histone deposition during adenovirus DNA replication.\",\n \"abstract\": \"In infected cells, the chromatin structure of the adenovirus genome DNA plays critical roles in its genome functions. Previously, we reported that in early phases of infection, incoming viral DNA is associated with both viral core protein VII and cellular histones. Here we show that in late phases of infection, newly synthesized viral DNA is also associated with histones. We also found that the knockdown of CAF-1, a histone chaperone that functions in the replication-coupled deposition of histones, does not affect the level of histone H3 bound on viral chromatin, although CAF-1 is accumulated at viral DNA replication foci together with PCNA. Chromatin immunoprecipitation assays using epitope-tagged histone H3 demonstrated that histone variant H3.3, which is deposited onto the cellular genome in a replication-independent manner, is selectively associated with both incoming and newly synthesized viral DNAs. Microscopic analyses indicated that histones but not USF1, a transcription factor that regulates viral late gene expression, are excluded from viral DNA replication foci and that this is achieved by the oligomerization of the DNA binding protein (DBP). Taken together, these results suggest that histone deposition onto newly synthesized viral DNA is most likely uncoupled with viral DNA replication, and a possible role of DBP oligomerization in this replication-uncoupled histone deposition is discussed.\",\n \"corpus_id\": 1445380,\n \"score\": 2\n },\n {\n \"doc_id\": \"22754652\",\n \"title\": \"Latest insights on adenovirus structure and assembly.\",\n \"abstract\": \"Adenovirus (AdV) capsid organization is considerably complex, not only because of its large size (~950 Å) and triangulation number (pseudo T = 25), but also because it contains four types of minor proteins in specialized locations modulating the quasi-equivalent icosahedral interactions. Up until 2009, only its major components (hexon, penton, and fiber) had separately been described in atomic detail. Their relationships within the virion, and the location of minor coat proteins, were inferred from combining the known crystal structures with increasingly more detailed cryo-electron microscopy (cryoEM) maps. There was no structural information on assembly intermediates. Later on that year, two reports described the structural differences between the mature and immature adenoviral particle, starting to shed light on the different stages of viral assembly, and giving further insights into the roles of core and minor coat proteins during morphogenesis [1,2]. Finally, in 2010, two papers describing the atomic resolution structure of the complete virion appeared [3,4]. These reports represent a veritable tour de force for two structural biology techniques: X-ray crystallography and cryoEM, as this is the largest macromolecular complex solved at high resolution by either of them. In particular, the cryoEM analysis provided an unprecedented clear picture of the complex protein networks shaping the icosahedral shell. Here I review these latest developments in the field of AdV structural studies.\",\n \"corpus_id\": 15455524,\n \"score\": 2\n },\n {\n \"doc_id\": \"22811519\",\n \"title\": \"The adenovirus L4-22K protein is multifunctional and is an integral component of crucial aspects of infection.\",\n \"abstract\": \"A variety of cellular and viral processes are coordinately regulated during adenovirus (Ad) infection to achieve optimal virus production. The Ad late gene product L4-22K has been associated with disparate activities during infection, including the regulation of late gene expression, viral DNA packaging, and infectious virus production. We generated and characterized two L4-22K mutant viruses to further explore L4-22K functions during viral infection. Our results show that L4-22K is indeed important for temporal control of viral gene expression not only because it activates late gene expression but also because it suppresses early gene expression. We also show that the L4-22K protein binds to viral packaging sequences in vivo and is essential to recruit two other packaging proteins, IVa2 and L1-52/55K, to this region. The elimination of L4-22K gave rise to the production of only empty virus capsids and not mature virions, which confirms that the L4-22K protein is required for Ad genome packaging. Finally, L4-22K contributes to adenovirus-induced cell death by regulating the expression of the adenovirus death protein. Thus, the adenovirus L4-22K protein is multifunctional and an integral component of crucial aspects of infection.\",\n \"corpus_id\": 31270881,\n \"score\": 2\n },\n {\n \"doc_id\": \"23388198\",\n \"title\": \"Adenoviral E2 IVa2 protein interacts with L4 33K protein and E2 DNA-binding protein.\",\n \"abstract\": \"Adenovirus (AdV) is thought to follow a sequential assembly pathway similar to that observed in dsDNA bacteriophages and herpesviruses. First, empty capsids are assembled, and then the genome is packaged through a ring-like structure, referred to as a portal, located at a unique vertex. In human AdV serotype 5 (HAdV5), the IVa2 protein initiates specific recognition of viral genome by associating with the viral packaging domain located between nucleotides 220 and 400 of the genome. IVa2 is located at a unique vertex on mature capsids and plays an essential role during genome packaging, most likely by acting as a DNA packaging ATPase. In this study, we demonstrated interactions among IVa2, 33K and DNA-binding protein (DBP) in virus-infected cells by in vivo cross-linking of HAdV5-infected cells followed by Western blot, and co-immunoprecipitation of IVa2, 33K and DBP from nuclear extracts of HAdV5-infected cells. Confocal microscopy demonstrated co-localization of IVa2, 33K and DBP in virus-infected cells and also in cells transfected with IVa2, 33K and DBP genes. Immunogold electron microscopy of purified HAdV5 showed the presence of IVa2, 33K or DBP at a single site on the virus particles. Our results provide indirect evidence that IVa2, 33K and DBP may form a complex at a unique vertex on viral capsids and cooperate in genome packaging.\",\n \"corpus_id\": 12599446,\n \"score\": 2\n },\n {\n \"doc_id\": \"23552425\",\n \"title\": \"The adenovirus L4-33K protein regulates both late gene expression patterns and viral DNA packaging.\",\n \"abstract\": \"The adenovirus (Ad) L4-33K protein has been linked to disparate functions during infection. L4-33K is a virus-encoded alternative RNA splicing factor which activates splicing of viral late gene transcripts that contain weak 3' splice sites. Additionally, L4-33K has been indicated to play a role in adenovirus assembly. We generated and characterized an Ad5 L4-33K mutant virus to further explore its function(s) during infection. Infectivity, viral genome replication, and most viral gene expression of the L4-33K mutant virus are comparable to those of the wild-type virus, except for a prominent decrease in the levels of the late proteins IIIa and pVI. The L4-33K mutant virus produces only empty capsids, indicating a defect in viral DNA packaging. We demonstrate that L4-33K does not preferentially bind to viral packaging sequences in vivo, and mutation of L4-33K does not interfere with the binding of the known viral packaging proteins IVa2, L4-22K, L1-52/55K, and IIIa to the packaging sequences in vivo. Collectively, these results demonstrate that the phenotype of an Ad5 L4-33K mutant virus is complex. The L4-33K protein regulates the accumulation of selective Ad late gene mRNAs and is involved in the proper transition of gene expression during the late phase of infection. The L4-33K protein also plays a role in adenovirus morphogenesis by promoting the packaging of the viral genome into the empty capsid. These results demonstrate the multifunctional nature of the L4-33K protein and its involvement in several different and critical aspects of viral infection.\",\n \"corpus_id\": 32056891,\n \"score\": 2\n },\n {\n \"doc_id\": \"23637408\",\n \"title\": \"The adenovirus L4-22K protein has distinct functions in the posttranscriptional regulation of gene expression and encapsidation of the viral genome.\",\n \"abstract\": \"The adenovirus L4-22K protein is multifunctional and critical for different aspects of viral infection. Packaging of the viral genome into an empty capsid absolutely requires the L4-22K protein to bind to packaging sequences in cooperation with other viral proteins. Additionally, the L4-22K protein is important for the temporal switch from the early to late phase of infection by regulating both early and late gene expression. To better understand the molecular mechanisms of these key functions of the L4-22K protein, we focused our studies on the role of conserved pairs of cysteine and histidine residues in the C-terminal region of L4-22K. We found that mutation of the cysteine residues affected the production of infectious progeny virus but did not interfere with the ability of the L4-22K protein to regulate viral gene expression. These results demonstrate that these two functions of L4-22K may be uncoupled. Mutation of the histidine residues resulted in a mutant with a similar phenotype as a virus deficient in the L4-22K protein, where both viral genome packaging and viral gene expression patterns were disrupted. Interestingly, both mutant L4-22K proteins bound to adenovirus packaging sequences, indicating that the paired cysteine and histidine residues do not function as a zinc finger DNA binding motif. Our results reveal that the L4-22K protein controls viral gene expression at the posttranscriptional level and regulates the accumulation of the L4-33K protein, another critical viral regulator, at the level of alternative pre-mRNA splicing.\",\n \"corpus_id\": 19966284,\n \"score\": 2\n },\n {\n \"doc_id\": \"24227847\",\n \"title\": \"Processing of the l1 52/55k protein by the adenovirus protease: a new substrate and new insights into virion maturation.\",\n \"abstract\": \"Late in adenovirus assembly, the viral protease (AVP) becomes activated and cleaves multiple copies of three capsid and three core proteins. Proteolytic maturation is an absolute requirement to render the viral particle infectious. We show here that the L1 52/55k protein, which is present in empty capsids but not in mature virions and is required for genome packaging, is the seventh substrate for AVP. A new estimate on its copy number indicates that there are about 50 molecules of the L1 52/55k protein in the immature virus particle. Using a quasi-in vivo situation, i.e., the addition of recombinant AVP to mildly disrupted immature virus particles, we show that cleavage of L1 52/55k is DNA dependent, as is the cleavage of the other viral precursor proteins, and occurs at multiple sites, many not conforming to AVP consensus cleavage sites. Proteolytic processing of L1 52/55k disrupts its interactions with other capsid and core proteins, providing a mechanism for its removal during viral maturation. Our results support a model in which the role of L1 52/55k protein during assembly consists in tethering the viral core to the icosahedral shell and in which maturation proceeds simultaneously with packaging, before the viral particle is sealed.\",\n \"corpus_id\": 870372,\n \"score\": 2\n },\n {\n \"doc_id\": \"24854002\",\n \"title\": \"Conserved regions of bovine adenovirus-3 pVIII contain functional domains involved in nuclear localization and packaging in mature infectious virions.\",\n \"abstract\": \"Adenoviruses are non-enveloped DNA viruses that replicate in the nucleus of infected cells. One of the core proteins, named pVIII, is a minor capsid protein connecting the core with the inner surface of the capsid. Here, we report the characterization of minor capsid protein pVIII encoded by the L6 region of bovine adenovirus (BAdV)-3. Anti-pVIII serum detected a 24 kDa protein at 12-48 h post-infection and an additional 8 kDa protein at 24-48 h post-infection. While the 24 kDa protein was detected in empty capsids, only the C-terminal-cleaved 8 kDa protein was detected in the mature virion, suggesting that amino acids147-216 of the conserved C-terminus of BAdV-3 pVIII are incorporated in mature virions. Detection of hexon protein associated with both precursor (24 kDa) and cleaved (8 kDa) forms of pVIII suggest that the C-terminus of pVIII interacts with the hexon. The pVIII protein predominantly localizes to the nucleus of BAdV-3-infected cells utilizing the classical importin α/β dependent nuclear import pathway. Analysis of mutant pVIII demonstrated that amino acids 52-72 of the conserved N-terminus bind to importin α-3 with high affinity and are required for the nuclear localization.\",\n \"corpus_id\": 46563611,\n \"score\": 2\n },\n {\n \"doc_id\": \"25421887\",\n \"title\": \"Structure, function and dynamics in adenovirus maturation.\",\n \"abstract\": \"Here we review the current knowledge on maturation of adenovirus, a non-enveloped icosahedral eukaryotic virus. The adenovirus dsDNA genome fills the capsid in complex with a large amount of histone-like viral proteins, forming the core. Maturation involves proteolytic cleavage of several capsid and core precursor proteins by the viral protease (AVP). AVP uses a peptide cleaved from one of its targets as a \\\"molecular sled\\\" to slide on the viral genome and reach its substrates, in a remarkable example of one-dimensional chemistry. Immature adenovirus containing the precursor proteins lacks infectivity because of its inability to uncoat. The immature core is more compact and stable than the mature one, due to the condensing action of unprocessed core polypeptides; shell precursors underpin the vertex region and the connections between capsid and core. Maturation makes the virion metastable, priming it for stepwise uncoating by facilitating vertex release and loosening the condensed genome and its attachment to the icosahedral shell. The packaging scaffold protein L1 52/55k is also a substrate for AVP. Proteolytic processing of L1 52/55k disrupts its interactions with other virion components, providing a mechanism for its removal during maturation. Finally, possible roles for maturation of the terminal protein are discussed.\",\n \"corpus_id\": 18742961,\n \"score\": 2\n },\n {\n \"doc_id\": \"25954255\",\n \"title\": \"Adenoviral L4 33K forms ring-like oligomers and stimulates ATPase activity of IVa2: implications in viral genome packaging.\",\n \"abstract\": \"The mechanism of genome packaging in adenoviruses (AdVs) is presumed to be similar to that of dsDNA viruses including herpesviruses and dsDNA phages. First, the empty capsids are assembled after which the viral genome is pushed through a unique vertex by a motor which consists of three minimal components: an ATPase, a small terminase and a portal. Various components of this motor exist as ring-like structures forming a central channel through which the DNA travels during packaging. In AdV, the IVa2 protein is believed to function as a packaging ATPase, however, the equivalents of the small terminase and the portal have not been identified in AdVs. IVa2 interacts with another viral protein late region 4 (L4) 33K which is important for genome packaging. Both IVa2 and 33K are expressed at high levels during the late stage of virus infection. The oligomeric state of IVa2 and 33K was analyzed in virus-infected cells, IVa2 and 33K transfected cells, AdV particles, or as recombinant purified proteins. Electron microscopy of the purified proteins showed ring-like oligomers for both proteins which is consistent with their putative roles as a part of the packaging motor. We found that the ATPase activity of IVa2 is stimulated in the presence of 33K and the AdV genome. Our results suggest that the 33K functions analogous to the small terminase proteins and so will be part of the packaging motor complex.\",\n \"corpus_id\": 6119398,\n \"score\": 2\n },\n {\n \"doc_id\": \"26178997\",\n \"title\": \"Structures of Adenovirus Incomplete Particles Clarify Capsid Architecture and Show Maturation Changes of Packaging Protein L1 52/55k.\",\n \"abstract\": \"UNLABELLED: Adenovirus is one of the most complex icosahedral, nonenveloped viruses. Even after its structure was solved at near-atomic resolution by both cryo-electron microscopy and X-ray crystallography, the location of minor coat proteins is still a subject of debate. The elaborated capsid architecture is the product of a correspondingly complex assembly process, about which many aspects remain unknown. Genome encapsidation involves the concerted action of five virus proteins, and proteolytic processing by the virus protease is needed to prime the virion for sequential uncoating. Protein L1 52/55k is required for packaging, and multiple cleavages by the maturation protease facilitate its release from the nascent virion. Light-density particles are routinely produced in adenovirus infections and are thought to represent assembly intermediates. Here, we present the molecular and structural characterization of two different types of human adenovirus light particles produced by a mutant with delayed packaging. We show that these particles lack core polypeptide V but do not lack the density corresponding to this protein in the X-ray structure, thereby adding support to the adenovirus cryo-electron microscopy model. The two types of light particles present different degrees of proteolytic processing. Their structures provide the first glimpse of the organization of L1 52/55k protein inside the capsid shell and of how this organization changes upon partial maturation. Immature, full-length L1 52/55k is poised beneath the vertices to engage the virus genome. Upon proteolytic processing, L1 52/55k disengages from the capsid shell, facilitating genome release during uncoating. IMPORTANCE: Adenoviruses have been extensively characterized as experimental systems in molecular biology, as human pathogens, and as therapeutic vectors. However, a clear picture of many aspects of their basic biology is still lacking. Two of these aspects are the location of minor coat proteins in the capsid and the molecular details of capsid assembly. Here, we provide evidence supporting one of the two current models for capsid architecture. We also show for the first time the location of the packaging protein L1 52/55k in particles lacking the virus genome and how this location changes during maturation. Our results contribute to clarifying standing questions in adenovirus capsid architecture and provide new details on the role of L1 52/55k protein in assembly.\",\n \"corpus_id\": 5903737,\n \"score\": 2\n },\n {\n \"doc_id\": \"26491163\",\n \"title\": \"A Single Maturation Cleavage Site in Adenovirus Impacts Cell Entry and Capsid Assembly.\",\n \"abstract\": \"UNLABELLED: Proteolytic maturation drives the conversion of stable, immature virus particles to a mature, metastable state primed for cell infection. In the case of human adenovirus, this proteolytic cleavage is mediated by the virally encoded protease AVP. Protein VI, an internal capsid cement protein and substrate for AVP, is cleaved at two sites, one of which is near the N terminus of the protein. In mature capsids, the 33 residues at the N terminus of protein VI (pVIn) are sequestered inside the cavity formed by peripentonal hexon trimers at the 5-fold vertex. Here, we describe a glycine-to-alanine mutation in the N-terminal cleavage site of protein VI that profoundly impacts proteolytic processing, the generation of infectious particles, and cell entry. The phenotypic effects associated with this mutant provide a mechanistic framework for understanding the multifunctional nature of protein VI. Based on our findings, we propose that the primary function of the pVIn peptide is to mediate interactions between protein VI and hexon during virus replication, driving hexon nuclear accumulation and particle assembly. Once particles are assembled, AVP-mediated cleavage facilitates the release of the membrane lytic region at the amino terminus of mature VI, allowing it to lyse the endosome during cell infection. These findings highlight the importance of a single maturation cleavage site for both infectious particle production and cell entry and emphasize the exquisite spatiotemporal regulation governing adenovirus assembly and disassembly. IMPORTANCE: Postassembly virus maturation is a cornerstone principle in virology. However, a mechanistic understanding of how icosahedral viruses utilize this process to transform immature capsids into infection-competent particles is largely lacking. Adenovirus maturation involves proteolytic processing of seven precursor proteins. There is currently no information for the role of each independent cleavage event in the generation of infectious virions. To address this, we investigated the proteolytic maturation of one adenovirus precursor molecule, protein VI. Structurally, protein VI cements the outer capsid shell and links it to the viral core. Functionally, protein VI is involved in endosome disruption, subcellular trafficking, transcription activation, and virus assembly. Our studies demonstrate that the multifunctional nature of protein VI is largely linked to its maturation. Through mutational analysis, we show that disrupting the N-terminal cleavage of preprotein VI has major deleterious effects on the assembly of infectious virions and their subsequent ability to infect host cells.\",\n \"corpus_id\": 3870130,\n \"score\": 2\n },\n {\n \"doc_id\": \"26764008\",\n \"title\": \"Morphological, Biochemical, and Functional Study of Viral Replication Compartments Isolated from Adenovirus-Infected Cells.\",\n \"abstract\": \"UNLABELLED: Adenovirus (Ad) replication compartments (RC) are nuclear microenvironments where the viral genome is replicated and a coordinated program of late gene expression is established. These virus-induced nuclear sites seem to behave as central hubs for the regulation of virus-host cell interactions, since proteins that promote efficient viral replication as well as factors that participate in the antiviral response are coopted and concentrated there. To gain further insight into the activities of viral RC, here we report, for the first time, the morphology, composition, and activities of RC isolated from Ad-infected cells. Morphological analyses of isolated RC particles by superresolution microscopy showed that they were indistinguishable from RC within infected cells and that they displayed a dynamic compartmentalization. Furthermore, the RC-containing fractions (RCf) proved to be functional, as they directed de novo synthesis of viral DNA and RNA as well as RNA splicing, activities that are associated with RC in vivo. A detailed analysis of the production of viral late mRNA from RCf at different times postinfection revealed that viral mRNA splicing occurs in RC and that the synthesis, posttranscriptional processing, and release from RC to the nucleoplasm of individual viral late transcripts are spatiotemporally separate events. The results presented here demonstrate that RCf are a powerful system for detailed study into RC structure, composition, and activities and, as a result, the determination of the molecular mechanisms that induce the formation of these viral sites of adenoviruses and other nuclear-replicating viruses. IMPORTANCE: RC may represent molecular hubs where many aspects of virus-host cell interaction are controlled. Here, we show by superresolution microscopy that RCf have morphologies similar to those of RC within Ad-infected cells and that they appear to be compartmentalized, as nucleolin and DBP display different localization in the periphery of these viral sites. RCf proved to be functional, as they direct de novo synthesis of viral DNA and mRNA, allowing the detailed study of the regulation of viral genome replication and expression. Furthermore, we show that the synthesis and splicing of individual viral late mRNA occurs in RC and that they are subject to different temporal patterns of regulation, from their synthesis to their splicing and release from RC to the nucleoplasm. Hence, RCf represent a novel system to study molecular mechanisms that are orchestrated in viral RC to take control of the infected cell and promote an efficient viral replication cycle.\",\n \"corpus_id\": 6160153,\n \"score\": 2\n },\n {\n \"doc_id\": \"27721809\",\n \"title\": \"Components of Adenovirus Genome Packaging.\",\n \"abstract\": \"Adenoviruses (AdVs) are icosahedral viruses with double-stranded DNA (dsDNA) genomes. Genome packaging in AdV is thought to be similar to that seen in dsDNA containing icosahedral bacteriophages and herpesviruses. Specific recognition of the AdV genome is mediated by a packaging domain located close to the left end of the viral genome and is mediated by the viral packaging machinery. Our understanding of the role of various components of the viral packaging machinery in AdV genome packaging has greatly advanced in recent years. Characterization of empty capsids assembled in the absence of one or more components involved in packaging, identification of the unique vertex, and demonstration of the role of IVa2, the putative packaging ATPase, in genome packaging have provided compelling evidence that AdVs follow a sequential assembly pathway. This review provides a detailed discussion on the functions of the various viral and cellular factors involved in AdV genome packaging. We conclude by briefly discussing the roles of the empty capsids, assembly intermediates, scaffolding proteins, portal vertex and DNA encapsidating enzymes in AdV assembly and packaging.\",\n \"corpus_id\": 15315707,\n \"score\": 2\n },\n {\n \"doc_id\": \"28628648\",\n \"title\": \"The adenovirus major core protein VII is dispensable for virion assembly but is essential for lytic infection.\",\n \"abstract\": \"The Adenovirus (Ad) genome within the capsid is tightly associated with a virus-encoded, histone-like core protein-protein VII. Two other Ad core proteins, V and X/μ, also are located within the virion and are loosely associated with viral DNA. Core protein VII remains associated with the Ad genome during the early phase of infection. It is not known if naked Ad DNA is packaged into the capsid, as with dsDNA bacteriophage and herpesviruses, followed by the encapsidation of viral core proteins, or if a unique packaging mechanism exists with Ad where a DNA-protein complex is simultaneously packaged into the virion. The latter model would require an entirely new molecular mechanism for packaging compared to known viral packaging motors. We characterized a virus with a conditional knockout of core protein VII. Remarkably, virus particles were assembled efficiently in the absence of protein VII. No changes in protein composition were evident with VII-virus particles, including the abundance of core protein V, but changes in the proteolytic processing of some capsid proteins were evident. Virus particles that lack protein VII enter the cell, but incoming virions did not escape efficiently from endosomes. This greatly diminished all subsequent aspects of the infectious cycle. These results reveal that the Ad major core protein VII is not required to condense viral DNA within the capsid, but rather plays an unexpected role during virus maturation and the early stages of infection. These results establish a new paradigm pertaining to the Ad assembly mechanism and reveal a new and important role of protein VII in early stages of infection.\",\n \"corpus_id\": 7448978,\n \"score\": 2\n },\n {\n \"doc_id\": \"18674782\",\n \"title\": \"DNA packaging motor assembly intermediate of bacteriophage phi29.\",\n \"abstract\": \"Unraveling the structure and assembly of the DNA packaging ATPases of the tailed double-stranded DNA bacteriophages is integral to understanding the mechanism of DNA translocation. Here, the bacteriophage phi29 packaging ATPase gene product 16 (gp16) was overexpressed in soluble form in Bacillus subtilis (pSAC), purified to near homogeneity, and assembled to the phi29 precursor capsid (prohead) to produce a packaging motor intermediate that was fully active in in vitro DNA packaging. The formation of higher oligomers of the gp16 from monomers was concentration dependent and was characterized by analytical ultracentrifugation, gel filtration, and electron microscopy. The binding of multiple copies of gp16 to the prohead was dependent on the presence of an oligomer of 174- or 120-base prohead RNA (pRNA) fixed to the head-tail connector at the unique portal vertex of the prohead. The use of mutant pRNAs demonstrated that gp16 bound specifically to the A-helix of pRNA, and ribonuclease footprinting of gp16 on pRNA showed that gp16 protected the CC residues of the CCA bulge (residues 18-20) of the A-helix. The binding of gp16 to the prohead/pRNA to constitute the complete and active packaging motor was confirmed by cryo-electron microscopy three-dimensional reconstruction of the prohead/pRNA/gp16 complex. The complex was capable of supercoiling DNA-gp3 as observed previously for gp16 alone; therefore, the binding of gp16 to the prohead, rather than first to DNA-gp3, represents an alternative packaging motor assembly pathway.\",\n \"corpus_id\": 20765445,\n \"score\": 1\n },\n {\n \"doc_id\": \"19196470\",\n \"title\": \"Packaging of viral RNAs in virions of adenoviruses.\",\n \"abstract\": \"Earlier, we detected viral RNAs packaged in the porcine adenovirus (PAdV) -3 virions. Using Southern blot analysis, we further demonstrated that the viral RNAs were predominantly packaged in CsCl purified mature capsids (containing viral genome) than empty/intermediate capsids. Some of the packaged viral RNAs appear to be polyadenylated. Real-time reverse transcription (RT)-PCR analysis indicated that the copy number of the tested viral mRNAs encoding E1Bsmall and fiber proteins was less than one per full capsid. Moreover, detection of viral RNA packaged in CsCl purified human adenovirus (HAdV) -5 virions indicates that the viral RNA packaging might be a common phenomenon in members of Adenoviridae family. Further quantitative analysis of viral protein, DNA, and RNA in CsCl purified mature and empty/intermediate capsids of recombinant HAdV-5 expressing enhanced green fluorescent protein indicated that the traceable viral RNA detected in empty/intermediate capsids seems associated with the presence of traceable viral genomic DNA. Taken together, our data suggest that the viral RNAs may be passively packaged in adenovirus virion during encapsidation of viral genomic DNA in cell nuclei. Thus, viral RNA packaging may be a characteristic feature of adenoviral genomic DNA encapsidation.\",\n \"corpus_id\": 15462435,\n \"score\": 1\n },\n {\n \"doc_id\": \"19846532\",\n \"title\": \"African swine fever virus polyprotein pp62 is essential for viral core development.\",\n \"abstract\": \"One of the most characteristic features of African swine fever virus gene expression is its use of two polyproteins, pp220 and pp62, to produce several structural proteins that account for approximately 32% of the total protein virion mass. Equimolecular amounts of these proteins are the major components of the core shell, a thick protein layer that lies beneath the inner envelope, surrounding the viral nucleoid. Polyprotein pp220, which is located immediately underneath the internal envelope, is essential for the encapsidation of the core of the viral particle. In its absence, the infection produces essentially coreless particles. In this study we analyzed, by means of an IPTG (isopropyl-beta-d-thiogalactopyranoside)-inducible virus, the role of polyprotein pp62 in virus assembly. Polyprotein pp62 is indispensable for viral replication. The repression of polyprotein pp62 expression does not alter late gene expression or the proteolytic processing of the polyprotein pp220. However, it has a profound impact on the subcellular localization of polyprotein pp220. Electron microscopy studies revealed that polyprotein pp62 is necessary for the correct assembly and maturation of the core of the viral particle. Its repression leads to the appearance of a significant fraction of empty particles, to an increase in the number of immature-like particles, and to the accumulation of defective particles. Immunoelectron microscopy analysis showed a clear correlation between the amount of polyprotein pp62, the quantity of polyprotein pp220, and the state of development of the core, suggesting that the complete absence of polyprotein pp62 during morphogenesis would produce a homogenous population of empty particles.\",\n \"corpus_id\": 206807788,\n \"score\": 1\n },\n {\n \"doc_id\": \"20060706\",\n \"title\": \"Genome packaging in viruses.\",\n \"abstract\": \"Genome packaging is a fundamental process in a viral life cycle. Many viruses assemble preformed capsids into which the genomic material is subsequently packaged. These viruses use a packaging motor protein that is driven by the hydrolysis of ATP to condense the nucleic acids into a confined space. How these motor proteins package viral genomes had been poorly understood until recently, when a few X-ray crystal structures and cryo-electron microscopy (cryo-EM) structures became available. Here we discuss various aspects of genome packaging and compare the mechanisms proposed for packaging motors on the basis of structural information.\",\n \"corpus_id\": 19551835,\n \"score\": 1\n },\n {\n \"doc_id\": \"22734445\",\n \"title\": \"Influence of loxP insertion upstream of the cis-acting packaging domain on adenovirus packaging efficiency.\",\n \"abstract\": \"First-generation AdV enables efficient gene transduction, although its immunogenicity is an important problem in vivo. Helper-dependent AdV (HD-AdV) is one possible solution to this problem. The construction of HD-AdV requires a helper virus, in which the viral packaging domain is flanked by two inserted loxP to hamper its packaging in Cre-expressing 293 cells. Here, we constructed 19L viruses containing loxP at 191 nt from the left end of the genome upstream of the packaging domain, 15L viruses bearing loxP at 143 nt, and a control ΔL virus lacking loxP at these positions. The 19L position is used worldwide, and the 15L position has been reported to result in a lower titer than that of 19L. When the titers were compared for six pairs of 19L and 15L AdV, the 19L AdV produced titers similar to, or sometimes lower than, the 15L and ΔL AdV, unlike the results of previous reports. We next chose one pair of 15L and 19L AdV that produced titers similar to that of ΔL and a competitor AdV lacking loxP for use in a competition assay. When a small amount of the competitor AdV was co-infected, both the 15L and the 19L AdV, but not ΔL, gradually became minority components during subsequent viral passages. Therefore, the loxP insertions at 143 nt and 191 nt decreased the viral packaging efficiency.\",\n \"corpus_id\": 24286363,\n \"score\": 1\n },\n {\n \"doc_id\": \"23737056\",\n \"title\": \"Assembly of simple icosahedral viruses.\",\n \"abstract\": \"Icosahedral viruses exhibit elegant pathways of capsid assembly and maturation regulated by symmetry principles. Assembly is a dynamic process driven by consecutive and genetically programmed morphogenetic interactions between protein subunits. The non-symmetric capsid subunits are gathered by hydrophobic contacts and non-covalent interactions in assembly intermediates, which serve as blocks to build a symmetric capsid. In some cases, non-symmetric interactions among intermediates are involved in assembly, highlighting the remarkable capacity of capsid proteins to fold into demanding conformations compatible with a closed protein shell. In this chapter, the morphogenesis of structurally simple icosahedral viruses, including representative members of the parvoviruses, picornaviruses or polyomaviruses as paradigms, is described in some detail. Icosahedral virus assembly may occur in different subcellular compartments and involve a panoplia of cellular and viral factors, chaperones, and protein modifications that, in general, are still poorly characterized. Mechanisms of viral genome encapsidation may imply direct interactions between the genome and the assembly intermediates, or active packaging into a preformed empty capsid. High stability of intermediates and proteolytic cleavages during viral maturation usually contribute to the overall irreversible character of the assembly process. These and other simple icosahedral viruses were pioneer models to understand basic principles of virus assembly, continue to be leading subjects of morphogenetic analyses, and have inspired ongoing studies on the assembly of larger viruses and cellular and synthetic macromolecular complexes.\",\n \"corpus_id\": 24767972,\n \"score\": 1\n },\n {\n \"doc_id\": \"24706827\",\n \"title\": \"Solving a Levinthal's paradox for virus assembly identifies a unique antiviral strategy.\",\n \"abstract\": \"One of the important puzzles in virology is how viruses assemble the protein containers that package their genomes rapidly and efficiently in vivo while avoiding triggering their hosts' antiviral defenses. Viral assembly appears directed toward a relatively small subset of the vast number of all possible assembly intermediates and pathways, akin to Levinthal's paradox for the folding of polypeptide chains. Using an in silico assembly model, we demonstrate that this reduction in complexity can be understood if aspects of in vivo assembly, which have mostly been neglected in in vitro experimental and theoretical modeling assembly studies, are included in the analysis. In particular, we show that the increasing viral coat protein concentration that occurs in infected cells plays unexpected and vital roles in avoiding potential kinetic assembly traps, significantly reducing the number of assembly pathways and assembly initiation sites, and resulting in enhanced assembly efficiency and genome packaging specificity. Because capsid assembly is a vital determinant of the overall fitness of a virus in the infection process, these insights have important consequences for our understanding of how selection impacts on the evolution of viral quasispecies. These results moreover suggest strategies for optimizing the production of protein nanocontainers for drug delivery and of virus-like particles for vaccination. We demonstrate here in silico that drugs targeting the specific RNA-capsid protein contacts can delay assembly, reduce viral load, and lead to an increase of misencapsidation of cellular RNAs, hence opening up unique avenues for antiviral therapy.\",\n \"corpus_id\": 7956841,\n \"score\": 1\n },\n {\n \"doc_id\": \"24784448\",\n \"title\": \"Overexpression of Ad5 precursor terminal protein accelerates recombinant adenovirus packaging and amplification in HEK-293 packaging cells.\",\n \"abstract\": \"Recombinant adenoviruses are one of the most common vehicles for efficient in vitro and in vivo gene deliveries. Here, we investigate whether exogenous precursor terminal protein (pTP) expression in 293 cells improves the efficiency of adenovirus packaging and amplification. We used a piggyBac transposon-based vector and engineered a stable 293 line that expresses high level of Ad5 pTP, designated as 293pTP. Using the AdBMP6-GLuc that expresses green fluorescent protein (GFP), BMP6 and Gaussia luciferase, we found that the infectivity of AdBMP6-GLuc viral samples packaged in 293pTP cells was titrated up to 19.3 times higher than that packaged in parental 293 cells. AdBMP6-GLuc viral samples packaged in 293pTP cells exhibited significantly higher transduction efficiency in 143B and immortalized mouse embryonic fibroblast (iMEF) cells, as assessed by fluorescence-activated cell sorting analysis of GFP-positive cells, the luciferase activity assay and BMP6-induced osteogenic marker alkaline phosphatase activities in iMEFs. When adenovirus amplification efficiency was analyzed, we found that 293pTP cells infected with AdBMP6-GLuc yielded up to 12.6 times higher titer than that in parental 293 cells, especially at lower multiplicities of infection. These results strongly suggest that exogenous pTP expression may accelerate the packaging and amplification of recombinant adenoviruses. Thus, the engineered 293pTP cells should be a superior packaging line for efficient adenovirus production.\",\n \"corpus_id\": 205145088,\n \"score\": 1\n },\n {\n \"doc_id\": \"27521148\",\n \"title\": \"Deletion of pV affects integrity of capsid causing defect in the infectivity of bovine adenovirus-3.\",\n \"abstract\": \"Members of the genus Mastadenovirus including bovine adenovirus 3 (BAdV-3) encode a genus-specific unique protein named pV. The pV encoded by BAdV-3 is a protein of 423 aa showing 40.9 % identity to pV of human adenovirus 2. Here, we report the construction and analysis of recombinant BAdV-3 (BAV.dV) containing deletion of pV. The BAV.dV could only be isolated in CRL.pV cells expressing pV, suggesting that pV appears essential for the infection of BAdV-3. Analysis of BAV.dV suggested that despite affecting some late gene expression in virus-infected cells, there was no significant difference in the incorporation of viral proteins in the mature virions. Moreover, analysis of mature virions revealed degraded capsids leading to change in morphology and infectivity of BAV.dV. Furthermore, analysis of the genome sequence of different clones of BAV.dV passaged in different cell lines revealed no mutations in core proteins pVII and pX\\\\Mu suggesting that the replication defect may not be rescued. Our results suggest that pV is required for proper viral assembly of BAdV-3 as lack of pV produces aberrant capsids. Moreover, altered capsids lead to the production of non-infectious BAV.dV virions.\",\n \"corpus_id\": 24839525,\n \"score\": 1\n },\n {\n \"doc_id\": \"28528442\",\n \"title\": \"Herpesvirus Capsid Assembly and DNA Packaging.\",\n \"abstract\": \"Herpes simplex virus type I (HSV-1) is the causative agent of several pathologies ranging in severity from the common cold sore to life-threatening encephalitic infection. During productive lytic infection, over 80 viral proteins are expressed in a highly regulated manner, resulting in the replication of viral genomes and assembly of progeny virions. The virion of all herpesviruses consists of an external membrane envelope, a proteinaceous layer called the tegument, and an icosahedral capsid containing the double-stranded linear DNA genome. The capsid shell of HSV-1 is built from four structural proteins: a major capsid protein, VP5, which forms the capsomers (hexons and pentons), the triplex consisting of VP19C and VP23 found between the capsomers, and VP26 which binds to VP5 on hexons but not pentons. In addition, the dodecameric pUL6 portal complex occupies 1 of the 12 capsid vertices, and the capsid vertex specific component (CVSC), a heterotrimer complex of pUL17, pUL25, and pUL36, binds specifically to the triplexes adjacent to each penton. The capsid is assembled in the nucleus where the viral genome is packaged into newly assembled closed capsid shells. Cleavage and packaging of replicated, concatemeric viral DNA requires the seven viral proteins encoded by the UL6, UL15, UL17, UL25, UL28, UL32, and UL33 genes. Considerable advances have been made in understanding the structure of the herpesvirus capsid and the function of several of the DNA packaging proteins by applying biochemical, genetic, and structural techniques. This review is a summary of recent advances with respect to the structure of the HSV-1 virion capsid and what is known about the function of the seven packaging proteins and their interactions with each other and with the capsid shell.\",\n \"corpus_id\": 4054191,\n \"score\": 1\n },\n {\n \"doc_id\": \"29167340\",\n \"title\": \"Human Adenovirus Core Protein V Is Targeted by the Host SUMOylation Machinery To Limit Essential Viral Functions.\",\n \"abstract\": \"Human adenoviruses (HAdV) are nonenveloped viruses containing a linear, double-stranded DNA genome surrounded by an icosahedral capsid. To allow proper viral replication, the genome is imported through the nuclear pore complex associated with viral core proteins. Until now, the role of these incoming virion proteins during the early phase of infection was poorly understood. The core protein V is speculated to bridge the core and the surrounding capsid. It binds the genome in a sequence-independent manner and localizes in the nucleus of infected cells, accumulating at nucleoli. Here, we show that protein V contains conserved SUMO conjugation motifs (SCMs). Mutation of these consensus motifs resulted in reduced SUMOylation of the protein; thus, protein V represents a novel target of the host SUMOylation machinery. To understand the role of protein V SUMO posttranslational modification during productive HAdV infection, we generated a replication-competent HAdV with SCM mutations within the protein V coding sequence. Phenotypic analyses revealed that these SCM mutations are beneficial for adenoviral replication. Blocking protein V SUMOylation at specific sites shifts the onset of viral DNA replication to earlier time points during infection and promotes viral gene expression. Simultaneously, the altered kinetics within the viral life cycle are accompanied by more efficient proteasomal degradation of host determinants and increased virus progeny production than that observed during wild-type infection. Taken together, our studies show that protein V SUMOylation reduces virus growth; hence, protein V SUMOylation represents an important novel aspect of the host antiviral strategy to limit virus replication and thereby points to potential intervention strategies. IMPORTANCE Many decades of research have revealed that HAdV structural proteins promote viral entry and mainly physical stability of the viral genome in the capsid. Our work over the last years showed that this concept needs expansion as the functions are more diverse. We showed that capsid protein VI regulates the antiviral response by modulation of the transcription factor Daxx during infection. Moreover, core protein VII interacts with SPOC1 restriction factor, which is beneficial for efficient viral gene expression. Here, we were able to show that core protein V also represents a novel substrate of the host SUMOylation machinery and contains several conserved SCMs; mutation of these consensus motifs reduced SUMOylation of the protein. Unexpectedly, we observed that introducing these mutations into HAdV promotes adenoviral replication. In conclusion, we offer novel insights into adenovirus core proteins and provide evidence that SUMOylation of HAdV factors regulates replication efficiency.\",\n \"corpus_id\": 4970916,\n \"score\": 1\n },\n {\n \"doc_id\": \"18077717\",\n \"title\": \"The essential human cytomegalovirus gene UL52 is required for cleavage-packaging of the viral genome.\",\n \"abstract\": \"Replication of human cytomegalovirus (HCMV) produces large DNA concatemers of head-to-tail-linked viral genomes that upon packaging into capsids are cut into unit-length genomes. The mechanisms underlying cleavage-packaging and the subsequent steps prior to nuclear egress of DNA-filled capsids are incompletely understood. The hitherto uncharacterized product of the essential HCMV UL52 gene was proposed to participate in these processes. To investigate the function of pUL52, we constructed a DeltaUL52 mutant as well as a complementing cell line. We found that replication of viral DNA was not impaired in noncomplementing cells infected with the DeltaUL52 virus, but viral concatemers remained uncleaved. Since the subnuclear localization of the known cleavage-packaging proteins pUL56, pUL89, and pUL104 was unchanged in DeltaUL52-infected fibroblasts, pUL52 does not seem to act via these proteins. Electron microscopy studies revealed only B capsids in the nuclei of DeltaUL52-infected cells, indicating that the mutant virus has a defect in encapsidation of viral DNA. Generation of recombinant HCMV genomes encoding epitope-tagged pUL52 versions showed that only the N-terminally tagged pUL52 supported viral growth, suggesting that the C terminus is crucial for its function. pUL52 was expressed as a 75-kDa protein with true late kinetics. It localized preferentially to the nuclei of infected cells and was found to enclose the replication compartments. Taken together, our results demonstrate an essential role for pUL52 in cleavage-packaging of HCMV DNA. Given its unique subnuclear localization, the function of pUL52 might be distinct from that of other cleavage-packaging proteins.\",\n \"corpus_id\": 18247659,\n \"score\": 0\n },\n {\n \"doc_id\": \"19812148\",\n \"title\": \"Effects of major capsid proteins, capsid assembly, and DNA cleavage/packaging on the pUL17/pUL25 complex of herpes simplex virus 1.\",\n \"abstract\": \"The U(L)17 and U(L)25 proteins (pU(L)17 and pU(L)25, respectively) of herpes simplex virus 1 are located at the external surface of capsids and are essential for DNA packaging and DNA retention in the capsid, respectively. The current studies were undertaken to determine whether DNA packaging or capsid assembly affected the pU(L)17/pU(L)25 interaction. We found that pU(L)17 and pU(L)25 coimmunoprecipitated from cells infected with wild-type virus, whereas the major capsid protein VP5 (encoded by the U(L)19 gene) did not coimmunoprecipitate with these proteins under stringent conditions. In addition, pU(L)17 (i) coimmunoprecipitated with pU(L)25 in the absence of other viral proteins, (ii) coimmunoprecipitated with pU(L)25 from lysates of infected cells in the presence or absence of VP5, (iii) did not coimmunoprecipitate efficiently with pU(L)25 in the absence of the triplex protein VP23 (encoded by the U(L)18 gene), (iv) required pU(L)25 for proper solubilization and localization within the viral replication compartment, (v) was essential for the sole nuclear localization of pU(L)25, and (vi) required capsid proteins VP5 and VP23 for nuclear localization and normal levels of immunoreactivity in an indirect immunofluorescence assay. Proper localization of pU(L)25 in infected cell nuclei required pU(L)17, pU(L)32, and the major capsid proteins VP5 and VP23, but not the DNA packaging protein pU(L)15. The data suggest that VP23 or triplexes augment the pU(L)17/pU(L)25 interaction and that VP23 and VP5 induce conformational changes in pU(L)17 and pU(L)25, exposing epitopes that are otherwise partially masked in infected cells. These conformational changes can occur in the absence of DNA packaging. The data indicate that the pU(L)17/pU(L)25 complex requires multiple viral proteins and functions for proper localization and biochemical behavior in the infected cell.\",\n \"corpus_id\": 7579552,\n \"score\": 0\n },\n {\n \"doc_id\": \"20181717\",\n \"title\": \"Mutational analysis of the herpes simplex virus type 1 UL25 DNA packaging protein reveals regions that are important after the viral DNA has been packaged.\",\n \"abstract\": \"The herpes simplex virus type 1 (HSV-1) UL25 gene encodes a minor capsid protein, pUL25, that is essential for packaging the full-length viral genome. Six regions which contain disordered residues have been identified in the high-resolution structure of pUL25. To investigate the significance of these flexible regions, a panel of plasmids was generated encoding mutant proteins, with each member lacking the disordered residues in one of the six regions. In addition, UL25 constructs were produced, which specified proteins that contained missense mutations individually affecting two of the four regions on the surface of pUL25 predicted from evolutionary trace analysis to be important in protein-protein interactions. The impacts of these mutations on viral DNA packaging, virus assembly, and growth were examined. Of the nine mutant proteins analyzed, five failed to complement the growth of a UL25 deletion mutant in Vero cells. These noncomplementing proteins fell into three classes. Proteins in one class did not alter the DNA packaging phenotype of an HSV-1 UL25 deletion mutant, whereas proteins from the other two classes allowed the UL25 null mutant to package full-length viral DNA. Subsequent analysis of the latter classes of mutant proteins demonstrated that one class enabled the null virus to release enveloped virus particles from U2OS cells, whereas the other class prevented egress of mature HSV-1 capsids from the nucleus. These findings reveal a new role for pUL25 in virion assembly, consistent with its flexible structure and location on the capsid.\",\n \"corpus_id\": 9107079,\n \"score\": 0\n },\n {\n \"doc_id\": \"20845949\",\n \"title\": \"Trapping of hepatitis B virus capsid assembly intermediates by phenylpropenamide assembly accelerators.\",\n \"abstract\": \"Understanding the biological self-assembly process of virus capsids is key to understanding the viral life cycle, as well as serving as a platform for the design of assembly-based antiviral drugs. Here we identify and characterize the phenylpropenamide family of small molecules, known to have antiviral activity in vivo, as assembly effectors of the hepatitis B virus (HBV) capsid. We have found two representative phenylpropenamides to be assembly accelerators, increasing the rate of assembly with only modest increases in the stability of the HBV capsids; these data provide a physical-chemical basis for their antiviral activity. Unlike previously described HBV assembly effectors, the phenylpropenamides do not misdirect assembly; rather, the accelerated reactions proceed on-path to produce morphologically normal capsids. However, capsid assembly in the presence of phenylpropenamides is characterized by kinetic trapping of assembly intermediates. These traps resolve under conditions close to physiological, but we found that trapped intermediates persist under conditions that favor phenylpropenamide binding and strong core protein-protein interactions. The phenylpropenamides serve as chemical probes of the HBV capsid assembly pathway by trapping on-path assembly intermediates, illustrating the governing influence of reaction kinetics on capsid assembly.\",\n \"corpus_id\": 106032,\n \"score\": 0\n },\n {\n \"doc_id\": \"21347350\",\n \"title\": \"NS2 protein of hepatitis C virus interacts with structural and non-structural proteins towards virus assembly.\",\n \"abstract\": \"Growing experimental evidence indicates that, in addition to the physical virion components, the non-structural proteins of hepatitis C virus (HCV) are intimately involved in orchestrating morphogenesis. Since it is dispensable for HCV RNA replication, the non-structural viral protein NS2 is suggested to play a central role in HCV particle assembly. However, despite genetic evidences, we have almost no understanding about NS2 protein-protein interactions and their role in the production of infectious particles. Here, we used co-immunoprecipitation and/or fluorescence resonance energy transfer with fluorescence lifetime imaging microscopy analyses to study the interactions between NS2 and the viroporin p7 and the HCV glycoprotein E2. In addition, we used alanine scanning insertion mutagenesis as well as other mutations in the context of an infectious virus to investigate the functional role of NS2 in HCV assembly. Finally, the subcellular localization of NS2 and several mutants was analyzed by confocal microscopy. Our data demonstrate molecular interactions between NS2 and p7 and E2. Furthermore, we show that, in the context of an infectious virus, NS2 accumulates over time in endoplasmic reticulum-derived dotted structures and colocalizes with both the envelope glycoproteins and components of the replication complex in close proximity to the HCV core protein and lipid droplets, a location that has been shown to be essential for virus assembly. We show that NS2 transmembrane region is crucial for both E2 interaction and subcellular localization. Moreover, specific mutations in core, envelope proteins, p7 and NS5A reported to abolish viral assembly changed the subcellular localization of NS2 protein. Together, these observations indicate that NS2 protein attracts the envelope proteins at the assembly site and it crosstalks with non-structural proteins for virus assembly.\",\n \"corpus_id\": 18422988,\n \"score\": 0\n },\n {\n \"doc_id\": \"21762796\",\n \"title\": \"Visualizing HIV-1 assembly.\",\n \"abstract\": \"The assembly of an HIV-1 particle is a complex, multistep process involving several viral and cellular proteins, RNAs and lipids. While many macroscopic and fixed-cell microscopic techniques have provided important insights into the structure of HIV-1 particles and the mechanisms by which they assemble, analysis of individual particles and their assembly in living cells offers the potential of surmounting many of the limitations inherent in other approaches. In this review, we discuss how the recent application of live-cell microscopic imaging techniques has increased our understanding of the process of HIV-1 particle assembly. In particular, we focus on recent studies that have employed total internal reflection fluorescence microscopy and other single-virion imaging techniques in live cells. These approaches have illuminated the dynamics of Gag protein assembly, viral RNA packaging and ESCRT (endosomal sorting complex required for transport) protein recruitment at the level of individual viral particles. Overall, the particular advantages of individual particle imaging in living cells have yielded findings that would have been difficult or impossible to obtain using macroscopic or fixed-cell microscopic techniques.\",\n \"corpus_id\": 10910761,\n \"score\": 0\n },\n {\n \"doc_id\": \"22019738\",\n \"title\": \"Stepwise expansion of the bacteriophage ϕ6 procapsid: possible packaging intermediates.\",\n \"abstract\": \"The initial assembly product of bacteriophage ϕ6, the procapsid, undergoes major structural transformation during the sequential packaging of its three segments of single-stranded RNA. The procapsid, a compact icosahedrally symmetric particle with deeply recessed vertices, expands to the spherical mature capsid, increasing the volume available to accommodate the genome by 2.5-fold. It has been proposed that expansion and packaging are linked, with each stage in expansion presenting a binding site for a particular RNA segment. To investigate procapsid transformability, we induced expansion by acidification, heating, and elevated salt concentration. Cryo-electron microscopy reconstructions after all three treatments yielded the same partially expanded particle. Analysis by cryo-electron tomography showed that all vertices of a given capsid were either in a compact or an expanded state, indicating a highly cooperative transition. To benchmark the mature capsid, we analyzed filled (in vivo packaged) capsids. When these particles were induced to release their RNA, they reverted to the same intermediate state as expanded procapsids (intermediate 1) or to a second, further expanded state (intermediate 2). This partial reversibility of expansion suggests that the mature spherical capsid conformation is obtained only when sufficient outward pressure is exerted by packaged RNA. The observation of two intermediates is consistent with the proposed three-step packaging process. The model is further supported by the observation that a mutant capable of packaging the second RNA segment without previously packaging the first segment has enhanced susceptibility for switching spontaneously from the procapsid to the first intermediate state.\",\n \"corpus_id\": 12492657,\n \"score\": 0\n },\n {\n \"doc_id\": \"23175377\",\n \"title\": \"The human cytomegalovirus UL51 protein is essential for viral genome cleavage-packaging and interacts with the terminase subunits pUL56 and pUL89.\",\n \"abstract\": \"Cleavage of human cytomegalovirus (HCMV) genomes as well as their packaging into capsids is an enzymatic process mediated by viral proteins and therefore a promising target for antiviral therapy. The HCMV proteins pUL56 and pUL89 form the terminase and play a central role in cleavage-packaging, but several additional viral proteins, including pUL51, had been suggested to contribute to this process, although they remain largely uncharacterized. To study the function of pUL51 in infected cells, we constructed HCMV mutants encoding epitope-tagged versions of pUL51 and used a conditionally replicating virus (HCMV-UL51-ddFKBP), in which pUL51 levels could be regulated by a synthetic ligand. In cells infected with HCMV-UL51-ddFKBP, viral DNA replication was not affected when pUL51 was knocked down. However, no unit-length genomes and no DNA-filled C capsids were found, indicating that cleavage of concatemeric HCMV DNA and genome packaging into capsids did not occur in the absence of pUL51. pUL51 was expressed mainly with late kinetics and was targeted to nuclear replication compartments, where it colocalized with pUL56 and pUL89. Upon pUL51 knockdown, pUL56 and pUL89 were no longer detectable in replication compartments, suggesting that pUL51 is needed for their correct subnuclear localization. Moreover, pUL51 was found in a complex with the terminase subunits pUL56 and pUL89. Our data provide evidence that pUL51 is crucial for HCMV genome cleavage-packaging and may represent a third component of the viral terminase complex. Interference with the interactions between the terminase subunits by antiviral drugs could be a strategy to disrupt the HCMV replication cycle.\",\n \"corpus_id\": 2274085,\n \"score\": 0\n },\n {\n \"doc_id\": \"23658526\",\n \"title\": \"hepatitis c Virus p7 is critical for capsid assembly and envelopment.\",\n \"abstract\": \"Hepatitis C virus (HCV) p7 is a membrane-associated ion channel protein crucial for virus production. To analyze how p7 contributes to this process, we dissected HCV morphogenesis into sub-steps including recruitment of HCV core to lipid droplets (LD), virus capsid assembly, unloading of core protein from LDs and subsequent membrane envelopment of capsids. Interestingly, we observed accumulation of slowly sedimenting capsid-like structures lacking the viral envelope in cells transfected with HCV p7 mutant genomes which possess a defect in virion production. Concomitantly, core protein was enriched at the surface of LDs. This indicates a defect in core/capsid unloading from LDs and subsequent membrane envelopment rather than defective trafficking of core to this cellular organelle. Protease and ribonuclease digestion protection assays, rate zonal centrifugation and native, two dimensional gel electrophoresis revealed increased amounts of high-order, non-enveloped core protein complexes unable to protect viral RNA in cells transfected with p7 mutant genomes. These results suggest accumulation of capsid assembly intermediates that had not yet completely incorporated viral RNA in the absence of functional p7. Thus, functional p7 is necessary for the final steps of capsid assembly as well as for capsid envelopment. These results support a model where capsid assembly is linked with membrane envelopment of nascent RNA-containing core protein multimers, a process coordinated by p7. In summary, we provide novel insights into the sequence of HCV assembly events and essential functions of p7.\",\n \"corpus_id\": 559775,\n \"score\": 0\n },\n {\n \"doc_id\": \"24722756\",\n \"title\": \"Binding of glutathione to enterovirus capsids is essential for virion morphogenesis.\",\n \"abstract\": \"Enteroviruses (family of the Picornaviridae) cover a large group of medically important human pathogens for which no antiviral treatment is approved. Although these viruses have been extensively studied, some aspects of the viral life cycle, in particular morphogenesis, are yet poorly understood. We report the discovery of TP219 as a novel inhibitor of the replication of several enteroviruses, including coxsackievirus and poliovirus. We show that TP219 binds directly glutathione (GSH), thereby rapidly depleting intracellular GSH levels and that this interferes with virus morphogenesis without affecting viral RNA replication. The inhibitory effect on assembly was shown not to depend on an altered reducing environment. Using TP219, we show that GSH is an essential stabilizing cofactor during the transition of protomeric particles into pentameric particles. Sequential passaging of coxsackievirus B3 in the presence of low GSH-levels selected for GSH-independent mutants that harbored a surface-exposed methionine in VP1 at the interface between two protomers. In line with this observation, enteroviruses that already contained this surface-exposed methionine, such as EV71, did not rely on GSH for virus morphogenesis. Biochemical and microscopical analysis provided strong evidence for a direct interaction between GSH and wildtype VP1 and a role for this interaction in localizing assembly intermediates to replication sites. Consistently, the interaction between GSH and mutant VP1 was abolished resulting in a relocalization of the assembly intermediates to replication sites independent from GSH. This study thus reveals GSH as a novel stabilizing host factor essential for the production of infectious enterovirus progeny and provides new insights into the poorly understood process of morphogenesis.\",\n \"corpus_id\": 5849001,\n \"score\": 0\n },\n {\n \"doc_id\": \"25078694\",\n \"title\": \"Dynamic and nucleolin-dependent localization of human cytomegalovirus UL84 to the periphery of viral replication compartments and nucleoli.\",\n \"abstract\": \"Protein-protein and protein-nucleic acid interactions within subcellular compartments are required for viral genome replication. To understand the localization of the human cytomegalovirus viral replication factor UL84 relative to other proteins involved in viral DNA synthesis and to replicating viral DNA in infected cells, we created a recombinant virus expressing a FLAG-tagged version of UL84 (UL84FLAG) and used this virus in immunofluorescence assays. UL84FLAG localization differed at early and late times of infection, transitioning from diffuse distribution throughout the nucleus to exclusion from the interior of replication compartments, with some concentration at the periphery of replication compartments with newly labeled DNA and the viral DNA polymerase subunit UL44. Early in infection, UL84FLAG colocalized with the viral single-stranded DNA binding protein UL57, but colocalization became less prominent as infection progressed. A portion of UL84FLAG also colocalized with the host nucleolar protein nucleolin at the peripheries of both replication compartments and nucleoli. Small interfering RNA (siRNA)-mediated knockdown of nucleolin resulted in a dramatic elimination of UL84FLAG from replication compartments and other parts of the nucleus and its accumulation in the cytoplasm. Reciprocal coimmunoprecipitation of viral proteins from infected cell lysates revealed association of UL84, UL44, and nucleolin. These results indicate that UL84 localization during infection is dynamic, which is likely relevant to its functions, and suggest that its nuclear and subnuclear localization is highly dependent on direct or indirect interactions with nucleolin. Importance: The protein-protein interactions among viral and cellular proteins required for replication of the human cytomegalovirus (HCMV) DNA genome are poorly understood. We sought to understand how an enigmatic HCMV protein critical for virus replication, UL84, localizes relative to other viral and cellular proteins required for HCMV genome replication and replicating viral DNA. We found that UL84 localizes with viral proteins, viral DNA, and the cellular nucleolar protein nucleolin in the subnuclear replication compartments in which viral DNA replication occurs. Unexpectedly, we also found localization of UL84 with nucleolin in nucleoli and showed that the presence of nucleolin is involved in localization of UL84 to the nucleus. These results add to previous work showing the importance of nucleolin in replication compartment architecture and viral DNA synthesis and are relevant to understanding UL84 function.\",\n \"corpus_id\": 44478320,\n \"score\": 0\n },\n {\n \"doc_id\": \"25428366\",\n \"title\": \"Sequential packaging of RNA genomic segments during the assembly of Bluetongue virus.\",\n \"abstract\": \"Bluetongue virus (BTV), a member of the Orbivirus genus within the Reoviridae family, has a genome of 10 double-stranded RNA segments, with three distinct size classes. Although the packaging of the viral genome is evidently highly specific such that every virus particle contains a set of 10 RNA segments, the order and mechanism of packaging are not understood. In this study we have combined the use of a cell-free in vitro assembly system with a novel RNA-RNA interaction assay to investigate the mechanism of single-stranded (ss) RNAs packaging during nascent capsid assembly. Exclusion of single or multiple ssRNA segments in the packaging reaction or their addition in different order significantly altered the outcome and suggested a particular role for the smallest segment, S10. Our data suggests that genome packaging probably initiates with the smallest segment which triggers RNA-RNA interaction with other smaller segments forming a complex network. Subsequently, the medium to larger size ssRNAs are recruited until the complete genome is packaging into the capsid. The untranslated regions of the smallest RNA segment, S10, is critical for the instigation of this process. We suggest that the selective packaging observed in BTV may also apply to other members of the Reoviridae family.\",\n \"corpus_id\": 10647694,\n \"score\": 0\n },\n {\n \"doc_id\": \"25635339\",\n \"title\": \"Electron microscopic analysis of rotavirus assembly-replication intermediates.\",\n \"abstract\": \"Rotaviruses (RVs) replicate their segmented, double-stranded RNA genomes in tandem with early virion assembly. In this study, we sought to gain insight into the ultrastructure of RV assembly-replication intermediates (RIs) using transmission electron microscopy (EM). Specifically, we examined a replicase-competent, subcellular fraction that contains all known RV RIs. Three never-before-seen complexes were visualized in this fraction. Using in vitro reconstitution, we showed that ~15-nm doughnut-shaped proteins in strings were nonstructural protein 2 (NSP2) bound to viral RNA transcripts. Moreover, using immunoaffinity-capture EM, we revealed that ~20-nm pebble-shaped complexes contain the viral RNA polymerase (VP1) and RNA capping enzyme (VP3). Finally, using a gel purification method, we demonstrated that ~30-70-nm electron-dense, particle-shaped complexes represent replicase-competent core RIs, containing VP1, VP3, and NSP2 as well as capsid proteins VP2 and VP6. The results of this study raise new questions about the interactions among viral proteins and RNA during the concerted assembly-replicase process.\",\n \"corpus_id\": 9140979,\n \"score\": 0\n },\n {\n \"doc_id\": \"25717105\",\n \"title\": \"Gammaherpesvirus Tegument Protein ORF33 Is Associated With Intranuclear Capsids at an Early Stage of the Tegumentation Process.\",\n \"abstract\": \"UNLABELLED: Herpesvirus nascent capsids, after assembly in the nucleus, must acquire a variety of tegument proteins during maturation. However, little is known about the identity of the tegument proteins that are associated with capsids in the nucleus or the molecular mechanisms involved in the nuclear egress of capsids into the cytoplasm, especially for the two human gammaherpesviruses Epstein-Barr virus (EBV) and Kaposi's sarcoma-associated herpesvirus (KSHV), due to a lack of efficient lytic replication systems. Murine gammaherpesvirus 68 (MHV-68) is genetically related to human gammaherpesviruses and serves as an excellent model to study the de novo lytic replication of gammaherpesviruses. We have previously shown that open reading frame 33 (ORF33) of MHV-68 is a tegument protein of mature virions and is essential for virion assembly and egress. However, it remains unclear how ORF33 is incorporated into virions. In this study, we first show that the endogenous ORF33 protein colocalizes with capsid proteins at discrete areas in the nucleus during viral infection. Cosedimentation analysis as well as an immunoprecipitation assay demonstrated that ORF33 is associated with both nuclear and cytoplasmic capsids. An immunogold labeling experiment using an anti-ORF33 monoclonal antibody revealed that ORF33-rich areas in the nucleus are surrounded by immature capsids. Moreover, ORF33 is associated with nucleocapsids prior to primary envelopment as well as with mature virions in the cytoplasm. Finally, we show that ORF33 interacts with two capsid proteins, suggesting that nucleocapsids may interact with ORF33 in a direct manner. In summary, we identified ORF33 to be a tegument protein that is associated with intranuclear capsids prior to primary envelopment, likely through interacting with capsid proteins in a direct manner. IMPORTANCE: Morphogenesis is an essential step in virus propagation that leads to the generation of progeny virions. For herpesviruses, this is a complicated process that starts in the nucleus. Although the process of capsid assembly and genome packaging is relatively well understood, how capsids acquire tegument (the layer between the capsid and the envelope in a herpesvirus virion) and whether the initial tegumentation process takes place in the nucleus remain unclear. We previously showed that ORF33 of MHV-68 is a tegument protein and functions in both the nuclear egress of capsids and final virion maturation in the cytoplasm. In the present study, we show that ORF33 is associated with intranuclear capsids prior to primary envelopment and identify novel interactions between ORF33 and two capsid proteins. Our work provides new insights into the association between tegument proteins and nucleocapsids at an early stage of the virion maturation process for herpesviruses.\",\n \"corpus_id\": 46101752,\n \"score\": 0\n },\n {\n \"doc_id\": \"25863879\",\n \"title\": \"The vaccinia virus E6 protein influences virion protein localization during virus assembly.\",\n \"abstract\": \"Vaccinia virus mutants in which expression of the virion core protein gene E6R is repressed are defective in virion morphogenesis. E6 deficient infections fail to properly package viroplasm into viral membranes, resulting in an accumulation of empty immature virions and large aggregates of viroplasm. We have used immunogold electron microscopy and immunofluorescence confocal microscopy to assess the intracellular localization of several virion structural proteins and enzymes during E6R mutant infections. We find that during E6R mutant infections virion membrane proteins and virion transcription enzymes maintain a normal localization within viral factories while several major core and lateral body proteins accumulate in aggregated virosomes. The results support a model in which vaccinia virions are assembled from at least three substructures, the membrane, the viroplasm and a \\\"pre-nucleocapsid\\\", and that the E6 protein is essential for maintaining proper localization of the seven-protein complex and the viroplasm during assembly.\",\n \"corpus_id\": 426850,\n \"score\": 0\n },\n {\n \"doc_id\": \"25986309\",\n \"title\": \"The Role of Packaging Sites in Efficient and Specific Virus Assembly.\",\n \"abstract\": \"During the life cycle of many single-stranded RNA viruses, including many human pathogens, a protein shell called the capsid spontaneously assembles around the viral genome. Understanding the mechanisms by which capsid proteins selectively assemble around the viral RNA amidst diverse host RNAs is a key question in virology. In one proposed mechanism, short sequences (packaging sites) within the genomic RNA promote rapid and efficient assembly through specific interactions with the capsid proteins. In this work, we develop a coarse-grained particle-based computational model for capsid proteins and RNA that represents protein-RNA interactions arising both from nonspecific electrostatics and from specific packaging site interactions. Using Brownian dynamics simulations, we explore how the efficiency and specificity of assembly depend on solution conditions (which control protein-protein and nonspecific protein-RNA interactions) and the strength and number of packaging sites. We identify distinct regions in parameter space in which packaging sites lead to highly specific assembly via different mechanisms and others in which packaging sites lead to kinetic traps. We relate these computational predictions to in vitro assays for specificity in which cognate viral RNAs compete against non-cognate RNAs for assembly by capsid proteins.\",\n \"corpus_id\": 3591269,\n \"score\": 0\n },\n {\n \"doc_id\": \"26051211\",\n \"title\": \"An alphavirus temperature-sensitive capsid mutant reveals stages of nucleocapsid assembly.\",\n \"abstract\": \"Alphaviruses have a nucleocapsid core composed of the RNA genome surrounded by an icosahedral lattice of capsid protein. An insertion after position 186 in the capsid protein produced a strongly temperature-sensitive growth phenotype. Even when the structural proteins were synthesized at the permissive temperature (28°C), subsequent incubation of the cells at the non-permissive temperature (37°C) dramatically decreased mutant capsid protein stability and particle assembly. Electron microscopy confirmed the presence of cytoplasmic nucleocapsids in mutant-infected cells cultured at the permissive temperature, but these nucleocapsids were not stable to sucrose gradient separation. In contrast, nucleocapsids isolated from mutant virus particles had similar stability to that of wildtype virus. Our data support a model in which cytoplasmic nucleocapsids go through a maturation step during packaging into virus particles. The insertion site lies in the interface between capsid proteins in the assembled nucleocapsid, suggesting the region where such a stabilizing transition occurs.\",\n \"corpus_id\": 20534693,\n \"score\": 0\n },\n {\n \"doc_id\": \"26178992\",\n \"title\": \"RNA and Nucleocapsid Are Dispensable for Mature HIV-1 Capsid Assembly.\",\n \"abstract\": \"UNLABELLED: Human immunodeficiency virus type 1 (HIV-1) is released from infected cells in an immature, noninfectious form in which the structural polyprotein Gag is arranged in a hexameric lattice, forming an incomplete spherical shell. Maturation to the infectious form is mediated by the viral protease, which cleaves Gag at five sites, releasing the CA (capsid) protein, which forms a conical capsid encasing the condensed RNA genome. The pathway of this structural rearrangement is currently not understood, and it is unclear how cone assembly is initiated. RNA represents an integral structural component of retroviruses, and the viral nucleoprotein core has previously been proposed to nucleate mature capsid assembly. We addressed this hypothesis by replacing the RNA-binding NC (nucleocapsid) domain of HIV-1 Gag and the adjacent spacer peptide 2 (SP2) by a leucine zipper (LZ) protein-protein interaction domain [Gag(LZ)] in the viral context. We found that Gag(LZ)-carrying virus [HIV(LZ)] was efficiently released and viral polyproteins were proteolytically processed, though with reduced efficiency. Cryo-electron tomography revealed that the particles lacked a condensed nucleoprotein and contained an increased proportion of aberrant core morphologies caused either by the absence of RNA or by altered Gag processing. Nevertheless, a significant proportion of HIV(LZ) particles contained mature capsids with the wild-type morphology. These results clearly demonstrate that the nucleoprotein complex is dispensable as a nucleator for mature HIV-1 capsid assembly in the viral context. IMPORTANCE: Formation of a closed conical capsid encasing the viral RNA genome is essential for HIV-1 infectivity. It is currently unclear what viral components initiate and regulate the formation of the capsid during virus morphogenesis, but it has been proposed that the ribonucleoprotein complex plays a role. To test this, we prepared virus-like particles lacking the viral nucleocapsid protein and RNA and analyzed their three-dimensional structure by cryo-electron tomography. While most virions displayed an abnormal morphology under these conditions, some particles showed a normal mature morphology with closed conical capsids. These data demonstrate that the presence of RNA and the nucleocapsid protein is not required for the formation of a mature, cone-shaped HIV-1 capsid.\",\n \"corpus_id\": 34671999,\n \"score\": 0\n },\n {\n \"doc_id\": \"26552701\",\n \"title\": \"Assembly and Release of Hepatitis B Virus.\",\n \"abstract\": \"The hepatitis B virus (HBV) core protein is a dynamic and versatile protein that directs many viral processes. During capsid assembly, core protein allosteric changes ensure efficient formation of a stable capsid that assembles while packaging viral RNA-polymerase complex. Reverse transcription of the RNA genome as well as transport of the capsid to multiple cellular compartments are directed by dynamic phosphorylation and structural changes of core protein. Subsequently, interactions of the capsid with the surface proteins and/or host proteins trigger envelopment and release of the viral capsids or the transport to the nucleus. Held together by many weak protein-protein interactions, the viral capsid is an extraordinary metastable machine that is stable enough to persist in the cellular and extracellular environment but dissociates to allow release of the viral genome at the right time during infection.\",\n \"corpus_id\": 41325114,\n \"score\": 0\n },\n {\n \"doc_id\": \"26657148\",\n \"title\": \"Mechanisms of assembly and genome packaging in an RNA virus revealed by high-resolution cryo-EM.\",\n \"abstract\": \"Cowpea mosaic virus is a plant-infecting member of the Picornavirales and is of major interest in the development of biotechnology applications. Despite the availability of >100 crystal structures of Picornavirales capsids, relatively little is known about the mechanisms of capsid assembly and genome encapsidation. Here we have determined cryo-electron microscopy reconstructions for the wild-type virus and an empty virus-like particle, to 3.4 Å and 3.0 Å resolution, respectively, and built de novo atomic models of their capsids. These new structures reveal the C-terminal region of the small coat protein subunit, which is essential for virus assembly and which was missing from previously determined crystal structures, as well as residues that bind to the viral genome. These observations allow us to develop a new model for genome encapsidation and capsid assembly.\",\n \"corpus_id\": 17500124,\n \"score\": 0\n },\n {\n \"doc_id\": \"26912613\",\n \"title\": \"Nucleic Acid Binding by Mason-Pfizer Monkey Virus CA Promotes Virus Assembly and Genome Packaging.\",\n \"abstract\": \"UNLABELLED: The Gag polyprotein of retroviruses drives immature virus assembly by forming hexameric protein lattices. The assembly is primarily mediated by protein-protein interactions between capsid (CA) domains and by interactions between nucleocapsid (NC) domains and RNA. Specific interactions between NC and the viral RNA are required for genome packaging. Previously reported cryoelectron microscopy analysis of immature Mason-Pfizer monkey virus (M-PMV) particles suggested that a basic region (residues RKK) in CA may serve as an additional binding site for nucleic acids. Here, we have introduced mutations into the RKK region in both bacterial and proviral M-PMV vectors and have assessed their impact on M-PMV assembly, structure, RNA binding, budding/release, nuclear trafficking, and infectivity using in vitro and in vivo systems. Our data indicate that the RKK region binds and structures nucleic acid that serves to promote virus particle assembly in the cytoplasm. Moreover, the RKK region appears to be important for recruitment of viral genomic RNA into Gag particles, and this function could be linked to changes in nuclear trafficking. Together these observations suggest that in M-PMV, direct interactions between CA and nucleic acid play important functions in the late stages of the viral life cycle. IMPORTANCE: Assembly of retrovirus particles is driven by the Gag polyprotein, which can self-assemble to form virus particles and interact with RNA to recruit the viral genome into the particles. Generally, the capsid domains of Gag contribute to essential protein-protein interactions during assembly, while the nucleocapsid domain interacts with RNA. The interactions between the nucleocapsid domain and RNA are important both for identifying the genome and for self-assembly of Gag molecules. Here, we show that a region of basic residues in the capsid protein of the betaretrovirus Mason-Pfizer monkey virus (M-PMV) contributes to interaction of Gag with nucleic acid. This interaction appears to provide a critical scaffolding function that promotes assembly of virus particles in the cytoplasm. It is also crucial for packaging the viral genome and thus for infectivity. These data indicate that, surprisingly, interactions between the capsid domain and RNA play an important role in the assembly of M-PMV.\",\n \"corpus_id\": 4766834,\n \"score\": 0\n },\n {\n \"doc_id\": \"27226558\",\n \"title\": \"Cellular Casein Kinase 2 and Protein Phosphatase 2A Modulate Replication Site Assembly of Bluetongue Virus.\",\n \"abstract\": \"A number of cytoplasmic replicating viruses produce cytoplasmic inclusion bodies or protein aggregates; however, a hallmark of viruses of the Reoviridae family is that they utilize these sites for purposes of replication and capsid assembly, functioning as viral assembly factories. Here we have used bluetongue virus (BTV) as a model system for this broad family of important viruses to understand the mechanisms regulating inclusion body assembly. Newly synthesized viral proteins interact with sequestered viral RNA molecules prior to capsid assembly and double-stranded RNA synthesis within viral inclusion bodies (VIBs). VIBs are predominantly comprised of a BTV-encoded non-structural protein 2 (NS2). Previous in vitro studies indicated that casein kinase 2 (CK2) mediated the phosphorylation of NS2, which regulated the propensity of NS2 to form larger aggregates. Using targeted pharmacological reagents, specific mutation in the viral genome by reverse genetics and confocal microscopy, here we demonstrate that CK2 activity is important for BTV replication. Furthermore, we show that a novel host cell factor, protein phosphatase 2A, is involved in NS2 dephosphorylation and that, together with CK2, it regulates VIB morphology and virus replication. Thus, these two host enzymes influence the dynamic nature of VIB assembly/disassembly, and these concerted activities may be relevant to the assembly and the release of these cores from VIBs.\",\n \"corpus_id\": 205358194,\n \"score\": 0\n },\n {\n \"doc_id\": \"27428992\",\n \"title\": \"Coordination of Genomic RNA Packaging with Viral Assembly in HIV-1.\",\n \"abstract\": \"The tremendous progress made in unraveling the complexities of human immunodeficiency virus (HIV) replication has resulted in a library of drugs to target key aspects of the replication cycle of the virus. Yet, despite this accumulated wealth of knowledge, we still have much to learn about certain viral processes. One of these is virus assembly, where the viral genome and proteins come together to form infectious progeny. Here we review this topic from the perspective of how the route to production of an infectious virion is orchestrated by the viral genome, and we compare and contrast aspects of the assembly mechanisms employed by HIV-1 with those of other RNA viruses.\",\n \"corpus_id\": 1530448,\n \"score\": 0\n },\n {\n \"doc_id\": \"27881644\",\n \"title\": \"Suppression of Adenovirus Replication by Cardiotonic Steroids.\",\n \"abstract\": \"The dependence of adenovirus on the host pre-RNA splicing machinery for expression of its complete genome potentially makes it vulnerable to modulators of RNA splicing, such as digoxin and digitoxin. Both drugs reduced the yields of four human adenoviruses (HAdV-A31, -B35, and -C5 and a species D conjunctivitis isolate) by at least 2 to 3 logs by affecting one or more steps needed for genome replication. Immediate early E1A protein levels are unaffected by the drugs, but synthesis of the delayed protein E4orf6 and the major late capsid protein hexon is compromised. Quantitative reverse transcription-PCR (qRT-PCR) analyses revealed that both drugs altered E1A RNA splicing (favoring the production of 13S over 12S RNA) early in infection and partially blocked the transition from 12S and 13S to 9S RNA at late stages of virus replication. Expression of multiple late viral protein mRNAs was lost in the presence of either drug, consistent with the observed block in viral DNA replication. The antiviral effect was dependent on the continued presence of the drug and was rapidly reversible. RIDK34, a derivative of convallotoxin, although having more potent antiviral activity, did not show an improved selectivity index. All three drugs reduced metabolic activity to some degree without evidence of cell death. By blocking adenovirus replication at one or more steps beyond the onset of E1A expression and prior to genome replication, digoxin and digitoxin show potential as antiviral agents for treatment of serious adenovirus infections. Furthermore, understanding the mechanism(s) by which digoxin and digitoxin inhibit adenovirus replication will guide the development of novel antiviral therapies. IMPORTANCE: Despite human adenoviruses being a common and, in some instances, life-threating pathogen in humans, there are few well-tolerated therapies. In this report, we demonstrate that two cardiotonic steroids already in use in humans, digoxin and digitoxin, are potent inhibitors of multiple adenovirus species. A synthetic derivative of the cardiotonic steroid convallotoxin was even more potent than digoxin and digitoxin when tested with HAdV-C5. These drugs alter the cascade of adenovirus gene expression, acting after initiation of early gene expression to block viral DNA replication and synthesis of viral structural proteins. These findings validate a novel approach to treating adenovirus infections through the modulation of host cell processes.\",\n \"corpus_id\": 24206090,\n \"score\": 0\n },\n {\n \"doc_id\": \"28082593\",\n \"title\": \"Assembly of a nucleus-like structure during viral replication in bacteria.\",\n \"abstract\": \"We observed the assembly of a nucleus-like structure in bacteria during viral infection. Using fluorescence microscopy and cryo-electron tomography, we showed that Pseudomonas chlororaphis phage 201φ2-1 assembled a compartment that separated viral DNA from the cytoplasm. The phage compartment was centered by a bipolar tubulin-based spindle, and it segregated phage and bacterial proteins according to function. Proteins involved in DNA replication and transcription localized inside the compartment, whereas proteins involved in translation and nucleotide synthesis localized outside. Later during infection, viral capsids assembled on the cytoplasmic membrane and moved to the surface of the compartment for DNA packaging. Ultimately, viral particles were released from the compartment and the cell lysed. These results demonstrate that phages have evolved a specialized structure to compartmentalize viral replication.\",\n \"corpus_id\": 206654602,\n \"score\": 0\n },\n {\n \"doc_id\": \"29444942\",\n \"title\": \"A Functional Link between RNA Replication and Virion Assembly in the Potyvirus Plum Pox Virus.\",\n \"abstract\": \"Accurate assembly of viral particles in the potyvirus Plum pox virus (PPV) has been shown to depend on the contribution of the multifunctional viral protein HCPro. In this study, we show that other viral factors, in addition to the capsid protein (CP) and HCPro, are necessary for the formation of stable PPV virions. The CP produced in Nicotiana benthamiana leaves from a subviral RNA termed LONG, which expresses a truncated polyprotein that lacks P1 and HCPro, together with HCPro supplied in trans, was assembled into virus-like particles and remained stable after in vitro incubation. In contrast, deletions in multiple regions of the LONG coding sequence prevented the CP stabilization mediated by HCPro. In particular, we demonstrated that the first 178 amino acids of P3, but not a specific nucleotide sequence coding for them, are required for CP stability and proper assembly of PPV particles. Using a sequential coagroinfiltration assay, we observed that the subviral LONG RNA replicates and locally spreads in N. benthamiana leaves expressing an RNA silencing suppressor. The analysis of the effect of both point and deletion mutations affecting RNA replication in LONG and full-length PPV demonstrated that this process is essential for the assembly of stable viral particles. Interestingly, in spite of this requirement, the CP produced by a nonreplicating viral RNA can be stably assembled into virions as long as it is coexpressed with a replication-proficient RNA. Altogether, these results highlight the importance of coupling encapsidation to other viral processes to secure a successful infection. IMPORTANCE Viruses of the family Potyviridae are among the most dangerous threats for basically every important crop, and such socioeconomical relevance has made them a subject of many research studies. In spite of this, very little is currently known about proteins and processes controlling viral genome encapsidation by the coat protein. In the case of Plum pox virus (genus Potyvirus), for instance, we have previously shown that the multitasking viral factor HCPro plays a role in the production of stable virions. Here, by using this potyvirus as a model, we move further to show that additional factors are also necessary for the efficient production of potyviral particles. More importantly, a comprehensive screening for such factors led us to the identification of a functional link between virus replication and packaging, unraveling a previously unknown connection of these two key events of the potyviral infection cycle.\",\n \"corpus_id\": 4826578,\n \"score\": 0\n },\n {\n \"doc_id\": \"29558394\",\n \"title\": \"Alphavirus Nucleocapsid Packaging and Assembly.\",\n \"abstract\": \"Alphavirus nucleocapsids are assembled in the cytoplasm of infected cells from 240 copies of the capsid protein and the approximately 11 kb positive strand genomic RNA. However, the challenge of how the capsid specifically selects its RNA package and assembles around it has remained an elusive one to solve. In this review, we will summarize what is known about the alphavirus capsid protein, the packaging signal, and their roles in the mechanism of packaging and assembly. We will review the discovery of the packaging signal and how there is as much evidence for, as well as against, its requirement to specify packaging of the genomic RNA. Finally, we will compare this model with those of other viral systems including particular reference to a relatively new idea of RNA packaging based on the presence of multiple minimal packaging signals throughout the genome known as the two stage mechanism. This review will provide a basis for further investigating the fundamental ways of how RNA viruses are able to select their own cargo from the relative chaos that is the cytoplasm.\",\n \"corpus_id\": 3986519,\n \"score\": 0\n }\n]","isConversational":false}}},{"rowIdx":73,"cells":{"query":{"kind":"string","value":"{\n \"doc_id\": \"22889878\",\n \"title\": \"Crystal structure of Plasmodium falciparum thioredoxin reductase, a validated drug target.\",\n \"abstract\": \"Plasmodium falciparum is the vector of the most prevalent and deadly form of malaria, and, among the Plasmodium species, it is the one with the highest rate of drug resistance. At the basis of a rational drug design project there is the selection and characterization of suitable target(s). Thioredoxin reductase, the first protection against reactive oxygen species in the erythrocytic phase of the parasite, is essential for its survival. Hence it represents a good target for the design of new anti-malarial active compounds. In this paper we present the first crystal structure of recombinant P. falciparum thioredoxin reductase (PfTrxR) at 2.9Å and discuss its differences with respect to the human orthologue. The most important one resides in the dimer interface, which offers a good binding site for selective non competitive inhibitors. The striking conservation of this feature among the Plasmodium parasites, but not among other Apicomplexa parasites neither in mammals, boosts its exploitability.\",\n \"corpus_id\": 26123546\n}"},"candidates":{"kind":"list like","value":[{"doc_id":"18980703","title":"Differential inhibition of high and low Mr thioredoxin reductases of parasites by organotelluriums supports the concept that low Mr thioredoxin reductases are good drug targets.","abstract":"Thioredoxin reductase (TrxR), a NADPH-dependent disulfide oxidoreductase, is vital in numerous cellular processes including defence against reactive oxygen species, cell proliferation and signal transduction. TrxRs occur in 2 forms, a high Mr enzyme characterized by those of mammals, the malaria parasite Plasmodium falciparum and some worms, and a low Mr form is present in bacteria, fungi, plants and some protozoan parasites. Our hypothesis is that the differences between the forms can be exploited in the development of selective inhibitors. In this study, cyclodextrin- and sulfonic acid-derived organotelluriums known to inhibit mammalian TrxR were investigated for their relative efficacy against P. falciparum TrxR (PfTrxR), a high Mr enzyme, and Trichomonas vaginalis TrxR (TvTrxR), a low Mr form of TrxR. The results suggest that selective inhibition of low Mr TrxRs is a feasible goal.","corpus_id":9065841,"score":2},{"doc_id":"19360125","title":"Identification of proteins targeted by the thioredoxin superfamily in Plasmodium falciparum.","abstract":"The malarial parasite Plasmodium falciparum possesses a functional thioredoxin and glutathione system comprising the dithiol-containing redox proteins thioredoxin (Trx) and glutaredoxin (Grx), as well as plasmoredoxin (Plrx), which is exclusively found in Plasmodium species. All three proteins belong to the thioredoxin superfamily and share a conserved Cys-X-X-Cys motif at the active site. Only a few of their target proteins, which are likely to be involved in redox reactions, are currently known. The aim of the present study was to extend our knowledge of the Trx-, Grx-, and Plrx-interactome in Plasmodium. Based on the reaction mechanism, we generated active site mutants of Trx and Grx lacking the resolving cysteine residue. These mutants were bound to affinity columns to trap target proteins from P. falciparum cell extracts after formation of intermolecular disulfide bonds. Covalently linked proteins were eluted with dithiothreitol and analyzed by mass spectrometry. For Trx and Grx, we were able to isolate 17 putatively redox-regulated proteins each. Furthermore, the approach was successfully established for Plrx, leading to the identification of 21 potential target proteins. In addition to confirming known interaction partners, we captured potential target proteins involved in various processes including protein biosynthesis, energy metabolism, and signal transduction. The identification of three enzymes involved in S-adenosylmethionine (SAM) metabolism furthermore suggests that redox control is required to balance the metabolic fluxes of SAM between methyl-group transfer reactions and polyamine synthesis. To substantiate our data, the binding of the redoxins to S-adenosyl-L-homocysteine hydrolase and ornithine aminotransferase (OAT) were verified using BIAcore surface plasmon resonance. In enzymatic assays, Trx was furthermore shown to enhance the activity of OAT. Our approach led to the discovery of several putatively redox-regulated proteins, thereby contributing to our understanding of the redox interactome in malarial parasites.","corpus_id":12087168,"score":2},{"doc_id":"19724080","title":"Structural model of the Plasmodium falciparum thioredoxin reductase:a novel target for antimalarial drugs.","abstract":"BACKGROUND: Malaria, a scourge of mankind, imposes a huge socioeconomic burden in tropical countries. Emergence of multi-drug resistant malarial parasites impels us to explore novel drug targets. Thioredoxin reductase is a promising antimalarial drug target. METHODS: The Thioredoxin reductase enzyme of Plasmodium falciparum was characterized in silico and protein disorder was predicted using available online tools. Since the crystal structure of Thioredoxin reductase of P. falciparum is not yet available, its three-dimensional structure was constructed by homology modeling using the high-resolution Thioredoxin reductase type 2 of mouse as a template. Obtained model was further refined by Molecular Dynamics (MD). RESULTS: The model was stable during the simulation with the equilibrium root mean square deviation (RMSD) value of 1.2 A. Stereochemical evaluation revealed that 99.1% residues of the constructed model lie in the most favoured and allowed regions, thus, indicating a good quality model. CONCLUSION: Results of this study will provide an insight into the structure of the Thioredoxin reductase of malarial parasite and aid in rational drug designing.","corpus_id":12230573,"score":2},{"doc_id":"20335080","title":"Development of binding assays to screen ligands for Plasmodium falciparum thioredoxin and glutathione reductases by ultrafiltration and liquid chromatography/mass spectrometry.","abstract":"To identify potential lead compounds for malaria drug discovery, ultrafiltration and liquid chromatography and mass spectrometry (UF and LC/MS) based binding assays were developed for the first time for Plasmodium falciparum thioredoxin (PfTrxR) and glutathione (PfGR) reductases. In the binding assays, curcuminoids (bis-demethoxycurcumin 1, demethoxycurcumin 2, and curcumin 3) were used to study the binding affinity for PfTrxR and PfGR enzymes. The optimum binding was observed when the curcumimoids mixture (1 microM) was incubated with 1 microM PfTrxR and 0.5 microM PfGR enzymes separately for 60 min at 25 degrees C. The peak areas of the ligands in the chromatogram corresponding to incubation with active PfTrxR and PfGR enzymes increased by 1.6- and 2.0-fold respectively compared to the chromatogram of test compounds incubated with denatured enzymes. Further, binding assay experiments were carried out for compound 2 under non-competitive and competitive incubation conditions with 1 microM PfTrxR and 0.5 microM PfGR enzymes, separately. The binding affinity of compound 2 was higher for both the enzymes under non-competitive incubation conditions. To validate the binding assay developed, we have tested bis-2,4-dinitrophenyl sulfide (4) which is reported as an inhibitor of PfTrxR and PfGR enzymes. Compound 4 showed greater binding affinity for both enzymes under competitive incubation conditions. The relative peak area of compound 4 increased by 3.2- and 6-fold when incubated with active PfTrxR (1 microM) and PfGR (0.5 microM) enzymes respectively compared to the peak areas of the compound in control experiments. The current method developed has a potential for automated high-throughput screening to rapidly determine the binding affinity of ligands for these enzymes.","corpus_id":2886568,"score":2},{"doc_id":"21203490","title":"Compartmentation of redox metabolism in malaria parasites.","abstract":"Malaria, caused by the apicomplexan parasite Plasmodium, still represents a major threat to human health and welfare and leads to about one million human deaths annually. Plasmodium is a rapidly multiplying unicellular organism undergoing a complex developmental cycle in man and mosquito - a life style that requires rapid adaptation to various environments. In order to deal with high fluxes of reactive oxygen species and maintain redox regulatory processes and pathogenicity, Plasmodium depends upon an adequate redox balance. By systematically studying the subcellular localization of the major antioxidant and redox regulatory proteins, we obtained the first complete map of redox compartmentation in Plasmodium falciparum. We demonstrate the targeting of two plasmodial peroxiredoxins and a putative glyoxalase system to the apicoplast, a non-photosynthetic plastid. We furthermore obtained a complete picture of the compartmentation of thioredoxin- and glutaredoxin-like proteins. Notably, for the two major antioxidant redox-enzymes--glutathione reductase and thioredoxin reductase--Plasmodium makes use of alternative-translation-initiation (ATI) to achieve differential targeting. Dual localization of proteins effected by ATI is likely to occur also in other Apicomplexa and might open new avenues for therapeutic intervention.","corpus_id":8837078,"score":2},{"doc_id":"21353756","title":"Screening of natural compounds for ligands to PfTrxR by ultrafiltration and LC-MS based binding assay.","abstract":"In our study, we have screened 133 structurally diverse natural compounds from the MEGx® collection of AnalytiCon Discovery and three synthetic hispolone analogs for binding affinity to Plasmodium falciparum thioredoxin reductase (PfTrxR) using an ultrafiltration (UF) and liquid chromatography (LC/MS) based ligand-binding assay newly developed in our laboratory. PfTrxR catalyzes the reduction of thioredoxin (PfTrx) protein. In reduced form, PfTrx is essentially involved in the antioxidative defense and redox regulation of P. falciparum. Nine compounds (yohimbine (1), catharanthine (2), vobasine (3), gnetifolin E (4), quinidine N-oxide (5), 11-hydroxycoronaridine (6), hispolone (7), hispolone methyl ether (8), and hernagine (9)) displayed binding affinity for PfTrxR at 1μM. The ranking order of compound's binding affinities for PfTrxR is 7>6>2>4>5>8>1>9>3. On the other hand, compounds 6, 7, 2 and 8 demonstrated specific binding to the active site of PfTrxR, when ligands were tested in an equimolar mixture of 1 μM.","corpus_id":11210527,"score":2},{"doc_id":"21567357","title":"Identification of oleamide in Guatteria recurvisepala by LC/MS-based Plasmodium falciparum thioredoxin reductase ligand binding method.","abstract":"Our current research on applications of mass spectrometry to natural product drug discovery against malaria aims to screen plant extracts for new ligands to Plasmodium falciparum thioredoxin reductase (PfTrxR) followed by their identification and structure elucidation. PfTrxR is involved in the antioxidant defense and redox regulation of the parasite and is validated as a promising target for therapeutic intervention against malaria. In the present study, detannified methanol extracts from Guatteria recurvisepala, Licania kallunkiae, and Topobea watsonii were screened for ligands to PfTrxR using ultrafiltration and liquid chromatography/mass spectrometry-based binding experiments. The PfTrxR ligand identified in the extract of Guatteria recurvisepala displayed a relative binding affinity of 3.5-fold when incubated with 1 μM PfTrxR. The ligand corresponding to the protonated molecule m/z 282.2792 [M+ H]+ was eluted at a retention time of 17.95 min in a 20-min gradient of 95% B consisting of (A) 0.1%formic acid in 95% H₂O-5% ACN, and (B) 0.1% formic acid in 95% ACN-5% H₂O in an LC-QTOF-MS.Tandem MS of the protonated molecule m/z 282.2792 [M + H]+, C₁₈H₃₆NO (DBE: 2; error: 1.13 ppm) resulted in two daughter ions m/z 265.2516[M + H-NH₃]+ (DBE: 3; error: 0.35 ppm) and m/z 247.2405 [M + H-NH₃-H₂O] +, (DBE: 4; error:2.26 ppm). The PfTrxR ligand was identified as oleamide and confirmed by comparison of the retention time, molecular formula, accurate mass,and double bond equivalence with the standard oleamide. This is the first report on the identification of oleamide as a PfTrxR ligand from Guatteria recurvisepala R. E. Fr. and the corresponding in vitro activity against P. falciparum strain K1 (IC₅₀ 4.29 μg/mL).","corpus_id":38294373,"score":2},{"doc_id":"21750537","title":"Crystal structure of the human thioredoxin reductase-thioredoxin complex.","abstract":"Thioredoxin reductase 1 (TrxR1) is a homodimeric flavoprotein crucially involved in the regulation of cellular redox homeostasis, growth, and differentiation. Its importance in various diseases makes TrxR1 a highly interesting drug target. Here we present the first crystal structures of human TrxR1 in complex with its substrate thioredoxin (Trx). The carboxy-terminal redox centre is found about 20 Å apart from the amino-terminal redox centre, with no major conformational changes in TrxR or Trx. Thus, our structure confirms that the enzyme uses a flexible C-terminal arm for electron transport to its substrates, which is stabilized by a guiding bar for controlled transfer. This notion is supported by mutational analyses. Furthermore, essential residues of the interface region were characterized both structurally and functionally. The structure provides templates for future drug design, and contributes to our understanding of redox regulatory processes in mammals.","corpus_id":35983486,"score":2},{"doc_id":"22177949","title":"Investigation of a potential mechanism for the inhibition of SmTGR by Auranofin and its implications for Plasmodium falciparum inhibition.","abstract":"Schistosoma mansoni and Plasmodium falciparum are pathogen parasites that spend part of their lives in the blood stream of the human host and are therefore heavily exposed to fluxes of toxic reactive oxygen species (ROS). SmTGR, an essential enzyme of the S. mansoni ROS detoxification machinery, is known to be inhibited by Auranofin although the inhibition mechanism has not been completely clarified. Auranofin also kills P. falciparum, even if its molecular targets are unknown. Here, we used computational and docking techniques to investigate the molecular mechanism of interaction between SmTGR and Auranofin. Furthermore, we took advantage of the homology relationship and of docking studies to assess if PfTR, the SmTGR malaria parasite homologue, can be a putative target for Auranofin. Our findings support a recently hypothesized molecular mechanism of inhibition for SmTGR and suggest that PfTR is indeed a possible and attractive drug target in P. falciparum.","corpus_id":26487877,"score":2},{"doc_id":"22612231","title":"Discovery and biochemical characterization of Plasmodium thioredoxin reductase inhibitors from an antimalarial set.","abstract":"Plasmodium falciparum is the most prevalent and deadly species of the human malaria parasites, and thioredoxin reductase (TrxR) is an enzyme involved in the redox response to oxidative stress. Essential for P. falciparum survival, the enzyme has been highlighted as a promising target for novel antimalarial drugs. Here we report the discovery and characterization of seven molecules from an antimalarial set of 13533 compounds through single-target TrxR biochemical screens. We have produced high-purity, full-length, recombinant native enzyme from four Plasmodium species, and thioredoxin substrates from P. falciparum and Rattus norvegicus. The enzymes were screened using a unique, high-throughput, in vitro native substrate assay, and we have observed selectivity between the Plasmodium species and the mammalian form of the enzyme. This has indicated differences in their biomolecular profiles and has provided valuable insights into the biochemical mechanisms of action of compounds with proven antimalarial activity.","corpus_id":9981259,"score":2},{"doc_id":"22847705","title":"Development of liquid chromatography/mass spectrometry based screening assay for PfTrxR inhibitors using relative quantitation of intact thioredoxin.","abstract":"RATIONALE: Plasmodium falciparum (Pf) thioredoxin reductase (TrxR) catalyzes the reduction of thioredoxin disulfide (Trx-S(2)) to thioredoxin dithiol (Trx-(SH)(2)) that is essential for antioxidant defense mechanism and DNA synthesis in the parasite and is a validated drug target for new antimalarial agents. METHODS: In this study, we have developed a liquid chromatography/mass spectrometry (LC/MS)-based functional assay to identify inhibitors of PfTrxR by quantifying the product formed (Trx-(SH)(2)) in the enzymatic reaction. Relative quantitation of the reaction product (intact Trx-(SH)(2)) was carried out using an Agilent 6520 QTOF mass spectrometer equipped with a positive mode electrospray ionization (ESI) source. RESULTS: The calibration curve prepared for Trx-(SH)(2) at concentrations ranging from 1.8 to 116.5 µg/mL was linear (R(2) >0.998). The limit of detection (LOD) and limit of quantification (LOQ) of Trx-(SH)(2) were at 0.45 and 1.8 µg/mL respectively. To validate the developed functional assay we have screened reference compounds 1, 2 and 3 for their PfTrxR inhibitory activity and ten natural compounds (at 10 μM) which were earlier identified as ligands of PfTrxR by a UF-LC/MS based binding assay. CONCLUSIONS: The developed LC/MS-based functional assay for identification of inhibitors of PfTrxR is a sensitive and reliable method that is also amendable for high-throughput format. This is the first representation of a relative quantitation of intact Trx-(SH)(2) using LC/MS.","corpus_id":25713067,"score":2},{"doc_id":"22939033","title":"Thioredoxin and glutathione systems in Plasmodium falciparum.","abstract":"Despite a 50% decrease in malaria infections between 2000 and 2010, malaria is still one of the three leading infectious diseases with an estimated 216 million cases worldwide in 2010. More than 90% of all malaria infections were caused by Plasmodium falciparum, a unicellular eukaryotic parasite that faces oxidative stress challenges while developing in Anopheles mosquitoes and humans. Reactive oxygen and nitrogen species threatening the parasite are either endogenously produced by heme derived from hemoglobin degradation or they are from exogenous sources such as the host immune defense. In order to maintain the intracellular redox balance, P. falciparum employs a complex thioredoxin and glutathione system based on the thioredoxin reductase/thioredoxin and glutathione reductase/glutathione couples. P. falciparum thioredoxin reductase reduces thioredoxin and a range of low molecular weight compounds, while glutathione reductase is highly specific for its substrate glutathione disulfide. Since Plasmodium spp. lack catalase and a classical glutathione peroxidase, their redox balance depends on a complex set of five peroxiredoxins differentially located in the cytosol, apicoplast, mitochondria, and nucleus with partially overlapping substrate preferences. Moreover, P. falciparum employs a set of members belonging to the thioredoxin superfamily such as three thioredoxins, two thioredoxin-like proteins, a dithiol and three monocysteine glutaredoxins, and a redox-active plasmoredoxin with largely redundant functions. This review aims at summarizing our current knowledge on the functional redox networks of the malaria parasite P. falciparum.","corpus_id":8493014,"score":2},{"doc_id":"23845423","title":"Crystal structure of the Plasmodium falciparum thioredoxin reductase-thioredoxin complex.","abstract":"Over the last decades, malaria parasites have been rapidly developing resistance against antimalarial drugs, which underlines the need for novel drug targets. Thioredoxin reductase (TrxR) is crucially involved in redox homeostasis and essential for Plasmodium falciparum. Here, we report the first crystal structure of P. falciparum TrxR bound to its substrate thioredoxin 1. Upon complex formation, the flexible C-terminal arm and an insertion loop of PfTrxR are rearranged, suggesting that the C-terminal arm changes its conformation during catalysis similar to human TrxR. Striking differences between P. falciparum and human TrxR are a Plasmodium-specific insertion and the conformation of the C-terminal arm, which lead to considerable differences in thioredoxin binding and disulfide reduction. Moreover, we functionally analyzed amino acid residues involved in substrate binding and in the architecture of the intersubunit cavity, which is a known binding site for disulfide reductase inhibitors. Cell biological experiments indicate that P. falciparum TrxR is indeed targeted in the parasite by specific inhibitors with antimalarial activity. Differences between P. falciparum and human TrxR and details on substrate reduction and inhibitor binding provide the first solid basis for structure-based drug development and lead optimization.","corpus_id":206212834,"score":2},{"doc_id":"24175748","title":"Targeting the redox metabolism of Plasmodium falciparum.","abstract":"Targeting the redox metabolism of Plasmodium falciparum to create a fatal overload of oxidative stress is a route to explore the discovery of new antimalarial drugs. There are three main possibilities to target the redox metabolism of P. falciparum at the erythrocytic stage: selective targeting and inhibition of a redox P. falciparum protein or enzyme; oxidant drugs targeting essential parasite components and heme by-products; and redox cycler drugs targeting the parasitized red blood cell. Oxidants and redox cycler agents, with or without specific targets, may disrupt the fragile parasitized erythrocyte redox-dependent architecture given that: redox equilibrium plays a vital role at the erythrocytic stage; P. falciparum possesses major NADPH-dependent redox systems, such as glutathione and thioredoxin ones; and the protein-NADPH-dependent phosphorylation-dephosphorylation process is involved in building new permeation pathways and channels for the nutrient-waste import-export traffic of the parasite.","corpus_id":19246212,"score":2},{"doc_id":"24443991","title":"Determination of antiplasmodial activity and binding affinity of curcumin and demethoxycurcumin towards PfTrxR.","abstract":"In our study, the inhibitory activity of curcuminoids towards Plasmodium falciparum thioredoxin reductase (PfTrxR) was determined using LC-MS-based functional assay and showed that only demethoxycurcumin (DMC) inhibited PfTrxR (IC50: 2 μM). In silico molecular modelling was used to ascertain and further confirm that the binding affinities of curcumin and DMC are towards the dimer interface of PfTrxR. The in vitro antiplasmodial activities of curcumin and DMC were evaluated and shown to be active against chloroquine (CQ)-sensitive (D6 clone) and moderately active against CQ-resistant (W2 clone) strains of Plasmodium falciparum while no cytotoxicity was observed against Vero cells.","corpus_id":205839668,"score":2},{"doc_id":"25198774","title":"PfalDB: an integrated drug target and chemical database for Plasmodium falciparum.","abstract":"Plasmodium falciparum is one of the deadliest protozoan parasite species among those that cause malaria. Uncontrolled use of antimalarial drugs has resulted in evolutionary selection pressure favoring high levels of resistance to antimalarials; currently P.falciparum shows resistance to all classes of antimalarials. Therefore it is essential to identify novel drug targets, and design selective anti-malarials which can overcome resistance. While many drug targets are freely available in various public domain resources, a single comprehensive source of data containing easily searchable and retrievable information is currently lacking. To facilitate the total integration and mining of data emerging from different drug consortia and also to prioritize drug targets for structure-based drug design, an open-access, inclusive comprehensive database for Plasmodium falciparum was established. Meta data of known/modeled structures along with binding site parameters of drug targets have been included in the database. Additionally, chemical compounds showing a positive inhibitory assay against Plasmodium falciparum or known drug targets have also been provided. The database is accessible at http://pfaldb.jnu.ac.in. The database provides diverse information regarding the structure, sequence, stage specific gene expression, pathway, action mechanism, essentiality and druggability for each drug target, and literature to assess the validation status of individual drug targets. It also includes information on individual anti-malarials with their activity and bioassay.","corpus_id":21959986,"score":2},{"doc_id":"26111176","title":"Plasmodium falciparum Thioredoxin Reductase (PfTrxR) and Its Role as a Target for New Antimalarial Discovery.","abstract":"The growing resistance to current antimalarial drugs is a major concern for global public health. The pressing need for new antimalarials has led to an increase in research focused on the Plasmodium parasites that cause human malaria. Thioredoxin reductase (TrxR), an enzyme needed to maintain redox equilibrium in Plasmodium species, is a promising target for new antimalarials. This review paper provides an overview of the structure and function of TrxR, discusses similarities and differences between the thioredoxin reductases (TrxRs) of different Plasmodium species and the human forms of the enzyme, gives an overview of modeling Plasmodium infections in animals, and suggests the role of Trx functions in antimalarial drug resistance. TrxR of Plasmodium falciparum is a central focus of this paper since it is the only Plasmodium TrxR that has been crystallized and P. falciparum is the species that causes most malaria cases. It is anticipated that the information summarized here will give insight and stimulate new directions in which research might be most beneficial.","corpus_id":8764389,"score":2},{"doc_id":"27043496","title":"Preliminary LC-MS Based Screening for Inhibitors of Plasmodium falciparum Thioredoxin Reductase (PfTrxR) among a Set of Antimalarials from the Malaria Box.","abstract":"Plasmodium falciparum thioredoxin reductase (PfTrxR) has been identified as a potential drug target to combat growing antimalarial drug resistance. Medicines for Malaria Venture (MMV) has pre-screened and identified a set of 400 antimalarial compounds called the Malaria Box. From those, we have evaluated their mechanisms of action through inhibition of PfTrxR and found new active chemical scaffolds. Five compounds with significant PfTrxR inhibitory activity, with IC50 values ranging from 0.9-7.5 µM against the target enzyme, were found out of the Malaria Box.","corpus_id":39018362,"score":2},{"doc_id":"19888680","title":"NMR assignments of oxidised thioredoxin from Plasmodium falciparum.","abstract":"During its life cycle, the malaria parasite Plasmodium falciparum is found intracellular to human erythrocytes, where its survival and ability to multiply critically depends on the control of the environment redox state. Thioredoxin is a small protein containing 104 amino acids that is part of the parasite specific redox system. During the catalytic cycle it alternates between a reduced and oxidised form. Here we report the complete resonance assignment of Plasmodium falciparum thioredoxin in its oxidized form by heteronuclear multidimensional spectroscopy. The obtained chemical shifts differ significantly from those reported earlier for this protein in its reduced state.","corpus_id":2456950,"score":1},{"doc_id":"22355694","title":"Structural insights into thioredoxin-2: a component of malaria parasite protein secretion machinery.","abstract":"Thioredoxins are vital components of Plasmodium proteome and act as both reducing agents and protein disulfide reductases. The malaria parasite P. falciparum thioredoxin-2 (PfTrx-2) is part of the multi-protein complex embedded within the parasite parasitophorous vacuolar membrane (PVM) which purportedly directs protein secretion. We have characterized structural and enzymatic features of PfTrx-2, and we show that PfTrx-2 adopts a canonical thioredoxin fold but with significant structural differences in its N-terminus. Our confocal localization data suggest distinct PVM residency of PfTrx-2. Based on the crystal structure of PfTrx-2, we screened and tested small molecule drug-like libraries for compounds which target unique structural features of PfTrx-2. Disruption of PfTrx-2 interactions using specific inhibitors may result in a dysfunctional parasite translocon that is rendered unable to secrete pathogenic proteins into hosts. This approach therefore offers a new focus for anti-malarial drug development.","corpus_id":16902108,"score":1},{"doc_id":"22392134","title":"Cloning and characterization of Plasmodium vivax thioredoxin peroxidase-1.","abstract":"Reactive oxygen species produced from hemoglobin digestion and the host immune system could have adverse effects on malaria parasites. To protect themselves, malaria parasites are highly dependent on the antioxidant enzymes, including superoxide dismutases and thioredoxin-dependent peroxidases. To date, several thioredoxin peroxidases (TPx) have been characterized in Plasmodium falciparum, but the TPx in Plasmodium vivax has not yet been characterized. The complete sequence of gene coding for thioredoxin peroxidase-1 of P. vivax (PvTPx-1) was amplified by PCR and cloned. Using the recombinant PvTPx-1 (rPvTPx-1), polyclonal antibody was produced in mice for immunolocalization of the enzyme in the parasite. The antioxidant activity of rPvTPx-1 was evaluated by mixed-function oxidation assay. PvTPx-1 has two conserved cysteine residues in the amino acid sequence at the positions 50 and 170 which formed a dimer under a non-reducing condition. Using a thiol mixed-function oxidation assay, the antioxidant activity of rPvTPx-1 was revealed. Indirect immunofluorescence microscopy with the specific antibody indicated that PvTPx-1 was expressed in the cytoplasm of the erythrocytic stage of the parasite in a dots-like pattern. The results suggest that P. vivax uses TPx-1 to reduce and detoxify hydrogen peroxides in order to maintain their redox homeostasis and proliferation in the host body.","corpus_id":14643225,"score":1},{"doc_id":"23649394","title":"[Structural biology for developing antimalarial compounds].","abstract":"The human malaria parasite Plasmodium falciparum is responsible for the death of more than a million people each year. The emergence of strains of this malaria parasite resistant to conventional drug therapy has stimulated the search for antimalarial compounds with novel modes of action. Here the structure-function relationship studies for two Plasmodium proteins are presented. One example is the structural studies for S-adenosyl-L-homocysteine hydrolase from Plasmodium falciparum (PfSAHH) and the other example is those for 1-deoxy-D-xylulose reductoisomerase from Plasmodium falciparum (PfDXR). In the former study, the clue for design of species specific PfSAHH inhibitors was obtained by the structural comparison of the active site of PfSAHH with that of human SAHH (HsSAHH). Our study revealed that the inhibitor selectivity depends on the difference of only one amino acid residue in the active site; Cys59 in PfSAHH vs. Thr60 in HsSAHH. In the latter study, the inhibition of PfDXR enzyme by fosmidomycin has proved to be efficient in the treatment of uncomplicated malaria in recent clinical trials conducted in Gabon and Thailand. Our crystal structure analyses of PfDXR/inhibitor complexes revealed the molecular basis of fosmidomycin's action in P. falciparum. We expect that the structure-function relationship studies on Plasmodium proteins are useful for developing the more effective antimalarial compounds.","corpus_id":34691633,"score":1},{"doc_id":"25475729","title":"Crystal structure and solution characterization of the thioredoxin-2 from Plasmodium falciparum, a constituent of an essential parasitic protein export complex.","abstract":"Survival of the malaria parasite Plasmodium falciparum when it infects red blood cells depends upon its ability to export hundreds of its proteins beyond an encasing vacuole. Protein export is mediated by a parasite-derived protein complex, the Plasmodium translocon of exported proteins (PTEX), and requires unfolding of the different cargos prior to their translocation across the vacuolar membrane. Unfolding is performed by the AAA+protein unfoldase HSP101/ClpB2 and the thioredoxin-2 enzyme (TRX2). Protein trafficking is dramatically impaired in parasites with defective HSP101 or lacking TRX2. These two PTEX subunits drive export and are targets for the design of a novel class of antimalarials: protein export inhibitors. To rationalize inhibitor design, we solved the crystal structure of Pfal-TRX2 at 2.2-Å resolution. Within the asymmetric unit, the three different copies of this protein disulfide reductase sample its two redox catalytic states. Size exclusion chromatography and small-angle X-ray scattering (SAXS) analyses demonstrate that Pfal-TRX2 is monomeric in solution. A non-conserved N-terminal extension precedes the canonical thioredoxin-fold; although it is not observed in our structure, our solution analysis suggests it is flexible in contrast to Plasmodium thioredoxin-1. This represents a first step towards the reconstitution of the entire PTEX for mechanistic and structural studies.","corpus_id":205936634,"score":1},{"doc_id":"28755265","title":"An in silico strategy for identification of novel drug targets against Plasmodium falciparum.","abstract":"The apicomplexan parasite Plasmodium falciparum is responsible for global malaria burden. With the reported resistance to artemisinin chemotherapy, there is an urgent need to maintain early phase drug discovery and identify novel drug targets for successful eradication of the pathogen from the host. In our previous work on comparative genomics study for identification of putative essential genes and therapeutic candidates in P. falciparum, we predicted 11 proteins as anti-malarial drug targets from PlasmoDB database. In this paper, we made an attempt for identification of novel drug targets in P. falciparum genome using a sequence of computational methods from Malaria Parasite Metabolic Pathway database. The study reported the identification of 71 proteins as potential drug targets for anti-malarial interventions. Furthermore, homology modeling and molecular dynamic simulation study of one of the potential drug targets, aminodeoxychorismate lyase, was carried to predict the 3D structure of the protein. Structure and ligand-based drug designing reported MMV019742 from Pathogen Box and TCAMS-141515 from GSK-TCAMS library as potential hits. The reliability of the binding mode of the inhibitors is confirmed by GROMACS for a simulation time of 20 ns in water environment. This will be helpful for experimental validation of the small-molecule inhibitor.","corpus_id":4048428,"score":1},{"doc_id":"18037315","title":"In silico screening against wild-type and mutant Plasmodium falciparum dihydrofolate reductase.","abstract":"Modeling studies were performed on known inhibitors of wild-type as well as quadruple mutant Plasmodium falciparum dihydrofolate reductase (DHFR). GOLD was used to dock 31 pyrimethamine derivatives into the active site of DHFR obtained from the X-ray crystal structures 1J3I.pdb and 1J3K.pdb. Predicted binding affinities from a scoring function were analyzed and evaluated in order to develop criteria for selecting compounds having a greater chance of activity versus wild-type and resistant strains of P. falciparum for future high-throughput screening experiments.","corpus_id":8425934,"score":0},{"doc_id":"19146480","title":"Exploiting structural analysis, in silico screening, and serendipity to identify novel inhibitors of drug-resistant falciparum malaria.","abstract":"Plasmodium falciparum thymidylate synthase-dihydrofolate reductase (TS-DHFR) is an essential enzyme in folate biosynthesis and a major malarial drug target. This bifunctional enzyme thus presents different design approaches for developing novel inhibitors against drug-resistant mutants. We performed a high-throughput in silico screen of a database of diverse, drug-like molecules against a non-active-site pocket of TS-DHFR. The top compounds from this virtual screen were evaluated by in vitro enzymatic and cellular culture studies. Three compounds active to 20 microM IC(50)'s in both wildtype and antifolate-resistant P. falciparum parasites were identified; moreover, no inhibition of human DHFR enzyme was observed, indicating that the inhibitory effects appeared to be parasite-specific. Notably, all three compounds had a biguanide scaffold. However, relative free energy of binding calculations suggested that the compounds might preferentially interact with the active site over the screened non-active-site region. To resolve the two possible modes of binding, co-crystallization studies of the compounds complexed with TS-DHFR enzyme were performed. Surprisingly, the structural analysis revealed that these novel, biguanide compounds do indeed bind at the active site of DHFR and additionally revealed the molecular basis by which they overcome drug resistance. To our knowledge, these are the first co-crystal structures of novel, biguanide, non-WR99210 compounds that are active against folate-resistant malaria parasites in cell culture.","corpus_id":25802336,"score":0},{"doc_id":"19174148","title":"Plasmodium falciparum signal peptide peptidase is a promising drug target against blood stage malaria.","abstract":"The resistance of malaria parasites to current anti-malarial drugs is an issue of major concern globally. Recently we identified a Plasmodium falciparum cell membrane aspartyl protease, which binds to erythrocyte band 3, and is involved in merozoite invasion. Here we report the complete primary structure of P. falciparum signal peptide peptidase (PfSPP), and demonstrate that it is essential for parasite invasion and growth in human erythrocytes. Gene silencing suggests that PfSPP may be essential for parasite survival in human erythrocytes. Remarkably, mammalian signal peptide peptidase inhibitors (Z-LL)(2)-ketone and L-685,458 effectively inhibited malaria parasite invasion as well as growth in human erythrocytes. In contrast, DAPT, an inhibitor of a related gamma-secretase/presenilin-1, was ineffective. Thus, SPP inhibitors specific for PfSPP may function as potent anti-malarial drugs against the blood stage malaria.","corpus_id":38590623,"score":0},{"doc_id":"19196988","title":"Structural basis for the inhibition of the essential Plasmodium falciparum M1 neutral aminopeptidase.","abstract":"Plasmodium falciparum parasites are responsible for the major global disease malaria, which results in >2 million deaths each year. With the rise of drug-resistant malarial parasites, novel drug targets and lead compounds are urgently required for the development of new therapeutic strategies. Here, we address this important problem by targeting the malarial neutral aminopeptidases that are involved in the terminal stages of hemoglobin digestion and essential for the provision of amino acids used for parasite growth and development within the erythrocyte. We characterize the structure and substrate specificity of one such aminopeptidase, PfA-M1, a validated drug target. The X-ray crystal structure of PfA-M1 alone and in complex with the generic inhibitor, bestatin, and a phosphinate dipeptide analogue with potent in vitro and in vivo antimalarial activity, hPheP[CH(2)]Phe, reveals features within the protease active site that are critical to its function as an aminopeptidase and can be exploited for drug development. These results set the groundwork for the development of antimalarial therapeutics that target the neutral aminopeptidases of the parasite.","corpus_id":26034035,"score":0},{"doc_id":"19285084","title":"Crystal structures of the histo-aspartic protease (HAP) from Plasmodium falciparum.","abstract":"The structures of recombinant histo-aspartic protease (HAP) from malaria-causing parasite Plasmodium falciparum as apoenzyme and in complex with two inhibitors, pepstatin A and KNI-10006, were solved at 2.5-, 3.3-, and 3.05-A resolutions, respectively. In the apoenzyme crystals, HAP forms a tight dimer not seen previously in any aspartic protease. The interactions between the monomers affect the conformation of two flexible loops, the functionally important \"flap\" (residues 70-83) and its structural equivalent in the C-terminal domain (residues 238-245), as well as the orientation of helix 225-235. The flap is found in an open conformation in the apoenzyme. Unexpectedly, the active site of the apoenzyme contains a zinc ion tightly bound to His32 and Asp215 from one monomer and to Glu278A from the other monomer, with the coordination of Zn resembling that seen in metalloproteases. The flap is closed in the structure of the pepstatin A complex, whereas it is open in the complex with KNI-10006. Although the binding mode of pepstatin A is significantly different from that in other pepsin-like aspartic proteases, its location in the active site makes unlikely the previously proposed hypothesis that HAP is a serine protease. The binding mode of KNI-10006 is unusual compared with the binding of other inhibitors from the KNI series to aspartic proteases. The novel features of the HAP active site could facilitate design of specific inhibitors used in the development of antimalarial drugs.","corpus_id":16254507,"score":0},{"doc_id":"19827093","title":"The crystal structures of macrophage migration inhibitory factor from Plasmodium falciparum and Plasmodium berghei.","abstract":"Malaria, caused by Plasmodium falciparum and related parasites, is responsible for millions of deaths each year, mainly from complications arising from the blood stages of its life cycle. Macrophage migration inhibitory factor (MIF), a protein expressed by the parasite during these stages, has been characterized in mammals as a cytokine involved in a broad spectrum of immune responses. It also possesses two catalytic activities, a tautomerase and an oxidoreductase, though the physiological significance of neither reaction is known. Here, we have determined the crystal structure of MIF from two malaria parasites, Plasmodium falciparum and Plasmodium berghei at 2.2 A and 1.8 A, respectively. The structures have an alpha/beta fold and each reveals a trimer, in agreement with the results of analytical ultracentrifugation. We observed open and closed active sites, these being distinguished by movements of proline-1, the catalytic base in the tautomerase reaction. These states correlate with the covalent modification of cysteine 2 to form a mercaptoethanol adduct, an observation confirmed by mass spectrometry. The Plasmodium MIFs have a different pattern of conserved cysteine residues to the mammalian MIFs and the side chain of Cys58, which is implicated in the oxidoreductase activity, is buried. This observation and the evident redox reactivity of Cys2 suggest quite different oxidoreductase characteristics. Finally, we show in pull-down assays that Plasmodium MIF binds to the cell surface receptor CD74, a known mammalian MIF receptor implying that parasite MIF has the ability to interfere with, or modulate, host MIF activity through a competitive binding mechanism.","corpus_id":13241233,"score":0},{"doc_id":"19845508","title":"Comparison of the cellular and biochemical properties of Plasmodium falciparum choline and ethanolamine kinases.","abstract":"The proliferation of the malaria-causing parasite Plasmodium falciparum within the erythrocyte is concomitant with massive phosphatidylcholine and phosphatidylethanolamine biosynthesis. Based on pharmacological and genetic data, de novo biosynthesis pathways of both phospholipids appear to be essential for parasite survival. The present study characterizes PfCK (P. falciparum choline kinase) and PfEK (P. falciparum ethanolamine kinase), which catalyse the first enzymatic steps of these essential metabolic pathways. Recombinant PfCK and PfEK were expressed as His6-tagged fusion proteins from overexpressing Escherichia coli strains, then purified to homogeneity and characterized. Using murine polyclonal antibodies against recombinant kinases, PfCK and PfEK were shown to be localized within the parasite cytoplasm. Protein expression levels increased during erythrocytic development. PfCK and PfEK appeared to be specific to their respective substrates and followed Michaelis-Menten kinetics. The Km value of PfCK for choline was 135.3+/-15.5 microM. PfCK was also able to phosphorylate ethanolamine with a very low affinity. PfEK was found to be an ethanolamine-specific kinase (Km=475.7+/-80.2 microM for ethanolamine). The quaternary ammonium compound hemicholinium-3 and an ethanolamine analogue, 2-amino-1-butanol, selectively inhibited PfCK or PfEK. In contrast, the bis-thiazolium compound T3, which was designed as a choline analogue and is currently in clinical trials for antimalarial treatment, affected PfCK and PfEK activities similarly. Inhibition exerted by T3 was competitive for both PfCK and PfEK and correlated with the impairment of cellular phosphatidylcholine biosynthesis. Comparative analyses of sequences and structures for both kinase types gave insights into their specific inhibition profiles and into the dual capacity of T3 to inhibit both PfCK and PfEK.","corpus_id":5875081,"score":0},{"doc_id":"20133789","title":"Structure of the Plasmodium falciparum M17 aminopeptidase and significance for the design of drugs targeting the neutral exopeptidases.","abstract":"Current therapeutics and prophylactics for malaria are under severe challenge as a result of the rapid emergence of drug-resistant parasites. The human malaria parasite Plasmodium falciparum expresses two neutral aminopeptidases, PfA-M1 and PfA-M17, which function in regulating the intracellular pool of amino acids required for growth and development inside the red blood cell. These enzymes are essential for parasite viability and are validated therapeutic targets. We previously reported the X-ray crystal structure of the monomeric PfA-M1 and proposed a mechanism for substrate entry and free amino acid release from the active site. Here, we present the X-ray crystal structure of the hexameric leucine aminopeptidase, PfA-M17, alone and in complex with two inhibitors with antimalarial activity. The six active sites of the PfA-M17 hexamer are arranged in a disc-like fashion so that they are orientated inwards to form a central catalytic cavity; flexible loops that sit at each of the six entrances to the catalytic cavern function to regulate substrate access. In stark contrast to PfA-M1, PfA-M17 has a narrow and hydrophobic primary specificity pocket which accounts for its highly restricted substrate specificity. We also explicate the essential roles for the metal-binding centers in these enzymes (two in PfA-M17 and one in PfA-M1) in both substrate and drug binding. Our detailed understanding of the PfA-M1 and PfA-M17 active sites now permits a rational approach in the development of a unique class of two-target and/or combination antimalarial therapy.","corpus_id":25137010,"score":0},{"doc_id":"20480551","title":"Targeting Plasmodium falciparum purine salvage enzymes: a look at structure-based drug development.","abstract":"New antimalarials are needed due to the rapid development of resistance to currently deployed drugs. Because Plasmodium species are unable to synthesize purines, purine salvage pathways have been proposed as novel anti-malarial targets. The purine salvage pathway in Plasmodium is streamlined with adenosine deaminase (ADA), purine nucleoside phosphorylase (PNP) and hypoxanthine-xanthine-guanine-phosphoribosyltransferase (HXGPRT) representing the major pathway for purine acquisition. Plasmodium falciparum enzymes PfADA and PfPNP have unique dual specificity that enable them to act upon methylthiopurines resulting from polyamine synthesis. Thus Plasmodium ADA and PNP function in both purine salvage and purine recycling. Genetic studies have confirmed the importance of Plasmodium PNP for viability of malaria parasites. Immucillins, powerful picomolar transition state inhibitors of PNP, are active against cultured Plasmodium falciparum and inhibit all Plasmodium PNPs tested. Several immucillins have undergone human clinical trials, and these compounds represent a new class of compounds with potential activity against human malarias.","corpus_id":45808723,"score":0},{"doc_id":"20702404","title":"Novel inhibitors of Plasmodium falciparum dihydroorotate dehydrogenase with anti-malarial activity in the mouse model.","abstract":"Plasmodium falciparum, the causative agent of the most deadly form of human malaria, is unable to salvage pyrimidines and must rely on de novo biosynthesis for survival. Dihydroorotate dehydrogenase (DHODH) catalyzes the rate-limiting step in the pyrimidine biosynthetic pathway and represents a potential target for anti-malarial therapy. A high throughput screen and subsequent medicinal chemistry program identified a series of N-alkyl-5-(1H-benzimidazol-1-yl)thiophene-2-carboxamides with low nanomolar in vitro potency against DHODH from P. falciparum, P. vivax, and P. berghei. The compounds were selective for the parasite enzymes over human DHODH, and x-ray structural data on the analog Genz-667348, demonstrated that species selectivity could be attributed to amino acid differences in the inhibitor-binding site. Compounds from this series demonstrated in vitro potency against the 3D7 and Dd2 strains of P. falciparum, good tolerability and oral exposure in the mouse, and ED(50) values in the 4-day murine P. berghei efficacy model of 13-21 mg/kg/day with oral twice-daily dosing. In particular, treatment with Genz-667348 at 100 mg/kg/day resulted in sterile cure. Two recent analogs of Genz-667348 are currently undergoing pilot toxicity testing to determine suitability as clinical development candidates.","corpus_id":22125990,"score":0},{"doc_id":"21205898","title":"Validation of isoleucine utilization targets in Plasmodium falciparum.","abstract":"Intraerythrocytic malaria parasites can obtain nearly their entire amino acid requirement by degrading host cell hemoglobin. The sole exception is isoleucine, which is not present in adult human hemoglobin and must be obtained exogenously. We evaluated two compounds for their potential to interfere with isoleucine utilization. Mupirocin, a clinically used antibacterial, kills Plasmodium falciparum parasites at nanomolar concentrations. Thiaisoleucine, an isoleucine analog, also has antimalarial activity. To identify targets of the two compounds, we selected parasites resistant to either mupirocin or thiaisoleucine. Mutants were analyzed by genome-wide high-density tiling microarrays, DNA sequencing, and copy number variation analysis. The genomes of three independent mupirocin-resistant parasite clones had all acquired either amplifications encompassing or SNPs within the chromosomally encoded organellar (apicoplast) isoleucyl-tRNA synthetase. Thiaisoleucine-resistant parasites had a mutation in the cytoplasmic isoleucyl-tRNA synthetase. The role of this mutation in thiaisoleucine resistance was confirmed by allelic replacement. This approach is generally useful for elucidation of new targets in P. falciparum. Our study shows that isoleucine utilization is an essential pathway that can be targeted for antimalarial drug development.","corpus_id":3471462,"score":0},{"doc_id":"21428877","title":"Falcipains, Plasmodium falciparum cysteine proteases as key drug targets against malaria.","abstract":"There is a high demand for new drugs against malaria, which takes millions of lives annually. The abuse of classical antimalarials from the late 1940's to the early 1980's has bred resistant parasites, which led to the use of more potent drugs that ended up by refueling the resistance cycle. An example is chloroquine, once highly effective but now virtually useless against malaria. Structure-based rational drug design relies on high-resolution target structures to allow for screening of selective ligands/inhibitors. For the past two decades, and especially after the unveiling of the Plasmodium falciparum genome in 2002, enzymes of this lethal malaria parasite species have been increasingly attracting the attention of Medicinal Chemists worldwide as promising drug targets. There is particular emphasis on proteases having key roles on the degradation of host's hemoglobin within the food vacuole of blood-stage parasites, as these depend on such process for their survival. Among such enzymes, Plasmepsins (aspartic proteases) and, especially, Falcipains (cysteine proteases) are highly promising antimalarial drug targets. The present review will focus on the computational approaches made so far towards the unraveling of the structure, function and inhibition of Falcipains that, by virtue of their quite specific features, are excellent targets for highly selective inhibitors.","corpus_id":19312471,"score":0},{"doc_id":"21554743","title":"Selection of drug resistant mutants from random library of Plasmodium falciparum dihydrofolate reductase in Plasmodium berghei model.","abstract":"BACKGROUND: The prevalence of drug resistance amongst the human malaria Plasmodium species has most commonly been associated with genomic mutation within the parasites. This phenomenon necessitates evolutionary predictive studies of possible resistance mutations, which may occur when a new drug is introduced. Therefore, identification of possible new Plasmodium falciparum dihydrofolate reductase (PfDHFR) mutants that confer resistance to antifolate drugs is essential in the process of antifolate anti-malarial drug development. METHODS: A system to identify mutations in Pfdhfr gene that confer antifolate drug resistance using an animal Plasmodium parasite model was developed. By using error-prone PCR and Plasmodium transfection technologies, libraries of Pfdhfr mutant were generated and then episomally transfected to Plasmodium berghei parasites, from which pyrimethamine-resistant PfDHFR mutants were selected. RESULTS: The principal mutation found from this experiment was S108N, coincident with the first pyrimethamine-resistance mutation isolated from the field. A transgenic P. berghei, in which endogenous Pbdhfr allele was replaced with the mutant PfdhfrS108N, was generated and confirmed to have normal growth rate comparing to parental non-transgenic parasite and also confer resistance to pyrimethamine. CONCLUSION: This study demonstrated the power of the transgenic P. berghei system to predict drug-resistant Pfdhfr mutations in an in vivo parasite/host setting. The system could be utilized for identification of possible novel drug-resistant mutants that could arise against new antifolate compounds and for prediction the evolution of resistance mutations.","corpus_id":8888211,"score":0},{"doc_id":"21801743","title":"Structural analysis of chorismate synthase from Plasmodium falciparum: a novel target for antimalaria drug discovery.","abstract":"The shikimate pathway in Plasmodium falciparum provides several targets for designing novel antiparasitic agents for the treatment of malaria. Chorismate synthase (CS) is a key enzyme in the shikimate pathway which catalyzes the seventh and final step of the pathway. P. falciparum chorismate synthase (PfCS) is unique in terms of enzymatic behavior, cellular localization and in having two additional amino acid inserts compared to any other CS. The structure of PfCS along with cofactor FMN was predicted by homology modeling using crystal structure of Helicobacter pylori chorismate synthase (HpCS). The quality of the model was validated using structure analysis servers and molecular dynamics. Dimeric form of PfCS was generated and the FMN binding mechanism involving movement of loop near active site has been proposed. Active site pocket has been identified and substrate 5-enolpyruvylshikimate 3-phosphate (EPSP) along with screened potent inhibitors has been docked. The study resulted in identification of putative inhibitors of PfCS with binding efficiency in nanomolar range. The selected putative inhibitors could lead to the development of anti-malarial drugs.","corpus_id":22208796,"score":0},{"doc_id":"21843142","title":"Support vector machine based prediction of P. falciparum proteasome inhibitors and development of focused library by molecular docking.","abstract":"The emergence and spread of Plasmodium falciparum resistance to existing antimalarials emphasize the impelling search for novel drug targets and chemotherapeutic compounds. The ubiquitin-proteasome system plays a major role in overall protein turnover, in eukaryotic cells including plasmodia. 20S β subunit is the catalytic core of this proteolytic machinery, and hence most of the inhibitors developed are being targeted towards this component. Inhibition of the proteasome is established as a promising strategy to develop novel antimalarial drugs. The present study reports identification of novel drug-like 20S proteasome inhibitors with potential activity against the 20S β subunit of P. falciparum using a combination of ligand based (Support Vector Machines) and receptor based (molecular docking) techniques. The robust learning and generalizing capability of Support Vector Machines (SVM) has been exploited to classify proteasome inhibitors and non-inhibitors, targeted towards P. falciparum 20S proteasome. SVM model has been trained using 170 molecular descriptors of 64 inhibitors and 208 putative non-inhibitors of 20S proteasome. The non-linear classifier based on Radial Basis Function (RBF) kernel yielded highest classification accuracy in comparison to the linear classifier. The best classifier had 5-fold Cross-Validation (CV) accuracy of 97% and Area Under Curve (AUC) of 0.99 reflecting good accuracy of the model. The SVM model rapidly classified compounds with potential proteasomal activity. Subsequently, molecular docking studies aided the generation of focused collection of compounds with good binding affinity towards the substrate-binding site of 20S β subunit. The novel drug-like 20S proteasome inhibitors identified in this study can be a good starting point to develop novel antimalarial drugs.","corpus_id":32951082,"score":0},{"doc_id":"22117061","title":"Structure and reaction mechanism of phosphoethanolamine methyltransferase from the malaria parasite Plasmodium falciparum: an antiparasitic drug target.","abstract":"In the malarial parasite Plasmodium falciparum, a multifunctional phosphoethanolamine methyltransferase (PfPMT) catalyzes the methylation of phosphoethanolamine (pEA) to phosphocholine for membrane biogenesis. This pathway is also found in plant and nematodes, but PMT from these organisms use multiple methyltransferase domains for the S-adenosylmethionine (AdoMet) reactions. Because PfPMT is essential for normal growth and survival of Plasmodium and is not found in humans, it is an antiparasitic target. Here we describe the 1.55 Å resolution crystal structure of PfPMT in complex with AdoMet by single-wavelength anomalous dispersion phasing. In addition, 1.19-1.52 Å resolution structures of PfPMT with pEA (substrate), phosphocholine (product), sinefungin (inhibitor), and both pEA and S-adenosylhomocysteine bound were determined. These structures suggest that domain rearrangements occur upon ligand binding and provide insight on active site architecture defining the AdoMet and phosphobase binding sites. Functional characterization of 27 site-directed mutants identifies critical active site residues and suggests that Tyr-19 and His-132 form a catalytic dyad. Kinetic analysis, isothermal titration calorimetry, and protein crystallography of the Y19F and H132A mutants suggest a reaction mechanism for the PMT. Not only are Tyr-19 and His-132 required for phosphobase methylation, but they also form a \"catalytic\" latch that locks ligands in the active site and orders the site for catalysis. This study provides the first insight on this antiparasitic target enzyme essential for survival of the malaria parasite; however, further studies of the multidomain PMT from plants and nematodes are needed to understand the evolutionary division of metabolic function in the phosphobase pathway of these organisms.","corpus_id":3203009,"score":0},{"doc_id":"22543039","title":"Plasmodium subtilisin-like protease 1 (SUB1): insights into the active-site structure, specificity and function of a pan-malaria drug target.","abstract":"Release of the malaria merozoite from its host erythrocyte (egress) and invasion of a fresh cell are crucial steps in the life cycle of the malaria pathogen. Subtilisin-like protease 1 (SUB1) is a parasite serine protease implicated in both processes. In the most dangerous human malarial species, Plasmodium falciparum, SUB1 has previously been shown to have several parasite-derived substrates, proteolytic cleavage of which is important both for egress and maturation of the merozoite surface to enable invasion. Here we have used molecular modelling, existing knowledge of SUB1 substrates, and recombinant expression and characterisation of additional Plasmodium SUB1 orthologues, to examine the active site architecture and substrate specificity of P. falciparum SUB1 and its orthologues from the two other major human malaria pathogens Plasmodium vivax and Plasmodium knowlesi, as well as from the rodent malaria species, Plasmodium berghei. Our results reveal a number of unusual features of the SUB1 substrate binding cleft, including a requirement to interact with both prime and non-prime side residues of the substrate recognition motif. Cleavage of conserved parasite substrates is mediated by SUB1 in all parasite species examined, and the importance of this is supported by evidence for species-specific co-evolution of protease and substrates. Two peptidyl alpha-ketoamides based on an authentic PfSUB1 substrate inhibit all SUB1 orthologues examined, with inhibitory potency enhanced by the presence of a carboxyl moiety designed to introduce prime side interactions with the protease. Our findings demonstrate that it should be possible to develop 'pan-reactive' drug-like compounds that inhibit SUB1 in all three major human malaria pathogens, enabling production of broad-spectrum antimalarial drugs targeting SUB1.","corpus_id":34527491,"score":0},{"doc_id":"22709581","title":"X-ray crystal structure and specificity of the Plasmodium falciparum malaria aminopeptidase PfM18AAP.","abstract":"The malarial aminopeptidases have emerged as promising new drug targets for the development of novel antimalarial drugs. The M18AAP of Plasmodium falciparum malaria is a metallo-aminopeptidase that we show demonstrates a highly restricted specificity for peptides with an N-terminal Glu or Asp residue. Thus, the enzyme may function alongside other aminopeptidases in effecting the complete degradation or turnover of proteins, such as host hemoglobin, which provides a free amino acid pool for the growing parasite. Inhibition of PfM18AAP's function using antisense RNA is detrimental to the intra-erythrocytic malaria parasite and, hence, it has been proposed as a potential novel drug target. We report the X-ray crystal structure of the PfM18AAP aminopeptidase and reveal its complex dodecameric assembly arranged via dimer and trimer units that interact to form a large tetrahedron shape that completely encloses the 12 active sites within a central cavity. The four entry points to the catalytic lumen are each guarded by 12 large flexible loops that could control substrate entry into the catalytic sites. PfM18AAP thus resembles a proteasomal-like machine with multiple active sites able to degrade peptide substrates that enter the central lumen. The Plasmodium enzyme shows significant structural differences around the active site when compared to recently determined structures of its mammalian and human homologs, which provides a platform from which a rational approach to inhibitor design of new malaria-specific drugs can begin.","corpus_id":21866725,"score":0},{"doc_id":"23035243","title":"Malarial dihydrofolate reductase as a paradigm for drug development against a resistance-compromised target.","abstract":"Malarial dihydrofolate reductase (DHFR) is the target of antifolate antimalarial drugs such as pyrimethamine and cycloguanil, the clinical efficacy of which have been compromised by resistance arising through mutations at various sites on the enzyme. Here, we describe the use of cocrystal structures with inhibitors and substrates, along with efficacy and pharmacokinetic profiling for the design, characterization, and preclinical development of a selective, highly efficacious, and orally available antimalarial drug candidate that potently inhibits both wild-type and clinically relevant mutated forms of Plasmodium falciparum (Pf) DHFR. Important structural characteristics of P218 include pyrimidine side-chain flexibility and a carboxylate group that makes charge-mediated hydrogen bonds with conserved Arg122 (PfDHFR-TS amino acid numbering). An analogous interaction of P218 with human DHFR is disfavored because of three species-dependent amino acid substitutions in the vicinity of the conserved Arg. Thus, P218 binds to the active site of PfDHFR in a substantially different fashion from the human enzyme, which is the basis for its high selectivity. Unlike pyrimethamine, P218 binds both wild-type and mutant PfDHFR in a slow-on/slow-off tight-binding mode, which prolongs the target residence time. P218, when bound to PfDHFR-TS, resides almost entirely within the envelope mapped out by the dihydrofolate substrate, which may make it less susceptible to resistance mutations. The high in vivo efficacy in a SCID mouse model of P. falciparum malaria, good oral bioavailability, favorable enzyme selectivity, and good safety characteristics of P218 make it a potential candidate for further development.","corpus_id":28088781,"score":0},{"doc_id":"23353582","title":"In silico identification of novel inhibitors against Plasmodium falciparum dihydroorate dehydrogenase.","abstract":"Plasmodium falciparum causes the most fatal form of malaria and accounts for over 1 million deaths annually, yet currently used drug therapies are compromised by resistance. The malaria parasite cannot salvage pyrimidines and relies on de novo biosynthesis for survival. The enzyme dihydrooratate dehydrogenase (DHODH), a mitochondrial flavoenzyme, catalyzes the rate-limiting step of this pathway and is therefore an attractive anti-malarial chemotherapeutic target. In an effort to design new and potential anti-malarials, structure-based pharmacophore mapping, molecular docking, binding energy calculations and binding affinity predictions were employed in a virtual screening strategy to design new and potent P. falciparum dihydrooratate dehydrogenase (PfDHODH) inhibitors. A structure-based pharmacophore model was generated which consist of important interactions as observed in co-crystal of PfDHODH enzyme. The developed model was used to retrieve molecules from ChemBridge database, a freely available commercial database. A total of 87 molecules mapped on the modeled pharmacophore from the database. The retrieved hits were further screened by docking simulation, binding energy calculations and biding affinity predictions using genetic optimization for ligand docking (GOLD) and MOE. Based on these results, finally 26 chemo-types molecules were predicted as new, potential and structurally diverse PfDHODH inhibitors.","corpus_id":11653555,"score":0},{"doc_id":"23633587","title":"Structural analysis of malaria-parasite lysyl-tRNA synthetase provides a platform for drug development.","abstract":"Aminoacyl-tRNA synthetases are essential enzymes that transmit information from the genetic code to proteins in cells and are targets for antipathogen drug development. Elucidation of the crystal structure of cytoplasmic lysyl-tRNA synthetase from the malaria parasite Plasmodium falciparum (PfLysRS) has allowed direct comparison with human LysRS. The authors' data suggest that PfLysRS is dimeric in solution, whereas the human counterpart can also adopt tetrameric forms. It is shown for the first time that PfLysRS is capable of synthesizing the signalling molecule Ap4a (diadenosine tetraphosphate) using ATP as a substrate. The PfLysRS crystal structure is in the apo form, such that binding to ATP will require rotameric changes in four conserved residues. Differences in the active-site regions of parasite and human LysRSs suggest the possibility of exploiting PfLysRS for selective inhibition. These investigations on PfLysRS further validate malarial LysRSs as attractive antimalarial targets and provide new structural space for the development of inhibitors that target pathogen LysRSs selectively.","corpus_id":34079431,"score":0},{"doc_id":"23665145","title":"Crystal structures of Plasmodium falciparum cytosolic tryptophanyl-tRNA synthetase and its potential as a target for structure-guided drug design.","abstract":"Malaria, most commonly caused by the parasite Plasmodium falciparum, is a devastating disease that remains a large global health burden. Lack of vaccines and drug resistance necessitate the continual development of new drugs and exploration of new drug targets. Due to their essential role in protein synthesis, aminoacyl-tRNA synthetases are potential anti-malaria drug targets. Here we report the crystal structures of P. falciparum cytosolic tryptophanyl-tRNA synthetase (Pf-cTrpRS) in its ligand-free state and tryptophanyl-adenylate (WAMP)-bound state at 2.34 Å and 2.40 Å resolutions, respectively. Large conformational changes are observed when the ligand-free protein is bound to WAMP. Multiple residues, completely surrounding the active site pocket, collapse onto WAMP. Comparison of the structures to those of human cytosolic TrpRS (Hs-cTrpRS) provides information about the possibility of targeting Pf-cTrpRS for inhibitor development. There is a high degree of similarity between Pf-cTrpRS and Hs-cTrpRS within the active site. However, the large motion that Pf-cTrpRS undergoes during transitions between different functional states avails an opportunity to arrive at compounds which selectively perturb the motion, and may provide a starting point for the development of new anti-malaria therapeutics.","corpus_id":5443658,"score":0},{"doc_id":"23750298","title":"In silico analysis of Plasmodium species specific UvrD helicase.","abstract":"Malaria is still a devastating disease caused by the mosquito-transmitted parasite Plasmodium, particularly Plasmodium falciparum. During the last few years the situation has worsened in many ways, mainly due to malarial parasites becoming increasingly resistant to several anti-malarial drugs. Thus there is an urgent need to find alternate ways to control malaria and therefore it is necessary to identify new drug targets and new classes of anti-malarial drugs. A malaria vaccine would be the ultimate weapon to fight this deadly disease but unfortunately despite encouraging advances a vaccine is not likely soon. DNA helicases from the PcrA/UvrD/Rep (PUR) subfamily are important for the survival of the various organisms, mainly pathogenic bacteria. Members from this subfamily can be targeted and inhibited by a variety of synthetic compounds. Using bioinformatics analysis we have shown that UvrD from this subfamily is the only member present in the P. falciparum genome, while PcrA and Rep are absent in the genome. UvrD from the parasite shows no homology to any protein or enzyme from human and thus can be considered as a strong potential drug target. In the present study we report an in silico analysis of this important enzyme from a variety of Plasmodium species. The results suggest that among all the species of Plasmodium, P. falciparum contains the largest UvrD and this enzyme is variable at the sequence and structural level.","corpus_id":10375376,"score":0},{"doc_id":"24063369","title":"Design, synthesis, and biological and crystallographic evaluation of novel inhibitors of Plasmodium falciparum enoyl-ACP-reductase (PfFabI).","abstract":"Malaria, a disease of worldwide significance, is responsible for over one million deaths annually. The liver-stage of Plasmodium's life cycle is the first, obligatory, but clinically silent step in malaria infection. The P. falciparum type II fatty acid biosynthesis pathway (PfFAS-II) has been found to be essential for complete liver-stage development and has been regarded as a potential antimalarial target for the development of drugs for malaria prophylaxis and liver-stage eradication. In this paper, new coumarin-based triclosan analogues are reported and their biological profile is explored in terms of inhibitory potency against enzymes of the PfFAS-II pathway. Among the tested compounds, 7 and 8 showed the highest inhibitory potency against Pf enoyl-ACP-reductase (PfFabI), followed by 15 and 3. Finally, we determined the crystal structures of compounds 7 and 11 in complex with PfFabI to identify their mode of binding and to confirm outcomes of docking simulations.","corpus_id":42443710,"score":0},{"doc_id":"24410837","title":"Crystal structures of IspF from Plasmodium falciparum and Burkholderia cenocepacia: comparisons inform antimicrobial drug target assessment.","abstract":"BACKGROUND: 2C-methyl-D-erythritol-2,4-cyclodiphosphate synthase (IspF) catalyzes the conversion of 4-diphosphocytidyl-2C-methyl-D-erythritol-2-phosphate to 2C-methyl-D-erythritol-2,4-cyclodiphosphate and cytidine monophosphate in production of isoprenoid-precursors via the methylerythritol phosphate biosynthetic pathway. IspF is found in the protozoan Plasmodium falciparum, a parasite that causes cerebral malaria, as well as in many Gram-negative bacteria such as Burkholderia cenocepacia. IspF represents a potential target for development of broad-spectrum antimicrobial drugs since it is proven or inferred as essential in these pathogens and absent from mammals. Structural studies of IspF from these two important yet distinct pathogens, and comparisons with orthologues have been carried out to generate reagents, to support and inform a structure-based approach to early stage drug discovery. RESULTS: Efficient recombinant protein production and crystallization protocols were developed, and high-resolution crystal structures of IspF from P. falciparum (Emphasis/Emphasis>IspF) and B. cenocepacia (BcIspF) in complex with cytidine nucleotides determined. Comparisons with orthologues, indicate a high degree of order and conservation in parts of the active site where Zn2+ is bound and where recognition of the cytidine moiety of substrate occurs. However, conformational flexibility is noted in that area of the active site responsible for binding the methylerythritol component of substrate. Unexpectedly, one structure of BcIspF revealed two molecules of cytidine monophosphate in the active site, and another identified citrate coordinating to the catalytic Zn2+. In both cases interactions with ligands appear to help order a flexible loop at one side of the active site. Difficulties were encountered when attempting to derive complex structures with other ligands. CONCLUSIONS: High-resolution crystal structures of IspF from two important human pathogens have been obtained and compared to orthologues. The studies reveal new data on ligand binding, with citrate coordinating to the active site Zn2+ and when present in high concentrations cytidine monophosphate displays two binding modes in the active site. Ligand binding appears to order a part of the active site involved in substrate recognition. The high degree of structural conservation in and around the IspF active site suggests that any structural model might be suitable to support a program of structure-based drug discovery.","corpus_id":1849890,"score":0},{"doc_id":"24742318","title":"Molecular characterization of Plasmodium falciparum uracil-DNA glycosylase and its potential as a new anti-malarial drug target.","abstract":"BACKGROUND: Based on resistance of currently used anti-malarials, a new anti-malarial drug target against Plasmodium falciparum is urgently needed. Damaged DNA cannot be transcribed without prior DNA repair; therefore, uracil-DNA glycosylase, playing an important role in base excision repair, may act as a candidate for a new anti-malarial drug target. METHODS: Initially, the native PfUDG from parasite crude extract was partially purified using two columns, and the glycosylase activity was monitored. The existence of malarial UDG activity prompted the recombinant expression of PfUDG for further characterization. The PfUDG from chloroquine and pyrimethamine resistant P. falciparum strain K1 was amplified, cloned into the expression vector, and expressed in Escherichia coli. The recombinant PfUDG was analysed by SDS-PAGE and identified by LC-MS/MS. The three dimensional structure was modelled. Biochemical properties were characterized. Inhibitory effects of 12 uracil-derivatives on PfUDG activity were investigated. Inhibition of parasite growth was determined in vitro using SYBR Green I and compared with results from human cytotoxicity tests. RESULTS: The native PfUDG was partially purified with a specific activity of 1,811.7 units/mg (113.2 fold purification). After cloning of 966-bp PCR product, the 40-kDa hexa-histidine tagged PfUDG was expressed and identified. The amino acid sequence of PfUDG showed only 24.8% similarity compared with the human enzyme. The biochemical characteristics of PfUDGs were quite similar. They were inhibited by uracil glycosylase inhibitor protein as found in other organisms. Interestingly, recombinant PfUDG was inhibited by two uracil-derived compounds; 1-methoxyethyl-6-(p-n-octylanilino)uracil (IC50 of 16.75 μM) and 6-(phenylhydrazino)uracil (IC50 of 77.5 μM). Both compounds also inhibited parasite growth with IC50s of 15.6 and 12.8 μM, respectively. Moreover, 1-methoxyethyl-6-(p-n-octylanilino)uracil was not toxic to HepG2 cells, with IC50 of > 160 μM while 6-(phenylhydrazino)uracil exhibited cytoxicity, with IC50 of 27.5 μM. CONCLUSIONS: The recombinant PfUDG was expressed, characterized and compared to partially purified native PfUDG. Their characteristics were not significantly different. PfUDG differs from human enzyme in its size and predicted amino acid sequence. Two uracil derivatives inhibited PfUDG and parasite growth; however, only one non-cytotoxic compound was found. Therefore, this selective compound can act as a lead compound for anti-malarial development in the future.","corpus_id":15488694,"score":0},{"doc_id":"24864210","title":"Exploring Drug Targets in Isoprenoid Biosynthetic Pathway for Plasmodium falciparum.","abstract":"Emergence of rapid drug resistance to existing antimalarial drugs in Plasmodium falciparum has created the need for prediction of novel targets as well as leads derived from original molecules with improved activity against a validated drug target. The malaria parasite has a plant plastid-like apicoplast. To overcome the problem of falciparum malaria, the metabolic pathways in parasite apicoplast have been used as antimalarial drug targets. Among several pathways in apicoplast, isoprenoid biosynthesis is one of the important pathways for parasite as its multiplication in human erythrocytes requires isoprenoids. Therefore targeting this pathway and exploring leads with improved activity is a highly attractive approach. This report has explored progress towards the study of proteins and inhibitors of isoprenoid biosynthesis pathway. For more comprehensive analysis, antimalarial drug-protein interaction has been covered.","corpus_id":15423736,"score":0},{"doc_id":"24934654","title":"Identification of inhibitors of Plasmodium falciparum RuvB1 helicase using biochemical assays.","abstract":"Human malaria is a major parasitic infection, and the situation has worsened mainly due to the emergence of resistant malaria parasites to several anti-malarial drugs. Thus, an urgent need to find suitable drug targets has led to the development of newer classes of anti-malarial drugs. Helicases have been targeted to develop therapeutics for viral, bacterial, and other microorganism infections. Recently, Plasmodium falciparum RuvB ATPases/helicases have been characterized and proposed as a suitable antimalarial drug target. In the present study, the screening of various compounds was done and the results suggest that PfRuvB1 ATPase activity is inhibited considerably by the novobiocin and partially by cisplatin and ciprofloxacin. Helicase assay of PfRuvB1 in the presence of various compounds suggest novobiocin, actinomycin, and ethidium bromide as potent inhibitors. Novobiocin inhibits the helicase activity of PfRuvB1 possibly by blocking the ATPase activity of PfRuvB1. This study is unique in respect to the identification of novobiocin as inhibitor of PfRuvB1, partially by competing with ATP binding at its active site and provides evidence for PfRuvB1 as target of novobiocin after DNA gyrase-B and HSP90. These studies will certainly help the pharmacologist to design and develop some novel inhibitor specific to PfRuvB1, which may serve as suitable chemotherapeutics to target malaria.","corpus_id":16643632,"score":0},{"doc_id":"25738296","title":"Hemoglobin Degrading Proteases of Plasmodium falciparum as Antimalarial Drug Targets.","abstract":"Plasmepsins, falcipains and aminopeptidases are Plasmodium falciparum proteases involved in human host hemoglobin degradation and other processes like erythrocyte invasion and rupture. Antimalarial drug resistance and natural selection in parasite are important reasons that create the urgent need of novel targets and lead compounds to overcome the burden of malaria. This report explored progress of the study covering proteases and their inhibitors specific to hemoglobin degradation. Additionally, in silico predicted antimalarial targets, balancing selection and drug-protein interaction are included.","corpus_id":23198963,"score":0},{"doc_id":"26130467","title":"Structural mapping of the ClpB ATPases of Plasmodium falciparum: Targeting protein folding and secretion for antimalarial drug design.","abstract":"Caseinolytic chaperones and proteases (Clp) belong to the AAA+ protein superfamily and are part of the protein quality control machinery in cells. The eukaryotic parasite Plasmodium falciparum, the causative agent of malaria, has evolved an elaborate network of Clp proteins including two distinct ClpB ATPases. ClpB1 and ClpB2 are involved in different aspects of parasitic proteostasis. ClpB1 is present in the apicoplast, a parasite-specific and plastid-like organelle hosting various metabolic pathways necessary for parasite growth. ClpB2 localizes to the parasitophorous vacuole membrane where it drives protein export as core subunit of a parasite-derived protein secretion complex, the Plasmodium Translocon of Exported proteins (PTEX); this process is central to parasite virulence and survival in the human host. The functional associations of these two chaperones with parasite-specific metabolism and protein secretion make them prime drug targets. ClpB proteins function as unfoldases and disaggregases and share a common architecture consisting of four domains-a variable N-terminal domain that binds different protein substrates, followed by two highly conserved catalytic ATPase domains, and a C-terminal domain. Here, we report and compare the first crystal structures of the N terminal domains of ClpB1 and ClpB2 from Plasmodium and analyze their molecular surfaces. Solution scattering analysis of the N domain of ClpB2 shows that the average solution conformation is similar to the crystalline structure. These structures represent the first step towards the characterization of these two malarial chaperones and the reconstitution of the entire PTEX to aid structure-based design of novel anti-malarial drugs.","corpus_id":3449763,"score":0},{"doc_id":"26198663","title":"Plasmodium falciparum glucose-6-phosphate dehydrogenase 6-phosphogluconolactonase is a potential drug target.","abstract":"The malarial parasite Plasmodium falciparum is exposed to substantial redox challenges during its complex life cycle. In intraerythrocytic parasites, haemoglobin breakdown is a major source of reactive oxygen species. Deficiencies in human glucose-6-phosphate dehydrogenase, the initial enzyme in the pentose phosphate pathway (PPP), lead to a disturbed redox equilibrium in infected erythrocytes and partial protection against severe malaria. In P. falciparum, the first two reactions of the PPP are catalysed by the bifunctional enzyme glucose-6-phosphate dehydrogenase 6-phosphogluconolactonase (PfGluPho). This enzyme differs structurally from its human counterparts and represents a potential target for drugs. In the present study we used epitope tagging of endogenous PfGluPho to verify that the enzyme localises to the parasite cytosol. Furthermore, attempted double crossover disruption of the PfGluPho gene indicates that the enzyme is essential for the growth of blood stage parasites. As a further step towards targeting PfGluPho pharmacologically, ellagic acid was characterised as a potent PfGluPho inhibitor with an IC50 of 76 nM. Interestingly, pro-oxidative drugs or treatment of the parasites with H2O2 only slightly altered PfGluPho expression or activity under the conditions tested. Furthermore, metabolic profiling suggested that pro-oxidative drugs do not significantly perturb the abundance of PPP intermediates. These data indicate that PfGluPho is essential in asexual parasites, but that the oxidative arm of the PPP is not strongly regulated in response to oxidative challenge.","corpus_id":46398163,"score":0},{"doc_id":"26863983","title":"Structure- and function-based design of Plasmodium-selective proteasome inhibitors.","abstract":"The proteasome is a multi-component protease complex responsible for regulating key processes such as the cell cycle and antigen presentation. Compounds that target the proteasome are potentially valuable tools for the treatment of pathogens that depend on proteasome function for survival and replication. In particular, proteasome inhibitors have been shown to be toxic for the malaria parasite Plasmodium falciparum at all stages of its life cycle. Most compounds that have been tested against the parasite also inhibit the mammalian proteasome, resulting in toxicity that precludes their use as therapeutic agents. Therefore, better definition of the substrate specificity and structural properties of the Plasmodium proteasome could enable the development of compounds with sufficient selectivity to allow their use as anti-malarial agents. To accomplish this goal, here we use a substrate profiling method to uncover differences in the specificities of the human and P. falciparum proteasome. We design inhibitors based on amino-acid preferences specific to the parasite proteasome, and find that they preferentially inhibit the β2-subunit. We determine the structure of the P. falciparum 20S proteasome bound to the inhibitor using cryo-electron microscopy and single-particle analysis, to a resolution of 3.6 Å. These data reveal the unusually open P. falciparum β2 active site and provide valuable information about active-site architecture that can be used to further refine inhibitor design. Furthermore, consistent with the recent finding that the proteasome is important for stress pathways associated with resistance of artemisinin family anti-malarials, we observe growth inhibition synergism with low doses of this β2-selective inhibitor in artemisinin-sensitive and -resistant parasites. Finally, we demonstrate that a parasite-selective inhibitor could be used to attenuate parasite growth in vivo without appreciable toxicity to the host. Thus, the Plasmodium proteasome is a chemically tractable target that could be exploited by next-generation anti-malarial agents.","corpus_id":4410450,"score":0},{"doc_id":"27487482","title":"Crystal Structure of the Apicoplast DNA Polymerase from Plasmodium falciparum: The First Look at a Plastidic A-Family DNA Polymerase.","abstract":"Plasmodium falciparum, the primary cause of malaria, contains a non-photosynthetic plastid called the apicoplast. The apicoplast exists in most members of the phylum Apicomplexa and has its own genome along with organelle-specific enzymes for its replication. The only DNA polymerase found in the apicoplast (apPOL) was putatively acquired through horizontal gene transfer from a bacteriophage and is classified as an atypical A-family polymerase. Here, we present its crystal structure at a resolution of 2.9Å. P. falciparum apPOL, the first structural representative of a plastidic A-family polymerase, diverges from typical A-family members in two of three previously identified signature motifs and in a region not implicated by sequence. Moreover, apPOL has an additional N-terminal subdomain, the absence of which severely diminishes its 3' to 5' exonuclease activity. A compound known to be toxic to Plasmodium is a potent inhibitor of apPOL, suggesting that apPOL is a viable drug target. The structure provides new insights into the structural diversity of A-family polymerases and may facilitate structurally guided antimalarial drug design.","corpus_id":26767933,"score":0},{"doc_id":"28003005","title":"Targeting cysteine proteases from Plasmodium falciparum: A general overview, rational drug design and computational approaches for drug discovery.","abstract":"The Plasmodium falciparum cysteine proteases, also known as falcipains, are involved in different erythrocytic cycle processes of the malaria parasite, e.g. hydrolysis of host haemoglobin, erythrocyte invasion, and erythrocyte rupture. With the biochemical characterization of four falcipains so far, FP-2 (falcipain-2) and FP-3 (falcipain-3), members of the papain-like CAC1 family, are essential haemoglobinases. They could therefore be referred to as potential anti-malarial drug targets in the search for novel therapies, which could ease the burden caused by the increasing resistance to current anti-malarial drugs. This review provides a summary of the most important results, highlighting the drug design approaches essential for the understanding of the mechanism of inhibition and discovery of inhibitors against cysteine proteases from P. falciparum. Rational and computer-aided drug discovery approaches for the design of promising falcipain inhibitors are described herein, with a focus on a variety of structure-based and ligand-based modeling approaches. Moreover, the key features of ligand recognition against these targets are emphasized. This review would be of interest to scientists engaged in the development of drug design strategies to target the cysteine proteases, FP-2 and FP-3.","corpus_id":4397880,"score":0},{"doc_id":"28195463","title":"Target Elucidation by Cocrystal Structures of NADH-Ubiquinone Oxidoreductase of Plasmodium falciparum (PfNDH2) with Small Molecule To Eliminate Drug-Resistant Malaria.","abstract":"Drug-resistant malarial strains have been continuously emerging recently, which posts a great challenge for the global health. Therefore, new antimalarial drugs with novel targeting mechanisms are urgently needed for fighting drug-resistant malaria. NADH-ubiquinone oxidoreductase of Plasmodium falciparum (PfNDH2) represents a viable target for antimalarial drug development. However, the absence of structural information on PfNDH2 limited rational drug design and further development. Herein, we report high resolution crystal structures of the PfNDH2 protein for the first time in Apo-, NADH-, and RYL-552 (a new inhibitor)-bound states. The PfNDH2 inhibitor exhibits excellent potency against both drug-resistant strains in vitro and parasite-infected mice in vivo via a potential allosteric mechanism. Furthermore, it was found that the inhibitor can be used in combination with dihydroartemisinin (DHA) synergistically. These findings not only are important for malarial PfNDH2 protein-based drug development but could also have broad implications for other NDH2-containing pathogenic microorganisms such as Mycobacterium tuberculosis.","corpus_id":36645667,"score":0},{"doc_id":"29269266","title":"Biochemical studies of membrane bound Plasmodium falciparum mitochondrial L-malate:quinone oxidoreductase, a potential drug target.","abstract":"Plasmodium falciparum is an apicomplexan parasite that causes the most severe malaria in humans. Due to a lack of effective vaccines and emerging of drug resistance parasites, development of drugs with novel mechanisms of action and few side effects are imperative. To this end, ideal drug targets are those essential to parasite viability as well as absent in their mammalian hosts. The mitochondrial electron transport chain (ETC) of P. falciparum is one source of such potential targets because enzymes, such as L-malate:quinone oxidoreductase (PfMQO), in this pathway are absent humans. PfMQO catalyzes the oxidation of L-malate to oxaloacetate and the simultaneous reduction of ubiquinone to ubiquinol. It is a membrane protein, involved in three pathways (ETC, the tricarboxylic acid cycle and the fumarate cycle) and has been shown to be essential for parasite survival, at least, in the intra-erythrocytic asexual stage. These findings indicate that PfMQO would be a valuable drug target for development of antimalarial with novel mechanism of action. Up to this point in time, difficulty in producing active recombinant mitochondrial MQO has hampered biochemical characterization and targeted drug discovery with MQO. Here we report for the first time recombinant PfMQO overexpressed in bacterial membrane and the first biochemical study. Furthermore, about 113 compounds, consisting of ubiquinone binding site inhibitors and antiparasitic agents, were screened resulting in the discovery of ferulenol as a potent PfMQO inhibitor. Finally, ferulenol was shown to inhibit parasite growth and showed strong synergism in combination with atovaquone, a well-described anti-malarial and bc1 complex inhibitor.","corpus_id":46768644,"score":0}],"string":"[\n {\n \"doc_id\": \"18980703\",\n \"title\": \"Differential inhibition of high and low Mr thioredoxin reductases of parasites by organotelluriums supports the concept that low Mr thioredoxin reductases are good drug targets.\",\n \"abstract\": \"Thioredoxin reductase (TrxR), a NADPH-dependent disulfide oxidoreductase, is vital in numerous cellular processes including defence against reactive oxygen species, cell proliferation and signal transduction. TrxRs occur in 2 forms, a high Mr enzyme characterized by those of mammals, the malaria parasite Plasmodium falciparum and some worms, and a low Mr form is present in bacteria, fungi, plants and some protozoan parasites. Our hypothesis is that the differences between the forms can be exploited in the development of selective inhibitors. In this study, cyclodextrin- and sulfonic acid-derived organotelluriums known to inhibit mammalian TrxR were investigated for their relative efficacy against P. falciparum TrxR (PfTrxR), a high Mr enzyme, and Trichomonas vaginalis TrxR (TvTrxR), a low Mr form of TrxR. The results suggest that selective inhibition of low Mr TrxRs is a feasible goal.\",\n \"corpus_id\": 9065841,\n \"score\": 2\n },\n {\n \"doc_id\": \"19360125\",\n \"title\": \"Identification of proteins targeted by the thioredoxin superfamily in Plasmodium falciparum.\",\n \"abstract\": \"The malarial parasite Plasmodium falciparum possesses a functional thioredoxin and glutathione system comprising the dithiol-containing redox proteins thioredoxin (Trx) and glutaredoxin (Grx), as well as plasmoredoxin (Plrx), which is exclusively found in Plasmodium species. All three proteins belong to the thioredoxin superfamily and share a conserved Cys-X-X-Cys motif at the active site. Only a few of their target proteins, which are likely to be involved in redox reactions, are currently known. The aim of the present study was to extend our knowledge of the Trx-, Grx-, and Plrx-interactome in Plasmodium. Based on the reaction mechanism, we generated active site mutants of Trx and Grx lacking the resolving cysteine residue. These mutants were bound to affinity columns to trap target proteins from P. falciparum cell extracts after formation of intermolecular disulfide bonds. Covalently linked proteins were eluted with dithiothreitol and analyzed by mass spectrometry. For Trx and Grx, we were able to isolate 17 putatively redox-regulated proteins each. Furthermore, the approach was successfully established for Plrx, leading to the identification of 21 potential target proteins. In addition to confirming known interaction partners, we captured potential target proteins involved in various processes including protein biosynthesis, energy metabolism, and signal transduction. The identification of three enzymes involved in S-adenosylmethionine (SAM) metabolism furthermore suggests that redox control is required to balance the metabolic fluxes of SAM between methyl-group transfer reactions and polyamine synthesis. To substantiate our data, the binding of the redoxins to S-adenosyl-L-homocysteine hydrolase and ornithine aminotransferase (OAT) were verified using BIAcore surface plasmon resonance. In enzymatic assays, Trx was furthermore shown to enhance the activity of OAT. Our approach led to the discovery of several putatively redox-regulated proteins, thereby contributing to our understanding of the redox interactome in malarial parasites.\",\n \"corpus_id\": 12087168,\n \"score\": 2\n },\n {\n \"doc_id\": \"19724080\",\n \"title\": \"Structural model of the Plasmodium falciparum thioredoxin reductase:a novel target for antimalarial drugs.\",\n \"abstract\": \"BACKGROUND: Malaria, a scourge of mankind, imposes a huge socioeconomic burden in tropical countries. Emergence of multi-drug resistant malarial parasites impels us to explore novel drug targets. Thioredoxin reductase is a promising antimalarial drug target. METHODS: The Thioredoxin reductase enzyme of Plasmodium falciparum was characterized in silico and protein disorder was predicted using available online tools. Since the crystal structure of Thioredoxin reductase of P. falciparum is not yet available, its three-dimensional structure was constructed by homology modeling using the high-resolution Thioredoxin reductase type 2 of mouse as a template. Obtained model was further refined by Molecular Dynamics (MD). RESULTS: The model was stable during the simulation with the equilibrium root mean square deviation (RMSD) value of 1.2 A. Stereochemical evaluation revealed that 99.1% residues of the constructed model lie in the most favoured and allowed regions, thus, indicating a good quality model. CONCLUSION: Results of this study will provide an insight into the structure of the Thioredoxin reductase of malarial parasite and aid in rational drug designing.\",\n \"corpus_id\": 12230573,\n \"score\": 2\n },\n {\n \"doc_id\": \"20335080\",\n \"title\": \"Development of binding assays to screen ligands for Plasmodium falciparum thioredoxin and glutathione reductases by ultrafiltration and liquid chromatography/mass spectrometry.\",\n \"abstract\": \"To identify potential lead compounds for malaria drug discovery, ultrafiltration and liquid chromatography and mass spectrometry (UF and LC/MS) based binding assays were developed for the first time for Plasmodium falciparum thioredoxin (PfTrxR) and glutathione (PfGR) reductases. In the binding assays, curcuminoids (bis-demethoxycurcumin 1, demethoxycurcumin 2, and curcumin 3) were used to study the binding affinity for PfTrxR and PfGR enzymes. The optimum binding was observed when the curcumimoids mixture (1 microM) was incubated with 1 microM PfTrxR and 0.5 microM PfGR enzymes separately for 60 min at 25 degrees C. The peak areas of the ligands in the chromatogram corresponding to incubation with active PfTrxR and PfGR enzymes increased by 1.6- and 2.0-fold respectively compared to the chromatogram of test compounds incubated with denatured enzymes. Further, binding assay experiments were carried out for compound 2 under non-competitive and competitive incubation conditions with 1 microM PfTrxR and 0.5 microM PfGR enzymes, separately. The binding affinity of compound 2 was higher for both the enzymes under non-competitive incubation conditions. To validate the binding assay developed, we have tested bis-2,4-dinitrophenyl sulfide (4) which is reported as an inhibitor of PfTrxR and PfGR enzymes. Compound 4 showed greater binding affinity for both enzymes under competitive incubation conditions. The relative peak area of compound 4 increased by 3.2- and 6-fold when incubated with active PfTrxR (1 microM) and PfGR (0.5 microM) enzymes respectively compared to the peak areas of the compound in control experiments. The current method developed has a potential for automated high-throughput screening to rapidly determine the binding affinity of ligands for these enzymes.\",\n \"corpus_id\": 2886568,\n \"score\": 2\n },\n {\n \"doc_id\": \"21203490\",\n \"title\": \"Compartmentation of redox metabolism in malaria parasites.\",\n \"abstract\": \"Malaria, caused by the apicomplexan parasite Plasmodium, still represents a major threat to human health and welfare and leads to about one million human deaths annually. Plasmodium is a rapidly multiplying unicellular organism undergoing a complex developmental cycle in man and mosquito - a life style that requires rapid adaptation to various environments. In order to deal with high fluxes of reactive oxygen species and maintain redox regulatory processes and pathogenicity, Plasmodium depends upon an adequate redox balance. By systematically studying the subcellular localization of the major antioxidant and redox regulatory proteins, we obtained the first complete map of redox compartmentation in Plasmodium falciparum. We demonstrate the targeting of two plasmodial peroxiredoxins and a putative glyoxalase system to the apicoplast, a non-photosynthetic plastid. We furthermore obtained a complete picture of the compartmentation of thioredoxin- and glutaredoxin-like proteins. Notably, for the two major antioxidant redox-enzymes--glutathione reductase and thioredoxin reductase--Plasmodium makes use of alternative-translation-initiation (ATI) to achieve differential targeting. Dual localization of proteins effected by ATI is likely to occur also in other Apicomplexa and might open new avenues for therapeutic intervention.\",\n \"corpus_id\": 8837078,\n \"score\": 2\n },\n {\n \"doc_id\": \"21353756\",\n \"title\": \"Screening of natural compounds for ligands to PfTrxR by ultrafiltration and LC-MS based binding assay.\",\n \"abstract\": \"In our study, we have screened 133 structurally diverse natural compounds from the MEGx® collection of AnalytiCon Discovery and three synthetic hispolone analogs for binding affinity to Plasmodium falciparum thioredoxin reductase (PfTrxR) using an ultrafiltration (UF) and liquid chromatography (LC/MS) based ligand-binding assay newly developed in our laboratory. PfTrxR catalyzes the reduction of thioredoxin (PfTrx) protein. In reduced form, PfTrx is essentially involved in the antioxidative defense and redox regulation of P. falciparum. Nine compounds (yohimbine (1), catharanthine (2), vobasine (3), gnetifolin E (4), quinidine N-oxide (5), 11-hydroxycoronaridine (6), hispolone (7), hispolone methyl ether (8), and hernagine (9)) displayed binding affinity for PfTrxR at 1μM. The ranking order of compound's binding affinities for PfTrxR is 7>6>2>4>5>8>1>9>3. On the other hand, compounds 6, 7, 2 and 8 demonstrated specific binding to the active site of PfTrxR, when ligands were tested in an equimolar mixture of 1 μM.\",\n \"corpus_id\": 11210527,\n \"score\": 2\n },\n {\n \"doc_id\": \"21567357\",\n \"title\": \"Identification of oleamide in Guatteria recurvisepala by LC/MS-based Plasmodium falciparum thioredoxin reductase ligand binding method.\",\n \"abstract\": \"Our current research on applications of mass spectrometry to natural product drug discovery against malaria aims to screen plant extracts for new ligands to Plasmodium falciparum thioredoxin reductase (PfTrxR) followed by their identification and structure elucidation. PfTrxR is involved in the antioxidant defense and redox regulation of the parasite and is validated as a promising target for therapeutic intervention against malaria. In the present study, detannified methanol extracts from Guatteria recurvisepala, Licania kallunkiae, and Topobea watsonii were screened for ligands to PfTrxR using ultrafiltration and liquid chromatography/mass spectrometry-based binding experiments. The PfTrxR ligand identified in the extract of Guatteria recurvisepala displayed a relative binding affinity of 3.5-fold when incubated with 1 μM PfTrxR. The ligand corresponding to the protonated molecule m/z 282.2792 [M+ H]+ was eluted at a retention time of 17.95 min in a 20-min gradient of 95% B consisting of (A) 0.1%formic acid in 95% H₂O-5% ACN, and (B) 0.1% formic acid in 95% ACN-5% H₂O in an LC-QTOF-MS.Tandem MS of the protonated molecule m/z 282.2792 [M + H]+, C₁₈H₃₆NO (DBE: 2; error: 1.13 ppm) resulted in two daughter ions m/z 265.2516[M + H-NH₃]+ (DBE: 3; error: 0.35 ppm) and m/z 247.2405 [M + H-NH₃-H₂O] +, (DBE: 4; error:2.26 ppm). The PfTrxR ligand was identified as oleamide and confirmed by comparison of the retention time, molecular formula, accurate mass,and double bond equivalence with the standard oleamide. This is the first report on the identification of oleamide as a PfTrxR ligand from Guatteria recurvisepala R. E. Fr. and the corresponding in vitro activity against P. falciparum strain K1 (IC₅₀ 4.29 μg/mL).\",\n \"corpus_id\": 38294373,\n \"score\": 2\n },\n {\n \"doc_id\": \"21750537\",\n \"title\": \"Crystal structure of the human thioredoxin reductase-thioredoxin complex.\",\n \"abstract\": \"Thioredoxin reductase 1 (TrxR1) is a homodimeric flavoprotein crucially involved in the regulation of cellular redox homeostasis, growth, and differentiation. Its importance in various diseases makes TrxR1 a highly interesting drug target. Here we present the first crystal structures of human TrxR1 in complex with its substrate thioredoxin (Trx). The carboxy-terminal redox centre is found about 20 Å apart from the amino-terminal redox centre, with no major conformational changes in TrxR or Trx. Thus, our structure confirms that the enzyme uses a flexible C-terminal arm for electron transport to its substrates, which is stabilized by a guiding bar for controlled transfer. This notion is supported by mutational analyses. Furthermore, essential residues of the interface region were characterized both structurally and functionally. The structure provides templates for future drug design, and contributes to our understanding of redox regulatory processes in mammals.\",\n \"corpus_id\": 35983486,\n \"score\": 2\n },\n {\n \"doc_id\": \"22177949\",\n \"title\": \"Investigation of a potential mechanism for the inhibition of SmTGR by Auranofin and its implications for Plasmodium falciparum inhibition.\",\n \"abstract\": \"Schistosoma mansoni and Plasmodium falciparum are pathogen parasites that spend part of their lives in the blood stream of the human host and are therefore heavily exposed to fluxes of toxic reactive oxygen species (ROS). SmTGR, an essential enzyme of the S. mansoni ROS detoxification machinery, is known to be inhibited by Auranofin although the inhibition mechanism has not been completely clarified. Auranofin also kills P. falciparum, even if its molecular targets are unknown. Here, we used computational and docking techniques to investigate the molecular mechanism of interaction between SmTGR and Auranofin. Furthermore, we took advantage of the homology relationship and of docking studies to assess if PfTR, the SmTGR malaria parasite homologue, can be a putative target for Auranofin. Our findings support a recently hypothesized molecular mechanism of inhibition for SmTGR and suggest that PfTR is indeed a possible and attractive drug target in P. falciparum.\",\n \"corpus_id\": 26487877,\n \"score\": 2\n },\n {\n \"doc_id\": \"22612231\",\n \"title\": \"Discovery and biochemical characterization of Plasmodium thioredoxin reductase inhibitors from an antimalarial set.\",\n \"abstract\": \"Plasmodium falciparum is the most prevalent and deadly species of the human malaria parasites, and thioredoxin reductase (TrxR) is an enzyme involved in the redox response to oxidative stress. Essential for P. falciparum survival, the enzyme has been highlighted as a promising target for novel antimalarial drugs. Here we report the discovery and characterization of seven molecules from an antimalarial set of 13533 compounds through single-target TrxR biochemical screens. We have produced high-purity, full-length, recombinant native enzyme from four Plasmodium species, and thioredoxin substrates from P. falciparum and Rattus norvegicus. The enzymes were screened using a unique, high-throughput, in vitro native substrate assay, and we have observed selectivity between the Plasmodium species and the mammalian form of the enzyme. This has indicated differences in their biomolecular profiles and has provided valuable insights into the biochemical mechanisms of action of compounds with proven antimalarial activity.\",\n \"corpus_id\": 9981259,\n \"score\": 2\n },\n {\n \"doc_id\": \"22847705\",\n \"title\": \"Development of liquid chromatography/mass spectrometry based screening assay for PfTrxR inhibitors using relative quantitation of intact thioredoxin.\",\n \"abstract\": \"RATIONALE: Plasmodium falciparum (Pf) thioredoxin reductase (TrxR) catalyzes the reduction of thioredoxin disulfide (Trx-S(2)) to thioredoxin dithiol (Trx-(SH)(2)) that is essential for antioxidant defense mechanism and DNA synthesis in the parasite and is a validated drug target for new antimalarial agents. METHODS: In this study, we have developed a liquid chromatography/mass spectrometry (LC/MS)-based functional assay to identify inhibitors of PfTrxR by quantifying the product formed (Trx-(SH)(2)) in the enzymatic reaction. Relative quantitation of the reaction product (intact Trx-(SH)(2)) was carried out using an Agilent 6520 QTOF mass spectrometer equipped with a positive mode electrospray ionization (ESI) source. RESULTS: The calibration curve prepared for Trx-(SH)(2) at concentrations ranging from 1.8 to 116.5 µg/mL was linear (R(2) >0.998). The limit of detection (LOD) and limit of quantification (LOQ) of Trx-(SH)(2) were at 0.45 and 1.8 µg/mL respectively. To validate the developed functional assay we have screened reference compounds 1, 2 and 3 for their PfTrxR inhibitory activity and ten natural compounds (at 10 μM) which were earlier identified as ligands of PfTrxR by a UF-LC/MS based binding assay. CONCLUSIONS: The developed LC/MS-based functional assay for identification of inhibitors of PfTrxR is a sensitive and reliable method that is also amendable for high-throughput format. This is the first representation of a relative quantitation of intact Trx-(SH)(2) using LC/MS.\",\n \"corpus_id\": 25713067,\n \"score\": 2\n },\n {\n \"doc_id\": \"22939033\",\n \"title\": \"Thioredoxin and glutathione systems in Plasmodium falciparum.\",\n \"abstract\": \"Despite a 50% decrease in malaria infections between 2000 and 2010, malaria is still one of the three leading infectious diseases with an estimated 216 million cases worldwide in 2010. More than 90% of all malaria infections were caused by Plasmodium falciparum, a unicellular eukaryotic parasite that faces oxidative stress challenges while developing in Anopheles mosquitoes and humans. Reactive oxygen and nitrogen species threatening the parasite are either endogenously produced by heme derived from hemoglobin degradation or they are from exogenous sources such as the host immune defense. In order to maintain the intracellular redox balance, P. falciparum employs a complex thioredoxin and glutathione system based on the thioredoxin reductase/thioredoxin and glutathione reductase/glutathione couples. P. falciparum thioredoxin reductase reduces thioredoxin and a range of low molecular weight compounds, while glutathione reductase is highly specific for its substrate glutathione disulfide. Since Plasmodium spp. lack catalase and a classical glutathione peroxidase, their redox balance depends on a complex set of five peroxiredoxins differentially located in the cytosol, apicoplast, mitochondria, and nucleus with partially overlapping substrate preferences. Moreover, P. falciparum employs a set of members belonging to the thioredoxin superfamily such as three thioredoxins, two thioredoxin-like proteins, a dithiol and three monocysteine glutaredoxins, and a redox-active plasmoredoxin with largely redundant functions. This review aims at summarizing our current knowledge on the functional redox networks of the malaria parasite P. falciparum.\",\n \"corpus_id\": 8493014,\n \"score\": 2\n },\n {\n \"doc_id\": \"23845423\",\n \"title\": \"Crystal structure of the Plasmodium falciparum thioredoxin reductase-thioredoxin complex.\",\n \"abstract\": \"Over the last decades, malaria parasites have been rapidly developing resistance against antimalarial drugs, which underlines the need for novel drug targets. Thioredoxin reductase (TrxR) is crucially involved in redox homeostasis and essential for Plasmodium falciparum. Here, we report the first crystal structure of P. falciparum TrxR bound to its substrate thioredoxin 1. Upon complex formation, the flexible C-terminal arm and an insertion loop of PfTrxR are rearranged, suggesting that the C-terminal arm changes its conformation during catalysis similar to human TrxR. Striking differences between P. falciparum and human TrxR are a Plasmodium-specific insertion and the conformation of the C-terminal arm, which lead to considerable differences in thioredoxin binding and disulfide reduction. Moreover, we functionally analyzed amino acid residues involved in substrate binding and in the architecture of the intersubunit cavity, which is a known binding site for disulfide reductase inhibitors. Cell biological experiments indicate that P. falciparum TrxR is indeed targeted in the parasite by specific inhibitors with antimalarial activity. Differences between P. falciparum and human TrxR and details on substrate reduction and inhibitor binding provide the first solid basis for structure-based drug development and lead optimization.\",\n \"corpus_id\": 206212834,\n \"score\": 2\n },\n {\n \"doc_id\": \"24175748\",\n \"title\": \"Targeting the redox metabolism of Plasmodium falciparum.\",\n \"abstract\": \"Targeting the redox metabolism of Plasmodium falciparum to create a fatal overload of oxidative stress is a route to explore the discovery of new antimalarial drugs. There are three main possibilities to target the redox metabolism of P. falciparum at the erythrocytic stage: selective targeting and inhibition of a redox P. falciparum protein or enzyme; oxidant drugs targeting essential parasite components and heme by-products; and redox cycler drugs targeting the parasitized red blood cell. Oxidants and redox cycler agents, with or without specific targets, may disrupt the fragile parasitized erythrocyte redox-dependent architecture given that: redox equilibrium plays a vital role at the erythrocytic stage; P. falciparum possesses major NADPH-dependent redox systems, such as glutathione and thioredoxin ones; and the protein-NADPH-dependent phosphorylation-dephosphorylation process is involved in building new permeation pathways and channels for the nutrient-waste import-export traffic of the parasite.\",\n \"corpus_id\": 19246212,\n \"score\": 2\n },\n {\n \"doc_id\": \"24443991\",\n \"title\": \"Determination of antiplasmodial activity and binding affinity of curcumin and demethoxycurcumin towards PfTrxR.\",\n \"abstract\": \"In our study, the inhibitory activity of curcuminoids towards Plasmodium falciparum thioredoxin reductase (PfTrxR) was determined using LC-MS-based functional assay and showed that only demethoxycurcumin (DMC) inhibited PfTrxR (IC50: 2 μM). In silico molecular modelling was used to ascertain and further confirm that the binding affinities of curcumin and DMC are towards the dimer interface of PfTrxR. The in vitro antiplasmodial activities of curcumin and DMC were evaluated and shown to be active against chloroquine (CQ)-sensitive (D6 clone) and moderately active against CQ-resistant (W2 clone) strains of Plasmodium falciparum while no cytotoxicity was observed against Vero cells.\",\n \"corpus_id\": 205839668,\n \"score\": 2\n },\n {\n \"doc_id\": \"25198774\",\n \"title\": \"PfalDB: an integrated drug target and chemical database for Plasmodium falciparum.\",\n \"abstract\": \"Plasmodium falciparum is one of the deadliest protozoan parasite species among those that cause malaria. Uncontrolled use of antimalarial drugs has resulted in evolutionary selection pressure favoring high levels of resistance to antimalarials; currently P.falciparum shows resistance to all classes of antimalarials. Therefore it is essential to identify novel drug targets, and design selective anti-malarials which can overcome resistance. While many drug targets are freely available in various public domain resources, a single comprehensive source of data containing easily searchable and retrievable information is currently lacking. To facilitate the total integration and mining of data emerging from different drug consortia and also to prioritize drug targets for structure-based drug design, an open-access, inclusive comprehensive database for Plasmodium falciparum was established. Meta data of known/modeled structures along with binding site parameters of drug targets have been included in the database. Additionally, chemical compounds showing a positive inhibitory assay against Plasmodium falciparum or known drug targets have also been provided. The database is accessible at http://pfaldb.jnu.ac.in. The database provides diverse information regarding the structure, sequence, stage specific gene expression, pathway, action mechanism, essentiality and druggability for each drug target, and literature to assess the validation status of individual drug targets. It also includes information on individual anti-malarials with their activity and bioassay.\",\n \"corpus_id\": 21959986,\n \"score\": 2\n },\n {\n \"doc_id\": \"26111176\",\n \"title\": \"Plasmodium falciparum Thioredoxin Reductase (PfTrxR) and Its Role as a Target for New Antimalarial Discovery.\",\n \"abstract\": \"The growing resistance to current antimalarial drugs is a major concern for global public health. The pressing need for new antimalarials has led to an increase in research focused on the Plasmodium parasites that cause human malaria. Thioredoxin reductase (TrxR), an enzyme needed to maintain redox equilibrium in Plasmodium species, is a promising target for new antimalarials. This review paper provides an overview of the structure and function of TrxR, discusses similarities and differences between the thioredoxin reductases (TrxRs) of different Plasmodium species and the human forms of the enzyme, gives an overview of modeling Plasmodium infections in animals, and suggests the role of Trx functions in antimalarial drug resistance. TrxR of Plasmodium falciparum is a central focus of this paper since it is the only Plasmodium TrxR that has been crystallized and P. falciparum is the species that causes most malaria cases. It is anticipated that the information summarized here will give insight and stimulate new directions in which research might be most beneficial.\",\n \"corpus_id\": 8764389,\n \"score\": 2\n },\n {\n \"doc_id\": \"27043496\",\n \"title\": \"Preliminary LC-MS Based Screening for Inhibitors of Plasmodium falciparum Thioredoxin Reductase (PfTrxR) among a Set of Antimalarials from the Malaria Box.\",\n \"abstract\": \"Plasmodium falciparum thioredoxin reductase (PfTrxR) has been identified as a potential drug target to combat growing antimalarial drug resistance. Medicines for Malaria Venture (MMV) has pre-screened and identified a set of 400 antimalarial compounds called the Malaria Box. From those, we have evaluated their mechanisms of action through inhibition of PfTrxR and found new active chemical scaffolds. Five compounds with significant PfTrxR inhibitory activity, with IC50 values ranging from 0.9-7.5 µM against the target enzyme, were found out of the Malaria Box.\",\n \"corpus_id\": 39018362,\n \"score\": 2\n },\n {\n \"doc_id\": \"19888680\",\n \"title\": \"NMR assignments of oxidised thioredoxin from Plasmodium falciparum.\",\n \"abstract\": \"During its life cycle, the malaria parasite Plasmodium falciparum is found intracellular to human erythrocytes, where its survival and ability to multiply critically depends on the control of the environment redox state. Thioredoxin is a small protein containing 104 amino acids that is part of the parasite specific redox system. During the catalytic cycle it alternates between a reduced and oxidised form. Here we report the complete resonance assignment of Plasmodium falciparum thioredoxin in its oxidized form by heteronuclear multidimensional spectroscopy. The obtained chemical shifts differ significantly from those reported earlier for this protein in its reduced state.\",\n \"corpus_id\": 2456950,\n \"score\": 1\n },\n {\n \"doc_id\": \"22355694\",\n \"title\": \"Structural insights into thioredoxin-2: a component of malaria parasite protein secretion machinery.\",\n \"abstract\": \"Thioredoxins are vital components of Plasmodium proteome and act as both reducing agents and protein disulfide reductases. The malaria parasite P. falciparum thioredoxin-2 (PfTrx-2) is part of the multi-protein complex embedded within the parasite parasitophorous vacuolar membrane (PVM) which purportedly directs protein secretion. We have characterized structural and enzymatic features of PfTrx-2, and we show that PfTrx-2 adopts a canonical thioredoxin fold but with significant structural differences in its N-terminus. Our confocal localization data suggest distinct PVM residency of PfTrx-2. Based on the crystal structure of PfTrx-2, we screened and tested small molecule drug-like libraries for compounds which target unique structural features of PfTrx-2. Disruption of PfTrx-2 interactions using specific inhibitors may result in a dysfunctional parasite translocon that is rendered unable to secrete pathogenic proteins into hosts. This approach therefore offers a new focus for anti-malarial drug development.\",\n \"corpus_id\": 16902108,\n \"score\": 1\n },\n {\n \"doc_id\": \"22392134\",\n \"title\": \"Cloning and characterization of Plasmodium vivax thioredoxin peroxidase-1.\",\n \"abstract\": \"Reactive oxygen species produced from hemoglobin digestion and the host immune system could have adverse effects on malaria parasites. To protect themselves, malaria parasites are highly dependent on the antioxidant enzymes, including superoxide dismutases and thioredoxin-dependent peroxidases. To date, several thioredoxin peroxidases (TPx) have been characterized in Plasmodium falciparum, but the TPx in Plasmodium vivax has not yet been characterized. The complete sequence of gene coding for thioredoxin peroxidase-1 of P. vivax (PvTPx-1) was amplified by PCR and cloned. Using the recombinant PvTPx-1 (rPvTPx-1), polyclonal antibody was produced in mice for immunolocalization of the enzyme in the parasite. The antioxidant activity of rPvTPx-1 was evaluated by mixed-function oxidation assay. PvTPx-1 has two conserved cysteine residues in the amino acid sequence at the positions 50 and 170 which formed a dimer under a non-reducing condition. Using a thiol mixed-function oxidation assay, the antioxidant activity of rPvTPx-1 was revealed. Indirect immunofluorescence microscopy with the specific antibody indicated that PvTPx-1 was expressed in the cytoplasm of the erythrocytic stage of the parasite in a dots-like pattern. The results suggest that P. vivax uses TPx-1 to reduce and detoxify hydrogen peroxides in order to maintain their redox homeostasis and proliferation in the host body.\",\n \"corpus_id\": 14643225,\n \"score\": 1\n },\n {\n \"doc_id\": \"23649394\",\n \"title\": \"[Structural biology for developing antimalarial compounds].\",\n \"abstract\": \"The human malaria parasite Plasmodium falciparum is responsible for the death of more than a million people each year. The emergence of strains of this malaria parasite resistant to conventional drug therapy has stimulated the search for antimalarial compounds with novel modes of action. Here the structure-function relationship studies for two Plasmodium proteins are presented. One example is the structural studies for S-adenosyl-L-homocysteine hydrolase from Plasmodium falciparum (PfSAHH) and the other example is those for 1-deoxy-D-xylulose reductoisomerase from Plasmodium falciparum (PfDXR). In the former study, the clue for design of species specific PfSAHH inhibitors was obtained by the structural comparison of the active site of PfSAHH with that of human SAHH (HsSAHH). Our study revealed that the inhibitor selectivity depends on the difference of only one amino acid residue in the active site; Cys59 in PfSAHH vs. Thr60 in HsSAHH. In the latter study, the inhibition of PfDXR enzyme by fosmidomycin has proved to be efficient in the treatment of uncomplicated malaria in recent clinical trials conducted in Gabon and Thailand. Our crystal structure analyses of PfDXR/inhibitor complexes revealed the molecular basis of fosmidomycin's action in P. falciparum. We expect that the structure-function relationship studies on Plasmodium proteins are useful for developing the more effective antimalarial compounds.\",\n \"corpus_id\": 34691633,\n \"score\": 1\n },\n {\n \"doc_id\": \"25475729\",\n \"title\": \"Crystal structure and solution characterization of the thioredoxin-2 from Plasmodium falciparum, a constituent of an essential parasitic protein export complex.\",\n \"abstract\": \"Survival of the malaria parasite Plasmodium falciparum when it infects red blood cells depends upon its ability to export hundreds of its proteins beyond an encasing vacuole. Protein export is mediated by a parasite-derived protein complex, the Plasmodium translocon of exported proteins (PTEX), and requires unfolding of the different cargos prior to their translocation across the vacuolar membrane. Unfolding is performed by the AAA+protein unfoldase HSP101/ClpB2 and the thioredoxin-2 enzyme (TRX2). Protein trafficking is dramatically impaired in parasites with defective HSP101 or lacking TRX2. These two PTEX subunits drive export and are targets for the design of a novel class of antimalarials: protein export inhibitors. To rationalize inhibitor design, we solved the crystal structure of Pfal-TRX2 at 2.2-Å resolution. Within the asymmetric unit, the three different copies of this protein disulfide reductase sample its two redox catalytic states. Size exclusion chromatography and small-angle X-ray scattering (SAXS) analyses demonstrate that Pfal-TRX2 is monomeric in solution. A non-conserved N-terminal extension precedes the canonical thioredoxin-fold; although it is not observed in our structure, our solution analysis suggests it is flexible in contrast to Plasmodium thioredoxin-1. This represents a first step towards the reconstitution of the entire PTEX for mechanistic and structural studies.\",\n \"corpus_id\": 205936634,\n \"score\": 1\n },\n {\n \"doc_id\": \"28755265\",\n \"title\": \"An in silico strategy for identification of novel drug targets against Plasmodium falciparum.\",\n \"abstract\": \"The apicomplexan parasite Plasmodium falciparum is responsible for global malaria burden. With the reported resistance to artemisinin chemotherapy, there is an urgent need to maintain early phase drug discovery and identify novel drug targets for successful eradication of the pathogen from the host. In our previous work on comparative genomics study for identification of putative essential genes and therapeutic candidates in P. falciparum, we predicted 11 proteins as anti-malarial drug targets from PlasmoDB database. In this paper, we made an attempt for identification of novel drug targets in P. falciparum genome using a sequence of computational methods from Malaria Parasite Metabolic Pathway database. The study reported the identification of 71 proteins as potential drug targets for anti-malarial interventions. Furthermore, homology modeling and molecular dynamic simulation study of one of the potential drug targets, aminodeoxychorismate lyase, was carried to predict the 3D structure of the protein. Structure and ligand-based drug designing reported MMV019742 from Pathogen Box and TCAMS-141515 from GSK-TCAMS library as potential hits. The reliability of the binding mode of the inhibitors is confirmed by GROMACS for a simulation time of 20 ns in water environment. This will be helpful for experimental validation of the small-molecule inhibitor.\",\n \"corpus_id\": 4048428,\n \"score\": 1\n },\n {\n \"doc_id\": \"18037315\",\n \"title\": \"In silico screening against wild-type and mutant Plasmodium falciparum dihydrofolate reductase.\",\n \"abstract\": \"Modeling studies were performed on known inhibitors of wild-type as well as quadruple mutant Plasmodium falciparum dihydrofolate reductase (DHFR). GOLD was used to dock 31 pyrimethamine derivatives into the active site of DHFR obtained from the X-ray crystal structures 1J3I.pdb and 1J3K.pdb. Predicted binding affinities from a scoring function were analyzed and evaluated in order to develop criteria for selecting compounds having a greater chance of activity versus wild-type and resistant strains of P. falciparum for future high-throughput screening experiments.\",\n \"corpus_id\": 8425934,\n \"score\": 0\n },\n {\n \"doc_id\": \"19146480\",\n \"title\": \"Exploiting structural analysis, in silico screening, and serendipity to identify novel inhibitors of drug-resistant falciparum malaria.\",\n \"abstract\": \"Plasmodium falciparum thymidylate synthase-dihydrofolate reductase (TS-DHFR) is an essential enzyme in folate biosynthesis and a major malarial drug target. This bifunctional enzyme thus presents different design approaches for developing novel inhibitors against drug-resistant mutants. We performed a high-throughput in silico screen of a database of diverse, drug-like molecules against a non-active-site pocket of TS-DHFR. The top compounds from this virtual screen were evaluated by in vitro enzymatic and cellular culture studies. Three compounds active to 20 microM IC(50)'s in both wildtype and antifolate-resistant P. falciparum parasites were identified; moreover, no inhibition of human DHFR enzyme was observed, indicating that the inhibitory effects appeared to be parasite-specific. Notably, all three compounds had a biguanide scaffold. However, relative free energy of binding calculations suggested that the compounds might preferentially interact with the active site over the screened non-active-site region. To resolve the two possible modes of binding, co-crystallization studies of the compounds complexed with TS-DHFR enzyme were performed. Surprisingly, the structural analysis revealed that these novel, biguanide compounds do indeed bind at the active site of DHFR and additionally revealed the molecular basis by which they overcome drug resistance. To our knowledge, these are the first co-crystal structures of novel, biguanide, non-WR99210 compounds that are active against folate-resistant malaria parasites in cell culture.\",\n \"corpus_id\": 25802336,\n \"score\": 0\n },\n {\n \"doc_id\": \"19174148\",\n \"title\": \"Plasmodium falciparum signal peptide peptidase is a promising drug target against blood stage malaria.\",\n \"abstract\": \"The resistance of malaria parasites to current anti-malarial drugs is an issue of major concern globally. Recently we identified a Plasmodium falciparum cell membrane aspartyl protease, which binds to erythrocyte band 3, and is involved in merozoite invasion. Here we report the complete primary structure of P. falciparum signal peptide peptidase (PfSPP), and demonstrate that it is essential for parasite invasion and growth in human erythrocytes. Gene silencing suggests that PfSPP may be essential for parasite survival in human erythrocytes. Remarkably, mammalian signal peptide peptidase inhibitors (Z-LL)(2)-ketone and L-685,458 effectively inhibited malaria parasite invasion as well as growth in human erythrocytes. In contrast, DAPT, an inhibitor of a related gamma-secretase/presenilin-1, was ineffective. Thus, SPP inhibitors specific for PfSPP may function as potent anti-malarial drugs against the blood stage malaria.\",\n \"corpus_id\": 38590623,\n \"score\": 0\n },\n {\n \"doc_id\": \"19196988\",\n \"title\": \"Structural basis for the inhibition of the essential Plasmodium falciparum M1 neutral aminopeptidase.\",\n \"abstract\": \"Plasmodium falciparum parasites are responsible for the major global disease malaria, which results in >2 million deaths each year. With the rise of drug-resistant malarial parasites, novel drug targets and lead compounds are urgently required for the development of new therapeutic strategies. Here, we address this important problem by targeting the malarial neutral aminopeptidases that are involved in the terminal stages of hemoglobin digestion and essential for the provision of amino acids used for parasite growth and development within the erythrocyte. We characterize the structure and substrate specificity of one such aminopeptidase, PfA-M1, a validated drug target. The X-ray crystal structure of PfA-M1 alone and in complex with the generic inhibitor, bestatin, and a phosphinate dipeptide analogue with potent in vitro and in vivo antimalarial activity, hPheP[CH(2)]Phe, reveals features within the protease active site that are critical to its function as an aminopeptidase and can be exploited for drug development. These results set the groundwork for the development of antimalarial therapeutics that target the neutral aminopeptidases of the parasite.\",\n \"corpus_id\": 26034035,\n \"score\": 0\n },\n {\n \"doc_id\": \"19285084\",\n \"title\": \"Crystal structures of the histo-aspartic protease (HAP) from Plasmodium falciparum.\",\n \"abstract\": \"The structures of recombinant histo-aspartic protease (HAP) from malaria-causing parasite Plasmodium falciparum as apoenzyme and in complex with two inhibitors, pepstatin A and KNI-10006, were solved at 2.5-, 3.3-, and 3.05-A resolutions, respectively. In the apoenzyme crystals, HAP forms a tight dimer not seen previously in any aspartic protease. The interactions between the monomers affect the conformation of two flexible loops, the functionally important \\\"flap\\\" (residues 70-83) and its structural equivalent in the C-terminal domain (residues 238-245), as well as the orientation of helix 225-235. The flap is found in an open conformation in the apoenzyme. Unexpectedly, the active site of the apoenzyme contains a zinc ion tightly bound to His32 and Asp215 from one monomer and to Glu278A from the other monomer, with the coordination of Zn resembling that seen in metalloproteases. The flap is closed in the structure of the pepstatin A complex, whereas it is open in the complex with KNI-10006. Although the binding mode of pepstatin A is significantly different from that in other pepsin-like aspartic proteases, its location in the active site makes unlikely the previously proposed hypothesis that HAP is a serine protease. The binding mode of KNI-10006 is unusual compared with the binding of other inhibitors from the KNI series to aspartic proteases. The novel features of the HAP active site could facilitate design of specific inhibitors used in the development of antimalarial drugs.\",\n \"corpus_id\": 16254507,\n \"score\": 0\n },\n {\n \"doc_id\": \"19827093\",\n \"title\": \"The crystal structures of macrophage migration inhibitory factor from Plasmodium falciparum and Plasmodium berghei.\",\n \"abstract\": \"Malaria, caused by Plasmodium falciparum and related parasites, is responsible for millions of deaths each year, mainly from complications arising from the blood stages of its life cycle. Macrophage migration inhibitory factor (MIF), a protein expressed by the parasite during these stages, has been characterized in mammals as a cytokine involved in a broad spectrum of immune responses. It also possesses two catalytic activities, a tautomerase and an oxidoreductase, though the physiological significance of neither reaction is known. Here, we have determined the crystal structure of MIF from two malaria parasites, Plasmodium falciparum and Plasmodium berghei at 2.2 A and 1.8 A, respectively. The structures have an alpha/beta fold and each reveals a trimer, in agreement with the results of analytical ultracentrifugation. We observed open and closed active sites, these being distinguished by movements of proline-1, the catalytic base in the tautomerase reaction. These states correlate with the covalent modification of cysteine 2 to form a mercaptoethanol adduct, an observation confirmed by mass spectrometry. The Plasmodium MIFs have a different pattern of conserved cysteine residues to the mammalian MIFs and the side chain of Cys58, which is implicated in the oxidoreductase activity, is buried. This observation and the evident redox reactivity of Cys2 suggest quite different oxidoreductase characteristics. Finally, we show in pull-down assays that Plasmodium MIF binds to the cell surface receptor CD74, a known mammalian MIF receptor implying that parasite MIF has the ability to interfere with, or modulate, host MIF activity through a competitive binding mechanism.\",\n \"corpus_id\": 13241233,\n \"score\": 0\n },\n {\n \"doc_id\": \"19845508\",\n \"title\": \"Comparison of the cellular and biochemical properties of Plasmodium falciparum choline and ethanolamine kinases.\",\n \"abstract\": \"The proliferation of the malaria-causing parasite Plasmodium falciparum within the erythrocyte is concomitant with massive phosphatidylcholine and phosphatidylethanolamine biosynthesis. Based on pharmacological and genetic data, de novo biosynthesis pathways of both phospholipids appear to be essential for parasite survival. The present study characterizes PfCK (P. falciparum choline kinase) and PfEK (P. falciparum ethanolamine kinase), which catalyse the first enzymatic steps of these essential metabolic pathways. Recombinant PfCK and PfEK were expressed as His6-tagged fusion proteins from overexpressing Escherichia coli strains, then purified to homogeneity and characterized. Using murine polyclonal antibodies against recombinant kinases, PfCK and PfEK were shown to be localized within the parasite cytoplasm. Protein expression levels increased during erythrocytic development. PfCK and PfEK appeared to be specific to their respective substrates and followed Michaelis-Menten kinetics. The Km value of PfCK for choline was 135.3+/-15.5 microM. PfCK was also able to phosphorylate ethanolamine with a very low affinity. PfEK was found to be an ethanolamine-specific kinase (Km=475.7+/-80.2 microM for ethanolamine). The quaternary ammonium compound hemicholinium-3 and an ethanolamine analogue, 2-amino-1-butanol, selectively inhibited PfCK or PfEK. In contrast, the bis-thiazolium compound T3, which was designed as a choline analogue and is currently in clinical trials for antimalarial treatment, affected PfCK and PfEK activities similarly. Inhibition exerted by T3 was competitive for both PfCK and PfEK and correlated with the impairment of cellular phosphatidylcholine biosynthesis. Comparative analyses of sequences and structures for both kinase types gave insights into their specific inhibition profiles and into the dual capacity of T3 to inhibit both PfCK and PfEK.\",\n \"corpus_id\": 5875081,\n \"score\": 0\n },\n {\n \"doc_id\": \"20133789\",\n \"title\": \"Structure of the Plasmodium falciparum M17 aminopeptidase and significance for the design of drugs targeting the neutral exopeptidases.\",\n \"abstract\": \"Current therapeutics and prophylactics for malaria are under severe challenge as a result of the rapid emergence of drug-resistant parasites. The human malaria parasite Plasmodium falciparum expresses two neutral aminopeptidases, PfA-M1 and PfA-M17, which function in regulating the intracellular pool of amino acids required for growth and development inside the red blood cell. These enzymes are essential for parasite viability and are validated therapeutic targets. We previously reported the X-ray crystal structure of the monomeric PfA-M1 and proposed a mechanism for substrate entry and free amino acid release from the active site. Here, we present the X-ray crystal structure of the hexameric leucine aminopeptidase, PfA-M17, alone and in complex with two inhibitors with antimalarial activity. The six active sites of the PfA-M17 hexamer are arranged in a disc-like fashion so that they are orientated inwards to form a central catalytic cavity; flexible loops that sit at each of the six entrances to the catalytic cavern function to regulate substrate access. In stark contrast to PfA-M1, PfA-M17 has a narrow and hydrophobic primary specificity pocket which accounts for its highly restricted substrate specificity. We also explicate the essential roles for the metal-binding centers in these enzymes (two in PfA-M17 and one in PfA-M1) in both substrate and drug binding. Our detailed understanding of the PfA-M1 and PfA-M17 active sites now permits a rational approach in the development of a unique class of two-target and/or combination antimalarial therapy.\",\n \"corpus_id\": 25137010,\n \"score\": 0\n },\n {\n \"doc_id\": \"20480551\",\n \"title\": \"Targeting Plasmodium falciparum purine salvage enzymes: a look at structure-based drug development.\",\n \"abstract\": \"New antimalarials are needed due to the rapid development of resistance to currently deployed drugs. Because Plasmodium species are unable to synthesize purines, purine salvage pathways have been proposed as novel anti-malarial targets. The purine salvage pathway in Plasmodium is streamlined with adenosine deaminase (ADA), purine nucleoside phosphorylase (PNP) and hypoxanthine-xanthine-guanine-phosphoribosyltransferase (HXGPRT) representing the major pathway for purine acquisition. Plasmodium falciparum enzymes PfADA and PfPNP have unique dual specificity that enable them to act upon methylthiopurines resulting from polyamine synthesis. Thus Plasmodium ADA and PNP function in both purine salvage and purine recycling. Genetic studies have confirmed the importance of Plasmodium PNP for viability of malaria parasites. Immucillins, powerful picomolar transition state inhibitors of PNP, are active against cultured Plasmodium falciparum and inhibit all Plasmodium PNPs tested. Several immucillins have undergone human clinical trials, and these compounds represent a new class of compounds with potential activity against human malarias.\",\n \"corpus_id\": 45808723,\n \"score\": 0\n },\n {\n \"doc_id\": \"20702404\",\n \"title\": \"Novel inhibitors of Plasmodium falciparum dihydroorotate dehydrogenase with anti-malarial activity in the mouse model.\",\n \"abstract\": \"Plasmodium falciparum, the causative agent of the most deadly form of human malaria, is unable to salvage pyrimidines and must rely on de novo biosynthesis for survival. Dihydroorotate dehydrogenase (DHODH) catalyzes the rate-limiting step in the pyrimidine biosynthetic pathway and represents a potential target for anti-malarial therapy. A high throughput screen and subsequent medicinal chemistry program identified a series of N-alkyl-5-(1H-benzimidazol-1-yl)thiophene-2-carboxamides with low nanomolar in vitro potency against DHODH from P. falciparum, P. vivax, and P. berghei. The compounds were selective for the parasite enzymes over human DHODH, and x-ray structural data on the analog Genz-667348, demonstrated that species selectivity could be attributed to amino acid differences in the inhibitor-binding site. Compounds from this series demonstrated in vitro potency against the 3D7 and Dd2 strains of P. falciparum, good tolerability and oral exposure in the mouse, and ED(50) values in the 4-day murine P. berghei efficacy model of 13-21 mg/kg/day with oral twice-daily dosing. In particular, treatment with Genz-667348 at 100 mg/kg/day resulted in sterile cure. Two recent analogs of Genz-667348 are currently undergoing pilot toxicity testing to determine suitability as clinical development candidates.\",\n \"corpus_id\": 22125990,\n \"score\": 0\n },\n {\n \"doc_id\": \"21205898\",\n \"title\": \"Validation of isoleucine utilization targets in Plasmodium falciparum.\",\n \"abstract\": \"Intraerythrocytic malaria parasites can obtain nearly their entire amino acid requirement by degrading host cell hemoglobin. The sole exception is isoleucine, which is not present in adult human hemoglobin and must be obtained exogenously. We evaluated two compounds for their potential to interfere with isoleucine utilization. Mupirocin, a clinically used antibacterial, kills Plasmodium falciparum parasites at nanomolar concentrations. Thiaisoleucine, an isoleucine analog, also has antimalarial activity. To identify targets of the two compounds, we selected parasites resistant to either mupirocin or thiaisoleucine. Mutants were analyzed by genome-wide high-density tiling microarrays, DNA sequencing, and copy number variation analysis. The genomes of three independent mupirocin-resistant parasite clones had all acquired either amplifications encompassing or SNPs within the chromosomally encoded organellar (apicoplast) isoleucyl-tRNA synthetase. Thiaisoleucine-resistant parasites had a mutation in the cytoplasmic isoleucyl-tRNA synthetase. The role of this mutation in thiaisoleucine resistance was confirmed by allelic replacement. This approach is generally useful for elucidation of new targets in P. falciparum. Our study shows that isoleucine utilization is an essential pathway that can be targeted for antimalarial drug development.\",\n \"corpus_id\": 3471462,\n \"score\": 0\n },\n {\n \"doc_id\": \"21428877\",\n \"title\": \"Falcipains, Plasmodium falciparum cysteine proteases as key drug targets against malaria.\",\n \"abstract\": \"There is a high demand for new drugs against malaria, which takes millions of lives annually. The abuse of classical antimalarials from the late 1940's to the early 1980's has bred resistant parasites, which led to the use of more potent drugs that ended up by refueling the resistance cycle. An example is chloroquine, once highly effective but now virtually useless against malaria. Structure-based rational drug design relies on high-resolution target structures to allow for screening of selective ligands/inhibitors. For the past two decades, and especially after the unveiling of the Plasmodium falciparum genome in 2002, enzymes of this lethal malaria parasite species have been increasingly attracting the attention of Medicinal Chemists worldwide as promising drug targets. There is particular emphasis on proteases having key roles on the degradation of host's hemoglobin within the food vacuole of blood-stage parasites, as these depend on such process for their survival. Among such enzymes, Plasmepsins (aspartic proteases) and, especially, Falcipains (cysteine proteases) are highly promising antimalarial drug targets. The present review will focus on the computational approaches made so far towards the unraveling of the structure, function and inhibition of Falcipains that, by virtue of their quite specific features, are excellent targets for highly selective inhibitors.\",\n \"corpus_id\": 19312471,\n \"score\": 0\n },\n {\n \"doc_id\": \"21554743\",\n \"title\": \"Selection of drug resistant mutants from random library of Plasmodium falciparum dihydrofolate reductase in Plasmodium berghei model.\",\n \"abstract\": \"BACKGROUND: The prevalence of drug resistance amongst the human malaria Plasmodium species has most commonly been associated with genomic mutation within the parasites. This phenomenon necessitates evolutionary predictive studies of possible resistance mutations, which may occur when a new drug is introduced. Therefore, identification of possible new Plasmodium falciparum dihydrofolate reductase (PfDHFR) mutants that confer resistance to antifolate drugs is essential in the process of antifolate anti-malarial drug development. METHODS: A system to identify mutations in Pfdhfr gene that confer antifolate drug resistance using an animal Plasmodium parasite model was developed. By using error-prone PCR and Plasmodium transfection technologies, libraries of Pfdhfr mutant were generated and then episomally transfected to Plasmodium berghei parasites, from which pyrimethamine-resistant PfDHFR mutants were selected. RESULTS: The principal mutation found from this experiment was S108N, coincident with the first pyrimethamine-resistance mutation isolated from the field. A transgenic P. berghei, in which endogenous Pbdhfr allele was replaced with the mutant PfdhfrS108N, was generated and confirmed to have normal growth rate comparing to parental non-transgenic parasite and also confer resistance to pyrimethamine. CONCLUSION: This study demonstrated the power of the transgenic P. berghei system to predict drug-resistant Pfdhfr mutations in an in vivo parasite/host setting. The system could be utilized for identification of possible novel drug-resistant mutants that could arise against new antifolate compounds and for prediction the evolution of resistance mutations.\",\n \"corpus_id\": 8888211,\n \"score\": 0\n },\n {\n \"doc_id\": \"21801743\",\n \"title\": \"Structural analysis of chorismate synthase from Plasmodium falciparum: a novel target for antimalaria drug discovery.\",\n \"abstract\": \"The shikimate pathway in Plasmodium falciparum provides several targets for designing novel antiparasitic agents for the treatment of malaria. Chorismate synthase (CS) is a key enzyme in the shikimate pathway which catalyzes the seventh and final step of the pathway. P. falciparum chorismate synthase (PfCS) is unique in terms of enzymatic behavior, cellular localization and in having two additional amino acid inserts compared to any other CS. The structure of PfCS along with cofactor FMN was predicted by homology modeling using crystal structure of Helicobacter pylori chorismate synthase (HpCS). The quality of the model was validated using structure analysis servers and molecular dynamics. Dimeric form of PfCS was generated and the FMN binding mechanism involving movement of loop near active site has been proposed. Active site pocket has been identified and substrate 5-enolpyruvylshikimate 3-phosphate (EPSP) along with screened potent inhibitors has been docked. The study resulted in identification of putative inhibitors of PfCS with binding efficiency in nanomolar range. The selected putative inhibitors could lead to the development of anti-malarial drugs.\",\n \"corpus_id\": 22208796,\n \"score\": 0\n },\n {\n \"doc_id\": \"21843142\",\n \"title\": \"Support vector machine based prediction of P. falciparum proteasome inhibitors and development of focused library by molecular docking.\",\n \"abstract\": \"The emergence and spread of Plasmodium falciparum resistance to existing antimalarials emphasize the impelling search for novel drug targets and chemotherapeutic compounds. The ubiquitin-proteasome system plays a major role in overall protein turnover, in eukaryotic cells including plasmodia. 20S β subunit is the catalytic core of this proteolytic machinery, and hence most of the inhibitors developed are being targeted towards this component. Inhibition of the proteasome is established as a promising strategy to develop novel antimalarial drugs. The present study reports identification of novel drug-like 20S proteasome inhibitors with potential activity against the 20S β subunit of P. falciparum using a combination of ligand based (Support Vector Machines) and receptor based (molecular docking) techniques. The robust learning and generalizing capability of Support Vector Machines (SVM) has been exploited to classify proteasome inhibitors and non-inhibitors, targeted towards P. falciparum 20S proteasome. SVM model has been trained using 170 molecular descriptors of 64 inhibitors and 208 putative non-inhibitors of 20S proteasome. The non-linear classifier based on Radial Basis Function (RBF) kernel yielded highest classification accuracy in comparison to the linear classifier. The best classifier had 5-fold Cross-Validation (CV) accuracy of 97% and Area Under Curve (AUC) of 0.99 reflecting good accuracy of the model. The SVM model rapidly classified compounds with potential proteasomal activity. Subsequently, molecular docking studies aided the generation of focused collection of compounds with good binding affinity towards the substrate-binding site of 20S β subunit. The novel drug-like 20S proteasome inhibitors identified in this study can be a good starting point to develop novel antimalarial drugs.\",\n \"corpus_id\": 32951082,\n \"score\": 0\n },\n {\n \"doc_id\": \"22117061\",\n \"title\": \"Structure and reaction mechanism of phosphoethanolamine methyltransferase from the malaria parasite Plasmodium falciparum: an antiparasitic drug target.\",\n \"abstract\": \"In the malarial parasite Plasmodium falciparum, a multifunctional phosphoethanolamine methyltransferase (PfPMT) catalyzes the methylation of phosphoethanolamine (pEA) to phosphocholine for membrane biogenesis. This pathway is also found in plant and nematodes, but PMT from these organisms use multiple methyltransferase domains for the S-adenosylmethionine (AdoMet) reactions. Because PfPMT is essential for normal growth and survival of Plasmodium and is not found in humans, it is an antiparasitic target. Here we describe the 1.55 Å resolution crystal structure of PfPMT in complex with AdoMet by single-wavelength anomalous dispersion phasing. In addition, 1.19-1.52 Å resolution structures of PfPMT with pEA (substrate), phosphocholine (product), sinefungin (inhibitor), and both pEA and S-adenosylhomocysteine bound were determined. These structures suggest that domain rearrangements occur upon ligand binding and provide insight on active site architecture defining the AdoMet and phosphobase binding sites. Functional characterization of 27 site-directed mutants identifies critical active site residues and suggests that Tyr-19 and His-132 form a catalytic dyad. Kinetic analysis, isothermal titration calorimetry, and protein crystallography of the Y19F and H132A mutants suggest a reaction mechanism for the PMT. Not only are Tyr-19 and His-132 required for phosphobase methylation, but they also form a \\\"catalytic\\\" latch that locks ligands in the active site and orders the site for catalysis. This study provides the first insight on this antiparasitic target enzyme essential for survival of the malaria parasite; however, further studies of the multidomain PMT from plants and nematodes are needed to understand the evolutionary division of metabolic function in the phosphobase pathway of these organisms.\",\n \"corpus_id\": 3203009,\n \"score\": 0\n },\n {\n \"doc_id\": \"22543039\",\n \"title\": \"Plasmodium subtilisin-like protease 1 (SUB1): insights into the active-site structure, specificity and function of a pan-malaria drug target.\",\n \"abstract\": \"Release of the malaria merozoite from its host erythrocyte (egress) and invasion of a fresh cell are crucial steps in the life cycle of the malaria pathogen. Subtilisin-like protease 1 (SUB1) is a parasite serine protease implicated in both processes. In the most dangerous human malarial species, Plasmodium falciparum, SUB1 has previously been shown to have several parasite-derived substrates, proteolytic cleavage of which is important both for egress and maturation of the merozoite surface to enable invasion. Here we have used molecular modelling, existing knowledge of SUB1 substrates, and recombinant expression and characterisation of additional Plasmodium SUB1 orthologues, to examine the active site architecture and substrate specificity of P. falciparum SUB1 and its orthologues from the two other major human malaria pathogens Plasmodium vivax and Plasmodium knowlesi, as well as from the rodent malaria species, Plasmodium berghei. Our results reveal a number of unusual features of the SUB1 substrate binding cleft, including a requirement to interact with both prime and non-prime side residues of the substrate recognition motif. Cleavage of conserved parasite substrates is mediated by SUB1 in all parasite species examined, and the importance of this is supported by evidence for species-specific co-evolution of protease and substrates. Two peptidyl alpha-ketoamides based on an authentic PfSUB1 substrate inhibit all SUB1 orthologues examined, with inhibitory potency enhanced by the presence of a carboxyl moiety designed to introduce prime side interactions with the protease. Our findings demonstrate that it should be possible to develop 'pan-reactive' drug-like compounds that inhibit SUB1 in all three major human malaria pathogens, enabling production of broad-spectrum antimalarial drugs targeting SUB1.\",\n \"corpus_id\": 34527491,\n \"score\": 0\n },\n {\n \"doc_id\": \"22709581\",\n \"title\": \"X-ray crystal structure and specificity of the Plasmodium falciparum malaria aminopeptidase PfM18AAP.\",\n \"abstract\": \"The malarial aminopeptidases have emerged as promising new drug targets for the development of novel antimalarial drugs. The M18AAP of Plasmodium falciparum malaria is a metallo-aminopeptidase that we show demonstrates a highly restricted specificity for peptides with an N-terminal Glu or Asp residue. Thus, the enzyme may function alongside other aminopeptidases in effecting the complete degradation or turnover of proteins, such as host hemoglobin, which provides a free amino acid pool for the growing parasite. Inhibition of PfM18AAP's function using antisense RNA is detrimental to the intra-erythrocytic malaria parasite and, hence, it has been proposed as a potential novel drug target. We report the X-ray crystal structure of the PfM18AAP aminopeptidase and reveal its complex dodecameric assembly arranged via dimer and trimer units that interact to form a large tetrahedron shape that completely encloses the 12 active sites within a central cavity. The four entry points to the catalytic lumen are each guarded by 12 large flexible loops that could control substrate entry into the catalytic sites. PfM18AAP thus resembles a proteasomal-like machine with multiple active sites able to degrade peptide substrates that enter the central lumen. The Plasmodium enzyme shows significant structural differences around the active site when compared to recently determined structures of its mammalian and human homologs, which provides a platform from which a rational approach to inhibitor design of new malaria-specific drugs can begin.\",\n \"corpus_id\": 21866725,\n \"score\": 0\n },\n {\n \"doc_id\": \"23035243\",\n \"title\": \"Malarial dihydrofolate reductase as a paradigm for drug development against a resistance-compromised target.\",\n \"abstract\": \"Malarial dihydrofolate reductase (DHFR) is the target of antifolate antimalarial drugs such as pyrimethamine and cycloguanil, the clinical efficacy of which have been compromised by resistance arising through mutations at various sites on the enzyme. Here, we describe the use of cocrystal structures with inhibitors and substrates, along with efficacy and pharmacokinetic profiling for the design, characterization, and preclinical development of a selective, highly efficacious, and orally available antimalarial drug candidate that potently inhibits both wild-type and clinically relevant mutated forms of Plasmodium falciparum (Pf) DHFR. Important structural characteristics of P218 include pyrimidine side-chain flexibility and a carboxylate group that makes charge-mediated hydrogen bonds with conserved Arg122 (PfDHFR-TS amino acid numbering). An analogous interaction of P218 with human DHFR is disfavored because of three species-dependent amino acid substitutions in the vicinity of the conserved Arg. Thus, P218 binds to the active site of PfDHFR in a substantially different fashion from the human enzyme, which is the basis for its high selectivity. Unlike pyrimethamine, P218 binds both wild-type and mutant PfDHFR in a slow-on/slow-off tight-binding mode, which prolongs the target residence time. P218, when bound to PfDHFR-TS, resides almost entirely within the envelope mapped out by the dihydrofolate substrate, which may make it less susceptible to resistance mutations. The high in vivo efficacy in a SCID mouse model of P. falciparum malaria, good oral bioavailability, favorable enzyme selectivity, and good safety characteristics of P218 make it a potential candidate for further development.\",\n \"corpus_id\": 28088781,\n \"score\": 0\n },\n {\n \"doc_id\": \"23353582\",\n \"title\": \"In silico identification of novel inhibitors against Plasmodium falciparum dihydroorate dehydrogenase.\",\n \"abstract\": \"Plasmodium falciparum causes the most fatal form of malaria and accounts for over 1 million deaths annually, yet currently used drug therapies are compromised by resistance. The malaria parasite cannot salvage pyrimidines and relies on de novo biosynthesis for survival. The enzyme dihydrooratate dehydrogenase (DHODH), a mitochondrial flavoenzyme, catalyzes the rate-limiting step of this pathway and is therefore an attractive anti-malarial chemotherapeutic target. In an effort to design new and potential anti-malarials, structure-based pharmacophore mapping, molecular docking, binding energy calculations and binding affinity predictions were employed in a virtual screening strategy to design new and potent P. falciparum dihydrooratate dehydrogenase (PfDHODH) inhibitors. A structure-based pharmacophore model was generated which consist of important interactions as observed in co-crystal of PfDHODH enzyme. The developed model was used to retrieve molecules from ChemBridge database, a freely available commercial database. A total of 87 molecules mapped on the modeled pharmacophore from the database. The retrieved hits were further screened by docking simulation, binding energy calculations and biding affinity predictions using genetic optimization for ligand docking (GOLD) and MOE. Based on these results, finally 26 chemo-types molecules were predicted as new, potential and structurally diverse PfDHODH inhibitors.\",\n \"corpus_id\": 11653555,\n \"score\": 0\n },\n {\n \"doc_id\": \"23633587\",\n \"title\": \"Structural analysis of malaria-parasite lysyl-tRNA synthetase provides a platform for drug development.\",\n \"abstract\": \"Aminoacyl-tRNA synthetases are essential enzymes that transmit information from the genetic code to proteins in cells and are targets for antipathogen drug development. Elucidation of the crystal structure of cytoplasmic lysyl-tRNA synthetase from the malaria parasite Plasmodium falciparum (PfLysRS) has allowed direct comparison with human LysRS. The authors' data suggest that PfLysRS is dimeric in solution, whereas the human counterpart can also adopt tetrameric forms. It is shown for the first time that PfLysRS is capable of synthesizing the signalling molecule Ap4a (diadenosine tetraphosphate) using ATP as a substrate. The PfLysRS crystal structure is in the apo form, such that binding to ATP will require rotameric changes in four conserved residues. Differences in the active-site regions of parasite and human LysRSs suggest the possibility of exploiting PfLysRS for selective inhibition. These investigations on PfLysRS further validate malarial LysRSs as attractive antimalarial targets and provide new structural space for the development of inhibitors that target pathogen LysRSs selectively.\",\n \"corpus_id\": 34079431,\n \"score\": 0\n },\n {\n \"doc_id\": \"23665145\",\n \"title\": \"Crystal structures of Plasmodium falciparum cytosolic tryptophanyl-tRNA synthetase and its potential as a target for structure-guided drug design.\",\n \"abstract\": \"Malaria, most commonly caused by the parasite Plasmodium falciparum, is a devastating disease that remains a large global health burden. Lack of vaccines and drug resistance necessitate the continual development of new drugs and exploration of new drug targets. Due to their essential role in protein synthesis, aminoacyl-tRNA synthetases are potential anti-malaria drug targets. Here we report the crystal structures of P. falciparum cytosolic tryptophanyl-tRNA synthetase (Pf-cTrpRS) in its ligand-free state and tryptophanyl-adenylate (WAMP)-bound state at 2.34 Å and 2.40 Å resolutions, respectively. Large conformational changes are observed when the ligand-free protein is bound to WAMP. Multiple residues, completely surrounding the active site pocket, collapse onto WAMP. Comparison of the structures to those of human cytosolic TrpRS (Hs-cTrpRS) provides information about the possibility of targeting Pf-cTrpRS for inhibitor development. There is a high degree of similarity between Pf-cTrpRS and Hs-cTrpRS within the active site. However, the large motion that Pf-cTrpRS undergoes during transitions between different functional states avails an opportunity to arrive at compounds which selectively perturb the motion, and may provide a starting point for the development of new anti-malaria therapeutics.\",\n \"corpus_id\": 5443658,\n \"score\": 0\n },\n {\n \"doc_id\": \"23750298\",\n \"title\": \"In silico analysis of Plasmodium species specific UvrD helicase.\",\n \"abstract\": \"Malaria is still a devastating disease caused by the mosquito-transmitted parasite Plasmodium, particularly Plasmodium falciparum. During the last few years the situation has worsened in many ways, mainly due to malarial parasites becoming increasingly resistant to several anti-malarial drugs. Thus there is an urgent need to find alternate ways to control malaria and therefore it is necessary to identify new drug targets and new classes of anti-malarial drugs. A malaria vaccine would be the ultimate weapon to fight this deadly disease but unfortunately despite encouraging advances a vaccine is not likely soon. DNA helicases from the PcrA/UvrD/Rep (PUR) subfamily are important for the survival of the various organisms, mainly pathogenic bacteria. Members from this subfamily can be targeted and inhibited by a variety of synthetic compounds. Using bioinformatics analysis we have shown that UvrD from this subfamily is the only member present in the P. falciparum genome, while PcrA and Rep are absent in the genome. UvrD from the parasite shows no homology to any protein or enzyme from human and thus can be considered as a strong potential drug target. In the present study we report an in silico analysis of this important enzyme from a variety of Plasmodium species. The results suggest that among all the species of Plasmodium, P. falciparum contains the largest UvrD and this enzyme is variable at the sequence and structural level.\",\n \"corpus_id\": 10375376,\n \"score\": 0\n },\n {\n \"doc_id\": \"24063369\",\n \"title\": \"Design, synthesis, and biological and crystallographic evaluation of novel inhibitors of Plasmodium falciparum enoyl-ACP-reductase (PfFabI).\",\n \"abstract\": \"Malaria, a disease of worldwide significance, is responsible for over one million deaths annually. The liver-stage of Plasmodium's life cycle is the first, obligatory, but clinically silent step in malaria infection. The P. falciparum type II fatty acid biosynthesis pathway (PfFAS-II) has been found to be essential for complete liver-stage development and has been regarded as a potential antimalarial target for the development of drugs for malaria prophylaxis and liver-stage eradication. In this paper, new coumarin-based triclosan analogues are reported and their biological profile is explored in terms of inhibitory potency against enzymes of the PfFAS-II pathway. Among the tested compounds, 7 and 8 showed the highest inhibitory potency against Pf enoyl-ACP-reductase (PfFabI), followed by 15 and 3. Finally, we determined the crystal structures of compounds 7 and 11 in complex with PfFabI to identify their mode of binding and to confirm outcomes of docking simulations.\",\n \"corpus_id\": 42443710,\n \"score\": 0\n },\n {\n \"doc_id\": \"24410837\",\n \"title\": \"Crystal structures of IspF from Plasmodium falciparum and Burkholderia cenocepacia: comparisons inform antimicrobial drug target assessment.\",\n \"abstract\": \"BACKGROUND: 2C-methyl-D-erythritol-2,4-cyclodiphosphate synthase (IspF) catalyzes the conversion of 4-diphosphocytidyl-2C-methyl-D-erythritol-2-phosphate to 2C-methyl-D-erythritol-2,4-cyclodiphosphate and cytidine monophosphate in production of isoprenoid-precursors via the methylerythritol phosphate biosynthetic pathway. IspF is found in the protozoan Plasmodium falciparum, a parasite that causes cerebral malaria, as well as in many Gram-negative bacteria such as Burkholderia cenocepacia. IspF represents a potential target for development of broad-spectrum antimicrobial drugs since it is proven or inferred as essential in these pathogens and absent from mammals. Structural studies of IspF from these two important yet distinct pathogens, and comparisons with orthologues have been carried out to generate reagents, to support and inform a structure-based approach to early stage drug discovery. RESULTS: Efficient recombinant protein production and crystallization protocols were developed, and high-resolution crystal structures of IspF from P. falciparum (Emphasis/Emphasis>IspF) and B. cenocepacia (BcIspF) in complex with cytidine nucleotides determined. Comparisons with orthologues, indicate a high degree of order and conservation in parts of the active site where Zn2+ is bound and where recognition of the cytidine moiety of substrate occurs. However, conformational flexibility is noted in that area of the active site responsible for binding the methylerythritol component of substrate. Unexpectedly, one structure of BcIspF revealed two molecules of cytidine monophosphate in the active site, and another identified citrate coordinating to the catalytic Zn2+. In both cases interactions with ligands appear to help order a flexible loop at one side of the active site. Difficulties were encountered when attempting to derive complex structures with other ligands. CONCLUSIONS: High-resolution crystal structures of IspF from two important human pathogens have been obtained and compared to orthologues. The studies reveal new data on ligand binding, with citrate coordinating to the active site Zn2+ and when present in high concentrations cytidine monophosphate displays two binding modes in the active site. Ligand binding appears to order a part of the active site involved in substrate recognition. The high degree of structural conservation in and around the IspF active site suggests that any structural model might be suitable to support a program of structure-based drug discovery.\",\n \"corpus_id\": 1849890,\n \"score\": 0\n },\n {\n \"doc_id\": \"24742318\",\n \"title\": \"Molecular characterization of Plasmodium falciparum uracil-DNA glycosylase and its potential as a new anti-malarial drug target.\",\n \"abstract\": \"BACKGROUND: Based on resistance of currently used anti-malarials, a new anti-malarial drug target against Plasmodium falciparum is urgently needed. Damaged DNA cannot be transcribed without prior DNA repair; therefore, uracil-DNA glycosylase, playing an important role in base excision repair, may act as a candidate for a new anti-malarial drug target. METHODS: Initially, the native PfUDG from parasite crude extract was partially purified using two columns, and the glycosylase activity was monitored. The existence of malarial UDG activity prompted the recombinant expression of PfUDG for further characterization. The PfUDG from chloroquine and pyrimethamine resistant P. falciparum strain K1 was amplified, cloned into the expression vector, and expressed in Escherichia coli. The recombinant PfUDG was analysed by SDS-PAGE and identified by LC-MS/MS. The three dimensional structure was modelled. Biochemical properties were characterized. Inhibitory effects of 12 uracil-derivatives on PfUDG activity were investigated. Inhibition of parasite growth was determined in vitro using SYBR Green I and compared with results from human cytotoxicity tests. RESULTS: The native PfUDG was partially purified with a specific activity of 1,811.7 units/mg (113.2 fold purification). After cloning of 966-bp PCR product, the 40-kDa hexa-histidine tagged PfUDG was expressed and identified. The amino acid sequence of PfUDG showed only 24.8% similarity compared with the human enzyme. The biochemical characteristics of PfUDGs were quite similar. They were inhibited by uracil glycosylase inhibitor protein as found in other organisms. Interestingly, recombinant PfUDG was inhibited by two uracil-derived compounds; 1-methoxyethyl-6-(p-n-octylanilino)uracil (IC50 of 16.75 μM) and 6-(phenylhydrazino)uracil (IC50 of 77.5 μM). Both compounds also inhibited parasite growth with IC50s of 15.6 and 12.8 μM, respectively. Moreover, 1-methoxyethyl-6-(p-n-octylanilino)uracil was not toxic to HepG2 cells, with IC50 of > 160 μM while 6-(phenylhydrazino)uracil exhibited cytoxicity, with IC50 of 27.5 μM. CONCLUSIONS: The recombinant PfUDG was expressed, characterized and compared to partially purified native PfUDG. Their characteristics were not significantly different. PfUDG differs from human enzyme in its size and predicted amino acid sequence. Two uracil derivatives inhibited PfUDG and parasite growth; however, only one non-cytotoxic compound was found. Therefore, this selective compound can act as a lead compound for anti-malarial development in the future.\",\n \"corpus_id\": 15488694,\n \"score\": 0\n },\n {\n \"doc_id\": \"24864210\",\n \"title\": \"Exploring Drug Targets in Isoprenoid Biosynthetic Pathway for Plasmodium falciparum.\",\n \"abstract\": \"Emergence of rapid drug resistance to existing antimalarial drugs in Plasmodium falciparum has created the need for prediction of novel targets as well as leads derived from original molecules with improved activity against a validated drug target. The malaria parasite has a plant plastid-like apicoplast. To overcome the problem of falciparum malaria, the metabolic pathways in parasite apicoplast have been used as antimalarial drug targets. Among several pathways in apicoplast, isoprenoid biosynthesis is one of the important pathways for parasite as its multiplication in human erythrocytes requires isoprenoids. Therefore targeting this pathway and exploring leads with improved activity is a highly attractive approach. This report has explored progress towards the study of proteins and inhibitors of isoprenoid biosynthesis pathway. For more comprehensive analysis, antimalarial drug-protein interaction has been covered.\",\n \"corpus_id\": 15423736,\n \"score\": 0\n },\n {\n \"doc_id\": \"24934654\",\n \"title\": \"Identification of inhibitors of Plasmodium falciparum RuvB1 helicase using biochemical assays.\",\n \"abstract\": \"Human malaria is a major parasitic infection, and the situation has worsened mainly due to the emergence of resistant malaria parasites to several anti-malarial drugs. Thus, an urgent need to find suitable drug targets has led to the development of newer classes of anti-malarial drugs. Helicases have been targeted to develop therapeutics for viral, bacterial, and other microorganism infections. Recently, Plasmodium falciparum RuvB ATPases/helicases have been characterized and proposed as a suitable antimalarial drug target. In the present study, the screening of various compounds was done and the results suggest that PfRuvB1 ATPase activity is inhibited considerably by the novobiocin and partially by cisplatin and ciprofloxacin. Helicase assay of PfRuvB1 in the presence of various compounds suggest novobiocin, actinomycin, and ethidium bromide as potent inhibitors. Novobiocin inhibits the helicase activity of PfRuvB1 possibly by blocking the ATPase activity of PfRuvB1. This study is unique in respect to the identification of novobiocin as inhibitor of PfRuvB1, partially by competing with ATP binding at its active site and provides evidence for PfRuvB1 as target of novobiocin after DNA gyrase-B and HSP90. These studies will certainly help the pharmacologist to design and develop some novel inhibitor specific to PfRuvB1, which may serve as suitable chemotherapeutics to target malaria.\",\n \"corpus_id\": 16643632,\n \"score\": 0\n },\n {\n \"doc_id\": \"25738296\",\n \"title\": \"Hemoglobin Degrading Proteases of Plasmodium falciparum as Antimalarial Drug Targets.\",\n \"abstract\": \"Plasmepsins, falcipains and aminopeptidases are Plasmodium falciparum proteases involved in human host hemoglobin degradation and other processes like erythrocyte invasion and rupture. Antimalarial drug resistance and natural selection in parasite are important reasons that create the urgent need of novel targets and lead compounds to overcome the burden of malaria. This report explored progress of the study covering proteases and their inhibitors specific to hemoglobin degradation. Additionally, in silico predicted antimalarial targets, balancing selection and drug-protein interaction are included.\",\n \"corpus_id\": 23198963,\n \"score\": 0\n },\n {\n \"doc_id\": \"26130467\",\n \"title\": \"Structural mapping of the ClpB ATPases of Plasmodium falciparum: Targeting protein folding and secretion for antimalarial drug design.\",\n \"abstract\": \"Caseinolytic chaperones and proteases (Clp) belong to the AAA+ protein superfamily and are part of the protein quality control machinery in cells. The eukaryotic parasite Plasmodium falciparum, the causative agent of malaria, has evolved an elaborate network of Clp proteins including two distinct ClpB ATPases. ClpB1 and ClpB2 are involved in different aspects of parasitic proteostasis. ClpB1 is present in the apicoplast, a parasite-specific and plastid-like organelle hosting various metabolic pathways necessary for parasite growth. ClpB2 localizes to the parasitophorous vacuole membrane where it drives protein export as core subunit of a parasite-derived protein secretion complex, the Plasmodium Translocon of Exported proteins (PTEX); this process is central to parasite virulence and survival in the human host. The functional associations of these two chaperones with parasite-specific metabolism and protein secretion make them prime drug targets. ClpB proteins function as unfoldases and disaggregases and share a common architecture consisting of four domains-a variable N-terminal domain that binds different protein substrates, followed by two highly conserved catalytic ATPase domains, and a C-terminal domain. Here, we report and compare the first crystal structures of the N terminal domains of ClpB1 and ClpB2 from Plasmodium and analyze their molecular surfaces. Solution scattering analysis of the N domain of ClpB2 shows that the average solution conformation is similar to the crystalline structure. These structures represent the first step towards the characterization of these two malarial chaperones and the reconstitution of the entire PTEX to aid structure-based design of novel anti-malarial drugs.\",\n \"corpus_id\": 3449763,\n \"score\": 0\n },\n {\n \"doc_id\": \"26198663\",\n \"title\": \"Plasmodium falciparum glucose-6-phosphate dehydrogenase 6-phosphogluconolactonase is a potential drug target.\",\n \"abstract\": \"The malarial parasite Plasmodium falciparum is exposed to substantial redox challenges during its complex life cycle. In intraerythrocytic parasites, haemoglobin breakdown is a major source of reactive oxygen species. Deficiencies in human glucose-6-phosphate dehydrogenase, the initial enzyme in the pentose phosphate pathway (PPP), lead to a disturbed redox equilibrium in infected erythrocytes and partial protection against severe malaria. In P. falciparum, the first two reactions of the PPP are catalysed by the bifunctional enzyme glucose-6-phosphate dehydrogenase 6-phosphogluconolactonase (PfGluPho). This enzyme differs structurally from its human counterparts and represents a potential target for drugs. In the present study we used epitope tagging of endogenous PfGluPho to verify that the enzyme localises to the parasite cytosol. Furthermore, attempted double crossover disruption of the PfGluPho gene indicates that the enzyme is essential for the growth of blood stage parasites. As a further step towards targeting PfGluPho pharmacologically, ellagic acid was characterised as a potent PfGluPho inhibitor with an IC50 of 76 nM. Interestingly, pro-oxidative drugs or treatment of the parasites with H2O2 only slightly altered PfGluPho expression or activity under the conditions tested. Furthermore, metabolic profiling suggested that pro-oxidative drugs do not significantly perturb the abundance of PPP intermediates. These data indicate that PfGluPho is essential in asexual parasites, but that the oxidative arm of the PPP is not strongly regulated in response to oxidative challenge.\",\n \"corpus_id\": 46398163,\n \"score\": 0\n },\n {\n \"doc_id\": \"26863983\",\n \"title\": \"Structure- and function-based design of Plasmodium-selective proteasome inhibitors.\",\n \"abstract\": \"The proteasome is a multi-component protease complex responsible for regulating key processes such as the cell cycle and antigen presentation. Compounds that target the proteasome are potentially valuable tools for the treatment of pathogens that depend on proteasome function for survival and replication. In particular, proteasome inhibitors have been shown to be toxic for the malaria parasite Plasmodium falciparum at all stages of its life cycle. Most compounds that have been tested against the parasite also inhibit the mammalian proteasome, resulting in toxicity that precludes their use as therapeutic agents. Therefore, better definition of the substrate specificity and structural properties of the Plasmodium proteasome could enable the development of compounds with sufficient selectivity to allow their use as anti-malarial agents. To accomplish this goal, here we use a substrate profiling method to uncover differences in the specificities of the human and P. falciparum proteasome. We design inhibitors based on amino-acid preferences specific to the parasite proteasome, and find that they preferentially inhibit the β2-subunit. We determine the structure of the P. falciparum 20S proteasome bound to the inhibitor using cryo-electron microscopy and single-particle analysis, to a resolution of 3.6 Å. These data reveal the unusually open P. falciparum β2 active site and provide valuable information about active-site architecture that can be used to further refine inhibitor design. Furthermore, consistent with the recent finding that the proteasome is important for stress pathways associated with resistance of artemisinin family anti-malarials, we observe growth inhibition synergism with low doses of this β2-selective inhibitor in artemisinin-sensitive and -resistant parasites. Finally, we demonstrate that a parasite-selective inhibitor could be used to attenuate parasite growth in vivo without appreciable toxicity to the host. Thus, the Plasmodium proteasome is a chemically tractable target that could be exploited by next-generation anti-malarial agents.\",\n \"corpus_id\": 4410450,\n \"score\": 0\n },\n {\n \"doc_id\": \"27487482\",\n \"title\": \"Crystal Structure of the Apicoplast DNA Polymerase from Plasmodium falciparum: The First Look at a Plastidic A-Family DNA Polymerase.\",\n \"abstract\": \"Plasmodium falciparum, the primary cause of malaria, contains a non-photosynthetic plastid called the apicoplast. The apicoplast exists in most members of the phylum Apicomplexa and has its own genome along with organelle-specific enzymes for its replication. The only DNA polymerase found in the apicoplast (apPOL) was putatively acquired through horizontal gene transfer from a bacteriophage and is classified as an atypical A-family polymerase. Here, we present its crystal structure at a resolution of 2.9Å. P. falciparum apPOL, the first structural representative of a plastidic A-family polymerase, diverges from typical A-family members in two of three previously identified signature motifs and in a region not implicated by sequence. Moreover, apPOL has an additional N-terminal subdomain, the absence of which severely diminishes its 3' to 5' exonuclease activity. A compound known to be toxic to Plasmodium is a potent inhibitor of apPOL, suggesting that apPOL is a viable drug target. The structure provides new insights into the structural diversity of A-family polymerases and may facilitate structurally guided antimalarial drug design.\",\n \"corpus_id\": 26767933,\n \"score\": 0\n },\n {\n \"doc_id\": \"28003005\",\n \"title\": \"Targeting cysteine proteases from Plasmodium falciparum: A general overview, rational drug design and computational approaches for drug discovery.\",\n \"abstract\": \"The Plasmodium falciparum cysteine proteases, also known as falcipains, are involved in different erythrocytic cycle processes of the malaria parasite, e.g. hydrolysis of host haemoglobin, erythrocyte invasion, and erythrocyte rupture. With the biochemical characterization of four falcipains so far, FP-2 (falcipain-2) and FP-3 (falcipain-3), members of the papain-like CAC1 family, are essential haemoglobinases. They could therefore be referred to as potential anti-malarial drug targets in the search for novel therapies, which could ease the burden caused by the increasing resistance to current anti-malarial drugs. This review provides a summary of the most important results, highlighting the drug design approaches essential for the understanding of the mechanism of inhibition and discovery of inhibitors against cysteine proteases from P. falciparum. Rational and computer-aided drug discovery approaches for the design of promising falcipain inhibitors are described herein, with a focus on a variety of structure-based and ligand-based modeling approaches. Moreover, the key features of ligand recognition against these targets are emphasized. This review would be of interest to scientists engaged in the development of drug design strategies to target the cysteine proteases, FP-2 and FP-3.\",\n \"corpus_id\": 4397880,\n \"score\": 0\n },\n {\n \"doc_id\": \"28195463\",\n \"title\": \"Target Elucidation by Cocrystal Structures of NADH-Ubiquinone Oxidoreductase of Plasmodium falciparum (PfNDH2) with Small Molecule To Eliminate Drug-Resistant Malaria.\",\n \"abstract\": \"Drug-resistant malarial strains have been continuously emerging recently, which posts a great challenge for the global health. Therefore, new antimalarial drugs with novel targeting mechanisms are urgently needed for fighting drug-resistant malaria. NADH-ubiquinone oxidoreductase of Plasmodium falciparum (PfNDH2) represents a viable target for antimalarial drug development. However, the absence of structural information on PfNDH2 limited rational drug design and further development. Herein, we report high resolution crystal structures of the PfNDH2 protein for the first time in Apo-, NADH-, and RYL-552 (a new inhibitor)-bound states. The PfNDH2 inhibitor exhibits excellent potency against both drug-resistant strains in vitro and parasite-infected mice in vivo via a potential allosteric mechanism. Furthermore, it was found that the inhibitor can be used in combination with dihydroartemisinin (DHA) synergistically. These findings not only are important for malarial PfNDH2 protein-based drug development but could also have broad implications for other NDH2-containing pathogenic microorganisms such as Mycobacterium tuberculosis.\",\n \"corpus_id\": 36645667,\n \"score\": 0\n },\n {\n \"doc_id\": \"29269266\",\n \"title\": \"Biochemical studies of membrane bound Plasmodium falciparum mitochondrial L-malate:quinone oxidoreductase, a potential drug target.\",\n \"abstract\": \"Plasmodium falciparum is an apicomplexan parasite that causes the most severe malaria in humans. Due to a lack of effective vaccines and emerging of drug resistance parasites, development of drugs with novel mechanisms of action and few side effects are imperative. To this end, ideal drug targets are those essential to parasite viability as well as absent in their mammalian hosts. The mitochondrial electron transport chain (ETC) of P. falciparum is one source of such potential targets because enzymes, such as L-malate:quinone oxidoreductase (PfMQO), in this pathway are absent humans. PfMQO catalyzes the oxidation of L-malate to oxaloacetate and the simultaneous reduction of ubiquinone to ubiquinol. It is a membrane protein, involved in three pathways (ETC, the tricarboxylic acid cycle and the fumarate cycle) and has been shown to be essential for parasite survival, at least, in the intra-erythrocytic asexual stage. These findings indicate that PfMQO would be a valuable drug target for development of antimalarial with novel mechanism of action. Up to this point in time, difficulty in producing active recombinant mitochondrial MQO has hampered biochemical characterization and targeted drug discovery with MQO. Here we report for the first time recombinant PfMQO overexpressed in bacterial membrane and the first biochemical study. Furthermore, about 113 compounds, consisting of ubiquinone binding site inhibitors and antiparasitic agents, were screened resulting in the discovery of ferulenol as a potent PfMQO inhibitor. Finally, ferulenol was shown to inhibit parasite growth and showed strong synergism in combination with atovaquone, a well-described anti-malarial and bc1 complex inhibitor.\",\n \"corpus_id\": 46768644,\n \"score\": 0\n }\n]","isConversational":false}}},{"rowIdx":74,"cells":{"query":{"kind":"string","value":"{\n \"doc_id\": \"28359768\",\n \"title\": \"On the Science of Consciousness: Epistemological Reflections and Clinical Implications.\",\n \"abstract\": \"Consciousness has been one of the most important and tantalizing issues ever since the origin of philosophy and medicine. The concept of consciousness and the so-called \\\"hard problem\\\" (i.e., the mind-brain relationship) are highly complex topics that have yet to be elucidated, involving the realms of both science and philosophy with profound epistemological implications. In the lively debate on the foundations of the science of consciousness there are several potential biases of an essentially philosophical nature, such as those related to the paradigm and axioms adopted, and the ostensible logical contradiction between monism and dualism. Their origin dates back largely to Descartes' thinking and the birth of the new sciences as a compromise with the Inquisition, but they have been handed down through the Enlightenment and Positivism. A proper investigation of consciousness and the world of subjectivity demands a careful reflection on the paradigm of scientific medicine to identify possible flaws and overcome the limits of the mechanistic-reductionist approach.\",\n \"corpus_id\": 2909347\n}"},"candidates":{"kind":"list like","value":[{"doc_id":"19505026","title":"[Individual consciousness].","abstract":"The main modern concepts on the consciousness nature are considered. Together with the dualistic concepts, there exist concepts the adherents of which find it possible to get to know the origin of consciousness on the basis of natural science. A critical analysis of those concepts brings the author to the conclusion that they do not solve the main problem of individual consciousness: how subjective elements of consciousness arise in the brain as a result of objectively registered processes. The main reason of failures to solve said problem is considered by the author in the fact that the subjective categories of consciousness are not really subject to science. Nevertheless, it does not mean the dualism is to be inevitably accepted. In fact, the subjective categories arise in the limits of a life the area of which is substantially wider than that of science. An original information and physical hypothesis is being set up that provides for necessary premises and conditions enabling the origination of subjective categories of consciousness during the progressive natural evolution of living systems.","corpus_id":36838608,"score":2},{"doc_id":"20589952","title":"A natural science approach to consciousness.","abstract":"We begin with premises about natural science, its fundamental protocols and its limitations. With those in mind, we construct alternative descriptive models of consciousness, each comprising a synthesis of recent literature in cognitive science. Presuming that consciousness arose through natural selection, we eliminate the subset of alternatives that lack selectable physical phenotypes, leaving the subset with limited free will (mostly in the form of free won't). We argue that membership in this subset implies a two-way exchange of energy between the conscious mental realm and the physical realm of the brain. We propose an analogy between the mental and physical phases of energy and the phases (e.g., gas/liquid) of matter, and a possible realization in the form of a generic resonator. As candidate undergirdings of such a system, we propose astroglial-pyramidal cell and electromagnetic-field models. Finally, we consider the problem of identification of the presence of consciousness in other beings or in machines.","corpus_id":18684426,"score":2},{"doc_id":"21033194","title":"Science, conscience, consciousness.","abstract":"Descartes' metaphysics lays the foundation for the special sciences, and the notion of consciousness (\"conscientia\") belongs to metaphysics rather than to psychology. I argue that as a metaphysical notion, \"consciousness\" refers to an epistemic version of moral conscience. As a consequence, the activity on which science is based turns out to be conscientious thought. The consciousness that makes science possible is a double awareness: the awareness of what one is thinking, of what one should be doing, and of the possibility of a gap between the two.","corpus_id":22907051,"score":2},{"doc_id":"21033196","title":"Kant and the scientific study of consciousness.","abstract":"We argue that Kant's views about consciousness, the mind-body problem and the status of psychology as a science all differ drastically from the way in which these topics are conjoined in present debates about the prominent idea of a science of consciousness. Kant never used the concept of consciousness in the now dominant sense of phenomenal qualia; his discussions of the mind-body problem center not on the reducibility of mental properties but of substances; and his views about the possibility of psychology as a science did not employ the requirement of a mechanistic explanation, but of a quantification of phenomena. This shows strikingly how deeply philosophical problems and conceptions can change even if they look similar on the surface.","corpus_id":22053209,"score":2},{"doc_id":"21971695","title":"[The so-called body-mind problem].","abstract":"Das so genannte Leib-Seele-Problem. THE PROBLEM: Even psychosomatic researchers seem to want to avoid the so-called body-mind problem, which is actually a mind-brain problem. In line with Beckermann (2008), the first the four possible positions on the mind-brain problem are presented. The debate over the past 100 years has revolved around the question of whether mental events are ontologically independent of brain physiology or whether they are in fact entirely determined by it. Such a physicalism approach based on properties (i.e., mental characteristics or phenomena are physical or can be completely reduced to physical characteristics), however, is diametrically opposed to some of our strongest intuitions, e.g., that computers will never be able to develop qualities of human experience (qualia) and thus become subjects in the first person singular. Yet we are equally unable to prove the fundamental impossibility of such a development. THESIS: In this stalemate situation, a differentiation was undertaken by Gottlob Frege (1892) which could be of help: Expressed in today's language, a distinction is made between the sense of an expression, its contextual presentation (e.g., where there is a difference between \"the evening star\" and \"the morning star\"), on the one hand, and its so-called reference (the object to which it refers, here the planet Venus in both cases) on the other. The school of Gestalt psychology that developed in Berlin at the start of the last century similarly posited a \"psychophysical level of the CNS,\" a continuum in a pattern of electrical field forces which manifests itself first in cerebral physiological-neuronal processes as well as in other perspectives such as consciousness and experience. A subsequent speculative concept then extends this model to assume also an (as yet) unknown Alpha configuration as being a common reference of two sense contents: (1) the results of the neurophysiological third-person perspective and (2) of the emotional-cognitive first-person perspectives. Only through the latter will Alpha be able to become self-conscious and an instance acting in his world. RESULTS: Only through the latter will Alpha be able to become self-conscious and an instance acting in his world. The postulate of an Alpha configuration thus retains the possibility of a biology not (yet) accessible to our knowledge, such that our fundamental conviction regarding the holism of soma and psyche can be maintained for us as medical practitioners and scientific physicians. Our patients need both, our medical-scientific competence (3rd-person perspective) as well as our empathic sensibility in exploring their phenomenal experience (1st-person perspective). They need us as medical artists.","corpus_id":297834,"score":2},{"doc_id":"21988251","title":"Science, self, and immortality.","abstract":"The following considers the concept of scientific naturalism in relation to life after death and contrasts three alternative perspectives on immortality of the soul, including naturalistic fatalism, otherworldly optimism, and long-suffering hope.","corpus_id":2591321,"score":2},{"doc_id":"22577305","title":"Consciousness regained? Philosophical arguments for and against reductive physicalism.","abstract":"This paper is an overview of recent discussions concerning the mind-body problem, which is being addressed at the interface between philosophy and neuroscience. It focuses on phenomenal features of consciousness or \"qualia,\" which are distinguished from various related issues. Then follows a discussion of various influential skeptical arguments that question the possibility of reductive explanations of qualia in physicalist terms: knowledge arguments, conceivability arguments, the argument of multiple realizability, and the explanatory gap argument. None of the arguments is found to be very convincing. It does not necessarily follow that reductive physicalism is the only option, but it is defensible. However, constant conceptual and methodological reflection is required, alongside ongoing research, to keep such a view free from dogmatism and naivety.","corpus_id":16921142,"score":2},{"doc_id":"22654125","title":"The Vegetative State and the Science of Consciousness.","abstract":"Consciousness in experimental subjects is typically inferred from reports and other forms of voluntary behaviour. A wealth of everyday experience confirms that healthy subjects do not ordinarily behave in these ways unless they are conscious. Investigation of consciousness in vegetative state patients has been based on the search for neural evidence that such broad functional capacities are preserved in some vegetative state patients. We call this the standard approach. To date, the results of the standard approach have suggested that some vegetative state patients might indeed be conscious, although they fall short of being demonstrative. The fact that some vegetative state patients show evidence of consciousness according to the standard approach is remarkable, for the standard approach to consciousness is rather conservative, and leaves open the pressing question of how to ascertain whether patients who fail such tests are conscious or not. We argue for a cluster-based 'natural kind' methodology that is adequate to that task, both as a replacement for the approach that currently informs research into the presence or absence of consciousness in vegetative state patients and as a methodology for the science of consciousness more generally.","corpus_id":8896305,"score":2},{"doc_id":"23073546","title":"[What can qualia be? The monistic views].","abstract":"Phenomenal properties, also named qualia (that is, the qualities of human experiences, e.g. the senses of red, of salt, of pain, qua senses) create a hard problem for philosophy. It is claimed that phenomenal properties are radically different to the physical ones: they are intrinsic (their essence is totally confined within the limits of their existence), they depend on mind, they are accessible only privately, by introspection and they are infallible, in the sense that the experience of a quale is identical to its existence. On the contrary, physical properties are dispositional (their essence is defined through their causal consequences), they exist independently of mind, they are accessible to public observation and are liable to verification or falsification. The faculty of philosophy, named philosophy of mind, is systematically interested in qualia. In the present paper some of the main monistic philosophical approaches to qualia are discussed. The main common characteristic of monistic views is that (contrary to dualistic views) they purport that: two radically different substances cannot exist, side by side, within the same world (our world). Thus, there are either physical properties, or phenomenal properties, but not both. The monistic theories, supporting that in our world there are only physical properties, or properties totally reducible into physical ones, are named physicalism (or according to a more traditional nomination, materialism). On the other hand, monistic theories maintaining that all existing properties are phenomenal, or properties reducible into phenomenal ones, are named phenomenalism. The main arguments for physicalism are: (a) the scientific principle of the causal closure of the universe (every event has one physical cause), (b) the dependence of every well-studied mental phenomenon, from a physical phenomenal, such as the function of the neural system. Dualists counterattack physicalism with mental experiments (such as, the experiments concerning philosophical zombies) in order to demonstrate that qualia are irreducible entities. The main physicalistic options are eliminativism, the theories of identity, functionalism and representationalism. The main argument for phenomenalism is that physical properties and physical knowledge of them, as well, are reducible into and derived from experiences. On the other hand, opponents of phenomenalism retort that our world comprises spatiotemporal parts inaccessible to experience (f.e. the microworld of atomic physics, the world before the appearance of intelligent beings). Yet, some phenomenalists claim that phenomenal properties can be either real (experienced) or potentially real (what one would experience if one could observe this or that spatiotemporal part of the world). According to a third, agnosticistic opinion, named mysterianism, the human mind lacks the capacity of bridging the explanatory gap between physical and phenomenal identities. Many opponents of this theory claim the historically proved ability of human mind to find solutions for difficult problems of our world through scientific knowledge and based on it natural philosophy.","corpus_id":24773763,"score":2},{"doc_id":"23882252","title":"On the autonomy of the concept of disease in psychiatry.","abstract":"Does the reference to a mental realm in using the notion of mental disorder lead to a dilemma that consists in either implying a Cartesian account of the mind-body relation or in the need to give up a notion of mental disorder in its own right? Many psychiatrists seem to believe that denying substance dualism requires a purely neurophysiological stance for explaining mental disorder. However, this conviction is based on a limited awareness of the philosophical debate on the mind-body problem. This article discusses the reasonableness of the concept of mental disorder in relation to reductionist and eliminativist strategies in the philosophy of mind. It is concluded that we need a psychological level of explanation that cannot be reduced to neurophysiological findings in order to make sense of mental disorder.","corpus_id":561485,"score":2},{"doc_id":"24309878","title":"Implications of spiritual experiences to the understanding of mind-brain relationship.","abstract":"OBJECTIVE: While there has been a large increase in scientific studies on spirituality, there has been too few of studies of the core of spirituality: spiritual experiences (SE), which often involve altered states of consciousness, reports of anomalous experiences and of consciousness beyond the body. This paper argues that SE, although usually neglected in debates regarding mind-brain relationship (MBR), may provide the much needed enlargement of the empirical basis for advancing the understanding of the MBR. METHODS: This paper briefly presents and discusses recent scientific investigations on some types of SE (meditative states, end of life and near death experiences, mediumship and alleged memories of previous lives) and their implications to MBR. RESULTS: Neurofunctional studies of SE have shown that they are related to but not necessarily caused by complex functional patterns in several brain areas. The study of meditative states, as voluntarily induced mind states that influence brain states has been a privileged venue to investigate top-down (mind over brain) causation. End of life and near death experiences offer cases of unexpected adequate mental function under severe brain damage and/or dysfunction. Scientific investigations of several types of SE have provided evidence against materialistic reductionist views of mind. CONCLUSIONS: The recent trend to scientifically investigate SE has already produced interesting and thought-provoking findings that deserve careful further exploration. Because of their potential implication, these findings may also contribute to the understanding of MBR, which remains an important, yet poorly explored way to investigate human nature.","corpus_id":21157227,"score":2},{"doc_id":"24974626","title":"[Is the brain the creator of psychic phenomena or is a paradigm shift inevitable?].","abstract":"¿Es el cerebro el creador de los fenómenos psíquicos o es ineludible un cambio de paradigma? Every day new scientific information is appearing that cannot be explained using the classical Newtonian model and is calling for the emergence of a new paradigm that would include the explanation of such phenomena as telepathy, clairvoyance, presentiment, precognition, out of the body experiences, psychic healing, after-death communication, near-death experiences and reincarnation. The materialist paradigm which considers the brain as the sole cause of consciousness and psychic phenomena has been challenged by a new paradigm that seems to demonstrate that there is not a cause-effect relationship between brain activity and psychic phenomena but only a correlation between them, since these phenomena can be experienced without the body and appear to have an extra-cerebral origin (cosmic field, cosmic consciousness?). Of course, the brain is intensely involved in the manifestation of consciousness in our daily life but this is not equivalent to affirm that brain creates consciousness. Recent findings force us to consider a non-physical, spiritual and transpersonal aspect of reality.","corpus_id":24110348,"score":2},{"doc_id":"25892488","title":"Epistemological implications of near-death experiences and other non-ordinary mental expressions: Moving beyond the concept of altered state of consciousness.","abstract":"During the last decades an increasing interest has developed in the so-called altered state of consciousness (ASCs); among these, near-death experiences (NDEs) are one of the most intriguing and debated examples. NDEs are deep and universal experiences with a clear phenomenology and incidence, while some of their features challenge the current views of human consciousness (focused on neural circuits and based on the concept of mind as a byproduct of brain circuitry) with relevant epistemological and historical implications. The origin of the ruling mechanist-reductionist paradigm can be traced back to Descartes' radical separation of res cogitans and res extensa and the conflict between the nascent science and the Inquisition; this led to removing the subjective properties of mind from the field of scientific interest, relegating them to philosophy and theology in order to enable the development of modern science. However, the physics of the 20th century has eventually moved beyond the classical paradigm, permitting a profound renewal of scientific interest in the mind. Modern research on NDEs has contributed to reopening the debate surrounding the Cartesian separation, the mind-brain relationship and the nature of consciousness. It is now time to reappraise the relevance, strengths, and weaknesses of the available scientific interpretations of NDEs, their relationship with other ASCs, as well as the very concept of ASC; the latter looks to be ill-founded, suggesting the need for: (a) a revision of the conventional approach to subjective phenomena, including both the third- and first-person perspective; and (b) a deep reflection on the possible links between different non-ordinary mental expression, as regards both their phenomenology and mechanisms from a non-pathological perspective.","corpus_id":18815739,"score":2},{"doc_id":"26308870","title":"Attributions of consciousness.","abstract":"UNLABELLED: Many philosophers and brain scientists hold that explaining consciousness is one of the major outstanding problems facing modern science today. One type of consciousness in particular-phenomenal consciousness-is thought to be especially problematic. The reasons given for believing that this phenomenon exists in the first place, however, often hinge on the claim that its existence is simply obvious in ordinary perceptual experience. Such claims motivate the study of people's intuitions about consciousness. In recent years a number of researchers in experimental philosophy of mind have begun to shed light on this area, investigating how people understand and attribute those mental states that have been thought to be phenomenally conscious. In this article, we discuss the philosophical concept of phenomenal consciousness and detail the work that has been done on the question of whether lay people have this concept. WIREs Cogn Sci 2014, 5:635-648. doi: 10.1002/wcs.1320 For further resources related to this article, please visit the WIREs website. CONFLICT OF INTEREST: The author has declared no conflicts of interest for this article.","corpus_id":45317588,"score":2},{"doc_id":"26321981","title":"Pedagogical tools to explore Cartesian mind-body dualism in the classroom: philosophical arguments and neuroscience illusions.","abstract":"A fundamental discussion in lower-level undergraduate neuroscience and psychology courses is Descartes's \"radical\" or \"mind-body\" dualism. According to Descartes, our thinking mind, the res cogitans, is separate from the body as physical matter or substance, the res extensa. Since the transmission of sensory stimuli from the body to the mind is a physical capacity shared with animals, it can be confused, misled, or uncertain (e.g., bodily senses imply that ice and water are different substances). True certainty thus arises from within the mind and its capacity to doubt physical stimuli. Since this doubting mind is a thinking thing that is distinct from bodily stimuli, truth and certainty are reached through the doubting mind as cogito ergo sum, or the certainty of itself as it thinks: hence Descartes's famous maxim, I think, therefore I am. However, in the last century of Western philosophy, with nervous system investigation, and with recent advances in neuroscience, the potential avenues to explore student's understanding of the epistemology and effects of Cartesian mind-body dualism has expanded. This article further explores this expansion, highlighting pedagogical practices and tools instructors can use to enhance a psychology student's understanding of Cartesian dualistic epistemology, in order to think more critically about its implicit assumptions and effects on learning. It does so in two ways: first, by offering instructors an alternative philosophical perspective to dualistic thinking: a mind-body holism that is antithetical to the assumed binaries of dualistic epistemology. Second, it supplements this philosophical argument with a practical component: simple mind-body illusions that instructors may use to demonstrate contrary epistemologies to students. Combining these short philosophical and neuroscience arguments thereby acts as a pedagogical tool to open new conceptual spaces within which learning may occur.","corpus_id":7282992,"score":2},{"doc_id":"27412020","title":"[The mind-brain problem (I): onto-epistemological foundations].","abstract":"El problema mente-cerebro (I): fundamentos ontoepistemologicos. INTRODUCTION: Throughout the history of thought, science and philosophy have addressed the problem of mind-brain from different epistemic perspectives. The first covers specific areas of reality and constructs hypotheses with limited scope and multiple inter-scientific connectivity with the aim of validating theoretical models; the second extends its systemic architecture to all that is real (including scientific activity). DEVELOPMENT: The complexity of the mind-brain problem requires the generation of a link connecting the disciplines of philosophy and science; our onto-epistemological presuppositions therefore fall within the framework of a scientifically-oriented philosophy (scientific philosophy). Emergentist materialism is defended as a coherent and verifiable philosophical-scientific solution, as opposed to other proposals developed on the basis of different ontological models (for example, interactionist dualism, functionalism, theory of identity, epiphenomenalism, and so on). CONCLUSIONS: An answer to the mind-brain problem is only feasible if based on a philosophically grounded cognitive neuroscience: emergentist materialism -an ontological postulate- holds that the mind is an emergent property (qualitative novelty) of the brain; scientific realism -an epistemological postulate- holds that cognitive neuroscience is the basic theoretical-experimental tool that allows cognitive access to both the brain and its neurocognitive processes. We consider that on the basis of this philosophical reasoning, cognitive neuroscience acquires epistemic legitimacy to be able to undertake the study of the most genuinely human mental process: consciousness.","corpus_id":3789708,"score":2},{"doc_id":"29504485","title":"Framing the Mind-Body Problem in Contemporary Neuroscientific and Sunni Islamic Theological Discourse.","abstract":"Famously posed by seventeenth-century French philosopher René Descartes, the mind-body problem remains unresolved in western philosophy and science, with both disciplines unable to move convincingly beyond the dualistic model. The persistence of dualism calls for a reframing of the problem through interdisciplinary modes of inquiry that include non-western points of view. One such perspective is Islamic theology of the soul, which, while approaching the problem from a distinct point of view, also adopts a position commensurate with (substance) dualism. Using this point of convergence as a conceptual starting point, we argue that bringing into dialogue contemporary neuroscientific, philosophy of mind, and Sunni Islamic theological discourses may provide a fruitful way of reframing the age-old mind-body problem. This paper provides an overview of how these three discourses have approached the issue of the mind-body (-soul) problem. Juxtaposing these three discourses, we hope, may ignite further scholarly dialogue and investigation.","corpus_id":3676219,"score":2},{"doc_id":"29727520","title":"The mind-body problem.","abstract":"The mind-body problem is the problem of explaining how the happenings of our mental lives are related to physical states, events and processes. Proposed solutions to the problem vary by whether and how they endorse physicalism, the claim that mental states are ultimately \"nothing over and above\" physical states, and by how they understand the interactions between mental and physical states. Physicalist solutions to the mind-body problem have been dominant in the last century, with the variety of physicalism endorsed (reductive or nonreductive) depending upon both the outcome of philosophical arguments and methodological developments in the cognitive and neural sciences. After outlining the dominant contemporary approach to the mind-body problem, I examine the prospects for a solution in light of developments in the cognitive sciences, especially the scientific study of consciousness. This article is categorized under: Philosophy > Consciousness Philosophy > Metaphysics Philosophy > Foundations of Cognitive Science.","corpus_id":19237639,"score":2},{"doc_id":"18723943","title":"Reflections on humanizing biomedicine.","abstract":"Although biomedicine is responsible for the \"miracles\" of modern medicine, paradoxically it has also led to a quality-of-care crisis in which many patients feel disenfranchised from the health-care industry. To address this crisis, several medical commentators make an appeal for humanizing biomedicine, which has led to shifts in the philosophical boundaries of medical knowledge and practice. In this paper, the metaphysical, epistemological, and ethical boundaries of biomedicine and its humanized versions are investigated and compared to one another. Biomedicine is founded on a metaphysical position of mechanistic monism, an epistemology of objective knowing, and an ethic of emotionally detached concern. In humanizing modern medicine, these boundaries are often shifted to a metaphysical position of dualism/holism, an epistemology of subject knowing, and an ethic of empathic care. In a concluding section, the question is discussed whether these shifts in the philosophical boundaries are adequate to resolve the quality-of-care crisis.","corpus_id":22848400,"score":1},{"doc_id":"19012586","title":"Descartes' dreams.","abstract":"René Descartes is often regarded as the 'father of modern philosophy'. He was a key figure in instigating the scientific revolution that has been so influential in shaping our modern world. He has been revered and reviled in almost equal measure for this role; on the one hand seen as liberating science from religion, on the other as splitting soul from body and man from nature. He dates the founding of his philosophical methods to the night of 10(th) November 1619 and in particular to three powerful dreams he had that night. This article utilizes Descartes' own interpretations of the dreams, supported by biographical material, as well as contemporary neuroscientific and psychoanalytic theory, to reach a new understanding of them. It is argued that the dreams can be understood as depicting Descartes' personal journey from a state of mind-body dissociation to one of mind-body deintegration. This personal journey may have implications for a parallel journey from Renaissance to modern culture and from modernity to post-modern culture.","corpus_id":23703343,"score":1},{"doc_id":"19093679","title":"Whither the psychology of religion: a spirituality-focused discussion of Paloutzian and Park's (2005). Handbook of the psychology of religion and spirituality.","abstract":"Presuming Rayburn's (2006: Child & Family Behavior Therapy, 28, 86-92) review of (Paloutzian and Park's, (2005, New York: The Guilford Press) [corrected] Handbook of the Psychology of Religion and Spirituality [corrected] and sketching an alternative paradigm, this review focuses on the Handbook's virtual conflation of religion and spirituality; relates this conflation to the hegemony of Protestant theology in North American psychology of religion; highlights the Handbook's lack of attention to [corrected] spirituality per se, which--if [corrected] not inseparably linked with theism, but, rather, [corrected] related to the self-transcending, meaning-making dimension of the human mind--could [corrected] provide an explanatory breakthrough in the field of the psychology of religion and of the social sciences overall; and sees Handbook's advocacy for a \"multilevel interdisciplinary paradigm\" as a regrettable acceptance of the failed, long-term strategy of the field of psychology in general.","corpus_id":40692533,"score":1},{"doc_id":"21037408","title":"The philosophical \"mind-body problem\" and its relevance for the relationship between psychiatry and the neurosciences.","abstract":"Parallel to psychiatry, \"philosophy of mind\" investigates the relationship between mind (mental domain) and body/brain (physical domain). Unlike older forms of philosophy of mind, contemporary analytical philosophy is not exclusively based on introspection and conceptual analysis, but also draws upon the empirical methods and findings of the sciences. This article outlines the conceptual framework of the \"mind-body problem\" as formulated in contemporary analytical philosophy and argues that this philosophical debate has potentially far-reaching implications for psychiatry as a clinical-scientific discipline, especially for its own autonomy and its relationship to neurology/neuroscience. This point is illustrated by a conceptual analysis of the five principles formulated in Kandel's 1998 article \"A New Intellectual Framework for Psychiatry.\" Kandel's position in the philosophical mind-body debate is ambiguous, ranging from reductive physicalism (psychophysical identity theory) to non-reductive physicalism (in which the mental \"supervenes\" on the physical) to epiphenomenalist dualism or even emergent dualism. We illustrate how these diverging interpretations result in radically different views on the identity of psychiatry and its relationship with the rapidly expanding domain of neurology/neuroscience.","corpus_id":414110,"score":1},{"doc_id":"22622355","title":"Science, practice and mythology: a definition and examination of the implications of scientism in medicine.","abstract":"Scientism is a philosophy which purports to define what the world 'really is'. It adopts what the philosopher Thomas Nagel called 'an epistemological criterion of reality', defining what is real as that which can be discovered by certain quite specific methods of investigation. As a consequence all features of experience not revealed by those methods are deemed 'subjective' in a way that suggests they are either not real, or lie beyond the scope of meaningful rational inquiry. This devalues capacities that (we argue) are in fact essential components of good reasoning and virtuous practice. Ultimately, the implications of scientism for statements of value undermine value-judgements essential for science itself to have a sound basis. Scientism has implications, therefore, for ontology, epistemology and also for which claims we can assert as objective truths about the world. Adopting scientism as a world view will have consequences for reasoning and decision-making in clinical and other contexts. We analyse the implications of this approach and conclude that we need to reject scientism if we are to avoid stifling virtuous practice and to develop richer conceptions of human reasoning.","corpus_id":13445258,"score":1},{"doc_id":"22627668","title":"Epistemology of psychiatry.","abstract":"In historical and epistemological terms, psychiatry is a new discipline born during the 19th century. Rooted in both the natural and social sciences, psychiatric objects of inquiry, namely mental symptoms and mental disorders, are hybrid, constituted by the blending of components arising from disparate sources of knowledge ranging from the biological to the semantic in its widest sense. This poses problems for psychiatric research and therapy. Whilst conventional pluralism may be a convenient approach to manage aspects of psychiatric practice, it lacks the capacity to analyse psychiatric objects in their entirety. For the latter, psychiatry demands a new, tailored regional epistemology. This paper outlines the main features of an epistemology specific to the needs of psychiatry. It highlights the relational approach that needs to be taken and illustrates the usefulness of this approach by analysing the structure of psychiatric objects, exploring the manner in which they may be inscribed in the brain, and identifying the need to periodically recalibrate the language of psychiatry.","corpus_id":23136420,"score":1},{"doc_id":"22865511","title":"Haunted by the ghost in the machine. Commentary on \"The spirituality of human consciousness: a Catholic evaluation of some current neuro-scientific interpretations\".","abstract":"Metaphysical and epistemological dualism informs much contemporary discussion of the relationships of science and religion, in particular in relation to the neurosciences and the religious understanding of the human person. This dualism is a foundational artifact of modern culture; however, contemporary scientific research and historical theological scholarship encourage a more holistic view wherein human personhood is most fittingly understood as an emergent phenomenon of, but not simply reducible to, evolutionary and developmental neurobiology.","corpus_id":30268188,"score":1},{"doc_id":"23562082","title":"Beyond the pineal gland assumption: a neuroanatomical appraisal of dualism in Descartes' philosophy.","abstract":"OBJECTIVE: The problem of the substantial union of the soul and the body and therefore the mechanisms of interaction between them represents the core of the Cartesian dualistic philosophy. This philosophy is based upon a neuroanatomical obvious misconception, consisting mainly on a wrong intraventricular position of the pineal gland and its capacity of movement to act as a valve regulating the flow of animal spirits. Should we consider the Cartesian neurophysiology as a purely anatomical descriptive work and therefore totally incorrect, or rather as a theoretical conception supporting his dualistic philosophy? METHOD: From the various pre-Cartesian theories on the pineal organ, we try to explain how Descartes used his original conception of neuroanatomy to serve his dualistic philosophy. Moreover, we present an appraisal of the Cartesian neuroanatomical corpus from an anatomical but also metaphysical and theological perspectives. RESULTS: A new interpretation of Descartes' writings and an analysis of the secondary related literature shed the light on the voluntary anatomical approximations aiming to build an ad hoc neurophysiology that allows Descartes' soul-body theory. CONCLUSION: By its central position within the brain mass and its particular shape, the pineal gland raised diverse metaphysical theories regarding its function, but the most original theory remains certainly its role as the seat of soul in René Descartes' philosophy and more precisely the organ where soul and body interact. The author emphasizes on the critics raised by Descartes' theories on the soul-body interaction through the role of the pineal gland.","corpus_id":9140909,"score":1},{"doc_id":"24468878","title":"Disorders of consciousness after acquired brain injury: the state of the science.","abstract":"The concept of consciousness continues to defy definition and elude the grasp of philosophical and scientific efforts to formulate a testable construct that maps to human experience. Severe acquired brain injury results in the dissolution of consciousness, providing a natural model from which key insights about consciousness may be drawn. In the clinical setting, neurologists and neurorehabilitation specialists are called on to discern the level of consciousness in patients who are unable to communicate through word or gesture, and to project outcomes and recommend approaches to treatment. Standards of care are not available to guide clinical decision-making for this population, often leading to inconsistent, inaccurate and inappropriate care. In this Review, we describe the state of the science with regard to clinical management of patients with prolonged disorders of consciousness. We review consciousness-altering pathophysiological mechanisms, specific clinical syndromes, and novel diagnostic and prognostic applications of advanced neuroimaging and electrophysiological procedures. We conclude with a provocative discussion of bioethical and medicolegal issues that are unique to this population and have a profound impact on care, as well as raising questions of broad societal interest.","corpus_id":205515762,"score":1},{"doc_id":"25116396","title":"Nursing and the new biology: towards a realist, anti-reductionist approach to nursing knowledge.","abstract":"As a system of knowledge, nursing has utilized a range of subjects and reconstituted them to reflect the thinking and practice of health care. Often drawn to a holistic model, nursing finds it difficult to resist the reductionist tendencies in biological and medical thinking. In this paper I will propose a relational approach to knowledge that is able to address this issue. The paper argues that biology is not characterized by one stable theory but is often a contentious topic and employs philosophically diverse models in its scientific research. Biology need not be seen as a reductionist science, but reductionism is nonetheless an important current within biological thinking. These reductionist currents can undermine nursing knowledge in four main ways. Firstly, that the conclusions drawn from reductionism go far beyond their data based on an approach that prioritizes biological explanations and eliminates others. Secondly, that the methods employed by biologists are sometimes weak, and the limitations are insufficiently acknowledged. Thirdly, that the assumptions that drive the research agenda are problematic, and finally that uncritical application of these ideas can be potentially disastrous for nursing practice. These issues are explored through an examination of the problems reductionism poses for the issue of gender, mental health, and altruism. I then propose an approach based on critical realism that adopts an anti-reductionist philosophy that utilizes the conceptual tools of emergence and a relational ontology.","corpus_id":43796680,"score":1},{"doc_id":"25164301","title":"Explaining how the mind works: on the relation between cognitive science and philosophy.","abstract":"In this paper, we argue that under certain prevalent interpretations of the nature and aims of cognitive science, theories of cognition generate a forced choice between a conception of cognition which depends on the possibility of a private language, and a conception of cognition which depends on mereological confusions. We argue, further, that this should not pose a fundamental problem for cognitive scientists since a plausible interpretation of the nature and aims of cognitive science is available that does not generate this forced choice. The crucial difference between these interpretations is that on the one hand the aim of theories of cognition is to tell us what thinking (etc.) is, and on the other it is to tell us what is causally necessary if an intelligent creature is to be able to think. Our argument draws heavily on a Wittgensteinian conception of philosophy in which no philosophical theory can explain what thinking, perceiving, remembering, etc. are, either. The positive, strictly therapeutic, purpose of a philosophy of cognitive science should be to show that, since the traditional problems which constitute the philosophy of mind are chimerical, there is nothing for philosophical theorizing in cognitive science to achieve.","corpus_id":9272647,"score":1},{"doc_id":"25292274","title":"New epistemological foundations for cultural psychology: from an atomistic to a self-organizing view of living systems.","abstract":"An epistemological foundation for cultural psychology is essential to neuro- and behavioural sciences for the challenge psychological sciences must currently face: searching for an explanation of how a brain can become a mind and how individuals assign a sense to the world and their life. Biological systems are very likely determined by physical and chemical laws of spontaneous self-organization and endogenous constraints but, even if the major result of the Darwinian revolution is \"the discovery that living species are their story\", the modern synthesis of the evolution theory adopted only continuist and gradualist hypotheses. This nourished the analogy between the theory of natural selection and the theory of operant conditioning, thereby supporting empiricist associationism and the methodological positivism of behavioural and \"classical\" cognitive psychologists. Current scientific contributions provide evidence to the need for psychotherapy and psychopathology of a new epistemological approach in order to connect research stemming from animal models, up to the most abstract levels of personal meaning. The complex system oriented approach, here described, called \"post-rationalism\", shaped by a change initiated by evolutionary epistemology. The regulation of emotions initially develops within interpersonal relationships and evolves during both phylogeny and ontogeny, according to complex self-organization processes, leading to the acquisition of Self-organizing abilities and the construction of personal meaning. Endorsing the epistemological similarities of neo-Darwinism and behaviourism, and differentiating from this, the above mentioned approach, emphasises the fact that clinical and psycho-therapeutical practice must be founded on the laws of biological organisation: the ongoing activity of neurobiological systems, including the more abstract domains of thought and language.","corpus_id":16755223,"score":1},{"doc_id":"25363442","title":"Interpreting \"Mind-Cure\": William James and the \"chief task…of the science of human nature\".","abstract":"The private papers of the philosopher-psychologist, William James, indicate that he frequented several mental healers during his life, undertaking 100-200 therapeutic sessions concerning a range of symptoms from angina to insomnia. The success of the mind-cure movement constituted for James both a corroboration, and an extension, of the new research into the subconscious self and the psychogenesis of disease. Epistemologically, the experiences of those converts to the \"mind-cure religion\" exemplified his conviction that positivistic scientific enquiry can only reveal only one part of a wider reality. Metaphysically their reports comprised a powerful body of support for the existence of a \"higher consciousness,\" a supernatural world of some description. The positing of such a source of \"supernormal\" healing power was, for James, the best way to reconcile the accounts of those who had been regenerated, via their faith, despite having exhausted all natural reserves of energy and will.","corpus_id":25125104,"score":1},{"doc_id":"25452738","title":"Closing in on the constitution of consciousness.","abstract":"The science of consciousness is a nascent and thriving field of research that is founded on identifying the minimally sufficient neural correlates of consciousness. However, I have argued that it is the neural constitution of consciousness that science seeks to understand and that there are no evident strategies for distinguishing the correlates and constitution of (phenomenal) consciousness. Here I review this correlation/constitution distinction problem and challenge the existing foundations of consciousness science. I present the main analyses from a longer paper in press on this issue, focusing on recording, inhibition, stimulation, and combined inhibition/stimulation strategies, including proposal of the Jenga analogy to illustrate why identifying the minimally sufficient neural correlates of consciousness should not be considered the ultimate target of consciousness science. Thereafter I suggest that while combined inhibition and stimulation strategies might identify some constitutive neural activities-indeed minimally sufficient constitutive neural activities-such strategies fail to identify the whole neural constitution of consciousness and thus the correlation/constitution distinction problem is not fully solved. Various clarifications, potential objections and related scientific and philosophical issues are also discussed and I conclude by proposing new foundational claims for consciousness science.","corpus_id":7928552,"score":1},{"doc_id":"25546646","title":"[Reductionist approaches of complex problems: an epistemological and ethical reflection].","abstract":"Abordajes reduccionistas de problemáticas complejas: una reflexión epistemológica y ética. Reductionism is a constitutive feature of the \"standard view\" or inherited conception in philosophy of science, such as Enrique Marí says in his book \"Elements of comparative epistemology\". Whereas the \"standard view\" is one of the articulators of scientism - epistemological hegemonic position in the contexts of education, innovation, evaluation and application of techno-scientific knowledge - imposed an analysis of this concept as a necessary condition for its overcoming. This article intends to define the meaning and scope of the epistemological reductionism within the framework of the biomedical sciences, on the basis of their genealogy, and then moving in the explicitation of the multiple ways that invest for, finally, realize the consequences of his naive acceptance - or perhaps downright accomplice, of a great part of the scientific community. The consequences are presented in the field of theory, but very particularly in the field of praxis. Establishing the ethical implications of the epistemological reductionism in the theory and practice of Biomedical Sciences is the objective of this work.","corpus_id":31548919,"score":1},{"doc_id":"25682384","title":"Only one mind: an artist's exploration of consciousness.","abstract":"The aim of this article is to critique the contemporary scientific reduction of mind to brain and to explore the imaginal realm of consciousness. Through the author's own practice as an engraver, and through the researches and discoveries of free-thinking scientists, philosophers and artists, this realm of the \"One Mind\" is revealed to be timeless and universal.","corpus_id":31276538,"score":1},{"doc_id":"25756252","title":"[When science becomes technology: epistemological and ethical consequences of the Adduction].","abstract":"Quando la scienza diviene tecnologia: conseguenze epistemologiche ed etiche della Adduzione. Notwithstanding that the sciences are every day closest to technology, the Philosophy of Science has not yet well realized the epistemological and ethical differences that make different the \"Traditional Naturalistic Science\" (TNS) and the technological, artefactual, intrusive science that I called: \"Post-Modern Meta-Naturalistic Science\" (P-MM-NS). The first type of science has as a primary scope the knowledge of nature, using a methodology that departs from the methodic doubt, realizes a hypothesis, defines the aim(s), adopts a protocol, interprets and discusses the results, inferentially derives the conclusions, according to the classical philosophical reasonings of induction, deduction, abduction. In my philosophical reasoning, I realized that P-MM-NS follows an absolutely different epistemological procedure. The technological science prefigures a scope, produces a non-natural technically-modified object, gives for sure the occurrence of the effect for which the object has been manufactured. This means that only \"in retrospect\" it will ascertain whether or not the promised effect has occurred, considering that any technical artifact could be rejected by that natural environment in which it has been, acritically, delivered, without knowing how to remedy in case of an unexpected effect. In such a circumstance, the technological science has totally failed in its scope and effect, The potential failure of the predicted effect will prove that P-MM-NS follows a logical reasoning that is substantially and formally \"sui generis\" with respect to the epistemology and ethics of NS. This divergence from the classic reasoning of induction, deduction, abduction, has been called by me: \"Adduction\", because of the following considerations: the scientific procedure doesn't depart from the methodic doubt and hypothesis, only declares a scope, for which it is produced a technically-manufactured object, and gives for sure which will be the expected effect, but, not knowing how to remedy to negative results in case of a failure. It is, thus, clearly visible that the adduction is a type of logical reasoning that is self-referential and tautogical, being only based on a declaration of intents, adducted for justifying the production of a technical artifact, assuring an effect without suspecting that it could not respond to the promised scope.","corpus_id":-1,"score":1},{"doc_id":"26143599","title":"Why natural science needs phenomenological philosophy.","abstract":"Through an exploration of theoretical physics, this paper suggests the need for regrounding natural science in phenomenological philosophy. To begin, the philosophical roots of the prevailing scientific paradigm are traced to the thinking of Plato, Descartes, and Newton. The crisis in modern science is then investigated, tracking developments in physics, science's premier discipline. Einsteinian special relativity is interpreted as a response to the threat of discontinuity implied by the Michelson-Morley experiment, a challenge to classical objectivism that Einstein sought to counteract. We see that Einstein's efforts to banish discontinuity ultimately fall into the \"black hole\" predicted in his general theory of relativity. The unavoidable discontinuity that haunts Einstein's theory is also central to quantum mechanics. Here too the attempt has been made to manage discontinuity, only to have this strategy thwarted in the end by the intractable problem of quantum gravity. The irrepressible discontinuity manifested in the phenomena of modern physics proves to be linked to a merging of subject and object that flies in the face of Cartesian philosophy. To accommodate these radically non-classical phenomena, a new philosophical foundation is called for: phenomenology. Phenomenological philosophy is elaborated through Merleau-Ponty's concept of depth and is then brought into focus for use in theoretical physics via qualitative work with topology and hypercomplex numbers. In the final part of this paper, a detailed summary is offered of the specific application of topological phenomenology to quantum gravity that was systematically articulated in The Self-Evolving Cosmos (Rosen, 2008a).","corpus_id":207336376,"score":1},{"doc_id":"26978563","title":"Are Allopathic and Holistic Medicine Incommensurable?","abstract":"The shift from the Aristotelian to the Newtonian scientific paradigm gave birth to progresses in the natural, hard sciences and contributed to the emergence of modernity. Allopathic medicine gradually implemented those progresses, transforming itself into contemporary biomedicine. In the early 20th century, replacement of Newtonian physics by quantum mechanics and Einstein's theory of relativity resulted in a new paradigm shift in the natural, hard sciences. This shift gave birth to post-modern perceptions, which attempt to put those changes in context. Within this new context, holistic therapeutic approaches are considered more compatible with the new paradigm. Different paradigms in the natural, hard sciences are considered to be incommensurable (in the Kuhnian sense). This incommensurability is also transferred to the different societal contexts, the different «Weltanschauungen» that rely on different scientific paradigms. However, drawing on arguments that range from historical and philosophical to practical and sociological ones, we argue that, although based on different scientific paradigms, allopathic and holistic medicine are not incommensurable, but rather complementary. This may be related to the inherent attributes of medicine, a fact that reinforces the debate on its epistemological status.","corpus_id":36644651,"score":1},{"doc_id":"27271129","title":"Ancient Ethical Practices of Dualism and Ethical Implications for Future Paradigms in Nursing.","abstract":"Paradigms contain theoretical structures to guide scientific disciplines. Since ancient times, Cartesian dualism has been a prominent philosophy incorporated in the practice of medicine. The discipline of nursing has continued the body-mind emphasis with similar paradigmatic thinking and theories of nursing that separate body and mind. Future trends for paradigm and nursing theory development are harkening to former ways of thinking. In this article the author discusses the origins of Cartesian dualism and implications for its current usage. The author shall illuminate what it potentially means to engage in dualism in nursing and discuss possible ethical implications for future paradigm and theory development in nursing.","corpus_id":5217760,"score":1},{"doc_id":"18582293","title":"Critical realism: a philosophical framework for the study of gender and mental health.","abstract":"This paper explores gender and mental health with particular reference to the emerging philosophical field of critical realism. This philosophy suggests a shared ontology and epistemology for the natural and social sciences. Until recently, most of the debate surrounding gender and mental health has been guided either implicitly or explicitly within a positivist or constructivist philosophy. With this in mind, key areas of critical realism are explored in relation to gender and mental health, and contrasted with the positions of positivism and constructivism. It is argued that critical realism offers an alternative philosophical framework for the exploration of gender issues within mental health care.","corpus_id":22203664,"score":0},{"doc_id":"18816337","title":"The logic of turmoil: some epistemological and clinical considerations on emotional experience and the infinite.","abstract":"The idea of the infinite has its origins in the very beginnings of western philosophy and was developed significantly by modern philosophers such as Galileo and Leibniz. Freud discovered the Unconscious which does not respect the laws of classical logic, flouting its fundamental principle of non-contradiction. This opened the way to a new epistemology in which classical logic coexists with an aberrant logic of infinite affects. Matte Blanco reorganized this Freudian revolution in logic and introduced the concept of bi-logic, which is an intermingling of symmetric and Aristotelic logics. The authors explore some epistemological and clinical aspects of the functioning of the deep unconscious where the emergence of infinity threatens to overwhelm the containing function of thought, connecting this topic to some of Bion's propositions. They then suggest that bodily experiences can be considered a prime source of the logic of turmoil, and link a psychoanalytic consideration of the infinite to the mind-body relation. Emotional catastrophe is seen both as a defect-a breakdown of the unfolding function which translates unconscious material into conscious experience-and as the consequence of affective bodily pressures. These pressures function in turn as symmetrizing or infinitizing operators. Two clinical vignettes are presented to exemplify the hypotheses.","corpus_id":29590245,"score":0},{"doc_id":"18840335","title":"[A reflection on \"nursing science\"].","abstract":"Una reflexión en torno a las \"ciencias de la enfermería\" The present article provides a reflection on the concept of \"nursing science\", a concept that is increasingly used in Spain. The article begins by discussing the scientific paradigms of nursing, continues briefly with the notion of science, and subsequently addresses the concept of nursing science more thoroughly in a three-fold manner. First, we reflect on the center of interest or essence of the discipline of nursing: nursing care. Then, we address the influence of the distinct paradigms in the understanding of this center of interest and support the development of nursing knowledge from a multiple paradigmatic perspective. Lastly, we contrast nursing science and nursing practice in an attempt to explain their interdependence and mutual need within an eminently practical discipline: the discipline of nursing.","corpus_id":12825715,"score":0},{"doc_id":"19337202","title":"Epistemologic inquiries in evidence-based medicine.","abstract":"BACKGROUND: Since the term \"evidence-based medicine\" (EBM) first appeared in the scientific literature in 1991, the concept has had considerable influence in many parts of the world. Most professional societies, the public,and funding agencies have accepted EBM with remarkable enthusiasm. The concept of evidence-based practice is now applied in management, education, criminology, and social work. Yet, EBM has attracted controversy: its critics allege that EBM uses a narrow concept of evidence and a naive conception of the relationships between evidence, theory, and practice. They also contend that EBM presents itself as a radical restructuring of medical knowledge that discredits more traditional ways of knowing in medicine, largely in the interests of people with a particular investment in the enterprise of large-scale clinical trials. Because EBM proposes aspecific relationship between theory, evidence, and knowledge, its theoretical basis can be understood as an epistemological system. Undertaking epistemological inquiry is important because the adoption of a particular epistemological view defines how science is conducted. METHODS: In this paper, we challenge this critical view of EBM by examining how EBM fits into broad epistemological debates within the philosophy of science. We consider how EBM relates to some classical debates regarding the nature of science and knowledge. We investigate EBM from the perspective of major epistemological theories (logical-positivism/inductivism, deductivism/falsificationism/theory-ladeness of observations, explanationism/holism, instrumentalism, underdetermination theory by evidence). RESULTS: We first explore the relationship between evidence and knowledge and discuss philosophical support for the main way that evidence is used in medicine: (1) in the philosophical tradition that \"rational thinkers respect their evidence,\" we show that EBM refers to making medical decisions that are consistent with evidence, (2) as a reliable sign, symptom, or mark to enhance reasonableness or truthfulness of some particular claim (\"evidence as a guide to truth\"), and (3) to serve as a neutral arbiter among competing views. Our analysis indicates that EBM does not have a rigorous epistemological stance. In fact, EBM enthusiastically draws on all major traditions of philosophical theories of scientific evidence. CONCLUSIONS: Our findings indicate that EBM should not be construed as a new scientific or philosophical theory that changes the nature of medicine or our understanding thereof. Rather, we should consider EBM as a continuously evolving heuristic structure for optimizing clinical practice.","corpus_id":16468941,"score":0},{"doc_id":"19794882","title":"Translational science: epistemology and the investigative process.","abstract":"The term \"translational science\" has recently become very popular with its usage appearing to be almost exclusively related to medicine, in particular, the \"translation\" of biological knowledge into medical practice. Taking the perspective that translational science is somehow different than science and that sound science is grounded in an epistemology developed over millennia, it seems imperative that the meaning of translational science be carefully examined, especially how the scientific epistemology manifests itself in translational science. This paper examines epistemological issues relating mainly to modeling in translational science, with a focus on optimal operator synthesis. It goes on to discuss the implications of epistemology on the nature of collaborations conducive to the translational investigative process. The philosophical concepts are illustrated by considering intervention in gene regulatory networks.","corpus_id":14906792,"score":0},{"doc_id":"20017878","title":"Professional knowledge and the epistemology of reflective practice.","abstract":"Reflective practice is one of the most popular theories of professional knowledge in the last 20 years and has been widely adopted by nursing, health, and social care professions. The term was coined by Donald Schön in his influential books The Reflective Practitioner, and Educating the Reflective Practitioner, and has garnered the unprecedented attention of theorists and practitioners of professional education and practice. Reflective practice has been integrated into professional preparatory programmes, continuing education programmes, and by the regulatory bodies of a wide range of health and social care professions. Yet, despite its popularity and widespread adoption, a problem frequently raised in the literature concerns the lack of conceptual clarity surrounding the term reflective practice. This paper seeks to respond to this problem by offering an analysis of the epistemology of reflective practice as revealed through a critical examination of philosophical influences within the theory. The aim is to discern philosophical underpinnings of reflective practice in order to advance increasingly coherent interpretations, and to consider the implications for conceptions of professional knowledge in professional life. The paper briefly examines major philosophical underpinnings in reflective practice to explicate central themes that inform the epistemological assumptions of the theory. The study draws on the work of Donald Schön, and on texts from four philosophers: John Dewey, Nelson Goodman, Michael Polanyi, and Gilbert Ryle. Five central epistemological themes in reflective practice are illuminated: (1) a broad critique of technical rationality; (2) professional practice knowledge as artistry; (3) constructivist assumptions in the theory; (4) the significance of tacit knowledge for professional practice knowledge; and (5) overcoming mind body dualism to recognize the knowledge revealed in intelligent action. The paper reveals that the theory of reflective practice is concerned with deep epistemological questions of significance to conceptions of knowledge in health and social care professions.","corpus_id":5230304,"score":0},{"doc_id":"20589363","title":"Epistemology.","abstract":"This entry begins by presenting the origin, history and etymology of the term, as well as a short definition of epistemology as the discipline that deals with the nature, origin, validity and limits of knowledge. Then we focus on the classical platonic analysis of knowledge as truth justified belief. Against the backdrop of this platonic notion we present other relevant perspectives. It is essential to follow the history of the relation between origin and justification of knowledge until the contemporary separation of both problems. The study of the origin of knowledge seems to require a naturalized epistemology, while the problem of justification is usually approached from a philosophical point of view, whether coherentist, foundationalist or fallibilist. However, currently some authors are advocating for a full naturalized epistemology, while others are extending the philosophical point of view also to the genesis of knowledge.","corpus_id":-1,"score":0},{"doc_id":"21449197","title":"[Introduction to epistemology in nursing sciences].","abstract":"Introduction à l'épistémologie en sciences infirmières. The development of nursing research is one of the stages in the process for the professionalization of nurses. An epistemological reflection which took place gradually became necessary. Today, three traditions derived from the positivist, interpretative and critical approaches orientate reflections on nursing sciences, not without some controversy and debate.","corpus_id":32814863,"score":0},{"doc_id":"21567307","title":"[Ludovico Geymonat: The problem of historical epistemology].","abstract":"Ludovico Geymonat le Problème de L'épistémologie Historique Ludovico Geymonat: Das Probllem der Historischen Eepistemologie Ludovico Geymonat: Il Probllema dell'Epistemologia Storica. The study of the various inspirations of Ludovico Geymonat's epistemology (positivism and neopositivism, neorationalism, historicism and dialectical materialism) illustrates the way in which for the Italian philosopher the problem of objectivity of knowledge remains inseparable from the historicity of the sciences. Geymonat's epistemological approach associates scientific progress to its objectivity.","corpus_id":7848520,"score":0},{"doc_id":"21657127","title":"Grasping the spirit in nature: Anschauung in Ørsted's epistemology of science and beauty.","abstract":"The intersection between art, poetry, philosophy and science was the leitmotif which guided the lives and careers of romantic natural philosophers including that of the Danish natural philosopher, H. C. Ørsted. A simple model of orsted's career would be one in which it was framed by two periods of philosophical speculation: the youth's curious and idealistic interest in new attractive thoughts and the experienced man's mature reflections at the end of his life. We suggest that a closer look at the epistemological aspects of his works on the theory of beauty reveals a connection between this late work and his early philosophical work including experimental philosophy, but also with the work in teaching and textbook writing, that lies in between. The latter includes Ørsted's view on the application of mathematics in natural philosophy as well as his failed attempt at a genetic presentation of elementary geometry.","corpus_id":9088751,"score":0},{"doc_id":"21836785","title":"Notes on a few issues in the philosophy of psychiatry.","abstract":"THE FIRST PART CALLED THE PREAMBLE TACKLES: (a) the issues of silence and speech, and life and disease; (b) whether we need to know some or all of the truth, and how are exact science and philosophical reason related; (c) the phenomenon of Why, How, and What; (d) how are mind and brain related; (e) what is robust eclecticism, empirical/scientific enquiry, replicability/refutability, and the role of diagnosis and medical model in psychiatry; (f) bioethics and the four principles of beneficence, non-malfeasance, autonomy, and justice; (g) the four concepts of disease, illness, sickness, and disorder; how confusion is confounded by these concepts but clarity is imperative if we want to make sense out of them; and how psychiatry is an interim medical discipline. THE SECOND PART CALLED THE ISSUES DEALS WITH: (a) the concepts of nature and nurture; the biological and the psychosocial; and psychiatric disease and brain pathophysiology; (b) biology, Freud and the reinvention of psychiatry; (c) critics of psychiatry, mind-body problem and paradigm shifts in psychiatry; (d) the biological, the psychoanalytic, the psychosocial and the cognitive; (e) the issues of clarity, reductionism, and integration; (f) what are the fool-proof criteria, which are false leads, and what is the need for questioning assumptions in psychiatry. The third part is called Psychiatric Disorder, Psychiatric Ethics, and Psychiatry Connected Disciplines. It includes topics like (a) psychiatric disorder, mental health, and mental phenomena; (b) issues in psychiatric ethics; (c) social psychiatry, liaison psychiatry, psychosomatic medicine, forensic psychiatry, and neuropsychiatry. The fourth part is called Antipsychiatry, Blunting Creativity, etc. It includes topics like (a) antipsychiatry revisited; (b) basic arguments of antipsychiatry, Szasz, etc.; ( c) psychiatric classification and value judgment; (d) conformity, labeling, and blunting creativity. The fifth part is called The Role of Philosophy, Religion, and Spirituality in Psychiatry. It includes topics like (a) relevance of philosophy to psychiatry; (b) psychiatry, religion, spirituality, and culture; (c) ancient Indian concepts and contemporary psychiatry; (d) Indian holism and Western reductionism; (e) science, humanism, and the nomothetic-idiographic orientation. The last part, called Final Goal, talks of the need for a grand unified theory. The whole discussion is put in the form of refutable points.","corpus_id":23082100,"score":0},{"doc_id":"22397137","title":"[Science in the crosshairs of enlightenment. Significance of hypothetical thinking].","abstract":"Wissenschaft im Fadenkreuz der Aufklärung. Zur Tragweite des hypothetischen Denkens. To further the enlightenment primarily or even only by means of science was the hope of most representatives of the movement of the enlightenment which gave its name to a whole period of European cultural history. Only a few of its representatives, like Montesquieu and Rousseau, doubted for good reasons, whether and how the goals of the enlightenment can be reached at all by the means of science alone. In his Discours préliminaires to the Encyclopédie D'Alembert still wanted to limit science proper to the narrower field of those kinds of research which were strictly based on observations and calculations alone. In this way he remained committed to Descartes' ideal method of receiving authentic knowledge only by deduction from evident axioms or fundamental theorems. Pascal's casual discovery of the calculation of probabilities allowed to apply mathematics on the hidden laws of the apparent casualties of the human life world. Bacon's project of empirical science as a rational and methodological art of conducting experiments could replace the methodological ideal of science more geometrico. Lichtenberg's refined sensibility for the subjunctive linguistic forms of hypothetical thinking indicates a new understanding of inventing and testing hypotheses as the two most important methods of the experimental sciences when compared to the formal sciences of logic and mathematics. Whoever is studying the history of science of modern times in the cross wire of the enlightenment, will realize soon that science has always been in need of being illuminated about its own chances, risks and side effects. The project of enlightenment through science had to be complemented by the project of an enlightenment about science right from its beginning. Because of the implicit risks and side effects the project of enlightenment has to be enlightenment despite of science and because of science. On the one hand, as a special form of human practice the sciences are directed towards theoretical goals and practical purposes such that their agents cannot be conscious of all aspects of their practices in advance and reflect about all of them at the same time. On the other hand, the agents of such scientific practices are rarely trained, to analyze the cognitive implications of their own actions with the conceptual means of philosophical analysis. Furthermore, the agents of scientific research are hardly able to foresee the theoretical results of their research or even predict the chances and risks of eventual applications with the methods of the social sciences. Despite of the chastening experiences with the ambivalence of the theoretical results and practical applications of the modern sciences and despite of the illuminating effects of modern history and theory of science, contemporary scientists are not fully conscious yet of what they are really doing and what science really is. The contemplative ideal of scientific investigations for their own sake has been replaced in modern times by the practical ideal of scientific research in the service of humanity. The emancipation of the modem sciences from philosophical authorities and religious institutions has freed at first the sciences from alien restrictions to their self-chosen objects and purposes of research. However, the increasing economic constraints and the political dependences prevented even more so that scientists could realize the autonomy which the representatives of the enlightenment had been hoping for. KANT defined the goal of enlightenment as \"man's emergence from his self-incurred immaturity\". Quoting HORACE'S Sapere aude! he appealed to the courage of his comrades to use their own reason without the guidance of others in philosophical and especially in religious matters. Intellectual maturity as the proper goal of the enlightenment remained to be an undelivered promise despite of the emancipation of the sciences from traditional philosophical authorities and religious institutions. It is not only arguable whether or not enlightenment in this understanding is possible for most people, but also whether it is even desirable for all people considering the implicit ambivalence of the modern sciences. Kant's main philosophical works can be adequately interpreted as the first and unique attempt to understand the potential of the cognitive capacities of human beings about the chances and risks of enlightenment itself by means of a critical inquiry. This holds especially for the practical fruits of the enlightenment as, e.g., with respect to the emancipation from superstition and the appeal to religious tolerance, to the republican idea of the state and the establishment of civil and human rights, to the humanization of the law and execution of legal penalty as well as the unalienable rights of each individual human being.","corpus_id":34330323,"score":0},{"doc_id":"23483470","title":"[Philosophy within the context of neurosciences].","abstract":"La filosofia en el marco de las neurociencias. Based on the interrelation between science and philosophy, this article addresses the impact of neurosciences on the philosophical issues posed by today's society, especially those related with epistemology and the philosophy of science. To do so, the different approaches in the cognitive sciences are taken into account, with special attention paid to those that have to do with social, embodied and situated cognition versus a more individual, rational and abstract cognition. This initial framework is taken as the starting point with which to analyse the ways of representing knowledge and the characteristics of the cognoscente agent.","corpus_id":22650139,"score":0},{"doc_id":"23640189","title":"Reflection: medicines for children--science alone is not enough.","abstract":"PURPOSE: Access to medicines filling children's therapeutic needs is a long-standing global problem. The problem has been recognised and initiatives for correction were adopted in the USA in the late 1990s, and in the European Union in the first decade of this century. Paediatric medicines are particularly problematic in middle- and low-income countries, where most of the children of the world live. METHODS: A paediatric medicines initiative involving the WHO in parallel with the US and EU initiatives was seen as important by the global paediatric and paediatric clinical pharmacology community, but the WHO was resistant to getting involved. RESULTS: Advocacy, networking, cooperation, persistence, hard work and some luck were needed to get the \"Better medicines for children\" resolution 60.20 adopted by the World Health Assembly in May 2007. CONCLUSION: Science has been a key enabler of the developments leading to and following the adoption of the paediatric initiatives, but as the example of the WHO shows, science alone was not enough to make the change.","corpus_id":30362156,"score":0},{"doc_id":"24596845","title":"A brief philosophical encounter with science and medicine.","abstract":"We show a lot of respect for science today. To back up our claims, we tend to appeal to scientific methods. It seems that we all agree that these methods are effective for gaining the truth. We can ask why science has its special status as a supplier of knowledge about our external world and our bodies. Of course, one should not always trust what scientists say. Nonetheless, epistemological justification of scientific claims is really a big project for philosophers of science. Philosophers of science are interested in knowing how science proves what it does claim and why it gives us good reasons to take these claims seriously. These questions are epistemological questions. Epistemology is a branch of philosophy which deals with knowledge claims and justification. Besides epistemological questions, metaphysical and ethical issues in science are worthy of philosophical scrutiny. This paper gives a short survey of these intellectually demanding issues.","corpus_id":9014233,"score":0},{"doc_id":"25007445","title":"[Scientific revolution and embryology: rejection or transformation of antiquity? A comparison between the procreation teachings of Cesare Cremonini, William Harvey und René Descartes].","abstract":"Wissenschaftliche Revolution und Embryologie: Ablehnung oder Transformation der Antike? Ein Vergleich zwischen den Zeugungslehren Cesare Cremoninis, William Harveys und René Descartes. In this paper I address the issue of the theoretical and epistemological status of embryology at the rise of the so-called \"Scientific Revolution\" (also in the first half of the seventeenth-century) and raise the question, in what sense and to what extent the historiographical concept of \"Scientific Revolution\" is applicable to the domain of embryology. To achieve this aim I compare the theories of three protagonists of the medical, scientific and philosophical debate of that age, namely Cesare Cremonini, William Harvey and René Descartes, who had very different views on the world structure and human nature and a very different concept of science, but who shared, as concerns embryological issues, an epigenetic conception of the development of the embryo. Their theories are discussed and compared in light of following questions: 1) What do Cremonini's, Harvey's and Descartes's embryological theories exactly aim to?; 2) In developing their theories, do these thinkers deal explicitly or implicitly with the Aristotelian and the Galenic embryological paradigm?; 3)Do they refer polemically to the Aristotelian and the Galenic tradition and what theoretical and/or rhetorical function have these polemical references?; 4) Do the embryological theories of Cremonini, Harvey and Descartes reflect the century-long dispute between \"(Aristotelian) philosophers\" and \"(Galenic) doctors\"?; 5) How is represented embryology as a 'scientific' and/or 'theoretical' domain? And what relationship between concepts of 'truth', 'research', 'tradition' and 'scientific progress' is implied or proposed in the embryological works of these three thinkers? What kind of use do Cremonini, Harvey and Descartes make of the argumenta ex ratione and of those ex experientia?","corpus_id":44398371,"score":0},{"doc_id":"25281293","title":"Conceiving \"personality\": Psychologist's challenges and basic fundamentals of the Transdisciplinary Philosophy-of-Science Paradigm for Research on Individuals.","abstract":"Scientists exploring individuals, as such scientists are individuals themselves and thus not independent from their objects of research, encounter profound challenges; in particular, high risks for anthropo-, ethno- and ego-centric biases and various fallacies in reasoning. The Transdisciplinary Philosophy-of-Science Paradigm for Research on Individuals (TPS-Paradigm) aims to tackle these challenges by exploring and making explicit the philosophical presuppositions that are being made and the metatheories and methodologies that are used in the field. This article introduces basic fundamentals of the TPS-Paradigm including the epistemological principle of complementarity and metatheoretical concepts for exploring individuals as living organisms. Centrally, the TPS-Paradigm considers three metatheoretical properties (spatial location in relation to individuals' bodies, temporal extension, and physicality versus \"non-physicality\") that can be conceived in different forms for various kinds of phenomena explored in individuals (morphology, physiology, behaviour, the psyche, semiotic representations, artificially modified outer appearances and contexts). These properties, as they determine the phenomena's accessibility in everyday life and research, are used to elaborate philosophy-of-science foundations and to derive general methodological implications for the elementary problem of phenomenon-methodology matching and for scientific quantification of the various kinds of phenomena studied. On the basis of these foundations, the article explores the metatheories and methodologies that are used or needed to empirically study each given kind of phenomenon in individuals in general. Building on these general implications, the article derives special implications for exploring individuals' \"personality\", which the TPS-Paradigm conceives of as individual-specificity in all of the various kinds of phenomena studied in individuals.","corpus_id":16259191,"score":0},{"doc_id":"25644235","title":"Habermasian knowledge interests: epistemological implications for health sciences.","abstract":"The Habermasian concept of 'interest' has had a profound effect on the characterization of scientific disciplines. Going beyond issues unrelated to the theory itself, intra-theoretical interest characterizes the specific ways of approaching any science-related discipline, defining research topics and methodologies. This approach was developed by Jürgen Habermas in relation to empirical-analytical sciences, historical-hermeneutics sciences, and critical sciences; however, he did not make any specific references to health sciences. This article aims to contribute to shaping a general epistemological framework for health sciences, as well as its specific implications for the medical and nursing areas, via an analysis of the basic knowledge interests developed by Habermas.","corpus_id":12030588,"score":0},{"doc_id":"27339891","title":"Research philosophy in pharmacy practice: necessity and relevance.","abstract":"OBJECTIVE: Pharmacy practice has gradually evolved with the paradigm shifted towards patient-focused practice or medicines optimisation. The advancement of pharmacy-related research has contributed to this progression, but the philosophy of research remained unexplored. This review was thus aimed to outline the succinct concept of research philosophy and its application in pharmacy practice research. KEY FINDINGS: Research philosophy has been introduced to offer an alternative way to think about problem-driven research that is normally conducted. To clarify the research philosophy, four research paradigms, i.e. positivism (or empiricism), postpositivism (or realism), interpretivism (or constructivism) and pragmatism, are investigated according to philosophical realms, i.e. ontology, epistemology, axiology and logic of inquiry. With the application of research philosophy, some examples of quantitative and qualitative research were elaborated along with the conventional research approach. Understanding research philosophy is crucial for pharmacy researchers and pharmacists, as it underpins the choice of methodology and data collection. CONCLUSIONS: The review provides the overview of research philosophy and its application in pharmacy practice research. Further discussion on this vital issue is warranted to help generate quality evidence for pharmacy practice.","corpus_id":205198550,"score":0},{"doc_id":"27925104","title":"Epistemology of nursing care: a reflection on its foundations.","abstract":"Epistemologia do cuidado de enfermagem: uma reflexão sobre suas bases. Objective:: to reflect on nursing care and its epistemology from its historical, theoretical, philosophical, spiritual dimensions and as a social practice. Method:: discussions originated in the discipline \"Epistemology of caring\", from the graduate nursing program of the School of Nursing, Federal University of Minas Gerais, and in critical analysis of nursing literature together with the professional practice of the authors. Results:: we identified the necessity of developing a critical conscience on health care provision, research, and teaching, as well as on challenges in maintaining high standards of working interpersonal relationships, which has a profound impact on population health. Conclusion:: we suggest the rescue of integrality, humanization, unity, and spirituality in researches and practices of individual, familiar, and community care, as an advance in incorporating epistemology of caring in nursing.","corpus_id":7275618,"score":0},{"doc_id":"29147898","title":"\"Don't Mind the Gap!\" Reflections on Improvement Science as a Paradigm.","abstract":"Responding to this issue's invitation to bring new disciplinary insights to the field of improvement science, this article takes as its starting point one of the field's guiding metaphors: the imperative to \"mind the gap\". Drawing on insights from anthropology, history, and philosophy, the article reflects on the origins and implications of this metaphoric imperative, and suggests some ways in which it might be in tension with the means and ends of improvement. If the industrial origins of improvement science in the twentieth century inform a metaphor of gaps, chasms, and spaces of misalignment as invariably imperfect and potentially dangerous, and therefore requiring bridging or closure, other currents that feed the discipline of improvement science suggest the potential value and uses of spaces of openness and ambiguity. These currents include the science of complex adaptive systems, and certain precepts of philosophical pragmatism acknowledged to inform improvement science. Going a step further, I reflect on whether or not these two contrasting approaches within improvement science should be treated as incommensurable paradigms, and what each approach tells us about the very possibility of accommodating seemingly irreconcilable or incommensurable approaches within improvement science.","corpus_id":4924880,"score":0},{"doc_id":"29280271","title":"Nursing as concrete philosophy, Part I: Risjord on nursing knowledge.","abstract":"This essay addresses the problem of the essentiality of nursing knowledge and what kind of theory, if any, is essential to nursing practice. The overarching aim of the essay was to argue for the thesis that nursing may be described as a kind of philosophical activity, and, consequently, that philosophy is the kind of \"theory\" that is essential to nursing practice and to the nursing discipline at large. The essay consists of two papers. The present paper, Part I, is a critical examination of Mark Risjord's discussion of the problem of the theory-practice gap in his Nursing Knowledge: Practice, Science, Philosophy, from 2010. According to Risjord, the cause of the theory-practice gap originates in an erroneous conception of science (logical positivism) which had a decisive influence upon the way nursing scholars appropriated theoretical frameworks for the nursing discipline. This philosophical influence is considered in effect to have generated the theory-practice gap. In order to bridge the gap, Risjord suggests, the nursing discipline needs to adopt a standpoint epistemology conjoined with a postpositivist conception of scientific theory. In this way, a legitimate brand of nursing science may be developed and the theory-practice gap overcome. I will argue that neither Risjord's diagnosis of the problem, nor his recommended cure, may succeed in rescuing the nursing discipline from the theory-practice gap. Rather, the real cause of the theory-practice gap, I will claim, derives from an erroneous conception of nursing (not of science), namely the conception of nursing as a kind of science (roughly speaking). On my view, to overcome the gap, the nursing discipline needs to make salient the inherently philosophical character of nursing. In the second paper (Part II), I will continue the discussion of nursing knowledge and delineate the thesis of nursing as a kind of concrete philosophy.","corpus_id":3323520,"score":0}],"string":"[\n {\n \"doc_id\": \"19505026\",\n \"title\": \"[Individual consciousness].\",\n \"abstract\": \"The main modern concepts on the consciousness nature are considered. Together with the dualistic concepts, there exist concepts the adherents of which find it possible to get to know the origin of consciousness on the basis of natural science. A critical analysis of those concepts brings the author to the conclusion that they do not solve the main problem of individual consciousness: how subjective elements of consciousness arise in the brain as a result of objectively registered processes. The main reason of failures to solve said problem is considered by the author in the fact that the subjective categories of consciousness are not really subject to science. Nevertheless, it does not mean the dualism is to be inevitably accepted. In fact, the subjective categories arise in the limits of a life the area of which is substantially wider than that of science. An original information and physical hypothesis is being set up that provides for necessary premises and conditions enabling the origination of subjective categories of consciousness during the progressive natural evolution of living systems.\",\n \"corpus_id\": 36838608,\n \"score\": 2\n },\n {\n \"doc_id\": \"20589952\",\n \"title\": \"A natural science approach to consciousness.\",\n \"abstract\": \"We begin with premises about natural science, its fundamental protocols and its limitations. With those in mind, we construct alternative descriptive models of consciousness, each comprising a synthesis of recent literature in cognitive science. Presuming that consciousness arose through natural selection, we eliminate the subset of alternatives that lack selectable physical phenotypes, leaving the subset with limited free will (mostly in the form of free won't). We argue that membership in this subset implies a two-way exchange of energy between the conscious mental realm and the physical realm of the brain. We propose an analogy between the mental and physical phases of energy and the phases (e.g., gas/liquid) of matter, and a possible realization in the form of a generic resonator. As candidate undergirdings of such a system, we propose astroglial-pyramidal cell and electromagnetic-field models. Finally, we consider the problem of identification of the presence of consciousness in other beings or in machines.\",\n \"corpus_id\": 18684426,\n \"score\": 2\n },\n {\n \"doc_id\": \"21033194\",\n \"title\": \"Science, conscience, consciousness.\",\n \"abstract\": \"Descartes' metaphysics lays the foundation for the special sciences, and the notion of consciousness (\\\"conscientia\\\") belongs to metaphysics rather than to psychology. I argue that as a metaphysical notion, \\\"consciousness\\\" refers to an epistemic version of moral conscience. As a consequence, the activity on which science is based turns out to be conscientious thought. The consciousness that makes science possible is a double awareness: the awareness of what one is thinking, of what one should be doing, and of the possibility of a gap between the two.\",\n \"corpus_id\": 22907051,\n \"score\": 2\n },\n {\n \"doc_id\": \"21033196\",\n \"title\": \"Kant and the scientific study of consciousness.\",\n \"abstract\": \"We argue that Kant's views about consciousness, the mind-body problem and the status of psychology as a science all differ drastically from the way in which these topics are conjoined in present debates about the prominent idea of a science of consciousness. Kant never used the concept of consciousness in the now dominant sense of phenomenal qualia; his discussions of the mind-body problem center not on the reducibility of mental properties but of substances; and his views about the possibility of psychology as a science did not employ the requirement of a mechanistic explanation, but of a quantification of phenomena. This shows strikingly how deeply philosophical problems and conceptions can change even if they look similar on the surface.\",\n \"corpus_id\": 22053209,\n \"score\": 2\n },\n {\n \"doc_id\": \"21971695\",\n \"title\": \"[The so-called body-mind problem].\",\n \"abstract\": \"Das so genannte Leib-Seele-Problem. THE PROBLEM: Even psychosomatic researchers seem to want to avoid the so-called body-mind problem, which is actually a mind-brain problem. In line with Beckermann (2008), the first the four possible positions on the mind-brain problem are presented. The debate over the past 100 years has revolved around the question of whether mental events are ontologically independent of brain physiology or whether they are in fact entirely determined by it. Such a physicalism approach based on properties (i.e., mental characteristics or phenomena are physical or can be completely reduced to physical characteristics), however, is diametrically opposed to some of our strongest intuitions, e.g., that computers will never be able to develop qualities of human experience (qualia) and thus become subjects in the first person singular. Yet we are equally unable to prove the fundamental impossibility of such a development. THESIS: In this stalemate situation, a differentiation was undertaken by Gottlob Frege (1892) which could be of help: Expressed in today's language, a distinction is made between the sense of an expression, its contextual presentation (e.g., where there is a difference between \\\"the evening star\\\" and \\\"the morning star\\\"), on the one hand, and its so-called reference (the object to which it refers, here the planet Venus in both cases) on the other. The school of Gestalt psychology that developed in Berlin at the start of the last century similarly posited a \\\"psychophysical level of the CNS,\\\" a continuum in a pattern of electrical field forces which manifests itself first in cerebral physiological-neuronal processes as well as in other perspectives such as consciousness and experience. A subsequent speculative concept then extends this model to assume also an (as yet) unknown Alpha configuration as being a common reference of two sense contents: (1) the results of the neurophysiological third-person perspective and (2) of the emotional-cognitive first-person perspectives. Only through the latter will Alpha be able to become self-conscious and an instance acting in his world. RESULTS: Only through the latter will Alpha be able to become self-conscious and an instance acting in his world. The postulate of an Alpha configuration thus retains the possibility of a biology not (yet) accessible to our knowledge, such that our fundamental conviction regarding the holism of soma and psyche can be maintained for us as medical practitioners and scientific physicians. Our patients need both, our medical-scientific competence (3rd-person perspective) as well as our empathic sensibility in exploring their phenomenal experience (1st-person perspective). They need us as medical artists.\",\n \"corpus_id\": 297834,\n \"score\": 2\n },\n {\n \"doc_id\": \"21988251\",\n \"title\": \"Science, self, and immortality.\",\n \"abstract\": \"The following considers the concept of scientific naturalism in relation to life after death and contrasts three alternative perspectives on immortality of the soul, including naturalistic fatalism, otherworldly optimism, and long-suffering hope.\",\n \"corpus_id\": 2591321,\n \"score\": 2\n },\n {\n \"doc_id\": \"22577305\",\n \"title\": \"Consciousness regained? Philosophical arguments for and against reductive physicalism.\",\n \"abstract\": \"This paper is an overview of recent discussions concerning the mind-body problem, which is being addressed at the interface between philosophy and neuroscience. It focuses on phenomenal features of consciousness or \\\"qualia,\\\" which are distinguished from various related issues. Then follows a discussion of various influential skeptical arguments that question the possibility of reductive explanations of qualia in physicalist terms: knowledge arguments, conceivability arguments, the argument of multiple realizability, and the explanatory gap argument. None of the arguments is found to be very convincing. It does not necessarily follow that reductive physicalism is the only option, but it is defensible. However, constant conceptual and methodological reflection is required, alongside ongoing research, to keep such a view free from dogmatism and naivety.\",\n \"corpus_id\": 16921142,\n \"score\": 2\n },\n {\n \"doc_id\": \"22654125\",\n \"title\": \"The Vegetative State and the Science of Consciousness.\",\n \"abstract\": \"Consciousness in experimental subjects is typically inferred from reports and other forms of voluntary behaviour. A wealth of everyday experience confirms that healthy subjects do not ordinarily behave in these ways unless they are conscious. Investigation of consciousness in vegetative state patients has been based on the search for neural evidence that such broad functional capacities are preserved in some vegetative state patients. We call this the standard approach. To date, the results of the standard approach have suggested that some vegetative state patients might indeed be conscious, although they fall short of being demonstrative. The fact that some vegetative state patients show evidence of consciousness according to the standard approach is remarkable, for the standard approach to consciousness is rather conservative, and leaves open the pressing question of how to ascertain whether patients who fail such tests are conscious or not. We argue for a cluster-based 'natural kind' methodology that is adequate to that task, both as a replacement for the approach that currently informs research into the presence or absence of consciousness in vegetative state patients and as a methodology for the science of consciousness more generally.\",\n \"corpus_id\": 8896305,\n \"score\": 2\n },\n {\n \"doc_id\": \"23073546\",\n \"title\": \"[What can qualia be? The monistic views].\",\n \"abstract\": \"Phenomenal properties, also named qualia (that is, the qualities of human experiences, e.g. the senses of red, of salt, of pain, qua senses) create a hard problem for philosophy. It is claimed that phenomenal properties are radically different to the physical ones: they are intrinsic (their essence is totally confined within the limits of their existence), they depend on mind, they are accessible only privately, by introspection and they are infallible, in the sense that the experience of a quale is identical to its existence. On the contrary, physical properties are dispositional (their essence is defined through their causal consequences), they exist independently of mind, they are accessible to public observation and are liable to verification or falsification. The faculty of philosophy, named philosophy of mind, is systematically interested in qualia. In the present paper some of the main monistic philosophical approaches to qualia are discussed. The main common characteristic of monistic views is that (contrary to dualistic views) they purport that: two radically different substances cannot exist, side by side, within the same world (our world). Thus, there are either physical properties, or phenomenal properties, but not both. The monistic theories, supporting that in our world there are only physical properties, or properties totally reducible into physical ones, are named physicalism (or according to a more traditional nomination, materialism). On the other hand, monistic theories maintaining that all existing properties are phenomenal, or properties reducible into phenomenal ones, are named phenomenalism. The main arguments for physicalism are: (a) the scientific principle of the causal closure of the universe (every event has one physical cause), (b) the dependence of every well-studied mental phenomenon, from a physical phenomenal, such as the function of the neural system. Dualists counterattack physicalism with mental experiments (such as, the experiments concerning philosophical zombies) in order to demonstrate that qualia are irreducible entities. The main physicalistic options are eliminativism, the theories of identity, functionalism and representationalism. The main argument for phenomenalism is that physical properties and physical knowledge of them, as well, are reducible into and derived from experiences. On the other hand, opponents of phenomenalism retort that our world comprises spatiotemporal parts inaccessible to experience (f.e. the microworld of atomic physics, the world before the appearance of intelligent beings). Yet, some phenomenalists claim that phenomenal properties can be either real (experienced) or potentially real (what one would experience if one could observe this or that spatiotemporal part of the world). According to a third, agnosticistic opinion, named mysterianism, the human mind lacks the capacity of bridging the explanatory gap between physical and phenomenal identities. Many opponents of this theory claim the historically proved ability of human mind to find solutions for difficult problems of our world through scientific knowledge and based on it natural philosophy.\",\n \"corpus_id\": 24773763,\n \"score\": 2\n },\n {\n \"doc_id\": \"23882252\",\n \"title\": \"On the autonomy of the concept of disease in psychiatry.\",\n \"abstract\": \"Does the reference to a mental realm in using the notion of mental disorder lead to a dilemma that consists in either implying a Cartesian account of the mind-body relation or in the need to give up a notion of mental disorder in its own right? Many psychiatrists seem to believe that denying substance dualism requires a purely neurophysiological stance for explaining mental disorder. However, this conviction is based on a limited awareness of the philosophical debate on the mind-body problem. This article discusses the reasonableness of the concept of mental disorder in relation to reductionist and eliminativist strategies in the philosophy of mind. It is concluded that we need a psychological level of explanation that cannot be reduced to neurophysiological findings in order to make sense of mental disorder.\",\n \"corpus_id\": 561485,\n \"score\": 2\n },\n {\n \"doc_id\": \"24309878\",\n \"title\": \"Implications of spiritual experiences to the understanding of mind-brain relationship.\",\n \"abstract\": \"OBJECTIVE: While there has been a large increase in scientific studies on spirituality, there has been too few of studies of the core of spirituality: spiritual experiences (SE), which often involve altered states of consciousness, reports of anomalous experiences and of consciousness beyond the body. This paper argues that SE, although usually neglected in debates regarding mind-brain relationship (MBR), may provide the much needed enlargement of the empirical basis for advancing the understanding of the MBR. METHODS: This paper briefly presents and discusses recent scientific investigations on some types of SE (meditative states, end of life and near death experiences, mediumship and alleged memories of previous lives) and their implications to MBR. RESULTS: Neurofunctional studies of SE have shown that they are related to but not necessarily caused by complex functional patterns in several brain areas. The study of meditative states, as voluntarily induced mind states that influence brain states has been a privileged venue to investigate top-down (mind over brain) causation. End of life and near death experiences offer cases of unexpected adequate mental function under severe brain damage and/or dysfunction. Scientific investigations of several types of SE have provided evidence against materialistic reductionist views of mind. CONCLUSIONS: The recent trend to scientifically investigate SE has already produced interesting and thought-provoking findings that deserve careful further exploration. Because of their potential implication, these findings may also contribute to the understanding of MBR, which remains an important, yet poorly explored way to investigate human nature.\",\n \"corpus_id\": 21157227,\n \"score\": 2\n },\n {\n \"doc_id\": \"24974626\",\n \"title\": \"[Is the brain the creator of psychic phenomena or is a paradigm shift inevitable?].\",\n \"abstract\": \"¿Es el cerebro el creador de los fenómenos psíquicos o es ineludible un cambio de paradigma? Every day new scientific information is appearing that cannot be explained using the classical Newtonian model and is calling for the emergence of a new paradigm that would include the explanation of such phenomena as telepathy, clairvoyance, presentiment, precognition, out of the body experiences, psychic healing, after-death communication, near-death experiences and reincarnation. The materialist paradigm which considers the brain as the sole cause of consciousness and psychic phenomena has been challenged by a new paradigm that seems to demonstrate that there is not a cause-effect relationship between brain activity and psychic phenomena but only a correlation between them, since these phenomena can be experienced without the body and appear to have an extra-cerebral origin (cosmic field, cosmic consciousness?). Of course, the brain is intensely involved in the manifestation of consciousness in our daily life but this is not equivalent to affirm that brain creates consciousness. Recent findings force us to consider a non-physical, spiritual and transpersonal aspect of reality.\",\n \"corpus_id\": 24110348,\n \"score\": 2\n },\n {\n \"doc_id\": \"25892488\",\n \"title\": \"Epistemological implications of near-death experiences and other non-ordinary mental expressions: Moving beyond the concept of altered state of consciousness.\",\n \"abstract\": \"During the last decades an increasing interest has developed in the so-called altered state of consciousness (ASCs); among these, near-death experiences (NDEs) are one of the most intriguing and debated examples. NDEs are deep and universal experiences with a clear phenomenology and incidence, while some of their features challenge the current views of human consciousness (focused on neural circuits and based on the concept of mind as a byproduct of brain circuitry) with relevant epistemological and historical implications. The origin of the ruling mechanist-reductionist paradigm can be traced back to Descartes' radical separation of res cogitans and res extensa and the conflict between the nascent science and the Inquisition; this led to removing the subjective properties of mind from the field of scientific interest, relegating them to philosophy and theology in order to enable the development of modern science. However, the physics of the 20th century has eventually moved beyond the classical paradigm, permitting a profound renewal of scientific interest in the mind. Modern research on NDEs has contributed to reopening the debate surrounding the Cartesian separation, the mind-brain relationship and the nature of consciousness. It is now time to reappraise the relevance, strengths, and weaknesses of the available scientific interpretations of NDEs, their relationship with other ASCs, as well as the very concept of ASC; the latter looks to be ill-founded, suggesting the need for: (a) a revision of the conventional approach to subjective phenomena, including both the third- and first-person perspective; and (b) a deep reflection on the possible links between different non-ordinary mental expression, as regards both their phenomenology and mechanisms from a non-pathological perspective.\",\n \"corpus_id\": 18815739,\n \"score\": 2\n },\n {\n \"doc_id\": \"26308870\",\n \"title\": \"Attributions of consciousness.\",\n \"abstract\": \"UNLABELLED: Many philosophers and brain scientists hold that explaining consciousness is one of the major outstanding problems facing modern science today. One type of consciousness in particular-phenomenal consciousness-is thought to be especially problematic. The reasons given for believing that this phenomenon exists in the first place, however, often hinge on the claim that its existence is simply obvious in ordinary perceptual experience. Such claims motivate the study of people's intuitions about consciousness. In recent years a number of researchers in experimental philosophy of mind have begun to shed light on this area, investigating how people understand and attribute those mental states that have been thought to be phenomenally conscious. In this article, we discuss the philosophical concept of phenomenal consciousness and detail the work that has been done on the question of whether lay people have this concept. WIREs Cogn Sci 2014, 5:635-648. doi: 10.1002/wcs.1320 For further resources related to this article, please visit the WIREs website. CONFLICT OF INTEREST: The author has declared no conflicts of interest for this article.\",\n \"corpus_id\": 45317588,\n \"score\": 2\n },\n {\n \"doc_id\": \"26321981\",\n \"title\": \"Pedagogical tools to explore Cartesian mind-body dualism in the classroom: philosophical arguments and neuroscience illusions.\",\n \"abstract\": \"A fundamental discussion in lower-level undergraduate neuroscience and psychology courses is Descartes's \\\"radical\\\" or \\\"mind-body\\\" dualism. According to Descartes, our thinking mind, the res cogitans, is separate from the body as physical matter or substance, the res extensa. Since the transmission of sensory stimuli from the body to the mind is a physical capacity shared with animals, it can be confused, misled, or uncertain (e.g., bodily senses imply that ice and water are different substances). True certainty thus arises from within the mind and its capacity to doubt physical stimuli. Since this doubting mind is a thinking thing that is distinct from bodily stimuli, truth and certainty are reached through the doubting mind as cogito ergo sum, or the certainty of itself as it thinks: hence Descartes's famous maxim, I think, therefore I am. However, in the last century of Western philosophy, with nervous system investigation, and with recent advances in neuroscience, the potential avenues to explore student's understanding of the epistemology and effects of Cartesian mind-body dualism has expanded. This article further explores this expansion, highlighting pedagogical practices and tools instructors can use to enhance a psychology student's understanding of Cartesian dualistic epistemology, in order to think more critically about its implicit assumptions and effects on learning. It does so in two ways: first, by offering instructors an alternative philosophical perspective to dualistic thinking: a mind-body holism that is antithetical to the assumed binaries of dualistic epistemology. Second, it supplements this philosophical argument with a practical component: simple mind-body illusions that instructors may use to demonstrate contrary epistemologies to students. Combining these short philosophical and neuroscience arguments thereby acts as a pedagogical tool to open new conceptual spaces within which learning may occur.\",\n \"corpus_id\": 7282992,\n \"score\": 2\n },\n {\n \"doc_id\": \"27412020\",\n \"title\": \"[The mind-brain problem (I): onto-epistemological foundations].\",\n \"abstract\": \"El problema mente-cerebro (I): fundamentos ontoepistemologicos. INTRODUCTION: Throughout the history of thought, science and philosophy have addressed the problem of mind-brain from different epistemic perspectives. The first covers specific areas of reality and constructs hypotheses with limited scope and multiple inter-scientific connectivity with the aim of validating theoretical models; the second extends its systemic architecture to all that is real (including scientific activity). DEVELOPMENT: The complexity of the mind-brain problem requires the generation of a link connecting the disciplines of philosophy and science; our onto-epistemological presuppositions therefore fall within the framework of a scientifically-oriented philosophy (scientific philosophy). Emergentist materialism is defended as a coherent and verifiable philosophical-scientific solution, as opposed to other proposals developed on the basis of different ontological models (for example, interactionist dualism, functionalism, theory of identity, epiphenomenalism, and so on). CONCLUSIONS: An answer to the mind-brain problem is only feasible if based on a philosophically grounded cognitive neuroscience: emergentist materialism -an ontological postulate- holds that the mind is an emergent property (qualitative novelty) of the brain; scientific realism -an epistemological postulate- holds that cognitive neuroscience is the basic theoretical-experimental tool that allows cognitive access to both the brain and its neurocognitive processes. We consider that on the basis of this philosophical reasoning, cognitive neuroscience acquires epistemic legitimacy to be able to undertake the study of the most genuinely human mental process: consciousness.\",\n \"corpus_id\": 3789708,\n \"score\": 2\n },\n {\n \"doc_id\": \"29504485\",\n \"title\": \"Framing the Mind-Body Problem in Contemporary Neuroscientific and Sunni Islamic Theological Discourse.\",\n \"abstract\": \"Famously posed by seventeenth-century French philosopher René Descartes, the mind-body problem remains unresolved in western philosophy and science, with both disciplines unable to move convincingly beyond the dualistic model. The persistence of dualism calls for a reframing of the problem through interdisciplinary modes of inquiry that include non-western points of view. One such perspective is Islamic theology of the soul, which, while approaching the problem from a distinct point of view, also adopts a position commensurate with (substance) dualism. Using this point of convergence as a conceptual starting point, we argue that bringing into dialogue contemporary neuroscientific, philosophy of mind, and Sunni Islamic theological discourses may provide a fruitful way of reframing the age-old mind-body problem. This paper provides an overview of how these three discourses have approached the issue of the mind-body (-soul) problem. Juxtaposing these three discourses, we hope, may ignite further scholarly dialogue and investigation.\",\n \"corpus_id\": 3676219,\n \"score\": 2\n },\n {\n \"doc_id\": \"29727520\",\n \"title\": \"The mind-body problem.\",\n \"abstract\": \"The mind-body problem is the problem of explaining how the happenings of our mental lives are related to physical states, events and processes. Proposed solutions to the problem vary by whether and how they endorse physicalism, the claim that mental states are ultimately \\\"nothing over and above\\\" physical states, and by how they understand the interactions between mental and physical states. Physicalist solutions to the mind-body problem have been dominant in the last century, with the variety of physicalism endorsed (reductive or nonreductive) depending upon both the outcome of philosophical arguments and methodological developments in the cognitive and neural sciences. After outlining the dominant contemporary approach to the mind-body problem, I examine the prospects for a solution in light of developments in the cognitive sciences, especially the scientific study of consciousness. This article is categorized under: Philosophy > Consciousness Philosophy > Metaphysics Philosophy > Foundations of Cognitive Science.\",\n \"corpus_id\": 19237639,\n \"score\": 2\n },\n {\n \"doc_id\": \"18723943\",\n \"title\": \"Reflections on humanizing biomedicine.\",\n \"abstract\": \"Although biomedicine is responsible for the \\\"miracles\\\" of modern medicine, paradoxically it has also led to a quality-of-care crisis in which many patients feel disenfranchised from the health-care industry. To address this crisis, several medical commentators make an appeal for humanizing biomedicine, which has led to shifts in the philosophical boundaries of medical knowledge and practice. In this paper, the metaphysical, epistemological, and ethical boundaries of biomedicine and its humanized versions are investigated and compared to one another. Biomedicine is founded on a metaphysical position of mechanistic monism, an epistemology of objective knowing, and an ethic of emotionally detached concern. In humanizing modern medicine, these boundaries are often shifted to a metaphysical position of dualism/holism, an epistemology of subject knowing, and an ethic of empathic care. In a concluding section, the question is discussed whether these shifts in the philosophical boundaries are adequate to resolve the quality-of-care crisis.\",\n \"corpus_id\": 22848400,\n \"score\": 1\n },\n {\n \"doc_id\": \"19012586\",\n \"title\": \"Descartes' dreams.\",\n \"abstract\": \"René Descartes is often regarded as the 'father of modern philosophy'. He was a key figure in instigating the scientific revolution that has been so influential in shaping our modern world. He has been revered and reviled in almost equal measure for this role; on the one hand seen as liberating science from religion, on the other as splitting soul from body and man from nature. He dates the founding of his philosophical methods to the night of 10(th) November 1619 and in particular to three powerful dreams he had that night. This article utilizes Descartes' own interpretations of the dreams, supported by biographical material, as well as contemporary neuroscientific and psychoanalytic theory, to reach a new understanding of them. It is argued that the dreams can be understood as depicting Descartes' personal journey from a state of mind-body dissociation to one of mind-body deintegration. This personal journey may have implications for a parallel journey from Renaissance to modern culture and from modernity to post-modern culture.\",\n \"corpus_id\": 23703343,\n \"score\": 1\n },\n {\n \"doc_id\": \"19093679\",\n \"title\": \"Whither the psychology of religion: a spirituality-focused discussion of Paloutzian and Park's (2005). Handbook of the psychology of religion and spirituality.\",\n \"abstract\": \"Presuming Rayburn's (2006: Child & Family Behavior Therapy, 28, 86-92) review of (Paloutzian and Park's, (2005, New York: The Guilford Press) [corrected] Handbook of the Psychology of Religion and Spirituality [corrected] and sketching an alternative paradigm, this review focuses on the Handbook's virtual conflation of religion and spirituality; relates this conflation to the hegemony of Protestant theology in North American psychology of religion; highlights the Handbook's lack of attention to [corrected] spirituality per se, which--if [corrected] not inseparably linked with theism, but, rather, [corrected] related to the self-transcending, meaning-making dimension of the human mind--could [corrected] provide an explanatory breakthrough in the field of the psychology of religion and of the social sciences overall; and sees Handbook's advocacy for a \\\"multilevel interdisciplinary paradigm\\\" as a regrettable acceptance of the failed, long-term strategy of the field of psychology in general.\",\n \"corpus_id\": 40692533,\n \"score\": 1\n },\n {\n \"doc_id\": \"21037408\",\n \"title\": \"The philosophical \\\"mind-body problem\\\" and its relevance for the relationship between psychiatry and the neurosciences.\",\n \"abstract\": \"Parallel to psychiatry, \\\"philosophy of mind\\\" investigates the relationship between mind (mental domain) and body/brain (physical domain). Unlike older forms of philosophy of mind, contemporary analytical philosophy is not exclusively based on introspection and conceptual analysis, but also draws upon the empirical methods and findings of the sciences. This article outlines the conceptual framework of the \\\"mind-body problem\\\" as formulated in contemporary analytical philosophy and argues that this philosophical debate has potentially far-reaching implications for psychiatry as a clinical-scientific discipline, especially for its own autonomy and its relationship to neurology/neuroscience. This point is illustrated by a conceptual analysis of the five principles formulated in Kandel's 1998 article \\\"A New Intellectual Framework for Psychiatry.\\\" Kandel's position in the philosophical mind-body debate is ambiguous, ranging from reductive physicalism (psychophysical identity theory) to non-reductive physicalism (in which the mental \\\"supervenes\\\" on the physical) to epiphenomenalist dualism or even emergent dualism. We illustrate how these diverging interpretations result in radically different views on the identity of psychiatry and its relationship with the rapidly expanding domain of neurology/neuroscience.\",\n \"corpus_id\": 414110,\n \"score\": 1\n },\n {\n \"doc_id\": \"22622355\",\n \"title\": \"Science, practice and mythology: a definition and examination of the implications of scientism in medicine.\",\n \"abstract\": \"Scientism is a philosophy which purports to define what the world 'really is'. It adopts what the philosopher Thomas Nagel called 'an epistemological criterion of reality', defining what is real as that which can be discovered by certain quite specific methods of investigation. As a consequence all features of experience not revealed by those methods are deemed 'subjective' in a way that suggests they are either not real, or lie beyond the scope of meaningful rational inquiry. This devalues capacities that (we argue) are in fact essential components of good reasoning and virtuous practice. Ultimately, the implications of scientism for statements of value undermine value-judgements essential for science itself to have a sound basis. Scientism has implications, therefore, for ontology, epistemology and also for which claims we can assert as objective truths about the world. Adopting scientism as a world view will have consequences for reasoning and decision-making in clinical and other contexts. We analyse the implications of this approach and conclude that we need to reject scientism if we are to avoid stifling virtuous practice and to develop richer conceptions of human reasoning.\",\n \"corpus_id\": 13445258,\n \"score\": 1\n },\n {\n \"doc_id\": \"22627668\",\n \"title\": \"Epistemology of psychiatry.\",\n \"abstract\": \"In historical and epistemological terms, psychiatry is a new discipline born during the 19th century. Rooted in both the natural and social sciences, psychiatric objects of inquiry, namely mental symptoms and mental disorders, are hybrid, constituted by the blending of components arising from disparate sources of knowledge ranging from the biological to the semantic in its widest sense. This poses problems for psychiatric research and therapy. Whilst conventional pluralism may be a convenient approach to manage aspects of psychiatric practice, it lacks the capacity to analyse psychiatric objects in their entirety. For the latter, psychiatry demands a new, tailored regional epistemology. This paper outlines the main features of an epistemology specific to the needs of psychiatry. It highlights the relational approach that needs to be taken and illustrates the usefulness of this approach by analysing the structure of psychiatric objects, exploring the manner in which they may be inscribed in the brain, and identifying the need to periodically recalibrate the language of psychiatry.\",\n \"corpus_id\": 23136420,\n \"score\": 1\n },\n {\n \"doc_id\": \"22865511\",\n \"title\": \"Haunted by the ghost in the machine. Commentary on \\\"The spirituality of human consciousness: a Catholic evaluation of some current neuro-scientific interpretations\\\".\",\n \"abstract\": \"Metaphysical and epistemological dualism informs much contemporary discussion of the relationships of science and religion, in particular in relation to the neurosciences and the religious understanding of the human person. This dualism is a foundational artifact of modern culture; however, contemporary scientific research and historical theological scholarship encourage a more holistic view wherein human personhood is most fittingly understood as an emergent phenomenon of, but not simply reducible to, evolutionary and developmental neurobiology.\",\n \"corpus_id\": 30268188,\n \"score\": 1\n },\n {\n \"doc_id\": \"23562082\",\n \"title\": \"Beyond the pineal gland assumption: a neuroanatomical appraisal of dualism in Descartes' philosophy.\",\n \"abstract\": \"OBJECTIVE: The problem of the substantial union of the soul and the body and therefore the mechanisms of interaction between them represents the core of the Cartesian dualistic philosophy. This philosophy is based upon a neuroanatomical obvious misconception, consisting mainly on a wrong intraventricular position of the pineal gland and its capacity of movement to act as a valve regulating the flow of animal spirits. Should we consider the Cartesian neurophysiology as a purely anatomical descriptive work and therefore totally incorrect, or rather as a theoretical conception supporting his dualistic philosophy? METHOD: From the various pre-Cartesian theories on the pineal organ, we try to explain how Descartes used his original conception of neuroanatomy to serve his dualistic philosophy. Moreover, we present an appraisal of the Cartesian neuroanatomical corpus from an anatomical but also metaphysical and theological perspectives. RESULTS: A new interpretation of Descartes' writings and an analysis of the secondary related literature shed the light on the voluntary anatomical approximations aiming to build an ad hoc neurophysiology that allows Descartes' soul-body theory. CONCLUSION: By its central position within the brain mass and its particular shape, the pineal gland raised diverse metaphysical theories regarding its function, but the most original theory remains certainly its role as the seat of soul in René Descartes' philosophy and more precisely the organ where soul and body interact. The author emphasizes on the critics raised by Descartes' theories on the soul-body interaction through the role of the pineal gland.\",\n \"corpus_id\": 9140909,\n \"score\": 1\n },\n {\n \"doc_id\": \"24468878\",\n \"title\": \"Disorders of consciousness after acquired brain injury: the state of the science.\",\n \"abstract\": \"The concept of consciousness continues to defy definition and elude the grasp of philosophical and scientific efforts to formulate a testable construct that maps to human experience. Severe acquired brain injury results in the dissolution of consciousness, providing a natural model from which key insights about consciousness may be drawn. In the clinical setting, neurologists and neurorehabilitation specialists are called on to discern the level of consciousness in patients who are unable to communicate through word or gesture, and to project outcomes and recommend approaches to treatment. Standards of care are not available to guide clinical decision-making for this population, often leading to inconsistent, inaccurate and inappropriate care. In this Review, we describe the state of the science with regard to clinical management of patients with prolonged disorders of consciousness. We review consciousness-altering pathophysiological mechanisms, specific clinical syndromes, and novel diagnostic and prognostic applications of advanced neuroimaging and electrophysiological procedures. We conclude with a provocative discussion of bioethical and medicolegal issues that are unique to this population and have a profound impact on care, as well as raising questions of broad societal interest.\",\n \"corpus_id\": 205515762,\n \"score\": 1\n },\n {\n \"doc_id\": \"25116396\",\n \"title\": \"Nursing and the new biology: towards a realist, anti-reductionist approach to nursing knowledge.\",\n \"abstract\": \"As a system of knowledge, nursing has utilized a range of subjects and reconstituted them to reflect the thinking and practice of health care. Often drawn to a holistic model, nursing finds it difficult to resist the reductionist tendencies in biological and medical thinking. In this paper I will propose a relational approach to knowledge that is able to address this issue. The paper argues that biology is not characterized by one stable theory but is often a contentious topic and employs philosophically diverse models in its scientific research. Biology need not be seen as a reductionist science, but reductionism is nonetheless an important current within biological thinking. These reductionist currents can undermine nursing knowledge in four main ways. Firstly, that the conclusions drawn from reductionism go far beyond their data based on an approach that prioritizes biological explanations and eliminates others. Secondly, that the methods employed by biologists are sometimes weak, and the limitations are insufficiently acknowledged. Thirdly, that the assumptions that drive the research agenda are problematic, and finally that uncritical application of these ideas can be potentially disastrous for nursing practice. These issues are explored through an examination of the problems reductionism poses for the issue of gender, mental health, and altruism. I then propose an approach based on critical realism that adopts an anti-reductionist philosophy that utilizes the conceptual tools of emergence and a relational ontology.\",\n \"corpus_id\": 43796680,\n \"score\": 1\n },\n {\n \"doc_id\": \"25164301\",\n \"title\": \"Explaining how the mind works: on the relation between cognitive science and philosophy.\",\n \"abstract\": \"In this paper, we argue that under certain prevalent interpretations of the nature and aims of cognitive science, theories of cognition generate a forced choice between a conception of cognition which depends on the possibility of a private language, and a conception of cognition which depends on mereological confusions. We argue, further, that this should not pose a fundamental problem for cognitive scientists since a plausible interpretation of the nature and aims of cognitive science is available that does not generate this forced choice. The crucial difference between these interpretations is that on the one hand the aim of theories of cognition is to tell us what thinking (etc.) is, and on the other it is to tell us what is causally necessary if an intelligent creature is to be able to think. Our argument draws heavily on a Wittgensteinian conception of philosophy in which no philosophical theory can explain what thinking, perceiving, remembering, etc. are, either. The positive, strictly therapeutic, purpose of a philosophy of cognitive science should be to show that, since the traditional problems which constitute the philosophy of mind are chimerical, there is nothing for philosophical theorizing in cognitive science to achieve.\",\n \"corpus_id\": 9272647,\n \"score\": 1\n },\n {\n \"doc_id\": \"25292274\",\n \"title\": \"New epistemological foundations for cultural psychology: from an atomistic to a self-organizing view of living systems.\",\n \"abstract\": \"An epistemological foundation for cultural psychology is essential to neuro- and behavioural sciences for the challenge psychological sciences must currently face: searching for an explanation of how a brain can become a mind and how individuals assign a sense to the world and their life. Biological systems are very likely determined by physical and chemical laws of spontaneous self-organization and endogenous constraints but, even if the major result of the Darwinian revolution is \\\"the discovery that living species are their story\\\", the modern synthesis of the evolution theory adopted only continuist and gradualist hypotheses. This nourished the analogy between the theory of natural selection and the theory of operant conditioning, thereby supporting empiricist associationism and the methodological positivism of behavioural and \\\"classical\\\" cognitive psychologists. Current scientific contributions provide evidence to the need for psychotherapy and psychopathology of a new epistemological approach in order to connect research stemming from animal models, up to the most abstract levels of personal meaning. The complex system oriented approach, here described, called \\\"post-rationalism\\\", shaped by a change initiated by evolutionary epistemology. The regulation of emotions initially develops within interpersonal relationships and evolves during both phylogeny and ontogeny, according to complex self-organization processes, leading to the acquisition of Self-organizing abilities and the construction of personal meaning. Endorsing the epistemological similarities of neo-Darwinism and behaviourism, and differentiating from this, the above mentioned approach, emphasises the fact that clinical and psycho-therapeutical practice must be founded on the laws of biological organisation: the ongoing activity of neurobiological systems, including the more abstract domains of thought and language.\",\n \"corpus_id\": 16755223,\n \"score\": 1\n },\n {\n \"doc_id\": \"25363442\",\n \"title\": \"Interpreting \\\"Mind-Cure\\\": William James and the \\\"chief task…of the science of human nature\\\".\",\n \"abstract\": \"The private papers of the philosopher-psychologist, William James, indicate that he frequented several mental healers during his life, undertaking 100-200 therapeutic sessions concerning a range of symptoms from angina to insomnia. The success of the mind-cure movement constituted for James both a corroboration, and an extension, of the new research into the subconscious self and the psychogenesis of disease. Epistemologically, the experiences of those converts to the \\\"mind-cure religion\\\" exemplified his conviction that positivistic scientific enquiry can only reveal only one part of a wider reality. Metaphysically their reports comprised a powerful body of support for the existence of a \\\"higher consciousness,\\\" a supernatural world of some description. The positing of such a source of \\\"supernormal\\\" healing power was, for James, the best way to reconcile the accounts of those who had been regenerated, via their faith, despite having exhausted all natural reserves of energy and will.\",\n \"corpus_id\": 25125104,\n \"score\": 1\n },\n {\n \"doc_id\": \"25452738\",\n \"title\": \"Closing in on the constitution of consciousness.\",\n \"abstract\": \"The science of consciousness is a nascent and thriving field of research that is founded on identifying the minimally sufficient neural correlates of consciousness. However, I have argued that it is the neural constitution of consciousness that science seeks to understand and that there are no evident strategies for distinguishing the correlates and constitution of (phenomenal) consciousness. Here I review this correlation/constitution distinction problem and challenge the existing foundations of consciousness science. I present the main analyses from a longer paper in press on this issue, focusing on recording, inhibition, stimulation, and combined inhibition/stimulation strategies, including proposal of the Jenga analogy to illustrate why identifying the minimally sufficient neural correlates of consciousness should not be considered the ultimate target of consciousness science. Thereafter I suggest that while combined inhibition and stimulation strategies might identify some constitutive neural activities-indeed minimally sufficient constitutive neural activities-such strategies fail to identify the whole neural constitution of consciousness and thus the correlation/constitution distinction problem is not fully solved. Various clarifications, potential objections and related scientific and philosophical issues are also discussed and I conclude by proposing new foundational claims for consciousness science.\",\n \"corpus_id\": 7928552,\n \"score\": 1\n },\n {\n \"doc_id\": \"25546646\",\n \"title\": \"[Reductionist approaches of complex problems: an epistemological and ethical reflection].\",\n \"abstract\": \"Abordajes reduccionistas de problemáticas complejas: una reflexión epistemológica y ética. Reductionism is a constitutive feature of the \\\"standard view\\\" or inherited conception in philosophy of science, such as Enrique Marí says in his book \\\"Elements of comparative epistemology\\\". Whereas the \\\"standard view\\\" is one of the articulators of scientism - epistemological hegemonic position in the contexts of education, innovation, evaluation and application of techno-scientific knowledge - imposed an analysis of this concept as a necessary condition for its overcoming. This article intends to define the meaning and scope of the epistemological reductionism within the framework of the biomedical sciences, on the basis of their genealogy, and then moving in the explicitation of the multiple ways that invest for, finally, realize the consequences of his naive acceptance - or perhaps downright accomplice, of a great part of the scientific community. The consequences are presented in the field of theory, but very particularly in the field of praxis. Establishing the ethical implications of the epistemological reductionism in the theory and practice of Biomedical Sciences is the objective of this work.\",\n \"corpus_id\": 31548919,\n \"score\": 1\n },\n {\n \"doc_id\": \"25682384\",\n \"title\": \"Only one mind: an artist's exploration of consciousness.\",\n \"abstract\": \"The aim of this article is to critique the contemporary scientific reduction of mind to brain and to explore the imaginal realm of consciousness. Through the author's own practice as an engraver, and through the researches and discoveries of free-thinking scientists, philosophers and artists, this realm of the \\\"One Mind\\\" is revealed to be timeless and universal.\",\n \"corpus_id\": 31276538,\n \"score\": 1\n },\n {\n \"doc_id\": \"25756252\",\n \"title\": \"[When science becomes technology: epistemological and ethical consequences of the Adduction].\",\n \"abstract\": \"Quando la scienza diviene tecnologia: conseguenze epistemologiche ed etiche della Adduzione. Notwithstanding that the sciences are every day closest to technology, the Philosophy of Science has not yet well realized the epistemological and ethical differences that make different the \\\"Traditional Naturalistic Science\\\" (TNS) and the technological, artefactual, intrusive science that I called: \\\"Post-Modern Meta-Naturalistic Science\\\" (P-MM-NS). The first type of science has as a primary scope the knowledge of nature, using a methodology that departs from the methodic doubt, realizes a hypothesis, defines the aim(s), adopts a protocol, interprets and discusses the results, inferentially derives the conclusions, according to the classical philosophical reasonings of induction, deduction, abduction. In my philosophical reasoning, I realized that P-MM-NS follows an absolutely different epistemological procedure. The technological science prefigures a scope, produces a non-natural technically-modified object, gives for sure the occurrence of the effect for which the object has been manufactured. This means that only \\\"in retrospect\\\" it will ascertain whether or not the promised effect has occurred, considering that any technical artifact could be rejected by that natural environment in which it has been, acritically, delivered, without knowing how to remedy in case of an unexpected effect. In such a circumstance, the technological science has totally failed in its scope and effect, The potential failure of the predicted effect will prove that P-MM-NS follows a logical reasoning that is substantially and formally \\\"sui generis\\\" with respect to the epistemology and ethics of NS. This divergence from the classic reasoning of induction, deduction, abduction, has been called by me: \\\"Adduction\\\", because of the following considerations: the scientific procedure doesn't depart from the methodic doubt and hypothesis, only declares a scope, for which it is produced a technically-manufactured object, and gives for sure which will be the expected effect, but, not knowing how to remedy to negative results in case of a failure. It is, thus, clearly visible that the adduction is a type of logical reasoning that is self-referential and tautogical, being only based on a declaration of intents, adducted for justifying the production of a technical artifact, assuring an effect without suspecting that it could not respond to the promised scope.\",\n \"corpus_id\": -1,\n \"score\": 1\n },\n {\n \"doc_id\": \"26143599\",\n \"title\": \"Why natural science needs phenomenological philosophy.\",\n \"abstract\": \"Through an exploration of theoretical physics, this paper suggests the need for regrounding natural science in phenomenological philosophy. To begin, the philosophical roots of the prevailing scientific paradigm are traced to the thinking of Plato, Descartes, and Newton. The crisis in modern science is then investigated, tracking developments in physics, science's premier discipline. Einsteinian special relativity is interpreted as a response to the threat of discontinuity implied by the Michelson-Morley experiment, a challenge to classical objectivism that Einstein sought to counteract. We see that Einstein's efforts to banish discontinuity ultimately fall into the \\\"black hole\\\" predicted in his general theory of relativity. The unavoidable discontinuity that haunts Einstein's theory is also central to quantum mechanics. Here too the attempt has been made to manage discontinuity, only to have this strategy thwarted in the end by the intractable problem of quantum gravity. The irrepressible discontinuity manifested in the phenomena of modern physics proves to be linked to a merging of subject and object that flies in the face of Cartesian philosophy. To accommodate these radically non-classical phenomena, a new philosophical foundation is called for: phenomenology. Phenomenological philosophy is elaborated through Merleau-Ponty's concept of depth and is then brought into focus for use in theoretical physics via qualitative work with topology and hypercomplex numbers. In the final part of this paper, a detailed summary is offered of the specific application of topological phenomenology to quantum gravity that was systematically articulated in The Self-Evolving Cosmos (Rosen, 2008a).\",\n \"corpus_id\": 207336376,\n \"score\": 1\n },\n {\n \"doc_id\": \"26978563\",\n \"title\": \"Are Allopathic and Holistic Medicine Incommensurable?\",\n \"abstract\": \"The shift from the Aristotelian to the Newtonian scientific paradigm gave birth to progresses in the natural, hard sciences and contributed to the emergence of modernity. Allopathic medicine gradually implemented those progresses, transforming itself into contemporary biomedicine. In the early 20th century, replacement of Newtonian physics by quantum mechanics and Einstein's theory of relativity resulted in a new paradigm shift in the natural, hard sciences. This shift gave birth to post-modern perceptions, which attempt to put those changes in context. Within this new context, holistic therapeutic approaches are considered more compatible with the new paradigm. Different paradigms in the natural, hard sciences are considered to be incommensurable (in the Kuhnian sense). This incommensurability is also transferred to the different societal contexts, the different «Weltanschauungen» that rely on different scientific paradigms. However, drawing on arguments that range from historical and philosophical to practical and sociological ones, we argue that, although based on different scientific paradigms, allopathic and holistic medicine are not incommensurable, but rather complementary. This may be related to the inherent attributes of medicine, a fact that reinforces the debate on its epistemological status.\",\n \"corpus_id\": 36644651,\n \"score\": 1\n },\n {\n \"doc_id\": \"27271129\",\n \"title\": \"Ancient Ethical Practices of Dualism and Ethical Implications for Future Paradigms in Nursing.\",\n \"abstract\": \"Paradigms contain theoretical structures to guide scientific disciplines. Since ancient times, Cartesian dualism has been a prominent philosophy incorporated in the practice of medicine. The discipline of nursing has continued the body-mind emphasis with similar paradigmatic thinking and theories of nursing that separate body and mind. Future trends for paradigm and nursing theory development are harkening to former ways of thinking. In this article the author discusses the origins of Cartesian dualism and implications for its current usage. The author shall illuminate what it potentially means to engage in dualism in nursing and discuss possible ethical implications for future paradigm and theory development in nursing.\",\n \"corpus_id\": 5217760,\n \"score\": 1\n },\n {\n \"doc_id\": \"18582293\",\n \"title\": \"Critical realism: a philosophical framework for the study of gender and mental health.\",\n \"abstract\": \"This paper explores gender and mental health with particular reference to the emerging philosophical field of critical realism. This philosophy suggests a shared ontology and epistemology for the natural and social sciences. Until recently, most of the debate surrounding gender and mental health has been guided either implicitly or explicitly within a positivist or constructivist philosophy. With this in mind, key areas of critical realism are explored in relation to gender and mental health, and contrasted with the positions of positivism and constructivism. It is argued that critical realism offers an alternative philosophical framework for the exploration of gender issues within mental health care.\",\n \"corpus_id\": 22203664,\n \"score\": 0\n },\n {\n \"doc_id\": \"18816337\",\n \"title\": \"The logic of turmoil: some epistemological and clinical considerations on emotional experience and the infinite.\",\n \"abstract\": \"The idea of the infinite has its origins in the very beginnings of western philosophy and was developed significantly by modern philosophers such as Galileo and Leibniz. Freud discovered the Unconscious which does not respect the laws of classical logic, flouting its fundamental principle of non-contradiction. This opened the way to a new epistemology in which classical logic coexists with an aberrant logic of infinite affects. Matte Blanco reorganized this Freudian revolution in logic and introduced the concept of bi-logic, which is an intermingling of symmetric and Aristotelic logics. The authors explore some epistemological and clinical aspects of the functioning of the deep unconscious where the emergence of infinity threatens to overwhelm the containing function of thought, connecting this topic to some of Bion's propositions. They then suggest that bodily experiences can be considered a prime source of the logic of turmoil, and link a psychoanalytic consideration of the infinite to the mind-body relation. Emotional catastrophe is seen both as a defect-a breakdown of the unfolding function which translates unconscious material into conscious experience-and as the consequence of affective bodily pressures. These pressures function in turn as symmetrizing or infinitizing operators. Two clinical vignettes are presented to exemplify the hypotheses.\",\n \"corpus_id\": 29590245,\n \"score\": 0\n },\n {\n \"doc_id\": \"18840335\",\n \"title\": \"[A reflection on \\\"nursing science\\\"].\",\n \"abstract\": \"Una reflexión en torno a las \\\"ciencias de la enfermería\\\" The present article provides a reflection on the concept of \\\"nursing science\\\", a concept that is increasingly used in Spain. The article begins by discussing the scientific paradigms of nursing, continues briefly with the notion of science, and subsequently addresses the concept of nursing science more thoroughly in a three-fold manner. First, we reflect on the center of interest or essence of the discipline of nursing: nursing care. Then, we address the influence of the distinct paradigms in the understanding of this center of interest and support the development of nursing knowledge from a multiple paradigmatic perspective. Lastly, we contrast nursing science and nursing practice in an attempt to explain their interdependence and mutual need within an eminently practical discipline: the discipline of nursing.\",\n \"corpus_id\": 12825715,\n \"score\": 0\n },\n {\n \"doc_id\": \"19337202\",\n \"title\": \"Epistemologic inquiries in evidence-based medicine.\",\n \"abstract\": \"BACKGROUND: Since the term \\\"evidence-based medicine\\\" (EBM) first appeared in the scientific literature in 1991, the concept has had considerable influence in many parts of the world. Most professional societies, the public,and funding agencies have accepted EBM with remarkable enthusiasm. The concept of evidence-based practice is now applied in management, education, criminology, and social work. Yet, EBM has attracted controversy: its critics allege that EBM uses a narrow concept of evidence and a naive conception of the relationships between evidence, theory, and practice. They also contend that EBM presents itself as a radical restructuring of medical knowledge that discredits more traditional ways of knowing in medicine, largely in the interests of people with a particular investment in the enterprise of large-scale clinical trials. Because EBM proposes aspecific relationship between theory, evidence, and knowledge, its theoretical basis can be understood as an epistemological system. Undertaking epistemological inquiry is important because the adoption of a particular epistemological view defines how science is conducted. METHODS: In this paper, we challenge this critical view of EBM by examining how EBM fits into broad epistemological debates within the philosophy of science. We consider how EBM relates to some classical debates regarding the nature of science and knowledge. We investigate EBM from the perspective of major epistemological theories (logical-positivism/inductivism, deductivism/falsificationism/theory-ladeness of observations, explanationism/holism, instrumentalism, underdetermination theory by evidence). RESULTS: We first explore the relationship between evidence and knowledge and discuss philosophical support for the main way that evidence is used in medicine: (1) in the philosophical tradition that \\\"rational thinkers respect their evidence,\\\" we show that EBM refers to making medical decisions that are consistent with evidence, (2) as a reliable sign, symptom, or mark to enhance reasonableness or truthfulness of some particular claim (\\\"evidence as a guide to truth\\\"), and (3) to serve as a neutral arbiter among competing views. Our analysis indicates that EBM does not have a rigorous epistemological stance. In fact, EBM enthusiastically draws on all major traditions of philosophical theories of scientific evidence. CONCLUSIONS: Our findings indicate that EBM should not be construed as a new scientific or philosophical theory that changes the nature of medicine or our understanding thereof. Rather, we should consider EBM as a continuously evolving heuristic structure for optimizing clinical practice.\",\n \"corpus_id\": 16468941,\n \"score\": 0\n },\n {\n \"doc_id\": \"19794882\",\n \"title\": \"Translational science: epistemology and the investigative process.\",\n \"abstract\": \"The term \\\"translational science\\\" has recently become very popular with its usage appearing to be almost exclusively related to medicine, in particular, the \\\"translation\\\" of biological knowledge into medical practice. Taking the perspective that translational science is somehow different than science and that sound science is grounded in an epistemology developed over millennia, it seems imperative that the meaning of translational science be carefully examined, especially how the scientific epistemology manifests itself in translational science. This paper examines epistemological issues relating mainly to modeling in translational science, with a focus on optimal operator synthesis. It goes on to discuss the implications of epistemology on the nature of collaborations conducive to the translational investigative process. The philosophical concepts are illustrated by considering intervention in gene regulatory networks.\",\n \"corpus_id\": 14906792,\n \"score\": 0\n },\n {\n \"doc_id\": \"20017878\",\n \"title\": \"Professional knowledge and the epistemology of reflective practice.\",\n \"abstract\": \"Reflective practice is one of the most popular theories of professional knowledge in the last 20 years and has been widely adopted by nursing, health, and social care professions. The term was coined by Donald Schön in his influential books The Reflective Practitioner, and Educating the Reflective Practitioner, and has garnered the unprecedented attention of theorists and practitioners of professional education and practice. Reflective practice has been integrated into professional preparatory programmes, continuing education programmes, and by the regulatory bodies of a wide range of health and social care professions. Yet, despite its popularity and widespread adoption, a problem frequently raised in the literature concerns the lack of conceptual clarity surrounding the term reflective practice. This paper seeks to respond to this problem by offering an analysis of the epistemology of reflective practice as revealed through a critical examination of philosophical influences within the theory. The aim is to discern philosophical underpinnings of reflective practice in order to advance increasingly coherent interpretations, and to consider the implications for conceptions of professional knowledge in professional life. The paper briefly examines major philosophical underpinnings in reflective practice to explicate central themes that inform the epistemological assumptions of the theory. The study draws on the work of Donald Schön, and on texts from four philosophers: John Dewey, Nelson Goodman, Michael Polanyi, and Gilbert Ryle. Five central epistemological themes in reflective practice are illuminated: (1) a broad critique of technical rationality; (2) professional practice knowledge as artistry; (3) constructivist assumptions in the theory; (4) the significance of tacit knowledge for professional practice knowledge; and (5) overcoming mind body dualism to recognize the knowledge revealed in intelligent action. The paper reveals that the theory of reflective practice is concerned with deep epistemological questions of significance to conceptions of knowledge in health and social care professions.\",\n \"corpus_id\": 5230304,\n \"score\": 0\n },\n {\n \"doc_id\": \"20589363\",\n \"title\": \"Epistemology.\",\n \"abstract\": \"This entry begins by presenting the origin, history and etymology of the term, as well as a short definition of epistemology as the discipline that deals with the nature, origin, validity and limits of knowledge. Then we focus on the classical platonic analysis of knowledge as truth justified belief. Against the backdrop of this platonic notion we present other relevant perspectives. It is essential to follow the history of the relation between origin and justification of knowledge until the contemporary separation of both problems. The study of the origin of knowledge seems to require a naturalized epistemology, while the problem of justification is usually approached from a philosophical point of view, whether coherentist, foundationalist or fallibilist. However, currently some authors are advocating for a full naturalized epistemology, while others are extending the philosophical point of view also to the genesis of knowledge.\",\n \"corpus_id\": -1,\n \"score\": 0\n },\n {\n \"doc_id\": \"21449197\",\n \"title\": \"[Introduction to epistemology in nursing sciences].\",\n \"abstract\": \"Introduction à l'épistémologie en sciences infirmières. The development of nursing research is one of the stages in the process for the professionalization of nurses. An epistemological reflection which took place gradually became necessary. Today, three traditions derived from the positivist, interpretative and critical approaches orientate reflections on nursing sciences, not without some controversy and debate.\",\n \"corpus_id\": 32814863,\n \"score\": 0\n },\n {\n \"doc_id\": \"21567307\",\n \"title\": \"[Ludovico Geymonat: The problem of historical epistemology].\",\n \"abstract\": \"Ludovico Geymonat le Problème de L'épistémologie Historique Ludovico Geymonat: Das Probllem der Historischen Eepistemologie Ludovico Geymonat: Il Probllema dell'Epistemologia Storica. The study of the various inspirations of Ludovico Geymonat's epistemology (positivism and neopositivism, neorationalism, historicism and dialectical materialism) illustrates the way in which for the Italian philosopher the problem of objectivity of knowledge remains inseparable from the historicity of the sciences. Geymonat's epistemological approach associates scientific progress to its objectivity.\",\n \"corpus_id\": 7848520,\n \"score\": 0\n },\n {\n \"doc_id\": \"21657127\",\n \"title\": \"Grasping the spirit in nature: Anschauung in Ørsted's epistemology of science and beauty.\",\n \"abstract\": \"The intersection between art, poetry, philosophy and science was the leitmotif which guided the lives and careers of romantic natural philosophers including that of the Danish natural philosopher, H. C. Ørsted. A simple model of orsted's career would be one in which it was framed by two periods of philosophical speculation: the youth's curious and idealistic interest in new attractive thoughts and the experienced man's mature reflections at the end of his life. We suggest that a closer look at the epistemological aspects of his works on the theory of beauty reveals a connection between this late work and his early philosophical work including experimental philosophy, but also with the work in teaching and textbook writing, that lies in between. The latter includes Ørsted's view on the application of mathematics in natural philosophy as well as his failed attempt at a genetic presentation of elementary geometry.\",\n \"corpus_id\": 9088751,\n \"score\": 0\n },\n {\n \"doc_id\": \"21836785\",\n \"title\": \"Notes on a few issues in the philosophy of psychiatry.\",\n \"abstract\": \"THE FIRST PART CALLED THE PREAMBLE TACKLES: (a) the issues of silence and speech, and life and disease; (b) whether we need to know some or all of the truth, and how are exact science and philosophical reason related; (c) the phenomenon of Why, How, and What; (d) how are mind and brain related; (e) what is robust eclecticism, empirical/scientific enquiry, replicability/refutability, and the role of diagnosis and medical model in psychiatry; (f) bioethics and the four principles of beneficence, non-malfeasance, autonomy, and justice; (g) the four concepts of disease, illness, sickness, and disorder; how confusion is confounded by these concepts but clarity is imperative if we want to make sense out of them; and how psychiatry is an interim medical discipline. THE SECOND PART CALLED THE ISSUES DEALS WITH: (a) the concepts of nature and nurture; the biological and the psychosocial; and psychiatric disease and brain pathophysiology; (b) biology, Freud and the reinvention of psychiatry; (c) critics of psychiatry, mind-body problem and paradigm shifts in psychiatry; (d) the biological, the psychoanalytic, the psychosocial and the cognitive; (e) the issues of clarity, reductionism, and integration; (f) what are the fool-proof criteria, which are false leads, and what is the need for questioning assumptions in psychiatry. The third part is called Psychiatric Disorder, Psychiatric Ethics, and Psychiatry Connected Disciplines. It includes topics like (a) psychiatric disorder, mental health, and mental phenomena; (b) issues in psychiatric ethics; (c) social psychiatry, liaison psychiatry, psychosomatic medicine, forensic psychiatry, and neuropsychiatry. The fourth part is called Antipsychiatry, Blunting Creativity, etc. It includes topics like (a) antipsychiatry revisited; (b) basic arguments of antipsychiatry, Szasz, etc.; ( c) psychiatric classification and value judgment; (d) conformity, labeling, and blunting creativity. The fifth part is called The Role of Philosophy, Religion, and Spirituality in Psychiatry. It includes topics like (a) relevance of philosophy to psychiatry; (b) psychiatry, religion, spirituality, and culture; (c) ancient Indian concepts and contemporary psychiatry; (d) Indian holism and Western reductionism; (e) science, humanism, and the nomothetic-idiographic orientation. The last part, called Final Goal, talks of the need for a grand unified theory. The whole discussion is put in the form of refutable points.\",\n \"corpus_id\": 23082100,\n \"score\": 0\n },\n {\n \"doc_id\": \"22397137\",\n \"title\": \"[Science in the crosshairs of enlightenment. Significance of hypothetical thinking].\",\n \"abstract\": \"Wissenschaft im Fadenkreuz der Aufklärung. Zur Tragweite des hypothetischen Denkens. To further the enlightenment primarily or even only by means of science was the hope of most representatives of the movement of the enlightenment which gave its name to a whole period of European cultural history. Only a few of its representatives, like Montesquieu and Rousseau, doubted for good reasons, whether and how the goals of the enlightenment can be reached at all by the means of science alone. In his Discours préliminaires to the Encyclopédie D'Alembert still wanted to limit science proper to the narrower field of those kinds of research which were strictly based on observations and calculations alone. In this way he remained committed to Descartes' ideal method of receiving authentic knowledge only by deduction from evident axioms or fundamental theorems. Pascal's casual discovery of the calculation of probabilities allowed to apply mathematics on the hidden laws of the apparent casualties of the human life world. Bacon's project of empirical science as a rational and methodological art of conducting experiments could replace the methodological ideal of science more geometrico. Lichtenberg's refined sensibility for the subjunctive linguistic forms of hypothetical thinking indicates a new understanding of inventing and testing hypotheses as the two most important methods of the experimental sciences when compared to the formal sciences of logic and mathematics. Whoever is studying the history of science of modern times in the cross wire of the enlightenment, will realize soon that science has always been in need of being illuminated about its own chances, risks and side effects. The project of enlightenment through science had to be complemented by the project of an enlightenment about science right from its beginning. Because of the implicit risks and side effects the project of enlightenment has to be enlightenment despite of science and because of science. On the one hand, as a special form of human practice the sciences are directed towards theoretical goals and practical purposes such that their agents cannot be conscious of all aspects of their practices in advance and reflect about all of them at the same time. On the other hand, the agents of such scientific practices are rarely trained, to analyze the cognitive implications of their own actions with the conceptual means of philosophical analysis. Furthermore, the agents of scientific research are hardly able to foresee the theoretical results of their research or even predict the chances and risks of eventual applications with the methods of the social sciences. Despite of the chastening experiences with the ambivalence of the theoretical results and practical applications of the modern sciences and despite of the illuminating effects of modern history and theory of science, contemporary scientists are not fully conscious yet of what they are really doing and what science really is. The contemplative ideal of scientific investigations for their own sake has been replaced in modern times by the practical ideal of scientific research in the service of humanity. The emancipation of the modem sciences from philosophical authorities and religious institutions has freed at first the sciences from alien restrictions to their self-chosen objects and purposes of research. However, the increasing economic constraints and the political dependences prevented even more so that scientists could realize the autonomy which the representatives of the enlightenment had been hoping for. KANT defined the goal of enlightenment as \\\"man's emergence from his self-incurred immaturity\\\". Quoting HORACE'S Sapere aude! he appealed to the courage of his comrades to use their own reason without the guidance of others in philosophical and especially in religious matters. Intellectual maturity as the proper goal of the enlightenment remained to be an undelivered promise despite of the emancipation of the sciences from traditional philosophical authorities and religious institutions. It is not only arguable whether or not enlightenment in this understanding is possible for most people, but also whether it is even desirable for all people considering the implicit ambivalence of the modern sciences. Kant's main philosophical works can be adequately interpreted as the first and unique attempt to understand the potential of the cognitive capacities of human beings about the chances and risks of enlightenment itself by means of a critical inquiry. This holds especially for the practical fruits of the enlightenment as, e.g., with respect to the emancipation from superstition and the appeal to religious tolerance, to the republican idea of the state and the establishment of civil and human rights, to the humanization of the law and execution of legal penalty as well as the unalienable rights of each individual human being.\",\n \"corpus_id\": 34330323,\n \"score\": 0\n },\n {\n \"doc_id\": \"23483470\",\n \"title\": \"[Philosophy within the context of neurosciences].\",\n \"abstract\": \"La filosofia en el marco de las neurociencias. Based on the interrelation between science and philosophy, this article addresses the impact of neurosciences on the philosophical issues posed by today's society, especially those related with epistemology and the philosophy of science. To do so, the different approaches in the cognitive sciences are taken into account, with special attention paid to those that have to do with social, embodied and situated cognition versus a more individual, rational and abstract cognition. This initial framework is taken as the starting point with which to analyse the ways of representing knowledge and the characteristics of the cognoscente agent.\",\n \"corpus_id\": 22650139,\n \"score\": 0\n },\n {\n \"doc_id\": \"23640189\",\n \"title\": \"Reflection: medicines for children--science alone is not enough.\",\n \"abstract\": \"PURPOSE: Access to medicines filling children's therapeutic needs is a long-standing global problem. The problem has been recognised and initiatives for correction were adopted in the USA in the late 1990s, and in the European Union in the first decade of this century. Paediatric medicines are particularly problematic in middle- and low-income countries, where most of the children of the world live. METHODS: A paediatric medicines initiative involving the WHO in parallel with the US and EU initiatives was seen as important by the global paediatric and paediatric clinical pharmacology community, but the WHO was resistant to getting involved. RESULTS: Advocacy, networking, cooperation, persistence, hard work and some luck were needed to get the \\\"Better medicines for children\\\" resolution 60.20 adopted by the World Health Assembly in May 2007. CONCLUSION: Science has been a key enabler of the developments leading to and following the adoption of the paediatric initiatives, but as the example of the WHO shows, science alone was not enough to make the change.\",\n \"corpus_id\": 30362156,\n \"score\": 0\n },\n {\n \"doc_id\": \"24596845\",\n \"title\": \"A brief philosophical encounter with science and medicine.\",\n \"abstract\": \"We show a lot of respect for science today. To back up our claims, we tend to appeal to scientific methods. It seems that we all agree that these methods are effective for gaining the truth. We can ask why science has its special status as a supplier of knowledge about our external world and our bodies. Of course, one should not always trust what scientists say. Nonetheless, epistemological justification of scientific claims is really a big project for philosophers of science. Philosophers of science are interested in knowing how science proves what it does claim and why it gives us good reasons to take these claims seriously. These questions are epistemological questions. Epistemology is a branch of philosophy which deals with knowledge claims and justification. Besides epistemological questions, metaphysical and ethical issues in science are worthy of philosophical scrutiny. This paper gives a short survey of these intellectually demanding issues.\",\n \"corpus_id\": 9014233,\n \"score\": 0\n },\n {\n \"doc_id\": \"25007445\",\n \"title\": \"[Scientific revolution and embryology: rejection or transformation of antiquity? A comparison between the procreation teachings of Cesare Cremonini, William Harvey und René Descartes].\",\n \"abstract\": \"Wissenschaftliche Revolution und Embryologie: Ablehnung oder Transformation der Antike? Ein Vergleich zwischen den Zeugungslehren Cesare Cremoninis, William Harveys und René Descartes. In this paper I address the issue of the theoretical and epistemological status of embryology at the rise of the so-called \\\"Scientific Revolution\\\" (also in the first half of the seventeenth-century) and raise the question, in what sense and to what extent the historiographical concept of \\\"Scientific Revolution\\\" is applicable to the domain of embryology. To achieve this aim I compare the theories of three protagonists of the medical, scientific and philosophical debate of that age, namely Cesare Cremonini, William Harvey and René Descartes, who had very different views on the world structure and human nature and a very different concept of science, but who shared, as concerns embryological issues, an epigenetic conception of the development of the embryo. Their theories are discussed and compared in light of following questions: 1) What do Cremonini's, Harvey's and Descartes's embryological theories exactly aim to?; 2) In developing their theories, do these thinkers deal explicitly or implicitly with the Aristotelian and the Galenic embryological paradigm?; 3)Do they refer polemically to the Aristotelian and the Galenic tradition and what theoretical and/or rhetorical function have these polemical references?; 4) Do the embryological theories of Cremonini, Harvey and Descartes reflect the century-long dispute between \\\"(Aristotelian) philosophers\\\" and \\\"(Galenic) doctors\\\"?; 5) How is represented embryology as a 'scientific' and/or 'theoretical' domain? And what relationship between concepts of 'truth', 'research', 'tradition' and 'scientific progress' is implied or proposed in the embryological works of these three thinkers? What kind of use do Cremonini, Harvey and Descartes make of the argumenta ex ratione and of those ex experientia?\",\n \"corpus_id\": 44398371,\n \"score\": 0\n },\n {\n \"doc_id\": \"25281293\",\n \"title\": \"Conceiving \\\"personality\\\": Psychologist's challenges and basic fundamentals of the Transdisciplinary Philosophy-of-Science Paradigm for Research on Individuals.\",\n \"abstract\": \"Scientists exploring individuals, as such scientists are individuals themselves and thus not independent from their objects of research, encounter profound challenges; in particular, high risks for anthropo-, ethno- and ego-centric biases and various fallacies in reasoning. The Transdisciplinary Philosophy-of-Science Paradigm for Research on Individuals (TPS-Paradigm) aims to tackle these challenges by exploring and making explicit the philosophical presuppositions that are being made and the metatheories and methodologies that are used in the field. This article introduces basic fundamentals of the TPS-Paradigm including the epistemological principle of complementarity and metatheoretical concepts for exploring individuals as living organisms. Centrally, the TPS-Paradigm considers three metatheoretical properties (spatial location in relation to individuals' bodies, temporal extension, and physicality versus \\\"non-physicality\\\") that can be conceived in different forms for various kinds of phenomena explored in individuals (morphology, physiology, behaviour, the psyche, semiotic representations, artificially modified outer appearances and contexts). These properties, as they determine the phenomena's accessibility in everyday life and research, are used to elaborate philosophy-of-science foundations and to derive general methodological implications for the elementary problem of phenomenon-methodology matching and for scientific quantification of the various kinds of phenomena studied. On the basis of these foundations, the article explores the metatheories and methodologies that are used or needed to empirically study each given kind of phenomenon in individuals in general. Building on these general implications, the article derives special implications for exploring individuals' \\\"personality\\\", which the TPS-Paradigm conceives of as individual-specificity in all of the various kinds of phenomena studied in individuals.\",\n \"corpus_id\": 16259191,\n \"score\": 0\n },\n {\n \"doc_id\": \"25644235\",\n \"title\": \"Habermasian knowledge interests: epistemological implications for health sciences.\",\n \"abstract\": \"The Habermasian concept of 'interest' has had a profound effect on the characterization of scientific disciplines. Going beyond issues unrelated to the theory itself, intra-theoretical interest characterizes the specific ways of approaching any science-related discipline, defining research topics and methodologies. This approach was developed by Jürgen Habermas in relation to empirical-analytical sciences, historical-hermeneutics sciences, and critical sciences; however, he did not make any specific references to health sciences. This article aims to contribute to shaping a general epistemological framework for health sciences, as well as its specific implications for the medical and nursing areas, via an analysis of the basic knowledge interests developed by Habermas.\",\n \"corpus_id\": 12030588,\n \"score\": 0\n },\n {\n \"doc_id\": \"27339891\",\n \"title\": \"Research philosophy in pharmacy practice: necessity and relevance.\",\n \"abstract\": \"OBJECTIVE: Pharmacy practice has gradually evolved with the paradigm shifted towards patient-focused practice or medicines optimisation. The advancement of pharmacy-related research has contributed to this progression, but the philosophy of research remained unexplored. This review was thus aimed to outline the succinct concept of research philosophy and its application in pharmacy practice research. KEY FINDINGS: Research philosophy has been introduced to offer an alternative way to think about problem-driven research that is normally conducted. To clarify the research philosophy, four research paradigms, i.e. positivism (or empiricism), postpositivism (or realism), interpretivism (or constructivism) and pragmatism, are investigated according to philosophical realms, i.e. ontology, epistemology, axiology and logic of inquiry. With the application of research philosophy, some examples of quantitative and qualitative research were elaborated along with the conventional research approach. Understanding research philosophy is crucial for pharmacy researchers and pharmacists, as it underpins the choice of methodology and data collection. CONCLUSIONS: The review provides the overview of research philosophy and its application in pharmacy practice research. Further discussion on this vital issue is warranted to help generate quality evidence for pharmacy practice.\",\n \"corpus_id\": 205198550,\n \"score\": 0\n },\n {\n \"doc_id\": \"27925104\",\n \"title\": \"Epistemology of nursing care: a reflection on its foundations.\",\n \"abstract\": \"Epistemologia do cuidado de enfermagem: uma reflexão sobre suas bases. Objective:: to reflect on nursing care and its epistemology from its historical, theoretical, philosophical, spiritual dimensions and as a social practice. Method:: discussions originated in the discipline \\\"Epistemology of caring\\\", from the graduate nursing program of the School of Nursing, Federal University of Minas Gerais, and in critical analysis of nursing literature together with the professional practice of the authors. Results:: we identified the necessity of developing a critical conscience on health care provision, research, and teaching, as well as on challenges in maintaining high standards of working interpersonal relationships, which has a profound impact on population health. Conclusion:: we suggest the rescue of integrality, humanization, unity, and spirituality in researches and practices of individual, familiar, and community care, as an advance in incorporating epistemology of caring in nursing.\",\n \"corpus_id\": 7275618,\n \"score\": 0\n },\n {\n \"doc_id\": \"29147898\",\n \"title\": \"\\\"Don't Mind the Gap!\\\" Reflections on Improvement Science as a Paradigm.\",\n \"abstract\": \"Responding to this issue's invitation to bring new disciplinary insights to the field of improvement science, this article takes as its starting point one of the field's guiding metaphors: the imperative to \\\"mind the gap\\\". Drawing on insights from anthropology, history, and philosophy, the article reflects on the origins and implications of this metaphoric imperative, and suggests some ways in which it might be in tension with the means and ends of improvement. If the industrial origins of improvement science in the twentieth century inform a metaphor of gaps, chasms, and spaces of misalignment as invariably imperfect and potentially dangerous, and therefore requiring bridging or closure, other currents that feed the discipline of improvement science suggest the potential value and uses of spaces of openness and ambiguity. These currents include the science of complex adaptive systems, and certain precepts of philosophical pragmatism acknowledged to inform improvement science. Going a step further, I reflect on whether or not these two contrasting approaches within improvement science should be treated as incommensurable paradigms, and what each approach tells us about the very possibility of accommodating seemingly irreconcilable or incommensurable approaches within improvement science.\",\n \"corpus_id\": 4924880,\n \"score\": 0\n },\n {\n \"doc_id\": \"29280271\",\n \"title\": \"Nursing as concrete philosophy, Part I: Risjord on nursing knowledge.\",\n \"abstract\": \"This essay addresses the problem of the essentiality of nursing knowledge and what kind of theory, if any, is essential to nursing practice. The overarching aim of the essay was to argue for the thesis that nursing may be described as a kind of philosophical activity, and, consequently, that philosophy is the kind of \\\"theory\\\" that is essential to nursing practice and to the nursing discipline at large. The essay consists of two papers. The present paper, Part I, is a critical examination of Mark Risjord's discussion of the problem of the theory-practice gap in his Nursing Knowledge: Practice, Science, Philosophy, from 2010. According to Risjord, the cause of the theory-practice gap originates in an erroneous conception of science (logical positivism) which had a decisive influence upon the way nursing scholars appropriated theoretical frameworks for the nursing discipline. This philosophical influence is considered in effect to have generated the theory-practice gap. In order to bridge the gap, Risjord suggests, the nursing discipline needs to adopt a standpoint epistemology conjoined with a postpositivist conception of scientific theory. In this way, a legitimate brand of nursing science may be developed and the theory-practice gap overcome. I will argue that neither Risjord's diagnosis of the problem, nor his recommended cure, may succeed in rescuing the nursing discipline from the theory-practice gap. Rather, the real cause of the theory-practice gap, I will claim, derives from an erroneous conception of nursing (not of science), namely the conception of nursing as a kind of science (roughly speaking). On my view, to overcome the gap, the nursing discipline needs to make salient the inherently philosophical character of nursing. In the second paper (Part II), I will continue the discussion of nursing knowledge and delineate the thesis of nursing as a kind of concrete philosophy.\",\n \"corpus_id\": 3323520,\n \"score\": 0\n }\n]","isConversational":false}}},{"rowIdx":75,"cells":{"query":{"kind":"string","value":"{\n \"doc_id\": \"29333233\",\n \"title\": \"On the primacy and irreducible nature of first-person versus third-person information.\",\n \"abstract\": \"In this essay, we will support the claim that at the current level of scientific advancement a) some first-person accounts cannot be reduced to their third-person neural and psychophysiological correlates and b) that these first-person accounts are the only information to reckon when it is necessary to analyse qualia contents. Consequently, for many phenomena, first-person accounts are the only reliable source of information available and the knowledge of their neural and psychophysical correlates don't offer any additional information about them.\",\n \"corpus_id\": 746895\n}"},"candidates":{"kind":"list like","value":[{"doc_id":"20157986","title":"Networks of conscious experience: computational neuroscience in understanding life, death, and consciousness.","abstract":"We demonstrate brain locations appearing to correlate with consciousness, but not being directly responsible for it. Technology reveals that brain activity is associated with consciousness but is not equivalent to it. We examine how consciousness occurs at critical levels of complexity. Conventional explanations portray consciousness as an emergent property of classical computer-like activities in the brain's neural networks. Prevailing views in this camp are that patterns of neural network activities correlate with mental states, that synchronous network oscillations in the thalamus and cerebral cortex temporally bind information, and that consciousness emerges as a novel property of computational complexity among neurons. A hard-wired theory is enigmatic for explaining consciousness because the nature of subjective experience, or 'qualia'- 'inner life' - is a \"hard problem\" to understand; binding spatially distributed brain activity into unitary objects, and a coherent sense of self, or 'oneness' is difficult to explain as is the transition from pre- to conscious states. Consciousness is non-computable and involves factors that are neither random nor algorithmic - consciousness cannot be simulated; explanations are also needed for free will and for subjective time flow. Convention argues that neurons and their chemical synapses are the fundamental units of information in the brain, and that conscious experience emerges when a critical level of complexity is reached in the brain's neural networks. The basic idea is that the mind is a computer functioning in the brain. In fitting the brain to a computational view, such explanations omit incompatible neurophysiological details, including widespread apparent randomness at all levels of neural processes (is it really noise, or underlying levels of complexity?); glial cells (which account for some 80% of the brain); dendritic-dendritic processing; electrotonic gap junctions; cytoplasmic/cytoskeletal activities; living state (the brain is alive!); and absence of testable hypotheses in emergence theory. There is no threshold or rationale specified; rather, consciousness 'just happens'. Consciousness then involves an awareness of what we are sensing or experiencing and some ability to control or coordinate voluntary actions. These issues of life, death, and consciousness are discussed in the context of Mike, the headless chicken, who survived for 18 months, and in the context of consciousness with high degrees of intellectual and cognitive function in a congenitally anencephalic brain; additionally, in the reanimation work of Soviet scientists in the 1920-30s, and in auditory sentence processing in patients in comatose, vegetative, and minimally conscious states.","corpus_id":40003252,"score":2},{"doc_id":"21493099","title":"Neural correlates of consciousness reconsidered.","abstract":"It is widely accepted among philosophers that neuroscientists are conducting a search for the neural correlates of consciousness, or NCC. Chalmers (2000) conceptualized this research program as the attempt to correlate the contents of conscious experience with the contents of representations in specific neural populations. A notable claim on behalf of this interpretation is that the neutral language of \"correlates\" frees us from philosophical disputes over the mind/body relation, allowing the science to move independently. But the experimental paradigms and explanatory canons of neuroscience are not neutral about the mechanical relation between consciousness and the brain. I argue that NCC research is best characterized as an attempt to locate a causally relevant neural mechanism and not as an effort to identify a discrete neural representation, the content of which correlates with some actual experience. It might be said that the first C in \"NCC\" should stand for \"causes\" rather than \"correlates.\"","corpus_id":37669419,"score":2},{"doc_id":"23073546","title":"[What can qualia be? The monistic views].","abstract":"Phenomenal properties, also named qualia (that is, the qualities of human experiences, e.g. the senses of red, of salt, of pain, qua senses) create a hard problem for philosophy. It is claimed that phenomenal properties are radically different to the physical ones: they are intrinsic (their essence is totally confined within the limits of their existence), they depend on mind, they are accessible only privately, by introspection and they are infallible, in the sense that the experience of a quale is identical to its existence. On the contrary, physical properties are dispositional (their essence is defined through their causal consequences), they exist independently of mind, they are accessible to public observation and are liable to verification or falsification. The faculty of philosophy, named philosophy of mind, is systematically interested in qualia. In the present paper some of the main monistic philosophical approaches to qualia are discussed. The main common characteristic of monistic views is that (contrary to dualistic views) they purport that: two radically different substances cannot exist, side by side, within the same world (our world). Thus, there are either physical properties, or phenomenal properties, but not both. The monistic theories, supporting that in our world there are only physical properties, or properties totally reducible into physical ones, are named physicalism (or according to a more traditional nomination, materialism). On the other hand, monistic theories maintaining that all existing properties are phenomenal, or properties reducible into phenomenal ones, are named phenomenalism. The main arguments for physicalism are: (a) the scientific principle of the causal closure of the universe (every event has one physical cause), (b) the dependence of every well-studied mental phenomenon, from a physical phenomenal, such as the function of the neural system. Dualists counterattack physicalism with mental experiments (such as, the experiments concerning philosophical zombies) in order to demonstrate that qualia are irreducible entities. The main physicalistic options are eliminativism, the theories of identity, functionalism and representationalism. The main argument for phenomenalism is that physical properties and physical knowledge of them, as well, are reducible into and derived from experiences. On the other hand, opponents of phenomenalism retort that our world comprises spatiotemporal parts inaccessible to experience (f.e. the microworld of atomic physics, the world before the appearance of intelligent beings). Yet, some phenomenalists claim that phenomenal properties can be either real (experienced) or potentially real (what one would experience if one could observe this or that spatiotemporal part of the world). According to a third, agnosticistic opinion, named mysterianism, the human mind lacks the capacity of bridging the explanatory gap between physical and phenomenal identities. Many opponents of this theory claim the historically proved ability of human mind to find solutions for difficult problems of our world through scientific knowledge and based on it natural philosophy.","corpus_id":24773763,"score":2},{"doc_id":"23165867","title":"Integrated information theory of consciousness: an updated account.","abstract":"This article presents an updated account of integrated information theory of consciousness (IIT) and some of its implications. IIT stems from thought experiments that lead to phenomenological axioms and ontological postulates. The information axiom asserts that every experience is one out of many, i.e. specific - it is what it is by differing in its particular way from a large repertoire of alternatives. The integration axiom asserts that each experience is one, i.e. unified - it cannot be reduced to independent components. The exclusion axiom asserts that every experience is definite - it is limited to particular things and not others and flows at a particular speed and resolution. IIT formalizes these intuitions with three postulates. The information postulate states that only \"differences that make a difference\" from the intrinsic perspective of a system matter: a mechanism generates cause-effect information if its present state has specific past causes and specific future effects within a system. The integration postulate states that only information that is irreducible matters: mechanisms generate integrated information only to the extent that the information they generate cannot be partitioned into that generated within independent components. The exclusion postulate states that only maxima of integrated information matter: a mechanism specifies only one maximally irreducible set of past causes and future effects - a concept. A complex is a set of elements specifying a maximally irreducible constellation of concepts, where the maximum is evaluated at the optimal spatio-temporal scale. Its concepts specify a maximally integrated conceptual information structure or quale, which is identical with an experience. Finally, changes in information integration upon exposure to the environment reflect a system's ability to match the causal structure of the world. After introducing an updated definition of information integration and related quantities, the article presents some theoretical considerations about the relationship between information and causation and about the relational structure of concepts within a quale. It also explores the relationship between the temporal grain size of information integration and the dynamic of metastable states in the corticothalamic complex. Finally, it summarizes how IIT accounts for empirical findings about the neural substrate of consciousness, and how various aspects of phenomenology may in principle be addressed in terms of the geometry of information integration.","corpus_id":13920052,"score":2},{"doc_id":"23467765","title":"Consciousness and the invention of Morel.","abstract":"A scientific study of consciousness should take into consideration both objective and subjective measures of conscious experiences. To this date, very few studies have tried to integrate third-person data, or data about the neurophysiological correlates of conscious states, with first-person data, or data about subjective experience. Inspired by Morel's invention (Casares, 1940), a literary machine capable of reproducing sensory-dependent external reality, this article suggests that combination of virtual reality techniques and brain reading technologies, that is, decoding of conscious states by brain activity alone, can offer this integration. It is also proposed that the multimodal, simulating, and integrative capacities of the dreaming brain render it an \"endogenous\" Morel's machine, which can potentially be used in studying consciousness, but not always in a reliable way. Both the literary machine and dreaming could contribute to a better understanding of conscious states.","corpus_id":14109744,"score":2},{"doc_id":"23802335","title":"Integrated information theory of consciousness: an updated account.","abstract":"This article presents an updated account of integrated information theory of consciousness (liT) and some of its implications. /IT stems from thought experiments that lead to phenomenological axioms (existence, compositionality, information, integration, exclusion) and corresponding ontological postulates. The information axiom asserts that every experience is spec~fic - it is what it is by differing in its particular way from a large repertoire of alternatives. The integration axiom asserts that each experience is unified- it cannot be reduced to independent components. The exclusion axiom asserts that every experience is definite - it is limited to particular things and not others and flows at a particular speed and resolution. /IT formalizes these intuitions with postulates. The information postulate states that only \"differences that make a difference\" from the intrinsic perpective of a system matter: a mechanism generates cause-effect information if its present state has selective past causes and selective future effects within a system. The integration postulate states that only information that is irreducible matters: mechanisms generate integrated information only to the extent that the information they generate cannot be partitioned into that generated within independent components. The exclusion postulate states that only maxima of integrated information matter: a mechanism specifies only one maximally irreducible set of past causes and future effects - a concept. A complex is a set of elements specifying a maximally irreducible constellation of concepts, where the maximum is evaluated over elements and at the optimal spatiatemporal scale. Its concepts specify a maximally integrated conceptual information structure or quale, which is identical with an experience. Finally, changes in information integration upon exposure to the environment reflect a system's ability to match the causal structure of the world. After introducing an updated definition of information integration and related quantities, the article presents some theoretical considerations about the relationship between information and causation and about the relational structure of concepts within a qua/e. It also explores the relationship between the temporal grain size of information integration and the dynamic of metastable states in the corticothalamic complex. Finally, it summarizes how liT accounts for empirical findings about the neural substrate of consciousness, and how various aspects of phenomenology may in principle be addressed in terms of the geometry of information integration.","corpus_id":6113590,"score":2},{"doc_id":"23883758","title":"Merging second-person and first-person neuroscience.","abstract":"Schilbach et al. contrast second-person and third-person approaches to social neuroscience. We discuss relations between second-person and first-person approaches, arguing that they cannot be studied in isolation. Contingency is central for converging first- and second-person approaches. Studies of embodiment show how contingencies scaffold first-person perspective and how the transition from a third- to a second-person perspective fundamentally involves first-person contributions.","corpus_id":54587375,"score":2},{"doc_id":"24168487","title":"Bodily self-consciousness, and the primacy of self related signals such as the 1(st) person perspective and self-location.","abstract":"Abstract G&K provide a new and interesting perspective on consciousness, by arguing that consciousness is a product of social perception. Based on the overlap between the neural mechanisms underlying spatial awareness of other people and oneself, out-of-body experiences (OBEs), and social perception the authors argue that consciousness is based on the brain signals that represent other people and their spatial awareness. Although we generally welcome the authors efforts, we (1) would like to emphasize that consciousness has two distinct spatial aspects, namely self-location and first-person perspective, (2) cite evidence about distinct developmental and brain mechanisms concerning first- versus third-person perceptions and cogitations and (3) argue for a primacy of multisensory own body perception over social perception and awareness as a neurobiological foundation of consciousness.","corpus_id":-1,"score":2},{"doc_id":"24236862","title":"How can we construct a science of consciousness?","abstract":"This chapter gives an overview of the projects facing a science of consciousness. Such a science must integrate third-person data about behavior and brain processes with first-person data about conscious experience. Empirical projects for integrating these data include those of contrasting conscious and unconscious processes, investigating the contents of consciousness, finding neural correlates of consciousness, and eventually inferring underlying principles connecting consciousness with physical processes. These projects are discussed with reference to current experimental research on consciousness. Some obstacles that a science of consciousness faces are also discussed.","corpus_id":42133770,"score":2},{"doc_id":"24672510","title":"Structural qualia: a solution to the hard problem of consciousness.","abstract":"The hard problem of consciousness has been often claimed to be unsolvable by the methods of traditional empirical sciences. It has been argued that all the objects of empirical sciences can be fully analyzed in structural terms but that consciousness is (or has) something over and above its structure. However, modern neuroscience has introduced a theoretical framework in which also the apparently non-structural aspects of consciousness, namely the so called qualia or qualitative properties, can be analyzed in structural terms. That framework allows us to see qualia as something compositional with internal structures that fully determine their qualitative nature. Moreover, those internal structures can be identified which certain neural patterns. Thus consciousness as a whole can be seen as a complex neural pattern that misperceives some of its own highly complex structural properties as monadic and qualitative. Such neural pattern is analyzable in fully structural terms and thereby the hard problem is solved.","corpus_id":15323989,"score":2},{"doc_id":"25071677","title":"The measurement of consciousness: a framework for the scientific study of consciousness.","abstract":"Scientists studying consciousness are attempting to identify correlations between measurements of consciousness and the physical world. Consciousness can only be measured through first-person reports, which raises problems about the accuracy of first-person reports, the possibility of non-reportable consciousness and the causal closure of the physical world. Many of these issues could be resolved by assuming that consciousness is entirely physical or functional. However, this would sacrifice the theory-neutrality that is a key attraction of a correlates-based approach to the study of consciousness. This paper puts forward a different solution that uses a framework of definitions and assumptions to explain how consciousness can be measured. This addresses the problems associated with first-person reports and avoids the issues with the causal closure of the physical world. This framework is compatible with most of the current theories of consciousness and it leads to a distinction between two types of correlates of consciousness.","corpus_id":11598675,"score":2},{"doc_id":"25202297","title":"It is time to combine the two main traditions in the research on the neural correlates of consciousness: C = L × D.","abstract":"Research on neural correlates of consciousness has been conducted and carried out mostly from within two relatively autonomous paradigmatic traditions - studying the specific contents of conscious experience and their brain-process correlates and studying the level of consciousness. In the present paper we offer a theoretical integration suggesting that an emphasis has to be put on understanding the mechanisms of consciousness (and not a mere correlates) and in doing this, the two paradigmatic traditions must be combined. We argue that consciousness emerges as a result of interaction of brain mechanisms specialized for representing the specific contents of perception/cognition - the data - and mechanisms specialized for regulating the level of activity of whatever data the content-carrying specific mechanisms happen to represent. Each of these mechanisms are necessary because without the contents there is no conscious experience and without the required level of activity the processed contents remain unconscious. Together the two mechanisms, when activated up to a necessary degree each, provide conditions sufficient for conscious experience to emerge. This proposal is related to pertinent experimental evidence.","corpus_id":2490484,"score":2},{"doc_id":"25892488","title":"Epistemological implications of near-death experiences and other non-ordinary mental expressions: Moving beyond the concept of altered state of consciousness.","abstract":"During the last decades an increasing interest has developed in the so-called altered state of consciousness (ASCs); among these, near-death experiences (NDEs) are one of the most intriguing and debated examples. NDEs are deep and universal experiences with a clear phenomenology and incidence, while some of their features challenge the current views of human consciousness (focused on neural circuits and based on the concept of mind as a byproduct of brain circuitry) with relevant epistemological and historical implications. The origin of the ruling mechanist-reductionist paradigm can be traced back to Descartes' radical separation of res cogitans and res extensa and the conflict between the nascent science and the Inquisition; this led to removing the subjective properties of mind from the field of scientific interest, relegating them to philosophy and theology in order to enable the development of modern science. However, the physics of the 20th century has eventually moved beyond the classical paradigm, permitting a profound renewal of scientific interest in the mind. Modern research on NDEs has contributed to reopening the debate surrounding the Cartesian separation, the mind-brain relationship and the nature of consciousness. It is now time to reappraise the relevance, strengths, and weaknesses of the available scientific interpretations of NDEs, their relationship with other ASCs, as well as the very concept of ASC; the latter looks to be ill-founded, suggesting the need for: (a) a revision of the conventional approach to subjective phenomena, including both the third- and first-person perspective; and (b) a deep reflection on the possible links between different non-ordinary mental expression, as regards both their phenomenology and mechanisms from a non-pathological perspective.","corpus_id":18815739,"score":2},{"doc_id":"26074839","title":"Neurophenomenology revisited: second-person methods for the study of human consciousness.","abstract":"In the study of consciousness, neurophenomenology was originally established as a novel research program attempting to reconcile two apparently irreconcilable methodologies in psychology: qualitative and quantitative methods. Its potential relies on Francisco Varela's idea of reciprocal constraints, in which first-person accounts and neurophysiological data mutually inform each other. However, since its first conceptualization, neurophenomenology has encountered methodological problems. These problems have emerged mainly because of the difficulty of obtaining and analyzing subjective reports in a systematic manner. However, more recently, several interview techniques for describing subjective accounts have been developed, collectively known as \"second-person methods.\" Second-person methods refer to interview techniques that solicit both verbal and non-verbal information from participants in order to obtain systematic and detailed subjective reports. Here, we examine the potential for employing second-person methodologies in the neurophenomenological study of consciousness and we propose three practical ideas for developing a second-person neurophenomenological method. Thus, we first describe second-person methodologies available in the literature for analyzing subjective reports, identifying specific constraints on the status of the first-, second- and third- person methods. Second, we analyze two experimental studies that explicitly incorporate second-person methods for traversing the \"gap\" between phenomenology and neuroscience. Third, we analyze the challenges that second-person accounts face in establishing an objective methodology for comparing results across different participants and interviewers: this is the \"validation\" problem. Finally, we synthesize the common aspects of the interview methods described above. In conclusion, our arguments emphasize that second-person methods represent a powerful approach for closing the gap between the experiential and the neurobiological levels of description in the study of human consciousness.","corpus_id":374435,"score":2},{"doc_id":"26444360","title":"Emergence Of Consciousness And Qualia From A Complex Brain.","abstract":"Qualia are private conscious experiences of which the associated feelings can be reported to other people. Whether qualia are amenable to scientific exploration has often been questioned, which is challenged by the present article. The following arguments are given: 1. the configuration of the brain changes continuously and irreversibly, because of genetic and environmental influences and interhuman communication; 2. qualia and consciousness are processes, rather than states; 3. private feelings, including those associated with qualia, should be positioned in the context of a personal brain as being developed during life; 4. consciousness and qualia should be understood in the context of general system theory, thus concluding that isolated, in vitro, properties of neurons and other brain constituents might marginally contribute to the understanding of higher brain functions, mind or qualia; 5. current in vivo approaches have too little resolution power - in terms of space and time - to delineate individual and subjective brain processes. When subtle personalized properties of the nervous system can be assessed in vivo or in vitro, qualia can scientifically be investigated. We discuss some approaches to overcome these barriers.","corpus_id":8441610,"score":2},{"doc_id":"26748074","title":"Using category theory to assess the relationship between consciousness and integrated information theory.","abstract":"One of the most mysterious phenomena in science is the nature of conscious experience. Due to its subjective nature, a reductionist approach is having a hard time in addressing some fundamental questions about consciousness. These questions are squarely and quantitatively tackled by a recently developed theoretical framework, called integrated information theory (IIT) of consciousness. In particular, IIT proposes that a maximally irreducible conceptual structure (MICS) is identical to conscious experience. However, there has been no principled way to assess the claimed identity. Here, we propose to apply a mathematical formalism, category theory, to assess the proposed identity and suggest that it is important to consider if there exists a proper translation between the domain of conscious experience and that of the MICS. If such translation exists, we postulate that questions in one domain can be answered in the other domain; very difficult questions in the domain of consciousness can be resolved in the domain of mathematics. We claim that it is possible to empirically test if such a functor exists, by using a combination of neuroscientific and computational approaches. Our general, principled and empirical framework allows us to assess the relationship between the domain of consciousness and the domain of mathematical structures, including those suggested by IIT.","corpus_id":13900169,"score":2},{"doc_id":"20402245","title":"Representing human hands haptically or visually from first-person versus third-person perspectives.","abstract":"Humans can recognise human body parts haptically as well as visually. We employed a mental-rotation task to determine whether participants could adopt a third-person perspective when judging the laterality of life-like human hands. Female participants adopted either a first-person or a third-person perspective using vision (experiment 1) or haptics (experiment 2), with hands presented at various orientations within a horizontal plane. In the first-person perspective task, most participants responded more slowly as hand orientation increasingly deviated from the participant's upright orientation, regardless of modality. In the visual third-person perspective task, most participants responded more slowly as hand orientation increasingly deviated from the experimenter's upright orientation; in contrast, less than half of the participants produced this same inverted U-shaped response-time function haptically. In experiment 3, participants were explicitly instructed to adopt a third-person perspective haptically by mentally rotating the rubber hand to the experimenter's upright orientation. Most participants produced an inverted U-shaped function. Collectively, these results suggest that humans can accurately assume a third-person perspective when hands are explored haptically or visually. With less explicit instructions, however, the canonical orientation for hand representation may be more strongly influenced haptically than visually by body-based heuristics, and less easily modified by perspective instructions.","corpus_id":19177750,"score":1},{"doc_id":"20531262","title":"The primacy of intersubjectivity.","abstract":"The most important result of phenomenological research is the discovery of inherent intersubjectivity. Strategies for reporting phenomenological research and recognizing its intersubjective aspects are discussed. In addition to its significance for the practice of nurturing care, intersubjectivity is discussed in response to criticism of phenomenology as ungeneralizeable research. As the philosophical foundation of all research, phenomenology's singular position as a philosophy and research methodology is discussed.","corpus_id":2022053,"score":1},{"doc_id":"21713178","title":"The nature of consciousness in the visually deprived brain.","abstract":"Vision plays a central role in how we represent and interact with the world around us. The primacy of vision is structurally imbedded in cortical organization as about one-third of the cortical surface in primates is involved in visual processes. Consequently, the loss of vision, either at birth or later in life, affects brain organization and the way the world is perceived and acted upon. In this paper, we address a number of issues on the nature of consciousness in people deprived of vision. Do brains from sighted and blind individuals differ, and how? How does the brain of someone who has never had any visual perception form an image of the external world? What is the subjective correlate of activity in the visual cortex of a subject who has never seen in life? More in general, what can we learn about the functional development of the human brain in physiological conditions by studying blindness? We discuss findings from animal research as well from recent psychophysical and functional brain imaging studies in sighted and blind individuals that shed some new light on the answers to these questions.","corpus_id":2287638,"score":1},{"doc_id":"21971695","title":"[The so-called body-mind problem].","abstract":"Das so genannte Leib-Seele-Problem. THE PROBLEM: Even psychosomatic researchers seem to want to avoid the so-called body-mind problem, which is actually a mind-brain problem. In line with Beckermann (2008), the first the four possible positions on the mind-brain problem are presented. The debate over the past 100 years has revolved around the question of whether mental events are ontologically independent of brain physiology or whether they are in fact entirely determined by it. Such a physicalism approach based on properties (i.e., mental characteristics or phenomena are physical or can be completely reduced to physical characteristics), however, is diametrically opposed to some of our strongest intuitions, e.g., that computers will never be able to develop qualities of human experience (qualia) and thus become subjects in the first person singular. Yet we are equally unable to prove the fundamental impossibility of such a development. THESIS: In this stalemate situation, a differentiation was undertaken by Gottlob Frege (1892) which could be of help: Expressed in today's language, a distinction is made between the sense of an expression, its contextual presentation (e.g., where there is a difference between \"the evening star\" and \"the morning star\"), on the one hand, and its so-called reference (the object to which it refers, here the planet Venus in both cases) on the other. The school of Gestalt psychology that developed in Berlin at the start of the last century similarly posited a \"psychophysical level of the CNS,\" a continuum in a pattern of electrical field forces which manifests itself first in cerebral physiological-neuronal processes as well as in other perspectives such as consciousness and experience. A subsequent speculative concept then extends this model to assume also an (as yet) unknown Alpha configuration as being a common reference of two sense contents: (1) the results of the neurophysiological third-person perspective and (2) of the emotional-cognitive first-person perspectives. Only through the latter will Alpha be able to become self-conscious and an instance acting in his world. RESULTS: Only through the latter will Alpha be able to become self-conscious and an instance acting in his world. The postulate of an Alpha configuration thus retains the possibility of a biology not (yet) accessible to our knowledge, such that our fundamental conviction regarding the holism of soma and psyche can be maintained for us as medical practitioners and scientific physicians. Our patients need both, our medical-scientific competence (3rd-person perspective) as well as our empathic sensibility in exploring their phenomenal experience (1st-person perspective). They need us as medical artists.","corpus_id":297834,"score":1},{"doc_id":"22461776","title":"How to Begin to Overcome the Ambiguity Present in Differentiation between Contents and Levels of Consciousness?","abstract":"Recently, a welcome trend has emerged - in addition to the traditional studies on contents and states of consciousness, levels of consciousness have become a matter of research. However, there are some conceptual and methodological difficulties with this research - the labels used for empirical measurement of levels are ambiguous and underspecified while the research on neural correlates of consciousness has not been well linked to psychophysical approaches to studying the levels of consciousness. This article suggests a perspective on how to advance the psychophysics of measuring the levels by precisely specifying level-specific contents and how to relate the distinction between contents and levels to the distinction between the underlying brain mechanisms necessary for processing contents and regulating the level of consciousness.","corpus_id":13388403,"score":1},{"doc_id":"24130538","title":"Visual perspective and the characteristics of mind wandering.","abstract":"When the mind wanders away from the here-and-now toward imaginary events, it typically does so from one of two visual vantage points-a first-person perspective (i.e., the world is seen as it is in everyday life) or a third-person perspective (i.e., the world is seen from the viewpoint of an outside observer). While extant evidence has detailed consequences that ensue from the utilization of these distinct points of view, less is known about their more basic properties. Here, we investigated the prevalence, demographics and qualities associated with the visual perspective that people spontaneously adopt when the mind wanders. The results from a cross-cultural survey (N = 400) revealed that almost half of the participants (46%) typically utilize a third-person perspective when mind wandering. Further, culture and gender were shown to impact the distribution of first- and third-person imagers. Specifically, a first-person perspective was more common among participants from Western nations and females, while participants from Eastern cultures resonated more strongly with a third-person perspective. Moreover, these factors were also shown to impact qualities (e.g., temporal locus, vividness) of mental imagery. Taken together, the current findings elucidate the prevalence of first- and third-person visual perspectives and detail individual differences that influence the qualia of mind wandering.","corpus_id":10981877,"score":1},{"doc_id":"24742205","title":"Neural correlates of moral judgments in first- and third-person perspectives: implications for neuroethics and beyond.","abstract":"BACKGROUND: There appears to be an inconsistency in experimental paradigms used in fMRI research on moral judgments. As stimuli, moral dilemmas or moral statements/ pictures that induce emotional reactions are usually employed; a main difference between these stimuli is the perspective of the participants reflecting first-person (moral dilemmas) or third-person perspective (moral reactions). The present study employed functional magnetic resonance imaging (fMRI) in order to investigate the neural correlates of moral judgments in either first- or third-person perspective. RESULTS: Our results indicate that different neural mechanisms appear to be involved in these perspectives. Although conjunction analysis revealed common activation in the anterior medial prefrontal cortex, third person-perspective elicited unique activations in hippocampus and visual cortex. The common activation can be explained by the role the anterior medial prefrontal cortex may play in integrating different information types and also by its involvement in theory of mind. Our results also indicate that the so-called \"actor-observer bias\" affects moral evaluation in the third-person perspective, possibly due to the involvement of the hippocampus. We suggest two possible ways in which the hippocampus may support the process of moral judgment: by the engagement of episodic memory and its role in understanding the behaviors and emotions of others. CONCLUSION: We posit that these findings demonstrate that first or third person perspectives in moral cognition involve distinct neural processes, that are important to different aspects of moral judgments. These results are important to a deepened understanding of neural correlates of moral cognition-the so-called \"first tradition\" of neuroethics, with the caveat that any results must be interpreted and employed with prudence, so as to heed neuroethics \"second tradition\" that sustains the pragmatic evaluation of outcomes, capabilities and limitations of neuroscientific techniques and technologies.","corpus_id":9310894,"score":1},{"doc_id":"25376588","title":"Are Informant Reports of Personality More Internally Consistent Than Self Reports of Personality?","abstract":"The present study examined whether informant-reported personality was more or less internally consistent than self-reported personality in an epidemiological community sample (n = 1,449). Results indicated that across the 5 NEO (Neuroticism-Extraversion-Openness) personality factors and the 10 personality disorder trait dimensions, informant reports tended to be more internally consistent than self reports, as indicated by equal or higher Cronbach's alpha scores and higher average interitem correlations. In addition, the informant reports collectively outperformed the self reports for predicting responses on a global measure of health, indicating that the informant reports are not only more reliable than self reports, but they can also be useful in predicting an external criterion. Collectively these findings indicate that informant reports tend to have greater internal consistency than self reports.","corpus_id":31189113,"score":1},{"doc_id":"28760626","title":"How do the brain's time and space mediate consciousness and its different dimensions? Temporo-spatial theory of consciousness (TTC).","abstract":"Time and space are the basic building blocks of nature. As a unique existent in nature, our brain exists in time and takes up space. The brain's activity itself also constitutes and spreads in its own (intrinsic) time and space that is crucial for consciousness. Consciousness is a complex phenomenon including different dimensions: level/state, content/form, phenomenal aspects, and cognitive features. We propose a Temporo-spatial Theory of Consciousness (TTC) focusing primarily on the temporal and spatial features of the brain activity. We postulate four different neuronal mechanisms accounting for the different dimensions of consciousness: (i) \"temporo-spatial nestedness\" of the spontaneous activity accounts for the level/state of consciousness as neural predisposition of consciousness (NPC); (ii) \"temporo-spatial alignment\" of the pre-stimulus activity accounts for the content/form of consciousness as neural prerequisite of consciousness (preNCC); (iii) \"temporo-spatial expansion\" of early stimulus-induced activity accounts for phenomenal consciousness as neural correlates of consciousness (NCC); (iv) \"temporo-spatial globalization\" of late stimulus-induced activity accounts for the cognitive features of consciousness as neural consequence of consciousness (NCCcon).","corpus_id":24713088,"score":1},{"doc_id":"18434246","title":"Determinants of Internet use as a preferred source of information on personal health.","abstract":"OBJECTIVE: To understand the personal, social and cultural factors likely to explain recourse to the Internet as a preferred source of personal health information. DESIGN: A cross-sectional survey was conducted among a population of 2923 Internet users visiting a firmly established website that offers information on personal health. Multiple regression analysis was performed to identify the determinants of site use. MEASUREMENT: The analysis template comprised four classes of determinants likely to explain Internet use: beliefs, intentions, user satisfaction and socio-demographic characteristics. Seven-point Likert scales were used. An analysis of the psychometric qualities of the variables provided compelling evidence of the construct's validity and reliability. A confirmatory factor analysis confirmed the correspondence with the factors predicted by the theoretical model. FINDINGS: The regression analysis explained 35% of the variance in Internet use. Use was directly associated with five factors: perceived usefulness, importance given to written media in searches for health information, concern for personal health, importance given to the opinions of physicians and other health professionals, and the trust placed in the information available on the site itself. CONCLUSION: This study confirms the importance of the credibility of information on the frequency of Internet use as a preferred source of information on personal health. It also shows the potentially influential role of the Internet in the development of personal knowledge of health issues.","corpus_id":24534095,"score":0},{"doc_id":"19338113","title":"Position of the American Dietetic Association: functional foods.","abstract":"All foods are functional at some physiological level, but it is the position of the American Dietetic Association (ADA) that functional foods that include whole foods and fortified, enriched, or enhanced foods have a potentially beneficial effect on health when consumed as part of a varied diet on a regular basis, at effective levels. ADA supports research to further define the health benefits and risks of individual functional foods and their physiologically active components. Health claims on food products, including functional foods, should be based on the significant scientific agreement standard of evidence and ADA supports label claims based on such strong scientific substantiation. Food and nutrition professionals will continue to work with the food industry, allied health professionals, the government, the scientific community, and the media to ensure that the public has accurate information regarding functional foods and thus should continue to educate themselves on this emerging area of food and nutrition science. Knowledge of the role of physiologically active food components, from plant, animal, and microbial food sources, has changed the role of diet in health. Functional foods have evolved as food and nutrition science has advanced beyond the treatment of deficiency syndromes to reduction of disease risk and health promotion. This position paper reviews the definition of functional foods, their regulation, and the scientific evidence supporting this evolving area of food and nutrition. Foods can no longer be evaluated only in terms of macronutrient and micronutrient content alone. Analyzing the content of other physiologically active components and evaluating their role in health promotion will be necessary. The availability of health-promoting functional foods in the US diet has the potential to help ensure a healthier population. However, each functional food should be evaluated on the basis of scientific evidence to ensure appropriate integration into a varied diet.","corpus_id":39013158,"score":0},{"doc_id":"19361993","title":"Public versus personal information for mate copying in an invertebrate.","abstract":"Organisms require information to make decisions about fitness-affecting resources, such as mates. Animals may extract \"personal information\" about potential mates by observing their physical characteristics or extract additional \"public information\" by observing their mating performance [1]. Mate copying by females [2-6] is a form of public information use that may reduce uncertainty about male quality, allowing more adaptive choices [2]. Experimental studies have produced evidence that female mate copying occurs in several species of fish [3], birds [5-7], and mammals [8], including humans [9]. We report the first evidence that a female invertebrate can exploit public information to select mates. In a first experiment, Drosophila melanogaster female prospectors increased their time in the attraction zones of poor-condition males, but not of good-condition males, after having observed them with a model female. This suggests that females appraised prospective mates by exploiting public information and did so mainly when it contrasted with personal information. In a second experiment, prospector females preferably mated with males of the color type they had previously observed copulating over males of the rejected color type, suggesting that female Drosophila can generalize socially learned information. The complexity of Drosophila decision-making suggests an unprecedented level of cognition in invertebrates. Our findings have implications for evolution given that socially learned mate preferences may lead to reproductive isolation, setting the stage for speciation [10].","corpus_id":12667396,"score":0},{"doc_id":"19692271","title":"I can see it both ways: first- and third-person visual perspectives at retrieval.","abstract":"The number of studies examining visual perspective during retrieval has recently grown. However, the way in which perspective has been conceptualized differs across studies. Some studies have suggested perspective is experienced as either a first-person or a third-person perspective, whereas others have suggested both perspectives can be experienced during a single retrieval attempt. This aspect of perspective was examined across three studies, which used different measurement techniques commonly used in studies of perspective. Results suggest that individuals can experience more than one perspective when recalling events. Furthermore, the experience of the two perspectives correlated differentially with ratings of vividness, suggesting that the two perspectives should not be considered in opposition of one another. We also found evidence of a gender effect in the experience of perspective, with females experiencing third-person perspectives more often than males. Future studies should allow for the experience of more than one perspective during retrieval.","corpus_id":1111690,"score":0},{"doc_id":"19814826","title":"Information management to enable personalized medicine: stakeholder roles in building clinical decision support.","abstract":"BACKGROUND: Advances in technology and the scientific understanding of disease processes are presenting new opportunities to improve health through individualized approaches to patient management referred to as personalized medicine. Future health care strategies that deploy genomic technologies and molecular therapies will bring opportunities to prevent, predict, and pre-empt disease processes but will be dependent on knowledge management capabilities for health care providers that are not currently available. A key cornerstone to the potential application of this knowledge will be effective use of electronic health records. In particular, appropriate clinical use of genomic test results and molecularly-targeted therapies present important challenges in patient management that can be effectively addressed using electronic clinical decision support technologies. DISCUSSION: Approaches to shaping future health information needs for personalized medicine were undertaken by a work group of the American Health Information Community. A needs assessment for clinical decision support in electronic health record systems to support personalized medical practices was conducted to guide health future development activities. Further, a suggested action plan was developed for government, researchers and research institutions, developers of electronic information tools (including clinical guidelines, and quality measures), and standards development organizations to meet the needs for personalized approaches to medical practice. In this article, we focus these activities on stakeholder organizations as an operational framework to help identify and coordinate needs and opportunities for clinical decision support tools to enable personalized medicine. SUMMARY: This perspective addresses conceptual approaches that can be undertaken to develop and apply clinical decision support in electronic health record systems to achieve personalized medical care. In addition, to represent meaningful benefits to personalized decision-making, a comparison of current and future applications of clinical decision support to enable individualized medical treatment plans is presented. If clinical decision support tools are to impact outcomes in a clear and positive manner, their development and deployment must therefore consider the needs of the providers, including specific practice needs, information workflow, and practice environment.","corpus_id":1002325,"score":0},{"doc_id":"19930262","title":"The nature (and nurture) of personality disorders.","abstract":"Personality disorders have a long history in the literature but a short scientific history. The point prevalence of personality disorders is 10%, but the lifetime prevalence is probably 30-40%. Genetic factors contribute to around 40-50% of the variation in the development of personality disorders. The effect of shared environment is very small or non-existent. Some researchers have tried to promote gene-environment interaction. However, in reality, the studies investigated gene-situation interaction, as the \"environment\" may in reality be partly of a genetic nature. Thus, we are dealing with an unknown part of gene-gene interaction. Gene-experience (not gene-environment) correlations are the rule in human life. Personality disorders co-occur (are comorbid) with symptom disorders (Axis I) and correlate with common personality dimensions. Possibly, the concept of personality disorder could merge with dysfunctional personality types. But it is likely that the concept will survive on its own.","corpus_id":35862425,"score":0},{"doc_id":"20665336","title":"Correlates and phenomenology of first and third person memories.","abstract":"The present research addressed fundamental questions about the visual perspective of autobiographical memories: Are stable personality characteristics associated with visual perspective? Does visual perspective influence the memory's phenomenological qualities? Participants in Study 1 (N=1684) completed individual-difference measures and indicated the perspective from which they generally retrieve memories. Participants in Study 2 (N=706) retrieved a memory from their natural or manipulated perspective, rated its phenomenology, and completed the same individual-difference measures. Dissociation and anxiety were associated with third person retrieval style; the Big Five personality traits were primarily unrelated to perspective. Compared to third person memories, naturally occurring first person memories were higher on Vividness, Coherence, Accessibility, Sensory Detail, Emotional Intensity, and Time Perspective, and lower on Distancing; manipulating perspective eliminated these differences. Visual perspective is associated with clinically relevant constructs and, although associated with the memory's phenomenology, perspective does not shape it.","corpus_id":13797339,"score":0},{"doc_id":"21278049","title":"Review of extracting information from the Social Web for health personalization.","abstract":"In recent years the Web has come into its own as a social platform where health consumers are actively creating and consuming Web content. Moreover, as the Web matures, consumers are gaining access to personalized applications adapted to their health needs and interests. The creation of personalized Web applications relies on extracted information about the users and the content to personalize. The Social Web itself provides many sources of information that can be used to extract information for personalization apart from traditional Web forms and questionnaires. This paper provides a review of different approaches for extracting information from the Social Web for health personalization. We reviewed research literature across different fields addressing the disclosure of health information in the Social Web, techniques to extract that information, and examples of personalized health applications. In addition, the paper includes a discussion of technical and socioethical challenges related to the extraction of information for health personalization.","corpus_id":7037794,"score":0},{"doc_id":"21357240","title":"Young children's selective trust in informants.","abstract":"Young children readily act on information from adults, setting aside their own prior convictions and even continuing to trust informants who make claims that are manifestly false. Such credulity is consistent with a long-standing philosophical and scientific conception of young children as prone to indiscriminate trust. Against this conception, we argue that children trust some informants more than others. In particular, they use two major heuristics. First, they keep track of the history of potential informants. Faced with conflicting claims, they endorse claims made by someone who has provided reliable care or reliable information in the past. Second, they monitor the cultural standing of potential informants. Faced with conflicting claims, children endorse claims made by someone who belongs to a consensus and whose behaviour abides by, rather than deviating from, the norms of their group. The first heuristic is likely to promote receptivity to information offered by familiar caregivers, whereas the second heuristic is likely to promote a broader receptivity to informants from the same culture.","corpus_id":2110951,"score":0},{"doc_id":"21858422","title":"The mind as skills and dispositions: on normativity and mediation.","abstract":"On the occasion of the critique of Alfredo Gaete and Carlos Cornejo, this article explains and extends the hybrid theory of the mind that I recently presented in this journal. Taking inspiration from Rom Harré's program for a hybrid psychology, the theory is supposed to be integrative and aims to broaden Harré's hybrid psychology by including not just the brain, but also the body, social practices, and technological artifacts as mediators of the mind. The mind is understood not as a substance of any kind, but as a set of skills and dispositions to act, think, and feel. This implies a normative view of the mind, according to which psychological phenomena do not simply happen, but are done, and can consequently be done more or less well. I provide arguments in favor of grounding psychology in normativity rather than conscious experience, and I explain why the emphasis on mediators does not represent a threat to the ontological primacy of the person in psychology.","corpus_id":36141213,"score":0},{"doc_id":"22023911","title":"Mirror-view reverses somatoparaphrenia: dissociation between first- and third-person perspectives on body ownership.","abstract":"Right-hemisphere stroke can lead to the somatoparaphrenic delusion that parts of one's own body belong to someone else. To our knowledge, no previous study has experimentally assessed the sense of body part ownership in somatoparaphrenic patients when they see the body from a third-person perspective, as in a mirror. In alternating trials, we provided either direct first-person perspective vision of the arms, or indirect third-person perspective vision via a mirror in the frontal plane. We tested body ownership in these conditions in five patients with right-hemisphere lesions with left hemiplegia and neglect, including two patients with this somatoparaphrenic delusion. The somatoparaphrenic patients systematically attributed the ownership of their left plegic hands to someone else in direct view, but showed a statistically significant increase in ownership of the left hand in mirror view trials, as compared with the three control patients. Depending on the view offered (mirror or direct), judgements of ownership and disownership of the same limb could alternate within a few seconds. The patients did not particularly remark on these dramatic and repeated alterations between ownership and disownership. Conditions of direct- and mirror-view with simultaneous touch of the hand by the experimenter showed the same patterns of results as conditions without touch. This study provides the first experimental evidence that limb disownership can be altered using self-observation in a mirror, and in turn suggests dissociation between first- and third-person visual perspectives on the body. Furthermore, the fact that reinstatement of ownership by third-person perspective did not permanently abolish somatoparaphrenia suggests that the subjective sense of body ownership remained dominated by an impaired first-person representation of the body that could not be updated, nor integrated with other signals. More generally, our findings suggest that a neural network involving the perisylvian areas of the right hemisphere may be necessary for the integration of multiple representations of one's body and for a higher order re-representation of various bodily signals into a first-person sense of body ownership. We suggest that other areas, possibly including the occipital cortex, may be involved in the recognition of the body from a third-person visual perspective. We thus propose that somatoparaphrenia can be regarded as a neurogenic dissociation between the 'subjectively felt' and 'objectively seen' body. This recalls the developmental finding that young infants cannot link their 'felt body' with the view of themselves in a mirror.","corpus_id":25892919,"score":0},{"doc_id":"22117462","title":"[The psychophysiological condition of first year students with different levels of physical activity].","abstract":"The psychophysiological condition of (male) first year students who participate in sport or don't participate in sport during studies was studied. R. M. Bayevsky's method was used to establish the level of stress on regulatory mechanisms. The functional level of the nervous system, stability of neural responses, and the level of functional abilities of the developed functional system were evaluated using the variation chronoreflexometric method. It was established that an improvement of mental capacity indicators (increase of memory capacity, reduction of the amount of mistakes made, growth of the level of functional abilities and reduction of the latency period of the visual-motor response) was accompanied by a growth of stress on the body's regulatory systems which was more pronounced with regard to those test participants whose level of physical activity was low. This fact is proof that physical activity reduces the body's \"adaptation price\" to the changing conditions of the environment. The optimal realisation of a person's adaptive systemic reactions is provided for by the dynamic interaction of the functional systems, which form a complex correlation in the body's somatovegetative, motor and psychoemotional spheres of activity.","corpus_id":22233503,"score":0},{"doc_id":"23205018","title":"The current and future status of the concealed information test for field use.","abstract":"The Concealed Information Test (CIT) is a psychophysiological technique for examining whether a person has knowledge of crime-relevant information. Many laboratory studies have shown that the CIT has good scientific validity. However, the CIT has seldom been used for actual criminal investigations. One successful exception is its use by the Japanese police. In Japan, the CIT has been widely used for criminal investigations, although its probative force in court is not strong. In this paper, we first review the current use of the field CIT in Japan. Then, we discuss two possible approaches to increase its probative force: sophisticated statistical judgment methods and combining new psychophysiological measures with classic autonomic measures. On the basis of these considerations, we propose several suggestions for future practice and research involving the field CIT.","corpus_id":14655244,"score":0},{"doc_id":"24189291","title":"The nature and evolution of insight in schizophrenia: a multi-informant longitudinal study of first-episode versus chronic patients.","abstract":"BACKGROUND AND AIMS: This study investigated a novel distinction between two possible sources of poor insight in schizophrenia: primary unawareness, in which the ill person is not aware that other people think one has a problem, and secondary unawareness (or disagreement), in which a person does appreciate that other people think one has a problem. A secondary goal was to compare the evolution of insight in first-episode and chronic schizophrenia. METHODS: Sixty-eight first-episode and 51 chronic patients were administered two versions of the Scale of Unawareness of Mental Disorder (SUMD) at three time points: hospital admission, discharge, and 6-month post-discharge. In the first standard SUMD version, they were asked about their own opinions, whereas in the second modified version, they were asked about their best guess of their doctor's opinion. RESULTS: While overall level of unawareness remained stable within each single episode, there were significant Type of Unawareness (primary versus secondary) by Clinical Status (admission versus discharge versus 6-month post-discharge) and Type of Unawareness by Phase of Illness (first-episode versus chronic) interaction effects. More specifically, in the first-episode group, primary unawareness steadily decreased over time. In contrast, in the chronic group, primary unawareness decreased markedly during hospitalization and returned to baseline after discharge. CONCLUSIONS: These results provide preliminary support for the notion that impaired insight is an additive outcome of primary unawareness and disagreement, and that change in insight over time occurs mostly at the level of their relative proportion as opposed to their overall sum. Implications for studying and treating poor insight in schizophrenia are discussed.","corpus_id":42405152,"score":0},{"doc_id":"24453321","title":"Suboptimal use of neural information in a mammalian auditory system.","abstract":"Establishing neural determinants of psychophysical performance requires both behavioral and neurophysiological metrics amenable to correlative analyses. It is often assumed that organisms use neural information optimally, such that any information available in a neural code that could improve behavioral performance is used. Studies have shown that detection of amplitude-modulated (AM) auditory tones by humans is correlated to neural synchrony thresholds, as recorded in rabbit at the level of the inferior colliculus, the first level of the ascending auditory pathway where neurons are tuned to AM stimuli. Behavioral thresholds in rabbit, however, are ∼10 dB higher (i.e., 3 times less sensitive) than in humans, and are better correlated to rate-based than temporal coding schemes in the auditory midbrain. The behavioral and physiological results shown here illustrate an unexpected, suboptimal utilization of available neural information that could provide new insights into the mechanisms that link neuronal function to behavior.","corpus_id":11991198,"score":0},{"doc_id":"24547754","title":"Students working with multiple conflicting documents on a scientific issue: relations between epistemic cognition while reading and sourcing and argumentation in essays.","abstract":"BACKGROUND: There is burgeoning research within educational psychology on both epistemic cognition and multiple-documents literacy, as well as on relationships between the two constructs. AIM: To examine relationships between epistemic cognition concerning the justification of knowledge claims and sourcing and argumentation skills. SAMPLE: Participants were 51 Norwegian undergraduates. METHOD: Three dimensions of justification were identified in think-aloud protocols based on students' reading of six documents presenting conflicting claims on the controversial scientific issue of cell phone radiation and health risks: justification by authority, personal justification and justification by multiple sources. Hierarchical multiple regression analyses were performed to examine the unique predictability of these dimensions for essay performance after removing variance associated with prior knowledge about the topic of the documents. RESULTS: After controlling for topic knowledge, justification by multiple sources uniquely predicted students' sourcing and argumentation in essays that they wrote after reading the documents, with students trying to justify knowledge claims by corroborating across several sources of information more likely to include explicit source citations, link sources and contents, and display better, more integrated argumentation in their essays. CONCLUSION: Findings are considered in the light of a theoretical framework for multiple-documents literacy adapted to the domain of science, and both theoretical and educational implications are discussed.","corpus_id":25334715,"score":0},{"doc_id":"24671136","title":"A cognitive ethology study of first- and third-person perspectives.","abstract":"The aim of the present study was to test the cognitive ethology approach, which seeks to link cognitions and behaviours as they operate in everyday life with those studied in controlled lab-based investigations. Our test bed was the understanding of first-person and third-person perspectives, which in lab-based investigations have been defined in a diverse and multi-faceted manner. We hypothesized that because these lab-based investigations seek to connect with how first- and third-person perspective operates in everyday life, then either some of the divergent lab-based definitions are missing their mark or the everyday conceptualization of first- and third-person perspective is multi-faceted. Our investigation revealed the latter. By applying a cognitive ethology approach we were able to determine that a) peoples' everyday understanding of perspective is diverse yet reliable, and b) a lab-based investigation that applies these diverse understandings in a controlled setting can accurately predict how people will perform. These findings provide a 'proof of concept' for the cognitive ethology approach. Moreover, the present data demonstrate that previous lab-based studies, that often had very different understandings of first- and third-person perspective, were each in and of themselves valid. That is, each is capturing part of a broader understanding of perspective in everyday life. Our results also revealed a novel social factor not included in traditional conceptualizations of first-person third-perspective, that of eye gaze, i.e., eye contact is equated strongly with first-person perspective and the lack of eye-contact with third-person perspective.","corpus_id":18904293,"score":0},{"doc_id":"24785813","title":"16. Information.","abstract":"Effective disaster management requires systems for data acquisition and information management that enable responders to rapidly collect, process, interpret, distribute, and access the data and information required for disaster management. Effective information sharing depends on the types of users, the type of damage, alterations of the functional status of the affected society, and how the information is structured. Those in need of information should be provided with the information necessary for their tasks and not be overloaded with unnecessary information that could serve as a distraction. Such information systems must be designed and exercised. To disseminate and share data with the relevant users, all disaster responses must include effective and reliable information systems. This information includes that acquired from repeated assessments in terms of available and needed human and material resources, which resources no longer are needed, and the status of the relief and recovery workers. It is through this information system that vital decisions are made that are congruent with the overall picture as perceived by the most relevant coordination and control centre. It is essential that information systems be designed and tested regularly as part of preparedness. Such systems must have the capacity to acquire, classify, and present information in an organised and useful manner.","corpus_id":206722695,"score":0},{"doc_id":"24821510","title":"Cultural differences in the primacy effect for person perception.","abstract":"Previous work has shown there are robust differences in how North Americans and East Asians form impressions of people. The present research examines whether the tendency to weigh initial information more heavily-the primacy effect-may be another component of these cultural differences. Specifically, we tested whether Americans would be more likely to use first impressions to guide person perception, compared to Japanese participants. In this experiment, participants read a vignette that described a target person's behaviour, then rated the target's personality. Before reading the vignette, some trait information was given to create an expectation about the target's personality. The data revealed that Americans used this initial information to guide their judgments of the target, whereas the Japanese sample based their judgments on all the information more evenly. Thus, Americans showed a stronger primacy effect in their impression formation than Japanese participants, who engaged in more data-driven processing.","corpus_id":3711355,"score":0},{"doc_id":"24845204","title":"The diagnosis of death and the irreducibility of the human person.","abstract":"If, as Karol Wojtyla had insisted, the human person is fundamentally irreducible to any natural, biological, social, or even cosmological function, then the diagnosis of death on any of the purely functionalistic grounds available to medical science presents a serious ethical problem. Perhaps we can no longer treat the question of death merely as a medical \"diagnosis,\" regarding, on that basis, the appropriateness of organ transplantation as a purely medical judgment, ethically accountable only to professional standards of care. We will explore this problem from within a personalistic philosophical, and theological framework, according to which the irreducibility of the human person provides the central referent for an analysis of the reductionistic tendencies of contemporary thinking concerning the \"diagnosis of death.\"","corpus_id":20263777,"score":0},{"doc_id":"25259560","title":"A qualitative study on the use of personal information technology by persons with spinal cord injury.","abstract":"PURPOSE: Previous work has shown that information technology (IT), such as personal computers and other digital devices (e.g. tablets, laptops, etc.), software, online resources and hand-held communication tools (e.g. cellphones), has benefits for health and well-being for persons with chronic health conditions. To date, the ways that persons with spinal cord injury (SCI) use IT in their daily activities has not been fully explored. Thus, the purpose of the study was to obtain an in-depth perspective of how people with SCI regularly use IT to gain insight on ways IT can be used to support health and well-being in the community for this population. METHODS: Semi-structured interviews were conducted with community-dwelling persons with SCI (N = 10) who identified themselves as frequent-or-daily-users of IT. Qualitative content analysis was used to identify the ways that persons with SCI use personal IT. RESULTS: Ten themes related to IT use were identified: (1) Modifications allowing access to IT; (2) Convenience of IT and its perceived value; (3) IT as a scheduler/planner; (4) Challenges; (5) Contributions of IT to participation; (6) Access to information; (7) Influence of IT on well-being; (8) IT as a connector; (9) Issues of IT acquisition; and (10) Desires for future devices/technology. CONCLUSIONS: The findings suggest that IT use by people with SCI contributes to general health and well-being, by increasing access to SCI-related health information and opportunity for social participation. Despite the benefits offered by IT, persons with SCI have identified a degree of skepticism about the reliability and applicability of the health information they find online. Future work on developing and implementing IT for health and well-being post-SCI should take into account consumers' perspectives to facilitate uptake. Implications for Rehabilitation There is a need for a more refined understanding of how people with spinal cord injury (SCI) use information technology (IT) in their daily lives in order to understand how IT can support health and well-being post-injury in the community. IT use holds implications for the physical and mental well-being of persons with SCI. IT allows access to a variety of information, and facilitates participation in the community. The enthusiasm for the use of IT is tempered by a degree of skepticism about the reliability and applicability of the health information available online. This highlights the need to raise awareness of existing sources vetted for this population, and to develop content that meets the particular health needs for SCI.","corpus_id":25745097,"score":0},{"doc_id":"25417640","title":"Accuracy of Judgments of Personality Based on Textual Information on Major Life Domains.","abstract":"We studied the accuracy of personality impressions relying on textual information on important life domains. Specifically, how is accuracy moderated by the trait being judged, information being provided, judgeability of target persons, and perceptiveness of judges? A sample of 208 students was recruited in groups of four mutual acquaintances who described themselves and each other on a measure of the Five-Factor Model of personality. Moreover, they wrote essays on their hobbies, friends, family, academic studies, and plans for the future and provided self-reports on possible predictors of expressive accuracy. The essays were delivered to 130 strangers who reported their impressions of the personality of the targets and provided self-reports on possible predictors of perceptive accuracy. Accuracy was measured by correlating these impressions with the descriptions of the targets by their acquaintances. The judges used the available information efficiently. Overall, impressions of Openness to Experience were most accurate, but accuracy depended on the information being provided. Several predictors of expressive and perceptive accuracy were identified using Biesanz's (2010) social accuracy model. The results advance our understanding of factors contributing to and moderating the accuracy of personality impressions based on textual information.","corpus_id":1223281,"score":0},{"doc_id":"25494630","title":"Evidence-informed person-centred health care (part II): are 'cognitive biases plus' underlying the EBM paradigm responsible for undermining the quality of evidence?","abstract":"INTRODUCTION: Recently, some leaders of the evidence-based medicine (EBM) movement drew attention to the \"unintended\" negative consequences associated with EBM. The term 'cognitive biases plus' was introduced in part I to encompass cognitive biases, conflicts of interests, fallacies and certain behaviours. HYPOTHESIS: 'Cognitive biases plus' in those closely involved in creating and promoting the EBM paradigm are responsible for their (1) inability to anticipate and then recognize flaws in the tenets of EBM; (2) discounting alternative views; and (3) delaying reform. METHODS: A narrative review style was used, with methods as in part I. APPRAISAL OF LITERATURE: Over the past two decades there has been mounting qualitative and quantitative methodological evidence to suggest that the faith placed in (1) the EBM hierarchy with randomized controlled trials and systematic reviews at the summit; (2) the reliability of biostatistical methods to quantitate data; and (3) the primacy of sources of pre-appraised evidence, is seriously misplaced. Consequently, the evidence that informs person-centred care is compromised. DISCUSSION: Arguments focusing on 'cognitive biases plus' are offered to support our hypothesis. To the best of our knowledge, EBM proponents have not provided an explanation. CONCLUSIONS: Reform is urgently needed to minimize continuing risks to patients. If our hypothesis is correct, then in addition to the suggestions made in part I, deficiencies in the paradigm must be corrected. Meaningful solutions are only possible if the biases of scientific inbreeding and groupthink are minimized by collaboration between EBM leaders and those who have been sounding warning bells.","corpus_id":46137,"score":0},{"doc_id":"25528086","title":"Is it always me first? Effects of self-tagging on third-person perspective-taking.","abstract":"Self-relevant information is associated with facilitation of perceptual and memory processes. In 2 experiments, participants verified the number of dots within a virtual room that were visible to a given perspective, corresponding to participants' own first-person perspectives or the third-person perspectives for self- and other-associated avatars. Perspectives were either congruent or incongruent with respect to the number of dots visible to each. In Experiment 1, we examined perspective taking for self- and other-associated avatars relative to one another; both avatars appeared simultaneously in the virtual room, and participants made judgments based on the prompted avatar's perspective. In Experiment 2, we examined perspective taking for each avatar relative to the first-person perspective; only 1 avatar was visible in the virtual room (Self or Other, varying by trial), and participants made judgments based on their first-person view or the avatar's perspective. Experiment 2 also included a replication of the third-person paradigm used in Experiment 1. Results from Experiment 1 (replicated in Experiment 2) demonstrated an advantage for judgments of the Self (vs. Other) avatar's perspective; both avatars elicited reliable interference effects of similar magnitude. Results from Experiment 2 further demonstrated that participants prioritized the first-person (vs. third-person) perspective, and that the presence of the Self (vs. Other) avatar improved performance for the first- and third-person perspectives when those perspectives were congruent. Taken together, these findings suggest that self-relevant perspectives are prioritized when they are actively engaged and when they can be subsumed within the first-person view. Such prioritization appears to occur by strategic means.","corpus_id":4985388,"score":0},{"doc_id":"25594153","title":"First-person and third-person verbs in visual motion-perception regions.","abstract":"Verb-related activity is consistently found in the left posterior lateral cortex (PLTC), encompassing also regions that respond to visual-motion perception. Besides motion, those regions appear sensitive to distinctions among the entities beyond motion, including that between first- vs. third-person (\"third-person bias\"). In two experiments, using functional magnetic resonance imaging (fMRI), we studied whether the implied subject (first/third-person) and/or the semantic content (motor/non-motor) of verbs modulate the neural activity in the left PLTC-regions responsive during basic- and biological-motion perception. In those sites, we found higher activity for verbs than for nouns. This activity was modulated by the person (but not the semantic content) of the verbs, with stronger response to third- than first-person verbs. The third-person bias elicited by verbs supports a role of motion-processing regions in encoding information about the entity beyond (and independently from) motion, and sets in a new light the role of these regions in verb processing.","corpus_id":20166449,"score":0},{"doc_id":"25597036","title":"The researcher as experimental subject: using self-experimentation to access experiences, understand social phenomena, and stimulate reflexivity.","abstract":"The current article argues that researcher-as-subject self-experimentation can provide valuable insight and systematic knowledge to social psychologists. This approach, the modus operandi of experimental psychology when the field was in its infancy, has been largely eclipsed by an almost exclusive focus on participant-as-subject other-experimentation. Drawing from the non-experimental first-person traditions of autoethnography, participant observation, and phenomenology, we argue that participating as both observer and subject within one's own social psychological experiment affords researchers at least three potential benefits: (1) access to \"social qualia,\" that is, the subjective experience of social phenomena; (2) improved mental models of social phenomena, potentially stimulating new research questions; and (3) an enhanced ability to be reflexive about the given experiment. To support our position, we provide first-person self-reflections from researchers who have self-experimented with transformed social interactions involving Milgram's cyranoid method. We close by offering guidelines on how one might approach self-experimentation, and discuss a variety of first-person perspective ethnographic technologies that can be incorporated into the practice.","corpus_id":33909867,"score":0},{"doc_id":"26567205","title":"Consumer Perception of Genetically Modified Organisms and Sources of Information.","abstract":"Genetically modified organisms (GMOs) have been available for commercial purchase since the 1990s, allowing producers to increase crop yields through bioengineering that creates herbicide-resistant and insect-resistant varieties. However, consumer knowledge about GMOs has not increased at the same rate as the adoption of GMO crops. Consumers worldwide are displaying limited understanding, misconceptions, and even unfamiliarity with GMO food products. Many consumers report that they receive information about GMO food products from the media, Internet, and other news sources. These sources may be less reliable than scientific experts whom consumers trust more to present the facts. Although many in the United States support mandatory GMO labeling (similar to current European standards), consumer awareness of current GMO labeling is low. A distinction must also be made between GMO familiarity and scientific understanding, because those who are more familiar with it tend to be more resistant to bioengineering, whereas those with higher scientific knowledge scores tend to have less negative attitudes toward GMOs. This brings to question the relation between scientific literacy, sources of information, and overall consumer knowledge and perception of GMO foods.","corpus_id":11162085,"score":0},{"doc_id":"27065345","title":"The information-anchoring model of first offers: When moving first helps versus hurts negotiators.","abstract":"Does making the first offer increase or impair a negotiator's outcomes? Past research has found evidence supporting both claims. To reconcile these contradictory findings, we developed and tested an integrative model-the Information-Anchoring Model of First Offers. The model predicts when and why making the first offer helps versus hurts. We suggest that first offers have 2 effects. First, they serve as anchors that pull final settlements toward the initial first-offer value; this anchor function often produces a first-mover advantage. Second, first offers can convey information on the senders' priorities, which makes the sender vulnerable to exploitation and increases the risk of a first-mover disadvantage. To test this model, 3 experiments manipulated the information that senders communicated in their first offer. When senders did not reveal their priorities, the first-mover advantage was replicated. However, when first offers revealed senders' priorities explicitly, implicitly, or both, a first-mover disadvantage emerged. Negotiators' social value orientation moderated this effect: A first-mover disadvantage occurred when senders faced proself recipients who exploited priority information, but not with prosocial recipients. Moderated mediation analyses supported the model assumptions: Proself recipients used their integrative insight to feign priorities in their low-priority issues and thereby claimed more individual value than senders. The final discussion reviews theoretical and applied implications of the Information-Anchoring Model of First Offers. ( PsycINFO Database Record","corpus_id":34365662,"score":0},{"doc_id":"27067632","title":"Children's understanding of first- and third-person perspectives in complement clauses and false-belief tasks.","abstract":"De Villiers (Lingua, 2007, Vol. 117, pp. 1858-1878) and others have claimed that children come to understand false belief as they acquire linguistic constructions for representing a proposition and the speaker's epistemic attitude toward that proposition. In the current study, English-speaking children of 3 and 4years of age (N=64) were asked to interpret propositional attitude constructions with a first- or third-person subject of the propositional attitude (e.g., \"I think the sticker is in the red box\" or \"The cow thinks the sticker is in the red box\", respectively). They were also assessed for an understanding of their own and others' false beliefs. We found that 4-year-olds showed a better understanding of both third-person propositional attitude constructions and false belief than their younger peers. No significant developmental differences were found for first-person propositional attitude constructions. The older children also showed a better understanding of their own false beliefs than of others' false beliefs. In addition, regression analyses suggest that the older children's comprehension of their own false beliefs was mainly related to their understanding of third-person propositional attitude constructions. These results indicate that we need to take a closer look at the propositional attitude constructions that are supposed to support children's false-belief reasoning. Children may come to understand their own and others' beliefs in different ways, and this may affect both their use and understanding of propositional attitude constructions and their performance in various types of false-belief tasks.","corpus_id":34323014,"score":0},{"doc_id":"27474914","title":"The occipital place area represents first-person perspective motion information through scenes.","abstract":"Neuroimaging studies have identified multiple scene-selective regions in human cortex, but the precise role each region plays in scene processing is not yet clear. It was recently hypothesized that two regions, the occipital place area (OPA) and the retrosplenial complex (RSC), play a direct role in navigation, while a third region, the parahippocampal place area (PPA), does not. Some evidence suggests a further division of labor even among regions involved in navigation: While RSC is thought to support navigation through the broader environment, OPA may be involved in navigation through the immediately visible environment, although this role for OPA has never been tested. Here we predict that OPA represents first-person perspective motion information through scenes, a critical cue for such \"visually-guided navigation\", consistent with the hypothesized role for OPA. Response magnitudes were measured in OPA (as well as RSC and PPA) to i) video clips of first-person perspective motion through scenes (\"Dynamic Scenes\"), and ii) static images taken from these same movies, rearranged such that first-person perspective motion could not be inferred (\"Static Scenes\"). As predicted, OPA responded significantly more to the Dynamic than Static Scenes, relative to both RSC and PPA. The selective response in OPA to Dynamic Scenes was not due to domain-general motion sensitivity or to low-level information inherited from early visual regions. Taken together, these findings suggest the novel hypothesis that OPA may support visually-guided navigation, insofar as first-person perspective motion information is useful for such navigation, while RSC and PPA support other aspects of navigation and scene recognition.","corpus_id":22736033,"score":0},{"doc_id":"27708754","title":"Apparent Biological Motion in First and Third Person Perspective.","abstract":"Apparent biological motion is the perception of plausible movements when two alternating images depicting the initial and final phase of an action are presented at specific stimulus onset asynchronies. Here, we show lower subjective apparent biological motion perception when actions are observed from a first relative to a third visual perspective. These findings are discussed within the context of sensorimotor contributions to body ownership.","corpus_id":14756284,"score":0},{"doc_id":"27744988","title":"Information prescriptions.","abstract":"Information prescriptions (IPs) are intended to guide people to relevant and reliable sources of information on, for example, conditions and treatments, services and support groups.","corpus_id":28986553,"score":0},{"doc_id":"28934559","title":"Psychological Perspectives on Interrogation.","abstract":"Proponents of \"enhanced interrogation techniques\" in the United States have claimed that such methods are necessary for obtaining information from uncooperative terrorism subjects. In the present article, we offer an informed, academic perspective on such claims. Psychological theory and research shows that harsh interrogation methods are ineffective. First, they are likely to increase resistance by the subject rather than facilitate cooperation. Second, the threatening and adversarial nature of harsh interrogation is often inimical to the goal of facilitating the retrieval of information from memory and therefore reduces the likelihood that a subject will provide reports that are extensive, detailed, and accurate. Third, harsh interrogation methods make lie detection difficult. Analyzing speech content and eliciting verifiable details are the most reliable cues to assessing credibility; however, to elicit such cues subjects must be encouraged to provide extensive narratives, something that does not occur in harsh interrogations. Evidence is accumulating for the effectiveness of rapport-based information-gathering approaches as an alternative to harsh interrogations. Such approaches promote cooperation, enhance recall of relevant and reliable information, and facilitate assessments of credibility. Given the available evidence that torture is ineffective, why might some laypersons, policymakers, and interrogation personnel support the use of torture? We conclude our review by offering a psychological perspective on this important question.","corpus_id":5147951,"score":0},{"doc_id":"29118785","title":"Advance Directives as Support of Autonomy for Persons with Dementia? A Pilot Study among Persons with Dementia and Their Informal Caregivers.","abstract":"Background: Advance directives could be an important instrument to support a person's will once he/she is not able to consent anymore - if composed competently. A survey was conducted to identify the level of knowledge concerning possibilities and limits of advance directives. Methods: The study was conducted as part of the Bavarian Dementia Survey (BayDem). Data were collected from January 2014 to December 2015 by structured face-to-face interviews. Study participants were persons with dementia and their informal caregivers (n = 74). Results: In total, 66% reported having written an advance directive. Concerning the participants' knowledge about possibilities and limitations of advance directives, a lack of knowledge was noted about the possibility to revoke an advance directive. Furthermore, 70% of informal caregivers and 56% of persons with dementia were not aware of the possibility to include dementia-specific terms in the advance directive. Conclusion: It is necessary to optimize structures for public information and education concerning the topic of advance directives for persons with dementia.","corpus_id":13062896,"score":0},{"doc_id":"29281736","title":"Characterizing first and third person viewpoints and their alternation for embodied interaction in virtual reality.","abstract":"Empirical research on the bodily self has shown that the body representation is malleable, and prone to manipulation when conflicting sensory stimuli are presented. Using Virtual Reality (VR) we assessed the effects of manipulating multisensory feedback (full body control and visuo-tactile congruence) and visual perspective (first and third person perspective) on the sense of embodying a virtual body that was exposed to a virtual threat. We also investigated how subjects behave when the possibility of alternating between first and third person perspective at will was presented. Our results support that illusory ownership of a virtual body can be achieved in both first and third person perspectives under congruent visuo-motor-tactile condition. However, subjective body ownership and reaction to threat were generally stronger for first person perspective and alternating condition than for third person perspective. This suggests that the possibility of alternating perspective is compatible with a strong sense of embodiment, which is meaningful for the design of new embodied VR experiences.","corpus_id":33581414,"score":0}],"string":"[\n {\n \"doc_id\": \"20157986\",\n \"title\": \"Networks of conscious experience: computational neuroscience in understanding life, death, and consciousness.\",\n \"abstract\": \"We demonstrate brain locations appearing to correlate with consciousness, but not being directly responsible for it. Technology reveals that brain activity is associated with consciousness but is not equivalent to it. We examine how consciousness occurs at critical levels of complexity. Conventional explanations portray consciousness as an emergent property of classical computer-like activities in the brain's neural networks. Prevailing views in this camp are that patterns of neural network activities correlate with mental states, that synchronous network oscillations in the thalamus and cerebral cortex temporally bind information, and that consciousness emerges as a novel property of computational complexity among neurons. A hard-wired theory is enigmatic for explaining consciousness because the nature of subjective experience, or 'qualia'- 'inner life' - is a \\\"hard problem\\\" to understand; binding spatially distributed brain activity into unitary objects, and a coherent sense of self, or 'oneness' is difficult to explain as is the transition from pre- to conscious states. Consciousness is non-computable and involves factors that are neither random nor algorithmic - consciousness cannot be simulated; explanations are also needed for free will and for subjective time flow. Convention argues that neurons and their chemical synapses are the fundamental units of information in the brain, and that conscious experience emerges when a critical level of complexity is reached in the brain's neural networks. The basic idea is that the mind is a computer functioning in the brain. In fitting the brain to a computational view, such explanations omit incompatible neurophysiological details, including widespread apparent randomness at all levels of neural processes (is it really noise, or underlying levels of complexity?); glial cells (which account for some 80% of the brain); dendritic-dendritic processing; electrotonic gap junctions; cytoplasmic/cytoskeletal activities; living state (the brain is alive!); and absence of testable hypotheses in emergence theory. There is no threshold or rationale specified; rather, consciousness 'just happens'. Consciousness then involves an awareness of what we are sensing or experiencing and some ability to control or coordinate voluntary actions. These issues of life, death, and consciousness are discussed in the context of Mike, the headless chicken, who survived for 18 months, and in the context of consciousness with high degrees of intellectual and cognitive function in a congenitally anencephalic brain; additionally, in the reanimation work of Soviet scientists in the 1920-30s, and in auditory sentence processing in patients in comatose, vegetative, and minimally conscious states.\",\n \"corpus_id\": 40003252,\n \"score\": 2\n },\n {\n \"doc_id\": \"21493099\",\n \"title\": \"Neural correlates of consciousness reconsidered.\",\n \"abstract\": \"It is widely accepted among philosophers that neuroscientists are conducting a search for the neural correlates of consciousness, or NCC. Chalmers (2000) conceptualized this research program as the attempt to correlate the contents of conscious experience with the contents of representations in specific neural populations. A notable claim on behalf of this interpretation is that the neutral language of \\\"correlates\\\" frees us from philosophical disputes over the mind/body relation, allowing the science to move independently. But the experimental paradigms and explanatory canons of neuroscience are not neutral about the mechanical relation between consciousness and the brain. I argue that NCC research is best characterized as an attempt to locate a causally relevant neural mechanism and not as an effort to identify a discrete neural representation, the content of which correlates with some actual experience. It might be said that the first C in \\\"NCC\\\" should stand for \\\"causes\\\" rather than \\\"correlates.\\\"\",\n \"corpus_id\": 37669419,\n \"score\": 2\n },\n {\n \"doc_id\": \"23073546\",\n \"title\": \"[What can qualia be? The monistic views].\",\n \"abstract\": \"Phenomenal properties, also named qualia (that is, the qualities of human experiences, e.g. the senses of red, of salt, of pain, qua senses) create a hard problem for philosophy. It is claimed that phenomenal properties are radically different to the physical ones: they are intrinsic (their essence is totally confined within the limits of their existence), they depend on mind, they are accessible only privately, by introspection and they are infallible, in the sense that the experience of a quale is identical to its existence. On the contrary, physical properties are dispositional (their essence is defined through their causal consequences), they exist independently of mind, they are accessible to public observation and are liable to verification or falsification. The faculty of philosophy, named philosophy of mind, is systematically interested in qualia. In the present paper some of the main monistic philosophical approaches to qualia are discussed. The main common characteristic of monistic views is that (contrary to dualistic views) they purport that: two radically different substances cannot exist, side by side, within the same world (our world). Thus, there are either physical properties, or phenomenal properties, but not both. The monistic theories, supporting that in our world there are only physical properties, or properties totally reducible into physical ones, are named physicalism (or according to a more traditional nomination, materialism). On the other hand, monistic theories maintaining that all existing properties are phenomenal, or properties reducible into phenomenal ones, are named phenomenalism. The main arguments for physicalism are: (a) the scientific principle of the causal closure of the universe (every event has one physical cause), (b) the dependence of every well-studied mental phenomenon, from a physical phenomenal, such as the function of the neural system. Dualists counterattack physicalism with mental experiments (such as, the experiments concerning philosophical zombies) in order to demonstrate that qualia are irreducible entities. The main physicalistic options are eliminativism, the theories of identity, functionalism and representationalism. The main argument for phenomenalism is that physical properties and physical knowledge of them, as well, are reducible into and derived from experiences. On the other hand, opponents of phenomenalism retort that our world comprises spatiotemporal parts inaccessible to experience (f.e. the microworld of atomic physics, the world before the appearance of intelligent beings). Yet, some phenomenalists claim that phenomenal properties can be either real (experienced) or potentially real (what one would experience if one could observe this or that spatiotemporal part of the world). According to a third, agnosticistic opinion, named mysterianism, the human mind lacks the capacity of bridging the explanatory gap between physical and phenomenal identities. Many opponents of this theory claim the historically proved ability of human mind to find solutions for difficult problems of our world through scientific knowledge and based on it natural philosophy.\",\n \"corpus_id\": 24773763,\n \"score\": 2\n },\n {\n \"doc_id\": \"23165867\",\n \"title\": \"Integrated information theory of consciousness: an updated account.\",\n \"abstract\": \"This article presents an updated account of integrated information theory of consciousness (IIT) and some of its implications. IIT stems from thought experiments that lead to phenomenological axioms and ontological postulates. The information axiom asserts that every experience is one out of many, i.e. specific - it is what it is by differing in its particular way from a large repertoire of alternatives. The integration axiom asserts that each experience is one, i.e. unified - it cannot be reduced to independent components. The exclusion axiom asserts that every experience is definite - it is limited to particular things and not others and flows at a particular speed and resolution. IIT formalizes these intuitions with three postulates. The information postulate states that only \\\"differences that make a difference\\\" from the intrinsic perspective of a system matter: a mechanism generates cause-effect information if its present state has specific past causes and specific future effects within a system. The integration postulate states that only information that is irreducible matters: mechanisms generate integrated information only to the extent that the information they generate cannot be partitioned into that generated within independent components. The exclusion postulate states that only maxima of integrated information matter: a mechanism specifies only one maximally irreducible set of past causes and future effects - a concept. A complex is a set of elements specifying a maximally irreducible constellation of concepts, where the maximum is evaluated at the optimal spatio-temporal scale. Its concepts specify a maximally integrated conceptual information structure or quale, which is identical with an experience. Finally, changes in information integration upon exposure to the environment reflect a system's ability to match the causal structure of the world. After introducing an updated definition of information integration and related quantities, the article presents some theoretical considerations about the relationship between information and causation and about the relational structure of concepts within a quale. It also explores the relationship between the temporal grain size of information integration and the dynamic of metastable states in the corticothalamic complex. Finally, it summarizes how IIT accounts for empirical findings about the neural substrate of consciousness, and how various aspects of phenomenology may in principle be addressed in terms of the geometry of information integration.\",\n \"corpus_id\": 13920052,\n \"score\": 2\n },\n {\n \"doc_id\": \"23467765\",\n \"title\": \"Consciousness and the invention of Morel.\",\n \"abstract\": \"A scientific study of consciousness should take into consideration both objective and subjective measures of conscious experiences. To this date, very few studies have tried to integrate third-person data, or data about the neurophysiological correlates of conscious states, with first-person data, or data about subjective experience. Inspired by Morel's invention (Casares, 1940), a literary machine capable of reproducing sensory-dependent external reality, this article suggests that combination of virtual reality techniques and brain reading technologies, that is, decoding of conscious states by brain activity alone, can offer this integration. It is also proposed that the multimodal, simulating, and integrative capacities of the dreaming brain render it an \\\"endogenous\\\" Morel's machine, which can potentially be used in studying consciousness, but not always in a reliable way. Both the literary machine and dreaming could contribute to a better understanding of conscious states.\",\n \"corpus_id\": 14109744,\n \"score\": 2\n },\n {\n \"doc_id\": \"23802335\",\n \"title\": \"Integrated information theory of consciousness: an updated account.\",\n \"abstract\": \"This article presents an updated account of integrated information theory of consciousness (liT) and some of its implications. /IT stems from thought experiments that lead to phenomenological axioms (existence, compositionality, information, integration, exclusion) and corresponding ontological postulates. The information axiom asserts that every experience is spec~fic - it is what it is by differing in its particular way from a large repertoire of alternatives. The integration axiom asserts that each experience is unified- it cannot be reduced to independent components. The exclusion axiom asserts that every experience is definite - it is limited to particular things and not others and flows at a particular speed and resolution. /IT formalizes these intuitions with postulates. The information postulate states that only \\\"differences that make a difference\\\" from the intrinsic perpective of a system matter: a mechanism generates cause-effect information if its present state has selective past causes and selective future effects within a system. The integration postulate states that only information that is irreducible matters: mechanisms generate integrated information only to the extent that the information they generate cannot be partitioned into that generated within independent components. The exclusion postulate states that only maxima of integrated information matter: a mechanism specifies only one maximally irreducible set of past causes and future effects - a concept. A complex is a set of elements specifying a maximally irreducible constellation of concepts, where the maximum is evaluated over elements and at the optimal spatiatemporal scale. Its concepts specify a maximally integrated conceptual information structure or quale, which is identical with an experience. Finally, changes in information integration upon exposure to the environment reflect a system's ability to match the causal structure of the world. After introducing an updated definition of information integration and related quantities, the article presents some theoretical considerations about the relationship between information and causation and about the relational structure of concepts within a qua/e. It also explores the relationship between the temporal grain size of information integration and the dynamic of metastable states in the corticothalamic complex. Finally, it summarizes how liT accounts for empirical findings about the neural substrate of consciousness, and how various aspects of phenomenology may in principle be addressed in terms of the geometry of information integration.\",\n \"corpus_id\": 6113590,\n \"score\": 2\n },\n {\n \"doc_id\": \"23883758\",\n \"title\": \"Merging second-person and first-person neuroscience.\",\n \"abstract\": \"Schilbach et al. contrast second-person and third-person approaches to social neuroscience. We discuss relations between second-person and first-person approaches, arguing that they cannot be studied in isolation. Contingency is central for converging first- and second-person approaches. Studies of embodiment show how contingencies scaffold first-person perspective and how the transition from a third- to a second-person perspective fundamentally involves first-person contributions.\",\n \"corpus_id\": 54587375,\n \"score\": 2\n },\n {\n \"doc_id\": \"24168487\",\n \"title\": \"Bodily self-consciousness, and the primacy of self related signals such as the 1(st) person perspective and self-location.\",\n \"abstract\": \"Abstract G&K provide a new and interesting perspective on consciousness, by arguing that consciousness is a product of social perception. Based on the overlap between the neural mechanisms underlying spatial awareness of other people and oneself, out-of-body experiences (OBEs), and social perception the authors argue that consciousness is based on the brain signals that represent other people and their spatial awareness. Although we generally welcome the authors efforts, we (1) would like to emphasize that consciousness has two distinct spatial aspects, namely self-location and first-person perspective, (2) cite evidence about distinct developmental and brain mechanisms concerning first- versus third-person perceptions and cogitations and (3) argue for a primacy of multisensory own body perception over social perception and awareness as a neurobiological foundation of consciousness.\",\n \"corpus_id\": -1,\n \"score\": 2\n },\n {\n \"doc_id\": \"24236862\",\n \"title\": \"How can we construct a science of consciousness?\",\n \"abstract\": \"This chapter gives an overview of the projects facing a science of consciousness. Such a science must integrate third-person data about behavior and brain processes with first-person data about conscious experience. Empirical projects for integrating these data include those of contrasting conscious and unconscious processes, investigating the contents of consciousness, finding neural correlates of consciousness, and eventually inferring underlying principles connecting consciousness with physical processes. These projects are discussed with reference to current experimental research on consciousness. Some obstacles that a science of consciousness faces are also discussed.\",\n \"corpus_id\": 42133770,\n \"score\": 2\n },\n {\n \"doc_id\": \"24672510\",\n \"title\": \"Structural qualia: a solution to the hard problem of consciousness.\",\n \"abstract\": \"The hard problem of consciousness has been often claimed to be unsolvable by the methods of traditional empirical sciences. It has been argued that all the objects of empirical sciences can be fully analyzed in structural terms but that consciousness is (or has) something over and above its structure. However, modern neuroscience has introduced a theoretical framework in which also the apparently non-structural aspects of consciousness, namely the so called qualia or qualitative properties, can be analyzed in structural terms. That framework allows us to see qualia as something compositional with internal structures that fully determine their qualitative nature. Moreover, those internal structures can be identified which certain neural patterns. Thus consciousness as a whole can be seen as a complex neural pattern that misperceives some of its own highly complex structural properties as monadic and qualitative. Such neural pattern is analyzable in fully structural terms and thereby the hard problem is solved.\",\n \"corpus_id\": 15323989,\n \"score\": 2\n },\n {\n \"doc_id\": \"25071677\",\n \"title\": \"The measurement of consciousness: a framework for the scientific study of consciousness.\",\n \"abstract\": \"Scientists studying consciousness are attempting to identify correlations between measurements of consciousness and the physical world. Consciousness can only be measured through first-person reports, which raises problems about the accuracy of first-person reports, the possibility of non-reportable consciousness and the causal closure of the physical world. Many of these issues could be resolved by assuming that consciousness is entirely physical or functional. However, this would sacrifice the theory-neutrality that is a key attraction of a correlates-based approach to the study of consciousness. This paper puts forward a different solution that uses a framework of definitions and assumptions to explain how consciousness can be measured. This addresses the problems associated with first-person reports and avoids the issues with the causal closure of the physical world. This framework is compatible with most of the current theories of consciousness and it leads to a distinction between two types of correlates of consciousness.\",\n \"corpus_id\": 11598675,\n \"score\": 2\n },\n {\n \"doc_id\": \"25202297\",\n \"title\": \"It is time to combine the two main traditions in the research on the neural correlates of consciousness: C = L × D.\",\n \"abstract\": \"Research on neural correlates of consciousness has been conducted and carried out mostly from within two relatively autonomous paradigmatic traditions - studying the specific contents of conscious experience and their brain-process correlates and studying the level of consciousness. In the present paper we offer a theoretical integration suggesting that an emphasis has to be put on understanding the mechanisms of consciousness (and not a mere correlates) and in doing this, the two paradigmatic traditions must be combined. We argue that consciousness emerges as a result of interaction of brain mechanisms specialized for representing the specific contents of perception/cognition - the data - and mechanisms specialized for regulating the level of activity of whatever data the content-carrying specific mechanisms happen to represent. Each of these mechanisms are necessary because without the contents there is no conscious experience and without the required level of activity the processed contents remain unconscious. Together the two mechanisms, when activated up to a necessary degree each, provide conditions sufficient for conscious experience to emerge. This proposal is related to pertinent experimental evidence.\",\n \"corpus_id\": 2490484,\n \"score\": 2\n },\n {\n \"doc_id\": \"25892488\",\n \"title\": \"Epistemological implications of near-death experiences and other non-ordinary mental expressions: Moving beyond the concept of altered state of consciousness.\",\n \"abstract\": \"During the last decades an increasing interest has developed in the so-called altered state of consciousness (ASCs); among these, near-death experiences (NDEs) are one of the most intriguing and debated examples. NDEs are deep and universal experiences with a clear phenomenology and incidence, while some of their features challenge the current views of human consciousness (focused on neural circuits and based on the concept of mind as a byproduct of brain circuitry) with relevant epistemological and historical implications. The origin of the ruling mechanist-reductionist paradigm can be traced back to Descartes' radical separation of res cogitans and res extensa and the conflict between the nascent science and the Inquisition; this led to removing the subjective properties of mind from the field of scientific interest, relegating them to philosophy and theology in order to enable the development of modern science. However, the physics of the 20th century has eventually moved beyond the classical paradigm, permitting a profound renewal of scientific interest in the mind. Modern research on NDEs has contributed to reopening the debate surrounding the Cartesian separation, the mind-brain relationship and the nature of consciousness. It is now time to reappraise the relevance, strengths, and weaknesses of the available scientific interpretations of NDEs, their relationship with other ASCs, as well as the very concept of ASC; the latter looks to be ill-founded, suggesting the need for: (a) a revision of the conventional approach to subjective phenomena, including both the third- and first-person perspective; and (b) a deep reflection on the possible links between different non-ordinary mental expression, as regards both their phenomenology and mechanisms from a non-pathological perspective.\",\n \"corpus_id\": 18815739,\n \"score\": 2\n },\n {\n \"doc_id\": \"26074839\",\n \"title\": \"Neurophenomenology revisited: second-person methods for the study of human consciousness.\",\n \"abstract\": \"In the study of consciousness, neurophenomenology was originally established as a novel research program attempting to reconcile two apparently irreconcilable methodologies in psychology: qualitative and quantitative methods. Its potential relies on Francisco Varela's idea of reciprocal constraints, in which first-person accounts and neurophysiological data mutually inform each other. However, since its first conceptualization, neurophenomenology has encountered methodological problems. These problems have emerged mainly because of the difficulty of obtaining and analyzing subjective reports in a systematic manner. However, more recently, several interview techniques for describing subjective accounts have been developed, collectively known as \\\"second-person methods.\\\" Second-person methods refer to interview techniques that solicit both verbal and non-verbal information from participants in order to obtain systematic and detailed subjective reports. Here, we examine the potential for employing second-person methodologies in the neurophenomenological study of consciousness and we propose three practical ideas for developing a second-person neurophenomenological method. Thus, we first describe second-person methodologies available in the literature for analyzing subjective reports, identifying specific constraints on the status of the first-, second- and third- person methods. Second, we analyze two experimental studies that explicitly incorporate second-person methods for traversing the \\\"gap\\\" between phenomenology and neuroscience. Third, we analyze the challenges that second-person accounts face in establishing an objective methodology for comparing results across different participants and interviewers: this is the \\\"validation\\\" problem. Finally, we synthesize the common aspects of the interview methods described above. In conclusion, our arguments emphasize that second-person methods represent a powerful approach for closing the gap between the experiential and the neurobiological levels of description in the study of human consciousness.\",\n \"corpus_id\": 374435,\n \"score\": 2\n },\n {\n \"doc_id\": \"26444360\",\n \"title\": \"Emergence Of Consciousness And Qualia From A Complex Brain.\",\n \"abstract\": \"Qualia are private conscious experiences of which the associated feelings can be reported to other people. Whether qualia are amenable to scientific exploration has often been questioned, which is challenged by the present article. The following arguments are given: 1. the configuration of the brain changes continuously and irreversibly, because of genetic and environmental influences and interhuman communication; 2. qualia and consciousness are processes, rather than states; 3. private feelings, including those associated with qualia, should be positioned in the context of a personal brain as being developed during life; 4. consciousness and qualia should be understood in the context of general system theory, thus concluding that isolated, in vitro, properties of neurons and other brain constituents might marginally contribute to the understanding of higher brain functions, mind or qualia; 5. current in vivo approaches have too little resolution power - in terms of space and time - to delineate individual and subjective brain processes. When subtle personalized properties of the nervous system can be assessed in vivo or in vitro, qualia can scientifically be investigated. We discuss some approaches to overcome these barriers.\",\n \"corpus_id\": 8441610,\n \"score\": 2\n },\n {\n \"doc_id\": \"26748074\",\n \"title\": \"Using category theory to assess the relationship between consciousness and integrated information theory.\",\n \"abstract\": \"One of the most mysterious phenomena in science is the nature of conscious experience. Due to its subjective nature, a reductionist approach is having a hard time in addressing some fundamental questions about consciousness. These questions are squarely and quantitatively tackled by a recently developed theoretical framework, called integrated information theory (IIT) of consciousness. In particular, IIT proposes that a maximally irreducible conceptual structure (MICS) is identical to conscious experience. However, there has been no principled way to assess the claimed identity. Here, we propose to apply a mathematical formalism, category theory, to assess the proposed identity and suggest that it is important to consider if there exists a proper translation between the domain of conscious experience and that of the MICS. If such translation exists, we postulate that questions in one domain can be answered in the other domain; very difficult questions in the domain of consciousness can be resolved in the domain of mathematics. We claim that it is possible to empirically test if such a functor exists, by using a combination of neuroscientific and computational approaches. Our general, principled and empirical framework allows us to assess the relationship between the domain of consciousness and the domain of mathematical structures, including those suggested by IIT.\",\n \"corpus_id\": 13900169,\n \"score\": 2\n },\n {\n \"doc_id\": \"20402245\",\n \"title\": \"Representing human hands haptically or visually from first-person versus third-person perspectives.\",\n \"abstract\": \"Humans can recognise human body parts haptically as well as visually. We employed a mental-rotation task to determine whether participants could adopt a third-person perspective when judging the laterality of life-like human hands. Female participants adopted either a first-person or a third-person perspective using vision (experiment 1) or haptics (experiment 2), with hands presented at various orientations within a horizontal plane. In the first-person perspective task, most participants responded more slowly as hand orientation increasingly deviated from the participant's upright orientation, regardless of modality. In the visual third-person perspective task, most participants responded more slowly as hand orientation increasingly deviated from the experimenter's upright orientation; in contrast, less than half of the participants produced this same inverted U-shaped response-time function haptically. In experiment 3, participants were explicitly instructed to adopt a third-person perspective haptically by mentally rotating the rubber hand to the experimenter's upright orientation. Most participants produced an inverted U-shaped function. Collectively, these results suggest that humans can accurately assume a third-person perspective when hands are explored haptically or visually. With less explicit instructions, however, the canonical orientation for hand representation may be more strongly influenced haptically than visually by body-based heuristics, and less easily modified by perspective instructions.\",\n \"corpus_id\": 19177750,\n \"score\": 1\n },\n {\n \"doc_id\": \"20531262\",\n \"title\": \"The primacy of intersubjectivity.\",\n \"abstract\": \"The most important result of phenomenological research is the discovery of inherent intersubjectivity. Strategies for reporting phenomenological research and recognizing its intersubjective aspects are discussed. In addition to its significance for the practice of nurturing care, intersubjectivity is discussed in response to criticism of phenomenology as ungeneralizeable research. As the philosophical foundation of all research, phenomenology's singular position as a philosophy and research methodology is discussed.\",\n \"corpus_id\": 2022053,\n \"score\": 1\n },\n {\n \"doc_id\": \"21713178\",\n \"title\": \"The nature of consciousness in the visually deprived brain.\",\n \"abstract\": \"Vision plays a central role in how we represent and interact with the world around us. The primacy of vision is structurally imbedded in cortical organization as about one-third of the cortical surface in primates is involved in visual processes. Consequently, the loss of vision, either at birth or later in life, affects brain organization and the way the world is perceived and acted upon. In this paper, we address a number of issues on the nature of consciousness in people deprived of vision. Do brains from sighted and blind individuals differ, and how? How does the brain of someone who has never had any visual perception form an image of the external world? What is the subjective correlate of activity in the visual cortex of a subject who has never seen in life? More in general, what can we learn about the functional development of the human brain in physiological conditions by studying blindness? We discuss findings from animal research as well from recent psychophysical and functional brain imaging studies in sighted and blind individuals that shed some new light on the answers to these questions.\",\n \"corpus_id\": 2287638,\n \"score\": 1\n },\n {\n \"doc_id\": \"21971695\",\n \"title\": \"[The so-called body-mind problem].\",\n \"abstract\": \"Das so genannte Leib-Seele-Problem. THE PROBLEM: Even psychosomatic researchers seem to want to avoid the so-called body-mind problem, which is actually a mind-brain problem. In line with Beckermann (2008), the first the four possible positions on the mind-brain problem are presented. The debate over the past 100 years has revolved around the question of whether mental events are ontologically independent of brain physiology or whether they are in fact entirely determined by it. Such a physicalism approach based on properties (i.e., mental characteristics or phenomena are physical or can be completely reduced to physical characteristics), however, is diametrically opposed to some of our strongest intuitions, e.g., that computers will never be able to develop qualities of human experience (qualia) and thus become subjects in the first person singular. Yet we are equally unable to prove the fundamental impossibility of such a development. THESIS: In this stalemate situation, a differentiation was undertaken by Gottlob Frege (1892) which could be of help: Expressed in today's language, a distinction is made between the sense of an expression, its contextual presentation (e.g., where there is a difference between \\\"the evening star\\\" and \\\"the morning star\\\"), on the one hand, and its so-called reference (the object to which it refers, here the planet Venus in both cases) on the other. The school of Gestalt psychology that developed in Berlin at the start of the last century similarly posited a \\\"psychophysical level of the CNS,\\\" a continuum in a pattern of electrical field forces which manifests itself first in cerebral physiological-neuronal processes as well as in other perspectives such as consciousness and experience. A subsequent speculative concept then extends this model to assume also an (as yet) unknown Alpha configuration as being a common reference of two sense contents: (1) the results of the neurophysiological third-person perspective and (2) of the emotional-cognitive first-person perspectives. Only through the latter will Alpha be able to become self-conscious and an instance acting in his world. RESULTS: Only through the latter will Alpha be able to become self-conscious and an instance acting in his world. The postulate of an Alpha configuration thus retains the possibility of a biology not (yet) accessible to our knowledge, such that our fundamental conviction regarding the holism of soma and psyche can be maintained for us as medical practitioners and scientific physicians. Our patients need both, our medical-scientific competence (3rd-person perspective) as well as our empathic sensibility in exploring their phenomenal experience (1st-person perspective). They need us as medical artists.\",\n \"corpus_id\": 297834,\n \"score\": 1\n },\n {\n \"doc_id\": \"22461776\",\n \"title\": \"How to Begin to Overcome the Ambiguity Present in Differentiation between Contents and Levels of Consciousness?\",\n \"abstract\": \"Recently, a welcome trend has emerged - in addition to the traditional studies on contents and states of consciousness, levels of consciousness have become a matter of research. However, there are some conceptual and methodological difficulties with this research - the labels used for empirical measurement of levels are ambiguous and underspecified while the research on neural correlates of consciousness has not been well linked to psychophysical approaches to studying the levels of consciousness. This article suggests a perspective on how to advance the psychophysics of measuring the levels by precisely specifying level-specific contents and how to relate the distinction between contents and levels to the distinction between the underlying brain mechanisms necessary for processing contents and regulating the level of consciousness.\",\n \"corpus_id\": 13388403,\n \"score\": 1\n },\n {\n \"doc_id\": \"24130538\",\n \"title\": \"Visual perspective and the characteristics of mind wandering.\",\n \"abstract\": \"When the mind wanders away from the here-and-now toward imaginary events, it typically does so from one of two visual vantage points-a first-person perspective (i.e., the world is seen as it is in everyday life) or a third-person perspective (i.e., the world is seen from the viewpoint of an outside observer). While extant evidence has detailed consequences that ensue from the utilization of these distinct points of view, less is known about their more basic properties. Here, we investigated the prevalence, demographics and qualities associated with the visual perspective that people spontaneously adopt when the mind wanders. The results from a cross-cultural survey (N = 400) revealed that almost half of the participants (46%) typically utilize a third-person perspective when mind wandering. Further, culture and gender were shown to impact the distribution of first- and third-person imagers. Specifically, a first-person perspective was more common among participants from Western nations and females, while participants from Eastern cultures resonated more strongly with a third-person perspective. Moreover, these factors were also shown to impact qualities (e.g., temporal locus, vividness) of mental imagery. Taken together, the current findings elucidate the prevalence of first- and third-person visual perspectives and detail individual differences that influence the qualia of mind wandering.\",\n \"corpus_id\": 10981877,\n \"score\": 1\n },\n {\n \"doc_id\": \"24742205\",\n \"title\": \"Neural correlates of moral judgments in first- and third-person perspectives: implications for neuroethics and beyond.\",\n \"abstract\": \"BACKGROUND: There appears to be an inconsistency in experimental paradigms used in fMRI research on moral judgments. As stimuli, moral dilemmas or moral statements/ pictures that induce emotional reactions are usually employed; a main difference between these stimuli is the perspective of the participants reflecting first-person (moral dilemmas) or third-person perspective (moral reactions). The present study employed functional magnetic resonance imaging (fMRI) in order to investigate the neural correlates of moral judgments in either first- or third-person perspective. RESULTS: Our results indicate that different neural mechanisms appear to be involved in these perspectives. Although conjunction analysis revealed common activation in the anterior medial prefrontal cortex, third person-perspective elicited unique activations in hippocampus and visual cortex. The common activation can be explained by the role the anterior medial prefrontal cortex may play in integrating different information types and also by its involvement in theory of mind. Our results also indicate that the so-called \\\"actor-observer bias\\\" affects moral evaluation in the third-person perspective, possibly due to the involvement of the hippocampus. We suggest two possible ways in which the hippocampus may support the process of moral judgment: by the engagement of episodic memory and its role in understanding the behaviors and emotions of others. CONCLUSION: We posit that these findings demonstrate that first or third person perspectives in moral cognition involve distinct neural processes, that are important to different aspects of moral judgments. These results are important to a deepened understanding of neural correlates of moral cognition-the so-called \\\"first tradition\\\" of neuroethics, with the caveat that any results must be interpreted and employed with prudence, so as to heed neuroethics \\\"second tradition\\\" that sustains the pragmatic evaluation of outcomes, capabilities and limitations of neuroscientific techniques and technologies.\",\n \"corpus_id\": 9310894,\n \"score\": 1\n },\n {\n \"doc_id\": \"25376588\",\n \"title\": \"Are Informant Reports of Personality More Internally Consistent Than Self Reports of Personality?\",\n \"abstract\": \"The present study examined whether informant-reported personality was more or less internally consistent than self-reported personality in an epidemiological community sample (n = 1,449). Results indicated that across the 5 NEO (Neuroticism-Extraversion-Openness) personality factors and the 10 personality disorder trait dimensions, informant reports tended to be more internally consistent than self reports, as indicated by equal or higher Cronbach's alpha scores and higher average interitem correlations. In addition, the informant reports collectively outperformed the self reports for predicting responses on a global measure of health, indicating that the informant reports are not only more reliable than self reports, but they can also be useful in predicting an external criterion. Collectively these findings indicate that informant reports tend to have greater internal consistency than self reports.\",\n \"corpus_id\": 31189113,\n \"score\": 1\n },\n {\n \"doc_id\": \"28760626\",\n \"title\": \"How do the brain's time and space mediate consciousness and its different dimensions? Temporo-spatial theory of consciousness (TTC).\",\n \"abstract\": \"Time and space are the basic building blocks of nature. As a unique existent in nature, our brain exists in time and takes up space. The brain's activity itself also constitutes and spreads in its own (intrinsic) time and space that is crucial for consciousness. Consciousness is a complex phenomenon including different dimensions: level/state, content/form, phenomenal aspects, and cognitive features. We propose a Temporo-spatial Theory of Consciousness (TTC) focusing primarily on the temporal and spatial features of the brain activity. We postulate four different neuronal mechanisms accounting for the different dimensions of consciousness: (i) \\\"temporo-spatial nestedness\\\" of the spontaneous activity accounts for the level/state of consciousness as neural predisposition of consciousness (NPC); (ii) \\\"temporo-spatial alignment\\\" of the pre-stimulus activity accounts for the content/form of consciousness as neural prerequisite of consciousness (preNCC); (iii) \\\"temporo-spatial expansion\\\" of early stimulus-induced activity accounts for phenomenal consciousness as neural correlates of consciousness (NCC); (iv) \\\"temporo-spatial globalization\\\" of late stimulus-induced activity accounts for the cognitive features of consciousness as neural consequence of consciousness (NCCcon).\",\n \"corpus_id\": 24713088,\n \"score\": 1\n },\n {\n \"doc_id\": \"18434246\",\n \"title\": \"Determinants of Internet use as a preferred source of information on personal health.\",\n \"abstract\": \"OBJECTIVE: To understand the personal, social and cultural factors likely to explain recourse to the Internet as a preferred source of personal health information. DESIGN: A cross-sectional survey was conducted among a population of 2923 Internet users visiting a firmly established website that offers information on personal health. Multiple regression analysis was performed to identify the determinants of site use. MEASUREMENT: The analysis template comprised four classes of determinants likely to explain Internet use: beliefs, intentions, user satisfaction and socio-demographic characteristics. Seven-point Likert scales were used. An analysis of the psychometric qualities of the variables provided compelling evidence of the construct's validity and reliability. A confirmatory factor analysis confirmed the correspondence with the factors predicted by the theoretical model. FINDINGS: The regression analysis explained 35% of the variance in Internet use. Use was directly associated with five factors: perceived usefulness, importance given to written media in searches for health information, concern for personal health, importance given to the opinions of physicians and other health professionals, and the trust placed in the information available on the site itself. CONCLUSION: This study confirms the importance of the credibility of information on the frequency of Internet use as a preferred source of information on personal health. It also shows the potentially influential role of the Internet in the development of personal knowledge of health issues.\",\n \"corpus_id\": 24534095,\n \"score\": 0\n },\n {\n \"doc_id\": \"19338113\",\n \"title\": \"Position of the American Dietetic Association: functional foods.\",\n \"abstract\": \"All foods are functional at some physiological level, but it is the position of the American Dietetic Association (ADA) that functional foods that include whole foods and fortified, enriched, or enhanced foods have a potentially beneficial effect on health when consumed as part of a varied diet on a regular basis, at effective levels. ADA supports research to further define the health benefits and risks of individual functional foods and their physiologically active components. Health claims on food products, including functional foods, should be based on the significant scientific agreement standard of evidence and ADA supports label claims based on such strong scientific substantiation. Food and nutrition professionals will continue to work with the food industry, allied health professionals, the government, the scientific community, and the media to ensure that the public has accurate information regarding functional foods and thus should continue to educate themselves on this emerging area of food and nutrition science. Knowledge of the role of physiologically active food components, from plant, animal, and microbial food sources, has changed the role of diet in health. Functional foods have evolved as food and nutrition science has advanced beyond the treatment of deficiency syndromes to reduction of disease risk and health promotion. This position paper reviews the definition of functional foods, their regulation, and the scientific evidence supporting this evolving area of food and nutrition. Foods can no longer be evaluated only in terms of macronutrient and micronutrient content alone. Analyzing the content of other physiologically active components and evaluating their role in health promotion will be necessary. The availability of health-promoting functional foods in the US diet has the potential to help ensure a healthier population. However, each functional food should be evaluated on the basis of scientific evidence to ensure appropriate integration into a varied diet.\",\n \"corpus_id\": 39013158,\n \"score\": 0\n },\n {\n \"doc_id\": \"19361993\",\n \"title\": \"Public versus personal information for mate copying in an invertebrate.\",\n \"abstract\": \"Organisms require information to make decisions about fitness-affecting resources, such as mates. Animals may extract \\\"personal information\\\" about potential mates by observing their physical characteristics or extract additional \\\"public information\\\" by observing their mating performance [1]. Mate copying by females [2-6] is a form of public information use that may reduce uncertainty about male quality, allowing more adaptive choices [2]. Experimental studies have produced evidence that female mate copying occurs in several species of fish [3], birds [5-7], and mammals [8], including humans [9]. We report the first evidence that a female invertebrate can exploit public information to select mates. In a first experiment, Drosophila melanogaster female prospectors increased their time in the attraction zones of poor-condition males, but not of good-condition males, after having observed them with a model female. This suggests that females appraised prospective mates by exploiting public information and did so mainly when it contrasted with personal information. In a second experiment, prospector females preferably mated with males of the color type they had previously observed copulating over males of the rejected color type, suggesting that female Drosophila can generalize socially learned information. The complexity of Drosophila decision-making suggests an unprecedented level of cognition in invertebrates. Our findings have implications for evolution given that socially learned mate preferences may lead to reproductive isolation, setting the stage for speciation [10].\",\n \"corpus_id\": 12667396,\n \"score\": 0\n },\n {\n \"doc_id\": \"19692271\",\n \"title\": \"I can see it both ways: first- and third-person visual perspectives at retrieval.\",\n \"abstract\": \"The number of studies examining visual perspective during retrieval has recently grown. However, the way in which perspective has been conceptualized differs across studies. Some studies have suggested perspective is experienced as either a first-person or a third-person perspective, whereas others have suggested both perspectives can be experienced during a single retrieval attempt. This aspect of perspective was examined across three studies, which used different measurement techniques commonly used in studies of perspective. Results suggest that individuals can experience more than one perspective when recalling events. Furthermore, the experience of the two perspectives correlated differentially with ratings of vividness, suggesting that the two perspectives should not be considered in opposition of one another. We also found evidence of a gender effect in the experience of perspective, with females experiencing third-person perspectives more often than males. Future studies should allow for the experience of more than one perspective during retrieval.\",\n \"corpus_id\": 1111690,\n \"score\": 0\n },\n {\n \"doc_id\": \"19814826\",\n \"title\": \"Information management to enable personalized medicine: stakeholder roles in building clinical decision support.\",\n \"abstract\": \"BACKGROUND: Advances in technology and the scientific understanding of disease processes are presenting new opportunities to improve health through individualized approaches to patient management referred to as personalized medicine. Future health care strategies that deploy genomic technologies and molecular therapies will bring opportunities to prevent, predict, and pre-empt disease processes but will be dependent on knowledge management capabilities for health care providers that are not currently available. A key cornerstone to the potential application of this knowledge will be effective use of electronic health records. In particular, appropriate clinical use of genomic test results and molecularly-targeted therapies present important challenges in patient management that can be effectively addressed using electronic clinical decision support technologies. DISCUSSION: Approaches to shaping future health information needs for personalized medicine were undertaken by a work group of the American Health Information Community. A needs assessment for clinical decision support in electronic health record systems to support personalized medical practices was conducted to guide health future development activities. Further, a suggested action plan was developed for government, researchers and research institutions, developers of electronic information tools (including clinical guidelines, and quality measures), and standards development organizations to meet the needs for personalized approaches to medical practice. In this article, we focus these activities on stakeholder organizations as an operational framework to help identify and coordinate needs and opportunities for clinical decision support tools to enable personalized medicine. SUMMARY: This perspective addresses conceptual approaches that can be undertaken to develop and apply clinical decision support in electronic health record systems to achieve personalized medical care. In addition, to represent meaningful benefits to personalized decision-making, a comparison of current and future applications of clinical decision support to enable individualized medical treatment plans is presented. If clinical decision support tools are to impact outcomes in a clear and positive manner, their development and deployment must therefore consider the needs of the providers, including specific practice needs, information workflow, and practice environment.\",\n \"corpus_id\": 1002325,\n \"score\": 0\n },\n {\n \"doc_id\": \"19930262\",\n \"title\": \"The nature (and nurture) of personality disorders.\",\n \"abstract\": \"Personality disorders have a long history in the literature but a short scientific history. The point prevalence of personality disorders is 10%, but the lifetime prevalence is probably 30-40%. Genetic factors contribute to around 40-50% of the variation in the development of personality disorders. The effect of shared environment is very small or non-existent. Some researchers have tried to promote gene-environment interaction. However, in reality, the studies investigated gene-situation interaction, as the \\\"environment\\\" may in reality be partly of a genetic nature. Thus, we are dealing with an unknown part of gene-gene interaction. Gene-experience (not gene-environment) correlations are the rule in human life. Personality disorders co-occur (are comorbid) with symptom disorders (Axis I) and correlate with common personality dimensions. Possibly, the concept of personality disorder could merge with dysfunctional personality types. But it is likely that the concept will survive on its own.\",\n \"corpus_id\": 35862425,\n \"score\": 0\n },\n {\n \"doc_id\": \"20665336\",\n \"title\": \"Correlates and phenomenology of first and third person memories.\",\n \"abstract\": \"The present research addressed fundamental questions about the visual perspective of autobiographical memories: Are stable personality characteristics associated with visual perspective? Does visual perspective influence the memory's phenomenological qualities? Participants in Study 1 (N=1684) completed individual-difference measures and indicated the perspective from which they generally retrieve memories. Participants in Study 2 (N=706) retrieved a memory from their natural or manipulated perspective, rated its phenomenology, and completed the same individual-difference measures. Dissociation and anxiety were associated with third person retrieval style; the Big Five personality traits were primarily unrelated to perspective. Compared to third person memories, naturally occurring first person memories were higher on Vividness, Coherence, Accessibility, Sensory Detail, Emotional Intensity, and Time Perspective, and lower on Distancing; manipulating perspective eliminated these differences. Visual perspective is associated with clinically relevant constructs and, although associated with the memory's phenomenology, perspective does not shape it.\",\n \"corpus_id\": 13797339,\n \"score\": 0\n },\n {\n \"doc_id\": \"21278049\",\n \"title\": \"Review of extracting information from the Social Web for health personalization.\",\n \"abstract\": \"In recent years the Web has come into its own as a social platform where health consumers are actively creating and consuming Web content. Moreover, as the Web matures, consumers are gaining access to personalized applications adapted to their health needs and interests. The creation of personalized Web applications relies on extracted information about the users and the content to personalize. The Social Web itself provides many sources of information that can be used to extract information for personalization apart from traditional Web forms and questionnaires. This paper provides a review of different approaches for extracting information from the Social Web for health personalization. We reviewed research literature across different fields addressing the disclosure of health information in the Social Web, techniques to extract that information, and examples of personalized health applications. In addition, the paper includes a discussion of technical and socioethical challenges related to the extraction of information for health personalization.\",\n \"corpus_id\": 7037794,\n \"score\": 0\n },\n {\n \"doc_id\": \"21357240\",\n \"title\": \"Young children's selective trust in informants.\",\n \"abstract\": \"Young children readily act on information from adults, setting aside their own prior convictions and even continuing to trust informants who make claims that are manifestly false. Such credulity is consistent with a long-standing philosophical and scientific conception of young children as prone to indiscriminate trust. Against this conception, we argue that children trust some informants more than others. In particular, they use two major heuristics. First, they keep track of the history of potential informants. Faced with conflicting claims, they endorse claims made by someone who has provided reliable care or reliable information in the past. Second, they monitor the cultural standing of potential informants. Faced with conflicting claims, children endorse claims made by someone who belongs to a consensus and whose behaviour abides by, rather than deviating from, the norms of their group. The first heuristic is likely to promote receptivity to information offered by familiar caregivers, whereas the second heuristic is likely to promote a broader receptivity to informants from the same culture.\",\n \"corpus_id\": 2110951,\n \"score\": 0\n },\n {\n \"doc_id\": \"21858422\",\n \"title\": \"The mind as skills and dispositions: on normativity and mediation.\",\n \"abstract\": \"On the occasion of the critique of Alfredo Gaete and Carlos Cornejo, this article explains and extends the hybrid theory of the mind that I recently presented in this journal. Taking inspiration from Rom Harré's program for a hybrid psychology, the theory is supposed to be integrative and aims to broaden Harré's hybrid psychology by including not just the brain, but also the body, social practices, and technological artifacts as mediators of the mind. The mind is understood not as a substance of any kind, but as a set of skills and dispositions to act, think, and feel. This implies a normative view of the mind, according to which psychological phenomena do not simply happen, but are done, and can consequently be done more or less well. I provide arguments in favor of grounding psychology in normativity rather than conscious experience, and I explain why the emphasis on mediators does not represent a threat to the ontological primacy of the person in psychology.\",\n \"corpus_id\": 36141213,\n \"score\": 0\n },\n {\n \"doc_id\": \"22023911\",\n \"title\": \"Mirror-view reverses somatoparaphrenia: dissociation between first- and third-person perspectives on body ownership.\",\n \"abstract\": \"Right-hemisphere stroke can lead to the somatoparaphrenic delusion that parts of one's own body belong to someone else. To our knowledge, no previous study has experimentally assessed the sense of body part ownership in somatoparaphrenic patients when they see the body from a third-person perspective, as in a mirror. In alternating trials, we provided either direct first-person perspective vision of the arms, or indirect third-person perspective vision via a mirror in the frontal plane. We tested body ownership in these conditions in five patients with right-hemisphere lesions with left hemiplegia and neglect, including two patients with this somatoparaphrenic delusion. The somatoparaphrenic patients systematically attributed the ownership of their left plegic hands to someone else in direct view, but showed a statistically significant increase in ownership of the left hand in mirror view trials, as compared with the three control patients. Depending on the view offered (mirror or direct), judgements of ownership and disownership of the same limb could alternate within a few seconds. The patients did not particularly remark on these dramatic and repeated alterations between ownership and disownership. Conditions of direct- and mirror-view with simultaneous touch of the hand by the experimenter showed the same patterns of results as conditions without touch. This study provides the first experimental evidence that limb disownership can be altered using self-observation in a mirror, and in turn suggests dissociation between first- and third-person visual perspectives on the body. Furthermore, the fact that reinstatement of ownership by third-person perspective did not permanently abolish somatoparaphrenia suggests that the subjective sense of body ownership remained dominated by an impaired first-person representation of the body that could not be updated, nor integrated with other signals. More generally, our findings suggest that a neural network involving the perisylvian areas of the right hemisphere may be necessary for the integration of multiple representations of one's body and for a higher order re-representation of various bodily signals into a first-person sense of body ownership. We suggest that other areas, possibly including the occipital cortex, may be involved in the recognition of the body from a third-person visual perspective. We thus propose that somatoparaphrenia can be regarded as a neurogenic dissociation between the 'subjectively felt' and 'objectively seen' body. This recalls the developmental finding that young infants cannot link their 'felt body' with the view of themselves in a mirror.\",\n \"corpus_id\": 25892919,\n \"score\": 0\n },\n {\n \"doc_id\": \"22117462\",\n \"title\": \"[The psychophysiological condition of first year students with different levels of physical activity].\",\n \"abstract\": \"The psychophysiological condition of (male) first year students who participate in sport or don't participate in sport during studies was studied. R. M. Bayevsky's method was used to establish the level of stress on regulatory mechanisms. The functional level of the nervous system, stability of neural responses, and the level of functional abilities of the developed functional system were evaluated using the variation chronoreflexometric method. It was established that an improvement of mental capacity indicators (increase of memory capacity, reduction of the amount of mistakes made, growth of the level of functional abilities and reduction of the latency period of the visual-motor response) was accompanied by a growth of stress on the body's regulatory systems which was more pronounced with regard to those test participants whose level of physical activity was low. This fact is proof that physical activity reduces the body's \\\"adaptation price\\\" to the changing conditions of the environment. The optimal realisation of a person's adaptive systemic reactions is provided for by the dynamic interaction of the functional systems, which form a complex correlation in the body's somatovegetative, motor and psychoemotional spheres of activity.\",\n \"corpus_id\": 22233503,\n \"score\": 0\n },\n {\n \"doc_id\": \"23205018\",\n \"title\": \"The current and future status of the concealed information test for field use.\",\n \"abstract\": \"The Concealed Information Test (CIT) is a psychophysiological technique for examining whether a person has knowledge of crime-relevant information. Many laboratory studies have shown that the CIT has good scientific validity. However, the CIT has seldom been used for actual criminal investigations. One successful exception is its use by the Japanese police. In Japan, the CIT has been widely used for criminal investigations, although its probative force in court is not strong. In this paper, we first review the current use of the field CIT in Japan. Then, we discuss two possible approaches to increase its probative force: sophisticated statistical judgment methods and combining new psychophysiological measures with classic autonomic measures. On the basis of these considerations, we propose several suggestions for future practice and research involving the field CIT.\",\n \"corpus_id\": 14655244,\n \"score\": 0\n },\n {\n \"doc_id\": \"24189291\",\n \"title\": \"The nature and evolution of insight in schizophrenia: a multi-informant longitudinal study of first-episode versus chronic patients.\",\n \"abstract\": \"BACKGROUND AND AIMS: This study investigated a novel distinction between two possible sources of poor insight in schizophrenia: primary unawareness, in which the ill person is not aware that other people think one has a problem, and secondary unawareness (or disagreement), in which a person does appreciate that other people think one has a problem. A secondary goal was to compare the evolution of insight in first-episode and chronic schizophrenia. METHODS: Sixty-eight first-episode and 51 chronic patients were administered two versions of the Scale of Unawareness of Mental Disorder (SUMD) at three time points: hospital admission, discharge, and 6-month post-discharge. In the first standard SUMD version, they were asked about their own opinions, whereas in the second modified version, they were asked about their best guess of their doctor's opinion. RESULTS: While overall level of unawareness remained stable within each single episode, there were significant Type of Unawareness (primary versus secondary) by Clinical Status (admission versus discharge versus 6-month post-discharge) and Type of Unawareness by Phase of Illness (first-episode versus chronic) interaction effects. More specifically, in the first-episode group, primary unawareness steadily decreased over time. In contrast, in the chronic group, primary unawareness decreased markedly during hospitalization and returned to baseline after discharge. CONCLUSIONS: These results provide preliminary support for the notion that impaired insight is an additive outcome of primary unawareness and disagreement, and that change in insight over time occurs mostly at the level of their relative proportion as opposed to their overall sum. Implications for studying and treating poor insight in schizophrenia are discussed.\",\n \"corpus_id\": 42405152,\n \"score\": 0\n },\n {\n \"doc_id\": \"24453321\",\n \"title\": \"Suboptimal use of neural information in a mammalian auditory system.\",\n \"abstract\": \"Establishing neural determinants of psychophysical performance requires both behavioral and neurophysiological metrics amenable to correlative analyses. It is often assumed that organisms use neural information optimally, such that any information available in a neural code that could improve behavioral performance is used. Studies have shown that detection of amplitude-modulated (AM) auditory tones by humans is correlated to neural synchrony thresholds, as recorded in rabbit at the level of the inferior colliculus, the first level of the ascending auditory pathway where neurons are tuned to AM stimuli. Behavioral thresholds in rabbit, however, are ∼10 dB higher (i.e., 3 times less sensitive) than in humans, and are better correlated to rate-based than temporal coding schemes in the auditory midbrain. The behavioral and physiological results shown here illustrate an unexpected, suboptimal utilization of available neural information that could provide new insights into the mechanisms that link neuronal function to behavior.\",\n \"corpus_id\": 11991198,\n \"score\": 0\n },\n {\n \"doc_id\": \"24547754\",\n \"title\": \"Students working with multiple conflicting documents on a scientific issue: relations between epistemic cognition while reading and sourcing and argumentation in essays.\",\n \"abstract\": \"BACKGROUND: There is burgeoning research within educational psychology on both epistemic cognition and multiple-documents literacy, as well as on relationships between the two constructs. AIM: To examine relationships between epistemic cognition concerning the justification of knowledge claims and sourcing and argumentation skills. SAMPLE: Participants were 51 Norwegian undergraduates. METHOD: Three dimensions of justification were identified in think-aloud protocols based on students' reading of six documents presenting conflicting claims on the controversial scientific issue of cell phone radiation and health risks: justification by authority, personal justification and justification by multiple sources. Hierarchical multiple regression analyses were performed to examine the unique predictability of these dimensions for essay performance after removing variance associated with prior knowledge about the topic of the documents. RESULTS: After controlling for topic knowledge, justification by multiple sources uniquely predicted students' sourcing and argumentation in essays that they wrote after reading the documents, with students trying to justify knowledge claims by corroborating across several sources of information more likely to include explicit source citations, link sources and contents, and display better, more integrated argumentation in their essays. CONCLUSION: Findings are considered in the light of a theoretical framework for multiple-documents literacy adapted to the domain of science, and both theoretical and educational implications are discussed.\",\n \"corpus_id\": 25334715,\n \"score\": 0\n },\n {\n \"doc_id\": \"24671136\",\n \"title\": \"A cognitive ethology study of first- and third-person perspectives.\",\n \"abstract\": \"The aim of the present study was to test the cognitive ethology approach, which seeks to link cognitions and behaviours as they operate in everyday life with those studied in controlled lab-based investigations. Our test bed was the understanding of first-person and third-person perspectives, which in lab-based investigations have been defined in a diverse and multi-faceted manner. We hypothesized that because these lab-based investigations seek to connect with how first- and third-person perspective operates in everyday life, then either some of the divergent lab-based definitions are missing their mark or the everyday conceptualization of first- and third-person perspective is multi-faceted. Our investigation revealed the latter. By applying a cognitive ethology approach we were able to determine that a) peoples' everyday understanding of perspective is diverse yet reliable, and b) a lab-based investigation that applies these diverse understandings in a controlled setting can accurately predict how people will perform. These findings provide a 'proof of concept' for the cognitive ethology approach. Moreover, the present data demonstrate that previous lab-based studies, that often had very different understandings of first- and third-person perspective, were each in and of themselves valid. That is, each is capturing part of a broader understanding of perspective in everyday life. Our results also revealed a novel social factor not included in traditional conceptualizations of first-person third-perspective, that of eye gaze, i.e., eye contact is equated strongly with first-person perspective and the lack of eye-contact with third-person perspective.\",\n \"corpus_id\": 18904293,\n \"score\": 0\n },\n {\n \"doc_id\": \"24785813\",\n \"title\": \"16. Information.\",\n \"abstract\": \"Effective disaster management requires systems for data acquisition and information management that enable responders to rapidly collect, process, interpret, distribute, and access the data and information required for disaster management. Effective information sharing depends on the types of users, the type of damage, alterations of the functional status of the affected society, and how the information is structured. Those in need of information should be provided with the information necessary for their tasks and not be overloaded with unnecessary information that could serve as a distraction. Such information systems must be designed and exercised. To disseminate and share data with the relevant users, all disaster responses must include effective and reliable information systems. This information includes that acquired from repeated assessments in terms of available and needed human and material resources, which resources no longer are needed, and the status of the relief and recovery workers. It is through this information system that vital decisions are made that are congruent with the overall picture as perceived by the most relevant coordination and control centre. It is essential that information systems be designed and tested regularly as part of preparedness. Such systems must have the capacity to acquire, classify, and present information in an organised and useful manner.\",\n \"corpus_id\": 206722695,\n \"score\": 0\n },\n {\n \"doc_id\": \"24821510\",\n \"title\": \"Cultural differences in the primacy effect for person perception.\",\n \"abstract\": \"Previous work has shown there are robust differences in how North Americans and East Asians form impressions of people. The present research examines whether the tendency to weigh initial information more heavily-the primacy effect-may be another component of these cultural differences. Specifically, we tested whether Americans would be more likely to use first impressions to guide person perception, compared to Japanese participants. In this experiment, participants read a vignette that described a target person's behaviour, then rated the target's personality. Before reading the vignette, some trait information was given to create an expectation about the target's personality. The data revealed that Americans used this initial information to guide their judgments of the target, whereas the Japanese sample based their judgments on all the information more evenly. Thus, Americans showed a stronger primacy effect in their impression formation than Japanese participants, who engaged in more data-driven processing.\",\n \"corpus_id\": 3711355,\n \"score\": 0\n },\n {\n \"doc_id\": \"24845204\",\n \"title\": \"The diagnosis of death and the irreducibility of the human person.\",\n \"abstract\": \"If, as Karol Wojtyla had insisted, the human person is fundamentally irreducible to any natural, biological, social, or even cosmological function, then the diagnosis of death on any of the purely functionalistic grounds available to medical science presents a serious ethical problem. Perhaps we can no longer treat the question of death merely as a medical \\\"diagnosis,\\\" regarding, on that basis, the appropriateness of organ transplantation as a purely medical judgment, ethically accountable only to professional standards of care. We will explore this problem from within a personalistic philosophical, and theological framework, according to which the irreducibility of the human person provides the central referent for an analysis of the reductionistic tendencies of contemporary thinking concerning the \\\"diagnosis of death.\\\"\",\n \"corpus_id\": 20263777,\n \"score\": 0\n },\n {\n \"doc_id\": \"25259560\",\n \"title\": \"A qualitative study on the use of personal information technology by persons with spinal cord injury.\",\n \"abstract\": \"PURPOSE: Previous work has shown that information technology (IT), such as personal computers and other digital devices (e.g. tablets, laptops, etc.), software, online resources and hand-held communication tools (e.g. cellphones), has benefits for health and well-being for persons with chronic health conditions. To date, the ways that persons with spinal cord injury (SCI) use IT in their daily activities has not been fully explored. Thus, the purpose of the study was to obtain an in-depth perspective of how people with SCI regularly use IT to gain insight on ways IT can be used to support health and well-being in the community for this population. METHODS: Semi-structured interviews were conducted with community-dwelling persons with SCI (N = 10) who identified themselves as frequent-or-daily-users of IT. Qualitative content analysis was used to identify the ways that persons with SCI use personal IT. RESULTS: Ten themes related to IT use were identified: (1) Modifications allowing access to IT; (2) Convenience of IT and its perceived value; (3) IT as a scheduler/planner; (4) Challenges; (5) Contributions of IT to participation; (6) Access to information; (7) Influence of IT on well-being; (8) IT as a connector; (9) Issues of IT acquisition; and (10) Desires for future devices/technology. CONCLUSIONS: The findings suggest that IT use by people with SCI contributes to general health and well-being, by increasing access to SCI-related health information and opportunity for social participation. Despite the benefits offered by IT, persons with SCI have identified a degree of skepticism about the reliability and applicability of the health information they find online. Future work on developing and implementing IT for health and well-being post-SCI should take into account consumers' perspectives to facilitate uptake. Implications for Rehabilitation There is a need for a more refined understanding of how people with spinal cord injury (SCI) use information technology (IT) in their daily lives in order to understand how IT can support health and well-being post-injury in the community. IT use holds implications for the physical and mental well-being of persons with SCI. IT allows access to a variety of information, and facilitates participation in the community. The enthusiasm for the use of IT is tempered by a degree of skepticism about the reliability and applicability of the health information available online. This highlights the need to raise awareness of existing sources vetted for this population, and to develop content that meets the particular health needs for SCI.\",\n \"corpus_id\": 25745097,\n \"score\": 0\n },\n {\n \"doc_id\": \"25417640\",\n \"title\": \"Accuracy of Judgments of Personality Based on Textual Information on Major Life Domains.\",\n \"abstract\": \"We studied the accuracy of personality impressions relying on textual information on important life domains. Specifically, how is accuracy moderated by the trait being judged, information being provided, judgeability of target persons, and perceptiveness of judges? A sample of 208 students was recruited in groups of four mutual acquaintances who described themselves and each other on a measure of the Five-Factor Model of personality. Moreover, they wrote essays on their hobbies, friends, family, academic studies, and plans for the future and provided self-reports on possible predictors of expressive accuracy. The essays were delivered to 130 strangers who reported their impressions of the personality of the targets and provided self-reports on possible predictors of perceptive accuracy. Accuracy was measured by correlating these impressions with the descriptions of the targets by their acquaintances. The judges used the available information efficiently. Overall, impressions of Openness to Experience were most accurate, but accuracy depended on the information being provided. Several predictors of expressive and perceptive accuracy were identified using Biesanz's (2010) social accuracy model. The results advance our understanding of factors contributing to and moderating the accuracy of personality impressions based on textual information.\",\n \"corpus_id\": 1223281,\n \"score\": 0\n },\n {\n \"doc_id\": \"25494630\",\n \"title\": \"Evidence-informed person-centred health care (part II): are 'cognitive biases plus' underlying the EBM paradigm responsible for undermining the quality of evidence?\",\n \"abstract\": \"INTRODUCTION: Recently, some leaders of the evidence-based medicine (EBM) movement drew attention to the \\\"unintended\\\" negative consequences associated with EBM. The term 'cognitive biases plus' was introduced in part I to encompass cognitive biases, conflicts of interests, fallacies and certain behaviours. HYPOTHESIS: 'Cognitive biases plus' in those closely involved in creating and promoting the EBM paradigm are responsible for their (1) inability to anticipate and then recognize flaws in the tenets of EBM; (2) discounting alternative views; and (3) delaying reform. METHODS: A narrative review style was used, with methods as in part I. APPRAISAL OF LITERATURE: Over the past two decades there has been mounting qualitative and quantitative methodological evidence to suggest that the faith placed in (1) the EBM hierarchy with randomized controlled trials and systematic reviews at the summit; (2) the reliability of biostatistical methods to quantitate data; and (3) the primacy of sources of pre-appraised evidence, is seriously misplaced. Consequently, the evidence that informs person-centred care is compromised. DISCUSSION: Arguments focusing on 'cognitive biases plus' are offered to support our hypothesis. To the best of our knowledge, EBM proponents have not provided an explanation. CONCLUSIONS: Reform is urgently needed to minimize continuing risks to patients. If our hypothesis is correct, then in addition to the suggestions made in part I, deficiencies in the paradigm must be corrected. Meaningful solutions are only possible if the biases of scientific inbreeding and groupthink are minimized by collaboration between EBM leaders and those who have been sounding warning bells.\",\n \"corpus_id\": 46137,\n \"score\": 0\n },\n {\n \"doc_id\": \"25528086\",\n \"title\": \"Is it always me first? Effects of self-tagging on third-person perspective-taking.\",\n \"abstract\": \"Self-relevant information is associated with facilitation of perceptual and memory processes. In 2 experiments, participants verified the number of dots within a virtual room that were visible to a given perspective, corresponding to participants' own first-person perspectives or the third-person perspectives for self- and other-associated avatars. Perspectives were either congruent or incongruent with respect to the number of dots visible to each. In Experiment 1, we examined perspective taking for self- and other-associated avatars relative to one another; both avatars appeared simultaneously in the virtual room, and participants made judgments based on the prompted avatar's perspective. In Experiment 2, we examined perspective taking for each avatar relative to the first-person perspective; only 1 avatar was visible in the virtual room (Self or Other, varying by trial), and participants made judgments based on their first-person view or the avatar's perspective. Experiment 2 also included a replication of the third-person paradigm used in Experiment 1. Results from Experiment 1 (replicated in Experiment 2) demonstrated an advantage for judgments of the Self (vs. Other) avatar's perspective; both avatars elicited reliable interference effects of similar magnitude. Results from Experiment 2 further demonstrated that participants prioritized the first-person (vs. third-person) perspective, and that the presence of the Self (vs. Other) avatar improved performance for the first- and third-person perspectives when those perspectives were congruent. Taken together, these findings suggest that self-relevant perspectives are prioritized when they are actively engaged and when they can be subsumed within the first-person view. Such prioritization appears to occur by strategic means.\",\n \"corpus_id\": 4985388,\n \"score\": 0\n },\n {\n \"doc_id\": \"25594153\",\n \"title\": \"First-person and third-person verbs in visual motion-perception regions.\",\n \"abstract\": \"Verb-related activity is consistently found in the left posterior lateral cortex (PLTC), encompassing also regions that respond to visual-motion perception. Besides motion, those regions appear sensitive to distinctions among the entities beyond motion, including that between first- vs. third-person (\\\"third-person bias\\\"). In two experiments, using functional magnetic resonance imaging (fMRI), we studied whether the implied subject (first/third-person) and/or the semantic content (motor/non-motor) of verbs modulate the neural activity in the left PLTC-regions responsive during basic- and biological-motion perception. In those sites, we found higher activity for verbs than for nouns. This activity was modulated by the person (but not the semantic content) of the verbs, with stronger response to third- than first-person verbs. The third-person bias elicited by verbs supports a role of motion-processing regions in encoding information about the entity beyond (and independently from) motion, and sets in a new light the role of these regions in verb processing.\",\n \"corpus_id\": 20166449,\n \"score\": 0\n },\n {\n \"doc_id\": \"25597036\",\n \"title\": \"The researcher as experimental subject: using self-experimentation to access experiences, understand social phenomena, and stimulate reflexivity.\",\n \"abstract\": \"The current article argues that researcher-as-subject self-experimentation can provide valuable insight and systematic knowledge to social psychologists. This approach, the modus operandi of experimental psychology when the field was in its infancy, has been largely eclipsed by an almost exclusive focus on participant-as-subject other-experimentation. Drawing from the non-experimental first-person traditions of autoethnography, participant observation, and phenomenology, we argue that participating as both observer and subject within one's own social psychological experiment affords researchers at least three potential benefits: (1) access to \\\"social qualia,\\\" that is, the subjective experience of social phenomena; (2) improved mental models of social phenomena, potentially stimulating new research questions; and (3) an enhanced ability to be reflexive about the given experiment. To support our position, we provide first-person self-reflections from researchers who have self-experimented with transformed social interactions involving Milgram's cyranoid method. We close by offering guidelines on how one might approach self-experimentation, and discuss a variety of first-person perspective ethnographic technologies that can be incorporated into the practice.\",\n \"corpus_id\": 33909867,\n \"score\": 0\n },\n {\n \"doc_id\": \"26567205\",\n \"title\": \"Consumer Perception of Genetically Modified Organisms and Sources of Information.\",\n \"abstract\": \"Genetically modified organisms (GMOs) have been available for commercial purchase since the 1990s, allowing producers to increase crop yields through bioengineering that creates herbicide-resistant and insect-resistant varieties. However, consumer knowledge about GMOs has not increased at the same rate as the adoption of GMO crops. Consumers worldwide are displaying limited understanding, misconceptions, and even unfamiliarity with GMO food products. Many consumers report that they receive information about GMO food products from the media, Internet, and other news sources. These sources may be less reliable than scientific experts whom consumers trust more to present the facts. Although many in the United States support mandatory GMO labeling (similar to current European standards), consumer awareness of current GMO labeling is low. A distinction must also be made between GMO familiarity and scientific understanding, because those who are more familiar with it tend to be more resistant to bioengineering, whereas those with higher scientific knowledge scores tend to have less negative attitudes toward GMOs. This brings to question the relation between scientific literacy, sources of information, and overall consumer knowledge and perception of GMO foods.\",\n \"corpus_id\": 11162085,\n \"score\": 0\n },\n {\n \"doc_id\": \"27065345\",\n \"title\": \"The information-anchoring model of first offers: When moving first helps versus hurts negotiators.\",\n \"abstract\": \"Does making the first offer increase or impair a negotiator's outcomes? Past research has found evidence supporting both claims. To reconcile these contradictory findings, we developed and tested an integrative model-the Information-Anchoring Model of First Offers. The model predicts when and why making the first offer helps versus hurts. We suggest that first offers have 2 effects. First, they serve as anchors that pull final settlements toward the initial first-offer value; this anchor function often produces a first-mover advantage. Second, first offers can convey information on the senders' priorities, which makes the sender vulnerable to exploitation and increases the risk of a first-mover disadvantage. To test this model, 3 experiments manipulated the information that senders communicated in their first offer. When senders did not reveal their priorities, the first-mover advantage was replicated. However, when first offers revealed senders' priorities explicitly, implicitly, or both, a first-mover disadvantage emerged. Negotiators' social value orientation moderated this effect: A first-mover disadvantage occurred when senders faced proself recipients who exploited priority information, but not with prosocial recipients. Moderated mediation analyses supported the model assumptions: Proself recipients used their integrative insight to feign priorities in their low-priority issues and thereby claimed more individual value than senders. The final discussion reviews theoretical and applied implications of the Information-Anchoring Model of First Offers. ( PsycINFO Database Record\",\n \"corpus_id\": 34365662,\n \"score\": 0\n },\n {\n \"doc_id\": \"27067632\",\n \"title\": \"Children's understanding of first- and third-person perspectives in complement clauses and false-belief tasks.\",\n \"abstract\": \"De Villiers (Lingua, 2007, Vol. 117, pp. 1858-1878) and others have claimed that children come to understand false belief as they acquire linguistic constructions for representing a proposition and the speaker's epistemic attitude toward that proposition. In the current study, English-speaking children of 3 and 4years of age (N=64) were asked to interpret propositional attitude constructions with a first- or third-person subject of the propositional attitude (e.g., \\\"I think the sticker is in the red box\\\" or \\\"The cow thinks the sticker is in the red box\\\", respectively). They were also assessed for an understanding of their own and others' false beliefs. We found that 4-year-olds showed a better understanding of both third-person propositional attitude constructions and false belief than their younger peers. No significant developmental differences were found for first-person propositional attitude constructions. The older children also showed a better understanding of their own false beliefs than of others' false beliefs. In addition, regression analyses suggest that the older children's comprehension of their own false beliefs was mainly related to their understanding of third-person propositional attitude constructions. These results indicate that we need to take a closer look at the propositional attitude constructions that are supposed to support children's false-belief reasoning. Children may come to understand their own and others' beliefs in different ways, and this may affect both their use and understanding of propositional attitude constructions and their performance in various types of false-belief tasks.\",\n \"corpus_id\": 34323014,\n \"score\": 0\n },\n {\n \"doc_id\": \"27474914\",\n \"title\": \"The occipital place area represents first-person perspective motion information through scenes.\",\n \"abstract\": \"Neuroimaging studies have identified multiple scene-selective regions in human cortex, but the precise role each region plays in scene processing is not yet clear. It was recently hypothesized that two regions, the occipital place area (OPA) and the retrosplenial complex (RSC), play a direct role in navigation, while a third region, the parahippocampal place area (PPA), does not. Some evidence suggests a further division of labor even among regions involved in navigation: While RSC is thought to support navigation through the broader environment, OPA may be involved in navigation through the immediately visible environment, although this role for OPA has never been tested. Here we predict that OPA represents first-person perspective motion information through scenes, a critical cue for such \\\"visually-guided navigation\\\", consistent with the hypothesized role for OPA. Response magnitudes were measured in OPA (as well as RSC and PPA) to i) video clips of first-person perspective motion through scenes (\\\"Dynamic Scenes\\\"), and ii) static images taken from these same movies, rearranged such that first-person perspective motion could not be inferred (\\\"Static Scenes\\\"). As predicted, OPA responded significantly more to the Dynamic than Static Scenes, relative to both RSC and PPA. The selective response in OPA to Dynamic Scenes was not due to domain-general motion sensitivity or to low-level information inherited from early visual regions. Taken together, these findings suggest the novel hypothesis that OPA may support visually-guided navigation, insofar as first-person perspective motion information is useful for such navigation, while RSC and PPA support other aspects of navigation and scene recognition.\",\n \"corpus_id\": 22736033,\n \"score\": 0\n },\n {\n \"doc_id\": \"27708754\",\n \"title\": \"Apparent Biological Motion in First and Third Person Perspective.\",\n \"abstract\": \"Apparent biological motion is the perception of plausible movements when two alternating images depicting the initial and final phase of an action are presented at specific stimulus onset asynchronies. Here, we show lower subjective apparent biological motion perception when actions are observed from a first relative to a third visual perspective. These findings are discussed within the context of sensorimotor contributions to body ownership.\",\n \"corpus_id\": 14756284,\n \"score\": 0\n },\n {\n \"doc_id\": \"27744988\",\n \"title\": \"Information prescriptions.\",\n \"abstract\": \"Information prescriptions (IPs) are intended to guide people to relevant and reliable sources of information on, for example, conditions and treatments, services and support groups.\",\n \"corpus_id\": 28986553,\n \"score\": 0\n },\n {\n \"doc_id\": \"28934559\",\n \"title\": \"Psychological Perspectives on Interrogation.\",\n \"abstract\": \"Proponents of \\\"enhanced interrogation techniques\\\" in the United States have claimed that such methods are necessary for obtaining information from uncooperative terrorism subjects. In the present article, we offer an informed, academic perspective on such claims. Psychological theory and research shows that harsh interrogation methods are ineffective. First, they are likely to increase resistance by the subject rather than facilitate cooperation. Second, the threatening and adversarial nature of harsh interrogation is often inimical to the goal of facilitating the retrieval of information from memory and therefore reduces the likelihood that a subject will provide reports that are extensive, detailed, and accurate. Third, harsh interrogation methods make lie detection difficult. Analyzing speech content and eliciting verifiable details are the most reliable cues to assessing credibility; however, to elicit such cues subjects must be encouraged to provide extensive narratives, something that does not occur in harsh interrogations. Evidence is accumulating for the effectiveness of rapport-based information-gathering approaches as an alternative to harsh interrogations. Such approaches promote cooperation, enhance recall of relevant and reliable information, and facilitate assessments of credibility. Given the available evidence that torture is ineffective, why might some laypersons, policymakers, and interrogation personnel support the use of torture? We conclude our review by offering a psychological perspective on this important question.\",\n \"corpus_id\": 5147951,\n \"score\": 0\n },\n {\n \"doc_id\": \"29118785\",\n \"title\": \"Advance Directives as Support of Autonomy for Persons with Dementia? A Pilot Study among Persons with Dementia and Their Informal Caregivers.\",\n \"abstract\": \"Background: Advance directives could be an important instrument to support a person's will once he/she is not able to consent anymore - if composed competently. A survey was conducted to identify the level of knowledge concerning possibilities and limits of advance directives. Methods: The study was conducted as part of the Bavarian Dementia Survey (BayDem). Data were collected from January 2014 to December 2015 by structured face-to-face interviews. Study participants were persons with dementia and their informal caregivers (n = 74). Results: In total, 66% reported having written an advance directive. Concerning the participants' knowledge about possibilities and limitations of advance directives, a lack of knowledge was noted about the possibility to revoke an advance directive. Furthermore, 70% of informal caregivers and 56% of persons with dementia were not aware of the possibility to include dementia-specific terms in the advance directive. Conclusion: It is necessary to optimize structures for public information and education concerning the topic of advance directives for persons with dementia.\",\n \"corpus_id\": 13062896,\n \"score\": 0\n },\n {\n \"doc_id\": \"29281736\",\n \"title\": \"Characterizing first and third person viewpoints and their alternation for embodied interaction in virtual reality.\",\n \"abstract\": \"Empirical research on the bodily self has shown that the body representation is malleable, and prone to manipulation when conflicting sensory stimuli are presented. Using Virtual Reality (VR) we assessed the effects of manipulating multisensory feedback (full body control and visuo-tactile congruence) and visual perspective (first and third person perspective) on the sense of embodying a virtual body that was exposed to a virtual threat. We also investigated how subjects behave when the possibility of alternating between first and third person perspective at will was presented. Our results support that illusory ownership of a virtual body can be achieved in both first and third person perspectives under congruent visuo-motor-tactile condition. However, subjective body ownership and reaction to threat were generally stronger for first person perspective and alternating condition than for third person perspective. This suggests that the possibility of alternating perspective is compatible with a strong sense of embodiment, which is meaningful for the design of new embodied VR experiences.\",\n \"corpus_id\": 33581414,\n \"score\": 0\n }\n]","isConversational":false}}},{"rowIdx":76,"cells":{"query":{"kind":"string","value":"{\n \"doc_id\": \"27083189\",\n \"title\": \"Fasciola hepatica calcium-binding protein FhCaBP2: structure of the dynein light chain-like domain.\",\n \"abstract\": \"The common liver fluke Fasciola hepatica causes an increasing burden on human and animal health, partly because of the spread of drug-resistant isolates. As a consequence, there is considerable interest in developing new drugs to combat liver fluke infections. A group of potential targets is a family of calcium-binding proteins which combine an N-terminal domain with two EF-hand motifs and a C-terminal domain with predicted similarity to dynein light chains (DLC-like domain). The function of these proteins is unknown, although in several species, they have been localised to the tegument, an important structure at the host-parasite interface. Here, we report the X-ray crystal structure of the DLC-like domain of F. hepatica calcium-binding protein 2 (FhCaBP2), solved using single-wavelength anomalous diffraction and refined at 2.3 Å resolution in two different crystal forms. The FhCaBP2 DLC-like domain has a structure similar to other DLC domains, with an anti-parallel β-sheet packed against an α-helical hairpin. Like other DLC domains, it dimerises through its β2-strand, which extends in an arch and forms the fifth strand in an extended β-sheet of the other monomer. The structure provides molecular details of the dimerisation of FhCaBP2, the first example from this family of parasite proteins.\",\n \"corpus_id\": 18643300\n}"},"candidates":{"kind":"list like","value":[{"doc_id":"18467191","title":"Plasmodium possesses dynein light chain classes that are unique and conserved across species.","abstract":"Plasmodium belongs to the phylum Apicomplexa. Within the Apicomplexa, Plasmodium, Toxoplasma and Cryptosporidium are parasites of considerable medical importance while Theileria and Eimeria are animal pathogens. P. falciparum is particularly important as it causes malaria, resulting in more than 1 million deaths each year. The malaria parasite actively invades the host cell in which it propagates and several proteins associated with the apical organelles have been implicated to be crucial in the invasion process. The biogenesis of the apical organelles is not well understood, but several studies indicate that microtubule-based vesicular transport is involved. Vesicular transport proteins are also present in Plasmodium and are presumed to be involved in transcellular transport in infected erythrocytes. Dynein is a multi-subunit motor protein involved in microtubule-based vesicular transport. In this study, we analyzed the cytoplasmic dynein light chains (Dlcs) of P. falciparum since they provide adaptor surface to the cargoes and are likely to be involved in differential transport. Dlcs consist of three different families: TcTex1/2, LC8 and LC7/roadblock. The data presented demonstrate that P. falciparum Dlcs sequences and functional domains show high sequence similarity within the species, but that only the Dlc group 1 (LC8) has a high similarity to human orthologues. TcTex1 and LC7/roadblock have low similarity to human orthologues. This sequence variation could be targeted for vaccine or drug development.","corpus_id":19344029,"score":2},{"doc_id":"18996374","title":"Schistosoma spp.: Isolation of microtubule associated proteins in the tegument and the definition of dynein light chains components.","abstract":"Schistosomes are parasitic blood flukes that reside in human mesenteric veins or urinary bladder veins, depending on species of the parasite. The syncytial tegument of these parasites represents a dynamic interface that regulates nutritional and immunological interactions between the parasite and the host. It is known that the components for biogenesis and maintenance of the tegument are supplied via vesicles from the nucleated cell bodies beneath the syncytium and muscle layer. To investigate the common motor components of vesicular transport in the tegument of schistomes, we extracted Schistosoma mansoni tegumental microtubule associated proteins utilizing detergent/high-salt procedure and raised antiserum against these proteins. The antiserum was applied to screen Schistosoma haematobium lambda gt11 expression library and some of the isolated clones were sequenced. Blast search for the sequences against NCBI database identified clones that are dynein light chains and myosin genes. Further analysis of schistosome dynein genes in the databases identified three families of dynein light chains (Dlcs). The Tctex family protein sequences are significantly different from the mammalian homologs and, therefore, offer a potential vaccine/drug target against schistosomes.","corpus_id":42587114,"score":2},{"doc_id":"21078120","title":"FH8--a small EF-hand protein from Fasciola hepatica.","abstract":"Vaccine and drug development for fasciolasis rely on a thorough understanding of the mechanisms involved in parasite-host interactions. FH8 is an 8 kDa protein secreted by the parasite Fasciola hepatica in the early stages of infection. Sequence analysis revealed that FH8 has two EF-hand Ca(2+)-binding motifs, and our experimental data show that the protein binds Ca(2+) and that this induces conformational alterations, thus causing it to behave like a sensor protein. Moreover, FH8 displays low affinity for Ca(2+) (K(obs) = 10(4) m(-1)) and is highly stable in its apo and Ca(2+)-loaded states. Homology models were built for FH8 in both states. It has only one globular domain, with two binding sites and appropriate groups in the positions for coordination of the metal ions. However, an unusually high content of positively charged amino acids in one of the binding sites, when compared with the prototypical sensor proteins, potentially affects the protein's affinity for Ca(2+). The only Cys present in FH8, conserved in the homologous proteins of other helminth parasites, is located on the surface, allowing the formation of dimers, detected on SDS gels. These findings reflect specificities of FH8, which are most probably related to its roles both in the parasite and in the host.","corpus_id":2838269,"score":2},{"doc_id":"22019596","title":"Exploring the Fasciola hepatica tegument proteome.","abstract":"The surface tegument of the liver fluke Fasciola hepatica is a syncytial cytoplasmic layer bounded externally by a plasma membrane and covered by a glycocalyx, which constitutes the interface between the parasite and its ruminant host. The tegument's interaction with the immune system during the fluke's protracted migration from the gut lumen through the peritoneal cavity and liver parenchyma to the lumen of the bile duct, plays a key role in the fluke's establishment or elimination. However, little is known about proteins of the tegument surface or its secretions. We applied techniques developed for the blood fluke, Schistosoma mansoni, to enrich a tegument surface membrane preparation and analyse its composition by tandem mass spectrometry using new transcript databases for F. hepatica. We increased the membrane and secretory pathway components of the final preparation to ∼30%, whilst eliminating contaminating proteases. We identified a series of proteins or transcripts shared with the schistosome tegument including annexins, a tetraspanin, carbonic anhydrase and an orthologue of a host protein (CD59) that inhibits complement fixation. Unique to F. hepatica, we also found proteins with lectin, cubulin and von Willebrand factor domains plus 10 proteins with leader sequences or transmembrane helices. Many of these surface proteins are potential vaccine candidates. We were hampered in collecting tegument secretions by the propensity of liver flukes, unlike blood flukes, to vomit their gut contents. We analysed both the 'vomitus' and a second supernatant released from haematin-depleted flukes. We identified many proteases, some novel, as well as a second protein with a von Willebrand factor domain. This study demonstrates that components of the tegumental surface of F. hepatica can be defined using proteomic approaches, but also indicates the need to prevent vomiting if tegument secretions are to be characterised.","corpus_id":26084615,"score":2},{"doc_id":"22366577","title":"Analysis of a calcium-binding EF-hand protein family in Fasciola gigantica.","abstract":"Transcriptome data supports the notion of a Platyhelminthes-specific protein family that is characterized by combination of two N-terminal EF-hands and a C-terminal dynein light chain-like domain. Family members in schistosomes induce an IgE response that has been connected with resistance to reinfection in schistosomiasis and is considered as a marker of protection. In the present study, we have compared three homologs of the liver fluke Fasciola gigantica for their immunological properties in mouse. Antisera raised against the recombinant proteins detected the native proteins in tegumental type tissues and epithelial linings of excretory system and intestinal tract. The recombinant EF-hand domains induced strong IgG and IgE responses in immunised mice while only weak to moderate responses were observed against the complete recombinant proteins and their DLC-like domains. Parasite crude worm and tegumental extract antisera reacted predominantly with one isoform and its EF-hand domain. Sera of F. gigantica infected mice did not react with the recombinant proteins. The RNA products of the three genes were detected from the metacercarial up to the adult stage. These observations indicate that the investigated EF-hand proteins are not at the frontier of humoral host/parasite interaction in acute fascioliasis gigantica in mouse but are acting as intracellular proteins in tissues that interface with the parasite's environment or tubular tracts.","corpus_id":30508089,"score":2},{"doc_id":"22642211","title":"A proteomic approach to investigate the distribution and abundance of surface and internal Fasciola hepatica proteins during the chronic stage of natural liver fluke infection in cattle.","abstract":"Fasciola hepatica, a trematode helminth, causes an economically important disease (fasciolosis) in ruminants worldwide. Proteomic analysis of the parasite provides valuable information to understand the relationship between the parasite and its host. Previous studies have identified various parasite proteins, some of which are considered as vaccine candidates or important drug targets. However, the approximate distribution and abundance of the proteins on the surface and within internal parts of the liver fluke are unknown. In this study, two fractions including surface protein fraction (representing surface part of the parasite, near subplasma membrane of the tegument and above the basal membrane of the tegument) and internal protein fraction (representing internal part of the parasite, mainly deeper sides of the tegument including subbasal membrane and other further internal elements of the parasite) were obtained. Components of these two fractions were investigated by an advanced proteomics approach using a high-definition mass spectrometer with nano electrospray ionization source coupled to a high-performance liquid chromatography system (nanoUPLC-ESI-qTOF-MS). FABP1 was found highly abundant in the SPF fraction. Potentially novel F. hepatica proteins showing homology with AKT interacting protein (Xenopus tropicalis), sterol O-acyltransferase 2 (Homo sapiens), and integrin beta 7 (Mus musculus) were identified with high quantities in only the surface fraction of the parasite and may be possible candidates for future control strategies.","corpus_id":6255669,"score":2},{"doc_id":"22773043","title":"FhCaBP4: a Fasciola hepatica calcium-binding protein with EF-hand and dynein light chain domains.","abstract":"In trematodes, there is a family of proteins which combine EF-hand-containing domains with dynein light chain (DLC)-like domains. A member of this family from the liver fluke, Fasciola hepatica-FhCaBP4-has been identified and characterised biochemically. FhCaBP4 has an N-terminal domain containing two imperfect EF-hand sequences and a C-terminal dynein light chain-like domain. Molecular modelling predicted that the two domains are joined by a flexible linker. Native gel electrophoresis demonstrated that FhCaBP4 binds to calcium, manganese, barium and strontium ions, but not to magnesium or zinc ions. The hydrophobic, fluorescent probe 8-anilinonaphthalene-1-sulphonate bound more tightly to FhCaBP4 in the presence of calcium ions. This suggests that the protein undergoes a conformational change on ion binding which increases the number of non-polar residues on the surface. FhCaBP4 was protected from limited proteolysis by the calmodulin antagonist W7, but not by trifluoperazine or praziquantel. Protein-protein cross-linking experiments showed that FhCaBP4 underwent calcium ion-dependent dimerisation. Since DLCs are commonly dimeric, it is likely that FhCaBP4 dimerises through this domain. The molecular model reveals that the calcium ion-binding site is located close to a key sequence in the DLC-like domain, suggesting a plausible mechanism for calcium-dependent dimerisation.","corpus_id":18776459,"score":2},{"doc_id":"23142130","title":"FhCaBP3: a Fasciola hepatica calcium binding protein with EF-hand and dynein light chain domains.","abstract":"A DNA sequence encoding a protein with predicted EF-hand and dynein light chain binding domains was identified in a Fasciola hepatica EST library. Sequence analysis of the encoded protein revealed that the most similar known protein was the Fasciola gigantica protein FgCaBP3 and so this newly identified protein was named FhCaBP3. Molecular modelling of FhCaBP3 predicted a highly flexible N-terminal region, followed by a domain containing two EF-hand motifs the second of which is likely to be a functioning divalent ion binding site. The C-terminal domain of the protein contains a dynein light chain like region. Interestingly, molecular modelling predicts that calcium ion binding to the N-terminal domain destabilises the β-sheet structure of the C-terminal domain. FhCaBP3 can be expressed in, and purified from, Escherichia coli. The recombinant protein dimerises and the absence of calcium ions appeared to promote dimerisation. Native gel shift assays demonstrated that the protein bound to calcium and manganese ions, but not to magnesium, barium, zinc, strontium, nickel, copper or cadmium ions. FhCaBP3 interacted with the calmodulin antagonists trifluoperazine, N-(6-aminohexyl)-5-chloro-1-naphthalenesulfonamide and chlorpromazine as well as the myosin regulatory light chain-binding drug praziquantel. Despite sequence and structural similarities to other members of the same protein family from F. hepatica, FhCaBP3 has different biochemical properties to the other well characterised family members, FH22 and FhCaBP4. This suggests that each member of this trematode calcium-binding family has discrete functional roles within the organism.","corpus_id":9112646,"score":2},{"doc_id":"24915098","title":"Preliminary crystallographic studies of a Schistosoma mansoni antigen (Sm21.7) dynein light-chain (DLC) domain.","abstract":"Schistosomiasis is an inflammatory chronic disease that represents a major health problem in tropical and subtropical countries. The drug of choice for treatment, praziquantel, is effective in killing adult worms but fails to kill immature forms and prevent reinfection. One prominent antigen candidate for an anti-schistosomiasis vaccine is the protein Sm21.7 (184 amino-acid residues) from Schistosoma mansoni, a tegumental protein capable of reducing the worm burden in a murine immunization model. In the present work, the Sm21.7 gene was cloned and expressed in Escherichia coli and the full-length protein was purified to homogeneity. Crystals of recombinant Sm21.7 suitable for X-ray diffraction were obtained using PEG monomethyl ether 2000 as a precipitant. X-ray diffraction images of a native crystal (at 2.05 Å resolution) and a quick-cryosoaked NaI derivative (at 1.95 Å resolution) were collected on the W01B-MX2 beamline at the Laboratório Nacional de Luz Síncrotron (LNLS, Brazilian Synchrotron Light Laboratory/MCT). Both crystals belonged to the hexagonal space group P6122, with similar unit-cell parameters a=b=108.5, c=55.8 Å. SIRAS-derived phases were used to generate the first electron-density map, from which a partial three-dimensional model of Sm21.7 (from Gln89 to Asn184) was automatically constructed. Anaysis of dissolved crystals by SDS-PAGE confirmed that the protein was cleaved in the crystallization drop and only the Sm21.7 C-terminal domain was crystallized. The structure of the Sm21.7 C-terminal domain will help in the localization of the epitopes responsible for its protective immune responses, constituting important progress in the development of an anti-schistosomiasis vaccine.","corpus_id":27932347,"score":2},{"doc_id":"26152524","title":"FhCaBP2: a Fasciola hepatica calcium-binding protein with EF-hand and dynein light chain domains.","abstract":"FhCaBP2 is a Fasciola hepatica protein which belongs to a family of helminth calcium-binding proteins which combine an N-terminal domain containing two EF-hand motifs and a C-terminal dynein light chain-like (DLC-like) domain. Its predicted structure showed two globular domains joined by a flexible linker. Recombinant FhCaBP2 interacted reversibly with calcium and manganese ions, but not with magnesium, barium, strontium, copper (II), colbalt (II), iron (II), nickel, lead or potassium ions. Cadmium (II) ions appeared to bind non-site-specifically and destabilize the protein. Interaction with either calcium or magnesium ions results in a conformational change in which the protein's surface becomes more hydrophobic. The EF-hand domain alone was able to interact with calcium and manganese ions; the DLC-like domain was not. Alteration of a residue (Asp-58 to Ala) in the second EF-hand motif in this domain abolished ion-binding activity. This suggests that the second EF-hand is the one responsible for ion-binding. FhCaBP2 homodimerizes and the extent of dimerization was not affected by calcium ions or by the aspartate to alanine substitution in the second EF-hand. The isolated EF-hand and DLC-like domains are both capable of homodimerization. FhCaBP2 interacted with the calmodulin antagonists trifluoperazine, chlorpromazine, thiamylal and W7. Interestingly, while chlorpromazine and thiamylal interacted with the EF-hand domain (as expected), trifluoperazine and W7 bound to the DLC-like domain. Overall, FhCaBP2 has distinct biochemical properties compared with other members of this protein family from Fasciola hepatica, a fact which supports the hypothesis that these proteins have different physiological roles.","corpus_id":54562582,"score":2},{"doc_id":"27528745","title":"A mysterious family of calcium-binding proteins from parasitic worms.","abstract":"There is a family of proteins from parasitic worms which combine N-terminal EF-hand domains with C-terminal dynein light chain-like domains. Data are accumulating on the biochemistry and cell biology of these proteins. However, little is known about their functions in vivo Schistosoma mansoni expresses 13 family members (SmTAL1-SmTAL13). Three of these (SmTAL1, SmTAL2 and SmTAL3) have been subjected to biochemical analysis which demonstrated that they have different molecular properties. Although their overall folds are predicted to be similar, small changes in the EF-hand domains result in differences in their ion binding properties. Whereas SmTAL1 and SmTAL2 are able to bind calcium (and some other) ions, SmTAL3 appears to be unable to bind any divalent cations. Similar biochemical diversity has been seen in the CaBP proteins from Fasciola hepatica Four family members are known (FhCaBP1-4). All of these bind to calcium ions. However, FhCaBP4 dimerizes in the presence of calcium ions, FhCaBP3 dimerizes in the absence of calcium ions and FhCaBP2 dimerizes regardless of the prevailing calcium ion concentration. In both the SmTAL and FhCaBP families, the proteins also differ in their ability to bind calmodulin antagonists and related drugs. Interestingly, SmTAL1 interacts with praziquantel (the drug of choice for treating schistosomiasis). The pharmacological significance (if any) of this finding is unknown.","corpus_id":206155869,"score":2},{"doc_id":"27693219","title":"FhCaBP1 (FH22): A Fasciola hepatica calcium-binding protein with EF-hand and dynein light chain domains.","abstract":"FH22 has been previously identified as a calcium-binding protein from the common liver fluke, Fasciola hepatica. It is part of a family of at least four proteins in this organism which combine an EF-hand containing N-terminal domain with a C-terminal dynein light chain-like domain. Here we report further biochemical properties of FH22, which we propose should be renamed FhCaBP1 for consistency with other family members. Molecular modelling predicted that the two domains are linked by a flexible region and that the second EF-hand in the N-terminal domain is most likely the calcium ion binding site. Native gel electrophoresis demonstrated that the protein binds both calcium and manganese ions, but not cadmium, magnesium, strontium, barium, cobalt, copper(II), iron (II), nickel, zinc, lead or potassium ions. Calcium ion binding alters the conformation of the protein and increases its stability towards thermal denaturation. FhCaBP1 is a dimer in solution and calcium ions have no detectable effect on the protein's ability to dimerise. FhCaBP1 binds to the calmodulin antagonists trifluoperazine and chlorpromazine. Overall, the FhCaBP1's biochemical properties are most similar to FhCaBP2 a fact consistent with the close sequence and predicted structural similarity between the two proteins.","corpus_id":34616309,"score":2},{"doc_id":"28273846","title":"Molecular and Structural Characterization of the Tegumental 20.6-kDa Protein in Clonorchis sinensis as a Potential Druggable Target.","abstract":"The tegument, representing the membrane-bound outer surface of platyhelminth parasites, plays an important role for the regulation of the host immune response and parasite survival. A comprehensive understanding of tegumental proteins can provide drug candidates for use against helminth-associated diseases, such as clonorchiasis caused by the liver fluke Clonorchis sinensis. However, little is known regarding the physicochemical properties of C. sinensis teguments. In this study, a novel 20.6-kDa tegumental protein of the C. sinensis adult worm (CsTegu20.6) was identified and characterized by molecular and in silico methods. The complete coding sequence of 525 bp was derived from cDNA clones and encodes a protein of 175 amino acids. Homology search using BLASTX showed CsTegu20.6 identity ranging from 29% to 39% with previously-known tegumental proteins in C. sinensis. Domain analysis indicated the presence of a calcium-binding EF-hand domain containing a basic helix-loop-helix structure and a dynein light chain domain exhibiting a ferredoxin fold. We used a modified method to obtain the accurate tertiary structure of the CsTegu20.6 protein because of the unavailability of appropriate templates. The CsTegu20.6 protein sequence was split into two domains based on the disordered region, and then, the structure of each domain was modeled using I-TASSER. A final full-length structure was obtained by combining two structures and refining the whole structure. A refined CsTegu20.6 structure was used to identify a potential CsTegu20.6 inhibitor based on protein structure-compound interaction analysis. The recombinant proteins were expressed in Escherichia coli and purified by nickel-nitrilotriacetic acid affinity chromatography. In C. sinensis, CsTegu20.6 mRNAs were abundant in adult and metacercariae, but not in the egg. Immunohistochemistry revealed that CsTegu20.6 localized to the surface of the tegument in the adult fluke. Collectively, our results contribute to a better understanding of the structural and functional characteristics of CsTegu20.6 and homologs of flukes. One compound is proposed as a putative inhibitor of CsTegu20.6 to facilitate further studies for anthelmintics.","corpus_id":22530851,"score":2},{"doc_id":"28496122","title":"Structural insights into a 20.8-kDa tegumental-allergen-like (TAL) protein from Clonorchis sinensis.","abstract":"Survival of Clonorchis sinensis, a cause of human clonorchiasis, requires tegument proteins, which are localized to the tegumental outer surface membrane. These proteins play an important role in a host response and parasite survival. Thus, these proteins are interesting molecular targets for vaccine and drug development. Here, we have determined two crystal structures of the calmodulin like domain (amino acid [aa] positions 1-81) and dynein light chain (DLC)-like domain (aa 83-177) of a 20.8-kDa tegumental-allergen-like protein from Clonorchis sinensis (CsTAL3). The calmodulin like domain has two Ca(2+)-binding sites (named CB1 and CB2), but Ca(2+) binds to only one site, CB1. The DLC-like domain has a dimeric conformation; the interface is formed mainly by hydrogen bonds between the main chain atoms. In addition, we have determined full-length structure of CsTAL3 in solution and showed the conformational change of CsTAL3 induced by Ca(2+) ion binding using small-angle X-ray scattering analysis and molecular dynamics simulations. The Ca(2+)-bound form has a more extended conformation than the Ca(2+)-free from does. These structural and biochemical analyses will advance the understanding of the biology of this liver fluke and may contribute to our understanding of the molecular mechanism of calcium-responsive and tegumental-allergen-like proteins.","corpus_id":11559130,"score":2},{"doc_id":"18031748","title":"Human fascioliasis and the presence of hybrid/introgressed forms of Fasciola hepatica and Fasciola gigantica in Vietnam.","abstract":"The two species common of liver fluke, Fasciola hepatica and Fasciola gigantica, cause human fascioliasis. Hybrids between these species, and introgressed forms of Fasciola, are known from temperate and subtropical regions of eastern Asia. Here, we report the presence of hybrid and/or introgressed liver flukes in Vietnam where it has recently been recognised that human fascioliasis is an important zoonotic disease. Specimens examined came from domestic stock (cattle and buffalo) at slaughter and also from human patients. DNA sequences were obtained from the nuclear ribosomal second internal transcribed spacer (ITS-2) and from portions of two mitochondrial protein-coding genes. Mitochondrial sequences in every case were similar to those of Fasciola gigantica. Nuclear ITS-2 sequences belonged to one or other of the Fasciola species, or, sequences from both were found in the same individual worm. This study extends the known range of hybrids or introgressed forms of Fasciola into tropical regions of Asia.","corpus_id":41832791,"score":1},{"doc_id":"18160404","title":"Structural and functional relationships in the virulence-associated cathepsin L proteases of the parasitic liver fluke, Fasciola hepatica.","abstract":"The helminth parasite Fasciola hepatica secretes cysteine proteases to facilitate tissue invasion, migration, and development within the mammalian host. The major proteases cathepsin L1 (FheCL1) and cathepsin L2 (FheCL2) were recombinantly produced and biochemically characterized. By using site-directed mutagenesis, we show that residues at position 67 and 205, which lie within the S2 pocket of the active site, are critical in determining the substrate and inhibitor specificity. FheCL1 exhibits a broader specificity and a higher substrate turnover rate compared with FheCL2. However, FheCL2 can efficiently cleave substrates with a Pro in the P2 position and degrade collagen within the triple helices at physiological pH, an activity that among cysteine proteases has only been reported for human cathepsin K. The 1.4-A three-dimensional structure of the FheCL1 was determined by x-ray crystallography, and the three-dimensional structure of FheCL2 was constructed via homology-based modeling. Analysis and comparison of these structures and our biochemical data with those of human cathepsins L and K provided an interpretation of the substrate-recognition mechanisms of these major parasite proteases. Furthermore, our studies suggest that a configuration involving residue 67 and the \"gatekeeper\" residues 157 and 158 situated at the entrance of the active site pocket create a topology that endows FheCL2 with its unusual collagenolytic activity. The emergence of a specialized collagenolytic function in Fasciola likely contributes to the success of this tissue-invasive parasite.","corpus_id":25829733,"score":1},{"doc_id":"18190913","title":"Fasciola hepatica and Fasciola gigantica: cloning and characterisation of 70 kDa heat-shock proteins reveals variation in HSP70 gene expression between parasite species recovered from sheep.","abstract":"Fasciola hepatica and Fasciola gigantica are trematode parasites responsible for fasciolosis, a disease of ruminant animals which is also increasingly recognised as a disease in humans. By biochemical and in silico methods, we have cloned and characterised the 70 kDa heat-shock proteins (HSP70s) of F. hepatica and F. gigantica. The nucleotide and protein sequences for HSP70 were found to be 98% and 99% identical between liver fluke species, respectively, and to encode conserved amino acid motifs that are of putative functional importance. Western blot analysis demonstrated that HSP70 proteins were expressed at a higher level in F. gigantica recovered from sheep relative to F. hepatica, but HSP70 was not detected in the excretory-secretory products of these liver fluke samples. Real-time reverse-transcriptase PCR analysis of HSP70 expression in parasites from sheep, but not cattle, showed HSP70 expression to be higher in F. gigantica than F. hepatica. These results suggest that hosts refractory to F. gigantica are associated with higher HSP70 expression by this parasite and that HSP70 expression may represent a biochemical marker of the stress response of F. gigantica.","corpus_id":10389393,"score":1},{"doc_id":"18237745","title":"The crystal structure of plant-specific calcium-binding protein AtCBL2 in complex with the regulatory domain of AtCIPK14.","abstract":"Calcium signals mediate a multitude of plant responses to external stimuli. Calcineurin B-like (CBL) proteins and their target kinases, CBL-interacting protein kinases (CIPKs), represent important relays in plant calcium signaling. CBL interacts with CIPK through a conserved motif (NAF/FISL motif) within the C-terminal regulatory domain. To better understand the functional role of the CBL-CIPK system, we determined the crystal structure of AtCBL2 in complex with the regulatory domain of AtCIPK14 at 1.2 A resolution. The NAF/FISL motif is inserted into a hydrophobic crevice within AtCBL2, accompanied by a large displacement of the helices and loop on the opposite side of the NAF/FISL motif from the C-terminal region, which shields the hydrophobic crevice in free form. Ca(2+) are coordinated within four EF hands in AtCBL2 in bound form. This calcium coordination pattern differs from that in the structure of the SOS3-SOS2 complex previously reported. Structural comparison of the two structures shows that the recognition of CBL by CIPK is performed in a similar manner, but inherent interactions confer binding affinity and specificity.","corpus_id":44426665,"score":1},{"doc_id":"18612418","title":"Development of functional genomic tools in trematodes: RNA interference and luciferase reporter gene activity in Fasciola hepatica.","abstract":"The growing availability of sequence information from diverse parasites through genomic and transcriptomic projects offer new opportunities for the identification of key mediators in the parasite-host interaction. Functional genomics approaches and methods for the manipulation of genes are essential tools for deciphering the roles of genes and to identify new intervention targets in parasites. Exciting advances in functional genomics for parasitic helminths are starting to occur, with transgene expression and RNA interference (RNAi) reported in several species of nematodes, but the area is still in its infancy in flatworms, with reports in just three species. While advancing in model organisms, there is a need to rapidly extend these technologies to other parasites responsible for several chronic diseases of humans and cattle. In order to extend these approaches to less well studied parasitic worms, we developed a test method for the presence of a viable RNAi pathway by silencing the exogenous reporter gene, firefly luciferase (fLUC). We established the method in the human blood fluke Schistosoma mansoni and then confirmed its utility in the liver fluke Fasciola hepatica. We transformed newly excysted juveniles of F. hepatica by electroporation with mRNA of fLUC and three hours later were able to detect luciferase enzyme activity, concentrated mainly in the digestive ceca. Subsequently, we tested the presence of an active RNAi pathway in F. hepatica by knocking down the exogenous luciferase activity by introduction into the transformed parasites of double-stranded RNA (dsRNA) specific for fLUC. In addition, we tested the RNAi pathway targeting an endogenous F. hepatica gene encoding leucine aminopeptidase (FhLAP), and observed a significant reduction in specific mRNA levels. In summary, these studies demonstrated the utility of RNAi targeting reporter fLUC as a reporter gene assay to establish the presence of an intact RNAi pathway in helminth parasites. These could facilitate the study of gene function and the identification of relevant targets for intervention in organisms that are by other means intractable. More specifically, these results open new perspectives for functional genomics of F. hepatica, which hopefully can lead to the development of new interventions for fascioliasis.","corpus_id":15936304,"score":1},{"doc_id":"18620002","title":"The Fasciola hepatica thioredoxin: High resolution structure reveals two oxidation states.","abstract":"The Fasciola hepatica thioredoxin protein structure has been determined to 1.45A resolution. This is the first example of a single crystal structure to show the active site cysteine residues in both the reduced and disulfide oxidised form. Consistent with this observation the process of oxidation appears to require very little rearrangement of the surrounding protein structure. The F. hepatica thioredoxin structure has been compared to other thioredoxin protein structures already known and is found to be highly conserved. The F. hepatica protein is most similar to that of the thioredoxin from its human and animal hosts but it resembles other parasitic thioredoxins with regard to having no additional cysteine residues and is therefore not regulated by transient disulfide bond formation as proposed for thioredoxins from higher eukaryotic species.","corpus_id":43847142,"score":1},{"doc_id":"18775726","title":"Crystal-structure and biochemical characterization of recombinant human calcyphosine delineates a novel EF-hand-containing protein family.","abstract":"Calcyphosine is an EF-hand protein involved in both Ca(2+)-phosphatidylinositol and cyclic AMP signal cascades, as well as in other cellular functions. The crystal structure of Ca(2+)-loaded calcyphosine was determined up to 2.65 A resolution and reveals a protein containing two pairs of Ca(2+)-binding EF-hand motifs. Calcyphosine shares a highly similar overall topology with calmodulin. However, there are striking differences between EF-hand 4, both N-terminal and C-terminal regions, and interdomain linkers. The C-terminal domain of calcyphosine possesses a large hydrophobic pocket in the presence of calcium ions that might be implicated in ligand binding, while its N-terminal hydrophobic pocket is almost shielded by an additional terminal helix. Calcyphosine is largely monomeric, regardless of the presence of Ca(2+). Differences in structure, oligomeric state in the presence and in the absence of Ca(2+), a highly conserved sequence with low similarity to other proteins, and phylogeny define a new EF-hand-containing family of calcyphosine proteins that extends from arthropods to humans.","corpus_id":18129251,"score":1},{"doc_id":"18948118","title":"The interplay of ligand binding and quaternary structure in the diverse interactions of dynein light chain LC8.","abstract":"Dynein light chain LC8 is a small, dimeric, and very highly conserved globular protein that is an integral part of the dynein and myosin molecular motors but appears to have a broader role in multiple protein complexes unrelated to molecular motors. LC8 binds to two families of targets: those having a KXTQT sequence fingerprint and those having a GIQVD fingerprint. All known LC8 binding partners containing these fingerprints share a common binding site on LC8 that raises the question of what determines binding specificity. Here, we present the crystal structure of apo-LC8 at 1.7-A resolution, which, when compared with the crystal structures of several LC8 complexes, gives insight into the mechanism underlying the binding diversity of LC8. Peptide binding is associated with a shift in quaternary structure that expands the hydrophobic binding surface available to the ligand, in addition to changes in tertiary structure and ordering of LC8 around the binding groove. The observed quaternary shift suggests a mechanism by which binding at one of the two identical sites can influence binding at the other. NMR spectra of titrations with peptides from each fingerprint family show evidence of allosteric interaction between the two binding sites, to a differing degree in the two ligand families. Allosteric interaction between the binding sites may be a mechanism to promote simultaneous binding of ligands from the same family, providing a physiological role for the two fingerprints.","corpus_id":20840777,"score":1},{"doc_id":"19443417","title":"An integrated transcriptomics and proteomics analysis of the secretome of the helminth pathogen Fasciola hepatica: proteins associated with invasion and infection of the mammalian host.","abstract":"To infect their mammalian hosts, Fasciola hepatica larvae must penetrate and traverse the intestinal wall of the duodenum, move through the peritoneum, and penetrate the liver. After migrating through and feeding on the liver, causing extensive tissue damage, the parasites move to their final niche in the bile ducts where they mature and produce eggs. Here we integrated a transcriptomics and proteomics approach to profile Fasciola secretory proteins that are involved in host-pathogen interactions and to correlate changes in their expression with the migration of the parasite. Prediction of F. hepatica secretory proteins from 14,031 expressed sequence tags (ESTs) available from the Wellcome Trust Sanger Centre using the semiautomated EST2Secretome pipeline showed that the major components of adult parasite secretions are proteolytic enzymes including cathepsin L, cathepsin B, and asparaginyl endopeptidase cysteine proteases as well as novel trypsin-like serine proteases and carboxypeptidases. Proteomics analysis of proteins secreted by infective larvae, immature flukes, and adult F. hepatica showed that these proteases are developmentally regulated and correlate with the passage of the parasite through host tissues and its encounters with different host macromolecules. Proteases such as FhCL3 and cathepsin B have specific functions in larvae activation and intestinal wall penetration, whereas FhCL1, FhCL2, and FhCL5 are required for liver penetration and tissue and blood feeding. Besides proteases, the parasites secrete an array of antioxidants that are also highly regulated according to their migration through host tissues. However, whereas the proteases of F. hepatica are secreted into the parasite gut via a classical endoplasmic reticulum/Golgi pathway, we speculate that the antioxidants, which all lack a signal sequence, are released via a non-classical trans-tegumental pathway.","corpus_id":3715533,"score":1},{"doc_id":"20006979","title":"Elucidating the transcriptome of Fasciola hepatica - a key to fundamental and biotechnological discoveries for a neglected parasite.","abstract":"Liver flukes of animals are parasitic flatworms (Platyhelminthes: Digenea) of major socioeconomic importance in many countries. Key representatives, such as Fasciola hepatica and F. gigantica, cause \"liver fluke disease\" (= fascioliasis), which is of major animal health significance worldwide. In particular, F. hepatica is a leading cause of production losses to the livestock (mainly sheep and cattle) and meat industries due to clinical disease, reduced weight gain and milk production, and deaths. This parasite is also a major food-borne pathogen of humans throughout parts of the Middle East, Asia and South America. Currently, there is a significant focus on the development of new approaches for the prevention and control of fascioliasis in livestock. Recent technological advances in genomics and bioinformatics provide unique opportunities for the identification and prevalidation of drug targets and vaccines through a better understanding of the biology of F. hepatica and related species as well as their relationship with their hosts at the molecular level. Surprisingly, despite the widespread socioeconomic impact of fascioliasis, genomic datasets for F. hepatica are scant, limiting the molecular biological research of this parasite. The present article explores specifically the transcriptome of the adult stage of F. hepatica using an integrated genomic-bioinformatic platform. The analysis of the current data reveals numerous molecules of biological relevance, some of which are inferred to be involved in key biological processes or pathways that could serve as targets for new trematocidal drugs or vaccines. Improved insights into the transcriptome of F. hepatica should pave the way for future, comparative analysis of the transcriptomes of other developmental stages of this and related parasites, such as F. gigantica, cancer-causing flatworms (Clonorchis sinensis and Opisthorchis viverrini) and blood flukes (Schistosoma mansoni and S. japonicum). Prediction of the essentiality of genes and their products, molecular network connectivity of trematode genes as well as experimental exploration of function should also add value to the genomic discovery efforts in the future, focused on biotechnological outcomes.","corpus_id":206179664,"score":1},{"doc_id":"20089359","title":"Proteomic analysis of embryonic Fasciola hepatica: characterization and antigenic potential of a developmentally regulated heat shock protein.","abstract":"Fasciola hepatica is responsible for human disease and economic livestock loss on a global scale. We report the first post-genomic investigation of cellular proteins expressed by embryonic F. hepatica via two-dimensional electrophoresis, image analysis and tandem mass spectrometry. Antioxidant proteins and protein chaperones are prominently expressed by embryonic F. hepatica. Molecular differences between the egg and other characterized F. hepatica lifecycle stages were noted. Furthermore, proteins expressed within liver fluke eggs differ to those isolated from the well-characterized eggs of the human blood flatworm Schistosoma mansoni were revealed. Plasticity in expression of major proteins, particularly a prominently expressed 65kDa protein cluster was seen between natural populations of embryonating F. hepatica eggs suggesting that liver fluke embryogenisis is a plastic process. Immunoblotting revealed that the abundant 65kDa protein cluster is recognised by infection sera from three F. hepatica challenged host species. Mass spectrometry and BLAST analyses demonstrated that the 65kDa antigen shows homology to egg antigens of other flatworm parasites, and is represented in a F. hepatica EST database constructed from adult fluke transcripts. EST clones encoding the egg antigen were re-sequenced, predicting two forms of the protein. Four clones predict a 312 aa polypeptide, three clones encode a putative 110 amino acid extension at the N-terminus which may be involved in protein secretion, although this extension was not expressed by natively extracted proteins. Consistent expression of alpha crystallin domains confirmed the protein to be a member of the alpha crystallin containing small heat shock protein (AC/sHSP) superfamily. AC/sHSPs are ubiquitous in nature, however, this is the first time a member of this protein superfamily has been described from F. hepatica. The antigenic AC/sHSP was named Fh-HSP35alpha based on predictions of molecular weight. Production of recombinant Fh-HSP35alpha reveals considerable mass discrepancy between native and recombinant proteins, although descriptions of other characterized flatworm AC/sHSPs, suggest that the native form is a dimer. Immunoblot analyses confirm that the recombinant protein is recognised by F. hepatica challenged hosts, but does not react with sera from non-infected animals. We discuss the potential of recombinant Fh-HSP35alpha as an egg-based diagnostic marker for liver fluke infection.","corpus_id":25029074,"score":1},{"doc_id":"20374642","title":"Survey of transcripts expressed by the invasive juvenile stage of the liver fluke Fasciola hepatica.","abstract":"BACKGROUND: The common liver fluke Fasciola hepatica is the agent of a zoonosis with significant economic consequences in livestock production worldwide, and increasing relevance to human health in developing countries. Although flukicidal drugs are available, re-infection and emerging resistance are demanding new efficient and inexpensive control strategies. Understanding the molecular mechanisms underlying the host-parasite interaction provide relevant clues in this search, while enlightening the physiological adaptations to parasitism. Genomics and transcriptomics are still in their infancy in F. hepatica, with very scarce information available from the invasive newly excysted juveniles (NEJ). Here we provide an initial glimpse to the transcriptomics of the NEJ, the first stage to interact with the mammalian host. RESULTS: We catalogued more than 500 clusters generated from the analysis of F. hepatica juvenile expressed sequence tags (EST), several of them not detected in the adult stage. A set of putative F. hepatica specific transcripts, and a group of sequences conserved exclusively in flatworms were identified. These novel sequences along with a set of parasite transcripts absent in the host genomes are putative new targets for future anti-parasitic drugs or vaccine development. Comparisons of the F. hepatica sequences with other metazoans genomes or EST databases were consistent with the basal positioning of flatworms in the bilaterian phylogeny. Notably, GC content, codon usage and amino acid frequencies are remarkably different in Schistosomes to F. hepatica and other trematodes. Functional annotation of predicted proteins showed a general representation of diverse biological functions. Besides proteases and antioxidant enzymes expected to participate in the early interaction with the host, various proteins involved in gene expression, protein synthesis, cell signaling and mitochondrial enzymes were identified. Differential expression of secreted protease gene family members between juvenile and adult stages may respond to different needs during host colonization. CONCLUSION: The knowledge of the genes expressed by the invasive stage of Fasciola hepatica is a starting point to unravel key aspects of this parasite's biology. The integration of the emerging transcriptomics, and proteomics data and the advent of functional genomics tools in this organism are positioning F. hepatica as an interesting model for trematode biology.","corpus_id":13863138,"score":1},{"doc_id":"21766237","title":"Effect of Fasciola hepatica proteins on the functioning of rat hepatocytes.","abstract":"Fasciolosis is a hepatic parasitic infection that affects many mammal species and creates a great economic and veterinary problem. Molecular mechanisms of parasite-hepatocyte interactions have not been precisely characterized yet. Therefore, the aim of the study was to investigate alterations in the metabolic activity of rat liver cells exposed to Fasciola hepatica somatic proteins. Hepatocytes were incubated with 0-1 mg/ml of fluke's somatic proteins for various periods of time. Afterward, changes in hepatocytes metabolic activity were determined with MTT and enzyme leakage tests. Hepatocytes' capacity to synthesize albumin was also investigated. It was observed that protein concentration, as well as longevity of their action, influenced metabolic activity of rat liver cells. Diminution of hepatocytes survival rate, an increase in enzyme leakage and altered synthetic capacity after treatment with parasite's proteins were reported. It is concluded that somatic proteins of F. hepatica may play an important role in liver cell damaging.","corpus_id":17281291,"score":1},{"doc_id":"21782972","title":"Cloning, expression, and characterization of a novel Opisthorchis viverrini calcium-binding EF-hand protein.","abstract":"A novel 22.8 kDa of Opisthorchis viverrini (Ov) calcium-binding EF-hand protein (Ov CaBP) was identified and isolated from an immunoscreening of the adult stage Ov cDNA library by using a human cholangiocarcinoma (CCA) serum. This protein was related to other calcium-binding proteins and conserved among the trematodes. Ov CaBP shared 98% amino acid identity to 22.8 kDa of Clonorchis sinensis CaBP and both were classified as a new group of CaBP EF-hand protein by multiple sequence alignment and phylogenetic tree analysis. The open reading frame of Ov CaBP was 585 bp which encoded for 194 amino acids. The N-terminal part is composed of two calcium-binding EF-hand motifs whereas the C-terminal part contains a dynein light chain motif (DLC). In addition, transcription analysis by RT-PCR revealed that it was constitutively transcribed in all stages, including metacercariae, juvenile, and adult. Furthermore, recombinant Ov CaBP protein (rOv CaBP) was expressed as a soluble protein and antibody generated against this rOv CaBP protein was capable of detecting Ov CaBP in the Ov somatic extracts but not in Ov ES products. This anti-rOv CaBP serum was also used to localize Ov CaBP in Ov infected hamster's liver sections which the distribution of Ov CaBP was located in gut epithelium, miracidia in eggs and slightly in parenchyma. Moreover, rOv CaBP protein showed a calcium-binding property in non-denaturing gel mobility shift assay.","corpus_id":24096855,"score":1},{"doc_id":"21920370","title":"Crystal structure of cardiac troponin C regulatory domain in complex with cadmium and deoxycholic acid reveals novel conformation.","abstract":"The amino-terminal regulatory domain of cardiac troponin C (cNTnC) plays an important role as the calcium sensor for the troponin complex. Calcium binding to cNTnC results in conformational changes that trigger a cascade of events that lead to cardiac muscle contraction. The cardiac N-terminal domain of TnC consists of two EF-hand calcium binding motifs, one of which is dysfunctional in binding calcium. Nevertheless, the defunct EF-hand still maintains a role in cNTnC function. For its structural analysis by X-ray crystallography, human cNTnC with the wild-type primary sequence was crystallized under a novel crystallization condition. The crystal structure was solved by the single-wavelength anomalous dispersion method and refined to 2.2 Å resolution. The structure displays several novel features. Firstly, both EF-hand motifs coordinate cadmium ions derived from the crystallization milieu. Secondly, the ion coordination in the defunct EF-hand motif accompanies unusual changes in the protein conformation. Thirdly, deoxycholic acid, also derived from the crystallization milieu, is bound in the central hydrophobic cavity. This is reminiscent of the interactions observed for cardiac calcium sensitizer drugs that bind to the same core region and maintain the \"open\" conformational state of calcium-bound cNTnC. The cadmium ion coordination in the defunct EF-hand indicates that this vestigial calcium binding site retains the structural and functional elements that allow it to coordinate a cadmium ion. However, it is a result of, or concomitant with, large and unusual structural changes in cNTnC.","corpus_id":6629342,"score":1},{"doc_id":"22015384","title":"Identification and characterization of a novel 21.6-kDa tegumental protein from Clonorchis sinensis.","abstract":"Tegumental proteins form a membrane-bound outer surface and are thus involved in host-parasite interactions and parasite survival. A complementary DNA clone encoding a novel 21.6-kDa tegumental protein (CsTegu21.6, accession number JF911532) was identified in a sequence library for the adult Clonorchis sinensis liver fluke. The complete coding sequence was 564 bp and encoded a protein of 188 amino acids. A BLASTX search revealed identities from 43 to 47% with previously identified tegumental proteins in C. sinensis and other helminthic parasites. Multiple alignment of the amino acids of CsTegu21.6 with those of four other C. sinensis tegumental proteins, CsTegu21.1, CsTegu22.3, CsTegu20.8 and CsTegu31.8, revealed pair-wise sequence identities ranging from 24 to 31.8%. A calcium-binding EF-hand domain containing a basic helix-loop-helix structure at the N terminus and a dynein light chain domain at the C terminus were found in CsTegu21.6; these motifs are common in tegumental proteins. CsTegu21.6 was specifically observed on the tegument of adult worms using immunolocalization analysis.","corpus_id":15730390,"score":1},{"doc_id":"22240114","title":"Characterization and differential expression of a ferritin protein from Fasciola hepatica.","abstract":"Ferritins are proteins that play a central role in maintaining intracellular iron balance. A cDNA clone of Fasciola hepatica (687 bp long) encoding a putative 228-amino acid polypeptide (FhFtn-1) homologous with ferritins of vertebrates and invertebrates was identified. FhFtn-1 contains a conserved motif of the ferroxidase center typical of vertebrate ferritins. Phylogenetic tree analysis showed that FhFtn-1 clusters with two ferritins of Paragonimus westermani, which suggests a common ancestry for the ferritins of these two trematodes. Recombinant FhFtn-1 protein expressed and purified from an Escherichia coli system showed iron-uptake ability. Moreover, FhFtn-1 showed strong reactivity with sera from rabbits infected with F. hepatica for 2-12 weeks, which suggests that this protein could be a potential antigen for immunodiagnosis of fascioliasis. qPCR analysis demonstrated that FhFtn-1-mRNA is expressed at significantly higher levels in adults and unembryonated eggs than in juveniles or miracidia. These results represent the first characterization of a ferritin protein from the liver fluke F. hepatica.","corpus_id":33515370,"score":1},{"doc_id":"22727910","title":"A novel calmodulin-like protein from the liver fluke, Fasciola hepatica.","abstract":"An 18.2 kDa protein from the liver fluke, Fasciola hepatica has been identified and characterised. The protein shows strongest sequence similarity to egg antigen proteins from Schistosoma mansoni, Schistosoma japonicum and Clonorchis sinensis. The protein is predicted to adopt a calmodulin-like fold; it thus represents the third calmodulin-like protein to be characterised in F. hepatica and has been named FhCaM3. Compared to the classical calmodulin structure there are some variations. Most noticeably, the central, linker helix is disrupted by a cysteine residue. Alkaline native gel electrophoresis showed that FhCaM3 binds calcium ions. This binding event increases the ability of the protein to bind the hydrophobic fluorescent probe 8-anilinonaphthalene-1-sulphonate, consistent with an increase in surface hydrophobicity as seen in other calmodulins. FhCaM3 binds to the calmodulin antagonists trifluoperazine and W7, but not to the myosin regulatory light chain binding compound praziquantel. Immunolocalisation demonstrated that the protein is found in eggs and vitelline cells. Given the critical role of calcium ions in egg formation and hatching this suggests that FhCaM3 may play a role in calcium signalling in these processes. Consequently the antagonism of FhCaM3 may, potentially, offer a method for inhibiting egg production and thus reducing the spread of infection.","corpus_id":23927989,"score":1},{"doc_id":"22819963","title":"A plasma membrane Ca(2+)-ATPase (PMCA) from the liver fluke, Fasciola hepatica.","abstract":"Fasciolosis is a parasitic infection by the liver fluke Fasciola hepatica, which costs the global agricultural community over US $2 billion per year. Its prevalence is rising due to factors such as climate change and drug resistance. ATP-dependent membrane transporters are considered good potential drug targets as they are essential for cellular processes and are in an exposed, accessible position in the cell. Immunolocalisation studies demonstrated that a plasma membrane calcium ATPase (PMCA) was localised to the parenchymal tissue in F. hepatica. The coding sequence for a F. hepatica PMCA (FhPMCA) has been obtained. This sequence encodes a 1,163 amino acid protein which contains motifs which are commonly conserved in PMCAs. Molecular modelling predicted that the protein has 10 transmembrane segments which include a potential calcium ion binding site and phosphorylation motif. FhPMCA interacts with the calmodulin-like protein FhCaM1, but not the related proteins FhCaM2 or FhCaM3, in a calcium-ion dependent manner. This interaction occurs through a region in the C-terminal region of FhPMCA which most likely adopts an α-helical conformation. When FhPMCA was heterologously expressed in a budding yeast strain deleted for its PMCA (Pmc1p), it restored viability. Microsomes prepared from these yeast cells had calcium ion stimulated ATPase activity which was inhibited by the known PMCA inhibitors, bisphenol and eosin. The potential of FhPMCA as a new drug target is discussed.","corpus_id":26115371,"score":1},{"doc_id":"23770026","title":"Characterization and differential expression of cathepsin L3 alleles from Fasciola hepatica.","abstract":"Fasciola hepatica infections cause significant global problems in veterinary and human medicine, including causing huge losses in cattle and sheep production. F. hepatica host infection is a multistage process and flukes express papain-like cysteine proteases, termed cathepsins, which play pivotal roles in virulence through host entry, tissue migration and immune evasion. Expression of these proteases is developmentally regulated. Recent studies indicate that excystment of infective larvae is dependent on cysteine proteases and together FhCL3 and FhCB account for over 80% of total protease activity detectable in newly excysted juvenile (NEJ) fluke. This paper focuses on members of the cathepsin L gene family, specifically those belonging to the CL3 clade. The cDNA of two novel cathepsin L3 proteases--FhCL3-1 and FhCL3-2 were cloned. The mRNA transcript expression levels for these enzymes were significantly different at various time points in life development stages obtained in vitro, from dormant metacercariae to NEJ 24h after excystment. Maximum expression levels were observed in NEJ immediately after excystment. In all stages examined by Real Time PCR, FhCL3-2 was expressed at a higher level compared to FhCL3-1 which was expressed only at very low levels. Western blot and immunohistochemical analysis also indicated higher expression of the FhCL3-2 allele and its secretory nature. The ability of antibody responses from rats and sheep challenged with F. hepatica to recognize recombinant FhCL3-1 and FhCL3-2 was shown to differ. Differences were also confirmed through the use of anti-rFhCL3-1 and anti-rFhCL3-2 sera in Western blot analysis of juvenile excretory/secretory (ES) material separated by 2D electrophoresis. These results indicate analysis of relative expression of parasite virulence factors from different populations is required, as this will likely impact the effectiveness of vaccines based on these antigens.","corpus_id":37671585,"score":1},{"doc_id":"24566472","title":"Biochemical characterisation of glyceraldehyde 3-phosphate dehydrogenase (GAPDH) from the liver fluke, Fasciola hepatica.","abstract":"Glyceraldehyde 3-phosphate dehydrogenase (GAPDH) catalyses one of the two steps in glycolysis which generate the reduced coenzyme NADH. This reaction precedes the two ATP generating steps. Thus, inhibition of GAPDH will lead to substantially reduced energy generation. Consequently, there has been considerable interest in developing GAPDH inhibitors as anti-cancer and anti-parasitic agents. Here, we describe the biochemical characterisation of GAPDH from the common liver fluke Fasciola hepatica (FhGAPDH). The primary sequence of FhGAPDH is similar to that from other trematodes and the predicted structure shows high similarity to those from other animals including the mammalian hosts. FhGAPDH lacks a binding pocket which has been exploited in the design of novel antitrypanosomal compounds. The protein can be expressed in, and purified from Escherichia coli; the recombinant protein was active and showed no cooperativity towards glyceraldehyde 3-phosphate as a substrate. In the absence of ligands, FhGAPDH was a mixture of homodimers and tetramers, as judged by protein-protein crosslinking and analytical gel filtration. The addition of either NAD⁺ or glyceraldehyde 3-phosphate shifted this equilibrium towards a compact dimer. Thermal scanning fluorimetry demonstrated that this form was considerably more stable than the unliganded one. These responses to ligand binding differ from those seen in mammalian enzymes. These differences could be exploited in the discovery of reagents which selectively disrupt the function of FhGAPDH.","corpus_id":11247617,"score":1},{"doc_id":"24680784","title":"A structural analysis of the AAA+ domains in Saccharomyces cerevisiae cytoplasmic dynein.","abstract":"Dyneins are large protein complexes that act as microtubule based molecular motors. The dynein heavy chain contains a motor domain which is a member of the AAA+ protein family (ATPases Associated with diverse cellular Activities). Proteins of the AAA+ family show a diverse range of functionalities, but share a related core AAA+ domain, which often assembles into hexameric rings. Dynein is unusual because it has all six AAA+ domains linked together, in one long polypeptide. The dynein motor domain generates movement by coupling ATP driven conformational changes in the AAA+ ring to the swing of a motile element called the linker. Dynein binds to its microtubule track via a long antiparallel coiled-coil stalk that emanates from the AAA+ ring. Recently the first high resolution structures of the dynein motor domain were published. Here we provide a detailed structural analysis of the six AAA+ domains using our Saccharomycescerevisiae crystal structure. We describe how structural similarities in the dynein AAA+ domains suggest they share a common evolutionary origin. We analyse how the different AAA+ domains have diverged from each other. We discuss how this is related to the function of dynein as a motor protein and how the AAA+ domains of dynein compare to those of other AAA+ proteins.","corpus_id":12086629,"score":1},{"doc_id":"24733753","title":"Generating a detailed protein profile of Fasciola hepatica during the chronic stage of infection in cattle.","abstract":"Fasciola hepatica is a trematode helminth causing a damaging disease, fasciolosis, in ruminants and humans. Comprehensive proteomic studies broaden our knowledge of the parasite's protein profile, and provide new insights into the development of more effective strategies to deal with fasciolosis. The objective of this study was to generate a comprehensive profile of F. hepatica proteins expressed during the chronic stage of infection in cattle by building on previous efforts in this area. The approach included an improved sample preparation procedure for surface and internal layers of the parasite, the application of nano-UPLC-ESI-qTOF-MS (nano-ultra-performance LC and ESI quadrupole TOF MS) integrated with different acquisition methods and in silico database search against various protein databases and a transcript database including a new assembly of publically available EST. Of a total of 776 identified proteins, 206 and 332 were specific to the surface and internal layers of the parasite, respectively. Furthermore, 238 proteins were common to both layers, with comparative differences of 172 proteins detected. Specific proteins not previously identified in F. hepatica, but shown to be immunomodulatory or potential drug targets for other parasites, are discussed.","corpus_id":24946104,"score":1},{"doc_id":"25225247","title":"Fasciola hepatica fatty acid binding protein induces the alternative activation of human macrophages.","abstract":"The liver fluke Fasciola hepatica is a highly evolved parasite that uses sophisticated mechanisms to evade the host immune response. The immunosuppressive capabilities of the parasite have been associated with antigens secreted through the parasite's tegument, called excretory-secretory products (ESPs). Proteomic studies have identified the fatty acid binding protein (FABP) as one of molecules present in the parasite ESPs. Although FABP has been investigated for potential use in the development of vaccines against fascioliasis, its direct interaction with cells of immune system has not been studied. In this study, FABP was purified in native form from soluble extracts of F. hepatica adult flukes using a combination of molecular sieving chromatography and preparative isoelectric focusing. The immunological effect of the purified protein, termed Fh12, was assayed in vitro using monocyte-derived macrophages (MDM) obtained from healthy human donors. Results from the assay indicate that Fh12 produced a significantly increased arginase expression and activity and induced the expression of chitinase-3-like protein (CHI3L1). The assay also showed that Fh12 downregulated the production of nitric oxide (NO) and the expression of nitric oxide synthase (NOS2). This indicates that Fh12 induced the production of alternatively activated macrophages (AAMϕ). The results also demonstrated the ability of Fh12 to downregulate the secretion of the proinflammatory and inflammatory cytokines tumor necrosis factor alpha (TNF-α), interleukin-12 (IL-12), and IL-1βB, even after stimulation with lipopolysaccharide (LPS), as well as its ability to stimulate the overexpression of IL-10. These results suggest a potent anti-inflammatory role for Fh12, which could occur via targeting of Toll-like receptor 4 (TLR4).","corpus_id":35747966,"score":1},{"doc_id":"25272277","title":"A Ras-like domain in the light intermediate chain bridges the dynein motor to a cargo-binding region.","abstract":"Cytoplasmic dynein, a microtubule-based motor protein, transports many intracellular cargos by means of its light intermediate chain (LIC). In this study, we have determined the crystal structure of the conserved LIC domain, which binds the motor heavy chain, from a thermophilic fungus. We show that the LIC has a Ras-like fold with insertions that distinguish it from Ras and other previously described G proteins. Despite having a G protein fold, the fungal LIC has lost its ability to bind nucleotide, while the human LIC1 binds GDP preferentially over GTP. We show that the LIC G domain binds the dynein heavy chain using a conserved patch of aromatic residues, whereas the less conserved C-terminal domain binds several Rab effectors involved in membrane transport. These studies provide the first structural information and insight into the evolutionary origin of the LIC as well as revealing how this critical subunit connects the dynein motor to cargo.","corpus_id":18376103,"score":1},{"doc_id":"25312846","title":"DYNLL2 dynein light chain binds to an extended linear motif of myosin 5a tail that has structural plasticity.","abstract":"LC8 dynein light chains (DYNLL) are conserved homodimeric eukaryotic hub proteins that participate in diverse cellular processes. Among the binding partners of DYNLL2, myosin 5a (myo5a) is a motor protein involved in cargo transport. Here we provide a profound characterization of the DYNLL2 binding motif of myo5a in free and DYNLL2-bound form by using nuclear magnetic resonance spectroscopy, X-ray crystallography, and molecular dynamics simulations. In the free form, the DYNLL2 binding region, located in an intrinsically disordered domain of the myo5a tail, has a nascent helical character. The motif becomes structured and folds into a β-strand upon binding to DYNLL2. Despite differences of the myo5a sequence from the consensus binding motif, one peptide is accommodated in each of the parallel DYNLL2 binding grooves, as for all other known partners. Interestingly, while the core motif shows a similar interaction pattern in the binding groove as seen in other complexes, the flanking residues make several additional contacts, thereby lengthening the binding motif. The N-terminal extension folds back and partially blocks the free edge of the β-sheet formed by the binding motif itself. The C-terminal extension contacts the dimer interface and interacts with symmetry-related residues of the second myo5a peptide. The involvement of flanking residues of the core binding site of myo5a could modify the quaternary structure of the full-length myo5a and affect its biological functions. Our results deepen the knowledge of the diverse partner recognition of DYNLL proteins and provide an example of a Janus-faced linear motif.","corpus_id":6627026,"score":1},{"doc_id":"25450768","title":"Structure of the microtubule-binding domain of flagellar dynein.","abstract":"Flagellar dyneins are essential microtubule motors in eukaryotes, as they drive the beating motions of cilia and flagella. Unlike myosin and kinesin motors, the track binding mechanism of dyneins and the regulation between the strong and weak binding states remain obscure. Here we report the solution structure of the microtubule-binding domain of flagellar dynein-c/DHC9 (dynein-c MTBD). The structure reveals a similar overall helix-rich fold to that of the MTBD of cytoplasmic dynein (cytoplasmic MTBD), but dynein-c MTBD has an additional flap, consisting of an antiparallel b sheet. The flap is positively charged and highly flexible. Despite the structural similarity to cytoplasmic MTBD, dynein-c MTBD shows only a small change in the microtubule- binding affinity depending on the registry change of coiled coil-sliding, whereby lacks the apparent strong binding state. The surface charge distribution of dynein-c MTBD also differs from that of cytoplasmic MTBD, which suggests a difference in the microtubule-binding mechanism.","corpus_id":-1,"score":1},{"doc_id":"25879787","title":"TGF-β superfamily members from the helminth Fasciola hepatica show intrinsic effects on viability and development.","abstract":"The helminth Fasciola hepatica causes fasciolosis throughout the world, a major disease of livestock and an emerging zoonotic disease in humans. Sustainable control mechanisms such as vaccination are urgently required. To discover potential vaccine targets we undertook a genome screen to identify members of the transforming growth factor (TGF) family of proteins. Herein we describe the discovery of three ligands belonging to this superfamily and the cloning and characterisation of an activin/TGF like molecule we term FhTLM. FhTLM has a limited expression pattern both temporally across the parasite stages but also spatially within the worm. Furthermore, a recombinant form of this protein is able to enhance the rate (or magnitude) of multiple developmental processes of the parasite indicating a conserved role for this protein superfamily in the developmental biology of a major trematode parasite. Our study demonstrates for the first time the existence of this protein superfamily within F. hepatica and assigns a function to one of the three identified ligands. Moreover further exploration of this superfamily may yield future targets for diagnostic or vaccination purposes due to its stage restricted expression and functional role.","corpus_id":18584829,"score":1},{"doc_id":"27049013","title":"Current Threat of Triclabendazole Resistance in Fasciola hepatica.","abstract":"Triclabendazole (TCBZ) is the only chemical that kills early immature and adult Fasciola hepatica (liver fluke) but widespread resistance to the drug greatly compromises fluke control in livestock and humans. The mode of action of TCBZ and mechanism(s) underlying parasite resistance to the drug are not known. Due to the high prevalence of TCBZ resistance (TCBZ-R), effective management of drug resistance is now critical for sustainable livestock production. Here, we discuss the current status of TCBZ-R in F. hepatica, the global distribution of resistance observed in livestock, the possible mechanism(s) of drug action, the proposed mechanisms and genetic basis of resistance, and the prospects for future control of liver fluke infections using an integrated parasite management (IPM) approach.","corpus_id":3704331,"score":1},{"doc_id":"27466253","title":"Fasciola hepatica Surface Tegument: Glycoproteins at the Interface of Parasite and Host.","abstract":"Fasciola hepatica, commonly known as liver fluke, is a trematode that causes Fasciolosis in ruminants and humans. The outer tegumental coat of F. hepatica (FhTeg) is a complex metabolically active biological matrix that is continually exposed to the host immune system and therefore makes a good vaccine target. F. hepatica tegumental coat is highly glycosylated and helminth-derived immunogenic oligosaccharide motifs and glycoproteins are currently being investigated as novel vaccine candidates. This report presents the first systematic characterization of FhTeg glycosylation using lectin microarrays to characterize carbohydrates motifs present, and lectin histochemistry to localize these on the F. hepatica tegument. We discovered that FhTeg glycoproteins are predominantly oligomannose oligosaccharides that are expressed on the spines, suckers and tegumental coat of F. hepatica and lectin blot analysis confirmed the abundance of N- glycosylated proteins. Although some oligosaccharides are widely distributed on the fluke surface other subsets are restricted to distinct anatomical regions. We selectively enriched for FhTeg mannosylated glycoprotein subsets using lectin affinity chromatography and identified 369 proteins by mass spectrometric analysis. Among these proteins are a number of potential vaccine candidates with known immune modulatory properties including proteases, protease inhibitors, paramyosin, Venom Allergen-like II, Enolase and two proteins, nardilysin and TRIL, that have not been previously associated with F. hepatica Furthermore, we provide a comprehensive insight regarding the putative glycosylation of FhTeg components that could highlight the importance of further studies examining glycoconjugates in host-parasite interactions in the context of F. hepatica infection and the development of an effective vaccine.","corpus_id":10218556,"score":1},{"doc_id":"27864381","title":"Dynein light chain DLC-1 promotes localization and function of the PUF protein FBF-2 in germline progenitor cells.","abstract":"PUF family translational repressors are conserved developmental regulators, but the molecular function provided by the regions flanking the PUF RNA-binding domain is unknown. In C. elegans, the PUF proteins FBF-1 and FBF-2 support germline progenitor maintenance by repressing production of meiotic proteins and use distinct mechanisms to repress their target mRNAs. We identify dynein light chain DLC-1 as an important regulator of FBF-2 function. DLC-1 directly binds to FBF-2 outside of the RNA-binding domain and promotes FBF-2 localization and function. By contrast, DLC-1 does not interact with FBF-1 and does not contribute to FBF-1 activity. Surprisingly, we find that the contribution of DLC-1 to FBF-2 activity is independent of the dynein motor. Our findings suggest that PUF protein localization and activity are mediated by sequences flanking the RNA-binding domain that bind specific molecular partners. Furthermore, these results identify a new role for DLC-1 in post-transcriptional regulation of gene expression.","corpus_id":6288352,"score":1},{"doc_id":"27866265","title":"Proteomic analysis of Fasciola hepatica excretory and secretory products (FhESPs) involved in interacting with host PBMCs and cytokines by shotgun LC-MS/MS.","abstract":"Fasciola hepatica is a helminth parasite with a worldwide distribution, which can cause chronic liver disease, fasciolosis, leading to economic losses in the livestock and public health in many countries. Control is mostly reliant on the use of drugs, and as a result, drug resistance has now emerged. The identification of F. hepatica genes involved in interaction between the parasite and host immune system is utmost important to elucidate the evasion mechanisms of the parasite and develop more effective strategies against fasciolosis. In this study, we aimed to identify molecules in F. hepatica excretory and secretory products (FhESPs) interacting with the host peripheral blood mononuclear cells (PBMCs), Th1-like cytokines (IL2 and IFN-γ), and Th17-like cytokines (IL17) by Co-IP combined with tandem mass spectrometry. The results showed that 14, 16, and 9 proteins in FhESPs could bind with IL2, IL17, and IFN-γ, respectively, which indicated that adult F. hepatica may evade the host immune responses through directly interplaying with cytokines. In addition, nine proteins in FhESPs could adhere to PBMCs. Our findings provided potential targets as immuno-regulators, and will be helpful to elucidate the molecular basis of host-parasite interactions and search for new potential proteins as vaccine and drug target candidates.","corpus_id":22343498,"score":1},{"doc_id":"27940066","title":"Fasciola hepatica demonstrates high levels of genetic diversity, a lack of population structure and high gene flow: possible implications for drug resistance.","abstract":"Fasciola hepatica, the liver fluke, is a trematode parasite of considerable economic importance to the livestock industry and is a re-emerging zoonosis that poses a risk to human health in F. hepatica-endemic areas worldwide. Drug resistance is a substantial threat to the current and future control of F. hepatica, yet little is known about how the biology of the parasite influences the development and spread of resistance. Given that F. hepatica can self-fertilise and therefore inbreed, there is the potential for greater population differentiation and an increased likelihood of recessive alleles, such as drug resistance genes, coming together. This could be compounded by clonal expansion within the snail intermediate host and aggregation of parasites of the same genotype on pasture. Alternatively, widespread movement of animals that typically occurs in the UK could promote high levels of gene flow and prevent population differentiation. We identified clonal parasites with identical multilocus genotypes in 61% of hosts. Despite this, 84% of 1579 adult parasites had unique multilocus genotypes, which supports high levels of genotypic diversity within F. hepatica populations. Our analyses indicate a selfing rate no greater than 2%, suggesting that this diversity is in part due to the propensity for F. hepatica to cross-fertilise. Finally, although we identified high genetic diversity within a given host, there was little evidence for differentiation between populations from different hosts, indicating a single panmictic population. This implies that, once those emerge, anthelmintic resistance genes have the potential to spread rapidly through liver fluke populations.","corpus_id":19054145,"score":1},{"doc_id":"28060841","title":"Genomes of Fasciola hepatica from the Americas Reveal Colonization with Neorickettsia Endobacteria Related to the Agents of Potomac Horse and Human Sennetsu Fevers.","abstract":"Food borne trematodes (FBTs) are an assemblage of platyhelminth parasites transmitted through the food chain, four of which are recognized as neglected tropical diseases (NTDs). Fascioliasis stands out among the other NTDs due to its broad and significant impact on both human and animal health, as Fasciola sp., are also considered major pathogens of domesticated ruminants. Here we present a reference genome sequence of the common liver fluke, Fasciola hepatica isolated from sheep, complementing previously reported isolate from cattle. A total of 14,642 genes were predicted from the 1.14 GB genome of the liver fluke. Comparative genomics indicated that F. hepatica Oregon and related food-borne trematodes are metabolically less constrained than schistosomes and cestodes, taking advantage of the richer millieux offered by the hepatobiliary organs. Protease families differentially expanded between diverse trematodes may facilitate migration and survival within the heterogeneous environments and niches within the mammalian host. Surprisingly, the sequencing of Oregon and Uruguay F. hepatica isolates led to the first discovery of an endobacteria in this species. Two contigs from the F. hepatica Oregon assembly were joined to complete the 859,205 bp genome of a novel Neorickettsia endobacterium (nFh) closely related to the etiological agents of human Sennetsu and Potomac horse fevers. Immunohistochemical studies targeting a Neorickettsia surface protein found nFh in specific organs and tissues of the adult trematode including the female reproductive tract, eggs, the Mehlis' gland, seminal vesicle, and oral suckers, suggesting putative routes for fluke-to-fluke and fluke-to-host transmission. The genomes of F. hepatica and nFh will serve as a resource for further exploration of the biology of F. hepatica, and specifically its newly discovered trans-kingdom interaction with nFh and the impact of both species on disease in ruminants and humans.","corpus_id":3356027,"score":1},{"doc_id":"28348084","title":"Delineating distinct heme-scavenging and -binding functions of domains in MF6p/helminth defense molecule (HDM) proteins from parasitic flatworms.","abstract":"MF6p/FhHDM-1 is a small protein secreted by the parasitic flatworm (trematode) Fasciola hepatica that belongs to a broad family of heme-binding proteins (MF6p/helminth defense molecules (HDMs)). MF6p/HDMs are of interest for understanding heme homeostasis in trematodes and as potential targets for the development of new flukicides. Moreover, interest in these molecules has also increased because of their immunomodulatory properties. Here we have extended our previous findings on the mechanism of MF6p/HDM-heme interactions and mapped the protein regions required for heme binding and for other biological functions. Our data revealed that MF6p/FhHDM-1 forms high-molecular-weight complexes when associated with heme and that these complexes are reorganized by a stacking procedure to form fibril-like and granular nanostructures. Furthermore, we showed that MF6p/FhHDM-1 is a transitory heme-binding protein as protein·heme complexes can be disrupted by contact with an apoprotein (e.g. apomyoglobin) with higher affinity for heme. We also demonstrated that (i) the heme-binding region is located in the MF6p/FhHDM-1 C-terminal moiety, which also inhibits the peroxidase-like activity of heme, and (ii) MF6p/HDMs from other trematodes, such as Opisthorchis viverrini and Paragonimus westermani, also bind heme. Finally, we observed that the N-terminal, but not the C-terminal, moiety of MF6p/HDMs has a predicted structural analogy with cell-penetrating peptides and that both the entire protein and the peptide corresponding to the N-terminal moiety of MF6p/FhHDM-1 interact in vitro with cell membranes in hemin-preconditioned erythrocytes. Our findings suggest that MF6p/HDMs can transport heme in trematodes and thereby shield the parasite from the harmful effects of heme.","corpus_id":40844086,"score":1},{"doc_id":"29476869","title":"Advances in Fasciola hepatica research using 'omics' technologies.","abstract":"The liver fluke Fasciola hepatica is an economically important pathogen of livestock worldwide, as well as being an important neglected zoonosis. Parasite control is reliant on the use of drugs, particularly triclabendazole, which is effective against multiple parasite stages. However, the spread of parasites resistant to triclabendazole has intensified the pursuit for novel control strategies. Emerging 'omics' technologies are helping advance our understanding of liver fluke biology, specifically the molecules that act at the host-parasite interface and are central to infection, virulence and long-term survival within the definitive host. This review discusses the technological sequencing advances that have facilitated the unbiased analysis of liver fluke biology, resulting in an extensive range of 'omics' datasets. In addition, we highlight the 'omics' studies of host responses to F. hepatica infection that, when combined with the parasite datasets, provide the opportunity for integrated analyses of host-parasite interactions. These extensive datasets will form the foundation for future in-depth analysis of F. hepatica biology and development, and the search for new drug or vaccine interventions.","corpus_id":3693486,"score":1},{"doc_id":"29529855","title":"Comparative Characterization of Four Calcium-Binding EF Hand Proteins from Opisthorchis viverrini.","abstract":"Four isoforms of calcium binding proteins containing 2 EF hand motifs and a dynein light chain-like domain in the human liver fluke Opisthorchis viverrini, namely OvCaBP1, 2, 3, and 4, were characterized. They had molecular weights of 22.7, 21.6, 23.7, and 22.5 kDa, respectively and showed 37.2-42.1% sequence identity to CaBP22.8 of O. viverrini. All were detected in 2- and 4-week-old immature and mature parasites. Additionally, OvCaBP4 was found in newly excysted juveniles. Polyclonal antibodies against each isoform were generated to detect the native proteins in parasite extracts by Western blot analysis. All OvCaBPs were detected in soluble and insoluble crude worm extracts and in the excretory-secretory product, at approximate sizes of 21-23 kDa. The ion-binding properties of the proteins were analyzed by mobility shift assays with the divalent cations Ca2+, Mg2+, Zn2+, and Cu2+. All OvCaBPs showed mobility shifts with Ca2+ and Zn2+. OvCaBP1 showed also positive results with Mg2+ and Cu2+. As tegumental proteins, OvCaBP1, 2, and 3 are interesting drug targets for the treatment of opisthorchiasis.","corpus_id":2316517,"score":1},{"doc_id":"20726552","title":"Comparative proteomic analysis of triclabendazole response in the liver fluke Fasciola hepatica.","abstract":"Control of Fasciola hepatica infections of livestock in the absence of vaccines depends largely on the chemical triclabendazole (TCBZ) because it is effective against immature and adult parasites. Overdependence on a single drug and improper application is considered a significant factor in increasing global reports of fluke resistant to TCBZ. The mode(s) of action and biological target(s) of TCBZ are not confirmed, delaying detection and the monitoring of early TCBZ resistance. In this study, to further understand liver fluke response to TCBZ, the soluble proteomes of TCBZ-resistant and TCBZ-susceptible isolates of F. hepatica were compared with and without in vitro exposure to the metabolically active form of the parent drug triclabendazole sulphoxide (TCBZ-SO), via two-dimensional gel electrophoresis (2-DE). Gel image analysis revealed proteins displaying altered synthesis patterns and responses both between isolates and under TCBZ-SO exposure. These proteins were identified by mass spectrometry supported by a F. hepatica expressed sequence tag (EST) data set. The TCBZ responding proteins were grouped into three categories; structural proteins, energy metabolism proteins, and \"stress\" response proteins. This single proteomic investigation supported the reductionist experiments from many laboratories that collectively suggest TCBZ has a range of effects on liver fluke metabolism. Proteomics highlighted differences in the innate proteome profile of different fluke isolates that may influence future therapy and diagnostics design. Two of the TCBZ responding proteins, a glutathione transferase and a fatty acid binding protein, were cloned, produced as recombinants, and both found to bind TCBZ-SO at physiologically relevant concentrations, which may indicate a role in TCBZ metabolism and resistance.","corpus_id":27345424,"score":0},{"doc_id":"21308846","title":"Crystal structure of the sensory domain of Escherichia coli CadC, a member of the ToxR-like protein family.","abstract":"The membrane-integral transcriptional activator CadC comprises sensory and transcriptional regulatory functions within one polypeptide chain. Its C-terminal periplasmic domain, CadC(pd), is responsible for sensing of environmental pH as well as for binding of the feedback inhibitor cadaverine. Here we describe the crystal structure of CadC(pd) (residues 188-512) solved at a resolution of 1.8 Å via multiple wavelength anomalous dispersion (MAD) using a ReCl(6)(2-) derivative. CadC(pd) reveals a novel fold comprising two subdomains: an N-terminal subdomain dominated by a β-sheet in contact with three α-helices and a C-terminal subdomain formed by an eleven-membered α-helical bundle, which is oriented almost perpendicular to the helices in the first subdomain. Further to the native protein, crystal structures were also solved for its variants D471N and D471E, which show functionally different behavior in pH sensing. Interestingly, in the heavy metal derivative of CadC(pd) used for MAD phasing a ReCl(6)(2-) ion was found in a cavity located between the two subdomains. Amino acid side chains that coordinate this complex ion are conserved in CadC homologues from various bacterial species, suggesting a function of the cavity in the binding of cadaverine, which was supported by docking studies. Notably, CadC(pd) forms a homo-dimer in solution, which can be explained by an extended, albeit rather polar interface between two symmetry-related monomers in the crystal structure. The occurrence of several acidic residues in this region suggests protonation-dependent changes in the mode of dimerization, which could eventually trigger transcriptional activation by CadC in the bacterial cytoplasm.","corpus_id":28544446,"score":0},{"doc_id":"21539810","title":"Crystal structure of the middle domain of human poly(A)-binding protein-interacting protein 1.","abstract":"In eukaryotes, the poly(A)-binding protein (PABP) is one of the important factors for initiation of messenger RNA translation. PABP activity is regulated by the PABP-interacting proteins (Paips), which include Paip1, Paip2A, and Paip2B. Human Paip1 has three different isoforms. Here, we report the crystal structure of the middle domain of Paip1 isoform 2 (Paip1M) as determined by single-wavelength anomalous dispersion phasing. The structure reveals a crescent-shaped domain consisting of 10 α-helices and two antiparallel β-strands forming a β-hairpin. The 10 α-helices are arranged as five HEAT repeats which form a double layer of α helices with a convex and a concave surface. Despite low sequence identity, the overall fold of Paip1M is similar to the middle domain of human eIF4GII and yeast eIF4GI. Moreover, the amino-acid sequence motif and the local structure of eIF4G involved in binding of eIF4A, are conserved in Paip1. The structure reported here is the first of a member of the Paip family, thereby filling a gap in our understanding of initiation of eukaryotic mRNA translation in three dimensions.","corpus_id":45850805,"score":0},{"doc_id":"21589904","title":"A family of helminth molecules that modulate innate cell responses via molecular mimicry of host antimicrobial peptides.","abstract":"Over the last decade a significant number of studies have highlighted the central role of host antimicrobial (or defence) peptides in modulating the response of innate immune cells to pathogen-associated ligands. In humans, the most widely studied antimicrobial peptide is LL-37, a 37-residue peptide containing an amphipathic helix that is released via proteolytic cleavage of the precursor protein CAP18. Owing to its ability to protect against lethal endotoxaemia and clinically-relevant bacterial infections, LL-37 and its derivatives are seen as attractive candidates for anti-sepsis therapies. We have identified a novel family of molecules secreted by parasitic helminths (helminth defence molecules; HDMs) that exhibit similar biochemical and functional characteristics to human defence peptides, particularly CAP18. The HDM secreted by Fasciola hepatica (FhHDM-1) adopts a predominantly α-helical structure in solution. Processing of FhHDM-1 by F. hepatica cathepsin L1 releases a 34-residue C-terminal fragment containing a conserved amphipathic helix. This is analogous to the proteolytic processing of CAP18 to release LL-37, which modulates innate cell activation by classical toll-like receptor (TLR) ligands such as lipopolysaccharide (LPS). We show that full-length recombinant FhHDM-1 and a peptide analogue of the amphipathic C-terminus bind directly to LPS in a concentration-dependent manner, reducing its interaction with both LPS-binding protein (LBP) and the surface of macrophages. Furthermore, FhHDM-1 and the amphipathic C-terminal peptide protect mice against LPS-induced inflammation by significantly reducing the release of inflammatory mediators from macrophages. We propose that HDMs, by mimicking the function of host defence peptides, represent a novel family of innate cell modulators with therapeutic potential in anti-sepsis treatments and prevention of inflammation.","corpus_id":11573203,"score":0},{"doc_id":"24324649","title":"Crystal structures of the human G3BP1 NTF2-like domain visualize FxFG Nup repeat specificity.","abstract":"Ras GTPase Activating Protein SH3 Domain Binding Protein (G3BP) is a potential anti-cancer drug target implicated in several cellular functions. We have used protein crystallography to solve crystal structures of the human G3BP1 NTF2-like domain both alone and in complex with an FxFG Nup repeat peptide. Despite high structural similarity, the FxFG binding site is located between two alpha helices in the G3BP1 NTF2-like domain and not at the dimer interface as observed for nuclear transport factor 2. ITC studies showed specificity towards the FxFG motif but not FG and GLFG motifs. The unliganded form of the G3BP1 NTF2-like domain was solved in two crystal forms to resolutions of 1.6 and 3.3 Å in space groups P212121 and P6322 based on two different constructs, residues 1-139 and 11-139, respectively. Crystal packing of the N-terminal residues against a symmetry related molecule in the P212121 crystal form might indicate a novel ligand binding site that, however, remains to be validated. The crystal structures give insight into the nuclear transportation mechanisms of G3BP and provide a basis for future structure based drug design.","corpus_id":1523159,"score":0},{"doc_id":"25602718","title":"Distribution of Fasciola hepatica and F. gigantica in the endemic area of Guilan, Iran: Relationships between zonal overlap and phenotypic traits.","abstract":"Fascioliasis is a zoonotic disease emerging in numerous parts of the world. In any endemic area, the characterisation of scenarios and patterns of infection must always be considered the starting point before implementing any control measure. Fascioliasis is a parasitic disease of different epidemiological, pathological and control characteristics depending on the endemic area and the causal agent, Fasciola hepatica and Fasciolagigantica. Classically it has been accepted that F. hepatica is present worldwide, while the distribution of the two species overlaps in many areas of Africa and Asia. Fascioliasis caused by F. hepatica, F. gigantica and intermediate forms is present in Guilan province, a complicated epidemiological situation where the highest human infection rates have been described in Iran. Morphometric tools were used to analyse the possible relationship between liver-fluke metric traits and geographical and altitudinal distribution. This is the first study in which a detailed distribution of both Fasciola species is analysed in a human fascioliasis endemic area with a zonal overlap transmission pattern. An accurate analysis was conducted to phenotypically discriminate between fasciolids from naturally infected livestock (cattle, buffaloes, sheep and goats). The distribution of the % F. hepatica-like (F.h.) and F. gigantica-like (F.g.) flukes detected in each liver versus altitude (m) in each group was analysed. The presence of F.g. specimens mainly in locations below sea level (average: 11.23% F.h., 88.77% F.g.), the presence of both species with similar intensity at 1-99m (average: 56.95% F.h., 43.05% F.g.) and the presence of F.h. specimens mainly from 100 to 999m (average: 71.69% F.h., 28.31% F.g.) as well as in locations with an altitude above 1000m (average: 97.48% F.h., 2.52% F.g.) are noteworthy. A significant positive correlation was obtained between altitude and % F.h., and a significant negative correlation was obtained between altitude and % F.g. The results show that F.g. populations in cattle, buffaloes and sheep share larger size values, but smaller specimens are present mainly in lowland populations located below sea level, independently of the host species (cattle, buffalo). F.g. from lowland cattle presented larger worm size variability. Four different fascioliasis transmission areas may be distinguished in Guilan: (a) lowland coastal areas neighbouring the Caspian Sea shore, below sea level, where basically F. gigantica-like specimens are found; (b) a coastal plain with an altitude between 1 and 100m where both species co-exist; (c) areas with altitude values of 100-999m where mainly F. hepatica-like specimens are found; (d) highland mountainous areas, where basically F. hepatica-like specimens are found. The study of the influence of the host species on the liver fluke was also carried out by a size-out analysis. This is the first report concerning the decisive influence exercised by the host species on the metric traits of F. gigantica adults.","corpus_id":2878496,"score":0},{"doc_id":"26623254","title":"Partial Hepatectomy for the Resistant Fasciola Hepatica Infection in a Child.","abstract":"Fascioliasis is an emerging and important chronic parasitic disease caused by two trematode liver fluke species: Fasciola hepatica (F. hepatica) and Fasciola gigantica (F. gigantica) infecting several herbivorous mammals including cattle, goats, sheep, and humans. We report a 9-year-old girl who suffered from F. hepatica infection and underwent right hepatectomy because of increasing abdominal pain resistant to anthelmintic chemotherapy. When anthelmintic drug treatment is not effective and abdominal pain persists, surgical resection including hepatectomy should be kept in mind for resistant F. hepatica infection.","corpus_id":19257513,"score":0},{"doc_id":"27466369","title":"Structure of the Single-lobe Myosin Light Chain C in Complex with the Light Chain-binding Domains of Myosin-1C Provides Insights into Divergent IQ Motif Recognition.","abstract":"Myosin light chains are key regulators of class 1 myosins and typically comprise two domains, with calmodulin being the archetypal example. They bind IQ motifs within the myosin neck region and amplify conformational changes in the motor domain. A single lobe light chain, myosin light chain C (MlcC), was recently identified and shown to specifically bind to two sequentially divergent IQ motifs of the Dictyostelium myosin-1C. To provide a molecular basis of this interaction, the structures of apo-MlcC and a 2:1 MlcC·myosin-1C neck complex were determined. The two non-functional EF-hand motifs of MlcC pack together to form a globular four-helix bundle that opens up to expose a central hydrophobic groove, which interacts with the N-terminal portion of the divergent IQ1 and IQ2 motifs. The N- and C-terminal regions of MlcC make critical contacts that contribute to its specific interactions with the myosin-1C divergent IQ motifs, which are contacts that deviate from the traditional mode of calmodulin-IQ recognition.","corpus_id":205361333,"score":0},{"doc_id":"29474932","title":"Profiling G protein-coupled receptors of Fasciola hepatica identifies orphan rhodopsins unique to phylum Platyhelminthes.","abstract":"G protein-coupled receptors (GPCRs) are established drug targets. Despite their considerable appeal as targets for next-generation anthelmintics, poor understanding of their diversity and function in parasitic helminths has thwarted progress towards GPCR-targeted anti-parasite drugs. This study facilitates GPCR research in the liver fluke, Fasciola hepatica, by generating the first profile of GPCRs from the F. hepatica genome. Our dataset describes 147 high confidence GPCRs, representing the largest cohort of GPCRs, and the largest set of in silico ligand-receptor predictions, yet reported in any parasitic helminth. All GPCRs fall within the established GRAFS nomenclature; comprising three glutamate, 135 rhodopsin, two adhesion, five frizzled, one smoothened, and one secretin GPCR. Stringent annotation pipelines identified 18 highly diverged rhodopsins in F. hepatica that maintained core rhodopsin signatures, but lacked significant similarity with non-flatworm sequences, providing a new sub-group of potential flukicide targets. These facilitated identification of a larger cohort of 76 related sequences from available flatworm genomes, representing new members of existing groups (PROF1/Srfb, Rho-L, Rho-R, Srfa, Srfc) of flatworm-specific rhodopsins. These receptors imply flatworm specific GPCR functions, and/or co-evolution with unique flatworm ligands, and could facilitate the development of exquisitely selective anthelmintics. Ligand binding domain sequence conservation relative to deorphanised rhodopsins enabled high confidence ligand-receptor matching of seventeen receptors activated by acetylcholine, neuropeptide F/Y, octopamine or serotonin. RNA-Seq analyses showed expression of 101 GPCRs across various developmental stages, with the majority expressed most highly in the pathogenic intra-mammalian juvenile parasites. These data identify a broad complement of GPCRs in F. hepatica, including rhodopsins likely to have key functions in neuromuscular control and sensory perception, as well as frizzled and adhesion/secretin families implicated, in other species, in growth, development and reproduction. This catalogue of liver fluke GPCRs provides a platform for new avenues into our understanding of flatworm biology and anthelmintic discovery.","corpus_id":4481527,"score":0}],"string":"[\n {\n \"doc_id\": \"18467191\",\n \"title\": \"Plasmodium possesses dynein light chain classes that are unique and conserved across species.\",\n \"abstract\": \"Plasmodium belongs to the phylum Apicomplexa. Within the Apicomplexa, Plasmodium, Toxoplasma and Cryptosporidium are parasites of considerable medical importance while Theileria and Eimeria are animal pathogens. P. falciparum is particularly important as it causes malaria, resulting in more than 1 million deaths each year. The malaria parasite actively invades the host cell in which it propagates and several proteins associated with the apical organelles have been implicated to be crucial in the invasion process. The biogenesis of the apical organelles is not well understood, but several studies indicate that microtubule-based vesicular transport is involved. Vesicular transport proteins are also present in Plasmodium and are presumed to be involved in transcellular transport in infected erythrocytes. Dynein is a multi-subunit motor protein involved in microtubule-based vesicular transport. In this study, we analyzed the cytoplasmic dynein light chains (Dlcs) of P. falciparum since they provide adaptor surface to the cargoes and are likely to be involved in differential transport. Dlcs consist of three different families: TcTex1/2, LC8 and LC7/roadblock. The data presented demonstrate that P. falciparum Dlcs sequences and functional domains show high sequence similarity within the species, but that only the Dlc group 1 (LC8) has a high similarity to human orthologues. TcTex1 and LC7/roadblock have low similarity to human orthologues. This sequence variation could be targeted for vaccine or drug development.\",\n \"corpus_id\": 19344029,\n \"score\": 2\n },\n {\n \"doc_id\": \"18996374\",\n \"title\": \"Schistosoma spp.: Isolation of microtubule associated proteins in the tegument and the definition of dynein light chains components.\",\n \"abstract\": \"Schistosomes are parasitic blood flukes that reside in human mesenteric veins or urinary bladder veins, depending on species of the parasite. The syncytial tegument of these parasites represents a dynamic interface that regulates nutritional and immunological interactions between the parasite and the host. It is known that the components for biogenesis and maintenance of the tegument are supplied via vesicles from the nucleated cell bodies beneath the syncytium and muscle layer. To investigate the common motor components of vesicular transport in the tegument of schistomes, we extracted Schistosoma mansoni tegumental microtubule associated proteins utilizing detergent/high-salt procedure and raised antiserum against these proteins. The antiserum was applied to screen Schistosoma haematobium lambda gt11 expression library and some of the isolated clones were sequenced. Blast search for the sequences against NCBI database identified clones that are dynein light chains and myosin genes. Further analysis of schistosome dynein genes in the databases identified three families of dynein light chains (Dlcs). The Tctex family protein sequences are significantly different from the mammalian homologs and, therefore, offer a potential vaccine/drug target against schistosomes.\",\n \"corpus_id\": 42587114,\n \"score\": 2\n },\n {\n \"doc_id\": \"21078120\",\n \"title\": \"FH8--a small EF-hand protein from Fasciola hepatica.\",\n \"abstract\": \"Vaccine and drug development for fasciolasis rely on a thorough understanding of the mechanisms involved in parasite-host interactions. FH8 is an 8 kDa protein secreted by the parasite Fasciola hepatica in the early stages of infection. Sequence analysis revealed that FH8 has two EF-hand Ca(2+)-binding motifs, and our experimental data show that the protein binds Ca(2+) and that this induces conformational alterations, thus causing it to behave like a sensor protein. Moreover, FH8 displays low affinity for Ca(2+) (K(obs) = 10(4) m(-1)) and is highly stable in its apo and Ca(2+)-loaded states. Homology models were built for FH8 in both states. It has only one globular domain, with two binding sites and appropriate groups in the positions for coordination of the metal ions. However, an unusually high content of positively charged amino acids in one of the binding sites, when compared with the prototypical sensor proteins, potentially affects the protein's affinity for Ca(2+). The only Cys present in FH8, conserved in the homologous proteins of other helminth parasites, is located on the surface, allowing the formation of dimers, detected on SDS gels. These findings reflect specificities of FH8, which are most probably related to its roles both in the parasite and in the host.\",\n \"corpus_id\": 2838269,\n \"score\": 2\n },\n {\n \"doc_id\": \"22019596\",\n \"title\": \"Exploring the Fasciola hepatica tegument proteome.\",\n \"abstract\": \"The surface tegument of the liver fluke Fasciola hepatica is a syncytial cytoplasmic layer bounded externally by a plasma membrane and covered by a glycocalyx, which constitutes the interface between the parasite and its ruminant host. The tegument's interaction with the immune system during the fluke's protracted migration from the gut lumen through the peritoneal cavity and liver parenchyma to the lumen of the bile duct, plays a key role in the fluke's establishment or elimination. However, little is known about proteins of the tegument surface or its secretions. We applied techniques developed for the blood fluke, Schistosoma mansoni, to enrich a tegument surface membrane preparation and analyse its composition by tandem mass spectrometry using new transcript databases for F. hepatica. We increased the membrane and secretory pathway components of the final preparation to ∼30%, whilst eliminating contaminating proteases. We identified a series of proteins or transcripts shared with the schistosome tegument including annexins, a tetraspanin, carbonic anhydrase and an orthologue of a host protein (CD59) that inhibits complement fixation. Unique to F. hepatica, we also found proteins with lectin, cubulin and von Willebrand factor domains plus 10 proteins with leader sequences or transmembrane helices. Many of these surface proteins are potential vaccine candidates. We were hampered in collecting tegument secretions by the propensity of liver flukes, unlike blood flukes, to vomit their gut contents. We analysed both the 'vomitus' and a second supernatant released from haematin-depleted flukes. We identified many proteases, some novel, as well as a second protein with a von Willebrand factor domain. This study demonstrates that components of the tegumental surface of F. hepatica can be defined using proteomic approaches, but also indicates the need to prevent vomiting if tegument secretions are to be characterised.\",\n \"corpus_id\": 26084615,\n \"score\": 2\n },\n {\n \"doc_id\": \"22366577\",\n \"title\": \"Analysis of a calcium-binding EF-hand protein family in Fasciola gigantica.\",\n \"abstract\": \"Transcriptome data supports the notion of a Platyhelminthes-specific protein family that is characterized by combination of two N-terminal EF-hands and a C-terminal dynein light chain-like domain. Family members in schistosomes induce an IgE response that has been connected with resistance to reinfection in schistosomiasis and is considered as a marker of protection. In the present study, we have compared three homologs of the liver fluke Fasciola gigantica for their immunological properties in mouse. Antisera raised against the recombinant proteins detected the native proteins in tegumental type tissues and epithelial linings of excretory system and intestinal tract. The recombinant EF-hand domains induced strong IgG and IgE responses in immunised mice while only weak to moderate responses were observed against the complete recombinant proteins and their DLC-like domains. Parasite crude worm and tegumental extract antisera reacted predominantly with one isoform and its EF-hand domain. Sera of F. gigantica infected mice did not react with the recombinant proteins. The RNA products of the three genes were detected from the metacercarial up to the adult stage. These observations indicate that the investigated EF-hand proteins are not at the frontier of humoral host/parasite interaction in acute fascioliasis gigantica in mouse but are acting as intracellular proteins in tissues that interface with the parasite's environment or tubular tracts.\",\n \"corpus_id\": 30508089,\n \"score\": 2\n },\n {\n \"doc_id\": \"22642211\",\n \"title\": \"A proteomic approach to investigate the distribution and abundance of surface and internal Fasciola hepatica proteins during the chronic stage of natural liver fluke infection in cattle.\",\n \"abstract\": \"Fasciola hepatica, a trematode helminth, causes an economically important disease (fasciolosis) in ruminants worldwide. Proteomic analysis of the parasite provides valuable information to understand the relationship between the parasite and its host. Previous studies have identified various parasite proteins, some of which are considered as vaccine candidates or important drug targets. However, the approximate distribution and abundance of the proteins on the surface and within internal parts of the liver fluke are unknown. In this study, two fractions including surface protein fraction (representing surface part of the parasite, near subplasma membrane of the tegument and above the basal membrane of the tegument) and internal protein fraction (representing internal part of the parasite, mainly deeper sides of the tegument including subbasal membrane and other further internal elements of the parasite) were obtained. Components of these two fractions were investigated by an advanced proteomics approach using a high-definition mass spectrometer with nano electrospray ionization source coupled to a high-performance liquid chromatography system (nanoUPLC-ESI-qTOF-MS). FABP1 was found highly abundant in the SPF fraction. Potentially novel F. hepatica proteins showing homology with AKT interacting protein (Xenopus tropicalis), sterol O-acyltransferase 2 (Homo sapiens), and integrin beta 7 (Mus musculus) were identified with high quantities in only the surface fraction of the parasite and may be possible candidates for future control strategies.\",\n \"corpus_id\": 6255669,\n \"score\": 2\n },\n {\n \"doc_id\": \"22773043\",\n \"title\": \"FhCaBP4: a Fasciola hepatica calcium-binding protein with EF-hand and dynein light chain domains.\",\n \"abstract\": \"In trematodes, there is a family of proteins which combine EF-hand-containing domains with dynein light chain (DLC)-like domains. A member of this family from the liver fluke, Fasciola hepatica-FhCaBP4-has been identified and characterised biochemically. FhCaBP4 has an N-terminal domain containing two imperfect EF-hand sequences and a C-terminal dynein light chain-like domain. Molecular modelling predicted that the two domains are joined by a flexible linker. Native gel electrophoresis demonstrated that FhCaBP4 binds to calcium, manganese, barium and strontium ions, but not to magnesium or zinc ions. The hydrophobic, fluorescent probe 8-anilinonaphthalene-1-sulphonate bound more tightly to FhCaBP4 in the presence of calcium ions. This suggests that the protein undergoes a conformational change on ion binding which increases the number of non-polar residues on the surface. FhCaBP4 was protected from limited proteolysis by the calmodulin antagonist W7, but not by trifluoperazine or praziquantel. Protein-protein cross-linking experiments showed that FhCaBP4 underwent calcium ion-dependent dimerisation. Since DLCs are commonly dimeric, it is likely that FhCaBP4 dimerises through this domain. The molecular model reveals that the calcium ion-binding site is located close to a key sequence in the DLC-like domain, suggesting a plausible mechanism for calcium-dependent dimerisation.\",\n \"corpus_id\": 18776459,\n \"score\": 2\n },\n {\n \"doc_id\": \"23142130\",\n \"title\": \"FhCaBP3: a Fasciola hepatica calcium binding protein with EF-hand and dynein light chain domains.\",\n \"abstract\": \"A DNA sequence encoding a protein with predicted EF-hand and dynein light chain binding domains was identified in a Fasciola hepatica EST library. Sequence analysis of the encoded protein revealed that the most similar known protein was the Fasciola gigantica protein FgCaBP3 and so this newly identified protein was named FhCaBP3. Molecular modelling of FhCaBP3 predicted a highly flexible N-terminal region, followed by a domain containing two EF-hand motifs the second of which is likely to be a functioning divalent ion binding site. The C-terminal domain of the protein contains a dynein light chain like region. Interestingly, molecular modelling predicts that calcium ion binding to the N-terminal domain destabilises the β-sheet structure of the C-terminal domain. FhCaBP3 can be expressed in, and purified from, Escherichia coli. The recombinant protein dimerises and the absence of calcium ions appeared to promote dimerisation. Native gel shift assays demonstrated that the protein bound to calcium and manganese ions, but not to magnesium, barium, zinc, strontium, nickel, copper or cadmium ions. FhCaBP3 interacted with the calmodulin antagonists trifluoperazine, N-(6-aminohexyl)-5-chloro-1-naphthalenesulfonamide and chlorpromazine as well as the myosin regulatory light chain-binding drug praziquantel. Despite sequence and structural similarities to other members of the same protein family from F. hepatica, FhCaBP3 has different biochemical properties to the other well characterised family members, FH22 and FhCaBP4. This suggests that each member of this trematode calcium-binding family has discrete functional roles within the organism.\",\n \"corpus_id\": 9112646,\n \"score\": 2\n },\n {\n \"doc_id\": \"24915098\",\n \"title\": \"Preliminary crystallographic studies of a Schistosoma mansoni antigen (Sm21.7) dynein light-chain (DLC) domain.\",\n \"abstract\": \"Schistosomiasis is an inflammatory chronic disease that represents a major health problem in tropical and subtropical countries. The drug of choice for treatment, praziquantel, is effective in killing adult worms but fails to kill immature forms and prevent reinfection. One prominent antigen candidate for an anti-schistosomiasis vaccine is the protein Sm21.7 (184 amino-acid residues) from Schistosoma mansoni, a tegumental protein capable of reducing the worm burden in a murine immunization model. In the present work, the Sm21.7 gene was cloned and expressed in Escherichia coli and the full-length protein was purified to homogeneity. Crystals of recombinant Sm21.7 suitable for X-ray diffraction were obtained using PEG monomethyl ether 2000 as a precipitant. X-ray diffraction images of a native crystal (at 2.05 Å resolution) and a quick-cryosoaked NaI derivative (at 1.95 Å resolution) were collected on the W01B-MX2 beamline at the Laboratório Nacional de Luz Síncrotron (LNLS, Brazilian Synchrotron Light Laboratory/MCT). Both crystals belonged to the hexagonal space group P6122, with similar unit-cell parameters a=b=108.5, c=55.8 Å. SIRAS-derived phases were used to generate the first electron-density map, from which a partial three-dimensional model of Sm21.7 (from Gln89 to Asn184) was automatically constructed. Anaysis of dissolved crystals by SDS-PAGE confirmed that the protein was cleaved in the crystallization drop and only the Sm21.7 C-terminal domain was crystallized. The structure of the Sm21.7 C-terminal domain will help in the localization of the epitopes responsible for its protective immune responses, constituting important progress in the development of an anti-schistosomiasis vaccine.\",\n \"corpus_id\": 27932347,\n \"score\": 2\n },\n {\n \"doc_id\": \"26152524\",\n \"title\": \"FhCaBP2: a Fasciola hepatica calcium-binding protein with EF-hand and dynein light chain domains.\",\n \"abstract\": \"FhCaBP2 is a Fasciola hepatica protein which belongs to a family of helminth calcium-binding proteins which combine an N-terminal domain containing two EF-hand motifs and a C-terminal dynein light chain-like (DLC-like) domain. Its predicted structure showed two globular domains joined by a flexible linker. Recombinant FhCaBP2 interacted reversibly with calcium and manganese ions, but not with magnesium, barium, strontium, copper (II), colbalt (II), iron (II), nickel, lead or potassium ions. Cadmium (II) ions appeared to bind non-site-specifically and destabilize the protein. Interaction with either calcium or magnesium ions results in a conformational change in which the protein's surface becomes more hydrophobic. The EF-hand domain alone was able to interact with calcium and manganese ions; the DLC-like domain was not. Alteration of a residue (Asp-58 to Ala) in the second EF-hand motif in this domain abolished ion-binding activity. This suggests that the second EF-hand is the one responsible for ion-binding. FhCaBP2 homodimerizes and the extent of dimerization was not affected by calcium ions or by the aspartate to alanine substitution in the second EF-hand. The isolated EF-hand and DLC-like domains are both capable of homodimerization. FhCaBP2 interacted with the calmodulin antagonists trifluoperazine, chlorpromazine, thiamylal and W7. Interestingly, while chlorpromazine and thiamylal interacted with the EF-hand domain (as expected), trifluoperazine and W7 bound to the DLC-like domain. Overall, FhCaBP2 has distinct biochemical properties compared with other members of this protein family from Fasciola hepatica, a fact which supports the hypothesis that these proteins have different physiological roles.\",\n \"corpus_id\": 54562582,\n \"score\": 2\n },\n {\n \"doc_id\": \"27528745\",\n \"title\": \"A mysterious family of calcium-binding proteins from parasitic worms.\",\n \"abstract\": \"There is a family of proteins from parasitic worms which combine N-terminal EF-hand domains with C-terminal dynein light chain-like domains. Data are accumulating on the biochemistry and cell biology of these proteins. However, little is known about their functions in vivo Schistosoma mansoni expresses 13 family members (SmTAL1-SmTAL13). Three of these (SmTAL1, SmTAL2 and SmTAL3) have been subjected to biochemical analysis which demonstrated that they have different molecular properties. Although their overall folds are predicted to be similar, small changes in the EF-hand domains result in differences in their ion binding properties. Whereas SmTAL1 and SmTAL2 are able to bind calcium (and some other) ions, SmTAL3 appears to be unable to bind any divalent cations. Similar biochemical diversity has been seen in the CaBP proteins from Fasciola hepatica Four family members are known (FhCaBP1-4). All of these bind to calcium ions. However, FhCaBP4 dimerizes in the presence of calcium ions, FhCaBP3 dimerizes in the absence of calcium ions and FhCaBP2 dimerizes regardless of the prevailing calcium ion concentration. In both the SmTAL and FhCaBP families, the proteins also differ in their ability to bind calmodulin antagonists and related drugs. Interestingly, SmTAL1 interacts with praziquantel (the drug of choice for treating schistosomiasis). The pharmacological significance (if any) of this finding is unknown.\",\n \"corpus_id\": 206155869,\n \"score\": 2\n },\n {\n \"doc_id\": \"27693219\",\n \"title\": \"FhCaBP1 (FH22): A Fasciola hepatica calcium-binding protein with EF-hand and dynein light chain domains.\",\n \"abstract\": \"FH22 has been previously identified as a calcium-binding protein from the common liver fluke, Fasciola hepatica. It is part of a family of at least four proteins in this organism which combine an EF-hand containing N-terminal domain with a C-terminal dynein light chain-like domain. Here we report further biochemical properties of FH22, which we propose should be renamed FhCaBP1 for consistency with other family members. Molecular modelling predicted that the two domains are linked by a flexible region and that the second EF-hand in the N-terminal domain is most likely the calcium ion binding site. Native gel electrophoresis demonstrated that the protein binds both calcium and manganese ions, but not cadmium, magnesium, strontium, barium, cobalt, copper(II), iron (II), nickel, zinc, lead or potassium ions. Calcium ion binding alters the conformation of the protein and increases its stability towards thermal denaturation. FhCaBP1 is a dimer in solution and calcium ions have no detectable effect on the protein's ability to dimerise. FhCaBP1 binds to the calmodulin antagonists trifluoperazine and chlorpromazine. Overall, the FhCaBP1's biochemical properties are most similar to FhCaBP2 a fact consistent with the close sequence and predicted structural similarity between the two proteins.\",\n \"corpus_id\": 34616309,\n \"score\": 2\n },\n {\n \"doc_id\": \"28273846\",\n \"title\": \"Molecular and Structural Characterization of the Tegumental 20.6-kDa Protein in Clonorchis sinensis as a Potential Druggable Target.\",\n \"abstract\": \"The tegument, representing the membrane-bound outer surface of platyhelminth parasites, plays an important role for the regulation of the host immune response and parasite survival. A comprehensive understanding of tegumental proteins can provide drug candidates for use against helminth-associated diseases, such as clonorchiasis caused by the liver fluke Clonorchis sinensis. However, little is known regarding the physicochemical properties of C. sinensis teguments. In this study, a novel 20.6-kDa tegumental protein of the C. sinensis adult worm (CsTegu20.6) was identified and characterized by molecular and in silico methods. The complete coding sequence of 525 bp was derived from cDNA clones and encodes a protein of 175 amino acids. Homology search using BLASTX showed CsTegu20.6 identity ranging from 29% to 39% with previously-known tegumental proteins in C. sinensis. Domain analysis indicated the presence of a calcium-binding EF-hand domain containing a basic helix-loop-helix structure and a dynein light chain domain exhibiting a ferredoxin fold. We used a modified method to obtain the accurate tertiary structure of the CsTegu20.6 protein because of the unavailability of appropriate templates. The CsTegu20.6 protein sequence was split into two domains based on the disordered region, and then, the structure of each domain was modeled using I-TASSER. A final full-length structure was obtained by combining two structures and refining the whole structure. A refined CsTegu20.6 structure was used to identify a potential CsTegu20.6 inhibitor based on protein structure-compound interaction analysis. The recombinant proteins were expressed in Escherichia coli and purified by nickel-nitrilotriacetic acid affinity chromatography. In C. sinensis, CsTegu20.6 mRNAs were abundant in adult and metacercariae, but not in the egg. Immunohistochemistry revealed that CsTegu20.6 localized to the surface of the tegument in the adult fluke. Collectively, our results contribute to a better understanding of the structural and functional characteristics of CsTegu20.6 and homologs of flukes. One compound is proposed as a putative inhibitor of CsTegu20.6 to facilitate further studies for anthelmintics.\",\n \"corpus_id\": 22530851,\n \"score\": 2\n },\n {\n \"doc_id\": \"28496122\",\n \"title\": \"Structural insights into a 20.8-kDa tegumental-allergen-like (TAL) protein from Clonorchis sinensis.\",\n \"abstract\": \"Survival of Clonorchis sinensis, a cause of human clonorchiasis, requires tegument proteins, which are localized to the tegumental outer surface membrane. These proteins play an important role in a host response and parasite survival. Thus, these proteins are interesting molecular targets for vaccine and drug development. Here, we have determined two crystal structures of the calmodulin like domain (amino acid [aa] positions 1-81) and dynein light chain (DLC)-like domain (aa 83-177) of a 20.8-kDa tegumental-allergen-like protein from Clonorchis sinensis (CsTAL3). The calmodulin like domain has two Ca(2+)-binding sites (named CB1 and CB2), but Ca(2+) binds to only one site, CB1. The DLC-like domain has a dimeric conformation; the interface is formed mainly by hydrogen bonds between the main chain atoms. In addition, we have determined full-length structure of CsTAL3 in solution and showed the conformational change of CsTAL3 induced by Ca(2+) ion binding using small-angle X-ray scattering analysis and molecular dynamics simulations. The Ca(2+)-bound form has a more extended conformation than the Ca(2+)-free from does. These structural and biochemical analyses will advance the understanding of the biology of this liver fluke and may contribute to our understanding of the molecular mechanism of calcium-responsive and tegumental-allergen-like proteins.\",\n \"corpus_id\": 11559130,\n \"score\": 2\n },\n {\n \"doc_id\": \"18031748\",\n \"title\": \"Human fascioliasis and the presence of hybrid/introgressed forms of Fasciola hepatica and Fasciola gigantica in Vietnam.\",\n \"abstract\": \"The two species common of liver fluke, Fasciola hepatica and Fasciola gigantica, cause human fascioliasis. Hybrids between these species, and introgressed forms of Fasciola, are known from temperate and subtropical regions of eastern Asia. Here, we report the presence of hybrid and/or introgressed liver flukes in Vietnam where it has recently been recognised that human fascioliasis is an important zoonotic disease. Specimens examined came from domestic stock (cattle and buffalo) at slaughter and also from human patients. DNA sequences were obtained from the nuclear ribosomal second internal transcribed spacer (ITS-2) and from portions of two mitochondrial protein-coding genes. Mitochondrial sequences in every case were similar to those of Fasciola gigantica. Nuclear ITS-2 sequences belonged to one or other of the Fasciola species, or, sequences from both were found in the same individual worm. This study extends the known range of hybrids or introgressed forms of Fasciola into tropical regions of Asia.\",\n \"corpus_id\": 41832791,\n \"score\": 1\n },\n {\n \"doc_id\": \"18160404\",\n \"title\": \"Structural and functional relationships in the virulence-associated cathepsin L proteases of the parasitic liver fluke, Fasciola hepatica.\",\n \"abstract\": \"The helminth parasite Fasciola hepatica secretes cysteine proteases to facilitate tissue invasion, migration, and development within the mammalian host. The major proteases cathepsin L1 (FheCL1) and cathepsin L2 (FheCL2) were recombinantly produced and biochemically characterized. By using site-directed mutagenesis, we show that residues at position 67 and 205, which lie within the S2 pocket of the active site, are critical in determining the substrate and inhibitor specificity. FheCL1 exhibits a broader specificity and a higher substrate turnover rate compared with FheCL2. However, FheCL2 can efficiently cleave substrates with a Pro in the P2 position and degrade collagen within the triple helices at physiological pH, an activity that among cysteine proteases has only been reported for human cathepsin K. The 1.4-A three-dimensional structure of the FheCL1 was determined by x-ray crystallography, and the three-dimensional structure of FheCL2 was constructed via homology-based modeling. Analysis and comparison of these structures and our biochemical data with those of human cathepsins L and K provided an interpretation of the substrate-recognition mechanisms of these major parasite proteases. Furthermore, our studies suggest that a configuration involving residue 67 and the \\\"gatekeeper\\\" residues 157 and 158 situated at the entrance of the active site pocket create a topology that endows FheCL2 with its unusual collagenolytic activity. The emergence of a specialized collagenolytic function in Fasciola likely contributes to the success of this tissue-invasive parasite.\",\n \"corpus_id\": 25829733,\n \"score\": 1\n },\n {\n \"doc_id\": \"18190913\",\n \"title\": \"Fasciola hepatica and Fasciola gigantica: cloning and characterisation of 70 kDa heat-shock proteins reveals variation in HSP70 gene expression between parasite species recovered from sheep.\",\n \"abstract\": \"Fasciola hepatica and Fasciola gigantica are trematode parasites responsible for fasciolosis, a disease of ruminant animals which is also increasingly recognised as a disease in humans. By biochemical and in silico methods, we have cloned and characterised the 70 kDa heat-shock proteins (HSP70s) of F. hepatica and F. gigantica. The nucleotide and protein sequences for HSP70 were found to be 98% and 99% identical between liver fluke species, respectively, and to encode conserved amino acid motifs that are of putative functional importance. Western blot analysis demonstrated that HSP70 proteins were expressed at a higher level in F. gigantica recovered from sheep relative to F. hepatica, but HSP70 was not detected in the excretory-secretory products of these liver fluke samples. Real-time reverse-transcriptase PCR analysis of HSP70 expression in parasites from sheep, but not cattle, showed HSP70 expression to be higher in F. gigantica than F. hepatica. These results suggest that hosts refractory to F. gigantica are associated with higher HSP70 expression by this parasite and that HSP70 expression may represent a biochemical marker of the stress response of F. gigantica.\",\n \"corpus_id\": 10389393,\n \"score\": 1\n },\n {\n \"doc_id\": \"18237745\",\n \"title\": \"The crystal structure of plant-specific calcium-binding protein AtCBL2 in complex with the regulatory domain of AtCIPK14.\",\n \"abstract\": \"Calcium signals mediate a multitude of plant responses to external stimuli. Calcineurin B-like (CBL) proteins and their target kinases, CBL-interacting protein kinases (CIPKs), represent important relays in plant calcium signaling. CBL interacts with CIPK through a conserved motif (NAF/FISL motif) within the C-terminal regulatory domain. To better understand the functional role of the CBL-CIPK system, we determined the crystal structure of AtCBL2 in complex with the regulatory domain of AtCIPK14 at 1.2 A resolution. The NAF/FISL motif is inserted into a hydrophobic crevice within AtCBL2, accompanied by a large displacement of the helices and loop on the opposite side of the NAF/FISL motif from the C-terminal region, which shields the hydrophobic crevice in free form. Ca(2+) are coordinated within four EF hands in AtCBL2 in bound form. This calcium coordination pattern differs from that in the structure of the SOS3-SOS2 complex previously reported. Structural comparison of the two structures shows that the recognition of CBL by CIPK is performed in a similar manner, but inherent interactions confer binding affinity and specificity.\",\n \"corpus_id\": 44426665,\n \"score\": 1\n },\n {\n \"doc_id\": \"18612418\",\n \"title\": \"Development of functional genomic tools in trematodes: RNA interference and luciferase reporter gene activity in Fasciola hepatica.\",\n \"abstract\": \"The growing availability of sequence information from diverse parasites through genomic and transcriptomic projects offer new opportunities for the identification of key mediators in the parasite-host interaction. Functional genomics approaches and methods for the manipulation of genes are essential tools for deciphering the roles of genes and to identify new intervention targets in parasites. Exciting advances in functional genomics for parasitic helminths are starting to occur, with transgene expression and RNA interference (RNAi) reported in several species of nematodes, but the area is still in its infancy in flatworms, with reports in just three species. While advancing in model organisms, there is a need to rapidly extend these technologies to other parasites responsible for several chronic diseases of humans and cattle. In order to extend these approaches to less well studied parasitic worms, we developed a test method for the presence of a viable RNAi pathway by silencing the exogenous reporter gene, firefly luciferase (fLUC). We established the method in the human blood fluke Schistosoma mansoni and then confirmed its utility in the liver fluke Fasciola hepatica. We transformed newly excysted juveniles of F. hepatica by electroporation with mRNA of fLUC and three hours later were able to detect luciferase enzyme activity, concentrated mainly in the digestive ceca. Subsequently, we tested the presence of an active RNAi pathway in F. hepatica by knocking down the exogenous luciferase activity by introduction into the transformed parasites of double-stranded RNA (dsRNA) specific for fLUC. In addition, we tested the RNAi pathway targeting an endogenous F. hepatica gene encoding leucine aminopeptidase (FhLAP), and observed a significant reduction in specific mRNA levels. In summary, these studies demonstrated the utility of RNAi targeting reporter fLUC as a reporter gene assay to establish the presence of an intact RNAi pathway in helminth parasites. These could facilitate the study of gene function and the identification of relevant targets for intervention in organisms that are by other means intractable. More specifically, these results open new perspectives for functional genomics of F. hepatica, which hopefully can lead to the development of new interventions for fascioliasis.\",\n \"corpus_id\": 15936304,\n \"score\": 1\n },\n {\n \"doc_id\": \"18620002\",\n \"title\": \"The Fasciola hepatica thioredoxin: High resolution structure reveals two oxidation states.\",\n \"abstract\": \"The Fasciola hepatica thioredoxin protein structure has been determined to 1.45A resolution. This is the first example of a single crystal structure to show the active site cysteine residues in both the reduced and disulfide oxidised form. Consistent with this observation the process of oxidation appears to require very little rearrangement of the surrounding protein structure. The F. hepatica thioredoxin structure has been compared to other thioredoxin protein structures already known and is found to be highly conserved. The F. hepatica protein is most similar to that of the thioredoxin from its human and animal hosts but it resembles other parasitic thioredoxins with regard to having no additional cysteine residues and is therefore not regulated by transient disulfide bond formation as proposed for thioredoxins from higher eukaryotic species.\",\n \"corpus_id\": 43847142,\n \"score\": 1\n },\n {\n \"doc_id\": \"18775726\",\n \"title\": \"Crystal-structure and biochemical characterization of recombinant human calcyphosine delineates a novel EF-hand-containing protein family.\",\n \"abstract\": \"Calcyphosine is an EF-hand protein involved in both Ca(2+)-phosphatidylinositol and cyclic AMP signal cascades, as well as in other cellular functions. The crystal structure of Ca(2+)-loaded calcyphosine was determined up to 2.65 A resolution and reveals a protein containing two pairs of Ca(2+)-binding EF-hand motifs. Calcyphosine shares a highly similar overall topology with calmodulin. However, there are striking differences between EF-hand 4, both N-terminal and C-terminal regions, and interdomain linkers. The C-terminal domain of calcyphosine possesses a large hydrophobic pocket in the presence of calcium ions that might be implicated in ligand binding, while its N-terminal hydrophobic pocket is almost shielded by an additional terminal helix. Calcyphosine is largely monomeric, regardless of the presence of Ca(2+). Differences in structure, oligomeric state in the presence and in the absence of Ca(2+), a highly conserved sequence with low similarity to other proteins, and phylogeny define a new EF-hand-containing family of calcyphosine proteins that extends from arthropods to humans.\",\n \"corpus_id\": 18129251,\n \"score\": 1\n },\n {\n \"doc_id\": \"18948118\",\n \"title\": \"The interplay of ligand binding and quaternary structure in the diverse interactions of dynein light chain LC8.\",\n \"abstract\": \"Dynein light chain LC8 is a small, dimeric, and very highly conserved globular protein that is an integral part of the dynein and myosin molecular motors but appears to have a broader role in multiple protein complexes unrelated to molecular motors. LC8 binds to two families of targets: those having a KXTQT sequence fingerprint and those having a GIQVD fingerprint. All known LC8 binding partners containing these fingerprints share a common binding site on LC8 that raises the question of what determines binding specificity. Here, we present the crystal structure of apo-LC8 at 1.7-A resolution, which, when compared with the crystal structures of several LC8 complexes, gives insight into the mechanism underlying the binding diversity of LC8. Peptide binding is associated with a shift in quaternary structure that expands the hydrophobic binding surface available to the ligand, in addition to changes in tertiary structure and ordering of LC8 around the binding groove. The observed quaternary shift suggests a mechanism by which binding at one of the two identical sites can influence binding at the other. NMR spectra of titrations with peptides from each fingerprint family show evidence of allosteric interaction between the two binding sites, to a differing degree in the two ligand families. Allosteric interaction between the binding sites may be a mechanism to promote simultaneous binding of ligands from the same family, providing a physiological role for the two fingerprints.\",\n \"corpus_id\": 20840777,\n \"score\": 1\n },\n {\n \"doc_id\": \"19443417\",\n \"title\": \"An integrated transcriptomics and proteomics analysis of the secretome of the helminth pathogen Fasciola hepatica: proteins associated with invasion and infection of the mammalian host.\",\n \"abstract\": \"To infect their mammalian hosts, Fasciola hepatica larvae must penetrate and traverse the intestinal wall of the duodenum, move through the peritoneum, and penetrate the liver. After migrating through and feeding on the liver, causing extensive tissue damage, the parasites move to their final niche in the bile ducts where they mature and produce eggs. Here we integrated a transcriptomics and proteomics approach to profile Fasciola secretory proteins that are involved in host-pathogen interactions and to correlate changes in their expression with the migration of the parasite. Prediction of F. hepatica secretory proteins from 14,031 expressed sequence tags (ESTs) available from the Wellcome Trust Sanger Centre using the semiautomated EST2Secretome pipeline showed that the major components of adult parasite secretions are proteolytic enzymes including cathepsin L, cathepsin B, and asparaginyl endopeptidase cysteine proteases as well as novel trypsin-like serine proteases and carboxypeptidases. Proteomics analysis of proteins secreted by infective larvae, immature flukes, and adult F. hepatica showed that these proteases are developmentally regulated and correlate with the passage of the parasite through host tissues and its encounters with different host macromolecules. Proteases such as FhCL3 and cathepsin B have specific functions in larvae activation and intestinal wall penetration, whereas FhCL1, FhCL2, and FhCL5 are required for liver penetration and tissue and blood feeding. Besides proteases, the parasites secrete an array of antioxidants that are also highly regulated according to their migration through host tissues. However, whereas the proteases of F. hepatica are secreted into the parasite gut via a classical endoplasmic reticulum/Golgi pathway, we speculate that the antioxidants, which all lack a signal sequence, are released via a non-classical trans-tegumental pathway.\",\n \"corpus_id\": 3715533,\n \"score\": 1\n },\n {\n \"doc_id\": \"20006979\",\n \"title\": \"Elucidating the transcriptome of Fasciola hepatica - a key to fundamental and biotechnological discoveries for a neglected parasite.\",\n \"abstract\": \"Liver flukes of animals are parasitic flatworms (Platyhelminthes: Digenea) of major socioeconomic importance in many countries. Key representatives, such as Fasciola hepatica and F. gigantica, cause \\\"liver fluke disease\\\" (= fascioliasis), which is of major animal health significance worldwide. In particular, F. hepatica is a leading cause of production losses to the livestock (mainly sheep and cattle) and meat industries due to clinical disease, reduced weight gain and milk production, and deaths. This parasite is also a major food-borne pathogen of humans throughout parts of the Middle East, Asia and South America. Currently, there is a significant focus on the development of new approaches for the prevention and control of fascioliasis in livestock. Recent technological advances in genomics and bioinformatics provide unique opportunities for the identification and prevalidation of drug targets and vaccines through a better understanding of the biology of F. hepatica and related species as well as their relationship with their hosts at the molecular level. Surprisingly, despite the widespread socioeconomic impact of fascioliasis, genomic datasets for F. hepatica are scant, limiting the molecular biological research of this parasite. The present article explores specifically the transcriptome of the adult stage of F. hepatica using an integrated genomic-bioinformatic platform. The analysis of the current data reveals numerous molecules of biological relevance, some of which are inferred to be involved in key biological processes or pathways that could serve as targets for new trematocidal drugs or vaccines. Improved insights into the transcriptome of F. hepatica should pave the way for future, comparative analysis of the transcriptomes of other developmental stages of this and related parasites, such as F. gigantica, cancer-causing flatworms (Clonorchis sinensis and Opisthorchis viverrini) and blood flukes (Schistosoma mansoni and S. japonicum). Prediction of the essentiality of genes and their products, molecular network connectivity of trematode genes as well as experimental exploration of function should also add value to the genomic discovery efforts in the future, focused on biotechnological outcomes.\",\n \"corpus_id\": 206179664,\n \"score\": 1\n },\n {\n \"doc_id\": \"20089359\",\n \"title\": \"Proteomic analysis of embryonic Fasciola hepatica: characterization and antigenic potential of a developmentally regulated heat shock protein.\",\n \"abstract\": \"Fasciola hepatica is responsible for human disease and economic livestock loss on a global scale. We report the first post-genomic investigation of cellular proteins expressed by embryonic F. hepatica via two-dimensional electrophoresis, image analysis and tandem mass spectrometry. Antioxidant proteins and protein chaperones are prominently expressed by embryonic F. hepatica. Molecular differences between the egg and other characterized F. hepatica lifecycle stages were noted. Furthermore, proteins expressed within liver fluke eggs differ to those isolated from the well-characterized eggs of the human blood flatworm Schistosoma mansoni were revealed. Plasticity in expression of major proteins, particularly a prominently expressed 65kDa protein cluster was seen between natural populations of embryonating F. hepatica eggs suggesting that liver fluke embryogenisis is a plastic process. Immunoblotting revealed that the abundant 65kDa protein cluster is recognised by infection sera from three F. hepatica challenged host species. Mass spectrometry and BLAST analyses demonstrated that the 65kDa antigen shows homology to egg antigens of other flatworm parasites, and is represented in a F. hepatica EST database constructed from adult fluke transcripts. EST clones encoding the egg antigen were re-sequenced, predicting two forms of the protein. Four clones predict a 312 aa polypeptide, three clones encode a putative 110 amino acid extension at the N-terminus which may be involved in protein secretion, although this extension was not expressed by natively extracted proteins. Consistent expression of alpha crystallin domains confirmed the protein to be a member of the alpha crystallin containing small heat shock protein (AC/sHSP) superfamily. AC/sHSPs are ubiquitous in nature, however, this is the first time a member of this protein superfamily has been described from F. hepatica. The antigenic AC/sHSP was named Fh-HSP35alpha based on predictions of molecular weight. Production of recombinant Fh-HSP35alpha reveals considerable mass discrepancy between native and recombinant proteins, although descriptions of other characterized flatworm AC/sHSPs, suggest that the native form is a dimer. Immunoblot analyses confirm that the recombinant protein is recognised by F. hepatica challenged hosts, but does not react with sera from non-infected animals. We discuss the potential of recombinant Fh-HSP35alpha as an egg-based diagnostic marker for liver fluke infection.\",\n \"corpus_id\": 25029074,\n \"score\": 1\n },\n {\n \"doc_id\": \"20374642\",\n \"title\": \"Survey of transcripts expressed by the invasive juvenile stage of the liver fluke Fasciola hepatica.\",\n \"abstract\": \"BACKGROUND: The common liver fluke Fasciola hepatica is the agent of a zoonosis with significant economic consequences in livestock production worldwide, and increasing relevance to human health in developing countries. Although flukicidal drugs are available, re-infection and emerging resistance are demanding new efficient and inexpensive control strategies. Understanding the molecular mechanisms underlying the host-parasite interaction provide relevant clues in this search, while enlightening the physiological adaptations to parasitism. Genomics and transcriptomics are still in their infancy in F. hepatica, with very scarce information available from the invasive newly excysted juveniles (NEJ). Here we provide an initial glimpse to the transcriptomics of the NEJ, the first stage to interact with the mammalian host. RESULTS: We catalogued more than 500 clusters generated from the analysis of F. hepatica juvenile expressed sequence tags (EST), several of them not detected in the adult stage. A set of putative F. hepatica specific transcripts, and a group of sequences conserved exclusively in flatworms were identified. These novel sequences along with a set of parasite transcripts absent in the host genomes are putative new targets for future anti-parasitic drugs or vaccine development. Comparisons of the F. hepatica sequences with other metazoans genomes or EST databases were consistent with the basal positioning of flatworms in the bilaterian phylogeny. Notably, GC content, codon usage and amino acid frequencies are remarkably different in Schistosomes to F. hepatica and other trematodes. Functional annotation of predicted proteins showed a general representation of diverse biological functions. Besides proteases and antioxidant enzymes expected to participate in the early interaction with the host, various proteins involved in gene expression, protein synthesis, cell signaling and mitochondrial enzymes were identified. Differential expression of secreted protease gene family members between juvenile and adult stages may respond to different needs during host colonization. CONCLUSION: The knowledge of the genes expressed by the invasive stage of Fasciola hepatica is a starting point to unravel key aspects of this parasite's biology. The integration of the emerging transcriptomics, and proteomics data and the advent of functional genomics tools in this organism are positioning F. hepatica as an interesting model for trematode biology.\",\n \"corpus_id\": 13863138,\n \"score\": 1\n },\n {\n \"doc_id\": \"21766237\",\n \"title\": \"Effect of Fasciola hepatica proteins on the functioning of rat hepatocytes.\",\n \"abstract\": \"Fasciolosis is a hepatic parasitic infection that affects many mammal species and creates a great economic and veterinary problem. Molecular mechanisms of parasite-hepatocyte interactions have not been precisely characterized yet. Therefore, the aim of the study was to investigate alterations in the metabolic activity of rat liver cells exposed to Fasciola hepatica somatic proteins. Hepatocytes were incubated with 0-1 mg/ml of fluke's somatic proteins for various periods of time. Afterward, changes in hepatocytes metabolic activity were determined with MTT and enzyme leakage tests. Hepatocytes' capacity to synthesize albumin was also investigated. It was observed that protein concentration, as well as longevity of their action, influenced metabolic activity of rat liver cells. Diminution of hepatocytes survival rate, an increase in enzyme leakage and altered synthetic capacity after treatment with parasite's proteins were reported. It is concluded that somatic proteins of F. hepatica may play an important role in liver cell damaging.\",\n \"corpus_id\": 17281291,\n \"score\": 1\n },\n {\n \"doc_id\": \"21782972\",\n \"title\": \"Cloning, expression, and characterization of a novel Opisthorchis viverrini calcium-binding EF-hand protein.\",\n \"abstract\": \"A novel 22.8 kDa of Opisthorchis viverrini (Ov) calcium-binding EF-hand protein (Ov CaBP) was identified and isolated from an immunoscreening of the adult stage Ov cDNA library by using a human cholangiocarcinoma (CCA) serum. This protein was related to other calcium-binding proteins and conserved among the trematodes. Ov CaBP shared 98% amino acid identity to 22.8 kDa of Clonorchis sinensis CaBP and both were classified as a new group of CaBP EF-hand protein by multiple sequence alignment and phylogenetic tree analysis. The open reading frame of Ov CaBP was 585 bp which encoded for 194 amino acids. The N-terminal part is composed of two calcium-binding EF-hand motifs whereas the C-terminal part contains a dynein light chain motif (DLC). In addition, transcription analysis by RT-PCR revealed that it was constitutively transcribed in all stages, including metacercariae, juvenile, and adult. Furthermore, recombinant Ov CaBP protein (rOv CaBP) was expressed as a soluble protein and antibody generated against this rOv CaBP protein was capable of detecting Ov CaBP in the Ov somatic extracts but not in Ov ES products. This anti-rOv CaBP serum was also used to localize Ov CaBP in Ov infected hamster's liver sections which the distribution of Ov CaBP was located in gut epithelium, miracidia in eggs and slightly in parenchyma. Moreover, rOv CaBP protein showed a calcium-binding property in non-denaturing gel mobility shift assay.\",\n \"corpus_id\": 24096855,\n \"score\": 1\n },\n {\n \"doc_id\": \"21920370\",\n \"title\": \"Crystal structure of cardiac troponin C regulatory domain in complex with cadmium and deoxycholic acid reveals novel conformation.\",\n \"abstract\": \"The amino-terminal regulatory domain of cardiac troponin C (cNTnC) plays an important role as the calcium sensor for the troponin complex. Calcium binding to cNTnC results in conformational changes that trigger a cascade of events that lead to cardiac muscle contraction. The cardiac N-terminal domain of TnC consists of two EF-hand calcium binding motifs, one of which is dysfunctional in binding calcium. Nevertheless, the defunct EF-hand still maintains a role in cNTnC function. For its structural analysis by X-ray crystallography, human cNTnC with the wild-type primary sequence was crystallized under a novel crystallization condition. The crystal structure was solved by the single-wavelength anomalous dispersion method and refined to 2.2 Å resolution. The structure displays several novel features. Firstly, both EF-hand motifs coordinate cadmium ions derived from the crystallization milieu. Secondly, the ion coordination in the defunct EF-hand motif accompanies unusual changes in the protein conformation. Thirdly, deoxycholic acid, also derived from the crystallization milieu, is bound in the central hydrophobic cavity. This is reminiscent of the interactions observed for cardiac calcium sensitizer drugs that bind to the same core region and maintain the \\\"open\\\" conformational state of calcium-bound cNTnC. The cadmium ion coordination in the defunct EF-hand indicates that this vestigial calcium binding site retains the structural and functional elements that allow it to coordinate a cadmium ion. However, it is a result of, or concomitant with, large and unusual structural changes in cNTnC.\",\n \"corpus_id\": 6629342,\n \"score\": 1\n },\n {\n \"doc_id\": \"22015384\",\n \"title\": \"Identification and characterization of a novel 21.6-kDa tegumental protein from Clonorchis sinensis.\",\n \"abstract\": \"Tegumental proteins form a membrane-bound outer surface and are thus involved in host-parasite interactions and parasite survival. A complementary DNA clone encoding a novel 21.6-kDa tegumental protein (CsTegu21.6, accession number JF911532) was identified in a sequence library for the adult Clonorchis sinensis liver fluke. The complete coding sequence was 564 bp and encoded a protein of 188 amino acids. A BLASTX search revealed identities from 43 to 47% with previously identified tegumental proteins in C. sinensis and other helminthic parasites. Multiple alignment of the amino acids of CsTegu21.6 with those of four other C. sinensis tegumental proteins, CsTegu21.1, CsTegu22.3, CsTegu20.8 and CsTegu31.8, revealed pair-wise sequence identities ranging from 24 to 31.8%. A calcium-binding EF-hand domain containing a basic helix-loop-helix structure at the N terminus and a dynein light chain domain at the C terminus were found in CsTegu21.6; these motifs are common in tegumental proteins. CsTegu21.6 was specifically observed on the tegument of adult worms using immunolocalization analysis.\",\n \"corpus_id\": 15730390,\n \"score\": 1\n },\n {\n \"doc_id\": \"22240114\",\n \"title\": \"Characterization and differential expression of a ferritin protein from Fasciola hepatica.\",\n \"abstract\": \"Ferritins are proteins that play a central role in maintaining intracellular iron balance. A cDNA clone of Fasciola hepatica (687 bp long) encoding a putative 228-amino acid polypeptide (FhFtn-1) homologous with ferritins of vertebrates and invertebrates was identified. FhFtn-1 contains a conserved motif of the ferroxidase center typical of vertebrate ferritins. Phylogenetic tree analysis showed that FhFtn-1 clusters with two ferritins of Paragonimus westermani, which suggests a common ancestry for the ferritins of these two trematodes. Recombinant FhFtn-1 protein expressed and purified from an Escherichia coli system showed iron-uptake ability. Moreover, FhFtn-1 showed strong reactivity with sera from rabbits infected with F. hepatica for 2-12 weeks, which suggests that this protein could be a potential antigen for immunodiagnosis of fascioliasis. qPCR analysis demonstrated that FhFtn-1-mRNA is expressed at significantly higher levels in adults and unembryonated eggs than in juveniles or miracidia. These results represent the first characterization of a ferritin protein from the liver fluke F. hepatica.\",\n \"corpus_id\": 33515370,\n \"score\": 1\n },\n {\n \"doc_id\": \"22727910\",\n \"title\": \"A novel calmodulin-like protein from the liver fluke, Fasciola hepatica.\",\n \"abstract\": \"An 18.2 kDa protein from the liver fluke, Fasciola hepatica has been identified and characterised. The protein shows strongest sequence similarity to egg antigen proteins from Schistosoma mansoni, Schistosoma japonicum and Clonorchis sinensis. The protein is predicted to adopt a calmodulin-like fold; it thus represents the third calmodulin-like protein to be characterised in F. hepatica and has been named FhCaM3. Compared to the classical calmodulin structure there are some variations. Most noticeably, the central, linker helix is disrupted by a cysteine residue. Alkaline native gel electrophoresis showed that FhCaM3 binds calcium ions. This binding event increases the ability of the protein to bind the hydrophobic fluorescent probe 8-anilinonaphthalene-1-sulphonate, consistent with an increase in surface hydrophobicity as seen in other calmodulins. FhCaM3 binds to the calmodulin antagonists trifluoperazine and W7, but not to the myosin regulatory light chain binding compound praziquantel. Immunolocalisation demonstrated that the protein is found in eggs and vitelline cells. Given the critical role of calcium ions in egg formation and hatching this suggests that FhCaM3 may play a role in calcium signalling in these processes. Consequently the antagonism of FhCaM3 may, potentially, offer a method for inhibiting egg production and thus reducing the spread of infection.\",\n \"corpus_id\": 23927989,\n \"score\": 1\n },\n {\n \"doc_id\": \"22819963\",\n \"title\": \"A plasma membrane Ca(2+)-ATPase (PMCA) from the liver fluke, Fasciola hepatica.\",\n \"abstract\": \"Fasciolosis is a parasitic infection by the liver fluke Fasciola hepatica, which costs the global agricultural community over US $2 billion per year. Its prevalence is rising due to factors such as climate change and drug resistance. ATP-dependent membrane transporters are considered good potential drug targets as they are essential for cellular processes and are in an exposed, accessible position in the cell. Immunolocalisation studies demonstrated that a plasma membrane calcium ATPase (PMCA) was localised to the parenchymal tissue in F. hepatica. The coding sequence for a F. hepatica PMCA (FhPMCA) has been obtained. This sequence encodes a 1,163 amino acid protein which contains motifs which are commonly conserved in PMCAs. Molecular modelling predicted that the protein has 10 transmembrane segments which include a potential calcium ion binding site and phosphorylation motif. FhPMCA interacts with the calmodulin-like protein FhCaM1, but not the related proteins FhCaM2 or FhCaM3, in a calcium-ion dependent manner. This interaction occurs through a region in the C-terminal region of FhPMCA which most likely adopts an α-helical conformation. When FhPMCA was heterologously expressed in a budding yeast strain deleted for its PMCA (Pmc1p), it restored viability. Microsomes prepared from these yeast cells had calcium ion stimulated ATPase activity which was inhibited by the known PMCA inhibitors, bisphenol and eosin. The potential of FhPMCA as a new drug target is discussed.\",\n \"corpus_id\": 26115371,\n \"score\": 1\n },\n {\n \"doc_id\": \"23770026\",\n \"title\": \"Characterization and differential expression of cathepsin L3 alleles from Fasciola hepatica.\",\n \"abstract\": \"Fasciola hepatica infections cause significant global problems in veterinary and human medicine, including causing huge losses in cattle and sheep production. F. hepatica host infection is a multistage process and flukes express papain-like cysteine proteases, termed cathepsins, which play pivotal roles in virulence through host entry, tissue migration and immune evasion. Expression of these proteases is developmentally regulated. Recent studies indicate that excystment of infective larvae is dependent on cysteine proteases and together FhCL3 and FhCB account for over 80% of total protease activity detectable in newly excysted juvenile (NEJ) fluke. This paper focuses on members of the cathepsin L gene family, specifically those belonging to the CL3 clade. The cDNA of two novel cathepsin L3 proteases--FhCL3-1 and FhCL3-2 were cloned. The mRNA transcript expression levels for these enzymes were significantly different at various time points in life development stages obtained in vitro, from dormant metacercariae to NEJ 24h after excystment. Maximum expression levels were observed in NEJ immediately after excystment. In all stages examined by Real Time PCR, FhCL3-2 was expressed at a higher level compared to FhCL3-1 which was expressed only at very low levels. Western blot and immunohistochemical analysis also indicated higher expression of the FhCL3-2 allele and its secretory nature. The ability of antibody responses from rats and sheep challenged with F. hepatica to recognize recombinant FhCL3-1 and FhCL3-2 was shown to differ. Differences were also confirmed through the use of anti-rFhCL3-1 and anti-rFhCL3-2 sera in Western blot analysis of juvenile excretory/secretory (ES) material separated by 2D electrophoresis. These results indicate analysis of relative expression of parasite virulence factors from different populations is required, as this will likely impact the effectiveness of vaccines based on these antigens.\",\n \"corpus_id\": 37671585,\n \"score\": 1\n },\n {\n \"doc_id\": \"24566472\",\n \"title\": \"Biochemical characterisation of glyceraldehyde 3-phosphate dehydrogenase (GAPDH) from the liver fluke, Fasciola hepatica.\",\n \"abstract\": \"Glyceraldehyde 3-phosphate dehydrogenase (GAPDH) catalyses one of the two steps in glycolysis which generate the reduced coenzyme NADH. This reaction precedes the two ATP generating steps. Thus, inhibition of GAPDH will lead to substantially reduced energy generation. Consequently, there has been considerable interest in developing GAPDH inhibitors as anti-cancer and anti-parasitic agents. Here, we describe the biochemical characterisation of GAPDH from the common liver fluke Fasciola hepatica (FhGAPDH). The primary sequence of FhGAPDH is similar to that from other trematodes and the predicted structure shows high similarity to those from other animals including the mammalian hosts. FhGAPDH lacks a binding pocket which has been exploited in the design of novel antitrypanosomal compounds. The protein can be expressed in, and purified from Escherichia coli; the recombinant protein was active and showed no cooperativity towards glyceraldehyde 3-phosphate as a substrate. In the absence of ligands, FhGAPDH was a mixture of homodimers and tetramers, as judged by protein-protein crosslinking and analytical gel filtration. The addition of either NAD⁺ or glyceraldehyde 3-phosphate shifted this equilibrium towards a compact dimer. Thermal scanning fluorimetry demonstrated that this form was considerably more stable than the unliganded one. These responses to ligand binding differ from those seen in mammalian enzymes. These differences could be exploited in the discovery of reagents which selectively disrupt the function of FhGAPDH.\",\n \"corpus_id\": 11247617,\n \"score\": 1\n },\n {\n \"doc_id\": \"24680784\",\n \"title\": \"A structural analysis of the AAA+ domains in Saccharomyces cerevisiae cytoplasmic dynein.\",\n \"abstract\": \"Dyneins are large protein complexes that act as microtubule based molecular motors. The dynein heavy chain contains a motor domain which is a member of the AAA+ protein family (ATPases Associated with diverse cellular Activities). Proteins of the AAA+ family show a diverse range of functionalities, but share a related core AAA+ domain, which often assembles into hexameric rings. Dynein is unusual because it has all six AAA+ domains linked together, in one long polypeptide. The dynein motor domain generates movement by coupling ATP driven conformational changes in the AAA+ ring to the swing of a motile element called the linker. Dynein binds to its microtubule track via a long antiparallel coiled-coil stalk that emanates from the AAA+ ring. Recently the first high resolution structures of the dynein motor domain were published. Here we provide a detailed structural analysis of the six AAA+ domains using our Saccharomycescerevisiae crystal structure. We describe how structural similarities in the dynein AAA+ domains suggest they share a common evolutionary origin. We analyse how the different AAA+ domains have diverged from each other. We discuss how this is related to the function of dynein as a motor protein and how the AAA+ domains of dynein compare to those of other AAA+ proteins.\",\n \"corpus_id\": 12086629,\n \"score\": 1\n },\n {\n \"doc_id\": \"24733753\",\n \"title\": \"Generating a detailed protein profile of Fasciola hepatica during the chronic stage of infection in cattle.\",\n \"abstract\": \"Fasciola hepatica is a trematode helminth causing a damaging disease, fasciolosis, in ruminants and humans. Comprehensive proteomic studies broaden our knowledge of the parasite's protein profile, and provide new insights into the development of more effective strategies to deal with fasciolosis. The objective of this study was to generate a comprehensive profile of F. hepatica proteins expressed during the chronic stage of infection in cattle by building on previous efforts in this area. The approach included an improved sample preparation procedure for surface and internal layers of the parasite, the application of nano-UPLC-ESI-qTOF-MS (nano-ultra-performance LC and ESI quadrupole TOF MS) integrated with different acquisition methods and in silico database search against various protein databases and a transcript database including a new assembly of publically available EST. Of a total of 776 identified proteins, 206 and 332 were specific to the surface and internal layers of the parasite, respectively. Furthermore, 238 proteins were common to both layers, with comparative differences of 172 proteins detected. Specific proteins not previously identified in F. hepatica, but shown to be immunomodulatory or potential drug targets for other parasites, are discussed.\",\n \"corpus_id\": 24946104,\n \"score\": 1\n },\n {\n \"doc_id\": \"25225247\",\n \"title\": \"Fasciola hepatica fatty acid binding protein induces the alternative activation of human macrophages.\",\n \"abstract\": \"The liver fluke Fasciola hepatica is a highly evolved parasite that uses sophisticated mechanisms to evade the host immune response. The immunosuppressive capabilities of the parasite have been associated with antigens secreted through the parasite's tegument, called excretory-secretory products (ESPs). Proteomic studies have identified the fatty acid binding protein (FABP) as one of molecules present in the parasite ESPs. Although FABP has been investigated for potential use in the development of vaccines against fascioliasis, its direct interaction with cells of immune system has not been studied. In this study, FABP was purified in native form from soluble extracts of F. hepatica adult flukes using a combination of molecular sieving chromatography and preparative isoelectric focusing. The immunological effect of the purified protein, termed Fh12, was assayed in vitro using monocyte-derived macrophages (MDM) obtained from healthy human donors. Results from the assay indicate that Fh12 produced a significantly increased arginase expression and activity and induced the expression of chitinase-3-like protein (CHI3L1). The assay also showed that Fh12 downregulated the production of nitric oxide (NO) and the expression of nitric oxide synthase (NOS2). This indicates that Fh12 induced the production of alternatively activated macrophages (AAMϕ). The results also demonstrated the ability of Fh12 to downregulate the secretion of the proinflammatory and inflammatory cytokines tumor necrosis factor alpha (TNF-α), interleukin-12 (IL-12), and IL-1βB, even after stimulation with lipopolysaccharide (LPS), as well as its ability to stimulate the overexpression of IL-10. These results suggest a potent anti-inflammatory role for Fh12, which could occur via targeting of Toll-like receptor 4 (TLR4).\",\n \"corpus_id\": 35747966,\n \"score\": 1\n },\n {\n \"doc_id\": \"25272277\",\n \"title\": \"A Ras-like domain in the light intermediate chain bridges the dynein motor to a cargo-binding region.\",\n \"abstract\": \"Cytoplasmic dynein, a microtubule-based motor protein, transports many intracellular cargos by means of its light intermediate chain (LIC). In this study, we have determined the crystal structure of the conserved LIC domain, which binds the motor heavy chain, from a thermophilic fungus. We show that the LIC has a Ras-like fold with insertions that distinguish it from Ras and other previously described G proteins. Despite having a G protein fold, the fungal LIC has lost its ability to bind nucleotide, while the human LIC1 binds GDP preferentially over GTP. We show that the LIC G domain binds the dynein heavy chain using a conserved patch of aromatic residues, whereas the less conserved C-terminal domain binds several Rab effectors involved in membrane transport. These studies provide the first structural information and insight into the evolutionary origin of the LIC as well as revealing how this critical subunit connects the dynein motor to cargo.\",\n \"corpus_id\": 18376103,\n \"score\": 1\n },\n {\n \"doc_id\": \"25312846\",\n \"title\": \"DYNLL2 dynein light chain binds to an extended linear motif of myosin 5a tail that has structural plasticity.\",\n \"abstract\": \"LC8 dynein light chains (DYNLL) are conserved homodimeric eukaryotic hub proteins that participate in diverse cellular processes. Among the binding partners of DYNLL2, myosin 5a (myo5a) is a motor protein involved in cargo transport. Here we provide a profound characterization of the DYNLL2 binding motif of myo5a in free and DYNLL2-bound form by using nuclear magnetic resonance spectroscopy, X-ray crystallography, and molecular dynamics simulations. In the free form, the DYNLL2 binding region, located in an intrinsically disordered domain of the myo5a tail, has a nascent helical character. The motif becomes structured and folds into a β-strand upon binding to DYNLL2. Despite differences of the myo5a sequence from the consensus binding motif, one peptide is accommodated in each of the parallel DYNLL2 binding grooves, as for all other known partners. Interestingly, while the core motif shows a similar interaction pattern in the binding groove as seen in other complexes, the flanking residues make several additional contacts, thereby lengthening the binding motif. The N-terminal extension folds back and partially blocks the free edge of the β-sheet formed by the binding motif itself. The C-terminal extension contacts the dimer interface and interacts with symmetry-related residues of the second myo5a peptide. The involvement of flanking residues of the core binding site of myo5a could modify the quaternary structure of the full-length myo5a and affect its biological functions. Our results deepen the knowledge of the diverse partner recognition of DYNLL proteins and provide an example of a Janus-faced linear motif.\",\n \"corpus_id\": 6627026,\n \"score\": 1\n },\n {\n \"doc_id\": \"25450768\",\n \"title\": \"Structure of the microtubule-binding domain of flagellar dynein.\",\n \"abstract\": \"Flagellar dyneins are essential microtubule motors in eukaryotes, as they drive the beating motions of cilia and flagella. Unlike myosin and kinesin motors, the track binding mechanism of dyneins and the regulation between the strong and weak binding states remain obscure. Here we report the solution structure of the microtubule-binding domain of flagellar dynein-c/DHC9 (dynein-c MTBD). The structure reveals a similar overall helix-rich fold to that of the MTBD of cytoplasmic dynein (cytoplasmic MTBD), but dynein-c MTBD has an additional flap, consisting of an antiparallel b sheet. The flap is positively charged and highly flexible. Despite the structural similarity to cytoplasmic MTBD, dynein-c MTBD shows only a small change in the microtubule- binding affinity depending on the registry change of coiled coil-sliding, whereby lacks the apparent strong binding state. The surface charge distribution of dynein-c MTBD also differs from that of cytoplasmic MTBD, which suggests a difference in the microtubule-binding mechanism.\",\n \"corpus_id\": -1,\n \"score\": 1\n },\n {\n \"doc_id\": \"25879787\",\n \"title\": \"TGF-β superfamily members from the helminth Fasciola hepatica show intrinsic effects on viability and development.\",\n \"abstract\": \"The helminth Fasciola hepatica causes fasciolosis throughout the world, a major disease of livestock and an emerging zoonotic disease in humans. Sustainable control mechanisms such as vaccination are urgently required. To discover potential vaccine targets we undertook a genome screen to identify members of the transforming growth factor (TGF) family of proteins. Herein we describe the discovery of three ligands belonging to this superfamily and the cloning and characterisation of an activin/TGF like molecule we term FhTLM. FhTLM has a limited expression pattern both temporally across the parasite stages but also spatially within the worm. Furthermore, a recombinant form of this protein is able to enhance the rate (or magnitude) of multiple developmental processes of the parasite indicating a conserved role for this protein superfamily in the developmental biology of a major trematode parasite. Our study demonstrates for the first time the existence of this protein superfamily within F. hepatica and assigns a function to one of the three identified ligands. Moreover further exploration of this superfamily may yield future targets for diagnostic or vaccination purposes due to its stage restricted expression and functional role.\",\n \"corpus_id\": 18584829,\n \"score\": 1\n },\n {\n \"doc_id\": \"27049013\",\n \"title\": \"Current Threat of Triclabendazole Resistance in Fasciola hepatica.\",\n \"abstract\": \"Triclabendazole (TCBZ) is the only chemical that kills early immature and adult Fasciola hepatica (liver fluke) but widespread resistance to the drug greatly compromises fluke control in livestock and humans. The mode of action of TCBZ and mechanism(s) underlying parasite resistance to the drug are not known. Due to the high prevalence of TCBZ resistance (TCBZ-R), effective management of drug resistance is now critical for sustainable livestock production. Here, we discuss the current status of TCBZ-R in F. hepatica, the global distribution of resistance observed in livestock, the possible mechanism(s) of drug action, the proposed mechanisms and genetic basis of resistance, and the prospects for future control of liver fluke infections using an integrated parasite management (IPM) approach.\",\n \"corpus_id\": 3704331,\n \"score\": 1\n },\n {\n \"doc_id\": \"27466253\",\n \"title\": \"Fasciola hepatica Surface Tegument: Glycoproteins at the Interface of Parasite and Host.\",\n \"abstract\": \"Fasciola hepatica, commonly known as liver fluke, is a trematode that causes Fasciolosis in ruminants and humans. The outer tegumental coat of F. hepatica (FhTeg) is a complex metabolically active biological matrix that is continually exposed to the host immune system and therefore makes a good vaccine target. F. hepatica tegumental coat is highly glycosylated and helminth-derived immunogenic oligosaccharide motifs and glycoproteins are currently being investigated as novel vaccine candidates. This report presents the first systematic characterization of FhTeg glycosylation using lectin microarrays to characterize carbohydrates motifs present, and lectin histochemistry to localize these on the F. hepatica tegument. We discovered that FhTeg glycoproteins are predominantly oligomannose oligosaccharides that are expressed on the spines, suckers and tegumental coat of F. hepatica and lectin blot analysis confirmed the abundance of N- glycosylated proteins. Although some oligosaccharides are widely distributed on the fluke surface other subsets are restricted to distinct anatomical regions. We selectively enriched for FhTeg mannosylated glycoprotein subsets using lectin affinity chromatography and identified 369 proteins by mass spectrometric analysis. Among these proteins are a number of potential vaccine candidates with known immune modulatory properties including proteases, protease inhibitors, paramyosin, Venom Allergen-like II, Enolase and two proteins, nardilysin and TRIL, that have not been previously associated with F. hepatica Furthermore, we provide a comprehensive insight regarding the putative glycosylation of FhTeg components that could highlight the importance of further studies examining glycoconjugates in host-parasite interactions in the context of F. hepatica infection and the development of an effective vaccine.\",\n \"corpus_id\": 10218556,\n \"score\": 1\n },\n {\n \"doc_id\": \"27864381\",\n \"title\": \"Dynein light chain DLC-1 promotes localization and function of the PUF protein FBF-2 in germline progenitor cells.\",\n \"abstract\": \"PUF family translational repressors are conserved developmental regulators, but the molecular function provided by the regions flanking the PUF RNA-binding domain is unknown. In C. elegans, the PUF proteins FBF-1 and FBF-2 support germline progenitor maintenance by repressing production of meiotic proteins and use distinct mechanisms to repress their target mRNAs. We identify dynein light chain DLC-1 as an important regulator of FBF-2 function. DLC-1 directly binds to FBF-2 outside of the RNA-binding domain and promotes FBF-2 localization and function. By contrast, DLC-1 does not interact with FBF-1 and does not contribute to FBF-1 activity. Surprisingly, we find that the contribution of DLC-1 to FBF-2 activity is independent of the dynein motor. Our findings suggest that PUF protein localization and activity are mediated by sequences flanking the RNA-binding domain that bind specific molecular partners. Furthermore, these results identify a new role for DLC-1 in post-transcriptional regulation of gene expression.\",\n \"corpus_id\": 6288352,\n \"score\": 1\n },\n {\n \"doc_id\": \"27866265\",\n \"title\": \"Proteomic analysis of Fasciola hepatica excretory and secretory products (FhESPs) involved in interacting with host PBMCs and cytokines by shotgun LC-MS/MS.\",\n \"abstract\": \"Fasciola hepatica is a helminth parasite with a worldwide distribution, which can cause chronic liver disease, fasciolosis, leading to economic losses in the livestock and public health in many countries. Control is mostly reliant on the use of drugs, and as a result, drug resistance has now emerged. The identification of F. hepatica genes involved in interaction between the parasite and host immune system is utmost important to elucidate the evasion mechanisms of the parasite and develop more effective strategies against fasciolosis. In this study, we aimed to identify molecules in F. hepatica excretory and secretory products (FhESPs) interacting with the host peripheral blood mononuclear cells (PBMCs), Th1-like cytokines (IL2 and IFN-γ), and Th17-like cytokines (IL17) by Co-IP combined with tandem mass spectrometry. The results showed that 14, 16, and 9 proteins in FhESPs could bind with IL2, IL17, and IFN-γ, respectively, which indicated that adult F. hepatica may evade the host immune responses through directly interplaying with cytokines. In addition, nine proteins in FhESPs could adhere to PBMCs. Our findings provided potential targets as immuno-regulators, and will be helpful to elucidate the molecular basis of host-parasite interactions and search for new potential proteins as vaccine and drug target candidates.\",\n \"corpus_id\": 22343498,\n \"score\": 1\n },\n {\n \"doc_id\": \"27940066\",\n \"title\": \"Fasciola hepatica demonstrates high levels of genetic diversity, a lack of population structure and high gene flow: possible implications for drug resistance.\",\n \"abstract\": \"Fasciola hepatica, the liver fluke, is a trematode parasite of considerable economic importance to the livestock industry and is a re-emerging zoonosis that poses a risk to human health in F. hepatica-endemic areas worldwide. Drug resistance is a substantial threat to the current and future control of F. hepatica, yet little is known about how the biology of the parasite influences the development and spread of resistance. Given that F. hepatica can self-fertilise and therefore inbreed, there is the potential for greater population differentiation and an increased likelihood of recessive alleles, such as drug resistance genes, coming together. This could be compounded by clonal expansion within the snail intermediate host and aggregation of parasites of the same genotype on pasture. Alternatively, widespread movement of animals that typically occurs in the UK could promote high levels of gene flow and prevent population differentiation. We identified clonal parasites with identical multilocus genotypes in 61% of hosts. Despite this, 84% of 1579 adult parasites had unique multilocus genotypes, which supports high levels of genotypic diversity within F. hepatica populations. Our analyses indicate a selfing rate no greater than 2%, suggesting that this diversity is in part due to the propensity for F. hepatica to cross-fertilise. Finally, although we identified high genetic diversity within a given host, there was little evidence for differentiation between populations from different hosts, indicating a single panmictic population. This implies that, once those emerge, anthelmintic resistance genes have the potential to spread rapidly through liver fluke populations.\",\n \"corpus_id\": 19054145,\n \"score\": 1\n },\n {\n \"doc_id\": \"28060841\",\n \"title\": \"Genomes of Fasciola hepatica from the Americas Reveal Colonization with Neorickettsia Endobacteria Related to the Agents of Potomac Horse and Human Sennetsu Fevers.\",\n \"abstract\": \"Food borne trematodes (FBTs) are an assemblage of platyhelminth parasites transmitted through the food chain, four of which are recognized as neglected tropical diseases (NTDs). Fascioliasis stands out among the other NTDs due to its broad and significant impact on both human and animal health, as Fasciola sp., are also considered major pathogens of domesticated ruminants. Here we present a reference genome sequence of the common liver fluke, Fasciola hepatica isolated from sheep, complementing previously reported isolate from cattle. A total of 14,642 genes were predicted from the 1.14 GB genome of the liver fluke. Comparative genomics indicated that F. hepatica Oregon and related food-borne trematodes are metabolically less constrained than schistosomes and cestodes, taking advantage of the richer millieux offered by the hepatobiliary organs. Protease families differentially expanded between diverse trematodes may facilitate migration and survival within the heterogeneous environments and niches within the mammalian host. Surprisingly, the sequencing of Oregon and Uruguay F. hepatica isolates led to the first discovery of an endobacteria in this species. Two contigs from the F. hepatica Oregon assembly were joined to complete the 859,205 bp genome of a novel Neorickettsia endobacterium (nFh) closely related to the etiological agents of human Sennetsu and Potomac horse fevers. Immunohistochemical studies targeting a Neorickettsia surface protein found nFh in specific organs and tissues of the adult trematode including the female reproductive tract, eggs, the Mehlis' gland, seminal vesicle, and oral suckers, suggesting putative routes for fluke-to-fluke and fluke-to-host transmission. The genomes of F. hepatica and nFh will serve as a resource for further exploration of the biology of F. hepatica, and specifically its newly discovered trans-kingdom interaction with nFh and the impact of both species on disease in ruminants and humans.\",\n \"corpus_id\": 3356027,\n \"score\": 1\n },\n {\n \"doc_id\": \"28348084\",\n \"title\": \"Delineating distinct heme-scavenging and -binding functions of domains in MF6p/helminth defense molecule (HDM) proteins from parasitic flatworms.\",\n \"abstract\": \"MF6p/FhHDM-1 is a small protein secreted by the parasitic flatworm (trematode) Fasciola hepatica that belongs to a broad family of heme-binding proteins (MF6p/helminth defense molecules (HDMs)). MF6p/HDMs are of interest for understanding heme homeostasis in trematodes and as potential targets for the development of new flukicides. Moreover, interest in these molecules has also increased because of their immunomodulatory properties. Here we have extended our previous findings on the mechanism of MF6p/HDM-heme interactions and mapped the protein regions required for heme binding and for other biological functions. Our data revealed that MF6p/FhHDM-1 forms high-molecular-weight complexes when associated with heme and that these complexes are reorganized by a stacking procedure to form fibril-like and granular nanostructures. Furthermore, we showed that MF6p/FhHDM-1 is a transitory heme-binding protein as protein·heme complexes can be disrupted by contact with an apoprotein (e.g. apomyoglobin) with higher affinity for heme. We also demonstrated that (i) the heme-binding region is located in the MF6p/FhHDM-1 C-terminal moiety, which also inhibits the peroxidase-like activity of heme, and (ii) MF6p/HDMs from other trematodes, such as Opisthorchis viverrini and Paragonimus westermani, also bind heme. Finally, we observed that the N-terminal, but not the C-terminal, moiety of MF6p/HDMs has a predicted structural analogy with cell-penetrating peptides and that both the entire protein and the peptide corresponding to the N-terminal moiety of MF6p/FhHDM-1 interact in vitro with cell membranes in hemin-preconditioned erythrocytes. Our findings suggest that MF6p/HDMs can transport heme in trematodes and thereby shield the parasite from the harmful effects of heme.\",\n \"corpus_id\": 40844086,\n \"score\": 1\n },\n {\n \"doc_id\": \"29476869\",\n \"title\": \"Advances in Fasciola hepatica research using 'omics' technologies.\",\n \"abstract\": \"The liver fluke Fasciola hepatica is an economically important pathogen of livestock worldwide, as well as being an important neglected zoonosis. Parasite control is reliant on the use of drugs, particularly triclabendazole, which is effective against multiple parasite stages. However, the spread of parasites resistant to triclabendazole has intensified the pursuit for novel control strategies. Emerging 'omics' technologies are helping advance our understanding of liver fluke biology, specifically the molecules that act at the host-parasite interface and are central to infection, virulence and long-term survival within the definitive host. This review discusses the technological sequencing advances that have facilitated the unbiased analysis of liver fluke biology, resulting in an extensive range of 'omics' datasets. In addition, we highlight the 'omics' studies of host responses to F. hepatica infection that, when combined with the parasite datasets, provide the opportunity for integrated analyses of host-parasite interactions. These extensive datasets will form the foundation for future in-depth analysis of F. hepatica biology and development, and the search for new drug or vaccine interventions.\",\n \"corpus_id\": 3693486,\n \"score\": 1\n },\n {\n \"doc_id\": \"29529855\",\n \"title\": \"Comparative Characterization of Four Calcium-Binding EF Hand Proteins from Opisthorchis viverrini.\",\n \"abstract\": \"Four isoforms of calcium binding proteins containing 2 EF hand motifs and a dynein light chain-like domain in the human liver fluke Opisthorchis viverrini, namely OvCaBP1, 2, 3, and 4, were characterized. They had molecular weights of 22.7, 21.6, 23.7, and 22.5 kDa, respectively and showed 37.2-42.1% sequence identity to CaBP22.8 of O. viverrini. All were detected in 2- and 4-week-old immature and mature parasites. Additionally, OvCaBP4 was found in newly excysted juveniles. Polyclonal antibodies against each isoform were generated to detect the native proteins in parasite extracts by Western blot analysis. All OvCaBPs were detected in soluble and insoluble crude worm extracts and in the excretory-secretory product, at approximate sizes of 21-23 kDa. The ion-binding properties of the proteins were analyzed by mobility shift assays with the divalent cations Ca2+, Mg2+, Zn2+, and Cu2+. All OvCaBPs showed mobility shifts with Ca2+ and Zn2+. OvCaBP1 showed also positive results with Mg2+ and Cu2+. As tegumental proteins, OvCaBP1, 2, and 3 are interesting drug targets for the treatment of opisthorchiasis.\",\n \"corpus_id\": 2316517,\n \"score\": 1\n },\n {\n \"doc_id\": \"20726552\",\n \"title\": \"Comparative proteomic analysis of triclabendazole response in the liver fluke Fasciola hepatica.\",\n \"abstract\": \"Control of Fasciola hepatica infections of livestock in the absence of vaccines depends largely on the chemical triclabendazole (TCBZ) because it is effective against immature and adult parasites. Overdependence on a single drug and improper application is considered a significant factor in increasing global reports of fluke resistant to TCBZ. The mode(s) of action and biological target(s) of TCBZ are not confirmed, delaying detection and the monitoring of early TCBZ resistance. In this study, to further understand liver fluke response to TCBZ, the soluble proteomes of TCBZ-resistant and TCBZ-susceptible isolates of F. hepatica were compared with and without in vitro exposure to the metabolically active form of the parent drug triclabendazole sulphoxide (TCBZ-SO), via two-dimensional gel electrophoresis (2-DE). Gel image analysis revealed proteins displaying altered synthesis patterns and responses both between isolates and under TCBZ-SO exposure. These proteins were identified by mass spectrometry supported by a F. hepatica expressed sequence tag (EST) data set. The TCBZ responding proteins were grouped into three categories; structural proteins, energy metabolism proteins, and \\\"stress\\\" response proteins. This single proteomic investigation supported the reductionist experiments from many laboratories that collectively suggest TCBZ has a range of effects on liver fluke metabolism. Proteomics highlighted differences in the innate proteome profile of different fluke isolates that may influence future therapy and diagnostics design. Two of the TCBZ responding proteins, a glutathione transferase and a fatty acid binding protein, were cloned, produced as recombinants, and both found to bind TCBZ-SO at physiologically relevant concentrations, which may indicate a role in TCBZ metabolism and resistance.\",\n \"corpus_id\": 27345424,\n \"score\": 0\n },\n {\n \"doc_id\": \"21308846\",\n \"title\": \"Crystal structure of the sensory domain of Escherichia coli CadC, a member of the ToxR-like protein family.\",\n \"abstract\": \"The membrane-integral transcriptional activator CadC comprises sensory and transcriptional regulatory functions within one polypeptide chain. Its C-terminal periplasmic domain, CadC(pd), is responsible for sensing of environmental pH as well as for binding of the feedback inhibitor cadaverine. Here we describe the crystal structure of CadC(pd) (residues 188-512) solved at a resolution of 1.8 Å via multiple wavelength anomalous dispersion (MAD) using a ReCl(6)(2-) derivative. CadC(pd) reveals a novel fold comprising two subdomains: an N-terminal subdomain dominated by a β-sheet in contact with three α-helices and a C-terminal subdomain formed by an eleven-membered α-helical bundle, which is oriented almost perpendicular to the helices in the first subdomain. Further to the native protein, crystal structures were also solved for its variants D471N and D471E, which show functionally different behavior in pH sensing. Interestingly, in the heavy metal derivative of CadC(pd) used for MAD phasing a ReCl(6)(2-) ion was found in a cavity located between the two subdomains. Amino acid side chains that coordinate this complex ion are conserved in CadC homologues from various bacterial species, suggesting a function of the cavity in the binding of cadaverine, which was supported by docking studies. Notably, CadC(pd) forms a homo-dimer in solution, which can be explained by an extended, albeit rather polar interface between two symmetry-related monomers in the crystal structure. The occurrence of several acidic residues in this region suggests protonation-dependent changes in the mode of dimerization, which could eventually trigger transcriptional activation by CadC in the bacterial cytoplasm.\",\n \"corpus_id\": 28544446,\n \"score\": 0\n },\n {\n \"doc_id\": \"21539810\",\n \"title\": \"Crystal structure of the middle domain of human poly(A)-binding protein-interacting protein 1.\",\n \"abstract\": \"In eukaryotes, the poly(A)-binding protein (PABP) is one of the important factors for initiation of messenger RNA translation. PABP activity is regulated by the PABP-interacting proteins (Paips), which include Paip1, Paip2A, and Paip2B. Human Paip1 has three different isoforms. Here, we report the crystal structure of the middle domain of Paip1 isoform 2 (Paip1M) as determined by single-wavelength anomalous dispersion phasing. The structure reveals a crescent-shaped domain consisting of 10 α-helices and two antiparallel β-strands forming a β-hairpin. The 10 α-helices are arranged as five HEAT repeats which form a double layer of α helices with a convex and a concave surface. Despite low sequence identity, the overall fold of Paip1M is similar to the middle domain of human eIF4GII and yeast eIF4GI. Moreover, the amino-acid sequence motif and the local structure of eIF4G involved in binding of eIF4A, are conserved in Paip1. The structure reported here is the first of a member of the Paip family, thereby filling a gap in our understanding of initiation of eukaryotic mRNA translation in three dimensions.\",\n \"corpus_id\": 45850805,\n \"score\": 0\n },\n {\n \"doc_id\": \"21589904\",\n \"title\": \"A family of helminth molecules that modulate innate cell responses via molecular mimicry of host antimicrobial peptides.\",\n \"abstract\": \"Over the last decade a significant number of studies have highlighted the central role of host antimicrobial (or defence) peptides in modulating the response of innate immune cells to pathogen-associated ligands. In humans, the most widely studied antimicrobial peptide is LL-37, a 37-residue peptide containing an amphipathic helix that is released via proteolytic cleavage of the precursor protein CAP18. Owing to its ability to protect against lethal endotoxaemia and clinically-relevant bacterial infections, LL-37 and its derivatives are seen as attractive candidates for anti-sepsis therapies. We have identified a novel family of molecules secreted by parasitic helminths (helminth defence molecules; HDMs) that exhibit similar biochemical and functional characteristics to human defence peptides, particularly CAP18. The HDM secreted by Fasciola hepatica (FhHDM-1) adopts a predominantly α-helical structure in solution. Processing of FhHDM-1 by F. hepatica cathepsin L1 releases a 34-residue C-terminal fragment containing a conserved amphipathic helix. This is analogous to the proteolytic processing of CAP18 to release LL-37, which modulates innate cell activation by classical toll-like receptor (TLR) ligands such as lipopolysaccharide (LPS). We show that full-length recombinant FhHDM-1 and a peptide analogue of the amphipathic C-terminus bind directly to LPS in a concentration-dependent manner, reducing its interaction with both LPS-binding protein (LBP) and the surface of macrophages. Furthermore, FhHDM-1 and the amphipathic C-terminal peptide protect mice against LPS-induced inflammation by significantly reducing the release of inflammatory mediators from macrophages. We propose that HDMs, by mimicking the function of host defence peptides, represent a novel family of innate cell modulators with therapeutic potential in anti-sepsis treatments and prevention of inflammation.\",\n \"corpus_id\": 11573203,\n \"score\": 0\n },\n {\n \"doc_id\": \"24324649\",\n \"title\": \"Crystal structures of the human G3BP1 NTF2-like domain visualize FxFG Nup repeat specificity.\",\n \"abstract\": \"Ras GTPase Activating Protein SH3 Domain Binding Protein (G3BP) is a potential anti-cancer drug target implicated in several cellular functions. We have used protein crystallography to solve crystal structures of the human G3BP1 NTF2-like domain both alone and in complex with an FxFG Nup repeat peptide. Despite high structural similarity, the FxFG binding site is located between two alpha helices in the G3BP1 NTF2-like domain and not at the dimer interface as observed for nuclear transport factor 2. ITC studies showed specificity towards the FxFG motif but not FG and GLFG motifs. The unliganded form of the G3BP1 NTF2-like domain was solved in two crystal forms to resolutions of 1.6 and 3.3 Å in space groups P212121 and P6322 based on two different constructs, residues 1-139 and 11-139, respectively. Crystal packing of the N-terminal residues against a symmetry related molecule in the P212121 crystal form might indicate a novel ligand binding site that, however, remains to be validated. The crystal structures give insight into the nuclear transportation mechanisms of G3BP and provide a basis for future structure based drug design.\",\n \"corpus_id\": 1523159,\n \"score\": 0\n },\n {\n \"doc_id\": \"25602718\",\n \"title\": \"Distribution of Fasciola hepatica and F. gigantica in the endemic area of Guilan, Iran: Relationships between zonal overlap and phenotypic traits.\",\n \"abstract\": \"Fascioliasis is a zoonotic disease emerging in numerous parts of the world. In any endemic area, the characterisation of scenarios and patterns of infection must always be considered the starting point before implementing any control measure. Fascioliasis is a parasitic disease of different epidemiological, pathological and control characteristics depending on the endemic area and the causal agent, Fasciola hepatica and Fasciolagigantica. Classically it has been accepted that F. hepatica is present worldwide, while the distribution of the two species overlaps in many areas of Africa and Asia. Fascioliasis caused by F. hepatica, F. gigantica and intermediate forms is present in Guilan province, a complicated epidemiological situation where the highest human infection rates have been described in Iran. Morphometric tools were used to analyse the possible relationship between liver-fluke metric traits and geographical and altitudinal distribution. This is the first study in which a detailed distribution of both Fasciola species is analysed in a human fascioliasis endemic area with a zonal overlap transmission pattern. An accurate analysis was conducted to phenotypically discriminate between fasciolids from naturally infected livestock (cattle, buffaloes, sheep and goats). The distribution of the % F. hepatica-like (F.h.) and F. gigantica-like (F.g.) flukes detected in each liver versus altitude (m) in each group was analysed. The presence of F.g. specimens mainly in locations below sea level (average: 11.23% F.h., 88.77% F.g.), the presence of both species with similar intensity at 1-99m (average: 56.95% F.h., 43.05% F.g.) and the presence of F.h. specimens mainly from 100 to 999m (average: 71.69% F.h., 28.31% F.g.) as well as in locations with an altitude above 1000m (average: 97.48% F.h., 2.52% F.g.) are noteworthy. A significant positive correlation was obtained between altitude and % F.h., and a significant negative correlation was obtained between altitude and % F.g. The results show that F.g. populations in cattle, buffaloes and sheep share larger size values, but smaller specimens are present mainly in lowland populations located below sea level, independently of the host species (cattle, buffalo). F.g. from lowland cattle presented larger worm size variability. Four different fascioliasis transmission areas may be distinguished in Guilan: (a) lowland coastal areas neighbouring the Caspian Sea shore, below sea level, where basically F. gigantica-like specimens are found; (b) a coastal plain with an altitude between 1 and 100m where both species co-exist; (c) areas with altitude values of 100-999m where mainly F. hepatica-like specimens are found; (d) highland mountainous areas, where basically F. hepatica-like specimens are found. The study of the influence of the host species on the liver fluke was also carried out by a size-out analysis. This is the first report concerning the decisive influence exercised by the host species on the metric traits of F. gigantica adults.\",\n \"corpus_id\": 2878496,\n \"score\": 0\n },\n {\n \"doc_id\": \"26623254\",\n \"title\": \"Partial Hepatectomy for the Resistant Fasciola Hepatica Infection in a Child.\",\n \"abstract\": \"Fascioliasis is an emerging and important chronic parasitic disease caused by two trematode liver fluke species: Fasciola hepatica (F. hepatica) and Fasciola gigantica (F. gigantica) infecting several herbivorous mammals including cattle, goats, sheep, and humans. We report a 9-year-old girl who suffered from F. hepatica infection and underwent right hepatectomy because of increasing abdominal pain resistant to anthelmintic chemotherapy. When anthelmintic drug treatment is not effective and abdominal pain persists, surgical resection including hepatectomy should be kept in mind for resistant F. hepatica infection.\",\n \"corpus_id\": 19257513,\n \"score\": 0\n },\n {\n \"doc_id\": \"27466369\",\n \"title\": \"Structure of the Single-lobe Myosin Light Chain C in Complex with the Light Chain-binding Domains of Myosin-1C Provides Insights into Divergent IQ Motif Recognition.\",\n \"abstract\": \"Myosin light chains are key regulators of class 1 myosins and typically comprise two domains, with calmodulin being the archetypal example. They bind IQ motifs within the myosin neck region and amplify conformational changes in the motor domain. A single lobe light chain, myosin light chain C (MlcC), was recently identified and shown to specifically bind to two sequentially divergent IQ motifs of the Dictyostelium myosin-1C. To provide a molecular basis of this interaction, the structures of apo-MlcC and a 2:1 MlcC·myosin-1C neck complex were determined. The two non-functional EF-hand motifs of MlcC pack together to form a globular four-helix bundle that opens up to expose a central hydrophobic groove, which interacts with the N-terminal portion of the divergent IQ1 and IQ2 motifs. The N- and C-terminal regions of MlcC make critical contacts that contribute to its specific interactions with the myosin-1C divergent IQ motifs, which are contacts that deviate from the traditional mode of calmodulin-IQ recognition.\",\n \"corpus_id\": 205361333,\n \"score\": 0\n },\n {\n \"doc_id\": \"29474932\",\n \"title\": \"Profiling G protein-coupled receptors of Fasciola hepatica identifies orphan rhodopsins unique to phylum Platyhelminthes.\",\n \"abstract\": \"G protein-coupled receptors (GPCRs) are established drug targets. Despite their considerable appeal as targets for next-generation anthelmintics, poor understanding of their diversity and function in parasitic helminths has thwarted progress towards GPCR-targeted anti-parasite drugs. This study facilitates GPCR research in the liver fluke, Fasciola hepatica, by generating the first profile of GPCRs from the F. hepatica genome. Our dataset describes 147 high confidence GPCRs, representing the largest cohort of GPCRs, and the largest set of in silico ligand-receptor predictions, yet reported in any parasitic helminth. All GPCRs fall within the established GRAFS nomenclature; comprising three glutamate, 135 rhodopsin, two adhesion, five frizzled, one smoothened, and one secretin GPCR. Stringent annotation pipelines identified 18 highly diverged rhodopsins in F. hepatica that maintained core rhodopsin signatures, but lacked significant similarity with non-flatworm sequences, providing a new sub-group of potential flukicide targets. These facilitated identification of a larger cohort of 76 related sequences from available flatworm genomes, representing new members of existing groups (PROF1/Srfb, Rho-L, Rho-R, Srfa, Srfc) of flatworm-specific rhodopsins. These receptors imply flatworm specific GPCR functions, and/or co-evolution with unique flatworm ligands, and could facilitate the development of exquisitely selective anthelmintics. Ligand binding domain sequence conservation relative to deorphanised rhodopsins enabled high confidence ligand-receptor matching of seventeen receptors activated by acetylcholine, neuropeptide F/Y, octopamine or serotonin. RNA-Seq analyses showed expression of 101 GPCRs across various developmental stages, with the majority expressed most highly in the pathogenic intra-mammalian juvenile parasites. These data identify a broad complement of GPCRs in F. hepatica, including rhodopsins likely to have key functions in neuromuscular control and sensory perception, as well as frizzled and adhesion/secretin families implicated, in other species, in growth, development and reproduction. This catalogue of liver fluke GPCRs provides a platform for new avenues into our understanding of flatworm biology and anthelmintic discovery.\",\n \"corpus_id\": 4481527,\n \"score\": 0\n }\n]","isConversational":false}}},{"rowIdx":77,"cells":{"query":{"kind":"string","value":"{\n \"doc_id\": \"29460862\",\n \"title\": \"Host preferences and feeding patterns of Anopheles sinensis Wiedemann in three sites of Shandong province, China.\",\n \"abstract\": \"Background & objectives: Anopheles sinensis Wiedemann is a major vector of malaria and is among the dominant species in Shandong province of China. Knowledge of the blood-feeding patterns of mosquitoes is crucial for elimination of malaria vectors. However, little information is available on the blood-feeding behaviour of An. sinensis mosquitoes in Shandong province. This study was carried out to compare the blood-feeding behaviour of An. sinensis in malaria-endemic areas of Shandong province China. Methods: Adult Anopheles mosquitoes were collected from three malaria-endemic areas (Jimo, Yinan and Shanxian), during the peak months of mosquito population (August and September) from 2014 to 2015. Indoor-resting mosquitoes and outdoor-resting blood-fed females were sampled in the morning hours (0600 to 0900 hrs) from 10 randomly selected houses using pyrethrum spray catch method, and sweeping with an insect net. ELISA was used for the identification of blood meal. The blood meal of each mosquito was tested against antisera specific to human, pig, dog, cow, goat, horse (mule) and fowl. Results: At all indoor study locations of Jimo, Yinan and Shanxian, 59.4, 68.1 and 98.8% blood-engorged female An. sinensis collected from cattle sheds fed almost exclusively on bovines, respectively. For outdoor locations, at Jimo site, 27.27 and 49.55% An. sinensis fed on cattle and pigs; at Yinan, 30.42% fed on cattle and 36.88% fed both on cattle and goats, while no pig antibodies were detected. At Shanxian, percent of An. sinensis that fed on cattle, pigs and cattle-goat was 20.72, 27.62 and 21.78%, respectively. Interpretation & conclusion: The analysis of An. sinensis blood meals in all the three studied areas from human houses, cattle sheds, pig sheds and mixed dwellings revealed that An. sinensis prefers cattle hosts, and can feed on other available animal hosts if the cattle hosts are absent, and the mosquitoes readily feed on humans when domestic animals (cattle and pigs) are not nearby for feeding. The analysis of blood meal revealed that An. sinensis follow opportunistic feeding in Shandong province, China.\",\n \"corpus_id\": 3442265\n}"},"candidates":{"kind":"list like","value":[{"doc_id":"18538036","title":"The resting sites and blood-meal sources of Anopheles minimus in Taiwan.","abstract":"BACKGROUND: The WHO declared Taiwan free from malaria in 1965, but in 2003 the reporting of two introduced cases in a rural area suggested a possible local transmission of this disease. Therefore, understanding the resting sites and the blood sources of Anopheles minimus is crucial in order to provide information for implementing vector control strategies. METHODS: During a two-year survey, mosquitoes were collected in houses and their surrounding areas and at the bank of larval habitats by backpack aspirators in 17 villages in rural areas of southern and eastern Taiwan for 1 hr. On the same day, blacklight traps were hung downward overnight. Blood-fed mosquito samples were analysed by PCR. RESULTS: Of the 195 total households surveyed by backpack aspirators, no Anopheles adults were collected inside the houses, while a single Anopheles minimus and a single Anopheles maculatus were collected outside of the houses. On the same day, 23 An. minimus, two An. maculatus, two Anopheles ludlowae, two Anopheles sinensis, and one Anopheles tessellatus were collected along the bank of larval habitats. In blacklight traps hung outside of the houses in the villages, 69 An. minimus, 62 An. ludlowae, 31 An. sinensis, and 19 An. maculatus were collected. In larval habitats, 98 An. ludlowae, 64 An. minimus, 49 An. sinensis, and 14 An. maculatus were collected. Of a total of 10 blood-fed samples, An. minimus fed on four animals including bovine (60%), dogs (20%), pig (10%), and non-chicken avian (10%). CONCLUSION: Anopheles minimus, an opportunist feeder in Taiwan, was not collected inside the houses, but was found outside of the houses in villages and surrounding larval habitats. Therefore, an outdoor transmission of malaria is likely to occur and, thus, the bed nets, which are favoured for controlling the late biting of An. minimus, should be a very efficient and effective method for those local residents who sleep outdoors. Additionally, space spray of insecticides for Anopheles at night, as well as residual spray inside animal huts and selective larval habitats, are also helpful to control female adults.","corpus_id":2098821,"score":2},{"doc_id":"21559055","title":"Seasonal abundance and host-feeding patterns of anopheline vectors in malaria endemic area of iran.","abstract":"Seasonal abundance and tendency to feed on humans are important parameters to measure for effective control of malaria vectors. The objective of this study was to describe relation between feeding pattern, abundance, and resting behavior of four malaria vectors in southern Iran. This study was conducted in ten indicator villages (based on malaria incidence and entomological indices) in mountainous/hilly and plain regions situated south and southeastern Iran. Mosquito vectors were collected from indoor as well as outdoor shelters and the blood meals were examined by ELISA test. Over all 7654 female Anopheles spp. were captured, the most common species were Anopheles stephensi, An. culicifacies, An. fluviatilis, and An. d'thali. The overall human blood index was 37.50%, 19.83%, 16.4%, and 30.1% for An. fluviatilis, An. stephensi, An. culicifacies, and An. d'thali, respectively. In addition, An. fluviatilis fed on human blood during the entire year but the feeding behavior of An. stephensi and An. culicifacies varied according to seasons. Overall, the abundance of the female mosquito positive to human blood was 4.25% per human shelter versus 17.5% per animal shelter. This result indicates that the vectors had tendency to rest in animal shelters after feeding on human. Therefore, vector control measure should be planned based on such as feeding pattern, abundance, and resting behavior of these vectors in the area.","corpus_id":17230409,"score":2},{"doc_id":"21569546","title":"Plasmodium falciparum transmission and aridity: a Kenyan experience from the dry lands of Baringo and its implications for Anopheles arabiensis control.","abstract":"BACKGROUND: The ecology of malaria vectors particularly in semi-arid areas of Africa is poorly understood. Accurate knowledge on this subject will boost current efforts to reduce the burden of malaria in sub-Saharan Africa. The objective of this study was to describe the dynamics of malaria transmission in two model semi-arid sites (Kamarimar and Tirion) in Baringo in Kenya. METHODS: Adult mosquitoes were collected indoors by pyrethrum spray collections (PSC) and outdoors by Centers for Disease Control (CDC) light traps and identified to species by morphological characteristics. Sibling species of Anopheles gambiae complex were further characterized by rDNA. PCR and enzyme-linked immuno-sorbent assays (ELISA) were used to test for Plasmodium falciparum circumsporozoite proteins and host blood meal sources respectively. RESULTS: Anopheles arabiensis was not only the most dominant mosquito species in both study sites but also the only sibling species of An. gambiae s.l. present in the area. Other species identified in the study area were Anopheles funestus, Anopheles pharoensis and Anopheles coustani. For Kamarimar but not Tirion, the human blood index (HBI) for light trap samples was significantly higher than for PSC samples (Kamarimar, 0.63 and 0.11, Tirion, 0.48 and 0.43). The HBI for light trap samples was significantly higher in Kamarimar than in Tirion while that of PSC samples was significantly higher in Tirion than in Kamarimar. Entomological inoculation rates (EIR) were only detected for one month in Kamarimar and 3 months in Tirion. The number of houses in a homestead, number of people sleeping in the house, quality of the house, presence or absence of domestic animals, and distance to the animal shelter and the nearest larval habitat were significant predictors of An. arabiensis occurrence. CONCLUSION: Malaria transmission in the study area is seasonal with An. arabiensis as the dominant vector. The fact this species feeds readily on humans and domestic animals suggest that zooprophylaxis may be a plausible malaria control strategy in semi-arid areas of Africa. The results also suggest that certain household characteristics may increase the risk of malaria transmission.","corpus_id":1035329,"score":2},{"doc_id":"21727666","title":"Seasonal prevalence & resting behaviour of Anopheles minimus Theobald & An. fluviatilis James (Diptera: Culicidae) in east-central India.","abstract":"BACKGROUND & OBJECTIVES: Anopheles minimus has recently been reported to have re-appeared in Keonjhar district of Orissa after a period of about 45 years of launching the malaria eradication programme. An. minimus and An. fluviatilis were the incriminated major malaria vectors in the district, endemic for falciparum malaria. The information on seasonal prevalence and resting behaviour of the vectors is crucial for implementing appropriate malaria control measures. Therefore, a study was undertaken on seasonal prevalence and resting behaviour of An. minimus and An. fluviatilis in this district. METHODS: Seven randomly selected villages of Keonjhar district, Orissa, were studied during August 2005 to November 2007. Daytime resting collections indoors and outdoors were made covering three seasons of the year. The Anopheles mosquitoes obtained from different habitats were identified. Collections were maintained separately according to different sites as well as heights of the walls in human dwellings. RESULTS: Among the indoor collections, the densities of An. minimus and An. fluviatilis were higher in human dwellings than cattle sheds. An. fluviatilis was the predominant (41.5%) species followed by An. minimus (26.3%) in human dwellings. The density of both the vector species in human dwellings peaked during rainy and winter seasons followed by summer. Walls were the most preferred site by these vectors for resting and the maximum number was collected at a height of 3 to 4 ft. INTERPRETATION & CONCLUSIONS: The resting behaviour of the vector species increases their contact with the sprayed walls and therefore, a quality residual spraying of human dwellings focusing indoor walls could interrupt the malaria transmission in this area.","corpus_id":15447460,"score":2},{"doc_id":"22115320","title":"The abundance and host-seeking behavior of culicine species (Diptera: Culicidae) and Anopheles sinensis in Yongcheng city, People's Republic of China.","abstract":"BACKGROUND: The knowledge of mosquito species diversity and the level of anthropophily exhibited by each species in a region are of great importance to the integrated vector control. Culicine species are the primary vectors of Japanese encephalitis (JE) virus and filariasis in China. Anopheles sinensis plays a major role in the maintenance of Plasmodium vivax malaria transmission in China. The goal of this study was to compare the abundance and host-seeking behavior of culicine species and An. sinensis in Yongcheng city, a representative region of P. vivax malaria. Specifically, we wished to determine the relative attractiveness of different animal baits versus human bait to culicine species and An. sinensis. RESULTS: Culex tritaeniorhynchus was the most prevalent mosquito species and An. sinensis was the sole potential vector of P. vivax malaria in Yongcheng city. There were significant differences (P < 0.01) in the abundance of both An. sinensis and Cx. tritaeniorhynchus collected in distinct baited traps. The relative attractiveness of animal versus human bait was similar towards both An. sinensis and Cx. tritaeniorhynchus. The ranking derived from the mean number of mosquitoes per bait indicated that pigs, goats and calves frequently attracted more mosquitoes than the other hosts tested (dogs, humans, and chickens). These trends were similar across all capture nights at three distinct villages. The human blood index (HBI) of female An. sinensis was 2.94% when computed with mixed meals while 3.70% computed with only the single meal. 19:00~21:00 was the primary peak of host-seeking female An. sinensis while 4:00~5:00 was the smaller peak at night. There was significant correlation between the density of female An. sinensis and the average relative humidity (P < 0.05) in Wangshanzhuang village. CONCLUSIONS: Pigs, goats and calves were more attractive to An. sinensis and Cx. tritaeniorhynchus than dogs, humans, and chickens. Female An. sinensis host-seeking activity mainly occurred from 19:00 to 21:00. Thus, we propose that future vector control against An. sinensis and Cx. tritaeniorhynchus in the areas along the Huang-Huai River of central China should target the interface of human activity with domestic animals and adopt before human hosts go to bed at night.","corpus_id":2559019,"score":2},{"doc_id":"22336191","title":"Blood-feeding patterns of Anopheles mosquitoes in a malaria-endemic area of Bangladesh.","abstract":"BACKGROUND: Blood-feeding patterns of mosquitoes are crucial for incriminating malaria vectors. However, little information is available on the host preferences of Anopheles mosquitoes in Bangladesh. Therefore, the objective of the present study was to determine the hematophagic tendencies of the anophelines inhabiting a malaria-endemic area of Bangladesh. METHODS: Adult Anopheles mosquitoes were collected using light traps (LTs), pyrethrum spray (PS), and human bait (HB) from a malaria-endemic village (Kumari, Bandarban, Bangladesh) during the peak months of malaria transmission (August-September). Enzyme-linked immunosorbent assay (ELISA) and polymerase chain reaction (PCR) were performed to identify the host blood meals of Anopheles mosquitoes. RESULTS: In total, 2456 female anopheline mosquitoes representing 21 species were collected from the study area. Anopheles vagus Doenitz (35.71%) was the dominant species followed by An. philippinensis Ludlow (26.67%) and An. minimus s.l. Theobald (5.78%). All species were collected by LTs set indoors (n = 1094), 19 species were from outdoors (n = 784), whereas, six by PS (n = 549) and four species by HB (n = 29). Anopheline species composition significantly differed between every possible combination of the three collection methods (χ(2) test, P < 0.001). Host blood meals were successfully detected from 1318 (53.66%) Anopheles samples belonging to 17 species. Values of the human blood index (HBI) of anophelines collected from indoors and outdoors were 6.96% and 11.73%, respectively. The highest values of HBI were found in An. baimai Baimaii (80%), followed by An. minimus s.l. ( 43.64%) and An. annularis Van den Wulp (37.50%). Anopheles baimai (B(i) = 0.63) and An. minimus s.l. ( B(i) = 0.24) showed strong relative preferences (B(i)) for humans among all hosts (human, bovine, goats/sheep, and others). Anopheles annularis, An. maculatus s.l. Theobald, and An. pallidus Theobald exhibited opportunistic blood-feeding behavior, in that they fed on either humans or animals, depending on whichever was accessible. The remaining 12 species preferred bovines as hosts. CONCLUSIONS: The observed high anthropophilic nature of An. baimai, An. minimus s.l., and An. annularis revealed these species to be important malaria vectors in hilly areas of Bangladesh. Higher values of HBI in outdoor-resting mosquitoes indicated that indoor collection alone is not adequate for evaluating malaria transmission in the area.","corpus_id":547702,"score":2},{"doc_id":"22676415","title":"Host feeding patterns and preference of Anopheles minimus (Diptera: Culicidae) in a malaria endemic area of western Thailand: baseline site description.","abstract":"BACKGROUND: Host feeding patterns of Anopheles minimus in relation to ambient environmental conditions were observed during a 2-year period at Tum Sua Village, located in Mae Sot District, Tak Province, in western Thailand, where An. minimus is found in abundance and regarded as the most predominant malaria vector species. Detailed information on mosquito behavior is important for understanding the epidemiology of disease transmission and developing more effective and efficient vector control methods. METHODS: Adult mosquitoes were collected every 2 months for two consecutive nights from 1800 to 0600 hrs. Three collection methods were used; indoor human-landing collections (HLC), outdoor HLC, and outdoor cattle-bait collections (CBC). RESULTS: A total of 7,663 female Anopheles mosquitoes were collected of which 5,392 were identified as members of 3 different species complexes, the most prevalent being Anopheles minimus complex (50.36%), followed by Anopheles maculatus complex (19.68%) and Anopheles dirus complex (0.33%). An. minimus s.s. comprised virtually all (> 99.8 percent) of Minimus Complex species captured. Blood feeding behavior of An. minimus was more pronounced during the second half of the evening, showing a slight preference to blood feed outdoors (~60%) versus inside structures. Significantly (P < 0.0001) more An. minimus were collected from human-baited methods compared with a tethered cow, indicating a more anthropophilic feeding behavior. Although a significant difference in total number of mosquitoes from the HLC was recorded between the first and second year, the mean biting frequency over the course of the evening hours remained similar. CONCLUSIONS: The Human landing activity of An. minimus in Tum Sua Village showed a stronger preference/attraction for humans compared to a cow-baited collection method. This study supports the incrimination of An. minimus as the primary malaria vector in the area. A better understanding of mosquito behavior related to host preference, and the temporal and spatial blood feeding activity will help facilitate the design of vector control strategies and effectiveness of vector control management programs in Thailand.","corpus_id":18063759,"score":2},{"doc_id":"22776520","title":"Vector capacity of Anopheles sinensis in malaria outbreak areas of central China.","abstract":"BACKGROUND: Both falciparum and vivax malaria were historically prevalent in China with high incidence. With the control efforts, the annual incidence in the whole country has reduced to 0.0001% except in some areas in the southern borders after 2000. Despite this, the re-emergence or outbreak of malaria was unavoidable in central China during 2005-2007. In order to understand the role of the vector in the transmission of malaria during the outbreak period, the vector capacity of An. sinensis in Huanghuai valley of central China was investigated. FINDINGS: The study was undertaken in two sites, namely Huaiyuan county of Anhui province and Yongcheng county of Henan province. In each county, malaria cases were recorded for recent years, and transmission risk factors for each study village including anti-mosquito facilities and total number of livestock were recorded by visiting each household in the study sites. The specimens of mosquitoes were collected in two villages, and population density and species in each study site were recorded after the identification of different species, and the blood-fed mosquitoes were tested by ring precipitation test. Finally, various indicators were calculated to estimate vector capacity or dynamics, including mosquito biting rate (MBR), human blood index (HBI), and the parous rates (M). Finally, the vector capacity, as an important indicator of malaria transmission to predict the potential recurrence of malaria, was estimated and compared in each study site. About 93.0% of 80 households in Huaiyuan and 89.3% of 192 households in Yongcheng had anti-mosquito facilities. No cattle or pigs were found, only less than 10 sheep were found in each study village. A total of 94 and 107 Anopheles spp. mosquitos were captured in two study sites, respectively, and all of An. sinensis were morphologically identified. It was found that mosquito blood-feeding peak was between 9:00 pm and 12:00 pm. Man biting rate of An. sinensis was 6.0957 and 5.8621 (mosquitoes/people/night) estimated by using half-night human bait trap method and full-capture method, respectively. Human blood indexes (HBI) were 0.6667 (6/9) and 0.6429 (18/28), and man-biting habits were 0.2667 and 0.2572 in two sites, respectively. Therefore, the expectation of infective life and vector capacity of An. sinensis was 0.3649-0.4761 and 0.5502-0.7740, respectively, in Huanhuai valley of central China where the outbreak occurred, which is much higher than that in the previous years without malaria outbreak. CONCLUSIONS: This study suggests that vivax malaria outbreak in Huanhuai valley is highly related to the enhancement in vector capacity of An. sinensis for P. vivax, which is attributed to the local residents' habits and the remarkable drop in the number of large livestock leading to disappearance of traditional biological barriers.","corpus_id":17026,"score":2},{"doc_id":"23433306","title":"Blood meal origins and insecticide susceptibility of Anopheles arabiensis from Chano in South-West Ethiopia.","abstract":"BACKGROUND: Anopheles arabiensis, the main malaria vector in Ethiopia, shows both anthropophilic and zoophilic behaviours. Insecticide resistance is increasing, and alternative methods of vector control are needed. The objectives of this study were to determine the blood meal origins and the susceptibility to insecticides of An. arabiensis from Chano village near Arba Minch in South-West Ethiopia. METHODS: Blood meal sources of anopheline mosquitoes collected using Centers for Disease Control and Prevention (CDC) light traps and pyrethrum spray catches (PSC) from human dwellings, and hand-held mouth aspirators from outdoor pit shelters were analysed using a direct enzyme-linked-immunosorbent assay (ELISA). The susceptibility of An. arabiensis to pyrethroid insecticides (alphacypermethrin, lambdacyhalothrin, deltamethrin, and cyfluthrin) and DDT was assessed using females reared from larval and pupal collections from natural breeding sites. RESULTS: The blood meal origins of 2967 freshly fed Anopheles mosquitoes were determined. An. arabiensis was the predominant species (75%), and it fed mainly on cattle. The densities of both freshly fed An. arabiensis and those fed on human blood followed similar seasonal patterns. The overall human blood index (HBI) of An. arabiensis, including mixed blood meals, was 44% and the bovine blood index (BBI) was 69%. The HBI of An. arabiensis from CDC light trap collections was 75% and this was higher than those for PSC (38%) and outdoor pit shelter collections (13%), while the BBI was 65% for PSC, 68% for outdoor pit shelters and 72% for CDC light traps. More freshly fed and human blood-fed An. arabiensis were sampled from houses close to the shore of Lake Abaya (the major breeding site).A high proportion of An. arabiensis was resistant to the pyrethroid insecticides, with a mortality rate of 56% for lambdacyhalothrin, 50% for cyfluthrin and alphacypermethrin, 47% for deltamethrin, and 10% for DDT. CONCLUSION: Anopheles arabiensis is the predominant species of anopheline mosquito in this region, and cattle are the main source of its blood meals. The greater tendency of this species to feed on cattle justifies the application of insecticides on cattle to control it. However, An. arabiensis has already developed resistance to the available pyrethroid insecticides, and alternative insecticides are needed for malaria vector control.","corpus_id":17249470,"score":2},{"doc_id":"23768077","title":"Susceptibility of Anopheles sinensis to Plasmodium vivax in malarial outbreak areas of central China.","abstract":"BACKGROUND: Anopheles sinensis, Anopheles anthropophagus, Anopheles minimus and Anopheles dirus are the major vectors of malaria transmission in China. Anopheles sinensis is considered a secondary vector due to its relatively low malaria-transmission ability. However, in 2005, an outbreak of over 40,000 Plasmodium vivax malaria cases was reported in areas where Anopheles sinensis was the only major vector. Therefore, it is necessary to reassess the malaria transmission ability of this vector species in China. METHODS: Laboratory colonies of An. sinensis and An. anthropophagus, and first-generation progeny (F1) of An. sinensis that had been collected in central China, were infected by direct membrane feeding assay with mono-vivax gametocyte-containing blood collected from vivax-infected patients. The mosquitoes were kept for 7 to 14 days post-blood feeding to allow parasites to develop into oocysts and sporozoites. Infectivity was measured by dissecting midguts and salivary glands. The presence of oocysts and sporozoites was determined by microscopy at 7 and 14 days post-blood feeding, and the numbers of gametocytes and asexual parasites, as well as mosquito parasite infections, were determined. RESULTS: The positive oocyst and sporozoite feed rates of the 142 pairs of lab-colony An. sinensis and An. anthropophagus were not significantly different, and the same results were found with the 10 pairs of laboratory and F1 An. sinensis. An. sinensis had more oocysts/midgut at 7 days post-feeding than An. anthropophagus, but the gametocytemia, asexual parasitemia, and ratio of macrogametocytes to microgametocytes, did not correlate with either oocyst or sporozoite infection. However, in the oocyst-positive mosquitoes, there was a correlation between gametocytemia and the average oocyst number/midgut. CONCLUSIONS: The susceptibility of An. sinensis (both laboratory and F1) to P. vivax-infected blood is similar to Anopheles anthropophagus, when evaluated by membrane feeding assay under laboratory conditions. In recent years, in central China, the vivax malaria transmission ability of An. sinensis has probably been underestimated. Further studies of this species in other regions are needed. An. sinensis could also be a good candidate vector for evaluating candidate malaria transmission-blocking vaccines (TBV).","corpus_id":1492680,"score":2},{"doc_id":"24252367","title":"Spatio-temporal analysis of host preferences and feeding patterns of malaria vectors in the sylvo-pastoral area of Senegal: impact of landscape classes.","abstract":"BACKGROUND: The study of vector feeding behaviour is an important step in the understanding of the epidemiology of vector borne diseases. The main objective of this work was to study the spatio-temporal host preferences and blood-feeding patterns of malaria vectors in a pastoral area of Senegal where cattle breeding is the main human activity. METHODS: Malaria vectors were collected indoors by pyrethrum spray catch in 16 villages belonging to 4 different landscape classes (wooded savanna, shrubby savanna, bare soils and steppe). Blood meals sources were determined using a direct enzyme-linked immunosorbent assay (ELISA). RESULTS: The blood meal origins of 1886 freshly fed An. gambiae s.l. were determined. Among these blood meals, most were taken on a single host: 40.1% on human and 37.1% on animal. The range in proportions of blood meals taken from human were 25-62.4% in wooded savanna villages, 23.5-61.9% in shrubby savanna villages, 31.3-70% in bare soils villages and 57.7-68.7 in steppe villages. Blood meals taken from bovines were very heterogeneous with two clusters localized in the Northeast and Southwest axis of the study area that corresponds to the distribution of the main water ponds. Patent mixed blood meals taken from human and non-human were significantly higher than those taken from two animals, the highest proportions being observed in September (shrubby savanna, bare soils and steppe villages) or October (wooded savanna villages). CONCLUSIONS: These observations suggest that in this pastoral area, differences in feeding patterns of malaria vectors are merely linked to the specific localization of villages and are not influenced by landscape class distribution. In addition, the temporal variations in the anthropophilic rates are influenced by the presence of standing water in the study area.","corpus_id":14205629,"score":2},{"doc_id":"24589247","title":"Insecticide resistance of Anopheles sinensis and An. vagus in Hainan Island, a malaria-endemic area of China.","abstract":"BACKGROUND: Malaria is one of the most important public health problems in Southeast Asia, including Hainan Island, China. Vector control is the main malaria control measure, and insecticide resistance is a major concern for the effectiveness of chemical insecticide control programs. The objective of this study is to determine the resistance status of the main malaria vector species to pyrethroids and other insecticides recommended by the World Health Organization (WHO) for indoor residual sprays. METHODS: The larvae and pupae of Anopheles mosquitoes were sampled from multiple sites in Hainan Island, and five sites yielded sufficient mosquitoes for insecticide susceptibility bioassays. Bioassays of female adult mosquitoes three days after emergence were conducted in the two most abundant species, Anopheles sinensis and An. vagus, using three insecticides (0.05% deltamethrin, 4% DDT, and 5% malathion) and following the WHO standard tube assay procedure. P450 monooxygenase, glutathione S-transferase and carboxylesterase activities were measured. Mutations at the knockdown resistance (kdr) gene and the ace-1 gene were detected by DNA sequencing and PCR-RFLP analysis, respectively. RESULTS: An. sinensis and An. vagus were the predominant Anopheles mosquito species. An. sinensis was found to be resistant to DDT and deltamethrin. An. vagus was susceptible to deltamethrin but resistant to DDT and malathion. Low kdr mutation (L1014F) frequency (<10%) was detected in An. sinensis, but no kdr mutation was detected in An. vagus populations. Modest to high (45%-75%) ace-1 mutation frequency was found in An. sinensis populations, but no ace-1 mutation was detected in An. vagus populations. Significantly higher P450 monooxygenase and carboxylesterase activities were detected in deltamethrin-resistant An. sinensis, and significantly higher P450 monooxygenase, glutathione S-transferase and carboxylesterase activities were found in malathion-resistant An. vagus mosquitoes. CONCLUSIONS: Multiple insecticide resistance was found in An. sinensis and An. vagus in Hainan Island, a malaria-endemic area of China. Cost-effective integrated vector control programs that go beyond synthetic insecticides are urgently needed.","corpus_id":14417787,"score":2},{"doc_id":"24822373","title":"[Identification of mammalian blood meals in anopheline mosquitoes from four counties of Yunnan Province by multiple PCR].","abstract":"From June to August 2012, the blood-sucking mosquitoes were captured around cattle-sheds and human houses in Yuanjiang County, Qiaojia County, Yongshan County, and Jinghong City of Yunan Province. Blood samples from mosquitoes were collected on filter paper. Multiplex PCR assay was used to detect the blood meal samples. Among the 145 mosquitoes captured, 123 were Anopheles sinensis (84.8%) and 22 A. minimus (15.2%). Among the blood samples, corresponding bands were amplified in 134 samples. The result showed that the blood meals were from pigs (n = 104), cows (n = 22), dogs (n = 4), human (n=2), cow and pig (n = 1), pig and human (n = 1). Human blood index of A. sinensis and A. minimus was 0.018 and 0.045, respectively.","corpus_id":21283349,"score":2},{"doc_id":"25782250","title":"[Sequence analysis of ribosomal DNA internal transcribed spacer 2 of sympatric populations of Anopheles sinensis of different feeding preferences].","abstract":"OBJECTIVE: To investigate the existence of genetic divergence of sympatric populations of Anopheles sinensis of different feeding preferences based on the rDNA-ITS2 sequence differences. METHODS: A large number of wild anopheles populations were trapped all night by man-baited net and calf-baited net that had been set up between high-density natural villages of An. sinensis populations and vector-breeding sites, from which two groups of An. sinensis were separated by morphological identification and brought back to the lab for conventional breeding. A large closed greenhouse which temperature and humidity was appropriate was selected as research settings of mark-release-recapture methods by female mosquitoes, in the center of which above An. sinensis populations baited by man and calf and respectively correspondingly marked by red and yellow phosphors were released in together, in each side of which An. sinensis were recaptured simultaneously by man-baited net and calf-baited net. An. sinensis populations trapped by man twice were brought back to the lab and bred with man-blood, correspondingly ones trapped by calf with calf-blood. Man-preferring and calf-preferring strains were screened respectively from An. sinensis which had been baited by man and calf by the mark-release-recapture methods after parent and F1 mosquitoes, and sequencing and aligning of both rDNA-ITS2 were conducted via PCR amplification. RESULTS: The recapture ratios of wild parental mosquitoes An. sinensis of man-preferring group by man-baited net and calf-baited net were 54.07% (339/627) and 45.93% (288/627) respectively, and ones of calf-preferring group by man-baited net and calf-baited net were 58.01% (409/705) and 41.99% (296/ 705) respectively. Two groups of parental mosquitoes trended towards selecting the original blood hosts in host-seeking preference (Χ2 = 19.42, P < 0.01). The recapture ratios of F1 mosquitoes An. sinensis of man-preferring group by man-baited net and calf-baited net were 63.43% (765/1 206) and 36.57% (441/1 206), and ones of calf-preferring group by man-baited net and calf-baited net were 68.22% (1 039/1 523) and 31.78% (484/1 523). Two groups of F1 mosquitoes had more significant characteristics of selecting the original blood hosts in host-seeking preference (Χ2 = 271.69, P < 0.01) and showed the genetic differentiation phenomenon, but the results of sequencing and aligning of the rDNA-ITS2 via PCR amplification showed no difference in base sequence between the two strains and both were 469 bp. CONCLUSIONS: The genetic divergence based on the rDNA-ITS2 sequence does not happen in An. sinensis sympatric populations of different feeding preferences.","corpus_id":20139419,"score":2},{"doc_id":"25843138","title":"Host feeding patterns of mosquitoes in a rural malaria-endemic region in hainan island, china.","abstract":"Malaria is endemic in Wangxia Village of Hainan Island. In this area little is known about the host seeking behavior and feeding habit of mosquitoes. Three sites representing the most common habitat types in the village were selected to study the host seeking behavior and feeding habit of mosquitoes. Of the total 9 species belonging to 4 genera (Armigeres, Culex, Aedes, and Anopheles) collected in Wangxia Village, Culex tritaeniorhynchus and Cx. pipiens quinquefasciatus were the most commonly collected species. Armigeres subalbatus and Anopheles sinensis were moderately common species. Blood meal analysis confirmed that Cx. tritaeniorhynchus and Cx. p. quinquefasciatus fed on multiple hosts, mainly poultry but occasionally other animals. Anopheles sinensis, a vector of malaria, fed predominately on cattle hosts, followed by humans. Anopheles maculatus and An. barbirostris fed on both humans and domestic animals. Our results indicate that most mosquitoes in this area preferred domestic animals over humans and showed a tendency to feed on multiple hosts within the same gonotrophic cycle. Therefore, the potential role of domestic animals in arbovirus transmission should be evaluated as part of a strategy for controlling mosquito-borne diseases in this region.","corpus_id":8236412,"score":2},{"doc_id":"25880316","title":"Development of insecticide resistance in malaria vector Anopheles sinensis populations from Shandong province in China.","abstract":"BACKGROUND: Anopheles sinensis is a major vector of malaria and among the dominant species in Shandong province of China. Insecticide resistance is an important threat to vector-borne disease control. However, there are only few reports about insecticide resistance of An. sinensis populations from Shandong province. METHODS: From 2003 to 2012, six districts in Shandong province were selected as the study areas. Insecticide susceptibility bioassay were tested on F1 progeny of An. sinensis to 4% DDT, 0.05% deltamethrin, 0.15% cyfluthrin, and 5% malathion, using the standard WHO resistance tube assay. RESULTS: The resistance status of An. sinensis showed a significant decrease in the mortality rates in DDT, deltamethrin and cyfluthrin during the past ten years. Whereas obvious increase of mortality to malathion was observed throughout the assay, ranging from 47.37% to 86.62%.","corpus_id":7544460,"score":2},{"doc_id":"25888824","title":"Historical survey of the kdr mutations in the populations of Anopheles sinensis in China in 1996-2014.","abstract":"BACKGROUND: Anopheles sinensis has become an important malaria vector in China. The long-term extensive utilization of pyrethroids for ITNs and IRS for mosquito control in the last three decades has resulted in the occurrence of resistant An. sinensis populations in many regions. Knockdown resistance (kdr), caused by point mutations in the VGSC gene, is one of the mechanisms that confer resistance to DDT and pyrethroids. Recently, several investigations revealed the kdr occurrence in some An. sinensis populations, however, no kdr data were available earlier than 2009. A survey tracking the dynamics of the kdr mutations in past decades would provide invaluable information to understand how the kdr alleles spread in mosquito populations temporally and spatially. METHODS: A survey was conducted on the kdr alleles at condon 1014 of the VGSC gene and their distributions in 733 specimens of An. sinensis and 232 specimens of the other eight member species of the Anopheles hyrcanus group that were collected from 17 provinces in China in 1996-2014. RESULTS: A total of three kdr alleles, TTT (F), TTG (F) and TGT (C) were detected, and TGT (C) and TTT (F) were already present in the specimens from Jiangsu and Shandong as early as 1997. The TTT (F) was the most frequent mutant allele, and largely distributed in central China, namely Shandong, Jiangsu, Anhui, Henan, Shanghai, Jiangxi and Hubei. When data were analysed in three time intervals, 1996-2001, 2005-2009, 2010-2014, the prevalence of kdr alleles increased progressively over time in the populations in central China. In contrast, the kdr alleles were less frequent in the samples from other regions, especially in Yunnan and Hainan, despite the documented presence of pyrethroid resistant populations in those regions. Interestingly, no mutant alleles were detected in all 232 specimens of eight other species in the An. hyrcanus group. CONCLUSION: The survey revealed that the kdr occurrence and accumulation in the An. sinensis populations were more frequent in central China than in the other regions, suggesting that the kdr mutations may contribute significantly to the pyrethroid resistance in the mosquitoes in central China.","corpus_id":14046359,"score":2},{"doc_id":"25902680","title":"[Experimental observation on host preference of Anopheles sinensis].","abstract":"OBJECTIVE: To observe the host preference of Anopheles sinensis captured by outdoor human or cattle baits. METHODS: A large number of non-blood-fed An. sinensis females were collected by overnight trapping outdoor with human and cattle in the rice paddy field in Shan County of Shandong Province, and took back to the lab, and individually labeled as human baits group and cattle baits group, fed with mouse blood. The host preference of parent, F1 and F25 generations of the two groups were observed by mark-release-recapture methods in a large greenhouse. RESULTS: The recapture rates of parent, F1 and F25 generations were 39.02% (1332/3414), 37.97% (2583/6803), and 30.55% (1523/4986), respectively. In parent generation, the proportion of mosquitoes from human baits group and cattle baits group collected by human-bait and cattle-bait was 54.07% (339/627) and 58.01% (409/705), respectively (χ2=19.42, P<0.01); in F1 generation, that of the two groups was 51.03% (669/1311) and 55.11% (701/1272), respectively (χ2= 9.75, P<0.01); in F25 generation, that of the two groups was 51.98% (342/658) and 52.37 (453/865), respectively (χ2=2.82, P>0.05). CONCLUSION: After culture for 25 generations in an experimental condition, the host preference for human or cattle of An. sinensis maybe change.","corpus_id":42962031,"score":2},{"doc_id":"26964528","title":"Determinants of host feeding success by Anopheles farauti.","abstract":"BACKGROUND: The proportion of blood meals that mosquitoes take from a host species is a function of the interplay of extrinsic (abundance and location of potential hosts) and intrinsic (innate preference) factors. A mark-release-recapture experiment addressed whether host preference in a population of Anopheles farauti was uniform or if there were anthropophilic and zoophilic subpopulations. The corresponding fitness associated with selecting different hosts for blood meals was compared by measuring fecundity. METHODS: The attractiveness of humans for blood meals by An. farauti in the Solomon Islands was compared to pigs using tent traps. Host fidelity was assessed by mark-release-recapture experiments in which different colour dusts were linked to the host to which the mosquito was first attracted. Outdoor resting An. farauti were captured on barrier screens and the human blood index (HBI) as well as the feeding index were calculated. The fecundity of individual An. farauti after feeding on either humans or pigs was assessed from blood-fed mosquitoes held in individual oviposition chambers. RESULTS: Anopheles farauti were more attracted to humans than pigs at a ratio of 1.31:1.00. The mark-release-recapture experiment found evidence for An. farauti being a single population regarding host preference. The HBI of outdoor resting An. farauti was 0.93 and the feeding index was 1.29. Anopheles farauti that fed on a human host laid more eggs but had a longer oviposition time compared to An. farauti that had blood fed on a pig. CONCLUSIONS: One of the strongest drivers for host species preference was the relative abundance of the different host species. Here, An. farauti have a slight preference for humans over pigs as blood meal sources. However, the limited availability of alternative hosts relative to humans in the Solomon Islands ensures a very high proportion of blood meals are obtained from humans, and thus, the transmission potential of malaria by An. farauti is high.","corpus_id":5644824,"score":2},{"doc_id":"27118141","title":"Determination of the foraging behaviour and blood meal source of malaria vector mosquitoes in Trincomalee District of Sri Lanka using a multiplex real time polymerase chain reaction assay.","abstract":"BACKGROUND: Studies of host preference patterns in blood-feeding anopheline mosquitoes are crucial to incriminating malaria vectors. However, little information is available on host preferences of Anopheles mosquitoes in Sri Lanka. METHODS: Adult Anopheles mosquitoes were collected from five selected sentinel sites in Trincomalee District during June-September 2011. Each blood-fed mosquito was processed on filter papers. DNA was extracted using the dried blood meal protocol of the QIAmp DNA mini kit. A multiplexed, real-time PCR assay targeting eight animals was developed for two panels to identify the host meal of Anopheles. Human blood index (HBI), forage ratio (FR) and host feeding index (HFI) were calculated. RESULTS: A total of 280 field-caught, freshly engorged female mosquitoes belonging to 12 anopheline species were analysed. The overall HBI and HFI in the present study were low indicating that humans were not the preferred host for the tested anopheline species. Nevertheless, a small proportion engorged Anopheles aconitus, Anopheles culicifacies, Anopheles barbirostris, Anopheles annularis, Anopheles subpictus, Anopheles peditaeniatus, Anopheles pseudojamesi, and Anopheles barbumbrosus contained human blood. CONCLUSION: The presence of human blood in mosquito species indicates the possibility of them transmitting malaria. Further studies on vector competence are needed to determine the role of each of the above anopheline species as efficient vectors of malaria.","corpus_id":18000347,"score":2},{"doc_id":"27353581","title":"Biting behaviour of Anopheles funestus populations in Mutare and Mutasa districts, Manicaland province, Zimbabwe: Implications for the malaria control programme.","abstract":"BACKGROUND & OBJECTIVES: Biting behaviour of Anopheles funestus in Mutare and Mutasa districts, Zimbabwe, is little understood. An investigation was conducted to primarily compare indoor and outdoor biting behaviour of the mosquito, as well as blood meal sources and sporozoite rates. METHODS: Monthly adult anopheline sampling was conducted from October 2013 to September 2014 using Centers for Disease Control light-traps, pyrethrum spray catch and artificial pit shelter methods. Mosquitoes sampled by light-traps were divided into two cohorts. In one cohort, traps were left overnight and mosquitoes were collected the following morning, while in the other set, mosquitoes were collected hourly from 1800-0600 hrs . Collected females were identified using morphological characters and categorised according to their abdominal status. Polymerase chain reaction was used to identify An. funestus sibling species and blood meal sources. Infection rate was tested by enzyme-linked immunosorbent assay. RESULTS: Morphological identification showed that indoor and outdoor catches comprised Anopheles funestus (98.3%) and Anopheles gambiae s.l. ( 1.7%). Of the 2268 mosquitoes collected, 66.2% were caught by light-traps, and 33.8% were caught resting indoors and outdoors. Anopheles funestus and An. gambiae s.l. were trapped more abundantly indoors (68%) than outdoors (32%). Both indoor and outdoor An. funestus densities were higher in wet (4.3) than dry season (1.8). In Burma Valley and Zindi areas, An. funestus demonstrated variable nocturnal indoor and outdoor flight activity rhythms, with two peaks during the night; between 2200-2300 hrs and 0200- 0400 hrs. Human blood index in An. funestus was 0.64, with Plasmodium falciparum infection rate of 1.8%. INTERPRETATION & CONCLUSION: The present work highlighted important information on the host-seeking behaviour, blood meal sources and infection rates in An. funestus. The information would be helpful in improving the vector control strategies.","corpus_id":10342064,"score":2},{"doc_id":"27681543","title":"A reassessment of the artificial infection of three predominant mosquito species with Plasmodium vivax in Shandong Province, China.","abstract":"BACKGROUND & OBJECTIVES: Under certain ecological circumstances, pathogens are able to rapidly adapt to new vectors. The great capacity of Plasmodium spp. to adapt to new anopheline mosquito vectors on different continents and the continuous ecological changes attributed to humans might promote their adaptation to culicine vectors, which are known to infect humans. Based on our current knowledge, it is difficult to predict whether such adaptations will occur. This study was aimed to determine the infection susceptibility of Anopheles sinensis, Culex tritaeniorhynchus and Cx. pipiens pallens to Plasmodium vivax in Shandong Province of China. METHODS: The susceptibility of the three predominant species of mosquitoes -An. sinensis, Cx. tritaeniorhynchus and Cx. pipiens pallens in Shandong Province was compared with a direct membrane feeding assay with 15 batches of Shandong strain mono-infected gametocyte-containing blood collected from Plasmodium vivax-infected patients. Infectivity was measured by dissecting the midguts and salivary glands of the mosquitoes. The presence of oocysts and sporozoites was determined by microscopy at 6 and 22 days post-blood feeding. RESULTS: From the 15 batches of mosquitoes that were fed infected blood, oocysts and sporozoites were detected only in 7th, 13th and 15th batches of infection for An. sinensis, and no oocysts or sporozoites were detected in Cx. tritaeniorhynchus or Cx. pipiens pallens. The positive rate of An. sinensis infection was 21.2, 13 and 36.3% in the three batches of mosquitoes, with an average infection rate of 23.5%. INTERPRETATION & CONCLUSION: The susceptibility of An. sinensis to P. vivax was very high in Shandong Province. Cx. tritaeniorhynchus and Cx. pipiens pallens failed to exhibit susceptibility to P. vivax.","corpus_id":40990673,"score":2},{"doc_id":"28719327","title":"Extensive Resistance of Anopheles sinensis to Insecticides in Malaria-Endemic Areas of Hainan Province, China.","abstract":"Anopheles sinensis is one of the major malaria vectors and among the dominant species in Hainan Province, China. The resistance of An. sinensis to insecticides is an important threat to malaria control. However, few reports on insecticide resistance of An. sinensis were reported in this area. Eight districts in Hainan Province were selected as the study areas. Insecticide susceptibility bioassays were tested on wild-caught female mosquitoes of An. sinensis to 4% dichlorodiphenyltrichloroethane (DDT), 0.05% deltamethrin, and 5% malathion by using the World Health Organization standard resistance tube assay procedure. All the tested An. sinensis mosquitoes demonstrated resistance to 4% DDT, with less than 72% mortality in the standard assay. The populations from Baisha and Qiongzhong demonstrated possible resistance to 0.05% deltamethrin, with 94-95% mortality, whereas the populations from other districts demonstrated resistance to 0.05% deltamethrin in the standard assay. The populations from Baisha, Qiongzhong, and Dongfang demonstrated susceptibility to 5% malathion, but the populations from other districts demonstrated resistance. These results facilitate the improvement of effective control strategies for malaria vector mosquitoes in Hainan.","corpus_id":31960372,"score":2},{"doc_id":"28764710","title":"Host attraction and biting behaviour of Anopheles mosquitoes in South Halmahera, Indonesia.","abstract":"BACKGROUND: Indonesia is home to a variety of malaria vectors whose specific bionomic traits remain largely uncharacterized. Species-specific behaviours, such as host feeding preferences, impact the dynamics of malaria transmission and the effectiveness of vector control interventions. METHODS: To examine species-specific host attraction and feeding behaviours, a Latin square design was used to compare Anopheles mosquitoes attracted to human, cow, and goat-baited tents. Anopheles mosquitoes were collected hourly from the inside walls of each baited tent. Species were morphologically and then molecularly identified using rDNA ITS2 sequences. The head and thorax of individual specimens were analysed for Plasmodium DNA using PCR. Bloodmeals were identified using a multiplex PCR. RESULTS: A total of 1024, 137, and 74 Anopheles were collected over 12 nights in cow, goat, and human-baited tents, respectively. The species were identified as Anopheles kochi, Anopheles farauti s.s., Anopheles hackeri, Anopheles hinesorum, Anopheles indefinitus, Anopheles punctulatus, Anopheles tessellatus, Anopheles vagus, and Anopheles vanus, many of which are known to transmit human malaria. Molecular analysis of blood meals revealed a high level of feeding on multiple host species in a single night. Anopheles kochi, An. indefinitus, and An. vanus were infected with Plasmodium vivax at rates comparable to primary malaria vectors. CONCLUSIONS: The species distributions of Anopheles mosquitoes attracted to human, goat, and cow hosts were similar. Eight of nine sporozoite positive samples were captured with animal-baited traps, indicating that even predominantly zoophilic mosquitoes may be contributing to malaria transmission. Multiple host feeding and flexibility in blood feeding behaviour have important implications for malaria transmission, malaria control, and the effectiveness of intervention and monitoring methods, particularly those that target human-feeding vectors.","corpus_id":4961842,"score":2},{"doc_id":"29162093","title":"Receptivity to malaria in the China-Myanmar border in Yingjiang County, Yunnan Province, China.","abstract":"BACKGROUND: The re-establishment of malaria has become an important public health issue in and out of China, and receptivity to this disease is key to its re-emergence. Yingjiang is one of the few counties with locally acquired malaria cases in the China-Myanmar border in China. This study aimed to understand receptivity to malaria in Yingjiang County, China, from June to October 2016. METHODS: Light-traps were employed to capture the mosquitoes in 17 villages in eight towns which were categorized into four elevation levels: level 1, 0-599 m; level 2, 600-1199 m; level 3, 1200-1799 m; and level 4, > 1800 m. Species richness, diversity, dominance and evenness were used to picture the community structure. Similarity in species composition was compared between different elevation levels. Data of seasonal abundance of mosquitoes, human biting rate, density of light-trap-captured adult mosquitoes and larvae, parous rate, and height distribution (density) of Anopheles minimus and Anopheles sinensis were collected in two towns (Na Bang and Ping Yuan) each month from June to October, 2016. RESULTS: Over the study period, 10,053 Anopheles mosquitoes were collected from the eight towns, and 15 Anopheles species were identified, the most-common of which were An. sinensis (75.4%), Anopheles kunmingensis (15.6%), and An. minimus (3.5%). Anopheles minimus was the major malaria vector in low-elevation areas (< 600 m, i.e., Na Bang town), and An. sinensis in medium-elevation areas (600-1200 m, i.e., Ping Yuan town). In Na Bang, the peak human-biting rate of An. minimus at the inner and outer sites of the village occurred in June and August 2016, with 5/bait/night and 15/bait/night, respectively. In Ping Yuan, the peak human-biting rate of An. sinensis was in August, with 9/bait/night at the inner site and 21/bait/night at the outer site. The two towns exhibited seasonal abundance with high density of the two adult vectors: The peak density of An. minimus was in June and that of An. sinensis was in August. Meanwhile, the peak larval density of An. minimus was in July, but that of An. sinensis decreased during the investigation season; the slightly acidic water suited the growth of these vectors. The parous rates of An. sinensis and An. minimus were 90.46 and 93.33%, respectively. CONCLUSIONS: The Anopheles community was spread across different elevation levels. Its structure was complex and stable during the entire epidemic season in low-elevation areas at the border. The high human-biting rates, adult and larval densities, and parous rates of the two Anopheles vectors reveal an exceedingly high receptivity to malaria in the China-Myanmar border in Yingjiang County.","corpus_id":7740480,"score":2},{"doc_id":"18297310","title":"Blood-feeding patterns of Culex quinquefasciatus and other culicines and implications for disease transmission in Mwea rice scheme, Kenya.","abstract":"Studies were conducted in Mwea Rice Scheme, Kenya during the period April 2005 and January 2007 to determine the host-feeding pattern of culicine mosquitoes. Mosquitoes were collected indoors and outdoors and tested for human, bovine, goat, and donkey blood meals by an Enzyme-Linked Immunosorbent Assay. A total of 1,714 blood-engorged samples comprising Culex quinquefasciatus Say (96.1%), Culex annulioris Theobald (1.8%), Culex poicilipes Theobald (0.9%), Aedes cuminsi Theobald (1.0%), Aedes taylori Edwards (0.1%), and Mansonia africana Theobald (0.1%) were tested. Except for A. taylori, in which the single blood meal tested was of bovine origin, the other species fed mostly on both bovine (range 73.3-100%) and goats (range 50-100%). Donkeys were also common hosts for all species (range 19.4-23.5%) except A. taylori and M. africana. C. quinquefasciatus was the only species containing human blood meals (0.04), and indoor collected populations of this species had significantly higher frequency of human blood meals (9.8%) compared with outdoor-collected populations (3.0%). Mixed blood feeding was dominant among culicine species comprising 50.0%, 73.3%, 73.5%, 80.6%, and 94.1% of the samples for M. africana, C. poicilipes, C. quinquefasciatus, C. annulioris, and A. cuminsi, respectively. Ten mixed blood meal combinations including a mixture of all the four hosts were observed in C. quinquefasciatus, compared to one blood meal combination for M. Africana, and two combinations for C. poicilipes, C. annulioris, and A. cuminsi. Mixed bovine and goat blood meal was the most common combination among the five culicine species followed by a mixture of donkey, bovine, and goat blood meals. We conclude that culicine species in Mwea are least likely to be vectors of lymphatic filariasis due to their high \"preference\" for livestock over human hosts, but they present an increased risk for arbovirus transmission particularly Rift Valley Fever virus, in which domestic animals serve as amplification hosts.","corpus_id":26124116,"score":1},{"doc_id":"18312667","title":"Host choice and multiple blood feeding behaviour of malaria vectors and other anophelines in Mwea rice scheme, Kenya.","abstract":"BACKGROUND: Studies were conducted between April 2004 and February 2006 to determine the blood-feeding pattern of Anopheles mosquitoes in Mwea Kenya. METHODS: Samples were collected indoors by pyrethrum spay catch and outdoors by Centers for Disease Control light traps and processed for blood meal analysis by an Enzyme-linked Immunosorbent Assay. RESULTS: A total of 3,333 blood-fed Anopheles mosquitoes representing four Anopheles species were collected and 2,796 of the samples were assayed, with Anopheles arabiensis comprising 76.2% (n = 2,542) followed in decreasing order by Anopheles coustani 8.9% (n = 297), Anopheles pharoensis 8.2% (n = 272) and Anopheles funestus 6.7% (n = 222). All mosquito species had a high preference for bovine (range 56.3-71.4%) over human (range 1.1-23.9%) or goat (0.1-2.2%) blood meals. Some individuals from all the four species were found to contain mixed blood meals. The bovine blood index (BBI) for An. arabiensis was significantly higher for populations collected indoors (71.8%), than populations collected outdoors (41.3%), but the human blood index (HBI) did not differ significantly between the two populations. In contrast, BBI for indoor collected An. funestus (51.4%) was significantly lower than for outdoor collected populations (78.0%) and the HBI was significantly higher indoors (28.7%) than outdoors (2.4%). Anthropophily of An. funestus was lowest within the rice scheme, moderate in unplanned rice agro-ecosystem, and highest within the non-irrigated agro-ecosystem. Anthropophily of An. arabiensis was significantly higher in the non-irrigated agro-ecosystem than in the other agro-ecosystems. CONCLUSION: These findings suggest that rice cultivation has an effect on host choice by Anopheles mosquitoes. The study further indicate that zooprophylaxis may be a potential strategy for malaria control, but there is need to assess how domestic animals may influence arboviruses epidemiology before adapting the strategy.","corpus_id":1717904,"score":1},{"doc_id":"19485771","title":"Host-feeding patterns of Aedes albopictus (Diptera: Culicidae) in urban and rural contexts within Rome province, Italy.","abstract":"Knowledge of the frequency of contact between a mosquito species and its different hosts is essential to understand the role of each vector species in the transmission of diseases to humans and/or animals. However, no data are so far available on the feeding habits of Aedes albopictus in Italy or in other recently colonized temperate regions of Europe, due to difficulties in collecting blood-fed females of this diurnal and exophilic species. We analyzed Ae. albopictus host-feeding patterns in two urban and two rural sites within the area of Rome (Italy). Ae. albopictus was collected using sticky-traps and the blood-meal origin of 303 females was determined by direct dot-ELISA. The blood-fed sample, although representing only 4% of the total Ae. albopictus collected, demonstrates the useful application of sticky-trap in studying the feeding behavior of the species. The human blood index was significantly different among sites, ranging from 79-96% in urban sites to 23-55% in rural sites, where horses and bovines represented the most bitten hosts. The results obtained confirm the plastic feeding behavior shown by Ae. albopictus in its original range of distribution and highlights the high potential of this species as a vector of human pathogens in urban areas of Italy, where both humans and the mosquito itself may reach very high densities.","corpus_id":20034869,"score":1},{"doc_id":"19724081","title":"Effects of long-lasting insecticidal nets and zooprophylaxis on mosquito feeding behaviour and density in Mwea, central Kenya.","abstract":"BACKGROUND & OBJECTIVES: Zooprophylaxis is a strategy that can control malaria by attracting mosquitoes to domestic animals that act as dead-end hosts. The objective of this study was to establish the effects of zooprophylaxis and long-lasting insecticidal nets (LLINs) on malaria transmission in an agro-based ecosystem with seasonal transmission. METHODS: The mosquito samples were collected indoors using the space spray catch method before and after intervention between October 2005 and March 2006 to determine the mosquito densities and the feeding patterns of Anopheles spp in Mwea, Kenya. RESULTS: A total of 4148 mosquito samples were collected, out of which 11 (0.2%) were tested positive for sporozoites. Ten were Anopheles gambiae species and one was An. funestus species. Results on blood meal ELISA showed that in the household categories that used bednets and kept one cow there was a decrease in relative change ratio (post-/pre-intervention) of 87.5 and 19.6% (p <0.05) in human and cattle blood intake respectively. For households that kept 2-4 cattle and used bednets, there was a decrease in cattle blood index (CBI) by 61.9% and an increase in human blood index (HBI) by 2%, which was not significant (p <0.05). In households with <4 cattle and bednet, there was significant reduction (p >0.05) in CBI of 37.5% as compared to the reduction of 10.3% in HBI. The ratios of man biting rates (MBR) decreased significantly, as you move up from households with one cattle with or without LLINs to households with more than four cattle with or without LLINs with a regression coefficient of -0.96; SE = 0.834; p = 0.017. Similarly, the HBI decreased significantly with the regression coefficient of 0.239; SE = 0.039; p = 0.015 (p <0.05) especially in households with >4 cattle. INTERPRETATION & CONCLUSION: This study demonstrated that there were additive effects of zooprophylaxis and LLINs in the control of mosquito density and reduction of human risk to the mosquito bites. However, in Integrated Vector Management (IVM), the number of animals per household should not be more than four.","corpus_id":8730204,"score":1},{"doc_id":"20578953","title":"Host-feeding preference of the mosquito, Culex quinquefasciatus, in Yucatan State, Mexico.","abstract":"Studies were conducted to determine the host-feeding preference of Culex quinquefasciatus Say (Diptera: Culicidae) in relation to the availability of human and domestic animals in the city of Merida, Yucatan State, Mexico. Mosquitoes were collected in the backyards of houses using resting wooden boxes. Collections were made five times per week from January to December 2005. DNA was extracted from engorged females and tested by PCR using universal avian- and mammalian-specific primers. DNA extracted from avian-derived blood was further analyzed by PCR using primers that differentiate among the birds of three avian orders: Passeriformes, Columbiformes and Galliformes. PCR products obtained from mammalian-derived blood were subjected to restriction enzyme digestion to differentiate between human-, dog-, cat-, pig-, and horse-derived blood meals. Overall, 82% of engorged mosquitoes had fed on birds, and 18% had fed on mammals. The most frequent vertebrate hosts were Galliformes (47.1%), Passeriformes (23.8%), Columbiformes (11.2%) birds, and dogs (8.8%). The overall human blood index was 6.7%. The overall forage ratio for humans was 0.1, indicating that humans were not a preferred host for Cx. quinquefasciatus in Merida.","corpus_id":1700431,"score":1},{"doc_id":"21826902","title":"[An investigation on malaria vectors in western part of China-Myanmar border].","abstract":"OBJECTIVE: To reveal the distribution and composition of malaria-transmitting vectors on the western part of China-Myanmar border. METHODS: An entomological survey of malaria vectors was carried out in six villages of Yingjiang County and Xidong County on China-Myanmar border between August and September, 2008. Mosquitoes in human dwellings and cattle sheds were collected by overnight trapping with ovitrap light. The mosquitoes were firstly identified morphologically, and then Anopheles minimus A and C, An. aconitus, and An. jeyporiensis were identified by using multiplex PCR. Some mosquitoes were selected to extract the total genomic DNA, and detect sporozoites by nested PCR. RESULTS: A total of 4571 mosquitoes were captured with 54.32% (2483/4571) of anopheline mosquitoes. There was significant difference in Anopheles species composition in human dwellings and cattle sheda The main species in human dwellings were An. kochi, An. minimus, and An. sinensis, while the principal species in cattle sheds consist of An. kochi (223), An. annularis (184), An. vagus (131), and An jeyporiensis (129). Furthermore, the composition in human dwellings of villages with and without cattle was significantly different. An. minimus (260) and An. kochi (49) werethe most important species in villages with cattle, whereas An. kochi (481) and An. sinensis (124) were the key species in villages without cattle. A total of 1075 mosquitoes were examined for sporozoites and 9 mosquitoes were found to be infected. Only three species, Le. An. minimus (7/408), An aconiaus (1/125) and An. pseudowillmori (1/101) were infected with malaria parasite. All sporozoites were identified as Plasmodium falcipoarum by sequencing, the target fragment was 204 bp. CONCLUSION: The species composition of mosquitoes is complex in the study sites on the western part of China-Myanmar border, and An. minimus is the major malaria vector. Additionally, An. aconitus and An.pseudowillmori are also confirmed as potential malaria vector in this area.","corpus_id":26923987,"score":1},{"doc_id":"22165904","title":"Impact of insecticide-treated bed nets on malaria transmission indices on the south coast of Kenya.","abstract":"BACKGROUND: Besides significantly reducing malaria vector densities, prolonged usage of bed nets has been linked to decline of Anopheles gambiae s.s. relative to Anopheles arabiensis, changes in host feeding preference of malaria vectors, and behavioural shifts to exophagy (outdoor biting) for the two important malaria vectors in Africa, An. gambiae s.l. and Anopheles funestus. In southern coastal Kenya, bed net use was negligible in 1997-1998 when Anopheles funestus and An. gambiae s.s. were the primary malaria vectors, with An. arabiensis and Anopheles merus playing a secondary role. Since 2001, bed net use has increased progressively and reached high levels by 2009-2010 with corresponding decline in malaria transmission. METHODS: To evaluate the impact of the substantial increase in household bed net use within this area on vector density, vector composition, and human-vector contact, indoor and outdoor resting mosquitoes were collected in the same region during 2009-2010 using pyrethrum spray catches and clay pots for indoor and outdoor collections respectively. Information on bed net use per sleeping spaces and factors influencing mosquito density were determined in the same houses using Poisson regression analysis. Species distribution was determined, and number of mosquitoes per house, human-biting rates (HBR), and entomological inoculation rate (EIR) were compared to those reported for the same area during 1997-1998, when bed net coverage had been minimal. RESULTS: Compared to 1997-1998, a significant decline in the relative proportion of An. gambiae s.s. among collected mosquitoes was noted, coupled with a proportionate increase of An. arabiensis. Following > 5 years of 60-86% coverage with bed nets, the density, human biting rate and EIR of indoor resting mosquitoes were reduced by more than 92% for An. funestus and by 75% for An. gambiae s.l. In addition, the host feeding choice of both vectors shifted more toward non-human vertebrates. Besides bed net use, malaria vector abundance was also influenced by type of house construction and according to whether one sleeps on a bed or a mat (both of these are associated with household wealth). Mosquito density was positively associated with presence of domestic animals. CONCLUSIONS: These entomological indices indicate a much reduced human biting rate and a diminishing role of An. gambiae s.s. in malaria transmission following high bed net coverage. While increasing bed net coverage beyond the current levels may not significantly reduce the transmission potential of An. arabiensis, it is anticipated that increasing or at least sustaining high bed net coverage will result in a diminished role for An. funestus in malaria transmission.","corpus_id":245708,"score":1},{"doc_id":"22910571","title":"Anopheles gambiae and Anopheles arabiensis population densities and infectivity in Kopere village, Western Kenya.","abstract":"INTRODUCTION: This study was conducted in a sugar belt region of western Kenya interfacing epidemic and endemic malaria transmission. We investigated Anopheles gambiae sensu stricto (ss) and Anopheles arabiensis species compositions and densities, human host choice, and infectivity. METHODOLOGY: Mosquitoes were captured using pyrethrum spray catch technique and first identified based on morphology; species were confirmed by PCR. Blood meal preference and sporozoite rates were determined by ELISA. Parity rates and entomological inoculation rates (EIR) were determined. Seasonal densities were compared against environmental temperatures, relative humidity and rainfall. RESULTS: In total 2,426 An. gambiae were collected. Out of 1,687 female blood-fed mosquitoes, 272 were randomly selected for entomological tests. An. gambiae ss and An. arabiensis comprised 75% (205/272) and 25% (68/272) of the selection, respectively. An. gambiae ss had higher preference for human blood (97%; n=263/272) compared with An. arabiensis, which mostly fed on bovines (88%; n=239/272). The sporozoite and parity rates were 6% (16/272) and 66% (179/272) for An. gambiae ss and 2% (4/272) and 53% (144/272) for An. arabiensis respectively, while EIR was 0.78 infective bites/person/night. Climate (ANOVA; F=14.2; DF=23) and temperature alone (r=0.626; t=3.75; p=0.001) were significantly correlated with vector densities. CONCLUSION: An. gambiae ss are the most efficient malaria vector mosquito species in Kopere village. Because An. gambiae ss largely rests and feeds indoors, use of indoor residual spray and insecticide-treated nets is likely the most suitable approach to malaria vector control in Kopere village and other parts of Kenya where this species is abundant.","corpus_id":8130926,"score":1},{"doc_id":"23253167","title":"The fitness of African malaria vectors in the presence and limitation of host behaviour.","abstract":"BACKGROUND: Host responses are important sources of selection upon the host species range of ectoparasites and phytophagous insects. However little is known about the role of host responses in defining the host species range of malaria vectors. This study aimed to estimate the relative importance of host behaviour to the feeding success and fitness of African malaria vectors, and assess its ability to predict their known host species preferences in nature. METHODS: Paired evaluations of the feeding success and fitness of African vectors Anopheles arabiensis and Anopheles gambiae sensu stricto in the presence and limitation of host behaviour were conducted in a semi-field system (SFS) at Ifakara Health Institute, Tanzania. In one set of trials, mosquitoes were released within the SFS and allowed to forage overnight on a host that was free to exhibit a natural behaviour in response to insect biting. In the other, mosquitoes were allowed to feed directly on from the skin surface of immobile hosts. The feeding success and subsequent fitness of vectors under these conditions were investigated on six host types (humans, calves, chickens, cows, dogs and goats) to assess whether physical movements of preferred host species (cattle for An. arabiensis, humans for An. gambiae s.s.) were less effective at preventing mosquito bites than those of common alternatives. RESULTS: Anopheles arabiensis generally had greater feeding success when applied directly to host skin than when foraging on unrestricted hosts (in five of six host species). However, An. gambiae s.s. obtained blood meals from free and restrained hosts with similar success from most host types (four out of six). Overall, the blood meal size, oviposition rate, fecundity and post-feeding survival of mosquito vectors were significantly higher after feeding on hosts free to exhibit behaviour, than those who were immobilized during feeding trials. CONCLUSIONS: Allowing hosts to move freely during exposure to mosquitoes was associated with moderate reductions in mosquito feeding success, but no detrimental impact to the subsequent fitness of mosquitoes that were able to feed upon them. This suggests that physical defensive behaviours exhibited by common host species including humans do not impose substantial fitness costs on African malaria vectors.","corpus_id":8726081,"score":1},{"doc_id":"24034528","title":"The Anopheles community and the role of Anopheles minimus on malaria transmission on the China-Myanmar border.","abstract":"BACKGROUND: Malaria around the China-Myanmar border is a serious health problem in the countries of South-East Asia. An. minimus is a principle malaria vector with a wide geographic distribution in this area. Malaria is endemic along the boundary between Yunnan province in China and the Kachin State of Myanmar where the local Anopheles community (species composition) and the malaria transmission vectors have never been clarified. METHODS: Adult Anopheles specimens were collected using CDC light traps in four villages along the border of China and Myanmar from May 2012 to April 2013. Morphological and molecular identification of mosquito adults confirmed the species of Anopheles. Blood-meal identification using the female abdomens was conducted using multiplex PCR. For sporozoite detection in An. minimus, sets of 10 female salivary glands were pooled and identified with SSU rDNA using nested PCR. Monthly abundance of An. minimus populations during the year was documented. The diversity of Anopheles and the role of An. minimus on malaria transmission in this border area were analyzed. RESULTS: 4,833 adult mosquitoes in the genus Anopheles were collected and morphologically identified to species or species complex. The Anopheles community is comprised of 13 species, and 78.83% of our total specimens belonged to An. minimus s.l., followed by An. maculatus (5.55%) and the An. culicifacies complex (4.03%). The quantity of trapped An. minimus in the rainy season of malaria transmission was greater than during the non-malarial dry season, and a peak was found in May 2012. An. minimus fed on the blood of four animals: humans (79.8%), cattle (10.6%), pigs (5.8%) and dogs (3.8%). 1,500 females of An. minimus were pooled into 150 samples and tested for sporozoites: only 1 pooled sample was found to have sporozoites of Plasmodium vivax. CONCLUSION: Anopheles is abundant with An. minimus being the dominant species and having a high human blood index along the China-Myanmar border. The sporozoites in An. minimus were determined to be Plasmodium vivax with a 0.07-0.7% infection rate.","corpus_id":7811668,"score":1},{"doc_id":"24822345","title":"[Taxonomic status of Anopheles yatsushiroensis in Rongcheng City of Shandong Province].","abstract":"OBJECTIVE: To clarify the taxonomic status of Anopheles yatsushiroensis in Rongcheng City of Shandong Province. METHODS: By the end of August 2009, Anopheles yatsushiroensis were collected in the western suburbs of Wangjia Village of Rongcheng City, and raised for the next generation of various types of adult mosquitoes. Through morphological identification of filial generation various types, mosquito feet of 1-2 mosquitoes of various types were taken for complete DNA extraction, and complete sequence analysis of rDNA-ITS2 alignment was made by PCR. Multiple sequnence comparison was carried out with those previously documented by DNAstar7.1, including An. yatsushiroensis in Shandong Province (YSD, AY306128), An. yatsushiroensis in Sichuan Province (YSC, AY170925), An. yatsushiroensis in Liaoning Province (YLN, AY170923) and An. yatsushiroensis from South Korea (YK, AF146749). RESULTS: 56 An. yatsushiroensis with blood meal were collected in Rongcheng City, of which 7 successfully laid eggs, and received 354 adult mosquitoes of filiar generation, including 240 An. yatsushiroensis (Y type), 8 An. pullus (P type) and 106 hybrid type (H). The rDNA-ITS2 sequence alignment homology between single-parent female offspring of adult mosquitoes and various types of An. yatsushiroensis segments (JN865249, JN865246, JN865247, JN865248) was 98.7-100%, and the rDNA-ITS2 sequence alignment homology to those from Sichuan (YSC), Liaoning (YLN) and Korea (YK) was 98.5%-99.3%, 98.7%-99.6% and 98.7 to 100%, respectively, while to the original An. yatsushiroensis from Rongcheng (YSD), it was only 67.1%-68.5%. CONCLUSION: There are Y, P and H types of An. yatsushiroensis in Rongcheng City, Shandong Province, but the rDNA-ITS2 sequence is close to An. pullus. The local distribution of An. pullus is deduced.","corpus_id":23128146,"score":1},{"doc_id":"24885668","title":"Individual experience affects host choice in malaria vector mosquitoes.","abstract":"BACKGROUND: Despite epidemiological importance, few studies have explored whether individual experience and learning could affect the vertebrate host choice of mosquito disease vectors. Here, we investigated whether a first successful blood meal can modulate mosquito preference during a second blood meal. METHODS: In no-choice situations, females of the mosquito Anopheles coluzzii, one of the primary African malaria vectors, were first allowed to feed on either human, rabbit or guinea pig. Four days later in dual-choice situations, the same mosquitoes were allowed to choose between the two uncommon hosts, rabbit and guinea pig, as a source of blood. ELISA assays were then used to determine which host mosquitoes fed on. RESULTS: Our results indicate that, overall, mosquitoes preferred to feed on rabbit over guinea pig and that the nature of the first blood meal had a significant impact on the mosquito host choice during the second blood meal. Compared to mosquitoes that previously fed on guinea pigs or humans, mosquitoes that fed on rabbits were less likely to choose this host species during a second exposition. The decreased preference for rabbit was observed four days after mosquitoes were first exposed to this host, suggesting that the effect lasts at least the duration of a gonotrophic cycle. Furthermore, this effect was observed after only one successful blood meal. Fitness measurements on mosquitoes fed on the three different vertebrate hosts showed that the origin of the blood meal affected mosquito longevity but not fecundity. In particular, human-fed mosquitoes lived longer than guinea pig-fed or rabbit-fed mosquitoes. CONCLUSIONS: Our study demonstrates that individual experience affects host choice in this mosquito species and might have strong repercussions on biting patterns in natural conditions and hence on malaria transmission.","corpus_id":16954046,"score":1},{"doc_id":"25424266","title":"Biting patterns and host preference of Anopheles epiroticus in Chang Island, Trat Province, eastern Thailand.","abstract":"A study of species diversity of Anopheles mosquitoes, biting patterns, and seasonal abundance of important mosquito vectors was conducted in two villages of Chang Island, Trat Province, in eastern Thailand, one located along the coast and the other in the low hills of the central interior of the island. Of 5,399 captured female anophelines, 70.25% belong to the subgenus Cellia and remaining specimens to the subgenus Anopheles. Five important putative malaria vectors were molecularly identified, including Anopheles epiroticus, Anopheles dirus, Anopheles sawadwongporni, Anopheles maculatus, and Anopheles minimus. Anopheles epiroticus was the most commonly collected species in the coastal site, whereas An. dirus was found to be most abundant in the forest-hill site. From both locations, a greater number of mosquitoes was collected during the dry season compared to the wet. Anopheles epiroticus showed greater exophagic and zoophilic behavior with the highest blood feeding densities occurring between 18:00 and 19:00. In contrast, An. dirus demonstrated an activity peak between midnight and 01:00. We conclude that An. epiroticus and An. dirus, in coastal and inland areas, respectively, appear to be the most epidemiologically important malaria vectors on Chang Island. As no studies of vector competency specific to Chang Island have been conducted, our conclusions that these two species play a primary role in malaria transmission are based on evidence from other localities in Thailand and mainland Southeast Asia. This information serves as a basis for designing improved vector control programs that target specific species, and if integrated with other interventions could result in the elimination of malaria transmission on the island.","corpus_id":25934909,"score":1},{"doc_id":"25890038","title":"Knockdown resistance of Anopheles sinensis in Henan province, China.","abstract":"BACKGROUND: Vivax malaria was historically epidemic in Henan Province of China and Anopheles sinensis was the main vectors and poor farming communities bare the greatest burden of disease. Knockdown resistance in An. sinensis is one of the mechanisms of resistance against pyrethroids. In the present study, the frequency of mutations from An. sinensis was examined in Henan province, China. METHODS: Anopheles was collected from Kaifeng, Tongbai, Tanghe, Pingqiao, Shihe, and Yongcheng counties of Henan province in 2013. Molecular identification of Anopheles species was conducted by polymerase chain reaction (PCR) amplifying the internal transcribed spacer 2 (ITS2). Part of the IIS6 domain of the para-type sodium channel protein gene was polymerase chain reaction-amplified and directly sequenced. Frequency and geographic difference of kdr gene mutant types were analysed. RESULTS: 208 Anopheles were received molecular identification, of which 169 (81.25%) were An. sinensis, 25 (12.02%) were Anopheles yatsushiroensis, and 12 (5.77%) were Anopheles lesteri. A 325 bp fragment of the para-type sodium channel gene including position 1014 was successfully sequenced from 139 Anopheles, of which 125 (89.93%) were An. sinensis, 12 (8.63%) were An. yatsushiroensis, 2 (1.44%) were An. lesteri. The molecular analyses revealed that mutations existed at codon 1014 in An. sinensis but not in An. yatsushiroensis and An. lesteri. Frequency of kdr mutation was 73.60% (92/125) from population of An. sinensis in Henan province, of which L1014F (TTT + TTC) allele frequencies accounted for 46.40% (58/125), and was higher than that of L1014C(TGT) which accounted for 27.20% (34/125) ( χ2 = 55.423, P < 0.001). The frequency of kdr mutation in Kaifeng county was 100% (49/49), and was higher than that of 37.93% (11/29) in Tongbai, 54.55% (6/11) in Pingqiao, 50.00% (3/3) in Shihe, and 62.50% (10/16) in Yongcheng county, respectively (χ2 = 39.538, P < 0.001; χ2 = 24.298, P < 0.001; χ2 = 25.913, P < 0.001; χ2 = 20.244, P < 0.001). While 92.86% (13/14) frequency of kdr mutation was found in Tanghe county, which was higher than that in Tongbai county (χ2 = 11.550, P = 0.0018). CONCLUSIONS: A high frequency of kdr gene mutations from population of An. sinensis in Henan province was found.","corpus_id":1628079,"score":1},{"doc_id":"25927429","title":"Underestimation of foraging behaviour by standard field methods in malaria vector mosquitoes in southern Africa.","abstract":"BACKGROUND: Defining the anopheline mosquito vectors and their foraging behaviour in malaria endemic areas is crucial for disease control and surveillance. The standard protocol for molecular identification of host blood meals in mosquitoes is to morphologically identify fed mosquitoes and then perform polymerase chain reaction (PCR), precipitin tests, or ELISA assays. The purpose of this study was to determine the extent to which the feeding rate and human blood indices (HBIs) of malaria vectors were underestimated when molecular confirmation by PCR was performed on both visually fed and unfed mosquitoes. METHODS: In association with the Southern Africa International Centers of Excellence in Malaria Research (ICEMR), mosquito collections were performed at three sites: Choma district in southern Zambia, Nchelenge district in northern Zambia, and Mutasa district in eastern Zimbabwe. All anophelines were classified visually as fed or unfed, and tested for blood meal species using PCR methods. The HBIs of visually fed mosquitoes were compared to the HBIs of overall PCR confirmed fed mosquitoes by Pearson's Chi-Square Test of Independence. RESULTS: The mosquito collections consisted of Anopheles arabiensis from Choma, Anopheles funestus s.s., Anopheles gambiae s.s. and Anopheles leesoni from Nchelenge, and An. funestus s.s. and An. leesoni from Mutasa. The malaria vectors at all three sites had large human blood indices (HBI) suggesting high anthropophily. When only visually fed mosquitoes tested by PCR for blood meal species were compared to testing those classified as both visually fed and unfed mosquitoes, it was found that the proportion blooded was underestimated by up to 18.7%. For most Anopheles species at each site, there was a statistically significant relationship (P < 0.05) between the HBIs of visually fed mosquitoes and that of the overall PCR confirmed fed mosquitoes. CONCLUSION: The impact on HBI of analysing both visually fed and unfed mosquitoes varied from site to site. This discrepancy may be due to partial blood feeding behaviour by mosquitoes, digestion of blood meals, sample condition, and/or expertise of entomology field staff. It is important to perform molecular testing on all mosquitoes to accurately characterize vector feeding behaviour and develop interventions in malaria endemic areas.","corpus_id":13525284,"score":1},{"doc_id":"25963759","title":"Host-feeding preference of Phlebotomus orientalis (Diptera: Psychodidae) in an endemic focus of visceral leishmaniasis in northern Ethiopia.","abstract":"BACKGROUND: Blood-feeding behavior studies are important for estimating the efficiency of pathogen transmission and assessing the relative human disease risk. However, in Ethiopia and other parts of East Africa there are large remaining gaps in identifying the feeding habits of Phlebotomus orientalis, the vector of Leishmania donovani. The aim of the study was to determine the blood feeding patterns of P. orientalis in Tahtay Adiyabo district, northern Ethiopia. METHODS: For bloodmeal analysis, sandflies were collected from three different villages of Tahtay Adiyabo district using CDC light traps, sticky traps, and pyrethrum spray catches. Bloodmeal of engorged female sandflies was identified using cytochrome (cyt) b-PCR and reverse-line blotting (RLB) and enzyme linked immunosorbent assay (ELISA) assays. RESULTS: Most (637/641) of the females analyzed were P. orientalis. Successful identification of the host from bloodmeals was achieved in 83.03 and 92.1% using cyt b PCR-RLB and ELISA, respectively. Bloodmeal analysis of P. orientalis females revealed that they have a range of hosts with predominant preference to bovines followed by donkey, human, goat, sheep, dog, and camel. CONCLUSION: Results obtained from bloodmeal analyses demonstrate that the feeding preference of P. orientalis is mainly zoophilic, which could vary depending on the availability of hosts.","corpus_id":14225285,"score":1},{"doc_id":"26209103","title":"Early biting of the Anopheles gambiae s.s. and its challenges to vector control using insecticide treated nets in western Kenya highlands.","abstract":"Long term use of insecticides in malaria vector control has been shown to alter the behavior of vectors. Such behavioral shifts have the potential of undermining the effectiveness of insecticide-based control interventions. The effects of insecticide treated nets (ITNs) use on the composition, biting/feeding and sporozoite rates of Anopheles gambiae s.l. mosquitoes in Musilongo village, Vihiga County of western Kenya highlands were investigated. Adult mosquitoes were collected in selected sleeping spaces inside six randomly selected houses using miniature Centre for Disease Control and Prevention (CDC) light traps. Mosquito sampling in each house was conducted twice every week for 16 consecutive months (May 2010-August 2012). At each sampling a single trap was set in the selected space inside each house such that it collected mosquitoes alternatively from 18:00 to 21:00h and 21:00 to 06:00h every week. All collected mosquitoes were morphologically identified. Female Anopheles mosquitoes were classified according to their physiological status as unfed, fed, partially gravid and gravid, sorted and counted. Members of the A. gambiae complex were identified using a Polymerase chain reaction (PCR) method. Enzyme-linked-immunosorbent assay (ELISA) was used to determine blood meal sources and Plasmodium infection rates in A. gambiae s.l. mosquitoes. Blood meal tests were conducted on DNA extracted from gut contents of blood fed A. gambiae s.l. The head and thorax section of dried samples of A. gambiae s.l. were used in testing for the presence of Plasmodium falciparum (Pf) sporozoites. Overall, 735 adult female Anopheles comprising 708 [96.3%] A. gambiae s.l. and 27 [3.7%] Anopheles funestus mosquitoes were collected. A. gambiae s.l. population collected comprised, 615 [86.9%] unfed and 38 [5.4%] fed adult mosquitoes. The rest were either partially or fully gravid. The proportion of A. gambiae s.l. biting indoors within 18:00-21:00h was 15.8% (103/653) at a rate of 3.2bites per person per hour compared to 84.2% biting from 21:00-06:00h at a rate of 3.8 bites/per/h. An estimated 97.7% A. gambiae ss and 2.3% A. arabiensis constituted the indoor biting A. gambiae s.l. The population of An. gambiae s.l. biting from 18:00 to 21:00h had a Plasmodium faciparum (pf) sporozoite rate of 3.8% compared to 3.5% observed in populations biting within 21:00-06:00h. Human blood constituted 89% of An. gambiae s.l. blood meal sources. The risk of malaria transmission from 21:00 to 06:00h was approximately 5 fold the risk within 18:00-21:00h. Majority of the infective female A. gambiae s.l. adults were biting deep into the night than in the early hours of the night. Humans remain the preferred source of blood meal for A. gambiae s.s. the dominant malaria vector in the highlands. ITNs remain a fundamental control intervention against malaria transmission since female blood seekers were more during bed time than pre-bed time. Advocacy on enhanced net availability, integrity and usage in Kenyan highlands can reduce Pf transmission. Additional complementary interventions are required to control the biting and parasite transmission encountered before bed-time.","corpus_id":33009745,"score":1},{"doc_id":"26684464","title":"Zoophagic behaviour of anopheline mosquitoes in southwest Ethiopia: opportunity for malaria vector control.","abstract":"BACKGROUND: Increased understanding of the feeding behaviours of malaria vectors is important to determine the frequency of human-vector contact and to implement effective vector control interventions. Here we assess the relative feeding preferences of Anopheles mosquitoes in relation to cattle and human host abundance in southwest Ethiopia. METHODS: We collected female Anopheles mosquitoes bi-weekly using Centers for Disease Control and prevention (CDC) light traps, pyrethrum spray catches (PSCs) and by aspirating from artificial pit shelters, and determined mosquito blood meal origins using a direct enzyme-linked immunosorbent assay (ELISA). RESULTS: Both Anopheles arabiensis Patton and An. marshalli (Theobald) showed preference of bovine blood meal over humans regardless of higher human population sizes. The relative feeding preference of An. arabiensis on bovine blood meal was 4.7 times higher than that of human blood. Anopheles marshalli was 6 times more likely to feed on bovine blood meal than humans. The HBI of An. arabiensis and An. marshalli significantly varied between the collection methods, whereas the bovine feeding patterns was not substantially influenced by collection methods. Even though the highest HBI of An. arabiensis and An. marshalli was from indoor CDC traps collections, a substantial number of An. arabiensis (65 %) and An. marshalli (63 %) had contact with cattle. Anopheles arabiensis (44 %) and An. marshalli (41 %) had clearly taken bovine blood meals outdoors, but they rested indoors. CONCLUSION: Anopheles mosquitoes are zoophagic and mainly feed on bovine blood meals than humans. Hence, it is important to consider treatment of cattle with appropriate insecticide to control the zoophagic malaria vectors in southwest Ethiopia. Systemic insecticides like ivermectin and its member eprinomectin could be investigated to control the pyrethroid insecticides resistant vectors.","corpus_id":16206708,"score":1},{"doc_id":"26857915","title":"Malaria vectors and their blood-meal sources in an area of high bed net ownership in the western Kenya highlands.","abstract":"BACKGROUND: Blood-meal sources of malaria vectors affect their capacity to transmit the disease. Most efficient malaria vectors prefer human hosts. However, with increasing personal protection measures it becomes more difficult for them to find human hosts. Here recent malaria vector blood-meal sources in western Kenya highlands were investigated. METHODS: Adult mosquitoes resting indoors, outdoors and exiting through windows were collected in three study areas within the western Kenya highlands from June 2011 to June 2013. A census of people, livestock and of insecticide-treated nets was done per house. Mosquito blood-meal sources were determined as human, goat, bovine or chicken using enzyme-linked-immunosorbent assays. RESULTS: Most (86.3 %) households possessed at least one bed net, 57.2 % had domesticated animals and 83.6 % had people sharing houses with livestock at night. Most (94.9 %) unfed malaria vectors were caught exiting through windows. Overall, 53.1 % of Anopheles gambiae sensu stricto obtained blood-meals from humans, 26.5 % from goats and 18.4 % from bovines. Single blood-meal sources by An. gambiae s.s. from humans were 26.5 %, 8.2 % from bovines and 2.0 % from goats. Mixed blood-meal sources by An. gambiae s.s. identified included: 24.5 % human/goat, 10.2 % human/bovine, 8.2 % human/bovine/goat and also 8.2 % bovine/goat. One An. arabiensis mosquito obtained blood-meal only from humans. CONCLUSION: An unusually high frequency of animal and mixed human-animal blood meals in the major malaria vector An. gambiae s.s. was revealed in the western Kenya highlands where bed net coverage is above the WHO target. The shift in blood-meal sources from humans to livestock is most likely the vectors' response to increased bed net coverage and the close location of livestock frequently in the same house as people at night. Livestock-targeted interventions should be considered under these circumstances to address residual malaria transmission.","corpus_id":14385673,"score":1},{"doc_id":"26960327","title":"Anopheles farauti is a homogeneous population that blood feeds early and outdoors in the Solomon Islands.","abstract":"BACKGROUND: In the 1970s, Anopheles farauti in the Solomon Island responded to indoor residual spraying with DDT by increasingly feeding more outdoors and earlier in the evening. Although long-lasting insecticidal nets (LLINs) are now the primary malaria vector control intervention in the Solomon Islands, only a small proportion of An. farauti still seek blood meals indoors and late at night where they are vulnerable to being killed by contract with the insecticides in LLINs. The effectiveness of LLINs and indoor residual spraying (IRS) in controlling malaria transmission where the vectors are exophagic and early biting will depend on whether the predominant outdoor or early biting phenotypes are associated with a subpopulation of the vectors present. METHODS: Mark-release-recapture experiments were conducted in the Solomon Islands to determine if individual An. farauti repeat the same behaviours over successive feeding cycles. The two behavioural phenotypes examined were those on which the WHO recommended malaria vector control strategies, LLINs and IRS, depend: indoor and late night biting. RESULTS: Evidence was found for An. farauti being a single population regarding time (early evening or late night) and location (indoor or outdoor) of blood feeding. Individual An. farauti did not consistently repeat behavioural phenotypes expressed for blood feeding (e.g., while most mosquitoes that fed early and outdoors, and would repeat those behaviours, some fed late at night or indoors in the next feeding cycle). CONCLUSIONS: The finding that An. farauti is a homogeneous population is significant, because during the multiple feeding cycles required to complete the extrinsic incubation period, many individual female anophelines will enter houses late at night and be exposed to the insecticides used in LLINs or IRS. This explains, in part, the control that LLINs and IRS have exerted against a predominantly outdoor feeding vector, such as An. farauti. These findings may be relevant to many of the outdoor feeding vectors that dominate transmission in much of the malaria endemic world and justifies continued use of LLINs. However, the population-level tendency of mosquitoes to feed outdoors and early in the evening does require complementary interventions to accelerate malaria control towards elimination.","corpus_id":16023064,"score":1},{"doc_id":"26969430","title":"Frequent blood feeding enables insecticide-treated nets to reduce transmission by mosquitoes that bite predominately outdoors.","abstract":"BACKGROUND: The effectiveness of vector control on malaria transmission by long-lasting insecticidal nets (LLINs) and indoor residual spraying (IRS) depends on the vectors entering houses to blood feed and rest when people are inside houses. In the Solomon Islands, significant reductions in malaria have been achieved in the past 20 years with insecticide-treated bed nets, IRS, improved diagnosis and treatment with artemisinin combination therapies; despite the preference of the primary vector, Anopheles farauti, to feed outdoors and early in the evening and thereby avoid potential exposure to insecticides. Rational development of tools to complement LLINs and IRS by attacking vectors outdoor requires detailed knowledge of the biology and behaviours of the target species. METHODS: Malaria transmission in Central Province, Solomon Islands was estimated by measuring the components comprising the entomological inoculation rate (EIR) as well as the vectorial capacity of An. farauti. In addition, the daily and seasonal biting behaviour of An. farauti, was examined and the duration of the feeding cycle was estimated with a mark-release-recapture experiment. RESULTS: Anopheles farauti was highly exophagic with 72% captured by human landing catches (HLC) outside of houses. Three-quarters (76%) of blood feeding on humans was estimated to occur before 21.00 h. When the hourly location of humans was considered, the proportion of exposure to mosquito bites on humans occurring indoors (πi) was only 0.130 ± 0.129. Peak densities of host seeking An. farauti occurred between October and January. The annual EIR was estimated to be 2.5 for 2012 and 33.2 for 2013. The length of the feeding cycle was 2.1 days. CONCLUSIONS: The short duration of the feeding cycle by this species offers an explanation for the substantial control of malaria that has been achieved in the Solomon Islands by LLINs and IRS. Anopheles farauti is primarily exophagic and early biting, with 13% of mosquitoes entering houses to feed late at night during each feeding cycle. The two-day feeding cycle of An. farauti requires females to take 5-6 blood meals before the extrinsic incubation period (EIP) is completed; and this could translate into substantial population-level mortality by LLINs or IRS before females would be infectious to humans with Plasmodium falciparum and Plasmodium vivax. Although An. farauti is primarily exophagic, the indoor vector control tools recommended by the World Health Organization (LLINs and IRS) can still provide an important level of control. Nonetheless, elimination will likely require vector control tools that target other bionomic vulnerabilities to suppress transmission outdoors and that complement the control provided by LLINs and IRS.","corpus_id":11747863,"score":1},{"doc_id":"27093890","title":"Most outdoor malaria transmission by behaviourally-resistant Anopheles arabiensis is mediated by mosquitoes that have previously been inside houses.","abstract":"BACKGROUND: Anopheles arabiensis is stereotypical of diverse vectors that mediate residual malaria transmission globally, because it can feed outdoors upon humans or cattle, or enter but then rapidly exit houses without fatal exposure to insecticidal nets or sprays. METHODS: Life histories of a well-characterized An. arabiensis population were simulated with a simple but process-explicit deterministic model and relevance to other vectors examined through sensitivity analysis. RESULTS: Where most humans use bed nets, two thirds of An. arabiensis blood feeds and half of malaria transmission events were estimated to occur outdoors. However, it was also estimated that most successful feeds and almost all (>98 %) transmission events are preceded by unsuccessful attempts to attack humans indoors. The estimated proportion of vector blood meals ultimately obtained from humans indoors is dramatically attenuated by availability of alternative hosts, or partial ability to attack humans outdoors. However, the estimated proportion of mosquitoes old enough to transmit malaria, and which have previously entered a house at least once, is far less sensitive to both variables. For vectors with similarly modest preference for cattle over humans and similar ability to evade fatal indoor insecticide exposure once indoors, >80 % of predicted feeding events by mosquitoes old enough to transmit malaria are preceded by at least one house entry event, so long as ≥40 % of attempts to attack humans occur indoors and humans outnumber cattle ≥4-fold. CONCLUSIONS: While the exact numerical results predicted by such a simple deterministic model should be considered only approximate and illustrative, the derived conclusions are remarkably insensitive to substantive deviations from the input parameter values measured for this particular An. arabiensis population. This life-history analysis, therefore, identifies a clear, broadly-important opportunity for more effective suppression of residual malaria transmission by An. arabiensis in Africa and other important vectors of residual transmission across the tropics. Improved control of predominantly outdoor residual transmission by An. arabiensis, and other modestly zoophagic vectors like Anopheles darlingi, which frequently enter but then rapidly exit from houses, may be readily achieved by improving existing technology for killing mosquitoes indoors.","corpus_id":15774826,"score":1},{"doc_id":"27259984","title":"Host-feeding patterns of mosquito species in Germany.","abstract":"BACKGROUND: Mosquito-borne pathogens are of growing importance in many countries of Europe including Germany. At the same time, the transmission cycles of most mosquito-borne pathogens (e.g. viruses or filarial parasites) are not completely understood. There is especially a lack of knowledge about the vector capacity of the different mosquito species, which is strongly influenced by their host-feeding patterns. While this kind of information is important to identify the relevant vector species, e.g. to direct efficient control measures, studies about the host-feeding patterns of mosquito species in Germany are scarce and outdated. METHODS: Between 2012 and 2015, 775 blood-fed mosquito specimens were collected. Sampling was conducted with Heavy Duty Encephalitis Vector Survey traps, Biogents Sentinel traps, gravid traps, hand-held aspirators, sweep nets, and human-bait collection. The host species for each mosquito specimen was identified with polymerase chain reactions and subsequent Sanger sequencing of the cytochrome b gene. RESULTS: A total of 32 host species were identified for 23 mosquito species, covering 21 mammalian species (including humans) and eleven bird species. Three mosquito species accounted for nearly three quarters of all collected blood-fed mosquitoes: Aedes vexans (363 specimens, 46.8 % of all mosquito specimens), Culex pipiens pipiens form pipiens (100, 12.9 %) and Ochlerotatus cantans (99, 12.8 %). Non-human mammals dominated the host species (572 specimens, 73.8 % of all mosquito specimens), followed by humans (152, 19.6 %) and birds (51, 6.6 %). The most common host species were roe deer (Capreolus capreolus; 258 mosquito specimens, 33.3 % of all mosquito specimens, 65 % of all mosquito species), humans (Homo sapiens; 152, 19.6 %, 90 %), cattle (Bos taurus; 101, 13.0 %, 60 %), and wild boar (Sus scrofa; 116, 15.0 %, 50 %). There were no statistically significant differences in the spatial-temporal host-feeding patterns of the three most common mosquito species. CONCLUSIONS: Although the collected blood-fed mosquito species had a strong overlap of host species, two different host-feeding groups were identified with mosquito species feeding on (i) non-human mammals and humans or (ii) birds, non-human mammals, and humans, which make them potential vectors of pathogens only between mammals or between mammals and birds, respectively. Due to the combination of their host-feeding patterns and wide distribution in Germany, Cx. pipiens pipiens form pipiens and Cx. torrentium are potentially most important vectors for pathogens transmitted from birds to humans and the species Ae. vexans for pathogens transmitted from non-human mammals to humans. Finally, the presented study indicated a much broader host range compared to the classifications found in the literature for some of the species, which highlights the need for studies on the host-feeding patterns of mosquitoes to further assess their vector capacity and the disease ecology in Europe.","corpus_id":2794703,"score":1},{"doc_id":"27317557","title":"Evaluation of a topical formulation of eprinomectin against Anopheles arabiensis when administered to Zebu cattle (Bos indicus) under field conditions.","abstract":"BACKGROUND: Although vector control strategies, such as insecticide-treated bed nets (ITNs) and indoor residual spraying (IRS) have been effective in Kenya the transmission of malaria continues to afflict western Kenya. This residual transmission is driven in part by Anopheles arabiensis, known for its opportunistic blood feeding behaviour and propensity to feed outdoors. The objective of this research was to evaluate the efficacy of the drug eprinomectin at reducing malaria vector density when applied to cattle (Bos indicus), the primary source of blood for An. arabiensis, under field conditions. METHODS: A pilot study was carried out in the Samia District of western Kenya from September to October of 2014. Treatment and control areas were randomly designated and comprised of 50 homes per study area. Before cattle treatments, baseline mosquito counts were performed after pyrethrum spray. Cows in the treatment area were administered topical applications of eprinomectin at 0.5 mg/kg once a week for two consecutive weeks. Mosquito collections were performed once each week for two weeks following the eprinomectin treatments. Mosquitoes were first identified morphologically and with molecular confirmation, then screened for sporozoite presence and host blood using PCR-based methods. RESULTS: The indoor resting density of An. arabiensis was significantly reduced by 38 % in the treatment area compared to the control area at one-week post-treatment (Control mean females per hut = 1.33 95 % CI [1.08, 1.64]; Treatment = 0.79 [0.56, 1.07]). An increase in the indoor resting density of Anopheles gambiae s.s. and Anopheles funestus s.s. was observed in the treatment area in the absence of An. arabiensis. At two weeks post-treatment, the total number of mosquitoes for any species per hut was not significantly different between the treatment and control areas. No change was observed in An. arabiensis host preference as a result of treatment. CONCLUSIONS: Systemic drugs may be an important tool by which to supplement existing vector control interventions by significantly impacting outdoor malaria transmission driven by An. arabiensis through the treatment of cattle.","corpus_id":16717421,"score":1},{"doc_id":"27439360","title":"Chicken volatiles repel host-seeking malaria mosquitoes.","abstract":"BACKGROUND: Anopheles arabiensis is a dominant vector of malaria in sub-Saharan Africa, which feeds indoors and outdoors on human and other vertebrate hosts, making it a difficult species to control with existing control methods. Novel methods that reduce human-vector interactions are, therefore, required to improve the impact of vector control programmes. Investigating the mechanisms underlying the host discrimination process in An. arabiensis could provide valuable knowledge leading to the development of novel control technologies. In this study, a host census and blood meal analysis were conducted to determine the host selection behaviour of An. arabiensis. Since mosquitoes select and discriminate among hosts primarily using olfaction, the volatile headspace of the preferred non-human host and non-host species, were collected. Using combined gas chromatography and electroantennographic detection analysis followed by combined gas chromatography and mass spectrometry, the bioactive compounds in the headspace collections were identified. The efficiency of the identified non-host compounds to repel host-seeking malaria mosquitoes was tested under field conditions. RESULTS: The host census and blood meal analyses demonstrated that An. arabiensis strongly prefers human blood when host seeking indoors, while it randomly feeds on cattle, goats and sheep when found outdoors. However, An. arabiensis avoids chickens despite their relatively high abundance, indicating that chickens are a non-host species for this vector. Eleven bioactive compounds were found in the headspace of the non-host species. Six of these were species-specific, out of which four were identified using combined gas chromatography and mass spectrometry. When tested in the field, the chicken-specific compounds, isobutyl butyrate, naphthalene, hexadecane and trans-limonene oxide, and the generic host compounds, limonene, cis-limonene oxide and β-myrcene, significantly reduced trap catches within the house compared to a negative control. A significant reduction in trap catch was also observed when suspending a caged chicken next to the trap. CONCLUSIONS: Non-host volatiles repel host-seeking An. arabiensis and thus play a significant role in host discrimination. As such, this study demonstrates that non-host volatiles can provide protection to humans at risk of mosquito-vectored diseases in combination with established control programmes.","corpus_id":6144262,"score":1},{"doc_id":"27631375","title":"The Genetic Basis of Host Preference and Resting Behavior in the Major African Malaria Vector, Anopheles arabiensis.","abstract":"Malaria transmission is dependent on the propensity of Anopheles mosquitoes to bite humans (anthropophily) instead of other dead end hosts. Recent increases in the usage of Long Lasting Insecticide Treated Nets (LLINs) in Africa have been associated with reductions in highly anthropophilic and endophilic vectors such as Anopheles gambiae s.s., leaving species with a broader host range, such as Anopheles arabiensis, as the most prominent remaining source of transmission in many settings. An. arabiensis appears to be more of a generalist in terms of its host choice and resting behavior, which may be due to phenotypic plasticity and/or segregating allelic variation. To investigate the genetic basis of host choice and resting behavior in An. arabiensis we sequenced the genomes of 23 human-fed and 25 cattle-fed mosquitoes collected both in-doors and out-doors in the Kilombero Valley, Tanzania. We identified a total of 4,820,851 SNPs, which were used to conduct the first genome-wide estimates of \"SNP heritability\" for host choice and resting behavior in this species. A genetic component was detected for host choice (human vs cow fed; permuted P = 0.002), but there was no evidence of a genetic component for resting behavior (indoors versus outside; permuted P = 0.465). A principal component analysis (PCA) segregated individuals based on genomic variation into three groups which were characterized by differences at the 2Rb and/or 3Ra paracentromeric chromosome inversions. There was a non-random distribution of cattle-fed mosquitoes between the PCA clusters, suggesting that alleles linked to the 2Rb and/or 3Ra inversions may influence host choice. Using a novel inversion genotyping assay, we detected a significant enrichment of the standard arrangement (non-inverted) of 3Ra among cattle-fed mosquitoes (N = 129) versus all non-cattle-fed individuals (N = 234; χ2, p = 0.007). Thus, tracking the frequency of the 3Ra in An. arabiensis populations may be of use to infer selection on host choice behavior within these vector populations; possibly in response to vector control. Controlled host-choice assays are needed to discern whether the observed genetic component has a direct relationship with innate host preference. A better understanding of the genetic basis for host feeding behavior in An. arabiensis may also open avenues for novel vector control strategies based on driving genes for zoophily into wild mosquito populations.","corpus_id":16646011,"score":1},{"doc_id":"27716416","title":"Human-biting activities of Anopheles species in south-central Ethiopia.","abstract":"BACKGROUND: Indoor residual spraying (IRS) and long-lasting insecticidal nets (LLINs) are the key malaria vector control interventions in Ethiopia. The success of these interventions rely on their efficacy to repel or kill indoor feeding and resting mosquitoes. This study was undertaken to monitor human-biting patterns of Anopheles species in south-central Ethiopia. METHODS: Human-biting patterns of anophelines were monitored for 40 nights in three houses using human landing catches (HLC) both indoors and outdoors between July and November 2014, in Edo Kontola village, south-central Ethiopia. This time coincides with the major malaria transmission season in Ethiopia, which is usually between September and November. Adult mosquitoes were collected from 19:00 to 06:00 h and identified to species. Comparisons of HLC data were done using incidence rate ratio (IRR) calculated by negative binomial regression. The nocturnal biting activities of each Anopheles species was expressed as mean number of mosquitoes landing per person per hour. To assess malaria infections in Anopheles mosquitoes the presence of Plasmodium falciparum and P. vivax circumsporozoite proteins (CSP) were determined by enzyme-linked immunosorbent assay (ELISA). RESULTS: Altogether 3,408 adult female anophelines were collected, 2,610 (76.6 %) outdoors and 798 (23.4 %) indoors. Anopheles zeimanni was the predominant species (66.5 %) followed by An. arabiensis (24.8 %), An. pharoensis (6.8 %) and An. funestus (s.l.) ( 1.8 %). The overall mean anopheline density was 3.3 times higher outdoors than indoors (65.3 vs 19.9/person/night, IRR: 3.3, 95 % CI: 1.1-5.1, P = 0.001). The mean density of An. zeimanni, An. pharoensis and An. funestus (s.l.) collected outdoors was significantly higher than indoors for each species (P < 0.05). However, the mean An. arabiensis density outdoors was similar to that indoors (11.8 vs 9.4/person/night, IRR: 1.3, 95 % CI: 0.8-1.9, P = 0.335). The mean hourly human-biting density of An. arabiensis was greater outdoors than indoors and peaked between 21:00 and 22:00 h. However, An. arabiensis parous population showed high indoor man biting activities during bedtimes (22:00 to 05:00 h) when the local people were indoor and potentially protected by IRS and LLINs. All mosquito samples tested for CSP antigen were found negative to malaria parasites. CONCLUSIONS: Results show much greater mosquito human-biting activities occurring outdoors than indoors and during early parts of the night, implying higher outdoor malaria transmission potential in the area. However, high bedtime (22:00 to 05:00 h) indoor biting activities of parous An. arabiensis suggest high potential intervention impact of IRS and LLINs on indoor malaria transmission.","corpus_id":14913998,"score":1},{"doc_id":"28222769","title":"Plasticity of host selection by malaria vectors of Papua New Guinea.","abstract":"BACKGROUND: Host selection is an important determinant of vectorial capacity because malaria transmission increases when mosquitoes feed more on humans than non-humans. Host selection also affects the outcome of long-lasting insecticidal nets (LLIN). Despite the recent nationwide implementation of LLIN-based malaria control program in Papua New Guinea (PNG), little is known about the host selection of the local Anopheles vectors. This study investigated the host selection of Anopheles vectors in PNG. METHODS: Blood-engorged mosquitoes were sampled using the barrier screen method and blood meals analyzed for vertebrate host source with PCR-amplification of the mitochondrial cytochrome b gene. Abundance of common hosts was estimated in surveys. The test of homogeneity of proportions and the Manly resource selection ratio were used to determine if hosts were selected in proportion to their abundance. RESULTS: Two thousand four hundred and forty blood fed Anopheles females of seven species were sampled from five villages in Madang, PNG. Of 2,142 samples tested, 2,061 (96.2%) yielded a definitive host source; all were human, pig, or dog. Hosts were not selected in proportion to their abundance, but rather were under-selected or over-selected by the mosquitoes. Four species, Anopheles farauti (sensu stricto) (s.s.), Anopheles punctulatus (s.s.), Anopheles farauti no. 4 and Anopheles longirostris, over-selected humans in villages with low LLIN usage, but over-selected pigs in villages with high LLIN usage. Anopheles koliensis consistently over-selected humans despite high LLIN usage, and Anopheles bancroftii over-selected pigs. CONCLUSIONS: The plasticity of host selection of an Anopheles species depends on its opportunistic, anthropophilic or zoophilic behavior, and on the extent of host availability and LLIN usage where the mosquitoes forage for hosts. The high anthropophily of An. koliensis increases the likelihood of contacting the LLIN inside houses. This allows its population size to be reduced to levels insufficient to support transmission. In contrast, by feeding on alternative hosts the likelihood of the opportunistic species to contact LLIN is lower, making them difficult to control. By maintaining high population size, the proportion that feed on humans outdoors can sustain residual transmission despite high LLIN usage in the village.","corpus_id":4699384,"score":1},{"doc_id":"28283033","title":"Resting and feeding preferences of Anopheles stephensi in an urban setting, perennial for malaria.","abstract":"BACKGROUND: The Indian city of Chennai is endemic for malaria and the known local malaria vector is Anopheles stephensi. Plasmodium vivax is the predominant malaria parasite species, though Plasmodium falciparum is present at low levels. The urban ecotype of malaria prevails in Chennai with perennial transmission despite vector surveillance by the Urban Malaria Scheme (UMS) of the National Vector Borne Disease Control Programme (NVBDCP). Understanding the feeding and resting preferences, together with the transmission potential of adult vectors in the area is essential in effective planning and execution of improved vector control measures. METHODS: A yearlong survey was carried out in cattle sheds and human dwellings to check the resting, feeding preferences and transmission potential of An. stephensi. The gonotrophic status, age structure, resting and host seeking preferences were studied. The infection rate in An. stephensi and Anopheles subpictus were analysed by circumsporozoite ELISA (CS-ELISA). RESULTS: Adult vectors were found more frequently and at higher densities in cattle sheds than human dwellings. The overall Human Blood Index (HBI) was 0.009 indicating the vectors to be strongly zoophilic. Among the vectors collected from human dwellings, 94.2% were from thatched structures and the remaining 5.8% from tiled and asbestos structures. 57.75% of the dissected vectors were nulliparous whereas, 35.83% were monoparous and the rest 6.42% biparous. Sporozoite positivity rate was 0.55% (4/720) and 1.92% (1/52) for An. stephensi collected from cattle sheds and human dwellings, respectively. One adult An. subpictus (1/155) was also found to be infected with P. falciparum. CONCLUSIONS: Control of the adult vector populations can be successful only by understanding the resting and feeding preferences. The present study indicates that adult vectors predominantly feed on cattle and cattle sheds are the preferred resting place, possibly due to easy availability of blood meal source and lack of any insecticide or repellent pressure. Hence targeting these resting sites with cost effective, socially acceptable intervention tools, together with effective larval source management to reduce vector breeding, could provide an improved integrated vector management strategy to help drive down malaria transmission and assist in India's plan to eliminate malaria by 2030.","corpus_id":3484664,"score":1},{"doc_id":"28797253","title":"First record of Anopheles stephensi in Sri Lanka: a potential challenge for prevention of malaria reintroduction.","abstract":"BACKGROUND: The major malaria vector in Sri Lanka is reported to be Anopheles culicifacies with Anopheles subpictus, Anopheles annularis, and Anopheles varuna considered as potential vectors. The occurrence of Anopheles stephensi, which is the key vector of urban malaria in India and the Middle East, had never been reported from Sri Lanka. METHODS: A series of entomological investigations were carried out by the Anti Malaria Campaign, Ministry of Health, Sri Lanka during December 2016 to April 2017 in two localities of the Mannar District in the Northern Province of the country. Adult mosquito collections were done through indoor and outdoor resting collections, animal and human biting collections and emergence traps. Potential mosquito breeding sites were investigated through larval surveys. The larvae and adults of An. stephensi were initially identified using morphological keys, and subsequently confirmed by sequencing the barcode region of the cytochrome c oxidase I (COI) gene. RESULTS: This is the first report of the presence of An. stephensi in the island of Mannar in the Northern Province of Sri Lanka. Anopheles stephensi (36.65%) was the most abundant anopheline species in the larval habitats in Mannar. It was found breeding together with An. culicifacies (20.7%), An. subpictus (13.5%) and An. varuna (28.13%). Anopheles stephensi was found to be abundantly breeding in built wells used for domestic purposes. Adult females of An. stephensi were observed in emergence trap collections (93.9%), human landing catches all night (79.2%), pyrethrum spray sheet collections (38.6%), outdoor collections (8.3%), donkey-baited trap collections (14.3), and cattle-baited net trap collections (0.7%). CONCLUSIONS: Sri Lanka was certified as malaria-free by the WHO in September 2016, however, this new finding may pose a serious challenge to the efforts of the Ministry of Health to prevent the re-introduction of malaria transmission in the country, considering the role that An. stephensi could play in urban and high vulnerability areas of Sri Lanka.","corpus_id":13653737,"score":1},{"doc_id":"29110670","title":"Indoor and outdoor malaria vector surveillance in western Kenya: implications for better understanding of residual transmission.","abstract":"BACKGROUND: The widespread use of indoor-based malaria vector control interventions has been shown to alter the behaviour of vectors in Africa. There is an increasing concern that such changes could sustain residual transmission. This study was conducted to assess vector species composition, feeding behaviour and their contribution to indoor and outdoor malaria transmission in western Kenya. METHODS: Anopheles mosquito collections were carried out from September 2015 to April 2016 in Ahero and Iguhu sites, western Kenya using CDC light traps (indoor and outdoor), pyrethrum spray catches (PSCs) (indoor) and pit shelters (outdoor). Species within Anopheles gambiae s.l. and Anopheles funestus s.l. were identified using polymerase chain reaction (PCR). Enzyme-linked immunosorbent assay (ELISA) was used to determine mosquito blood meal sources and sporozoite infections. RESULTS: A total of 10,864 female Anopheles mosquitoes comprising An. gambiae s.l. ( 71.4%), An. funestus s.l. ( 12.3%), Anopheles coustani (9.2%) and Anopheles pharoensis (7.1%) were collected. The majority (61.8%) of the anopheline mosquitoes were collected outdoors. PCR result (n = 581) revealed that 98.9% An. arabiensis and 1.1% An. gambiae s.s. constituted An. gambiae s.l. in Ahero while this was 87% An. gambiae s.s. and 13% An. arabiensis in Iguhu. Of the 108 An. funestus s.l. analysed by PCR, 98.1% belonged to An. funestus s.s. and 1.9% to Anopheles leesoni. The human blood index (HBI) and bovine blood index (BBI) of An. arabiensis was 2.5 and 73.1%, respectively. Anopheles gambiae s.s. had HBI and BBI of 50 and 28%, respectively. The HBI and BBI of An. funestus was 60 and 22.3%, respectively. Forage ratio estimate revealed that An. arabiensis preferred to feed on cattle, An. gambiae s.s. showed preference for both human and cattle, while An. funestus preferred human over other hosts. In Ahero, the sporozoite rates for An. arabiensis and An. funestus were 0.16 and 1.8%, respectively, whereas in Iguhu, the sporozoite rates for An. gambiae s.s. and An. funestus were 2.3 and 2.4%, respectively. In Ahero, the estimated indoor and outdoor entomological inoculation rate (EIR) was 108.6 infective bites/person/year (79.0 from An. funestus and 29.6 from An. arabiensis) and 43.5 infective bites/person/year (27.9 from An. arabiensis and 15.6 from An. funestus), respectively. In Iguhu, the estimated indoor and outdoor EIR was 24.5 infective bites/person/year (18.8 from An. gambiae s.s. and 5.7 from An. funestus) and 5.5 infective bites/person/year (all from An. gambiae s.s.), respectively. CONCLUSION: Anopheles gambiae s.s. showed an increasing tendency to feed on cattle. Anopheles arabiensis was highly zoophagic, whereas An. funestus showed anthropophagic behaviour. While the majority of malaria transmission occurred indoor, the magnitude of outdoor transmission was considerably high. Additional control tools that complement the existing interventions are required to control residual transmission.","corpus_id":2213801,"score":1},{"doc_id":"29310656","title":"Comparative evaluation of anopheline sampling methods in three localities in Indonesia.","abstract":"BACKGROUND: The effectiveness of vector control efforts can vary based on the interventions used and local mosquito behaviour and adaptability. In many settings, biting patterns of Anopheles mosquitoes can shift in response to interventions targeting indoor-biting mosquitoes, often resulting in higher proportions of mosquitoes feeding outside or at times when people are not protected. These behaviourally resistant mosquitoes have been shown to sustain residual malaria transmission and limit control efforts. Therefore, it is important to accurately sample mosquitoes to understand their behaviour. METHODS: A variety of traps were evaluated in three geographically diverse sites in malaria-endemic Indonesia to investigate local mosquito feeding behaviour and determine effective traps for surveillance. RESULTS: Eight traps were evaluated in three sites: Canti village, Lampung, Kaliharjo village, Purworejo, and Saketa village, Halmahera, Indonesia, including the gold standard human landing collection (HLC) and a variety of traps targeting host-seeking and resting mosquitoes both indoors and outdoors. Trapping, using indoor and outdoor HLC, the Ifakara tent trap C, goat and human-occupied tents, resting pots and boxes, and CDC miniature light traps was conducted for 16 nights in two sites and 8 nights in a third site, using a Latin square design. Trap efficacy varied by site, with outdoor HLC yielding the highest catch rates in Canti and Kaliharjo and a goat-baited tent trap proving most effective in Saketa. In Canti village, anthropophilic Anopheles sundaicus were caught indoors and outdoors using HLCs, peaking in the early morning. In Kaliharjo, a variety of mosquitoes were caught, mostly outdoors throughout the night. HLC was ineffective in Saketa, the only site where a goat-baited tent trap was tested. This trap was effective in catching zoophilic vectors outdoors before midnight. CONCLUSIONS: Different trapping methods were suitable for different species, likely reflecting differences in behaviour among species. The three villages, each located on a different island in the Indonesian archipelago, contained mosquito populations with unique behaviours. These data suggest that the effectiveness of specific vector monitoring and control measures may vary by location.","corpus_id":28888560,"score":1},{"doc_id":"29479733","title":"Studies on the resting behaviour and host choice of Anopheles gambiae and An. arabiensis from Muleba, Tanzania.","abstract":"The relative efficacy of a mechanical (Prokopack) collection method vs. manual aspiration in the collection of resting mosquitoes was evaluated in northern Tanzania before and after an intervention using indoor residual spraying and longlasting insecticide-treated nets. In smoke-free houses mosquitoes were collected from the roof and walls, but in smoky houses mosquitoes were found predominantly on the walls. Anopheles gambiae (Diptera: Culicidae) constituted 97.7% of the 312 An. gambiae complex specimens identified before but only 19.3% of the 183 identified after the intervention. A single sampling with the Prokopack collected a third of the available insects. Anopheles gambiae completed its gonotrophic development indoors, whereas Anopheles arabiensis did so outdoors. In both species gonotrophic development took 2 days. Most unfed resting An. arabiensis collected outdoors were virgins, whereas the majority of engorged insects were parous (with well-contracted sacs). Daily survival was estimated to be 80.0%. Only 9.4% of the engorged An. arabiensis collected outdoors and 47.1% of those collected indoors had fed on humans. Using the Prokopack sampler is more efficient than manual methods for the collection of resting mosquitoes. Malaria transmission may have been affected by a change in vector composition resulting from a change in feeding, rather than reduced survival. Monitoring the proportions of members of the An. gambiae complex may provide signals of an impending breakdown in control.","corpus_id":3539415,"score":1},{"doc_id":"29669580","title":"The bionomics of the malaria vector Anopheles rufipes Gough, 1910 and its susceptibility to deltamethrin insecticide in North Cameroon.","abstract":"BACKGROUND: Following the recent discovery of the role of Anopheles rufipes Gough, 1910 in human malaria transmission in the northern savannah of Cameroon, we report here additional information on its feeding and resting habits and its susceptibility to the pyrethroid insecticide deltamethrin. METHODS: From 2011 to 2015, mosquito samples were collected in 38 locations across Garoua, Mayo Oulo and Pitoa health districts in North Cameroon. Adult anophelines collected using outdoor clay pots, window exit traps and indoor spray catches were checked for feeding status, blood meal origin and Plasmodium circumsporozoite protein. The susceptibility of field-collected An. rufipes to deltamethrin was assessed using WHO standard procedures. RESULTS: Of 9327 adult Anopheles collected in the 38 study sites, An. rufipes (6.5%) was overall the fifth most abundant malaria vector species following An. arabiensis (52.4%), An. funestus (s.l.) ( 20.8%), An. coluzzii (12.6%) and An. gambiae (6.8%). This species was found outdoors (51.2%) or entering houses (48.8%) in 35 suburban and rural locations, together with main vector species. Apart from human blood with index of 37%, An. rufipes also fed on animals including cows (52%), sheep (49%), pigs (16%), chickens (2%) and horses (1%). The overall parasite infection rate of this species was 0.4% based on the detection of P. falciparum circumsporozoite proteins in two of 517 specimens tested. Among the 21 An. rufipes populations assessed for deltamethrin susceptibility, seven populations were classified as \"susceptible\" (mortality ≥ 98%) , ten as \"probable resistant\" with a mortality range of 90-97% and four as \"resistant\" with a mortality range of 80-89%. CONCLUSIONS: This study revealed changeable resting and feeding behaviour of An. rufipes, as well as further evidence on its ability to carry human malaria parasites in North Cameroon. Besides, this species is developing physiological resistance to deltamethrin insecticide which is used in treated nets and agriculture throughout the country, and should be regarded as one of potential targets for the control of residual malaria parasite transmission in Africa.","corpus_id":4939805,"score":1},{"doc_id":"28849536","title":"Diversity of tick species on domestic animals in Shandong Province, China, using DNA barcoding.","abstract":"Ticks are considered to be second only to mosquitoes as vectors of diseases. In recent years, severe fever with thrombocytopenia syndrome, a new emerging tick-borne disease has been detected in many areas of China, including Shandong Province, Eastern China. Here, we report the tick species diversity based on surveys between 2014 and 2016 covering 16 locations in seven cities of Shandong. Based on DNA barcoding, 1859 ticks belonging to three species were identified: Haemaphysalis longicornis, Rhipicephalus turanicus and Haemaphysalis verticalis. Samples of the same species clustered together in a neighbor-joining phylogenetic tree, with intraspecific distances between 0 and 3.0% and interspecific distances ranged between 15.5 and 24.3%. Goats and dogs were the major hosts of ticks and H. longicornis was regarded as predominant tick species of Shandong. In order to reduce tick populations and prevent tick-borne diseases, effective control measures should be implemented on human and domestic animals, respectively.","corpus_id":34695622,"score":0}],"string":"[\n {\n \"doc_id\": \"18538036\",\n \"title\": \"The resting sites and blood-meal sources of Anopheles minimus in Taiwan.\",\n \"abstract\": \"BACKGROUND: The WHO declared Taiwan free from malaria in 1965, but in 2003 the reporting of two introduced cases in a rural area suggested a possible local transmission of this disease. Therefore, understanding the resting sites and the blood sources of Anopheles minimus is crucial in order to provide information for implementing vector control strategies. METHODS: During a two-year survey, mosquitoes were collected in houses and their surrounding areas and at the bank of larval habitats by backpack aspirators in 17 villages in rural areas of southern and eastern Taiwan for 1 hr. On the same day, blacklight traps were hung downward overnight. Blood-fed mosquito samples were analysed by PCR. RESULTS: Of the 195 total households surveyed by backpack aspirators, no Anopheles adults were collected inside the houses, while a single Anopheles minimus and a single Anopheles maculatus were collected outside of the houses. On the same day, 23 An. minimus, two An. maculatus, two Anopheles ludlowae, two Anopheles sinensis, and one Anopheles tessellatus were collected along the bank of larval habitats. In blacklight traps hung outside of the houses in the villages, 69 An. minimus, 62 An. ludlowae, 31 An. sinensis, and 19 An. maculatus were collected. In larval habitats, 98 An. ludlowae, 64 An. minimus, 49 An. sinensis, and 14 An. maculatus were collected. Of a total of 10 blood-fed samples, An. minimus fed on four animals including bovine (60%), dogs (20%), pig (10%), and non-chicken avian (10%). CONCLUSION: Anopheles minimus, an opportunist feeder in Taiwan, was not collected inside the houses, but was found outside of the houses in villages and surrounding larval habitats. Therefore, an outdoor transmission of malaria is likely to occur and, thus, the bed nets, which are favoured for controlling the late biting of An. minimus, should be a very efficient and effective method for those local residents who sleep outdoors. Additionally, space spray of insecticides for Anopheles at night, as well as residual spray inside animal huts and selective larval habitats, are also helpful to control female adults.\",\n \"corpus_id\": 2098821,\n \"score\": 2\n },\n {\n \"doc_id\": \"21559055\",\n \"title\": \"Seasonal abundance and host-feeding patterns of anopheline vectors in malaria endemic area of iran.\",\n \"abstract\": \"Seasonal abundance and tendency to feed on humans are important parameters to measure for effective control of malaria vectors. The objective of this study was to describe relation between feeding pattern, abundance, and resting behavior of four malaria vectors in southern Iran. This study was conducted in ten indicator villages (based on malaria incidence and entomological indices) in mountainous/hilly and plain regions situated south and southeastern Iran. Mosquito vectors were collected from indoor as well as outdoor shelters and the blood meals were examined by ELISA test. Over all 7654 female Anopheles spp. were captured, the most common species were Anopheles stephensi, An. culicifacies, An. fluviatilis, and An. d'thali. The overall human blood index was 37.50%, 19.83%, 16.4%, and 30.1% for An. fluviatilis, An. stephensi, An. culicifacies, and An. d'thali, respectively. In addition, An. fluviatilis fed on human blood during the entire year but the feeding behavior of An. stephensi and An. culicifacies varied according to seasons. Overall, the abundance of the female mosquito positive to human blood was 4.25% per human shelter versus 17.5% per animal shelter. This result indicates that the vectors had tendency to rest in animal shelters after feeding on human. Therefore, vector control measure should be planned based on such as feeding pattern, abundance, and resting behavior of these vectors in the area.\",\n \"corpus_id\": 17230409,\n \"score\": 2\n },\n {\n \"doc_id\": \"21569546\",\n \"title\": \"Plasmodium falciparum transmission and aridity: a Kenyan experience from the dry lands of Baringo and its implications for Anopheles arabiensis control.\",\n \"abstract\": \"BACKGROUND: The ecology of malaria vectors particularly in semi-arid areas of Africa is poorly understood. Accurate knowledge on this subject will boost current efforts to reduce the burden of malaria in sub-Saharan Africa. The objective of this study was to describe the dynamics of malaria transmission in two model semi-arid sites (Kamarimar and Tirion) in Baringo in Kenya. METHODS: Adult mosquitoes were collected indoors by pyrethrum spray collections (PSC) and outdoors by Centers for Disease Control (CDC) light traps and identified to species by morphological characteristics. Sibling species of Anopheles gambiae complex were further characterized by rDNA. PCR and enzyme-linked immuno-sorbent assays (ELISA) were used to test for Plasmodium falciparum circumsporozoite proteins and host blood meal sources respectively. RESULTS: Anopheles arabiensis was not only the most dominant mosquito species in both study sites but also the only sibling species of An. gambiae s.l. present in the area. Other species identified in the study area were Anopheles funestus, Anopheles pharoensis and Anopheles coustani. For Kamarimar but not Tirion, the human blood index (HBI) for light trap samples was significantly higher than for PSC samples (Kamarimar, 0.63 and 0.11, Tirion, 0.48 and 0.43). The HBI for light trap samples was significantly higher in Kamarimar than in Tirion while that of PSC samples was significantly higher in Tirion than in Kamarimar. Entomological inoculation rates (EIR) were only detected for one month in Kamarimar and 3 months in Tirion. The number of houses in a homestead, number of people sleeping in the house, quality of the house, presence or absence of domestic animals, and distance to the animal shelter and the nearest larval habitat were significant predictors of An. arabiensis occurrence. CONCLUSION: Malaria transmission in the study area is seasonal with An. arabiensis as the dominant vector. The fact this species feeds readily on humans and domestic animals suggest that zooprophylaxis may be a plausible malaria control strategy in semi-arid areas of Africa. The results also suggest that certain household characteristics may increase the risk of malaria transmission.\",\n \"corpus_id\": 1035329,\n \"score\": 2\n },\n {\n \"doc_id\": \"21727666\",\n \"title\": \"Seasonal prevalence & resting behaviour of Anopheles minimus Theobald & An. fluviatilis James (Diptera: Culicidae) in east-central India.\",\n \"abstract\": \"BACKGROUND & OBJECTIVES: Anopheles minimus has recently been reported to have re-appeared in Keonjhar district of Orissa after a period of about 45 years of launching the malaria eradication programme. An. minimus and An. fluviatilis were the incriminated major malaria vectors in the district, endemic for falciparum malaria. The information on seasonal prevalence and resting behaviour of the vectors is crucial for implementing appropriate malaria control measures. Therefore, a study was undertaken on seasonal prevalence and resting behaviour of An. minimus and An. fluviatilis in this district. METHODS: Seven randomly selected villages of Keonjhar district, Orissa, were studied during August 2005 to November 2007. Daytime resting collections indoors and outdoors were made covering three seasons of the year. The Anopheles mosquitoes obtained from different habitats were identified. Collections were maintained separately according to different sites as well as heights of the walls in human dwellings. RESULTS: Among the indoor collections, the densities of An. minimus and An. fluviatilis were higher in human dwellings than cattle sheds. An. fluviatilis was the predominant (41.5%) species followed by An. minimus (26.3%) in human dwellings. The density of both the vector species in human dwellings peaked during rainy and winter seasons followed by summer. Walls were the most preferred site by these vectors for resting and the maximum number was collected at a height of 3 to 4 ft. INTERPRETATION & CONCLUSIONS: The resting behaviour of the vector species increases their contact with the sprayed walls and therefore, a quality residual spraying of human dwellings focusing indoor walls could interrupt the malaria transmission in this area.\",\n \"corpus_id\": 15447460,\n \"score\": 2\n },\n {\n \"doc_id\": \"22115320\",\n \"title\": \"The abundance and host-seeking behavior of culicine species (Diptera: Culicidae) and Anopheles sinensis in Yongcheng city, People's Republic of China.\",\n \"abstract\": \"BACKGROUND: The knowledge of mosquito species diversity and the level of anthropophily exhibited by each species in a region are of great importance to the integrated vector control. Culicine species are the primary vectors of Japanese encephalitis (JE) virus and filariasis in China. Anopheles sinensis plays a major role in the maintenance of Plasmodium vivax malaria transmission in China. The goal of this study was to compare the abundance and host-seeking behavior of culicine species and An. sinensis in Yongcheng city, a representative region of P. vivax malaria. Specifically, we wished to determine the relative attractiveness of different animal baits versus human bait to culicine species and An. sinensis. RESULTS: Culex tritaeniorhynchus was the most prevalent mosquito species and An. sinensis was the sole potential vector of P. vivax malaria in Yongcheng city. There were significant differences (P < 0.01) in the abundance of both An. sinensis and Cx. tritaeniorhynchus collected in distinct baited traps. The relative attractiveness of animal versus human bait was similar towards both An. sinensis and Cx. tritaeniorhynchus. The ranking derived from the mean number of mosquitoes per bait indicated that pigs, goats and calves frequently attracted more mosquitoes than the other hosts tested (dogs, humans, and chickens). These trends were similar across all capture nights at three distinct villages. The human blood index (HBI) of female An. sinensis was 2.94% when computed with mixed meals while 3.70% computed with only the single meal. 19:00~21:00 was the primary peak of host-seeking female An. sinensis while 4:00~5:00 was the smaller peak at night. There was significant correlation between the density of female An. sinensis and the average relative humidity (P < 0.05) in Wangshanzhuang village. CONCLUSIONS: Pigs, goats and calves were more attractive to An. sinensis and Cx. tritaeniorhynchus than dogs, humans, and chickens. Female An. sinensis host-seeking activity mainly occurred from 19:00 to 21:00. Thus, we propose that future vector control against An. sinensis and Cx. tritaeniorhynchus in the areas along the Huang-Huai River of central China should target the interface of human activity with domestic animals and adopt before human hosts go to bed at night.\",\n \"corpus_id\": 2559019,\n \"score\": 2\n },\n {\n \"doc_id\": \"22336191\",\n \"title\": \"Blood-feeding patterns of Anopheles mosquitoes in a malaria-endemic area of Bangladesh.\",\n \"abstract\": \"BACKGROUND: Blood-feeding patterns of mosquitoes are crucial for incriminating malaria vectors. However, little information is available on the host preferences of Anopheles mosquitoes in Bangladesh. Therefore, the objective of the present study was to determine the hematophagic tendencies of the anophelines inhabiting a malaria-endemic area of Bangladesh. METHODS: Adult Anopheles mosquitoes were collected using light traps (LTs), pyrethrum spray (PS), and human bait (HB) from a malaria-endemic village (Kumari, Bandarban, Bangladesh) during the peak months of malaria transmission (August-September). Enzyme-linked immunosorbent assay (ELISA) and polymerase chain reaction (PCR) were performed to identify the host blood meals of Anopheles mosquitoes. RESULTS: In total, 2456 female anopheline mosquitoes representing 21 species were collected from the study area. Anopheles vagus Doenitz (35.71%) was the dominant species followed by An. philippinensis Ludlow (26.67%) and An. minimus s.l. Theobald (5.78%). All species were collected by LTs set indoors (n = 1094), 19 species were from outdoors (n = 784), whereas, six by PS (n = 549) and four species by HB (n = 29). Anopheline species composition significantly differed between every possible combination of the three collection methods (χ(2) test, P < 0.001). Host blood meals were successfully detected from 1318 (53.66%) Anopheles samples belonging to 17 species. Values of the human blood index (HBI) of anophelines collected from indoors and outdoors were 6.96% and 11.73%, respectively. The highest values of HBI were found in An. baimai Baimaii (80%), followed by An. minimus s.l. ( 43.64%) and An. annularis Van den Wulp (37.50%). Anopheles baimai (B(i) = 0.63) and An. minimus s.l. ( B(i) = 0.24) showed strong relative preferences (B(i)) for humans among all hosts (human, bovine, goats/sheep, and others). Anopheles annularis, An. maculatus s.l. Theobald, and An. pallidus Theobald exhibited opportunistic blood-feeding behavior, in that they fed on either humans or animals, depending on whichever was accessible. The remaining 12 species preferred bovines as hosts. CONCLUSIONS: The observed high anthropophilic nature of An. baimai, An. minimus s.l., and An. annularis revealed these species to be important malaria vectors in hilly areas of Bangladesh. Higher values of HBI in outdoor-resting mosquitoes indicated that indoor collection alone is not adequate for evaluating malaria transmission in the area.\",\n \"corpus_id\": 547702,\n \"score\": 2\n },\n {\n \"doc_id\": \"22676415\",\n \"title\": \"Host feeding patterns and preference of Anopheles minimus (Diptera: Culicidae) in a malaria endemic area of western Thailand: baseline site description.\",\n \"abstract\": \"BACKGROUND: Host feeding patterns of Anopheles minimus in relation to ambient environmental conditions were observed during a 2-year period at Tum Sua Village, located in Mae Sot District, Tak Province, in western Thailand, where An. minimus is found in abundance and regarded as the most predominant malaria vector species. Detailed information on mosquito behavior is important for understanding the epidemiology of disease transmission and developing more effective and efficient vector control methods. METHODS: Adult mosquitoes were collected every 2 months for two consecutive nights from 1800 to 0600 hrs. Three collection methods were used; indoor human-landing collections (HLC), outdoor HLC, and outdoor cattle-bait collections (CBC). RESULTS: A total of 7,663 female Anopheles mosquitoes were collected of which 5,392 were identified as members of 3 different species complexes, the most prevalent being Anopheles minimus complex (50.36%), followed by Anopheles maculatus complex (19.68%) and Anopheles dirus complex (0.33%). An. minimus s.s. comprised virtually all (> 99.8 percent) of Minimus Complex species captured. Blood feeding behavior of An. minimus was more pronounced during the second half of the evening, showing a slight preference to blood feed outdoors (~60%) versus inside structures. Significantly (P < 0.0001) more An. minimus were collected from human-baited methods compared with a tethered cow, indicating a more anthropophilic feeding behavior. Although a significant difference in total number of mosquitoes from the HLC was recorded between the first and second year, the mean biting frequency over the course of the evening hours remained similar. CONCLUSIONS: The Human landing activity of An. minimus in Tum Sua Village showed a stronger preference/attraction for humans compared to a cow-baited collection method. This study supports the incrimination of An. minimus as the primary malaria vector in the area. A better understanding of mosquito behavior related to host preference, and the temporal and spatial blood feeding activity will help facilitate the design of vector control strategies and effectiveness of vector control management programs in Thailand.\",\n \"corpus_id\": 18063759,\n \"score\": 2\n },\n {\n \"doc_id\": \"22776520\",\n \"title\": \"Vector capacity of Anopheles sinensis in malaria outbreak areas of central China.\",\n \"abstract\": \"BACKGROUND: Both falciparum and vivax malaria were historically prevalent in China with high incidence. With the control efforts, the annual incidence in the whole country has reduced to 0.0001% except in some areas in the southern borders after 2000. Despite this, the re-emergence or outbreak of malaria was unavoidable in central China during 2005-2007. In order to understand the role of the vector in the transmission of malaria during the outbreak period, the vector capacity of An. sinensis in Huanghuai valley of central China was investigated. FINDINGS: The study was undertaken in two sites, namely Huaiyuan county of Anhui province and Yongcheng county of Henan province. In each county, malaria cases were recorded for recent years, and transmission risk factors for each study village including anti-mosquito facilities and total number of livestock were recorded by visiting each household in the study sites. The specimens of mosquitoes were collected in two villages, and population density and species in each study site were recorded after the identification of different species, and the blood-fed mosquitoes were tested by ring precipitation test. Finally, various indicators were calculated to estimate vector capacity or dynamics, including mosquito biting rate (MBR), human blood index (HBI), and the parous rates (M). Finally, the vector capacity, as an important indicator of malaria transmission to predict the potential recurrence of malaria, was estimated and compared in each study site. About 93.0% of 80 households in Huaiyuan and 89.3% of 192 households in Yongcheng had anti-mosquito facilities. No cattle or pigs were found, only less than 10 sheep were found in each study village. A total of 94 and 107 Anopheles spp. mosquitos were captured in two study sites, respectively, and all of An. sinensis were morphologically identified. It was found that mosquito blood-feeding peak was between 9:00 pm and 12:00 pm. Man biting rate of An. sinensis was 6.0957 and 5.8621 (mosquitoes/people/night) estimated by using half-night human bait trap method and full-capture method, respectively. Human blood indexes (HBI) were 0.6667 (6/9) and 0.6429 (18/28), and man-biting habits were 0.2667 and 0.2572 in two sites, respectively. Therefore, the expectation of infective life and vector capacity of An. sinensis was 0.3649-0.4761 and 0.5502-0.7740, respectively, in Huanhuai valley of central China where the outbreak occurred, which is much higher than that in the previous years without malaria outbreak. CONCLUSIONS: This study suggests that vivax malaria outbreak in Huanhuai valley is highly related to the enhancement in vector capacity of An. sinensis for P. vivax, which is attributed to the local residents' habits and the remarkable drop in the number of large livestock leading to disappearance of traditional biological barriers.\",\n \"corpus_id\": 17026,\n \"score\": 2\n },\n {\n \"doc_id\": \"23433306\",\n \"title\": \"Blood meal origins and insecticide susceptibility of Anopheles arabiensis from Chano in South-West Ethiopia.\",\n \"abstract\": \"BACKGROUND: Anopheles arabiensis, the main malaria vector in Ethiopia, shows both anthropophilic and zoophilic behaviours. Insecticide resistance is increasing, and alternative methods of vector control are needed. The objectives of this study were to determine the blood meal origins and the susceptibility to insecticides of An. arabiensis from Chano village near Arba Minch in South-West Ethiopia. METHODS: Blood meal sources of anopheline mosquitoes collected using Centers for Disease Control and Prevention (CDC) light traps and pyrethrum spray catches (PSC) from human dwellings, and hand-held mouth aspirators from outdoor pit shelters were analysed using a direct enzyme-linked-immunosorbent assay (ELISA). The susceptibility of An. arabiensis to pyrethroid insecticides (alphacypermethrin, lambdacyhalothrin, deltamethrin, and cyfluthrin) and DDT was assessed using females reared from larval and pupal collections from natural breeding sites. RESULTS: The blood meal origins of 2967 freshly fed Anopheles mosquitoes were determined. An. arabiensis was the predominant species (75%), and it fed mainly on cattle. The densities of both freshly fed An. arabiensis and those fed on human blood followed similar seasonal patterns. The overall human blood index (HBI) of An. arabiensis, including mixed blood meals, was 44% and the bovine blood index (BBI) was 69%. The HBI of An. arabiensis from CDC light trap collections was 75% and this was higher than those for PSC (38%) and outdoor pit shelter collections (13%), while the BBI was 65% for PSC, 68% for outdoor pit shelters and 72% for CDC light traps. More freshly fed and human blood-fed An. arabiensis were sampled from houses close to the shore of Lake Abaya (the major breeding site).A high proportion of An. arabiensis was resistant to the pyrethroid insecticides, with a mortality rate of 56% for lambdacyhalothrin, 50% for cyfluthrin and alphacypermethrin, 47% for deltamethrin, and 10% for DDT. CONCLUSION: Anopheles arabiensis is the predominant species of anopheline mosquito in this region, and cattle are the main source of its blood meals. The greater tendency of this species to feed on cattle justifies the application of insecticides on cattle to control it. However, An. arabiensis has already developed resistance to the available pyrethroid insecticides, and alternative insecticides are needed for malaria vector control.\",\n \"corpus_id\": 17249470,\n \"score\": 2\n },\n {\n \"doc_id\": \"23768077\",\n \"title\": \"Susceptibility of Anopheles sinensis to Plasmodium vivax in malarial outbreak areas of central China.\",\n \"abstract\": \"BACKGROUND: Anopheles sinensis, Anopheles anthropophagus, Anopheles minimus and Anopheles dirus are the major vectors of malaria transmission in China. Anopheles sinensis is considered a secondary vector due to its relatively low malaria-transmission ability. However, in 2005, an outbreak of over 40,000 Plasmodium vivax malaria cases was reported in areas where Anopheles sinensis was the only major vector. Therefore, it is necessary to reassess the malaria transmission ability of this vector species in China. METHODS: Laboratory colonies of An. sinensis and An. anthropophagus, and first-generation progeny (F1) of An. sinensis that had been collected in central China, were infected by direct membrane feeding assay with mono-vivax gametocyte-containing blood collected from vivax-infected patients. The mosquitoes were kept for 7 to 14 days post-blood feeding to allow parasites to develop into oocysts and sporozoites. Infectivity was measured by dissecting midguts and salivary glands. The presence of oocysts and sporozoites was determined by microscopy at 7 and 14 days post-blood feeding, and the numbers of gametocytes and asexual parasites, as well as mosquito parasite infections, were determined. RESULTS: The positive oocyst and sporozoite feed rates of the 142 pairs of lab-colony An. sinensis and An. anthropophagus were not significantly different, and the same results were found with the 10 pairs of laboratory and F1 An. sinensis. An. sinensis had more oocysts/midgut at 7 days post-feeding than An. anthropophagus, but the gametocytemia, asexual parasitemia, and ratio of macrogametocytes to microgametocytes, did not correlate with either oocyst or sporozoite infection. However, in the oocyst-positive mosquitoes, there was a correlation between gametocytemia and the average oocyst number/midgut. CONCLUSIONS: The susceptibility of An. sinensis (both laboratory and F1) to P. vivax-infected blood is similar to Anopheles anthropophagus, when evaluated by membrane feeding assay under laboratory conditions. In recent years, in central China, the vivax malaria transmission ability of An. sinensis has probably been underestimated. Further studies of this species in other regions are needed. An. sinensis could also be a good candidate vector for evaluating candidate malaria transmission-blocking vaccines (TBV).\",\n \"corpus_id\": 1492680,\n \"score\": 2\n },\n {\n \"doc_id\": \"24252367\",\n \"title\": \"Spatio-temporal analysis of host preferences and feeding patterns of malaria vectors in the sylvo-pastoral area of Senegal: impact of landscape classes.\",\n \"abstract\": \"BACKGROUND: The study of vector feeding behaviour is an important step in the understanding of the epidemiology of vector borne diseases. The main objective of this work was to study the spatio-temporal host preferences and blood-feeding patterns of malaria vectors in a pastoral area of Senegal where cattle breeding is the main human activity. METHODS: Malaria vectors were collected indoors by pyrethrum spray catch in 16 villages belonging to 4 different landscape classes (wooded savanna, shrubby savanna, bare soils and steppe). Blood meals sources were determined using a direct enzyme-linked immunosorbent assay (ELISA). RESULTS: The blood meal origins of 1886 freshly fed An. gambiae s.l. were determined. Among these blood meals, most were taken on a single host: 40.1% on human and 37.1% on animal. The range in proportions of blood meals taken from human were 25-62.4% in wooded savanna villages, 23.5-61.9% in shrubby savanna villages, 31.3-70% in bare soils villages and 57.7-68.7 in steppe villages. Blood meals taken from bovines were very heterogeneous with two clusters localized in the Northeast and Southwest axis of the study area that corresponds to the distribution of the main water ponds. Patent mixed blood meals taken from human and non-human were significantly higher than those taken from two animals, the highest proportions being observed in September (shrubby savanna, bare soils and steppe villages) or October (wooded savanna villages). CONCLUSIONS: These observations suggest that in this pastoral area, differences in feeding patterns of malaria vectors are merely linked to the specific localization of villages and are not influenced by landscape class distribution. In addition, the temporal variations in the anthropophilic rates are influenced by the presence of standing water in the study area.\",\n \"corpus_id\": 14205629,\n \"score\": 2\n },\n {\n \"doc_id\": \"24589247\",\n \"title\": \"Insecticide resistance of Anopheles sinensis and An. vagus in Hainan Island, a malaria-endemic area of China.\",\n \"abstract\": \"BACKGROUND: Malaria is one of the most important public health problems in Southeast Asia, including Hainan Island, China. Vector control is the main malaria control measure, and insecticide resistance is a major concern for the effectiveness of chemical insecticide control programs. The objective of this study is to determine the resistance status of the main malaria vector species to pyrethroids and other insecticides recommended by the World Health Organization (WHO) for indoor residual sprays. METHODS: The larvae and pupae of Anopheles mosquitoes were sampled from multiple sites in Hainan Island, and five sites yielded sufficient mosquitoes for insecticide susceptibility bioassays. Bioassays of female adult mosquitoes three days after emergence were conducted in the two most abundant species, Anopheles sinensis and An. vagus, using three insecticides (0.05% deltamethrin, 4% DDT, and 5% malathion) and following the WHO standard tube assay procedure. P450 monooxygenase, glutathione S-transferase and carboxylesterase activities were measured. Mutations at the knockdown resistance (kdr) gene and the ace-1 gene were detected by DNA sequencing and PCR-RFLP analysis, respectively. RESULTS: An. sinensis and An. vagus were the predominant Anopheles mosquito species. An. sinensis was found to be resistant to DDT and deltamethrin. An. vagus was susceptible to deltamethrin but resistant to DDT and malathion. Low kdr mutation (L1014F) frequency (<10%) was detected in An. sinensis, but no kdr mutation was detected in An. vagus populations. Modest to high (45%-75%) ace-1 mutation frequency was found in An. sinensis populations, but no ace-1 mutation was detected in An. vagus populations. Significantly higher P450 monooxygenase and carboxylesterase activities were detected in deltamethrin-resistant An. sinensis, and significantly higher P450 monooxygenase, glutathione S-transferase and carboxylesterase activities were found in malathion-resistant An. vagus mosquitoes. CONCLUSIONS: Multiple insecticide resistance was found in An. sinensis and An. vagus in Hainan Island, a malaria-endemic area of China. Cost-effective integrated vector control programs that go beyond synthetic insecticides are urgently needed.\",\n \"corpus_id\": 14417787,\n \"score\": 2\n },\n {\n \"doc_id\": \"24822373\",\n \"title\": \"[Identification of mammalian blood meals in anopheline mosquitoes from four counties of Yunnan Province by multiple PCR].\",\n \"abstract\": \"From June to August 2012, the blood-sucking mosquitoes were captured around cattle-sheds and human houses in Yuanjiang County, Qiaojia County, Yongshan County, and Jinghong City of Yunan Province. Blood samples from mosquitoes were collected on filter paper. Multiplex PCR assay was used to detect the blood meal samples. Among the 145 mosquitoes captured, 123 were Anopheles sinensis (84.8%) and 22 A. minimus (15.2%). Among the blood samples, corresponding bands were amplified in 134 samples. The result showed that the blood meals were from pigs (n = 104), cows (n = 22), dogs (n = 4), human (n=2), cow and pig (n = 1), pig and human (n = 1). Human blood index of A. sinensis and A. minimus was 0.018 and 0.045, respectively.\",\n \"corpus_id\": 21283349,\n \"score\": 2\n },\n {\n \"doc_id\": \"25782250\",\n \"title\": \"[Sequence analysis of ribosomal DNA internal transcribed spacer 2 of sympatric populations of Anopheles sinensis of different feeding preferences].\",\n \"abstract\": \"OBJECTIVE: To investigate the existence of genetic divergence of sympatric populations of Anopheles sinensis of different feeding preferences based on the rDNA-ITS2 sequence differences. METHODS: A large number of wild anopheles populations were trapped all night by man-baited net and calf-baited net that had been set up between high-density natural villages of An. sinensis populations and vector-breeding sites, from which two groups of An. sinensis were separated by morphological identification and brought back to the lab for conventional breeding. A large closed greenhouse which temperature and humidity was appropriate was selected as research settings of mark-release-recapture methods by female mosquitoes, in the center of which above An. sinensis populations baited by man and calf and respectively correspondingly marked by red and yellow phosphors were released in together, in each side of which An. sinensis were recaptured simultaneously by man-baited net and calf-baited net. An. sinensis populations trapped by man twice were brought back to the lab and bred with man-blood, correspondingly ones trapped by calf with calf-blood. Man-preferring and calf-preferring strains were screened respectively from An. sinensis which had been baited by man and calf by the mark-release-recapture methods after parent and F1 mosquitoes, and sequencing and aligning of both rDNA-ITS2 were conducted via PCR amplification. RESULTS: The recapture ratios of wild parental mosquitoes An. sinensis of man-preferring group by man-baited net and calf-baited net were 54.07% (339/627) and 45.93% (288/627) respectively, and ones of calf-preferring group by man-baited net and calf-baited net were 58.01% (409/705) and 41.99% (296/ 705) respectively. Two groups of parental mosquitoes trended towards selecting the original blood hosts in host-seeking preference (Χ2 = 19.42, P < 0.01). The recapture ratios of F1 mosquitoes An. sinensis of man-preferring group by man-baited net and calf-baited net were 63.43% (765/1 206) and 36.57% (441/1 206), and ones of calf-preferring group by man-baited net and calf-baited net were 68.22% (1 039/1 523) and 31.78% (484/1 523). Two groups of F1 mosquitoes had more significant characteristics of selecting the original blood hosts in host-seeking preference (Χ2 = 271.69, P < 0.01) and showed the genetic differentiation phenomenon, but the results of sequencing and aligning of the rDNA-ITS2 via PCR amplification showed no difference in base sequence between the two strains and both were 469 bp. CONCLUSIONS: The genetic divergence based on the rDNA-ITS2 sequence does not happen in An. sinensis sympatric populations of different feeding preferences.\",\n \"corpus_id\": 20139419,\n \"score\": 2\n },\n {\n \"doc_id\": \"25843138\",\n \"title\": \"Host feeding patterns of mosquitoes in a rural malaria-endemic region in hainan island, china.\",\n \"abstract\": \"Malaria is endemic in Wangxia Village of Hainan Island. In this area little is known about the host seeking behavior and feeding habit of mosquitoes. Three sites representing the most common habitat types in the village were selected to study the host seeking behavior and feeding habit of mosquitoes. Of the total 9 species belonging to 4 genera (Armigeres, Culex, Aedes, and Anopheles) collected in Wangxia Village, Culex tritaeniorhynchus and Cx. pipiens quinquefasciatus were the most commonly collected species. Armigeres subalbatus and Anopheles sinensis were moderately common species. Blood meal analysis confirmed that Cx. tritaeniorhynchus and Cx. p. quinquefasciatus fed on multiple hosts, mainly poultry but occasionally other animals. Anopheles sinensis, a vector of malaria, fed predominately on cattle hosts, followed by humans. Anopheles maculatus and An. barbirostris fed on both humans and domestic animals. Our results indicate that most mosquitoes in this area preferred domestic animals over humans and showed a tendency to feed on multiple hosts within the same gonotrophic cycle. Therefore, the potential role of domestic animals in arbovirus transmission should be evaluated as part of a strategy for controlling mosquito-borne diseases in this region.\",\n \"corpus_id\": 8236412,\n \"score\": 2\n },\n {\n \"doc_id\": \"25880316\",\n \"title\": \"Development of insecticide resistance in malaria vector Anopheles sinensis populations from Shandong province in China.\",\n \"abstract\": \"BACKGROUND: Anopheles sinensis is a major vector of malaria and among the dominant species in Shandong province of China. Insecticide resistance is an important threat to vector-borne disease control. However, there are only few reports about insecticide resistance of An. sinensis populations from Shandong province. METHODS: From 2003 to 2012, six districts in Shandong province were selected as the study areas. Insecticide susceptibility bioassay were tested on F1 progeny of An. sinensis to 4% DDT, 0.05% deltamethrin, 0.15% cyfluthrin, and 5% malathion, using the standard WHO resistance tube assay. RESULTS: The resistance status of An. sinensis showed a significant decrease in the mortality rates in DDT, deltamethrin and cyfluthrin during the past ten years. Whereas obvious increase of mortality to malathion was observed throughout the assay, ranging from 47.37% to 86.62%.\",\n \"corpus_id\": 7544460,\n \"score\": 2\n },\n {\n \"doc_id\": \"25888824\",\n \"title\": \"Historical survey of the kdr mutations in the populations of Anopheles sinensis in China in 1996-2014.\",\n \"abstract\": \"BACKGROUND: Anopheles sinensis has become an important malaria vector in China. The long-term extensive utilization of pyrethroids for ITNs and IRS for mosquito control in the last three decades has resulted in the occurrence of resistant An. sinensis populations in many regions. Knockdown resistance (kdr), caused by point mutations in the VGSC gene, is one of the mechanisms that confer resistance to DDT and pyrethroids. Recently, several investigations revealed the kdr occurrence in some An. sinensis populations, however, no kdr data were available earlier than 2009. A survey tracking the dynamics of the kdr mutations in past decades would provide invaluable information to understand how the kdr alleles spread in mosquito populations temporally and spatially. METHODS: A survey was conducted on the kdr alleles at condon 1014 of the VGSC gene and their distributions in 733 specimens of An. sinensis and 232 specimens of the other eight member species of the Anopheles hyrcanus group that were collected from 17 provinces in China in 1996-2014. RESULTS: A total of three kdr alleles, TTT (F), TTG (F) and TGT (C) were detected, and TGT (C) and TTT (F) were already present in the specimens from Jiangsu and Shandong as early as 1997. The TTT (F) was the most frequent mutant allele, and largely distributed in central China, namely Shandong, Jiangsu, Anhui, Henan, Shanghai, Jiangxi and Hubei. When data were analysed in three time intervals, 1996-2001, 2005-2009, 2010-2014, the prevalence of kdr alleles increased progressively over time in the populations in central China. In contrast, the kdr alleles were less frequent in the samples from other regions, especially in Yunnan and Hainan, despite the documented presence of pyrethroid resistant populations in those regions. Interestingly, no mutant alleles were detected in all 232 specimens of eight other species in the An. hyrcanus group. CONCLUSION: The survey revealed that the kdr occurrence and accumulation in the An. sinensis populations were more frequent in central China than in the other regions, suggesting that the kdr mutations may contribute significantly to the pyrethroid resistance in the mosquitoes in central China.\",\n \"corpus_id\": 14046359,\n \"score\": 2\n },\n {\n \"doc_id\": \"25902680\",\n \"title\": \"[Experimental observation on host preference of Anopheles sinensis].\",\n \"abstract\": \"OBJECTIVE: To observe the host preference of Anopheles sinensis captured by outdoor human or cattle baits. METHODS: A large number of non-blood-fed An. sinensis females were collected by overnight trapping outdoor with human and cattle in the rice paddy field in Shan County of Shandong Province, and took back to the lab, and individually labeled as human baits group and cattle baits group, fed with mouse blood. The host preference of parent, F1 and F25 generations of the two groups were observed by mark-release-recapture methods in a large greenhouse. RESULTS: The recapture rates of parent, F1 and F25 generations were 39.02% (1332/3414), 37.97% (2583/6803), and 30.55% (1523/4986), respectively. In parent generation, the proportion of mosquitoes from human baits group and cattle baits group collected by human-bait and cattle-bait was 54.07% (339/627) and 58.01% (409/705), respectively (χ2=19.42, P<0.01); in F1 generation, that of the two groups was 51.03% (669/1311) and 55.11% (701/1272), respectively (χ2= 9.75, P<0.01); in F25 generation, that of the two groups was 51.98% (342/658) and 52.37 (453/865), respectively (χ2=2.82, P>0.05). CONCLUSION: After culture for 25 generations in an experimental condition, the host preference for human or cattle of An. sinensis maybe change.\",\n \"corpus_id\": 42962031,\n \"score\": 2\n },\n {\n \"doc_id\": \"26964528\",\n \"title\": \"Determinants of host feeding success by Anopheles farauti.\",\n \"abstract\": \"BACKGROUND: The proportion of blood meals that mosquitoes take from a host species is a function of the interplay of extrinsic (abundance and location of potential hosts) and intrinsic (innate preference) factors. A mark-release-recapture experiment addressed whether host preference in a population of Anopheles farauti was uniform or if there were anthropophilic and zoophilic subpopulations. The corresponding fitness associated with selecting different hosts for blood meals was compared by measuring fecundity. METHODS: The attractiveness of humans for blood meals by An. farauti in the Solomon Islands was compared to pigs using tent traps. Host fidelity was assessed by mark-release-recapture experiments in which different colour dusts were linked to the host to which the mosquito was first attracted. Outdoor resting An. farauti were captured on barrier screens and the human blood index (HBI) as well as the feeding index were calculated. The fecundity of individual An. farauti after feeding on either humans or pigs was assessed from blood-fed mosquitoes held in individual oviposition chambers. RESULTS: Anopheles farauti were more attracted to humans than pigs at a ratio of 1.31:1.00. The mark-release-recapture experiment found evidence for An. farauti being a single population regarding host preference. The HBI of outdoor resting An. farauti was 0.93 and the feeding index was 1.29. Anopheles farauti that fed on a human host laid more eggs but had a longer oviposition time compared to An. farauti that had blood fed on a pig. CONCLUSIONS: One of the strongest drivers for host species preference was the relative abundance of the different host species. Here, An. farauti have a slight preference for humans over pigs as blood meal sources. However, the limited availability of alternative hosts relative to humans in the Solomon Islands ensures a very high proportion of blood meals are obtained from humans, and thus, the transmission potential of malaria by An. farauti is high.\",\n \"corpus_id\": 5644824,\n \"score\": 2\n },\n {\n \"doc_id\": \"27118141\",\n \"title\": \"Determination of the foraging behaviour and blood meal source of malaria vector mosquitoes in Trincomalee District of Sri Lanka using a multiplex real time polymerase chain reaction assay.\",\n \"abstract\": \"BACKGROUND: Studies of host preference patterns in blood-feeding anopheline mosquitoes are crucial to incriminating malaria vectors. However, little information is available on host preferences of Anopheles mosquitoes in Sri Lanka. METHODS: Adult Anopheles mosquitoes were collected from five selected sentinel sites in Trincomalee District during June-September 2011. Each blood-fed mosquito was processed on filter papers. DNA was extracted using the dried blood meal protocol of the QIAmp DNA mini kit. A multiplexed, real-time PCR assay targeting eight animals was developed for two panels to identify the host meal of Anopheles. Human blood index (HBI), forage ratio (FR) and host feeding index (HFI) were calculated. RESULTS: A total of 280 field-caught, freshly engorged female mosquitoes belonging to 12 anopheline species were analysed. The overall HBI and HFI in the present study were low indicating that humans were not the preferred host for the tested anopheline species. Nevertheless, a small proportion engorged Anopheles aconitus, Anopheles culicifacies, Anopheles barbirostris, Anopheles annularis, Anopheles subpictus, Anopheles peditaeniatus, Anopheles pseudojamesi, and Anopheles barbumbrosus contained human blood. CONCLUSION: The presence of human blood in mosquito species indicates the possibility of them transmitting malaria. Further studies on vector competence are needed to determine the role of each of the above anopheline species as efficient vectors of malaria.\",\n \"corpus_id\": 18000347,\n \"score\": 2\n },\n {\n \"doc_id\": \"27353581\",\n \"title\": \"Biting behaviour of Anopheles funestus populations in Mutare and Mutasa districts, Manicaland province, Zimbabwe: Implications for the malaria control programme.\",\n \"abstract\": \"BACKGROUND & OBJECTIVES: Biting behaviour of Anopheles funestus in Mutare and Mutasa districts, Zimbabwe, is little understood. An investigation was conducted to primarily compare indoor and outdoor biting behaviour of the mosquito, as well as blood meal sources and sporozoite rates. METHODS: Monthly adult anopheline sampling was conducted from October 2013 to September 2014 using Centers for Disease Control light-traps, pyrethrum spray catch and artificial pit shelter methods. Mosquitoes sampled by light-traps were divided into two cohorts. In one cohort, traps were left overnight and mosquitoes were collected the following morning, while in the other set, mosquitoes were collected hourly from 1800-0600 hrs . Collected females were identified using morphological characters and categorised according to their abdominal status. Polymerase chain reaction was used to identify An. funestus sibling species and blood meal sources. Infection rate was tested by enzyme-linked immunosorbent assay. RESULTS: Morphological identification showed that indoor and outdoor catches comprised Anopheles funestus (98.3%) and Anopheles gambiae s.l. ( 1.7%). Of the 2268 mosquitoes collected, 66.2% were caught by light-traps, and 33.8% were caught resting indoors and outdoors. Anopheles funestus and An. gambiae s.l. were trapped more abundantly indoors (68%) than outdoors (32%). Both indoor and outdoor An. funestus densities were higher in wet (4.3) than dry season (1.8). In Burma Valley and Zindi areas, An. funestus demonstrated variable nocturnal indoor and outdoor flight activity rhythms, with two peaks during the night; between 2200-2300 hrs and 0200- 0400 hrs. Human blood index in An. funestus was 0.64, with Plasmodium falciparum infection rate of 1.8%. INTERPRETATION & CONCLUSION: The present work highlighted important information on the host-seeking behaviour, blood meal sources and infection rates in An. funestus. The information would be helpful in improving the vector control strategies.\",\n \"corpus_id\": 10342064,\n \"score\": 2\n },\n {\n \"doc_id\": \"27681543\",\n \"title\": \"A reassessment of the artificial infection of three predominant mosquito species with Plasmodium vivax in Shandong Province, China.\",\n \"abstract\": \"BACKGROUND & OBJECTIVES: Under certain ecological circumstances, pathogens are able to rapidly adapt to new vectors. The great capacity of Plasmodium spp. to adapt to new anopheline mosquito vectors on different continents and the continuous ecological changes attributed to humans might promote their adaptation to culicine vectors, which are known to infect humans. Based on our current knowledge, it is difficult to predict whether such adaptations will occur. This study was aimed to determine the infection susceptibility of Anopheles sinensis, Culex tritaeniorhynchus and Cx. pipiens pallens to Plasmodium vivax in Shandong Province of China. METHODS: The susceptibility of the three predominant species of mosquitoes -An. sinensis, Cx. tritaeniorhynchus and Cx. pipiens pallens in Shandong Province was compared with a direct membrane feeding assay with 15 batches of Shandong strain mono-infected gametocyte-containing blood collected from Plasmodium vivax-infected patients. Infectivity was measured by dissecting the midguts and salivary glands of the mosquitoes. The presence of oocysts and sporozoites was determined by microscopy at 6 and 22 days post-blood feeding. RESULTS: From the 15 batches of mosquitoes that were fed infected blood, oocysts and sporozoites were detected only in 7th, 13th and 15th batches of infection for An. sinensis, and no oocysts or sporozoites were detected in Cx. tritaeniorhynchus or Cx. pipiens pallens. The positive rate of An. sinensis infection was 21.2, 13 and 36.3% in the three batches of mosquitoes, with an average infection rate of 23.5%. INTERPRETATION & CONCLUSION: The susceptibility of An. sinensis to P. vivax was very high in Shandong Province. Cx. tritaeniorhynchus and Cx. pipiens pallens failed to exhibit susceptibility to P. vivax.\",\n \"corpus_id\": 40990673,\n \"score\": 2\n },\n {\n \"doc_id\": \"28719327\",\n \"title\": \"Extensive Resistance of Anopheles sinensis to Insecticides in Malaria-Endemic Areas of Hainan Province, China.\",\n \"abstract\": \"Anopheles sinensis is one of the major malaria vectors and among the dominant species in Hainan Province, China. The resistance of An. sinensis to insecticides is an important threat to malaria control. However, few reports on insecticide resistance of An. sinensis were reported in this area. Eight districts in Hainan Province were selected as the study areas. Insecticide susceptibility bioassays were tested on wild-caught female mosquitoes of An. sinensis to 4% dichlorodiphenyltrichloroethane (DDT), 0.05% deltamethrin, and 5% malathion by using the World Health Organization standard resistance tube assay procedure. All the tested An. sinensis mosquitoes demonstrated resistance to 4% DDT, with less than 72% mortality in the standard assay. The populations from Baisha and Qiongzhong demonstrated possible resistance to 0.05% deltamethrin, with 94-95% mortality, whereas the populations from other districts demonstrated resistance to 0.05% deltamethrin in the standard assay. The populations from Baisha, Qiongzhong, and Dongfang demonstrated susceptibility to 5% malathion, but the populations from other districts demonstrated resistance. These results facilitate the improvement of effective control strategies for malaria vector mosquitoes in Hainan.\",\n \"corpus_id\": 31960372,\n \"score\": 2\n },\n {\n \"doc_id\": \"28764710\",\n \"title\": \"Host attraction and biting behaviour of Anopheles mosquitoes in South Halmahera, Indonesia.\",\n \"abstract\": \"BACKGROUND: Indonesia is home to a variety of malaria vectors whose specific bionomic traits remain largely uncharacterized. Species-specific behaviours, such as host feeding preferences, impact the dynamics of malaria transmission and the effectiveness of vector control interventions. METHODS: To examine species-specific host attraction and feeding behaviours, a Latin square design was used to compare Anopheles mosquitoes attracted to human, cow, and goat-baited tents. Anopheles mosquitoes were collected hourly from the inside walls of each baited tent. Species were morphologically and then molecularly identified using rDNA ITS2 sequences. The head and thorax of individual specimens were analysed for Plasmodium DNA using PCR. Bloodmeals were identified using a multiplex PCR. RESULTS: A total of 1024, 137, and 74 Anopheles were collected over 12 nights in cow, goat, and human-baited tents, respectively. The species were identified as Anopheles kochi, Anopheles farauti s.s., Anopheles hackeri, Anopheles hinesorum, Anopheles indefinitus, Anopheles punctulatus, Anopheles tessellatus, Anopheles vagus, and Anopheles vanus, many of which are known to transmit human malaria. Molecular analysis of blood meals revealed a high level of feeding on multiple host species in a single night. Anopheles kochi, An. indefinitus, and An. vanus were infected with Plasmodium vivax at rates comparable to primary malaria vectors. CONCLUSIONS: The species distributions of Anopheles mosquitoes attracted to human, goat, and cow hosts were similar. Eight of nine sporozoite positive samples were captured with animal-baited traps, indicating that even predominantly zoophilic mosquitoes may be contributing to malaria transmission. Multiple host feeding and flexibility in blood feeding behaviour have important implications for malaria transmission, malaria control, and the effectiveness of intervention and monitoring methods, particularly those that target human-feeding vectors.\",\n \"corpus_id\": 4961842,\n \"score\": 2\n },\n {\n \"doc_id\": \"29162093\",\n \"title\": \"Receptivity to malaria in the China-Myanmar border in Yingjiang County, Yunnan Province, China.\",\n \"abstract\": \"BACKGROUND: The re-establishment of malaria has become an important public health issue in and out of China, and receptivity to this disease is key to its re-emergence. Yingjiang is one of the few counties with locally acquired malaria cases in the China-Myanmar border in China. This study aimed to understand receptivity to malaria in Yingjiang County, China, from June to October 2016. METHODS: Light-traps were employed to capture the mosquitoes in 17 villages in eight towns which were categorized into four elevation levels: level 1, 0-599 m; level 2, 600-1199 m; level 3, 1200-1799 m; and level 4, > 1800 m. Species richness, diversity, dominance and evenness were used to picture the community structure. Similarity in species composition was compared between different elevation levels. Data of seasonal abundance of mosquitoes, human biting rate, density of light-trap-captured adult mosquitoes and larvae, parous rate, and height distribution (density) of Anopheles minimus and Anopheles sinensis were collected in two towns (Na Bang and Ping Yuan) each month from June to October, 2016. RESULTS: Over the study period, 10,053 Anopheles mosquitoes were collected from the eight towns, and 15 Anopheles species were identified, the most-common of which were An. sinensis (75.4%), Anopheles kunmingensis (15.6%), and An. minimus (3.5%). Anopheles minimus was the major malaria vector in low-elevation areas (< 600 m, i.e., Na Bang town), and An. sinensis in medium-elevation areas (600-1200 m, i.e., Ping Yuan town). In Na Bang, the peak human-biting rate of An. minimus at the inner and outer sites of the village occurred in June and August 2016, with 5/bait/night and 15/bait/night, respectively. In Ping Yuan, the peak human-biting rate of An. sinensis was in August, with 9/bait/night at the inner site and 21/bait/night at the outer site. The two towns exhibited seasonal abundance with high density of the two adult vectors: The peak density of An. minimus was in June and that of An. sinensis was in August. Meanwhile, the peak larval density of An. minimus was in July, but that of An. sinensis decreased during the investigation season; the slightly acidic water suited the growth of these vectors. The parous rates of An. sinensis and An. minimus were 90.46 and 93.33%, respectively. CONCLUSIONS: The Anopheles community was spread across different elevation levels. Its structure was complex and stable during the entire epidemic season in low-elevation areas at the border. The high human-biting rates, adult and larval densities, and parous rates of the two Anopheles vectors reveal an exceedingly high receptivity to malaria in the China-Myanmar border in Yingjiang County.\",\n \"corpus_id\": 7740480,\n \"score\": 2\n },\n {\n \"doc_id\": \"18297310\",\n \"title\": \"Blood-feeding patterns of Culex quinquefasciatus and other culicines and implications for disease transmission in Mwea rice scheme, Kenya.\",\n \"abstract\": \"Studies were conducted in Mwea Rice Scheme, Kenya during the period April 2005 and January 2007 to determine the host-feeding pattern of culicine mosquitoes. Mosquitoes were collected indoors and outdoors and tested for human, bovine, goat, and donkey blood meals by an Enzyme-Linked Immunosorbent Assay. A total of 1,714 blood-engorged samples comprising Culex quinquefasciatus Say (96.1%), Culex annulioris Theobald (1.8%), Culex poicilipes Theobald (0.9%), Aedes cuminsi Theobald (1.0%), Aedes taylori Edwards (0.1%), and Mansonia africana Theobald (0.1%) were tested. Except for A. taylori, in which the single blood meal tested was of bovine origin, the other species fed mostly on both bovine (range 73.3-100%) and goats (range 50-100%). Donkeys were also common hosts for all species (range 19.4-23.5%) except A. taylori and M. africana. C. quinquefasciatus was the only species containing human blood meals (0.04), and indoor collected populations of this species had significantly higher frequency of human blood meals (9.8%) compared with outdoor-collected populations (3.0%). Mixed blood feeding was dominant among culicine species comprising 50.0%, 73.3%, 73.5%, 80.6%, and 94.1% of the samples for M. africana, C. poicilipes, C. quinquefasciatus, C. annulioris, and A. cuminsi, respectively. Ten mixed blood meal combinations including a mixture of all the four hosts were observed in C. quinquefasciatus, compared to one blood meal combination for M. Africana, and two combinations for C. poicilipes, C. annulioris, and A. cuminsi. Mixed bovine and goat blood meal was the most common combination among the five culicine species followed by a mixture of donkey, bovine, and goat blood meals. We conclude that culicine species in Mwea are least likely to be vectors of lymphatic filariasis due to their high \\\"preference\\\" for livestock over human hosts, but they present an increased risk for arbovirus transmission particularly Rift Valley Fever virus, in which domestic animals serve as amplification hosts.\",\n \"corpus_id\": 26124116,\n \"score\": 1\n },\n {\n \"doc_id\": \"18312667\",\n \"title\": \"Host choice and multiple blood feeding behaviour of malaria vectors and other anophelines in Mwea rice scheme, Kenya.\",\n \"abstract\": \"BACKGROUND: Studies were conducted between April 2004 and February 2006 to determine the blood-feeding pattern of Anopheles mosquitoes in Mwea Kenya. METHODS: Samples were collected indoors by pyrethrum spay catch and outdoors by Centers for Disease Control light traps and processed for blood meal analysis by an Enzyme-linked Immunosorbent Assay. RESULTS: A total of 3,333 blood-fed Anopheles mosquitoes representing four Anopheles species were collected and 2,796 of the samples were assayed, with Anopheles arabiensis comprising 76.2% (n = 2,542) followed in decreasing order by Anopheles coustani 8.9% (n = 297), Anopheles pharoensis 8.2% (n = 272) and Anopheles funestus 6.7% (n = 222). All mosquito species had a high preference for bovine (range 56.3-71.4%) over human (range 1.1-23.9%) or goat (0.1-2.2%) blood meals. Some individuals from all the four species were found to contain mixed blood meals. The bovine blood index (BBI) for An. arabiensis was significantly higher for populations collected indoors (71.8%), than populations collected outdoors (41.3%), but the human blood index (HBI) did not differ significantly between the two populations. In contrast, BBI for indoor collected An. funestus (51.4%) was significantly lower than for outdoor collected populations (78.0%) and the HBI was significantly higher indoors (28.7%) than outdoors (2.4%). Anthropophily of An. funestus was lowest within the rice scheme, moderate in unplanned rice agro-ecosystem, and highest within the non-irrigated agro-ecosystem. Anthropophily of An. arabiensis was significantly higher in the non-irrigated agro-ecosystem than in the other agro-ecosystems. CONCLUSION: These findings suggest that rice cultivation has an effect on host choice by Anopheles mosquitoes. The study further indicate that zooprophylaxis may be a potential strategy for malaria control, but there is need to assess how domestic animals may influence arboviruses epidemiology before adapting the strategy.\",\n \"corpus_id\": 1717904,\n \"score\": 1\n },\n {\n \"doc_id\": \"19485771\",\n \"title\": \"Host-feeding patterns of Aedes albopictus (Diptera: Culicidae) in urban and rural contexts within Rome province, Italy.\",\n \"abstract\": \"Knowledge of the frequency of contact between a mosquito species and its different hosts is essential to understand the role of each vector species in the transmission of diseases to humans and/or animals. However, no data are so far available on the feeding habits of Aedes albopictus in Italy or in other recently colonized temperate regions of Europe, due to difficulties in collecting blood-fed females of this diurnal and exophilic species. We analyzed Ae. albopictus host-feeding patterns in two urban and two rural sites within the area of Rome (Italy). Ae. albopictus was collected using sticky-traps and the blood-meal origin of 303 females was determined by direct dot-ELISA. The blood-fed sample, although representing only 4% of the total Ae. albopictus collected, demonstrates the useful application of sticky-trap in studying the feeding behavior of the species. The human blood index was significantly different among sites, ranging from 79-96% in urban sites to 23-55% in rural sites, where horses and bovines represented the most bitten hosts. The results obtained confirm the plastic feeding behavior shown by Ae. albopictus in its original range of distribution and highlights the high potential of this species as a vector of human pathogens in urban areas of Italy, where both humans and the mosquito itself may reach very high densities.\",\n \"corpus_id\": 20034869,\n \"score\": 1\n },\n {\n \"doc_id\": \"19724081\",\n \"title\": \"Effects of long-lasting insecticidal nets and zooprophylaxis on mosquito feeding behaviour and density in Mwea, central Kenya.\",\n \"abstract\": \"BACKGROUND & OBJECTIVES: Zooprophylaxis is a strategy that can control malaria by attracting mosquitoes to domestic animals that act as dead-end hosts. The objective of this study was to establish the effects of zooprophylaxis and long-lasting insecticidal nets (LLINs) on malaria transmission in an agro-based ecosystem with seasonal transmission. METHODS: The mosquito samples were collected indoors using the space spray catch method before and after intervention between October 2005 and March 2006 to determine the mosquito densities and the feeding patterns of Anopheles spp in Mwea, Kenya. RESULTS: A total of 4148 mosquito samples were collected, out of which 11 (0.2%) were tested positive for sporozoites. Ten were Anopheles gambiae species and one was An. funestus species. Results on blood meal ELISA showed that in the household categories that used bednets and kept one cow there was a decrease in relative change ratio (post-/pre-intervention) of 87.5 and 19.6% (p <0.05) in human and cattle blood intake respectively. For households that kept 2-4 cattle and used bednets, there was a decrease in cattle blood index (CBI) by 61.9% and an increase in human blood index (HBI) by 2%, which was not significant (p <0.05). In households with <4 cattle and bednet, there was significant reduction (p >0.05) in CBI of 37.5% as compared to the reduction of 10.3% in HBI. The ratios of man biting rates (MBR) decreased significantly, as you move up from households with one cattle with or without LLINs to households with more than four cattle with or without LLINs with a regression coefficient of -0.96; SE = 0.834; p = 0.017. Similarly, the HBI decreased significantly with the regression coefficient of 0.239; SE = 0.039; p = 0.015 (p <0.05) especially in households with >4 cattle. INTERPRETATION & CONCLUSION: This study demonstrated that there were additive effects of zooprophylaxis and LLINs in the control of mosquito density and reduction of human risk to the mosquito bites. However, in Integrated Vector Management (IVM), the number of animals per household should not be more than four.\",\n \"corpus_id\": 8730204,\n \"score\": 1\n },\n {\n \"doc_id\": \"20578953\",\n \"title\": \"Host-feeding preference of the mosquito, Culex quinquefasciatus, in Yucatan State, Mexico.\",\n \"abstract\": \"Studies were conducted to determine the host-feeding preference of Culex quinquefasciatus Say (Diptera: Culicidae) in relation to the availability of human and domestic animals in the city of Merida, Yucatan State, Mexico. Mosquitoes were collected in the backyards of houses using resting wooden boxes. Collections were made five times per week from January to December 2005. DNA was extracted from engorged females and tested by PCR using universal avian- and mammalian-specific primers. DNA extracted from avian-derived blood was further analyzed by PCR using primers that differentiate among the birds of three avian orders: Passeriformes, Columbiformes and Galliformes. PCR products obtained from mammalian-derived blood were subjected to restriction enzyme digestion to differentiate between human-, dog-, cat-, pig-, and horse-derived blood meals. Overall, 82% of engorged mosquitoes had fed on birds, and 18% had fed on mammals. The most frequent vertebrate hosts were Galliformes (47.1%), Passeriformes (23.8%), Columbiformes (11.2%) birds, and dogs (8.8%). The overall human blood index was 6.7%. The overall forage ratio for humans was 0.1, indicating that humans were not a preferred host for Cx. quinquefasciatus in Merida.\",\n \"corpus_id\": 1700431,\n \"score\": 1\n },\n {\n \"doc_id\": \"21826902\",\n \"title\": \"[An investigation on malaria vectors in western part of China-Myanmar border].\",\n \"abstract\": \"OBJECTIVE: To reveal the distribution and composition of malaria-transmitting vectors on the western part of China-Myanmar border. METHODS: An entomological survey of malaria vectors was carried out in six villages of Yingjiang County and Xidong County on China-Myanmar border between August and September, 2008. Mosquitoes in human dwellings and cattle sheds were collected by overnight trapping with ovitrap light. The mosquitoes were firstly identified morphologically, and then Anopheles minimus A and C, An. aconitus, and An. jeyporiensis were identified by using multiplex PCR. Some mosquitoes were selected to extract the total genomic DNA, and detect sporozoites by nested PCR. RESULTS: A total of 4571 mosquitoes were captured with 54.32% (2483/4571) of anopheline mosquitoes. There was significant difference in Anopheles species composition in human dwellings and cattle sheda The main species in human dwellings were An. kochi, An. minimus, and An. sinensis, while the principal species in cattle sheds consist of An. kochi (223), An. annularis (184), An. vagus (131), and An jeyporiensis (129). Furthermore, the composition in human dwellings of villages with and without cattle was significantly different. An. minimus (260) and An. kochi (49) werethe most important species in villages with cattle, whereas An. kochi (481) and An. sinensis (124) were the key species in villages without cattle. A total of 1075 mosquitoes were examined for sporozoites and 9 mosquitoes were found to be infected. Only three species, Le. An. minimus (7/408), An aconiaus (1/125) and An. pseudowillmori (1/101) were infected with malaria parasite. All sporozoites were identified as Plasmodium falcipoarum by sequencing, the target fragment was 204 bp. CONCLUSION: The species composition of mosquitoes is complex in the study sites on the western part of China-Myanmar border, and An. minimus is the major malaria vector. Additionally, An. aconitus and An.pseudowillmori are also confirmed as potential malaria vector in this area.\",\n \"corpus_id\": 26923987,\n \"score\": 1\n },\n {\n \"doc_id\": \"22165904\",\n \"title\": \"Impact of insecticide-treated bed nets on malaria transmission indices on the south coast of Kenya.\",\n \"abstract\": \"BACKGROUND: Besides significantly reducing malaria vector densities, prolonged usage of bed nets has been linked to decline of Anopheles gambiae s.s. relative to Anopheles arabiensis, changes in host feeding preference of malaria vectors, and behavioural shifts to exophagy (outdoor biting) for the two important malaria vectors in Africa, An. gambiae s.l. and Anopheles funestus. In southern coastal Kenya, bed net use was negligible in 1997-1998 when Anopheles funestus and An. gambiae s.s. were the primary malaria vectors, with An. arabiensis and Anopheles merus playing a secondary role. Since 2001, bed net use has increased progressively and reached high levels by 2009-2010 with corresponding decline in malaria transmission. METHODS: To evaluate the impact of the substantial increase in household bed net use within this area on vector density, vector composition, and human-vector contact, indoor and outdoor resting mosquitoes were collected in the same region during 2009-2010 using pyrethrum spray catches and clay pots for indoor and outdoor collections respectively. Information on bed net use per sleeping spaces and factors influencing mosquito density were determined in the same houses using Poisson regression analysis. Species distribution was determined, and number of mosquitoes per house, human-biting rates (HBR), and entomological inoculation rate (EIR) were compared to those reported for the same area during 1997-1998, when bed net coverage had been minimal. RESULTS: Compared to 1997-1998, a significant decline in the relative proportion of An. gambiae s.s. among collected mosquitoes was noted, coupled with a proportionate increase of An. arabiensis. Following > 5 years of 60-86% coverage with bed nets, the density, human biting rate and EIR of indoor resting mosquitoes were reduced by more than 92% for An. funestus and by 75% for An. gambiae s.l. In addition, the host feeding choice of both vectors shifted more toward non-human vertebrates. Besides bed net use, malaria vector abundance was also influenced by type of house construction and according to whether one sleeps on a bed or a mat (both of these are associated with household wealth). Mosquito density was positively associated with presence of domestic animals. CONCLUSIONS: These entomological indices indicate a much reduced human biting rate and a diminishing role of An. gambiae s.s. in malaria transmission following high bed net coverage. While increasing bed net coverage beyond the current levels may not significantly reduce the transmission potential of An. arabiensis, it is anticipated that increasing or at least sustaining high bed net coverage will result in a diminished role for An. funestus in malaria transmission.\",\n \"corpus_id\": 245708,\n \"score\": 1\n },\n {\n \"doc_id\": \"22910571\",\n \"title\": \"Anopheles gambiae and Anopheles arabiensis population densities and infectivity in Kopere village, Western Kenya.\",\n \"abstract\": \"INTRODUCTION: This study was conducted in a sugar belt region of western Kenya interfacing epidemic and endemic malaria transmission. We investigated Anopheles gambiae sensu stricto (ss) and Anopheles arabiensis species compositions and densities, human host choice, and infectivity. METHODOLOGY: Mosquitoes were captured using pyrethrum spray catch technique and first identified based on morphology; species were confirmed by PCR. Blood meal preference and sporozoite rates were determined by ELISA. Parity rates and entomological inoculation rates (EIR) were determined. Seasonal densities were compared against environmental temperatures, relative humidity and rainfall. RESULTS: In total 2,426 An. gambiae were collected. Out of 1,687 female blood-fed mosquitoes, 272 were randomly selected for entomological tests. An. gambiae ss and An. arabiensis comprised 75% (205/272) and 25% (68/272) of the selection, respectively. An. gambiae ss had higher preference for human blood (97%; n=263/272) compared with An. arabiensis, which mostly fed on bovines (88%; n=239/272). The sporozoite and parity rates were 6% (16/272) and 66% (179/272) for An. gambiae ss and 2% (4/272) and 53% (144/272) for An. arabiensis respectively, while EIR was 0.78 infective bites/person/night. Climate (ANOVA; F=14.2; DF=23) and temperature alone (r=0.626; t=3.75; p=0.001) were significantly correlated with vector densities. CONCLUSION: An. gambiae ss are the most efficient malaria vector mosquito species in Kopere village. Because An. gambiae ss largely rests and feeds indoors, use of indoor residual spray and insecticide-treated nets is likely the most suitable approach to malaria vector control in Kopere village and other parts of Kenya where this species is abundant.\",\n \"corpus_id\": 8130926,\n \"score\": 1\n },\n {\n \"doc_id\": \"23253167\",\n \"title\": \"The fitness of African malaria vectors in the presence and limitation of host behaviour.\",\n \"abstract\": \"BACKGROUND: Host responses are important sources of selection upon the host species range of ectoparasites and phytophagous insects. However little is known about the role of host responses in defining the host species range of malaria vectors. This study aimed to estimate the relative importance of host behaviour to the feeding success and fitness of African malaria vectors, and assess its ability to predict their known host species preferences in nature. METHODS: Paired evaluations of the feeding success and fitness of African vectors Anopheles arabiensis and Anopheles gambiae sensu stricto in the presence and limitation of host behaviour were conducted in a semi-field system (SFS) at Ifakara Health Institute, Tanzania. In one set of trials, mosquitoes were released within the SFS and allowed to forage overnight on a host that was free to exhibit a natural behaviour in response to insect biting. In the other, mosquitoes were allowed to feed directly on from the skin surface of immobile hosts. The feeding success and subsequent fitness of vectors under these conditions were investigated on six host types (humans, calves, chickens, cows, dogs and goats) to assess whether physical movements of preferred host species (cattle for An. arabiensis, humans for An. gambiae s.s.) were less effective at preventing mosquito bites than those of common alternatives. RESULTS: Anopheles arabiensis generally had greater feeding success when applied directly to host skin than when foraging on unrestricted hosts (in five of six host species). However, An. gambiae s.s. obtained blood meals from free and restrained hosts with similar success from most host types (four out of six). Overall, the blood meal size, oviposition rate, fecundity and post-feeding survival of mosquito vectors were significantly higher after feeding on hosts free to exhibit behaviour, than those who were immobilized during feeding trials. CONCLUSIONS: Allowing hosts to move freely during exposure to mosquitoes was associated with moderate reductions in mosquito feeding success, but no detrimental impact to the subsequent fitness of mosquitoes that were able to feed upon them. This suggests that physical defensive behaviours exhibited by common host species including humans do not impose substantial fitness costs on African malaria vectors.\",\n \"corpus_id\": 8726081,\n \"score\": 1\n },\n {\n \"doc_id\": \"24034528\",\n \"title\": \"The Anopheles community and the role of Anopheles minimus on malaria transmission on the China-Myanmar border.\",\n \"abstract\": \"BACKGROUND: Malaria around the China-Myanmar border is a serious health problem in the countries of South-East Asia. An. minimus is a principle malaria vector with a wide geographic distribution in this area. Malaria is endemic along the boundary between Yunnan province in China and the Kachin State of Myanmar where the local Anopheles community (species composition) and the malaria transmission vectors have never been clarified. METHODS: Adult Anopheles specimens were collected using CDC light traps in four villages along the border of China and Myanmar from May 2012 to April 2013. Morphological and molecular identification of mosquito adults confirmed the species of Anopheles. Blood-meal identification using the female abdomens was conducted using multiplex PCR. For sporozoite detection in An. minimus, sets of 10 female salivary glands were pooled and identified with SSU rDNA using nested PCR. Monthly abundance of An. minimus populations during the year was documented. The diversity of Anopheles and the role of An. minimus on malaria transmission in this border area were analyzed. RESULTS: 4,833 adult mosquitoes in the genus Anopheles were collected and morphologically identified to species or species complex. The Anopheles community is comprised of 13 species, and 78.83% of our total specimens belonged to An. minimus s.l., followed by An. maculatus (5.55%) and the An. culicifacies complex (4.03%). The quantity of trapped An. minimus in the rainy season of malaria transmission was greater than during the non-malarial dry season, and a peak was found in May 2012. An. minimus fed on the blood of four animals: humans (79.8%), cattle (10.6%), pigs (5.8%) and dogs (3.8%). 1,500 females of An. minimus were pooled into 150 samples and tested for sporozoites: only 1 pooled sample was found to have sporozoites of Plasmodium vivax. CONCLUSION: Anopheles is abundant with An. minimus being the dominant species and having a high human blood index along the China-Myanmar border. The sporozoites in An. minimus were determined to be Plasmodium vivax with a 0.07-0.7% infection rate.\",\n \"corpus_id\": 7811668,\n \"score\": 1\n },\n {\n \"doc_id\": \"24822345\",\n \"title\": \"[Taxonomic status of Anopheles yatsushiroensis in Rongcheng City of Shandong Province].\",\n \"abstract\": \"OBJECTIVE: To clarify the taxonomic status of Anopheles yatsushiroensis in Rongcheng City of Shandong Province. METHODS: By the end of August 2009, Anopheles yatsushiroensis were collected in the western suburbs of Wangjia Village of Rongcheng City, and raised for the next generation of various types of adult mosquitoes. Through morphological identification of filial generation various types, mosquito feet of 1-2 mosquitoes of various types were taken for complete DNA extraction, and complete sequence analysis of rDNA-ITS2 alignment was made by PCR. Multiple sequnence comparison was carried out with those previously documented by DNAstar7.1, including An. yatsushiroensis in Shandong Province (YSD, AY306128), An. yatsushiroensis in Sichuan Province (YSC, AY170925), An. yatsushiroensis in Liaoning Province (YLN, AY170923) and An. yatsushiroensis from South Korea (YK, AF146749). RESULTS: 56 An. yatsushiroensis with blood meal were collected in Rongcheng City, of which 7 successfully laid eggs, and received 354 adult mosquitoes of filiar generation, including 240 An. yatsushiroensis (Y type), 8 An. pullus (P type) and 106 hybrid type (H). The rDNA-ITS2 sequence alignment homology between single-parent female offspring of adult mosquitoes and various types of An. yatsushiroensis segments (JN865249, JN865246, JN865247, JN865248) was 98.7-100%, and the rDNA-ITS2 sequence alignment homology to those from Sichuan (YSC), Liaoning (YLN) and Korea (YK) was 98.5%-99.3%, 98.7%-99.6% and 98.7 to 100%, respectively, while to the original An. yatsushiroensis from Rongcheng (YSD), it was only 67.1%-68.5%. CONCLUSION: There are Y, P and H types of An. yatsushiroensis in Rongcheng City, Shandong Province, but the rDNA-ITS2 sequence is close to An. pullus. The local distribution of An. pullus is deduced.\",\n \"corpus_id\": 23128146,\n \"score\": 1\n },\n {\n \"doc_id\": \"24885668\",\n \"title\": \"Individual experience affects host choice in malaria vector mosquitoes.\",\n \"abstract\": \"BACKGROUND: Despite epidemiological importance, few studies have explored whether individual experience and learning could affect the vertebrate host choice of mosquito disease vectors. Here, we investigated whether a first successful blood meal can modulate mosquito preference during a second blood meal. METHODS: In no-choice situations, females of the mosquito Anopheles coluzzii, one of the primary African malaria vectors, were first allowed to feed on either human, rabbit or guinea pig. Four days later in dual-choice situations, the same mosquitoes were allowed to choose between the two uncommon hosts, rabbit and guinea pig, as a source of blood. ELISA assays were then used to determine which host mosquitoes fed on. RESULTS: Our results indicate that, overall, mosquitoes preferred to feed on rabbit over guinea pig and that the nature of the first blood meal had a significant impact on the mosquito host choice during the second blood meal. Compared to mosquitoes that previously fed on guinea pigs or humans, mosquitoes that fed on rabbits were less likely to choose this host species during a second exposition. The decreased preference for rabbit was observed four days after mosquitoes were first exposed to this host, suggesting that the effect lasts at least the duration of a gonotrophic cycle. Furthermore, this effect was observed after only one successful blood meal. Fitness measurements on mosquitoes fed on the three different vertebrate hosts showed that the origin of the blood meal affected mosquito longevity but not fecundity. In particular, human-fed mosquitoes lived longer than guinea pig-fed or rabbit-fed mosquitoes. CONCLUSIONS: Our study demonstrates that individual experience affects host choice in this mosquito species and might have strong repercussions on biting patterns in natural conditions and hence on malaria transmission.\",\n \"corpus_id\": 16954046,\n \"score\": 1\n },\n {\n \"doc_id\": \"25424266\",\n \"title\": \"Biting patterns and host preference of Anopheles epiroticus in Chang Island, Trat Province, eastern Thailand.\",\n \"abstract\": \"A study of species diversity of Anopheles mosquitoes, biting patterns, and seasonal abundance of important mosquito vectors was conducted in two villages of Chang Island, Trat Province, in eastern Thailand, one located along the coast and the other in the low hills of the central interior of the island. Of 5,399 captured female anophelines, 70.25% belong to the subgenus Cellia and remaining specimens to the subgenus Anopheles. Five important putative malaria vectors were molecularly identified, including Anopheles epiroticus, Anopheles dirus, Anopheles sawadwongporni, Anopheles maculatus, and Anopheles minimus. Anopheles epiroticus was the most commonly collected species in the coastal site, whereas An. dirus was found to be most abundant in the forest-hill site. From both locations, a greater number of mosquitoes was collected during the dry season compared to the wet. Anopheles epiroticus showed greater exophagic and zoophilic behavior with the highest blood feeding densities occurring between 18:00 and 19:00. In contrast, An. dirus demonstrated an activity peak between midnight and 01:00. We conclude that An. epiroticus and An. dirus, in coastal and inland areas, respectively, appear to be the most epidemiologically important malaria vectors on Chang Island. As no studies of vector competency specific to Chang Island have been conducted, our conclusions that these two species play a primary role in malaria transmission are based on evidence from other localities in Thailand and mainland Southeast Asia. This information serves as a basis for designing improved vector control programs that target specific species, and if integrated with other interventions could result in the elimination of malaria transmission on the island.\",\n \"corpus_id\": 25934909,\n \"score\": 1\n },\n {\n \"doc_id\": \"25890038\",\n \"title\": \"Knockdown resistance of Anopheles sinensis in Henan province, China.\",\n \"abstract\": \"BACKGROUND: Vivax malaria was historically epidemic in Henan Province of China and Anopheles sinensis was the main vectors and poor farming communities bare the greatest burden of disease. Knockdown resistance in An. sinensis is one of the mechanisms of resistance against pyrethroids. In the present study, the frequency of mutations from An. sinensis was examined in Henan province, China. METHODS: Anopheles was collected from Kaifeng, Tongbai, Tanghe, Pingqiao, Shihe, and Yongcheng counties of Henan province in 2013. Molecular identification of Anopheles species was conducted by polymerase chain reaction (PCR) amplifying the internal transcribed spacer 2 (ITS2). Part of the IIS6 domain of the para-type sodium channel protein gene was polymerase chain reaction-amplified and directly sequenced. Frequency and geographic difference of kdr gene mutant types were analysed. RESULTS: 208 Anopheles were received molecular identification, of which 169 (81.25%) were An. sinensis, 25 (12.02%) were Anopheles yatsushiroensis, and 12 (5.77%) were Anopheles lesteri. A 325 bp fragment of the para-type sodium channel gene including position 1014 was successfully sequenced from 139 Anopheles, of which 125 (89.93%) were An. sinensis, 12 (8.63%) were An. yatsushiroensis, 2 (1.44%) were An. lesteri. The molecular analyses revealed that mutations existed at codon 1014 in An. sinensis but not in An. yatsushiroensis and An. lesteri. Frequency of kdr mutation was 73.60% (92/125) from population of An. sinensis in Henan province, of which L1014F (TTT + TTC) allele frequencies accounted for 46.40% (58/125), and was higher than that of L1014C(TGT) which accounted for 27.20% (34/125) ( χ2 = 55.423, P < 0.001). The frequency of kdr mutation in Kaifeng county was 100% (49/49), and was higher than that of 37.93% (11/29) in Tongbai, 54.55% (6/11) in Pingqiao, 50.00% (3/3) in Shihe, and 62.50% (10/16) in Yongcheng county, respectively (χ2 = 39.538, P < 0.001; χ2 = 24.298, P < 0.001; χ2 = 25.913, P < 0.001; χ2 = 20.244, P < 0.001). While 92.86% (13/14) frequency of kdr mutation was found in Tanghe county, which was higher than that in Tongbai county (χ2 = 11.550, P = 0.0018). CONCLUSIONS: A high frequency of kdr gene mutations from population of An. sinensis in Henan province was found.\",\n \"corpus_id\": 1628079,\n \"score\": 1\n },\n {\n \"doc_id\": \"25927429\",\n \"title\": \"Underestimation of foraging behaviour by standard field methods in malaria vector mosquitoes in southern Africa.\",\n \"abstract\": \"BACKGROUND: Defining the anopheline mosquito vectors and their foraging behaviour in malaria endemic areas is crucial for disease control and surveillance. The standard protocol for molecular identification of host blood meals in mosquitoes is to morphologically identify fed mosquitoes and then perform polymerase chain reaction (PCR), precipitin tests, or ELISA assays. The purpose of this study was to determine the extent to which the feeding rate and human blood indices (HBIs) of malaria vectors were underestimated when molecular confirmation by PCR was performed on both visually fed and unfed mosquitoes. METHODS: In association with the Southern Africa International Centers of Excellence in Malaria Research (ICEMR), mosquito collections were performed at three sites: Choma district in southern Zambia, Nchelenge district in northern Zambia, and Mutasa district in eastern Zimbabwe. All anophelines were classified visually as fed or unfed, and tested for blood meal species using PCR methods. The HBIs of visually fed mosquitoes were compared to the HBIs of overall PCR confirmed fed mosquitoes by Pearson's Chi-Square Test of Independence. RESULTS: The mosquito collections consisted of Anopheles arabiensis from Choma, Anopheles funestus s.s., Anopheles gambiae s.s. and Anopheles leesoni from Nchelenge, and An. funestus s.s. and An. leesoni from Mutasa. The malaria vectors at all three sites had large human blood indices (HBI) suggesting high anthropophily. When only visually fed mosquitoes tested by PCR for blood meal species were compared to testing those classified as both visually fed and unfed mosquitoes, it was found that the proportion blooded was underestimated by up to 18.7%. For most Anopheles species at each site, there was a statistically significant relationship (P < 0.05) between the HBIs of visually fed mosquitoes and that of the overall PCR confirmed fed mosquitoes. CONCLUSION: The impact on HBI of analysing both visually fed and unfed mosquitoes varied from site to site. This discrepancy may be due to partial blood feeding behaviour by mosquitoes, digestion of blood meals, sample condition, and/or expertise of entomology field staff. It is important to perform molecular testing on all mosquitoes to accurately characterize vector feeding behaviour and develop interventions in malaria endemic areas.\",\n \"corpus_id\": 13525284,\n \"score\": 1\n },\n {\n \"doc_id\": \"25963759\",\n \"title\": \"Host-feeding preference of Phlebotomus orientalis (Diptera: Psychodidae) in an endemic focus of visceral leishmaniasis in northern Ethiopia.\",\n \"abstract\": \"BACKGROUND: Blood-feeding behavior studies are important for estimating the efficiency of pathogen transmission and assessing the relative human disease risk. However, in Ethiopia and other parts of East Africa there are large remaining gaps in identifying the feeding habits of Phlebotomus orientalis, the vector of Leishmania donovani. The aim of the study was to determine the blood feeding patterns of P. orientalis in Tahtay Adiyabo district, northern Ethiopia. METHODS: For bloodmeal analysis, sandflies were collected from three different villages of Tahtay Adiyabo district using CDC light traps, sticky traps, and pyrethrum spray catches. Bloodmeal of engorged female sandflies was identified using cytochrome (cyt) b-PCR and reverse-line blotting (RLB) and enzyme linked immunosorbent assay (ELISA) assays. RESULTS: Most (637/641) of the females analyzed were P. orientalis. Successful identification of the host from bloodmeals was achieved in 83.03 and 92.1% using cyt b PCR-RLB and ELISA, respectively. Bloodmeal analysis of P. orientalis females revealed that they have a range of hosts with predominant preference to bovines followed by donkey, human, goat, sheep, dog, and camel. CONCLUSION: Results obtained from bloodmeal analyses demonstrate that the feeding preference of P. orientalis is mainly zoophilic, which could vary depending on the availability of hosts.\",\n \"corpus_id\": 14225285,\n \"score\": 1\n },\n {\n \"doc_id\": \"26209103\",\n \"title\": \"Early biting of the Anopheles gambiae s.s. and its challenges to vector control using insecticide treated nets in western Kenya highlands.\",\n \"abstract\": \"Long term use of insecticides in malaria vector control has been shown to alter the behavior of vectors. Such behavioral shifts have the potential of undermining the effectiveness of insecticide-based control interventions. The effects of insecticide treated nets (ITNs) use on the composition, biting/feeding and sporozoite rates of Anopheles gambiae s.l. mosquitoes in Musilongo village, Vihiga County of western Kenya highlands were investigated. Adult mosquitoes were collected in selected sleeping spaces inside six randomly selected houses using miniature Centre for Disease Control and Prevention (CDC) light traps. Mosquito sampling in each house was conducted twice every week for 16 consecutive months (May 2010-August 2012). At each sampling a single trap was set in the selected space inside each house such that it collected mosquitoes alternatively from 18:00 to 21:00h and 21:00 to 06:00h every week. All collected mosquitoes were morphologically identified. Female Anopheles mosquitoes were classified according to their physiological status as unfed, fed, partially gravid and gravid, sorted and counted. Members of the A. gambiae complex were identified using a Polymerase chain reaction (PCR) method. Enzyme-linked-immunosorbent assay (ELISA) was used to determine blood meal sources and Plasmodium infection rates in A. gambiae s.l. mosquitoes. Blood meal tests were conducted on DNA extracted from gut contents of blood fed A. gambiae s.l. The head and thorax section of dried samples of A. gambiae s.l. were used in testing for the presence of Plasmodium falciparum (Pf) sporozoites. Overall, 735 adult female Anopheles comprising 708 [96.3%] A. gambiae s.l. and 27 [3.7%] Anopheles funestus mosquitoes were collected. A. gambiae s.l. population collected comprised, 615 [86.9%] unfed and 38 [5.4%] fed adult mosquitoes. The rest were either partially or fully gravid. The proportion of A. gambiae s.l. biting indoors within 18:00-21:00h was 15.8% (103/653) at a rate of 3.2bites per person per hour compared to 84.2% biting from 21:00-06:00h at a rate of 3.8 bites/per/h. An estimated 97.7% A. gambiae ss and 2.3% A. arabiensis constituted the indoor biting A. gambiae s.l. The population of An. gambiae s.l. biting from 18:00 to 21:00h had a Plasmodium faciparum (pf) sporozoite rate of 3.8% compared to 3.5% observed in populations biting within 21:00-06:00h. Human blood constituted 89% of An. gambiae s.l. blood meal sources. The risk of malaria transmission from 21:00 to 06:00h was approximately 5 fold the risk within 18:00-21:00h. Majority of the infective female A. gambiae s.l. adults were biting deep into the night than in the early hours of the night. Humans remain the preferred source of blood meal for A. gambiae s.s. the dominant malaria vector in the highlands. ITNs remain a fundamental control intervention against malaria transmission since female blood seekers were more during bed time than pre-bed time. Advocacy on enhanced net availability, integrity and usage in Kenyan highlands can reduce Pf transmission. Additional complementary interventions are required to control the biting and parasite transmission encountered before bed-time.\",\n \"corpus_id\": 33009745,\n \"score\": 1\n },\n {\n \"doc_id\": \"26684464\",\n \"title\": \"Zoophagic behaviour of anopheline mosquitoes in southwest Ethiopia: opportunity for malaria vector control.\",\n \"abstract\": \"BACKGROUND: Increased understanding of the feeding behaviours of malaria vectors is important to determine the frequency of human-vector contact and to implement effective vector control interventions. Here we assess the relative feeding preferences of Anopheles mosquitoes in relation to cattle and human host abundance in southwest Ethiopia. METHODS: We collected female Anopheles mosquitoes bi-weekly using Centers for Disease Control and prevention (CDC) light traps, pyrethrum spray catches (PSCs) and by aspirating from artificial pit shelters, and determined mosquito blood meal origins using a direct enzyme-linked immunosorbent assay (ELISA). RESULTS: Both Anopheles arabiensis Patton and An. marshalli (Theobald) showed preference of bovine blood meal over humans regardless of higher human population sizes. The relative feeding preference of An. arabiensis on bovine blood meal was 4.7 times higher than that of human blood. Anopheles marshalli was 6 times more likely to feed on bovine blood meal than humans. The HBI of An. arabiensis and An. marshalli significantly varied between the collection methods, whereas the bovine feeding patterns was not substantially influenced by collection methods. Even though the highest HBI of An. arabiensis and An. marshalli was from indoor CDC traps collections, a substantial number of An. arabiensis (65 %) and An. marshalli (63 %) had contact with cattle. Anopheles arabiensis (44 %) and An. marshalli (41 %) had clearly taken bovine blood meals outdoors, but they rested indoors. CONCLUSION: Anopheles mosquitoes are zoophagic and mainly feed on bovine blood meals than humans. Hence, it is important to consider treatment of cattle with appropriate insecticide to control the zoophagic malaria vectors in southwest Ethiopia. Systemic insecticides like ivermectin and its member eprinomectin could be investigated to control the pyrethroid insecticides resistant vectors.\",\n \"corpus_id\": 16206708,\n \"score\": 1\n },\n {\n \"doc_id\": \"26857915\",\n \"title\": \"Malaria vectors and their blood-meal sources in an area of high bed net ownership in the western Kenya highlands.\",\n \"abstract\": \"BACKGROUND: Blood-meal sources of malaria vectors affect their capacity to transmit the disease. Most efficient malaria vectors prefer human hosts. However, with increasing personal protection measures it becomes more difficult for them to find human hosts. Here recent malaria vector blood-meal sources in western Kenya highlands were investigated. METHODS: Adult mosquitoes resting indoors, outdoors and exiting through windows were collected in three study areas within the western Kenya highlands from June 2011 to June 2013. A census of people, livestock and of insecticide-treated nets was done per house. Mosquito blood-meal sources were determined as human, goat, bovine or chicken using enzyme-linked-immunosorbent assays. RESULTS: Most (86.3 %) households possessed at least one bed net, 57.2 % had domesticated animals and 83.6 % had people sharing houses with livestock at night. Most (94.9 %) unfed malaria vectors were caught exiting through windows. Overall, 53.1 % of Anopheles gambiae sensu stricto obtained blood-meals from humans, 26.5 % from goats and 18.4 % from bovines. Single blood-meal sources by An. gambiae s.s. from humans were 26.5 %, 8.2 % from bovines and 2.0 % from goats. Mixed blood-meal sources by An. gambiae s.s. identified included: 24.5 % human/goat, 10.2 % human/bovine, 8.2 % human/bovine/goat and also 8.2 % bovine/goat. One An. arabiensis mosquito obtained blood-meal only from humans. CONCLUSION: An unusually high frequency of animal and mixed human-animal blood meals in the major malaria vector An. gambiae s.s. was revealed in the western Kenya highlands where bed net coverage is above the WHO target. The shift in blood-meal sources from humans to livestock is most likely the vectors' response to increased bed net coverage and the close location of livestock frequently in the same house as people at night. Livestock-targeted interventions should be considered under these circumstances to address residual malaria transmission.\",\n \"corpus_id\": 14385673,\n \"score\": 1\n },\n {\n \"doc_id\": \"26960327\",\n \"title\": \"Anopheles farauti is a homogeneous population that blood feeds early and outdoors in the Solomon Islands.\",\n \"abstract\": \"BACKGROUND: In the 1970s, Anopheles farauti in the Solomon Island responded to indoor residual spraying with DDT by increasingly feeding more outdoors and earlier in the evening. Although long-lasting insecticidal nets (LLINs) are now the primary malaria vector control intervention in the Solomon Islands, only a small proportion of An. farauti still seek blood meals indoors and late at night where they are vulnerable to being killed by contract with the insecticides in LLINs. The effectiveness of LLINs and indoor residual spraying (IRS) in controlling malaria transmission where the vectors are exophagic and early biting will depend on whether the predominant outdoor or early biting phenotypes are associated with a subpopulation of the vectors present. METHODS: Mark-release-recapture experiments were conducted in the Solomon Islands to determine if individual An. farauti repeat the same behaviours over successive feeding cycles. The two behavioural phenotypes examined were those on which the WHO recommended malaria vector control strategies, LLINs and IRS, depend: indoor and late night biting. RESULTS: Evidence was found for An. farauti being a single population regarding time (early evening or late night) and location (indoor or outdoor) of blood feeding. Individual An. farauti did not consistently repeat behavioural phenotypes expressed for blood feeding (e.g., while most mosquitoes that fed early and outdoors, and would repeat those behaviours, some fed late at night or indoors in the next feeding cycle). CONCLUSIONS: The finding that An. farauti is a homogeneous population is significant, because during the multiple feeding cycles required to complete the extrinsic incubation period, many individual female anophelines will enter houses late at night and be exposed to the insecticides used in LLINs or IRS. This explains, in part, the control that LLINs and IRS have exerted against a predominantly outdoor feeding vector, such as An. farauti. These findings may be relevant to many of the outdoor feeding vectors that dominate transmission in much of the malaria endemic world and justifies continued use of LLINs. However, the population-level tendency of mosquitoes to feed outdoors and early in the evening does require complementary interventions to accelerate malaria control towards elimination.\",\n \"corpus_id\": 16023064,\n \"score\": 1\n },\n {\n \"doc_id\": \"26969430\",\n \"title\": \"Frequent blood feeding enables insecticide-treated nets to reduce transmission by mosquitoes that bite predominately outdoors.\",\n \"abstract\": \"BACKGROUND: The effectiveness of vector control on malaria transmission by long-lasting insecticidal nets (LLINs) and indoor residual spraying (IRS) depends on the vectors entering houses to blood feed and rest when people are inside houses. In the Solomon Islands, significant reductions in malaria have been achieved in the past 20 years with insecticide-treated bed nets, IRS, improved diagnosis and treatment with artemisinin combination therapies; despite the preference of the primary vector, Anopheles farauti, to feed outdoors and early in the evening and thereby avoid potential exposure to insecticides. Rational development of tools to complement LLINs and IRS by attacking vectors outdoor requires detailed knowledge of the biology and behaviours of the target species. METHODS: Malaria transmission in Central Province, Solomon Islands was estimated by measuring the components comprising the entomological inoculation rate (EIR) as well as the vectorial capacity of An. farauti. In addition, the daily and seasonal biting behaviour of An. farauti, was examined and the duration of the feeding cycle was estimated with a mark-release-recapture experiment. RESULTS: Anopheles farauti was highly exophagic with 72% captured by human landing catches (HLC) outside of houses. Three-quarters (76%) of blood feeding on humans was estimated to occur before 21.00 h. When the hourly location of humans was considered, the proportion of exposure to mosquito bites on humans occurring indoors (πi) was only 0.130 ± 0.129. Peak densities of host seeking An. farauti occurred between October and January. The annual EIR was estimated to be 2.5 for 2012 and 33.2 for 2013. The length of the feeding cycle was 2.1 days. CONCLUSIONS: The short duration of the feeding cycle by this species offers an explanation for the substantial control of malaria that has been achieved in the Solomon Islands by LLINs and IRS. Anopheles farauti is primarily exophagic and early biting, with 13% of mosquitoes entering houses to feed late at night during each feeding cycle. The two-day feeding cycle of An. farauti requires females to take 5-6 blood meals before the extrinsic incubation period (EIP) is completed; and this could translate into substantial population-level mortality by LLINs or IRS before females would be infectious to humans with Plasmodium falciparum and Plasmodium vivax. Although An. farauti is primarily exophagic, the indoor vector control tools recommended by the World Health Organization (LLINs and IRS) can still provide an important level of control. Nonetheless, elimination will likely require vector control tools that target other bionomic vulnerabilities to suppress transmission outdoors and that complement the control provided by LLINs and IRS.\",\n \"corpus_id\": 11747863,\n \"score\": 1\n },\n {\n \"doc_id\": \"27093890\",\n \"title\": \"Most outdoor malaria transmission by behaviourally-resistant Anopheles arabiensis is mediated by mosquitoes that have previously been inside houses.\",\n \"abstract\": \"BACKGROUND: Anopheles arabiensis is stereotypical of diverse vectors that mediate residual malaria transmission globally, because it can feed outdoors upon humans or cattle, or enter but then rapidly exit houses without fatal exposure to insecticidal nets or sprays. METHODS: Life histories of a well-characterized An. arabiensis population were simulated with a simple but process-explicit deterministic model and relevance to other vectors examined through sensitivity analysis. RESULTS: Where most humans use bed nets, two thirds of An. arabiensis blood feeds and half of malaria transmission events were estimated to occur outdoors. However, it was also estimated that most successful feeds and almost all (>98 %) transmission events are preceded by unsuccessful attempts to attack humans indoors. The estimated proportion of vector blood meals ultimately obtained from humans indoors is dramatically attenuated by availability of alternative hosts, or partial ability to attack humans outdoors. However, the estimated proportion of mosquitoes old enough to transmit malaria, and which have previously entered a house at least once, is far less sensitive to both variables. For vectors with similarly modest preference for cattle over humans and similar ability to evade fatal indoor insecticide exposure once indoors, >80 % of predicted feeding events by mosquitoes old enough to transmit malaria are preceded by at least one house entry event, so long as ≥40 % of attempts to attack humans occur indoors and humans outnumber cattle ≥4-fold. CONCLUSIONS: While the exact numerical results predicted by such a simple deterministic model should be considered only approximate and illustrative, the derived conclusions are remarkably insensitive to substantive deviations from the input parameter values measured for this particular An. arabiensis population. This life-history analysis, therefore, identifies a clear, broadly-important opportunity for more effective suppression of residual malaria transmission by An. arabiensis in Africa and other important vectors of residual transmission across the tropics. Improved control of predominantly outdoor residual transmission by An. arabiensis, and other modestly zoophagic vectors like Anopheles darlingi, which frequently enter but then rapidly exit from houses, may be readily achieved by improving existing technology for killing mosquitoes indoors.\",\n \"corpus_id\": 15774826,\n \"score\": 1\n },\n {\n \"doc_id\": \"27259984\",\n \"title\": \"Host-feeding patterns of mosquito species in Germany.\",\n \"abstract\": \"BACKGROUND: Mosquito-borne pathogens are of growing importance in many countries of Europe including Germany. At the same time, the transmission cycles of most mosquito-borne pathogens (e.g. viruses or filarial parasites) are not completely understood. There is especially a lack of knowledge about the vector capacity of the different mosquito species, which is strongly influenced by their host-feeding patterns. While this kind of information is important to identify the relevant vector species, e.g. to direct efficient control measures, studies about the host-feeding patterns of mosquito species in Germany are scarce and outdated. METHODS: Between 2012 and 2015, 775 blood-fed mosquito specimens were collected. Sampling was conducted with Heavy Duty Encephalitis Vector Survey traps, Biogents Sentinel traps, gravid traps, hand-held aspirators, sweep nets, and human-bait collection. The host species for each mosquito specimen was identified with polymerase chain reactions and subsequent Sanger sequencing of the cytochrome b gene. RESULTS: A total of 32 host species were identified for 23 mosquito species, covering 21 mammalian species (including humans) and eleven bird species. Three mosquito species accounted for nearly three quarters of all collected blood-fed mosquitoes: Aedes vexans (363 specimens, 46.8 % of all mosquito specimens), Culex pipiens pipiens form pipiens (100, 12.9 %) and Ochlerotatus cantans (99, 12.8 %). Non-human mammals dominated the host species (572 specimens, 73.8 % of all mosquito specimens), followed by humans (152, 19.6 %) and birds (51, 6.6 %). The most common host species were roe deer (Capreolus capreolus; 258 mosquito specimens, 33.3 % of all mosquito specimens, 65 % of all mosquito species), humans (Homo sapiens; 152, 19.6 %, 90 %), cattle (Bos taurus; 101, 13.0 %, 60 %), and wild boar (Sus scrofa; 116, 15.0 %, 50 %). There were no statistically significant differences in the spatial-temporal host-feeding patterns of the three most common mosquito species. CONCLUSIONS: Although the collected blood-fed mosquito species had a strong overlap of host species, two different host-feeding groups were identified with mosquito species feeding on (i) non-human mammals and humans or (ii) birds, non-human mammals, and humans, which make them potential vectors of pathogens only between mammals or between mammals and birds, respectively. Due to the combination of their host-feeding patterns and wide distribution in Germany, Cx. pipiens pipiens form pipiens and Cx. torrentium are potentially most important vectors for pathogens transmitted from birds to humans and the species Ae. vexans for pathogens transmitted from non-human mammals to humans. Finally, the presented study indicated a much broader host range compared to the classifications found in the literature for some of the species, which highlights the need for studies on the host-feeding patterns of mosquitoes to further assess their vector capacity and the disease ecology in Europe.\",\n \"corpus_id\": 2794703,\n \"score\": 1\n },\n {\n \"doc_id\": \"27317557\",\n \"title\": \"Evaluation of a topical formulation of eprinomectin against Anopheles arabiensis when administered to Zebu cattle (Bos indicus) under field conditions.\",\n \"abstract\": \"BACKGROUND: Although vector control strategies, such as insecticide-treated bed nets (ITNs) and indoor residual spraying (IRS) have been effective in Kenya the transmission of malaria continues to afflict western Kenya. This residual transmission is driven in part by Anopheles arabiensis, known for its opportunistic blood feeding behaviour and propensity to feed outdoors. The objective of this research was to evaluate the efficacy of the drug eprinomectin at reducing malaria vector density when applied to cattle (Bos indicus), the primary source of blood for An. arabiensis, under field conditions. METHODS: A pilot study was carried out in the Samia District of western Kenya from September to October of 2014. Treatment and control areas were randomly designated and comprised of 50 homes per study area. Before cattle treatments, baseline mosquito counts were performed after pyrethrum spray. Cows in the treatment area were administered topical applications of eprinomectin at 0.5 mg/kg once a week for two consecutive weeks. Mosquito collections were performed once each week for two weeks following the eprinomectin treatments. Mosquitoes were first identified morphologically and with molecular confirmation, then screened for sporozoite presence and host blood using PCR-based methods. RESULTS: The indoor resting density of An. arabiensis was significantly reduced by 38 % in the treatment area compared to the control area at one-week post-treatment (Control mean females per hut = 1.33 95 % CI [1.08, 1.64]; Treatment = 0.79 [0.56, 1.07]). An increase in the indoor resting density of Anopheles gambiae s.s. and Anopheles funestus s.s. was observed in the treatment area in the absence of An. arabiensis. At two weeks post-treatment, the total number of mosquitoes for any species per hut was not significantly different between the treatment and control areas. No change was observed in An. arabiensis host preference as a result of treatment. CONCLUSIONS: Systemic drugs may be an important tool by which to supplement existing vector control interventions by significantly impacting outdoor malaria transmission driven by An. arabiensis through the treatment of cattle.\",\n \"corpus_id\": 16717421,\n \"score\": 1\n },\n {\n \"doc_id\": \"27439360\",\n \"title\": \"Chicken volatiles repel host-seeking malaria mosquitoes.\",\n \"abstract\": \"BACKGROUND: Anopheles arabiensis is a dominant vector of malaria in sub-Saharan Africa, which feeds indoors and outdoors on human and other vertebrate hosts, making it a difficult species to control with existing control methods. Novel methods that reduce human-vector interactions are, therefore, required to improve the impact of vector control programmes. Investigating the mechanisms underlying the host discrimination process in An. arabiensis could provide valuable knowledge leading to the development of novel control technologies. In this study, a host census and blood meal analysis were conducted to determine the host selection behaviour of An. arabiensis. Since mosquitoes select and discriminate among hosts primarily using olfaction, the volatile headspace of the preferred non-human host and non-host species, were collected. Using combined gas chromatography and electroantennographic detection analysis followed by combined gas chromatography and mass spectrometry, the bioactive compounds in the headspace collections were identified. The efficiency of the identified non-host compounds to repel host-seeking malaria mosquitoes was tested under field conditions. RESULTS: The host census and blood meal analyses demonstrated that An. arabiensis strongly prefers human blood when host seeking indoors, while it randomly feeds on cattle, goats and sheep when found outdoors. However, An. arabiensis avoids chickens despite their relatively high abundance, indicating that chickens are a non-host species for this vector. Eleven bioactive compounds were found in the headspace of the non-host species. Six of these were species-specific, out of which four were identified using combined gas chromatography and mass spectrometry. When tested in the field, the chicken-specific compounds, isobutyl butyrate, naphthalene, hexadecane and trans-limonene oxide, and the generic host compounds, limonene, cis-limonene oxide and β-myrcene, significantly reduced trap catches within the house compared to a negative control. A significant reduction in trap catch was also observed when suspending a caged chicken next to the trap. CONCLUSIONS: Non-host volatiles repel host-seeking An. arabiensis and thus play a significant role in host discrimination. As such, this study demonstrates that non-host volatiles can provide protection to humans at risk of mosquito-vectored diseases in combination with established control programmes.\",\n \"corpus_id\": 6144262,\n \"score\": 1\n },\n {\n \"doc_id\": \"27631375\",\n \"title\": \"The Genetic Basis of Host Preference and Resting Behavior in the Major African Malaria Vector, Anopheles arabiensis.\",\n \"abstract\": \"Malaria transmission is dependent on the propensity of Anopheles mosquitoes to bite humans (anthropophily) instead of other dead end hosts. Recent increases in the usage of Long Lasting Insecticide Treated Nets (LLINs) in Africa have been associated with reductions in highly anthropophilic and endophilic vectors such as Anopheles gambiae s.s., leaving species with a broader host range, such as Anopheles arabiensis, as the most prominent remaining source of transmission in many settings. An. arabiensis appears to be more of a generalist in terms of its host choice and resting behavior, which may be due to phenotypic plasticity and/or segregating allelic variation. To investigate the genetic basis of host choice and resting behavior in An. arabiensis we sequenced the genomes of 23 human-fed and 25 cattle-fed mosquitoes collected both in-doors and out-doors in the Kilombero Valley, Tanzania. We identified a total of 4,820,851 SNPs, which were used to conduct the first genome-wide estimates of \\\"SNP heritability\\\" for host choice and resting behavior in this species. A genetic component was detected for host choice (human vs cow fed; permuted P = 0.002), but there was no evidence of a genetic component for resting behavior (indoors versus outside; permuted P = 0.465). A principal component analysis (PCA) segregated individuals based on genomic variation into three groups which were characterized by differences at the 2Rb and/or 3Ra paracentromeric chromosome inversions. There was a non-random distribution of cattle-fed mosquitoes between the PCA clusters, suggesting that alleles linked to the 2Rb and/or 3Ra inversions may influence host choice. Using a novel inversion genotyping assay, we detected a significant enrichment of the standard arrangement (non-inverted) of 3Ra among cattle-fed mosquitoes (N = 129) versus all non-cattle-fed individuals (N = 234; χ2, p = 0.007). Thus, tracking the frequency of the 3Ra in An. arabiensis populations may be of use to infer selection on host choice behavior within these vector populations; possibly in response to vector control. Controlled host-choice assays are needed to discern whether the observed genetic component has a direct relationship with innate host preference. A better understanding of the genetic basis for host feeding behavior in An. arabiensis may also open avenues for novel vector control strategies based on driving genes for zoophily into wild mosquito populations.\",\n \"corpus_id\": 16646011,\n \"score\": 1\n },\n {\n \"doc_id\": \"27716416\",\n \"title\": \"Human-biting activities of Anopheles species in south-central Ethiopia.\",\n \"abstract\": \"BACKGROUND: Indoor residual spraying (IRS) and long-lasting insecticidal nets (LLINs) are the key malaria vector control interventions in Ethiopia. The success of these interventions rely on their efficacy to repel or kill indoor feeding and resting mosquitoes. This study was undertaken to monitor human-biting patterns of Anopheles species in south-central Ethiopia. METHODS: Human-biting patterns of anophelines were monitored for 40 nights in three houses using human landing catches (HLC) both indoors and outdoors between July and November 2014, in Edo Kontola village, south-central Ethiopia. This time coincides with the major malaria transmission season in Ethiopia, which is usually between September and November. Adult mosquitoes were collected from 19:00 to 06:00 h and identified to species. Comparisons of HLC data were done using incidence rate ratio (IRR) calculated by negative binomial regression. The nocturnal biting activities of each Anopheles species was expressed as mean number of mosquitoes landing per person per hour. To assess malaria infections in Anopheles mosquitoes the presence of Plasmodium falciparum and P. vivax circumsporozoite proteins (CSP) were determined by enzyme-linked immunosorbent assay (ELISA). RESULTS: Altogether 3,408 adult female anophelines were collected, 2,610 (76.6 %) outdoors and 798 (23.4 %) indoors. Anopheles zeimanni was the predominant species (66.5 %) followed by An. arabiensis (24.8 %), An. pharoensis (6.8 %) and An. funestus (s.l.) ( 1.8 %). The overall mean anopheline density was 3.3 times higher outdoors than indoors (65.3 vs 19.9/person/night, IRR: 3.3, 95 % CI: 1.1-5.1, P = 0.001). The mean density of An. zeimanni, An. pharoensis and An. funestus (s.l.) collected outdoors was significantly higher than indoors for each species (P < 0.05). However, the mean An. arabiensis density outdoors was similar to that indoors (11.8 vs 9.4/person/night, IRR: 1.3, 95 % CI: 0.8-1.9, P = 0.335). The mean hourly human-biting density of An. arabiensis was greater outdoors than indoors and peaked between 21:00 and 22:00 h. However, An. arabiensis parous population showed high indoor man biting activities during bedtimes (22:00 to 05:00 h) when the local people were indoor and potentially protected by IRS and LLINs. All mosquito samples tested for CSP antigen were found negative to malaria parasites. CONCLUSIONS: Results show much greater mosquito human-biting activities occurring outdoors than indoors and during early parts of the night, implying higher outdoor malaria transmission potential in the area. However, high bedtime (22:00 to 05:00 h) indoor biting activities of parous An. arabiensis suggest high potential intervention impact of IRS and LLINs on indoor malaria transmission.\",\n \"corpus_id\": 14913998,\n \"score\": 1\n },\n {\n \"doc_id\": \"28222769\",\n \"title\": \"Plasticity of host selection by malaria vectors of Papua New Guinea.\",\n \"abstract\": \"BACKGROUND: Host selection is an important determinant of vectorial capacity because malaria transmission increases when mosquitoes feed more on humans than non-humans. Host selection also affects the outcome of long-lasting insecticidal nets (LLIN). Despite the recent nationwide implementation of LLIN-based malaria control program in Papua New Guinea (PNG), little is known about the host selection of the local Anopheles vectors. This study investigated the host selection of Anopheles vectors in PNG. METHODS: Blood-engorged mosquitoes were sampled using the barrier screen method and blood meals analyzed for vertebrate host source with PCR-amplification of the mitochondrial cytochrome b gene. Abundance of common hosts was estimated in surveys. The test of homogeneity of proportions and the Manly resource selection ratio were used to determine if hosts were selected in proportion to their abundance. RESULTS: Two thousand four hundred and forty blood fed Anopheles females of seven species were sampled from five villages in Madang, PNG. Of 2,142 samples tested, 2,061 (96.2%) yielded a definitive host source; all were human, pig, or dog. Hosts were not selected in proportion to their abundance, but rather were under-selected or over-selected by the mosquitoes. Four species, Anopheles farauti (sensu stricto) (s.s.), Anopheles punctulatus (s.s.), Anopheles farauti no. 4 and Anopheles longirostris, over-selected humans in villages with low LLIN usage, but over-selected pigs in villages with high LLIN usage. Anopheles koliensis consistently over-selected humans despite high LLIN usage, and Anopheles bancroftii over-selected pigs. CONCLUSIONS: The plasticity of host selection of an Anopheles species depends on its opportunistic, anthropophilic or zoophilic behavior, and on the extent of host availability and LLIN usage where the mosquitoes forage for hosts. The high anthropophily of An. koliensis increases the likelihood of contacting the LLIN inside houses. This allows its population size to be reduced to levels insufficient to support transmission. In contrast, by feeding on alternative hosts the likelihood of the opportunistic species to contact LLIN is lower, making them difficult to control. By maintaining high population size, the proportion that feed on humans outdoors can sustain residual transmission despite high LLIN usage in the village.\",\n \"corpus_id\": 4699384,\n \"score\": 1\n },\n {\n \"doc_id\": \"28283033\",\n \"title\": \"Resting and feeding preferences of Anopheles stephensi in an urban setting, perennial for malaria.\",\n \"abstract\": \"BACKGROUND: The Indian city of Chennai is endemic for malaria and the known local malaria vector is Anopheles stephensi. Plasmodium vivax is the predominant malaria parasite species, though Plasmodium falciparum is present at low levels. The urban ecotype of malaria prevails in Chennai with perennial transmission despite vector surveillance by the Urban Malaria Scheme (UMS) of the National Vector Borne Disease Control Programme (NVBDCP). Understanding the feeding and resting preferences, together with the transmission potential of adult vectors in the area is essential in effective planning and execution of improved vector control measures. METHODS: A yearlong survey was carried out in cattle sheds and human dwellings to check the resting, feeding preferences and transmission potential of An. stephensi. The gonotrophic status, age structure, resting and host seeking preferences were studied. The infection rate in An. stephensi and Anopheles subpictus were analysed by circumsporozoite ELISA (CS-ELISA). RESULTS: Adult vectors were found more frequently and at higher densities in cattle sheds than human dwellings. The overall Human Blood Index (HBI) was 0.009 indicating the vectors to be strongly zoophilic. Among the vectors collected from human dwellings, 94.2% were from thatched structures and the remaining 5.8% from tiled and asbestos structures. 57.75% of the dissected vectors were nulliparous whereas, 35.83% were monoparous and the rest 6.42% biparous. Sporozoite positivity rate was 0.55% (4/720) and 1.92% (1/52) for An. stephensi collected from cattle sheds and human dwellings, respectively. One adult An. subpictus (1/155) was also found to be infected with P. falciparum. CONCLUSIONS: Control of the adult vector populations can be successful only by understanding the resting and feeding preferences. The present study indicates that adult vectors predominantly feed on cattle and cattle sheds are the preferred resting place, possibly due to easy availability of blood meal source and lack of any insecticide or repellent pressure. Hence targeting these resting sites with cost effective, socially acceptable intervention tools, together with effective larval source management to reduce vector breeding, could provide an improved integrated vector management strategy to help drive down malaria transmission and assist in India's plan to eliminate malaria by 2030.\",\n \"corpus_id\": 3484664,\n \"score\": 1\n },\n {\n \"doc_id\": \"28797253\",\n \"title\": \"First record of Anopheles stephensi in Sri Lanka: a potential challenge for prevention of malaria reintroduction.\",\n \"abstract\": \"BACKGROUND: The major malaria vector in Sri Lanka is reported to be Anopheles culicifacies with Anopheles subpictus, Anopheles annularis, and Anopheles varuna considered as potential vectors. The occurrence of Anopheles stephensi, which is the key vector of urban malaria in India and the Middle East, had never been reported from Sri Lanka. METHODS: A series of entomological investigations were carried out by the Anti Malaria Campaign, Ministry of Health, Sri Lanka during December 2016 to April 2017 in two localities of the Mannar District in the Northern Province of the country. Adult mosquito collections were done through indoor and outdoor resting collections, animal and human biting collections and emergence traps. Potential mosquito breeding sites were investigated through larval surveys. The larvae and adults of An. stephensi were initially identified using morphological keys, and subsequently confirmed by sequencing the barcode region of the cytochrome c oxidase I (COI) gene. RESULTS: This is the first report of the presence of An. stephensi in the island of Mannar in the Northern Province of Sri Lanka. Anopheles stephensi (36.65%) was the most abundant anopheline species in the larval habitats in Mannar. It was found breeding together with An. culicifacies (20.7%), An. subpictus (13.5%) and An. varuna (28.13%). Anopheles stephensi was found to be abundantly breeding in built wells used for domestic purposes. Adult females of An. stephensi were observed in emergence trap collections (93.9%), human landing catches all night (79.2%), pyrethrum spray sheet collections (38.6%), outdoor collections (8.3%), donkey-baited trap collections (14.3), and cattle-baited net trap collections (0.7%). CONCLUSIONS: Sri Lanka was certified as malaria-free by the WHO in September 2016, however, this new finding may pose a serious challenge to the efforts of the Ministry of Health to prevent the re-introduction of malaria transmission in the country, considering the role that An. stephensi could play in urban and high vulnerability areas of Sri Lanka.\",\n \"corpus_id\": 13653737,\n \"score\": 1\n },\n {\n \"doc_id\": \"29110670\",\n \"title\": \"Indoor and outdoor malaria vector surveillance in western Kenya: implications for better understanding of residual transmission.\",\n \"abstract\": \"BACKGROUND: The widespread use of indoor-based malaria vector control interventions has been shown to alter the behaviour of vectors in Africa. There is an increasing concern that such changes could sustain residual transmission. This study was conducted to assess vector species composition, feeding behaviour and their contribution to indoor and outdoor malaria transmission in western Kenya. METHODS: Anopheles mosquito collections were carried out from September 2015 to April 2016 in Ahero and Iguhu sites, western Kenya using CDC light traps (indoor and outdoor), pyrethrum spray catches (PSCs) (indoor) and pit shelters (outdoor). Species within Anopheles gambiae s.l. and Anopheles funestus s.l. were identified using polymerase chain reaction (PCR). Enzyme-linked immunosorbent assay (ELISA) was used to determine mosquito blood meal sources and sporozoite infections. RESULTS: A total of 10,864 female Anopheles mosquitoes comprising An. gambiae s.l. ( 71.4%), An. funestus s.l. ( 12.3%), Anopheles coustani (9.2%) and Anopheles pharoensis (7.1%) were collected. The majority (61.8%) of the anopheline mosquitoes were collected outdoors. PCR result (n = 581) revealed that 98.9% An. arabiensis and 1.1% An. gambiae s.s. constituted An. gambiae s.l. in Ahero while this was 87% An. gambiae s.s. and 13% An. arabiensis in Iguhu. Of the 108 An. funestus s.l. analysed by PCR, 98.1% belonged to An. funestus s.s. and 1.9% to Anopheles leesoni. The human blood index (HBI) and bovine blood index (BBI) of An. arabiensis was 2.5 and 73.1%, respectively. Anopheles gambiae s.s. had HBI and BBI of 50 and 28%, respectively. The HBI and BBI of An. funestus was 60 and 22.3%, respectively. Forage ratio estimate revealed that An. arabiensis preferred to feed on cattle, An. gambiae s.s. showed preference for both human and cattle, while An. funestus preferred human over other hosts. In Ahero, the sporozoite rates for An. arabiensis and An. funestus were 0.16 and 1.8%, respectively, whereas in Iguhu, the sporozoite rates for An. gambiae s.s. and An. funestus were 2.3 and 2.4%, respectively. In Ahero, the estimated indoor and outdoor entomological inoculation rate (EIR) was 108.6 infective bites/person/year (79.0 from An. funestus and 29.6 from An. arabiensis) and 43.5 infective bites/person/year (27.9 from An. arabiensis and 15.6 from An. funestus), respectively. In Iguhu, the estimated indoor and outdoor EIR was 24.5 infective bites/person/year (18.8 from An. gambiae s.s. and 5.7 from An. funestus) and 5.5 infective bites/person/year (all from An. gambiae s.s.), respectively. CONCLUSION: Anopheles gambiae s.s. showed an increasing tendency to feed on cattle. Anopheles arabiensis was highly zoophagic, whereas An. funestus showed anthropophagic behaviour. While the majority of malaria transmission occurred indoor, the magnitude of outdoor transmission was considerably high. Additional control tools that complement the existing interventions are required to control residual transmission.\",\n \"corpus_id\": 2213801,\n \"score\": 1\n },\n {\n \"doc_id\": \"29310656\",\n \"title\": \"Comparative evaluation of anopheline sampling methods in three localities in Indonesia.\",\n \"abstract\": \"BACKGROUND: The effectiveness of vector control efforts can vary based on the interventions used and local mosquito behaviour and adaptability. In many settings, biting patterns of Anopheles mosquitoes can shift in response to interventions targeting indoor-biting mosquitoes, often resulting in higher proportions of mosquitoes feeding outside or at times when people are not protected. These behaviourally resistant mosquitoes have been shown to sustain residual malaria transmission and limit control efforts. Therefore, it is important to accurately sample mosquitoes to understand their behaviour. METHODS: A variety of traps were evaluated in three geographically diverse sites in malaria-endemic Indonesia to investigate local mosquito feeding behaviour and determine effective traps for surveillance. RESULTS: Eight traps were evaluated in three sites: Canti village, Lampung, Kaliharjo village, Purworejo, and Saketa village, Halmahera, Indonesia, including the gold standard human landing collection (HLC) and a variety of traps targeting host-seeking and resting mosquitoes both indoors and outdoors. Trapping, using indoor and outdoor HLC, the Ifakara tent trap C, goat and human-occupied tents, resting pots and boxes, and CDC miniature light traps was conducted for 16 nights in two sites and 8 nights in a third site, using a Latin square design. Trap efficacy varied by site, with outdoor HLC yielding the highest catch rates in Canti and Kaliharjo and a goat-baited tent trap proving most effective in Saketa. In Canti village, anthropophilic Anopheles sundaicus were caught indoors and outdoors using HLCs, peaking in the early morning. In Kaliharjo, a variety of mosquitoes were caught, mostly outdoors throughout the night. HLC was ineffective in Saketa, the only site where a goat-baited tent trap was tested. This trap was effective in catching zoophilic vectors outdoors before midnight. CONCLUSIONS: Different trapping methods were suitable for different species, likely reflecting differences in behaviour among species. The three villages, each located on a different island in the Indonesian archipelago, contained mosquito populations with unique behaviours. These data suggest that the effectiveness of specific vector monitoring and control measures may vary by location.\",\n \"corpus_id\": 28888560,\n \"score\": 1\n },\n {\n \"doc_id\": \"29479733\",\n \"title\": \"Studies on the resting behaviour and host choice of Anopheles gambiae and An. arabiensis from Muleba, Tanzania.\",\n \"abstract\": \"The relative efficacy of a mechanical (Prokopack) collection method vs. manual aspiration in the collection of resting mosquitoes was evaluated in northern Tanzania before and after an intervention using indoor residual spraying and longlasting insecticide-treated nets. In smoke-free houses mosquitoes were collected from the roof and walls, but in smoky houses mosquitoes were found predominantly on the walls. Anopheles gambiae (Diptera: Culicidae) constituted 97.7% of the 312 An. gambiae complex specimens identified before but only 19.3% of the 183 identified after the intervention. A single sampling with the Prokopack collected a third of the available insects. Anopheles gambiae completed its gonotrophic development indoors, whereas Anopheles arabiensis did so outdoors. In both species gonotrophic development took 2 days. Most unfed resting An. arabiensis collected outdoors were virgins, whereas the majority of engorged insects were parous (with well-contracted sacs). Daily survival was estimated to be 80.0%. Only 9.4% of the engorged An. arabiensis collected outdoors and 47.1% of those collected indoors had fed on humans. Using the Prokopack sampler is more efficient than manual methods for the collection of resting mosquitoes. Malaria transmission may have been affected by a change in vector composition resulting from a change in feeding, rather than reduced survival. Monitoring the proportions of members of the An. gambiae complex may provide signals of an impending breakdown in control.\",\n \"corpus_id\": 3539415,\n \"score\": 1\n },\n {\n \"doc_id\": \"29669580\",\n \"title\": \"The bionomics of the malaria vector Anopheles rufipes Gough, 1910 and its susceptibility to deltamethrin insecticide in North Cameroon.\",\n \"abstract\": \"BACKGROUND: Following the recent discovery of the role of Anopheles rufipes Gough, 1910 in human malaria transmission in the northern savannah of Cameroon, we report here additional information on its feeding and resting habits and its susceptibility to the pyrethroid insecticide deltamethrin. METHODS: From 2011 to 2015, mosquito samples were collected in 38 locations across Garoua, Mayo Oulo and Pitoa health districts in North Cameroon. Adult anophelines collected using outdoor clay pots, window exit traps and indoor spray catches were checked for feeding status, blood meal origin and Plasmodium circumsporozoite protein. The susceptibility of field-collected An. rufipes to deltamethrin was assessed using WHO standard procedures. RESULTS: Of 9327 adult Anopheles collected in the 38 study sites, An. rufipes (6.5%) was overall the fifth most abundant malaria vector species following An. arabiensis (52.4%), An. funestus (s.l.) ( 20.8%), An. coluzzii (12.6%) and An. gambiae (6.8%). This species was found outdoors (51.2%) or entering houses (48.8%) in 35 suburban and rural locations, together with main vector species. Apart from human blood with index of 37%, An. rufipes also fed on animals including cows (52%), sheep (49%), pigs (16%), chickens (2%) and horses (1%). The overall parasite infection rate of this species was 0.4% based on the detection of P. falciparum circumsporozoite proteins in two of 517 specimens tested. Among the 21 An. rufipes populations assessed for deltamethrin susceptibility, seven populations were classified as \\\"susceptible\\\" (mortality ≥ 98%) , ten as \\\"probable resistant\\\" with a mortality range of 90-97% and four as \\\"resistant\\\" with a mortality range of 80-89%. CONCLUSIONS: This study revealed changeable resting and feeding behaviour of An. rufipes, as well as further evidence on its ability to carry human malaria parasites in North Cameroon. Besides, this species is developing physiological resistance to deltamethrin insecticide which is used in treated nets and agriculture throughout the country, and should be regarded as one of potential targets for the control of residual malaria parasite transmission in Africa.\",\n \"corpus_id\": 4939805,\n \"score\": 1\n },\n {\n \"doc_id\": \"28849536\",\n \"title\": \"Diversity of tick species on domestic animals in Shandong Province, China, using DNA barcoding.\",\n \"abstract\": \"Ticks are considered to be second only to mosquitoes as vectors of diseases. In recent years, severe fever with thrombocytopenia syndrome, a new emerging tick-borne disease has been detected in many areas of China, including Shandong Province, Eastern China. Here, we report the tick species diversity based on surveys between 2014 and 2016 covering 16 locations in seven cities of Shandong. Based on DNA barcoding, 1859 ticks belonging to three species were identified: Haemaphysalis longicornis, Rhipicephalus turanicus and Haemaphysalis verticalis. Samples of the same species clustered together in a neighbor-joining phylogenetic tree, with intraspecific distances between 0 and 3.0% and interspecific distances ranged between 15.5 and 24.3%. Goats and dogs were the major hosts of ticks and H. longicornis was regarded as predominant tick species of Shandong. In order to reduce tick populations and prevent tick-borne diseases, effective control measures should be implemented on human and domestic animals, respectively.\",\n \"corpus_id\": 34695622,\n \"score\": 0\n }\n]","isConversational":false}}},{"rowIdx":78,"cells":{"query":{"kind":"string","value":"{\n \"doc_id\": \"27681543\",\n \"title\": \"A reassessment of the artificial infection of three predominant mosquito species with Plasmodium vivax in Shandong Province, China.\",\n \"abstract\": \"BACKGROUND & OBJECTIVES: Under certain ecological circumstances, pathogens are able to rapidly adapt to new vectors. The great capacity of Plasmodium spp. to adapt to new anopheline mosquito vectors on different continents and the continuous ecological changes attributed to humans might promote their adaptation to culicine vectors, which are known to infect humans. Based on our current knowledge, it is difficult to predict whether such adaptations will occur. This study was aimed to determine the infection susceptibility of Anopheles sinensis, Culex tritaeniorhynchus and Cx. pipiens pallens to Plasmodium vivax in Shandong Province of China. METHODS: The susceptibility of the three predominant species of mosquitoes -An. sinensis, Cx. tritaeniorhynchus and Cx. pipiens pallens in Shandong Province was compared with a direct membrane feeding assay with 15 batches of Shandong strain mono-infected gametocyte-containing blood collected from Plasmodium vivax-infected patients. Infectivity was measured by dissecting the midguts and salivary glands of the mosquitoes. The presence of oocysts and sporozoites was determined by microscopy at 6 and 22 days post-blood feeding. RESULTS: From the 15 batches of mosquitoes that were fed infected blood, oocysts and sporozoites were detected only in 7th, 13th and 15th batches of infection for An. sinensis, and no oocysts or sporozoites were detected in Cx. tritaeniorhynchus or Cx. pipiens pallens. The positive rate of An. sinensis infection was 21.2, 13 and 36.3% in the three batches of mosquitoes, with an average infection rate of 23.5%. INTERPRETATION & CONCLUSION: The susceptibility of An. sinensis to P. vivax was very high in Shandong Province. Cx. tritaeniorhynchus and Cx. pipiens pallens failed to exhibit susceptibility to P. vivax.\",\n \"corpus_id\": 40990673\n}"},"candidates":{"kind":"list like","value":[{"doc_id":"18627630","title":"Competency of Anopheles stephensi mysorensis strain for Plasmodium vivax and the role of inhibitory carbohydrates to block its sporogonic cycle.","abstract":"BACKGROUND: Despite the abundance of studies conducted on the role of mosquitoes in malaria transmission, the biology and interaction of Plasmodium with its insect host still holds many mysteries. This paper provides the first study to follow the sporogonic cycle of Plasmodium vivax in a wild insecticide-resistant mysorensis strain of Anopheles stephensi, a major vector of vivax malaria in south-eastern Iran. The study subsequently demonstrates that host-parasite sugar binding interactions are critical to the development of this parasite in the salivary glands of its mosquito host. The identity of the receptors or sugars involved was revealed by a receptor \"pre-saturation\" strategy in which sugars fed to the mosquitoes inhibited normal host-parasite interactions. METHODS: Anopheles stephensi mysorensis mosquitoes were artificially infected with P. vivax by feeding on the blood of gametocytaemic volunteers reporting to local malaria clinics in the Sistan-Baluchistan province of south-eastern Iran. In order to determine the inhibitory effect of carbohydrates on sporogonic development, vector mosquitoes were allowed to ingest blood meals containing both gametocytes and added carbohydrates. The carbohydrates tested were GlcNAc, GalNAc, arabinose, fucose, mannose, lactose, glucose and galactose. Sporogonic development was assessed by survival of the parasite at both the oocyst and sporozoite stages. RESULTS: Oocyst development was observed among nearly 6% of the fed control mosquitoes but the overall number of mosquitoes exhibiting sporozoite invasion of the salivary glands was 47.5% lower than the number supporting oocysts in their midgut. Of the tested carbohydrates, only arabinose and fucose slightly perturbed the development of P. vivax oocysts at the basal side of the mosquito midgut, and the remaining sugars caused no reductions in oocyst development. Strikingly however, sporozoites were completely absent from the salivary glands of mosquitoes treated with mannose, GalNAc, and lactose. CONCLUSION: The study indicates that An. stephensi in southern Iran has the potential to survive long enough to be re-infected and transmit vivax malaria several times, based on the average adult female longevity (about 30 days) and its gonotrophic cycle (2-3 days) during the malaria transmission season. Certain sugar binding interactions are important for the development of P. vivax sporozoites, and this information may be instrumental for the development of transmission blocking strategies.","corpus_id":13170758,"score":2},{"doc_id":"19196130","title":"Distribution of arboviruses and mosquitoes in northwestern Yunnan Province, China.","abstract":"From July to September in 2005 and 2006, a survey was conducted to identify mosquito species and mosquito-borne arboviruses at elevations ranging from 900-3280 m between 24 degrees 00' N and 29 degrees 00' N latitude in the northwestern part of Yunnan Province, China. A total of 54,879 mosquitoes representing 15 species and 4 genera was collected using UV light traps at 59 sites. Culex tritaeniorhynchus and Anopheles sinensis were the most abundant species. The density of mosquitoes as well as the diversity of species decreased with increasing altitude. A total of 21,008 mosquitoes in 281 pools representing all of the 15 species was tested for the presence of viruses using cell culture. Viruses identified included Japanese encephalitis virus (13 isolates), Getah virus (five isolates), Banna virus (three isolates), Kadipiro virus (five isolates), and Densovirus (seven isolates). These isolates were obtained from Culex tritaeniorhynchus (20 isolates), Anopheles sinensis (three isolates), Armigeres subalbatus (six isolates), Culex pipiens quinquefasciatus (two isolates), and from unidentified, mixed mosquitoes (two isolates). Most of the isolates were from collections made at elevations below 2,500 m. Vector Borne Zoonotic Dis. 0, 000-000.","corpus_id":32104034,"score":2},{"doc_id":"19284634","title":"The susceptibility of Anopheles lesteri to infection with Korean strain of Plasmodium vivax.","abstract":"BACKGROUND: Following its recent re-emergence, malaria has gained renewed attention as a serious infectious disease in Korea. Three species of the Hyrcanusgroup, Anopheles lesteri, Anopheles sinensis and Anopheles pullus, have long been suspected malaria vectors. However, opinions about their vector ability are controversial. The present study was designed with the aim of determining the susceptibility of these mosquitoes to a Korean isolate of Plasmodium vivax. Also, An. sinensis is primarily suspected to be vector of malaria in Korea, but in Thailand, the same species is described to have less medical importance. Therefore, comparative susceptibility of Thai and Korean strains of An. sinensis with Thai strain of P. vivax may be helpful to understand whether these geographically different strains exhibit differences in their susceptibility or not. METHODS: The comparative susceptibility of An. lesteri, An. sinensis and An. pullus was studied by feeding laboratory-reared mosquitoes on blood from patients carrying gametocytes from Korea and Thailand. RESULTS: In experimental feeding with Korean strain of P. vivax, oocysts developed in An. lesteri, An. sinensis and An. pullus. Salivary gland sporozoites were detected only in An. lesteri and An. sinensis but not in An. pullus. Large differences were found in the number of sporozoites in the salivary glands, with An. lesteri carrying much higher densities, up to 2,105 sporozoites in a single microscope field of 750 x 560 muM, whereas a maximum of 14 sporozoites were found in any individual salivary gland of An. sinensis. Similar results were obtained from a susceptibility test of two different strains of An. sinensis to Thai isolate of P. vivax, and differences in vector susceptibility according to geographical variation were not detected. CONCLUSION: The high sporozoite rate and sporozoite loads of An. lesteri indicate that this species is highly susceptible to infection with P. vivax. Anopheles sinensis appears to have a markedly reduced ability to develop salivary gland infection, whilst in An. pullus, no sporozoites were found in the salivary glands. Provided that the survival rate of An. lesteri is sufficiently high in the field, it would be a highly competent vector of vivax malaria.","corpus_id":15517110,"score":2},{"doc_id":"19629522","title":"Mosquito blood-meal analysis for avian malaria study in wild bird communities: laboratory verification and application to Culex sasai (Diptera: Culicidae) collected in Tokyo, Japan.","abstract":"We conducted laboratory experiments to verify molecular techniques of avian malaria parasite detection distinguishing between an infected mosquito (oocysts on midgut wall) and infective mosquito (sporozoites in salivary glands) in parallel with blood-meal identification from individual blood-fed mosquitoes prior to application to field survey for avian malaria. Domestic fowl infected with Plasmodium gallinaceum was exposed to a vector and non-vector mosquito species, Aedes aegypti and Culex pipiens pallens, respectively, to compare the time course of polymerase chain reaction (PCR) detection for parasite between competent and refractory mosquitoes. DNA of the domestic fowl was detectable for at least 3 days after blood feeding. The PCR-based detection of P. gallinaceum from the abdomen and thorax of A. aegypti corresponded to the microscopic observation of oocysts and sporozoites. Therefore, this PCR-based method was considered useful as one of the criteria to assess developmental stages of Plasmodium spp. in mosquito species collected in the field. We applied the same PCR-based method to 21 blood-fed C. sasai mosquitoes collected in Rinshi-no-mori Park in urban Tokyo, Japan. Of 15 blood meals of C. sasai successfully identified, 86.7% were avian-derived, 13.3% were bovine-derived. Plasmodium DNA was amplified from the abdomen of three C. sasai specimens having an avian blood meal from the Great Tit (Parus major), Pale Thrush (Turdus pallidus), and Jungle Crow (Corvus macrorhynchos). This is the first field study on host-feeding habits of C. sasai in relation to the potential role as a vector for avian malaria parasites transmitted in the Japanese wild bird community.","corpus_id":24616221,"score":2},{"doc_id":"19646275","title":"Implementation of a novel PCR based method for detecting malaria parasites from naturally infected mosquitoes in Papua New Guinea.","abstract":"BACKGROUND: Detection of Plasmodium species in mosquitoes is important for designing vector control studies. However, most of the PCR-based detection methods show some potential limitations. The objective of this study was to introduce an effective PCR-based method for detecting Plasmodium vivax and Plasmodium falciparum from the field-caught mosquitoes of Papua New Guinea. METHODS: A method has been developed to concurrently detect mitochondrial cytochrome b (Cyt b) of four human Plasmodium species using PCR (Cytb-PCR). To particularly discriminate P. falciparum from P. vivax, Plasmodium ovale and Plasmodium malariae, a polymerase chain reaction-repeated fragment length polymorphism (PCR-RFLP) has further been developed to use with this method. However, due to limited samples number of P. ovale and P. malariae; this study was mainly confined to P. vivax and P. falciparum. The efficiency of Cytb-PCR was evaluated by comparing it with two 'gold standards' enzyme linked immunosorbent assay specific for circumsporozoite protein (CS-ELISA) using artificially infected mosquitoes; and nested PCR specific for small subunit ribosomal RNA (SSUrRNA) using field caught mosquitoes collected from three areas (Kaboibus, Wingei, and Jawia) of the East Sepic Province of Papua New Guinea. RESULTS: A total of 90 mosquitoes were artificially infected with three strains of Plasmodium: P. vivax-210 (n = 30), P. vivax-247 (n = 30) and P. falciparum (n = 30). These infected mosquitoes along with another 32 unfed mosquitoes were first checked for the presence of Plasmodium infection by CS-ELISA, and later the same samples were compared with the Cytb-PCR. CS-ELISA for P. vivax-210, P. vivax-247 and P. falciparum detected positive infection in 30, 19 and 18 mosquitoes respectively; whereas Cytb-PCR detected 27, 16 and 16 infections, respectively. The comparison revealed a close agreement between the two assays (kappa = 0.862, 0.842 and 0.894, respectively for Pv-210, Pv-247 and P. falciparum groups). It was found that the eight CS-ELISA-positive mosquitoes detected negative by Cytb-PCR were false-positive results. The lowest detection limit of this Cytb-PCR was 10 sporozoites. A highly concordance result was also found between nested PCR and Cytb-PCR using 107 field caught mosquitoes, and both tests concordantly detected P. falciparum in an Anopheles punctulatus mosquito collected from Kaboibus. Both tests thus suggested an overall sporozoite rate of 0.9% (1/107) in the study areas. Subsequently, PCR-RFLP efficiently discriminated P. falciparum from P. vivax for all of the Cytb-PCR positive samples. CONCLUSION: A single step PCR based method has been introduced here that is highly sensitive, efficient and reliable for identifying P. vivax and P. falciparum from mosquitoes. The reliability of the technique was confirmed by its ability to detect Plasmodium as efficiently as those of CS-ELISA and nested PCR. Application of the assay offers the opportunity to detect vector species of Papua New Guinea and may contribute for designing further vector control programmes.","corpus_id":7933136,"score":2},{"doc_id":"19769059","title":"Bloodmeal identification and detection of avian malaria parasite from mosquitoes (Diptera: Culicidae) inhabiting coastal areas of Tokyo Bay, Japan.","abstract":"Bloodmeal identification and the detection of avian malaria parasite from mosquitoes (Diptera: Culicidae) were carried out by polymerase chain reaction-based methods for field samples collected in coastal areas of Tokyo Bay, Japan, from April to October 2007. The following seven mosquito species were collected: Aedes albopictus (Skuse), Culex pipiens pallens Coquillett, Culex pipiens form molestus Forskal, Culex tritaeniorhynchus Giles, Culex inatomii Kamimura & Wada, Culex bitaeniorhynchus Giles, and Lutzia vorax Edwards. Forty blood-fed mosquitoes were collected and 95% of bloodmeals of Cx. pipiens pallens were avian-derived, whereas only mammalian bloodmeals were identified for Ae. albopictus. Plasmodium DNA was amplified from 65% (15/23) of blood-fed Cx. pipiens pallens and unfed females of Cx. pipiens pallens and Cx. pipiens form molestus with a minimum infection rate of 29.9 and 13.5, respectively. One unfed female of Lt. vorax was also positive for Plasmodium parasites. Five genetically distinct lineages of Plasmodium were identified, with 0.21 to 5.86% sequence divergence. Rinshi-8, the most prevalent lineage at our study site, was identical to the published sequence of Plasmodium relictum-P5.","corpus_id":26714838,"score":2},{"doc_id":"20939372","title":"Experimental studies on comparison of the potential vector competence of four species of Culex mosquitoes in China to transmit West Nile virus.","abstract":"To assess the risk that indigenous mosquitoes in China are capable of transmitting and sustaining West Nile virus (WNV), four important Culex mosquito species, Culex tritaeniorhynchus, Culex modestus, Culex pipiens pallens, and Culex pipiens quinquefasciatus, were allowed to feed on the artificial infectious blood meal with WNV dose of 10(6.8) plaque-forming unit/ml and tested approximately 2 wk later to determine infection and transmission rates. The results indicated that four Culex mosquitoes were competent laboratory vectors of WNV. The infection rates and transmission rates were statistical differences among different species of mosquito (chi2 = 20.620, P = 0.000; chi2 = 15.020, P = 0.005, respectively). The highest infection rate and transmission rate were obtained with Cx. tritaeniorhynchus (87.5 and 74.2%, respectively).","corpus_id":1063109,"score":2},{"doc_id":"21292875","title":"Plasmodium vivax sporozoite production in Anopheles albimanus mosquitoes for vaccine clinical trials.","abstract":"Vaccine development for Plasmodium vivax malaria is underway. A model to assess the protective efficacy of vaccine candidates in humans is urgently needed. Given the lack of continuous P. vivax cultures, we developed a system to infect Anopheles albimanus mosquitoes using blood from P. vivax-infected patients and determined parameters for challenge of malaria-naive volunteers by mosquito bite. Absence of co-infections in parasitized blood was confirmed by tests consistent with blood bank screening. A total of 119 experiments were conducted using batches of 900-4,500 mosquitoes fed by an artificial membrane feeding method. Optimal conditions for mosquito probing and infection were determined. Presence of oocyst and sporozoites were assessed on Days 7-8 and 14-15, respectively, and conditions to choose batches of infected mosquitoes for sporozoite challenge were established. Procedures to infect volunteers took a 2-hour period including verification of inoculum dose. Anopheles albimanus mosquitoes represent a valuable resource for P. vivax sporozoite challenge of volunteers.","corpus_id":10469297,"score":2},{"doc_id":"21762577","title":"Co-infections of Plasmodium knowlesi, P. falciparum, and P. vivax among Humans and Anopheles dirus Mosquitoes, Southern Vietnam.","abstract":"A single Anopheles dirus mosquito carrying sporozoites of Plasmodium knowlesi, P. falciparum, and P. vivax was recently discovered in Khanh Phu, southern Vietnam. Further sampling of humans and mosquitoes in this area during 2009-2010 showed P. knowlesi infections in 32 (26%) persons with malaria (n = 125) and in 31 (43%) sporozoite-positive An. dirus mosquitoes (n = 73). Co-infections of P. knowlesi and P. vivax were predominant in mosquitoes and humans, while single P. knowlesi infections were found only in mosquitoes. P. knowlesi-co-infected patients were largely asymptomatic and were concentrated among ethnic minority families who commonly spend nights in the forest. P. knowlesi carriers were significantly younger than those infected with other malaria parasite species. These results imply that even if human malaria could be eliminated, forests that harbor An. dirus mosquitoes and macaque monkeys will remain a reservoir for the zoonotic transmission of P. knowlesi.","corpus_id":2509421,"score":2},{"doc_id":"22017097","title":"Preliminary vivax malaria vector competence for three members of the Anopheles hyrcanus group in the Republic of Korea.","abstract":"In a study on the comparative susceptibility of Anopheles kleini, An. lesteri, and An. sinensis to Plasmodium vivax, we examined the feeding of laboratory-reared mosquitoes on blood of a patient carrying gametocytes from the Republic of Korea. Sporozoites in salivary glands from day 14 postfeeding were detected in An. kleini and An. lesteri with numbers high enough to initiate infection, while no sporozoites were detected in the salivary glands of An. sinensis. This result suggests that An. kleini and An. lesteri could be vivax malaria vectors in the Republic of Korea.","corpus_id":36958050,"score":2},{"doc_id":"22072836","title":"Mosquito species composition and Plasmodium vivax infection rates on Baengnyeong-do (island), Republic of Korea.","abstract":"Vivax malaria is a significant military and civilian health threat in the north of the Republic of Korea (ROK). The island of Baengnyeong-do is the westernmost point of the ROK and is located close to the southwestern coast of the Democratic People's Republic of Korea (DPRK). Mosquitoes were collected using a black light trap on Baengnyeong-do, and Anopheles spp. were assayed by PCR, to identify the species, and screened for sporozoites of Plasmodium vivax. Of a subsample of 257 mosquitoes, Anopheles lesteri was the most frequently collected (49.8%), followed by Anopheles sinensis (22.6%), Anopheles pullus (18.7%), Anopheles kleini (7.8%), and Anopheles belenrae (1.2%). The overall sporozoite rate was 3.1%, with the highest rates observed in An. kleini (15.0%), An. sinensis (5.2%), and An. lesteri (1.6%). No sporozoite positive An. pullus or An. belenrae were observed. The results extend our knowledge of the distribution and potential role in malaria transmission of An. kleini, An. lesteri, and An. sinensis, for an area previously considered to be at a low risk for contracting vivax malaria.","corpus_id":10740609,"score":2},{"doc_id":"22115320","title":"The abundance and host-seeking behavior of culicine species (Diptera: Culicidae) and Anopheles sinensis in Yongcheng city, People's Republic of China.","abstract":"BACKGROUND: The knowledge of mosquito species diversity and the level of anthropophily exhibited by each species in a region are of great importance to the integrated vector control. Culicine species are the primary vectors of Japanese encephalitis (JE) virus and filariasis in China. Anopheles sinensis plays a major role in the maintenance of Plasmodium vivax malaria transmission in China. The goal of this study was to compare the abundance and host-seeking behavior of culicine species and An. sinensis in Yongcheng city, a representative region of P. vivax malaria. Specifically, we wished to determine the relative attractiveness of different animal baits versus human bait to culicine species and An. sinensis. RESULTS: Culex tritaeniorhynchus was the most prevalent mosquito species and An. sinensis was the sole potential vector of P. vivax malaria in Yongcheng city. There were significant differences (P < 0.01) in the abundance of both An. sinensis and Cx. tritaeniorhynchus collected in distinct baited traps. The relative attractiveness of animal versus human bait was similar towards both An. sinensis and Cx. tritaeniorhynchus. The ranking derived from the mean number of mosquitoes per bait indicated that pigs, goats and calves frequently attracted more mosquitoes than the other hosts tested (dogs, humans, and chickens). These trends were similar across all capture nights at three distinct villages. The human blood index (HBI) of female An. sinensis was 2.94% when computed with mixed meals while 3.70% computed with only the single meal. 19:00~21:00 was the primary peak of host-seeking female An. sinensis while 4:00~5:00 was the smaller peak at night. There was significant correlation between the density of female An. sinensis and the average relative humidity (P < 0.05) in Wangshanzhuang village. CONCLUSIONS: Pigs, goats and calves were more attractive to An. sinensis and Cx. tritaeniorhynchus than dogs, humans, and chickens. Female An. sinensis host-seeking activity mainly occurred from 19:00 to 21:00. Thus, we propose that future vector control against An. sinensis and Cx. tritaeniorhynchus in the areas along the Huang-Huai River of central China should target the interface of human activity with domestic animals and adopt before human hosts go to bed at night.","corpus_id":2559019,"score":2},{"doc_id":"22276651","title":"Vector competence of five common mosquito species in the People's Republic of China for Western equine encephalitis virus.","abstract":"Two strains of the Western equine encephalitis virus (WEEV) were first detected and isolated in China in 2001. The maintenance and transmission cycles of WEEV in China are currently not well understood, and the mosquito vectors involved in these cycles are unknown. To understand the ability of the local mosquitoes in China to transmit WEEV, the vector competence of five mosquito species, namely, Culex pipiens pallens Coquillett, Cx. p. quinquefasciatus Say, Aedes (Stegomyia) albopictus Skuse, Ae. ( Stegomyia) aegypti Linnaeus, and C. tritaeniorhynchus Giles, for WEEV were evaluated. Infection rates for Cx. p. pallens, Cx. p. quinquefasciatus, Cx. tritaeniorhynchus, Ae. Albopictus, and Ae. aegypti were 46%, 60%, 80%, 37%, and 25%, respectively. Dissemination rates for the same species were 60%, 61%, 75%, 55%, and 50%, respectively. Transmission rates were 41%, 53%, 57%, and 45% for Cx. p. pallens, Cx. p. quinquefasciatus, Ae. Albopictus, and Ae. Aegypti, respectively. Infection rates were significantly different between species, but the difference between dissemination and transmission rates were nonsignificant. These results suggest that several local mosquito species in China are competent laboratory vectors for WEEV.","corpus_id":8024842,"score":2},{"doc_id":"22382193","title":"Mosquito biting activity on humans & detection of Plasmodium falciparum infection in Anopheles stephensi in Goa, India.","abstract":"BACKGROUND & OBJECTIVES: Knowledge of the bionomics of mosquitoes, especially of disease vectors, is essential to plan appropriate vector avoidance and control strategies. Information on biting activity of vectors during the night hours in different seasons is important for choosing personal protection measures. This study was carried out to find out the composition of mosquito fauna biting on humans and seasonal biting trends in Goa, India. METHODS: Biting activities of all mosquitoes including vectors were studied from 1800 to 0600 h during 85 nights using human volunteers in 14 different localities of three distinct ecotypes in Goa. Seasonal biting trends of vector species were analysed and compared. Seasonal biting periodicity during different phases of night was also studied using William's mean. RESULTS: A total of 4,191 mosquitoes of five genera and 23 species were collected. Ten species belonged to Anopheles, eight to Culex, three to Aedes and one each to Mansonia and Armigeres. Eleven vector species had human hosts, including malaria vectors Anopheles stephensi (1.3%), An. fluviatilis (1.8%), and An. culicifacies (0.76%); filariasis vectors Culex quinquefasciatus (40.8%) and Mansonia uniformis (1.8%); Japanese encephalitis vectors Cx. tritaeniorhynchus (17.4%), Cx. vishnui (7.7%), Cx. pseudovishnui (0.1%), and Cx. gelidus (2.4%); and dengue and chikungunya vectors Aedes albopictus (0.9%) and Ae. aegypti (0.6%). Two An. stephensi of the total 831 female anophelines, were found positive for P. falciparum sporozoites. The entomological inoculation rate (EIR) of P. falciparum was 18.1 and 2.35 for Panaji city and Goa, respectively. INTERPRETATION & CONCLUSIONS: Most of the mosquito vector species were collected in all seasons and throughout the scotophase. Biting rates of different vector species differed during different phases of night and seasons. Personal protection methods could be used to stop vector-host contact.","corpus_id":30476903,"score":2},{"doc_id":"22403307","title":"Mosquito infection studies with Aotus monkeys and humans infected with the Chesson strain of Plasmodiun vivax.","abstract":"Oocyst counts were compared between mosquitoes that fed on humans versus mosquitoes that fed on Aotus monkeys, both of which were infected with the Chesson strain of Plasmodium vivax. Oocyst counts obtained from mosquitoes fed on humans were almost 10-fold higher in number. Mosquitoes were more likely to be infected and with a higher rate of infection when they fed on monkeys before the peak in the asexual parasite count. Mosquitoes that fed on humans were more likely to be more heavily infected when fed after the peak in the asexual count. Of several species of owl monkeys, Aotus vociferans was infected at a higher frequency. On the basis of oocyst counts, Anopheles dirus were the most susceptible and An. maculatus were the least susceptible of the mosquito species tested.","corpus_id":20460805,"score":2},{"doc_id":"22776520","title":"Vector capacity of Anopheles sinensis in malaria outbreak areas of central China.","abstract":"BACKGROUND: Both falciparum and vivax malaria were historically prevalent in China with high incidence. With the control efforts, the annual incidence in the whole country has reduced to 0.0001% except in some areas in the southern borders after 2000. Despite this, the re-emergence or outbreak of malaria was unavoidable in central China during 2005-2007. In order to understand the role of the vector in the transmission of malaria during the outbreak period, the vector capacity of An. sinensis in Huanghuai valley of central China was investigated. FINDINGS: The study was undertaken in two sites, namely Huaiyuan county of Anhui province and Yongcheng county of Henan province. In each county, malaria cases were recorded for recent years, and transmission risk factors for each study village including anti-mosquito facilities and total number of livestock were recorded by visiting each household in the study sites. The specimens of mosquitoes were collected in two villages, and population density and species in each study site were recorded after the identification of different species, and the blood-fed mosquitoes were tested by ring precipitation test. Finally, various indicators were calculated to estimate vector capacity or dynamics, including mosquito biting rate (MBR), human blood index (HBI), and the parous rates (M). Finally, the vector capacity, as an important indicator of malaria transmission to predict the potential recurrence of malaria, was estimated and compared in each study site. About 93.0% of 80 households in Huaiyuan and 89.3% of 192 households in Yongcheng had anti-mosquito facilities. No cattle or pigs were found, only less than 10 sheep were found in each study village. A total of 94 and 107 Anopheles spp. mosquitos were captured in two study sites, respectively, and all of An. sinensis were morphologically identified. It was found that mosquito blood-feeding peak was between 9:00 pm and 12:00 pm. Man biting rate of An. sinensis was 6.0957 and 5.8621 (mosquitoes/people/night) estimated by using half-night human bait trap method and full-capture method, respectively. Human blood indexes (HBI) were 0.6667 (6/9) and 0.6429 (18/28), and man-biting habits were 0.2667 and 0.2572 in two sites, respectively. Therefore, the expectation of infective life and vector capacity of An. sinensis was 0.3649-0.4761 and 0.5502-0.7740, respectively, in Huanhuai valley of central China where the outbreak occurred, which is much higher than that in the previous years without malaria outbreak. CONCLUSIONS: This study suggests that vivax malaria outbreak in Huanhuai valley is highly related to the enhancement in vector capacity of An. sinensis for P. vivax, which is attributed to the local residents' habits and the remarkable drop in the number of large livestock leading to disappearance of traditional biological barriers.","corpus_id":17026,"score":2},{"doc_id":"23243112","title":"Mosquito species composition and Plasmodium vivax infection rates for Korean army bases near the demilitarized zone in the Republic of Korea, 2011.","abstract":"Vivax malaria is a significant military and civilian health threat in northern Republic of Korea (ROK). Mosquito collections were performed at two ROK army installations, Paju near the demilitarized zone (DMZ) using black light traps in 2011. The DMZ, a 4 km wide border, is the northernmost point of the ROK and separates the ROK from the Democratic People's Republic of Korea (DPRK). Anopheles spp. were identified by polymerase chain reaction and screened for Plasmodium vivax sporozoites. Of 4,354 female Anopheles mosquitoes identified, Anopheles kleini (61.8%) was the most frequently collected, followed by Anopheles pullus (16.0%), Anopheles belenrae (9.0%), Anopheles sinensis (7.4%), Anopheles sineroides (4.2%), and Anopheles lesteri (1.6%). Anopheles kleini, An. pullus, and An. sineroides showed the highest population densities in June, whereas population densities were highest for An. belenrae, An. lesteri, and An. sinensis in August. The maximum likelihood estimation (estimated number of positive mosquitoes/1,000) for P. vivax was highest for An. lesteri (28.9), followed by An. sineroides (23.3), An. belenrae (15.8), An. sinensis (9.6), An. pullus (5.8) and An. kleini (4.2). The seasonal maximum likelihood estimation (MLE) values were variable among Anopheles species. Anopheles belenrae, An. Pullus, and An. sineroides showed the highest seasonal MLE's in July, whereas An. lesteri and An. sinensis exhibited the highest seasonal MLEs in September and An. kleini during August. This is the first report implicating An. sineroides as a vector of P. vivax in the ROK, and extends our knowledge of the distribution and potential role in malaria transmission.","corpus_id":9395322,"score":2},{"doc_id":"23373272","title":"[Establishment of early warning system of malaria epidemic situation in Jiangsu Province I impact of temperature on development of Plasmodium vivax in Anopheles sinensis in Jiangsu Province].","abstract":"OBJECTIVE: To observe the developmental threshold temperature and the effective accumulated temperature of Plasmodium vivax sporozoites in Anopheles sinensis in Jiangsu Province, and to analyze the impact of temperature on the development of Plasmodium vivax. METHODS: The Anopheles sinensis mosquitoes were maintained under different temperatures of 16 +/- 0.5, 19 +/- 0.5, 22 +/- 0.5, 25 +/- 0.5, 28 +/- 0.5 degrees C and 31 +/- 0.5 degrees C in incubators after membrane feeding with Plasmodium vivax infected blood at laboratory. The salivary glands of Anopheles sinensis were dissected to confirm the development of sporozoite under different temperatures, and the developmental threshold temperature and the effective accumulated temperature of Plasmodium vivax sporozoites in Anopheles sinensis were calculated. The theoretical number of generations of Plasmodium vivax in Anopheles sinensis per year was calculated based on the average monthly temperatures of 13 municipalities in Jiangsu Province. RESULTS: The average developmental threshold temperature of Plasmodium vivax in Anopheles sinensis in Jiangsu Province was 15.31 degrees C, the average effective accumulated temperature was 109.81 day-degrees, and the optimal temperature for the proliferation of Plasmodium vivax was 25-28 degrees C. The theoretical generation number of Plasmodium vivax in sinensis in south Jiangsu was 1-3 generations being more than that in the north of the province. CONCLUSIONS: Temperature is one of the important influencing factors for the development of Plasmodium. The chance for Anopheles sinensis to transmit malaria increases under the temperature of 25-28 degrees C. However, other factors should be considered in the establishment of early warning system of malaria.","corpus_id":37355768,"score":2},{"doc_id":"23658824","title":"An impossible journey? The development of Plasmodium falciparum NF54 in Culex quinquefasciatus.","abstract":"Although Anopheles mosquitoes are the vectors for human Plasmodium spp., there are also other mosquito species-among them culicines (Culex spp., Aedes spp.)-present in malaria-endemic areas. Culicine mosquitoes transmit arboviruses and filarial worms to humans and are vectors for avian Plasmodium spp., but have never been observed to transmit human Plasmodium spp. When ingested by a culicine mosquito, parasites could either face an environment that does not allow development due to biologic incompatibility or be actively killed by the mosquito's immune system. In the latter case, the molecular mechanism of killing must be sufficiently powerful that Plasmodium is not able to overcome it. To investigate how human malaria parasites develop in culicine mosquitoes, we infected Culex quinquefasciatus with Plasmodium falciparum NF54 and monitored development of parasites in the blood bolus and midgut epithelium at different time points. Our results reveal that ookinetes develop in the midgut lumen of C. quinquefasciatus in slightly lower numbers than in Anopheles gambiae G3. After 30 hours, parasites have invaded the midgut and can be observed on the basal side of the midgut epithelium by confocal and transmission electron microscopy. Very few of the parasites in C. quinquefasciatus are alive, most of them are lysed. Eight days after the mosquito's blood meal, no oocysts can be found in C. quinquefasciatus. Our results suggest that the mosquito immune system could be involved in parasite killing early in development after ookinetes have crossed the midgut epithelium and come in contact with the mosquito hemolymph.","corpus_id":16989353,"score":2},{"doc_id":"23768077","title":"Susceptibility of Anopheles sinensis to Plasmodium vivax in malarial outbreak areas of central China.","abstract":"BACKGROUND: Anopheles sinensis, Anopheles anthropophagus, Anopheles minimus and Anopheles dirus are the major vectors of malaria transmission in China. Anopheles sinensis is considered a secondary vector due to its relatively low malaria-transmission ability. However, in 2005, an outbreak of over 40,000 Plasmodium vivax malaria cases was reported in areas where Anopheles sinensis was the only major vector. Therefore, it is necessary to reassess the malaria transmission ability of this vector species in China. METHODS: Laboratory colonies of An. sinensis and An. anthropophagus, and first-generation progeny (F1) of An. sinensis that had been collected in central China, were infected by direct membrane feeding assay with mono-vivax gametocyte-containing blood collected from vivax-infected patients. The mosquitoes were kept for 7 to 14 days post-blood feeding to allow parasites to develop into oocysts and sporozoites. Infectivity was measured by dissecting midguts and salivary glands. The presence of oocysts and sporozoites was determined by microscopy at 7 and 14 days post-blood feeding, and the numbers of gametocytes and asexual parasites, as well as mosquito parasite infections, were determined. RESULTS: The positive oocyst and sporozoite feed rates of the 142 pairs of lab-colony An. sinensis and An. anthropophagus were not significantly different, and the same results were found with the 10 pairs of laboratory and F1 An. sinensis. An. sinensis had more oocysts/midgut at 7 days post-feeding than An. anthropophagus, but the gametocytemia, asexual parasitemia, and ratio of macrogametocytes to microgametocytes, did not correlate with either oocyst or sporozoite infection. However, in the oocyst-positive mosquitoes, there was a correlation between gametocytemia and the average oocyst number/midgut. CONCLUSIONS: The susceptibility of An. sinensis (both laboratory and F1) to P. vivax-infected blood is similar to Anopheles anthropophagus, when evaluated by membrane feeding assay under laboratory conditions. In recent years, in central China, the vivax malaria transmission ability of An. sinensis has probably been underestimated. Further studies of this species in other regions are needed. An. sinensis could also be a good candidate vector for evaluating candidate malaria transmission-blocking vaccines (TBV).","corpus_id":1492680,"score":2},{"doc_id":"24034528","title":"The Anopheles community and the role of Anopheles minimus on malaria transmission on the China-Myanmar border.","abstract":"BACKGROUND: Malaria around the China-Myanmar border is a serious health problem in the countries of South-East Asia. An. minimus is a principle malaria vector with a wide geographic distribution in this area. Malaria is endemic along the boundary between Yunnan province in China and the Kachin State of Myanmar where the local Anopheles community (species composition) and the malaria transmission vectors have never been clarified. METHODS: Adult Anopheles specimens were collected using CDC light traps in four villages along the border of China and Myanmar from May 2012 to April 2013. Morphological and molecular identification of mosquito adults confirmed the species of Anopheles. Blood-meal identification using the female abdomens was conducted using multiplex PCR. For sporozoite detection in An. minimus, sets of 10 female salivary glands were pooled and identified with SSU rDNA using nested PCR. Monthly abundance of An. minimus populations during the year was documented. The diversity of Anopheles and the role of An. minimus on malaria transmission in this border area were analyzed. RESULTS: 4,833 adult mosquitoes in the genus Anopheles were collected and morphologically identified to species or species complex. The Anopheles community is comprised of 13 species, and 78.83% of our total specimens belonged to An. minimus s.l., followed by An. maculatus (5.55%) and the An. culicifacies complex (4.03%). The quantity of trapped An. minimus in the rainy season of malaria transmission was greater than during the non-malarial dry season, and a peak was found in May 2012. An. minimus fed on the blood of four animals: humans (79.8%), cattle (10.6%), pigs (5.8%) and dogs (3.8%). 1,500 females of An. minimus were pooled into 150 samples and tested for sporozoites: only 1 pooled sample was found to have sporozoites of Plasmodium vivax. CONCLUSION: Anopheles is abundant with An. minimus being the dominant species and having a high human blood index along the China-Myanmar border. The sporozoites in An. minimus were determined to be Plasmodium vivax with a 0.07-0.7% infection rate.","corpus_id":7811668,"score":2},{"doc_id":"24146951","title":"Mosquitoes of Western Yunnan Province, China: seasonal abundance, diversity, and arbovirus associations.","abstract":"OBJECTIVE: The western borderland between Yunnan Province, China, and Myanmar is characterized by a climate that facilitates year-round production of mosquitoes. Numerous mosquito-transmitted viruses, including Japanese encephalitis virus circulate in this area. This project was to describe seasonal patterns in mosquito species abundance and arbovirus activity in the mosquito populations. METHODS: Mosquitoes were collected in Mangshi and Ruili cities of Dehong Prefecture near the border of China and Burma in Yunnan Province, the Peoples Republic of China in 2010. We monitored mosquito species abundance for a 12-month period using ultraviolet light, carbon dioxide baited CDC light and gravid traps; and tested the captured mosquitoes for the presence of virus to evaluate mosquito-virus associations in rural/agricultural settings in the area. RESULTS: A total of 43 species of mosquitoes from seven genera were collected, including 15 Culex species, 15 Anopheles spp., four Aedes spp., three Armigeres spp., one Mimomyia spp., two Uranotaenia spp. and three Mansonia spp.. Species richness and diversity varied between Mangshi and Ruili. Culex tritaeniorhynchus, Culex quinquefasciatus, Anopheles sinensis and Anopheles peditaeniatus were the most abundant species in both sampling sites. Ultraviolet light traps collected more specimens than CDC light traps baited with dry ice, though both collected the same variety of mosquito species. The CDC gravid trap was the most effective trap for capture of Culex quinquefasciatus, a species underrepresented in light trap collections. A total of 26 virus strains were isolated, which included 13 strains of Japanese encephalitis virus, four strains of Getah virus, one strain of Oya virus, one strain from the orbivirus genus, and seven strains of Culex pipien pallens densovirus. CONCLUSIONS: The present study illustrates the value of monitoring mosquito populations and mosquito-transmitted viruses year-round in areas where the climate supports year-round adult mosquito activity.","corpus_id":4032496,"score":2},{"doc_id":"24359307","title":"Experimental Plasmodium vivax infection of key Anopheles species from the Brazilian Amazon.","abstract":"BACKGROUND: Anopheles darlingi is the major malaria vector in countries located in the Amazon region. Anopheles aquasalis and Anopheles albitarsis s.l. are also proven vectors in this region. Anopheles nuneztovari s.l. and Anopheles triannulatus s.l. were found infected with Plasmodium vivax; however, their status as vectors is not yet well defined. Knowledge of susceptibility of Amazon anopheline populations to Plasmodium infection is necessary to better understand their vector capacity. Laboratory colonization of An. darlingi, the main Amazon vector, has proven to be difficult and presently An. aquasalis is the only available autonomous colony. METHODS: Larvae of An. darlingi, An. albitarsis s.l., An. nuneztovari s.l. and An. triannulatus s.l. were collected in the field and reared until adult stage. Adults of An. aquasalis were obtained from a well-established colony. Mosquitoes were blood-fed using a membrane-feeding device containing infected blood from malarial patients. The infection of the distinct Anopheles species was evaluated by the impact variance of the following parameters: (a) parasitaemia density; (b) blood serum inactivation of the infective bloodmeal; (c) influence of gametocyte number on infection rates and number of oocysts. The goal of this work was to compare the susceptibility to P. vivax of four field-collected Anopheles species with colonized An. aquasalis. RESULTS: All Anopheles species tested were susceptible to P. vivax infection, nevertheless the proportion of infected mosquitoes and the infection intensity measured by oocyst number varied significantly among species. Inactivation of the blood serum prior to mosquito feeding increased infection rates in An. darlingi and An. triannulatus s.l., but was diminished in An. albitarsis s.l. and An. aquasalis. There was a positive correlation between gametocyte density and the infection rate in all tests (Z = -8.37; p < 0.001) but varied among the mosquito species. Anopheles albitarsis s.l., An. aquasalis and An. nuneztovari s.l. had higher infection rates than An. darlingi. CONCLUSION: All field-collected Anopheles species, as well as colonized An. aquasalis are susceptible to experimental P. vivax infections by membrane feeding assays. Anopheles darlingi, An. albitarsis s.l. and An. aquasalis are very susceptible to P. vivax infection. However, colonized An. aquasalis mosquitoes showed the higher infection intensity represented by infection rate and oocyst numbers. This study is the first to characterize experimental development of Plasmodium infections in Amazon Anopheles vectors and also to endorse that P. vivax infection of colonized An. aquasalis is a feasible laboratory model.","corpus_id":15098984,"score":2},{"doc_id":"24534811","title":"Infection of laboratory-colonized Anopheles darlingi mosquitoes by Plasmodium vivax.","abstract":"Anopheles darlingi Root is the most important malaria vector in the Amazonia region of South America. However, continuous propagation of An. darlingi in the laboratory has been elusive, limiting entomological, genetic/genomic, and vector-pathogen interaction studies of this mosquito species. Here, we report the establishment of an An. darlingi colony derived from wild-caught mosquitoes obtained in the northeastern Peruvian Amazon region of Iquitos in the Loreto Department. We show that the numbers of eggs, larvae, pupae, and adults continue to rise at least to the F6 generation. Comparison of feeding Plasmodium vivax ex vivo of F4 and F5 to F1 generation mosquitoes showed the comparable presence of oocysts and sporozoites, with numbers that corresponded to blood-stage asexual parasitemia and gametocytemia, confirming P. vivax vectorial capacity in the colonized mosquitoes. These results provide new avenues for research on An. darlingi biology and study of An. darlingi-Plasmodium interactions.","corpus_id":13500805,"score":2},{"doc_id":"24820559","title":"Infection and dissemination of West Nile virus in China by the potential vector, Culex pipiens pallens.","abstract":"The distribution of the West Nile virus (WNV) in the organs and tissues of the mosquito Culex pipiens pallens, a potential vector of WNV in China, was investigated up to 14 days after oral infection. The WNV antigen was detected in paraffin-embedded mosquitoes using immunocytochemistry and viral titers of post-infected mosquitoes determined by plaque assay. Viral titers sharply decreased 24 h post-infection, were undetectable for the first few days, then rose over the course of infection. The first midgut infection appeared after one day, and the overall infection rate (based on midgut infection) was 43.9%. Other tissues, including hindgut, foregut, ovarian follicles, Malpighian tubules, and ommatidia, showed weak WNV antigens as early as three days post-infection. Staining in the salivary glands first appeared after seven days, and the salivary gland infection rate on the 14th day was 37.5%. Specimens with no detectable WNV antigens in any tissues, and with positive results confined to the midgut, anterior midgut, and hindgut, were observed on the 14th day. The route of viral dissemination from the midgut, and the relative importance of amplifying tissues in mosquitoes' susceptibility to infection, were evaluated. The results indicate that Cx. p. pallens has the ability to harbor WNV throughout its alimentary system and that midgut epithelial cells may be the initial site of the replication of this virus in this species.","corpus_id":27558654,"score":2},{"doc_id":"25059361","title":"[Investigation on mosquitoes and mosquito-borne viruses in Dehong prefecture, Yunnan province, 2007 and 2010].","abstract":"OBJECTIVE: To investigate the distribution patterns of mosquito and mosquito-borne viruses in Dehong prefecture, Yunnan province, China. METHODS: Mosquito samples were collected using the mosquito traps from five counties of Dehong prefecture on July, 2007 and 2010. Mosquito were cell cultured for viral isolation, and positive isolates were identified using RT-PCR and sequence analysis. RESULTS: A total of 43 634 mosquito comprised of 29 species representing six genera were collected. Culex tritaeniorhynchus and Anopheles sinensis comprised 78.69% and 14.77% of the total. Six strains of viruses were isolated from the mosquito pools. RT-PCR and phylogenetic analysis revealed three strains from Cx. tritaeniorhynchus, identified as genotype I Japanese encephalitis virus (JEV). One strain was identified from Cx. tritaeniorhynchus, as Getah virus (GETV). Two strains isolated from Cx. tritaeniorhynchus and Anopheles vagus were identified as Culex pipiens pallens Densovirus (CppDNV). CONCLUSION: Cx. tritaeniorhynchus had been the major species of mosquito and mainly transmitting vector of mosquito-borne viruses in Dehong prefecture. Genotype I JEV, GETV and CppDNV were the vectors causing transmission of mosquito-borne diseases in this area. Data from phylogenetic analysis showed that these newly discovered isolates seemed to have had close relationship with those viruses previously circulating in Yunnan and other provinces of China.","corpus_id":25080206,"score":2},{"doc_id":"25224069","title":"Monitoring Plasmodium vivax chloroquine sensitivity along China-Myanmar border of Yunnan Province, China during 2008-2013.","abstract":"BACKGROUND: Plasmodium vivax is the most widespread of the malaria parasites infecting human hosts. In malaria-eliminating settings, both imported and local malaria predominantly occurs in border areas, and most of them are P. vivax. Chloroquine (CQ) is the first-line drug for P. vivax treatment in China. To understand CQ sensitivity in P. vivax, in vivo monitoring of CQ resistance was conducted along the China-Myanmar border from 2008 to 2013. METHODS: Eligible patients with mono-infections of P. vivax were recruited to this study after obtaining full informed consent. CQ tablets for different categories of kg body weight ranges were given once a day for three days. Patients were followed up for 28 days. PCR was conducted to distinguish between re-infection and recrudescence, to confirm the Plasmodium species. The data were entered and analysed by the Kaplan-Meier method. Treatment outcome and sensitivity were classified according to the WHO recommended standards. RESULTS: 603 patients were completed valid follow-up. The fever clearance time and asexual parasite clearance times were, respectively, 22.2 ± 10.2 and 38.1 ± 12.6 hours. 594 (98.5%) patients were adequate clinical and parasitological response (ACPR), and nine (1.5%) patients, who were late clinical failure (LCF) or resistant response level I (RI), were imported from the neighbouring districts of Myanmar. CONCLUSION: In terms of efficacy, CQ is still effective for vivax malaria treatment. Plasmodium vivax CQ sensitivity had not significantly changed along the China-Myanmar border of Yunnan Province, China.","corpus_id":15343343,"score":2},{"doc_id":"25481362","title":"Enhancing longevity of Plasmodium vivax and P. falciparum sporozoites after dissection from mosquito salivary glands.","abstract":"The pre-erythrocytic stages of Plasmodium vivax and Plasmodium falciparum remain challenging for experimental research in part due to limited access to sporozoites. An important factor limiting availability is the laboratory support required for producing infected mosquitoes and the ephemeral nature of isolated extracellular sporozoites. This study was undertaken to investigate methods to improve the availability of this limited resource by extending the longevity of the extracellular sporozoites after mosquito dissection. Our goal in this study was to determine whether buffer conditions more closely mimicking the insect microenvironment could prolong longevity of ex vivo P. vivax and P. falciparum sporozoites. The study compared the current standard dissection buffer RPMI1640 to Hank's Balanced Salt Solution with 1g/L glucose (HBSS-1) or 2g/L glucose (HBSS-2) and Grace's Insect Medium for ability to extend longevity of ex vivo P. vivax and P. falciparum sporozoites. The effect of each buffer on sporozoite viability was evaluated by measuring sporozoite gliding motility at 0, 4, 8, and 24h post-dissection from mosquito salivary glands. Comparisons of mean gliding percentages of ex vivo sporozoites in the different buffers and time points found that RPMI and Grace's both showed strong gliding at 0h. In contrast, by 4h post-dissection sporozoites in RPMI consistently had the lowest gliding activity, whereas sporozoites in Grace's had significantly more gliding compared to all other buffers at almost all time points. Our results indicate that P. vivax and P. falciparum sporozoites maintained in insect media rather than the standard dissection buffer RPMI and HBSS retain viability better over time.","corpus_id":207314427,"score":2},{"doc_id":"25502034","title":"Measure post-bloodmeal dispersal of mosquitoes and duration of radioactivity by using the isotope ³²P.","abstract":"The radioactive isotope (32)P-labeled disodium phosphate (Na₂H(32)PO₄) was injected via the jugular vein into a cow kept in a shed in Maozhuang Village, Cao Township of Shanxian County, China. Over the following 5 d, mosquitoes feeding on the cow were captured at distances up to 400 m to determine dispersal distance. The duration of radioactivity in the cow and marked mosquitoes was 10 d. The results showed that after blood feeding, Anopheles sinensis and Culex tritaeniorhynchus temporarily rested in the cattle shed and then flew outdoors. In contrast, Culex pipiens pallens remained in the cattle shed after feeding. These findings confirmed that local An. sinensis and Cx. tritaeniorhynchus were partially endophilic and tended to rest out of doors, whereas Cx. pipiens pallens was endophilic. For marked An. sinensis and Cx. tritaeniorhynchus, there was a significant tendency for dispersal to be in a northeast and east direction, probably because of the presence of heavy shading by an agricultural field, a small river for mosquito oviposition sites, and locations downwind from the blood source. The furthest flight distances for An. sinensis and Cx. tritaeniorhynchus were 210 and 240 m; therefore, control of these mosquitoes should include resting places indoors and outdoors within a radius of 250 m from confirmed cases.","corpus_id":205170445,"score":2},{"doc_id":"25958156","title":"Complete sporogony of Plasmodium relictum (lineage pGRW4) in mosquitoes Culex pipiens pipiens, with implications on avian malaria epidemiology.","abstract":"Plasmodium relictum (lineage pGRW4) causes malaria in birds and is actively transmitted in countries with warm climates and also temperate regions of the New World. In Europe, the lineage pGRW4 has been frequently reported in many species of Afrotropical migrants after their arrival from wintering grounds, but is rare in European resident birds. Obstacles for transmission of this parasite in Europe have not been identified. Culex quinquefasciatus is an effective vector of pGRW4 malaria, but this mosquito is absent from temperate regions of Eurasia. It remains unclear if the lineage pGRW4 completes sporogony in European species of mosquitoes. Here we compare the sporogonic development of P. relictum (pGRW4) in experimentally infected mosquitoes Culex pipiens pipiens form molestus, C. quinquefasciatus, and Ochlerotatus cantans. The pGRW4 parasite was isolated from a garden warbler Sylvia borin, multiplied, and used to infect laboratory-reared Culex spp. and wild-caught Ochlerotatus mosquitoes by allowing them to take blood meals on infected birds. The exposed females were maintained at a mean laboratory temperature of 19 °C, which ranged between 14 °C at night and 24 °C during daytime. They were dissected on intervals to study the development of sporogonic stages. Only ookinetes developed in O. cantans; sporogonic development was abortive. The parasite completed sporogony in both Culex species, with similar patterns of development, and sporozoites were reported in the salivary glands 16 days after infection. The presence of sporogonic stages of the lineage pGRW4 in mosquitoes was confirmed by PCR-based testing of (1) the sporozoites present in salivary glands and (2) the single oocysts, which were obtained by laser microdissection from infected mosquito midguts. This study shows that P. relictum (pGRW4) completes sporogony in C. p. pipiens at relatively low temperatures. We conclude that there are no restrictions for spreading this bird infection in Europe from the point of view of vector availability and temperature necessary for sporogony. Other factors should be considered and were discussed for the explanation of rare reports of this malaria parasite in Europe.","corpus_id":17252261,"score":2},{"doc_id":"25975552","title":"[Isolation and identification of mosquito-borne arboviruses in Yuncheng city, Shanxi province, 2012].","abstract":"OBJECTIVE: To investigate the species and distribution of mosquitoes and mosquito-borne arboviruses in Yuncheng city of Shanxi province, China. METHODS: Mosquito samples were collected in 19 collection sites from Linyi county and Yongji city in Yuncheng city, in August, 2012. After identification and classification, all the specimens were homogenized and centrifuged to acquire supernatant before being inoculated to both C6/36 and BHK21 cells for viral isolation. Positive isolates were identified with arbovirus species-specific primers under RT-PCR, for further sequencing and phylogenetic analysis. RESULTS: A total of 10 455 mosquitoes of 7 species in 4 genuese were collected. The predominant mosquito species in Linyi county was Culex pipens pallens (91.96%, 3 911/4 253), but the one in Yongji city was Culex tritaeniorhynchus (72.85%, 4 518/6 202). A total of 23 strains of viruses were isolated from the mosquito pools. 15 strains from Culex tritaeniorhynchus and Culex pipens pallens were identified as genotype I Japanese encephalitis virus (JEV). Four strains from Culex pipens pallens were identified as Culex flavivirus (CxFV). Three strains from Culex pipens pallens were identified as Culex pipiens pallens densovirus (CppDNV). One strain from Armigeres subalbatus and Aedes albopictus was identified as Getah virus (GETV). CONCLUSION: Four kinds of arboviruses were isolated from the mosquito pools, including GETV and CxFV, which were isolated and documented in Shanxi province for the first time. In the city of Yuncheng, Culex tritaeniorhynchus had been the predominant species and major vector for transmitting JEV. Genotype I JEV remained the major JEV circulating in the local natural environment.","corpus_id":43359136,"score":2},{"doc_id":"26259952","title":"The suitability of laboratory-bred Anopheles cracens for the production of Plasmodium vivax sporozoites.","abstract":"BACKGROUND: A stenogamous colony of Anopheles cracens (A. dirus B) established 20 years ago in a Thai insectary proved susceptible to Plasmodium vivax. However, routine sporozoite production by feeding on field-collected blood samples has not been described. The setting-up of an A. cracens colony in an insectary on the Thai-Myanmar border and the process of using P. vivax field samples for the production of infectious sporozoites are described. METHODS: The colony was started in 2012 from egg batches that were sent from the Department of Parasitology, Faculty of Medicine, University of Chiang Mai, to the Shoklo Malaria Research Unit (SMRU), on wet filter paper in sealed Petri dishes. From May 2013 to December 2014, P. vivax-infected blood samples collected from patients seeking care at SMRU clinics were used for membrane feeding assays and sporozoite production. RESULTS: Mosquitoes were fed on blood samples from 55 patients, and for 38 (69 %) this led to the production sporozoites. The average number of sporozoites obtained per mosquito was 26,112 (range 328-79,310). Gametocytaemia was not correlated with mosquito infectiousness (p = 0.82), or with the number of the sporozoites produced (Spearman's ρ = -0.016, p = 0.905). Infectiousness did not vary with the date of collection or the age of the patient. Mosquito survival was not correlated with sporozoite load (Spearman's ρ = 0.179, p = 0.282). CONCLUSION: Consistent and routine P. vivax sporozoites production confirms that A. cracens is highly susceptible to P. vivax infection. Laboratory-bred colonies of this vector are suitable for experimental transmission protocols and thus constitute a valuable resource.","corpus_id":11072837,"score":2},{"doc_id":"26666959","title":"Sporogony and sporozoite rates of avian malaria parasites in wild Culex pipiens pallens and C. inatomii in Japan.","abstract":"BACKGROUND: Malaria infection in mosquitoes is traditionally detected by microscopic examination for Plasmodium oocysts and sporozoites. Although PCR is now widely used, the presence of parasite DNA in a mosquito does not prove that sporogony is achieved. Thus, detection of sporozoites by microscopy is still required to definitively identify vector mosquitoes. The aim of this study was to confirm sporogony of avian Plasmodium spp. in Culex pipiens pallens and C. inatomii caught from the wild. FINDINGS: Mosquitoes collected at two sites in Japan were dissected and examined by microscopy for Plasmodium oocysts and sporozoites. DNA was extracted from the midgut and salivary gland of infected mosquitoes, and the infecting Plasmodium species was identified by sequencing 478 bp of cytochrome b. Oocysts, or both oocysts and sporozoites, were found in 3.94 and 0.46 % of C. p. pallens and C. inatomii, respectively. Four (CXPIP09, GRW4, GRW11 and SGS1) and three cytochrome b lineages (CXINA01, CXINA02 and CXQUI01) were confirmed to achieve sporogony in C. p. pallens and C. inatomii, respectively. One mosquito each of C. p. pallens and C. inatomii was co-infected with two different Plasmodium lineages. CONCLUSIONS: These findings demonstrate that C. p. pallens and C. inatomii are natural vectors of four and three lineages of avian Plasmodium spp., respectively. The data indicate that a systematic procedure combining microscopy and PCR is a feasible and reliable approach to identify natural vectors of wildlife malaria.","corpus_id":6537285,"score":2},{"doc_id":"26816489","title":"Resistance Level of Mosquito Species (Diptera: Culicidae) from Shandong Province, China.","abstract":"This study describes the aquatic habitats, species composition, and the insecticide resistance level of the mosquito Culex pipiens pallens in Shandong Province, China. A cross-sectional survey of mosquito larval habitats was conducted from May to November 2014 to determine the species composition and larval abundance. Larvae were collected using the standard dipping technique, and a total of four habitat types were sampled. The fourth instar larvae of Cx. pipiens pallens collected in each habitat type were tested for resistance to five insecticides according to a WHO bioassay. A total of 7,281 mosquito larvae were collected, of which 399 (5.48%) were categorized as Anopheles mosquito larvae (An. sinensis), 6636 (91.14%) as culicine larvae (Cx. pipiens pallens, Cx. tritaeniorhynchus, Cx. halifaxii, and Cx. bitaeniorhynchus), 213 (2.93%) as Armigeres larvae, and 33 (0.45%) as Aedes larvae (Aedes albopictus). In addition, a total of 1,149 mosquito pupae were collected. Culex larvae were distributed in all habitats investigated. Tukeys HSD analysis showed that roadside drainages were the most productive habitat type for Culex larvae. Armigeres species were found only in drains, Aedes only in water tanks, and Anopheles in water that was comparatively clear and rich in emergent plants. Bioassay showed that the maximum resistance level of Cx. pipiens pallens was to deltamethrin, while it was lowest to plifenate. The productivity of various mosquitoes in different habitat types is very heterogeneous. It is particularly important to modify human activity and the environment to achieve effective mosquito vector control. For effective larval control, the type of habitat should be considered, and the most productive habitat type should be given priority in mosquito abatement programs.","corpus_id":8282206,"score":2},{"doc_id":"26822406","title":"Plasmodium vivax gametocyte infectivity in sub-microscopic infections.","abstract":"BACKGROUND: The use of molecular techniques has put in the spotlight the existence of a large mass of malaria sub-microscopic infections among apparently healthy populations. These sub-microscopic infections are considered an important pool for maintained malaria transmission. METHODS: In order to assess the appearance of Plasmodium vivax gametocytes in circulation, gametocyte density and the parasite infectivity to Anopheles mosquitoes, a study was designed to compare three groups of volunteers either experimentally infected with P. vivax sporozoites (early infections; n = 16) or naturally infected patients (acute malaria, n = 16 and asymptomatic, n = 14). In order to determine gametocyte stage, a quantitative reverse transcriptase PCR (RT-qPCR) assay targeting two sexual stage-specific molecular markers was used. Parasite infectivity was assessed by membrane feeding assays (MFA). RESULTS: In early infections P. vivax gametocytes could be detected starting at day 7 without giving rise to infected mosquitoes during 13 days of follow-up. Asymptomatic carriers, with presumably long-lasting infections, presented the highest proportion of mature gametocytes and were as infective as acute patients. CONCLUSIONS: This study shows the potential role of P. vivax asymptomatic carriers in malaria transmission should be considered when new policies are envisioned to redirect malaria control strategies towards targeting asymptomatic infections as a tool for malaria elimination.","corpus_id":3912235,"score":2},{"doc_id":"26944051","title":"Small-scale land-use variability affects Anopheles spp. distribution and concomitant Plasmodium infection in humans and mosquito vectors in southeastern Madagascar.","abstract":"BACKGROUND: Deforestation and land-use change have the potential to alter human exposure to malaria. A large percentage of Madagascar's original forest cover has been lost to slash-and-burn agriculture, and malaria is one of the top causes of mortality on the island. In this study, the influence of land-use on the distribution of Plasmodium vectors and concomitant Plasmodium infection in humans and mosquito vectors was examined in the southeastern rainforests of Madagascar. METHODS: From June to August 2013, health assessments were conducted on individuals living in sixty randomly selected households in six villages bordering Ranomafana National Park. Humans were screened for malaria using species-specific rapid diagnostic tests (RDTs), and surveyed about insecticide-treated bed net (ITN) usage. Concurrently, mosquitoes were captured in villages and associated forest and agricultural sites. All captured female Anopheline mosquitoes were screened for Plasmodium spp. using a circumsporozoite enzyme-linked immunosorbent assay (csELISA). RESULTS: Anopheles spp. dominated the mosquito communities of agricultural and village land-use sites, accounting for 41.4 and 31.4 % of mosquitoes captured respectively, whereas Anopheles spp. accounted for only 1.6 % of mosquitoes captured from forest sites. Interestingly, most Anopheles spp. ( 67.7 %) were captured in agricultural sites in close proximity to animal pens, and 90.8 % of Anopheles mosquitoes captured in agricultural sites were known vectors of malaria. Three Anopheline mosquitoes (0.7 %) were positive for malaria (Plasmodium vivax-210) and all positive mosquitoes were collected from agricultural or village land-use sites. Ten humans (3.7 %) tested were positive for P. falciparum, and 23.3 % of those surveyed reported never sleeping under ITNs. CONCLUSIONS: This study presents the first report of malaria surveillance in humans and the environment in southeastern Madagascar. These findings suggest that even during the winter, malaria species are present in both humans and mosquitoes; with P. falciparum found in humans, and evidence of P. vivax-210 in mosquito vectors. The presence of P. vivax in resident vectors, but not humans may relate to the high incidence of humans lacking the Duffy protein. The majority of mosquito vectors were found in agricultural land-use sites, in particular near livestock pens. These findings have the potential to inform and improve targeted malaria control and prevention strategies in the region.","corpus_id":15259771,"score":2},{"doc_id":"26969510","title":"A method to preserve low parasitaemia Plasmodium-infected avian blood for host and vector infectivity assays.","abstract":"BACKGROUND: Avian malaria vector competence studies are needed to understand more succinctly complex avian parasite-vector-relations. The lack of vector competence trials may be attributed to the difficulty of obtaining gametocytes for the majority of Plasmodium species and lineages. To conduct avian malaria infectivity assays for those Plasmodium spp. and lineages that are refractory to in vitro cultivation, it is necessary to obtain and preserve for short periods sufficient viable merozoites to infect naïve donor birds to be used as gametocyte donors to infect mosquitoes. Currently, there is only one described method for long-term storage of Plasmodium spp.-infected wild avian blood and it is reliable at a parasitaemia of at least 1%. However, most naturally infected wild-caught birds have a parasitaemia of much less that 1%. To address this problem, a method for short-term storage of infected wild avian blood with low parasitaemia (even ≤ 0.0005%) has been explored and validated. METHODS: To obtain viable infective merozoites, blood was collected from wild birds using a syringe containing the anticoagulant and the red blood cell preservative citrate phosphate dextrose adenine solution (CPDA). Each blood sample was stored at 4 °C for up to 48 h providing sufficient time to determine the species and parasitaemia of Plasmodium spp. in the blood by morphological examination before injecting into donor canaries. Plasmodium spp.--infected blood was inoculated intravenously into canaries and once infection was established, Culex stigmatosoma, Cx. pipiens and Cx. quinquefasciatus mosquitoes were then allowed to feed on the infected canaries to validate the efficacy of this method for mosquito vector competence assays. RESULTS: Storage of Plasmodium spp.--infected donor blood at 4 °C yielded viable parasites for 48 h. All five experimentally-infected canaries developed clinical signs and were infectious. Pathologic examination of three canaries that later died revealed splenic lesions typical of avian malaria infection. Mosquito infectivity assays demonstrated that Cx. stigmatosoma and Cx. pipiens were competent vectors for Plasmodium cathemerium. CONCLUSIONS: A simple method of collecting and preserving avian whole blood with malaria parasites of low parasitaemia (≤ 0.0005%) was developed that remained viable for further experimental bird and mosquito infectivity assays. This method allows researchers interested in conducting infectivity assays on target Plasmodium spp. to collect these parasites directly from nature with minimal impact on wild birds.","corpus_id":14794735,"score":2},{"doc_id":"27355210","title":"Optimization of a Membrane Feeding Assay for Plasmodium vivax Infection in Anopheles albimanus.","abstract":"INTRODUCTION: Individuals exposed to malaria infections for a long time develop immune responses capable of blocking Plasmodium transmission to mosquito vectors, potentially limiting parasite spreading in nature. Development of a malaria TB vaccine requires a better understanding of the mechanisms and main effectors responsible for transmission blocking (TB) responses. The lack of an in vitro culture system for Plasmodium vivax has been an important drawback for development of a standardized method to assess TB responses to this parasite. This study evaluated host, vector, and parasite factors that may influence Anopheles mosquito infection in order to develop an efficient and reliable assay to assess the TB immunity. METHODS/PRINCIPAL FINDINGS: A total of 94 P. vivax infected patients were enrolled as parasite donors or subjects of direct mosquito feeding in two malaria endemic regions of Colombia (Tierralta, and Buenaventura). Parasite infectiousness was assessed by membrane feeding assay or direct feeding assay using laboratory reared Anopheles mosquitoes. Infection was measured by qPCR and by microscopically examining mosquito midguts at day 7 for the presence of oocysts. Best infectivity was attained in four day old mosquitoes fed at a density of 100 mosquitos/cage. Membrane feeding assays produced statistically significant better infections than direct feeding assays in parasite donors; cytokine profiles showed increased IFN-γ, TNF and IL-1 levels in non-infectious individuals. Mosquito infections and parasite maturation were more reliably assessed by PCR compared to microscopy. CONCLUSIONS: We evaluated mosquito, parasite and host factors that may affect the outcome of parasite transmission as measured by artificial membrane feeding assays. Results have led us to conclude that: 1) optimal mosquito infectivity occurs with mosquitoes four days after emergence at a cage density of 100; 2) mosquito infectivity is best quantified by PCR as it may be underestimated by microscopy; 3) host cellular immune response did not appear to significantly affect mosquito infectivity; and 4) no statistically significant difference was observed in transmission between mosquitoes directly feeding on humans and artificial membrane feeding assays.","corpus_id":5028754,"score":2},{"doc_id":"27493248","title":"Vector Competence of Anopheles kleini and Anopheles sinensis (Diptera: Culicidae) From the Republic of Korea to Vivax Malaria-Infected Blood From Patients From Thailand.","abstract":"In total, 1,300 each of Anopheles kleini Rueda and Anopheles sinensis Wiedemann sensu stricto (s.s.) females (colonized from the Republic of Korea) and Anopheles dirus Peyton & Harrison (Thai strain) were allowed to feed on blood from Thai malaria patients naturally infected with Plasmodium vivax The overall oocyst infection rates for An. dirus, An. kleini, and An. sinensis s.s. were 77.4, 46.1, and 45.9%, respectively. The mean number of oocysts was significantly higher for An. dirus (82.7) compared with An. kleini (6.1) and An. sinensis s.s. ( 8.6), whereas the mean number of oocysts for An. kleini and An. sinensis s.s. was similar. The overall sporozoite infection rates for An. dirus, An. kleini, and An. sinensis s.s. dissected on days 14-15, 21, and 28 days post-feed were significantly higher for An. dirus (90.0%) than An. kleini (5.4%), whereas An. kleini sporozoite rates were significantly higher than An. sinensis s.s. ( <0.1%). The overall sporozoite indices for positive females with +3 (100-1,000 sporozoites) and +4 (>1,000 sporozoites) salivary gland indices were significantly higher for An. dirus (85.7%), compared with An. kleini (47.1%). Only one An. sinensis s.s. had sporozoites (+2; >10-100 sporozoites). These results indicate that An. kleini is a competent vector of vivax malaria. Although An. sinensis s.s. develops relatively high numbers of oocysts, it is considered a very poor vector of vivax malaria due to a salivary gland barrier.","corpus_id":23349915,"score":2},{"doc_id":"27658591","title":"Characteristics of Imported Malaria and Species of Plasmodium Involved in Shandong Province, China (2012-2014).","abstract":"Malaria remains a serious public health problem in Shandong Province, China; therefore, it is important to explore the characteristics of the current malaria prevalence situation in the province. In this study, data of malaria cases reported in Shandong during 2012-2014 were analyzed, and Plasmodium species were confirmed by smear microscopy and nested-PCR. A total of 374 malaria cases were reported, 80.8% of which were reported from 6 prefectures. Of all cases, P. falciparum was dominant (81.3%), followed by P. vivax (11.8%); P. ovale and P. malariae together accounted for 6.4% of cases. Notably, for the first time since 2012, no indigenous case had been reported in Shandong Province, a situation that continued through 2014. Total 95.2% of cases were imported from Africa. The ratio of male/female was 92.5:1, and 96.8% of cases occurred in people 20-54 years of age. Farmers or laborers represented 77.5% of cases. No significant trends of monthly pattern were found in the reported cases. All patients were in good condition after treatment, except for 3 who died. These results indicate that imported malaria has increased significantly since 2012 in Shandong Province, especially for P. falciparum, and there is an emergence of species diversity.","corpus_id":17868138,"score":2},{"doc_id":"27756355","title":"Similar trends of susceptibility in Anopheles arabiensis and Anopheles pharoensis to Plasmodium vivax infection in Ethiopia.","abstract":"BACKGROUND: Around half of the global population is living in areas at risk of malaria infection. Plasmodium vivax malaria has become increasingly prevalent and responsible for a high health and socio-economic burden in Ethiopia. The availability of gametocyte carriers and mosquito species susceptible to P. vivax infection are vital for malaria transmission. Determining the susceptibility of vector species to parasite infection in space and time is important in vector control programs. This study assesses the susceptibility of Anopheles arabiensis, An. pharoensis and An. coustani group to Plasmodium vivax infection in Ethiopia. METHODS: Larvae of An. arabiensis, An. pharoensis and An. coustani group were collected from an array of breeding sites and reared to adult under controlled conditions. Batches of adult female mosquitoes of the three species were allowed to feed in parallel on the same infected blood with gametocytes drawn from Plasmodium vivax infected patients by Direct Membrane Feeding Assays (DMFA). Fed mosquitoes were kept in an incubator under controlled laboratory conditions. Seven days after each feeding assay, mosquitoes were dissected for midgut oocyst microscopy and enumeration. Data were analysed using R statistical software package version 3.1.0. RESULTS: Over all, 8,139 adult female mosquitoes were exposed to P. vivax infection. Of the exposed mosquitoes 16.64 % (95 % CI: 1,354-8,139) were properly fed and survived until dissection. The infection rate in An. arabiensis and An. pharoensis was 31.72 % (95 % CI: 28.35-35.08) and 28.80 % (95 % CI: 25.31-32.28), respectively. The intensity of infection for An. arabiensis and An. pharoensis was 2.5 (95 % CI: 1.9-3.2) and 1.4 (95 % CI: 1.1-1.8), respectively. Gametocyte density was positively correlated to infection rate and intensity of infection in An. arabiensis as well as An. pharoensis. No An. coustani group mosquitoes were found infected, though almost four hundred mosquitoes were successfully fed and dissected. All groups received blood from the same infected blood source containing gametocytes in parallel. There was no significant difference in susceptibility rates between An. arabiensis and An. pharoensis (P = 0.215). CONCLUSIONS: Anopheles arabiensis and An. pharoensis showed similar susceptibility to P. vivax infection. However, An. coustani group was not permissive for the development of P. vivax parasites.","corpus_id":10505738,"score":2},{"doc_id":"29082435","title":"Natural Plasmodium vivax infections in Anopheles mosquitoes in a malaria endemic area of northeastern Thailand.","abstract":"There was recently an outbreak of malaria in Ubon Ratchathani Province, northeastern Thailand. In the absence of information on malaria vector transmission dynamics, this study aimed to identify the anopheline vectors and their role in malaria transmission. Adult female Anopheles mosquitoes were collected monthly by human-landing catch in Na Chaluai District of Ubon Ratchathani Province during January 2014-December 2015. Field-captured mosquitoes were identified to species using morphology-based keys and molecular assays (allele-specific polymerase chain reaction, AS-PCR), and analysed for the presence of Plasmodium falciparum and Plasmodium vivax using an enzyme-linked immunosorbent assay (ELISA) for the detection of circumsporozoite proteins (CSP). A total of 1,229 Anopheles females belonging to 13 species were collected. Four anopheline taxa were most abundant: Members of the Anopheles barbirostris complex, comprising 38% of the specimens, species of the Anopheles hyrcanus group (18%), Anopheles nivipes (17%) and Anopheles philippinensis (12%). The other nine species comprised 15% of the collections. Plasmodium infections were detected in two of 668 pooled samples of heads/thoraces, Anopheles dirus (1/29) and An. philippinensis (1/97). The An. dirus pool had a mixed infection of P. vivax-210 and P. vivax-247, whereas the An. philippinensis pool was positive only for the latter protein variant. Both positive ELISA samples were confirmed by nested PCR. This study is the first to incriminate An. dirus and An. philippinensis as natural malaria vectors in the area where the outbreak occurred. This information can assist in designing and implementing a more effective malaria control programme in the province.","corpus_id":3753470,"score":2},{"doc_id":"29460862","title":"Host preferences and feeding patterns of Anopheles sinensis Wiedemann in three sites of Shandong province, China.","abstract":"Background & objectives: Anopheles sinensis Wiedemann is a major vector of malaria and is among the dominant species in Shandong province of China. Knowledge of the blood-feeding patterns of mosquitoes is crucial for elimination of malaria vectors. However, little information is available on the blood-feeding behaviour of An. sinensis mosquitoes in Shandong province. This study was carried out to compare the blood-feeding behaviour of An. sinensis in malaria-endemic areas of Shandong province China. Methods: Adult Anopheles mosquitoes were collected from three malaria-endemic areas (Jimo, Yinan and Shanxian), during the peak months of mosquito population (August and September) from 2014 to 2015. Indoor-resting mosquitoes and outdoor-resting blood-fed females were sampled in the morning hours (0600 to 0900 hrs) from 10 randomly selected houses using pyrethrum spray catch method, and sweeping with an insect net. ELISA was used for the identification of blood meal. The blood meal of each mosquito was tested against antisera specific to human, pig, dog, cow, goat, horse (mule) and fowl. Results: At all indoor study locations of Jimo, Yinan and Shanxian, 59.4, 68.1 and 98.8% blood-engorged female An. sinensis collected from cattle sheds fed almost exclusively on bovines, respectively. For outdoor locations, at Jimo site, 27.27 and 49.55% An. sinensis fed on cattle and pigs; at Yinan, 30.42% fed on cattle and 36.88% fed both on cattle and goats, while no pig antibodies were detected. At Shanxian, percent of An. sinensis that fed on cattle, pigs and cattle-goat was 20.72, 27.62 and 21.78%, respectively. Interpretation & conclusion: The analysis of An. sinensis blood meals in all the three studied areas from human houses, cattle sheds, pig sheds and mixed dwellings revealed that An. sinensis prefers cattle hosts, and can feed on other available animal hosts if the cattle hosts are absent, and the mosquitoes readily feed on humans when domestic animals (cattle and pigs) are not nearby for feeding. The analysis of blood meal revealed that An. sinensis follow opportunistic feeding in Shandong province, China.","corpus_id":3442265,"score":2},{"doc_id":"21340364","title":"Susceptibility of Anopheles campestris-like and Anopheles barbirostris species complexes to Plasmodium falciparum and Plasmodium vivax in Thailand.","abstract":"Nine colonies of five sibling species members of Anopheles barbirostris complexes were experimentally infected with Plasmodium falciparum and Plasmodium vivax. They were then dissected eight and 14 days after feeding for oocyst and sporozoite rates, respectively, and compared with Anopheles cracens. The results revealed that Anopheles campestris-like Forms E (Chiang Mai) and F (Udon Thani) as well as An. barbirostris species A3 and A4 were non-potential vectors for P. falciparum because 0% oocyst rates were obtained, in comparison to the 86.67-100% oocyst rates recovered from An. cracens. Likewise, An. campestris-like Forms E (Sa Kaeo) and F (Ayuttaya), as well as An. barbirostris species A4, were non-potential vectors for P. vivax because 0% sporozoite rates were obtained, in comparison to the 85.71-92.31% sporozoite rates recovered from An. cracens. An. barbirostris species A1, A2 and A3 were low potential vectors for P. vivax because 9.09%, 6.67% and 11.76% sporozoite rates were obtained, respectively, in comparison to the 85.71-92.31% sporozoite rates recovered from An. cracens. An. campestris-like Forms B and E (Chiang Mai) were high-potential vectors for P. vivax because 66.67% and 64.29% sporozoite rates were obtained, respectively, in comparison to 90% sporozoite rates recovered from An. cracens.","corpus_id":7408328,"score":1},{"doc_id":"22296040","title":"Correlation of Pfg377 ortholog gene expression of Plasmodium vivax and mosquito infection.","abstract":"OBJECTIVE: To determine the expression of Pfg377 ortholog gene in Plasmodium vivax, and examine its correlation with mosquito infection. METHODS: Seventy clinical blood samples positive for P. vivax by microscopy, were used for the mosquito infectivity assay. Infectivity to female Anopheles dirus was determined from oocyst counts. The transcripts of Pfg377 ortholog gene of P. vivax from blood samples infective and non-infective to mosquitoes were examined using quantitative real-time reverse transcriptase-polymerase chain reaction (RT-PCR). RESULTS: Of 70 P. vivax positive blood samples, 50 (71.4%) samples were mosquito-infective and 20 (28.6%) were not. In infective samples, the expression level of Pfg377 ortholog gene was significantly higher than in the non-infective group (P<0.05). In infective samples, the expression level of Pfg377 ortholog gene at ≥100 copies/ml of blood cut-off point correlated with ≥10 oocysts/mosquito cut-off point of average oocyst numbers and with ≥50% cut-off point of per cent infected mosquitoes (Pearson's chi-square correlation, P=0.014 and P=0.026, respectively). CONCLUSION: The cut-off point of the expression level of Pfg377 ortholog gene could be used to predict the infectiousness of P. vivax gametocytes leading to mosquito infection and parasite transmission in the field.","corpus_id":22279310,"score":1},{"doc_id":"22627302","title":"Distribution of mosquitoes and mosquito-borne viruses along the China-Myanmar border in Yunnan Province.","abstract":"A total of 54,673 mosquitoes were collected at 11 sites located near the China-Myanmar border in the western part of Yunnan Province during July and August 2007. There were 29 species in 4 genera identified from the collections, including 12 species of Culex, 12 species of Anopheles, 3 species of Aedes, and 2 species of Armigeres. Culex tritaeniorhynchus Giles (67.9%, 37,119/54,673) and Anopheles sinensis Wiedemann (25.9%, 14,170/54,673) were the most abundant species in this investigation. Virus was isolated using BHK-21 and C6/36 cells from 22 of 510 mosquito pools. Isolates included Japanese encephalitis virus (JEV) and Getah virus (GETV), which were identified by serological and molecular methods. Twenty JEV strains were isolated from Cx. tritaeniorhynchus (15 isolates), An. sinensis (3 isolates), and Armigeres subalbatus Coquillett (2 isolates), and 2 GETV strains were isolated from Culex pseudovishnui Colless and Cx. tritaeniorhynchus. This study suggests that Ar. subalbatus is a potentially important local vector because of the high JEV infection ratio found in this species. Enzootic JEV transmission persists in this area and therefore, surveillance for human disease caused by JEV and GETV should be conducted in the region.","corpus_id":18671765,"score":1},{"doc_id":"23181931","title":"Anopheles plumbeus (Diptera: Culicidae) in Europe: a mere nuisance mosquito or potential malaria vector?","abstract":"BACKGROUND: Anopheles plumbeus has been recognized as a minor vector for human malaria in Europe since the beginning of the 20th century. In recent years this tree hole breeding mosquito species appears to have exploited novel breeding sites, including large and organically rich man-made containers, with consequently larger mosquito populations in close vicinity to humans. This lead to investigate whether current populations of An. plumbeus would be able to efficiently transmit Plasmodium falciparum, the parasite responsible for the most deadly form of malaria. METHODS: Anopheles plumbeus immatures were collected from a liquid manure pit in Switzerland and transferred as adults to the CEPIA (Institut Pasteur, France) where they were fed on P. falciparum gametocytes produced in vitro. Anopheles gambiae mosquitoes served as controls. Development of P. falciparum in both mosquito species was followed by microscopical detection of oocysts on mosquito midguts and by sporozoite detection in the head/thorax by PCR and microscopy. RESULTS: A total of 293 wild An. plumbeus females from four independent collections successfully fed through a membrane on blood containing P. falciparum gametocytes. Oocysts were observed in mosquito midguts and P. falciparum DNA was detected in head-thorax samples in all four experiments, demonstrating, on a large mosquito sample, that An. plumbeus is indeed receptive to P. falciparum NF54 and able to produce sporozoites. Importantly, the proportion of sporozoites-infected An. plumbeus was almost similar to that of An. gambiae (31 to 88% An. plumbeus versus 67 to 97% An. gambiae). However, the number of sporozoites produced was significantly lower in infected An. plumbeus. CONCLUSION: The results show that a sample of field-caught An. plumbeus has a moderate to high receptivity towards P. falciparum. Considering the increased mobility of humans between Europe and malaria endemic countries and changes in environment and climate, these data strongly suggest that An. plumbeus could act as a vector for malaria and thus significantly contribute to increasing the malaria transmission risk in Central-Western Europe. In locations showing high vulnerability to the presence of gametocyte carriers, the risk of transmission of malaria by An. plumbeus should be considered.","corpus_id":1877118,"score":1},{"doc_id":"24979183","title":"Complete sporogony of Plasmodium relictum (lineages pSGS1 and pGRW11) in mosquito Culex pipiens pipiens form molestus, with implications to avian malaria epidemiology.","abstract":"Plasmodium parasites (Plasmodiidae) cause malaria in many species of terrestrial vertebrates and are transmitted mainly by mosquitoes (Culicidae). Avian malaria is often caused by Plasmodium relictum , a cosmopolitan hemosporidian infection. Numerous genetic lineages of P. relictum have been described. However, it remains unclear if these lineages can be transmitted by Culex pipiens pipiens form molestus, which is widespread but has been insufficiently investigated as a possible vector of avian malaria. The aim of this study was to test experimentally if 2 common P. relictum lineages complete sporogony in the experimentally infected insects. The mosquitoes were cultivated under laboratory conditions. Unfed females were allowed to take blood meals on domestic canaries experimentally infected with the lineages pSGS1 and pGRW11 of P. relictum . These lineages are widespread and cause malaria in many species of birds. Infected female flies were examined for sporogonic development of each parasite lineage. Both exposed groups were maintained under the same laboratory conditions. Mosquitoes were dissected at intervals, and the midguts and salivary glands were prepared in order to detect sporogonic stages. Numerous ookinetes, oocysts, and sporozoites of both parasite lineages were observed. Polymerase chain reaction confirmed the presence of corresponding parasite lineages in the experimentally infected insects. Sporogonic stages of both lineages were morphologically similar and developed synchronously in this mosquito; however, the lineage pGRW11 developed a significantly greater number of oocysts than did the lineage pSGS1. This study shows that Culex p. pipiens f. molestus is susceptible to 2 widespread lineages of P. relictum and worth more attention in avian malaria epidemiology. We recommend C. p. pipiens f. molestus for experimental research of avian malaria parasites, principally because it willingly takes blood meals on birds and because it is easy to establish and maintain new colonies of this insect under laboratory conditions using wild-sampled eggs, larvae, or imago.","corpus_id":25648185,"score":1},{"doc_id":"25843138","title":"Host feeding patterns of mosquitoes in a rural malaria-endemic region in hainan island, china.","abstract":"Malaria is endemic in Wangxia Village of Hainan Island. In this area little is known about the host seeking behavior and feeding habit of mosquitoes. Three sites representing the most common habitat types in the village were selected to study the host seeking behavior and feeding habit of mosquitoes. Of the total 9 species belonging to 4 genera (Armigeres, Culex, Aedes, and Anopheles) collected in Wangxia Village, Culex tritaeniorhynchus and Cx. pipiens quinquefasciatus were the most commonly collected species. Armigeres subalbatus and Anopheles sinensis were moderately common species. Blood meal analysis confirmed that Cx. tritaeniorhynchus and Cx. p. quinquefasciatus fed on multiple hosts, mainly poultry but occasionally other animals. Anopheles sinensis, a vector of malaria, fed predominately on cattle hosts, followed by humans. Anopheles maculatus and An. barbirostris fed on both humans and domestic animals. Our results indicate that most mosquitoes in this area preferred domestic animals over humans and showed a tendency to feed on multiple hosts within the same gonotrophic cycle. Therefore, the potential role of domestic animals in arbovirus transmission should be evaluated as part of a strategy for controlling mosquito-borne diseases in this region.","corpus_id":8236412,"score":1},{"doc_id":"26118548","title":"Distribution and phylogenetic analysis of Culex flavivirus in mosquitoes in China.","abstract":"Culex flavivirus (CxFV) is an insect-specific virus of the genus Flavivirus. CxFV strains have been isolated from Cx. pipiens, Cx. quinquefasciatus, and other Cx. species in Asia, Africa, North America, Central America and South America. CxFV was isolated for the first time in China in 2006. As this is a novel flavivirus, we explored the distribution and genetic characteristics of Culex flavivirus in China. A total of 46,649 mosquitoes were collected in seven provinces between 2004 and 2012 and were analysed in 871 pools. 29 CxFV RNAs from Cx. pipiens, Cx. tritaeniorhynchus, Anopheles Sinensis, and Culex spp. tested positive for CxFV in real-time RT-PCR. 6 CxFV strains were isolated from Cx. species collected in Shandong, Henan, and Shaanxi provinces, while no virus or viral RNA was detected in samples from Sichuan, Chongqing, Hubei, and Fujian. Phylogenetic analysis of the envelope gene indicated that Chinese strains formed a robust subgroup of genotype 1, together with viruses from the United States and Japan. This study demonstrates that the geographic distribution of CxFV in China is widespread, but geographical boundaries to spread are apparent. Our findings suggest that CxFV can infect various mosquito species in nature.","corpus_id":14530000,"score":1},{"doc_id":"26805471","title":"Species composition, co-occurrence, association and affinity indices of mosquito larvae (Diptera: Culicidae) in Mazandaran Province, northern Iran.","abstract":"Although considerable progress has been made in the past years in management of mosquito borne diseases such as malaria, dengue, yellow fever and West Nile fever through research in biology and ecology of the vectors, these diseases are still major threats to human health. Therefore, more research is required for better management of the diseases. This investigation provides information on the composition, co-occurrence, association and affinity indices of mosquito larvae in Mazandaran Province, northern Iran. In a large scale field study, mosquito larvae were collected from 120 sentinel sites in 16 counties in Mazandaran Province, using standard 350 ml dipper. Sampling took place monthly from May to December 2014. Collected larvae were mounted on glass slides using de Faure's medium and were diagnosed using morphological characters. Totally, 19,840 larvae were collected including three genera and 16 species from 120 larval habitats, as follows: Anopheles claviger, Anopheles hyrcanus, Anopheles maculipennis s.l., Anopheles marteri, Anopheles plumbeus, Anopheles pseudopictus, Culex pipiens, Culex tritaeniorhynchus, Culex torrentium, Culex perexiguus, Culex territans, Culex mimeticus, Culex hortensis, Culiseta annulata, Culiseta longiareolata, and Culiseta morsitans. Predominant species were Cx. pipiens and An. maculipennis s.l. which show the highest co-occurrence. The pair of species An. hyrcanus/An. pseudopictus showed significant affinity and association. High co-occurrence of the predominant species Cx. pipiens and An. maculipennis s.l. in the study area is of considerable importance in terms of vector ecology. It was also revealed that An. pseudopictus/An. hyrcanus often occur sympatrically indicating their common habitat requirements. The information may be equally important when vector control measures are considered.","corpus_id":205239654,"score":1},{"doc_id":"27301693","title":"High susceptibility of wild Anopheles funestus to infection with natural Plasmodium falciparum gametocytes using membrane feeding assays.","abstract":"BACKGROUND: Anopheles funestus is a major vector of malaria in sub-Saharan Africa. However, because it is difficult to colonize, research on this mosquito species has lagged behind other vectors, particularly the understanding of its susceptibility and interactions with the Plasmodium parasite. The present study reports one of the first experimental infections of progeny from wild-caught An. funestus with the P. falciparum parasite providing a realistic avenue for the characterisation of immune responses associated with this infection. METHODS: Wild-fed resting An. funestus females were collected using electric aspirators and kept in cages for four days until they were fully gravid and ready to oviposit. The resulting eggs were reared to adults F1 mosquitoes under insectary conditions. Three to five day-old An. funestus F1 females were fed with infected blood taken from gametocyte carriers using an artificial glass-parafilm feeding system. Feeding rate was recorded and fed mosquitoes were dissected at day 7 to count oocysts in midguts. Parallel experiments were performed with the known Plasmodium-susceptible An. coluzzii Ngousso laboratory strain, to monitor our blood handling procedures and infectivity of gametocytes. RESULTS: The results revealed that An. funestus displays high and similar level of susceptibility to Plasmodium infection compared to An. coluzzii, and suggest that our methodology produces robust feeding and infection rates in wild An. funestus progeny. The prevalence of infection in An. funestus mosquitoes was 38.52 % (range 6.25-100 %) and the median oocyst number was 12.5 (range 1-139). In parallel, the prevalence in An. coluzzii was 39.92 % (range 6.85-97.5 %), while the median oocyst number was 32.1 (range 1-351). CONCLUSIONS: Overall, our observations are in line with the fact that both species are readily infected with P. falciparum, the most common and dangerous malaria parasite in sub-Saharan Africa, and since An. funestus is widespread throughout Africa, malaria vector control research and implementation needs to seriously address this vector species too. Additionally, the present work indicates that it is feasible to generate large number of wild F1 infected An. funestus mosquitoes using membrane feeding assays, which can be used for comprehensive study of interactions with the Plasmodium parasite.","corpus_id":1404544,"score":1},{"doc_id":"27444629","title":"The mitochondrial genomes of Culex tritaeniorhynchus and Culex pipiens pallens (Diptera: Culicidae) and comparison analysis with two other Culex species.","abstract":"BACKGROUND: Culex tritaeniorhynchus and Culex pipiens pallens are the major vectors of the Japanese encephalitis virus and Wuchereria bancrofti, the causative agent of filariasis. The knowledge of mitochondrial genomes has been widely useful for the studies on molecular evolution, phylogenetics and population genetics. METHODS: In this study, we sequenced and annotated the mitochondrial (mt) genomes of Cx. tritaeniorhynchus and Cx. p. pallens, and performed a comparative analysis including four known mt genomes of species of the subgenus Culex (Culex). The phylogenetic relationships of Cx. tritaeniorhynchus, Cx. p. pallens and four known Culex mt genome sequences were reconstructed by maximum likelihood based on concatenated protein-coding gene sequences. RESULTS: Culex tritaeniorhynchus and Cx. p. pallens mt genomes are 14,844 bp and 15,617 bp long, both consists of 13 PCGs, 22 tRNAs, 2 rRNAs and 1 CR (not sequenced for Cx. tritaeniorhynchus). The initiation and termination codons of PCGs are ATN and TAA, respectively, except for COI starting with TCG, and COI and COII terminated with T. tRNAs have the typical clover-leaf secondary structures except for trnS ((AGN)) that is lacking the DHU stem. 16S rRNA and 12S rRNA secondary structures were drawn for the first time for mosquito mt genomes. The control region of Cx. p. pallens mt genome is 747 bp long and with four tandem repeat structures. Phylogenetic analyses demonstrated that the mt genome of Cx. tritaeniorhynchus was significantly separated from the remaining five mt genomes of Culex spp. Culex p. pipiens, Cx. p. pallens and Cx. p. quinquefasciatus formed a monophyletic clade with Cx. p. quinquefasciatus linked in the middle of the clade, and Cx. p. pallens should have the same taxonomic level as Culex p. pipiens and Cx. p. quinquefasciatus. CONCLUSIONS: The mt genomes of Cx. tritaeniorhynchus and Cx. p. pallens share the same gene composition and order with those of two other Culex species. Culex p. pallens of the Pipiens complex should have the same taxonomic level as Culex p. pipiens and Cx. p. quinquefasciatus investigated. We enriched the Culex mt genome data and provided a reference basis for further Culex mt genome sequencing and analyses.","corpus_id":13947030,"score":1},{"doc_id":"28962620","title":"Avian Plasmodium in Eastern Austrian mosquitoes.","abstract":"BACKGROUND: Insect vectors, namely mosquitoes (Diptera: Culicidae), are compulsory for malaria parasites (Plasmodium spp.) to complete their life cycle. Despite this, little is known about vector competence of different mosquito species for the transmission of avian malaria parasites. METHODS: In this study, nested PCR was used to determine Plasmodium spp. occurrence in pools of whole individuals, as well as the diversity of mitochondrial cytochrome b gene sequences in wild-caught mosquitoes sampled across Eastern Austria in 2013-2015. RESULTS: A total of 45,749 mosquitoes in 2628 pools were collected, of which 169 pools (6.43%) comprising 9 mosquito species were positive for avian Plasmodium, with the majority of positives in mosquitoes of Culex pipiens s.l./Culex torrentium. Six different avian Plasmodium lineages were found, the most common were Plasmodium vaughani SYAT05, Plasmodium sp. Linn1 and Plasmodium relictum SGS1. In 2014, mosquitoes of the Culex pipiens complex were genetically identified and Culex pipiens f. pipiens presented with the highest number of avian Plasmodium positives (n = 37; 16.74%). Despite this, the minimum infection rate (MIR) was highest in Culex torrentium (5.36%) and Culex pipiens f. pipiens/f. molestus hybrids (5.26%). During 2014 and 2015, seasonal and annual changes in Plasmodium lineage distribution were also observed. In both years P. vaughani SYAT05 dominated at the beginning of the sampling period to be replaced later in the year by P. relictum SGS1 (2014) and Plasmodium sp. Linn1 (2015). CONCLUSIONS: This is the first large-scale study of avian Plasmodium parasites in Austrian mosquitoes. These results are of special interest, because molecular identification of the taxa of the Cx. pipiens complex and Cx. torrentium enabled the determination of Plasmodium prevalence in the different mosquito taxa and hybrids of this complex. Since pools of whole insects were used, it is not possible to assert any vector competence in any of the examined mosquitoes, but the results are nonetheless valuable in providing an overview of avian Plasmodium species and lineages present in Austria.","corpus_id":27785142,"score":1},{"doc_id":"29536705","title":"[Analysis of population genetic diversity of mosquitoes from Shandong Province based on mitochondrial DNA cytochrome oxidase subunit I gene fragment].","abstract":"OBJECTIVE: To explore the characteristics of gene sequence of mtDNA-COⅠ of Culex pipiens pallens from different geographical regions in Shandong Province and different resistant strains from the lab and five common mosquito species, and analyze the genetic diversity of these mosquitoes. METHODS: Adult mosquitoes were collected from Jinan, Jining, Qingdao cities and other places in Shandong Province. The sensitive, dichlorvos-resistant, pyrethroid-resistant and propoxur-resistant strains were reared in the lab. Five species of mosquito (Cx. pipiens pallens, Cx. tritaeniorhynchus, Anopheles sinensis, Aedes albopictus, and Armigeres subalbatus) were collected from Jining City and identified in the lab. mtDNA-COⅠwas specifically amplified by PCR and sequenced. The gene sequences were compared and analyzed by the biological information systems, and the phylogenetic tree was constructed. RESULTS: The amplified mtDNA-COⅠfragments of Cx. pipiens pallens from eight different cities and four different resistant strains were 528 bp in length, with 67.4% A+T contents and two mutation sites. The nucleotide sequence homology among the different geographic strains was 99.95% and the gene sequences of the four resistant strains were the same, showing a high homogeny. The amplified mtDNA-COⅠfragments of the five species of mosquitoes were 528 bp with 408 conserved sites, 120 variable sites, 42 parsimony informative sites and 78 singleton sites. The A+T contents were between 65.7% and 68.0%. The nucleotide sequence homology among the different mosquito species was between 86.17% and 92.05%, and the molecular identification was consistent with the traditional morphological identification. The molecular phylogenetic study showed that the different species were clustered at their own branch at the species and genus levels, while genera Armigeres was distantly related to the others. CONCLUSIONS: mtDNA-COⅠcould not serve as the molecular marker to analyze the population genetic variation and phylogenesis of Cx. pipiens pallens from different geographical regions and different resistant strains, but it has species and genus specificities, which could be used for the identification of the mosquito species and genus.","corpus_id":3847185,"score":1},{"doc_id":"29723510","title":"Infection of mosquitoes from in vitro cultivated Plasmodium knowlesi H strain.","abstract":"In vitro studies of sexual blood stages of the most fatal malaria species, Plasmodium falciparum, have revealed key processes by which gametocytes develop and transmit infection from humans to anopheline mosquitoes. However, most malaria cases outside sub-Saharan Africa are caused by other Plasmodium spp., frequently Plasmodium vivax and Plasmodium knowlesi, a zoonotic parasite of macaque monkeys. Gametocytes of P. vivax and P. knowlesi exhibit distinct morphology, faster development, and a shorter life span compared with gametocytes of P. falciparum, reflecting the evolutionary separation and biological differences of these species. Unlike P. falciparum, P. vivax cannot be cultivated in vitro, necessitating access to infected primates for laboratory studies. In contrast, P. knowlesi asexual stages have been successfully adapted to cultures in macaque and human red blood cells, but these stages have not been reported to produce gametocytes infective to mosquitoes. Here, we show that gametocyte production and sporadic, low-level mosquito infectivity of a P. knowlesi strain was not improved by application of a \"crash\" method commonly used to induce gametocytes in P. falciparum cultures. However, Percoll-gradient purified schizonts from this strain yielded highly synchronised populations that, in three of six experiments, produced infections at an average rate of 0.97-9.1 oocysts in Anopheles dirus mosquitoes. Oocyst counts were most abundant in mosquitoes that were fed from the synchronised cultures 36 h after schizont purification. Gametocytes in these cultures occurred at low prevalence and were difficult to observe. Transcription from orthologs of P. falciparum gametocyte-specific markers did not correlate with infectivity of the P. knowlesi parasites to mosquitoes. The ability to infect mosquitoes from in vitro-cultivated P. knowlesi will support research on the unique features of this emerging pathogen and facilitate comparative studies of transmission by the different human malarias.","corpus_id":19141194,"score":1},{"doc_id":"21194433","title":"Insecticide resistance and malaria transmission: infection rate and oocyst burden in Culex pipiens mosquitoes infected with Plasmodium relictum.","abstract":"BACKGROUND: The control of most vectors of malaria is threatened by the spread of insecticide resistance. One factor that has been hitherto largely overlooked is the potential effects of insecticide resistance on the ability of mosquitoes to transmit malaria: are insecticide-resistant mosquitoes as good vectors of Plasmodium as susceptible ones? The drastic physiological changes that accompany the evolution of insecticide resistance may indeed alter the ability of vectors to transmit diseases, a possibility that, if confirmed, could have major epidemiological consequences. METHODS: Using a novel experimental system consisting of the avian malaria parasite (Plasmodium relictum) and its natural vector (the mosquito Culex pipiens), two of the most common mechanisms of insecticide resistance (esterase overproduction and acetylcholinesterase modification) were investigated for their effect on mosquito infection rate and parasite burden. For this purpose two types of experiments were carried out using (i) insecticide-resistant and susceptible laboratory isogenic lines of Cx. pipiens and (ii) wild Cx. pipiens collected from a population where insecticide resistant and susceptible mosquitoes coexist in sympatry. RESULTS: The isogenic line and wild-caught mosquito experiments were highly consistent in showing no effect of either esterase overproduction or of acetylcholinesterase modification on either the infection rate or on the oocyst burden of mosquitoes. The only determinant of these traits was blood meal size, which was similar across the different insecticide resistant categories in both experiments. CONCLUSIONS: Insecticide resistance was found to have no effect on Plasmodium development within the mosquito. This is the first time this question has been addressed using a natural mosquito-Plasmodium combination, while taking care to standardize the genetic background against which the insecticide resistance genes operate. Infection rate and oocyst burden are but two of the factors that determine the vectorial capacity of mosquitoes. Other key determinants of parasite transmission, such as mosquito longevity and behaviour, or the parasite's incubation time, need to be investigated before concluding on whether insecticide resistance influences the ability of mosquitoes to transmit malaria.","corpus_id":2887708,"score":0},{"doc_id":"21290944","title":"Evaluation of octenol and Lurex as baits in Mosquito Magnet Pro traps to collect vector mosquitoes in China.","abstract":"The effectiveness of the attractants 1-octen-3-ol (octenol) and L-lactic acid (Lurex) on the collection of Aedes albopictus, Culex tritaeniorhynchus, Cx. pipiens pallens, and Anopheles sinensis was first evaluated in Mosquito Magnet Pro traps in Yamenkou and Badachu residential areas, Beijing City, and Lishui area, Zhejiang Province, China. The Mosquito Magnet Pro traps baited with octenol collected significantly more Ae. albopictus, Cx. tritaeniorhynchus, and An. sinensis, but fewer Cx. pipiens pallens than collection by the traps alone. There were no significant differences in the numbers of Cx. pipiens pallens, Cx. tritaeniorhynchus, and An. sinensis collected by Mosquito Magnet Pro traps baited with Lurex compared to the traps alone, but the Mosquito Magnet Pro traps baited with Lurex collected significantly more Ae. albopictus than the number collected by the traps alone at 2 areas in Beijing.","corpus_id":42023971,"score":0},{"doc_id":"28693607","title":"Dynamics of Plasmodium vivax sporogony in wild Anopheles stephensi in a malaria-endemic region of Western India.","abstract":"BACKGROUND: In global efforts to track mosquito infectivity and parasite elimination, controlled mosquito-feeding experiments can help in understanding the dynamics of parasite development in vectors. Anopheles stephensi is often accepted as the major urban malaria vector that transmits Plasmodium in Goa and elsewhere in South Asia. However, much needs to be learned about the interactions of Plasmodium vivax with An. stephensi. As a component of the US NIH International Center of Excellence for Malaria Research (ICEMR) for Malaria Evolution in South Asia (MESA), a series of membrane-feeding experiments with wild An. stephensi and P. vivax were carried out to better understand this vector-parasite interaction. METHODS: Wild An. stephensi larvae and pupae were collected from curing water in construction sites in the city of Ponda, Goa, India. The larvae and pupae were reared at the MESA ICEMR insectary within the National Institute of Malaria Research (NIMR) field unit in Goa until they emerged into adult mosquitoes. Blood for membrane-feeding experiments was obtained from malaria patients at the local Goa Medical College and Hospital who volunteered for the study. Parasites were counted by Miller reticule technique and correlation between gametocytaemia/parasitaemia and successful mosquito infection was studied. RESULTS: A weak but significant correlation was found between patient blood gametocytaemia/parasitaemia and mosquito oocyst load. No correlation was observed between gametocytaemia/parasitaemia and oocyst infection rates, and between gametocyte sex ratio and oocyst load. When it came to development of the parasite in the mosquito, a strong positive correlation was observed between oocyst midgut levels and sporozoite infection rates, and between oocyst levels and salivary gland sporozoite loads. Kinetic studies showed that sporozoites appeared in the salivary gland as early as day 7, post-infection. CONCLUSIONS: This is the first study in India to carry out membrane-feeding experiments with wild An. stephensi and P. vivax. A wide range of mosquito infection loads and infection rates were observed, pointing to a strong interplay between parasite, vector and human factors. Most of the present observations are in agreement with feeding experiments conducted with P. vivax elsewhere in the world.","corpus_id":4574883,"score":0},{"doc_id":"29536711","title":"[Overwintering surveillance of Culex pipiens pallens in Shandong Province].","abstract":"OBJECTIVE: To understand the ecological habits of Culex pipiens pallens in Shandong Province in winter. METHODS: From December 2015 to January 2016, the overwintering conditions of Cx. pipiens pallens were investigated in Shandong Province. RESULTS: In Shandong Province, in rural districts, the overwintering places of Cx. pipiens pallens were basements, wells and caves; and in urban areas, they were air raid shelters, holes of city walls, sewers and flower cellars. CONCLUSIONS: In Shandong Province, the overwintering places of Cx. pipiens pallens are mainly basements and holes, which are under high temperature and humidity, and away from light. Its larvae cannot overwinter.","corpus_id":43009797,"score":0}],"string":"[\n {\n \"doc_id\": \"18627630\",\n \"title\": \"Competency of Anopheles stephensi mysorensis strain for Plasmodium vivax and the role of inhibitory carbohydrates to block its sporogonic cycle.\",\n \"abstract\": \"BACKGROUND: Despite the abundance of studies conducted on the role of mosquitoes in malaria transmission, the biology and interaction of Plasmodium with its insect host still holds many mysteries. This paper provides the first study to follow the sporogonic cycle of Plasmodium vivax in a wild insecticide-resistant mysorensis strain of Anopheles stephensi, a major vector of vivax malaria in south-eastern Iran. The study subsequently demonstrates that host-parasite sugar binding interactions are critical to the development of this parasite in the salivary glands of its mosquito host. The identity of the receptors or sugars involved was revealed by a receptor \\\"pre-saturation\\\" strategy in which sugars fed to the mosquitoes inhibited normal host-parasite interactions. METHODS: Anopheles stephensi mysorensis mosquitoes were artificially infected with P. vivax by feeding on the blood of gametocytaemic volunteers reporting to local malaria clinics in the Sistan-Baluchistan province of south-eastern Iran. In order to determine the inhibitory effect of carbohydrates on sporogonic development, vector mosquitoes were allowed to ingest blood meals containing both gametocytes and added carbohydrates. The carbohydrates tested were GlcNAc, GalNAc, arabinose, fucose, mannose, lactose, glucose and galactose. Sporogonic development was assessed by survival of the parasite at both the oocyst and sporozoite stages. RESULTS: Oocyst development was observed among nearly 6% of the fed control mosquitoes but the overall number of mosquitoes exhibiting sporozoite invasion of the salivary glands was 47.5% lower than the number supporting oocysts in their midgut. Of the tested carbohydrates, only arabinose and fucose slightly perturbed the development of P. vivax oocysts at the basal side of the mosquito midgut, and the remaining sugars caused no reductions in oocyst development. Strikingly however, sporozoites were completely absent from the salivary glands of mosquitoes treated with mannose, GalNAc, and lactose. CONCLUSION: The study indicates that An. stephensi in southern Iran has the potential to survive long enough to be re-infected and transmit vivax malaria several times, based on the average adult female longevity (about 30 days) and its gonotrophic cycle (2-3 days) during the malaria transmission season. Certain sugar binding interactions are important for the development of P. vivax sporozoites, and this information may be instrumental for the development of transmission blocking strategies.\",\n \"corpus_id\": 13170758,\n \"score\": 2\n },\n {\n \"doc_id\": \"19196130\",\n \"title\": \"Distribution of arboviruses and mosquitoes in northwestern Yunnan Province, China.\",\n \"abstract\": \"From July to September in 2005 and 2006, a survey was conducted to identify mosquito species and mosquito-borne arboviruses at elevations ranging from 900-3280 m between 24 degrees 00' N and 29 degrees 00' N latitude in the northwestern part of Yunnan Province, China. A total of 54,879 mosquitoes representing 15 species and 4 genera was collected using UV light traps at 59 sites. Culex tritaeniorhynchus and Anopheles sinensis were the most abundant species. The density of mosquitoes as well as the diversity of species decreased with increasing altitude. A total of 21,008 mosquitoes in 281 pools representing all of the 15 species was tested for the presence of viruses using cell culture. Viruses identified included Japanese encephalitis virus (13 isolates), Getah virus (five isolates), Banna virus (three isolates), Kadipiro virus (five isolates), and Densovirus (seven isolates). These isolates were obtained from Culex tritaeniorhynchus (20 isolates), Anopheles sinensis (three isolates), Armigeres subalbatus (six isolates), Culex pipiens quinquefasciatus (two isolates), and from unidentified, mixed mosquitoes (two isolates). Most of the isolates were from collections made at elevations below 2,500 m. Vector Borne Zoonotic Dis. 0, 000-000.\",\n \"corpus_id\": 32104034,\n \"score\": 2\n },\n {\n \"doc_id\": \"19284634\",\n \"title\": \"The susceptibility of Anopheles lesteri to infection with Korean strain of Plasmodium vivax.\",\n \"abstract\": \"BACKGROUND: Following its recent re-emergence, malaria has gained renewed attention as a serious infectious disease in Korea. Three species of the Hyrcanusgroup, Anopheles lesteri, Anopheles sinensis and Anopheles pullus, have long been suspected malaria vectors. However, opinions about their vector ability are controversial. The present study was designed with the aim of determining the susceptibility of these mosquitoes to a Korean isolate of Plasmodium vivax. Also, An. sinensis is primarily suspected to be vector of malaria in Korea, but in Thailand, the same species is described to have less medical importance. Therefore, comparative susceptibility of Thai and Korean strains of An. sinensis with Thai strain of P. vivax may be helpful to understand whether these geographically different strains exhibit differences in their susceptibility or not. METHODS: The comparative susceptibility of An. lesteri, An. sinensis and An. pullus was studied by feeding laboratory-reared mosquitoes on blood from patients carrying gametocytes from Korea and Thailand. RESULTS: In experimental feeding with Korean strain of P. vivax, oocysts developed in An. lesteri, An. sinensis and An. pullus. Salivary gland sporozoites were detected only in An. lesteri and An. sinensis but not in An. pullus. Large differences were found in the number of sporozoites in the salivary glands, with An. lesteri carrying much higher densities, up to 2,105 sporozoites in a single microscope field of 750 x 560 muM, whereas a maximum of 14 sporozoites were found in any individual salivary gland of An. sinensis. Similar results were obtained from a susceptibility test of two different strains of An. sinensis to Thai isolate of P. vivax, and differences in vector susceptibility according to geographical variation were not detected. CONCLUSION: The high sporozoite rate and sporozoite loads of An. lesteri indicate that this species is highly susceptible to infection with P. vivax. Anopheles sinensis appears to have a markedly reduced ability to develop salivary gland infection, whilst in An. pullus, no sporozoites were found in the salivary glands. Provided that the survival rate of An. lesteri is sufficiently high in the field, it would be a highly competent vector of vivax malaria.\",\n \"corpus_id\": 15517110,\n \"score\": 2\n },\n {\n \"doc_id\": \"19629522\",\n \"title\": \"Mosquito blood-meal analysis for avian malaria study in wild bird communities: laboratory verification and application to Culex sasai (Diptera: Culicidae) collected in Tokyo, Japan.\",\n \"abstract\": \"We conducted laboratory experiments to verify molecular techniques of avian malaria parasite detection distinguishing between an infected mosquito (oocysts on midgut wall) and infective mosquito (sporozoites in salivary glands) in parallel with blood-meal identification from individual blood-fed mosquitoes prior to application to field survey for avian malaria. Domestic fowl infected with Plasmodium gallinaceum was exposed to a vector and non-vector mosquito species, Aedes aegypti and Culex pipiens pallens, respectively, to compare the time course of polymerase chain reaction (PCR) detection for parasite between competent and refractory mosquitoes. DNA of the domestic fowl was detectable for at least 3 days after blood feeding. The PCR-based detection of P. gallinaceum from the abdomen and thorax of A. aegypti corresponded to the microscopic observation of oocysts and sporozoites. Therefore, this PCR-based method was considered useful as one of the criteria to assess developmental stages of Plasmodium spp. in mosquito species collected in the field. We applied the same PCR-based method to 21 blood-fed C. sasai mosquitoes collected in Rinshi-no-mori Park in urban Tokyo, Japan. Of 15 blood meals of C. sasai successfully identified, 86.7% were avian-derived, 13.3% were bovine-derived. Plasmodium DNA was amplified from the abdomen of three C. sasai specimens having an avian blood meal from the Great Tit (Parus major), Pale Thrush (Turdus pallidus), and Jungle Crow (Corvus macrorhynchos). This is the first field study on host-feeding habits of C. sasai in relation to the potential role as a vector for avian malaria parasites transmitted in the Japanese wild bird community.\",\n \"corpus_id\": 24616221,\n \"score\": 2\n },\n {\n \"doc_id\": \"19646275\",\n \"title\": \"Implementation of a novel PCR based method for detecting malaria parasites from naturally infected mosquitoes in Papua New Guinea.\",\n \"abstract\": \"BACKGROUND: Detection of Plasmodium species in mosquitoes is important for designing vector control studies. However, most of the PCR-based detection methods show some potential limitations. The objective of this study was to introduce an effective PCR-based method for detecting Plasmodium vivax and Plasmodium falciparum from the field-caught mosquitoes of Papua New Guinea. METHODS: A method has been developed to concurrently detect mitochondrial cytochrome b (Cyt b) of four human Plasmodium species using PCR (Cytb-PCR). To particularly discriminate P. falciparum from P. vivax, Plasmodium ovale and Plasmodium malariae, a polymerase chain reaction-repeated fragment length polymorphism (PCR-RFLP) has further been developed to use with this method. However, due to limited samples number of P. ovale and P. malariae; this study was mainly confined to P. vivax and P. falciparum. The efficiency of Cytb-PCR was evaluated by comparing it with two 'gold standards' enzyme linked immunosorbent assay specific for circumsporozoite protein (CS-ELISA) using artificially infected mosquitoes; and nested PCR specific for small subunit ribosomal RNA (SSUrRNA) using field caught mosquitoes collected from three areas (Kaboibus, Wingei, and Jawia) of the East Sepic Province of Papua New Guinea. RESULTS: A total of 90 mosquitoes were artificially infected with three strains of Plasmodium: P. vivax-210 (n = 30), P. vivax-247 (n = 30) and P. falciparum (n = 30). These infected mosquitoes along with another 32 unfed mosquitoes were first checked for the presence of Plasmodium infection by CS-ELISA, and later the same samples were compared with the Cytb-PCR. CS-ELISA for P. vivax-210, P. vivax-247 and P. falciparum detected positive infection in 30, 19 and 18 mosquitoes respectively; whereas Cytb-PCR detected 27, 16 and 16 infections, respectively. The comparison revealed a close agreement between the two assays (kappa = 0.862, 0.842 and 0.894, respectively for Pv-210, Pv-247 and P. falciparum groups). It was found that the eight CS-ELISA-positive mosquitoes detected negative by Cytb-PCR were false-positive results. The lowest detection limit of this Cytb-PCR was 10 sporozoites. A highly concordance result was also found between nested PCR and Cytb-PCR using 107 field caught mosquitoes, and both tests concordantly detected P. falciparum in an Anopheles punctulatus mosquito collected from Kaboibus. Both tests thus suggested an overall sporozoite rate of 0.9% (1/107) in the study areas. Subsequently, PCR-RFLP efficiently discriminated P. falciparum from P. vivax for all of the Cytb-PCR positive samples. CONCLUSION: A single step PCR based method has been introduced here that is highly sensitive, efficient and reliable for identifying P. vivax and P. falciparum from mosquitoes. The reliability of the technique was confirmed by its ability to detect Plasmodium as efficiently as those of CS-ELISA and nested PCR. Application of the assay offers the opportunity to detect vector species of Papua New Guinea and may contribute for designing further vector control programmes.\",\n \"corpus_id\": 7933136,\n \"score\": 2\n },\n {\n \"doc_id\": \"19769059\",\n \"title\": \"Bloodmeal identification and detection of avian malaria parasite from mosquitoes (Diptera: Culicidae) inhabiting coastal areas of Tokyo Bay, Japan.\",\n \"abstract\": \"Bloodmeal identification and the detection of avian malaria parasite from mosquitoes (Diptera: Culicidae) were carried out by polymerase chain reaction-based methods for field samples collected in coastal areas of Tokyo Bay, Japan, from April to October 2007. The following seven mosquito species were collected: Aedes albopictus (Skuse), Culex pipiens pallens Coquillett, Culex pipiens form molestus Forskal, Culex tritaeniorhynchus Giles, Culex inatomii Kamimura & Wada, Culex bitaeniorhynchus Giles, and Lutzia vorax Edwards. Forty blood-fed mosquitoes were collected and 95% of bloodmeals of Cx. pipiens pallens were avian-derived, whereas only mammalian bloodmeals were identified for Ae. albopictus. Plasmodium DNA was amplified from 65% (15/23) of blood-fed Cx. pipiens pallens and unfed females of Cx. pipiens pallens and Cx. pipiens form molestus with a minimum infection rate of 29.9 and 13.5, respectively. One unfed female of Lt. vorax was also positive for Plasmodium parasites. Five genetically distinct lineages of Plasmodium were identified, with 0.21 to 5.86% sequence divergence. Rinshi-8, the most prevalent lineage at our study site, was identical to the published sequence of Plasmodium relictum-P5.\",\n \"corpus_id\": 26714838,\n \"score\": 2\n },\n {\n \"doc_id\": \"20939372\",\n \"title\": \"Experimental studies on comparison of the potential vector competence of four species of Culex mosquitoes in China to transmit West Nile virus.\",\n \"abstract\": \"To assess the risk that indigenous mosquitoes in China are capable of transmitting and sustaining West Nile virus (WNV), four important Culex mosquito species, Culex tritaeniorhynchus, Culex modestus, Culex pipiens pallens, and Culex pipiens quinquefasciatus, were allowed to feed on the artificial infectious blood meal with WNV dose of 10(6.8) plaque-forming unit/ml and tested approximately 2 wk later to determine infection and transmission rates. The results indicated that four Culex mosquitoes were competent laboratory vectors of WNV. The infection rates and transmission rates were statistical differences among different species of mosquito (chi2 = 20.620, P = 0.000; chi2 = 15.020, P = 0.005, respectively). The highest infection rate and transmission rate were obtained with Cx. tritaeniorhynchus (87.5 and 74.2%, respectively).\",\n \"corpus_id\": 1063109,\n \"score\": 2\n },\n {\n \"doc_id\": \"21292875\",\n \"title\": \"Plasmodium vivax sporozoite production in Anopheles albimanus mosquitoes for vaccine clinical trials.\",\n \"abstract\": \"Vaccine development for Plasmodium vivax malaria is underway. A model to assess the protective efficacy of vaccine candidates in humans is urgently needed. Given the lack of continuous P. vivax cultures, we developed a system to infect Anopheles albimanus mosquitoes using blood from P. vivax-infected patients and determined parameters for challenge of malaria-naive volunteers by mosquito bite. Absence of co-infections in parasitized blood was confirmed by tests consistent with blood bank screening. A total of 119 experiments were conducted using batches of 900-4,500 mosquitoes fed by an artificial membrane feeding method. Optimal conditions for mosquito probing and infection were determined. Presence of oocyst and sporozoites were assessed on Days 7-8 and 14-15, respectively, and conditions to choose batches of infected mosquitoes for sporozoite challenge were established. Procedures to infect volunteers took a 2-hour period including verification of inoculum dose. Anopheles albimanus mosquitoes represent a valuable resource for P. vivax sporozoite challenge of volunteers.\",\n \"corpus_id\": 10469297,\n \"score\": 2\n },\n {\n \"doc_id\": \"21762577\",\n \"title\": \"Co-infections of Plasmodium knowlesi, P. falciparum, and P. vivax among Humans and Anopheles dirus Mosquitoes, Southern Vietnam.\",\n \"abstract\": \"A single Anopheles dirus mosquito carrying sporozoites of Plasmodium knowlesi, P. falciparum, and P. vivax was recently discovered in Khanh Phu, southern Vietnam. Further sampling of humans and mosquitoes in this area during 2009-2010 showed P. knowlesi infections in 32 (26%) persons with malaria (n = 125) and in 31 (43%) sporozoite-positive An. dirus mosquitoes (n = 73). Co-infections of P. knowlesi and P. vivax were predominant in mosquitoes and humans, while single P. knowlesi infections were found only in mosquitoes. P. knowlesi-co-infected patients were largely asymptomatic and were concentrated among ethnic minority families who commonly spend nights in the forest. P. knowlesi carriers were significantly younger than those infected with other malaria parasite species. These results imply that even if human malaria could be eliminated, forests that harbor An. dirus mosquitoes and macaque monkeys will remain a reservoir for the zoonotic transmission of P. knowlesi.\",\n \"corpus_id\": 2509421,\n \"score\": 2\n },\n {\n \"doc_id\": \"22017097\",\n \"title\": \"Preliminary vivax malaria vector competence for three members of the Anopheles hyrcanus group in the Republic of Korea.\",\n \"abstract\": \"In a study on the comparative susceptibility of Anopheles kleini, An. lesteri, and An. sinensis to Plasmodium vivax, we examined the feeding of laboratory-reared mosquitoes on blood of a patient carrying gametocytes from the Republic of Korea. Sporozoites in salivary glands from day 14 postfeeding were detected in An. kleini and An. lesteri with numbers high enough to initiate infection, while no sporozoites were detected in the salivary glands of An. sinensis. This result suggests that An. kleini and An. lesteri could be vivax malaria vectors in the Republic of Korea.\",\n \"corpus_id\": 36958050,\n \"score\": 2\n },\n {\n \"doc_id\": \"22072836\",\n \"title\": \"Mosquito species composition and Plasmodium vivax infection rates on Baengnyeong-do (island), Republic of Korea.\",\n \"abstract\": \"Vivax malaria is a significant military and civilian health threat in the north of the Republic of Korea (ROK). The island of Baengnyeong-do is the westernmost point of the ROK and is located close to the southwestern coast of the Democratic People's Republic of Korea (DPRK). Mosquitoes were collected using a black light trap on Baengnyeong-do, and Anopheles spp. were assayed by PCR, to identify the species, and screened for sporozoites of Plasmodium vivax. Of a subsample of 257 mosquitoes, Anopheles lesteri was the most frequently collected (49.8%), followed by Anopheles sinensis (22.6%), Anopheles pullus (18.7%), Anopheles kleini (7.8%), and Anopheles belenrae (1.2%). The overall sporozoite rate was 3.1%, with the highest rates observed in An. kleini (15.0%), An. sinensis (5.2%), and An. lesteri (1.6%). No sporozoite positive An. pullus or An. belenrae were observed. The results extend our knowledge of the distribution and potential role in malaria transmission of An. kleini, An. lesteri, and An. sinensis, for an area previously considered to be at a low risk for contracting vivax malaria.\",\n \"corpus_id\": 10740609,\n \"score\": 2\n },\n {\n \"doc_id\": \"22115320\",\n \"title\": \"The abundance and host-seeking behavior of culicine species (Diptera: Culicidae) and Anopheles sinensis in Yongcheng city, People's Republic of China.\",\n \"abstract\": \"BACKGROUND: The knowledge of mosquito species diversity and the level of anthropophily exhibited by each species in a region are of great importance to the integrated vector control. Culicine species are the primary vectors of Japanese encephalitis (JE) virus and filariasis in China. Anopheles sinensis plays a major role in the maintenance of Plasmodium vivax malaria transmission in China. The goal of this study was to compare the abundance and host-seeking behavior of culicine species and An. sinensis in Yongcheng city, a representative region of P. vivax malaria. Specifically, we wished to determine the relative attractiveness of different animal baits versus human bait to culicine species and An. sinensis. RESULTS: Culex tritaeniorhynchus was the most prevalent mosquito species and An. sinensis was the sole potential vector of P. vivax malaria in Yongcheng city. There were significant differences (P < 0.01) in the abundance of both An. sinensis and Cx. tritaeniorhynchus collected in distinct baited traps. The relative attractiveness of animal versus human bait was similar towards both An. sinensis and Cx. tritaeniorhynchus. The ranking derived from the mean number of mosquitoes per bait indicated that pigs, goats and calves frequently attracted more mosquitoes than the other hosts tested (dogs, humans, and chickens). These trends were similar across all capture nights at three distinct villages. The human blood index (HBI) of female An. sinensis was 2.94% when computed with mixed meals while 3.70% computed with only the single meal. 19:00~21:00 was the primary peak of host-seeking female An. sinensis while 4:00~5:00 was the smaller peak at night. There was significant correlation between the density of female An. sinensis and the average relative humidity (P < 0.05) in Wangshanzhuang village. CONCLUSIONS: Pigs, goats and calves were more attractive to An. sinensis and Cx. tritaeniorhynchus than dogs, humans, and chickens. Female An. sinensis host-seeking activity mainly occurred from 19:00 to 21:00. Thus, we propose that future vector control against An. sinensis and Cx. tritaeniorhynchus in the areas along the Huang-Huai River of central China should target the interface of human activity with domestic animals and adopt before human hosts go to bed at night.\",\n \"corpus_id\": 2559019,\n \"score\": 2\n },\n {\n \"doc_id\": \"22276651\",\n \"title\": \"Vector competence of five common mosquito species in the People's Republic of China for Western equine encephalitis virus.\",\n \"abstract\": \"Two strains of the Western equine encephalitis virus (WEEV) were first detected and isolated in China in 2001. The maintenance and transmission cycles of WEEV in China are currently not well understood, and the mosquito vectors involved in these cycles are unknown. To understand the ability of the local mosquitoes in China to transmit WEEV, the vector competence of five mosquito species, namely, Culex pipiens pallens Coquillett, Cx. p. quinquefasciatus Say, Aedes (Stegomyia) albopictus Skuse, Ae. ( Stegomyia) aegypti Linnaeus, and C. tritaeniorhynchus Giles, for WEEV were evaluated. Infection rates for Cx. p. pallens, Cx. p. quinquefasciatus, Cx. tritaeniorhynchus, Ae. Albopictus, and Ae. aegypti were 46%, 60%, 80%, 37%, and 25%, respectively. Dissemination rates for the same species were 60%, 61%, 75%, 55%, and 50%, respectively. Transmission rates were 41%, 53%, 57%, and 45% for Cx. p. pallens, Cx. p. quinquefasciatus, Ae. Albopictus, and Ae. Aegypti, respectively. Infection rates were significantly different between species, but the difference between dissemination and transmission rates were nonsignificant. These results suggest that several local mosquito species in China are competent laboratory vectors for WEEV.\",\n \"corpus_id\": 8024842,\n \"score\": 2\n },\n {\n \"doc_id\": \"22382193\",\n \"title\": \"Mosquito biting activity on humans & detection of Plasmodium falciparum infection in Anopheles stephensi in Goa, India.\",\n \"abstract\": \"BACKGROUND & OBJECTIVES: Knowledge of the bionomics of mosquitoes, especially of disease vectors, is essential to plan appropriate vector avoidance and control strategies. Information on biting activity of vectors during the night hours in different seasons is important for choosing personal protection measures. This study was carried out to find out the composition of mosquito fauna biting on humans and seasonal biting trends in Goa, India. METHODS: Biting activities of all mosquitoes including vectors were studied from 1800 to 0600 h during 85 nights using human volunteers in 14 different localities of three distinct ecotypes in Goa. Seasonal biting trends of vector species were analysed and compared. Seasonal biting periodicity during different phases of night was also studied using William's mean. RESULTS: A total of 4,191 mosquitoes of five genera and 23 species were collected. Ten species belonged to Anopheles, eight to Culex, three to Aedes and one each to Mansonia and Armigeres. Eleven vector species had human hosts, including malaria vectors Anopheles stephensi (1.3%), An. fluviatilis (1.8%), and An. culicifacies (0.76%); filariasis vectors Culex quinquefasciatus (40.8%) and Mansonia uniformis (1.8%); Japanese encephalitis vectors Cx. tritaeniorhynchus (17.4%), Cx. vishnui (7.7%), Cx. pseudovishnui (0.1%), and Cx. gelidus (2.4%); and dengue and chikungunya vectors Aedes albopictus (0.9%) and Ae. aegypti (0.6%). Two An. stephensi of the total 831 female anophelines, were found positive for P. falciparum sporozoites. The entomological inoculation rate (EIR) of P. falciparum was 18.1 and 2.35 for Panaji city and Goa, respectively. INTERPRETATION & CONCLUSIONS: Most of the mosquito vector species were collected in all seasons and throughout the scotophase. Biting rates of different vector species differed during different phases of night and seasons. Personal protection methods could be used to stop vector-host contact.\",\n \"corpus_id\": 30476903,\n \"score\": 2\n },\n {\n \"doc_id\": \"22403307\",\n \"title\": \"Mosquito infection studies with Aotus monkeys and humans infected with the Chesson strain of Plasmodiun vivax.\",\n \"abstract\": \"Oocyst counts were compared between mosquitoes that fed on humans versus mosquitoes that fed on Aotus monkeys, both of which were infected with the Chesson strain of Plasmodium vivax. Oocyst counts obtained from mosquitoes fed on humans were almost 10-fold higher in number. Mosquitoes were more likely to be infected and with a higher rate of infection when they fed on monkeys before the peak in the asexual parasite count. Mosquitoes that fed on humans were more likely to be more heavily infected when fed after the peak in the asexual count. Of several species of owl monkeys, Aotus vociferans was infected at a higher frequency. On the basis of oocyst counts, Anopheles dirus were the most susceptible and An. maculatus were the least susceptible of the mosquito species tested.\",\n \"corpus_id\": 20460805,\n \"score\": 2\n },\n {\n \"doc_id\": \"22776520\",\n \"title\": \"Vector capacity of Anopheles sinensis in malaria outbreak areas of central China.\",\n \"abstract\": \"BACKGROUND: Both falciparum and vivax malaria were historically prevalent in China with high incidence. With the control efforts, the annual incidence in the whole country has reduced to 0.0001% except in some areas in the southern borders after 2000. Despite this, the re-emergence or outbreak of malaria was unavoidable in central China during 2005-2007. In order to understand the role of the vector in the transmission of malaria during the outbreak period, the vector capacity of An. sinensis in Huanghuai valley of central China was investigated. FINDINGS: The study was undertaken in two sites, namely Huaiyuan county of Anhui province and Yongcheng county of Henan province. In each county, malaria cases were recorded for recent years, and transmission risk factors for each study village including anti-mosquito facilities and total number of livestock were recorded by visiting each household in the study sites. The specimens of mosquitoes were collected in two villages, and population density and species in each study site were recorded after the identification of different species, and the blood-fed mosquitoes were tested by ring precipitation test. Finally, various indicators were calculated to estimate vector capacity or dynamics, including mosquito biting rate (MBR), human blood index (HBI), and the parous rates (M). Finally, the vector capacity, as an important indicator of malaria transmission to predict the potential recurrence of malaria, was estimated and compared in each study site. About 93.0% of 80 households in Huaiyuan and 89.3% of 192 households in Yongcheng had anti-mosquito facilities. No cattle or pigs were found, only less than 10 sheep were found in each study village. A total of 94 and 107 Anopheles spp. mosquitos were captured in two study sites, respectively, and all of An. sinensis were morphologically identified. It was found that mosquito blood-feeding peak was between 9:00 pm and 12:00 pm. Man biting rate of An. sinensis was 6.0957 and 5.8621 (mosquitoes/people/night) estimated by using half-night human bait trap method and full-capture method, respectively. Human blood indexes (HBI) were 0.6667 (6/9) and 0.6429 (18/28), and man-biting habits were 0.2667 and 0.2572 in two sites, respectively. Therefore, the expectation of infective life and vector capacity of An. sinensis was 0.3649-0.4761 and 0.5502-0.7740, respectively, in Huanhuai valley of central China where the outbreak occurred, which is much higher than that in the previous years without malaria outbreak. CONCLUSIONS: This study suggests that vivax malaria outbreak in Huanhuai valley is highly related to the enhancement in vector capacity of An. sinensis for P. vivax, which is attributed to the local residents' habits and the remarkable drop in the number of large livestock leading to disappearance of traditional biological barriers.\",\n \"corpus_id\": 17026,\n \"score\": 2\n },\n {\n \"doc_id\": \"23243112\",\n \"title\": \"Mosquito species composition and Plasmodium vivax infection rates for Korean army bases near the demilitarized zone in the Republic of Korea, 2011.\",\n \"abstract\": \"Vivax malaria is a significant military and civilian health threat in northern Republic of Korea (ROK). Mosquito collections were performed at two ROK army installations, Paju near the demilitarized zone (DMZ) using black light traps in 2011. The DMZ, a 4 km wide border, is the northernmost point of the ROK and separates the ROK from the Democratic People's Republic of Korea (DPRK). Anopheles spp. were identified by polymerase chain reaction and screened for Plasmodium vivax sporozoites. Of 4,354 female Anopheles mosquitoes identified, Anopheles kleini (61.8%) was the most frequently collected, followed by Anopheles pullus (16.0%), Anopheles belenrae (9.0%), Anopheles sinensis (7.4%), Anopheles sineroides (4.2%), and Anopheles lesteri (1.6%). Anopheles kleini, An. pullus, and An. sineroides showed the highest population densities in June, whereas population densities were highest for An. belenrae, An. lesteri, and An. sinensis in August. The maximum likelihood estimation (estimated number of positive mosquitoes/1,000) for P. vivax was highest for An. lesteri (28.9), followed by An. sineroides (23.3), An. belenrae (15.8), An. sinensis (9.6), An. pullus (5.8) and An. kleini (4.2). The seasonal maximum likelihood estimation (MLE) values were variable among Anopheles species. Anopheles belenrae, An. Pullus, and An. sineroides showed the highest seasonal MLE's in July, whereas An. lesteri and An. sinensis exhibited the highest seasonal MLEs in September and An. kleini during August. This is the first report implicating An. sineroides as a vector of P. vivax in the ROK, and extends our knowledge of the distribution and potential role in malaria transmission.\",\n \"corpus_id\": 9395322,\n \"score\": 2\n },\n {\n \"doc_id\": \"23373272\",\n \"title\": \"[Establishment of early warning system of malaria epidemic situation in Jiangsu Province I impact of temperature on development of Plasmodium vivax in Anopheles sinensis in Jiangsu Province].\",\n \"abstract\": \"OBJECTIVE: To observe the developmental threshold temperature and the effective accumulated temperature of Plasmodium vivax sporozoites in Anopheles sinensis in Jiangsu Province, and to analyze the impact of temperature on the development of Plasmodium vivax. METHODS: The Anopheles sinensis mosquitoes were maintained under different temperatures of 16 +/- 0.5, 19 +/- 0.5, 22 +/- 0.5, 25 +/- 0.5, 28 +/- 0.5 degrees C and 31 +/- 0.5 degrees C in incubators after membrane feeding with Plasmodium vivax infected blood at laboratory. The salivary glands of Anopheles sinensis were dissected to confirm the development of sporozoite under different temperatures, and the developmental threshold temperature and the effective accumulated temperature of Plasmodium vivax sporozoites in Anopheles sinensis were calculated. The theoretical number of generations of Plasmodium vivax in Anopheles sinensis per year was calculated based on the average monthly temperatures of 13 municipalities in Jiangsu Province. RESULTS: The average developmental threshold temperature of Plasmodium vivax in Anopheles sinensis in Jiangsu Province was 15.31 degrees C, the average effective accumulated temperature was 109.81 day-degrees, and the optimal temperature for the proliferation of Plasmodium vivax was 25-28 degrees C. The theoretical generation number of Plasmodium vivax in sinensis in south Jiangsu was 1-3 generations being more than that in the north of the province. CONCLUSIONS: Temperature is one of the important influencing factors for the development of Plasmodium. The chance for Anopheles sinensis to transmit malaria increases under the temperature of 25-28 degrees C. However, other factors should be considered in the establishment of early warning system of malaria.\",\n \"corpus_id\": 37355768,\n \"score\": 2\n },\n {\n \"doc_id\": \"23658824\",\n \"title\": \"An impossible journey? The development of Plasmodium falciparum NF54 in Culex quinquefasciatus.\",\n \"abstract\": \"Although Anopheles mosquitoes are the vectors for human Plasmodium spp., there are also other mosquito species-among them culicines (Culex spp., Aedes spp.)-present in malaria-endemic areas. Culicine mosquitoes transmit arboviruses and filarial worms to humans and are vectors for avian Plasmodium spp., but have never been observed to transmit human Plasmodium spp. When ingested by a culicine mosquito, parasites could either face an environment that does not allow development due to biologic incompatibility or be actively killed by the mosquito's immune system. In the latter case, the molecular mechanism of killing must be sufficiently powerful that Plasmodium is not able to overcome it. To investigate how human malaria parasites develop in culicine mosquitoes, we infected Culex quinquefasciatus with Plasmodium falciparum NF54 and monitored development of parasites in the blood bolus and midgut epithelium at different time points. Our results reveal that ookinetes develop in the midgut lumen of C. quinquefasciatus in slightly lower numbers than in Anopheles gambiae G3. After 30 hours, parasites have invaded the midgut and can be observed on the basal side of the midgut epithelium by confocal and transmission electron microscopy. Very few of the parasites in C. quinquefasciatus are alive, most of them are lysed. Eight days after the mosquito's blood meal, no oocysts can be found in C. quinquefasciatus. Our results suggest that the mosquito immune system could be involved in parasite killing early in development after ookinetes have crossed the midgut epithelium and come in contact with the mosquito hemolymph.\",\n \"corpus_id\": 16989353,\n \"score\": 2\n },\n {\n \"doc_id\": \"23768077\",\n \"title\": \"Susceptibility of Anopheles sinensis to Plasmodium vivax in malarial outbreak areas of central China.\",\n \"abstract\": \"BACKGROUND: Anopheles sinensis, Anopheles anthropophagus, Anopheles minimus and Anopheles dirus are the major vectors of malaria transmission in China. Anopheles sinensis is considered a secondary vector due to its relatively low malaria-transmission ability. However, in 2005, an outbreak of over 40,000 Plasmodium vivax malaria cases was reported in areas where Anopheles sinensis was the only major vector. Therefore, it is necessary to reassess the malaria transmission ability of this vector species in China. METHODS: Laboratory colonies of An. sinensis and An. anthropophagus, and first-generation progeny (F1) of An. sinensis that had been collected in central China, were infected by direct membrane feeding assay with mono-vivax gametocyte-containing blood collected from vivax-infected patients. The mosquitoes were kept for 7 to 14 days post-blood feeding to allow parasites to develop into oocysts and sporozoites. Infectivity was measured by dissecting midguts and salivary glands. The presence of oocysts and sporozoites was determined by microscopy at 7 and 14 days post-blood feeding, and the numbers of gametocytes and asexual parasites, as well as mosquito parasite infections, were determined. RESULTS: The positive oocyst and sporozoite feed rates of the 142 pairs of lab-colony An. sinensis and An. anthropophagus were not significantly different, and the same results were found with the 10 pairs of laboratory and F1 An. sinensis. An. sinensis had more oocysts/midgut at 7 days post-feeding than An. anthropophagus, but the gametocytemia, asexual parasitemia, and ratio of macrogametocytes to microgametocytes, did not correlate with either oocyst or sporozoite infection. However, in the oocyst-positive mosquitoes, there was a correlation between gametocytemia and the average oocyst number/midgut. CONCLUSIONS: The susceptibility of An. sinensis (both laboratory and F1) to P. vivax-infected blood is similar to Anopheles anthropophagus, when evaluated by membrane feeding assay under laboratory conditions. In recent years, in central China, the vivax malaria transmission ability of An. sinensis has probably been underestimated. Further studies of this species in other regions are needed. An. sinensis could also be a good candidate vector for evaluating candidate malaria transmission-blocking vaccines (TBV).\",\n \"corpus_id\": 1492680,\n \"score\": 2\n },\n {\n \"doc_id\": \"24034528\",\n \"title\": \"The Anopheles community and the role of Anopheles minimus on malaria transmission on the China-Myanmar border.\",\n \"abstract\": \"BACKGROUND: Malaria around the China-Myanmar border is a serious health problem in the countries of South-East Asia. An. minimus is a principle malaria vector with a wide geographic distribution in this area. Malaria is endemic along the boundary between Yunnan province in China and the Kachin State of Myanmar where the local Anopheles community (species composition) and the malaria transmission vectors have never been clarified. METHODS: Adult Anopheles specimens were collected using CDC light traps in four villages along the border of China and Myanmar from May 2012 to April 2013. Morphological and molecular identification of mosquito adults confirmed the species of Anopheles. Blood-meal identification using the female abdomens was conducted using multiplex PCR. For sporozoite detection in An. minimus, sets of 10 female salivary glands were pooled and identified with SSU rDNA using nested PCR. Monthly abundance of An. minimus populations during the year was documented. The diversity of Anopheles and the role of An. minimus on malaria transmission in this border area were analyzed. RESULTS: 4,833 adult mosquitoes in the genus Anopheles were collected and morphologically identified to species or species complex. The Anopheles community is comprised of 13 species, and 78.83% of our total specimens belonged to An. minimus s.l., followed by An. maculatus (5.55%) and the An. culicifacies complex (4.03%). The quantity of trapped An. minimus in the rainy season of malaria transmission was greater than during the non-malarial dry season, and a peak was found in May 2012. An. minimus fed on the blood of four animals: humans (79.8%), cattle (10.6%), pigs (5.8%) and dogs (3.8%). 1,500 females of An. minimus were pooled into 150 samples and tested for sporozoites: only 1 pooled sample was found to have sporozoites of Plasmodium vivax. CONCLUSION: Anopheles is abundant with An. minimus being the dominant species and having a high human blood index along the China-Myanmar border. The sporozoites in An. minimus were determined to be Plasmodium vivax with a 0.07-0.7% infection rate.\",\n \"corpus_id\": 7811668,\n \"score\": 2\n },\n {\n \"doc_id\": \"24146951\",\n \"title\": \"Mosquitoes of Western Yunnan Province, China: seasonal abundance, diversity, and arbovirus associations.\",\n \"abstract\": \"OBJECTIVE: The western borderland between Yunnan Province, China, and Myanmar is characterized by a climate that facilitates year-round production of mosquitoes. Numerous mosquito-transmitted viruses, including Japanese encephalitis virus circulate in this area. This project was to describe seasonal patterns in mosquito species abundance and arbovirus activity in the mosquito populations. METHODS: Mosquitoes were collected in Mangshi and Ruili cities of Dehong Prefecture near the border of China and Burma in Yunnan Province, the Peoples Republic of China in 2010. We monitored mosquito species abundance for a 12-month period using ultraviolet light, carbon dioxide baited CDC light and gravid traps; and tested the captured mosquitoes for the presence of virus to evaluate mosquito-virus associations in rural/agricultural settings in the area. RESULTS: A total of 43 species of mosquitoes from seven genera were collected, including 15 Culex species, 15 Anopheles spp., four Aedes spp., three Armigeres spp., one Mimomyia spp., two Uranotaenia spp. and three Mansonia spp.. Species richness and diversity varied between Mangshi and Ruili. Culex tritaeniorhynchus, Culex quinquefasciatus, Anopheles sinensis and Anopheles peditaeniatus were the most abundant species in both sampling sites. Ultraviolet light traps collected more specimens than CDC light traps baited with dry ice, though both collected the same variety of mosquito species. The CDC gravid trap was the most effective trap for capture of Culex quinquefasciatus, a species underrepresented in light trap collections. A total of 26 virus strains were isolated, which included 13 strains of Japanese encephalitis virus, four strains of Getah virus, one strain of Oya virus, one strain from the orbivirus genus, and seven strains of Culex pipien pallens densovirus. CONCLUSIONS: The present study illustrates the value of monitoring mosquito populations and mosquito-transmitted viruses year-round in areas where the climate supports year-round adult mosquito activity.\",\n \"corpus_id\": 4032496,\n \"score\": 2\n },\n {\n \"doc_id\": \"24359307\",\n \"title\": \"Experimental Plasmodium vivax infection of key Anopheles species from the Brazilian Amazon.\",\n \"abstract\": \"BACKGROUND: Anopheles darlingi is the major malaria vector in countries located in the Amazon region. Anopheles aquasalis and Anopheles albitarsis s.l. are also proven vectors in this region. Anopheles nuneztovari s.l. and Anopheles triannulatus s.l. were found infected with Plasmodium vivax; however, their status as vectors is not yet well defined. Knowledge of susceptibility of Amazon anopheline populations to Plasmodium infection is necessary to better understand their vector capacity. Laboratory colonization of An. darlingi, the main Amazon vector, has proven to be difficult and presently An. aquasalis is the only available autonomous colony. METHODS: Larvae of An. darlingi, An. albitarsis s.l., An. nuneztovari s.l. and An. triannulatus s.l. were collected in the field and reared until adult stage. Adults of An. aquasalis were obtained from a well-established colony. Mosquitoes were blood-fed using a membrane-feeding device containing infected blood from malarial patients. The infection of the distinct Anopheles species was evaluated by the impact variance of the following parameters: (a) parasitaemia density; (b) blood serum inactivation of the infective bloodmeal; (c) influence of gametocyte number on infection rates and number of oocysts. The goal of this work was to compare the susceptibility to P. vivax of four field-collected Anopheles species with colonized An. aquasalis. RESULTS: All Anopheles species tested were susceptible to P. vivax infection, nevertheless the proportion of infected mosquitoes and the infection intensity measured by oocyst number varied significantly among species. Inactivation of the blood serum prior to mosquito feeding increased infection rates in An. darlingi and An. triannulatus s.l., but was diminished in An. albitarsis s.l. and An. aquasalis. There was a positive correlation between gametocyte density and the infection rate in all tests (Z = -8.37; p < 0.001) but varied among the mosquito species. Anopheles albitarsis s.l., An. aquasalis and An. nuneztovari s.l. had higher infection rates than An. darlingi. CONCLUSION: All field-collected Anopheles species, as well as colonized An. aquasalis are susceptible to experimental P. vivax infections by membrane feeding assays. Anopheles darlingi, An. albitarsis s.l. and An. aquasalis are very susceptible to P. vivax infection. However, colonized An. aquasalis mosquitoes showed the higher infection intensity represented by infection rate and oocyst numbers. This study is the first to characterize experimental development of Plasmodium infections in Amazon Anopheles vectors and also to endorse that P. vivax infection of colonized An. aquasalis is a feasible laboratory model.\",\n \"corpus_id\": 15098984,\n \"score\": 2\n },\n {\n \"doc_id\": \"24534811\",\n \"title\": \"Infection of laboratory-colonized Anopheles darlingi mosquitoes by Plasmodium vivax.\",\n \"abstract\": \"Anopheles darlingi Root is the most important malaria vector in the Amazonia region of South America. However, continuous propagation of An. darlingi in the laboratory has been elusive, limiting entomological, genetic/genomic, and vector-pathogen interaction studies of this mosquito species. Here, we report the establishment of an An. darlingi colony derived from wild-caught mosquitoes obtained in the northeastern Peruvian Amazon region of Iquitos in the Loreto Department. We show that the numbers of eggs, larvae, pupae, and adults continue to rise at least to the F6 generation. Comparison of feeding Plasmodium vivax ex vivo of F4 and F5 to F1 generation mosquitoes showed the comparable presence of oocysts and sporozoites, with numbers that corresponded to blood-stage asexual parasitemia and gametocytemia, confirming P. vivax vectorial capacity in the colonized mosquitoes. These results provide new avenues for research on An. darlingi biology and study of An. darlingi-Plasmodium interactions.\",\n \"corpus_id\": 13500805,\n \"score\": 2\n },\n {\n \"doc_id\": \"24820559\",\n \"title\": \"Infection and dissemination of West Nile virus in China by the potential vector, Culex pipiens pallens.\",\n \"abstract\": \"The distribution of the West Nile virus (WNV) in the organs and tissues of the mosquito Culex pipiens pallens, a potential vector of WNV in China, was investigated up to 14 days after oral infection. The WNV antigen was detected in paraffin-embedded mosquitoes using immunocytochemistry and viral titers of post-infected mosquitoes determined by plaque assay. Viral titers sharply decreased 24 h post-infection, were undetectable for the first few days, then rose over the course of infection. The first midgut infection appeared after one day, and the overall infection rate (based on midgut infection) was 43.9%. Other tissues, including hindgut, foregut, ovarian follicles, Malpighian tubules, and ommatidia, showed weak WNV antigens as early as three days post-infection. Staining in the salivary glands first appeared after seven days, and the salivary gland infection rate on the 14th day was 37.5%. Specimens with no detectable WNV antigens in any tissues, and with positive results confined to the midgut, anterior midgut, and hindgut, were observed on the 14th day. The route of viral dissemination from the midgut, and the relative importance of amplifying tissues in mosquitoes' susceptibility to infection, were evaluated. The results indicate that Cx. p. pallens has the ability to harbor WNV throughout its alimentary system and that midgut epithelial cells may be the initial site of the replication of this virus in this species.\",\n \"corpus_id\": 27558654,\n \"score\": 2\n },\n {\n \"doc_id\": \"25059361\",\n \"title\": \"[Investigation on mosquitoes and mosquito-borne viruses in Dehong prefecture, Yunnan province, 2007 and 2010].\",\n \"abstract\": \"OBJECTIVE: To investigate the distribution patterns of mosquito and mosquito-borne viruses in Dehong prefecture, Yunnan province, China. METHODS: Mosquito samples were collected using the mosquito traps from five counties of Dehong prefecture on July, 2007 and 2010. Mosquito were cell cultured for viral isolation, and positive isolates were identified using RT-PCR and sequence analysis. RESULTS: A total of 43 634 mosquito comprised of 29 species representing six genera were collected. Culex tritaeniorhynchus and Anopheles sinensis comprised 78.69% and 14.77% of the total. Six strains of viruses were isolated from the mosquito pools. RT-PCR and phylogenetic analysis revealed three strains from Cx. tritaeniorhynchus, identified as genotype I Japanese encephalitis virus (JEV). One strain was identified from Cx. tritaeniorhynchus, as Getah virus (GETV). Two strains isolated from Cx. tritaeniorhynchus and Anopheles vagus were identified as Culex pipiens pallens Densovirus (CppDNV). CONCLUSION: Cx. tritaeniorhynchus had been the major species of mosquito and mainly transmitting vector of mosquito-borne viruses in Dehong prefecture. Genotype I JEV, GETV and CppDNV were the vectors causing transmission of mosquito-borne diseases in this area. Data from phylogenetic analysis showed that these newly discovered isolates seemed to have had close relationship with those viruses previously circulating in Yunnan and other provinces of China.\",\n \"corpus_id\": 25080206,\n \"score\": 2\n },\n {\n \"doc_id\": \"25224069\",\n \"title\": \"Monitoring Plasmodium vivax chloroquine sensitivity along China-Myanmar border of Yunnan Province, China during 2008-2013.\",\n \"abstract\": \"BACKGROUND: Plasmodium vivax is the most widespread of the malaria parasites infecting human hosts. In malaria-eliminating settings, both imported and local malaria predominantly occurs in border areas, and most of them are P. vivax. Chloroquine (CQ) is the first-line drug for P. vivax treatment in China. To understand CQ sensitivity in P. vivax, in vivo monitoring of CQ resistance was conducted along the China-Myanmar border from 2008 to 2013. METHODS: Eligible patients with mono-infections of P. vivax were recruited to this study after obtaining full informed consent. CQ tablets for different categories of kg body weight ranges were given once a day for three days. Patients were followed up for 28 days. PCR was conducted to distinguish between re-infection and recrudescence, to confirm the Plasmodium species. The data were entered and analysed by the Kaplan-Meier method. Treatment outcome and sensitivity were classified according to the WHO recommended standards. RESULTS: 603 patients were completed valid follow-up. The fever clearance time and asexual parasite clearance times were, respectively, 22.2 ± 10.2 and 38.1 ± 12.6 hours. 594 (98.5%) patients were adequate clinical and parasitological response (ACPR), and nine (1.5%) patients, who were late clinical failure (LCF) or resistant response level I (RI), were imported from the neighbouring districts of Myanmar. CONCLUSION: In terms of efficacy, CQ is still effective for vivax malaria treatment. Plasmodium vivax CQ sensitivity had not significantly changed along the China-Myanmar border of Yunnan Province, China.\",\n \"corpus_id\": 15343343,\n \"score\": 2\n },\n {\n \"doc_id\": \"25481362\",\n \"title\": \"Enhancing longevity of Plasmodium vivax and P. falciparum sporozoites after dissection from mosquito salivary glands.\",\n \"abstract\": \"The pre-erythrocytic stages of Plasmodium vivax and Plasmodium falciparum remain challenging for experimental research in part due to limited access to sporozoites. An important factor limiting availability is the laboratory support required for producing infected mosquitoes and the ephemeral nature of isolated extracellular sporozoites. This study was undertaken to investigate methods to improve the availability of this limited resource by extending the longevity of the extracellular sporozoites after mosquito dissection. Our goal in this study was to determine whether buffer conditions more closely mimicking the insect microenvironment could prolong longevity of ex vivo P. vivax and P. falciparum sporozoites. The study compared the current standard dissection buffer RPMI1640 to Hank's Balanced Salt Solution with 1g/L glucose (HBSS-1) or 2g/L glucose (HBSS-2) and Grace's Insect Medium for ability to extend longevity of ex vivo P. vivax and P. falciparum sporozoites. The effect of each buffer on sporozoite viability was evaluated by measuring sporozoite gliding motility at 0, 4, 8, and 24h post-dissection from mosquito salivary glands. Comparisons of mean gliding percentages of ex vivo sporozoites in the different buffers and time points found that RPMI and Grace's both showed strong gliding at 0h. In contrast, by 4h post-dissection sporozoites in RPMI consistently had the lowest gliding activity, whereas sporozoites in Grace's had significantly more gliding compared to all other buffers at almost all time points. Our results indicate that P. vivax and P. falciparum sporozoites maintained in insect media rather than the standard dissection buffer RPMI and HBSS retain viability better over time.\",\n \"corpus_id\": 207314427,\n \"score\": 2\n },\n {\n \"doc_id\": \"25502034\",\n \"title\": \"Measure post-bloodmeal dispersal of mosquitoes and duration of radioactivity by using the isotope ³²P.\",\n \"abstract\": \"The radioactive isotope (32)P-labeled disodium phosphate (Na₂H(32)PO₄) was injected via the jugular vein into a cow kept in a shed in Maozhuang Village, Cao Township of Shanxian County, China. Over the following 5 d, mosquitoes feeding on the cow were captured at distances up to 400 m to determine dispersal distance. The duration of radioactivity in the cow and marked mosquitoes was 10 d. The results showed that after blood feeding, Anopheles sinensis and Culex tritaeniorhynchus temporarily rested in the cattle shed and then flew outdoors. In contrast, Culex pipiens pallens remained in the cattle shed after feeding. These findings confirmed that local An. sinensis and Cx. tritaeniorhynchus were partially endophilic and tended to rest out of doors, whereas Cx. pipiens pallens was endophilic. For marked An. sinensis and Cx. tritaeniorhynchus, there was a significant tendency for dispersal to be in a northeast and east direction, probably because of the presence of heavy shading by an agricultural field, a small river for mosquito oviposition sites, and locations downwind from the blood source. The furthest flight distances for An. sinensis and Cx. tritaeniorhynchus were 210 and 240 m; therefore, control of these mosquitoes should include resting places indoors and outdoors within a radius of 250 m from confirmed cases.\",\n \"corpus_id\": 205170445,\n \"score\": 2\n },\n {\n \"doc_id\": \"25958156\",\n \"title\": \"Complete sporogony of Plasmodium relictum (lineage pGRW4) in mosquitoes Culex pipiens pipiens, with implications on avian malaria epidemiology.\",\n \"abstract\": \"Plasmodium relictum (lineage pGRW4) causes malaria in birds and is actively transmitted in countries with warm climates and also temperate regions of the New World. In Europe, the lineage pGRW4 has been frequently reported in many species of Afrotropical migrants after their arrival from wintering grounds, but is rare in European resident birds. Obstacles for transmission of this parasite in Europe have not been identified. Culex quinquefasciatus is an effective vector of pGRW4 malaria, but this mosquito is absent from temperate regions of Eurasia. It remains unclear if the lineage pGRW4 completes sporogony in European species of mosquitoes. Here we compare the sporogonic development of P. relictum (pGRW4) in experimentally infected mosquitoes Culex pipiens pipiens form molestus, C. quinquefasciatus, and Ochlerotatus cantans. The pGRW4 parasite was isolated from a garden warbler Sylvia borin, multiplied, and used to infect laboratory-reared Culex spp. and wild-caught Ochlerotatus mosquitoes by allowing them to take blood meals on infected birds. The exposed females were maintained at a mean laboratory temperature of 19 °C, which ranged between 14 °C at night and 24 °C during daytime. They were dissected on intervals to study the development of sporogonic stages. Only ookinetes developed in O. cantans; sporogonic development was abortive. The parasite completed sporogony in both Culex species, with similar patterns of development, and sporozoites were reported in the salivary glands 16 days after infection. The presence of sporogonic stages of the lineage pGRW4 in mosquitoes was confirmed by PCR-based testing of (1) the sporozoites present in salivary glands and (2) the single oocysts, which were obtained by laser microdissection from infected mosquito midguts. This study shows that P. relictum (pGRW4) completes sporogony in C. p. pipiens at relatively low temperatures. We conclude that there are no restrictions for spreading this bird infection in Europe from the point of view of vector availability and temperature necessary for sporogony. Other factors should be considered and were discussed for the explanation of rare reports of this malaria parasite in Europe.\",\n \"corpus_id\": 17252261,\n \"score\": 2\n },\n {\n \"doc_id\": \"25975552\",\n \"title\": \"[Isolation and identification of mosquito-borne arboviruses in Yuncheng city, Shanxi province, 2012].\",\n \"abstract\": \"OBJECTIVE: To investigate the species and distribution of mosquitoes and mosquito-borne arboviruses in Yuncheng city of Shanxi province, China. METHODS: Mosquito samples were collected in 19 collection sites from Linyi county and Yongji city in Yuncheng city, in August, 2012. After identification and classification, all the specimens were homogenized and centrifuged to acquire supernatant before being inoculated to both C6/36 and BHK21 cells for viral isolation. Positive isolates were identified with arbovirus species-specific primers under RT-PCR, for further sequencing and phylogenetic analysis. RESULTS: A total of 10 455 mosquitoes of 7 species in 4 genuese were collected. The predominant mosquito species in Linyi county was Culex pipens pallens (91.96%, 3 911/4 253), but the one in Yongji city was Culex tritaeniorhynchus (72.85%, 4 518/6 202). A total of 23 strains of viruses were isolated from the mosquito pools. 15 strains from Culex tritaeniorhynchus and Culex pipens pallens were identified as genotype I Japanese encephalitis virus (JEV). Four strains from Culex pipens pallens were identified as Culex flavivirus (CxFV). Three strains from Culex pipens pallens were identified as Culex pipiens pallens densovirus (CppDNV). One strain from Armigeres subalbatus and Aedes albopictus was identified as Getah virus (GETV). CONCLUSION: Four kinds of arboviruses were isolated from the mosquito pools, including GETV and CxFV, which were isolated and documented in Shanxi province for the first time. In the city of Yuncheng, Culex tritaeniorhynchus had been the predominant species and major vector for transmitting JEV. Genotype I JEV remained the major JEV circulating in the local natural environment.\",\n \"corpus_id\": 43359136,\n \"score\": 2\n },\n {\n \"doc_id\": \"26259952\",\n \"title\": \"The suitability of laboratory-bred Anopheles cracens for the production of Plasmodium vivax sporozoites.\",\n \"abstract\": \"BACKGROUND: A stenogamous colony of Anopheles cracens (A. dirus B) established 20 years ago in a Thai insectary proved susceptible to Plasmodium vivax. However, routine sporozoite production by feeding on field-collected blood samples has not been described. The setting-up of an A. cracens colony in an insectary on the Thai-Myanmar border and the process of using P. vivax field samples for the production of infectious sporozoites are described. METHODS: The colony was started in 2012 from egg batches that were sent from the Department of Parasitology, Faculty of Medicine, University of Chiang Mai, to the Shoklo Malaria Research Unit (SMRU), on wet filter paper in sealed Petri dishes. From May 2013 to December 2014, P. vivax-infected blood samples collected from patients seeking care at SMRU clinics were used for membrane feeding assays and sporozoite production. RESULTS: Mosquitoes were fed on blood samples from 55 patients, and for 38 (69 %) this led to the production sporozoites. The average number of sporozoites obtained per mosquito was 26,112 (range 328-79,310). Gametocytaemia was not correlated with mosquito infectiousness (p = 0.82), or with the number of the sporozoites produced (Spearman's ρ = -0.016, p = 0.905). Infectiousness did not vary with the date of collection or the age of the patient. Mosquito survival was not correlated with sporozoite load (Spearman's ρ = 0.179, p = 0.282). CONCLUSION: Consistent and routine P. vivax sporozoites production confirms that A. cracens is highly susceptible to P. vivax infection. Laboratory-bred colonies of this vector are suitable for experimental transmission protocols and thus constitute a valuable resource.\",\n \"corpus_id\": 11072837,\n \"score\": 2\n },\n {\n \"doc_id\": \"26666959\",\n \"title\": \"Sporogony and sporozoite rates of avian malaria parasites in wild Culex pipiens pallens and C. inatomii in Japan.\",\n \"abstract\": \"BACKGROUND: Malaria infection in mosquitoes is traditionally detected by microscopic examination for Plasmodium oocysts and sporozoites. Although PCR is now widely used, the presence of parasite DNA in a mosquito does not prove that sporogony is achieved. Thus, detection of sporozoites by microscopy is still required to definitively identify vector mosquitoes. The aim of this study was to confirm sporogony of avian Plasmodium spp. in Culex pipiens pallens and C. inatomii caught from the wild. FINDINGS: Mosquitoes collected at two sites in Japan were dissected and examined by microscopy for Plasmodium oocysts and sporozoites. DNA was extracted from the midgut and salivary gland of infected mosquitoes, and the infecting Plasmodium species was identified by sequencing 478 bp of cytochrome b. Oocysts, or both oocysts and sporozoites, were found in 3.94 and 0.46 % of C. p. pallens and C. inatomii, respectively. Four (CXPIP09, GRW4, GRW11 and SGS1) and three cytochrome b lineages (CXINA01, CXINA02 and CXQUI01) were confirmed to achieve sporogony in C. p. pallens and C. inatomii, respectively. One mosquito each of C. p. pallens and C. inatomii was co-infected with two different Plasmodium lineages. CONCLUSIONS: These findings demonstrate that C. p. pallens and C. inatomii are natural vectors of four and three lineages of avian Plasmodium spp., respectively. The data indicate that a systematic procedure combining microscopy and PCR is a feasible and reliable approach to identify natural vectors of wildlife malaria.\",\n \"corpus_id\": 6537285,\n \"score\": 2\n },\n {\n \"doc_id\": \"26816489\",\n \"title\": \"Resistance Level of Mosquito Species (Diptera: Culicidae) from Shandong Province, China.\",\n \"abstract\": \"This study describes the aquatic habitats, species composition, and the insecticide resistance level of the mosquito Culex pipiens pallens in Shandong Province, China. A cross-sectional survey of mosquito larval habitats was conducted from May to November 2014 to determine the species composition and larval abundance. Larvae were collected using the standard dipping technique, and a total of four habitat types were sampled. The fourth instar larvae of Cx. pipiens pallens collected in each habitat type were tested for resistance to five insecticides according to a WHO bioassay. A total of 7,281 mosquito larvae were collected, of which 399 (5.48%) were categorized as Anopheles mosquito larvae (An. sinensis), 6636 (91.14%) as culicine larvae (Cx. pipiens pallens, Cx. tritaeniorhynchus, Cx. halifaxii, and Cx. bitaeniorhynchus), 213 (2.93%) as Armigeres larvae, and 33 (0.45%) as Aedes larvae (Aedes albopictus). In addition, a total of 1,149 mosquito pupae were collected. Culex larvae were distributed in all habitats investigated. Tukeys HSD analysis showed that roadside drainages were the most productive habitat type for Culex larvae. Armigeres species were found only in drains, Aedes only in water tanks, and Anopheles in water that was comparatively clear and rich in emergent plants. Bioassay showed that the maximum resistance level of Cx. pipiens pallens was to deltamethrin, while it was lowest to plifenate. The productivity of various mosquitoes in different habitat types is very heterogeneous. It is particularly important to modify human activity and the environment to achieve effective mosquito vector control. For effective larval control, the type of habitat should be considered, and the most productive habitat type should be given priority in mosquito abatement programs.\",\n \"corpus_id\": 8282206,\n \"score\": 2\n },\n {\n \"doc_id\": \"26822406\",\n \"title\": \"Plasmodium vivax gametocyte infectivity in sub-microscopic infections.\",\n \"abstract\": \"BACKGROUND: The use of molecular techniques has put in the spotlight the existence of a large mass of malaria sub-microscopic infections among apparently healthy populations. These sub-microscopic infections are considered an important pool for maintained malaria transmission. METHODS: In order to assess the appearance of Plasmodium vivax gametocytes in circulation, gametocyte density and the parasite infectivity to Anopheles mosquitoes, a study was designed to compare three groups of volunteers either experimentally infected with P. vivax sporozoites (early infections; n = 16) or naturally infected patients (acute malaria, n = 16 and asymptomatic, n = 14). In order to determine gametocyte stage, a quantitative reverse transcriptase PCR (RT-qPCR) assay targeting two sexual stage-specific molecular markers was used. Parasite infectivity was assessed by membrane feeding assays (MFA). RESULTS: In early infections P. vivax gametocytes could be detected starting at day 7 without giving rise to infected mosquitoes during 13 days of follow-up. Asymptomatic carriers, with presumably long-lasting infections, presented the highest proportion of mature gametocytes and were as infective as acute patients. CONCLUSIONS: This study shows the potential role of P. vivax asymptomatic carriers in malaria transmission should be considered when new policies are envisioned to redirect malaria control strategies towards targeting asymptomatic infections as a tool for malaria elimination.\",\n \"corpus_id\": 3912235,\n \"score\": 2\n },\n {\n \"doc_id\": \"26944051\",\n \"title\": \"Small-scale land-use variability affects Anopheles spp. distribution and concomitant Plasmodium infection in humans and mosquito vectors in southeastern Madagascar.\",\n \"abstract\": \"BACKGROUND: Deforestation and land-use change have the potential to alter human exposure to malaria. A large percentage of Madagascar's original forest cover has been lost to slash-and-burn agriculture, and malaria is one of the top causes of mortality on the island. In this study, the influence of land-use on the distribution of Plasmodium vectors and concomitant Plasmodium infection in humans and mosquito vectors was examined in the southeastern rainforests of Madagascar. METHODS: From June to August 2013, health assessments were conducted on individuals living in sixty randomly selected households in six villages bordering Ranomafana National Park. Humans were screened for malaria using species-specific rapid diagnostic tests (RDTs), and surveyed about insecticide-treated bed net (ITN) usage. Concurrently, mosquitoes were captured in villages and associated forest and agricultural sites. All captured female Anopheline mosquitoes were screened for Plasmodium spp. using a circumsporozoite enzyme-linked immunosorbent assay (csELISA). RESULTS: Anopheles spp. dominated the mosquito communities of agricultural and village land-use sites, accounting for 41.4 and 31.4 % of mosquitoes captured respectively, whereas Anopheles spp. accounted for only 1.6 % of mosquitoes captured from forest sites. Interestingly, most Anopheles spp. ( 67.7 %) were captured in agricultural sites in close proximity to animal pens, and 90.8 % of Anopheles mosquitoes captured in agricultural sites were known vectors of malaria. Three Anopheline mosquitoes (0.7 %) were positive for malaria (Plasmodium vivax-210) and all positive mosquitoes were collected from agricultural or village land-use sites. Ten humans (3.7 %) tested were positive for P. falciparum, and 23.3 % of those surveyed reported never sleeping under ITNs. CONCLUSIONS: This study presents the first report of malaria surveillance in humans and the environment in southeastern Madagascar. These findings suggest that even during the winter, malaria species are present in both humans and mosquitoes; with P. falciparum found in humans, and evidence of P. vivax-210 in mosquito vectors. The presence of P. vivax in resident vectors, but not humans may relate to the high incidence of humans lacking the Duffy protein. The majority of mosquito vectors were found in agricultural land-use sites, in particular near livestock pens. These findings have the potential to inform and improve targeted malaria control and prevention strategies in the region.\",\n \"corpus_id\": 15259771,\n \"score\": 2\n },\n {\n \"doc_id\": \"26969510\",\n \"title\": \"A method to preserve low parasitaemia Plasmodium-infected avian blood for host and vector infectivity assays.\",\n \"abstract\": \"BACKGROUND: Avian malaria vector competence studies are needed to understand more succinctly complex avian parasite-vector-relations. The lack of vector competence trials may be attributed to the difficulty of obtaining gametocytes for the majority of Plasmodium species and lineages. To conduct avian malaria infectivity assays for those Plasmodium spp. and lineages that are refractory to in vitro cultivation, it is necessary to obtain and preserve for short periods sufficient viable merozoites to infect naïve donor birds to be used as gametocyte donors to infect mosquitoes. Currently, there is only one described method for long-term storage of Plasmodium spp.-infected wild avian blood and it is reliable at a parasitaemia of at least 1%. However, most naturally infected wild-caught birds have a parasitaemia of much less that 1%. To address this problem, a method for short-term storage of infected wild avian blood with low parasitaemia (even ≤ 0.0005%) has been explored and validated. METHODS: To obtain viable infective merozoites, blood was collected from wild birds using a syringe containing the anticoagulant and the red blood cell preservative citrate phosphate dextrose adenine solution (CPDA). Each blood sample was stored at 4 °C for up to 48 h providing sufficient time to determine the species and parasitaemia of Plasmodium spp. in the blood by morphological examination before injecting into donor canaries. Plasmodium spp.--infected blood was inoculated intravenously into canaries and once infection was established, Culex stigmatosoma, Cx. pipiens and Cx. quinquefasciatus mosquitoes were then allowed to feed on the infected canaries to validate the efficacy of this method for mosquito vector competence assays. RESULTS: Storage of Plasmodium spp.--infected donor blood at 4 °C yielded viable parasites for 48 h. All five experimentally-infected canaries developed clinical signs and were infectious. Pathologic examination of three canaries that later died revealed splenic lesions typical of avian malaria infection. Mosquito infectivity assays demonstrated that Cx. stigmatosoma and Cx. pipiens were competent vectors for Plasmodium cathemerium. CONCLUSIONS: A simple method of collecting and preserving avian whole blood with malaria parasites of low parasitaemia (≤ 0.0005%) was developed that remained viable for further experimental bird and mosquito infectivity assays. This method allows researchers interested in conducting infectivity assays on target Plasmodium spp. to collect these parasites directly from nature with minimal impact on wild birds.\",\n \"corpus_id\": 14794735,\n \"score\": 2\n },\n {\n \"doc_id\": \"27355210\",\n \"title\": \"Optimization of a Membrane Feeding Assay for Plasmodium vivax Infection in Anopheles albimanus.\",\n \"abstract\": \"INTRODUCTION: Individuals exposed to malaria infections for a long time develop immune responses capable of blocking Plasmodium transmission to mosquito vectors, potentially limiting parasite spreading in nature. Development of a malaria TB vaccine requires a better understanding of the mechanisms and main effectors responsible for transmission blocking (TB) responses. The lack of an in vitro culture system for Plasmodium vivax has been an important drawback for development of a standardized method to assess TB responses to this parasite. This study evaluated host, vector, and parasite factors that may influence Anopheles mosquito infection in order to develop an efficient and reliable assay to assess the TB immunity. METHODS/PRINCIPAL FINDINGS: A total of 94 P. vivax infected patients were enrolled as parasite donors or subjects of direct mosquito feeding in two malaria endemic regions of Colombia (Tierralta, and Buenaventura). Parasite infectiousness was assessed by membrane feeding assay or direct feeding assay using laboratory reared Anopheles mosquitoes. Infection was measured by qPCR and by microscopically examining mosquito midguts at day 7 for the presence of oocysts. Best infectivity was attained in four day old mosquitoes fed at a density of 100 mosquitos/cage. Membrane feeding assays produced statistically significant better infections than direct feeding assays in parasite donors; cytokine profiles showed increased IFN-γ, TNF and IL-1 levels in non-infectious individuals. Mosquito infections and parasite maturation were more reliably assessed by PCR compared to microscopy. CONCLUSIONS: We evaluated mosquito, parasite and host factors that may affect the outcome of parasite transmission as measured by artificial membrane feeding assays. Results have led us to conclude that: 1) optimal mosquito infectivity occurs with mosquitoes four days after emergence at a cage density of 100; 2) mosquito infectivity is best quantified by PCR as it may be underestimated by microscopy; 3) host cellular immune response did not appear to significantly affect mosquito infectivity; and 4) no statistically significant difference was observed in transmission between mosquitoes directly feeding on humans and artificial membrane feeding assays.\",\n \"corpus_id\": 5028754,\n \"score\": 2\n },\n {\n \"doc_id\": \"27493248\",\n \"title\": \"Vector Competence of Anopheles kleini and Anopheles sinensis (Diptera: Culicidae) From the Republic of Korea to Vivax Malaria-Infected Blood From Patients From Thailand.\",\n \"abstract\": \"In total, 1,300 each of Anopheles kleini Rueda and Anopheles sinensis Wiedemann sensu stricto (s.s.) females (colonized from the Republic of Korea) and Anopheles dirus Peyton & Harrison (Thai strain) were allowed to feed on blood from Thai malaria patients naturally infected with Plasmodium vivax The overall oocyst infection rates for An. dirus, An. kleini, and An. sinensis s.s. were 77.4, 46.1, and 45.9%, respectively. The mean number of oocysts was significantly higher for An. dirus (82.7) compared with An. kleini (6.1) and An. sinensis s.s. ( 8.6), whereas the mean number of oocysts for An. kleini and An. sinensis s.s. was similar. The overall sporozoite infection rates for An. dirus, An. kleini, and An. sinensis s.s. dissected on days 14-15, 21, and 28 days post-feed were significantly higher for An. dirus (90.0%) than An. kleini (5.4%), whereas An. kleini sporozoite rates were significantly higher than An. sinensis s.s. ( <0.1%). The overall sporozoite indices for positive females with +3 (100-1,000 sporozoites) and +4 (>1,000 sporozoites) salivary gland indices were significantly higher for An. dirus (85.7%), compared with An. kleini (47.1%). Only one An. sinensis s.s. had sporozoites (+2; >10-100 sporozoites). These results indicate that An. kleini is a competent vector of vivax malaria. Although An. sinensis s.s. develops relatively high numbers of oocysts, it is considered a very poor vector of vivax malaria due to a salivary gland barrier.\",\n \"corpus_id\": 23349915,\n \"score\": 2\n },\n {\n \"doc_id\": \"27658591\",\n \"title\": \"Characteristics of Imported Malaria and Species of Plasmodium Involved in Shandong Province, China (2012-2014).\",\n \"abstract\": \"Malaria remains a serious public health problem in Shandong Province, China; therefore, it is important to explore the characteristics of the current malaria prevalence situation in the province. In this study, data of malaria cases reported in Shandong during 2012-2014 were analyzed, and Plasmodium species were confirmed by smear microscopy and nested-PCR. A total of 374 malaria cases were reported, 80.8% of which were reported from 6 prefectures. Of all cases, P. falciparum was dominant (81.3%), followed by P. vivax (11.8%); P. ovale and P. malariae together accounted for 6.4% of cases. Notably, for the first time since 2012, no indigenous case had been reported in Shandong Province, a situation that continued through 2014. Total 95.2% of cases were imported from Africa. The ratio of male/female was 92.5:1, and 96.8% of cases occurred in people 20-54 years of age. Farmers or laborers represented 77.5% of cases. No significant trends of monthly pattern were found in the reported cases. All patients were in good condition after treatment, except for 3 who died. These results indicate that imported malaria has increased significantly since 2012 in Shandong Province, especially for P. falciparum, and there is an emergence of species diversity.\",\n \"corpus_id\": 17868138,\n \"score\": 2\n },\n {\n \"doc_id\": \"27756355\",\n \"title\": \"Similar trends of susceptibility in Anopheles arabiensis and Anopheles pharoensis to Plasmodium vivax infection in Ethiopia.\",\n \"abstract\": \"BACKGROUND: Around half of the global population is living in areas at risk of malaria infection. Plasmodium vivax malaria has become increasingly prevalent and responsible for a high health and socio-economic burden in Ethiopia. The availability of gametocyte carriers and mosquito species susceptible to P. vivax infection are vital for malaria transmission. Determining the susceptibility of vector species to parasite infection in space and time is important in vector control programs. This study assesses the susceptibility of Anopheles arabiensis, An. pharoensis and An. coustani group to Plasmodium vivax infection in Ethiopia. METHODS: Larvae of An. arabiensis, An. pharoensis and An. coustani group were collected from an array of breeding sites and reared to adult under controlled conditions. Batches of adult female mosquitoes of the three species were allowed to feed in parallel on the same infected blood with gametocytes drawn from Plasmodium vivax infected patients by Direct Membrane Feeding Assays (DMFA). Fed mosquitoes were kept in an incubator under controlled laboratory conditions. Seven days after each feeding assay, mosquitoes were dissected for midgut oocyst microscopy and enumeration. Data were analysed using R statistical software package version 3.1.0. RESULTS: Over all, 8,139 adult female mosquitoes were exposed to P. vivax infection. Of the exposed mosquitoes 16.64 % (95 % CI: 1,354-8,139) were properly fed and survived until dissection. The infection rate in An. arabiensis and An. pharoensis was 31.72 % (95 % CI: 28.35-35.08) and 28.80 % (95 % CI: 25.31-32.28), respectively. The intensity of infection for An. arabiensis and An. pharoensis was 2.5 (95 % CI: 1.9-3.2) and 1.4 (95 % CI: 1.1-1.8), respectively. Gametocyte density was positively correlated to infection rate and intensity of infection in An. arabiensis as well as An. pharoensis. No An. coustani group mosquitoes were found infected, though almost four hundred mosquitoes were successfully fed and dissected. All groups received blood from the same infected blood source containing gametocytes in parallel. There was no significant difference in susceptibility rates between An. arabiensis and An. pharoensis (P = 0.215). CONCLUSIONS: Anopheles arabiensis and An. pharoensis showed similar susceptibility to P. vivax infection. However, An. coustani group was not permissive for the development of P. vivax parasites.\",\n \"corpus_id\": 10505738,\n \"score\": 2\n },\n {\n \"doc_id\": \"29082435\",\n \"title\": \"Natural Plasmodium vivax infections in Anopheles mosquitoes in a malaria endemic area of northeastern Thailand.\",\n \"abstract\": \"There was recently an outbreak of malaria in Ubon Ratchathani Province, northeastern Thailand. In the absence of information on malaria vector transmission dynamics, this study aimed to identify the anopheline vectors and their role in malaria transmission. Adult female Anopheles mosquitoes were collected monthly by human-landing catch in Na Chaluai District of Ubon Ratchathani Province during January 2014-December 2015. Field-captured mosquitoes were identified to species using morphology-based keys and molecular assays (allele-specific polymerase chain reaction, AS-PCR), and analysed for the presence of Plasmodium falciparum and Plasmodium vivax using an enzyme-linked immunosorbent assay (ELISA) for the detection of circumsporozoite proteins (CSP). A total of 1,229 Anopheles females belonging to 13 species were collected. Four anopheline taxa were most abundant: Members of the Anopheles barbirostris complex, comprising 38% of the specimens, species of the Anopheles hyrcanus group (18%), Anopheles nivipes (17%) and Anopheles philippinensis (12%). The other nine species comprised 15% of the collections. Plasmodium infections were detected in two of 668 pooled samples of heads/thoraces, Anopheles dirus (1/29) and An. philippinensis (1/97). The An. dirus pool had a mixed infection of P. vivax-210 and P. vivax-247, whereas the An. philippinensis pool was positive only for the latter protein variant. Both positive ELISA samples were confirmed by nested PCR. This study is the first to incriminate An. dirus and An. philippinensis as natural malaria vectors in the area where the outbreak occurred. This information can assist in designing and implementing a more effective malaria control programme in the province.\",\n \"corpus_id\": 3753470,\n \"score\": 2\n },\n {\n \"doc_id\": \"29460862\",\n \"title\": \"Host preferences and feeding patterns of Anopheles sinensis Wiedemann in three sites of Shandong province, China.\",\n \"abstract\": \"Background & objectives: Anopheles sinensis Wiedemann is a major vector of malaria and is among the dominant species in Shandong province of China. Knowledge of the blood-feeding patterns of mosquitoes is crucial for elimination of malaria vectors. However, little information is available on the blood-feeding behaviour of An. sinensis mosquitoes in Shandong province. This study was carried out to compare the blood-feeding behaviour of An. sinensis in malaria-endemic areas of Shandong province China. Methods: Adult Anopheles mosquitoes were collected from three malaria-endemic areas (Jimo, Yinan and Shanxian), during the peak months of mosquito population (August and September) from 2014 to 2015. Indoor-resting mosquitoes and outdoor-resting blood-fed females were sampled in the morning hours (0600 to 0900 hrs) from 10 randomly selected houses using pyrethrum spray catch method, and sweeping with an insect net. ELISA was used for the identification of blood meal. The blood meal of each mosquito was tested against antisera specific to human, pig, dog, cow, goat, horse (mule) and fowl. Results: At all indoor study locations of Jimo, Yinan and Shanxian, 59.4, 68.1 and 98.8% blood-engorged female An. sinensis collected from cattle sheds fed almost exclusively on bovines, respectively. For outdoor locations, at Jimo site, 27.27 and 49.55% An. sinensis fed on cattle and pigs; at Yinan, 30.42% fed on cattle and 36.88% fed both on cattle and goats, while no pig antibodies were detected. At Shanxian, percent of An. sinensis that fed on cattle, pigs and cattle-goat was 20.72, 27.62 and 21.78%, respectively. Interpretation & conclusion: The analysis of An. sinensis blood meals in all the three studied areas from human houses, cattle sheds, pig sheds and mixed dwellings revealed that An. sinensis prefers cattle hosts, and can feed on other available animal hosts if the cattle hosts are absent, and the mosquitoes readily feed on humans when domestic animals (cattle and pigs) are not nearby for feeding. The analysis of blood meal revealed that An. sinensis follow opportunistic feeding in Shandong province, China.\",\n \"corpus_id\": 3442265,\n \"score\": 2\n },\n {\n \"doc_id\": \"21340364\",\n \"title\": \"Susceptibility of Anopheles campestris-like and Anopheles barbirostris species complexes to Plasmodium falciparum and Plasmodium vivax in Thailand.\",\n \"abstract\": \"Nine colonies of five sibling species members of Anopheles barbirostris complexes were experimentally infected with Plasmodium falciparum and Plasmodium vivax. They were then dissected eight and 14 days after feeding for oocyst and sporozoite rates, respectively, and compared with Anopheles cracens. The results revealed that Anopheles campestris-like Forms E (Chiang Mai) and F (Udon Thani) as well as An. barbirostris species A3 and A4 were non-potential vectors for P. falciparum because 0% oocyst rates were obtained, in comparison to the 86.67-100% oocyst rates recovered from An. cracens. Likewise, An. campestris-like Forms E (Sa Kaeo) and F (Ayuttaya), as well as An. barbirostris species A4, were non-potential vectors for P. vivax because 0% sporozoite rates were obtained, in comparison to the 85.71-92.31% sporozoite rates recovered from An. cracens. An. barbirostris species A1, A2 and A3 were low potential vectors for P. vivax because 9.09%, 6.67% and 11.76% sporozoite rates were obtained, respectively, in comparison to the 85.71-92.31% sporozoite rates recovered from An. cracens. An. campestris-like Forms B and E (Chiang Mai) were high-potential vectors for P. vivax because 66.67% and 64.29% sporozoite rates were obtained, respectively, in comparison to 90% sporozoite rates recovered from An. cracens.\",\n \"corpus_id\": 7408328,\n \"score\": 1\n },\n {\n \"doc_id\": \"22296040\",\n \"title\": \"Correlation of Pfg377 ortholog gene expression of Plasmodium vivax and mosquito infection.\",\n \"abstract\": \"OBJECTIVE: To determine the expression of Pfg377 ortholog gene in Plasmodium vivax, and examine its correlation with mosquito infection. METHODS: Seventy clinical blood samples positive for P. vivax by microscopy, were used for the mosquito infectivity assay. Infectivity to female Anopheles dirus was determined from oocyst counts. The transcripts of Pfg377 ortholog gene of P. vivax from blood samples infective and non-infective to mosquitoes were examined using quantitative real-time reverse transcriptase-polymerase chain reaction (RT-PCR). RESULTS: Of 70 P. vivax positive blood samples, 50 (71.4%) samples were mosquito-infective and 20 (28.6%) were not. In infective samples, the expression level of Pfg377 ortholog gene was significantly higher than in the non-infective group (P<0.05). In infective samples, the expression level of Pfg377 ortholog gene at ≥100 copies/ml of blood cut-off point correlated with ≥10 oocysts/mosquito cut-off point of average oocyst numbers and with ≥50% cut-off point of per cent infected mosquitoes (Pearson's chi-square correlation, P=0.014 and P=0.026, respectively). CONCLUSION: The cut-off point of the expression level of Pfg377 ortholog gene could be used to predict the infectiousness of P. vivax gametocytes leading to mosquito infection and parasite transmission in the field.\",\n \"corpus_id\": 22279310,\n \"score\": 1\n },\n {\n \"doc_id\": \"22627302\",\n \"title\": \"Distribution of mosquitoes and mosquito-borne viruses along the China-Myanmar border in Yunnan Province.\",\n \"abstract\": \"A total of 54,673 mosquitoes were collected at 11 sites located near the China-Myanmar border in the western part of Yunnan Province during July and August 2007. There were 29 species in 4 genera identified from the collections, including 12 species of Culex, 12 species of Anopheles, 3 species of Aedes, and 2 species of Armigeres. Culex tritaeniorhynchus Giles (67.9%, 37,119/54,673) and Anopheles sinensis Wiedemann (25.9%, 14,170/54,673) were the most abundant species in this investigation. Virus was isolated using BHK-21 and C6/36 cells from 22 of 510 mosquito pools. Isolates included Japanese encephalitis virus (JEV) and Getah virus (GETV), which were identified by serological and molecular methods. Twenty JEV strains were isolated from Cx. tritaeniorhynchus (15 isolates), An. sinensis (3 isolates), and Armigeres subalbatus Coquillett (2 isolates), and 2 GETV strains were isolated from Culex pseudovishnui Colless and Cx. tritaeniorhynchus. This study suggests that Ar. subalbatus is a potentially important local vector because of the high JEV infection ratio found in this species. Enzootic JEV transmission persists in this area and therefore, surveillance for human disease caused by JEV and GETV should be conducted in the region.\",\n \"corpus_id\": 18671765,\n \"score\": 1\n },\n {\n \"doc_id\": \"23181931\",\n \"title\": \"Anopheles plumbeus (Diptera: Culicidae) in Europe: a mere nuisance mosquito or potential malaria vector?\",\n \"abstract\": \"BACKGROUND: Anopheles plumbeus has been recognized as a minor vector for human malaria in Europe since the beginning of the 20th century. In recent years this tree hole breeding mosquito species appears to have exploited novel breeding sites, including large and organically rich man-made containers, with consequently larger mosquito populations in close vicinity to humans. This lead to investigate whether current populations of An. plumbeus would be able to efficiently transmit Plasmodium falciparum, the parasite responsible for the most deadly form of malaria. METHODS: Anopheles plumbeus immatures were collected from a liquid manure pit in Switzerland and transferred as adults to the CEPIA (Institut Pasteur, France) where they were fed on P. falciparum gametocytes produced in vitro. Anopheles gambiae mosquitoes served as controls. Development of P. falciparum in both mosquito species was followed by microscopical detection of oocysts on mosquito midguts and by sporozoite detection in the head/thorax by PCR and microscopy. RESULTS: A total of 293 wild An. plumbeus females from four independent collections successfully fed through a membrane on blood containing P. falciparum gametocytes. Oocysts were observed in mosquito midguts and P. falciparum DNA was detected in head-thorax samples in all four experiments, demonstrating, on a large mosquito sample, that An. plumbeus is indeed receptive to P. falciparum NF54 and able to produce sporozoites. Importantly, the proportion of sporozoites-infected An. plumbeus was almost similar to that of An. gambiae (31 to 88% An. plumbeus versus 67 to 97% An. gambiae). However, the number of sporozoites produced was significantly lower in infected An. plumbeus. CONCLUSION: The results show that a sample of field-caught An. plumbeus has a moderate to high receptivity towards P. falciparum. Considering the increased mobility of humans between Europe and malaria endemic countries and changes in environment and climate, these data strongly suggest that An. plumbeus could act as a vector for malaria and thus significantly contribute to increasing the malaria transmission risk in Central-Western Europe. In locations showing high vulnerability to the presence of gametocyte carriers, the risk of transmission of malaria by An. plumbeus should be considered.\",\n \"corpus_id\": 1877118,\n \"score\": 1\n },\n {\n \"doc_id\": \"24979183\",\n \"title\": \"Complete sporogony of Plasmodium relictum (lineages pSGS1 and pGRW11) in mosquito Culex pipiens pipiens form molestus, with implications to avian malaria epidemiology.\",\n \"abstract\": \"Plasmodium parasites (Plasmodiidae) cause malaria in many species of terrestrial vertebrates and are transmitted mainly by mosquitoes (Culicidae). Avian malaria is often caused by Plasmodium relictum , a cosmopolitan hemosporidian infection. Numerous genetic lineages of P. relictum have been described. However, it remains unclear if these lineages can be transmitted by Culex pipiens pipiens form molestus, which is widespread but has been insufficiently investigated as a possible vector of avian malaria. The aim of this study was to test experimentally if 2 common P. relictum lineages complete sporogony in the experimentally infected insects. The mosquitoes were cultivated under laboratory conditions. Unfed females were allowed to take blood meals on domestic canaries experimentally infected with the lineages pSGS1 and pGRW11 of P. relictum . These lineages are widespread and cause malaria in many species of birds. Infected female flies were examined for sporogonic development of each parasite lineage. Both exposed groups were maintained under the same laboratory conditions. Mosquitoes were dissected at intervals, and the midguts and salivary glands were prepared in order to detect sporogonic stages. Numerous ookinetes, oocysts, and sporozoites of both parasite lineages were observed. Polymerase chain reaction confirmed the presence of corresponding parasite lineages in the experimentally infected insects. Sporogonic stages of both lineages were morphologically similar and developed synchronously in this mosquito; however, the lineage pGRW11 developed a significantly greater number of oocysts than did the lineage pSGS1. This study shows that Culex p. pipiens f. molestus is susceptible to 2 widespread lineages of P. relictum and worth more attention in avian malaria epidemiology. We recommend C. p. pipiens f. molestus for experimental research of avian malaria parasites, principally because it willingly takes blood meals on birds and because it is easy to establish and maintain new colonies of this insect under laboratory conditions using wild-sampled eggs, larvae, or imago.\",\n \"corpus_id\": 25648185,\n \"score\": 1\n },\n {\n \"doc_id\": \"25843138\",\n \"title\": \"Host feeding patterns of mosquitoes in a rural malaria-endemic region in hainan island, china.\",\n \"abstract\": \"Malaria is endemic in Wangxia Village of Hainan Island. In this area little is known about the host seeking behavior and feeding habit of mosquitoes. Three sites representing the most common habitat types in the village were selected to study the host seeking behavior and feeding habit of mosquitoes. Of the total 9 species belonging to 4 genera (Armigeres, Culex, Aedes, and Anopheles) collected in Wangxia Village, Culex tritaeniorhynchus and Cx. pipiens quinquefasciatus were the most commonly collected species. Armigeres subalbatus and Anopheles sinensis were moderately common species. Blood meal analysis confirmed that Cx. tritaeniorhynchus and Cx. p. quinquefasciatus fed on multiple hosts, mainly poultry but occasionally other animals. Anopheles sinensis, a vector of malaria, fed predominately on cattle hosts, followed by humans. Anopheles maculatus and An. barbirostris fed on both humans and domestic animals. Our results indicate that most mosquitoes in this area preferred domestic animals over humans and showed a tendency to feed on multiple hosts within the same gonotrophic cycle. Therefore, the potential role of domestic animals in arbovirus transmission should be evaluated as part of a strategy for controlling mosquito-borne diseases in this region.\",\n \"corpus_id\": 8236412,\n \"score\": 1\n },\n {\n \"doc_id\": \"26118548\",\n \"title\": \"Distribution and phylogenetic analysis of Culex flavivirus in mosquitoes in China.\",\n \"abstract\": \"Culex flavivirus (CxFV) is an insect-specific virus of the genus Flavivirus. CxFV strains have been isolated from Cx. pipiens, Cx. quinquefasciatus, and other Cx. species in Asia, Africa, North America, Central America and South America. CxFV was isolated for the first time in China in 2006. As this is a novel flavivirus, we explored the distribution and genetic characteristics of Culex flavivirus in China. A total of 46,649 mosquitoes were collected in seven provinces between 2004 and 2012 and were analysed in 871 pools. 29 CxFV RNAs from Cx. pipiens, Cx. tritaeniorhynchus, Anopheles Sinensis, and Culex spp. tested positive for CxFV in real-time RT-PCR. 6 CxFV strains were isolated from Cx. species collected in Shandong, Henan, and Shaanxi provinces, while no virus or viral RNA was detected in samples from Sichuan, Chongqing, Hubei, and Fujian. Phylogenetic analysis of the envelope gene indicated that Chinese strains formed a robust subgroup of genotype 1, together with viruses from the United States and Japan. This study demonstrates that the geographic distribution of CxFV in China is widespread, but geographical boundaries to spread are apparent. Our findings suggest that CxFV can infect various mosquito species in nature.\",\n \"corpus_id\": 14530000,\n \"score\": 1\n },\n {\n \"doc_id\": \"26805471\",\n \"title\": \"Species composition, co-occurrence, association and affinity indices of mosquito larvae (Diptera: Culicidae) in Mazandaran Province, northern Iran.\",\n \"abstract\": \"Although considerable progress has been made in the past years in management of mosquito borne diseases such as malaria, dengue, yellow fever and West Nile fever through research in biology and ecology of the vectors, these diseases are still major threats to human health. Therefore, more research is required for better management of the diseases. This investigation provides information on the composition, co-occurrence, association and affinity indices of mosquito larvae in Mazandaran Province, northern Iran. In a large scale field study, mosquito larvae were collected from 120 sentinel sites in 16 counties in Mazandaran Province, using standard 350 ml dipper. Sampling took place monthly from May to December 2014. Collected larvae were mounted on glass slides using de Faure's medium and were diagnosed using morphological characters. Totally, 19,840 larvae were collected including three genera and 16 species from 120 larval habitats, as follows: Anopheles claviger, Anopheles hyrcanus, Anopheles maculipennis s.l., Anopheles marteri, Anopheles plumbeus, Anopheles pseudopictus, Culex pipiens, Culex tritaeniorhynchus, Culex torrentium, Culex perexiguus, Culex territans, Culex mimeticus, Culex hortensis, Culiseta annulata, Culiseta longiareolata, and Culiseta morsitans. Predominant species were Cx. pipiens and An. maculipennis s.l. which show the highest co-occurrence. The pair of species An. hyrcanus/An. pseudopictus showed significant affinity and association. High co-occurrence of the predominant species Cx. pipiens and An. maculipennis s.l. in the study area is of considerable importance in terms of vector ecology. It was also revealed that An. pseudopictus/An. hyrcanus often occur sympatrically indicating their common habitat requirements. The information may be equally important when vector control measures are considered.\",\n \"corpus_id\": 205239654,\n \"score\": 1\n },\n {\n \"doc_id\": \"27301693\",\n \"title\": \"High susceptibility of wild Anopheles funestus to infection with natural Plasmodium falciparum gametocytes using membrane feeding assays.\",\n \"abstract\": \"BACKGROUND: Anopheles funestus is a major vector of malaria in sub-Saharan Africa. However, because it is difficult to colonize, research on this mosquito species has lagged behind other vectors, particularly the understanding of its susceptibility and interactions with the Plasmodium parasite. The present study reports one of the first experimental infections of progeny from wild-caught An. funestus with the P. falciparum parasite providing a realistic avenue for the characterisation of immune responses associated with this infection. METHODS: Wild-fed resting An. funestus females were collected using electric aspirators and kept in cages for four days until they were fully gravid and ready to oviposit. The resulting eggs were reared to adults F1 mosquitoes under insectary conditions. Three to five day-old An. funestus F1 females were fed with infected blood taken from gametocyte carriers using an artificial glass-parafilm feeding system. Feeding rate was recorded and fed mosquitoes were dissected at day 7 to count oocysts in midguts. Parallel experiments were performed with the known Plasmodium-susceptible An. coluzzii Ngousso laboratory strain, to monitor our blood handling procedures and infectivity of gametocytes. RESULTS: The results revealed that An. funestus displays high and similar level of susceptibility to Plasmodium infection compared to An. coluzzii, and suggest that our methodology produces robust feeding and infection rates in wild An. funestus progeny. The prevalence of infection in An. funestus mosquitoes was 38.52 % (range 6.25-100 %) and the median oocyst number was 12.5 (range 1-139). In parallel, the prevalence in An. coluzzii was 39.92 % (range 6.85-97.5 %), while the median oocyst number was 32.1 (range 1-351). CONCLUSIONS: Overall, our observations are in line with the fact that both species are readily infected with P. falciparum, the most common and dangerous malaria parasite in sub-Saharan Africa, and since An. funestus is widespread throughout Africa, malaria vector control research and implementation needs to seriously address this vector species too. Additionally, the present work indicates that it is feasible to generate large number of wild F1 infected An. funestus mosquitoes using membrane feeding assays, which can be used for comprehensive study of interactions with the Plasmodium parasite.\",\n \"corpus_id\": 1404544,\n \"score\": 1\n },\n {\n \"doc_id\": \"27444629\",\n \"title\": \"The mitochondrial genomes of Culex tritaeniorhynchus and Culex pipiens pallens (Diptera: Culicidae) and comparison analysis with two other Culex species.\",\n \"abstract\": \"BACKGROUND: Culex tritaeniorhynchus and Culex pipiens pallens are the major vectors of the Japanese encephalitis virus and Wuchereria bancrofti, the causative agent of filariasis. The knowledge of mitochondrial genomes has been widely useful for the studies on molecular evolution, phylogenetics and population genetics. METHODS: In this study, we sequenced and annotated the mitochondrial (mt) genomes of Cx. tritaeniorhynchus and Cx. p. pallens, and performed a comparative analysis including four known mt genomes of species of the subgenus Culex (Culex). The phylogenetic relationships of Cx. tritaeniorhynchus, Cx. p. pallens and four known Culex mt genome sequences were reconstructed by maximum likelihood based on concatenated protein-coding gene sequences. RESULTS: Culex tritaeniorhynchus and Cx. p. pallens mt genomes are 14,844 bp and 15,617 bp long, both consists of 13 PCGs, 22 tRNAs, 2 rRNAs and 1 CR (not sequenced for Cx. tritaeniorhynchus). The initiation and termination codons of PCGs are ATN and TAA, respectively, except for COI starting with TCG, and COI and COII terminated with T. tRNAs have the typical clover-leaf secondary structures except for trnS ((AGN)) that is lacking the DHU stem. 16S rRNA and 12S rRNA secondary structures were drawn for the first time for mosquito mt genomes. The control region of Cx. p. pallens mt genome is 747 bp long and with four tandem repeat structures. Phylogenetic analyses demonstrated that the mt genome of Cx. tritaeniorhynchus was significantly separated from the remaining five mt genomes of Culex spp. Culex p. pipiens, Cx. p. pallens and Cx. p. quinquefasciatus formed a monophyletic clade with Cx. p. quinquefasciatus linked in the middle of the clade, and Cx. p. pallens should have the same taxonomic level as Culex p. pipiens and Cx. p. quinquefasciatus. CONCLUSIONS: The mt genomes of Cx. tritaeniorhynchus and Cx. p. pallens share the same gene composition and order with those of two other Culex species. Culex p. pallens of the Pipiens complex should have the same taxonomic level as Culex p. pipiens and Cx. p. quinquefasciatus investigated. We enriched the Culex mt genome data and provided a reference basis for further Culex mt genome sequencing and analyses.\",\n \"corpus_id\": 13947030,\n \"score\": 1\n },\n {\n \"doc_id\": \"28962620\",\n \"title\": \"Avian Plasmodium in Eastern Austrian mosquitoes.\",\n \"abstract\": \"BACKGROUND: Insect vectors, namely mosquitoes (Diptera: Culicidae), are compulsory for malaria parasites (Plasmodium spp.) to complete their life cycle. Despite this, little is known about vector competence of different mosquito species for the transmission of avian malaria parasites. METHODS: In this study, nested PCR was used to determine Plasmodium spp. occurrence in pools of whole individuals, as well as the diversity of mitochondrial cytochrome b gene sequences in wild-caught mosquitoes sampled across Eastern Austria in 2013-2015. RESULTS: A total of 45,749 mosquitoes in 2628 pools were collected, of which 169 pools (6.43%) comprising 9 mosquito species were positive for avian Plasmodium, with the majority of positives in mosquitoes of Culex pipiens s.l./Culex torrentium. Six different avian Plasmodium lineages were found, the most common were Plasmodium vaughani SYAT05, Plasmodium sp. Linn1 and Plasmodium relictum SGS1. In 2014, mosquitoes of the Culex pipiens complex were genetically identified and Culex pipiens f. pipiens presented with the highest number of avian Plasmodium positives (n = 37; 16.74%). Despite this, the minimum infection rate (MIR) was highest in Culex torrentium (5.36%) and Culex pipiens f. pipiens/f. molestus hybrids (5.26%). During 2014 and 2015, seasonal and annual changes in Plasmodium lineage distribution were also observed. In both years P. vaughani SYAT05 dominated at the beginning of the sampling period to be replaced later in the year by P. relictum SGS1 (2014) and Plasmodium sp. Linn1 (2015). CONCLUSIONS: This is the first large-scale study of avian Plasmodium parasites in Austrian mosquitoes. These results are of special interest, because molecular identification of the taxa of the Cx. pipiens complex and Cx. torrentium enabled the determination of Plasmodium prevalence in the different mosquito taxa and hybrids of this complex. Since pools of whole insects were used, it is not possible to assert any vector competence in any of the examined mosquitoes, but the results are nonetheless valuable in providing an overview of avian Plasmodium species and lineages present in Austria.\",\n \"corpus_id\": 27785142,\n \"score\": 1\n },\n {\n \"doc_id\": \"29536705\",\n \"title\": \"[Analysis of population genetic diversity of mosquitoes from Shandong Province based on mitochondrial DNA cytochrome oxidase subunit I gene fragment].\",\n \"abstract\": \"OBJECTIVE: To explore the characteristics of gene sequence of mtDNA-COⅠ of Culex pipiens pallens from different geographical regions in Shandong Province and different resistant strains from the lab and five common mosquito species, and analyze the genetic diversity of these mosquitoes. METHODS: Adult mosquitoes were collected from Jinan, Jining, Qingdao cities and other places in Shandong Province. The sensitive, dichlorvos-resistant, pyrethroid-resistant and propoxur-resistant strains were reared in the lab. Five species of mosquito (Cx. pipiens pallens, Cx. tritaeniorhynchus, Anopheles sinensis, Aedes albopictus, and Armigeres subalbatus) were collected from Jining City and identified in the lab. mtDNA-COⅠwas specifically amplified by PCR and sequenced. The gene sequences were compared and analyzed by the biological information systems, and the phylogenetic tree was constructed. RESULTS: The amplified mtDNA-COⅠfragments of Cx. pipiens pallens from eight different cities and four different resistant strains were 528 bp in length, with 67.4% A+T contents and two mutation sites. The nucleotide sequence homology among the different geographic strains was 99.95% and the gene sequences of the four resistant strains were the same, showing a high homogeny. The amplified mtDNA-COⅠfragments of the five species of mosquitoes were 528 bp with 408 conserved sites, 120 variable sites, 42 parsimony informative sites and 78 singleton sites. The A+T contents were between 65.7% and 68.0%. The nucleotide sequence homology among the different mosquito species was between 86.17% and 92.05%, and the molecular identification was consistent with the traditional morphological identification. The molecular phylogenetic study showed that the different species were clustered at their own branch at the species and genus levels, while genera Armigeres was distantly related to the others. CONCLUSIONS: mtDNA-COⅠcould not serve as the molecular marker to analyze the population genetic variation and phylogenesis of Cx. pipiens pallens from different geographical regions and different resistant strains, but it has species and genus specificities, which could be used for the identification of the mosquito species and genus.\",\n \"corpus_id\": 3847185,\n \"score\": 1\n },\n {\n \"doc_id\": \"29723510\",\n \"title\": \"Infection of mosquitoes from in vitro cultivated Plasmodium knowlesi H strain.\",\n \"abstract\": \"In vitro studies of sexual blood stages of the most fatal malaria species, Plasmodium falciparum, have revealed key processes by which gametocytes develop and transmit infection from humans to anopheline mosquitoes. However, most malaria cases outside sub-Saharan Africa are caused by other Plasmodium spp., frequently Plasmodium vivax and Plasmodium knowlesi, a zoonotic parasite of macaque monkeys. Gametocytes of P. vivax and P. knowlesi exhibit distinct morphology, faster development, and a shorter life span compared with gametocytes of P. falciparum, reflecting the evolutionary separation and biological differences of these species. Unlike P. falciparum, P. vivax cannot be cultivated in vitro, necessitating access to infected primates for laboratory studies. In contrast, P. knowlesi asexual stages have been successfully adapted to cultures in macaque and human red blood cells, but these stages have not been reported to produce gametocytes infective to mosquitoes. Here, we show that gametocyte production and sporadic, low-level mosquito infectivity of a P. knowlesi strain was not improved by application of a \\\"crash\\\" method commonly used to induce gametocytes in P. falciparum cultures. However, Percoll-gradient purified schizonts from this strain yielded highly synchronised populations that, in three of six experiments, produced infections at an average rate of 0.97-9.1 oocysts in Anopheles dirus mosquitoes. Oocyst counts were most abundant in mosquitoes that were fed from the synchronised cultures 36 h after schizont purification. Gametocytes in these cultures occurred at low prevalence and were difficult to observe. Transcription from orthologs of P. falciparum gametocyte-specific markers did not correlate with infectivity of the P. knowlesi parasites to mosquitoes. The ability to infect mosquitoes from in vitro-cultivated P. knowlesi will support research on the unique features of this emerging pathogen and facilitate comparative studies of transmission by the different human malarias.\",\n \"corpus_id\": 19141194,\n \"score\": 1\n },\n {\n \"doc_id\": \"21194433\",\n \"title\": \"Insecticide resistance and malaria transmission: infection rate and oocyst burden in Culex pipiens mosquitoes infected with Plasmodium relictum.\",\n \"abstract\": \"BACKGROUND: The control of most vectors of malaria is threatened by the spread of insecticide resistance. One factor that has been hitherto largely overlooked is the potential effects of insecticide resistance on the ability of mosquitoes to transmit malaria: are insecticide-resistant mosquitoes as good vectors of Plasmodium as susceptible ones? The drastic physiological changes that accompany the evolution of insecticide resistance may indeed alter the ability of vectors to transmit diseases, a possibility that, if confirmed, could have major epidemiological consequences. METHODS: Using a novel experimental system consisting of the avian malaria parasite (Plasmodium relictum) and its natural vector (the mosquito Culex pipiens), two of the most common mechanisms of insecticide resistance (esterase overproduction and acetylcholinesterase modification) were investigated for their effect on mosquito infection rate and parasite burden. For this purpose two types of experiments were carried out using (i) insecticide-resistant and susceptible laboratory isogenic lines of Cx. pipiens and (ii) wild Cx. pipiens collected from a population where insecticide resistant and susceptible mosquitoes coexist in sympatry. RESULTS: The isogenic line and wild-caught mosquito experiments were highly consistent in showing no effect of either esterase overproduction or of acetylcholinesterase modification on either the infection rate or on the oocyst burden of mosquitoes. The only determinant of these traits was blood meal size, which was similar across the different insecticide resistant categories in both experiments. CONCLUSIONS: Insecticide resistance was found to have no effect on Plasmodium development within the mosquito. This is the first time this question has been addressed using a natural mosquito-Plasmodium combination, while taking care to standardize the genetic background against which the insecticide resistance genes operate. Infection rate and oocyst burden are but two of the factors that determine the vectorial capacity of mosquitoes. Other key determinants of parasite transmission, such as mosquito longevity and behaviour, or the parasite's incubation time, need to be investigated before concluding on whether insecticide resistance influences the ability of mosquitoes to transmit malaria.\",\n \"corpus_id\": 2887708,\n \"score\": 0\n },\n {\n \"doc_id\": \"21290944\",\n \"title\": \"Evaluation of octenol and Lurex as baits in Mosquito Magnet Pro traps to collect vector mosquitoes in China.\",\n \"abstract\": \"The effectiveness of the attractants 1-octen-3-ol (octenol) and L-lactic acid (Lurex) on the collection of Aedes albopictus, Culex tritaeniorhynchus, Cx. pipiens pallens, and Anopheles sinensis was first evaluated in Mosquito Magnet Pro traps in Yamenkou and Badachu residential areas, Beijing City, and Lishui area, Zhejiang Province, China. The Mosquito Magnet Pro traps baited with octenol collected significantly more Ae. albopictus, Cx. tritaeniorhynchus, and An. sinensis, but fewer Cx. pipiens pallens than collection by the traps alone. There were no significant differences in the numbers of Cx. pipiens pallens, Cx. tritaeniorhynchus, and An. sinensis collected by Mosquito Magnet Pro traps baited with Lurex compared to the traps alone, but the Mosquito Magnet Pro traps baited with Lurex collected significantly more Ae. albopictus than the number collected by the traps alone at 2 areas in Beijing.\",\n \"corpus_id\": 42023971,\n \"score\": 0\n },\n {\n \"doc_id\": \"28693607\",\n \"title\": \"Dynamics of Plasmodium vivax sporogony in wild Anopheles stephensi in a malaria-endemic region of Western India.\",\n \"abstract\": \"BACKGROUND: In global efforts to track mosquito infectivity and parasite elimination, controlled mosquito-feeding experiments can help in understanding the dynamics of parasite development in vectors. Anopheles stephensi is often accepted as the major urban malaria vector that transmits Plasmodium in Goa and elsewhere in South Asia. However, much needs to be learned about the interactions of Plasmodium vivax with An. stephensi. As a component of the US NIH International Center of Excellence for Malaria Research (ICEMR) for Malaria Evolution in South Asia (MESA), a series of membrane-feeding experiments with wild An. stephensi and P. vivax were carried out to better understand this vector-parasite interaction. METHODS: Wild An. stephensi larvae and pupae were collected from curing water in construction sites in the city of Ponda, Goa, India. The larvae and pupae were reared at the MESA ICEMR insectary within the National Institute of Malaria Research (NIMR) field unit in Goa until they emerged into adult mosquitoes. Blood for membrane-feeding experiments was obtained from malaria patients at the local Goa Medical College and Hospital who volunteered for the study. Parasites were counted by Miller reticule technique and correlation between gametocytaemia/parasitaemia and successful mosquito infection was studied. RESULTS: A weak but significant correlation was found between patient blood gametocytaemia/parasitaemia and mosquito oocyst load. No correlation was observed between gametocytaemia/parasitaemia and oocyst infection rates, and between gametocyte sex ratio and oocyst load. When it came to development of the parasite in the mosquito, a strong positive correlation was observed between oocyst midgut levels and sporozoite infection rates, and between oocyst levels and salivary gland sporozoite loads. Kinetic studies showed that sporozoites appeared in the salivary gland as early as day 7, post-infection. CONCLUSIONS: This is the first study in India to carry out membrane-feeding experiments with wild An. stephensi and P. vivax. A wide range of mosquito infection loads and infection rates were observed, pointing to a strong interplay between parasite, vector and human factors. Most of the present observations are in agreement with feeding experiments conducted with P. vivax elsewhere in the world.\",\n \"corpus_id\": 4574883,\n \"score\": 0\n },\n {\n \"doc_id\": \"29536711\",\n \"title\": \"[Overwintering surveillance of Culex pipiens pallens in Shandong Province].\",\n \"abstract\": \"OBJECTIVE: To understand the ecological habits of Culex pipiens pallens in Shandong Province in winter. METHODS: From December 2015 to January 2016, the overwintering conditions of Cx. pipiens pallens were investigated in Shandong Province. RESULTS: In Shandong Province, in rural districts, the overwintering places of Cx. pipiens pallens were basements, wells and caves; and in urban areas, they were air raid shelters, holes of city walls, sewers and flower cellars. CONCLUSIONS: In Shandong Province, the overwintering places of Cx. pipiens pallens are mainly basements and holes, which are under high temperature and humidity, and away from light. Its larvae cannot overwinter.\",\n \"corpus_id\": 43009797,\n \"score\": 0\n }\n]","isConversational":false}}},{"rowIdx":79,"cells":{"query":{"kind":"string","value":"{\n \"doc_id\": \"25502034\",\n \"title\": \"Measure post-bloodmeal dispersal of mosquitoes and duration of radioactivity by using the isotope ³²P.\",\n \"abstract\": \"The radioactive isotope (32)P-labeled disodium phosphate (Na₂H(32)PO₄) was injected via the jugular vein into a cow kept in a shed in Maozhuang Village, Cao Township of Shanxian County, China. Over the following 5 d, mosquitoes feeding on the cow were captured at distances up to 400 m to determine dispersal distance. The duration of radioactivity in the cow and marked mosquitoes was 10 d. The results showed that after blood feeding, Anopheles sinensis and Culex tritaeniorhynchus temporarily rested in the cattle shed and then flew outdoors. In contrast, Culex pipiens pallens remained in the cattle shed after feeding. These findings confirmed that local An. sinensis and Cx. tritaeniorhynchus were partially endophilic and tended to rest out of doors, whereas Cx. pipiens pallens was endophilic. For marked An. sinensis and Cx. tritaeniorhynchus, there was a significant tendency for dispersal to be in a northeast and east direction, probably because of the presence of heavy shading by an agricultural field, a small river for mosquito oviposition sites, and locations downwind from the blood source. The furthest flight distances for An. sinensis and Cx. tritaeniorhynchus were 210 and 240 m; therefore, control of these mosquitoes should include resting places indoors and outdoors within a radius of 250 m from confirmed cases.\",\n \"corpus_id\": 205170445\n}"},"candidates":{"kind":"list like","value":[{"doc_id":"18493314","title":"Stable isotope analysis can potentially identify completely-digested bloodmeals in mosquitoes.","abstract":"BACKGROUND: Vertebrate bloodfeeding is a critical component of a mosquito's ability to transmit pathogens that cause diseases such as malaria, dengue fever and viral encephalitis. Due to degradation by the digestive process, current methods to identify mosquito bloodmeal sources are only useful for approximately 36 hours post-feeding. A critical need exists for technologies to extend this window and gain a more complete picture of mosquito feeding behavior for epidemiological studies. Stable isotopes are useful for investigating organism feeding behavior because the isotopic ratio of an organism's tissues reflects that of the material it ingests. METHODOLOGY/PRINCIPAL FINDINGS: Proof-of-principle data indicates that after bloodfeeding, Aedes albopictus mosquitoes acquire diagnostic Carbon and Nitrogen stable isotope profiles from their vertebrate hosts that can be accurately identified one week post-feeding, approximately 4 days after the entire bloodmeal has been digested. Total C/N ratio served as a biomarker marker for bloodfeeding (P<0.02), while deltaN was the most informative variable which could distinguish between unfed, chicken-fed and human-fed mosquitoes (P<0.01). By plotting C/N vs. deltaN, all feeding treatments could be identified in a double-blind analysis. CONCLUSIONS/SIGNIFICANCE: These proof-of-principle experiments indicate that analysis of stable isotopes can be used to distinguish bloodfed from unfed mosquitoes, and also distinguish between different vertebrate bloodmeal sources even after all blood has been digested. The development of stable isotope-based assays for mosquito bloodmeal identification may be a powerful tool to investigate mosquito feeding ecology and the dynamics of vector-borne pathogens.","corpus_id":18008036,"score":2},{"doc_id":"18567443","title":"Control of mosquito vectors of tropical infectious diseases: (1) bioefficacy of mosquito coils containing several pyrethroids and a synergist.","abstract":"The bioefficacy of mosquito coils containing several pyrethroids were tested in a 25 m3 room against Culex pipiens quinquefasciatus, Aedes aegypti and Anopheles dirus. The test results were compared with tests against Culex pipiens pallens in Japan. Based on the KT50 values (the 50% knockdown time) of mosquito coils containing dl, d-T80-allethrin, d, d-T-prallethrin and methoxymethyl-tetrafluorobenzyl tetramethyl-cyclopropanecarboxylate (K-3050) at doses of 0.05-0.5% (w/w) with or without a synergist, the pyrethroid susceptibility of the four mosquito species was as follows: Cx. p. quinquefasciatus was several times more tolerant to pyrethroids than Cx. p. pallens, Ae. aegypti was a further several times more tolerant than Cx. p. quinquefasciatus, and An. dirus was more susceptible than Cx. p. pallens (KT50 value: about half of Cx. p. pallens). The order of their susceptibilities is common for pyrethroids. Mosquito coils containing d, d-T-prallethrin and K-3050 at doses of 0.05-0.2% (w/w) and N-(2-ethylhexyl)bicycle-[2,2,1]-hept-5-ene-2,3-dicarboxyimide as a synergist at a ratio of 2 times the active ingredient were highly effective against Ae. aegypti, the most important mosquito vector for dengue fever.","corpus_id":1927230,"score":2},{"doc_id":"18939684","title":"A mark-release-recapture study on dispersal and flight distance of Culex pipiens pallens in an urban area of Japan.","abstract":"A mark-release-recapture of Culex pipiens pallens was conducted in an urban area of Japan during June 26-29, 2007. Larvae naturally occurring in rain gutters were collected and reared to adults in a laboratory. A total of 10,183 emerging female Cx. pipiens pallens of 4-8 days old were marked with fluorescent dye and released from one site. Recapture was made on 4 consecutive days using 41 Centers for Disease Control and Prevention traps with 1 kg of dry ice and human landing collection, and 121 marked females were recaptured. The overall recapture rate was 0.01. The mean distance traveled by the recaptured females was estimated as 470, 287, 326, and 517 m on days 1-4, respectively. The maximum flight distance of host-seeking Cx. pipiens pallens was estimated as 1,217 m based on the relationship between distance from the release site to the collection site and the total number of recaptures/traps. The population size of female Cx. pipiens pallens in the study area was estimated as 100,904 +/- 8,509. The size of operational area for the control of Cx. pipiens pallens in urban area is discussed.","corpus_id":826613,"score":2},{"doc_id":"18939686","title":"Diversity of riceland mosquitoes and factors affecting their occurrence and distribution in Mwea, Kenya.","abstract":"Knowledge of mosquito species diversity, occurrence, and distribution is an essential component of vector ecology and a guiding principle to formulation and implementation of integrated vector management programs. A 12-month entomological survey was conducted to determine the diversity of riceland mosquitoes and factors affecting their occurrence and distribution at 3 sites targeted for malaria vector control in Mwea, Kenya. Adult mosquitoes were sampled indoors by pyrethrum spray catch and outdoors by the Centers for Disease Control and Prevention light traps. Mosquitoes were then morphologically identified to species using taxonomic keys. The characteristics of houses sampled for indoor resting mosquitoes, including number of people sleeping in each house the night preceding collection, presence of bed nets, location of the house, size of eaves, wall type, presence of cattle and distance of the house to the cowshed, and proximity to larval habitats, were recorded. Of the 191,378 mosquitoes collected, 95% were identified morphologically to species and comprised 25 species from 5 genera. Common species included Anopheles arabiensis (53.5%), Culex quinquefasciatus (35.5%), An. pharoensis (4.7%), An. coustani (2.5%), and An. funestus (1.6%). Shannon's species diversity and evenness indices did not differ significantly among the 3 study sites. There was a marked house-to-house variation in the average number of mosquitoes captured. The number of people sleeping in the house the night preceding collection, size of eaves, distance to the cowshed, and the nearest larval habitat were significant predictors of occurrence of either or both An. arabiensis and Cx. quinquefasciatus. The peak abundance of An. arabiensis coincided with land preparation and the first few weeks after transplanting of rice seedlings, and that of Cx. quinquefasciatus coincided with land preparation, late stage of rice development, and short rains. After transplanting of rice seedlings, the populations of Cx. quinquefasciatus were collected more outdoors than indoors, suggesting a shift from endophily to exophily. These results demonstrate that irrigated rice cultivation has a strong impact on mosquito species occurrence, distribution, abundance, and behavior, and that certain house characteristics increase the degree of human-vector contact.","corpus_id":22837595,"score":2},{"doc_id":"18939969","title":"Risk factors for house-entry by culicine mosquitoes in a rural town and satellite villages in The Gambia.","abstract":"UNLABELLED: BACKGROUND: Screening doors, windows and eaves of houses should reduce house entry by eusynanthropic insects, including the common African house mosquito Culex pipiens quinquefasciatus and other culicines. In the pre-intervention year of a randomized controlled trial investigating the protective effects of house screening against mosquito house entry, a multi-factorial risk factor analysis study was used to identify factors influencing house entry by culicines of nuisance biting and medical importance. These factors were house location, architecture, human occupancy and their mosquito control activities, and the number and type of domestic animals within the compound. RESULTS: 40,407 culicines were caught; the dominant species were Culex thalassius, Cx. pipiens s.l., Mansonia africanus, M. uniformis and Aedes aegypti. There were four times more Cx. pipiens s.l. in Farafenni town (geometric mean/trap/night = 8.1, 95% confidence intervals, CIs = 7.2-9.1) than in surrounding villages (2.1, 1.9-2.3), but over five times more other culicines in the villages (25.1, 22.1-28.7) than in town (4.6, 4.2-5.2). The presence of Cx. pipiens s.l. was reduced in both settings if the house had closed eaves (odds ratios, OR town = 0.62, 95% CIs = 0.49-0.77; OR village = 0.49, 0.33-0.73), but increased per additional person in the trapping room (OR town = 1.16, 1.09-1.24; OR village = 1.10, 1.02-1.18). In the town only, Cx. pipiens s.l. numbers were reduced if houses had a thatched roof (OR = 0.70, 0.51-0.96), for each additional cow tethered near the house (OR = 0.73, 0.65-0.82) and with increasing distance from a pit latrine (OR = 0.97, 0.95-0.99). In the villages a reduction in Cx. pipiens s.l. numbers correlated with increased horses in the compound (OR = 0.90, 0.82-0.99). The presence of all other culicines was reduced in houses with closed eaves (both locations), with horses tethered outside (village only) and with increasing room height (town only), but increased with additional people in the trapping room and where cows were tethered outside (both locations). CONCLUSION: The findings of this study advocate eave closure and pit latrine treatment in all locations, and zooprophylaxis using horses in rural areas, as simple control measures that could reduce the number of culicines found indoors.","corpus_id":1649665,"score":2},{"doc_id":"19769051","title":"Determination of mosquito (Diptera: Culicidae) bloodmeal sources in Western Australia: implications for arbovirus transmission.","abstract":"A double-antibody enzyme-linked immunosorbent assay was used to determine the bloodmeal sources of adult mosquitoes (Diptera: Culicidae) collected in encephalitis vector surveillance mosquito traps in Western Australia between May 1993 and August 2004. In total, 2,606 blood-fed mosquitoes, representing 29 mosquito species, were tested, and 81.7% reacted with one or more of the primary antibodies. Aedes camptorhynchus (Thomson) and Culex annulirostris Skuse were the most common species tested, making up 47.2% (1,234) and 35.6% (930), respectively. These species obtained bloodmeals from a variety of vertebrate hosts but particularly marsupials and cows. In contrast, Culex pullus Theobald (72.7%; 24/33), Culiseta atra (Lee) (70.0%; 7/10), Culex globocoxitus Dobrotworsky (54.5%; 12/22), and Culex quinquefasciatus Say (39.3%; 22/56) often obtained bloodmeals from birds. Although Ae. camptorhynchus and Cx. annulirostris are well established vectors of arboviruses, other mosquitoes also may have a role in enzootic and/ or epizootic transmission.","corpus_id":22213969,"score":2},{"doc_id":"19769059","title":"Bloodmeal identification and detection of avian malaria parasite from mosquitoes (Diptera: Culicidae) inhabiting coastal areas of Tokyo Bay, Japan.","abstract":"Bloodmeal identification and the detection of avian malaria parasite from mosquitoes (Diptera: Culicidae) were carried out by polymerase chain reaction-based methods for field samples collected in coastal areas of Tokyo Bay, Japan, from April to October 2007. The following seven mosquito species were collected: Aedes albopictus (Skuse), Culex pipiens pallens Coquillett, Culex pipiens form molestus Forskal, Culex tritaeniorhynchus Giles, Culex inatomii Kamimura & Wada, Culex bitaeniorhynchus Giles, and Lutzia vorax Edwards. Forty blood-fed mosquitoes were collected and 95% of bloodmeals of Cx. pipiens pallens were avian-derived, whereas only mammalian bloodmeals were identified for Ae. albopictus. Plasmodium DNA was amplified from 65% (15/23) of blood-fed Cx. pipiens pallens and unfed females of Cx. pipiens pallens and Cx. pipiens form molestus with a minimum infection rate of 29.9 and 13.5, respectively. One unfed female of Lt. vorax was also positive for Plasmodium parasites. Five genetically distinct lineages of Plasmodium were identified, with 0.21 to 5.86% sequence divergence. Rinshi-8, the most prevalent lineage at our study site, was identical to the published sequence of Plasmodium relictum-P5.","corpus_id":26714838,"score":2},{"doc_id":"20939372","title":"Experimental studies on comparison of the potential vector competence of four species of Culex mosquitoes in China to transmit West Nile virus.","abstract":"To assess the risk that indigenous mosquitoes in China are capable of transmitting and sustaining West Nile virus (WNV), four important Culex mosquito species, Culex tritaeniorhynchus, Culex modestus, Culex pipiens pallens, and Culex pipiens quinquefasciatus, were allowed to feed on the artificial infectious blood meal with WNV dose of 10(6.8) plaque-forming unit/ml and tested approximately 2 wk later to determine infection and transmission rates. The results indicated that four Culex mosquitoes were competent laboratory vectors of WNV. The infection rates and transmission rates were statistical differences among different species of mosquito (chi2 = 20.620, P = 0.000; chi2 = 15.020, P = 0.005, respectively). The highest infection rate and transmission rate were obtained with Cx. tritaeniorhynchus (87.5 and 74.2%, respectively).","corpus_id":1063109,"score":2},{"doc_id":"21044196","title":"Seasonal changes in the feeding pattern of Culex pipiens pallens govern the transmission dynamics of multiple lineages of avian malaria parasites in Japanese wild bird community.","abstract":"Heterogeneity in the transmission of mosquito-borne pathogens is determined largely by distribution patterns of mosquito bites among wild animal populations. Although mosquitoes are crucial for transmission of avian malaria parasites, little is known about the ecology of natural vectors. We examined bloodmeal and parasite incidence in Culex pipiens pallens by a polymerase chain reaction (PCR)-based procedure to determine how the feeding pattern of mosquitoes govern transmission dynamics of avian malaria parasites in Japanese wild birds. We collected 881 unfed and 486 blood-fed Cx. pipiens pallens resting on vegetation in a park in Tokyo. The mosquitoes were separated into abdomen and thorax prior to PCR screening. Abdomens of unfed mosquitoes were combined into 95 pools. From these, we amplified Plasmodium DNA in 32 (33.7%) pools. Among blood-fed mosquitoes, 371 individuals were screened for blood-sources and Plasmodium parasites. Plasmodium DNA was amplified from mosquitoes fed on 6 of 13 avian species identified as blood-sources. Ten Plasmodium lineages were identified on the basis of 478 bp of the cytochrome b gene, with 0.2-10% sequence divergence. The three commonest Plasmodium lineages (CXPIP09, SGS1 and PADOM02) were detected in both the abdomens and thoraxes of mosquitoes, strongly suggesting transmission of these lineages. Jungle crow (Corvus macrorhynchos) served as a natural host for the three commonest Plasmodium lineages and made up 63.8% of blood-sources. As a significant increase in feeding of vector mosquitoes on jungle crows coincided with their breeding season, jungle crows were considered to be the primary reservoir of Plasmodium transmission in this study.","corpus_id":205363381,"score":2},{"doc_id":"21246936","title":"Haematophageous vector monitoring in Djibouti city from 2008 to 2009: first records of Culex pipiens ssp. torridus (IGLISCH), and Anopheles sergentii (theobald).","abstract":"The Horn of Africa represents a region formerly known to be highly susceptible to mosquito-borne infectious diseases. In order to monitor and analyze the current presence and threat of vector mosquitoes, continuous and standardized trapping using CDC light traps without an additional CO2-generator has been carried out at six selected monitoring sites located in Djibouti City, from August 2008 until December 2009. An overall of 620 haematophageous Diptera were trapped, 603 (97.3%) were mosquitoes, 10 (1.6%) were sand flies, and 7 (1.1%) were biting midges, respectively. Genus distribution of mosquitoes revealed that 600 (99.5%) were Culex spp., 2 (0.3%) were Anopheles sergentii, and 1 (0.2%) was Aedes aegypti. Culex species were represented by Cx. quinquefasciatus (78.5%), and Cx. pipiens ssp. torridus (21.5%). The later species was first detected focally in early December 2009 showing a strongly increasing population density resulting in a maximum trap rate of 25 mosquitoes per trap night. Sand flies were all Sergentomyia antennata, and biting midges of the genus Culicoides were represented by C. nubeculosus (71.4%) and C. vexans (28.6 %). The findings included the first records for Cx. pipiens ssp. torridus and An. sergentii in Djibouti. However, none of the captured female Culex spp, the known vector for West Nile Virus, showed positive results for viral nucleic acids using WNV RT-real time PCR system. Also, females An. sergentii were Plasmodium falciparum and P. vivax circumsporozoite protein negative.","corpus_id":6965137,"score":2},{"doc_id":"21290944","title":"Evaluation of octenol and Lurex as baits in Mosquito Magnet Pro traps to collect vector mosquitoes in China.","abstract":"The effectiveness of the attractants 1-octen-3-ol (octenol) and L-lactic acid (Lurex) on the collection of Aedes albopictus, Culex tritaeniorhynchus, Cx. pipiens pallens, and Anopheles sinensis was first evaluated in Mosquito Magnet Pro traps in Yamenkou and Badachu residential areas, Beijing City, and Lishui area, Zhejiang Province, China. The Mosquito Magnet Pro traps baited with octenol collected significantly more Ae. albopictus, Cx. tritaeniorhynchus, and An. sinensis, but fewer Cx. pipiens pallens than collection by the traps alone. There were no significant differences in the numbers of Cx. pipiens pallens, Cx. tritaeniorhynchus, and An. sinensis collected by Mosquito Magnet Pro traps baited with Lurex compared to the traps alone, but the Mosquito Magnet Pro traps baited with Lurex collected significantly more Ae. albopictus than the number collected by the traps alone at 2 areas in Beijing.","corpus_id":42023971,"score":2},{"doc_id":"21476444","title":"Emergence of Culex pipiens from overwintering hibernacula.","abstract":"Overwintering populations of Culex pipiens, the principal enzootic vector of West Nile virus in the northeastern USA, were studied over 3 consecutive winters from 2006 to 2008, using mark-recapture techniques to determine when Cx. pipiens females began to disperse from overwintering hibernacula and how their survival influenced early season populations. In February of each year, Cx. pipiens were aspirated and marked using fluorescent powder; 4,067, 752, and 3,070 diapausing Cx. pipiens were marked in each successive year. Mosquitoes were then trapped from mid-April to early May of each year using 19 Centers for Disease Control and Prevention (CDC) light traps and 16 CDC gravid traps. A total of 348, 39, and 111 Culex mosquitoes were captured in the spring of 2006, 2007, and 2008, respectively. The number of mosquitoes marked in overwintering habitats is generally positively correlated with the number of mosquitoes recaptured in the early spring (linear regression, R2 = 0.79, P = 0.04), yet results also suggest that seasonal variations beyond overwintering population size are likely important in determining the success of emergent populations. A single marked Cx. pipiens was captured in both 2006 and 2008. In 2006, the mosquito was captured 0.5 km from its overwintering site while in 2008 the mosquito was captured 0.3 km from its overwintering site. In all study years, mosquitoes consistently began exiting overwintering hibernacula the 3rd week of April, yet evidence of earlier exodus was observed in 2007, when outside temperatures were significantly higher in preceding days and months.","corpus_id":1375270,"score":2},{"doc_id":"21875691","title":"\"Bird biting\" mosquitoes and human disease: a review of the role of Culex pipiens complex mosquitoes in epidemiology.","abstract":"The transmission of vector-borne pathogens is greatly influenced by the ecology of their vector, which is in turn shaped by genetic ancestry, the environment, and the hosts that are fed on. One group of vectors, the mosquitoes in the Culex pipiens complex, play key roles in the transmission of a range of pathogens including several viruses such as West Nile and St. Louis encephalitis viruses, avian malaria (Plasmodium spp.), and filarial worms. The Cx. pipiens complex includes Culex pipiens pipiens with two forms, pipiens and molestus, Culex pipiens pallens, Culex quinquefasciatus, Culex australicus, and Culex globocoxitus. While several members of the complex have limited geographic distributions, Cx. pipienspipiens and Cx. quinquefasciatus are found in all known urban and sub-urban temperate and tropical regions, respectively, across the world, where they are often principal disease vectors. In addition, hybrids are common in areas of overlap. Although gaps in our knowledge still remain, the advent of genetic tools has greatly enhanced our understanding of the history of speciation, domestication, dispersal, and hybridization. We review the taxonomy, genetics, evolution, behavior, and ecology of members of the Cx. pipiens complex and their role in the transmission of medically important pathogens. The adaptation of Cx. pipiens complex mosquitoes to human-altered environments led to their global distribution through dispersal via humans and, combined with their mixed feeding patterns on birds and mammals (including humans), increased the transmission of several avian pathogens to humans. We highlight several unanswered questions that will increase our ability to control diseases transmitted by these mosquitoes.","corpus_id":13770917,"score":2},{"doc_id":"21980773","title":"Mosquitoes (Diptera: Culicidae) in relation to the risk of disease transmission in El Ismailia Governorate, Egypt.","abstract":"Mosquito were surveyed (Nov. 2009 - March 2010) in El Ismailia Governorate. Nine species were reported: Culex pipiens, Cx. perexiguus, Cx. antennatus, Anopheles tenebrosus, An. pharoensis, An. multicolor, Ochlerotatus detritus, Oc. caspius and Culiseta longiareolata. Culex pipiens was the predominant species (ca. 87% larvae and 57% adults). For the 3 common species, Cx. pipiens, Cx. perexiguus, and Cx. antennatus the following were examined: (1) the type and characteristics (temperature and pH) of the breeding habitats and their relation to the larval density and (2) the relation of adult indoor density to the indoor and outdoor temperature and RH. The abundance of mosquito vectors in El Ismailia with its old history of vector transmitted diseases contributes to the risk of mosquito borne disease transmission in this area. This would assist in the control activities.","corpus_id":39591553,"score":2},{"doc_id":"22115320","title":"The abundance and host-seeking behavior of culicine species (Diptera: Culicidae) and Anopheles sinensis in Yongcheng city, People's Republic of China.","abstract":"BACKGROUND: The knowledge of mosquito species diversity and the level of anthropophily exhibited by each species in a region are of great importance to the integrated vector control. Culicine species are the primary vectors of Japanese encephalitis (JE) virus and filariasis in China. Anopheles sinensis plays a major role in the maintenance of Plasmodium vivax malaria transmission in China. The goal of this study was to compare the abundance and host-seeking behavior of culicine species and An. sinensis in Yongcheng city, a representative region of P. vivax malaria. Specifically, we wished to determine the relative attractiveness of different animal baits versus human bait to culicine species and An. sinensis. RESULTS: Culex tritaeniorhynchus was the most prevalent mosquito species and An. sinensis was the sole potential vector of P. vivax malaria in Yongcheng city. There were significant differences (P < 0.01) in the abundance of both An. sinensis and Cx. tritaeniorhynchus collected in distinct baited traps. The relative attractiveness of animal versus human bait was similar towards both An. sinensis and Cx. tritaeniorhynchus. The ranking derived from the mean number of mosquitoes per bait indicated that pigs, goats and calves frequently attracted more mosquitoes than the other hosts tested (dogs, humans, and chickens). These trends were similar across all capture nights at three distinct villages. The human blood index (HBI) of female An. sinensis was 2.94% when computed with mixed meals while 3.70% computed with only the single meal. 19:00~21:00 was the primary peak of host-seeking female An. sinensis while 4:00~5:00 was the smaller peak at night. There was significant correlation between the density of female An. sinensis and the average relative humidity (P < 0.05) in Wangshanzhuang village. CONCLUSIONS: Pigs, goats and calves were more attractive to An. sinensis and Cx. tritaeniorhynchus than dogs, humans, and chickens. Female An. sinensis host-seeking activity mainly occurred from 19:00 to 21:00. Thus, we propose that future vector control against An. sinensis and Cx. tritaeniorhynchus in the areas along the Huang-Huai River of central China should target the interface of human activity with domestic animals and adopt before human hosts go to bed at night.","corpus_id":2559019,"score":2},{"doc_id":"22308769","title":"Dispersal of Culex mosquitoes (Diptera: Culicidae) from a wastewater treatment facility.","abstract":"A mark-recapture project examined dispersal and flight distances of Culex mosquitoes from a wastewater treatment plant in Albany, NY, during 2007 and 2008. A self-marking device was constructed to mark egressing mosquitoes with fluorescent marking powder. Mosquitoes were recaptured using 30 CDC miniature light traps located within a 2.0 km radius of the marking site. A total of 13 and 10 marked Culex mosquitoes were recaptured in 2007 and 2008, respectively. Culex mosquitoes traveled a minimum of 0.16 km, a maximum of 1.98 km and, following correction for decreasing trap density with distance, had a mean distance traveled of 1.33 km. Characterizing the dispersal patterns of these mosquitoes is important for understanding the distribution of West Nile virus and other pathogens.","corpus_id":41665921,"score":2},{"doc_id":"22308772","title":"Evaluation of a stable isotope method to mark naturally-breeding larval mosquitoes for adult dispersal studies.","abstract":"Understanding mosquito dispersal is critically important for vector-borne disease control and prevention. Mark-release-recapture methods using various marking techniques have made substantial contributions to the study of mosquito biology. However, the ability to mark naturally breeding mosquitoes noninvasively and with life-long retention has remained problematic. Here, we describe a method to mark naturally breeding mosquitoes with stable isotopes. Culex pipiens f. molestus mosquitoes were provisioned as larvae in laboratory experiments with 15N-labeled potassium nitrate and 13C-labeled glucose. Larval enrichment was sufficient to differentiate marked adult mosquitoes from unmarked control mosquitoes and the natural source population from Chicago Illinois, using either delta 15N or delta 13C. Isotopic retention lasted for at least 55 d for adult male and females mosquitoes. There were no consistent effects of isotopic enrichment on immature mosquito survival or adult mosquito body size. We then applied this marking technique to naturally breeding Culex pipiens mosquitoes in suburban Chicago, IL, and for the first time, report successful isotopic enrichment of mosquitoes in the field. This stable isotope marking technique will facilitate studies of mosquito dispersal.","corpus_id":18177233,"score":2},{"doc_id":"22548540","title":"Analysis of post-blood meal flight distances in mosquitoes utilizing zoo animal blood meals.","abstract":"We assessed the post-blood meal flight distance of four mosquito species in a unique environment using blood meal analysis. Mosquitoes were trapped at the Rio Grande Zoo in Albuquerque, NM, and the blood source of blood-engorged mosquitoes was identified. The distance from the enclosure of the animal serving as a blood source to the trap site was then determined. We found that mosquitoes captured at the zoo flew no more than 170 m with an average distance of 106.7 m after taking a blood meal. This is the first study in which the flight distance of wild mosquitoes has been assessed using blood meal analysis and the first in which zoo animals have served as the exclusive source of blood meals.","corpus_id":42980754,"score":2},{"doc_id":"22627302","title":"Distribution of mosquitoes and mosquito-borne viruses along the China-Myanmar border in Yunnan Province.","abstract":"A total of 54,673 mosquitoes were collected at 11 sites located near the China-Myanmar border in the western part of Yunnan Province during July and August 2007. There were 29 species in 4 genera identified from the collections, including 12 species of Culex, 12 species of Anopheles, 3 species of Aedes, and 2 species of Armigeres. Culex tritaeniorhynchus Giles (67.9%, 37,119/54,673) and Anopheles sinensis Wiedemann (25.9%, 14,170/54,673) were the most abundant species in this investigation. Virus was isolated using BHK-21 and C6/36 cells from 22 of 510 mosquito pools. Isolates included Japanese encephalitis virus (JEV) and Getah virus (GETV), which were identified by serological and molecular methods. Twenty JEV strains were isolated from Cx. tritaeniorhynchus (15 isolates), An. sinensis (3 isolates), and Armigeres subalbatus Coquillett (2 isolates), and 2 GETV strains were isolated from Culex pseudovishnui Colless and Cx. tritaeniorhynchus. This study suggests that Ar. subalbatus is a potentially important local vector because of the high JEV infection ratio found in this species. Enzootic JEV transmission persists in this area and therefore, surveillance for human disease caused by JEV and GETV should be conducted in the region.","corpus_id":18671765,"score":2},{"doc_id":"22679881","title":"Host-feeding patterns of Culex pipiens and other potential mosquito vectors (Diptera: Culicidae) of West Nile virus (Flaviviridae) collected in Portugal.","abstract":"The host blood-feeding patterns of mosquito vectors affects the likelihood of human exposure to zoonotic pathogens, including West Nile Virus (family Flaviviridae, genus Flavivirus, WNV). In Portugal, data are unavailable regarding the blood-feeding habits of common mosquito species, including Culex pipiens L., considered the primary vector of WNV to humans. The sources of bloodmeals in 203 blood-fed mosquitoes of nine species collected from June 2007 to November 2010 in 34 Portuguese counties were analyzed by sequencing cytochrome-b partial fragments. Cx. pipiens was the most common species collected and successfully analyzed (n = 135/78). In addition, blood-fed females of the following species were analyzed: Ochlerotatus caspius Pallas (n = 20), Culex theileri Theobald (n = 16), Anopheles maculipennis s.l. Meigen (n = 10), Culiseta longiareolata Macquart (n = 7), Aedes aegypti L. (n = 6), Culex perexiguus Theobald (n = 3), Culiseta annulata Schrank (n = 3), and Ochlerotatus detritus Haliday (n = 3). The Cx. pipiens mosquitoes fed predominantly on birds (n = 55/78, 70.5%), with a high diversity of avian species used as hosts, although human blood was identified in 18 specimens (18/78, 23.1%). No significant differences were found between the host-feeding patterns of blood-fed Cx. pipiens collected in residential and nonresidential habitats. The occurrence of human derived blood meals and the presence of a mix avian-human bloodmeal accordingly suggest this species as a potential vector of WNV. Therefore, in Portugal, Cx. pipiens may play a role both in the avian-to-avian enzootic WNV cycle and in the avian-to-mammal transmission. In this context, the identity of Cx. pipiens (considering the forms molestus and pipiens) and the potential consequence on feeding behavior and WNV transmission are discussed.","corpus_id":44445656,"score":2},{"doc_id":"23226489","title":"Dispersal range of Anopheles sinensis in Yongcheng City, China by mark-release-recapture methods.","abstract":"BACKGROUND: Studying the dispersal range of Anopheles sinensis is of major importance for understanding the transition from malaria control to elimination. However, no data are available regarding the dispersal range of An. sinensis in China. The aim of the present study was to study the dispersal range of An. sinensis and provide the scientific basis for the development of effective control measures for malaria elimination in China. METHODOLOGY/PRINCIPAL FINDINGS: Mark-Release-Recapture (MRR) experiments were conducted with 3000 adult wild An. sinensis in 2010 and 3000 newly emerged wild An. sinensis in 2011 in two villages of Yongcheng City in Henan Province. Marked An. sinensis were recaptured daily for ten successive days using light traps. The overall recapture rates were 0.83% (95% CI, 0.50%~1.16%) in 2010 and 1.33% (95% CI, 0.92%~1.74%) in 2011. There was no significant difference in the recapture rates of wild An. sinensis and newly emerged An. sinensis. The majority of An. sinensis were captured due east at study site I compared with most in the west at study site II. Eighty percent and 90% of the marked An. sinensis were recaptured within a radius of 100 m from the release point in study site I and II, respectively, with a maximum dispersal range of 400 m within the period of this study. CONCLUSIONS/SIGNIFICANCE: Our results indicate that local An. sinensis may have limited dispersal ranges. Therefore, control efforts should target breeding and resting sites in proximity of the villages.","corpus_id":170597,"score":2},{"doc_id":"23270171","title":"Host-feeding pattern of Culex theileri (Diptera: Culicidae), potential vector of Dirofilaria immitis in the Canary Islands, Spain.","abstract":"To identify the host range of potential vectors of Dirofilaria immitis Leidy, the causal agent of canine dirofilariasis, we studied the bloodmeal origin of mosquitoes trapped on two of the Canary Islands, Gran Canaria and Tenerife, where this disease is considered hyperendemic. On Gran Canaria, mosquitoes were captured using Centers for Disease Control and Prevention (CDC) traps (outdoors) and resting in a bathroom (indoors). Only CDC traps were used to capture mosquitoes in Tenerife. The species captured in decreasing order of abundance were Culex theileri Theobald, Culex pipiens L., Culiseta longiareolata Macquart, Anopheles atroparvus van Thiel, and Anopheles cinereus Theobald. The origins of bloodmeals were identified for 121 Cx. theileri and 4 Cx. pipiens after amplification and sequencing of a fragment of the vertebrate cytochrome oxidase I (COI) gene. Cx. theileri fed on goats, sheep, dogs, cattle, cats, humans, and chickens, and Cx. pipiens fed on goats and chickens. A lower success of bloodmeal identification was obtained in mosquitoes captured resting indoors than outdoors in CDC traps, probably because of a longer time period between feeding and capture. Although most Cx. theileri fed on ruminants, this species also fed on different mammal species susceptible to dirofiliarasis, including humans, suggesting it could play a role on parasite transmission.","corpus_id":27484126,"score":2},{"doc_id":"23379959","title":"Barrier screens: a method to sample blood-fed and host-seeking exophilic mosquitoes.","abstract":"BACKGROUND: Determining the proportion of blood meals on humans by outdoor-feeding and resting mosquitoes is challenging. This is largely due to the difficulty of finding an adequate and unbiased sample of resting, engorged mosquitoes to enable the identification of host blood meal sources. This is particularly difficult in the south-west Pacific countries of Indonesia, the Solomon Islands and Papua New Guinea where thick vegetation constitutes the primary resting sites for the exophilic mosquitoes that are the primary malaria and filariasis vectors. METHODS: Barrier screens of shade-cloth netting attached to bamboo poles were constructed between villages and likely areas where mosquitoes might seek blood meals or rest. Flying mosquitoes, obstructed by the barrier screens, would temporarily stop and could then be captured by aspiration at hourly intervals throughout the night. RESULTS: In the three countries where this method was evaluated, blood-fed females of Anopheles farauti, Anopheles bancroftii, Anopheles longirostris, Anopheles sundaicus, Anopheles vagus, Anopheles kochi, Anopheles annularis, Anopheles tessellatus, Culex vishnui, Culex quinquefasciatus and Mansonia spp were collected while resting on the barrier screens. In addition, female Anopheles punctulatus and Armigeres spp as well as male An. farauti, Cx. vishnui, Cx. quinquefasciatus and Aedes species were similarly captured. CONCLUSIONS: Building barrier screens as temporary resting sites in areas where mosquitoes were likely to fly was an extremely time-effective method for collecting an unbiased representative sample of engorged mosquitoes for determining the human blood index.","corpus_id":13723361,"score":2},{"doc_id":"23540117","title":"Ecological and genetic analyses of the complete genomes of Culex flavivirus strains isolated from Culex tritaeniorhynchus and Culex pipiens (Diptera: Culicidae) group mosquitoes.","abstract":"Culex flavivirus (CxFV) is an insect-specific flavivirus that was first reported in 2007 in Japan. CxFV strains were isolated from Culex tritaeniorhynchus Giles and Culex pipiens L. group mosquitoes and genetically characterized in Toyama Prefecture, Japan, from 2004 to 2009, to reveal host specificity, mode of transmission, and seasonal and geographical distribution. The minimum infection rate (MIR) of CxFV within Cx. tritaeniorhynchus populations was 0.3 and much lower than that within Cx. pipiens group (17.9). The complete genome sequences of 11 CxFV isolates (four from Cx. tritaeniorhynchus and seven from Cx. pipiens group) consisted of 10,835-10,837 nucleotides. When these 11 isolates and five reference strains (NIID-21-2 and Tokyo strains from Japan, Iowa07 and HOU24518 strains from the United States, H0901 strain from China) were compared, there were 95.2-99.2% nucleotide and 98.1-99.8% amino acid identities. Phylogenetic analysis showed that the 11 isolates were divided into four clusters. One cluster consisted of five isolates from Cx. pipiens group and Cx. tritaeniorhynchus from one site and their nucleotide sequences almost completely matched. One cluster consisted of an isolate with a unique sequence from a Cx. pipiens group mosquito captured in an aircraft from Taiwan, suggesting that it was introduced from abroad. CxFV strains were divided into several groups according to countries when nucleotide sequences of CxFV available in GenBank and 11 Toyama isolates were compared. These results suggest that CxFV is maintained in nature among Culex mosquitoes in a mosquito habitat-specific but not a species-specific manner.","corpus_id":23364714,"score":2},{"doc_id":"23642138","title":"Taxis assays measure directional movement of mosquitoes to olfactory cues.","abstract":"BACKGROUND: Malaria control methods targeting indoor-biting mosquitoes have limited impact on vectors that feed and rest outdoors. Exploiting mosquito olfactory behaviour to reduce blood-feeding outdoors might be a sustainable approach to complement existing control strategies. Methodologies that can objectively quantify responses to odour under realistic field conditions and allow high-throughput screening of many compounds are required for development of effective odour-based control strategies. METHODS: The olfactory responses of laboratory-reared Anopheles gambiae in a semi-field tunnel and A. arabiensis females in an outdoor field setting to three stimuli, namely whole human odour, a synthetic blend of carboxylic acids plus carbon dioxide and CO(2) alone at four distances up to 100 metres were measured in two experiments using three-chambered taxis boxes that allow mosquito responses to natural or experimentally-introduced odour cues to be quantified. RESULTS: Taxis box assays could detect both activation of flight and directional mosquito movement. Significantly more (6-18%) A. arabiensis mosquitoes were attracted to natural human odour in the field up to 30 metres compared to controls, and blended synthetic human odours attracted 20% more A. gambiae in the semi-field tunnel up to 70 metres. Whereas CO(2) elicited no response in A. arabiensis in the open field, it was attractive to A. gambiae up to 50 metres (65% attraction compared to 36% in controls). CONCLUSIONS: We have developed a simple reproducible system to allow for the comparison of compounds that are active over medium- to long-ranges in semi-field or full-field environments. Knowing the natural range of attraction of anopheline mosquitoes to potential blood sources has substantial implications for the design of malaria control strategies, and adds to the understanding of olfactory behaviour in mosquitoes. This experimental strategy could also be extended from malaria vectors to other motile arthropods of medical, veterinary and agricultural significance.","corpus_id":2078629,"score":2},{"doc_id":"23697019","title":"Population ecology of mosquitoes and the status of bancroftian filariasis in El Dakahlia Governorate, the Nile delta, Egypt.","abstract":"Mosquitoes were surveyed (Oct. 2010 & Apr. - Oct. 2011) in some localities representing 13 centers of El-Dakahlia Governorate. Six mosquito species were collected: Culex pipiens, Cx. antennatus, Cx. perexiguus, Ochlerotatus detritus, Anopheles pharoensis and An. tenebrosus. Culex pipiens was predominating (ca 79% larvae, 51% adults). Culex antennatus and Cx. perexiguus were also common. Of the Four types of the breeding habitats, the drainage canals were the most productive (53.4% larvae). For the three common species, the compiled larval density increases as water temp. increased and decreases as pH increased while adult indoor density increases as indoor and outdoor temp. and indoor RH increased and decreases as outdoor RH increased. Cx. pipiens significantly associated with Cx. antennatus (CAB=0.88 & I=0.48) while Cx. antennatus has a moderate association with Cx. perexiguus (CAB=0.47 & I=0.36). Out of 908 examined blood samples from ten centers, 7.49% were infected with Wuchereria bancrofti. The highest infection rates in some centers were associated with high indoor densities of Cx. pipiens females, the main filariasis vector. The situation necessitates a wide vector control program to minimize lymphatic filariasis transmission in this Governorate.","corpus_id":20976502,"score":2},{"doc_id":"23786327","title":"Sympatric occurrence of Culex pipiens (Diptera, Culicidae) biotypes pipiens, molestus and their hybrids in Portugal, Western Europe: feeding patterns and habitat determinants.","abstract":"Culex (Culex) pipiens (Diptera: Culicidae) has two recognized biotypes, pipiens and molestus, which differ in physiology and behaviour; this difference may influence vectorial capacity for West Nile virus (WNV). Our goal was first to determine the presence of Cx. pipiens populations in 31 locations in Portugal and to subsequently analyse their host-feeding preferences and habitat determinants. Molecular identification of Cx. pipiens forms and their hybrids was performed in 97 females; bloodmeal sources were identified in 59 engorged specimens. Overall, 61.9% of specimens were identified as Cx. pipiens f. pipiens, 20.6% as Cx. pipiens f. molestus, and 17.5% as hybrid forms. Culex pipiens f. pipiens fed preferentially on birds, and Cx. pipiens f. molestus on humans. Hybrid forms fed mostly on birds, but human bloodmeals were common. With reference to habitat, Cx. pipiens f. pipiens and hybrid forms were positively correlated with peri-urban habitats. Our results confirm the sympatric presence of different Cx. pipiens biotypes in 14 of the 31 locations studied. Peri-urban areas were a common habitat of all biotypes and may represent zones of hybridization. The feeding preferences and sympatric distribution of the Cx. pipiens biotypes observed in Portugal favour the epizootic circulation of WNV and the occurrence of disease outbreaks of WNV.","corpus_id":206198574,"score":2},{"doc_id":"23835922","title":"Larvicidal, oviposition, and ovicidal effects of Artemisia annua (Asterales: Asteraceae) against Aedes aegypti, Anopheles sinensis, and Culex quinquefasciatus (Diptera: Culicidae).","abstract":"This study focuses on the larvicidal, oviposition, and ovicidal effects of a crude extract of Artemisia annua against Aedes aegypti, Anopheles sinensis, and Culex quinquefasciatus. Dried cells of Artemisia annua from cell suspension cultures were extracted using hexane. The extract showed moderate larvicidal effects against mosquitoes. At 24-h post treatment, the LC50 values for Anopheles sinensis, Aedes aegypti, and Culex quinquefasciatus were recorded as 244.55, 276.14, and 374.99 ppm, respectively. The percentage mortality of larvae was directly proportional to the tested concentration. Anopheles sinensis was found to be the most susceptible species, whereas Culex quinquefasciatus was the most tolerant to the Artemisia annua extract. The results indicated that the Artemisia annua extract showed concentration-dependent oviposition deterrent activity and had a strong deterrent effect. At 500 ppm, the percentage effective repellency was more than 85% compared with the control group for all the species, with oviposition activity index values of -0.94, -0.95, and -0.78 for Aedes aegypti, Anopheles sinensis, and Culex quinquefasciatus, respectively. In the ovicidal assay, the percentage hatchability of eggs after treatment with 500 ppm of Artemisia annua extract was significantly lower than the control, with values of 48.84 ± 4.08, 38.42 ± 3.67, and 79.35 ± 2.09% for Aedes aegypti, Anopheles sinensis, and Culex quinquefasciatus, respectively. Artemisia annua was found to be more effective against Aedes aegypti and Anopheles sinensis compared with Culex quinquefasciatus. This study indicated that crude extract of A. annua could be a potential alternative for use in vector management programs.","corpus_id":9113080,"score":2},{"doc_id":"24060238","title":"Mosquitoes established in Lhasa city, Tibet, China.","abstract":"BACKGROUND: In 2009, residents of Lhasa city, Tibet Autonomous Region (TAR), China reported large numbers of mosquitoes and bites from these insects. It is unclear whether this was a new phenomenon, which species were involved, and whether these mosquitoes had established themselves in the local circumstances. METHODS: The present study was undertaken in six urban sites of Chengguan district Lhasa city, Tibet. Adult mosquitoes were collected by bed net trap, labor hour method and light trap in August 2009 and August 2012. The trapped adult mosquitoes were initially counted and identified according to morphological criteria, and a proportion of mosquitoes were examined more closely using a multiplex PCR assay. RESULTS: 907 mosquitoes of the Culex pipiens complex were collected in this study. Among them, 595 were females and 312 were males. There was no significant difference in mosquito density monitored by bed net trap and labor hour method in 2009 and 2012. Of 105 mosquitoes identified by multiplex PCR, 36 were pure mosquitoes (34.29%) while 69 were hybrids (65.71%). The same subspecies of Culex pipiens complex were observed by bed net trap, labor hour method and light trap in 2009 and 2012. CONCLUSION: The local Culex pipiens complex comprises the subspecies Cx. pipiens pipiens, Cx. pipiens pallens, Cx. pipiens quinquefasciatus and its hybrids. Mosquitoes in the Cx. pipiens complex, known to be, potentially, vectors of periodic filariasis and encephalitis, are now present from one season to the next, and appear to be established in Lhasa City, TAR.","corpus_id":1225470,"score":2},{"doc_id":"24146951","title":"Mosquitoes of Western Yunnan Province, China: seasonal abundance, diversity, and arbovirus associations.","abstract":"OBJECTIVE: The western borderland between Yunnan Province, China, and Myanmar is characterized by a climate that facilitates year-round production of mosquitoes. Numerous mosquito-transmitted viruses, including Japanese encephalitis virus circulate in this area. This project was to describe seasonal patterns in mosquito species abundance and arbovirus activity in the mosquito populations. METHODS: Mosquitoes were collected in Mangshi and Ruili cities of Dehong Prefecture near the border of China and Burma in Yunnan Province, the Peoples Republic of China in 2010. We monitored mosquito species abundance for a 12-month period using ultraviolet light, carbon dioxide baited CDC light and gravid traps; and tested the captured mosquitoes for the presence of virus to evaluate mosquito-virus associations in rural/agricultural settings in the area. RESULTS: A total of 43 species of mosquitoes from seven genera were collected, including 15 Culex species, 15 Anopheles spp., four Aedes spp., three Armigeres spp., one Mimomyia spp., two Uranotaenia spp. and three Mansonia spp.. Species richness and diversity varied between Mangshi and Ruili. Culex tritaeniorhynchus, Culex quinquefasciatus, Anopheles sinensis and Anopheles peditaeniatus were the most abundant species in both sampling sites. Ultraviolet light traps collected more specimens than CDC light traps baited with dry ice, though both collected the same variety of mosquito species. The CDC gravid trap was the most effective trap for capture of Culex quinquefasciatus, a species underrepresented in light trap collections. A total of 26 virus strains were isolated, which included 13 strains of Japanese encephalitis virus, four strains of Getah virus, one strain of Oya virus, one strain from the orbivirus genus, and seven strains of Culex pipien pallens densovirus. CONCLUSIONS: The present study illustrates the value of monitoring mosquito populations and mosquito-transmitted viruses year-round in areas where the climate supports year-round adult mosquito activity.","corpus_id":4032496,"score":2},{"doc_id":"24180110","title":"Flight capacity of adult Culex pipiens pallens (Diptera: Culicidae) in relation to gender and day-age.","abstract":"Culex pipiens pallens (L.) is the most common mosquito in houses of central and northern China. It is the primary vector of lymphatic filariasis and Japanese encephalitis. The flight range of mosquitoes is an important factor predicting the risk area of transmission of mosquito-borne pathogens to vertebrate hosts. The flight performance of Cx. pipiens pallens was measured with a 26-channel computer-monitored flight-mill system. We found that females had longer flight capability than males for total flight distance (TFD) and total flight duration (TFDr), and females flew faster than males based on mean flight velocity. No significant difference in flight capability was found between different age-groups in males. However, certain age-groups of females showed significant differences in TFDr and TFD. Specifically, TFD and TFDr tended to be shortest for 5- and 6-d-old females. These significant differences in flight capability between ages and genders provide insights to determine the size of operational area to achieve effective control of Cx. pipiens pallens and minimize the risk of the related mosquito-borne epidemic diseases of lymphatic filariasis and Japanese encephalitis.","corpus_id":40597234,"score":2},{"doc_id":"24180115","title":"Feeding behavior and spatial distribution of Culex mosquitoes (Diptera: Culicidae) in wetland areas of the Czech Republic.","abstract":"Mosquito feeding behavior determines the degree of vector-host contact and may have a serious impact on the risk of pathogen transmission, including that of the West Nile virus (WNV). To measure the role of Culex mosquitoes as WNV vectors, host-seeking females were collected using animal-baited traps containing live birds (quail) or mammals (rabbits) and CO2-baited Center for Disease Control and Prevention traps placed in several wetland areas in the Czech Republic. Culex pipiens (L.) and Culex modestus (F.) were the most frequently collected species. Although Cx. modestus did not distinguish between baits, Cx. pipiens was collected significantly more frequently in bird-baited traps. Based on mitochondrial DNA analysis of bloodmeals from engorged females collected by CO2-baited traps situated within reed beds, a diverse group of birds were the predominant hosts (93.7%), followed by mammals (4.2%) including humans, and amphibians (2.1%). Among birds, Anseriformes were fed upon most frequently by Cx. modestus, whereas Cx. pipiens fed most frequently on Passeriformes. To measure the infection risk and confirm the distribution of mosquito species in various biotopes, transects of CO2-baited CDC traps were operated from wetland reed beds into upland vegetated areas. Even though both Culex species occurred in all biotopes sampled and frequently dispersed hundreds of meters away from fishpond shore vegetation, the spatial distribution of Cx. modestus was significantly associated with reed beds at wetlands. The first detection of WNV (subtype RabV) in Cx. modestus in Bohemia and confirmation of WNV presence in Cx. pipiens in Moravia together with observed feeding behavior supports the presumed role of both Culex species in the avian-to-avian enzootic WNV cycle and in avian-to-mammal transmission in the Czech Republic.","corpus_id":38698605,"score":2},{"doc_id":"24534672","title":"Serosal cuticle formation and distinct degrees of desiccation resistance in embryos of the mosquito vectors Aedes aegypti, Anopheles aquasalis and Culex quinquefasciatus.","abstract":"Given their medical importance, mosquitoes have been studied as vectors of parasites since the late 1800's. However, there are still many gaps concerning some aspects of their biology, such as embryogenesis. The embryonic desiccation resistance (EDR), already described in Aedes and Anopheles gambiae mosquitoes, is a peculiar trait. Freshly laid eggs are susceptible to water loss, a condition that can impair their viability. EDR is acquired during embryogenesis through the formation of the serosal cuticle (SC), protecting eggs from desiccation. Nevertheless, conservation of both traits (SC presence and EDR acquisition) throughout mosquito evolution is unknown. Comparative physiological studies with mosquito embryos from different genera, exhibiting distinct evolutionary histories and habits is a feasible approach. In this sense, the process of EDR acquisition of Aedes aegypti, Anopheles aquasalis and Culex quinquefasciatus at 25°C was evaluated. Completion of embryogenesis occurs in Ae. aegypti, An. aquasalis and Cx. quinquefasciatus at, respectively 77.4, 51.3 and 34.3hours after egg laying, Cx. quinquefasciatus embryonic development taking less than half the time of Ae. aegypti. In all cases, EDR is acquired in correlation with SC formation. For both Ae. aegypti and An. aquasalis, EDR and SC appear at 21% of total embryonic development, corresponding to the morphological stage of complete germ band elongation/beginning of germ band retraction. Although phylogenetically closer to Ae. aegypti than to An. aquasalis, Cx. quinquefasciatus acquires both EDR and serosal cuticle later, with 35% of total development, when the embryo already progresses to the middle of germ band retraction. EDR confers distinct egg viability in these species. While Ae. aegypti eggs demonstrated high viability when left up to 72hours in a dry environment, those of An. aquasalis and Cx. quinquefasciatus supported these conditions for only 24 and 5hours, respectively. Our data suggest that serosa development is at least partially uncoupled from embryo development and that, depending upon the mosquito species, EDR bestows distinct levels of egg viability.","corpus_id":5628681,"score":2},{"doc_id":"24676212","title":"Dispersal of adult culex mosquitoes in an urban west nile virus hotspot: a mark-capture study incorporating stable isotope enrichment of natural larval habitats.","abstract":"Dispersal is a critical life history behavior for mosquitoes and is important for the spread of mosquito-borne disease. We implemented the first stable isotope mark-capture study to measure mosquito dispersal, focusing on Culex pipiens in southwest suburban Chicago, Illinois, a hotspot of West Nile virus (WNV) transmission. We enriched nine catch basins in 2010 and 2011 with 15N-potassium nitrate and detected dispersal of enriched adult females emerging from these catch basins using CDC light and gravid traps to distances as far as 3 km. We detected 12 isotopically enriched pools of mosquitoes out of 2,442 tested during the two years and calculated a mean dispersal distance of 1.15 km and maximum flight range of 2.48 km. According to a logistic distribution function, 90% of the female Culex mosquitoes stayed within 3 km of their larval habitat, which corresponds with the distance-limited genetic variation of WNV observed in this study region. This study provides new insights on the dispersal of the most important vector of WNV in the eastern United States and demonstrates the utility of stable isotope enrichment for studying the biology of mosquitoes in other disease systems.","corpus_id":8710958,"score":2},{"doc_id":"24822373","title":"[Identification of mammalian blood meals in anopheline mosquitoes from four counties of Yunnan Province by multiple PCR].","abstract":"From June to August 2012, the blood-sucking mosquitoes were captured around cattle-sheds and human houses in Yuanjiang County, Qiaojia County, Yongshan County, and Jinghong City of Yunan Province. Blood samples from mosquitoes were collected on filter paper. Multiplex PCR assay was used to detect the blood meal samples. Among the 145 mosquitoes captured, 123 were Anopheles sinensis (84.8%) and 22 A. minimus (15.2%). Among the blood samples, corresponding bands were amplified in 134 samples. The result showed that the blood meals were from pigs (n = 104), cows (n = 22), dogs (n = 4), human (n=2), cow and pig (n = 1), pig and human (n = 1). Human blood index of A. sinensis and A. minimus was 0.018 and 0.045, respectively.","corpus_id":21283349,"score":2},{"doc_id":"24897862","title":"Molecular identification of bloodmeals from sand flies and mosquitoes collected in Israel.","abstract":"In Israel, sand flies are the vectors of Leishmania Ross and mosquitoes are the vectors of West Nile Virus. In the Judean Desert and Tiberias, the sand fly Phlebotomus sergenti Parrot is the vector of Leishmania tropica (Wright) and the rock hyrax (Procavia capensis Pallas) is considered the main reservoir animal. The main vectors of West Nile Virus are Culex pipiens L. and Culex perexiguus Theobald. Bloodmeals of engorged field-caught female sand flies and mosquitoes are an important source for defining host preferences. Recent progress in DNA molecular techniques has enabled the accurate identification of blood sources within the arthropod gut. In this study, we applied molecular approach for species-specific identification based on polymerase chain reaction and nucleotide sequence analysis of polymorphic regions along two mitochondrial genes, 12S and 16S rRNA. The research was carried out on 261 engorged female sand flies collected in the Judean Desert and Tiberias and 50 engorged female mosquitoes collected in Tel-Aviv and Arava. Species identification of bloodmeals was successful in 92% of the samples. Rock hyrax was the most abundant host in bloodmeals of P. sergenti, while human blood was found in only seven (3%) females. L. tropica DNA was detected in three P. sergenti females from Tiberias that contained rock hyrax blood. Avian sequences were detected in 67% (10 of 15) of the identified bloodmeals from Cx. perexiguus and in 10% (3 of 29) of the identified meals from Cx. pipiens. Human sequences were found in 14% of the identified bloodmeals from Cx. pipiens. The successful analysis of the majority of the bloodmeals performed on wild sand flies and mosquitoes suggests that bloodmeal identification can be applied as one of the routine procedures in vector surveillance programs.","corpus_id":36866910,"score":2},{"doc_id":"25059361","title":"[Investigation on mosquitoes and mosquito-borne viruses in Dehong prefecture, Yunnan province, 2007 and 2010].","abstract":"OBJECTIVE: To investigate the distribution patterns of mosquito and mosquito-borne viruses in Dehong prefecture, Yunnan province, China. METHODS: Mosquito samples were collected using the mosquito traps from five counties of Dehong prefecture on July, 2007 and 2010. Mosquito were cell cultured for viral isolation, and positive isolates were identified using RT-PCR and sequence analysis. RESULTS: A total of 43 634 mosquito comprised of 29 species representing six genera were collected. Culex tritaeniorhynchus and Anopheles sinensis comprised 78.69% and 14.77% of the total. Six strains of viruses were isolated from the mosquito pools. RT-PCR and phylogenetic analysis revealed three strains from Cx. tritaeniorhynchus, identified as genotype I Japanese encephalitis virus (JEV). One strain was identified from Cx. tritaeniorhynchus, as Getah virus (GETV). Two strains isolated from Cx. tritaeniorhynchus and Anopheles vagus were identified as Culex pipiens pallens Densovirus (CppDNV). CONCLUSION: Cx. tritaeniorhynchus had been the major species of mosquito and mainly transmitting vector of mosquito-borne viruses in Dehong prefecture. Genotype I JEV, GETV and CppDNV were the vectors causing transmission of mosquito-borne diseases in this area. Data from phylogenetic analysis showed that these newly discovered isolates seemed to have had close relationship with those viruses previously circulating in Yunnan and other provinces of China.","corpus_id":25080206,"score":2},{"doc_id":"25445747","title":"Study of mosquito fauna in rice ecosystems around Hanoi, northern Vietnam.","abstract":"Species of the Culex vishnui subgroup, Cx. fuscocephala and Cx. gelidus, which are known Japanese encephalitis (JE) vectors, are distributed in rice agroecosystems in Asian countries. Hence, although ecological studies of rice agroecosystems in northern Vietnam are necessary, very few integrated studies of breeding habitats of mosquitoes, including JE vectors, have been conducted. We carried out a field study and investigated the mosquito fauna in six rice production areas in northern Vietnam during the rainy and dry seasons of 2009. Mosquitoes and potential mosquito predators were collected from aquatic habitats by using larval dippers. We collected 1780 Culex individuals (including 254 Cx. tritaeniorhynchus; 113 Cx. vishnui, 58 Cx. vishnui complex, consisting of Cx. vishnui and Cx. pseudovishnui; 12 Cx. gelidus; 1 Cx. bitaeniorhynchus; and 1 Cx. fuscocephala), 148 Anopheles individuals (including 5 An. vagus), 1 Mansonia annulifera, and 1 Mimomyia chamberlaini during the rainy season. During the dry season, we collected 176 Culex individuals (including 33 Cx. vishnui, 24 Cx. tritaeniorhynchus, 8 Cx. vishnui complex, and 1 Cx. gelidus) and 186 Anopheles individuals (including 9 An. tessellatus, 2 An. kochi, and 2 An. barbumbrosus). We found mosquitoes in all aquatic habitats, namely, rice fields, ditches, ponds, wetlands, irrigation canals, and rice nurseries, and Cx. tritaeniorhynchus and Cx. vishnui complex were found in all the above six areas. Heteroptera such as Micronecta, Veliidae, and Pleidae were abundant and widely distributed in both the seasons. The abundance of mosquito larvae was higher in the rice fields, ditches, and ponds during the rainy season than during the dry season. Cx. tritaeniorhynchus, Cx. vishnui complex, Cx. fuscocephala, and Cx. gelidus were abundant in rice agroecosystems (rice fields, ditches, ponds, and wetlands) in northern Vietnam, and their abundance was high during the rainy season. These findings deepen our understanding of mosquito ecology and strengthen mosquito control strategies to be applied in rice ecosystems Vietnam in the future.","corpus_id":45726294,"score":2},{"doc_id":"25843138","title":"Host feeding patterns of mosquitoes in a rural malaria-endemic region in hainan island, china.","abstract":"Malaria is endemic in Wangxia Village of Hainan Island. In this area little is known about the host seeking behavior and feeding habit of mosquitoes. Three sites representing the most common habitat types in the village were selected to study the host seeking behavior and feeding habit of mosquitoes. Of the total 9 species belonging to 4 genera (Armigeres, Culex, Aedes, and Anopheles) collected in Wangxia Village, Culex tritaeniorhynchus and Cx. pipiens quinquefasciatus were the most commonly collected species. Armigeres subalbatus and Anopheles sinensis were moderately common species. Blood meal analysis confirmed that Cx. tritaeniorhynchus and Cx. p. quinquefasciatus fed on multiple hosts, mainly poultry but occasionally other animals. Anopheles sinensis, a vector of malaria, fed predominately on cattle hosts, followed by humans. Anopheles maculatus and An. barbirostris fed on both humans and domestic animals. Our results indicate that most mosquitoes in this area preferred domestic animals over humans and showed a tendency to feed on multiple hosts within the same gonotrophic cycle. Therefore, the potential role of domestic animals in arbovirus transmission should be evaluated as part of a strategy for controlling mosquito-borne diseases in this region.","corpus_id":8236412,"score":2},{"doc_id":"25975552","title":"[Isolation and identification of mosquito-borne arboviruses in Yuncheng city, Shanxi province, 2012].","abstract":"OBJECTIVE: To investigate the species and distribution of mosquitoes and mosquito-borne arboviruses in Yuncheng city of Shanxi province, China. METHODS: Mosquito samples were collected in 19 collection sites from Linyi county and Yongji city in Yuncheng city, in August, 2012. After identification and classification, all the specimens were homogenized and centrifuged to acquire supernatant before being inoculated to both C6/36 and BHK21 cells for viral isolation. Positive isolates were identified with arbovirus species-specific primers under RT-PCR, for further sequencing and phylogenetic analysis. RESULTS: A total of 10 455 mosquitoes of 7 species in 4 genuese were collected. The predominant mosquito species in Linyi county was Culex pipens pallens (91.96%, 3 911/4 253), but the one in Yongji city was Culex tritaeniorhynchus (72.85%, 4 518/6 202). A total of 23 strains of viruses were isolated from the mosquito pools. 15 strains from Culex tritaeniorhynchus and Culex pipens pallens were identified as genotype I Japanese encephalitis virus (JEV). Four strains from Culex pipens pallens were identified as Culex flavivirus (CxFV). Three strains from Culex pipens pallens were identified as Culex pipiens pallens densovirus (CppDNV). One strain from Armigeres subalbatus and Aedes albopictus was identified as Getah virus (GETV). CONCLUSION: Four kinds of arboviruses were isolated from the mosquito pools, including GETV and CxFV, which were isolated and documented in Shanxi province for the first time. In the city of Yuncheng, Culex tritaeniorhynchus had been the predominant species and major vector for transmitting JEV. Genotype I JEV remained the major JEV circulating in the local natural environment.","corpus_id":43359136,"score":2},{"doc_id":"26118548","title":"Distribution and phylogenetic analysis of Culex flavivirus in mosquitoes in China.","abstract":"Culex flavivirus (CxFV) is an insect-specific virus of the genus Flavivirus. CxFV strains have been isolated from Cx. pipiens, Cx. quinquefasciatus, and other Cx. species in Asia, Africa, North America, Central America and South America. CxFV was isolated for the first time in China in 2006. As this is a novel flavivirus, we explored the distribution and genetic characteristics of Culex flavivirus in China. A total of 46,649 mosquitoes were collected in seven provinces between 2004 and 2012 and were analysed in 871 pools. 29 CxFV RNAs from Cx. pipiens, Cx. tritaeniorhynchus, Anopheles Sinensis, and Culex spp. tested positive for CxFV in real-time RT-PCR. 6 CxFV strains were isolated from Cx. species collected in Shandong, Henan, and Shaanxi provinces, while no virus or viral RNA was detected in samples from Sichuan, Chongqing, Hubei, and Fujian. Phylogenetic analysis of the envelope gene indicated that Chinese strains formed a robust subgroup of genotype 1, together with viruses from the United States and Japan. This study demonstrates that the geographic distribution of CxFV in China is widespread, but geographical boundaries to spread are apparent. Our findings suggest that CxFV can infect various mosquito species in nature.","corpus_id":14530000,"score":2},{"doc_id":"26309323","title":"Influence of Bloodmeal Source on Reproductive Output of the Potential West Nile Vector, Culex theileri (Diptera: Culicidae).","abstract":"Culex theileri Theobald (Diptera: Culicidae) has a wide Afrotropical, southern Palaearctic, northern Oriental, and European distribution. It is mainly considered as a mammophilic mosquito and also feeds on birds and serves as a vector for various zoonotic diseases including West Nile virus. Despite its broad distribution and evidence indicating that Cx. theileri is a competent vector of human and domestic animal pathogens, basic biological and ecological features of this species have not been well investigated. We evaluated the impact of bloodmeal source (human, chicken, cow, and a double bloodmeal such as human and cow or chicken and cow and mixed bloodmeals [cow, chicken, and human] via artificial feeding) on fecundity, hatching rates, developmental times, and viability from egg to adult for laboratory colonized Cx. theileri. Fecundity in mosquitoes that took a chicken bloodmeal, a double bloodmeal and mixed bloodmeals was significantly higher than in females fed on a single cow or single human blood. This is the first study about the bloodmeal sources effect on laboratory-reared Cx. theileri populations and these findings contribute to our understanding of the impact of bloodmeal source on reproduction in Cx. theileri. As it is known that Cx. theileri is a vector for West Nile virus, the potential impacts of bloodmeal source on virus transmission are discussed.","corpus_id":207239092,"score":2},{"doc_id":"26666683","title":"Evaluation of CDC light traps for mosquito surveillance in a malaria endemic area on the Thai-Myanmar border.","abstract":"BACKGROUND: Centers for Disease Control and Prevention miniature light traps (CDC-LT) baited with CO2 are a routine tool for adult mosquito sampling used in entomological surveys, and for monitoring and surveillance of disease vectors. The present study was aimed at evaluating the performance of baited and unbaited CDC-LT for indoor and outdoor trapping of endemic mosquito species in northwestern Thailand. METHODS: CDC-LT (n = 112) with and without dry ice baits were set both indoors and outdoors in 88 selected houses for stretches of 5 consecutive nights per month in 7 villages in Tha Song Yang district, Tak province between January 2011 and March 2013. Individual traps were repeatedly placed in the same location for a median of 6 (range 1-10) times. Mosquitoes were identified by morphological characteristics and classified into blood-fed, empty, male/female and gravid. Absolute mosquito numbers were converted to capture rates (i.e., mosquitoes per trap and year). Capture rates were compared using multilevel negative binomial regression to account for multiple trap placements and adjust for regional and seasonal differences. RESULTS: A total of 6,668 mosquitoes from 9 genera were collected from 576 individual CDC-LT placements. Culex was the predominant captured genus (46 %), followed by anopheline mosquitoes (45 %). Overall, CO2 baited traps captured significantly more Culex (especially Culex vishnui Theobald) and Anopheles mosquitoes per unit time (adjusted capture rate ratio (aCRR) 1.64 and 1.38, respectively). Armigeres spp. mosquitoes were trapped in outdoor traps with significantly higher frequency (aCRR: 1.50), whereas Aedes albopictus (Skuse) had a tendency to be trapped more frequently indoors (aCRR: 1.89, p = 0.07). Furthermore, capture rate ratios between CO2 baited and non-baited CDC-LT were significantly influenced by seasonality and indoor vs. outdoor trap placement. CONCLUSION: The present study shows that CDC-LT with CO2 baiting capture significantly more Culex and Anopheles mosquitoes, some of which (e.g., Cx. vishnui, Cx. quinquefasciatus Say, An. minimus s.l. Theobald, An. maculatus s.l. Theobald) represent important disease vectors in Thailand. This study also shows significant differences in the capture efficiency of CDC-LT when placed indoors or outdoors and in different seasons. Our study thus provides important guidelines for more targeted future vector trapping studies on the Thai-Myanmar border, which is an important cross-border malaria transmission region in Thailand.","corpus_id":17500377,"score":2},{"doc_id":"26726881","title":"Sampling Design Influences the Observed Dominance of Culex tritaeniorhynchus: Considerations for Future Studies of Japanese Encephalitis Virus Transmission.","abstract":"Mosquito sampling during Japanese encephalitis virus (JEV)-associated studies, particularly in India, has usually been conducted via aspirators or light traps to catch mosquitoes around cattle, which are dead-end hosts for JEV. High numbers of Culex tritaeniorhynchus, relative to other species, have often been caught during these studies. Less frequently, studies have involved sampling outdoor resting mosquitoes. We aimed to compare the relative abundance of mosquito species between these two previously used mosquito sampling methods. From September to December 2013 entomological surveys were undertaken in eight villages in a Japanese encephalitis (JE) endemic area of Bangladesh. Light traps were used to collect active mosquitoes in households, and resting boxes and a Bina Pani Das hop cage were used near oviposition sites to collect resting mosquitoes. Numbers of humans and domestic animals present in households where light traps were set were recorded. In five villages Cx. tritaeniorhynchus was more likely to be selected from light trap samples near hosts than resting collection samples near oviposition sites, according to log odds ratio tests. The opposite was true for Cx. pseudovishnui and Armigeres subalbatus, which can also transmit JEV. Culex tritaeniorhynchus constituted 59% of the mosquitoes sampled from households with cattle, 28% from households without cattle and 17% in resting collections. In contrast Cx. pseudovishnui constituted 5.4% of the sample from households with cattle, 16% from households with no cattle and 27% from resting collections, while Ar. subalbatus constituted 0.15%, 0.38%, and 8.4% of these samples respectively. These observations may be due to differences in timing of biting activity, host preference and host-seeking strategy rather than differences in population density. We suggest that future studies aiming to implicate vector species in transmission of JEV should consider focusing catches around hosts able to transmit JEV.","corpus_id":21083882,"score":2},{"doc_id":"26739652","title":"Survivorship and fecundity of Culex pipiens pallens feeding on flowering plants and seed pods with differential preferences.","abstract":"Adult mosquitoes rely on ingestion of sugar from plants to survive, swarm and mate. Culex pipiens pallens Coguillett is the primary vector of lymphatic filariasis and epidemic encephalitis. Little is known about the effect of feeding on different sugar sources on the survivorship and fecundity of Cx. pipiens pallens. In the present study, newly emerged mosquitoes were exposed to several flowering plant and seed pod species with different olfactory preferences, and the survival times of mosquitoes exposed to these sugar sources were determined. The proportions of mosquitoes that ingested sugar from host plants were investigated by cold anthrone tests. The numbers of eggs per egg raft laid by mosquitoes were compared when they were provided with different sugar sources and one blood meal. The results revealed that feeding on different kinds of sugar sources significantly affected female and male mosquitoes' survival times. Cold anthrone tests indicated that the proportions of sugar-positive mosquitoes from different nutritional regimes within 24h corresponded to the preference rankings of Cx. pipiens pallens to these sugar sources, and rapid declines in the proportions of surviving individuals might be attributed to their insufficient ingestion of sugar from nutritional regimes. Feeding on different sugar sources strongly affected the proportions of engorged mosquitoes, and females that had fed on their preferred sugar sources laid more eggs than mosquitoes provided with less preferred sugar sources. The results would provide insights in developing mosquito control strategies that target the sugar feeding behavior of mosquitoes.","corpus_id":87595,"score":2},{"doc_id":"26805471","title":"Species composition, co-occurrence, association and affinity indices of mosquito larvae (Diptera: Culicidae) in Mazandaran Province, northern Iran.","abstract":"Although considerable progress has been made in the past years in management of mosquito borne diseases such as malaria, dengue, yellow fever and West Nile fever through research in biology and ecology of the vectors, these diseases are still major threats to human health. Therefore, more research is required for better management of the diseases. This investigation provides information on the composition, co-occurrence, association and affinity indices of mosquito larvae in Mazandaran Province, northern Iran. In a large scale field study, mosquito larvae were collected from 120 sentinel sites in 16 counties in Mazandaran Province, using standard 350 ml dipper. Sampling took place monthly from May to December 2014. Collected larvae were mounted on glass slides using de Faure's medium and were diagnosed using morphological characters. Totally, 19,840 larvae were collected including three genera and 16 species from 120 larval habitats, as follows: Anopheles claviger, Anopheles hyrcanus, Anopheles maculipennis s.l., Anopheles marteri, Anopheles plumbeus, Anopheles pseudopictus, Culex pipiens, Culex tritaeniorhynchus, Culex torrentium, Culex perexiguus, Culex territans, Culex mimeticus, Culex hortensis, Culiseta annulata, Culiseta longiareolata, and Culiseta morsitans. Predominant species were Cx. pipiens and An. maculipennis s.l. which show the highest co-occurrence. The pair of species An. hyrcanus/An. pseudopictus showed significant affinity and association. High co-occurrence of the predominant species Cx. pipiens and An. maculipennis s.l. in the study area is of considerable importance in terms of vector ecology. It was also revealed that An. pseudopictus/An. hyrcanus often occur sympatrically indicating their common habitat requirements. The information may be equally important when vector control measures are considered.","corpus_id":205239654,"score":2},{"doc_id":"26816489","title":"Resistance Level of Mosquito Species (Diptera: Culicidae) from Shandong Province, China.","abstract":"This study describes the aquatic habitats, species composition, and the insecticide resistance level of the mosquito Culex pipiens pallens in Shandong Province, China. A cross-sectional survey of mosquito larval habitats was conducted from May to November 2014 to determine the species composition and larval abundance. Larvae were collected using the standard dipping technique, and a total of four habitat types were sampled. The fourth instar larvae of Cx. pipiens pallens collected in each habitat type were tested for resistance to five insecticides according to a WHO bioassay. A total of 7,281 mosquito larvae were collected, of which 399 (5.48%) were categorized as Anopheles mosquito larvae (An. sinensis), 6636 (91.14%) as culicine larvae (Cx. pipiens pallens, Cx. tritaeniorhynchus, Cx. halifaxii, and Cx. bitaeniorhynchus), 213 (2.93%) as Armigeres larvae, and 33 (0.45%) as Aedes larvae (Aedes albopictus). In addition, a total of 1,149 mosquito pupae were collected. Culex larvae were distributed in all habitats investigated. Tukeys HSD analysis showed that roadside drainages were the most productive habitat type for Culex larvae. Armigeres species were found only in drains, Aedes only in water tanks, and Anopheles in water that was comparatively clear and rich in emergent plants. Bioassay showed that the maximum resistance level of Cx. pipiens pallens was to deltamethrin, while it was lowest to plifenate. The productivity of various mosquitoes in different habitat types is very heterogeneous. It is particularly important to modify human activity and the environment to achieve effective mosquito vector control. For effective larval control, the type of habitat should be considered, and the most productive habitat type should be given priority in mosquito abatement programs.","corpus_id":8282206,"score":2},{"doc_id":"27308279","title":"Evaluation of Isotope (32)P Method to Mark Culex pipiens (Diptera: Culicidae) in a Laboratory.","abstract":"BACKGROUND: The aim of the current study was to develop a marking technique as an internal marker to mark post blood meal mosquitoes by using stable phosphate isotope (32)P and determine the optimal concentration of it. METHODS: An isotonic physiological saline solution, containing different concentration of radioactive isotope (32)P-labeled disodium phosphate (Na2H(32)PO4) was injected into rabbits via the jugular vein in the laboratory. Emerged Cx. pipiens were marked after feeding on rabbit. At the same time, the labeled conditions of emerged Cx. pipiens were also measured by placing feces of No. 6 rabbit into containers with mosquito larvae and pupae inside. RESULTS: According to the label condition of Cx. pipiens after taking blood and the effect of different dosage Na2H(32)PO4 on rabbit health, the optimal concentration of radioactive isotope was determined, that is, 0.1211 mCi/kg. By placing feces of No. 6 rabbit into containers with mosquito larvae and pupae inside, the emerged mosquitoes were also labeled. Therefore, feeding mosquitoes on the animal injected with radioactive Na2H(32)PO4 was more practical for detecting and tracing mosquitoes. CONCLUSION: The method was less time-consuming, more sensitive and safer. This marking method will facilitate post-bloodmeal studies of mosquitoes and other blood-sucking insects.","corpus_id":31021691,"score":2},{"doc_id":"27444629","title":"The mitochondrial genomes of Culex tritaeniorhynchus and Culex pipiens pallens (Diptera: Culicidae) and comparison analysis with two other Culex species.","abstract":"BACKGROUND: Culex tritaeniorhynchus and Culex pipiens pallens are the major vectors of the Japanese encephalitis virus and Wuchereria bancrofti, the causative agent of filariasis. The knowledge of mitochondrial genomes has been widely useful for the studies on molecular evolution, phylogenetics and population genetics. METHODS: In this study, we sequenced and annotated the mitochondrial (mt) genomes of Cx. tritaeniorhynchus and Cx. p. pallens, and performed a comparative analysis including four known mt genomes of species of the subgenus Culex (Culex). The phylogenetic relationships of Cx. tritaeniorhynchus, Cx. p. pallens and four known Culex mt genome sequences were reconstructed by maximum likelihood based on concatenated protein-coding gene sequences. RESULTS: Culex tritaeniorhynchus and Cx. p. pallens mt genomes are 14,844 bp and 15,617 bp long, both consists of 13 PCGs, 22 tRNAs, 2 rRNAs and 1 CR (not sequenced for Cx. tritaeniorhynchus). The initiation and termination codons of PCGs are ATN and TAA, respectively, except for COI starting with TCG, and COI and COII terminated with T. tRNAs have the typical clover-leaf secondary structures except for trnS ((AGN)) that is lacking the DHU stem. 16S rRNA and 12S rRNA secondary structures were drawn for the first time for mosquito mt genomes. The control region of Cx. p. pallens mt genome is 747 bp long and with four tandem repeat structures. Phylogenetic analyses demonstrated that the mt genome of Cx. tritaeniorhynchus was significantly separated from the remaining five mt genomes of Culex spp. Culex p. pipiens, Cx. p. pallens and Cx. p. quinquefasciatus formed a monophyletic clade with Cx. p. quinquefasciatus linked in the middle of the clade, and Cx. p. pallens should have the same taxonomic level as Culex p. pipiens and Cx. p. quinquefasciatus. CONCLUSIONS: The mt genomes of Cx. tritaeniorhynchus and Cx. p. pallens share the same gene composition and order with those of two other Culex species. Culex p. pallens of the Pipiens complex should have the same taxonomic level as Culex p. pipiens and Cx. p. quinquefasciatus investigated. We enriched the Culex mt genome data and provided a reference basis for further Culex mt genome sequencing and analyses.","corpus_id":13947030,"score":2},{"doc_id":"27456936","title":"Laboratory evaluation of differential attraction of Culex pipiens pallens to fruit-based sugar baits.","abstract":"Mosquito adults usually need to obtain sugar from floral nectaries and damaged fruits/seed pods to replenish their energy reserves. The newly developed attractive toxic sugar baits have been successfully applied in controlling various mosquito species outdoors. However, the attraction of Culex pipiens pallens to different fruit-based sugar baits remains unknown. In the present study, we selected nine common fruit species, prepared the fruit-based sugar solutions, and investigated the attractiveness of different sugar baits to newly emerged Cx. pipiens pallens in the laboratory. The results showed that when tested against the 5% brown sugar solution, all the sugar baits were significantly attractive to both females and males. When tested together in the mesh-covered cage, there was a significant difference on the attractiveness between different fruit-based sugar baits. The most attractive fruit species included Broussonetia papyrifera, Cucumis melo, C. melo var. saccharinus, Amygdalus persica and Pyrus bretschneideri, and their seed pods could be potentially used as ingredients in ATSB for controlling mosquitoes outdoors.","corpus_id":30962330,"score":2},{"doc_id":"27681543","title":"A reassessment of the artificial infection of three predominant mosquito species with Plasmodium vivax in Shandong Province, China.","abstract":"BACKGROUND & OBJECTIVES: Under certain ecological circumstances, pathogens are able to rapidly adapt to new vectors. The great capacity of Plasmodium spp. to adapt to new anopheline mosquito vectors on different continents and the continuous ecological changes attributed to humans might promote their adaptation to culicine vectors, which are known to infect humans. Based on our current knowledge, it is difficult to predict whether such adaptations will occur. This study was aimed to determine the infection susceptibility of Anopheles sinensis, Culex tritaeniorhynchus and Cx. pipiens pallens to Plasmodium vivax in Shandong Province of China. METHODS: The susceptibility of the three predominant species of mosquitoes -An. sinensis, Cx. tritaeniorhynchus and Cx. pipiens pallens in Shandong Province was compared with a direct membrane feeding assay with 15 batches of Shandong strain mono-infected gametocyte-containing blood collected from Plasmodium vivax-infected patients. Infectivity was measured by dissecting the midguts and salivary glands of the mosquitoes. The presence of oocysts and sporozoites was determined by microscopy at 6 and 22 days post-blood feeding. RESULTS: From the 15 batches of mosquitoes that were fed infected blood, oocysts and sporozoites were detected only in 7th, 13th and 15th batches of infection for An. sinensis, and no oocysts or sporozoites were detected in Cx. tritaeniorhynchus or Cx. pipiens pallens. The positive rate of An. sinensis infection was 21.2, 13 and 36.3% in the three batches of mosquitoes, with an average infection rate of 23.5%. INTERPRETATION & CONCLUSION: The susceptibility of An. sinensis to P. vivax was very high in Shandong Province. Cx. tritaeniorhynchus and Cx. pipiens pallens failed to exhibit susceptibility to P. vivax.","corpus_id":40990673,"score":2},{"doc_id":"28135281","title":"Dispersal of male and female Culex quinquefasciatus and Aedes albopictus mosquitoes using stable isotope enrichment.","abstract":"The dispersal patterns of mosquito vectors are important drivers of vector-borne infectious disease dynamics and understanding movement patterns is pivotal to devise successful intervention strategies. Here, we investigate the dispersal patterns of two globally important mosquito vectors, Aedes albopictus and Culex quinquefasciatus, by marking naturally-occurring larvae with stable isotopes (13C or 15N). Marked individuals were captured with 32 CDC light trap, 32 gravid trap, and 16 BG Sentinel at different locations within two-kilometer radii of six larval habitats enriched with either 13C or 15N. In total, 720 trap nights from July to August 2013 yielded a total of 32,140 Cx. quinquefasciatus and 7,722 Ae. albopictus. Overall, 69 marked female mosquitoes and 24 marked male mosquitoes were captured throughout the study period. The distance that Cx. quinquefasciatus females traveled differed for host-seeking and oviposition-seeking traps, with females seeking oviposition sites traveling further than those seeking hosts. Our analysis suggests that 41% of Cx. quinquefasciatus females that were host-seeking occurred 1-2 kilometer from their respective natal site, while 59% remained within a kilometer of their natal site. In contrast, 59% of Cx. quinquefasciatus females that were seeking oviposition sites occurred between 1-2 kilometer away from their larval habitat, while 15% occurred > 2 kilometer away from their natal site. Our analysis estimated that approximately 100% of Ae. albopictus females remained within 1 km of their respective natal site, with 79% occurring within 250m. In addition, we found that male Ae. albopictus dispersed farther than females, suggesting male-biased dispersal in this Ae. albopictus population. This study provides important insights on the dispersal patterns of two globally relevant vector species, and will be important in planning next generation vector control strategies that mitigate mosquito-borne disease through sterile insect techniques, novel Wolbachia infection, and gene drive strategies.","corpus_id":8086573,"score":2},{"doc_id":"28347323","title":"Blood-feeding patterns of native mosquitoes and insights into their potential role as pathogen vectors in the Thames estuary region of the United Kingdom.","abstract":"BACKGROUND: The range of vertebrate hosts on which species of mosquito blood-feed is an important parameter for identifying potential vectors and in assessing the risk of incursion and establishment of vector-borne pathogens. In the United Kingdom, studies of mosquito host range have collected relatively few specimens and used techniques that could only broadly identify host species. This study conducted intensive collection and analysis of mosquitoes from a grazing marsh environment in southeast England. This site provides extensive wetland habitat for resident and migratory birds and has abundant human nuisance biting mosquitoes. The aim was to identify the blood-feeding patterns of mosquito species present at the site which could contribute to the transmission of pathogens. METHODS: Twice-weekly collections of mosquitoes were made from Elmley Nature Reserve, Kent, between June and October 2014. Mosquitoes were collected using resting boxes, by aspiration from man-made structures and using a Mosquito Magnet Pro baited with 1-octen-3-ol. Blood-fed specimens were classified according to the degree of blood meal digestion using the Sella scale and vertebrate origin determined using sequencing of a fragment of the mitochondrial cytochrome C oxidase subunit I gene. Mosquitoes that were morphologically cryptic were identified to species level using multiplex PCR and sequencing methods. RESULTS: A total of 20,666 mosquitoes of 11 species were collected, and 2,159 (10.4%) were blood-fed (Sella scale II-VI); of these 1,341 blood-fed specimens were selected for blood meal analysis. Vertebrate origin was successfully identified in 964 specimens (72%). Collections of blood-fed individuals were dominated by Anopheles maculipennis complex (73.5%), Culiseta annulata (21.2%) and Culex pipiens form pipiens (10.4%). Nineteen vertebrate hosts comprising five mammals and 14 birds were identified as hosts for mosquitoes, including two migratory bird species. Feeding on birds by Culex modestus and Anopheles atroparvus populations in England was demonstrated. CONCLUSIONS: This study expands the vertebrate host range of mosquitoes in the Thames estuary region of the UK. Feeding on both resident and migratory bird species by potential arbovirus vectors including Cx. pipiens f. pipiens and Cx. modestus indicates the potential for enzootic transmission of an introduced arbovirus between migratory and local bird species by native mosquito species.","corpus_id":69573,"score":2},{"doc_id":"29325101","title":"Fauna, Ecological Characteristics, and Checklist of the Mosquitoes in Mazandaran Province, Northern Iran.","abstract":"Mosquitoes are important vectors of human and animal diseases. This study updates current knowledge on fauna, dominance, and distribution of mosquitoes in Mazandaran Province, Northern Iran, to inform disease control effort. Larval collections, using standard dippers or droppers, and adult collections, using total catches, shelter pits, CDC light traps, and human landing catches, were performed monthly in 30 villages across 16 counties, from May to December 2014. Ovitraps, baited with hay infusion as oviposition attractants or stimulants for Aedes (Stegomyia) mosquitoes, were installed in each village and inspected weekly for eggs. Lactophenol and Berlese media were used for preserving and mounting specimens. Overall, 36,024 mosquito specimens (19,840 larvae and 16,184 adults) belonging to 4 genera and 20 species were morphologically identified. The dominance and distribution indices showed that Culex pipiens s.s. was the eudominant species with a constant distribution of larvae (D = 69.07%, C = 100%) and adults (D = 31.86%, C = 100%), followed by Cx tritaeniorhynchus (D = 38.14%, C = 100%) and Anopheles maculipennis s.l. ( D = 11.05%, C = 100%) as adults. Aedes vexans was the dominant (7.85%) species, but it had a sporadic (20%) distribution. Culex torrentium and Culiseta morsitans were added as the new species to the checklist of mosquitoes in Mazandaran Province. Due to the potential role, Cx. pipiens s.s. as a vector of various pathogens, further ecological studies are recommended.","corpus_id":24540035,"score":2},{"doc_id":"29460862","title":"Host preferences and feeding patterns of Anopheles sinensis Wiedemann in three sites of Shandong province, China.","abstract":"Background & objectives: Anopheles sinensis Wiedemann is a major vector of malaria and is among the dominant species in Shandong province of China. Knowledge of the blood-feeding patterns of mosquitoes is crucial for elimination of malaria vectors. However, little information is available on the blood-feeding behaviour of An. sinensis mosquitoes in Shandong province. This study was carried out to compare the blood-feeding behaviour of An. sinensis in malaria-endemic areas of Shandong province China. Methods: Adult Anopheles mosquitoes were collected from three malaria-endemic areas (Jimo, Yinan and Shanxian), during the peak months of mosquito population (August and September) from 2014 to 2015. Indoor-resting mosquitoes and outdoor-resting blood-fed females were sampled in the morning hours (0600 to 0900 hrs) from 10 randomly selected houses using pyrethrum spray catch method, and sweeping with an insect net. ELISA was used for the identification of blood meal. The blood meal of each mosquito was tested against antisera specific to human, pig, dog, cow, goat, horse (mule) and fowl. Results: At all indoor study locations of Jimo, Yinan and Shanxian, 59.4, 68.1 and 98.8% blood-engorged female An. sinensis collected from cattle sheds fed almost exclusively on bovines, respectively. For outdoor locations, at Jimo site, 27.27 and 49.55% An. sinensis fed on cattle and pigs; at Yinan, 30.42% fed on cattle and 36.88% fed both on cattle and goats, while no pig antibodies were detected. At Shanxian, percent of An. sinensis that fed on cattle, pigs and cattle-goat was 20.72, 27.62 and 21.78%, respectively. Interpretation & conclusion: The analysis of An. sinensis blood meals in all the three studied areas from human houses, cattle sheds, pig sheds and mixed dwellings revealed that An. sinensis prefers cattle hosts, and can feed on other available animal hosts if the cattle hosts are absent, and the mosquitoes readily feed on humans when domestic animals (cattle and pigs) are not nearby for feeding. The analysis of blood meal revealed that An. sinensis follow opportunistic feeding in Shandong province, China.","corpus_id":3442265,"score":2},{"doc_id":"29536705","title":"[Analysis of population genetic diversity of mosquitoes from Shandong Province based on mitochondrial DNA cytochrome oxidase subunit I gene fragment].","abstract":"OBJECTIVE: To explore the characteristics of gene sequence of mtDNA-COⅠ of Culex pipiens pallens from different geographical regions in Shandong Province and different resistant strains from the lab and five common mosquito species, and analyze the genetic diversity of these mosquitoes. METHODS: Adult mosquitoes were collected from Jinan, Jining, Qingdao cities and other places in Shandong Province. The sensitive, dichlorvos-resistant, pyrethroid-resistant and propoxur-resistant strains were reared in the lab. Five species of mosquito (Cx. pipiens pallens, Cx. tritaeniorhynchus, Anopheles sinensis, Aedes albopictus, and Armigeres subalbatus) were collected from Jining City and identified in the lab. mtDNA-COⅠwas specifically amplified by PCR and sequenced. The gene sequences were compared and analyzed by the biological information systems, and the phylogenetic tree was constructed. RESULTS: The amplified mtDNA-COⅠfragments of Cx. pipiens pallens from eight different cities and four different resistant strains were 528 bp in length, with 67.4% A+T contents and two mutation sites. The nucleotide sequence homology among the different geographic strains was 99.95% and the gene sequences of the four resistant strains were the same, showing a high homogeny. The amplified mtDNA-COⅠfragments of the five species of mosquitoes were 528 bp with 408 conserved sites, 120 variable sites, 42 parsimony informative sites and 78 singleton sites. The A+T contents were between 65.7% and 68.0%. The nucleotide sequence homology among the different mosquito species was between 86.17% and 92.05%, and the molecular identification was consistent with the traditional morphological identification. The molecular phylogenetic study showed that the different species were clustered at their own branch at the species and genus levels, while genera Armigeres was distantly related to the others. CONCLUSIONS: mtDNA-COⅠcould not serve as the molecular marker to analyze the population genetic variation and phylogenesis of Cx. pipiens pallens from different geographical regions and different resistant strains, but it has species and genus specificities, which could be used for the identification of the mosquito species and genus.","corpus_id":3847185,"score":2},{"doc_id":"19287362","title":"Species composition of mosquito fauna in Ranau, Sabah, Malaysia.","abstract":"The adult population and species composition of mosquitoes collected in Ranau, Sabah are described. A total of 5956 mosquitoes representing 8 genera and 41 species were collected using human landing catch, indoor and outdoor. Anopheles maculatus was the most common species (15.6%) followed by Culex quinquefasciatus (12.8%), Culex pseudovishnui (12.1%), Anopheles balabacensis (11.1%), Culex vishnui (9.7%), Aedes vexans (9.6%), Culex tritaeniorhyncus (6.6%), Anopheles donaldi (5.6%) and others in very small percentage.","corpus_id":10985009,"score":1},{"doc_id":"21943071","title":"The role of cow urine in the oviposition site preference of culicine and Anopheles mosquitoes.","abstract":"BACKGROUND: Chemical and behavioural ecology of mosquitoes plays an important role in the development of chemical cue based vector control. To date, studies available have focused on evaluating mosquito attractants and repellents of synthetic and human origins. This study, however, was aimed at seasonal evaluation of the efficiency of cow urine in producing oviposition cues to Anopheles gambiae s.l. and Culex quinquefasciatus in both laboratory and field conditions. METHODS: Oviposition response evaluation in laboratory conditions was carried out in mosquito rearing cages. The oviposition substrates were located in parallel or in diagonal positions inside the cage. Urine evaluation against gravid females of An. arabiensis and Cx. quinquefasciatus was carried out at Day 1, Day 3 and Day 7. Five millilitres (mls) of cow urine was added to oviposition substrate while de-chlorinated water was used as a control. In field experiments, 500 mls of cow urine was added in artificial habitats with 2500 mls of de-chlorinated water and 2 kgs of soil. The experiment was monitored for thirty consecutive days, eggs were collected daily from the habitats at 7.00 hrs. Data analysis was performed using parametric and non-parametric tests for treatments and controls while attraction of the oviposition substrate in each species was presented using Oviposition Activity Index (OAI). RESULTS: The OAI was positive with ageing of cattle urine in culicine species in both laboratory and field experiments. The OAI for anopheline species was positive with fresh urine. The OAI during the rainy season was positive for all species tested while in the dry season the OAI for culicine spp and Anopheles gambiae s.l., changed with time from positive to negative values. Based on linear model analysis, seasons and treatments had a significant effect on the number of eggs laid in habitats, even though the number of days had no effect. CONCLUSION: Oviposition substrates treated with cow urine in both laboratory and field conditions have shown that cow urine left to age from 1-7 days has an influence on oviposition behavioural response in mosquitoes. The analysis of microbial colonies for decaying urine should be investigated along with its associated by-products.","corpus_id":2824080,"score":1},{"doc_id":"22276651","title":"Vector competence of five common mosquito species in the People's Republic of China for Western equine encephalitis virus.","abstract":"Two strains of the Western equine encephalitis virus (WEEV) were first detected and isolated in China in 2001. The maintenance and transmission cycles of WEEV in China are currently not well understood, and the mosquito vectors involved in these cycles are unknown. To understand the ability of the local mosquitoes in China to transmit WEEV, the vector competence of five mosquito species, namely, Culex pipiens pallens Coquillett, Cx. p. quinquefasciatus Say, Aedes (Stegomyia) albopictus Skuse, Ae. ( Stegomyia) aegypti Linnaeus, and C. tritaeniorhynchus Giles, for WEEV were evaluated. Infection rates for Cx. p. pallens, Cx. p. quinquefasciatus, Cx. tritaeniorhynchus, Ae. Albopictus, and Ae. aegypti were 46%, 60%, 80%, 37%, and 25%, respectively. Dissemination rates for the same species were 60%, 61%, 75%, 55%, and 50%, respectively. Transmission rates were 41%, 53%, 57%, and 45% for Cx. p. pallens, Cx. p. quinquefasciatus, Ae. Albopictus, and Ae. Aegypti, respectively. Infection rates were significantly different between species, but the difference between dissemination and transmission rates were nonsignificant. These results suggest that several local mosquito species in China are competent laboratory vectors for WEEV.","corpus_id":8024842,"score":1},{"doc_id":"25987223","title":"Pyrethroid resistance in Culex pipiens mosquitoes.","abstract":"Mosquitoes within the Culex pipiens complex are widely distributed and important in the transmission of many human diseases. Insecticides, pyrethroids in particular, remain a mainstay for control of these important vectors. In this paper we review what is known about the levels, mechanisms and fitness costs of pyrethroid resistance in Cx. pipiens. Pyrethroid resistance in Cx. pipiens is a global problem, and resistance ratios of up to 7000-fold have been found in larvae of field collected mosquitoes. However, there is considerable variation between populations, indicating significant geographic heterogeneity of the resistance. The two major mechanisms of resistance to pyrethroids in Culex are mutations in Vssc (target site insensitivity) and overexpression of cytochrome P450(s) (increased detoxification). The most frequently reported Vssc mutation is L1014F (i.e. kdr), which has been found throughout the world. The L1014S mutation has been found in Cx. p. pallens from Japan and China, and in Cx. p. pipiens from China. The L1014C mutation has only been reported for Cx. p. pipens molestus from China and the V1016G mutation has only been reported from Saudi Arabia. Studies on the P450s of Cx. pipiens have identified several that are overexpressed (measured as transcript levels) in pyrethroid resistant strains. CYP9M10 is consistently overexpressed in pyrethroid resistant Cx. pipiens from at least seven countries, suggesting this P450 might be of global importance in resistance. Both CYP9M10-mediated pyrethroid resistance and kdr have fitness costs in the absence of insecticides under certain environmental conditions. Research needs and future directions are discussed.","corpus_id":25006251,"score":1}],"string":"[\n {\n \"doc_id\": \"18493314\",\n \"title\": \"Stable isotope analysis can potentially identify completely-digested bloodmeals in mosquitoes.\",\n \"abstract\": \"BACKGROUND: Vertebrate bloodfeeding is a critical component of a mosquito's ability to transmit pathogens that cause diseases such as malaria, dengue fever and viral encephalitis. Due to degradation by the digestive process, current methods to identify mosquito bloodmeal sources are only useful for approximately 36 hours post-feeding. A critical need exists for technologies to extend this window and gain a more complete picture of mosquito feeding behavior for epidemiological studies. Stable isotopes are useful for investigating organism feeding behavior because the isotopic ratio of an organism's tissues reflects that of the material it ingests. METHODOLOGY/PRINCIPAL FINDINGS: Proof-of-principle data indicates that after bloodfeeding, Aedes albopictus mosquitoes acquire diagnostic Carbon and Nitrogen stable isotope profiles from their vertebrate hosts that can be accurately identified one week post-feeding, approximately 4 days after the entire bloodmeal has been digested. Total C/N ratio served as a biomarker marker for bloodfeeding (P<0.02), while deltaN was the most informative variable which could distinguish between unfed, chicken-fed and human-fed mosquitoes (P<0.01). By plotting C/N vs. deltaN, all feeding treatments could be identified in a double-blind analysis. CONCLUSIONS/SIGNIFICANCE: These proof-of-principle experiments indicate that analysis of stable isotopes can be used to distinguish bloodfed from unfed mosquitoes, and also distinguish between different vertebrate bloodmeal sources even after all blood has been digested. The development of stable isotope-based assays for mosquito bloodmeal identification may be a powerful tool to investigate mosquito feeding ecology and the dynamics of vector-borne pathogens.\",\n \"corpus_id\": 18008036,\n \"score\": 2\n },\n {\n \"doc_id\": \"18567443\",\n \"title\": \"Control of mosquito vectors of tropical infectious diseases: (1) bioefficacy of mosquito coils containing several pyrethroids and a synergist.\",\n \"abstract\": \"The bioefficacy of mosquito coils containing several pyrethroids were tested in a 25 m3 room against Culex pipiens quinquefasciatus, Aedes aegypti and Anopheles dirus. The test results were compared with tests against Culex pipiens pallens in Japan. Based on the KT50 values (the 50% knockdown time) of mosquito coils containing dl, d-T80-allethrin, d, d-T-prallethrin and methoxymethyl-tetrafluorobenzyl tetramethyl-cyclopropanecarboxylate (K-3050) at doses of 0.05-0.5% (w/w) with or without a synergist, the pyrethroid susceptibility of the four mosquito species was as follows: Cx. p. quinquefasciatus was several times more tolerant to pyrethroids than Cx. p. pallens, Ae. aegypti was a further several times more tolerant than Cx. p. quinquefasciatus, and An. dirus was more susceptible than Cx. p. pallens (KT50 value: about half of Cx. p. pallens). The order of their susceptibilities is common for pyrethroids. Mosquito coils containing d, d-T-prallethrin and K-3050 at doses of 0.05-0.2% (w/w) and N-(2-ethylhexyl)bicycle-[2,2,1]-hept-5-ene-2,3-dicarboxyimide as a synergist at a ratio of 2 times the active ingredient were highly effective against Ae. aegypti, the most important mosquito vector for dengue fever.\",\n \"corpus_id\": 1927230,\n \"score\": 2\n },\n {\n \"doc_id\": \"18939684\",\n \"title\": \"A mark-release-recapture study on dispersal and flight distance of Culex pipiens pallens in an urban area of Japan.\",\n \"abstract\": \"A mark-release-recapture of Culex pipiens pallens was conducted in an urban area of Japan during June 26-29, 2007. Larvae naturally occurring in rain gutters were collected and reared to adults in a laboratory. A total of 10,183 emerging female Cx. pipiens pallens of 4-8 days old were marked with fluorescent dye and released from one site. Recapture was made on 4 consecutive days using 41 Centers for Disease Control and Prevention traps with 1 kg of dry ice and human landing collection, and 121 marked females were recaptured. The overall recapture rate was 0.01. The mean distance traveled by the recaptured females was estimated as 470, 287, 326, and 517 m on days 1-4, respectively. The maximum flight distance of host-seeking Cx. pipiens pallens was estimated as 1,217 m based on the relationship between distance from the release site to the collection site and the total number of recaptures/traps. The population size of female Cx. pipiens pallens in the study area was estimated as 100,904 +/- 8,509. The size of operational area for the control of Cx. pipiens pallens in urban area is discussed.\",\n \"corpus_id\": 826613,\n \"score\": 2\n },\n {\n \"doc_id\": \"18939686\",\n \"title\": \"Diversity of riceland mosquitoes and factors affecting their occurrence and distribution in Mwea, Kenya.\",\n \"abstract\": \"Knowledge of mosquito species diversity, occurrence, and distribution is an essential component of vector ecology and a guiding principle to formulation and implementation of integrated vector management programs. A 12-month entomological survey was conducted to determine the diversity of riceland mosquitoes and factors affecting their occurrence and distribution at 3 sites targeted for malaria vector control in Mwea, Kenya. Adult mosquitoes were sampled indoors by pyrethrum spray catch and outdoors by the Centers for Disease Control and Prevention light traps. Mosquitoes were then morphologically identified to species using taxonomic keys. The characteristics of houses sampled for indoor resting mosquitoes, including number of people sleeping in each house the night preceding collection, presence of bed nets, location of the house, size of eaves, wall type, presence of cattle and distance of the house to the cowshed, and proximity to larval habitats, were recorded. Of the 191,378 mosquitoes collected, 95% were identified morphologically to species and comprised 25 species from 5 genera. Common species included Anopheles arabiensis (53.5%), Culex quinquefasciatus (35.5%), An. pharoensis (4.7%), An. coustani (2.5%), and An. funestus (1.6%). Shannon's species diversity and evenness indices did not differ significantly among the 3 study sites. There was a marked house-to-house variation in the average number of mosquitoes captured. The number of people sleeping in the house the night preceding collection, size of eaves, distance to the cowshed, and the nearest larval habitat were significant predictors of occurrence of either or both An. arabiensis and Cx. quinquefasciatus. The peak abundance of An. arabiensis coincided with land preparation and the first few weeks after transplanting of rice seedlings, and that of Cx. quinquefasciatus coincided with land preparation, late stage of rice development, and short rains. After transplanting of rice seedlings, the populations of Cx. quinquefasciatus were collected more outdoors than indoors, suggesting a shift from endophily to exophily. These results demonstrate that irrigated rice cultivation has a strong impact on mosquito species occurrence, distribution, abundance, and behavior, and that certain house characteristics increase the degree of human-vector contact.\",\n \"corpus_id\": 22837595,\n \"score\": 2\n },\n {\n \"doc_id\": \"18939969\",\n \"title\": \"Risk factors for house-entry by culicine mosquitoes in a rural town and satellite villages in The Gambia.\",\n \"abstract\": \"UNLABELLED: BACKGROUND: Screening doors, windows and eaves of houses should reduce house entry by eusynanthropic insects, including the common African house mosquito Culex pipiens quinquefasciatus and other culicines. In the pre-intervention year of a randomized controlled trial investigating the protective effects of house screening against mosquito house entry, a multi-factorial risk factor analysis study was used to identify factors influencing house entry by culicines of nuisance biting and medical importance. These factors were house location, architecture, human occupancy and their mosquito control activities, and the number and type of domestic animals within the compound. RESULTS: 40,407 culicines were caught; the dominant species were Culex thalassius, Cx. pipiens s.l., Mansonia africanus, M. uniformis and Aedes aegypti. There were four times more Cx. pipiens s.l. in Farafenni town (geometric mean/trap/night = 8.1, 95% confidence intervals, CIs = 7.2-9.1) than in surrounding villages (2.1, 1.9-2.3), but over five times more other culicines in the villages (25.1, 22.1-28.7) than in town (4.6, 4.2-5.2). The presence of Cx. pipiens s.l. was reduced in both settings if the house had closed eaves (odds ratios, OR town = 0.62, 95% CIs = 0.49-0.77; OR village = 0.49, 0.33-0.73), but increased per additional person in the trapping room (OR town = 1.16, 1.09-1.24; OR village = 1.10, 1.02-1.18). In the town only, Cx. pipiens s.l. numbers were reduced if houses had a thatched roof (OR = 0.70, 0.51-0.96), for each additional cow tethered near the house (OR = 0.73, 0.65-0.82) and with increasing distance from a pit latrine (OR = 0.97, 0.95-0.99). In the villages a reduction in Cx. pipiens s.l. numbers correlated with increased horses in the compound (OR = 0.90, 0.82-0.99). The presence of all other culicines was reduced in houses with closed eaves (both locations), with horses tethered outside (village only) and with increasing room height (town only), but increased with additional people in the trapping room and where cows were tethered outside (both locations). CONCLUSION: The findings of this study advocate eave closure and pit latrine treatment in all locations, and zooprophylaxis using horses in rural areas, as simple control measures that could reduce the number of culicines found indoors.\",\n \"corpus_id\": 1649665,\n \"score\": 2\n },\n {\n \"doc_id\": \"19769051\",\n \"title\": \"Determination of mosquito (Diptera: Culicidae) bloodmeal sources in Western Australia: implications for arbovirus transmission.\",\n \"abstract\": \"A double-antibody enzyme-linked immunosorbent assay was used to determine the bloodmeal sources of adult mosquitoes (Diptera: Culicidae) collected in encephalitis vector surveillance mosquito traps in Western Australia between May 1993 and August 2004. In total, 2,606 blood-fed mosquitoes, representing 29 mosquito species, were tested, and 81.7% reacted with one or more of the primary antibodies. Aedes camptorhynchus (Thomson) and Culex annulirostris Skuse were the most common species tested, making up 47.2% (1,234) and 35.6% (930), respectively. These species obtained bloodmeals from a variety of vertebrate hosts but particularly marsupials and cows. In contrast, Culex pullus Theobald (72.7%; 24/33), Culiseta atra (Lee) (70.0%; 7/10), Culex globocoxitus Dobrotworsky (54.5%; 12/22), and Culex quinquefasciatus Say (39.3%; 22/56) often obtained bloodmeals from birds. Although Ae. camptorhynchus and Cx. annulirostris are well established vectors of arboviruses, other mosquitoes also may have a role in enzootic and/ or epizootic transmission.\",\n \"corpus_id\": 22213969,\n \"score\": 2\n },\n {\n \"doc_id\": \"19769059\",\n \"title\": \"Bloodmeal identification and detection of avian malaria parasite from mosquitoes (Diptera: Culicidae) inhabiting coastal areas of Tokyo Bay, Japan.\",\n \"abstract\": \"Bloodmeal identification and the detection of avian malaria parasite from mosquitoes (Diptera: Culicidae) were carried out by polymerase chain reaction-based methods for field samples collected in coastal areas of Tokyo Bay, Japan, from April to October 2007. The following seven mosquito species were collected: Aedes albopictus (Skuse), Culex pipiens pallens Coquillett, Culex pipiens form molestus Forskal, Culex tritaeniorhynchus Giles, Culex inatomii Kamimura & Wada, Culex bitaeniorhynchus Giles, and Lutzia vorax Edwards. Forty blood-fed mosquitoes were collected and 95% of bloodmeals of Cx. pipiens pallens were avian-derived, whereas only mammalian bloodmeals were identified for Ae. albopictus. Plasmodium DNA was amplified from 65% (15/23) of blood-fed Cx. pipiens pallens and unfed females of Cx. pipiens pallens and Cx. pipiens form molestus with a minimum infection rate of 29.9 and 13.5, respectively. One unfed female of Lt. vorax was also positive for Plasmodium parasites. Five genetically distinct lineages of Plasmodium were identified, with 0.21 to 5.86% sequence divergence. Rinshi-8, the most prevalent lineage at our study site, was identical to the published sequence of Plasmodium relictum-P5.\",\n \"corpus_id\": 26714838,\n \"score\": 2\n },\n {\n \"doc_id\": \"20939372\",\n \"title\": \"Experimental studies on comparison of the potential vector competence of four species of Culex mosquitoes in China to transmit West Nile virus.\",\n \"abstract\": \"To assess the risk that indigenous mosquitoes in China are capable of transmitting and sustaining West Nile virus (WNV), four important Culex mosquito species, Culex tritaeniorhynchus, Culex modestus, Culex pipiens pallens, and Culex pipiens quinquefasciatus, were allowed to feed on the artificial infectious blood meal with WNV dose of 10(6.8) plaque-forming unit/ml and tested approximately 2 wk later to determine infection and transmission rates. The results indicated that four Culex mosquitoes were competent laboratory vectors of WNV. The infection rates and transmission rates were statistical differences among different species of mosquito (chi2 = 20.620, P = 0.000; chi2 = 15.020, P = 0.005, respectively). The highest infection rate and transmission rate were obtained with Cx. tritaeniorhynchus (87.5 and 74.2%, respectively).\",\n \"corpus_id\": 1063109,\n \"score\": 2\n },\n {\n \"doc_id\": \"21044196\",\n \"title\": \"Seasonal changes in the feeding pattern of Culex pipiens pallens govern the transmission dynamics of multiple lineages of avian malaria parasites in Japanese wild bird community.\",\n \"abstract\": \"Heterogeneity in the transmission of mosquito-borne pathogens is determined largely by distribution patterns of mosquito bites among wild animal populations. Although mosquitoes are crucial for transmission of avian malaria parasites, little is known about the ecology of natural vectors. We examined bloodmeal and parasite incidence in Culex pipiens pallens by a polymerase chain reaction (PCR)-based procedure to determine how the feeding pattern of mosquitoes govern transmission dynamics of avian malaria parasites in Japanese wild birds. We collected 881 unfed and 486 blood-fed Cx. pipiens pallens resting on vegetation in a park in Tokyo. The mosquitoes were separated into abdomen and thorax prior to PCR screening. Abdomens of unfed mosquitoes were combined into 95 pools. From these, we amplified Plasmodium DNA in 32 (33.7%) pools. Among blood-fed mosquitoes, 371 individuals were screened for blood-sources and Plasmodium parasites. Plasmodium DNA was amplified from mosquitoes fed on 6 of 13 avian species identified as blood-sources. Ten Plasmodium lineages were identified on the basis of 478 bp of the cytochrome b gene, with 0.2-10% sequence divergence. The three commonest Plasmodium lineages (CXPIP09, SGS1 and PADOM02) were detected in both the abdomens and thoraxes of mosquitoes, strongly suggesting transmission of these lineages. Jungle crow (Corvus macrorhynchos) served as a natural host for the three commonest Plasmodium lineages and made up 63.8% of blood-sources. As a significant increase in feeding of vector mosquitoes on jungle crows coincided with their breeding season, jungle crows were considered to be the primary reservoir of Plasmodium transmission in this study.\",\n \"corpus_id\": 205363381,\n \"score\": 2\n },\n {\n \"doc_id\": \"21246936\",\n \"title\": \"Haematophageous vector monitoring in Djibouti city from 2008 to 2009: first records of Culex pipiens ssp. torridus (IGLISCH), and Anopheles sergentii (theobald).\",\n \"abstract\": \"The Horn of Africa represents a region formerly known to be highly susceptible to mosquito-borne infectious diseases. In order to monitor and analyze the current presence and threat of vector mosquitoes, continuous and standardized trapping using CDC light traps without an additional CO2-generator has been carried out at six selected monitoring sites located in Djibouti City, from August 2008 until December 2009. An overall of 620 haematophageous Diptera were trapped, 603 (97.3%) were mosquitoes, 10 (1.6%) were sand flies, and 7 (1.1%) were biting midges, respectively. Genus distribution of mosquitoes revealed that 600 (99.5%) were Culex spp., 2 (0.3%) were Anopheles sergentii, and 1 (0.2%) was Aedes aegypti. Culex species were represented by Cx. quinquefasciatus (78.5%), and Cx. pipiens ssp. torridus (21.5%). The later species was first detected focally in early December 2009 showing a strongly increasing population density resulting in a maximum trap rate of 25 mosquitoes per trap night. Sand flies were all Sergentomyia antennata, and biting midges of the genus Culicoides were represented by C. nubeculosus (71.4%) and C. vexans (28.6 %). The findings included the first records for Cx. pipiens ssp. torridus and An. sergentii in Djibouti. However, none of the captured female Culex spp, the known vector for West Nile Virus, showed positive results for viral nucleic acids using WNV RT-real time PCR system. Also, females An. sergentii were Plasmodium falciparum and P. vivax circumsporozoite protein negative.\",\n \"corpus_id\": 6965137,\n \"score\": 2\n },\n {\n \"doc_id\": \"21290944\",\n \"title\": \"Evaluation of octenol and Lurex as baits in Mosquito Magnet Pro traps to collect vector mosquitoes in China.\",\n \"abstract\": \"The effectiveness of the attractants 1-octen-3-ol (octenol) and L-lactic acid (Lurex) on the collection of Aedes albopictus, Culex tritaeniorhynchus, Cx. pipiens pallens, and Anopheles sinensis was first evaluated in Mosquito Magnet Pro traps in Yamenkou and Badachu residential areas, Beijing City, and Lishui area, Zhejiang Province, China. The Mosquito Magnet Pro traps baited with octenol collected significantly more Ae. albopictus, Cx. tritaeniorhynchus, and An. sinensis, but fewer Cx. pipiens pallens than collection by the traps alone. There were no significant differences in the numbers of Cx. pipiens pallens, Cx. tritaeniorhynchus, and An. sinensis collected by Mosquito Magnet Pro traps baited with Lurex compared to the traps alone, but the Mosquito Magnet Pro traps baited with Lurex collected significantly more Ae. albopictus than the number collected by the traps alone at 2 areas in Beijing.\",\n \"corpus_id\": 42023971,\n \"score\": 2\n },\n {\n \"doc_id\": \"21476444\",\n \"title\": \"Emergence of Culex pipiens from overwintering hibernacula.\",\n \"abstract\": \"Overwintering populations of Culex pipiens, the principal enzootic vector of West Nile virus in the northeastern USA, were studied over 3 consecutive winters from 2006 to 2008, using mark-recapture techniques to determine when Cx. pipiens females began to disperse from overwintering hibernacula and how their survival influenced early season populations. In February of each year, Cx. pipiens were aspirated and marked using fluorescent powder; 4,067, 752, and 3,070 diapausing Cx. pipiens were marked in each successive year. Mosquitoes were then trapped from mid-April to early May of each year using 19 Centers for Disease Control and Prevention (CDC) light traps and 16 CDC gravid traps. A total of 348, 39, and 111 Culex mosquitoes were captured in the spring of 2006, 2007, and 2008, respectively. The number of mosquitoes marked in overwintering habitats is generally positively correlated with the number of mosquitoes recaptured in the early spring (linear regression, R2 = 0.79, P = 0.04), yet results also suggest that seasonal variations beyond overwintering population size are likely important in determining the success of emergent populations. A single marked Cx. pipiens was captured in both 2006 and 2008. In 2006, the mosquito was captured 0.5 km from its overwintering site while in 2008 the mosquito was captured 0.3 km from its overwintering site. In all study years, mosquitoes consistently began exiting overwintering hibernacula the 3rd week of April, yet evidence of earlier exodus was observed in 2007, when outside temperatures were significantly higher in preceding days and months.\",\n \"corpus_id\": 1375270,\n \"score\": 2\n },\n {\n \"doc_id\": \"21875691\",\n \"title\": \"\\\"Bird biting\\\" mosquitoes and human disease: a review of the role of Culex pipiens complex mosquitoes in epidemiology.\",\n \"abstract\": \"The transmission of vector-borne pathogens is greatly influenced by the ecology of their vector, which is in turn shaped by genetic ancestry, the environment, and the hosts that are fed on. One group of vectors, the mosquitoes in the Culex pipiens complex, play key roles in the transmission of a range of pathogens including several viruses such as West Nile and St. Louis encephalitis viruses, avian malaria (Plasmodium spp.), and filarial worms. The Cx. pipiens complex includes Culex pipiens pipiens with two forms, pipiens and molestus, Culex pipiens pallens, Culex quinquefasciatus, Culex australicus, and Culex globocoxitus. While several members of the complex have limited geographic distributions, Cx. pipienspipiens and Cx. quinquefasciatus are found in all known urban and sub-urban temperate and tropical regions, respectively, across the world, where they are often principal disease vectors. In addition, hybrids are common in areas of overlap. Although gaps in our knowledge still remain, the advent of genetic tools has greatly enhanced our understanding of the history of speciation, domestication, dispersal, and hybridization. We review the taxonomy, genetics, evolution, behavior, and ecology of members of the Cx. pipiens complex and their role in the transmission of medically important pathogens. The adaptation of Cx. pipiens complex mosquitoes to human-altered environments led to their global distribution through dispersal via humans and, combined with their mixed feeding patterns on birds and mammals (including humans), increased the transmission of several avian pathogens to humans. We highlight several unanswered questions that will increase our ability to control diseases transmitted by these mosquitoes.\",\n \"corpus_id\": 13770917,\n \"score\": 2\n },\n {\n \"doc_id\": \"21980773\",\n \"title\": \"Mosquitoes (Diptera: Culicidae) in relation to the risk of disease transmission in El Ismailia Governorate, Egypt.\",\n \"abstract\": \"Mosquito were surveyed (Nov. 2009 - March 2010) in El Ismailia Governorate. Nine species were reported: Culex pipiens, Cx. perexiguus, Cx. antennatus, Anopheles tenebrosus, An. pharoensis, An. multicolor, Ochlerotatus detritus, Oc. caspius and Culiseta longiareolata. Culex pipiens was the predominant species (ca. 87% larvae and 57% adults). For the 3 common species, Cx. pipiens, Cx. perexiguus, and Cx. antennatus the following were examined: (1) the type and characteristics (temperature and pH) of the breeding habitats and their relation to the larval density and (2) the relation of adult indoor density to the indoor and outdoor temperature and RH. The abundance of mosquito vectors in El Ismailia with its old history of vector transmitted diseases contributes to the risk of mosquito borne disease transmission in this area. This would assist in the control activities.\",\n \"corpus_id\": 39591553,\n \"score\": 2\n },\n {\n \"doc_id\": \"22115320\",\n \"title\": \"The abundance and host-seeking behavior of culicine species (Diptera: Culicidae) and Anopheles sinensis in Yongcheng city, People's Republic of China.\",\n \"abstract\": \"BACKGROUND: The knowledge of mosquito species diversity and the level of anthropophily exhibited by each species in a region are of great importance to the integrated vector control. Culicine species are the primary vectors of Japanese encephalitis (JE) virus and filariasis in China. Anopheles sinensis plays a major role in the maintenance of Plasmodium vivax malaria transmission in China. The goal of this study was to compare the abundance and host-seeking behavior of culicine species and An. sinensis in Yongcheng city, a representative region of P. vivax malaria. Specifically, we wished to determine the relative attractiveness of different animal baits versus human bait to culicine species and An. sinensis. RESULTS: Culex tritaeniorhynchus was the most prevalent mosquito species and An. sinensis was the sole potential vector of P. vivax malaria in Yongcheng city. There were significant differences (P < 0.01) in the abundance of both An. sinensis and Cx. tritaeniorhynchus collected in distinct baited traps. The relative attractiveness of animal versus human bait was similar towards both An. sinensis and Cx. tritaeniorhynchus. The ranking derived from the mean number of mosquitoes per bait indicated that pigs, goats and calves frequently attracted more mosquitoes than the other hosts tested (dogs, humans, and chickens). These trends were similar across all capture nights at three distinct villages. The human blood index (HBI) of female An. sinensis was 2.94% when computed with mixed meals while 3.70% computed with only the single meal. 19:00~21:00 was the primary peak of host-seeking female An. sinensis while 4:00~5:00 was the smaller peak at night. There was significant correlation between the density of female An. sinensis and the average relative humidity (P < 0.05) in Wangshanzhuang village. CONCLUSIONS: Pigs, goats and calves were more attractive to An. sinensis and Cx. tritaeniorhynchus than dogs, humans, and chickens. Female An. sinensis host-seeking activity mainly occurred from 19:00 to 21:00. Thus, we propose that future vector control against An. sinensis and Cx. tritaeniorhynchus in the areas along the Huang-Huai River of central China should target the interface of human activity with domestic animals and adopt before human hosts go to bed at night.\",\n \"corpus_id\": 2559019,\n \"score\": 2\n },\n {\n \"doc_id\": \"22308769\",\n \"title\": \"Dispersal of Culex mosquitoes (Diptera: Culicidae) from a wastewater treatment facility.\",\n \"abstract\": \"A mark-recapture project examined dispersal and flight distances of Culex mosquitoes from a wastewater treatment plant in Albany, NY, during 2007 and 2008. A self-marking device was constructed to mark egressing mosquitoes with fluorescent marking powder. Mosquitoes were recaptured using 30 CDC miniature light traps located within a 2.0 km radius of the marking site. A total of 13 and 10 marked Culex mosquitoes were recaptured in 2007 and 2008, respectively. Culex mosquitoes traveled a minimum of 0.16 km, a maximum of 1.98 km and, following correction for decreasing trap density with distance, had a mean distance traveled of 1.33 km. Characterizing the dispersal patterns of these mosquitoes is important for understanding the distribution of West Nile virus and other pathogens.\",\n \"corpus_id\": 41665921,\n \"score\": 2\n },\n {\n \"doc_id\": \"22308772\",\n \"title\": \"Evaluation of a stable isotope method to mark naturally-breeding larval mosquitoes for adult dispersal studies.\",\n \"abstract\": \"Understanding mosquito dispersal is critically important for vector-borne disease control and prevention. Mark-release-recapture methods using various marking techniques have made substantial contributions to the study of mosquito biology. However, the ability to mark naturally breeding mosquitoes noninvasively and with life-long retention has remained problematic. Here, we describe a method to mark naturally breeding mosquitoes with stable isotopes. Culex pipiens f. molestus mosquitoes were provisioned as larvae in laboratory experiments with 15N-labeled potassium nitrate and 13C-labeled glucose. Larval enrichment was sufficient to differentiate marked adult mosquitoes from unmarked control mosquitoes and the natural source population from Chicago Illinois, using either delta 15N or delta 13C. Isotopic retention lasted for at least 55 d for adult male and females mosquitoes. There were no consistent effects of isotopic enrichment on immature mosquito survival or adult mosquito body size. We then applied this marking technique to naturally breeding Culex pipiens mosquitoes in suburban Chicago, IL, and for the first time, report successful isotopic enrichment of mosquitoes in the field. This stable isotope marking technique will facilitate studies of mosquito dispersal.\",\n \"corpus_id\": 18177233,\n \"score\": 2\n },\n {\n \"doc_id\": \"22548540\",\n \"title\": \"Analysis of post-blood meal flight distances in mosquitoes utilizing zoo animal blood meals.\",\n \"abstract\": \"We assessed the post-blood meal flight distance of four mosquito species in a unique environment using blood meal analysis. Mosquitoes were trapped at the Rio Grande Zoo in Albuquerque, NM, and the blood source of blood-engorged mosquitoes was identified. The distance from the enclosure of the animal serving as a blood source to the trap site was then determined. We found that mosquitoes captured at the zoo flew no more than 170 m with an average distance of 106.7 m after taking a blood meal. This is the first study in which the flight distance of wild mosquitoes has been assessed using blood meal analysis and the first in which zoo animals have served as the exclusive source of blood meals.\",\n \"corpus_id\": 42980754,\n \"score\": 2\n },\n {\n \"doc_id\": \"22627302\",\n \"title\": \"Distribution of mosquitoes and mosquito-borne viruses along the China-Myanmar border in Yunnan Province.\",\n \"abstract\": \"A total of 54,673 mosquitoes were collected at 11 sites located near the China-Myanmar border in the western part of Yunnan Province during July and August 2007. There were 29 species in 4 genera identified from the collections, including 12 species of Culex, 12 species of Anopheles, 3 species of Aedes, and 2 species of Armigeres. Culex tritaeniorhynchus Giles (67.9%, 37,119/54,673) and Anopheles sinensis Wiedemann (25.9%, 14,170/54,673) were the most abundant species in this investigation. Virus was isolated using BHK-21 and C6/36 cells from 22 of 510 mosquito pools. Isolates included Japanese encephalitis virus (JEV) and Getah virus (GETV), which were identified by serological and molecular methods. Twenty JEV strains were isolated from Cx. tritaeniorhynchus (15 isolates), An. sinensis (3 isolates), and Armigeres subalbatus Coquillett (2 isolates), and 2 GETV strains were isolated from Culex pseudovishnui Colless and Cx. tritaeniorhynchus. This study suggests that Ar. subalbatus is a potentially important local vector because of the high JEV infection ratio found in this species. Enzootic JEV transmission persists in this area and therefore, surveillance for human disease caused by JEV and GETV should be conducted in the region.\",\n \"corpus_id\": 18671765,\n \"score\": 2\n },\n {\n \"doc_id\": \"22679881\",\n \"title\": \"Host-feeding patterns of Culex pipiens and other potential mosquito vectors (Diptera: Culicidae) of West Nile virus (Flaviviridae) collected in Portugal.\",\n \"abstract\": \"The host blood-feeding patterns of mosquito vectors affects the likelihood of human exposure to zoonotic pathogens, including West Nile Virus (family Flaviviridae, genus Flavivirus, WNV). In Portugal, data are unavailable regarding the blood-feeding habits of common mosquito species, including Culex pipiens L., considered the primary vector of WNV to humans. The sources of bloodmeals in 203 blood-fed mosquitoes of nine species collected from June 2007 to November 2010 in 34 Portuguese counties were analyzed by sequencing cytochrome-b partial fragments. Cx. pipiens was the most common species collected and successfully analyzed (n = 135/78). In addition, blood-fed females of the following species were analyzed: Ochlerotatus caspius Pallas (n = 20), Culex theileri Theobald (n = 16), Anopheles maculipennis s.l. Meigen (n = 10), Culiseta longiareolata Macquart (n = 7), Aedes aegypti L. (n = 6), Culex perexiguus Theobald (n = 3), Culiseta annulata Schrank (n = 3), and Ochlerotatus detritus Haliday (n = 3). The Cx. pipiens mosquitoes fed predominantly on birds (n = 55/78, 70.5%), with a high diversity of avian species used as hosts, although human blood was identified in 18 specimens (18/78, 23.1%). No significant differences were found between the host-feeding patterns of blood-fed Cx. pipiens collected in residential and nonresidential habitats. The occurrence of human derived blood meals and the presence of a mix avian-human bloodmeal accordingly suggest this species as a potential vector of WNV. Therefore, in Portugal, Cx. pipiens may play a role both in the avian-to-avian enzootic WNV cycle and in the avian-to-mammal transmission. In this context, the identity of Cx. pipiens (considering the forms molestus and pipiens) and the potential consequence on feeding behavior and WNV transmission are discussed.\",\n \"corpus_id\": 44445656,\n \"score\": 2\n },\n {\n \"doc_id\": \"23226489\",\n \"title\": \"Dispersal range of Anopheles sinensis in Yongcheng City, China by mark-release-recapture methods.\",\n \"abstract\": \"BACKGROUND: Studying the dispersal range of Anopheles sinensis is of major importance for understanding the transition from malaria control to elimination. However, no data are available regarding the dispersal range of An. sinensis in China. The aim of the present study was to study the dispersal range of An. sinensis and provide the scientific basis for the development of effective control measures for malaria elimination in China. METHODOLOGY/PRINCIPAL FINDINGS: Mark-Release-Recapture (MRR) experiments were conducted with 3000 adult wild An. sinensis in 2010 and 3000 newly emerged wild An. sinensis in 2011 in two villages of Yongcheng City in Henan Province. Marked An. sinensis were recaptured daily for ten successive days using light traps. The overall recapture rates were 0.83% (95% CI, 0.50%~1.16%) in 2010 and 1.33% (95% CI, 0.92%~1.74%) in 2011. There was no significant difference in the recapture rates of wild An. sinensis and newly emerged An. sinensis. The majority of An. sinensis were captured due east at study site I compared with most in the west at study site II. Eighty percent and 90% of the marked An. sinensis were recaptured within a radius of 100 m from the release point in study site I and II, respectively, with a maximum dispersal range of 400 m within the period of this study. CONCLUSIONS/SIGNIFICANCE: Our results indicate that local An. sinensis may have limited dispersal ranges. Therefore, control efforts should target breeding and resting sites in proximity of the villages.\",\n \"corpus_id\": 170597,\n \"score\": 2\n },\n {\n \"doc_id\": \"23270171\",\n \"title\": \"Host-feeding pattern of Culex theileri (Diptera: Culicidae), potential vector of Dirofilaria immitis in the Canary Islands, Spain.\",\n \"abstract\": \"To identify the host range of potential vectors of Dirofilaria immitis Leidy, the causal agent of canine dirofilariasis, we studied the bloodmeal origin of mosquitoes trapped on two of the Canary Islands, Gran Canaria and Tenerife, where this disease is considered hyperendemic. On Gran Canaria, mosquitoes were captured using Centers for Disease Control and Prevention (CDC) traps (outdoors) and resting in a bathroom (indoors). Only CDC traps were used to capture mosquitoes in Tenerife. The species captured in decreasing order of abundance were Culex theileri Theobald, Culex pipiens L., Culiseta longiareolata Macquart, Anopheles atroparvus van Thiel, and Anopheles cinereus Theobald. The origins of bloodmeals were identified for 121 Cx. theileri and 4 Cx. pipiens after amplification and sequencing of a fragment of the vertebrate cytochrome oxidase I (COI) gene. Cx. theileri fed on goats, sheep, dogs, cattle, cats, humans, and chickens, and Cx. pipiens fed on goats and chickens. A lower success of bloodmeal identification was obtained in mosquitoes captured resting indoors than outdoors in CDC traps, probably because of a longer time period between feeding and capture. Although most Cx. theileri fed on ruminants, this species also fed on different mammal species susceptible to dirofiliarasis, including humans, suggesting it could play a role on parasite transmission.\",\n \"corpus_id\": 27484126,\n \"score\": 2\n },\n {\n \"doc_id\": \"23379959\",\n \"title\": \"Barrier screens: a method to sample blood-fed and host-seeking exophilic mosquitoes.\",\n \"abstract\": \"BACKGROUND: Determining the proportion of blood meals on humans by outdoor-feeding and resting mosquitoes is challenging. This is largely due to the difficulty of finding an adequate and unbiased sample of resting, engorged mosquitoes to enable the identification of host blood meal sources. This is particularly difficult in the south-west Pacific countries of Indonesia, the Solomon Islands and Papua New Guinea where thick vegetation constitutes the primary resting sites for the exophilic mosquitoes that are the primary malaria and filariasis vectors. METHODS: Barrier screens of shade-cloth netting attached to bamboo poles were constructed between villages and likely areas where mosquitoes might seek blood meals or rest. Flying mosquitoes, obstructed by the barrier screens, would temporarily stop and could then be captured by aspiration at hourly intervals throughout the night. RESULTS: In the three countries where this method was evaluated, blood-fed females of Anopheles farauti, Anopheles bancroftii, Anopheles longirostris, Anopheles sundaicus, Anopheles vagus, Anopheles kochi, Anopheles annularis, Anopheles tessellatus, Culex vishnui, Culex quinquefasciatus and Mansonia spp were collected while resting on the barrier screens. In addition, female Anopheles punctulatus and Armigeres spp as well as male An. farauti, Cx. vishnui, Cx. quinquefasciatus and Aedes species were similarly captured. CONCLUSIONS: Building barrier screens as temporary resting sites in areas where mosquitoes were likely to fly was an extremely time-effective method for collecting an unbiased representative sample of engorged mosquitoes for determining the human blood index.\",\n \"corpus_id\": 13723361,\n \"score\": 2\n },\n {\n \"doc_id\": \"23540117\",\n \"title\": \"Ecological and genetic analyses of the complete genomes of Culex flavivirus strains isolated from Culex tritaeniorhynchus and Culex pipiens (Diptera: Culicidae) group mosquitoes.\",\n \"abstract\": \"Culex flavivirus (CxFV) is an insect-specific flavivirus that was first reported in 2007 in Japan. CxFV strains were isolated from Culex tritaeniorhynchus Giles and Culex pipiens L. group mosquitoes and genetically characterized in Toyama Prefecture, Japan, from 2004 to 2009, to reveal host specificity, mode of transmission, and seasonal and geographical distribution. The minimum infection rate (MIR) of CxFV within Cx. tritaeniorhynchus populations was 0.3 and much lower than that within Cx. pipiens group (17.9). The complete genome sequences of 11 CxFV isolates (four from Cx. tritaeniorhynchus and seven from Cx. pipiens group) consisted of 10,835-10,837 nucleotides. When these 11 isolates and five reference strains (NIID-21-2 and Tokyo strains from Japan, Iowa07 and HOU24518 strains from the United States, H0901 strain from China) were compared, there were 95.2-99.2% nucleotide and 98.1-99.8% amino acid identities. Phylogenetic analysis showed that the 11 isolates were divided into four clusters. One cluster consisted of five isolates from Cx. pipiens group and Cx. tritaeniorhynchus from one site and their nucleotide sequences almost completely matched. One cluster consisted of an isolate with a unique sequence from a Cx. pipiens group mosquito captured in an aircraft from Taiwan, suggesting that it was introduced from abroad. CxFV strains were divided into several groups according to countries when nucleotide sequences of CxFV available in GenBank and 11 Toyama isolates were compared. These results suggest that CxFV is maintained in nature among Culex mosquitoes in a mosquito habitat-specific but not a species-specific manner.\",\n \"corpus_id\": 23364714,\n \"score\": 2\n },\n {\n \"doc_id\": \"23642138\",\n \"title\": \"Taxis assays measure directional movement of mosquitoes to olfactory cues.\",\n \"abstract\": \"BACKGROUND: Malaria control methods targeting indoor-biting mosquitoes have limited impact on vectors that feed and rest outdoors. Exploiting mosquito olfactory behaviour to reduce blood-feeding outdoors might be a sustainable approach to complement existing control strategies. Methodologies that can objectively quantify responses to odour under realistic field conditions and allow high-throughput screening of many compounds are required for development of effective odour-based control strategies. METHODS: The olfactory responses of laboratory-reared Anopheles gambiae in a semi-field tunnel and A. arabiensis females in an outdoor field setting to three stimuli, namely whole human odour, a synthetic blend of carboxylic acids plus carbon dioxide and CO(2) alone at four distances up to 100 metres were measured in two experiments using three-chambered taxis boxes that allow mosquito responses to natural or experimentally-introduced odour cues to be quantified. RESULTS: Taxis box assays could detect both activation of flight and directional mosquito movement. Significantly more (6-18%) A. arabiensis mosquitoes were attracted to natural human odour in the field up to 30 metres compared to controls, and blended synthetic human odours attracted 20% more A. gambiae in the semi-field tunnel up to 70 metres. Whereas CO(2) elicited no response in A. arabiensis in the open field, it was attractive to A. gambiae up to 50 metres (65% attraction compared to 36% in controls). CONCLUSIONS: We have developed a simple reproducible system to allow for the comparison of compounds that are active over medium- to long-ranges in semi-field or full-field environments. Knowing the natural range of attraction of anopheline mosquitoes to potential blood sources has substantial implications for the design of malaria control strategies, and adds to the understanding of olfactory behaviour in mosquitoes. This experimental strategy could also be extended from malaria vectors to other motile arthropods of medical, veterinary and agricultural significance.\",\n \"corpus_id\": 2078629,\n \"score\": 2\n },\n {\n \"doc_id\": \"23697019\",\n \"title\": \"Population ecology of mosquitoes and the status of bancroftian filariasis in El Dakahlia Governorate, the Nile delta, Egypt.\",\n \"abstract\": \"Mosquitoes were surveyed (Oct. 2010 & Apr. - Oct. 2011) in some localities representing 13 centers of El-Dakahlia Governorate. Six mosquito species were collected: Culex pipiens, Cx. antennatus, Cx. perexiguus, Ochlerotatus detritus, Anopheles pharoensis and An. tenebrosus. Culex pipiens was predominating (ca 79% larvae, 51% adults). Culex antennatus and Cx. perexiguus were also common. Of the Four types of the breeding habitats, the drainage canals were the most productive (53.4% larvae). For the three common species, the compiled larval density increases as water temp. increased and decreases as pH increased while adult indoor density increases as indoor and outdoor temp. and indoor RH increased and decreases as outdoor RH increased. Cx. pipiens significantly associated with Cx. antennatus (CAB=0.88 & I=0.48) while Cx. antennatus has a moderate association with Cx. perexiguus (CAB=0.47 & I=0.36). Out of 908 examined blood samples from ten centers, 7.49% were infected with Wuchereria bancrofti. The highest infection rates in some centers were associated with high indoor densities of Cx. pipiens females, the main filariasis vector. The situation necessitates a wide vector control program to minimize lymphatic filariasis transmission in this Governorate.\",\n \"corpus_id\": 20976502,\n \"score\": 2\n },\n {\n \"doc_id\": \"23786327\",\n \"title\": \"Sympatric occurrence of Culex pipiens (Diptera, Culicidae) biotypes pipiens, molestus and their hybrids in Portugal, Western Europe: feeding patterns and habitat determinants.\",\n \"abstract\": \"Culex (Culex) pipiens (Diptera: Culicidae) has two recognized biotypes, pipiens and molestus, which differ in physiology and behaviour; this difference may influence vectorial capacity for West Nile virus (WNV). Our goal was first to determine the presence of Cx. pipiens populations in 31 locations in Portugal and to subsequently analyse their host-feeding preferences and habitat determinants. Molecular identification of Cx. pipiens forms and their hybrids was performed in 97 females; bloodmeal sources were identified in 59 engorged specimens. Overall, 61.9% of specimens were identified as Cx. pipiens f. pipiens, 20.6% as Cx. pipiens f. molestus, and 17.5% as hybrid forms. Culex pipiens f. pipiens fed preferentially on birds, and Cx. pipiens f. molestus on humans. Hybrid forms fed mostly on birds, but human bloodmeals were common. With reference to habitat, Cx. pipiens f. pipiens and hybrid forms were positively correlated with peri-urban habitats. Our results confirm the sympatric presence of different Cx. pipiens biotypes in 14 of the 31 locations studied. Peri-urban areas were a common habitat of all biotypes and may represent zones of hybridization. The feeding preferences and sympatric distribution of the Cx. pipiens biotypes observed in Portugal favour the epizootic circulation of WNV and the occurrence of disease outbreaks of WNV.\",\n \"corpus_id\": 206198574,\n \"score\": 2\n },\n {\n \"doc_id\": \"23835922\",\n \"title\": \"Larvicidal, oviposition, and ovicidal effects of Artemisia annua (Asterales: Asteraceae) against Aedes aegypti, Anopheles sinensis, and Culex quinquefasciatus (Diptera: Culicidae).\",\n \"abstract\": \"This study focuses on the larvicidal, oviposition, and ovicidal effects of a crude extract of Artemisia annua against Aedes aegypti, Anopheles sinensis, and Culex quinquefasciatus. Dried cells of Artemisia annua from cell suspension cultures were extracted using hexane. The extract showed moderate larvicidal effects against mosquitoes. At 24-h post treatment, the LC50 values for Anopheles sinensis, Aedes aegypti, and Culex quinquefasciatus were recorded as 244.55, 276.14, and 374.99 ppm, respectively. The percentage mortality of larvae was directly proportional to the tested concentration. Anopheles sinensis was found to be the most susceptible species, whereas Culex quinquefasciatus was the most tolerant to the Artemisia annua extract. The results indicated that the Artemisia annua extract showed concentration-dependent oviposition deterrent activity and had a strong deterrent effect. At 500 ppm, the percentage effective repellency was more than 85% compared with the control group for all the species, with oviposition activity index values of -0.94, -0.95, and -0.78 for Aedes aegypti, Anopheles sinensis, and Culex quinquefasciatus, respectively. In the ovicidal assay, the percentage hatchability of eggs after treatment with 500 ppm of Artemisia annua extract was significantly lower than the control, with values of 48.84 ± 4.08, 38.42 ± 3.67, and 79.35 ± 2.09% for Aedes aegypti, Anopheles sinensis, and Culex quinquefasciatus, respectively. Artemisia annua was found to be more effective against Aedes aegypti and Anopheles sinensis compared with Culex quinquefasciatus. This study indicated that crude extract of A. annua could be a potential alternative for use in vector management programs.\",\n \"corpus_id\": 9113080,\n \"score\": 2\n },\n {\n \"doc_id\": \"24060238\",\n \"title\": \"Mosquitoes established in Lhasa city, Tibet, China.\",\n \"abstract\": \"BACKGROUND: In 2009, residents of Lhasa city, Tibet Autonomous Region (TAR), China reported large numbers of mosquitoes and bites from these insects. It is unclear whether this was a new phenomenon, which species were involved, and whether these mosquitoes had established themselves in the local circumstances. METHODS: The present study was undertaken in six urban sites of Chengguan district Lhasa city, Tibet. Adult mosquitoes were collected by bed net trap, labor hour method and light trap in August 2009 and August 2012. The trapped adult mosquitoes were initially counted and identified according to morphological criteria, and a proportion of mosquitoes were examined more closely using a multiplex PCR assay. RESULTS: 907 mosquitoes of the Culex pipiens complex were collected in this study. Among them, 595 were females and 312 were males. There was no significant difference in mosquito density monitored by bed net trap and labor hour method in 2009 and 2012. Of 105 mosquitoes identified by multiplex PCR, 36 were pure mosquitoes (34.29%) while 69 were hybrids (65.71%). The same subspecies of Culex pipiens complex were observed by bed net trap, labor hour method and light trap in 2009 and 2012. CONCLUSION: The local Culex pipiens complex comprises the subspecies Cx. pipiens pipiens, Cx. pipiens pallens, Cx. pipiens quinquefasciatus and its hybrids. Mosquitoes in the Cx. pipiens complex, known to be, potentially, vectors of periodic filariasis and encephalitis, are now present from one season to the next, and appear to be established in Lhasa City, TAR.\",\n \"corpus_id\": 1225470,\n \"score\": 2\n },\n {\n \"doc_id\": \"24146951\",\n \"title\": \"Mosquitoes of Western Yunnan Province, China: seasonal abundance, diversity, and arbovirus associations.\",\n \"abstract\": \"OBJECTIVE: The western borderland between Yunnan Province, China, and Myanmar is characterized by a climate that facilitates year-round production of mosquitoes. Numerous mosquito-transmitted viruses, including Japanese encephalitis virus circulate in this area. This project was to describe seasonal patterns in mosquito species abundance and arbovirus activity in the mosquito populations. METHODS: Mosquitoes were collected in Mangshi and Ruili cities of Dehong Prefecture near the border of China and Burma in Yunnan Province, the Peoples Republic of China in 2010. We monitored mosquito species abundance for a 12-month period using ultraviolet light, carbon dioxide baited CDC light and gravid traps; and tested the captured mosquitoes for the presence of virus to evaluate mosquito-virus associations in rural/agricultural settings in the area. RESULTS: A total of 43 species of mosquitoes from seven genera were collected, including 15 Culex species, 15 Anopheles spp., four Aedes spp., three Armigeres spp., one Mimomyia spp., two Uranotaenia spp. and three Mansonia spp.. Species richness and diversity varied between Mangshi and Ruili. Culex tritaeniorhynchus, Culex quinquefasciatus, Anopheles sinensis and Anopheles peditaeniatus were the most abundant species in both sampling sites. Ultraviolet light traps collected more specimens than CDC light traps baited with dry ice, though both collected the same variety of mosquito species. The CDC gravid trap was the most effective trap for capture of Culex quinquefasciatus, a species underrepresented in light trap collections. A total of 26 virus strains were isolated, which included 13 strains of Japanese encephalitis virus, four strains of Getah virus, one strain of Oya virus, one strain from the orbivirus genus, and seven strains of Culex pipien pallens densovirus. CONCLUSIONS: The present study illustrates the value of monitoring mosquito populations and mosquito-transmitted viruses year-round in areas where the climate supports year-round adult mosquito activity.\",\n \"corpus_id\": 4032496,\n \"score\": 2\n },\n {\n \"doc_id\": \"24180110\",\n \"title\": \"Flight capacity of adult Culex pipiens pallens (Diptera: Culicidae) in relation to gender and day-age.\",\n \"abstract\": \"Culex pipiens pallens (L.) is the most common mosquito in houses of central and northern China. It is the primary vector of lymphatic filariasis and Japanese encephalitis. The flight range of mosquitoes is an important factor predicting the risk area of transmission of mosquito-borne pathogens to vertebrate hosts. The flight performance of Cx. pipiens pallens was measured with a 26-channel computer-monitored flight-mill system. We found that females had longer flight capability than males for total flight distance (TFD) and total flight duration (TFDr), and females flew faster than males based on mean flight velocity. No significant difference in flight capability was found between different age-groups in males. However, certain age-groups of females showed significant differences in TFDr and TFD. Specifically, TFD and TFDr tended to be shortest for 5- and 6-d-old females. These significant differences in flight capability between ages and genders provide insights to determine the size of operational area to achieve effective control of Cx. pipiens pallens and minimize the risk of the related mosquito-borne epidemic diseases of lymphatic filariasis and Japanese encephalitis.\",\n \"corpus_id\": 40597234,\n \"score\": 2\n },\n {\n \"doc_id\": \"24180115\",\n \"title\": \"Feeding behavior and spatial distribution of Culex mosquitoes (Diptera: Culicidae) in wetland areas of the Czech Republic.\",\n \"abstract\": \"Mosquito feeding behavior determines the degree of vector-host contact and may have a serious impact on the risk of pathogen transmission, including that of the West Nile virus (WNV). To measure the role of Culex mosquitoes as WNV vectors, host-seeking females were collected using animal-baited traps containing live birds (quail) or mammals (rabbits) and CO2-baited Center for Disease Control and Prevention traps placed in several wetland areas in the Czech Republic. Culex pipiens (L.) and Culex modestus (F.) were the most frequently collected species. Although Cx. modestus did not distinguish between baits, Cx. pipiens was collected significantly more frequently in bird-baited traps. Based on mitochondrial DNA analysis of bloodmeals from engorged females collected by CO2-baited traps situated within reed beds, a diverse group of birds were the predominant hosts (93.7%), followed by mammals (4.2%) including humans, and amphibians (2.1%). Among birds, Anseriformes were fed upon most frequently by Cx. modestus, whereas Cx. pipiens fed most frequently on Passeriformes. To measure the infection risk and confirm the distribution of mosquito species in various biotopes, transects of CO2-baited CDC traps were operated from wetland reed beds into upland vegetated areas. Even though both Culex species occurred in all biotopes sampled and frequently dispersed hundreds of meters away from fishpond shore vegetation, the spatial distribution of Cx. modestus was significantly associated with reed beds at wetlands. The first detection of WNV (subtype RabV) in Cx. modestus in Bohemia and confirmation of WNV presence in Cx. pipiens in Moravia together with observed feeding behavior supports the presumed role of both Culex species in the avian-to-avian enzootic WNV cycle and in avian-to-mammal transmission in the Czech Republic.\",\n \"corpus_id\": 38698605,\n \"score\": 2\n },\n {\n \"doc_id\": \"24534672\",\n \"title\": \"Serosal cuticle formation and distinct degrees of desiccation resistance in embryos of the mosquito vectors Aedes aegypti, Anopheles aquasalis and Culex quinquefasciatus.\",\n \"abstract\": \"Given their medical importance, mosquitoes have been studied as vectors of parasites since the late 1800's. However, there are still many gaps concerning some aspects of their biology, such as embryogenesis. The embryonic desiccation resistance (EDR), already described in Aedes and Anopheles gambiae mosquitoes, is a peculiar trait. Freshly laid eggs are susceptible to water loss, a condition that can impair their viability. EDR is acquired during embryogenesis through the formation of the serosal cuticle (SC), protecting eggs from desiccation. Nevertheless, conservation of both traits (SC presence and EDR acquisition) throughout mosquito evolution is unknown. Comparative physiological studies with mosquito embryos from different genera, exhibiting distinct evolutionary histories and habits is a feasible approach. In this sense, the process of EDR acquisition of Aedes aegypti, Anopheles aquasalis and Culex quinquefasciatus at 25°C was evaluated. Completion of embryogenesis occurs in Ae. aegypti, An. aquasalis and Cx. quinquefasciatus at, respectively 77.4, 51.3 and 34.3hours after egg laying, Cx. quinquefasciatus embryonic development taking less than half the time of Ae. aegypti. In all cases, EDR is acquired in correlation with SC formation. For both Ae. aegypti and An. aquasalis, EDR and SC appear at 21% of total embryonic development, corresponding to the morphological stage of complete germ band elongation/beginning of germ band retraction. Although phylogenetically closer to Ae. aegypti than to An. aquasalis, Cx. quinquefasciatus acquires both EDR and serosal cuticle later, with 35% of total development, when the embryo already progresses to the middle of germ band retraction. EDR confers distinct egg viability in these species. While Ae. aegypti eggs demonstrated high viability when left up to 72hours in a dry environment, those of An. aquasalis and Cx. quinquefasciatus supported these conditions for only 24 and 5hours, respectively. Our data suggest that serosa development is at least partially uncoupled from embryo development and that, depending upon the mosquito species, EDR bestows distinct levels of egg viability.\",\n \"corpus_id\": 5628681,\n \"score\": 2\n },\n {\n \"doc_id\": \"24676212\",\n \"title\": \"Dispersal of adult culex mosquitoes in an urban west nile virus hotspot: a mark-capture study incorporating stable isotope enrichment of natural larval habitats.\",\n \"abstract\": \"Dispersal is a critical life history behavior for mosquitoes and is important for the spread of mosquito-borne disease. We implemented the first stable isotope mark-capture study to measure mosquito dispersal, focusing on Culex pipiens in southwest suburban Chicago, Illinois, a hotspot of West Nile virus (WNV) transmission. We enriched nine catch basins in 2010 and 2011 with 15N-potassium nitrate and detected dispersal of enriched adult females emerging from these catch basins using CDC light and gravid traps to distances as far as 3 km. We detected 12 isotopically enriched pools of mosquitoes out of 2,442 tested during the two years and calculated a mean dispersal distance of 1.15 km and maximum flight range of 2.48 km. According to a logistic distribution function, 90% of the female Culex mosquitoes stayed within 3 km of their larval habitat, which corresponds with the distance-limited genetic variation of WNV observed in this study region. This study provides new insights on the dispersal of the most important vector of WNV in the eastern United States and demonstrates the utility of stable isotope enrichment for studying the biology of mosquitoes in other disease systems.\",\n \"corpus_id\": 8710958,\n \"score\": 2\n },\n {\n \"doc_id\": \"24822373\",\n \"title\": \"[Identification of mammalian blood meals in anopheline mosquitoes from four counties of Yunnan Province by multiple PCR].\",\n \"abstract\": \"From June to August 2012, the blood-sucking mosquitoes were captured around cattle-sheds and human houses in Yuanjiang County, Qiaojia County, Yongshan County, and Jinghong City of Yunan Province. Blood samples from mosquitoes were collected on filter paper. Multiplex PCR assay was used to detect the blood meal samples. Among the 145 mosquitoes captured, 123 were Anopheles sinensis (84.8%) and 22 A. minimus (15.2%). Among the blood samples, corresponding bands were amplified in 134 samples. The result showed that the blood meals were from pigs (n = 104), cows (n = 22), dogs (n = 4), human (n=2), cow and pig (n = 1), pig and human (n = 1). Human blood index of A. sinensis and A. minimus was 0.018 and 0.045, respectively.\",\n \"corpus_id\": 21283349,\n \"score\": 2\n },\n {\n \"doc_id\": \"24897862\",\n \"title\": \"Molecular identification of bloodmeals from sand flies and mosquitoes collected in Israel.\",\n \"abstract\": \"In Israel, sand flies are the vectors of Leishmania Ross and mosquitoes are the vectors of West Nile Virus. In the Judean Desert and Tiberias, the sand fly Phlebotomus sergenti Parrot is the vector of Leishmania tropica (Wright) and the rock hyrax (Procavia capensis Pallas) is considered the main reservoir animal. The main vectors of West Nile Virus are Culex pipiens L. and Culex perexiguus Theobald. Bloodmeals of engorged field-caught female sand flies and mosquitoes are an important source for defining host preferences. Recent progress in DNA molecular techniques has enabled the accurate identification of blood sources within the arthropod gut. In this study, we applied molecular approach for species-specific identification based on polymerase chain reaction and nucleotide sequence analysis of polymorphic regions along two mitochondrial genes, 12S and 16S rRNA. The research was carried out on 261 engorged female sand flies collected in the Judean Desert and Tiberias and 50 engorged female mosquitoes collected in Tel-Aviv and Arava. Species identification of bloodmeals was successful in 92% of the samples. Rock hyrax was the most abundant host in bloodmeals of P. sergenti, while human blood was found in only seven (3%) females. L. tropica DNA was detected in three P. sergenti females from Tiberias that contained rock hyrax blood. Avian sequences were detected in 67% (10 of 15) of the identified bloodmeals from Cx. perexiguus and in 10% (3 of 29) of the identified meals from Cx. pipiens. Human sequences were found in 14% of the identified bloodmeals from Cx. pipiens. The successful analysis of the majority of the bloodmeals performed on wild sand flies and mosquitoes suggests that bloodmeal identification can be applied as one of the routine procedures in vector surveillance programs.\",\n \"corpus_id\": 36866910,\n \"score\": 2\n },\n {\n \"doc_id\": \"25059361\",\n \"title\": \"[Investigation on mosquitoes and mosquito-borne viruses in Dehong prefecture, Yunnan province, 2007 and 2010].\",\n \"abstract\": \"OBJECTIVE: To investigate the distribution patterns of mosquito and mosquito-borne viruses in Dehong prefecture, Yunnan province, China. METHODS: Mosquito samples were collected using the mosquito traps from five counties of Dehong prefecture on July, 2007 and 2010. Mosquito were cell cultured for viral isolation, and positive isolates were identified using RT-PCR and sequence analysis. RESULTS: A total of 43 634 mosquito comprised of 29 species representing six genera were collected. Culex tritaeniorhynchus and Anopheles sinensis comprised 78.69% and 14.77% of the total. Six strains of viruses were isolated from the mosquito pools. RT-PCR and phylogenetic analysis revealed three strains from Cx. tritaeniorhynchus, identified as genotype I Japanese encephalitis virus (JEV). One strain was identified from Cx. tritaeniorhynchus, as Getah virus (GETV). Two strains isolated from Cx. tritaeniorhynchus and Anopheles vagus were identified as Culex pipiens pallens Densovirus (CppDNV). CONCLUSION: Cx. tritaeniorhynchus had been the major species of mosquito and mainly transmitting vector of mosquito-borne viruses in Dehong prefecture. Genotype I JEV, GETV and CppDNV were the vectors causing transmission of mosquito-borne diseases in this area. Data from phylogenetic analysis showed that these newly discovered isolates seemed to have had close relationship with those viruses previously circulating in Yunnan and other provinces of China.\",\n \"corpus_id\": 25080206,\n \"score\": 2\n },\n {\n \"doc_id\": \"25445747\",\n \"title\": \"Study of mosquito fauna in rice ecosystems around Hanoi, northern Vietnam.\",\n \"abstract\": \"Species of the Culex vishnui subgroup, Cx. fuscocephala and Cx. gelidus, which are known Japanese encephalitis (JE) vectors, are distributed in rice agroecosystems in Asian countries. Hence, although ecological studies of rice agroecosystems in northern Vietnam are necessary, very few integrated studies of breeding habitats of mosquitoes, including JE vectors, have been conducted. We carried out a field study and investigated the mosquito fauna in six rice production areas in northern Vietnam during the rainy and dry seasons of 2009. Mosquitoes and potential mosquito predators were collected from aquatic habitats by using larval dippers. We collected 1780 Culex individuals (including 254 Cx. tritaeniorhynchus; 113 Cx. vishnui, 58 Cx. vishnui complex, consisting of Cx. vishnui and Cx. pseudovishnui; 12 Cx. gelidus; 1 Cx. bitaeniorhynchus; and 1 Cx. fuscocephala), 148 Anopheles individuals (including 5 An. vagus), 1 Mansonia annulifera, and 1 Mimomyia chamberlaini during the rainy season. During the dry season, we collected 176 Culex individuals (including 33 Cx. vishnui, 24 Cx. tritaeniorhynchus, 8 Cx. vishnui complex, and 1 Cx. gelidus) and 186 Anopheles individuals (including 9 An. tessellatus, 2 An. kochi, and 2 An. barbumbrosus). We found mosquitoes in all aquatic habitats, namely, rice fields, ditches, ponds, wetlands, irrigation canals, and rice nurseries, and Cx. tritaeniorhynchus and Cx. vishnui complex were found in all the above six areas. Heteroptera such as Micronecta, Veliidae, and Pleidae were abundant and widely distributed in both the seasons. The abundance of mosquito larvae was higher in the rice fields, ditches, and ponds during the rainy season than during the dry season. Cx. tritaeniorhynchus, Cx. vishnui complex, Cx. fuscocephala, and Cx. gelidus were abundant in rice agroecosystems (rice fields, ditches, ponds, and wetlands) in northern Vietnam, and their abundance was high during the rainy season. These findings deepen our understanding of mosquito ecology and strengthen mosquito control strategies to be applied in rice ecosystems Vietnam in the future.\",\n \"corpus_id\": 45726294,\n \"score\": 2\n },\n {\n \"doc_id\": \"25843138\",\n \"title\": \"Host feeding patterns of mosquitoes in a rural malaria-endemic region in hainan island, china.\",\n \"abstract\": \"Malaria is endemic in Wangxia Village of Hainan Island. In this area little is known about the host seeking behavior and feeding habit of mosquitoes. Three sites representing the most common habitat types in the village were selected to study the host seeking behavior and feeding habit of mosquitoes. Of the total 9 species belonging to 4 genera (Armigeres, Culex, Aedes, and Anopheles) collected in Wangxia Village, Culex tritaeniorhynchus and Cx. pipiens quinquefasciatus were the most commonly collected species. Armigeres subalbatus and Anopheles sinensis were moderately common species. Blood meal analysis confirmed that Cx. tritaeniorhynchus and Cx. p. quinquefasciatus fed on multiple hosts, mainly poultry but occasionally other animals. Anopheles sinensis, a vector of malaria, fed predominately on cattle hosts, followed by humans. Anopheles maculatus and An. barbirostris fed on both humans and domestic animals. Our results indicate that most mosquitoes in this area preferred domestic animals over humans and showed a tendency to feed on multiple hosts within the same gonotrophic cycle. Therefore, the potential role of domestic animals in arbovirus transmission should be evaluated as part of a strategy for controlling mosquito-borne diseases in this region.\",\n \"corpus_id\": 8236412,\n \"score\": 2\n },\n {\n \"doc_id\": \"25975552\",\n \"title\": \"[Isolation and identification of mosquito-borne arboviruses in Yuncheng city, Shanxi province, 2012].\",\n \"abstract\": \"OBJECTIVE: To investigate the species and distribution of mosquitoes and mosquito-borne arboviruses in Yuncheng city of Shanxi province, China. METHODS: Mosquito samples were collected in 19 collection sites from Linyi county and Yongji city in Yuncheng city, in August, 2012. After identification and classification, all the specimens were homogenized and centrifuged to acquire supernatant before being inoculated to both C6/36 and BHK21 cells for viral isolation. Positive isolates were identified with arbovirus species-specific primers under RT-PCR, for further sequencing and phylogenetic analysis. RESULTS: A total of 10 455 mosquitoes of 7 species in 4 genuese were collected. The predominant mosquito species in Linyi county was Culex pipens pallens (91.96%, 3 911/4 253), but the one in Yongji city was Culex tritaeniorhynchus (72.85%, 4 518/6 202). A total of 23 strains of viruses were isolated from the mosquito pools. 15 strains from Culex tritaeniorhynchus and Culex pipens pallens were identified as genotype I Japanese encephalitis virus (JEV). Four strains from Culex pipens pallens were identified as Culex flavivirus (CxFV). Three strains from Culex pipens pallens were identified as Culex pipiens pallens densovirus (CppDNV). One strain from Armigeres subalbatus and Aedes albopictus was identified as Getah virus (GETV). CONCLUSION: Four kinds of arboviruses were isolated from the mosquito pools, including GETV and CxFV, which were isolated and documented in Shanxi province for the first time. In the city of Yuncheng, Culex tritaeniorhynchus had been the predominant species and major vector for transmitting JEV. Genotype I JEV remained the major JEV circulating in the local natural environment.\",\n \"corpus_id\": 43359136,\n \"score\": 2\n },\n {\n \"doc_id\": \"26118548\",\n \"title\": \"Distribution and phylogenetic analysis of Culex flavivirus in mosquitoes in China.\",\n \"abstract\": \"Culex flavivirus (CxFV) is an insect-specific virus of the genus Flavivirus. CxFV strains have been isolated from Cx. pipiens, Cx. quinquefasciatus, and other Cx. species in Asia, Africa, North America, Central America and South America. CxFV was isolated for the first time in China in 2006. As this is a novel flavivirus, we explored the distribution and genetic characteristics of Culex flavivirus in China. A total of 46,649 mosquitoes were collected in seven provinces between 2004 and 2012 and were analysed in 871 pools. 29 CxFV RNAs from Cx. pipiens, Cx. tritaeniorhynchus, Anopheles Sinensis, and Culex spp. tested positive for CxFV in real-time RT-PCR. 6 CxFV strains were isolated from Cx. species collected in Shandong, Henan, and Shaanxi provinces, while no virus or viral RNA was detected in samples from Sichuan, Chongqing, Hubei, and Fujian. Phylogenetic analysis of the envelope gene indicated that Chinese strains formed a robust subgroup of genotype 1, together with viruses from the United States and Japan. This study demonstrates that the geographic distribution of CxFV in China is widespread, but geographical boundaries to spread are apparent. Our findings suggest that CxFV can infect various mosquito species in nature.\",\n \"corpus_id\": 14530000,\n \"score\": 2\n },\n {\n \"doc_id\": \"26309323\",\n \"title\": \"Influence of Bloodmeal Source on Reproductive Output of the Potential West Nile Vector, Culex theileri (Diptera: Culicidae).\",\n \"abstract\": \"Culex theileri Theobald (Diptera: Culicidae) has a wide Afrotropical, southern Palaearctic, northern Oriental, and European distribution. It is mainly considered as a mammophilic mosquito and also feeds on birds and serves as a vector for various zoonotic diseases including West Nile virus. Despite its broad distribution and evidence indicating that Cx. theileri is a competent vector of human and domestic animal pathogens, basic biological and ecological features of this species have not been well investigated. We evaluated the impact of bloodmeal source (human, chicken, cow, and a double bloodmeal such as human and cow or chicken and cow and mixed bloodmeals [cow, chicken, and human] via artificial feeding) on fecundity, hatching rates, developmental times, and viability from egg to adult for laboratory colonized Cx. theileri. Fecundity in mosquitoes that took a chicken bloodmeal, a double bloodmeal and mixed bloodmeals was significantly higher than in females fed on a single cow or single human blood. This is the first study about the bloodmeal sources effect on laboratory-reared Cx. theileri populations and these findings contribute to our understanding of the impact of bloodmeal source on reproduction in Cx. theileri. As it is known that Cx. theileri is a vector for West Nile virus, the potential impacts of bloodmeal source on virus transmission are discussed.\",\n \"corpus_id\": 207239092,\n \"score\": 2\n },\n {\n \"doc_id\": \"26666683\",\n \"title\": \"Evaluation of CDC light traps for mosquito surveillance in a malaria endemic area on the Thai-Myanmar border.\",\n \"abstract\": \"BACKGROUND: Centers for Disease Control and Prevention miniature light traps (CDC-LT) baited with CO2 are a routine tool for adult mosquito sampling used in entomological surveys, and for monitoring and surveillance of disease vectors. The present study was aimed at evaluating the performance of baited and unbaited CDC-LT for indoor and outdoor trapping of endemic mosquito species in northwestern Thailand. METHODS: CDC-LT (n = 112) with and without dry ice baits were set both indoors and outdoors in 88 selected houses for stretches of 5 consecutive nights per month in 7 villages in Tha Song Yang district, Tak province between January 2011 and March 2013. Individual traps were repeatedly placed in the same location for a median of 6 (range 1-10) times. Mosquitoes were identified by morphological characteristics and classified into blood-fed, empty, male/female and gravid. Absolute mosquito numbers were converted to capture rates (i.e., mosquitoes per trap and year). Capture rates were compared using multilevel negative binomial regression to account for multiple trap placements and adjust for regional and seasonal differences. RESULTS: A total of 6,668 mosquitoes from 9 genera were collected from 576 individual CDC-LT placements. Culex was the predominant captured genus (46 %), followed by anopheline mosquitoes (45 %). Overall, CO2 baited traps captured significantly more Culex (especially Culex vishnui Theobald) and Anopheles mosquitoes per unit time (adjusted capture rate ratio (aCRR) 1.64 and 1.38, respectively). Armigeres spp. mosquitoes were trapped in outdoor traps with significantly higher frequency (aCRR: 1.50), whereas Aedes albopictus (Skuse) had a tendency to be trapped more frequently indoors (aCRR: 1.89, p = 0.07). Furthermore, capture rate ratios between CO2 baited and non-baited CDC-LT were significantly influenced by seasonality and indoor vs. outdoor trap placement. CONCLUSION: The present study shows that CDC-LT with CO2 baiting capture significantly more Culex and Anopheles mosquitoes, some of which (e.g., Cx. vishnui, Cx. quinquefasciatus Say, An. minimus s.l. Theobald, An. maculatus s.l. Theobald) represent important disease vectors in Thailand. This study also shows significant differences in the capture efficiency of CDC-LT when placed indoors or outdoors and in different seasons. Our study thus provides important guidelines for more targeted future vector trapping studies on the Thai-Myanmar border, which is an important cross-border malaria transmission region in Thailand.\",\n \"corpus_id\": 17500377,\n \"score\": 2\n },\n {\n \"doc_id\": \"26726881\",\n \"title\": \"Sampling Design Influences the Observed Dominance of Culex tritaeniorhynchus: Considerations for Future Studies of Japanese Encephalitis Virus Transmission.\",\n \"abstract\": \"Mosquito sampling during Japanese encephalitis virus (JEV)-associated studies, particularly in India, has usually been conducted via aspirators or light traps to catch mosquitoes around cattle, which are dead-end hosts for JEV. High numbers of Culex tritaeniorhynchus, relative to other species, have often been caught during these studies. Less frequently, studies have involved sampling outdoor resting mosquitoes. We aimed to compare the relative abundance of mosquito species between these two previously used mosquito sampling methods. From September to December 2013 entomological surveys were undertaken in eight villages in a Japanese encephalitis (JE) endemic area of Bangladesh. Light traps were used to collect active mosquitoes in households, and resting boxes and a Bina Pani Das hop cage were used near oviposition sites to collect resting mosquitoes. Numbers of humans and domestic animals present in households where light traps were set were recorded. In five villages Cx. tritaeniorhynchus was more likely to be selected from light trap samples near hosts than resting collection samples near oviposition sites, according to log odds ratio tests. The opposite was true for Cx. pseudovishnui and Armigeres subalbatus, which can also transmit JEV. Culex tritaeniorhynchus constituted 59% of the mosquitoes sampled from households with cattle, 28% from households without cattle and 17% in resting collections. In contrast Cx. pseudovishnui constituted 5.4% of the sample from households with cattle, 16% from households with no cattle and 27% from resting collections, while Ar. subalbatus constituted 0.15%, 0.38%, and 8.4% of these samples respectively. These observations may be due to differences in timing of biting activity, host preference and host-seeking strategy rather than differences in population density. We suggest that future studies aiming to implicate vector species in transmission of JEV should consider focusing catches around hosts able to transmit JEV.\",\n \"corpus_id\": 21083882,\n \"score\": 2\n },\n {\n \"doc_id\": \"26739652\",\n \"title\": \"Survivorship and fecundity of Culex pipiens pallens feeding on flowering plants and seed pods with differential preferences.\",\n \"abstract\": \"Adult mosquitoes rely on ingestion of sugar from plants to survive, swarm and mate. Culex pipiens pallens Coguillett is the primary vector of lymphatic filariasis and epidemic encephalitis. Little is known about the effect of feeding on different sugar sources on the survivorship and fecundity of Cx. pipiens pallens. In the present study, newly emerged mosquitoes were exposed to several flowering plant and seed pod species with different olfactory preferences, and the survival times of mosquitoes exposed to these sugar sources were determined. The proportions of mosquitoes that ingested sugar from host plants were investigated by cold anthrone tests. The numbers of eggs per egg raft laid by mosquitoes were compared when they were provided with different sugar sources and one blood meal. The results revealed that feeding on different kinds of sugar sources significantly affected female and male mosquitoes' survival times. Cold anthrone tests indicated that the proportions of sugar-positive mosquitoes from different nutritional regimes within 24h corresponded to the preference rankings of Cx. pipiens pallens to these sugar sources, and rapid declines in the proportions of surviving individuals might be attributed to their insufficient ingestion of sugar from nutritional regimes. Feeding on different sugar sources strongly affected the proportions of engorged mosquitoes, and females that had fed on their preferred sugar sources laid more eggs than mosquitoes provided with less preferred sugar sources. The results would provide insights in developing mosquito control strategies that target the sugar feeding behavior of mosquitoes.\",\n \"corpus_id\": 87595,\n \"score\": 2\n },\n {\n \"doc_id\": \"26805471\",\n \"title\": \"Species composition, co-occurrence, association and affinity indices of mosquito larvae (Diptera: Culicidae) in Mazandaran Province, northern Iran.\",\n \"abstract\": \"Although considerable progress has been made in the past years in management of mosquito borne diseases such as malaria, dengue, yellow fever and West Nile fever through research in biology and ecology of the vectors, these diseases are still major threats to human health. Therefore, more research is required for better management of the diseases. This investigation provides information on the composition, co-occurrence, association and affinity indices of mosquito larvae in Mazandaran Province, northern Iran. In a large scale field study, mosquito larvae were collected from 120 sentinel sites in 16 counties in Mazandaran Province, using standard 350 ml dipper. Sampling took place monthly from May to December 2014. Collected larvae were mounted on glass slides using de Faure's medium and were diagnosed using morphological characters. Totally, 19,840 larvae were collected including three genera and 16 species from 120 larval habitats, as follows: Anopheles claviger, Anopheles hyrcanus, Anopheles maculipennis s.l., Anopheles marteri, Anopheles plumbeus, Anopheles pseudopictus, Culex pipiens, Culex tritaeniorhynchus, Culex torrentium, Culex perexiguus, Culex territans, Culex mimeticus, Culex hortensis, Culiseta annulata, Culiseta longiareolata, and Culiseta morsitans. Predominant species were Cx. pipiens and An. maculipennis s.l. which show the highest co-occurrence. The pair of species An. hyrcanus/An. pseudopictus showed significant affinity and association. High co-occurrence of the predominant species Cx. pipiens and An. maculipennis s.l. in the study area is of considerable importance in terms of vector ecology. It was also revealed that An. pseudopictus/An. hyrcanus often occur sympatrically indicating their common habitat requirements. The information may be equally important when vector control measures are considered.\",\n \"corpus_id\": 205239654,\n \"score\": 2\n },\n {\n \"doc_id\": \"26816489\",\n \"title\": \"Resistance Level of Mosquito Species (Diptera: Culicidae) from Shandong Province, China.\",\n \"abstract\": \"This study describes the aquatic habitats, species composition, and the insecticide resistance level of the mosquito Culex pipiens pallens in Shandong Province, China. A cross-sectional survey of mosquito larval habitats was conducted from May to November 2014 to determine the species composition and larval abundance. Larvae were collected using the standard dipping technique, and a total of four habitat types were sampled. The fourth instar larvae of Cx. pipiens pallens collected in each habitat type were tested for resistance to five insecticides according to a WHO bioassay. A total of 7,281 mosquito larvae were collected, of which 399 (5.48%) were categorized as Anopheles mosquito larvae (An. sinensis), 6636 (91.14%) as culicine larvae (Cx. pipiens pallens, Cx. tritaeniorhynchus, Cx. halifaxii, and Cx. bitaeniorhynchus), 213 (2.93%) as Armigeres larvae, and 33 (0.45%) as Aedes larvae (Aedes albopictus). In addition, a total of 1,149 mosquito pupae were collected. Culex larvae were distributed in all habitats investigated. Tukeys HSD analysis showed that roadside drainages were the most productive habitat type for Culex larvae. Armigeres species were found only in drains, Aedes only in water tanks, and Anopheles in water that was comparatively clear and rich in emergent plants. Bioassay showed that the maximum resistance level of Cx. pipiens pallens was to deltamethrin, while it was lowest to plifenate. The productivity of various mosquitoes in different habitat types is very heterogeneous. It is particularly important to modify human activity and the environment to achieve effective mosquito vector control. For effective larval control, the type of habitat should be considered, and the most productive habitat type should be given priority in mosquito abatement programs.\",\n \"corpus_id\": 8282206,\n \"score\": 2\n },\n {\n \"doc_id\": \"27308279\",\n \"title\": \"Evaluation of Isotope (32)P Method to Mark Culex pipiens (Diptera: Culicidae) in a Laboratory.\",\n \"abstract\": \"BACKGROUND: The aim of the current study was to develop a marking technique as an internal marker to mark post blood meal mosquitoes by using stable phosphate isotope (32)P and determine the optimal concentration of it. METHODS: An isotonic physiological saline solution, containing different concentration of radioactive isotope (32)P-labeled disodium phosphate (Na2H(32)PO4) was injected into rabbits via the jugular vein in the laboratory. Emerged Cx. pipiens were marked after feeding on rabbit. At the same time, the labeled conditions of emerged Cx. pipiens were also measured by placing feces of No. 6 rabbit into containers with mosquito larvae and pupae inside. RESULTS: According to the label condition of Cx. pipiens after taking blood and the effect of different dosage Na2H(32)PO4 on rabbit health, the optimal concentration of radioactive isotope was determined, that is, 0.1211 mCi/kg. By placing feces of No. 6 rabbit into containers with mosquito larvae and pupae inside, the emerged mosquitoes were also labeled. Therefore, feeding mosquitoes on the animal injected with radioactive Na2H(32)PO4 was more practical for detecting and tracing mosquitoes. CONCLUSION: The method was less time-consuming, more sensitive and safer. This marking method will facilitate post-bloodmeal studies of mosquitoes and other blood-sucking insects.\",\n \"corpus_id\": 31021691,\n \"score\": 2\n },\n {\n \"doc_id\": \"27444629\",\n \"title\": \"The mitochondrial genomes of Culex tritaeniorhynchus and Culex pipiens pallens (Diptera: Culicidae) and comparison analysis with two other Culex species.\",\n \"abstract\": \"BACKGROUND: Culex tritaeniorhynchus and Culex pipiens pallens are the major vectors of the Japanese encephalitis virus and Wuchereria bancrofti, the causative agent of filariasis. The knowledge of mitochondrial genomes has been widely useful for the studies on molecular evolution, phylogenetics and population genetics. METHODS: In this study, we sequenced and annotated the mitochondrial (mt) genomes of Cx. tritaeniorhynchus and Cx. p. pallens, and performed a comparative analysis including four known mt genomes of species of the subgenus Culex (Culex). The phylogenetic relationships of Cx. tritaeniorhynchus, Cx. p. pallens and four known Culex mt genome sequences were reconstructed by maximum likelihood based on concatenated protein-coding gene sequences. RESULTS: Culex tritaeniorhynchus and Cx. p. pallens mt genomes are 14,844 bp and 15,617 bp long, both consists of 13 PCGs, 22 tRNAs, 2 rRNAs and 1 CR (not sequenced for Cx. tritaeniorhynchus). The initiation and termination codons of PCGs are ATN and TAA, respectively, except for COI starting with TCG, and COI and COII terminated with T. tRNAs have the typical clover-leaf secondary structures except for trnS ((AGN)) that is lacking the DHU stem. 16S rRNA and 12S rRNA secondary structures were drawn for the first time for mosquito mt genomes. The control region of Cx. p. pallens mt genome is 747 bp long and with four tandem repeat structures. Phylogenetic analyses demonstrated that the mt genome of Cx. tritaeniorhynchus was significantly separated from the remaining five mt genomes of Culex spp. Culex p. pipiens, Cx. p. pallens and Cx. p. quinquefasciatus formed a monophyletic clade with Cx. p. quinquefasciatus linked in the middle of the clade, and Cx. p. pallens should have the same taxonomic level as Culex p. pipiens and Cx. p. quinquefasciatus. CONCLUSIONS: The mt genomes of Cx. tritaeniorhynchus and Cx. p. pallens share the same gene composition and order with those of two other Culex species. Culex p. pallens of the Pipiens complex should have the same taxonomic level as Culex p. pipiens and Cx. p. quinquefasciatus investigated. We enriched the Culex mt genome data and provided a reference basis for further Culex mt genome sequencing and analyses.\",\n \"corpus_id\": 13947030,\n \"score\": 2\n },\n {\n \"doc_id\": \"27456936\",\n \"title\": \"Laboratory evaluation of differential attraction of Culex pipiens pallens to fruit-based sugar baits.\",\n \"abstract\": \"Mosquito adults usually need to obtain sugar from floral nectaries and damaged fruits/seed pods to replenish their energy reserves. The newly developed attractive toxic sugar baits have been successfully applied in controlling various mosquito species outdoors. However, the attraction of Culex pipiens pallens to different fruit-based sugar baits remains unknown. In the present study, we selected nine common fruit species, prepared the fruit-based sugar solutions, and investigated the attractiveness of different sugar baits to newly emerged Cx. pipiens pallens in the laboratory. The results showed that when tested against the 5% brown sugar solution, all the sugar baits were significantly attractive to both females and males. When tested together in the mesh-covered cage, there was a significant difference on the attractiveness between different fruit-based sugar baits. The most attractive fruit species included Broussonetia papyrifera, Cucumis melo, C. melo var. saccharinus, Amygdalus persica and Pyrus bretschneideri, and their seed pods could be potentially used as ingredients in ATSB for controlling mosquitoes outdoors.\",\n \"corpus_id\": 30962330,\n \"score\": 2\n },\n {\n \"doc_id\": \"27681543\",\n \"title\": \"A reassessment of the artificial infection of three predominant mosquito species with Plasmodium vivax in Shandong Province, China.\",\n \"abstract\": \"BACKGROUND & OBJECTIVES: Under certain ecological circumstances, pathogens are able to rapidly adapt to new vectors. The great capacity of Plasmodium spp. to adapt to new anopheline mosquito vectors on different continents and the continuous ecological changes attributed to humans might promote their adaptation to culicine vectors, which are known to infect humans. Based on our current knowledge, it is difficult to predict whether such adaptations will occur. This study was aimed to determine the infection susceptibility of Anopheles sinensis, Culex tritaeniorhynchus and Cx. pipiens pallens to Plasmodium vivax in Shandong Province of China. METHODS: The susceptibility of the three predominant species of mosquitoes -An. sinensis, Cx. tritaeniorhynchus and Cx. pipiens pallens in Shandong Province was compared with a direct membrane feeding assay with 15 batches of Shandong strain mono-infected gametocyte-containing blood collected from Plasmodium vivax-infected patients. Infectivity was measured by dissecting the midguts and salivary glands of the mosquitoes. The presence of oocysts and sporozoites was determined by microscopy at 6 and 22 days post-blood feeding. RESULTS: From the 15 batches of mosquitoes that were fed infected blood, oocysts and sporozoites were detected only in 7th, 13th and 15th batches of infection for An. sinensis, and no oocysts or sporozoites were detected in Cx. tritaeniorhynchus or Cx. pipiens pallens. The positive rate of An. sinensis infection was 21.2, 13 and 36.3% in the three batches of mosquitoes, with an average infection rate of 23.5%. INTERPRETATION & CONCLUSION: The susceptibility of An. sinensis to P. vivax was very high in Shandong Province. Cx. tritaeniorhynchus and Cx. pipiens pallens failed to exhibit susceptibility to P. vivax.\",\n \"corpus_id\": 40990673,\n \"score\": 2\n },\n {\n \"doc_id\": \"28135281\",\n \"title\": \"Dispersal of male and female Culex quinquefasciatus and Aedes albopictus mosquitoes using stable isotope enrichment.\",\n \"abstract\": \"The dispersal patterns of mosquito vectors are important drivers of vector-borne infectious disease dynamics and understanding movement patterns is pivotal to devise successful intervention strategies. Here, we investigate the dispersal patterns of two globally important mosquito vectors, Aedes albopictus and Culex quinquefasciatus, by marking naturally-occurring larvae with stable isotopes (13C or 15N). Marked individuals were captured with 32 CDC light trap, 32 gravid trap, and 16 BG Sentinel at different locations within two-kilometer radii of six larval habitats enriched with either 13C or 15N. In total, 720 trap nights from July to August 2013 yielded a total of 32,140 Cx. quinquefasciatus and 7,722 Ae. albopictus. Overall, 69 marked female mosquitoes and 24 marked male mosquitoes were captured throughout the study period. The distance that Cx. quinquefasciatus females traveled differed for host-seeking and oviposition-seeking traps, with females seeking oviposition sites traveling further than those seeking hosts. Our analysis suggests that 41% of Cx. quinquefasciatus females that were host-seeking occurred 1-2 kilometer from their respective natal site, while 59% remained within a kilometer of their natal site. In contrast, 59% of Cx. quinquefasciatus females that were seeking oviposition sites occurred between 1-2 kilometer away from their larval habitat, while 15% occurred > 2 kilometer away from their natal site. Our analysis estimated that approximately 100% of Ae. albopictus females remained within 1 km of their respective natal site, with 79% occurring within 250m. In addition, we found that male Ae. albopictus dispersed farther than females, suggesting male-biased dispersal in this Ae. albopictus population. This study provides important insights on the dispersal patterns of two globally relevant vector species, and will be important in planning next generation vector control strategies that mitigate mosquito-borne disease through sterile insect techniques, novel Wolbachia infection, and gene drive strategies.\",\n \"corpus_id\": 8086573,\n \"score\": 2\n },\n {\n \"doc_id\": \"28347323\",\n \"title\": \"Blood-feeding patterns of native mosquitoes and insights into their potential role as pathogen vectors in the Thames estuary region of the United Kingdom.\",\n \"abstract\": \"BACKGROUND: The range of vertebrate hosts on which species of mosquito blood-feed is an important parameter for identifying potential vectors and in assessing the risk of incursion and establishment of vector-borne pathogens. In the United Kingdom, studies of mosquito host range have collected relatively few specimens and used techniques that could only broadly identify host species. This study conducted intensive collection and analysis of mosquitoes from a grazing marsh environment in southeast England. This site provides extensive wetland habitat for resident and migratory birds and has abundant human nuisance biting mosquitoes. The aim was to identify the blood-feeding patterns of mosquito species present at the site which could contribute to the transmission of pathogens. METHODS: Twice-weekly collections of mosquitoes were made from Elmley Nature Reserve, Kent, between June and October 2014. Mosquitoes were collected using resting boxes, by aspiration from man-made structures and using a Mosquito Magnet Pro baited with 1-octen-3-ol. Blood-fed specimens were classified according to the degree of blood meal digestion using the Sella scale and vertebrate origin determined using sequencing of a fragment of the mitochondrial cytochrome C oxidase subunit I gene. Mosquitoes that were morphologically cryptic were identified to species level using multiplex PCR and sequencing methods. RESULTS: A total of 20,666 mosquitoes of 11 species were collected, and 2,159 (10.4%) were blood-fed (Sella scale II-VI); of these 1,341 blood-fed specimens were selected for blood meal analysis. Vertebrate origin was successfully identified in 964 specimens (72%). Collections of blood-fed individuals were dominated by Anopheles maculipennis complex (73.5%), Culiseta annulata (21.2%) and Culex pipiens form pipiens (10.4%). Nineteen vertebrate hosts comprising five mammals and 14 birds were identified as hosts for mosquitoes, including two migratory bird species. Feeding on birds by Culex modestus and Anopheles atroparvus populations in England was demonstrated. CONCLUSIONS: This study expands the vertebrate host range of mosquitoes in the Thames estuary region of the UK. Feeding on both resident and migratory bird species by potential arbovirus vectors including Cx. pipiens f. pipiens and Cx. modestus indicates the potential for enzootic transmission of an introduced arbovirus between migratory and local bird species by native mosquito species.\",\n \"corpus_id\": 69573,\n \"score\": 2\n },\n {\n \"doc_id\": \"29325101\",\n \"title\": \"Fauna, Ecological Characteristics, and Checklist of the Mosquitoes in Mazandaran Province, Northern Iran.\",\n \"abstract\": \"Mosquitoes are important vectors of human and animal diseases. This study updates current knowledge on fauna, dominance, and distribution of mosquitoes in Mazandaran Province, Northern Iran, to inform disease control effort. Larval collections, using standard dippers or droppers, and adult collections, using total catches, shelter pits, CDC light traps, and human landing catches, were performed monthly in 30 villages across 16 counties, from May to December 2014. Ovitraps, baited with hay infusion as oviposition attractants or stimulants for Aedes (Stegomyia) mosquitoes, were installed in each village and inspected weekly for eggs. Lactophenol and Berlese media were used for preserving and mounting specimens. Overall, 36,024 mosquito specimens (19,840 larvae and 16,184 adults) belonging to 4 genera and 20 species were morphologically identified. The dominance and distribution indices showed that Culex pipiens s.s. was the eudominant species with a constant distribution of larvae (D = 69.07%, C = 100%) and adults (D = 31.86%, C = 100%), followed by Cx tritaeniorhynchus (D = 38.14%, C = 100%) and Anopheles maculipennis s.l. ( D = 11.05%, C = 100%) as adults. Aedes vexans was the dominant (7.85%) species, but it had a sporadic (20%) distribution. Culex torrentium and Culiseta morsitans were added as the new species to the checklist of mosquitoes in Mazandaran Province. Due to the potential role, Cx. pipiens s.s. as a vector of various pathogens, further ecological studies are recommended.\",\n \"corpus_id\": 24540035,\n \"score\": 2\n },\n {\n \"doc_id\": \"29460862\",\n \"title\": \"Host preferences and feeding patterns of Anopheles sinensis Wiedemann in three sites of Shandong province, China.\",\n \"abstract\": \"Background & objectives: Anopheles sinensis Wiedemann is a major vector of malaria and is among the dominant species in Shandong province of China. Knowledge of the blood-feeding patterns of mosquitoes is crucial for elimination of malaria vectors. However, little information is available on the blood-feeding behaviour of An. sinensis mosquitoes in Shandong province. This study was carried out to compare the blood-feeding behaviour of An. sinensis in malaria-endemic areas of Shandong province China. Methods: Adult Anopheles mosquitoes were collected from three malaria-endemic areas (Jimo, Yinan and Shanxian), during the peak months of mosquito population (August and September) from 2014 to 2015. Indoor-resting mosquitoes and outdoor-resting blood-fed females were sampled in the morning hours (0600 to 0900 hrs) from 10 randomly selected houses using pyrethrum spray catch method, and sweeping with an insect net. ELISA was used for the identification of blood meal. The blood meal of each mosquito was tested against antisera specific to human, pig, dog, cow, goat, horse (mule) and fowl. Results: At all indoor study locations of Jimo, Yinan and Shanxian, 59.4, 68.1 and 98.8% blood-engorged female An. sinensis collected from cattle sheds fed almost exclusively on bovines, respectively. For outdoor locations, at Jimo site, 27.27 and 49.55% An. sinensis fed on cattle and pigs; at Yinan, 30.42% fed on cattle and 36.88% fed both on cattle and goats, while no pig antibodies were detected. At Shanxian, percent of An. sinensis that fed on cattle, pigs and cattle-goat was 20.72, 27.62 and 21.78%, respectively. Interpretation & conclusion: The analysis of An. sinensis blood meals in all the three studied areas from human houses, cattle sheds, pig sheds and mixed dwellings revealed that An. sinensis prefers cattle hosts, and can feed on other available animal hosts if the cattle hosts are absent, and the mosquitoes readily feed on humans when domestic animals (cattle and pigs) are not nearby for feeding. The analysis of blood meal revealed that An. sinensis follow opportunistic feeding in Shandong province, China.\",\n \"corpus_id\": 3442265,\n \"score\": 2\n },\n {\n \"doc_id\": \"29536705\",\n \"title\": \"[Analysis of population genetic diversity of mosquitoes from Shandong Province based on mitochondrial DNA cytochrome oxidase subunit I gene fragment].\",\n \"abstract\": \"OBJECTIVE: To explore the characteristics of gene sequence of mtDNA-COⅠ of Culex pipiens pallens from different geographical regions in Shandong Province and different resistant strains from the lab and five common mosquito species, and analyze the genetic diversity of these mosquitoes. METHODS: Adult mosquitoes were collected from Jinan, Jining, Qingdao cities and other places in Shandong Province. The sensitive, dichlorvos-resistant, pyrethroid-resistant and propoxur-resistant strains were reared in the lab. Five species of mosquito (Cx. pipiens pallens, Cx. tritaeniorhynchus, Anopheles sinensis, Aedes albopictus, and Armigeres subalbatus) were collected from Jining City and identified in the lab. mtDNA-COⅠwas specifically amplified by PCR and sequenced. The gene sequences were compared and analyzed by the biological information systems, and the phylogenetic tree was constructed. RESULTS: The amplified mtDNA-COⅠfragments of Cx. pipiens pallens from eight different cities and four different resistant strains were 528 bp in length, with 67.4% A+T contents and two mutation sites. The nucleotide sequence homology among the different geographic strains was 99.95% and the gene sequences of the four resistant strains were the same, showing a high homogeny. The amplified mtDNA-COⅠfragments of the five species of mosquitoes were 528 bp with 408 conserved sites, 120 variable sites, 42 parsimony informative sites and 78 singleton sites. The A+T contents were between 65.7% and 68.0%. The nucleotide sequence homology among the different mosquito species was between 86.17% and 92.05%, and the molecular identification was consistent with the traditional morphological identification. The molecular phylogenetic study showed that the different species were clustered at their own branch at the species and genus levels, while genera Armigeres was distantly related to the others. CONCLUSIONS: mtDNA-COⅠcould not serve as the molecular marker to analyze the population genetic variation and phylogenesis of Cx. pipiens pallens from different geographical regions and different resistant strains, but it has species and genus specificities, which could be used for the identification of the mosquito species and genus.\",\n \"corpus_id\": 3847185,\n \"score\": 2\n },\n {\n \"doc_id\": \"19287362\",\n \"title\": \"Species composition of mosquito fauna in Ranau, Sabah, Malaysia.\",\n \"abstract\": \"The adult population and species composition of mosquitoes collected in Ranau, Sabah are described. A total of 5956 mosquitoes representing 8 genera and 41 species were collected using human landing catch, indoor and outdoor. Anopheles maculatus was the most common species (15.6%) followed by Culex quinquefasciatus (12.8%), Culex pseudovishnui (12.1%), Anopheles balabacensis (11.1%), Culex vishnui (9.7%), Aedes vexans (9.6%), Culex tritaeniorhyncus (6.6%), Anopheles donaldi (5.6%) and others in very small percentage.\",\n \"corpus_id\": 10985009,\n \"score\": 1\n },\n {\n \"doc_id\": \"21943071\",\n \"title\": \"The role of cow urine in the oviposition site preference of culicine and Anopheles mosquitoes.\",\n \"abstract\": \"BACKGROUND: Chemical and behavioural ecology of mosquitoes plays an important role in the development of chemical cue based vector control. To date, studies available have focused on evaluating mosquito attractants and repellents of synthetic and human origins. This study, however, was aimed at seasonal evaluation of the efficiency of cow urine in producing oviposition cues to Anopheles gambiae s.l. and Culex quinquefasciatus in both laboratory and field conditions. METHODS: Oviposition response evaluation in laboratory conditions was carried out in mosquito rearing cages. The oviposition substrates were located in parallel or in diagonal positions inside the cage. Urine evaluation against gravid females of An. arabiensis and Cx. quinquefasciatus was carried out at Day 1, Day 3 and Day 7. Five millilitres (mls) of cow urine was added to oviposition substrate while de-chlorinated water was used as a control. In field experiments, 500 mls of cow urine was added in artificial habitats with 2500 mls of de-chlorinated water and 2 kgs of soil. The experiment was monitored for thirty consecutive days, eggs were collected daily from the habitats at 7.00 hrs. Data analysis was performed using parametric and non-parametric tests for treatments and controls while attraction of the oviposition substrate in each species was presented using Oviposition Activity Index (OAI). RESULTS: The OAI was positive with ageing of cattle urine in culicine species in both laboratory and field experiments. The OAI for anopheline species was positive with fresh urine. The OAI during the rainy season was positive for all species tested while in the dry season the OAI for culicine spp and Anopheles gambiae s.l., changed with time from positive to negative values. Based on linear model analysis, seasons and treatments had a significant effect on the number of eggs laid in habitats, even though the number of days had no effect. CONCLUSION: Oviposition substrates treated with cow urine in both laboratory and field conditions have shown that cow urine left to age from 1-7 days has an influence on oviposition behavioural response in mosquitoes. The analysis of microbial colonies for decaying urine should be investigated along with its associated by-products.\",\n \"corpus_id\": 2824080,\n \"score\": 1\n },\n {\n \"doc_id\": \"22276651\",\n \"title\": \"Vector competence of five common mosquito species in the People's Republic of China for Western equine encephalitis virus.\",\n \"abstract\": \"Two strains of the Western equine encephalitis virus (WEEV) were first detected and isolated in China in 2001. The maintenance and transmission cycles of WEEV in China are currently not well understood, and the mosquito vectors involved in these cycles are unknown. To understand the ability of the local mosquitoes in China to transmit WEEV, the vector competence of five mosquito species, namely, Culex pipiens pallens Coquillett, Cx. p. quinquefasciatus Say, Aedes (Stegomyia) albopictus Skuse, Ae. ( Stegomyia) aegypti Linnaeus, and C. tritaeniorhynchus Giles, for WEEV were evaluated. Infection rates for Cx. p. pallens, Cx. p. quinquefasciatus, Cx. tritaeniorhynchus, Ae. Albopictus, and Ae. aegypti were 46%, 60%, 80%, 37%, and 25%, respectively. Dissemination rates for the same species were 60%, 61%, 75%, 55%, and 50%, respectively. Transmission rates were 41%, 53%, 57%, and 45% for Cx. p. pallens, Cx. p. quinquefasciatus, Ae. Albopictus, and Ae. Aegypti, respectively. Infection rates were significantly different between species, but the difference between dissemination and transmission rates were nonsignificant. These results suggest that several local mosquito species in China are competent laboratory vectors for WEEV.\",\n \"corpus_id\": 8024842,\n \"score\": 1\n },\n {\n \"doc_id\": \"25987223\",\n \"title\": \"Pyrethroid resistance in Culex pipiens mosquitoes.\",\n \"abstract\": \"Mosquitoes within the Culex pipiens complex are widely distributed and important in the transmission of many human diseases. Insecticides, pyrethroids in particular, remain a mainstay for control of these important vectors. In this paper we review what is known about the levels, mechanisms and fitness costs of pyrethroid resistance in Cx. pipiens. Pyrethroid resistance in Cx. pipiens is a global problem, and resistance ratios of up to 7000-fold have been found in larvae of field collected mosquitoes. However, there is considerable variation between populations, indicating significant geographic heterogeneity of the resistance. The two major mechanisms of resistance to pyrethroids in Culex are mutations in Vssc (target site insensitivity) and overexpression of cytochrome P450(s) (increased detoxification). The most frequently reported Vssc mutation is L1014F (i.e. kdr), which has been found throughout the world. The L1014S mutation has been found in Cx. p. pallens from Japan and China, and in Cx. p. pipiens from China. The L1014C mutation has only been reported for Cx. p. pipens molestus from China and the V1016G mutation has only been reported from Saudi Arabia. Studies on the P450s of Cx. pipiens have identified several that are overexpressed (measured as transcript levels) in pyrethroid resistant strains. CYP9M10 is consistently overexpressed in pyrethroid resistant Cx. pipiens from at least seven countries, suggesting this P450 might be of global importance in resistance. Both CYP9M10-mediated pyrethroid resistance and kdr have fitness costs in the absence of insecticides under certain environmental conditions. Research needs and future directions are discussed.\",\n \"corpus_id\": 25006251,\n \"score\": 1\n }\n]","isConversational":false}}},{"rowIdx":80,"cells":{"query":{"kind":"string","value":"{\n \"doc_id\": \"19578149\",\n \"title\": \"Serratia nematodiphila sp. nov., associated symbiotically with the entomopathogenic nematode Heterorhabditidoides chongmingensis (Rhabditida: Rhabditidae).\",\n \"abstract\": \"A novel red-pigmented, Gram-negative, motile, fluorescent, rod-shaped strain, DZ0503SBS1(T), with a single lateral flagellum, was isolated from the intestine of the nematode Heterorhabditidoides chongmingensis. Comparative 16S rRNA gene sequence analysis indicated that the strain is a member of the genus Serratia, sharing highest sequence similarities with Serratia marcescens subsp. sakuensis JCM 11315(T) (99.8 %), S. marcescens subsp. marcescens DSM 30121(T) (99.5 %) and Serratia ureilytica LMG 22860(T) (98.3 %). Similarities between the rpoB gene sequence of strain DZ0503SBS1(T) and those of S. marcescens subsp. sakuensis JCM 11315(T), S. marcescens subsp. marcescens DSM 30121(T) and S. ureilytica LMG 22860(T) were 98.0, 97.4 and 98.3 %, respectively. DNA-DNA hybridization values of strain DZ0503SBS1(T) with S. marcescens subsp. sakuensis JCM 11315(T), S. marcescens subsp. marcescens DSM 30121(T) and S. ureilytica LMG 22860(T) were 68.2, 65.1 and 53.0 %, respectively. The major isoprenoid quinone of strain DZ0503SBS1(T) was Q-8 and the predominant fatty acids were C(16 : 0) (34.76 %), cyclo-C(17 : 0) (20.03 %) and cyclo-C(19 : 0)omega8c (17.24 %). The cyclo-C(19 : 0)omega8c content (17.24 %) was significantly different from those found in S. marcescens subsp. sakuensis JCM 11315(T) and S. marcescens subsp. marcescens DSM 30121(T). Some characteristics of strain DZ0503SBS1(T), i.e. fluorescence and its symbiotic association with nematodes, have not been reported previously in any species of the genus Serratia. Phenotypic and biochemical characteristics and molecular data show that strain DZ0503SBS1(T) represents a novel species, for which the name Serratia nematodiphila sp. nov. is proposed; the type strain is DZ0503SBS1(T) (=KCTC 22130(T) =CGMCC 1.6853(T)).\",\n \"corpus_id\": 32795700\n}"},"candidates":{"kind":"list like","value":[{"doc_id":"18175681","title":"Sanguibacter antarcticus sp. nov., isolated from Antarctic sea sand.","abstract":"A Gram-positive, yellow-pigmented bacterium, strain KOPRI 21702(T), was isolated from sea sand on King George Island, Antarctica. Cells were irregular rods with peritrichous flagella; their optimum growth temperature was 23-26 degrees C. Phylogenetic analysis based on 16S rRNA gene sequences revealed that the Antarctic isolate formed a distinct phyletic line in a clade of the genus Sanguibacter and showed highest sequence similarity (97.7%) to the type strain of Sanguibacter keddieii. The major isoprenoid quinone, predominant cellular fatty acids and DNA G+C content were consistent with placement of the Antarctic isolate in the genus Sanguibacter. Phylogenetic analysis and differences in physiological and biochemical characteristics between strain KOPRI 21702(T) and the four recognized Sanguibacter species indicate that the isolate represents a novel species of this genus. The name Sanguibacter antarcticus sp. nov. (type strain KOPRI 21702(T) =KCTC 13143(T) =JCM 14623(T) =DSM 18966(T)) is proposed for this isolate.","corpus_id":206183960,"score":2},{"doc_id":"18319455","title":"Burkholderia sediminicola sp. nov., isolated from freshwater sediment.","abstract":"A Gram-negative, motile and rod-shaped bacterium, designated HU2-65W(T), was isolated from freshwater sediment. The strain possessed ubiquinone 8 as the predominant isoprenoid quinone and contained major amounts of omega7-cis-octadecenoic acid and hexadecanoic acid in its cell envelope, which are properties shared by members of the genus Burkholderia. On the basis of 16S rRNA gene sequence similarity, strain HU2-65W(T) was most closely related to the type strain of Burkholderia xenovorans (98.4 %). The DNA G+C content of strain HU2-65W(T) was 61.2 mol%, and DNA-DNA relatedness values to type strains of closely related species were found to be much lower than 70 %, indicating that the strain represents a separate genomic species within the genus Burkholderia. Strain HU2-65W(T) was also differentiated from other species of the genus by physiological and biochemical characteristics. Consequently, strain HU2-65W(T) is considered to represent a single, novel species of the genus Burkholderia, for which the name Burkholderia sediminicola sp. nov. is proposed, with the type strain HU2-65W(T) (=KCTC 22086(T) =LMG 24238(T)).","corpus_id":23738894,"score":2},{"doc_id":"18319480","title":"Labrys portucalensis sp. nov., a fluorobenzene-degrading bacterium isolated from an industrially contaminated sediment in northern Portugal.","abstract":"A detailed classification of a novel bacterial strain, designated F11(T), capable of degrading fluorobenzene as a sole carbon and energy source, was performed by using a polyphasic approach. This Gram-negative, rod-shaped, non-motile, non-spore-forming, aerobic bacterium was isolated from a sediment sample collected from an industrially contaminated site in northern Portugal. The predominant whole-cell fatty acids were C(19 : 0) cyclo omega8c, C(16 : 0), C(18 : 1)omega7c, C(18 : 0), C(18 : 0) 3-OH and C(16 : 0) 3-OH. The G+C content of the DNA was 62.9 mol% and the major respiratory quinone was ubiquinone 10 (UQ-10). 16S rRNA gene sequence analysis revealed that strain F11(T) was a member of the class Alphaproteobacteria and was phylogenetically related to the genus Labrys, having sequence similarities of 95.6 and 93.1 % to the type strains of Labrys monachus and Labrys methylaminiphilus, respectively. DNA-DNA hybridization experiments revealed levels of relatedness of <70 % between strain F11(T) and the type strains of L. monachus and L. methylaminiphilus (38.6 and 34.1 %, respectively), justifying the classification of strain F11(T) as representing a novel species of the genus Labrys. The name Labrys portucalensis sp. nov. is proposed for this organism. The type strain is F11(T) (=LMG 23412(T)=DSM 17916(T)).","corpus_id":14436728,"score":2},{"doc_id":"18398165","title":"Flavobacterium anhuiense sp. nov., isolated from field soil.","abstract":"A novel strain, D3T, isolated from a field-soil sample obtained from Anhui Province, PR China, was characterized taxonomically by using a polyphasic approach. The cells were Gram-negative, yellow-pigmented rods devoid of flagella, but showing gliding motility. The organism was able to grow at 5-37 degrees C and at pH 4.0-10.0. A comparative 16S rRNA gene sequence analysis indicated that strain D3T is a member of the genus Flavobacterium, sharing highest sequence similarity with the type strain of Flavobacterium defluvii (96.7 %). The major isoprenoid quinone was MK-6 and the predominant fatty acids were iso-C15 : 0, summed feature 3 (C16 : 1 omega 7c and/or iso-C15 : 0 2-OH) and C16 : 0. The DNA G+C content was 31.4 mol%. On the basis of phylogenetic and phenotypic data, strain D3T represents a novel species within the genus Flavobacterium, for which the name Flavobacterium anhuiense sp. nov. is proposed. The type strain is D3T (=KCTC 22128T = CGMCC 1.6859T).","corpus_id":9876913,"score":2},{"doc_id":"18410943","title":"Heterorhabditidoides chongmingensis gen. nov., sp. nov. (Rhabditida: Rhabditidae), a novel member of the entomopathogenic nematodes.","abstract":"During a recent soil sample survey in Eastern China, a new entomopathogenic nematode species, collected from the Chongming Islands in the southern-eastern area of Shanghai, was discovered. Morphological characteristics of different developmental stages of the nematode combined with molecular data showed that this nematode is a new genus of Rhabditidae, and described as Heterorhabditidoides chongmingensis gen. nov., sp. nov., for that it shares more morphological characteristics with heterorhabditids than with steinernematids. For males, the papillae formula of bursa is 1, 2, 3, 3, with constant papillae number in the terminal group, stoma tubular-shaped and about 1.5 head width; cheilorhabdions cuticularized, esophageal collar present and long, median bulb present. For infective juveniles, EP=90 (80-105)microm, ES=104 (92-120)microm, tail length=111 (89-159)microm, and a=19.1 (15-21). The percentages of the nucleotides A, T, C and G in the ITS1 regions of the new species are significantly different from those of heterorhabditids and other rhabditids. Molecular phylogenetic trees based on 18S rDNA and the internal transcribed spacer (ITS) sequences data revealed that the new entomopathogenic nematode species forms a monophyletic group, which is a sister group of the clade comprised of some genera of Rhabditidae.","corpus_id":9633949,"score":2},{"doc_id":"18523187","title":"Shinella kummerowiae sp. nov., a symbiotic bacterium isolated from root nodules of the herbal legume Kummerowia stipulacea.","abstract":"Bacterial strain CCBAU 25048(T) was isolated from root nodules of Kummerowia stipulacea grown in Shandong province of China. Cells of the strain were Gram-negative, strictly aerobic, non-spore-forming, motile short rods. Phylogeny of 16S rRNA gene sequences revealed that the strain belonged to the genus Shinella, a member of family Rhizobiaceae. Its closest phylogenetic relatives were Shinella granuli Ch06(T) and Shinella zoogloeoides IAM 12669(T), respectively showing 98.3 and 98.9 % 16S rRNA gene sequence similarity. Strain CCBAU 25048(T) had DNA-DNA relatedness of 43.5 and 34.8 %, respectively, with S. zoogloeoides JCM 20728(T) and S. granuli JCM 13254(T). In addition, in TP-RAPD analysis, different patterns were obtained for these three strains and some rhizobial strains. The nifH, nodC and nodD sequences of CCBAU 25048(T) were identical or very similar to those of bean-nodulating Rhizobium tropici strains. Several phenotypic characteristics, including the use of citrate and d-ribose as carbon sources and growth at pH 11.0, as well as the fatty acid composition, could differentiate CCBAU 25048(T) from the two defined Shinella species. Therefore, a novel species Shinella kummerowiae sp. nov. is proposed, with strain CCBAU 25048(T) (=JCM 14778(T) =LMG 24136(T)) as the type strain.","corpus_id":9720510,"score":2},{"doc_id":"18523189","title":"Massilia aerilata sp. nov., isolated from an air sample.","abstract":"A novel aerobic, Gram-negative, rod-shaped, motile bacterium, designated strain 5516S-11(T), was isolated from air samples collected in the Suwon region of the Republic of Korea. Analysis of the 16S rRNA gene sequence indicated that the organism belongs to the genus Massilia; the highest sequence similarity (97.2 %) was found with respect to Massilia aurea DSM 18055(T). Cells of strain 5516S-11(T) contained ubiquinone Q-8 as the predominant isoprenoid quinone and possessed summed feature 3 (C(16 : 1)omega7c/iso-C(15 : 0) 2-OH; 35.2 %), C(16 : 0) (30.6 %) and C(18 : 1)omega7c (11.7 %) as the major fatty acids. DNA-DNA hybridization revealed 32 % relatedness between strain 5516S-11(T) and M. aurea DSM 18055(T). The G+C content of the DNA of strain 5516S-11(T) was 68.9 mol%. It is clear from the genotypic and phenotypic data presented that strain 5516S-11(T) represents a novel species of the genus Massilia, for which the name Massilia aerilata sp. nov. is proposed. The type strain is 5516S-11(T) (=KACC 12505(T) =DSM 19289(T)).","corpus_id":19979053,"score":2},{"doc_id":"18523192","title":"Cronobacter gen. nov., a new genus to accommodate the biogroups of Enterobacter sakazakii, and proposal of Cronobacter sakazakii gen. nov., comb. nov., Cronobacter malonaticus sp. nov., Cronobacter turicensis sp. nov., Cronobacter muytjensii sp. nov., Cronobacter dublinensis sp. nov., Cronobacter genomospecies 1, and of three subspecies, Cronobacter dublinensis subsp. dublinensis subsp. nov., Cronobacter dublinensis subsp. lausannensis subsp. nov. and Cronobacter dublinensis subsp. lactaridi subsp. nov.","abstract":"[Enterobacter] sakazakii is an opportunistic pathogen that can cause infections in neonates. This study further clarifies the taxonomy of isolates described as [E.] sakazakii and completes the formal description of the proposed reclassification of these organisms as novel species and subspecies within a proposed novel genus, Cronobacter gen. nov. [E.] sakazakii was first defined in 1980, however recent polyphasic taxonomic analysis has determined that this group of organisms consists of several genomospecies. In this study, the phenotypic descriptions of the proposed novel species are expanded using Biotype 100 and Biolog Phenotype MicroArray data. Further DNA-DNA hybridization experiments showed that malonate-positive strains within the [E.] sakazakii genomospecies represent a distinct species, not a subspecies. DNA-DNA hybridizations also determined that phenotypically different strains within the proposed species, Cronobacter dublinensis sp. nov., belong to the same species and can be considered as novel subspecies. Based on these analyses, the following alternative classifications are proposed: Cronobacter sakazakii gen. nov., comb. nov. [type strain ATCC 29544(T) (=NCTC 11467(T))]; Cronobacter malonaticus sp. nov. [type strain CDC 1058-77(T) (=LMG 23826(T)=DSM 18702(T))]; Cronobacter turicensis sp. nov. [type strain z3032(T) (=LMG 23827(T)=DSM 18703(T))]; Cronobacter muytjensii sp. nov. [type strain ATCC 51329(T) (=CIP 103581(T))]; Cronobacter dublinensis sp. nov. [type strain DES187(T) (=LMG 23823(T)=DSM 18705(T))]; Cronobacter dublinensis subsp. dublinensis subsp. nov. [type strain DES187(T) (=LMG 23823(T)=DSM 18705(T))]; Cronobacter dublinensis subsp. lausannensis subsp. nov. [type strain E515(T) (=LMG 23824=DSM 18706(T))], and Cronobacter dublinensis subsp. lactaridi subsp. nov. [type strain E464(T) (=LMG 23825(T)=DSM 18707(T))].","corpus_id":6609941,"score":2},{"doc_id":"18974964","title":"Aliihoeflea aestuarii gen. nov., sp. nov., a novel bacterium isolated from tidal flat sediment.","abstract":"A novel Gram-negative and rod-shaped bacterium, designated N8(T), was isolated from tidal flat sediment. Phylogenetic analysis based on 16S rRNA gene sequences showed that N8(T) strain is associated with the family Phyllobacteriaceae: two uncultured clones (98.4 and 99.8% 16S rRNA gene sequence similarity) and the genus Mesorhizobium (< or =97.0%). The novel strain formed a separate clade with uncultured clones in the phylogenetic tree based on 16S rRNA gene sequences. Cellular fatty acid profiles predominately comprised C(18:1) omega7c and C(19:0) cyclo omega8c. The major isoprenoid quinone is ubiquinone-10 and genomic DNA G+C content is 53.4 mol%. The polyphasic taxonomic study indicates that the novel strain N8(T) represents a novel species of the new genus in the family Phyllobacteriaceae, named Aliihoeflea aestuarii. The type strain is N8(T) (= KCTC 22052(T)= JCM 15118(T)= DSM 19536(T)).","corpus_id":11546957,"score":2},{"doc_id":"18984696","title":"Photorhabdus temperata subsp. cinerea subsp. nov., isolated from Heterorhabditis nematodes.","abstract":"During the characterization of symbiotic bacteria of Hungarian entomopathogenic nematode isolates, a number of bacteria (including strain 3107(T)) isolated from Heterorhabditis downesi and Heterorhabditis megidis showed only moderate 16S rRNA gene sequence similarity to the type strains of all described Photorhabdus species and subspecies. On the basis of the 16S rRNA gene sequence, the phylogenetic relationships of these isolates were uncertain, because of the low bootstrap values. Using gyrB sequences for phylogenetic analysis, these isolates were shown to be part of the species Photorhabdus temperata, with clear separation from both Palaearctic and American strains (phylogenetic distances are 6.9 and 7.9 %, respectively). Physiological properties and carbon-source utilization profiles supported the phylogenetic position of these strains; therefore, a novel subspecies, Photorhabdus temperata subsp. cinerea subsp. nov. is proposed, with the type strain 3107(T) (=DSM 19724(T) =NCAIM B 02271(T)).","corpus_id":37286848,"score":2},{"doc_id":"18984707","title":"Paenibacillus taichungensis sp. nov., from soil in Taiwan.","abstract":"Among a large collection of Taiwanese soil isolates, a novel Gram-variable, rod-shaped, motile, endospore-forming bacterial strain, strain V10537(T), was subjected to a polyphasic study including 16S rRNA and gyrB gene sequence analysis, DNA-DNA hybridization experiments, cell wall peptidoglycan type, cellular fatty acid composition analysis and comparative phenotypic characterization. 16S rRNA gene sequence analysis indicated that the organism belonged to the genus Paenibacillus. Strain V10537(T) possessed meso-diaminopimelic acid as the diagnostic diamino acid of the peptidoglycan. It contained menaquinone MK-7 as the predominant isoprenoid quinone and anteiso-C(15 : 0) (53.6 %) and C(16 : 0) (19.0 %) as the major fatty acids. Phylogenetically, the most closely related species to strain V10537(T) were Paenibacillus pabuli, Paenibacillus xylanilyticus, Paenibacillus amylolyticus, Paenibacillus barcinonensis and Paenibacillus illinoisensis, with 16S rRNA gene sequence similarities of 99.5, 98.8, 98.3, 98.2 and 98.1 % to the respective type strains. The gyrB gene sequence similarities between strain V10537(T) and these strains were 76.9-85.0 %. DNA-DNA hybridization experiments showed levels of relatedness of 8.5-45.6 % between strain V10537(T) and these strains. The DNA G+C content of strain V10537(T) was 46.7 mol%. Strain V10537(T) was clearly distinguishable from other Paenibacillus species and thus represents a novel species of the genus Paenibacillus, for which the name Paenibacillus taichungensis sp. nov. is proposed. The type strain is V10537(T) (=BCRC 17757(T) =DSM 19942(T)).","corpus_id":206185903,"score":2},{"doc_id":"19244422","title":"Dyella ginsengisoli sp. nov., isolated from soil of a ginseng field in South Korea.","abstract":"A Gram-negative, aerobic, yellow-pigmented, non-spore-forming, motile, rod-shaped bacterium, designated strain Gsoil 3046(T), was isolated from soil from a ginseng field in Pocheon Province, South Korea, and was characterized taxonomically by using a polyphasic approach. A comparative analysis of 16S rRNA gene sequences revealed that strain Gsoil 3046(T) belongs to the family Xanthomonadaceae in the Gammaproteobacteria. The greatest sequence similarity was found with respect to Dyella koreensis KCTC 12359(T) (97.7 %), Dyella japonica IAM 15069(T) (97.4 %), Frateuria aurantia DSM 6220(T) (96.7 %), Fulvimonas soli LMG 19981(T) (96.2 %) and Luteibacter rhizovicinus DSM 16549(T) (96.0 %). The phylogenetic distances from other recognized species within the family Xanthomonadaceae, including Dyella yeojuensis KACC 11405(T), were greater than 4.0 % (i.e. the sequence similarities were less than 96.0 %). DNA-DNA hybridization experiments showed that the levels of DNA-DNA relatedness between strain Gsoil 3046(T) and its phylogenetically closest neighbours were below 25 %. The G+C content of the genomic DNA was 66.6 mol%. In addition, the presence of ubiquinone Q-8 as the predominant respiratory quinone, iso-C(17 : 1)omega9c, iso-C(16 : 0), iso-C(15 : 0) and iso-C(17 : 0) as the major cellular fatty acids and iso-C(13 : 0) 3-OH and iso-C(11 : 0) 3-OH as the major hydroxy fatty acids supported the affiliation of strain Gsoil 3046(T) to the genus Dyella. On the basis of its phenotypic properties and phylogenetic distinctiveness, strain Gsoil 3046(T) represents a novel species in the genus Dyella, for which the name Dyella ginsengisoli sp. nov. is proposed. The type strain is Gsoil 3046(T) (=KCTC 12599(T)=DSM 18387(T)).","corpus_id":23095888,"score":2},{"doc_id":"19329624","title":"Salinivibrio siamensis sp. nov., from fermented fish (pla-ra) in Thailand.","abstract":"A Gram-negative, facultatively anaerobic, moderately halophilic bacterium, strain ND1-1(T), was isolated from fermented fish (pla-ra) in Thailand. The cells were curved rods, motile and non-endospore-forming. The novel strain grew optimally at 37 degrees C, at pH 8 and in the presence of 9-10 % (w/v) NaCl. The predominant respiratory lipoquinone was Q-8. The major cellular fatty acids were C(16 : 0) and C(12 : 0). Polar lipid analysis revealed the presence of phosphatidylethanolamine, phosphatidylglycerol and diphosphatidylglycerol. The DNA G+C content was 49.0 mol%. Comparative 16S rRNA gene sequence analyses indicated that strain ND1-1(T) was closely related to Salinivibrio costicola, which comprises three subspecies, and Salinivibrio proteolyticus with gene sequence similarities of 98.3-98.6 %. Strain ND1-1(T) showed low levels of DNA-DNA relatedness with S. costicola subsp. costicola JCM 15095(T) (33.2 %), S. costicola subsp. alcaliphilus DSM 16359(T) (38.4 %), S. costicola subsp. vallismortis JCM 15096(T) (59.7 %), and S. proteolyticus AF-2004(T) (42.1 %). On the basis of the physiological and biochemical characteristics and the molecular data presented, strain ND1-1(T) should be classified as a novel species of the genus Salinivibrio for which the name Salinivibrio siamensis sp. nov. is proposed. The type strain is ND1-1(T) (=JCM 14472(T)=PCU 301(T)=TISTR 1810(T)).","corpus_id":2373959,"score":2},{"doc_id":"19406774","title":"Saccharibacillus kuerlensis sp. nov., isolated from a desert soil.","abstract":"A taxonomic study was performed on strain HR1(T), which was isolated from a desert soil sample collected from Xinjiang Province (China). Cells were aerobic, Gram-positive-staining, pink-pigmented, sporulating rods with a single lateral flagellum. The organism can grow at 15-42 degrees C and pH 5.0-10.0, optimally at 30-37 degrees C and pH 6.0-8.0. Growth is inhibited by 6 % NaCl. Analysis of almost-complete 16S rRNA gene sequence revealed that the isolate represents a distinct taxon within the genus Saccharibacillus; Saccharibacillus sacchari LMG 24085(T) was the nearest relative (97.9 % sequence similarity). DNA-DNA hybridization showed 29.6 % genetic relatedness between strain HR1(T) and S. sacchari LMG 24085(T). The major isoprenoid quinone was MK-7 and the predominant fatty acid was anteiso-C(15 : 0) (50.3 %). The G+C content of the DNA was 50.5 mol%. Therefore, based on phenotypic criteria and the phylogenetic position, strain HR1(T) belongs to a previously unidentified species of the genus Saccharibacillus, for which the name Saccharibacillus kuerlensis sp. nov. is proposed. The type strain is HR1(T) (=KCTC 13182(T) =JCM 14865(T) =CGMCC 1.6964(T)).","corpus_id":39604488,"score":2},{"doc_id":"19406814","title":"Marinobacterium nitratireducens sp. nov. and Marinobacterium sediminicola sp. nov., isolated from marine sediment.","abstract":"Two strains, CN44(T) and CN47(T), isolated from marine sediment of the East China Sea, were characterized by using a polyphasic approach. The isolates were Gram-negative, strictly aerobic, non-spore-forming rods. The chemotaxonomic characteristics of these isolates included the presence of C(18 : 1)omega7c, C(16 : 0), iso-C(15 : 0) 2-OH and/or C(16 : 1)omega7c and C(10 : 0) 3-OH as the major cellular fatty acids and Q-8 as the predominant ubiquinone. The DNA G+C contents of strains CN44(T) and CN47(T) were 62.5 and 56.3 mol%, respectively. Phylogenetic analyses based on 16S rRNA gene sequences revealed that strain CN44(T) was related to members of the genus Marinobacterium. The most closely related described organism was the type strain of Marinobacterium rhizophilum (95.3 % sequence similarity). Strain CN47(T) showed the highest sequence similarity to the type strain of Marinobacterium stanieri (97.8 %) and <97 % similarity to other type strains of described Marinobacterium species. The level of DNA-DNA relatedness between strain CN47(T) and M. stanieri DSM 7027(T) was 46 %. On the basis of phenotypic and genotypic properties, strains CN44(T) and CN47(T) represent two novel species within the genus Marinobacterium, for which the names Marinobacterium nitratireducens sp. nov. (type strain, CN44(T) =CGMCC 1.7286(T) =JCM 15523(T)) and Marinobacterium sediminicola sp. nov. (type strain, CN47(T) =CGMCC 1.7287(T) =JCM 15524(T)) are proposed.","corpus_id":35719126,"score":2},{"doc_id":"19502301","title":"Marispirillum indicum gen. nov., sp. nov., isolated from a deep-sea environment.","abstract":"A taxonomic study was carried out on strain B142(T), which was isolated from a crude-oil-degrading microbial consortium via enrichment with deep water from the Indian Ocean. Cells of the isolate were Gram-negative, oxidase-negative, catalase-positive, helical in shape, motile by means of polar flagella (three per cell) and moderately halophilic. Growth was observed at salinities of 0.5-12 % and at temperatures of 10-41 degrees C. The micro-organism was capable of denitrification, but was unable to degrade Tween 80 or gelatin. The predominant fatty acids were C(16 : 1)omega7c and/or iso-C(15 :0 )2-OH (6.4 %), C(16 : 0) (15.7 %), C(18 : 1)omega7c (45 %), C(18 : 0) (6.8 %) and C(19 : 0)omega8c cyclo (6.7 %). The G+C content of the chromosomal DNA was 67.3 mol%. Comparisons of 16S rRNA gene sequences showed that strain B142(T) was most closely related to the type strains of two Insolitispirillum peregrinum subspecies (93.0-93.1 % sequence similarity), two Novispirillum itersonii subspecies (92.8-92.9 %) and Caenispirillum bisanense (91.7 %); sequence similarities with respect to other taxa were below 90.5 %. Phylogenetic analyses based on 16S rRNA gene sequences showed that strain B142(T) formed a distinct evolutionary lineage within the family Rhodospirillaceae. Strain B142(T) was distinguishable from phylogenetically related genera with regard to several phenotypic properties. On the basis of phenotypic and phylogenetic data, therefore, strain B142(T) represents a novel genus and species, for which the name Marispirillum indicum gen. nov., sp. nov. is proposed. The type strain is B142(T) (=CCTCC AB 208225(T)=LMG 24627(T)=MCCC 1A01235(T)).","corpus_id":22261987,"score":2},{"doc_id":"19502309","title":"Pseudidiomarina donghaiensis sp. nov. and Pseudidiomarina maritima sp. nov., isolated from the East China Sea.","abstract":"Two Gram-negative, aerobic, motile, rod-shaped bacteria, designated strains 908033(T) and 908087(T), were isolated from a seawater sample collected from the East China Sea. Chemotaxonomic characteristics of the two isolates included the presence of iso-C(15 : 0), iso-C(17 : 0) and iso-C(17 : 1)omega9c as the major cellular fatty acids and Q-8 as the predominant ubiquinone. The genomic DNA G+C contents of strains 908033(T) and 908087(T) were 45.5 and 45.2 mol%, respectively. Phylogenetic analyses based on 16S rRNA gene sequences revealed that the new isolates were related to members of the genus Pseudidiomarina, showing levels of similarity of 95.8-96.6 % with the type strains of recognized species of the genus. The results of DNA-DNA hybridization experiments among these two isolates and Pseudidiomarina sediminum CICC 10319(T), in combination with chemotaxonomic and phenotypic data, demonstrated that the new isolates represent two novel species of the genus Pseudidiomarina, for which the names Pseudidiomarina donghaiensis sp. nov. (type strain 908033(T)=CGMCC 1.7284(T)=JCM 15533(T)) and Pseudidiomarina maritima sp. nov. (type strain 908087(T)=CGMCC 1.7285(T)=JCM 15534(T)) are proposed.","corpus_id":1703729,"score":2},{"doc_id":"19502317","title":"Description of Paenisporosarcina quisquiliarum gen. nov., sp. nov., and reclassification of Sporosarcina macmurdoensis Reddy et al. 2003 as Paenisporosarcina macmurdoensis comb. nov.","abstract":"In the course of a study of the prokaryotic diversity of a landfill site in Chandigarh, India, a strain designated SK 55(T) was isolated and characterized using a polyphasic approach. Its 16S rRNA gene sequence showed closest similarity (98.3 %) to that of Sporosarcina macmurdoensis CMS 21w(T). The sequence similarity to strains of other hitherto described species of Sporosarcina was less than 95.5 %. Strain SK 55(T) contains peptidoglycan of the A4alpha type (l-Lys-d-Asp), MK-8 and MK-7 as the major menaquinones and iso-C(15 : 0) as the major fatty acid. Strain SK 55(T), Sporosarcina macmurdoensis and Sporosarcina ureae, the type species of the genus, had some polar lipids in common (diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, a phospholipid and an unknown lipid). However, an aminolipid, an aminophospholipid and an unknown lipid found in the former two organisms are similar, though not identical, but quite different from the profile of S. ureae. The genomic DNA G+C contents of strain SK 55(T) (46.0 mol%) and S. macmurdoensis CMS 21w(T) (44.0 mol%) are higher than those reported for the majority of species of Sporosarcina (36-42 mol%). As revealed by 16S rRNA gene sequence analysis, strain SK 55(T) and S. macmurdoensis CMS 21w(T) form a clade which is distinct from the clade occupied by other species of Sporosarcina. On the basis of phenotypic characteristics including chemotaxonomic data and analysis of the 16S rRNA gene sequence, we conclude that strain SK 55(T) should be considered as a member of a novel genus and species, for which the name Paenisporosarcina quisquiliarum gen. nov., sp. nov. is proposed. The type strain of Paenisporosarcina quisquiliarum is SK 55(T) (=MTCC7604(T) =JCM 14041(T)). S. macmurdoensis CMS 21w(T) shows more similarity in its 16S rRNA gene sequence (98.3 %), DNA G+C content and polar lipid profile to strain SK 55(T) than to S. ureae DSM 2281(T). Phylogenetically, it forms a coherent cluster with strain SK 55(T) which is separate from the Sporosarcina cluster. Moreover, iso-C(15 : 0), anteiso-C(15 : 0) and C(16 : 1)omega7c alcohol are the three major fatty acids in both S. macmurdoensis CMS 21w(T) and SK 55(T). All these data suggest that S. macmurdoensis should be a member of the genus Paenisporosarcina. However, S. macmurdoensis can be differentiated from SK 55(T) in several physiological and biochemical characteristics, especially in the patterns of oxidation and acid production from carbohydrates. The genomic relatedness of S. macmurdoensis CMS 21w(T) and strain SK 55(T) was also very low (18.0 %). It is therefore logical to transfer Sporosarcina macmurdoensis to the newly created genus as Paenisporosarcina macmurdoensis comb. nov. The type strain is CMS 21w(T) (=MTCC4670(T) =DSM 15428(T)).","corpus_id":9277832,"score":2},{"doc_id":"19542119","title":"Marinobacter lacisalsi sp. nov., a moderately halophilic bacterium isolated from the saline-wetland wildfowl reserve Fuente de Piedra in southern Spain.","abstract":"A Gram-negative, non-spore-forming, motile, moderately halophilic, aerobic, rod-shaped bacterium, designated strain FP2.5(T), was isolated from the inland hypersaline lake Fuente de Piedra, a saline-wetland wildfowl reserve located in the province of Málaga in southern Spain. Strain FP2.5(T) was subjected to a polyphasic taxonomic study. It produced colonies with a light-yellow pigment. Strain FP2.5(T) grew at salinities of 3-15 % (w/v) and at temperatures of 20-40 degrees C. The pH range for growth was 5-9. Strain FP2.5(T) was able to utilize various organic acids as sole carbon and energy source. Its major fatty acids were C(16 : 0), C(18 : 1)omega9c and C(16 : 1)omega9c. The DNA G+C content was 58.6 mol%. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain FP2.5(T) appeared to be a member of the genus Marinobacter and clustered closely with the type strains of Marinobacter segnicrescens, Marinobacter bryozoorum and Marinobacter gudaonensis (levels of 16S rRNA gene sequence similarity of 98.1, 97.4 and 97.2 %, respectively). However, DNA-DNA relatedness between the new isolate and the type strains of its closest related Marinobacter species was low; levels of DNA-DNA relatedness between strain FP2.5(T) and M. segnicrescens LMG 23928(T), M. bryozoorum DSM 15401(T) and M. gudaonensis DSM 18066(T) were 36.3, 32.1 and 24.9 %, respectively. On the basis of phenotypic characteristics, phylogenetic analysis and DNA-DNA relatedness data, strain FP2.5(T) is considered to represent a novel species of the genus Marinobacter, for which the name Marinobacter lacisalsi sp. nov. is proposed. The type strain is FP2.5(T) (=CECT 7297(T)=LMG 24237(T)).","corpus_id":21001674,"score":2},{"doc_id":"19542120","title":"Flavobacterium chungangense sp. nov., isolated from a freshwater lake.","abstract":"A yellow-pigmented, rod-shaped, Gram-staining-negative, aerobic bacterial strain, designated CJ7(T), was isolated from a freshwater lake at Chung-Ang University in Anseong, South Korea. Results from 16S rRNA gene sequence analysis revealed that the isolate was phylogenetically affiliated with members of the genus Flavobacterium. Strain CJ7(T) showed sequence similarity values of 91.5-98.0 % to the type strains of recognized Flavobacterium species. The DNA-DNA relatedness between strain CJ7(T) and Flavobacterium hercynium DSM 18292(T), which showed the highest 16S rRNA gene sequence similarity, was 25.4 %. The predominant cellular fatty acids were iso-C(15 : 0) (18.3 %), summed feature 3 (comprising iso-C(15 : 0) 2-OH and/or C(16 : 1)omega7c) (16.1 %), iso-C(17 : 0) 3-OH (8.9 %), iso-C(15 : 0) 3-OH (7.2 %), iso-C(17 : 1)omega9c (6.1 %) and iso-C(15 : 1) (5.9 %). Flexirubin-type pigments were absent. The major isoprenoid quinone was menaquinone-6. The DNA G+C content was 34.5 mol%. The results obtained from this study, with a polyphasic taxonomic approach, suggested that strain CJ7(T) represents a novel species of the genus Flavobacterium for which the name Flavobacterium chungangense sp. nov. is proposed. The type strain is CJ7(T) (=KACC 13353(T)=JCM 15651(T)).","corpus_id":23608270,"score":2},{"doc_id":"19542122","title":"Paenibacillus tundrae sp. nov. and Paenibacillus xylanexedens sp. nov., psychrotolerant, xylan-degrading bacteria from Alaskan tundra.","abstract":"Eight psychrotolerant, xylan-degrading strains of bacteria that were catalase-positive, oxidase-negative and able to reduce nitrate to nitrite were isolated from soil beneath moist non-acidic and acidic tundra in northern Alaska. The DNA G+C contents for the strains ranged from 46.4-50.3 mol%. Phylogenetic analysis based on 16S rRNA gene sequences revealed that each strain belonged to the genus Paenibacillus. The highest level of 16S rRNA gene similarity was found between the eight strains and Paenibacillus amylolyticus NRRL NRS-290(T) (98.9-99.1 %). However, despite relatively high 16S rRNA gene similarity, DNA-DNA hybridization, repetitive elements genotyping and phenotypic analysis revealed that at least two of the strains differed from P. amylolyticus NRRL NRS-290(T). DNA-DNA hybridization values between strain A10b(T) and P. amylolyticus NRRL NRS-290(T) (4.3 %), between strain B22a(T) and P. amylolyticus NRRL NRS-290(T) (48.8 %) and between strain A10b(T) and strain B22a(T) (11.0 %) were below those recommended by the ad hoc committee for those belonging to the same species. Significant phenotypic features that differentiate these novel strains from P. amylolyticus included their inability to utilize l-arabinose and ability to utilize glycogen as sole carbon sources. Unlike strains 1B4a and B22a(T), strains A6a and A10b(T) produced ethanol as an end product of glucose fermentation, utilized acetic acid and 2,3-butanediol and did not utilize d-gluconic acid. MK-7 was the major isoprenoid quinone and anteiso-C(15 : 0) was the most abundant fatty acid for strains A10b(T) and B22a(T). On the basis of these results, strains A10b(T) and B22a(T) are each considered to represent a novel species of the genus Paenibacillus, for which the names Paenibacillus tundrae sp. nov. and Paenibacillus xylanexedens sp. nov. are proposed, respectively. The type strain of Paenibacillus tundrae sp. nov. is A10b(T) (=NRRL B-51094(T)=DSM 21291(T)). The type strain of Paenibacillus xylanexedens sp. nov. is B22a(T) (=NRRL B-51090(T)=DSM 21292(T)).","corpus_id":206165968,"score":2},{"doc_id":"19542125","title":"Massilia niabensis sp. nov. and Massilia niastensis sp. nov., isolated from air samples.","abstract":"Two bacterial isolates, designated strains 5420S-26(T) and 5516S-1(T), were recovered from air samples collected in Suwon, Korea. Cells of both strains were aerobic, Gram-negative, motile rods. Phylogenetically, these strains were positioned within the radius of the genus Massilia. 16S rRNA gene sequence analysis showed that the strains shared 97.3 % sequence similarity and had sequence similarities of 94.9-98.1 % with respect to type strains of species belonging to the genus Massilia. In DNA-DNA hybridization tests, the two strains showed <39 % relatedness with respect to strains of closely related species of the genus Massilia and 27 % relatedness to each other. Both strains contained Q-8 as the predominant isoprenoid quinone and possessed summed feature 3 (comprising C(16 : 1)omega7c and/or iso-C(15 : 0) 2-OH) as the major fatty acid. Strain 5516S-1(T) was found to contain the fatty acid C(20 : 0) (in small amounts), a feature that served to distinguish it from both 5420S-26(T) and recognized members of the genus Massilia. The DNA G+C contents of 5420S-26(T) and 5516S-1(T) were 67.8 and 66.6 mol%, respectively. Phylogenetic, phenotypic and chemotaxonomic data accumulated in this study revealed that 5420S-26(T) and 5516S-1(T) represent novel species of the genus Massilia, for which the names Massilia niabensis sp. nov. (type strain 5420S-26(T) =KACC 12632(T) =DSM 21312(T)) and Massilia niastensis sp. nov. (type strain 5516S-1(T) =KACC 12599(T) =DSM 21313(T)) are proposed, respectively.","corpus_id":26995066,"score":2},{"doc_id":"19542127","title":"Tenacibaculum crassostreae sp. nov., isolated from the Pacific oyster, Crassostrea gigas.","abstract":"A rod-shaped, yellow-pigmented, aerobic, Gram-negative bacterium, designated strain JO-1(T), was isolated from an apparently healthy Pacific oyster, Crassostrea gigas, collected at Wan Island, Korea. It grew at 15-37 degrees C (optimum 30 degrees C) only in the presence of sea salts. Strain JO-1(T) hydrolysed casein, Tween 80 and starch. The major fatty acids were iso-C(15 : 0) (23.8 %), summed feature 3 (comprising C(16 : 1)omega7c and/or iso-C(15 : 0) 2-OH; 14.5 %) and iso-C(15 : 1) G (14.1 %). Analysis of the 16S rRNA gene sequence indicated that strain JO-1(T) was a member of the genus Tenacibaculum in the family Flavobacteriaceae, with sequence similarity of 94.6-97.8 % to the type strains of recognized members of the genus. The G+C content of the genomic DNA was 31.4 mol%. DNA-DNA relatedness levels between strain JO-1(T) and the five closest relatives, Tenacibaculum litoreum KCCM 42115(T), T. lutimaris KCTC 12302(T), T. aestuarii KCTC 12569(T), T. mesophilum DSM 13764(T) and T. adriaticum JCM 14633(T), were less than 28 %. Phylogenetic analyses and differences in physiological and biochemical characteristics suggested that strain JO-1(T) (=KCTC 22329(T) =JCM 15428(T)) should be classified as the type strain of a novel species within the genus Tenacibaculum, for which the name Tenacibaculum crassostreae sp. nov. is proposed.","corpus_id":206166480,"score":2},{"doc_id":"19542132","title":"Dyella soli sp. nov. and Dyella terrae sp. nov., isolated from soil.","abstract":"Two novel strains isolated from soils, JS12-10(T) and JS14-6(T), were characterized using a polyphasic approach to determine their taxonomic positions. These isolates were found to be aerobic, Gram-negative, motile with one polar flagellum, non-spore-forming and rod-shaped. Phenotypic and fatty acid data supported the affiliation of JS12-10(T) and JS14-6(T) to the genus Dyella. However, chemotaxonomic data and DNA-DNA relatedness values allowed differentiation of these strains from other Dyella species with validly published names. Strains JS12-10(T) and JS14-6(T) showed the highest 16S rRNA gene sequence similarities with Dyella ginsengisoli Gsoil 3046(T) (98.4 %) and Dyella japonica XD53(T) (97.9 %), respectively, and the 16S rRNA gene sequence similarity between them was 97.1 %. DNA-DNA hybridization values between the novel isolates and strains of other recognized Dyella species were 29-38 %. Therefore, strains JS12-10(T) and JS14-6(T) represent two novel species of the genus Dyella, for which the names Dyella soli sp. nov. (type strain JS12-10(T) =KACC 12747(T) =JCM 15423(T)) and Dyella terrae sp. nov. (type strain JS14-6(T) =KACC 12748(T) =JCM 15424(T)) are proposed.","corpus_id":23680513,"score":2},{"doc_id":"19542144","title":"Sediminibacillus albus sp. nov., a moderately halophilic, Gram-positive bacterium isolated from a hypersaline lake, and emended description of the genus Sediminibacillus Carrasco et al. 2008.","abstract":"A moderately halophilic, Gram-positive-staining, endospore-forming, rod-shaped and strictly aerobic bacterium, designated strain NHBX5(T), was isolated from Lake Nanhuobuxun in China. Strain NHBX5(T) was able to grow at NaCl concentrations of 0-22 % (w/v) (optimally at 7 %, w/v), at pH 6.0-9.0 (optimally at pH 7.5) and at temperatures of 10-45 degrees C (optimally at 37 degrees C). The cell-wall peptidoglycan of strain NHBX5(T) contained meso-diaminopimelic acid as the diagnostic diamino acid. The predominant isoprenoid quinone was MK-7. The major cellular fatty acids were anteiso-C(15 : 0) and anteiso-C(17 : 0). The polar lipids were phosphatidylglycerol, diphosphatidylglycerol and a glycolipid. The genomic DNA G+C content of strain NHBX5(T) was 44.9 mol%. Phylogenetic analysis based on 16S rRNA gene sequence comparisons revealed that strain NHBX5(T) was most closely related to Sediminibacillus halophilus EN8d(T) (98.6 % gene sequence similarity). The level of DNA-DNA relatedness between strain NHBX5(T) and S. halophilus CGMCC 1.6199(T) was 34.6 %. Based on the data presented, strain NHBX5(T) represents a novel species of the genus Sediminibacillus, for which the name Sediminibacillus albus sp. nov. is proposed. The type strain is NHBX5(T) (=DSM 19340(T) =CGMCC 1.6502(T)). In addition, an emended description of the genus Sediminibacillus is presented.","corpus_id":206165836,"score":2},{"doc_id":"19542147","title":"Roseomonas frigidaquae sp. nov., isolated from a water-cooling system.","abstract":"A non-motile, coccobacilli-shaped, pale-pink-pigmented bacterium, designated strain CW67(T), was isolated from a water-cooling system in Gwangyang, Republic of Korea. Cells were found to be Gram-negative, catalase-positive and oxidase-positive, the major fatty acids were C(18 : 1)omega7c (43.6 %) and C(16 : 0) (15.8 %), the predominant respiratory lipoquinone was Q-10 and the DNA G+C content was 69.5 mol%. A phylogenetic tree based on 16S rRNA gene sequence comparisons showed that strain CW67(T) forms an evolutionary lineage within the radiation of the genus Roseomonas and that its closest relative is Roseomonas gilardii subsp. rosea MDA5605(T) (94.7 % sequence similarity). Evidence from this polyphasic study showed that strain CW67(T) could not be assigned to any recognized species. It therefore represents a novel species, for which the name Roseomonas frigidaquae sp. nov. is proposed, with CW67(T) (=KCTC 22211(T) =JCM 15073(T)) as the type strain.","corpus_id":29260423,"score":2},{"doc_id":"19567564","title":"Microvirga guangxiensis sp. nov., a novel alphaproteobacterium from soil, and emended description of the genus Microvirga.","abstract":"A Gram-negative-staining bacterium, designated strain 25BT, was isolated from a soil sample from a rice field in Guangxi Province, China, and its taxonomic position was investigated by using a polyphasic approach. Cells were rod-shaped, non-spore-forming, non-motile and strictly aerobic. Strain 25BT grew optimally at 37 degrees C and pH 7.0. The predominant fatty acids of this soil isolate were C18:1omega7c, C19:0 cyclo omega8c and C16:0. Phylogenetic analysis based on the almost-complete 16S rRNA gene sequence showed that strain 25BT formed a monophyletic clade with the type strain of Microvirga subterranea; the two organisms shared 97.2% 16S rRNA gene sequence similarity. However, the two strains shared low DNA-DNA relatedness. Strain 25BT was also readily distinguishable from Microvirga subterranea DSM 14364T by various phenotypic characteristics. The combination of genotypic and phenotypic data suggests that the isolate represents a novel species of the genus Microvirga, for which the name Microvirga guangxiensis sp. nov. is proposed. The type strain is 25BT (=CGMCC 1.7666T=JCM 15710T).","corpus_id":19982151,"score":2},{"doc_id":"19628599","title":"Maritimimonas rapanae gen. nov., sp. nov., isolated from gut microflora of the veined rapa whelk, Rapana venosa.","abstract":"A yellow-pigmented, Gram-negative, aerobic bacterial strain comprising rod-shaped cells devoid of flagellar and gliding motility, designated strain A31(T), was isolated from a veined rapa whelk (Rapana venosa) collected from the South Sea, Republic of Korea. Results from 16S rRNA gene sequence analysis indicated that the isolate belonged to the family Flavobacteriaceae; the highest level of nucleotide sequence similarity (92.6 %) was observed with Tenacibaculum aestuarii KCTC 12569(T). The predominant cellular fatty acids were iso-C(15 : 1) G (24.2 %), iso-C(15 : 0) (20.1 %) and iso-C(17 : 0) 3-OH (11.2 %). Flexirubin-type pigments were absent. The major isoprenoid quinone was MK-6. The DNA G+C content was 31.7 mol%. Data from a polyphasic taxonomic study suggested that the isolate represents a novel species in a new genus of the family Flavobacteriaceae, for which the name Maritimimonas rapanae gen. nov., sp. nov. is proposed. The type strain of Maritimimonas rapanae is A31(T) (=KCTC 22186(T) =JCM 15075(T)).","corpus_id":206167678,"score":2},{"doc_id":"19654345","title":"Paenibacillus aestuarii sp. nov., isolated from an estuarine wetland.","abstract":"A novel bacterial strain designated CJ25(T) was isolated from the estuarine wetland of the Han river in Korea. Identification of this strain was carried out on the basis of polyphasic taxonomy. The isolate was Gram-staining-positive, rod-shaped, non-pigmented and motile. Phylogenetic analysis based on the 16S rRNA gene sequence revealed that the isolate was closely related to Paenibacillus chondroitinus DSM 5051(T) with 96.1 % similarity. The predominant fatty acids were anteiso-C(15 : 0) (50.25 %), iso-C(16 : 0) (18.54 %) and iso-C(15 : 0) (10.00 %). The major isoprenoid quinone was MK-7. The G+C content of genomic DNA was 50 mol%. According to physiological data and 16S rRNA gene sequence analysis, the isolate was discriminated from related members of the genus Paenibacillus. Therefore, strain CJ25(T) represents a novel species of the genus Paenibacillus, for which the name Paenibacillus aestuarii sp. nov. is proposed. The type strain is CJ25(T) (=KACC 13125(T) =JCM 15521(T)).","corpus_id":41243520,"score":2},{"doc_id":"19661503","title":"Kaistia terrae sp. nov., isolated from a wetland in Korea.","abstract":"An ivory-coloured bacterium, designated strain 5YN7-3(T), was isolated from a wetland, Yongneup, Korea. Cells of the strain were aerobic, Gram-stain-negative, non-motile and short rods. 16S rRNA gene sequence analysis demonstrated that strain 5YN7-3(T) belongs to the order Rhizobiales of the class Alphaproteobacteria and is closely related to Kaistia soli 5YN9-8(T) (97.8 %), Kaistia granuli Ko04(T) (97.6 %) and Kaistia adipata Chj404(T) (97.4 %). Strain 5YN7-3(T) showed DNA-DNA hybridization values of 28, 22 and 35 % with K. granuli Ko04(T), K. soli 5YN9-8(T) and K. adipata Chj404(T), respectively. The major fatty acids were C(18 : 1)omega7c (51.2 %), C(19 : 0) cyclo omega8c (25.0 %), C(18 : 0) (12.9 %) and C(16 : 0) (10.8 %) (>10 % of total fatty acids). Ubiquinone-10 was the major isoprenoid quinone and the DNA G+C content was 66.5 mol%. The phenotypic characteristics in combination with 16S rRNA gene sequence analysis and DNA-DNA hybridization data clearly define strain 5YN7-3(T) as a novel species of the genus Kaistia, for which the name Kaistia terrae sp. nov. is proposed. The type strain is 5YN7-3(T) (=KACC 12910(T) =DSM 21341(T)).","corpus_id":23256186,"score":2},{"doc_id":"20127465","title":"Methylobacterium dankookense sp. nov., isolated from drinking water.","abstract":"A pink-pigmented bacterium, designated SW08-7(T) was isolated from the drinking water of a water purifier. Cells were Gram-negative, rod-shaped, strictly aerobic, and non-spore-forming. It grew optimally at 25 degrees C, pH 6 approximately 7. Phylogenese analysis based on 16S rRNA gene sequence showed that strain SW08-7(T) belongs to the genus Methylobacterium. The highest 16S rRNA gene sequence similarities were found to Methylobacterium mesophilicum JCM 2829(T) (96.9%), Methylobacterium brachiatum B0021(T) (96.9%), Methylobacterium phyllosphaerae CBMB27(T) (96.6%), Methylobacterium radiotolerans JCM 2831(T) (96.6%), and Methylobacterium hispanicum GP34(T) (96.5%). DNA-DNA hybridization experiment revealed low-level (28.5%) of DNA-DNA relatedness between strain SW08-7(T) and Methylobacterium hispanicum. The genomic DNA G+C content was 68.9 mol% and the major isoprenoid quinone was Q-10. The major cellular fatty acid of strain SW08-7(T) was C(18:1) omega7c (79.8+/-2.1%). Results of phylogenetic, phenotypic, and biochemical analyses revealed that strain SW08-7(T) could be classified as representing a novel species of genus Methylobacterium, for which the name Methylobacterium dankookense sp. nov. is proposed. The type strain is SW08-7(T) (=KCTC 22512(T) =DSM 22415(1)).","corpus_id":21564976,"score":2},{"doc_id":"20952545","title":"Tistrella bauzanensis sp. nov., isolated from soil.","abstract":"A Gram-reaction-negative, strictly aerobic, motile, rod-shaped bacterium, designated strain BZ78(T), was isolated from soil from an industrial site. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain BZ78(T) belonged to the family Rhodospirillaceae and formed a coherent cluster with the type strain of Tistrella mobilis (98.3 % pairwise similarity). The predominant cellular fatty acids of strain BZ78(T) were C₁₈:₁ω7c (58.3 %), C₁₉:₀ω8c cyclo (11.5 %), C₁₈:₁ 2-OH (10.9 %) and C₁₄:₀ 3-OH (6.4 %). The predominant ubiquinone was Q-10. The genomic DNA G+C content of strain BZ78(T) was 65.8 mol%. On the basis of phenotypic characteristics, phylogenetic analysis and DNA-DNA relatedness data, strain BZ78(T) is considered to represent a novel species of the genus Tistrella, for which the name Tistrella bauzanensis sp. nov. is proposed. The type strain is BZ78(T) ( = DSM 22817(T) = CGMCC 1.10188(T) = LMG 26047(T)).","corpus_id":10202663,"score":2},{"doc_id":"20952549","title":"Lysobacter korlensis sp. nov. and Lysobacter bugurensis sp. nov., isolated from soil.","abstract":"Two Gram-reaction-negative, rod-shaped, gliding, yellow-pigmented bacterial strains, designated ZLD-17(T) and ZLD-29(T), were isolated from arid soil samples collected from Xinjiang Province, north-west China, and subjected to analysis using a polyphasic taxonomic approach. Both novel strains required 1.0-2.0 % (w/v) sea salts for optimal growth. Phylogenetic analysis based on 16S rRNA gene sequences indicated that these two strains belong to the genus Lysobacter within the class Gammaproteobacteria. Strain ZLD-17(T) showed highest 16S rRNA gene sequence similarities to Lysobacter capsici KCTC 22007(T) (96.9 %), Lysobacter spongiicola DSM 21749(T) (96.8 %) and Lysobacter koreensis KCTC 12204(T) (96.8 %), whereas strain ZLD-29(T) showed highest sequence similarities to Lysobacter niastensis DSM 18481(T) (96.0 %) and Lysobacter enzymogenes DSM 2043(T) (95.9 %). 16S rRNA gene sequence similarity between ZLD-17(T) and ZLD-29(T) was 96.1 %. The DNA G+C contents of strains ZLD-17(T) and ZLD-29(T) were 67.9 and 68.2 mol%, respectively. The major cellular fatty acids of both strains were summed feature 3 (iso-C₁₅:₀ 2-OH and/or C₁₆:₁ω7c), iso-C₁₇:₁ω9c, iso-C₁₆:₀, C₁₆:₀ and iso-C₁₁:₀ 3-OH; their predominant isoprenoid quinone was Q-8 and their major polar lipids were diphosphatidylglycerol, phosphatidylethanolamine and phosphatidylglycerol. Based on their phenotypic characteristics, phylogenetic position as determined by 16S rRNA gene sequence analysis and chemotaxonomic data, strains ZLD-17(T) ( = CCTCC AB 207174(T) = KCTC 23076(T)) and ZLD-29(T) ( = CCTCC AB 207175(T) = KCTC 23077(T)) represent two novel species of the genus Lysobacter, for which the names Lysobacter korlensis sp. nov. and Lysobacter bugurensis sp. nov. are proposed, respectively.","corpus_id":41356058,"score":2},{"doc_id":"21037038","title":"Pseudomonas bauzanensis sp. nov., isolated from soil.","abstract":"A Gram-negative, aerobic, motile rod, designated BZ93(T), was isolated from soil from an industrial site. The strain grew at 5-30 °C. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain BZ93(T) was related to members of the genus Pseudomonas and was related most closely to Pseudomonas xiamenensis C10-2(T) (97.8 % 16S rRNA gene sequence similarity) and Pseudomonas pertucinogena IFO 14163(T) (97.4 %). The predominant cellular fatty acids of strain BZ93(T) were C(18 : 1)ω7c (54.8 %), summed feature 3 (C(16 : 1)ω7c and/or iso-C(15 : 0) 2-OH; 10.3 %), C(16 : 0) (9.9 %) and C(17 : 0) cyclo (7.4 %). The major quinone was ubiquinone 9. The major phospholipids were phosphatidylethanolamine, diphosphatidylglycerol, phosphatidylglycerol and an unknown phospholipid. The genomic DNA G+C content was 61.8 mol%. On the basis of phenotypic characteristics, phylogenetic analysis and DNA-DNA relatedness, a novel species, Pseudomonas bauzanensis sp. nov., is proposed. The type strain is BZ93(T) ( = DSM 22558(T) = CGMCC 1.9095(T) = LMG 26048(T)).","corpus_id":30576964,"score":2},{"doc_id":"21717323","title":"Flavobacterium koreense sp. nov., Flavobacterium chungnamense sp. nov., and Flavobacterium cheonanense sp. nov., isolated from a freshwater reservoir.","abstract":"Taxonomic studies were performed on three strains isolated from Cheonho reservoir in Cheonan, Korea. The isolates were Gram-negative, aerobic, rod-shaped, non-motile, catalase-positive, and oxidase-positive. Colonies on solid media were cream-yellow, smooth, shiny, and circular. Phylogenetic analysis of the 16S rRNA gene sequences revealed that these strains belong to the genus Flavobacterium. The strains shared 98.6-99.4% sequence similarity with each other and showed less than 97% similarity with members of the genus Flavobacterium with validly published names. The DNA-DNA hybridization results confirmed the separate genomic status of strains ARSA-42(T), ARSA-103(T), and ARSA-108(T). The isolates contained menaqui-none-6 as the predominant menaquinone and iso-C(15:0), iso-C(15:0) 3-OH, iso-Ci(15:1) G, and iso-C(16:0) 3-OH as the major fatty acids. The genomic DNA G+C content of the isolates were 31.4-33.2 mol%. According to the phenotypic and genotypic data, these organisms are classified as representative of three novel species in the genus Flavobacterium, and the name Flavobacterium koreense sp. nov. (strain ARSA-42(T) =KCTC 23182(T) =JCM 17066(T) =KACC 14969(T)), Flavobacterium chungnamense sp. nov. (strain ARSA-103(T) =KCTC 23183(T) =JCM 17068(T) =KACC 14971(T)), and Flavobacterium cheonanense sp. nov. (strain ARSA-108(T) =KCTC 23184(T) =JCM 17069(T) =KACC 14972) are proposed.","corpus_id":19444004,"score":2},{"doc_id":"22247212","title":"Kaistia defluvii sp. nov., isolated from river sediment.","abstract":"A Gram-stain-negative, aerobic, non-motile, rod- and coccus-shaped bacterium, designated strain B6-12(T), was isolated from sediment collected from the River Geumho in South Korea. In comparative 16S rRNA gene sequence analysis, the novel strain appeared to be affiliated with the class Alphaproteobacteria and to be most closely related to Kaistia adipata KCTC 12095(T), Kaistia dalseonensis DSM 18800(T), Kaistia geumhonensis DSM 18799(T), Kaistia granuli KCTC 12575(T), Kaistia soli KACC 12605(T) and Kaistia terrae KACC 12910(T), with sequence similarities of 96.2-99.1%. The predominant ubiquinone in the isolate was Q-10, major fatty acids were C(18:0), C(18:1)ω7c and C(19:0)ω8c cyclo, and genomic DNA G+C content was 63.0 mol%. Based on the phylogenetic and chemotaxonomic evidence and the results of DNA-DNA hybridizations, strain B6-12(T) represents a novel species in the genus Kaistia, for which the name Kaistia defluvii sp. nov. is proposed. The type strain is B6-12(T) ( = KCTC 23766(T) = JCM 18034(T)).","corpus_id":30343928,"score":2},{"doc_id":"22922533","title":"Xenorhabdus ishibashii sp. nov., isolated from the entomopathogenic nematode Steinernema aciari.","abstract":"Gram-negative bacteria of the genus Xenorhabdus exhibit a mutualistic association with steinernematid entomopathogenic nematodes and a pathogenic relationship with insects. Here we describe two isolates of the entomopathogenic nematode Steinernema aciari collected from China and Japan. 16S rRNA gene sequence similarity and phylogenetic analysis indicated that the isolates obtained from S. aciari belonged to the genus Xenorhabdus. Multilocus sequence analysis based on five universal protein-coding gene sequences revealed that the isolates were closely related to Xenorhabdus ehlersii DSM 16337(T) and Xenorhabdus griffiniae ID10(T) but that they exhibited <97 % sequence similarity with these reference strains, which indicated that the isolates were distinct from previously described species. Based on these genetic differences and several differential phenotypic traits, we propose that the isolates represent a novel species of the genus Xenorhabdus, for which we propose the name Xenorhabdus ishibashii sp. nov. The type strain is GDh7(T) ( = DSM 22670(T) = CGMCC 1.9166(T)).","corpus_id":46314950,"score":2},{"doc_id":"23243096","title":"Caulobacter daechungensis sp. nov., a stalked bacterium isolated from a eutrophic reservoir.","abstract":"A Gram-stain-negative, aerobic, non-spore-forming, curved, rod-shaped bacterium, H-E3-2(T), was isolated from a water sample taken from Daechung Reservoir, Republic of Korea, during the late-blooming period of cyanobacteria. Strain H-E3-2(T) was motile with a single polar flagellum or non-motile (stalked cell). Comparative 16S rRNA gene sequence studies showed the isolate had a clear affiliation with the class Alphaproteobacteria and was most closely related to Caulobacter fusiformis ATCC 15257(T) and Caulobacter mirabilis LMG 24261(T), showing 97.6 and 97.3 % 16S rRNA gene sequence similarity, respectively, and 95.3-96.3 % similarity to all other species of the genus Caulobacter. The predominant ubiquinone was Q-10. The major fatty acids were summed feature 8 (C18 : 1ω6c and/or C18 : 1ω7c) and C16 : 0. The G+C content of the genomic DNA of strain H-E3-2(T) was 64.7 mol%. DNA-DNA hybridization values of strain H-E3-2(T) with C. fusiformis ATCC 15257(T) and C. mirabilis LMG 24261(T) were 21.2 and 19.7 %, respectively. Thus, based on the results of polyphasic analysis, it is proposed that strain H-E3-2(T) represents a novel species of the genus Caulobacter, for which the name Caulobacter daechungensis sp. nov. is proposed. The type strain is H-E3-2(T) ( = KCTC 32211(T) = JCM 18689(T)).","corpus_id":206178457,"score":2},{"doc_id":"23416574","title":"Devosia submarina sp. nov., isolated from deep-sea surface sediments.","abstract":"The taxonomic status of two aerobic, Gram-stain-negative, orange-reddish pigmented, motile, rod-shaped bacteria, designated KMM 9415(T) and KMM 9416, isolated from a deep surface-sediment sample from the Sea of Japan, was defined. Comparative 16S rRNA gene sequence analysis of strains KMM 9415(T) and KMM 9416 revealed their affiliation to the genus Devosia with a high sequence similarity of 98.5 % to both Devosia psychrophila DSM 22950(T) and Devosia glacialis LMG 26051(T). The novel strains were characterized by the predominance of the fatty acid C18 : 1ω7c followed by C16 : 1 and C16 : 0. The major isoprenoid quinone was Q-10 and the polar lipids comprised phosphatidylglycerol, phosphatidic acid and unknown glycolipids. The DNA-DNA hybridization value of 88 % between the novel strains KMM 9415(T) and KMM 9416 confirmed their assignment to the same species. The values of DNA relatedness determined for strain KMM 9415(T) and the closely related strains D. psychrophila DSM 22950(T) and D. glacialis LMG 26051(T) were 21 % and 23 %, respectively. Based on distinctive phenotypic characteristics, phylogenetic analysis and DNA-DNA relatedness, it can be concluded that the novel strains KMM 9415(T) and KMM 9416 represent a novel species within the genus Devosia, for which the name Devosia submarina sp. nov. is proposed. The type strain is the strain KMM 9415(T) (= NRIC 0884(T) = JCM 18935(T)).","corpus_id":25539634,"score":2},{"doc_id":"23482845","title":"Heterorhabditidoides rugaoensis n. sp. (Rhabditida: Rhabditidae), a Novel Highly Pathogenic Entomopathogenic Nematode Member of Rhabditidae.","abstract":"A novel entomopathogenic nematode species, Heterorhabditidoides rugaoensis n. sp. RG081015, collected from Rugao, China, is described. The new species is morphologically very similar to H. chongmingensis but can be distinguished from it on the basis of some morphological characteristics, combined with molecular data and a cross-hybridization test. Males of the new species can be recognized on the basis of body length averaging 1396.2 μm; lateral field with one ridge; metastome isoglottoid with one hemispherical swellings comprised of two to three well-developed warts; asymmetric spicules; peloderan bursa. In IJs, EP = 134.5 μm; ES = 149.3 μm; tail length = 82.5 μm; and a = 20.5. Hermaphroditic females have four to five lateral ridges. The 18S rDNA and ITS sequences of the two nematodes share 99% and 98% identity, respectively. Phylogenetic trees of 18S rDNA and ITS indicate that the new species is most closely related to H. chongmingensis; thus, the two nematodes belong to the same genus. Failure of cross-hybridization between them indicates that nematode strain RG081015 is a novel species and is described herein as H. rugaoensis n. sp. The LC50 of the novel species against Galleria mellonella were 24.35 IJs / ml within 48 hours of infection. Morphological characteristics, genetic similarity analyses, and phylogenetic relationships provide strong evidence that some species of Oscheius/Insectivora-group should be reassigned to the genus Heterorhabditidoides.","corpus_id":18010469,"score":2},{"doc_id":"23606482","title":"Dyadobacter tibetensis sp. nov., isolated from glacial ice core.","abstract":"A Gram-stain-negative, rod-shaped, aerobic, non-motile bacterium, designated Y620-1(T), was isolated from a glacier on the Tibetan Plateau, China. The 16S rRNA gene sequence of the novel isolate shared 93.6-95.1 % similarity with type strains of species of the genus Dyadobacter. The major fatty acids of strain Y620-1(T) were summed feature 3 (C16 : 1ω7c and/or iso-C15 : 0 2-OH), iso-C15 : 0, C16 : 1ω5c and iso-C17 : 0 3-OH. The predominant isoprenoid quinone and polar lipid were MK-7 and phosphatidylethanolamine (PE), respectively. The DNA G+C content was 44.4±0.3 mol% (Tm). Flexirubin-type pigment was produced. The novel isolate was classified in the genus Dyadobacter, but a number of phenotypic characteristics distinguished the novel isolate from type strains of species of the genus Dyadobacter. From these genotypic and phenotypic data, it is evident that strain Y620-1(T) represents a novel species of the genus Dyadobacter, for which the name Dyadobacter tibetensis sp. nov. is proposed. The type strain is Y620-1(T) ( = JCM 18589(T) = CGMCC 1.12215(T)).","corpus_id":27706358,"score":2},{"doc_id":"23918786","title":"Pseudomonas guguanensis sp. nov., a gammaproteobacterium isolated from a hot spring.","abstract":"An aerobic, Gram-stain-negative, rod-shaped bacterium (designated strain CC-G9A(T)), motile by a polar-flagellum, was isolated from a hot spring water sample in Taiwan. Strain CC-G9A(T) could grow at 20-42 °C, pH 6.0-10.0 and tolerate up to 7% (w/v) NaCl. The 16S rRNA gene sequence analysis of strain CC-G9A(T) showed pairwise sequence similarity to Pseudomonas mendocina LMG 1223(T) (97.7%), Pseudomonas alcaligenes ATCC 14909(T) (97.8 %), Pseudomonas alcaliphila DSM 17744(T) (97.8 %), Pseudomonas toyotomiensis JCM 15604(T) (97.6 %), Pseudomonas oleovorans subsp. lubricantis DSM 21016(T) (97.6 %) and Pseudomonas argentinensis BCRC 17807(T) (97.5 %), and lower sequence similarity to other species of the genus Pseudomonas. According to DNA-DNA association analysis, the relatedness of strain CC-G9A(T) to P. mendocina BCRC 10458(T), P. alcaliphila DSM 17744(T), P. alcaligenes BCRC 11893(T), P. oleovorans subsp. lubricantis DSM 21016(T), P. argentinensis BCRC 17807(T) and P. oleovorans subsp. oleovorans BCRC 11902 was 55.1±3.1, 13.7±1.5, 14.1±1.8, 58.5±1.1, 28.9±2.0 and 28.6±1.8 %, respectively. The evolutionary trees reconstructed based on 16S rRNA, gyrB and rpoB gene sequences revealed varying phylogenetic neighbourhoods of strain CC-G9A(T) with regard to the most closely related type strains. The predominant quinone system was ubiquinone (Q-9) and the DNA G+C content was 64.3±1.3 mol%. The major fatty acids were C10 : 0 3-OH, C12 : 0, C12 : 0 3-OH, C16 : 0 and summed features 3 and 8 consisting of C16 : 1ω7c/C16 : 1ω6c and C18 : 1ω7c/C18 : 1ω6c, respectively. The major polar lipids were diphosphatidylglycerol, phosphatidylcholine, phosphatidylethanolamine and phosphatidylglycerol. According to distinct phylogenetic, phenotypic and chemotaxonomic features, strain CC-G9A(T) is proposed to represent a novel species within the genus Pseudomonas for which the name Pseudomonas guguanensis sp. nov. is proposed. The type strain is CC-G9A(T) ( = BCRC 80438(T) = JCM 18416(T)).","corpus_id":206178039,"score":2},{"doc_id":"23918787","title":"Pseudomonas guangdongensis sp. nov., isolated from an electroactive biofilm, and emended description of the genus Pseudomonas Migula 1894.","abstract":"A Gram-negative, straight to slightly curved rod-shaped bacterium, motile with peritrichous flagella, designated SgZ-6(T), was isolated from an electroactive biofilm and was characterized by means of a polyphasic approach. Growth occurred with 0-5.0 % (w/v) NaCl (optimum 1 %), at pH 6.0-10.0 (optimum pH 7.0) and at 10-42 °C (optimum 30 °C) in trypticase soya broth. Phylogenetic analyses based on the 16S rRNA and gyrB genes identified the isolate as a member of a novel species of the genus Pseudomonas. Strain SgZ-6(T) exhibited the highest 16S rRNA gene sequence similarity to 'Pseudomonas linyingensis' CGMCC 1.10701 (97.5 %), followed by Pseudomonas sagittaria JCM 18195(T) (97.4 %), P. oleovorans subsp. lubricantis DSM 21016(T) (96.6 %), P. tuomuerensis JCM 14085(T) (96.5 %) and P. alcaliphila JCM 10630(T) (96.4 %). Strain SgZ-6(T) showed the highest gyrB gene sequence similarity of 93.7 % to 'P. linyingensis' CGMCC 1.10701 among all type strains of genus Pseudomonas. DNA-DNA pairing studies showed that strain SgZ-6(T) displayed 47.1 and 40.3 % relatedness to 'P. linyingensis' CGMCC 1.10701 and P. sagittaria JCM 18195(T), respectively. The major isoprenoid quinone was ubiquinone 9 (Q-9). The whole-cell fatty acids consisted mainly of summed feature 3 (C16 : 1ω6c and/or C16 : 1ω7c), C16 : 0 and summed feature 8 (C18 : 1ω6c and/or C18 : 1ω7c). The DNA G+C content of the genomic DNA was 68.1 mol%. On the basis of phenotypic, chemotaxonomic and phylogenetic data, strain SgZ-6(T) is proposed to represent a novel species of the genus Pseudomonas, for which the name Pseudomonas guangdongensis sp. nov. is proposed. The type strain is SgZ-6(T) ( = CCTCC AB 2012022(T) = KACC 16606(T)). An emended description of the genus Pseudomonas is also proposed.","corpus_id":27637805,"score":2},{"doc_id":"24664580","title":"Thalassomonas eurytherma sp. nov., a marine proteobacterium.","abstract":"Two Gram-staining-negative, aerobic, rod-shaped bacterial strains, designated Za6a-12(T) and Za6a-17, were isolated from seawater of the East China Sea. Cells of Za6a-12(T) and Za6a-17 were approximately 1.5-2.0 µm×0.5-0.7 µm and motile by a single polar flagellum. Strains grew optimally at pH 7.5-8.0, 28 °C, and in the presence of 2.5-3.0% (w/v) NaCl. Chemotaxonomic analysis showed that the predominant respiratory quinone of strains Za6a-12(T) and Za6a-17 was ubiquinone-8 (>97%), and the major fatty acids were C(14 : 0), C(16 : 1)ω7c and/or iso-C(15 : 0) 2-OH, C(16 : 0) and C(17 : 1)ω8c. Their DNA G+C contents were 42.7 mol% and 42.8 mol%, respectively. 16S rRNA gene sequence analysis revealed that the isolates belonged to the genus Thalassomonas and showed the highest sequence similarity to Thalassomonas loyana CBMAI 722(T) (95.9%). Strains Za6a-12(T) and Za6a-17 could be differentiated from T. loyana CBMAI 722(T) according to their phenotypic and chemotaxonomic features, DNA G+C contents and fatty acid composition. On the basis of these features, we propose strains Za6a-12(T) and Za6a-17 to be representatives of a novel species of the genus Thalassomonas with the name Thalassomonas eurytherma sp. nov. suggested. Strain Za6a-12(T) ( = CGMCC 1.12115(T) = JCM 18482(T)) is the type strain of this novel species.","corpus_id":20301774,"score":2},{"doc_id":"24944336","title":"Martelella radicis sp. nov. and Martelella mangrovi sp. nov., isolated from mangrove sediment.","abstract":"Two Gram-stain-negative, non-motile, rod-shaped bacterial strains, designated BM5-7(T) and BM9-1(T) were isolated from soil of the root system of a mangrove forest. Phylogenetic analysis based on 16S rRNA gene sequences showed that the two isolates belong to the genus Martelella. The chemotaxonomic characteristics of these isolates included the presence of C19 : 0 cyclo ω8c and C18 : 1ω7c as the major cellular fatty acids and Q-10 as the dominant ubiquinone. The genomic DNA G+C contents of strains BM5-7(T) and BM9-1(T) were 61.0 and 59.7 mol% (HPLC method), respectively. The 16S rRNA gene sequence similarity between the two strains was 98.1 %, but DNA-DNA hybridization indicated 44 % relatedness. Strains BM5-7(T) and BM9-1(T) exhibited 16S rRNA gene sequence similarities of 98.0-99.2 % and 97.7-98.1 %, respectively, with type strains of Martelella endophytica and Martelella mediterranea. Combined data from phenotypic, phylogenetic and DNA-DNA relatedness studies demonstrated that strains BM5-7(T) and BM9-1(T) are representatives of two novel species of the genus Martelella, for which the names Martelella radicis sp. nov. (type strain BM5-7(T) = DSM 28101(T) = LMG 27958(T)) and Martelella mangrovi sp. nov. (type strain BM9-1(T) = DSM 28102(T) = LMG 27959(T)) are proposed.","corpus_id":206182687,"score":2},{"doc_id":"25122614","title":"Sulfitobacter geojensis sp. nov., Sulfitobacter noctilucae sp. nov., and Sulfitobacter noctilucicola sp. nov., isolated from coastal seawater.","abstract":"Four Gram-stain-negative, aerobic, rod-shaped bacterial strains, MM-124, MM-126, NB-68 and NB-77, were isolated from the coastal seawater or a region with a bloom of sea sparkle around Geoje island in Korea. The sequence similarity values of the 16S rRNA gene between the isolates and Sulfitobacter mediterraneus DSM 12244(T) ranged from 97.7 to 98.2%, and phylogenetic relationships suggested that they belong to a phylogenetic branch that includes the genera Sulfitobacter and Roseobacter. The isoprenoid quinone of all three novel strains was ubiquinone-10 and the major fatty acid was cis-vaccenic acid, as in other species of the genus Sulfitobacter. However, there were several differences in the morphological, physiological and biochemical characteristics among the four strains and the reference species of the genus Sulfitobacter. Moreover, the average nucleotide identity values between the three sequenced isolates and the reference strains were below 76.33, indicating that genomic variation exists between the isolates and reference strains. Chemotaxonomic characteristics together with phylogenetic affiliations and genomic distances illustrate that strains MM-124, NB-68 and NB-77 represent novel species of the genus Sulfitobacter, for which the names Sulfitobacter geojensis sp. nov. (type strain MM-124(T) =KCTC 32124(T) =JCM 18835(T)), Sulfitobacter noctilucae sp. nov. (type strain NB-68(T) =KCTC 32122(T) =JCM 18833(T)) and Sulfitobacter noctilucicola sp. nov. (type strain NB-77(T) =KCTC 32123(T) =JCM 18834(T)) are proposed.","corpus_id":20504994,"score":2},{"doc_id":"25281728","title":"Serratia myotis sp. nov. and Serratia vespertilionis sp. nov., isolated from bats hibernating in caves.","abstract":"During the study of bacteria associated with bats affected by white-nose syndrome hibernating in caves in the Czech Republic, we isolated two facultatively anaerobic, Gram-stain-negative bacteria, designated strains 12(T) and 52(T). Strains 12(T) and 52(T) were motile, rod-like bacteria (0.5-0.6 µm in diameter; 1-1.3 µm long), with optimal growth at 20-35 °C and pH 6-8. On the basis of the almost complete sequence of their 16S rRNA genes they should be classified within the genus Serratia; the closest relatives to strains 12(T) and 52(T) were Serratia quinivorans DSM 4597(T) (99.5 % similarity in 16S rRNA gene sequences) and Serratia ficaria DSM 4569(T) (99.5% similarity in 16S rRNA gene sequences), respectively. DNA-DNA relatedness between strain 12(T) and S. quinivorans DSM 4597(T) was only 37.1% and between strain 52(T) and S. ficaria DSM 4569(T) was only 56.2%. Both values are far below the 70% threshold value for species delineation. In view of these data, we propose the inclusion of the two isolates in the genus Serratia as representatives of Serratia myotis sp. nov. (type strain 12(T) =CECT 8594(T) =DSM 28726(T)) and Serratia vespertilionis sp. nov. (type strain 52(T) =CECT 8595(T) =DSM 28727(T)).","corpus_id":43187151,"score":2},{"doc_id":"25444874","title":"Genome sequence of Serratia nematodiphila DSM 21420T, a symbiotic bacterium from entomopathogenic nematode.","abstract":"Serratia nematodiphila DSM 21420(T) (=CGMCC 1.6853(T), DZ0503SBS1(T)), isolated from the intestine of Heterorhabditidoides chongmingensis, has been known to have symbiotic-pathogenic life cycle, on the multilateral relationships with entomopathogenic nematode and insect pest. In order to better understanding of this rare feature in Serratia species, we present here the genome sequence of S. nematodiphila DSM 21420(T) with the significance of first genome sequence in this species.","corpus_id":20175431,"score":2},{"doc_id":"25634950","title":"Pedobacter daejeonensis sp. nov. and Pedobacter trunci sp. nov., isolated from an ancient tree trunk, and emended description of the genus Pedobacter.","abstract":"Two Gram-stain-negative, yellow, aerobic and rod-shaped bacterial isolates, designated THG-DN3.18(T) and THG-DN3.19(T), were isolated from an ancient tree trunk from Daejeon, South Korea. 16S rRNA gene sequence similarity showed that both strains belong to the genus Pedobacter within the family Sphingobacteriaceae . Strain THG-DN3.18(T) exhibited maximum sequence similarity with Pedobacter boryungensis KCTC 23344(T) (98.5%) while strain THG-DN3.19(T) exhibited maximum sequence similarity with Pedobacter nyackensis LMG 24260(T) (97.3%). In DNA-DNA hybridization tests, the two strains showed less than 35% relatedness with respect to closely related species of the genus Pedobacter . Both strains contained iso-C(15 : 0) and C(16 : 1)ω6c and/or C(16 : 1)ω7c (summed feature 3) as the predominant fatty acids and MK-7 as the major isoprenoid quinone. The DNA G+C contents of strains THG-DN3.18(T) and THG-DN3.19(T) were 35.5 and 40.1 mol%, respectively. The genotypic analysis, biochemical properties, and phenotypic and chemotaxonomic characteristics indicate that strains THG-DN3.18(T) and THG-DN3.19(T) represent novel species of the genus Pedobacter , for which the names Pedobacter daejeonensis sp. nov. and Pedobacter trunci sp. nov. are proposed. The type strains are THG-DN3.18(T) ( = KCTC 42230(T) = JCM 30352(T)) and THG-DN3.19(T) ( = KCTC 42233(T) = JCM 30353(T)), respectively.","corpus_id":25962317,"score":2},{"doc_id":"25716888","title":"Enterobacillus tribolii gen. nov., sp. nov., a novel member of the family Enterobacteriaceae, isolated from the gut of a red flour beetle, Tribolium castaneum.","abstract":"Two novel Gram-stain negative facultative anaerobic, motile, rod-shaped bacterial strains IG-V01(T) and IG-V01b were isolated from the gut of red flour beetles, Tribolium castaneum. The 16S rRNA gene sequences of strains IG-V01(T) and IG-V01b were found to have their highest sequence similarity (96.5% and 96.4%) with Serratia nematodiphila DZ0503SBS1(T) (Enterobacteriaceae family) respectively. Strains IG-V01(T) and IG-V01b share 100% 16S rRNA gene sequence similarity and exhibit very similar phenotypic characteristics. In addition, they show 89.7% genomic relatedness (DNA-DNA hybridisation). Major fatty acids were identified to be C(16:0) (38.3%), C(17:0) cyclo (19.5-20%) and C(14:0) (11.2-11.3%). Cells contain phosphatidylethanolamine and diphosphatidylglycerol as predominant polar lipids. Genomic DNA G+C content (mol%) was determined to be 51.5-51.7. A polyphasic approach employing the study of morphological, physiological, chemotaxonomic, genomic and phylogenetic analysis revealed that the two newly isolated strains cannot be placed in any of the existing genera of the family Enterobacteriaceae. Therefore, it is proposed that strains IG-V01(T) and IG-V01b belong to a novel genus within the family Enterobacteriaceae, and represent a new species Enterobacillus tribolii gen. nov., sp. nov., with the type strain =IG-V01(T) = KCTC 42159(T) = MCC 2532(T).","corpus_id":7877444,"score":2},{"doc_id":"25977284","title":"Shimia sagamensis sp. nov., a marine bacterium isolated from cold-seep sediment.","abstract":"A novel marine bacterial strain designated JAMH 011(T) was isolated from the cold-seep sediment in Sagami Bay, Japan. Cells were Gram-stain-negative, rod-shaped, non-spore-forming, aerobic chemo-organotrophs and motile by means of a single polar flagellum. Growth occurred at temperatures below 31 °C, with the optimum at 25 °C. The major respiratory quinone was Q-10. The predominant fatty acid was C18 : 1ω7c. On the basis of 16S rRNA gene sequence analysis, the isolated strain was closely affiliated with members of the genus Shimia in the class Alphaproteobacteria, and the 16S rRNA gene sequence similarity of the novel isolate with the type strain of the closest related species, Shimia haliotis WM35(T), was 98.1%. The DNA G+C content of the novel strain was 57.3 mol%. The hybridization values for DNA-DNA relatedness between strain JAMH 011(T) and reference strains belonging to the genus Shimia were less than 9.4 ± 0.7%. Based on differences in taxonomic characteristics, the isolated strain represents a novel species of the genus Shimia, for which the name Shimia sagamensis sp. nov. is proposed. The type strain is JAMH 011(T) ( = JCM 30583(T) = DSM 29734(T)).","corpus_id":38247529,"score":2},{"doc_id":"26338019","title":"Salibacterium halotolerans gen. nov. sp. nov., a novel bacterium isolated from a salt pan, reclassification of Bacillus qingdaonensis as Salibacterium qingdaonense comb. nov. and Bacillus halochares as Salibacterium halochares comb. nov.","abstract":"Two novel Gram-stain-positive, rod shaped, non-motile, non-endospore forming bacterial strains S7T and IB5 were isolated from Khavda, in India. Based on the 16S rRNA gene sequence analysis they were identified as belonging to the class Bacilli, order Bacillales, family Bacillaceae and were most closely related to Bacillus qingdaonensis CGMCC 1.6134T (97.3 %, sequence similarity), Bacillus halochares LMG 24571T (96.9 %), Bacillus salarius KCTC 3912T (95.6 %) and Bacillus aidingensis DSM 18341T (95.3 %). However, these strains shared only 88.2 % 16S rRNA gene sequence similarity with Bacillus subtilis subsp. subtilis DSM 10T, indicating that the strains S7T and IB5 might not be the members of the genus Bacillus. The DNA-DNA relatedness of these strains with B. qingdaonensis CGMCC 1.6134T was 42.9 + 0.8. The cell-wall peptidoglycan of strains S7Tand IB5 contains meso-diaminopimelic acid. Polar lipids include diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, a phospholipid and three unknown lipids. The predominant isoprenoid quinone was MK-7. Anteiso-C15:0 (38.4 %) was the predominant fatty acid. The results of phylogenetic, chemotaxonomic and biochemical tests allowed a clear differentiation of strains S7T and IB5, which represents a novel member of the family, for which the name Salibacterium halotolerans gen. nov. sp. nov. is proposed. The type strain is S7T (= KCTC 33658T = CGMCC 1.15324T). Based on the present study, it is also suggested to transfer B. qingdaonensis and B. halochares to this new genus, as Salibacterium qingdaonense comb. nov. and Salibacterium halochares comb. nov., respectively.","corpus_id":26054899,"score":2},{"doc_id":"26537514","title":"Serratia aquatilis sp. nov., isolated from drinking water systems.","abstract":"A crème-white-pigmented, oxidase-negative bacterium (strain 2015-2462-01T), isolated from a drinking water system was investigated in detail for its taxonomic allocation. Cells of the isolate were rod shaped and stained Gram-negative. A comparison of the 16S rRNA gene sequence of strain 2015-2462-01T with sequences of type strains of most closely related Serratia species showed highest sequence similarities to Serratia fonticola (98.4%), Serratia protaemaculans (97.8%), Serratia liquefaciens and Serratia grimesii (both 97.7%). 16S rRNA gene sequence similarities to all other Serratia species were below 97.4%. Multilocus sequence analyses (MLSA) on the basis of concatenated partial gyrB, rpoB, infB and atpD sequences showed a clear distinction of strain 2015-2462-01T from the closest related type strains of the Serratia species. The fatty acid profile of the strain consisted of the major fatty acids C14:0, C16:0, C16:1 ω7c, C17:0 cyclo, and C18:1 ω7c. DNA-DNA hybridizations between 2015-2462-01T and type strain of Serratia fonticola ATCC 29844T resulted in a similarity values of 27% (reciprocal 20%). This DNA-DNA hybridization result in combination with the MLSA results and the differentiating biochemical properties indicated, that strain 2015-2462-01T represents a novel Serratia species, for which the name Serratia aquatilis sp. nov. (type strain 2015-2462-01T = LMG 29119T = CCM 8626T), is proposed.","corpus_id":29017121,"score":2},{"doc_id":"26541594","title":"Comamonas phosphati sp. nov., a novel bacterium isolated from a phosphate mine.","abstract":"A Gram-negative, facultatively anaerobic, non-pigmented, non-sporulating, rod-shaped bacterial strain WYH 22-41T was isolated from a phosphate mine in Yunnan Province, China. The cells were motile with a single polar flagellum. The 16S rRNA gene of strain WYH 22-41T was phylogenetically related to the corresponding gene of Comamonas terrae DSM 27221T (98.4%), Comamonas odontotermitis LMG 23579T (97.6%) and Comamonas aquatica LMG 2370T (97.4%). DNA-DNA hybridizations of strain WYH 22-41T with these three strains showed relatedness of 33.2%, 20.5% and 27.7%, respectively. The DNA G+C content of strain WYH 22-41T was 62.4 mol%. The predominant respiratory quinone was ubiquinone-8. The major polar lipids were diphosphatidylglycerol, phosphatidylethanolamine, and phosphatidylglycerol. The major fatty acids of strain WYH 22-41T were C16 : 0, C17 : 0 cyclo, summed feature 3 (C16 : 1 ω6c and/or C16 : 1 ω7c) and summed feature 8 (C18 : 1 ω6c and/or C18 : 1 ω7c). On the basis of its phenotypic properties, phylogenetic characteristics, DNA-DNA hybridization, as well as whole-cell fatty acid composition, strain WYH 22-41T represents a novel species of the genus Comamonas, for which the name Comamonas phosphati sp. nov. is proposed. The type strain is WYH 22-41T (=CGMCC 1.12294T = DSM 26017T).","corpus_id":22979125,"score":2},{"doc_id":"26637822","title":"Luteimonas notoginsengisoli sp. nov., isolated from rhizosphere soil.","abstract":"A Gram-staining-negative, yellow pigmented strain, designated as SYP-B804T, was isolated from the rhizospheric soil of Panax notoginseng. The strain was rod shaped with single polar flagellum. The optimum temperature and pH required for growth of the strain was observed at 28-32 °C and 7-8, respectively. The 16S rRNA gene sequence analysis indicated that the strain SYP-B804T showed highest 16S rRNA gene sequence similarity with Luteimonas mephitis DSM 12574T (98.0 %). However, the DNA-DNA relatedness value between them (38.1±0.6 %) was less than the threshold value for the delineation of genomic species. Ubiquinone-8 (Q-8) was the predominant quinone. The major fatty acids were iso-C15:0 and iso-C17:1 ω9c. The major polar lipids of the strain were diphosphatidylglycerol, phosphatidylglycerol and phosphatidylethanolamine. The G+C content of the genomic DNA was 71%. On the basis of phenotypic, chemotaxonomic and molecular characteristics, the strain SYP-B804T merits recognition as a representative of a novel species of the genus Luteimonas, for which the name Luteimonas notoginsengisoli sp. nov. is proposed with SYP-B804T (=KCTC 42211T=JCM 30329T) as the type strain.","corpus_id":12469428,"score":2},{"doc_id":"28853686","title":"Serratia oryzae sp. nov., isolated from rice stems.","abstract":"A novel endophytic bacterium, strain J11-6T, was isolated from rice stems. Its taxonomic position was investigated using a polyphasic approach. The novel strain was Gram-staining-negative, facultatively anaerobic, motile and rod-shaped. Although the results of phylogenetic analysis based on 16S rRNA gene sequences indicated that J11-6T represented a member of the genus Rahnella, multilocus sequence analysis (MLSA) on the basis of concatenated partial atpD, gyrB, rpoB and infB gene sequences showed a clear distinction of J11-6T from the type strains of species of the genus Rahnella but indicated that it lay within the clade of the genus Serratia. The phylogenetically closest species were Serratia fonticola and Serratia aquatilis on the basis of the results of the MLSA phylogenetic analysis. The predominant cellular fatty acids were C16 : 1ω7c (38.7 %) and C16 : 0 (25.0 %). The DNA G+C content was 53.2 mol%. The DNA-DNA relatedness was 17.4 % between J11-6T and Rahnella aquatilis CIP 78.65T, and 29.2 % between J11-6T and S. fonticola LMG 7882T which indicates that this strain represents a novel species of the genus Serratia. Characterization by genotypic and phenotypic analysis indicated that J11-6T (=ACCC 19934T=KCTC 52529T) represents a novel species of the genus Serratia, for which the name Serratia oryzae sp. nov. is proposed.","corpus_id":24881970,"score":2},{"doc_id":"18175699","title":"Actibacter sediminis gen. nov., sp. nov., a marine bacterium of the family Flavobacteriaceae isolated from tidal flat sediment.","abstract":"A yellow-pigmented, Gram-negative, aerobic bacterial strain comprising rod-shaped cells devoid of flagellar and gliding motility, designated strain JC2129(T), was isolated from tidal flat sediment of Dongmak on Ganghwa Island, South Korea. Results from a 16S rRNA gene sequence analysis indicated that the isolate belonged to the family Flavobacteriaceae; the highest level of nucleotide sequence similarity (91.9%) occurred with Polaribacter dokdonensis DSW-5(T). The predominant cellular fatty acids were iso-C(15:0) (19.8%), iso-C(15:1) G (14.0%), iso-C(17:0) 3-OH (13.7%) and iso-C(13:0) (6.4%). Flexirubin-type pigments were absent. The major isoprenoid quinone was MK-6. The DNA G+C content was 43-45 mol%. Data from a polyphasic taxonomy study suggested that the isolate represents a novel genus and species in the family Flavobacteriaceae, for which the name Actibacter sediminis gen. nov., sp. nov. is proposed. The type strain of Actibacter sediminis is JC2129(T) (=KCTC 12704(T) =JCM 14002(T)).","corpus_id":7089875,"score":1},{"doc_id":"19502335","title":"Bacillus solisalsi sp. nov., a halotolerant, alkaliphilic bacterium isolated from soil around a salt lake.","abstract":"A novel Gram-positive, motile, rod-shaped bacterium isolated from a saline soil in China was characterized by a polyphasic taxonomic approach. The strain, designated YC1(T), was halotolerant [tolerating up to 15 % (w/v) NaCl] and alkaliphilic (growing at a broad pH range of 5-13). 16S rRNA gene sequence analysis revealed that the isolate belonged to the genus Bacillus, showing highest similarity to Bacillus macauensis JCM 13285(T) (98.0 %). However, DNA-DNA hybridization indicated low levels of genomic relatedness with B. macauensis JCM 13285(T) (8.5 %). The major isoprenoid quinone was MK-7 and the cellular fatty acid profile consisted of significant amounts of iso-C(15 : 0) (38.6 %) and anteiso-C(15 : 0) (35.9 %). The predominant polar lipids were diphosphatidylglycerol, phosphatidylglycerol and phosphatidylethanolamine. The G+C content of the genomic DNA was 41.8 mol%. On the basis of the polyphasic evidence from this study, strain YC1(T) (=KCTC 13181(T)=CGMCC 1.6854(T)) should be classified as the type strain of a novel species of the genus Bacillus, for which the name Bacillus solisalsi sp. nov. is proposed.","corpus_id":206165166,"score":1},{"doc_id":"19528203","title":"Sediminimonas qiaohouensis gen. nov., sp. nov., a member of the Roseobacter clade in the order Rhodobacterales.","abstract":"Two aerobic bacterial strains, YIM B024(T) and YIM B025, were isolated from a salt mine in Yunnan, south-west China. Both strains showed almost the same physiological properties. Cells were Gram-negative, non-motile, non-spore-forming rods. The novel strains grew at 15-37 degrees C, pH 6.5-9.0 and 0.25-20 % (w/v) NaCl; optimum growth was observed at 28-30 degrees C, pH 7.0-8.5 and 1.5-10 % NaCl. Oxidase, catalase and nitrate-reducing activities were detected. The two strains were closely related to each other with a 16S rRNA gene sequence similarity of 100 %. DNA-DNA hybridization experiments revealed high relatedness values (90+/-0.4 %) between strains YIM B024(T) and YIM B025, which suggested that these two new strains constituted a single species. Phylogenetic analysis based on 16S rRNA gene sequences indicated that the two isolates formed a loose cluster with members of the genus Roseivivax in the Roseobacter clade, but were clearly separated from this genus. The levels of 16S rRNA gene sequence similarity between the two isolates and members of the genus Roseivivax ranged from 92.4 to 93.9 %. The major polar lipids comprised diphosphatidylglycerol, phosphatidylglycerol, phosphatidylcholine and four unknown phospholipids. The major cellular fatty acids were C(18 : 1)omega7c, C(16 : 0), C(18 : 1)omega9c, 11-methyl C(18 : 1)omega7c and C(19 : 0) cyclo omega8c. The sole respiratory quinone was Q-10 and the genomic DNA G+C content was 63.0-64.1 mol%. The distinct phylogenetic position and a combination of phenotypic and chemotaxonomic characteristics supported the proposal of the new isolates as representing a novel species in a new genus, for which the name Sediminimonas qiaohouensis gen. nov., sp. nov. is proposed. The type strain of the type species is YIM B024(T) (=KCTC 22349(T)=CCTCC AA 208033(T)).","corpus_id":5079226,"score":1},{"doc_id":"19542113","title":"Bacillus korlensis sp. nov., a moderately halotolerant bacterium isolated from a sand soil sample in China.","abstract":"A Gram-positive-staining, rod-shaped, motile, spore-forming and moderately halotolerant bacterium, designated ZLC-26(T), was isolated from a sand soil sample collected from Xinjiang Province, China, and was characterized by using a polyphasic taxonomic approach. This isolate grew optimally at 30-37 degrees C and pH 7-8. It grew with 0-8% NaCl (optimum, 0-2 %). Comparative 16S rRNA gene sequence analysis showed that strain ZLC-26(T) was closely related to members of the genus Bacillus, exhibiting the highest 16S rRNA gene sequence similarities to Bacillus nealsonii DSM 15077(T) (97.1 %), B. shackletonii LMG 18435(T) (97.0 %), B. siralis 171544(T) (97.0 %), B. circulans IAM 12462(T) (96.7 %) and B. pocheonensis Gsoil 420(T) (96.7 %). Strain ZLC-26(T) contained MK-7 as the predominant menaquinone. The diagnostic diamino acid in the cell-wall peptidoglycan was meso-diaminopimelic acid. The major cellular fatty acids were iso-C(15 : 0), C(16 : 1)omega11c and anteiso-C(15 : 0). The DNA G+C content was 38.2 mol%. These chemotaxonomic results supported the affiliation of strain ZLC-26(T) to the genus Bacillus. However, low DNA-DNA relatedness values and distinguishing phenotypic characteristics allowed genotypic and phenotypic differentiation of strain ZLC-26(T) from recognized Bacillus species. On the basis of the evidence presented, strain ZLC-26(T) is considered to represent a novel species of the genus Bacillus, for which the name Bacillus korlensis sp. nov. is proposed. The type strain is ZLC-26(T) (=CCTCC AB 207172(T)=NRRL B-51302(T)).","corpus_id":28213615,"score":0}],"string":"[\n {\n \"doc_id\": \"18175681\",\n \"title\": \"Sanguibacter antarcticus sp. nov., isolated from Antarctic sea sand.\",\n \"abstract\": \"A Gram-positive, yellow-pigmented bacterium, strain KOPRI 21702(T), was isolated from sea sand on King George Island, Antarctica. Cells were irregular rods with peritrichous flagella; their optimum growth temperature was 23-26 degrees C. Phylogenetic analysis based on 16S rRNA gene sequences revealed that the Antarctic isolate formed a distinct phyletic line in a clade of the genus Sanguibacter and showed highest sequence similarity (97.7%) to the type strain of Sanguibacter keddieii. The major isoprenoid quinone, predominant cellular fatty acids and DNA G+C content were consistent with placement of the Antarctic isolate in the genus Sanguibacter. Phylogenetic analysis and differences in physiological and biochemical characteristics between strain KOPRI 21702(T) and the four recognized Sanguibacter species indicate that the isolate represents a novel species of this genus. The name Sanguibacter antarcticus sp. nov. (type strain KOPRI 21702(T) =KCTC 13143(T) =JCM 14623(T) =DSM 18966(T)) is proposed for this isolate.\",\n \"corpus_id\": 206183960,\n \"score\": 2\n },\n {\n \"doc_id\": \"18319455\",\n \"title\": \"Burkholderia sediminicola sp. nov., isolated from freshwater sediment.\",\n \"abstract\": \"A Gram-negative, motile and rod-shaped bacterium, designated HU2-65W(T), was isolated from freshwater sediment. The strain possessed ubiquinone 8 as the predominant isoprenoid quinone and contained major amounts of omega7-cis-octadecenoic acid and hexadecanoic acid in its cell envelope, which are properties shared by members of the genus Burkholderia. On the basis of 16S rRNA gene sequence similarity, strain HU2-65W(T) was most closely related to the type strain of Burkholderia xenovorans (98.4 %). The DNA G+C content of strain HU2-65W(T) was 61.2 mol%, and DNA-DNA relatedness values to type strains of closely related species were found to be much lower than 70 %, indicating that the strain represents a separate genomic species within the genus Burkholderia. Strain HU2-65W(T) was also differentiated from other species of the genus by physiological and biochemical characteristics. Consequently, strain HU2-65W(T) is considered to represent a single, novel species of the genus Burkholderia, for which the name Burkholderia sediminicola sp. nov. is proposed, with the type strain HU2-65W(T) (=KCTC 22086(T) =LMG 24238(T)).\",\n \"corpus_id\": 23738894,\n \"score\": 2\n },\n {\n \"doc_id\": \"18319480\",\n \"title\": \"Labrys portucalensis sp. nov., a fluorobenzene-degrading bacterium isolated from an industrially contaminated sediment in northern Portugal.\",\n \"abstract\": \"A detailed classification of a novel bacterial strain, designated F11(T), capable of degrading fluorobenzene as a sole carbon and energy source, was performed by using a polyphasic approach. This Gram-negative, rod-shaped, non-motile, non-spore-forming, aerobic bacterium was isolated from a sediment sample collected from an industrially contaminated site in northern Portugal. The predominant whole-cell fatty acids were C(19 : 0) cyclo omega8c, C(16 : 0), C(18 : 1)omega7c, C(18 : 0), C(18 : 0) 3-OH and C(16 : 0) 3-OH. The G+C content of the DNA was 62.9 mol% and the major respiratory quinone was ubiquinone 10 (UQ-10). 16S rRNA gene sequence analysis revealed that strain F11(T) was a member of the class Alphaproteobacteria and was phylogenetically related to the genus Labrys, having sequence similarities of 95.6 and 93.1 % to the type strains of Labrys monachus and Labrys methylaminiphilus, respectively. DNA-DNA hybridization experiments revealed levels of relatedness of <70 % between strain F11(T) and the type strains of L. monachus and L. methylaminiphilus (38.6 and 34.1 %, respectively), justifying the classification of strain F11(T) as representing a novel species of the genus Labrys. The name Labrys portucalensis sp. nov. is proposed for this organism. The type strain is F11(T) (=LMG 23412(T)=DSM 17916(T)).\",\n \"corpus_id\": 14436728,\n \"score\": 2\n },\n {\n \"doc_id\": \"18398165\",\n \"title\": \"Flavobacterium anhuiense sp. nov., isolated from field soil.\",\n \"abstract\": \"A novel strain, D3T, isolated from a field-soil sample obtained from Anhui Province, PR China, was characterized taxonomically by using a polyphasic approach. The cells were Gram-negative, yellow-pigmented rods devoid of flagella, but showing gliding motility. The organism was able to grow at 5-37 degrees C and at pH 4.0-10.0. A comparative 16S rRNA gene sequence analysis indicated that strain D3T is a member of the genus Flavobacterium, sharing highest sequence similarity with the type strain of Flavobacterium defluvii (96.7 %). The major isoprenoid quinone was MK-6 and the predominant fatty acids were iso-C15 : 0, summed feature 3 (C16 : 1 omega 7c and/or iso-C15 : 0 2-OH) and C16 : 0. The DNA G+C content was 31.4 mol%. On the basis of phylogenetic and phenotypic data, strain D3T represents a novel species within the genus Flavobacterium, for which the name Flavobacterium anhuiense sp. nov. is proposed. The type strain is D3T (=KCTC 22128T = CGMCC 1.6859T).\",\n \"corpus_id\": 9876913,\n \"score\": 2\n },\n {\n \"doc_id\": \"18410943\",\n \"title\": \"Heterorhabditidoides chongmingensis gen. nov., sp. nov. (Rhabditida: Rhabditidae), a novel member of the entomopathogenic nematodes.\",\n \"abstract\": \"During a recent soil sample survey in Eastern China, a new entomopathogenic nematode species, collected from the Chongming Islands in the southern-eastern area of Shanghai, was discovered. Morphological characteristics of different developmental stages of the nematode combined with molecular data showed that this nematode is a new genus of Rhabditidae, and described as Heterorhabditidoides chongmingensis gen. nov., sp. nov., for that it shares more morphological characteristics with heterorhabditids than with steinernematids. For males, the papillae formula of bursa is 1, 2, 3, 3, with constant papillae number in the terminal group, stoma tubular-shaped and about 1.5 head width; cheilorhabdions cuticularized, esophageal collar present and long, median bulb present. For infective juveniles, EP=90 (80-105)microm, ES=104 (92-120)microm, tail length=111 (89-159)microm, and a=19.1 (15-21). The percentages of the nucleotides A, T, C and G in the ITS1 regions of the new species are significantly different from those of heterorhabditids and other rhabditids. Molecular phylogenetic trees based on 18S rDNA and the internal transcribed spacer (ITS) sequences data revealed that the new entomopathogenic nematode species forms a monophyletic group, which is a sister group of the clade comprised of some genera of Rhabditidae.\",\n \"corpus_id\": 9633949,\n \"score\": 2\n },\n {\n \"doc_id\": \"18523187\",\n \"title\": \"Shinella kummerowiae sp. nov., a symbiotic bacterium isolated from root nodules of the herbal legume Kummerowia stipulacea.\",\n \"abstract\": \"Bacterial strain CCBAU 25048(T) was isolated from root nodules of Kummerowia stipulacea grown in Shandong province of China. Cells of the strain were Gram-negative, strictly aerobic, non-spore-forming, motile short rods. Phylogeny of 16S rRNA gene sequences revealed that the strain belonged to the genus Shinella, a member of family Rhizobiaceae. Its closest phylogenetic relatives were Shinella granuli Ch06(T) and Shinella zoogloeoides IAM 12669(T), respectively showing 98.3 and 98.9 % 16S rRNA gene sequence similarity. Strain CCBAU 25048(T) had DNA-DNA relatedness of 43.5 and 34.8 %, respectively, with S. zoogloeoides JCM 20728(T) and S. granuli JCM 13254(T). In addition, in TP-RAPD analysis, different patterns were obtained for these three strains and some rhizobial strains. The nifH, nodC and nodD sequences of CCBAU 25048(T) were identical or very similar to those of bean-nodulating Rhizobium tropici strains. Several phenotypic characteristics, including the use of citrate and d-ribose as carbon sources and growth at pH 11.0, as well as the fatty acid composition, could differentiate CCBAU 25048(T) from the two defined Shinella species. Therefore, a novel species Shinella kummerowiae sp. nov. is proposed, with strain CCBAU 25048(T) (=JCM 14778(T) =LMG 24136(T)) as the type strain.\",\n \"corpus_id\": 9720510,\n \"score\": 2\n },\n {\n \"doc_id\": \"18523189\",\n \"title\": \"Massilia aerilata sp. nov., isolated from an air sample.\",\n \"abstract\": \"A novel aerobic, Gram-negative, rod-shaped, motile bacterium, designated strain 5516S-11(T), was isolated from air samples collected in the Suwon region of the Republic of Korea. Analysis of the 16S rRNA gene sequence indicated that the organism belongs to the genus Massilia; the highest sequence similarity (97.2 %) was found with respect to Massilia aurea DSM 18055(T). Cells of strain 5516S-11(T) contained ubiquinone Q-8 as the predominant isoprenoid quinone and possessed summed feature 3 (C(16 : 1)omega7c/iso-C(15 : 0) 2-OH; 35.2 %), C(16 : 0) (30.6 %) and C(18 : 1)omega7c (11.7 %) as the major fatty acids. DNA-DNA hybridization revealed 32 % relatedness between strain 5516S-11(T) and M. aurea DSM 18055(T). The G+C content of the DNA of strain 5516S-11(T) was 68.9 mol%. It is clear from the genotypic and phenotypic data presented that strain 5516S-11(T) represents a novel species of the genus Massilia, for which the name Massilia aerilata sp. nov. is proposed. The type strain is 5516S-11(T) (=KACC 12505(T) =DSM 19289(T)).\",\n \"corpus_id\": 19979053,\n \"score\": 2\n },\n {\n \"doc_id\": \"18523192\",\n \"title\": \"Cronobacter gen. nov., a new genus to accommodate the biogroups of Enterobacter sakazakii, and proposal of Cronobacter sakazakii gen. nov., comb. nov., Cronobacter malonaticus sp. nov., Cronobacter turicensis sp. nov., Cronobacter muytjensii sp. nov., Cronobacter dublinensis sp. nov., Cronobacter genomospecies 1, and of three subspecies, Cronobacter dublinensis subsp. dublinensis subsp. nov., Cronobacter dublinensis subsp. lausannensis subsp. nov. and Cronobacter dublinensis subsp. lactaridi subsp. nov.\",\n \"abstract\": \"[Enterobacter] sakazakii is an opportunistic pathogen that can cause infections in neonates. This study further clarifies the taxonomy of isolates described as [E.] sakazakii and completes the formal description of the proposed reclassification of these organisms as novel species and subspecies within a proposed novel genus, Cronobacter gen. nov. [E.] sakazakii was first defined in 1980, however recent polyphasic taxonomic analysis has determined that this group of organisms consists of several genomospecies. In this study, the phenotypic descriptions of the proposed novel species are expanded using Biotype 100 and Biolog Phenotype MicroArray data. Further DNA-DNA hybridization experiments showed that malonate-positive strains within the [E.] sakazakii genomospecies represent a distinct species, not a subspecies. DNA-DNA hybridizations also determined that phenotypically different strains within the proposed species, Cronobacter dublinensis sp. nov., belong to the same species and can be considered as novel subspecies. Based on these analyses, the following alternative classifications are proposed: Cronobacter sakazakii gen. nov., comb. nov. [type strain ATCC 29544(T) (=NCTC 11467(T))]; Cronobacter malonaticus sp. nov. [type strain CDC 1058-77(T) (=LMG 23826(T)=DSM 18702(T))]; Cronobacter turicensis sp. nov. [type strain z3032(T) (=LMG 23827(T)=DSM 18703(T))]; Cronobacter muytjensii sp. nov. [type strain ATCC 51329(T) (=CIP 103581(T))]; Cronobacter dublinensis sp. nov. [type strain DES187(T) (=LMG 23823(T)=DSM 18705(T))]; Cronobacter dublinensis subsp. dublinensis subsp. nov. [type strain DES187(T) (=LMG 23823(T)=DSM 18705(T))]; Cronobacter dublinensis subsp. lausannensis subsp. nov. [type strain E515(T) (=LMG 23824=DSM 18706(T))], and Cronobacter dublinensis subsp. lactaridi subsp. nov. [type strain E464(T) (=LMG 23825(T)=DSM 18707(T))].\",\n \"corpus_id\": 6609941,\n \"score\": 2\n },\n {\n \"doc_id\": \"18974964\",\n \"title\": \"Aliihoeflea aestuarii gen. nov., sp. nov., a novel bacterium isolated from tidal flat sediment.\",\n \"abstract\": \"A novel Gram-negative and rod-shaped bacterium, designated N8(T), was isolated from tidal flat sediment. Phylogenetic analysis based on 16S rRNA gene sequences showed that N8(T) strain is associated with the family Phyllobacteriaceae: two uncultured clones (98.4 and 99.8% 16S rRNA gene sequence similarity) and the genus Mesorhizobium (< or =97.0%). The novel strain formed a separate clade with uncultured clones in the phylogenetic tree based on 16S rRNA gene sequences. Cellular fatty acid profiles predominately comprised C(18:1) omega7c and C(19:0) cyclo omega8c. The major isoprenoid quinone is ubiquinone-10 and genomic DNA G+C content is 53.4 mol%. The polyphasic taxonomic study indicates that the novel strain N8(T) represents a novel species of the new genus in the family Phyllobacteriaceae, named Aliihoeflea aestuarii. The type strain is N8(T) (= KCTC 22052(T)= JCM 15118(T)= DSM 19536(T)).\",\n \"corpus_id\": 11546957,\n \"score\": 2\n },\n {\n \"doc_id\": \"18984696\",\n \"title\": \"Photorhabdus temperata subsp. cinerea subsp. nov., isolated from Heterorhabditis nematodes.\",\n \"abstract\": \"During the characterization of symbiotic bacteria of Hungarian entomopathogenic nematode isolates, a number of bacteria (including strain 3107(T)) isolated from Heterorhabditis downesi and Heterorhabditis megidis showed only moderate 16S rRNA gene sequence similarity to the type strains of all described Photorhabdus species and subspecies. On the basis of the 16S rRNA gene sequence, the phylogenetic relationships of these isolates were uncertain, because of the low bootstrap values. Using gyrB sequences for phylogenetic analysis, these isolates were shown to be part of the species Photorhabdus temperata, with clear separation from both Palaearctic and American strains (phylogenetic distances are 6.9 and 7.9 %, respectively). Physiological properties and carbon-source utilization profiles supported the phylogenetic position of these strains; therefore, a novel subspecies, Photorhabdus temperata subsp. cinerea subsp. nov. is proposed, with the type strain 3107(T) (=DSM 19724(T) =NCAIM B 02271(T)).\",\n \"corpus_id\": 37286848,\n \"score\": 2\n },\n {\n \"doc_id\": \"18984707\",\n \"title\": \"Paenibacillus taichungensis sp. nov., from soil in Taiwan.\",\n \"abstract\": \"Among a large collection of Taiwanese soil isolates, a novel Gram-variable, rod-shaped, motile, endospore-forming bacterial strain, strain V10537(T), was subjected to a polyphasic study including 16S rRNA and gyrB gene sequence analysis, DNA-DNA hybridization experiments, cell wall peptidoglycan type, cellular fatty acid composition analysis and comparative phenotypic characterization. 16S rRNA gene sequence analysis indicated that the organism belonged to the genus Paenibacillus. Strain V10537(T) possessed meso-diaminopimelic acid as the diagnostic diamino acid of the peptidoglycan. It contained menaquinone MK-7 as the predominant isoprenoid quinone and anteiso-C(15 : 0) (53.6 %) and C(16 : 0) (19.0 %) as the major fatty acids. Phylogenetically, the most closely related species to strain V10537(T) were Paenibacillus pabuli, Paenibacillus xylanilyticus, Paenibacillus amylolyticus, Paenibacillus barcinonensis and Paenibacillus illinoisensis, with 16S rRNA gene sequence similarities of 99.5, 98.8, 98.3, 98.2 and 98.1 % to the respective type strains. The gyrB gene sequence similarities between strain V10537(T) and these strains were 76.9-85.0 %. DNA-DNA hybridization experiments showed levels of relatedness of 8.5-45.6 % between strain V10537(T) and these strains. The DNA G+C content of strain V10537(T) was 46.7 mol%. Strain V10537(T) was clearly distinguishable from other Paenibacillus species and thus represents a novel species of the genus Paenibacillus, for which the name Paenibacillus taichungensis sp. nov. is proposed. The type strain is V10537(T) (=BCRC 17757(T) =DSM 19942(T)).\",\n \"corpus_id\": 206185903,\n \"score\": 2\n },\n {\n \"doc_id\": \"19244422\",\n \"title\": \"Dyella ginsengisoli sp. nov., isolated from soil of a ginseng field in South Korea.\",\n \"abstract\": \"A Gram-negative, aerobic, yellow-pigmented, non-spore-forming, motile, rod-shaped bacterium, designated strain Gsoil 3046(T), was isolated from soil from a ginseng field in Pocheon Province, South Korea, and was characterized taxonomically by using a polyphasic approach. A comparative analysis of 16S rRNA gene sequences revealed that strain Gsoil 3046(T) belongs to the family Xanthomonadaceae in the Gammaproteobacteria. The greatest sequence similarity was found with respect to Dyella koreensis KCTC 12359(T) (97.7 %), Dyella japonica IAM 15069(T) (97.4 %), Frateuria aurantia DSM 6220(T) (96.7 %), Fulvimonas soli LMG 19981(T) (96.2 %) and Luteibacter rhizovicinus DSM 16549(T) (96.0 %). The phylogenetic distances from other recognized species within the family Xanthomonadaceae, including Dyella yeojuensis KACC 11405(T), were greater than 4.0 % (i.e. the sequence similarities were less than 96.0 %). DNA-DNA hybridization experiments showed that the levels of DNA-DNA relatedness between strain Gsoil 3046(T) and its phylogenetically closest neighbours were below 25 %. The G+C content of the genomic DNA was 66.6 mol%. In addition, the presence of ubiquinone Q-8 as the predominant respiratory quinone, iso-C(17 : 1)omega9c, iso-C(16 : 0), iso-C(15 : 0) and iso-C(17 : 0) as the major cellular fatty acids and iso-C(13 : 0) 3-OH and iso-C(11 : 0) 3-OH as the major hydroxy fatty acids supported the affiliation of strain Gsoil 3046(T) to the genus Dyella. On the basis of its phenotypic properties and phylogenetic distinctiveness, strain Gsoil 3046(T) represents a novel species in the genus Dyella, for which the name Dyella ginsengisoli sp. nov. is proposed. The type strain is Gsoil 3046(T) (=KCTC 12599(T)=DSM 18387(T)).\",\n \"corpus_id\": 23095888,\n \"score\": 2\n },\n {\n \"doc_id\": \"19329624\",\n \"title\": \"Salinivibrio siamensis sp. nov., from fermented fish (pla-ra) in Thailand.\",\n \"abstract\": \"A Gram-negative, facultatively anaerobic, moderately halophilic bacterium, strain ND1-1(T), was isolated from fermented fish (pla-ra) in Thailand. The cells were curved rods, motile and non-endospore-forming. The novel strain grew optimally at 37 degrees C, at pH 8 and in the presence of 9-10 % (w/v) NaCl. The predominant respiratory lipoquinone was Q-8. The major cellular fatty acids were C(16 : 0) and C(12 : 0). Polar lipid analysis revealed the presence of phosphatidylethanolamine, phosphatidylglycerol and diphosphatidylglycerol. The DNA G+C content was 49.0 mol%. Comparative 16S rRNA gene sequence analyses indicated that strain ND1-1(T) was closely related to Salinivibrio costicola, which comprises three subspecies, and Salinivibrio proteolyticus with gene sequence similarities of 98.3-98.6 %. Strain ND1-1(T) showed low levels of DNA-DNA relatedness with S. costicola subsp. costicola JCM 15095(T) (33.2 %), S. costicola subsp. alcaliphilus DSM 16359(T) (38.4 %), S. costicola subsp. vallismortis JCM 15096(T) (59.7 %), and S. proteolyticus AF-2004(T) (42.1 %). On the basis of the physiological and biochemical characteristics and the molecular data presented, strain ND1-1(T) should be classified as a novel species of the genus Salinivibrio for which the name Salinivibrio siamensis sp. nov. is proposed. The type strain is ND1-1(T) (=JCM 14472(T)=PCU 301(T)=TISTR 1810(T)).\",\n \"corpus_id\": 2373959,\n \"score\": 2\n },\n {\n \"doc_id\": \"19406774\",\n \"title\": \"Saccharibacillus kuerlensis sp. nov., isolated from a desert soil.\",\n \"abstract\": \"A taxonomic study was performed on strain HR1(T), which was isolated from a desert soil sample collected from Xinjiang Province (China). Cells were aerobic, Gram-positive-staining, pink-pigmented, sporulating rods with a single lateral flagellum. The organism can grow at 15-42 degrees C and pH 5.0-10.0, optimally at 30-37 degrees C and pH 6.0-8.0. Growth is inhibited by 6 % NaCl. Analysis of almost-complete 16S rRNA gene sequence revealed that the isolate represents a distinct taxon within the genus Saccharibacillus; Saccharibacillus sacchari LMG 24085(T) was the nearest relative (97.9 % sequence similarity). DNA-DNA hybridization showed 29.6 % genetic relatedness between strain HR1(T) and S. sacchari LMG 24085(T). The major isoprenoid quinone was MK-7 and the predominant fatty acid was anteiso-C(15 : 0) (50.3 %). The G+C content of the DNA was 50.5 mol%. Therefore, based on phenotypic criteria and the phylogenetic position, strain HR1(T) belongs to a previously unidentified species of the genus Saccharibacillus, for which the name Saccharibacillus kuerlensis sp. nov. is proposed. The type strain is HR1(T) (=KCTC 13182(T) =JCM 14865(T) =CGMCC 1.6964(T)).\",\n \"corpus_id\": 39604488,\n \"score\": 2\n },\n {\n \"doc_id\": \"19406814\",\n \"title\": \"Marinobacterium nitratireducens sp. nov. and Marinobacterium sediminicola sp. nov., isolated from marine sediment.\",\n \"abstract\": \"Two strains, CN44(T) and CN47(T), isolated from marine sediment of the East China Sea, were characterized by using a polyphasic approach. The isolates were Gram-negative, strictly aerobic, non-spore-forming rods. The chemotaxonomic characteristics of these isolates included the presence of C(18 : 1)omega7c, C(16 : 0), iso-C(15 : 0) 2-OH and/or C(16 : 1)omega7c and C(10 : 0) 3-OH as the major cellular fatty acids and Q-8 as the predominant ubiquinone. The DNA G+C contents of strains CN44(T) and CN47(T) were 62.5 and 56.3 mol%, respectively. Phylogenetic analyses based on 16S rRNA gene sequences revealed that strain CN44(T) was related to members of the genus Marinobacterium. The most closely related described organism was the type strain of Marinobacterium rhizophilum (95.3 % sequence similarity). Strain CN47(T) showed the highest sequence similarity to the type strain of Marinobacterium stanieri (97.8 %) and <97 % similarity to other type strains of described Marinobacterium species. The level of DNA-DNA relatedness between strain CN47(T) and M. stanieri DSM 7027(T) was 46 %. On the basis of phenotypic and genotypic properties, strains CN44(T) and CN47(T) represent two novel species within the genus Marinobacterium, for which the names Marinobacterium nitratireducens sp. nov. (type strain, CN44(T) =CGMCC 1.7286(T) =JCM 15523(T)) and Marinobacterium sediminicola sp. nov. (type strain, CN47(T) =CGMCC 1.7287(T) =JCM 15524(T)) are proposed.\",\n \"corpus_id\": 35719126,\n \"score\": 2\n },\n {\n \"doc_id\": \"19502301\",\n \"title\": \"Marispirillum indicum gen. nov., sp. nov., isolated from a deep-sea environment.\",\n \"abstract\": \"A taxonomic study was carried out on strain B142(T), which was isolated from a crude-oil-degrading microbial consortium via enrichment with deep water from the Indian Ocean. Cells of the isolate were Gram-negative, oxidase-negative, catalase-positive, helical in shape, motile by means of polar flagella (three per cell) and moderately halophilic. Growth was observed at salinities of 0.5-12 % and at temperatures of 10-41 degrees C. The micro-organism was capable of denitrification, but was unable to degrade Tween 80 or gelatin. The predominant fatty acids were C(16 : 1)omega7c and/or iso-C(15 :0 )2-OH (6.4 %), C(16 : 0) (15.7 %), C(18 : 1)omega7c (45 %), C(18 : 0) (6.8 %) and C(19 : 0)omega8c cyclo (6.7 %). The G+C content of the chromosomal DNA was 67.3 mol%. Comparisons of 16S rRNA gene sequences showed that strain B142(T) was most closely related to the type strains of two Insolitispirillum peregrinum subspecies (93.0-93.1 % sequence similarity), two Novispirillum itersonii subspecies (92.8-92.9 %) and Caenispirillum bisanense (91.7 %); sequence similarities with respect to other taxa were below 90.5 %. Phylogenetic analyses based on 16S rRNA gene sequences showed that strain B142(T) formed a distinct evolutionary lineage within the family Rhodospirillaceae. Strain B142(T) was distinguishable from phylogenetically related genera with regard to several phenotypic properties. On the basis of phenotypic and phylogenetic data, therefore, strain B142(T) represents a novel genus and species, for which the name Marispirillum indicum gen. nov., sp. nov. is proposed. The type strain is B142(T) (=CCTCC AB 208225(T)=LMG 24627(T)=MCCC 1A01235(T)).\",\n \"corpus_id\": 22261987,\n \"score\": 2\n },\n {\n \"doc_id\": \"19502309\",\n \"title\": \"Pseudidiomarina donghaiensis sp. nov. and Pseudidiomarina maritima sp. nov., isolated from the East China Sea.\",\n \"abstract\": \"Two Gram-negative, aerobic, motile, rod-shaped bacteria, designated strains 908033(T) and 908087(T), were isolated from a seawater sample collected from the East China Sea. Chemotaxonomic characteristics of the two isolates included the presence of iso-C(15 : 0), iso-C(17 : 0) and iso-C(17 : 1)omega9c as the major cellular fatty acids and Q-8 as the predominant ubiquinone. The genomic DNA G+C contents of strains 908033(T) and 908087(T) were 45.5 and 45.2 mol%, respectively. Phylogenetic analyses based on 16S rRNA gene sequences revealed that the new isolates were related to members of the genus Pseudidiomarina, showing levels of similarity of 95.8-96.6 % with the type strains of recognized species of the genus. The results of DNA-DNA hybridization experiments among these two isolates and Pseudidiomarina sediminum CICC 10319(T), in combination with chemotaxonomic and phenotypic data, demonstrated that the new isolates represent two novel species of the genus Pseudidiomarina, for which the names Pseudidiomarina donghaiensis sp. nov. (type strain 908033(T)=CGMCC 1.7284(T)=JCM 15533(T)) and Pseudidiomarina maritima sp. nov. (type strain 908087(T)=CGMCC 1.7285(T)=JCM 15534(T)) are proposed.\",\n \"corpus_id\": 1703729,\n \"score\": 2\n },\n {\n \"doc_id\": \"19502317\",\n \"title\": \"Description of Paenisporosarcina quisquiliarum gen. nov., sp. nov., and reclassification of Sporosarcina macmurdoensis Reddy et al. 2003 as Paenisporosarcina macmurdoensis comb. nov.\",\n \"abstract\": \"In the course of a study of the prokaryotic diversity of a landfill site in Chandigarh, India, a strain designated SK 55(T) was isolated and characterized using a polyphasic approach. Its 16S rRNA gene sequence showed closest similarity (98.3 %) to that of Sporosarcina macmurdoensis CMS 21w(T). The sequence similarity to strains of other hitherto described species of Sporosarcina was less than 95.5 %. Strain SK 55(T) contains peptidoglycan of the A4alpha type (l-Lys-d-Asp), MK-8 and MK-7 as the major menaquinones and iso-C(15 : 0) as the major fatty acid. Strain SK 55(T), Sporosarcina macmurdoensis and Sporosarcina ureae, the type species of the genus, had some polar lipids in common (diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, a phospholipid and an unknown lipid). However, an aminolipid, an aminophospholipid and an unknown lipid found in the former two organisms are similar, though not identical, but quite different from the profile of S. ureae. The genomic DNA G+C contents of strain SK 55(T) (46.0 mol%) and S. macmurdoensis CMS 21w(T) (44.0 mol%) are higher than those reported for the majority of species of Sporosarcina (36-42 mol%). As revealed by 16S rRNA gene sequence analysis, strain SK 55(T) and S. macmurdoensis CMS 21w(T) form a clade which is distinct from the clade occupied by other species of Sporosarcina. On the basis of phenotypic characteristics including chemotaxonomic data and analysis of the 16S rRNA gene sequence, we conclude that strain SK 55(T) should be considered as a member of a novel genus and species, for which the name Paenisporosarcina quisquiliarum gen. nov., sp. nov. is proposed. The type strain of Paenisporosarcina quisquiliarum is SK 55(T) (=MTCC7604(T) =JCM 14041(T)). S. macmurdoensis CMS 21w(T) shows more similarity in its 16S rRNA gene sequence (98.3 %), DNA G+C content and polar lipid profile to strain SK 55(T) than to S. ureae DSM 2281(T). Phylogenetically, it forms a coherent cluster with strain SK 55(T) which is separate from the Sporosarcina cluster. Moreover, iso-C(15 : 0), anteiso-C(15 : 0) and C(16 : 1)omega7c alcohol are the three major fatty acids in both S. macmurdoensis CMS 21w(T) and SK 55(T). All these data suggest that S. macmurdoensis should be a member of the genus Paenisporosarcina. However, S. macmurdoensis can be differentiated from SK 55(T) in several physiological and biochemical characteristics, especially in the patterns of oxidation and acid production from carbohydrates. The genomic relatedness of S. macmurdoensis CMS 21w(T) and strain SK 55(T) was also very low (18.0 %). It is therefore logical to transfer Sporosarcina macmurdoensis to the newly created genus as Paenisporosarcina macmurdoensis comb. nov. The type strain is CMS 21w(T) (=MTCC4670(T) =DSM 15428(T)).\",\n \"corpus_id\": 9277832,\n \"score\": 2\n },\n {\n \"doc_id\": \"19542119\",\n \"title\": \"Marinobacter lacisalsi sp. nov., a moderately halophilic bacterium isolated from the saline-wetland wildfowl reserve Fuente de Piedra in southern Spain.\",\n \"abstract\": \"A Gram-negative, non-spore-forming, motile, moderately halophilic, aerobic, rod-shaped bacterium, designated strain FP2.5(T), was isolated from the inland hypersaline lake Fuente de Piedra, a saline-wetland wildfowl reserve located in the province of Málaga in southern Spain. Strain FP2.5(T) was subjected to a polyphasic taxonomic study. It produced colonies with a light-yellow pigment. Strain FP2.5(T) grew at salinities of 3-15 % (w/v) and at temperatures of 20-40 degrees C. The pH range for growth was 5-9. Strain FP2.5(T) was able to utilize various organic acids as sole carbon and energy source. Its major fatty acids were C(16 : 0), C(18 : 1)omega9c and C(16 : 1)omega9c. The DNA G+C content was 58.6 mol%. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain FP2.5(T) appeared to be a member of the genus Marinobacter and clustered closely with the type strains of Marinobacter segnicrescens, Marinobacter bryozoorum and Marinobacter gudaonensis (levels of 16S rRNA gene sequence similarity of 98.1, 97.4 and 97.2 %, respectively). However, DNA-DNA relatedness between the new isolate and the type strains of its closest related Marinobacter species was low; levels of DNA-DNA relatedness between strain FP2.5(T) and M. segnicrescens LMG 23928(T), M. bryozoorum DSM 15401(T) and M. gudaonensis DSM 18066(T) were 36.3, 32.1 and 24.9 %, respectively. On the basis of phenotypic characteristics, phylogenetic analysis and DNA-DNA relatedness data, strain FP2.5(T) is considered to represent a novel species of the genus Marinobacter, for which the name Marinobacter lacisalsi sp. nov. is proposed. The type strain is FP2.5(T) (=CECT 7297(T)=LMG 24237(T)).\",\n \"corpus_id\": 21001674,\n \"score\": 2\n },\n {\n \"doc_id\": \"19542120\",\n \"title\": \"Flavobacterium chungangense sp. nov., isolated from a freshwater lake.\",\n \"abstract\": \"A yellow-pigmented, rod-shaped, Gram-staining-negative, aerobic bacterial strain, designated CJ7(T), was isolated from a freshwater lake at Chung-Ang University in Anseong, South Korea. Results from 16S rRNA gene sequence analysis revealed that the isolate was phylogenetically affiliated with members of the genus Flavobacterium. Strain CJ7(T) showed sequence similarity values of 91.5-98.0 % to the type strains of recognized Flavobacterium species. The DNA-DNA relatedness between strain CJ7(T) and Flavobacterium hercynium DSM 18292(T), which showed the highest 16S rRNA gene sequence similarity, was 25.4 %. The predominant cellular fatty acids were iso-C(15 : 0) (18.3 %), summed feature 3 (comprising iso-C(15 : 0) 2-OH and/or C(16 : 1)omega7c) (16.1 %), iso-C(17 : 0) 3-OH (8.9 %), iso-C(15 : 0) 3-OH (7.2 %), iso-C(17 : 1)omega9c (6.1 %) and iso-C(15 : 1) (5.9 %). Flexirubin-type pigments were absent. The major isoprenoid quinone was menaquinone-6. The DNA G+C content was 34.5 mol%. The results obtained from this study, with a polyphasic taxonomic approach, suggested that strain CJ7(T) represents a novel species of the genus Flavobacterium for which the name Flavobacterium chungangense sp. nov. is proposed. The type strain is CJ7(T) (=KACC 13353(T)=JCM 15651(T)).\",\n \"corpus_id\": 23608270,\n \"score\": 2\n },\n {\n \"doc_id\": \"19542122\",\n \"title\": \"Paenibacillus tundrae sp. nov. and Paenibacillus xylanexedens sp. nov., psychrotolerant, xylan-degrading bacteria from Alaskan tundra.\",\n \"abstract\": \"Eight psychrotolerant, xylan-degrading strains of bacteria that were catalase-positive, oxidase-negative and able to reduce nitrate to nitrite were isolated from soil beneath moist non-acidic and acidic tundra in northern Alaska. The DNA G+C contents for the strains ranged from 46.4-50.3 mol%. Phylogenetic analysis based on 16S rRNA gene sequences revealed that each strain belonged to the genus Paenibacillus. The highest level of 16S rRNA gene similarity was found between the eight strains and Paenibacillus amylolyticus NRRL NRS-290(T) (98.9-99.1 %). However, despite relatively high 16S rRNA gene similarity, DNA-DNA hybridization, repetitive elements genotyping and phenotypic analysis revealed that at least two of the strains differed from P. amylolyticus NRRL NRS-290(T). DNA-DNA hybridization values between strain A10b(T) and P. amylolyticus NRRL NRS-290(T) (4.3 %), between strain B22a(T) and P. amylolyticus NRRL NRS-290(T) (48.8 %) and between strain A10b(T) and strain B22a(T) (11.0 %) were below those recommended by the ad hoc committee for those belonging to the same species. Significant phenotypic features that differentiate these novel strains from P. amylolyticus included their inability to utilize l-arabinose and ability to utilize glycogen as sole carbon sources. Unlike strains 1B4a and B22a(T), strains A6a and A10b(T) produced ethanol as an end product of glucose fermentation, utilized acetic acid and 2,3-butanediol and did not utilize d-gluconic acid. MK-7 was the major isoprenoid quinone and anteiso-C(15 : 0) was the most abundant fatty acid for strains A10b(T) and B22a(T). On the basis of these results, strains A10b(T) and B22a(T) are each considered to represent a novel species of the genus Paenibacillus, for which the names Paenibacillus tundrae sp. nov. and Paenibacillus xylanexedens sp. nov. are proposed, respectively. The type strain of Paenibacillus tundrae sp. nov. is A10b(T) (=NRRL B-51094(T)=DSM 21291(T)). The type strain of Paenibacillus xylanexedens sp. nov. is B22a(T) (=NRRL B-51090(T)=DSM 21292(T)).\",\n \"corpus_id\": 206165968,\n \"score\": 2\n },\n {\n \"doc_id\": \"19542125\",\n \"title\": \"Massilia niabensis sp. nov. and Massilia niastensis sp. nov., isolated from air samples.\",\n \"abstract\": \"Two bacterial isolates, designated strains 5420S-26(T) and 5516S-1(T), were recovered from air samples collected in Suwon, Korea. Cells of both strains were aerobic, Gram-negative, motile rods. Phylogenetically, these strains were positioned within the radius of the genus Massilia. 16S rRNA gene sequence analysis showed that the strains shared 97.3 % sequence similarity and had sequence similarities of 94.9-98.1 % with respect to type strains of species belonging to the genus Massilia. In DNA-DNA hybridization tests, the two strains showed <39 % relatedness with respect to strains of closely related species of the genus Massilia and 27 % relatedness to each other. Both strains contained Q-8 as the predominant isoprenoid quinone and possessed summed feature 3 (comprising C(16 : 1)omega7c and/or iso-C(15 : 0) 2-OH) as the major fatty acid. Strain 5516S-1(T) was found to contain the fatty acid C(20 : 0) (in small amounts), a feature that served to distinguish it from both 5420S-26(T) and recognized members of the genus Massilia. The DNA G+C contents of 5420S-26(T) and 5516S-1(T) were 67.8 and 66.6 mol%, respectively. Phylogenetic, phenotypic and chemotaxonomic data accumulated in this study revealed that 5420S-26(T) and 5516S-1(T) represent novel species of the genus Massilia, for which the names Massilia niabensis sp. nov. (type strain 5420S-26(T) =KACC 12632(T) =DSM 21312(T)) and Massilia niastensis sp. nov. (type strain 5516S-1(T) =KACC 12599(T) =DSM 21313(T)) are proposed, respectively.\",\n \"corpus_id\": 26995066,\n \"score\": 2\n },\n {\n \"doc_id\": \"19542127\",\n \"title\": \"Tenacibaculum crassostreae sp. nov., isolated from the Pacific oyster, Crassostrea gigas.\",\n \"abstract\": \"A rod-shaped, yellow-pigmented, aerobic, Gram-negative bacterium, designated strain JO-1(T), was isolated from an apparently healthy Pacific oyster, Crassostrea gigas, collected at Wan Island, Korea. It grew at 15-37 degrees C (optimum 30 degrees C) only in the presence of sea salts. Strain JO-1(T) hydrolysed casein, Tween 80 and starch. The major fatty acids were iso-C(15 : 0) (23.8 %), summed feature 3 (comprising C(16 : 1)omega7c and/or iso-C(15 : 0) 2-OH; 14.5 %) and iso-C(15 : 1) G (14.1 %). Analysis of the 16S rRNA gene sequence indicated that strain JO-1(T) was a member of the genus Tenacibaculum in the family Flavobacteriaceae, with sequence similarity of 94.6-97.8 % to the type strains of recognized members of the genus. The G+C content of the genomic DNA was 31.4 mol%. DNA-DNA relatedness levels between strain JO-1(T) and the five closest relatives, Tenacibaculum litoreum KCCM 42115(T), T. lutimaris KCTC 12302(T), T. aestuarii KCTC 12569(T), T. mesophilum DSM 13764(T) and T. adriaticum JCM 14633(T), were less than 28 %. Phylogenetic analyses and differences in physiological and biochemical characteristics suggested that strain JO-1(T) (=KCTC 22329(T) =JCM 15428(T)) should be classified as the type strain of a novel species within the genus Tenacibaculum, for which the name Tenacibaculum crassostreae sp. nov. is proposed.\",\n \"corpus_id\": 206166480,\n \"score\": 2\n },\n {\n \"doc_id\": \"19542132\",\n \"title\": \"Dyella soli sp. nov. and Dyella terrae sp. nov., isolated from soil.\",\n \"abstract\": \"Two novel strains isolated from soils, JS12-10(T) and JS14-6(T), were characterized using a polyphasic approach to determine their taxonomic positions. These isolates were found to be aerobic, Gram-negative, motile with one polar flagellum, non-spore-forming and rod-shaped. Phenotypic and fatty acid data supported the affiliation of JS12-10(T) and JS14-6(T) to the genus Dyella. However, chemotaxonomic data and DNA-DNA relatedness values allowed differentiation of these strains from other Dyella species with validly published names. Strains JS12-10(T) and JS14-6(T) showed the highest 16S rRNA gene sequence similarities with Dyella ginsengisoli Gsoil 3046(T) (98.4 %) and Dyella japonica XD53(T) (97.9 %), respectively, and the 16S rRNA gene sequence similarity between them was 97.1 %. DNA-DNA hybridization values between the novel isolates and strains of other recognized Dyella species were 29-38 %. Therefore, strains JS12-10(T) and JS14-6(T) represent two novel species of the genus Dyella, for which the names Dyella soli sp. nov. (type strain JS12-10(T) =KACC 12747(T) =JCM 15423(T)) and Dyella terrae sp. nov. (type strain JS14-6(T) =KACC 12748(T) =JCM 15424(T)) are proposed.\",\n \"corpus_id\": 23680513,\n \"score\": 2\n },\n {\n \"doc_id\": \"19542144\",\n \"title\": \"Sediminibacillus albus sp. nov., a moderately halophilic, Gram-positive bacterium isolated from a hypersaline lake, and emended description of the genus Sediminibacillus Carrasco et al. 2008.\",\n \"abstract\": \"A moderately halophilic, Gram-positive-staining, endospore-forming, rod-shaped and strictly aerobic bacterium, designated strain NHBX5(T), was isolated from Lake Nanhuobuxun in China. Strain NHBX5(T) was able to grow at NaCl concentrations of 0-22 % (w/v) (optimally at 7 %, w/v), at pH 6.0-9.0 (optimally at pH 7.5) and at temperatures of 10-45 degrees C (optimally at 37 degrees C). The cell-wall peptidoglycan of strain NHBX5(T) contained meso-diaminopimelic acid as the diagnostic diamino acid. The predominant isoprenoid quinone was MK-7. The major cellular fatty acids were anteiso-C(15 : 0) and anteiso-C(17 : 0). The polar lipids were phosphatidylglycerol, diphosphatidylglycerol and a glycolipid. The genomic DNA G+C content of strain NHBX5(T) was 44.9 mol%. Phylogenetic analysis based on 16S rRNA gene sequence comparisons revealed that strain NHBX5(T) was most closely related to Sediminibacillus halophilus EN8d(T) (98.6 % gene sequence similarity). The level of DNA-DNA relatedness between strain NHBX5(T) and S. halophilus CGMCC 1.6199(T) was 34.6 %. Based on the data presented, strain NHBX5(T) represents a novel species of the genus Sediminibacillus, for which the name Sediminibacillus albus sp. nov. is proposed. The type strain is NHBX5(T) (=DSM 19340(T) =CGMCC 1.6502(T)). In addition, an emended description of the genus Sediminibacillus is presented.\",\n \"corpus_id\": 206165836,\n \"score\": 2\n },\n {\n \"doc_id\": \"19542147\",\n \"title\": \"Roseomonas frigidaquae sp. nov., isolated from a water-cooling system.\",\n \"abstract\": \"A non-motile, coccobacilli-shaped, pale-pink-pigmented bacterium, designated strain CW67(T), was isolated from a water-cooling system in Gwangyang, Republic of Korea. Cells were found to be Gram-negative, catalase-positive and oxidase-positive, the major fatty acids were C(18 : 1)omega7c (43.6 %) and C(16 : 0) (15.8 %), the predominant respiratory lipoquinone was Q-10 and the DNA G+C content was 69.5 mol%. A phylogenetic tree based on 16S rRNA gene sequence comparisons showed that strain CW67(T) forms an evolutionary lineage within the radiation of the genus Roseomonas and that its closest relative is Roseomonas gilardii subsp. rosea MDA5605(T) (94.7 % sequence similarity). Evidence from this polyphasic study showed that strain CW67(T) could not be assigned to any recognized species. It therefore represents a novel species, for which the name Roseomonas frigidaquae sp. nov. is proposed, with CW67(T) (=KCTC 22211(T) =JCM 15073(T)) as the type strain.\",\n \"corpus_id\": 29260423,\n \"score\": 2\n },\n {\n \"doc_id\": \"19567564\",\n \"title\": \"Microvirga guangxiensis sp. nov., a novel alphaproteobacterium from soil, and emended description of the genus Microvirga.\",\n \"abstract\": \"A Gram-negative-staining bacterium, designated strain 25BT, was isolated from a soil sample from a rice field in Guangxi Province, China, and its taxonomic position was investigated by using a polyphasic approach. Cells were rod-shaped, non-spore-forming, non-motile and strictly aerobic. Strain 25BT grew optimally at 37 degrees C and pH 7.0. The predominant fatty acids of this soil isolate were C18:1omega7c, C19:0 cyclo omega8c and C16:0. Phylogenetic analysis based on the almost-complete 16S rRNA gene sequence showed that strain 25BT formed a monophyletic clade with the type strain of Microvirga subterranea; the two organisms shared 97.2% 16S rRNA gene sequence similarity. However, the two strains shared low DNA-DNA relatedness. Strain 25BT was also readily distinguishable from Microvirga subterranea DSM 14364T by various phenotypic characteristics. The combination of genotypic and phenotypic data suggests that the isolate represents a novel species of the genus Microvirga, for which the name Microvirga guangxiensis sp. nov. is proposed. The type strain is 25BT (=CGMCC 1.7666T=JCM 15710T).\",\n \"corpus_id\": 19982151,\n \"score\": 2\n },\n {\n \"doc_id\": \"19628599\",\n \"title\": \"Maritimimonas rapanae gen. nov., sp. nov., isolated from gut microflora of the veined rapa whelk, Rapana venosa.\",\n \"abstract\": \"A yellow-pigmented, Gram-negative, aerobic bacterial strain comprising rod-shaped cells devoid of flagellar and gliding motility, designated strain A31(T), was isolated from a veined rapa whelk (Rapana venosa) collected from the South Sea, Republic of Korea. Results from 16S rRNA gene sequence analysis indicated that the isolate belonged to the family Flavobacteriaceae; the highest level of nucleotide sequence similarity (92.6 %) was observed with Tenacibaculum aestuarii KCTC 12569(T). The predominant cellular fatty acids were iso-C(15 : 1) G (24.2 %), iso-C(15 : 0) (20.1 %) and iso-C(17 : 0) 3-OH (11.2 %). Flexirubin-type pigments were absent. The major isoprenoid quinone was MK-6. The DNA G+C content was 31.7 mol%. Data from a polyphasic taxonomic study suggested that the isolate represents a novel species in a new genus of the family Flavobacteriaceae, for which the name Maritimimonas rapanae gen. nov., sp. nov. is proposed. The type strain of Maritimimonas rapanae is A31(T) (=KCTC 22186(T) =JCM 15075(T)).\",\n \"corpus_id\": 206167678,\n \"score\": 2\n },\n {\n \"doc_id\": \"19654345\",\n \"title\": \"Paenibacillus aestuarii sp. nov., isolated from an estuarine wetland.\",\n \"abstract\": \"A novel bacterial strain designated CJ25(T) was isolated from the estuarine wetland of the Han river in Korea. Identification of this strain was carried out on the basis of polyphasic taxonomy. The isolate was Gram-staining-positive, rod-shaped, non-pigmented and motile. Phylogenetic analysis based on the 16S rRNA gene sequence revealed that the isolate was closely related to Paenibacillus chondroitinus DSM 5051(T) with 96.1 % similarity. The predominant fatty acids were anteiso-C(15 : 0) (50.25 %), iso-C(16 : 0) (18.54 %) and iso-C(15 : 0) (10.00 %). The major isoprenoid quinone was MK-7. The G+C content of genomic DNA was 50 mol%. According to physiological data and 16S rRNA gene sequence analysis, the isolate was discriminated from related members of the genus Paenibacillus. Therefore, strain CJ25(T) represents a novel species of the genus Paenibacillus, for which the name Paenibacillus aestuarii sp. nov. is proposed. The type strain is CJ25(T) (=KACC 13125(T) =JCM 15521(T)).\",\n \"corpus_id\": 41243520,\n \"score\": 2\n },\n {\n \"doc_id\": \"19661503\",\n \"title\": \"Kaistia terrae sp. nov., isolated from a wetland in Korea.\",\n \"abstract\": \"An ivory-coloured bacterium, designated strain 5YN7-3(T), was isolated from a wetland, Yongneup, Korea. Cells of the strain were aerobic, Gram-stain-negative, non-motile and short rods. 16S rRNA gene sequence analysis demonstrated that strain 5YN7-3(T) belongs to the order Rhizobiales of the class Alphaproteobacteria and is closely related to Kaistia soli 5YN9-8(T) (97.8 %), Kaistia granuli Ko04(T) (97.6 %) and Kaistia adipata Chj404(T) (97.4 %). Strain 5YN7-3(T) showed DNA-DNA hybridization values of 28, 22 and 35 % with K. granuli Ko04(T), K. soli 5YN9-8(T) and K. adipata Chj404(T), respectively. The major fatty acids were C(18 : 1)omega7c (51.2 %), C(19 : 0) cyclo omega8c (25.0 %), C(18 : 0) (12.9 %) and C(16 : 0) (10.8 %) (>10 % of total fatty acids). Ubiquinone-10 was the major isoprenoid quinone and the DNA G+C content was 66.5 mol%. The phenotypic characteristics in combination with 16S rRNA gene sequence analysis and DNA-DNA hybridization data clearly define strain 5YN7-3(T) as a novel species of the genus Kaistia, for which the name Kaistia terrae sp. nov. is proposed. The type strain is 5YN7-3(T) (=KACC 12910(T) =DSM 21341(T)).\",\n \"corpus_id\": 23256186,\n \"score\": 2\n },\n {\n \"doc_id\": \"20127465\",\n \"title\": \"Methylobacterium dankookense sp. nov., isolated from drinking water.\",\n \"abstract\": \"A pink-pigmented bacterium, designated SW08-7(T) was isolated from the drinking water of a water purifier. Cells were Gram-negative, rod-shaped, strictly aerobic, and non-spore-forming. It grew optimally at 25 degrees C, pH 6 approximately 7. Phylogenese analysis based on 16S rRNA gene sequence showed that strain SW08-7(T) belongs to the genus Methylobacterium. The highest 16S rRNA gene sequence similarities were found to Methylobacterium mesophilicum JCM 2829(T) (96.9%), Methylobacterium brachiatum B0021(T) (96.9%), Methylobacterium phyllosphaerae CBMB27(T) (96.6%), Methylobacterium radiotolerans JCM 2831(T) (96.6%), and Methylobacterium hispanicum GP34(T) (96.5%). DNA-DNA hybridization experiment revealed low-level (28.5%) of DNA-DNA relatedness between strain SW08-7(T) and Methylobacterium hispanicum. The genomic DNA G+C content was 68.9 mol% and the major isoprenoid quinone was Q-10. The major cellular fatty acid of strain SW08-7(T) was C(18:1) omega7c (79.8+/-2.1%). Results of phylogenetic, phenotypic, and biochemical analyses revealed that strain SW08-7(T) could be classified as representing a novel species of genus Methylobacterium, for which the name Methylobacterium dankookense sp. nov. is proposed. The type strain is SW08-7(T) (=KCTC 22512(T) =DSM 22415(1)).\",\n \"corpus_id\": 21564976,\n \"score\": 2\n },\n {\n \"doc_id\": \"20952545\",\n \"title\": \"Tistrella bauzanensis sp. nov., isolated from soil.\",\n \"abstract\": \"A Gram-reaction-negative, strictly aerobic, motile, rod-shaped bacterium, designated strain BZ78(T), was isolated from soil from an industrial site. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain BZ78(T) belonged to the family Rhodospirillaceae and formed a coherent cluster with the type strain of Tistrella mobilis (98.3 % pairwise similarity). The predominant cellular fatty acids of strain BZ78(T) were C₁₈:₁ω7c (58.3 %), C₁₉:₀ω8c cyclo (11.5 %), C₁₈:₁ 2-OH (10.9 %) and C₁₄:₀ 3-OH (6.4 %). The predominant ubiquinone was Q-10. The genomic DNA G+C content of strain BZ78(T) was 65.8 mol%. On the basis of phenotypic characteristics, phylogenetic analysis and DNA-DNA relatedness data, strain BZ78(T) is considered to represent a novel species of the genus Tistrella, for which the name Tistrella bauzanensis sp. nov. is proposed. The type strain is BZ78(T) ( = DSM 22817(T) = CGMCC 1.10188(T) = LMG 26047(T)).\",\n \"corpus_id\": 10202663,\n \"score\": 2\n },\n {\n \"doc_id\": \"20952549\",\n \"title\": \"Lysobacter korlensis sp. nov. and Lysobacter bugurensis sp. nov., isolated from soil.\",\n \"abstract\": \"Two Gram-reaction-negative, rod-shaped, gliding, yellow-pigmented bacterial strains, designated ZLD-17(T) and ZLD-29(T), were isolated from arid soil samples collected from Xinjiang Province, north-west China, and subjected to analysis using a polyphasic taxonomic approach. Both novel strains required 1.0-2.0 % (w/v) sea salts for optimal growth. Phylogenetic analysis based on 16S rRNA gene sequences indicated that these two strains belong to the genus Lysobacter within the class Gammaproteobacteria. Strain ZLD-17(T) showed highest 16S rRNA gene sequence similarities to Lysobacter capsici KCTC 22007(T) (96.9 %), Lysobacter spongiicola DSM 21749(T) (96.8 %) and Lysobacter koreensis KCTC 12204(T) (96.8 %), whereas strain ZLD-29(T) showed highest sequence similarities to Lysobacter niastensis DSM 18481(T) (96.0 %) and Lysobacter enzymogenes DSM 2043(T) (95.9 %). 16S rRNA gene sequence similarity between ZLD-17(T) and ZLD-29(T) was 96.1 %. The DNA G+C contents of strains ZLD-17(T) and ZLD-29(T) were 67.9 and 68.2 mol%, respectively. The major cellular fatty acids of both strains were summed feature 3 (iso-C₁₅:₀ 2-OH and/or C₁₆:₁ω7c), iso-C₁₇:₁ω9c, iso-C₁₆:₀, C₁₆:₀ and iso-C₁₁:₀ 3-OH; their predominant isoprenoid quinone was Q-8 and their major polar lipids were diphosphatidylglycerol, phosphatidylethanolamine and phosphatidylglycerol. Based on their phenotypic characteristics, phylogenetic position as determined by 16S rRNA gene sequence analysis and chemotaxonomic data, strains ZLD-17(T) ( = CCTCC AB 207174(T) = KCTC 23076(T)) and ZLD-29(T) ( = CCTCC AB 207175(T) = KCTC 23077(T)) represent two novel species of the genus Lysobacter, for which the names Lysobacter korlensis sp. nov. and Lysobacter bugurensis sp. nov. are proposed, respectively.\",\n \"corpus_id\": 41356058,\n \"score\": 2\n },\n {\n \"doc_id\": \"21037038\",\n \"title\": \"Pseudomonas bauzanensis sp. nov., isolated from soil.\",\n \"abstract\": \"A Gram-negative, aerobic, motile rod, designated BZ93(T), was isolated from soil from an industrial site. The strain grew at 5-30 °C. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain BZ93(T) was related to members of the genus Pseudomonas and was related most closely to Pseudomonas xiamenensis C10-2(T) (97.8 % 16S rRNA gene sequence similarity) and Pseudomonas pertucinogena IFO 14163(T) (97.4 %). The predominant cellular fatty acids of strain BZ93(T) were C(18 : 1)ω7c (54.8 %), summed feature 3 (C(16 : 1)ω7c and/or iso-C(15 : 0) 2-OH; 10.3 %), C(16 : 0) (9.9 %) and C(17 : 0) cyclo (7.4 %). The major quinone was ubiquinone 9. The major phospholipids were phosphatidylethanolamine, diphosphatidylglycerol, phosphatidylglycerol and an unknown phospholipid. The genomic DNA G+C content was 61.8 mol%. On the basis of phenotypic characteristics, phylogenetic analysis and DNA-DNA relatedness, a novel species, Pseudomonas bauzanensis sp. nov., is proposed. The type strain is BZ93(T) ( = DSM 22558(T) = CGMCC 1.9095(T) = LMG 26048(T)).\",\n \"corpus_id\": 30576964,\n \"score\": 2\n },\n {\n \"doc_id\": \"21717323\",\n \"title\": \"Flavobacterium koreense sp. nov., Flavobacterium chungnamense sp. nov., and Flavobacterium cheonanense sp. nov., isolated from a freshwater reservoir.\",\n \"abstract\": \"Taxonomic studies were performed on three strains isolated from Cheonho reservoir in Cheonan, Korea. The isolates were Gram-negative, aerobic, rod-shaped, non-motile, catalase-positive, and oxidase-positive. Colonies on solid media were cream-yellow, smooth, shiny, and circular. Phylogenetic analysis of the 16S rRNA gene sequences revealed that these strains belong to the genus Flavobacterium. The strains shared 98.6-99.4% sequence similarity with each other and showed less than 97% similarity with members of the genus Flavobacterium with validly published names. The DNA-DNA hybridization results confirmed the separate genomic status of strains ARSA-42(T), ARSA-103(T), and ARSA-108(T). The isolates contained menaqui-none-6 as the predominant menaquinone and iso-C(15:0), iso-C(15:0) 3-OH, iso-Ci(15:1) G, and iso-C(16:0) 3-OH as the major fatty acids. The genomic DNA G+C content of the isolates were 31.4-33.2 mol%. According to the phenotypic and genotypic data, these organisms are classified as representative of three novel species in the genus Flavobacterium, and the name Flavobacterium koreense sp. nov. (strain ARSA-42(T) =KCTC 23182(T) =JCM 17066(T) =KACC 14969(T)), Flavobacterium chungnamense sp. nov. (strain ARSA-103(T) =KCTC 23183(T) =JCM 17068(T) =KACC 14971(T)), and Flavobacterium cheonanense sp. nov. (strain ARSA-108(T) =KCTC 23184(T) =JCM 17069(T) =KACC 14972) are proposed.\",\n \"corpus_id\": 19444004,\n \"score\": 2\n },\n {\n \"doc_id\": \"22247212\",\n \"title\": \"Kaistia defluvii sp. nov., isolated from river sediment.\",\n \"abstract\": \"A Gram-stain-negative, aerobic, non-motile, rod- and coccus-shaped bacterium, designated strain B6-12(T), was isolated from sediment collected from the River Geumho in South Korea. In comparative 16S rRNA gene sequence analysis, the novel strain appeared to be affiliated with the class Alphaproteobacteria and to be most closely related to Kaistia adipata KCTC 12095(T), Kaistia dalseonensis DSM 18800(T), Kaistia geumhonensis DSM 18799(T), Kaistia granuli KCTC 12575(T), Kaistia soli KACC 12605(T) and Kaistia terrae KACC 12910(T), with sequence similarities of 96.2-99.1%. The predominant ubiquinone in the isolate was Q-10, major fatty acids were C(18:0), C(18:1)ω7c and C(19:0)ω8c cyclo, and genomic DNA G+C content was 63.0 mol%. Based on the phylogenetic and chemotaxonomic evidence and the results of DNA-DNA hybridizations, strain B6-12(T) represents a novel species in the genus Kaistia, for which the name Kaistia defluvii sp. nov. is proposed. The type strain is B6-12(T) ( = KCTC 23766(T) = JCM 18034(T)).\",\n \"corpus_id\": 30343928,\n \"score\": 2\n },\n {\n \"doc_id\": \"22922533\",\n \"title\": \"Xenorhabdus ishibashii sp. nov., isolated from the entomopathogenic nematode Steinernema aciari.\",\n \"abstract\": \"Gram-negative bacteria of the genus Xenorhabdus exhibit a mutualistic association with steinernematid entomopathogenic nematodes and a pathogenic relationship with insects. Here we describe two isolates of the entomopathogenic nematode Steinernema aciari collected from China and Japan. 16S rRNA gene sequence similarity and phylogenetic analysis indicated that the isolates obtained from S. aciari belonged to the genus Xenorhabdus. Multilocus sequence analysis based on five universal protein-coding gene sequences revealed that the isolates were closely related to Xenorhabdus ehlersii DSM 16337(T) and Xenorhabdus griffiniae ID10(T) but that they exhibited <97 % sequence similarity with these reference strains, which indicated that the isolates were distinct from previously described species. Based on these genetic differences and several differential phenotypic traits, we propose that the isolates represent a novel species of the genus Xenorhabdus, for which we propose the name Xenorhabdus ishibashii sp. nov. The type strain is GDh7(T) ( = DSM 22670(T) = CGMCC 1.9166(T)).\",\n \"corpus_id\": 46314950,\n \"score\": 2\n },\n {\n \"doc_id\": \"23243096\",\n \"title\": \"Caulobacter daechungensis sp. nov., a stalked bacterium isolated from a eutrophic reservoir.\",\n \"abstract\": \"A Gram-stain-negative, aerobic, non-spore-forming, curved, rod-shaped bacterium, H-E3-2(T), was isolated from a water sample taken from Daechung Reservoir, Republic of Korea, during the late-blooming period of cyanobacteria. Strain H-E3-2(T) was motile with a single polar flagellum or non-motile (stalked cell). Comparative 16S rRNA gene sequence studies showed the isolate had a clear affiliation with the class Alphaproteobacteria and was most closely related to Caulobacter fusiformis ATCC 15257(T) and Caulobacter mirabilis LMG 24261(T), showing 97.6 and 97.3 % 16S rRNA gene sequence similarity, respectively, and 95.3-96.3 % similarity to all other species of the genus Caulobacter. The predominant ubiquinone was Q-10. The major fatty acids were summed feature 8 (C18 : 1ω6c and/or C18 : 1ω7c) and C16 : 0. The G+C content of the genomic DNA of strain H-E3-2(T) was 64.7 mol%. DNA-DNA hybridization values of strain H-E3-2(T) with C. fusiformis ATCC 15257(T) and C. mirabilis LMG 24261(T) were 21.2 and 19.7 %, respectively. Thus, based on the results of polyphasic analysis, it is proposed that strain H-E3-2(T) represents a novel species of the genus Caulobacter, for which the name Caulobacter daechungensis sp. nov. is proposed. The type strain is H-E3-2(T) ( = KCTC 32211(T) = JCM 18689(T)).\",\n \"corpus_id\": 206178457,\n \"score\": 2\n },\n {\n \"doc_id\": \"23416574\",\n \"title\": \"Devosia submarina sp. nov., isolated from deep-sea surface sediments.\",\n \"abstract\": \"The taxonomic status of two aerobic, Gram-stain-negative, orange-reddish pigmented, motile, rod-shaped bacteria, designated KMM 9415(T) and KMM 9416, isolated from a deep surface-sediment sample from the Sea of Japan, was defined. Comparative 16S rRNA gene sequence analysis of strains KMM 9415(T) and KMM 9416 revealed their affiliation to the genus Devosia with a high sequence similarity of 98.5 % to both Devosia psychrophila DSM 22950(T) and Devosia glacialis LMG 26051(T). The novel strains were characterized by the predominance of the fatty acid C18 : 1ω7c followed by C16 : 1 and C16 : 0. The major isoprenoid quinone was Q-10 and the polar lipids comprised phosphatidylglycerol, phosphatidic acid and unknown glycolipids. The DNA-DNA hybridization value of 88 % between the novel strains KMM 9415(T) and KMM 9416 confirmed their assignment to the same species. The values of DNA relatedness determined for strain KMM 9415(T) and the closely related strains D. psychrophila DSM 22950(T) and D. glacialis LMG 26051(T) were 21 % and 23 %, respectively. Based on distinctive phenotypic characteristics, phylogenetic analysis and DNA-DNA relatedness, it can be concluded that the novel strains KMM 9415(T) and KMM 9416 represent a novel species within the genus Devosia, for which the name Devosia submarina sp. nov. is proposed. The type strain is the strain KMM 9415(T) (= NRIC 0884(T) = JCM 18935(T)).\",\n \"corpus_id\": 25539634,\n \"score\": 2\n },\n {\n \"doc_id\": \"23482845\",\n \"title\": \"Heterorhabditidoides rugaoensis n. sp. (Rhabditida: Rhabditidae), a Novel Highly Pathogenic Entomopathogenic Nematode Member of Rhabditidae.\",\n \"abstract\": \"A novel entomopathogenic nematode species, Heterorhabditidoides rugaoensis n. sp. RG081015, collected from Rugao, China, is described. The new species is morphologically very similar to H. chongmingensis but can be distinguished from it on the basis of some morphological characteristics, combined with molecular data and a cross-hybridization test. Males of the new species can be recognized on the basis of body length averaging 1396.2 μm; lateral field with one ridge; metastome isoglottoid with one hemispherical swellings comprised of two to three well-developed warts; asymmetric spicules; peloderan bursa. In IJs, EP = 134.5 μm; ES = 149.3 μm; tail length = 82.5 μm; and a = 20.5. Hermaphroditic females have four to five lateral ridges. The 18S rDNA and ITS sequences of the two nematodes share 99% and 98% identity, respectively. Phylogenetic trees of 18S rDNA and ITS indicate that the new species is most closely related to H. chongmingensis; thus, the two nematodes belong to the same genus. Failure of cross-hybridization between them indicates that nematode strain RG081015 is a novel species and is described herein as H. rugaoensis n. sp. The LC50 of the novel species against Galleria mellonella were 24.35 IJs / ml within 48 hours of infection. Morphological characteristics, genetic similarity analyses, and phylogenetic relationships provide strong evidence that some species of Oscheius/Insectivora-group should be reassigned to the genus Heterorhabditidoides.\",\n \"corpus_id\": 18010469,\n \"score\": 2\n },\n {\n \"doc_id\": \"23606482\",\n \"title\": \"Dyadobacter tibetensis sp. nov., isolated from glacial ice core.\",\n \"abstract\": \"A Gram-stain-negative, rod-shaped, aerobic, non-motile bacterium, designated Y620-1(T), was isolated from a glacier on the Tibetan Plateau, China. The 16S rRNA gene sequence of the novel isolate shared 93.6-95.1 % similarity with type strains of species of the genus Dyadobacter. The major fatty acids of strain Y620-1(T) were summed feature 3 (C16 : 1ω7c and/or iso-C15 : 0 2-OH), iso-C15 : 0, C16 : 1ω5c and iso-C17 : 0 3-OH. The predominant isoprenoid quinone and polar lipid were MK-7 and phosphatidylethanolamine (PE), respectively. The DNA G+C content was 44.4±0.3 mol% (Tm). Flexirubin-type pigment was produced. The novel isolate was classified in the genus Dyadobacter, but a number of phenotypic characteristics distinguished the novel isolate from type strains of species of the genus Dyadobacter. From these genotypic and phenotypic data, it is evident that strain Y620-1(T) represents a novel species of the genus Dyadobacter, for which the name Dyadobacter tibetensis sp. nov. is proposed. The type strain is Y620-1(T) ( = JCM 18589(T) = CGMCC 1.12215(T)).\",\n \"corpus_id\": 27706358,\n \"score\": 2\n },\n {\n \"doc_id\": \"23918786\",\n \"title\": \"Pseudomonas guguanensis sp. nov., a gammaproteobacterium isolated from a hot spring.\",\n \"abstract\": \"An aerobic, Gram-stain-negative, rod-shaped bacterium (designated strain CC-G9A(T)), motile by a polar-flagellum, was isolated from a hot spring water sample in Taiwan. Strain CC-G9A(T) could grow at 20-42 °C, pH 6.0-10.0 and tolerate up to 7% (w/v) NaCl. The 16S rRNA gene sequence analysis of strain CC-G9A(T) showed pairwise sequence similarity to Pseudomonas mendocina LMG 1223(T) (97.7%), Pseudomonas alcaligenes ATCC 14909(T) (97.8 %), Pseudomonas alcaliphila DSM 17744(T) (97.8 %), Pseudomonas toyotomiensis JCM 15604(T) (97.6 %), Pseudomonas oleovorans subsp. lubricantis DSM 21016(T) (97.6 %) and Pseudomonas argentinensis BCRC 17807(T) (97.5 %), and lower sequence similarity to other species of the genus Pseudomonas. According to DNA-DNA association analysis, the relatedness of strain CC-G9A(T) to P. mendocina BCRC 10458(T), P. alcaliphila DSM 17744(T), P. alcaligenes BCRC 11893(T), P. oleovorans subsp. lubricantis DSM 21016(T), P. argentinensis BCRC 17807(T) and P. oleovorans subsp. oleovorans BCRC 11902 was 55.1±3.1, 13.7±1.5, 14.1±1.8, 58.5±1.1, 28.9±2.0 and 28.6±1.8 %, respectively. The evolutionary trees reconstructed based on 16S rRNA, gyrB and rpoB gene sequences revealed varying phylogenetic neighbourhoods of strain CC-G9A(T) with regard to the most closely related type strains. The predominant quinone system was ubiquinone (Q-9) and the DNA G+C content was 64.3±1.3 mol%. The major fatty acids were C10 : 0 3-OH, C12 : 0, C12 : 0 3-OH, C16 : 0 and summed features 3 and 8 consisting of C16 : 1ω7c/C16 : 1ω6c and C18 : 1ω7c/C18 : 1ω6c, respectively. The major polar lipids were diphosphatidylglycerol, phosphatidylcholine, phosphatidylethanolamine and phosphatidylglycerol. According to distinct phylogenetic, phenotypic and chemotaxonomic features, strain CC-G9A(T) is proposed to represent a novel species within the genus Pseudomonas for which the name Pseudomonas guguanensis sp. nov. is proposed. The type strain is CC-G9A(T) ( = BCRC 80438(T) = JCM 18416(T)).\",\n \"corpus_id\": 206178039,\n \"score\": 2\n },\n {\n \"doc_id\": \"23918787\",\n \"title\": \"Pseudomonas guangdongensis sp. nov., isolated from an electroactive biofilm, and emended description of the genus Pseudomonas Migula 1894.\",\n \"abstract\": \"A Gram-negative, straight to slightly curved rod-shaped bacterium, motile with peritrichous flagella, designated SgZ-6(T), was isolated from an electroactive biofilm and was characterized by means of a polyphasic approach. Growth occurred with 0-5.0 % (w/v) NaCl (optimum 1 %), at pH 6.0-10.0 (optimum pH 7.0) and at 10-42 °C (optimum 30 °C) in trypticase soya broth. Phylogenetic analyses based on the 16S rRNA and gyrB genes identified the isolate as a member of a novel species of the genus Pseudomonas. Strain SgZ-6(T) exhibited the highest 16S rRNA gene sequence similarity to 'Pseudomonas linyingensis' CGMCC 1.10701 (97.5 %), followed by Pseudomonas sagittaria JCM 18195(T) (97.4 %), P. oleovorans subsp. lubricantis DSM 21016(T) (96.6 %), P. tuomuerensis JCM 14085(T) (96.5 %) and P. alcaliphila JCM 10630(T) (96.4 %). Strain SgZ-6(T) showed the highest gyrB gene sequence similarity of 93.7 % to 'P. linyingensis' CGMCC 1.10701 among all type strains of genus Pseudomonas. DNA-DNA pairing studies showed that strain SgZ-6(T) displayed 47.1 and 40.3 % relatedness to 'P. linyingensis' CGMCC 1.10701 and P. sagittaria JCM 18195(T), respectively. The major isoprenoid quinone was ubiquinone 9 (Q-9). The whole-cell fatty acids consisted mainly of summed feature 3 (C16 : 1ω6c and/or C16 : 1ω7c), C16 : 0 and summed feature 8 (C18 : 1ω6c and/or C18 : 1ω7c). The DNA G+C content of the genomic DNA was 68.1 mol%. On the basis of phenotypic, chemotaxonomic and phylogenetic data, strain SgZ-6(T) is proposed to represent a novel species of the genus Pseudomonas, for which the name Pseudomonas guangdongensis sp. nov. is proposed. The type strain is SgZ-6(T) ( = CCTCC AB 2012022(T) = KACC 16606(T)). An emended description of the genus Pseudomonas is also proposed.\",\n \"corpus_id\": 27637805,\n \"score\": 2\n },\n {\n \"doc_id\": \"24664580\",\n \"title\": \"Thalassomonas eurytherma sp. nov., a marine proteobacterium.\",\n \"abstract\": \"Two Gram-staining-negative, aerobic, rod-shaped bacterial strains, designated Za6a-12(T) and Za6a-17, were isolated from seawater of the East China Sea. Cells of Za6a-12(T) and Za6a-17 were approximately 1.5-2.0 µm×0.5-0.7 µm and motile by a single polar flagellum. Strains grew optimally at pH 7.5-8.0, 28 °C, and in the presence of 2.5-3.0% (w/v) NaCl. Chemotaxonomic analysis showed that the predominant respiratory quinone of strains Za6a-12(T) and Za6a-17 was ubiquinone-8 (>97%), and the major fatty acids were C(14 : 0), C(16 : 1)ω7c and/or iso-C(15 : 0) 2-OH, C(16 : 0) and C(17 : 1)ω8c. Their DNA G+C contents were 42.7 mol% and 42.8 mol%, respectively. 16S rRNA gene sequence analysis revealed that the isolates belonged to the genus Thalassomonas and showed the highest sequence similarity to Thalassomonas loyana CBMAI 722(T) (95.9%). Strains Za6a-12(T) and Za6a-17 could be differentiated from T. loyana CBMAI 722(T) according to their phenotypic and chemotaxonomic features, DNA G+C contents and fatty acid composition. On the basis of these features, we propose strains Za6a-12(T) and Za6a-17 to be representatives of a novel species of the genus Thalassomonas with the name Thalassomonas eurytherma sp. nov. suggested. Strain Za6a-12(T) ( = CGMCC 1.12115(T) = JCM 18482(T)) is the type strain of this novel species.\",\n \"corpus_id\": 20301774,\n \"score\": 2\n },\n {\n \"doc_id\": \"24944336\",\n \"title\": \"Martelella radicis sp. nov. and Martelella mangrovi sp. nov., isolated from mangrove sediment.\",\n \"abstract\": \"Two Gram-stain-negative, non-motile, rod-shaped bacterial strains, designated BM5-7(T) and BM9-1(T) were isolated from soil of the root system of a mangrove forest. Phylogenetic analysis based on 16S rRNA gene sequences showed that the two isolates belong to the genus Martelella. The chemotaxonomic characteristics of these isolates included the presence of C19 : 0 cyclo ω8c and C18 : 1ω7c as the major cellular fatty acids and Q-10 as the dominant ubiquinone. The genomic DNA G+C contents of strains BM5-7(T) and BM9-1(T) were 61.0 and 59.7 mol% (HPLC method), respectively. The 16S rRNA gene sequence similarity between the two strains was 98.1 %, but DNA-DNA hybridization indicated 44 % relatedness. Strains BM5-7(T) and BM9-1(T) exhibited 16S rRNA gene sequence similarities of 98.0-99.2 % and 97.7-98.1 %, respectively, with type strains of Martelella endophytica and Martelella mediterranea. Combined data from phenotypic, phylogenetic and DNA-DNA relatedness studies demonstrated that strains BM5-7(T) and BM9-1(T) are representatives of two novel species of the genus Martelella, for which the names Martelella radicis sp. nov. (type strain BM5-7(T) = DSM 28101(T) = LMG 27958(T)) and Martelella mangrovi sp. nov. (type strain BM9-1(T) = DSM 28102(T) = LMG 27959(T)) are proposed.\",\n \"corpus_id\": 206182687,\n \"score\": 2\n },\n {\n \"doc_id\": \"25122614\",\n \"title\": \"Sulfitobacter geojensis sp. nov., Sulfitobacter noctilucae sp. nov., and Sulfitobacter noctilucicola sp. nov., isolated from coastal seawater.\",\n \"abstract\": \"Four Gram-stain-negative, aerobic, rod-shaped bacterial strains, MM-124, MM-126, NB-68 and NB-77, were isolated from the coastal seawater or a region with a bloom of sea sparkle around Geoje island in Korea. The sequence similarity values of the 16S rRNA gene between the isolates and Sulfitobacter mediterraneus DSM 12244(T) ranged from 97.7 to 98.2%, and phylogenetic relationships suggested that they belong to a phylogenetic branch that includes the genera Sulfitobacter and Roseobacter. The isoprenoid quinone of all three novel strains was ubiquinone-10 and the major fatty acid was cis-vaccenic acid, as in other species of the genus Sulfitobacter. However, there were several differences in the morphological, physiological and biochemical characteristics among the four strains and the reference species of the genus Sulfitobacter. Moreover, the average nucleotide identity values between the three sequenced isolates and the reference strains were below 76.33, indicating that genomic variation exists between the isolates and reference strains. Chemotaxonomic characteristics together with phylogenetic affiliations and genomic distances illustrate that strains MM-124, NB-68 and NB-77 represent novel species of the genus Sulfitobacter, for which the names Sulfitobacter geojensis sp. nov. (type strain MM-124(T) =KCTC 32124(T) =JCM 18835(T)), Sulfitobacter noctilucae sp. nov. (type strain NB-68(T) =KCTC 32122(T) =JCM 18833(T)) and Sulfitobacter noctilucicola sp. nov. (type strain NB-77(T) =KCTC 32123(T) =JCM 18834(T)) are proposed.\",\n \"corpus_id\": 20504994,\n \"score\": 2\n },\n {\n \"doc_id\": \"25281728\",\n \"title\": \"Serratia myotis sp. nov. and Serratia vespertilionis sp. nov., isolated from bats hibernating in caves.\",\n \"abstract\": \"During the study of bacteria associated with bats affected by white-nose syndrome hibernating in caves in the Czech Republic, we isolated two facultatively anaerobic, Gram-stain-negative bacteria, designated strains 12(T) and 52(T). Strains 12(T) and 52(T) were motile, rod-like bacteria (0.5-0.6 µm in diameter; 1-1.3 µm long), with optimal growth at 20-35 °C and pH 6-8. On the basis of the almost complete sequence of their 16S rRNA genes they should be classified within the genus Serratia; the closest relatives to strains 12(T) and 52(T) were Serratia quinivorans DSM 4597(T) (99.5 % similarity in 16S rRNA gene sequences) and Serratia ficaria DSM 4569(T) (99.5% similarity in 16S rRNA gene sequences), respectively. DNA-DNA relatedness between strain 12(T) and S. quinivorans DSM 4597(T) was only 37.1% and between strain 52(T) and S. ficaria DSM 4569(T) was only 56.2%. Both values are far below the 70% threshold value for species delineation. In view of these data, we propose the inclusion of the two isolates in the genus Serratia as representatives of Serratia myotis sp. nov. (type strain 12(T) =CECT 8594(T) =DSM 28726(T)) and Serratia vespertilionis sp. nov. (type strain 52(T) =CECT 8595(T) =DSM 28727(T)).\",\n \"corpus_id\": 43187151,\n \"score\": 2\n },\n {\n \"doc_id\": \"25444874\",\n \"title\": \"Genome sequence of Serratia nematodiphila DSM 21420T, a symbiotic bacterium from entomopathogenic nematode.\",\n \"abstract\": \"Serratia nematodiphila DSM 21420(T) (=CGMCC 1.6853(T), DZ0503SBS1(T)), isolated from the intestine of Heterorhabditidoides chongmingensis, has been known to have symbiotic-pathogenic life cycle, on the multilateral relationships with entomopathogenic nematode and insect pest. In order to better understanding of this rare feature in Serratia species, we present here the genome sequence of S. nematodiphila DSM 21420(T) with the significance of first genome sequence in this species.\",\n \"corpus_id\": 20175431,\n \"score\": 2\n },\n {\n \"doc_id\": \"25634950\",\n \"title\": \"Pedobacter daejeonensis sp. nov. and Pedobacter trunci sp. nov., isolated from an ancient tree trunk, and emended description of the genus Pedobacter.\",\n \"abstract\": \"Two Gram-stain-negative, yellow, aerobic and rod-shaped bacterial isolates, designated THG-DN3.18(T) and THG-DN3.19(T), were isolated from an ancient tree trunk from Daejeon, South Korea. 16S rRNA gene sequence similarity showed that both strains belong to the genus Pedobacter within the family Sphingobacteriaceae . Strain THG-DN3.18(T) exhibited maximum sequence similarity with Pedobacter boryungensis KCTC 23344(T) (98.5%) while strain THG-DN3.19(T) exhibited maximum sequence similarity with Pedobacter nyackensis LMG 24260(T) (97.3%). In DNA-DNA hybridization tests, the two strains showed less than 35% relatedness with respect to closely related species of the genus Pedobacter . Both strains contained iso-C(15 : 0) and C(16 : 1)ω6c and/or C(16 : 1)ω7c (summed feature 3) as the predominant fatty acids and MK-7 as the major isoprenoid quinone. The DNA G+C contents of strains THG-DN3.18(T) and THG-DN3.19(T) were 35.5 and 40.1 mol%, respectively. The genotypic analysis, biochemical properties, and phenotypic and chemotaxonomic characteristics indicate that strains THG-DN3.18(T) and THG-DN3.19(T) represent novel species of the genus Pedobacter , for which the names Pedobacter daejeonensis sp. nov. and Pedobacter trunci sp. nov. are proposed. The type strains are THG-DN3.18(T) ( = KCTC 42230(T) = JCM 30352(T)) and THG-DN3.19(T) ( = KCTC 42233(T) = JCM 30353(T)), respectively.\",\n \"corpus_id\": 25962317,\n \"score\": 2\n },\n {\n \"doc_id\": \"25716888\",\n \"title\": \"Enterobacillus tribolii gen. nov., sp. nov., a novel member of the family Enterobacteriaceae, isolated from the gut of a red flour beetle, Tribolium castaneum.\",\n \"abstract\": \"Two novel Gram-stain negative facultative anaerobic, motile, rod-shaped bacterial strains IG-V01(T) and IG-V01b were isolated from the gut of red flour beetles, Tribolium castaneum. The 16S rRNA gene sequences of strains IG-V01(T) and IG-V01b were found to have their highest sequence similarity (96.5% and 96.4%) with Serratia nematodiphila DZ0503SBS1(T) (Enterobacteriaceae family) respectively. Strains IG-V01(T) and IG-V01b share 100% 16S rRNA gene sequence similarity and exhibit very similar phenotypic characteristics. In addition, they show 89.7% genomic relatedness (DNA-DNA hybridisation). Major fatty acids were identified to be C(16:0) (38.3%), C(17:0) cyclo (19.5-20%) and C(14:0) (11.2-11.3%). Cells contain phosphatidylethanolamine and diphosphatidylglycerol as predominant polar lipids. Genomic DNA G+C content (mol%) was determined to be 51.5-51.7. A polyphasic approach employing the study of morphological, physiological, chemotaxonomic, genomic and phylogenetic analysis revealed that the two newly isolated strains cannot be placed in any of the existing genera of the family Enterobacteriaceae. Therefore, it is proposed that strains IG-V01(T) and IG-V01b belong to a novel genus within the family Enterobacteriaceae, and represent a new species Enterobacillus tribolii gen. nov., sp. nov., with the type strain =IG-V01(T) = KCTC 42159(T) = MCC 2532(T).\",\n \"corpus_id\": 7877444,\n \"score\": 2\n },\n {\n \"doc_id\": \"25977284\",\n \"title\": \"Shimia sagamensis sp. nov., a marine bacterium isolated from cold-seep sediment.\",\n \"abstract\": \"A novel marine bacterial strain designated JAMH 011(T) was isolated from the cold-seep sediment in Sagami Bay, Japan. Cells were Gram-stain-negative, rod-shaped, non-spore-forming, aerobic chemo-organotrophs and motile by means of a single polar flagellum. Growth occurred at temperatures below 31 °C, with the optimum at 25 °C. The major respiratory quinone was Q-10. The predominant fatty acid was C18 : 1ω7c. On the basis of 16S rRNA gene sequence analysis, the isolated strain was closely affiliated with members of the genus Shimia in the class Alphaproteobacteria, and the 16S rRNA gene sequence similarity of the novel isolate with the type strain of the closest related species, Shimia haliotis WM35(T), was 98.1%. The DNA G+C content of the novel strain was 57.3 mol%. The hybridization values for DNA-DNA relatedness between strain JAMH 011(T) and reference strains belonging to the genus Shimia were less than 9.4 ± 0.7%. Based on differences in taxonomic characteristics, the isolated strain represents a novel species of the genus Shimia, for which the name Shimia sagamensis sp. nov. is proposed. The type strain is JAMH 011(T) ( = JCM 30583(T) = DSM 29734(T)).\",\n \"corpus_id\": 38247529,\n \"score\": 2\n },\n {\n \"doc_id\": \"26338019\",\n \"title\": \"Salibacterium halotolerans gen. nov. sp. nov., a novel bacterium isolated from a salt pan, reclassification of Bacillus qingdaonensis as Salibacterium qingdaonense comb. nov. and Bacillus halochares as Salibacterium halochares comb. nov.\",\n \"abstract\": \"Two novel Gram-stain-positive, rod shaped, non-motile, non-endospore forming bacterial strains S7T and IB5 were isolated from Khavda, in India. Based on the 16S rRNA gene sequence analysis they were identified as belonging to the class Bacilli, order Bacillales, family Bacillaceae and were most closely related to Bacillus qingdaonensis CGMCC 1.6134T (97.3 %, sequence similarity), Bacillus halochares LMG 24571T (96.9 %), Bacillus salarius KCTC 3912T (95.6 %) and Bacillus aidingensis DSM 18341T (95.3 %). However, these strains shared only 88.2 % 16S rRNA gene sequence similarity with Bacillus subtilis subsp. subtilis DSM 10T, indicating that the strains S7T and IB5 might not be the members of the genus Bacillus. The DNA-DNA relatedness of these strains with B. qingdaonensis CGMCC 1.6134T was 42.9 + 0.8. The cell-wall peptidoglycan of strains S7Tand IB5 contains meso-diaminopimelic acid. Polar lipids include diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, a phospholipid and three unknown lipids. The predominant isoprenoid quinone was MK-7. Anteiso-C15:0 (38.4 %) was the predominant fatty acid. The results of phylogenetic, chemotaxonomic and biochemical tests allowed a clear differentiation of strains S7T and IB5, which represents a novel member of the family, for which the name Salibacterium halotolerans gen. nov. sp. nov. is proposed. The type strain is S7T (= KCTC 33658T = CGMCC 1.15324T). Based on the present study, it is also suggested to transfer B. qingdaonensis and B. halochares to this new genus, as Salibacterium qingdaonense comb. nov. and Salibacterium halochares comb. nov., respectively.\",\n \"corpus_id\": 26054899,\n \"score\": 2\n },\n {\n \"doc_id\": \"26537514\",\n \"title\": \"Serratia aquatilis sp. nov., isolated from drinking water systems.\",\n \"abstract\": \"A crème-white-pigmented, oxidase-negative bacterium (strain 2015-2462-01T), isolated from a drinking water system was investigated in detail for its taxonomic allocation. Cells of the isolate were rod shaped and stained Gram-negative. A comparison of the 16S rRNA gene sequence of strain 2015-2462-01T with sequences of type strains of most closely related Serratia species showed highest sequence similarities to Serratia fonticola (98.4%), Serratia protaemaculans (97.8%), Serratia liquefaciens and Serratia grimesii (both 97.7%). 16S rRNA gene sequence similarities to all other Serratia species were below 97.4%. Multilocus sequence analyses (MLSA) on the basis of concatenated partial gyrB, rpoB, infB and atpD sequences showed a clear distinction of strain 2015-2462-01T from the closest related type strains of the Serratia species. The fatty acid profile of the strain consisted of the major fatty acids C14:0, C16:0, C16:1 ω7c, C17:0 cyclo, and C18:1 ω7c. DNA-DNA hybridizations between 2015-2462-01T and type strain of Serratia fonticola ATCC 29844T resulted in a similarity values of 27% (reciprocal 20%). This DNA-DNA hybridization result in combination with the MLSA results and the differentiating biochemical properties indicated, that strain 2015-2462-01T represents a novel Serratia species, for which the name Serratia aquatilis sp. nov. (type strain 2015-2462-01T = LMG 29119T = CCM 8626T), is proposed.\",\n \"corpus_id\": 29017121,\n \"score\": 2\n },\n {\n \"doc_id\": \"26541594\",\n \"title\": \"Comamonas phosphati sp. nov., a novel bacterium isolated from a phosphate mine.\",\n \"abstract\": \"A Gram-negative, facultatively anaerobic, non-pigmented, non-sporulating, rod-shaped bacterial strain WYH 22-41T was isolated from a phosphate mine in Yunnan Province, China. The cells were motile with a single polar flagellum. The 16S rRNA gene of strain WYH 22-41T was phylogenetically related to the corresponding gene of Comamonas terrae DSM 27221T (98.4%), Comamonas odontotermitis LMG 23579T (97.6%) and Comamonas aquatica LMG 2370T (97.4%). DNA-DNA hybridizations of strain WYH 22-41T with these three strains showed relatedness of 33.2%, 20.5% and 27.7%, respectively. The DNA G+C content of strain WYH 22-41T was 62.4 mol%. The predominant respiratory quinone was ubiquinone-8. The major polar lipids were diphosphatidylglycerol, phosphatidylethanolamine, and phosphatidylglycerol. The major fatty acids of strain WYH 22-41T were C16 : 0, C17 : 0 cyclo, summed feature 3 (C16 : 1 ω6c and/or C16 : 1 ω7c) and summed feature 8 (C18 : 1 ω6c and/or C18 : 1 ω7c). On the basis of its phenotypic properties, phylogenetic characteristics, DNA-DNA hybridization, as well as whole-cell fatty acid composition, strain WYH 22-41T represents a novel species of the genus Comamonas, for which the name Comamonas phosphati sp. nov. is proposed. The type strain is WYH 22-41T (=CGMCC 1.12294T = DSM 26017T).\",\n \"corpus_id\": 22979125,\n \"score\": 2\n },\n {\n \"doc_id\": \"26637822\",\n \"title\": \"Luteimonas notoginsengisoli sp. nov., isolated from rhizosphere soil.\",\n \"abstract\": \"A Gram-staining-negative, yellow pigmented strain, designated as SYP-B804T, was isolated from the rhizospheric soil of Panax notoginseng. The strain was rod shaped with single polar flagellum. The optimum temperature and pH required for growth of the strain was observed at 28-32 °C and 7-8, respectively. The 16S rRNA gene sequence analysis indicated that the strain SYP-B804T showed highest 16S rRNA gene sequence similarity with Luteimonas mephitis DSM 12574T (98.0 %). However, the DNA-DNA relatedness value between them (38.1±0.6 %) was less than the threshold value for the delineation of genomic species. Ubiquinone-8 (Q-8) was the predominant quinone. The major fatty acids were iso-C15:0 and iso-C17:1 ω9c. The major polar lipids of the strain were diphosphatidylglycerol, phosphatidylglycerol and phosphatidylethanolamine. The G+C content of the genomic DNA was 71%. On the basis of phenotypic, chemotaxonomic and molecular characteristics, the strain SYP-B804T merits recognition as a representative of a novel species of the genus Luteimonas, for which the name Luteimonas notoginsengisoli sp. nov. is proposed with SYP-B804T (=KCTC 42211T=JCM 30329T) as the type strain.\",\n \"corpus_id\": 12469428,\n \"score\": 2\n },\n {\n \"doc_id\": \"28853686\",\n \"title\": \"Serratia oryzae sp. nov., isolated from rice stems.\",\n \"abstract\": \"A novel endophytic bacterium, strain J11-6T, was isolated from rice stems. Its taxonomic position was investigated using a polyphasic approach. The novel strain was Gram-staining-negative, facultatively anaerobic, motile and rod-shaped. Although the results of phylogenetic analysis based on 16S rRNA gene sequences indicated that J11-6T represented a member of the genus Rahnella, multilocus sequence analysis (MLSA) on the basis of concatenated partial atpD, gyrB, rpoB and infB gene sequences showed a clear distinction of J11-6T from the type strains of species of the genus Rahnella but indicated that it lay within the clade of the genus Serratia. The phylogenetically closest species were Serratia fonticola and Serratia aquatilis on the basis of the results of the MLSA phylogenetic analysis. The predominant cellular fatty acids were C16 : 1ω7c (38.7 %) and C16 : 0 (25.0 %). The DNA G+C content was 53.2 mol%. The DNA-DNA relatedness was 17.4 % between J11-6T and Rahnella aquatilis CIP 78.65T, and 29.2 % between J11-6T and S. fonticola LMG 7882T which indicates that this strain represents a novel species of the genus Serratia. Characterization by genotypic and phenotypic analysis indicated that J11-6T (=ACCC 19934T=KCTC 52529T) represents a novel species of the genus Serratia, for which the name Serratia oryzae sp. nov. is proposed.\",\n \"corpus_id\": 24881970,\n \"score\": 2\n },\n {\n \"doc_id\": \"18175699\",\n \"title\": \"Actibacter sediminis gen. nov., sp. nov., a marine bacterium of the family Flavobacteriaceae isolated from tidal flat sediment.\",\n \"abstract\": \"A yellow-pigmented, Gram-negative, aerobic bacterial strain comprising rod-shaped cells devoid of flagellar and gliding motility, designated strain JC2129(T), was isolated from tidal flat sediment of Dongmak on Ganghwa Island, South Korea. Results from a 16S rRNA gene sequence analysis indicated that the isolate belonged to the family Flavobacteriaceae; the highest level of nucleotide sequence similarity (91.9%) occurred with Polaribacter dokdonensis DSW-5(T). The predominant cellular fatty acids were iso-C(15:0) (19.8%), iso-C(15:1) G (14.0%), iso-C(17:0) 3-OH (13.7%) and iso-C(13:0) (6.4%). Flexirubin-type pigments were absent. The major isoprenoid quinone was MK-6. The DNA G+C content was 43-45 mol%. Data from a polyphasic taxonomy study suggested that the isolate represents a novel genus and species in the family Flavobacteriaceae, for which the name Actibacter sediminis gen. nov., sp. nov. is proposed. The type strain of Actibacter sediminis is JC2129(T) (=KCTC 12704(T) =JCM 14002(T)).\",\n \"corpus_id\": 7089875,\n \"score\": 1\n },\n {\n \"doc_id\": \"19502335\",\n \"title\": \"Bacillus solisalsi sp. nov., a halotolerant, alkaliphilic bacterium isolated from soil around a salt lake.\",\n \"abstract\": \"A novel Gram-positive, motile, rod-shaped bacterium isolated from a saline soil in China was characterized by a polyphasic taxonomic approach. The strain, designated YC1(T), was halotolerant [tolerating up to 15 % (w/v) NaCl] and alkaliphilic (growing at a broad pH range of 5-13). 16S rRNA gene sequence analysis revealed that the isolate belonged to the genus Bacillus, showing highest similarity to Bacillus macauensis JCM 13285(T) (98.0 %). However, DNA-DNA hybridization indicated low levels of genomic relatedness with B. macauensis JCM 13285(T) (8.5 %). The major isoprenoid quinone was MK-7 and the cellular fatty acid profile consisted of significant amounts of iso-C(15 : 0) (38.6 %) and anteiso-C(15 : 0) (35.9 %). The predominant polar lipids were diphosphatidylglycerol, phosphatidylglycerol and phosphatidylethanolamine. The G+C content of the genomic DNA was 41.8 mol%. On the basis of the polyphasic evidence from this study, strain YC1(T) (=KCTC 13181(T)=CGMCC 1.6854(T)) should be classified as the type strain of a novel species of the genus Bacillus, for which the name Bacillus solisalsi sp. nov. is proposed.\",\n \"corpus_id\": 206165166,\n \"score\": 1\n },\n {\n \"doc_id\": \"19528203\",\n \"title\": \"Sediminimonas qiaohouensis gen. nov., sp. nov., a member of the Roseobacter clade in the order Rhodobacterales.\",\n \"abstract\": \"Two aerobic bacterial strains, YIM B024(T) and YIM B025, were isolated from a salt mine in Yunnan, south-west China. Both strains showed almost the same physiological properties. Cells were Gram-negative, non-motile, non-spore-forming rods. The novel strains grew at 15-37 degrees C, pH 6.5-9.0 and 0.25-20 % (w/v) NaCl; optimum growth was observed at 28-30 degrees C, pH 7.0-8.5 and 1.5-10 % NaCl. Oxidase, catalase and nitrate-reducing activities were detected. The two strains were closely related to each other with a 16S rRNA gene sequence similarity of 100 %. DNA-DNA hybridization experiments revealed high relatedness values (90+/-0.4 %) between strains YIM B024(T) and YIM B025, which suggested that these two new strains constituted a single species. Phylogenetic analysis based on 16S rRNA gene sequences indicated that the two isolates formed a loose cluster with members of the genus Roseivivax in the Roseobacter clade, but were clearly separated from this genus. The levels of 16S rRNA gene sequence similarity between the two isolates and members of the genus Roseivivax ranged from 92.4 to 93.9 %. The major polar lipids comprised diphosphatidylglycerol, phosphatidylglycerol, phosphatidylcholine and four unknown phospholipids. The major cellular fatty acids were C(18 : 1)omega7c, C(16 : 0), C(18 : 1)omega9c, 11-methyl C(18 : 1)omega7c and C(19 : 0) cyclo omega8c. The sole respiratory quinone was Q-10 and the genomic DNA G+C content was 63.0-64.1 mol%. The distinct phylogenetic position and a combination of phenotypic and chemotaxonomic characteristics supported the proposal of the new isolates as representing a novel species in a new genus, for which the name Sediminimonas qiaohouensis gen. nov., sp. nov. is proposed. The type strain of the type species is YIM B024(T) (=KCTC 22349(T)=CCTCC AA 208033(T)).\",\n \"corpus_id\": 5079226,\n \"score\": 1\n },\n {\n \"doc_id\": \"19542113\",\n \"title\": \"Bacillus korlensis sp. nov., a moderately halotolerant bacterium isolated from a sand soil sample in China.\",\n \"abstract\": \"A Gram-positive-staining, rod-shaped, motile, spore-forming and moderately halotolerant bacterium, designated ZLC-26(T), was isolated from a sand soil sample collected from Xinjiang Province, China, and was characterized by using a polyphasic taxonomic approach. This isolate grew optimally at 30-37 degrees C and pH 7-8. It grew with 0-8% NaCl (optimum, 0-2 %). Comparative 16S rRNA gene sequence analysis showed that strain ZLC-26(T) was closely related to members of the genus Bacillus, exhibiting the highest 16S rRNA gene sequence similarities to Bacillus nealsonii DSM 15077(T) (97.1 %), B. shackletonii LMG 18435(T) (97.0 %), B. siralis 171544(T) (97.0 %), B. circulans IAM 12462(T) (96.7 %) and B. pocheonensis Gsoil 420(T) (96.7 %). Strain ZLC-26(T) contained MK-7 as the predominant menaquinone. The diagnostic diamino acid in the cell-wall peptidoglycan was meso-diaminopimelic acid. The major cellular fatty acids were iso-C(15 : 0), C(16 : 1)omega11c and anteiso-C(15 : 0). The DNA G+C content was 38.2 mol%. These chemotaxonomic results supported the affiliation of strain ZLC-26(T) to the genus Bacillus. However, low DNA-DNA relatedness values and distinguishing phenotypic characteristics allowed genotypic and phenotypic differentiation of strain ZLC-26(T) from recognized Bacillus species. On the basis of the evidence presented, strain ZLC-26(T) is considered to represent a novel species of the genus Bacillus, for which the name Bacillus korlensis sp. nov. is proposed. The type strain is ZLC-26(T) (=CCTCC AB 207172(T)=NRRL B-51302(T)).\",\n \"corpus_id\": 28213615,\n \"score\": 0\n }\n]","isConversational":false}}},{"rowIdx":81,"cells":{"query":{"kind":"string","value":"{\n \"doc_id\": \"25176387\",\n \"title\": \"Anti-glycation and anti-oxidation properties of Capsicum frutescens and Curcuma longa fruits: possible role in prevention of diabetic complication.\",\n \"abstract\": \"The accumulation of advanced glycationend products (AGE's) in the body, due to the non-enzymatic glycation of proteins is associated with several pathological conditions like aging and diabetes mellitus. Hence a plant having anti-glycation and anti-oxidation potentials may serve as therapeutic agent for diabetic complications and aging. In this study the anti-glycation and anti-oxidation properties of crude methanolic extracts of fruits of Capsicum frutescens and Curcuma longa were investigated. Among the two C. frutescens had more anti-glycation ability with a minimum inhibitory concentration (MIC50) of 90βg/mLas compared to 324βg/mL MIC50 of C. longa. Curcuma longa had the more anti-oxidation potential i.e. 35.01, 30.83 and 28.08% at 0.5mg, 0.25mg and 0.125mg respectively.\",\n \"corpus_id\": 46560489\n}"},"candidates":{"kind":"list like","value":[{"doc_id":"18167045","title":"Glycation inhibitory activity and the identification of an active compound in Plantago asiatica extract.","abstract":"The glycation reaction involves a series of non-enzymatic reactions between the carbonyl group on reducing sugars and the amino group on proteins leading to the formation of advanced glycation end-products (AGEs), which are acknowledged to be involved in the pathogenesis of diabetic and aging-related complications. Consequently, the development of AGE inhibitors is considered to have therapeutic potential in patients with diabetes or age-related diseases. The preliminary results showed that a methanol extract (PAE) of Plantago asiatica, which is traditionally used as a folk medicine in Asian countries to treat fever, cough, wound etc., had strong glycation inhibitory activity. The effects of the extract on AGE fluorescence were dose-dependent, reaching 41% inhibition at 0.1 microg/mL of extract. The purified principle from PAE was identified as plantamajoside. As well as antioxidant activities, in vitro glycation inhibitory activities with 10 and 25 mm plantamajoside were higher than those with 10 and 25 mm aminoguanidine. The results demonstrate that PAE and plantamajoside had significant effects on in vitro AGE formation, and the glycation inhibitory activity and antioxidant activity of plantamajoside were comparable to those obtained using millimolar concentrations of the standard antiglycation agent aminoguanidine, and the antioxidant ascorbate, respectively.","corpus_id":24664890,"score":2},{"doc_id":"18350451","title":"Polyphenolic extract of Ichnocarpus frutescens attenuates diabetic complications in streptozotocin-treated diabetic rats.","abstract":"Diabetic nephropathy is one of the major complications of diabetes. Oxidative stress is implicated as an important mechanism by which diabetes causes nephropathy. The aim of the study was to examine the involvement of oxidative stress in the progression of nephropathy in STZ diabetic animals and to evaluate the potential of polyphenolic extract (PPE) in the treatment of diabetes mellitus. In this study, we examined whether prolonged oral administration of polyphenolic extract of Ichnocarpus frutescens could prevent the progress or improve the outcome of diabetic nephropathy induced by oxidative stress in STZ diabetic rats. Intraperitoneal glucose tolerance test (IPGTT) revealed a significant decrease in blood glucose levels at 180 min after glucose loading in Wistar albino rats fed with PPE. During the eight weeks of experimental period, diabetic rats exhibited wide range of symptoms, including loss of body weight, hyperglycemia, polyuria, proteinuria, renal enlargement, and total renal dysfunction. A significant increase in TBARS level was observed in diabetic kidney, which was accompanied by a significant decrease in enzymatic and non-enzymatic antioxidant levels. After eight weeks, PPE-treated groups showed a lower level of blood glucose compared with non-treated STZ diabetic rats. The increases in urinary albumin and protein after eight weeks of treatment were significantly inhibited by prolonged treatment with PPE. In addition, PPE attenuates the adverse effects on hepatic biomarkers. We found that PPE can effectively protect against aldose reductase activity and protein damage (albumin glycation), and showed that its action was mainly due to enriched polyphenolic content. Our results also showed that treatment with PPE normalized the increase in hyperalgesia (i.e., the response to thermal stimuli) associated with the induction of diabetes by STZ. PPE administration in diabetic rats clearly ameliorated diabetic complications, suggesting not only a natural antioxidant but also supportive therapy for the treatment of type II diabetes.","corpus_id":205592916,"score":2},{"doc_id":"18421073","title":"The anti-inflammatory effects of Curcuma longa and Berberis aristata in endotoxin-induced uveitis in rabbits.","abstract":"PURPOSE: To investigate the anti-inflammatory effect of topical application of Curcuma longa (C. longa) and Berberis aristata (B. aristata) aqueous extracts on experimental uveitis in the rabbit. METHODS: Anterior uveitis was induced in rabbits by intravitreal injection of lipopolysaccharide from Escherichia coli after pretreatment with C. longa and B. aristata aqueous extracts. Subsequently, the anti-inflammatory activity of C. longa and B. aristata was evaluated by grading the clinical signs and histopathologic changes and estimating the inflammatory cell count, protein, and TNF-alpha levels in the aqueous humor. RESULTS: The anterior segment inflammation in the control group was significantly higher than in both the extract-treated groups, as observed by clinical and histopathologic grading. The inflammatory cell count in the control group was 30.75 +/- 7.33 x 10(5) cells/mL, whereas it was 2.39 +/- 0.59 x 10(5) (P < 0.001 vs. control) and 11.56 +/- 2.44 x 10(5) (P = 0.001 vs. control) cells/mL in the C. longa- and B. aristata-treated groups, respectively. The protein content of the aqueous humor was 18.14 +/- 4.98, 3.16 +/- 0.55 (P < 0.001 vs. control), and 8.24 +/- 1.42 (P < 0.01 vs. control) mg/mL in the control, C. longa-, and B. aristata-treated groups, respectively. The aqueous TNF-alpha level in the control group was 976.29 +/- 66.38 pg/mL and was 311.96 +/- 28.50 (P < 0.0001 vs. control) and 654.09 +/- 47.66 (P < 0.001vs. control) pg/mL in the C. longa- and B. aristata-treated groups, respectively. CONCLUSIONS: Topical instillation of aqueous extracts of C. longa and B. aristata showed potent anti-inflammatory activity against endotoxin-induced uveitis in rabbits.","corpus_id":15207070,"score":2},{"doc_id":"18820805","title":"[The role of advanced glycation end-products (AGEs) in the development of vascular diabetic complications].","abstract":"O papel dos produtos finais da glicação avançada (AGEs) no desencadeamento das complicações vasculares do diabetes. The advanced glycation end-products (AGEs) constitute a class of heterogeneous molecules formed by amino-carbonyl reactions of a non-enzymatic nature, which occur at an accelerated rate in the hyperglycemic state of diabetes. Considered important pathogenic mediators of diabetic complications, AGEs are capable of irreversibly modifying the chemical properties and functions of diverse biological structures. In this review, recent data from literature is presented describing the pathways of AGEs formation, their metabolism, the main mechanisms of action of these substances in the triggering of pathological processes associated with diabetes, as well as methods of AGEs determination in biological samples. This text also points to new perspectives in anti-AGE therapies, an example of which is the studies involved with the action of natural compounds of food, which can represent a potential coadjuvant therapy for people with diabetes or other pathologies associated with the degenerative accumulation of AGEs.","corpus_id":7407948,"score":2},{"doc_id":"18949134","title":"Free radical scavenging profile and myeloperoxidase inhibition of extracts from antidiabetic plants: Bauhinia forficata and Cissus sicyoides.","abstract":"There is abundant evidence that reactive oxygen species are implicated in several physiological and pathological processes. To protect biological targets from oxidative damage, antioxidants must react with radicals and other reactive species faster than biological substrates do. The aim of the present study was to determine the in vitro antioxidant activity of aqueous extracts from leaves of Bauhinia forficata Link (Fabaceae-Caesalpinioideae) and Cissus sicyoides L. (Vitaceae) (two medicinal plants used popularly in the control of diabetes mellitus), using several different assay systems, namely, 2,2'-azino-bis(3-ethylbenzothiazoline-6-sulfonic acid) (ABTS) decolorization, superoxide anion radical (O2(.-)) scavenging and myeloperoxidase (MPO) activity. In the ABTS assay for total antioxidant activity, B. forficata showed IC50 = 8.00+/-0.07 microg/mL, while C. sicyoides showed IC50 = 13.0+/-0.2 microg/mL. However, the extract of C. sicyoides had a stronger effect on O2(.-) (IC50 = 60.0+/-2.3 microg/mL) than the extract of B. forficata (IC50 = 90.0+/-4.4 microg/mL). B. forficata also had a stronger inhibitory effect on MPO activity, as measured by guaiacol oxidation, than C. sicyoides. These results indicate that aqueous extracts of leaves of B. forficata and C. sicyoides are a potential source of natural antioxidants and may be helpful in the prevention of diabetic complications associated with oxidative stress.","corpus_id":18394945,"score":2},{"doc_id":"18986599","title":"Prevention of non-enzymic glycation of proteins by dietary agents: prospects for alleviating diabetic complications.","abstract":"The accumulation of advanced glycation endproducts (AGE) due to non-enzymic glycation of proteins has been implicated in several pathophysiologies associated with ageing and diabetes. The formation of AGE is accelerated in hyperglycaemic conditions, which alter the structure and function of long-lived proteins. Thus inhibition of the formation of AGE is believed to play a role in the prevention of diabetic complications. In the present study we evaluated the antiglycating effect of aqueous extracts of various plant-based foods. The effect of aqueous extracts of these agents in terms of their ability to prevent the accumulation of AGE due to fructose-mediated in vitro glycation of eye lens soluble proteins was investigated. The degree of protein glycation in the absence and presence of dietary extracts was assessed by different complementary methods, i.e. non-tryptophan AGE fluorescence, AGE-induced cross-linking by SDS-PAGE and glyco-oxidative damage by carbonyl assay. Five out of the seventeen agents tested showed significant inhibitory potential against in vitro protein glycation in a dose-dependent manner. Prominent among them were ginger, cumin, cinnamon, black pepper and green tea, which inhibited in vitro AGE formation to lens proteins 40-90 % at 1.0 mg/ml concentration. Assessing their potential to reduce the amount of glycated protein using boronate affinity chromatography and also their ability to prevent the formation of specific antigenic-AGE structures by immunodetection further substantiated the importance of ginger, cumin and cinnamon in reducing AGE burden. These findings indicate the potential of some dietary components to prevent and/or inhibit protein glycation. Thus these dietary agents may be able to be exploited for controlling AGE-mediated diabetic pathological conditions in vivo.","corpus_id":25490281,"score":2},{"doc_id":"19489690","title":"Hyperglycemia and glycation in diabetic complications.","abstract":"Diabetes mellitus is a multifactorial disease, classically influenced by genetic determinants of individual susceptibility and by environmental accelerating factors, such as lifestyle. It is considered a major health concern,as its incidence is increasing at an alarming rate, and the high invalidating effects of its long-term complications affect macro- and microvasculature, heart, kidney, eye, and nerves. Increasing evidence indicates that hyperglycemia is the initiating cause of the tissue damage occurring in diabetes, either through repeated acute changes in cellular glucose metabolism, or through the long-term accumulation of glycated biomolecules and advanced glycation end products (AGEs). AGEs represent a heterogeneous group of chemical products resulting from a nonenzymatic reaction between reducing sugars and proteins, lipids, nucleic acids, or a combination of these. The glycation process (glucose fixation) affects circulating proteins (serum albumin, lipoprotein, insulin, hemoglobin),whereas the formation of AGEs implicates reactive intermediates such as methylglyoxal. AGEs form cross-links on long-lived extracellular matrix proteins or react with their specific receptor RAGE, resulting inoxidative stress and proinflammatory signaling implicated in endothelium dysfunction, arterial stiffening, and microvascular complications. This review summarizes the mechanism of glycation and of AGEs formation and the role of hyperglycemia, AGEs, and oxidative stress in the pathophysiology of diabetic complications.","corpus_id":20627439,"score":2},{"doc_id":"19954478","title":"Advanced glycation end products and receptor-oxidative stress system in diabetic vascular complications.","abstract":"Reducing sugars can react non-enzymatically with amino groups of protein to form Amadori products. These early glycation products undergo further complex reactions, such as rearrangement, dehydration, and condensation, to become irreversibly cross-linked, heterogeneous fluorescent derivatives, termed advanced glycation end products (AGEs). The formation and accumulation of AGEs have been known to progress at an accelerated rate in patients with diabetes mellitus, thus being involved in the development and progression of diabetic micro- and macroangiopathy. Indeed, there is accumulating evidence that an interaction between an AGE and its receptor (RAGE) generates oxidative stress and subsequently evokes vascular inflammation and thrombosis, thereby playing a central role in diabetic vascular complications. In this paper, we review the pathophysiological role of AGE-RAGE-oxidative stress system and its therapeutic interventions in diabetic micro- and macroangiopathy.","corpus_id":11190337,"score":2},{"doc_id":"20184132","title":"[Glycation and protein crosslinking in the diabetes and ageing pathogenesis].","abstract":"Glicación y entrecruzamiento de proteínas en la patogénesis de la diabetes y el envejecimiento. Long exposition to hyperglycemia is associated with development of vascular diseases in diabetic patients. Many of these effects are mediated by non-enzymatic glycosylation (glycation) of proteins and formation of advanced glycation end-products (AGEs). This phenomenon is accelerated in conditions where glucose concentration is chronically high, as it happens in diabetes mellitus. AGE formation is associated with structure-function alterations of proteins such as collagen, and particularly in tissues where these products are accumulated. A number of studies have demonstrated that AGEs can act as mediators, not only for the development of chronic complications of diabetes, but also in those related to ageing, nephropathy, Alzheimer's disease and erectile dysfunction, among others. In this paper, information generated about formation and accumulation of AGEs, including its biological effects and their participation in the development of complications in diabetes mellitus and other process such as ageing is revised. In addition, therapeutic strategies and a new methodology to measure glycation products are also considered.","corpus_id":34662516,"score":2},{"doc_id":"20451573","title":"Antihyperglycemic activity and inhibition of advanced glycation end product formation by Cuminum cyminum in streptozotocin induced diabetic rats.","abstract":"Cuminum cyminum is widely used as a spice in many countries. The aim of the present study was to investigate the effect of methanolic extract of seeds of C. cyminum (CC) on diabetes, oxidative stress and formation of advanced glycated end products (AGE) and obtain comparison with glibenclamide. In vitro studies indicated that CC inhibited free radicals and AGE formation. Treatment of streptozotocin-diabetic rats with CC and glibenclamide for 28 days caused a reduction in blood glucose, glycosylated hemoglobin, creatinine, blood urea nitrogen and improved serum insulin and glycogen (liver and skeletal muscle) content when compared to diabetic control rats. Significant reduction in renal oxidative stress and AGE was observed with CC when compared to diabetic control and glibenclamide. CC and glibenclamide improved antioxidant status in kidney and pancreas of diabetic rats. Diabetic rats showed increase in rat tail tendon collagen, glycated collagen, collagen linked fluorescence and reduction in pepsin digestion. Treatment with CC significantly improved these parameters when compared to diabetic control and glibenclamide group. Though the antidiabetic effect of CC was comparable to glibenclamide it had better effect in controlling oxidative stress and inhibiting the AGE formation, which are implicated in the pathogenesis of diabetic microvascular complications.","corpus_id":7433711,"score":2},{"doc_id":"20717877","title":"Inhibition of advanced glycation end product formation by medicinal plant extracts correlates with phenolic metabolites and antioxidant activity.","abstract":"Nonenzymatic formation of advanced glycation end products (AGEs) is accelerated under hyperglycemic conditions characteristic of type 2 diabetes mellitus and contributes to the development of vascular complications. As such, inhibition of AGE formation represents a potential therapeutic target for the prevention and treatment of diabetic complications. In the present study, ethanolic extracts of 17 medicinal plants were assessed for inhibitory effects on in vitro AGE formation through fluorometric and immunochemical detection of fluorescent AGEs and N(ε)-(carboxymethyl)lysine adducts of albumin (CML-BSA), respectively. Most extracts inhibited fluorescent AGE formation with IC (50) values ranging from 0.4 to 38.6 µg/mL and all extracts reduced CML-BSA formation but to differing degrees. Results obtained through both methods were highly correlated. Antiglycation activities were positively correlated with total phenolic content, free radical scavenging activity and reduction in malonyldiadehyde levels following oxidation of low-density lipoprotein, but negatively correlated with lag time to formation of conjugated dienes. Together, these results provide evidence that antioxidant phenolic metabolites mediate the antiglycation activity of our medicinal plant collection, a relationship that likely extends to other medicinal and food plants.","corpus_id":9813185,"score":2},{"doc_id":"21120596","title":"Anti-inflammatory and anti-oxidant properties of Curcuma longa (turmeric) versus Zingiber officinale (ginger) rhizomes in rat adjuvant-induced arthritis.","abstract":"Turmeric (rich in curcuminoids) and ginger (rich in gingerols and shogaols) rhizomes have been widely used as dietary spices and to treat different diseases in Ayurveda/Chinese medicine since antiquity. Here, we compared the anti-inflammatory/anti-oxidant activity of these two plants in rat adjuvant-induced arthritis (AIA). Both plants (at dose 200 mg/kg body weight) significantly suppressed (but with different degrees) the incidence and severity of arthritis by increasing/decreasing the production of anti-inflammatory/pro-inflammatory cytokines, respectively, and activating the anti-oxidant defence system. The anti-arthritic activity of turmeric exceeded that of ginger and indomethacin (a non-steroidal anti-inflammatory drug), especially when the treatment started from the day of arthritis induction. The percentage of disease recovery was 4.6-8.3% and 10.2% more in turmeric compared with ginger and indomethacin (P < 0.05), respectively. The present study proves the anti-inflammatory/anti-oxidant activity of turmeric over ginger and indomethacin, which may have beneficial effects against rheumatoid arthritis onset/progression as shown in AIA rat model.","corpus_id":10202571,"score":2},{"doc_id":"21341505","title":"[Non-enzymatic glycation of proteins: from diabetes to cancer].","abstract":"Incubation of proteins with glucose leads to their non-enzymatic glycation and formation of Amadori products known as an early glycation product. Oxidative cleavage of Amadori products is considered as a major route to advanced glycation endproducts (AGEs) formation in vivo. Nonenzymatic glycation of proteins or Maillard reaction is increased in diabetes mellitus due to hyperglycemia and leads to several complications such as blindness, heart disease, nerve damage and kidney failure. Accumulation of the early and advanced glycation products in plasma and tissues of diabetic patients and causes production of autoantibodies against corresponding products. The advanced glycation products are also associated with other diseases like cancer. This review summarizes current knowledge of these stage specific glycated products as common and early diagnostic biomarkers for the associated diseases and the complications with the aim of a novel therapeutic target for the diseases.","corpus_id":32051578,"score":2},{"doc_id":"21440603","title":"Role of advanced glycation end products (AGEs) and oxidative stress in vascular complications in diabetes.","abstract":"BACKGROUND: A non-enzymatic reaction between reducing sugars and amino groups of proteins, lipids and nucleic acids contributes to the aging of macromolecules, whose process has been known to progress at an accelerated rate under hyperglycemic and/or oxidative stress conditions. Over a course of days to weeks, early glycation products undergo further reactions such as rearrangements and dehydration to become irreversibly cross-linked, fluorescent protein derivatives termed advanced glycation end products (AGEs). SCOPE OF REVIEW: In this paper, we review the role of AGE-oxidative stress axis and its therapeutic interventions in vascular complications in diabetes. MAJOR CONCLUSIONS: AGEs elicit oxidative stress generation and subsequently cause inflammatory and thrombogenic reactions in various types of cells via interaction with a receptor for AGEs (RAGE), thereby being involved in vascular complications in diabetes. In addition, mitochondrial superoxide generation has been shown to play an important role in the formation and accumulation of AGEs under diabetic conditions. Further, we have recently found that a pathophysiological crosstalk between AGE-RAGE axis and renin-angiotensin system (RAS) could contribute to the progression of vascular damage in diabetes. GENERAL SIGNIFICANCE: These observations suggest that inhibition of AGE-RAGE-oxidative stress axis or blockade of its interaction with RAS is a novel therapeutic strategy for preventing vascular complications in diabetes.","corpus_id":39308860,"score":2},{"doc_id":"21457747","title":"Phytochemical profile, antioxidant, anti-inflammatory and hypoglycemic potential of hydroalcoholic extracts from Citrus medica L. cv Diamante flowers, leaves and fruits at two maturity stages.","abstract":"Since the past decade consumption of certain foods has been reported to have a positive effect on health. The object of the study was to determine for the first time the chemical composition and the antioxidant, anti-inflammatory and hypoglycemic potential of Citrus medica L. cv Diamante flowers, leaves and fruits (endocarp and mesocarp) at two maturity stages. Flowers and leaves were characterized by the highest total phenols and flavonoids content. A declining trend was observed during maturity of fruits for both phenols and flavonoids. The antioxidant activity evaluated by the β-carotene bleaching test showed a strong activity for flowers and endocarp of mature fruits with IC50 values of 2.8 μg/mL and 3.5 μg/mL, respectively, after 30 min of incubation. Interestingly, the mature fruits endocarp (IC50 value of 426.0 μg/mL) could inhibit α-amylase with an IC50 value 2-fold higher than immature fruits. None of the tested extracts affected the proliferation of human skin fibroblasts 142BR. The obtained results suggest a potential use of C. medica L. cv Diamante as new valuable Citrus species with functional properties for food or nutraceutical product on the basis of high content of phytochemicals.","corpus_id":8351905,"score":2},{"doc_id":"22151933","title":"Topical vesicular formulations of Curcuma longa extract on recuperating the ultraviolet radiation-damaged skin.","abstract":"BACKGROUND: Ultraviolet radiations generate reactive oxygen species, leading to adverse effects on skin properties. Botanical extracts are multifunctional in nature having various properties like photoprotection, anti-aging, moisturizing, antioxidant, astringent, anti-irritant, and antimicrobial activity. AIMS: The aim of this study was to formulate creams having Curcuma longa extract loaded novel vesicular systems (liposomes, ethosomes, and transfersomes) and study their photoprotective effect by assessment of skin hydration (Cutometer) and sebum content (Sebumeter). METHODS: The alcoholic C. longa extract loaded liposomes, ethosomes, and transfersomes having 0.5-2.0% w/w extract were prepared, evaluated for size, entrapment efficiency, and incorporated into the cream. Their long-term interaction with skin (6 weeks) was compared in terms of their effects on skin hydration and sebum content. RESULTS: Vesicular size obtained was in the range 167.3 ± 3.0 to 262.4 ± 2.4 nm with low polydispersity index (0.2-0.3) and high entrapment efficiency. The efficacy was in the order C. longa extract loaded transfersomal creams > C. longa extract loaded ethosomal creams > C. longa extract loaded liposomal creams > C. longa extract loaded creams > Empty transfersome loaded cream > Empty ethosome loaded cream > Empty liposome loaded cream > Base cream. CONCLUSIONS: The photoprotective properties of the constituents of C. longa extract and hydrant, moisturizing lipid components of nano vesicles with better skin penetration resulted in improvement in skin properties like skin hydration and sebum content. The herbal extract loaded nano vesicles incorporated in cream could be used as photoprotective formulations.","corpus_id":32714749,"score":2},{"doc_id":"22268395","title":"Natural products as anti-glycation agents: possible therapeutic potential for diabetic complications.","abstract":"Diabetes mellitus is characterised by hyperglycaemia, lipidaemia and oxidative stress and predisposes affected individuals to long-term complications afflicting the eyes, skin, kidneys, nerves and blood vessels. Increased protein glycation and the subsequent build-up of tissue advanced glycation endproducts (AGEs) contribute towards the pathogenesis of diabetic complications. Protein glycation is accompanied by generation of free radicals through autoxidation of glucose and glycated proteins and via interaction of AGEs with their cell surface receptors (referred to as RAGE). Glycationderived free radicals can damage proteins, lipids and nucleic acids and contribute towards oxidative stress in diabetes. There is interest in compounds with anti-glycation activity as they may offer therapeutic potential in delaying or preventing the onset of diabetic complications. Although many different compounds are under study, only a few have successfully entered clinical trials but none have yet been approved for clinical use. Whilst the search for new synthetic inhibitors of glycation continues, little attention has been paid to anti-glycation compounds from natural sources. In the last few decades the traditional system of medicine has become a topic of global interest. Various studies have indicated that dietary supplementation with combined anti-glycation and antioxidant nutrients may be a safe and simple complement to traditional therapies targeting diabetic complications. Data for forty two plants/constituents studied for anti-glycation activity is presented in this review and some commonly used medicinal plants that possess anti-glycation activity are discussed in detail including their active ingredients, mechanism of action and therapeutic potential.","corpus_id":21407008,"score":2},{"doc_id":"22530890","title":"In vitro anti-glycation and anti-oxidant properties of synthesized Schiff bases.","abstract":"A series of mono, bis and mixed Schiff bases (1-7) were synthesised and evaluated for potential anti-glycation and anti-oxidant activities using the bovine serum albumin-glucose assay and 2,2-diphenyl-1-picrylhydrazyl (DPPH) free radical assay respectively. All compounds showed significant (p<0.05) antiglycating activities with IC50 values (4.02x10(-24)±0.1-2.88x10(-1)±1.35 mM) which were lower than the standard positive control aminoguanidine (IC50: 1.51x10(-3)±2.11 mM). Moreover, compounds 1-7 were found to possess significant (p<0.05) DPPH radical scavenging properties with SC50 values (1.31x10(-19)±0.05 to 2.25x10(-1)±1.24 mM) lower than the standard ascorbic acid (SC50: 5.50x10(-3)±2.11 mM). Compound 6 was found to be the most potent anti-glycating molecule (IC50 value: 4.02x10(-24)±0.1 mM) while compound 5 was the most potent anti-oxidant molecule (SC50: 1.31x10(-19)±0.05 mM); both being significantly lower (p<0.05) than the respective positive controls used. The present data showed that the number of phenolic OH together with structural changes influence both the anti-glycation and anti-oxidant observed herein. This study provides for the first time a series of potential template molecules for possible pharmaceutical applications that warrant further investigation as potential anti-glycation and anti-oxidant agents which could be of importance in metabolic diseases including diabetes mellitus.","corpus_id":22068375,"score":2},{"doc_id":"22868139","title":"Curcuma longa and Curcuma mangga leaves exhibit functional food property.","abstract":"Although leaves of Curcuma mangga and Curcuma longa are used in food preparations, the bioactive components in it are not known. In this study, antioxidant, antiinflammatory and anticancer activities of leave extracts and its isolates were investigated using established bioassay procedures in our laboratory. The leaf extracts of both plants gave similar bioassay and chromatographic profiles. The methanolic and water extracts of C. mangga (CMM and CMW) and C. longa (CLM and CLW), at 100 μg/mL, inhibited lipid peroxidation (LPO) by 78%, 63%, 81% and 43%, cyclooxygenase enzymes COX-1 by 55%, 33%, 43% and 24% and COX-2 by 65%, 55%, 77% and 69%, respectively. At same concentration, CMM, CMW, CLM and CLW showed growth inhibition of human tumour cell lines by 0-46%. Therefore, a bioassay-guided isolation of water and methanolic extracts of C. longa was carried out and afforded nine isolates. At 25 μg/mL, these compounds inhibited LPO by 11-87%, COX-1 and -2 enzymes by 0-35% and 0-82% and growth of human tumour cells by 0-36%, respectively.","corpus_id":3108079,"score":2},{"doc_id":"22923199","title":"The in vitro protective effects of curcumin and demethoxycurcumin in Curcuma longa extract on advanced glycation end products-induced mesangial cell apoptosis and oxidative stress.","abstract":"Curcuma longa L. (CLL), a traditional herbal medicine, has been widely used for the prevention of diabetic vascular complications in recent years. However, the protective effects of curcuminoids in CLL on the AGEs-induced damage to mesangial cell are not fully understood. In this present study, dihydroethidium, superoxide dismutase kit, malondialdehyde kit, and acridine orange/ethidium bromide staining methods were used to evaluate the activities of curcumin and demethoxycurcumin (10(-11)-10(-9) M) on AGEs-induced oxidative stress and apoptosis, which were associated with the damage to mesangial cell. The results showed that these two compounds could significantly restore advanced glycation end products (AGEs)-induced apoptosis to normal levels (IC50 = 3.874 × 10(-11) M for curcumin and IC50 = 6.085 × 10(-11) M for demethoxycurcumin) and reduce remarkably reactive oxygen species generation in mesangial cell. Furthermore, curcumin and demethoxycurcumin dramatically elevated AGEs-decreased superoxide dismutase activity while significantly reducing AGEs-increased malondialdehyde content in cell culture supernatant. Our results suggest that both curcumin and demethoxycurcumin have a significant protective potential to the prevention of diabetic nephropathy.","corpus_id":12829704,"score":2},{"doc_id":"23047487","title":"Evaluation of the antioxidant and anti-glication effects of the hexane extract from Piper auritum leaves in vitro and beneficial activity on oxidative stress and advanced glycation end-product-mediated renal injury in streptozotocin-treated diabetic rats.","abstract":"The aim of this study was to investigate the antioxidant activity of hexane extracts from leaves of Piper auritum (HS). Eight complementary in vitro test methods were used, including inhibition of DPPH· radicals, nitric oxide, superoxide anion, ion-chelating, ABTS, oxygen radical absorbance capacity, β-carotene bleaching and peroxy radical scavenging. The results indicated that HS possesses high antioxidant activity. To add to these finding we tested the effect against oxidative stress in liver, pancreas and kidney in diabetic rats. Low levels of SOD, CAT, GPx and GSH in diabetic rats were reverted to near normal values after treatment with HS. These results suggest that P. auritum prevents oxidative stress, acting as a suppressor of liver cell damage. Given the link between glycation and oxidation, we proposed that HS might possess significant in vitro antiglycation activity. Our data confirmed the inhibitory effect of HS on bovine serum albumin, serum glycosylated protein, glycation of LDL, and glycation hemoglobin. The effect of HS on diabetic renal damage was investigated using streptozotocin-induced diabetic rats. The oral administration of HS at a dose of 200 and 400 mg/kg body weight/day for 28 days significantly reduced advanced glycation endproduct (AGE) formation, elevated renal glucose and thiobarbituric acid-reactive substance levels in the kidneys of diabetic rats. This implies that HS would alleviate the oxidative stress under diabetes through the inhibition of lipid peroxidation. These findings indicate that oxidative stress is increased in the diabetic rat kidney and that HS can prevent renal damage associated with diabetes by attenuating the oxidative stress.","corpus_id":16963703,"score":2},{"doc_id":"23167275","title":"Chemical analysis and biological activities of Cupressus sempervirens var. horizontalis essential oils.","abstract":"CONTEXT: Safe and effective antioxidants are regarded as a cornerstone for the prevention and treatment of several types of disorders. OBJECTIVE: The present study aimed to investigate the antioxidant and anti-glycation properties of branchlet and fruit oils of Cupressus sempervirens L. var. horizontalis (Mill.) Gord. ( Cupressaceae). MATERIALS AND METHODS: Essential oils were extracted from the branchlets and fruits of C. sempervirens var. horizontalis using the steam distillation method. A gas chromatography-mass spectrometry method was employed for the compositional analysis of essential oils. In order to evaluate antioxidant activities of oils at different concentrations (180, 220 and 260 μg mL(-1)), linoleic acid peroxidation test and peroxyl radical mediated hemolysis of red blood cells (RBC) assay were used. Linoleic acid peroxidation was monitored for 4 h and determined during each hour of incubation. Antiglycation effects of oils at 200, 400 and 600 μg mL(-1) were assessed using hemoglobin and insulin glycation assays. RESULTS: Overall, 10 volatile components were identified, amounting for 88.2 and 93.2% of branchlet and fruit oils, respectively. α-Pinene and δ-3-carene were major components of both branchlet (46.2 and 22.7%) and fruit (59.2 and 14.9%) oils. Hemoglobin glycation was inhibited by both branchlet (44.8, 62.6 and 54.0% at 200, 400 and 600 μg mL(-1), respectively) and fruit (41.0, 62.8 and 48.5%) oils. As for the insulin glycation, inhibitory rates were 66.1, 69.2 and 73.8% for branchlet oil, and 80.0, 76.9 and 81.5% for fruit oil (at 200, 400 and 600 μg mL(-1), respectively). RBC hemolysis was also inhibited by both branchlet (49.9, 38.5 and 15.0% at 180, 220 and 260 μg mL(-1), respectively) and fruit (45.9, 38.6 and 25.0%) oil. Finally, the oils mitigated linoleic acid peroxidation which was peaked after 4 h for both branchlet (39.5, 35.6 and 53.4% at 180, 220 and 260 μg mL(-1), respectively) and fruit (47.5, 58.6 and 59.8%) oil. CONCLUSIONS: The present findings suggest that essential oils obtained from the branchlets and fruits of C. sempervirens var. horizontalis possess antioxidant and, in particular, antiglycation properties. These activities may find implication in the prevention of diabetic and cardiovascular complications. However, further investigations are required to justify the traditional medical applications of the plant.","corpus_id":20386770,"score":2},{"doc_id":"23297565","title":"Antiglycation and antioxidation properties of Juglans regia and Calendula officinalis: possible role in reducing diabetic complications and slowing down ageing.","abstract":"OBJECTIVE: Accumulation of advanced glycation end products (AGEs) in the body due to the non-enzymatic glycation of proteins and oxidation is associated with aging and diabetes mellitus. In this study we wanted to investigate the antiglycation and antioxidation potential of two medicinal plants: Juglans regia and Calendula officinalis. METHODS: In-vitro investigation was carried out to discover the antiglycation and antioxidation potential of J. regia and C. officinalis. Using an Ultraviolet Double-beam Spectrophotometer, we evaluated the antiglycation property of the crude methanolic extracts of J. regia and C. officinalis by assessing their ability to inhibit the Maillard reaction. Employing the same instrument we also measured the antioxidation potential of these plant extracts using the nitric oxide (NO) free radical-scavenging assay. RESULTS: J. regia had greater antiglycation ability, with a minimum inhibitory concentration (MIC50) of 28 microg/mL as compared with that of C. officinalis (270 microg/mL). C. officinalis had greater antioxidation potential (26.10, 22.07 and 16.06% at 0.5 mg, 0.25 mg and 0.125 mg, respectively, as compared with 18.15, 16.50 and 16.06% of J. regia, respectively). CONCLUSION: J. regia and C. officinalis inhibited the Maillard reaction and prevented oxidation in-vitro. Hence, the extracts of these plants could have therapeutic uses in curbing chronic diabetic complications and slowing down aging.","corpus_id":10454102,"score":2},{"doc_id":"23768830","title":"Antioxidant and anti-glycation activities correlates with phenolic composition of tropical medicinal herbs.","abstract":"OBJECTIVE: To determine the contribution of total phenolic content (TPC) in glycation inhibitory activity of common tropical medicinal food and spices with potential antioxidative properties. METHODS: In vitro glucose-bovine serum albumin (BSA) assay was used. Ethanolic extracts of ten common household condiments/herbs (Allium sativum, Zingiber officinale, Thymus vulgaris, Petroselinum crispum, Murraya koenigii Spreng, Mentha piperita L., Curcuma longa L., Allium cepa L., Allium fistulosum and Coriandrum sativum L.) were evaluated for antioxidative activity by 2,2-diphenyl-2-picrylhydrazyl (DPPH), and ferric reducing antioxidant power (FRAP) and the TPC, flavonoid and tannins content were determined. RESULTS: Findings showed good correlation between TPC/DPPH (r = 0.8), TPC/FRAP (r = 0.8), TPC/anti-glycation (r = 0.9), DPPH/anti-glycation (r = 0.6), FRAP/anti-glycation (r = 0.9), Flavonoid/anti-glycation (r = 0.7) and Tannins/anti-glycation (r = 0.8) and relatively fair correlation for TPC/Flavonoids (r = 0.5) and TPC/Tannins (r = 0.5). Results imply that these plants are potential sources of natural antioxidants which have free radical scavenging activity and might be used for reducing oxidative stress. CONCLUSIONS: The positive glycation inhibitory and antioxidative activities of these tropical herbs suggest a possible role in targeting ageing, diabetic complications and oxidative stress related diseases.","corpus_id":3411406,"score":2},{"doc_id":"24093976","title":"Do plants mediate their anti-diabetic effects through anti-oxidant and anti-apoptotic actions? an in vitro assay of 3 Indian medicinal plants.","abstract":"BACKGROUND: Both experimental and clinical studies suggest that oxidative stress plays a major role in the pathogenesis of both types of diabetes mellitus. This oxidative stress leads to β-cell destruction by apoptosis. Hence exploring agents modulating oxidative stress is an effective strategy in the treatment of both Type I and Type II diabetes. Plants are a major source of anti-oxidants and exert protective effects against oxidative stress in biological systems. Phyllanthus emblica, Curcuma longa and Tinospora cordifolia are three such plants widely used in Ayurveda for their anti-hyperglycemic activity. Additionally their anti-oxidant properties have been scientifically validated in various experimental in vitro and in vivo models. Hence the present in vitro study was planned to assess whether the anti-hyperglycemic effects of the hydro-alcoholic extracts of Phyllanthus emblica (Pe) and Curcuma longa (Cl) and aqueous extract of Tinospora cordifolia (Tc) are mediated through their antioxidant and/or anti-apoptotic property in a streptozotocin induced stress model. METHODS: RINm5F cell line was used as a model of pancreatic β-cells against stress induced by streptozotocin (2 mM). Non-toxic concentrations of the plant extracts were identified using MTT assay. Lipid peroxidation through MDA release, modulation of apoptosis and insulin release were the variables measured to assess streptozotocin induced damage and protection afforded by the plant extracts. RESULTS: All 3 plants extracts significantly inhibited MDA release from RIN cells indicating protective effect against STZ induced oxidative damage. They also exhibited a dose dependent anti-apoptotic effect as seen by a decrease in the sub G0 population in response to STZ. None of the plant extracts affected insulin secretion from the cells to a great extent. CONCLUSION: The present study thus demonstrated that the protective effect of the selected medicinal plants against oxidative stress induced by STZ in vitro, which was exerted through their anti-oxidant and anti-apoptotic actions.","corpus_id":15294246,"score":2},{"doc_id":"24374440","title":"Protective effect of crude Curcuma longa and its methanolic extract in alloxanized rabbits.","abstract":"Curcuma longa (C. longa) is commonly found in different areas of Pakistan. It has been locally utilized as a traditional medicine. The aim of this study was to evaluate the antidiabetic, hepatoprotective and total antioxidant effect of the crude drug and its methanolic extract in rabbits. Diabetes was induced with alloxan (180mg/kg). Two major groups were designed, curative and protective groups. In curative group the crude drug and its methanolic extract was orally administered to the diabetic animals and acute study was performed. On the other hand in protective group the crude drug and its methanolic extract were administered for eight days prior to the diabetes induction. Results indicated that in Curative group the crude and methanolic extract of C. longa significantly improved the levels of serum glucose, serum transaminases and antioxidant activity (AOA). In protective group, serum glucose, serum transaminases were not significantly increased by alloxan, in both crude as well as methanolic extract group. This study shows that C. longa acts as antidiabetic, hepatoprotective and antioxidant in diabetes especially type 1 diabetes.","corpus_id":24316741,"score":2},{"doc_id":"24448675","title":"Investigating wild berries as a dietary approach to reducing the formation of advanced glycation endproducts: chemical correlates of in vitro antiglycation activity.","abstract":"Evidence supports the health promoting benefits of berries, particularly with regard to the prevention and management of chronic diseases such cardio- and cerebrovascular disease, diabetes and Alzheimer's disease. Two related pathophysiological features common to many of these conditions are oxidative stress and the accumulation of advanced glycation endproducts (AGEs). Whereas antioxidant properties are well-established in several species of berries and are believed central to their protective mechanisms, few studies have investigated the effects of berries on AGE formation. Here, employing a series of complementary in vitro assays, we evaluated a collection of wild berry extracts for 1) inhibitory effects on fluorescent-AGE and Nε- (carboxymethyl)lysine-albumin adduct formation, 2) radical scavenging activity and 3) total phenolic and anthocyanin content. All samples reduced AGE formation in a concentration-dependent manner that correlated positively with each extract's total phenolic content and, to a lesser degree, total anthocyanin content. Inhibition of AGE formation was similarly related to radical scavenging activities. Adding antiglycation activity to the list of established functional properties ascribed to berries and their phenolic metabolites, our data provide further insight into the active compounds and protective mechanisms through which berry consumption may aid in the prevention and treatment of chronic diseases associated with AGE accumulation and toxicity. As widely available, safe and nutritious foods, berries represent a promising dietary intervention worthy of further investigation.","corpus_id":14469293,"score":2},{"doc_id":"24497740","title":"Comparative assessment on in vitro antioxidant activities of ethanol extracts of Averrhoa bilimbi, Gymnema sylvestre and Capsicum frutescens.","abstract":"BACKGROUND: Averrhoa bilimbi, Gymnema sylvestre and Capsicum frutescens are medicinal plants commonly used as traditional medicine for the treatment of various diseases. The present study was designed to investigate the antioxidant activities of Ethanolic extract of A. bilimbi, G. sylvestre and C. frutescens. MATERIALS AND METHODS: The antioxidant activity of the extracts were evaluated using total phenolic and flavonoid contents, ferric reducing power and the free radical scavenging activity against 1,1-diphenyl-2-picrylhydrazyl (DPPH). RESULTS: Total phenolic and flavonoid contents were higher in G. sylvestre (53.63636 ± 0.454545 mg/g gallic acid equivalent) and C. frutescens (26.66667 ± 2.081666 mg/g quercetin equivalent) respectively. Reducing power of the crude ethanol extracts increased with the concentrations of the extracts and all the extracts showed moderate free radical scavenging activity against DPPH. The plant extract displayed moderate phenolic and flavonoid contents compared to gallic acid and quercetin equivalent respectively, whereas also exhibited significant scavenging of DPPH radical and reducing power compared with ascorbic acid as standard. CONCLUSION: Our study suggests that G. sylvestre has significant antioxidant activity. The antioxidant compound of this plant might be a therapeutic candidate against oxidative stress related diseases. Different sub-fraction of A. bilimbi and C. frutescens should be studied further to assess the effect. Further study is necessary for isolation and characterization of the active antioxidant agents for better treatment.","corpus_id":20730258,"score":2},{"doc_id":"24597145","title":"Antioxidant potential and oxidative DNA damage preventive activity of unexplored endemic species of Curcuma.","abstract":"Free radical scavenging activity, ferrous ion chelating capacity, reducing power and genoprotective effect of the aqueous leaf extracts of four unexplored endemic Curcuma spp. ( C. vamana, C. neilgherrensis, C. mutabilis, C. haritha) were found to be dose-dependent and were highest in C. vamana. DNA protection property of the extracts was evaluated against H202/UV-induced oxidative damage. DNA-methyl green displacement assay showed that these extracts were free of DNA intercalating compounds. Further, hemolysis assay also showed that the extracts were non-toxic to human erythrocytes. The results highlight C. vamana as a promising source for herbal preparations possessing high antioxidant potential and genoprotective activity.","corpus_id":33937115,"score":2},{"doc_id":"24634591","title":"Advanced glycation end products and diabetic complications.","abstract":"During long standing hyperglycaemic state in diabetes mellitus, glucose forms covalent adducts with the plasma proteins through a non-enzymatic process known as glycation. Protein glycation and formation of advanced glycation end products (AGEs) play an important role in the pathogenesis of diabetic complications like retinopathy, nephropathy, neuropathy, cardiomyopathy along with some other diseases such as rheumatoid arthritis, osteoporosis and aging. Glycation of proteins interferes with their normal functions by disrupting molecular conformation, altering enzymatic activity, and interfering with receptor functioning. AGEs form intra- and extracellular cross linking not only with proteins, but with some other endogenous key molecules including lipids and nucleic acids to contribute in the development of diabetic complications. Recent studies suggest that AGEs interact with plasma membrane localized receptors for AGEs (RAGE) to alter intracellular signaling, gene expression, release of pro-inflammatory molecules and free radicals. The present review discusses the glycation of plasma proteins such as albumin, fibrinogen, globulins and collagen to form different types of AGEs. Furthermore, the role of AGEs in the pathogenesis of diabetic complications including retinopathy, cataract, neuropathy, nephropathy and cardiomyopathy is also discussed.","corpus_id":3034045,"score":2},{"doc_id":"24650229","title":"Pharmacological importance of an ethnobotanical plant: Capsicum annuum L.","abstract":"Capsicum annuum L., a fruit plant from tropical and subtropical regions, contains a range of essential nutrients and bioactive compounds which are known to exhibit a range of bioactivities including free radical scavenging (antioxidant), antimicrobial, antiviral, anti-inflammatory and anticancer. This review aims to give a comprehensive overview of the literature published on pharmacological behaviours of C. annuum L.","corpus_id":12600252,"score":2},{"doc_id":"24772978","title":"Inhibitory effect of Piper betle Linn. leaf extract on protein glycation--quantification and characterization of the antiglycation components.","abstract":"Piper betle Linn. is a Pan-Asiatic plant having several beneficial properties. Protein glycation and advanced glycation end products (AGEs) formation are associated with different pathophysiological conditions, including diabetes mellitus. Our study aims to find the effect of methanolic extract of P. betle leaves on in vitro protein glycation in bovine serum albumin (BSA)-glucose model. The extract inhibits glucose-induced glycation, thiol group modification and carbonyl formation in BSA in dose-dependent manner. It inhibits different stages of protein glycation, as demonstrated by using glycation models: hemoglobin-delta-gluconolactone (for early stage, Amadori product formation), BSA-methylglyoxal (for middle stage, formation of oxidative cleavage products) and BSA-glucose (for last stage, formation of AGEs) systems. Several phenolic compounds are isolated from the extract. Considering their relative amounts present in the extract, rutin appears to be the most active antiglycating agent. The extract of P. betle leaf may thus have beneficial effect in preventing protein glycation and associated complications in pathological conditions.","corpus_id":978810,"score":2},{"doc_id":"24967413","title":"Dietary intake of Curcuma longa and Emblica officinalis increases life span in Drosophila melanogaster.","abstract":"Intake of food and nutrition plays a major role in affecting aging process and longevity. However, the precise mechanisms underlying the ageing process are still unclear. To this respect, diet has been considered to be a determinant of ageing process. In order to better illustrate this, we used Drosophila melanogaster as a model and fed them orally with different concentrations of two commonly used Indian medicinal plant products, Curcuma longa (rhizome) and Emblica officinalis (fruit). The results revealed significant increase in life span of Drosophila flies on exposure to both the plant products, more efficiently by C. Longa than by E. officinalis. In order to understand whether the increase in lifespan was due to high-antioxidant properties of these medicinal plants, we performed enzymatic assays to assess the SOD and catalase activities in case of both treated and control Drosophila flies. Interestingly, the results support the free radical theory of aging as both these plant derivatives show high reactive oxygen species (ROS) scavenging activities.","corpus_id":16408821,"score":2},{"doc_id":"25477660","title":"In vitro antidiabetic and inhibitory potential of turmeric (Curcuma longa L) rhizome against cellular and LDL oxidation and angiotensin converting enzyme.","abstract":"Turmeric (Curcuma longa L) rhizome extracts were evaluated for their antidiabetic, antihypertensive and antioxidant potentials. α-Glucosidase (0.4 μg/mL) and α-amylase (0.4 μg/mL) inhibitory potential of turmeric ethyl acetate extract was significantly higher than those of the reference drug acarbose (17.1 μg/mL and 290.6 μg/mL respectively). Protein glycation inhibitory potential of ethyl acetate extract was 800 times higher than that of ascorbic acid. High potential of ethyl acetate extract to scavenge free radicals and to reduce LDL oxidation and cellular oxidative stress was also revealed. The positive correlation obtained between the free radical scavenging capacity of the extracts and their antiglycation potential further confirmed the role of antioxidants in controlling glycation reactions. Ethyl acetate extract was also found as effective in reducing hypertension by inhibiting angiotensin converting enzyme (ACE). Antidiabetic, ACE inhibitory and antioxidant capacities of the extracts were in the order of their curcumin contents.","corpus_id":27369814,"score":2},{"doc_id":"25657787","title":"Inhibition of protein glycation by essential oils of branchlets and fruits of Juniperus communis subsp. hemisphaerica.","abstract":"Oxidative stress and protein glycation play pivotal roles in the pathophysiology of diabetes mellitus and its vascular complications. The present study aimed to investigate the anti-glycation properties of essential oils obtained from different parts of Juniperus communis subsp. hemisphaerica. The branchlets of male tree (BMT) and branchlets of female (BFT) tree, and fruits of J. communis subsp. hemisphaerica were extracted using steam distillation method. The oils were phytochemically analyzed using gas chromatography-mass spectrometry. Anti-glycation properties were evaluated using hemoglobin and insulin glycation assays. Overall, 18 volatile components were identified in the J. communis subsp. hemisphaerica oils, amounting to 82.1%, 100.0% and 96.4% of the BMT, BFT and fruit oils, respectively. Promising inhibitory activity was observed from all concentrations of the tested oils in the hemoglobin and insulin glycation assays. The inhibitory activities peaked to 89.9% (BFT oil; 200 μg mL(-1)) and 81.0% (BFT oil; 600 μg mL(-1)) in the hemoglobin and insulin glycation assays, respectively. The evidence from this study suggests that essential oils obtained from the fruits and branchlets of J. communis subsp. hemisphaerica possess anti-glycation properties. These activities may find implication for the prevention and treatment of diabetic complications.","corpus_id":1598856,"score":2},{"doc_id":"26088351","title":"Curcumin: a natural product for diabetes and its complications.","abstract":"Curcumin is the yellow-colored bioactive constituent of the perennial plant, Curcuma longa L., which possesses a wide range of physiological and pharmacological properties such as antioxidant, anti-inflammatory, anticancer, neuroprotective and anti-diabetic activities. Anti-diabetic activity of curcumin may be due to its potent ability to suppress oxidative stress and inflammation. Moreover, it shows a beneficial role on the diabetesinduced endothelial dysfunction and induces a down-regulation of nuclear factor-kappa B. Curcumin possesses a protective role against advanced glycation as well as collagen crosslinking and through this way, mitigates advanced glycation end products-induced complications of diabetes. Curcumin also reduces blood glucose, and the levels of glycosylated hemoglobin in diabetic rat through the regulation of polyol pathway. It also suppresses increased bone resorption through the inhibition of osteoclastogenesis and expression of the AP-1 transcription factors, c-fos and c-jun, in diabetic animals. Overall, scientific literature shows that curcumin possesses anti-diabetic effects and mitigates diabetes complications. Here we report a systematical discussion on the beneficial role of curcumin on diabetes and its complications with emphasis on its molecular mechanisms of actions.","corpus_id":37630935,"score":2},{"doc_id":"26417319","title":"Combined anti-ages and antioxidant activities of different solvent extracts of Solanum elaeagnifolium Cav (Solanacea) fruits during ripening and related to their phytochemical compositions.","abstract":"Oxidative stress and advanced glycation end products (AGEs) are known as key factors for the development of diabetic complications such as retinopathy, cataract as well as atherosclerosis and neurodegenerative diseases, including Alzheimer's diseases. In this context, natural products have been previously identified as promising sources for antioxidant and anti-glycation compounds. The current study focuses on the evaluation of antioxidant and glycation inhibitory activities of different solvent extracts of Solanum elaeagnifolium Cav (Solanaceae) fruits at different ripening stages. The results showed that antioxidant and anti-AGEs activities were significantly influenced by solvents polarities and ripening stages of S. elaeagnifolium Cav. With one exception, methanolic extract of overripe S. elaeagnifolium Cav fruit showed important protective effects against cellular oxidative stress. The aqueous extract showed the highest ABTS(+) scavenging ability. Principal component analysis showed that total phenolic and flavonoid contents correlated well with observed antioxidants and anti-glycation activities. These results bring attention to the possible use of S. elaeagnifolium Cav as a valuable source of bioactive compounds exhibiting antioxidant effects and potentially alleviating diabetic complications.","corpus_id":11530325,"score":2},{"doc_id":"26966424","title":"The protective effects of pomelo extract (Citrus grandis L. Osbeck) against fructose-mediated protein oxidation and glycation.","abstract":"Chronic hyperglycemia induces non-enzymatic protein glycation, which plays an important role in the development of diabetic complications. Immense efforts have been made to determine effective antiglycation compounds from natural products. Pomelo has shown beneficial effects for human health. The objective of this study was to determine the antiglycation effect of pomelo extract against fructose-mediated protein oxidation and glycation. Our results showed that the pomelo extract (0.25 - 2.00 mg/mL) significantly inhibited the overall formation of advanced glycation end products (AGEs) in a concentration-dependent manner. The pomelo extract markedly decreased the level of fructosamine, which is directly associated with reduction in formation of AGEs and N (ε)-(carboxymethyl)lysine (CML). In addition, the pomelo extract inhibited protein oxidation through its ability to prevent the loss of thiol groups and reduced protein carbonyl formation. We characterized the active components in the pomelo extract by using high-performance liquid chromatography (HPLC), which showed that the pomelo extract contained naringin (11.90 ± 0.21 mg/g dried extract), hesperidin (12.04 ± 0.12 mg/g dried extract), neohesperidin (25.4 ± 0.12 mg/g dried extract), and naringenin (9.20 ± 0.19 mg/g dried extract). Our findings could provide a new insight into the antiglycation properties of the extract of the naturally occurring fruit pomelo for preventing AGE-mediated diabetic complications.","corpus_id":14090794,"score":2},{"doc_id":"27103908","title":"Prevention of non-enzymatic glycosylation (glycation): Implication in the treatment of diabetic complication.","abstract":"Non-enzymatic glycosylation (glycation) plays an important role in the development of physiological and pathophysiological processes such as aging, diabetes, atherosclerosis, neurodegenerative diseases and chronic renal failure. Preventing glycation can minimize diabetic complications. Glycation can be prevented by the natural defence system in the body, synthetic inhibitors and natural inhibitors. Synthetic inhibitors may prevent glycation through several possible mechanisms. They might inhibit the glycation by interfering with the attachment of sugars with proteins, by inhibiting the late stage of glycation or by preventing Amadori product formation. Furthermore, their ability to scavenge free radicals and to break cross-links might be other mechanisms responsible for their potential to inhibit glycation. Naturally occurring phytochemicals/products have been found to be relatively non-toxic as compared to synthetic compounds, and are inexpensive and available in an ingestible form. A large number of plants and natural biomolecules have been shown to have antidiabetic effects. Several hypoglycaemic compounds have anti-oxidant properties. The present review describes the various ways in which glycation can be prevented.","corpus_id":42690278,"score":2},{"doc_id":"27213445","title":"The Possible Role of Flavonoids in the Prevention of Diabetic Complications.","abstract":"Type 2 diabetes mellitus is a disease that affects many metabolic pathways. It is associated with insulin resistance, impaired insulin signaling, β-cell dysfunction, abnormal glucose levels, altered lipid metabolism, sub-clinical inflammation and increased oxidative stress. These and other unknown mechanisms lead to micro- and macro-complications, such as neuropathy, retinopathy, nephropathy and cardiovascular disease. Based on several in vitro animal models and some human studies, flavonoids appear to play a role in many of the metabolic processes involved in type 2 diabetes mellitus. In this review, we seek to highlight the most recent papers focusing on the relationship between flavonoids and main diabetic complications.","corpus_id":9637140,"score":2},{"doc_id":"27495289","title":"In-Vitro dual inhibition of protein glycation, and oxidation by some Arabian plants.","abstract":"BACKGROUND: Diabetes mellitus is a metabolic disorder of epidemic proportion, projected to become the major cause of morbidity and mortality in the world in future. Despite extensive research in understanding this disease at molecular level, and the discovery of new drugs, diabetes and its complications remain largely untreated. Many of the late diabetic complications are associated with the glycation of proteins in the body. Natural flora has long been a rich source for therapeutic agents, especially against diabetes. The present study deals with the anti-glycation properties of some medicinally important plants of Arabian region. METHODS: Twenty-six medicinal plants, commonly found in different regions of Arabian Peninsula, were evaluated for their protein anti-glycation activity by using BSA-MG glycation assay in-vitro. The extracts were incubated with BSA and MG at 37 °C for 9 days, each sample was then examined for the presence of fluorescence (λex 330 nm, and λem 420 nm), which represent the extent of protein glycation. Antioxidant activity was evaluated by using 1,1-diphenyl- 2-picrylhydrazyl (DPPH), iron chelation, and superoxide radical scavenging asaays. RESULTS: The data revealed that out of 26 medicinal plants, five plants viz. Sida cordifolia, Plumbago zeylanica, Tribulus terrestris, Glycyrrhiza glabra, and Rosa indica were active against the in-vitro protein glycation with IC50 values between 0.408- 1.690 mg/mL. Among the active plants, Glycyrrhiza glabra L. was found to be the most potent (IC50 = 0.408 ± 0.027 mg/mL), followed by Rosa indica (IC50 = 0.596 ± 0.0179 mg/mL), and Sida cordifolia L. (IC50 = 0.63 ± 0.009 mg/mL). The antioxidant potential of these plant extracts were also determined by using DPPH (2,2-diphenyl-1-picrylhydrazyl), iron chelation, and superoxide anion radical scavenging assays. Among five plants, Sida cordifolia exhibited a potent anti-oxidant activity in both DPPH and superoxide anion radical scavenging assays (IC50 = 0.005 ± 0.0004, and 0.078 ± 0.002 mg/mL, respectively), followed by Rosa indica (IC50 = 0.023 ± 0.0005 and 0.141 ± 0.003 mg/mL, respectively). CONCLUSIONS: Protein glycation in hyperglycemic conditions involve oxidative changes. Therefore dual inhibition of protein glycation and oxidation are desirable properties in any test substance investigated for therapeutic purposes.","corpus_id":14581877,"score":2},{"doc_id":"27901193","title":"Physicochemical/photophysical characterization and angiogenic properties of Curcuma longa essential oil.","abstract":"This study analyzed the physicochemical and photophysical properties of essential oil of Curcuma longa and its angiogenic potential. The results showed that curcumin is the main fluorescent component present in the oil, although the amount is relatively small. The experimental chorioallantoic membrane model was used to evaluate angiogenic activity, showing a significant increase in the vascular network of Curcuma longa and positive control groups when compared to the neutral and inhibitor controls (P <0.05), but no significant difference was found between Curcuma longa essential oil and the positive control (P >0.05). Histological analysis showed extensive neovascularization, hyperemia and inflammation in the positive control group and Curcuma longa when compared to other controls (P <0.05), characteristic factors of the angiogenesis process. In conclusion, Curcuma longa oil showed considerable proangiogenic activity and could be a potential compound in medical applications.","corpus_id":3690599,"score":2},{"doc_id":"28053889","title":"Antioxidant, antiglycation and insulinotrophic properties of Coccinia grandis (L.) in vitro: Possible role in prevention of diabetic complications.","abstract":"In an attempt to develop Complementary and Alternative Medicine (CAM) for the treatment of diabetes and related complications, the antidiabetic potential of the mature unripe fruits of Coccinia grandis (CGF) was evaluated. Oxidative stress and glycation plays an important role in manifesting of diabetes and vascular complications. Agents with antioxidant and antiglycation properties may retard these pathological alterations. In this study, the edible plant Coccinia grandis was assessed for in vitro estimation of antioxidant and antiglycation potential and its insulinotrophic properties in RINm5F cells. Antioxidant activity was evaluated as DPPH (1,1-diphenyl-2-picrylhydrazyl), hydrogen peroxide and superoxide anion scavenging activities, whereas the protein glycation inhibitory potential was evaluated using in vitro albumin-fructose glycation model. Glycation inhibition was estimated by different biochemical parameters viz. fructosamine, protein carbonyl group and protein aggregation using thioflavin T fluorescence. C. grandis extract exerted a dose dependent radical scavenging activity and exhibited a significant antiglycation potential. The extract also showed a significant insulinotrophic property with 1.28 and 1.71-fold increase in insulin release when compared to control at 0.25 and 0.50 mg/mL, respectively. These data suggest the possible antidiabetic role of CGF extract, presumably by its antioxidant, antiglycation and insulin secretory effects. Present findings provide experimental evidence that the fruits of C. grandis have potential antidiabetic activity which might be used as a functional food and safe remedy for the treatment of diabetes and associated complications. This study also revealed that the plant can be a promising source for development of natural antiglycating agents and novel insulin secretagogues.","corpus_id":26098992,"score":2},{"doc_id":"28068085","title":"Cyclocurcumin, an Antivasoconstrictive Constituent of Curcuma longa (Turmeric).","abstract":"Despite the increasing attention on the therapeutic potential of Curcuma longa (turmeric), the biological activities of curcuminoids other than curcumin are not well understood. Here, we investigated antivasoconstrictive activities of C. longa extract and its ingredients using freshly isolated rat aortic rings. C. longa extract significantly suppressed agonist-stimulated vasoconstriction, and cyclocurcumin was found to be the most potent (IC50 against phenylephrine-induced vasoconstriction: 14.9 ± 1.0 μM) among the 10 tested ingredients including four curcuminoids. Cyclocurcumin significantly inhibited contraction of vascular smooth muscle, which was mediated by the suppression of myosin-light-chain phosphorylation and calcium influx via the L-type calcium channel. The inhibitory effect of cyclocurcumin was observed to be reversible and without cytotoxicity. Taken together, we demonstrated that cyclocurcumin, a bioactive ingredient in C. longa, may have a therapeutic potential as a novel antivasoconstrictive natural product.","corpus_id":4490231,"score":2},{"doc_id":"29169285","title":"Relaxant effect of Curcuma longa on rat tracheal smooth muscle and its possible mechanisms.","abstract":"CONTEXT: Turmeric is a spice obtained from the root of Curcuma longa L. (Zingiberaceae) with anti-aging, anticancer, anti-Alzheimer's disease, antioxidant and other medicinal properties. OBJECTIVE: The relaxant effect of C. longa on rat tracheal smooth muscle and its possible mechanisms were investigated in this study. MATERIALS AND METHODS: The relaxant effects of four cumulative concentrations of hydro-ethanol extract of C. longa (6.25, 12.5, 25, 50 mg/mL) were studied on tracheal smooth muscle precontracted by methacholine or KCl in non-incubated or incubated with different substances including propranolol, diltiazem, L-NAME, glibenclamide, atropine, chlorpheniramine, indomethacin and papaverine. The duration of the study was 84 days. RESULTS: In non-incubated tracheal smooth muscle, the extract of C. longa showed significant concentration-dependent relaxant effects (p < 0.001 for all concentrations on both KCl and methacholine-induced contraction). There was no significant difference in the relaxant effects between C. longa and theophylline in both methacholine and KCl-induced contraction conditions. In tissues incubated with propranolol, diltiazem, L-NAME and glibenclamide on methacholine-induced contraction and in tissues incubated with atropine, chlorpheniramine, indomethacin and papaverine on KCl-induced contraction, the extract also showed significant concentration-dependent relaxant effects (p < 0.001). EC50 values of C. longa between non-incubated (16.22 ± 0.62) and incubated tissues (atropine: 13.03 ± 0.55, chlorpheniramine: 12.94 ± 0.68, indomethacin: 14.80 ± 0.57 and papaverine: 16.16 ± 1.42) were not significantly different. CONCLUSIONS: Tracheal smooth muscle relaxant effects of C. longa, were comparable to those of theophylline, which could be due to the presence of methylxanthines or its possible interaction with non-adrenergic non-cholinergic nervous system.","corpus_id":24612650,"score":2},{"doc_id":"29232190","title":"The effects of Curcuma longa and curcumin on reproductive systems.","abstract":"OBJECTIVE: Curcuma longa (C. longa) was used in some countries such as China and India for various medicinal purposes. Curcumin, the active component of C. longa, is commonly used as a coloring agent in foods, drugs, and cosmetics. C. longa and curcumin have been known to act as antioxidant, anti-inflammatory, anti-mutagen, and anti-carcinogenic agents. Th e attempt of the present review was to give an effort on a detailed literature survey concentrated on the protective effects of C. longa and curcumin on the reproductive organs activity. METHODS: The databases such as, PubMed, Web of Science, Google Scholar, Scopus, and Iran- Medex, were considered. The search terms were \"testis\" or \"ovary\" and \"Curcuma longa\", \"curcumin\", \"antioxidant effect\", \"anti-inflammatory effect\" and \"anti-cancer effect\". RESULTS: C. longa and curcumin inhibited the production of the tumor necrosis factor-α (TNF-α) and prostaglandin E2 (PGE2) and increased the caspases (3, 8 and 9) activities in HL-60 prostate cancer. Furthermore, C. longa and curcumin suppressed the vascular endothelial growth factor (VEGF), phosphorylated signal transducers and activators of the transcription 3 (STAT) and matrix metalloproteinase-9 (MMP-9) in ovarian cancer cell line. CONCLUSION: C. longa and curcumin might decrease the risk of cancer and other malignant diseases in the reproductive system. C. longa and curcumin have a protective effect on the reproductive organs activity such as, anti-inflammatory, anti-apoptotic, and antioxidant effects in normal cells but showed pro-apoptotic effects in the malignant cells. Therefore, different effects of C. longa and curcumin are dependent on the doses and the type of cells used in various models studied.","corpus_id":31096998,"score":2},{"doc_id":"29274842","title":"Antioxidant and anti-glycation capacities of some medicinal plants and their potential inhibitory against digestive enzymes related to type 2 diabetes mellitus.","abstract":"ETHNOPHARMACOLOGICAL RELEVANCE: Plants preparations are used by traditional medicine in the treatment of various diseases, such as type-2 diabetes mellitus. Some medicinal plants are capable of controlling the complications of this metabolic disease at different levels, for example, providing antioxidant compounds that act against oxidative stress and protein glycation and others which are capable of inhibiting the catalysis of digestive enzymes and thus contribute to the reduction of hyperglycemia and hyperlipidemia. Our objective was to investigate the antioxidant and anti-glycation activities of some medicinal plants and their potential inhibitory against α-amylase, α-glucosidase and pancreatic lipase activities. MATERIAL AND METHODS: Based on the ethnobotanical researches carried out by academic studies conducted at the Federal University of Uberlandia, ten plants traditionally used in the treatment of type-2 diabetes mellitus were selected. Ethanol (EtOH) and hexane (Hex) extracts of specific parts of these plants were used in enzymatic assays to evaluate their inhibitory potential against α-amylase, α-glucosidase and lipase, as well as their antioxidant (DPPH, ORAC and FRAP) and anti-glycation (BSA/fructose model) capacities. RESULTS: The results indicate that EtOH extract of four of the ten analyzed plants exhibited more than 70% of antioxidant and anti-glycation capacities, and α-amylase and lipase inhibitory activities; no extract was able to inhibit more than 40% the α-glucosidase activity. The EtOH extracts of Bauhinia forficata and Syzygium. cumini inhibited α-amylase (IC50 8.17 ± 2.24 and 401.8 ± 14.7 μg/mL, respectively), whereas EtOH extracts of B. forficata, Chamomilla recutita and Echinodorus grandiflorus inhibited lipase (IC50 59.6 ± 10.8, 264.2 ± 87.2 and 115.8 ± 57.1 μg/mL, respectively). In addition, EtOH extracts of B. forficata, S. cumini, C. recutita and E. grandiflorus showed, respectively, higher antioxidant capacity (DPPH IC50 0.7 ± 0.1, 2.5 ± 0.2, 1.3 ± 0.2 and 35.3 ± 9.0 μg/mL) and anti-glycation activity (IC50 22.7 ± 4.4, 246.2 ± 81.7, 18.5 ± 2.8 and 339.0 ± 91.0 μg/mL). CONCLUSIONS: EtOH extracts of four of the ten species popularly cited for treatment of type 2 diabetes mellitus have shown promising antioxidant and anti-glycation properties, as well as the ability to inhibit the digestive enzymes α-amylase and lipase. Thus, our results open new possibilities for further studies in order to evaluate the antidiabetic potential of these medicinal plants.","corpus_id":24576820,"score":2},{"doc_id":"29480231","title":"Alpha-Synuclein Glycation and the Action of Anti-Diabetic Agents in Parkinson's Disease.","abstract":"Parkinson's disease (PD) is a neurodegenerative disorder with complex etiology and variable pathology. While a subset of cases is associated with single-gene mutations, the majority originates from a combination of factors we do not fully understand. Thus, understanding the underlying causes of PD is indispensable for the development of novel therapeutics. Glycation, the non-enzymatic reaction between reactive dicarbonyls and amino groups, gives rise to a variety of different reaction products known as advanced glycation end products (AGEs). AGEs accumulate over a proteins life-time, and increased levels of glycation reaction products play a role in diabetic complications. It is now also becoming evident that PD patients also display perturbed sugar metabolism and protein glycation, including that of alpha-synuclein, a key player in PD. Here, we hypothesize that anti-diabetic drugs targeting the levels of glycation precursors, or promoting the clearance of glycated proteins may also prove beneficial for PD patients.","corpus_id":3867626,"score":2},{"doc_id":"29618440","title":"Synergistic potential of Zingiber officinale and Curcuma longa to ameliorate diabetic-dyslipidemia.","abstract":"To find the cure of world's one of the leading morbid and mortal disorders; diabetes mellitus and its most prevalent complication, 'diabetic-dyslipidemia', is one of the leading health challenges of 21st century. The use of phytomedicine is a glimmer of hope in this scenario. Studies of current decade have shown that methanolic extracts of Zingiber officinale and Curcuma longa have highly effective therapeutic potentials against the aforesaid disorders, however, which of the extracts has more potential is still unclear. Furthermore, synergistic effect of the extracts has never been studied. Forty-eight Albino adult rats of either sex were randomly divided into eight groups. A-D groups were containing healthy rats while E-H groups were of induced diabetic-dyslipidemic rats. For forty-two days, rats of each group were given either distilled water or Zingiber officinale methanolic extract (ZOME) or Curcuma longa methanolic extract (CLME) or ZOME+CLME therapies at dose rate of 300mg/100 mL dist. H2O/kg body wt/day. FPG and lipid profiles were estimated before and after the trial, and were statistically analyzed by one-way ANOVA along with Post-hoc Tukey's multiple comparison tests. Although, ZOME and CLME significantly (P<0.05) lowered fasting plasma glucose (FPG) levels and controlled lipid profiles in diabetic-dyslipidemic rats; yet, synergistic therapy of both extracts (ZOME+CLME) most significantly (P<0.05) controlled all parameters of diabetic-dyslipidemia (78.00±1.06mg/dL FPG, 62.00±0.58mg/dL TG, 66.50±0.76mg/dL cholesterol, 32.00±0.36mg/dL HDL, 22.43±0.64 mg/dL LDL, and 12.40±0.12mg/dL VLDL). Our findings may be useful to formulate new medicines having multiple potentials to control diabetes mellitus, dyslipidemia, and diabetic-dyslipidemia.","corpus_id":4598978,"score":2},{"doc_id":"29624265","title":"CURCUMA LONGA AS MEDICINAL HERB IN THE TREATMENT OF DIABET- IC COMPLICATIONS.","abstract":"Curcuma longa L. (turmeric) of ginger family (Zingiberaceae) belongs to the group of oldest cultivated spice plants in the south-east Asian countries. For many years rhizome of this plant has been used also as a safe and active drug for the treatment of various.chronic diseases, especially of diabetes mellitus (DM). The active substance of turmeric - curcumin (diferuloylmethane), possesses multiple therapeutic properties. In recent years, many detailed research (tests in vito and in vivo) along with clinical trials have revealed its very valuable biological activities related to its anti-inflammatory, antioxidant and cancer preventive properties, which are presented in numerous publications (1-6). At the molecular level it has been stated that curcumin inhibits cell proliferation, metastasis creation and apoptosis. Currently, great attention has been focused on curcumin as a blocker of TNF-s, which are the principal mediators of most inflammation-related disturbances (7). The main cause of blocking the broadly extended pharmacological and clinical investigations of curcumin is its extremely low solubility in water and in organ fluids. This feature consequently limits its systemic bioavailability and makes use of curcumin as a therapeutic remedy (to date) difficult. The primary aim of presently conducted research is to achieve increased solubilization and bioavailability of this promising nontoxic agent.","corpus_id":4646629,"score":2},{"doc_id":"29624857","title":"Impact of wedelolactone in the anti-glycation and anti-diabetic activity in experimental diabetic animals.","abstract":"The glycation reaction is the addition of free carbonyl group of reducing sugar to the free amino groups of proteins, lipoproteins and nucleic acids which results in the formation of an Amadori product which may ultimately lead to the generation of advanced glycation products (AGEs). The impact of AGEs on proteins consequently generates free radicals, \"a key player\" for the pathogenesis of diabetes mellitus. Gel electrophoresis was carried out to see the visual changes taking place as a result of the glycation reaction. In this study, the anti-glycation and anti-diabetic effect of wedelolactone (WED) was seen both in vitro and in vivo. WED reverted various biochemical markers in streptozotocin-induced diabetic rats along-with the improvements in the oxidative stress markers. It also decreased the levels of the glycated serum protein and fasting blood glucose. Broadly, WED not only inhibited glycation in vitro but also proved to be an effective in vivo anti-glycating agent. © 2018 IUBMB Life, 70(6):547-552, 2018.","corpus_id":4634609,"score":2},{"doc_id":"29732511","title":"Protective effects of Curcuma longa against neurobehavioral and neurochemical damage caused by cerium chloride in mice.","abstract":"Cerium chloride (CeCl3) is considered an environmental pollutant and a potent neurotoxic agent. Medicinal plants have many bioactive compounds that provide protection against damage caused by such pollutants. Curcuma longa is a bioactive compound-rich plant with very important antioxidant properties. To study the preventive and healing effects of Curcuma longa on cerium-damaged mouse brains, we intraperitoneally injected cerium chloride (CeCl3, 20 mg/kg BW) along with Curcuma longa extract, administrated by gavage (100 mg/kg BW), into mice for 60 days. We then examined mouse behavior, brain tissue damage, and brain oxidative stress parameters. Our results revealed a significant modification in the behavior of the CeCl3-treated mice. In addition, CeCl3 induced a significant increment in lipid peroxidation, carbonyl protein (PCO), and advanced oxidation protein product levels, as well as a significant reduction in superoxide dismutase (SOD) and glutathione peroxidase (GPx) activities. Acetylcholinesterase (AChE) activity remarkably increased in the brain of CeCl3-treated mice. Histopathological observations confirmed these results. Curcuma longa attenuated CeCl3-induced oxidative stress and increased the activities of antioxidant enzymes. It also decreased AChE activity in the CeCl3-damaged mouse brain that was confirmed by histopathology. In conclusion, this study suggests that Curcuma longa has a neuroprotective effect against CeCl3-induced damage in the brain.","corpus_id":21389098,"score":2},{"doc_id":"18361755","title":"Influence of ripening stage on health benefits properties of Capsicum annuum var. acuminatum L.: in vitro studies.","abstract":"ABSTRACT In the present study the in vitro hypoglycemic and anti-acetylcholinesterase activities of hot pepper fruits (Capsicum annuum var. acuminatum L.) at different ripening stages were investigated. The mature, green-stage fruits had the highest activity against alpha-amylase and alpha-glucosidase with 50% inhibitory concentration (IC(50)) values of 55.88 and 76.11 microg/mL, respectively, while C. annuum var. acuminatum in the prematurity green stage exhibited the highest acetylcholinesterase inhibition property (IC(50) = 84.30 microg/mL), using the Ellman method. This study highlights the biochemical rationale for chemopreventive significance in health benefits when consuming this variety of pepper.","corpus_id":30445637,"score":1},{"doc_id":"18668490","title":"Dietary red chilli (Capsicum frutescens L.) is insulinotropic rather than hypoglycemic in type 2 diabetes model of rats.","abstract":"The present study was conducted to clarify whether a low or a high, but tolerable, dietary dose of red chilli (RC) can ameliorate the diabetes related complications in a high-fat (HF) diet-fed streptozotocin (STZ)-induced type 2 diabetes model of rats. Five-week-old male Sprague Dawley rats were fed a HF diet for 2 weeks then randomly divided into four groups namely: normal control (NC), diabetic control (DBC), red chilli low (RCL, 0.5%) and red chilli high (RCH, 2.0%) groups. Diabetes was induced by an intraperitoneal (i.p.) injection of STZ (40 mg/kg BW) in all groups except the NC group. After 4 weeks feeding of experimental diets, the fasting blood glucose concentrations in both RC fed groups were not significantly different. The serum insulin concentration was significantly (p < 0.05) increased in the RCH group compared with the DBC and RCL groups. Blood HbA1c, liver weight, liver glycogen and serum lipids were not influenced by the feeding of RC-containing diets. The data of this study suggest that 2% dietary RC is insulinotropic rather than hypoglycemic at least in this experimental condition.","corpus_id":9846280,"score":1},{"doc_id":"19447589","title":"Cyclophosphamide-induced oxidative stress in brain: protective effect of hot short pepper (Capsicum frutescens L. var. abbreviatum).","abstract":"This study sought to characterize the distribution of phenols and antioxidant activities in hot short pepper (Capsicum frutescens var. abbreviatum) and their inhibition of cyclophosphamide-induced oxidative stress in rat's brain. The total phenol content and antioxidant activities of pepper flesh (pericarp) and seeds were determined in vitro and in vivo. The results of the study revealed that intraperitoneal administration of cyclophosphamide (75mg/kg of body weight) caused a significant increase (P<0.05) in the malondialdehyde (MDA) content of the brain; however, there was a significant decrease (P<0.05) in the brain MDA content, in those of rats fed diet containing pepper; the flesh showed a higher inhibitory effect. In addition, dietary inclusion of the pepper (seed and flesh) also caused a dose-dependent inhibition of serum glutamate oxaloacetate transaminase (SGOT), glutamate pyruvate transaminase (SGPT), alkaline phosphatase and total bilirubin; likewise, dietary inclusion of the flesh inhibited MDA production than the seeds. The higher inhibition of oxidative stress in brain and serum enzymes and metabolites by the flesh could be attributed to its significantly higher (P<0.05) total phenol content, reducing power and free-radical scavenging ability. Therefore, dietary hot short pepper (Capsicum frutescens L. var. abbreviatum) could prevent cyclophosphamide-induced oxidative stress in brain; although the flesh is a better protectant, the possible contributory role of the seeds cannot be neglected. However, this protective effect of the pepper could be attributed to their antioxidant properties.","corpus_id":25190576,"score":1},{"doc_id":"20226481","title":"[Pentosidine: a new biomarker in diabetes mellitus complications].","abstract":"Pentosidina: un nuevo biomarcador de las complicaciones en la diabetes mellitus. Diabetes mellitus causes an increase of morbidity and mortality. Advanced glycosilation end products (AGE) are formed by non-enzymatic glycation between proteins and reducing sugars as glucose. Oxidative reactions (glycoxidations) are essential for the formation of some AGE, for example pentosidine. Increased concentrations of pentosidine can be found in pathological conditions associated with hyperglycaemia and also related to increased oxidative stress. In individuals with diabetes mellitus, pentosidine formation and accumulation is developed at an accelerated rate in cells without insulin control for glucose uptake. Pentosidine has a pivotal role in diabetic complications, probably as a consequence of the diverse properties of this compound, which alters the structure and function of molecules in biological systems. The following review discusses the alterations in the concentration of pentosidine in the body, particularly in relation to changes occurring in diabetes and its complications such as vascular and bone disease, nephropathy, neuropathy and retinopathy. Novel therapeutic approaches which can prevent or ameliorate the toxic effects of AGE in the initiation and progression of diabetic complications are reviewed.","corpus_id":10102290,"score":1},{"doc_id":"23376105","title":"Sutherlandia frutescens prevents changes in diabetes-related gene expression in a fructose-induced insulin resistant cell model.","abstract":"ETHNOPHARMACOLOGICAL RELEVANCE: The African medicinal plant Sutherlandia frutescens (L.) R.Br. ( Fabaceae) is traditionally used to treat diabetes and has been shown to have anti-diabetic properties in animal models. The present study investigated the capacity of an aqueous extract of Sutherlandia frutescens to prevent insulin resistance (a precursor of type 2 diabetes) in a human liver cell culture and to identify genes regulated by Sutherlandia frutescens treatment. MATERIALS AND METHODS: A combination of insulin and fructose was used to generate an in vitro model of insulin resistance in human liver cells to compare untreated control, insulin resistant and Sutherlandia frutescens treated insulin resistant cultures. Insulin resistance and its prevention by Sutherlandia frutescens were measured by glucose uptake, gluconeogenesis and lipid accumulation in the cell cultures. Changes in gene expression were quantified using the RT(2)Profiler(TM) PCR Array of 84 diabetes-related genes. RESULTS: The insulin resistant Chang liver cells took up significantly less 2-[(3)H]-deoxyglucose (p<0.05) than controls, released more glucose into the culture medium (p<0.05) and accumulated more intracellular lipid (p<0.05). Simultaneous treatment with Sutherlandia frutescens prevented development of these insulin resistance parameters (p<0.05). A total of 27 potential gene targets of Sutherlandia frutescens were significantly up or down regulated in the Sutherlandia frutescens treated insulin resistant cells. The gene VAMP3, which plays a role in vesicle transport, was down-regulated by insulin resistance, and up-regulated by Sutherlandia frutescens. Twenty six other genes encoding vesicle transporters, receptors, signalling molecules, transcription factors, and metabolic enzymes were significantly regulated by Sutherlandia frutescens. CONCLUSION: These results confirm that Sutherlandia frutescens can prevent insulin resistance in hepatocytes. The identified changes in gene expression indicate several potential mechanisms of anti-diabetic action for Sutherlandia frutescens, reflecting the multiple bioactive compounds previously identified in aqueous extracts of Sutherlandia frutescens.","corpus_id":25071583,"score":1},{"doc_id":"23426539","title":"DIA-2, a polyherbal formulation ameliorates hyperglycemia and protein-oxidation without increasing the body weight in type II diabetic rats.","abstract":"BACKGROUND: The dried bulbs of Allium sativum (Garlic) and leaves of Lagerstroemia speciosa (Banaba) are used as medicinal food for the treatment of diabetes and other ailments. AIM: The present study was undertaken to ascertain whether the combination of both garlic and banaba extract produces synergistic therapeutic effect in diabetic state. METHODS: In the in vitro studies, the effect of standardized aqueous extract of Allium sativum (ASE), methanolic extract of Lagerstroemia speciosa (LSE) and their mixture (1:1 ratio), DIA-2 on insulin stimulated glucose uptake in 3T3-L1 cells, erythrocyte sorbitol accumulation and protein glycation were evaluated. Impetus from the in vitro findings triggered to screen the anti-diabetic potential of DIA-2 in rat model of type II diabetes and associated oxidative stress. In the in vivo studies, acute oral toxicity of DIA-2 was determined following OECD-423 guidelines in female rats. Anti-diabetic activity of DIA-2 was investigated in high fat diet/low dose streptozotocin induced type II diabetes at four dose levels (62.5, 125, 250 and 500 mg/kg b.w) in rats. RESULTS: Combination of ASE and LSE produced synergistic and a dose dependent increase in glucose uptake in 3T3 adipocyte cell lines when compared to the individual extracts. A similar effect was observed in the inhibition of sorbitol accumulation and protein glycation tests. DIA-2 restored the glucose and lipid level near to normal level without gain in body weight which is the most commonly encountered side effect with the use of conventional antidiabetic agents, particularly insulin, insulin secretagogues, sulfonylureas and thiazolidinediones. DIA-2 also decreased hepatic protein carbonyl content levels significantly in the diabetic rats. CONCLUSIONS: The study concluded that DIA-2 posses potent anti-diabetic activity and anti-oxidant effects.","corpus_id":32090286,"score":1},{"doc_id":"24235936","title":"Comparative anti-inflammatory properties of Capsaicin and ethyl-aAcetate extract of Capsicum frutescens linn [Solanaceae] in rats.","abstract":"BACKGROUND: The analgesic effect of capsaicin (the active ingredient in Capsicum frutescens Linn. [ Solanaceae]) had been reported in several studies. Current research is being directed at producing analgesics, anti-inflammatory agents with better side effect profile. OBJECTIVES: To investigate if either the ethyl acetate extract of Capsicum frutescens Linn. [ Solanaceae] (CFE) or capsaicin (Fluka Biotechnika-CPF) (in addition to the known analgesic properties) has any anti-inflammatory effect comparable to nonsteroidal anti-inflammatory analgesics (NSAIDS). METHODS: The effects of ethyl acetate extract of Capsicum frutescens Linn. [ Solanaceae] (CFE) and capsaicin (Fluka Biotechnika-CPF) was examined on rat hind paw. Inflammation was induced in the rat's hind paw by subplantar injections of fresh egg albumin (0.5 ml/kg). Diclofenac (100 mg/kg) was used as the reference anti-inflammatory agent for comparison, while distilled water was used as the placebo. The leucocytes count, corticosterone and C - reactive protein (CRP) levels were measured as biomarkers of inflammation. Data obtained were pooled and analysed using repeated ANOVA, in a general linear model with the CPSS software. RESULTS: Sub-plantar injections of fresh egg albumin (0.5 ml/kg) produced profound and time-related oedema in the rat hind paw of the 'control' rats. Diclofenac (DIC, 100 mg/kg, i.p.) and reference capsaicin (CPF, 2.5 mg/kg, i.p.) significantly inhibited paw swelling at (p<0.05-0.001) (CI 95%) compared to distilled water-treated 'controls'. While the corticosterone levels were all very low in 7 rats treated with capsaicin, the leucocytes count was within normal range in 9 rats. However, in 16 specimens randomly assigned for CRP levels, there were very high CRP readings, up to a magnitude of 10 times the normal range. CONCLUSIONS: Capsaicin in both forms (CFE and CPF) produced anti-inflammatory effects that were comparable to diclofenac in the experimental rat model at p<0.05. It may be concluded that capsaicin has both analgesic and anti-inflammatory properties.","corpus_id":8360143,"score":1},{"doc_id":"20525746","title":"Hydraulic connections of leaves and fruit to the parent plant in Capsicum frutescens (hot pepper) during fruit ripening.","abstract":"BACKGROUND AND AIMS: The hydraulic architecture and water relations of fruits and leaves of Capsicum frutescens were measured before and during the fruiting phase in order to estimate the eventual impact of xylem cavitation and embolism on the hydraulic isolation of fruits and leaves before maturation/abscission. METHODS: Measurements were performed at three different growth stages: (1) actively growing plants with some flowers before anthesis (GS1), (2) plants with about 50 % fully expanded leaves and immature fruits (GS2) and (3) plants with mature fruits and senescing basal leaves (GS3). Leaf conductance to water vapour as well as leaf and fruit water potential were measured. Hydraulic measurements were made using both the high-pressure flow meter (HPFM) and the vacuum chamber (VC) technique. KEY RESULTS: The hydraulic architecture of hot pepper plants during the fruiting phase was clearly addressed to favour water supply to growing fruits. Hydraulic measurements revealed that leaves of GS1 plants as well as leaves and fruit peduncles of GS2 plants were free from significant xylem embolism. Substantial increases in leaf petiole and fruit peduncle resistivity were recorded in GS3 plants irrespective of the hydraulic technique used. The higher fraction of resistivity measured using the VC technique compared with the HPFM technique was apparently due to conduit embolism. CONCLUSIONS: The present study is the first to look at the hydraulics of leaves and fruits during growth and maturation through direct, simultaneous measurements of water status and xylem efficiency of both plant regions at different hours of the day.","corpus_id":24669270,"score":0}],"string":"[\n {\n \"doc_id\": \"18167045\",\n \"title\": \"Glycation inhibitory activity and the identification of an active compound in Plantago asiatica extract.\",\n \"abstract\": \"The glycation reaction involves a series of non-enzymatic reactions between the carbonyl group on reducing sugars and the amino group on proteins leading to the formation of advanced glycation end-products (AGEs), which are acknowledged to be involved in the pathogenesis of diabetic and aging-related complications. Consequently, the development of AGE inhibitors is considered to have therapeutic potential in patients with diabetes or age-related diseases. The preliminary results showed that a methanol extract (PAE) of Plantago asiatica, which is traditionally used as a folk medicine in Asian countries to treat fever, cough, wound etc., had strong glycation inhibitory activity. The effects of the extract on AGE fluorescence were dose-dependent, reaching 41% inhibition at 0.1 microg/mL of extract. The purified principle from PAE was identified as plantamajoside. As well as antioxidant activities, in vitro glycation inhibitory activities with 10 and 25 mm plantamajoside were higher than those with 10 and 25 mm aminoguanidine. The results demonstrate that PAE and plantamajoside had significant effects on in vitro AGE formation, and the glycation inhibitory activity and antioxidant activity of plantamajoside were comparable to those obtained using millimolar concentrations of the standard antiglycation agent aminoguanidine, and the antioxidant ascorbate, respectively.\",\n \"corpus_id\": 24664890,\n \"score\": 2\n },\n {\n \"doc_id\": \"18350451\",\n \"title\": \"Polyphenolic extract of Ichnocarpus frutescens attenuates diabetic complications in streptozotocin-treated diabetic rats.\",\n \"abstract\": \"Diabetic nephropathy is one of the major complications of diabetes. Oxidative stress is implicated as an important mechanism by which diabetes causes nephropathy. The aim of the study was to examine the involvement of oxidative stress in the progression of nephropathy in STZ diabetic animals and to evaluate the potential of polyphenolic extract (PPE) in the treatment of diabetes mellitus. In this study, we examined whether prolonged oral administration of polyphenolic extract of Ichnocarpus frutescens could prevent the progress or improve the outcome of diabetic nephropathy induced by oxidative stress in STZ diabetic rats. Intraperitoneal glucose tolerance test (IPGTT) revealed a significant decrease in blood glucose levels at 180 min after glucose loading in Wistar albino rats fed with PPE. During the eight weeks of experimental period, diabetic rats exhibited wide range of symptoms, including loss of body weight, hyperglycemia, polyuria, proteinuria, renal enlargement, and total renal dysfunction. A significant increase in TBARS level was observed in diabetic kidney, which was accompanied by a significant decrease in enzymatic and non-enzymatic antioxidant levels. After eight weeks, PPE-treated groups showed a lower level of blood glucose compared with non-treated STZ diabetic rats. The increases in urinary albumin and protein after eight weeks of treatment were significantly inhibited by prolonged treatment with PPE. In addition, PPE attenuates the adverse effects on hepatic biomarkers. We found that PPE can effectively protect against aldose reductase activity and protein damage (albumin glycation), and showed that its action was mainly due to enriched polyphenolic content. Our results also showed that treatment with PPE normalized the increase in hyperalgesia (i.e., the response to thermal stimuli) associated with the induction of diabetes by STZ. PPE administration in diabetic rats clearly ameliorated diabetic complications, suggesting not only a natural antioxidant but also supportive therapy for the treatment of type II diabetes.\",\n \"corpus_id\": 205592916,\n \"score\": 2\n },\n {\n \"doc_id\": \"18421073\",\n \"title\": \"The anti-inflammatory effects of Curcuma longa and Berberis aristata in endotoxin-induced uveitis in rabbits.\",\n \"abstract\": \"PURPOSE: To investigate the anti-inflammatory effect of topical application of Curcuma longa (C. longa) and Berberis aristata (B. aristata) aqueous extracts on experimental uveitis in the rabbit. METHODS: Anterior uveitis was induced in rabbits by intravitreal injection of lipopolysaccharide from Escherichia coli after pretreatment with C. longa and B. aristata aqueous extracts. Subsequently, the anti-inflammatory activity of C. longa and B. aristata was evaluated by grading the clinical signs and histopathologic changes and estimating the inflammatory cell count, protein, and TNF-alpha levels in the aqueous humor. RESULTS: The anterior segment inflammation in the control group was significantly higher than in both the extract-treated groups, as observed by clinical and histopathologic grading. The inflammatory cell count in the control group was 30.75 +/- 7.33 x 10(5) cells/mL, whereas it was 2.39 +/- 0.59 x 10(5) (P < 0.001 vs. control) and 11.56 +/- 2.44 x 10(5) (P = 0.001 vs. control) cells/mL in the C. longa- and B. aristata-treated groups, respectively. The protein content of the aqueous humor was 18.14 +/- 4.98, 3.16 +/- 0.55 (P < 0.001 vs. control), and 8.24 +/- 1.42 (P < 0.01 vs. control) mg/mL in the control, C. longa-, and B. aristata-treated groups, respectively. The aqueous TNF-alpha level in the control group was 976.29 +/- 66.38 pg/mL and was 311.96 +/- 28.50 (P < 0.0001 vs. control) and 654.09 +/- 47.66 (P < 0.001vs. control) pg/mL in the C. longa- and B. aristata-treated groups, respectively. CONCLUSIONS: Topical instillation of aqueous extracts of C. longa and B. aristata showed potent anti-inflammatory activity against endotoxin-induced uveitis in rabbits.\",\n \"corpus_id\": 15207070,\n \"score\": 2\n },\n {\n \"doc_id\": \"18820805\",\n \"title\": \"[The role of advanced glycation end-products (AGEs) in the development of vascular diabetic complications].\",\n \"abstract\": \"O papel dos produtos finais da glicação avançada (AGEs) no desencadeamento das complicações vasculares do diabetes. The advanced glycation end-products (AGEs) constitute a class of heterogeneous molecules formed by amino-carbonyl reactions of a non-enzymatic nature, which occur at an accelerated rate in the hyperglycemic state of diabetes. Considered important pathogenic mediators of diabetic complications, AGEs are capable of irreversibly modifying the chemical properties and functions of diverse biological structures. In this review, recent data from literature is presented describing the pathways of AGEs formation, their metabolism, the main mechanisms of action of these substances in the triggering of pathological processes associated with diabetes, as well as methods of AGEs determination in biological samples. This text also points to new perspectives in anti-AGE therapies, an example of which is the studies involved with the action of natural compounds of food, which can represent a potential coadjuvant therapy for people with diabetes or other pathologies associated with the degenerative accumulation of AGEs.\",\n \"corpus_id\": 7407948,\n \"score\": 2\n },\n {\n \"doc_id\": \"18949134\",\n \"title\": \"Free radical scavenging profile and myeloperoxidase inhibition of extracts from antidiabetic plants: Bauhinia forficata and Cissus sicyoides.\",\n \"abstract\": \"There is abundant evidence that reactive oxygen species are implicated in several physiological and pathological processes. To protect biological targets from oxidative damage, antioxidants must react with radicals and other reactive species faster than biological substrates do. The aim of the present study was to determine the in vitro antioxidant activity of aqueous extracts from leaves of Bauhinia forficata Link (Fabaceae-Caesalpinioideae) and Cissus sicyoides L. (Vitaceae) (two medicinal plants used popularly in the control of diabetes mellitus), using several different assay systems, namely, 2,2'-azino-bis(3-ethylbenzothiazoline-6-sulfonic acid) (ABTS) decolorization, superoxide anion radical (O2(.-)) scavenging and myeloperoxidase (MPO) activity. In the ABTS assay for total antioxidant activity, B. forficata showed IC50 = 8.00+/-0.07 microg/mL, while C. sicyoides showed IC50 = 13.0+/-0.2 microg/mL. However, the extract of C. sicyoides had a stronger effect on O2(.-) (IC50 = 60.0+/-2.3 microg/mL) than the extract of B. forficata (IC50 = 90.0+/-4.4 microg/mL). B. forficata also had a stronger inhibitory effect on MPO activity, as measured by guaiacol oxidation, than C. sicyoides. These results indicate that aqueous extracts of leaves of B. forficata and C. sicyoides are a potential source of natural antioxidants and may be helpful in the prevention of diabetic complications associated with oxidative stress.\",\n \"corpus_id\": 18394945,\n \"score\": 2\n },\n {\n \"doc_id\": \"18986599\",\n \"title\": \"Prevention of non-enzymic glycation of proteins by dietary agents: prospects for alleviating diabetic complications.\",\n \"abstract\": \"The accumulation of advanced glycation endproducts (AGE) due to non-enzymic glycation of proteins has been implicated in several pathophysiologies associated with ageing and diabetes. The formation of AGE is accelerated in hyperglycaemic conditions, which alter the structure and function of long-lived proteins. Thus inhibition of the formation of AGE is believed to play a role in the prevention of diabetic complications. In the present study we evaluated the antiglycating effect of aqueous extracts of various plant-based foods. The effect of aqueous extracts of these agents in terms of their ability to prevent the accumulation of AGE due to fructose-mediated in vitro glycation of eye lens soluble proteins was investigated. The degree of protein glycation in the absence and presence of dietary extracts was assessed by different complementary methods, i.e. non-tryptophan AGE fluorescence, AGE-induced cross-linking by SDS-PAGE and glyco-oxidative damage by carbonyl assay. Five out of the seventeen agents tested showed significant inhibitory potential against in vitro protein glycation in a dose-dependent manner. Prominent among them were ginger, cumin, cinnamon, black pepper and green tea, which inhibited in vitro AGE formation to lens proteins 40-90 % at 1.0 mg/ml concentration. Assessing their potential to reduce the amount of glycated protein using boronate affinity chromatography and also their ability to prevent the formation of specific antigenic-AGE structures by immunodetection further substantiated the importance of ginger, cumin and cinnamon in reducing AGE burden. These findings indicate the potential of some dietary components to prevent and/or inhibit protein glycation. Thus these dietary agents may be able to be exploited for controlling AGE-mediated diabetic pathological conditions in vivo.\",\n \"corpus_id\": 25490281,\n \"score\": 2\n },\n {\n \"doc_id\": \"19489690\",\n \"title\": \"Hyperglycemia and glycation in diabetic complications.\",\n \"abstract\": \"Diabetes mellitus is a multifactorial disease, classically influenced by genetic determinants of individual susceptibility and by environmental accelerating factors, such as lifestyle. It is considered a major health concern,as its incidence is increasing at an alarming rate, and the high invalidating effects of its long-term complications affect macro- and microvasculature, heart, kidney, eye, and nerves. Increasing evidence indicates that hyperglycemia is the initiating cause of the tissue damage occurring in diabetes, either through repeated acute changes in cellular glucose metabolism, or through the long-term accumulation of glycated biomolecules and advanced glycation end products (AGEs). AGEs represent a heterogeneous group of chemical products resulting from a nonenzymatic reaction between reducing sugars and proteins, lipids, nucleic acids, or a combination of these. The glycation process (glucose fixation) affects circulating proteins (serum albumin, lipoprotein, insulin, hemoglobin),whereas the formation of AGEs implicates reactive intermediates such as methylglyoxal. AGEs form cross-links on long-lived extracellular matrix proteins or react with their specific receptor RAGE, resulting inoxidative stress and proinflammatory signaling implicated in endothelium dysfunction, arterial stiffening, and microvascular complications. This review summarizes the mechanism of glycation and of AGEs formation and the role of hyperglycemia, AGEs, and oxidative stress in the pathophysiology of diabetic complications.\",\n \"corpus_id\": 20627439,\n \"score\": 2\n },\n {\n \"doc_id\": \"19954478\",\n \"title\": \"Advanced glycation end products and receptor-oxidative stress system in diabetic vascular complications.\",\n \"abstract\": \"Reducing sugars can react non-enzymatically with amino groups of protein to form Amadori products. These early glycation products undergo further complex reactions, such as rearrangement, dehydration, and condensation, to become irreversibly cross-linked, heterogeneous fluorescent derivatives, termed advanced glycation end products (AGEs). The formation and accumulation of AGEs have been known to progress at an accelerated rate in patients with diabetes mellitus, thus being involved in the development and progression of diabetic micro- and macroangiopathy. Indeed, there is accumulating evidence that an interaction between an AGE and its receptor (RAGE) generates oxidative stress and subsequently evokes vascular inflammation and thrombosis, thereby playing a central role in diabetic vascular complications. In this paper, we review the pathophysiological role of AGE-RAGE-oxidative stress system and its therapeutic interventions in diabetic micro- and macroangiopathy.\",\n \"corpus_id\": 11190337,\n \"score\": 2\n },\n {\n \"doc_id\": \"20184132\",\n \"title\": \"[Glycation and protein crosslinking in the diabetes and ageing pathogenesis].\",\n \"abstract\": \"Glicación y entrecruzamiento de proteínas en la patogénesis de la diabetes y el envejecimiento. Long exposition to hyperglycemia is associated with development of vascular diseases in diabetic patients. Many of these effects are mediated by non-enzymatic glycosylation (glycation) of proteins and formation of advanced glycation end-products (AGEs). This phenomenon is accelerated in conditions where glucose concentration is chronically high, as it happens in diabetes mellitus. AGE formation is associated with structure-function alterations of proteins such as collagen, and particularly in tissues where these products are accumulated. A number of studies have demonstrated that AGEs can act as mediators, not only for the development of chronic complications of diabetes, but also in those related to ageing, nephropathy, Alzheimer's disease and erectile dysfunction, among others. In this paper, information generated about formation and accumulation of AGEs, including its biological effects and their participation in the development of complications in diabetes mellitus and other process such as ageing is revised. In addition, therapeutic strategies and a new methodology to measure glycation products are also considered.\",\n \"corpus_id\": 34662516,\n \"score\": 2\n },\n {\n \"doc_id\": \"20451573\",\n \"title\": \"Antihyperglycemic activity and inhibition of advanced glycation end product formation by Cuminum cyminum in streptozotocin induced diabetic rats.\",\n \"abstract\": \"Cuminum cyminum is widely used as a spice in many countries. The aim of the present study was to investigate the effect of methanolic extract of seeds of C. cyminum (CC) on diabetes, oxidative stress and formation of advanced glycated end products (AGE) and obtain comparison with glibenclamide. In vitro studies indicated that CC inhibited free radicals and AGE formation. Treatment of streptozotocin-diabetic rats with CC and glibenclamide for 28 days caused a reduction in blood glucose, glycosylated hemoglobin, creatinine, blood urea nitrogen and improved serum insulin and glycogen (liver and skeletal muscle) content when compared to diabetic control rats. Significant reduction in renal oxidative stress and AGE was observed with CC when compared to diabetic control and glibenclamide. CC and glibenclamide improved antioxidant status in kidney and pancreas of diabetic rats. Diabetic rats showed increase in rat tail tendon collagen, glycated collagen, collagen linked fluorescence and reduction in pepsin digestion. Treatment with CC significantly improved these parameters when compared to diabetic control and glibenclamide group. Though the antidiabetic effect of CC was comparable to glibenclamide it had better effect in controlling oxidative stress and inhibiting the AGE formation, which are implicated in the pathogenesis of diabetic microvascular complications.\",\n \"corpus_id\": 7433711,\n \"score\": 2\n },\n {\n \"doc_id\": \"20717877\",\n \"title\": \"Inhibition of advanced glycation end product formation by medicinal plant extracts correlates with phenolic metabolites and antioxidant activity.\",\n \"abstract\": \"Nonenzymatic formation of advanced glycation end products (AGEs) is accelerated under hyperglycemic conditions characteristic of type 2 diabetes mellitus and contributes to the development of vascular complications. As such, inhibition of AGE formation represents a potential therapeutic target for the prevention and treatment of diabetic complications. In the present study, ethanolic extracts of 17 medicinal plants were assessed for inhibitory effects on in vitro AGE formation through fluorometric and immunochemical detection of fluorescent AGEs and N(ε)-(carboxymethyl)lysine adducts of albumin (CML-BSA), respectively. Most extracts inhibited fluorescent AGE formation with IC (50) values ranging from 0.4 to 38.6 µg/mL and all extracts reduced CML-BSA formation but to differing degrees. Results obtained through both methods were highly correlated. Antiglycation activities were positively correlated with total phenolic content, free radical scavenging activity and reduction in malonyldiadehyde levels following oxidation of low-density lipoprotein, but negatively correlated with lag time to formation of conjugated dienes. Together, these results provide evidence that antioxidant phenolic metabolites mediate the antiglycation activity of our medicinal plant collection, a relationship that likely extends to other medicinal and food plants.\",\n \"corpus_id\": 9813185,\n \"score\": 2\n },\n {\n \"doc_id\": \"21120596\",\n \"title\": \"Anti-inflammatory and anti-oxidant properties of Curcuma longa (turmeric) versus Zingiber officinale (ginger) rhizomes in rat adjuvant-induced arthritis.\",\n \"abstract\": \"Turmeric (rich in curcuminoids) and ginger (rich in gingerols and shogaols) rhizomes have been widely used as dietary spices and to treat different diseases in Ayurveda/Chinese medicine since antiquity. Here, we compared the anti-inflammatory/anti-oxidant activity of these two plants in rat adjuvant-induced arthritis (AIA). Both plants (at dose 200 mg/kg body weight) significantly suppressed (but with different degrees) the incidence and severity of arthritis by increasing/decreasing the production of anti-inflammatory/pro-inflammatory cytokines, respectively, and activating the anti-oxidant defence system. The anti-arthritic activity of turmeric exceeded that of ginger and indomethacin (a non-steroidal anti-inflammatory drug), especially when the treatment started from the day of arthritis induction. The percentage of disease recovery was 4.6-8.3% and 10.2% more in turmeric compared with ginger and indomethacin (P < 0.05), respectively. The present study proves the anti-inflammatory/anti-oxidant activity of turmeric over ginger and indomethacin, which may have beneficial effects against rheumatoid arthritis onset/progression as shown in AIA rat model.\",\n \"corpus_id\": 10202571,\n \"score\": 2\n },\n {\n \"doc_id\": \"21341505\",\n \"title\": \"[Non-enzymatic glycation of proteins: from diabetes to cancer].\",\n \"abstract\": \"Incubation of proteins with glucose leads to their non-enzymatic glycation and formation of Amadori products known as an early glycation product. Oxidative cleavage of Amadori products is considered as a major route to advanced glycation endproducts (AGEs) formation in vivo. Nonenzymatic glycation of proteins or Maillard reaction is increased in diabetes mellitus due to hyperglycemia and leads to several complications such as blindness, heart disease, nerve damage and kidney failure. Accumulation of the early and advanced glycation products in plasma and tissues of diabetic patients and causes production of autoantibodies against corresponding products. The advanced glycation products are also associated with other diseases like cancer. This review summarizes current knowledge of these stage specific glycated products as common and early diagnostic biomarkers for the associated diseases and the complications with the aim of a novel therapeutic target for the diseases.\",\n \"corpus_id\": 32051578,\n \"score\": 2\n },\n {\n \"doc_id\": \"21440603\",\n \"title\": \"Role of advanced glycation end products (AGEs) and oxidative stress in vascular complications in diabetes.\",\n \"abstract\": \"BACKGROUND: A non-enzymatic reaction between reducing sugars and amino groups of proteins, lipids and nucleic acids contributes to the aging of macromolecules, whose process has been known to progress at an accelerated rate under hyperglycemic and/or oxidative stress conditions. Over a course of days to weeks, early glycation products undergo further reactions such as rearrangements and dehydration to become irreversibly cross-linked, fluorescent protein derivatives termed advanced glycation end products (AGEs). SCOPE OF REVIEW: In this paper, we review the role of AGE-oxidative stress axis and its therapeutic interventions in vascular complications in diabetes. MAJOR CONCLUSIONS: AGEs elicit oxidative stress generation and subsequently cause inflammatory and thrombogenic reactions in various types of cells via interaction with a receptor for AGEs (RAGE), thereby being involved in vascular complications in diabetes. In addition, mitochondrial superoxide generation has been shown to play an important role in the formation and accumulation of AGEs under diabetic conditions. Further, we have recently found that a pathophysiological crosstalk between AGE-RAGE axis and renin-angiotensin system (RAS) could contribute to the progression of vascular damage in diabetes. GENERAL SIGNIFICANCE: These observations suggest that inhibition of AGE-RAGE-oxidative stress axis or blockade of its interaction with RAS is a novel therapeutic strategy for preventing vascular complications in diabetes.\",\n \"corpus_id\": 39308860,\n \"score\": 2\n },\n {\n \"doc_id\": \"21457747\",\n \"title\": \"Phytochemical profile, antioxidant, anti-inflammatory and hypoglycemic potential of hydroalcoholic extracts from Citrus medica L. cv Diamante flowers, leaves and fruits at two maturity stages.\",\n \"abstract\": \"Since the past decade consumption of certain foods has been reported to have a positive effect on health. The object of the study was to determine for the first time the chemical composition and the antioxidant, anti-inflammatory and hypoglycemic potential of Citrus medica L. cv Diamante flowers, leaves and fruits (endocarp and mesocarp) at two maturity stages. Flowers and leaves were characterized by the highest total phenols and flavonoids content. A declining trend was observed during maturity of fruits for both phenols and flavonoids. The antioxidant activity evaluated by the β-carotene bleaching test showed a strong activity for flowers and endocarp of mature fruits with IC50 values of 2.8 μg/mL and 3.5 μg/mL, respectively, after 30 min of incubation. Interestingly, the mature fruits endocarp (IC50 value of 426.0 μg/mL) could inhibit α-amylase with an IC50 value 2-fold higher than immature fruits. None of the tested extracts affected the proliferation of human skin fibroblasts 142BR. The obtained results suggest a potential use of C. medica L. cv Diamante as new valuable Citrus species with functional properties for food or nutraceutical product on the basis of high content of phytochemicals.\",\n \"corpus_id\": 8351905,\n \"score\": 2\n },\n {\n \"doc_id\": \"22151933\",\n \"title\": \"Topical vesicular formulations of Curcuma longa extract on recuperating the ultraviolet radiation-damaged skin.\",\n \"abstract\": \"BACKGROUND: Ultraviolet radiations generate reactive oxygen species, leading to adverse effects on skin properties. Botanical extracts are multifunctional in nature having various properties like photoprotection, anti-aging, moisturizing, antioxidant, astringent, anti-irritant, and antimicrobial activity. AIMS: The aim of this study was to formulate creams having Curcuma longa extract loaded novel vesicular systems (liposomes, ethosomes, and transfersomes) and study their photoprotective effect by assessment of skin hydration (Cutometer) and sebum content (Sebumeter). METHODS: The alcoholic C. longa extract loaded liposomes, ethosomes, and transfersomes having 0.5-2.0% w/w extract were prepared, evaluated for size, entrapment efficiency, and incorporated into the cream. Their long-term interaction with skin (6 weeks) was compared in terms of their effects on skin hydration and sebum content. RESULTS: Vesicular size obtained was in the range 167.3 ± 3.0 to 262.4 ± 2.4 nm with low polydispersity index (0.2-0.3) and high entrapment efficiency. The efficacy was in the order C. longa extract loaded transfersomal creams > C. longa extract loaded ethosomal creams > C. longa extract loaded liposomal creams > C. longa extract loaded creams > Empty transfersome loaded cream > Empty ethosome loaded cream > Empty liposome loaded cream > Base cream. CONCLUSIONS: The photoprotective properties of the constituents of C. longa extract and hydrant, moisturizing lipid components of nano vesicles with better skin penetration resulted in improvement in skin properties like skin hydration and sebum content. The herbal extract loaded nano vesicles incorporated in cream could be used as photoprotective formulations.\",\n \"corpus_id\": 32714749,\n \"score\": 2\n },\n {\n \"doc_id\": \"22268395\",\n \"title\": \"Natural products as anti-glycation agents: possible therapeutic potential for diabetic complications.\",\n \"abstract\": \"Diabetes mellitus is characterised by hyperglycaemia, lipidaemia and oxidative stress and predisposes affected individuals to long-term complications afflicting the eyes, skin, kidneys, nerves and blood vessels. Increased protein glycation and the subsequent build-up of tissue advanced glycation endproducts (AGEs) contribute towards the pathogenesis of diabetic complications. Protein glycation is accompanied by generation of free radicals through autoxidation of glucose and glycated proteins and via interaction of AGEs with their cell surface receptors (referred to as RAGE). Glycationderived free radicals can damage proteins, lipids and nucleic acids and contribute towards oxidative stress in diabetes. There is interest in compounds with anti-glycation activity as they may offer therapeutic potential in delaying or preventing the onset of diabetic complications. Although many different compounds are under study, only a few have successfully entered clinical trials but none have yet been approved for clinical use. Whilst the search for new synthetic inhibitors of glycation continues, little attention has been paid to anti-glycation compounds from natural sources. In the last few decades the traditional system of medicine has become a topic of global interest. Various studies have indicated that dietary supplementation with combined anti-glycation and antioxidant nutrients may be a safe and simple complement to traditional therapies targeting diabetic complications. Data for forty two plants/constituents studied for anti-glycation activity is presented in this review and some commonly used medicinal plants that possess anti-glycation activity are discussed in detail including their active ingredients, mechanism of action and therapeutic potential.\",\n \"corpus_id\": 21407008,\n \"score\": 2\n },\n {\n \"doc_id\": \"22530890\",\n \"title\": \"In vitro anti-glycation and anti-oxidant properties of synthesized Schiff bases.\",\n \"abstract\": \"A series of mono, bis and mixed Schiff bases (1-7) were synthesised and evaluated for potential anti-glycation and anti-oxidant activities using the bovine serum albumin-glucose assay and 2,2-diphenyl-1-picrylhydrazyl (DPPH) free radical assay respectively. All compounds showed significant (p<0.05) antiglycating activities with IC50 values (4.02x10(-24)±0.1-2.88x10(-1)±1.35 mM) which were lower than the standard positive control aminoguanidine (IC50: 1.51x10(-3)±2.11 mM). Moreover, compounds 1-7 were found to possess significant (p<0.05) DPPH radical scavenging properties with SC50 values (1.31x10(-19)±0.05 to 2.25x10(-1)±1.24 mM) lower than the standard ascorbic acid (SC50: 5.50x10(-3)±2.11 mM). Compound 6 was found to be the most potent anti-glycating molecule (IC50 value: 4.02x10(-24)±0.1 mM) while compound 5 was the most potent anti-oxidant molecule (SC50: 1.31x10(-19)±0.05 mM); both being significantly lower (p<0.05) than the respective positive controls used. The present data showed that the number of phenolic OH together with structural changes influence both the anti-glycation and anti-oxidant observed herein. This study provides for the first time a series of potential template molecules for possible pharmaceutical applications that warrant further investigation as potential anti-glycation and anti-oxidant agents which could be of importance in metabolic diseases including diabetes mellitus.\",\n \"corpus_id\": 22068375,\n \"score\": 2\n },\n {\n \"doc_id\": \"22868139\",\n \"title\": \"Curcuma longa and Curcuma mangga leaves exhibit functional food property.\",\n \"abstract\": \"Although leaves of Curcuma mangga and Curcuma longa are used in food preparations, the bioactive components in it are not known. In this study, antioxidant, antiinflammatory and anticancer activities of leave extracts and its isolates were investigated using established bioassay procedures in our laboratory. The leaf extracts of both plants gave similar bioassay and chromatographic profiles. The methanolic and water extracts of C. mangga (CMM and CMW) and C. longa (CLM and CLW), at 100 μg/mL, inhibited lipid peroxidation (LPO) by 78%, 63%, 81% and 43%, cyclooxygenase enzymes COX-1 by 55%, 33%, 43% and 24% and COX-2 by 65%, 55%, 77% and 69%, respectively. At same concentration, CMM, CMW, CLM and CLW showed growth inhibition of human tumour cell lines by 0-46%. Therefore, a bioassay-guided isolation of water and methanolic extracts of C. longa was carried out and afforded nine isolates. At 25 μg/mL, these compounds inhibited LPO by 11-87%, COX-1 and -2 enzymes by 0-35% and 0-82% and growth of human tumour cells by 0-36%, respectively.\",\n \"corpus_id\": 3108079,\n \"score\": 2\n },\n {\n \"doc_id\": \"22923199\",\n \"title\": \"The in vitro protective effects of curcumin and demethoxycurcumin in Curcuma longa extract on advanced glycation end products-induced mesangial cell apoptosis and oxidative stress.\",\n \"abstract\": \"Curcuma longa L. (CLL), a traditional herbal medicine, has been widely used for the prevention of diabetic vascular complications in recent years. However, the protective effects of curcuminoids in CLL on the AGEs-induced damage to mesangial cell are not fully understood. In this present study, dihydroethidium, superoxide dismutase kit, malondialdehyde kit, and acridine orange/ethidium bromide staining methods were used to evaluate the activities of curcumin and demethoxycurcumin (10(-11)-10(-9) M) on AGEs-induced oxidative stress and apoptosis, which were associated with the damage to mesangial cell. The results showed that these two compounds could significantly restore advanced glycation end products (AGEs)-induced apoptosis to normal levels (IC50 = 3.874 × 10(-11) M for curcumin and IC50 = 6.085 × 10(-11) M for demethoxycurcumin) and reduce remarkably reactive oxygen species generation in mesangial cell. Furthermore, curcumin and demethoxycurcumin dramatically elevated AGEs-decreased superoxide dismutase activity while significantly reducing AGEs-increased malondialdehyde content in cell culture supernatant. Our results suggest that both curcumin and demethoxycurcumin have a significant protective potential to the prevention of diabetic nephropathy.\",\n \"corpus_id\": 12829704,\n \"score\": 2\n },\n {\n \"doc_id\": \"23047487\",\n \"title\": \"Evaluation of the antioxidant and anti-glication effects of the hexane extract from Piper auritum leaves in vitro and beneficial activity on oxidative stress and advanced glycation end-product-mediated renal injury in streptozotocin-treated diabetic rats.\",\n \"abstract\": \"The aim of this study was to investigate the antioxidant activity of hexane extracts from leaves of Piper auritum (HS). Eight complementary in vitro test methods were used, including inhibition of DPPH· radicals, nitric oxide, superoxide anion, ion-chelating, ABTS, oxygen radical absorbance capacity, β-carotene bleaching and peroxy radical scavenging. The results indicated that HS possesses high antioxidant activity. To add to these finding we tested the effect against oxidative stress in liver, pancreas and kidney in diabetic rats. Low levels of SOD, CAT, GPx and GSH in diabetic rats were reverted to near normal values after treatment with HS. These results suggest that P. auritum prevents oxidative stress, acting as a suppressor of liver cell damage. Given the link between glycation and oxidation, we proposed that HS might possess significant in vitro antiglycation activity. Our data confirmed the inhibitory effect of HS on bovine serum albumin, serum glycosylated protein, glycation of LDL, and glycation hemoglobin. The effect of HS on diabetic renal damage was investigated using streptozotocin-induced diabetic rats. The oral administration of HS at a dose of 200 and 400 mg/kg body weight/day for 28 days significantly reduced advanced glycation endproduct (AGE) formation, elevated renal glucose and thiobarbituric acid-reactive substance levels in the kidneys of diabetic rats. This implies that HS would alleviate the oxidative stress under diabetes through the inhibition of lipid peroxidation. These findings indicate that oxidative stress is increased in the diabetic rat kidney and that HS can prevent renal damage associated with diabetes by attenuating the oxidative stress.\",\n \"corpus_id\": 16963703,\n \"score\": 2\n },\n {\n \"doc_id\": \"23167275\",\n \"title\": \"Chemical analysis and biological activities of Cupressus sempervirens var. horizontalis essential oils.\",\n \"abstract\": \"CONTEXT: Safe and effective antioxidants are regarded as a cornerstone for the prevention and treatment of several types of disorders. OBJECTIVE: The present study aimed to investigate the antioxidant and anti-glycation properties of branchlet and fruit oils of Cupressus sempervirens L. var. horizontalis (Mill.) Gord. ( Cupressaceae). MATERIALS AND METHODS: Essential oils were extracted from the branchlets and fruits of C. sempervirens var. horizontalis using the steam distillation method. A gas chromatography-mass spectrometry method was employed for the compositional analysis of essential oils. In order to evaluate antioxidant activities of oils at different concentrations (180, 220 and 260 μg mL(-1)), linoleic acid peroxidation test and peroxyl radical mediated hemolysis of red blood cells (RBC) assay were used. Linoleic acid peroxidation was monitored for 4 h and determined during each hour of incubation. Antiglycation effects of oils at 200, 400 and 600 μg mL(-1) were assessed using hemoglobin and insulin glycation assays. RESULTS: Overall, 10 volatile components were identified, amounting for 88.2 and 93.2% of branchlet and fruit oils, respectively. α-Pinene and δ-3-carene were major components of both branchlet (46.2 and 22.7%) and fruit (59.2 and 14.9%) oils. Hemoglobin glycation was inhibited by both branchlet (44.8, 62.6 and 54.0% at 200, 400 and 600 μg mL(-1), respectively) and fruit (41.0, 62.8 and 48.5%) oils. As for the insulin glycation, inhibitory rates were 66.1, 69.2 and 73.8% for branchlet oil, and 80.0, 76.9 and 81.5% for fruit oil (at 200, 400 and 600 μg mL(-1), respectively). RBC hemolysis was also inhibited by both branchlet (49.9, 38.5 and 15.0% at 180, 220 and 260 μg mL(-1), respectively) and fruit (45.9, 38.6 and 25.0%) oil. Finally, the oils mitigated linoleic acid peroxidation which was peaked after 4 h for both branchlet (39.5, 35.6 and 53.4% at 180, 220 and 260 μg mL(-1), respectively) and fruit (47.5, 58.6 and 59.8%) oil. CONCLUSIONS: The present findings suggest that essential oils obtained from the branchlets and fruits of C. sempervirens var. horizontalis possess antioxidant and, in particular, antiglycation properties. These activities may find implication in the prevention of diabetic and cardiovascular complications. However, further investigations are required to justify the traditional medical applications of the plant.\",\n \"corpus_id\": 20386770,\n \"score\": 2\n },\n {\n \"doc_id\": \"23297565\",\n \"title\": \"Antiglycation and antioxidation properties of Juglans regia and Calendula officinalis: possible role in reducing diabetic complications and slowing down ageing.\",\n \"abstract\": \"OBJECTIVE: Accumulation of advanced glycation end products (AGEs) in the body due to the non-enzymatic glycation of proteins and oxidation is associated with aging and diabetes mellitus. In this study we wanted to investigate the antiglycation and antioxidation potential of two medicinal plants: Juglans regia and Calendula officinalis. METHODS: In-vitro investigation was carried out to discover the antiglycation and antioxidation potential of J. regia and C. officinalis. Using an Ultraviolet Double-beam Spectrophotometer, we evaluated the antiglycation property of the crude methanolic extracts of J. regia and C. officinalis by assessing their ability to inhibit the Maillard reaction. Employing the same instrument we also measured the antioxidation potential of these plant extracts using the nitric oxide (NO) free radical-scavenging assay. RESULTS: J. regia had greater antiglycation ability, with a minimum inhibitory concentration (MIC50) of 28 microg/mL as compared with that of C. officinalis (270 microg/mL). C. officinalis had greater antioxidation potential (26.10, 22.07 and 16.06% at 0.5 mg, 0.25 mg and 0.125 mg, respectively, as compared with 18.15, 16.50 and 16.06% of J. regia, respectively). CONCLUSION: J. regia and C. officinalis inhibited the Maillard reaction and prevented oxidation in-vitro. Hence, the extracts of these plants could have therapeutic uses in curbing chronic diabetic complications and slowing down aging.\",\n \"corpus_id\": 10454102,\n \"score\": 2\n },\n {\n \"doc_id\": \"23768830\",\n \"title\": \"Antioxidant and anti-glycation activities correlates with phenolic composition of tropical medicinal herbs.\",\n \"abstract\": \"OBJECTIVE: To determine the contribution of total phenolic content (TPC) in glycation inhibitory activity of common tropical medicinal food and spices with potential antioxidative properties. METHODS: In vitro glucose-bovine serum albumin (BSA) assay was used. Ethanolic extracts of ten common household condiments/herbs (Allium sativum, Zingiber officinale, Thymus vulgaris, Petroselinum crispum, Murraya koenigii Spreng, Mentha piperita L., Curcuma longa L., Allium cepa L., Allium fistulosum and Coriandrum sativum L.) were evaluated for antioxidative activity by 2,2-diphenyl-2-picrylhydrazyl (DPPH), and ferric reducing antioxidant power (FRAP) and the TPC, flavonoid and tannins content were determined. RESULTS: Findings showed good correlation between TPC/DPPH (r = 0.8), TPC/FRAP (r = 0.8), TPC/anti-glycation (r = 0.9), DPPH/anti-glycation (r = 0.6), FRAP/anti-glycation (r = 0.9), Flavonoid/anti-glycation (r = 0.7) and Tannins/anti-glycation (r = 0.8) and relatively fair correlation for TPC/Flavonoids (r = 0.5) and TPC/Tannins (r = 0.5). Results imply that these plants are potential sources of natural antioxidants which have free radical scavenging activity and might be used for reducing oxidative stress. CONCLUSIONS: The positive glycation inhibitory and antioxidative activities of these tropical herbs suggest a possible role in targeting ageing, diabetic complications and oxidative stress related diseases.\",\n \"corpus_id\": 3411406,\n \"score\": 2\n },\n {\n \"doc_id\": \"24093976\",\n \"title\": \"Do plants mediate their anti-diabetic effects through anti-oxidant and anti-apoptotic actions? an in vitro assay of 3 Indian medicinal plants.\",\n \"abstract\": \"BACKGROUND: Both experimental and clinical studies suggest that oxidative stress plays a major role in the pathogenesis of both types of diabetes mellitus. This oxidative stress leads to β-cell destruction by apoptosis. Hence exploring agents modulating oxidative stress is an effective strategy in the treatment of both Type I and Type II diabetes. Plants are a major source of anti-oxidants and exert protective effects against oxidative stress in biological systems. Phyllanthus emblica, Curcuma longa and Tinospora cordifolia are three such plants widely used in Ayurveda for their anti-hyperglycemic activity. Additionally their anti-oxidant properties have been scientifically validated in various experimental in vitro and in vivo models. Hence the present in vitro study was planned to assess whether the anti-hyperglycemic effects of the hydro-alcoholic extracts of Phyllanthus emblica (Pe) and Curcuma longa (Cl) and aqueous extract of Tinospora cordifolia (Tc) are mediated through their antioxidant and/or anti-apoptotic property in a streptozotocin induced stress model. METHODS: RINm5F cell line was used as a model of pancreatic β-cells against stress induced by streptozotocin (2 mM). Non-toxic concentrations of the plant extracts were identified using MTT assay. Lipid peroxidation through MDA release, modulation of apoptosis and insulin release were the variables measured to assess streptozotocin induced damage and protection afforded by the plant extracts. RESULTS: All 3 plants extracts significantly inhibited MDA release from RIN cells indicating protective effect against STZ induced oxidative damage. They also exhibited a dose dependent anti-apoptotic effect as seen by a decrease in the sub G0 population in response to STZ. None of the plant extracts affected insulin secretion from the cells to a great extent. CONCLUSION: The present study thus demonstrated that the protective effect of the selected medicinal plants against oxidative stress induced by STZ in vitro, which was exerted through their anti-oxidant and anti-apoptotic actions.\",\n \"corpus_id\": 15294246,\n \"score\": 2\n },\n {\n \"doc_id\": \"24374440\",\n \"title\": \"Protective effect of crude Curcuma longa and its methanolic extract in alloxanized rabbits.\",\n \"abstract\": \"Curcuma longa (C. longa) is commonly found in different areas of Pakistan. It has been locally utilized as a traditional medicine. The aim of this study was to evaluate the antidiabetic, hepatoprotective and total antioxidant effect of the crude drug and its methanolic extract in rabbits. Diabetes was induced with alloxan (180mg/kg). Two major groups were designed, curative and protective groups. In curative group the crude drug and its methanolic extract was orally administered to the diabetic animals and acute study was performed. On the other hand in protective group the crude drug and its methanolic extract were administered for eight days prior to the diabetes induction. Results indicated that in Curative group the crude and methanolic extract of C. longa significantly improved the levels of serum glucose, serum transaminases and antioxidant activity (AOA). In protective group, serum glucose, serum transaminases were not significantly increased by alloxan, in both crude as well as methanolic extract group. This study shows that C. longa acts as antidiabetic, hepatoprotective and antioxidant in diabetes especially type 1 diabetes.\",\n \"corpus_id\": 24316741,\n \"score\": 2\n },\n {\n \"doc_id\": \"24448675\",\n \"title\": \"Investigating wild berries as a dietary approach to reducing the formation of advanced glycation endproducts: chemical correlates of in vitro antiglycation activity.\",\n \"abstract\": \"Evidence supports the health promoting benefits of berries, particularly with regard to the prevention and management of chronic diseases such cardio- and cerebrovascular disease, diabetes and Alzheimer's disease. Two related pathophysiological features common to many of these conditions are oxidative stress and the accumulation of advanced glycation endproducts (AGEs). Whereas antioxidant properties are well-established in several species of berries and are believed central to their protective mechanisms, few studies have investigated the effects of berries on AGE formation. Here, employing a series of complementary in vitro assays, we evaluated a collection of wild berry extracts for 1) inhibitory effects on fluorescent-AGE and Nε- (carboxymethyl)lysine-albumin adduct formation, 2) radical scavenging activity and 3) total phenolic and anthocyanin content. All samples reduced AGE formation in a concentration-dependent manner that correlated positively with each extract's total phenolic content and, to a lesser degree, total anthocyanin content. Inhibition of AGE formation was similarly related to radical scavenging activities. Adding antiglycation activity to the list of established functional properties ascribed to berries and their phenolic metabolites, our data provide further insight into the active compounds and protective mechanisms through which berry consumption may aid in the prevention and treatment of chronic diseases associated with AGE accumulation and toxicity. As widely available, safe and nutritious foods, berries represent a promising dietary intervention worthy of further investigation.\",\n \"corpus_id\": 14469293,\n \"score\": 2\n },\n {\n \"doc_id\": \"24497740\",\n \"title\": \"Comparative assessment on in vitro antioxidant activities of ethanol extracts of Averrhoa bilimbi, Gymnema sylvestre and Capsicum frutescens.\",\n \"abstract\": \"BACKGROUND: Averrhoa bilimbi, Gymnema sylvestre and Capsicum frutescens are medicinal plants commonly used as traditional medicine for the treatment of various diseases. The present study was designed to investigate the antioxidant activities of Ethanolic extract of A. bilimbi, G. sylvestre and C. frutescens. MATERIALS AND METHODS: The antioxidant activity of the extracts were evaluated using total phenolic and flavonoid contents, ferric reducing power and the free radical scavenging activity against 1,1-diphenyl-2-picrylhydrazyl (DPPH). RESULTS: Total phenolic and flavonoid contents were higher in G. sylvestre (53.63636 ± 0.454545 mg/g gallic acid equivalent) and C. frutescens (26.66667 ± 2.081666 mg/g quercetin equivalent) respectively. Reducing power of the crude ethanol extracts increased with the concentrations of the extracts and all the extracts showed moderate free radical scavenging activity against DPPH. The plant extract displayed moderate phenolic and flavonoid contents compared to gallic acid and quercetin equivalent respectively, whereas also exhibited significant scavenging of DPPH radical and reducing power compared with ascorbic acid as standard. CONCLUSION: Our study suggests that G. sylvestre has significant antioxidant activity. The antioxidant compound of this plant might be a therapeutic candidate against oxidative stress related diseases. Different sub-fraction of A. bilimbi and C. frutescens should be studied further to assess the effect. Further study is necessary for isolation and characterization of the active antioxidant agents for better treatment.\",\n \"corpus_id\": 20730258,\n \"score\": 2\n },\n {\n \"doc_id\": \"24597145\",\n \"title\": \"Antioxidant potential and oxidative DNA damage preventive activity of unexplored endemic species of Curcuma.\",\n \"abstract\": \"Free radical scavenging activity, ferrous ion chelating capacity, reducing power and genoprotective effect of the aqueous leaf extracts of four unexplored endemic Curcuma spp. ( C. vamana, C. neilgherrensis, C. mutabilis, C. haritha) were found to be dose-dependent and were highest in C. vamana. DNA protection property of the extracts was evaluated against H202/UV-induced oxidative damage. DNA-methyl green displacement assay showed that these extracts were free of DNA intercalating compounds. Further, hemolysis assay also showed that the extracts were non-toxic to human erythrocytes. The results highlight C. vamana as a promising source for herbal preparations possessing high antioxidant potential and genoprotective activity.\",\n \"corpus_id\": 33937115,\n \"score\": 2\n },\n {\n \"doc_id\": \"24634591\",\n \"title\": \"Advanced glycation end products and diabetic complications.\",\n \"abstract\": \"During long standing hyperglycaemic state in diabetes mellitus, glucose forms covalent adducts with the plasma proteins through a non-enzymatic process known as glycation. Protein glycation and formation of advanced glycation end products (AGEs) play an important role in the pathogenesis of diabetic complications like retinopathy, nephropathy, neuropathy, cardiomyopathy along with some other diseases such as rheumatoid arthritis, osteoporosis and aging. Glycation of proteins interferes with their normal functions by disrupting molecular conformation, altering enzymatic activity, and interfering with receptor functioning. AGEs form intra- and extracellular cross linking not only with proteins, but with some other endogenous key molecules including lipids and nucleic acids to contribute in the development of diabetic complications. Recent studies suggest that AGEs interact with plasma membrane localized receptors for AGEs (RAGE) to alter intracellular signaling, gene expression, release of pro-inflammatory molecules and free radicals. The present review discusses the glycation of plasma proteins such as albumin, fibrinogen, globulins and collagen to form different types of AGEs. Furthermore, the role of AGEs in the pathogenesis of diabetic complications including retinopathy, cataract, neuropathy, nephropathy and cardiomyopathy is also discussed.\",\n \"corpus_id\": 3034045,\n \"score\": 2\n },\n {\n \"doc_id\": \"24650229\",\n \"title\": \"Pharmacological importance of an ethnobotanical plant: Capsicum annuum L.\",\n \"abstract\": \"Capsicum annuum L., a fruit plant from tropical and subtropical regions, contains a range of essential nutrients and bioactive compounds which are known to exhibit a range of bioactivities including free radical scavenging (antioxidant), antimicrobial, antiviral, anti-inflammatory and anticancer. This review aims to give a comprehensive overview of the literature published on pharmacological behaviours of C. annuum L.\",\n \"corpus_id\": 12600252,\n \"score\": 2\n },\n {\n \"doc_id\": \"24772978\",\n \"title\": \"Inhibitory effect of Piper betle Linn. leaf extract on protein glycation--quantification and characterization of the antiglycation components.\",\n \"abstract\": \"Piper betle Linn. is a Pan-Asiatic plant having several beneficial properties. Protein glycation and advanced glycation end products (AGEs) formation are associated with different pathophysiological conditions, including diabetes mellitus. Our study aims to find the effect of methanolic extract of P. betle leaves on in vitro protein glycation in bovine serum albumin (BSA)-glucose model. The extract inhibits glucose-induced glycation, thiol group modification and carbonyl formation in BSA in dose-dependent manner. It inhibits different stages of protein glycation, as demonstrated by using glycation models: hemoglobin-delta-gluconolactone (for early stage, Amadori product formation), BSA-methylglyoxal (for middle stage, formation of oxidative cleavage products) and BSA-glucose (for last stage, formation of AGEs) systems. Several phenolic compounds are isolated from the extract. Considering their relative amounts present in the extract, rutin appears to be the most active antiglycating agent. The extract of P. betle leaf may thus have beneficial effect in preventing protein glycation and associated complications in pathological conditions.\",\n \"corpus_id\": 978810,\n \"score\": 2\n },\n {\n \"doc_id\": \"24967413\",\n \"title\": \"Dietary intake of Curcuma longa and Emblica officinalis increases life span in Drosophila melanogaster.\",\n \"abstract\": \"Intake of food and nutrition plays a major role in affecting aging process and longevity. However, the precise mechanisms underlying the ageing process are still unclear. To this respect, diet has been considered to be a determinant of ageing process. In order to better illustrate this, we used Drosophila melanogaster as a model and fed them orally with different concentrations of two commonly used Indian medicinal plant products, Curcuma longa (rhizome) and Emblica officinalis (fruit). The results revealed significant increase in life span of Drosophila flies on exposure to both the plant products, more efficiently by C. Longa than by E. officinalis. In order to understand whether the increase in lifespan was due to high-antioxidant properties of these medicinal plants, we performed enzymatic assays to assess the SOD and catalase activities in case of both treated and control Drosophila flies. Interestingly, the results support the free radical theory of aging as both these plant derivatives show high reactive oxygen species (ROS) scavenging activities.\",\n \"corpus_id\": 16408821,\n \"score\": 2\n },\n {\n \"doc_id\": \"25477660\",\n \"title\": \"In vitro antidiabetic and inhibitory potential of turmeric (Curcuma longa L) rhizome against cellular and LDL oxidation and angiotensin converting enzyme.\",\n \"abstract\": \"Turmeric (Curcuma longa L) rhizome extracts were evaluated for their antidiabetic, antihypertensive and antioxidant potentials. α-Glucosidase (0.4 μg/mL) and α-amylase (0.4 μg/mL) inhibitory potential of turmeric ethyl acetate extract was significantly higher than those of the reference drug acarbose (17.1 μg/mL and 290.6 μg/mL respectively). Protein glycation inhibitory potential of ethyl acetate extract was 800 times higher than that of ascorbic acid. High potential of ethyl acetate extract to scavenge free radicals and to reduce LDL oxidation and cellular oxidative stress was also revealed. The positive correlation obtained between the free radical scavenging capacity of the extracts and their antiglycation potential further confirmed the role of antioxidants in controlling glycation reactions. Ethyl acetate extract was also found as effective in reducing hypertension by inhibiting angiotensin converting enzyme (ACE). Antidiabetic, ACE inhibitory and antioxidant capacities of the extracts were in the order of their curcumin contents.\",\n \"corpus_id\": 27369814,\n \"score\": 2\n },\n {\n \"doc_id\": \"25657787\",\n \"title\": \"Inhibition of protein glycation by essential oils of branchlets and fruits of Juniperus communis subsp. hemisphaerica.\",\n \"abstract\": \"Oxidative stress and protein glycation play pivotal roles in the pathophysiology of diabetes mellitus and its vascular complications. The present study aimed to investigate the anti-glycation properties of essential oils obtained from different parts of Juniperus communis subsp. hemisphaerica. The branchlets of male tree (BMT) and branchlets of female (BFT) tree, and fruits of J. communis subsp. hemisphaerica were extracted using steam distillation method. The oils were phytochemically analyzed using gas chromatography-mass spectrometry. Anti-glycation properties were evaluated using hemoglobin and insulin glycation assays. Overall, 18 volatile components were identified in the J. communis subsp. hemisphaerica oils, amounting to 82.1%, 100.0% and 96.4% of the BMT, BFT and fruit oils, respectively. Promising inhibitory activity was observed from all concentrations of the tested oils in the hemoglobin and insulin glycation assays. The inhibitory activities peaked to 89.9% (BFT oil; 200 μg mL(-1)) and 81.0% (BFT oil; 600 μg mL(-1)) in the hemoglobin and insulin glycation assays, respectively. The evidence from this study suggests that essential oils obtained from the fruits and branchlets of J. communis subsp. hemisphaerica possess anti-glycation properties. These activities may find implication for the prevention and treatment of diabetic complications.\",\n \"corpus_id\": 1598856,\n \"score\": 2\n },\n {\n \"doc_id\": \"26088351\",\n \"title\": \"Curcumin: a natural product for diabetes and its complications.\",\n \"abstract\": \"Curcumin is the yellow-colored bioactive constituent of the perennial plant, Curcuma longa L., which possesses a wide range of physiological and pharmacological properties such as antioxidant, anti-inflammatory, anticancer, neuroprotective and anti-diabetic activities. Anti-diabetic activity of curcumin may be due to its potent ability to suppress oxidative stress and inflammation. Moreover, it shows a beneficial role on the diabetesinduced endothelial dysfunction and induces a down-regulation of nuclear factor-kappa B. Curcumin possesses a protective role against advanced glycation as well as collagen crosslinking and through this way, mitigates advanced glycation end products-induced complications of diabetes. Curcumin also reduces blood glucose, and the levels of glycosylated hemoglobin in diabetic rat through the regulation of polyol pathway. It also suppresses increased bone resorption through the inhibition of osteoclastogenesis and expression of the AP-1 transcription factors, c-fos and c-jun, in diabetic animals. Overall, scientific literature shows that curcumin possesses anti-diabetic effects and mitigates diabetes complications. Here we report a systematical discussion on the beneficial role of curcumin on diabetes and its complications with emphasis on its molecular mechanisms of actions.\",\n \"corpus_id\": 37630935,\n \"score\": 2\n },\n {\n \"doc_id\": \"26417319\",\n \"title\": \"Combined anti-ages and antioxidant activities of different solvent extracts of Solanum elaeagnifolium Cav (Solanacea) fruits during ripening and related to their phytochemical compositions.\",\n \"abstract\": \"Oxidative stress and advanced glycation end products (AGEs) are known as key factors for the development of diabetic complications such as retinopathy, cataract as well as atherosclerosis and neurodegenerative diseases, including Alzheimer's diseases. In this context, natural products have been previously identified as promising sources for antioxidant and anti-glycation compounds. The current study focuses on the evaluation of antioxidant and glycation inhibitory activities of different solvent extracts of Solanum elaeagnifolium Cav (Solanaceae) fruits at different ripening stages. The results showed that antioxidant and anti-AGEs activities were significantly influenced by solvents polarities and ripening stages of S. elaeagnifolium Cav. With one exception, methanolic extract of overripe S. elaeagnifolium Cav fruit showed important protective effects against cellular oxidative stress. The aqueous extract showed the highest ABTS(+) scavenging ability. Principal component analysis showed that total phenolic and flavonoid contents correlated well with observed antioxidants and anti-glycation activities. These results bring attention to the possible use of S. elaeagnifolium Cav as a valuable source of bioactive compounds exhibiting antioxidant effects and potentially alleviating diabetic complications.\",\n \"corpus_id\": 11530325,\n \"score\": 2\n },\n {\n \"doc_id\": \"26966424\",\n \"title\": \"The protective effects of pomelo extract (Citrus grandis L. Osbeck) against fructose-mediated protein oxidation and glycation.\",\n \"abstract\": \"Chronic hyperglycemia induces non-enzymatic protein glycation, which plays an important role in the development of diabetic complications. Immense efforts have been made to determine effective antiglycation compounds from natural products. Pomelo has shown beneficial effects for human health. The objective of this study was to determine the antiglycation effect of pomelo extract against fructose-mediated protein oxidation and glycation. Our results showed that the pomelo extract (0.25 - 2.00 mg/mL) significantly inhibited the overall formation of advanced glycation end products (AGEs) in a concentration-dependent manner. The pomelo extract markedly decreased the level of fructosamine, which is directly associated with reduction in formation of AGEs and N (ε)-(carboxymethyl)lysine (CML). In addition, the pomelo extract inhibited protein oxidation through its ability to prevent the loss of thiol groups and reduced protein carbonyl formation. We characterized the active components in the pomelo extract by using high-performance liquid chromatography (HPLC), which showed that the pomelo extract contained naringin (11.90 ± 0.21 mg/g dried extract), hesperidin (12.04 ± 0.12 mg/g dried extract), neohesperidin (25.4 ± 0.12 mg/g dried extract), and naringenin (9.20 ± 0.19 mg/g dried extract). Our findings could provide a new insight into the antiglycation properties of the extract of the naturally occurring fruit pomelo for preventing AGE-mediated diabetic complications.\",\n \"corpus_id\": 14090794,\n \"score\": 2\n },\n {\n \"doc_id\": \"27103908\",\n \"title\": \"Prevention of non-enzymatic glycosylation (glycation): Implication in the treatment of diabetic complication.\",\n \"abstract\": \"Non-enzymatic glycosylation (glycation) plays an important role in the development of physiological and pathophysiological processes such as aging, diabetes, atherosclerosis, neurodegenerative diseases and chronic renal failure. Preventing glycation can minimize diabetic complications. Glycation can be prevented by the natural defence system in the body, synthetic inhibitors and natural inhibitors. Synthetic inhibitors may prevent glycation through several possible mechanisms. They might inhibit the glycation by interfering with the attachment of sugars with proteins, by inhibiting the late stage of glycation or by preventing Amadori product formation. Furthermore, their ability to scavenge free radicals and to break cross-links might be other mechanisms responsible for their potential to inhibit glycation. Naturally occurring phytochemicals/products have been found to be relatively non-toxic as compared to synthetic compounds, and are inexpensive and available in an ingestible form. A large number of plants and natural biomolecules have been shown to have antidiabetic effects. Several hypoglycaemic compounds have anti-oxidant properties. The present review describes the various ways in which glycation can be prevented.\",\n \"corpus_id\": 42690278,\n \"score\": 2\n },\n {\n \"doc_id\": \"27213445\",\n \"title\": \"The Possible Role of Flavonoids in the Prevention of Diabetic Complications.\",\n \"abstract\": \"Type 2 diabetes mellitus is a disease that affects many metabolic pathways. It is associated with insulin resistance, impaired insulin signaling, β-cell dysfunction, abnormal glucose levels, altered lipid metabolism, sub-clinical inflammation and increased oxidative stress. These and other unknown mechanisms lead to micro- and macro-complications, such as neuropathy, retinopathy, nephropathy and cardiovascular disease. Based on several in vitro animal models and some human studies, flavonoids appear to play a role in many of the metabolic processes involved in type 2 diabetes mellitus. In this review, we seek to highlight the most recent papers focusing on the relationship between flavonoids and main diabetic complications.\",\n \"corpus_id\": 9637140,\n \"score\": 2\n },\n {\n \"doc_id\": \"27495289\",\n \"title\": \"In-Vitro dual inhibition of protein glycation, and oxidation by some Arabian plants.\",\n \"abstract\": \"BACKGROUND: Diabetes mellitus is a metabolic disorder of epidemic proportion, projected to become the major cause of morbidity and mortality in the world in future. Despite extensive research in understanding this disease at molecular level, and the discovery of new drugs, diabetes and its complications remain largely untreated. Many of the late diabetic complications are associated with the glycation of proteins in the body. Natural flora has long been a rich source for therapeutic agents, especially against diabetes. The present study deals with the anti-glycation properties of some medicinally important plants of Arabian region. METHODS: Twenty-six medicinal plants, commonly found in different regions of Arabian Peninsula, were evaluated for their protein anti-glycation activity by using BSA-MG glycation assay in-vitro. The extracts were incubated with BSA and MG at 37 °C for 9 days, each sample was then examined for the presence of fluorescence (λex 330 nm, and λem 420 nm), which represent the extent of protein glycation. Antioxidant activity was evaluated by using 1,1-diphenyl- 2-picrylhydrazyl (DPPH), iron chelation, and superoxide radical scavenging asaays. RESULTS: The data revealed that out of 26 medicinal plants, five plants viz. Sida cordifolia, Plumbago zeylanica, Tribulus terrestris, Glycyrrhiza glabra, and Rosa indica were active against the in-vitro protein glycation with IC50 values between 0.408- 1.690 mg/mL. Among the active plants, Glycyrrhiza glabra L. was found to be the most potent (IC50 = 0.408 ± 0.027 mg/mL), followed by Rosa indica (IC50 = 0.596 ± 0.0179 mg/mL), and Sida cordifolia L. (IC50 = 0.63 ± 0.009 mg/mL). The antioxidant potential of these plant extracts were also determined by using DPPH (2,2-diphenyl-1-picrylhydrazyl), iron chelation, and superoxide anion radical scavenging assays. Among five plants, Sida cordifolia exhibited a potent anti-oxidant activity in both DPPH and superoxide anion radical scavenging assays (IC50 = 0.005 ± 0.0004, and 0.078 ± 0.002 mg/mL, respectively), followed by Rosa indica (IC50 = 0.023 ± 0.0005 and 0.141 ± 0.003 mg/mL, respectively). CONCLUSIONS: Protein glycation in hyperglycemic conditions involve oxidative changes. Therefore dual inhibition of protein glycation and oxidation are desirable properties in any test substance investigated for therapeutic purposes.\",\n \"corpus_id\": 14581877,\n \"score\": 2\n },\n {\n \"doc_id\": \"27901193\",\n \"title\": \"Physicochemical/photophysical characterization and angiogenic properties of Curcuma longa essential oil.\",\n \"abstract\": \"This study analyzed the physicochemical and photophysical properties of essential oil of Curcuma longa and its angiogenic potential. The results showed that curcumin is the main fluorescent component present in the oil, although the amount is relatively small. The experimental chorioallantoic membrane model was used to evaluate angiogenic activity, showing a significant increase in the vascular network of Curcuma longa and positive control groups when compared to the neutral and inhibitor controls (P <0.05), but no significant difference was found between Curcuma longa essential oil and the positive control (P >0.05). Histological analysis showed extensive neovascularization, hyperemia and inflammation in the positive control group and Curcuma longa when compared to other controls (P <0.05), characteristic factors of the angiogenesis process. In conclusion, Curcuma longa oil showed considerable proangiogenic activity and could be a potential compound in medical applications.\",\n \"corpus_id\": 3690599,\n \"score\": 2\n },\n {\n \"doc_id\": \"28053889\",\n \"title\": \"Antioxidant, antiglycation and insulinotrophic properties of Coccinia grandis (L.) in vitro: Possible role in prevention of diabetic complications.\",\n \"abstract\": \"In an attempt to develop Complementary and Alternative Medicine (CAM) for the treatment of diabetes and related complications, the antidiabetic potential of the mature unripe fruits of Coccinia grandis (CGF) was evaluated. Oxidative stress and glycation plays an important role in manifesting of diabetes and vascular complications. Agents with antioxidant and antiglycation properties may retard these pathological alterations. In this study, the edible plant Coccinia grandis was assessed for in vitro estimation of antioxidant and antiglycation potential and its insulinotrophic properties in RINm5F cells. Antioxidant activity was evaluated as DPPH (1,1-diphenyl-2-picrylhydrazyl), hydrogen peroxide and superoxide anion scavenging activities, whereas the protein glycation inhibitory potential was evaluated using in vitro albumin-fructose glycation model. Glycation inhibition was estimated by different biochemical parameters viz. fructosamine, protein carbonyl group and protein aggregation using thioflavin T fluorescence. C. grandis extract exerted a dose dependent radical scavenging activity and exhibited a significant antiglycation potential. The extract also showed a significant insulinotrophic property with 1.28 and 1.71-fold increase in insulin release when compared to control at 0.25 and 0.50 mg/mL, respectively. These data suggest the possible antidiabetic role of CGF extract, presumably by its antioxidant, antiglycation and insulin secretory effects. Present findings provide experimental evidence that the fruits of C. grandis have potential antidiabetic activity which might be used as a functional food and safe remedy for the treatment of diabetes and associated complications. This study also revealed that the plant can be a promising source for development of natural antiglycating agents and novel insulin secretagogues.\",\n \"corpus_id\": 26098992,\n \"score\": 2\n },\n {\n \"doc_id\": \"28068085\",\n \"title\": \"Cyclocurcumin, an Antivasoconstrictive Constituent of Curcuma longa (Turmeric).\",\n \"abstract\": \"Despite the increasing attention on the therapeutic potential of Curcuma longa (turmeric), the biological activities of curcuminoids other than curcumin are not well understood. Here, we investigated antivasoconstrictive activities of C. longa extract and its ingredients using freshly isolated rat aortic rings. C. longa extract significantly suppressed agonist-stimulated vasoconstriction, and cyclocurcumin was found to be the most potent (IC50 against phenylephrine-induced vasoconstriction: 14.9 ± 1.0 μM) among the 10 tested ingredients including four curcuminoids. Cyclocurcumin significantly inhibited contraction of vascular smooth muscle, which was mediated by the suppression of myosin-light-chain phosphorylation and calcium influx via the L-type calcium channel. The inhibitory effect of cyclocurcumin was observed to be reversible and without cytotoxicity. Taken together, we demonstrated that cyclocurcumin, a bioactive ingredient in C. longa, may have a therapeutic potential as a novel antivasoconstrictive natural product.\",\n \"corpus_id\": 4490231,\n \"score\": 2\n },\n {\n \"doc_id\": \"29169285\",\n \"title\": \"Relaxant effect of Curcuma longa on rat tracheal smooth muscle and its possible mechanisms.\",\n \"abstract\": \"CONTEXT: Turmeric is a spice obtained from the root of Curcuma longa L. (Zingiberaceae) with anti-aging, anticancer, anti-Alzheimer's disease, antioxidant and other medicinal properties. OBJECTIVE: The relaxant effect of C. longa on rat tracheal smooth muscle and its possible mechanisms were investigated in this study. MATERIALS AND METHODS: The relaxant effects of four cumulative concentrations of hydro-ethanol extract of C. longa (6.25, 12.5, 25, 50 mg/mL) were studied on tracheal smooth muscle precontracted by methacholine or KCl in non-incubated or incubated with different substances including propranolol, diltiazem, L-NAME, glibenclamide, atropine, chlorpheniramine, indomethacin and papaverine. The duration of the study was 84 days. RESULTS: In non-incubated tracheal smooth muscle, the extract of C. longa showed significant concentration-dependent relaxant effects (p < 0.001 for all concentrations on both KCl and methacholine-induced contraction). There was no significant difference in the relaxant effects between C. longa and theophylline in both methacholine and KCl-induced contraction conditions. In tissues incubated with propranolol, diltiazem, L-NAME and glibenclamide on methacholine-induced contraction and in tissues incubated with atropine, chlorpheniramine, indomethacin and papaverine on KCl-induced contraction, the extract also showed significant concentration-dependent relaxant effects (p < 0.001). EC50 values of C. longa between non-incubated (16.22 ± 0.62) and incubated tissues (atropine: 13.03 ± 0.55, chlorpheniramine: 12.94 ± 0.68, indomethacin: 14.80 ± 0.57 and papaverine: 16.16 ± 1.42) were not significantly different. CONCLUSIONS: Tracheal smooth muscle relaxant effects of C. longa, were comparable to those of theophylline, which could be due to the presence of methylxanthines or its possible interaction with non-adrenergic non-cholinergic nervous system.\",\n \"corpus_id\": 24612650,\n \"score\": 2\n },\n {\n \"doc_id\": \"29232190\",\n \"title\": \"The effects of Curcuma longa and curcumin on reproductive systems.\",\n \"abstract\": \"OBJECTIVE: Curcuma longa (C. longa) was used in some countries such as China and India for various medicinal purposes. Curcumin, the active component of C. longa, is commonly used as a coloring agent in foods, drugs, and cosmetics. C. longa and curcumin have been known to act as antioxidant, anti-inflammatory, anti-mutagen, and anti-carcinogenic agents. Th e attempt of the present review was to give an effort on a detailed literature survey concentrated on the protective effects of C. longa and curcumin on the reproductive organs activity. METHODS: The databases such as, PubMed, Web of Science, Google Scholar, Scopus, and Iran- Medex, were considered. The search terms were \\\"testis\\\" or \\\"ovary\\\" and \\\"Curcuma longa\\\", \\\"curcumin\\\", \\\"antioxidant effect\\\", \\\"anti-inflammatory effect\\\" and \\\"anti-cancer effect\\\". RESULTS: C. longa and curcumin inhibited the production of the tumor necrosis factor-α (TNF-α) and prostaglandin E2 (PGE2) and increased the caspases (3, 8 and 9) activities in HL-60 prostate cancer. Furthermore, C. longa and curcumin suppressed the vascular endothelial growth factor (VEGF), phosphorylated signal transducers and activators of the transcription 3 (STAT) and matrix metalloproteinase-9 (MMP-9) in ovarian cancer cell line. CONCLUSION: C. longa and curcumin might decrease the risk of cancer and other malignant diseases in the reproductive system. C. longa and curcumin have a protective effect on the reproductive organs activity such as, anti-inflammatory, anti-apoptotic, and antioxidant effects in normal cells but showed pro-apoptotic effects in the malignant cells. Therefore, different effects of C. longa and curcumin are dependent on the doses and the type of cells used in various models studied.\",\n \"corpus_id\": 31096998,\n \"score\": 2\n },\n {\n \"doc_id\": \"29274842\",\n \"title\": \"Antioxidant and anti-glycation capacities of some medicinal plants and their potential inhibitory against digestive enzymes related to type 2 diabetes mellitus.\",\n \"abstract\": \"ETHNOPHARMACOLOGICAL RELEVANCE: Plants preparations are used by traditional medicine in the treatment of various diseases, such as type-2 diabetes mellitus. Some medicinal plants are capable of controlling the complications of this metabolic disease at different levels, for example, providing antioxidant compounds that act against oxidative stress and protein glycation and others which are capable of inhibiting the catalysis of digestive enzymes and thus contribute to the reduction of hyperglycemia and hyperlipidemia. Our objective was to investigate the antioxidant and anti-glycation activities of some medicinal plants and their potential inhibitory against α-amylase, α-glucosidase and pancreatic lipase activities. MATERIAL AND METHODS: Based on the ethnobotanical researches carried out by academic studies conducted at the Federal University of Uberlandia, ten plants traditionally used in the treatment of type-2 diabetes mellitus were selected. Ethanol (EtOH) and hexane (Hex) extracts of specific parts of these plants were used in enzymatic assays to evaluate their inhibitory potential against α-amylase, α-glucosidase and lipase, as well as their antioxidant (DPPH, ORAC and FRAP) and anti-glycation (BSA/fructose model) capacities. RESULTS: The results indicate that EtOH extract of four of the ten analyzed plants exhibited more than 70% of antioxidant and anti-glycation capacities, and α-amylase and lipase inhibitory activities; no extract was able to inhibit more than 40% the α-glucosidase activity. The EtOH extracts of Bauhinia forficata and Syzygium. cumini inhibited α-amylase (IC50 8.17 ± 2.24 and 401.8 ± 14.7 μg/mL, respectively), whereas EtOH extracts of B. forficata, Chamomilla recutita and Echinodorus grandiflorus inhibited lipase (IC50 59.6 ± 10.8, 264.2 ± 87.2 and 115.8 ± 57.1 μg/mL, respectively). In addition, EtOH extracts of B. forficata, S. cumini, C. recutita and E. grandiflorus showed, respectively, higher antioxidant capacity (DPPH IC50 0.7 ± 0.1, 2.5 ± 0.2, 1.3 ± 0.2 and 35.3 ± 9.0 μg/mL) and anti-glycation activity (IC50 22.7 ± 4.4, 246.2 ± 81.7, 18.5 ± 2.8 and 339.0 ± 91.0 μg/mL). CONCLUSIONS: EtOH extracts of four of the ten species popularly cited for treatment of type 2 diabetes mellitus have shown promising antioxidant and anti-glycation properties, as well as the ability to inhibit the digestive enzymes α-amylase and lipase. Thus, our results open new possibilities for further studies in order to evaluate the antidiabetic potential of these medicinal plants.\",\n \"corpus_id\": 24576820,\n \"score\": 2\n },\n {\n \"doc_id\": \"29480231\",\n \"title\": \"Alpha-Synuclein Glycation and the Action of Anti-Diabetic Agents in Parkinson's Disease.\",\n \"abstract\": \"Parkinson's disease (PD) is a neurodegenerative disorder with complex etiology and variable pathology. While a subset of cases is associated with single-gene mutations, the majority originates from a combination of factors we do not fully understand. Thus, understanding the underlying causes of PD is indispensable for the development of novel therapeutics. Glycation, the non-enzymatic reaction between reactive dicarbonyls and amino groups, gives rise to a variety of different reaction products known as advanced glycation end products (AGEs). AGEs accumulate over a proteins life-time, and increased levels of glycation reaction products play a role in diabetic complications. It is now also becoming evident that PD patients also display perturbed sugar metabolism and protein glycation, including that of alpha-synuclein, a key player in PD. Here, we hypothesize that anti-diabetic drugs targeting the levels of glycation precursors, or promoting the clearance of glycated proteins may also prove beneficial for PD patients.\",\n \"corpus_id\": 3867626,\n \"score\": 2\n },\n {\n \"doc_id\": \"29618440\",\n \"title\": \"Synergistic potential of Zingiber officinale and Curcuma longa to ameliorate diabetic-dyslipidemia.\",\n \"abstract\": \"To find the cure of world's one of the leading morbid and mortal disorders; diabetes mellitus and its most prevalent complication, 'diabetic-dyslipidemia', is one of the leading health challenges of 21st century. The use of phytomedicine is a glimmer of hope in this scenario. Studies of current decade have shown that methanolic extracts of Zingiber officinale and Curcuma longa have highly effective therapeutic potentials against the aforesaid disorders, however, which of the extracts has more potential is still unclear. Furthermore, synergistic effect of the extracts has never been studied. Forty-eight Albino adult rats of either sex were randomly divided into eight groups. A-D groups were containing healthy rats while E-H groups were of induced diabetic-dyslipidemic rats. For forty-two days, rats of each group were given either distilled water or Zingiber officinale methanolic extract (ZOME) or Curcuma longa methanolic extract (CLME) or ZOME+CLME therapies at dose rate of 300mg/100 mL dist. H2O/kg body wt/day. FPG and lipid profiles were estimated before and after the trial, and were statistically analyzed by one-way ANOVA along with Post-hoc Tukey's multiple comparison tests. Although, ZOME and CLME significantly (P<0.05) lowered fasting plasma glucose (FPG) levels and controlled lipid profiles in diabetic-dyslipidemic rats; yet, synergistic therapy of both extracts (ZOME+CLME) most significantly (P<0.05) controlled all parameters of diabetic-dyslipidemia (78.00±1.06mg/dL FPG, 62.00±0.58mg/dL TG, 66.50±0.76mg/dL cholesterol, 32.00±0.36mg/dL HDL, 22.43±0.64 mg/dL LDL, and 12.40±0.12mg/dL VLDL). Our findings may be useful to formulate new medicines having multiple potentials to control diabetes mellitus, dyslipidemia, and diabetic-dyslipidemia.\",\n \"corpus_id\": 4598978,\n \"score\": 2\n },\n {\n \"doc_id\": \"29624265\",\n \"title\": \"CURCUMA LONGA AS MEDICINAL HERB IN THE TREATMENT OF DIABET- IC COMPLICATIONS.\",\n \"abstract\": \"Curcuma longa L. (turmeric) of ginger family (Zingiberaceae) belongs to the group of oldest cultivated spice plants in the south-east Asian countries. For many years rhizome of this plant has been used also as a safe and active drug for the treatment of various.chronic diseases, especially of diabetes mellitus (DM). The active substance of turmeric - curcumin (diferuloylmethane), possesses multiple therapeutic properties. In recent years, many detailed research (tests in vito and in vivo) along with clinical trials have revealed its very valuable biological activities related to its anti-inflammatory, antioxidant and cancer preventive properties, which are presented in numerous publications (1-6). At the molecular level it has been stated that curcumin inhibits cell proliferation, metastasis creation and apoptosis. Currently, great attention has been focused on curcumin as a blocker of TNF-s, which are the principal mediators of most inflammation-related disturbances (7). The main cause of blocking the broadly extended pharmacological and clinical investigations of curcumin is its extremely low solubility in water and in organ fluids. This feature consequently limits its systemic bioavailability and makes use of curcumin as a therapeutic remedy (to date) difficult. The primary aim of presently conducted research is to achieve increased solubilization and bioavailability of this promising nontoxic agent.\",\n \"corpus_id\": 4646629,\n \"score\": 2\n },\n {\n \"doc_id\": \"29624857\",\n \"title\": \"Impact of wedelolactone in the anti-glycation and anti-diabetic activity in experimental diabetic animals.\",\n \"abstract\": \"The glycation reaction is the addition of free carbonyl group of reducing sugar to the free amino groups of proteins, lipoproteins and nucleic acids which results in the formation of an Amadori product which may ultimately lead to the generation of advanced glycation products (AGEs). The impact of AGEs on proteins consequently generates free radicals, \\\"a key player\\\" for the pathogenesis of diabetes mellitus. Gel electrophoresis was carried out to see the visual changes taking place as a result of the glycation reaction. In this study, the anti-glycation and anti-diabetic effect of wedelolactone (WED) was seen both in vitro and in vivo. WED reverted various biochemical markers in streptozotocin-induced diabetic rats along-with the improvements in the oxidative stress markers. It also decreased the levels of the glycated serum protein and fasting blood glucose. Broadly, WED not only inhibited glycation in vitro but also proved to be an effective in vivo anti-glycating agent. © 2018 IUBMB Life, 70(6):547-552, 2018.\",\n \"corpus_id\": 4634609,\n \"score\": 2\n },\n {\n \"doc_id\": \"29732511\",\n \"title\": \"Protective effects of Curcuma longa against neurobehavioral and neurochemical damage caused by cerium chloride in mice.\",\n \"abstract\": \"Cerium chloride (CeCl3) is considered an environmental pollutant and a potent neurotoxic agent. Medicinal plants have many bioactive compounds that provide protection against damage caused by such pollutants. Curcuma longa is a bioactive compound-rich plant with very important antioxidant properties. To study the preventive and healing effects of Curcuma longa on cerium-damaged mouse brains, we intraperitoneally injected cerium chloride (CeCl3, 20 mg/kg BW) along with Curcuma longa extract, administrated by gavage (100 mg/kg BW), into mice for 60 days. We then examined mouse behavior, brain tissue damage, and brain oxidative stress parameters. Our results revealed a significant modification in the behavior of the CeCl3-treated mice. In addition, CeCl3 induced a significant increment in lipid peroxidation, carbonyl protein (PCO), and advanced oxidation protein product levels, as well as a significant reduction in superoxide dismutase (SOD) and glutathione peroxidase (GPx) activities. Acetylcholinesterase (AChE) activity remarkably increased in the brain of CeCl3-treated mice. Histopathological observations confirmed these results. Curcuma longa attenuated CeCl3-induced oxidative stress and increased the activities of antioxidant enzymes. It also decreased AChE activity in the CeCl3-damaged mouse brain that was confirmed by histopathology. In conclusion, this study suggests that Curcuma longa has a neuroprotective effect against CeCl3-induced damage in the brain.\",\n \"corpus_id\": 21389098,\n \"score\": 2\n },\n {\n \"doc_id\": \"18361755\",\n \"title\": \"Influence of ripening stage on health benefits properties of Capsicum annuum var. acuminatum L.: in vitro studies.\",\n \"abstract\": \"ABSTRACT In the present study the in vitro hypoglycemic and anti-acetylcholinesterase activities of hot pepper fruits (Capsicum annuum var. acuminatum L.) at different ripening stages were investigated. The mature, green-stage fruits had the highest activity against alpha-amylase and alpha-glucosidase with 50% inhibitory concentration (IC(50)) values of 55.88 and 76.11 microg/mL, respectively, while C. annuum var. acuminatum in the prematurity green stage exhibited the highest acetylcholinesterase inhibition property (IC(50) = 84.30 microg/mL), using the Ellman method. This study highlights the biochemical rationale for chemopreventive significance in health benefits when consuming this variety of pepper.\",\n \"corpus_id\": 30445637,\n \"score\": 1\n },\n {\n \"doc_id\": \"18668490\",\n \"title\": \"Dietary red chilli (Capsicum frutescens L.) is insulinotropic rather than hypoglycemic in type 2 diabetes model of rats.\",\n \"abstract\": \"The present study was conducted to clarify whether a low or a high, but tolerable, dietary dose of red chilli (RC) can ameliorate the diabetes related complications in a high-fat (HF) diet-fed streptozotocin (STZ)-induced type 2 diabetes model of rats. Five-week-old male Sprague Dawley rats were fed a HF diet for 2 weeks then randomly divided into four groups namely: normal control (NC), diabetic control (DBC), red chilli low (RCL, 0.5%) and red chilli high (RCH, 2.0%) groups. Diabetes was induced by an intraperitoneal (i.p.) injection of STZ (40 mg/kg BW) in all groups except the NC group. After 4 weeks feeding of experimental diets, the fasting blood glucose concentrations in both RC fed groups were not significantly different. The serum insulin concentration was significantly (p < 0.05) increased in the RCH group compared with the DBC and RCL groups. Blood HbA1c, liver weight, liver glycogen and serum lipids were not influenced by the feeding of RC-containing diets. The data of this study suggest that 2% dietary RC is insulinotropic rather than hypoglycemic at least in this experimental condition.\",\n \"corpus_id\": 9846280,\n \"score\": 1\n },\n {\n \"doc_id\": \"19447589\",\n \"title\": \"Cyclophosphamide-induced oxidative stress in brain: protective effect of hot short pepper (Capsicum frutescens L. var. abbreviatum).\",\n \"abstract\": \"This study sought to characterize the distribution of phenols and antioxidant activities in hot short pepper (Capsicum frutescens var. abbreviatum) and their inhibition of cyclophosphamide-induced oxidative stress in rat's brain. The total phenol content and antioxidant activities of pepper flesh (pericarp) and seeds were determined in vitro and in vivo. The results of the study revealed that intraperitoneal administration of cyclophosphamide (75mg/kg of body weight) caused a significant increase (P<0.05) in the malondialdehyde (MDA) content of the brain; however, there was a significant decrease (P<0.05) in the brain MDA content, in those of rats fed diet containing pepper; the flesh showed a higher inhibitory effect. In addition, dietary inclusion of the pepper (seed and flesh) also caused a dose-dependent inhibition of serum glutamate oxaloacetate transaminase (SGOT), glutamate pyruvate transaminase (SGPT), alkaline phosphatase and total bilirubin; likewise, dietary inclusion of the flesh inhibited MDA production than the seeds. The higher inhibition of oxidative stress in brain and serum enzymes and metabolites by the flesh could be attributed to its significantly higher (P<0.05) total phenol content, reducing power and free-radical scavenging ability. Therefore, dietary hot short pepper (Capsicum frutescens L. var. abbreviatum) could prevent cyclophosphamide-induced oxidative stress in brain; although the flesh is a better protectant, the possible contributory role of the seeds cannot be neglected. However, this protective effect of the pepper could be attributed to their antioxidant properties.\",\n \"corpus_id\": 25190576,\n \"score\": 1\n },\n {\n \"doc_id\": \"20226481\",\n \"title\": \"[Pentosidine: a new biomarker in diabetes mellitus complications].\",\n \"abstract\": \"Pentosidina: un nuevo biomarcador de las complicaciones en la diabetes mellitus. Diabetes mellitus causes an increase of morbidity and mortality. Advanced glycosilation end products (AGE) are formed by non-enzymatic glycation between proteins and reducing sugars as glucose. Oxidative reactions (glycoxidations) are essential for the formation of some AGE, for example pentosidine. Increased concentrations of pentosidine can be found in pathological conditions associated with hyperglycaemia and also related to increased oxidative stress. In individuals with diabetes mellitus, pentosidine formation and accumulation is developed at an accelerated rate in cells without insulin control for glucose uptake. Pentosidine has a pivotal role in diabetic complications, probably as a consequence of the diverse properties of this compound, which alters the structure and function of molecules in biological systems. The following review discusses the alterations in the concentration of pentosidine in the body, particularly in relation to changes occurring in diabetes and its complications such as vascular and bone disease, nephropathy, neuropathy and retinopathy. Novel therapeutic approaches which can prevent or ameliorate the toxic effects of AGE in the initiation and progression of diabetic complications are reviewed.\",\n \"corpus_id\": 10102290,\n \"score\": 1\n },\n {\n \"doc_id\": \"23376105\",\n \"title\": \"Sutherlandia frutescens prevents changes in diabetes-related gene expression in a fructose-induced insulin resistant cell model.\",\n \"abstract\": \"ETHNOPHARMACOLOGICAL RELEVANCE: The African medicinal plant Sutherlandia frutescens (L.) R.Br. ( Fabaceae) is traditionally used to treat diabetes and has been shown to have anti-diabetic properties in animal models. The present study investigated the capacity of an aqueous extract of Sutherlandia frutescens to prevent insulin resistance (a precursor of type 2 diabetes) in a human liver cell culture and to identify genes regulated by Sutherlandia frutescens treatment. MATERIALS AND METHODS: A combination of insulin and fructose was used to generate an in vitro model of insulin resistance in human liver cells to compare untreated control, insulin resistant and Sutherlandia frutescens treated insulin resistant cultures. Insulin resistance and its prevention by Sutherlandia frutescens were measured by glucose uptake, gluconeogenesis and lipid accumulation in the cell cultures. Changes in gene expression were quantified using the RT(2)Profiler(TM) PCR Array of 84 diabetes-related genes. RESULTS: The insulin resistant Chang liver cells took up significantly less 2-[(3)H]-deoxyglucose (p<0.05) than controls, released more glucose into the culture medium (p<0.05) and accumulated more intracellular lipid (p<0.05). Simultaneous treatment with Sutherlandia frutescens prevented development of these insulin resistance parameters (p<0.05). A total of 27 potential gene targets of Sutherlandia frutescens were significantly up or down regulated in the Sutherlandia frutescens treated insulin resistant cells. The gene VAMP3, which plays a role in vesicle transport, was down-regulated by insulin resistance, and up-regulated by Sutherlandia frutescens. Twenty six other genes encoding vesicle transporters, receptors, signalling molecules, transcription factors, and metabolic enzymes were significantly regulated by Sutherlandia frutescens. CONCLUSION: These results confirm that Sutherlandia frutescens can prevent insulin resistance in hepatocytes. The identified changes in gene expression indicate several potential mechanisms of anti-diabetic action for Sutherlandia frutescens, reflecting the multiple bioactive compounds previously identified in aqueous extracts of Sutherlandia frutescens.\",\n \"corpus_id\": 25071583,\n \"score\": 1\n },\n {\n \"doc_id\": \"23426539\",\n \"title\": \"DIA-2, a polyherbal formulation ameliorates hyperglycemia and protein-oxidation without increasing the body weight in type II diabetic rats.\",\n \"abstract\": \"BACKGROUND: The dried bulbs of Allium sativum (Garlic) and leaves of Lagerstroemia speciosa (Banaba) are used as medicinal food for the treatment of diabetes and other ailments. AIM: The present study was undertaken to ascertain whether the combination of both garlic and banaba extract produces synergistic therapeutic effect in diabetic state. METHODS: In the in vitro studies, the effect of standardized aqueous extract of Allium sativum (ASE), methanolic extract of Lagerstroemia speciosa (LSE) and their mixture (1:1 ratio), DIA-2 on insulin stimulated glucose uptake in 3T3-L1 cells, erythrocyte sorbitol accumulation and protein glycation were evaluated. Impetus from the in vitro findings triggered to screen the anti-diabetic potential of DIA-2 in rat model of type II diabetes and associated oxidative stress. In the in vivo studies, acute oral toxicity of DIA-2 was determined following OECD-423 guidelines in female rats. Anti-diabetic activity of DIA-2 was investigated in high fat diet/low dose streptozotocin induced type II diabetes at four dose levels (62.5, 125, 250 and 500 mg/kg b.w) in rats. RESULTS: Combination of ASE and LSE produced synergistic and a dose dependent increase in glucose uptake in 3T3 adipocyte cell lines when compared to the individual extracts. A similar effect was observed in the inhibition of sorbitol accumulation and protein glycation tests. DIA-2 restored the glucose and lipid level near to normal level without gain in body weight which is the most commonly encountered side effect with the use of conventional antidiabetic agents, particularly insulin, insulin secretagogues, sulfonylureas and thiazolidinediones. DIA-2 also decreased hepatic protein carbonyl content levels significantly in the diabetic rats. CONCLUSIONS: The study concluded that DIA-2 posses potent anti-diabetic activity and anti-oxidant effects.\",\n \"corpus_id\": 32090286,\n \"score\": 1\n },\n {\n \"doc_id\": \"24235936\",\n \"title\": \"Comparative anti-inflammatory properties of Capsaicin and ethyl-aAcetate extract of Capsicum frutescens linn [Solanaceae] in rats.\",\n \"abstract\": \"BACKGROUND: The analgesic effect of capsaicin (the active ingredient in Capsicum frutescens Linn. [ Solanaceae]) had been reported in several studies. Current research is being directed at producing analgesics, anti-inflammatory agents with better side effect profile. OBJECTIVES: To investigate if either the ethyl acetate extract of Capsicum frutescens Linn. [ Solanaceae] (CFE) or capsaicin (Fluka Biotechnika-CPF) (in addition to the known analgesic properties) has any anti-inflammatory effect comparable to nonsteroidal anti-inflammatory analgesics (NSAIDS). METHODS: The effects of ethyl acetate extract of Capsicum frutescens Linn. [ Solanaceae] (CFE) and capsaicin (Fluka Biotechnika-CPF) was examined on rat hind paw. Inflammation was induced in the rat's hind paw by subplantar injections of fresh egg albumin (0.5 ml/kg). Diclofenac (100 mg/kg) was used as the reference anti-inflammatory agent for comparison, while distilled water was used as the placebo. The leucocytes count, corticosterone and C - reactive protein (CRP) levels were measured as biomarkers of inflammation. Data obtained were pooled and analysed using repeated ANOVA, in a general linear model with the CPSS software. RESULTS: Sub-plantar injections of fresh egg albumin (0.5 ml/kg) produced profound and time-related oedema in the rat hind paw of the 'control' rats. Diclofenac (DIC, 100 mg/kg, i.p.) and reference capsaicin (CPF, 2.5 mg/kg, i.p.) significantly inhibited paw swelling at (p<0.05-0.001) (CI 95%) compared to distilled water-treated 'controls'. While the corticosterone levels were all very low in 7 rats treated with capsaicin, the leucocytes count was within normal range in 9 rats. However, in 16 specimens randomly assigned for CRP levels, there were very high CRP readings, up to a magnitude of 10 times the normal range. CONCLUSIONS: Capsaicin in both forms (CFE and CPF) produced anti-inflammatory effects that were comparable to diclofenac in the experimental rat model at p<0.05. It may be concluded that capsaicin has both analgesic and anti-inflammatory properties.\",\n \"corpus_id\": 8360143,\n \"score\": 1\n },\n {\n \"doc_id\": \"20525746\",\n \"title\": \"Hydraulic connections of leaves and fruit to the parent plant in Capsicum frutescens (hot pepper) during fruit ripening.\",\n \"abstract\": \"BACKGROUND AND AIMS: The hydraulic architecture and water relations of fruits and leaves of Capsicum frutescens were measured before and during the fruiting phase in order to estimate the eventual impact of xylem cavitation and embolism on the hydraulic isolation of fruits and leaves before maturation/abscission. METHODS: Measurements were performed at three different growth stages: (1) actively growing plants with some flowers before anthesis (GS1), (2) plants with about 50 % fully expanded leaves and immature fruits (GS2) and (3) plants with mature fruits and senescing basal leaves (GS3). Leaf conductance to water vapour as well as leaf and fruit water potential were measured. Hydraulic measurements were made using both the high-pressure flow meter (HPFM) and the vacuum chamber (VC) technique. KEY RESULTS: The hydraulic architecture of hot pepper plants during the fruiting phase was clearly addressed to favour water supply to growing fruits. Hydraulic measurements revealed that leaves of GS1 plants as well as leaves and fruit peduncles of GS2 plants were free from significant xylem embolism. Substantial increases in leaf petiole and fruit peduncle resistivity were recorded in GS3 plants irrespective of the hydraulic technique used. The higher fraction of resistivity measured using the VC technique compared with the HPFM technique was apparently due to conduit embolism. CONCLUSIONS: The present study is the first to look at the hydraulics of leaves and fruits during growth and maturation through direct, simultaneous measurements of water status and xylem efficiency of both plant regions at different hours of the day.\",\n \"corpus_id\": 24669270,\n \"score\": 0\n }\n]","isConversational":false}}},{"rowIdx":82,"cells":{"query":{"kind":"string","value":"{\n \"doc_id\": \"18712298\",\n \"title\": \"An introduction to protein contact prediction.\",\n \"abstract\": \"A fundamental problem in molecular biology is the prediction of the three-dimensional structure of a protein from its amino acid sequence. However, molecular modeling to find the structure is at present intractable and is likely to remain so for some time, hence intermediate steps such as predicting which residues pairs are in contact have been developed. Predicted contact pairs have been used for fold prediction, as an initial condition or constraint for molecular modeling, and as a filter to rank multiple models arising from homology modeling. As contact prediction has advanced it is becoming more common for 3D structure predictors to integrate contact prediction into structure building, as this often gives information that is orthogonal to that produced by other methods. This chapter shows how evolutionary information contained in protein sequences and multiple sequence alignments can be used to predict protein structure, and the state-of-the-art predictors and their methodologies are reviewed.\",\n \"corpus_id\": 38457709\n}"},"candidates":{"kind":"list like","value":[{"doc_id":"18000015","title":"Correlated substitution analysis and the prediction of amino acid structural contacts.","abstract":"It has long been suspected that analysis of correlated amino acid substitutions should uncover pairs or clusters of sites that are spatially proximal in mature protein structures. Accordingly, methods based on different mathematical principles such as information theory, correlation coefficients and maximum likelihood have been developed to identify co-evolving amino acids from multiple sequence alignments. Sets of pairs of sites whose behaviour is identified by these methods as correlated are often significantly enriched in pairs of spatially proximal residues. However, relatively high levels of false-positive predictions typically render such methods, in isolation, of little use in the ab initio prediction of protein structure. Misleading signal (or problems with the estimation of significance levels) can be caused by phylogenetic correlations between homologous sequences and from correlation due to factors other than spatial proximity (for example, correlation of sites which are not spatially close but which are involved in common functional properties of the protein). In recent years, several workers have suggested that information from correlated substitutions should be combined with other sources of information (secondary structure, solvent accessibility, evolutionary rates) in an attempt to reduce the proportion of false-positive predictions. We review methods for the detection of correlated amino acid substitutions, compare their relative performance in contact prediction and predict future directions in the field.","corpus_id":8551320,"score":2},{"doc_id":"18057019","title":"Mutual information without the influence of phylogeny or entropy dramatically improves residue contact prediction.","abstract":"MOTIVATION: Compensating alterations during the evolution of protein families give rise to coevolving positions that contain important structural and functional information. However, a high background composed of random noise and phylogenetic components interferes with the identification of coevolving positions. RESULTS: We have developed a rapid, simple and general method based on information theory that accurately estimates the level of background mutual information for each pair of positions in a given protein family. Removal of this background results in a metric, MIp, that correctly identifies substantially more coevolving positions in protein families than any existing method. A significant fraction of these positions coevolve strongly with one or only a few positions. The vast majority of such position pairs are in contact in representative structures. The identification of strongly coevolving position pairs can be used to impose significant structural limitations and should be an important additional constraint for ab initio protein folding. AVAILABILITY: Alignments and program files can be found in the Supplementary Information.","corpus_id":37134831,"score":2},{"doc_id":"18075167","title":"The pros and cons of predicting protein contact maps.","abstract":"Is there any reason why we should predict contact maps (CMs)? The question is one of the several 'NP-hard' questions that arise when striving for feasible solutions of the protein folding problem. At some point, theoreticians started thinking that a possible alternative to an unsolvable problem was to predict a simplified version of the protein structure: a CM. In this chapter, we will clarify that whenever problems are difficult they remain at least as difficult in the process of finding approximate solutions or heuristic approaches. However, humans rarely give up, as it is stimulating to find solutions in the face of difficulties. CMs of proteins are an interesting and useful representation of protein structures. These two-dimensional representations capture all the important features of a protein fold. We will review the general characteristics of CMs and the methods developed to study and predict them, and we will highlight some new ideas on how to improve CM predictions.","corpus_id":22637229,"score":2},{"doc_id":"18511466","title":"Using inferred residue contacts to distinguish between correct and incorrect protein models.","abstract":"MOTIVATION: The de novo prediction of 3D protein structure is enjoying a period of dramatic improvements. Often, a remaining difficulty is to select the model closest to the true structure from a group of low-energy candidates. To what extent can inter-residue contact predictions from multiple sequence alignments, information which is orthogonal to that used in most structure prediction algorithms, be used to identify those models most similar to the native protein structure? RESULTS: We present a Bayesian inference procedure to identify residue pairs that are spatially proximal in a protein structure. The method takes as input a multiple sequence alignment, and outputs an accurate posterior probability of proximity for each residue pair. We exploit a recent metagenomic sequencing project to create large, diverse and informative multiple sequence alignments for a test set of 1656 known protein structures. The method infers spatially proximal residue pairs in this test set with good accuracy: top-ranked predictions achieve an average accuracy of 38% (for an average 21-fold improvement over random predictions) in cross-validation tests. Notably, the accuracy of predicted 3D models generated by a range of structure prediction algorithms strongly correlates with how well the models satisfy probable residue contacts inferred via our method. This correlation allows for confident rejection of incorrect structural models. AVAILABILITY: An implementation of the method is freely available at http://www.doe-mbi.ucla.edu/services.","corpus_id":9668801,"score":2},{"doc_id":"18513429","title":"Protein contact order prediction from primary sequences.","abstract":"BACKGROUND: Contact order is a topological descriptor that has been shown to be correlated with several interesting protein properties such as protein folding rates and protein transition state placements. Contact order has also been used to select for viable protein folds from ab initio protein structure prediction programs. For proteins of known three-dimensional structure, their contact order can be calculated directly. However, for proteins with unknown three-dimensional structure, there is no effective prediction method currently available. RESULTS: In this paper, we propose several simple yet very effective methods to predict contact order from the amino acid sequence only. One set of methods is based on a weighted linear combination of predicted secondary structure content and amino acid composition. Depending on the number of components used in these equations it is possible to achieve a correlation coefficient of 0.857-0.870 between the observed and predicted contact order. A second method, based on sequence similarity to known three-dimensional structures, is able to achieve a correlation coefficient of 0.977. We have also developed a much more robust implementation for calculating contact order directly from PDB coordinates that works for > 99% PDB files. All of these contact order predictors and calculators have been implemented as a web server (see Availability and requirements section for URL). CONCLUSION: Protein contact order can be effectively predicted from the primary sequence, at the absence of three-dimensional structure. Three factors, percentage of residues in alpha helices, percentage of residues in beta strands, and sequence length, appear to be strongly correlated with the absolute contact order.","corpus_id":13146198,"score":2},{"doc_id":"18572239","title":"Homology-based modeling of 3D structures of protein-protein complexes using alignments of modified sequence profiles.","abstract":"Customary practice in predicting 3D structures of protein-protein complexes is employment of various docking methods when the structures of separate monomers are known a priori. The alternative approach, i.e. the template-based prediction with pure sequence information as a starting point, is still considered as being inferior mostly due to presumption that the pool of available structures of protein-protein complexes, which can serve as putative templates, is not sufficiently large. Recently, however, several labs have developed databases containing thousands of 3D structures of protein-protein complexes, which enable statistically reliable testing of homology-based algorithms. In this paper we report the results on homology-based modeling of 3D structures of protein complexes using alignments of modified sequence profiles. The method, called HOMology-BAsed COmplex Prediction (HOMBACOP), has two distinctive features: (I) extra weight on aligning interfacial residues in the dynamical programming algorithm, and (II) increased gap penalties for the interfacial segments. The method was tested against our recently developed ProtCom database and against the Boston University protein-protein BENCHMARK. In both cases, models generated were compared to the models built on basis of customarily protein structure initiative (PSI)-BLAST sequence alignments. It was found that existence of homologous (by the means of PSI-BLAST) templates (44% of cases) enables both methods to produce models of good quality, with the profiles method outperforming the PSI-BLAST models (with respect to the percentage of correctly predicted residues on the complex interface and fraction of native interfacial contacts). The models were evaluated according to the CAPRI assessment criteria and about two thirds of the models were found to fall into acceptable and medium-quality categories. The same comparison of a larger set of 463 protein complexes showed again that profiles generate better models. We further demonstrate, using our ProtCom database, the suitability of the profile alignment algorithm in detecting remote homologues between query and template sequences, where the PSI-BLAST method fails.","corpus_id":-1,"score":2},{"doc_id":"18710876","title":"Optimal contact map alignment of protein-protein interfaces.","abstract":"The long-standing problem of constructing protein structure alignments is of central importance in computational biology. The main goal is to provide an alignment of residue correspondences, in order to identify homologous residues across chains. A critical next step of this is the alignment of protein complexes and their interfaces. Here, we introduce the program CMAPi, a two-dimensional dynamic programming algorithm that, given a pair of protein complexes, optimally aligns the contact maps of their interfaces: it produces polynomial-time near-optimal alignments in the case of multiple complexes. We demonstrate the efficacy of our algorithm on complexes from PPI families listed in the SCOPPI database and from highly divergent cytokine families. In comparison to existing techniques, CMAPi generates more accurate alignments of interacting residues within families of interacting proteins, especially for sequences with low similarity. While previous methods that use an all-atom based representation of the interface have been successful, CMAPi's use of a contact map representation allows it to be more tolerant to conformational changes and thus to align more of the interaction surface. These improved interface alignments should enhance homology modeling and threading methods for predicting PPIs by providing a basis for generating template profiles for sequence-structure alignment.","corpus_id":9317504,"score":2},{"doc_id":"18712297","title":"Protein structure prediction.","abstract":"Protein structure prediction has matured over the past few years to the point that even fully automated methods can provide reasonably accurate three-dimensional models of protein structures. However, until now it has not been possible to develop programs able to perform as well as human experts, who are still capable of systematically producing better models than automated servers. Although the precise details of protein structure prediction procedures are different for virtually every protein, this chapter describes a generic procedure to obtain a three-dimensional protein model starting from the amino acid sequence. This procedure takes advantage both of programs and servers that have been shown to perform best in blind tests and of the current knowledge about evolutionary relationships between proteins, gained from detailed analyses of protein sequence, structure, and functional data.","corpus_id":20247094,"score":2},{"doc_id":"19075747","title":"Advances and pitfalls in protein structure prediction.","abstract":"Three dimensional protein structures are crucial for understanding biology at both molecular and system level. Despite the advances in experimental structural biology, the pace of sequence deposition into databanks considerably exceeds that of structure determination. Inevitably the functional annotation of genes and genomes requires the exploitation of bioinformatics methods for protein sequence comparison and structure prediction. Hence monitoring objectively the state of art of the field is of paramount importance, in order to make best use of computational protein models to address biological questions. This review describes some relevant issues in the field of structural bioinformatics, emphasizig both open basic questions and the progress being continuously achieved. It is reasonably expected that these bioinformatics methods will increasingly contribute to the biomedical, pharmaceutical and biotechnological research.","corpus_id":24602529,"score":2},{"doc_id":"19091011","title":"Real value prediction of protein solvent accessibility using enhanced PSSM features.","abstract":"BACKGROUND: Prediction of protein solvent accessibility, also called accessible surface area (ASA) prediction, is an important step for tertiary structure prediction directly from one-dimensional sequences. Traditionally, predicting solvent accessibility is regarded as either a two- (exposed or buried) or three-state (exposed, intermediate or buried) classification problem. However, the states of solvent accessibility are not well-defined in real protein structures. Thus, a number of methods have been developed to directly predict the real value ASA based on evolutionary information such as position specific scoring matrix (PSSM). RESULTS: This study enhances the PSSM-based features for real value ASA prediction by considering the physicochemical properties and solvent propensities of amino acid types. We propose a systematic method for identifying residue groups with respect to protein solvent accessibility. The amino acid columns in the PSSM profile that belong to a certain residue group are merged to generate novel features. Finally, support vector regression (SVR) is adopted to construct a real value ASA predictor. Experimental results demonstrate that the features produced by the proposed selection process are informative for ASA prediction. CONCLUSION: Experimental results based on a widely used benchmark reveal that the proposed method performs best among several of existing packages for performing ASA prediction. Furthermore, the feature selection mechanism incorporated in this study can be applied to other regression problems using the PSSM. The program and data are available from the authors upon request.","corpus_id":3026054,"score":2},{"doc_id":"19153136","title":"Sequence-based prediction of protein interaction sites with an integrative method.","abstract":"MOTIVATION: Identification of protein interaction sites has significant impact on understanding protein function, elucidating signal transduction networks and drug design studies. With the exponentially growing protein sequence data, predictive methods using sequence information only for protein interaction site prediction have drawn increasing interest. In this article, we propose a predictive model for identifying protein interaction sites. Without using any structure data, the proposed method extracts a wide range of features from protein sequences. A random forest-based integrative model is developed to effectively utilize these features and to deal with the imbalanced data classification problem commonly encountered in binding site predictions. RESULTS: We evaluate the predictive method using 2829 interface residues and 24,616 non-interface residues extracted from 99 polypeptide chains in the Protein Data Bank. The experimental results show that the proposed method performs significantly better than two other sequence-based predictive methods and can reliably predict residues involved in protein interaction sites. Furthermore, we apply the method to predict interaction sites and to construct three protein complexes: the DnaK molecular chaperone system, 1YUW and 1DKG, which provide new insight into the sequence-function relationship. We show that the predicted interaction sites can be valuable as a first approach for guiding experimental methods investigating protein-protein interactions and localizing the specific interface residues. AVAILABILITY: Datasets and software are available at http://ittc.ku.edu/~xwchen/bindingsite/prediction.","corpus_id":2113859,"score":2},{"doc_id":"19623489","title":"Protein structure prediction based on sequence similarity.","abstract":"The observation that similar protein sequences fold into similar three-dimensional structures provides a basis for the methods which predict structural features of a novel protein based on the similarity between its sequence and sequences of known protein structures. Similarity over entire sequence or large sequence fragment(s) enables prediction and modeling of entire structural domains while statistics derived from distributions of local features of known protein structures make it possible to predict such features in proteins with unknown structures. The accuracy of models of protein structures is sufficient for many practical purposes such as analysis of point mutation effects, enzymatic reactions, interaction interfaces of protein complexes, and active sites. Protein models are also used for phasing of crystallographic data and, in some cases, for drug design. By using models one can avoid the costly and time-consuming process of experimental structure determination. The purpose of this chapter is to give a practical review of the most popular protein structure prediction methods based on sequence similarity and to outline a practical approach to protein structure prediction. While the main focus of this chapter is on template-based protein structure prediction, it also provides references to other methods and programs which play an important role in protein structure prediction.","corpus_id":206671298,"score":2},{"doc_id":"20221928","title":"Protein secondary structure prediction.","abstract":"While the prediction of a native protein structure from sequence continues to remain a challenging problem, over the past decades computational methods have become quite successful in exploiting the mechanisms behind secondary structure formation. The great effort expended in this area has resulted in the development of a vast number of secondary structure prediction methods. Especially the combination of well-optimized/sensitive machine-learning algorithms and inclusion of homologous sequence information has led to increased prediction accuracies of up to 80%. In this chapter, we will first introduce some basic notions and provide a brief history of secondary structure prediction advances. Then a comprehensive overview of state-of-the-art prediction methods will be given. Finally, we will discuss open questions and challenges in this field and provide some practical recommendations for the user.","corpus_id":5082916,"score":2},{"doc_id":"22079474","title":"Protein contact map prediction using multi-stage hybrid intelligence inference systems.","abstract":"Proteins are one of the most important molecules in organisms. Protein function can be inferred from its 3D structure. The gap between the number of discovered protein sequences and the number of structures determined by the experimental methods is increasing. Accurate prediction of protein contact map is an important step toward the reconstruction of the protein's 3D structure. In spite of continuous progress in developing contact map predictors, highly accurate prediction is still unresolved problem. In this paper, we introduce a new predictor, JUSTcon, which consists of multiple parallel stages that are based on adaptive neuro-fuzzy inference System (ANFIS) and K nearest neighbors (KNNs) classifier. A smart filtering operation is performed on the final outputs to ensure normal connectivity behaviors of amino acids pairs. The window size of the filter is selected by a simple expert system. The dataset was divided into testing dataset of 50 proteins and training dataset of 450 proteins. The system produced an average accuracy of 45.2% for the sequence separation of six amino acids. In addition, JUSTcon outperformed SVMcon and PROFcon predictors in the cases of large separation distances. JUSTcon produced an average accuracy of 15% for the sequence separation of 24 amino acids after applying it on CASP9 targets.","corpus_id":722206,"score":2},{"doc_id":"22168237","title":"MSACompro: protein multiple sequence alignment using predicted secondary structure, solvent accessibility, and residue-residue contacts.","abstract":"BACKGROUND: Multiple Sequence Alignment (MSA) is a basic tool for bioinformatics research and analysis. It has been used essentially in almost all bioinformatics tasks such as protein structure modeling, gene and protein function prediction, DNA motif recognition, and phylogenetic analysis. Therefore, improving the accuracy of multiple sequence alignment is important for advancing many bioinformatics fields. RESULTS: We designed and developed a new method, MSACompro, to synergistically incorporate predicted secondary structure, relative solvent accessibility, and residue-residue contact information into the currently most accurate posterior probability-based MSA methods to improve the accuracy of multiple sequence alignments. The method is different from the multiple sequence alignment methods (e.g. 3D-Coffee) that use the tertiary structure information of some sequences since the structural information of our method is fully predicted from sequences. To the best of our knowledge, applying predicted relative solvent accessibility and contact map to multiple sequence alignment is novel. The rigorous benchmarking of our method to the standard benchmarks (i.e. BAliBASE, SABmark and OXBENCH) clearly demonstrated that incorporating predicted protein structural information improves the multiple sequence alignment accuracy over the leading multiple protein sequence alignment tools without using this information, such as MSAProbs, ProbCons, Probalign, T-coffee, MAFFT and MUSCLE. And the performance of the method is comparable to the state-of-the-art method PROMALS of using structural features and additional homologous sequences by slightly lower scores. CONCLUSION: MSACompro is an efficient and reliable multiple protein sequence alignment tool that can effectively incorporate predicted protein structural information into multiple sequence alignment. The software is available at http://sysbio.rnet.missouri.edu/multicom_toolbox/.","corpus_id":2304721,"score":2},{"doc_id":"22194819","title":"Structural constraints on the covariance matrix derived from multiple aligned protein sequences.","abstract":"Residue contact predictions were calculated based on the mutual information observed between pairs of positions in large multiple protein sequence alignments. Where previously only the statistical properties of these data have been considered important, we introduce new measures to impose constraints that make the contact map more consistent with a three dimensional structure. These included global (bulk) properties and local secondary structure properties. The latter allowed the contact constraints to be employed at the level of filtering pairs of secondary structure contacts which led to a more efficient (lower-level) implementation in the PLATO structure prediction server. Where previously the measure of success with this method had been whether the correct fold was predicted in the top 10 ranked models, with the current implementation, our summary statistic is the number of correct folds included in the top 10 models--which is on average over 50 percent.","corpus_id":11108935,"score":2},{"doc_id":"22669913","title":"CMWeb: an interactive on-line tool for analysing residue-residue contacts and contact prediction methods.","abstract":"A contact map is a 2D derivative of the 3D structure of proteins, containing various residue-residue (RR) contacts within the structure. Contact maps can be used for the reconstruction of structure with high accuracy and can be predicted from the amino acid sequence. Therefore understanding the various properties of contact maps is an important step in protein structure prediction. For investigating basic properties of contact formation and contact clusters we set up an integrated system called Contact Map Web Viewer, or CMWeb for short. The server can be used to visualize contact maps, to link contacts and to show them both in 3D structures and in multiple sequence alignments and to calculate various statistics on contacts. Moreover, we have implemented five contact prediction methods in the CMWeb server to visualize the predicted and real RR contacts in one contact map. The results of other RR contact prediction methods can be uploaded as a benchmark test onto the server as well. All of these functionality is behind a web server, thus for using our application only a Java-capable web browser is needed, no further program installation is required. The CMWeb is freely accessible at http://cmweb.enzim.hu.","corpus_id":32314824,"score":2},{"doc_id":"22847931","title":"Deep architectures for protein contact map prediction.","abstract":"MOTIVATION: Residue-residue contact prediction is important for protein structure prediction and other applications. However, the accuracy of current contact predictors often barely exceeds 20% on long-range contacts, falling short of the level required for ab initio structure prediction. RESULTS: Here, we develop a novel machine learning approach for contact map prediction using three steps of increasing resolution. First, we use 2D recursive neural networks to predict coarse contacts and orientations between secondary structure elements. Second, we use an energy-based method to align secondary structure elements and predict contact probabilities between residues in contacting alpha-helices or strands. Third, we use a deep neural network architecture to organize and progressively refine the prediction of contacts, integrating information over both space and time. We train the architecture on a large set of non-redundant proteins and test it on a large set of non-homologous domains, as well as on the set of protein domains used for contact prediction in the two most recent CASP8 and CASP9 experiments. For long-range contacts, the accuracy of the new CMAPpro predictor is close to 30%, a significant increase over existing approaches. AVAILABILITY: CMAPpro is available as part of the SCRATCH suite at http://scratch.proteomics.ics.uci.edu/. CONTACT: pfbaldi@uci.edu SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.","corpus_id":3031721,"score":2},{"doc_id":"23047561","title":"Predicting protein residue-residue contacts using deep networks and boosting.","abstract":"MOTIVATION: Protein residue-residue contacts continue to play a larger and larger role in protein tertiary structure modeling and evaluation. Yet, while the importance of contact information increases, the performance of sequence-based contact predictors has improved slowly. New approaches and methods are needed to spur further development and progress in the field. RESULTS: Here we present DNCON, a new sequence-based residue-residue contact predictor using deep networks and boosting techniques. Making use of graphical processing units and CUDA parallel computing technology, we are able to train large boosted ensembles of residue-residue contact predictors achieving state-of-the-art performance. AVAILABILITY: The web server of the prediction method (DNCON) is available at http://iris.rnet.missouri.edu/dncon/. CONTACT: chengji@missouri.edu SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.","corpus_id":3160846,"score":2},{"doc_id":"23342110","title":"Prediction of contact residue pairs based on co-substitution between sites in protein structures.","abstract":"Residue-residue interactions that fold a protein into a unique three-dimensional structure and make it play a specific function impose structural and functional constraints in varying degrees on each residue site. Selective constraints on residue sites are recorded in amino acid orders in homologous sequences and also in the evolutionary trace of amino acid substitutions. A challenge is to extract direct dependences between residue sites by removing phylogenetic correlations and indirect dependences through other residues within a protein or even through other molecules. Rapid growth of protein families with unknown folds requires an accurate de novo prediction method for protein structure. Recent attempts of disentangling direct from indirect dependences of amino acid types between residue positions in multiple sequence alignments have revealed that inferred residue-residue proximities can be sufficient information to predict a protein fold without the use of known three-dimensional structures. Here, we propose an alternative method of inferring coevolving site pairs from concurrent and compensatory substitutions between sites in each branch of a phylogenetic tree. Substitution probability and physico-chemical changes (volume, charge, hydrogen-bonding capability, and others) accompanied by substitutions at each site in each branch of a phylogenetic tree are estimated with the likelihood of each substitution, and their direct correlations between sites are used to detect concurrent and compensatory substitutions. In order to extract direct dependences between sites, partial correlation coefficients of the characteristic changes along branches between sites, in which linear multiple dependences on feature vectors at other sites are removed, are calculated and used to rank coevolving site pairs. Accuracy of contact prediction based on the present coevolution score is comparable to that achieved by a maximum entropy model of protein sequences for 15 protein families taken from the Pfam release 26.0. Besides, this excellent accuracy indicates that compensatory substitutions are significant in protein evolution.","corpus_id":17351177,"score":2},{"doc_id":"23418186","title":"Prediction of contact matrix for protein-protein interaction.","abstract":"MOTIVATION: Prediction of protein-protein interaction has become an important part of systems biology in reverse engineering the biological networks for better understanding the molecular biology of the cell. Although significant progress has been made in terms of prediction accuracy, most computational methods only predict whether two proteins interact but not their interacting residues-the information that can be very valuable for understanding the interaction mechanisms and designing modulation of the interaction. In this work, we developed a computational method to predict the interacting residue pairs-contact matrix for interacting protein domains, whose rows and columns correspond to the residues in the two interacting domains respectively and whose values (1 or 0) indicate whether the corresponding residues (do or do not) interact. RESULTS: Our method is based on supervised learning using support vector machines. For each domain involved in a given domain-domain interaction (DDI), an interaction profile hidden Markov model (ipHMM) is first built for the domain family, and then each residue position for a member domain sequence is represented as a 20-dimension vector of Fisher scores, characterizing how similar it is as compared with the family profile at that position. Each element of the contact matrix for a sequence pair is now represented by a feature vector from concatenating the vectors of the two corresponding residues, and the task is to predict the element value (1 or 0) from the feature vector. A support vector machine is trained for a given DDI, using either a consensus contact matrix or contact matrices for individual sequence pairs, and is tested by leave-one-out cross validation. The performance averaged over a set of 115 DDIs collected from the 3 DID database shows significant improvement (sensitivity up to 85%, and specificity up to 85%), as compared with a multiple sequence alignment-based method (sensitivity 57%, and specificity 78%) previously reported in the literature. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.","corpus_id":16693916,"score":2},{"doc_id":"23626696","title":"CNNcon: improved protein contact maps prediction using cascaded neural networks.","abstract":"BACKGROUNDS: Despite continuing progress in X-ray crystallography and high-field NMR spectroscopy for determination of three-dimensional protein structures, the number of unsolved and newly discovered sequences grows much faster than that of determined structures. Protein modeling methods can possibly bridge this huge sequence-structure gap with the development of computational science. A grand challenging problem is to predict three-dimensional protein structure from its primary structure (residues sequence) alone. However, predicting residue contact maps is a crucial and promising intermediate step towards final three-dimensional structure prediction. Better predictions of local and non-local contacts between residues can transform protein sequence alignment to structure alignment, which can finally improve template based three-dimensional protein structure predictors greatly. METHODS: CNNcon, an improved multiple neural networks based contact map predictor using six sub-networks and one final cascade-network, was developed in this paper. Both the sub-networks and the final cascade-network were trained and tested with their corresponding data sets. While for testing, the target protein was first coded and then input to its corresponding sub-networks for prediction. After that, the intermediate results were input to the cascade-network to finish the final prediction. RESULTS: The CNNcon can accurately predict 58.86% in average of contacts at a distance cutoff of 8 Å for proteins with lengths ranging from 51 to 450. The comparison results show that the present method performs better than the compared state-of-the-art predictors. Particularly, the prediction accuracy keeps steady with the increase of protein sequence length. It indicates that the CNNcon overcomes the thin density problem, with which other current predictors have trouble. This advantage makes the method valuable to the prediction of long length proteins. As a result, the effective prediction of long length proteins could be possible by the CNNcon.","corpus_id":9628402,"score":2},{"doc_id":"23680395","title":"Prediction of contacts from correlated sequence substitutions.","abstract":"Recent work has led to a substantial improvement in the accuracy of predictions of contacts between amino acids using evolutionary information derived from multiple sequence alignments. Where large numbers of diverse sequence relatives are available and can be aligned to the sequence of a protein of unknown structure it is now possible to generate high-resolution models without recourse to the structure of a template. In this review we describe these exciting new techniques and critically assess the state-of-the-art in contact prediction in the light of these. While concentrating on methods, we also discuss applications to protein and RNA structure prediction as well as potential future developments.","corpus_id":41447316,"score":2},{"doc_id":"23738436","title":"Prediction of protein contacts from correlated sequence substitutions.","abstract":"Recent work has led to a substantial improvement in the accuracy of predictions of contacts between amino acids using evolutionary information derived from multiple sequence alignments. Where large numbers of diverse sequence relatives are available and can be aligned to the sequence of a protein of unknown structure, it is now possible to generate high-resolution models without recourse to the structure of a template. In this review, we describe these exciting new techniques and critically assess the state of the art in contact prediction in light of them. We discuss areas for immediate research and development as well as potential future developments.","corpus_id":7200012,"score":2},{"doc_id":"23873510","title":"Assessment of CASP10 contact-assisted predictions.","abstract":"In CASP10, for the first time, contact-assisted structure predictions have been assessed. Sets of pairs of contacting residues from target structures were provided to predictors for a second round of prediction after the initial round in which they were given only sequences. The objective of the experiment was to measure model quality improvement resulting from the added contact information and thereby assess and help develop so-called hybrid prediction methods--methods where some experimentally determined distance constraints are used to augment de novo computational prediction methods. The results of the experiment were, overall, quite promising.","corpus_id":637088,"score":2},{"doc_id":"24009338","title":"Assessing the utility of coevolution-based residue-residue contact predictions in a sequence- and structure-rich era.","abstract":"Recently developed methods have shown considerable promise in predicting residue-residue contacts in protein 3D structures using evolutionary covariance information. However, these methods require large numbers of evolutionarily related sequences to robustly assess the extent of residue covariation, and the larger the protein family, the more likely that contact information is unnecessary because a reasonable model can be built based on the structure of a homolog. Here we describe a method that integrates sequence coevolution and structural context information using a pseudolikelihood approach, allowing more accurate contact predictions from fewer homologous sequences. We rigorously assess the utility of predicted contacts for protein structure prediction using large and representative sequence and structure databases from recent structure prediction experiments. We find that contact predictions are likely to be accurate when the number of aligned sequences (with sequence redundancy reduced to 90%) is greater than five times the length of the protein, and that accurate predictions are likely to be useful for structure modeling if the aligned sequences are more similar to the protein of interest than to the closest homolog of known structure. These conditions are currently met by 422 of the protein families collected in the Pfam database.","corpus_id":32974151,"score":2},{"doc_id":"24410833","title":"Toward an accurate prediction of inter-residue distances in proteins using 2D recursive neural networks.","abstract":"BACKGROUND: Protein inter-residue contact maps provide a translation and rotation invariant topological representation of a protein. They can be used as an intermediary step in protein structure predictions. However, the prediction of contact maps represents an unbalanced problem as far fewer examples of contacts than non-contacts exist in a protein structure. In this study we explore the possibility of completely eliminating the unbalanced nature of the contact map prediction problem by predicting real-value distances between residues. Predicting full inter-residue distance maps and applying them in protein structure predictions has been relatively unexplored in the past. RESULTS: We initially demonstrate that the use of native-like distance maps is able to reproduce 3D structures almost identical to the targets, giving an average RMSD of 0.5Å. In addition, the corrupted physical maps with an introduced random error of ±6Å are able to reconstruct the targets within an average RMSD of 2Å.After demonstrating the reconstruction potential of distance maps, we develop two classes of predictors using two-dimensional recursive neural networks: an ab initio predictor that relies only on the protein sequence and evolutionary information, and a template-based predictor in which additional structural homology information is provided. We find that the ab initio predictor is able to reproduce distances with an RMSD of 6Å, regardless of the evolutionary content provided. Furthermore, we show that the template-based predictor exploits both sequence and structure information even in cases of dubious homology and outperforms the best template hit with a clear margin of up to 3.7Å.Lastly, we demonstrate the ability of the two predictors to reconstruct the CASP9 targets shorter than 200 residues producing the results similar to the state of the machine learning art approach implemented in the Distill server. CONCLUSIONS: The methodology presented here, if complemented by more complex reconstruction protocols, can represent a possible path to improve machine learning algorithms for 3D protein structure prediction. Moreover, it can be used as an intermediary step in protein structure predictions either on its own or complemented by NMR restraints.","corpus_id":8181390,"score":2},{"doc_id":"24573474","title":"Direct coupling analysis for protein contact prediction.","abstract":"During evolution, structure, and function of proteins are remarkably conserved, whereas amino-acid sequences vary strongly between homologous proteins. Structural conservation constrains sequence variability and forces different residues to coevolve, i.e., to show correlated patterns of amino-acid occurrences. However, residue correlation may result from direct coupling, e.g., by a contact in the folded protein, or be induced indirectly via intermediate residues. To use empirically observed correlations for predicting residue-residue contacts, direct and indirect effects have to be disentangled. Here we present mechanistic details on how to achieve this using a methodology called Direct Coupling Analysis (DCA). DCA has been shown to produce highly accurate estimates of amino-acid pairs that have direct reciprocal constraints in evolution. Specifically, we provide instructions and protocols on how to use the algorithmic implementations of DCA starting from data extraction to predicted-contact visualization in contact maps or representative protein structures.","corpus_id":9919396,"score":2},{"doc_id":"24637808","title":"De novo structure prediction of globular proteins aided by sequence variation-derived contacts.","abstract":"The advent of high accuracy residue-residue intra-protein contact prediction methods enabled a significant boost in the quality of de novo structure predictions. Here, we investigate the potential benefits of combining a well-established fragment-based folding algorithm--FRAGFOLD, with PSICOV, a contact prediction method which uses sparse inverse covariance estimation to identify co-varying sites in multiple sequence alignments. Using a comprehensive set of 150 diverse globular target proteins, up to 266 amino acids in length, we are able to address the effectiveness and some limitations of such approaches to globular proteins in practice. Overall we find that using fragment assembly with both statistical potentials and predicted contacts is significantly better than either statistical potentials or contacts alone. Results show up to nearly 80% of correct predictions (TM-score ≥0.5) within analysed dataset and a mean TM-score of 0.54. Unsuccessful modelling cases emerged either from conformational sampling problems, or insufficient contact prediction accuracy. Nevertheless, a strong dependency of the quality of final models on the fraction of satisfied predicted long-range contacts was observed. This not only highlights the importance of these contacts on determining the protein fold, but also (combined with other ensemble-derived qualities) provides a powerful guide as to the choice of correct models and the global quality of the selected model. A proposed quality assessment scoring function achieves 0.93 precision and 0.77 recall for the discrimination of correct folds on our dataset of decoys. These findings suggest the approach is well-suited for blind predictions on a variety of globular proteins of unknown 3D structure, provided that enough homologous sequences are available to construct a large and accurate multiple sequence alignment for the initial contact prediction step.","corpus_id":14448556,"score":2},{"doc_id":"25255213","title":"Sequence co-evolution gives 3D contacts and structures of protein complexes.","abstract":"Protein-protein interactions are fundamental to many biological processes. Experimental screens have identified tens of thousands of interactions, and structural biology has provided detailed functional insight for select 3D protein complexes. An alternative rich source of information about protein interactions is the evolutionary sequence record. Building on earlier work, we show that analysis of correlated evolutionary sequence changes across proteins identifies residues that are close in space with sufficient accuracy to determine the three-dimensional structure of the protein complexes. We evaluate prediction performance in blinded tests on 76 complexes of known 3D structure, predict protein-protein contacts in 32 complexes of unknown structure, and demonstrate how evolutionary couplings can be used to distinguish between interacting and non-interacting protein pairs in a large complex. With the current growth of sequences, we expect that the method can be generalized to genome-wide elucidation of protein-protein interaction networks and used for interaction predictions at residue resolution.","corpus_id":32630002,"score":2},{"doc_id":"25299132","title":"Improving contact prediction along three dimensions.","abstract":"Correlation patterns in multiple sequence alignments of homologous proteins can be exploited to infer information on the three-dimensional structure of their members. The typical pipeline to address this task, which we in this paper refer to as the three dimensions of contact prediction, is to (i) filter and align the raw sequence data representing the evolutionarily related proteins; (ii) choose a predictive model to describe a sequence alignment; (iii) infer the model parameters and interpret them in terms of structural properties, such as an accurate contact map. We show here that all three dimensions are important for overall prediction success. In particular, we show that it is possible to improve significantly along the second dimension by going beyond the pair-wise Potts models from statistical physics, which have hitherto been the focus of the field. These (simple) extensions are motivated by multiple sequence alignments often containing long stretches of gaps which, as a data feature, would be rather untypical for independent samples drawn from a Potts model. Using a large test set of proteins we show that the combined improvements along the three dimensions are as large as any reported to date.","corpus_id":1117908,"score":2},{"doc_id":"25338092","title":"Combining physicochemical and evolutionary information for protein contact prediction.","abstract":"We introduce a novel contact prediction method that achieves high prediction accuracy by combining evolutionary and physicochemical information about native contacts. We obtain evolutionary information from multiple-sequence alignments and physicochemical information from predicted ab initio protein structures. These structures represent low-energy states in an energy landscape and thus capture the physicochemical information encoded in the energy function. Such low-energy structures are likely to contain native contacts, even if their overall fold is not native. To differentiate native from non-native contacts in those structures, we develop a graph-based representation of the structural context of contacts. We then use this representation to train an support vector machine classifier to identify most likely native contacts in otherwise non-native structures. The resulting contact predictions are highly accurate. As a result of combining two sources of information--evolutionary and physicochemical--we maintain prediction accuracy even when only few sequence homologs are present. We show that the predicted contacts help to improve ab initio structure prediction. A web service is available at http://compbio.robotics.tu-berlin.de/epc-map/.","corpus_id":4274795,"score":2},{"doc_id":"25375897","title":"Improved contact predictions using the recognition of protein like contact patterns.","abstract":"Given sufficient large protein families, and using a global statistical inference approach, it is possible to obtain sufficient accuracy in protein residue contact predictions to predict the structure of many proteins. However, these approaches do not consider the fact that the contacts in a protein are neither randomly, nor independently distributed, but actually follow precise rules governed by the structure of the protein and thus are interdependent. Here, we present PconsC2, a novel method that uses a deep learning approach to identify protein-like contact patterns to improve contact predictions. A substantial enhancement can be seen for all contacts independently on the number of aligned sequences, residue separation or secondary structure type, but is largest for β-sheet containing proteins. In addition to being superior to earlier methods based on statistical inferences, in comparison to state of the art methods using machine learning, PconsC2 is superior for families with more than 100 effective sequence homologs. The improved contact prediction enables improved structure prediction.","corpus_id":18540524,"score":2},{"doc_id":"25431331","title":"MetaPSICOV: combining coevolution methods for accurate prediction of contacts and long range hydrogen bonding in proteins.","abstract":"MOTIVATION: Recent developments of statistical techniques to infer direct evolutionary couplings between residue pairs have rendered covariation-based contact prediction a viable means for accurate 3D modelling of proteins, with no information other than the sequence required. To extend the usefulness of contact prediction, we have designed a new meta-predictor (MetaPSICOV) which combines three distinct approaches for inferring covariation signals from multiple sequence alignments, considers a broad range of other sequence-derived features and, uniquely, a range of metrics which describe both the local and global quality of the input multiple sequence alignment. Finally, we use a two-stage predictor, where the second stage filters the output of the first stage. This two-stage predictor is additionally evaluated on its ability to accurately predict the long range network of hydrogen bonds, including correctly assigning the donor and acceptor residues. RESULTS: Using the original PSICOV benchmark set of 150 protein families, MetaPSICOV achieves a mean precision of 0.54 for top-L predicted long range contacts-around 60% higher than PSICOV, and around 40% better than CCMpred. In de novo protein structure prediction using FRAGFOLD, MetaPSICOV is able to improve the TM-scores of models by a median of 0.05 compared with PSICOV. Lastly, for predicting long range hydrogen bonding, MetaPSICOV-HB achieves a precision of 0.69 for the top-L/10 hydrogen bonds compared with just 0.26 for the baseline MetaPSICOV. AVAILABILITY AND IMPLEMENTATION: MetaPSICOV is available as a freely available web server at http://bioinf.cs.ucl.ac.uk/MetaPSICOV. Raw data (predicted contact lists and 3D models) and source code can be downloaded from http://bioinf.cs.ucl.ac.uk/downloads/MetaPSICOV. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.","corpus_id":2985369,"score":2},{"doc_id":"25548928","title":"Advances in protein contact map prediction based on machine learning.","abstract":"A protein contact map is a simplified, two-dimensional version of the three-dimensional protein structure. Protein contact map is proved to be crucial in forming the three-dimensional structure. Contact map prediction has now become an indispensable and promising intermediate step towards final three-dimensional structure prediction, while directed sequence-structure prediction hits its bottlenecks. In this article, different evaluation scores of prediction efficiency are compared. Next, the state of the art and future perspectives of contact map methods are reviewed and special attention is paid to those relying on machine learning algorithms. Details of neural network based methods as well as a list of machine learning based methods are given. Finally, bottlenecks and potential improvements of contact map predictions are discussed.","corpus_id":20881869,"score":2},{"doc_id":"26502070","title":"CAB-Align: A Flexible Protein Structure Alignment Method Based on the Residue-Residue Contact Area.","abstract":"Proteins are flexible, and this flexibility has an essential functional role. Flexibility can be observed in loop regions, rearrangements between secondary structure elements, and conformational changes between entire domains. However, most protein structure alignment methods treat protein structures as rigid bodies. Thus, these methods fail to identify the equivalences of residue pairs in regions with flexibility. In this study, we considered that the evolutionary relationship between proteins corresponds directly to the residue-residue physical contacts rather than the three-dimensional (3D) coordinates of proteins. Thus, we developed a new protein structure alignment method, contact area-based alignment (CAB-align), which uses the residue-residue contact area to identify regions of similarity. The main purpose of CAB-align is to identify homologous relationships at the residue level between related protein structures. The CAB-align procedure comprises two main steps: First, a rigid-body alignment method based on local and global 3D structure superposition is employed to generate a sufficient number of initial alignments. Then, iterative dynamic programming is executed to find the optimal alignment. We evaluated the performance and advantages of CAB-align based on four main points: (1) agreement with the gold standard alignment, (2) alignment quality based on an evolutionary relationship without 3D coordinate superposition, (3) consistency of the multiple alignments, and (4) classification agreement with the gold standard classification. Comparisons of CAB-align with other state-of-the-art protein structure alignment methods (TM-align, FATCAT, and DaliLite) using our benchmark dataset showed that CAB-align performed robustly in obtaining high-quality alignments and generating consistent multiple alignments with high coverage and accuracy rates, and it performed extremely well when discriminating between homologous and nonhomologous pairs of proteins in both single and multi-domain comparisons. The CAB-align software is freely available to academic users as stand-alone software at http://www.pharm.kitasato-u.ac.jp/bmd/bmd/Publications.html.","corpus_id":17375188,"score":2},{"doc_id":"27112569","title":"CoinFold: a web server for protein contact prediction and contact-assisted protein folding.","abstract":"CoinFold (http://raptorx2.uchicago.edu/ContactMap/) is a web server for protein contact prediction and contact-assisted de novo structure prediction. CoinFold predicts contacts by integrating joint multi-family evolutionary coupling (EC) analysis and supervised machine learning. This joint EC analysis is unique in that it not only uses residue coevolution information in the target protein family, but also that in the related families which may have divergent sequences but similar folds. The supervised learning further improves contact prediction accuracy by making use of sequence profile, contact (distance) potential and other information. Finally, this server predicts tertiary structure of a sequence by feeding its predicted contacts and secondary structure to the CNS suite. Tested on the CASP and CAMEO targets, this server shows significant advantages over existing ones of similar category in both contact and tertiary structure prediction.","corpus_id":3731114,"score":2},{"doc_id":"27115648","title":"Protein Residue Contacts and Prediction Methods.","abstract":"In the field of computational structural proteomics, contact predictions have shown new prospects of solving the longstanding problem of ab initio protein structure prediction. In the last few years, application of deep learning algorithms and availability of large protein sequence databases, combined with improvement in methods that derive contacts from multiple sequence alignments, have shown a huge increase in the precision of contact prediction. In addition, these predicted contacts have also been used to build three-dimensional models from scratch. In this chapter, we briefly discuss many elements of protein residue-residue contacts and the methods available for prediction, focusing on a state-of-the-art contact prediction tool, DNcon. Illustrating with a case study, we describe how DNcon can be used to make ab initio contact predictions for a given protein sequence and discuss how the predicted contacts may be analyzed and evaluated.","corpus_id":22725123,"score":2},{"doc_id":"27307635","title":"CMsearch: simultaneous exploration of protein sequence space and structure space improves not only protein homology detection but also protein structure prediction.","abstract":"MOTIVATION: Protein homology detection, a fundamental problem in computational biology, is an indispensable step toward predicting protein structures and understanding protein functions. Despite the advances in recent decades on sequence alignment, threading and alignment-free methods, protein homology detection remains a challenging open problem. Recently, network methods that try to find transitive paths in the protein structure space demonstrate the importance of incorporating network information of the structure space. Yet, current methods merge the sequence space and the structure space into a single space, and thus introduce inconsistency in combining different sources of information. METHOD: We present a novel network-based protein homology detection method, CMsearch, based on cross-modal learning. Instead of exploring a single network built from the mixture of sequence and structure space information, CMsearch builds two separate networks to represent the sequence space and the structure space. It then learns sequence-structure correlation by simultaneously taking sequence information, structure information, sequence space information and structure space information into consideration. RESULTS: We tested CMsearch on two challenging tasks, protein homology detection and protein structure prediction, by querying all 8332 PDB40 proteins. Our results demonstrate that CMsearch is insensitive to the similarity metrics used to define the sequence and the structure spaces. By using HMM-HMM alignment as the sequence similarity metric, CMsearch clearly outperforms state-of-the-art homology detection methods and the CASP-winning template-based protein structure prediction methods. AVAILABILITY AND IMPLEMENTATION: Our program is freely available for download from http://sfb.kaust.edu.sa/Pages/Software.aspx CONTACT: : xin.gao@kaust.edu.sa SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.","corpus_id":12245606,"score":2},{"doc_id":"27787823","title":"Assessing Predicted Contacts for Building Protein Three-Dimensional Models.","abstract":"Recent successes of contact-guided protein structure prediction methods have revived interest in solving the long-standing problem of ab initio protein structure prediction. With homology modeling failing for many protein sequences that do not have templates, contact-guided structure prediction has shown promise, and consequently, contact prediction has gained a lot of interest recently. Although a few dozen contact prediction tools are already currently available as web servers and downloadables, not enough research has been done towards using existing measures like precision and recall to evaluate these contacts with the goal of building three-dimensional models. Moreover, when we do not have a native structure for a set of predicted contacts, the only analysis we can perform is a simple contact map visualization of the predicted contacts. A wider and more rigorous assessment of the predicted contacts is needed, in order to build tertiary structure models. This chapter discusses instructions and protocols for using tools and applying techniques in order to assess predicted contacts for building three-dimensional models.","corpus_id":4873322,"score":2},{"doc_id":"28056090","title":"Accurate De Novo Prediction of Protein Contact Map by Ultra-Deep Learning Model.","abstract":"MOTIVATION: Protein contacts contain key information for the understanding of protein structure and function and thus, contact prediction from sequence is an important problem. Recently exciting progress has been made on this problem, but the predicted contacts for proteins without many sequence homologs is still of low quality and not very useful for de novo structure prediction. METHOD: This paper presents a new deep learning method that predicts contacts by integrating both evolutionary coupling (EC) and sequence conservation information through an ultra-deep neural network formed by two deep residual neural networks. The first residual network conducts a series of 1-dimensional convolutional transformation of sequential features; the second residual network conducts a series of 2-dimensional convolutional transformation of pairwise information including output of the first residual network, EC information and pairwise potential. By using very deep residual networks, we can accurately model contact occurrence patterns and complex sequence-structure relationship and thus, obtain higher-quality contact prediction regardless of how many sequence homologs are available for proteins in question. RESULTS: Our method greatly outperforms existing methods and leads to much more accurate contact-assisted folding. Tested on 105 CASP11 targets, 76 past CAMEO hard targets, and 398 membrane proteins, the average top L long-range prediction accuracy obtained by our method, one representative EC method CCMpred and the CASP11 winner MetaPSICOV is 0.47, 0.21 and 0.30, respectively; the average top L/10 long-range accuracy of our method, CCMpred and MetaPSICOV is 0.77, 0.47 and 0.59, respectively. Ab initio folding using our predicted contacts as restraints but without any force fields can yield correct folds (i.e., TMscore>0.6) for 203 of the 579 test proteins, while that using MetaPSICOV- and CCMpred-predicted contacts can do so for only 79 and 62 of them, respectively. Our contact-assisted models also have much better quality than template-based models especially for membrane proteins. The 3D models built from our contact prediction have TMscore>0.5 for 208 of the 398 membrane proteins, while those from homology modeling have TMscore>0.5 for only 10 of them. Further, even if trained mostly by soluble proteins, our deep learning method works very well on membrane proteins. In the recent blind CAMEO benchmark, our fully-automated web server implementing this method successfully folded 6 targets with a new fold and only 0.3L-2.3L effective sequence homologs, including one β protein of 182 residues, one α+β protein of 125 residues, one α protein of 140 residues, one α protein of 217 residues, one α/β of 260 residues and one α protein of 462 residues. Our method also achieved the highest F1 score on free-modeling targets in the latest CASP (Critical Assessment of Structure Prediction), although it was not fully implemented back then. AVAILABILITY: http://raptorx.uchicago.edu/ContactMap/.","corpus_id":605957,"score":2},{"doc_id":"18235992","title":"PRINTR: prediction of RNA binding sites in proteins using SVM and profiles.","abstract":"Protein-RNA interactions play a key role in a number of biological processes such as protein synthesis, mRNA processing, assembly and function of ribosomes and eukaryotic spliceosomes. A reliable identification of RNA-binding sites in RNA-binding proteins is important for functional annotation and site-directed mutagenesis. We developed a novel method for the prediction of protein residues that interact with RNA using support vector machine (SVM) and position-specific scoring matrices (PSSMs). Two cases have been considered in the prediction of protein residues at RNA-binding surfaces. One is given the sequence information of a protein chain that is known to interact with RNA; the other is given the structural information. Thus, five different inputs have been tested. Coupled with PSI-BLAST profiles and predicted secondary structure, the present approach yields a Matthews correlation coefficient (MCC) of 0.432 by a 7-fold cross-validation, which is the best among all previous reported RNA-binding sites prediction methods. When given the structural information, we have obtained the MCC value of 0.457, with PSSMs, observed secondary structure and solvent accessibility information assigned by DSSP as input. A web server implementing the prediction method is available at the following URL: http://210.42.106.80/printr/ .","corpus_id":1035800,"score":1},{"doc_id":"18464326","title":"A different look at the quality of modeled three-dimensional protein structures.","abstract":"Measuring the accuracy of protein three-dimensional structures is one of the most important problems in protein structure prediction. For structure-based drug design, the accuracy of the binding site is far more important than the accuracy of any other region of the protein. We have developed an automated method for assessing the quality of a protein model by focusing on the set of residues in the small molecule binding site. Small molecule binding sites typically involve multiple regions of the protein coming together in space, and their accuracy has been observed to be sensitive to even small alignment errors. In addition, ligand binding sites contain the critical information required for drug design, making their accuracy particularly important. We analyzed the accuracy of the binding sites on two sets of protein models: the predictions submitted by the top-performing CASP7 groups, and the models generated by four widely used homology modeling packages. The results of our CASP7 analysis significantly differ from the previous findings, implying that the binding site measure does not correlate with the traditional model quality measures used in the structure prediction benchmarks. For the modeling programs, the resolution of binding sites is extremely sensitive to the degree of sequence homology between the query and the template, even when the most accurate alignments are used in the homology modeling process.","corpus_id":13639028,"score":1},{"doc_id":"18689810","title":"Detection of 3D atomic similarities and their use in the discrimination of small molecule protein-binding sites.","abstract":"MOTIVATION: Current computational methods for the prediction of function from structure are restricted to the detection of similarities and subsequent transfer of functional annotation. In a significant minority of cases, global sequence or structural (fold) similarities do not provide clues about protein function. In these cases, one alternative is to detect local binding site similarities. These may still reflect more distant evolutionary relationships as well as unique physico-chemical constraints necessary for binding similar ligands, thus helping pinpoint the function. In the present work, we ask the following question: is it possible to discriminate within a dataset of non-homologous proteins those that bind similar ligands based on their binding site similarities? METHODS: We implement a graph-matching-based method for the detection of 3D atomic similarities introducing some simplifications that allow us to extend its applicability to the analysis of large allatom binding site models. This method, called IsoCleft, does not require atoms to be connected either in sequence or space. We apply the method to a cognate-ligand bound dataset of non-homologous proteins. We define a family of binding site models with decreasing knowledge about the identity of the ligand-interacting atoms to uncouple the questions of predicting the location of the binding site and detecting binding site similarities. Furthermore, we calculate the individual contributions of binding site size, chemical composition and geometry to prediction performance. RESULTS: We find that it is possible to discriminate between different ligand-binding sites. In other words, there is a certain uniqueness in the set of atoms that are in contact to specific ligand scaffolds. This uniqueness is restricted to the atoms in close proximity of the ligand in which case, size and chemical composition alone are sufficient to discriminate binding sites. Discrimination ability decreases with decreasing knowledge about the identity of the ligand-interacting binding site atoms. The decrease is quite abrupt when considering size and chemical composition alone, but much slower when including geometry. We also observe that certain ligands are easier to discriminate. Interestingly, the subset of binding site atoms belonging to highly conserved residues is not sufficient to discriminate binding sites, implying that convergently evolved binding sites arrived at dissimilar solutions. AVAILABILITY: IsoCleft can be obtained from the authors.","corpus_id":25624257,"score":1},{"doc_id":"18704938","title":"Prediction of helix-helix contacts and interacting helices in polytopic membrane proteins using neural networks.","abstract":"Despite rapidly increasing numbers of available 3D structures, membrane proteins still account for less than 1% of all structures in the Protein Data Bank. Recent high-resolution structures indicate a clearly broader structural diversity of membrane proteins than initially anticipated, motivating the development of reliable structure prediction methods specifically tailored for this class of molecules. One important prediction target capturing all major aspects of a protein's 3D structure is its contact map. Our analysis shows that computational methods trained to predict residue contacts in globular proteins perform poorly when applied to membrane proteins. We have recently published a method to identify interacting alpha-helices in membrane proteins based on the analysis of coevolving residues in predicted transmembrane regions. Here, we present a substantially improved algorithm for the same problem, which uses a newly developed neural network approach to predict helix-helix contacts. In addition to the input features commonly used for contact prediction of soluble proteins, such as windowed residue profiles and residue distance in the sequence, our network also incorporates features that apply to membrane proteins only, such as residue position within the transmembrane segment and its orientation toward the lipophilic environment. The obtained neural network can predict contacts between residues in transmembrane segments with nearly 26% accuracy. It is therefore the first published contact predictor developed specifically for membrane proteins performing with equal accuracy to state-of-the-art contact predictors available for soluble proteins. The predicted helix-helix contacts were employed in a second step to identify interacting helices. For our dataset consisting of 62 membrane proteins of solved structure, we gained an accuracy of 78.1%. Because the reliable prediction of helix interaction patterns is an important step in the classification and prediction of membrane protein folds, our method will be a helpful tool in compiling a structural census of membrane proteins.","corpus_id":7928484,"score":1},{"doc_id":"19003998","title":"Accurate prediction for atomic-level protein design and its application in diversifying the near-optimal sequence space.","abstract":"The task of engineering a protein to assume a target three-dimensional structure is known as protein design. Computational search algorithms are devised to predict a minimal energy amino acid sequence for a particular structure. In practice, however, an ensemble of low-energy sequences is often sought. Primarily, this is performed because an individual predicted low-energy sequence may not necessarily fold to the target structure because of both inaccuracies in modeling protein energetics and the nonoptimal nature of search algorithms employed. Additionally, some low-energy sequences may be overly stable and thus lack the dynamic flexibility required for biological functionality. Furthermore, the investigation of low-energy sequence ensembles will provide crucial insights into the pseudo-physical energy force fields that have been derived to describe structural energetics for protein design. Significantly, numerous studies have predicted low-energy sequences, which were subsequently synthesized and demonstrated to fold to desired structures. However, the characterization of the sequence space defined by such energy functions as compatible with a target structure has not been performed in full detail. This issue is critical for protein design scientists to successfully continue using these force fields at an ever-increasing pace and scale. In this paper, we present a conceptually novel algorithm that rapidly predicts the set of lowest energy sequences for a given structure. Based on the theory of probabilistic graphical models, it performs efficient inspection and partitioning of the near-optimal sequence space, without making any assumptions of positional independence. We benchmark its performance on a diverse set of relevant protein design examples and show that it consistently yields sequences of lower energy than those derived from state-of-the-art techniques. Thus, we find that previously presented search techniques do not fully depict the low-energy space as precisely. Examination of the predicted ensembles indicates that, for each structure, the amino acid identity at a majority of positions must be chosen extremely selectively so as to not incur significant energetic penalties. We investigate this high degree of similarity and demonstrate how more diverse near-optimal sequences can be predicted in order to systematically overcome this bottleneck for computational design. Finally, we exploit this in-depth analysis of a collection of the lowest energy sequences to suggest an explanation for previously observed experimental design results. The novel methodologies introduced here accurately portray the sequence space compatible with a protein structure and further supply a scheme to yield heterogeneous low-energy sequences, thus providing a powerful instrument for future work on protein design.","corpus_id":8014671,"score":1},{"doc_id":"19046430","title":"A discriminative method for protein remote homology detection and fold recognition combining Top-n-grams and latent semantic analysis.","abstract":"BACKGROUND: Protein remote homology detection and fold recognition are central problems in bioinformatics. Currently, discriminative methods based on support vector machine (SVM) are the most effective and accurate methods for solving these problems. A key step to improve the performance of the SVM-based methods is to find a suitable representation of protein sequences. RESULTS: In this paper, a novel building block of proteins called Top-n-grams is presented, which contains the evolutionary information extracted from the protein sequence frequency profiles. The protein sequence frequency profiles are calculated from the multiple sequence alignments outputted by PSI-BLAST and converted into Top-n-grams. The protein sequences are transformed into fixed-dimension feature vectors by the occurrence times of each Top-n-gram. The training vectors are evaluated by SVM to train classifiers which are then used to classify the test protein sequences. We demonstrate that the prediction performance of remote homology detection and fold recognition can be improved by combining Top-n-grams and latent semantic analysis (LSA), which is an efficient feature extraction technique from natural language processing. When tested on superfamily and fold benchmarks, the method combining Top-n-grams and LSA gives significantly better results compared to related methods. CONCLUSION: The method based on Top-n-grams significantly outperforms the methods based on many other building blocks including N-grams, patterns, motifs and binary profiles. Therefore, Top-n-gram is a good building block of the protein sequences and can be widely used in many tasks of the computational biology, such as the sequence alignment, the prediction of domain boundary, the designation of knowledge-based potentials and the prediction of protein binding sites.","corpus_id":10752257,"score":1},{"doc_id":"19173310","title":"Prediction of 3D metal binding sites from translated gene sequences based on remote-homology templates.","abstract":"Database-scale analysis was performed to determine whether structural models, based on remote homologues, are effective in predicting 3D transition metal binding sites in proteins directly from translated gene sequences. The extent by which side chain modeling alone reduces sensitivity and selectivity is shown to be <10%. Surprisingly, selectivity was not dependent on the level of sequence homology between template and target, or on the presence of a metal ion in the structural template. Applying a modification of the CHED algorithm (Babor et al., Proteins 2008;70:208-217) and machine learning filters, a selectivity of approximately 90% was achieved for protein sequences using unrelated structural templates over a sequence identity range of 18-100%. Below approximately 18% identity, the number of analyzable target-template pairs and predictability of metal binding sites falls off sharply. A full third of structural templates were found to have target partners only in the remote homology range of 18-30%. In this range, nonmetal-binding templates are calculated to be the majority and serve to predict with 50% sensitivity at the geometric level. Overall, sensitivity at the geometric level for targets having templates in the 18-30% sequence identity range is 73%, with an average of one false positive site per true site. Protein sequences described as \"unknown\" in the UniProt database and composed largely of unidentified genome project sequences were studied and metal binding sites predicted. A web server for prediction of metal binding sites from protein sequence is provided.","corpus_id":21577128,"score":1},{"doc_id":"19180183","title":"Prediction of protein-protein interaction sites in sequences and 3D structures by random forests.","abstract":"Identifying interaction sites in proteins provides important clues to the function of a protein and is becoming increasingly relevant in topics such as systems biology and drug discovery. Although there are numerous papers on the prediction of interaction sites using information derived from structure, there are only a few case reports on the prediction of interaction residues based solely on protein sequence. Here, a sliding window approach is combined with the Random Forests method to predict protein interaction sites using (i) a combination of sequence- and structure-derived parameters and (ii) sequence information alone. For sequence-based prediction we achieved a precision of 84% with a 26% recall and an F-measure of 40%. When combined with structural information, the prediction performance increases to a precision of 76% and a recall of 38% with an F-measure of 51%. We also present an attempt to rationalize the sliding window size and demonstrate that a nine-residue window is the most suitable for predictor construction. Finally, we demonstrate the applicability of our prediction methods by modeling the Ras-Raf complex using predicted interaction sites as target binding interfaces. Our results suggest that it is possible to predict protein interaction sites with quite a high accuracy using only sequence information.","corpus_id":5697364,"score":1},{"doc_id":"19422056","title":"Beyond the Twilight Zone: automated prediction of structural properties of proteins by recursive neural networks and remote homology information.","abstract":"The prediction of 1D structural properties of proteins is an important step toward the prediction of protein structure and function, not only in the ab initio case but also when homology information to known structures is available. Despite this the vast majority of 1D predictors do not incorporate homology information into the prediction process. We develop a novel structural alignment method, SAMD, which we use to build alignments of putative remote homologues that we compress into templates of structural frequency profiles. We use these templates as additional input to ensembles of recursive neural networks, which we specialise for the prediction of query sequences that show only remote homology to any Protein Data Bank structure. We predict four 1D structural properties - secondary structure, relative solvent accessibility, backbone structural motifs, and contact density. Secondary structure prediction accuracy, tested by five-fold cross-validation on a large set of proteins allowing less than 25% sequence identity between training and test set and query sequences and templates, exceeds 82%, outperforming its ab initio counterpart, other state-of-the-art secondary structure predictors (Jpred 3 and PSIPRED) and two other systems based on PSI-BLAST and COMPASS templates. We show that structural information from homologues improves prediction accuracy well beyond the Twilight Zone of sequence similarity, even below 5% sequence identity, for all four structural properties. Significant improvement over the extraction of structural information directly from PDB templates suggests that the combination of sequence and template information is more informative than templates alone.","corpus_id":21505025,"score":1},{"doc_id":"19734152","title":"Algorithms for optimal protein structure alignment.","abstract":"MOTIVATION: Structural alignment is an important tool for understanding the evolutionary relationships between proteins. However, finding the best pairwise structural alignment is difficult, due to the infinite number of possible superpositions of two structures. Unlike the sequence alignment problem, which has a polynomial time solution, the structural alignment problem has not been even classified as solvable. RESULTS: We study one of the most widely used measures of protein structural similarity, defined as the number of pairs of residues in two proteins that can be superimposed under a predefined distance cutoff. We prove that, for any two proteins, this measure can be optimized for all but finitely many distance cutoffs. Our method leads to a series of algorithms for optimizing other structure similarity measures, including the measures commonly used in protein structure prediction experiments. We also present a polynomial time algorithm for finding a near-optimal superposition of two proteins. Aside from having a relatively low cost, the algorithm for near-optimal solution returns a superposition of provable quality. In other words, the difference between the score of the returned superposition and the score of an optimal superposition can be explicitly computed and used to determine whether the returned superposition is, in fact, the best superposition. CONTACT: poleksic@cs.uni.edu SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.","corpus_id":23621754,"score":1},{"doc_id":"23110141","title":"Accurate prediction of protein catalytic residues by side chain orientation and residue contact density.","abstract":"Prediction of protein catalytic residues provides useful information for the studies of protein functions. Most of the existing methods combine both structure and sequence information but heavily rely on sequence conservation from multiple sequence alignments. The contribution of structure information is usually less than that of sequence conservation in existing methods. We found a novel structure feature, residue side chain orientation, which is the first structure-based feature that achieves prediction results comparable to that of evolutionary sequence conservation. We developed a structure-based method, Enzyme Catalytic residue SIde-chain Arrangement (EXIA), which is based on residue side chain orientations and backbone flexibility of protein structure. The prediction that uses EXIA outperforms existing structure-based features. The prediction quality of combing EXIA and sequence conservation exceeds that of the state-of-the-art prediction methods. EXIA is designed to predict catalytic residues from single protein structure without needing sequence or structure alignments. It provides invaluable information when there is no sufficient or reliable homology information for target protein. We found that catalytic residues have very special side chain orientation and designed the EXIA method based on the newly discovered feature. It was also found that EXIA performs well for a dataset of enzymes without any bounded ligand in their crystallographic structures.","corpus_id":17268599,"score":1},{"doc_id":"23314126","title":"Predicting protein β-sheet contacts using a maximum entropy-based correlated mutation measure.","abstract":"MOTIVATION: The problem of ab initio protein folding is one of the most difficult in modern computational biology. The prediction of residue contacts within a protein provides a more tractable immediate step. Recently introduced maximum entropy-based correlated mutation measures (CMMs), such as direct information, have been successful in predicting residue contacts. However, most correlated mutation studies focus on proteins that have large good-quality multiple sequence alignments (MSA) because the power of correlated mutation analysis falls as the size of the MSA decreases. However, even with small autogenerated MSAs, maximum entropy-based CMMs contain information. To make use of this information, in this article, we focus not on general residue contacts but contacts between residues in β-sheets. The strong constraints and prior knowledge associated with β-contacts are ideally suited for prediction using a method that incorporates an often noisy CMM. RESULTS: Using contrastive divergence, a statistical machine learning technique, we have calculated a maximum entropy-based CMM. We have integrated this measure with a new probabilistic model for β-contact prediction, which is used to predict both residue- and strand-level contacts. Using our model on a standard non-redundant dataset, we significantly outperform a 2D recurrent neural network architecture, achieving a 5% improvement in true positives at the 5% false-positive rate at the residue level. At the strand level, our approach is competitive with the state-of-the-art single methods achieving precision of 61.0% and recall of 55.4%, while not requiring residue solvent accessibility as an input. AVAILABILITY: http://www2.warwick.ac.uk/fac/sci/systemsbiology/research/software/","corpus_id":9728230,"score":1},{"doc_id":"25330970","title":"De novo membrane protein structure prediction.","abstract":"Recent advances in identifying residue-residue contacts from large multiple sequence alignments have enabled impressive gains to be made in the field of protein structure prediction. In this chapter, we discuss these advances and provide a step-by-step guide to applying the latest tools to the de novo modelling of alpha-helical transmembrane proteins. As a practical example, we demonstrate the process of building an accurate 3D model of a G protein-coupled receptor, correctly orientated in the membrane, using only its primary protein sequence.","corpus_id":24129100,"score":1},{"doc_id":"27171127","title":"Critical assessment of methods of protein structure prediction: Progress and new directions in round XI.","abstract":"Modeling of protein structure from amino acid sequence now plays a major role in structural biology. Here we report new developments and progress from the CASP11 community experiment, assessing the state of the art in structure modeling. Notable points include the following: (1) New methods for predicting three dimensional contacts resulted in a few spectacular template free models in this CASP, whereas models based on sequence homology to proteins with experimental structure continue to be the most accurate. ( 2) Refinement of initial protein models, primarily using molecular dynamics related approaches, has now advanced to the point where the best methods can consistently (though slightly) improve nearly all models. ( 3) The use of relatively sparse NMR constraints dramatically improves the accuracy of models, and another type of sparse data, chemical crosslinking, introduced in this CASP, also shows promise for producing better models. ( 4) A new emphasis on modeling protein complexes, in collaboration with CAPRI, has produced interesting results, but also shows the need for more focus on this area. ( 5) Methods for estimating the accuracy of models have advanced to the point where they are of considerable practical use. ( 6) A first assessment demonstrates that models can sometimes successfully address biological questions that motivate experimental structure determination. ( 7) There is continuing progress in accuracy of modeling regions of structure not directly available by comparative modeling, while there is marginal or no progress in some other areas. Proteins 2016; 84(Suppl 1):4-14. © 2016 Wiley Periodicals, Inc.","corpus_id":206409570,"score":1},{"doc_id":"27220237","title":"[MOLECULAR EVOLUTION OF ION CHANNELS: AMINO ACID SEQUENCES AND 3D STRUCTURES].","abstract":"An integral part of modern evolutionary biology is comparative analysis of structure and function of macromolecules such as proteins. The first and critical step to understand evolution of homologous proteins is their amino acid sequence alignment. However, standard algorithms fop not provide unambiguous sequence alignments for proteins of poor homology. More reliable results can be obtained by comparing experimental 3D structures obtained at atomic resolution, for instance, with the aid of X-ray structural analysis. If such structures are lacking, homology modeling is used, which may take into account indirect experimental data on functional roles of individual amino-acid residues. An important problem is that the sequence alignment, which reflects genetic modifications, does not necessarily correspond to the functional homology. The latter depends on three-dimensional structures which are critical for natural selection. Since alignment techniques relying only on the analysis of primary structures carry no information on the functional properties of proteins, including 3D structures into consideration is very important. Here we consider several examples involving ion channels and demonstrate that alignment of their three-dimensional structures can significantly improve sequence alignments obtained by traditional methods.","corpus_id":15224112,"score":1},{"doc_id":"29297299","title":"A sparse autoencoder-based deep neural network for protein solvent accessibility and contact number prediction.","abstract":"BACKGROUND: Direct prediction of the three-dimensional (3D) structures of proteins from one-dimensional (1D) sequences is a challenging problem. Significant structural characteristics such as solvent accessibility and contact number are essential for deriving restrains in modeling protein folding and protein 3D structure. Thus, accurately predicting these features is a critical step for 3D protein structure building. RESULTS: In this study, we present DeepSacon, a computational method that can effectively predict protein solvent accessibility and contact number by using a deep neural network, which is built based on stacked autoencoder and a dropout method. The results demonstrate that our proposed DeepSacon achieves a significant improvement in the prediction quality compared with the state-of-the-art methods. We obtain 0.70 three-state accuracy for solvent accessibility, 0.33 15-state accuracy and 0.74 Pearson Correlation Coefficient (PCC) for the contact number on the 5729 monomeric soluble globular protein dataset. We also evaluate the performance on the CASP11 benchmark dataset, DeepSacon achieves 0.68 three-state accuracy and 0.69 PCC for solvent accessibility and contact number, respectively. CONCLUSIONS: We have shown that DeepSacon can reliably predict solvent accessibility and contact number with stacked sparse autoencoder and a dropout approach.","corpus_id":19404395,"score":1},{"doc_id":"29625561","title":"COZOID: contact zone identifier for visual analysis of protein-protein interactions.","abstract":"BACKGROUND: Studying the patterns of protein-protein interactions (PPIs) is fundamental for understanding the structure and function of protein complexes. The exploration of the vast space of possible mutual configurations of interacting proteins and their contact zones is very time consuming and requires the proteomic expert knowledge. RESULTS: In this paper, we propose a novel tool containing a set of visual abstraction techniques for the guided exploration of PPI configuration space. It helps proteomic experts to select the most relevant configurations and explore their contact zones at different levels of detail. The system integrates a set of methods that follow and support the workflow of proteomics experts. The first visual abstraction method, the Matrix view, is based on customized interactive heat maps and provides the users with an overview of all possible residue-residue contacts in all PPI configurations and their interactive filtering. In this step, the user can traverse all input PPI configurations and obtain an overview of their interacting amino acids. Then, the models containing a particular pair of interacting amino acids can be selectively picked and traversed. Detailed information on the individual amino acids in the contact zones and their properties is presented in the Contact-Zone list-view. The list-view provides a comparative tool to rank the best models based on the similarity of their contacts to the template-structure contacts. All these techniques are interactively linked with other proposed methods, the Exploded view and the Open-Book view, which represent individual configurations in three-dimensional space. These representations solve the high overlap problem associated with many configurations. Using these views, the structural alignment of the best models can also be visually confirmed. CONCLUSIONS: We developed a system for the exploration of large sets of protein-protein complexes in a fast and intuitive way. The usefulness of our system has been tested and verified on several docking structures covering the three major types of PPIs, including coiled-coil, pocket-string, and surface-surface interactions. Our case studies prove that our tool helps to analyse and filter protein-protein complexes in a fraction of the time compared to using previously available techniques.","corpus_id":4651784,"score":1},{"doc_id":"19768443","title":"Proteomic tools for the analysis of cytoskeleton proteins.","abstract":"Proteomic tools have become an essential part of the tool kit of the molecular biologist, and provide techniques for detecting homologous sequences, recognizing functional domains, modeling, and analyzing the three-dimensional structure for any given protein sequence. Although a wealth of structural and functional information is available for a large number of members of the various classes of cytoskeletal proteins, many more members remain uncharacterized. These computational tools that are freely and easily accessible to the scientific community provide an excellent starting point to predict the structural and functional properties of such partially or fully uncharacterized protein sequences, and can lead to elegantly designed experiments to probe the hypothesized function. This chapter discusses various proteomic analysis tools with a focus on protein structure and function predictions.","corpus_id":41951596,"score":0},{"doc_id":"24272431","title":"Introduction to bioinformatics.","abstract":"Bioinformatics is an interdisciplinary field mainly involving molecular biology and genetics, computer science, mathematics, and statistics. Data intensive, large-scale biological problems are addressed from a computational point of view. The most common problems are modeling biological processes at the molecular level and making inferences from collected data. A bioinformatics solution usually involves the following steps: Collect statistics from biological data. Build a computational model. Solve a computational modeling problem. Test and evaluate a computational algorithm. This chapter gives a brief introduction to bioinformatics by first providing an introduction to biological terminology and then discussing some classical bioinformatics problems organized by the types of data sources. Sequence analysis is the analysis of DNA and protein sequences for clues regarding function and includes subproblems such as identification of homologs, multiple sequence alignment, searching sequence patterns, and evolutionary analyses. Protein structures are three-dimensional data and the associated problems are structure prediction (secondary and tertiary), analysis of protein structures for clues regarding function, and structural alignment. Gene expression data is usually represented as matrices and analysis of microarray data mostly involves statistics analysis, classification, and clustering approaches. Biological networks such as gene regulatory networks, metabolic pathways, and protein-protein interaction networks are usually modeled as graphs and graph theoretic approaches are used to solve associated problems such as construction and analysis of large-scale networks.","corpus_id":40174170,"score":0}],"string":"[\n {\n \"doc_id\": \"18000015\",\n \"title\": \"Correlated substitution analysis and the prediction of amino acid structural contacts.\",\n \"abstract\": \"It has long been suspected that analysis of correlated amino acid substitutions should uncover pairs or clusters of sites that are spatially proximal in mature protein structures. Accordingly, methods based on different mathematical principles such as information theory, correlation coefficients and maximum likelihood have been developed to identify co-evolving amino acids from multiple sequence alignments. Sets of pairs of sites whose behaviour is identified by these methods as correlated are often significantly enriched in pairs of spatially proximal residues. However, relatively high levels of false-positive predictions typically render such methods, in isolation, of little use in the ab initio prediction of protein structure. Misleading signal (or problems with the estimation of significance levels) can be caused by phylogenetic correlations between homologous sequences and from correlation due to factors other than spatial proximity (for example, correlation of sites which are not spatially close but which are involved in common functional properties of the protein). In recent years, several workers have suggested that information from correlated substitutions should be combined with other sources of information (secondary structure, solvent accessibility, evolutionary rates) in an attempt to reduce the proportion of false-positive predictions. We review methods for the detection of correlated amino acid substitutions, compare their relative performance in contact prediction and predict future directions in the field.\",\n \"corpus_id\": 8551320,\n \"score\": 2\n },\n {\n \"doc_id\": \"18057019\",\n \"title\": \"Mutual information without the influence of phylogeny or entropy dramatically improves residue contact prediction.\",\n \"abstract\": \"MOTIVATION: Compensating alterations during the evolution of protein families give rise to coevolving positions that contain important structural and functional information. However, a high background composed of random noise and phylogenetic components interferes with the identification of coevolving positions. RESULTS: We have developed a rapid, simple and general method based on information theory that accurately estimates the level of background mutual information for each pair of positions in a given protein family. Removal of this background results in a metric, MIp, that correctly identifies substantially more coevolving positions in protein families than any existing method. A significant fraction of these positions coevolve strongly with one or only a few positions. The vast majority of such position pairs are in contact in representative structures. The identification of strongly coevolving position pairs can be used to impose significant structural limitations and should be an important additional constraint for ab initio protein folding. AVAILABILITY: Alignments and program files can be found in the Supplementary Information.\",\n \"corpus_id\": 37134831,\n \"score\": 2\n },\n {\n \"doc_id\": \"18075167\",\n \"title\": \"The pros and cons of predicting protein contact maps.\",\n \"abstract\": \"Is there any reason why we should predict contact maps (CMs)? The question is one of the several 'NP-hard' questions that arise when striving for feasible solutions of the protein folding problem. At some point, theoreticians started thinking that a possible alternative to an unsolvable problem was to predict a simplified version of the protein structure: a CM. In this chapter, we will clarify that whenever problems are difficult they remain at least as difficult in the process of finding approximate solutions or heuristic approaches. However, humans rarely give up, as it is stimulating to find solutions in the face of difficulties. CMs of proteins are an interesting and useful representation of protein structures. These two-dimensional representations capture all the important features of a protein fold. We will review the general characteristics of CMs and the methods developed to study and predict them, and we will highlight some new ideas on how to improve CM predictions.\",\n \"corpus_id\": 22637229,\n \"score\": 2\n },\n {\n \"doc_id\": \"18511466\",\n \"title\": \"Using inferred residue contacts to distinguish between correct and incorrect protein models.\",\n \"abstract\": \"MOTIVATION: The de novo prediction of 3D protein structure is enjoying a period of dramatic improvements. Often, a remaining difficulty is to select the model closest to the true structure from a group of low-energy candidates. To what extent can inter-residue contact predictions from multiple sequence alignments, information which is orthogonal to that used in most structure prediction algorithms, be used to identify those models most similar to the native protein structure? RESULTS: We present a Bayesian inference procedure to identify residue pairs that are spatially proximal in a protein structure. The method takes as input a multiple sequence alignment, and outputs an accurate posterior probability of proximity for each residue pair. We exploit a recent metagenomic sequencing project to create large, diverse and informative multiple sequence alignments for a test set of 1656 known protein structures. The method infers spatially proximal residue pairs in this test set with good accuracy: top-ranked predictions achieve an average accuracy of 38% (for an average 21-fold improvement over random predictions) in cross-validation tests. Notably, the accuracy of predicted 3D models generated by a range of structure prediction algorithms strongly correlates with how well the models satisfy probable residue contacts inferred via our method. This correlation allows for confident rejection of incorrect structural models. AVAILABILITY: An implementation of the method is freely available at http://www.doe-mbi.ucla.edu/services.\",\n \"corpus_id\": 9668801,\n \"score\": 2\n },\n {\n \"doc_id\": \"18513429\",\n \"title\": \"Protein contact order prediction from primary sequences.\",\n \"abstract\": \"BACKGROUND: Contact order is a topological descriptor that has been shown to be correlated with several interesting protein properties such as protein folding rates and protein transition state placements. Contact order has also been used to select for viable protein folds from ab initio protein structure prediction programs. For proteins of known three-dimensional structure, their contact order can be calculated directly. However, for proteins with unknown three-dimensional structure, there is no effective prediction method currently available. RESULTS: In this paper, we propose several simple yet very effective methods to predict contact order from the amino acid sequence only. One set of methods is based on a weighted linear combination of predicted secondary structure content and amino acid composition. Depending on the number of components used in these equations it is possible to achieve a correlation coefficient of 0.857-0.870 between the observed and predicted contact order. A second method, based on sequence similarity to known three-dimensional structures, is able to achieve a correlation coefficient of 0.977. We have also developed a much more robust implementation for calculating contact order directly from PDB coordinates that works for > 99% PDB files. All of these contact order predictors and calculators have been implemented as a web server (see Availability and requirements section for URL). CONCLUSION: Protein contact order can be effectively predicted from the primary sequence, at the absence of three-dimensional structure. Three factors, percentage of residues in alpha helices, percentage of residues in beta strands, and sequence length, appear to be strongly correlated with the absolute contact order.\",\n \"corpus_id\": 13146198,\n \"score\": 2\n },\n {\n \"doc_id\": \"18572239\",\n \"title\": \"Homology-based modeling of 3D structures of protein-protein complexes using alignments of modified sequence profiles.\",\n \"abstract\": \"Customary practice in predicting 3D structures of protein-protein complexes is employment of various docking methods when the structures of separate monomers are known a priori. The alternative approach, i.e. the template-based prediction with pure sequence information as a starting point, is still considered as being inferior mostly due to presumption that the pool of available structures of protein-protein complexes, which can serve as putative templates, is not sufficiently large. Recently, however, several labs have developed databases containing thousands of 3D structures of protein-protein complexes, which enable statistically reliable testing of homology-based algorithms. In this paper we report the results on homology-based modeling of 3D structures of protein complexes using alignments of modified sequence profiles. The method, called HOMology-BAsed COmplex Prediction (HOMBACOP), has two distinctive features: (I) extra weight on aligning interfacial residues in the dynamical programming algorithm, and (II) increased gap penalties for the interfacial segments. The method was tested against our recently developed ProtCom database and against the Boston University protein-protein BENCHMARK. In both cases, models generated were compared to the models built on basis of customarily protein structure initiative (PSI)-BLAST sequence alignments. It was found that existence of homologous (by the means of PSI-BLAST) templates (44% of cases) enables both methods to produce models of good quality, with the profiles method outperforming the PSI-BLAST models (with respect to the percentage of correctly predicted residues on the complex interface and fraction of native interfacial contacts). The models were evaluated according to the CAPRI assessment criteria and about two thirds of the models were found to fall into acceptable and medium-quality categories. The same comparison of a larger set of 463 protein complexes showed again that profiles generate better models. We further demonstrate, using our ProtCom database, the suitability of the profile alignment algorithm in detecting remote homologues between query and template sequences, where the PSI-BLAST method fails.\",\n \"corpus_id\": -1,\n \"score\": 2\n },\n {\n \"doc_id\": \"18710876\",\n \"title\": \"Optimal contact map alignment of protein-protein interfaces.\",\n \"abstract\": \"The long-standing problem of constructing protein structure alignments is of central importance in computational biology. The main goal is to provide an alignment of residue correspondences, in order to identify homologous residues across chains. A critical next step of this is the alignment of protein complexes and their interfaces. Here, we introduce the program CMAPi, a two-dimensional dynamic programming algorithm that, given a pair of protein complexes, optimally aligns the contact maps of their interfaces: it produces polynomial-time near-optimal alignments in the case of multiple complexes. We demonstrate the efficacy of our algorithm on complexes from PPI families listed in the SCOPPI database and from highly divergent cytokine families. In comparison to existing techniques, CMAPi generates more accurate alignments of interacting residues within families of interacting proteins, especially for sequences with low similarity. While previous methods that use an all-atom based representation of the interface have been successful, CMAPi's use of a contact map representation allows it to be more tolerant to conformational changes and thus to align more of the interaction surface. These improved interface alignments should enhance homology modeling and threading methods for predicting PPIs by providing a basis for generating template profiles for sequence-structure alignment.\",\n \"corpus_id\": 9317504,\n \"score\": 2\n },\n {\n \"doc_id\": \"18712297\",\n \"title\": \"Protein structure prediction.\",\n \"abstract\": \"Protein structure prediction has matured over the past few years to the point that even fully automated methods can provide reasonably accurate three-dimensional models of protein structures. However, until now it has not been possible to develop programs able to perform as well as human experts, who are still capable of systematically producing better models than automated servers. Although the precise details of protein structure prediction procedures are different for virtually every protein, this chapter describes a generic procedure to obtain a three-dimensional protein model starting from the amino acid sequence. This procedure takes advantage both of programs and servers that have been shown to perform best in blind tests and of the current knowledge about evolutionary relationships between proteins, gained from detailed analyses of protein sequence, structure, and functional data.\",\n \"corpus_id\": 20247094,\n \"score\": 2\n },\n {\n \"doc_id\": \"19075747\",\n \"title\": \"Advances and pitfalls in protein structure prediction.\",\n \"abstract\": \"Three dimensional protein structures are crucial for understanding biology at both molecular and system level. Despite the advances in experimental structural biology, the pace of sequence deposition into databanks considerably exceeds that of structure determination. Inevitably the functional annotation of genes and genomes requires the exploitation of bioinformatics methods for protein sequence comparison and structure prediction. Hence monitoring objectively the state of art of the field is of paramount importance, in order to make best use of computational protein models to address biological questions. This review describes some relevant issues in the field of structural bioinformatics, emphasizig both open basic questions and the progress being continuously achieved. It is reasonably expected that these bioinformatics methods will increasingly contribute to the biomedical, pharmaceutical and biotechnological research.\",\n \"corpus_id\": 24602529,\n \"score\": 2\n },\n {\n \"doc_id\": \"19091011\",\n \"title\": \"Real value prediction of protein solvent accessibility using enhanced PSSM features.\",\n \"abstract\": \"BACKGROUND: Prediction of protein solvent accessibility, also called accessible surface area (ASA) prediction, is an important step for tertiary structure prediction directly from one-dimensional sequences. Traditionally, predicting solvent accessibility is regarded as either a two- (exposed or buried) or three-state (exposed, intermediate or buried) classification problem. However, the states of solvent accessibility are not well-defined in real protein structures. Thus, a number of methods have been developed to directly predict the real value ASA based on evolutionary information such as position specific scoring matrix (PSSM). RESULTS: This study enhances the PSSM-based features for real value ASA prediction by considering the physicochemical properties and solvent propensities of amino acid types. We propose a systematic method for identifying residue groups with respect to protein solvent accessibility. The amino acid columns in the PSSM profile that belong to a certain residue group are merged to generate novel features. Finally, support vector regression (SVR) is adopted to construct a real value ASA predictor. Experimental results demonstrate that the features produced by the proposed selection process are informative for ASA prediction. CONCLUSION: Experimental results based on a widely used benchmark reveal that the proposed method performs best among several of existing packages for performing ASA prediction. Furthermore, the feature selection mechanism incorporated in this study can be applied to other regression problems using the PSSM. The program and data are available from the authors upon request.\",\n \"corpus_id\": 3026054,\n \"score\": 2\n },\n {\n \"doc_id\": \"19153136\",\n \"title\": \"Sequence-based prediction of protein interaction sites with an integrative method.\",\n \"abstract\": \"MOTIVATION: Identification of protein interaction sites has significant impact on understanding protein function, elucidating signal transduction networks and drug design studies. With the exponentially growing protein sequence data, predictive methods using sequence information only for protein interaction site prediction have drawn increasing interest. In this article, we propose a predictive model for identifying protein interaction sites. Without using any structure data, the proposed method extracts a wide range of features from protein sequences. A random forest-based integrative model is developed to effectively utilize these features and to deal with the imbalanced data classification problem commonly encountered in binding site predictions. RESULTS: We evaluate the predictive method using 2829 interface residues and 24,616 non-interface residues extracted from 99 polypeptide chains in the Protein Data Bank. The experimental results show that the proposed method performs significantly better than two other sequence-based predictive methods and can reliably predict residues involved in protein interaction sites. Furthermore, we apply the method to predict interaction sites and to construct three protein complexes: the DnaK molecular chaperone system, 1YUW and 1DKG, which provide new insight into the sequence-function relationship. We show that the predicted interaction sites can be valuable as a first approach for guiding experimental methods investigating protein-protein interactions and localizing the specific interface residues. AVAILABILITY: Datasets and software are available at http://ittc.ku.edu/~xwchen/bindingsite/prediction.\",\n \"corpus_id\": 2113859,\n \"score\": 2\n },\n {\n \"doc_id\": \"19623489\",\n \"title\": \"Protein structure prediction based on sequence similarity.\",\n \"abstract\": \"The observation that similar protein sequences fold into similar three-dimensional structures provides a basis for the methods which predict structural features of a novel protein based on the similarity between its sequence and sequences of known protein structures. Similarity over entire sequence or large sequence fragment(s) enables prediction and modeling of entire structural domains while statistics derived from distributions of local features of known protein structures make it possible to predict such features in proteins with unknown structures. The accuracy of models of protein structures is sufficient for many practical purposes such as analysis of point mutation effects, enzymatic reactions, interaction interfaces of protein complexes, and active sites. Protein models are also used for phasing of crystallographic data and, in some cases, for drug design. By using models one can avoid the costly and time-consuming process of experimental structure determination. The purpose of this chapter is to give a practical review of the most popular protein structure prediction methods based on sequence similarity and to outline a practical approach to protein structure prediction. While the main focus of this chapter is on template-based protein structure prediction, it also provides references to other methods and programs which play an important role in protein structure prediction.\",\n \"corpus_id\": 206671298,\n \"score\": 2\n },\n {\n \"doc_id\": \"20221928\",\n \"title\": \"Protein secondary structure prediction.\",\n \"abstract\": \"While the prediction of a native protein structure from sequence continues to remain a challenging problem, over the past decades computational methods have become quite successful in exploiting the mechanisms behind secondary structure formation. The great effort expended in this area has resulted in the development of a vast number of secondary structure prediction methods. Especially the combination of well-optimized/sensitive machine-learning algorithms and inclusion of homologous sequence information has led to increased prediction accuracies of up to 80%. In this chapter, we will first introduce some basic notions and provide a brief history of secondary structure prediction advances. Then a comprehensive overview of state-of-the-art prediction methods will be given. Finally, we will discuss open questions and challenges in this field and provide some practical recommendations for the user.\",\n \"corpus_id\": 5082916,\n \"score\": 2\n },\n {\n \"doc_id\": \"22079474\",\n \"title\": \"Protein contact map prediction using multi-stage hybrid intelligence inference systems.\",\n \"abstract\": \"Proteins are one of the most important molecules in organisms. Protein function can be inferred from its 3D structure. The gap between the number of discovered protein sequences and the number of structures determined by the experimental methods is increasing. Accurate prediction of protein contact map is an important step toward the reconstruction of the protein's 3D structure. In spite of continuous progress in developing contact map predictors, highly accurate prediction is still unresolved problem. In this paper, we introduce a new predictor, JUSTcon, which consists of multiple parallel stages that are based on adaptive neuro-fuzzy inference System (ANFIS) and K nearest neighbors (KNNs) classifier. A smart filtering operation is performed on the final outputs to ensure normal connectivity behaviors of amino acids pairs. The window size of the filter is selected by a simple expert system. The dataset was divided into testing dataset of 50 proteins and training dataset of 450 proteins. The system produced an average accuracy of 45.2% for the sequence separation of six amino acids. In addition, JUSTcon outperformed SVMcon and PROFcon predictors in the cases of large separation distances. JUSTcon produced an average accuracy of 15% for the sequence separation of 24 amino acids after applying it on CASP9 targets.\",\n \"corpus_id\": 722206,\n \"score\": 2\n },\n {\n \"doc_id\": \"22168237\",\n \"title\": \"MSACompro: protein multiple sequence alignment using predicted secondary structure, solvent accessibility, and residue-residue contacts.\",\n \"abstract\": \"BACKGROUND: Multiple Sequence Alignment (MSA) is a basic tool for bioinformatics research and analysis. It has been used essentially in almost all bioinformatics tasks such as protein structure modeling, gene and protein function prediction, DNA motif recognition, and phylogenetic analysis. Therefore, improving the accuracy of multiple sequence alignment is important for advancing many bioinformatics fields. RESULTS: We designed and developed a new method, MSACompro, to synergistically incorporate predicted secondary structure, relative solvent accessibility, and residue-residue contact information into the currently most accurate posterior probability-based MSA methods to improve the accuracy of multiple sequence alignments. The method is different from the multiple sequence alignment methods (e.g. 3D-Coffee) that use the tertiary structure information of some sequences since the structural information of our method is fully predicted from sequences. To the best of our knowledge, applying predicted relative solvent accessibility and contact map to multiple sequence alignment is novel. The rigorous benchmarking of our method to the standard benchmarks (i.e. BAliBASE, SABmark and OXBENCH) clearly demonstrated that incorporating predicted protein structural information improves the multiple sequence alignment accuracy over the leading multiple protein sequence alignment tools without using this information, such as MSAProbs, ProbCons, Probalign, T-coffee, MAFFT and MUSCLE. And the performance of the method is comparable to the state-of-the-art method PROMALS of using structural features and additional homologous sequences by slightly lower scores. CONCLUSION: MSACompro is an efficient and reliable multiple protein sequence alignment tool that can effectively incorporate predicted protein structural information into multiple sequence alignment. The software is available at http://sysbio.rnet.missouri.edu/multicom_toolbox/.\",\n \"corpus_id\": 2304721,\n \"score\": 2\n },\n {\n \"doc_id\": \"22194819\",\n \"title\": \"Structural constraints on the covariance matrix derived from multiple aligned protein sequences.\",\n \"abstract\": \"Residue contact predictions were calculated based on the mutual information observed between pairs of positions in large multiple protein sequence alignments. Where previously only the statistical properties of these data have been considered important, we introduce new measures to impose constraints that make the contact map more consistent with a three dimensional structure. These included global (bulk) properties and local secondary structure properties. The latter allowed the contact constraints to be employed at the level of filtering pairs of secondary structure contacts which led to a more efficient (lower-level) implementation in the PLATO structure prediction server. Where previously the measure of success with this method had been whether the correct fold was predicted in the top 10 ranked models, with the current implementation, our summary statistic is the number of correct folds included in the top 10 models--which is on average over 50 percent.\",\n \"corpus_id\": 11108935,\n \"score\": 2\n },\n {\n \"doc_id\": \"22669913\",\n \"title\": \"CMWeb: an interactive on-line tool for analysing residue-residue contacts and contact prediction methods.\",\n \"abstract\": \"A contact map is a 2D derivative of the 3D structure of proteins, containing various residue-residue (RR) contacts within the structure. Contact maps can be used for the reconstruction of structure with high accuracy and can be predicted from the amino acid sequence. Therefore understanding the various properties of contact maps is an important step in protein structure prediction. For investigating basic properties of contact formation and contact clusters we set up an integrated system called Contact Map Web Viewer, or CMWeb for short. The server can be used to visualize contact maps, to link contacts and to show them both in 3D structures and in multiple sequence alignments and to calculate various statistics on contacts. Moreover, we have implemented five contact prediction methods in the CMWeb server to visualize the predicted and real RR contacts in one contact map. The results of other RR contact prediction methods can be uploaded as a benchmark test onto the server as well. All of these functionality is behind a web server, thus for using our application only a Java-capable web browser is needed, no further program installation is required. The CMWeb is freely accessible at http://cmweb.enzim.hu.\",\n \"corpus_id\": 32314824,\n \"score\": 2\n },\n {\n \"doc_id\": \"22847931\",\n \"title\": \"Deep architectures for protein contact map prediction.\",\n \"abstract\": \"MOTIVATION: Residue-residue contact prediction is important for protein structure prediction and other applications. However, the accuracy of current contact predictors often barely exceeds 20% on long-range contacts, falling short of the level required for ab initio structure prediction. RESULTS: Here, we develop a novel machine learning approach for contact map prediction using three steps of increasing resolution. First, we use 2D recursive neural networks to predict coarse contacts and orientations between secondary structure elements. Second, we use an energy-based method to align secondary structure elements and predict contact probabilities between residues in contacting alpha-helices or strands. Third, we use a deep neural network architecture to organize and progressively refine the prediction of contacts, integrating information over both space and time. We train the architecture on a large set of non-redundant proteins and test it on a large set of non-homologous domains, as well as on the set of protein domains used for contact prediction in the two most recent CASP8 and CASP9 experiments. For long-range contacts, the accuracy of the new CMAPpro predictor is close to 30%, a significant increase over existing approaches. AVAILABILITY: CMAPpro is available as part of the SCRATCH suite at http://scratch.proteomics.ics.uci.edu/. CONTACT: pfbaldi@uci.edu SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.\",\n \"corpus_id\": 3031721,\n \"score\": 2\n },\n {\n \"doc_id\": \"23047561\",\n \"title\": \"Predicting protein residue-residue contacts using deep networks and boosting.\",\n \"abstract\": \"MOTIVATION: Protein residue-residue contacts continue to play a larger and larger role in protein tertiary structure modeling and evaluation. Yet, while the importance of contact information increases, the performance of sequence-based contact predictors has improved slowly. New approaches and methods are needed to spur further development and progress in the field. RESULTS: Here we present DNCON, a new sequence-based residue-residue contact predictor using deep networks and boosting techniques. Making use of graphical processing units and CUDA parallel computing technology, we are able to train large boosted ensembles of residue-residue contact predictors achieving state-of-the-art performance. AVAILABILITY: The web server of the prediction method (DNCON) is available at http://iris.rnet.missouri.edu/dncon/. CONTACT: chengji@missouri.edu SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.\",\n \"corpus_id\": 3160846,\n \"score\": 2\n },\n {\n \"doc_id\": \"23342110\",\n \"title\": \"Prediction of contact residue pairs based on co-substitution between sites in protein structures.\",\n \"abstract\": \"Residue-residue interactions that fold a protein into a unique three-dimensional structure and make it play a specific function impose structural and functional constraints in varying degrees on each residue site. Selective constraints on residue sites are recorded in amino acid orders in homologous sequences and also in the evolutionary trace of amino acid substitutions. A challenge is to extract direct dependences between residue sites by removing phylogenetic correlations and indirect dependences through other residues within a protein or even through other molecules. Rapid growth of protein families with unknown folds requires an accurate de novo prediction method for protein structure. Recent attempts of disentangling direct from indirect dependences of amino acid types between residue positions in multiple sequence alignments have revealed that inferred residue-residue proximities can be sufficient information to predict a protein fold without the use of known three-dimensional structures. Here, we propose an alternative method of inferring coevolving site pairs from concurrent and compensatory substitutions between sites in each branch of a phylogenetic tree. Substitution probability and physico-chemical changes (volume, charge, hydrogen-bonding capability, and others) accompanied by substitutions at each site in each branch of a phylogenetic tree are estimated with the likelihood of each substitution, and their direct correlations between sites are used to detect concurrent and compensatory substitutions. In order to extract direct dependences between sites, partial correlation coefficients of the characteristic changes along branches between sites, in which linear multiple dependences on feature vectors at other sites are removed, are calculated and used to rank coevolving site pairs. Accuracy of contact prediction based on the present coevolution score is comparable to that achieved by a maximum entropy model of protein sequences for 15 protein families taken from the Pfam release 26.0. Besides, this excellent accuracy indicates that compensatory substitutions are significant in protein evolution.\",\n \"corpus_id\": 17351177,\n \"score\": 2\n },\n {\n \"doc_id\": \"23418186\",\n \"title\": \"Prediction of contact matrix for protein-protein interaction.\",\n \"abstract\": \"MOTIVATION: Prediction of protein-protein interaction has become an important part of systems biology in reverse engineering the biological networks for better understanding the molecular biology of the cell. Although significant progress has been made in terms of prediction accuracy, most computational methods only predict whether two proteins interact but not their interacting residues-the information that can be very valuable for understanding the interaction mechanisms and designing modulation of the interaction. In this work, we developed a computational method to predict the interacting residue pairs-contact matrix for interacting protein domains, whose rows and columns correspond to the residues in the two interacting domains respectively and whose values (1 or 0) indicate whether the corresponding residues (do or do not) interact. RESULTS: Our method is based on supervised learning using support vector machines. For each domain involved in a given domain-domain interaction (DDI), an interaction profile hidden Markov model (ipHMM) is first built for the domain family, and then each residue position for a member domain sequence is represented as a 20-dimension vector of Fisher scores, characterizing how similar it is as compared with the family profile at that position. Each element of the contact matrix for a sequence pair is now represented by a feature vector from concatenating the vectors of the two corresponding residues, and the task is to predict the element value (1 or 0) from the feature vector. A support vector machine is trained for a given DDI, using either a consensus contact matrix or contact matrices for individual sequence pairs, and is tested by leave-one-out cross validation. The performance averaged over a set of 115 DDIs collected from the 3 DID database shows significant improvement (sensitivity up to 85%, and specificity up to 85%), as compared with a multiple sequence alignment-based method (sensitivity 57%, and specificity 78%) previously reported in the literature. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.\",\n \"corpus_id\": 16693916,\n \"score\": 2\n },\n {\n \"doc_id\": \"23626696\",\n \"title\": \"CNNcon: improved protein contact maps prediction using cascaded neural networks.\",\n \"abstract\": \"BACKGROUNDS: Despite continuing progress in X-ray crystallography and high-field NMR spectroscopy for determination of three-dimensional protein structures, the number of unsolved and newly discovered sequences grows much faster than that of determined structures. Protein modeling methods can possibly bridge this huge sequence-structure gap with the development of computational science. A grand challenging problem is to predict three-dimensional protein structure from its primary structure (residues sequence) alone. However, predicting residue contact maps is a crucial and promising intermediate step towards final three-dimensional structure prediction. Better predictions of local and non-local contacts between residues can transform protein sequence alignment to structure alignment, which can finally improve template based three-dimensional protein structure predictors greatly. METHODS: CNNcon, an improved multiple neural networks based contact map predictor using six sub-networks and one final cascade-network, was developed in this paper. Both the sub-networks and the final cascade-network were trained and tested with their corresponding data sets. While for testing, the target protein was first coded and then input to its corresponding sub-networks for prediction. After that, the intermediate results were input to the cascade-network to finish the final prediction. RESULTS: The CNNcon can accurately predict 58.86% in average of contacts at a distance cutoff of 8 Å for proteins with lengths ranging from 51 to 450. The comparison results show that the present method performs better than the compared state-of-the-art predictors. Particularly, the prediction accuracy keeps steady with the increase of protein sequence length. It indicates that the CNNcon overcomes the thin density problem, with which other current predictors have trouble. This advantage makes the method valuable to the prediction of long length proteins. As a result, the effective prediction of long length proteins could be possible by the CNNcon.\",\n \"corpus_id\": 9628402,\n \"score\": 2\n },\n {\n \"doc_id\": \"23680395\",\n \"title\": \"Prediction of contacts from correlated sequence substitutions.\",\n \"abstract\": \"Recent work has led to a substantial improvement in the accuracy of predictions of contacts between amino acids using evolutionary information derived from multiple sequence alignments. Where large numbers of diverse sequence relatives are available and can be aligned to the sequence of a protein of unknown structure it is now possible to generate high-resolution models without recourse to the structure of a template. In this review we describe these exciting new techniques and critically assess the state-of-the-art in contact prediction in the light of these. While concentrating on methods, we also discuss applications to protein and RNA structure prediction as well as potential future developments.\",\n \"corpus_id\": 41447316,\n \"score\": 2\n },\n {\n \"doc_id\": \"23738436\",\n \"title\": \"Prediction of protein contacts from correlated sequence substitutions.\",\n \"abstract\": \"Recent work has led to a substantial improvement in the accuracy of predictions of contacts between amino acids using evolutionary information derived from multiple sequence alignments. Where large numbers of diverse sequence relatives are available and can be aligned to the sequence of a protein of unknown structure, it is now possible to generate high-resolution models without recourse to the structure of a template. In this review, we describe these exciting new techniques and critically assess the state of the art in contact prediction in light of them. We discuss areas for immediate research and development as well as potential future developments.\",\n \"corpus_id\": 7200012,\n \"score\": 2\n },\n {\n \"doc_id\": \"23873510\",\n \"title\": \"Assessment of CASP10 contact-assisted predictions.\",\n \"abstract\": \"In CASP10, for the first time, contact-assisted structure predictions have been assessed. Sets of pairs of contacting residues from target structures were provided to predictors for a second round of prediction after the initial round in which they were given only sequences. The objective of the experiment was to measure model quality improvement resulting from the added contact information and thereby assess and help develop so-called hybrid prediction methods--methods where some experimentally determined distance constraints are used to augment de novo computational prediction methods. The results of the experiment were, overall, quite promising.\",\n \"corpus_id\": 637088,\n \"score\": 2\n },\n {\n \"doc_id\": \"24009338\",\n \"title\": \"Assessing the utility of coevolution-based residue-residue contact predictions in a sequence- and structure-rich era.\",\n \"abstract\": \"Recently developed methods have shown considerable promise in predicting residue-residue contacts in protein 3D structures using evolutionary covariance information. However, these methods require large numbers of evolutionarily related sequences to robustly assess the extent of residue covariation, and the larger the protein family, the more likely that contact information is unnecessary because a reasonable model can be built based on the structure of a homolog. Here we describe a method that integrates sequence coevolution and structural context information using a pseudolikelihood approach, allowing more accurate contact predictions from fewer homologous sequences. We rigorously assess the utility of predicted contacts for protein structure prediction using large and representative sequence and structure databases from recent structure prediction experiments. We find that contact predictions are likely to be accurate when the number of aligned sequences (with sequence redundancy reduced to 90%) is greater than five times the length of the protein, and that accurate predictions are likely to be useful for structure modeling if the aligned sequences are more similar to the protein of interest than to the closest homolog of known structure. These conditions are currently met by 422 of the protein families collected in the Pfam database.\",\n \"corpus_id\": 32974151,\n \"score\": 2\n },\n {\n \"doc_id\": \"24410833\",\n \"title\": \"Toward an accurate prediction of inter-residue distances in proteins using 2D recursive neural networks.\",\n \"abstract\": \"BACKGROUND: Protein inter-residue contact maps provide a translation and rotation invariant topological representation of a protein. They can be used as an intermediary step in protein structure predictions. However, the prediction of contact maps represents an unbalanced problem as far fewer examples of contacts than non-contacts exist in a protein structure. In this study we explore the possibility of completely eliminating the unbalanced nature of the contact map prediction problem by predicting real-value distances between residues. Predicting full inter-residue distance maps and applying them in protein structure predictions has been relatively unexplored in the past. RESULTS: We initially demonstrate that the use of native-like distance maps is able to reproduce 3D structures almost identical to the targets, giving an average RMSD of 0.5Å. In addition, the corrupted physical maps with an introduced random error of ±6Å are able to reconstruct the targets within an average RMSD of 2Å.After demonstrating the reconstruction potential of distance maps, we develop two classes of predictors using two-dimensional recursive neural networks: an ab initio predictor that relies only on the protein sequence and evolutionary information, and a template-based predictor in which additional structural homology information is provided. We find that the ab initio predictor is able to reproduce distances with an RMSD of 6Å, regardless of the evolutionary content provided. Furthermore, we show that the template-based predictor exploits both sequence and structure information even in cases of dubious homology and outperforms the best template hit with a clear margin of up to 3.7Å.Lastly, we demonstrate the ability of the two predictors to reconstruct the CASP9 targets shorter than 200 residues producing the results similar to the state of the machine learning art approach implemented in the Distill server. CONCLUSIONS: The methodology presented here, if complemented by more complex reconstruction protocols, can represent a possible path to improve machine learning algorithms for 3D protein structure prediction. Moreover, it can be used as an intermediary step in protein structure predictions either on its own or complemented by NMR restraints.\",\n \"corpus_id\": 8181390,\n \"score\": 2\n },\n {\n \"doc_id\": \"24573474\",\n \"title\": \"Direct coupling analysis for protein contact prediction.\",\n \"abstract\": \"During evolution, structure, and function of proteins are remarkably conserved, whereas amino-acid sequences vary strongly between homologous proteins. Structural conservation constrains sequence variability and forces different residues to coevolve, i.e., to show correlated patterns of amino-acid occurrences. However, residue correlation may result from direct coupling, e.g., by a contact in the folded protein, or be induced indirectly via intermediate residues. To use empirically observed correlations for predicting residue-residue contacts, direct and indirect effects have to be disentangled. Here we present mechanistic details on how to achieve this using a methodology called Direct Coupling Analysis (DCA). DCA has been shown to produce highly accurate estimates of amino-acid pairs that have direct reciprocal constraints in evolution. Specifically, we provide instructions and protocols on how to use the algorithmic implementations of DCA starting from data extraction to predicted-contact visualization in contact maps or representative protein structures.\",\n \"corpus_id\": 9919396,\n \"score\": 2\n },\n {\n \"doc_id\": \"24637808\",\n \"title\": \"De novo structure prediction of globular proteins aided by sequence variation-derived contacts.\",\n \"abstract\": \"The advent of high accuracy residue-residue intra-protein contact prediction methods enabled a significant boost in the quality of de novo structure predictions. Here, we investigate the potential benefits of combining a well-established fragment-based folding algorithm--FRAGFOLD, with PSICOV, a contact prediction method which uses sparse inverse covariance estimation to identify co-varying sites in multiple sequence alignments. Using a comprehensive set of 150 diverse globular target proteins, up to 266 amino acids in length, we are able to address the effectiveness and some limitations of such approaches to globular proteins in practice. Overall we find that using fragment assembly with both statistical potentials and predicted contacts is significantly better than either statistical potentials or contacts alone. Results show up to nearly 80% of correct predictions (TM-score ≥0.5) within analysed dataset and a mean TM-score of 0.54. Unsuccessful modelling cases emerged either from conformational sampling problems, or insufficient contact prediction accuracy. Nevertheless, a strong dependency of the quality of final models on the fraction of satisfied predicted long-range contacts was observed. This not only highlights the importance of these contacts on determining the protein fold, but also (combined with other ensemble-derived qualities) provides a powerful guide as to the choice of correct models and the global quality of the selected model. A proposed quality assessment scoring function achieves 0.93 precision and 0.77 recall for the discrimination of correct folds on our dataset of decoys. These findings suggest the approach is well-suited for blind predictions on a variety of globular proteins of unknown 3D structure, provided that enough homologous sequences are available to construct a large and accurate multiple sequence alignment for the initial contact prediction step.\",\n \"corpus_id\": 14448556,\n \"score\": 2\n },\n {\n \"doc_id\": \"25255213\",\n \"title\": \"Sequence co-evolution gives 3D contacts and structures of protein complexes.\",\n \"abstract\": \"Protein-protein interactions are fundamental to many biological processes. Experimental screens have identified tens of thousands of interactions, and structural biology has provided detailed functional insight for select 3D protein complexes. An alternative rich source of information about protein interactions is the evolutionary sequence record. Building on earlier work, we show that analysis of correlated evolutionary sequence changes across proteins identifies residues that are close in space with sufficient accuracy to determine the three-dimensional structure of the protein complexes. We evaluate prediction performance in blinded tests on 76 complexes of known 3D structure, predict protein-protein contacts in 32 complexes of unknown structure, and demonstrate how evolutionary couplings can be used to distinguish between interacting and non-interacting protein pairs in a large complex. With the current growth of sequences, we expect that the method can be generalized to genome-wide elucidation of protein-protein interaction networks and used for interaction predictions at residue resolution.\",\n \"corpus_id\": 32630002,\n \"score\": 2\n },\n {\n \"doc_id\": \"25299132\",\n \"title\": \"Improving contact prediction along three dimensions.\",\n \"abstract\": \"Correlation patterns in multiple sequence alignments of homologous proteins can be exploited to infer information on the three-dimensional structure of their members. The typical pipeline to address this task, which we in this paper refer to as the three dimensions of contact prediction, is to (i) filter and align the raw sequence data representing the evolutionarily related proteins; (ii) choose a predictive model to describe a sequence alignment; (iii) infer the model parameters and interpret them in terms of structural properties, such as an accurate contact map. We show here that all three dimensions are important for overall prediction success. In particular, we show that it is possible to improve significantly along the second dimension by going beyond the pair-wise Potts models from statistical physics, which have hitherto been the focus of the field. These (simple) extensions are motivated by multiple sequence alignments often containing long stretches of gaps which, as a data feature, would be rather untypical for independent samples drawn from a Potts model. Using a large test set of proteins we show that the combined improvements along the three dimensions are as large as any reported to date.\",\n \"corpus_id\": 1117908,\n \"score\": 2\n },\n {\n \"doc_id\": \"25338092\",\n \"title\": \"Combining physicochemical and evolutionary information for protein contact prediction.\",\n \"abstract\": \"We introduce a novel contact prediction method that achieves high prediction accuracy by combining evolutionary and physicochemical information about native contacts. We obtain evolutionary information from multiple-sequence alignments and physicochemical information from predicted ab initio protein structures. These structures represent low-energy states in an energy landscape and thus capture the physicochemical information encoded in the energy function. Such low-energy structures are likely to contain native contacts, even if their overall fold is not native. To differentiate native from non-native contacts in those structures, we develop a graph-based representation of the structural context of contacts. We then use this representation to train an support vector machine classifier to identify most likely native contacts in otherwise non-native structures. The resulting contact predictions are highly accurate. As a result of combining two sources of information--evolutionary and physicochemical--we maintain prediction accuracy even when only few sequence homologs are present. We show that the predicted contacts help to improve ab initio structure prediction. A web service is available at http://compbio.robotics.tu-berlin.de/epc-map/.\",\n \"corpus_id\": 4274795,\n \"score\": 2\n },\n {\n \"doc_id\": \"25375897\",\n \"title\": \"Improved contact predictions using the recognition of protein like contact patterns.\",\n \"abstract\": \"Given sufficient large protein families, and using a global statistical inference approach, it is possible to obtain sufficient accuracy in protein residue contact predictions to predict the structure of many proteins. However, these approaches do not consider the fact that the contacts in a protein are neither randomly, nor independently distributed, but actually follow precise rules governed by the structure of the protein and thus are interdependent. Here, we present PconsC2, a novel method that uses a deep learning approach to identify protein-like contact patterns to improve contact predictions. A substantial enhancement can be seen for all contacts independently on the number of aligned sequences, residue separation or secondary structure type, but is largest for β-sheet containing proteins. In addition to being superior to earlier methods based on statistical inferences, in comparison to state of the art methods using machine learning, PconsC2 is superior for families with more than 100 effective sequence homologs. The improved contact prediction enables improved structure prediction.\",\n \"corpus_id\": 18540524,\n \"score\": 2\n },\n {\n \"doc_id\": \"25431331\",\n \"title\": \"MetaPSICOV: combining coevolution methods for accurate prediction of contacts and long range hydrogen bonding in proteins.\",\n \"abstract\": \"MOTIVATION: Recent developments of statistical techniques to infer direct evolutionary couplings between residue pairs have rendered covariation-based contact prediction a viable means for accurate 3D modelling of proteins, with no information other than the sequence required. To extend the usefulness of contact prediction, we have designed a new meta-predictor (MetaPSICOV) which combines three distinct approaches for inferring covariation signals from multiple sequence alignments, considers a broad range of other sequence-derived features and, uniquely, a range of metrics which describe both the local and global quality of the input multiple sequence alignment. Finally, we use a two-stage predictor, where the second stage filters the output of the first stage. This two-stage predictor is additionally evaluated on its ability to accurately predict the long range network of hydrogen bonds, including correctly assigning the donor and acceptor residues. RESULTS: Using the original PSICOV benchmark set of 150 protein families, MetaPSICOV achieves a mean precision of 0.54 for top-L predicted long range contacts-around 60% higher than PSICOV, and around 40% better than CCMpred. In de novo protein structure prediction using FRAGFOLD, MetaPSICOV is able to improve the TM-scores of models by a median of 0.05 compared with PSICOV. Lastly, for predicting long range hydrogen bonding, MetaPSICOV-HB achieves a precision of 0.69 for the top-L/10 hydrogen bonds compared with just 0.26 for the baseline MetaPSICOV. AVAILABILITY AND IMPLEMENTATION: MetaPSICOV is available as a freely available web server at http://bioinf.cs.ucl.ac.uk/MetaPSICOV. Raw data (predicted contact lists and 3D models) and source code can be downloaded from http://bioinf.cs.ucl.ac.uk/downloads/MetaPSICOV. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.\",\n \"corpus_id\": 2985369,\n \"score\": 2\n },\n {\n \"doc_id\": \"25548928\",\n \"title\": \"Advances in protein contact map prediction based on machine learning.\",\n \"abstract\": \"A protein contact map is a simplified, two-dimensional version of the three-dimensional protein structure. Protein contact map is proved to be crucial in forming the three-dimensional structure. Contact map prediction has now become an indispensable and promising intermediate step towards final three-dimensional structure prediction, while directed sequence-structure prediction hits its bottlenecks. In this article, different evaluation scores of prediction efficiency are compared. Next, the state of the art and future perspectives of contact map methods are reviewed and special attention is paid to those relying on machine learning algorithms. Details of neural network based methods as well as a list of machine learning based methods are given. Finally, bottlenecks and potential improvements of contact map predictions are discussed.\",\n \"corpus_id\": 20881869,\n \"score\": 2\n },\n {\n \"doc_id\": \"26502070\",\n \"title\": \"CAB-Align: A Flexible Protein Structure Alignment Method Based on the Residue-Residue Contact Area.\",\n \"abstract\": \"Proteins are flexible, and this flexibility has an essential functional role. Flexibility can be observed in loop regions, rearrangements between secondary structure elements, and conformational changes between entire domains. However, most protein structure alignment methods treat protein structures as rigid bodies. Thus, these methods fail to identify the equivalences of residue pairs in regions with flexibility. In this study, we considered that the evolutionary relationship between proteins corresponds directly to the residue-residue physical contacts rather than the three-dimensional (3D) coordinates of proteins. Thus, we developed a new protein structure alignment method, contact area-based alignment (CAB-align), which uses the residue-residue contact area to identify regions of similarity. The main purpose of CAB-align is to identify homologous relationships at the residue level between related protein structures. The CAB-align procedure comprises two main steps: First, a rigid-body alignment method based on local and global 3D structure superposition is employed to generate a sufficient number of initial alignments. Then, iterative dynamic programming is executed to find the optimal alignment. We evaluated the performance and advantages of CAB-align based on four main points: (1) agreement with the gold standard alignment, (2) alignment quality based on an evolutionary relationship without 3D coordinate superposition, (3) consistency of the multiple alignments, and (4) classification agreement with the gold standard classification. Comparisons of CAB-align with other state-of-the-art protein structure alignment methods (TM-align, FATCAT, and DaliLite) using our benchmark dataset showed that CAB-align performed robustly in obtaining high-quality alignments and generating consistent multiple alignments with high coverage and accuracy rates, and it performed extremely well when discriminating between homologous and nonhomologous pairs of proteins in both single and multi-domain comparisons. The CAB-align software is freely available to academic users as stand-alone software at http://www.pharm.kitasato-u.ac.jp/bmd/bmd/Publications.html.\",\n \"corpus_id\": 17375188,\n \"score\": 2\n },\n {\n \"doc_id\": \"27112569\",\n \"title\": \"CoinFold: a web server for protein contact prediction and contact-assisted protein folding.\",\n \"abstract\": \"CoinFold (http://raptorx2.uchicago.edu/ContactMap/) is a web server for protein contact prediction and contact-assisted de novo structure prediction. CoinFold predicts contacts by integrating joint multi-family evolutionary coupling (EC) analysis and supervised machine learning. This joint EC analysis is unique in that it not only uses residue coevolution information in the target protein family, but also that in the related families which may have divergent sequences but similar folds. The supervised learning further improves contact prediction accuracy by making use of sequence profile, contact (distance) potential and other information. Finally, this server predicts tertiary structure of a sequence by feeding its predicted contacts and secondary structure to the CNS suite. Tested on the CASP and CAMEO targets, this server shows significant advantages over existing ones of similar category in both contact and tertiary structure prediction.\",\n \"corpus_id\": 3731114,\n \"score\": 2\n },\n {\n \"doc_id\": \"27115648\",\n \"title\": \"Protein Residue Contacts and Prediction Methods.\",\n \"abstract\": \"In the field of computational structural proteomics, contact predictions have shown new prospects of solving the longstanding problem of ab initio protein structure prediction. In the last few years, application of deep learning algorithms and availability of large protein sequence databases, combined with improvement in methods that derive contacts from multiple sequence alignments, have shown a huge increase in the precision of contact prediction. In addition, these predicted contacts have also been used to build three-dimensional models from scratch. In this chapter, we briefly discuss many elements of protein residue-residue contacts and the methods available for prediction, focusing on a state-of-the-art contact prediction tool, DNcon. Illustrating with a case study, we describe how DNcon can be used to make ab initio contact predictions for a given protein sequence and discuss how the predicted contacts may be analyzed and evaluated.\",\n \"corpus_id\": 22725123,\n \"score\": 2\n },\n {\n \"doc_id\": \"27307635\",\n \"title\": \"CMsearch: simultaneous exploration of protein sequence space and structure space improves not only protein homology detection but also protein structure prediction.\",\n \"abstract\": \"MOTIVATION: Protein homology detection, a fundamental problem in computational biology, is an indispensable step toward predicting protein structures and understanding protein functions. Despite the advances in recent decades on sequence alignment, threading and alignment-free methods, protein homology detection remains a challenging open problem. Recently, network methods that try to find transitive paths in the protein structure space demonstrate the importance of incorporating network information of the structure space. Yet, current methods merge the sequence space and the structure space into a single space, and thus introduce inconsistency in combining different sources of information. METHOD: We present a novel network-based protein homology detection method, CMsearch, based on cross-modal learning. Instead of exploring a single network built from the mixture of sequence and structure space information, CMsearch builds two separate networks to represent the sequence space and the structure space. It then learns sequence-structure correlation by simultaneously taking sequence information, structure information, sequence space information and structure space information into consideration. RESULTS: We tested CMsearch on two challenging tasks, protein homology detection and protein structure prediction, by querying all 8332 PDB40 proteins. Our results demonstrate that CMsearch is insensitive to the similarity metrics used to define the sequence and the structure spaces. By using HMM-HMM alignment as the sequence similarity metric, CMsearch clearly outperforms state-of-the-art homology detection methods and the CASP-winning template-based protein structure prediction methods. AVAILABILITY AND IMPLEMENTATION: Our program is freely available for download from http://sfb.kaust.edu.sa/Pages/Software.aspx CONTACT: : xin.gao@kaust.edu.sa SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.\",\n \"corpus_id\": 12245606,\n \"score\": 2\n },\n {\n \"doc_id\": \"27787823\",\n \"title\": \"Assessing Predicted Contacts for Building Protein Three-Dimensional Models.\",\n \"abstract\": \"Recent successes of contact-guided protein structure prediction methods have revived interest in solving the long-standing problem of ab initio protein structure prediction. With homology modeling failing for many protein sequences that do not have templates, contact-guided structure prediction has shown promise, and consequently, contact prediction has gained a lot of interest recently. Although a few dozen contact prediction tools are already currently available as web servers and downloadables, not enough research has been done towards using existing measures like precision and recall to evaluate these contacts with the goal of building three-dimensional models. Moreover, when we do not have a native structure for a set of predicted contacts, the only analysis we can perform is a simple contact map visualization of the predicted contacts. A wider and more rigorous assessment of the predicted contacts is needed, in order to build tertiary structure models. This chapter discusses instructions and protocols for using tools and applying techniques in order to assess predicted contacts for building three-dimensional models.\",\n \"corpus_id\": 4873322,\n \"score\": 2\n },\n {\n \"doc_id\": \"28056090\",\n \"title\": \"Accurate De Novo Prediction of Protein Contact Map by Ultra-Deep Learning Model.\",\n \"abstract\": \"MOTIVATION: Protein contacts contain key information for the understanding of protein structure and function and thus, contact prediction from sequence is an important problem. Recently exciting progress has been made on this problem, but the predicted contacts for proteins without many sequence homologs is still of low quality and not very useful for de novo structure prediction. METHOD: This paper presents a new deep learning method that predicts contacts by integrating both evolutionary coupling (EC) and sequence conservation information through an ultra-deep neural network formed by two deep residual neural networks. The first residual network conducts a series of 1-dimensional convolutional transformation of sequential features; the second residual network conducts a series of 2-dimensional convolutional transformation of pairwise information including output of the first residual network, EC information and pairwise potential. By using very deep residual networks, we can accurately model contact occurrence patterns and complex sequence-structure relationship and thus, obtain higher-quality contact prediction regardless of how many sequence homologs are available for proteins in question. RESULTS: Our method greatly outperforms existing methods and leads to much more accurate contact-assisted folding. Tested on 105 CASP11 targets, 76 past CAMEO hard targets, and 398 membrane proteins, the average top L long-range prediction accuracy obtained by our method, one representative EC method CCMpred and the CASP11 winner MetaPSICOV is 0.47, 0.21 and 0.30, respectively; the average top L/10 long-range accuracy of our method, CCMpred and MetaPSICOV is 0.77, 0.47 and 0.59, respectively. Ab initio folding using our predicted contacts as restraints but without any force fields can yield correct folds (i.e., TMscore>0.6) for 203 of the 579 test proteins, while that using MetaPSICOV- and CCMpred-predicted contacts can do so for only 79 and 62 of them, respectively. Our contact-assisted models also have much better quality than template-based models especially for membrane proteins. The 3D models built from our contact prediction have TMscore>0.5 for 208 of the 398 membrane proteins, while those from homology modeling have TMscore>0.5 for only 10 of them. Further, even if trained mostly by soluble proteins, our deep learning method works very well on membrane proteins. In the recent blind CAMEO benchmark, our fully-automated web server implementing this method successfully folded 6 targets with a new fold and only 0.3L-2.3L effective sequence homologs, including one β protein of 182 residues, one α+β protein of 125 residues, one α protein of 140 residues, one α protein of 217 residues, one α/β of 260 residues and one α protein of 462 residues. Our method also achieved the highest F1 score on free-modeling targets in the latest CASP (Critical Assessment of Structure Prediction), although it was not fully implemented back then. AVAILABILITY: http://raptorx.uchicago.edu/ContactMap/.\",\n \"corpus_id\": 605957,\n \"score\": 2\n },\n {\n \"doc_id\": \"18235992\",\n \"title\": \"PRINTR: prediction of RNA binding sites in proteins using SVM and profiles.\",\n \"abstract\": \"Protein-RNA interactions play a key role in a number of biological processes such as protein synthesis, mRNA processing, assembly and function of ribosomes and eukaryotic spliceosomes. A reliable identification of RNA-binding sites in RNA-binding proteins is important for functional annotation and site-directed mutagenesis. We developed a novel method for the prediction of protein residues that interact with RNA using support vector machine (SVM) and position-specific scoring matrices (PSSMs). Two cases have been considered in the prediction of protein residues at RNA-binding surfaces. One is given the sequence information of a protein chain that is known to interact with RNA; the other is given the structural information. Thus, five different inputs have been tested. Coupled with PSI-BLAST profiles and predicted secondary structure, the present approach yields a Matthews correlation coefficient (MCC) of 0.432 by a 7-fold cross-validation, which is the best among all previous reported RNA-binding sites prediction methods. When given the structural information, we have obtained the MCC value of 0.457, with PSSMs, observed secondary structure and solvent accessibility information assigned by DSSP as input. A web server implementing the prediction method is available at the following URL: http://210.42.106.80/printr/ .\",\n \"corpus_id\": 1035800,\n \"score\": 1\n },\n {\n \"doc_id\": \"18464326\",\n \"title\": \"A different look at the quality of modeled three-dimensional protein structures.\",\n \"abstract\": \"Measuring the accuracy of protein three-dimensional structures is one of the most important problems in protein structure prediction. For structure-based drug design, the accuracy of the binding site is far more important than the accuracy of any other region of the protein. We have developed an automated method for assessing the quality of a protein model by focusing on the set of residues in the small molecule binding site. Small molecule binding sites typically involve multiple regions of the protein coming together in space, and their accuracy has been observed to be sensitive to even small alignment errors. In addition, ligand binding sites contain the critical information required for drug design, making their accuracy particularly important. We analyzed the accuracy of the binding sites on two sets of protein models: the predictions submitted by the top-performing CASP7 groups, and the models generated by four widely used homology modeling packages. The results of our CASP7 analysis significantly differ from the previous findings, implying that the binding site measure does not correlate with the traditional model quality measures used in the structure prediction benchmarks. For the modeling programs, the resolution of binding sites is extremely sensitive to the degree of sequence homology between the query and the template, even when the most accurate alignments are used in the homology modeling process.\",\n \"corpus_id\": 13639028,\n \"score\": 1\n },\n {\n \"doc_id\": \"18689810\",\n \"title\": \"Detection of 3D atomic similarities and their use in the discrimination of small molecule protein-binding sites.\",\n \"abstract\": \"MOTIVATION: Current computational methods for the prediction of function from structure are restricted to the detection of similarities and subsequent transfer of functional annotation. In a significant minority of cases, global sequence or structural (fold) similarities do not provide clues about protein function. In these cases, one alternative is to detect local binding site similarities. These may still reflect more distant evolutionary relationships as well as unique physico-chemical constraints necessary for binding similar ligands, thus helping pinpoint the function. In the present work, we ask the following question: is it possible to discriminate within a dataset of non-homologous proteins those that bind similar ligands based on their binding site similarities? METHODS: We implement a graph-matching-based method for the detection of 3D atomic similarities introducing some simplifications that allow us to extend its applicability to the analysis of large allatom binding site models. This method, called IsoCleft, does not require atoms to be connected either in sequence or space. We apply the method to a cognate-ligand bound dataset of non-homologous proteins. We define a family of binding site models with decreasing knowledge about the identity of the ligand-interacting atoms to uncouple the questions of predicting the location of the binding site and detecting binding site similarities. Furthermore, we calculate the individual contributions of binding site size, chemical composition and geometry to prediction performance. RESULTS: We find that it is possible to discriminate between different ligand-binding sites. In other words, there is a certain uniqueness in the set of atoms that are in contact to specific ligand scaffolds. This uniqueness is restricted to the atoms in close proximity of the ligand in which case, size and chemical composition alone are sufficient to discriminate binding sites. Discrimination ability decreases with decreasing knowledge about the identity of the ligand-interacting binding site atoms. The decrease is quite abrupt when considering size and chemical composition alone, but much slower when including geometry. We also observe that certain ligands are easier to discriminate. Interestingly, the subset of binding site atoms belonging to highly conserved residues is not sufficient to discriminate binding sites, implying that convergently evolved binding sites arrived at dissimilar solutions. AVAILABILITY: IsoCleft can be obtained from the authors.\",\n \"corpus_id\": 25624257,\n \"score\": 1\n },\n {\n \"doc_id\": \"18704938\",\n \"title\": \"Prediction of helix-helix contacts and interacting helices in polytopic membrane proteins using neural networks.\",\n \"abstract\": \"Despite rapidly increasing numbers of available 3D structures, membrane proteins still account for less than 1% of all structures in the Protein Data Bank. Recent high-resolution structures indicate a clearly broader structural diversity of membrane proteins than initially anticipated, motivating the development of reliable structure prediction methods specifically tailored for this class of molecules. One important prediction target capturing all major aspects of a protein's 3D structure is its contact map. Our analysis shows that computational methods trained to predict residue contacts in globular proteins perform poorly when applied to membrane proteins. We have recently published a method to identify interacting alpha-helices in membrane proteins based on the analysis of coevolving residues in predicted transmembrane regions. Here, we present a substantially improved algorithm for the same problem, which uses a newly developed neural network approach to predict helix-helix contacts. In addition to the input features commonly used for contact prediction of soluble proteins, such as windowed residue profiles and residue distance in the sequence, our network also incorporates features that apply to membrane proteins only, such as residue position within the transmembrane segment and its orientation toward the lipophilic environment. The obtained neural network can predict contacts between residues in transmembrane segments with nearly 26% accuracy. It is therefore the first published contact predictor developed specifically for membrane proteins performing with equal accuracy to state-of-the-art contact predictors available for soluble proteins. The predicted helix-helix contacts were employed in a second step to identify interacting helices. For our dataset consisting of 62 membrane proteins of solved structure, we gained an accuracy of 78.1%. Because the reliable prediction of helix interaction patterns is an important step in the classification and prediction of membrane protein folds, our method will be a helpful tool in compiling a structural census of membrane proteins.\",\n \"corpus_id\": 7928484,\n \"score\": 1\n },\n {\n \"doc_id\": \"19003998\",\n \"title\": \"Accurate prediction for atomic-level protein design and its application in diversifying the near-optimal sequence space.\",\n \"abstract\": \"The task of engineering a protein to assume a target three-dimensional structure is known as protein design. Computational search algorithms are devised to predict a minimal energy amino acid sequence for a particular structure. In practice, however, an ensemble of low-energy sequences is often sought. Primarily, this is performed because an individual predicted low-energy sequence may not necessarily fold to the target structure because of both inaccuracies in modeling protein energetics and the nonoptimal nature of search algorithms employed. Additionally, some low-energy sequences may be overly stable and thus lack the dynamic flexibility required for biological functionality. Furthermore, the investigation of low-energy sequence ensembles will provide crucial insights into the pseudo-physical energy force fields that have been derived to describe structural energetics for protein design. Significantly, numerous studies have predicted low-energy sequences, which were subsequently synthesized and demonstrated to fold to desired structures. However, the characterization of the sequence space defined by such energy functions as compatible with a target structure has not been performed in full detail. This issue is critical for protein design scientists to successfully continue using these force fields at an ever-increasing pace and scale. In this paper, we present a conceptually novel algorithm that rapidly predicts the set of lowest energy sequences for a given structure. Based on the theory of probabilistic graphical models, it performs efficient inspection and partitioning of the near-optimal sequence space, without making any assumptions of positional independence. We benchmark its performance on a diverse set of relevant protein design examples and show that it consistently yields sequences of lower energy than those derived from state-of-the-art techniques. Thus, we find that previously presented search techniques do not fully depict the low-energy space as precisely. Examination of the predicted ensembles indicates that, for each structure, the amino acid identity at a majority of positions must be chosen extremely selectively so as to not incur significant energetic penalties. We investigate this high degree of similarity and demonstrate how more diverse near-optimal sequences can be predicted in order to systematically overcome this bottleneck for computational design. Finally, we exploit this in-depth analysis of a collection of the lowest energy sequences to suggest an explanation for previously observed experimental design results. The novel methodologies introduced here accurately portray the sequence space compatible with a protein structure and further supply a scheme to yield heterogeneous low-energy sequences, thus providing a powerful instrument for future work on protein design.\",\n \"corpus_id\": 8014671,\n \"score\": 1\n },\n {\n \"doc_id\": \"19046430\",\n \"title\": \"A discriminative method for protein remote homology detection and fold recognition combining Top-n-grams and latent semantic analysis.\",\n \"abstract\": \"BACKGROUND: Protein remote homology detection and fold recognition are central problems in bioinformatics. Currently, discriminative methods based on support vector machine (SVM) are the most effective and accurate methods for solving these problems. A key step to improve the performance of the SVM-based methods is to find a suitable representation of protein sequences. RESULTS: In this paper, a novel building block of proteins called Top-n-grams is presented, which contains the evolutionary information extracted from the protein sequence frequency profiles. The protein sequence frequency profiles are calculated from the multiple sequence alignments outputted by PSI-BLAST and converted into Top-n-grams. The protein sequences are transformed into fixed-dimension feature vectors by the occurrence times of each Top-n-gram. The training vectors are evaluated by SVM to train classifiers which are then used to classify the test protein sequences. We demonstrate that the prediction performance of remote homology detection and fold recognition can be improved by combining Top-n-grams and latent semantic analysis (LSA), which is an efficient feature extraction technique from natural language processing. When tested on superfamily and fold benchmarks, the method combining Top-n-grams and LSA gives significantly better results compared to related methods. CONCLUSION: The method based on Top-n-grams significantly outperforms the methods based on many other building blocks including N-grams, patterns, motifs and binary profiles. Therefore, Top-n-gram is a good building block of the protein sequences and can be widely used in many tasks of the computational biology, such as the sequence alignment, the prediction of domain boundary, the designation of knowledge-based potentials and the prediction of protein binding sites.\",\n \"corpus_id\": 10752257,\n \"score\": 1\n },\n {\n \"doc_id\": \"19173310\",\n \"title\": \"Prediction of 3D metal binding sites from translated gene sequences based on remote-homology templates.\",\n \"abstract\": \"Database-scale analysis was performed to determine whether structural models, based on remote homologues, are effective in predicting 3D transition metal binding sites in proteins directly from translated gene sequences. The extent by which side chain modeling alone reduces sensitivity and selectivity is shown to be <10%. Surprisingly, selectivity was not dependent on the level of sequence homology between template and target, or on the presence of a metal ion in the structural template. Applying a modification of the CHED algorithm (Babor et al., Proteins 2008;70:208-217) and machine learning filters, a selectivity of approximately 90% was achieved for protein sequences using unrelated structural templates over a sequence identity range of 18-100%. Below approximately 18% identity, the number of analyzable target-template pairs and predictability of metal binding sites falls off sharply. A full third of structural templates were found to have target partners only in the remote homology range of 18-30%. In this range, nonmetal-binding templates are calculated to be the majority and serve to predict with 50% sensitivity at the geometric level. Overall, sensitivity at the geometric level for targets having templates in the 18-30% sequence identity range is 73%, with an average of one false positive site per true site. Protein sequences described as \\\"unknown\\\" in the UniProt database and composed largely of unidentified genome project sequences were studied and metal binding sites predicted. A web server for prediction of metal binding sites from protein sequence is provided.\",\n \"corpus_id\": 21577128,\n \"score\": 1\n },\n {\n \"doc_id\": \"19180183\",\n \"title\": \"Prediction of protein-protein interaction sites in sequences and 3D structures by random forests.\",\n \"abstract\": \"Identifying interaction sites in proteins provides important clues to the function of a protein and is becoming increasingly relevant in topics such as systems biology and drug discovery. Although there are numerous papers on the prediction of interaction sites using information derived from structure, there are only a few case reports on the prediction of interaction residues based solely on protein sequence. Here, a sliding window approach is combined with the Random Forests method to predict protein interaction sites using (i) a combination of sequence- and structure-derived parameters and (ii) sequence information alone. For sequence-based prediction we achieved a precision of 84% with a 26% recall and an F-measure of 40%. When combined with structural information, the prediction performance increases to a precision of 76% and a recall of 38% with an F-measure of 51%. We also present an attempt to rationalize the sliding window size and demonstrate that a nine-residue window is the most suitable for predictor construction. Finally, we demonstrate the applicability of our prediction methods by modeling the Ras-Raf complex using predicted interaction sites as target binding interfaces. Our results suggest that it is possible to predict protein interaction sites with quite a high accuracy using only sequence information.\",\n \"corpus_id\": 5697364,\n \"score\": 1\n },\n {\n \"doc_id\": \"19422056\",\n \"title\": \"Beyond the Twilight Zone: automated prediction of structural properties of proteins by recursive neural networks and remote homology information.\",\n \"abstract\": \"The prediction of 1D structural properties of proteins is an important step toward the prediction of protein structure and function, not only in the ab initio case but also when homology information to known structures is available. Despite this the vast majority of 1D predictors do not incorporate homology information into the prediction process. We develop a novel structural alignment method, SAMD, which we use to build alignments of putative remote homologues that we compress into templates of structural frequency profiles. We use these templates as additional input to ensembles of recursive neural networks, which we specialise for the prediction of query sequences that show only remote homology to any Protein Data Bank structure. We predict four 1D structural properties - secondary structure, relative solvent accessibility, backbone structural motifs, and contact density. Secondary structure prediction accuracy, tested by five-fold cross-validation on a large set of proteins allowing less than 25% sequence identity between training and test set and query sequences and templates, exceeds 82%, outperforming its ab initio counterpart, other state-of-the-art secondary structure predictors (Jpred 3 and PSIPRED) and two other systems based on PSI-BLAST and COMPASS templates. We show that structural information from homologues improves prediction accuracy well beyond the Twilight Zone of sequence similarity, even below 5% sequence identity, for all four structural properties. Significant improvement over the extraction of structural information directly from PDB templates suggests that the combination of sequence and template information is more informative than templates alone.\",\n \"corpus_id\": 21505025,\n \"score\": 1\n },\n {\n \"doc_id\": \"19734152\",\n \"title\": \"Algorithms for optimal protein structure alignment.\",\n \"abstract\": \"MOTIVATION: Structural alignment is an important tool for understanding the evolutionary relationships between proteins. However, finding the best pairwise structural alignment is difficult, due to the infinite number of possible superpositions of two structures. Unlike the sequence alignment problem, which has a polynomial time solution, the structural alignment problem has not been even classified as solvable. RESULTS: We study one of the most widely used measures of protein structural similarity, defined as the number of pairs of residues in two proteins that can be superimposed under a predefined distance cutoff. We prove that, for any two proteins, this measure can be optimized for all but finitely many distance cutoffs. Our method leads to a series of algorithms for optimizing other structure similarity measures, including the measures commonly used in protein structure prediction experiments. We also present a polynomial time algorithm for finding a near-optimal superposition of two proteins. Aside from having a relatively low cost, the algorithm for near-optimal solution returns a superposition of provable quality. In other words, the difference between the score of the returned superposition and the score of an optimal superposition can be explicitly computed and used to determine whether the returned superposition is, in fact, the best superposition. CONTACT: poleksic@cs.uni.edu SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.\",\n \"corpus_id\": 23621754,\n \"score\": 1\n },\n {\n \"doc_id\": \"23110141\",\n \"title\": \"Accurate prediction of protein catalytic residues by side chain orientation and residue contact density.\",\n \"abstract\": \"Prediction of protein catalytic residues provides useful information for the studies of protein functions. Most of the existing methods combine both structure and sequence information but heavily rely on sequence conservation from multiple sequence alignments. The contribution of structure information is usually less than that of sequence conservation in existing methods. We found a novel structure feature, residue side chain orientation, which is the first structure-based feature that achieves prediction results comparable to that of evolutionary sequence conservation. We developed a structure-based method, Enzyme Catalytic residue SIde-chain Arrangement (EXIA), which is based on residue side chain orientations and backbone flexibility of protein structure. The prediction that uses EXIA outperforms existing structure-based features. The prediction quality of combing EXIA and sequence conservation exceeds that of the state-of-the-art prediction methods. EXIA is designed to predict catalytic residues from single protein structure without needing sequence or structure alignments. It provides invaluable information when there is no sufficient or reliable homology information for target protein. We found that catalytic residues have very special side chain orientation and designed the EXIA method based on the newly discovered feature. It was also found that EXIA performs well for a dataset of enzymes without any bounded ligand in their crystallographic structures.\",\n \"corpus_id\": 17268599,\n \"score\": 1\n },\n {\n \"doc_id\": \"23314126\",\n \"title\": \"Predicting protein β-sheet contacts using a maximum entropy-based correlated mutation measure.\",\n \"abstract\": \"MOTIVATION: The problem of ab initio protein folding is one of the most difficult in modern computational biology. The prediction of residue contacts within a protein provides a more tractable immediate step. Recently introduced maximum entropy-based correlated mutation measures (CMMs), such as direct information, have been successful in predicting residue contacts. However, most correlated mutation studies focus on proteins that have large good-quality multiple sequence alignments (MSA) because the power of correlated mutation analysis falls as the size of the MSA decreases. However, even with small autogenerated MSAs, maximum entropy-based CMMs contain information. To make use of this information, in this article, we focus not on general residue contacts but contacts between residues in β-sheets. The strong constraints and prior knowledge associated with β-contacts are ideally suited for prediction using a method that incorporates an often noisy CMM. RESULTS: Using contrastive divergence, a statistical machine learning technique, we have calculated a maximum entropy-based CMM. We have integrated this measure with a new probabilistic model for β-contact prediction, which is used to predict both residue- and strand-level contacts. Using our model on a standard non-redundant dataset, we significantly outperform a 2D recurrent neural network architecture, achieving a 5% improvement in true positives at the 5% false-positive rate at the residue level. At the strand level, our approach is competitive with the state-of-the-art single methods achieving precision of 61.0% and recall of 55.4%, while not requiring residue solvent accessibility as an input. AVAILABILITY: http://www2.warwick.ac.uk/fac/sci/systemsbiology/research/software/\",\n \"corpus_id\": 9728230,\n \"score\": 1\n },\n {\n \"doc_id\": \"25330970\",\n \"title\": \"De novo membrane protein structure prediction.\",\n \"abstract\": \"Recent advances in identifying residue-residue contacts from large multiple sequence alignments have enabled impressive gains to be made in the field of protein structure prediction. In this chapter, we discuss these advances and provide a step-by-step guide to applying the latest tools to the de novo modelling of alpha-helical transmembrane proteins. As a practical example, we demonstrate the process of building an accurate 3D model of a G protein-coupled receptor, correctly orientated in the membrane, using only its primary protein sequence.\",\n \"corpus_id\": 24129100,\n \"score\": 1\n },\n {\n \"doc_id\": \"27171127\",\n \"title\": \"Critical assessment of methods of protein structure prediction: Progress and new directions in round XI.\",\n \"abstract\": \"Modeling of protein structure from amino acid sequence now plays a major role in structural biology. Here we report new developments and progress from the CASP11 community experiment, assessing the state of the art in structure modeling. Notable points include the following: (1) New methods for predicting three dimensional contacts resulted in a few spectacular template free models in this CASP, whereas models based on sequence homology to proteins with experimental structure continue to be the most accurate. ( 2) Refinement of initial protein models, primarily using molecular dynamics related approaches, has now advanced to the point where the best methods can consistently (though slightly) improve nearly all models. ( 3) The use of relatively sparse NMR constraints dramatically improves the accuracy of models, and another type of sparse data, chemical crosslinking, introduced in this CASP, also shows promise for producing better models. ( 4) A new emphasis on modeling protein complexes, in collaboration with CAPRI, has produced interesting results, but also shows the need for more focus on this area. ( 5) Methods for estimating the accuracy of models have advanced to the point where they are of considerable practical use. ( 6) A first assessment demonstrates that models can sometimes successfully address biological questions that motivate experimental structure determination. ( 7) There is continuing progress in accuracy of modeling regions of structure not directly available by comparative modeling, while there is marginal or no progress in some other areas. Proteins 2016; 84(Suppl 1):4-14. © 2016 Wiley Periodicals, Inc.\",\n \"corpus_id\": 206409570,\n \"score\": 1\n },\n {\n \"doc_id\": \"27220237\",\n \"title\": \"[MOLECULAR EVOLUTION OF ION CHANNELS: AMINO ACID SEQUENCES AND 3D STRUCTURES].\",\n \"abstract\": \"An integral part of modern evolutionary biology is comparative analysis of structure and function of macromolecules such as proteins. The first and critical step to understand evolution of homologous proteins is their amino acid sequence alignment. However, standard algorithms fop not provide unambiguous sequence alignments for proteins of poor homology. More reliable results can be obtained by comparing experimental 3D structures obtained at atomic resolution, for instance, with the aid of X-ray structural analysis. If such structures are lacking, homology modeling is used, which may take into account indirect experimental data on functional roles of individual amino-acid residues. An important problem is that the sequence alignment, which reflects genetic modifications, does not necessarily correspond to the functional homology. The latter depends on three-dimensional structures which are critical for natural selection. Since alignment techniques relying only on the analysis of primary structures carry no information on the functional properties of proteins, including 3D structures into consideration is very important. Here we consider several examples involving ion channels and demonstrate that alignment of their three-dimensional structures can significantly improve sequence alignments obtained by traditional methods.\",\n \"corpus_id\": 15224112,\n \"score\": 1\n },\n {\n \"doc_id\": \"29297299\",\n \"title\": \"A sparse autoencoder-based deep neural network for protein solvent accessibility and contact number prediction.\",\n \"abstract\": \"BACKGROUND: Direct prediction of the three-dimensional (3D) structures of proteins from one-dimensional (1D) sequences is a challenging problem. Significant structural characteristics such as solvent accessibility and contact number are essential for deriving restrains in modeling protein folding and protein 3D structure. Thus, accurately predicting these features is a critical step for 3D protein structure building. RESULTS: In this study, we present DeepSacon, a computational method that can effectively predict protein solvent accessibility and contact number by using a deep neural network, which is built based on stacked autoencoder and a dropout method. The results demonstrate that our proposed DeepSacon achieves a significant improvement in the prediction quality compared with the state-of-the-art methods. We obtain 0.70 three-state accuracy for solvent accessibility, 0.33 15-state accuracy and 0.74 Pearson Correlation Coefficient (PCC) for the contact number on the 5729 monomeric soluble globular protein dataset. We also evaluate the performance on the CASP11 benchmark dataset, DeepSacon achieves 0.68 three-state accuracy and 0.69 PCC for solvent accessibility and contact number, respectively. CONCLUSIONS: We have shown that DeepSacon can reliably predict solvent accessibility and contact number with stacked sparse autoencoder and a dropout approach.\",\n \"corpus_id\": 19404395,\n \"score\": 1\n },\n {\n \"doc_id\": \"29625561\",\n \"title\": \"COZOID: contact zone identifier for visual analysis of protein-protein interactions.\",\n \"abstract\": \"BACKGROUND: Studying the patterns of protein-protein interactions (PPIs) is fundamental for understanding the structure and function of protein complexes. The exploration of the vast space of possible mutual configurations of interacting proteins and their contact zones is very time consuming and requires the proteomic expert knowledge. RESULTS: In this paper, we propose a novel tool containing a set of visual abstraction techniques for the guided exploration of PPI configuration space. It helps proteomic experts to select the most relevant configurations and explore their contact zones at different levels of detail. The system integrates a set of methods that follow and support the workflow of proteomics experts. The first visual abstraction method, the Matrix view, is based on customized interactive heat maps and provides the users with an overview of all possible residue-residue contacts in all PPI configurations and their interactive filtering. In this step, the user can traverse all input PPI configurations and obtain an overview of their interacting amino acids. Then, the models containing a particular pair of interacting amino acids can be selectively picked and traversed. Detailed information on the individual amino acids in the contact zones and their properties is presented in the Contact-Zone list-view. The list-view provides a comparative tool to rank the best models based on the similarity of their contacts to the template-structure contacts. All these techniques are interactively linked with other proposed methods, the Exploded view and the Open-Book view, which represent individual configurations in three-dimensional space. These representations solve the high overlap problem associated with many configurations. Using these views, the structural alignment of the best models can also be visually confirmed. CONCLUSIONS: We developed a system for the exploration of large sets of protein-protein complexes in a fast and intuitive way. The usefulness of our system has been tested and verified on several docking structures covering the three major types of PPIs, including coiled-coil, pocket-string, and surface-surface interactions. Our case studies prove that our tool helps to analyse and filter protein-protein complexes in a fraction of the time compared to using previously available techniques.\",\n \"corpus_id\": 4651784,\n \"score\": 1\n },\n {\n \"doc_id\": \"19768443\",\n \"title\": \"Proteomic tools for the analysis of cytoskeleton proteins.\",\n \"abstract\": \"Proteomic tools have become an essential part of the tool kit of the molecular biologist, and provide techniques for detecting homologous sequences, recognizing functional domains, modeling, and analyzing the three-dimensional structure for any given protein sequence. Although a wealth of structural and functional information is available for a large number of members of the various classes of cytoskeletal proteins, many more members remain uncharacterized. These computational tools that are freely and easily accessible to the scientific community provide an excellent starting point to predict the structural and functional properties of such partially or fully uncharacterized protein sequences, and can lead to elegantly designed experiments to probe the hypothesized function. This chapter discusses various proteomic analysis tools with a focus on protein structure and function predictions.\",\n \"corpus_id\": 41951596,\n \"score\": 0\n },\n {\n \"doc_id\": \"24272431\",\n \"title\": \"Introduction to bioinformatics.\",\n \"abstract\": \"Bioinformatics is an interdisciplinary field mainly involving molecular biology and genetics, computer science, mathematics, and statistics. Data intensive, large-scale biological problems are addressed from a computational point of view. The most common problems are modeling biological processes at the molecular level and making inferences from collected data. A bioinformatics solution usually involves the following steps: Collect statistics from biological data. Build a computational model. Solve a computational modeling problem. Test and evaluate a computational algorithm. This chapter gives a brief introduction to bioinformatics by first providing an introduction to biological terminology and then discussing some classical bioinformatics problems organized by the types of data sources. Sequence analysis is the analysis of DNA and protein sequences for clues regarding function and includes subproblems such as identification of homologs, multiple sequence alignment, searching sequence patterns, and evolutionary analyses. Protein structures are three-dimensional data and the associated problems are structure prediction (secondary and tertiary), analysis of protein structures for clues regarding function, and structural alignment. Gene expression data is usually represented as matrices and analysis of microarray data mostly involves statistics analysis, classification, and clustering approaches. Biological networks such as gene regulatory networks, metabolic pathways, and protein-protein interaction networks are usually modeled as graphs and graph theoretic approaches are used to solve associated problems such as construction and analysis of large-scale networks.\",\n \"corpus_id\": 40174170,\n \"score\": 0\n }\n]","isConversational":false}}},{"rowIdx":83,"cells":{"query":{"kind":"string","value":"{\n \"doc_id\": \"28729956\",\n \"title\": \"Predicting the host of influenza viruses based on the word vector.\",\n \"abstract\": \"Newly emerging influenza viruses continue to threaten public health. A rapid determination of the host range of newly discovered influenza viruses would assist in early assessment of their risk. Here, we attempted to predict the host of influenza viruses using the Support Vector Machine (SVM) classifier based on the word vector, a new representation and feature extraction method for biological sequences. The results show that the length of the word within the word vector, the sequence type (DNA or protein) and the species from which the sequences were derived for generating the word vector all influence the performance of models in predicting the host of influenza viruses. In nearly all cases, the models built on the surface proteins hemagglutinin (HA) and neuraminidase (NA) (or their genes) produced better results than internal influenza proteins (or their genes). The best performance was achieved when the model was built on the HA gene based on word vectors (words of three-letters long) generated from DNA sequences of the influenza virus. This results in accuracies of 99.7% for avian, 96.9% for human and 90.6% for swine influenza viruses. Compared to the method of sequence homology best-hit searches using the Basic Local Alignment Search Tool (BLAST), the word vector-based models still need further improvements in predicting the host of influenza A viruses.\",\n \"corpus_id\": 25481671\n}"},"candidates":{"kind":"list like","value":[{"doc_id":"21109586","title":"Charting the host adaptation of influenza viruses.","abstract":"Four influenza pandemics have struck the human population during the last 100 years causing substantial morbidity and mortality. The pandemics were caused by the introduction of a new virus into the human population from an avian or swine host or through the mixing of virus segments from an animal host with a human virus to create a new reassortant subtype virus. Understanding which changes have contributed to the adaptation of the virus to the human host is essential in assessing the pandemic potential of current and future animal viruses. Here, we develop a measure of the level of adaptation of a given virus strain to a particular host. We show that adaptation to the human host has been gradual with a timescale of decades and that none of the virus proteins have yet achieved full adaptation to the selective constraints. When the measure is applied to historical data, our results indicate that the 1918 influenza virus had undergone a period of preadaptation prior to the 1918 pandemic. Yet, ancestral reconstruction of the avian virus that founded the classical swine and 1918 human influenza lineages shows no evidence that this virus was exceptionally preadapted to humans. These results indicate that adaptation to humans occurred following the initial host shift from birds to mammals, including a significant amount prior to 1918. The 2009 pandemic virus seems to have undergone preadaptation to human-like selective constraints during its period of circulation in swine. Ancestral reconstruction along the human virus tree indicates that mutations that have increased the adaptation of the virus have occurred preferentially along the trunk of the tree. The method should be helpful in assessing the potential of current viruses to found future epidemics or pandemics.","corpus_id":18123073,"score":2},{"doc_id":"24418567","title":"Accurate classification and hemagglutinin amino acid signatures for influenza A virus host-origin association and subtyping.","abstract":"Host-origin classification and signatures of influenza A viruses were investigated based on the HA protein for tracking of the HA host of origin. Hidden Markov models (HMMs), decision trees and associative classification for each influenza A virus subtype and its major hosts (human, avian, swine) were generated. Features of the HA protein signatures that were host-and subtype-specific were sought. Host-associated signatures that occurred in different subtypes of the virus were identified. Evaluation of the classification models based on ROC curves and support and confidence ratings for the amino acid class-association rules was performed. Host classification based on the HA subtype achieved accuracies between 91.2% and 100% using decision trees after feature selection. Host-specific class association rules for avian-host origins gave better support and confidence ratings, followed by human and finally swine origin. This finding indicated the lower specificity of the swine host, perhaps pointing to its ability to mix different strains.","corpus_id":3939071,"score":2},{"doc_id":"25521718","title":"Predicting host tropism of influenza A virus proteins using random forest.","abstract":"BACKGROUND: Majority of influenza A viruses reside and circulate among animal populations, seldom infecting humans due to host range restriction. Yet when some avian strains do acquire the ability to overcome species barrier, they might become adapted to humans, replicating efficiently and causing diseases, leading to potential pandemic. With the huge influenza A virus reservoir in wild birds, it is a cause for concern when a new influenza strain emerges with the ability to cross host species barrier, as shown in light of the recent H7N9 outbreak in China. Several influenza proteins have been shown to be major determinants in host tropism. Further understanding and determining host tropism would be important in identifying zoonotic influenza virus strains capable of crossing species barrier and infecting humans. RESULTS: In this study, computational models for 11 influenza proteins have been constructed using the machine learning algorithm random forest for prediction of host tropism. The prediction models were trained on influenza protein sequences isolated from both avian and human samples, which were transformed into amino acid physicochemical properties feature vectors. The results were highly accurate prediction models (ACC>96.57; AUC>0.980; MCC>0.916) capable of determining host tropism of individual influenza proteins. In addition, features from all 11 proteins were used to construct a combined model to predict host tropism of influenza virus strains. This would help assess a novel influenza strain's host range capability. CONCLUSIONS: From the prediction models constructed, all achieved high prediction performance, indicating clear distinctions in both avian and human proteins. When used together as a host tropism prediction system, zoonotic strains could potentially be identified based on different protein prediction results. Understanding and predicting host tropism of influenza proteins lay an important foundation for future work in constructing computation models capable of directly predicting interspecies transmission of influenza viruses. The models are available for prediction at http://fluleap.bic.nus.edu.sg.","corpus_id":6263991,"score":2},{"doc_id":"26915079","title":"Distinct Host Tropism Protein Signatures to Identify Possible Zoonotic Influenza A Viruses.","abstract":"Zoonotic influenza A viruses constantly pose a health threat to humans as novel strains occasionally emerge from the avian population to cause human infections. Many past epidemic as well as pandemic strains have originated from avian species. While most viruses are restricted to their primary hosts, zoonotic strains can sometimes arise from mutations or reassortment, leading them to acquire the capability to escape host species barrier and successfully infect a new host. Phylogenetic analyses and genetic markers are useful in tracing the origins of zoonotic infections, but there are still no effective means to identify high risk strains prior to an outbreak. Here we show that distinct host tropism protein signatures can be used to identify possible zoonotic strains in avian species which have the potential to cause human infections. We have discovered that influenza A viruses can now be classified into avian, human, or zoonotic strains based on their host tropism protein signatures. Analysis of all influenza A viruses with complete proteome using the host tropism prediction system, based on machine learning classifications of avian and human viral proteins has uncovered distinct signatures of zoonotic strains as mosaics of avian and human viral proteins. This is in contrast with typical avian or human strains where they show mostly avian or human viral proteins in their signatures respectively. Moreover, we have found that zoonotic strains from the same influenza outbreaks carry similar host tropism protein signatures characteristic of a common ancestry. Our results demonstrate that the distinct host tropism protein signature in zoonotic strains may prove useful in influenza surveillance to rapidly identify potential high risk strains circulating in avian species, which may grant us the foresight in anticipating an impending influenza outbreak.","corpus_id":24472396,"score":2},{"doc_id":"28361670","title":"Prediction of virus-host infectious association by supervised learning methods.","abstract":"BACKGROUND: The study of virus-host infectious association is important for understanding the functions and dynamics of microbial communities. Both cellular and fractionated viral metagenomic data generate a large number of viral contigs with missing host information. Although relative simple methods based on the similarity between the word frequency vectors of viruses and bacterial hosts have been developed to study virus-host associations, the problem is significantly understudied. We hypothesize that machine learning methods based on word frequencies can be efficiently used to study virus-host infectious associations. METHODS: We investigate four different representations of word frequencies of viral sequences including the relative word frequency and three normalized word frequencies by subtracting the number of expected from the observed word counts. We also study five machine learning methods including logistic regression, support vector machine, random forest, Gaussian naive Bayes and Bernoulli naive Bayes for separating infectious from non-infectious viruses for nine bacterial host genera with at least 45 infecting viruses. Area under the receiver operating characteristic curve (AUC) is used to compare the performance of different machine learning method and feature combinations. We then evaluate the performance of the best method for the identification of the hosts of contigs in metagenomic studies. We also develop a maximum likelihood method to estimate the fraction of true infectious viruses for a given host in viral tagging experiments. RESULTS: Based on nine bacterial host genera with at least 45 infectious viruses, we show that random forest together with the relative word frequency vector performs the best in identifying viruses infecting particular hosts. For all the nine host genera, the AUC is over 0.85 and for five of them, the AUC is higher than 0.98 when the word size is 6 indicating the high accuracy of using machine learning approaches for identifying viruses infecting particular hosts. We also show that our method can predict the hosts of viral contigs of length at least 1kbps in metagenomic studies with high accuracy. The random forest together with word frequency vector outperforms current available methods based on Manhattan and [Formula: see text] dissimilarity measures. Based on word frequencies, we estimate that about 95% of the identified T4-like viruses in viral tagging experiment infect Synechococcus, while only about 29% of the identified non-T4-like viruses and 30% of the contigs in the study potentially infect Synechococcus. CONCLUSIONS: The random forest machine learning method together with the relative word frequencies as features of viruses can be used to predict viruses and viral contigs for specific bacterial hosts. The maximum likelihood approach can be used to estimate the fraction of true infectious associated viruses in viral tagging experiments.","corpus_id":5452774,"score":2},{"doc_id":"28587080","title":"Predicting Zoonotic Risk of Influenza A Viruses from Host Tropism Protein Signature Using Random Forest.","abstract":"Influenza A viruses remain a significant health problem, especially when a novel subtype emerges from the avian population to cause severe outbreaks in humans. Zoonotic viruses arise from the animal population as a result of mutations and reassortments, giving rise to novel strains with the capability to evade the host species barrier and cause human infections. Despite progress in understanding interspecies transmission of influenza viruses, we are no closer to predicting zoonotic strains that can lead to an outbreak. We have previously discovered distinct host tropism protein signatures of avian, human and zoonotic influenza strains obtained from host tropism predictions on individual protein sequences. Here, we apply machine learning approaches on the signatures to build a computational model capable of predicting zoonotic strains. The zoonotic strain prediction model can classify avian, human or zoonotic strains with high accuracy, as well as providing an estimated zoonotic risk. This would therefore allow us to quickly determine if an influenza virus strain has the potential to be zoonotic using only protein sequences. The swift identification of potential zoonotic strains in the animal population using the zoonotic strain prediction model could provide us with an early indication of an imminent influenza outbreak.","corpus_id":430918,"score":2},{"doc_id":"29060087","title":"Prediction of Influenza A virus infections in humans using an Artificial Neural Network learning approach.","abstract":"The Influenza type A virus can be considered as one of the most severe viruses that can infect multiple species with often fatal consequences to the hosts. The Haemagglutinin (HA) gene of the virus has the potential to be a target for antiviral drug development realised through accurate identification of its sub-types and possible the targeted hosts. In this paper, to accurately predict if an Influenza type A virus has the capability to infect human hosts, by using only the HA gene, is therefore developed and tested. The predictive model follows three main steps; (i) decoding the protein sequences into numerical signals using EIIP amino acid scale, (ii) analysing these sequences by using Discrete Fourier Transform (DFT) and extracting DFT-based features, (iii) using a predictive model, based on Artificial Neural Networks and using the features generated by DFT. In this analysis, from the Influenza Research Database, 30724, 18236 and 8157 HA protein sequences were collected for Human, Avian and Swine respectively. Given this set of the proteins, the proposed method yielded 97.36% (± 0.04%), 97.26% (± 0.26%), 0.978 (± 0.004), 0.963 (± 0.005) and 0.945 (±0.005) for the training accuracy validation accuracy, precision, recall and Mathews Correlation Coefficient (MCC) respectively, based on a 10-fold cross-validation. The classification model generated by using one of the largest dataset, if not the largest, yields promising results that could lead to early detection of such species and help develop precautionary measurements for possible human infections.","corpus_id":2583056,"score":2},{"doc_id":"29236050","title":"Molecular Markers for Interspecies Transmission of Avian Influenza Viruses in Mammalian Hosts.","abstract":"In the last decade, a wide range of avian influenza viruses (AIVs) have infected various mammalian hosts and continuously threaten both human and animal health. It is a result of overcoming the inter-species barrier which is mostly associated with gene reassortment and accumulation of mutations in their gene segments. Several recent studies have shed insights into the phenotypic and genetic changes that are involved in the interspecies transmission of AIVs. These studies have a major focus on transmission from avian to mammalian species due to the high zoonotic potential of the viruses. As more mammalian species have been infected with these viruses, there is higher risk of genetic evolution of these viruses that may lead to the next human pandemic which represents and raises public health concern. Thus, understanding the mechanism of interspecies transmission and molecular determinants through which the emerging AIVs can acquire the ability to transmit to humans and other mammals is an important key in evaluating the potential risk caused by AIVs among humans. Here, we summarize previous and recent studies on molecular markers that are specifically involved in the transmission of avian-derived influenza viruses to various mammalian hosts including humans, pigs, horses, dogs, and marine mammals.","corpus_id":29923745,"score":2},{"doc_id":"18785841","title":"Host restriction of avian influenza viruses at the level of the ribonucleoproteins.","abstract":"Although transmission of avian influenza viruses to mammals, particularly humans, has been repeatedly documented, adaptation and sustained transmission in the new host is a rare event that in the case of humans may result in pandemics. Host restriction involves multiple genetic determinants. Among the known determinants of host range, key determinants have been identified on the genes coding for the nucleoprotein and polymerase proteins that, together with the viral RNA segments, form the ribonucleoproteins (RNPs). The RNP genes form host-specific lineages and harbor host-associated genetic signatures. The functional significance of these determinants has been studied by reassortment and reverse genetics experiments, underlining the influence of the global genetic context. In some instances the molecular mechanisms have been approached, pointing to the importance of the polymerase activity and interaction with cellular host factors. Better knowledge of determinants of host restriction will allow monitoring of the pandemic potential of avian influenza viruses.","corpus_id":1603988,"score":1},{"doc_id":"19687042","title":"Within-host variation of avian influenza viruses.","abstract":"The emergence and spread of H5N1 avian influenza viruses from Asia through to Europe and Africa pose a significant animal disease problem and have raised concerns that the virus may pose a pandemic threat to humans. The epizootological factors that have influenced the wide distribution of the virus are complex, and the variety of viruses currently circulating reflects these factors. Sequence analysis of the virus genes sheds light on the H5N1 virus evolution during its emergence and spread, but the degree of virus variation at the level of an individual infected bird has been described in only a few studies. Here, we describe some results of a study in which turkeys, ducks and chickens were infected with either one of two H5N1 or one of three H7N1 viruses, and the degree of sequence variation within an individual infected avian host was examined. We developed 'deep amplicon' sequence analysis for this work, and the methods and results provide a background framework for application to disease outbreaks in the field.","corpus_id":5894654,"score":1},{"doc_id":"22595002","title":"Prediction of protein-protein interactions between viruses and human by an SVM model.","abstract":"BACKGROUND: Several computational methods have been developed to predict protein-protein interactions from amino acid sequences, but most of those methods are intended for the interactions within a species rather than for interactions across different species. Methods for predicting interactions between homogeneous proteins are not appropriate for finding those between heterogeneous proteins since they do not distinguish the interactions between proteins of the same species from those of different species. RESULTS: We developed a new method for representing a protein sequence of variable length in a frequency vector of fixed length, which encodes the relative frequency of three consecutive amino acids of a sequence. We built a support vector machine (SVM) model to predict human proteins that interact with virus proteins. In two types of viruses, human papillomaviruses (HPV) and hepatitis C virus (HCV), our SVM model achieved an average accuracy above 80%, which is higher than that of another SVM model with a different representation scheme. Using the SVM model and Gene Ontology (GO) annotations of proteins, we predicted new interactions between virus proteins and human proteins. CONCLUSIONS: Encoding the relative frequency of amino acid triplets of a protein sequence is a simple yet powerful representation method for predicting protein-protein interactions across different species. The representation method has several advantages: (1) it enables a prediction model to achieve a better performance than other representations, (2) it generates feature vectors of fixed length regardless of the sequence length, and (3) the same representation is applicable to different types of proteins.","corpus_id":9388262,"score":1},{"doc_id":"23777174","title":"Predicting transmission of avian influenza A viruses from avian to human by using informative physicochemical properties.","abstract":"Some strains of avian influenza A virus (AIV) can directly transmit from their natural hosts to humans. These avian-to-human transmissions have continuously been reported to cause human deaths worldwide since 1997. Predicting whether AIV strains can transmit from avian to human is valuable for early warning of AIV strains with human pandemic potential. In this study, we constructed a computational model to predict avian-to-human transmission of AIV based on physicochemical properties. Initially, ninety signature positions in the inner protein sequences were extracted with the entropy method. These positions were then encoded with 531 physicochemical features. Subsequently, the optimal subset of these physicochemical features was mined with several feature selection methods. Finally, a support vector machine (SVM) model named A2H was established to integrate the selected optimal features. The experimental results of cross-validation and an independent test show that A2H has the capability of predicting transmission of AIV from avian to human.","corpus_id":23120853,"score":1},{"doc_id":"26038511","title":"Host adaptation and transmission of influenza A viruses in mammals.","abstract":"A wide range of influenza A viruses of pigs and birds have infected humans in the last decade, sometimes with severe clinical consequences. Each of these so-called zoonotic infections provides an opportunity for virus adaptation to the new host. Fortunately, most of these human infections do not yield viruses with the ability of sustained human-to-human transmission. However, animal influenza viruses have acquired the ability of sustained transmission between humans to cause pandemics on rare occasions in the past, and therefore, influenza virus zoonoses continue to represent threats to public health. Numerous recent studies have shed new light on the mechanisms of adaptation and transmission of avian and swine influenza A viruses in mammals. In particular, several studies provided insights into the genetic and phenotypic traits of influenza A viruses that may determine airborne transmission. Here, we summarize recent studies on molecular determinants of virulence and adaptation of animal influenza A virus and discuss the phenotypic traits associated with airborne transmission of newly emerging influenza A viruses. Increased understanding of the determinants and mechanisms of virulence and transmission may aid in assessing the risks posed by animal influenza viruses to human health, and preparedness for such risks.","corpus_id":10701239,"score":1},{"doc_id":"18370034","title":"A brief introduction to the avian influenza virus.","abstract":"The avian influenza (AI) virus is type A influenza isolated from and adapted to an avian host. Type A influenza belongs to the orthomyxovirdae virus family, is enveloped, and is pleiomorphic with a size ranging from 80-120 nm (reviewed in [1]). Type A influenza strains are classified by the serological subtypes of the primary viral surface proteins, the hemagglutinin (HA) and neuraminidase (NA). The HA has 16 subtypes (H1-H16) and contains neutralizing epitopes. Antibodies against the NA are not neutralizing, and there are nine neuraminidase or \"N\" subtypes. The \"H\" and N subtypes seem to be able to assort into any combination, and many of the 144 possible combinations have been found in natural reservoir species, although some combinations are more common than others. All 16 subtypes have been found in ducks, gulls, or shorebirds, the natural reservoir host species of the virus. However, in these species certain subtypes are more common than others; for example, H3, H4, and H6 are most common in ducks in North America [2, 3] and although there is no clear association between host range or host restriction based on HA subtype, some subtypes are more common in some species than others, i.e., H1 and H3 in swine, H3 in horses, and H5 and H7 in chickens.","corpus_id":24480926,"score":0},{"doc_id":"18722814","title":"A feature vector integration approach for a generalized support vector machine pairwise homology algorithm.","abstract":"Due to the exponential growth of sequenced genomes, the need to quickly provide accurate annotation for existing and new sequences is paramount to facilitate biological research. Current sequence comparison approaches fail to detect homologous relationships when sequence similarity is low. Support vector machine (SVM) algorithms approach this problem by transforming all proteins into a feature space of equal dimension based on protein properties, such as sequence similarity scores against a basis set of proteins or motifs. This multivariate representation of the protein space is then used to build a classifier specific to a pre-defined protein family. However, this approach is not well suited to large-scale annotation. We have developed a SVM approach that formulates remote homology as a single classifier that answers the pairwise comparison problem by integrating the two feature vectors for a pair of sequences into a single vector representation that can be used to build a classifier that separates sequence pairs into homologs and non-homologs. This pairwise SVM approach significantly improves the task of remote homology detection on the benchmark dataset, quantified as the area under the receiver operating characteristic curve; 0.97 versus 0.73 and 0.70 for PSI-BLAST and Basic Local Alignment Search Tool (BLAST), respectively.","corpus_id":206908061,"score":0},{"doc_id":"18941631","title":"Evolution of highly pathogenic H5N1 avian influenza viruses in Vietnam between 2001 and 2007.","abstract":"Highly pathogenic avian influenza (HPAI) H5N1 viruses have caused dramatic economic losses to the poultry industry of Vietnam and continue to pose a serious threat to public health. As of June 2008, Vietnam had reported nearly one third of worldwide laboratory confirmed human H5N1 infections. To better understand the emergence, spread and evolution of H5N1 in Vietnam we studied over 300 H5N1 avian influenza viruses isolated from Vietnam since their first detection in 2001. Our phylogenetic analyses indicated that six genetically distinct H5N1 viruses were introduced into Vietnam during the past seven years. The H5N1 lineage that evolved following the introduction in 2003 of the A/duck/Hong Kong/821/2002-like viruses, with clade 1 hemagglutinin (HA), continued to predominate in southern Vietnam as of May 2007. A virus with a clade 2.3.4 HA newly introduced into northern Vietnam in 2007, reassorted with pre-existing clade 1 viruses, resulting in the emergence of novel genotypes with neuraminidase (NA) and/or internal gene segments from clade 1 viruses. A total of nine distinct genotypes have been present in Vietnam since 2001, including five that were circulating in 2007. At least four of these genotypes appear to have originated in Vietnam and represent novel H5N1 viruses not reported elsewhere. Geographic and temporal analyses of H5N1 infection dynamics in poultry suggest that the majority of viruses containing new genes were first detected in northern Vietnam and subsequently spread to southern Vietnam after reassorting with pre-existing local viruses in northern Vietnam. Although the routes of entry and spread of H5N1 in Vietnam remain speculative, enhanced poultry import controls and virologic surveillance efforts may help curb the entry and spread of new HPAI viral genes.","corpus_id":2797526,"score":0},{"doc_id":"19276438","title":"The public health impact of avian influenza viruses.","abstract":"Influenza viruses with novel hemagglutinin and 1 or more accompanying genes derived from avian influenza viruses sporadically emerge in humans and have the potential to result in a pandemic if the virus causes disease and spreads efficiently in a population that lacks immunity to the novel hemagglutinin. Since 1997, multiple avian influenza virus subtypes have been transmitted directly from domestic poultry to humans and have caused a spectrum of human disease, from asymptomatic to severe and fatal. To assess the pandemic risk that avian influenza viruses pose, we have used multiple strategies to better understand the capacity of avian viruses to infect, cause disease, and transmit among mammals, including humans. Seroepidemiologic studies that evaluate the frequency and risk of human infection with avian influenza viruses in populations with exposure to domestic or wild birds can provide a better understanding of the pandemic potential of avian influenza subtypes. Investigations conducted in Hong Kong following the first H5N1 outbreak in humans in 1997 determined that exposure to poultry in live bird markets was a key risk factor for human disease. Among poultry workers, butchering and exposure to sick poultry were risk factors for antibody to H5 virus, which provided evidence for infection. A second risk assessment tool, the ferret, can be used to evaluate the level of virulence and potential for host-to-host transmission of avian influenza viruses in this naturally susceptible host. Avian viruses isolated from humans exhibit a level of virulence and transmissibility in ferrets that generally reflects that seen in humans. The ferret model thus provides a means to monitor emerging avian influenza viruses for pandemic risk, as well as to evaluate laboratory-generated reassortants and mutants to better understand the molecular basis of influenza virus transmissibility. Taken together, such studies provide valuable information with which we can assess the public health risk of avian influenza viruses.","corpus_id":19832067,"score":0},{"doc_id":"19447141","title":"Amplification of four genes of influenza A viruses using a degenerate primer set in a one step RT-PCR method.","abstract":"We designed a degenerate primer set that yielded full-length amplification of hemagglutinin (HA), neuraminidase (NA), matrix (M), and non-structural protein (NSP) genes of influenza A viruses in a single reaction mixture. These four genes were amplified from 15 HA (1-15) and 9 NA (1-9) subtypes of influenza A viruses of avian (n=16) origin. In addition, 272 field isolates of avian origin were tested by this method. Full-length amplification of HA, NA, M, and NSP genes was obtained in 242 (88.9%), 254 (93.4%), 268 (98.5%), and 268 (98.5%) isolates, respectively. No gene was amplified in four isolates. Of these four isolates, two were subtyped as H4N6, one as H7N7, and one as H10N7. Amplification was successful for all 4 genes of H1N1, H2N3, and H3N2 isolates of swine influenza. Also, all four genes were amplified in one equine influenza (H3N8) isolate and seven isolates of human origin (H1N1 and H3N2). This appears to be the first study using degenerate primer set for full-length amplification of four genes of influenza A viruses in a single reaction. Further studies are needed to determine if this primer set can be used for subtyping of influenza virus isolates.","corpus_id":15148655,"score":0},{"doc_id":"19460353","title":"Isolation and genetic characterization of avian-like H1N1 and novel ressortant H1N2 influenza viruses from pigs in China.","abstract":"As pigs are susceptible to both human and avian influenza viruses, they have been proposed to be intermediate hosts or mixing vessels for the generation of pandemic influenza viruses through reassortment or adaptation to the mammalian host. In this study, we reported avian-like H1N1 and novel ressortant H1N2 influenza viruses from pigs in China. Homology and phylogenetic analyses showed that the H1N1 virus (A/swine/Zhejiang/1/07) was closely to avian-like H1N1 viruses and seemed to be derived from the European swine H1N1 viruses, which was for the first time reported in China; and the two H1N2 viruses (A/swine/Shanghai/1/07 and A/swine/Guangxi/13/06) were novel ressortant H1N2 influenza viruses containing genes from the classical swine (HA, NP, M and NS), human (NA and PB1) and avian (PB2 and PA) lineages, which indicted that the reassortment among human, avian, and swine influenza viruses had taken place in pigs in China and resulted in the generation of new viruses. The isolation of avian-like H1N1 influenza virus originated from the European swine H1N1 viruses, especially the emergence of two novel ressortant H1N2 influenza viruses provides further evidence that pigs serve as intermediate hosts or \"mixing vessels\", and swine influenza virus surveillance in China should be given a high priority.","corpus_id":36688594,"score":0},{"doc_id":"19486316","title":"The role of swine in the generation of novel influenza viruses.","abstract":"The ecology of influenza A viruses is very complicated involving multiple host species and viral genes. Avian species have variable susceptibility to influenza A viruses with wild aquatic birds being the reservoir for this group of pathogens. Occasionally, influenza A viruses are transmitted to mammals from avian species, which can lead to the development of human pandemic strains by direct or indirect transmission to man. Because swine are also susceptible to infection with avian and human influenza viruses, genetic reassortment between these viruses and/or swine influenza viruses can occur. The potential to generate novel influenza viruses has resulted in swine being labelled 'mixing vessels'. The mixing vessel theory is one mechanism by which unique viruses can be transmitted from an avian reservoir to man. Although swine can generate novel influenza viruses capable of infecting man, at present, it is difficult to predict which viruses, if any, will cause a human pandemic. Clearly, the ecology of influenza A viruses is dynamic and can impact human health, companion animals, as well as the health of livestock and poultry for production of valuable protein commodities. For these reasons, influenza is, and will continue to be, a serious threat to the wellbeing of mankind.","corpus_id":30630155,"score":0},{"doc_id":"19546028","title":"Structural and evolutionary characteristics of HA, NA, NS and M genes of clinical influenza A/H3N2 viruses passaged in human and canine cells.","abstract":"BACKGROUND: Canine (MDCK) cells and chicken eggs are usually used for isolation of human influenza viruses. Viruses isolated by these procedures often differ from those present in the clinical specimens, since adaptive changes occur during virus transmission from the human host to cells of heterologous origin. OBJECTIVES: To minimize these species-dependent changes, CACO-2 cells derived from human intestinal epithelium were used to isolate virus from influenza patients. STUDY DESIGN: Influenza A viruses of subtype H3N2 were primarily isolated in CACO-2 and then passaged in parallel in CACO-2 and MDCK cells. Structural properties of passaged virus variants were compared and analyzed for evolutionary relationships. RESULTS: Influenza viruses were isolated in CACO-2 with higher efficiency than in MDCK and chicken eggs. The following observations were made: (i) recent isolates showed an about 2-fold increase in the number of glycosylation sites of HA and NA when compared to isolates from 1968 to 1970; (ii) during passages of clinical strains in CACO-2 and MDCK cells HA and NA mutated cooperatively with strain-specific variations implying that functioning of the HA-NA complex varied from strain to strain in one influenza outbreak; (iii) there were no amino acid exchanges in the HA receptor binding site although the viruses acquired the ability to agglutinate avian erythrocytes after passage in MDCK cells, suggesting that virus adsorption is regulated by several factors; (iv) quasispecies characterized by deletion of 66 nucleotides (22 amino acids) in the stalk region of the NA gene was dominant in naso-pharyngeal washes of all patients whereas during passaging in CACO-2 cells this deleted genotype in isolates from different patients was either stably retained as prevalent quasispecies or rapidly replaced for that one containing full length NA gene; (v) the M2 protein of clinical viruses was sensitive to amantadine; (vi) the NS segment of human viruses, unlike the most of avian ones, contained an additional positive-sense open reading frame encoding a hypothetical 25kD polypeptide (negative strand protein, NSP). CONCLUSIONS: The data suggest that (i) clinical influenza viruses can be isolated from respiratory tract of humans more effectively in human than in canine cells; (ii) heterologous virus population circulates during one influenza outbreak; (iii) increasing numbers of glycosylation sites on HA and NA and stalk shortening of NA take place during virus evolution in humans.","corpus_id":12056097,"score":0},{"doc_id":"19673419","title":"[Rescue of H3N2 subtype swine influenza virus and substitution of hemagglutinin, neuraminidase].","abstract":"OBJECTIVE: To study the mechanisms of trans-species transmission of influenza virus for developing novel vaccine of influenza in future. METHODS: We rescued H3N2 subtype swine influenza virus strain A/Swine/Henan/S4/01 successfully by a plasmid-base reverse genetics. Eight gene segments were synthesized by reverse transcriptase-PCR and cloned into bidirection expression vector pHW2000. We cotransfected 8 recombinant plasmids into 293T and MDCK cells and got the rescued virus rgH3N2. Then we replaced Hemagglutinin, Neuraminidase of rgH3N2 by Hemagglutinin, Neuraminidase gene from Human influenza virus, Avian influenza virus, Equine influenza virus. RESULTS: The rescued virus rgH3N2 and the wild type virus shared similar biological properties such as in titers of 50% embryo infective, 50% tissue culture infective dose and stability tests. The rescued virus titer in MDCK cell culture was measured by hemagglutination assay and the maximum virus titre of 1:64 hemagglutination unit was obtained after infection of MDCK cell for 60 h, The hemagglutination titre was 1:256 after several passages in embryonated eggs. With various combinations of HA, NA genes, we successfully generated high-yield reassortant viruses rgH1N1, rgH4N6 and rgH3N8 in embryonated eggs and MDCK cells. CONCLUSION: The successful rescue of reassortment viruses establish the foundation for the molecular mechanism research on how the swine influenza virus breakthrough the intermediate barriers and the function of HA, NA during transmitting among species, Also it is feasible to be used for developing novel vaccine of H3N2 subtype Swine influenza in future.","corpus_id":38606120,"score":0},{"doc_id":"19939933","title":"Molecular determinants of adaptation of highly pathogenic avian influenza H7N7 viruses to efficient replication in the human host.","abstract":"Two viruses isolated during the highly pathogenic avian influenza (HPAI) H7N7 virus outbreak in The Netherlands in 2003, one isolated from a person with conjunctivitis and one from a person who died as the result of infection, were used for an in vitro study of influenza A virus pathogenicity factors. The two HPAI H7N7 viruses differed in 15 amino acid positions in five gene segments. Assays were designed to investigate the role of each of these substitutions in attachment and entry, transcription and genome replication, and virus production and release as determined by hemagglutinin (HA), polymerase proteins, nonstructural protein 1 (NS1), and neuraminidase (NA). These in vitro studies confirmed the roles of the E627K substitution in basic polymerase 2 (PB2) and the A143T substitution in HA in pathogenicity observed in a mouse model previously. However, the in vitro studies identified a contribution of acidic polymerase (PA) and NA to the efficient replication in human cells of the fatal case virus, despite the fact that these are rarely marked as determinants of pathogenicity in in vivo studies. With the exception of PB2 E627K, all substitutions contributing to enhanced replication of the fatal case virus in vitro were present in poultry viruses prior to transmission to the human fatal case, indicating that viruses with enhanced replication efficiency in the mammalian host can be generated in poultry. Thus, detailed in vitro analyses of mutations facilitating replication of avian influenza viruses in mammalian cells are important to assess the zoonotic risk posed by these viruses and, in addition, highlight the value of in vitro studies to complement animal models.","corpus_id":10015180,"score":0},{"doc_id":"20134234","title":"Comparative study of the nucleotide bias between the novel H1N1 and H5N1 subtypes of influenza A viruses using bioinformatics techniques.","abstract":"Novel influenza A (H1N1) is a newly emerged flu virus which was first detected in April, 2009. Unlike the avian influenza (H5N1), this virus has been known to be able to spread from human to human directly. Although it is uncertain that how severe this novel H1N1 virus will be in terms of human illness, illness may be more widespread because most people will not have immunity to it. In this study, we compared the codon usage bias between the novel H1N1 influenza A viruses and other viruses such as H1N1 and H5N1 subtypes to investigate the genomic patterns of novel influenza A (H1N1). Totally 1,675 nucleotide sequences of the hemagglutinin (HA) and neuraminidase (NA) genes of influenza A virus including H1N1 and H5N1 subtypes occurred from 2004 to 2009 were used. As a result, we found that the novel H1N1 influenza A viruses showed the most close correlations with the swine-origin H1N1 subtypes than other H1N1 viruses in the result from not only the analysis of nucleotide compositions, but also the phylogenetic analysis. Although the genetic sequences of novel H1N1 subtypes were not exactly same as the other H1N1 subtypes, the HA and NA genes of novel H1N1s showed very similar codon usage patterns with other H1N1 subtypes, especially with the swine-origin H1N1 influenza A viruses. Our findings strongly suggested that those novel H1N1 viruses seemed to be originated from the swine-host H1N1 viruses in terms of the codon usage patterns.","corpus_id":24039349,"score":0},{"doc_id":"20484565","title":"Viral reassortment and transmission after co-infection of pigs with classical H1N1 and triple-reassortant H3N2 swine influenza viruses.","abstract":"Triple-reassortant swine influenza viruses circulating in North American pigs contain the internal genes derived from swine (matrix, non-structural and nucleoprotein), human [polymerase basic 1 (PB1)] and avian (polymerase acidic and PB2) influenza viruses forming a constellation of genes that is well conserved and is called the triple-reassortant internal gene (TRIG) cassette. In contrast, the external genes [haemagglutinin (HA) and neuraminidase (NA)] are less conserved, reflecting multiple reassortant events that have produced viruses with different combinations of HA and NA genes. This study hypothesized that maintenance of the TRIG cassette confers a selective advantage to the virus. To test this hypothesis, pigs were co-infected with the triple-reassortant H3N2 A/Swine/Texas/4199-2/98 (Tx/98) and the classical H1N1 A/Swine/Iowa/15/1930 viruses and co-housed with a group of sentinel animals. This direct contact group was subsequently moved into contact with a second group of naïve animals. Four different subtypes (H1N1, H1N2, H3N1 and H3N2) of influenza virus were identified in bronchoalveolar lavage fluid collected from the lungs of the experimentally infected pigs, with most of the viruses containing TRIG from the Tx/98 virus. Interestingly, only the intact H3N2 Tx/98 virus was transmitted from the infected pigs to the direct-contact animals and from them to the second contact group of pigs. These results demonstrated that multiple reassortments can occur within a host; however, only specific gene constellations are readily transmissible. It was concluded that certain HA and NA gene pairs, in conjunction with the TRIG cassette, may have a competitive advantage over other combinations for transmission and maintenance in swine.","corpus_id":18293879,"score":0},{"doc_id":"20591213","title":"Interspecies and intraspecies transmission of influenza A viruses: viral, host and environmental factors.","abstract":"Influenza A viruses are enveloped viruses belonging to the family Orthomyxoviridae that encompasses four more genera: Influenza B, Influenza C, Isavirus and Thogotovirus. Type A viruses belong to the only genus that is highly infectious to a variety of mammalian and avian species. They are divided into subtypes based on two surface glycoproteins, the hemagglutinin (HA) and neuraminidase (NA). So far, 16 HA and 9 NA subtypes have been identified worldwide, making a possible combination of 144 subtypes between both proteins. Generally, individual viruses are host-specific, however, interspecies transmission of influenza A viruses is not uncommon. All of the HA and NA subtypes have been isolated from wild birds; however, infections in humans and other mammalian species are limited to a few subtypes. The replication of individual influenza A virus in a specific host is dependent on many factors including, viral proteins, host system and environmental conditions. In this review, the key findings that contribute to the transmission of influenza A viruses amongst different species are summarized.","corpus_id":34951469,"score":0},{"doc_id":"20600474","title":"Repository of Eurasian influenza A virus hemagglutinin and neuraminidase reverse genetics vectors and recombinant viruses.","abstract":"Reverse genetics can be used to produce recombinant influenza A viruses containing virtually every desired combination of hemagglutinin (HA) and neuraminidase (NA) genes using the virus backbone of choice. Here, a repository of plasmids and recombinant viruses representing all contemporary Eurasian HA and NA subtypes, H1-H16 and N1-N9, was established. HA and NA genes were selected based on sequence analyses of influenza virus genes available from public databases. Prototype Eurasian HA and NA genes were cloned in bidirectional reverse genetics plasmids. Recombinant viruses based on the virus backbone of A/PR/8/34, and containing a variety of HA and NA genes were produced in 293T cells. Virus stocks were produced in MDCK cells and embryonated chicken eggs. These plasmids and viruses may be useful for numerous purposes, including influenza virus research projects, vaccination studies, and to serve as reference reagents in diagnostic settings.","corpus_id":23733821,"score":0},{"doc_id":"21209922","title":"A complete analysis of HA and NA genes of influenza A viruses.","abstract":"BACKGROUND: More and more nucleotide sequences of type A influenza virus are available in public databases. Although these sequences have been the focus of many molecular epidemiological and phylogenetic analyses, most studies only deal with a few representative sequences. In this paper, we present a complete analysis of all Haemagglutinin (HA) and Neuraminidase (NA) gene sequences available to allow large scale analyses of the evolution and epidemiology of type A influenza. METHODOLOGY/PRINCIPAL FINDINGS: This paper describes an analysis and complete classification of all HA and NA gene sequences available in public databases using multivariate and phylogenetic methods. CONCLUSIONS/SIGNIFICANCE: We analyzed 18,975 HA sequences and divided them into 280 subgroups according to multivariate and phylogenetic analyses. Similarly, we divided 11,362 NA sequences into 202 subgroups. Compared to previous analyses, this work is more detailed and comprehensive, especially for the bigger datasets. Therefore, it can be used to show the full and complex phylogenetic diversity and provides a framework for studying the molecular evolution and epidemiology of type A influenza virus. For more than 85% of type A influenza HA and NA sequences into GenBank, they are categorized in one unambiguous and unique group. Therefore, our results are a kind of genetic and phylogenetic annotation for influenza HA and NA sequences. In addition, sequences of swine influenza viruses come from 56 HA and 45 NA subgroups. Most of these subgroups also include viruses from other hosts indicating cross species transmission of the viruses between pigs and other hosts. Furthermore, the phylogenetic diversity of swine influenza viruses from Eurasia is greater than that of North American strains and both of them are becoming more diverse. Apart from viruses from human, pigs, birds and horses, viruses from other species show very low phylogenetic diversity. This might indicate that viruses have not become established in these species. Based on current evidence, there is no simple pattern of inter-hemisphere transmission of avian influenza viruses and it appears to happen sporadically. However, for H6 subtype avian influenza viruses, such transmissions might have happened very frequently and multiple and bidirectional transmission events might exist.","corpus_id":12829449,"score":0},{"doc_id":"21507270","title":"Positive selection on hemagglutinin and neuraminidase genes of H1N1 influenza viruses.","abstract":"BACKGROUND: Since its emergence in March 2009, the pandemic 2009 H1N1 influenza A virus has posed a serious threat to public health. To trace the evolutionary path of these new pathogens, we performed a selection-pressure analysis of a large number of hemagglutinin (HA) and neuraminidase (NA) gene sequences of H1N1 influenza viruses from different hosts. RESULTS: Phylogenetic analysis revealed that both HA and NA genes have evolved into five distinct clusters, with further analyses indicating that the pandemic 2009 strains have experienced the strongest positive selection. We also found evidence of strong selection acting on the seasonal human H1N1 isolates. However, swine viruses from North America and Eurasia were under weak positive selection, while there was no significant evidence of positive selection acting on the avian isolates. A site-by-site analysis revealed that the positively selected sites were located in both of the cleaved products of HA (HA1 and HA2), as well as NA. In addition, the pandemic 2009 strains were subject to differential selection pressures compared to seasonal human, North American swine and Eurasian swine H1N1 viruses. CONCLUSIONS: Most of these positively and/or differentially selected sites were situated in the B-cell and/or T-cell antigenic regions, suggesting that selection at these sites might be responsible for the antigenic variation of the viruses. Moreover, some sites were also associated with glycosylation and receptor-binding ability. Thus, selection at these positions might have helped the pandemic 2009 H1N1 viruses to adapt to the new hosts after they were introduced from pigs to humans. Positive selection on position 274 of NA protein, associated with drug resistance, might account for the prevalence of drug-resistant variants of seasonal human H1N1 influenza viruses, but there was no evidence that positive selection was responsible for the spread of the drug resistance of the pandemic H1N1 strains.","corpus_id":5199018,"score":0},{"doc_id":"21849451","title":"Comparative analysis of avian influenza virus diversity in poultry and humans during a highly pathogenic avian influenza A (H7N7) virus outbreak.","abstract":"Although increasing data have become available that link human adaptation with specific molecular changes in nonhuman influenza viruses, the molecular changes of these viruses during a large highly pathogenic avian influenza virus (HPAI) outbreak in poultry along with avian-to-human transmission have never been documented. By comprehensive virologic analysis of combined veterinary and human samples obtained during a large HPAI A (H7N7) outbreak in the Netherlands in 2003, we mapped the acquisition of human adaptation markers to identify the public health risk associated with an HPAI outbreak in poultry. Full-length hemagglutinin (HA), neuraminidase (NA), and PB2 sequencing of A (H7N7) viruses obtained from 45 human cases showed amino acid variations at different codons in HA (n=20), NA (n=23), and PB2 (n=23). Identification of the avian sources of human virus infections based on 232 farm sequences demonstrated that for each gene about 50% of the variation was already present in poultry. Polygenic accumulation and farm-to-farm spread of known virulence and human adaptation markers in A (H7N7) virus-infected poultry occurred prior to farm-to-human transmission. These include the independent emergence of HA A143T mutants, accumulation of four NA mutations, and farm-to-farm spread of virus variants harboring mammalian host determinants D701N and S714I in PB2. This implies that HPAI viruses with pandemic potential can emerge directly from poultry. Since the public health risk of an avian influenza virus outbreak in poultry can rapidly change, we recommend virologic monitoring for human adaptation markers among poultry as well as among humans during the course of an outbreak in poultry.","corpus_id":5528879,"score":0},{"doc_id":"21880750","title":"Tissue tropism of swine influenza viruses and reassortants in ex vivo cultures of the human respiratory tract and conjunctiva.","abstract":"The 2009 pandemic influenza H1N1 (H1N1pdm) virus was generated by reassortment of swine influenza viruses of different lineages. This was the first influenza pandemic to emerge in over 4 decades and the first to occur after the realization that influenza pandemics arise from influenza viruses of animals. In order to understand the biological determinants of pandemic emergence, it is relevant to compare the tropism of different lineages of swine influenza viruses and reassortants derived from them with that of 2009 pandemic H1N1 (H1N1pdm) and seasonal influenza H1N1 viruses in ex vivo cultures of the human nasopharynx, bronchus, alveoli, and conjunctiva. We hypothesized that virus which can transmit efficiently between humans replicated well in the human upper airways. As previously reported, H1N1pdm and seasonal H1N1 viruses replicated efficiently in the nasopharyngeal, bronchial, and alveolar epithelium. In contrast, representative viruses from the classical swine (CS) (H1N1) lineage could not infect human respiratory epithelium; Eurasian avian-like swine (EA) (H1N1) viruses only infected alveolar epithelium and North American triple-reassortant (TRIG) viruses only infected the bronchial epithelium albeit inefficiently. Interestingly, a naturally occurring triple-reassortant swine virus, A/SW/HK/915/04 (H1N2), with a matrix gene segment of EA swine derivation (i.e., differing from H1N1pdm only in lacking a neuraminidase [NA] gene of EA derivation) readily infected and replicated in human nasopharyngeal and bronchial epithelia but not in the lung. A recombinant sw915 with the NA from H1N1pdm retained its tropism for the bronchus and acquired additional replication competence for alveolar epithelium. In contrast to H1N1pdm, none of the swine viruses tested nor seasonal H1N1 had tropism in human conjunctiva. Recombinant viruses generated by swapping the surface proteins (hemagglutinin and NA) of H1N1pdm and seasonal H1N1 virus demonstrated that these two gene segments together are key determinants of conjunctival tropism. Overall, these findings suggest that ex vivo cultures of the human respiratory tract provide a useful biological model for assessing the human health risk of swine influenza viruses.","corpus_id":40025853,"score":0},{"doc_id":"22230579","title":"Cloned cDNA of A/swine/Iowa/15/1930 internal genes as a candidate backbone for reverse genetics vaccine against influenza A viruses.","abstract":"Reverse genetics viruses for influenza vaccine production usually utilize the internal genes of the egg-adapted A/Puerto Rico/8/34 (PR8) strain. This egg-adapted strain provides high production yield in embryonated eggs but does not necessarily give the best yield in mammalian cell culture. In order to generate a reverse genetics viral backbone that is well-adapted to high growth in mammalian cell culture, a swine influenza isolate A/swine/Iowa/15/30 (H1N1) (rg1930) that was shown to give high yield in Madin-Darby canine kidney (MDCK) cells was used as the internal gene donor for reverse genetics plasmids. In this report, the internal genes from rg1930 were used for construction of reverse genetics viruses carrying a cleavage site-modified hemagglutinin (HA) gene and neuraminidase (NA) gene from a highly pathogenic H5N1 virus. The resulting virus (rg1930H5N1) was low pathogenic in vivo. Inactivated rg1930H5N1 vaccine completely protected chickens from morbidity and mortality after challenge with highly pathogenic H5N1. Protective immunity was obtained when chickens were immunized with an inactivated vaccine consisting of at least 2(9) HA units of the rg1930H5N1 virus. In comparison to the PR8-based reverse genetics viruses carrying the same HA and NA genes from an H5N1 virus, rg1930 based viruses yielded higher viral titers in MDCK and Vero cells. In addition, the reverse genetics derived H3N2 and H5N2 viruses with the rg1930 backbone replicated in MDCK cells better than the cognate viruses with the rgPR8 backbone. It is concluded that this newly established reverse genetics backbone system could serve as a candidate for a master donor strain for development of inactivated influenza vaccines in cell-based systems.","corpus_id":2179136,"score":0},{"doc_id":"22355413","title":"Prediction of biological functions on glycosylation site migrations in human influenza H1N1 viruses.","abstract":"Protein glycosylation alteration is typically employed by various viruses for escaping immune pressures from their hosts. Our previous work had shown that not only the increase of glycosylation sites (glycosites) numbers, but also glycosite migration might be involved in the evolution of human seasonal influenza H1N1 viruses. More importantly, glycosite migration was likely a more effectively alteration way for the host adaption of human influenza H1N1 viruses. In this study, we provided more bioinformatics and statistic evidences for further predicting the significant biological functions of glycosite migration in the host adaptation of human influenza H1N1 viruses, by employing homology modeling and in silico protein glycosylation of representative HA and NA proteins as well as amino acid variability analysis at antigenic sites of HA and NA. The results showed that glycosite migrations in human influenza viruses have at least five possible functions: to more effectively mask the antigenic sites, to more effectively protect the enzymatic cleavage sites of neuraminidase (NA), to stabilize the polymeric structures, to regulate the receptor binding and catalytic activities and to balance the binding activity of hemagglutinin (HA) with the release activity of NA. The information here can provide some constructive suggestions for the function research related to protein glycosylation of influenza viruses, although these predictions still need to be supported by experimental data.","corpus_id":6621767,"score":0},{"doc_id":"22465746","title":"Production and characterization of mammalian virus-like particles from modified vaccinia virus Ankara vectors expressing influenza H5N1 hemagglutinin and neuraminidase.","abstract":"Several studies have described the production of influenza virus-like particles (VLP) using a variety of platform systems. These VLPs are non-replicating particles that spontaneously self-assemble from expressed influenza virus proteins and have been proposed as vaccine candidates for both seasonal and pandemic influenza. Although still in the early stages of development and evaluation as influenza vaccines, influenza VLPs have a variety of other valuable uses such as examining and understanding correlates of protection against influenza and investigating virus-cell interactions. The most common production system for influenza VLPs is the baculovirus-insect cell expression which has several attractive features including the ease in which new gene combinations can be constructed, the immunogenicity elicited and protection afforded by the produced VLPs, and the scalability offered by the system. However, there are differences between the influenza VLPs produced by baculovirus expression systems in insect cells and the influenza viruses produced for use as current vaccines or the virus produced during a productive clinical infection. We describe here the development of a modified vaccinia virus Ankara (MVA) system to generate mammalian influenza VLPs containing influenza H5N1 proteins. The MVA vector system is flexible for manipulating and generating various VLP constructs, expresses high level of influenza hemagglutinin (HA), neuraminidase (NA), and matrix (M) proteins, and can be scaled up to produce VLPs in quantities sufficient for in vivo studies. We show that mammalian VLPs are generated from recombinant MVA vectors expressing H5N1 HA alone, but that increased VLP production can be achieved if NA is co-expressed. These mammalian H5N1 influenza VLPs have properties in common with live virus, as shown by electron microscopy analysis, their ability to hemagglutinate red blood cells, express neuraminidase activity, and to bind influenza specific antibodies. Importantly, these VLPs are able to elicit a protective immune response in a mouse challenge model, suggesting their utility in dissecting the correlates of immunity in such models. Mammalian derived VLPs may also provide a useful tool for studying virus-cell interactions and may have potential for development as pandemic vaccines.","corpus_id":22788930,"score":0},{"doc_id":"22718832","title":"Functional balance of the hemagglutinin and neuraminidase activities accompanies the emergence of the 2009 H1N1 influenza pandemic.","abstract":"The 2009 H1N1 influenza pandemic is the first human pandemic in decades and was of swine origin. Although swine are believed to be an intermediate host in the emergence of new human influenza viruses, there is still little known about the host barriers that keep swine influenza viruses from entering the human population. We surveyed swine progenitors and human viruses from the 2009 pandemic and measured the activities of the hemagglutinin (HA) and neuraminidase (NA), which are the two viral surface proteins that interact with host glycan receptors. A functional balance of these two activities (HA binding and NA cleavage) is found in human viruses but not in the swine progenitors. The human 2009 H1N1 pandemic virus exhibited both low HA avidity for glycan receptors as a result of mutations near the receptor binding site and weak NA enzymatic activity. Thus, a functional match between the hemagglutinin and neuraminidase appears to be necessary for efficient transmission between humans and may be an indicator of the pandemic potential of zoonotic viruses.","corpus_id":27952692,"score":0},{"doc_id":"23202513","title":"Rapid detection and differentiation of swine-origin influenza A virus (H1N1/2009) from other seasonal influenza A viruses.","abstract":"We previously developed a rapid and simple gold nanoparticle(NP)-based genomic microarray assay for identification of the avian H5N1 virus and its discrimination from other influenza A virus strains (H1N1, H3N2). In this study, we expanded the platform to detect the 2009 swine-origin influenza A virus (H1N1/2009). Multiple specific capture and intermediate oligonucleotides were designed for the matrix (M), hemagglutinin (HA), and neuraminidase (NA) genes of the H1N1/2009 virus. The H1N1/2009 microarrays were printed in the same format as those of the seasonal influenza H1N1 and H3N2 for the HA, NA, and M genes. Viral RNA was tested using capture-target-intermediate oligonucleotide hybridization and gold NP-mediated silver staining. The signal from the 4 capture-target-intermediates of the HA and NA genes was specific for H1N1/2009 virus and showed no cross hybridization with viral RNA from other influenza strains H1N1, H3N2, and H5N1. All of the 3 M gene captures showed strong affinity with H1N1/2009 viral RNA, with 2 out of the 3 M gene captures showing cross hybridization with the H1N1, H3N2, and H5N1 samples tested. The current assay was able to detect H1N1/2009 and distinguish it from other influenza A viruses. This new method may be useful for simultaneous detection and subtyping of influenza A viruses and can be rapidly modified to detect other emerging influenza strains in public health settings.","corpus_id":8510715,"score":0},{"doc_id":"23429089","title":"Composition of hemagglutinin and neuraminidase affects the antigen yield of influenza A(H1N1)pdm09 candidate vaccine viruses.","abstract":"To improve the hemagglutinin (HA) antigen yield of influenza A(H1N1)pdm09 candidate vaccine viruses, we generated 7:1, 6:2, and 5:3 genetic reassortant viruses between wild-type (H1N1)pdm09 (A/California/7/2009) (Cal7) and a high-yielding master virus, A/Puerto Rico/8/34 (PR8). These viruses contained the HA; HA and neuraminidase (NA); and HA, NA, and M genes, respectively, derived from Cal7, on a PR8 backbone. The influence of the amino acid residue at position 223 in Cal7 HA on virus growth and HA antigen yield differed between these reassortant viruses. NIIDRG-7, a 7:1 virus possessing arginine at position 223, exhibited a 10-fold higher 50% egg infectious dose (EID(50)) (10.0 log(10)EID(50)/ml) than the 5:3 and 6:2 viruses. It also had 1.5- to 3-fold higher protein (13.8 μg/ml of allantoic fluids) and HA antigen (4.1 μg/ml of allantoic fluids) yields than the 5:3 and 6:2 viruses, which possessed identical Cal7 HA proteins. However, the HA antigen yield of the other 7:1 virus, which possessed glutamine at position 223 was 60% of that of NIIDRG-7. In addition, a novel 6:2 virus possessing Cal7 HA and the NA of A/Wisconsin/10/98 (a triple reassortant swine-like H1N1 virus), produced 107% of the HA yield of NIIDRG-7. In this study, we showed that the balance between HA and NA in the influenza A(H1N1)pdm09 virus affects its protein and antigen yield.","corpus_id":8475880,"score":0},{"doc_id":"23929468","title":"Complete Genome Sequences of Novel Reassortant H1N2 Swine Influenza Viruses Isolated from Pigs in the Republic of Korea.","abstract":"Novel reassortant swine H1N2 influenza viruses were isolated from pigs in a commercial slaughterhouse in the Republic of Korea. Genome sequence analyses revealed that these isolates contain segments from Eurasian avian-like swine (hemagglutinin [HA]), Korean swine H1N2 (neuraminidase [NA]), and North American H3N2pM-like (remaining genes) viruses. Further characterization is needed to gauge the potential threats of these viruses to public health.","corpus_id":29570839,"score":0},{"doc_id":"24051313","title":"Influenza a virus with a human-like n2 gene is circulating in pigs.","abstract":"A novel reassortant influenza A virus, H1avN2hu, has been found in Danish swine. The virus contains an H1 gene similar to the hemagglutinin (HA) gene of H1N1 avian-like swine viruses and an N2 gene most closely related to the neuraminidase (NA) gene of human H3N2 viruses from the mid-1990s.","corpus_id":29890690,"score":0},{"doc_id":"24150926","title":"Hemagglutinin and neuraminidase genes of influenza B viruses circulating in Riyadh, Saudi Arabia during 2010-2011: evolution and sequence analysis.","abstract":"Influenza viruses are known as continuing threats to human public health every year worldwide. Evolutionary dynamics of influenza B viruses in humans are in a unique progression having two lineages; B/Yam and B/Vic-like viruses, which are circulating simultaneously worldwide. There is a considerable lack of data on influenza B viruses circulating in Saudi Arabia. During the winter-spring season of 2010-2011, 80 nasopharyngeal aspirates were collected from hospitalized patients with flu-like symptoms in Riyadh. Screening of samples by one-step RT-PCR identified three (3.8%) influenza B viruses. Sequencing of hemagglutinin (HA) and neuraminidase (NA) genes was performed to analyze influenza B viruses circulating in Riyadh as compared to the globally circulating strains. Several common and six unique amino acid substitutions were observed for both HA and NA genes of influenza B Saudi strains. Three unique substitutions (T182A, D196N, and K254R) were identified in HA gene of the B/Yam-like Riyadh strains. In NA gene, a unique common substitution (D53G) was found in all Riyadh strains, while two unique substitutions (L38P, G233R) were recognized only in B/Vic-like Riyadh strains. Riyadh strains were also found to contain N-glycosylation site in HA gene of both B/Vic and B/Yam lineages at positions 197-199 (NET) and 196-198 (NNK/DNK), respectively. The significance of these mutations on the antigenicity of both lineages is discussed herein. The unique changes observed in HA and NA genes of influenza B Riyadh strains support strongly the need for continuous surveillance and monitoring of new evolving strains that might pose threat to the Saudi community.","corpus_id":2898522,"score":0},{"doc_id":"24155384","title":"Activation of influenza A viruses by host proteases from swine airway epithelium.","abstract":"Pigs are important natural hosts of influenza A viruses, and due to their susceptibility to swine, avian, and human viruses, they may serve as intermediate hosts supporting adaptation and genetic reassortment. Cleavage of the influenza virus surface glycoprotein hemagglutinin (HA) by host cell proteases is essential for viral infectivity. Most influenza viruses, including human and swine viruses, are activated at a monobasic HA cleavage site, and we previously identified TMPRSS2 and HAT to be relevant proteases present in human airways. We investigated the proteolytic activation of influenza viruses in primary porcine tracheal and bronchial epithelial cells (PTEC and PBEC, respectively). Human H1N1 and H3N2 viruses replicated efficiently in PTECs and PBECs, and viruses containing cleaved HA were released from infected cells. Moreover, the cells supported the proteolytic activation of HA at the stage of entry. We found that swine proteases homologous to TMPRSS2 and HAT, designated swTMPRSS2 and swAT, respectively, were expressed in several parts of the porcine respiratory tract. Both proteases cloned from primary PBECs were shown to activate HA with a monobasic cleavage site upon coexpression and support multicycle replication of influenza viruses. swAT was predominantly localized at the plasma membrane, where it was present as an active protease that mediated activation of incoming virus. In contrast, swTMPRSS2 accumulated in the trans-Golgi network, suggesting that it cleaves HA in this compartment. In conclusion, our data show that HA activation in porcine airways may occur by similar proteases and at similar stages of the viral life cycle as in human airways.","corpus_id":20076045,"score":0},{"doc_id":"24371061","title":"Evaluation of three live attenuated H2 pandemic influenza vaccine candidates in mice and ferrets.","abstract":"UNLABELLED: H2 influenza viruses have not circulated in humans since 1968, and therefore a significant portion of the population would be susceptible to infection should H2 influenza viruses reemerge. H2 influenza viruses continue to circulate in avian reservoirs worldwide, and these reservoirs are a potential source from which these viruses could emerge. Three reassortant cold-adapted (ca) H2 pandemic influenza vaccine candidates with hemagglutinin (HA) and neuraminidase (NA) genes derived from the wild-type A/Japan/305/1957 (H2N2) (Jap/57), A/mallard/6750/1978 (H2N2) (mal/78), or A/swine/MO/4296424/2006 (H2N3) (sw/06) viruses and the internal protein gene segments from the A/Ann Arbor/6/60 ca virus were generated by plasmid-based reverse genetics (Jap/57 ca, mal/78 ca, and sw/06 ca, respectively). The vaccine candidates exhibited the in vitro phenotypes of temperature sensitivity and cold adaptation and were restricted in replication in the respiratory tract of ferrets. In mice and ferrets, the vaccines elicited neutralizing antibodies and conferred protection against homologous wild-type virus challenge. Of the three candidates, the sw/06 ca vaccine elicited cross-reactive antibodies and provided significant protection against the greatest number of heterologous viruses. These observations suggest that the sw/06 ca vaccine should be further evaluated in a clinical trial as an H2 pandemic influenza vaccine candidate. IMPORTANCE: Influenza pandemics arise when novel influenza viruses are introduced into a population with little prior immunity to the new virus and often result in higher rates of illness and death than annual seasonal influenza epidemics. An influenza H2 subtype virus caused a pandemic in 1957, and H2 viruses circulated in humans till 1968. H2 influenza viruses continue to circulate in birds, and the development of an H2 influenza vaccine candidate is therefore considered a priority in preparing for future pandemics. However, we cannot predict whether a human H2 virus will reemerge or a novel avian H2 virus will emerge. We identified three viruses as suitable candidates for further evaluation as vaccines to protect against H2 influenza viruses and evaluated the immune responses and protection that these three vaccines provided in mice and ferrets.","corpus_id":25925133,"score":0},{"doc_id":"24404173","title":"ClassyFlu: classification of influenza A viruses with Discriminatively trained profile-HMMs.","abstract":"Accurate and rapid characterization of influenza A virus (IAV) hemagglutinin (HA) and neuraminidase (NA) sequences with respect to subtype and clade is at the basis of extended diagnostic services and implicit to molecular epidemiologic studies. ClassyFlu is a new tool and web service for the classification of IAV sequences of the HA and NA gene into subtypes and phylogenetic clades using discriminatively trained profile hidden Markov models (HMMs), one for each subtype or clade. ClassyFlu merely requires as input unaligned, full-length or partial HA or NA DNA sequences. It enables rapid and highly accurate assignment of HA sequences to subtypes H1-H17 but particularly focusses on the finer grained assignment of sequences of highly pathogenic avian influenza viruses of subtype H5N1 according to the cladistics proposed by the H5N1 Evolution Working Group. NA sequences are classified into subtypes N1-N10. ClassyFlu was compared to semiautomatic classification approaches using BLAST and phylogenetics and additionally for H5 sequences to the new \"Highly Pathogenic H5N1 Clade Classification Tool\" (IRD-CT) proposed by the Influenza Research Database. Our results show that both web tools (ClassyFlu and IRD-CT), although based on different methods, are nearly equivalent in performance and both are more accurate and faster than semiautomatic classification. A retraining of ClassyFlu to altered cladistics as well as an extension of ClassyFlu to other IAV genome segments or fragments thereof is undemanding. This is exemplified by unambiguous assignment to a distinct cluster within subtype H7 of sequences of H7N9 viruses which emerged in China early in 2013 and caused more than 130 human infections. http://bioinf.uni-greifswald.de/ClassyFlu is a free web service. For local execution, the ClassyFlu source code in PERL is freely available.","corpus_id":14408947,"score":0},{"doc_id":"24429367","title":"The M segment of the 2009 pandemic influenza virus confers increased neuraminidase activity, filamentous morphology, and efficient contact transmissibility to A/Puerto Rico/8/1934-based reassortant viruses.","abstract":"UNLABELLED: The 2009 H1N1 lineage represented the first detection of a novel, highly transmissible influenza A virus genotype: six gene segments originated from the North American triple-reassortant swine lineage, and two segments, NA and M, derived from the Eurasian avian-like swine lineage. As neither parental lineage transmits efficiently between humans, the adaptations and mechanisms underlying the pandemic spread of the swine-origin 2009 strain are not clear. To help identify determinants of transmission, we used reverse genetics to introduce gene segments of an early pandemic isolate, A/Netherlands/602/2009 [H1N1] (NL602), into the background of A/Puerto Rico/8/1934 [H1N1] (PR8) and evaluated the resultant viruses in a guinea pig transmission model. Whereas the NL602 virus spread efficiently, the PR8 virus did not transmit. Swapping of the HA, NA, and M segments of NL602 into the PR8 background yielded a virus with indistinguishable contact transmissibility to the wild-type pandemic strain. Consistent with earlier reports, the pandemic M segment alone accounted for much of the improvement in transmission. To aid in understanding how the M segment might affect transmission, we evaluated neuraminidase activity and virion morphology of reassortant viruses. Transmission was found to correlate with higher neuraminidase activity and a more filamentous morphology. Importantly, we found that introduction of the pandemic M segment alone resulted in an increase in the neuraminidase activity of two pairs of otherwise isogenic PR8-based viruses. Thus, our data demonstrate the surprising result that functions encoded by the influenza A virus M segment impact neuraminidase activity and, perhaps through this mechanism, have a potent effect on transmissibility. IMPORTANCE: Our work uncovers a previously unappreciated mechanism through which the influenza A virus M segment can alter the receptor-destroying activity of an influenza virus. Concomitant with changes to neuraminidase activity, the M segment impacts the morphology of the influenza A virion and transmissibility of the virus in the guinea pig model. We suggest that changes in NA activity underlie the ability of the influenza M segment to influence virus transmissibility. Furthermore, we show that coadapted M, NA, and HA segments are required to provide optimal transmissibility to an influenza virus. The M-NA functional interaction we describe appears to underlie the prominent role of the 2009 pandemic M segment in supporting efficient transmission and may be a highly important means by which influenza A viruses restore HA/NA balance following reassortment or transfer to new host environments.","corpus_id":5992849,"score":0},{"doc_id":"24523938","title":"Phylogenetic analysis of a swine influenza A(H3N2) virus isolated in Korea in 2012.","abstract":"Influenza A virus (IAV) can infect avian and mammalian species, including humans. The genome nature of IAVs may contribute to viral adaptation in different animal hosts, resulting in gene reassortment and the reproduction of variants with optimal fitness. As seen again in the 2009 swine-origin influenza A H1N1 pandemic, pigs are known to be susceptible to swine, avian, and human IAVs and can serve as a 'mixing vessel' for the generation of novel IAV variants. To this end, the emergence of swine influenza viruses must be kept under close surveillance. Herein, we report the isolation and phylogenetic study of a swine IAV, A/swine/Korea/PL01/2012 (swPL01, H3N2 subtype). After screening nasopharyngeal samples from pigs in the Gyeongsangnam-do region of Korea from December 2011 to May 2012, we isolated the swPL01 virus and sequenced its all of 8 genome segments (polymerase basic 2, PB2; polymerase basic 1, PB1; polymerase acidic, PA; hemagglutinin, HA; nucleocapsid protein, NP; neuraminidase, NA; matrix protein, M; and nonstructural protein, NS). The phylogenetic study, analyzed with reference strains registered in the National Center for Biotechnology Information (NCBI) database, indicated that the swPL01 virus was similar to the North American triple-reassortant swine strains and that the HA gene of the swPL01 virus was categorized into swine H3 cluster IV. The swPL01 virus had the M gene of the triple-reassortant swine H3N2 viruses, whereas that of other contemporary strains in Korea was transferred from the 2009 pandemic H1N1 virus. These data suggest the possibility that various swine H3N2 viruses may co-circulate in Korea, which underlines the importance of a sustained surveillance system against swine IAVs.","corpus_id":4586165,"score":0},{"doc_id":"24579700","title":"T-cell immunity to influenza A viruses.","abstract":"Influenza infection remains a global threat to human health. Influenza viruses are normally controlled by antibodies specific for the surface glycoproteins hemagglutinin (HA) and neuraminidase (NA). Standard influenza vaccines are aimed at inducing these antibodies, but they must be administered annually and can be rendered ineffective since different strains circulate from year to year and vary considerably in their individual HA and NA profiles. Influenza-specific T cells have been shown to be protective in animal models and typically recognize the more conserved internal influenza proteins. Improving our understanding of influenza-specific T-cell responses, including immunodominance, specific epitope sequences, strain-related epitope variation, host/virus interaction, and the balance between immunity versus immunopathology, will be important to improve future T-cell-based vaccines, which promise broader strain coverage and longer-lasting protection than current standard vaccines.","corpus_id":34087472,"score":0},{"doc_id":"24582528","title":"Bat-derived influenza-like viruses H17N10 and H18N11.","abstract":"Shorebirds and waterfowls are believed to be the reservoir hosts for influenza viruses, whereas swine putatively act as mixing vessels. The recent identification of two influenza-like virus genomes (designated H17N10 and H18N11) from bats has challenged this notion. A crucial question concerns the role bats might play in influenza virus ecology. Structural and functional studies of the two major surface envelope proteins, hemagglutinin (HA) and neuraminidase (NA), demonstrate that neither has canonical HA or NA functions found in influenza viruses. However, putative functional modules and domains in other encoded proteins are conserved, and the N-terminal domain of the H17N10 polymerase subunit PA has a classical structure and function. Therefore, potential genomic reassortments of such influenza-like viruses with canonical influenza viruses cannot be excluded at this point and should be assessed.","corpus_id":7606490,"score":0},{"doc_id":"24809455","title":"Understanding the undelaying mechanism of HA-subtyping in the level of physic-chemical characteristics of protein.","abstract":"The evolution of the influenza A virus to increase its host range is a major concern worldwide. Molecular mechanisms of increasing host range are largely unknown. Influenza surface proteins play determining roles in reorganization of host-sialic acid receptors and host range. In an attempt to uncover the physic-chemical attributes which govern HA subtyping, we performed a large scale functional analysis of over 7000 sequences of 16 different HA subtypes. Large number (896) of physic-chemical protein characteristics were calculated for each HA sequence. Then, 10 different attribute weighting algorithms were used to find the key characteristics distinguishing HA subtypes. Furthermore, to discover machine leaning models which can predict HA subtypes, various Decision Tree, Support Vector Machine, Naïve Bayes, and Neural Network models were trained on calculated protein characteristics dataset as well as 10 trimmed datasets generated by attribute weighting algorithms. The prediction accuracies of the machine learning methods were evaluated by 10-fold cross validation. The results highlighted the frequency of Gln (selected by 80% of attribute weighting algorithms), percentage/frequency of Tyr, percentage of Cys, and frequencies of Try and Glu (selected by 70% of attribute weighting algorithms) as the key features that are associated with HA subtyping. Random Forest tree induction algorithm and RBF kernel function of SVM (scaled by grid search) showed high accuracy of 98% in clustering and predicting HA subtypes based on protein attributes. Decision tree models were successful in monitoring the short mutation/reassortment paths by which influenza virus can gain the key protein structure of another HA subtype and increase its host range in a short period of time with less energy consumption. Extracting and mining a large number of amino acid attributes of HA subtypes of influenza A virus through supervised algorithms represent a new avenue for understanding and predicting possible future structure of influenza pandemics.","corpus_id":14595349,"score":0},{"doc_id":"25047593","title":"In silico structural homology modelling and docking for assessment of pandemic potential of a novel H7N9 influenza virus and its ability to be neutralized by existing anti-hemagglutinin antibodies.","abstract":"The unpredictable nature of pandemic influenza and difficulties in early prediction of pandemic potential of new isolates present a major challenge for health planners. Vaccine manufacturers, in particular, are reluctant to commit resources to development of a new vaccine until after a pandemic is declared. We hypothesized that a structural bioinformatics approach utilising homology-based molecular modelling and docking approaches would assist prediction of pandemic potential of new influenza strains alongside more traditional laboratory and sequence-based methods. The newly emerged Chinese A/Hangzhou/1/2013 (H7N9) influenza virus provided a real-life opportunity to test this hypothesis. We used sequence data and a homology-based approach to construct a 3D-structural model of H7-Hangzhou hemagglutinin (HA) protein. This model was then used to perform docking to human and avian sialic acid receptors to assess respective binding affinities. The model was also used to perform docking simulations with known neutralizing antibodies to assess their ability to neutralize the newly emerged virus. The model predicted H7N9 could bind to human sialic acid receptors thereby indicating pandemic potential. The model also confirmed that existing antibodies against the HA head region are unable to neutralise H7N9 whereas antibodies, e.g. Cr9114, targeting the HA stalk region should bind with high affinity to H7N9. This indicates that existing stalk antibodies initially raised against H5N1 or other influenza A viruses could be therapeutically beneficial in prevention and/or treatment of H7N9 infections. The subsequent publication of the H7N9 HA crystal structure confirmed the accuracy of our in-silico structural model. Antibody docking studies performed using the H7N9 HA crystal structure supported the model's prediction that existing stalk antibodies could cross-neutralise the H7N9 virus. This study demonstrates the value of using in-silico structural modelling approaches to complement physical studies in characterization of new influenza viruses.","corpus_id":16990134,"score":0},{"doc_id":"25122789","title":"The matrix gene segment destabilizes the acid and thermal stability of the hemagglutinin of pandemic live attenuated influenza virus vaccines.","abstract":"UNLABELLED: The threat of future influenza pandemics and their potential for rapid spread, morbidity, and mortality has led to the development of pandemic vaccines. We generated seven reassortant pandemic live attenuated influenza vaccines (pLAIVs) with the hemagglutinin (HA) and neuraminidase (NA) genes derived from animal influenza viruses on the backbone of the six internal protein gene segments of the temperature sensitive, cold-adapted (ca) A/Ann Arbor/60 (H2N2) virus (AA/60 ca) of the licensed seasonal LAIV. The pLAIV viruses were moderately to highly restricted in replication in seronegative adults; we sought to determine the biological basis for this restriction. Avian influenza viruses generally replicate at higher temperatures than human influenza viruses and, although they shared the same backbone, the pLAIV viruses had a lower shutoff temperature than seasonal LAIV viruses, suggesting that the HA and NA influence the degree of temperature sensitivity. The pH of HA activation of highly pathogenic avian influenza viruses was greater than human and low-pathogenicity avian influenza viruses, as reported by others. However, pLAIV viruses had a consistently higher pH of HA activation and reduced HA thermostability compared to the corresponding wild-type parental viruses. From studies with single-gene reassortant viruses bearing one gene segment from the AA/60 ca virus in recombinant H5N1 or pH1N1 viruses, we found that the lower HA thermal stability and increased pH of HA activation were associated with the AA/60 M gene. Together, the impaired HA acid and thermal stability and temperature sensitivity likely contributed to the restricted replication of the pLAIV viruses we observed in seronegative adults. IMPORTANCE: There is increasing evidence that the HA stability of influenza viruses depends on the virus strain and host species and that HA stability can influence replication, virulence, and transmission of influenza A viruses in different species. We investigated the HA stability of pandemic live attenuated influenza vaccine (pLAIV) viruses and observed that the pLAIV viruses consistently had a less stable HA than the corresponding wild-type influenza viruses. The reduced HA stability and temperature sensitivity of the pLAIV viruses may account for their restricted replication in clinical trials.","corpus_id":40923043,"score":0},{"doc_id":"25762737","title":"Swine Influenza Virus PA and Neuraminidase Gene Reassortment into Human H1N1 Influenza Virus Is Associated with an Altered Pathogenic Phenotype Linked to Increased MIP-2 Expression.","abstract":"UNLABELLED: Swine are susceptible to infection by both avian and human influenza viruses, and this feature is thought to contribute to novel reassortant influenza viruses. In this study, the influenza virus reassortment rate in swine and human cells was determined. Coinfection of swine cells with 2009 pandemic H1N1 virus (huH1N1) and an endemic swine H1N2 (A/swine/Illinois/02860/09) virus (swH1N2) resulted in a 23% reassortment rate that was independent of α2,3- or α2,6-sialic acid distribution on the cells. The reassortants had altered pathogenic phenotypes linked to introduction of the swine virus PA and neuraminidase (NA) into huH1N1. In mice, the huH1N1 PA and NA mediated increased MIP-2 expression early postinfection, resulting in substantial pulmonary neutrophilia with enhanced lung pathology and disease. The findings support the notion that swine are a mixing vessel for influenza virus reassortants independent of sialic acid distribution. These results show the potential for continued reassortment of the 2009 pandemic H1N1 virus with endemic swine viruses and for reassortants to have increased pathogenicity linked to the swine virus NA and PA genes which are associated with increased pulmonary neutrophil trafficking that is related to MIP-2 expression. IMPORTANCE: Influenza A viruses can change rapidly via reassortment to create a novel virus, and reassortment can result in possible pandemics. Reassortments among subtypes from avian and human viruses led to the 1957 (H2N2 subtype) and 1968 (H3N2 subtype) human influenza pandemics. Recent analyses of circulating isolates have shown that multiple genes can be recombined from human, avian, and swine influenza viruses, leading to triple reassortants. Understanding the factors that can affect influenza A virus reassortment is needed for the establishment of disease intervention strategies that may reduce or preclude pandemics. The findings from this study show that swine cells provide a mixing vessel for influenza virus reassortment independent of differential sialic acid distribution. The findings also establish that circulating neuraminidase (NA) and PA genes could alter the pathogenic phenotype of the pandemic H1N1 virus, resulting in enhanced disease. The identification of such factors provides a framework for pandemic modeling and surveillance.","corpus_id":206790500,"score":0},{"doc_id":"25810540","title":"Pandemic Swine H1N1 Influenza Viruses with Almost Undetectable Neuraminidase Activity Are Not Transmitted via Aerosols in Ferrets and Are Inhibited by Human Mucus but Not Swine Mucus.","abstract":"UNLABELLED: A balance between the functions of the influenza virus surface proteins hemagglutinin (HA) and neuraminidase (NA) is thought to be important for the transmission of viruses between humans. Here we describe two pandemic H1N1 viruses, A/swine/Virginia/1814-1/2012 and A/swine/Virginia/1814-2/2012 (pH1N1low-1 and -2, respectively), that were isolated from swine symptomatic for influenza. The enzymatic activity of the NA of these viruses was almost undetectable, while the HA binding affinity for α2,6 sialic acids was greater than that of the highly homologous pH1N1 viruses A/swine/Pennsylvania/2436/2012 and A/swine/Minnesota/2499/2012 (pH1N1-1 and -2), which exhibited better-balanced HA and NA activities. The in vitro growth kinetics of pH1N1low and pH1N1 viruses were similar, but aerosol transmission of pH1N1low-1 was abrogated and transmission via direct contact in ferrets was significantly impaired compared to pH1N1-1, which transmitted by direct and aerosol contact. In normal human bronchial epithelial cells, pH1N1low-1 was significantly inhibited by mucus but pH1N1-1 was not. In Madin-Darby canine kidney cell cultures overlaid with human or swine mucus, human mucus inhibited pH1N1low-1 but swine mucus did not. These data show that the interaction between viruses and mucus may be an important factor in viral transmissibility and could be a barrier for interspecies transmission between humans and swine for influenza viruses. IMPORTANCE: A balance between the functions of the influenza virus surface proteins hemagglutinin (HA) and neuraminidase (NA) is thought to be important for transmission of viruses from swine to humans. Here we show that a swine virus with extremely functionally mismatched HA and NAs (pH1N1low-1) cannot transmit via aerosol in ferrets, while another highly homologous virus with HA and NAs that are better matched functionally (pH1N1-1) can transmit via aerosol. These viruses show similar growth kinetics in Madin-Darby canine kidney (MDCK) cells, but pH1N1low-1 is significantly inhibited by mucus in normal human bronchial epithelial cells whereas pH1N1-1 is not. Further, human mucus could inhibit these viruses, but swine mucus could not. These data show that the interaction between viruses and mucus may be an important factor in viral transmissibility and could be a species barrier between humans and swine for influenza viruses.","corpus_id":43108163,"score":0},{"doc_id":"25812763","title":"Transmission of influenza A viruses.","abstract":"Influenza A viruses cause respiratory infections that range from asymptomatic to deadly in humans. Widespread outbreaks (pandemics) are attributable to 'novel' viruses that possess a viral hemagglutinin (HA) gene to which humans lack immunity. After a pandemic, these novel viruses form stable virus lineages in humans and circulate until they are replaced by other novel viruses. The factors and mechanisms that facilitate virus transmission among hosts and the establishment of novel lineages are not completely understood, but the HA and basic polymerase 2 (PB2) proteins are thought to play essential roles in these processes by enabling avian influenza viruses to infect mammals and replicate efficiently in their new host. Here, we summarize our current knowledge of the contributions of HA, PB2, and other viral components to virus transmission and the formation of new virus lineages.","corpus_id":25306860,"score":0},{"doc_id":"26049044","title":"Evolutionary trajectories and diagnostic challenges of potentially zoonotic avian influenza viruses H5N1 and H9N2 co-circulating in Egypt.","abstract":"In Egypt, since 2006, descendants of the highly pathogenic avian influenza virus (HP AIV) H5N1 of clade 2.2 continue to cause sharp losses in poultry production and seriously threaten public health. Potentially zoonotic H9N2 viruses established an endemic status in poultry in Egypt as well and co-circulate with HP AIV H5N1 rising concerns of reassortments between H9N2 and H5N1 viruses along with an increase of mixed infections of poultry. Nucleotide sequences of whole genomes of 15 different isolates (H5N1: 7; H9N2: 8), and of the hemagglutinin (HA) and neuraminidase (NA) encoding segments of nine further clinical samples (H5N1: 2; H9N2: 7) from 2013 and 2014 were generated and analysed. The HA of H5N1 viruses clustered with clade 2.2.1 while the H9 HA formed three distinguishable subgroups within cluster B viruses. BEAST analysis revealed that H9N2 viruses are likely present in Egypt since 2009. Several previously undescribed substituting mutations putatively associated with host tropism and virulence modulation were detected in different proteins of the analysed H9N2 and H5N1 viruses. Reassortment between HP AIV H5N1 and H9N2 is anticipated in Egypt, and timely detection of such events is of public health concern. As a rapid tool for detection of such reassortants discriminative SYBR-Green reverse transcription real-time PCR assays (SG-RT-qPCR), targeting the internal genes of the Egyptian H5N1 and H9N2 viruses were developed for the rapid screening of viral RNAs from both virus isolates and clinical samples. However, in accordance to Sanger sequencing, no reassortants were found by SG-RT-qPCR. Nevertheless, the complex epidemiology of avian influenza in poultry in Egypt will require sustained close observation. Further development and continuing adaptation of rapid and cost-effective screening assays such as the SG-RT-qPCR protocol developed here are at the basis of efforts for improvement the currently critical situation.","corpus_id":1763820,"score":0},{"doc_id":"26091504","title":"In Silico Prediction and Experimental Confirmation of HA Residues Conferring Enhanced Human Receptor Specificity of H5N1 Influenza A Viruses.","abstract":"Newly emerging influenza A viruses (IAV) pose a major threat to human health by causing seasonal epidemics and/or pandemics, the latter often facilitated by the lack of pre-existing immunity in the general population. Early recognition of candidate pandemic influenza viruses (CPIV) is of crucial importance for restricting virus transmission and developing appropriate therapeutic and prophylactic strategies including effective vaccines. Often, the pandemic potential of newly emerging IAV is only fully recognized once the virus starts to spread efficiently causing serious disease in humans. Here, we used a novel phylogenetic algorithm based on the informational spectrum method (ISM) to identify potential CPIV by predicting mutations in the viral hemagglutinin (HA) gene that are likely to (differentially) affect critical interactions between the HA protein and target cells from bird and human origin, respectively. Predictions were subsequently validated by generating pseudotyped retrovirus particles and genetically engineered IAV containing these mutations and characterizing potential effects on virus entry and replication in cells expressing human and avian IAV receptors, respectively. Our data suggest that the ISM-based algorithm is suitable to identify CPIV among IAV strains that are circulating in animal hosts and thus may be a new tool for assessing pandemic risks associated with specific strains.","corpus_id":25331462,"score":0},{"doc_id":"26292325","title":"Unique Determinants of Neuraminidase Inhibitor Resistance among N3, N7, and N9 Avian Influenza Viruses.","abstract":"UNLABELLED: Human infections with avian influenza viruses are a serious public health concern. The neuraminidase (NA) inhibitors (NAIs) are the frontline anti-influenza drugs and are the major option for treatment of newly emerging influenza. Therefore, it is essential to identify the molecular markers of NAI resistance among specific NA subtypes of avian influenza viruses to help guide clinical management. NAI-resistant substitutions in NA subtypes other than N1 and N2 have been poorly studied. Here, we identified NA amino acid substitutions associated with NAI resistance among influenza viruses of N3, N7, and N9 subtypes which have been associated with zoonotic transmission. We applied random mutagenesis and generated recombinant influenza viruses carrying single or double NA substitution(s) with seven internal genes from A/Puerto Rico/8/1934 (H1N1) virus. In a fluorescence-based NA inhibition assay, we identified three categories of NA substitutions associated with reduced inhibition by NAIs (oseltamivir, zanamivir, and peramivir): (i) novel subtype-specific substitutions in or near the enzyme catalytic site (R152W, A246T, and D293N, N2 numbering), (ii) subtype-independent substitutions (E119G/V and/or D and R292K), and (iii) substitutions previously reported in other subtypes (Q136K, I222M, and E276D). Our data show that although some markers of resistance are present across NA subtypes, other subtype-specific markers can only be determined empirically. IMPORTANCE: The number of humans infected with avian influenza viruses is increasing, raising concerns of the emergence of avian influenza viruses resistant to neuraminidase (NA) inhibitors (NAIs). Since most studies have focused on NAI-resistance in human influenza viruses, we investigated the molecular changes in NA that could confer NAI resistance in avian viruses grown in immortalized monolayer cells, especially those of the N3, N7, and N9 subtypes, which have caused human infections. We identified not only numerous NAI-resistant substitutions previously reported in other NA subtypes but also several novel changes conferring reduced susceptibility to NAIs, which are subtype specific. The findings indicate that some resistance markers are common across NA subtypes, but other markers need to be determined empirically for each subtype. The study also implies that antiviral surveillance monitoring could play a critical role in the clinical management of influenza virus infection and an essential component of pandemic preparedness.","corpus_id":25503607,"score":0},{"doc_id":"26311895","title":"Novel Reassortant Human-Like H3N2 and H3N1 Influenza A Viruses Detected in Pigs Are Virulent and Antigenically Distinct from Swine Viruses Endemic to the United States.","abstract":"UNLABELLED: Human-like swine H3 influenza A viruses (IAV) were detected by the USDA surveillance system. We characterized two novel swine human-like H3N2 and H3N1 viruses with hemagglutinin (HA) genes similar to those in human seasonal H3 strains and internal genes closely related to those of 2009 H1N1 pandemic viruses. The H3N2 neuraminidase (NA) was of the contemporary human N2 lineage, while the H3N1 NA was of the classical swine N1 lineage. Both viruses were antigenically distant from swine H3 viruses that circulate in the United States and from swine vaccine strains and also showed antigenic drift from human seasonal H3N2 viruses. Their pathogenicity and transmission in pigs were compared to those of a human H3N2 virus with a common HA ancestry. Both swine human-like H3 viruses efficiently infected pigs and were transmitted to indirect contacts, whereas the human H3N2 virus did so much less efficiently. To evaluate the role of genes from the swine isolates in their pathogenesis, reverse genetics-generated reassortants between the swine human-like H3N1 virus and the seasonal human H3N2 virus were tested in pigs. The contribution of the gene segments to virulence was complex, with the swine HA and internal genes showing effects in vivo. The experimental infections indicate that these novel H3 viruses are virulent and can sustain onward transmission in pigs, and the naturally occurring mutations in the HA were associated with antigenic divergence from H3 IAV from humans and swine. Consequently, these viruses could have a significant impact on the swine industry if they were to cause more widespread outbreaks, and the potential risk of these emerging swine IAV to humans should be considered. IMPORTANCE: Pigs are important hosts in the evolution of influenza A viruses (IAV). Human-to-swine transmissions of IAV have resulted in the circulation of reassortant viruses containing human-origin genes in pigs, greatly contributing to the diversity of IAV in swine worldwide. New human-like H3N2 and H3N1 viruses that contain a mix of human and swine gene segments were recently detected by the USDA surveillance system. The human-like viruses efficiently infected pigs and resulted in onward airborne transmission, likely due to the multiple changes identified between human and swine H3 viruses. The human-like swine viruses are distinct from contemporary U.S. H3 swine viruses and from the strains used in swine vaccines, which could have a significant impact on the swine industry due to a lack of population immunity. Additionally, public health experts should consider an appropriate assessment of the risk of these emerging swine H3 viruses for the human population.","corpus_id":24388382,"score":0},{"doc_id":"27314023","title":"Using the Relevance Vector Machine Model Combined with Local Phase Quantization to Predict Protein-Protein Interactions from Protein Sequences.","abstract":"We propose a novel computational method known as RVM-LPQ that combines the Relevance Vector Machine (RVM) model and Local Phase Quantization (LPQ) to predict PPIs from protein sequences. The main improvements are the results of representing protein sequences using the LPQ feature representation on a Position Specific Scoring Matrix (PSSM), reducing the influence of noise using a Principal Component Analysis (PCA), and using a Relevance Vector Machine (RVM) based classifier. We perform 5-fold cross-validation experiments on Yeast and Human datasets, and we achieve very high accuracies of 92.65% and 97.62%, respectively, which is significantly better than previous works. To further evaluate the proposed method, we compare it with the state-of-the-art support vector machine (SVM) classifier on the Yeast dataset. The experimental results demonstrate that our RVM-LPQ method is obviously better than the SVM-based method. The promising experimental results show the efficiency and simplicity of the proposed method, which can be an automatic decision support tool for future proteomics research.","corpus_id":479168,"score":0},{"doc_id":"28082971","title":"Tracking the Evolution of Polymerase Genes of Influenza A Viruses during Interspecies Transmission between Avian and Swine Hosts.","abstract":"Human influenza pandemics have historically been caused by reassortant influenza A viruses using genes from human and avian viruses. This genetic reassortment between human and avian viruses has been known to occur in swine during viral circulation, as swine are capable of circulating both avian and human viruses. Therefore, avian-to-swine transmission of viruses plays an important role in the emergence of new pandemic strains. The amino acids at several positions on PB2, PB1, and PA are known to determine the host range of influenza A viruses. In this paper, we track viral transmission between avian and swine to investigate the evolution on polymerase genes associated with their hosts. We traced viral transmissions between avian and swine hosts by using nucleotide sequences of avian viruses and swine viruses registered in the NCBI GenBank. Using BLAST and the reciprocal best hits technique, we found 32, 33, and 30 pairs of avian and swine nucleotide sequences that may be associated with avian-to-swine transmissions for PB2, PB1, and PA genes, respectively. Then, we examined the amino acid substitutions involved in these sporadic transmissions. On average, avian-to-swine transmission pairs had 5.47, 3.73, and 5.13 amino acid substitutions on PB2, PB1, and PA, respectively. However, amino acid substitutions were distributed over the positions, and few positions showed common substitutions in the multiple transmission events. Statistical tests on the number of repeated amino acid substitutions suggested that no specific positions on PB2 and PA may be required for avian viruses to infect swine. We also found that avian viruses that transmitted to swine tend to process I478V substitutions on PB2 before interspecies transmission events. Furthermore, most mutations occurred after the interspecies transmissions, possibly due to selective viral adaptation to swine.","corpus_id":10366069,"score":0},{"doc_id":"28492483","title":"PCVMZM: Using the Probabilistic Classification Vector Machines Model Combined with a Zernike Moments Descriptor to Predict Protein-Protein Interactions from Protein Sequences.","abstract":"Protein-protein interactions (PPIs) are essential for most living organisms' process. Thus, detecting PPIs is extremely important to understand the molecular mechanisms of biological systems. Although many PPIs data have been generated by high-throughput technologies for a variety of organisms, the whole interatom is still far from complete. In addition, the high-throughput technologies for detecting PPIs has some unavoidable defects, including time consumption, high cost, and high error rate. In recent years, with the development of machine learning, computational methods have been broadly used to predict PPIs, and can achieve good prediction rate. In this paper, we present here PCVMZM, a computational method based on a Probabilistic Classification Vector Machines (PCVM) model and Zernike moments (ZM) descriptor for predicting the PPIs from protein amino acids sequences. Specifically, a Zernike moments (ZM) descriptor is used to extract protein evolutionary information from Position-Specific Scoring Matrix (PSSM) generated by Position-Specific Iterated Basic Local Alignment Search Tool (PSI-BLAST). Then, PCVM classifier is used to infer the interactions among protein. When performed on PPIs datasets of Yeast and H. Pylori, the proposed method can achieve the average prediction accuracy of 94.48% and 91.25%, respectively. In order to further evaluate the performance of the proposed method, the state-of-the-art support vector machines (SVM) classifier is used and compares with the PCVM model. Experimental results on the Yeast dataset show that the performance of PCVM classifier is better than that of SVM classifier. The experimental results indicate that our proposed method is robust, powerful and feasible, which can be used as a helpful tool for proteomics research.","corpus_id":4418482,"score":0}],"string":"[\n {\n \"doc_id\": \"21109586\",\n \"title\": \"Charting the host adaptation of influenza viruses.\",\n \"abstract\": \"Four influenza pandemics have struck the human population during the last 100 years causing substantial morbidity and mortality. The pandemics were caused by the introduction of a new virus into the human population from an avian or swine host or through the mixing of virus segments from an animal host with a human virus to create a new reassortant subtype virus. Understanding which changes have contributed to the adaptation of the virus to the human host is essential in assessing the pandemic potential of current and future animal viruses. Here, we develop a measure of the level of adaptation of a given virus strain to a particular host. We show that adaptation to the human host has been gradual with a timescale of decades and that none of the virus proteins have yet achieved full adaptation to the selective constraints. When the measure is applied to historical data, our results indicate that the 1918 influenza virus had undergone a period of preadaptation prior to the 1918 pandemic. Yet, ancestral reconstruction of the avian virus that founded the classical swine and 1918 human influenza lineages shows no evidence that this virus was exceptionally preadapted to humans. These results indicate that adaptation to humans occurred following the initial host shift from birds to mammals, including a significant amount prior to 1918. The 2009 pandemic virus seems to have undergone preadaptation to human-like selective constraints during its period of circulation in swine. Ancestral reconstruction along the human virus tree indicates that mutations that have increased the adaptation of the virus have occurred preferentially along the trunk of the tree. The method should be helpful in assessing the potential of current viruses to found future epidemics or pandemics.\",\n \"corpus_id\": 18123073,\n \"score\": 2\n },\n {\n \"doc_id\": \"24418567\",\n \"title\": \"Accurate classification and hemagglutinin amino acid signatures for influenza A virus host-origin association and subtyping.\",\n \"abstract\": \"Host-origin classification and signatures of influenza A viruses were investigated based on the HA protein for tracking of the HA host of origin. Hidden Markov models (HMMs), decision trees and associative classification for each influenza A virus subtype and its major hosts (human, avian, swine) were generated. Features of the HA protein signatures that were host-and subtype-specific were sought. Host-associated signatures that occurred in different subtypes of the virus were identified. Evaluation of the classification models based on ROC curves and support and confidence ratings for the amino acid class-association rules was performed. Host classification based on the HA subtype achieved accuracies between 91.2% and 100% using decision trees after feature selection. Host-specific class association rules for avian-host origins gave better support and confidence ratings, followed by human and finally swine origin. This finding indicated the lower specificity of the swine host, perhaps pointing to its ability to mix different strains.\",\n \"corpus_id\": 3939071,\n \"score\": 2\n },\n {\n \"doc_id\": \"25521718\",\n \"title\": \"Predicting host tropism of influenza A virus proteins using random forest.\",\n \"abstract\": \"BACKGROUND: Majority of influenza A viruses reside and circulate among animal populations, seldom infecting humans due to host range restriction. Yet when some avian strains do acquire the ability to overcome species barrier, they might become adapted to humans, replicating efficiently and causing diseases, leading to potential pandemic. With the huge influenza A virus reservoir in wild birds, it is a cause for concern when a new influenza strain emerges with the ability to cross host species barrier, as shown in light of the recent H7N9 outbreak in China. Several influenza proteins have been shown to be major determinants in host tropism. Further understanding and determining host tropism would be important in identifying zoonotic influenza virus strains capable of crossing species barrier and infecting humans. RESULTS: In this study, computational models for 11 influenza proteins have been constructed using the machine learning algorithm random forest for prediction of host tropism. The prediction models were trained on influenza protein sequences isolated from both avian and human samples, which were transformed into amino acid physicochemical properties feature vectors. The results were highly accurate prediction models (ACC>96.57; AUC>0.980; MCC>0.916) capable of determining host tropism of individual influenza proteins. In addition, features from all 11 proteins were used to construct a combined model to predict host tropism of influenza virus strains. This would help assess a novel influenza strain's host range capability. CONCLUSIONS: From the prediction models constructed, all achieved high prediction performance, indicating clear distinctions in both avian and human proteins. When used together as a host tropism prediction system, zoonotic strains could potentially be identified based on different protein prediction results. Understanding and predicting host tropism of influenza proteins lay an important foundation for future work in constructing computation models capable of directly predicting interspecies transmission of influenza viruses. The models are available for prediction at http://fluleap.bic.nus.edu.sg.\",\n \"corpus_id\": 6263991,\n \"score\": 2\n },\n {\n \"doc_id\": \"26915079\",\n \"title\": \"Distinct Host Tropism Protein Signatures to Identify Possible Zoonotic Influenza A Viruses.\",\n \"abstract\": \"Zoonotic influenza A viruses constantly pose a health threat to humans as novel strains occasionally emerge from the avian population to cause human infections. Many past epidemic as well as pandemic strains have originated from avian species. While most viruses are restricted to their primary hosts, zoonotic strains can sometimes arise from mutations or reassortment, leading them to acquire the capability to escape host species barrier and successfully infect a new host. Phylogenetic analyses and genetic markers are useful in tracing the origins of zoonotic infections, but there are still no effective means to identify high risk strains prior to an outbreak. Here we show that distinct host tropism protein signatures can be used to identify possible zoonotic strains in avian species which have the potential to cause human infections. We have discovered that influenza A viruses can now be classified into avian, human, or zoonotic strains based on their host tropism protein signatures. Analysis of all influenza A viruses with complete proteome using the host tropism prediction system, based on machine learning classifications of avian and human viral proteins has uncovered distinct signatures of zoonotic strains as mosaics of avian and human viral proteins. This is in contrast with typical avian or human strains where they show mostly avian or human viral proteins in their signatures respectively. Moreover, we have found that zoonotic strains from the same influenza outbreaks carry similar host tropism protein signatures characteristic of a common ancestry. Our results demonstrate that the distinct host tropism protein signature in zoonotic strains may prove useful in influenza surveillance to rapidly identify potential high risk strains circulating in avian species, which may grant us the foresight in anticipating an impending influenza outbreak.\",\n \"corpus_id\": 24472396,\n \"score\": 2\n },\n {\n \"doc_id\": \"28361670\",\n \"title\": \"Prediction of virus-host infectious association by supervised learning methods.\",\n \"abstract\": \"BACKGROUND: The study of virus-host infectious association is important for understanding the functions and dynamics of microbial communities. Both cellular and fractionated viral metagenomic data generate a large number of viral contigs with missing host information. Although relative simple methods based on the similarity between the word frequency vectors of viruses and bacterial hosts have been developed to study virus-host associations, the problem is significantly understudied. We hypothesize that machine learning methods based on word frequencies can be efficiently used to study virus-host infectious associations. METHODS: We investigate four different representations of word frequencies of viral sequences including the relative word frequency and three normalized word frequencies by subtracting the number of expected from the observed word counts. We also study five machine learning methods including logistic regression, support vector machine, random forest, Gaussian naive Bayes and Bernoulli naive Bayes for separating infectious from non-infectious viruses for nine bacterial host genera with at least 45 infecting viruses. Area under the receiver operating characteristic curve (AUC) is used to compare the performance of different machine learning method and feature combinations. We then evaluate the performance of the best method for the identification of the hosts of contigs in metagenomic studies. We also develop a maximum likelihood method to estimate the fraction of true infectious viruses for a given host in viral tagging experiments. RESULTS: Based on nine bacterial host genera with at least 45 infectious viruses, we show that random forest together with the relative word frequency vector performs the best in identifying viruses infecting particular hosts. For all the nine host genera, the AUC is over 0.85 and for five of them, the AUC is higher than 0.98 when the word size is 6 indicating the high accuracy of using machine learning approaches for identifying viruses infecting particular hosts. We also show that our method can predict the hosts of viral contigs of length at least 1kbps in metagenomic studies with high accuracy. The random forest together with word frequency vector outperforms current available methods based on Manhattan and [Formula: see text] dissimilarity measures. Based on word frequencies, we estimate that about 95% of the identified T4-like viruses in viral tagging experiment infect Synechococcus, while only about 29% of the identified non-T4-like viruses and 30% of the contigs in the study potentially infect Synechococcus. CONCLUSIONS: The random forest machine learning method together with the relative word frequencies as features of viruses can be used to predict viruses and viral contigs for specific bacterial hosts. The maximum likelihood approach can be used to estimate the fraction of true infectious associated viruses in viral tagging experiments.\",\n \"corpus_id\": 5452774,\n \"score\": 2\n },\n {\n \"doc_id\": \"28587080\",\n \"title\": \"Predicting Zoonotic Risk of Influenza A Viruses from Host Tropism Protein Signature Using Random Forest.\",\n \"abstract\": \"Influenza A viruses remain a significant health problem, especially when a novel subtype emerges from the avian population to cause severe outbreaks in humans. Zoonotic viruses arise from the animal population as a result of mutations and reassortments, giving rise to novel strains with the capability to evade the host species barrier and cause human infections. Despite progress in understanding interspecies transmission of influenza viruses, we are no closer to predicting zoonotic strains that can lead to an outbreak. We have previously discovered distinct host tropism protein signatures of avian, human and zoonotic influenza strains obtained from host tropism predictions on individual protein sequences. Here, we apply machine learning approaches on the signatures to build a computational model capable of predicting zoonotic strains. The zoonotic strain prediction model can classify avian, human or zoonotic strains with high accuracy, as well as providing an estimated zoonotic risk. This would therefore allow us to quickly determine if an influenza virus strain has the potential to be zoonotic using only protein sequences. The swift identification of potential zoonotic strains in the animal population using the zoonotic strain prediction model could provide us with an early indication of an imminent influenza outbreak.\",\n \"corpus_id\": 430918,\n \"score\": 2\n },\n {\n \"doc_id\": \"29060087\",\n \"title\": \"Prediction of Influenza A virus infections in humans using an Artificial Neural Network learning approach.\",\n \"abstract\": \"The Influenza type A virus can be considered as one of the most severe viruses that can infect multiple species with often fatal consequences to the hosts. The Haemagglutinin (HA) gene of the virus has the potential to be a target for antiviral drug development realised through accurate identification of its sub-types and possible the targeted hosts. In this paper, to accurately predict if an Influenza type A virus has the capability to infect human hosts, by using only the HA gene, is therefore developed and tested. The predictive model follows three main steps; (i) decoding the protein sequences into numerical signals using EIIP amino acid scale, (ii) analysing these sequences by using Discrete Fourier Transform (DFT) and extracting DFT-based features, (iii) using a predictive model, based on Artificial Neural Networks and using the features generated by DFT. In this analysis, from the Influenza Research Database, 30724, 18236 and 8157 HA protein sequences were collected for Human, Avian and Swine respectively. Given this set of the proteins, the proposed method yielded 97.36% (± 0.04%), 97.26% (± 0.26%), 0.978 (± 0.004), 0.963 (± 0.005) and 0.945 (±0.005) for the training accuracy validation accuracy, precision, recall and Mathews Correlation Coefficient (MCC) respectively, based on a 10-fold cross-validation. The classification model generated by using one of the largest dataset, if not the largest, yields promising results that could lead to early detection of such species and help develop precautionary measurements for possible human infections.\",\n \"corpus_id\": 2583056,\n \"score\": 2\n },\n {\n \"doc_id\": \"29236050\",\n \"title\": \"Molecular Markers for Interspecies Transmission of Avian Influenza Viruses in Mammalian Hosts.\",\n \"abstract\": \"In the last decade, a wide range of avian influenza viruses (AIVs) have infected various mammalian hosts and continuously threaten both human and animal health. It is a result of overcoming the inter-species barrier which is mostly associated with gene reassortment and accumulation of mutations in their gene segments. Several recent studies have shed insights into the phenotypic and genetic changes that are involved in the interspecies transmission of AIVs. These studies have a major focus on transmission from avian to mammalian species due to the high zoonotic potential of the viruses. As more mammalian species have been infected with these viruses, there is higher risk of genetic evolution of these viruses that may lead to the next human pandemic which represents and raises public health concern. Thus, understanding the mechanism of interspecies transmission and molecular determinants through which the emerging AIVs can acquire the ability to transmit to humans and other mammals is an important key in evaluating the potential risk caused by AIVs among humans. Here, we summarize previous and recent studies on molecular markers that are specifically involved in the transmission of avian-derived influenza viruses to various mammalian hosts including humans, pigs, horses, dogs, and marine mammals.\",\n \"corpus_id\": 29923745,\n \"score\": 2\n },\n {\n \"doc_id\": \"18785841\",\n \"title\": \"Host restriction of avian influenza viruses at the level of the ribonucleoproteins.\",\n \"abstract\": \"Although transmission of avian influenza viruses to mammals, particularly humans, has been repeatedly documented, adaptation and sustained transmission in the new host is a rare event that in the case of humans may result in pandemics. Host restriction involves multiple genetic determinants. Among the known determinants of host range, key determinants have been identified on the genes coding for the nucleoprotein and polymerase proteins that, together with the viral RNA segments, form the ribonucleoproteins (RNPs). The RNP genes form host-specific lineages and harbor host-associated genetic signatures. The functional significance of these determinants has been studied by reassortment and reverse genetics experiments, underlining the influence of the global genetic context. In some instances the molecular mechanisms have been approached, pointing to the importance of the polymerase activity and interaction with cellular host factors. Better knowledge of determinants of host restriction will allow monitoring of the pandemic potential of avian influenza viruses.\",\n \"corpus_id\": 1603988,\n \"score\": 1\n },\n {\n \"doc_id\": \"19687042\",\n \"title\": \"Within-host variation of avian influenza viruses.\",\n \"abstract\": \"The emergence and spread of H5N1 avian influenza viruses from Asia through to Europe and Africa pose a significant animal disease problem and have raised concerns that the virus may pose a pandemic threat to humans. The epizootological factors that have influenced the wide distribution of the virus are complex, and the variety of viruses currently circulating reflects these factors. Sequence analysis of the virus genes sheds light on the H5N1 virus evolution during its emergence and spread, but the degree of virus variation at the level of an individual infected bird has been described in only a few studies. Here, we describe some results of a study in which turkeys, ducks and chickens were infected with either one of two H5N1 or one of three H7N1 viruses, and the degree of sequence variation within an individual infected avian host was examined. We developed 'deep amplicon' sequence analysis for this work, and the methods and results provide a background framework for application to disease outbreaks in the field.\",\n \"corpus_id\": 5894654,\n \"score\": 1\n },\n {\n \"doc_id\": \"22595002\",\n \"title\": \"Prediction of protein-protein interactions between viruses and human by an SVM model.\",\n \"abstract\": \"BACKGROUND: Several computational methods have been developed to predict protein-protein interactions from amino acid sequences, but most of those methods are intended for the interactions within a species rather than for interactions across different species. Methods for predicting interactions between homogeneous proteins are not appropriate for finding those between heterogeneous proteins since they do not distinguish the interactions between proteins of the same species from those of different species. RESULTS: We developed a new method for representing a protein sequence of variable length in a frequency vector of fixed length, which encodes the relative frequency of three consecutive amino acids of a sequence. We built a support vector machine (SVM) model to predict human proteins that interact with virus proteins. In two types of viruses, human papillomaviruses (HPV) and hepatitis C virus (HCV), our SVM model achieved an average accuracy above 80%, which is higher than that of another SVM model with a different representation scheme. Using the SVM model and Gene Ontology (GO) annotations of proteins, we predicted new interactions between virus proteins and human proteins. CONCLUSIONS: Encoding the relative frequency of amino acid triplets of a protein sequence is a simple yet powerful representation method for predicting protein-protein interactions across different species. The representation method has several advantages: (1) it enables a prediction model to achieve a better performance than other representations, (2) it generates feature vectors of fixed length regardless of the sequence length, and (3) the same representation is applicable to different types of proteins.\",\n \"corpus_id\": 9388262,\n \"score\": 1\n },\n {\n \"doc_id\": \"23777174\",\n \"title\": \"Predicting transmission of avian influenza A viruses from avian to human by using informative physicochemical properties.\",\n \"abstract\": \"Some strains of avian influenza A virus (AIV) can directly transmit from their natural hosts to humans. These avian-to-human transmissions have continuously been reported to cause human deaths worldwide since 1997. Predicting whether AIV strains can transmit from avian to human is valuable for early warning of AIV strains with human pandemic potential. In this study, we constructed a computational model to predict avian-to-human transmission of AIV based on physicochemical properties. Initially, ninety signature positions in the inner protein sequences were extracted with the entropy method. These positions were then encoded with 531 physicochemical features. Subsequently, the optimal subset of these physicochemical features was mined with several feature selection methods. Finally, a support vector machine (SVM) model named A2H was established to integrate the selected optimal features. The experimental results of cross-validation and an independent test show that A2H has the capability of predicting transmission of AIV from avian to human.\",\n \"corpus_id\": 23120853,\n \"score\": 1\n },\n {\n \"doc_id\": \"26038511\",\n \"title\": \"Host adaptation and transmission of influenza A viruses in mammals.\",\n \"abstract\": \"A wide range of influenza A viruses of pigs and birds have infected humans in the last decade, sometimes with severe clinical consequences. Each of these so-called zoonotic infections provides an opportunity for virus adaptation to the new host. Fortunately, most of these human infections do not yield viruses with the ability of sustained human-to-human transmission. However, animal influenza viruses have acquired the ability of sustained transmission between humans to cause pandemics on rare occasions in the past, and therefore, influenza virus zoonoses continue to represent threats to public health. Numerous recent studies have shed new light on the mechanisms of adaptation and transmission of avian and swine influenza A viruses in mammals. In particular, several studies provided insights into the genetic and phenotypic traits of influenza A viruses that may determine airborne transmission. Here, we summarize recent studies on molecular determinants of virulence and adaptation of animal influenza A virus and discuss the phenotypic traits associated with airborne transmission of newly emerging influenza A viruses. Increased understanding of the determinants and mechanisms of virulence and transmission may aid in assessing the risks posed by animal influenza viruses to human health, and preparedness for such risks.\",\n \"corpus_id\": 10701239,\n \"score\": 1\n },\n {\n \"doc_id\": \"18370034\",\n \"title\": \"A brief introduction to the avian influenza virus.\",\n \"abstract\": \"The avian influenza (AI) virus is type A influenza isolated from and adapted to an avian host. Type A influenza belongs to the orthomyxovirdae virus family, is enveloped, and is pleiomorphic with a size ranging from 80-120 nm (reviewed in [1]). Type A influenza strains are classified by the serological subtypes of the primary viral surface proteins, the hemagglutinin (HA) and neuraminidase (NA). The HA has 16 subtypes (H1-H16) and contains neutralizing epitopes. Antibodies against the NA are not neutralizing, and there are nine neuraminidase or \\\"N\\\" subtypes. The \\\"H\\\" and N subtypes seem to be able to assort into any combination, and many of the 144 possible combinations have been found in natural reservoir species, although some combinations are more common than others. All 16 subtypes have been found in ducks, gulls, or shorebirds, the natural reservoir host species of the virus. However, in these species certain subtypes are more common than others; for example, H3, H4, and H6 are most common in ducks in North America [2, 3] and although there is no clear association between host range or host restriction based on HA subtype, some subtypes are more common in some species than others, i.e., H1 and H3 in swine, H3 in horses, and H5 and H7 in chickens.\",\n \"corpus_id\": 24480926,\n \"score\": 0\n },\n {\n \"doc_id\": \"18722814\",\n \"title\": \"A feature vector integration approach for a generalized support vector machine pairwise homology algorithm.\",\n \"abstract\": \"Due to the exponential growth of sequenced genomes, the need to quickly provide accurate annotation for existing and new sequences is paramount to facilitate biological research. Current sequence comparison approaches fail to detect homologous relationships when sequence similarity is low. Support vector machine (SVM) algorithms approach this problem by transforming all proteins into a feature space of equal dimension based on protein properties, such as sequence similarity scores against a basis set of proteins or motifs. This multivariate representation of the protein space is then used to build a classifier specific to a pre-defined protein family. However, this approach is not well suited to large-scale annotation. We have developed a SVM approach that formulates remote homology as a single classifier that answers the pairwise comparison problem by integrating the two feature vectors for a pair of sequences into a single vector representation that can be used to build a classifier that separates sequence pairs into homologs and non-homologs. This pairwise SVM approach significantly improves the task of remote homology detection on the benchmark dataset, quantified as the area under the receiver operating characteristic curve; 0.97 versus 0.73 and 0.70 for PSI-BLAST and Basic Local Alignment Search Tool (BLAST), respectively.\",\n \"corpus_id\": 206908061,\n \"score\": 0\n },\n {\n \"doc_id\": \"18941631\",\n \"title\": \"Evolution of highly pathogenic H5N1 avian influenza viruses in Vietnam between 2001 and 2007.\",\n \"abstract\": \"Highly pathogenic avian influenza (HPAI) H5N1 viruses have caused dramatic economic losses to the poultry industry of Vietnam and continue to pose a serious threat to public health. As of June 2008, Vietnam had reported nearly one third of worldwide laboratory confirmed human H5N1 infections. To better understand the emergence, spread and evolution of H5N1 in Vietnam we studied over 300 H5N1 avian influenza viruses isolated from Vietnam since their first detection in 2001. Our phylogenetic analyses indicated that six genetically distinct H5N1 viruses were introduced into Vietnam during the past seven years. The H5N1 lineage that evolved following the introduction in 2003 of the A/duck/Hong Kong/821/2002-like viruses, with clade 1 hemagglutinin (HA), continued to predominate in southern Vietnam as of May 2007. A virus with a clade 2.3.4 HA newly introduced into northern Vietnam in 2007, reassorted with pre-existing clade 1 viruses, resulting in the emergence of novel genotypes with neuraminidase (NA) and/or internal gene segments from clade 1 viruses. A total of nine distinct genotypes have been present in Vietnam since 2001, including five that were circulating in 2007. At least four of these genotypes appear to have originated in Vietnam and represent novel H5N1 viruses not reported elsewhere. Geographic and temporal analyses of H5N1 infection dynamics in poultry suggest that the majority of viruses containing new genes were first detected in northern Vietnam and subsequently spread to southern Vietnam after reassorting with pre-existing local viruses in northern Vietnam. Although the routes of entry and spread of H5N1 in Vietnam remain speculative, enhanced poultry import controls and virologic surveillance efforts may help curb the entry and spread of new HPAI viral genes.\",\n \"corpus_id\": 2797526,\n \"score\": 0\n },\n {\n \"doc_id\": \"19276438\",\n \"title\": \"The public health impact of avian influenza viruses.\",\n \"abstract\": \"Influenza viruses with novel hemagglutinin and 1 or more accompanying genes derived from avian influenza viruses sporadically emerge in humans and have the potential to result in a pandemic if the virus causes disease and spreads efficiently in a population that lacks immunity to the novel hemagglutinin. Since 1997, multiple avian influenza virus subtypes have been transmitted directly from domestic poultry to humans and have caused a spectrum of human disease, from asymptomatic to severe and fatal. To assess the pandemic risk that avian influenza viruses pose, we have used multiple strategies to better understand the capacity of avian viruses to infect, cause disease, and transmit among mammals, including humans. Seroepidemiologic studies that evaluate the frequency and risk of human infection with avian influenza viruses in populations with exposure to domestic or wild birds can provide a better understanding of the pandemic potential of avian influenza subtypes. Investigations conducted in Hong Kong following the first H5N1 outbreak in humans in 1997 determined that exposure to poultry in live bird markets was a key risk factor for human disease. Among poultry workers, butchering and exposure to sick poultry were risk factors for antibody to H5 virus, which provided evidence for infection. A second risk assessment tool, the ferret, can be used to evaluate the level of virulence and potential for host-to-host transmission of avian influenza viruses in this naturally susceptible host. Avian viruses isolated from humans exhibit a level of virulence and transmissibility in ferrets that generally reflects that seen in humans. The ferret model thus provides a means to monitor emerging avian influenza viruses for pandemic risk, as well as to evaluate laboratory-generated reassortants and mutants to better understand the molecular basis of influenza virus transmissibility. Taken together, such studies provide valuable information with which we can assess the public health risk of avian influenza viruses.\",\n \"corpus_id\": 19832067,\n \"score\": 0\n },\n {\n \"doc_id\": \"19447141\",\n \"title\": \"Amplification of four genes of influenza A viruses using a degenerate primer set in a one step RT-PCR method.\",\n \"abstract\": \"We designed a degenerate primer set that yielded full-length amplification of hemagglutinin (HA), neuraminidase (NA), matrix (M), and non-structural protein (NSP) genes of influenza A viruses in a single reaction mixture. These four genes were amplified from 15 HA (1-15) and 9 NA (1-9) subtypes of influenza A viruses of avian (n=16) origin. In addition, 272 field isolates of avian origin were tested by this method. Full-length amplification of HA, NA, M, and NSP genes was obtained in 242 (88.9%), 254 (93.4%), 268 (98.5%), and 268 (98.5%) isolates, respectively. No gene was amplified in four isolates. Of these four isolates, two were subtyped as H4N6, one as H7N7, and one as H10N7. Amplification was successful for all 4 genes of H1N1, H2N3, and H3N2 isolates of swine influenza. Also, all four genes were amplified in one equine influenza (H3N8) isolate and seven isolates of human origin (H1N1 and H3N2). This appears to be the first study using degenerate primer set for full-length amplification of four genes of influenza A viruses in a single reaction. Further studies are needed to determine if this primer set can be used for subtyping of influenza virus isolates.\",\n \"corpus_id\": 15148655,\n \"score\": 0\n },\n {\n \"doc_id\": \"19460353\",\n \"title\": \"Isolation and genetic characterization of avian-like H1N1 and novel ressortant H1N2 influenza viruses from pigs in China.\",\n \"abstract\": \"As pigs are susceptible to both human and avian influenza viruses, they have been proposed to be intermediate hosts or mixing vessels for the generation of pandemic influenza viruses through reassortment or adaptation to the mammalian host. In this study, we reported avian-like H1N1 and novel ressortant H1N2 influenza viruses from pigs in China. Homology and phylogenetic analyses showed that the H1N1 virus (A/swine/Zhejiang/1/07) was closely to avian-like H1N1 viruses and seemed to be derived from the European swine H1N1 viruses, which was for the first time reported in China; and the two H1N2 viruses (A/swine/Shanghai/1/07 and A/swine/Guangxi/13/06) were novel ressortant H1N2 influenza viruses containing genes from the classical swine (HA, NP, M and NS), human (NA and PB1) and avian (PB2 and PA) lineages, which indicted that the reassortment among human, avian, and swine influenza viruses had taken place in pigs in China and resulted in the generation of new viruses. The isolation of avian-like H1N1 influenza virus originated from the European swine H1N1 viruses, especially the emergence of two novel ressortant H1N2 influenza viruses provides further evidence that pigs serve as intermediate hosts or \\\"mixing vessels\\\", and swine influenza virus surveillance in China should be given a high priority.\",\n \"corpus_id\": 36688594,\n \"score\": 0\n },\n {\n \"doc_id\": \"19486316\",\n \"title\": \"The role of swine in the generation of novel influenza viruses.\",\n \"abstract\": \"The ecology of influenza A viruses is very complicated involving multiple host species and viral genes. Avian species have variable susceptibility to influenza A viruses with wild aquatic birds being the reservoir for this group of pathogens. Occasionally, influenza A viruses are transmitted to mammals from avian species, which can lead to the development of human pandemic strains by direct or indirect transmission to man. Because swine are also susceptible to infection with avian and human influenza viruses, genetic reassortment between these viruses and/or swine influenza viruses can occur. The potential to generate novel influenza viruses has resulted in swine being labelled 'mixing vessels'. The mixing vessel theory is one mechanism by which unique viruses can be transmitted from an avian reservoir to man. Although swine can generate novel influenza viruses capable of infecting man, at present, it is difficult to predict which viruses, if any, will cause a human pandemic. Clearly, the ecology of influenza A viruses is dynamic and can impact human health, companion animals, as well as the health of livestock and poultry for production of valuable protein commodities. For these reasons, influenza is, and will continue to be, a serious threat to the wellbeing of mankind.\",\n \"corpus_id\": 30630155,\n \"score\": 0\n },\n {\n \"doc_id\": \"19546028\",\n \"title\": \"Structural and evolutionary characteristics of HA, NA, NS and M genes of clinical influenza A/H3N2 viruses passaged in human and canine cells.\",\n \"abstract\": \"BACKGROUND: Canine (MDCK) cells and chicken eggs are usually used for isolation of human influenza viruses. Viruses isolated by these procedures often differ from those present in the clinical specimens, since adaptive changes occur during virus transmission from the human host to cells of heterologous origin. OBJECTIVES: To minimize these species-dependent changes, CACO-2 cells derived from human intestinal epithelium were used to isolate virus from influenza patients. STUDY DESIGN: Influenza A viruses of subtype H3N2 were primarily isolated in CACO-2 and then passaged in parallel in CACO-2 and MDCK cells. Structural properties of passaged virus variants were compared and analyzed for evolutionary relationships. RESULTS: Influenza viruses were isolated in CACO-2 with higher efficiency than in MDCK and chicken eggs. The following observations were made: (i) recent isolates showed an about 2-fold increase in the number of glycosylation sites of HA and NA when compared to isolates from 1968 to 1970; (ii) during passages of clinical strains in CACO-2 and MDCK cells HA and NA mutated cooperatively with strain-specific variations implying that functioning of the HA-NA complex varied from strain to strain in one influenza outbreak; (iii) there were no amino acid exchanges in the HA receptor binding site although the viruses acquired the ability to agglutinate avian erythrocytes after passage in MDCK cells, suggesting that virus adsorption is regulated by several factors; (iv) quasispecies characterized by deletion of 66 nucleotides (22 amino acids) in the stalk region of the NA gene was dominant in naso-pharyngeal washes of all patients whereas during passaging in CACO-2 cells this deleted genotype in isolates from different patients was either stably retained as prevalent quasispecies or rapidly replaced for that one containing full length NA gene; (v) the M2 protein of clinical viruses was sensitive to amantadine; (vi) the NS segment of human viruses, unlike the most of avian ones, contained an additional positive-sense open reading frame encoding a hypothetical 25kD polypeptide (negative strand protein, NSP). CONCLUSIONS: The data suggest that (i) clinical influenza viruses can be isolated from respiratory tract of humans more effectively in human than in canine cells; (ii) heterologous virus population circulates during one influenza outbreak; (iii) increasing numbers of glycosylation sites on HA and NA and stalk shortening of NA take place during virus evolution in humans.\",\n \"corpus_id\": 12056097,\n \"score\": 0\n },\n {\n \"doc_id\": \"19673419\",\n \"title\": \"[Rescue of H3N2 subtype swine influenza virus and substitution of hemagglutinin, neuraminidase].\",\n \"abstract\": \"OBJECTIVE: To study the mechanisms of trans-species transmission of influenza virus for developing novel vaccine of influenza in future. METHODS: We rescued H3N2 subtype swine influenza virus strain A/Swine/Henan/S4/01 successfully by a plasmid-base reverse genetics. Eight gene segments were synthesized by reverse transcriptase-PCR and cloned into bidirection expression vector pHW2000. We cotransfected 8 recombinant plasmids into 293T and MDCK cells and got the rescued virus rgH3N2. Then we replaced Hemagglutinin, Neuraminidase of rgH3N2 by Hemagglutinin, Neuraminidase gene from Human influenza virus, Avian influenza virus, Equine influenza virus. RESULTS: The rescued virus rgH3N2 and the wild type virus shared similar biological properties such as in titers of 50% embryo infective, 50% tissue culture infective dose and stability tests. The rescued virus titer in MDCK cell culture was measured by hemagglutination assay and the maximum virus titre of 1:64 hemagglutination unit was obtained after infection of MDCK cell for 60 h, The hemagglutination titre was 1:256 after several passages in embryonated eggs. With various combinations of HA, NA genes, we successfully generated high-yield reassortant viruses rgH1N1, rgH4N6 and rgH3N8 in embryonated eggs and MDCK cells. CONCLUSION: The successful rescue of reassortment viruses establish the foundation for the molecular mechanism research on how the swine influenza virus breakthrough the intermediate barriers and the function of HA, NA during transmitting among species, Also it is feasible to be used for developing novel vaccine of H3N2 subtype Swine influenza in future.\",\n \"corpus_id\": 38606120,\n \"score\": 0\n },\n {\n \"doc_id\": \"19939933\",\n \"title\": \"Molecular determinants of adaptation of highly pathogenic avian influenza H7N7 viruses to efficient replication in the human host.\",\n \"abstract\": \"Two viruses isolated during the highly pathogenic avian influenza (HPAI) H7N7 virus outbreak in The Netherlands in 2003, one isolated from a person with conjunctivitis and one from a person who died as the result of infection, were used for an in vitro study of influenza A virus pathogenicity factors. The two HPAI H7N7 viruses differed in 15 amino acid positions in five gene segments. Assays were designed to investigate the role of each of these substitutions in attachment and entry, transcription and genome replication, and virus production and release as determined by hemagglutinin (HA), polymerase proteins, nonstructural protein 1 (NS1), and neuraminidase (NA). These in vitro studies confirmed the roles of the E627K substitution in basic polymerase 2 (PB2) and the A143T substitution in HA in pathogenicity observed in a mouse model previously. However, the in vitro studies identified a contribution of acidic polymerase (PA) and NA to the efficient replication in human cells of the fatal case virus, despite the fact that these are rarely marked as determinants of pathogenicity in in vivo studies. With the exception of PB2 E627K, all substitutions contributing to enhanced replication of the fatal case virus in vitro were present in poultry viruses prior to transmission to the human fatal case, indicating that viruses with enhanced replication efficiency in the mammalian host can be generated in poultry. Thus, detailed in vitro analyses of mutations facilitating replication of avian influenza viruses in mammalian cells are important to assess the zoonotic risk posed by these viruses and, in addition, highlight the value of in vitro studies to complement animal models.\",\n \"corpus_id\": 10015180,\n \"score\": 0\n },\n {\n \"doc_id\": \"20134234\",\n \"title\": \"Comparative study of the nucleotide bias between the novel H1N1 and H5N1 subtypes of influenza A viruses using bioinformatics techniques.\",\n \"abstract\": \"Novel influenza A (H1N1) is a newly emerged flu virus which was first detected in April, 2009. Unlike the avian influenza (H5N1), this virus has been known to be able to spread from human to human directly. Although it is uncertain that how severe this novel H1N1 virus will be in terms of human illness, illness may be more widespread because most people will not have immunity to it. In this study, we compared the codon usage bias between the novel H1N1 influenza A viruses and other viruses such as H1N1 and H5N1 subtypes to investigate the genomic patterns of novel influenza A (H1N1). Totally 1,675 nucleotide sequences of the hemagglutinin (HA) and neuraminidase (NA) genes of influenza A virus including H1N1 and H5N1 subtypes occurred from 2004 to 2009 were used. As a result, we found that the novel H1N1 influenza A viruses showed the most close correlations with the swine-origin H1N1 subtypes than other H1N1 viruses in the result from not only the analysis of nucleotide compositions, but also the phylogenetic analysis. Although the genetic sequences of novel H1N1 subtypes were not exactly same as the other H1N1 subtypes, the HA and NA genes of novel H1N1s showed very similar codon usage patterns with other H1N1 subtypes, especially with the swine-origin H1N1 influenza A viruses. Our findings strongly suggested that those novel H1N1 viruses seemed to be originated from the swine-host H1N1 viruses in terms of the codon usage patterns.\",\n \"corpus_id\": 24039349,\n \"score\": 0\n },\n {\n \"doc_id\": \"20484565\",\n \"title\": \"Viral reassortment and transmission after co-infection of pigs with classical H1N1 and triple-reassortant H3N2 swine influenza viruses.\",\n \"abstract\": \"Triple-reassortant swine influenza viruses circulating in North American pigs contain the internal genes derived from swine (matrix, non-structural and nucleoprotein), human [polymerase basic 1 (PB1)] and avian (polymerase acidic and PB2) influenza viruses forming a constellation of genes that is well conserved and is called the triple-reassortant internal gene (TRIG) cassette. In contrast, the external genes [haemagglutinin (HA) and neuraminidase (NA)] are less conserved, reflecting multiple reassortant events that have produced viruses with different combinations of HA and NA genes. This study hypothesized that maintenance of the TRIG cassette confers a selective advantage to the virus. To test this hypothesis, pigs were co-infected with the triple-reassortant H3N2 A/Swine/Texas/4199-2/98 (Tx/98) and the classical H1N1 A/Swine/Iowa/15/1930 viruses and co-housed with a group of sentinel animals. This direct contact group was subsequently moved into contact with a second group of naïve animals. Four different subtypes (H1N1, H1N2, H3N1 and H3N2) of influenza virus were identified in bronchoalveolar lavage fluid collected from the lungs of the experimentally infected pigs, with most of the viruses containing TRIG from the Tx/98 virus. Interestingly, only the intact H3N2 Tx/98 virus was transmitted from the infected pigs to the direct-contact animals and from them to the second contact group of pigs. These results demonstrated that multiple reassortments can occur within a host; however, only specific gene constellations are readily transmissible. It was concluded that certain HA and NA gene pairs, in conjunction with the TRIG cassette, may have a competitive advantage over other combinations for transmission and maintenance in swine.\",\n \"corpus_id\": 18293879,\n \"score\": 0\n },\n {\n \"doc_id\": \"20591213\",\n \"title\": \"Interspecies and intraspecies transmission of influenza A viruses: viral, host and environmental factors.\",\n \"abstract\": \"Influenza A viruses are enveloped viruses belonging to the family Orthomyxoviridae that encompasses four more genera: Influenza B, Influenza C, Isavirus and Thogotovirus. Type A viruses belong to the only genus that is highly infectious to a variety of mammalian and avian species. They are divided into subtypes based on two surface glycoproteins, the hemagglutinin (HA) and neuraminidase (NA). So far, 16 HA and 9 NA subtypes have been identified worldwide, making a possible combination of 144 subtypes between both proteins. Generally, individual viruses are host-specific, however, interspecies transmission of influenza A viruses is not uncommon. All of the HA and NA subtypes have been isolated from wild birds; however, infections in humans and other mammalian species are limited to a few subtypes. The replication of individual influenza A virus in a specific host is dependent on many factors including, viral proteins, host system and environmental conditions. In this review, the key findings that contribute to the transmission of influenza A viruses amongst different species are summarized.\",\n \"corpus_id\": 34951469,\n \"score\": 0\n },\n {\n \"doc_id\": \"20600474\",\n \"title\": \"Repository of Eurasian influenza A virus hemagglutinin and neuraminidase reverse genetics vectors and recombinant viruses.\",\n \"abstract\": \"Reverse genetics can be used to produce recombinant influenza A viruses containing virtually every desired combination of hemagglutinin (HA) and neuraminidase (NA) genes using the virus backbone of choice. Here, a repository of plasmids and recombinant viruses representing all contemporary Eurasian HA and NA subtypes, H1-H16 and N1-N9, was established. HA and NA genes were selected based on sequence analyses of influenza virus genes available from public databases. Prototype Eurasian HA and NA genes were cloned in bidirectional reverse genetics plasmids. Recombinant viruses based on the virus backbone of A/PR/8/34, and containing a variety of HA and NA genes were produced in 293T cells. Virus stocks were produced in MDCK cells and embryonated chicken eggs. These plasmids and viruses may be useful for numerous purposes, including influenza virus research projects, vaccination studies, and to serve as reference reagents in diagnostic settings.\",\n \"corpus_id\": 23733821,\n \"score\": 0\n },\n {\n \"doc_id\": \"21209922\",\n \"title\": \"A complete analysis of HA and NA genes of influenza A viruses.\",\n \"abstract\": \"BACKGROUND: More and more nucleotide sequences of type A influenza virus are available in public databases. Although these sequences have been the focus of many molecular epidemiological and phylogenetic analyses, most studies only deal with a few representative sequences. In this paper, we present a complete analysis of all Haemagglutinin (HA) and Neuraminidase (NA) gene sequences available to allow large scale analyses of the evolution and epidemiology of type A influenza. METHODOLOGY/PRINCIPAL FINDINGS: This paper describes an analysis and complete classification of all HA and NA gene sequences available in public databases using multivariate and phylogenetic methods. CONCLUSIONS/SIGNIFICANCE: We analyzed 18,975 HA sequences and divided them into 280 subgroups according to multivariate and phylogenetic analyses. Similarly, we divided 11,362 NA sequences into 202 subgroups. Compared to previous analyses, this work is more detailed and comprehensive, especially for the bigger datasets. Therefore, it can be used to show the full and complex phylogenetic diversity and provides a framework for studying the molecular evolution and epidemiology of type A influenza virus. For more than 85% of type A influenza HA and NA sequences into GenBank, they are categorized in one unambiguous and unique group. Therefore, our results are a kind of genetic and phylogenetic annotation for influenza HA and NA sequences. In addition, sequences of swine influenza viruses come from 56 HA and 45 NA subgroups. Most of these subgroups also include viruses from other hosts indicating cross species transmission of the viruses between pigs and other hosts. Furthermore, the phylogenetic diversity of swine influenza viruses from Eurasia is greater than that of North American strains and both of them are becoming more diverse. Apart from viruses from human, pigs, birds and horses, viruses from other species show very low phylogenetic diversity. This might indicate that viruses have not become established in these species. Based on current evidence, there is no simple pattern of inter-hemisphere transmission of avian influenza viruses and it appears to happen sporadically. However, for H6 subtype avian influenza viruses, such transmissions might have happened very frequently and multiple and bidirectional transmission events might exist.\",\n \"corpus_id\": 12829449,\n \"score\": 0\n },\n {\n \"doc_id\": \"21507270\",\n \"title\": \"Positive selection on hemagglutinin and neuraminidase genes of H1N1 influenza viruses.\",\n \"abstract\": \"BACKGROUND: Since its emergence in March 2009, the pandemic 2009 H1N1 influenza A virus has posed a serious threat to public health. To trace the evolutionary path of these new pathogens, we performed a selection-pressure analysis of a large number of hemagglutinin (HA) and neuraminidase (NA) gene sequences of H1N1 influenza viruses from different hosts. RESULTS: Phylogenetic analysis revealed that both HA and NA genes have evolved into five distinct clusters, with further analyses indicating that the pandemic 2009 strains have experienced the strongest positive selection. We also found evidence of strong selection acting on the seasonal human H1N1 isolates. However, swine viruses from North America and Eurasia were under weak positive selection, while there was no significant evidence of positive selection acting on the avian isolates. A site-by-site analysis revealed that the positively selected sites were located in both of the cleaved products of HA (HA1 and HA2), as well as NA. In addition, the pandemic 2009 strains were subject to differential selection pressures compared to seasonal human, North American swine and Eurasian swine H1N1 viruses. CONCLUSIONS: Most of these positively and/or differentially selected sites were situated in the B-cell and/or T-cell antigenic regions, suggesting that selection at these sites might be responsible for the antigenic variation of the viruses. Moreover, some sites were also associated with glycosylation and receptor-binding ability. Thus, selection at these positions might have helped the pandemic 2009 H1N1 viruses to adapt to the new hosts after they were introduced from pigs to humans. Positive selection on position 274 of NA protein, associated with drug resistance, might account for the prevalence of drug-resistant variants of seasonal human H1N1 influenza viruses, but there was no evidence that positive selection was responsible for the spread of the drug resistance of the pandemic H1N1 strains.\",\n \"corpus_id\": 5199018,\n \"score\": 0\n },\n {\n \"doc_id\": \"21849451\",\n \"title\": \"Comparative analysis of avian influenza virus diversity in poultry and humans during a highly pathogenic avian influenza A (H7N7) virus outbreak.\",\n \"abstract\": \"Although increasing data have become available that link human adaptation with specific molecular changes in nonhuman influenza viruses, the molecular changes of these viruses during a large highly pathogenic avian influenza virus (HPAI) outbreak in poultry along with avian-to-human transmission have never been documented. By comprehensive virologic analysis of combined veterinary and human samples obtained during a large HPAI A (H7N7) outbreak in the Netherlands in 2003, we mapped the acquisition of human adaptation markers to identify the public health risk associated with an HPAI outbreak in poultry. Full-length hemagglutinin (HA), neuraminidase (NA), and PB2 sequencing of A (H7N7) viruses obtained from 45 human cases showed amino acid variations at different codons in HA (n=20), NA (n=23), and PB2 (n=23). Identification of the avian sources of human virus infections based on 232 farm sequences demonstrated that for each gene about 50% of the variation was already present in poultry. Polygenic accumulation and farm-to-farm spread of known virulence and human adaptation markers in A (H7N7) virus-infected poultry occurred prior to farm-to-human transmission. These include the independent emergence of HA A143T mutants, accumulation of four NA mutations, and farm-to-farm spread of virus variants harboring mammalian host determinants D701N and S714I in PB2. This implies that HPAI viruses with pandemic potential can emerge directly from poultry. Since the public health risk of an avian influenza virus outbreak in poultry can rapidly change, we recommend virologic monitoring for human adaptation markers among poultry as well as among humans during the course of an outbreak in poultry.\",\n \"corpus_id\": 5528879,\n \"score\": 0\n },\n {\n \"doc_id\": \"21880750\",\n \"title\": \"Tissue tropism of swine influenza viruses and reassortants in ex vivo cultures of the human respiratory tract and conjunctiva.\",\n \"abstract\": \"The 2009 pandemic influenza H1N1 (H1N1pdm) virus was generated by reassortment of swine influenza viruses of different lineages. This was the first influenza pandemic to emerge in over 4 decades and the first to occur after the realization that influenza pandemics arise from influenza viruses of animals. In order to understand the biological determinants of pandemic emergence, it is relevant to compare the tropism of different lineages of swine influenza viruses and reassortants derived from them with that of 2009 pandemic H1N1 (H1N1pdm) and seasonal influenza H1N1 viruses in ex vivo cultures of the human nasopharynx, bronchus, alveoli, and conjunctiva. We hypothesized that virus which can transmit efficiently between humans replicated well in the human upper airways. As previously reported, H1N1pdm and seasonal H1N1 viruses replicated efficiently in the nasopharyngeal, bronchial, and alveolar epithelium. In contrast, representative viruses from the classical swine (CS) (H1N1) lineage could not infect human respiratory epithelium; Eurasian avian-like swine (EA) (H1N1) viruses only infected alveolar epithelium and North American triple-reassortant (TRIG) viruses only infected the bronchial epithelium albeit inefficiently. Interestingly, a naturally occurring triple-reassortant swine virus, A/SW/HK/915/04 (H1N2), with a matrix gene segment of EA swine derivation (i.e., differing from H1N1pdm only in lacking a neuraminidase [NA] gene of EA derivation) readily infected and replicated in human nasopharyngeal and bronchial epithelia but not in the lung. A recombinant sw915 with the NA from H1N1pdm retained its tropism for the bronchus and acquired additional replication competence for alveolar epithelium. In contrast to H1N1pdm, none of the swine viruses tested nor seasonal H1N1 had tropism in human conjunctiva. Recombinant viruses generated by swapping the surface proteins (hemagglutinin and NA) of H1N1pdm and seasonal H1N1 virus demonstrated that these two gene segments together are key determinants of conjunctival tropism. Overall, these findings suggest that ex vivo cultures of the human respiratory tract provide a useful biological model for assessing the human health risk of swine influenza viruses.\",\n \"corpus_id\": 40025853,\n \"score\": 0\n },\n {\n \"doc_id\": \"22230579\",\n \"title\": \"Cloned cDNA of A/swine/Iowa/15/1930 internal genes as a candidate backbone for reverse genetics vaccine against influenza A viruses.\",\n \"abstract\": \"Reverse genetics viruses for influenza vaccine production usually utilize the internal genes of the egg-adapted A/Puerto Rico/8/34 (PR8) strain. This egg-adapted strain provides high production yield in embryonated eggs but does not necessarily give the best yield in mammalian cell culture. In order to generate a reverse genetics viral backbone that is well-adapted to high growth in mammalian cell culture, a swine influenza isolate A/swine/Iowa/15/30 (H1N1) (rg1930) that was shown to give high yield in Madin-Darby canine kidney (MDCK) cells was used as the internal gene donor for reverse genetics plasmids. In this report, the internal genes from rg1930 were used for construction of reverse genetics viruses carrying a cleavage site-modified hemagglutinin (HA) gene and neuraminidase (NA) gene from a highly pathogenic H5N1 virus. The resulting virus (rg1930H5N1) was low pathogenic in vivo. Inactivated rg1930H5N1 vaccine completely protected chickens from morbidity and mortality after challenge with highly pathogenic H5N1. Protective immunity was obtained when chickens were immunized with an inactivated vaccine consisting of at least 2(9) HA units of the rg1930H5N1 virus. In comparison to the PR8-based reverse genetics viruses carrying the same HA and NA genes from an H5N1 virus, rg1930 based viruses yielded higher viral titers in MDCK and Vero cells. In addition, the reverse genetics derived H3N2 and H5N2 viruses with the rg1930 backbone replicated in MDCK cells better than the cognate viruses with the rgPR8 backbone. It is concluded that this newly established reverse genetics backbone system could serve as a candidate for a master donor strain for development of inactivated influenza vaccines in cell-based systems.\",\n \"corpus_id\": 2179136,\n \"score\": 0\n },\n {\n \"doc_id\": \"22355413\",\n \"title\": \"Prediction of biological functions on glycosylation site migrations in human influenza H1N1 viruses.\",\n \"abstract\": \"Protein glycosylation alteration is typically employed by various viruses for escaping immune pressures from their hosts. Our previous work had shown that not only the increase of glycosylation sites (glycosites) numbers, but also glycosite migration might be involved in the evolution of human seasonal influenza H1N1 viruses. More importantly, glycosite migration was likely a more effectively alteration way for the host adaption of human influenza H1N1 viruses. In this study, we provided more bioinformatics and statistic evidences for further predicting the significant biological functions of glycosite migration in the host adaptation of human influenza H1N1 viruses, by employing homology modeling and in silico protein glycosylation of representative HA and NA proteins as well as amino acid variability analysis at antigenic sites of HA and NA. The results showed that glycosite migrations in human influenza viruses have at least five possible functions: to more effectively mask the antigenic sites, to more effectively protect the enzymatic cleavage sites of neuraminidase (NA), to stabilize the polymeric structures, to regulate the receptor binding and catalytic activities and to balance the binding activity of hemagglutinin (HA) with the release activity of NA. The information here can provide some constructive suggestions for the function research related to protein glycosylation of influenza viruses, although these predictions still need to be supported by experimental data.\",\n \"corpus_id\": 6621767,\n \"score\": 0\n },\n {\n \"doc_id\": \"22465746\",\n \"title\": \"Production and characterization of mammalian virus-like particles from modified vaccinia virus Ankara vectors expressing influenza H5N1 hemagglutinin and neuraminidase.\",\n \"abstract\": \"Several studies have described the production of influenza virus-like particles (VLP) using a variety of platform systems. These VLPs are non-replicating particles that spontaneously self-assemble from expressed influenza virus proteins and have been proposed as vaccine candidates for both seasonal and pandemic influenza. Although still in the early stages of development and evaluation as influenza vaccines, influenza VLPs have a variety of other valuable uses such as examining and understanding correlates of protection against influenza and investigating virus-cell interactions. The most common production system for influenza VLPs is the baculovirus-insect cell expression which has several attractive features including the ease in which new gene combinations can be constructed, the immunogenicity elicited and protection afforded by the produced VLPs, and the scalability offered by the system. However, there are differences between the influenza VLPs produced by baculovirus expression systems in insect cells and the influenza viruses produced for use as current vaccines or the virus produced during a productive clinical infection. We describe here the development of a modified vaccinia virus Ankara (MVA) system to generate mammalian influenza VLPs containing influenza H5N1 proteins. The MVA vector system is flexible for manipulating and generating various VLP constructs, expresses high level of influenza hemagglutinin (HA), neuraminidase (NA), and matrix (M) proteins, and can be scaled up to produce VLPs in quantities sufficient for in vivo studies. We show that mammalian VLPs are generated from recombinant MVA vectors expressing H5N1 HA alone, but that increased VLP production can be achieved if NA is co-expressed. These mammalian H5N1 influenza VLPs have properties in common with live virus, as shown by electron microscopy analysis, their ability to hemagglutinate red blood cells, express neuraminidase activity, and to bind influenza specific antibodies. Importantly, these VLPs are able to elicit a protective immune response in a mouse challenge model, suggesting their utility in dissecting the correlates of immunity in such models. Mammalian derived VLPs may also provide a useful tool for studying virus-cell interactions and may have potential for development as pandemic vaccines.\",\n \"corpus_id\": 22788930,\n \"score\": 0\n },\n {\n \"doc_id\": \"22718832\",\n \"title\": \"Functional balance of the hemagglutinin and neuraminidase activities accompanies the emergence of the 2009 H1N1 influenza pandemic.\",\n \"abstract\": \"The 2009 H1N1 influenza pandemic is the first human pandemic in decades and was of swine origin. Although swine are believed to be an intermediate host in the emergence of new human influenza viruses, there is still little known about the host barriers that keep swine influenza viruses from entering the human population. We surveyed swine progenitors and human viruses from the 2009 pandemic and measured the activities of the hemagglutinin (HA) and neuraminidase (NA), which are the two viral surface proteins that interact with host glycan receptors. A functional balance of these two activities (HA binding and NA cleavage) is found in human viruses but not in the swine progenitors. The human 2009 H1N1 pandemic virus exhibited both low HA avidity for glycan receptors as a result of mutations near the receptor binding site and weak NA enzymatic activity. Thus, a functional match between the hemagglutinin and neuraminidase appears to be necessary for efficient transmission between humans and may be an indicator of the pandemic potential of zoonotic viruses.\",\n \"corpus_id\": 27952692,\n \"score\": 0\n },\n {\n \"doc_id\": \"23202513\",\n \"title\": \"Rapid detection and differentiation of swine-origin influenza A virus (H1N1/2009) from other seasonal influenza A viruses.\",\n \"abstract\": \"We previously developed a rapid and simple gold nanoparticle(NP)-based genomic microarray assay for identification of the avian H5N1 virus and its discrimination from other influenza A virus strains (H1N1, H3N2). In this study, we expanded the platform to detect the 2009 swine-origin influenza A virus (H1N1/2009). Multiple specific capture and intermediate oligonucleotides were designed for the matrix (M), hemagglutinin (HA), and neuraminidase (NA) genes of the H1N1/2009 virus. The H1N1/2009 microarrays were printed in the same format as those of the seasonal influenza H1N1 and H3N2 for the HA, NA, and M genes. Viral RNA was tested using capture-target-intermediate oligonucleotide hybridization and gold NP-mediated silver staining. The signal from the 4 capture-target-intermediates of the HA and NA genes was specific for H1N1/2009 virus and showed no cross hybridization with viral RNA from other influenza strains H1N1, H3N2, and H5N1. All of the 3 M gene captures showed strong affinity with H1N1/2009 viral RNA, with 2 out of the 3 M gene captures showing cross hybridization with the H1N1, H3N2, and H5N1 samples tested. The current assay was able to detect H1N1/2009 and distinguish it from other influenza A viruses. This new method may be useful for simultaneous detection and subtyping of influenza A viruses and can be rapidly modified to detect other emerging influenza strains in public health settings.\",\n \"corpus_id\": 8510715,\n \"score\": 0\n },\n {\n \"doc_id\": \"23429089\",\n \"title\": \"Composition of hemagglutinin and neuraminidase affects the antigen yield of influenza A(H1N1)pdm09 candidate vaccine viruses.\",\n \"abstract\": \"To improve the hemagglutinin (HA) antigen yield of influenza A(H1N1)pdm09 candidate vaccine viruses, we generated 7:1, 6:2, and 5:3 genetic reassortant viruses between wild-type (H1N1)pdm09 (A/California/7/2009) (Cal7) and a high-yielding master virus, A/Puerto Rico/8/34 (PR8). These viruses contained the HA; HA and neuraminidase (NA); and HA, NA, and M genes, respectively, derived from Cal7, on a PR8 backbone. The influence of the amino acid residue at position 223 in Cal7 HA on virus growth and HA antigen yield differed between these reassortant viruses. NIIDRG-7, a 7:1 virus possessing arginine at position 223, exhibited a 10-fold higher 50% egg infectious dose (EID(50)) (10.0 log(10)EID(50)/ml) than the 5:3 and 6:2 viruses. It also had 1.5- to 3-fold higher protein (13.8 μg/ml of allantoic fluids) and HA antigen (4.1 μg/ml of allantoic fluids) yields than the 5:3 and 6:2 viruses, which possessed identical Cal7 HA proteins. However, the HA antigen yield of the other 7:1 virus, which possessed glutamine at position 223 was 60% of that of NIIDRG-7. In addition, a novel 6:2 virus possessing Cal7 HA and the NA of A/Wisconsin/10/98 (a triple reassortant swine-like H1N1 virus), produced 107% of the HA yield of NIIDRG-7. In this study, we showed that the balance between HA and NA in the influenza A(H1N1)pdm09 virus affects its protein and antigen yield.\",\n \"corpus_id\": 8475880,\n \"score\": 0\n },\n {\n \"doc_id\": \"23929468\",\n \"title\": \"Complete Genome Sequences of Novel Reassortant H1N2 Swine Influenza Viruses Isolated from Pigs in the Republic of Korea.\",\n \"abstract\": \"Novel reassortant swine H1N2 influenza viruses were isolated from pigs in a commercial slaughterhouse in the Republic of Korea. Genome sequence analyses revealed that these isolates contain segments from Eurasian avian-like swine (hemagglutinin [HA]), Korean swine H1N2 (neuraminidase [NA]), and North American H3N2pM-like (remaining genes) viruses. Further characterization is needed to gauge the potential threats of these viruses to public health.\",\n \"corpus_id\": 29570839,\n \"score\": 0\n },\n {\n \"doc_id\": \"24051313\",\n \"title\": \"Influenza a virus with a human-like n2 gene is circulating in pigs.\",\n \"abstract\": \"A novel reassortant influenza A virus, H1avN2hu, has been found in Danish swine. The virus contains an H1 gene similar to the hemagglutinin (HA) gene of H1N1 avian-like swine viruses and an N2 gene most closely related to the neuraminidase (NA) gene of human H3N2 viruses from the mid-1990s.\",\n \"corpus_id\": 29890690,\n \"score\": 0\n },\n {\n \"doc_id\": \"24150926\",\n \"title\": \"Hemagglutinin and neuraminidase genes of influenza B viruses circulating in Riyadh, Saudi Arabia during 2010-2011: evolution and sequence analysis.\",\n \"abstract\": \"Influenza viruses are known as continuing threats to human public health every year worldwide. Evolutionary dynamics of influenza B viruses in humans are in a unique progression having two lineages; B/Yam and B/Vic-like viruses, which are circulating simultaneously worldwide. There is a considerable lack of data on influenza B viruses circulating in Saudi Arabia. During the winter-spring season of 2010-2011, 80 nasopharyngeal aspirates were collected from hospitalized patients with flu-like symptoms in Riyadh. Screening of samples by one-step RT-PCR identified three (3.8%) influenza B viruses. Sequencing of hemagglutinin (HA) and neuraminidase (NA) genes was performed to analyze influenza B viruses circulating in Riyadh as compared to the globally circulating strains. Several common and six unique amino acid substitutions were observed for both HA and NA genes of influenza B Saudi strains. Three unique substitutions (T182A, D196N, and K254R) were identified in HA gene of the B/Yam-like Riyadh strains. In NA gene, a unique common substitution (D53G) was found in all Riyadh strains, while two unique substitutions (L38P, G233R) were recognized only in B/Vic-like Riyadh strains. Riyadh strains were also found to contain N-glycosylation site in HA gene of both B/Vic and B/Yam lineages at positions 197-199 (NET) and 196-198 (NNK/DNK), respectively. The significance of these mutations on the antigenicity of both lineages is discussed herein. The unique changes observed in HA and NA genes of influenza B Riyadh strains support strongly the need for continuous surveillance and monitoring of new evolving strains that might pose threat to the Saudi community.\",\n \"corpus_id\": 2898522,\n \"score\": 0\n },\n {\n \"doc_id\": \"24155384\",\n \"title\": \"Activation of influenza A viruses by host proteases from swine airway epithelium.\",\n \"abstract\": \"Pigs are important natural hosts of influenza A viruses, and due to their susceptibility to swine, avian, and human viruses, they may serve as intermediate hosts supporting adaptation and genetic reassortment. Cleavage of the influenza virus surface glycoprotein hemagglutinin (HA) by host cell proteases is essential for viral infectivity. Most influenza viruses, including human and swine viruses, are activated at a monobasic HA cleavage site, and we previously identified TMPRSS2 and HAT to be relevant proteases present in human airways. We investigated the proteolytic activation of influenza viruses in primary porcine tracheal and bronchial epithelial cells (PTEC and PBEC, respectively). Human H1N1 and H3N2 viruses replicated efficiently in PTECs and PBECs, and viruses containing cleaved HA were released from infected cells. Moreover, the cells supported the proteolytic activation of HA at the stage of entry. We found that swine proteases homologous to TMPRSS2 and HAT, designated swTMPRSS2 and swAT, respectively, were expressed in several parts of the porcine respiratory tract. Both proteases cloned from primary PBECs were shown to activate HA with a monobasic cleavage site upon coexpression and support multicycle replication of influenza viruses. swAT was predominantly localized at the plasma membrane, where it was present as an active protease that mediated activation of incoming virus. In contrast, swTMPRSS2 accumulated in the trans-Golgi network, suggesting that it cleaves HA in this compartment. In conclusion, our data show that HA activation in porcine airways may occur by similar proteases and at similar stages of the viral life cycle as in human airways.\",\n \"corpus_id\": 20076045,\n \"score\": 0\n },\n {\n \"doc_id\": \"24371061\",\n \"title\": \"Evaluation of three live attenuated H2 pandemic influenza vaccine candidates in mice and ferrets.\",\n \"abstract\": \"UNLABELLED: H2 influenza viruses have not circulated in humans since 1968, and therefore a significant portion of the population would be susceptible to infection should H2 influenza viruses reemerge. H2 influenza viruses continue to circulate in avian reservoirs worldwide, and these reservoirs are a potential source from which these viruses could emerge. Three reassortant cold-adapted (ca) H2 pandemic influenza vaccine candidates with hemagglutinin (HA) and neuraminidase (NA) genes derived from the wild-type A/Japan/305/1957 (H2N2) (Jap/57), A/mallard/6750/1978 (H2N2) (mal/78), or A/swine/MO/4296424/2006 (H2N3) (sw/06) viruses and the internal protein gene segments from the A/Ann Arbor/6/60 ca virus were generated by plasmid-based reverse genetics (Jap/57 ca, mal/78 ca, and sw/06 ca, respectively). The vaccine candidates exhibited the in vitro phenotypes of temperature sensitivity and cold adaptation and were restricted in replication in the respiratory tract of ferrets. In mice and ferrets, the vaccines elicited neutralizing antibodies and conferred protection against homologous wild-type virus challenge. Of the three candidates, the sw/06 ca vaccine elicited cross-reactive antibodies and provided significant protection against the greatest number of heterologous viruses. These observations suggest that the sw/06 ca vaccine should be further evaluated in a clinical trial as an H2 pandemic influenza vaccine candidate. IMPORTANCE: Influenza pandemics arise when novel influenza viruses are introduced into a population with little prior immunity to the new virus and often result in higher rates of illness and death than annual seasonal influenza epidemics. An influenza H2 subtype virus caused a pandemic in 1957, and H2 viruses circulated in humans till 1968. H2 influenza viruses continue to circulate in birds, and the development of an H2 influenza vaccine candidate is therefore considered a priority in preparing for future pandemics. However, we cannot predict whether a human H2 virus will reemerge or a novel avian H2 virus will emerge. We identified three viruses as suitable candidates for further evaluation as vaccines to protect against H2 influenza viruses and evaluated the immune responses and protection that these three vaccines provided in mice and ferrets.\",\n \"corpus_id\": 25925133,\n \"score\": 0\n },\n {\n \"doc_id\": \"24404173\",\n \"title\": \"ClassyFlu: classification of influenza A viruses with Discriminatively trained profile-HMMs.\",\n \"abstract\": \"Accurate and rapid characterization of influenza A virus (IAV) hemagglutinin (HA) and neuraminidase (NA) sequences with respect to subtype and clade is at the basis of extended diagnostic services and implicit to molecular epidemiologic studies. ClassyFlu is a new tool and web service for the classification of IAV sequences of the HA and NA gene into subtypes and phylogenetic clades using discriminatively trained profile hidden Markov models (HMMs), one for each subtype or clade. ClassyFlu merely requires as input unaligned, full-length or partial HA or NA DNA sequences. It enables rapid and highly accurate assignment of HA sequences to subtypes H1-H17 but particularly focusses on the finer grained assignment of sequences of highly pathogenic avian influenza viruses of subtype H5N1 according to the cladistics proposed by the H5N1 Evolution Working Group. NA sequences are classified into subtypes N1-N10. ClassyFlu was compared to semiautomatic classification approaches using BLAST and phylogenetics and additionally for H5 sequences to the new \\\"Highly Pathogenic H5N1 Clade Classification Tool\\\" (IRD-CT) proposed by the Influenza Research Database. Our results show that both web tools (ClassyFlu and IRD-CT), although based on different methods, are nearly equivalent in performance and both are more accurate and faster than semiautomatic classification. A retraining of ClassyFlu to altered cladistics as well as an extension of ClassyFlu to other IAV genome segments or fragments thereof is undemanding. This is exemplified by unambiguous assignment to a distinct cluster within subtype H7 of sequences of H7N9 viruses which emerged in China early in 2013 and caused more than 130 human infections. http://bioinf.uni-greifswald.de/ClassyFlu is a free web service. For local execution, the ClassyFlu source code in PERL is freely available.\",\n \"corpus_id\": 14408947,\n \"score\": 0\n },\n {\n \"doc_id\": \"24429367\",\n \"title\": \"The M segment of the 2009 pandemic influenza virus confers increased neuraminidase activity, filamentous morphology, and efficient contact transmissibility to A/Puerto Rico/8/1934-based reassortant viruses.\",\n \"abstract\": \"UNLABELLED: The 2009 H1N1 lineage represented the first detection of a novel, highly transmissible influenza A virus genotype: six gene segments originated from the North American triple-reassortant swine lineage, and two segments, NA and M, derived from the Eurasian avian-like swine lineage. As neither parental lineage transmits efficiently between humans, the adaptations and mechanisms underlying the pandemic spread of the swine-origin 2009 strain are not clear. To help identify determinants of transmission, we used reverse genetics to introduce gene segments of an early pandemic isolate, A/Netherlands/602/2009 [H1N1] (NL602), into the background of A/Puerto Rico/8/1934 [H1N1] (PR8) and evaluated the resultant viruses in a guinea pig transmission model. Whereas the NL602 virus spread efficiently, the PR8 virus did not transmit. Swapping of the HA, NA, and M segments of NL602 into the PR8 background yielded a virus with indistinguishable contact transmissibility to the wild-type pandemic strain. Consistent with earlier reports, the pandemic M segment alone accounted for much of the improvement in transmission. To aid in understanding how the M segment might affect transmission, we evaluated neuraminidase activity and virion morphology of reassortant viruses. Transmission was found to correlate with higher neuraminidase activity and a more filamentous morphology. Importantly, we found that introduction of the pandemic M segment alone resulted in an increase in the neuraminidase activity of two pairs of otherwise isogenic PR8-based viruses. Thus, our data demonstrate the surprising result that functions encoded by the influenza A virus M segment impact neuraminidase activity and, perhaps through this mechanism, have a potent effect on transmissibility. IMPORTANCE: Our work uncovers a previously unappreciated mechanism through which the influenza A virus M segment can alter the receptor-destroying activity of an influenza virus. Concomitant with changes to neuraminidase activity, the M segment impacts the morphology of the influenza A virion and transmissibility of the virus in the guinea pig model. We suggest that changes in NA activity underlie the ability of the influenza M segment to influence virus transmissibility. Furthermore, we show that coadapted M, NA, and HA segments are required to provide optimal transmissibility to an influenza virus. The M-NA functional interaction we describe appears to underlie the prominent role of the 2009 pandemic M segment in supporting efficient transmission and may be a highly important means by which influenza A viruses restore HA/NA balance following reassortment or transfer to new host environments.\",\n \"corpus_id\": 5992849,\n \"score\": 0\n },\n {\n \"doc_id\": \"24523938\",\n \"title\": \"Phylogenetic analysis of a swine influenza A(H3N2) virus isolated in Korea in 2012.\",\n \"abstract\": \"Influenza A virus (IAV) can infect avian and mammalian species, including humans. The genome nature of IAVs may contribute to viral adaptation in different animal hosts, resulting in gene reassortment and the reproduction of variants with optimal fitness. As seen again in the 2009 swine-origin influenza A H1N1 pandemic, pigs are known to be susceptible to swine, avian, and human IAVs and can serve as a 'mixing vessel' for the generation of novel IAV variants. To this end, the emergence of swine influenza viruses must be kept under close surveillance. Herein, we report the isolation and phylogenetic study of a swine IAV, A/swine/Korea/PL01/2012 (swPL01, H3N2 subtype). After screening nasopharyngeal samples from pigs in the Gyeongsangnam-do region of Korea from December 2011 to May 2012, we isolated the swPL01 virus and sequenced its all of 8 genome segments (polymerase basic 2, PB2; polymerase basic 1, PB1; polymerase acidic, PA; hemagglutinin, HA; nucleocapsid protein, NP; neuraminidase, NA; matrix protein, M; and nonstructural protein, NS). The phylogenetic study, analyzed with reference strains registered in the National Center for Biotechnology Information (NCBI) database, indicated that the swPL01 virus was similar to the North American triple-reassortant swine strains and that the HA gene of the swPL01 virus was categorized into swine H3 cluster IV. The swPL01 virus had the M gene of the triple-reassortant swine H3N2 viruses, whereas that of other contemporary strains in Korea was transferred from the 2009 pandemic H1N1 virus. These data suggest the possibility that various swine H3N2 viruses may co-circulate in Korea, which underlines the importance of a sustained surveillance system against swine IAVs.\",\n \"corpus_id\": 4586165,\n \"score\": 0\n },\n {\n \"doc_id\": \"24579700\",\n \"title\": \"T-cell immunity to influenza A viruses.\",\n \"abstract\": \"Influenza infection remains a global threat to human health. Influenza viruses are normally controlled by antibodies specific for the surface glycoproteins hemagglutinin (HA) and neuraminidase (NA). Standard influenza vaccines are aimed at inducing these antibodies, but they must be administered annually and can be rendered ineffective since different strains circulate from year to year and vary considerably in their individual HA and NA profiles. Influenza-specific T cells have been shown to be protective in animal models and typically recognize the more conserved internal influenza proteins. Improving our understanding of influenza-specific T-cell responses, including immunodominance, specific epitope sequences, strain-related epitope variation, host/virus interaction, and the balance between immunity versus immunopathology, will be important to improve future T-cell-based vaccines, which promise broader strain coverage and longer-lasting protection than current standard vaccines.\",\n \"corpus_id\": 34087472,\n \"score\": 0\n },\n {\n \"doc_id\": \"24582528\",\n \"title\": \"Bat-derived influenza-like viruses H17N10 and H18N11.\",\n \"abstract\": \"Shorebirds and waterfowls are believed to be the reservoir hosts for influenza viruses, whereas swine putatively act as mixing vessels. The recent identification of two influenza-like virus genomes (designated H17N10 and H18N11) from bats has challenged this notion. A crucial question concerns the role bats might play in influenza virus ecology. Structural and functional studies of the two major surface envelope proteins, hemagglutinin (HA) and neuraminidase (NA), demonstrate that neither has canonical HA or NA functions found in influenza viruses. However, putative functional modules and domains in other encoded proteins are conserved, and the N-terminal domain of the H17N10 polymerase subunit PA has a classical structure and function. Therefore, potential genomic reassortments of such influenza-like viruses with canonical influenza viruses cannot be excluded at this point and should be assessed.\",\n \"corpus_id\": 7606490,\n \"score\": 0\n },\n {\n \"doc_id\": \"24809455\",\n \"title\": \"Understanding the undelaying mechanism of HA-subtyping in the level of physic-chemical characteristics of protein.\",\n \"abstract\": \"The evolution of the influenza A virus to increase its host range is a major concern worldwide. Molecular mechanisms of increasing host range are largely unknown. Influenza surface proteins play determining roles in reorganization of host-sialic acid receptors and host range. In an attempt to uncover the physic-chemical attributes which govern HA subtyping, we performed a large scale functional analysis of over 7000 sequences of 16 different HA subtypes. Large number (896) of physic-chemical protein characteristics were calculated for each HA sequence. Then, 10 different attribute weighting algorithms were used to find the key characteristics distinguishing HA subtypes. Furthermore, to discover machine leaning models which can predict HA subtypes, various Decision Tree, Support Vector Machine, Naïve Bayes, and Neural Network models were trained on calculated protein characteristics dataset as well as 10 trimmed datasets generated by attribute weighting algorithms. The prediction accuracies of the machine learning methods were evaluated by 10-fold cross validation. The results highlighted the frequency of Gln (selected by 80% of attribute weighting algorithms), percentage/frequency of Tyr, percentage of Cys, and frequencies of Try and Glu (selected by 70% of attribute weighting algorithms) as the key features that are associated with HA subtyping. Random Forest tree induction algorithm and RBF kernel function of SVM (scaled by grid search) showed high accuracy of 98% in clustering and predicting HA subtypes based on protein attributes. Decision tree models were successful in monitoring the short mutation/reassortment paths by which influenza virus can gain the key protein structure of another HA subtype and increase its host range in a short period of time with less energy consumption. Extracting and mining a large number of amino acid attributes of HA subtypes of influenza A virus through supervised algorithms represent a new avenue for understanding and predicting possible future structure of influenza pandemics.\",\n \"corpus_id\": 14595349,\n \"score\": 0\n },\n {\n \"doc_id\": \"25047593\",\n \"title\": \"In silico structural homology modelling and docking for assessment of pandemic potential of a novel H7N9 influenza virus and its ability to be neutralized by existing anti-hemagglutinin antibodies.\",\n \"abstract\": \"The unpredictable nature of pandemic influenza and difficulties in early prediction of pandemic potential of new isolates present a major challenge for health planners. Vaccine manufacturers, in particular, are reluctant to commit resources to development of a new vaccine until after a pandemic is declared. We hypothesized that a structural bioinformatics approach utilising homology-based molecular modelling and docking approaches would assist prediction of pandemic potential of new influenza strains alongside more traditional laboratory and sequence-based methods. The newly emerged Chinese A/Hangzhou/1/2013 (H7N9) influenza virus provided a real-life opportunity to test this hypothesis. We used sequence data and a homology-based approach to construct a 3D-structural model of H7-Hangzhou hemagglutinin (HA) protein. This model was then used to perform docking to human and avian sialic acid receptors to assess respective binding affinities. The model was also used to perform docking simulations with known neutralizing antibodies to assess their ability to neutralize the newly emerged virus. The model predicted H7N9 could bind to human sialic acid receptors thereby indicating pandemic potential. The model also confirmed that existing antibodies against the HA head region are unable to neutralise H7N9 whereas antibodies, e.g. Cr9114, targeting the HA stalk region should bind with high affinity to H7N9. This indicates that existing stalk antibodies initially raised against H5N1 or other influenza A viruses could be therapeutically beneficial in prevention and/or treatment of H7N9 infections. The subsequent publication of the H7N9 HA crystal structure confirmed the accuracy of our in-silico structural model. Antibody docking studies performed using the H7N9 HA crystal structure supported the model's prediction that existing stalk antibodies could cross-neutralise the H7N9 virus. This study demonstrates the value of using in-silico structural modelling approaches to complement physical studies in characterization of new influenza viruses.\",\n \"corpus_id\": 16990134,\n \"score\": 0\n },\n {\n \"doc_id\": \"25122789\",\n \"title\": \"The matrix gene segment destabilizes the acid and thermal stability of the hemagglutinin of pandemic live attenuated influenza virus vaccines.\",\n \"abstract\": \"UNLABELLED: The threat of future influenza pandemics and their potential for rapid spread, morbidity, and mortality has led to the development of pandemic vaccines. We generated seven reassortant pandemic live attenuated influenza vaccines (pLAIVs) with the hemagglutinin (HA) and neuraminidase (NA) genes derived from animal influenza viruses on the backbone of the six internal protein gene segments of the temperature sensitive, cold-adapted (ca) A/Ann Arbor/60 (H2N2) virus (AA/60 ca) of the licensed seasonal LAIV. The pLAIV viruses were moderately to highly restricted in replication in seronegative adults; we sought to determine the biological basis for this restriction. Avian influenza viruses generally replicate at higher temperatures than human influenza viruses and, although they shared the same backbone, the pLAIV viruses had a lower shutoff temperature than seasonal LAIV viruses, suggesting that the HA and NA influence the degree of temperature sensitivity. The pH of HA activation of highly pathogenic avian influenza viruses was greater than human and low-pathogenicity avian influenza viruses, as reported by others. However, pLAIV viruses had a consistently higher pH of HA activation and reduced HA thermostability compared to the corresponding wild-type parental viruses. From studies with single-gene reassortant viruses bearing one gene segment from the AA/60 ca virus in recombinant H5N1 or pH1N1 viruses, we found that the lower HA thermal stability and increased pH of HA activation were associated with the AA/60 M gene. Together, the impaired HA acid and thermal stability and temperature sensitivity likely contributed to the restricted replication of the pLAIV viruses we observed in seronegative adults. IMPORTANCE: There is increasing evidence that the HA stability of influenza viruses depends on the virus strain and host species and that HA stability can influence replication, virulence, and transmission of influenza A viruses in different species. We investigated the HA stability of pandemic live attenuated influenza vaccine (pLAIV) viruses and observed that the pLAIV viruses consistently had a less stable HA than the corresponding wild-type influenza viruses. The reduced HA stability and temperature sensitivity of the pLAIV viruses may account for their restricted replication in clinical trials.\",\n \"corpus_id\": 40923043,\n \"score\": 0\n },\n {\n \"doc_id\": \"25762737\",\n \"title\": \"Swine Influenza Virus PA and Neuraminidase Gene Reassortment into Human H1N1 Influenza Virus Is Associated with an Altered Pathogenic Phenotype Linked to Increased MIP-2 Expression.\",\n \"abstract\": \"UNLABELLED: Swine are susceptible to infection by both avian and human influenza viruses, and this feature is thought to contribute to novel reassortant influenza viruses. In this study, the influenza virus reassortment rate in swine and human cells was determined. Coinfection of swine cells with 2009 pandemic H1N1 virus (huH1N1) and an endemic swine H1N2 (A/swine/Illinois/02860/09) virus (swH1N2) resulted in a 23% reassortment rate that was independent of α2,3- or α2,6-sialic acid distribution on the cells. The reassortants had altered pathogenic phenotypes linked to introduction of the swine virus PA and neuraminidase (NA) into huH1N1. In mice, the huH1N1 PA and NA mediated increased MIP-2 expression early postinfection, resulting in substantial pulmonary neutrophilia with enhanced lung pathology and disease. The findings support the notion that swine are a mixing vessel for influenza virus reassortants independent of sialic acid distribution. These results show the potential for continued reassortment of the 2009 pandemic H1N1 virus with endemic swine viruses and for reassortants to have increased pathogenicity linked to the swine virus NA and PA genes which are associated with increased pulmonary neutrophil trafficking that is related to MIP-2 expression. IMPORTANCE: Influenza A viruses can change rapidly via reassortment to create a novel virus, and reassortment can result in possible pandemics. Reassortments among subtypes from avian and human viruses led to the 1957 (H2N2 subtype) and 1968 (H3N2 subtype) human influenza pandemics. Recent analyses of circulating isolates have shown that multiple genes can be recombined from human, avian, and swine influenza viruses, leading to triple reassortants. Understanding the factors that can affect influenza A virus reassortment is needed for the establishment of disease intervention strategies that may reduce or preclude pandemics. The findings from this study show that swine cells provide a mixing vessel for influenza virus reassortment independent of differential sialic acid distribution. The findings also establish that circulating neuraminidase (NA) and PA genes could alter the pathogenic phenotype of the pandemic H1N1 virus, resulting in enhanced disease. The identification of such factors provides a framework for pandemic modeling and surveillance.\",\n \"corpus_id\": 206790500,\n \"score\": 0\n },\n {\n \"doc_id\": \"25810540\",\n \"title\": \"Pandemic Swine H1N1 Influenza Viruses with Almost Undetectable Neuraminidase Activity Are Not Transmitted via Aerosols in Ferrets and Are Inhibited by Human Mucus but Not Swine Mucus.\",\n \"abstract\": \"UNLABELLED: A balance between the functions of the influenza virus surface proteins hemagglutinin (HA) and neuraminidase (NA) is thought to be important for the transmission of viruses between humans. Here we describe two pandemic H1N1 viruses, A/swine/Virginia/1814-1/2012 and A/swine/Virginia/1814-2/2012 (pH1N1low-1 and -2, respectively), that were isolated from swine symptomatic for influenza. The enzymatic activity of the NA of these viruses was almost undetectable, while the HA binding affinity for α2,6 sialic acids was greater than that of the highly homologous pH1N1 viruses A/swine/Pennsylvania/2436/2012 and A/swine/Minnesota/2499/2012 (pH1N1-1 and -2), which exhibited better-balanced HA and NA activities. The in vitro growth kinetics of pH1N1low and pH1N1 viruses were similar, but aerosol transmission of pH1N1low-1 was abrogated and transmission via direct contact in ferrets was significantly impaired compared to pH1N1-1, which transmitted by direct and aerosol contact. In normal human bronchial epithelial cells, pH1N1low-1 was significantly inhibited by mucus but pH1N1-1 was not. In Madin-Darby canine kidney cell cultures overlaid with human or swine mucus, human mucus inhibited pH1N1low-1 but swine mucus did not. These data show that the interaction between viruses and mucus may be an important factor in viral transmissibility and could be a barrier for interspecies transmission between humans and swine for influenza viruses. IMPORTANCE: A balance between the functions of the influenza virus surface proteins hemagglutinin (HA) and neuraminidase (NA) is thought to be important for transmission of viruses from swine to humans. Here we show that a swine virus with extremely functionally mismatched HA and NAs (pH1N1low-1) cannot transmit via aerosol in ferrets, while another highly homologous virus with HA and NAs that are better matched functionally (pH1N1-1) can transmit via aerosol. These viruses show similar growth kinetics in Madin-Darby canine kidney (MDCK) cells, but pH1N1low-1 is significantly inhibited by mucus in normal human bronchial epithelial cells whereas pH1N1-1 is not. Further, human mucus could inhibit these viruses, but swine mucus could not. These data show that the interaction between viruses and mucus may be an important factor in viral transmissibility and could be a species barrier between humans and swine for influenza viruses.\",\n \"corpus_id\": 43108163,\n \"score\": 0\n },\n {\n \"doc_id\": \"25812763\",\n \"title\": \"Transmission of influenza A viruses.\",\n \"abstract\": \"Influenza A viruses cause respiratory infections that range from asymptomatic to deadly in humans. Widespread outbreaks (pandemics) are attributable to 'novel' viruses that possess a viral hemagglutinin (HA) gene to which humans lack immunity. After a pandemic, these novel viruses form stable virus lineages in humans and circulate until they are replaced by other novel viruses. The factors and mechanisms that facilitate virus transmission among hosts and the establishment of novel lineages are not completely understood, but the HA and basic polymerase 2 (PB2) proteins are thought to play essential roles in these processes by enabling avian influenza viruses to infect mammals and replicate efficiently in their new host. Here, we summarize our current knowledge of the contributions of HA, PB2, and other viral components to virus transmission and the formation of new virus lineages.\",\n \"corpus_id\": 25306860,\n \"score\": 0\n },\n {\n \"doc_id\": \"26049044\",\n \"title\": \"Evolutionary trajectories and diagnostic challenges of potentially zoonotic avian influenza viruses H5N1 and H9N2 co-circulating in Egypt.\",\n \"abstract\": \"In Egypt, since 2006, descendants of the highly pathogenic avian influenza virus (HP AIV) H5N1 of clade 2.2 continue to cause sharp losses in poultry production and seriously threaten public health. Potentially zoonotic H9N2 viruses established an endemic status in poultry in Egypt as well and co-circulate with HP AIV H5N1 rising concerns of reassortments between H9N2 and H5N1 viruses along with an increase of mixed infections of poultry. Nucleotide sequences of whole genomes of 15 different isolates (H5N1: 7; H9N2: 8), and of the hemagglutinin (HA) and neuraminidase (NA) encoding segments of nine further clinical samples (H5N1: 2; H9N2: 7) from 2013 and 2014 were generated and analysed. The HA of H5N1 viruses clustered with clade 2.2.1 while the H9 HA formed three distinguishable subgroups within cluster B viruses. BEAST analysis revealed that H9N2 viruses are likely present in Egypt since 2009. Several previously undescribed substituting mutations putatively associated with host tropism and virulence modulation were detected in different proteins of the analysed H9N2 and H5N1 viruses. Reassortment between HP AIV H5N1 and H9N2 is anticipated in Egypt, and timely detection of such events is of public health concern. As a rapid tool for detection of such reassortants discriminative SYBR-Green reverse transcription real-time PCR assays (SG-RT-qPCR), targeting the internal genes of the Egyptian H5N1 and H9N2 viruses were developed for the rapid screening of viral RNAs from both virus isolates and clinical samples. However, in accordance to Sanger sequencing, no reassortants were found by SG-RT-qPCR. Nevertheless, the complex epidemiology of avian influenza in poultry in Egypt will require sustained close observation. Further development and continuing adaptation of rapid and cost-effective screening assays such as the SG-RT-qPCR protocol developed here are at the basis of efforts for improvement the currently critical situation.\",\n \"corpus_id\": 1763820,\n \"score\": 0\n },\n {\n \"doc_id\": \"26091504\",\n \"title\": \"In Silico Prediction and Experimental Confirmation of HA Residues Conferring Enhanced Human Receptor Specificity of H5N1 Influenza A Viruses.\",\n \"abstract\": \"Newly emerging influenza A viruses (IAV) pose a major threat to human health by causing seasonal epidemics and/or pandemics, the latter often facilitated by the lack of pre-existing immunity in the general population. Early recognition of candidate pandemic influenza viruses (CPIV) is of crucial importance for restricting virus transmission and developing appropriate therapeutic and prophylactic strategies including effective vaccines. Often, the pandemic potential of newly emerging IAV is only fully recognized once the virus starts to spread efficiently causing serious disease in humans. Here, we used a novel phylogenetic algorithm based on the informational spectrum method (ISM) to identify potential CPIV by predicting mutations in the viral hemagglutinin (HA) gene that are likely to (differentially) affect critical interactions between the HA protein and target cells from bird and human origin, respectively. Predictions were subsequently validated by generating pseudotyped retrovirus particles and genetically engineered IAV containing these mutations and characterizing potential effects on virus entry and replication in cells expressing human and avian IAV receptors, respectively. Our data suggest that the ISM-based algorithm is suitable to identify CPIV among IAV strains that are circulating in animal hosts and thus may be a new tool for assessing pandemic risks associated with specific strains.\",\n \"corpus_id\": 25331462,\n \"score\": 0\n },\n {\n \"doc_id\": \"26292325\",\n \"title\": \"Unique Determinants of Neuraminidase Inhibitor Resistance among N3, N7, and N9 Avian Influenza Viruses.\",\n \"abstract\": \"UNLABELLED: Human infections with avian influenza viruses are a serious public health concern. The neuraminidase (NA) inhibitors (NAIs) are the frontline anti-influenza drugs and are the major option for treatment of newly emerging influenza. Therefore, it is essential to identify the molecular markers of NAI resistance among specific NA subtypes of avian influenza viruses to help guide clinical management. NAI-resistant substitutions in NA subtypes other than N1 and N2 have been poorly studied. Here, we identified NA amino acid substitutions associated with NAI resistance among influenza viruses of N3, N7, and N9 subtypes which have been associated with zoonotic transmission. We applied random mutagenesis and generated recombinant influenza viruses carrying single or double NA substitution(s) with seven internal genes from A/Puerto Rico/8/1934 (H1N1) virus. In a fluorescence-based NA inhibition assay, we identified three categories of NA substitutions associated with reduced inhibition by NAIs (oseltamivir, zanamivir, and peramivir): (i) novel subtype-specific substitutions in or near the enzyme catalytic site (R152W, A246T, and D293N, N2 numbering), (ii) subtype-independent substitutions (E119G/V and/or D and R292K), and (iii) substitutions previously reported in other subtypes (Q136K, I222M, and E276D). Our data show that although some markers of resistance are present across NA subtypes, other subtype-specific markers can only be determined empirically. IMPORTANCE: The number of humans infected with avian influenza viruses is increasing, raising concerns of the emergence of avian influenza viruses resistant to neuraminidase (NA) inhibitors (NAIs). Since most studies have focused on NAI-resistance in human influenza viruses, we investigated the molecular changes in NA that could confer NAI resistance in avian viruses grown in immortalized monolayer cells, especially those of the N3, N7, and N9 subtypes, which have caused human infections. We identified not only numerous NAI-resistant substitutions previously reported in other NA subtypes but also several novel changes conferring reduced susceptibility to NAIs, which are subtype specific. The findings indicate that some resistance markers are common across NA subtypes, but other markers need to be determined empirically for each subtype. The study also implies that antiviral surveillance monitoring could play a critical role in the clinical management of influenza virus infection and an essential component of pandemic preparedness.\",\n \"corpus_id\": 25503607,\n \"score\": 0\n },\n {\n \"doc_id\": \"26311895\",\n \"title\": \"Novel Reassortant Human-Like H3N2 and H3N1 Influenza A Viruses Detected in Pigs Are Virulent and Antigenically Distinct from Swine Viruses Endemic to the United States.\",\n \"abstract\": \"UNLABELLED: Human-like swine H3 influenza A viruses (IAV) were detected by the USDA surveillance system. We characterized two novel swine human-like H3N2 and H3N1 viruses with hemagglutinin (HA) genes similar to those in human seasonal H3 strains and internal genes closely related to those of 2009 H1N1 pandemic viruses. The H3N2 neuraminidase (NA) was of the contemporary human N2 lineage, while the H3N1 NA was of the classical swine N1 lineage. Both viruses were antigenically distant from swine H3 viruses that circulate in the United States and from swine vaccine strains and also showed antigenic drift from human seasonal H3N2 viruses. Their pathogenicity and transmission in pigs were compared to those of a human H3N2 virus with a common HA ancestry. Both swine human-like H3 viruses efficiently infected pigs and were transmitted to indirect contacts, whereas the human H3N2 virus did so much less efficiently. To evaluate the role of genes from the swine isolates in their pathogenesis, reverse genetics-generated reassortants between the swine human-like H3N1 virus and the seasonal human H3N2 virus were tested in pigs. The contribution of the gene segments to virulence was complex, with the swine HA and internal genes showing effects in vivo. The experimental infections indicate that these novel H3 viruses are virulent and can sustain onward transmission in pigs, and the naturally occurring mutations in the HA were associated with antigenic divergence from H3 IAV from humans and swine. Consequently, these viruses could have a significant impact on the swine industry if they were to cause more widespread outbreaks, and the potential risk of these emerging swine IAV to humans should be considered. IMPORTANCE: Pigs are important hosts in the evolution of influenza A viruses (IAV). Human-to-swine transmissions of IAV have resulted in the circulation of reassortant viruses containing human-origin genes in pigs, greatly contributing to the diversity of IAV in swine worldwide. New human-like H3N2 and H3N1 viruses that contain a mix of human and swine gene segments were recently detected by the USDA surveillance system. The human-like viruses efficiently infected pigs and resulted in onward airborne transmission, likely due to the multiple changes identified between human and swine H3 viruses. The human-like swine viruses are distinct from contemporary U.S. H3 swine viruses and from the strains used in swine vaccines, which could have a significant impact on the swine industry due to a lack of population immunity. Additionally, public health experts should consider an appropriate assessment of the risk of these emerging swine H3 viruses for the human population.\",\n \"corpus_id\": 24388382,\n \"score\": 0\n },\n {\n \"doc_id\": \"27314023\",\n \"title\": \"Using the Relevance Vector Machine Model Combined with Local Phase Quantization to Predict Protein-Protein Interactions from Protein Sequences.\",\n \"abstract\": \"We propose a novel computational method known as RVM-LPQ that combines the Relevance Vector Machine (RVM) model and Local Phase Quantization (LPQ) to predict PPIs from protein sequences. The main improvements are the results of representing protein sequences using the LPQ feature representation on a Position Specific Scoring Matrix (PSSM), reducing the influence of noise using a Principal Component Analysis (PCA), and using a Relevance Vector Machine (RVM) based classifier. We perform 5-fold cross-validation experiments on Yeast and Human datasets, and we achieve very high accuracies of 92.65% and 97.62%, respectively, which is significantly better than previous works. To further evaluate the proposed method, we compare it with the state-of-the-art support vector machine (SVM) classifier on the Yeast dataset. The experimental results demonstrate that our RVM-LPQ method is obviously better than the SVM-based method. The promising experimental results show the efficiency and simplicity of the proposed method, which can be an automatic decision support tool for future proteomics research.\",\n \"corpus_id\": 479168,\n \"score\": 0\n },\n {\n \"doc_id\": \"28082971\",\n \"title\": \"Tracking the Evolution of Polymerase Genes of Influenza A Viruses during Interspecies Transmission between Avian and Swine Hosts.\",\n \"abstract\": \"Human influenza pandemics have historically been caused by reassortant influenza A viruses using genes from human and avian viruses. This genetic reassortment between human and avian viruses has been known to occur in swine during viral circulation, as swine are capable of circulating both avian and human viruses. Therefore, avian-to-swine transmission of viruses plays an important role in the emergence of new pandemic strains. The amino acids at several positions on PB2, PB1, and PA are known to determine the host range of influenza A viruses. In this paper, we track viral transmission between avian and swine to investigate the evolution on polymerase genes associated with their hosts. We traced viral transmissions between avian and swine hosts by using nucleotide sequences of avian viruses and swine viruses registered in the NCBI GenBank. Using BLAST and the reciprocal best hits technique, we found 32, 33, and 30 pairs of avian and swine nucleotide sequences that may be associated with avian-to-swine transmissions for PB2, PB1, and PA genes, respectively. Then, we examined the amino acid substitutions involved in these sporadic transmissions. On average, avian-to-swine transmission pairs had 5.47, 3.73, and 5.13 amino acid substitutions on PB2, PB1, and PA, respectively. However, amino acid substitutions were distributed over the positions, and few positions showed common substitutions in the multiple transmission events. Statistical tests on the number of repeated amino acid substitutions suggested that no specific positions on PB2 and PA may be required for avian viruses to infect swine. We also found that avian viruses that transmitted to swine tend to process I478V substitutions on PB2 before interspecies transmission events. Furthermore, most mutations occurred after the interspecies transmissions, possibly due to selective viral adaptation to swine.\",\n \"corpus_id\": 10366069,\n \"score\": 0\n },\n {\n \"doc_id\": \"28492483\",\n \"title\": \"PCVMZM: Using the Probabilistic Classification Vector Machines Model Combined with a Zernike Moments Descriptor to Predict Protein-Protein Interactions from Protein Sequences.\",\n \"abstract\": \"Protein-protein interactions (PPIs) are essential for most living organisms' process. Thus, detecting PPIs is extremely important to understand the molecular mechanisms of biological systems. Although many PPIs data have been generated by high-throughput technologies for a variety of organisms, the whole interatom is still far from complete. In addition, the high-throughput technologies for detecting PPIs has some unavoidable defects, including time consumption, high cost, and high error rate. In recent years, with the development of machine learning, computational methods have been broadly used to predict PPIs, and can achieve good prediction rate. In this paper, we present here PCVMZM, a computational method based on a Probabilistic Classification Vector Machines (PCVM) model and Zernike moments (ZM) descriptor for predicting the PPIs from protein amino acids sequences. Specifically, a Zernike moments (ZM) descriptor is used to extract protein evolutionary information from Position-Specific Scoring Matrix (PSSM) generated by Position-Specific Iterated Basic Local Alignment Search Tool (PSI-BLAST). Then, PCVM classifier is used to infer the interactions among protein. When performed on PPIs datasets of Yeast and H. Pylori, the proposed method can achieve the average prediction accuracy of 94.48% and 91.25%, respectively. In order to further evaluate the performance of the proposed method, the state-of-the-art support vector machines (SVM) classifier is used and compares with the PCVM model. Experimental results on the Yeast dataset show that the performance of PCVM classifier is better than that of SVM classifier. The experimental results indicate that our proposed method is robust, powerful and feasible, which can be used as a helpful tool for proteomics research.\",\n \"corpus_id\": 4418482,\n \"score\": 0\n }\n]","isConversational":false}}},{"rowIdx":84,"cells":{"query":{"kind":"string","value":"{\n \"doc_id\": \"28649418\",\n \"title\": \"Facilitating access to health research through a participatory research register: a feasibility study in outpatient clinics.\",\n \"abstract\": \"BACKGROUND: A research register (Reach West) has been established to facilitate recruitment of people and patients to health-related research. We conducted a prospective feasibility study to investigate the practicality of recruiting through outpatient clinics. METHODS: Patients over 18 years of age attending dental, eye or oncology outpatient clinics in an acute hospital in the West of England were provided with the opportunity to participate in Reach West. In Phase I, recruitment packs were handed to clinic attendees who could place completed consent forms in secure drop-box or return them later on-line or by post. In Phase II, recruitment packs were posted directly to patients with consent forms to be returned by post or on-line. Response rates by age, sex, postcode (for level of deprivation), and clinic type were recorded for those agreeing to participate on paper or on-line. RESULTS: In Phase I, 2,314 of 4,500 (51.4%) of recruitment packs were handed out to clinic attendees, and 114 (5%) consented to join Reach West. In Phase II, 7,173 of 9000 packs were posted (79.7%), and 387 (5.4%) consented to participate. The overall consent rate was 6% (580), with the majority doing so on paper (87%) rather than on-line. The sample was balanced by sex, but mostly comprised people over 50 years located in less deprived postcodes. Non-staff costs for postal recruitment were lower than hand-outs in clinic (£6.84 compared with £8.05 per participant). CONCLUSIONS: Recruiting participants to the Reach West register was feasible among those with oncology, dental or eye outpatient appointments by post or with packs given out in the clinic. Response rates were similar to those achieved for other registers. Recruitment of participants can be achieved through outpatient clinics but other strategies will also be required to attract large numbers of participants and more diverse populations.\",\n \"corpus_id\": 23061549\n}"},"candidates":{"kind":"list like","value":[{"doc_id":"24139174","title":"Acceptability and perceived barriers and facilitators to creating a national research register to enable 'direct to patient' enrolment into research: the Scottish Health Research Register (SHARE).","abstract":"BACKGROUND: Difficulties with recruitment pose a major, increasingly recognised challenge to the viability of research. We sought to explore whether a register of volunteers interested in research participation, with data linkage to electronic health records to identify suitable research participants, would prove acceptable to healthcare staff, patients and researchers. METHODS: We undertook a qualitative study in which a maximum variation sampling approach was adopted. Focus groups and interviews were conducted with patients, general practitioners (GP), practice managers and health service researchers in two Scottish health boards. Analysis was primarily thematic to identify a range of issues and concerns for all stakeholder groups. RESULTS: The concept of a national research register was, in general, acceptable to all stakeholder groups and was widely regarded as beneficial for research and for society. Patients, however, highlighted a number of conditions which should be met in the design of a register to expedite confidence and facilitate recruitment. They also gave their perceptions on how a register should operate and be promoted, favouring a range of media. GPs and practice managers were primarily concerned with the security and confidentiality of patient data and the impact a register may have on their workload. Researchers were supportive of the initiative seeing advantages in more rapid access to a wider pool of patients. They did raise concerns that GPs may be able to block access to personal patient data held in general practice clinical systems and that the register may not be representative of the whole population. CONCLUSIONS: This work suggests that patients, healthcare staff and researchers have a favourable view of the potential benefits of a national register to identify people who are potentially eligible and willing to participate in health related research. It has highlighted a number of issues for the developers to incorporate in the design of research registers.","corpus_id":5761028,"score":2},{"doc_id":"25354322","title":"Effectiveness of a community research registry to recruit minority and underserved adults for health research.","abstract":"BACKGROUND: Recruiting minorities and underserved populations into population-based studies is a long standing challenge. This study examined the feasibility of recruiting adults from a community research registry. METHODS: Ethnically diverse, bilingual staff attended health fairs, inviting adults to join a registry. We examined rates of successful contact, scheduling, and participation for studies that used the registry. RESULTS: Five studies queried 6,886 research registry members (48% Hispanic and 38% black) and attempted to contact 2,301 potentially eligible participants; eligibility criteria varied across studies. We successfully contacted 1,130 members, 51.9% were scheduled to participate and of those, 60.8% completed their study appointment. Non-Hispanic whites were less likely than Hispanics to be interested, but among those scheduling an appointment, participation did not differ by race/ethnicity. CONCLUSION: Community research registries are a feasible and efficient method for recruiting minority and underserved adults and may address disparities in access to and participation in health research.","corpus_id":20553211,"score":2},{"doc_id":"26769574","title":"Research participation registers can increase opportunities for patients and the public to participate in health services research.","abstract":"Members of the public and patients repeatedly indicate their willingness to take part in research, but current United Kingdom research governance involves complex rules about gaining consent. Research participation registers that seek consent from participants to be approached about future studies have several potential benefits, including: increased research participation across clinical and healthy populations; simplified recruitment to health care research; support for people's autonomy in decision making; and improved efficiency and generalizability of research. These potential benefits have to be balanced against ethical and governance considerations. With appropriate processes in place, seeking prospective consent from patients and members of the public to be approached about future studies could potentially increase public participation in health research without compromising informed consent and other ethical principles.","corpus_id":3364244,"score":2},{"doc_id":"27724888","title":"A consumer register: an acceptable and cost-effective alternative for accessing patient populations.","abstract":"BACKGROUND: Population-based registries are increasingly used to recruit patient samples for research, however, they have several limitations including low consent and participation rates, and potential selection bias. To improve access to samples for research, the utility of a new model of recruitment termed the 'Consumer Register', that allows for direct patient recruitment from hospitals, was examined. This paper reports: (i) consent rates onto the register; (ii) preferred methods and frequency of contact; and (iii) the feasibility of establishing the register, including: (a) cost per person recruited to the register; (b) the differential cost and consent rates of volunteer versus paid data collectors; and (c) participant completion rates. METHODS: A cross-sectional survey was conducted in five outpatient clinics in Australia. Patients were approached by volunteers or paid data collectors and asked to complete a touch-screen electronic survey. Consenting individuals were asked to indicate their willingness and preferences for enrolment onto a research register. Descriptive statistics were used to examine patient preferences and linear regression used to model the success of volunteer versus paid data collectors. The opportunity and financial costs of establishing the register were calculated. RESULTS: A total of 1947 patients (80.6 %) consented to complete the survey, of which, 1486 (76.3 %) completed the questionnaire. Of the completers, the majority (69.4 %, or 1032 participants) were willing to be listed on the register and preferred to be contacted by email (50.3 %). Almost 39 % of completers were willing to be contacted three or more times in a 12 month period. The annual opportunity cost of resources consumed by the register was valued at $37,187, giving an opportunity cost per person recruited to the register of $36. After amortising fixed costs, the annual financial outlay was $23,004 or $22 per person recruited to the register. Use of volunteer data collectors contributed to an annual saving of $14,183, however paid data collectors achieved significantly higher consent rates. Successful enrolment onto the register was completed for 42 % of the sample. CONCLUSIONS: A Consumer Register is a promising and feasible alternative to population-based registries, with the majority of participants willing to be contacted multiple times via low-resource methods such as email. There is an effectiveness/cost trade off in the use of paid versus volunteer data collectors.","corpus_id":4485730,"score":2},{"doc_id":"28148535","title":"Cohort profile: the Scottish Research register SHARE. A register of people interested in research participation linked to NHS data sets.","abstract":"PURPOSE: Recruitment to trials is often difficult. Many trials fail to meet recruitment targets resulting in underpowered studies which waste resources and the time of those who participated. While there is evidence that many people are willing to take part in research, particularly if it involves a condition from which they suffer, researchers are unable to easily contact such people often relying on busy clinicians to identify them. Many clinicians perceive themselves as too busy to take part in research activities. The Scottish Health Research Register SHARE adopts an approach which asks the public to consent to their data held in National Health Service databases to be used to determine their suitability for research projects. Additionally, participants can consent for spare blood, left after routine venepuncture to be automatically identified in the laboratory and stored for future research studies. PARTICIPANTS: Anyone over the age of 16 years in Scotland can participate. Participants are approached through a range of methods including directly at outpatient clinics and general practitioners practices, leaflets with hospital letters and personal email from employers. FINDINGS TO DATE: SHARE has recruited around 130 000 people. SHARE has demonstrated that it can quickly and efficiently recruit to studies, over 20 until now. In addition, it can be used to administer questionnaire studies by email and recruit to patient and public involvement groups. FUTURE PLANS: SHARE continues to steadily recruit with the ambition of eventually achieving 1 000 000 people in Scotland. We are steadily increasing the number of data sets we use for identifying participants. We are adding a mobile app which will facilitate dissemination about research and allow the collection of physiological and activity data if desired. We anticipate that SHARE will soon become the main source of health research recruitment in Scotland.","corpus_id":-1,"score":2},{"doc_id":"22621621","title":"Survey of patient and public perceptions of electronic health records for healthcare, policy and research: study protocol.","abstract":"BACKGROUND: Immediate access to patients' complete health records via electronic databases could improve healthcare and facilitate health research. However, the possible benefits of a national electronic health records (EHR) system must be balanced against public concerns about data security and personal privacy. Successful development of EHR requires better understanding of the views of the public and those most affected by EHR: users of the National Health Service. This study aims to explore the correlation between personal healthcare experience (including number of healthcare contacts and number and type of longer term conditions) and views relating to development of EHR for healthcare, health services planning and policy and health research. METHODS/DESIGN: A multi-site cross-sectional self-complete questionnaire designed and piloted for use in waiting rooms was administered to patients from randomly selected outpatients' clinics at a university teaching hospital (431 beds) and general practice surgeries from the four primary care trusts within the catchment area of the hospital. All patients entering the selected outpatients clinics and general practice surgeries were invited to take part in the survey during August-September 2011. Statistical analyses will be conducted using descriptive techniques to present respondents' overall views about electronic health records and logistic regression to explore associations between these views and participants' personal circumstances, experiences, sociodemographics and more specific views about electronic health records. DISCUSSION: The study design and implementation were successful, resulting in unusually high response rates and overall recruitment (85.5%, 5336 responses). Rates for face-to-face recruitment in previous work are variable, but typically lower (mean 76.7%, SD 20). We discuss details of how we collected the data to provide insight into how we obtained this unusually high response rate.","corpus_id":6083131,"score":1},{"doc_id":"22783770","title":"Analysis and validation of a Parkinson's disease register as a recruitment tool for clinical studies.","abstract":"Promotion of research is a key strategy of the National Health Service (NHS). Currently, many patients are not afforded the opportunity to participate in clinical studies. A register of research-interested patients has the potential to maximise inclusivity. We have established a register of research-interested patients with Parkinson's disease within the South West of England, with pragmatic inclusion criteria and multiple recruitment routes. We undertook an analysis of the register, investigation of its utility as a recruitment tool and a survey of recruiters. There were 529 active participants; 30% were self-referred and 70% were recruited by a healthcare practitioner. Response rate to annual questionnaires was 86.5%. Staff time required for pack preparation, recruitment and data entry was 15 min per new recruit and 5 min per follow-up questionnaire. In total, 85% of recruiters viewed the register positively. A single mailing to participants resulted in a recruitment rate that significantly exceeded that achieved by traditional recruitment methods.","corpus_id":43150694,"score":1},{"doc_id":"24845592","title":"Permission to contact (PTC)--a strategy to enhance patient engagement in translational research.","abstract":"UNLABELLED: Improving patient recruitment and consent to participate in clinical studies is an important issue. The process of consent involves three steps: patient referral for contact, the preliminary interview to determine patient interest, and the informed consent discussion. We hypothesized that putting the first step of the consent process into a 'Permission to Contact' (PTC) platform would improve patient engagement, would improve the efficiency of the other steps of the process, and would be acceptable to diverse patient groups. METHODS: To test this hypothesis, four PTC platforms were established in three types of outpatient health clinics (cancer, cardiac, maternal health) in different British Columbia health centers. Each began as a research project where clinic personnel were engaged, clinic flow processes were mapped, and a design for each PTC was derived by consensus. All patients at these clinics were asked for 'permission to be contacted for future research purposes.' Patient approach and permission response rates were assessed and operational costs were estimated. RESULTS: Overall permission rates were high for all projects, but ranged from 94% of 'cancer' patients to 80% of 'congenital heart' patients who were approached (p<0.0001). Sustainability was demonstrated by stable enrollment levels after several years, and ongoing costs averaged $25 (range $12-$39) for each 'permission' across all four platforms. CONCLUSIONS: A PTC platform is a feasible mechanism to engage patients in research programs such as biobanking. It is well supported by clinic staff and receives high engagement and acceptance from patients. Patient-approach rates vary in different clinics, likely due to both clinic and PTC process factors, but this strategy provides an efficient means of engaging patients in research and sets the stage for enhanced enrollment into translational research programs.","corpus_id":24695002,"score":1},{"doc_id":"25318374","title":"The DiReCT study - improving recruitment into clinical trials: a mixed methods study investigating the ethical acceptability, feasibility and recruitment yield of the cohort multiple randomised controlled trials design.","abstract":"BACKGROUND: The 'cohort multiple Randomised Controlled Trial' (cmRCT) design has been proposed as a potential solution to poor recruitment into clinical trials. The design randomly selects participants eligible for experimental treatments from a pre-enrolled cohort of patients, recruiting participants to multiple trials from a single cohort. Controls remain unaware of their participation in specific trials. METHODS: We undertook a mixed methods study to determine the ethical acceptability, the proportion of patients in a routine service consenting to cohort participation, the proportion of these who would consent to being hypothetically randomly selected to receive new treatments, and the views of clinicians on the acceptability of the design. We submitted our cmRCT design for ethical review and recruited participants from people with anxiety and depression attending a community mental health service of twenty-one clinicians. We recorded the proportion of patients who were offered participation in the DiReCT study and the proportion that consented to researcher contact, medical record sharing, and who accepted to be randomly allocated to active treatment procedures in future hypothetical unspecified clinical trials. We used a thematic framework analysis to analyse clinician interviews. RESULTS: We obtained a favourable ethical opinion from the UK Health Research Authority. Clinicians approached 131/752 (17%) potentially eligible participants for consent. Of these 131, 84 (64%) initially consented to be contacted by a researcher and all but one consented to being randomised into future trials. We confirmed consent for 71 (54%) of participants approached by clinicians, of whom 69 (53%) consented to being randomised into hypothetical future trials, 9% (69/752) of all potentially eligible patients. The interviewed clinicians described issues impacting on their ability to recruit participants in terms of clinical concerns for patient wellbeing, work pressure, their views of both general research and the specific DiReCT study, and how they viewed patients' responses to being offered participation in the study. CONCLUSIONS: The cmRCT system offers the potential to improve the recruitment into clinical trials and is acceptable ethically and to many patients. Overcoming the multiple factors driving the difficulties clinicians experience in patient recruitment is likely to require the application of significant implementation science-informed effort.","corpus_id":16397039,"score":1},{"doc_id":"25552589","title":"Confidentiality in participatory research: Challenges from one study.","abstract":"AIM: This article presents key ethical challenges that were encountered when conducting a participatory qualitative research project with a very specific, small group of nurses, in this case with practice development nurses in Malta. BACKGROUND: With the small number of nurses employed in practice development roles in Malta, there are numerous difficulties of maintaining confidentiality. Poorly constructed interventions by the researcher could have resulted in detrimental effects to research participants and the overall trustworthiness of the research. Generally, ethical guidelines for research exist to reinforce validity of research; however, there is not an established consensus on how these strategies can be utilised in some types of qualitative field work. RESEARCH DESIGN: The researcher used an exploratory case study methodology. The sample consisted of 10 participants who were interviewed twice using face-to-face interviews, over a period of 2 months. ETHICAL CONSIDERATIONS: The study was ethically reviewed by the University Research Ethics Committee and the Faculty Research Ethics Committee, University of Malta. The participants referred to in this article have been given adequate information about the study and their consent has been obtained. DISCUSSION: Numerous strategies for ensuring confidentiality during recruitment of the participants, during data collection, during transcription and data analysis and during dissemination of research results assisted the researcher in responding to potential and actual ethical issues. CONCLUSION: This article emphasises the main strategies that can be used to respond to ethical challenges when researching with a small easily identifiable group. The learning discussed here may be relevant to or even transferable to other similar research studies or research contexts. These methods fostered a greater credibility throughout the research process and predisposed the participants to greater trust, and thus, they disclosed their experiences and speak more freely, thus enhancing the quality of the study.","corpus_id":206611350,"score":1},{"doc_id":"25834643","title":"Linking a research register to clinical records in older adults' mental health services: a mixed-methods study.","abstract":"INTRODUCTION: Patients can provide consent to have their clinical records linked to a research register, a process known as consent for contact (C4C). There is evidence about how to engage people with mental illness in C4C, but nothing specific to older adults. This is a priority area for research (for example, dementia trials), although sign-up rates to C4C are lower than for younger populations. Through this study we seek to understand these disparities. METHODS: This was a two-stage cross-sectional observational study. In phase one, focus groups with service users, carers and clinicians informed a framework for clinicians to explain C4C to those on their caseload. In phase two, clinicians explained C4C to 26 service users (and carers where applicable). These conversations were recorded, and their content was analysed. Service users and carers were then interviewed to provide further feedback on their conversations with clinicians. A total of 31 service users, 24 carers and 13 clinical staff took part across the two phases. RESULTS: In phase one, service users and carers sought assurance of the right to refuse participation in further studies (after joining C4C). Clinicians expressed concerns over legal and practical implications of ascertaining mental capacity and best interest. In phase two, clinicians' explanations were less thorough than similar explanations given to younger adults with psychosis. Clinicians omitted details of service users' right to stipulate contact arrangements, which was significantly associated with whether service users/carers agreed to join. Common reasons for joining C4C included altruism and the chance to speak to new people. Few participants refused to join, but reasons included avoidance of stress (potentially alleviated through the presence of a carer). CONCLUSIONS: Implementing C4C in older adults' services requires clinicians to deliver concise, simple explanations to individuals and their carers where applicable. Older adults can be suspicious of unsolicited contact; thus, explanations must emphasise freedom to negotiate suitable contact arrangements. Hearing about research opportunities can be in the best interests of older adults, but communicating these opportunities requires a tailored approach.","corpus_id":16818270,"score":1},{"doc_id":"25971412","title":"Consenting for contact? Linking electronic health records to a research register within psychosis services, a mixed method study.","abstract":"BACKGROUND: Research registers of potential participants linked to Electronic Health Records (EHRs) provide a basis for screening and identifying people suitable for studies. Such a system relies upon people joining the register and giving permission for their record to be used in this way. This study describes the process of training clinicians to explain EHR-linked research registers to service users, and to recruit them onto the register. METHOD: Training materials were developed for clinicians to help them describe the register to service users. These materials were based upon findings from focus groups reported elsewhere, they were then tested with 31 clinicians in early intervention psychosis services and each clinician discussed the register with service users on their caseload (n = 100 service users). Consultations were recorded and analysed in relation to their coverage of the training criteria. Service users also provided data on the acceptability of the process from their perspective. The content of clinicians' explanations to service users was described, and then compared against the likelihood of service users joining the register. Interpretive statistics (t-test and Chi-Squared) were used to explore differences between consultations in which service users agreed to join the register, and consultations where they did not agree to join. RESULTS: Service users appeared more likely to join the register if they felt control over what they signed up to, this necessitated understanding that they could decide when, how often, and by whom they were contacted, that joining the register did not automatically enlist them to future studies, and that they could change their mind in future. Clinicians' explanations did not always include that researchers would be able to see the service users' EHR. Service users often confused the idea of signing up to the register and signing up to studies themselves. Confidentiality was not well explained, but service users were not always concerned by confidentiality. CONCLUSION: EHR-linked research registers provide recruitment opportunities, and help service users to find out about research. Implementing these registers within mental health settings requires a trained clinical workforce and an informed service user population.","corpus_id":17812677,"score":1},{"doc_id":"26599631","title":"Development of the CHARIOT Research Register for the Prevention of Alzheimer's Dementia and Other Late Onset Neurodegenerative Diseases.","abstract":"BACKGROUND: Identifying cognitively healthy people at high risk of developing dementia is an ever-increasing focus. These individuals are essential for inclusion in observational studies into the natural history of the prodromal and early disease stages and for interventional studies aimed at prevention or disease modification. The success of this research is dependent on having access to a well characterised, representative and sufficiently large population of individuals. Access to such a population remains challenging as clinical research has, historically, focussed on patients with dementia referred to secondary and tertiary services. The primary care system in the United Kingdom allows access to a true prodromal population prior to symptoms emerging and specialist referral. We report the development and recruitment rates of the CHARIOT register, a primary care-based recruitment register for research into the prevention of dementia. The CHARIOT register was designed specifically to support recruitment into observational natural history studies of pre-symptomatic or prodromal dementia stages, and primary or secondary prevention pharmaceutical trials or other prevention strategies for dementia and other cognitive problems associated with ageing. METHODS: Participants were recruited through searches of general practice lists across the west and central London regions. Invitations were posted to individuals aged between 60 and 85 years, without a diagnosis of dementia. Upon consent, a minimum data set of demographic and contact details was extracted from the patient's electronic health record. RESULTS: To date, 123 surgeries participated in the register, recruiting a total of 24,509 participants-a response rate of 22.3%. The age, gender and ethnicity profiles of participants closely match that of the overall eligible population. Higher response rates tended to be associated with larger practices (r = 0.34), practices with a larger older population (r = 0.27), less socioeconomically disadvantaged practices (r = 0.68), and practices with a higher proportion of White patients (r = 0.82). DISCUSSION: Response rates are comparable to other registers reported in the literature, and indicate good interest and support for a research register and for participation in research for the prevention of age-related neurodegenerative diseases and dementia. We consider that the simplicity of the approach means that this system is easily scalable and replicable across the UK and internationally.","corpus_id":4913645,"score":1},{"doc_id":"27503859","title":"Facilitating mental health research for patients, clinicians and researchers: a mixed-method study.","abstract":"OBJECTIVES: Research registers using Consent for Contact (C4C) can facilitate recruitment into mental health research studies, allowing investigators to contact patients based on clinical records information. We investigated whether such a register was useful for mental health research, seeking the perspectives of patients and research investigators. SETTING AND DESIGN: In 2012, a C4C register was developed in a large secondary mental health provider within the UK; almost 9000 patients have joined. This mixed-method study audited the effectiveness of the register. PARTICIPANTS: A 'mystery shopper' exercise was conducted, and patients (n=21) were recruited to ask clinicians about the availability of research opportunities. Structured interviews were conducted with patients (n=52) about their experiences of being on the register. Similar interviews were conducted with 18 investigators from 19 studies, who had attempted to use the register to recruit participants. OUTCOME MEASURES: The impact of C4C on study recruitment, and whether it helped patients learn about research. RESULTS: So far, the register has provided 928 individuals with 1085 research opportunities (in 60% of cases, the individual agreed to participate in the study). Clinicians were willing to link patients to research opportunities, but often lacked information about studies. For patients, the register provided opportunities which they may not otherwise have; 27 of 52 had participated in studies since joining the register (18 participating for the first time). Most investigators used the register to supplement recruitment to their studies, but described problems in prescreening potential participants from a clinical record for complex studies. CONCLUSIONS: Although the register helped investigators recruit for studies, and provided patients with research opportunities, clinicians' input is still useful for identifying suitable participants. C4C registers should be adapted to provide clinicians with automatically updated information on local studies allowing them to match patients on their caseload with active studies.","corpus_id":6801068,"score":1},{"doc_id":"27557678","title":"Electronic health records to facilitate clinical research.","abstract":"Electronic health records (EHRs) provide opportunities to enhance patient care, embed performance measures in clinical practice, and facilitate clinical research. Concerns have been raised about the increasing recruitment challenges in trials, burdensome and obtrusive data collection, and uncertain generalizability of the results. Leveraging electronic health records to counterbalance these trends is an area of intense interest. The initial applications of electronic health records, as the primary data source is envisioned for observational studies, embedded pragmatic or post-marketing registry-based randomized studies, or comparative effectiveness studies. Advancing this approach to randomized clinical trials, electronic health records may potentially be used to assess study feasibility, to facilitate patient recruitment, and streamline data collection at baseline and follow-up. Ensuring data security and privacy, overcoming the challenges associated with linking diverse systems and maintaining infrastructure for repeat use of high quality data, are some of the challenges associated with using electronic health records in clinical research. Collaboration between academia, industry, regulatory bodies, policy makers, patients, and electronic health record vendors is critical for the greater use of electronic health records in clinical research. This manuscript identifies the key steps required to advance the role of electronic health records in cardiovascular clinical research.","corpus_id":16614338,"score":1},{"doc_id":"18714713","title":"Feasibility of gaining access to women in jail for health interventions.","abstract":"UNLABELLED: Female jail populations are comprised of women at high-risk for an array of psychological and physical health problems. Jails offer an opportune site to deliver clinical health interventions to women who often quickly cycle back into the community. In contrast with prison population studies, many investigators have encountered recruitment problems when attempting to engage the jailed population in clinical research. This study addressed the feasibility of recruiting detained women for eligibility for clinical research. METHODS: Commitments to the Women's Facility at the Rhode Island Department of Corrections were chronicled for 40 months, from February 2004 to June 2007. Research staff, working 8 a.m. to 5 p.m., Monday through Friday, attempted to screen all detained women for a randomized clinical trial. RESULTS: During the 40-month study period, 4,131 individual women had 8,010 commitments to the facility. Staff was able to gain access to nearly 50% of women. Of the inaccessible women, 65% were released in less than 24 hours. In total, 88% of accessed women agreed to be screened for study participation. No significant differences were observed by race/ethnicity or age between women who were screened and those who were not. CONCLUSIONS: Clinical research with the female jail population is feasible. The jail setting requires researchers to plan for short-commitment lengths and high rates of recidivism to optimize screening and recruitment in this population.","corpus_id":44250910,"score":0},{"doc_id":"19566931","title":"Strategies for achieving a high response rate in a home interview survey.","abstract":"BACKGROUND: Response rates in surveys have been falling over the last 20 years, leading to the need for novel approaches to enhance recruitment. This study describes strategies used to maximise recruitment to a home interview survey of mothers with young children living in areas of high deprivation. METHODS: Mothers of two year old children received a letter from their GP inviting them to take part in a survey on diet. Participants were subsequently recruited by a researcher. The researcher first tried to contact potential participants by telephone, to discuss the study and make an appointment to conduct a home interview. Where telephone numbers for women could not be obtained from GP records, web searches of publicly available databases were conducted. After obtaining correct telephone numbers, up to six attempts were made to establish contact by telephone. If this was unsuccessful, a postal request for telephone contact was made. Where no telephone contact was achieved, the researcher sent up to two appointments by post to conduct a home interview. RESULTS: Participating GPs invited 372 women to take part in a home based interview study. GP practices provided telephone numbers for 162 women, of which 134 were valid numbers. The researcher identified a further 187 numbers from electronic directories. Further searches of GP records by practice staff yielded another 38 telephone numbers. Thus, telephone numbers were obtained for 99% of potential participants. The recruitment rate from telephone contacts was 77%. Most of the gain was achieved within four calls. For the remaining women, contact by post and home visits resulted in 18 further interviews, corresponding to 35% of the women not recruited by telephone. The final interview rate was 82%. This was possible because personal contact was established with 95% of potential participants. CONCLUSION: This study achieved a high response rate in a hard to reach group. This was mainly achieved by first establishing contact by telephone. The use of multiple sources identified the telephone numbers of almost all the sample. Multiple attempts at telephone contact followed by postal approaches led to a high home interview rate.","corpus_id":5711328,"score":0},{"doc_id":"19845656","title":"Recruiting older adults to health research studies: A systematic review.","abstract":"AIM: To provide a systematic review of papers comparing the effectiveness of different strategies to recruit older adults (aged 50 years and over) to participate in health research studies, to guide successful recruitment in future research. METHODS: Four major databases were searched for papers published between 1995 and 2008 with: target group aged 50 years or over; participants allocated to receive one of two or more recruitment strategies; and an outcome measure of response rate or enrolment in study. RESULTS: Twelve papers were included in the review. CONCLUSION: For postal questionnaires, recruitment strategies used with older adults had comparable outcomes to those used to recruit from the general population. For other types of studies, strategies involving face-to-face contact may be more effective than indirect methods, but this needs to be balanced against feasibility. Overall, little evidence on the topic exists and more rigorous investigation is necessary.","corpus_id":37661332,"score":0},{"doc_id":"19930724","title":"Trials and tribulations of recruiting 2,000 older women onto a clinical trial investigating falls and fractures: Vital D study.","abstract":"BACKGROUND: Randomised, placebo-controlled trials are needed to provide evidence demonstrating safe, effective interventions that reduce falls and fractures in the elderly. The quality of a clinical trial is dependent on successful recruitment of the target participant group. This paper documents the successes and failures of recruiting over 2,000 women aged at least 70 years and at higher risk of falls or fractures onto a placebo-controlled trial of six years duration. The characteristics of study participants at baseline are also described for this study. METHODS: The Vital D Study recruited older women identified at high risk of fracture through the use of an eligibility algorithm, adapted from identified risk factors for hip fracture. Participants were randomised to orally receive either 500,000 IU vitamin D3 (cholecalciferol) or placebo every autumn for five consecutive years. A variety of recruitment strategies were employed to attract potential participants. RESULTS: Of the 2,317 participants randomised onto the study, 74% (n = 1716/2317) were consented onto the study in the last five months of recruiting. This was largely due to the success of a targeted mail-out. Prior to this only 541 women were consented in the 18 months of recruiting. A total of 70% of all participants were recruited as a result of targeted mail-out. The response rate from the letters increased from 2 to 7% following revision of the material by a public relations company. Participant demographic or risk factor profile did not differ between those recruited by targeted mail-outs compared with other methods. CONCLUSION: The most successful recruitment strategy was the targeted mail-out and the response rate was no higher in the local region where the study had extensive exposure through other recruiting strategies. The strategies that were labour-intensive and did not result in successful recruitment include the activities directed towards the GP medical centres. Comprehensive recruitment programs employ overlapping strategies simultaneously with ongoing assessment of recruitment rates. In our experience, and others direct mail-outs work best although rights to privacy must be respected. TRIAL REGISTRATION: ISRCTN83409867 and ACTR12605000658617.","corpus_id":260502619,"score":0},{"doc_id":"20334748","title":"A randomised controlled multicentre trial of treatments for adolescent anorexia nervosa including assessment of cost-effectiveness and patient acceptability - the TOuCAN trial.","abstract":"OBJECTIVE: To evaluate the clinical effectiveness and cost-effectiveness of inpatient compared with outpatient treatment and general (routine) treatment in Child and Adolescent Mental Health Services (CAMHS) against specialist treatment for young people with anorexia nervosa. In addition, to determine young people's and their carers' satisfaction with these treatments. DESIGN: A population-based, pragmatic randomised controlled trial (RCT) was carried out on young people age 12 to 18 presenting to community CAMHS with anorexia nervosa. SETTING: Thirty-five English CAMHS in the north-west of England co-ordinated through specialist centres in Manchester and Liverpool. PARTICIPANTS: Two hundred and fifteen young people (199 female) were identified, of whom 167 (mean age 14 years 11 months) were randomised and 48 were followed up as a preference group. INTERVENTIONS: Randomised patients were allocated to either inpatient treatment in one of four units with considerable experience in the treatment of anorexia nervosa, a specialist outpatient programme delivered in one of two centres, or treatment as usual in general community CAMHS. The outpatient programmes spanned 6 months of treatment. The length of inpatient treatment was determined on a case-by-case basis on clinical need with outpatient follow-up to a minimum of 6 months. MAIN OUTCOME MEASURES: Follow-up assessments were carried out at 1, 2 and 5 years. The primary outcome measure was the Morgan-Russell Average Outcome Scale (MRAOS) and associated categorical outcomes. Secondary outcome measures included physical measures of weight, height, body mass index (BMI) and % weight for height. Research ratings included the Health of the National Outcome Scale for Children and Adolescents (HoNOSCA). Self report measures comprised the user version of HoNOSCA (HoNOSCA-SR), the Eating Disorder Inventory 2 (EDI-2), the Family Assessment Device (FAD) and the recent Mood and Feelings Questionnaire (MFQ). Information on resource use was collected in interview at 1, 2 and 5 years using the Child and Adolescent Service Use Schedule (CA-SUS). Satisfaction was measured quantitatively using a questionnaire designed for the study and qualitative (free) responses on it. The questionnaire data were supplemented by qualitative analysis of user and carer focus groups. RESULTS: Of the 167 patients randomised, 65% adhered to the allocated treatment. Adherence was lower for inpatient treatment (49%) than for general CAMHS (71%) or specialist outpatient treatment (77%) (p = 0.013). Every subject was traced at both 1 and 2 years, with the main outcome measure completed (through contact with the subject, family members or clinicians), by 94% at 1 year, 93% at 2 years, but only 47% at 5 years. A validated outcome category was assigned for 98% at 1 year, 96% at 2 years and 60% at 5 years. There was significant improvement in all groups at each time point, with the number achieving a good outcome being 19% at 1 year, 33% at 2 years and 64% (of those followed up) at 5 years. Analysis demonstrated no difference in treatment effectiveness of randomisation to inpatient compared with outpatient treatment, or, specialist over generalist treatment at any time point, when baseline characteristics were taken into account. Generalist CAMHS treatment was slightly more expensive over the first 2 years of the study, largely because greater numbers were subsequently admitted to hospital after the initial treatment phase. The specialist outpatient programme was the dominant treatment in terms of incremental cost-effectiveness. Specialist treatments had a higher probability of being more cost-effective than generalist treatments and outpatient treatment had a higher probability of being more cost-effective than inpatient care. Parental satisfaction with treatment was generally good, though better with specialist than generalist treatment. Young people's satisfaction was much more mixed, but again better with specialist treatment, including inpatient care. CONCLUSION: Poor adherence to randomisation (despite initial consent to it), limits the assessment of the treatment effect of inpatient care. However, this study provides little support for lengthy inpatient psychiatric treatment on clinical or health economic grounds. These findings are broadly consistent with existing guidelines on the treatment of anorexia nervosa, which suggest that outpatient treatments should be offered to the majority, with inpatient treatment offered in rare cases, though our findings lend little support to a stepped-care approach in which inpatient care is offered to outpatient non-responders. Outpatient care, supported by brief (medical) inpatient management for correction of acute complications may be a preferable approach. The health economic analysis and user views both support NICE guidelines, which suggest that anorexia nervosa should be managed in specialist services that have experience and expertise in its management. Comprehensive general CAMHS might, however, be well placed to manage milder cases. Further research should focus on the specific components of outpatient psychological therapies. Although family-based treatments are well established, trials have not established their effectiveness compared with good-quality individual psychological therapies and the combination of individual and family approaches is untested. Further research is needed to establish which patients (if any) might respond to inpatient psychiatric treatment when unresponsive to outpatient care, the positive and negative components of it and the optimum length of stay. TRIAL REGISTRATION: NRR number (National Research Register) N0484056615; Current Controlled Trials ISRCTN39345394.","corpus_id":42049325,"score":0},{"doc_id":"20353656","title":"An audit of smoking behaviours among patients attending two general dental practices in South Wales: an awareness-raising exercise for the dental team and patients.","abstract":"AIMS: This audit aimed to quantify the number of smokers attending two general dental practices. It also aimed to establish the demographic characteristics of these smokers in terms of age, gender and deprivation status, and to raise the awareness of practice staff about smoking cessation. METHODS: Data were collected from consecutive patients (aged over 16 years) attending two general dental practices over a period of one month. The information collected included smoking status, number of cigarettes smoked, age, gender, and postcode. A deprivation score (derived from the Welsh Index of Multiple Deprivation [WIMD] for 2008) was appended to each patient record in order to provide a measure of deprivation based on the postcode of the patient. Staff at both practices were involved in the audit. Staff were given a brief pre- and post-audit questionnaire to test their knowledge on smoking cessation. The audit standard was that no more than 29% of patients should be smokers. Where relevant, data were statistically tested using the chi-square test. RESULTS: Five hundred and sixty-one patients provided data on their smoking habits. It was found that 159 (28.3%) were smokers, smoking on average 12 cigarettes per day. The average age of the sample was 46 years and 242 (43.1%) were male. Forty-eight per cent of the sample was shown to be resident in a postcode considered to be deprived. Older patients were more likely to be nonsmokers (P=0.0001). Following the final audit meeting, correct answers among staff for knowledge of the National Institute for Health and Clinical Excellence guidelines regarding effective smoking-cessation practices improved from 6% to 71%. CONCLUSION: The issue of smoking cessation has been highlighted for two dental teams. Whether the audit will result in the delivery of smoking-cessation procedures within the dental practice settings cannot be established. It is clear that the desired smoking-cessation behaviours can now be contemplated by the dental teams. Further monitoring is required to establish outcomes as a result of the actions of the teams.","corpus_id":30829702,"score":0},{"doc_id":"20849598","title":"Engaging the oldest old in research: lessons from the Newcastle 85+ study.","abstract":"BACKGROUND: Those aged 85 and over, the oldest old, are now the fastest growing sector of the population. Information on their health is essential to inform future planning; however, there is a paucity of up-to-date information on the oldest old, who are often excluded from research. The aim of the Newcastle 85+ Study is to investigate the health of a cohort of 85-year-olds from a biological, medical and psychosocial perspective. This paper describes the methods employed for the successful recruitment, retention and evaluation of this cohort. METHODS: Participants were all individuals born in 1921 and registered with a participating general practice in Newcastle and North Tyneside, UK. Involvement comprised detailed health assessments, by a nurse, in their usual place of residence and/or review of their general practice medical records. RESULTS: Of the 1453 individuals eligible to participate, 72% (n = 1042) were recruited; 59% (n = 851) consented to both health assessment and review of general practice records. Key factors for successful involvement included protected time to engage with family and other key gatekeepers, minimising participant burden, through for example home based assessment, and flexibility of approach. Cognitive impairment is a significant issue; due consideration should be given to the ethical and legal issues of capacity and consent. Interim withdrawal rates at phase 2 (18 month post baseline), show 88 out of 854 participants (10%) had withdrawn with approval for continued use of data and materials and a further 2 participants (0.2%) had withdrawn and requested that all data be destroyed. Attrition due to death of participants within this same time frame was 135 (16%). CONCLUSION: Our recruitment rates were good and compared favourably with other similar UK and international longitudinal studies of the oldest old. The challenges of and successful strategies for involving, recruiting and retaining the oldest old in research, including those in institutions, are described to facilitate adequate representation of this growing population in future research into ageing.","corpus_id":11871450,"score":0},{"doc_id":"21916092","title":"Failure to attend out-patient clinics: is it in our DNA?","abstract":"PURPOSE: This paper aims to determine the reasons why patients miss clinic appointments and to ascertain patients' views on the implementation of reminder systems and penalty fees to reduce the rates of did not attend (DNAs). Overall, the paper seeks to establish novel ways to run a more efficient out-patient department (OPD) service to improve waiting times and access for patients to limited neurology resources. DESIGN/METHODOLOGY/APPROACH: A questionnaire-based study was approved by the audit committee and was offered to 204 out-patients attending the neurology clinics over a three-month period (July to September 2009). The patients' demographic details and non-attendance records were reviewed. The paper aimed to ascertain, from the patients' perspective, why people failed to attend clinic appointments. Each participant was asked their views on how they felt their public hospital service might reduce the number of DNAs at their neurology OPD. FINDINGS: A total of 204 patients took part. Participants had a mean age of 31 years (range 25-75 years) with a modal peak in the 26 to 35 age bracket. Almost 10 per cent of those surveyed admitted to missing a hospital out-patient appointment in the past. The most common reason was that they simply \"forgot\" (28 per cent). DNA rates by age range were proportionally similar to the overall age profile of attenders. Over 55 per cent said they would like a pre-appointment reminder via a mobile telephone text message, 19 per cent preferred a pre-appointment telephone call, and 19 per cent an e-mail. Of those surveyed, 47 per cent said they would be willing to pay a fee on booking that could be refunded on attending for their appointment. The majority of these felt Euro 20 was the most appropriate amount (39 per cent). The rate of acceptance for various fee amounts was uniform across age ranges. Over half (52 per cent) said that they would agree to a \"buddy\" system whereby the appointment reminder was sent to the patient but also a nominated friend or relative. ORIGINALITY/VALUE: Non-attendance rates at the neurology clinics in our institution are high with almost 10 per cent of attendees admitting to missing an appointment. One of the main reasons why people did not attend was because they simply \"forgot\" that they had an appointment and the patients favoured a text messaging reminder system to help reduce non-attendance. Almost half of the respondents said that they would be willing to pay a refundable booking fee.","corpus_id":22853807,"score":0},{"doc_id":"21995837","title":"Detecting referral and selection bias by the anonymous linkage of practice, hospital and clinic data using Secure and Private Record Linkage (SAPREL): case study from the evaluation of the Improved Access to Psychological Therapy (IAPT) service.","abstract":"BACKGROUND: The evaluation of demonstration sites set up to provide improved access to psychological therapies (IAPT) comprised the study of all people identified as having common mental health problems (CMHP), those referred to the IAPT service, and a sample of attenders studied in-depth. Information technology makes it feasible to link practice, hospital and IAPT clinic data to evaluate the representativeness of these samples. However, researchers do not have permission to browse and link these data without the patients' consent. OBJECTIVE: To demonstrate the use of a mixed deterministic-probabilistic method of secure and private record linkage (SAPREL)--to describe selection bias in subjects chosen for in-depth evaluation. METHOD: We extracted, pseudonymised and used fuzzy logic to link multiple health records without the researcher knowing the patient's identity. The method can be characterised as a three party protocol mainly using deterministic algorithms with dynamic linking strategies; though incorporating some elements of probabilistic linkage. Within the data providers' safe haven we extracted: Demographic data, hospital utilisation and IAPT clinic data; converted post code to index of multiple deprivation (IMD); and identified people with CMHP. We contrasted the age, gender, ethnicity and IMD for the in-depth evaluation sample with people referred to IAPT, use hospital services, and the population as a whole. RESULTS: The in IAPT-in-depth group had a mean age of 43.1 years; CI: 41.0-45.2 (n=166); the IAPT-referred 40.2 years; CI: 39.4-40.9 (n=1118); and those with CMHP 43.6 years SEM 0.15. ( n=12210). Whilst around 67% of those with a CMHP were women, compared to 70% of those referred to IAPT, and 75% of those subject to in-depth evaluation (Chi square p<0.001). The mean IMD score for the in-depth evaluation group was 36.6; CI: 34.2-38.9; (n=166); of those referred to IAPT 38.7; CI: 37.9-39.6; (n=1117); and of people with CMHP 37.6; CI 37.3-37.9; (n=12143). CONCLUSIONS: The sample studied in-depth were older, more likely female, and less deprived than people with CMHP, and fewer had recorded ethnic minority status. Anonymous linkage using SAPREL provides insight into the representativeness of a study population and possible adjustment for selection bias.","corpus_id":4896720,"score":0},{"doc_id":"22296428","title":"A demographic study to profile non-attenders at a gynaecology outpatient clinic.","abstract":"Missed outpatient appointments result in the inefficient utilisation of resources and have secondary effects on the health of the non-attenders, as well as on other patients who have to wait longer for their appointments. The first part of the study involved retrospective analysis of trends of non-attendance based on a computerised database of all gynaecology appointments over 12 months. The second comprised a prospective case-control study in which women who missed their gynaecology outpatient appointments (index cases) over 2 months were compared with patients who attended the same clinics matched for indication for referral (control cases). The overall non-attendance rate over 12 months was 16.1%, of whom 42% were recurrent non-attenders. Data from 105 defaulters were compared with 105 non-defaulters who attended the same clinics. Defaulters were significantly younger, single or separated and were more likely to be 'follow-ups' rather than new cases (all p < 0.05). Longer intervals between the appointment letter and actual appointment date was significantly related to non-attendance (p = 0.01) and there was a trend to a greater degree of smoking and alcohol ingestion in the defaulter group (p = 0.059). Comparison of other variables such as severity of symptoms, parity, source of referral and fluency of English did not reach statistical significance (p > 0.05). This prospective study has demonstrated certain profiles which are common to defaulters and which can be used to develop strategies to minimise non-attendance. Examples include reducing the time interval between sending the appointment letter and actual appointment date and selectively over-booking younger, single women who smoke.","corpus_id":26380120,"score":0},{"doc_id":"22397809","title":"Crowdsourced health research studies: an important emerging complement to clinical trials in the public health research ecosystem.","abstract":"BACKGROUND: Crowdsourced health research studies are the nexus of three contemporary trends: 1) citizen science (non-professionally trained individuals conducting science-related activities); 2) crowdsourcing (use of web-based technologies to recruit project participants); and 3) medicine 2.0 / health 2.0 (active participation of individuals in their health care particularly using web 2.0 technologies). Crowdsourced health research studies have arisen as a natural extension of the activities of health social networks (online health interest communities), and can be researcher-organized or participant-organized. In the last few years, professional researchers have been crowdsourcing cohorts from health social networks for the conduct of traditional studies. Participants have also begun to organize their own research studies through health social networks and health collaboration communities created especially for the purpose of self-experimentation and the investigation of health-related concerns. OBJECTIVE: The objective of this analysis is to undertake a comprehensive narrative review of crowdsourced health research studies. This review will assess the status, impact, and prospects of crowdsourced health research studies. METHODS: Crowdsourced health research studies were identified through a search of literature published from 2000 to 2011 and informal interviews conducted 2008-2011. Keyword terms related to crowdsourcing were sought in Medline/PubMed. Papers that presented results from human health studies that included crowdsourced populations were selected for inclusion. Crowdsourced health research studies not published in the scientific literature were identified by attending industry conferences and events, interviewing attendees, and reviewing related websites. RESULTS: Participatory health is a growing area with individuals using health social networks, crowdsourced studies, smartphone health applications, and personal health records to achieve positive outcomes for a variety of health conditions. PatientsLikeMe and 23andMe are the leading operators of researcher-organized, crowdsourced health research studies. These operators have published findings in the areas of disease research, drug response, user experience in crowdsourced studies, and genetic association. Quantified Self, Genomera, and DIYgenomics are communities of participant-organized health research studies where individuals conduct self-experimentation and group studies. Crowdsourced health research studies have a diversity of intended outcomes and levels of scientific rigor. CONCLUSIONS: Participatory health initiatives are becoming part of the public health ecosystem and their rapid growth is facilitated by Internet and social networking influences. Large-scale parameter-stratified cohorts have potential to facilitate a next-generation understanding of disease and drug response. Not only is the large size of crowdsourced cohorts an asset to medical discovery, too is the near-immediate speed at which medical findings might be tested and applied. Participatory health initiatives are expanding the scope of medicine from a traditional focus on disease cure to a personalized preventive approach. Crowdsourced health research studies are a promising complement and extension to traditional clinical trials as a model for the conduct of health research.","corpus_id":27693538,"score":0},{"doc_id":"22458706","title":"Costs and difficulties of recruiting patients to provide e-health support: pilot study in one primary care trust.","abstract":"BACKGROUND: Better use of e-health services by patients could improve outcomes and reduce costs but there are concerns about inequalities of access. Previous research in outpatients suggested that anonymous personal email support may help patients with long term conditions to use e-health, but recruiting earlier in their 'journey' may benefit patients more. This pilot study explored the feasibility and cost of recruiting patients for an e-health intervention in one primary care trust. METHODS: The sample comprised 46 practices with total patient population of 250,000. We approached all practices using various methods, seeking collaboration to recruit patients via methods agreed with each practice. A detailed research diary was kept of time spent recruiting practices and patients. Researcher time was used to estimate costs. Patients who consented to participate were offered email support for their use of the Internet for health. RESULTS: Eighteen practices agreed to take part; we recruited 27 patients, most (23/27) from five practices. Practices agreed to recruit patients for an e-health intervention via waiting room leaflets (16), posters (16), practice nurses (15), doctors giving patients leaflets (5), a study website link (7), inclusion in planned mailshots (2), and a special mailshot to patients selected from practice computers (1). After low recruitment response we also recruited directly in five practices through research assistants giving leaflets to patients in waiting rooms. Ten practices recruited no patients. Those practices that were more difficult to recruit were less likely to recruit patients. Leaving leaflets for practice staff to distribute and placing posters in the practice were not effective in recruiting patients. Leaflets handed out by practice nurses and website links were more successful. The practice with lowest costs per patient recruited (£70) used a special mailshot to selected patients. CONCLUSION: Recruitment via general practice was not successful and was therefore expensive. Direct to consumer methods and recruitment of patients in outpatients to offer email support may be more cost effective. If recruitment in general practice is required, contacting practices by letter and email, not following up non-responding practices, and recruiting patients with selected conditions by special mailshot may be the most cost-effective approach.","corpus_id":1268682,"score":0},{"doc_id":"22958055","title":"An international pilot study of an Internet-based platform to facilitate clinical research in epilepsy: the EpiNet project.","abstract":"PURPOSE: We created an epilepsy patient database that can be accessed via the Internet by neurologists from anywhere in the world. The database was designed to enroll and follow large cohorts of patients with specific epilepsy syndromes, and to facilitate recruitment of patients for investigator-initiated clinical trials. METHODS: The EpiNet database records physician-derived information regarding seizure type and frequency, epilepsy syndrome, etiology, drug history, and investigations. It can be accessed from any country by approved investigators via a secure, password-protected Website. All data are encrypted. The database is for both research and clinical purposes. Investigators were invited to register any patient with epilepsy, but were particularly encouraged to register patients when uncertain of the optimal management. Participation required approval from investigators' ethics committees and institutional review boards, and all patients or their caregiver provided written informed consent. Patients were not enrolled in clinical trials in this pilot study. KEY FINDINGS: The international pilot study recruited patients from September 2010 to November 2011. Sixty-four investigators or research assistants from 25 centers in 13 countries registered 1,050 patients. Patients with a wide range of epilepsy syndromes and etiologies were registered. Patients' ages ranged from 2 weeks to 90 years. SIGNIFICANCE: The Website was successfully used by doctors working in different health systems. The pilot study confirmed that this low-cost, collaborative approach to research has great potential. Large, multicenter cohort studies will commence in 2012, and randomized clinical trials are being planned. All epileptologists are invited to join this project.","corpus_id":27773996,"score":0},{"doc_id":"23235672","title":"Interventions for recruiting smokers into cessation programmes.","abstract":"BACKGROUND: Tobacco control is a top public health priority around the globe due to the high prevalence of cigarette smoking and its associated morbidity and mortality. Much effort has been focused on establishing the effectiveness of different smoking cessation strategies. This review, however, aims to address the initial challenge faced by smoking cessation programmes: recruitment of smokers. OBJECTIVES: The primary objective of this review was to determine the effectiveness of different strategies for recruiting smokers into cessation programmes. The secondary objective was to determine the impact that these strategies had on smoking cessation rates at least six months after enrolment into a cessation programme. SEARCH METHODS: We searched the specialised register of the Cochrane Tobacco Addiction Group using a search strategy which included the terms ('recruit$', 'invit$', 'enter', 'entry', 'enrolment') combined with ('smok$', 'cigarette', 'smoking cessation', 'tobacco') in the title, abstract or keyword fields. We searched MEDLINE, EMBASE, the Cochrane Central Register of Controlled Trials (CENTRAL), and registers of current and ongoing trials. We also searched the reference lists of included studies. SELECTION CRITERIA: We included randomised controlled trials and cluster randomised controlled trials that compared at least two different methods of recruiting current smokers into a smoking cessation programme. We also included those studies which focused on the effectiveness of a smoking cessation programme as long as the study involved multiple recruitment methods and reported results of the recruitment phase. DATA COLLECTION AND ANALYSIS: From each included study, we extracted data on the type of participants, type of recruitment strategies (i.e., setting, mode of communication used, intensity and duration) and comparisons, and on randomisation, allocation concealment, and blinding procedures. Our primary outcome was the proportion of smokers successfully recruited to each cessation programme compared to alternative modalities of recruitment. Our secondary outcome was smoking cessation for at least six months. Given the substantial heterogeneity across recruitment interventions and participants, we adopted a narrative synthesis approach for summarising results. MAIN RESULTS: This review includes 19 studies with a total of 14,890 participants. We categorised the included studies according to the modes used to deliver the recruitment strategy: head to head comparison of individual recruitment strategies; comparison of the same delivery mode but with different content or intensity; and the addition of another mode to an existing recruitment method. We identified three studies that made head-to-head comparisons of different types of recruitment strategies. Of these, only one study detected a significant effect, finding that a personal phone call was more effective than a generic invitation letter (RR 40.73, 95% CI 2.53 to 654.74). Five studies compared interventions using the same delivery modes but different content. Results showed that tailored messages through an interactive voice response system resulted in a higher recruitment rate than assessment of smoking status alone using the same system (RR 8.64, 95% CI 4.41 to 16.93), and that text messages indicating scarcity of places available were more effective than generic text message reminders (RR 1.45, 95% CI 1.07 to 1.96). One study compared interventions using the same delivery mode but different intensity and found that allowing for more phone call attempts to reach potential participants can result in better recruitment (RR 1.87, 95% CI 1.61 to 2.18). Finally, 10 studies investigated the effect of adding a recruitment mode to existing recruitment strategies. Findings showed that: adding a text message reminder or real quotes from participants to a personal phone call improved recruitment of participants (RR 3.38, 95% CI 1.26 to 9.08 and RR 29.07, 95% CI 1.74 to 485.70, respectively); that adding a personal phone call to an existing newsletter can also increase recruitment rates (RR 65.12, 95% CI 4.06 to 1045.4]); that a reactive-proactive recruitment phase is more effective than a proactive phase alone (63.8% versus 47.5%, RR not available); and that active recruitment at schools is more effective than passive recruitment (p < 0.001, denominator not available for calculation of RR). Additionally, a number of studies in this category showed that providing incentives can effectively increase the number of participants recruited into smoking cessation programmes. Out of the 19 included studies, only four reported on the effect of recruitment strategy on smoking cessation at six months or longer. Three of these studies compared strategies that used the same delivery mode with different content. Their results were non-significant. The remaining three studies evaluated adding an additional mode to an existing recruitment intervention. Only one of them showed a significant difference in the levels of smoking cessation that favoured the enhanced recruitment strategy, but this may have reflected the offer of incentives once in the programme rather than the recruitment strategy itself (RR at 15 or 18 months 2.60, 95% CI 1.48 to 4.56). AUTHORS' CONCLUSIONS: The substantial heterogeneity across the included studies restricts our ability to draw firm conclusions about the effectiveness of different recruitment strategies in relation to recruitment of participants into smoking cessation programmes or levels of smoking cessation. The limited evidence, however, suggests that the following elements may improve the recruitment of smokers into cessation programmes: personal, tailored interventions; recruitment methods that are proactive in nature; and more intensive recruitment strategies (i.e., those strategies that require increased contact with potential participants).","corpus_id":205198634,"score":0},{"doc_id":"23496916","title":"Recruitment and retention of participants in a pragmatic randomized intervention trial at three community health clinics: results and lessons learned.","abstract":"BACKGROUND: Obesity and hypertension and their associated health complications disproportionately affect communities of color and people of lower socioeconomic status. Recruitment and retention of these populations in research trials, and retention in weight loss trials has been an ongoing challenge. METHODS: Be Fit, Be Well was a pragmatic randomized weight loss and hypertension management trial of patients attending one of three community health centers in Boston, Massachusetts. Participants were asked to complete follow-up assessments every 6-months for two years. We describe challenges encountered and strategies implemented to recruit and retain trial participants over the 24-month intervention. We also identify baseline participant characteristics associated with retention status. Retention strategies included financial incentives, contact between assessment visits, building relationships with health center primary care providers (PCPs) and staff, and putting participant convenience first. RESULTS: Active refusal rates were low with 130 of 2,631 patients refusing participation (4.9%). Of 474 eligible persons completing telephone screening, 365 (77.0%) completed their baseline visit and were randomized into the study. The study population was predominantly non-Hispanic Black (71.2%), female (68.5%) and reported annual household income of less than $35,000 (70.1%). Recruitment strategies included use of passive approval of potential participants by PCPs, use of part-time staff, and outsourcing calls to a call center. A total of 314 (86.0%) people completed the 24-month visit. Retention levels varied across study visits and intervention condition. Most participants completed three or more visits (69.6%), with 205 (56.2%) completing all four. At 24-months, lower retention was observed for males and the intervention condition. Retention strategies included building strong relationships with clinic staff, flexibility in overcoming participant barriers through use of taxi vouchers, night and weekend appointments, and keeping participants engaged via newsletters and social gatherings. CONCLUSION: We were able to retain 86.0% of participants at 24-months. Recruitment and retention of high percentages of racial/ethnic minorities and lower income samples is possible with planning, coordination with a trusted community setting and staff (e.g. community health centers and RAs), adaptability and building strong relationships. TRIAL REGISTRATION: Clinicaltrials.gov Identifier: NCT00661817.","corpus_id":5835422,"score":0},{"doc_id":"23559527","title":"Building the research capacity of clinical physical therapists using a participatory action research approach.","abstract":"BACKGROUND: This 2-year study explored the experiences of clinical physical therapists who used a participatory action research (PAR) approach to learn about the practice of clinical research. OBJECTIVES: The aim of this study was to explore the experiences of physical therapists who were conducting clinical research, facilitated by a PAR approach. DESIGN: A mixed-methods research design was used. METHODS: Physical therapists completed questionnaires, were interviewed, and participated in focus groups prior to and after the 1-year intervention and 1 year later. The research facilitator took field notes. Questionnaire data were analyzed descriptively, and themes were developed from the qualitative data. Twenty-five therapists took part in 4 self-selected groups. RESULTS: Three groups actively participated in the PAR research projects (n=14). The remaining 11 therapists decided not to be involved in clinical research projects but took part in the study as participants. After 1 year, one group completed the data collection phase of their research project, and a second group completed their ethics application. The third group ceased their research project but hosted a journal club session. At completion of the study, the experiences of the physical therapists were positive, and their confidence in conducting research and orientation toward research had increased. The perceptions of physical therapists toward research, relationships among individuals, and how the clinical projects were structured influenced the success of the projects. LIMITATIONS: Only physical therapists of one hospital and no other health care practitioners were included in this study. CONCLUSIONS: Fourteen physical therapists divided among 3 PAR groups were overall positive about their experiences when they conducted a research project together. This finding shows that a PAR approach can be used as a novel tool to stimulate research participation in clinics.","corpus_id":207401509,"score":0},{"doc_id":"24055787","title":"Development of an electronic alcohol screening and brief intervention program for hospital outpatients with unhealthy alcohol use.","abstract":"BACKGROUND: Alcohol screening and brief intervention is recommended for widespread implementation in health care systems, but it is not used routinely in most countries for a variety of reasons. Electronic screening and brief intervention (e-SBI), in which patients complete a Web-based questionnaire and are provided with personalized feedback on their drinking, is a promising alternative to practitioner delivered intervention, but its efficacy in the hospital outpatient setting has not been established. OBJECTIVE: The objective of our study was to establish the feasibility of conducting a full-scale randomized controlled trial to determine whether e-SBI reduces alcohol consumption in hospital outpatients with hazardous or harmful drinking. METHODS: The study was conducted in the outpatient department of a large public hospital in Newcastle (population 540,000), Australia. Adults with appointments at a broad range of medical and surgical outpatient clinics were invited to complete an e-SBI program on a laptop, and to report their impressions via a short questionnaire. Follow-up assessments were conducted 2-8 weeks later by email and post. RESULTS: We approached 172 outpatients and 108/172 (62.8%) agreed to participate. Of the 106 patients capable of self-administering the e-SBI, 7/106 (6.6%) did not complete it (3 due to technical problems and 4 because they were called for their appointment), 15/106 (14.2%) indicated that they had not consumed any alcohol in the past 12 months, 43/106 (40.6%) screened negative for unhealthy alcohol use (scored less than 5 on the Alcohol Use Disorders Identification Test Consumption [AUDIT-C] questions), 33/106 (31.1%) screened positive for hazardous or harmful drinking (AUDIT-C score 5-9), and 8/106 (7.5%) screened positive for possible alcohol dependence (AUDIT-C score 10-12). Among the subgroup with hazardous or harmful drinking, 27/33 (82%) found the feedback on their drinking very, quite, or somewhat useful, 33/33 (100%) thought the intervention would appeal to most or some of the people who attend the service, and 22/30 (73%) completed the follow-up. We also found that some well established procedures used in trials of e-SBI in the primary care setting did not translate to the hospital outpatient setting (1) we experienced delays because the e-SBI program had to be developed and maintained by the health service's information technology staff for security reasons, (2) recruiting patients as they left the reception desk was impractical because patients tended to arrive at the beginning of the clinics with few arrivals thereafter, and (3) use of a laptop in a fixed location resulted in some patients rushing through the e-SBI so they could return to their seat in the area they had been advised to wait in. CONCLUSIONS: e-SBI is acceptable to outpatients and with some adaptation to organizational and physical conditions, it is feasible to recruit and screen patients and to deliver the intervention without disrupting normal service provision. This suggests that e-SBI could be provided routinely in this important setting if shown to be efficacious.","corpus_id":32350715,"score":0},{"doc_id":"24200825","title":"Network Oncology (NO)--a clinical cancer register for health services research and the evaluation of integrative therapeutic interventions in anthroposophic medicine.","abstract":"BACKGROUND: Concepts of integrative oncology (IO), as have been offered by anthroposophic medicine (AM) for decades, are gaining increasing interest and acceptance. Central aspects are multimodal therapeutic interventions, health-related quality of live, and patients' preference as well as therapeutic relationship and clinical outcome. Despite its broad application, IO lacks evaluation in clinical practice and complementary therapies are not monitored by any cancer registries. METHODS: To close this gap we established 'Network Oncology' (NO), a conjoint registry of German outpatient AM practitioners and AM hospitals. In this paper we present the project and a first data overview and compare it to epidemiological registers and current literature. RESULTS: NO has collected 10,405 cancer patients' records in 6 years. Compared to epidemiological registers our data show minor differences in disease entity distribution, age, and gender. There is an overproportional amount of young breast cancer patients in NO institutions indicating a demand for integrative therapies in this group. There is no difference between the UICC (Union for International Cancer Control) stages at first diagnosis and at admission to a NO facility. According to our data conventional therapies were less frequently administered after admission to a NO facility. Nevertheless, one third of the patients received their first conventional therapy in a NO facility. 80% of the patients received mistletoe preparations and 63% had nonpharmacotherapeutic, complementary interventions. CONCLUSION: Integrative oncological approaches attract a great number of patients visiting AM institutions. The NO provides an infrastructure to evaluate integrative interventions in AM, allows comparison to other clinical registers, and thus can contribute to health service research in this field.","corpus_id":207744003,"score":0},{"doc_id":"24228935","title":"Reflecting on the methodological challenges of recruiting to a United Kingdom-wide, multi-centre, randomised controlled trial in gynaecology outpatient settings.","abstract":"BACKGROUND: Successful recruitment of participants to any trial is central to its success. Trial results are routinely published, and recruitment is often cited to be slower and more difficult than anticipated. This article reflects on the methodological challenges of recruiting women with prolapse attending United Kingdom (UK) gynaecology outpatient clinics to a multi-centre randomised controlled trial (RCT) of physiotherapy, and the systems put in place in an attempt to address them. METHODS: Gynaecology outpatients with symptomatic prolapse were to be recruited over a 16-month period from 14 UK hospitals and one New Zealand hospital. Eligible women were informed about the trial by their gynaecologist and informed consent was obtained by the central trial office. Recruitment difficulties were encountered early on, and a number of strategies were employed to try to improve recruitment. RESULTS: Some strategies were more successful than others and they differed in the resources required. Actions that facilitated recruitment included increasing recruiting centres to 23 UK and two international hospitals, good centre support, using processes embedded in clinical practice, and good communication between the trial office, collaborators and participants. Collaborator incentives, whereby staff involved received the benefit immediately, were more successful than a nominal monetary payment per woman randomised. Barriers to recruitment included fewer eligible women than anticipated, patient's preference to receive active treatment rather than allocation to the control group, lack of support staff and high staff turnover. Geographical variations in Primary Care Trust Research Management and Governance approval systems and general practitioner (GP) referral procedures also impacted negatively on recruitment. CONCLUSIONS: Our article reflects on the methodological challenges of recruiting to a multi-centre RCT in a UK gynaecology setting. Effective interventions included increasing the number of recruiting centres and providing collaborator incentives. Barriers to recruitment included fewer eligible women than anticipated, patient's preference to be allocated to the treatment group, lack of support staff, and variations in approval systems and GP referral procedures. To improve the evidence base on clinical trial recruitment, trialists need to publish their experiences and lessons learned. Future RCTs should evaluate, where possible, the effect of strategies designed to improve recruitment and retention. TRIAL REGISTRATION: Current Controlled Trials ISRCTN35911035.","corpus_id":8416544,"score":0},{"doc_id":"24243869","title":"Health care professionals' views of paediatric outpatient non-attendance: implications for general practice.","abstract":"BACKGROUND: Non-attendance at paediatric hospital outpatient appointments poses potential risks to children's health and welfare. Prevention and management of missed appointments depends on the perceptions of clinicians and decision makers from both primary and secondary care, including general practitioners (GPs) who are integral to non-attendance follow-up. OBJECTIVES: To examine the views of clinical, managerial and executive health care staff regarding occurrence and management of non-attendance at general paediatric outpatient clinics. METHODS: A qualitative study using individual semi-structured interviews was carried out at three English Primary Care Trusts and a nearby children's hospital. Interviews were conducted with 37 staff, including GPs, hospital doctors, other health care professionals, managers, executives and commissioners. Participants were recruited through purposive and 'snowball' sampling methods. Data were analysed following a thematic framework approach. RESULTS: GPs focused on situational difficulties for families, while hospital-based staff emphasized the influence of parents' beliefs on attendance. Managers, executives and commissioners presented a broad overview of both factors, but with less detailed views. All groups discussed sociodemographic factors, with non-attendance thought to be more likely in 'chaotic families'. Hospital interviewees emphasized child protection issues and the need for thorough follow-up of missed appointments. However, GPs were reluctant to interfere with parental responsibilities. CONCLUSION: Parental motivation and practical and social barriers should be considered. Responsibilities regarding missed appointments are not clear across health care sectors, but GPs are uniquely placed to address non-attendance issues and are central to child safeguarding. Primary care policies and strategies could be introduced to reduce non-attendance and ensure children receive the care they require.","corpus_id":10890712,"score":0},{"doc_id":"24308359","title":"Electronic health records for biological sample collection: feasibility study of statin-induced myopathy using the Clinical Practice Research Datalink.","abstract":"AIMS: Electronic healthcare records (EHRs) are increasingly used to store clinical information. A secondary benefit of EHRs is their use, in an anonymized form, for observational research. The Clinical Practice Research Datalink (CPRD) contains EHRs from primary care in the UK and, despite 1083 peer-reviewed research publications, has never been used to obtain pharmacogenetic samples. Using a statin-induced myopathy paradigm, we evaluated using the CPRD to obtain patient samples for a pharmacogenetic study targeting 250 cases and 500 controls from UK general practitioner (GP) practices. METHODS: The CPRD identified potential patients fitting specific case-definition criteria (active rhabdomyolysis or creatine phosphokinase > four times the upper limit of normal), and corresponding GP practices were asked to invite patient participation. Consenting patients were requested to provide either saliva or blood samples and to complete an ethnicity questionnaire. Control subjects were recruited from the same GP practice (saliva) or a small number of practices (blood). Samples were forwarded for DNA extraction. RESULTS: Thirty-six months of recruitment yielded DNA samples from 149 statin-induced myopathy cases and 587 tolerant controls. Data show that contacting patients through their GP is a reliable method for obtaining samples without compromising anonymity. Saliva collection directly from patients was considerably less effective than blood sampling. After 10 months of recruitment, saliva sampling was suspended in favour of blood sampling. CONCLUSIONS: We demonstrate the potential of EHRs for identifying accurately phenotyped cases and controls for pharmacogenetic studies. Recruitment was successful only because of the willingness of GP practices to participate and the existence of strong doctor-patient relationships. The present study provides a model that can be implemented in future genetic analyses using EHRs.","corpus_id":15747443,"score":0},{"doc_id":"24495499","title":"Procedures of recruiting, obtaining informed consent, and compensating research participants in Qatar: findings from a qualitative investigation.","abstract":"BACKGROUND: Very few researchers have reported on procedures of recruiting, obtaining informed consent, and compensating participants in health research in the Arabian Gulf Region. Empirical research can inform the debate about whether to adjust these procedures for culturally diverse settings. Our objective was to delineate procedures related to recruiting, obtaining informed consent, and compensating health research participants in the extremely high-density multicultural setting of Qatar. METHODS: During a multistage mixed methods project, field observations and qualitative interviews were conducted in a general medicine clinic of a major medical center in Qatar. Participants were chosen based on gender, age, literacy, and preferred language, i.e., Arabic, English, Hindi and Urdu. Qualitative analysis identified themes about recruitment, informed consent, compensation, and other research procedures. RESULTS: A total of 153 individuals were approached and 84 enrolled; the latter showed a diverse age range (18 to 75 years); varied language representation: Arabic (n = 24), English (n = 20), Hindi (n = 20), and Urdu (n = 20); and balanced gender distribution: women (n = 43) and men (n = 41). Primary reasons for 30 declinations included concern about interview length and recording. The study achieved a 74% participation rate. Qualitative analytics revealed key themes about hesitation to participate, decisions about participation with family members as well as discussions with them as \"incidental research participants\", the informed consent process, privacy and gender rules of the interview environment, reactions to member checking and compensation, and motivation for participating. Vulnerability emerged as a recurring issue throughout the process among a minority of participants. CONCLUSIONS: This study from Qatar is the first to provide empirical data on recruitment, informed consent, compensation and other research procedures in a general adult population in the Middle East and Arabian Gulf. This investigation illustrates how potential research participants perceive research participation. Fundamentally, Western ethical research principles were applicable, but required flexibility and culturally informed adaptations.","corpus_id":15262678,"score":0},{"doc_id":"24690402","title":"Structured, intensive education maximising engagement, motivation and long-term change for children and young people with diabetes: a cluster randomised controlled trial with integral process and economic evaluation - the CASCADE study.","abstract":"BACKGROUND: Type 1 diabetes (T1D) in children and young people is increasing worldwide with a particular increase in children under the age of 5 years. Fewer than one in six children and young people achieve glycosylated fraction of haemoglobin (HbA1c) values in the range identified as providing best future outcomes. There is an urgent need for clinic-based pragmatic, feasible and effective interventions that improve both glycaemic control and quality of life (QoL). The intervention offers both structured education, to ensure young people know what they need to know, and a delivery model designed to motivate self-management. OBJECTIVE: To assess the feasibility of providing a clinic-based structured educational group programme incorporating psychological approaches to improve long-term glycaemic control, QoL and psychosocial functioning in a diverse range of young people. DESIGN: The study was a pragmatic, cluster randomised control trial with integral process and economic evaluation. SETTING: Twenty-eight paediatric diabetes services across London, south-east England and the Midlands. RANDOMISATION: Minimised by clinic size, age (paediatric or adolescent) and specialisation (district general hospital clinic or teaching hospital/tertiary clinic). ALLOCATION: Half of the sites were randomised to the intervention arm and half to the control arm. Allocation was concealed until after clinics had consented and the first participant was recruited. Where possible, families were blind to allocation until recruitment finished. PARTICIPANTS: Forty-three health-care practitioners (14 teams) were trained in the intervention. The study recruited 362 children aged 8-16 years, diagnosed with T1D for > 12 months, with a mean 12-month HbA1c level of ≥ 8.5%. INTERVENTION: Two 1-day workshops taught intervention delivery. A detailed manual and resources were provided. The intervention consists of four group education sessions led by a paediatric diabetes specialist nurse with another team member. OUTCOMES: The primary outcome was glycaemic control, assessed at the individual level using venous HbA1c values, measured at baseline, 12 and 24 months. Secondary outcomes were directly and indirectly related to diabetes management, including hypoglycaemic episodes, hospital admissions, diabetes regimen, knowledge, skills and responsibility for diabetes management, intervention compliance, clinic utilisation, emotional and behavioural adjustment, and general and diabetes-specific QoL. PROCESS EVALUATION: Questionnaires, semistructured interviews, informal discussion following observation sessions, fieldwork notes and case note review were used to collect qualitative and quantitative data from key stakeholder groups at specific time points in the trial. STATISTICAL ANALYSES: Primary and secondary analyses were intention-to-treat comparisons of outcomes at 12 and 24 months, using analysis of covariance with a random effect for clinic. Prespecified subgroup analyses based on age, gender, initial HbA1c value and socioeconomic status were estimated from models that included an interaction term. The economic analysis compared long-term costs and predicted quality-adjusted life-years (QALYs). RESULTS: The intervention did not improve HbA1c at 12 months [intervention effect 0.11; 95% confidence interval (CI) -0.28 to 0.50; p = 0.584] or 24 months (intervention effect 0.03; 95% CI -0.36 to 0.41; p = 0.891). A total of 298/362 patients (82.3%) provided blood samples at 12-month follow-up, and 284/362 (78.5%) provided blood samples at 24-month follow-up. Follow-up questionnaires were completed by 307 patients (85.3%) at 12 months and by 295 patients (81.5%) at 24 months. Intervention group parents at 12 months (95% CI 0.74; 0.03 to 1.52) and young people at 24 months (0.85; 95% CI 0.03 to 1.61) had higher scores on the diabetes family responsibility questionnaire. Young people reported reduced happiness with body weight at 12 months (-0.56; 95% CI -1.03 to -0.06). Only 68% of groups were run. Of the 180 families recruited, 96 (53%) attended at least one module. Reasons for low uptake included difficulties organising groups, and work and school commitments. Young people with higher HbA1c levels were less likely to attend. Parents and young people who attended groups described improved family relationships, improved knowledge and understanding, greater confidence and increased motivation to manage diabetes. Twenty-four months after the intervention, nearly half of the young people reported that the groups had made them want to try harder and that they had carried on trying. A high-quality, complex, pragmatic trial of structured education can be delivered alongside standard care in NHS diabetes clinics. Health-care providers benefited from behaviour change skill training and can deliver pragmatic aspects of a National Institute for Health and Care Excellence (NICE)-compliant structured education programme after relatively brief training. The process evaluation provides insight into aspects of the model, and highlights strengths and aspects that may have contributed to the failure to influence primary and secondary outcomes. Current NHS practice dominates CASCADE (Child and Adolescent Structured Competencies Approach to Diabetes Education) in that it achieves the same number of QALYs at a lower cost. The mean cost of providing the intervention was £5098 per site or £683 per child. Members of paediatric diabetes services trained to deliver the CASCADE structured education package using behaviour change techniques did not improve glycaemic control in patients compared with control subjects 1 and 2 years after the intervention. The training workshops for practitioners were well evaluated; however, more intensive training was needed. The intervention cost £683 per patient but was not cost-effective because it did not improve metabolic control. CONCLUSIONS: A high-quality, complex, pragmatic trial of structured education can be successfully conducted alongside standard care in NHS diabetes clinics. Pragmatic components of a NICE-compliant structured education programme can be successfully delivered following a relatively brief 2-day training while paediatric health-care professionals benefit from training in behaviour change skills. The study provides invaluable information on barriers and opportunities regarding future, similar interventions. A low dropout rate and good attendance for the subgroup that attended the intervention suggests there might be improved uptake if offered to young people with lower HbA1c. Testing whether this approach can be more successful with a robust ongoing supervisory element should be a target of further research. TRIAL REGISTRATION: Current Controlled Trials ISRCTN52537669. FUNDING: This project was funded by the NIHR Health Technology Assessment programme and will be published in full in Health Technology Assessment; Vol. 18, No. 20. See the NIHR Journals Library website for further project information.","corpus_id":21991999,"score":0},{"doc_id":"24793730","title":"Feasibility of integrating research data collection into routine clinical practice using the electronic health record.","abstract":"PURPOSE: The electronic health record is becoming central to routine medical practice and has the potential to facilitate large scale clinical research. We evaluated the completeness and accuracy of data collection using designated research fields integrated into a semistructured clinical note. We hypothesized that prospective research data collection as part of routine clinical charting is feasible, with a high rate of utilization (greater than 80%) and accuracy (kappa greater than 0.80). MATERIALS AND METHODS: Infants with congenital hydronephrosis were followed prospectively at a single institution. Existing functionality in the electronic health record was used for data collection by creation of 28 different data elements captured from a hydronephrosis note or phrase template. Completeness (percent utilization) was calculated and accuracy was assessed by comparing the structured data to manual chart review. Comparisons were conducted using the chi-square test, with 2-tailed p values <0.05 considered statistically significant. RESULTS: A total of 80 patients were eligible for manual chart review. Data were recorded through template use in 64 patients for an overall completeness of 80.0%. Of 28 elements 17 (60%) demonstrated \"almost perfect\" agreement (kappa greater than 0.80), and all variables reached at least \"moderate\" agreement (greater than 0.40). CONCLUSIONS: Integrating research fields into routine clinical practice is feasible by using semistructured clinical templates within an electronic health record. High completion and accuracy rates were captured from a variety of fields within a hydronephrosis template.","corpus_id":36863773,"score":0},{"doc_id":"24885915","title":"Effectiveness and cost-effectiveness of a group-based pain self-management intervention for patients undergoing total hip replacement: feasibility study for a randomized controlled trial.","abstract":"BACKGROUND: Total hip replacement (THR) is a common elective surgical procedure and can be effective for reducing chronic pain. However, waiting times can be considerable. A pain self-management intervention may provide patients with skills to more effectively manage their pain and its impact during their wait for surgery. This study aimed to evaluate the feasibility of conducting a randomized controlled trial to assess the effectiveness and cost-effectiveness of a group-based pain self-management course for patients undergoing THR. METHODS: Patients listed for a THR at one orthopedic center were posted a study invitation pack. Participants were randomized to attend a pain self-management course plus standard care or standard care only. The lay-led course was delivered by Arthritis Care and consisted of two half-day sessions prior to surgery and one full-day session after surgery. Participants provided outcome and resource-use data using a diary and postal questionnaires prior to surgery and one month, three months and six months after surgery. Brief telephone interviews were conducted with non-participants to explore barriers to participation. RESULTS: Invitations were sent to 385 eligible patients and 88 patients (23%) consented to participate. Interviews with 57 non-participants revealed the most common reasons for non-participation were views about the course and transport difficulties. Of the 43 patients randomized to the intervention group, 28 attended the pre-operative pain self-management sessions and 11 attended the post-operative sessions. Participant satisfaction with the course was high, and feedback highlighted that patients enjoyed the group format. Retention of participants was acceptable (83% of recruited patients completed follow-up) and questionnaire return rates were high (72% to 93%), with the exception of the pre-operative resource-use diary (35% return rate). Resource-use completion rates allowed for an economic evaluation from the health and social care payer perspective. CONCLUSIONS: This study highlights the importance of feasibility work prior to a randomized controlled trial to assess recruitment methods and rates, barriers to participation, logistics of scheduling group-based interventions, acceptability of the intervention and piloting resource use questionnaires to improve data available for economic evaluations. This information is of value to researchers and funders in the design and commissioning of future research. TRIAL REGISTRATION: Current Controlled Trials ISRCTN52305381.","corpus_id":10064675,"score":0},{"doc_id":"25486401","title":"Recruiting U.S. and Canadian college students via social media for participation in a web-based brief intervention study.","abstract":"OBJECTIVE: Recruiting young adults for health research is challenging. Social media provides wide access to potential research participants. We evaluated the feasibility of recruiting students via free message postings on Facebook and Twitter to participate in a web-based brief intervention study. The sample comprised students attending U.S. and Canadian universities. METHOD: During three semesters, institutional review board-approved recruitment messages were posted in 281 Facebook groups, 7 Facebook pages, and 27 message \"tweets\" on Twitter. RESULTS: A total of 708 eligible participants were recruited from Facebook. The mean enrollment rate per Facebook group was 0.21%; the rate was higher for host university groups (1.56%) compared with groups at other universities (0.10%). We recruited seven participants from Twitter. The sample was predominantly female (70%) with a mean age of 20.0 years. There were no significant differences between host university participants recruited through social media and traditional methods. The web-based intervention completion rate was 65%, and participants from the host university were more likely to complete the intervention than were groups at other universities (p = .01). CONCLUSIONS: Social media provides access to a large number of potential participants, and social media recruitment may be useful to researchers who can harness this broad reach. Facebook recruitment was feasible and free and resulted in a large number of enrolled participants. Social media recruitment for researchers at their own universities may be particularly fruitful. Despite wide access to students with Twitter, recruitment was slow. Social media recruitment allowed us to extend web-based intervention access to students in the United States and Canada.","corpus_id":39164230,"score":0},{"doc_id":"25759376","title":"Danish nationwide registers for public health and health-related research.","abstract":"AIMS: The Nordic countries have a strong tradition of using nationwide social and health registers for research purposes. The aim of the current paper is to provide an overview of the Danish population-based registers in public health and health-related research, and to discuss their strengths and limitations. METHODS: Danish registers on somatic and psychiatric hospital contacts as well as care provided by general practitioners were reviewed. The availability of demographic, individual-level variables of relevance for health-related research was summarized. RESULTS: Since 1968, every person living in Denmark has a unique identifier. This identifier is listed in Danish registers enabling linkage of information from a range of registers on an individual level. The nationwide coverage of all patient contacts at somatic and psychiatric hospitals, consultations with general practitioners, purchases of prescribed medications, and a complete follow-up with respect to causes of death support public health studies surveying trends of prevalence and incidence. Historical data on psychiatric and somatic hospitalizations since 1969 and 1977, respectively, allow an in-depth assessment of the burden of disease and time trends. Demographic characteristics of individuals and family units, together with information on education, employment, income, place of residence and migration, are provided by social registers. CONCLUSIONS: Register data are fully representative of the entire population with no loss to follow-up. Nationwide coverage also ensures a large sample to investigate events and conditions with low base rates. Clinical observations are limited and often only available for select patient populations. However, the opportunities available for public health research through linkage of register data with the increasing number of nationwide clinical databases, bio-banks and surveys entail promising perspectives for future research.","corpus_id":206723150,"score":0},{"doc_id":"25862756","title":"Introducing consultant outpatient clinics to community settings to improve access to paediatrics: an observational impact study.","abstract":"OBJECTIVES: In line with a national policy to move care 'closer to home', a specialist children's hospital in the National Health Service in England introduced consultant-led 'satellite' clinics to two community settings for general paediatric outpatient services. Objectives were to reduce non-attendance at appointments by providing care in more accessible locations and to create new physical clinic capacity. This study evaluated these satellite clinics to inform further development and identify lessons for stakeholders. METHODS: Impact of the satellite clinics was assessed by comparing community versus hospital-based clinics across the following measures: (1) non-attendance rates and associated factors (including patient characteristics and travel distance) using a logistic regression model; (2) percentage of appointments booked within local catchment area; (3) contribution to total clinic capacity; (4) time allocated to clinics and appointments; and (5) clinic efficiency, defined as the ratio of income to staff-related costs. RESULTS: Satellite clinics did not increase attendance beyond their contribution to shorter travel distance, which was associated with higher attendance. Children living in the most-deprived areas were 1.8 times more likely to miss appointments compared with those from least-deprived areas. The satellite clinics' contribution to activity in catchment areas and to total capacity was small. However, one of the two satellite clinics was efficient compared with most hospital-based clinics. CONCLUSIONS: Outpatient clinics were relocated in pragmatically chosen community settings using a 'drag and drop' service model. Such clinics have potential to improve access to specialist paediatric healthcare, but do not provide a panacea. Work is required to improve attendance as part of wider efforts to support vulnerable families. Satellite clinics highlight how improved management could contribute to better use of existing capacity.","corpus_id":21591162,"score":0},{"doc_id":"26251363","title":"A participatory study of teenagers and young adults views on access and participation in cancer research.","abstract":"PURPOSE: The purpose of this study was to elicit young people's views on access and participation in cancer research. METHODS: Eight young people aged 18-25 years with a previous cancer diagnosis aged 15-24 participated in a one day workshop utilising participatory methodology. The workshop consisted of four exercises: role play/scene setting; focus group examining thoughts and opinions of research access and participation; individual reflection on access to different types of research; and creative interpretation of the workshop. Further consultation with 222 young people with cancer was conducted using an electronic survey. RESULTS: Three themes emerged: • Patient choice: Young people thought it was their right to know all options about available research. Without knowledge of all available studies they would be unable to make an informed choice about participation. • Role of healthcare professionals as facilitators/barriers: Young people suggested non-clinical healthcare professionals such as social workers and youth support coordinators may be more suited to approaching young people about participation in psychosocial and health services research. • Value of the research: The what, when and how information was delivered was key in relaying the value of the study and assisting young people in their decision to participate. Further consultation showed approximately 70% wanted to find out about all available research. However, one third trusted healthcare professionals to decide which research studies to inform them of. CONCLUSION: Effective ways to support healthcare professionals approaching vulnerable populations about research are needed to ensure young people are empowered to make informed choices about research participation.","corpus_id":19123847,"score":0},{"doc_id":"26470880","title":"Participant recruitment into a randomised controlled trial of exercise therapy for people with multiple sclerosis.","abstract":"BACKGROUND: The success of a clinical trial is often dependant on whether recruitment targets can be met in the required time frame. Despite an increase in research into the benefits of exercise in people with multiple sclerosis (PwMS), no trial has reported detailed data on effective recruitment strategies for large-scale randomised controlled trials. The main purpose of this report is to provide a detailed outline of recruitment strategies, rates and estimated costs in the Exercise Intervention for Multiple Sclerosis (ExIMS) trial to identify best practices for future trials involving multiple sclerosis (MS) patient recruitment. METHODS: The ExIMS researchers recruited 120 PwMS to participate in a 12-week exercise intervention. Participants were randomly allocated to either exercise or usual-care control groups. Participants were sedentary, aged 18-65 years and had Expanded Disability Status Scale scores of 1.0-6.5. Recruitment strategies included attendance at MS outpatient clinics, consultant mail-out and trial awareness-raising activities. RESULTS: A total of 120 participants were recruited over the course of 34 months. To achieve this target, 369 potentially eligible and interested participants were identified. A total of 60 % of participants were recruited via MS clinics, 29.2 % from consultant mail-outs and 10.8 % through trial awareness. The randomisation yields were 33.2 %, 31.0 % and 68.4 % for MS clinic, consultant mail-outs and trial awareness strategies, respectively. The main reason for ineligibility was being too active (69.2 %), whilst for eligible participants the most common reason for non-participation was the need to travel to the study site (15.8 %). Recruitment via consultant mail-out was the most cost-effective strategy, with MS clinics being the most time-consuming and most costly. CONCLUSIONS: To reach recruitment targets in a timely fashion, a variety of methods were employed. Although consultant mail-outs were the most cost-effective recruitment strategy, use of this method alone would not have allowed us to obtain the predetermined number of participants in the required time period, thus leading to costly extensions of the project or failure to reach the number of participants required for sufficient statistical power. Thus, a multifaceted approach to recruitment is recommended for future trials. TRIAL REGISTRATION: International Standard Randomised Controlled Trial Registry number: ISRCTN41541516 ; date registered: 5 February 2009.","corpus_id":6013974,"score":0},{"doc_id":"26753864","title":"Genetics, lifestyle and environment. UK Biobank is an open access resource following the lives of 500,000 participants to improve the health of future generations.","abstract":"UK Biobank is a long-term prospective epidemiology study having recruited and now following the lives of 500,000 people in England, Scotland and Wales, aged 40-69 years when they joined the study (Sudlow et al., PLoS Med 12(3):e1001779, 2015). Participants were recruited by letter and asked to attend one of 22 assessment centres in towns and cities across Britain, where they provided consent, answered detailed questions about their health and lifestyle, had body measures taken and donated blood, urine and saliva. Participants provided consent for the long-term follow-up of their health via medical records, such as general practice and hospital records, cancer and death records. Samples are being stored long term for a wide range of analyses, including genetic. The resource is open to all bona fide scientists from the UK and overseas, academic and industry who register via its access management system. Summary of UK Biobank data can be viewed via its Data Showcase and the resource will be strengthened over time as the results of new analyses and studies are returned, health links and participants provide additional information about themselves. Some will attend full repeat assessment visits. UK Biobank is open for business, and it hopes researchers will find it a valuable tool to improve the health of future generations.","corpus_id":13910209,"score":0},{"doc_id":"26813669","title":"Patient responses to research recruitment and follow-up surveys: findings from a diverse multicultural health care setting in Qatar.","abstract":"BACKGROUND: Health care researchers working in the Arabian Gulf need information on how to optimize recruitment and retention of study participants in extremely culturally diverse settings. Implemented in Doha, Qatar in 2012 with 4 language groups, namely Arabic, English, Hindi, and Urdu, this research documents persons' responses to recruitment, consent, follow-up, and reminder procedures during psychometric testing of the Multicultural Assessment Instrument (MAI), a novel self- or interviewer-administered survey. METHODS: Bilingual research assistants recruited adults in outpatient clinics by approaching persons in particular who appeared to be from a target language group. Participants completed the MAI, a second acculturation instrument used for content-validity assessment, and a demographics questionnaire. Participants were asked to take the MAI again in 2-3 weeks, in person or by post, to assess test-retest reliability. Recruitment data were analyzed by using nonparametric statistics. RESULTS: Of 1503 persons approached during recruitment, 400 enrolled (27%)-100 per language group. The enrollment rates in the language groups were: Arabic-32%; English-33%; Hindi-18%; Urdu-30%. The groups varied somewhat in their preferences regarding consent procedure, follow-up survey administration, contact mode for follow-up reminders, and disclosure of personal mailing address (for postal follow-up). Over all, telephone was the preferred medium for follow-up reminders. Of 64 persons who accepted a research assistant's invitation for in-person follow-up, 40 participants completed the interview (follow-up rate, 63%); among 126 persons in the postal group with a deliverable address, 29 participants mailed back a completed follow-up survey (response rate, 23%). CONCLUSIONS: Researchers in the Arabian Gulf face challenges to successfully identify, enroll, and retain eligible study participants. Although bilingual assistants-often from the persons' own culture-recruited face-to-face, and our questionnaire contained no health care-related content, many persons were reluctant to participate. This occurrence was observed especially at follow-up, particularly among participants who had agreed to follow-up by post.","corpus_id":12322176,"score":0},{"doc_id":"26861942","title":"Dental practitioner recruitment for a randomized clinical trial in the field to evaluate the performance of a new glass ionomer restoration material.","abstract":"BACKGROUND: In 2009, we began recruiting dental practitioners across Germany to participate in a clinical trial to evaluate the clinical performance of EQUIA, a new glass ionomer restoration material. The aim of this paper is to discuss the outcomes of the dental practitioner recruitment and outline the process of establishing a practice-based research network. METHODS: Study proposals were sent to randomly selected dental offices in 29 cities in Germany. The proposals were sent until a minimum of 10 clinics in each city declared participation. Later on, briefing lectures informed the participating practitioners about the design, methods, and material application procedure. Participants were familiarized with the guidelines of Good Manufacturing Practice (GMP) and Good Epidemiological Practice (GEP). A questionnaire describing the characteristics of each dental office was filled out by the participating practitioner. Additionally, participation levels were characterized according to the socioeconomic status and geographic districts of residence in Germany (Regions 0 to 9). The associations between the characteristics were tested by the Kruskal-Wallis Test and Chi-squared test (P < 0.05). RESULTS: A total of 3194 private dental clinics were invited, 1712 clinics refused to participate, 1195 did not respond to the invitation, and 323 agreed to participate. Only 144 clinics participated in the lectures held in their cities and signed the participation agreement. Based on their geographic location, the highest participation was in Region 2 with a participation rate of 14.3%, and the lowest participation was in Region 6 with a participation rate of 1.7%. Regions with the lowest rate of unemployment and relatively higher rates of income (Regions 7 and 8) had the highest rate of refusals (86%). CONCLUSION: The initial results of the dental practitioner recruitment in this study suggest that the recruitment and pre-randomization design were successful, and by reaching out to a considerable number of private dental clinics to participate, we were able to recruit a smaller number of highly motivated dentists in this clinical study. Regional differences in socioeconomic status, practitioner specialization, and differences in patient health care insurance have to be considered when recruiting dental practitioners for clinical trials. TRIAL REGISTRATION: The trial has been registered at Deutsches Register Klinischer Studien (German register of clinical trials) on 6 September 2012 under DRKS-ID: DRKS00004220.","corpus_id":2930922,"score":0},{"doc_id":"26867046","title":"OPTIMA prelim: a randomised feasibility study of personalised care in the treatment of women with early breast cancer.","abstract":"BACKGROUND: There is uncertainty about the chemotherapy sensitivity of some oestrogen receptor (ER)-positive, human epidermal growth factor receptor 2 (HER2)-negative breast cancers. Multiparameter assays that measure the expression of several tumour genes simultaneously have been developed to guide the use of adjuvant chemotherapy for this breast cancer subtype. The assays provide prognostic information and have been claimed to predict chemotherapy sensitivity. There is a dearth of prospective validation studies. The Optimal Personalised Treatment of early breast cancer usIng Multiparameter Analysis preliminary study (OPTIMA prelim) is the feasibility phase of a randomised controlled trial (RCT) designed to validate the use of multiparameter assay directed chemotherapy decisions in the NHS. OBJECTIVES: OPTIMA prelim was designed to establish the acceptability to patients and clinicians of randomisation to test-driven treatment assignment compared with usual care and to select an assay for study in the main RCT. DESIGN: Partially blinded RCT with adaptive design. SETTING: Thirty-five UK hospitals. PARTICIPANTS: Patients aged ≥ 40 years with surgically treated ER-positive HER2-negative primary breast cancer and with 1-9 involved axillary nodes, or, if node negative, a tumour at least 30 mm in diameter. INTERVENTIONS: Randomisation between two treatment options. Option 1 was standard care consisting of chemotherapy followed by endocrine therapy. In option 2, an Oncotype DX(®) test (Genomic Health Inc., Redwood City, CA, USA) performed on the resected tumour was used to assign patients either to standard care [if 'recurrence score' (RS) was > 25] or to endocrine therapy alone (if RS was ≤ 25). Patients allocated chemotherapy were blind to their randomisation. MAIN OUTCOME MEASURES: The pre-specified success criteria were recruitment of 300 patients in no longer than 2 years and, for the final 150 patients, (1) an acceptance rate of at least 40%; (2) recruitment taking no longer than 6 months; and (3) chemotherapy starting within 6 weeks of consent in at least 85% of patients. RESULTS: Between September 2012 and 3 June 2014, 350 patients consented to join OPTIMA prelim and 313 were randomised; the final 150 patients were recruited in 6 months, of whom 92% assigned chemotherapy started treatment within 6 weeks. The acceptance rate for the 750 patients invited to participate was 47%. Twelve out of the 325 patients with data (3.7%, 95% confidence interval 1.7% to 5.8%) were deemed ineligible on central review of receptor status. Interviews with researchers and recordings of potential participant consultations made as part of the integral qualitative recruitment study provided insights into recruitment barriers and led to interventions designed to improve recruitment. Patient information was changed as the result of feedback from three patient focus groups. Additional multiparameter analysis was performed on 302 tumour samples. Although Oncotype DX, MammaPrint(®)/BluePrint(®) (Agendia Inc., Irvine, CA, USA), Prosigna(®) (NanoString Technologies Inc., Seattle, WA, USA), IHC4, IHC4 automated quantitative immunofluorescence (AQUA(®)) [NexCourse BreastTM (Genoptix Inc. Carlsbad, CA, USA)] and MammaTyper(®) (BioNTech Diagnostics GmbH, Mainz, Germany) categorised comparable numbers of tumours into low- or high-risk groups and/or equivalent molecular subtypes, there was only moderate agreement between tests at an individual tumour level (kappa ranges 0.33-0.60 and 0.39-0.55 for tests providing risks and subtypes, respectively). Health economics modelling showed the value of information to the NHS from further research into multiparameter testing is high irrespective of the test evaluated. Prosigna is currently the highest priority for further study. CONCLUSIONS: OPTIMA prelim has achieved its aims of demonstrating that a large UK clinical trial of multiparameter assay-based selection of chemotherapy in hormone-sensitive early breast cancer is feasible. The economic analysis shows that a trial would be economically worthwhile for the NHS. Based on the outcome of the OPTIMA prelim, a large-scale RCT to evaluate the clinical effectiveness and cost-effectiveness of multiparameter assay-directed chemotherapy decisions in hormone-sensitive HER2-negative early breast would be appropriate to take place in the NHS. TRIAL REGISTRATION: Current Controlled Trials ISRCTN42400492. FUNDING: This project was funded by the National Institute for Health Research (NIHR) Health Technology Assessment programme and will be published in full in Health Technology Assessment; Vol. 20, No. 10. See the NIHR Journals Library website for further project information. The Government of Ontario funded research at the Ontario Institute for Cancer Research. Robert C Stein received additional support from the NIHR University College London Hospitals Biomedical Research Centre.","corpus_id":33540975,"score":0},{"doc_id":"26977856","title":"Use of a 12 months' self-referral reminder to facilitate uptake of bowel scope (flexible sigmoidoscopy) screening in previous non-responders: a London-based feasibility study.","abstract":"BACKGROUND: In March 2013, NHS England extended its national Bowel Cancer Screening Programme to include 'one-off' Flexible Sigmoidoscopy screening (NHS Bowel Scope Screening, BSS) for men and women aged 55. With less than one in two people currently taking up the screening test offer, there is a strong public health mandate to develop system-friendly interventions to increase uptake while the programme is rolling out. This study aimed to assess the feasibility of sending a reminder to previous BSS non-responders, 12 months after the initial invitation, with consideration for its potential impact on uptake. METHOD: This study was conducted in the ethnically diverse London Boroughs of Brent and Harrow, where uptake is below the national average. Between September and November 2014, 160 previous non-responders were randomly selected to receive a reminder of the opportunity to self-refer 12 months after their initial invitation. The reminder included instructions on how to book an appointment, and provided options for the time and day of the appointment and the gender of the endoscopist performing the test. To address barriers to screening, the reminder was sent with a brief locally tailored information leaflet designed specifically for this study. Participants not responding within 4 weeks were sent a follow-up reminder, after which there was no further intervention. Self-referral rates were measured 8 weeks after the delivery of the follow-up reminder and accepted as final. RESULTS: Of the 155 participants who received the 12 months' reminder (returned to sender, n=5), 30 (19.4%) self-referred for an appointment, of which 24 (15.5%) attended and were successfully screened. Attendance rates differed by gender, with significantly more women attending an appointment than men (20.7% vs 8.8%, respectively; OR=2.73, 95% CI=1.02-7.35, P=0.05), but not by area (Brent vs Harrow) or area-level deprivation. Of the 30 people who self-referred for an appointment, 27 (90%) indicated a preference for a same-sex practitioner, whereas three (10%) gave no preference. Preference for a same-sex practitioner was higher among women than men (χ(2)=7.78, P<0.05), with only 67% of men (six of nine) requesting a same-sex practitioner, compared with 100% of women (n=21). CONCLUSIONS: Sending previous non-responders a 12 months' reminder letter with a brief information leaflet is a feasible and efficacious intervention, which merits further investigation in a randomised controlled trial.","corpus_id":6160026,"score":0},{"doc_id":"27780796","title":"Participant Recruitment and Engagement in Automated eHealth Trial Registration: Challenges and Opportunities for Recruiting Women Who Experience Violence.","abstract":"BACKGROUND: Automated eHealth Web-based research trials offer people an accessible, confidential opportunity to engage in research that matters to them. eHealth trials may be particularly useful for sensitive issues when seeking health care may be accompanied by shame and mistrust. Yet little is known about people's early engagement with eHealth trials, from recruitment to preintervention autoregistration processes. A recent randomized controlled trial that tested the effectiveness of an eHealth safety decision aid for New Zealand women in the general population who experienced intimate partner violence (isafe) provided the opportunity to examine recruitment and preintervention participant engagement with a fully automated Web-based registration process. The trial aimed to recruit 340 women within 24 months. OBJECTIVE: The objective of our study was to examine participant preintervention engagement and recruitment efficiency for the isafe trial, and to analyze dropout through the registration pathway, from recruitment to eligibility screening and consent, to completion of baseline measures. METHODS: In this case study, data collection sources included the trial recruitment log, Google Analytics reports, registration and program metadata, and costs. Analysis included a qualitative narrative of the recruitment experience and descriptive statistics of preintervention participant engagement and dropout rates. A Koyck model investigated the relationship between Web-based online marketing website advertisements (ads) and participant accrual. RESULTS: The isafe trial was launched on September 17, 2012. Placement of ads in an online classified advertising platform increased the average number of recruited participants per month from 2 to 25. Over the 23-month recruitment period, the registration website recorded 4176 unique visitors. Among 1003 women meeting eligibility criteria, 51.55% (517) consented to participate; among the 501 women who enrolled (consented, validated, and randomized), 412 (82.2%) were accrued (completed baseline assessments). The majority (n=52, 58%) of the 89 women who dropped out between enrollment and accrual never logged in to the allocated isafe website. Of every 4 accrued women, 3 (314/412, 76.2%) identified the classified ad as their referral source, followed by friends and family (52/412, 12.6%). Women recruited through a friend or relative were more likely to self-identify as indigenous Māori and live in the highest-deprivation areas. Ads increased the accrual rate by a factor of 74 (95% CI 49-112). CONCLUSIONS: Print advertisements, website links, and networking were costly and inefficient methods for recruiting participants to a Web-based eHealth trial. Researchers are advised to limit their recruitment efforts to Web-based online marketplace and classified advertising platforms, as in the isafe case, or to social media. Online classified advertising in \"Jobs-Other-volunteers\" successfully recruited a diverse sample of women experiencing intimate partner violence. Preintervention recruitment data provide critical information to inform future research and critical analysis of Web-based eHealth trials. CLINICALTRIAL: Australian New Zealand Clinical Trials Registry (ANZCTR): ACTRN12612000708853; https://www.anzctr.org.au/Trial/Registration/TrialReview.aspx?ACTRN=12612000708853 (Archived by WebCite at http://www.webcitation/6lMGuVXdK).","corpus_id":10775969,"score":0},{"doc_id":"28397521","title":"Improving access to health care in a rural regional hospital in South Africa: Why do patients miss their appointments?","abstract":"BACKGROUND: Access to health services is one of the Batho Pele ('people first') values and principles of the South African government since 1997. This necessitated some changes around public service systems, procedures, attitudes and behaviour. The challenges of providing health care to rural geographically spread populations include variations in socio-economic status, transport opportunities, access to appointment information and patient perceptions of costs and benefits of seeking health care. George hospital, situated in a rural area, serves 5000 outpatient visits monthly, with non-attendance rates of up to 40%. OBJECTIVES: The aim of this research was to gain a greater understanding of the reasons behind non-attendance of outpatient department clinics to allow locally driven, targeted interventions. METHODS: This was a descriptive study. We attempted to phone all patients who missed appointments over a 1-month period (n = 574). Only 20% were contactable with one person declining consent. Twenty-nine percent had no telephone number on hospital systems, 7% had incorrect numbers, 2% had died and 42% did not respond to three attempts. RESULTS: The main reasons for non-attendance included unaware of appointment date (16%), out of area (11%), confusion over date (11%), sick or admitted to hospital (10%), family member sick or died (7%), appointment should have been cancelled by clerical staff (6%) and transport (6%). Only 9% chose to miss their appointment. The other 24% had various reasons. CONCLUSIONS: Improved patient awareness of appointments, adjustments in referral systems and enabling appointment cancellation if indicated would directly improve over two-thirds of reasons for non-attendance. Understanding the underlying causes will help appointment planning, reduce wasted costs and have a significant impact on patient care.","corpus_id":-1,"score":0},{"doc_id":"28699815","title":"Improving recruitment to healthcare research studies: clinician judgements explored for opting mental health service users out of the time to change viewpoint survey.","abstract":"BACKGROUND: There are significant challenges across the research pathway, including participant recruitment. This paper aims to explore the impact of clinician recruitment decision-making on sampling for a national mental health survey. METHOD: Clinical teams in 20 English mental healthcare provider organisations screened caseload lists, opting-out people whom, in their judgement, should not be approached to participate in a survey about stigma and discrimination. The reasons for each individual opted-out were requested. We assess these reasons against study recruitment criteria and investigated the impact of variations in opt-out rates on response rates and study findings. RESULTS: Over 4 years (2009-2012), 37% (28,592 people) of the total eligible sampling frame were excluded. Exclusions comprised three categories: clinical teams did not screen their lists within recruitment period (12,392 people: 44%); protocol-specified exclusions (8364 people: 29%); clinician opt-outs queried by research team (other reasons were given) (7836, 28%). Response rates were influenced by decision-making variations. CONCLUSIONS: Large numbers of people were denied the opportunity to choose for themselves whether to participate or not in the Viewpoint Survey. The clinical research community, and their employing organisations, require support to better understand the value of research and best practice for research recruitment.","corpus_id":25545009,"score":0},{"doc_id":"28861532","title":"Perceptions of Barriers to and Facilitators of Participation in Health Research Among Transgender People.","abstract":"Purpose: Although transgender people may be at increased risk for a range of health problems, they have been the subject of relatively little health research. An important step toward expanding the evidence base is to understand and address the reasons for nonparticipation and dropout. The aim of this study was to explore the perceptions of barriers to and facilitators of participation in health research among a sample of transgender people in San Francisco, CA, and Atlanta, GA. Methods: Twelve in-person focus groups (FGs) were conducted; six (three with transwomen, three with transmen) were conducted in San Francisco and six FGs were conducted in Atlanta (three with transwomen and three with transmen). FGs were audiorecorded, transcribed, and uploaded to MaxQDA software for analysis. A codebook was used to code transcripts; new codes were added iteratively as they arose. All transcripts were coded by at least 2 of the 4 researchers and, after each transcript was coded, the researchers met to discuss any discrepancies, which were resolved by consensus. Results: Among 67 FG participants, 37 (55%) identified as transmen and 30 (45%) identified as transwomen. The average age of participants was ∼41 years (range 18-67) and the majority (61%) were non-Hispanic Whites. Several barriers that can hinder participation in health research were identified, including logistical concerns, issues related to mistrust, a lack of awareness about participation opportunities, and psychosocial/emotional concerns related to being \"outed.\" A broad range of facilitators were also identified, including the opportunity to gain knowledge, access medical services, and contribute to the transgender community. Conclusion: These findings provide insights about the perceived barriers to and facilitators of research participation and offer some guidance for researchers in our ongoing effort to engage the transgender community in health research.","corpus_id":523099,"score":0},{"doc_id":"28930210","title":"Right Place, Right Time: Preferences of Women with Ovarian Cancer for Delivery of CAM Education.","abstract":"The purpose of this pilot study was to assess the feasibility of on-site complementary and alternative medicine (CAM) education sessions to maximize quality of life for women with ovarian cancer. The pilot intervention consisted of four weekly sessions, each focusing the techniques and benefits of a particular CAM topic (e.g., nutrition, massage, relaxation). Participants were recruited from the Center for Women's Oncology at H. Lee Moffitt Cancer Center from 2010 to 2012. Eligible participants had an ovarian cancer diagnosis with a life expectancy of at least 12 months, and were 18 years or older. The Gynecologic Oncology research nurse invited women in the outpatient clinic who matched the eligibility criteria. The research nurse explained the study and provided an informed consent form and return envelope. Because ovarian cancer is not only a rare cancer but, also, most patients seen at Moffitt have recurrent or advanced disease, many women did not have an adequate ECOG score. Many women who consented had rapid changes in health status, with morbidity and mortality outpacing recruitment of the 20 needed to proceed with the four education sessions. Baseline and follow-up surveys were conducted to assess changes in QOL, knowledge, and satisfaction with the intervention. While 27 women consented and 24 women completed the baseline survey, only five women participated in the intervention. The five women who participated were all white, and at time of consenting had a mean age of 60 (SD 9.08) and an average of 102 months (SD 120.65) since diagnosis, and were all on active treatment, except for one. The intervention pilot did not encounter difficulties with regard to recruitment, but suffered problems in achieving an adequate number of women to launch the on-site sessions because of rapidly changing morbidity and significant mortality. The team recognized that a larger-scaled intervention comprised of on-site sessions was impractical and compared attendance rates with a more convenient format currently underway in the Women's Oncology program at Moffitt. While low participation prevented an intervention analysis of scientific merit, the study data is informative with regard to barriers, facilitators, and alternative methods for sharing useful information to women with advanced ovarian cancer. The comparison strongly suggested that CAM education for women compromised by the disease and treatment associated with ovarian cancer would best be delivered in the convenient-access format that allowed remote access to live and recorded discussions of specific topics.","corpus_id":7030283,"score":0},{"doc_id":"29152518","title":"Follow-up in patients with a burn-related emergency department visit: a feasibility study.","abstract":"Background: Data on epidemiology, costs, and outcomes of burn-related injuries presenting at emergency departments (EDs) are scarce. To obtain such information, a questionnaire study with an adequate response rate is imperative. There is evidence that optimized strategies can increase patient participation. However, it is unclear whether this applies to burn patients in an ED setting. The objective of this feasibility study was to optimize and evaluate patient recruitment strategy and follow-up methods in patients with burn injuries presenting at EDs. Methods: In a prospective cohort study with a 6-month follow-up, patients with burn-related injuries attending two large EDs during a 3-month study period were included. Eligible patients were quasi-randomly allocated to a standard or optimized recruitment strategy by week of the ED visit. The standard recruitment strategy consisted of an invitation letter to participate, an informed consent form, a questionnaire, and a franked return envelope. The optimized recruitment strategy was complemented by a stamped returned envelope, monetary incentive, sending a second copy of the questionnaire, and a reminder by telephone in non-responders. Response rates were calculated, and questionnaires were used to assess treatment, costs, and health-related quality of life. Results: A total of 87 patients were included of which 85 were eligible for the follow-up study. There was a higher response rate at 2 months in the optimized versus the standard recruitment strategy (43.6% vs. 20.0%; OR = 3.1 (95% CI 1.1-8.8)), although overall response is low. Non-response analyses showed no significant differences in patient, burn injury or treatment characteristics between responders versus non-responders. Conclusions: This study demonstrated that response rates can be increased with an optimized, but more labor-intensive recruitment strategy, although further optimization of recruitment and follow-up is needed. It is feasible to assess epidemiology, treatment, and costs after burn-related ED contacts.","corpus_id":7986461,"score":0},{"doc_id":"29164743","title":"Patient-initiated recruitment for clinical research: Evaluation of an outpatient letter research statement.","abstract":"BACKGROUND: UK Hospital Trusts are charged with increasing patients' research awareness and willingness to take part in research. This includes implementing strategies to encourage patient-initiated enquiries about participation. OBJECTIVES: To evaluate the impact of a research statement inserted in outpatient letters in one clinical service, and to derive suggestions on potential steps towards increasing patient-initiated recruitment. SETTING: A medical outpatient clinic of a research-active hospital trust, serving an inner-city multi-ethnic population across two boroughs. METHODS: Pre-intervention and post-intervention questionnaires were administered face-to-face to new patients. Questionnaires included closed questions and one open comments section. Data were analysed for frequencies, with thematic coding of open-ended responses. RESULTS: The response rates were 87% for the pre-intervention survey and 92% for the post-intervention survey. In the post-intervention survey, 85% of patients did not notice the research statement in the letter. More than half found the statement \"a little unclear,\" whilst one-third considered it \"clear.\" Three-quarters of respondents perceived the statement to be \"a little helpful.\" Only one person enquired about participating in clinical research having read the statement in the outpatient letter. CONCLUSION: The analysis suggests that simple, single-solution approaches such as including research statements in outpatient letters are unlikely to be sufficient to significantly facilitate patient-initiated recruitment. Recruitment efforts need to take into consideration the diversity of patient constituencies including the reasons they seek health care, and how patients can meaningfully access information (research literacy).","corpus_id":4510076,"score":0},{"doc_id":"29361929","title":"Interpreting population reach of a large, successful physical activity trial delivered through primary care.","abstract":"BACKGROUND: Failure to include socio-economically deprived or ethnic minority groups in physical activity (PA) trials may limit representativeness and could lead to implementation of interventions that then increase health inequalities. Randomised intervention trials often have low recruitment rates and rarely assess recruitment bias. A previous trial by the same team using similar methods recruited 30% of the eligible population but was in an affluent setting with few non-white residents and was limited to those over 60 years of age. METHODS: PACE-UP is a large, effective, population-based walking trial in inactive 45-75 year-olds that recruited through seven London general practices. Anonymised practice demographic data were available for all those invited, enabling investigation of inequalities in trial recruitment. Non-participants were invited to complete a questionnaire. RESULTS: From 10,927 postal invitations, 1150 (10.5%) completed baseline assessment. Participation rate ratios (95% CI), adjusted for age and gender as appropriate, were lower in men 0.59 (0.52, 0.67) than women, in those under 55 compared with those ≥65, 0.60 (0.51, 0.71), in the most deprived quintile compared with the least deprived 0.52 (0.39, 0.70) and in Asian individuals compared with whites 0.62 (0.50, 0.76). Black individuals were equally likely to participate as white individuals. Participation was also associated with having a co-morbidity or some degree of health limitation. The most common reasons for non-participation were considering themselves as being too active or lack of time. CONCLUSIONS: Conducting the trial in this diverse setting reduced overall response, with lower response in socio-economically deprived and Asian sub-groups. Trials with greater reach are likely to be more expensive in terms of recruitment and gains in generalizability need to be balanced with greater costs. Differential uptake of successful trial interventions may increase inequalities in PA levels and should be monitored. TRIAL REGISTRATION: ISRCTN.com ISRCTN98538934 . Registered 2nd March 2012.","corpus_id":13781395,"score":0},{"doc_id":"29713494","title":"Developing and feasibility testing of data collection methods for an economic evaluation of a supported selfmanagement programme for adults with a learning disability and type 2 diabetes.","abstract":"Background: The challenges of conducting research with hard to reach vulnerable groups are particularly pertinent for people with learning disabilities. Data collection methods for previous cost and cost-effectiveness analyses of health and social care interventions targeting people with learning disabilities have relied on health care/health insurance records or data collection forms completed by the service provider rather than by people with learning disabilities themselves. This paper reports on the development and testing of data collection methods for an economic evaluation within a randomised controlled trial (RCT) for a supported self-management programme for people with mild/moderate learning disabilities and type 2 diabetes. Methods: A case finding study was conducted to identify types of health and social care use and data collection methods employed in previous studies with this population. Based on this evidence, resource use questionnaires for completion by GP staff and interviewer-administered participant questionnaires (covering a wider cost perspective and health-related quality of life) were tested within a feasibility RCT. Interviewer-administered questionnaires included the EQ-5D-3L (the NICE recommended measure for use in economic evaluation). Participants were adults > 18 years with a mild or moderate learning disability and type 2 diabetes, with mental capacity to give consent to research participation. Results: Data collection for questionnaires completed by GP staff requesting data for the last 12 months proved time intensive and difficult. Whilst 82.3% (121/147) of questionnaires were returned, up to 17% of service use items were recorded as unknown. Subsequently, a shorter recall period (4 months) led to a higher return rate but with a higher rate of missing data. Missing data for interviewer-administered participant questionnaires was > 8% but the interviewers reported difficulty with participant recall. Almost 60% (48/80) of participants had difficulty completing the EQ-5D-3L. Conclusions: Further investigation as to how service use can be recorded is recommended. Concerns about the reliability of identifying service use data directly from participants with a learning disability due to challenges in completion, specifically around recall, remain. The degree of difficulty to complete EQ-5D-3L indicates concerns regarding the appropriateness of using this measure in its current form in research with this population. Trial registration: Current Controlled Trials ISRCTN41897033 (registered 21 January 2013).","corpus_id":5037512,"score":0},{"doc_id":"29728348","title":"The Acceptability and Feasibility of Implementing a Bio-Behavioral Enhanced Surveillance Tool for Sexually Transmitted Infections in England: Mixed-Methods Study.","abstract":"BACKGROUND: Sexually transmitted infection (STI) surveillance is vital for tracking the scale and pattern of epidemics; however, it often lacks data on the underlying drivers of STIs. OBJECTIVE: This study aimed to assess the acceptability and feasibility of implementing a bio-behavioral enhanced surveillance tool, comprising a self-administered Web-based survey among sexual health clinic attendees, as well as linking this to their electronic health records (EHR) held in England's national STI surveillance system. METHODS: Staff from 19 purposively selected sexual health clinics across England and men who have sex with men and black Caribbeans, because of high STI burden among these groups, were interviewed to assess the acceptability of the proposed bio-behavioral enhanced surveillance tool. Subsequently, sexual health clinic staff invited all attendees to complete a Web-based survey on drivers of STI risk using a study tablet or participants' own digital device. They recorded the number of attendees invited and participants' clinic numbers, which were used to link survey data to the EHR. Participants' online consent was obtained, separately for survey participation and linkage. In postimplementation phase, sexual health clinic staff were reinterviewed to assess the feasibility of implementing the bio-behavioral enhanced surveillance tool. Acceptability and feasibility of implementing the bio-behavioral enhanced surveillance tool were assessed by analyzing these qualitative and quantitative data. RESULTS: Prior to implementation of the bio-behavioral enhanced surveillance tool, sexual health clinic staff and attendees emphasized the importance of free internet/Wi-Fi access, confidentiality, and anonymity for increasing the acceptability of the bio-behavioral enhanced surveillance tool among attendees. Implementation of the bio-behavioral enhanced surveillance tool across sexual health clinics varied considerably and was influenced by sexual health clinics' culture of prioritization of research and innovation and availability of resources for implementing the surveys. Of the 7367 attendees invited, 85.28% (6283) agreed to participate. Of these, 72.97% (4585/6283) consented to participate in the survey, and 70.62% (4437/6283) were eligible and completed it. Of these, 91.19% (4046/4437) consented to EHR linkage, which did not differ by age or gender but was higher among gay/bisexual men than heterosexual men (95.50%, 722/756 vs 88.31%, 1073/1215; P<.003) and lower among black Caribbeans than white participants (87.25%, 568/651 vs 93.89%, 2181/2323; P<.002). Linkage was achieved for 88.88% (3596/4046) of consenting participants. CONCLUSIONS: Implementing a bio-behavioral enhanced surveillance tool in sexual health clinics was feasible and acceptable to staff and groups at STI risk; however, ensuring participants' confidentiality and anonymity and availability of resources is vital. Bio-behavioral enhanced surveillance tools could enable timely collection of detailed behavioral data for effective commissioning of sexual health services.","corpus_id":13712224,"score":0}],"string":"[\n {\n \"doc_id\": \"24139174\",\n \"title\": \"Acceptability and perceived barriers and facilitators to creating a national research register to enable 'direct to patient' enrolment into research: the Scottish Health Research Register (SHARE).\",\n \"abstract\": \"BACKGROUND: Difficulties with recruitment pose a major, increasingly recognised challenge to the viability of research. We sought to explore whether a register of volunteers interested in research participation, with data linkage to electronic health records to identify suitable research participants, would prove acceptable to healthcare staff, patients and researchers. METHODS: We undertook a qualitative study in which a maximum variation sampling approach was adopted. Focus groups and interviews were conducted with patients, general practitioners (GP), practice managers and health service researchers in two Scottish health boards. Analysis was primarily thematic to identify a range of issues and concerns for all stakeholder groups. RESULTS: The concept of a national research register was, in general, acceptable to all stakeholder groups and was widely regarded as beneficial for research and for society. Patients, however, highlighted a number of conditions which should be met in the design of a register to expedite confidence and facilitate recruitment. They also gave their perceptions on how a register should operate and be promoted, favouring a range of media. GPs and practice managers were primarily concerned with the security and confidentiality of patient data and the impact a register may have on their workload. Researchers were supportive of the initiative seeing advantages in more rapid access to a wider pool of patients. They did raise concerns that GPs may be able to block access to personal patient data held in general practice clinical systems and that the register may not be representative of the whole population. CONCLUSIONS: This work suggests that patients, healthcare staff and researchers have a favourable view of the potential benefits of a national register to identify people who are potentially eligible and willing to participate in health related research. It has highlighted a number of issues for the developers to incorporate in the design of research registers.\",\n \"corpus_id\": 5761028,\n \"score\": 2\n },\n {\n \"doc_id\": \"25354322\",\n \"title\": \"Effectiveness of a community research registry to recruit minority and underserved adults for health research.\",\n \"abstract\": \"BACKGROUND: Recruiting minorities and underserved populations into population-based studies is a long standing challenge. This study examined the feasibility of recruiting adults from a community research registry. METHODS: Ethnically diverse, bilingual staff attended health fairs, inviting adults to join a registry. We examined rates of successful contact, scheduling, and participation for studies that used the registry. RESULTS: Five studies queried 6,886 research registry members (48% Hispanic and 38% black) and attempted to contact 2,301 potentially eligible participants; eligibility criteria varied across studies. We successfully contacted 1,130 members, 51.9% were scheduled to participate and of those, 60.8% completed their study appointment. Non-Hispanic whites were less likely than Hispanics to be interested, but among those scheduling an appointment, participation did not differ by race/ethnicity. CONCLUSION: Community research registries are a feasible and efficient method for recruiting minority and underserved adults and may address disparities in access to and participation in health research.\",\n \"corpus_id\": 20553211,\n \"score\": 2\n },\n {\n \"doc_id\": \"26769574\",\n \"title\": \"Research participation registers can increase opportunities for patients and the public to participate in health services research.\",\n \"abstract\": \"Members of the public and patients repeatedly indicate their willingness to take part in research, but current United Kingdom research governance involves complex rules about gaining consent. Research participation registers that seek consent from participants to be approached about future studies have several potential benefits, including: increased research participation across clinical and healthy populations; simplified recruitment to health care research; support for people's autonomy in decision making; and improved efficiency and generalizability of research. These potential benefits have to be balanced against ethical and governance considerations. With appropriate processes in place, seeking prospective consent from patients and members of the public to be approached about future studies could potentially increase public participation in health research without compromising informed consent and other ethical principles.\",\n \"corpus_id\": 3364244,\n \"score\": 2\n },\n {\n \"doc_id\": \"27724888\",\n \"title\": \"A consumer register: an acceptable and cost-effective alternative for accessing patient populations.\",\n \"abstract\": \"BACKGROUND: Population-based registries are increasingly used to recruit patient samples for research, however, they have several limitations including low consent and participation rates, and potential selection bias. To improve access to samples for research, the utility of a new model of recruitment termed the 'Consumer Register', that allows for direct patient recruitment from hospitals, was examined. This paper reports: (i) consent rates onto the register; (ii) preferred methods and frequency of contact; and (iii) the feasibility of establishing the register, including: (a) cost per person recruited to the register; (b) the differential cost and consent rates of volunteer versus paid data collectors; and (c) participant completion rates. METHODS: A cross-sectional survey was conducted in five outpatient clinics in Australia. Patients were approached by volunteers or paid data collectors and asked to complete a touch-screen electronic survey. Consenting individuals were asked to indicate their willingness and preferences for enrolment onto a research register. Descriptive statistics were used to examine patient preferences and linear regression used to model the success of volunteer versus paid data collectors. The opportunity and financial costs of establishing the register were calculated. RESULTS: A total of 1947 patients (80.6 %) consented to complete the survey, of which, 1486 (76.3 %) completed the questionnaire. Of the completers, the majority (69.4 %, or 1032 participants) were willing to be listed on the register and preferred to be contacted by email (50.3 %). Almost 39 % of completers were willing to be contacted three or more times in a 12 month period. The annual opportunity cost of resources consumed by the register was valued at $37,187, giving an opportunity cost per person recruited to the register of $36. After amortising fixed costs, the annual financial outlay was $23,004 or $22 per person recruited to the register. Use of volunteer data collectors contributed to an annual saving of $14,183, however paid data collectors achieved significantly higher consent rates. Successful enrolment onto the register was completed for 42 % of the sample. CONCLUSIONS: A Consumer Register is a promising and feasible alternative to population-based registries, with the majority of participants willing to be contacted multiple times via low-resource methods such as email. There is an effectiveness/cost trade off in the use of paid versus volunteer data collectors.\",\n \"corpus_id\": 4485730,\n \"score\": 2\n },\n {\n \"doc_id\": \"28148535\",\n \"title\": \"Cohort profile: the Scottish Research register SHARE. A register of people interested in research participation linked to NHS data sets.\",\n \"abstract\": \"PURPOSE: Recruitment to trials is often difficult. Many trials fail to meet recruitment targets resulting in underpowered studies which waste resources and the time of those who participated. While there is evidence that many people are willing to take part in research, particularly if it involves a condition from which they suffer, researchers are unable to easily contact such people often relying on busy clinicians to identify them. Many clinicians perceive themselves as too busy to take part in research activities. The Scottish Health Research Register SHARE adopts an approach which asks the public to consent to their data held in National Health Service databases to be used to determine their suitability for research projects. Additionally, participants can consent for spare blood, left after routine venepuncture to be automatically identified in the laboratory and stored for future research studies. PARTICIPANTS: Anyone over the age of 16 years in Scotland can participate. Participants are approached through a range of methods including directly at outpatient clinics and general practitioners practices, leaflets with hospital letters and personal email from employers. FINDINGS TO DATE: SHARE has recruited around 130 000 people. SHARE has demonstrated that it can quickly and efficiently recruit to studies, over 20 until now. In addition, it can be used to administer questionnaire studies by email and recruit to patient and public involvement groups. FUTURE PLANS: SHARE continues to steadily recruit with the ambition of eventually achieving 1 000 000 people in Scotland. We are steadily increasing the number of data sets we use for identifying participants. We are adding a mobile app which will facilitate dissemination about research and allow the collection of physiological and activity data if desired. We anticipate that SHARE will soon become the main source of health research recruitment in Scotland.\",\n \"corpus_id\": -1,\n \"score\": 2\n },\n {\n \"doc_id\": \"22621621\",\n \"title\": \"Survey of patient and public perceptions of electronic health records for healthcare, policy and research: study protocol.\",\n \"abstract\": \"BACKGROUND: Immediate access to patients' complete health records via electronic databases could improve healthcare and facilitate health research. However, the possible benefits of a national electronic health records (EHR) system must be balanced against public concerns about data security and personal privacy. Successful development of EHR requires better understanding of the views of the public and those most affected by EHR: users of the National Health Service. This study aims to explore the correlation between personal healthcare experience (including number of healthcare contacts and number and type of longer term conditions) and views relating to development of EHR for healthcare, health services planning and policy and health research. METHODS/DESIGN: A multi-site cross-sectional self-complete questionnaire designed and piloted for use in waiting rooms was administered to patients from randomly selected outpatients' clinics at a university teaching hospital (431 beds) and general practice surgeries from the four primary care trusts within the catchment area of the hospital. All patients entering the selected outpatients clinics and general practice surgeries were invited to take part in the survey during August-September 2011. Statistical analyses will be conducted using descriptive techniques to present respondents' overall views about electronic health records and logistic regression to explore associations between these views and participants' personal circumstances, experiences, sociodemographics and more specific views about electronic health records. DISCUSSION: The study design and implementation were successful, resulting in unusually high response rates and overall recruitment (85.5%, 5336 responses). Rates for face-to-face recruitment in previous work are variable, but typically lower (mean 76.7%, SD 20). We discuss details of how we collected the data to provide insight into how we obtained this unusually high response rate.\",\n \"corpus_id\": 6083131,\n \"score\": 1\n },\n {\n \"doc_id\": \"22783770\",\n \"title\": \"Analysis and validation of a Parkinson's disease register as a recruitment tool for clinical studies.\",\n \"abstract\": \"Promotion of research is a key strategy of the National Health Service (NHS). Currently, many patients are not afforded the opportunity to participate in clinical studies. A register of research-interested patients has the potential to maximise inclusivity. We have established a register of research-interested patients with Parkinson's disease within the South West of England, with pragmatic inclusion criteria and multiple recruitment routes. We undertook an analysis of the register, investigation of its utility as a recruitment tool and a survey of recruiters. There were 529 active participants; 30% were self-referred and 70% were recruited by a healthcare practitioner. Response rate to annual questionnaires was 86.5%. Staff time required for pack preparation, recruitment and data entry was 15 min per new recruit and 5 min per follow-up questionnaire. In total, 85% of recruiters viewed the register positively. A single mailing to participants resulted in a recruitment rate that significantly exceeded that achieved by traditional recruitment methods.\",\n \"corpus_id\": 43150694,\n \"score\": 1\n },\n {\n \"doc_id\": \"24845592\",\n \"title\": \"Permission to contact (PTC)--a strategy to enhance patient engagement in translational research.\",\n \"abstract\": \"UNLABELLED: Improving patient recruitment and consent to participate in clinical studies is an important issue. The process of consent involves three steps: patient referral for contact, the preliminary interview to determine patient interest, and the informed consent discussion. We hypothesized that putting the first step of the consent process into a 'Permission to Contact' (PTC) platform would improve patient engagement, would improve the efficiency of the other steps of the process, and would be acceptable to diverse patient groups. METHODS: To test this hypothesis, four PTC platforms were established in three types of outpatient health clinics (cancer, cardiac, maternal health) in different British Columbia health centers. Each began as a research project where clinic personnel were engaged, clinic flow processes were mapped, and a design for each PTC was derived by consensus. All patients at these clinics were asked for 'permission to be contacted for future research purposes.' Patient approach and permission response rates were assessed and operational costs were estimated. RESULTS: Overall permission rates were high for all projects, but ranged from 94% of 'cancer' patients to 80% of 'congenital heart' patients who were approached (p<0.0001). Sustainability was demonstrated by stable enrollment levels after several years, and ongoing costs averaged $25 (range $12-$39) for each 'permission' across all four platforms. CONCLUSIONS: A PTC platform is a feasible mechanism to engage patients in research programs such as biobanking. It is well supported by clinic staff and receives high engagement and acceptance from patients. Patient-approach rates vary in different clinics, likely due to both clinic and PTC process factors, but this strategy provides an efficient means of engaging patients in research and sets the stage for enhanced enrollment into translational research programs.\",\n \"corpus_id\": 24695002,\n \"score\": 1\n },\n {\n \"doc_id\": \"25318374\",\n \"title\": \"The DiReCT study - improving recruitment into clinical trials: a mixed methods study investigating the ethical acceptability, feasibility and recruitment yield of the cohort multiple randomised controlled trials design.\",\n \"abstract\": \"BACKGROUND: The 'cohort multiple Randomised Controlled Trial' (cmRCT) design has been proposed as a potential solution to poor recruitment into clinical trials. The design randomly selects participants eligible for experimental treatments from a pre-enrolled cohort of patients, recruiting participants to multiple trials from a single cohort. Controls remain unaware of their participation in specific trials. METHODS: We undertook a mixed methods study to determine the ethical acceptability, the proportion of patients in a routine service consenting to cohort participation, the proportion of these who would consent to being hypothetically randomly selected to receive new treatments, and the views of clinicians on the acceptability of the design. We submitted our cmRCT design for ethical review and recruited participants from people with anxiety and depression attending a community mental health service of twenty-one clinicians. We recorded the proportion of patients who were offered participation in the DiReCT study and the proportion that consented to researcher contact, medical record sharing, and who accepted to be randomly allocated to active treatment procedures in future hypothetical unspecified clinical trials. We used a thematic framework analysis to analyse clinician interviews. RESULTS: We obtained a favourable ethical opinion from the UK Health Research Authority. Clinicians approached 131/752 (17%) potentially eligible participants for consent. Of these 131, 84 (64%) initially consented to be contacted by a researcher and all but one consented to being randomised into future trials. We confirmed consent for 71 (54%) of participants approached by clinicians, of whom 69 (53%) consented to being randomised into hypothetical future trials, 9% (69/752) of all potentially eligible patients. The interviewed clinicians described issues impacting on their ability to recruit participants in terms of clinical concerns for patient wellbeing, work pressure, their views of both general research and the specific DiReCT study, and how they viewed patients' responses to being offered participation in the study. CONCLUSIONS: The cmRCT system offers the potential to improve the recruitment into clinical trials and is acceptable ethically and to many patients. Overcoming the multiple factors driving the difficulties clinicians experience in patient recruitment is likely to require the application of significant implementation science-informed effort.\",\n \"corpus_id\": 16397039,\n \"score\": 1\n },\n {\n \"doc_id\": \"25552589\",\n \"title\": \"Confidentiality in participatory research: Challenges from one study.\",\n \"abstract\": \"AIM: This article presents key ethical challenges that were encountered when conducting a participatory qualitative research project with a very specific, small group of nurses, in this case with practice development nurses in Malta. BACKGROUND: With the small number of nurses employed in practice development roles in Malta, there are numerous difficulties of maintaining confidentiality. Poorly constructed interventions by the researcher could have resulted in detrimental effects to research participants and the overall trustworthiness of the research. Generally, ethical guidelines for research exist to reinforce validity of research; however, there is not an established consensus on how these strategies can be utilised in some types of qualitative field work. RESEARCH DESIGN: The researcher used an exploratory case study methodology. The sample consisted of 10 participants who were interviewed twice using face-to-face interviews, over a period of 2 months. ETHICAL CONSIDERATIONS: The study was ethically reviewed by the University Research Ethics Committee and the Faculty Research Ethics Committee, University of Malta. The participants referred to in this article have been given adequate information about the study and their consent has been obtained. DISCUSSION: Numerous strategies for ensuring confidentiality during recruitment of the participants, during data collection, during transcription and data analysis and during dissemination of research results assisted the researcher in responding to potential and actual ethical issues. CONCLUSION: This article emphasises the main strategies that can be used to respond to ethical challenges when researching with a small easily identifiable group. The learning discussed here may be relevant to or even transferable to other similar research studies or research contexts. These methods fostered a greater credibility throughout the research process and predisposed the participants to greater trust, and thus, they disclosed their experiences and speak more freely, thus enhancing the quality of the study.\",\n \"corpus_id\": 206611350,\n \"score\": 1\n },\n {\n \"doc_id\": \"25834643\",\n \"title\": \"Linking a research register to clinical records in older adults' mental health services: a mixed-methods study.\",\n \"abstract\": \"INTRODUCTION: Patients can provide consent to have their clinical records linked to a research register, a process known as consent for contact (C4C). There is evidence about how to engage people with mental illness in C4C, but nothing specific to older adults. This is a priority area for research (for example, dementia trials), although sign-up rates to C4C are lower than for younger populations. Through this study we seek to understand these disparities. METHODS: This was a two-stage cross-sectional observational study. In phase one, focus groups with service users, carers and clinicians informed a framework for clinicians to explain C4C to those on their caseload. In phase two, clinicians explained C4C to 26 service users (and carers where applicable). These conversations were recorded, and their content was analysed. Service users and carers were then interviewed to provide further feedback on their conversations with clinicians. A total of 31 service users, 24 carers and 13 clinical staff took part across the two phases. RESULTS: In phase one, service users and carers sought assurance of the right to refuse participation in further studies (after joining C4C). Clinicians expressed concerns over legal and practical implications of ascertaining mental capacity and best interest. In phase two, clinicians' explanations were less thorough than similar explanations given to younger adults with psychosis. Clinicians omitted details of service users' right to stipulate contact arrangements, which was significantly associated with whether service users/carers agreed to join. Common reasons for joining C4C included altruism and the chance to speak to new people. Few participants refused to join, but reasons included avoidance of stress (potentially alleviated through the presence of a carer). CONCLUSIONS: Implementing C4C in older adults' services requires clinicians to deliver concise, simple explanations to individuals and their carers where applicable. Older adults can be suspicious of unsolicited contact; thus, explanations must emphasise freedom to negotiate suitable contact arrangements. Hearing about research opportunities can be in the best interests of older adults, but communicating these opportunities requires a tailored approach.\",\n \"corpus_id\": 16818270,\n \"score\": 1\n },\n {\n \"doc_id\": \"25971412\",\n \"title\": \"Consenting for contact? Linking electronic health records to a research register within psychosis services, a mixed method study.\",\n \"abstract\": \"BACKGROUND: Research registers of potential participants linked to Electronic Health Records (EHRs) provide a basis for screening and identifying people suitable for studies. Such a system relies upon people joining the register and giving permission for their record to be used in this way. This study describes the process of training clinicians to explain EHR-linked research registers to service users, and to recruit them onto the register. METHOD: Training materials were developed for clinicians to help them describe the register to service users. These materials were based upon findings from focus groups reported elsewhere, they were then tested with 31 clinicians in early intervention psychosis services and each clinician discussed the register with service users on their caseload (n = 100 service users). Consultations were recorded and analysed in relation to their coverage of the training criteria. Service users also provided data on the acceptability of the process from their perspective. The content of clinicians' explanations to service users was described, and then compared against the likelihood of service users joining the register. Interpretive statistics (t-test and Chi-Squared) were used to explore differences between consultations in which service users agreed to join the register, and consultations where they did not agree to join. RESULTS: Service users appeared more likely to join the register if they felt control over what they signed up to, this necessitated understanding that they could decide when, how often, and by whom they were contacted, that joining the register did not automatically enlist them to future studies, and that they could change their mind in future. Clinicians' explanations did not always include that researchers would be able to see the service users' EHR. Service users often confused the idea of signing up to the register and signing up to studies themselves. Confidentiality was not well explained, but service users were not always concerned by confidentiality. CONCLUSION: EHR-linked research registers provide recruitment opportunities, and help service users to find out about research. Implementing these registers within mental health settings requires a trained clinical workforce and an informed service user population.\",\n \"corpus_id\": 17812677,\n \"score\": 1\n },\n {\n \"doc_id\": \"26599631\",\n \"title\": \"Development of the CHARIOT Research Register for the Prevention of Alzheimer's Dementia and Other Late Onset Neurodegenerative Diseases.\",\n \"abstract\": \"BACKGROUND: Identifying cognitively healthy people at high risk of developing dementia is an ever-increasing focus. These individuals are essential for inclusion in observational studies into the natural history of the prodromal and early disease stages and for interventional studies aimed at prevention or disease modification. The success of this research is dependent on having access to a well characterised, representative and sufficiently large population of individuals. Access to such a population remains challenging as clinical research has, historically, focussed on patients with dementia referred to secondary and tertiary services. The primary care system in the United Kingdom allows access to a true prodromal population prior to symptoms emerging and specialist referral. We report the development and recruitment rates of the CHARIOT register, a primary care-based recruitment register for research into the prevention of dementia. The CHARIOT register was designed specifically to support recruitment into observational natural history studies of pre-symptomatic or prodromal dementia stages, and primary or secondary prevention pharmaceutical trials or other prevention strategies for dementia and other cognitive problems associated with ageing. METHODS: Participants were recruited through searches of general practice lists across the west and central London regions. Invitations were posted to individuals aged between 60 and 85 years, without a diagnosis of dementia. Upon consent, a minimum data set of demographic and contact details was extracted from the patient's electronic health record. RESULTS: To date, 123 surgeries participated in the register, recruiting a total of 24,509 participants-a response rate of 22.3%. The age, gender and ethnicity profiles of participants closely match that of the overall eligible population. Higher response rates tended to be associated with larger practices (r = 0.34), practices with a larger older population (r = 0.27), less socioeconomically disadvantaged practices (r = 0.68), and practices with a higher proportion of White patients (r = 0.82). DISCUSSION: Response rates are comparable to other registers reported in the literature, and indicate good interest and support for a research register and for participation in research for the prevention of age-related neurodegenerative diseases and dementia. We consider that the simplicity of the approach means that this system is easily scalable and replicable across the UK and internationally.\",\n \"corpus_id\": 4913645,\n \"score\": 1\n },\n {\n \"doc_id\": \"27503859\",\n \"title\": \"Facilitating mental health research for patients, clinicians and researchers: a mixed-method study.\",\n \"abstract\": \"OBJECTIVES: Research registers using Consent for Contact (C4C) can facilitate recruitment into mental health research studies, allowing investigators to contact patients based on clinical records information. We investigated whether such a register was useful for mental health research, seeking the perspectives of patients and research investigators. SETTING AND DESIGN: In 2012, a C4C register was developed in a large secondary mental health provider within the UK; almost 9000 patients have joined. This mixed-method study audited the effectiveness of the register. PARTICIPANTS: A 'mystery shopper' exercise was conducted, and patients (n=21) were recruited to ask clinicians about the availability of research opportunities. Structured interviews were conducted with patients (n=52) about their experiences of being on the register. Similar interviews were conducted with 18 investigators from 19 studies, who had attempted to use the register to recruit participants. OUTCOME MEASURES: The impact of C4C on study recruitment, and whether it helped patients learn about research. RESULTS: So far, the register has provided 928 individuals with 1085 research opportunities (in 60% of cases, the individual agreed to participate in the study). Clinicians were willing to link patients to research opportunities, but often lacked information about studies. For patients, the register provided opportunities which they may not otherwise have; 27 of 52 had participated in studies since joining the register (18 participating for the first time). Most investigators used the register to supplement recruitment to their studies, but described problems in prescreening potential participants from a clinical record for complex studies. CONCLUSIONS: Although the register helped investigators recruit for studies, and provided patients with research opportunities, clinicians' input is still useful for identifying suitable participants. C4C registers should be adapted to provide clinicians with automatically updated information on local studies allowing them to match patients on their caseload with active studies.\",\n \"corpus_id\": 6801068,\n \"score\": 1\n },\n {\n \"doc_id\": \"27557678\",\n \"title\": \"Electronic health records to facilitate clinical research.\",\n \"abstract\": \"Electronic health records (EHRs) provide opportunities to enhance patient care, embed performance measures in clinical practice, and facilitate clinical research. Concerns have been raised about the increasing recruitment challenges in trials, burdensome and obtrusive data collection, and uncertain generalizability of the results. Leveraging electronic health records to counterbalance these trends is an area of intense interest. The initial applications of electronic health records, as the primary data source is envisioned for observational studies, embedded pragmatic or post-marketing registry-based randomized studies, or comparative effectiveness studies. Advancing this approach to randomized clinical trials, electronic health records may potentially be used to assess study feasibility, to facilitate patient recruitment, and streamline data collection at baseline and follow-up. Ensuring data security and privacy, overcoming the challenges associated with linking diverse systems and maintaining infrastructure for repeat use of high quality data, are some of the challenges associated with using electronic health records in clinical research. Collaboration between academia, industry, regulatory bodies, policy makers, patients, and electronic health record vendors is critical for the greater use of electronic health records in clinical research. This manuscript identifies the key steps required to advance the role of electronic health records in cardiovascular clinical research.\",\n \"corpus_id\": 16614338,\n \"score\": 1\n },\n {\n \"doc_id\": \"18714713\",\n \"title\": \"Feasibility of gaining access to women in jail for health interventions.\",\n \"abstract\": \"UNLABELLED: Female jail populations are comprised of women at high-risk for an array of psychological and physical health problems. Jails offer an opportune site to deliver clinical health interventions to women who often quickly cycle back into the community. In contrast with prison population studies, many investigators have encountered recruitment problems when attempting to engage the jailed population in clinical research. This study addressed the feasibility of recruiting detained women for eligibility for clinical research. METHODS: Commitments to the Women's Facility at the Rhode Island Department of Corrections were chronicled for 40 months, from February 2004 to June 2007. Research staff, working 8 a.m. to 5 p.m., Monday through Friday, attempted to screen all detained women for a randomized clinical trial. RESULTS: During the 40-month study period, 4,131 individual women had 8,010 commitments to the facility. Staff was able to gain access to nearly 50% of women. Of the inaccessible women, 65% were released in less than 24 hours. In total, 88% of accessed women agreed to be screened for study participation. No significant differences were observed by race/ethnicity or age between women who were screened and those who were not. CONCLUSIONS: Clinical research with the female jail population is feasible. The jail setting requires researchers to plan for short-commitment lengths and high rates of recidivism to optimize screening and recruitment in this population.\",\n \"corpus_id\": 44250910,\n \"score\": 0\n },\n {\n \"doc_id\": \"19566931\",\n \"title\": \"Strategies for achieving a high response rate in a home interview survey.\",\n \"abstract\": \"BACKGROUND: Response rates in surveys have been falling over the last 20 years, leading to the need for novel approaches to enhance recruitment. This study describes strategies used to maximise recruitment to a home interview survey of mothers with young children living in areas of high deprivation. METHODS: Mothers of two year old children received a letter from their GP inviting them to take part in a survey on diet. Participants were subsequently recruited by a researcher. The researcher first tried to contact potential participants by telephone, to discuss the study and make an appointment to conduct a home interview. Where telephone numbers for women could not be obtained from GP records, web searches of publicly available databases were conducted. After obtaining correct telephone numbers, up to six attempts were made to establish contact by telephone. If this was unsuccessful, a postal request for telephone contact was made. Where no telephone contact was achieved, the researcher sent up to two appointments by post to conduct a home interview. RESULTS: Participating GPs invited 372 women to take part in a home based interview study. GP practices provided telephone numbers for 162 women, of which 134 were valid numbers. The researcher identified a further 187 numbers from electronic directories. Further searches of GP records by practice staff yielded another 38 telephone numbers. Thus, telephone numbers were obtained for 99% of potential participants. The recruitment rate from telephone contacts was 77%. Most of the gain was achieved within four calls. For the remaining women, contact by post and home visits resulted in 18 further interviews, corresponding to 35% of the women not recruited by telephone. The final interview rate was 82%. This was possible because personal contact was established with 95% of potential participants. CONCLUSION: This study achieved a high response rate in a hard to reach group. This was mainly achieved by first establishing contact by telephone. The use of multiple sources identified the telephone numbers of almost all the sample. Multiple attempts at telephone contact followed by postal approaches led to a high home interview rate.\",\n \"corpus_id\": 5711328,\n \"score\": 0\n },\n {\n \"doc_id\": \"19845656\",\n \"title\": \"Recruiting older adults to health research studies: A systematic review.\",\n \"abstract\": \"AIM: To provide a systematic review of papers comparing the effectiveness of different strategies to recruit older adults (aged 50 years and over) to participate in health research studies, to guide successful recruitment in future research. METHODS: Four major databases were searched for papers published between 1995 and 2008 with: target group aged 50 years or over; participants allocated to receive one of two or more recruitment strategies; and an outcome measure of response rate or enrolment in study. RESULTS: Twelve papers were included in the review. CONCLUSION: For postal questionnaires, recruitment strategies used with older adults had comparable outcomes to those used to recruit from the general population. For other types of studies, strategies involving face-to-face contact may be more effective than indirect methods, but this needs to be balanced against feasibility. Overall, little evidence on the topic exists and more rigorous investigation is necessary.\",\n \"corpus_id\": 37661332,\n \"score\": 0\n },\n {\n \"doc_id\": \"19930724\",\n \"title\": \"Trials and tribulations of recruiting 2,000 older women onto a clinical trial investigating falls and fractures: Vital D study.\",\n \"abstract\": \"BACKGROUND: Randomised, placebo-controlled trials are needed to provide evidence demonstrating safe, effective interventions that reduce falls and fractures in the elderly. The quality of a clinical trial is dependent on successful recruitment of the target participant group. This paper documents the successes and failures of recruiting over 2,000 women aged at least 70 years and at higher risk of falls or fractures onto a placebo-controlled trial of six years duration. The characteristics of study participants at baseline are also described for this study. METHODS: The Vital D Study recruited older women identified at high risk of fracture through the use of an eligibility algorithm, adapted from identified risk factors for hip fracture. Participants were randomised to orally receive either 500,000 IU vitamin D3 (cholecalciferol) or placebo every autumn for five consecutive years. A variety of recruitment strategies were employed to attract potential participants. RESULTS: Of the 2,317 participants randomised onto the study, 74% (n = 1716/2317) were consented onto the study in the last five months of recruiting. This was largely due to the success of a targeted mail-out. Prior to this only 541 women were consented in the 18 months of recruiting. A total of 70% of all participants were recruited as a result of targeted mail-out. The response rate from the letters increased from 2 to 7% following revision of the material by a public relations company. Participant demographic or risk factor profile did not differ between those recruited by targeted mail-outs compared with other methods. CONCLUSION: The most successful recruitment strategy was the targeted mail-out and the response rate was no higher in the local region where the study had extensive exposure through other recruiting strategies. The strategies that were labour-intensive and did not result in successful recruitment include the activities directed towards the GP medical centres. Comprehensive recruitment programs employ overlapping strategies simultaneously with ongoing assessment of recruitment rates. In our experience, and others direct mail-outs work best although rights to privacy must be respected. TRIAL REGISTRATION: ISRCTN83409867 and ACTR12605000658617.\",\n \"corpus_id\": 260502619,\n \"score\": 0\n },\n {\n \"doc_id\": \"20334748\",\n \"title\": \"A randomised controlled multicentre trial of treatments for adolescent anorexia nervosa including assessment of cost-effectiveness and patient acceptability - the TOuCAN trial.\",\n \"abstract\": \"OBJECTIVE: To evaluate the clinical effectiveness and cost-effectiveness of inpatient compared with outpatient treatment and general (routine) treatment in Child and Adolescent Mental Health Services (CAMHS) against specialist treatment for young people with anorexia nervosa. In addition, to determine young people's and their carers' satisfaction with these treatments. DESIGN: A population-based, pragmatic randomised controlled trial (RCT) was carried out on young people age 12 to 18 presenting to community CAMHS with anorexia nervosa. SETTING: Thirty-five English CAMHS in the north-west of England co-ordinated through specialist centres in Manchester and Liverpool. PARTICIPANTS: Two hundred and fifteen young people (199 female) were identified, of whom 167 (mean age 14 years 11 months) were randomised and 48 were followed up as a preference group. INTERVENTIONS: Randomised patients were allocated to either inpatient treatment in one of four units with considerable experience in the treatment of anorexia nervosa, a specialist outpatient programme delivered in one of two centres, or treatment as usual in general community CAMHS. The outpatient programmes spanned 6 months of treatment. The length of inpatient treatment was determined on a case-by-case basis on clinical need with outpatient follow-up to a minimum of 6 months. MAIN OUTCOME MEASURES: Follow-up assessments were carried out at 1, 2 and 5 years. The primary outcome measure was the Morgan-Russell Average Outcome Scale (MRAOS) and associated categorical outcomes. Secondary outcome measures included physical measures of weight, height, body mass index (BMI) and % weight for height. Research ratings included the Health of the National Outcome Scale for Children and Adolescents (HoNOSCA). Self report measures comprised the user version of HoNOSCA (HoNOSCA-SR), the Eating Disorder Inventory 2 (EDI-2), the Family Assessment Device (FAD) and the recent Mood and Feelings Questionnaire (MFQ). Information on resource use was collected in interview at 1, 2 and 5 years using the Child and Adolescent Service Use Schedule (CA-SUS). Satisfaction was measured quantitatively using a questionnaire designed for the study and qualitative (free) responses on it. The questionnaire data were supplemented by qualitative analysis of user and carer focus groups. RESULTS: Of the 167 patients randomised, 65% adhered to the allocated treatment. Adherence was lower for inpatient treatment (49%) than for general CAMHS (71%) or specialist outpatient treatment (77%) (p = 0.013). Every subject was traced at both 1 and 2 years, with the main outcome measure completed (through contact with the subject, family members or clinicians), by 94% at 1 year, 93% at 2 years, but only 47% at 5 years. A validated outcome category was assigned for 98% at 1 year, 96% at 2 years and 60% at 5 years. There was significant improvement in all groups at each time point, with the number achieving a good outcome being 19% at 1 year, 33% at 2 years and 64% (of those followed up) at 5 years. Analysis demonstrated no difference in treatment effectiveness of randomisation to inpatient compared with outpatient treatment, or, specialist over generalist treatment at any time point, when baseline characteristics were taken into account. Generalist CAMHS treatment was slightly more expensive over the first 2 years of the study, largely because greater numbers were subsequently admitted to hospital after the initial treatment phase. The specialist outpatient programme was the dominant treatment in terms of incremental cost-effectiveness. Specialist treatments had a higher probability of being more cost-effective than generalist treatments and outpatient treatment had a higher probability of being more cost-effective than inpatient care. Parental satisfaction with treatment was generally good, though better with specialist than generalist treatment. Young people's satisfaction was much more mixed, but again better with specialist treatment, including inpatient care. CONCLUSION: Poor adherence to randomisation (despite initial consent to it), limits the assessment of the treatment effect of inpatient care. However, this study provides little support for lengthy inpatient psychiatric treatment on clinical or health economic grounds. These findings are broadly consistent with existing guidelines on the treatment of anorexia nervosa, which suggest that outpatient treatments should be offered to the majority, with inpatient treatment offered in rare cases, though our findings lend little support to a stepped-care approach in which inpatient care is offered to outpatient non-responders. Outpatient care, supported by brief (medical) inpatient management for correction of acute complications may be a preferable approach. The health economic analysis and user views both support NICE guidelines, which suggest that anorexia nervosa should be managed in specialist services that have experience and expertise in its management. Comprehensive general CAMHS might, however, be well placed to manage milder cases. Further research should focus on the specific components of outpatient psychological therapies. Although family-based treatments are well established, trials have not established their effectiveness compared with good-quality individual psychological therapies and the combination of individual and family approaches is untested. Further research is needed to establish which patients (if any) might respond to inpatient psychiatric treatment when unresponsive to outpatient care, the positive and negative components of it and the optimum length of stay. TRIAL REGISTRATION: NRR number (National Research Register) N0484056615; Current Controlled Trials ISRCTN39345394.\",\n \"corpus_id\": 42049325,\n \"score\": 0\n },\n {\n \"doc_id\": \"20353656\",\n \"title\": \"An audit of smoking behaviours among patients attending two general dental practices in South Wales: an awareness-raising exercise for the dental team and patients.\",\n \"abstract\": \"AIMS: This audit aimed to quantify the number of smokers attending two general dental practices. It also aimed to establish the demographic characteristics of these smokers in terms of age, gender and deprivation status, and to raise the awareness of practice staff about smoking cessation. METHODS: Data were collected from consecutive patients (aged over 16 years) attending two general dental practices over a period of one month. The information collected included smoking status, number of cigarettes smoked, age, gender, and postcode. A deprivation score (derived from the Welsh Index of Multiple Deprivation [WIMD] for 2008) was appended to each patient record in order to provide a measure of deprivation based on the postcode of the patient. Staff at both practices were involved in the audit. Staff were given a brief pre- and post-audit questionnaire to test their knowledge on smoking cessation. The audit standard was that no more than 29% of patients should be smokers. Where relevant, data were statistically tested using the chi-square test. RESULTS: Five hundred and sixty-one patients provided data on their smoking habits. It was found that 159 (28.3%) were smokers, smoking on average 12 cigarettes per day. The average age of the sample was 46 years and 242 (43.1%) were male. Forty-eight per cent of the sample was shown to be resident in a postcode considered to be deprived. Older patients were more likely to be nonsmokers (P=0.0001). Following the final audit meeting, correct answers among staff for knowledge of the National Institute for Health and Clinical Excellence guidelines regarding effective smoking-cessation practices improved from 6% to 71%. CONCLUSION: The issue of smoking cessation has been highlighted for two dental teams. Whether the audit will result in the delivery of smoking-cessation procedures within the dental practice settings cannot be established. It is clear that the desired smoking-cessation behaviours can now be contemplated by the dental teams. Further monitoring is required to establish outcomes as a result of the actions of the teams.\",\n \"corpus_id\": 30829702,\n \"score\": 0\n },\n {\n \"doc_id\": \"20849598\",\n \"title\": \"Engaging the oldest old in research: lessons from the Newcastle 85+ study.\",\n \"abstract\": \"BACKGROUND: Those aged 85 and over, the oldest old, are now the fastest growing sector of the population. Information on their health is essential to inform future planning; however, there is a paucity of up-to-date information on the oldest old, who are often excluded from research. The aim of the Newcastle 85+ Study is to investigate the health of a cohort of 85-year-olds from a biological, medical and psychosocial perspective. This paper describes the methods employed for the successful recruitment, retention and evaluation of this cohort. METHODS: Participants were all individuals born in 1921 and registered with a participating general practice in Newcastle and North Tyneside, UK. Involvement comprised detailed health assessments, by a nurse, in their usual place of residence and/or review of their general practice medical records. RESULTS: Of the 1453 individuals eligible to participate, 72% (n = 1042) were recruited; 59% (n = 851) consented to both health assessment and review of general practice records. Key factors for successful involvement included protected time to engage with family and other key gatekeepers, minimising participant burden, through for example home based assessment, and flexibility of approach. Cognitive impairment is a significant issue; due consideration should be given to the ethical and legal issues of capacity and consent. Interim withdrawal rates at phase 2 (18 month post baseline), show 88 out of 854 participants (10%) had withdrawn with approval for continued use of data and materials and a further 2 participants (0.2%) had withdrawn and requested that all data be destroyed. Attrition due to death of participants within this same time frame was 135 (16%). CONCLUSION: Our recruitment rates were good and compared favourably with other similar UK and international longitudinal studies of the oldest old. The challenges of and successful strategies for involving, recruiting and retaining the oldest old in research, including those in institutions, are described to facilitate adequate representation of this growing population in future research into ageing.\",\n \"corpus_id\": 11871450,\n \"score\": 0\n },\n {\n \"doc_id\": \"21916092\",\n \"title\": \"Failure to attend out-patient clinics: is it in our DNA?\",\n \"abstract\": \"PURPOSE: This paper aims to determine the reasons why patients miss clinic appointments and to ascertain patients' views on the implementation of reminder systems and penalty fees to reduce the rates of did not attend (DNAs). Overall, the paper seeks to establish novel ways to run a more efficient out-patient department (OPD) service to improve waiting times and access for patients to limited neurology resources. DESIGN/METHODOLOGY/APPROACH: A questionnaire-based study was approved by the audit committee and was offered to 204 out-patients attending the neurology clinics over a three-month period (July to September 2009). The patients' demographic details and non-attendance records were reviewed. The paper aimed to ascertain, from the patients' perspective, why people failed to attend clinic appointments. Each participant was asked their views on how they felt their public hospital service might reduce the number of DNAs at their neurology OPD. FINDINGS: A total of 204 patients took part. Participants had a mean age of 31 years (range 25-75 years) with a modal peak in the 26 to 35 age bracket. Almost 10 per cent of those surveyed admitted to missing a hospital out-patient appointment in the past. The most common reason was that they simply \\\"forgot\\\" (28 per cent). DNA rates by age range were proportionally similar to the overall age profile of attenders. Over 55 per cent said they would like a pre-appointment reminder via a mobile telephone text message, 19 per cent preferred a pre-appointment telephone call, and 19 per cent an e-mail. Of those surveyed, 47 per cent said they would be willing to pay a fee on booking that could be refunded on attending for their appointment. The majority of these felt Euro 20 was the most appropriate amount (39 per cent). The rate of acceptance for various fee amounts was uniform across age ranges. Over half (52 per cent) said that they would agree to a \\\"buddy\\\" system whereby the appointment reminder was sent to the patient but also a nominated friend or relative. ORIGINALITY/VALUE: Non-attendance rates at the neurology clinics in our institution are high with almost 10 per cent of attendees admitting to missing an appointment. One of the main reasons why people did not attend was because they simply \\\"forgot\\\" that they had an appointment and the patients favoured a text messaging reminder system to help reduce non-attendance. Almost half of the respondents said that they would be willing to pay a refundable booking fee.\",\n \"corpus_id\": 22853807,\n \"score\": 0\n },\n {\n \"doc_id\": \"21995837\",\n \"title\": \"Detecting referral and selection bias by the anonymous linkage of practice, hospital and clinic data using Secure and Private Record Linkage (SAPREL): case study from the evaluation of the Improved Access to Psychological Therapy (IAPT) service.\",\n \"abstract\": \"BACKGROUND: The evaluation of demonstration sites set up to provide improved access to psychological therapies (IAPT) comprised the study of all people identified as having common mental health problems (CMHP), those referred to the IAPT service, and a sample of attenders studied in-depth. Information technology makes it feasible to link practice, hospital and IAPT clinic data to evaluate the representativeness of these samples. However, researchers do not have permission to browse and link these data without the patients' consent. OBJECTIVE: To demonstrate the use of a mixed deterministic-probabilistic method of secure and private record linkage (SAPREL)--to describe selection bias in subjects chosen for in-depth evaluation. METHOD: We extracted, pseudonymised and used fuzzy logic to link multiple health records without the researcher knowing the patient's identity. The method can be characterised as a three party protocol mainly using deterministic algorithms with dynamic linking strategies; though incorporating some elements of probabilistic linkage. Within the data providers' safe haven we extracted: Demographic data, hospital utilisation and IAPT clinic data; converted post code to index of multiple deprivation (IMD); and identified people with CMHP. We contrasted the age, gender, ethnicity and IMD for the in-depth evaluation sample with people referred to IAPT, use hospital services, and the population as a whole. RESULTS: The in IAPT-in-depth group had a mean age of 43.1 years; CI: 41.0-45.2 (n=166); the IAPT-referred 40.2 years; CI: 39.4-40.9 (n=1118); and those with CMHP 43.6 years SEM 0.15. ( n=12210). Whilst around 67% of those with a CMHP were women, compared to 70% of those referred to IAPT, and 75% of those subject to in-depth evaluation (Chi square p<0.001). The mean IMD score for the in-depth evaluation group was 36.6; CI: 34.2-38.9; (n=166); of those referred to IAPT 38.7; CI: 37.9-39.6; (n=1117); and of people with CMHP 37.6; CI 37.3-37.9; (n=12143). CONCLUSIONS: The sample studied in-depth were older, more likely female, and less deprived than people with CMHP, and fewer had recorded ethnic minority status. Anonymous linkage using SAPREL provides insight into the representativeness of a study population and possible adjustment for selection bias.\",\n \"corpus_id\": 4896720,\n \"score\": 0\n },\n {\n \"doc_id\": \"22296428\",\n \"title\": \"A demographic study to profile non-attenders at a gynaecology outpatient clinic.\",\n \"abstract\": \"Missed outpatient appointments result in the inefficient utilisation of resources and have secondary effects on the health of the non-attenders, as well as on other patients who have to wait longer for their appointments. The first part of the study involved retrospective analysis of trends of non-attendance based on a computerised database of all gynaecology appointments over 12 months. The second comprised a prospective case-control study in which women who missed their gynaecology outpatient appointments (index cases) over 2 months were compared with patients who attended the same clinics matched for indication for referral (control cases). The overall non-attendance rate over 12 months was 16.1%, of whom 42% were recurrent non-attenders. Data from 105 defaulters were compared with 105 non-defaulters who attended the same clinics. Defaulters were significantly younger, single or separated and were more likely to be 'follow-ups' rather than new cases (all p < 0.05). Longer intervals between the appointment letter and actual appointment date was significantly related to non-attendance (p = 0.01) and there was a trend to a greater degree of smoking and alcohol ingestion in the defaulter group (p = 0.059). Comparison of other variables such as severity of symptoms, parity, source of referral and fluency of English did not reach statistical significance (p > 0.05). This prospective study has demonstrated certain profiles which are common to defaulters and which can be used to develop strategies to minimise non-attendance. Examples include reducing the time interval between sending the appointment letter and actual appointment date and selectively over-booking younger, single women who smoke.\",\n \"corpus_id\": 26380120,\n \"score\": 0\n },\n {\n \"doc_id\": \"22397809\",\n \"title\": \"Crowdsourced health research studies: an important emerging complement to clinical trials in the public health research ecosystem.\",\n \"abstract\": \"BACKGROUND: Crowdsourced health research studies are the nexus of three contemporary trends: 1) citizen science (non-professionally trained individuals conducting science-related activities); 2) crowdsourcing (use of web-based technologies to recruit project participants); and 3) medicine 2.0 / health 2.0 (active participation of individuals in their health care particularly using web 2.0 technologies). Crowdsourced health research studies have arisen as a natural extension of the activities of health social networks (online health interest communities), and can be researcher-organized or participant-organized. In the last few years, professional researchers have been crowdsourcing cohorts from health social networks for the conduct of traditional studies. Participants have also begun to organize their own research studies through health social networks and health collaboration communities created especially for the purpose of self-experimentation and the investigation of health-related concerns. OBJECTIVE: The objective of this analysis is to undertake a comprehensive narrative review of crowdsourced health research studies. This review will assess the status, impact, and prospects of crowdsourced health research studies. METHODS: Crowdsourced health research studies were identified through a search of literature published from 2000 to 2011 and informal interviews conducted 2008-2011. Keyword terms related to crowdsourcing were sought in Medline/PubMed. Papers that presented results from human health studies that included crowdsourced populations were selected for inclusion. Crowdsourced health research studies not published in the scientific literature were identified by attending industry conferences and events, interviewing attendees, and reviewing related websites. RESULTS: Participatory health is a growing area with individuals using health social networks, crowdsourced studies, smartphone health applications, and personal health records to achieve positive outcomes for a variety of health conditions. PatientsLikeMe and 23andMe are the leading operators of researcher-organized, crowdsourced health research studies. These operators have published findings in the areas of disease research, drug response, user experience in crowdsourced studies, and genetic association. Quantified Self, Genomera, and DIYgenomics are communities of participant-organized health research studies where individuals conduct self-experimentation and group studies. Crowdsourced health research studies have a diversity of intended outcomes and levels of scientific rigor. CONCLUSIONS: Participatory health initiatives are becoming part of the public health ecosystem and their rapid growth is facilitated by Internet and social networking influences. Large-scale parameter-stratified cohorts have potential to facilitate a next-generation understanding of disease and drug response. Not only is the large size of crowdsourced cohorts an asset to medical discovery, too is the near-immediate speed at which medical findings might be tested and applied. Participatory health initiatives are expanding the scope of medicine from a traditional focus on disease cure to a personalized preventive approach. Crowdsourced health research studies are a promising complement and extension to traditional clinical trials as a model for the conduct of health research.\",\n \"corpus_id\": 27693538,\n \"score\": 0\n },\n {\n \"doc_id\": \"22458706\",\n \"title\": \"Costs and difficulties of recruiting patients to provide e-health support: pilot study in one primary care trust.\",\n \"abstract\": \"BACKGROUND: Better use of e-health services by patients could improve outcomes and reduce costs but there are concerns about inequalities of access. Previous research in outpatients suggested that anonymous personal email support may help patients with long term conditions to use e-health, but recruiting earlier in their 'journey' may benefit patients more. This pilot study explored the feasibility and cost of recruiting patients for an e-health intervention in one primary care trust. METHODS: The sample comprised 46 practices with total patient population of 250,000. We approached all practices using various methods, seeking collaboration to recruit patients via methods agreed with each practice. A detailed research diary was kept of time spent recruiting practices and patients. Researcher time was used to estimate costs. Patients who consented to participate were offered email support for their use of the Internet for health. RESULTS: Eighteen practices agreed to take part; we recruited 27 patients, most (23/27) from five practices. Practices agreed to recruit patients for an e-health intervention via waiting room leaflets (16), posters (16), practice nurses (15), doctors giving patients leaflets (5), a study website link (7), inclusion in planned mailshots (2), and a special mailshot to patients selected from practice computers (1). After low recruitment response we also recruited directly in five practices through research assistants giving leaflets to patients in waiting rooms. Ten practices recruited no patients. Those practices that were more difficult to recruit were less likely to recruit patients. Leaving leaflets for practice staff to distribute and placing posters in the practice were not effective in recruiting patients. Leaflets handed out by practice nurses and website links were more successful. The practice with lowest costs per patient recruited (£70) used a special mailshot to selected patients. CONCLUSION: Recruitment via general practice was not successful and was therefore expensive. Direct to consumer methods and recruitment of patients in outpatients to offer email support may be more cost effective. If recruitment in general practice is required, contacting practices by letter and email, not following up non-responding practices, and recruiting patients with selected conditions by special mailshot may be the most cost-effective approach.\",\n \"corpus_id\": 1268682,\n \"score\": 0\n },\n {\n \"doc_id\": \"22958055\",\n \"title\": \"An international pilot study of an Internet-based platform to facilitate clinical research in epilepsy: the EpiNet project.\",\n \"abstract\": \"PURPOSE: We created an epilepsy patient database that can be accessed via the Internet by neurologists from anywhere in the world. The database was designed to enroll and follow large cohorts of patients with specific epilepsy syndromes, and to facilitate recruitment of patients for investigator-initiated clinical trials. METHODS: The EpiNet database records physician-derived information regarding seizure type and frequency, epilepsy syndrome, etiology, drug history, and investigations. It can be accessed from any country by approved investigators via a secure, password-protected Website. All data are encrypted. The database is for both research and clinical purposes. Investigators were invited to register any patient with epilepsy, but were particularly encouraged to register patients when uncertain of the optimal management. Participation required approval from investigators' ethics committees and institutional review boards, and all patients or their caregiver provided written informed consent. Patients were not enrolled in clinical trials in this pilot study. KEY FINDINGS: The international pilot study recruited patients from September 2010 to November 2011. Sixty-four investigators or research assistants from 25 centers in 13 countries registered 1,050 patients. Patients with a wide range of epilepsy syndromes and etiologies were registered. Patients' ages ranged from 2 weeks to 90 years. SIGNIFICANCE: The Website was successfully used by doctors working in different health systems. The pilot study confirmed that this low-cost, collaborative approach to research has great potential. Large, multicenter cohort studies will commence in 2012, and randomized clinical trials are being planned. All epileptologists are invited to join this project.\",\n \"corpus_id\": 27773996,\n \"score\": 0\n },\n {\n \"doc_id\": \"23235672\",\n \"title\": \"Interventions for recruiting smokers into cessation programmes.\",\n \"abstract\": \"BACKGROUND: Tobacco control is a top public health priority around the globe due to the high prevalence of cigarette smoking and its associated morbidity and mortality. Much effort has been focused on establishing the effectiveness of different smoking cessation strategies. This review, however, aims to address the initial challenge faced by smoking cessation programmes: recruitment of smokers. OBJECTIVES: The primary objective of this review was to determine the effectiveness of different strategies for recruiting smokers into cessation programmes. The secondary objective was to determine the impact that these strategies had on smoking cessation rates at least six months after enrolment into a cessation programme. SEARCH METHODS: We searched the specialised register of the Cochrane Tobacco Addiction Group using a search strategy which included the terms ('recruit$', 'invit$', 'enter', 'entry', 'enrolment') combined with ('smok$', 'cigarette', 'smoking cessation', 'tobacco') in the title, abstract or keyword fields. We searched MEDLINE, EMBASE, the Cochrane Central Register of Controlled Trials (CENTRAL), and registers of current and ongoing trials. We also searched the reference lists of included studies. SELECTION CRITERIA: We included randomised controlled trials and cluster randomised controlled trials that compared at least two different methods of recruiting current smokers into a smoking cessation programme. We also included those studies which focused on the effectiveness of a smoking cessation programme as long as the study involved multiple recruitment methods and reported results of the recruitment phase. DATA COLLECTION AND ANALYSIS: From each included study, we extracted data on the type of participants, type of recruitment strategies (i.e., setting, mode of communication used, intensity and duration) and comparisons, and on randomisation, allocation concealment, and blinding procedures. Our primary outcome was the proportion of smokers successfully recruited to each cessation programme compared to alternative modalities of recruitment. Our secondary outcome was smoking cessation for at least six months. Given the substantial heterogeneity across recruitment interventions and participants, we adopted a narrative synthesis approach for summarising results. MAIN RESULTS: This review includes 19 studies with a total of 14,890 participants. We categorised the included studies according to the modes used to deliver the recruitment strategy: head to head comparison of individual recruitment strategies; comparison of the same delivery mode but with different content or intensity; and the addition of another mode to an existing recruitment method. We identified three studies that made head-to-head comparisons of different types of recruitment strategies. Of these, only one study detected a significant effect, finding that a personal phone call was more effective than a generic invitation letter (RR 40.73, 95% CI 2.53 to 654.74). Five studies compared interventions using the same delivery modes but different content. Results showed that tailored messages through an interactive voice response system resulted in a higher recruitment rate than assessment of smoking status alone using the same system (RR 8.64, 95% CI 4.41 to 16.93), and that text messages indicating scarcity of places available were more effective than generic text message reminders (RR 1.45, 95% CI 1.07 to 1.96). One study compared interventions using the same delivery mode but different intensity and found that allowing for more phone call attempts to reach potential participants can result in better recruitment (RR 1.87, 95% CI 1.61 to 2.18). Finally, 10 studies investigated the effect of adding a recruitment mode to existing recruitment strategies. Findings showed that: adding a text message reminder or real quotes from participants to a personal phone call improved recruitment of participants (RR 3.38, 95% CI 1.26 to 9.08 and RR 29.07, 95% CI 1.74 to 485.70, respectively); that adding a personal phone call to an existing newsletter can also increase recruitment rates (RR 65.12, 95% CI 4.06 to 1045.4]); that a reactive-proactive recruitment phase is more effective than a proactive phase alone (63.8% versus 47.5%, RR not available); and that active recruitment at schools is more effective than passive recruitment (p < 0.001, denominator not available for calculation of RR). Additionally, a number of studies in this category showed that providing incentives can effectively increase the number of participants recruited into smoking cessation programmes. Out of the 19 included studies, only four reported on the effect of recruitment strategy on smoking cessation at six months or longer. Three of these studies compared strategies that used the same delivery mode with different content. Their results were non-significant. The remaining three studies evaluated adding an additional mode to an existing recruitment intervention. Only one of them showed a significant difference in the levels of smoking cessation that favoured the enhanced recruitment strategy, but this may have reflected the offer of incentives once in the programme rather than the recruitment strategy itself (RR at 15 or 18 months 2.60, 95% CI 1.48 to 4.56). AUTHORS' CONCLUSIONS: The substantial heterogeneity across the included studies restricts our ability to draw firm conclusions about the effectiveness of different recruitment strategies in relation to recruitment of participants into smoking cessation programmes or levels of smoking cessation. The limited evidence, however, suggests that the following elements may improve the recruitment of smokers into cessation programmes: personal, tailored interventions; recruitment methods that are proactive in nature; and more intensive recruitment strategies (i.e., those strategies that require increased contact with potential participants).\",\n \"corpus_id\": 205198634,\n \"score\": 0\n },\n {\n \"doc_id\": \"23496916\",\n \"title\": \"Recruitment and retention of participants in a pragmatic randomized intervention trial at three community health clinics: results and lessons learned.\",\n \"abstract\": \"BACKGROUND: Obesity and hypertension and their associated health complications disproportionately affect communities of color and people of lower socioeconomic status. Recruitment and retention of these populations in research trials, and retention in weight loss trials has been an ongoing challenge. METHODS: Be Fit, Be Well was a pragmatic randomized weight loss and hypertension management trial of patients attending one of three community health centers in Boston, Massachusetts. Participants were asked to complete follow-up assessments every 6-months for two years. We describe challenges encountered and strategies implemented to recruit and retain trial participants over the 24-month intervention. We also identify baseline participant characteristics associated with retention status. Retention strategies included financial incentives, contact between assessment visits, building relationships with health center primary care providers (PCPs) and staff, and putting participant convenience first. RESULTS: Active refusal rates were low with 130 of 2,631 patients refusing participation (4.9%). Of 474 eligible persons completing telephone screening, 365 (77.0%) completed their baseline visit and were randomized into the study. The study population was predominantly non-Hispanic Black (71.2%), female (68.5%) and reported annual household income of less than $35,000 (70.1%). Recruitment strategies included use of passive approval of potential participants by PCPs, use of part-time staff, and outsourcing calls to a call center. A total of 314 (86.0%) people completed the 24-month visit. Retention levels varied across study visits and intervention condition. Most participants completed three or more visits (69.6%), with 205 (56.2%) completing all four. At 24-months, lower retention was observed for males and the intervention condition. Retention strategies included building strong relationships with clinic staff, flexibility in overcoming participant barriers through use of taxi vouchers, night and weekend appointments, and keeping participants engaged via newsletters and social gatherings. CONCLUSION: We were able to retain 86.0% of participants at 24-months. Recruitment and retention of high percentages of racial/ethnic minorities and lower income samples is possible with planning, coordination with a trusted community setting and staff (e.g. community health centers and RAs), adaptability and building strong relationships. TRIAL REGISTRATION: Clinicaltrials.gov Identifier: NCT00661817.\",\n \"corpus_id\": 5835422,\n \"score\": 0\n },\n {\n \"doc_id\": \"23559527\",\n \"title\": \"Building the research capacity of clinical physical therapists using a participatory action research approach.\",\n \"abstract\": \"BACKGROUND: This 2-year study explored the experiences of clinical physical therapists who used a participatory action research (PAR) approach to learn about the practice of clinical research. OBJECTIVES: The aim of this study was to explore the experiences of physical therapists who were conducting clinical research, facilitated by a PAR approach. DESIGN: A mixed-methods research design was used. METHODS: Physical therapists completed questionnaires, were interviewed, and participated in focus groups prior to and after the 1-year intervention and 1 year later. The research facilitator took field notes. Questionnaire data were analyzed descriptively, and themes were developed from the qualitative data. Twenty-five therapists took part in 4 self-selected groups. RESULTS: Three groups actively participated in the PAR research projects (n=14). The remaining 11 therapists decided not to be involved in clinical research projects but took part in the study as participants. After 1 year, one group completed the data collection phase of their research project, and a second group completed their ethics application. The third group ceased their research project but hosted a journal club session. At completion of the study, the experiences of the physical therapists were positive, and their confidence in conducting research and orientation toward research had increased. The perceptions of physical therapists toward research, relationships among individuals, and how the clinical projects were structured influenced the success of the projects. LIMITATIONS: Only physical therapists of one hospital and no other health care practitioners were included in this study. CONCLUSIONS: Fourteen physical therapists divided among 3 PAR groups were overall positive about their experiences when they conducted a research project together. This finding shows that a PAR approach can be used as a novel tool to stimulate research participation in clinics.\",\n \"corpus_id\": 207401509,\n \"score\": 0\n },\n {\n \"doc_id\": \"24055787\",\n \"title\": \"Development of an electronic alcohol screening and brief intervention program for hospital outpatients with unhealthy alcohol use.\",\n \"abstract\": \"BACKGROUND: Alcohol screening and brief intervention is recommended for widespread implementation in health care systems, but it is not used routinely in most countries for a variety of reasons. Electronic screening and brief intervention (e-SBI), in which patients complete a Web-based questionnaire and are provided with personalized feedback on their drinking, is a promising alternative to practitioner delivered intervention, but its efficacy in the hospital outpatient setting has not been established. OBJECTIVE: The objective of our study was to establish the feasibility of conducting a full-scale randomized controlled trial to determine whether e-SBI reduces alcohol consumption in hospital outpatients with hazardous or harmful drinking. METHODS: The study was conducted in the outpatient department of a large public hospital in Newcastle (population 540,000), Australia. Adults with appointments at a broad range of medical and surgical outpatient clinics were invited to complete an e-SBI program on a laptop, and to report their impressions via a short questionnaire. Follow-up assessments were conducted 2-8 weeks later by email and post. RESULTS: We approached 172 outpatients and 108/172 (62.8%) agreed to participate. Of the 106 patients capable of self-administering the e-SBI, 7/106 (6.6%) did not complete it (3 due to technical problems and 4 because they were called for their appointment), 15/106 (14.2%) indicated that they had not consumed any alcohol in the past 12 months, 43/106 (40.6%) screened negative for unhealthy alcohol use (scored less than 5 on the Alcohol Use Disorders Identification Test Consumption [AUDIT-C] questions), 33/106 (31.1%) screened positive for hazardous or harmful drinking (AUDIT-C score 5-9), and 8/106 (7.5%) screened positive for possible alcohol dependence (AUDIT-C score 10-12). Among the subgroup with hazardous or harmful drinking, 27/33 (82%) found the feedback on their drinking very, quite, or somewhat useful, 33/33 (100%) thought the intervention would appeal to most or some of the people who attend the service, and 22/30 (73%) completed the follow-up. We also found that some well established procedures used in trials of e-SBI in the primary care setting did not translate to the hospital outpatient setting (1) we experienced delays because the e-SBI program had to be developed and maintained by the health service's information technology staff for security reasons, (2) recruiting patients as they left the reception desk was impractical because patients tended to arrive at the beginning of the clinics with few arrivals thereafter, and (3) use of a laptop in a fixed location resulted in some patients rushing through the e-SBI so they could return to their seat in the area they had been advised to wait in. CONCLUSIONS: e-SBI is acceptable to outpatients and with some adaptation to organizational and physical conditions, it is feasible to recruit and screen patients and to deliver the intervention without disrupting normal service provision. This suggests that e-SBI could be provided routinely in this important setting if shown to be efficacious.\",\n \"corpus_id\": 32350715,\n \"score\": 0\n },\n {\n \"doc_id\": \"24200825\",\n \"title\": \"Network Oncology (NO)--a clinical cancer register for health services research and the evaluation of integrative therapeutic interventions in anthroposophic medicine.\",\n \"abstract\": \"BACKGROUND: Concepts of integrative oncology (IO), as have been offered by anthroposophic medicine (AM) for decades, are gaining increasing interest and acceptance. Central aspects are multimodal therapeutic interventions, health-related quality of live, and patients' preference as well as therapeutic relationship and clinical outcome. Despite its broad application, IO lacks evaluation in clinical practice and complementary therapies are not monitored by any cancer registries. METHODS: To close this gap we established 'Network Oncology' (NO), a conjoint registry of German outpatient AM practitioners and AM hospitals. In this paper we present the project and a first data overview and compare it to epidemiological registers and current literature. RESULTS: NO has collected 10,405 cancer patients' records in 6 years. Compared to epidemiological registers our data show minor differences in disease entity distribution, age, and gender. There is an overproportional amount of young breast cancer patients in NO institutions indicating a demand for integrative therapies in this group. There is no difference between the UICC (Union for International Cancer Control) stages at first diagnosis and at admission to a NO facility. According to our data conventional therapies were less frequently administered after admission to a NO facility. Nevertheless, one third of the patients received their first conventional therapy in a NO facility. 80% of the patients received mistletoe preparations and 63% had nonpharmacotherapeutic, complementary interventions. CONCLUSION: Integrative oncological approaches attract a great number of patients visiting AM institutions. The NO provides an infrastructure to evaluate integrative interventions in AM, allows comparison to other clinical registers, and thus can contribute to health service research in this field.\",\n \"corpus_id\": 207744003,\n \"score\": 0\n },\n {\n \"doc_id\": \"24228935\",\n \"title\": \"Reflecting on the methodological challenges of recruiting to a United Kingdom-wide, multi-centre, randomised controlled trial in gynaecology outpatient settings.\",\n \"abstract\": \"BACKGROUND: Successful recruitment of participants to any trial is central to its success. Trial results are routinely published, and recruitment is often cited to be slower and more difficult than anticipated. This article reflects on the methodological challenges of recruiting women with prolapse attending United Kingdom (UK) gynaecology outpatient clinics to a multi-centre randomised controlled trial (RCT) of physiotherapy, and the systems put in place in an attempt to address them. METHODS: Gynaecology outpatients with symptomatic prolapse were to be recruited over a 16-month period from 14 UK hospitals and one New Zealand hospital. Eligible women were informed about the trial by their gynaecologist and informed consent was obtained by the central trial office. Recruitment difficulties were encountered early on, and a number of strategies were employed to try to improve recruitment. RESULTS: Some strategies were more successful than others and they differed in the resources required. Actions that facilitated recruitment included increasing recruiting centres to 23 UK and two international hospitals, good centre support, using processes embedded in clinical practice, and good communication between the trial office, collaborators and participants. Collaborator incentives, whereby staff involved received the benefit immediately, were more successful than a nominal monetary payment per woman randomised. Barriers to recruitment included fewer eligible women than anticipated, patient's preference to receive active treatment rather than allocation to the control group, lack of support staff and high staff turnover. Geographical variations in Primary Care Trust Research Management and Governance approval systems and general practitioner (GP) referral procedures also impacted negatively on recruitment. CONCLUSIONS: Our article reflects on the methodological challenges of recruiting to a multi-centre RCT in a UK gynaecology setting. Effective interventions included increasing the number of recruiting centres and providing collaborator incentives. Barriers to recruitment included fewer eligible women than anticipated, patient's preference to be allocated to the treatment group, lack of support staff, and variations in approval systems and GP referral procedures. To improve the evidence base on clinical trial recruitment, trialists need to publish their experiences and lessons learned. Future RCTs should evaluate, where possible, the effect of strategies designed to improve recruitment and retention. TRIAL REGISTRATION: Current Controlled Trials ISRCTN35911035.\",\n \"corpus_id\": 8416544,\n \"score\": 0\n },\n {\n \"doc_id\": \"24243869\",\n \"title\": \"Health care professionals' views of paediatric outpatient non-attendance: implications for general practice.\",\n \"abstract\": \"BACKGROUND: Non-attendance at paediatric hospital outpatient appointments poses potential risks to children's health and welfare. Prevention and management of missed appointments depends on the perceptions of clinicians and decision makers from both primary and secondary care, including general practitioners (GPs) who are integral to non-attendance follow-up. OBJECTIVES: To examine the views of clinical, managerial and executive health care staff regarding occurrence and management of non-attendance at general paediatric outpatient clinics. METHODS: A qualitative study using individual semi-structured interviews was carried out at three English Primary Care Trusts and a nearby children's hospital. Interviews were conducted with 37 staff, including GPs, hospital doctors, other health care professionals, managers, executives and commissioners. Participants were recruited through purposive and 'snowball' sampling methods. Data were analysed following a thematic framework approach. RESULTS: GPs focused on situational difficulties for families, while hospital-based staff emphasized the influence of parents' beliefs on attendance. Managers, executives and commissioners presented a broad overview of both factors, but with less detailed views. All groups discussed sociodemographic factors, with non-attendance thought to be more likely in 'chaotic families'. Hospital interviewees emphasized child protection issues and the need for thorough follow-up of missed appointments. However, GPs were reluctant to interfere with parental responsibilities. CONCLUSION: Parental motivation and practical and social barriers should be considered. Responsibilities regarding missed appointments are not clear across health care sectors, but GPs are uniquely placed to address non-attendance issues and are central to child safeguarding. Primary care policies and strategies could be introduced to reduce non-attendance and ensure children receive the care they require.\",\n \"corpus_id\": 10890712,\n \"score\": 0\n },\n {\n \"doc_id\": \"24308359\",\n \"title\": \"Electronic health records for biological sample collection: feasibility study of statin-induced myopathy using the Clinical Practice Research Datalink.\",\n \"abstract\": \"AIMS: Electronic healthcare records (EHRs) are increasingly used to store clinical information. A secondary benefit of EHRs is their use, in an anonymized form, for observational research. The Clinical Practice Research Datalink (CPRD) contains EHRs from primary care in the UK and, despite 1083 peer-reviewed research publications, has never been used to obtain pharmacogenetic samples. Using a statin-induced myopathy paradigm, we evaluated using the CPRD to obtain patient samples for a pharmacogenetic study targeting 250 cases and 500 controls from UK general practitioner (GP) practices. METHODS: The CPRD identified potential patients fitting specific case-definition criteria (active rhabdomyolysis or creatine phosphokinase > four times the upper limit of normal), and corresponding GP practices were asked to invite patient participation. Consenting patients were requested to provide either saliva or blood samples and to complete an ethnicity questionnaire. Control subjects were recruited from the same GP practice (saliva) or a small number of practices (blood). Samples were forwarded for DNA extraction. RESULTS: Thirty-six months of recruitment yielded DNA samples from 149 statin-induced myopathy cases and 587 tolerant controls. Data show that contacting patients through their GP is a reliable method for obtaining samples without compromising anonymity. Saliva collection directly from patients was considerably less effective than blood sampling. After 10 months of recruitment, saliva sampling was suspended in favour of blood sampling. CONCLUSIONS: We demonstrate the potential of EHRs for identifying accurately phenotyped cases and controls for pharmacogenetic studies. Recruitment was successful only because of the willingness of GP practices to participate and the existence of strong doctor-patient relationships. The present study provides a model that can be implemented in future genetic analyses using EHRs.\",\n \"corpus_id\": 15747443,\n \"score\": 0\n },\n {\n \"doc_id\": \"24495499\",\n \"title\": \"Procedures of recruiting, obtaining informed consent, and compensating research participants in Qatar: findings from a qualitative investigation.\",\n \"abstract\": \"BACKGROUND: Very few researchers have reported on procedures of recruiting, obtaining informed consent, and compensating participants in health research in the Arabian Gulf Region. Empirical research can inform the debate about whether to adjust these procedures for culturally diverse settings. Our objective was to delineate procedures related to recruiting, obtaining informed consent, and compensating health research participants in the extremely high-density multicultural setting of Qatar. METHODS: During a multistage mixed methods project, field observations and qualitative interviews were conducted in a general medicine clinic of a major medical center in Qatar. Participants were chosen based on gender, age, literacy, and preferred language, i.e., Arabic, English, Hindi and Urdu. Qualitative analysis identified themes about recruitment, informed consent, compensation, and other research procedures. RESULTS: A total of 153 individuals were approached and 84 enrolled; the latter showed a diverse age range (18 to 75 years); varied language representation: Arabic (n = 24), English (n = 20), Hindi (n = 20), and Urdu (n = 20); and balanced gender distribution: women (n = 43) and men (n = 41). Primary reasons for 30 declinations included concern about interview length and recording. The study achieved a 74% participation rate. Qualitative analytics revealed key themes about hesitation to participate, decisions about participation with family members as well as discussions with them as \\\"incidental research participants\\\", the informed consent process, privacy and gender rules of the interview environment, reactions to member checking and compensation, and motivation for participating. Vulnerability emerged as a recurring issue throughout the process among a minority of participants. CONCLUSIONS: This study from Qatar is the first to provide empirical data on recruitment, informed consent, compensation and other research procedures in a general adult population in the Middle East and Arabian Gulf. This investigation illustrates how potential research participants perceive research participation. Fundamentally, Western ethical research principles were applicable, but required flexibility and culturally informed adaptations.\",\n \"corpus_id\": 15262678,\n \"score\": 0\n },\n {\n \"doc_id\": \"24690402\",\n \"title\": \"Structured, intensive education maximising engagement, motivation and long-term change for children and young people with diabetes: a cluster randomised controlled trial with integral process and economic evaluation - the CASCADE study.\",\n \"abstract\": \"BACKGROUND: Type 1 diabetes (T1D) in children and young people is increasing worldwide with a particular increase in children under the age of 5 years. Fewer than one in six children and young people achieve glycosylated fraction of haemoglobin (HbA1c) values in the range identified as providing best future outcomes. There is an urgent need for clinic-based pragmatic, feasible and effective interventions that improve both glycaemic control and quality of life (QoL). The intervention offers both structured education, to ensure young people know what they need to know, and a delivery model designed to motivate self-management. OBJECTIVE: To assess the feasibility of providing a clinic-based structured educational group programme incorporating psychological approaches to improve long-term glycaemic control, QoL and psychosocial functioning in a diverse range of young people. DESIGN: The study was a pragmatic, cluster randomised control trial with integral process and economic evaluation. SETTING: Twenty-eight paediatric diabetes services across London, south-east England and the Midlands. RANDOMISATION: Minimised by clinic size, age (paediatric or adolescent) and specialisation (district general hospital clinic or teaching hospital/tertiary clinic). ALLOCATION: Half of the sites were randomised to the intervention arm and half to the control arm. Allocation was concealed until after clinics had consented and the first participant was recruited. Where possible, families were blind to allocation until recruitment finished. PARTICIPANTS: Forty-three health-care practitioners (14 teams) were trained in the intervention. The study recruited 362 children aged 8-16 years, diagnosed with T1D for > 12 months, with a mean 12-month HbA1c level of ≥ 8.5%. INTERVENTION: Two 1-day workshops taught intervention delivery. A detailed manual and resources were provided. The intervention consists of four group education sessions led by a paediatric diabetes specialist nurse with another team member. OUTCOMES: The primary outcome was glycaemic control, assessed at the individual level using venous HbA1c values, measured at baseline, 12 and 24 months. Secondary outcomes were directly and indirectly related to diabetes management, including hypoglycaemic episodes, hospital admissions, diabetes regimen, knowledge, skills and responsibility for diabetes management, intervention compliance, clinic utilisation, emotional and behavioural adjustment, and general and diabetes-specific QoL. PROCESS EVALUATION: Questionnaires, semistructured interviews, informal discussion following observation sessions, fieldwork notes and case note review were used to collect qualitative and quantitative data from key stakeholder groups at specific time points in the trial. STATISTICAL ANALYSES: Primary and secondary analyses were intention-to-treat comparisons of outcomes at 12 and 24 months, using analysis of covariance with a random effect for clinic. Prespecified subgroup analyses based on age, gender, initial HbA1c value and socioeconomic status were estimated from models that included an interaction term. The economic analysis compared long-term costs and predicted quality-adjusted life-years (QALYs). RESULTS: The intervention did not improve HbA1c at 12 months [intervention effect 0.11; 95% confidence interval (CI) -0.28 to 0.50; p = 0.584] or 24 months (intervention effect 0.03; 95% CI -0.36 to 0.41; p = 0.891). A total of 298/362 patients (82.3%) provided blood samples at 12-month follow-up, and 284/362 (78.5%) provided blood samples at 24-month follow-up. Follow-up questionnaires were completed by 307 patients (85.3%) at 12 months and by 295 patients (81.5%) at 24 months. Intervention group parents at 12 months (95% CI 0.74; 0.03 to 1.52) and young people at 24 months (0.85; 95% CI 0.03 to 1.61) had higher scores on the diabetes family responsibility questionnaire. Young people reported reduced happiness with body weight at 12 months (-0.56; 95% CI -1.03 to -0.06). Only 68% of groups were run. Of the 180 families recruited, 96 (53%) attended at least one module. Reasons for low uptake included difficulties organising groups, and work and school commitments. Young people with higher HbA1c levels were less likely to attend. Parents and young people who attended groups described improved family relationships, improved knowledge and understanding, greater confidence and increased motivation to manage diabetes. Twenty-four months after the intervention, nearly half of the young people reported that the groups had made them want to try harder and that they had carried on trying. A high-quality, complex, pragmatic trial of structured education can be delivered alongside standard care in NHS diabetes clinics. Health-care providers benefited from behaviour change skill training and can deliver pragmatic aspects of a National Institute for Health and Care Excellence (NICE)-compliant structured education programme after relatively brief training. The process evaluation provides insight into aspects of the model, and highlights strengths and aspects that may have contributed to the failure to influence primary and secondary outcomes. Current NHS practice dominates CASCADE (Child and Adolescent Structured Competencies Approach to Diabetes Education) in that it achieves the same number of QALYs at a lower cost. The mean cost of providing the intervention was £5098 per site or £683 per child. Members of paediatric diabetes services trained to deliver the CASCADE structured education package using behaviour change techniques did not improve glycaemic control in patients compared with control subjects 1 and 2 years after the intervention. The training workshops for practitioners were well evaluated; however, more intensive training was needed. The intervention cost £683 per patient but was not cost-effective because it did not improve metabolic control. CONCLUSIONS: A high-quality, complex, pragmatic trial of structured education can be successfully conducted alongside standard care in NHS diabetes clinics. Pragmatic components of a NICE-compliant structured education programme can be successfully delivered following a relatively brief 2-day training while paediatric health-care professionals benefit from training in behaviour change skills. The study provides invaluable information on barriers and opportunities regarding future, similar interventions. A low dropout rate and good attendance for the subgroup that attended the intervention suggests there might be improved uptake if offered to young people with lower HbA1c. Testing whether this approach can be more successful with a robust ongoing supervisory element should be a target of further research. TRIAL REGISTRATION: Current Controlled Trials ISRCTN52537669. FUNDING: This project was funded by the NIHR Health Technology Assessment programme and will be published in full in Health Technology Assessment; Vol. 18, No. 20. See the NIHR Journals Library website for further project information.\",\n \"corpus_id\": 21991999,\n \"score\": 0\n },\n {\n \"doc_id\": \"24793730\",\n \"title\": \"Feasibility of integrating research data collection into routine clinical practice using the electronic health record.\",\n \"abstract\": \"PURPOSE: The electronic health record is becoming central to routine medical practice and has the potential to facilitate large scale clinical research. We evaluated the completeness and accuracy of data collection using designated research fields integrated into a semistructured clinical note. We hypothesized that prospective research data collection as part of routine clinical charting is feasible, with a high rate of utilization (greater than 80%) and accuracy (kappa greater than 0.80). MATERIALS AND METHODS: Infants with congenital hydronephrosis were followed prospectively at a single institution. Existing functionality in the electronic health record was used for data collection by creation of 28 different data elements captured from a hydronephrosis note or phrase template. Completeness (percent utilization) was calculated and accuracy was assessed by comparing the structured data to manual chart review. Comparisons were conducted using the chi-square test, with 2-tailed p values <0.05 considered statistically significant. RESULTS: A total of 80 patients were eligible for manual chart review. Data were recorded through template use in 64 patients for an overall completeness of 80.0%. Of 28 elements 17 (60%) demonstrated \\\"almost perfect\\\" agreement (kappa greater than 0.80), and all variables reached at least \\\"moderate\\\" agreement (greater than 0.40). CONCLUSIONS: Integrating research fields into routine clinical practice is feasible by using semistructured clinical templates within an electronic health record. High completion and accuracy rates were captured from a variety of fields within a hydronephrosis template.\",\n \"corpus_id\": 36863773,\n \"score\": 0\n },\n {\n \"doc_id\": \"24885915\",\n \"title\": \"Effectiveness and cost-effectiveness of a group-based pain self-management intervention for patients undergoing total hip replacement: feasibility study for a randomized controlled trial.\",\n \"abstract\": \"BACKGROUND: Total hip replacement (THR) is a common elective surgical procedure and can be effective for reducing chronic pain. However, waiting times can be considerable. A pain self-management intervention may provide patients with skills to more effectively manage their pain and its impact during their wait for surgery. This study aimed to evaluate the feasibility of conducting a randomized controlled trial to assess the effectiveness and cost-effectiveness of a group-based pain self-management course for patients undergoing THR. METHODS: Patients listed for a THR at one orthopedic center were posted a study invitation pack. Participants were randomized to attend a pain self-management course plus standard care or standard care only. The lay-led course was delivered by Arthritis Care and consisted of two half-day sessions prior to surgery and one full-day session after surgery. Participants provided outcome and resource-use data using a diary and postal questionnaires prior to surgery and one month, three months and six months after surgery. Brief telephone interviews were conducted with non-participants to explore barriers to participation. RESULTS: Invitations were sent to 385 eligible patients and 88 patients (23%) consented to participate. Interviews with 57 non-participants revealed the most common reasons for non-participation were views about the course and transport difficulties. Of the 43 patients randomized to the intervention group, 28 attended the pre-operative pain self-management sessions and 11 attended the post-operative sessions. Participant satisfaction with the course was high, and feedback highlighted that patients enjoyed the group format. Retention of participants was acceptable (83% of recruited patients completed follow-up) and questionnaire return rates were high (72% to 93%), with the exception of the pre-operative resource-use diary (35% return rate). Resource-use completion rates allowed for an economic evaluation from the health and social care payer perspective. CONCLUSIONS: This study highlights the importance of feasibility work prior to a randomized controlled trial to assess recruitment methods and rates, barriers to participation, logistics of scheduling group-based interventions, acceptability of the intervention and piloting resource use questionnaires to improve data available for economic evaluations. This information is of value to researchers and funders in the design and commissioning of future research. TRIAL REGISTRATION: Current Controlled Trials ISRCTN52305381.\",\n \"corpus_id\": 10064675,\n \"score\": 0\n },\n {\n \"doc_id\": \"25486401\",\n \"title\": \"Recruiting U.S. and Canadian college students via social media for participation in a web-based brief intervention study.\",\n \"abstract\": \"OBJECTIVE: Recruiting young adults for health research is challenging. Social media provides wide access to potential research participants. We evaluated the feasibility of recruiting students via free message postings on Facebook and Twitter to participate in a web-based brief intervention study. The sample comprised students attending U.S. and Canadian universities. METHOD: During three semesters, institutional review board-approved recruitment messages were posted in 281 Facebook groups, 7 Facebook pages, and 27 message \\\"tweets\\\" on Twitter. RESULTS: A total of 708 eligible participants were recruited from Facebook. The mean enrollment rate per Facebook group was 0.21%; the rate was higher for host university groups (1.56%) compared with groups at other universities (0.10%). We recruited seven participants from Twitter. The sample was predominantly female (70%) with a mean age of 20.0 years. There were no significant differences between host university participants recruited through social media and traditional methods. The web-based intervention completion rate was 65%, and participants from the host university were more likely to complete the intervention than were groups at other universities (p = .01). CONCLUSIONS: Social media provides access to a large number of potential participants, and social media recruitment may be useful to researchers who can harness this broad reach. Facebook recruitment was feasible and free and resulted in a large number of enrolled participants. Social media recruitment for researchers at their own universities may be particularly fruitful. Despite wide access to students with Twitter, recruitment was slow. Social media recruitment allowed us to extend web-based intervention access to students in the United States and Canada.\",\n \"corpus_id\": 39164230,\n \"score\": 0\n },\n {\n \"doc_id\": \"25759376\",\n \"title\": \"Danish nationwide registers for public health and health-related research.\",\n \"abstract\": \"AIMS: The Nordic countries have a strong tradition of using nationwide social and health registers for research purposes. The aim of the current paper is to provide an overview of the Danish population-based registers in public health and health-related research, and to discuss their strengths and limitations. METHODS: Danish registers on somatic and psychiatric hospital contacts as well as care provided by general practitioners were reviewed. The availability of demographic, individual-level variables of relevance for health-related research was summarized. RESULTS: Since 1968, every person living in Denmark has a unique identifier. This identifier is listed in Danish registers enabling linkage of information from a range of registers on an individual level. The nationwide coverage of all patient contacts at somatic and psychiatric hospitals, consultations with general practitioners, purchases of prescribed medications, and a complete follow-up with respect to causes of death support public health studies surveying trends of prevalence and incidence. Historical data on psychiatric and somatic hospitalizations since 1969 and 1977, respectively, allow an in-depth assessment of the burden of disease and time trends. Demographic characteristics of individuals and family units, together with information on education, employment, income, place of residence and migration, are provided by social registers. CONCLUSIONS: Register data are fully representative of the entire population with no loss to follow-up. Nationwide coverage also ensures a large sample to investigate events and conditions with low base rates. Clinical observations are limited and often only available for select patient populations. However, the opportunities available for public health research through linkage of register data with the increasing number of nationwide clinical databases, bio-banks and surveys entail promising perspectives for future research.\",\n \"corpus_id\": 206723150,\n \"score\": 0\n },\n {\n \"doc_id\": \"25862756\",\n \"title\": \"Introducing consultant outpatient clinics to community settings to improve access to paediatrics: an observational impact study.\",\n \"abstract\": \"OBJECTIVES: In line with a national policy to move care 'closer to home', a specialist children's hospital in the National Health Service in England introduced consultant-led 'satellite' clinics to two community settings for general paediatric outpatient services. Objectives were to reduce non-attendance at appointments by providing care in more accessible locations and to create new physical clinic capacity. This study evaluated these satellite clinics to inform further development and identify lessons for stakeholders. METHODS: Impact of the satellite clinics was assessed by comparing community versus hospital-based clinics across the following measures: (1) non-attendance rates and associated factors (including patient characteristics and travel distance) using a logistic regression model; (2) percentage of appointments booked within local catchment area; (3) contribution to total clinic capacity; (4) time allocated to clinics and appointments; and (5) clinic efficiency, defined as the ratio of income to staff-related costs. RESULTS: Satellite clinics did not increase attendance beyond their contribution to shorter travel distance, which was associated with higher attendance. Children living in the most-deprived areas were 1.8 times more likely to miss appointments compared with those from least-deprived areas. The satellite clinics' contribution to activity in catchment areas and to total capacity was small. However, one of the two satellite clinics was efficient compared with most hospital-based clinics. CONCLUSIONS: Outpatient clinics were relocated in pragmatically chosen community settings using a 'drag and drop' service model. Such clinics have potential to improve access to specialist paediatric healthcare, but do not provide a panacea. Work is required to improve attendance as part of wider efforts to support vulnerable families. Satellite clinics highlight how improved management could contribute to better use of existing capacity.\",\n \"corpus_id\": 21591162,\n \"score\": 0\n },\n {\n \"doc_id\": \"26251363\",\n \"title\": \"A participatory study of teenagers and young adults views on access and participation in cancer research.\",\n \"abstract\": \"PURPOSE: The purpose of this study was to elicit young people's views on access and participation in cancer research. METHODS: Eight young people aged 18-25 years with a previous cancer diagnosis aged 15-24 participated in a one day workshop utilising participatory methodology. The workshop consisted of four exercises: role play/scene setting; focus group examining thoughts and opinions of research access and participation; individual reflection on access to different types of research; and creative interpretation of the workshop. Further consultation with 222 young people with cancer was conducted using an electronic survey. RESULTS: Three themes emerged: • Patient choice: Young people thought it was their right to know all options about available research. Without knowledge of all available studies they would be unable to make an informed choice about participation. • Role of healthcare professionals as facilitators/barriers: Young people suggested non-clinical healthcare professionals such as social workers and youth support coordinators may be more suited to approaching young people about participation in psychosocial and health services research. • Value of the research: The what, when and how information was delivered was key in relaying the value of the study and assisting young people in their decision to participate. Further consultation showed approximately 70% wanted to find out about all available research. However, one third trusted healthcare professionals to decide which research studies to inform them of. CONCLUSION: Effective ways to support healthcare professionals approaching vulnerable populations about research are needed to ensure young people are empowered to make informed choices about research participation.\",\n \"corpus_id\": 19123847,\n \"score\": 0\n },\n {\n \"doc_id\": \"26470880\",\n \"title\": \"Participant recruitment into a randomised controlled trial of exercise therapy for people with multiple sclerosis.\",\n \"abstract\": \"BACKGROUND: The success of a clinical trial is often dependant on whether recruitment targets can be met in the required time frame. Despite an increase in research into the benefits of exercise in people with multiple sclerosis (PwMS), no trial has reported detailed data on effective recruitment strategies for large-scale randomised controlled trials. The main purpose of this report is to provide a detailed outline of recruitment strategies, rates and estimated costs in the Exercise Intervention for Multiple Sclerosis (ExIMS) trial to identify best practices for future trials involving multiple sclerosis (MS) patient recruitment. METHODS: The ExIMS researchers recruited 120 PwMS to participate in a 12-week exercise intervention. Participants were randomly allocated to either exercise or usual-care control groups. Participants were sedentary, aged 18-65 years and had Expanded Disability Status Scale scores of 1.0-6.5. Recruitment strategies included attendance at MS outpatient clinics, consultant mail-out and trial awareness-raising activities. RESULTS: A total of 120 participants were recruited over the course of 34 months. To achieve this target, 369 potentially eligible and interested participants were identified. A total of 60 % of participants were recruited via MS clinics, 29.2 % from consultant mail-outs and 10.8 % through trial awareness. The randomisation yields were 33.2 %, 31.0 % and 68.4 % for MS clinic, consultant mail-outs and trial awareness strategies, respectively. The main reason for ineligibility was being too active (69.2 %), whilst for eligible participants the most common reason for non-participation was the need to travel to the study site (15.8 %). Recruitment via consultant mail-out was the most cost-effective strategy, with MS clinics being the most time-consuming and most costly. CONCLUSIONS: To reach recruitment targets in a timely fashion, a variety of methods were employed. Although consultant mail-outs were the most cost-effective recruitment strategy, use of this method alone would not have allowed us to obtain the predetermined number of participants in the required time period, thus leading to costly extensions of the project or failure to reach the number of participants required for sufficient statistical power. Thus, a multifaceted approach to recruitment is recommended for future trials. TRIAL REGISTRATION: International Standard Randomised Controlled Trial Registry number: ISRCTN41541516 ; date registered: 5 February 2009.\",\n \"corpus_id\": 6013974,\n \"score\": 0\n },\n {\n \"doc_id\": \"26753864\",\n \"title\": \"Genetics, lifestyle and environment. UK Biobank is an open access resource following the lives of 500,000 participants to improve the health of future generations.\",\n \"abstract\": \"UK Biobank is a long-term prospective epidemiology study having recruited and now following the lives of 500,000 people in England, Scotland and Wales, aged 40-69 years when they joined the study (Sudlow et al., PLoS Med 12(3):e1001779, 2015). Participants were recruited by letter and asked to attend one of 22 assessment centres in towns and cities across Britain, where they provided consent, answered detailed questions about their health and lifestyle, had body measures taken and donated blood, urine and saliva. Participants provided consent for the long-term follow-up of their health via medical records, such as general practice and hospital records, cancer and death records. Samples are being stored long term for a wide range of analyses, including genetic. The resource is open to all bona fide scientists from the UK and overseas, academic and industry who register via its access management system. Summary of UK Biobank data can be viewed via its Data Showcase and the resource will be strengthened over time as the results of new analyses and studies are returned, health links and participants provide additional information about themselves. Some will attend full repeat assessment visits. UK Biobank is open for business, and it hopes researchers will find it a valuable tool to improve the health of future generations.\",\n \"corpus_id\": 13910209,\n \"score\": 0\n },\n {\n \"doc_id\": \"26813669\",\n \"title\": \"Patient responses to research recruitment and follow-up surveys: findings from a diverse multicultural health care setting in Qatar.\",\n \"abstract\": \"BACKGROUND: Health care researchers working in the Arabian Gulf need information on how to optimize recruitment and retention of study participants in extremely culturally diverse settings. Implemented in Doha, Qatar in 2012 with 4 language groups, namely Arabic, English, Hindi, and Urdu, this research documents persons' responses to recruitment, consent, follow-up, and reminder procedures during psychometric testing of the Multicultural Assessment Instrument (MAI), a novel self- or interviewer-administered survey. METHODS: Bilingual research assistants recruited adults in outpatient clinics by approaching persons in particular who appeared to be from a target language group. Participants completed the MAI, a second acculturation instrument used for content-validity assessment, and a demographics questionnaire. Participants were asked to take the MAI again in 2-3 weeks, in person or by post, to assess test-retest reliability. Recruitment data were analyzed by using nonparametric statistics. RESULTS: Of 1503 persons approached during recruitment, 400 enrolled (27%)-100 per language group. The enrollment rates in the language groups were: Arabic-32%; English-33%; Hindi-18%; Urdu-30%. The groups varied somewhat in their preferences regarding consent procedure, follow-up survey administration, contact mode for follow-up reminders, and disclosure of personal mailing address (for postal follow-up). Over all, telephone was the preferred medium for follow-up reminders. Of 64 persons who accepted a research assistant's invitation for in-person follow-up, 40 participants completed the interview (follow-up rate, 63%); among 126 persons in the postal group with a deliverable address, 29 participants mailed back a completed follow-up survey (response rate, 23%). CONCLUSIONS: Researchers in the Arabian Gulf face challenges to successfully identify, enroll, and retain eligible study participants. Although bilingual assistants-often from the persons' own culture-recruited face-to-face, and our questionnaire contained no health care-related content, many persons were reluctant to participate. This occurrence was observed especially at follow-up, particularly among participants who had agreed to follow-up by post.\",\n \"corpus_id\": 12322176,\n \"score\": 0\n },\n {\n \"doc_id\": \"26861942\",\n \"title\": \"Dental practitioner recruitment for a randomized clinical trial in the field to evaluate the performance of a new glass ionomer restoration material.\",\n \"abstract\": \"BACKGROUND: In 2009, we began recruiting dental practitioners across Germany to participate in a clinical trial to evaluate the clinical performance of EQUIA, a new glass ionomer restoration material. The aim of this paper is to discuss the outcomes of the dental practitioner recruitment and outline the process of establishing a practice-based research network. METHODS: Study proposals were sent to randomly selected dental offices in 29 cities in Germany. The proposals were sent until a minimum of 10 clinics in each city declared participation. Later on, briefing lectures informed the participating practitioners about the design, methods, and material application procedure. Participants were familiarized with the guidelines of Good Manufacturing Practice (GMP) and Good Epidemiological Practice (GEP). A questionnaire describing the characteristics of each dental office was filled out by the participating practitioner. Additionally, participation levels were characterized according to the socioeconomic status and geographic districts of residence in Germany (Regions 0 to 9). The associations between the characteristics were tested by the Kruskal-Wallis Test and Chi-squared test (P < 0.05). RESULTS: A total of 3194 private dental clinics were invited, 1712 clinics refused to participate, 1195 did not respond to the invitation, and 323 agreed to participate. Only 144 clinics participated in the lectures held in their cities and signed the participation agreement. Based on their geographic location, the highest participation was in Region 2 with a participation rate of 14.3%, and the lowest participation was in Region 6 with a participation rate of 1.7%. Regions with the lowest rate of unemployment and relatively higher rates of income (Regions 7 and 8) had the highest rate of refusals (86%). CONCLUSION: The initial results of the dental practitioner recruitment in this study suggest that the recruitment and pre-randomization design were successful, and by reaching out to a considerable number of private dental clinics to participate, we were able to recruit a smaller number of highly motivated dentists in this clinical study. Regional differences in socioeconomic status, practitioner specialization, and differences in patient health care insurance have to be considered when recruiting dental practitioners for clinical trials. TRIAL REGISTRATION: The trial has been registered at Deutsches Register Klinischer Studien (German register of clinical trials) on 6 September 2012 under DRKS-ID: DRKS00004220.\",\n \"corpus_id\": 2930922,\n \"score\": 0\n },\n {\n \"doc_id\": \"26867046\",\n \"title\": \"OPTIMA prelim: a randomised feasibility study of personalised care in the treatment of women with early breast cancer.\",\n \"abstract\": \"BACKGROUND: There is uncertainty about the chemotherapy sensitivity of some oestrogen receptor (ER)-positive, human epidermal growth factor receptor 2 (HER2)-negative breast cancers. Multiparameter assays that measure the expression of several tumour genes simultaneously have been developed to guide the use of adjuvant chemotherapy for this breast cancer subtype. The assays provide prognostic information and have been claimed to predict chemotherapy sensitivity. There is a dearth of prospective validation studies. The Optimal Personalised Treatment of early breast cancer usIng Multiparameter Analysis preliminary study (OPTIMA prelim) is the feasibility phase of a randomised controlled trial (RCT) designed to validate the use of multiparameter assay directed chemotherapy decisions in the NHS. OBJECTIVES: OPTIMA prelim was designed to establish the acceptability to patients and clinicians of randomisation to test-driven treatment assignment compared with usual care and to select an assay for study in the main RCT. DESIGN: Partially blinded RCT with adaptive design. SETTING: Thirty-five UK hospitals. PARTICIPANTS: Patients aged ≥ 40 years with surgically treated ER-positive HER2-negative primary breast cancer and with 1-9 involved axillary nodes, or, if node negative, a tumour at least 30 mm in diameter. INTERVENTIONS: Randomisation between two treatment options. Option 1 was standard care consisting of chemotherapy followed by endocrine therapy. In option 2, an Oncotype DX(®) test (Genomic Health Inc., Redwood City, CA, USA) performed on the resected tumour was used to assign patients either to standard care [if 'recurrence score' (RS) was > 25] or to endocrine therapy alone (if RS was ≤ 25). Patients allocated chemotherapy were blind to their randomisation. MAIN OUTCOME MEASURES: The pre-specified success criteria were recruitment of 300 patients in no longer than 2 years and, for the final 150 patients, (1) an acceptance rate of at least 40%; (2) recruitment taking no longer than 6 months; and (3) chemotherapy starting within 6 weeks of consent in at least 85% of patients. RESULTS: Between September 2012 and 3 June 2014, 350 patients consented to join OPTIMA prelim and 313 were randomised; the final 150 patients were recruited in 6 months, of whom 92% assigned chemotherapy started treatment within 6 weeks. The acceptance rate for the 750 patients invited to participate was 47%. Twelve out of the 325 patients with data (3.7%, 95% confidence interval 1.7% to 5.8%) were deemed ineligible on central review of receptor status. Interviews with researchers and recordings of potential participant consultations made as part of the integral qualitative recruitment study provided insights into recruitment barriers and led to interventions designed to improve recruitment. Patient information was changed as the result of feedback from three patient focus groups. Additional multiparameter analysis was performed on 302 tumour samples. Although Oncotype DX, MammaPrint(®)/BluePrint(®) (Agendia Inc., Irvine, CA, USA), Prosigna(®) (NanoString Technologies Inc., Seattle, WA, USA), IHC4, IHC4 automated quantitative immunofluorescence (AQUA(®)) [NexCourse BreastTM (Genoptix Inc. Carlsbad, CA, USA)] and MammaTyper(®) (BioNTech Diagnostics GmbH, Mainz, Germany) categorised comparable numbers of tumours into low- or high-risk groups and/or equivalent molecular subtypes, there was only moderate agreement between tests at an individual tumour level (kappa ranges 0.33-0.60 and 0.39-0.55 for tests providing risks and subtypes, respectively). Health economics modelling showed the value of information to the NHS from further research into multiparameter testing is high irrespective of the test evaluated. Prosigna is currently the highest priority for further study. CONCLUSIONS: OPTIMA prelim has achieved its aims of demonstrating that a large UK clinical trial of multiparameter assay-based selection of chemotherapy in hormone-sensitive early breast cancer is feasible. The economic analysis shows that a trial would be economically worthwhile for the NHS. Based on the outcome of the OPTIMA prelim, a large-scale RCT to evaluate the clinical effectiveness and cost-effectiveness of multiparameter assay-directed chemotherapy decisions in hormone-sensitive HER2-negative early breast would be appropriate to take place in the NHS. TRIAL REGISTRATION: Current Controlled Trials ISRCTN42400492. FUNDING: This project was funded by the National Institute for Health Research (NIHR) Health Technology Assessment programme and will be published in full in Health Technology Assessment; Vol. 20, No. 10. See the NIHR Journals Library website for further project information. The Government of Ontario funded research at the Ontario Institute for Cancer Research. Robert C Stein received additional support from the NIHR University College London Hospitals Biomedical Research Centre.\",\n \"corpus_id\": 33540975,\n \"score\": 0\n },\n {\n \"doc_id\": \"26977856\",\n \"title\": \"Use of a 12 months' self-referral reminder to facilitate uptake of bowel scope (flexible sigmoidoscopy) screening in previous non-responders: a London-based feasibility study.\",\n \"abstract\": \"BACKGROUND: In March 2013, NHS England extended its national Bowel Cancer Screening Programme to include 'one-off' Flexible Sigmoidoscopy screening (NHS Bowel Scope Screening, BSS) for men and women aged 55. With less than one in two people currently taking up the screening test offer, there is a strong public health mandate to develop system-friendly interventions to increase uptake while the programme is rolling out. This study aimed to assess the feasibility of sending a reminder to previous BSS non-responders, 12 months after the initial invitation, with consideration for its potential impact on uptake. METHOD: This study was conducted in the ethnically diverse London Boroughs of Brent and Harrow, where uptake is below the national average. Between September and November 2014, 160 previous non-responders were randomly selected to receive a reminder of the opportunity to self-refer 12 months after their initial invitation. The reminder included instructions on how to book an appointment, and provided options for the time and day of the appointment and the gender of the endoscopist performing the test. To address barriers to screening, the reminder was sent with a brief locally tailored information leaflet designed specifically for this study. Participants not responding within 4 weeks were sent a follow-up reminder, after which there was no further intervention. Self-referral rates were measured 8 weeks after the delivery of the follow-up reminder and accepted as final. RESULTS: Of the 155 participants who received the 12 months' reminder (returned to sender, n=5), 30 (19.4%) self-referred for an appointment, of which 24 (15.5%) attended and were successfully screened. Attendance rates differed by gender, with significantly more women attending an appointment than men (20.7% vs 8.8%, respectively; OR=2.73, 95% CI=1.02-7.35, P=0.05), but not by area (Brent vs Harrow) or area-level deprivation. Of the 30 people who self-referred for an appointment, 27 (90%) indicated a preference for a same-sex practitioner, whereas three (10%) gave no preference. Preference for a same-sex practitioner was higher among women than men (χ(2)=7.78, P<0.05), with only 67% of men (six of nine) requesting a same-sex practitioner, compared with 100% of women (n=21). CONCLUSIONS: Sending previous non-responders a 12 months' reminder letter with a brief information leaflet is a feasible and efficacious intervention, which merits further investigation in a randomised controlled trial.\",\n \"corpus_id\": 6160026,\n \"score\": 0\n },\n {\n \"doc_id\": \"27780796\",\n \"title\": \"Participant Recruitment and Engagement in Automated eHealth Trial Registration: Challenges and Opportunities for Recruiting Women Who Experience Violence.\",\n \"abstract\": \"BACKGROUND: Automated eHealth Web-based research trials offer people an accessible, confidential opportunity to engage in research that matters to them. eHealth trials may be particularly useful for sensitive issues when seeking health care may be accompanied by shame and mistrust. Yet little is known about people's early engagement with eHealth trials, from recruitment to preintervention autoregistration processes. A recent randomized controlled trial that tested the effectiveness of an eHealth safety decision aid for New Zealand women in the general population who experienced intimate partner violence (isafe) provided the opportunity to examine recruitment and preintervention participant engagement with a fully automated Web-based registration process. The trial aimed to recruit 340 women within 24 months. OBJECTIVE: The objective of our study was to examine participant preintervention engagement and recruitment efficiency for the isafe trial, and to analyze dropout through the registration pathway, from recruitment to eligibility screening and consent, to completion of baseline measures. METHODS: In this case study, data collection sources included the trial recruitment log, Google Analytics reports, registration and program metadata, and costs. Analysis included a qualitative narrative of the recruitment experience and descriptive statistics of preintervention participant engagement and dropout rates. A Koyck model investigated the relationship between Web-based online marketing website advertisements (ads) and participant accrual. RESULTS: The isafe trial was launched on September 17, 2012. Placement of ads in an online classified advertising platform increased the average number of recruited participants per month from 2 to 25. Over the 23-month recruitment period, the registration website recorded 4176 unique visitors. Among 1003 women meeting eligibility criteria, 51.55% (517) consented to participate; among the 501 women who enrolled (consented, validated, and randomized), 412 (82.2%) were accrued (completed baseline assessments). The majority (n=52, 58%) of the 89 women who dropped out between enrollment and accrual never logged in to the allocated isafe website. Of every 4 accrued women, 3 (314/412, 76.2%) identified the classified ad as their referral source, followed by friends and family (52/412, 12.6%). Women recruited through a friend or relative were more likely to self-identify as indigenous Māori and live in the highest-deprivation areas. Ads increased the accrual rate by a factor of 74 (95% CI 49-112). CONCLUSIONS: Print advertisements, website links, and networking were costly and inefficient methods for recruiting participants to a Web-based eHealth trial. Researchers are advised to limit their recruitment efforts to Web-based online marketplace and classified advertising platforms, as in the isafe case, or to social media. Online classified advertising in \\\"Jobs-Other-volunteers\\\" successfully recruited a diverse sample of women experiencing intimate partner violence. Preintervention recruitment data provide critical information to inform future research and critical analysis of Web-based eHealth trials. CLINICALTRIAL: Australian New Zealand Clinical Trials Registry (ANZCTR): ACTRN12612000708853; https://www.anzctr.org.au/Trial/Registration/TrialReview.aspx?ACTRN=12612000708853 (Archived by WebCite at http://www.webcitation/6lMGuVXdK).\",\n \"corpus_id\": 10775969,\n \"score\": 0\n },\n {\n \"doc_id\": \"28397521\",\n \"title\": \"Improving access to health care in a rural regional hospital in South Africa: Why do patients miss their appointments?\",\n \"abstract\": \"BACKGROUND: Access to health services is one of the Batho Pele ('people first') values and principles of the South African government since 1997. This necessitated some changes around public service systems, procedures, attitudes and behaviour. The challenges of providing health care to rural geographically spread populations include variations in socio-economic status, transport opportunities, access to appointment information and patient perceptions of costs and benefits of seeking health care. George hospital, situated in a rural area, serves 5000 outpatient visits monthly, with non-attendance rates of up to 40%. OBJECTIVES: The aim of this research was to gain a greater understanding of the reasons behind non-attendance of outpatient department clinics to allow locally driven, targeted interventions. METHODS: This was a descriptive study. We attempted to phone all patients who missed appointments over a 1-month period (n = 574). Only 20% were contactable with one person declining consent. Twenty-nine percent had no telephone number on hospital systems, 7% had incorrect numbers, 2% had died and 42% did not respond to three attempts. RESULTS: The main reasons for non-attendance included unaware of appointment date (16%), out of area (11%), confusion over date (11%), sick or admitted to hospital (10%), family member sick or died (7%), appointment should have been cancelled by clerical staff (6%) and transport (6%). Only 9% chose to miss their appointment. The other 24% had various reasons. CONCLUSIONS: Improved patient awareness of appointments, adjustments in referral systems and enabling appointment cancellation if indicated would directly improve over two-thirds of reasons for non-attendance. Understanding the underlying causes will help appointment planning, reduce wasted costs and have a significant impact on patient care.\",\n \"corpus_id\": -1,\n \"score\": 0\n },\n {\n \"doc_id\": \"28699815\",\n \"title\": \"Improving recruitment to healthcare research studies: clinician judgements explored for opting mental health service users out of the time to change viewpoint survey.\",\n \"abstract\": \"BACKGROUND: There are significant challenges across the research pathway, including participant recruitment. This paper aims to explore the impact of clinician recruitment decision-making on sampling for a national mental health survey. METHOD: Clinical teams in 20 English mental healthcare provider organisations screened caseload lists, opting-out people whom, in their judgement, should not be approached to participate in a survey about stigma and discrimination. The reasons for each individual opted-out were requested. We assess these reasons against study recruitment criteria and investigated the impact of variations in opt-out rates on response rates and study findings. RESULTS: Over 4 years (2009-2012), 37% (28,592 people) of the total eligible sampling frame were excluded. Exclusions comprised three categories: clinical teams did not screen their lists within recruitment period (12,392 people: 44%); protocol-specified exclusions (8364 people: 29%); clinician opt-outs queried by research team (other reasons were given) (7836, 28%). Response rates were influenced by decision-making variations. CONCLUSIONS: Large numbers of people were denied the opportunity to choose for themselves whether to participate or not in the Viewpoint Survey. The clinical research community, and their employing organisations, require support to better understand the value of research and best practice for research recruitment.\",\n \"corpus_id\": 25545009,\n \"score\": 0\n },\n {\n \"doc_id\": \"28861532\",\n \"title\": \"Perceptions of Barriers to and Facilitators of Participation in Health Research Among Transgender People.\",\n \"abstract\": \"Purpose: Although transgender people may be at increased risk for a range of health problems, they have been the subject of relatively little health research. An important step toward expanding the evidence base is to understand and address the reasons for nonparticipation and dropout. The aim of this study was to explore the perceptions of barriers to and facilitators of participation in health research among a sample of transgender people in San Francisco, CA, and Atlanta, GA. Methods: Twelve in-person focus groups (FGs) were conducted; six (three with transwomen, three with transmen) were conducted in San Francisco and six FGs were conducted in Atlanta (three with transwomen and three with transmen). FGs were audiorecorded, transcribed, and uploaded to MaxQDA software for analysis. A codebook was used to code transcripts; new codes were added iteratively as they arose. All transcripts were coded by at least 2 of the 4 researchers and, after each transcript was coded, the researchers met to discuss any discrepancies, which were resolved by consensus. Results: Among 67 FG participants, 37 (55%) identified as transmen and 30 (45%) identified as transwomen. The average age of participants was ∼41 years (range 18-67) and the majority (61%) were non-Hispanic Whites. Several barriers that can hinder participation in health research were identified, including logistical concerns, issues related to mistrust, a lack of awareness about participation opportunities, and psychosocial/emotional concerns related to being \\\"outed.\\\" A broad range of facilitators were also identified, including the opportunity to gain knowledge, access medical services, and contribute to the transgender community. Conclusion: These findings provide insights about the perceived barriers to and facilitators of research participation and offer some guidance for researchers in our ongoing effort to engage the transgender community in health research.\",\n \"corpus_id\": 523099,\n \"score\": 0\n },\n {\n \"doc_id\": \"28930210\",\n \"title\": \"Right Place, Right Time: Preferences of Women with Ovarian Cancer for Delivery of CAM Education.\",\n \"abstract\": \"The purpose of this pilot study was to assess the feasibility of on-site complementary and alternative medicine (CAM) education sessions to maximize quality of life for women with ovarian cancer. The pilot intervention consisted of four weekly sessions, each focusing the techniques and benefits of a particular CAM topic (e.g., nutrition, massage, relaxation). Participants were recruited from the Center for Women's Oncology at H. Lee Moffitt Cancer Center from 2010 to 2012. Eligible participants had an ovarian cancer diagnosis with a life expectancy of at least 12 months, and were 18 years or older. The Gynecologic Oncology research nurse invited women in the outpatient clinic who matched the eligibility criteria. The research nurse explained the study and provided an informed consent form and return envelope. Because ovarian cancer is not only a rare cancer but, also, most patients seen at Moffitt have recurrent or advanced disease, many women did not have an adequate ECOG score. Many women who consented had rapid changes in health status, with morbidity and mortality outpacing recruitment of the 20 needed to proceed with the four education sessions. Baseline and follow-up surveys were conducted to assess changes in QOL, knowledge, and satisfaction with the intervention. While 27 women consented and 24 women completed the baseline survey, only five women participated in the intervention. The five women who participated were all white, and at time of consenting had a mean age of 60 (SD 9.08) and an average of 102 months (SD 120.65) since diagnosis, and were all on active treatment, except for one. The intervention pilot did not encounter difficulties with regard to recruitment, but suffered problems in achieving an adequate number of women to launch the on-site sessions because of rapidly changing morbidity and significant mortality. The team recognized that a larger-scaled intervention comprised of on-site sessions was impractical and compared attendance rates with a more convenient format currently underway in the Women's Oncology program at Moffitt. While low participation prevented an intervention analysis of scientific merit, the study data is informative with regard to barriers, facilitators, and alternative methods for sharing useful information to women with advanced ovarian cancer. The comparison strongly suggested that CAM education for women compromised by the disease and treatment associated with ovarian cancer would best be delivered in the convenient-access format that allowed remote access to live and recorded discussions of specific topics.\",\n \"corpus_id\": 7030283,\n \"score\": 0\n },\n {\n \"doc_id\": \"29152518\",\n \"title\": \"Follow-up in patients with a burn-related emergency department visit: a feasibility study.\",\n \"abstract\": \"Background: Data on epidemiology, costs, and outcomes of burn-related injuries presenting at emergency departments (EDs) are scarce. To obtain such information, a questionnaire study with an adequate response rate is imperative. There is evidence that optimized strategies can increase patient participation. However, it is unclear whether this applies to burn patients in an ED setting. The objective of this feasibility study was to optimize and evaluate patient recruitment strategy and follow-up methods in patients with burn injuries presenting at EDs. Methods: In a prospective cohort study with a 6-month follow-up, patients with burn-related injuries attending two large EDs during a 3-month study period were included. Eligible patients were quasi-randomly allocated to a standard or optimized recruitment strategy by week of the ED visit. The standard recruitment strategy consisted of an invitation letter to participate, an informed consent form, a questionnaire, and a franked return envelope. The optimized recruitment strategy was complemented by a stamped returned envelope, monetary incentive, sending a second copy of the questionnaire, and a reminder by telephone in non-responders. Response rates were calculated, and questionnaires were used to assess treatment, costs, and health-related quality of life. Results: A total of 87 patients were included of which 85 were eligible for the follow-up study. There was a higher response rate at 2 months in the optimized versus the standard recruitment strategy (43.6% vs. 20.0%; OR = 3.1 (95% CI 1.1-8.8)), although overall response is low. Non-response analyses showed no significant differences in patient, burn injury or treatment characteristics between responders versus non-responders. Conclusions: This study demonstrated that response rates can be increased with an optimized, but more labor-intensive recruitment strategy, although further optimization of recruitment and follow-up is needed. It is feasible to assess epidemiology, treatment, and costs after burn-related ED contacts.\",\n \"corpus_id\": 7986461,\n \"score\": 0\n },\n {\n \"doc_id\": \"29164743\",\n \"title\": \"Patient-initiated recruitment for clinical research: Evaluation of an outpatient letter research statement.\",\n \"abstract\": \"BACKGROUND: UK Hospital Trusts are charged with increasing patients' research awareness and willingness to take part in research. This includes implementing strategies to encourage patient-initiated enquiries about participation. OBJECTIVES: To evaluate the impact of a research statement inserted in outpatient letters in one clinical service, and to derive suggestions on potential steps towards increasing patient-initiated recruitment. SETTING: A medical outpatient clinic of a research-active hospital trust, serving an inner-city multi-ethnic population across two boroughs. METHODS: Pre-intervention and post-intervention questionnaires were administered face-to-face to new patients. Questionnaires included closed questions and one open comments section. Data were analysed for frequencies, with thematic coding of open-ended responses. RESULTS: The response rates were 87% for the pre-intervention survey and 92% for the post-intervention survey. In the post-intervention survey, 85% of patients did not notice the research statement in the letter. More than half found the statement \\\"a little unclear,\\\" whilst one-third considered it \\\"clear.\\\" Three-quarters of respondents perceived the statement to be \\\"a little helpful.\\\" Only one person enquired about participating in clinical research having read the statement in the outpatient letter. CONCLUSION: The analysis suggests that simple, single-solution approaches such as including research statements in outpatient letters are unlikely to be sufficient to significantly facilitate patient-initiated recruitment. Recruitment efforts need to take into consideration the diversity of patient constituencies including the reasons they seek health care, and how patients can meaningfully access information (research literacy).\",\n \"corpus_id\": 4510076,\n \"score\": 0\n },\n {\n \"doc_id\": \"29361929\",\n \"title\": \"Interpreting population reach of a large, successful physical activity trial delivered through primary care.\",\n \"abstract\": \"BACKGROUND: Failure to include socio-economically deprived or ethnic minority groups in physical activity (PA) trials may limit representativeness and could lead to implementation of interventions that then increase health inequalities. Randomised intervention trials often have low recruitment rates and rarely assess recruitment bias. A previous trial by the same team using similar methods recruited 30% of the eligible population but was in an affluent setting with few non-white residents and was limited to those over 60 years of age. METHODS: PACE-UP is a large, effective, population-based walking trial in inactive 45-75 year-olds that recruited through seven London general practices. Anonymised practice demographic data were available for all those invited, enabling investigation of inequalities in trial recruitment. Non-participants were invited to complete a questionnaire. RESULTS: From 10,927 postal invitations, 1150 (10.5%) completed baseline assessment. Participation rate ratios (95% CI), adjusted for age and gender as appropriate, were lower in men 0.59 (0.52, 0.67) than women, in those under 55 compared with those ≥65, 0.60 (0.51, 0.71), in the most deprived quintile compared with the least deprived 0.52 (0.39, 0.70) and in Asian individuals compared with whites 0.62 (0.50, 0.76). Black individuals were equally likely to participate as white individuals. Participation was also associated with having a co-morbidity or some degree of health limitation. The most common reasons for non-participation were considering themselves as being too active or lack of time. CONCLUSIONS: Conducting the trial in this diverse setting reduced overall response, with lower response in socio-economically deprived and Asian sub-groups. Trials with greater reach are likely to be more expensive in terms of recruitment and gains in generalizability need to be balanced with greater costs. Differential uptake of successful trial interventions may increase inequalities in PA levels and should be monitored. TRIAL REGISTRATION: ISRCTN.com ISRCTN98538934 . Registered 2nd March 2012.\",\n \"corpus_id\": 13781395,\n \"score\": 0\n },\n {\n \"doc_id\": \"29713494\",\n \"title\": \"Developing and feasibility testing of data collection methods for an economic evaluation of a supported selfmanagement programme for adults with a learning disability and type 2 diabetes.\",\n \"abstract\": \"Background: The challenges of conducting research with hard to reach vulnerable groups are particularly pertinent for people with learning disabilities. Data collection methods for previous cost and cost-effectiveness analyses of health and social care interventions targeting people with learning disabilities have relied on health care/health insurance records or data collection forms completed by the service provider rather than by people with learning disabilities themselves. This paper reports on the development and testing of data collection methods for an economic evaluation within a randomised controlled trial (RCT) for a supported self-management programme for people with mild/moderate learning disabilities and type 2 diabetes. Methods: A case finding study was conducted to identify types of health and social care use and data collection methods employed in previous studies with this population. Based on this evidence, resource use questionnaires for completion by GP staff and interviewer-administered participant questionnaires (covering a wider cost perspective and health-related quality of life) were tested within a feasibility RCT. Interviewer-administered questionnaires included the EQ-5D-3L (the NICE recommended measure for use in economic evaluation). Participants were adults > 18 years with a mild or moderate learning disability and type 2 diabetes, with mental capacity to give consent to research participation. Results: Data collection for questionnaires completed by GP staff requesting data for the last 12 months proved time intensive and difficult. Whilst 82.3% (121/147) of questionnaires were returned, up to 17% of service use items were recorded as unknown. Subsequently, a shorter recall period (4 months) led to a higher return rate but with a higher rate of missing data. Missing data for interviewer-administered participant questionnaires was > 8% but the interviewers reported difficulty with participant recall. Almost 60% (48/80) of participants had difficulty completing the EQ-5D-3L. Conclusions: Further investigation as to how service use can be recorded is recommended. Concerns about the reliability of identifying service use data directly from participants with a learning disability due to challenges in completion, specifically around recall, remain. The degree of difficulty to complete EQ-5D-3L indicates concerns regarding the appropriateness of using this measure in its current form in research with this population. Trial registration: Current Controlled Trials ISRCTN41897033 (registered 21 January 2013).\",\n \"corpus_id\": 5037512,\n \"score\": 0\n },\n {\n \"doc_id\": \"29728348\",\n \"title\": \"The Acceptability and Feasibility of Implementing a Bio-Behavioral Enhanced Surveillance Tool for Sexually Transmitted Infections in England: Mixed-Methods Study.\",\n \"abstract\": \"BACKGROUND: Sexually transmitted infection (STI) surveillance is vital for tracking the scale and pattern of epidemics; however, it often lacks data on the underlying drivers of STIs. OBJECTIVE: This study aimed to assess the acceptability and feasibility of implementing a bio-behavioral enhanced surveillance tool, comprising a self-administered Web-based survey among sexual health clinic attendees, as well as linking this to their electronic health records (EHR) held in England's national STI surveillance system. METHODS: Staff from 19 purposively selected sexual health clinics across England and men who have sex with men and black Caribbeans, because of high STI burden among these groups, were interviewed to assess the acceptability of the proposed bio-behavioral enhanced surveillance tool. Subsequently, sexual health clinic staff invited all attendees to complete a Web-based survey on drivers of STI risk using a study tablet or participants' own digital device. They recorded the number of attendees invited and participants' clinic numbers, which were used to link survey data to the EHR. Participants' online consent was obtained, separately for survey participation and linkage. In postimplementation phase, sexual health clinic staff were reinterviewed to assess the feasibility of implementing the bio-behavioral enhanced surveillance tool. Acceptability and feasibility of implementing the bio-behavioral enhanced surveillance tool were assessed by analyzing these qualitative and quantitative data. RESULTS: Prior to implementation of the bio-behavioral enhanced surveillance tool, sexual health clinic staff and attendees emphasized the importance of free internet/Wi-Fi access, confidentiality, and anonymity for increasing the acceptability of the bio-behavioral enhanced surveillance tool among attendees. Implementation of the bio-behavioral enhanced surveillance tool across sexual health clinics varied considerably and was influenced by sexual health clinics' culture of prioritization of research and innovation and availability of resources for implementing the surveys. Of the 7367 attendees invited, 85.28% (6283) agreed to participate. Of these, 72.97% (4585/6283) consented to participate in the survey, and 70.62% (4437/6283) were eligible and completed it. Of these, 91.19% (4046/4437) consented to EHR linkage, which did not differ by age or gender but was higher among gay/bisexual men than heterosexual men (95.50%, 722/756 vs 88.31%, 1073/1215; P<.003) and lower among black Caribbeans than white participants (87.25%, 568/651 vs 93.89%, 2181/2323; P<.002). Linkage was achieved for 88.88% (3596/4046) of consenting participants. CONCLUSIONS: Implementing a bio-behavioral enhanced surveillance tool in sexual health clinics was feasible and acceptable to staff and groups at STI risk; however, ensuring participants' confidentiality and anonymity and availability of resources is vital. Bio-behavioral enhanced surveillance tools could enable timely collection of detailed behavioral data for effective commissioning of sexual health services.\",\n \"corpus_id\": 13712224,\n \"score\": 0\n }\n]","isConversational":false}}},{"rowIdx":85,"cells":{"query":{"kind":"string","value":"{\n \"doc_id\": \"27821736\",\n \"title\": \"C-terminal domain of mammalian complexin-1 localizes to highly curved membranes.\",\n \"abstract\": \"In presynaptic nerve terminals, complexin regulates spontaneous \\\"mini\\\" neurotransmitter release and activates Ca(2+)-triggered synchronized neurotransmitter release. We studied the role of the C-terminal domain of mammalian complexin in these processes using single-particle optical imaging and electrophysiology. The C-terminal domain is important for regulating spontaneous release in neuronal cultures and suppressing Ca(2+)-independent fusion in vitro, but it is not essential for evoked release in neuronal cultures and in vitro. This domain interacts with membranes in a curvature-dependent fashion similar to a previous study with worm complexin [Snead D, Wragg RT, Dittman JS, Eliezer D (2014) Membrane curvature sensing by the C-terminal domain of complexin. Nat Commun 5:4955]. The curvature-sensing value of the C-terminal domain is comparable to that of α-synuclein. Upon replacement of the C-terminal domain with membrane-localizing elements, preferential localization to the synaptic vesicle membrane, but not to the plasma membrane, results in suppression of spontaneous release in neurons. Membrane localization had no measurable effect on evoked postsynaptic currents of AMPA-type glutamate receptors, but mislocalization to the plasma membrane increases both the variability and the mean of the synchronous decay time constant of NMDA-type glutamate receptor evoked postsynaptic currents.\",\n \"corpus_id\": 3911655\n}"},"candidates":{"kind":"list like","value":[{"doc_id":"18505837","title":"Complexins facilitate neurotransmitter release at excitatory and inhibitory synapses in mammalian central nervous system.","abstract":"Complexins (Cplxs) are key regulators of synaptic exocytosis, but whether they act as facilitators or inhibitors is currently being disputed controversially. We show that genetic deletion of all Cplxs expressed in the mouse brain causes a reduction in Ca(2+)-triggered and spontaneous neurotransmitter release at both excitatory and inhibitory synapses. Our results demonstrate that at mammalian central nervous system synapses, Cplxs facilitate neurotransmitter release and do not simply act as inhibitory clamps of the synaptic vesicle fusion machinery.","corpus_id":9354579,"score":2},{"doc_id":"19179400","title":"The carboxy-terminal domain of complexin I stimulates liposome fusion.","abstract":"Regulated exocytosis requires tight coupling of the membrane fusion machinery to a triggering signal and a fast response time. Complexins are part of this regulation and, together with synaptotagmins, control calcium-dependent exocytosis. Stimulatory and inhibitory functions have been reported for complexins. To test if complexins directly affect membrane fusion, we analyzed the 4 known mammalian complexin isoforms in a reconstituted fusion assay. In contrast to complexin III (CpxIII) and CpxIV, CpxI and CpxII stimulated soluble N-ethylmaleimide-sensitive factor attachment protein receptor (SNARE)-pin assembly and membrane fusion. This stimulatory effect required a preincubation at low temperature and was specific for neuronal t-SNAREs. Stimulation of membrane fusion was lost when the carboxy-terminal domain of CpxI was deleted or serine 115, a putative phosphorylation site, was mutated. Transfer of the carboxy-terminal domain of CpxI to CpxIII resulted in a stimulatory CpxIII-I chimera. Thus, the carboxy-terminal domains of CpxI and CpxII promote the fusion of high-curvature liposomes.","corpus_id":24553152,"score":2},{"doc_id":"21145004","title":"Complexin clamps asynchronous release by blocking a secondary Ca(2+) sensor via its accessory α helix.","abstract":"Complexin activates and clamps neurotransmitter release; impairing complexin function decreases synchronous, but increases spontaneous and asynchronous synaptic vesicle exocytosis. Here, we show that complexin-different from the Ca(2+) sensor synaptotagmin-1-activates synchronous exocytosis by promoting synaptic vesicle priming, but clamps spontaneous and asynchronous exocytosis-similar to synaptotagmin-1-by blocking a secondary Ca(2+) sensor. Activation and clamping functions of complexin depend on distinct, autonomously acting sequences, namely its N-terminal region and accessory α helix, respectively. Mutations designed to test whether the accessory α helix of complexin clamps exocytosis by inserting into SNARE-complexes support this hypothesis, suggesting that the accessory α helix blocks completion of trans-SNARE-complex assembly until Ca(2+) binding to synaptotagmin relieves this block. Moreover, a juxtamembranous mutation in the SNARE-protein synaptobrevin-2, which presumably impairs force transfer from nascent trans-SNARE complexes onto fusing membranes, also unclamps spontaneous fusion by disinhibiting a secondary Ca(2+) sensor. Thus, complexin performs mechanistically distinct activation and clamping functions that operate in conjunction with synaptotagmin-1 by controlling trans-SNARE-complex assembly.","corpus_id":14230300,"score":2},{"doc_id":"21215631","title":"Complexin maintains vesicles in the primed state in C. elegans.","abstract":"BACKGROUND: Complexin binds the SNARE complex at synapses and regulates exocytosis, but genetic studies indicate contradictory roles: in flies it predominantly inhibits synaptic vesicle fusion, whereas in mice it promotes evoked responses. RESULTS: Here we characterize the complexin mutant in the nematode Caenorhabditis elegans and reveal bipolar functions in neurotransmission: complexin inhibits spontaneous fusion of synaptic vesicles but is also essential for evoked responses. Complexin mutants exhibit a doubling of vesicle fusion in the absence of extracellular calcium. Even more profoundly, mutants exhibit an almost complete loss of evoked responses, and current amplitudes are reduced by 94%. One possible interpretation is that complexin is required for the stabilization of docked vesicles and that, in its absence, vesicles may fuse or undock from the plasma membrane. Consistent with this hypothesis, docked synaptic vesicles are reduced by 70% in complexin-1 mutants. CONCLUSION: These data suggest that the main function of complexin is to maintain the docked state both by inhibiting fusion and by promoting priming.","corpus_id":6117522,"score":2},{"doc_id":"22357870","title":"C-terminal complexin sequence is selectively required for clamping and priming but not for Ca2+ triggering of synaptic exocytosis.","abstract":"Complexins are small soluble proteins that bind to assembling SNARE complexes during synaptic vesicle exocytosis, which in turn mediates neurotransmitter release. Complexins are required for clamping of spontaneous \"mini \" release and for the priming and synaptotagmin-dependent Ca(2+) triggering of evoked release. Mammalian genomes encode four complexins that are composed of an N-terminal unstructured sequence that activates synaptic exocytosis, an accessory α-helix that clamps exocytosis, an essential central α-helix that binds to assembling SNARE complexes and is required for all of its functions, and a long, apparently unstructured C-terminal sequence whose function remains unclear. Here, we used cultured mouse neurons to show that the C-terminal sequence of complexin-1 is not required for its synaptotagmin-activating function but is essential for its priming and clamping functions. Wild-type complexin-3 did not clamp exocytosis but nevertheless fully primed and activated exocytosis. Strikingly, exchanging the complexin-1 C terminus for the complexin-3 C terminus abrogated clamping, whereas exchanging the complexin-3 C terminus for the complexin-1 C terminus enabled clamping. Analysis of point mutations in the complexin-1 C terminus identified two single amino-acid substitutions that impaired clamping without altering the activation function of complexin-1. Examination of release induced by stimulus trains revealed that clamping-deficient C-terminal complexin mutants produced a modest relative increase in delayed release. Overall, our results show that the relatively large C-terminal complexin-1 sequence acts in priming and clamping synaptic exocytosis and demonstrate that the clamping function is not conserved in complexin-3, presumably because of its distinct C-terminal sequences.","corpus_id":30991987,"score":2},{"doc_id":"23159779","title":"Differential regulation of evoked and spontaneous neurotransmitter release by C-terminal modifications of complexin.","abstract":"Complexins are small α-helical proteins that modulate neurotransmitter release by binding to SNARE complexes during synaptic vesicle exocytosis. They have been found to function as fusion clamps to inhibit spontaneous synaptic vesicle fusion in the absence of Ca(2+), while also promoting evoked neurotransmitter release following an action potential. Complexins consist of an N-terminal domain and an accessory α-helix that regulates the activating and inhibitory properties of the protein, respectively, and a central α-helix that binds the SNARE complex and is essential for both functions. In addition, complexins contain a largely unstructured C-terminal domain whose role in synaptic vesicle cycling is poorly defined. Here, we demonstrate that the C-terminus of Drosophila complexin (DmCpx) regulates localization to synapses and that alternative splicing of the C-terminus can differentially regulate spontaneous and evoked neurotransmitter release. Characterization of the single DmCpx gene by mRNA analysis revealed expression of two alternatively expressed isoforms, DmCpx7A and DmCpx7B, which encode proteins with different C-termini that contain or lack a membrane tethering prenylation domain. The predominant isoform, DmCpx7A, is further modified by RNA editing within this C-terminal region. Functional analysis of the splice isoforms showed that both are similarly localized to synaptic boutons at larval neuromuscular junctions, but have differential effects on the regulation of evoked and spontaneous fusion. These data indicate that the C-terminus of Drosophila complexin regulates both spontaneous and evoked release through separate mechanisms and that alternative splicing generates isoforms with distinct effects on the two major modes of synaptic vesicle fusion at synapses.","corpus_id":16488161,"score":2},{"doc_id":"23238737","title":"Complexin controls spontaneous and evoked neurotransmitter release by regulating the timing and properties of synaptotagmin activity.","abstract":"Neurotransmitter release following synaptic vesicle (SV) fusion is the fundamental mechanism for neuronal communication. Synaptic exocytosis is a specialized form of intercellular communication that shares a common SNARE-mediated fusion mechanism with other membrane trafficking pathways. The regulation of synaptic vesicle fusion kinetics and short-term plasticity is critical for rapid encoding and transmission of signals across synapses. Several families of SNARE-binding proteins have evolved to regulate synaptic exocytosis, including Synaptotagmin (SYT) and Complexin (CPX). Here, we demonstrate that Drosophila CPX controls evoked fusion occurring via the synchronous and asynchronous pathways. cpx(-/-) mutants show increased asynchronous release, while CPX overexpression largely eliminates the asynchronous component of fusion. We also find that SYT and CPX coregulate the kinetics and Ca(2+) co-operativity of neurotransmitter release. CPX functions as a positive regulator of release in part by coupling the Ca(2+) sensor SYT to the fusion machinery and synchronizing its activity to speed fusion. In contrast, syt(-/-); cpx(-/-) double mutants completely abolish the enhanced spontaneous release observe in cpx(-/-) mutants alone, indicating CPX acts as a fusion clamp to block premature exocytosis in part by preventing inappropriate activation of the SNARE machinery by SYT. CPX levels also control the size of synaptic vesicle pools, including the immediate releasable pool and the ready releasable pool-key elements of short-term plasticity that define the ability of synapses to sustain responses during burst firing. These observations indicate CPX regulates both spontaneous and evoked fusion by modulating the timing and properties of SYT activation during the synaptic vesicle cycle.","corpus_id":566304,"score":2},{"doc_id":"23352168","title":"Synaptic vesicles position complexin to block spontaneous fusion.","abstract":"Synapses continually replenish their synaptic vesicle (SV) pools while suppressing spontaneous fusion events, thus maintaining a high dynamic range in response to physiological stimuli. The presynaptic protein complexin can both promote and inhibit fusion through interactions between its α-helical domain and the SNARE complex. In addition, complexin's C-terminal half is required for the inhibition of spontaneous fusion in worm, fly, and mouse, although the molecular mechanism remains unexplained. We show here that complexin's C-terminal domain binds lipids through a novel protein motif, permitting complexin to inhibit spontaneous exocytosis in vivo by targeting complexin to SVs. We propose that the SV pool serves as a platform to sequester and position complexin where it can intercept the rapidly assembling SNAREs and control the rate of spontaneous fusion.","corpus_id":9485215,"score":2},{"doc_id":"23769723","title":"Molecular mechanisms of COMPLEXIN fusion clamp function in synaptic exocytosis revealed in a new Drosophila mutant.","abstract":"The COMPLEXIN (CPX) proteins play a critical role in synaptic vesicle fusion and neurotransmitter release. Previous studies demonstrated that CPX functions in both activation of evoked neurotransmitter release and inhibition/clamping of spontaneous synaptic vesicle fusion. Here we report a new cpx mutant in Drosophila melanogaster, cpx(1257), revealing spatially defined and separable pools of CPX which make distinct contributions to the activation and clamping functions. In cpx(1257), lack of only the last C-terminal amino acid of CPX is predicted to disrupt prenylation and membrane targeting of CPX. Immunocytochemical analysis established localization of wild-type CPX to active zone (AZ) regions containing neurotransmitter release sites as well as broader presynaptic membrane compartments including synaptic vesicles. Parallel biochemical studies confirmed CPX membrane association and demonstrated robust binding interactions of CPX with all three SNAREs. This is in contrast to the cpx(1257) mutant, in which AZ localization of CPX persists but general membrane localization and, surprisingly, the bulk of CPX-SNARE protein interactions are abolished. Furthermore, electrophysiological analysis of neuromuscular synapses revealed interesting differences between cpx(1257) and a cpx null mutant. The cpx null exhibited a marked decrease in the EPSC amplitude, slowed EPSC rise and decay times and an increased mEPSC frequency with respect to wild-type. In contrast, cpx(1257) exhibited a wild-type EPSC with an increased mEPSC frequency and thus a selective failure to clamp spontaneous release. These results indicate that spatially distinct and separable interactions of CPX with presynaptic membranes and SNARE proteins mediate separable activation and clamping functions of CPX in neurotransmitter release.","corpus_id":24750418,"score":2},{"doc_id":"23845424","title":"Subtle Interplay between synaptotagmin and complexin binding to the SNARE complex.","abstract":"Ca²⁺-triggered neurotransmitter release depends on the formation of SNARE complexes that bring the synaptic vesicle and plasma membranes together, on the Ca²⁺ sensor synaptotagmin-1 and on complexins, which play active and inhibitory roles. Release of the complexin inhibitory activity by binding of synaptotagmin-1 to the SNARE complex, causing complexin displacement, was proposed to trigger exocytosis. However, the validity of this model was questioned based on the observation of simultaneous binding of complexin-I and a fragment containing the synaptotagmin-1 C2 domains (C2AB) to membrane-anchored SNARE complex. Using diverse biophysical techniques, here we show that C2AB and complexin-I do not bind to each other but can indeed bind simultaneously to the SNARE complex in solution. Hence, the SNARE complex contains separate binding sites for both proteins. However, total internal reflection fluorescence microscopy experiments show that C2AB can displace a complexin-I fragment containing its central SNARE-binding helix and an inhibitory helix (Cpx26-83) from membrane-anchored SNARE complex under equilibrium conditions. Interestingly, full-length complexin-I binds more tightly to membrane-anchored SNARE complex than Cpx26-83, and it is not displaced by C2AB. These results show that interactions of N- and/or C-terminal sequences of complexin-I with the SNARE complex and/or phospholipids increase the affinity of complexin-I for the SNARE complex, hindering dissociation induced by C2AB. We propose a model whereby binding of synaptotagmin-1 to the SNARE complex directly or indirectly causes a rearrangement of the complexin-I inhibitory helix without inducing complexin-I dissociation, thus relieving the inhibitory activity and enabling cooperation between synaptotagmin-1 and complexin-I in triggering release.","corpus_id":30493743,"score":2},{"doc_id":"25122624","title":"Complexin inhibits spontaneous release and synchronizes Ca2+-triggered synaptic vesicle fusion by distinct mechanisms.","abstract":"Previously we showed that fast Ca(2+)-triggered vesicle fusion with reconstituted neuronal SNAREs and synaptotagmin-1 begins from an initial hemifusion-free membrane point contact, rather than a hemifusion diaphragm, using a single vesicle-vesicle lipid/content mixing assay (Diao et al., 2012). When complexin-1 was included, a more pronounced Ca(2+)-triggered fusion burst was observed, effectively synchronizing the process. Here we show that complexin-1 also reduces spontaneous fusion in the same assay. Moreover, distinct effects of several complexin-1 truncation mutants on spontaneous and Ca(2+)-triggered fusion closely mimic those observed in neuronal cultures. The very N-terminal domain is essential for synchronization of Ca(2+)-triggered fusion, but not for suppression of spontaneous fusion, whereas the opposite is true for the C-terminal domain. By systematically varying the complexin-1 concentration, we observed differences in titration behavior for spontaneous and Ca(2+)-triggered fusion. Taken together, complexin-1 utilizes distinct mechanisms for synchronization of Ca(2+)-triggered fusion and inhibition of spontaneous fusion.","corpus_id":584630,"score":2},{"doc_id":"25229806","title":"Membrane curvature sensing by the C-terminal domain of complexin.","abstract":"Complexin functions at presynaptic nerve terminals to inhibit spontaneous SNARE-mediated synaptic vesicle (SV) exocytosis, while enhancing stimulated neurotransmitter release. The C-terminal domain (CTD) of complexin is essential for its inhibitory function and has been implicated in localizing complexin to SVs via direct membrane interactions. Here we show that complexin's CTD is highly sensitive to membrane curvature, which it senses via tandem motifs, a C-terminal motif containing a mix of bulky hydrophobic and positively charged residues, and an adjacent amphipathic region that can bind membranes in either a disordered or a helical conformation. Helix formation requires membrane packing defects found on highly curved membrane surfaces. Mutations that disrupt helix formation without disrupting membrane binding compromise complexin's inhibitory function in vivo. Thus, this membrane curvature-dependent conformational transition, combined with curvature-sensitive binding by the adjacent C-terminal motif, constitute a novel mechanism for activating complexin's inhibitory function on the surface of SVs.","corpus_id":12334151,"score":2},{"doc_id":"25524119","title":"The mechanisms and functions of spontaneous neurotransmitter release.","abstract":"Fast synaptic communication in the brain requires synchronous vesicle fusion that is evoked by action potential-induced Ca(2+) influx. However, synaptic terminals also release neurotransmitters by spontaneous vesicle fusion, which is independent of presynaptic action potentials. A functional role for spontaneous neurotransmitter release events in the regulation of synaptic plasticity and homeostasis, as well as the regulation of certain behaviours, has been reported. In addition, there is evidence that the presynaptic mechanisms underlying spontaneous release of neurotransmitters and their postsynaptic targets are segregated from those of evoked neurotransmission. These findings challenge current assumptions about neuronal signalling and neurotransmission, as they indicate that spontaneous neurotransmission has an autonomous role in interneuronal communication that is distinct from that of evoked release.","corpus_id":26958246,"score":2},{"doc_id":"26806630","title":"Should I stop or should I go? The role of complexin in neurotransmitter release.","abstract":"When it comes to fusion with the neuronal cell membrane, does a synaptic vesicle have a choice whether to stop or to go? Recent work suggests that complexin, a tiny protein found within the synaptic terminal, contributes to the mechanism through which this choice is made. How complexin plays this consulting part and which synaptic vesicle proteins it interacts with remain open questions. Indeed, studies in mice and flies have led to the proposal of different models of complexin function. We suggest that understanding the modular nature of complexin will help us to unpick its role in synaptic vesicle release.","corpus_id":8974313,"score":2},{"doc_id":"27253060","title":"Complexin induces a conformational change at the membrane-proximal C-terminal end of the SNARE complex.","abstract":"Complexin regulates spontaneous and activates Ca(2+)-triggered neurotransmitter release, yet the molecular mechanisms are still unclear. Here we performed single molecule fluorescence resonance energy transfer experiments and uncovered two conformations of complexin-1 bound to the ternary SNARE complex. In the cis conformation, complexin-1 induces a conformational change at the membrane-proximal C-terminal end of the ternary SNARE complex that specifically depends on the N-terminal, accessory, and central domains of complexin-1. The complexin-1 induced conformation of the ternary SNARE complex may be related to a conformation that is juxtaposing the synaptic vesicle and plasma membranes. In the trans conformation, complexin-1 can simultaneously interact with a ternary SNARE complex via the central domain and a binary SNARE complex consisting of syntaxin-1A and SNAP-25A via the accessory domain. The cis conformation may be involved in activation of synchronous neurotransmitter release, whereas both conformations may be involved in regulating spontaneous release.","corpus_id":6244010,"score":2},{"doc_id":"27444020","title":"N-terminal domain of complexin independently activates calcium-triggered fusion.","abstract":"Complexin activates Ca(2+)-triggered neurotransmitter release and regulates spontaneous release in the presynaptic terminal by cooperating with the neuronal soluble N-ethylmaleimide-sensitive factor attachment protein receptors (SNAREs) and the Ca(2+)-sensor synaptotagmin. The N-terminal domain of complexin is important for activation, but its molecular mechanism is still poorly understood. Here, we observed that a split pair of N-terminal and central domain fragments of complexin is sufficient to activate Ca(2+)-triggered release using a reconstituted single-vesicle fusion assay, suggesting that the N-terminal domain acts as an independent module within the synaptic fusion machinery. The N-terminal domain can also interact independently with membranes, which is enhanced by a cooperative interaction with the neuronal SNARE complex. We show by mutagenesis that membrane binding of the N-terminal domain is essential for activation of Ca(2+)-triggered fusion. Consistent with the membrane-binding property, the N-terminal domain can be substituted by the influenza virus hemagglutinin fusion peptide, and this chimera also activates Ca(2+)-triggered fusion. Membrane binding of the N-terminal domain of complexin therefore cooperates with the other fusogenic elements of the synaptic fusion machinery during Ca(2+)-triggered release.","corpus_id":5847780,"score":2},{"doc_id":"28456331","title":"Complexin Binding to Membranes and Acceptor t-SNAREs Explains Its Clamping Effect on Fusion.","abstract":"Complexin-1 is a SNARE effector protein that decreases spontaneous neurotransmitter release and enhances evoked release. Complexin binds to the fully assembled four-helical neuronal SNARE core complex as revealed in competing molecular models derived from x-ray crystallography. Presently, it is unclear how complexin binding to the postfusion complex accounts for its effects upon spontaneous and evoked release in vivo. Using a combination of spectroscopic and imaging methods, we characterize in molecular detail how complexin binds to the 1:1 plasma membrane t-SNARE complex of syntaxin-1a and SNAP-25 while simultaneously binding the lipid bilayer at both its N- and C-terminal ends. These interactions are cooperative, and binding to the prefusion acceptor t-SNARE complex is stronger than to the postfusion core complex. This complexin interaction reduces the affinity of synaptobrevin-2 for the 1:1 complex, thereby retarding SNARE assembly and vesicle docking in vitro. The results provide the basis for molecular models that account for the observed clamping effect of complexin beginning with the acceptor t-SNARE complex and the subsequent activation of the clamped complex by Ca(2+) and synaptotagmin.","corpus_id":32826604,"score":2},{"doc_id":"28596722","title":"Unique Structural Features of Membrane-Bound C-Terminal Domain Motifs Modulate Complexin Inhibitory Function.","abstract":"Complexin is a small soluble presynaptic protein that interacts with neuronal SNARE proteins in order to regulate synaptic vesicle exocytosis. While the SNARE-binding central helix of complexin is required for both the inhibition of spontaneous fusion and the facilitation of synchronous fusion, the disordered C-terminal domain (CTD) of complexin is specifically required for its inhibitory function. The CTD of worm complexin binds to membranes via two distinct motifs, one of which undergoes a membrane curvature dependent structural transition that is required for efficient inhibition of neurotransmitter release, but the conformations of the membrane-bound motifs remain poorly characterized. Visualizing these conformations is required to clarify the mechanisms by which complexin membrane interactions regulate its function. Here, we employ optical and magnetic resonance spectroscopy to precisely define the boundaries of the two CTD membrane-binding motifs and to characterize their conformations. We show that the curvature dependent amphipathic helical motif features an irregular element of helical structure, likely a pi-bulge, and that this feature is important for complexin inhibitory function in vivo.","corpus_id":31171403,"score":2},{"doc_id":"28603484","title":"Evolutionary Divergence of the C-terminal Domain of Complexin Accounts for Functional Disparities between Vertebrate and Invertebrate Complexins.","abstract":"Complexin is a critical presynaptic protein that regulates both spontaneous and calcium-triggered neurotransmitter release in all synapses. Although the SNARE-binding central helix of complexin is highly conserved and required for all known complexin functions, the remainder of the protein has profoundly diverged across the animal kingdom. Striking disparities in complexin inhibitory activity are observed between vertebrate and invertebrate complexins but little is known about the source of these differences or their relevance to the underlying mechanism of complexin regulation. We found that mouse complexin 1 (mCpx1) failed to inhibit neurotransmitter secretion in Caenorhabditis elegans neuromuscular junctions lacking the worm complexin 1 (CPX-1). This lack of inhibition stemmed from differences in the C-terminal domain (CTD) of mCpx1. Previous studies revealed that the CTD selectively binds to highly curved membranes and directs complexin to synaptic vesicles. Although mouse and worm complexin have similar lipid binding affinity, their last few amino acids differ in both hydrophobicity and in lipid binding conformation, and these differences strongly impacted CPX-1 inhibitory function. Moreover, function was not maintained if a critical amphipathic helix in the worm CPX-1 CTD was replaced with the corresponding mCpx1 amphipathic helix. Invertebrate complexins generally shared more C-terminal similarity with vertebrate complexin 3 and 4 isoforms, and the amphipathic region of mouse complexin 3 significantly restored inhibitory function to worm CPX-1. We hypothesize that the CTD of complexin is essential in conferring an inhibitory function to complexin, and that this inhibitory activity has been attenuated in the vertebrate complexin 1 and 2 isoforms. Thus, evolutionary changes in the complexin CTD differentially shape its synaptic role across phylogeny.","corpus_id":10980323,"score":2},{"doc_id":"18499660","title":"Distinct domains of complexins bind SNARE complexes and clamp fusion in vitro.","abstract":"In regulated exocytosis, the core membrane fusion machinery proteins, the SNARE proteins, are assisted by a group of regulatory factors in order to couple membrane fusion to an increase of intracellular calcium ion (Ca(2+)) concentration. Complexin-I and synaptotagmin-I have been shown to be key elements for this tightly regulated process. Many studies suggest that complexin-I can arrest the fusion reaction and that synaptotagmin-I can release the complexin-I blockage in a calcium-dependent manner. Although the actual molecular mechanism by which they exert their function is still unknown, recent in vivo experiments postulate that domains of complexin-I produce different effects on neurotransmitter release. Herein, by using an in vitro flipped SNARE cell fusion assay, we have identified and characterized the minimal functional domains of complexin-I necessary to couple calcium and synaptotagmin-I to membrane fusion. Moreover, we provide evidence that other isoforms of complexin, complexin-II, -III, and -IV, can also be functionally coupled to synaptotagmin-I and calcium. These correspond closely to results from in vivo experiments, providing further validation of the physiological relevance of the flipped SNARE system.","corpus_id":22237326,"score":1},{"doc_id":"18503508","title":"Glucose/oxygen deprivation and reperfusion upregulate SNAREs and complexin in organotypic hippocampal slice cultures.","abstract":"Brain ischemia activates Ca(2+)-dependent synaptic vesicle exocytosis. The synaptosomal-associated protein 25 (SNAP-25) and syntaxin proteins, located on presynaptic terminals, are components of the SNARE (soluble N-ethylmaleimide-sensitive factor attachment protein receptor) complex and play a key role in regulating exocytosis. Changes in the expression of SNAREs could affect SNARE complex formation, fusion of vesicles with the presynaptic membrane, and release of neurotransmitters through exocytosis. To investigate the relationship of glucose/oxygen deprivation (GOD)/reperfusion-induced neuronal damage and alteration of presynaptic function, we examined the expression of SNAREs and complexin during GOD and reperfusion using organotypic hippocampal slice cultures. Microtubule-associated protein 2 (MAP-2) staining and transmission electron microscopy showed that neuronal damage increased in a time-dependent manner and both types of neuronal death can occur at different times during GOD and reperfusion. The immunoreactivity of SNAREs such as SNAP-25, vesicle-associated membrane protein and syntaxin and complexin increased in pyramidal cell bodies in the CA1 and CA3 areas in a time-dependent manner following reperfusion. Our data suggest that alteration of presynaptic function may play a partial role in delayed neuronal death during GOD and reperfusion in organotypic hippocampal slice cultures.","corpus_id":30447775,"score":1},{"doc_id":"18552825","title":"Complexin and Ca2+ stimulate SNARE-mediated membrane fusion.","abstract":"Ca(2+)-triggered, synchronized synaptic vesicle fusion underlies interneuronal communication. Complexin is a major binding partner of the SNARE complex, the core fusion machinery at the presynapse. The physiological data on complexin, however, have been at odds with each other, making delineation of its molecular function difficult. Here we report direct observation of two-faceted functions of complexin using the single-vesicle fluorescence fusion assay and EPR. We show that complexin I has two opposing effects on trans-SNARE assembly: inhibition of SNARE complex formation and stabilization of assembled SNARE complexes. Of note, SNARE-mediated fusion is markedly stimulated by complexin, and it is further accelerated by two orders of magnitude in response to an externally applied Ca(2+) wave. We suggest that SNARE complexes, complexins and phospholipids collectively form a complex substrate for Ca(2+) and Ca(2+)-sensing fusion effectors in neurotransmitter release.","corpus_id":17292787,"score":1},{"doc_id":"19128031","title":"Concurrent binding of complexin and synaptotagmin to liposome-embedded SNARE complexes.","abstract":"Synaptotagmin and complexin regulate SNARE-mediated synaptic vesicle exocytosis. It has been proposed that complexin clamps membrane fusion and that Ca(2+)-synaptotagmin displaces complexin from SNARE complexes to relieve this clamping activity. Using a reconstituted system, we demonstrate that complexin and synaptotagmin simultaneously bind to neuronal SNARE complexes and that both apo-synaptotagmin and complexin inhibit SNARE-mediated membrane fusion. Moreover, the clamping ability of apo-synaptotagmin occluded the clamping activity of complexin until the arrival of a Ca(2+) trigger, at which point synaptotagmin accelerated fusion while high concentrations of complexin inhibited fusion. Thus, the inhibitory patterns of synaptotagmin and complexin are different, suggesting that SNAREs assemble into distinct states along the fusion pathway. These data also suggest that during synaptotagmin-regulated vesicle-vesicle fusion, complexin does not function as a fusion clamp that is relieved by Ca(2+)-synaptotagmin.","corpus_id":15874033,"score":1},{"doc_id":"19164751","title":"Complexin controls the force transfer from SNARE complexes to membranes in fusion.","abstract":"Trans-SNAP receptor (SNARE, where SNAP is defined as soluble NSF attachment protein, and NSF is defined as N-ethylmaleimide-sensitive factor) complexes catalyze synaptic vesicle fusion and bind complexin, but the function of complexin binding to SNARE complexes remains unclear. Here we show that in neuronal synapses, complexin simultaneously suppressed spontaneous fusion and activated fast calcium ion-evoked fusion. The dual function of complexin required SNARE binding and also involved distinct amino-terminal sequences of complexin that localize to the point where trans-SNARE complexes insert into the fusing membranes, suggesting that complexin controls the force that trans-SNARE complexes apply onto the fusing membranes. Consistent with this hypothesis, a mutation in the membrane insertion sequence of the v-SNARE synaptobrevin/vesicle-associated membrane protein (VAMP) phenocopied the complexin loss-of-function state without impairing complexin binding to SNARE complexes. Thus, complexin probably activates and clamps the force transfer from assembled trans-SNARE complexes onto fusing membranes.","corpus_id":2220205,"score":1},{"doc_id":"19914185","title":"Tilting the balance between facilitatory and inhibitory functions of mammalian and Drosophila Complexins orchestrates synaptic vesicle exocytosis.","abstract":"SNARE-mediated synaptic exocytosis is orchestrated by facilitatory and inhibitory mechanisms. Genetic ablations of Complexins, a family of SNARE-complex-binding proteins, in mice and Drosophila cause apparently opposite effects on neurotransmitter release, leading to contradictory hypotheses of Complexin function. Reconstitution experiments with different fusion assays and Complexins also yield conflicting results. We therefore performed cross-species rescue experiments to compare the functions of murine and Drosophila Complexins in both mouse and fly synapses. We found that murine and Drosophila Complexins employ conserved mechanisms to regulate exocytosis despite their strikingly different overall effects on neurotransmitter release. Both Complexins contain distinct domains that facilitate or inhibit synaptic vesicle fusion, and the strength of each facilitatory or inhibitory function differs significantly between murine and Drosophila Complexins. Our results show that a relative shift in the balance of facilitatory and inhibitory functions results in differential regulation of neurotransmitter release by murine and Drosophila Complexins in vivo, reconciling previous incompatible findings.","corpus_id":8356420,"score":1},{"doc_id":"20026076","title":"Accessory alpha-helix of complexin I can displace VAMP2 locally in the complexin-SNARE quaternary complex.","abstract":"The calcium-triggered neurotransmitter release requires three SNARE (soluble N-ethylmaleimide-sensitive factor attachment protein receptor) proteins: synaptobrevin 2 (or vesicle-associated membrane protein 2) on the synaptic vesicle and syntaxin 1 and SNAP-25 (synaptosome-associated protein of 25 kDa) at the presynaptic plasma membrane. This minimal fusion machinery is believed to drive fusion of the vesicle to the presynaptic membrane. Complexin, also known as synaphin, is a neuronal cytosolic protein that acts as a major regulator of synaptic vesicle exocytosis. Stimulatory and inhibitory effects of complexin have both been reported, suggesting the duality of its function. To shed light on the molecular basis of the complexin's dual function, we have performed an EPR investigation of the complexin-SNARE quaternary complex. We found that the accessory alpha-helix (amino acids 27-48) by itself has the capacity to replace the C-terminus of the SNARE motif of vesicle-associated membrane protein 2 in the four-helix bundle and makes the SNARE complex weaker when the N-terminal region of complexin I (amino acids 1-26) is removed. However, the accessory alpha-helix remains detached from the SNARE core when the N-terminal region of complexin I is present. Thus, our data show the possibility that the balance between the activities of the accessory alpha-helix and the N-terminal domain might determine the final outcome of the complexin function, either stimulatory or inhibitory.","corpus_id":22886543,"score":1},{"doc_id":"20108313","title":"Structural studies of SNARE complex and its interaction with complexin by molecular dynamics simulation.","abstract":"Since neurotransmitter releasing into the synaptic space delivers electrical signals from presynaptic neural cell to the postsynaptic cell, neurotransmitter secretion must be much orchestrated. Crowded intracellular vesicles involving neurotransmitters present a question of the how secretory vesicles fuse onto the plasma membrane in a fast synchronized fashion. Complexin is one of the most experimentally studied proteins that regulate assembly of fusogenic four-helix SNARE complex to synchronized neurotransmitter secretion. We used MD simulation to investigate the interaction of complexin with the neural SNARE complex in detail. Our results show that the SNARE complex interacts with the complexin central helix by forming salt bridges and hydrogen bonds. Complexin also can interact with the Q-SNARE complex instead of synaptobrevin to decrease the Q-SNARE flexibility. The complexin alpha-accessory helix and the C-terminal region of synaptobrevin can interact with the same region of syntaxin. Although the alpha-accessory helix aids the tight binding of the central helix to the SNARE complex, its proximity with synaptobrevin causes the destabilization of syntaxin and Sn1 helices. This study suggests that the alpha-accessory helix of complexin can be an inhibiting factor for membrane fusion by competing with synaptobrevin for binding to the Q-SNARE complex.","corpus_id":28179005,"score":1},{"doc_id":"20400951","title":"Binding of the complexin N terminus to the SNARE complex potentiates synaptic-vesicle fusogenicity.","abstract":"Complexins facilitate and inhibit neurotransmitter release through distinct domains, and their function was proposed to be coupled to the Ca(2+) sensor synaptotagmin-1 (Syt1). However, the mechanisms underlying complexin function remain unclear. We now uncover an interaction between the complexin N terminus and the SNARE complex C terminus, and we show that disrupting this interaction abolishes the facilitatory function of complexins in mouse neurons. Analyses of hypertonically induced exocytosis show that complexins enhance synaptic-vesicle fusogenicity. Genetic experiments crossing complexin- and Syt1-null mice indicate a functional interaction between these proteins but also show that complexins can promote Ca(2+)-triggered release in the absence of Syt1. We propose that the complexin N terminus stabilizes the SNARE complex C terminus and/or helps release the inhibitory function of complexins, thereby activating the fusion machinery in a manner that may cooperate with Syt1 but does not require Syt1.","corpus_id":37974755,"score":1},{"doc_id":"20678575","title":"Comparative analysis of Drosophila and mammalian complexins as fusion clamps and facilitators of neurotransmitter release.","abstract":"The SNARE-binding protein complexin (Cpx) has been demonstrated to regulate synaptic vesicle fusion. Previous studies are consistent with Cpx functioning either as a synaptic vesicle fusion clamp to prevent premature exocytosis, or as a facilitator to directly stimulate release. Here we examined conserved roles of invertebrate and mammalian Cpx isoforms in the regulation of neurotransmitter release using the Drosophila neuromuscular junction as a model synapse. We find that SNARE binding by Cpx is required for its role as a fusion clamp. All four mammalian Cpx proteins (mCpx), which have been demonstrated to facilitate release, also function as fusion clamps when expressed in Drosophila cpx null mutants, though their clamping abilities vary between isoforms. Moreover, expression of mCpx I, II or III isoforms dramatically enhance evoked release compared to mCpx IV or Drosophila Cpx. Differences in the clamping and facilitating properties of complexin isoforms can be partially attributed to differences in the C-terminal membrane tethering domain. Our findings indicate that the function of complexins as fusion clamps and facilitators of fusion are conserved across evolution, and that these roles are genetically separable within an isoform and across different isoforms.","corpus_id":3190755,"score":1},{"doc_id":"21144993","title":"Complexin: does it deserve its name?","abstract":"Knockout and other perturbations of complexins have provided important insights and elicited controversies about their role in neurotransmitter release. New work by Yang et al. in this issue of Neuron adds important detail and complexity to existing concepts-particularly on the nature of a Ca(2+)-dependent complexin-synaptotagmin switch for the triggering of exocytosis. But it also provokes thoughts about alternative interpretations, which might result in a simpler model of complexin function.","corpus_id":8996828,"score":1},{"doc_id":"21215634","title":"Complexin has opposite effects on two modes of synaptic vesicle fusion.","abstract":"BACKGROUND: Synaptic transmission can occur in a binary or graded fashion, depending on whether transmitter release is triggered by action potentials or by gradual changes in membrane potential. Molecular differences of these two types of fusion events and their differential regulation in a physiological context have yet to be addressed. Complexin is a conserved SNARE-binding protein that has been proposed to regulate both spontaneous and stimulus-evoked synaptic vesicle (SV) fusion. RESULTS: Here we examine complexin function at a graded synapse in C. elegans. Null complexin (cpx-1) mutants are viable, although nervous system function is significantly impaired. Loss of CPX-1 results in a 3-fold increase in the rate of tonic synaptic transmission at the neuromuscular junction, whereas stimulus-evoked SV fusion is decreased 10-fold. A truncated CPX-1 missing its C-terminal domain can rescue stimulus-evoked synaptic vesicle exocytosis but fails to suppress tonic activity, demonstrating that these two modes of exocytosis can be distinguished at the molecular level. A CPX-1 variant with impaired SNARE binding also rescues evoked, but not tonic, neurotransmitter release. Finally, tonic, but not evoked, release can be rescued in a syntaxin point mutant by removing CPX-1. Rescue of either form of exocytosis partially restores locomotory behavior, indicating that both types of synaptic transmission are relevant. CONCLUSION: These observations suggest a dual role for CPX-1: suppressing SV exocytosis, driven by low levels of endogenous neural activity, while promoting synchronous fusion of SVs driven by a depolarizing stimulus. Thus, patterns of synaptic activity regulate complexin's inhibitory and permissive roles at a graded synapse.","corpus_id":14249171,"score":1},{"doc_id":"23536098","title":"Simultaneous monitoring of presynaptic transmitter release and postsynaptic receptor trafficking reveals an enhancement of presynaptic activity in metabotropic glutamate receptor-mediated long-term depression.","abstract":"Although the contribution of postsynaptic mechanisms to long-term synaptic plasticity has been studied extensively, understanding the contribution of presynaptic modifications to this process lags behind, primarily because of a lack of techniques with which to directly and quantifiably measure neurotransmitter release from synaptic terminals. Here, we developed a method to measure presynaptic activity through the biotinylation of vesicular transporters in vesicles fused with presynaptic membranes during neurotransmitter release. This method allowed us for the first time to selectively quantify the spontaneous or evoked release of glutamate or GABA at their respective synapses. Using this method to investigate presynaptic changes during the expression of group I metabotropic glutamate receptor (mGluR1/5)-mediated long-term depression (LTD) in cultured rat hippocampal neurons, we discovered that this form of LTD was associated with increased presynaptic release of glutamate, despite reduced miniature EPSCs measured with whole-cell recording. Moreover, we found that specific blockade of AMPA receptor (AMPAR) endocytosis with a membrane-permeable GluR2-derived peptide not only prevented the expression of LTD but also eliminated LTD-associated increase in presynaptic release. Thus, our work not only demonstrates that mGluR1/5-mediated LTD is associated with increased endocytosis of postsynaptic AMPARs but also reveals an unexpected homeostatic/compensatory increase in presynaptic release. In addition, this study indicates that biotinylation of vesicular transporters in live cultured neurons is a valuable tool for studying presynaptic function.","corpus_id":14958868,"score":1},{"doc_id":"23658160","title":"Stabilization of spontaneous neurotransmitter release at ribbon synapses by ribbon-specific subtypes of complexin.","abstract":"Ribbon synapses of tonically releasing sensory neurons must provide a large pool of releasable vesicles for sustained release, while minimizing spontaneous release in the absence of stimulation. Complexins are presynaptic proteins that may accomplish this dual task at conventional synapses by interacting with the molecular machinery of synaptic vesicle fusion at the active zone to retard spontaneous vesicle exocytosis yet facilitate release evoked by depolarization. However, ribbon synapses of photoreceptor cells and bipolar neurons in the retina express distinct complexin subtypes, perhaps reflecting the special requirements of these synapses for tonic release. To investigate the role of ribbon-specific complexins in transmitter release, we combined presynaptic voltage clamp, fluorescence imaging, electron microscopy, and behavioral assays of photoreceptive function in zebrafish. Acute interference with complexin function using a peptide derived from the SNARE-binding domain increased spontaneous synaptic vesicle fusion at ribbon synapses of retinal bipolar neurons without affecting release triggered by depolarization. Knockdown of complexin by injection of an antisense morpholino into zebrafish embryos prevented photoreceptor-driven migration of pigment in skin melanophores and caused the pigment distribution to remain in the dark-adapted state even when embryos were exposed to light. This suggests that loss of complexin function elevated spontaneous release in illuminated photoreceptors sufficiently to mimic the higher release rate normally associated with darkness, thus interfering with visual signaling. We conclude that visual system-specific complexins are required for proper illumination-dependent modulation of the rate of neurotransmitter release at visual system ribbon synapses.","corpus_id":17949179,"score":1},{"doc_id":"24083833","title":"Complexin-1 enhances the on-rate of vesicle docking via simultaneous SNARE and membrane interactions.","abstract":"In synaptic terminals, complexin is thought to have inhibitory and activating roles for spontaneous \"mini\" release and evoked synchronized neurotransmitter release, respectively. We used single vesicle-vesicle microscopy imaging to study the effect of complexin-1 on the on-rate of docking between vesicles that mimic synaptic vesicles and the plasma membrane. We found that complexin-1 enhances the on-rate of docking of synaptic vesicle mimics containing full-length synaptobrevin-2 and full-length synaptotagmin-1 to plasma membrane-mimicking vesicles containing full-length syntaxin-1A and SNAP-25A. This effect requires the C-terminal domain of complexin-1, which binds to the membrane, the presence of PS in the membrane, and the core region of complexin-1, which binds to the SNARE complex.","corpus_id":16318242,"score":1},{"doc_id":"24297916","title":"Deconstructing complexin function in activating and clamping Ca2+-triggered exocytosis by comparing knockout and knockdown phenotypes.","abstract":"Complexin, a presynaptic protein that avidly binds to assembled SNARE complexes, is widely acknowledged to activate Ca(2+)-triggered exocytosis. In addition, studies of invertebrate complexin mutants and of mouse neurons with a double knockdown (DKD) of complexin-1 and -2 suggested that complexin maintains the readily releasable pool (RRP) of vesicles and clamps spontaneous exocytosis. In contrast, studies of mouse neurons with a double knockout (DKO) of complexin-1 and -2, largely carried out in hippocampal autapses, did not detect changes in the RRP size or in spontaneous exocytosis. To clarify complexin function, we here directly compared in two different preparations, cultured cortical and olfactory bulb neurons, the phenotypes of complexin DKD and DKO neurons. We find that complexin-deficient DKD and DKO neurons invariably exhibit a ~50% decrease in vesicle priming. Moreover, the DKD consistently increased spontaneous exocytosis, but the DKO did so in cortical but not olfactory bulb neurons. Furthermore, the complexin DKD but not the complexin DKO caused a compensatory increase in complexin-3 and -4 mRNA levels; overexpression of complexin-3 but not complexin-1 increased spontaneous exocytosis. Complexin-3 but not complexin-1 contains a C-terminal lipid anchor attaching it to the plasma membrane; addition of a similar lipid anchor to complexin-1 converted complexin-1 from a clamp into an activator of spontaneous exocytosis. Viewed together, our data suggest that complexin generally functions in priming and Ca(2+) triggering of exocytosis, and additionally contributes to the control of spontaneous exocytosis dependent on the developmental history of a neuron and on the subcellular localization of the complexin.","corpus_id":467451,"score":1},{"doc_id":"24493260","title":"SNARE and regulatory proteins induce local membrane protrusions to prime docked vesicles for fast calcium-triggered fusion.","abstract":"Synaptic vesicles fuse with the plasma membrane in response to Ca(2+) influx, thereby releasing neurotransmitters into the synaptic cleft. The protein machinery that mediates this process, consisting of soluble N-ethylmaleimide-sensitive factor attachment protein receptors (SNAREs) and regulatory proteins, is well known, but the mechanisms by which these proteins prime synaptic membranes for fusion are debated. In this study, we applied large-scale, automated cryo-electron tomography to image an in vitro system that reconstitutes synaptic fusion. Our findings suggest that upon docking and priming of vesicles for fast Ca(2)(+)-triggered fusion, SNARE proteins act in concert with regulatory proteins to induce a local protrusion in the plasma membrane, directed towards the primed vesicle. The SNAREs and regulatory proteins thereby stabilize the membrane in a high-energy state from which the activation energy for fusion is profoundly reduced, allowing synchronous and instantaneous fusion upon release of the complexin clamp.","corpus_id":16062643,"score":1},{"doc_id":"24842998","title":"Re-examining how complexin inhibits neurotransmitter release.","abstract":"Complexins play activating and inhibitory functions in neurotransmitter release. The complexin accessory helix inhibits release and was proposed to insert into SNARE complexes to prevent their full assembly. This model was supported by 'superclamp' and 'poor-clamp' mutations that enhanced or decreased the complexin-I inhibitory activity in cell-cell fusion assays, and by the crystal structure of a superclamp mutant bound to a synaptobrevin-truncated SNARE complex. NMR studies now show that the complexin-I accessory helix does not insert into synaptobrevin-truncated SNARE complexes in solution, and electrophysiological data reveal that superclamp mutants have slightly stimulatory or no effects on neurotransmitter release, whereas a poor-clamp mutant inhibits release. Importantly, increasing or decreasing the negative charge of the complexin-I accessory helix inhibits or stimulates release, respectively. These results suggest a new model whereby the complexin accessory helix inhibits release through electrostatic (and perhaps steric) repulsion enabled by its location between the vesicle and plasma membranes. DOI: http://dx.doi.org/10.7554/eLife.02391.001.","corpus_id":16428795,"score":1},{"doc_id":"25716318","title":"Munc18a does not alter fusion rates mediated by neuronal SNAREs, synaptotagmin, and complexin.","abstract":"Sec1/Munc18 (SM) proteins are essential for membrane trafficking, but their molecular mechanism remains unclear. Using a single vesicle-vesicle content-mixing assay with reconstituted neuronal SNAREs, synaptotagmin-1, and complexin-1, we show that the neuronal SM protein Munc18a/nSec1 has no effect on the intrinsic kinetics of both spontaneous fusion and Ca(2+)-triggered fusion between vesicles that mimic synaptic vesicles and the plasma membrane. However, wild type Munc18a reduced vesicle association ∼50% when the vesicles bearing the t-SNAREs syntaxin-1A and SNAP-25 were preincubated with Munc18 for 30 min. Single molecule experiments with labeled SNAP-25 indicate that the reduction of vesicle association is a consequence of sequestration of syntaxin-1A by Munc18a and subsequent release of SNAP-25 (i.e. Munc18a captures syntaxin-1A via its high affinity interaction). Moreover, a phosphorylation mimic mutant of Munc18a with reduced affinity to syntaxin-1A results in less reduction of vesicle association. In summary, Munc18a does not directly affect fusion, although it has an effect on the t-SNARE complex, depending on the presence of other factors and experimental conditions. Our results suggest that Munc18a primarily acts at the prefusion stage.","corpus_id":25210663,"score":1},{"doc_id":"25740533","title":"Functional roles of complexin in neurotransmitter release at ribbon synapses of mouse retinal bipolar neurons.","abstract":"Ribbon synapses of photoreceptor cells and bipolar neurons in the retina signal graded changes in light intensity via sustained release of neurotransmitter. One molecular specialization of retinal ribbon synapses is the expression of complexin protein subtypes Cplx3 and Cplx4, whereas conventional synapses express Cplx1 and Cplx2. Because complexins bind to the molecular machinery for synaptic vesicle fusion (the SNARE complex) and modulate transmitter release at conventional synapses, we examined the roles of ribbon-specific complexin in regulating release at ribbon synapses of ON bipolar neurons from mouse retina. To interfere acutely with the interaction of native complexins with the SNARE complex, a peptide consisting of the highly conserved SNARE-binding domain of Cplx3 was introduced via a whole-cell patch pipette placed directly on the synaptic terminal, and vesicle fusion was monitored using capacitance measurements and FM-dye destaining. The inhibitory peptide, but not control peptides, increased spontaneous synaptic vesicle fusion, partially depleted reserve synaptic vesicles, and reduced fusion triggered by opening voltage-gated calcium channels under voltage clamp, without affecting the number of synaptic vesicles associated with ribbons, as revealed by electron microscopy of recorded terminals. The results are consistent with a dual role for ribbon-specific complexin, acting as a brake on the SNARE complex to prevent spontaneous fusion in the absence of calcium influx, while at the same time facilitating release evoked by depolarization.","corpus_id":14843378,"score":1},{"doc_id":"25809246","title":"Synaptic activity regulates the abundance and binding of complexin.","abstract":"Nervous system function relies on precise chemical communication between neurons at specialized junctions known as synapses. Complexin (CPX) is one of a small number of cytoplasmic proteins that are indispensable in controlling neurotransmitter release through SNARE and synaptic vesicle interactions. However, the mechanisms that recruit and stabilize CPX are poorly understood. The mobility of CPX tagged with photoactivatable green fluorescent protein (pGFP) was quantified in vivo using Caenorhabditis elegans. Although pGFP escaped the synapse within seconds, CPX-pGFP displayed both fast and slow decay components, requiring minutes for complete exchange of the synaptic pool. The longer synaptic residence time of CPX arose from both synaptic vesicle and SNARE interactions, and surprisingly, CPX mobility depended on synaptic activity. Moreover, mouse CPX-GFP reversibly dispersed out of hippocampal presynaptic terminals during stimulation, and blockade of vesicle fusion prevented CPX dispersion. Hence, synaptic CPX can rapidly redistribute and this exchange is influenced by neuronal activity, potentially contributing to use-dependent plasticity.","corpus_id":23658867,"score":1},{"doc_id":"25831964","title":"Re-visiting the trans insertion model for complexin clamping.","abstract":"We have previously proposed that complexin cross-links multiple pre-fusion SNARE complexes via a trans interaction to function as a clamp on SNARE-mediated neurotransmitter release. A recent NMR study was unable to detect the trans clamping interaction of complexin and therefore questioned the previous interpretation of the fluorescence resonance energy transfer and isothermal titration calorimetry data on which the trans clamping model was originally based. Here we present new biochemical data that underscore the validity of our previous interpretation and the continued relevancy of the trans insertion model for complexin clamping.","corpus_id":12502620,"score":1},{"doc_id":"26098518","title":"The Synaptic Vesicle Release Machinery.","abstract":"Extensive research has yielded crucial insights into the mechanism of neurotransmitter release, and working models for the functions of key proteins involved in release. The SNAREs Syntaxin-1, Synaptobrevin, and SNAP-25 play a central role in membrane fusion, forming SNARE complexes that bridge the vesicle and plasma membranes and that are disassembled by NSF-SNAPs. Exocytosis likely starts with Syntaxin-1 folded into a self-inhibited closed conformation that binds to Munc18-1. Munc13s open Syntaxin-1, orchestrating SNARE complex assembly in an NSF-SNAP-resistant manner together with Munc18-1. In the resulting primed state, with partially assembled SNARE complexes, fusion is inhibited by Synaptotagmin-1 and Complexins, which also perform active functions in release. Upon influx of Ca(2+), Synaptotagmin-1 activates fast release, likely by relieving the inhibition caused by Complexins and cooperating with the SNAREs in bringing the membranes together. Although alternative models exist and fundamental questions remain unanswered, a definitive description of the basic release mechanism may be available soon.","corpus_id":43024784,"score":1},{"doc_id":"26245303","title":"Complexins: small but capable.","abstract":"Despite intensive research, it is still unclear how an immediate and profound acceleration of exocytosis is triggered by appropriate Ca(2+)-stimuli in presynaptic terminals. This is due to the fact that the molecular mechanisms of \"docking\" and \"priming\" reactions, which set up secretory vesicles to fuse at millisecond time scale, are extremely hard to study. Yet, driven by a fruitful combination of in vitro and in vivo analyses, our mechanistic understanding of Ca(2+)-triggered vesicle fusion has certainly advanced in the past few years. In this review, we aim to highlight recent progress and emerging views on the molecular mechanisms, by which constitutively forming SNAREpins are organized in functional, tightly regulated units for synchronized release. In particular, we will focus on the role of the small regulatory factor complexin whose function in Ca(2+)-dependent exocytosis has been controversially discussed for more than a decade. Special emphasis will also be laid on the functional relationship of complexin and synaptotagmin, as both proteins possibly act as allies and/or antagonists to govern SNARE-mediated exocytosis.","corpus_id":2990515,"score":1},{"doc_id":"26338476","title":"Evolutionary conservation of complexins: from choanoflagellates to mice.","abstract":"Complexins are synaptic SNARE complex-binding proteins that cooperate with synaptotagmins in activating Ca(2+)-stimulated, synaptotagmin-dependent synaptic vesicle exocytosis and in clamping spontaneous, synaptotagmin-independent synaptic vesicle exocytosis. Here, we show that complexin sequences are conserved in some non-metazoan unicellular organisms and in all metazoans, suggesting that complexins are a universal feature of metazoans that predate metazoan evolution. We show that complexin from Nematostella vectensis, a cnidarian sea anemone far separated from mammals in metazoan evolution, functionally replaces mouse complexins in activating Ca(2+)-triggered exocytosis, but is unable to clamp spontaneous exocytosis. Thus, the activating function of complexins is likely conserved throughout metazoan evolution.","corpus_id":12939627,"score":1},{"doc_id":"26590346","title":"Phosphorylation of Complexin by PKA Regulates Activity-Dependent Spontaneous Neurotransmitter Release and Structural Synaptic Plasticity.","abstract":"Synaptic plasticity is a fundamental feature of the nervous system that allows adaptation to changing behavioral environments. Most studies of synaptic plasticity have examined the regulated trafficking of postsynaptic glutamate receptors that generates alterations in synaptic transmission. Whether and how changes in the presynaptic release machinery contribute to neuronal plasticity is less clear. The SNARE complex mediates neurotransmitter release in response to presynaptic Ca(2+) entry. Here we show that the SNARE fusion clamp Complexin undergoes activity-dependent phosphorylation that alters the basic properties of neurotransmission in Drosophila. Retrograde signaling following stimulation activates PKA-dependent phosphorylation of the Complexin C terminus that selectively and transiently enhances spontaneous release. Enhanced spontaneous release is required for activity-dependent synaptic growth. These data indicate that SNARE-dependent fusion mechanisms can be regulated in an activity-dependent manner and highlight the key role of spontaneous neurotransmitter release as a mediator of functional and structural plasticity.","corpus_id":11327307,"score":1},{"doc_id":"27806277","title":"Interaction of the Complexin Accessory Helix with Synaptobrevin Regulates Spontaneous Fusion.","abstract":"Neuronal transmitters are released from nerve terminals via the fusion of synaptic vesicles with the plasma membrane. Vesicles attach to membranes via a specialized protein machinery composed of membrane-attached (t-SNARE) and vesicle-attached (v-SNARE) proteins that zipper together to form a coiled-coil SNARE bundle that brings the two fusing membranes into close proximity. Neurotransmitter release may occur either in response to an action potential or through spontaneous fusion. A cytosolic protein, Complexin (Cpx), binds the SNARE complex and restricts spontaneous exocytosis by acting as a fusion clamp. We previously proposed a model in which the interaction between Cpx and the v-SNARE serves as a spring to prevent premature zippering of the SNARE complex, thereby reducing the likelihood of fusion. To test this model, we combined molecular-dynamics (MD) simulations and site-directed mutagenesis of Cpx and SNAREs in Drosophila. MD simulations of the Drosophila Cpx-SNARE complex demonstrated that Cpx's interaction with the v-SNARE promotes unraveling of the v-SNARE off the core SNARE bundle. We investigated clamping properties in the syx(3-69) paralytic mutant, which has a single-point mutation in the t-SNARE and displays enhanced spontaneous release. MD simulations demonstrated an altered interaction of Cpx with the SNARE bundle that hindered v-SNARE unraveling by Cpx, thus compromising clamping. We used our model to predict mutations that should enhance the ability of Cpx to prevent full assembly of the SNARE complex. MD simulations predicted that a weakened interaction between the Cpx accessory helix and the v-SNARE would enhance Cpx flexibility and thus promote separation of SNAREs, reducing spontaneous fusion. We generated transgenic Drosophila with mutations in Cpx and the v-SNARE that disrupted a salt bridge between these two proteins. As predicted, both lines demonstrated a selective inhibition in spontaneous release, suggesting that Cpx acts as a fusion clamp that restricts full SNARE zippering.","corpus_id":35760770,"score":1},{"doc_id":"28077717","title":"Complexin Mutants Reveal Partial Segregation between Recycling Pathways That Drive Evoked and Spontaneous Neurotransmission.","abstract":"Synaptic vesicles fuse at morphological specializations in the presynaptic terminal termed active zones (AZs). Vesicle fusion can occur spontaneously or in response to an action potential. Following fusion, vesicles are retrieved and recycled within nerve terminals. It is still unclear whether vesicles that fuse spontaneously or following evoked release share similar recycling mechanisms. Genetic deletion of the SNARE-binding protein complexin dramatically increases spontaneous fusion, with the protein serving as the synaptic vesicle fusion clamp at Drosophila synapses. We examined synaptic vesicle recycling pathways at complexin null neuromuscular junctions, where spontaneous release is dramatically enhanced. We combined loading of the lipophilic dye FM1-43 with photoconversion, electron microscopy, and electrophysiology to monitor evoked and spontaneous recycling vesicle pools. We found that the total number of recycling vesicles was equal to those retrieved through spontaneous and evoked pools, suggesting that retrieval following fusion is partially segregated for spontaneous and evoked release. In addition, the kinetics of FM1-43 destaining and synaptic depression measured in the presence of the vesicle-refilling blocker bafilomycin indicated that spontaneous and evoked recycling pools partially intermix during the release process. Finally, FM1-43 photoconversion combined with electron microscopy analysis indicated that spontaneous recycling preferentially involves synaptic vesicles in the vicinity of AZs, whereas vesicles recycled following evoked release involve a larger intraterminal pool. Together, these results suggest that spontaneous and evoked vesicles use separable recycling pathways and then partially intermix during subsequent rounds of fusion. SIGNIFICANCE STATEMENT: Neurotransmitter release involves fusion of synaptic vesicles with the plasma membrane in response to an action potential, or spontaneously in the absence of stimulation. Upon fusion, vesicles are retrieved and recycled, and it is unclear whether recycling pathways for evoked and spontaneous vesicles are segregated after fusion. We addressed this question by taking advantage of preparations lacking the synaptic protein complexin, which have elevated spontaneous release that enables reliable tracking of the spontaneous recycling pool. Our results suggest that spontaneous and evoked recycling pathways are segregated during the retrieval process but can partially intermix during stimulation.","corpus_id":-1,"score":1},{"doc_id":"28813412","title":"The primed SNARE-complexin-synaptotagmin complex for neuronal exocytosis.","abstract":"Synaptotagmin, complexin, and neuronal SNARE (soluble N-ethylmaleimide sensitive factor attachment protein receptor) proteins mediate evoked synchronous neurotransmitter release, but the molecular mechanisms mediating the cooperation between these molecules remain unclear. Here we determine crystal structures of the primed pre-fusion SNARE-complexin-synaptotagmin-1 complex. These structures reveal an unexpected tripartite interface between synaptotagmin-1 and both the SNARE complex and complexin. Simultaneously, a second synaptotagmin-1 molecule interacts with the other side of the SNARE complex via the previously identified primary interface. Mutations that disrupt either interface in solution also severely impair evoked synchronous release in neurons, suggesting that both interfaces are essential for the primed pre-fusion state. Ca(2+) binding to the synaptotagmin-1 molecules unlocks the complex, allows full zippering of the SNARE complex, and triggers membrane fusion. The tripartite SNARE-complexin-synaptotagmin-1 complex at a synaptic vesicle docking site has to be unlocked for triggered fusion to start, explaining the cooperation between complexin and synaptotagmin-1 in synchronizing evoked release on the sub-millisecond timescale.","corpus_id":205259313,"score":1},{"doc_id":"29535609","title":"Accessory and Central α-helices of Complexin Selectively Activate Ca2+ Triggering of Synaptic Exocytosis.","abstract":"Complexins, binding to assembling soluble NSF-attachment protein receptor (SNARE) complexes, activate Ca2+ triggered exocytosis and clamp spontaneous release in the presynaptic terminal. Functions of complexin are structural dependent and mechanistically distinct. To further understand the functional/structural dependence of complexin, here we show that the accessory and central α-helices of complexin are sufficient in activation of Ca2+ triggered vesicle fusion but not in clamping spontaneous release. Targeting the two α-helices to synaptic vesicle suppresses spontaneous release, thus further emphasizing the importance of curvature membrane localization in clamping function.","corpus_id":3513367,"score":1},{"doc_id":"19515924","title":"The unitary event underlying multiquantal EPSCs at a hair cell's ribbon synapse.","abstract":"EPSCs at the synapses of sensory receptors and of some CNS neurons include large events thought to represent the synchronous release of the neurotransmitter contained in several synaptic vesicles by a process known as multiquantal release. However, determination of the unitary, quantal size underlying such putatively multiquantal events has proven difficult at hair cell synapses, hindering confirmation that large EPSCs are in fact multiquantal. Here, we address this issue by performing presynaptic membrane capacitance measurements together with paired recordings at the ribbon synapses of adult hair cells. These simultaneous presynaptic and postsynaptic assays of exocytosis, together with electron microscopic estimates of single vesicle capacitance, allow us to estimate a single vesicle EPSC charge of approximately -45 fC, a value in close agreement with the mean postsynaptic charge transfer of uniformly small EPSCs recorded during periods of presynaptic hyperpolarization. By thus establishing the magnitude of the fundamental quantal event at this peripheral sensory synapse, we provide evidence that the majority of spontaneous and evoked EPSCs are multiquantal. Furthermore, we show that the prevalence of uniquantal versus multiquantal events is Ca2+ dependent. Paired recordings also reveal a tight correlation between membrane capacitance increase and evoked EPSC charge, indicating that glutamate release during prolonged hair cell depolarization does not significantly saturate or desensitize postsynaptic AMPA receptors. We propose that the large EPSCs reflect the highly synchronized release of multiple vesicles at single presynaptic ribbon-type active zones through a compound or coordinated vesicle fusion mechanism.","corpus_id":15204395,"score":0},{"doc_id":"20074062","title":"Role of C2 domain proteins during synaptic vesicle exocytosis.","abstract":"Neurotransmitter release is mediated by the fusion of synaptic vesicles with the presynaptic plasma membrane. Fusion is triggered by a rise in the intracellular calcium concentration and is dependent on the neuronal SNARE (soluble N-ethylmaleimide-sensitive fusion protein-attachment protein receptor) complex. A plethora of molecules such as members of the MUNC13, MUNC18, complexin and synaptotagmin families act along with the SNARE complex to enable calcium-regulated synaptic vesicle exocytosis. The synaptotagmins are localized to synaptic vesicles by an N-terminal transmembrane domain and contain two cytoplasmic C2 domains. Members of the synaptotagmin family are thought to translate the rise in intracellular calcium concentration into synaptic vesicle fusion. The C2 domains of synaptotagmin-1 bind membranes in a calcium-dependent manner and in response induce a high degree of membrane curvature, which is required for its ability to trigger membrane fusion in vitro and in vivo. Furthermore, members of the soluble DOC2 (double-C2 domain) protein family have similar properties. Taken together, these results suggest that C2 domain proteins such as the synaptotagmins and DOC2s promote membrane fusion by the induction of membrane curvature in the vicinity of the SNARE complex. Given the widespread expression of C2 domain proteins in secretory cells, it is proposed that promotion of SNARE-dependent membrane fusion by the induction of membrane curvature is a widespread phenomenon.","corpus_id":22170305,"score":0},{"doc_id":"20526850","title":"Realistic modelling of receptor activation in hippocampal excitatory synapses: analysis of multivesicular release, release location, temperature and synaptic cross-talk.","abstract":"Chemically mediated synaptic transmission results from fusion of synaptic vesicles with the presynaptic plasma membrane, subsequent release of the vesicular content into the cleft and binding to postsynaptic receptors. Previous modelling studies of excitatory neurotransmitter glutamate were based on simplified geometries failing to account for the biologically realistic synaptic environment, in particular, the presence of astrocytes, the geometry of extracellular space, and the neurotransmitter uptake mechanism. Using 3-dimensional reconstructions of hippocampal glutamatergic synapses including the surrounding astrocytic processes we have developed a biologically realistic model to analyse receptor activation in different conditions. We used the finite element method to simulate glutamate release, analyse glutamate diffusion following single and multiple vesicle release and binding at the postsynaptic site to AMPA and NMDA receptors. We demonstrate that: (1) the transmitter diffusion is highly temperature-sensitive; (2) release conditions and geometry more specifically affect AMPARs than NMDARs; (3) the sensitivities of AMPARs and NMDARs to simultaneous vesicular release are different; (4) in the case of multivesicle neurotransmitter release with variable delays, the binding of glutamate to AMPARs is additive up to 1 ms after the release, then becomes independent, but to NMDARs the binding is additive up to 33 ms; (5) the number of AMPARs varies more than the number of NMDRs in response to the input firing patterns; (6) the presence of astrocytes effectively blocks synaptic cross-talk; and (7) synaptic cross-talk, mediated by NMDARs but not AMPARs, is only possible after quasi-simultaneous multivesicular release at physiological temperature (35 degrees C) without intervening astrocytes, but not at 25 degrees C. Our simulations demonstrate the importance of temperature and ultrastructural synaptic environment in synaptic transmission and synaptic cross-talk.","corpus_id":29131577,"score":0},{"doc_id":"20829354","title":"Complexin 2 modulates vesicle-associated membrane protein (VAMP) 2-regulated zymogen granule exocytosis in pancreatic acini.","abstract":"Complexins are soluble proteins that regulate the activity of soluble N-ethylmaleimide-sensitive factor attachment protein receptor (SNARE) complexes necessary for vesicle fusion. Neuronal specific complexin 1 has inhibitory and stimulatory effects on exocytosis by clamping trans-SNARE complexes in a prefusion state and promoting conformational changes to facilitate membrane fusion following cell stimulation. Complexins are unable to bind to monomeric SNARE proteins but bind with high affinity to ternary SNARE complexes and with lower affinity to target SNARE complexes. Far less is understood about complexin function outside the nervous system. Pancreatic acini express the complexin 2 isoform by RT-PCR and immunoblotting. Immunofluorescence microscopy revealed complexin 2 localized along the apical plasma membrane consistent with a role in secretion. Accordingly, complexin 2 was found to interact with vesicle-associated membrane protein (VAMP) 2, syntaxins 3 and 4, but not with VAMP 8 or syntaxin 2. Introduction of recombinant complexin 2 into permeabilized acini inhibited Ca(2+)-stimulated secretion in a concentration-dependent manner with a maximal inhibition of nearly 50%. Mutations of the central α-helical domain reduced complexin 2 SNARE binding and concurrently abolished its inhibitory activity. Surprisingly, mutation of arginine 59 to histidine within the central α-helical domain did not alter SNARE binding and moreover, augmented Ca(2+)-stimulated secretion by 130% of control. Consistent with biochemical studies, complexin 2 colocalized with VAMP 2 along the apical plasma membrane following cholecystokinin-8 stimulation. These data demonstrate a functional role for complexin 2 outside the nervous system and indicate that it participates in the Ca(2+)-sensitive regulatory pathway for zymogen granule exocytosis.","corpus_id":205302672,"score":0},{"doc_id":"21098665","title":"Postsynaptic GluA1 enables acute retrograde enhancement of presynaptic function to coordinate adaptation to synaptic inactivity.","abstract":"Prolonged blockade of AMPA-type glutamate receptors in hippocampal neuron cultures leads to homeostatic enhancements of pre- and postsynaptic function that appear correlated at individual synapses, suggesting some form of transsynaptic coordination. The respective modifications are important for overall synaptic strength but their interrelationship, dynamics, and molecular underpinnings are unclear. Here we demonstrate that adaptation begins postsynaptically but is ultimately communicated to presynaptic terminals and expressed as an accelerated turnover of synaptic vesicles. Critical postsynaptic modifications occur over hours, but enable retrograde communication within minutes once AMPA receptor (AMPAR) blockade is removed, causing elevation of both spontaneous and evoked vesicle fusion. The retrograde signaling does not require spiking activity and can be interrupted by NBQX, philanthotoxin, postsynaptic BAPTA, or external sequestration of BDNF, consistent with the acute release of retrograde messenger, triggered by postsynaptic Ca(2+) elevation via Ca(2+)-permeable AMPARs.","corpus_id":14023628,"score":0},{"doc_id":"21110949","title":"Identification of complexin II in astrocytes: a possible regulator of glutamate release in these cells.","abstract":"Complexins are a family of SNARE complex-binding proteins which regulate neurotransmitter release by playing a crucial role in triggering fast exocytosis at the synapse. Current evidence indicates astrocytes can release glutamate via a vesicular mechanism similar to that at nerve terminals and thereby modulate synaptic activity. In addition, components of the biochemical machinery associated with synaptic release have been identified in these cells. However, whether complexins are also present in astrocytes and may therefore participate in the vesicular release of glutamate is a key issue that is yet to be determined. In the present study we therefore examined if astrocytes express complexin I (Cpx I) and/or complexin II (Cpx II). Our results indicate these cells contain Cpx II but not Cpx I in primary culture. In addition, serum deprivation for 24 h led to a 2.6-fold increase in Cpx II, suggesting this protein is responsive to insults. These findings point to Cpx II being a likely key modulator of synaptic activity at the level of these glial cells. Given the considered involvement of complexins in neurologic and psychiatric illness, astrocytic Cpx II represents a potentially important therapeutic target for the future treatment of such maladies.","corpus_id":205913901,"score":0},{"doc_id":"21272392","title":"Synaptic release at mammalian bipolar cell terminals.","abstract":"Bipolar cells play a vital role in the transfer of visual information across the vertebrate retina. The synaptic output of these neurons is regulated by factors that are extrinsic and intrinsic. Relatively little is known about the intrinsic factors that regulate neurotransmitter exocytosis. Much of what we know about intrinsic presynaptic mechanisms that regulate glutamate release has come from the study of the unusually large and accessible synaptic terminal of the goldfish rod-dominant bipolar cell, the Mb1 bipolar cell. However, over the past several years, examination of presynaptic mechanisms governing neurotransmitter release has been extended to the mammalian rod bipolar cell. In this review, we discuss the recent advances in our understanding of synaptic vesicle dynamics and neurotransmitter release in rodent rod bipolar cells and consider how these properties help to shape the synaptic output of the mammalian retina.","corpus_id":37079692,"score":0},{"doc_id":"22284181","title":"Postsynaptic complexin controls AMPA receptor exocytosis during LTP.","abstract":"Long-term potentiation (LTP) is a compelling synaptic correlate of learning and memory. LTP induction requires NMDA receptor (NMDAR) activation, which triggers SNARE-dependent exocytosis of AMPA receptors (AMPARs). However, the molecular mechanisms mediating AMPAR exocytosis induced by NMDAR activation remain largely unknown. Here, we show that complexin, a protein that regulates neurotransmitter release via binding to SNARE complexes, is essential for AMPAR exocytosis during LTP but not for the constitutive AMPAR exocytosis that maintains basal synaptic strength. The regulated postsynaptic AMPAR exocytosis during LTP requires binding of complexin to SNARE complexes. In hippocampal neurons, presynaptic complexin acts together with synaptotagmin-1 to mediate neurotransmitter release. However, postsynaptic synaptotagmin-1 is not required for complexin-dependent AMPAR exocytosis during LTP. These results suggest a complexin-dependent molecular mechanism for regulating AMPAR delivery to synapses, a mechanism that is surprisingly similar to presynaptic exocytosis but controlled by regulators other than synaptotagmin-1.","corpus_id":7486817,"score":0},{"doc_id":"23216578","title":"Regulators of synaptic transmission: roles in the pathogenesis and treatment of epilepsy.","abstract":"Synaptic transmission is the communication between a presynaptic and a postsynaptic neuron, and the subsequent processing of the signal. These processes are complex and highly regulated, reflecting their importance in normal brain functioning and homeostasis. Sustaining synaptic transmission depends on the continuing cycle of synaptic vesicle formation, release, and endocytosis, which requires proteins such as dynamin, syndapin, synapsin, and synaptic vesicle protein 2A. Synaptic transmission is regulated by diverse mechanisms, including presynaptic modulators of synaptic vesicle formation and release, postsynaptic receptors and signaling, and modulators of neurotransmission. Neurotransmitters released presynaptically can bind to their postsynaptic receptors, the inhibitory γ-aminobutyric acid (GABA)ergic receptors or the excitatory glutamate receptors. Once released, glutamate activates a variety of postsynaptic receptors including α-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid (AMPA), N-methyl-D-aspartate (NMDA), kainate, and metabotropic receptors. The activation of the receptors triggers downstream signaling cascades generating a vast array of effects, which can be modulated by a numerous auxiliary regulatory subunits. Moreover, different neuropeptides such as neuropeptide Y, brain-derived neurotrophic factor (BDNF), somatostatin, ghrelin, and galanin, act as regulators of diverse synaptic functions and along with the classic neurotransmitters. Abnormalities in the regulation of synaptic transmission play a critical role in the pathogenesis of numerous brain diseases, including epilepsy. This review focuses on the different mechanisms involved in the regulation of synaptic transmission, which may play a role in the pathogenesis of epilepsy: the presynaptic modulators of synaptic vesicle formation and release, postsynaptic receptors, and modulators of neurotransmission, including the mechanism by which drugs can modulate the frequency and severity of epileptic seizures.","corpus_id":27930716,"score":0},{"doc_id":"27335398","title":"Functional Roles of Complexin3 and Complexin4 at Mouse Photoreceptor Ribbon Synapses.","abstract":"UNLABELLED: Complexins (Cplxs) are SNARE complex regulators controlling the speed and Ca(2+) sensitivity of SNARE-mediated synaptic vesicle fusion. We have shown previously that photoreceptor ribbon synapses in mouse retina are equipped with Cplx3 and Cplx4 and that lack of both Cplxs perturbs photoreceptor ribbon synaptic function; however, Cplx3/4 function in photoreceptor synaptic transmission remained elusive. To investigate Cplx3/4 function in photoreceptor ribbon synapses, voltage-clamp recordings from postsynaptic horizontal cells were performed in horizontal slice preparations of Cplx3/4 wild-type (WT) and Cplx3/4 double knock-out (DKO) mice. We measured tonic activity in light and dark, current responses to changes in luminous intensity, and electrically evoked postsynaptic responses. Cplx3/4 decreased the frequency of tonic events and shifted their amplitude distribution to smaller values. Light responses were sustained in the presence of Cplx3/4, but transient in their absence. Finally, Cplx3/4 increased synaptic vesicle release evoked by electrical stimulation. Using electron microscopy, we quantified the number of synaptic vesicles at presynaptic ribbons after light or dark adaptation. In Cplx3/4 WT photoreceptors, the number of synaptic vesicles associated with the ribbon base close to the release site was significantly lower in light than in dark. This is in contrast to Cplx3/4 DKO photoreceptors, in which the number of ribbon-associated synaptic vesicles remained unchanged regardless of the adaptational state. Our results indicate a suppressing and a facilitating action of Cplx3/4 on Ca(2+)-dependent tonic and evoked neurotransmitter release, respectively, and a regulatory role in the adaptation-dependent availability of synaptic vesicles for release at photoreceptor ribbon synapses. SIGNIFICANCE STATEMENT: Synaptic vesicle fusion at active zones of chemical synapses is executed by SNARE complexes. Complexins (Cplxs) are SNARE complex regulators and photoreceptor ribbon synapses are equipped with Cplx3 and Cplx4. The absence of both Cplxs perturbs ribbon synaptic function. Because we lack information on Cplx function in photoreceptor synaptic transmission, we investigated Cplx function using voltage-clamp recordings from postsynaptic horizontal cells of Cplx3/4 wild-type and Cplx3/4 double knock-out mice and quantified synaptic vesicle number at the ribbon after light and dark adaptation using electron microscopy. The findings reveal a suppressing action of Cplx3/4 on tonic neurotransmitter release, a facilitating action on evoked release, and a regulatory role of Cplx3/4 in the adaptation-dependent availability of synaptic vesicles at mouse photoreceptor ribbon synapses.","corpus_id":41281024,"score":0},{"doc_id":"27881952","title":"Tissue-type Plasminogen Activator (tPA) Modulates the Postsynaptic Response of Cerebral Cortical Neurons to the Presynaptic Release of Glutamate.","abstract":"Tissue-type plasminogen activator (tPA) is a serine proteinase released by the presynaptic terminal of cerebral cortical neurons following membrane depolarization (Echeverry et al., 2010). Recent studies indicate that the release of tPA triggers the synaptic vesicle cycle and promotes the exocytosis (Wu et al., 2015) and endocytic retrieval (Yepes et al., 2016) of glutamate-containing synaptic vesicles. Here we used electron microscopy, proteomics, quantitative phosphoproteomics, biochemical analyses with extracts of the postsynaptic density (PSD), and an animal model of cerebral ischemia with mice overexpressing neuronal tPA to study whether the presynaptic release of tPA also has an effect on the postsynaptic terminal. We found that tPA has a bidirectional effect on the composition of the PSD of cerebral cortical neurons that is independent of the generation of plasmin and the presynaptic release of glutamate, but depends on the baseline level of neuronal activity and the extracellular concentrations of calcium (Ca(2+)). Accordingly, in neurons that are either inactive or incubated with low Ca(2+) concentrations tPA induces phosphorylation and accumulation in the PSD of the Ca(2+)/calmodulin-dependent protein kinase IIα (pCaMKIIα), followed by pCaMKIIα-mediated phosphorylation and synaptic recruitment of GluR1-containing α-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid (AMPA) receptors. In contrast, in neurons with previously increased baseline levels of pCaMKIIα in the PSD due to neuronal depolarization in vivo or incubation with high concentrations of either Ca(2+) or glutamate in vitro, tPA induces pCaMKIIα and pGluR1 dephosphorylation and their subsequent removal from the PSD. We found that these effects of tPA are mediated by synaptic N-methyl-D-aspartate (NMDA) receptors and cyclin-dependent kinase 5 (Cdk5)-induced phosphorylation of the protein phosphatase 1 (PP1) at T320. Our data indicate that by regulating the pCaMKIIα/PP1 balance in the PSD tPA acts as a homeostatic regulator of the postsynaptic response of cerebral cortical neurons to the presynaptic release of glutamate.","corpus_id":1138590,"score":0}],"string":"[\n {\n \"doc_id\": \"18505837\",\n \"title\": \"Complexins facilitate neurotransmitter release at excitatory and inhibitory synapses in mammalian central nervous system.\",\n \"abstract\": \"Complexins (Cplxs) are key regulators of synaptic exocytosis, but whether they act as facilitators or inhibitors is currently being disputed controversially. We show that genetic deletion of all Cplxs expressed in the mouse brain causes a reduction in Ca(2+)-triggered and spontaneous neurotransmitter release at both excitatory and inhibitory synapses. Our results demonstrate that at mammalian central nervous system synapses, Cplxs facilitate neurotransmitter release and do not simply act as inhibitory clamps of the synaptic vesicle fusion machinery.\",\n \"corpus_id\": 9354579,\n \"score\": 2\n },\n {\n \"doc_id\": \"19179400\",\n \"title\": \"The carboxy-terminal domain of complexin I stimulates liposome fusion.\",\n \"abstract\": \"Regulated exocytosis requires tight coupling of the membrane fusion machinery to a triggering signal and a fast response time. Complexins are part of this regulation and, together with synaptotagmins, control calcium-dependent exocytosis. Stimulatory and inhibitory functions have been reported for complexins. To test if complexins directly affect membrane fusion, we analyzed the 4 known mammalian complexin isoforms in a reconstituted fusion assay. In contrast to complexin III (CpxIII) and CpxIV, CpxI and CpxII stimulated soluble N-ethylmaleimide-sensitive factor attachment protein receptor (SNARE)-pin assembly and membrane fusion. This stimulatory effect required a preincubation at low temperature and was specific for neuronal t-SNAREs. Stimulation of membrane fusion was lost when the carboxy-terminal domain of CpxI was deleted or serine 115, a putative phosphorylation site, was mutated. Transfer of the carboxy-terminal domain of CpxI to CpxIII resulted in a stimulatory CpxIII-I chimera. Thus, the carboxy-terminal domains of CpxI and CpxII promote the fusion of high-curvature liposomes.\",\n \"corpus_id\": 24553152,\n \"score\": 2\n },\n {\n \"doc_id\": \"21145004\",\n \"title\": \"Complexin clamps asynchronous release by blocking a secondary Ca(2+) sensor via its accessory α helix.\",\n \"abstract\": \"Complexin activates and clamps neurotransmitter release; impairing complexin function decreases synchronous, but increases spontaneous and asynchronous synaptic vesicle exocytosis. Here, we show that complexin-different from the Ca(2+) sensor synaptotagmin-1-activates synchronous exocytosis by promoting synaptic vesicle priming, but clamps spontaneous and asynchronous exocytosis-similar to synaptotagmin-1-by blocking a secondary Ca(2+) sensor. Activation and clamping functions of complexin depend on distinct, autonomously acting sequences, namely its N-terminal region and accessory α helix, respectively. Mutations designed to test whether the accessory α helix of complexin clamps exocytosis by inserting into SNARE-complexes support this hypothesis, suggesting that the accessory α helix blocks completion of trans-SNARE-complex assembly until Ca(2+) binding to synaptotagmin relieves this block. Moreover, a juxtamembranous mutation in the SNARE-protein synaptobrevin-2, which presumably impairs force transfer from nascent trans-SNARE complexes onto fusing membranes, also unclamps spontaneous fusion by disinhibiting a secondary Ca(2+) sensor. Thus, complexin performs mechanistically distinct activation and clamping functions that operate in conjunction with synaptotagmin-1 by controlling trans-SNARE-complex assembly.\",\n \"corpus_id\": 14230300,\n \"score\": 2\n },\n {\n \"doc_id\": \"21215631\",\n \"title\": \"Complexin maintains vesicles in the primed state in C. elegans.\",\n \"abstract\": \"BACKGROUND: Complexin binds the SNARE complex at synapses and regulates exocytosis, but genetic studies indicate contradictory roles: in flies it predominantly inhibits synaptic vesicle fusion, whereas in mice it promotes evoked responses. RESULTS: Here we characterize the complexin mutant in the nematode Caenorhabditis elegans and reveal bipolar functions in neurotransmission: complexin inhibits spontaneous fusion of synaptic vesicles but is also essential for evoked responses. Complexin mutants exhibit a doubling of vesicle fusion in the absence of extracellular calcium. Even more profoundly, mutants exhibit an almost complete loss of evoked responses, and current amplitudes are reduced by 94%. One possible interpretation is that complexin is required for the stabilization of docked vesicles and that, in its absence, vesicles may fuse or undock from the plasma membrane. Consistent with this hypothesis, docked synaptic vesicles are reduced by 70% in complexin-1 mutants. CONCLUSION: These data suggest that the main function of complexin is to maintain the docked state both by inhibiting fusion and by promoting priming.\",\n \"corpus_id\": 6117522,\n \"score\": 2\n },\n {\n \"doc_id\": \"22357870\",\n \"title\": \"C-terminal complexin sequence is selectively required for clamping and priming but not for Ca2+ triggering of synaptic exocytosis.\",\n \"abstract\": \"Complexins are small soluble proteins that bind to assembling SNARE complexes during synaptic vesicle exocytosis, which in turn mediates neurotransmitter release. Complexins are required for clamping of spontaneous \\\"mini \\\" release and for the priming and synaptotagmin-dependent Ca(2+) triggering of evoked release. Mammalian genomes encode four complexins that are composed of an N-terminal unstructured sequence that activates synaptic exocytosis, an accessory α-helix that clamps exocytosis, an essential central α-helix that binds to assembling SNARE complexes and is required for all of its functions, and a long, apparently unstructured C-terminal sequence whose function remains unclear. Here, we used cultured mouse neurons to show that the C-terminal sequence of complexin-1 is not required for its synaptotagmin-activating function but is essential for its priming and clamping functions. Wild-type complexin-3 did not clamp exocytosis but nevertheless fully primed and activated exocytosis. Strikingly, exchanging the complexin-1 C terminus for the complexin-3 C terminus abrogated clamping, whereas exchanging the complexin-3 C terminus for the complexin-1 C terminus enabled clamping. Analysis of point mutations in the complexin-1 C terminus identified two single amino-acid substitutions that impaired clamping without altering the activation function of complexin-1. Examination of release induced by stimulus trains revealed that clamping-deficient C-terminal complexin mutants produced a modest relative increase in delayed release. Overall, our results show that the relatively large C-terminal complexin-1 sequence acts in priming and clamping synaptic exocytosis and demonstrate that the clamping function is not conserved in complexin-3, presumably because of its distinct C-terminal sequences.\",\n \"corpus_id\": 30991987,\n \"score\": 2\n },\n {\n \"doc_id\": \"23159779\",\n \"title\": \"Differential regulation of evoked and spontaneous neurotransmitter release by C-terminal modifications of complexin.\",\n \"abstract\": \"Complexins are small α-helical proteins that modulate neurotransmitter release by binding to SNARE complexes during synaptic vesicle exocytosis. They have been found to function as fusion clamps to inhibit spontaneous synaptic vesicle fusion in the absence of Ca(2+), while also promoting evoked neurotransmitter release following an action potential. Complexins consist of an N-terminal domain and an accessory α-helix that regulates the activating and inhibitory properties of the protein, respectively, and a central α-helix that binds the SNARE complex and is essential for both functions. In addition, complexins contain a largely unstructured C-terminal domain whose role in synaptic vesicle cycling is poorly defined. Here, we demonstrate that the C-terminus of Drosophila complexin (DmCpx) regulates localization to synapses and that alternative splicing of the C-terminus can differentially regulate spontaneous and evoked neurotransmitter release. Characterization of the single DmCpx gene by mRNA analysis revealed expression of two alternatively expressed isoforms, DmCpx7A and DmCpx7B, which encode proteins with different C-termini that contain or lack a membrane tethering prenylation domain. The predominant isoform, DmCpx7A, is further modified by RNA editing within this C-terminal region. Functional analysis of the splice isoforms showed that both are similarly localized to synaptic boutons at larval neuromuscular junctions, but have differential effects on the regulation of evoked and spontaneous fusion. These data indicate that the C-terminus of Drosophila complexin regulates both spontaneous and evoked release through separate mechanisms and that alternative splicing generates isoforms with distinct effects on the two major modes of synaptic vesicle fusion at synapses.\",\n \"corpus_id\": 16488161,\n \"score\": 2\n },\n {\n \"doc_id\": \"23238737\",\n \"title\": \"Complexin controls spontaneous and evoked neurotransmitter release by regulating the timing and properties of synaptotagmin activity.\",\n \"abstract\": \"Neurotransmitter release following synaptic vesicle (SV) fusion is the fundamental mechanism for neuronal communication. Synaptic exocytosis is a specialized form of intercellular communication that shares a common SNARE-mediated fusion mechanism with other membrane trafficking pathways. The regulation of synaptic vesicle fusion kinetics and short-term plasticity is critical for rapid encoding and transmission of signals across synapses. Several families of SNARE-binding proteins have evolved to regulate synaptic exocytosis, including Synaptotagmin (SYT) and Complexin (CPX). Here, we demonstrate that Drosophila CPX controls evoked fusion occurring via the synchronous and asynchronous pathways. cpx(-/-) mutants show increased asynchronous release, while CPX overexpression largely eliminates the asynchronous component of fusion. We also find that SYT and CPX coregulate the kinetics and Ca(2+) co-operativity of neurotransmitter release. CPX functions as a positive regulator of release in part by coupling the Ca(2+) sensor SYT to the fusion machinery and synchronizing its activity to speed fusion. In contrast, syt(-/-); cpx(-/-) double mutants completely abolish the enhanced spontaneous release observe in cpx(-/-) mutants alone, indicating CPX acts as a fusion clamp to block premature exocytosis in part by preventing inappropriate activation of the SNARE machinery by SYT. CPX levels also control the size of synaptic vesicle pools, including the immediate releasable pool and the ready releasable pool-key elements of short-term plasticity that define the ability of synapses to sustain responses during burst firing. These observations indicate CPX regulates both spontaneous and evoked fusion by modulating the timing and properties of SYT activation during the synaptic vesicle cycle.\",\n \"corpus_id\": 566304,\n \"score\": 2\n },\n {\n \"doc_id\": \"23352168\",\n \"title\": \"Synaptic vesicles position complexin to block spontaneous fusion.\",\n \"abstract\": \"Synapses continually replenish their synaptic vesicle (SV) pools while suppressing spontaneous fusion events, thus maintaining a high dynamic range in response to physiological stimuli. The presynaptic protein complexin can both promote and inhibit fusion through interactions between its α-helical domain and the SNARE complex. In addition, complexin's C-terminal half is required for the inhibition of spontaneous fusion in worm, fly, and mouse, although the molecular mechanism remains unexplained. We show here that complexin's C-terminal domain binds lipids through a novel protein motif, permitting complexin to inhibit spontaneous exocytosis in vivo by targeting complexin to SVs. We propose that the SV pool serves as a platform to sequester and position complexin where it can intercept the rapidly assembling SNAREs and control the rate of spontaneous fusion.\",\n \"corpus_id\": 9485215,\n \"score\": 2\n },\n {\n \"doc_id\": \"23769723\",\n \"title\": \"Molecular mechanisms of COMPLEXIN fusion clamp function in synaptic exocytosis revealed in a new Drosophila mutant.\",\n \"abstract\": \"The COMPLEXIN (CPX) proteins play a critical role in synaptic vesicle fusion and neurotransmitter release. Previous studies demonstrated that CPX functions in both activation of evoked neurotransmitter release and inhibition/clamping of spontaneous synaptic vesicle fusion. Here we report a new cpx mutant in Drosophila melanogaster, cpx(1257), revealing spatially defined and separable pools of CPX which make distinct contributions to the activation and clamping functions. In cpx(1257), lack of only the last C-terminal amino acid of CPX is predicted to disrupt prenylation and membrane targeting of CPX. Immunocytochemical analysis established localization of wild-type CPX to active zone (AZ) regions containing neurotransmitter release sites as well as broader presynaptic membrane compartments including synaptic vesicles. Parallel biochemical studies confirmed CPX membrane association and demonstrated robust binding interactions of CPX with all three SNAREs. This is in contrast to the cpx(1257) mutant, in which AZ localization of CPX persists but general membrane localization and, surprisingly, the bulk of CPX-SNARE protein interactions are abolished. Furthermore, electrophysiological analysis of neuromuscular synapses revealed interesting differences between cpx(1257) and a cpx null mutant. The cpx null exhibited a marked decrease in the EPSC amplitude, slowed EPSC rise and decay times and an increased mEPSC frequency with respect to wild-type. In contrast, cpx(1257) exhibited a wild-type EPSC with an increased mEPSC frequency and thus a selective failure to clamp spontaneous release. These results indicate that spatially distinct and separable interactions of CPX with presynaptic membranes and SNARE proteins mediate separable activation and clamping functions of CPX in neurotransmitter release.\",\n \"corpus_id\": 24750418,\n \"score\": 2\n },\n {\n \"doc_id\": \"23845424\",\n \"title\": \"Subtle Interplay between synaptotagmin and complexin binding to the SNARE complex.\",\n \"abstract\": \"Ca²⁺-triggered neurotransmitter release depends on the formation of SNARE complexes that bring the synaptic vesicle and plasma membranes together, on the Ca²⁺ sensor synaptotagmin-1 and on complexins, which play active and inhibitory roles. Release of the complexin inhibitory activity by binding of synaptotagmin-1 to the SNARE complex, causing complexin displacement, was proposed to trigger exocytosis. However, the validity of this model was questioned based on the observation of simultaneous binding of complexin-I and a fragment containing the synaptotagmin-1 C2 domains (C2AB) to membrane-anchored SNARE complex. Using diverse biophysical techniques, here we show that C2AB and complexin-I do not bind to each other but can indeed bind simultaneously to the SNARE complex in solution. Hence, the SNARE complex contains separate binding sites for both proteins. However, total internal reflection fluorescence microscopy experiments show that C2AB can displace a complexin-I fragment containing its central SNARE-binding helix and an inhibitory helix (Cpx26-83) from membrane-anchored SNARE complex under equilibrium conditions. Interestingly, full-length complexin-I binds more tightly to membrane-anchored SNARE complex than Cpx26-83, and it is not displaced by C2AB. These results show that interactions of N- and/or C-terminal sequences of complexin-I with the SNARE complex and/or phospholipids increase the affinity of complexin-I for the SNARE complex, hindering dissociation induced by C2AB. We propose a model whereby binding of synaptotagmin-1 to the SNARE complex directly or indirectly causes a rearrangement of the complexin-I inhibitory helix without inducing complexin-I dissociation, thus relieving the inhibitory activity and enabling cooperation between synaptotagmin-1 and complexin-I in triggering release.\",\n \"corpus_id\": 30493743,\n \"score\": 2\n },\n {\n \"doc_id\": \"25122624\",\n \"title\": \"Complexin inhibits spontaneous release and synchronizes Ca2+-triggered synaptic vesicle fusion by distinct mechanisms.\",\n \"abstract\": \"Previously we showed that fast Ca(2+)-triggered vesicle fusion with reconstituted neuronal SNAREs and synaptotagmin-1 begins from an initial hemifusion-free membrane point contact, rather than a hemifusion diaphragm, using a single vesicle-vesicle lipid/content mixing assay (Diao et al., 2012). When complexin-1 was included, a more pronounced Ca(2+)-triggered fusion burst was observed, effectively synchronizing the process. Here we show that complexin-1 also reduces spontaneous fusion in the same assay. Moreover, distinct effects of several complexin-1 truncation mutants on spontaneous and Ca(2+)-triggered fusion closely mimic those observed in neuronal cultures. The very N-terminal domain is essential for synchronization of Ca(2+)-triggered fusion, but not for suppression of spontaneous fusion, whereas the opposite is true for the C-terminal domain. By systematically varying the complexin-1 concentration, we observed differences in titration behavior for spontaneous and Ca(2+)-triggered fusion. Taken together, complexin-1 utilizes distinct mechanisms for synchronization of Ca(2+)-triggered fusion and inhibition of spontaneous fusion.\",\n \"corpus_id\": 584630,\n \"score\": 2\n },\n {\n \"doc_id\": \"25229806\",\n \"title\": \"Membrane curvature sensing by the C-terminal domain of complexin.\",\n \"abstract\": \"Complexin functions at presynaptic nerve terminals to inhibit spontaneous SNARE-mediated synaptic vesicle (SV) exocytosis, while enhancing stimulated neurotransmitter release. The C-terminal domain (CTD) of complexin is essential for its inhibitory function and has been implicated in localizing complexin to SVs via direct membrane interactions. Here we show that complexin's CTD is highly sensitive to membrane curvature, which it senses via tandem motifs, a C-terminal motif containing a mix of bulky hydrophobic and positively charged residues, and an adjacent amphipathic region that can bind membranes in either a disordered or a helical conformation. Helix formation requires membrane packing defects found on highly curved membrane surfaces. Mutations that disrupt helix formation without disrupting membrane binding compromise complexin's inhibitory function in vivo. Thus, this membrane curvature-dependent conformational transition, combined with curvature-sensitive binding by the adjacent C-terminal motif, constitute a novel mechanism for activating complexin's inhibitory function on the surface of SVs.\",\n \"corpus_id\": 12334151,\n \"score\": 2\n },\n {\n \"doc_id\": \"25524119\",\n \"title\": \"The mechanisms and functions of spontaneous neurotransmitter release.\",\n \"abstract\": \"Fast synaptic communication in the brain requires synchronous vesicle fusion that is evoked by action potential-induced Ca(2+) influx. However, synaptic terminals also release neurotransmitters by spontaneous vesicle fusion, which is independent of presynaptic action potentials. A functional role for spontaneous neurotransmitter release events in the regulation of synaptic plasticity and homeostasis, as well as the regulation of certain behaviours, has been reported. In addition, there is evidence that the presynaptic mechanisms underlying spontaneous release of neurotransmitters and their postsynaptic targets are segregated from those of evoked neurotransmission. These findings challenge current assumptions about neuronal signalling and neurotransmission, as they indicate that spontaneous neurotransmission has an autonomous role in interneuronal communication that is distinct from that of evoked release.\",\n \"corpus_id\": 26958246,\n \"score\": 2\n },\n {\n \"doc_id\": \"26806630\",\n \"title\": \"Should I stop or should I go? The role of complexin in neurotransmitter release.\",\n \"abstract\": \"When it comes to fusion with the neuronal cell membrane, does a synaptic vesicle have a choice whether to stop or to go? Recent work suggests that complexin, a tiny protein found within the synaptic terminal, contributes to the mechanism through which this choice is made. How complexin plays this consulting part and which synaptic vesicle proteins it interacts with remain open questions. Indeed, studies in mice and flies have led to the proposal of different models of complexin function. We suggest that understanding the modular nature of complexin will help us to unpick its role in synaptic vesicle release.\",\n \"corpus_id\": 8974313,\n \"score\": 2\n },\n {\n \"doc_id\": \"27253060\",\n \"title\": \"Complexin induces a conformational change at the membrane-proximal C-terminal end of the SNARE complex.\",\n \"abstract\": \"Complexin regulates spontaneous and activates Ca(2+)-triggered neurotransmitter release, yet the molecular mechanisms are still unclear. Here we performed single molecule fluorescence resonance energy transfer experiments and uncovered two conformations of complexin-1 bound to the ternary SNARE complex. In the cis conformation, complexin-1 induces a conformational change at the membrane-proximal C-terminal end of the ternary SNARE complex that specifically depends on the N-terminal, accessory, and central domains of complexin-1. The complexin-1 induced conformation of the ternary SNARE complex may be related to a conformation that is juxtaposing the synaptic vesicle and plasma membranes. In the trans conformation, complexin-1 can simultaneously interact with a ternary SNARE complex via the central domain and a binary SNARE complex consisting of syntaxin-1A and SNAP-25A via the accessory domain. The cis conformation may be involved in activation of synchronous neurotransmitter release, whereas both conformations may be involved in regulating spontaneous release.\",\n \"corpus_id\": 6244010,\n \"score\": 2\n },\n {\n \"doc_id\": \"27444020\",\n \"title\": \"N-terminal domain of complexin independently activates calcium-triggered fusion.\",\n \"abstract\": \"Complexin activates Ca(2+)-triggered neurotransmitter release and regulates spontaneous release in the presynaptic terminal by cooperating with the neuronal soluble N-ethylmaleimide-sensitive factor attachment protein receptors (SNAREs) and the Ca(2+)-sensor synaptotagmin. The N-terminal domain of complexin is important for activation, but its molecular mechanism is still poorly understood. Here, we observed that a split pair of N-terminal and central domain fragments of complexin is sufficient to activate Ca(2+)-triggered release using a reconstituted single-vesicle fusion assay, suggesting that the N-terminal domain acts as an independent module within the synaptic fusion machinery. The N-terminal domain can also interact independently with membranes, which is enhanced by a cooperative interaction with the neuronal SNARE complex. We show by mutagenesis that membrane binding of the N-terminal domain is essential for activation of Ca(2+)-triggered fusion. Consistent with the membrane-binding property, the N-terminal domain can be substituted by the influenza virus hemagglutinin fusion peptide, and this chimera also activates Ca(2+)-triggered fusion. Membrane binding of the N-terminal domain of complexin therefore cooperates with the other fusogenic elements of the synaptic fusion machinery during Ca(2+)-triggered release.\",\n \"corpus_id\": 5847780,\n \"score\": 2\n },\n {\n \"doc_id\": \"28456331\",\n \"title\": \"Complexin Binding to Membranes and Acceptor t-SNAREs Explains Its Clamping Effect on Fusion.\",\n \"abstract\": \"Complexin-1 is a SNARE effector protein that decreases spontaneous neurotransmitter release and enhances evoked release. Complexin binds to the fully assembled four-helical neuronal SNARE core complex as revealed in competing molecular models derived from x-ray crystallography. Presently, it is unclear how complexin binding to the postfusion complex accounts for its effects upon spontaneous and evoked release in vivo. Using a combination of spectroscopic and imaging methods, we characterize in molecular detail how complexin binds to the 1:1 plasma membrane t-SNARE complex of syntaxin-1a and SNAP-25 while simultaneously binding the lipid bilayer at both its N- and C-terminal ends. These interactions are cooperative, and binding to the prefusion acceptor t-SNARE complex is stronger than to the postfusion core complex. This complexin interaction reduces the affinity of synaptobrevin-2 for the 1:1 complex, thereby retarding SNARE assembly and vesicle docking in vitro. The results provide the basis for molecular models that account for the observed clamping effect of complexin beginning with the acceptor t-SNARE complex and the subsequent activation of the clamped complex by Ca(2+) and synaptotagmin.\",\n \"corpus_id\": 32826604,\n \"score\": 2\n },\n {\n \"doc_id\": \"28596722\",\n \"title\": \"Unique Structural Features of Membrane-Bound C-Terminal Domain Motifs Modulate Complexin Inhibitory Function.\",\n \"abstract\": \"Complexin is a small soluble presynaptic protein that interacts with neuronal SNARE proteins in order to regulate synaptic vesicle exocytosis. While the SNARE-binding central helix of complexin is required for both the inhibition of spontaneous fusion and the facilitation of synchronous fusion, the disordered C-terminal domain (CTD) of complexin is specifically required for its inhibitory function. The CTD of worm complexin binds to membranes via two distinct motifs, one of which undergoes a membrane curvature dependent structural transition that is required for efficient inhibition of neurotransmitter release, but the conformations of the membrane-bound motifs remain poorly characterized. Visualizing these conformations is required to clarify the mechanisms by which complexin membrane interactions regulate its function. Here, we employ optical and magnetic resonance spectroscopy to precisely define the boundaries of the two CTD membrane-binding motifs and to characterize their conformations. We show that the curvature dependent amphipathic helical motif features an irregular element of helical structure, likely a pi-bulge, and that this feature is important for complexin inhibitory function in vivo.\",\n \"corpus_id\": 31171403,\n \"score\": 2\n },\n {\n \"doc_id\": \"28603484\",\n \"title\": \"Evolutionary Divergence of the C-terminal Domain of Complexin Accounts for Functional Disparities between Vertebrate and Invertebrate Complexins.\",\n \"abstract\": \"Complexin is a critical presynaptic protein that regulates both spontaneous and calcium-triggered neurotransmitter release in all synapses. Although the SNARE-binding central helix of complexin is highly conserved and required for all known complexin functions, the remainder of the protein has profoundly diverged across the animal kingdom. Striking disparities in complexin inhibitory activity are observed between vertebrate and invertebrate complexins but little is known about the source of these differences or their relevance to the underlying mechanism of complexin regulation. We found that mouse complexin 1 (mCpx1) failed to inhibit neurotransmitter secretion in Caenorhabditis elegans neuromuscular junctions lacking the worm complexin 1 (CPX-1). This lack of inhibition stemmed from differences in the C-terminal domain (CTD) of mCpx1. Previous studies revealed that the CTD selectively binds to highly curved membranes and directs complexin to synaptic vesicles. Although mouse and worm complexin have similar lipid binding affinity, their last few amino acids differ in both hydrophobicity and in lipid binding conformation, and these differences strongly impacted CPX-1 inhibitory function. Moreover, function was not maintained if a critical amphipathic helix in the worm CPX-1 CTD was replaced with the corresponding mCpx1 amphipathic helix. Invertebrate complexins generally shared more C-terminal similarity with vertebrate complexin 3 and 4 isoforms, and the amphipathic region of mouse complexin 3 significantly restored inhibitory function to worm CPX-1. We hypothesize that the CTD of complexin is essential in conferring an inhibitory function to complexin, and that this inhibitory activity has been attenuated in the vertebrate complexin 1 and 2 isoforms. Thus, evolutionary changes in the complexin CTD differentially shape its synaptic role across phylogeny.\",\n \"corpus_id\": 10980323,\n \"score\": 2\n },\n {\n \"doc_id\": \"18499660\",\n \"title\": \"Distinct domains of complexins bind SNARE complexes and clamp fusion in vitro.\",\n \"abstract\": \"In regulated exocytosis, the core membrane fusion machinery proteins, the SNARE proteins, are assisted by a group of regulatory factors in order to couple membrane fusion to an increase of intracellular calcium ion (Ca(2+)) concentration. Complexin-I and synaptotagmin-I have been shown to be key elements for this tightly regulated process. Many studies suggest that complexin-I can arrest the fusion reaction and that synaptotagmin-I can release the complexin-I blockage in a calcium-dependent manner. Although the actual molecular mechanism by which they exert their function is still unknown, recent in vivo experiments postulate that domains of complexin-I produce different effects on neurotransmitter release. Herein, by using an in vitro flipped SNARE cell fusion assay, we have identified and characterized the minimal functional domains of complexin-I necessary to couple calcium and synaptotagmin-I to membrane fusion. Moreover, we provide evidence that other isoforms of complexin, complexin-II, -III, and -IV, can also be functionally coupled to synaptotagmin-I and calcium. These correspond closely to results from in vivo experiments, providing further validation of the physiological relevance of the flipped SNARE system.\",\n \"corpus_id\": 22237326,\n \"score\": 1\n },\n {\n \"doc_id\": \"18503508\",\n \"title\": \"Glucose/oxygen deprivation and reperfusion upregulate SNAREs and complexin in organotypic hippocampal slice cultures.\",\n \"abstract\": \"Brain ischemia activates Ca(2+)-dependent synaptic vesicle exocytosis. The synaptosomal-associated protein 25 (SNAP-25) and syntaxin proteins, located on presynaptic terminals, are components of the SNARE (soluble N-ethylmaleimide-sensitive factor attachment protein receptor) complex and play a key role in regulating exocytosis. Changes in the expression of SNAREs could affect SNARE complex formation, fusion of vesicles with the presynaptic membrane, and release of neurotransmitters through exocytosis. To investigate the relationship of glucose/oxygen deprivation (GOD)/reperfusion-induced neuronal damage and alteration of presynaptic function, we examined the expression of SNAREs and complexin during GOD and reperfusion using organotypic hippocampal slice cultures. Microtubule-associated protein 2 (MAP-2) staining and transmission electron microscopy showed that neuronal damage increased in a time-dependent manner and both types of neuronal death can occur at different times during GOD and reperfusion. The immunoreactivity of SNAREs such as SNAP-25, vesicle-associated membrane protein and syntaxin and complexin increased in pyramidal cell bodies in the CA1 and CA3 areas in a time-dependent manner following reperfusion. Our data suggest that alteration of presynaptic function may play a partial role in delayed neuronal death during GOD and reperfusion in organotypic hippocampal slice cultures.\",\n \"corpus_id\": 30447775,\n \"score\": 1\n },\n {\n \"doc_id\": \"18552825\",\n \"title\": \"Complexin and Ca2+ stimulate SNARE-mediated membrane fusion.\",\n \"abstract\": \"Ca(2+)-triggered, synchronized synaptic vesicle fusion underlies interneuronal communication. Complexin is a major binding partner of the SNARE complex, the core fusion machinery at the presynapse. The physiological data on complexin, however, have been at odds with each other, making delineation of its molecular function difficult. Here we report direct observation of two-faceted functions of complexin using the single-vesicle fluorescence fusion assay and EPR. We show that complexin I has two opposing effects on trans-SNARE assembly: inhibition of SNARE complex formation and stabilization of assembled SNARE complexes. Of note, SNARE-mediated fusion is markedly stimulated by complexin, and it is further accelerated by two orders of magnitude in response to an externally applied Ca(2+) wave. We suggest that SNARE complexes, complexins and phospholipids collectively form a complex substrate for Ca(2+) and Ca(2+)-sensing fusion effectors in neurotransmitter release.\",\n \"corpus_id\": 17292787,\n \"score\": 1\n },\n {\n \"doc_id\": \"19128031\",\n \"title\": \"Concurrent binding of complexin and synaptotagmin to liposome-embedded SNARE complexes.\",\n \"abstract\": \"Synaptotagmin and complexin regulate SNARE-mediated synaptic vesicle exocytosis. It has been proposed that complexin clamps membrane fusion and that Ca(2+)-synaptotagmin displaces complexin from SNARE complexes to relieve this clamping activity. Using a reconstituted system, we demonstrate that complexin and synaptotagmin simultaneously bind to neuronal SNARE complexes and that both apo-synaptotagmin and complexin inhibit SNARE-mediated membrane fusion. Moreover, the clamping ability of apo-synaptotagmin occluded the clamping activity of complexin until the arrival of a Ca(2+) trigger, at which point synaptotagmin accelerated fusion while high concentrations of complexin inhibited fusion. Thus, the inhibitory patterns of synaptotagmin and complexin are different, suggesting that SNAREs assemble into distinct states along the fusion pathway. These data also suggest that during synaptotagmin-regulated vesicle-vesicle fusion, complexin does not function as a fusion clamp that is relieved by Ca(2+)-synaptotagmin.\",\n \"corpus_id\": 15874033,\n \"score\": 1\n },\n {\n \"doc_id\": \"19164751\",\n \"title\": \"Complexin controls the force transfer from SNARE complexes to membranes in fusion.\",\n \"abstract\": \"Trans-SNAP receptor (SNARE, where SNAP is defined as soluble NSF attachment protein, and NSF is defined as N-ethylmaleimide-sensitive factor) complexes catalyze synaptic vesicle fusion and bind complexin, but the function of complexin binding to SNARE complexes remains unclear. Here we show that in neuronal synapses, complexin simultaneously suppressed spontaneous fusion and activated fast calcium ion-evoked fusion. The dual function of complexin required SNARE binding and also involved distinct amino-terminal sequences of complexin that localize to the point where trans-SNARE complexes insert into the fusing membranes, suggesting that complexin controls the force that trans-SNARE complexes apply onto the fusing membranes. Consistent with this hypothesis, a mutation in the membrane insertion sequence of the v-SNARE synaptobrevin/vesicle-associated membrane protein (VAMP) phenocopied the complexin loss-of-function state without impairing complexin binding to SNARE complexes. Thus, complexin probably activates and clamps the force transfer from assembled trans-SNARE complexes onto fusing membranes.\",\n \"corpus_id\": 2220205,\n \"score\": 1\n },\n {\n \"doc_id\": \"19914185\",\n \"title\": \"Tilting the balance between facilitatory and inhibitory functions of mammalian and Drosophila Complexins orchestrates synaptic vesicle exocytosis.\",\n \"abstract\": \"SNARE-mediated synaptic exocytosis is orchestrated by facilitatory and inhibitory mechanisms. Genetic ablations of Complexins, a family of SNARE-complex-binding proteins, in mice and Drosophila cause apparently opposite effects on neurotransmitter release, leading to contradictory hypotheses of Complexin function. Reconstitution experiments with different fusion assays and Complexins also yield conflicting results. We therefore performed cross-species rescue experiments to compare the functions of murine and Drosophila Complexins in both mouse and fly synapses. We found that murine and Drosophila Complexins employ conserved mechanisms to regulate exocytosis despite their strikingly different overall effects on neurotransmitter release. Both Complexins contain distinct domains that facilitate or inhibit synaptic vesicle fusion, and the strength of each facilitatory or inhibitory function differs significantly between murine and Drosophila Complexins. Our results show that a relative shift in the balance of facilitatory and inhibitory functions results in differential regulation of neurotransmitter release by murine and Drosophila Complexins in vivo, reconciling previous incompatible findings.\",\n \"corpus_id\": 8356420,\n \"score\": 1\n },\n {\n \"doc_id\": \"20026076\",\n \"title\": \"Accessory alpha-helix of complexin I can displace VAMP2 locally in the complexin-SNARE quaternary complex.\",\n \"abstract\": \"The calcium-triggered neurotransmitter release requires three SNARE (soluble N-ethylmaleimide-sensitive factor attachment protein receptor) proteins: synaptobrevin 2 (or vesicle-associated membrane protein 2) on the synaptic vesicle and syntaxin 1 and SNAP-25 (synaptosome-associated protein of 25 kDa) at the presynaptic plasma membrane. This minimal fusion machinery is believed to drive fusion of the vesicle to the presynaptic membrane. Complexin, also known as synaphin, is a neuronal cytosolic protein that acts as a major regulator of synaptic vesicle exocytosis. Stimulatory and inhibitory effects of complexin have both been reported, suggesting the duality of its function. To shed light on the molecular basis of the complexin's dual function, we have performed an EPR investigation of the complexin-SNARE quaternary complex. We found that the accessory alpha-helix (amino acids 27-48) by itself has the capacity to replace the C-terminus of the SNARE motif of vesicle-associated membrane protein 2 in the four-helix bundle and makes the SNARE complex weaker when the N-terminal region of complexin I (amino acids 1-26) is removed. However, the accessory alpha-helix remains detached from the SNARE core when the N-terminal region of complexin I is present. Thus, our data show the possibility that the balance between the activities of the accessory alpha-helix and the N-terminal domain might determine the final outcome of the complexin function, either stimulatory or inhibitory.\",\n \"corpus_id\": 22886543,\n \"score\": 1\n },\n {\n \"doc_id\": \"20108313\",\n \"title\": \"Structural studies of SNARE complex and its interaction with complexin by molecular dynamics simulation.\",\n \"abstract\": \"Since neurotransmitter releasing into the synaptic space delivers electrical signals from presynaptic neural cell to the postsynaptic cell, neurotransmitter secretion must be much orchestrated. Crowded intracellular vesicles involving neurotransmitters present a question of the how secretory vesicles fuse onto the plasma membrane in a fast synchronized fashion. Complexin is one of the most experimentally studied proteins that regulate assembly of fusogenic four-helix SNARE complex to synchronized neurotransmitter secretion. We used MD simulation to investigate the interaction of complexin with the neural SNARE complex in detail. Our results show that the SNARE complex interacts with the complexin central helix by forming salt bridges and hydrogen bonds. Complexin also can interact with the Q-SNARE complex instead of synaptobrevin to decrease the Q-SNARE flexibility. The complexin alpha-accessory helix and the C-terminal region of synaptobrevin can interact with the same region of syntaxin. Although the alpha-accessory helix aids the tight binding of the central helix to the SNARE complex, its proximity with synaptobrevin causes the destabilization of syntaxin and Sn1 helices. This study suggests that the alpha-accessory helix of complexin can be an inhibiting factor for membrane fusion by competing with synaptobrevin for binding to the Q-SNARE complex.\",\n \"corpus_id\": 28179005,\n \"score\": 1\n },\n {\n \"doc_id\": \"20400951\",\n \"title\": \"Binding of the complexin N terminus to the SNARE complex potentiates synaptic-vesicle fusogenicity.\",\n \"abstract\": \"Complexins facilitate and inhibit neurotransmitter release through distinct domains, and their function was proposed to be coupled to the Ca(2+) sensor synaptotagmin-1 (Syt1). However, the mechanisms underlying complexin function remain unclear. We now uncover an interaction between the complexin N terminus and the SNARE complex C terminus, and we show that disrupting this interaction abolishes the facilitatory function of complexins in mouse neurons. Analyses of hypertonically induced exocytosis show that complexins enhance synaptic-vesicle fusogenicity. Genetic experiments crossing complexin- and Syt1-null mice indicate a functional interaction between these proteins but also show that complexins can promote Ca(2+)-triggered release in the absence of Syt1. We propose that the complexin N terminus stabilizes the SNARE complex C terminus and/or helps release the inhibitory function of complexins, thereby activating the fusion machinery in a manner that may cooperate with Syt1 but does not require Syt1.\",\n \"corpus_id\": 37974755,\n \"score\": 1\n },\n {\n \"doc_id\": \"20678575\",\n \"title\": \"Comparative analysis of Drosophila and mammalian complexins as fusion clamps and facilitators of neurotransmitter release.\",\n \"abstract\": \"The SNARE-binding protein complexin (Cpx) has been demonstrated to regulate synaptic vesicle fusion. Previous studies are consistent with Cpx functioning either as a synaptic vesicle fusion clamp to prevent premature exocytosis, or as a facilitator to directly stimulate release. Here we examined conserved roles of invertebrate and mammalian Cpx isoforms in the regulation of neurotransmitter release using the Drosophila neuromuscular junction as a model synapse. We find that SNARE binding by Cpx is required for its role as a fusion clamp. All four mammalian Cpx proteins (mCpx), which have been demonstrated to facilitate release, also function as fusion clamps when expressed in Drosophila cpx null mutants, though their clamping abilities vary between isoforms. Moreover, expression of mCpx I, II or III isoforms dramatically enhance evoked release compared to mCpx IV or Drosophila Cpx. Differences in the clamping and facilitating properties of complexin isoforms can be partially attributed to differences in the C-terminal membrane tethering domain. Our findings indicate that the function of complexins as fusion clamps and facilitators of fusion are conserved across evolution, and that these roles are genetically separable within an isoform and across different isoforms.\",\n \"corpus_id\": 3190755,\n \"score\": 1\n },\n {\n \"doc_id\": \"21144993\",\n \"title\": \"Complexin: does it deserve its name?\",\n \"abstract\": \"Knockout and other perturbations of complexins have provided important insights and elicited controversies about their role in neurotransmitter release. New work by Yang et al. in this issue of Neuron adds important detail and complexity to existing concepts-particularly on the nature of a Ca(2+)-dependent complexin-synaptotagmin switch for the triggering of exocytosis. But it also provokes thoughts about alternative interpretations, which might result in a simpler model of complexin function.\",\n \"corpus_id\": 8996828,\n \"score\": 1\n },\n {\n \"doc_id\": \"21215634\",\n \"title\": \"Complexin has opposite effects on two modes of synaptic vesicle fusion.\",\n \"abstract\": \"BACKGROUND: Synaptic transmission can occur in a binary or graded fashion, depending on whether transmitter release is triggered by action potentials or by gradual changes in membrane potential. Molecular differences of these two types of fusion events and their differential regulation in a physiological context have yet to be addressed. Complexin is a conserved SNARE-binding protein that has been proposed to regulate both spontaneous and stimulus-evoked synaptic vesicle (SV) fusion. RESULTS: Here we examine complexin function at a graded synapse in C. elegans. Null complexin (cpx-1) mutants are viable, although nervous system function is significantly impaired. Loss of CPX-1 results in a 3-fold increase in the rate of tonic synaptic transmission at the neuromuscular junction, whereas stimulus-evoked SV fusion is decreased 10-fold. A truncated CPX-1 missing its C-terminal domain can rescue stimulus-evoked synaptic vesicle exocytosis but fails to suppress tonic activity, demonstrating that these two modes of exocytosis can be distinguished at the molecular level. A CPX-1 variant with impaired SNARE binding also rescues evoked, but not tonic, neurotransmitter release. Finally, tonic, but not evoked, release can be rescued in a syntaxin point mutant by removing CPX-1. Rescue of either form of exocytosis partially restores locomotory behavior, indicating that both types of synaptic transmission are relevant. CONCLUSION: These observations suggest a dual role for CPX-1: suppressing SV exocytosis, driven by low levels of endogenous neural activity, while promoting synchronous fusion of SVs driven by a depolarizing stimulus. Thus, patterns of synaptic activity regulate complexin's inhibitory and permissive roles at a graded synapse.\",\n \"corpus_id\": 14249171,\n \"score\": 1\n },\n {\n \"doc_id\": \"23536098\",\n \"title\": \"Simultaneous monitoring of presynaptic transmitter release and postsynaptic receptor trafficking reveals an enhancement of presynaptic activity in metabotropic glutamate receptor-mediated long-term depression.\",\n \"abstract\": \"Although the contribution of postsynaptic mechanisms to long-term synaptic plasticity has been studied extensively, understanding the contribution of presynaptic modifications to this process lags behind, primarily because of a lack of techniques with which to directly and quantifiably measure neurotransmitter release from synaptic terminals. Here, we developed a method to measure presynaptic activity through the biotinylation of vesicular transporters in vesicles fused with presynaptic membranes during neurotransmitter release. This method allowed us for the first time to selectively quantify the spontaneous or evoked release of glutamate or GABA at their respective synapses. Using this method to investigate presynaptic changes during the expression of group I metabotropic glutamate receptor (mGluR1/5)-mediated long-term depression (LTD) in cultured rat hippocampal neurons, we discovered that this form of LTD was associated with increased presynaptic release of glutamate, despite reduced miniature EPSCs measured with whole-cell recording. Moreover, we found that specific blockade of AMPA receptor (AMPAR) endocytosis with a membrane-permeable GluR2-derived peptide not only prevented the expression of LTD but also eliminated LTD-associated increase in presynaptic release. Thus, our work not only demonstrates that mGluR1/5-mediated LTD is associated with increased endocytosis of postsynaptic AMPARs but also reveals an unexpected homeostatic/compensatory increase in presynaptic release. In addition, this study indicates that biotinylation of vesicular transporters in live cultured neurons is a valuable tool for studying presynaptic function.\",\n \"corpus_id\": 14958868,\n \"score\": 1\n },\n {\n \"doc_id\": \"23658160\",\n \"title\": \"Stabilization of spontaneous neurotransmitter release at ribbon synapses by ribbon-specific subtypes of complexin.\",\n \"abstract\": \"Ribbon synapses of tonically releasing sensory neurons must provide a large pool of releasable vesicles for sustained release, while minimizing spontaneous release in the absence of stimulation. Complexins are presynaptic proteins that may accomplish this dual task at conventional synapses by interacting with the molecular machinery of synaptic vesicle fusion at the active zone to retard spontaneous vesicle exocytosis yet facilitate release evoked by depolarization. However, ribbon synapses of photoreceptor cells and bipolar neurons in the retina express distinct complexin subtypes, perhaps reflecting the special requirements of these synapses for tonic release. To investigate the role of ribbon-specific complexins in transmitter release, we combined presynaptic voltage clamp, fluorescence imaging, electron microscopy, and behavioral assays of photoreceptive function in zebrafish. Acute interference with complexin function using a peptide derived from the SNARE-binding domain increased spontaneous synaptic vesicle fusion at ribbon synapses of retinal bipolar neurons without affecting release triggered by depolarization. Knockdown of complexin by injection of an antisense morpholino into zebrafish embryos prevented photoreceptor-driven migration of pigment in skin melanophores and caused the pigment distribution to remain in the dark-adapted state even when embryos were exposed to light. This suggests that loss of complexin function elevated spontaneous release in illuminated photoreceptors sufficiently to mimic the higher release rate normally associated with darkness, thus interfering with visual signaling. We conclude that visual system-specific complexins are required for proper illumination-dependent modulation of the rate of neurotransmitter release at visual system ribbon synapses.\",\n \"corpus_id\": 17949179,\n \"score\": 1\n },\n {\n \"doc_id\": \"24083833\",\n \"title\": \"Complexin-1 enhances the on-rate of vesicle docking via simultaneous SNARE and membrane interactions.\",\n \"abstract\": \"In synaptic terminals, complexin is thought to have inhibitory and activating roles for spontaneous \\\"mini\\\" release and evoked synchronized neurotransmitter release, respectively. We used single vesicle-vesicle microscopy imaging to study the effect of complexin-1 on the on-rate of docking between vesicles that mimic synaptic vesicles and the plasma membrane. We found that complexin-1 enhances the on-rate of docking of synaptic vesicle mimics containing full-length synaptobrevin-2 and full-length synaptotagmin-1 to plasma membrane-mimicking vesicles containing full-length syntaxin-1A and SNAP-25A. This effect requires the C-terminal domain of complexin-1, which binds to the membrane, the presence of PS in the membrane, and the core region of complexin-1, which binds to the SNARE complex.\",\n \"corpus_id\": 16318242,\n \"score\": 1\n },\n {\n \"doc_id\": \"24297916\",\n \"title\": \"Deconstructing complexin function in activating and clamping Ca2+-triggered exocytosis by comparing knockout and knockdown phenotypes.\",\n \"abstract\": \"Complexin, a presynaptic protein that avidly binds to assembled SNARE complexes, is widely acknowledged to activate Ca(2+)-triggered exocytosis. In addition, studies of invertebrate complexin mutants and of mouse neurons with a double knockdown (DKD) of complexin-1 and -2 suggested that complexin maintains the readily releasable pool (RRP) of vesicles and clamps spontaneous exocytosis. In contrast, studies of mouse neurons with a double knockout (DKO) of complexin-1 and -2, largely carried out in hippocampal autapses, did not detect changes in the RRP size or in spontaneous exocytosis. To clarify complexin function, we here directly compared in two different preparations, cultured cortical and olfactory bulb neurons, the phenotypes of complexin DKD and DKO neurons. We find that complexin-deficient DKD and DKO neurons invariably exhibit a ~50% decrease in vesicle priming. Moreover, the DKD consistently increased spontaneous exocytosis, but the DKO did so in cortical but not olfactory bulb neurons. Furthermore, the complexin DKD but not the complexin DKO caused a compensatory increase in complexin-3 and -4 mRNA levels; overexpression of complexin-3 but not complexin-1 increased spontaneous exocytosis. Complexin-3 but not complexin-1 contains a C-terminal lipid anchor attaching it to the plasma membrane; addition of a similar lipid anchor to complexin-1 converted complexin-1 from a clamp into an activator of spontaneous exocytosis. Viewed together, our data suggest that complexin generally functions in priming and Ca(2+) triggering of exocytosis, and additionally contributes to the control of spontaneous exocytosis dependent on the developmental history of a neuron and on the subcellular localization of the complexin.\",\n \"corpus_id\": 467451,\n \"score\": 1\n },\n {\n \"doc_id\": \"24493260\",\n \"title\": \"SNARE and regulatory proteins induce local membrane protrusions to prime docked vesicles for fast calcium-triggered fusion.\",\n \"abstract\": \"Synaptic vesicles fuse with the plasma membrane in response to Ca(2+) influx, thereby releasing neurotransmitters into the synaptic cleft. The protein machinery that mediates this process, consisting of soluble N-ethylmaleimide-sensitive factor attachment protein receptors (SNAREs) and regulatory proteins, is well known, but the mechanisms by which these proteins prime synaptic membranes for fusion are debated. In this study, we applied large-scale, automated cryo-electron tomography to image an in vitro system that reconstitutes synaptic fusion. Our findings suggest that upon docking and priming of vesicles for fast Ca(2)(+)-triggered fusion, SNARE proteins act in concert with regulatory proteins to induce a local protrusion in the plasma membrane, directed towards the primed vesicle. The SNAREs and regulatory proteins thereby stabilize the membrane in a high-energy state from which the activation energy for fusion is profoundly reduced, allowing synchronous and instantaneous fusion upon release of the complexin clamp.\",\n \"corpus_id\": 16062643,\n \"score\": 1\n },\n {\n \"doc_id\": \"24842998\",\n \"title\": \"Re-examining how complexin inhibits neurotransmitter release.\",\n \"abstract\": \"Complexins play activating and inhibitory functions in neurotransmitter release. The complexin accessory helix inhibits release and was proposed to insert into SNARE complexes to prevent their full assembly. This model was supported by 'superclamp' and 'poor-clamp' mutations that enhanced or decreased the complexin-I inhibitory activity in cell-cell fusion assays, and by the crystal structure of a superclamp mutant bound to a synaptobrevin-truncated SNARE complex. NMR studies now show that the complexin-I accessory helix does not insert into synaptobrevin-truncated SNARE complexes in solution, and electrophysiological data reveal that superclamp mutants have slightly stimulatory or no effects on neurotransmitter release, whereas a poor-clamp mutant inhibits release. Importantly, increasing or decreasing the negative charge of the complexin-I accessory helix inhibits or stimulates release, respectively. These results suggest a new model whereby the complexin accessory helix inhibits release through electrostatic (and perhaps steric) repulsion enabled by its location between the vesicle and plasma membranes. DOI: http://dx.doi.org/10.7554/eLife.02391.001.\",\n \"corpus_id\": 16428795,\n \"score\": 1\n },\n {\n \"doc_id\": \"25716318\",\n \"title\": \"Munc18a does not alter fusion rates mediated by neuronal SNAREs, synaptotagmin, and complexin.\",\n \"abstract\": \"Sec1/Munc18 (SM) proteins are essential for membrane trafficking, but their molecular mechanism remains unclear. Using a single vesicle-vesicle content-mixing assay with reconstituted neuronal SNAREs, synaptotagmin-1, and complexin-1, we show that the neuronal SM protein Munc18a/nSec1 has no effect on the intrinsic kinetics of both spontaneous fusion and Ca(2+)-triggered fusion between vesicles that mimic synaptic vesicles and the plasma membrane. However, wild type Munc18a reduced vesicle association ∼50% when the vesicles bearing the t-SNAREs syntaxin-1A and SNAP-25 were preincubated with Munc18 for 30 min. Single molecule experiments with labeled SNAP-25 indicate that the reduction of vesicle association is a consequence of sequestration of syntaxin-1A by Munc18a and subsequent release of SNAP-25 (i.e. Munc18a captures syntaxin-1A via its high affinity interaction). Moreover, a phosphorylation mimic mutant of Munc18a with reduced affinity to syntaxin-1A results in less reduction of vesicle association. In summary, Munc18a does not directly affect fusion, although it has an effect on the t-SNARE complex, depending on the presence of other factors and experimental conditions. Our results suggest that Munc18a primarily acts at the prefusion stage.\",\n \"corpus_id\": 25210663,\n \"score\": 1\n },\n {\n \"doc_id\": \"25740533\",\n \"title\": \"Functional roles of complexin in neurotransmitter release at ribbon synapses of mouse retinal bipolar neurons.\",\n \"abstract\": \"Ribbon synapses of photoreceptor cells and bipolar neurons in the retina signal graded changes in light intensity via sustained release of neurotransmitter. One molecular specialization of retinal ribbon synapses is the expression of complexin protein subtypes Cplx3 and Cplx4, whereas conventional synapses express Cplx1 and Cplx2. Because complexins bind to the molecular machinery for synaptic vesicle fusion (the SNARE complex) and modulate transmitter release at conventional synapses, we examined the roles of ribbon-specific complexin in regulating release at ribbon synapses of ON bipolar neurons from mouse retina. To interfere acutely with the interaction of native complexins with the SNARE complex, a peptide consisting of the highly conserved SNARE-binding domain of Cplx3 was introduced via a whole-cell patch pipette placed directly on the synaptic terminal, and vesicle fusion was monitored using capacitance measurements and FM-dye destaining. The inhibitory peptide, but not control peptides, increased spontaneous synaptic vesicle fusion, partially depleted reserve synaptic vesicles, and reduced fusion triggered by opening voltage-gated calcium channels under voltage clamp, without affecting the number of synaptic vesicles associated with ribbons, as revealed by electron microscopy of recorded terminals. The results are consistent with a dual role for ribbon-specific complexin, acting as a brake on the SNARE complex to prevent spontaneous fusion in the absence of calcium influx, while at the same time facilitating release evoked by depolarization.\",\n \"corpus_id\": 14843378,\n \"score\": 1\n },\n {\n \"doc_id\": \"25809246\",\n \"title\": \"Synaptic activity regulates the abundance and binding of complexin.\",\n \"abstract\": \"Nervous system function relies on precise chemical communication between neurons at specialized junctions known as synapses. Complexin (CPX) is one of a small number of cytoplasmic proteins that are indispensable in controlling neurotransmitter release through SNARE and synaptic vesicle interactions. However, the mechanisms that recruit and stabilize CPX are poorly understood. The mobility of CPX tagged with photoactivatable green fluorescent protein (pGFP) was quantified in vivo using Caenorhabditis elegans. Although pGFP escaped the synapse within seconds, CPX-pGFP displayed both fast and slow decay components, requiring minutes for complete exchange of the synaptic pool. The longer synaptic residence time of CPX arose from both synaptic vesicle and SNARE interactions, and surprisingly, CPX mobility depended on synaptic activity. Moreover, mouse CPX-GFP reversibly dispersed out of hippocampal presynaptic terminals during stimulation, and blockade of vesicle fusion prevented CPX dispersion. Hence, synaptic CPX can rapidly redistribute and this exchange is influenced by neuronal activity, potentially contributing to use-dependent plasticity.\",\n \"corpus_id\": 23658867,\n \"score\": 1\n },\n {\n \"doc_id\": \"25831964\",\n \"title\": \"Re-visiting the trans insertion model for complexin clamping.\",\n \"abstract\": \"We have previously proposed that complexin cross-links multiple pre-fusion SNARE complexes via a trans interaction to function as a clamp on SNARE-mediated neurotransmitter release. A recent NMR study was unable to detect the trans clamping interaction of complexin and therefore questioned the previous interpretation of the fluorescence resonance energy transfer and isothermal titration calorimetry data on which the trans clamping model was originally based. Here we present new biochemical data that underscore the validity of our previous interpretation and the continued relevancy of the trans insertion model for complexin clamping.\",\n \"corpus_id\": 12502620,\n \"score\": 1\n },\n {\n \"doc_id\": \"26098518\",\n \"title\": \"The Synaptic Vesicle Release Machinery.\",\n \"abstract\": \"Extensive research has yielded crucial insights into the mechanism of neurotransmitter release, and working models for the functions of key proteins involved in release. The SNAREs Syntaxin-1, Synaptobrevin, and SNAP-25 play a central role in membrane fusion, forming SNARE complexes that bridge the vesicle and plasma membranes and that are disassembled by NSF-SNAPs. Exocytosis likely starts with Syntaxin-1 folded into a self-inhibited closed conformation that binds to Munc18-1. Munc13s open Syntaxin-1, orchestrating SNARE complex assembly in an NSF-SNAP-resistant manner together with Munc18-1. In the resulting primed state, with partially assembled SNARE complexes, fusion is inhibited by Synaptotagmin-1 and Complexins, which also perform active functions in release. Upon influx of Ca(2+), Synaptotagmin-1 activates fast release, likely by relieving the inhibition caused by Complexins and cooperating with the SNAREs in bringing the membranes together. Although alternative models exist and fundamental questions remain unanswered, a definitive description of the basic release mechanism may be available soon.\",\n \"corpus_id\": 43024784,\n \"score\": 1\n },\n {\n \"doc_id\": \"26245303\",\n \"title\": \"Complexins: small but capable.\",\n \"abstract\": \"Despite intensive research, it is still unclear how an immediate and profound acceleration of exocytosis is triggered by appropriate Ca(2+)-stimuli in presynaptic terminals. This is due to the fact that the molecular mechanisms of \\\"docking\\\" and \\\"priming\\\" reactions, which set up secretory vesicles to fuse at millisecond time scale, are extremely hard to study. Yet, driven by a fruitful combination of in vitro and in vivo analyses, our mechanistic understanding of Ca(2+)-triggered vesicle fusion has certainly advanced in the past few years. In this review, we aim to highlight recent progress and emerging views on the molecular mechanisms, by which constitutively forming SNAREpins are organized in functional, tightly regulated units for synchronized release. In particular, we will focus on the role of the small regulatory factor complexin whose function in Ca(2+)-dependent exocytosis has been controversially discussed for more than a decade. Special emphasis will also be laid on the functional relationship of complexin and synaptotagmin, as both proteins possibly act as allies and/or antagonists to govern SNARE-mediated exocytosis.\",\n \"corpus_id\": 2990515,\n \"score\": 1\n },\n {\n \"doc_id\": \"26338476\",\n \"title\": \"Evolutionary conservation of complexins: from choanoflagellates to mice.\",\n \"abstract\": \"Complexins are synaptic SNARE complex-binding proteins that cooperate with synaptotagmins in activating Ca(2+)-stimulated, synaptotagmin-dependent synaptic vesicle exocytosis and in clamping spontaneous, synaptotagmin-independent synaptic vesicle exocytosis. Here, we show that complexin sequences are conserved in some non-metazoan unicellular organisms and in all metazoans, suggesting that complexins are a universal feature of metazoans that predate metazoan evolution. We show that complexin from Nematostella vectensis, a cnidarian sea anemone far separated from mammals in metazoan evolution, functionally replaces mouse complexins in activating Ca(2+)-triggered exocytosis, but is unable to clamp spontaneous exocytosis. Thus, the activating function of complexins is likely conserved throughout metazoan evolution.\",\n \"corpus_id\": 12939627,\n \"score\": 1\n },\n {\n \"doc_id\": \"26590346\",\n \"title\": \"Phosphorylation of Complexin by PKA Regulates Activity-Dependent Spontaneous Neurotransmitter Release and Structural Synaptic Plasticity.\",\n \"abstract\": \"Synaptic plasticity is a fundamental feature of the nervous system that allows adaptation to changing behavioral environments. Most studies of synaptic plasticity have examined the regulated trafficking of postsynaptic glutamate receptors that generates alterations in synaptic transmission. Whether and how changes in the presynaptic release machinery contribute to neuronal plasticity is less clear. The SNARE complex mediates neurotransmitter release in response to presynaptic Ca(2+) entry. Here we show that the SNARE fusion clamp Complexin undergoes activity-dependent phosphorylation that alters the basic properties of neurotransmission in Drosophila. Retrograde signaling following stimulation activates PKA-dependent phosphorylation of the Complexin C terminus that selectively and transiently enhances spontaneous release. Enhanced spontaneous release is required for activity-dependent synaptic growth. These data indicate that SNARE-dependent fusion mechanisms can be regulated in an activity-dependent manner and highlight the key role of spontaneous neurotransmitter release as a mediator of functional and structural plasticity.\",\n \"corpus_id\": 11327307,\n \"score\": 1\n },\n {\n \"doc_id\": \"27806277\",\n \"title\": \"Interaction of the Complexin Accessory Helix with Synaptobrevin Regulates Spontaneous Fusion.\",\n \"abstract\": \"Neuronal transmitters are released from nerve terminals via the fusion of synaptic vesicles with the plasma membrane. Vesicles attach to membranes via a specialized protein machinery composed of membrane-attached (t-SNARE) and vesicle-attached (v-SNARE) proteins that zipper together to form a coiled-coil SNARE bundle that brings the two fusing membranes into close proximity. Neurotransmitter release may occur either in response to an action potential or through spontaneous fusion. A cytosolic protein, Complexin (Cpx), binds the SNARE complex and restricts spontaneous exocytosis by acting as a fusion clamp. We previously proposed a model in which the interaction between Cpx and the v-SNARE serves as a spring to prevent premature zippering of the SNARE complex, thereby reducing the likelihood of fusion. To test this model, we combined molecular-dynamics (MD) simulations and site-directed mutagenesis of Cpx and SNAREs in Drosophila. MD simulations of the Drosophila Cpx-SNARE complex demonstrated that Cpx's interaction with the v-SNARE promotes unraveling of the v-SNARE off the core SNARE bundle. We investigated clamping properties in the syx(3-69) paralytic mutant, which has a single-point mutation in the t-SNARE and displays enhanced spontaneous release. MD simulations demonstrated an altered interaction of Cpx with the SNARE bundle that hindered v-SNARE unraveling by Cpx, thus compromising clamping. We used our model to predict mutations that should enhance the ability of Cpx to prevent full assembly of the SNARE complex. MD simulations predicted that a weakened interaction between the Cpx accessory helix and the v-SNARE would enhance Cpx flexibility and thus promote separation of SNAREs, reducing spontaneous fusion. We generated transgenic Drosophila with mutations in Cpx and the v-SNARE that disrupted a salt bridge between these two proteins. As predicted, both lines demonstrated a selective inhibition in spontaneous release, suggesting that Cpx acts as a fusion clamp that restricts full SNARE zippering.\",\n \"corpus_id\": 35760770,\n \"score\": 1\n },\n {\n \"doc_id\": \"28077717\",\n \"title\": \"Complexin Mutants Reveal Partial Segregation between Recycling Pathways That Drive Evoked and Spontaneous Neurotransmission.\",\n \"abstract\": \"Synaptic vesicles fuse at morphological specializations in the presynaptic terminal termed active zones (AZs). Vesicle fusion can occur spontaneously or in response to an action potential. Following fusion, vesicles are retrieved and recycled within nerve terminals. It is still unclear whether vesicles that fuse spontaneously or following evoked release share similar recycling mechanisms. Genetic deletion of the SNARE-binding protein complexin dramatically increases spontaneous fusion, with the protein serving as the synaptic vesicle fusion clamp at Drosophila synapses. We examined synaptic vesicle recycling pathways at complexin null neuromuscular junctions, where spontaneous release is dramatically enhanced. We combined loading of the lipophilic dye FM1-43 with photoconversion, electron microscopy, and electrophysiology to monitor evoked and spontaneous recycling vesicle pools. We found that the total number of recycling vesicles was equal to those retrieved through spontaneous and evoked pools, suggesting that retrieval following fusion is partially segregated for spontaneous and evoked release. In addition, the kinetics of FM1-43 destaining and synaptic depression measured in the presence of the vesicle-refilling blocker bafilomycin indicated that spontaneous and evoked recycling pools partially intermix during the release process. Finally, FM1-43 photoconversion combined with electron microscopy analysis indicated that spontaneous recycling preferentially involves synaptic vesicles in the vicinity of AZs, whereas vesicles recycled following evoked release involve a larger intraterminal pool. Together, these results suggest that spontaneous and evoked vesicles use separable recycling pathways and then partially intermix during subsequent rounds of fusion. SIGNIFICANCE STATEMENT: Neurotransmitter release involves fusion of synaptic vesicles with the plasma membrane in response to an action potential, or spontaneously in the absence of stimulation. Upon fusion, vesicles are retrieved and recycled, and it is unclear whether recycling pathways for evoked and spontaneous vesicles are segregated after fusion. We addressed this question by taking advantage of preparations lacking the synaptic protein complexin, which have elevated spontaneous release that enables reliable tracking of the spontaneous recycling pool. Our results suggest that spontaneous and evoked recycling pathways are segregated during the retrieval process but can partially intermix during stimulation.\",\n \"corpus_id\": -1,\n \"score\": 1\n },\n {\n \"doc_id\": \"28813412\",\n \"title\": \"The primed SNARE-complexin-synaptotagmin complex for neuronal exocytosis.\",\n \"abstract\": \"Synaptotagmin, complexin, and neuronal SNARE (soluble N-ethylmaleimide sensitive factor attachment protein receptor) proteins mediate evoked synchronous neurotransmitter release, but the molecular mechanisms mediating the cooperation between these molecules remain unclear. Here we determine crystal structures of the primed pre-fusion SNARE-complexin-synaptotagmin-1 complex. These structures reveal an unexpected tripartite interface between synaptotagmin-1 and both the SNARE complex and complexin. Simultaneously, a second synaptotagmin-1 molecule interacts with the other side of the SNARE complex via the previously identified primary interface. Mutations that disrupt either interface in solution also severely impair evoked synchronous release in neurons, suggesting that both interfaces are essential for the primed pre-fusion state. Ca(2+) binding to the synaptotagmin-1 molecules unlocks the complex, allows full zippering of the SNARE complex, and triggers membrane fusion. The tripartite SNARE-complexin-synaptotagmin-1 complex at a synaptic vesicle docking site has to be unlocked for triggered fusion to start, explaining the cooperation between complexin and synaptotagmin-1 in synchronizing evoked release on the sub-millisecond timescale.\",\n \"corpus_id\": 205259313,\n \"score\": 1\n },\n {\n \"doc_id\": \"29535609\",\n \"title\": \"Accessory and Central α-helices of Complexin Selectively Activate Ca2+ Triggering of Synaptic Exocytosis.\",\n \"abstract\": \"Complexins, binding to assembling soluble NSF-attachment protein receptor (SNARE) complexes, activate Ca2+ triggered exocytosis and clamp spontaneous release in the presynaptic terminal. Functions of complexin are structural dependent and mechanistically distinct. To further understand the functional/structural dependence of complexin, here we show that the accessory and central α-helices of complexin are sufficient in activation of Ca2+ triggered vesicle fusion but not in clamping spontaneous release. Targeting the two α-helices to synaptic vesicle suppresses spontaneous release, thus further emphasizing the importance of curvature membrane localization in clamping function.\",\n \"corpus_id\": 3513367,\n \"score\": 1\n },\n {\n \"doc_id\": \"19515924\",\n \"title\": \"The unitary event underlying multiquantal EPSCs at a hair cell's ribbon synapse.\",\n \"abstract\": \"EPSCs at the synapses of sensory receptors and of some CNS neurons include large events thought to represent the synchronous release of the neurotransmitter contained in several synaptic vesicles by a process known as multiquantal release. However, determination of the unitary, quantal size underlying such putatively multiquantal events has proven difficult at hair cell synapses, hindering confirmation that large EPSCs are in fact multiquantal. Here, we address this issue by performing presynaptic membrane capacitance measurements together with paired recordings at the ribbon synapses of adult hair cells. These simultaneous presynaptic and postsynaptic assays of exocytosis, together with electron microscopic estimates of single vesicle capacitance, allow us to estimate a single vesicle EPSC charge of approximately -45 fC, a value in close agreement with the mean postsynaptic charge transfer of uniformly small EPSCs recorded during periods of presynaptic hyperpolarization. By thus establishing the magnitude of the fundamental quantal event at this peripheral sensory synapse, we provide evidence that the majority of spontaneous and evoked EPSCs are multiquantal. Furthermore, we show that the prevalence of uniquantal versus multiquantal events is Ca2+ dependent. Paired recordings also reveal a tight correlation between membrane capacitance increase and evoked EPSC charge, indicating that glutamate release during prolonged hair cell depolarization does not significantly saturate or desensitize postsynaptic AMPA receptors. We propose that the large EPSCs reflect the highly synchronized release of multiple vesicles at single presynaptic ribbon-type active zones through a compound or coordinated vesicle fusion mechanism.\",\n \"corpus_id\": 15204395,\n \"score\": 0\n },\n {\n \"doc_id\": \"20074062\",\n \"title\": \"Role of C2 domain proteins during synaptic vesicle exocytosis.\",\n \"abstract\": \"Neurotransmitter release is mediated by the fusion of synaptic vesicles with the presynaptic plasma membrane. Fusion is triggered by a rise in the intracellular calcium concentration and is dependent on the neuronal SNARE (soluble N-ethylmaleimide-sensitive fusion protein-attachment protein receptor) complex. A plethora of molecules such as members of the MUNC13, MUNC18, complexin and synaptotagmin families act along with the SNARE complex to enable calcium-regulated synaptic vesicle exocytosis. The synaptotagmins are localized to synaptic vesicles by an N-terminal transmembrane domain and contain two cytoplasmic C2 domains. Members of the synaptotagmin family are thought to translate the rise in intracellular calcium concentration into synaptic vesicle fusion. The C2 domains of synaptotagmin-1 bind membranes in a calcium-dependent manner and in response induce a high degree of membrane curvature, which is required for its ability to trigger membrane fusion in vitro and in vivo. Furthermore, members of the soluble DOC2 (double-C2 domain) protein family have similar properties. Taken together, these results suggest that C2 domain proteins such as the synaptotagmins and DOC2s promote membrane fusion by the induction of membrane curvature in the vicinity of the SNARE complex. Given the widespread expression of C2 domain proteins in secretory cells, it is proposed that promotion of SNARE-dependent membrane fusion by the induction of membrane curvature is a widespread phenomenon.\",\n \"corpus_id\": 22170305,\n \"score\": 0\n },\n {\n \"doc_id\": \"20526850\",\n \"title\": \"Realistic modelling of receptor activation in hippocampal excitatory synapses: analysis of multivesicular release, release location, temperature and synaptic cross-talk.\",\n \"abstract\": \"Chemically mediated synaptic transmission results from fusion of synaptic vesicles with the presynaptic plasma membrane, subsequent release of the vesicular content into the cleft and binding to postsynaptic receptors. Previous modelling studies of excitatory neurotransmitter glutamate were based on simplified geometries failing to account for the biologically realistic synaptic environment, in particular, the presence of astrocytes, the geometry of extracellular space, and the neurotransmitter uptake mechanism. Using 3-dimensional reconstructions of hippocampal glutamatergic synapses including the surrounding astrocytic processes we have developed a biologically realistic model to analyse receptor activation in different conditions. We used the finite element method to simulate glutamate release, analyse glutamate diffusion following single and multiple vesicle release and binding at the postsynaptic site to AMPA and NMDA receptors. We demonstrate that: (1) the transmitter diffusion is highly temperature-sensitive; (2) release conditions and geometry more specifically affect AMPARs than NMDARs; (3) the sensitivities of AMPARs and NMDARs to simultaneous vesicular release are different; (4) in the case of multivesicle neurotransmitter release with variable delays, the binding of glutamate to AMPARs is additive up to 1 ms after the release, then becomes independent, but to NMDARs the binding is additive up to 33 ms; (5) the number of AMPARs varies more than the number of NMDRs in response to the input firing patterns; (6) the presence of astrocytes effectively blocks synaptic cross-talk; and (7) synaptic cross-talk, mediated by NMDARs but not AMPARs, is only possible after quasi-simultaneous multivesicular release at physiological temperature (35 degrees C) without intervening astrocytes, but not at 25 degrees C. Our simulations demonstrate the importance of temperature and ultrastructural synaptic environment in synaptic transmission and synaptic cross-talk.\",\n \"corpus_id\": 29131577,\n \"score\": 0\n },\n {\n \"doc_id\": \"20829354\",\n \"title\": \"Complexin 2 modulates vesicle-associated membrane protein (VAMP) 2-regulated zymogen granule exocytosis in pancreatic acini.\",\n \"abstract\": \"Complexins are soluble proteins that regulate the activity of soluble N-ethylmaleimide-sensitive factor attachment protein receptor (SNARE) complexes necessary for vesicle fusion. Neuronal specific complexin 1 has inhibitory and stimulatory effects on exocytosis by clamping trans-SNARE complexes in a prefusion state and promoting conformational changes to facilitate membrane fusion following cell stimulation. Complexins are unable to bind to monomeric SNARE proteins but bind with high affinity to ternary SNARE complexes and with lower affinity to target SNARE complexes. Far less is understood about complexin function outside the nervous system. Pancreatic acini express the complexin 2 isoform by RT-PCR and immunoblotting. Immunofluorescence microscopy revealed complexin 2 localized along the apical plasma membrane consistent with a role in secretion. Accordingly, complexin 2 was found to interact with vesicle-associated membrane protein (VAMP) 2, syntaxins 3 and 4, but not with VAMP 8 or syntaxin 2. Introduction of recombinant complexin 2 into permeabilized acini inhibited Ca(2+)-stimulated secretion in a concentration-dependent manner with a maximal inhibition of nearly 50%. Mutations of the central α-helical domain reduced complexin 2 SNARE binding and concurrently abolished its inhibitory activity. Surprisingly, mutation of arginine 59 to histidine within the central α-helical domain did not alter SNARE binding and moreover, augmented Ca(2+)-stimulated secretion by 130% of control. Consistent with biochemical studies, complexin 2 colocalized with VAMP 2 along the apical plasma membrane following cholecystokinin-8 stimulation. These data demonstrate a functional role for complexin 2 outside the nervous system and indicate that it participates in the Ca(2+)-sensitive regulatory pathway for zymogen granule exocytosis.\",\n \"corpus_id\": 205302672,\n \"score\": 0\n },\n {\n \"doc_id\": \"21098665\",\n \"title\": \"Postsynaptic GluA1 enables acute retrograde enhancement of presynaptic function to coordinate adaptation to synaptic inactivity.\",\n \"abstract\": \"Prolonged blockade of AMPA-type glutamate receptors in hippocampal neuron cultures leads to homeostatic enhancements of pre- and postsynaptic function that appear correlated at individual synapses, suggesting some form of transsynaptic coordination. The respective modifications are important for overall synaptic strength but their interrelationship, dynamics, and molecular underpinnings are unclear. Here we demonstrate that adaptation begins postsynaptically but is ultimately communicated to presynaptic terminals and expressed as an accelerated turnover of synaptic vesicles. Critical postsynaptic modifications occur over hours, but enable retrograde communication within minutes once AMPA receptor (AMPAR) blockade is removed, causing elevation of both spontaneous and evoked vesicle fusion. The retrograde signaling does not require spiking activity and can be interrupted by NBQX, philanthotoxin, postsynaptic BAPTA, or external sequestration of BDNF, consistent with the acute release of retrograde messenger, triggered by postsynaptic Ca(2+) elevation via Ca(2+)-permeable AMPARs.\",\n \"corpus_id\": 14023628,\n \"score\": 0\n },\n {\n \"doc_id\": \"21110949\",\n \"title\": \"Identification of complexin II in astrocytes: a possible regulator of glutamate release in these cells.\",\n \"abstract\": \"Complexins are a family of SNARE complex-binding proteins which regulate neurotransmitter release by playing a crucial role in triggering fast exocytosis at the synapse. Current evidence indicates astrocytes can release glutamate via a vesicular mechanism similar to that at nerve terminals and thereby modulate synaptic activity. In addition, components of the biochemical machinery associated with synaptic release have been identified in these cells. However, whether complexins are also present in astrocytes and may therefore participate in the vesicular release of glutamate is a key issue that is yet to be determined. In the present study we therefore examined if astrocytes express complexin I (Cpx I) and/or complexin II (Cpx II). Our results indicate these cells contain Cpx II but not Cpx I in primary culture. In addition, serum deprivation for 24 h led to a 2.6-fold increase in Cpx II, suggesting this protein is responsive to insults. These findings point to Cpx II being a likely key modulator of synaptic activity at the level of these glial cells. Given the considered involvement of complexins in neurologic and psychiatric illness, astrocytic Cpx II represents a potentially important therapeutic target for the future treatment of such maladies.\",\n \"corpus_id\": 205913901,\n \"score\": 0\n },\n {\n \"doc_id\": \"21272392\",\n \"title\": \"Synaptic release at mammalian bipolar cell terminals.\",\n \"abstract\": \"Bipolar cells play a vital role in the transfer of visual information across the vertebrate retina. The synaptic output of these neurons is regulated by factors that are extrinsic and intrinsic. Relatively little is known about the intrinsic factors that regulate neurotransmitter exocytosis. Much of what we know about intrinsic presynaptic mechanisms that regulate glutamate release has come from the study of the unusually large and accessible synaptic terminal of the goldfish rod-dominant bipolar cell, the Mb1 bipolar cell. However, over the past several years, examination of presynaptic mechanisms governing neurotransmitter release has been extended to the mammalian rod bipolar cell. In this review, we discuss the recent advances in our understanding of synaptic vesicle dynamics and neurotransmitter release in rodent rod bipolar cells and consider how these properties help to shape the synaptic output of the mammalian retina.\",\n \"corpus_id\": 37079692,\n \"score\": 0\n },\n {\n \"doc_id\": \"22284181\",\n \"title\": \"Postsynaptic complexin controls AMPA receptor exocytosis during LTP.\",\n \"abstract\": \"Long-term potentiation (LTP) is a compelling synaptic correlate of learning and memory. LTP induction requires NMDA receptor (NMDAR) activation, which triggers SNARE-dependent exocytosis of AMPA receptors (AMPARs). However, the molecular mechanisms mediating AMPAR exocytosis induced by NMDAR activation remain largely unknown. Here, we show that complexin, a protein that regulates neurotransmitter release via binding to SNARE complexes, is essential for AMPAR exocytosis during LTP but not for the constitutive AMPAR exocytosis that maintains basal synaptic strength. The regulated postsynaptic AMPAR exocytosis during LTP requires binding of complexin to SNARE complexes. In hippocampal neurons, presynaptic complexin acts together with synaptotagmin-1 to mediate neurotransmitter release. However, postsynaptic synaptotagmin-1 is not required for complexin-dependent AMPAR exocytosis during LTP. These results suggest a complexin-dependent molecular mechanism for regulating AMPAR delivery to synapses, a mechanism that is surprisingly similar to presynaptic exocytosis but controlled by regulators other than synaptotagmin-1.\",\n \"corpus_id\": 7486817,\n \"score\": 0\n },\n {\n \"doc_id\": \"23216578\",\n \"title\": \"Regulators of synaptic transmission: roles in the pathogenesis and treatment of epilepsy.\",\n \"abstract\": \"Synaptic transmission is the communication between a presynaptic and a postsynaptic neuron, and the subsequent processing of the signal. These processes are complex and highly regulated, reflecting their importance in normal brain functioning and homeostasis. Sustaining synaptic transmission depends on the continuing cycle of synaptic vesicle formation, release, and endocytosis, which requires proteins such as dynamin, syndapin, synapsin, and synaptic vesicle protein 2A. Synaptic transmission is regulated by diverse mechanisms, including presynaptic modulators of synaptic vesicle formation and release, postsynaptic receptors and signaling, and modulators of neurotransmission. Neurotransmitters released presynaptically can bind to their postsynaptic receptors, the inhibitory γ-aminobutyric acid (GABA)ergic receptors or the excitatory glutamate receptors. Once released, glutamate activates a variety of postsynaptic receptors including α-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid (AMPA), N-methyl-D-aspartate (NMDA), kainate, and metabotropic receptors. The activation of the receptors triggers downstream signaling cascades generating a vast array of effects, which can be modulated by a numerous auxiliary regulatory subunits. Moreover, different neuropeptides such as neuropeptide Y, brain-derived neurotrophic factor (BDNF), somatostatin, ghrelin, and galanin, act as regulators of diverse synaptic functions and along with the classic neurotransmitters. Abnormalities in the regulation of synaptic transmission play a critical role in the pathogenesis of numerous brain diseases, including epilepsy. This review focuses on the different mechanisms involved in the regulation of synaptic transmission, which may play a role in the pathogenesis of epilepsy: the presynaptic modulators of synaptic vesicle formation and release, postsynaptic receptors, and modulators of neurotransmission, including the mechanism by which drugs can modulate the frequency and severity of epileptic seizures.\",\n \"corpus_id\": 27930716,\n \"score\": 0\n },\n {\n \"doc_id\": \"27335398\",\n \"title\": \"Functional Roles of Complexin3 and Complexin4 at Mouse Photoreceptor Ribbon Synapses.\",\n \"abstract\": \"UNLABELLED: Complexins (Cplxs) are SNARE complex regulators controlling the speed and Ca(2+) sensitivity of SNARE-mediated synaptic vesicle fusion. We have shown previously that photoreceptor ribbon synapses in mouse retina are equipped with Cplx3 and Cplx4 and that lack of both Cplxs perturbs photoreceptor ribbon synaptic function; however, Cplx3/4 function in photoreceptor synaptic transmission remained elusive. To investigate Cplx3/4 function in photoreceptor ribbon synapses, voltage-clamp recordings from postsynaptic horizontal cells were performed in horizontal slice preparations of Cplx3/4 wild-type (WT) and Cplx3/4 double knock-out (DKO) mice. We measured tonic activity in light and dark, current responses to changes in luminous intensity, and electrically evoked postsynaptic responses. Cplx3/4 decreased the frequency of tonic events and shifted their amplitude distribution to smaller values. Light responses were sustained in the presence of Cplx3/4, but transient in their absence. Finally, Cplx3/4 increased synaptic vesicle release evoked by electrical stimulation. Using electron microscopy, we quantified the number of synaptic vesicles at presynaptic ribbons after light or dark adaptation. In Cplx3/4 WT photoreceptors, the number of synaptic vesicles associated with the ribbon base close to the release site was significantly lower in light than in dark. This is in contrast to Cplx3/4 DKO photoreceptors, in which the number of ribbon-associated synaptic vesicles remained unchanged regardless of the adaptational state. Our results indicate a suppressing and a facilitating action of Cplx3/4 on Ca(2+)-dependent tonic and evoked neurotransmitter release, respectively, and a regulatory role in the adaptation-dependent availability of synaptic vesicles for release at photoreceptor ribbon synapses. SIGNIFICANCE STATEMENT: Synaptic vesicle fusion at active zones of chemical synapses is executed by SNARE complexes. Complexins (Cplxs) are SNARE complex regulators and photoreceptor ribbon synapses are equipped with Cplx3 and Cplx4. The absence of both Cplxs perturbs ribbon synaptic function. Because we lack information on Cplx function in photoreceptor synaptic transmission, we investigated Cplx function using voltage-clamp recordings from postsynaptic horizontal cells of Cplx3/4 wild-type and Cplx3/4 double knock-out mice and quantified synaptic vesicle number at the ribbon after light and dark adaptation using electron microscopy. The findings reveal a suppressing action of Cplx3/4 on tonic neurotransmitter release, a facilitating action on evoked release, and a regulatory role of Cplx3/4 in the adaptation-dependent availability of synaptic vesicles at mouse photoreceptor ribbon synapses.\",\n \"corpus_id\": 41281024,\n \"score\": 0\n },\n {\n \"doc_id\": \"27881952\",\n \"title\": \"Tissue-type Plasminogen Activator (tPA) Modulates the Postsynaptic Response of Cerebral Cortical Neurons to the Presynaptic Release of Glutamate.\",\n \"abstract\": \"Tissue-type plasminogen activator (tPA) is a serine proteinase released by the presynaptic terminal of cerebral cortical neurons following membrane depolarization (Echeverry et al., 2010). Recent studies indicate that the release of tPA triggers the synaptic vesicle cycle and promotes the exocytosis (Wu et al., 2015) and endocytic retrieval (Yepes et al., 2016) of glutamate-containing synaptic vesicles. Here we used electron microscopy, proteomics, quantitative phosphoproteomics, biochemical analyses with extracts of the postsynaptic density (PSD), and an animal model of cerebral ischemia with mice overexpressing neuronal tPA to study whether the presynaptic release of tPA also has an effect on the postsynaptic terminal. We found that tPA has a bidirectional effect on the composition of the PSD of cerebral cortical neurons that is independent of the generation of plasmin and the presynaptic release of glutamate, but depends on the baseline level of neuronal activity and the extracellular concentrations of calcium (Ca(2+)). Accordingly, in neurons that are either inactive or incubated with low Ca(2+) concentrations tPA induces phosphorylation and accumulation in the PSD of the Ca(2+)/calmodulin-dependent protein kinase IIα (pCaMKIIα), followed by pCaMKIIα-mediated phosphorylation and synaptic recruitment of GluR1-containing α-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid (AMPA) receptors. In contrast, in neurons with previously increased baseline levels of pCaMKIIα in the PSD due to neuronal depolarization in vivo or incubation with high concentrations of either Ca(2+) or glutamate in vitro, tPA induces pCaMKIIα and pGluR1 dephosphorylation and their subsequent removal from the PSD. We found that these effects of tPA are mediated by synaptic N-methyl-D-aspartate (NMDA) receptors and cyclin-dependent kinase 5 (Cdk5)-induced phosphorylation of the protein phosphatase 1 (PP1) at T320. Our data indicate that by regulating the pCaMKIIα/PP1 balance in the PSD tPA acts as a homeostatic regulator of the postsynaptic response of cerebral cortical neurons to the presynaptic release of glutamate.\",\n \"corpus_id\": 1138590,\n \"score\": 0\n }\n]","isConversational":false}}},{"rowIdx":86,"cells":{"query":{"kind":"string","value":"{\n \"doc_id\": \"25686604\",\n \"title\": \"ATG14 promotes membrane tethering and fusion of autophagosomes to endolysosomes.\",\n \"abstract\": \"Autophagy, an important catabolic pathway implicated in a broad spectrum of human diseases, begins by forming double membrane autophagosomes that engulf cytosolic cargo and ends by fusing autophagosomes with lysosomes for degradation. Membrane fusion activity is required for early biogenesis of autophagosomes and late degradation in lysosomes. However, the key regulatory mechanisms of autophagic membrane tethering and fusion remain largely unknown. Here we report that ATG14 (also known as beclin-1-associated autophagy-related key regulator (Barkor) or ATG14L), an essential autophagy-specific regulator of the class III phosphatidylinositol 3-kinase complex, promotes membrane tethering of protein-free liposomes, and enhances hemifusion and full fusion of proteoliposomes reconstituted with the target (t)-SNAREs (soluble N-ethylmaleimide-sensitive factor attachment protein receptors) syntaxin 17 (STX17) and SNAP29, and the vesicle (v)-SNARE VAMP8 (vesicle-associated membrane protein 8). ATG14 binds to the SNARE core domain of STX17 through its coiled-coil domain, and stabilizes the STX17-SNAP29 binary t-SNARE complex on autophagosomes. The STX17 binding, membrane tethering and fusion-enhancing activities of ATG14 require its homo-oligomerization by cysteine repeats. In ATG14 homo-oligomerization-defective cells, autophagosomes still efficiently form but their fusion with endolysosomes is blocked. Recombinant ATG14 homo-oligomerization mutants also completely lose their ability to promote membrane tethering and to enhance SNARE-mediated fusion in vitro. Taken together, our data suggest an autophagy-specific membrane fusion mechanism in which oligomeric ATG14 directly binds to STX17-SNAP29 binary t-SNARE complex on autophagosomes and primes it for VAMP8 interaction to promote autophagosome-endolysosome fusion.\",\n \"corpus_id\": 4404364\n}"},"candidates":{"kind":"list like","value":[{"doc_id":"19050071","title":"Identification of Barkor as a mammalian autophagy-specific factor for Beclin 1 and class III phosphatidylinositol 3-kinase.","abstract":"Autophagy mediates the cellular response to nutrient deprivation, protein aggregation, and pathogen invasion in human. Dysfunction of autophagy has been implicated in multiple human diseases including cancer. The identification of novel autophagy factors in mammalian cells will provide critical mechanistic insights into how this complicated cellular pathway responds to a broad range of challenges. Here, we report the cloning of an autophagy-specific protein that we called Barkor (Beclin 1-associated autophagy-related key regulator) through direct interaction with Beclin 1 in the human phosphatidylinositol 3-kinase class III complex. Barkor shares 18% sequence identity and 32% sequence similarity with yeast Atg14. Elimination of Barkor expression by RNA interference compromises starvation- and rapamycin-induced LC3 lipidation and autophagosome formation. Overexpression of Barkor leads to autophagy activation and increased number and enlarged volume of autophagosomes. Tellingly, Barkor is also required for suppression of the autophagy-mediated intracellular survival of Salmonella typhimurium in mammalian cells. Mechanistically, Barkor competes with UV radiation resistance associated gene product (UVRAG) for interaction with Beclin 1, and the complex formation of Barkor and Beclin1 is required for their localizations to autophagosomes. Therefore, we define a regulatory signaling pathway mediated by Barkor that positively controls autophagy through Beclin 1 and represents a potential target for drug development in the treatment of human diseases implicated in autophagic dysfunction.","corpus_id":205242712,"score":2},{"doc_id":"21518905","title":"Autophagosome targeting and membrane curvature sensing by Barkor/Atg14(L).","abstract":"The class III phosphatidylinositol 3-kinase (PI3KC3) is crucial for autophagosome biogenesis. It has been long speculated to nucleate the autophagosome membrane, but the biochemical mechanism of such nucleation activity remains unsolved. We recently identified Barkor/Atg14(L) as the targeting factor for PI3KC3 to autophagosome membrane. Here, we show that we have characterized the region of Barkor/Atg14(L) required for autophagosome targeting and identified the BATS [Barkor/Atg14(L) autophagosome targeting sequence] domain at the carboxyl terminus of Barkor. Bioinformatics and mutagenesis analyses revealed that the BATS domain binds to autophagosome membrane via the hydrophobic surface of an intrinsic amphipathic alpha helix. BATS puncta overlap with Atg16 and LC3, and partially with DFCP1, in a stress-inducible manner. Ectopically expressed BATS accumulates on highly curved tubules that likely represent intermediate autophagic structures. PI3KC3 recruitment and autophagy stimulation by Barkor/Atg14(L) require the BATS domain. Furthermore, our biochemical analyses indicate that the BATS domain directly binds to the membrane, and it favors membrane composed of phosphatidylinositol 3-phosphate [PtdIns(3)P] and phosphatidylinositol 4,5-biphosphate [PtdIns(4,5)P2]. By binding preferentially to curved membranes incorporated with PtdIns(3)P but not PtdIns(4,5)P2, the BATS domain is capable of sensing membrane curvature. Thus, we propose a novel model of PI3KC3 autophagosome membrane nucleation in which its autophagosome-specific adaptor, Barkor, accumulates on highly curved PtdIns(3)P enriched autophagic membrane via its BATS domain to sense and maintain membrane curvature.","corpus_id":7823697,"score":2},{"doc_id":"21784249","title":"SNARE proteins are required for macroautophagy.","abstract":"Macroautophagy mediates the degradation of long-lived proteins and organelles via the de novo formation of double-membrane autophagosomes that sequester cytoplasm and deliver it to the vacuole/lysosome; however, relatively little is known about autophagosome biogenesis. Atg8, a phosphatidylethanolamine-conjugated protein, was previously proposed to function in autophagosome membrane expansion, based on the observation that it mediates liposome tethering and hemifusion in vitro. We show here that with physiological concentrations of phosphatidylethanolamine, Atg8 does not act as a fusogen. Rather, we provide evidence for the involvement of exocytic Q/t-SNAREs in autophagosome formation, acting in the recruitment of key autophagy components to the site of autophagosome formation, and in regulating the organization of Atg9 into tubulovesicular clusters. Additionally, we found that the endosomal Q/t-SNARE Tlg2 and the R/v-SNAREs Sec22 and Ykt6 interact with Sso1-Sec9, and are required for normal Atg9 transport. Thus, multiple SNARE-mediated fusion events are likely to be involved in autophagosome biogenesis.","corpus_id":3842068,"score":2},{"doc_id":"23217709","title":"The hairpin-type tail-anchored SNARE syntaxin 17 targets to autophagosomes for fusion with endosomes/lysosomes.","abstract":"The lysosome is a degradative organelle, and its fusion with other organelles is strictly regulated. In contrast to fusion with the late endosome, the mechanisms underlying autophagosome-lysosome fusion remain unknown. Here, we identify syntaxin 17 (Stx17) as the autophagosomal SNARE required for fusion with the endosome/lysosome. Stx17 localizes to the outer membrane of completed autophagosomes but not to the isolation membrane (unclosed intermediate structures); for this reason, the lysosome does not fuse with the isolation membrane. Stx17 interacts with SNAP-29 and the endosomal/lysosomal SNARE VAMP8. Depletion of Stx17 causes accumulation of autophagosomes without degradation. Stx17 has a unique C-terminal hairpin structure mediated by two tandem transmembrane domains containing glycine zipper-like motifs, which is essential for its association with the autophagosomal membrane. These findings reveal a mechanism by which the SNARE protein is available to the completed autophagosome.","corpus_id":14736164,"score":2},{"doc_id":"23455425","title":"Autophagosomes form at ER-mitochondria contact sites.","abstract":"Autophagy is a tightly regulated intracellular bulk degradation/recycling system that has fundamental roles in cellular homeostasis. Autophagy is initiated by isolation membranes, which form and elongate as they engulf portions of the cytoplasm and organelles. Eventually isolation membranes close to form double membrane-bound autophagosomes and fuse with lysosomes to degrade their contents. The physiological role of autophagy has been determined since its discovery, but the origin of autophagosomal membranes has remained unclear. At present, there is much controversy about the organelle from which the membranes originate--the endoplasmic reticulum (ER), mitochondria and plasma membrane. Here we show that autophagosomes form at the ER-mitochondria contact site in mammalian cells. Imaging data reveal that the pre-autophagosome/autophagosome marker ATG14 (also known as ATG14L) relocalizes to the ER-mitochondria contact site after starvation, and the autophagosome-formation marker ATG5 also localizes at the site until formation is complete. Subcellular fractionation showed that ATG14 co-fractionates in the mitochondria-associated ER membrane fraction under starvation conditions. Disruption of the ER-mitochondria contact site prevents the formation of ATG14 puncta. The ER-resident SNARE protein syntaxin 17 (STX17) binds ATG14 and recruits it to the ER-mitochondria contact site. These results provide new insight into organelle biogenesis by demonstrating that the ER-mitochondria contact site is important in autophagosome formation.","corpus_id":205232769,"score":2},{"doc_id":"23466629","title":"Syntaxin 17: the autophagosomal SNARE.","abstract":"The phagophore (also called isolation membrane) elongates and encloses a portion of cytoplasm, resulting in formation of the autophagosome. After completion of autophagosome formation, the outer autophagosomal membrane becomes ready to fuse with the lysosome for degradation of enclosed cytoplasmic materials. However, the molecular mechanism for how the fusion of completed autophagosomes with the lysosome is regulated has not been fully understood. We discovered syntaxin 17 (STX17) as an autophagosomal soluble N-ethylmaleimide-sensitive factor attachment protein receptor (SNARE). STX17 has a hairpin-type structure mediated by two transmembrane domains, each containing glycine zipper motifs. This unique transmembrane structure contributes to its specific localization to completed autophagosomes but not to phagophores. STX17 interacts with SNAP29 and the lysosomal SNARE VAMP8, and all of these proteins are required for autophagosome-lysosome fusion. The late recruitment of STX17 to completed autophagosomes could prevent premature fusion of the lysosome with unclosed phagophores.","corpus_id":41343480,"score":2},{"doc_id":"24554770","title":"The HOPS complex mediates autophagosome-lysosome fusion through interaction with syntaxin 17.","abstract":"Membrane fusion is generally controlled by Rabs, soluble N-ethylmaleimide-sensitive factor attachment protein receptors (SNAREs), and tethering complexes. Syntaxin 17 (STX17) was recently identified as the autophagosomal SNARE required for autophagosome-lysosome fusion in mammals and Drosophila. In this study, to better understand the mechanism of autophagosome-lysosome fusion, we searched for STX17-interacting proteins. Immunoprecipitation and mass spectrometry analysis identified vacuolar protein sorting 33A (VPS33A) and VPS16, which are components of the homotypic fusion and protein sorting (HOPS)-tethering complex. We further confirmed that all HOPS components were coprecipitated with STX17. Knockdown of VPS33A, VPS16, or VPS39 blocked autophagic flux and caused accumulation of STX17- and microtubule-associated protein light chain (LC3)-positive autophagosomes. The endocytic pathway was also affected by knockdown of VPS33A, as previously reported, but not by knockdown of STX17. By contrast, ultraviolet irradiation resistance-associated gene (UVRAG), a known HOPS-interacting protein, did not interact with the STX17-HOPS complex and may not be directly involved in autophagosome-lysosome fusion. Collectively these results suggest that, in addition to its well-established function in the endocytic pathway, HOPS promotes autophagosome-lysosome fusion through interaction with STX17.","corpus_id":2100853,"score":2},{"doc_id":"25419848","title":"O-GlcNAc-modification of SNAP-29 regulates autophagosome maturation.","abstract":"The mechanism by which nutrient status regulates the fusion of autophagosomes with endosomes/lysosomes is poorly understood. Here, we report that O-linked β-N-acetylglucosamine (O-GlcNAc) transferase (OGT) mediates O-GlcNAcylation of the SNARE protein SNAP-29 and regulates autophagy in a nutrient-dependent manner. In mammalian cells, OGT knockdown, or mutating the O-GlcNAc sites in SNAP-29, promotes the formation of a SNAP-29-containing SNARE complex, increases fusion between autophagosomes and endosomes/lysosomes, and promotes autophagic flux. In Caenorhabditis elegans, depletion of ogt-1 has a similar effect on autophagy; moreover, expression of an O-GlcNAc-defective SNAP-29 mutant facilitates autophagic degradation of protein aggregates. O-GlcNAcylated SNAP-29 levels are reduced during starvation in mammalian cells and in C. elegans. Our study reveals a mechanism by which O-GlcNAc-modification integrates nutrient status with autophagosome maturation.","corpus_id":37822524,"score":2},{"doc_id":"25434465","title":"Sugar modification inhibits autophagosome-lysosome fusion.","abstract":"Autophagy is an intracellular degradation system that is mediated by orchestrated functions of membranes and proteins. A genetic screen in Caenorhabditis elegans revealed that O-linked N-acetylglucosamine modification of the SNARE protein SNAP-29 negatively regulates SNARE-dependent fusion between autophagosomes and lysosomes. This regulatory mechanism is conserved in mammals.","corpus_id":37079614,"score":2},{"doc_id":"25920502","title":"Toward an understanding of autophagosome-lysosome fusion: The unsuspected role of ATG14.","abstract":"Although largely overlooked relative to the process of phagophore formation, the mechanism through which autophagosomes fuse with lysosomes is a critical aspect of macroautophagy that is not fully understood. In particular, this step must be carefully regulated to prevent premature fusion of an incomplete autophagosome (that is, a phagophore) with a lysosome, because such an event would not allow access of the partially sequestered cargo to the lysosome lumen. The identification of the autophagosome-associated SNARE protein STX17 (syntaxin 17) provided some clue in the understanding of this process. STX17 is recruited specifically to mature autophagosomes, and functions in mediating autophagosome-lysosome fusion by forming a complex with the Qbc SNARE SNAP29 and the lysosomal R-SNARE VAMP8. Additionally, STX17 plays a role in the early events of autophagy by interacting with the phosphatidylinositol 3-kinase complex component ATG14. Upon autophagy induction STX17 is strictly required for ATG14 recruitment to the ER-mitochondria contact sites, a critical step for the assembly of the phagophore and therefore for autophagosome formation. In their recent paper, Diao and collaborators now show that the ATG14-STX17-SNAP29 interaction mediates autophagosome-lysosome tethering and fusion events, thus revealing a novel function of ATG14 in the later steps of the autophagy pathway.","corpus_id":3551891,"score":2},{"doc_id":"25945523","title":"ATG14 controls SNARE-mediated autophagosome fusion with a lysosome.","abstract":"Autophagosome fusion with a lysosome constitutes the last barrier for autophagic degradation. It is speculated that this fusion process is precisely and tightly regulated. Recent genetic evidence suggests that a set of SNARE proteins, including STX17, SNAP29, and VAMP8, are essential for the fusion between autophagosomes and lysosomes. However, it remains unclear whether these SNAREs are fusion competent and how their fusogenic activity is specifically regulated during autophagy. Using a combination of biochemical, cell biology, and genetic approaches, we demonstrated that fusogenic activity of the autophagic SNARE complex is temporally and spatially controlled by ATG14/Barkor/Atg14L, an essential autophagy-specific regulator of the class III phosphatidylinositol 3-kinase complex (PtdIns3K). ATG14 directly binds to the STX17-SNAP29 binary complex on autophagosomes and promotes STX17-SNAP29-VAMP8-mediated autophagosome fusion with lysosomes. ATG14 homo-oligomerization is required for SNARE binding and fusion promotion, but is dispensable for PtdIns3K stimulation and autophagosome biogenesis. Consequently, ATG14 homo-oligomerization is required for autophagosome fusion with a lysosome, but is dispensable for autophagosome biogenesis. These data support a key role of ATG14 in controlling autophagosome fusion with a lysosome.","corpus_id":6972001,"score":2},{"doc_id":"27885029","title":"The ATG conjugation systems are important for degradation of the inner autophagosomal membrane.","abstract":"In macroautophagy, cytoplasmic contents are sequestered into the double-membrane autophagosome, which fuses with the lysosome to become the autolysosome. It has been thought that the autophagy-related (ATG) conjugation systems are required for autophagosome formation. Here, we found that autophagosomal soluble N-ethylmaleimide-sensitive factor attachment protein receptor (SNARE) syntaxin 17-positive autophagosome-like structures could be generated even in the absence of the ATG conjugation systems, although at a reduced rate. These syntaxin 17-positive structures could further fuse with lysosomes, but degradation of the inner autophagosomal membrane was significantly delayed. Accordingly, autophagic activity in ATG conjugation-deficient cells was strongly suppressed. We suggest that the ATG conjugation systems, which are likely required for the closure (i.e., fission) of the autophagosomal edge, are not absolutely essential for autolysosome formation but are important for efficient degradation of the inner autophagosomal membrane.","corpus_id":39627761,"score":2},{"doc_id":"28077293","title":"Autophagosome Maturation and Fusion.","abstract":"Macroautophagy, or simply autophagy, is a degradative pathway that delivers cytoplasmic components, including cytosol and organelles, to the lysosome in double-membrane vesicles called autophagosomes. This process is initiated at the pre-autophagosomal structure or phagophore assembly site and involves a number of highly conserved autophagy-related proteins. These support the generation and conversion of an open membranous cistern known as the phagophore or isolation membrane into a closed autophagosome. Within this review, we will focus on recent insights into the molecular events following the sealing/completion of an autophagosome, which lead to its maturation and subsequent fusion with endosomes/lysosomes.","corpus_id":46790483,"score":2},{"doc_id":"28253966","title":"In Vitro Reconstitution of Autophagosome-Lysosome Fusion.","abstract":"SNARE (soluble N-ethylmaleimide-sensitive factor attachment protein receptors) proteins are a highly regulated class of membrane proteins lying in the center of membrane fusion. In conjunction with accessory proteins, SNAREs drive efficient merger of two distinct lipid bilayers into one interconnected structure. This chapter describes our fluorescence resonance energy transfer (FRET)-based proteoliposome fusion assays for the roles of various SNARE proteins, accessory proteins, and effects of different lipid compositions on membrane fusion involved in autophagy.","corpus_id":10899001,"score":2},{"doc_id":"28598244","title":"Accumulation of undegraded autophagosomes by expression of dominant-negative STX17 (syntaxin 17) mutants.","abstract":"Macroautophagy/autophagy, which is one of the main degradation systems in the cell, is mediated by a specialized organelle, the autophagosome. Purification of autophagosomes before fusion with lysosomes is important for both mechanistic and physiological studies of the autophagosome. Here, we report a simple method to accumulate undigested autophagosomes. Overexpression of the autophagosomal Qa-SNARE STX17 (syntaxin 17) lacking the N-terminal domain (NTD) or N-terminally tagged GFP-STX17 causes accumulation of autophagosomes. A HeLa cell line, which expresses GFP-STX17ΔNTD or full-length GFP-STX17 under the control of the tetracycline-responsive promoter, accumulates a large number of undigested autophagosomes devoid of lysosomal markers or early autophagy factors upon treatment with doxycycline. Using this inducible cell line, nascent autophagosomes can be easily purified by OptiPrep density-gradient centrifugation and immunoprecipitation. This novel method should be useful for further characterization of nascent autophagosomes.","corpus_id":205899963,"score":2},{"doc_id":"18032918","title":"BARgaining membranes for autophagosome formation: Regulation of autophagy and tumorigenesis by Bif-1/Endophilin B1.","abstract":"Autophagy is an intracellular system for the bulk degradation of cytoplasmic components enclosed within double-membrane structures known as autophagosomes. To date, many autophagy-related (Atg) genes have been identified by independent genetic screens for autophagy-defective mutants in yeast; however, the molecular machinery required for the biogenesis of autophagosomes in mammalian systems has yet to be determined.(1,2) Recently, we have reported that Bif-1 interacts with Beclin 1 through UVRAG and promotes the activation of class III phosphatidylinositol 3-kinase (PI3KC3) and the formation of autophagosomes.(3) Moreover, we have found that loss of Bif-1 promotes starvation-induced caspase activation, but prolongs cell survival by suppressing autophagydependent cell death, and enhances spontaneous tumorigenesis in mice. Bif-1 is a member of the endophilin family, which possesses membrane binding and liposome tubulation activities.(4) During nutrient deprivation, Bif-1 accumulates in punctate foci where it co-localizes with LC3, Atg5 and Atg9. Time-lapse microscopy analyses reveal that Bif-1-positive small vesicles expand by recruiting and fusing with Atg9-positive small membranes to form autophagosomes. Taken together, our findings highlight Bif-1 as a potential regulator of autophagosome biogenesis and as a tumor suppressor.","corpus_id":24936612,"score":1},{"doc_id":"18843052","title":"Beclin 1 forms two distinct phosphatidylinositol 3-kinase complexes with mammalian Atg14 and UVRAG.","abstract":"Class III phosphatidylinositol 3-kinase (PI3-kinase) regulates multiple membrane trafficking. In yeast, two distinct PI3-kinase complexes are known: complex I (Vps34, Vps15, Vps30/Atg6, and Atg14) is involved in autophagy, and complex II (Vps34, Vps15, Vps30/Atg6, and Vps38) functions in the vacuolar protein sorting pathway. Atg14 and Vps38 are important in inducing both complexes to exert distinct functions. In mammals, the counterparts of Vps34, Vps15, and Vps30/Atg6 have been identified as Vps34, p150, and Beclin 1, respectively. However, orthologues of Atg14 and Vps38 remain unknown. We identified putative mammalian homologues of Atg14 and Vps38. The Vps38 candidate is identical to UV irradiation resistance-associated gene (UVRAG), which has been reported as a Beclin 1-interacting protein. Although both human Atg14 and UVRAG interact with Beclin 1 and Vps34, Atg14, and UVRAG are not present in the same complex. Although Atg14 is present on autophagic isolation membranes, UVRAG primarily associates with Rab9-positive endosomes. Silencing of human Atg14 in HeLa cells suppresses autophagosome formation. The coiled-coil region of Atg14 required for binding with Vps34 and Beclin 1 is essential for autophagy. These results suggest that mammalian cells have at least two distinct class III PI3-kinase complexes, which may function in different membrane trafficking pathways.","corpus_id":32868891,"score":1},{"doc_id":"19270693","title":"Distinct regulation of autophagic activity by Atg14L and Rubicon associated with Beclin 1-phosphatidylinositol-3-kinase complex.","abstract":"Beclin 1, a mammalian autophagy protein that has been implicated in development, tumour suppression, neurodegeneration and cell death, exists in a complex with Vps34, the class III phosphatidylinositol-3-kinase (PI(3)K) that mediates multiple vesicle-trafficking processes including endocytosis and autophagy. However, the precise role of the Beclin 1-Vps34 complex in autophagy regulation remains to be elucidated. Combining mouse genetics and biochemistry, we have identified a large in vivo Beclin 1 complex containing the known proteins Vps34, p150/Vps15 and UVRAG, as well as two newly identified proteins, Atg14L (yeast Atg14-like) and Rubicon (RUN domain and cysteine-rich domain containing, Beclin 1-interacting protein). Characterization of the new proteins revealed that Atg14L enhances Vps34 lipid kinase activity and upregulates autophagy, whereas Rubicon reduces Vps34 activity and downregulates autophagy. We show that Beclin 1 and Atg14L synergistically promote the formation of double-membraned organelles that are associated with Atg5 and Atg12, whereas forced expression of Rubicon results in aberrant late endosomal/lysosomal structures and impaired autophagosome maturation. We hypothesize that by forming distinct protein complexes, Beclin 1 and its binding proteins orchestrate the precise function of the class III PI(3)K in regulating autophagy at multiple steps.","corpus_id":16601081,"score":1},{"doc_id":"19337031","title":"In vitro reconstitution of fusion between immature autophagosomes and endosomes.","abstract":"Autophagy is a highly conserved degradative pathway whereby a double membrane engulfs cytoplasmic constituents to form an autophagic vacuole or autophagosome. An essential requirement for efficient autophagy is the acquisition of an adequate degradative capacity by the autophagosomes. To acquire this capacity the immature autophagic vacuoles (AVis) obtain lysosomal hydrolases by fusion with endosomes. The current models suggest that at least two types of endosomes, early and late, fuse with AVis to form mature, degradative AVds. This fusion and maturation requires proteins also involved in endosome maturation such as Rab7. However, it is not known if there are molecular requirements unique to AVi-endosome fusion. To identify and investigate the molecular requirements of this fusion we developed a cell-free fusion assay based on content mixing, which occurs after fusion of isolated AVis and different endosomal fractions. Our assay shows that isolated AVis can fuse to a similar extent in vitro with both early and late endosomes. Furthermore, fusion between autophagosomes and endosomes requires cytosolic and endosomal proteins, but does not show a nucleotide-dependence, and is partially N-ethylmaleimide sensitive. We also demonstrate that the lipidated form of the autophagosomal protein LC3 is dispensable for this fusion event.","corpus_id":7451436,"score":1},{"doc_id":"20089838","title":"Combinational soluble N-ethylmaleimide-sensitive factor attachment protein receptor proteins VAMP8 and Vti1b mediate fusion of antimicrobial and canonical autophagosomes with lysosomes.","abstract":"Autophagy plays a crucial role in host defense, termed antimicrobial autophagy (xenophagy), as it functions to degrade intracellular foreign microbial invaders such as group A Streptococcus (GAS). Xenophagosomes undergo a stepwise maturation process consisting of a fusion event with lysosomes, after which the cargoes are degraded. However, the molecular mechanism underlying xenophagosome/lysosome fusion remains unclear. We examined the involvement of endocytic soluble N-ethylmaleimide-sensitive factor attachment protein receptors (SNAREs) in xenophagosome/lysosome fusion. Confocal microscopic analysis showed that SNAREs, including vesicle-associated membrane protein (VAMP)7, VAMP8, and vesicle transport through interaction with t-SNAREs homologue 1B (Vti1b), colocalized with green fluorescent protein-LC3 in xenophagosomes. Knockdown of Vti1b and VAMP8 with small interfering RNAs disturbed the colocalization of LC3 with lysosomal membrane protein (LAMP)1. The invasive efficiency of GAS into cells was not altered by knockdown of VAMP8 or Vti1b, whereas cellular bactericidal efficiency was significantly diminished, indicating that antimicrobial autophagy was functionally impaired. Knockdown of Vti1b and VAMP8 also disturbed colocalization of LC3 with LAMP1 in canonical autophagy, in which LC3-II proteins were negligibly degraded. In contrast, knockdown of Syntaxin 7 and Syntaxin 8 showed little effect on the autophagic fusion event. These findings strongly suggest that the combinational SNARE proteins VAMP8 and Vti1b mediate the fusion of antimicrobial and canonical autophagosomes with lysosomes, an essential event for autophagic degradation.","corpus_id":13268644,"score":1},{"doc_id":"20798834","title":"Cellular machinery to fuse antimicrobial autophagosome with lysosome.","abstract":"Autophagy is an intracellular bulk degradation/recycling system that turns over cellular constituents and also functions to degrade intracellular foreign microbial invaders by a process termed xenophagy (antimicrobial autophagy). We previously showed that intracellular group A Streptococcus (GAS) organisms are captured by xenophagosomes, then degraded following fusion with lysosomes. Very recently, we analyzed the molecular mechanism underlying xenophagosome/lysosome fusion and found that endocytic soluble N-ethylmaleimide-sensitive factor attachment protein receptors (SNAREs) were involved. Knockdown of the combinational SNARE proteins Vti1b and VAMP8 with siRNAs disturbed autophagic fusion with lysosomes, and cellular bactericidal efficiency was significantly diminished. Furthermore, knockdown of those SNAREs inhibited the fusion of canonical autophagosomes with lysosomes. In addition, important findings showed that Vti1b is derived from autophagic compartments, whereas VAMP8 originates from lysosomes. Together, these results strongly suggest that SNARE proteins Vti1b and VAMP8 mediate the fusion of antimicrobial and canonical autophagosomes with lysosomes, an essential event for autophagic degradation.","corpus_id":29550189,"score":1},{"doc_id":"21497758","title":"LC3 and GATE-16 N termini mediate membrane fusion processes required for autophagosome biogenesis.","abstract":"Autophagy is a unique membrane trafficking pathway describing the formation and targeting of double membrane autophagosomes to the vacuole/lysosome. The biogenesis of autophagosomes and their delivery to the vacuole/lysosome depend on multiple membrane fusion events. Using a cell-free system, we have investigated the ability of LC3 and GATE-16, two mammalian Atg8 orthologs, to mediate membrane fusion. We found that both proteins promote tethering and membrane fusion, mediated by the proteins' N-terminal α helices. We further show that short, 10 amino acid long synthetic peptides derived from the N terminus of LC3 or GATE-16 are sufficient to promote membrane fusion. Our data indicate that the fusion activity of LC3 is mediated by positively charged amino acids, whereas the activity of GATE-16 is mediated by hydrophobic interactions. Finally, we demonstrate that LC3 and GATE-16 N termini in general and specific residues needed for the fusion activity are essential for the proteins role in autophagosome biogenesis.","corpus_id":9354127,"score":1},{"doc_id":"21738011","title":"Membrane curvature response in autophagy.","abstract":"Membrane trafficking is key for signal transduction, cargo transportation, and in the case of autophagy, delivering cytoplasmic substrates to the lysosome for degradation. Autophagy requires the formation of a unique double membrane vesicle, the autophagosome. However, the mechanism by which the autophagosome forms is unknown. Our recent study focused on the role of Barkor/Atg14(L) in targeting the autophagy-specific class III phosphatidylinositol-3-kinase (PtdIns3KC3) complex to the early autophagosome has implicated this complex in autophagosome formation. This study found that the BATS domain of Barkor targets the PtdIns3KC3 complex to early autophagic structures and senses highly curved membranes enriched in phosphatidylinositol-3-phosphate (PtdIns(3)P). Consequently, this study uncovered an exciting new role for the PtdIns3KC3 complex as a potential inducer of autophagosome formation.","corpus_id":6595904,"score":1},{"doc_id":"21784250","title":"Autophagosome precursor maturation requires homotypic fusion.","abstract":"Autophagy is a catabolic process in which lysosomes degrade intracytoplasmic contents transported in double-membraned autophagosomes. Autophagosomes are formed by the elongation and fusion of phagophores, which can be derived from preautophagosomal structures coming from the plasma membrane and other sites like the endoplasmic reticulum and mitochondria. The mechanisms by which preautophagosomal structures elongate their membranes and mature toward fully formed autophagosomes still remain unknown. Here, we show that the maturation of the early Atg16L1 precursors requires homotypic fusion, which is essential for subsequent autophagosome formation. Atg16L1 precursor homotypic fusion depends on the SNARE protein VAMP7 together with partner SNAREs. Atg16L1 precursor homotypic fusion is a critical event in the early phases of autophagy that couples membrane acquisition and autophagosome biogenesis, as this step regulates the size of the vesicles, which in turn appears to influence their subsequent maturation into LC3-positive autophagosomes.","corpus_id":5377736,"score":1},{"doc_id":"22013444","title":"Atg14: a key player in orchestrating autophagy.","abstract":"Phosphorylation of phosphatidylinositol (PtdIns) by a PtdIns 3-kinase is an essential process in autophagy. Atg14, a specific subunit of one of the PtdIns 3-kinase complexes, targets the complex to the probable site of autophagosome formation, thereby, sorting the complex to function specifically in autophagy. The N-terminal half of Atg14, containing coiled-coil domains, is required to form the PtdIns 3-kinase complex and target it to the proper site. The C-terminal half of yeast Atg14 is suggested to be involved in the formation of a normal-sized autophagosome. The C-terminal half of mammalian Atg14 contains the Barkor/Atg14(L) autophagosome-targeting sequence (BATS) domain that preferentially binds to the highly curved membranes containing PtdIns(3)P and is proposed to target the PtdIns 3-kinase complex efficiently to the isolation membrane. Thus, the N- and C-terminal halves of Atg14 are likely to have an essential core function and a regulatory role, respectively.","corpus_id":9800350,"score":1},{"doc_id":"22342342","title":"A mammalian autophagosome maturation mechanism mediated by TECPR1 and the Atg12-Atg5 conjugate.","abstract":"Autophagy is a major catabolic pathway in eukaryotes associated with a broad spectrum of human diseases. In autophagy, autophagosomes carrying cellular cargoes fuse with lysosomes for degradation. However, the molecular mechanism underlying autophagosome maturation is largely unknown. Here we report that TECPR1 binds to the Atg12-Atg5 conjugate and phosphatidylinositol 3-phosphate (PtdIns[3]P) to promote autophagosome-lysosome fusion. TECPR1 and Atg16 form mutually exclusive complexes with the Atg12-Atg5 conjugate, and TECPR1 binds PtdIns(3)P upon association with the Atg12-Atg5 conjugate. Strikingly, TECPR1 localizes to and recruits Atg5 to autolysosome membrane. Consequently, elimination of TECPR1 leads to accumulation of autophagosomes and blocks autophagic degradation of LC3-II and p62. Finally, autophagosome maturation marked by GFP-mRFP-LC3 is defective in TECPR1-deficient cells. Thus, we propose that the concerted interactions among TECPR1, Atg12-Atg5, and PtdIns(3)P provide the fusion specificity between autophagosomes and lysosomes and that the assembly of this complex initiates the autophagosome maturation process.","corpus_id":206984358,"score":1},{"doc_id":"22617511","title":"A tethering coherent protein in autophagosome maturation.","abstract":"Autophagy is a cellular pathway that degrades damaged organelles, cytosol and microorganisms, thereby maintaining human health by preventing various diseases including cancers, neurodegenerative disorders and diabetes. In autophagy, autophagosomes carrying cellular cargoes fuse with lysosomes for degradation. The proper autophagosome-lysosome fusion is pivotal for efficient autophagy activity. However, the molecular mechanism that specifically directs the fusion process is not clear. Our study reported that lysosome-localized TECPR1 (TECtonin β-Propeller Repeat containing 1) binds the autophagosome-localized ATG12-ATG5 conjugate and recruits it to autolysosomes. TECPR1 also binds PtdIns3P in an ATG12-ATG5-dependent manner. Consequently, depletion of TECPR1 leads to a severe defect in autophagosome maturation. We propose that the interaction between TECPR1 and ATG12-ATG5 initiates the fusion between the autophagosome and lysosome, and TECPR1 is a TEthering Coherent PRotein in autophagosome maturation.","corpus_id":24620428,"score":1},{"doc_id":"22797916","title":"Beclin-1-interacting autophagy protein Atg14L targets the SNARE-associated protein Snapin to coordinate endocytic trafficking.","abstract":"Autophagy is a highly regulated membrane remodeling process that allows the lysosome-mediated degradation of cytoplasmic entities by sequestrating them in double-membrane autophagosomes. Autophagy is hence highly intertwined with the endocytic trafficking pathway, sharing similar molecular machinery. Atg14L, also known as Beclin 1-associated autophagy-related key regulator (Barkor), directly interacts with Beclin 1 through its coiled-coil domain and enhances phosphatidylinositol 3-phosphate kinase class III (PI3KC3) activity to induce autophagosome membrane nucleation, highlighting its essential role in the early stage of mammalian autophagy. Here, we report a novel function of Atg14L in the endocytic trafficking pathway wherein Atg14L binds to and colocalizes with the fusogenic SNARE effector protein Snapin to facilitate endosome maturation. Atg14L specifically binds to Snapin and this interaction effectively facilitates endosomal maturation without affecting autophagic cargo degradation. Consequently, atg14l knockdown significantly delayed the late stage of endocytic trafficking, as evidenced by the retarded kinetics of internalized surface receptor degradation. This phenotype was effectively complemented by wild-type Atg14L or Beclin 1-binding mutant, but not by its Snapin-binding mutant. Taken together, our study demonstrates that Atg14L functions as a multivalent trafficking effector that regulates endosome maturation as well as autophagosome formation, reflecting the complexity of the crosstalk between autophagic and endocytic vesicle trafficking in higher eukaryotes.","corpus_id":3179494,"score":1},{"doc_id":"23306003","title":"Connections between SNAREs and autophagy.","abstract":"Autophagy involves the sequestration of portions of cytoplasm by double-membraned autophagosomes, which are then trafficked to lysosomes. After autophagosome-lysosome fusion, the contents of the autophagosomes are degraded by lysosomal hydrolases. SNAREs [soluble N-ethylmaleimide-sensitive fusion (NSF) attachment protein receptors] are molecules that mediate vesicular fusion events. Here, we review recent data implicating SNAREs as having key roles both in the genesis of autophagosomes, as well as in autophagosome-lysosome fusion, and we discuss the implications of these findings in the context of a long-standing mystery: the origin of autophagosomes.","corpus_id":13918647,"score":1},{"doc_id":"24070471","title":"The Atg8 family: multifunctional ubiquitin-like key regulators of autophagy.","abstract":"Autophagy is an evolutionarily-conserved catabolic process initiated by the engulfment of cytosolic components in a crescent-shaped structure, called the phagophore, that expands and fuses to form a closed double-membrane vesicle, the autophagosome. Autophagosomes are subsequently targeted to the lysosome/vacuole with which they fuse to degrade their content. The formation of the autophagosome is carried out by a set of autophagy-related proteins (Atg), highly conserved from yeast to mammals. The Atg8s are Ubl (ubiquitin-like) proteins that play an essential role in autophagosome biogenesis. This family of proteins comprises a single member in yeast and several mammalian homologues grouped into three subfamilies: LC3 (light-chain 3), GABARAP (γ-aminobutyric acid receptor-associated protein) and GATE-16 (Golgi-associated ATPase enhancer of 16 kDa). The Atg8s are synthesized as cytosolic precursors, but can undergo a series of post-translational modifications leading to their tight association with autophagosomal structures following autophagy induction. Owing to this feature, the Atg8 proteins have been widely served as key molecules to monitor autophagosomes and autophagic activity. Studies in both yeast and mammalian systems have demonstrated that Atg8s play a dual role in the autophagosome formation process, coupling between selective incorporation of autophagy cargo and promoting autophagosome membrane expansion and closure. The membrane-remodelling activity of the Atg8 proteins is associated with their capacity to promote tethering and hemifusion of liposomes in vitro.","corpus_id":35414372,"score":1},{"doc_id":"24113031","title":"Evolutionarily conserved role and physiological relevance of a STX17/Syx17 (syntaxin 17)-containing SNARE complex in autophagosome fusion with endosomes and lysosomes.","abstract":"Phagophores engulf cytoplasmic material and give rise to autophagosomes, double-membrane vesicles mediating cargo transport to lysosomes for degradation. The regulation of autophagosome fusion with endosomes and lysosomes during autophagy has remained poorly characterized. Two recent papers conclude that STX17/syntaxin 17 (Syx17 in Drosophila) has an evolutionarily conserved role in autophagosome fusion with endosomes and lysosomes, acting in one SNARE complex with SNAP29 (ubisnap in Drosophila) and the endosomal/lysosomal VAMP8 (CG1599/Vamp7 in Drosophila). Surprisingly, a third report suggests that STX17 might also contribute to proper phagophore assembly. Although several experiments presented in the two human cell culture studies yielded controversial results, the essential role of STX17 in autophagic flux is now firmly established, both in cultured cells and in an animal model. Based on these data, we propose that genetic inhibition of STX17/Syx17 may be a more specific tool in autophagic flux experiments than currently used drug treatments, which impair all lysosomal degradation routes and also inactivate MTOR (mechanistic target of rapamycin), a major negative regulator of autophagy. Finally, the neuronal dysfunction and locomotion defects observed in Syx17 mutant animals point to the possible contribution of defective autophagosome clearance to various human diseases.","corpus_id":10593295,"score":1},{"doc_id":"24554766","title":"Interaction of the HOPS complex with Syntaxin 17 mediates autophagosome clearance in Drosophila.","abstract":"Homotypic fusion and vacuole protein sorting (HOPS) is a tethering complex required for trafficking to the vacuole/lysosome in yeast. Specific interaction of HOPS with certain SNARE (soluble NSF attachment protein receptor) proteins ensures the fusion of appropriate vesicles. HOPS function is less well characterized in metazoans. We show that all six HOPS subunits (Vps11 [vacuolar protein sorting 11]/CG32350, Vps18/Dor, Vps16A, Vps33A/Car, Vps39/CG7146, and Vps41/Lt) are required for fusion of autophagosomes with lysosomes in Drosophila. Loss of these genes results in large-scale accumulation of autophagosomes and blocks autophagic degradation under basal, starvation-induced, and developmental conditions. We find that HOPS colocalizes and interacts with Syntaxin 17 (Syx17), the recently identified autophagosomal SNARE required for fusion in Drosophila and mammals, suggesting their association is critical during tethering and fusion of autophagosomes with lysosomes. HOPS, but not Syx17, is also required for endocytic down-regulation of Notch and Boss in developing eyes and for proper trafficking to lysosomes and eye pigment granules. We also show that the formation of autophagosomes and their fusion with lysosomes is largely unaffected in null mutants of Vps38/UVRAG (UV radiation resistance associated), a suggested binding partner of HOPS in mammals, while endocytic breakdown and lysosome biogenesis is perturbed. Our results establish the role of HOPS and its likely mechanism of action during autophagy in metazoans.","corpus_id":1732539,"score":1},{"doc_id":"24832451","title":"Phosphoprotein of human parainfluenza virus type 3 blocks autophagosome-lysosome fusion to increase virus production.","abstract":"Autophagy is a multistep process in which cytoplasmic components, including invading pathogens, are captured by autophagosomes that subsequently fuse with degradative lysosomes. Negative-strand RNA viruses, including paramyxoviruses, have been shown to alter autophagy, but the molecular mechanisms remain largely unknown. We demonstrate that human parainfluenza virus type 3 (HPIV3) induces incomplete autophagy by blocking autophagosome-lysosome fusion, resulting in increased virus production. The viral phosphoprotein (P) is necessary and sufficient to inhibition autophagosome degradation. P binds to SNAP29 and inhibits its interaction with syntaxin17, thereby preventing these two host SNARE proteins from mediating autophagosome-lysome fusion. Incomplete autophagy and resultant autophagosome accumulation increase extracellular viral production but do not affect viral protein synthesis. These findings highlight how viruses can block autophagosome degradation by disrupting the function of SNARE proteins.","corpus_id":35762216,"score":1},{"doc_id":"25027988","title":"Getting ready for building: signaling and autophagosome biogenesis.","abstract":"Autophagy is the main cellular catabolic process responsible for degrading organelles and large protein aggregates. It is initiated by the formation of a unique membrane structure, the phagophore, which engulfs part of the cytoplasm and forms a double-membrane vesicle termed the autophagosome. Fusion of the outer autophagosomal membrane with the lysosome and degradation of the inner membrane contents complete the process. The extent of autophagy must be tightly regulated to avoid destruction of proteins and organelles essential for cell survival. Autophagic activity is thus regulated by external and internal cues, which initiate the formation of well-defined autophagy-related protein complexes that mediate autophagosome formation and selective cargo recruitment into these organelles. Autophagosome formation and the signaling pathways that regulate it have recently attracted substantial attention. In this review, we analyze the different signaling pathways that regulate autophagy and discuss recent progress in our understanding of autophagosome biogenesis.","corpus_id":2052205,"score":1},{"doc_id":"25086043","title":"Nrbf2 protein suppresses autophagy by modulating Atg14L protein-containing Beclin 1-Vps34 complex architecture and reducing intracellular phosphatidylinositol-3 phosphate levels.","abstract":"Autophagy is a tightly regulated lysosomal degradation pathway for maintaining cellular homeostasis and responding to stresses. Beclin 1 and its interacting proteins, including the class III phosphatidylinositol-3 kinase Vps34, play crucial roles in autophagy regulation in mammals. We identified nuclear receptor binding factor 2 (Nrbf2) as a Beclin 1-interacting protein from Becn1(-/-);Becn1-EGFP/+ mouse liver and brain. We also found that Nrbf2-Beclin 1 interaction required the N terminus of Nrbf2. We next used the human retinal pigment epithelial cell line RPE-1 as a model system and showed that transiently knocking down Nrbf2 by siRNA increased autophagic flux under both nutrient-rich and starvation conditions. To investigate the mechanism by which Nrbf2 regulates autophagy, we demonstrated that Nrbf2 interacted and colocalized with Atg14L, suggesting that Nrbf2 is a component of the Atg14L-containing Beclin 1-Vps34 complex. Moreover, ectopically expressed Nrbf2 formed cytosolic puncta that were positive for isolation membrane markers. These results suggest that Nrbf2 is involved in autophagosome biogenesis. Furthermore, we showed that Nrbf2 deficiency led to increased intracellular phosphatidylinositol-3 phosphate levels and diminished Atg14L-Vps34/Vps15 interactions, suggesting that Nrbf2-mediated Atg14L-Vps34/Vps15 interactions likely inhibit Vps34 activity. Therefore, we propose that Nrbf2 may interact with the Atg14L-containing Beclin 1-Vps34 protein complex to modulate protein-protein interactions within the complex, leading to suppression of Vps34 activity, autophagosome biogenesis, and autophagic flux. This work reveals a novel aspect of the intricate mechanism for the Beclin 1-Vps34 protein-protein interaction network to achieve precise control of autophagy.","corpus_id":25484134,"score":1},{"doc_id":"25343031","title":"Membrane tethering.","abstract":"Membrane trafficking depends on transport vesicles and carriers docking and fusing with the target organelle for the delivery of cargo. Membrane tethers and small guanosine triphosphatases (GTPases) mediate the docking of transport vesicles/carriers to enhance the efficiency of the subsequent SNARE (soluble N-ethylmaleimide-sensitive factor attachment protein receptor)-mediated fusion event with the target membrane bilayer. Different classes of membrane tethers and their specific intracellular location throughout the endomembrane system are now well defined. Recent biochemical and structural studies have led to a deeper understanding of the mechanism by which membrane tethers mediate docking of membrane carriers as well as an appreciation of the role of tethers in coordinating the correct SNARE complex and in regulating the organization of membrane compartments. This review will summarize the properties and roles of membrane tethers of both secretory and endocytic systems.","corpus_id":3946099,"score":1},{"doc_id":"25551675","title":"Multiple functions of the SNARE protein Snap29 in autophagy, endocytic, and exocytic trafficking during epithelial formation in Drosophila.","abstract":"How autophagic degradation is linked to endosomal trafficking routes is little known. Here we screened a collection of uncharacterized Drosophila mutants affecting membrane transport to identify new genes that also have a role in autophagy. We isolated a loss of function mutant in Snap29 (Synaptosomal-associated protein 29 kDa), the gene encoding the Drosophila homolog of the human protein SNAP29 and have characterized its function in vivo. Snap29 contains 2 soluble NSF attachment protein receptor (SNARE) domains and a asparagine-proline-phenylalanine (NPF motif) at its N terminus and rescue experiments indicate that both SNARE domains are required for function, whereas the NPF motif is in part dispensable. We find that Snap29 interacts with SNARE proteins, localizes to multiple trafficking organelles, and is required for protein trafficking and for proper Golgi apparatus morphology. Developing tissue lacking Snap29 displays distinctive epithelial architecture defects and accumulates large amounts of autophagosomes, highlighting a major role of Snap29 in autophagy and secretion. Mutants for autophagy genes do not display epithelial architecture or secretion defects, suggesting that the these alterations of the Snap29 mutant are unlikely to be caused by the impairment of autophagy. In contrast, we find evidence of elevated levels of hop-Stat92E (hopscotch-signal transducer and activator of transcription protein at 92E) ligand, receptor, and associated signaling, which might underlie the epithelial defects. In summary, our findings support a role of Snap29 at key steps of membrane trafficking, and predict that signaling defects may contribute to the pathogenesis of cerebral dysgenesis, neuropathy, ichthyosis, and palmoplantar keratoderma (CEDNIK), a human congenital syndrome due to loss of Snap29.","corpus_id":8165574,"score":1},{"doc_id":"26259518","title":"Impairment of autophagosome-lysosome fusion in the buff mutant mice with the VPS33A(D251E) mutation.","abstract":"The HOPS (homotypic fusion and protein sorting) complex functions in endocytic and autophagic pathways in both lower eukaryotes and mammalian cells through its involvement in fusion events between endosomes and lysosomes or autophagosomes and lysosomes. However, the differential molecular mechanisms underlying these fusion processes are largely unknown. Buff (bf) is a mouse mutant that carries an Asp251-to-Glu point mutation (D251E) in the VPS33A protein, a tethering protein and a core subunit of the HOPS complex. Bf mice showed impaired spontaneous locomotor activity, motor learning, and autophagic activity. Although the gross anatomy of the brain was apparently normal, the number of Purkinje cells was significantly reduced. Furthermore, we found that fusion between autophagosomes and lysosomes was defective in bf cells without compromising the endocytic pathway. The direct association of mutant VPS33A(D251E) with the autophagic SNARE complex, STX17 (syntaxin 17)-VAMP8-SNAP29, was enhanced. In addition, the VPS33A(D251E) mutation enhanced interactions with other HOPS subunits, namely VPS41, VPS39, VPS18, and VPS11, except for VPS16. Reduction of the interactions between VPS33A(Y440D) and several other HOPS subunits led to decreased association with STX17. These results suggest that the VPS33A(D251E) mutation plays dual roles by increasing the HOPS complex assembly and its association with the autophagic SNARE complex, which selectively affects the autophagosome-lysosome fusion that impairs basal autophagic activity and induces Purkinje cell loss.","corpus_id":205899003,"score":1},{"doc_id":"27099307","title":"The Autophagosomal SNARE Protein Syntaxin 17 Is an Essential Factor for the Hepatitis C Virus Life Cycle.","abstract":"UNLABELLED: Syntaxin 17 is an autophagosomal SNARE (soluble N-ethylmaleimide-sensitive factor attachment protein receptor) protein required for the fusion of autophagosomes with lysosomes to form autolysosomes and thereby to deliver the enclosed contents for degradation. Hepatitis C virus (HCV) induces autophagy. In light of the observation that the number of viral particles formed by HCV-infected cells is much greater than the number of infectious viral particles finally released by HCV-infected cells, the regulation of fusion between autophagosomes and lysosomes might fulfill a key function controlling the number of released virions. HCV-replicating cells possess a decreased amount of syntaxin 17 due to impaired expression and increased turnover of syntaxin 17. Overexpression of syntaxin 17 in HCV-replicating cells diminishes the number of released infectious viral particles and decreases the amount of intracellular retained viral particles by favoring the formation of autolysosomes, in which HCV particles are degraded. Inhibition of lysosomal acidification by bafilomycin rescues the decreased release of virions from syntaxin 17-overexpressing cells, while induction of autophagy by rapamycin enforces the impairment of release under these conditions. Vice versa, inhibition of syntaxin 17 expression by specific small interfering RNAs results in an elevated amount of intracellular retained viral particles and facilitates the release of HCV virions by impairment of autophagosome-lysosome fusion. HCV genome replication, however, is not affected by modulation of syntaxin 17 expression. These data identify syntaxin 17 to be a novel factor controlling the release of HCV. This is achieved by regulation of autophagosome-lysosome fusion, which affects the equilibrium between the release of infectious viral particles and lysosomal degradation of intracellular retained viral particles. IMPORTANCE: Hepatitis C virus (HCV) induces autophagy. Syntaxin 17 is an autophagosomal SNARE protein required for the fusion of autophagosomes with lysosomes. In HCV-infected cells, a major fraction of the de novo-synthesized viral particles is not released but is intracellularly degraded. In this context, the effect of HCV on the amount and distribution of syntaxin 17 and the relevance of syntaxin 17 for the viral life cycle were investigated. This study demonstrates that the amount of syntaxin 17 decreased in HCV-replicating cells. In addition, syntaxin 17 is identified to be a novel factor controlling the release of HCV, and the relevance of autophagosome-lysosome fusion as a regulator of the amount of released viral particles is revealed. Taken together, these findings indicate that syntaxin 17 is involved in the regulation of autophagosome-lysosome fusion and thereby affects the equilibrium between the release of infectious viral particles and the lysosomal degradation of intracellularly retained viral particles.","corpus_id":206795163,"score":1},{"doc_id":"27383850","title":"Identification of BECN1 and ATG14 Coiled-Coil Interface Residues That Are Important for Starvation-Induced Autophagy.","abstract":"Autophagy, an essential eukaryotic homeostasis pathway, allows the sequestration of unwanted, damaged, or harmful cytoplasmic components in vesicles called autophagosomes, permitting subsequent lysosomal degradation and nutrient recycling. Autophagosome nucleation is mediated by class III phosphatidylinositol-3-kinase complexes that include two key autophagy proteins, BECN1/Beclin 1 and ATG14/BARKOR, which form parallel heterodimers via their coiled-coil domains (CCDs). Here we present the 1.46 Å X-ray crystal structure of the antiparallel, human BECN1 CCD homodimer, which represents BECN1 oligomerization outside the autophagosome nucleation complex. We use circular dichroism and small-angle X-ray scattering (SAXS) to show that the ATG14 CCD is significantly disordered but becomes more helical in the BECN1:ATG14 heterodimer, although it is less well-folded than the BECN1 CCD homodimer. SAXS also indicates that the BECN1:ATG14 heterodimer is more curved than other BECN1-containing CCD dimers, which has important implications for the structure of the autophagosome nucleation complex. A model of the BECN1:ATG14 CCD heterodimer that agrees well with the SAXS data shows that BECN1 residues at the homodimer interface are also responsible for heterodimerization, allowing us to identify ATG14 interface residues. Finally, we verify the role of BECN1 and ATG14 interface residues in binding by assessing the impact of point mutations of these residues on co-immunoprecipitation of the partner and demonstrate that these mutations abrogate starvation-induced upregulation of autophagy but do not impact basal autophagy. Thus, this research provides insights into structures of the BECN1 CCD homodimer and the BECN1:ATG14 CCD heterodimer and identifies interface residues that are important for BECN1:ATG14 heterodimerization and for autophagy.","corpus_id":20237132,"score":1},{"doc_id":"27458136","title":"Syntaxin-17 delivers PINK1/parkin-dependent mitochondrial vesicles to the endolysosomal system.","abstract":"Mitochondria are considered autonomous organelles, physically separated from endocytic and biosynthetic pathways. However, recent work uncovered a PINK1/parkin-dependent vesicle transport pathway wherein oxidized or damaged mitochondrial content are selectively delivered to the late endosome/lysosome for degradation, providing evidence that mitochondria are indeed integrated within the endomembrane system. Given that mitochondria have not been shown to use canonical soluble NSF attachment protein receptor (SNARE) machinery for fusion, the mechanism by which mitochondrial-derived vesicles (MDVs) are targeted to the endosomal compartment has remained unclear. In this study, we identify syntaxin-17 as a core mitochondrial SNARE required for the delivery of stress-induced PINK1/parkin-dependent MDVs to the late endosome/lysosome. Syntaxin-17 remains associated with mature MDVs and forms a ternary SNARE complex with SNAP29 and VAMP7 to mediate MDV-endolysosome fusion in a manner dependent on the homotypic fusion and vacuole protein sorting (HOPS) tethering complex. Syntaxin-17 can be traced to the last eukaryotic common ancestor, hinting that the removal of damaged mitochondrial content may represent one of the earliest vesicle transport routes in the cell.","corpus_id":3941961,"score":1},{"doc_id":"27588602","title":"The Vici Syndrome Protein EPG5 Is a Rab7 Effector that Determines the Fusion Specificity of Autophagosomes with Late Endosomes/Lysosomes.","abstract":"Mutations in the human autophagy gene EPG5 cause the multisystem disorder Vici syndrome. Here we demonstrated that EPG5 is a Rab7 effector that determines the fusion specificity of autophagosomes with late endosomes/lysosomes. EPG5 is recruited to late endosomes/lysosomes by direct interaction with Rab7 and the late endosomal/lysosomal R-SNARE VAMP7/8. EPG5 also binds to LC3/LGG-1 (mammalian and C. elegans Atg8 homolog, respectively) and to assembled STX17-SNAP29 Qabc SNARE complexes on autophagosomes. EPG5 stabilizes and facilitates the assembly of STX17-SNAP29-VAMP7/8 trans-SNARE complexes, and promotes STX17-SNAP29-VAMP7-mediated fusion of reconstituted proteoliposomes. Loss of EPG5 activity causes abnormal fusion of autophagosomes with various endocytic vesicles, in part due to elevated assembly of STX17-SNAP25-VAMP8 complexes. SNAP25 knockdown partially suppresses the autophagy defect caused by EPG5 depletion. Our study reveals that EPG5 is a Rab7 effector involved in autophagosome maturation, providing insight into the molecular mechanism underlying Vici syndrome.","corpus_id":1202443,"score":1},{"doc_id":"27621469","title":"PtdIns(4,5)P2 signaling regulates ATG14 and autophagy.","abstract":"Autophagy is a regulated self-digestion pathway with fundamental roles in cell homeostasis and diseases. Autophagy is regulated by coordinated actions of a series of autophagy-related (ATG) proteins. The Barkor/ATG14(L)-VPS34 (a class III phosphatidylinositol 3-kinase) complex and its product phosphatidylinositol 3-phosphate [PtdIns(3)P] play key roles in autophagy initiation. ATG14 contains a C-terminal Barkor/ATG14(L) autophagosome-targeting sequence (BATS) domain that senses the curvature of PtdIns(3)P-containing membrane. The BATS domain also strongly binds PtdIns(4,5)P2, but the functional significance has been unclear. Here we show that ATG14 specifically interacts with type Iγ PIP kinase isoform 5 (PIPKIγi5), an enzyme that generates PtdIns(4,5)P2 in mammalian cells. Autophagosomes have associated PIPKIγi5 and PtdIns(4,5)P2 that are colocalized with late endosomes and the endoplasmic reticulum. PtdIns(4,5)P2 generation at these sites requires PIPKIγi5. Loss of PIPKIγi5 results in a loss of ATG14, UV irradiation resistance-associated gene, and Beclin 1 and a block of autophagy. PtdIns(4,5)P2 binding to the ATG14-BATS domain regulates ATG14 interaction with VPS34 and Beclin 1, and thus plays a key role in ATG14 complex assembly and autophagy initiation. This study identifies an unexpected role for PtdIns(4,5)P2 signaling in the regulation of ATG14 complex and autophagy.","corpus_id":205277858,"score":1},{"doc_id":"27628032","title":"LAMP-2 is required for incorporating syntaxin-17 into autophagosomes and for their fusion with lysosomes.","abstract":"Autophagy is an evolutionarily conserved process used for removing surplus and damaged proteins and organelles from the cytoplasm. The unwanted material is incorporated into autophagosomes that eventually fuse with lysosomes, leading to the degradation of their cargo. The fusion event is mediated by the interaction between the Qa-SNARE syntaxin-17 (STX17) on autophagosomes and the R-SNARE VAMP8 on lysosomes. Cells deficient in lysosome membrane-associated protein-2 (LAMP-2) have increased numbers of autophagosomes but the underlying mechanism is poorly understood. By transfecting LAMP-2-deficient and LAMP-1/2--double-deficient mouse embryonic fibroblasts (MEFs) with a tandem fluorescent-tagged LC3 we observed a failure of fusion between the autophagosomes and the lysosomes that could be rescued by complementation with LAMP-2A. Although we observed no change in expression and localization of VAMP8, its interacting partner STX17 was absent from autophagosomes of LAMP-2-deficient cells. Thus, LAMP-2 is essential for STX17 expression by the autophagosomes and this absence is sufficient to explain their failure to fuse with lysosomes. The results have clear implications for situations associated with a reduction of LAMP-2 expression.","corpus_id":13313475,"score":1},{"doc_id":"28306502","title":"Pacer Mediates the Function of Class III PI3K and HOPS Complexes in Autophagosome Maturation by Engaging Stx17.","abstract":"Class III PI3-kinase (PI3KC3) is essential for autophagy initiation, but whether PI3KC3 participates in other steps of autophagy remains unknown. The HOPS complex mediates the fusion of intracellular vesicles to lysosome, but how HOPS specifically tethers autophagosome to lysosome remains elusive. Here, we report Pacer (protein associated with UVRAG as autophagy enhancer) as a regulator of autophagy. Pacer localizes to autophagic structures and positively regulates autophagosome maturation. Mechanistically, Pacer antagonizes Rubicon to stimulate Vps34 kinase activity. Next, Pacer recruits PI3KC3 and HOPS complexes to the autophagosome for their site-specific activation by anchoring to the autophagosomal SNARE Stx17. Furthermore, Pacer is crucial for the degradation of hepatic lipid droplets, the suppression of Salmonella infection, and the clearance of protein aggregates. These results not only identify Pacer as a crucial multifunctional enhancer in autophagy but also uncover both the involvement of PI3KC3 and the mediators of HOPS's specific tethering activity in autophagosome maturation.","corpus_id":39480512,"score":1},{"doc_id":"28533369","title":"Phosphorylated Presenilin 1 decreases β-amyloid by facilitating autophagosome-lysosome fusion.","abstract":"Presenilin 1 (PS1), the catalytic subunit of the γ-secretase complex, cleaves βCTF to produce Aβ. We have shown that PS1 regulates Aβ levels by a unique bifunctional mechanism. In addition to its known role as the catalytic subunit of the γ-secretase complex, selective phosphorylation of PS1 on Ser367 decreases Aβ levels by increasing βCTF degradation through autophagy. Here, we report the molecular mechanism by which PS1 modulates βCTF degradation. We show that PS1 phosphorylated at Ser367, but not nonphosphorylated PS1, interacts with Annexin A2, which, in turn, interacts with the lysosomal N-ethylmaleimide-sensitive factor attachment protein receptor (SNARE) Vamp8. Annexin A2 facilitates the binding of Vamp8 to the autophagosomal SNARE Syntaxin 17 to modulate the fusion of autophagosomes with lysosomes. Thus, PS1 phosphorylated at Ser367 has an antiamyloidogenic function, promoting autophagosome-lysosome fusion and increasing βCTF degradation. Drugs designed to increase the level of PS1 phosphorylated at Ser367 should be useful in the treatment of Alzheimer's disease.","corpus_id":19054972,"score":1},{"doc_id":"28537477","title":"ATG conjugation-dependent degradation of the inner autophagosomal membrane is a key step for autophagosome maturation.","abstract":"Although the autophagy-related (ATG) conjugation systems are thought to be important for a late step of autophagosome formation, their precise function has been poorly understood because they are also required for localization of the most important autophagosomal marker LC3. In our recent study we found that, using the autophagosomal SNARE STX17 (syntaxin 17) as an alternative marker, autophagosome-like structures were generated in ATG conjugation system-deficient cells. Those structures could fuse with lysosomes but the degradation of the inner autophagosomal membrane was significantly delayed. We suggest that the ATG conjugation-dependent closure of autophagosomes causes the inner autophagosomal membrane to become sensitive to lysosomal degradation.","corpus_id":205899891,"score":1},{"doc_id":"28825857","title":"BORC Coordinates Encounter and Fusion of Lysosomes with Autophagosomes.","abstract":"Whereas the mechanisms involved in autophagosome formation have been extensively studied for the past 2 decades, those responsible for autophagosome-lysosome fusion have only recently begun to garner attention. In this study, we report that the multisubunit BORC complex, previously implicated in kinesin-dependent movement of lysosomes toward the cell periphery, is required for efficient autophagosome-lysosome fusion. Knockout (KO) of BORC subunits causes not only juxtanuclear clustering of lysosomes, but also increased levels of the autophagy protein LC3B-II and the receptor SQSTM1. Increases in LC3B-II occur without changes in basal MTORC1 activity and autophagy initiation. Instead, LC3B-II accumulation largely results from decreased lysosomal degradation. Further experiments show that BORC KO impairs both the encounter and fusion of autophagosomes with lysosomes. Reduced encounters result from an inability of lysosomes to move toward the peripheral cytoplasm, where many autophagosomes are formed. However, BORC KO also reduces the recruitment of the HOPS tethering complex to lysosomes and assembly of the STX17-VAMP8-SNAP29 trans-SNARE complex involved in autophagosome-lysosome fusion. Through these dual roles, BORC integrates the kinesin-dependent movement of lysosomes toward autophagosomes with HOPS-dependent autophagosome-lysosome fusion. These findings reveal a requirement for lysosome dispersal in autophagy that is independent of changes in MTORC1 signaling, and identify BORC as a novel regulator of autophagosome-lysosome fusion.","corpus_id":10700412,"score":1},{"doc_id":"29138318","title":"SNARE priming is essential for maturation of autophagosomes but not for their formation.","abstract":"Autophagy, a unique intracellular membrane-trafficking pathway, is initiated by the formation of an isolation membrane (phagophore) that engulfs cytoplasmic constituents, leading to generation of the autophagosome, a double-membrane vesicle, which is targeted to the lysosome. The outer autophagosomal membrane consequently fuses with the lysosomal membrane. Multiple membrane-fusion events mediated by SNARE molecules have been postulated to promote autophagy. αSNAP, the adaptor molecule for the SNARE-priming enzyme N-ethylmaleimide-sensitive factor (NSF) is known to be crucial for intracellular membrane fusion processes, but its role in autophagy remains unclear. Here we demonstrated that knockdown of αSNAP leads to inhibition of autophagy, manifested by an accumulation of sealed autophagosomes located in close proximity to lysosomes but not fused with them. Under these conditions, moreover, association of both Atg9 and the autophagy-related SNARE protein syntaxin17 with the autophagosome remained unaffected. Finally, our results suggested that under starvation conditions, the levels of αSNAP, although low, are nevertheless sufficient to partially promote the SNARE priming required for autophagy. Taken together, these findings indicate that while autophagosomal-lysosomal membrane fusion is sensitive to inhibition of SNARE priming, the initial stages of autophagosome biogenesis and autophagosome expansion remain resistant to its loss.","corpus_id":2617974,"score":1},{"doc_id":"29507186","title":"Increased O-GlcNAcylation of SNAP29 Drives Arsenic-Induced Autophagic Dysfunction.","abstract":"Environmental exposure to arsenic is linked to adverse health effects, including cancer and diabetes. Pleiotropic cellular effects are observed with arsenic exposure. Previously, we demonstrated that arsenic dysregulated the autophagy pathway at low, environmentally relevant concentrations. Here we show that arsenic blocks autophagy by preventing autophagosome-lysosome fusion. Specifically, arsenic disrupts formation of the STX17-SNAP29-VAMP8 SNARE complex, where SNAP29 mediates vesicle fusion through bridging STX17-containing autophagosomes to VAMP8-bearing lysosomes. Mechanistically, arsenic inhibits SNARE complex formation, at least in part, by enhancing O-GlcNAcylation of SNAP29. Transfection of O-GlcNAcylation-defective, but not wild-type, SNAP29 into clustered regularly interspaced short palindromic repeat (CRISPR)-mediated SNAP29 knockout cells abolishes arsenic-mediated autophagy inhibition. These findings reveal a mechanism by which low levels of arsenic perturb proteostasis through inhibition of SNARE complex formation, providing a possible therapeutic target for disease intervention in the more than 200 million people exposed to unsafe levels of arsenic.","corpus_id":3700206,"score":1},{"doc_id":"29694367","title":"Non-canonical role of the SNARE protein Ykt6 in autophagosome-lysosome fusion.","abstract":"The autophagosomal SNARE Syntaxin17 (Syx17) forms a complex with Snap29 and Vamp7/8 to promote autophagosome-lysosome fusion via multiple interactions with the tethering complex HOPS. Here we demonstrate that, unexpectedly, one more SNARE (Ykt6) is also required for autophagosome clearance in Drosophila. We find that loss of Ykt6 leads to large-scale accumulation of autophagosomes that are unable to fuse with lysosomes to form autolysosomes. Of note, loss of Syx5, the partner of Ykt6 in ER-Golgi trafficking does not prevent autolysosome formation, pointing to a more direct role of Ykt6 in fusion. Indeed, Ykt6 localizes to lysosomes and autolysosomes, and forms a SNARE complex with Syx17 and Snap29. Interestingly, Ykt6 can be outcompeted from this SNARE complex by Vamp7, and we demonstrate that overexpression of Vamp7 rescues the fusion defect of ykt6 loss of function cells. Finally, a point mutant form with an RQ amino acid change in the zero ionic layer of Ykt6 protein that is thought to be important for fusion-competent SNARE complex assembly retains normal autophagic activity and restores full viability in mutant animals, unlike palmitoylation or farnesylation site mutant Ykt6 forms. As Ykt6 and Vamp7 are both required for autophagosome-lysosome fusion and are mutually exclusive subunits in a Syx17-Snap29 complex, these data suggest that Vamp7 is directly involved in membrane fusion and Ykt6 acts as a non-conventional, regulatory SNARE in this process.","corpus_id":13680467,"score":1},{"doc_id":"19185015","title":"Comprehensive analysis of expression, subcellular localization, and cognate pairing of SNARE proteins in oligodendrocytes.","abstract":"Oligodendrocytes form the central nervous system myelin sheath by spiral wrapping of their plasma membrane around axons, necessitating a high rate of exocytic membrane addition to the growing myelin membrane. Membrane fusion is mediated by soluble N-ethylmaleimide-sensitive factor attachment protein receptor proteins (SNAREs), which act by specific pairing of vesicle (R)- and target (Q)-SNAREs. To characterize oligodendroglial SNAREs and their trafficking pathways, we performed a detailed expression analysis of SNAREs in differentiating cultured oligodendrocytes and myelin and determined their subcellular localization. Expression of the plasma membrane Q-SNAREs syntaxin 3, syntaxin 4, SNAP23, and the endosomal R-SNARE VAMP3/cellubrevin increased with oligodendroglial maturation, while the expression of SNAP29 decreased. Interestingly, syntaxin 3, syntaxin 4, and VAMP7/tetanustoxin-insensitive VAMP accumulated in myelin during development, suggesting a role in myelin membrane fusion. Coimmunoprecipitation from oligodendroglial cell lysates elucidated interactions between SNAREs: for example, Golgi-localized VAMP4 associated with syntaxin 6 and SNAP29. Furthermore, we identified a cognate core complex composed of VAMP3, syntaxin 4, and SNAP23, which may mediate fusion of endosome-derived vesicles with the plasma membrane. This study provides a comprehensive analysis of SNARE proteins in oligodendrocytes and assigns defined SNAREs to putative vesicle trafficking pathways in myelinating oligodendrocytes, thus facilitating future functional analysis of distinct SNAREs in oligodendroglial membrane traffic and myelination.","corpus_id":25612172,"score":0},{"doc_id":"19458617","title":"Reconstitution of Rab- and SNARE-dependent membrane fusion by synthetic endosomes.","abstract":"Rab GTPases and SNAREs (soluble N-ethylmaleimide-sensitive factor attachment protein receptors) are evolutionarily conserved essential components of the eukaryotic intracellular transport system. Although pairing of cognate SNAREs is sufficient to fuse membranes in vitro, a complete reconstitution of the Rab-SNARE machinery has never been achieved. Here we report the reconstitution of the early endosomal canine Rab5 GTPase, its key regulators and effectors together with SNAREs into proteoliposomes using a set of 17 recombinant human proteins. These vesicles behave like minimal 'synthetic' endosomes, fusing with purified early endosomes or with each other in vitro. Membrane fusion measured by content-mixing and morphological assays requires the cooperativity between Rab5 effectors and cognate SNAREs which, together, form a more efficient 'core machinery' than SNAREs alone. In reconstituting a fusion mechanism dependent on both a Rab GTPase and SNAREs, our work shows that the two machineries act coordinately to increase the specificity and efficiency of the membrane tethering and fusion process.","corpus_id":507806,"score":0},{"doc_id":"20937838","title":"Phosphoinositides function asymmetrically for membrane fusion, promoting tethering and 3Q-SNARE subcomplex assembly.","abstract":"Phosphatidylinositol 3-phosphate (PI(3)P) and phosphatidylinositol 4,5-bisphosphate (PI(4,5)P(2)) are essential for rapid SNARE-dependent fusion of yeast vacuoles and other organelles. These phosphoinositides also regulate the fusion of reconstituted proteoliposomes. The reconstituted reaction allows separate analysis of phosphoinositide-responsive subreactions: fusion with SNAREs alone, with the addition of the HOPS tethering factor, and with the further addition of the SNARE complex disassembly chaperones Sec17p and Sec18p. Using assays of membrane tethering, trans-SNARE pairing, and lipid mixing, we found that PI(3)P and PI(4,5)P(2) have distinct functions that are asymmetric with respect to R-SNARE (Nyv1p) and the 3Q-SNAREs (Vam3p, Vti1p, and Vam7p). Fusion reactions with the Q-SNAREs and R-SNARE on separate membranes showed that PI(3)P has two distinct functions. PI(3)P on Q-SNARE proteoliposomes promoted Vam7p binding and association with the other two Q-SNAREs. PI(3)P on R-SNARE proteoliposomes was recognized by the PX domain of Vam7p on Q-SNARE proteoliposomes to promote tethering, although this function could be supplanted by the tethering activity of HOPS. PI(4,5)P(2) stimulated fusion when it was on R-SNARE proteoliposomes, apposed to Q-SNARE proteoliposomes bearing PI(3)P. These functions are essential for the phosphoinositide-dependent synergy between HOPS and Sec17p/Sec18p in promoting rapid fusion.","corpus_id":205306048,"score":0},{"doc_id":"26986547","title":"The Atg17-Atg31-Atg29 complex and Atg11 regulate autophagosome-vacuole fusion.","abstract":"The macroautophagy (hereafter autophagy) process involves de novo formation of double-membrane autophagosomes; after sequestering cytoplasm these transient organelles fuse with the vacuole/lysosome. Genetic studies in yeasts have characterized more than 40 autophagy-related (Atg) proteins required for autophagy, and the majority of these proteins play roles in autophagosome formation. The fusion of autophagosomes with the vacuole is mediated by the Rab GTPase Ypt7, its guanine nucleotide exchange factor Mon1-Ccz1, and soluble N-ethylmaleimide-sensitive factor attachment protein receptor (SNARE) proteins. However, these factors are not autophagosome-vacuole fusion specific. We recently showed that 2 autophagy scaffold proteins, the Atg17-Atg31-Atg29 complex and Atg11, regulate autophagosome-vacuole fusion by recruiting the vacuolar SNARE Vam7 to the phagophore assembly site (PAS), where an autophagosome forms in yeast.","corpus_id":205899284,"score":0},{"doc_id":"27791468","title":"The STX6-VTI1B-VAMP3 complex facilitates xenophagy by regulating the fusion between recycling endosomes and autophagosomes.","abstract":"Macroautophagy/autophagy plays a critical role in immunity by directly degrading invading pathogens such as Group A Streptococcus (GAS), through a process that has been named xenophagy. We previously demonstrated that autophagic vacuoles directed against GAS, termed GAS-containing autophagosome-like vacuoles (GcAVs), use recycling endosomes (REs) as a membrane source. However, the precise molecular mechanism that facilitates the fusion between GcAVs and REs remains unclear. Here, we demonstrate that STX6 (syntaxin 6) is recruited to GcAVs and forms a complex with VTI1B and VAMP3 to regulate the GcAV-RE fusion that is required for xenophagy. STX6 targets the GcAV membrane through its tyrosine-based sorting motif and transmembrane domain, and localizes to TFRC (transferrin receptor)-positive punctate structures on GcAVs through its H2 SNARE domain. Knockdown and knockout experiments revealed that STX6 is required for the fusion between GcAVs and REs to promote clearance of intracellular GAS by autophagy. Moreover, VAMP3 and VTI1B interact with STX6 and localize on the TFRC-positive puncta on GcAVs, and are also involved in the RE-GcAV fusion. Furthermore, knockout of RABGEF1 impairs the RE-GcAV fusion and STX6-VAMP3 interaction. These findings demonstrate that RABGEF1 mediates RE fusion with GcAVs through the STX6-VAMP3-VTI1B complex, and reveal the SNARE dynamics involved in autophagosome formation in response to bacterial infection.","corpus_id":22869034,"score":0},{"doc_id":"28112172","title":"Sec3 promotes the initial binary t-SNARE complex assembly and membrane fusion.","abstract":"The soluble N-ethylmaleimide-sensitive factor-attachment protein receptors (SNAREs) constitute the core machinery for membrane fusion during eukaryotic cell vesicular trafficking. However, how the assembly of the SNARE complex is initiated is unknown. Here we report that Sec3, a component of the exocyst complex that mediates vesicle tethering during exocytosis, directly interacts with the t-SNARE protein Sso2. This interaction promotes the formation of an Sso2-Sec9 'binary' t-SNARE complex, the early rate-limiting step in SNARE complex assembly, and stimulates membrane fusion. The crystal structure of the Sec3-Sso2 complex suggests that Sec3 binding induces conformational changes of Sso2 that are crucial for the relief of its auto-inhibition. Interestingly, specific disruption of the Sec3-Sso2 interaction in cells blocks exocytosis without affecting the function of Sec3 in vesicle tethering. Our study reveals an activation mechanism for SNARE complex assembly, and uncovers a role of the exocyst in promoting membrane fusion in addition to vesicle tethering.","corpus_id":32784683,"score":0},{"doc_id":"28637767","title":"A short region upstream of the yeast vacuolar Qa-SNARE heptad-repeats promotes membrane fusion through enhanced SNARE complex assembly.","abstract":"Whereas SNARE (soluble N -ethylmaleimide-sensitive factor attachment protein receptor) heptad-repeats are well studied, SNAREs also have upstream N-domains of indeterminate function. The assembly of yeast vacuolar SNAREs into complexes for fusion can be studied in chemically defined reactions. Complementary proteoliposomes bearing a Rab:GTP and either the vacuolar R-SNARE or one of the three integrally anchored Q-SNAREs were incubated with the tethering/SM protein complex HOPS and the two other soluble SNAREs (lacking a transmembrane anchor) or their SNARE heptad-repeat domains. Fusion required a transmembrane-anchored R-SNARE on one membrane and an anchored Q-SNARE on the other. The N-domain of the Qb-SNARE was completely dispensable for fusion. Whereas fusion can be promoted by very high concentrations of the Qa-SNARE heptad-repeat domain alone, at physiological concentrations the Qa-SNARE heptad-repeat domain alone has almost no fusion activity. The 181-198 region of Qa, immediately upstream of the SNARE heptad-repeat domain, is required for normal fusion activity with HOPS. This region is needed for normal SNARE complex assembly.","corpus_id":20974035,"score":0},{"doc_id":"28677644","title":"2BC Non-Structural Protein of Enterovirus A71 Interacts with SNARE Proteins to Trigger Autolysosome Formation.","abstract":"Viruses have evolved unique strategies to evade or subvert autophagy machinery. Enterovirus A71 (EV-A71) induces autophagy during infection in vitro and in vivo. In this study, we report that EV-A71 triggers autolysosome formation during infection in human rhabdomyosarcoma (RD) cells to facilitate its replication. Blocking autophagosome-lysosome fusion with chloroquine inhibited virus RNA replication, resulting in lower viral titres, viral RNA copies and viral proteins. Overexpression of the non-structural protein 2BC of EV-A71 induced autolysosome formation. Yeast 2-hybrid and co-affinity purification assays showed that 2BC physically and specifically interacted with a N-ethylmaleimide-sensitive factor attachment receptor (SNARE) protein, syntaxin-17 (STX17). Co-immunoprecipitation assay further showed that 2BC binds to SNARE proteins, STX17 and synaptosome associated protein 29 (SNAP29). Transient knockdown of STX17, SNAP29, and microtubule-associated protein 1 light chain 3B (LC3B), crucial proteins in the fusion between autophagosomes and lysosomes) as well as the lysosomal-associated membrane protein 1 (LAMP1) impaired production of infectious EV-A71 in RD cells. Collectively, these results demonstrate that the generation of autolysosomes triggered by the 2BC non-structural protein is important for EV-A71 replication, revealing a potential molecular pathway targeted by the virus to exploit autophagy. This study opens the possibility for the development of novel antivirals that specifically target 2BC to inhibit formation of autolysosomes during EV-A71 infection.","corpus_id":4400316,"score":0},{"doc_id":"29088698","title":"A tethering complex drives the terminal stage of SNARE-dependent membrane fusion.","abstract":"Membrane fusion in eukaryotic cells mediates the biogenesis of organelles, vesicular traffic between them, and exo- and endocytosis of important signalling molecules, such as hormones and neurotransmitters. Distinct tasks in intracellular membrane fusion have been assigned to conserved protein systems. Tethering proteins mediate the initial recognition and attachment of membranes, whereas SNARE (soluble N-ethylmaleimide-sensitive factor attachment protein receptor) protein complexes are considered as the core fusion engine. SNARE complexes provide mechanical energy to distort membranes and drive them through a hemifusion intermediate towards the formation of a fusion pore. This last step is highly energy-demanding. Here we combine the in vivo and in vitro fusion of yeast vacuoles with molecular simulations to show that tethering proteins are critical for overcoming the final energy barrier to fusion pore formation. SNAREs alone drive vacuoles only into the hemifused state. Tethering proteins greatly increase the volume of SNARE complexes and deform the site of hemifusion, which lowers the energy barrier for pore opening and provides the driving force. Thereby, tethering proteins assume a crucial mechanical role in the terminal stage of membrane fusion that is likely to be conserved at multiple steps of vesicular traffic. We therefore propose that SNAREs and tethering proteins should be considered as a single, non-dissociable device that drives fusion. The core fusion machinery may then be larger and more complex than previously thought.","corpus_id":205261587,"score":0}],"string":"[\n {\n \"doc_id\": \"19050071\",\n \"title\": \"Identification of Barkor as a mammalian autophagy-specific factor for Beclin 1 and class III phosphatidylinositol 3-kinase.\",\n \"abstract\": \"Autophagy mediates the cellular response to nutrient deprivation, protein aggregation, and pathogen invasion in human. Dysfunction of autophagy has been implicated in multiple human diseases including cancer. The identification of novel autophagy factors in mammalian cells will provide critical mechanistic insights into how this complicated cellular pathway responds to a broad range of challenges. Here, we report the cloning of an autophagy-specific protein that we called Barkor (Beclin 1-associated autophagy-related key regulator) through direct interaction with Beclin 1 in the human phosphatidylinositol 3-kinase class III complex. Barkor shares 18% sequence identity and 32% sequence similarity with yeast Atg14. Elimination of Barkor expression by RNA interference compromises starvation- and rapamycin-induced LC3 lipidation and autophagosome formation. Overexpression of Barkor leads to autophagy activation and increased number and enlarged volume of autophagosomes. Tellingly, Barkor is also required for suppression of the autophagy-mediated intracellular survival of Salmonella typhimurium in mammalian cells. Mechanistically, Barkor competes with UV radiation resistance associated gene product (UVRAG) for interaction with Beclin 1, and the complex formation of Barkor and Beclin1 is required for their localizations to autophagosomes. Therefore, we define a regulatory signaling pathway mediated by Barkor that positively controls autophagy through Beclin 1 and represents a potential target for drug development in the treatment of human diseases implicated in autophagic dysfunction.\",\n \"corpus_id\": 205242712,\n \"score\": 2\n },\n {\n \"doc_id\": \"21518905\",\n \"title\": \"Autophagosome targeting and membrane curvature sensing by Barkor/Atg14(L).\",\n \"abstract\": \"The class III phosphatidylinositol 3-kinase (PI3KC3) is crucial for autophagosome biogenesis. It has been long speculated to nucleate the autophagosome membrane, but the biochemical mechanism of such nucleation activity remains unsolved. We recently identified Barkor/Atg14(L) as the targeting factor for PI3KC3 to autophagosome membrane. Here, we show that we have characterized the region of Barkor/Atg14(L) required for autophagosome targeting and identified the BATS [Barkor/Atg14(L) autophagosome targeting sequence] domain at the carboxyl terminus of Barkor. Bioinformatics and mutagenesis analyses revealed that the BATS domain binds to autophagosome membrane via the hydrophobic surface of an intrinsic amphipathic alpha helix. BATS puncta overlap with Atg16 and LC3, and partially with DFCP1, in a stress-inducible manner. Ectopically expressed BATS accumulates on highly curved tubules that likely represent intermediate autophagic structures. PI3KC3 recruitment and autophagy stimulation by Barkor/Atg14(L) require the BATS domain. Furthermore, our biochemical analyses indicate that the BATS domain directly binds to the membrane, and it favors membrane composed of phosphatidylinositol 3-phosphate [PtdIns(3)P] and phosphatidylinositol 4,5-biphosphate [PtdIns(4,5)P2]. By binding preferentially to curved membranes incorporated with PtdIns(3)P but not PtdIns(4,5)P2, the BATS domain is capable of sensing membrane curvature. Thus, we propose a novel model of PI3KC3 autophagosome membrane nucleation in which its autophagosome-specific adaptor, Barkor, accumulates on highly curved PtdIns(3)P enriched autophagic membrane via its BATS domain to sense and maintain membrane curvature.\",\n \"corpus_id\": 7823697,\n \"score\": 2\n },\n {\n \"doc_id\": \"21784249\",\n \"title\": \"SNARE proteins are required for macroautophagy.\",\n \"abstract\": \"Macroautophagy mediates the degradation of long-lived proteins and organelles via the de novo formation of double-membrane autophagosomes that sequester cytoplasm and deliver it to the vacuole/lysosome; however, relatively little is known about autophagosome biogenesis. Atg8, a phosphatidylethanolamine-conjugated protein, was previously proposed to function in autophagosome membrane expansion, based on the observation that it mediates liposome tethering and hemifusion in vitro. We show here that with physiological concentrations of phosphatidylethanolamine, Atg8 does not act as a fusogen. Rather, we provide evidence for the involvement of exocytic Q/t-SNAREs in autophagosome formation, acting in the recruitment of key autophagy components to the site of autophagosome formation, and in regulating the organization of Atg9 into tubulovesicular clusters. Additionally, we found that the endosomal Q/t-SNARE Tlg2 and the R/v-SNAREs Sec22 and Ykt6 interact with Sso1-Sec9, and are required for normal Atg9 transport. Thus, multiple SNARE-mediated fusion events are likely to be involved in autophagosome biogenesis.\",\n \"corpus_id\": 3842068,\n \"score\": 2\n },\n {\n \"doc_id\": \"23217709\",\n \"title\": \"The hairpin-type tail-anchored SNARE syntaxin 17 targets to autophagosomes for fusion with endosomes/lysosomes.\",\n \"abstract\": \"The lysosome is a degradative organelle, and its fusion with other organelles is strictly regulated. In contrast to fusion with the late endosome, the mechanisms underlying autophagosome-lysosome fusion remain unknown. Here, we identify syntaxin 17 (Stx17) as the autophagosomal SNARE required for fusion with the endosome/lysosome. Stx17 localizes to the outer membrane of completed autophagosomes but not to the isolation membrane (unclosed intermediate structures); for this reason, the lysosome does not fuse with the isolation membrane. Stx17 interacts with SNAP-29 and the endosomal/lysosomal SNARE VAMP8. Depletion of Stx17 causes accumulation of autophagosomes without degradation. Stx17 has a unique C-terminal hairpin structure mediated by two tandem transmembrane domains containing glycine zipper-like motifs, which is essential for its association with the autophagosomal membrane. These findings reveal a mechanism by which the SNARE protein is available to the completed autophagosome.\",\n \"corpus_id\": 14736164,\n \"score\": 2\n },\n {\n \"doc_id\": \"23455425\",\n \"title\": \"Autophagosomes form at ER-mitochondria contact sites.\",\n \"abstract\": \"Autophagy is a tightly regulated intracellular bulk degradation/recycling system that has fundamental roles in cellular homeostasis. Autophagy is initiated by isolation membranes, which form and elongate as they engulf portions of the cytoplasm and organelles. Eventually isolation membranes close to form double membrane-bound autophagosomes and fuse with lysosomes to degrade their contents. The physiological role of autophagy has been determined since its discovery, but the origin of autophagosomal membranes has remained unclear. At present, there is much controversy about the organelle from which the membranes originate--the endoplasmic reticulum (ER), mitochondria and plasma membrane. Here we show that autophagosomes form at the ER-mitochondria contact site in mammalian cells. Imaging data reveal that the pre-autophagosome/autophagosome marker ATG14 (also known as ATG14L) relocalizes to the ER-mitochondria contact site after starvation, and the autophagosome-formation marker ATG5 also localizes at the site until formation is complete. Subcellular fractionation showed that ATG14 co-fractionates in the mitochondria-associated ER membrane fraction under starvation conditions. Disruption of the ER-mitochondria contact site prevents the formation of ATG14 puncta. The ER-resident SNARE protein syntaxin 17 (STX17) binds ATG14 and recruits it to the ER-mitochondria contact site. These results provide new insight into organelle biogenesis by demonstrating that the ER-mitochondria contact site is important in autophagosome formation.\",\n \"corpus_id\": 205232769,\n \"score\": 2\n },\n {\n \"doc_id\": \"23466629\",\n \"title\": \"Syntaxin 17: the autophagosomal SNARE.\",\n \"abstract\": \"The phagophore (also called isolation membrane) elongates and encloses a portion of cytoplasm, resulting in formation of the autophagosome. After completion of autophagosome formation, the outer autophagosomal membrane becomes ready to fuse with the lysosome for degradation of enclosed cytoplasmic materials. However, the molecular mechanism for how the fusion of completed autophagosomes with the lysosome is regulated has not been fully understood. We discovered syntaxin 17 (STX17) as an autophagosomal soluble N-ethylmaleimide-sensitive factor attachment protein receptor (SNARE). STX17 has a hairpin-type structure mediated by two transmembrane domains, each containing glycine zipper motifs. This unique transmembrane structure contributes to its specific localization to completed autophagosomes but not to phagophores. STX17 interacts with SNAP29 and the lysosomal SNARE VAMP8, and all of these proteins are required for autophagosome-lysosome fusion. The late recruitment of STX17 to completed autophagosomes could prevent premature fusion of the lysosome with unclosed phagophores.\",\n \"corpus_id\": 41343480,\n \"score\": 2\n },\n {\n \"doc_id\": \"24554770\",\n \"title\": \"The HOPS complex mediates autophagosome-lysosome fusion through interaction with syntaxin 17.\",\n \"abstract\": \"Membrane fusion is generally controlled by Rabs, soluble N-ethylmaleimide-sensitive factor attachment protein receptors (SNAREs), and tethering complexes. Syntaxin 17 (STX17) was recently identified as the autophagosomal SNARE required for autophagosome-lysosome fusion in mammals and Drosophila. In this study, to better understand the mechanism of autophagosome-lysosome fusion, we searched for STX17-interacting proteins. Immunoprecipitation and mass spectrometry analysis identified vacuolar protein sorting 33A (VPS33A) and VPS16, which are components of the homotypic fusion and protein sorting (HOPS)-tethering complex. We further confirmed that all HOPS components were coprecipitated with STX17. Knockdown of VPS33A, VPS16, or VPS39 blocked autophagic flux and caused accumulation of STX17- and microtubule-associated protein light chain (LC3)-positive autophagosomes. The endocytic pathway was also affected by knockdown of VPS33A, as previously reported, but not by knockdown of STX17. By contrast, ultraviolet irradiation resistance-associated gene (UVRAG), a known HOPS-interacting protein, did not interact with the STX17-HOPS complex and may not be directly involved in autophagosome-lysosome fusion. Collectively these results suggest that, in addition to its well-established function in the endocytic pathway, HOPS promotes autophagosome-lysosome fusion through interaction with STX17.\",\n \"corpus_id\": 2100853,\n \"score\": 2\n },\n {\n \"doc_id\": \"25419848\",\n \"title\": \"O-GlcNAc-modification of SNAP-29 regulates autophagosome maturation.\",\n \"abstract\": \"The mechanism by which nutrient status regulates the fusion of autophagosomes with endosomes/lysosomes is poorly understood. Here, we report that O-linked β-N-acetylglucosamine (O-GlcNAc) transferase (OGT) mediates O-GlcNAcylation of the SNARE protein SNAP-29 and regulates autophagy in a nutrient-dependent manner. In mammalian cells, OGT knockdown, or mutating the O-GlcNAc sites in SNAP-29, promotes the formation of a SNAP-29-containing SNARE complex, increases fusion between autophagosomes and endosomes/lysosomes, and promotes autophagic flux. In Caenorhabditis elegans, depletion of ogt-1 has a similar effect on autophagy; moreover, expression of an O-GlcNAc-defective SNAP-29 mutant facilitates autophagic degradation of protein aggregates. O-GlcNAcylated SNAP-29 levels are reduced during starvation in mammalian cells and in C. elegans. Our study reveals a mechanism by which O-GlcNAc-modification integrates nutrient status with autophagosome maturation.\",\n \"corpus_id\": 37822524,\n \"score\": 2\n },\n {\n \"doc_id\": \"25434465\",\n \"title\": \"Sugar modification inhibits autophagosome-lysosome fusion.\",\n \"abstract\": \"Autophagy is an intracellular degradation system that is mediated by orchestrated functions of membranes and proteins. A genetic screen in Caenorhabditis elegans revealed that O-linked N-acetylglucosamine modification of the SNARE protein SNAP-29 negatively regulates SNARE-dependent fusion between autophagosomes and lysosomes. This regulatory mechanism is conserved in mammals.\",\n \"corpus_id\": 37079614,\n \"score\": 2\n },\n {\n \"doc_id\": \"25920502\",\n \"title\": \"Toward an understanding of autophagosome-lysosome fusion: The unsuspected role of ATG14.\",\n \"abstract\": \"Although largely overlooked relative to the process of phagophore formation, the mechanism through which autophagosomes fuse with lysosomes is a critical aspect of macroautophagy that is not fully understood. In particular, this step must be carefully regulated to prevent premature fusion of an incomplete autophagosome (that is, a phagophore) with a lysosome, because such an event would not allow access of the partially sequestered cargo to the lysosome lumen. The identification of the autophagosome-associated SNARE protein STX17 (syntaxin 17) provided some clue in the understanding of this process. STX17 is recruited specifically to mature autophagosomes, and functions in mediating autophagosome-lysosome fusion by forming a complex with the Qbc SNARE SNAP29 and the lysosomal R-SNARE VAMP8. Additionally, STX17 plays a role in the early events of autophagy by interacting with the phosphatidylinositol 3-kinase complex component ATG14. Upon autophagy induction STX17 is strictly required for ATG14 recruitment to the ER-mitochondria contact sites, a critical step for the assembly of the phagophore and therefore for autophagosome formation. In their recent paper, Diao and collaborators now show that the ATG14-STX17-SNAP29 interaction mediates autophagosome-lysosome tethering and fusion events, thus revealing a novel function of ATG14 in the later steps of the autophagy pathway.\",\n \"corpus_id\": 3551891,\n \"score\": 2\n },\n {\n \"doc_id\": \"25945523\",\n \"title\": \"ATG14 controls SNARE-mediated autophagosome fusion with a lysosome.\",\n \"abstract\": \"Autophagosome fusion with a lysosome constitutes the last barrier for autophagic degradation. It is speculated that this fusion process is precisely and tightly regulated. Recent genetic evidence suggests that a set of SNARE proteins, including STX17, SNAP29, and VAMP8, are essential for the fusion between autophagosomes and lysosomes. However, it remains unclear whether these SNAREs are fusion competent and how their fusogenic activity is specifically regulated during autophagy. Using a combination of biochemical, cell biology, and genetic approaches, we demonstrated that fusogenic activity of the autophagic SNARE complex is temporally and spatially controlled by ATG14/Barkor/Atg14L, an essential autophagy-specific regulator of the class III phosphatidylinositol 3-kinase complex (PtdIns3K). ATG14 directly binds to the STX17-SNAP29 binary complex on autophagosomes and promotes STX17-SNAP29-VAMP8-mediated autophagosome fusion with lysosomes. ATG14 homo-oligomerization is required for SNARE binding and fusion promotion, but is dispensable for PtdIns3K stimulation and autophagosome biogenesis. Consequently, ATG14 homo-oligomerization is required for autophagosome fusion with a lysosome, but is dispensable for autophagosome biogenesis. These data support a key role of ATG14 in controlling autophagosome fusion with a lysosome.\",\n \"corpus_id\": 6972001,\n \"score\": 2\n },\n {\n \"doc_id\": \"27885029\",\n \"title\": \"The ATG conjugation systems are important for degradation of the inner autophagosomal membrane.\",\n \"abstract\": \"In macroautophagy, cytoplasmic contents are sequestered into the double-membrane autophagosome, which fuses with the lysosome to become the autolysosome. It has been thought that the autophagy-related (ATG) conjugation systems are required for autophagosome formation. Here, we found that autophagosomal soluble N-ethylmaleimide-sensitive factor attachment protein receptor (SNARE) syntaxin 17-positive autophagosome-like structures could be generated even in the absence of the ATG conjugation systems, although at a reduced rate. These syntaxin 17-positive structures could further fuse with lysosomes, but degradation of the inner autophagosomal membrane was significantly delayed. Accordingly, autophagic activity in ATG conjugation-deficient cells was strongly suppressed. We suggest that the ATG conjugation systems, which are likely required for the closure (i.e., fission) of the autophagosomal edge, are not absolutely essential for autolysosome formation but are important for efficient degradation of the inner autophagosomal membrane.\",\n \"corpus_id\": 39627761,\n \"score\": 2\n },\n {\n \"doc_id\": \"28077293\",\n \"title\": \"Autophagosome Maturation and Fusion.\",\n \"abstract\": \"Macroautophagy, or simply autophagy, is a degradative pathway that delivers cytoplasmic components, including cytosol and organelles, to the lysosome in double-membrane vesicles called autophagosomes. This process is initiated at the pre-autophagosomal structure or phagophore assembly site and involves a number of highly conserved autophagy-related proteins. These support the generation and conversion of an open membranous cistern known as the phagophore or isolation membrane into a closed autophagosome. Within this review, we will focus on recent insights into the molecular events following the sealing/completion of an autophagosome, which lead to its maturation and subsequent fusion with endosomes/lysosomes.\",\n \"corpus_id\": 46790483,\n \"score\": 2\n },\n {\n \"doc_id\": \"28253966\",\n \"title\": \"In Vitro Reconstitution of Autophagosome-Lysosome Fusion.\",\n \"abstract\": \"SNARE (soluble N-ethylmaleimide-sensitive factor attachment protein receptors) proteins are a highly regulated class of membrane proteins lying in the center of membrane fusion. In conjunction with accessory proteins, SNAREs drive efficient merger of two distinct lipid bilayers into one interconnected structure. This chapter describes our fluorescence resonance energy transfer (FRET)-based proteoliposome fusion assays for the roles of various SNARE proteins, accessory proteins, and effects of different lipid compositions on membrane fusion involved in autophagy.\",\n \"corpus_id\": 10899001,\n \"score\": 2\n },\n {\n \"doc_id\": \"28598244\",\n \"title\": \"Accumulation of undegraded autophagosomes by expression of dominant-negative STX17 (syntaxin 17) mutants.\",\n \"abstract\": \"Macroautophagy/autophagy, which is one of the main degradation systems in the cell, is mediated by a specialized organelle, the autophagosome. Purification of autophagosomes before fusion with lysosomes is important for both mechanistic and physiological studies of the autophagosome. Here, we report a simple method to accumulate undigested autophagosomes. Overexpression of the autophagosomal Qa-SNARE STX17 (syntaxin 17) lacking the N-terminal domain (NTD) or N-terminally tagged GFP-STX17 causes accumulation of autophagosomes. A HeLa cell line, which expresses GFP-STX17ΔNTD or full-length GFP-STX17 under the control of the tetracycline-responsive promoter, accumulates a large number of undigested autophagosomes devoid of lysosomal markers or early autophagy factors upon treatment with doxycycline. Using this inducible cell line, nascent autophagosomes can be easily purified by OptiPrep density-gradient centrifugation and immunoprecipitation. This novel method should be useful for further characterization of nascent autophagosomes.\",\n \"corpus_id\": 205899963,\n \"score\": 2\n },\n {\n \"doc_id\": \"18032918\",\n \"title\": \"BARgaining membranes for autophagosome formation: Regulation of autophagy and tumorigenesis by Bif-1/Endophilin B1.\",\n \"abstract\": \"Autophagy is an intracellular system for the bulk degradation of cytoplasmic components enclosed within double-membrane structures known as autophagosomes. To date, many autophagy-related (Atg) genes have been identified by independent genetic screens for autophagy-defective mutants in yeast; however, the molecular machinery required for the biogenesis of autophagosomes in mammalian systems has yet to be determined.(1,2) Recently, we have reported that Bif-1 interacts with Beclin 1 through UVRAG and promotes the activation of class III phosphatidylinositol 3-kinase (PI3KC3) and the formation of autophagosomes.(3) Moreover, we have found that loss of Bif-1 promotes starvation-induced caspase activation, but prolongs cell survival by suppressing autophagydependent cell death, and enhances spontaneous tumorigenesis in mice. Bif-1 is a member of the endophilin family, which possesses membrane binding and liposome tubulation activities.(4) During nutrient deprivation, Bif-1 accumulates in punctate foci where it co-localizes with LC3, Atg5 and Atg9. Time-lapse microscopy analyses reveal that Bif-1-positive small vesicles expand by recruiting and fusing with Atg9-positive small membranes to form autophagosomes. Taken together, our findings highlight Bif-1 as a potential regulator of autophagosome biogenesis and as a tumor suppressor.\",\n \"corpus_id\": 24936612,\n \"score\": 1\n },\n {\n \"doc_id\": \"18843052\",\n \"title\": \"Beclin 1 forms two distinct phosphatidylinositol 3-kinase complexes with mammalian Atg14 and UVRAG.\",\n \"abstract\": \"Class III phosphatidylinositol 3-kinase (PI3-kinase) regulates multiple membrane trafficking. In yeast, two distinct PI3-kinase complexes are known: complex I (Vps34, Vps15, Vps30/Atg6, and Atg14) is involved in autophagy, and complex II (Vps34, Vps15, Vps30/Atg6, and Vps38) functions in the vacuolar protein sorting pathway. Atg14 and Vps38 are important in inducing both complexes to exert distinct functions. In mammals, the counterparts of Vps34, Vps15, and Vps30/Atg6 have been identified as Vps34, p150, and Beclin 1, respectively. However, orthologues of Atg14 and Vps38 remain unknown. We identified putative mammalian homologues of Atg14 and Vps38. The Vps38 candidate is identical to UV irradiation resistance-associated gene (UVRAG), which has been reported as a Beclin 1-interacting protein. Although both human Atg14 and UVRAG interact with Beclin 1 and Vps34, Atg14, and UVRAG are not present in the same complex. Although Atg14 is present on autophagic isolation membranes, UVRAG primarily associates with Rab9-positive endosomes. Silencing of human Atg14 in HeLa cells suppresses autophagosome formation. The coiled-coil region of Atg14 required for binding with Vps34 and Beclin 1 is essential for autophagy. These results suggest that mammalian cells have at least two distinct class III PI3-kinase complexes, which may function in different membrane trafficking pathways.\",\n \"corpus_id\": 32868891,\n \"score\": 1\n },\n {\n \"doc_id\": \"19270693\",\n \"title\": \"Distinct regulation of autophagic activity by Atg14L and Rubicon associated with Beclin 1-phosphatidylinositol-3-kinase complex.\",\n \"abstract\": \"Beclin 1, a mammalian autophagy protein that has been implicated in development, tumour suppression, neurodegeneration and cell death, exists in a complex with Vps34, the class III phosphatidylinositol-3-kinase (PI(3)K) that mediates multiple vesicle-trafficking processes including endocytosis and autophagy. However, the precise role of the Beclin 1-Vps34 complex in autophagy regulation remains to be elucidated. Combining mouse genetics and biochemistry, we have identified a large in vivo Beclin 1 complex containing the known proteins Vps34, p150/Vps15 and UVRAG, as well as two newly identified proteins, Atg14L (yeast Atg14-like) and Rubicon (RUN domain and cysteine-rich domain containing, Beclin 1-interacting protein). Characterization of the new proteins revealed that Atg14L enhances Vps34 lipid kinase activity and upregulates autophagy, whereas Rubicon reduces Vps34 activity and downregulates autophagy. We show that Beclin 1 and Atg14L synergistically promote the formation of double-membraned organelles that are associated with Atg5 and Atg12, whereas forced expression of Rubicon results in aberrant late endosomal/lysosomal structures and impaired autophagosome maturation. We hypothesize that by forming distinct protein complexes, Beclin 1 and its binding proteins orchestrate the precise function of the class III PI(3)K in regulating autophagy at multiple steps.\",\n \"corpus_id\": 16601081,\n \"score\": 1\n },\n {\n \"doc_id\": \"19337031\",\n \"title\": \"In vitro reconstitution of fusion between immature autophagosomes and endosomes.\",\n \"abstract\": \"Autophagy is a highly conserved degradative pathway whereby a double membrane engulfs cytoplasmic constituents to form an autophagic vacuole or autophagosome. An essential requirement for efficient autophagy is the acquisition of an adequate degradative capacity by the autophagosomes. To acquire this capacity the immature autophagic vacuoles (AVis) obtain lysosomal hydrolases by fusion with endosomes. The current models suggest that at least two types of endosomes, early and late, fuse with AVis to form mature, degradative AVds. This fusion and maturation requires proteins also involved in endosome maturation such as Rab7. However, it is not known if there are molecular requirements unique to AVi-endosome fusion. To identify and investigate the molecular requirements of this fusion we developed a cell-free fusion assay based on content mixing, which occurs after fusion of isolated AVis and different endosomal fractions. Our assay shows that isolated AVis can fuse to a similar extent in vitro with both early and late endosomes. Furthermore, fusion between autophagosomes and endosomes requires cytosolic and endosomal proteins, but does not show a nucleotide-dependence, and is partially N-ethylmaleimide sensitive. We also demonstrate that the lipidated form of the autophagosomal protein LC3 is dispensable for this fusion event.\",\n \"corpus_id\": 7451436,\n \"score\": 1\n },\n {\n \"doc_id\": \"20089838\",\n \"title\": \"Combinational soluble N-ethylmaleimide-sensitive factor attachment protein receptor proteins VAMP8 and Vti1b mediate fusion of antimicrobial and canonical autophagosomes with lysosomes.\",\n \"abstract\": \"Autophagy plays a crucial role in host defense, termed antimicrobial autophagy (xenophagy), as it functions to degrade intracellular foreign microbial invaders such as group A Streptococcus (GAS). Xenophagosomes undergo a stepwise maturation process consisting of a fusion event with lysosomes, after which the cargoes are degraded. However, the molecular mechanism underlying xenophagosome/lysosome fusion remains unclear. We examined the involvement of endocytic soluble N-ethylmaleimide-sensitive factor attachment protein receptors (SNAREs) in xenophagosome/lysosome fusion. Confocal microscopic analysis showed that SNAREs, including vesicle-associated membrane protein (VAMP)7, VAMP8, and vesicle transport through interaction with t-SNAREs homologue 1B (Vti1b), colocalized with green fluorescent protein-LC3 in xenophagosomes. Knockdown of Vti1b and VAMP8 with small interfering RNAs disturbed the colocalization of LC3 with lysosomal membrane protein (LAMP)1. The invasive efficiency of GAS into cells was not altered by knockdown of VAMP8 or Vti1b, whereas cellular bactericidal efficiency was significantly diminished, indicating that antimicrobial autophagy was functionally impaired. Knockdown of Vti1b and VAMP8 also disturbed colocalization of LC3 with LAMP1 in canonical autophagy, in which LC3-II proteins were negligibly degraded. In contrast, knockdown of Syntaxin 7 and Syntaxin 8 showed little effect on the autophagic fusion event. These findings strongly suggest that the combinational SNARE proteins VAMP8 and Vti1b mediate the fusion of antimicrobial and canonical autophagosomes with lysosomes, an essential event for autophagic degradation.\",\n \"corpus_id\": 13268644,\n \"score\": 1\n },\n {\n \"doc_id\": \"20798834\",\n \"title\": \"Cellular machinery to fuse antimicrobial autophagosome with lysosome.\",\n \"abstract\": \"Autophagy is an intracellular bulk degradation/recycling system that turns over cellular constituents and also functions to degrade intracellular foreign microbial invaders by a process termed xenophagy (antimicrobial autophagy). We previously showed that intracellular group A Streptococcus (GAS) organisms are captured by xenophagosomes, then degraded following fusion with lysosomes. Very recently, we analyzed the molecular mechanism underlying xenophagosome/lysosome fusion and found that endocytic soluble N-ethylmaleimide-sensitive factor attachment protein receptors (SNAREs) were involved. Knockdown of the combinational SNARE proteins Vti1b and VAMP8 with siRNAs disturbed autophagic fusion with lysosomes, and cellular bactericidal efficiency was significantly diminished. Furthermore, knockdown of those SNAREs inhibited the fusion of canonical autophagosomes with lysosomes. In addition, important findings showed that Vti1b is derived from autophagic compartments, whereas VAMP8 originates from lysosomes. Together, these results strongly suggest that SNARE proteins Vti1b and VAMP8 mediate the fusion of antimicrobial and canonical autophagosomes with lysosomes, an essential event for autophagic degradation.\",\n \"corpus_id\": 29550189,\n \"score\": 1\n },\n {\n \"doc_id\": \"21497758\",\n \"title\": \"LC3 and GATE-16 N termini mediate membrane fusion processes required for autophagosome biogenesis.\",\n \"abstract\": \"Autophagy is a unique membrane trafficking pathway describing the formation and targeting of double membrane autophagosomes to the vacuole/lysosome. The biogenesis of autophagosomes and their delivery to the vacuole/lysosome depend on multiple membrane fusion events. Using a cell-free system, we have investigated the ability of LC3 and GATE-16, two mammalian Atg8 orthologs, to mediate membrane fusion. We found that both proteins promote tethering and membrane fusion, mediated by the proteins' N-terminal α helices. We further show that short, 10 amino acid long synthetic peptides derived from the N terminus of LC3 or GATE-16 are sufficient to promote membrane fusion. Our data indicate that the fusion activity of LC3 is mediated by positively charged amino acids, whereas the activity of GATE-16 is mediated by hydrophobic interactions. Finally, we demonstrate that LC3 and GATE-16 N termini in general and specific residues needed for the fusion activity are essential for the proteins role in autophagosome biogenesis.\",\n \"corpus_id\": 9354127,\n \"score\": 1\n },\n {\n \"doc_id\": \"21738011\",\n \"title\": \"Membrane curvature response in autophagy.\",\n \"abstract\": \"Membrane trafficking is key for signal transduction, cargo transportation, and in the case of autophagy, delivering cytoplasmic substrates to the lysosome for degradation. Autophagy requires the formation of a unique double membrane vesicle, the autophagosome. However, the mechanism by which the autophagosome forms is unknown. Our recent study focused on the role of Barkor/Atg14(L) in targeting the autophagy-specific class III phosphatidylinositol-3-kinase (PtdIns3KC3) complex to the early autophagosome has implicated this complex in autophagosome formation. This study found that the BATS domain of Barkor targets the PtdIns3KC3 complex to early autophagic structures and senses highly curved membranes enriched in phosphatidylinositol-3-phosphate (PtdIns(3)P). Consequently, this study uncovered an exciting new role for the PtdIns3KC3 complex as a potential inducer of autophagosome formation.\",\n \"corpus_id\": 6595904,\n \"score\": 1\n },\n {\n \"doc_id\": \"21784250\",\n \"title\": \"Autophagosome precursor maturation requires homotypic fusion.\",\n \"abstract\": \"Autophagy is a catabolic process in which lysosomes degrade intracytoplasmic contents transported in double-membraned autophagosomes. Autophagosomes are formed by the elongation and fusion of phagophores, which can be derived from preautophagosomal structures coming from the plasma membrane and other sites like the endoplasmic reticulum and mitochondria. The mechanisms by which preautophagosomal structures elongate their membranes and mature toward fully formed autophagosomes still remain unknown. Here, we show that the maturation of the early Atg16L1 precursors requires homotypic fusion, which is essential for subsequent autophagosome formation. Atg16L1 precursor homotypic fusion depends on the SNARE protein VAMP7 together with partner SNAREs. Atg16L1 precursor homotypic fusion is a critical event in the early phases of autophagy that couples membrane acquisition and autophagosome biogenesis, as this step regulates the size of the vesicles, which in turn appears to influence their subsequent maturation into LC3-positive autophagosomes.\",\n \"corpus_id\": 5377736,\n \"score\": 1\n },\n {\n \"doc_id\": \"22013444\",\n \"title\": \"Atg14: a key player in orchestrating autophagy.\",\n \"abstract\": \"Phosphorylation of phosphatidylinositol (PtdIns) by a PtdIns 3-kinase is an essential process in autophagy. Atg14, a specific subunit of one of the PtdIns 3-kinase complexes, targets the complex to the probable site of autophagosome formation, thereby, sorting the complex to function specifically in autophagy. The N-terminal half of Atg14, containing coiled-coil domains, is required to form the PtdIns 3-kinase complex and target it to the proper site. The C-terminal half of yeast Atg14 is suggested to be involved in the formation of a normal-sized autophagosome. The C-terminal half of mammalian Atg14 contains the Barkor/Atg14(L) autophagosome-targeting sequence (BATS) domain that preferentially binds to the highly curved membranes containing PtdIns(3)P and is proposed to target the PtdIns 3-kinase complex efficiently to the isolation membrane. Thus, the N- and C-terminal halves of Atg14 are likely to have an essential core function and a regulatory role, respectively.\",\n \"corpus_id\": 9800350,\n \"score\": 1\n },\n {\n \"doc_id\": \"22342342\",\n \"title\": \"A mammalian autophagosome maturation mechanism mediated by TECPR1 and the Atg12-Atg5 conjugate.\",\n \"abstract\": \"Autophagy is a major catabolic pathway in eukaryotes associated with a broad spectrum of human diseases. In autophagy, autophagosomes carrying cellular cargoes fuse with lysosomes for degradation. However, the molecular mechanism underlying autophagosome maturation is largely unknown. Here we report that TECPR1 binds to the Atg12-Atg5 conjugate and phosphatidylinositol 3-phosphate (PtdIns[3]P) to promote autophagosome-lysosome fusion. TECPR1 and Atg16 form mutually exclusive complexes with the Atg12-Atg5 conjugate, and TECPR1 binds PtdIns(3)P upon association with the Atg12-Atg5 conjugate. Strikingly, TECPR1 localizes to and recruits Atg5 to autolysosome membrane. Consequently, elimination of TECPR1 leads to accumulation of autophagosomes and blocks autophagic degradation of LC3-II and p62. Finally, autophagosome maturation marked by GFP-mRFP-LC3 is defective in TECPR1-deficient cells. Thus, we propose that the concerted interactions among TECPR1, Atg12-Atg5, and PtdIns(3)P provide the fusion specificity between autophagosomes and lysosomes and that the assembly of this complex initiates the autophagosome maturation process.\",\n \"corpus_id\": 206984358,\n \"score\": 1\n },\n {\n \"doc_id\": \"22617511\",\n \"title\": \"A tethering coherent protein in autophagosome maturation.\",\n \"abstract\": \"Autophagy is a cellular pathway that degrades damaged organelles, cytosol and microorganisms, thereby maintaining human health by preventing various diseases including cancers, neurodegenerative disorders and diabetes. In autophagy, autophagosomes carrying cellular cargoes fuse with lysosomes for degradation. The proper autophagosome-lysosome fusion is pivotal for efficient autophagy activity. However, the molecular mechanism that specifically directs the fusion process is not clear. Our study reported that lysosome-localized TECPR1 (TECtonin β-Propeller Repeat containing 1) binds the autophagosome-localized ATG12-ATG5 conjugate and recruits it to autolysosomes. TECPR1 also binds PtdIns3P in an ATG12-ATG5-dependent manner. Consequently, depletion of TECPR1 leads to a severe defect in autophagosome maturation. We propose that the interaction between TECPR1 and ATG12-ATG5 initiates the fusion between the autophagosome and lysosome, and TECPR1 is a TEthering Coherent PRotein in autophagosome maturation.\",\n \"corpus_id\": 24620428,\n \"score\": 1\n },\n {\n \"doc_id\": \"22797916\",\n \"title\": \"Beclin-1-interacting autophagy protein Atg14L targets the SNARE-associated protein Snapin to coordinate endocytic trafficking.\",\n \"abstract\": \"Autophagy is a highly regulated membrane remodeling process that allows the lysosome-mediated degradation of cytoplasmic entities by sequestrating them in double-membrane autophagosomes. Autophagy is hence highly intertwined with the endocytic trafficking pathway, sharing similar molecular machinery. Atg14L, also known as Beclin 1-associated autophagy-related key regulator (Barkor), directly interacts with Beclin 1 through its coiled-coil domain and enhances phosphatidylinositol 3-phosphate kinase class III (PI3KC3) activity to induce autophagosome membrane nucleation, highlighting its essential role in the early stage of mammalian autophagy. Here, we report a novel function of Atg14L in the endocytic trafficking pathway wherein Atg14L binds to and colocalizes with the fusogenic SNARE effector protein Snapin to facilitate endosome maturation. Atg14L specifically binds to Snapin and this interaction effectively facilitates endosomal maturation without affecting autophagic cargo degradation. Consequently, atg14l knockdown significantly delayed the late stage of endocytic trafficking, as evidenced by the retarded kinetics of internalized surface receptor degradation. This phenotype was effectively complemented by wild-type Atg14L or Beclin 1-binding mutant, but not by its Snapin-binding mutant. Taken together, our study demonstrates that Atg14L functions as a multivalent trafficking effector that regulates endosome maturation as well as autophagosome formation, reflecting the complexity of the crosstalk between autophagic and endocytic vesicle trafficking in higher eukaryotes.\",\n \"corpus_id\": 3179494,\n \"score\": 1\n },\n {\n \"doc_id\": \"23306003\",\n \"title\": \"Connections between SNAREs and autophagy.\",\n \"abstract\": \"Autophagy involves the sequestration of portions of cytoplasm by double-membraned autophagosomes, which are then trafficked to lysosomes. After autophagosome-lysosome fusion, the contents of the autophagosomes are degraded by lysosomal hydrolases. SNAREs [soluble N-ethylmaleimide-sensitive fusion (NSF) attachment protein receptors] are molecules that mediate vesicular fusion events. Here, we review recent data implicating SNAREs as having key roles both in the genesis of autophagosomes, as well as in autophagosome-lysosome fusion, and we discuss the implications of these findings in the context of a long-standing mystery: the origin of autophagosomes.\",\n \"corpus_id\": 13918647,\n \"score\": 1\n },\n {\n \"doc_id\": \"24070471\",\n \"title\": \"The Atg8 family: multifunctional ubiquitin-like key regulators of autophagy.\",\n \"abstract\": \"Autophagy is an evolutionarily-conserved catabolic process initiated by the engulfment of cytosolic components in a crescent-shaped structure, called the phagophore, that expands and fuses to form a closed double-membrane vesicle, the autophagosome. Autophagosomes are subsequently targeted to the lysosome/vacuole with which they fuse to degrade their content. The formation of the autophagosome is carried out by a set of autophagy-related proteins (Atg), highly conserved from yeast to mammals. The Atg8s are Ubl (ubiquitin-like) proteins that play an essential role in autophagosome biogenesis. This family of proteins comprises a single member in yeast and several mammalian homologues grouped into three subfamilies: LC3 (light-chain 3), GABARAP (γ-aminobutyric acid receptor-associated protein) and GATE-16 (Golgi-associated ATPase enhancer of 16 kDa). The Atg8s are synthesized as cytosolic precursors, but can undergo a series of post-translational modifications leading to their tight association with autophagosomal structures following autophagy induction. Owing to this feature, the Atg8 proteins have been widely served as key molecules to monitor autophagosomes and autophagic activity. Studies in both yeast and mammalian systems have demonstrated that Atg8s play a dual role in the autophagosome formation process, coupling between selective incorporation of autophagy cargo and promoting autophagosome membrane expansion and closure. The membrane-remodelling activity of the Atg8 proteins is associated with their capacity to promote tethering and hemifusion of liposomes in vitro.\",\n \"corpus_id\": 35414372,\n \"score\": 1\n },\n {\n \"doc_id\": \"24113031\",\n \"title\": \"Evolutionarily conserved role and physiological relevance of a STX17/Syx17 (syntaxin 17)-containing SNARE complex in autophagosome fusion with endosomes and lysosomes.\",\n \"abstract\": \"Phagophores engulf cytoplasmic material and give rise to autophagosomes, double-membrane vesicles mediating cargo transport to lysosomes for degradation. The regulation of autophagosome fusion with endosomes and lysosomes during autophagy has remained poorly characterized. Two recent papers conclude that STX17/syntaxin 17 (Syx17 in Drosophila) has an evolutionarily conserved role in autophagosome fusion with endosomes and lysosomes, acting in one SNARE complex with SNAP29 (ubisnap in Drosophila) and the endosomal/lysosomal VAMP8 (CG1599/Vamp7 in Drosophila). Surprisingly, a third report suggests that STX17 might also contribute to proper phagophore assembly. Although several experiments presented in the two human cell culture studies yielded controversial results, the essential role of STX17 in autophagic flux is now firmly established, both in cultured cells and in an animal model. Based on these data, we propose that genetic inhibition of STX17/Syx17 may be a more specific tool in autophagic flux experiments than currently used drug treatments, which impair all lysosomal degradation routes and also inactivate MTOR (mechanistic target of rapamycin), a major negative regulator of autophagy. Finally, the neuronal dysfunction and locomotion defects observed in Syx17 mutant animals point to the possible contribution of defective autophagosome clearance to various human diseases.\",\n \"corpus_id\": 10593295,\n \"score\": 1\n },\n {\n \"doc_id\": \"24554766\",\n \"title\": \"Interaction of the HOPS complex with Syntaxin 17 mediates autophagosome clearance in Drosophila.\",\n \"abstract\": \"Homotypic fusion and vacuole protein sorting (HOPS) is a tethering complex required for trafficking to the vacuole/lysosome in yeast. Specific interaction of HOPS with certain SNARE (soluble NSF attachment protein receptor) proteins ensures the fusion of appropriate vesicles. HOPS function is less well characterized in metazoans. We show that all six HOPS subunits (Vps11 [vacuolar protein sorting 11]/CG32350, Vps18/Dor, Vps16A, Vps33A/Car, Vps39/CG7146, and Vps41/Lt) are required for fusion of autophagosomes with lysosomes in Drosophila. Loss of these genes results in large-scale accumulation of autophagosomes and blocks autophagic degradation under basal, starvation-induced, and developmental conditions. We find that HOPS colocalizes and interacts with Syntaxin 17 (Syx17), the recently identified autophagosomal SNARE required for fusion in Drosophila and mammals, suggesting their association is critical during tethering and fusion of autophagosomes with lysosomes. HOPS, but not Syx17, is also required for endocytic down-regulation of Notch and Boss in developing eyes and for proper trafficking to lysosomes and eye pigment granules. We also show that the formation of autophagosomes and their fusion with lysosomes is largely unaffected in null mutants of Vps38/UVRAG (UV radiation resistance associated), a suggested binding partner of HOPS in mammals, while endocytic breakdown and lysosome biogenesis is perturbed. Our results establish the role of HOPS and its likely mechanism of action during autophagy in metazoans.\",\n \"corpus_id\": 1732539,\n \"score\": 1\n },\n {\n \"doc_id\": \"24832451\",\n \"title\": \"Phosphoprotein of human parainfluenza virus type 3 blocks autophagosome-lysosome fusion to increase virus production.\",\n \"abstract\": \"Autophagy is a multistep process in which cytoplasmic components, including invading pathogens, are captured by autophagosomes that subsequently fuse with degradative lysosomes. Negative-strand RNA viruses, including paramyxoviruses, have been shown to alter autophagy, but the molecular mechanisms remain largely unknown. We demonstrate that human parainfluenza virus type 3 (HPIV3) induces incomplete autophagy by blocking autophagosome-lysosome fusion, resulting in increased virus production. The viral phosphoprotein (P) is necessary and sufficient to inhibition autophagosome degradation. P binds to SNAP29 and inhibits its interaction with syntaxin17, thereby preventing these two host SNARE proteins from mediating autophagosome-lysome fusion. Incomplete autophagy and resultant autophagosome accumulation increase extracellular viral production but do not affect viral protein synthesis. These findings highlight how viruses can block autophagosome degradation by disrupting the function of SNARE proteins.\",\n \"corpus_id\": 35762216,\n \"score\": 1\n },\n {\n \"doc_id\": \"25027988\",\n \"title\": \"Getting ready for building: signaling and autophagosome biogenesis.\",\n \"abstract\": \"Autophagy is the main cellular catabolic process responsible for degrading organelles and large protein aggregates. It is initiated by the formation of a unique membrane structure, the phagophore, which engulfs part of the cytoplasm and forms a double-membrane vesicle termed the autophagosome. Fusion of the outer autophagosomal membrane with the lysosome and degradation of the inner membrane contents complete the process. The extent of autophagy must be tightly regulated to avoid destruction of proteins and organelles essential for cell survival. Autophagic activity is thus regulated by external and internal cues, which initiate the formation of well-defined autophagy-related protein complexes that mediate autophagosome formation and selective cargo recruitment into these organelles. Autophagosome formation and the signaling pathways that regulate it have recently attracted substantial attention. In this review, we analyze the different signaling pathways that regulate autophagy and discuss recent progress in our understanding of autophagosome biogenesis.\",\n \"corpus_id\": 2052205,\n \"score\": 1\n },\n {\n \"doc_id\": \"25086043\",\n \"title\": \"Nrbf2 protein suppresses autophagy by modulating Atg14L protein-containing Beclin 1-Vps34 complex architecture and reducing intracellular phosphatidylinositol-3 phosphate levels.\",\n \"abstract\": \"Autophagy is a tightly regulated lysosomal degradation pathway for maintaining cellular homeostasis and responding to stresses. Beclin 1 and its interacting proteins, including the class III phosphatidylinositol-3 kinase Vps34, play crucial roles in autophagy regulation in mammals. We identified nuclear receptor binding factor 2 (Nrbf2) as a Beclin 1-interacting protein from Becn1(-/-);Becn1-EGFP/+ mouse liver and brain. We also found that Nrbf2-Beclin 1 interaction required the N terminus of Nrbf2. We next used the human retinal pigment epithelial cell line RPE-1 as a model system and showed that transiently knocking down Nrbf2 by siRNA increased autophagic flux under both nutrient-rich and starvation conditions. To investigate the mechanism by which Nrbf2 regulates autophagy, we demonstrated that Nrbf2 interacted and colocalized with Atg14L, suggesting that Nrbf2 is a component of the Atg14L-containing Beclin 1-Vps34 complex. Moreover, ectopically expressed Nrbf2 formed cytosolic puncta that were positive for isolation membrane markers. These results suggest that Nrbf2 is involved in autophagosome biogenesis. Furthermore, we showed that Nrbf2 deficiency led to increased intracellular phosphatidylinositol-3 phosphate levels and diminished Atg14L-Vps34/Vps15 interactions, suggesting that Nrbf2-mediated Atg14L-Vps34/Vps15 interactions likely inhibit Vps34 activity. Therefore, we propose that Nrbf2 may interact with the Atg14L-containing Beclin 1-Vps34 protein complex to modulate protein-protein interactions within the complex, leading to suppression of Vps34 activity, autophagosome biogenesis, and autophagic flux. This work reveals a novel aspect of the intricate mechanism for the Beclin 1-Vps34 protein-protein interaction network to achieve precise control of autophagy.\",\n \"corpus_id\": 25484134,\n \"score\": 1\n },\n {\n \"doc_id\": \"25343031\",\n \"title\": \"Membrane tethering.\",\n \"abstract\": \"Membrane trafficking depends on transport vesicles and carriers docking and fusing with the target organelle for the delivery of cargo. Membrane tethers and small guanosine triphosphatases (GTPases) mediate the docking of transport vesicles/carriers to enhance the efficiency of the subsequent SNARE (soluble N-ethylmaleimide-sensitive factor attachment protein receptor)-mediated fusion event with the target membrane bilayer. Different classes of membrane tethers and their specific intracellular location throughout the endomembrane system are now well defined. Recent biochemical and structural studies have led to a deeper understanding of the mechanism by which membrane tethers mediate docking of membrane carriers as well as an appreciation of the role of tethers in coordinating the correct SNARE complex and in regulating the organization of membrane compartments. This review will summarize the properties and roles of membrane tethers of both secretory and endocytic systems.\",\n \"corpus_id\": 3946099,\n \"score\": 1\n },\n {\n \"doc_id\": \"25551675\",\n \"title\": \"Multiple functions of the SNARE protein Snap29 in autophagy, endocytic, and exocytic trafficking during epithelial formation in Drosophila.\",\n \"abstract\": \"How autophagic degradation is linked to endosomal trafficking routes is little known. Here we screened a collection of uncharacterized Drosophila mutants affecting membrane transport to identify new genes that also have a role in autophagy. We isolated a loss of function mutant in Snap29 (Synaptosomal-associated protein 29 kDa), the gene encoding the Drosophila homolog of the human protein SNAP29 and have characterized its function in vivo. Snap29 contains 2 soluble NSF attachment protein receptor (SNARE) domains and a asparagine-proline-phenylalanine (NPF motif) at its N terminus and rescue experiments indicate that both SNARE domains are required for function, whereas the NPF motif is in part dispensable. We find that Snap29 interacts with SNARE proteins, localizes to multiple trafficking organelles, and is required for protein trafficking and for proper Golgi apparatus morphology. Developing tissue lacking Snap29 displays distinctive epithelial architecture defects and accumulates large amounts of autophagosomes, highlighting a major role of Snap29 in autophagy and secretion. Mutants for autophagy genes do not display epithelial architecture or secretion defects, suggesting that the these alterations of the Snap29 mutant are unlikely to be caused by the impairment of autophagy. In contrast, we find evidence of elevated levels of hop-Stat92E (hopscotch-signal transducer and activator of transcription protein at 92E) ligand, receptor, and associated signaling, which might underlie the epithelial defects. In summary, our findings support a role of Snap29 at key steps of membrane trafficking, and predict that signaling defects may contribute to the pathogenesis of cerebral dysgenesis, neuropathy, ichthyosis, and palmoplantar keratoderma (CEDNIK), a human congenital syndrome due to loss of Snap29.\",\n \"corpus_id\": 8165574,\n \"score\": 1\n },\n {\n \"doc_id\": \"26259518\",\n \"title\": \"Impairment of autophagosome-lysosome fusion in the buff mutant mice with the VPS33A(D251E) mutation.\",\n \"abstract\": \"The HOPS (homotypic fusion and protein sorting) complex functions in endocytic and autophagic pathways in both lower eukaryotes and mammalian cells through its involvement in fusion events between endosomes and lysosomes or autophagosomes and lysosomes. However, the differential molecular mechanisms underlying these fusion processes are largely unknown. Buff (bf) is a mouse mutant that carries an Asp251-to-Glu point mutation (D251E) in the VPS33A protein, a tethering protein and a core subunit of the HOPS complex. Bf mice showed impaired spontaneous locomotor activity, motor learning, and autophagic activity. Although the gross anatomy of the brain was apparently normal, the number of Purkinje cells was significantly reduced. Furthermore, we found that fusion between autophagosomes and lysosomes was defective in bf cells without compromising the endocytic pathway. The direct association of mutant VPS33A(D251E) with the autophagic SNARE complex, STX17 (syntaxin 17)-VAMP8-SNAP29, was enhanced. In addition, the VPS33A(D251E) mutation enhanced interactions with other HOPS subunits, namely VPS41, VPS39, VPS18, and VPS11, except for VPS16. Reduction of the interactions between VPS33A(Y440D) and several other HOPS subunits led to decreased association with STX17. These results suggest that the VPS33A(D251E) mutation plays dual roles by increasing the HOPS complex assembly and its association with the autophagic SNARE complex, which selectively affects the autophagosome-lysosome fusion that impairs basal autophagic activity and induces Purkinje cell loss.\",\n \"corpus_id\": 205899003,\n \"score\": 1\n },\n {\n \"doc_id\": \"27099307\",\n \"title\": \"The Autophagosomal SNARE Protein Syntaxin 17 Is an Essential Factor for the Hepatitis C Virus Life Cycle.\",\n \"abstract\": \"UNLABELLED: Syntaxin 17 is an autophagosomal SNARE (soluble N-ethylmaleimide-sensitive factor attachment protein receptor) protein required for the fusion of autophagosomes with lysosomes to form autolysosomes and thereby to deliver the enclosed contents for degradation. Hepatitis C virus (HCV) induces autophagy. In light of the observation that the number of viral particles formed by HCV-infected cells is much greater than the number of infectious viral particles finally released by HCV-infected cells, the regulation of fusion between autophagosomes and lysosomes might fulfill a key function controlling the number of released virions. HCV-replicating cells possess a decreased amount of syntaxin 17 due to impaired expression and increased turnover of syntaxin 17. Overexpression of syntaxin 17 in HCV-replicating cells diminishes the number of released infectious viral particles and decreases the amount of intracellular retained viral particles by favoring the formation of autolysosomes, in which HCV particles are degraded. Inhibition of lysosomal acidification by bafilomycin rescues the decreased release of virions from syntaxin 17-overexpressing cells, while induction of autophagy by rapamycin enforces the impairment of release under these conditions. Vice versa, inhibition of syntaxin 17 expression by specific small interfering RNAs results in an elevated amount of intracellular retained viral particles and facilitates the release of HCV virions by impairment of autophagosome-lysosome fusion. HCV genome replication, however, is not affected by modulation of syntaxin 17 expression. These data identify syntaxin 17 to be a novel factor controlling the release of HCV. This is achieved by regulation of autophagosome-lysosome fusion, which affects the equilibrium between the release of infectious viral particles and lysosomal degradation of intracellular retained viral particles. IMPORTANCE: Hepatitis C virus (HCV) induces autophagy. Syntaxin 17 is an autophagosomal SNARE protein required for the fusion of autophagosomes with lysosomes. In HCV-infected cells, a major fraction of the de novo-synthesized viral particles is not released but is intracellularly degraded. In this context, the effect of HCV on the amount and distribution of syntaxin 17 and the relevance of syntaxin 17 for the viral life cycle were investigated. This study demonstrates that the amount of syntaxin 17 decreased in HCV-replicating cells. In addition, syntaxin 17 is identified to be a novel factor controlling the release of HCV, and the relevance of autophagosome-lysosome fusion as a regulator of the amount of released viral particles is revealed. Taken together, these findings indicate that syntaxin 17 is involved in the regulation of autophagosome-lysosome fusion and thereby affects the equilibrium between the release of infectious viral particles and the lysosomal degradation of intracellularly retained viral particles.\",\n \"corpus_id\": 206795163,\n \"score\": 1\n },\n {\n \"doc_id\": \"27383850\",\n \"title\": \"Identification of BECN1 and ATG14 Coiled-Coil Interface Residues That Are Important for Starvation-Induced Autophagy.\",\n \"abstract\": \"Autophagy, an essential eukaryotic homeostasis pathway, allows the sequestration of unwanted, damaged, or harmful cytoplasmic components in vesicles called autophagosomes, permitting subsequent lysosomal degradation and nutrient recycling. Autophagosome nucleation is mediated by class III phosphatidylinositol-3-kinase complexes that include two key autophagy proteins, BECN1/Beclin 1 and ATG14/BARKOR, which form parallel heterodimers via their coiled-coil domains (CCDs). Here we present the 1.46 Å X-ray crystal structure of the antiparallel, human BECN1 CCD homodimer, which represents BECN1 oligomerization outside the autophagosome nucleation complex. We use circular dichroism and small-angle X-ray scattering (SAXS) to show that the ATG14 CCD is significantly disordered but becomes more helical in the BECN1:ATG14 heterodimer, although it is less well-folded than the BECN1 CCD homodimer. SAXS also indicates that the BECN1:ATG14 heterodimer is more curved than other BECN1-containing CCD dimers, which has important implications for the structure of the autophagosome nucleation complex. A model of the BECN1:ATG14 CCD heterodimer that agrees well with the SAXS data shows that BECN1 residues at the homodimer interface are also responsible for heterodimerization, allowing us to identify ATG14 interface residues. Finally, we verify the role of BECN1 and ATG14 interface residues in binding by assessing the impact of point mutations of these residues on co-immunoprecipitation of the partner and demonstrate that these mutations abrogate starvation-induced upregulation of autophagy but do not impact basal autophagy. Thus, this research provides insights into structures of the BECN1 CCD homodimer and the BECN1:ATG14 CCD heterodimer and identifies interface residues that are important for BECN1:ATG14 heterodimerization and for autophagy.\",\n \"corpus_id\": 20237132,\n \"score\": 1\n },\n {\n \"doc_id\": \"27458136\",\n \"title\": \"Syntaxin-17 delivers PINK1/parkin-dependent mitochondrial vesicles to the endolysosomal system.\",\n \"abstract\": \"Mitochondria are considered autonomous organelles, physically separated from endocytic and biosynthetic pathways. However, recent work uncovered a PINK1/parkin-dependent vesicle transport pathway wherein oxidized or damaged mitochondrial content are selectively delivered to the late endosome/lysosome for degradation, providing evidence that mitochondria are indeed integrated within the endomembrane system. Given that mitochondria have not been shown to use canonical soluble NSF attachment protein receptor (SNARE) machinery for fusion, the mechanism by which mitochondrial-derived vesicles (MDVs) are targeted to the endosomal compartment has remained unclear. In this study, we identify syntaxin-17 as a core mitochondrial SNARE required for the delivery of stress-induced PINK1/parkin-dependent MDVs to the late endosome/lysosome. Syntaxin-17 remains associated with mature MDVs and forms a ternary SNARE complex with SNAP29 and VAMP7 to mediate MDV-endolysosome fusion in a manner dependent on the homotypic fusion and vacuole protein sorting (HOPS) tethering complex. Syntaxin-17 can be traced to the last eukaryotic common ancestor, hinting that the removal of damaged mitochondrial content may represent one of the earliest vesicle transport routes in the cell.\",\n \"corpus_id\": 3941961,\n \"score\": 1\n },\n {\n \"doc_id\": \"27588602\",\n \"title\": \"The Vici Syndrome Protein EPG5 Is a Rab7 Effector that Determines the Fusion Specificity of Autophagosomes with Late Endosomes/Lysosomes.\",\n \"abstract\": \"Mutations in the human autophagy gene EPG5 cause the multisystem disorder Vici syndrome. Here we demonstrated that EPG5 is a Rab7 effector that determines the fusion specificity of autophagosomes with late endosomes/lysosomes. EPG5 is recruited to late endosomes/lysosomes by direct interaction with Rab7 and the late endosomal/lysosomal R-SNARE VAMP7/8. EPG5 also binds to LC3/LGG-1 (mammalian and C. elegans Atg8 homolog, respectively) and to assembled STX17-SNAP29 Qabc SNARE complexes on autophagosomes. EPG5 stabilizes and facilitates the assembly of STX17-SNAP29-VAMP7/8 trans-SNARE complexes, and promotes STX17-SNAP29-VAMP7-mediated fusion of reconstituted proteoliposomes. Loss of EPG5 activity causes abnormal fusion of autophagosomes with various endocytic vesicles, in part due to elevated assembly of STX17-SNAP25-VAMP8 complexes. SNAP25 knockdown partially suppresses the autophagy defect caused by EPG5 depletion. Our study reveals that EPG5 is a Rab7 effector involved in autophagosome maturation, providing insight into the molecular mechanism underlying Vici syndrome.\",\n \"corpus_id\": 1202443,\n \"score\": 1\n },\n {\n \"doc_id\": \"27621469\",\n \"title\": \"PtdIns(4,5)P2 signaling regulates ATG14 and autophagy.\",\n \"abstract\": \"Autophagy is a regulated self-digestion pathway with fundamental roles in cell homeostasis and diseases. Autophagy is regulated by coordinated actions of a series of autophagy-related (ATG) proteins. The Barkor/ATG14(L)-VPS34 (a class III phosphatidylinositol 3-kinase) complex and its product phosphatidylinositol 3-phosphate [PtdIns(3)P] play key roles in autophagy initiation. ATG14 contains a C-terminal Barkor/ATG14(L) autophagosome-targeting sequence (BATS) domain that senses the curvature of PtdIns(3)P-containing membrane. The BATS domain also strongly binds PtdIns(4,5)P2, but the functional significance has been unclear. Here we show that ATG14 specifically interacts with type Iγ PIP kinase isoform 5 (PIPKIγi5), an enzyme that generates PtdIns(4,5)P2 in mammalian cells. Autophagosomes have associated PIPKIγi5 and PtdIns(4,5)P2 that are colocalized with late endosomes and the endoplasmic reticulum. PtdIns(4,5)P2 generation at these sites requires PIPKIγi5. Loss of PIPKIγi5 results in a loss of ATG14, UV irradiation resistance-associated gene, and Beclin 1 and a block of autophagy. PtdIns(4,5)P2 binding to the ATG14-BATS domain regulates ATG14 interaction with VPS34 and Beclin 1, and thus plays a key role in ATG14 complex assembly and autophagy initiation. This study identifies an unexpected role for PtdIns(4,5)P2 signaling in the regulation of ATG14 complex and autophagy.\",\n \"corpus_id\": 205277858,\n \"score\": 1\n },\n {\n \"doc_id\": \"27628032\",\n \"title\": \"LAMP-2 is required for incorporating syntaxin-17 into autophagosomes and for their fusion with lysosomes.\",\n \"abstract\": \"Autophagy is an evolutionarily conserved process used for removing surplus and damaged proteins and organelles from the cytoplasm. The unwanted material is incorporated into autophagosomes that eventually fuse with lysosomes, leading to the degradation of their cargo. The fusion event is mediated by the interaction between the Qa-SNARE syntaxin-17 (STX17) on autophagosomes and the R-SNARE VAMP8 on lysosomes. Cells deficient in lysosome membrane-associated protein-2 (LAMP-2) have increased numbers of autophagosomes but the underlying mechanism is poorly understood. By transfecting LAMP-2-deficient and LAMP-1/2--double-deficient mouse embryonic fibroblasts (MEFs) with a tandem fluorescent-tagged LC3 we observed a failure of fusion between the autophagosomes and the lysosomes that could be rescued by complementation with LAMP-2A. Although we observed no change in expression and localization of VAMP8, its interacting partner STX17 was absent from autophagosomes of LAMP-2-deficient cells. Thus, LAMP-2 is essential for STX17 expression by the autophagosomes and this absence is sufficient to explain their failure to fuse with lysosomes. The results have clear implications for situations associated with a reduction of LAMP-2 expression.\",\n \"corpus_id\": 13313475,\n \"score\": 1\n },\n {\n \"doc_id\": \"28306502\",\n \"title\": \"Pacer Mediates the Function of Class III PI3K and HOPS Complexes in Autophagosome Maturation by Engaging Stx17.\",\n \"abstract\": \"Class III PI3-kinase (PI3KC3) is essential for autophagy initiation, but whether PI3KC3 participates in other steps of autophagy remains unknown. The HOPS complex mediates the fusion of intracellular vesicles to lysosome, but how HOPS specifically tethers autophagosome to lysosome remains elusive. Here, we report Pacer (protein associated with UVRAG as autophagy enhancer) as a regulator of autophagy. Pacer localizes to autophagic structures and positively regulates autophagosome maturation. Mechanistically, Pacer antagonizes Rubicon to stimulate Vps34 kinase activity. Next, Pacer recruits PI3KC3 and HOPS complexes to the autophagosome for their site-specific activation by anchoring to the autophagosomal SNARE Stx17. Furthermore, Pacer is crucial for the degradation of hepatic lipid droplets, the suppression of Salmonella infection, and the clearance of protein aggregates. These results not only identify Pacer as a crucial multifunctional enhancer in autophagy but also uncover both the involvement of PI3KC3 and the mediators of HOPS's specific tethering activity in autophagosome maturation.\",\n \"corpus_id\": 39480512,\n \"score\": 1\n },\n {\n \"doc_id\": \"28533369\",\n \"title\": \"Phosphorylated Presenilin 1 decreases β-amyloid by facilitating autophagosome-lysosome fusion.\",\n \"abstract\": \"Presenilin 1 (PS1), the catalytic subunit of the γ-secretase complex, cleaves βCTF to produce Aβ. We have shown that PS1 regulates Aβ levels by a unique bifunctional mechanism. In addition to its known role as the catalytic subunit of the γ-secretase complex, selective phosphorylation of PS1 on Ser367 decreases Aβ levels by increasing βCTF degradation through autophagy. Here, we report the molecular mechanism by which PS1 modulates βCTF degradation. We show that PS1 phosphorylated at Ser367, but not nonphosphorylated PS1, interacts with Annexin A2, which, in turn, interacts with the lysosomal N-ethylmaleimide-sensitive factor attachment protein receptor (SNARE) Vamp8. Annexin A2 facilitates the binding of Vamp8 to the autophagosomal SNARE Syntaxin 17 to modulate the fusion of autophagosomes with lysosomes. Thus, PS1 phosphorylated at Ser367 has an antiamyloidogenic function, promoting autophagosome-lysosome fusion and increasing βCTF degradation. Drugs designed to increase the level of PS1 phosphorylated at Ser367 should be useful in the treatment of Alzheimer's disease.\",\n \"corpus_id\": 19054972,\n \"score\": 1\n },\n {\n \"doc_id\": \"28537477\",\n \"title\": \"ATG conjugation-dependent degradation of the inner autophagosomal membrane is a key step for autophagosome maturation.\",\n \"abstract\": \"Although the autophagy-related (ATG) conjugation systems are thought to be important for a late step of autophagosome formation, their precise function has been poorly understood because they are also required for localization of the most important autophagosomal marker LC3. In our recent study we found that, using the autophagosomal SNARE STX17 (syntaxin 17) as an alternative marker, autophagosome-like structures were generated in ATG conjugation system-deficient cells. Those structures could fuse with lysosomes but the degradation of the inner autophagosomal membrane was significantly delayed. We suggest that the ATG conjugation-dependent closure of autophagosomes causes the inner autophagosomal membrane to become sensitive to lysosomal degradation.\",\n \"corpus_id\": 205899891,\n \"score\": 1\n },\n {\n \"doc_id\": \"28825857\",\n \"title\": \"BORC Coordinates Encounter and Fusion of Lysosomes with Autophagosomes.\",\n \"abstract\": \"Whereas the mechanisms involved in autophagosome formation have been extensively studied for the past 2 decades, those responsible for autophagosome-lysosome fusion have only recently begun to garner attention. In this study, we report that the multisubunit BORC complex, previously implicated in kinesin-dependent movement of lysosomes toward the cell periphery, is required for efficient autophagosome-lysosome fusion. Knockout (KO) of BORC subunits causes not only juxtanuclear clustering of lysosomes, but also increased levels of the autophagy protein LC3B-II and the receptor SQSTM1. Increases in LC3B-II occur without changes in basal MTORC1 activity and autophagy initiation. Instead, LC3B-II accumulation largely results from decreased lysosomal degradation. Further experiments show that BORC KO impairs both the encounter and fusion of autophagosomes with lysosomes. Reduced encounters result from an inability of lysosomes to move toward the peripheral cytoplasm, where many autophagosomes are formed. However, BORC KO also reduces the recruitment of the HOPS tethering complex to lysosomes and assembly of the STX17-VAMP8-SNAP29 trans-SNARE complex involved in autophagosome-lysosome fusion. Through these dual roles, BORC integrates the kinesin-dependent movement of lysosomes toward autophagosomes with HOPS-dependent autophagosome-lysosome fusion. These findings reveal a requirement for lysosome dispersal in autophagy that is independent of changes in MTORC1 signaling, and identify BORC as a novel regulator of autophagosome-lysosome fusion.\",\n \"corpus_id\": 10700412,\n \"score\": 1\n },\n {\n \"doc_id\": \"29138318\",\n \"title\": \"SNARE priming is essential for maturation of autophagosomes but not for their formation.\",\n \"abstract\": \"Autophagy, a unique intracellular membrane-trafficking pathway, is initiated by the formation of an isolation membrane (phagophore) that engulfs cytoplasmic constituents, leading to generation of the autophagosome, a double-membrane vesicle, which is targeted to the lysosome. The outer autophagosomal membrane consequently fuses with the lysosomal membrane. Multiple membrane-fusion events mediated by SNARE molecules have been postulated to promote autophagy. αSNAP, the adaptor molecule for the SNARE-priming enzyme N-ethylmaleimide-sensitive factor (NSF) is known to be crucial for intracellular membrane fusion processes, but its role in autophagy remains unclear. Here we demonstrated that knockdown of αSNAP leads to inhibition of autophagy, manifested by an accumulation of sealed autophagosomes located in close proximity to lysosomes but not fused with them. Under these conditions, moreover, association of both Atg9 and the autophagy-related SNARE protein syntaxin17 with the autophagosome remained unaffected. Finally, our results suggested that under starvation conditions, the levels of αSNAP, although low, are nevertheless sufficient to partially promote the SNARE priming required for autophagy. Taken together, these findings indicate that while autophagosomal-lysosomal membrane fusion is sensitive to inhibition of SNARE priming, the initial stages of autophagosome biogenesis and autophagosome expansion remain resistant to its loss.\",\n \"corpus_id\": 2617974,\n \"score\": 1\n },\n {\n \"doc_id\": \"29507186\",\n \"title\": \"Increased O-GlcNAcylation of SNAP29 Drives Arsenic-Induced Autophagic Dysfunction.\",\n \"abstract\": \"Environmental exposure to arsenic is linked to adverse health effects, including cancer and diabetes. Pleiotropic cellular effects are observed with arsenic exposure. Previously, we demonstrated that arsenic dysregulated the autophagy pathway at low, environmentally relevant concentrations. Here we show that arsenic blocks autophagy by preventing autophagosome-lysosome fusion. Specifically, arsenic disrupts formation of the STX17-SNAP29-VAMP8 SNARE complex, where SNAP29 mediates vesicle fusion through bridging STX17-containing autophagosomes to VAMP8-bearing lysosomes. Mechanistically, arsenic inhibits SNARE complex formation, at least in part, by enhancing O-GlcNAcylation of SNAP29. Transfection of O-GlcNAcylation-defective, but not wild-type, SNAP29 into clustered regularly interspaced short palindromic repeat (CRISPR)-mediated SNAP29 knockout cells abolishes arsenic-mediated autophagy inhibition. These findings reveal a mechanism by which low levels of arsenic perturb proteostasis through inhibition of SNARE complex formation, providing a possible therapeutic target for disease intervention in the more than 200 million people exposed to unsafe levels of arsenic.\",\n \"corpus_id\": 3700206,\n \"score\": 1\n },\n {\n \"doc_id\": \"29694367\",\n \"title\": \"Non-canonical role of the SNARE protein Ykt6 in autophagosome-lysosome fusion.\",\n \"abstract\": \"The autophagosomal SNARE Syntaxin17 (Syx17) forms a complex with Snap29 and Vamp7/8 to promote autophagosome-lysosome fusion via multiple interactions with the tethering complex HOPS. Here we demonstrate that, unexpectedly, one more SNARE (Ykt6) is also required for autophagosome clearance in Drosophila. We find that loss of Ykt6 leads to large-scale accumulation of autophagosomes that are unable to fuse with lysosomes to form autolysosomes. Of note, loss of Syx5, the partner of Ykt6 in ER-Golgi trafficking does not prevent autolysosome formation, pointing to a more direct role of Ykt6 in fusion. Indeed, Ykt6 localizes to lysosomes and autolysosomes, and forms a SNARE complex with Syx17 and Snap29. Interestingly, Ykt6 can be outcompeted from this SNARE complex by Vamp7, and we demonstrate that overexpression of Vamp7 rescues the fusion defect of ykt6 loss of function cells. Finally, a point mutant form with an RQ amino acid change in the zero ionic layer of Ykt6 protein that is thought to be important for fusion-competent SNARE complex assembly retains normal autophagic activity and restores full viability in mutant animals, unlike palmitoylation or farnesylation site mutant Ykt6 forms. As Ykt6 and Vamp7 are both required for autophagosome-lysosome fusion and are mutually exclusive subunits in a Syx17-Snap29 complex, these data suggest that Vamp7 is directly involved in membrane fusion and Ykt6 acts as a non-conventional, regulatory SNARE in this process.\",\n \"corpus_id\": 13680467,\n \"score\": 1\n },\n {\n \"doc_id\": \"19185015\",\n \"title\": \"Comprehensive analysis of expression, subcellular localization, and cognate pairing of SNARE proteins in oligodendrocytes.\",\n \"abstract\": \"Oligodendrocytes form the central nervous system myelin sheath by spiral wrapping of their plasma membrane around axons, necessitating a high rate of exocytic membrane addition to the growing myelin membrane. Membrane fusion is mediated by soluble N-ethylmaleimide-sensitive factor attachment protein receptor proteins (SNAREs), which act by specific pairing of vesicle (R)- and target (Q)-SNAREs. To characterize oligodendroglial SNAREs and their trafficking pathways, we performed a detailed expression analysis of SNAREs in differentiating cultured oligodendrocytes and myelin and determined their subcellular localization. Expression of the plasma membrane Q-SNAREs syntaxin 3, syntaxin 4, SNAP23, and the endosomal R-SNARE VAMP3/cellubrevin increased with oligodendroglial maturation, while the expression of SNAP29 decreased. Interestingly, syntaxin 3, syntaxin 4, and VAMP7/tetanustoxin-insensitive VAMP accumulated in myelin during development, suggesting a role in myelin membrane fusion. Coimmunoprecipitation from oligodendroglial cell lysates elucidated interactions between SNAREs: for example, Golgi-localized VAMP4 associated with syntaxin 6 and SNAP29. Furthermore, we identified a cognate core complex composed of VAMP3, syntaxin 4, and SNAP23, which may mediate fusion of endosome-derived vesicles with the plasma membrane. This study provides a comprehensive analysis of SNARE proteins in oligodendrocytes and assigns defined SNAREs to putative vesicle trafficking pathways in myelinating oligodendrocytes, thus facilitating future functional analysis of distinct SNAREs in oligodendroglial membrane traffic and myelination.\",\n \"corpus_id\": 25612172,\n \"score\": 0\n },\n {\n \"doc_id\": \"19458617\",\n \"title\": \"Reconstitution of Rab- and SNARE-dependent membrane fusion by synthetic endosomes.\",\n \"abstract\": \"Rab GTPases and SNAREs (soluble N-ethylmaleimide-sensitive factor attachment protein receptors) are evolutionarily conserved essential components of the eukaryotic intracellular transport system. Although pairing of cognate SNAREs is sufficient to fuse membranes in vitro, a complete reconstitution of the Rab-SNARE machinery has never been achieved. Here we report the reconstitution of the early endosomal canine Rab5 GTPase, its key regulators and effectors together with SNAREs into proteoliposomes using a set of 17 recombinant human proteins. These vesicles behave like minimal 'synthetic' endosomes, fusing with purified early endosomes or with each other in vitro. Membrane fusion measured by content-mixing and morphological assays requires the cooperativity between Rab5 effectors and cognate SNAREs which, together, form a more efficient 'core machinery' than SNAREs alone. In reconstituting a fusion mechanism dependent on both a Rab GTPase and SNAREs, our work shows that the two machineries act coordinately to increase the specificity and efficiency of the membrane tethering and fusion process.\",\n \"corpus_id\": 507806,\n \"score\": 0\n },\n {\n \"doc_id\": \"20937838\",\n \"title\": \"Phosphoinositides function asymmetrically for membrane fusion, promoting tethering and 3Q-SNARE subcomplex assembly.\",\n \"abstract\": \"Phosphatidylinositol 3-phosphate (PI(3)P) and phosphatidylinositol 4,5-bisphosphate (PI(4,5)P(2)) are essential for rapid SNARE-dependent fusion of yeast vacuoles and other organelles. These phosphoinositides also regulate the fusion of reconstituted proteoliposomes. The reconstituted reaction allows separate analysis of phosphoinositide-responsive subreactions: fusion with SNAREs alone, with the addition of the HOPS tethering factor, and with the further addition of the SNARE complex disassembly chaperones Sec17p and Sec18p. Using assays of membrane tethering, trans-SNARE pairing, and lipid mixing, we found that PI(3)P and PI(4,5)P(2) have distinct functions that are asymmetric with respect to R-SNARE (Nyv1p) and the 3Q-SNAREs (Vam3p, Vti1p, and Vam7p). Fusion reactions with the Q-SNAREs and R-SNARE on separate membranes showed that PI(3)P has two distinct functions. PI(3)P on Q-SNARE proteoliposomes promoted Vam7p binding and association with the other two Q-SNAREs. PI(3)P on R-SNARE proteoliposomes was recognized by the PX domain of Vam7p on Q-SNARE proteoliposomes to promote tethering, although this function could be supplanted by the tethering activity of HOPS. PI(4,5)P(2) stimulated fusion when it was on R-SNARE proteoliposomes, apposed to Q-SNARE proteoliposomes bearing PI(3)P. These functions are essential for the phosphoinositide-dependent synergy between HOPS and Sec17p/Sec18p in promoting rapid fusion.\",\n \"corpus_id\": 205306048,\n \"score\": 0\n },\n {\n \"doc_id\": \"26986547\",\n \"title\": \"The Atg17-Atg31-Atg29 complex and Atg11 regulate autophagosome-vacuole fusion.\",\n \"abstract\": \"The macroautophagy (hereafter autophagy) process involves de novo formation of double-membrane autophagosomes; after sequestering cytoplasm these transient organelles fuse with the vacuole/lysosome. Genetic studies in yeasts have characterized more than 40 autophagy-related (Atg) proteins required for autophagy, and the majority of these proteins play roles in autophagosome formation. The fusion of autophagosomes with the vacuole is mediated by the Rab GTPase Ypt7, its guanine nucleotide exchange factor Mon1-Ccz1, and soluble N-ethylmaleimide-sensitive factor attachment protein receptor (SNARE) proteins. However, these factors are not autophagosome-vacuole fusion specific. We recently showed that 2 autophagy scaffold proteins, the Atg17-Atg31-Atg29 complex and Atg11, regulate autophagosome-vacuole fusion by recruiting the vacuolar SNARE Vam7 to the phagophore assembly site (PAS), where an autophagosome forms in yeast.\",\n \"corpus_id\": 205899284,\n \"score\": 0\n },\n {\n \"doc_id\": \"27791468\",\n \"title\": \"The STX6-VTI1B-VAMP3 complex facilitates xenophagy by regulating the fusion between recycling endosomes and autophagosomes.\",\n \"abstract\": \"Macroautophagy/autophagy plays a critical role in immunity by directly degrading invading pathogens such as Group A Streptococcus (GAS), through a process that has been named xenophagy. We previously demonstrated that autophagic vacuoles directed against GAS, termed GAS-containing autophagosome-like vacuoles (GcAVs), use recycling endosomes (REs) as a membrane source. However, the precise molecular mechanism that facilitates the fusion between GcAVs and REs remains unclear. Here, we demonstrate that STX6 (syntaxin 6) is recruited to GcAVs and forms a complex with VTI1B and VAMP3 to regulate the GcAV-RE fusion that is required for xenophagy. STX6 targets the GcAV membrane through its tyrosine-based sorting motif and transmembrane domain, and localizes to TFRC (transferrin receptor)-positive punctate structures on GcAVs through its H2 SNARE domain. Knockdown and knockout experiments revealed that STX6 is required for the fusion between GcAVs and REs to promote clearance of intracellular GAS by autophagy. Moreover, VAMP3 and VTI1B interact with STX6 and localize on the TFRC-positive puncta on GcAVs, and are also involved in the RE-GcAV fusion. Furthermore, knockout of RABGEF1 impairs the RE-GcAV fusion and STX6-VAMP3 interaction. These findings demonstrate that RABGEF1 mediates RE fusion with GcAVs through the STX6-VAMP3-VTI1B complex, and reveal the SNARE dynamics involved in autophagosome formation in response to bacterial infection.\",\n \"corpus_id\": 22869034,\n \"score\": 0\n },\n {\n \"doc_id\": \"28112172\",\n \"title\": \"Sec3 promotes the initial binary t-SNARE complex assembly and membrane fusion.\",\n \"abstract\": \"The soluble N-ethylmaleimide-sensitive factor-attachment protein receptors (SNAREs) constitute the core machinery for membrane fusion during eukaryotic cell vesicular trafficking. However, how the assembly of the SNARE complex is initiated is unknown. Here we report that Sec3, a component of the exocyst complex that mediates vesicle tethering during exocytosis, directly interacts with the t-SNARE protein Sso2. This interaction promotes the formation of an Sso2-Sec9 'binary' t-SNARE complex, the early rate-limiting step in SNARE complex assembly, and stimulates membrane fusion. The crystal structure of the Sec3-Sso2 complex suggests that Sec3 binding induces conformational changes of Sso2 that are crucial for the relief of its auto-inhibition. Interestingly, specific disruption of the Sec3-Sso2 interaction in cells blocks exocytosis without affecting the function of Sec3 in vesicle tethering. Our study reveals an activation mechanism for SNARE complex assembly, and uncovers a role of the exocyst in promoting membrane fusion in addition to vesicle tethering.\",\n \"corpus_id\": 32784683,\n \"score\": 0\n },\n {\n \"doc_id\": \"28637767\",\n \"title\": \"A short region upstream of the yeast vacuolar Qa-SNARE heptad-repeats promotes membrane fusion through enhanced SNARE complex assembly.\",\n \"abstract\": \"Whereas SNARE (soluble N -ethylmaleimide-sensitive factor attachment protein receptor) heptad-repeats are well studied, SNAREs also have upstream N-domains of indeterminate function. The assembly of yeast vacuolar SNAREs into complexes for fusion can be studied in chemically defined reactions. Complementary proteoliposomes bearing a Rab:GTP and either the vacuolar R-SNARE or one of the three integrally anchored Q-SNAREs were incubated with the tethering/SM protein complex HOPS and the two other soluble SNAREs (lacking a transmembrane anchor) or their SNARE heptad-repeat domains. Fusion required a transmembrane-anchored R-SNARE on one membrane and an anchored Q-SNARE on the other. The N-domain of the Qb-SNARE was completely dispensable for fusion. Whereas fusion can be promoted by very high concentrations of the Qa-SNARE heptad-repeat domain alone, at physiological concentrations the Qa-SNARE heptad-repeat domain alone has almost no fusion activity. The 181-198 region of Qa, immediately upstream of the SNARE heptad-repeat domain, is required for normal fusion activity with HOPS. This region is needed for normal SNARE complex assembly.\",\n \"corpus_id\": 20974035,\n \"score\": 0\n },\n {\n \"doc_id\": \"28677644\",\n \"title\": \"2BC Non-Structural Protein of Enterovirus A71 Interacts with SNARE Proteins to Trigger Autolysosome Formation.\",\n \"abstract\": \"Viruses have evolved unique strategies to evade or subvert autophagy machinery. Enterovirus A71 (EV-A71) induces autophagy during infection in vitro and in vivo. In this study, we report that EV-A71 triggers autolysosome formation during infection in human rhabdomyosarcoma (RD) cells to facilitate its replication. Blocking autophagosome-lysosome fusion with chloroquine inhibited virus RNA replication, resulting in lower viral titres, viral RNA copies and viral proteins. Overexpression of the non-structural protein 2BC of EV-A71 induced autolysosome formation. Yeast 2-hybrid and co-affinity purification assays showed that 2BC physically and specifically interacted with a N-ethylmaleimide-sensitive factor attachment receptor (SNARE) protein, syntaxin-17 (STX17). Co-immunoprecipitation assay further showed that 2BC binds to SNARE proteins, STX17 and synaptosome associated protein 29 (SNAP29). Transient knockdown of STX17, SNAP29, and microtubule-associated protein 1 light chain 3B (LC3B), crucial proteins in the fusion between autophagosomes and lysosomes) as well as the lysosomal-associated membrane protein 1 (LAMP1) impaired production of infectious EV-A71 in RD cells. Collectively, these results demonstrate that the generation of autolysosomes triggered by the 2BC non-structural protein is important for EV-A71 replication, revealing a potential molecular pathway targeted by the virus to exploit autophagy. This study opens the possibility for the development of novel antivirals that specifically target 2BC to inhibit formation of autolysosomes during EV-A71 infection.\",\n \"corpus_id\": 4400316,\n \"score\": 0\n },\n {\n \"doc_id\": \"29088698\",\n \"title\": \"A tethering complex drives the terminal stage of SNARE-dependent membrane fusion.\",\n \"abstract\": \"Membrane fusion in eukaryotic cells mediates the biogenesis of organelles, vesicular traffic between them, and exo- and endocytosis of important signalling molecules, such as hormones and neurotransmitters. Distinct tasks in intracellular membrane fusion have been assigned to conserved protein systems. Tethering proteins mediate the initial recognition and attachment of membranes, whereas SNARE (soluble N-ethylmaleimide-sensitive factor attachment protein receptor) protein complexes are considered as the core fusion engine. SNARE complexes provide mechanical energy to distort membranes and drive them through a hemifusion intermediate towards the formation of a fusion pore. This last step is highly energy-demanding. Here we combine the in vivo and in vitro fusion of yeast vacuoles with molecular simulations to show that tethering proteins are critical for overcoming the final energy barrier to fusion pore formation. SNAREs alone drive vacuoles only into the hemifused state. Tethering proteins greatly increase the volume of SNARE complexes and deform the site of hemifusion, which lowers the energy barrier for pore opening and provides the driving force. Thereby, tethering proteins assume a crucial mechanical role in the terminal stage of membrane fusion that is likely to be conserved at multiple steps of vesicular traffic. We therefore propose that SNAREs and tethering proteins should be considered as a single, non-dissociable device that drives fusion. The core fusion machinery may then be larger and more complex than previously thought.\",\n \"corpus_id\": 205261587,\n \"score\": 0\n }\n]","isConversational":false}}},{"rowIdx":87,"cells":{"query":{"kind":"string","value":"{\n \"doc_id\": \"23534882\",\n \"title\": \"Accurate prediction of disorder in protein chains with a comprehensive and empirically designed consensus.\",\n \"abstract\": \"Availability of computational methods that predict disorder from protein sequences fuels rapid advancements in the protein disorder field. The most accurate predictions are usually obtained with consensus-based approaches. However, their design is performed in an ad hoc manner. We perform first-of-its-kind rational design where we empirically search for an optimal mixture of base methods, selected out of a comprehensive set of 20 modern predictors, and we explore several novel ways to build the consensus. Our method for the prediction of disorder based on Consensus of Predictors (disCoP) combines seven base methods, utilizes custom-designed set of selected 11 features that aggregate base predictions over a sequence window and uses binomial deviance loss-based regression to implement the consensus. Empirical tests performed on an independent benchmark set (with low-sequence similarity compared with proteins used to design disCoP), shows that disCoP provides statistically significant improvements with at least moderate magnitude of differences. disCoP outperforms 28 predictors, including other state-of-the-art consensuses, and achieves Area Under the ROC Curve of .85 and Matthews Correlation Coefficient of .5 compared with .83 and .48 of the best considered approach, respectively. Our consensus provides high rate of correct disorder predictions, especially when low rate of incorrect disorder predictions is desired. We are first to comprehensively assess predictions in the context of several functional types of disorder and we demonstrate that disCoP generates accurate predictions of disorder located at the post-translational modification sites (in particular phosphorylation sites) and in autoregulatory and flexible linker regions. disCoP is available at http://biomine.ece.ualberta.ca/disCoP/.\",\n \"corpus_id\": 6700404\n}"},"candidates":{"kind":"list like","value":[{"doc_id":"20823312","title":"Improved sequence-based prediction of disordered regions with multilayer fusion of multiple information sources.","abstract":"MOTIVATION: Intrinsically disordered proteins play a crucial role in numerous regulatory processes. Their abundance and ubiquity combined with a relatively low quantity of their annotations motivate research toward the development of computational models that predict disordered regions from protein sequences. Although the prediction quality of these methods continues to rise, novel and improved predictors are urgently needed. RESULTS: We propose a novel method, named MFDp (Multilayered Fusion-based Disorder predictor), that aims to improve over the current disorder predictors. MFDp is as an ensemble of 3 Support Vector Machines specialized for the prediction of short, long and generic disordered regions. It combines three complementary disorder predictors, sequence, sequence profiles, predicted secondary structure, solvent accessibility, backbone dihedral torsion angles, residue flexibility and B-factors. Our method utilizes a custom-designed set of features that are based on raw predictions and aggregated raw values and recognizes various types of disorder. The MFDp is compared at the residue level on two datasets against eight recent disorder predictors and top-performing methods from the most recent CASP8 experiment. In spite of using training chains with <or=25% similarity to the test sequences, our method consistently and significantly outperforms the other methods based on the MCC index. The MFDp outperforms modern disorder predictors for the binary disorder assignment and provides competitive real-valued predictions. The MFDp's outputs are also shown to outperform the other methods in the identification of proteins with long disordered regions. AVAILABILITY: http://biomine.ece.ualberta.ca/MFDp.html.","corpus_id":9371343,"score":2},{"doc_id":"21928402","title":"Evaluation of disorder predictions in CASP9.","abstract":"Lack of stable three-dimensional structure, or intrinsic disorder, is a common phenomenon in proteins. Naturally, unstructured regions are proven to be essential for carrying function by many proteins, and therefore identification of such regions is an important issue. CASP has been assessing the state of the art in predicting disorder regions from amino acid sequence since 2002. Here, we present the results of the evaluation of the disorder predictions submitted to CASP9. The assessment is based on the evaluation measures and procedures used in previous CASPs. The balanced accuracy and the Matthews correlation coefficient were chosen as basic measures for evaluating the correctness of binary classifications. The area under the receiver operating characteristic curve was the measure of choice for evaluating probability-based predictions of disorder. The CASP9 methods are shown to perform slightly better than the CASP7 methods but not better than the methods in CASP8. It was also shown that capability of most CASP9 methods to predict disorder decreases with increasing minimum disorder segment length.","corpus_id":206406180,"score":2},{"doc_id":"22044149","title":"Comprehensive comparative assessment of in-silico predictors of disordered regions.","abstract":"Intrinsic disorder is relatively common in proteins, plays important roles in numerous cellular activities, and its prevalence was implicated in various human diseases. However, annotations of the disorder lag behind the rapidly increasing number of known protein chains. The last decade observed development of a relatively large number of in-silico methods that predict the disorder using the protein sequence as their input. We perform a first-of-its kind comprehensive empirical evaluation of the disorder predictors which is characterized by three novel aspects, (1) we evaluate the quality of the disorder predictions at the residue, segment, and chain levels; (2) we consider a large number of published and accessible to the end user predictors that are evaluated on a relatively big dataset with close to 500 proteins; and (3) we assess statistical significance of differences between the considered methods. Our study reveals that there is no universally superior predictor and that the top-performing methods are complementary. We show that while recent consensus-based predictors outperform other considered methods for the residue-level predictions, some older methods perform better for the prediction of the disordered segments. Our analysis indicates that certain predictors are biased to under-predict the disorder, while some other solutions tend to over-predict the number of the disordered residues. We also evaluate the utility of the predicted residue-level disorder for prediction of proteins with long disordered segments and prediction of the chainlevel disorder content. Lastly, we provide recommendations concerning development of a new generation of consensusbased methods and specialized methods for improved prediction of the disorder content.","corpus_id":20615961,"score":2},{"doc_id":"22101336","title":"Uncertainty analysis in protein disorder prediction.","abstract":"UNLABELLED: A grand challenge in the proteomics and structural genomics era is the prediction of protein structure, including identification of those proteins that are partially or wholly unstructured. A number of predictors for identification of intrinsically disordered proteins (IDPs) have been developed over the last decade, but none can be taken as a fully reliable on its own. Using a single model for prediction is typically inadequate because prediction based on only the most accurate model ignores model uncertainty. In this paper, we present an empirical method to specify and measure uncertainty associated with disorder predictions. In particular, we analyze the uncertainty in the reference model itself and the uncertainty in data. This is achieved by training a set of models and developing several meta predictors on top of them. The best meta predictor achieved comparable or better results than any other single model, suggesting that incorporating different aspects of protein disorder prediction is important for the disorder prediction task. In addition, the best meta-predictor had more balanced sensitivity and specificity than any individual model. We also assessed the effects of changes in disorder prediction as a function of changes in the protein sequence. For collections of homologous sequences, we found that mutations caused many of the predicted disordered residues to be flipped to be predicted as ordered residues, while the reverse was observed much less frequently. These results suggest that disorder tendencies are more sensitive to allowed mutations than structure tendencies and the conservation of disorder is indeed less stable than conservation of structure. AVAILABILITY: five meta-predictors and four single models developed for this study will be publicly freely accessible for non-commercial use.","corpus_id":42312013,"score":2},{"doc_id":"22174273","title":"On the complementarity of the consensus-based disorder prediction.","abstract":"Intrinsic disorder in proteins plays important roles in transcriptional regulation, translation, and cellular signal transduction. The experimental annotation of the disorder lags behind the rapidly accumulating number of known protein chains, which motivates the development of computational predictors of disorder. Some of these methods address predictions of certain types/flavors of the disorder and recent years show that consensus-based predictors provide a viable way to improve predictive performance. However, the selection of the base predictors in a given consensus is usually performed in an ad-hock manner, based on their availability and with a premise that more is better. We perform first-of-its-kind investigation that analyzes complementarity among a dozen recent predictors to identify characteristics of (future) predictors that would lead to further consensus-based improvements in the predictive quality. The complementarity of a given set of three base predictors is expressed by the differences in their predictions when compared with each other and with their majority vote consensus. We propose a regression-based model that quantifies/predicts quality of the majority-vote consensus of a given triplet of predictors based on their individual predictive performance and their complementarity measured at the residue and the disorder segment levels. Our model shows that improved performance is associated with higher (lower) similarity between the three base predictors at the residue (segment) level and to their consensus prediction at the segment (residue) level. We also show that better consensuses utilize higher quality base methods. We use our model to predict the best-performing consensus on an independent test dataset and our empirical evaluation shows that this consensus outperforms individual methods and other consensus-based predictors based on the area under the ROC curve measure. Our study provides insights that could lead to the development of a new generation of the consensus-based disorder predictors.","corpus_id":1376243,"score":2},{"doc_id":"22190692","title":"ESpritz: accurate and fast prediction of protein disorder.","abstract":"MOTIVATION: Intrinsically disordered regions are key for the function of numerous proteins, and the scant available experimental annotations suggest the existence of different disorder flavors. While efficient predictions are required to annotate entire genomes, most existing methods require sequence profiles for disorder prediction, making them cumbersome for high-throughput applications. RESULTS: In this work, we present an ensemble of protein disorder predictors called ESpritz. These are based on bidirectional recursive neural networks and trained on three different flavors of disorder, including a novel NMR flexibility predictor. ESpritz can produce fast and accurate sequence-only predictions, annotating entire genomes in the order of hours on a single processor core. Alternatively, a slower but slightly more accurate ESpritz variant using sequence profiles can be used for applications requiring maximum performance. Two levels of prediction confidence allow either to maximize reasonable disorder detection or to limit expected false positives to 5%. ESpritz performs consistently well on the recent CASP9 data, reaching a S(w) measure of 54.82 and area under the receiver operator curve of 0.856. The fast predictor is four orders of magnitude faster and remains better than most publicly available CASP9 methods, making it ideal for genomic scale predictions. CONCLUSIONS: ESpritz predicts three flavors of disorder at two distinct false positive rates, either with a fast or slower and slightly more accurate approach. Given its state-of-the-art performance, it can be especially useful for high-throughput applications. AVAILABILITY: Both a web server for high-throughput analysis and a Linux executable version of ESpritz are available from: http://protein.bio.unipd.it/espritz/.","corpus_id":7257260,"score":2},{"doc_id":"22591473","title":"A sequence-based approach for predicting protein disordered regions.","abstract":"Protein disordered regions are associated with some critical cellular functions such as transcriptional regulation, translation and cellular signal transduction, and they are responsible for various diseases. Although experimental methods have been developed to determine these regions, they are time-consuming and expensive. Therefore, it is highly desired to develop computational methods that can provide us with this kind information in a rapid and inexpensive manner. Here we propose a sequence-based computational approach for predicting protein disordered regions by means of the Nearest Neighbor algorithm, in which conservation, amino acid factor and secondary structure status of each amino acid in a fixed-length sliding window are taken as the encoding features. Also, the feature selection based on mRMR (maximum Relevancy Minimum Redundancy) is applied to obtain an optimal 51-feature set that includes 39 conservation features and 12 secondary structure features. With the optimal 51 features, our predictor yielded quite promising MCC (Mathew's correlation coefficients): 0.371 on a rigorous benchmark dataset tested by 5-fold cross-validation and 0.219 on an independent test dataset. Our results suggest that conservation and secondary structure play important roles in intrinsically disordered proteins.","corpus_id":40663017,"score":2},{"doc_id":"23497251","title":"DNdisorder: predicting protein disorder using boosting and deep networks.","abstract":"BACKGROUND: A number of proteins contain regions which do not adopt a stable tertiary structure in their native state. Such regions known as disordered regions have been shown to participate in many vital cell functions and are increasingly being examined as drug targets. RESULTS: This work presents a new sequence based approach for the prediction of protein disorder. The method uses boosted ensembles of deep networks to make predictions and participated in the CASP10 experiment. In a 10 fold cross validation procedure on a dataset of 723 proteins, the method achieved an average balanced accuracy of 0.82 and an area under the ROC curve of 0.90. These results are achieved in part by a boosting procedure which is able to steadily increase balanced accuracy and the area under the ROC curve over several rounds. The method also compared competitively when evaluated against a number of state-of-the-art disorder predictors on CASP9 and CASP10 benchmark datasets. CONCLUSIONS: DNdisorder is available as a web service at http://iris.rnet.missouri.edu/dndisorder/.","corpus_id":5886678,"score":2},{"doc_id":"23710446","title":"A novel method of predicting protein disordered regions based on sequence features.","abstract":"With a large number of disordered proteins and their important functions discovered, it is highly desired to develop effective methods to computationally predict protein disordered regions. In this study, based on Random Forest (RF), Maximum Relevancy Minimum Redundancy (mRMR), and Incremental Feature Selection (IFS), we developed a new method to predict disordered regions in proteins. The mRMR criterion was used to rank the importance of all candidate features. Finally, top 128 features were selected from the ranked feature list to build the optimal model, including 92 Position Specific Scoring Matrix (PSSM) conservation score features and 36 secondary structure features. As a result, Matthews correlation coefficient (MCC) of 0.3895 was achieved on the training set by 10-fold cross-validation. On the basis of predicting results for each query sequence by using the method, we used the scanning and modification strategy to improve the performance. The accuracy (ACC) and MCC were increased by 4% and almost 0.2%, respectively, compared with other three popular predictors: DISOPRED, DISOclust, and OnD-CRF. The selected features may shed some light on the understanding of the formation mechanism of disordered structures, providing guidelines for experimental validation.","corpus_id":3131974,"score":2},{"doc_id":"23946100","title":"Assessment of protein disorder region predictions in CASP10.","abstract":"The article presents the assessment of disorder region predictions submitted to CASP10. The evaluation is based on the three measures tested in previous CASPs: (i) balanced accuracy, (ii) the Matthews correlation coefficient for the binary predictions, and (iii) the area under the curve in the receiver operating characteristic (ROC) analysis of predictions using probability annotation. We also performed new analyses such as comparison of the submitted predictions with those obtained with a Naïve disorder prediction method and with predictions from the disorder prediction databases D2P2 and MobiDB. On average, the methods participating in CASP10 demonstrated slightly better performance than those in CASP9.","corpus_id":27785748,"score":2},{"doc_id":"24093637","title":"MFSPSSMpred: identifying short disorder-to-order binding regions in disordered proteins based on contextual local evolutionary conservation.","abstract":"BACKGROUND: Molecular recognition features (MoRFs) are short binding regions located in longer intrinsically disordered protein regions. Although these short regions lack a stable structure in the natural state, they readily undergo disorder-to-order transitions upon binding to their partner molecules. MoRFs play critical roles in the molecular interaction network of a cell, and are associated with many human genetic diseases. Therefore, identification of MoRFs is an important step in understanding functional aspects of these proteins and in finding applications in drug design. RESULTS: Here, we propose a novel method for identifying MoRFs, named as MFSPSSMpred (Masked, Filtered and Smoothed Position-Specific Scoring Matrix-based Predictor). Firstly, a masking method is used to calculate the average local conservation scores of residues within a masking-window length in the position-specific scoring matrix (PSSM). Then, the scores below the average are filtered out. Finally, a smoothing method is used to incorporate the features of flanking regions for each residue to prepare the feature sets for prediction. Our method employs no predicted results from other classifiers as input, i.e., all features used in this method are extracted from the PSSM of sequence only. Experimental results show that, comparing with other methods tested on the same datasets, our method achieves the best performance: achieving 0.004~0.079 higher AUC than other methods when tested on TEST419, and achieving 0.045~0.212 higher AUC than other methods when tested on TEST2012. In addition, when tested on an independent membrane proteins-related dataset, MFSPSSMpred significantly outperformed the existing predictor MoRFpred. CONCLUSIONS: This study suggests that: 1) amino acid composition and physicochemical properties in the flanking regions of MoRFs are very different from those in the general non-MoRF regions; 2) MoRFs contain both highly conserved residues and highly variable residues and, on the whole, are highly locally conserved; and 3) combining contextual information with local conservation information of residues facilitates the prediction of MoRFs.","corpus_id":14617272,"score":2},{"doc_id":"24573480","title":"Prediction of intrinsic disorder in proteins using MFDp2.","abstract":"Intrinsically disordered proteins (IDPs) are either entirely disordered or contain disordered regions in their native state. IDPs were found to be abundant across all kingdoms of life, particularly in eukaryotes, and are implicated in numerous cellular processes. Experimental annotation of disorder lags behind the rapidly growing sizes of the protein databases and thus computational methods are used to close this gap and to investigate the disorder. MFDp2 is a novel webserver for accurate sequence-based prediction of protein disorder which also outputs well-described sequence-derived information that allows profiling the predicted disorder. We conveniently visualize sequence conservation, predicted secondary structure, relative solvent accessibility, and alignments to chains with annotated disorder. The webserver allows predictions for multiple proteins at the same time, includes help pages and tutorial, and the results can be downloaded as text-based (parsable) file. MFDp2 is freely available at http://biomine.ece.ualberta.ca/MFDp2/.","corpus_id":25163022,"score":2},{"doc_id":"25379372","title":"A novel approach for predicting disordered regions in a protein sequence.","abstract":"OBJECTIVES: A number of published predictors are based on various algorithms and disordered protein sequence properties. Although many predictors have been published, the study of protein disordered region prediction is ongoing because different prediction methods can find different disordered regions in a protein sequence. METHODS: Therefore we have used a new approach to find the more varying disordered regions for more efficient and accurate prediction of protein structures. In this study, we propose a novel approach called \"emerging subsequence (ES) mining\" without using the characteristics of the disordered protein. We first adapted the approach to generate emerging protein subsequences on public protein sequence data. Second, the disordered and ordered regions in a protein sequence were predicted by searching the generated emerging protein subsequence with a sliding window, which tends to overlap. Third, the scores of the overlapping regions were calculated based on support and growthrate values in both classes. Finally, the score of predicted regions in the target class were compared with the score of the source class, and the class having a higher score was selected. RESULTS: In this experiment, disordered sequence data and ordered sequence data was extracted from DisProt 6.02 and PDB respectively and used as training data. The test data come from CASP 9 and CASP 10 where disordered and ordered regions are known. CONCLUSION: Comparing with several published predictors, the results of the experiment show higher accuracy rates than with other existing methods.","corpus_id":17380116,"score":2},{"doc_id":"26090958","title":"DisoMCS: Accurately Predicting Protein Intrinsically Disordered Regions Using a Multi-Class Conservative Score Approach.","abstract":"UNLABELLED: The precise prediction of protein intrinsically disordered regions, which play a crucial role in biological procedures, is a necessary prerequisite to further the understanding of the principles and mechanisms of protein function. Here, we propose a novel predictor, DisoMCS, which is a more accurate predictor of protein intrinsically disordered regions. The DisoMCS bases on an original multi-class conservative score (MCS) obtained by sequence-order/disorder alignment. Initially, near-disorder regions are defined on fragments located at both the terminus of an ordered region connecting a disordered region. Then the multi-class conservative score is generated by sequence alignment against a known structure database and represented as order, near-disorder and disorder conservative scores. The MCS of each amino acid has three elements: order, near-disorder and disorder profiles. Finally, the MCS is exploited as features to identify disordered regions in sequences. DisoMCS utilizes a non-redundant data set as the training set, MCS and predicted secondary structure as features, and a conditional random field as the classification algorithm. In predicted near-disorder regions a residue is determined as an order or a disorder according to the optimized decision threshold. DisoMCS was evaluated by cross-validation, large-scale prediction, independent tests and CASP (Critical Assessment of Techniques for Protein Structure Prediction) tests. All results confirmed that DisoMCS was very competitive in terms of accuracy of prediction when compared with well-established publicly available disordered region predictors. It also indicated our approach was more accurate when a query has higher homologous with the knowledge database. AVAILABILITY: The DisoMCS is available at http://cal.tongji.edu.cn/disorder/.","corpus_id":7638704,"score":2},{"doc_id":"26198229","title":"An Overview of Practical Applications of Protein Disorder Prediction and Drive for Faster, More Accurate Predictions.","abstract":"Protein disordered regions are segments of a protein chain that do not adopt a stable structure. Thus far, a variety of protein disorder prediction methods have been developed and have been widely used, not only in traditional bioinformatics domains, including protein structure prediction, protein structure determination and function annotation, but also in many other biomedical fields. The relationship between intrinsically-disordered proteins and some human diseases has played a significant role in disorder prediction in disease identification and epidemiological investigations. Disordered proteins can also serve as potential targets for drug discovery with an emphasis on the disordered-to-ordered transition in the disordered binding regions, and this has led to substantial research in drug discovery or design based on protein disordered region prediction. Furthermore, protein disorder prediction has also been applied to healthcare by predicting the disease risk of mutations in patients and studying the mechanistic basis of diseases. As the applications of disorder prediction increase, so too does the need to make quick and accurate predictions. To fill this need, we also present a new approach to predict protein residue disorder using wide sequence windows that is applicable on the genomic scale.","corpus_id":10268104,"score":2},{"doc_id":"28369666","title":"Computational Prediction of Intrinsic Disorder in Proteins.","abstract":"Computational prediction of intrinsically disordered proteins (IDPs) is a mature research field. These methods predict disordered residues and regions in an input protein chain. More than 60 predictors of IDPs have been developed. This unit defines computational prediction of intrinsic disorder, summarizes major types of predictors of disorder, and provides details about three accurate and recently released methods. We demonstrate the use of these methods to predict intrinsic disorder for several illustrative proteins, provide insights into how predictions should be interpreted, and quantify and discuss predictive performance. Predictions can be freely and conveniently obtained using webservers. We point to the availability of databases that provide access to annotations of intrinsic disorder determined by structural studies and putative intrinsic disorder pre-computed by computational methods. Lastly, we also summarize experimental methods that can be used to validate computational predictions. © 2017 by John Wiley & Sons, Inc.","corpus_id":46283038,"score":2},{"doc_id":"28453683","title":"MobiDB-lite: fast and highly specific consensus prediction of intrinsic disorder in proteins.","abstract":"Motivation: Intrinsic disorder (ID) is established as an important feature of protein sequences. Its use in proteome annotation is however hampered by the availability of many methods with similar performance at the single residue level, which have mostly not been optimized to predict long ID regions of size comparable to domains. Results: Here, we have focused on providing a single consensus-based prediction, MobiDB-lite, optimized for highly specific (i.e. few false positive) predictions of long disorder. The method uses eight different predictors to derive a consensus which is then filtered for spurious short predictions. Consensus prediction is shown to outperform the single methods when annotating long ID regions. MobiDB-lite can be useful in large-scale annotation scenarios and has indeed already been integrated in the MobiDB, DisProt and InterPro databases. Availability and Implementation: MobiDB-lite is available as part of the MobiDB database from URL: http://mobidb.bio.unipd.it/. An executable can be downloaded from URL: http://protein.bio.unipd.it/mobidblite/. Contact: silvio.tosatto@unipd.it. Supplementary information: Supplementary data are available at Bioinformatics online.","corpus_id":52978257,"score":2},{"doc_id":"28516009","title":"MFDp2: Accurate predictor of disorder in proteins by fusion of disorder probabilities, content and profiles.","abstract":"Intrinsically disordered proteins (IDPs) are either entirely disordered or contain disordered regions in their native state. IDPs were found to be abundant in complex organisms and implicated in numerous cellular processes. Experimental annotation of disorder lags behind the rapidly growing sizes of the protein databases, and thus computational methods are used to close this gap and to investigate the disorder. MFDp2 is a novel content-rich and user-friendly web server for sequence-based prediction of protein disorder that builds upon our residue-level disorder predictor MFDp and chain-level disorder content predictor DisCon. It applies novel post-processing filters and uses sequence alignment to improve predictive quality. Using a new benchmark data set, which has reduced sequence identity to corresponding training data sets, MFDp2 is shown to provide competitive predictive quality when compared with MFDp and a comprehensive set of 13 other state-of-the-art predictors, including publicly available versions of the top predictors from CASP9. Our server obtains the highest Mathews Correlation Coefficient (MCC) and the second best Area Under the receiver operating characteristic Curve (AUC). In addition to the disorder predictions, our server also outputs well-described sequence-derived information that allows profiling the predicted disorder. We conveniently visualize sequence conservation, predicted secondary structure, relative solvent accessibility and alignments to chains with annotated disorder. We allow predictions for multiple proteins at the same time and each prediction can be downloaded as text-based (parsable) file. The web server, which includes help pages and tutorial, is freely available at biomine.ece.ualberta.ca/MFDp2/.","corpus_id":195671865,"score":2},{"doc_id":"28589442","title":"Comprehensive review of methods for prediction of intrinsic disorder and its molecular functions.","abstract":"Computational prediction of intrinsic disorder in protein sequences dates back to late 1970 and has flourished in the last two decades. We provide a brief historical overview, and we review over 30 recent predictors of disorder. We are the first to also cover predictors of molecular functions of disorder, including 13 methods that focus on disordered linkers and disordered protein-protein, protein-RNA, and protein-DNA binding regions. We overview their predictive models, usability, and predictive performance. We highlight newest methods and predictors that offer strong predictive performance measured based on recent comparative assessments. We conclude that the modern predictors are relatively accurate, enjoy widespread use, and many of them are fast. Their predictions are conveniently accessible to the end users, via web servers and databases that store pre-computed predictions for millions of proteins. However, research into methods that predict many not yet addressed functions of intrinsic disorder remains an outstanding challenge.","corpus_id":22179720,"score":2},{"doc_id":"29595057","title":"Accurately Predicting Disordered Regions of Proteins Using Rosetta ResidueDisorder Application.","abstract":"Although many proteins necessitate well-folded structures to properly instigate their biological functions, a large fraction of functioning proteins contain regions-known as intrinsically disordered protein regions-where stable structures are not likely to form. Notable functional roles of intrinsically disordered proteins are in transcriptional regulation, translation, and cellular signal transduction. Moreover, intrinsically disordered protein regions are highly abundant in many proteins associated with various human diseases, therefore these segments have become attractive drug targets for potential therapeutics. Over the past decades, numerous computational methods have been developed to accurately predict disordered regions of proteins. Here we introduce a user-friendly and reliable approach for the prediction of disordered protein regions using the structure prediction software Rosetta. Using 245 proteins from a benchmark data set (16 DisProt database proteins) and a test data set (229 proteins with NMR data), we use Rosetta to predict the global protein structures and then show that there is a statistically significant difference between Rosetta scores in disordered and ordered regions, with scores being less favorable in disordered regions. Furthermore, the difference in scores between ordered and disordered protein regions is sufficient to accurately identify disordered protein regions. As a result, our Rosetta ResidueDisorder method (benchmark data set prediction accuracy of 71.77% and independent test data set prediction accuracy of 65.37%) outperformed other established disorder prediction tools and did not exhibit a biased prediction toward either ordered or disordered regions. To facilitate usage, a Rosetta application has been developed for the Rosetta ResidueDisorder method.","corpus_id":4883675,"score":2},{"doc_id":"21682902","title":"In-silico prediction of disorder content using hybrid sequence representation.","abstract":"BACKGROUND: Intrinsically disordered proteins play important roles in various cellular activities and their prevalence was implicated in a number of human diseases. The knowledge of the content of the intrinsic disorder in proteins is useful for a variety of studies including estimation of the abundance of disorder in protein families, classes, and complete proteomes, and for the analysis of disorder-related protein functions. The above investigations currently utilize the disorder content derived from the per-residue disorder predictions. We show that these predictions may over-or under-predict the overall amount of disorder, which motivates development of novel tools for direct and accurate sequence-based prediction of the disorder content. RESULTS: We hypothesize that sequence-level aggregation of input information may provide more accurate content prediction when compared with the content extracted from the local window-based residue-level disorder predictors. We propose a novel predictor, DisCon, that takes advantage of a small set of 29 custom-designed descriptors that aggregate and hybridize information concerning sequence, evolutionary profiles, and predicted secondary structure, solvent accessibility, flexibility, and annotation of globular domains. Using these descriptors and a ridge regression model, DisCon predicts the content with low, 0.05, mean squared error and high, 0.68, Pearson correlation. This is a statistically significant improvement over the content computed from outputs of ten modern disorder predictors on a test dataset with proteins that share low sequence identity with the training sequences. The proposed predictive model is analyzed to discuss factors related to the prediction of the disorder content. CONCLUSIONS: DisCon is a high-quality alternative for high-throughput annotation of the disorder content. We also empirically demonstrate that the DisCon's predictions can be used to improve binary annotations of the disordered residues from the real-value disorder propensities generated by current residue-level disorder predictors. The web server that implements the DisCon is available at http://biomine.ece.ualberta.ca/DisCon/.","corpus_id":5354879,"score":1},{"doc_id":"22689782","title":"MoRFpred, a computational tool for sequence-based prediction and characterization of short disorder-to-order transitioning binding regions in proteins.","abstract":"MOTIVATION: Molecular recognition features (MoRFs) are short binding regions located within longer intrinsically disordered regions that bind to protein partners via disorder-to-order transitions. MoRFs are implicated in important processes including signaling and regulation. However, only a limited number of experimentally validated MoRFs is known, which motivates development of computational methods that predict MoRFs from protein chains. RESULTS: We introduce a new MoRF predictor, MoRFpred, which identifies all MoRF types (α, β, coil and complex). We develop a comprehensive dataset of annotated MoRFs to build and empirically compare our method. MoRFpred utilizes a novel design in which annotations generated by sequence alignment are fused with predictions generated by a Support Vector Machine (SVM), which uses a custom designed set of sequence-derived features. The features provide information about evolutionary profiles, selected physiochemical properties of amino acids, and predicted disorder, solvent accessibility and B-factors. Empirical evaluation on several datasets shows that MoRFpred outperforms related methods: α-MoRF-Pred that predicts α-MoRFs and ANCHOR which finds disordered regions that become ordered when bound to a globular partner. We show that our predicted (new) MoRF regions have non-random sequence similarity with native MoRFs. We use this observation along with the fact that predictions with higher probability are more accurate to identify putative MoRF regions. We also identify a few sequence-derived hallmarks of MoRFs. They are characterized by dips in the disorder predictions and higher hydrophobicity and stability when compared to adjacent (in the chain) residues. AVAILABILITY: http://biomine.ece.ualberta.ca/MoRFpred/; http://biomine.ece.ualberta.ca/MoRFpred/Supplement.pdf.","corpus_id":7599398,"score":1},{"doc_id":"23732563","title":"RAPID: fast and accurate sequence-based prediction of intrinsic disorder content on proteomic scale.","abstract":"Recent research in the protein intrinsic disorder was stimulated by the availability of accurate computational predictors. However, most of these methods are relatively slow, especially considering proteome-scale applications, and were shown to produce relatively large errors when estimating disorder at the protein- (in contrast to residue-) level, which is defined by the fraction/content of disordered residues. To this end, we propose a novel support vector Regression-based Accurate Predictor of Intrinsic Disorder (RAPID). Key advantages of RAPID are speed (prediction of an average-size eukaryotic proteome takes <1h on a modern desktop computer); sophisticated design (multiple, complementary information sources that are aggregated over an input chain are combined using feature selection); and high-quality and robust predictive performance. Empirical tests on two diverse benchmark datasets reveal that RAPID's predictive performance compares favorably to a comprehensive set of state-of-the-art disorder and disorder content predictors. Drawing on high speed and good predictive quality, RAPID was used to perform large-scale characterization of disorder in 200+ fully sequenced eukaryotic proteomes. Our analysis reveals interesting relations of disorder with structural coverage and chain length, and unusual distribution of fully disordered chains. We also performed a comprehensive (using 56000+ annotated chains, which doubles the scope of previous studies) investigation of cellular functions and localizations that are enriched in the disorder in the human proteome. RAPID, which allows for batch (proteome-wide) predictions, is available as a web server at http://biomine.ece.ualberta.ca/RAPID/.","corpus_id":38597868,"score":1},{"doc_id":"23798504","title":"Genome-scale prediction of proteins with long intrinsically disordered regions.","abstract":"Proteins with long disordered regions (LDRs), defined as having 30 or more consecutive disordered residues, are abundant in eukaryotes, and these regions are recognized as a distinct class of biologically functional domains. LDRs facilitate various cellular functions and are important for target selection in structural genomics. Motivated by the lack of methods that directly predict proteins with LDRs, we designed Super-fast predictor of proteins with Long Intrinsically DisordERed regions (SLIDER). SLIDER utilizes logistic regression that takes an empirically chosen set of numerical features, which consider selected physicochemical properties of amino acids, sequence complexity, and amino acid composition, as its inputs. Empirical tests show that SLIDER offers competitive predictive performance combined with low computational cost. It outperforms, by at least a modest margin, a comprehensive set of modern disorder predictors (that can indirectly predict LDRs) and is 16 times faster compared to the best currently available disorder predictor. Utilizing our time-efficient predictor, we characterized abundance and functional roles of proteins with LDRs over 110 eukaryotic proteomes. Similar to related studies, we found that eukaryotes have many (on average 30.3%) proteins with LDRs with majority of proteomes having between 25 and 40%, where higher abundance is characteristic to proteomes that have larger proteins. Our first-of-its-kind large-scale functional analysis shows that these proteins are enriched in a number of cellular functions and processes including certain binding events, regulation of catalytic activities, cellular component organization, biogenesis, biological regulation, and some metabolic and developmental processes. A webserver that implements SLIDER is available at http://biomine.ece.ualberta.ca/SLIDER/.","corpus_id":21229963,"score":1},{"doc_id":"24939692","title":"Exceptionally abundant exceptions: comprehensive characterization of intrinsic disorder in all domains of life.","abstract":"Recent years witnessed increased interest in intrinsically disordered proteins and regions. These proteins and regions are abundant and possess unique structural features and a broad functional repertoire that complements ordered proteins. However, modern studies on the abundance and functions of intrinsically disordered proteins and regions are relatively limited in size and scope of their analysis. To fill this gap, we performed a broad and detailed computational analysis of over 6 million proteins from 59 archaea, 471 bacterial, 110 eukaryotic and 325 viral proteomes. We used arguably more accurate consensus-based disorder predictions, and for the first time comprehensively characterized intrinsic disorder at proteomic and protein levels from all significant perspectives, including abundance, cellular localization, functional roles, evolution, and impact on structural coverage. We show that intrinsic disorder is more abundant and has a unique profile in eukaryotes. We map disorder into archaea, bacterial and eukaryotic cells, and demonstrate that it is preferentially located in some cellular compartments. Functional analysis that considers over 1,200 annotations shows that certain functions are exclusively implemented by intrinsically disordered proteins and regions, and that some of them are specific to certain domains of life. We reveal that disordered regions are often targets for various post-translational modifications, but primarily in the eukaryotes and viruses. Using a phylogenetic tree for 14 eukaryotic and 112 bacterial species, we analyzed relations between disorder, sequence conservation and evolutionary speed. We provide a complete analysis that clearly shows that intrinsic disorder is exceptionally and uniquely abundant in each domain of life.","corpus_id":15655242,"score":1},{"doc_id":"18293306","title":"Prediction of protein structural class using novel evolutionary collocation-based sequence representation.","abstract":"Knowledge of structural classes is useful in understanding of folding patterns in proteins. Although existing structural class prediction methods applied virtually all state-of-the-art classifiers, many of them use a relatively simple protein sequence representation that often includes amino acid (AA) composition. To this end, we propose a novel sequence representation that incorporates evolutionary information encoded using PSI-BLAST profile-based collocation of AA pairs. We used six benchmark datasets and five representative classifiers to quantify and compare the quality of the structural class prediction with the proposed representation. The best, classifier support vector machine achieved 61-96% accuracy on the six datasets. These predictions were comprehensively compared with a wide range of recently proposed methods for prediction of structural classes. Our comprehensive comparison shows superiority of the proposed representation, which results in error rate reductions that range between 14% and 26% when compared with predictions of the best-performing, previously published classifiers on the considered datasets. The study also shows that, for the benchmark dataset that includes sequences characterized by low identity (i.e., 25%, 30%, and 40%), the prediction accuracies are 20-35% lower than for the other three datasets that include sequences with a higher degree of similarity. In conclusion, the proposed representation is shown to substantially improve the accuracy of the structural class prediction. A web server that implements the presented prediction method is freely available at http://biomine.ece.ualberta.ca/Structural_Class/SCEC.html.","corpus_id":2074142,"score":0},{"doc_id":"18452616","title":"SCPRED: accurate prediction of protein structural class for sequences of twilight-zone similarity with predicting sequences.","abstract":"BACKGROUND: Protein structure prediction methods provide accurate results when a homologous protein is predicted, while poorer predictions are obtained in the absence of homologous templates. However, some protein chains that share twilight-zone pairwise identity can form similar folds and thus determining structural similarity without the sequence similarity would be desirable for the structure prediction. The folding type of a protein or its domain is defined as the structural class. Current structural class prediction methods that predict the four structural classes defined in SCOP provide up to 63% accuracy for the datasets in which sequence identity of any pair of sequences belongs to the twilight-zone. We propose SCPRED method that improves prediction accuracy for sequences that share twilight-zone pairwise similarity with sequences used for the prediction. RESULTS: SCPRED uses a support vector machine classifier that takes several custom-designed features as its input to predict the structural classes. Based on extensive design that considers over 2300 index-, composition- and physicochemical properties-based features along with features based on the predicted secondary structure and content, the classifier's input includes 8 features based on information extracted from the secondary structure predicted with PSI-PRED and one feature computed from the sequence. Tests performed with datasets of 1673 protein chains, in which any pair of sequences shares twilight-zone similarity, show that SCPRED obtains 80.3% accuracy when predicting the four SCOP-defined structural classes, which is superior when compared with over a dozen recent competing methods that are based on support vector machine, logistic regression, and ensemble of classifiers predictors. CONCLUSION: The SCPRED can accurately find similar structures for sequences that share low identity with sequence used for the prediction. The high predictive accuracy achieved by SCPRED is attributed to the design of the features, which are capable of separating the structural classes in spite of their low dimensionality. We also demonstrate that the SCPRED's predictions can be successfully used as a post-processing filter to improve performance of modern fold classification methods.","corpus_id":17815381,"score":0},{"doc_id":"19003998","title":"Accurate prediction for atomic-level protein design and its application in diversifying the near-optimal sequence space.","abstract":"The task of engineering a protein to assume a target three-dimensional structure is known as protein design. Computational search algorithms are devised to predict a minimal energy amino acid sequence for a particular structure. In practice, however, an ensemble of low-energy sequences is often sought. Primarily, this is performed because an individual predicted low-energy sequence may not necessarily fold to the target structure because of both inaccuracies in modeling protein energetics and the nonoptimal nature of search algorithms employed. Additionally, some low-energy sequences may be overly stable and thus lack the dynamic flexibility required for biological functionality. Furthermore, the investigation of low-energy sequence ensembles will provide crucial insights into the pseudo-physical energy force fields that have been derived to describe structural energetics for protein design. Significantly, numerous studies have predicted low-energy sequences, which were subsequently synthesized and demonstrated to fold to desired structures. However, the characterization of the sequence space defined by such energy functions as compatible with a target structure has not been performed in full detail. This issue is critical for protein design scientists to successfully continue using these force fields at an ever-increasing pace and scale. In this paper, we present a conceptually novel algorithm that rapidly predicts the set of lowest energy sequences for a given structure. Based on the theory of probabilistic graphical models, it performs efficient inspection and partitioning of the near-optimal sequence space, without making any assumptions of positional independence. We benchmark its performance on a diverse set of relevant protein design examples and show that it consistently yields sequences of lower energy than those derived from state-of-the-art techniques. Thus, we find that previously presented search techniques do not fully depict the low-energy space as precisely. Examination of the predicted ensembles indicates that, for each structure, the amino acid identity at a majority of positions must be chosen extremely selectively so as to not incur significant energetic penalties. We investigate this high degree of similarity and demonstrate how more diverse near-optimal sequences can be predicted in order to systematically overcome this bottleneck for computational design. Finally, we exploit this in-depth analysis of a collection of the lowest energy sequences to suggest an explanation for previously observed experimental design results. The novel methodologies introduced here accurately portray the sequence space compatible with a protein structure and further supply a scheme to yield heterogeneous low-energy sequences, thus providing a powerful instrument for future work on protein design.","corpus_id":8014671,"score":0},{"doc_id":"20003388","title":"Modular prediction of protein structural classes from sequences of twilight-zone identity with predicting sequences.","abstract":"BACKGROUND: Knowledge of structural class is used by numerous methods for identification of structural/functional characteristics of proteins and could be used for the detection of remote homologues, particularly for chains that share twilight-zone similarity. In contrast to existing sequence-based structural class predictors, which target four major classes and which are designed for high identity sequences, we predict seven classes from sequences that share twilight-zone identity with the training sequences. RESULTS: The proposed MODular Approach to Structural class prediction (MODAS) method is unique as it allows for selection of any subset of the classes. MODAS is also the first to utilize a novel, custom-built feature-based sequence representation that combines evolutionary profiles and predicted secondary structure. The features quantify information relevant to the definition of the classes including conservation of residues and arrangement and number of helix/strand segments. Our comprehensive design considers 8 feature selection methods and 4 classifiers to develop Support Vector Machine-based classifiers that are tailored for each of the seven classes. Tests on 5 twilight-zone and 1 high-similarity benchmark datasets and comparison with over two dozens of modern competing predictors show that MODAS provides the best overall accuracy that ranges between 80% and 96.7% (83.5% for the twilight-zone datasets), depending on the dataset. This translates into 19% and 8% error rate reduction when compared against the best performing competing method on two largest datasets. The proposed predictor provides accurate predictions at 58% accuracy for membrane proteins class, which is not considered by majority of existing methods, in spite that this class accounts for only 2% of the data. Our predictive model is analyzed to demonstrate how and why the input features are associated with the corresponding classes. CONCLUSIONS: The improved predictions stem from the novel features that express collocation of the secondary structure segments in the protein sequence and that combine evolutionary and secondary structure information. Our work demonstrates that conservation and arrangement of the secondary structure segments predicted along the protein chain can successfully predict structural classes which are defined based on the spatial arrangement of the secondary structures. A web server is available at http://biomine.ece.ualberta.ca/MODAS/.","corpus_id":5564894,"score":0},{"doc_id":"20730460","title":"iFC²: an integrated web-server for improved prediction of protein structural class, fold type, and secondary structure content.","abstract":"Several descriptors of protein structure at the sequence and residue levels have been recently proposed. They are widely adopted in the analysis and prediction of structural and functional characteristics of proteins. Numerous in silico methods have been developed for sequence-based prediction of these descriptors. However, many of them do not have a public web-server and only a few integrate multiple descriptors to improve the predictions. We introduce iFC² (integrated prediction of fold, class, and content) server that is the first to integrate three modern predictors of sequence-level descriptors. They concern fold type (PFRES), structural class (SCEC), and secondary structure content (PSSC-core). The server exploits relations between the three descriptors to implement a cross-evaluation procedure that improves over the predictions of the individual methods. The iFC² annotates fold and class predictions as potentially correct/incorrect. When tested on datasets with low-similarity chains, for the fold prediction iFC² labels 82% of the PFRES predictions as correct and the accuracy of these predictions equals 72%. The accuracy of the remaining 28% of the PFRES predictions equals 38%. Similarly, our server assigns correct labels for over 79% of SCEC predictions, which are shown to be 98% accurate, while the remaining SCEC predictions are only 15% accurate. These results are shown to be competitive when contrasted against recent relevant web-servers. Predictions on CASP8 targets show that the content predicted by iFC² is competitive when compared with the content computed from the tertiary structures predicted by three best-performing methods in CASP8. The iFC² server is available at http://biomine.ece.ualberta.ca/1D/1D.html .","corpus_id":6644489,"score":0},{"doc_id":"21064129","title":"Improved identification of outer membrane beta barrel proteins using primary sequence, predicted secondary structure, and evolutionary information.","abstract":"Membrane proteins (MPs) are difficult to identify in genomes and to crystallize, making it hard to determine their tertiary structures. MPs could be categorized into α-helical (AMP) and outer membrane proteins which mostly include beta barrel folds (OMBBs). The AMPs are relatively easy to predict from a protein sequence because they usually include several long membrane-spanning hydrophobic α-helices. The OMBBs play important roles in cell biology, they are targeted by multiple drugs, and they are more challenging to identify as they have shorter membrane-spanning regions which lack a folding pattern, that is, as consistent as in the case of the AMPs. Hence, accurate in silico methods for prediction of OMBBs from their primary sequences are needed. We present an accurate sequence-based predictor of OMBBs, called OMBBpred, which utilizes a Support Vector Machine classifier and a custom-designed set of 34 novel numerical descriptors derived from predicted secondary structures, hydrophobicity, and evolutionary information. Our method outperforms modern existing OMBB predictors and achieves accuracy of above 98% when tested on two existing benchmark datasets and 96% on a new large dataset. OMBBpred reduces the error rates of the second best method, depending on the dataset used, by between 13 and 65%, and generates predictions with high specificity of above 96%. Our solution is a useful tool for high-throughput discovery of the OMBBs on a genome scale and can be found at http://biomine.ece. ualberta.ca/OMBBpred/OMBBpred.htm.","corpus_id":23725010,"score":0},{"doc_id":"21082205","title":"Determination of protein folding kinetic types using sequence and predicted secondary structure and solvent accessibility.","abstract":"Proteins fold through a two-state (TS), with no visible intermediates, or a multi-state (MS), via at least one intermediate, process. We analyze sequence-derived factors that determine folding types by introducing a novel sequence-based folding type predictor called FOKIT. This method implements a logistic regression model with six input features which hybridize information concerning amino acid composition and predicted secondary structure and solvent accessibility. FOKIT provides predictions with average Matthews correlation coefficient (MCC) between 0.58 and 0.91 measured using out-of-sample tests on four benchmark datasets. These results are shown to be competitive or better than results of four modern predictors. We also show that FOKIT outperforms these methods when predicting chains that share low similarity with the chains used to build the model, which is an important advantage given the limited number of annotated chains. We demonstrate that inclusion of solvent accessibility helps in discrimination of the folding kinetic types and that three of the features constitute statistically significant markers that differentiate TS and MS folders. We found that the increased content of exposed Trp and buried Leu are indicative of the MS folding, which implies that the exposure/burial of certain hydrophobic residues may play important role in the formation of the folding intermediates. Our conclusions are supported by two case studies.","corpus_id":1068604,"score":0},{"doc_id":"21685077","title":"Sequence-based prediction of protein crystallization, purification and production propensity.","abstract":"MOTIVATION: X-ray crystallography-based protein structure determination, which accounts for majority of solved structures, is characterized by relatively low success rates. One solution is to build tools which support selection of targets that are more likely to crystallize. Several in silico methods that predict propensity of diffraction-quality crystallization from protein chains were developed. We show that the quality of their predictions drops when applied to more recent crystallization trails, which calls for new solutions. We propose a novel approach that alleviates drawbacks of the existing methods by using a recent dataset and improved protocol to annotate progress along the crystallization process, by predicting the success of the entire process and steps which result in the failed attempts, and by utilizing a compact and comprehensive set of sequence-derived inputs to generate accurate predictions. RESULTS: The proposed PPCpred (predictor of protein Production, Purification and Crystallization) predict propensity for production of diffraction-quality crystals, production of crystals, purification and production of the protein material. PPCpred utilizes comprehensive set of inputs based on energy and hydrophobicity indices, composition of certain amino acid types, predicted disorder, secondary structure and solvent accessibility, and content of certain buried and exposed residues. Our method significantly outperforms alignment-based predictions and several modern crystallization propensity predictors. Receiver operating characteristic (ROC) curves show that PPCpred is particularly useful for users who desire high true positive (TP) rates, i.e. low rate of mispredictions for solvable chains. Our model reveals several intuitive factors that influence the success of individual steps and the entire crystallization process, including the content of Cys, buried His and Ser, hydrophobic/hydrophilic segments and the number of predicted disordered segments. AVAILABILITY: http://biomine.ece.ualberta.ca/PPCpred/. CONTACT: lkurgan@ece.ualberta.ca.","corpus_id":14878897,"score":0},{"doc_id":"21919861","title":"CRYSpred: accurate sequence-based protein crystallization propensity prediction using sequence-derived structural characteristics.","abstract":"Relatively low success rates of X-ray crystallography, which is the most popular method for solving proteins structures, motivate development of novel methods that support selection of tractable protein targets. This aspect is particularly important in the context of the current structural genomics efforts that allow for a certain degree of flexibility in the target selection. We propose CRYSpred, a novel in-silico crystallization propensity predictor that uses a set of 15 novel features which utilize a broad range of inputs including charge, hydrophobicity, and amino acid composition derived from the protein chain, and the solvent accessibility and disorder predicted from the protein sequence. Our method outperforms seven modern crystallization propensity predictors on three, independent from training dataset, benchmark test datasets. The strong predictive performance offered by the CRYSpred is attributed to the careful design of the features, utilization of the comprehensive set of inputs, and the usage of the Support Vector Machine classifier. The inputs utilized by CRYSpred are well-aligned with the existing rules-of-thumb that are used in the structural genomics studies.","corpus_id":6091681,"score":0},{"doc_id":"22165846","title":"ATPsite: sequence-based prediction of ATP-binding residues.","abstract":"BACKGROUND: ATP is a ubiquitous nucleotide that provides energy for cellular activities, catalyzes chemical reactions, and is involved in cellular signalling. The knowledge of the ATP-protein interactions helps with annotation of protein functions and finds applications in drug design. The sequence to structure annotation gap motivates development of high-throughput sequence-based predictors of the ATP-binding residues. Moreover, our empirical tests show that the only existing predictor, ATPint, is characterized by relatively low predictive quality. METHODS: We propose a novel, high-throughput machine learning-based predictor, ATPsite, which identifies ATP-binding residues from protein sequences. Our predictor utilizes Support Vector Machine classifier and a comprehensive set of input features that are based on the sequence, evolutionary profiles, and the sequence-predicted structural descriptors including secondary structure, solvent accessibility, and dihedral angles. RESULTS: The ATPsite achieves significantly higher Mathews Correlation Coefficient (MCC) and Area Under the ROC Curve (AUC) values when compared with the existing methods including the ATPint, conservation-based rate4site, and alignment-based BLAST predictors. We also assessed the effectiveness of individual input types. The PSSM profile, the conservation scores, and certain features based on amino acid groups are shown to be more effective in predicting the ATP-binding residues than the remaining feature groups. CONCLUSIONS: Statistical tests show that ATPsite significantly outperforms existing solutions. The consensus of the ATPsite with the sequence-alignment based predictor is shown to give further improvements.","corpus_id":590014,"score":0},{"doc_id":"22272076","title":"Prediction of lysine ubiquitylation with ensemble classifier and feature selection.","abstract":"Ubiquitylation is an important process of post-translational modification. Correct identification of protein lysine ubiquitylation sites is of fundamental importance to understand the molecular mechanism of lysine ubiquitylation in biological systems. This paper develops a novel computational method to effectively identify the lysine ubiquitylation sites based on the ensemble approach. In the proposed method, 468 ubiquitylation sites from 323 proteins retrieved from the Swiss-Prot database were encoded into feature vectors by using four kinds of protein sequences information. An effective feature selection method was then applied to extract informative feature subsets. After different feature subsets were obtained by setting different starting points in the search procedure, they were used to train multiple random forests classifiers and then aggregated into a consensus classifier by majority voting. Evaluated by jackknife tests and independent tests respectively, the accuracy of the proposed predictor reached 76.82% for the training dataset and 79.16% for the test dataset, indicating that this predictor is a useful tool to predict lysine ubiquitylation sites. Furthermore, site-specific feature analysis was performed and it was shown that ubiquitylation is intimately correlated with the features of its surrounding sites in addition to features derived from the lysine site itself. The feature selection method is available upon request.","corpus_id":2877306,"score":0},{"doc_id":"22545993","title":"Accurate prediction of protein structural classes using functional domains and predicted secondary structure sequences.","abstract":"Protein structural class prediction is one of the challenging problems in bioinformatics. Previous methods directly based on the similarity of amino acid (AA) sequences have been shown to be insufficient for low-similarity protein data-sets. To improve the prediction accuracy for such low-similarity proteins, different methods have been recently proposed that explore the novel feature sets based on predicted secondary structure propensities. In this paper, we focus on protein structural class prediction using combinations of the novel features including secondary structure propensities as well as functional domain (FD) features extracted from the InterPro signature database. Our comprehensive experimental results based on several benchmark data-sets have shown that the integration of new FD features substantially improves the accuracy of structural class prediction for low-similarity proteins as they capture meaningful relationships among AA residues that are far away in protein sequence. The proposed prediction method has also been tested to predict structural classes for partially disordered proteins with the reasonable prediction accuracy, which is a more difficult problem comparing to structural class prediction for commonly used benchmark data-sets and has never been done before to the best of our knowledge. In addition, to avoid overfitting with a large number of features, feature selection is applied to select discriminating features that contribute to achieve high prediction accuracy. The selected features have been shown to achieve stable prediction performance across different benchmark data-sets.","corpus_id":28689690,"score":0},{"doc_id":"22555647","title":"AMS 4.0: consensus prediction of post-translational modifications in protein sequences.","abstract":"We present here the 2011 update of the AutoMotif Service (AMS 4.0) that predicts the wide selection of 88 different types of the single amino acid post-translational modifications (PTM) in protein sequences. The selection of experimentally confirmed modifications is acquired from the latest UniProt and Phospho. ELM databases for training. The sequence vicinity of each modified residue is represented using amino acids physico-chemical features encoded using high quality indices (HQI) obtaining by automatic clustering of known indices extracted from AAindex database. For each type of the numerical representation, the method builds the ensemble of Multi-Layer Perceptron (MLP) pattern classifiers, each optimising different objectives during the training (for example the recall, precision or area under the ROC curve (AUC)). The consensus is built using brainstorming technology, which combines multi-objective instances of machine learning algorithm, and the data fusion of different training objects representations, in order to boost the overall prediction accuracy of conserved short sequence motifs. The performance of AMS 4.0 is compared with the accuracy of previous versions, which were constructed using single machine learning methods (artificial neural networks, support vector machine). Our software improves the average AUC score of the earlier version by close to 7 % as calculated on the test datasets of all 88 PTM types. Moreover, for the selected most-difficult sequence motifs types it is able to improve the prediction performance by almost 32 %, when compared with previously used single machine learning methods. Summarising, the brainstorming consensus meta-learning methodology on the average boosts the AUC score up to around 89 %, averaged over all 88 PTM types. Detailed results for single machine learning methods and the consensus methodology are also provided, together with the comparison to previously published methods and state-of-the-art software tools. The source code and precompiled binaries of brainstorming tool are available at http://code.google.com/p/automotifserver/ under Apache 2.0 licensing.","corpus_id":16117028,"score":0},{"doc_id":"22723837","title":"Accurate prediction of protein structural class.","abstract":"Because of the increasing gap between the data from sequencing and structural genomics, the accurate prediction of the structural class of a protein domain solely from the primary sequence has remained a challenging problem in structural biology. Traditional sequence-based predictors generally select several sequence features and then feed them directly into a classification program to identify the structural class. The current best sequence-based predictor achieved an overall accuracy of 74.1% when tested on a widely used, non-homologous benchmark dataset 25PDB. In the present work, we built a multiple linear regression (MLR) model to convert the 440-dimensional (440D) sequence feature vector extracted from the Position Specific Scoring Matrix (PSSM) of a protein domain to a 4-dimensinal (4D) structural feature vector, which could then be used to predict the four major structural classes. We performed 10-fold cross-validation and jackknife tests of the method on a large non-homologous dataset containing 8,244 domains distributed among the four major classes. The performance of our approach outperformed all of the existing sequence-based methods and had an overall accuracy of 83.1%, which is even higher than the results of those predicted secondary structure-based methods.","corpus_id":17465367,"score":0},{"doc_id":"22761950","title":"BEST: improved prediction of B-cell epitopes from antigen sequences.","abstract":"Accurate identification of immunogenic regions in a given antigen chain is a difficult and actively pursued problem. Although accurate predictors for T-cell epitopes are already in place, the prediction of the B-cell epitopes requires further research. We overview the available approaches for the prediction of B-cell epitopes and propose a novel and accurate sequence-based solution. Our BEST (B-cell Epitope prediction using Support vector machine Tool) method predicts epitopes from antigen sequences, in contrast to some method that predict only from short sequence fragments, using a new architecture based on averaging selected scores generated from sliding 20-mers by a Support Vector Machine (SVM). The SVM predictor utilizes a comprehensive and custom designed set of inputs generated by combining information derived from the chain, sequence conservation, similarity to known (training) epitopes, and predicted secondary structure and relative solvent accessibility. Empirical evaluation on benchmark datasets demonstrates that BEST outperforms several modern sequence-based B-cell epitope predictors including ABCPred, method by Chen et al. (2007), BCPred, COBEpro, BayesB, and CBTOPE, when considering the predictions from antigen chains and from the chain fragments. Our method obtains a cross-validated area under the receiver operating characteristic curve (AUC) for the fragment-based prediction at 0.81 and 0.85, depending on the dataset. The AUCs of BEST on the benchmark sets of full antigen chains equal 0.57 and 0.6, which is significantly and slightly better than the next best method we tested. We also present case studies to contrast the propensity profiles generated by BEST and several other methods.","corpus_id":9088745,"score":0},{"doc_id":"23110141","title":"Accurate prediction of protein catalytic residues by side chain orientation and residue contact density.","abstract":"Prediction of protein catalytic residues provides useful information for the studies of protein functions. Most of the existing methods combine both structure and sequence information but heavily rely on sequence conservation from multiple sequence alignments. The contribution of structure information is usually less than that of sequence conservation in existing methods. We found a novel structure feature, residue side chain orientation, which is the first structure-based feature that achieves prediction results comparable to that of evolutionary sequence conservation. We developed a structure-based method, Enzyme Catalytic residue SIde-chain Arrangement (EXIA), which is based on residue side chain orientations and backbone flexibility of protein structure. The prediction that uses EXIA outperforms existing structure-based features. The prediction quality of combing EXIA and sequence conservation exceeds that of the state-of-the-art prediction methods. EXIA is designed to predict catalytic residues from single protein structure without needing sequence or structure alignments. It provides invaluable information when there is no sufficient or reliable homology information for target protein. We found that catalytic residues have very special side chain orientation and designed the EXIA method based on the newly discovered feature. It was also found that EXIA performs well for a dataset of enzymes without any bounded ligand in their crystallographic structures.","corpus_id":17268599,"score":0},{"doc_id":"23298369","title":"Comprehensively designed consensus of standalone secondary structure predictors improves Q3 by over 3%.","abstract":"Protein fold is defined by a spatial arrangement of three types of secondary structures (SSs) including helices, sheets, and coils/loops. Current methods that predict SS from sequences rely on complex machine learning-derived models and provide the three-state accuracy (Q3) at about 82%. Further improvements in predictive quality could be obtained with a consensus-based approach, which so far received limited attention. We perform first-of-its-kind comprehensive design of a SS consensus predictor (SScon), in which we consider 12 modern standalone SS predictors and utilize Support Vector Machine (SVM) to combine their predictions. Using a large benchmark data-set with 10 random training-test splits, we show that a simple, voting-based consensus of carefully selected base methods improves Q3 by 1.9% when compared to the best single predictor. Use of SVM provides additional 1.4% improvement with the overall Q3 at 85.6% and segment overlap (SOV3) at 83.7%, when compared to 82.3 and 80.9%, respectively, obtained by the best individual methods. We also show strong improvements when the consensus is based on ab-initio methods, with Q3 = 82.3% and SOV3 = 80.7% that match the results from the best template-based approaches. Our consensus reduces the number of significant errors where helix is confused with a strand, provides particularly good results for short helices and strands, and gives the most accurate estimates of the content of individual SSs in the chain. Case studies are used to visualize the improvements offered by the consensus at the residue level. A web-server and a standalone implementation of SScon are available at http://biomine.ece.ualberta.ca/SSCon/ .","corpus_id":31483068,"score":0},{"doc_id":"23504705","title":"Accurate prediction of hot spot residues through physicochemical characteristics of amino acid sequences.","abstract":"Hot spot residues of proteins are fundamental interface residues that help proteins perform their functions. Detecting hot spots by experimental methods is costly and time-consuming. Sequential and structural information has been widely used in the computational prediction of hot spots. However, structural information is not always available. In this article, we investigated the problem of identifying hot spots using only physicochemical characteristics extracted from amino acid sequences. We first extracted 132 relatively independent physicochemical features from a set of the 544 properties in AAindex1, an amino acid index database. Each feature was utilized to train a classification model with a novel encoding schema for hot spot prediction by the IBk algorithm, an extension of the K-nearest neighbor algorithm. The combinations of the individual classifiers were explored and the classifiers that appeared frequently in the top performing combinations were selected. The hot spot predictor was built based on an ensemble of these classifiers and to work in a voting manner. Experimental results demonstrated that our method effectively exploited the feature space and allowed flexible weights of features for different queries. On the commonly used hot spot benchmark sets, our method significantly outperformed other machine learning algorithms and state-of-the-art hot spot predictors. The program is available at http://sfb.kaust.edu.sa/pages/software.aspx.","corpus_id":5236261,"score":0},{"doc_id":"24846307","title":"RNABindRPlus: a predictor that combines machine learning and sequence homology-based methods to improve the reliability of predicted RNA-binding residues in proteins.","abstract":"Protein-RNA interactions are central to essential cellular processes such as protein synthesis and regulation of gene expression and play roles in human infectious and genetic diseases. Reliable identification of protein-RNA interfaces is critical for understanding the structural bases and functional implications of such interactions and for developing effective approaches to rational drug design. Sequence-based computational methods offer a viable, cost-effective way to identify putative RNA-binding residues in RNA-binding proteins. Here we report two novel approaches: (i) HomPRIP, a sequence homology-based method for predicting RNA-binding sites in proteins; (ii) RNABindRPlus, a new method that combines predictions from HomPRIP with those from an optimized Support Vector Machine (SVM) classifier trained on a benchmark dataset of 198 RNA-binding proteins. Although highly reliable, HomPRIP cannot make predictions for the unaligned parts of query proteins and its coverage is limited by the availability of close sequence homologs of the query protein with experimentally determined RNA-binding sites. RNABindRPlus overcomes these limitations. We compared the performance of HomPRIP and RNABindRPlus with that of several state-of-the-art predictors on two test sets, RB44 and RB111. On a subset of proteins for which homologs with experimentally determined interfaces could be reliably identified, HomPRIP outperformed all other methods achieving an MCC of 0.63 on RB44 and 0.83 on RB111. RNABindRPlus was able to predict RNA-binding residues of all proteins in both test sets, achieving an MCC of 0.55 and 0.37, respectively, and outperforming all other methods, including those that make use of structure-derived features of proteins. More importantly, RNABindRPlus outperforms all other methods for any choice of tradeoff between precision and recall. An important advantage of both HomPRIP and RNABindRPlus is that they rely on readily available sequence and sequence-derived features of RNA-binding proteins. A webserver implementation of both methods is freely available at http://einstein.cs.iastate.edu/RNABindRPlus/.","corpus_id":13527970,"score":0},{"doc_id":"25189131","title":"Enhancing protein-vitamin binding residues prediction by multiple heterogeneous subspace SVMs ensemble.","abstract":"BACKGROUND: Vitamins are typical ligands that play critical roles in various metabolic processes. The accurate identification of the vitamin-binding residues solely based on a protein sequence is of significant importance for the functional annotation of proteins, especially in the post-genomic era, when large volumes of protein sequences are accumulating quickly without being functionally annotated. RESULTS: In this paper, a new predictor called TargetVita is designed and implemented for predicting protein-vitamin binding residues using protein sequences. In TargetVita, features derived from the position-specific scoring matrix (PSSM), predicted protein secondary structure, and vitamin binding propensity are combined to form the original feature space; then, several feature subspaces are selected by performing different feature selection methods. Finally, based on the selected feature subspaces, heterogeneous SVMs are trained and then ensembled for performing prediction. CONCLUSIONS: The experimental results obtained with four separate vitamin-binding benchmark datasets demonstrate that the proposed TargetVita is superior to the state-of-the-art vitamin-specific predictor, and an average improvement of 10% in terms of the Matthews correlation coefficient (MCC) was achieved over independent validation tests. The TargetVita web server and the datasets used are freely available for academic use at http://csbio.njust.edu.cn/bioinf/TargetVita or http://www.csbio.sjtu.edu.cn/bioinf/TargetVita.","corpus_id":18756547,"score":0},{"doc_id":"25637562","title":"Computational identification of MoRFs in protein sequences.","abstract":"MOTIVATION: Intrinsically disordered regions of proteins play an essential role in the regulation of various biological processes. Key to their regulatory function is the binding of molecular recognition features (MoRFs) to globular protein domains in a process known as a disorder-to-order transition. Predicting the location of MoRFs in protein sequences with high accuracy remains an important computational challenge. METHOD: In this study, we introduce MoRFCHiBi, a new computational approach for fast and accurate prediction of MoRFs in protein sequences. MoRFCHiBi combines the outcomes of two support vector machine (SVM) models that take advantage of two different kernels with high noise tolerance. The first, SVMS, is designed to extract maximal information from the general contrast in amino acid compositions between MoRFs, their surrounding regions (Flanks), and the remainders of the sequences. The second, SVMT, is used to identify similarities between regions in a query sequence and MoRFs of the training set. RESULTS: We evaluated the performance of our predictor by comparing its results with those of two currently available MoRF predictors, MoRFpred and ANCHOR. Using three test sets that have previously been collected and used to evaluate MoRFpred and ANCHOR, we demonstrate that MoRFCHiBi outperforms the other predictors with respect to different evaluation metrics. In addition, MoRFCHiBi is downloadable and fast, which makes it useful as a component in other computational prediction tools. AVAILABILITY AND IMPLEMENTATION: http://www.chibi.ubc.ca/morf/.","corpus_id":16498676,"score":0},{"doc_id":"25713596","title":"Algorithmic approaches to protein-protein interaction site prediction.","abstract":"Interaction sites on protein surfaces mediate virtually all biological activities, and their identification holds promise for disease treatment and drug design. Novel algorithmic approaches for the prediction of these sites have been produced at a rapid rate, and the field has seen significant advancement over the past decade. However, the most current methods have not yet been reviewed in a systematic and comprehensive fashion. Herein, we describe the intricacies of the biological theory, datasets, and features required for modern protein-protein interaction site (PPIS) prediction, and present an integrative analysis of the state-of-the-art algorithms and their performance. First, the major sources of data used by predictors are reviewed, including training sets, evaluation sets, and methods for their procurement. Then, the features employed and their importance in the biological characterization of PPISs are explored. This is followed by a discussion of the methodologies adopted in contemporary prediction programs, as well as their relative performance on the datasets most recently used for evaluation. In addition, the potential utility that PPIS identification holds for rational drug design, hotspot prediction, and computational molecular docking is described. Finally, an analysis of the most promising areas for future development of the field is presented.","corpus_id":8720300,"score":0},{"doc_id":"25935161","title":"A comprehensive comparative review of sequence-based predictors of DNA- and RNA-binding residues.","abstract":"Motivated by the pressing need to characterize protein-DNA and protein-RNA interactions on large scale, we review a comprehensive set of 30 computational methods for high-throughput prediction of RNA- or DNA-binding residues from protein sequences. We summarize these predictors from several significant perspectives including their design, outputs and availability. We perform empirical assessment of methods that offer web servers using a new benchmark data set characterized by a more complete annotation that includes binding residues transferred from the same or similar proteins. We show that predictors of DNA-binding (RNA-binding) residues offer relatively strong predictive performance but they are unable to properly separate DNA- from RNA-binding residues. We design and empirically assess several types of consensuses and demonstrate that machine learning (ML)-based approaches provide improved predictive performance when compared with the individual predictors of DNA-binding residues or RNA-binding residues. We also formulate and execute first-of-its-kind study that targets combined prediction of DNA- and RNA-binding residues. We design and test three types of consensuses for this prediction and conclude that this novel approach that relies on ML design provides better predictive quality than individual predictors when tested on prediction of DNA- and RNA-binding residues individually. It also substantially improves discrimination between these two types of nucleic acids. Our results suggest that development of a new generation of predictors would benefit from using training data sets that combine both RNA- and DNA-binding proteins, designing new inputs that specifically target either DNA- or RNA-binding residues and pursuing combined prediction of DNA- and RNA-binding residues.","corpus_id":26243792,"score":0},{"doc_id":"26017462","title":"ADPRtool: A novel predicting model for identification of ASP-ADP-Ribosylation sites of human proteins.","abstract":"Post-translational modifications (PTMs) occur in the vast majority of proteins, and they are essential for many protein functions. Computational prediction of the residue location of PTMs enhances the functional characterization of proteins. ADP-Ribosylation is an important type of PTM, because it is implicated in apoptosis, DNA repair, regulation of cell proliferation, and protein synthesis. However, mass spectrometric approaches have difficulties in identifying a vast number of protein ADP-Ribosylation sites. Therefore, a computational method for predicting ADP-Ribosylation sites of human proteins seems useful and necessary. Four types of sequence features and an incremental feature selection technique are utilized to predict protein ADP-Ribosylation sites. The final feature set for ADPR prediction modeling is optimized, based on a minimum redundancy maximum relevance criterion, so as to make more accurate predictions on aspartic acid ADPR modified residues. Our prediction model, ADPRtool, is capable to predict Asp-ADP-Ribosylation sites with a total accuracy of 85.45%, which is as good as most computational PTM site predictors. By using a sequence-based computational method, a new ADP-Ribosylation site prediction model - ADPRtool, is developed, and it has shown great accuracies with total accuracy, Matthew's correlation coefficient and area under receiver operating characteristic curve.","corpus_id":13116260,"score":0},{"doc_id":"26020952","title":"Accurate prediction of immunogenic T-cell epitopes from epitope sequences using the genetic algorithm-based ensemble learning.","abstract":"BACKGROUND: T-cell epitopes play the important role in T-cell immune response, and they are critical components in the epitope-based vaccine design. Immunogenicity is the ability to trigger an immune response. The accurate prediction of immunogenic T-cell epitopes is significant for designing useful vaccines and understanding the immune system. METHODS: In this paper, we attempt to differentiate immunogenic epitopes from non-immunogenic epitopes based on their primary structures. First of all, we explore a variety of sequence-derived features, and analyze their relationship with epitope immunogenicity. To effectively utilize various features, a genetic algorithm (GA)-based ensemble method is proposed to determine the optimal feature subset and develop the high-accuracy ensemble model. In the GA optimization, a chromosome is to represent a feature subset in the search space. For each feature subset, the selected features are utilized to construct the base predictors, and an ensemble model is developed by taking the average of outputs from base predictors. The objective of GA is to search for the optimal feature subset, which leads to the ensemble model with the best cross validation AUC (area under ROC curve) on the training set. RESULTS: Two datasets named 'IMMA2' and 'PAAQD' are adopted as the benchmark datasets. Compared with the state-of-the-art methods POPI, POPISK, PAAQD and our previous method, the GA-based ensemble method produces much better performances, achieving the AUC score of 0.846 on IMMA2 dataset and the AUC score of 0.829 on PAAQD dataset. The statistical analysis demonstrates the performance improvements of GA-based ensemble method are statistically significant. CONCLUSIONS: The proposed method is a promising tool for predicting the immunogenic epitopes. The source codes and datasets are available in S1 File.","corpus_id":1329354,"score":0},{"doc_id":"26109352","title":"High-throughput prediction of RNA, DNA and protein binding regions mediated by intrinsic disorder.","abstract":"Intrinsically disordered proteins and regions (IDPs and IDRs) lack stable 3D structure under physiological conditions in-vitro, are common in eukaryotes, and facilitate interactions with RNA, DNA and proteins. Current methods for prediction of IDPs and IDRs do not provide insights into their functions, except for a handful of methods that address predictions of protein-binding regions. We report first-of-its-kind computational method DisoRDPbind for high-throughput prediction of RNA, DNA and protein binding residues located in IDRs from protein sequences. DisoRDPbind is implemented using a runtime-efficient multi-layered design that utilizes information extracted from physiochemical properties of amino acids, sequence complexity, putative secondary structure and disorder and sequence alignment. Empirical tests demonstrate that it provides accurate predictions that are competitive with other predictors of disorder-mediated protein binding regions and complementary to the methods that predict RNA- and DNA-binding residues annotated based on crystal structures. Application in Homo sapiens, Mus musculus, Caenorhabditis elegans and Drosophila melanogaster proteomes reveals that RNA- and DNA-binding proteins predicted by DisoRDPbind complement and overlap with the corresponding known binding proteins collected from several sources. Also, the number of the putative protein-binding regions predicted with DisoRDPbind correlates with the promiscuity of proteins in the corresponding protein-protein interaction networks. Webserver: http://biomine.ece.ualberta.ca/DisoRDPbind/.","corpus_id":13883311,"score":0},{"doc_id":"26478747","title":"Prediction of protein solvent accessibility using PSO-SVR with multiple sequence-derived features and weighted sliding window scheme.","abstract":"BACKGROUND: The prediction of solvent accessibility could provide valuable clues for analyzing protein structure and functions, such as protein 3-Dimensional structure and B-cell epitope prediction. To fully decipher the protein-protein interaction process, an initial but crucial step is to calculate the protein solvent accessibility, especially when the tertiary structure of the protein is unknown. Although some efforts have been put into the protein solvent accessibility prediction, the performance of existing methods is far from satisfaction. METHODS: In order to develop the high-accuracy model, we focus on some possible aspects concerning the prediction performance, including several sequence-derived features, a weighted sliding window scheme and the parameters optimization of machine learning approach. To address above issues, we take following strategies. Firstly, we explore various features which have been observed to be associated with the residue solvent accessibility. These discriminative features include protein evolutionary information, predicted protein secondary structure, native disorder, physicochemical propensities and several sequence-based structural descriptors of residues. Secondly, the different contributions of adjacent residues in sliding window are observed, thus a weighted sliding window scheme is proposed to differentiate the contributions of adjacent residues on the central residue. Thirdly, particle swarm optimization (PSO) is employed to search the global best parameters for the proposed predictor. RESULTS: Evaluated by 3-fold cross-validation, our method achieves the mean absolute error (MAE) of 14.1% and the person correlation coefficient (PCC) of 0.75 for our new-compiled dataset. When compared with the state-of-the-art prediction models in the two benchmark datasets, our method demonstrates better performance. Experimental results demonstrate that our PSAP achieves high performances and outperforms many existing predictors. A web server called PSAP is built and freely available at http://59.73.198.144:8088/SolventAccessibility/.","corpus_id":4912166,"score":0},{"doc_id":"27274091","title":"Consensus protein design.","abstract":"A popular and successful strategy in semi-rational design of protein stability is the use of evolutionary information encapsulated in homologous protein sequences. Consensus design is based on the hypothesis that at a given position, the respective consensus amino acid contributes more than average to the stability of the protein than non-conserved amino acids. Here, we review the consensus design approach, its theoretical underpinnings, successes, limitations and challenges, as well as providing a detailed guide to its application in protein engineering.","corpus_id":15164229,"score":0},{"doc_id":"27307636","title":"DFLpred: High-throughput prediction of disordered flexible linker regions in protein sequences.","abstract":"MOTIVATION: Disordered flexible linkers (DFLs) are disordered regions that serve as flexible linkers/spacers in multi-domain proteins or between structured constituents in domains. They are different from flexible linkers/residues because they are disordered and longer. Availability of experimentally annotated DFLs provides an opportunity to build high-throughput computational predictors of these regions from protein sequences. To date, there are no computational methods that directly predict DFLs and they can be found only indirectly by filtering predicted flexible residues with predictions of disorder. RESULTS: We conceptualized, developed and empirically assessed a first-of-its-kind sequence-based predictor of DFLs, DFLpred. This method outputs propensity to form DFLs for each residue in the input sequence. DFLpred uses a small set of empirically selected features that quantify propensities to form certain secondary structures, disordered regions and structured regions, which are processed by a fast linear model. Our high-throughput predictor can be used on the whole-proteome scale; it needs <1 h to predict entire proteome on a single CPU. When assessed on an independent test dataset with low sequence-identity proteins, it secures area under the receiver operating characteristic curve equal 0.715 and outperforms existing alternatives that include methods for the prediction of flexible linkers, flexible residues, intrinsically disordered residues and various combinations of these methods. Prediction on the complete human proteome reveals that about 10% of proteins have a large content of over 30% DFL residues. We also estimate that about 6000 DFL regions are long with ≥30 consecutive residues. AVAILABILITY AND IMPLEMENTATION: http://biomine.ece.ualberta.ca/DFLpred/ CONTACT: lkurgan@vcu.edu SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.","corpus_id":35835604,"score":0},{"doc_id":"27777222","title":"Comprehensive assessment and performance improvement of effector protein predictors for bacterial secretion systems III, IV and VI.","abstract":"Bacterial effector proteins secreted by various protein secretion systems play crucial roles in host-pathogen interactions. In this context, computational tools capable of accurately predicting effector proteins of the various types of bacterial secretion systems are highly desirable. Existing computational approaches use different machine learning (ML) techniques and heterogeneous features derived from protein sequences and/or structural information. These predictors differ not only in terms of the used ML methods but also with respect to the used curated data sets, the features selection and their prediction performance. Here, we provide a comprehensive survey and benchmarking of currently available tools for the prediction of effector proteins of bacterial types III, IV and VI secretion systems (T3SS, T4SS and T6SS, respectively). We review core algorithms, feature selection techniques, tool availability and applicability and evaluate the prediction performance based on carefully curated independent test data sets. In an effort to improve predictive performance, we constructed three ensemble models based on ML algorithms by integrating the output of all individual predictors reviewed. Our benchmarks demonstrate that these ensemble models outperform all the reviewed tools for the prediction of effector proteins of T3SS and T4SS. The webserver of the proposed ensemble methods for T3SS and T4SS effector protein prediction is freely available at http://tbooster.erc.monash.edu/index.jsp We anticipate that this survey will serve as a useful guide for interested users and that the new ensemble predictors will stimulate research into host-pathogen relationships and inspiration for the development of new bioinformatics tools for predicting effector proteins of T3SS, T4SS and T6SS.","corpus_id":3321295,"score":0},{"doc_id":"27787818","title":"Predicting Protein Secondary Structure Using Consensus Data Mining (CDM) Based on Empirical Statistics and Evolutionary Information.","abstract":"Predicting the secondary structure of a protein from its sequence still remains a challenging problem. The prediction accuracies remain around 80 %, and for very diverse methods. Using evolutionary information and machine learning algorithms in particular has had the most impact. In this chapter, we will first define secondary structures, then we will review the Consensus Data Mining (CDM) technique based on the robust GOR algorithm and Fragment Database Mining (FDM) approach. GOR V is an empirical method utilizing a sliding window approach to model the secondary structural elements of a protein by making use of generalized evolutionary information. FDM uses data mining from experimental structure fragments, and is able to successfully predict the secondary structure of a protein by combining experimentally determined structural fragments based on sequence similarities of the fragments. The CDM method combines predictions from GOR V and FDM in a hierarchical manner to produce consensus predictions for secondary structure. In other words, if sequence fragment are not available, then it uses GOR V to make the secondary structure prediction. The online server of CDM is available at http://gor.bb.iastate.edu/cdm/ .","corpus_id":4857477,"score":0},{"doc_id":"27787828","title":"Prediction of Disordered RNA, DNA, and Protein Binding Regions Using DisoRDPbind.","abstract":"Intrinsically disordered proteins and regions (IDPs and IDRs) are involved in a wide range of cellular functions and they often facilitate interactions with RNAs, DNAs, and proteins. Although many computational methods can predict IDPs and IDRs in protein sequences, only a few methods predict their functions and these functions primarily concern protein binding. We describe how to use the first computational method DisoRDPbind for high-throughput prediction of multiple functions of disordered regions. Our method predicts the RNA-, DNA-, and protein-binding residues located in IDRs in the input protein sequences. DisoRDPbind provides accurate predictions and is sufficiently fast to make predictions for full genomes. Our method is implemented as a user-friendly webserver that is freely available at http://biomine.ece.ualberta.ca/DisoRDPbind/ . We overview our predictor, discuss how to run the webserver, and show how to interpret the corresponding results. We also demonstrate the utility of our method based on two case studies, human BRCA1 protein that binds various proteins and DNA, and yeast 60S ribosomal protein L4 that interacts with proteins and RNA.","corpus_id":4869176,"score":0},{"doc_id":"27978812","title":"COUSCOus: improved protein contact prediction using an empirical Bayes covariance estimator.","abstract":"BACKGROUND: The post-genomic era with its wealth of sequences gave rise to a broad range of protein residue-residue contact detecting methods. Although various coevolution methods such as PSICOV, DCA and plmDCA provide correct contact predictions, they do not completely overlap. Hence, new approaches and improvements of existing methods are needed to motivate further development and progress in the field. We present a new contact detecting method, COUSCOus, by combining the best shrinkage approach, the empirical Bayes covariance estimator and GLasso. RESULTS: Using the original PSICOV benchmark dataset, COUSCOus achieves mean accuracies of 0.74, 0.62 and 0.55 for the top L/10 predicted long, medium and short range contacts, respectively. In addition, COUSCOus attains mean areas under the precision-recall curves of 0.25, 0.29 and 0.30 for long, medium and short contacts and outperforms PSICOV. We also observed that COUSCOus outperforms PSICOV w.r.t. Matthew's correlation coefficient criterion on full list of residue contacts. Furthermore, COUSCOus achieves on average 10% more gain in prediction accuracy compared to PSICOV on an independent test set composed of CASP11 protein targets. Finally, we showed that when using a simple random forest meta-classifier, by combining contact detecting techniques and sequence derived features, PSICOV predictions should be replaced by the more accurate COUSCOus predictions. CONCLUSION: We conclude that the consideration of superior covariance shrinkage approaches will boost several research fields that apply the GLasso procedure, amongst the presented one of residue-residue contact prediction as well as fields such as gene network reconstruction.","corpus_id":7377892,"score":0},{"doc_id":"28222000","title":"Fast prediction of protein methylation sites using a sequence-based feature selection technique.","abstract":"Protein methylation, an important post-translational modification, plays crucial roles in many cellular processes. The accurate prediction of protein methylation sites is fundamentally important for revealing the molecular mechanisms undergoing methylation. In recent years, computational prediction based on machine learning algorithms has emerged as a powerful and robust approach for identifying methylation sites, and much progress has been made in predictive performance improvement. However, the predictive performance of existing methods is not satisfactory in terms of overall accuracy. Motivated by this, we propose a novel random-forest-based predictor called MePred-RF, integrating several discriminative sequence-based feature descriptors and improving feature representation capability using a powerful feature selection technique. Importantly, unlike other methods based on multiple, complex information inputs, our proposed MePred-RF is based on sequence information alone. Comparative studies on benchmark datasets via vigorous jackknife tests indicate that our proposed MePred-RF method remarkably outperforms other state-of-the-art predictors, leading by a 4.5% average in terms of overall accuracy. A user-friendly webserver that implements the proposed method has been established for researchers' convenience, and is now freely available for public use through http://server.malab.cn/MePred---‑RF. We anticipate our research tool to be useful for the largescale prediction and analysis of protein methylation sites.","corpus_id":5263228,"score":0},{"doc_id":"29069295","title":"PaRSnIP: sequence-based protein solubility prediction using gradient boosting machine.","abstract":"Motivation: Protein solubility can be a decisive factor in both research and production efficiency, and in silico sequence-based predictors that can accurately estimate solubility outcomes are highly sought. Results: In this study, we present a novel approach termed PRotein SolubIlity Predictor (PaRSnIP), which uses a gradient boosting machine algorithm as well as an approximation of sequence and structural features of the protein of interest. Based on an independent test set, PaRSnIP outperformed other state-of-the-art sequence-based methods by more than 9% in accuracy and 0.17 in Matthew's correlation coefficient, with an overall accuracy of 74% and Matthew's correlation coefficient of 0.48. Additionally, PaRSnIP provides importance scores for all features used in training. We observed higher fractions of exposed residues to associate positively with protein solubility and tripeptide stretches with multiple histidines to associate negatively with solubility. The improved prediction accuracy of PaRSnIP should enable it to predict protein solubility with greater reliability and to screen for sequence variants with enhanced manufacturability. Availability and implementation: PaRSnIP software is available for download under GitHub (https://github.com/RedaRawi/PaRSnIP). Contact: gwo-yu.chuang@nih.gov. Supplementary information: Supplementary data are available at Bioinformatics online.","corpus_id":4576871,"score":0}],"string":"[\n {\n \"doc_id\": \"20823312\",\n \"title\": \"Improved sequence-based prediction of disordered regions with multilayer fusion of multiple information sources.\",\n \"abstract\": \"MOTIVATION: Intrinsically disordered proteins play a crucial role in numerous regulatory processes. Their abundance and ubiquity combined with a relatively low quantity of their annotations motivate research toward the development of computational models that predict disordered regions from protein sequences. Although the prediction quality of these methods continues to rise, novel and improved predictors are urgently needed. RESULTS: We propose a novel method, named MFDp (Multilayered Fusion-based Disorder predictor), that aims to improve over the current disorder predictors. MFDp is as an ensemble of 3 Support Vector Machines specialized for the prediction of short, long and generic disordered regions. It combines three complementary disorder predictors, sequence, sequence profiles, predicted secondary structure, solvent accessibility, backbone dihedral torsion angles, residue flexibility and B-factors. Our method utilizes a custom-designed set of features that are based on raw predictions and aggregated raw values and recognizes various types of disorder. The MFDp is compared at the residue level on two datasets against eight recent disorder predictors and top-performing methods from the most recent CASP8 experiment. In spite of using training chains with <or=25% similarity to the test sequences, our method consistently and significantly outperforms the other methods based on the MCC index. The MFDp outperforms modern disorder predictors for the binary disorder assignment and provides competitive real-valued predictions. The MFDp's outputs are also shown to outperform the other methods in the identification of proteins with long disordered regions. AVAILABILITY: http://biomine.ece.ualberta.ca/MFDp.html.\",\n \"corpus_id\": 9371343,\n \"score\": 2\n },\n {\n \"doc_id\": \"21928402\",\n \"title\": \"Evaluation of disorder predictions in CASP9.\",\n \"abstract\": \"Lack of stable three-dimensional structure, or intrinsic disorder, is a common phenomenon in proteins. Naturally, unstructured regions are proven to be essential for carrying function by many proteins, and therefore identification of such regions is an important issue. CASP has been assessing the state of the art in predicting disorder regions from amino acid sequence since 2002. Here, we present the results of the evaluation of the disorder predictions submitted to CASP9. The assessment is based on the evaluation measures and procedures used in previous CASPs. The balanced accuracy and the Matthews correlation coefficient were chosen as basic measures for evaluating the correctness of binary classifications. The area under the receiver operating characteristic curve was the measure of choice for evaluating probability-based predictions of disorder. The CASP9 methods are shown to perform slightly better than the CASP7 methods but not better than the methods in CASP8. It was also shown that capability of most CASP9 methods to predict disorder decreases with increasing minimum disorder segment length.\",\n \"corpus_id\": 206406180,\n \"score\": 2\n },\n {\n \"doc_id\": \"22044149\",\n \"title\": \"Comprehensive comparative assessment of in-silico predictors of disordered regions.\",\n \"abstract\": \"Intrinsic disorder is relatively common in proteins, plays important roles in numerous cellular activities, and its prevalence was implicated in various human diseases. However, annotations of the disorder lag behind the rapidly increasing number of known protein chains. The last decade observed development of a relatively large number of in-silico methods that predict the disorder using the protein sequence as their input. We perform a first-of-its kind comprehensive empirical evaluation of the disorder predictors which is characterized by three novel aspects, (1) we evaluate the quality of the disorder predictions at the residue, segment, and chain levels; (2) we consider a large number of published and accessible to the end user predictors that are evaluated on a relatively big dataset with close to 500 proteins; and (3) we assess statistical significance of differences between the considered methods. Our study reveals that there is no universally superior predictor and that the top-performing methods are complementary. We show that while recent consensus-based predictors outperform other considered methods for the residue-level predictions, some older methods perform better for the prediction of the disordered segments. Our analysis indicates that certain predictors are biased to under-predict the disorder, while some other solutions tend to over-predict the number of the disordered residues. We also evaluate the utility of the predicted residue-level disorder for prediction of proteins with long disordered segments and prediction of the chainlevel disorder content. Lastly, we provide recommendations concerning development of a new generation of consensusbased methods and specialized methods for improved prediction of the disorder content.\",\n \"corpus_id\": 20615961,\n \"score\": 2\n },\n {\n \"doc_id\": \"22101336\",\n \"title\": \"Uncertainty analysis in protein disorder prediction.\",\n \"abstract\": \"UNLABELLED: A grand challenge in the proteomics and structural genomics era is the prediction of protein structure, including identification of those proteins that are partially or wholly unstructured. A number of predictors for identification of intrinsically disordered proteins (IDPs) have been developed over the last decade, but none can be taken as a fully reliable on its own. Using a single model for prediction is typically inadequate because prediction based on only the most accurate model ignores model uncertainty. In this paper, we present an empirical method to specify and measure uncertainty associated with disorder predictions. In particular, we analyze the uncertainty in the reference model itself and the uncertainty in data. This is achieved by training a set of models and developing several meta predictors on top of them. The best meta predictor achieved comparable or better results than any other single model, suggesting that incorporating different aspects of protein disorder prediction is important for the disorder prediction task. In addition, the best meta-predictor had more balanced sensitivity and specificity than any individual model. We also assessed the effects of changes in disorder prediction as a function of changes in the protein sequence. For collections of homologous sequences, we found that mutations caused many of the predicted disordered residues to be flipped to be predicted as ordered residues, while the reverse was observed much less frequently. These results suggest that disorder tendencies are more sensitive to allowed mutations than structure tendencies and the conservation of disorder is indeed less stable than conservation of structure. AVAILABILITY: five meta-predictors and four single models developed for this study will be publicly freely accessible for non-commercial use.\",\n \"corpus_id\": 42312013,\n \"score\": 2\n },\n {\n \"doc_id\": \"22174273\",\n \"title\": \"On the complementarity of the consensus-based disorder prediction.\",\n \"abstract\": \"Intrinsic disorder in proteins plays important roles in transcriptional regulation, translation, and cellular signal transduction. The experimental annotation of the disorder lags behind the rapidly accumulating number of known protein chains, which motivates the development of computational predictors of disorder. Some of these methods address predictions of certain types/flavors of the disorder and recent years show that consensus-based predictors provide a viable way to improve predictive performance. However, the selection of the base predictors in a given consensus is usually performed in an ad-hock manner, based on their availability and with a premise that more is better. We perform first-of-its-kind investigation that analyzes complementarity among a dozen recent predictors to identify characteristics of (future) predictors that would lead to further consensus-based improvements in the predictive quality. The complementarity of a given set of three base predictors is expressed by the differences in their predictions when compared with each other and with their majority vote consensus. We propose a regression-based model that quantifies/predicts quality of the majority-vote consensus of a given triplet of predictors based on their individual predictive performance and their complementarity measured at the residue and the disorder segment levels. Our model shows that improved performance is associated with higher (lower) similarity between the three base predictors at the residue (segment) level and to their consensus prediction at the segment (residue) level. We also show that better consensuses utilize higher quality base methods. We use our model to predict the best-performing consensus on an independent test dataset and our empirical evaluation shows that this consensus outperforms individual methods and other consensus-based predictors based on the area under the ROC curve measure. Our study provides insights that could lead to the development of a new generation of the consensus-based disorder predictors.\",\n \"corpus_id\": 1376243,\n \"score\": 2\n },\n {\n \"doc_id\": \"22190692\",\n \"title\": \"ESpritz: accurate and fast prediction of protein disorder.\",\n \"abstract\": \"MOTIVATION: Intrinsically disordered regions are key for the function of numerous proteins, and the scant available experimental annotations suggest the existence of different disorder flavors. While efficient predictions are required to annotate entire genomes, most existing methods require sequence profiles for disorder prediction, making them cumbersome for high-throughput applications. RESULTS: In this work, we present an ensemble of protein disorder predictors called ESpritz. These are based on bidirectional recursive neural networks and trained on three different flavors of disorder, including a novel NMR flexibility predictor. ESpritz can produce fast and accurate sequence-only predictions, annotating entire genomes in the order of hours on a single processor core. Alternatively, a slower but slightly more accurate ESpritz variant using sequence profiles can be used for applications requiring maximum performance. Two levels of prediction confidence allow either to maximize reasonable disorder detection or to limit expected false positives to 5%. ESpritz performs consistently well on the recent CASP9 data, reaching a S(w) measure of 54.82 and area under the receiver operator curve of 0.856. The fast predictor is four orders of magnitude faster and remains better than most publicly available CASP9 methods, making it ideal for genomic scale predictions. CONCLUSIONS: ESpritz predicts three flavors of disorder at two distinct false positive rates, either with a fast or slower and slightly more accurate approach. Given its state-of-the-art performance, it can be especially useful for high-throughput applications. AVAILABILITY: Both a web server for high-throughput analysis and a Linux executable version of ESpritz are available from: http://protein.bio.unipd.it/espritz/.\",\n \"corpus_id\": 7257260,\n \"score\": 2\n },\n {\n \"doc_id\": \"22591473\",\n \"title\": \"A sequence-based approach for predicting protein disordered regions.\",\n \"abstract\": \"Protein disordered regions are associated with some critical cellular functions such as transcriptional regulation, translation and cellular signal transduction, and they are responsible for various diseases. Although experimental methods have been developed to determine these regions, they are time-consuming and expensive. Therefore, it is highly desired to develop computational methods that can provide us with this kind information in a rapid and inexpensive manner. Here we propose a sequence-based computational approach for predicting protein disordered regions by means of the Nearest Neighbor algorithm, in which conservation, amino acid factor and secondary structure status of each amino acid in a fixed-length sliding window are taken as the encoding features. Also, the feature selection based on mRMR (maximum Relevancy Minimum Redundancy) is applied to obtain an optimal 51-feature set that includes 39 conservation features and 12 secondary structure features. With the optimal 51 features, our predictor yielded quite promising MCC (Mathew's correlation coefficients): 0.371 on a rigorous benchmark dataset tested by 5-fold cross-validation and 0.219 on an independent test dataset. Our results suggest that conservation and secondary structure play important roles in intrinsically disordered proteins.\",\n \"corpus_id\": 40663017,\n \"score\": 2\n },\n {\n \"doc_id\": \"23497251\",\n \"title\": \"DNdisorder: predicting protein disorder using boosting and deep networks.\",\n \"abstract\": \"BACKGROUND: A number of proteins contain regions which do not adopt a stable tertiary structure in their native state. Such regions known as disordered regions have been shown to participate in many vital cell functions and are increasingly being examined as drug targets. RESULTS: This work presents a new sequence based approach for the prediction of protein disorder. The method uses boosted ensembles of deep networks to make predictions and participated in the CASP10 experiment. In a 10 fold cross validation procedure on a dataset of 723 proteins, the method achieved an average balanced accuracy of 0.82 and an area under the ROC curve of 0.90. These results are achieved in part by a boosting procedure which is able to steadily increase balanced accuracy and the area under the ROC curve over several rounds. The method also compared competitively when evaluated against a number of state-of-the-art disorder predictors on CASP9 and CASP10 benchmark datasets. CONCLUSIONS: DNdisorder is available as a web service at http://iris.rnet.missouri.edu/dndisorder/.\",\n \"corpus_id\": 5886678,\n \"score\": 2\n },\n {\n \"doc_id\": \"23710446\",\n \"title\": \"A novel method of predicting protein disordered regions based on sequence features.\",\n \"abstract\": \"With a large number of disordered proteins and their important functions discovered, it is highly desired to develop effective methods to computationally predict protein disordered regions. In this study, based on Random Forest (RF), Maximum Relevancy Minimum Redundancy (mRMR), and Incremental Feature Selection (IFS), we developed a new method to predict disordered regions in proteins. The mRMR criterion was used to rank the importance of all candidate features. Finally, top 128 features were selected from the ranked feature list to build the optimal model, including 92 Position Specific Scoring Matrix (PSSM) conservation score features and 36 secondary structure features. As a result, Matthews correlation coefficient (MCC) of 0.3895 was achieved on the training set by 10-fold cross-validation. On the basis of predicting results for each query sequence by using the method, we used the scanning and modification strategy to improve the performance. The accuracy (ACC) and MCC were increased by 4% and almost 0.2%, respectively, compared with other three popular predictors: DISOPRED, DISOclust, and OnD-CRF. The selected features may shed some light on the understanding of the formation mechanism of disordered structures, providing guidelines for experimental validation.\",\n \"corpus_id\": 3131974,\n \"score\": 2\n },\n {\n \"doc_id\": \"23946100\",\n \"title\": \"Assessment of protein disorder region predictions in CASP10.\",\n \"abstract\": \"The article presents the assessment of disorder region predictions submitted to CASP10. The evaluation is based on the three measures tested in previous CASPs: (i) balanced accuracy, (ii) the Matthews correlation coefficient for the binary predictions, and (iii) the area under the curve in the receiver operating characteristic (ROC) analysis of predictions using probability annotation. We also performed new analyses such as comparison of the submitted predictions with those obtained with a Naïve disorder prediction method and with predictions from the disorder prediction databases D2P2 and MobiDB. On average, the methods participating in CASP10 demonstrated slightly better performance than those in CASP9.\",\n \"corpus_id\": 27785748,\n \"score\": 2\n },\n {\n \"doc_id\": \"24093637\",\n \"title\": \"MFSPSSMpred: identifying short disorder-to-order binding regions in disordered proteins based on contextual local evolutionary conservation.\",\n \"abstract\": \"BACKGROUND: Molecular recognition features (MoRFs) are short binding regions located in longer intrinsically disordered protein regions. Although these short regions lack a stable structure in the natural state, they readily undergo disorder-to-order transitions upon binding to their partner molecules. MoRFs play critical roles in the molecular interaction network of a cell, and are associated with many human genetic diseases. Therefore, identification of MoRFs is an important step in understanding functional aspects of these proteins and in finding applications in drug design. RESULTS: Here, we propose a novel method for identifying MoRFs, named as MFSPSSMpred (Masked, Filtered and Smoothed Position-Specific Scoring Matrix-based Predictor). Firstly, a masking method is used to calculate the average local conservation scores of residues within a masking-window length in the position-specific scoring matrix (PSSM). Then, the scores below the average are filtered out. Finally, a smoothing method is used to incorporate the features of flanking regions for each residue to prepare the feature sets for prediction. Our method employs no predicted results from other classifiers as input, i.e., all features used in this method are extracted from the PSSM of sequence only. Experimental results show that, comparing with other methods tested on the same datasets, our method achieves the best performance: achieving 0.004~0.079 higher AUC than other methods when tested on TEST419, and achieving 0.045~0.212 higher AUC than other methods when tested on TEST2012. In addition, when tested on an independent membrane proteins-related dataset, MFSPSSMpred significantly outperformed the existing predictor MoRFpred. CONCLUSIONS: This study suggests that: 1) amino acid composition and physicochemical properties in the flanking regions of MoRFs are very different from those in the general non-MoRF regions; 2) MoRFs contain both highly conserved residues and highly variable residues and, on the whole, are highly locally conserved; and 3) combining contextual information with local conservation information of residues facilitates the prediction of MoRFs.\",\n \"corpus_id\": 14617272,\n \"score\": 2\n },\n {\n \"doc_id\": \"24573480\",\n \"title\": \"Prediction of intrinsic disorder in proteins using MFDp2.\",\n \"abstract\": \"Intrinsically disordered proteins (IDPs) are either entirely disordered or contain disordered regions in their native state. IDPs were found to be abundant across all kingdoms of life, particularly in eukaryotes, and are implicated in numerous cellular processes. Experimental annotation of disorder lags behind the rapidly growing sizes of the protein databases and thus computational methods are used to close this gap and to investigate the disorder. MFDp2 is a novel webserver for accurate sequence-based prediction of protein disorder which also outputs well-described sequence-derived information that allows profiling the predicted disorder. We conveniently visualize sequence conservation, predicted secondary structure, relative solvent accessibility, and alignments to chains with annotated disorder. The webserver allows predictions for multiple proteins at the same time, includes help pages and tutorial, and the results can be downloaded as text-based (parsable) file. MFDp2 is freely available at http://biomine.ece.ualberta.ca/MFDp2/.\",\n \"corpus_id\": 25163022,\n \"score\": 2\n },\n {\n \"doc_id\": \"25379372\",\n \"title\": \"A novel approach for predicting disordered regions in a protein sequence.\",\n \"abstract\": \"OBJECTIVES: A number of published predictors are based on various algorithms and disordered protein sequence properties. Although many predictors have been published, the study of protein disordered region prediction is ongoing because different prediction methods can find different disordered regions in a protein sequence. METHODS: Therefore we have used a new approach to find the more varying disordered regions for more efficient and accurate prediction of protein structures. In this study, we propose a novel approach called \\\"emerging subsequence (ES) mining\\\" without using the characteristics of the disordered protein. We first adapted the approach to generate emerging protein subsequences on public protein sequence data. Second, the disordered and ordered regions in a protein sequence were predicted by searching the generated emerging protein subsequence with a sliding window, which tends to overlap. Third, the scores of the overlapping regions were calculated based on support and growthrate values in both classes. Finally, the score of predicted regions in the target class were compared with the score of the source class, and the class having a higher score was selected. RESULTS: In this experiment, disordered sequence data and ordered sequence data was extracted from DisProt 6.02 and PDB respectively and used as training data. The test data come from CASP 9 and CASP 10 where disordered and ordered regions are known. CONCLUSION: Comparing with several published predictors, the results of the experiment show higher accuracy rates than with other existing methods.\",\n \"corpus_id\": 17380116,\n \"score\": 2\n },\n {\n \"doc_id\": \"26090958\",\n \"title\": \"DisoMCS: Accurately Predicting Protein Intrinsically Disordered Regions Using a Multi-Class Conservative Score Approach.\",\n \"abstract\": \"UNLABELLED: The precise prediction of protein intrinsically disordered regions, which play a crucial role in biological procedures, is a necessary prerequisite to further the understanding of the principles and mechanisms of protein function. Here, we propose a novel predictor, DisoMCS, which is a more accurate predictor of protein intrinsically disordered regions. The DisoMCS bases on an original multi-class conservative score (MCS) obtained by sequence-order/disorder alignment. Initially, near-disorder regions are defined on fragments located at both the terminus of an ordered region connecting a disordered region. Then the multi-class conservative score is generated by sequence alignment against a known structure database and represented as order, near-disorder and disorder conservative scores. The MCS of each amino acid has three elements: order, near-disorder and disorder profiles. Finally, the MCS is exploited as features to identify disordered regions in sequences. DisoMCS utilizes a non-redundant data set as the training set, MCS and predicted secondary structure as features, and a conditional random field as the classification algorithm. In predicted near-disorder regions a residue is determined as an order or a disorder according to the optimized decision threshold. DisoMCS was evaluated by cross-validation, large-scale prediction, independent tests and CASP (Critical Assessment of Techniques for Protein Structure Prediction) tests. All results confirmed that DisoMCS was very competitive in terms of accuracy of prediction when compared with well-established publicly available disordered region predictors. It also indicated our approach was more accurate when a query has higher homologous with the knowledge database. AVAILABILITY: The DisoMCS is available at http://cal.tongji.edu.cn/disorder/.\",\n \"corpus_id\": 7638704,\n \"score\": 2\n },\n {\n \"doc_id\": \"26198229\",\n \"title\": \"An Overview of Practical Applications of Protein Disorder Prediction and Drive for Faster, More Accurate Predictions.\",\n \"abstract\": \"Protein disordered regions are segments of a protein chain that do not adopt a stable structure. Thus far, a variety of protein disorder prediction methods have been developed and have been widely used, not only in traditional bioinformatics domains, including protein structure prediction, protein structure determination and function annotation, but also in many other biomedical fields. The relationship between intrinsically-disordered proteins and some human diseases has played a significant role in disorder prediction in disease identification and epidemiological investigations. Disordered proteins can also serve as potential targets for drug discovery with an emphasis on the disordered-to-ordered transition in the disordered binding regions, and this has led to substantial research in drug discovery or design based on protein disordered region prediction. Furthermore, protein disorder prediction has also been applied to healthcare by predicting the disease risk of mutations in patients and studying the mechanistic basis of diseases. As the applications of disorder prediction increase, so too does the need to make quick and accurate predictions. To fill this need, we also present a new approach to predict protein residue disorder using wide sequence windows that is applicable on the genomic scale.\",\n \"corpus_id\": 10268104,\n \"score\": 2\n },\n {\n \"doc_id\": \"28369666\",\n \"title\": \"Computational Prediction of Intrinsic Disorder in Proteins.\",\n \"abstract\": \"Computational prediction of intrinsically disordered proteins (IDPs) is a mature research field. These methods predict disordered residues and regions in an input protein chain. More than 60 predictors of IDPs have been developed. This unit defines computational prediction of intrinsic disorder, summarizes major types of predictors of disorder, and provides details about three accurate and recently released methods. We demonstrate the use of these methods to predict intrinsic disorder for several illustrative proteins, provide insights into how predictions should be interpreted, and quantify and discuss predictive performance. Predictions can be freely and conveniently obtained using webservers. We point to the availability of databases that provide access to annotations of intrinsic disorder determined by structural studies and putative intrinsic disorder pre-computed by computational methods. Lastly, we also summarize experimental methods that can be used to validate computational predictions. © 2017 by John Wiley & Sons, Inc.\",\n \"corpus_id\": 46283038,\n \"score\": 2\n },\n {\n \"doc_id\": \"28453683\",\n \"title\": \"MobiDB-lite: fast and highly specific consensus prediction of intrinsic disorder in proteins.\",\n \"abstract\": \"Motivation: Intrinsic disorder (ID) is established as an important feature of protein sequences. Its use in proteome annotation is however hampered by the availability of many methods with similar performance at the single residue level, which have mostly not been optimized to predict long ID regions of size comparable to domains. Results: Here, we have focused on providing a single consensus-based prediction, MobiDB-lite, optimized for highly specific (i.e. few false positive) predictions of long disorder. The method uses eight different predictors to derive a consensus which is then filtered for spurious short predictions. Consensus prediction is shown to outperform the single methods when annotating long ID regions. MobiDB-lite can be useful in large-scale annotation scenarios and has indeed already been integrated in the MobiDB, DisProt and InterPro databases. Availability and Implementation: MobiDB-lite is available as part of the MobiDB database from URL: http://mobidb.bio.unipd.it/. An executable can be downloaded from URL: http://protein.bio.unipd.it/mobidblite/. Contact: silvio.tosatto@unipd.it. Supplementary information: Supplementary data are available at Bioinformatics online.\",\n \"corpus_id\": 52978257,\n \"score\": 2\n },\n {\n \"doc_id\": \"28516009\",\n \"title\": \"MFDp2: Accurate predictor of disorder in proteins by fusion of disorder probabilities, content and profiles.\",\n \"abstract\": \"Intrinsically disordered proteins (IDPs) are either entirely disordered or contain disordered regions in their native state. IDPs were found to be abundant in complex organisms and implicated in numerous cellular processes. Experimental annotation of disorder lags behind the rapidly growing sizes of the protein databases, and thus computational methods are used to close this gap and to investigate the disorder. MFDp2 is a novel content-rich and user-friendly web server for sequence-based prediction of protein disorder that builds upon our residue-level disorder predictor MFDp and chain-level disorder content predictor DisCon. It applies novel post-processing filters and uses sequence alignment to improve predictive quality. Using a new benchmark data set, which has reduced sequence identity to corresponding training data sets, MFDp2 is shown to provide competitive predictive quality when compared with MFDp and a comprehensive set of 13 other state-of-the-art predictors, including publicly available versions of the top predictors from CASP9. Our server obtains the highest Mathews Correlation Coefficient (MCC) and the second best Area Under the receiver operating characteristic Curve (AUC). In addition to the disorder predictions, our server also outputs well-described sequence-derived information that allows profiling the predicted disorder. We conveniently visualize sequence conservation, predicted secondary structure, relative solvent accessibility and alignments to chains with annotated disorder. We allow predictions for multiple proteins at the same time and each prediction can be downloaded as text-based (parsable) file. The web server, which includes help pages and tutorial, is freely available at biomine.ece.ualberta.ca/MFDp2/.\",\n \"corpus_id\": 195671865,\n \"score\": 2\n },\n {\n \"doc_id\": \"28589442\",\n \"title\": \"Comprehensive review of methods for prediction of intrinsic disorder and its molecular functions.\",\n \"abstract\": \"Computational prediction of intrinsic disorder in protein sequences dates back to late 1970 and has flourished in the last two decades. We provide a brief historical overview, and we review over 30 recent predictors of disorder. We are the first to also cover predictors of molecular functions of disorder, including 13 methods that focus on disordered linkers and disordered protein-protein, protein-RNA, and protein-DNA binding regions. We overview their predictive models, usability, and predictive performance. We highlight newest methods and predictors that offer strong predictive performance measured based on recent comparative assessments. We conclude that the modern predictors are relatively accurate, enjoy widespread use, and many of them are fast. Their predictions are conveniently accessible to the end users, via web servers and databases that store pre-computed predictions for millions of proteins. However, research into methods that predict many not yet addressed functions of intrinsic disorder remains an outstanding challenge.\",\n \"corpus_id\": 22179720,\n \"score\": 2\n },\n {\n \"doc_id\": \"29595057\",\n \"title\": \"Accurately Predicting Disordered Regions of Proteins Using Rosetta ResidueDisorder Application.\",\n \"abstract\": \"Although many proteins necessitate well-folded structures to properly instigate their biological functions, a large fraction of functioning proteins contain regions-known as intrinsically disordered protein regions-where stable structures are not likely to form. Notable functional roles of intrinsically disordered proteins are in transcriptional regulation, translation, and cellular signal transduction. Moreover, intrinsically disordered protein regions are highly abundant in many proteins associated with various human diseases, therefore these segments have become attractive drug targets for potential therapeutics. Over the past decades, numerous computational methods have been developed to accurately predict disordered regions of proteins. Here we introduce a user-friendly and reliable approach for the prediction of disordered protein regions using the structure prediction software Rosetta. Using 245 proteins from a benchmark data set (16 DisProt database proteins) and a test data set (229 proteins with NMR data), we use Rosetta to predict the global protein structures and then show that there is a statistically significant difference between Rosetta scores in disordered and ordered regions, with scores being less favorable in disordered regions. Furthermore, the difference in scores between ordered and disordered protein regions is sufficient to accurately identify disordered protein regions. As a result, our Rosetta ResidueDisorder method (benchmark data set prediction accuracy of 71.77% and independent test data set prediction accuracy of 65.37%) outperformed other established disorder prediction tools and did not exhibit a biased prediction toward either ordered or disordered regions. To facilitate usage, a Rosetta application has been developed for the Rosetta ResidueDisorder method.\",\n \"corpus_id\": 4883675,\n \"score\": 2\n },\n {\n \"doc_id\": \"21682902\",\n \"title\": \"In-silico prediction of disorder content using hybrid sequence representation.\",\n \"abstract\": \"BACKGROUND: Intrinsically disordered proteins play important roles in various cellular activities and their prevalence was implicated in a number of human diseases. The knowledge of the content of the intrinsic disorder in proteins is useful for a variety of studies including estimation of the abundance of disorder in protein families, classes, and complete proteomes, and for the analysis of disorder-related protein functions. The above investigations currently utilize the disorder content derived from the per-residue disorder predictions. We show that these predictions may over-or under-predict the overall amount of disorder, which motivates development of novel tools for direct and accurate sequence-based prediction of the disorder content. RESULTS: We hypothesize that sequence-level aggregation of input information may provide more accurate content prediction when compared with the content extracted from the local window-based residue-level disorder predictors. We propose a novel predictor, DisCon, that takes advantage of a small set of 29 custom-designed descriptors that aggregate and hybridize information concerning sequence, evolutionary profiles, and predicted secondary structure, solvent accessibility, flexibility, and annotation of globular domains. Using these descriptors and a ridge regression model, DisCon predicts the content with low, 0.05, mean squared error and high, 0.68, Pearson correlation. This is a statistically significant improvement over the content computed from outputs of ten modern disorder predictors on a test dataset with proteins that share low sequence identity with the training sequences. The proposed predictive model is analyzed to discuss factors related to the prediction of the disorder content. CONCLUSIONS: DisCon is a high-quality alternative for high-throughput annotation of the disorder content. We also empirically demonstrate that the DisCon's predictions can be used to improve binary annotations of the disordered residues from the real-value disorder propensities generated by current residue-level disorder predictors. The web server that implements the DisCon is available at http://biomine.ece.ualberta.ca/DisCon/.\",\n \"corpus_id\": 5354879,\n \"score\": 1\n },\n {\n \"doc_id\": \"22689782\",\n \"title\": \"MoRFpred, a computational tool for sequence-based prediction and characterization of short disorder-to-order transitioning binding regions in proteins.\",\n \"abstract\": \"MOTIVATION: Molecular recognition features (MoRFs) are short binding regions located within longer intrinsically disordered regions that bind to protein partners via disorder-to-order transitions. MoRFs are implicated in important processes including signaling and regulation. However, only a limited number of experimentally validated MoRFs is known, which motivates development of computational methods that predict MoRFs from protein chains. RESULTS: We introduce a new MoRF predictor, MoRFpred, which identifies all MoRF types (α, β, coil and complex). We develop a comprehensive dataset of annotated MoRFs to build and empirically compare our method. MoRFpred utilizes a novel design in which annotations generated by sequence alignment are fused with predictions generated by a Support Vector Machine (SVM), which uses a custom designed set of sequence-derived features. The features provide information about evolutionary profiles, selected physiochemical properties of amino acids, and predicted disorder, solvent accessibility and B-factors. Empirical evaluation on several datasets shows that MoRFpred outperforms related methods: α-MoRF-Pred that predicts α-MoRFs and ANCHOR which finds disordered regions that become ordered when bound to a globular partner. We show that our predicted (new) MoRF regions have non-random sequence similarity with native MoRFs. We use this observation along with the fact that predictions with higher probability are more accurate to identify putative MoRF regions. We also identify a few sequence-derived hallmarks of MoRFs. They are characterized by dips in the disorder predictions and higher hydrophobicity and stability when compared to adjacent (in the chain) residues. AVAILABILITY: http://biomine.ece.ualberta.ca/MoRFpred/; http://biomine.ece.ualberta.ca/MoRFpred/Supplement.pdf.\",\n \"corpus_id\": 7599398,\n \"score\": 1\n },\n {\n \"doc_id\": \"23732563\",\n \"title\": \"RAPID: fast and accurate sequence-based prediction of intrinsic disorder content on proteomic scale.\",\n \"abstract\": \"Recent research in the protein intrinsic disorder was stimulated by the availability of accurate computational predictors. However, most of these methods are relatively slow, especially considering proteome-scale applications, and were shown to produce relatively large errors when estimating disorder at the protein- (in contrast to residue-) level, which is defined by the fraction/content of disordered residues. To this end, we propose a novel support vector Regression-based Accurate Predictor of Intrinsic Disorder (RAPID). Key advantages of RAPID are speed (prediction of an average-size eukaryotic proteome takes <1h on a modern desktop computer); sophisticated design (multiple, complementary information sources that are aggregated over an input chain are combined using feature selection); and high-quality and robust predictive performance. Empirical tests on two diverse benchmark datasets reveal that RAPID's predictive performance compares favorably to a comprehensive set of state-of-the-art disorder and disorder content predictors. Drawing on high speed and good predictive quality, RAPID was used to perform large-scale characterization of disorder in 200+ fully sequenced eukaryotic proteomes. Our analysis reveals interesting relations of disorder with structural coverage and chain length, and unusual distribution of fully disordered chains. We also performed a comprehensive (using 56000+ annotated chains, which doubles the scope of previous studies) investigation of cellular functions and localizations that are enriched in the disorder in the human proteome. RAPID, which allows for batch (proteome-wide) predictions, is available as a web server at http://biomine.ece.ualberta.ca/RAPID/.\",\n \"corpus_id\": 38597868,\n \"score\": 1\n },\n {\n \"doc_id\": \"23798504\",\n \"title\": \"Genome-scale prediction of proteins with long intrinsically disordered regions.\",\n \"abstract\": \"Proteins with long disordered regions (LDRs), defined as having 30 or more consecutive disordered residues, are abundant in eukaryotes, and these regions are recognized as a distinct class of biologically functional domains. LDRs facilitate various cellular functions and are important for target selection in structural genomics. Motivated by the lack of methods that directly predict proteins with LDRs, we designed Super-fast predictor of proteins with Long Intrinsically DisordERed regions (SLIDER). SLIDER utilizes logistic regression that takes an empirically chosen set of numerical features, which consider selected physicochemical properties of amino acids, sequence complexity, and amino acid composition, as its inputs. Empirical tests show that SLIDER offers competitive predictive performance combined with low computational cost. It outperforms, by at least a modest margin, a comprehensive set of modern disorder predictors (that can indirectly predict LDRs) and is 16 times faster compared to the best currently available disorder predictor. Utilizing our time-efficient predictor, we characterized abundance and functional roles of proteins with LDRs over 110 eukaryotic proteomes. Similar to related studies, we found that eukaryotes have many (on average 30.3%) proteins with LDRs with majority of proteomes having between 25 and 40%, where higher abundance is characteristic to proteomes that have larger proteins. Our first-of-its-kind large-scale functional analysis shows that these proteins are enriched in a number of cellular functions and processes including certain binding events, regulation of catalytic activities, cellular component organization, biogenesis, biological regulation, and some metabolic and developmental processes. A webserver that implements SLIDER is available at http://biomine.ece.ualberta.ca/SLIDER/.\",\n \"corpus_id\": 21229963,\n \"score\": 1\n },\n {\n \"doc_id\": \"24939692\",\n \"title\": \"Exceptionally abundant exceptions: comprehensive characterization of intrinsic disorder in all domains of life.\",\n \"abstract\": \"Recent years witnessed increased interest in intrinsically disordered proteins and regions. These proteins and regions are abundant and possess unique structural features and a broad functional repertoire that complements ordered proteins. However, modern studies on the abundance and functions of intrinsically disordered proteins and regions are relatively limited in size and scope of their analysis. To fill this gap, we performed a broad and detailed computational analysis of over 6 million proteins from 59 archaea, 471 bacterial, 110 eukaryotic and 325 viral proteomes. We used arguably more accurate consensus-based disorder predictions, and for the first time comprehensively characterized intrinsic disorder at proteomic and protein levels from all significant perspectives, including abundance, cellular localization, functional roles, evolution, and impact on structural coverage. We show that intrinsic disorder is more abundant and has a unique profile in eukaryotes. We map disorder into archaea, bacterial and eukaryotic cells, and demonstrate that it is preferentially located in some cellular compartments. Functional analysis that considers over 1,200 annotations shows that certain functions are exclusively implemented by intrinsically disordered proteins and regions, and that some of them are specific to certain domains of life. We reveal that disordered regions are often targets for various post-translational modifications, but primarily in the eukaryotes and viruses. Using a phylogenetic tree for 14 eukaryotic and 112 bacterial species, we analyzed relations between disorder, sequence conservation and evolutionary speed. We provide a complete analysis that clearly shows that intrinsic disorder is exceptionally and uniquely abundant in each domain of life.\",\n \"corpus_id\": 15655242,\n \"score\": 1\n },\n {\n \"doc_id\": \"18293306\",\n \"title\": \"Prediction of protein structural class using novel evolutionary collocation-based sequence representation.\",\n \"abstract\": \"Knowledge of structural classes is useful in understanding of folding patterns in proteins. Although existing structural class prediction methods applied virtually all state-of-the-art classifiers, many of them use a relatively simple protein sequence representation that often includes amino acid (AA) composition. To this end, we propose a novel sequence representation that incorporates evolutionary information encoded using PSI-BLAST profile-based collocation of AA pairs. We used six benchmark datasets and five representative classifiers to quantify and compare the quality of the structural class prediction with the proposed representation. The best, classifier support vector machine achieved 61-96% accuracy on the six datasets. These predictions were comprehensively compared with a wide range of recently proposed methods for prediction of structural classes. Our comprehensive comparison shows superiority of the proposed representation, which results in error rate reductions that range between 14% and 26% when compared with predictions of the best-performing, previously published classifiers on the considered datasets. The study also shows that, for the benchmark dataset that includes sequences characterized by low identity (i.e., 25%, 30%, and 40%), the prediction accuracies are 20-35% lower than for the other three datasets that include sequences with a higher degree of similarity. In conclusion, the proposed representation is shown to substantially improve the accuracy of the structural class prediction. A web server that implements the presented prediction method is freely available at http://biomine.ece.ualberta.ca/Structural_Class/SCEC.html.\",\n \"corpus_id\": 2074142,\n \"score\": 0\n },\n {\n \"doc_id\": \"18452616\",\n \"title\": \"SCPRED: accurate prediction of protein structural class for sequences of twilight-zone similarity with predicting sequences.\",\n \"abstract\": \"BACKGROUND: Protein structure prediction methods provide accurate results when a homologous protein is predicted, while poorer predictions are obtained in the absence of homologous templates. However, some protein chains that share twilight-zone pairwise identity can form similar folds and thus determining structural similarity without the sequence similarity would be desirable for the structure prediction. The folding type of a protein or its domain is defined as the structural class. Current structural class prediction methods that predict the four structural classes defined in SCOP provide up to 63% accuracy for the datasets in which sequence identity of any pair of sequences belongs to the twilight-zone. We propose SCPRED method that improves prediction accuracy for sequences that share twilight-zone pairwise similarity with sequences used for the prediction. RESULTS: SCPRED uses a support vector machine classifier that takes several custom-designed features as its input to predict the structural classes. Based on extensive design that considers over 2300 index-, composition- and physicochemical properties-based features along with features based on the predicted secondary structure and content, the classifier's input includes 8 features based on information extracted from the secondary structure predicted with PSI-PRED and one feature computed from the sequence. Tests performed with datasets of 1673 protein chains, in which any pair of sequences shares twilight-zone similarity, show that SCPRED obtains 80.3% accuracy when predicting the four SCOP-defined structural classes, which is superior when compared with over a dozen recent competing methods that are based on support vector machine, logistic regression, and ensemble of classifiers predictors. CONCLUSION: The SCPRED can accurately find similar structures for sequences that share low identity with sequence used for the prediction. The high predictive accuracy achieved by SCPRED is attributed to the design of the features, which are capable of separating the structural classes in spite of their low dimensionality. We also demonstrate that the SCPRED's predictions can be successfully used as a post-processing filter to improve performance of modern fold classification methods.\",\n \"corpus_id\": 17815381,\n \"score\": 0\n },\n {\n \"doc_id\": \"19003998\",\n \"title\": \"Accurate prediction for atomic-level protein design and its application in diversifying the near-optimal sequence space.\",\n \"abstract\": \"The task of engineering a protein to assume a target three-dimensional structure is known as protein design. Computational search algorithms are devised to predict a minimal energy amino acid sequence for a particular structure. In practice, however, an ensemble of low-energy sequences is often sought. Primarily, this is performed because an individual predicted low-energy sequence may not necessarily fold to the target structure because of both inaccuracies in modeling protein energetics and the nonoptimal nature of search algorithms employed. Additionally, some low-energy sequences may be overly stable and thus lack the dynamic flexibility required for biological functionality. Furthermore, the investigation of low-energy sequence ensembles will provide crucial insights into the pseudo-physical energy force fields that have been derived to describe structural energetics for protein design. Significantly, numerous studies have predicted low-energy sequences, which were subsequently synthesized and demonstrated to fold to desired structures. However, the characterization of the sequence space defined by such energy functions as compatible with a target structure has not been performed in full detail. This issue is critical for protein design scientists to successfully continue using these force fields at an ever-increasing pace and scale. In this paper, we present a conceptually novel algorithm that rapidly predicts the set of lowest energy sequences for a given structure. Based on the theory of probabilistic graphical models, it performs efficient inspection and partitioning of the near-optimal sequence space, without making any assumptions of positional independence. We benchmark its performance on a diverse set of relevant protein design examples and show that it consistently yields sequences of lower energy than those derived from state-of-the-art techniques. Thus, we find that previously presented search techniques do not fully depict the low-energy space as precisely. Examination of the predicted ensembles indicates that, for each structure, the amino acid identity at a majority of positions must be chosen extremely selectively so as to not incur significant energetic penalties. We investigate this high degree of similarity and demonstrate how more diverse near-optimal sequences can be predicted in order to systematically overcome this bottleneck for computational design. Finally, we exploit this in-depth analysis of a collection of the lowest energy sequences to suggest an explanation for previously observed experimental design results. The novel methodologies introduced here accurately portray the sequence space compatible with a protein structure and further supply a scheme to yield heterogeneous low-energy sequences, thus providing a powerful instrument for future work on protein design.\",\n \"corpus_id\": 8014671,\n \"score\": 0\n },\n {\n \"doc_id\": \"20003388\",\n \"title\": \"Modular prediction of protein structural classes from sequences of twilight-zone identity with predicting sequences.\",\n \"abstract\": \"BACKGROUND: Knowledge of structural class is used by numerous methods for identification of structural/functional characteristics of proteins and could be used for the detection of remote homologues, particularly for chains that share twilight-zone similarity. In contrast to existing sequence-based structural class predictors, which target four major classes and which are designed for high identity sequences, we predict seven classes from sequences that share twilight-zone identity with the training sequences. RESULTS: The proposed MODular Approach to Structural class prediction (MODAS) method is unique as it allows for selection of any subset of the classes. MODAS is also the first to utilize a novel, custom-built feature-based sequence representation that combines evolutionary profiles and predicted secondary structure. The features quantify information relevant to the definition of the classes including conservation of residues and arrangement and number of helix/strand segments. Our comprehensive design considers 8 feature selection methods and 4 classifiers to develop Support Vector Machine-based classifiers that are tailored for each of the seven classes. Tests on 5 twilight-zone and 1 high-similarity benchmark datasets and comparison with over two dozens of modern competing predictors show that MODAS provides the best overall accuracy that ranges between 80% and 96.7% (83.5% for the twilight-zone datasets), depending on the dataset. This translates into 19% and 8% error rate reduction when compared against the best performing competing method on two largest datasets. The proposed predictor provides accurate predictions at 58% accuracy for membrane proteins class, which is not considered by majority of existing methods, in spite that this class accounts for only 2% of the data. Our predictive model is analyzed to demonstrate how and why the input features are associated with the corresponding classes. CONCLUSIONS: The improved predictions stem from the novel features that express collocation of the secondary structure segments in the protein sequence and that combine evolutionary and secondary structure information. Our work demonstrates that conservation and arrangement of the secondary structure segments predicted along the protein chain can successfully predict structural classes which are defined based on the spatial arrangement of the secondary structures. A web server is available at http://biomine.ece.ualberta.ca/MODAS/.\",\n \"corpus_id\": 5564894,\n \"score\": 0\n },\n {\n \"doc_id\": \"20730460\",\n \"title\": \"iFC²: an integrated web-server for improved prediction of protein structural class, fold type, and secondary structure content.\",\n \"abstract\": \"Several descriptors of protein structure at the sequence and residue levels have been recently proposed. They are widely adopted in the analysis and prediction of structural and functional characteristics of proteins. Numerous in silico methods have been developed for sequence-based prediction of these descriptors. However, many of them do not have a public web-server and only a few integrate multiple descriptors to improve the predictions. We introduce iFC² (integrated prediction of fold, class, and content) server that is the first to integrate three modern predictors of sequence-level descriptors. They concern fold type (PFRES), structural class (SCEC), and secondary structure content (PSSC-core). The server exploits relations between the three descriptors to implement a cross-evaluation procedure that improves over the predictions of the individual methods. The iFC² annotates fold and class predictions as potentially correct/incorrect. When tested on datasets with low-similarity chains, for the fold prediction iFC² labels 82% of the PFRES predictions as correct and the accuracy of these predictions equals 72%. The accuracy of the remaining 28% of the PFRES predictions equals 38%. Similarly, our server assigns correct labels for over 79% of SCEC predictions, which are shown to be 98% accurate, while the remaining SCEC predictions are only 15% accurate. These results are shown to be competitive when contrasted against recent relevant web-servers. Predictions on CASP8 targets show that the content predicted by iFC² is competitive when compared with the content computed from the tertiary structures predicted by three best-performing methods in CASP8. The iFC² server is available at http://biomine.ece.ualberta.ca/1D/1D.html .\",\n \"corpus_id\": 6644489,\n \"score\": 0\n },\n {\n \"doc_id\": \"21064129\",\n \"title\": \"Improved identification of outer membrane beta barrel proteins using primary sequence, predicted secondary structure, and evolutionary information.\",\n \"abstract\": \"Membrane proteins (MPs) are difficult to identify in genomes and to crystallize, making it hard to determine their tertiary structures. MPs could be categorized into α-helical (AMP) and outer membrane proteins which mostly include beta barrel folds (OMBBs). The AMPs are relatively easy to predict from a protein sequence because they usually include several long membrane-spanning hydrophobic α-helices. The OMBBs play important roles in cell biology, they are targeted by multiple drugs, and they are more challenging to identify as they have shorter membrane-spanning regions which lack a folding pattern, that is, as consistent as in the case of the AMPs. Hence, accurate in silico methods for prediction of OMBBs from their primary sequences are needed. We present an accurate sequence-based predictor of OMBBs, called OMBBpred, which utilizes a Support Vector Machine classifier and a custom-designed set of 34 novel numerical descriptors derived from predicted secondary structures, hydrophobicity, and evolutionary information. Our method outperforms modern existing OMBB predictors and achieves accuracy of above 98% when tested on two existing benchmark datasets and 96% on a new large dataset. OMBBpred reduces the error rates of the second best method, depending on the dataset used, by between 13 and 65%, and generates predictions with high specificity of above 96%. Our solution is a useful tool for high-throughput discovery of the OMBBs on a genome scale and can be found at http://biomine.ece. ualberta.ca/OMBBpred/OMBBpred.htm.\",\n \"corpus_id\": 23725010,\n \"score\": 0\n },\n {\n \"doc_id\": \"21082205\",\n \"title\": \"Determination of protein folding kinetic types using sequence and predicted secondary structure and solvent accessibility.\",\n \"abstract\": \"Proteins fold through a two-state (TS), with no visible intermediates, or a multi-state (MS), via at least one intermediate, process. We analyze sequence-derived factors that determine folding types by introducing a novel sequence-based folding type predictor called FOKIT. This method implements a logistic regression model with six input features which hybridize information concerning amino acid composition and predicted secondary structure and solvent accessibility. FOKIT provides predictions with average Matthews correlation coefficient (MCC) between 0.58 and 0.91 measured using out-of-sample tests on four benchmark datasets. These results are shown to be competitive or better than results of four modern predictors. We also show that FOKIT outperforms these methods when predicting chains that share low similarity with the chains used to build the model, which is an important advantage given the limited number of annotated chains. We demonstrate that inclusion of solvent accessibility helps in discrimination of the folding kinetic types and that three of the features constitute statistically significant markers that differentiate TS and MS folders. We found that the increased content of exposed Trp and buried Leu are indicative of the MS folding, which implies that the exposure/burial of certain hydrophobic residues may play important role in the formation of the folding intermediates. Our conclusions are supported by two case studies.\",\n \"corpus_id\": 1068604,\n \"score\": 0\n },\n {\n \"doc_id\": \"21685077\",\n \"title\": \"Sequence-based prediction of protein crystallization, purification and production propensity.\",\n \"abstract\": \"MOTIVATION: X-ray crystallography-based protein structure determination, which accounts for majority of solved structures, is characterized by relatively low success rates. One solution is to build tools which support selection of targets that are more likely to crystallize. Several in silico methods that predict propensity of diffraction-quality crystallization from protein chains were developed. We show that the quality of their predictions drops when applied to more recent crystallization trails, which calls for new solutions. We propose a novel approach that alleviates drawbacks of the existing methods by using a recent dataset and improved protocol to annotate progress along the crystallization process, by predicting the success of the entire process and steps which result in the failed attempts, and by utilizing a compact and comprehensive set of sequence-derived inputs to generate accurate predictions. RESULTS: The proposed PPCpred (predictor of protein Production, Purification and Crystallization) predict propensity for production of diffraction-quality crystals, production of crystals, purification and production of the protein material. PPCpred utilizes comprehensive set of inputs based on energy and hydrophobicity indices, composition of certain amino acid types, predicted disorder, secondary structure and solvent accessibility, and content of certain buried and exposed residues. Our method significantly outperforms alignment-based predictions and several modern crystallization propensity predictors. Receiver operating characteristic (ROC) curves show that PPCpred is particularly useful for users who desire high true positive (TP) rates, i.e. low rate of mispredictions for solvable chains. Our model reveals several intuitive factors that influence the success of individual steps and the entire crystallization process, including the content of Cys, buried His and Ser, hydrophobic/hydrophilic segments and the number of predicted disordered segments. AVAILABILITY: http://biomine.ece.ualberta.ca/PPCpred/. CONTACT: lkurgan@ece.ualberta.ca.\",\n \"corpus_id\": 14878897,\n \"score\": 0\n },\n {\n \"doc_id\": \"21919861\",\n \"title\": \"CRYSpred: accurate sequence-based protein crystallization propensity prediction using sequence-derived structural characteristics.\",\n \"abstract\": \"Relatively low success rates of X-ray crystallography, which is the most popular method for solving proteins structures, motivate development of novel methods that support selection of tractable protein targets. This aspect is particularly important in the context of the current structural genomics efforts that allow for a certain degree of flexibility in the target selection. We propose CRYSpred, a novel in-silico crystallization propensity predictor that uses a set of 15 novel features which utilize a broad range of inputs including charge, hydrophobicity, and amino acid composition derived from the protein chain, and the solvent accessibility and disorder predicted from the protein sequence. Our method outperforms seven modern crystallization propensity predictors on three, independent from training dataset, benchmark test datasets. The strong predictive performance offered by the CRYSpred is attributed to the careful design of the features, utilization of the comprehensive set of inputs, and the usage of the Support Vector Machine classifier. The inputs utilized by CRYSpred are well-aligned with the existing rules-of-thumb that are used in the structural genomics studies.\",\n \"corpus_id\": 6091681,\n \"score\": 0\n },\n {\n \"doc_id\": \"22165846\",\n \"title\": \"ATPsite: sequence-based prediction of ATP-binding residues.\",\n \"abstract\": \"BACKGROUND: ATP is a ubiquitous nucleotide that provides energy for cellular activities, catalyzes chemical reactions, and is involved in cellular signalling. The knowledge of the ATP-protein interactions helps with annotation of protein functions and finds applications in drug design. The sequence to structure annotation gap motivates development of high-throughput sequence-based predictors of the ATP-binding residues. Moreover, our empirical tests show that the only existing predictor, ATPint, is characterized by relatively low predictive quality. METHODS: We propose a novel, high-throughput machine learning-based predictor, ATPsite, which identifies ATP-binding residues from protein sequences. Our predictor utilizes Support Vector Machine classifier and a comprehensive set of input features that are based on the sequence, evolutionary profiles, and the sequence-predicted structural descriptors including secondary structure, solvent accessibility, and dihedral angles. RESULTS: The ATPsite achieves significantly higher Mathews Correlation Coefficient (MCC) and Area Under the ROC Curve (AUC) values when compared with the existing methods including the ATPint, conservation-based rate4site, and alignment-based BLAST predictors. We also assessed the effectiveness of individual input types. The PSSM profile, the conservation scores, and certain features based on amino acid groups are shown to be more effective in predicting the ATP-binding residues than the remaining feature groups. CONCLUSIONS: Statistical tests show that ATPsite significantly outperforms existing solutions. The consensus of the ATPsite with the sequence-alignment based predictor is shown to give further improvements.\",\n \"corpus_id\": 590014,\n \"score\": 0\n },\n {\n \"doc_id\": \"22272076\",\n \"title\": \"Prediction of lysine ubiquitylation with ensemble classifier and feature selection.\",\n \"abstract\": \"Ubiquitylation is an important process of post-translational modification. Correct identification of protein lysine ubiquitylation sites is of fundamental importance to understand the molecular mechanism of lysine ubiquitylation in biological systems. This paper develops a novel computational method to effectively identify the lysine ubiquitylation sites based on the ensemble approach. In the proposed method, 468 ubiquitylation sites from 323 proteins retrieved from the Swiss-Prot database were encoded into feature vectors by using four kinds of protein sequences information. An effective feature selection method was then applied to extract informative feature subsets. After different feature subsets were obtained by setting different starting points in the search procedure, they were used to train multiple random forests classifiers and then aggregated into a consensus classifier by majority voting. Evaluated by jackknife tests and independent tests respectively, the accuracy of the proposed predictor reached 76.82% for the training dataset and 79.16% for the test dataset, indicating that this predictor is a useful tool to predict lysine ubiquitylation sites. Furthermore, site-specific feature analysis was performed and it was shown that ubiquitylation is intimately correlated with the features of its surrounding sites in addition to features derived from the lysine site itself. The feature selection method is available upon request.\",\n \"corpus_id\": 2877306,\n \"score\": 0\n },\n {\n \"doc_id\": \"22545993\",\n \"title\": \"Accurate prediction of protein structural classes using functional domains and predicted secondary structure sequences.\",\n \"abstract\": \"Protein structural class prediction is one of the challenging problems in bioinformatics. Previous methods directly based on the similarity of amino acid (AA) sequences have been shown to be insufficient for low-similarity protein data-sets. To improve the prediction accuracy for such low-similarity proteins, different methods have been recently proposed that explore the novel feature sets based on predicted secondary structure propensities. In this paper, we focus on protein structural class prediction using combinations of the novel features including secondary structure propensities as well as functional domain (FD) features extracted from the InterPro signature database. Our comprehensive experimental results based on several benchmark data-sets have shown that the integration of new FD features substantially improves the accuracy of structural class prediction for low-similarity proteins as they capture meaningful relationships among AA residues that are far away in protein sequence. The proposed prediction method has also been tested to predict structural classes for partially disordered proteins with the reasonable prediction accuracy, which is a more difficult problem comparing to structural class prediction for commonly used benchmark data-sets and has never been done before to the best of our knowledge. In addition, to avoid overfitting with a large number of features, feature selection is applied to select discriminating features that contribute to achieve high prediction accuracy. The selected features have been shown to achieve stable prediction performance across different benchmark data-sets.\",\n \"corpus_id\": 28689690,\n \"score\": 0\n },\n {\n \"doc_id\": \"22555647\",\n \"title\": \"AMS 4.0: consensus prediction of post-translational modifications in protein sequences.\",\n \"abstract\": \"We present here the 2011 update of the AutoMotif Service (AMS 4.0) that predicts the wide selection of 88 different types of the single amino acid post-translational modifications (PTM) in protein sequences. The selection of experimentally confirmed modifications is acquired from the latest UniProt and Phospho. ELM databases for training. The sequence vicinity of each modified residue is represented using amino acids physico-chemical features encoded using high quality indices (HQI) obtaining by automatic clustering of known indices extracted from AAindex database. For each type of the numerical representation, the method builds the ensemble of Multi-Layer Perceptron (MLP) pattern classifiers, each optimising different objectives during the training (for example the recall, precision or area under the ROC curve (AUC)). The consensus is built using brainstorming technology, which combines multi-objective instances of machine learning algorithm, and the data fusion of different training objects representations, in order to boost the overall prediction accuracy of conserved short sequence motifs. The performance of AMS 4.0 is compared with the accuracy of previous versions, which were constructed using single machine learning methods (artificial neural networks, support vector machine). Our software improves the average AUC score of the earlier version by close to 7 % as calculated on the test datasets of all 88 PTM types. Moreover, for the selected most-difficult sequence motifs types it is able to improve the prediction performance by almost 32 %, when compared with previously used single machine learning methods. Summarising, the brainstorming consensus meta-learning methodology on the average boosts the AUC score up to around 89 %, averaged over all 88 PTM types. Detailed results for single machine learning methods and the consensus methodology are also provided, together with the comparison to previously published methods and state-of-the-art software tools. The source code and precompiled binaries of brainstorming tool are available at http://code.google.com/p/automotifserver/ under Apache 2.0 licensing.\",\n \"corpus_id\": 16117028,\n \"score\": 0\n },\n {\n \"doc_id\": \"22723837\",\n \"title\": \"Accurate prediction of protein structural class.\",\n \"abstract\": \"Because of the increasing gap between the data from sequencing and structural genomics, the accurate prediction of the structural class of a protein domain solely from the primary sequence has remained a challenging problem in structural biology. Traditional sequence-based predictors generally select several sequence features and then feed them directly into a classification program to identify the structural class. The current best sequence-based predictor achieved an overall accuracy of 74.1% when tested on a widely used, non-homologous benchmark dataset 25PDB. In the present work, we built a multiple linear regression (MLR) model to convert the 440-dimensional (440D) sequence feature vector extracted from the Position Specific Scoring Matrix (PSSM) of a protein domain to a 4-dimensinal (4D) structural feature vector, which could then be used to predict the four major structural classes. We performed 10-fold cross-validation and jackknife tests of the method on a large non-homologous dataset containing 8,244 domains distributed among the four major classes. The performance of our approach outperformed all of the existing sequence-based methods and had an overall accuracy of 83.1%, which is even higher than the results of those predicted secondary structure-based methods.\",\n \"corpus_id\": 17465367,\n \"score\": 0\n },\n {\n \"doc_id\": \"22761950\",\n \"title\": \"BEST: improved prediction of B-cell epitopes from antigen sequences.\",\n \"abstract\": \"Accurate identification of immunogenic regions in a given antigen chain is a difficult and actively pursued problem. Although accurate predictors for T-cell epitopes are already in place, the prediction of the B-cell epitopes requires further research. We overview the available approaches for the prediction of B-cell epitopes and propose a novel and accurate sequence-based solution. Our BEST (B-cell Epitope prediction using Support vector machine Tool) method predicts epitopes from antigen sequences, in contrast to some method that predict only from short sequence fragments, using a new architecture based on averaging selected scores generated from sliding 20-mers by a Support Vector Machine (SVM). The SVM predictor utilizes a comprehensive and custom designed set of inputs generated by combining information derived from the chain, sequence conservation, similarity to known (training) epitopes, and predicted secondary structure and relative solvent accessibility. Empirical evaluation on benchmark datasets demonstrates that BEST outperforms several modern sequence-based B-cell epitope predictors including ABCPred, method by Chen et al. (2007), BCPred, COBEpro, BayesB, and CBTOPE, when considering the predictions from antigen chains and from the chain fragments. Our method obtains a cross-validated area under the receiver operating characteristic curve (AUC) for the fragment-based prediction at 0.81 and 0.85, depending on the dataset. The AUCs of BEST on the benchmark sets of full antigen chains equal 0.57 and 0.6, which is significantly and slightly better than the next best method we tested. We also present case studies to contrast the propensity profiles generated by BEST and several other methods.\",\n \"corpus_id\": 9088745,\n \"score\": 0\n },\n {\n \"doc_id\": \"23110141\",\n \"title\": \"Accurate prediction of protein catalytic residues by side chain orientation and residue contact density.\",\n \"abstract\": \"Prediction of protein catalytic residues provides useful information for the studies of protein functions. Most of the existing methods combine both structure and sequence information but heavily rely on sequence conservation from multiple sequence alignments. The contribution of structure information is usually less than that of sequence conservation in existing methods. We found a novel structure feature, residue side chain orientation, which is the first structure-based feature that achieves prediction results comparable to that of evolutionary sequence conservation. We developed a structure-based method, Enzyme Catalytic residue SIde-chain Arrangement (EXIA), which is based on residue side chain orientations and backbone flexibility of protein structure. The prediction that uses EXIA outperforms existing structure-based features. The prediction quality of combing EXIA and sequence conservation exceeds that of the state-of-the-art prediction methods. EXIA is designed to predict catalytic residues from single protein structure without needing sequence or structure alignments. It provides invaluable information when there is no sufficient or reliable homology information for target protein. We found that catalytic residues have very special side chain orientation and designed the EXIA method based on the newly discovered feature. It was also found that EXIA performs well for a dataset of enzymes without any bounded ligand in their crystallographic structures.\",\n \"corpus_id\": 17268599,\n \"score\": 0\n },\n {\n \"doc_id\": \"23298369\",\n \"title\": \"Comprehensively designed consensus of standalone secondary structure predictors improves Q3 by over 3%.\",\n \"abstract\": \"Protein fold is defined by a spatial arrangement of three types of secondary structures (SSs) including helices, sheets, and coils/loops. Current methods that predict SS from sequences rely on complex machine learning-derived models and provide the three-state accuracy (Q3) at about 82%. Further improvements in predictive quality could be obtained with a consensus-based approach, which so far received limited attention. We perform first-of-its-kind comprehensive design of a SS consensus predictor (SScon), in which we consider 12 modern standalone SS predictors and utilize Support Vector Machine (SVM) to combine their predictions. Using a large benchmark data-set with 10 random training-test splits, we show that a simple, voting-based consensus of carefully selected base methods improves Q3 by 1.9% when compared to the best single predictor. Use of SVM provides additional 1.4% improvement with the overall Q3 at 85.6% and segment overlap (SOV3) at 83.7%, when compared to 82.3 and 80.9%, respectively, obtained by the best individual methods. We also show strong improvements when the consensus is based on ab-initio methods, with Q3 = 82.3% and SOV3 = 80.7% that match the results from the best template-based approaches. Our consensus reduces the number of significant errors where helix is confused with a strand, provides particularly good results for short helices and strands, and gives the most accurate estimates of the content of individual SSs in the chain. Case studies are used to visualize the improvements offered by the consensus at the residue level. A web-server and a standalone implementation of SScon are available at http://biomine.ece.ualberta.ca/SSCon/ .\",\n \"corpus_id\": 31483068,\n \"score\": 0\n },\n {\n \"doc_id\": \"23504705\",\n \"title\": \"Accurate prediction of hot spot residues through physicochemical characteristics of amino acid sequences.\",\n \"abstract\": \"Hot spot residues of proteins are fundamental interface residues that help proteins perform their functions. Detecting hot spots by experimental methods is costly and time-consuming. Sequential and structural information has been widely used in the computational prediction of hot spots. However, structural information is not always available. In this article, we investigated the problem of identifying hot spots using only physicochemical characteristics extracted from amino acid sequences. We first extracted 132 relatively independent physicochemical features from a set of the 544 properties in AAindex1, an amino acid index database. Each feature was utilized to train a classification model with a novel encoding schema for hot spot prediction by the IBk algorithm, an extension of the K-nearest neighbor algorithm. The combinations of the individual classifiers were explored and the classifiers that appeared frequently in the top performing combinations were selected. The hot spot predictor was built based on an ensemble of these classifiers and to work in a voting manner. Experimental results demonstrated that our method effectively exploited the feature space and allowed flexible weights of features for different queries. On the commonly used hot spot benchmark sets, our method significantly outperformed other machine learning algorithms and state-of-the-art hot spot predictors. The program is available at http://sfb.kaust.edu.sa/pages/software.aspx.\",\n \"corpus_id\": 5236261,\n \"score\": 0\n },\n {\n \"doc_id\": \"24846307\",\n \"title\": \"RNABindRPlus: a predictor that combines machine learning and sequence homology-based methods to improve the reliability of predicted RNA-binding residues in proteins.\",\n \"abstract\": \"Protein-RNA interactions are central to essential cellular processes such as protein synthesis and regulation of gene expression and play roles in human infectious and genetic diseases. Reliable identification of protein-RNA interfaces is critical for understanding the structural bases and functional implications of such interactions and for developing effective approaches to rational drug design. Sequence-based computational methods offer a viable, cost-effective way to identify putative RNA-binding residues in RNA-binding proteins. Here we report two novel approaches: (i) HomPRIP, a sequence homology-based method for predicting RNA-binding sites in proteins; (ii) RNABindRPlus, a new method that combines predictions from HomPRIP with those from an optimized Support Vector Machine (SVM) classifier trained on a benchmark dataset of 198 RNA-binding proteins. Although highly reliable, HomPRIP cannot make predictions for the unaligned parts of query proteins and its coverage is limited by the availability of close sequence homologs of the query protein with experimentally determined RNA-binding sites. RNABindRPlus overcomes these limitations. We compared the performance of HomPRIP and RNABindRPlus with that of several state-of-the-art predictors on two test sets, RB44 and RB111. On a subset of proteins for which homologs with experimentally determined interfaces could be reliably identified, HomPRIP outperformed all other methods achieving an MCC of 0.63 on RB44 and 0.83 on RB111. RNABindRPlus was able to predict RNA-binding residues of all proteins in both test sets, achieving an MCC of 0.55 and 0.37, respectively, and outperforming all other methods, including those that make use of structure-derived features of proteins. More importantly, RNABindRPlus outperforms all other methods for any choice of tradeoff between precision and recall. An important advantage of both HomPRIP and RNABindRPlus is that they rely on readily available sequence and sequence-derived features of RNA-binding proteins. A webserver implementation of both methods is freely available at http://einstein.cs.iastate.edu/RNABindRPlus/.\",\n \"corpus_id\": 13527970,\n \"score\": 0\n },\n {\n \"doc_id\": \"25189131\",\n \"title\": \"Enhancing protein-vitamin binding residues prediction by multiple heterogeneous subspace SVMs ensemble.\",\n \"abstract\": \"BACKGROUND: Vitamins are typical ligands that play critical roles in various metabolic processes. The accurate identification of the vitamin-binding residues solely based on a protein sequence is of significant importance for the functional annotation of proteins, especially in the post-genomic era, when large volumes of protein sequences are accumulating quickly without being functionally annotated. RESULTS: In this paper, a new predictor called TargetVita is designed and implemented for predicting protein-vitamin binding residues using protein sequences. In TargetVita, features derived from the position-specific scoring matrix (PSSM), predicted protein secondary structure, and vitamin binding propensity are combined to form the original feature space; then, several feature subspaces are selected by performing different feature selection methods. Finally, based on the selected feature subspaces, heterogeneous SVMs are trained and then ensembled for performing prediction. CONCLUSIONS: The experimental results obtained with four separate vitamin-binding benchmark datasets demonstrate that the proposed TargetVita is superior to the state-of-the-art vitamin-specific predictor, and an average improvement of 10% in terms of the Matthews correlation coefficient (MCC) was achieved over independent validation tests. The TargetVita web server and the datasets used are freely available for academic use at http://csbio.njust.edu.cn/bioinf/TargetVita or http://www.csbio.sjtu.edu.cn/bioinf/TargetVita.\",\n \"corpus_id\": 18756547,\n \"score\": 0\n },\n {\n \"doc_id\": \"25637562\",\n \"title\": \"Computational identification of MoRFs in protein sequences.\",\n \"abstract\": \"MOTIVATION: Intrinsically disordered regions of proteins play an essential role in the regulation of various biological processes. Key to their regulatory function is the binding of molecular recognition features (MoRFs) to globular protein domains in a process known as a disorder-to-order transition. Predicting the location of MoRFs in protein sequences with high accuracy remains an important computational challenge. METHOD: In this study, we introduce MoRFCHiBi, a new computational approach for fast and accurate prediction of MoRFs in protein sequences. MoRFCHiBi combines the outcomes of two support vector machine (SVM) models that take advantage of two different kernels with high noise tolerance. The first, SVMS, is designed to extract maximal information from the general contrast in amino acid compositions between MoRFs, their surrounding regions (Flanks), and the remainders of the sequences. The second, SVMT, is used to identify similarities between regions in a query sequence and MoRFs of the training set. RESULTS: We evaluated the performance of our predictor by comparing its results with those of two currently available MoRF predictors, MoRFpred and ANCHOR. Using three test sets that have previously been collected and used to evaluate MoRFpred and ANCHOR, we demonstrate that MoRFCHiBi outperforms the other predictors with respect to different evaluation metrics. In addition, MoRFCHiBi is downloadable and fast, which makes it useful as a component in other computational prediction tools. AVAILABILITY AND IMPLEMENTATION: http://www.chibi.ubc.ca/morf/.\",\n \"corpus_id\": 16498676,\n \"score\": 0\n },\n {\n \"doc_id\": \"25713596\",\n \"title\": \"Algorithmic approaches to protein-protein interaction site prediction.\",\n \"abstract\": \"Interaction sites on protein surfaces mediate virtually all biological activities, and their identification holds promise for disease treatment and drug design. Novel algorithmic approaches for the prediction of these sites have been produced at a rapid rate, and the field has seen significant advancement over the past decade. However, the most current methods have not yet been reviewed in a systematic and comprehensive fashion. Herein, we describe the intricacies of the biological theory, datasets, and features required for modern protein-protein interaction site (PPIS) prediction, and present an integrative analysis of the state-of-the-art algorithms and their performance. First, the major sources of data used by predictors are reviewed, including training sets, evaluation sets, and methods for their procurement. Then, the features employed and their importance in the biological characterization of PPISs are explored. This is followed by a discussion of the methodologies adopted in contemporary prediction programs, as well as their relative performance on the datasets most recently used for evaluation. In addition, the potential utility that PPIS identification holds for rational drug design, hotspot prediction, and computational molecular docking is described. Finally, an analysis of the most promising areas for future development of the field is presented.\",\n \"corpus_id\": 8720300,\n \"score\": 0\n },\n {\n \"doc_id\": \"25935161\",\n \"title\": \"A comprehensive comparative review of sequence-based predictors of DNA- and RNA-binding residues.\",\n \"abstract\": \"Motivated by the pressing need to characterize protein-DNA and protein-RNA interactions on large scale, we review a comprehensive set of 30 computational methods for high-throughput prediction of RNA- or DNA-binding residues from protein sequences. We summarize these predictors from several significant perspectives including their design, outputs and availability. We perform empirical assessment of methods that offer web servers using a new benchmark data set characterized by a more complete annotation that includes binding residues transferred from the same or similar proteins. We show that predictors of DNA-binding (RNA-binding) residues offer relatively strong predictive performance but they are unable to properly separate DNA- from RNA-binding residues. We design and empirically assess several types of consensuses and demonstrate that machine learning (ML)-based approaches provide improved predictive performance when compared with the individual predictors of DNA-binding residues or RNA-binding residues. We also formulate and execute first-of-its-kind study that targets combined prediction of DNA- and RNA-binding residues. We design and test three types of consensuses for this prediction and conclude that this novel approach that relies on ML design provides better predictive quality than individual predictors when tested on prediction of DNA- and RNA-binding residues individually. It also substantially improves discrimination between these two types of nucleic acids. Our results suggest that development of a new generation of predictors would benefit from using training data sets that combine both RNA- and DNA-binding proteins, designing new inputs that specifically target either DNA- or RNA-binding residues and pursuing combined prediction of DNA- and RNA-binding residues.\",\n \"corpus_id\": 26243792,\n \"score\": 0\n },\n {\n \"doc_id\": \"26017462\",\n \"title\": \"ADPRtool: A novel predicting model for identification of ASP-ADP-Ribosylation sites of human proteins.\",\n \"abstract\": \"Post-translational modifications (PTMs) occur in the vast majority of proteins, and they are essential for many protein functions. Computational prediction of the residue location of PTMs enhances the functional characterization of proteins. ADP-Ribosylation is an important type of PTM, because it is implicated in apoptosis, DNA repair, regulation of cell proliferation, and protein synthesis. However, mass spectrometric approaches have difficulties in identifying a vast number of protein ADP-Ribosylation sites. Therefore, a computational method for predicting ADP-Ribosylation sites of human proteins seems useful and necessary. Four types of sequence features and an incremental feature selection technique are utilized to predict protein ADP-Ribosylation sites. The final feature set for ADPR prediction modeling is optimized, based on a minimum redundancy maximum relevance criterion, so as to make more accurate predictions on aspartic acid ADPR modified residues. Our prediction model, ADPRtool, is capable to predict Asp-ADP-Ribosylation sites with a total accuracy of 85.45%, which is as good as most computational PTM site predictors. By using a sequence-based computational method, a new ADP-Ribosylation site prediction model - ADPRtool, is developed, and it has shown great accuracies with total accuracy, Matthew's correlation coefficient and area under receiver operating characteristic curve.\",\n \"corpus_id\": 13116260,\n \"score\": 0\n },\n {\n \"doc_id\": \"26020952\",\n \"title\": \"Accurate prediction of immunogenic T-cell epitopes from epitope sequences using the genetic algorithm-based ensemble learning.\",\n \"abstract\": \"BACKGROUND: T-cell epitopes play the important role in T-cell immune response, and they are critical components in the epitope-based vaccine design. Immunogenicity is the ability to trigger an immune response. The accurate prediction of immunogenic T-cell epitopes is significant for designing useful vaccines and understanding the immune system. METHODS: In this paper, we attempt to differentiate immunogenic epitopes from non-immunogenic epitopes based on their primary structures. First of all, we explore a variety of sequence-derived features, and analyze their relationship with epitope immunogenicity. To effectively utilize various features, a genetic algorithm (GA)-based ensemble method is proposed to determine the optimal feature subset and develop the high-accuracy ensemble model. In the GA optimization, a chromosome is to represent a feature subset in the search space. For each feature subset, the selected features are utilized to construct the base predictors, and an ensemble model is developed by taking the average of outputs from base predictors. The objective of GA is to search for the optimal feature subset, which leads to the ensemble model with the best cross validation AUC (area under ROC curve) on the training set. RESULTS: Two datasets named 'IMMA2' and 'PAAQD' are adopted as the benchmark datasets. Compared with the state-of-the-art methods POPI, POPISK, PAAQD and our previous method, the GA-based ensemble method produces much better performances, achieving the AUC score of 0.846 on IMMA2 dataset and the AUC score of 0.829 on PAAQD dataset. The statistical analysis demonstrates the performance improvements of GA-based ensemble method are statistically significant. CONCLUSIONS: The proposed method is a promising tool for predicting the immunogenic epitopes. The source codes and datasets are available in S1 File.\",\n \"corpus_id\": 1329354,\n \"score\": 0\n },\n {\n \"doc_id\": \"26109352\",\n \"title\": \"High-throughput prediction of RNA, DNA and protein binding regions mediated by intrinsic disorder.\",\n \"abstract\": \"Intrinsically disordered proteins and regions (IDPs and IDRs) lack stable 3D structure under physiological conditions in-vitro, are common in eukaryotes, and facilitate interactions with RNA, DNA and proteins. Current methods for prediction of IDPs and IDRs do not provide insights into their functions, except for a handful of methods that address predictions of protein-binding regions. We report first-of-its-kind computational method DisoRDPbind for high-throughput prediction of RNA, DNA and protein binding residues located in IDRs from protein sequences. DisoRDPbind is implemented using a runtime-efficient multi-layered design that utilizes information extracted from physiochemical properties of amino acids, sequence complexity, putative secondary structure and disorder and sequence alignment. Empirical tests demonstrate that it provides accurate predictions that are competitive with other predictors of disorder-mediated protein binding regions and complementary to the methods that predict RNA- and DNA-binding residues annotated based on crystal structures. Application in Homo sapiens, Mus musculus, Caenorhabditis elegans and Drosophila melanogaster proteomes reveals that RNA- and DNA-binding proteins predicted by DisoRDPbind complement and overlap with the corresponding known binding proteins collected from several sources. Also, the number of the putative protein-binding regions predicted with DisoRDPbind correlates with the promiscuity of proteins in the corresponding protein-protein interaction networks. Webserver: http://biomine.ece.ualberta.ca/DisoRDPbind/.\",\n \"corpus_id\": 13883311,\n \"score\": 0\n },\n {\n \"doc_id\": \"26478747\",\n \"title\": \"Prediction of protein solvent accessibility using PSO-SVR with multiple sequence-derived features and weighted sliding window scheme.\",\n \"abstract\": \"BACKGROUND: The prediction of solvent accessibility could provide valuable clues for analyzing protein structure and functions, such as protein 3-Dimensional structure and B-cell epitope prediction. To fully decipher the protein-protein interaction process, an initial but crucial step is to calculate the protein solvent accessibility, especially when the tertiary structure of the protein is unknown. Although some efforts have been put into the protein solvent accessibility prediction, the performance of existing methods is far from satisfaction. METHODS: In order to develop the high-accuracy model, we focus on some possible aspects concerning the prediction performance, including several sequence-derived features, a weighted sliding window scheme and the parameters optimization of machine learning approach. To address above issues, we take following strategies. Firstly, we explore various features which have been observed to be associated with the residue solvent accessibility. These discriminative features include protein evolutionary information, predicted protein secondary structure, native disorder, physicochemical propensities and several sequence-based structural descriptors of residues. Secondly, the different contributions of adjacent residues in sliding window are observed, thus a weighted sliding window scheme is proposed to differentiate the contributions of adjacent residues on the central residue. Thirdly, particle swarm optimization (PSO) is employed to search the global best parameters for the proposed predictor. RESULTS: Evaluated by 3-fold cross-validation, our method achieves the mean absolute error (MAE) of 14.1% and the person correlation coefficient (PCC) of 0.75 for our new-compiled dataset. When compared with the state-of-the-art prediction models in the two benchmark datasets, our method demonstrates better performance. Experimental results demonstrate that our PSAP achieves high performances and outperforms many existing predictors. A web server called PSAP is built and freely available at http://59.73.198.144:8088/SolventAccessibility/.\",\n \"corpus_id\": 4912166,\n \"score\": 0\n },\n {\n \"doc_id\": \"27274091\",\n \"title\": \"Consensus protein design.\",\n \"abstract\": \"A popular and successful strategy in semi-rational design of protein stability is the use of evolutionary information encapsulated in homologous protein sequences. Consensus design is based on the hypothesis that at a given position, the respective consensus amino acid contributes more than average to the stability of the protein than non-conserved amino acids. Here, we review the consensus design approach, its theoretical underpinnings, successes, limitations and challenges, as well as providing a detailed guide to its application in protein engineering.\",\n \"corpus_id\": 15164229,\n \"score\": 0\n },\n {\n \"doc_id\": \"27307636\",\n \"title\": \"DFLpred: High-throughput prediction of disordered flexible linker regions in protein sequences.\",\n \"abstract\": \"MOTIVATION: Disordered flexible linkers (DFLs) are disordered regions that serve as flexible linkers/spacers in multi-domain proteins or between structured constituents in domains. They are different from flexible linkers/residues because they are disordered and longer. Availability of experimentally annotated DFLs provides an opportunity to build high-throughput computational predictors of these regions from protein sequences. To date, there are no computational methods that directly predict DFLs and they can be found only indirectly by filtering predicted flexible residues with predictions of disorder. RESULTS: We conceptualized, developed and empirically assessed a first-of-its-kind sequence-based predictor of DFLs, DFLpred. This method outputs propensity to form DFLs for each residue in the input sequence. DFLpred uses a small set of empirically selected features that quantify propensities to form certain secondary structures, disordered regions and structured regions, which are processed by a fast linear model. Our high-throughput predictor can be used on the whole-proteome scale; it needs <1 h to predict entire proteome on a single CPU. When assessed on an independent test dataset with low sequence-identity proteins, it secures area under the receiver operating characteristic curve equal 0.715 and outperforms existing alternatives that include methods for the prediction of flexible linkers, flexible residues, intrinsically disordered residues and various combinations of these methods. Prediction on the complete human proteome reveals that about 10% of proteins have a large content of over 30% DFL residues. We also estimate that about 6000 DFL regions are long with ≥30 consecutive residues. AVAILABILITY AND IMPLEMENTATION: http://biomine.ece.ualberta.ca/DFLpred/ CONTACT: lkurgan@vcu.edu SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.\",\n \"corpus_id\": 35835604,\n \"score\": 0\n },\n {\n \"doc_id\": \"27777222\",\n \"title\": \"Comprehensive assessment and performance improvement of effector protein predictors for bacterial secretion systems III, IV and VI.\",\n \"abstract\": \"Bacterial effector proteins secreted by various protein secretion systems play crucial roles in host-pathogen interactions. In this context, computational tools capable of accurately predicting effector proteins of the various types of bacterial secretion systems are highly desirable. Existing computational approaches use different machine learning (ML) techniques and heterogeneous features derived from protein sequences and/or structural information. These predictors differ not only in terms of the used ML methods but also with respect to the used curated data sets, the features selection and their prediction performance. Here, we provide a comprehensive survey and benchmarking of currently available tools for the prediction of effector proteins of bacterial types III, IV and VI secretion systems (T3SS, T4SS and T6SS, respectively). We review core algorithms, feature selection techniques, tool availability and applicability and evaluate the prediction performance based on carefully curated independent test data sets. In an effort to improve predictive performance, we constructed three ensemble models based on ML algorithms by integrating the output of all individual predictors reviewed. Our benchmarks demonstrate that these ensemble models outperform all the reviewed tools for the prediction of effector proteins of T3SS and T4SS. The webserver of the proposed ensemble methods for T3SS and T4SS effector protein prediction is freely available at http://tbooster.erc.monash.edu/index.jsp We anticipate that this survey will serve as a useful guide for interested users and that the new ensemble predictors will stimulate research into host-pathogen relationships and inspiration for the development of new bioinformatics tools for predicting effector proteins of T3SS, T4SS and T6SS.\",\n \"corpus_id\": 3321295,\n \"score\": 0\n },\n {\n \"doc_id\": \"27787818\",\n \"title\": \"Predicting Protein Secondary Structure Using Consensus Data Mining (CDM) Based on Empirical Statistics and Evolutionary Information.\",\n \"abstract\": \"Predicting the secondary structure of a protein from its sequence still remains a challenging problem. The prediction accuracies remain around 80 %, and for very diverse methods. Using evolutionary information and machine learning algorithms in particular has had the most impact. In this chapter, we will first define secondary structures, then we will review the Consensus Data Mining (CDM) technique based on the robust GOR algorithm and Fragment Database Mining (FDM) approach. GOR V is an empirical method utilizing a sliding window approach to model the secondary structural elements of a protein by making use of generalized evolutionary information. FDM uses data mining from experimental structure fragments, and is able to successfully predict the secondary structure of a protein by combining experimentally determined structural fragments based on sequence similarities of the fragments. The CDM method combines predictions from GOR V and FDM in a hierarchical manner to produce consensus predictions for secondary structure. In other words, if sequence fragment are not available, then it uses GOR V to make the secondary structure prediction. The online server of CDM is available at http://gor.bb.iastate.edu/cdm/ .\",\n \"corpus_id\": 4857477,\n \"score\": 0\n },\n {\n \"doc_id\": \"27787828\",\n \"title\": \"Prediction of Disordered RNA, DNA, and Protein Binding Regions Using DisoRDPbind.\",\n \"abstract\": \"Intrinsically disordered proteins and regions (IDPs and IDRs) are involved in a wide range of cellular functions and they often facilitate interactions with RNAs, DNAs, and proteins. Although many computational methods can predict IDPs and IDRs in protein sequences, only a few methods predict their functions and these functions primarily concern protein binding. We describe how to use the first computational method DisoRDPbind for high-throughput prediction of multiple functions of disordered regions. Our method predicts the RNA-, DNA-, and protein-binding residues located in IDRs in the input protein sequences. DisoRDPbind provides accurate predictions and is sufficiently fast to make predictions for full genomes. Our method is implemented as a user-friendly webserver that is freely available at http://biomine.ece.ualberta.ca/DisoRDPbind/ . We overview our predictor, discuss how to run the webserver, and show how to interpret the corresponding results. We also demonstrate the utility of our method based on two case studies, human BRCA1 protein that binds various proteins and DNA, and yeast 60S ribosomal protein L4 that interacts with proteins and RNA.\",\n \"corpus_id\": 4869176,\n \"score\": 0\n },\n {\n \"doc_id\": \"27978812\",\n \"title\": \"COUSCOus: improved protein contact prediction using an empirical Bayes covariance estimator.\",\n \"abstract\": \"BACKGROUND: The post-genomic era with its wealth of sequences gave rise to a broad range of protein residue-residue contact detecting methods. Although various coevolution methods such as PSICOV, DCA and plmDCA provide correct contact predictions, they do not completely overlap. Hence, new approaches and improvements of existing methods are needed to motivate further development and progress in the field. We present a new contact detecting method, COUSCOus, by combining the best shrinkage approach, the empirical Bayes covariance estimator and GLasso. RESULTS: Using the original PSICOV benchmark dataset, COUSCOus achieves mean accuracies of 0.74, 0.62 and 0.55 for the top L/10 predicted long, medium and short range contacts, respectively. In addition, COUSCOus attains mean areas under the precision-recall curves of 0.25, 0.29 and 0.30 for long, medium and short contacts and outperforms PSICOV. We also observed that COUSCOus outperforms PSICOV w.r.t. Matthew's correlation coefficient criterion on full list of residue contacts. Furthermore, COUSCOus achieves on average 10% more gain in prediction accuracy compared to PSICOV on an independent test set composed of CASP11 protein targets. Finally, we showed that when using a simple random forest meta-classifier, by combining contact detecting techniques and sequence derived features, PSICOV predictions should be replaced by the more accurate COUSCOus predictions. CONCLUSION: We conclude that the consideration of superior covariance shrinkage approaches will boost several research fields that apply the GLasso procedure, amongst the presented one of residue-residue contact prediction as well as fields such as gene network reconstruction.\",\n \"corpus_id\": 7377892,\n \"score\": 0\n },\n {\n \"doc_id\": \"28222000\",\n \"title\": \"Fast prediction of protein methylation sites using a sequence-based feature selection technique.\",\n \"abstract\": \"Protein methylation, an important post-translational modification, plays crucial roles in many cellular processes. The accurate prediction of protein methylation sites is fundamentally important for revealing the molecular mechanisms undergoing methylation. In recent years, computational prediction based on machine learning algorithms has emerged as a powerful and robust approach for identifying methylation sites, and much progress has been made in predictive performance improvement. However, the predictive performance of existing methods is not satisfactory in terms of overall accuracy. Motivated by this, we propose a novel random-forest-based predictor called MePred-RF, integrating several discriminative sequence-based feature descriptors and improving feature representation capability using a powerful feature selection technique. Importantly, unlike other methods based on multiple, complex information inputs, our proposed MePred-RF is based on sequence information alone. Comparative studies on benchmark datasets via vigorous jackknife tests indicate that our proposed MePred-RF method remarkably outperforms other state-of-the-art predictors, leading by a 4.5% average in terms of overall accuracy. A user-friendly webserver that implements the proposed method has been established for researchers' convenience, and is now freely available for public use through http://server.malab.cn/MePred---‑RF. We anticipate our research tool to be useful for the largescale prediction and analysis of protein methylation sites.\",\n \"corpus_id\": 5263228,\n \"score\": 0\n },\n {\n \"doc_id\": \"29069295\",\n \"title\": \"PaRSnIP: sequence-based protein solubility prediction using gradient boosting machine.\",\n \"abstract\": \"Motivation: Protein solubility can be a decisive factor in both research and production efficiency, and in silico sequence-based predictors that can accurately estimate solubility outcomes are highly sought. Results: In this study, we present a novel approach termed PRotein SolubIlity Predictor (PaRSnIP), which uses a gradient boosting machine algorithm as well as an approximation of sequence and structural features of the protein of interest. Based on an independent test set, PaRSnIP outperformed other state-of-the-art sequence-based methods by more than 9% in accuracy and 0.17 in Matthew's correlation coefficient, with an overall accuracy of 74% and Matthew's correlation coefficient of 0.48. Additionally, PaRSnIP provides importance scores for all features used in training. We observed higher fractions of exposed residues to associate positively with protein solubility and tripeptide stretches with multiple histidines to associate negatively with solubility. The improved prediction accuracy of PaRSnIP should enable it to predict protein solubility with greater reliability and to screen for sequence variants with enhanced manufacturability. Availability and implementation: PaRSnIP software is available for download under GitHub (https://github.com/RedaRawi/PaRSnIP). Contact: gwo-yu.chuang@nih.gov. Supplementary information: Supplementary data are available at Bioinformatics online.\",\n \"corpus_id\": 4576871,\n \"score\": 0\n }\n]","isConversational":false}}},{"rowIdx":88,"cells":{"query":{"kind":"string","value":"{\n \"doc_id\": \"27192562\",\n \"title\": \"Cellulose Structural Polymorphism in Plant Primary Cell Walls Investigated by High-Field 2D Solid-State NMR Spectroscopy and Density Functional Theory Calculations.\",\n \"abstract\": \"The native cellulose of bacterial, algal, and animal origins has been well studied structurally using X-ray and neutron diffraction and solid-state NMR spectroscopy, and is known to consist of varying proportions of two allomorphs, Iα and Iβ, which differ in hydrogen bonding, chain packing, and local conformation. In comparison, cellulose structure in plant primary cell walls is much less understood because plant cellulose has lower crystallinity and extensive interactions with matrix polysaccharides. Here we have combined two-dimensional magic-angle-spinning (MAS) solid-state nuclear magnetic resonance (solid-state NMR) spectroscopy at high magnetic fields with density functional theory (DFT) calculations to obtain detailed information about the structural polymorphism and spatial distributions of plant primary-wall cellulose. 2D (13)C-(13)C correlation spectra of uniformly (13)C-labeled cell walls of several model plants resolved seven sets of cellulose chemical shifts. Among these, five sets (denoted a-e) belong to cellulose in the interior of the microfibril while two sets (f and g) can be assigned to surface cellulose. Importantly, most of the interior cellulose (13)C chemical shifts differ significantly from the (13)C chemical shifts of the Iα and Iβ allomorphs, indicating that plant primary-wall cellulose has different conformations, packing, and hydrogen bonding from celluloses of other organisms. 2D (13)C-(13)C correlation experiments with long mixing times and with water polarization transfer revealed the spatial distributions and matrix-polysaccharide interactions of these cellulose structures. Celluloses f and g are well mixed chains on the microfibril surface, celluloses a and b are interior chains that are in molecular contact with the surface chains, while cellulose c resides in the core of the microfibril, outside spin diffusion contact with the surface. Interestingly, cellulose d, whose chemical shifts differ most significantly from those of bacterial, algal, and animal cellulose, interacts with hemicellulose, is poorly hydrated, and is targeted by the protein expansin during wall loosening. To obtain information about the C6 hydroxymethyl conformation of these plant celluloses, we carried out DFT calculations of (13)C chemical shifts, using the Iα and Iβ crystal structures as templates and varying the C5-C6 torsion angle. Comparison with the experimental chemical shifts suggests that all interior cellulose favor the tg conformation, but cellulose d also has a similar propensity to adopt the gt conformation. These results indicate that cellulose in plant primary cell walls, due to their interactions with matrix polysaccharides, and has polymorphic structures that are not a simple superposition of the Iα and Iβ allomorphs, thus distinguishing them from bacterial and animal celluloses.\",\n \"corpus_id\": 206523131\n}"},"candidates":{"kind":"list like","value":[{"doc_id":"19505136","title":"Localization of crystalline allomorphs in cellulose microfibril.","abstract":"We report an FTIR spectroscopic technique combined with intracrystalline deuteration and rehydrogenation of cellulose samples to investigate the localization of I(alpha) and I(beta) domains within a cellulose microfibril obtained from I(alpha)-rich algae. When Glaucocystis cellulose incompletely converted from I(alpha) to I(beta) was deuterated and rehydrogenated at elevated temperature, OD groups involved in hydrogen bonding in the I(beta) domain first reverted to OH, followed by those in the I(alpha) domain, suggesting that the I(alpha) core domain was surrounded by the I(beta) domain in an artificially induced sample. We concluded that this I(alpha) --> I(beta) conversion proceeded from the surface toward the core. Native celluloses from Valonia and Cladophora were first deuterated without changing the allomorphic composition, and rehydrogenation was studied from I(alpha)- and I(beta)-specific absorbances. Surprisingly, both absorbances changed synchronously, clearly indicating that the simple \"skin-core\" distribution model of I(alpha) and I(beta) domains is not realistic at least for these native celluloses.","corpus_id":192501,"score":2},{"doc_id":"21204530","title":"Structure and interactions of plant cell-wall polysaccharides by two- and three-dimensional magic-angle-spinning solid-state NMR.","abstract":"The polysaccharide-rich cell walls (CWs) of plants perform essential functions such as maintaining tensile strength and allowing plant growth. Using two- and three-dimensional magic-angle-spinning (MAS) solid-state NMR and uniformly (13)C-labeled Arabidopsis thaliana, we have assigned the resonances of the major polysaccharides in the intact and insoluble primary CW and determined the intermolecular contacts and dynamics of cellulose, hemicelluloses, and pectins. Cellulose microfibrils showed extensive interactions with pectins, while the main hemicellulose, xyloglucan, exhibited few cellulose cross-peaks, suggesting limited entrapment in the microfibrils rather than extensive surface coating. Site-resolved (13)C T(1) and (1)H T(1ρ) relaxation times indicate that the entrapped xyloglucan has motional properties that are intermediate between the rigid cellulose and the dynamic pectins. Xyloglucan absence in a triple knockout mutant caused the polysaccharides to undergo much faster motions than in the wild-type CW. These results suggest that load bearing in plant CWs is accomplished by a single network of all three types of polysaccharides instead of a cellulose-xyloglucan network, thus revising the existing paradigm of CW structure. The extensive pectin-cellulose interaction suggests a central role for pectins in maintaining the structure and function of plant CWs. This study demonstrates the power of multidimensional MAS NMR for molecular level investigation of the structure and dynamics of complex and energy-rich plant materials.","corpus_id":42980200,"score":2},{"doc_id":"21222085","title":"Using solid-state ¹³C NMR spectroscopy to study the molecular organisation of primary plant cell walls.","abstract":"Studies of the mobilities of polysaccharides or parts of polysaccharides in a cell-wall preparation may give clues about the molecular interactions among the polysaccharides in the cell wall and the relative locations of polysaccharides within the cell wall. A number of solid-state (13)C NMR techniques have been developed that can be used to investigate different types of polysaccharide mobilities: rigid, semi-rigid, mobile, and highly mobile. In this chapter, techniques are described for obtaining spectra from primary cell-wall preparations using CP/MAS, proton-rotating frame, proton spin-spin, spin-echo relaxation spectra, and single-pulse excitation. We also describe how proton spin relaxation editing can be used to obtain subspectra for cell-wall polysaccharides of different mobilities.","corpus_id":40079398,"score":2},{"doc_id":"22295909","title":"Solid-state selective (13)C excitation and spin diffusion NMR to resolve spatial dimensions in plant cell walls.","abstract":"The average spatial dimensions between major biopolymers within the plant cell wall can be resolved using a solid-state NMR technique referred to as a (13)C cross-polarization (CP) SELDOM (selectively by destruction of magnetization) with a mixing time delay for spin diffusion. Selective excitation of specific aromatic lignin carbons indicates that lignin is in close proximity to hemicellulose followed by amorphous and finally crystalline cellulose. (13)C spin diffusion time constants (T(SD)) were extracted using a two-site spin diffusion theory developed for (13)C nuclei under magic angle spinning (MAS) conditions. These time constants were then used to calculate an average lower-limit spin diffusion length between chemical groups within the plant cell wall. The results on untreated (13)C enriched corn stover stem reveal that the lignin carbons are, on average, located at distances ∼0.7-2.0 nm from the carbons in hemicellulose and cellulose, whereas the pretreated material had larger separations.","corpus_id":31170162,"score":2},{"doc_id":"22777793","title":"Multidimensional solid-state NMR studies of the structure and dynamics of pectic polysaccharides in uniformly 13C-labeled Arabidopsis primary cell walls.","abstract":"Plant cell wall (CW) polysaccharides are responsible for the mechanical strength and growth of plant cells; however, the high-resolution structure and dynamics of the CW polysaccharides are still poorly understood because of the insoluble nature of these molecules. Here, we use 2D and 3D magic-angle-spinning (MAS) solid-state NMR (SSNMR) to investigate the structural role of pectins in the plant CW. Intact and partially depectinated primary CWs of Arabidopsis thaliana were uniformly labeled with (13)C and their NMR spectra were compared. Recent (13)C resonance assignment of the major polysaccharides in Arabidopsis thaliana CWs allowed us to determine the effects of depectination on the intermolecular packing and dynamics of the remaining wall polysaccharides. 2D and 3D correlation spectra show the suppression of pectin signals, confirming partial pectin removal by chelating agents and sodium carbonate. Importantly, higher cross peaks are observed in 2D and 3D (13)C spectra of the depectinated CW, suggesting higher rigidity and denser packing of the remaining wall polysaccharides compared with the intact CW. (13)C spin-lattice relaxation times and (1)H rotating-frame spin-lattice relaxation times indicate that the polysaccharides are more rigid on both the nanosecond and microsecond timescales in the depectinated CW. Taken together, these results indicate that pectic polysaccharides are highly dynamic and endow the polysaccharide network of the primary CW with mobility and flexibility, which may be important for pectin functions. This study demonstrates the capability of multidimensional SSNMR to determine the intermolecular interactions and dynamic structures of complex plant materials under near-native conditions.","corpus_id":23964270,"score":2},{"doc_id":"22939331","title":"Exploring the conformational space of amorphous cellulose using NMR chemical shifts.","abstract":"(13)C-labeled amorphous cellulose and (13)C NMR chemical shifts by 2D (13)C-(13)C correlation spectroscopy were obtained in the regenerated solid-state from ionic liquids. On the basis of the assigned chemical shifts, combined with information from molecular dynamics and quantum chemistry computer simulations a twisted structure for amorphous cellulose is proposed exposing more hydrophilic surface than that of extended crystalline cellulose.","corpus_id":30709476,"score":2},{"doc_id":"23167456","title":"Pectin-cellulose interactions in the Arabidopsis primary cell wall from two-dimensional magic-angle-spinning solid-state nuclear magnetic resonance.","abstract":"The primary cell wall of higher plants consists of a mixture of polysaccharides whose spatial proximities and interactions with each other are not well understood. We recently obtained the first two-dimensional (2D) and three-dimensional high-resolution magic-angle-spinning (13)C solid-state nuclear magnetic resonance spectra of the uniformly (13)C-labeled primary cell wall of Arabidopsis thaliana, which allowed us to assign the majority of (13)C resonances of the three major classes of polysaccharides: cellulose, hemicellulose, and pectins. In this work, we measured the intensity buildup of (13)C-(13)C cross-peaks in a series of 2D (13)C correlation spectra to obtain semiquantitative information about the spatial proximities between different polysaccharides. Comparison of 2D spectra measured at different spin diffusion mixing times identified intermolecular pectin-cellulose cross-peaks as well as interior cellulose-surface cellulose cross-peaks. The intensity buildup time constants are only modestly longer for cellulose-pectin cross-peaks than for interior cellulose-surface cellulose cross-peaks, indicating that pectins come into direct contact with the cellulose microfibrils. Approximately 25-50% of the cellulose chains exhibit close contact with pectins. The (13)C magnetization of the wall polysaccharides is not fully equilibrated by 1.5 s, indicating that pectins and cellulose are not homogeneously mixed on the molecular level. We also assigned the (13)C signals of cell wall proteins, identifying common residues such as Pro, Hyp, Tyr, and Ala. The chemical shifts indicate significant coil and sheet conformations in these structural proteins. Interestingly, few cross- peaks were observed between the proteins and the polysaccharides. Taken together, these data indicate that the three major types of polysaccharides in the primary wall of Arabidopsis form a single cohesive network, while structural proteins form a relatively separate domain.","corpus_id":11561580,"score":2},{"doc_id":"23175754","title":"Structure of cellulose microfibrils in primary cell walls from collenchyma.","abstract":"In the primary walls of growing plant cells, the glucose polymer cellulose is assembled into long microfibrils a few nanometers in diameter. The rigidity and orientation of these microfibrils control cell expansion; therefore, cellulose synthesis is a key factor in the growth and morphogenesis of plants. Celery (Apium graveolens) collenchyma is a useful model system for the study of primary wall microfibril structure because its microfibrils are oriented with unusual uniformity, facilitating spectroscopic and diffraction experiments. Using a combination of x-ray and neutron scattering methods with vibrational and nuclear magnetic resonance spectroscopy, we show that celery collenchyma microfibrils were 2.9 to 3.0 nm in mean diameter, with a most probable structure containing 24 chains in cross section, arranged in eight hydrogen-bonded sheets of three chains, with extensive disorder in lateral packing, conformation, and hydrogen bonding. A similar 18-chain structure, and 24-chain structures of different shape, fitted the data less well. Conformational disorder was largely restricted to the surface chains, but disorder in chain packing was not. That is, in position and orientation, the surface chains conformed to the disordered lattice constituting the core of each microfibril. There was evidence that adjacent microfibrils were noncovalently aggregated together over part of their length, suggesting that the need to disrupt these aggregates might be a constraining factor in growth and in the hydrolysis of cellulose for biofuel production.","corpus_id":22599131,"score":2},{"doc_id":"24720372","title":"Structure and dynamics of Brachypodium primary cell wall polysaccharides from two-dimensional (13)C solid-state nuclear magnetic resonance spectroscopy.","abstract":"The polysaccharide structure and dynamics in the primary cell wall of the model grass Brachypodium distachyon are investigated for the first time using solid-state nuclear magnetic resonance (NMR). While both grass and non-grass cell walls contain cellulose as the main structural scaffold, the former contains xylan with arabinose and glucuronic acid substitutions as the main hemicellulose, with a small amount of xyloglucan (XyG) and pectins, while the latter contains XyG as the main hemicellulose and significant amounts of pectins. We labeled the Brachypodium cell wall with (13)C to allow two-dimensional (2D) (13)C correlation NMR experiments under magic-angle spinning. Well-resolved 2D spectra are obtained in which the (13)C signals of cellulose, glucuronoarabinoxylan (GAX), and other matrix polysaccharides can be assigned. The assigned (13)C chemical shifts indicate that there are a large number of arabinose and xylose linkages in the wall, and GAX is significantly branched at the developmental stage of 2 weeks. 2D (13)C-(13)C correlation spectra measured with long spin diffusion mixing times indicate that the branched GAX approaches cellulose microfibrils on the nanometer scale, contrary to the conventional model in which only unbranched GAX can bind cellulose. The GAX chains are highly dynamic, with average order parameters of ~0.4. Biexponential (13)C T1 and (1)H T1ρ relaxation indicates that there are two dynamically distinct domains in GAX: the more rigid domain may be responsible for cross-linking cellulose microfibrils, while the more mobile domain may fill the interfibrillar space. This dynamic heterogeneity is more pronounced than that of the non-grass hemicellulose, XyG, suggesting that GAX adopts the mixed characteristics of XyG and pectins. Moderate differences in cellulose rigidity are observed between the Brachypodium and Arabidopsis cell walls, suggesting different effects of the matrix polysaccharides on cellulose. These data provide the first molecular-level structural information about the three-dimensional organization of the polysaccharides in the grass primary wall.","corpus_id":25717651,"score":2},{"doc_id":"24984197","title":"Water-polysaccharide interactions in the primary cell wall of Arabidopsis thaliana from polarization transfer solid-state NMR.","abstract":"Polysaccharide-rich plant cell walls are hydrated under functional conditions, but the molecular interactions between water and polysaccharides in the wall have not been investigated. In this work, we employ polarization transfer solid-state NMR techniques to study the hydration of primary-wall polysaccharides of the model plant, Arabidopsis thaliana. By transferring water (1)H polarization to polysaccharides through distance- and mobility-dependent (1)H-(1)H dipolar couplings and detecting it through polysaccharide (13)C signals, we obtain information about water proximity to cellulose, hemicellulose, and pectins as well as water mobility. Both intact and partially extracted cell wall samples are studied. Our results show that water-pectin polarization transfer is much faster than water-cellulose polarization transfer in all samples, but the extent of extraction has a profound impact on the water-polysaccharide spin diffusion. Removal of calcium ions and the consequent extraction of homogalacturonan (HG) significantly slowed down spin diffusion, while further extraction of matrix polysaccharides restored the spin diffusion rate. These trends are observed in cell walls with similar water content, thus they reflect inherent differences in the mobility and spatial distribution of water. Combined with quantitative analysis of the polysaccharide contents, our results indicate that calcium ions and HG gelation increase the amount of bound water, which facilitates spin diffusion, while calcium removal disrupts the gel and gives rise to highly dynamic water, which slows down spin diffusion. The recovery of spin diffusion rates after more extensive extraction is attributed to increased water-exposed surface areas of the polysaccharides. Water-pectin spin diffusion precedes water-cellulose spin diffusion, lending support to the single-network model of plant primary walls in which a substantial fraction of the cellulose surface is surrounded by pectins.","corpus_id":207110985,"score":2},{"doc_id":"25739924","title":"Probing the molecular architecture of Arabidopsis thaliana secondary cell walls using two- and three-dimensional (13)C solid state nuclear magnetic resonance spectroscopy.","abstract":"The plant secondary cell wall is a thickened polysaccharide and phenolic structure, providing mechanical strength to cells, particularly in woody tissues. It is the main feedstock for the developing bioenergy and green chemistry industries. Despite the role that molecular architecture (the arrangement of biopolymers relative to each other, and their conformations) plays in dictating biomass properties, such as recalcitrance to breakdown, it is poorly understood. Here, unprocessed dry (13)C-labeled stems from the model plant Arabidopsis thaliana were analyzed by a variety of (13)C solid state magic angle spinning nuclear magnetic resonance methods, such as one-dimensional cross-polarization and direct polarization, two-dimensional refocused INADEQUATE, RFDR, PDSD, and three-dimensional DARR, demonstrating their viability for the study of native polymer arrangements in intact secondary cell walls. All carbon sites of the two main glucose environments in cellulose (previously assigned to microfibril surface and interior residues) are clearly resolved, as are carbon sites of the other major components of the secondary cell wall: xylan and lignin. The xylan carbon 4 chemical shift is markedly different from that reported previously for solution or primary cell wall xylan, indicating significant changes in the helical conformation in these dried stems. Furthermore, the shift span indicates that xylan adopts a wide range of conformations in this material, with very little in the 31 conformation typical of xylan in solution. Additionally, spatial connections of noncarbohydrate species were observed with both cellulose peaks conventionally assigned as \"surface\" and as \"interior\" cellulose environments, raising questions about the origin of these two cellulose signals.","corpus_id":10955354,"score":2},{"doc_id":"26355148","title":"Solid-state NMR investigations of cellulose structure and interactions with matrix polysaccharides in plant primary cell walls.","abstract":"Until recently, the 3D architecture of plant cell walls was poorly understood due to the lack of high-resolution techniques for characterizing the molecular structure, dynamics, and intermolecular interactions of the wall polysaccharides in these insoluble biomolecular mixtures. We introduced multidimensional solid-state NMR (SSNMR) spectroscopy, coupled with (13)C labelling of whole plants, to determine the spatial arrangements of macromolecules in near-native plant cell walls. Here we review key evidence from 2D and 3D correlation NMR spectra that show relatively few cellulose-hemicellulose cross peaks but many cellulose-pectin cross peaks, indicating that cellulose microfibrils are not extensively coated by hemicellulose and all three major polysaccharides exist in a single network rather than two separate networks as previously proposed. The number of glucan chains in the primary-wall cellulose microfibrils has been under active debate recently. We show detailed analysis of quantitative (13)C SSNMR spectra of cellulose in various wild-type (WT) and mutant Arabidopsis and Brachypodium primary cell walls, which consistently indicate that primary-wall cellulose microfibrils contain at least 24 glucan chains.","corpus_id":20917745,"score":2},{"doc_id":"27552739","title":"Multidimensional solid-state NMR spectroscopy of plant cell walls.","abstract":"Plant biomass has become an important source of bio-renewable energy in modern society. The molecular structure of plant cell walls is difficult to characterize by most atomic-resolution techniques due to the insoluble and disordered nature of the cell wall. Solid-state NMR (SSNMR) spectroscopy is uniquely suited for studying native hydrated plant cell walls at the molecular level with chemical resolution. Significant progress has been made in the last five years to elucidate the molecular structures and interactions of cellulose and matrix polysaccharides in plant cell walls. These studies have focused on primary cell walls of growing plants in both the dicotyledonous and grass families, as represented by the model plants Arabidopsis thaliana, Brachypodium distachyon, and Zea mays. To date, these SSNMR results have shown that 1) cellulose, hemicellulose, and pectins form a single network in the primary cell wall; 2) in dicot cell walls, the protein expansin targets the hemicellulose-enriched region of the cellulose microfibril for its wall-loosening function; and 3) primary wall cellulose has polymorphic structures that are distinct from the microbial cellulose structures. This article summarizes these key findings, and points out future directions of investigation to advance our fundamental understanding of plant cell wall structure and function.","corpus_id":10508705,"score":2},{"doc_id":"28000667","title":"Folding of xylan onto cellulose fibrils in plant cell walls revealed by solid-state NMR.","abstract":"Exploitation of plant lignocellulosic biomass is hampered by our ignorance of the molecular basis for its properties such as strength and digestibility. Xylan, the most prevalent non-cellulosic polysaccharide, binds to cellulose microfibrils. The nature of this interaction remains unclear, despite its importance. Here we show that the majority of xylan, which forms a threefold helical screw in solution, flattens into a twofold helical screw ribbon to bind intimately to cellulose microfibrils in the cell wall. (13)C solid-state magic-angle spinning (MAS) nuclear magnetic resonance (NMR) spectroscopy, supported by in silico predictions of chemical shifts, shows both two- and threefold screw xylan conformations are present in fresh Arabidopsis stems. The twofold screw xylan is spatially close to cellulose, and has similar rigidity to the cellulose microfibrils, but reverts to the threefold screw conformation in the cellulose-deficient irx3 mutant. The discovery that induced polysaccharide conformation underlies cell wall assembly provides new principles to understand biomass properties.","corpus_id":2602725,"score":2},{"doc_id":"29562125","title":"Direct Determination of Hydroxymethyl Conformations of Plant Cell Wall Cellulose Using 1H Polarization Transfer Solid-State NMR.","abstract":"In contrast to the well-studied crystalline cellulose of microbial and animal origins, cellulose in plant cell walls is disordered due to its interactions with matrix polysaccharides. Plant cell wall (PCW) is an undisputed source of sustainable global energy; therefore, it is important to determine the molecular structure of PCW cellulose. The most reactive component of cellulose is the exocyclic hydroxymethyl group: when it adopts the tg conformation, it stabilizes intrachain and interchain hydrogen bonding, while gt and gg conformations destabilize the hydrogen-bonding network. So far, information about the hydroxymethyl conformation in cellulose has been exclusively obtained from 13C chemical shifts of monosaccharides and oligosaccharides, which do not reflect the environment of cellulose in plant cell walls. Here, we use solid-state Nuclear Magnetic Resonance (ssNMR) spectroscopy to measure the hydroxymethyl torsion angle of cellulose in two model plants, by detecting distance-dependent polarization transfer between H4 and H6 protons in 2D 13C-13C correlation spectra. We show that the interior crystalline portion of cellulose microfibrils in Brachypodium and Arabidopsis cell walls exhibits H4-H6 polarization transfer curves that are indicative of a tg conformation, whereas surface cellulose chains exhibit slower H4-H6 polarization transfer that is best fit to the gt conformation. Joint constraints by the H4-H6 polarization transfer curves and 13C chemical shifts indicate that it is unlikely for interior cellulose to have a significant population of the gt and gg conformation mixed with the tg conformation, while surface cellulose may adopt a small percentage of the gg conformation. These results provide new constraints to the structure and matrix interactions of cellulose in plant cell walls, and represent the first direct determination of a torsion angle in an important noncrystalline carbohydrate polymer.","corpus_id":4450726,"score":2},{"doc_id":"18781703","title":"Spectral assignments and anisotropy data of cellulose I(alpha): 13C-NMR chemical shift data of cellulose I(alpha) determined by INADEQUATE and RAI techniques applied to uniformly 13C-labeled bacterial celluloses of different Gluconacetobacter xylinus strains.","abstract":"Solid-state (13)C-NMR spectroscopy was used to characterize native cellulose pellicles from two strains of Gluconacetobacter xylinus (ATCC 53582, ATCC 23769), which had been statically cultivated in Hestrin-Schramm (HS) medium containing fully (13)C-labeled beta-D-glucose-U-(13)C(6) as the sole source of carbon. For both samples, the (13)C-NMR chemical shifts were completely assigned for each (13)C-labeled site of cellulose I(alpha) with the aid of 2D refocused INADEQUATE NMR. To determine the principal chemical shift tensor components, a pulse sequence based on the recoupling of anisotropy information (RAI) was applied at 10 kHz MAS. The detailed (13)C tensors of cellulose I(alpha) from different bacterial celluloses are thus available now for the first time, and these results have been compared with previously published data of nonenriched material and with theoretical predictions.","corpus_id":43760876,"score":1},{"doc_id":"19133744","title":"Characterizing slight structural disorder in solids by combined solid-state NMR and first principles calculations.","abstract":"A general approach for structural interpretation of local disorder in partially ordered solids is proposed, combining high-resolution two-dimensional (2D) nuclear magnetic resonance (NMR) and first principles calculations. We show that small chemical shift variations of the order of a ppm can be interpreted in detailed structural terms with advanced density functional theory methods. Focusing on a model system of bisphosphinoamine, we demonstrate that the existence and the spatial range of small amplitude disorder can be probed using quantitative statistical analyses of 2D NMR line shapes obtained from through-space correlation experiments collected using variable mixing times. We show how low-energy vibration modes calculated from first principles can be conveniently used not as a cause of disorder but, instead, to generate a basis set of physically plausible local distortions to describe candidate static distributions of local geometries. Calculations of (31)P NMR isotropic chemical shifts are then used for the first time to simulate 2D correlation lineshapes associated with these distortions, which permit their evaluation as a potential source of disorder by comparison to experimental 2D cross-peaks between phosphorus sites. This new type of structural constraints allows the identification of changes in the bonding geometry that most likely contribute to the local structural disorder. We thus identify at least one type of structural deformation that is compatible with the experimental 2D NMR data and is also within the order of magnitude of the \"thermal ellipsoids\" associated with the uncertainties on the atomic positions of the X-ray diffraction structure.","corpus_id":44816685,"score":1},{"doc_id":"19817435","title":"Solid-state 13C NMR study of a composite of tobacco xyloglucan and Gluconacetobacter xylinus cellulose: molecular interactions between the component polysaccharides.","abstract":"To investigate possible molecular interactions between xyloglucans (XGs) and cellulose in plant cell walls, a model composite was produced using cellulose from the bacterium Gluconacetobacter xylinus and XG from the walls of a tobacco cell-suspension culture that had been incubated with (13)C-labeled glucose. Solid-state (13)C NMR with cross-polarization (CP) and magic-angle spinning (MAS) was used in combination with proton spin-relaxation editing to separate signals from crystalline (rigid) and less rigid domains of the composite. Signals from XG were confined to subspectra of less rigid domains, with no detectable signals from XG attached to surfaces of cellulose crystallites. Signal displacements indicated XGs were more rigid than the mobile coil (twisted backbone) conformation expected for unattached XGs. Similar (13)C chemical shifts were observed in a single-pulse excitation experiment. The results were not compatible with extensive hydrogen bonding between XG and cellulose, but were consistent with a composite structure in which cellulose crystallites were embedded in a matrix of XG with a semirigid (straightened backbone) conformation, that is, a matrix that is partly ordered rather than amorphous.","corpus_id":206868345,"score":1},{"doc_id":"21338135","title":"High-temperature behavior of cellulose I.","abstract":"We use molecular simulation to elucidate the structural behavior of small hydrated cellulose Iβ microfibrils heated to 227 °C (500 K) with two carbohydrate force fields. In contrast to the characteristic two-dimensional hydrogen-bonded layer sheets present in the cellulose Iβ crystal structure, we show that at high temperature a three-dimensional hydrogen bond network forms, made possible by hydroxymethyl groups changing conformation from trans-gauche (TG) to gauche-gauche (GG) in every second layer corresponding to \"center\" chains in cellulose Iβ and from TG to gauche-trans (GT) in the \"origin\" layer. The presence of a regular three-dimensional hydrogen bond network between neighboring sheets eliminates the possibility of twist, whereas two-dimensional hydrogen bonding allows for microfibril twist to occur. Structural features of this high-temperature phase as determined by molecular simulation may explain several experimental observations for which no detailed structural basis has been offered. This includes an explanation for the observed temperature and crystal size dependence for the extent of hydrogen/deuterium exchange, and diffraction patterns of cellulose at high temperature.","corpus_id":39581325,"score":1},{"doc_id":"21563791","title":"Natural-abundance solid-state 2H NMR spectroscopy at high magnetic field.","abstract":"High-resolution solid-state (2)H NMR spectroscopy provides a method for measuring (1)H NMR chemical shifts in solids and is advantageous over the direct measurement of high-resolution solid-state (1)H NMR spectra, as it requires only the application of routine magic angle sample spinning (MAS) and routine (1)H decoupling methods, in contrast to the requirement for complex pulse sequences for homonuclear (1)H decoupling and ultrafast MAS in the case of high-resolution solid-state (1)H NMR. However, a significant obstacle to the routine application of high-resolution solid-state (2)H NMR is the very low natural abundance of (2)H, with the consequent problem of inherently low sensitivity. Here, we explore the feasibility of measuring (2)H MAS NMR spectra of various solids with natural isotopic abundances at high magnetic field (850 MHz), focusing on samples of amino acids, peptides, collagen, and various organic solids. The results show that high-resolution solid-state (2)H NMR can be used successfully to measure isotropic (1)H chemical shifts in favorable cases, particularly for mobile functional groups, such as methyl and -N(+)H(3) groups, and in some cases phenyl groups. Furthermore, we demonstrate that routine (2)H MAS NMR measurements can be exploited for assessing the relative dynamics of different functional groups in a molecule and for assessing whole-molecule motions in the solid state. The magnitude and field-dependence of second-order shifts due to the (2)H quadrupole interaction are also investigated, on the basis of analysis of simulated and experimental (1)H and (2)H MAS NMR spectra of fully deuterated and selectively deuterated samples of the α polymorph of glycine at two different magnetic field strengths.","corpus_id":25181140,"score":1},{"doc_id":"21677972","title":"Hydrogen bonding and chemical shift assignments in carbazole functionalized isocyanides from solid-state NMR and first-principles calculations.","abstract":"Carbazole functionalized polyisocyanides are known to exhibit excellent electronic properties (E. Schwartz, et al., Chemistry of Materials, 2010, 22, 2597). The functionalities and properties of such materials crucially depend on the organization and stability of the polymer structure. We combine solid-state Nuclear Magnetic Resonance (NMR) experiments with first-principles calculations of isotropic chemical shifts, within the recently developed converse approach, to rationalize the origin of isotropic chemical shifts in the crystalline monomer l-isocyanoalanine 2-(9H-carbazol-9-yl) ethyl amide (monomer 1) and thereby gain insight into the structural organization of its polymer (polymer 2). The use of state-of-the-art solid-state NMR experiments combined with Density Functional Theory (DFT) based calculations allows an unambiguous assignment of all proton and carbon resonances of the monomer. We were able to identify the structure stabilising interactions in the crystal and understand the influence of the molecular packing in the crystal structure on the chemical shift data observed in the NMR spectra. Here the Nuclear Independent Chemical Shift (NICS) approach allows discriminating between 'physical' interactions amongst neighboring molecules such as ring-current effects and 'chemical' interactions such as hydrogen bonding. This analysis reveals that the isocyanide monomer is stabilized by multiple hydrogen bonds such as a bifurcated hydrogen bond involving -N-H, -C-H and O=C- moieties and Ar-H···C≡N- hydrogen bonding (Ar = aromatic group). Based on the geometrical arrangement it is postulated that the carbazole units are involved in the weak σ-π interactions giving rise to a Herringbone packing of the molecules. The chemical shift analysis of the polymer spectra readily establishes the existence of N-H···O=C hydrogen bonds despite the limited resolution exhibited by the polymer spectra. It is also elucidated that the relative arrangement of the carbazole units in the polymer differs significantly from that of the monomer.","corpus_id":20518868,"score":1},{"doc_id":"22044314","title":"Hydration and temperature dependence of 13C and 1H NMR spectra of the DMPC phospholipid membrane and complete resonance assignment of its crystalline state.","abstract":"Inhomogeneous line broadening due to conformational distributions of molecules is one of the troublesome problems in solid-state NMR spectroscopy. The best possible way to avoid it is to crystallize the sample. Here, we present a highly resolved (13)C cross-polarization (CP) magic angle spinning (MAS) NMR spectrum of the highly ordered crystalline 1,2-dimyrystoyl-sn-glycero-3-phosphocholine (DMPC) and completely assigned it using two-dimensional (2D) solid-state NMR spectra, dipolar heteronuclear correlation (HETCOR) spectra, scalar heteronuclear J coupling based chemical shift correlation (MAS-J-HMQC) spectra, and Dipolar Assisted Rotational Resonance (DARR) spectra. A comparison between assigned chemical shift values by solid-state NMR in this study and the calculated chemical shift values for X-ray crystal DMPC structures shows good agreement, indicating that the two isomers in the crystalline DMPC take the same conformation as the X-ray crystal structure. The phase diagram of the low hydration level of DMPC (3 ≤ n(W) ≤ 12) determined by (1)H and (13)C NMR spectra indicates that DMPC takes a crystalline state only in a very narrow region around n(W) = 4 and T < 313 K. These findings provide us with conformational information on crystalline DMPC and the physical properties of DMPC at a low hydration level and can possibly help us obtain a highly resolved solid-state NMR spectrum of microcrystalline membrane-associated protein samples.","corpus_id":24457741,"score":1},{"doc_id":"22129840","title":"DFT study of (17)O, (1)H and (13)C NMR chemical shifts in two forms of native cellulose, I(α) and I(β).","abstract":"This computational study is intended to shed light on the crystalline and molecular structure, together with the hydrogen bonding (H-bonding) differences between two forms of native cellulose. DFT calculations were carried out to characterize the (17)O, (1)H and (13)C nuclear magnetic resonance (NMR) parameters in cellulose I(α) and I(β) with the B3LYP functional employing the 6-311++G∗∗ and 6-31+G∗ basis sets. Geometry optimization revealed that the average HB length is shortened by 0.01-0.08Å when the chains are aligned, whereas the average bond angle increases by about 4-8° exhibiting the enhancement of HB strength. For the isolated cellotetramer chains, the isotropic (17)O-H chemical shifts were plotted as a function of HB length. Our results indicated that as the HB length in cellotetramer I(α) increases, the (17)O-H chemical shift isotropy increases, but this parameter changes in the opposite direction for the other structure. Moreover, B3LYP/6-311++G∗∗ calculations reveal that there is an acceptable correlation between the calculated (13)C chemical shifts of the two structures and their experimental values.","corpus_id":9458598,"score":1},{"doc_id":"22163913","title":"Sensing the structural differences in cellulose from apple and bacterial cell wall materials by Raman and FT-IR spectroscopy.","abstract":"Raman and Fourier Transform Infrared (FT-IR) spectroscopy was used for assessment of structural differences of celluloses of various origins. Investigated celluloses were: bacterial celluloses cultured in presence of pectin and/or xyloglucan, as well as commercial celluloses and cellulose extracted from apple parenchyma. FT-IR spectra were used to estimate of the I(β) content, whereas Raman spectra were used to evaluate the degree of crystallinity of the cellulose. The crystallinity index (X(C)(RAMAN)%) varied from -25% for apple cellulose to 53% for microcrystalline commercial cellulose. Considering bacterial cellulose, addition of xyloglucan has an impact on the percentage content of cellulose I(β). However, addition of only xyloglucan or only pectins to pure bacterial cellulose both resulted in a slight decrease of crystallinity. However, culturing bacterial cellulose in the presence of mixtures of xyloglucan and pectins results in an increase of crystallinity. The results confirmed that the higher degree of crystallinity, the broader the peak around 913 cm(-1). Among all bacterial celluloses the bacterial cellulose cultured in presence of xyloglucan and pectin (BCPX) has the most similar structure to those observed in natural primary cell walls.","corpus_id":16979107,"score":1},{"doc_id":"23774714","title":"Determining hydrogen-bond interactions in spider silk with 1H-13C HETCOR fast MAS solid-state NMR and DFT proton chemical shift calculations.","abstract":"Two-dimensional (2D) (1)H-(13)C heteronuclear correlation (HETCOR) solid-state NMR spectra collected with fast magic angle spinning (MAS) are used in conjunction with density functional theory (DFT) proton chemical shift calculations to determine the hydrogen-bonding strength for ordered β-sheet and disordered 310-helical structures in spider dragline silk. The hydrogen-bond strength is determined to be identical for both structures in spider silk with a 1.83-1.84 Å NH···OC hydrogen-bond distance.","corpus_id":205840285,"score":1},{"doc_id":"24065828","title":"Sensitivity-enhanced solid-state NMR detection of expansin's target in plant cell walls.","abstract":"Structure determination of protein binding to noncrystalline macromolecular assemblies such as plant cell walls (CWs) poses a significant structural biology challenge. CWs are loosened during growth by expansin proteins, which weaken the noncovalent network formed by cellulose, hemicellulose, and pectins, but the CW target of expansins has remained elusive because of the minute amount of the protein required for activity and the complex nature of the CW. Using solid-state NMR spectroscopy, combined with sensitivity-enhancing dynamic nuclear polarization (DNP) and differential isotopic labeling of expansin and polysaccharides, we have now determined the functional binding target of expansin in the Arabidopsis thaliana CW. By transferring the electron polarization of a biradical dopant to the nuclei, DNP allowed selective detection of (13)C spin diffusion from trace concentrations of (13)C, (15)N-labeled expansin in the CW to nearby polysaccharides. From the spin diffusion data of wild-type and mutant expansins, we conclude that to loosen the CW, expansin binds highly specific cellulose domains enriched in xyloglucan, whereas more abundant binding to pectins is unrelated to activity. Molecular dynamics simulations indicate short (13)C-(13)C distances of 4-6 Å between a hydrophobic surface of the cellulose microfibril and an aromatic motif on the expansin surface, consistent with the observed NMR signals. DNP-enhanced 2D (13)C correlation spectra further reveal that the expansin-bound cellulose has altered conformation and is enriched in xyloglucan, thus providing unique insight into the mechanism of CW loosening. DNP-enhanced NMR provides a powerful, generalizable approach for investigating protein binding to complex macromolecular targets.","corpus_id":21065255,"score":1},{"doc_id":"24760365","title":"Probing crystal structure and mesoscale assembly of cellulose microfibrils in plant cell walls, tunicate tests, and bacterial films using vibrational sum frequency generation (SFG) spectroscopy.","abstract":"This study reports that the noncentrosymmetry and phase synchronization requirements of the sum frequency generation (SFG) process can be used to distinguish the three-dimensional organization of crystalline cellulose distributed in amorphous matrices. Crystalline cellulose is produced as microfibrils with a few nanometer diameters by plants, tunicates, and bacteria. Crystalline cellulose microfibrils are embedded in wall matrix polymers and assembled into hierarchical structures that are precisely designed for specific biological and mechanical functions. The cellulose microfibril assemblies inside cell walls are extremely difficult to probe. The comparison of vibrational SFG spectra of uniaxially-aligned and disordered films of cellulose Iβ nanocrystals revealed that the spectral features cannot be fully explained with the crystallographic unit structure of cellulose. The overall SFG intensity, the alkyl peak shape, and the alkyl/hydroxyl intensity ratio are sensitive to the lateral packing and net directionality of the cellulose microfibrils within the SFG coherence length scale. It was also found that the OH SFG stretch peaks could be deconvoluted to find the polymorphic crystal structures of cellulose (Iα and Iβ). These findings were used to investigate the cellulose crystal structure and mesoscale cellulose microfibril packing in intact plant cell walls, tunicate tests, and bacterial films.","corpus_id":38622688,"score":1},{"doc_id":"24846814","title":"Effects of plant cell wall matrix polysaccharides on bacterial cellulose structure studied with vibrational sum frequency generation spectroscopy and X-ray diffraction.","abstract":"The crystallinity, allomorph content, and mesoscale ordering of cellulose produced by Gluconacetobacter xylinus cultured with different plant cell wall matrix polysaccharides were studied with vibrational sum frequency generation (SFG) spectroscopy and X-ray diffraction (XRD). Crystallinity and ordering were assessed as the intensity of SFG signals in the CH/CH2 stretch vibration region (and confirmed by XRD), while Iα content was assessed by the relative intensity of the OH stretch vibration at 3240 cm(-1). A key finding is that the presence of xyloglucan in the culture medium greatly reduced Iα allomorph content but with a relatively small effect on cellulose crystallinity, whereas xylan resulted in a larger decrease in crystallinity with a relatively small decrease in the Iα fraction. Arabinoxylan and various pectins had much weaker effects on cellulose structure as assessed by SFG and XRD. Homogalacturonan with calcium ion reduced the SFG signal, evidently by changing the ordering of cellulose microfibrils. We propose that the distinct effects of matrix polysaccharides on cellulose crystal structure result, at least in part, from selective interactions of the backbone and side chains of matrix polysaccharides with cellulose chains during the formation of the microfibril.","corpus_id":11759417,"score":1},{"doc_id":"25050643","title":"Theoretical study of the structural stability of molecular chain sheet models of cellulose crystal allomorphs.","abstract":"The structural stabilities of the molecular chain sheets constituting the crystal structures of the cellulose allomorphs Iα, Iβ, II, and IIII were investigated by density functional theory (DFT) optimization of the isolated chain sheet models with finite dimensions. The DFT-optimized chain sheet models of the two native cellulose crystals developed a right-handed twist with a similar amount of twisting. The DFT-optimized cellulose II (010) and (020) models twisted in opposite directions with right- and left-handed chirality, respectively. The cellulose IIII (1-10) model retained the initial flat structure after the DFT-optimization. The structural features of the DFT-optimized chain sheet models were reflected in the structures of the parent crystal models observed in solvated molecular dynamics (MD) simulations. The minor conformations of the hydroxymethyl groups proposed in the real crystal structures were detected in the MD crystal models and the DFT-optimized (010) model of cellulose II. The crystal chain packing and crystal conversions are interpreted in terms of principal chain sheet stacking.","corpus_id":8674241,"score":1},{"doc_id":"25584993","title":"Investigating albendazole desmotropes by solid-state NMR spectroscopy.","abstract":"Characterization of the molecular structure and physicochemical solid-state properties of the solid forms of pharmaceutical compounds is a key requirement for successful commercialization as potential active ingredients in drug products. These properties can ultimately have a critical effect on the solubility and bioavailability of the final drug product. Here, the desmotropy of Albendazole forms I and II was investigated at the atomic level. Ultrafast magic angle spinning (MAS) solid-state nuclear magnetic resonance (NMR) spectroscopy, together with powder X-ray diffraction, thermal analysis, and Fourier transform infrared spectroscopy, were performed on polycrystalline samples of the two solids in order to fully characterize and distinguish the two forms. High-resolution one-dimensional (1)H, (13)C, and (15)N together with two-dimensional (1)H/(1)H single quantum-single quantum, (1)H/(1)H single quantum-double quantum, and (1)H/(13)C chemical shift correlation solid-state NMR experiments under MAS conditions were extensively used to decipher the intramolecular and intermolecular hydrogen bonding interactions present in both solid forms. These experiments enabled the unequivocal identification of the tautomers of each desmotrope. Our results also revealed that both solid forms may be described as dimeric structures, with different intermolecular hydrogen bonds connecting the tautomers in each dimer.","corpus_id":10483551,"score":1},{"doc_id":"26036615","title":"Cellulose-Pectin Spatial Contacts Are Inherent to Never-Dried Arabidopsis Primary Cell Walls: Evidence from Solid-State Nuclear Magnetic Resonance.","abstract":"The structural role of pectins in plant primary cell walls is not yet well understood because of the complex and disordered nature of the cell wall polymers. We recently introduced multidimensional solid-state nuclear magnetic resonance spectroscopy to characterize the spatial proximities of wall polysaccharides. The data showed extensive cross peaks between pectins and cellulose in the primary wall of Arabidopsis (Arabidopsis thaliana), indicating subnanometer contacts between the two polysaccharides. This result was unexpected because stable pectin-cellulose interactions are not predicted by in vitro binding assays and prevailing cell wall models. To investigate whether the spatial contacts that give rise to the cross peaks are artifacts of sample preparation, we now compare never-dried Arabidopsis primary walls with dehydrated and rehydrated samples. One-dimensional (13)C spectra, two-dimensional (13)C-(13)C correlation spectra, water-polysaccharide correlation spectra, and dynamics data all indicate that the structure, mobility, and intermolecular contacts of the polysaccharides are indistinguishable between never-dried and rehydrated walls. Moreover, a partially depectinated cell wall in which 40% of homogalacturonan is extracted retains cellulose-pectin cross peaks, indicating that the cellulose-pectin contacts are not due to molecular crowding. The cross peaks are observed both at -20 °C and at ambient temperature, thus ruling out freezing as a cause of spatial contacts. These results indicate that rhamnogalacturonan I and a portion of homogalacturonan have significant interactions with cellulose microfibrils in the native primary wall. This pectin-cellulose association may be formed during wall biosynthesis and may involve pectin entrapment in or between cellulose microfibrils, which cannot be mimicked by in vitro binding assays.","corpus_id":9464878,"score":1},{"doc_id":"26717549","title":"Comparison of celery (Apium graveolens L.) collenchyma and parenchyma cell wall polysaccharides enabled by solid-state (13)C NMR.","abstract":"Collenchyma cells with their thickened walls are one of specific mechanical support tissues for plants, while parenchyma cells are thin walled and serve multiple functions. The parenchyma tissue is what you enjoy eating, while collenchyma, because of its fibrous nature, is not so attractive. Celery is a useful model for comparing the cell walls (CWs) of the two cell types such as collenchyma and parenchyma. However, to date, the structural characteristics of collenchyma and parenchyma cell walls from the same plant have not been compared. Monosaccharide composition suggested the collenchyma cell walls contained less pectin but more hemicellulose in comparison to parenchyma. High-resolution solid-state NMR spectra of highly mobile pectins revealed that the arabinan signals were more evident in the collenchyma spectrum, while galactan showed a much stronger resonance in the parenchyma spectrum. In addition, methyl esterified and non-esterified galacturonic acid signals were observed in parenchyma CWs, but only the latter one appeared in the collenchyma. The ratio of cellulose surface/interior obtained from CP/MAS spectra for collenchyma suggested the cellulose microfibrils were ~2.4 nm, while in the parenchyma, these were somewhat larger. X-ray diffraction indicated the size of the cellulose microfibrils were the same for both types of CWs.","corpus_id":25449914,"score":1},{"doc_id":"27474592","title":"(13)C NMR assignments of regenerated cellulose from solid-state 2D NMR spectroscopy.","abstract":"From the assignment of the solid-state (13)C NMR signals in the C4 region, distinct types of crystalline cellulose, cellulose at crystalline surfaces, and disordered cellulose can be identified and quantified. For regenerated cellulose, complete (13)C assignments of the other carbon regions have not previously been attainable, due to signal overlap. In this study, two-dimensional (2D) NMR correlation methods were used to resolve and assign (13)C signals for all carbon atoms in regenerated cellulose. (13)C-enriched bacterial nanocellulose was biosynthesized, dissolved, and coagulated as highly crystalline cellulose II. Specifically, four distinct (13)C signals were observed corresponding to conformationally different anhydroglucose units: two signals assigned to crystalline moieties and two signals assigned to non-crystalline species. The C1, C4 and C6 regions for cellulose II were fully examined by global spectral deconvolution, which yielded qualitative trends of the relative populations of the different cellulose moieties, as a function of wetting and drying treatments.","corpus_id":206450513,"score":1},{"doc_id":"28619057","title":"Polysaccharide compositions of collenchyma cell walls from celery (Apium graveolens L.) petioles.","abstract":"BACKGROUND: Collenchyma serves as a mechanical support tissue for many herbaceous plants. Previous work based on solid-state NMR and immunomicroscopy suggested collenchyma cell walls (CWs) may have similar polysaccharide compositions to those commonly found in eudicotyledon parenchyma walls, but no detailed chemical analysis was available. In this study, compositions and structures of cell wall polysaccharides of peripheral collenchyma from celery petioles were investigated. RESULTS: This is the first detailed investigation of the cell wall composition of collenchyma from any plant. Celery petioles were found to elongate throughout their length during early growth, but as they matured elongation was increasingly confined to the upper region, until elongation ceased. Mature, fully elongated, petioles were divided into three equal segments, upper, middle and lower, and peripheral collenchyma strands isolated from each. Cell walls (CWs) were prepared from the strands, which also yielded a HEPES buffer soluble fraction. The CWs were sequentially extracted with CDTA, Na2CO3, 1 M KOH and 4 M KOH. Monosaccharide compositions of the CWs showed that pectin was the most abundant polysaccharide [with homogalacturonan (HG) more abundant than rhamnogalacturonan I (RG-I) and rhamnogalacturonan II (RG-II)], followed by cellulose, and other polysaccharides, mainly xyloglucans, with smaller amounts of heteroxylans and heteromannans. CWs from different segments had similar compositions, but those from the upper segments had slightly more pectin than those from the lower two segments. Further, the pectin in the CWs of the upper segment had a higher degree of methyl esterification than the other segments. In addition to the anticipated water-soluble pectins, the HEPES-soluble fractions surprisingly contained large amounts of heteroxylans. The CDTA and Na2CO3 fractions were rich in HG and RG-I, the 1 M KOH fraction had abundant heteroxylans, the 4 M KOH fraction was rich in xyloglucan and heteromannans, and cellulose was predominant in the final residue. The structures of the xyloglucans, heteroxylans and heteromannans were deduced from the linkage analysis and were similar to those present in most eudicotyledon parenchyma CWs. Cross polarization with magic angle spinning (CP/MAS) NMR spectroscopy showed no apparent difference in the rigid and semi-rigid polysaccharides in the CWs of the three segments. Single-pulse excitation with magic-angle spinning (SPE/MAS) NMR spectroscopy, which detects highly mobile polysaccharides, showed the presence of arabinan, the detailed structure of which varied among the cell walls from the three segments. CONCLUSIONS: Celery collenchyma CWs have similar polysaccharide compositions to most eudicotyledon parenchyma CWs. However, celery collenchyma CWs have much higher XG content than celery parenchyma CWs. The degree of methyl esterification of pectin and the structures of the arabinan side chains of RG-I show some variation in the collenchyma CWs from the different segments. Unexpectedly, the HEPES-soluble fraction contained a large amount of heteroxylans.","corpus_id":24343520,"score":1},{"doc_id":"28674916","title":"(2)H-(13)C correlation solid-state NMR for investigating dynamics and water accessibilities of proteins and carbohydrates.","abstract":"Site-specific determination of molecular motion and water accessibility by indirect detection of (2)H NMR spectra has advantages over dipolar-coupling based techniques due to the large quadrupolar couplings and the ensuing high angular resolution. Recently, a Rotor Echo Short Pulse IRrAdiaTION mediated cross polarization ((RESPIRATION)CP) technique was developed, which allowed efficient transfer of (2)H magnetization to (13)C at moderate (2)H radiofrequency field strengths available on most commercial MAS probes. In this work, we investigate the (2)H-(13)C magnetization transfer characteristics of one-bond perdeuterated CD n spin systems and two-bond H/D exchanged C-(O)-D and C-(N)-D spin systems in carbohydrates and proteins. Our results show that multi-bond, broadband (2)H-(13)C polarization transfer can be achieved using (2)H radiofrequency fields of ~50 kHz, relatively short contact times of 1.3-1.7 ms, and with sufficiently high sensitivity to enable 2D (2)H-(13)C correlation experiments with undistorted (2)H spectra in the indirect dimension. To demonstrate the utility of this (2)H-(13)C technique for studying molecular motion, we show (2)H-(13)C correlation spectra of perdeuterated bacterial cellulose, whose surface glucan chains exhibit a motionally averaged C6 (2)H quadrupolar coupling that indicates fast trans-gauche isomerization about the C5-C6 bond. In comparison, the interior chains in the microfibril core are fully immobilized. Application of the (2)H-(13)C correlation experiment to H/D exchanged Arabidopsis primary cell walls show that the O-D quadrupolar spectra of the highest polysaccharide peaks can be fit to a two-component model, in which 74% of the spectral intensity, assigned to cellulose, has a near-rigid-limit coupling, while 26% of the intensity, assigned to matrix polysaccharides, has a weakened coupling of 50 kHz. The latter O-D quadrupolar order parameter of 0.22 is significantly smaller than previously reported C-D dipolar order parameters of 0.46-0.55 for pectins, suggesting that additional motions exist at the C-O bonds in the wall polysaccharides. (2)H-(13)C polarization transfer profiles are also compared between statistically deuterated and H/D exchanged GB1.","corpus_id":10869643,"score":1},{"doc_id":"28759814","title":"Evaluation of hydrogen bond networks in cellulose Iβ and II crystals using density functional theory and Car-Parrinello molecular dynamics.","abstract":"Crystal models of cellulose Iβ and II, which contain various hydrogen bonding (HB) networks, were analyzed using density functional theory and Car-Parrinello molecular dynamics (CPMD) simulations. From the CPMD trajectories, the power spectra of the velocity correlation functions of hydroxyl groups involved in hydrogen bonds were calculated. For the Iβ allomorph, HB network A, which is dominant according to the neutron diffraction data, was stable, and the power spectrum represented the essential features of the experimental IR spectra. In contrast, network B, which is a minor structure, was unstable because its hydroxymethyl groups reoriented during the CPMD simulation, yielding a different crystal structure to that determined by experiments. For the II allomorph, a HB network A is proposed based on diffraction data, whereas molecular modeling identifies an alternative network B. Our simulations showed that the interaction energies of the cellulose II (B) model are slightly more favorable than model II(A). However, the evaluation of the free energy should be waited for the accurate determination from the energy point of view. For the IR calculation, cellulose II (B) model reproduces the spectra better than model II (A).","corpus_id":13783281,"score":1},{"doc_id":"29565567","title":"Hydrogen Bond Dynamics of Cellulose through Inelastic Neutron Scattering Spectroscopy.","abstract":"This work explores the dynamics of hydrogen bond networks in cellulose through inelastic neutron scattering (INS) and periodic CASTEP calculations. Estimated spectra were based on the crystal structure of cellulose Iα and Iβ and replicate the INS spectrum of cellulose samples with remarkable similarity, allowing a reliable assignment of INS bands to vibrational modes of cellulose. Comparison of cellulose samples from varied sources, from bacterial to kraft pulp, allows the identification of characteristic INS bands, arising from C2-OH torsional motions, which easily identify which allomorph-Iα or Iβ-is prevalent. A high crystallinity index is revealed by the presence of well-defined INS bands associated with highly cooperative CH bending modes along the chain. Hydrating kraft cellulose samples clearly affects those INS bands related with the hydroxymethyl group, identified as the preferred binding site for water molecules. At high humidity content level, a significant proportion of the water molecules is aggregated in clusters within the amorphous cellulose domains. The formation of ice microcrystals leads to a partial disruption of the hydrogen-bond network, as can be concluded from the observed red-shift of the torsional OH vibrational modes. The full assignment and interpretation of cellulose's INS spectra herein provided is a sound basis for future use of INS spectroscopy in the characterization of functionalized cellulose fibers and composite materials.","corpus_id":4700982,"score":1},{"doc_id":"18098151","title":"Solid-state NMR studies and DFT calculations of flavonoids: baicalein, baicalin and wogonoside.","abstract":"Three flavonoids of pharmaceutical importance-baicalein, baicalin, and wogonoside-were isolated from a Chinese medicinal plant Scutellaria baicalensis Georgi and studied by 13C NMR in solution and solid state. Two-dimensional (2D) NMR spectroscopy in the liquid phase and dipolar dephasing (DD) experiments in magic-angle spinning (MAS) spectra enabled the assignment of 13C resonances. The cross-polarization (CP) time constants T(CH) and relaxation times T(H) (1rho) were obtained from the variable-contact time experiments. The principal elements of the 13C chemical shift tensor were determined in the spectra recorded under slow sample spinning (2 kHz) using phase-adjusted spinning sideband (PASS)-2D NMR technique, and were verified by density functional theory gauge-independent atomic orbital (DFT GIAO) calculations of shielding constants. Analysis of the 13C delta(ii) and comparison with shielding parameters calculated for different conformers of compounds 1-3 enabled the selection of the most reliable geometry in the solid phase. In all three compounds, an intramolecular hydrogen bond C5--OH...=C4 is formed; the existence of baicalein and baicalin with 'anticlockwise' orientation of OH groups is more probable.","corpus_id":44605780,"score":0},{"doc_id":"18523586","title":"High-resolution 3D structure determination of kaliotoxin by solid-state NMR spectroscopy.","abstract":"High-resolution solid-state NMR spectroscopy can provide structural information of proteins that cannot be studied by X-ray crystallography or solution NMR spectroscopy. Here we demonstrate that it is possible to determine a protein structure by solid-state NMR to a resolution comparable to that by solution NMR. Using an iterative assignment and structure calculation protocol, a large number of distance restraints was extracted from (1)H/(1)H mixing experiments recorded on a single uniformly labeled sample under magic angle spinning conditions. The calculated structure has a coordinate precision of 0.6 A and 1.3 A for the backbone and side chain heavy atoms, respectively, and deviates from the structure observed in solution. The approach is expected to be applicable to larger systems enabling the determination of high-resolution structures of amyloid or membrane proteins.","corpus_id":1633957,"score":0},{"doc_id":"18980301","title":"Investigation of silver-containing layered materials and their interactions with primary amines using solid-state 109Ag and 15N NMR spectroscopy and first principles calculations.","abstract":"Silver-containing layered networks of the form [Ag(L)] (L = 4-pyridinesulfonate or p-toluenesulfonate) were treated with primary amines in different ratios. The structures of the parent supramolecular networks are well-known; however, their interactions with primary amines lead to the formation of new layered materials for which single-crystal X-ray structures cannot be obtained. Solid-state (109)Ag, (15)N, and (13)C cross-polarization magic-angle spinning (CP/MAS) NMR experiments, in combination with powder X-ray diffraction experiments and ab initio calculations, are utilized to investigate the interactions between the primary amines and the parent materials, and to propose structural models for the new materials. (109)Ag chemical shift (CS) tensor parameters are extremely sensitive to changes in silver environments; hence, (1)H-(109)Ag CP/MAS NMR experiments are used to distinguish and characterize silver sites. The combination of (109)Ag and (15)N NMR experiments on starting materials and samples prepared with both (15)N-labeled and unlabeled amines permits the accurate measurements of indirect (1)J((109)Ag,(15)N) and (1)J((109)Ag,(14)N) spin-spin coupling constants, providing further information on structure and bonding in these systems. First principles calculations of silver CS tensors and (1)J((109)Ag,(14)N) coupling constants in model complexes aid in formulating the proposed structural models for the new materials, which are largely comprised of layers of silver-diamine cations.","corpus_id":24477410,"score":0},{"doc_id":"19177476","title":"The structure of (SCN)(x): a study using molecular and solid-state density functional theory calculations.","abstract":"A riddle solved! Despite its simple formula, the structure of the (SCN)(x) polymer has remained elusive since its first synthesis in 1929. From energetics as well as NMR chemical shifts, based on DFT calculations, we have strong evidence that it is indeed a tangle of linear chains, made up from N-linked S(2)C(2)N five-membered rings. Molecular fragments and crystal structures based on proposed structures for polythiocyanogen were studied by using molecular and solid-state electronic structure calculations at the density functional theory level. The energetics and chemical shifts from both types of calculations indicate that a planar N-linked chain consisting of 1,2,4-dithiazole five-membered rings with adjacent rings pointing in opposite directions is the most likely local structure of the (SCN)(x) polymer.","corpus_id":7390333,"score":0},{"doc_id":"19331396","title":"Solid state NMR study and density functional theory (DFT) calculations of structure and dynamics of poly(p-xylylenes).","abstract":"High resolution solid state (13)C nuclear magnetic resonance (SS NMR) measurements were carried out on poly(p-xylylene) (PPX). The samples comprised vapor-deposited specimens as well as pure alpha and beta polymorphs of this polymer. The measurements were performed using cross-polarization and magic angle spinning (CP/MAS) techniques. Density functional theory gauge-including-atomic-orbital (DFT GIAO) calculations of NMR shielding parameters (13)C sigma(ii) were performed for the optimized geometry and structure of a xylylene trimer, acquired from the X-ray data, including intermolecular interactions. Two-dimensional phase adjusted spinning sideband (2D PASS) correlation was employed for the assignment of the values of the principal elements (13)C delta(ii) of the chemical shift tensor (CST). A comparative analysis of shielding (sigma(ii)) versus chemical shift (delta(ii)) parameters showed substantial differences between the molecular dynamics of alpha and beta polymorphs. This observation was further supported by the measurements of (13)C T(1) relaxation times and the analysis of cross-polarization kinetics. Frequency switched Lee-Goldburg heteronuclear correlation (FSLG HETCOR) for the (1)H-(13)C system was used in order to analyze molecular packing in both polymorphs. As a result of all of the above measurements, new insight into the mechanism of thermal phase transition from the alpha to the beta polymorph of poly(p-xylylene) is presented.","corpus_id":30133585,"score":0},{"doc_id":"19663434","title":"Conformational studies of poly(9,9-dialkylfluorene)s in solution using NMR spectroscopy and density functional theory calculations.","abstract":"Relationships have been obtained between intermonomer torsional angle and NMR chemical shifts ((1)H and (13)C) for isolated chains of two of the most important poly(9,9-dialkylfluorenes), poly[9,9-bis(2-ethylhexyl)fluorene-2,7-diyl] (PF2/6) and the copolymer poly(9,9-dioctylfluorene-co-[2,1,3]benzothiadiazole-4,7-diyl) (F8BT), using DFT calculations. The correlations provide a model for NMR spectral data interpretation and the basis for analysis of conformational changes in poly(9,9-dialkylfluorene-2,7-diyl)s. The correlations obtained for PF2/6 indicate that the (13)C chemical shifts of the aromatic carbons close to the intermonomer connection (C1, C2, and C3) have minimum values at planar conformations (0 degrees and 180 degrees ) and maximum values at 90 degrees conformations. In contrast, the (1)H chemical shifts of the corresponding aromatic ortho protons (Ha and Hb) are greatest for planar conformations, and the minimum values are seen for 90 degrees conformations. For the F8BT copolymer, similar relationships are observed for the (1)H (Ha, Hb, and Hc) aromatic shifts. Considering the aromatic carbons of F8BT, the behavior of C2, C4, C5, and C6 is similar to that found for the PF2/6 carbons. However, C1 and C3 of the fluorene moiety behave differently with varying torsion angle. These are in close proximity to the fluorene-benzothiadiazole linkage and are markedly affected by interactions with the thiadiazole unit such that delta(C1) is a maximum for 180 degrees and a minimum for 0 degrees , whereas delta(C3) is a maximum for 0 degrees and minimum for 180 degrees. We have studied the (1)H and (13)C spectra of the two polymers at temperatures between -50 degrees C and +65 degrees C. The observed changes to higher or lower frequency in the aromatic resonances were analyzed using these theoretical relationships. Fluorescence studies on PF2/6 in chloroform solution suggest there are no significant interchain interactions under these conditions. This is supported by variable-temperature NMR results. Polymer-solvent and polymer intramolecular interactions were found to be present and influence all of the alkylic and one of the aromatic (1)H resonances (Hb). The detailed attribution of the (1)H and (13)C NMR spectra of the two polymers was made prior to the establishment of the relationships between torsion angle and NMR chemical shifts. This was carried out through DFT calculation of the (1)H and (13)C shielding constants of the monomers, coupled with distortionless enhancement by polarization transfer and heteronuclear correlation NMR spectra. Several DFT levels of calculation were tested for both optimization of structures and shielding constants calculation. The B3LYP/6-31G(d,p) method was found to perform well in both cases.","corpus_id":15939891,"score":0},{"doc_id":"19900275","title":"Characterisation of different polymorphs of tris(8-hydroxyquinolinato)aluminium(III) using solid-state NMR and DFT calculations.","abstract":"BACKGROUND: Organic light emitting devices (OLED) are becoming important and characterisation of them, in terms of structure, charge distribution, and intermolecular interactions, is important. Tris(8-hydroxyquinolinato)-aluminium(III), known as Alq3, an organomettalic complex has become a reference material of great importance in OLED. It is important to elucidate the structural details of Alq3 in its various isomeric and solvated forms. Solid-state nuclear magnetic resonance (NMR) is a useful tool for this which can also complement the information obtained with X-ray diffraction studies. RESULTS: We report here 27Al one-dimensional (1D) and two-dimensional (2D) multiple-quantum magic-angle spinning (MQMAS) NMR studies of the meridional (alpha-phase) and the facial (delta-phase) isomeric forms of Alq3. Quadrupolar parameters are estimated from the 1D spectra under MAS and anisotropic slices of the 2D spectra and also calculated using DFT (density functional theory) quantum-chemical calculations. We have also studied solvated phase of Alq3 containing ethanol in its lattice. We show that both the XRD patterns and the quadrupolar parameters of the solvated phase are different from both the alpha-phase and the delta-phase, although the fluorescence emission shows no substantial difference between the alpha-phase and the solvated phase. Moreover, we have shown that after the removal of ethanol from the matrix the solvated Alq3 has similar XRD patterns and quadrupolar parameters to that of the alpha-phase. CONCLUSION: The 2D MQMAS experiments have shown that all the different modifications of Alq3 have 27Al in single unique crystallographic site. The quadrupolar parameters predicted using the DFT calculation under the isodensity polarisable continuum model resemble closely the experimentally obtained values. The solvated phase of Alq3 containing ethanol has structural difference from the alpha-phase of Alq3 (containing meridional isomer) from the solid-state NMR studies. Solid-state NMR can hence be used as an effective complementary tool to XRD for characterisation and structural elucidation.","corpus_id":11159250,"score":0},{"doc_id":"20958031","title":"High-resolution (19)F MAS NMR spectroscopy: structural disorder and unusual J couplings in a fluorinated hydroxy-silicate.","abstract":"High-resolution (19)F magic angle spinning (MAS) NMR spectroscopy is used to study disorder and bonding in a crystalline solid. (19)F MAS NMR reveals four distinct F sites in a 50% fluorine-substituted deuterated hydrous magnesium silicate (clinohumite, 4Mg(2)SiO(4)·Mg(OD(1-x)F(x))(2) with x = 0.5), indicating extensive structural disorder. The four (19)F peaks can be assigned using density functional theory (DFT) calculations of NMR parameters for a number of structural models with a range of possible local F environments generated by F(-)/OH(-) substitution. These assignments are supported by two-dimensional (19)F double-quantum MAS NMR experiments that correlate F sites based on either spatial proximity (via dipolar couplings) or through-bond connectivity (via scalar, or J, couplings). The observation of (19)F-(19)F J couplings is unexpected as the fluorines coordinate Mg atoms and the Mg-F interaction is normally considered to be ionic in character (i.e., there is no formal F-Mg-F covalent bonding arrangement). However, DFT calculations predict significant (19)F-(19)F J couplings, and these are in good agreement with the splittings observed in a (19)F J-resolved MAS NMR experiment. The existence of these J couplings is discussed in relation to both the nature of bonding in the solid state and the occurrence of so-called \"through-space\" (19)F-(19)F J couplings in solution. Finally, we note that we have found similar structural disorder and spin-spin interactions in both synthetic and naturally occurring clinohumite samples.","corpus_id":26079475,"score":0},{"doc_id":"21175136","title":"Solid-state NMR and density functional theory studies of ionization states of thiamin.","abstract":"Thiamin diphosphate (ThDP) is a key coenzyme in sugar metabolism. The 4'-aminopyrimidine ring of ThDP cycles through several ionization and tautomeric states during enzyme catalysis, but it is not fully understood which states are adopted during the individual steps of the catalytic cycle. Thiamin has been synthesized with labels selectively inserted into the C2 and C6' positions, as well as into the amino group, creating [C2, C6'-(13)C(2)] thiamin and [N4'-(15)N] thiamin. Magic-angle spinning (MAS) NMR spectroscopy has been employed to record the (13)C and (15)N chemical shift anisotropy (CSA) tensors for C2, C6', and N4' atoms. Our results indicate that the isotropic chemical shifts as well as the principal components of the (13)C and (15)N CSA tensors are very sensitive to the protonation states in these compounds and, therefore, permit differentiating between the two ionization states, 4-aminopyrimidine and 4-aminopyrimidinium. Using density functional theory (DFT), we have calculated the magnetic shielding anisotropy tensors of C2, C6', and N4' and found excellent agreement between the computed and the experimental tensors. Our findings indicate that MAS NMR spectroscopy in conjunction with DFT calculations is a sensitive probe of ionization states in the thiamin cofactor. The results of this study will serve as a guide for characterization of ionization and tautomeric states of thiamin in complexes with thiamin-dependent enzymes.","corpus_id":32191231,"score":0},{"doc_id":"21384011","title":"Multinuclear solid state NMR investigation of two polymorphic forms of ciprofloxacin-saccharinate.","abstract":"Two polymorphic forms of a novel pharmaceutical compound, ciprofloxacin-saccharinate (CIP-SAC), are analyzed using one dimensional (1D) and two dimensional (2D) (1)H nuclear magnetic resonance (NMR) at fast magic angle spinning (MAS). Additionally (15)N spectroscopy and (1)H-(13)C correlation experiments were performed to complement our conclusions. The 1D (1)H NMR spectra of CIP and complexes reveal valuable information about the ionic bonding between ciprofloxacin and saccharine. Additionally, these spectra allow us to perform a clear characterization of each solid form, giving the number of molecules per unit cell in one of the polymorphs. From 2D (1)H-(1)H spectra obtained through double quantum correlations we can arrive at important conclusions about the hydrogen bonding, conformation, and intra and inter-molecular interactions present in these compounds. Comparing and contrasting the (1)H-(1)H correlation data obtained for both polymorphic forms and taking into account the single crystal structure data existing for the solid form CIP-SAC (II) was possible to extract some conclusions on the polymorph CIP-SAC (I) where no single crystal information is available. (1)H MAS NMR is shown to be an important tool in the field of polymorphism and for the characterization of multicomponent pharmaceutical compounds.","corpus_id":205764252,"score":0},{"doc_id":"21846145","title":"Solvation and crystal effects in bilirubin studied by NMR spectroscopy and density functional theory.","abstract":"The open-chain tetrapyrrole compound bilirubin was investigated in chloroform and dimethyl sulfoxide solutions by liquid-state NMR and as solid by (1)H, (13)C, and (15)N magic-angle spinning (MAS) solid-state NMR spectroscopy. Density functional theory (DFT) calculations were performed to interpret the data, using the B3LYP exchange-correlation functional to optimize geometries and to compute NMR chemical shieldings by the gauge-including atomic orbital method. The dependence of geometries and chemical shieldings on the size of the basis sets was investigated for the reference molecules tetramethylsilane, NH(3), and H(2)O, and for bilirubin as a monomer and in clusters consisting of up to six molecules. In order to assess the intrinsic errors of the B3LYP approximation in calculating NMR shieldings, complete basis set estimates were obtained for the nuclear shielding values of the reference molecules. The experimental liquid-state NMR data of bilirubin are well reproduced by a monomeric bilirubin molecule using the 6-311+G(2d,p) basis set for geometry optimization and for calculating chemical shieldings. To simulate the bilirubin crystal, a hexameric model was required. It was constructed from geometry-optimized monomers using information from the X-ray structure of bilirubin to fix the monomeric entities in space and refined by partial optimization. Combining experimental (1)H-(13)C and (1)H-(15)N NMR correlation spectroscopy and density functional theory, almost complete sets of (1)H, (13)C, and (15)N chemical shift assignments were obtained for both liquid and solid states. It is shown that monomeric bilirubin in chloroform solution is formed by 3-vinyl anti conformers, while bilirubin crystals are formed by 3-vinyl syn conformers. This conformational change leads to characteristic differences between the liquid- and solid-state NMR resonances.","corpus_id":5586220,"score":0},{"doc_id":"22225526","title":"Multinuclear solid-state nuclear magnetic resonance and density functional theory characterization of interaction tensors in taurine.","abstract":"A variety of experimental solid-state nuclear magnetic resonance (NMR) techniques has been used to characterize each of the elements in 2-aminoethane sulfonic acid (taurine). A combination of (15)N cross-polarization magic angle spinning (CPMAS), (14)N ultrawideline, and (14)N overtone experiments enabled a determination of the relative orientation of the nitrogen electric field gradient and chemical shift tensors. (17)O spectra recorded from an isotopically enriched taurine sample at multiple magnetic fields allowed the three nonequivalent oxygen sites to be distinguished, and NMR parameters calculated from a neutron diffraction structure using density functional theory allowed the assignment of the (17)O parameters to the correct crystallographic sites. This is the first time that a complete set of (17)O NMR tensors are reported for a sulfonate group. In combination with (1)H and (13)C MAS spectra, as well as a previously reported (33)S NMR study, this provides a very broad set of NMR data for this relatively simple organic molecule, making it a potentially useful structure on which to test DFT calculation methods (particularly for the quadrupolar nuclei (14)N, (17)O, and (33)S) or NMR crystallography approaches.","corpus_id":26290723,"score":0},{"doc_id":"23464364","title":"Protein structure determination with paramagnetic solid-state NMR spectroscopy.","abstract":"Many structures of the proteins and protein assemblies that play central roles in fundamental biological processes and disease pathogenesis are not readily accessible via the conventional techniques of single-crystal X-ray diffraction and solution-state nuclear magnetic resonance (NMR). On the other hand, many of these challenging biological systems are suitable targets for atomic-level structural and dynamic analysis by magic-angle spinning (MAS) solid-state NMR spectroscopy, a technique that has far less stringent limitations on the molecular size and crystalline state. Over the past decade, major advances in instrumentation and methodology have prompted rapid growth in the field of biological solid-state NMR. However, despite this progress, one challenge for the elucidation of three-dimensional (3D) protein structures via conventional MAS NMR methods is the relative lack of long-distance data. Specifically, extracting unambiguous interatomic distance restraints larger than ∼5 Å from through-space magnetic dipole-dipole couplings among the protein (1)H, (13)C, and (15)N nuclei has proven to be a considerable challenge for researchers. It is possible to circumvent this problem by extending the structural studies to include several analogs of the protein of interest, intentionally modified to contain covalently attached paramagnetic tags at selected sites. In these paramagnetic proteins, the hyperfine couplings between the nuclei and unpaired electrons can manifest themselves in NMR spectra in the form of relaxation enhancements of the nuclear spins that depend on the electron-nucleus distance. These effects can be significant for nuclei located up to ∼20 Å away from the paramagnetic center. In this Account, we discuss MAS NMR structural studies of nitroxide and EDTA-Cu(2+) labeled variants of a model 56 amino acid globular protein, B1 immunoglobulin-binding domain of protein G (GB1), in the microcrystalline solid phase. We used a set of six EDTA-Cu(2+)-tagged GB1 mutants to rapidly determine the global protein fold in a de novo fashion. Remarkably, these studies required quantitative measurements of only approximately four or five backbone amide (15)N longitudinal paramagnetic relaxation enhancements per residue, in the complete absence of the usual internuclear distance restraints. Importantly, this paramagnetic solid-state NMR methodology is general and can be directly applied to larger proteins and protein complexes for which a significant fraction of the signals can be assigned in standard 2D and 3D MAS NMR chemical shift correlation spectra.","corpus_id":14721048,"score":0},{"doc_id":"23738844","title":"Sum-frequency-generation vibration spectroscopy and density functional theory calculations with dispersion corrections (DFT-D2) for cellulose Iα and Iβ.","abstract":"Sum-frequency-generation (SFG) vibration spectroscopy selectively detects noncentrosymmetric vibrational modes in crystalline cellulose inside intact lignocellulose. However, SFG peak assignment in biomass samples is challenging due to the complexity of the SFG processes and the lack of reference SFG spectra from the two crystal forms synthesized in nature, cellulose Iα and Iβ. This paper compares SFG spectra of laterally aligned cellulose Iα and Iβ crystals with vibration frequencies calculated from density functional theory with dispersion corrections (DFT-D2). Two possible hydrogen-bond networks A and B ( Nishiyama et al. Biomacromolecules 2008 , 9 , 3133 ) were investigated for both polymorphs. From DFT-D2 calculations the energetically favorable structures for cellulose Iα and Iβ had CH2OH groups in tg conformations and network A hydrogen bonding. The calculated frequencies of C-H stretch modes agreed reasonably well with the peak positions observed with SFG and were localized vibrations; thus, peak assignments to specific alkyl groups were proposed. DFT-D2 calculations underestimated the distances between hydrogen-bonded oxygen atoms compared to the experimentally determined values; therefore, the OH stretching calculated frequencies were ~100 cm(-1) lower than observed. The SFG peak assignments through comparison with DFT-D2 calculations will guide the SFG analysis of the crystalline cellulose structure in plant cell walls and lignocellulose biomass.","corpus_id":24349408,"score":0},{"doc_id":"23918278","title":"Solid-state NMR analysis of a boron-containing pharmaceutical hydrochloride salt.","abstract":"A novel crystalline form of the boron-containing antibacterial drug (S)-3-(aminomethyl)-7-(3-hydroxypropoxy)benzo[c] [1,2]oxaborol-1(3H)-ol hydrochloride is studied by solid-state nuclear magnetic resonance (SSNMR) and single-crystal X-ray diffraction techniques. After determination of the crystal structure by X-ray diffraction, SSNMR spectroscopy of this form is performed to obtain structural information using experimental approaches based on dipolar correlation, chemical shift analysis, and quadrupolar interaction analysis. 1H SSNMR experiments at 16.4 T using magic-angle spinning (MAS) and homonuclear dipolar decoupling, 2D SSNMR experiments based on (1)H–(13)C and (1)H–(11)B dipolar heteronuclear correlation, and density functional theory (DFT) calculations are combined in a novel approach to obtain a nearly complete assignment of the (1)H spectrum of this crystalline phase. (11)B and (35)Cl chemical shift and quadrupolar parameters are obtained using the analysis of MAS spectra and are found to be accurately reproduced using DFT calculations. NMR chemical shielding and electric field gradient parameters obtained using these methods are related to hydrogen-bonding trends in the crystal structure. The results illustrate the increasing capability of SSNMR techniques involving (1)H, (11)B, and (35)Cl SSNMR in the analysis of the crystal structure of a pharmaceutical compound containing covalently bonded boron.","corpus_id":40929584,"score":0},{"doc_id":"23999926","title":"Global fold of human cannabinoid type 2 receptor probed by solid-state 13C-, 15N-MAS NMR and molecular dynamics simulations.","abstract":"The global fold of human cannabinoid type 2 (CB2 ) receptor in the agonist-bound active state in lipid bilayers was investigated by solid-state (13)C- and (15)N magic-angle spinning (MAS) NMR, in combination with chemical-shift prediction from a structural model of the receptor obtained by microsecond-long molecular dynamics (MD) simulations. Uniformly (13)C- and (15)N-labeled CB2 receptor was expressed in milligram quantities by bacterial fermentation, purified, and functionally reconstituted into liposomes. (13)C MAS NMR spectra were recorded without sensitivity enhancement for direct comparison of Cα, Cβ, and C=O bands of superimposed resonances with predictions from protein structures generated by MD. The experimental NMR spectra matched the calculated spectra reasonably well indicating agreement of the global fold of the protein between experiment and simulations. In particular, the (13) C chemical shift distribution of Cα resonances was shown to be very sensitive to both the primary amino acid sequence and the secondary structure of CB2. Thus the shape of the Cα band can be used as an indicator of CB2 global fold. The prediction from MD simulations indicated that upon receptor activation a rather limited number of amino acid residues, mainly located in the extracellular Loop 2 and the second half of intracellular Loop 3, change their chemical shifts significantly (≥ 1.5 ppm for carbons and ≥ 5.0 ppm for nitrogens). Simulated two-dimensional (13) Cα(i)-(13)C=O(i) and (13)C=O(i)-(15)NH(i + 1) dipolar-interaction correlation spectra provide guidance for selective amino acid labeling and signal assignment schemes to study the molecular mechanism of activation of CB2 by solid-state MAS NMR.","corpus_id":25483523,"score":0},{"doc_id":"24516184","title":"Density functional theory in the solid state.","abstract":"Density functional theory (DFT) has been used in many fields of the physical sciences, but none so successfully as in the solid state. From its origins in condensed matter physics, it has expanded into materials science, high-pressure physics and mineralogy, solid-state chemistry and more, powering entire computational subdisciplines. Modern DFT simulation codes can calculate a vast range of structural, chemical, optical, spectroscopic, elastic, vibrational and thermodynamic phenomena. The ability to predict structure-property relationships has revolutionized experimental fields, such as vibrational and solid-state NMR spectroscopy, where it is the primary method to analyse and interpret experimental spectra. In semiconductor physics, great progress has been made in the electronic structure of bulk and defect states despite the severe challenges presented by the description of excited states. Studies are no longer restricted to known crystallographic structures. DFT is increasingly used as an exploratory tool for materials discovery and computational experiments, culminating in ex nihilo crystal structure prediction, which addresses the long-standing difficult problem of how to predict crystal structure polymorphs from nothing but a specified chemical composition. We present an overview of the capabilities of solid-state DFT simulations in all of these topics, illustrated with recent examples using the CASTEP computer program.","corpus_id":7994033,"score":0},{"doc_id":"25133518","title":"Solid-state NMR analysis of a complex crystalline phase of ronacaleret hydrochloride.","abstract":"A crystalline phase of the pharmaceutical compound ronacaleret hydrochloride is studied by solid-state nuclear magnetic resonance (SSNMR) spectroscopy and single-crystal X-ray diffraction. The crystal structure is determined to contain two independent cationic molecules and chloride anions in the asymmetric unit, which combine with the covalent structure of the molecule to yield complex SSNMR spectra. Experimental approaches based on dipolar correlation, chemical shift tensor analysis, and quadrupolar interaction analysis are employed to obtain detailed information about this phase. Density functional theory (DFT) calculations are used to predict chemical shielding and electric field gradient (EFG) parameters for comparison with experiment. (1)H SSNMR experiments performed at 16.4 T using magic-angle spinning (MAS) and homonuclear dipolar decoupling provide information about hydrogen bonding and molecular connectivity that can be related to the crystal structure. (19)F and (13)C assignments for the Z' = 2 structure are obtained using DFT calculations, (19)F homonuclear dipolar correlation, and (13)C-(19)F heteronuclear dipolar correlation experiments. (35)Cl MAS experiments at 16.4 T observe two chlorine sites that are assigned using calculated chemical shielding and EFG parameters. SSNMR dipolar correlation experiments are used to extract (1)H-(13)C, (1)H-(15)N, (1)H-(19)F, (13)C-(19)F, and (1)H-(35)Cl through-space connectivity information for many positions of interest. The results allow for the evaluation of the performance of a suite of SSNMR experiments and computational approaches as applied to a complex but typical pharmaceutical solid phase.","corpus_id":20647613,"score":0},{"doc_id":"25306191","title":"On the crystal structure of the vaterite polymorph of CaCO3: a calcium-43 solid-state NMR and computational assessment.","abstract":"The vaterite polymorph of CaCO3 has puzzled crystallographers for decades in part due to difficulties in obtaining single crystals. The multiple proposed structures for the vaterite polymorph of CaCO3 are assessed using a combined (43)Ca solid-state nuclear magnetic resonance (SSNMR) spectroscopic and computational approach. A combination of improved experimental and computational methods, along with a calibrated chemical shift scale and (43)Ca nuclear quadrupole moment, allow for improved insights relative to our earlier work (Bryce et al., J. Am. Chem. Soc. 2008, 130, 9282). Here, we synthesize a (43)Ca isotopically-enriched sample of vaterite and perform high-resolution quadrupolar SSNMR experiments including magic-angle spinning (MAS), double-rotation (DOR), and multiple-quantum (MQ) MAS experiments at magnetic field strengths of 9.4 and 21.1T. We identify one crystallographically unique Ca(2+) site in vaterite with a slight distribution in both chemical shifts and quadrupolar parameters. Both the experimental (43)Ca electric field gradient tensor and the isotropic chemical shift for vaterite are compared to those calculated with the gauge-including projector-augmented-wave (GIPAW) DFT method in an attempt to identify the model that best represents the crystal structure of vaterite. Simulations of (43)Ca DOR and MAS NMR spectra based on the NMR parameters computed for a total of 18 structural models for vaterite allow us to distinguish between these models. Among these 18, the P3221 and C2 structures provide simulated spectra and diffractograms in best agreement with all experimental data.","corpus_id":23928342,"score":0},{"doc_id":"26114877","title":"Terahertz Spectroscopy and Solid-State Density Functional Theory Calculations of Cyanobenzaldehyde Isomers.","abstract":"Spectral signatures in the terahertz (THz) frequency region are mainly due to bulk vibrations of the molecules. These resonances are highly sensitive to the relative position of atoms in a molecule as well as the crystal packing arrangement. To understand the variation of THz resonances, THz spectra (2-10 THz) of three structural isomers: 2-, 3-, and 4-cyanobenzaldehyde have been studied. THz spectra obtained from Fourier transform infrared (FTIR) spectrometry of these isomers show that the resonances are distinctly different especially below 5 THz. For understanding the intermolecular interactions due to hydrogen bonds, four molecule cluster simulations of each of the isomers have been carried out using the B3LYP density functional with the 6-31G(d,p) basis set in Gaussian09 software and the compliance constants are obtained. However, to understand the exact reason behind the observed resonances, simulation of each isomer considering the full crystal structure is essential. The crystal structure of each isomer has been determined using X-ray diffraction (XRD) analysis for carrying out crystal structure simulations. Density functional theory (DFT) simulations using CRYSTAL14 software, utilizing the hybrid density functional B3LYP, have been carried out to understand the vibrational modes. The bond lengths and bond angles from the optimized structures are compared with the XRD results in terms of root-mean-square-deviation (RMSD) values. Very low RMSD values confirm the overall accuracy of the results. The simulations are able to predict most of the spectral features exhibited by the isomers. The results show that low frequency modes (<3 THz) are mediated through hydrogen bonds and are dominated by intermolecular vibrations.","corpus_id":28110208,"score":0},{"doc_id":"26372719","title":"Combining Nuclear Magnetic Resonance Spectroscopy and Density Functional Theory Calculations to Characterize Carvedilol Polymorphs.","abstract":"The experiments of carvedilol form II, form III and hydrate by (13) C and (15) N cross-polarization magic-angle spinning (CP MAS) are reported. The GIPAW (gauge-including projector-augmented wave) method from DFT (density functional theory) calculations was used to simulate (13) C and (15) N chemical shifts. A very good agreement was found for the comparison between the global results of experimental and calculated nuclear magnetic resonance (NMR) chemical shifts for carvedilol polymorphs. This work aims a comprehensive understanding of carvedilol crystalline forms employing solution and solid-state NMR as well as DFT calculations. © 2015 Wiley Periodicals, Inc. and the American Pharmacists Association J Pharm Sci.","corpus_id":5573445,"score":0},{"doc_id":"27018827","title":"Molecular and electron-spin structures of a ring-shaped mixed-valence polyoxovanadate (IV, V) studied by (11)B and (23)Na solid-state NMR spectroscopy and DFT calculations.","abstract":"(11)B and (23)Na solid-state nuclear magnetic resonance (NMR) spectra of ring-shaped paramagnetic crystals of H15[V7(IV)V5(V)B32O84Na4]·13H2O containing seven d(1) electrons from V(IV) were studied. Magic-angle-spinning (MAS) and multiple-quantum MAS NMR experiments were performed at moderate (9.4T) and ultrahigh magnetic fields (21.6T). The NMR parameters for quadrupole and isotropic chemical shift interactions were estimated by simulation of the NMR spectra and from relativistic density functional theory (DFT) calculations. Four Na ions incorporated into the framework were found to occupy four distinct sites with different populations. The DFT calculation showed that d(1) electrons with effectively one up-spin caused by strong antiferromagnetic interactions were delocalized over the 12V ions.","corpus_id":205236529,"score":0},{"doc_id":"27891541","title":"DFT calculations in the assignment of solid-state NMR and crystal structure elucidation of a lanthanum(iii) complex with dithiocarbamate and phenanthroline.","abstract":"The molecular, crystal, and electronic structures as well as spectroscopic properties of a mononuclear heteroleptic lanthanum(iii) complex with diethyldithiocarbamate and 1,10-phenanthroline ligands (3 : 1) were studied by solid-state (13)C and (15)N cross-polarisation (CP) magic-angle-spinning (MAS) NMR, X-ray diffraction (XRD), and first principles density functional theory (DFT) calculations. A substantially different powder XRD pattern and (13)C and (15)N CP-MAS NMR spectra indicated that the title compound is not isostructural to the previously reported analogous rare earth complexes with the space group P21/n. Both (13)C and (15)N CP-MAS NMR revealed the presence of six structurally different dithiocarbamate groups in the asymmetric unit cell, implying a non-centrosymmetric packing arrangement of molecules. This was supported by single-crystal X-ray crystallography showing that the title compound crystallised in the triclinic space group P1[combining macron]. In addition, the crystal structure also revealed that one of the dithiocarbamate ligands has a conformational disorder. NMR chemical shift calculations employing the periodic gauge including projector augmented wave (GIPAW) approach supported the assignment of the experimental (13)C and (15)N NMR spectra. However, the best correspondences were obtained with the structure where the atomic positions in the X-ray unit cell were optimised at the DFT level. The roles of the scalar and spin-orbit relativistic effects on NMR shielding were investigated using the zeroth-order regular approximation (ZORA) method with the outcome that already the scalar relativistic level qualitatively reproduces the experimental chemical shifts. The electronic properties of the complex were evaluated based on the results of the natural bond orbital (NBO) and topology of the electron density analyses. Overall, we apply a multidisciplinary approach acquiring comprehensive information about the solid-state structure and the metal-ligand bonding of the heteroleptic lanthanum complex.","corpus_id":38206398,"score":0}],"string":"[\n {\n \"doc_id\": \"19505136\",\n \"title\": \"Localization of crystalline allomorphs in cellulose microfibril.\",\n \"abstract\": \"We report an FTIR spectroscopic technique combined with intracrystalline deuteration and rehydrogenation of cellulose samples to investigate the localization of I(alpha) and I(beta) domains within a cellulose microfibril obtained from I(alpha)-rich algae. When Glaucocystis cellulose incompletely converted from I(alpha) to I(beta) was deuterated and rehydrogenated at elevated temperature, OD groups involved in hydrogen bonding in the I(beta) domain first reverted to OH, followed by those in the I(alpha) domain, suggesting that the I(alpha) core domain was surrounded by the I(beta) domain in an artificially induced sample. We concluded that this I(alpha) --> I(beta) conversion proceeded from the surface toward the core. Native celluloses from Valonia and Cladophora were first deuterated without changing the allomorphic composition, and rehydrogenation was studied from I(alpha)- and I(beta)-specific absorbances. Surprisingly, both absorbances changed synchronously, clearly indicating that the simple \\\"skin-core\\\" distribution model of I(alpha) and I(beta) domains is not realistic at least for these native celluloses.\",\n \"corpus_id\": 192501,\n \"score\": 2\n },\n {\n \"doc_id\": \"21204530\",\n \"title\": \"Structure and interactions of plant cell-wall polysaccharides by two- and three-dimensional magic-angle-spinning solid-state NMR.\",\n \"abstract\": \"The polysaccharide-rich cell walls (CWs) of plants perform essential functions such as maintaining tensile strength and allowing plant growth. Using two- and three-dimensional magic-angle-spinning (MAS) solid-state NMR and uniformly (13)C-labeled Arabidopsis thaliana, we have assigned the resonances of the major polysaccharides in the intact and insoluble primary CW and determined the intermolecular contacts and dynamics of cellulose, hemicelluloses, and pectins. Cellulose microfibrils showed extensive interactions with pectins, while the main hemicellulose, xyloglucan, exhibited few cellulose cross-peaks, suggesting limited entrapment in the microfibrils rather than extensive surface coating. Site-resolved (13)C T(1) and (1)H T(1ρ) relaxation times indicate that the entrapped xyloglucan has motional properties that are intermediate between the rigid cellulose and the dynamic pectins. Xyloglucan absence in a triple knockout mutant caused the polysaccharides to undergo much faster motions than in the wild-type CW. These results suggest that load bearing in plant CWs is accomplished by a single network of all three types of polysaccharides instead of a cellulose-xyloglucan network, thus revising the existing paradigm of CW structure. The extensive pectin-cellulose interaction suggests a central role for pectins in maintaining the structure and function of plant CWs. This study demonstrates the power of multidimensional MAS NMR for molecular level investigation of the structure and dynamics of complex and energy-rich plant materials.\",\n \"corpus_id\": 42980200,\n \"score\": 2\n },\n {\n \"doc_id\": \"21222085\",\n \"title\": \"Using solid-state ¹³C NMR spectroscopy to study the molecular organisation of primary plant cell walls.\",\n \"abstract\": \"Studies of the mobilities of polysaccharides or parts of polysaccharides in a cell-wall preparation may give clues about the molecular interactions among the polysaccharides in the cell wall and the relative locations of polysaccharides within the cell wall. A number of solid-state (13)C NMR techniques have been developed that can be used to investigate different types of polysaccharide mobilities: rigid, semi-rigid, mobile, and highly mobile. In this chapter, techniques are described for obtaining spectra from primary cell-wall preparations using CP/MAS, proton-rotating frame, proton spin-spin, spin-echo relaxation spectra, and single-pulse excitation. We also describe how proton spin relaxation editing can be used to obtain subspectra for cell-wall polysaccharides of different mobilities.\",\n \"corpus_id\": 40079398,\n \"score\": 2\n },\n {\n \"doc_id\": \"22295909\",\n \"title\": \"Solid-state selective (13)C excitation and spin diffusion NMR to resolve spatial dimensions in plant cell walls.\",\n \"abstract\": \"The average spatial dimensions between major biopolymers within the plant cell wall can be resolved using a solid-state NMR technique referred to as a (13)C cross-polarization (CP) SELDOM (selectively by destruction of magnetization) with a mixing time delay for spin diffusion. Selective excitation of specific aromatic lignin carbons indicates that lignin is in close proximity to hemicellulose followed by amorphous and finally crystalline cellulose. (13)C spin diffusion time constants (T(SD)) were extracted using a two-site spin diffusion theory developed for (13)C nuclei under magic angle spinning (MAS) conditions. These time constants were then used to calculate an average lower-limit spin diffusion length between chemical groups within the plant cell wall. The results on untreated (13)C enriched corn stover stem reveal that the lignin carbons are, on average, located at distances ∼0.7-2.0 nm from the carbons in hemicellulose and cellulose, whereas the pretreated material had larger separations.\",\n \"corpus_id\": 31170162,\n \"score\": 2\n },\n {\n \"doc_id\": \"22777793\",\n \"title\": \"Multidimensional solid-state NMR studies of the structure and dynamics of pectic polysaccharides in uniformly 13C-labeled Arabidopsis primary cell walls.\",\n \"abstract\": \"Plant cell wall (CW) polysaccharides are responsible for the mechanical strength and growth of plant cells; however, the high-resolution structure and dynamics of the CW polysaccharides are still poorly understood because of the insoluble nature of these molecules. Here, we use 2D and 3D magic-angle-spinning (MAS) solid-state NMR (SSNMR) to investigate the structural role of pectins in the plant CW. Intact and partially depectinated primary CWs of Arabidopsis thaliana were uniformly labeled with (13)C and their NMR spectra were compared. Recent (13)C resonance assignment of the major polysaccharides in Arabidopsis thaliana CWs allowed us to determine the effects of depectination on the intermolecular packing and dynamics of the remaining wall polysaccharides. 2D and 3D correlation spectra show the suppression of pectin signals, confirming partial pectin removal by chelating agents and sodium carbonate. Importantly, higher cross peaks are observed in 2D and 3D (13)C spectra of the depectinated CW, suggesting higher rigidity and denser packing of the remaining wall polysaccharides compared with the intact CW. (13)C spin-lattice relaxation times and (1)H rotating-frame spin-lattice relaxation times indicate that the polysaccharides are more rigid on both the nanosecond and microsecond timescales in the depectinated CW. Taken together, these results indicate that pectic polysaccharides are highly dynamic and endow the polysaccharide network of the primary CW with mobility and flexibility, which may be important for pectin functions. This study demonstrates the capability of multidimensional SSNMR to determine the intermolecular interactions and dynamic structures of complex plant materials under near-native conditions.\",\n \"corpus_id\": 23964270,\n \"score\": 2\n },\n {\n \"doc_id\": \"22939331\",\n \"title\": \"Exploring the conformational space of amorphous cellulose using NMR chemical shifts.\",\n \"abstract\": \"(13)C-labeled amorphous cellulose and (13)C NMR chemical shifts by 2D (13)C-(13)C correlation spectroscopy were obtained in the regenerated solid-state from ionic liquids. On the basis of the assigned chemical shifts, combined with information from molecular dynamics and quantum chemistry computer simulations a twisted structure for amorphous cellulose is proposed exposing more hydrophilic surface than that of extended crystalline cellulose.\",\n \"corpus_id\": 30709476,\n \"score\": 2\n },\n {\n \"doc_id\": \"23167456\",\n \"title\": \"Pectin-cellulose interactions in the Arabidopsis primary cell wall from two-dimensional magic-angle-spinning solid-state nuclear magnetic resonance.\",\n \"abstract\": \"The primary cell wall of higher plants consists of a mixture of polysaccharides whose spatial proximities and interactions with each other are not well understood. We recently obtained the first two-dimensional (2D) and three-dimensional high-resolution magic-angle-spinning (13)C solid-state nuclear magnetic resonance spectra of the uniformly (13)C-labeled primary cell wall of Arabidopsis thaliana, which allowed us to assign the majority of (13)C resonances of the three major classes of polysaccharides: cellulose, hemicellulose, and pectins. In this work, we measured the intensity buildup of (13)C-(13)C cross-peaks in a series of 2D (13)C correlation spectra to obtain semiquantitative information about the spatial proximities between different polysaccharides. Comparison of 2D spectra measured at different spin diffusion mixing times identified intermolecular pectin-cellulose cross-peaks as well as interior cellulose-surface cellulose cross-peaks. The intensity buildup time constants are only modestly longer for cellulose-pectin cross-peaks than for interior cellulose-surface cellulose cross-peaks, indicating that pectins come into direct contact with the cellulose microfibrils. Approximately 25-50% of the cellulose chains exhibit close contact with pectins. The (13)C magnetization of the wall polysaccharides is not fully equilibrated by 1.5 s, indicating that pectins and cellulose are not homogeneously mixed on the molecular level. We also assigned the (13)C signals of cell wall proteins, identifying common residues such as Pro, Hyp, Tyr, and Ala. The chemical shifts indicate significant coil and sheet conformations in these structural proteins. Interestingly, few cross- peaks were observed between the proteins and the polysaccharides. Taken together, these data indicate that the three major types of polysaccharides in the primary wall of Arabidopsis form a single cohesive network, while structural proteins form a relatively separate domain.\",\n \"corpus_id\": 11561580,\n \"score\": 2\n },\n {\n \"doc_id\": \"23175754\",\n \"title\": \"Structure of cellulose microfibrils in primary cell walls from collenchyma.\",\n \"abstract\": \"In the primary walls of growing plant cells, the glucose polymer cellulose is assembled into long microfibrils a few nanometers in diameter. The rigidity and orientation of these microfibrils control cell expansion; therefore, cellulose synthesis is a key factor in the growth and morphogenesis of plants. Celery (Apium graveolens) collenchyma is a useful model system for the study of primary wall microfibril structure because its microfibrils are oriented with unusual uniformity, facilitating spectroscopic and diffraction experiments. Using a combination of x-ray and neutron scattering methods with vibrational and nuclear magnetic resonance spectroscopy, we show that celery collenchyma microfibrils were 2.9 to 3.0 nm in mean diameter, with a most probable structure containing 24 chains in cross section, arranged in eight hydrogen-bonded sheets of three chains, with extensive disorder in lateral packing, conformation, and hydrogen bonding. A similar 18-chain structure, and 24-chain structures of different shape, fitted the data less well. Conformational disorder was largely restricted to the surface chains, but disorder in chain packing was not. That is, in position and orientation, the surface chains conformed to the disordered lattice constituting the core of each microfibril. There was evidence that adjacent microfibrils were noncovalently aggregated together over part of their length, suggesting that the need to disrupt these aggregates might be a constraining factor in growth and in the hydrolysis of cellulose for biofuel production.\",\n \"corpus_id\": 22599131,\n \"score\": 2\n },\n {\n \"doc_id\": \"24720372\",\n \"title\": \"Structure and dynamics of Brachypodium primary cell wall polysaccharides from two-dimensional (13)C solid-state nuclear magnetic resonance spectroscopy.\",\n \"abstract\": \"The polysaccharide structure and dynamics in the primary cell wall of the model grass Brachypodium distachyon are investigated for the first time using solid-state nuclear magnetic resonance (NMR). While both grass and non-grass cell walls contain cellulose as the main structural scaffold, the former contains xylan with arabinose and glucuronic acid substitutions as the main hemicellulose, with a small amount of xyloglucan (XyG) and pectins, while the latter contains XyG as the main hemicellulose and significant amounts of pectins. We labeled the Brachypodium cell wall with (13)C to allow two-dimensional (2D) (13)C correlation NMR experiments under magic-angle spinning. Well-resolved 2D spectra are obtained in which the (13)C signals of cellulose, glucuronoarabinoxylan (GAX), and other matrix polysaccharides can be assigned. The assigned (13)C chemical shifts indicate that there are a large number of arabinose and xylose linkages in the wall, and GAX is significantly branched at the developmental stage of 2 weeks. 2D (13)C-(13)C correlation spectra measured with long spin diffusion mixing times indicate that the branched GAX approaches cellulose microfibrils on the nanometer scale, contrary to the conventional model in which only unbranched GAX can bind cellulose. The GAX chains are highly dynamic, with average order parameters of ~0.4. Biexponential (13)C T1 and (1)H T1ρ relaxation indicates that there are two dynamically distinct domains in GAX: the more rigid domain may be responsible for cross-linking cellulose microfibrils, while the more mobile domain may fill the interfibrillar space. This dynamic heterogeneity is more pronounced than that of the non-grass hemicellulose, XyG, suggesting that GAX adopts the mixed characteristics of XyG and pectins. Moderate differences in cellulose rigidity are observed between the Brachypodium and Arabidopsis cell walls, suggesting different effects of the matrix polysaccharides on cellulose. These data provide the first molecular-level structural information about the three-dimensional organization of the polysaccharides in the grass primary wall.\",\n \"corpus_id\": 25717651,\n \"score\": 2\n },\n {\n \"doc_id\": \"24984197\",\n \"title\": \"Water-polysaccharide interactions in the primary cell wall of Arabidopsis thaliana from polarization transfer solid-state NMR.\",\n \"abstract\": \"Polysaccharide-rich plant cell walls are hydrated under functional conditions, but the molecular interactions between water and polysaccharides in the wall have not been investigated. In this work, we employ polarization transfer solid-state NMR techniques to study the hydration of primary-wall polysaccharides of the model plant, Arabidopsis thaliana. By transferring water (1)H polarization to polysaccharides through distance- and mobility-dependent (1)H-(1)H dipolar couplings and detecting it through polysaccharide (13)C signals, we obtain information about water proximity to cellulose, hemicellulose, and pectins as well as water mobility. Both intact and partially extracted cell wall samples are studied. Our results show that water-pectin polarization transfer is much faster than water-cellulose polarization transfer in all samples, but the extent of extraction has a profound impact on the water-polysaccharide spin diffusion. Removal of calcium ions and the consequent extraction of homogalacturonan (HG) significantly slowed down spin diffusion, while further extraction of matrix polysaccharides restored the spin diffusion rate. These trends are observed in cell walls with similar water content, thus they reflect inherent differences in the mobility and spatial distribution of water. Combined with quantitative analysis of the polysaccharide contents, our results indicate that calcium ions and HG gelation increase the amount of bound water, which facilitates spin diffusion, while calcium removal disrupts the gel and gives rise to highly dynamic water, which slows down spin diffusion. The recovery of spin diffusion rates after more extensive extraction is attributed to increased water-exposed surface areas of the polysaccharides. Water-pectin spin diffusion precedes water-cellulose spin diffusion, lending support to the single-network model of plant primary walls in which a substantial fraction of the cellulose surface is surrounded by pectins.\",\n \"corpus_id\": 207110985,\n \"score\": 2\n },\n {\n \"doc_id\": \"25739924\",\n \"title\": \"Probing the molecular architecture of Arabidopsis thaliana secondary cell walls using two- and three-dimensional (13)C solid state nuclear magnetic resonance spectroscopy.\",\n \"abstract\": \"The plant secondary cell wall is a thickened polysaccharide and phenolic structure, providing mechanical strength to cells, particularly in woody tissues. It is the main feedstock for the developing bioenergy and green chemistry industries. Despite the role that molecular architecture (the arrangement of biopolymers relative to each other, and their conformations) plays in dictating biomass properties, such as recalcitrance to breakdown, it is poorly understood. Here, unprocessed dry (13)C-labeled stems from the model plant Arabidopsis thaliana were analyzed by a variety of (13)C solid state magic angle spinning nuclear magnetic resonance methods, such as one-dimensional cross-polarization and direct polarization, two-dimensional refocused INADEQUATE, RFDR, PDSD, and three-dimensional DARR, demonstrating their viability for the study of native polymer arrangements in intact secondary cell walls. All carbon sites of the two main glucose environments in cellulose (previously assigned to microfibril surface and interior residues) are clearly resolved, as are carbon sites of the other major components of the secondary cell wall: xylan and lignin. The xylan carbon 4 chemical shift is markedly different from that reported previously for solution or primary cell wall xylan, indicating significant changes in the helical conformation in these dried stems. Furthermore, the shift span indicates that xylan adopts a wide range of conformations in this material, with very little in the 31 conformation typical of xylan in solution. Additionally, spatial connections of noncarbohydrate species were observed with both cellulose peaks conventionally assigned as \\\"surface\\\" and as \\\"interior\\\" cellulose environments, raising questions about the origin of these two cellulose signals.\",\n \"corpus_id\": 10955354,\n \"score\": 2\n },\n {\n \"doc_id\": \"26355148\",\n \"title\": \"Solid-state NMR investigations of cellulose structure and interactions with matrix polysaccharides in plant primary cell walls.\",\n \"abstract\": \"Until recently, the 3D architecture of plant cell walls was poorly understood due to the lack of high-resolution techniques for characterizing the molecular structure, dynamics, and intermolecular interactions of the wall polysaccharides in these insoluble biomolecular mixtures. We introduced multidimensional solid-state NMR (SSNMR) spectroscopy, coupled with (13)C labelling of whole plants, to determine the spatial arrangements of macromolecules in near-native plant cell walls. Here we review key evidence from 2D and 3D correlation NMR spectra that show relatively few cellulose-hemicellulose cross peaks but many cellulose-pectin cross peaks, indicating that cellulose microfibrils are not extensively coated by hemicellulose and all three major polysaccharides exist in a single network rather than two separate networks as previously proposed. The number of glucan chains in the primary-wall cellulose microfibrils has been under active debate recently. We show detailed analysis of quantitative (13)C SSNMR spectra of cellulose in various wild-type (WT) and mutant Arabidopsis and Brachypodium primary cell walls, which consistently indicate that primary-wall cellulose microfibrils contain at least 24 glucan chains.\",\n \"corpus_id\": 20917745,\n \"score\": 2\n },\n {\n \"doc_id\": \"27552739\",\n \"title\": \"Multidimensional solid-state NMR spectroscopy of plant cell walls.\",\n \"abstract\": \"Plant biomass has become an important source of bio-renewable energy in modern society. The molecular structure of plant cell walls is difficult to characterize by most atomic-resolution techniques due to the insoluble and disordered nature of the cell wall. Solid-state NMR (SSNMR) spectroscopy is uniquely suited for studying native hydrated plant cell walls at the molecular level with chemical resolution. Significant progress has been made in the last five years to elucidate the molecular structures and interactions of cellulose and matrix polysaccharides in plant cell walls. These studies have focused on primary cell walls of growing plants in both the dicotyledonous and grass families, as represented by the model plants Arabidopsis thaliana, Brachypodium distachyon, and Zea mays. To date, these SSNMR results have shown that 1) cellulose, hemicellulose, and pectins form a single network in the primary cell wall; 2) in dicot cell walls, the protein expansin targets the hemicellulose-enriched region of the cellulose microfibril for its wall-loosening function; and 3) primary wall cellulose has polymorphic structures that are distinct from the microbial cellulose structures. This article summarizes these key findings, and points out future directions of investigation to advance our fundamental understanding of plant cell wall structure and function.\",\n \"corpus_id\": 10508705,\n \"score\": 2\n },\n {\n \"doc_id\": \"28000667\",\n \"title\": \"Folding of xylan onto cellulose fibrils in plant cell walls revealed by solid-state NMR.\",\n \"abstract\": \"Exploitation of plant lignocellulosic biomass is hampered by our ignorance of the molecular basis for its properties such as strength and digestibility. Xylan, the most prevalent non-cellulosic polysaccharide, binds to cellulose microfibrils. The nature of this interaction remains unclear, despite its importance. Here we show that the majority of xylan, which forms a threefold helical screw in solution, flattens into a twofold helical screw ribbon to bind intimately to cellulose microfibrils in the cell wall. (13)C solid-state magic-angle spinning (MAS) nuclear magnetic resonance (NMR) spectroscopy, supported by in silico predictions of chemical shifts, shows both two- and threefold screw xylan conformations are present in fresh Arabidopsis stems. The twofold screw xylan is spatially close to cellulose, and has similar rigidity to the cellulose microfibrils, but reverts to the threefold screw conformation in the cellulose-deficient irx3 mutant. The discovery that induced polysaccharide conformation underlies cell wall assembly provides new principles to understand biomass properties.\",\n \"corpus_id\": 2602725,\n \"score\": 2\n },\n {\n \"doc_id\": \"29562125\",\n \"title\": \"Direct Determination of Hydroxymethyl Conformations of Plant Cell Wall Cellulose Using 1H Polarization Transfer Solid-State NMR.\",\n \"abstract\": \"In contrast to the well-studied crystalline cellulose of microbial and animal origins, cellulose in plant cell walls is disordered due to its interactions with matrix polysaccharides. Plant cell wall (PCW) is an undisputed source of sustainable global energy; therefore, it is important to determine the molecular structure of PCW cellulose. The most reactive component of cellulose is the exocyclic hydroxymethyl group: when it adopts the tg conformation, it stabilizes intrachain and interchain hydrogen bonding, while gt and gg conformations destabilize the hydrogen-bonding network. So far, information about the hydroxymethyl conformation in cellulose has been exclusively obtained from 13C chemical shifts of monosaccharides and oligosaccharides, which do not reflect the environment of cellulose in plant cell walls. Here, we use solid-state Nuclear Magnetic Resonance (ssNMR) spectroscopy to measure the hydroxymethyl torsion angle of cellulose in two model plants, by detecting distance-dependent polarization transfer between H4 and H6 protons in 2D 13C-13C correlation spectra. We show that the interior crystalline portion of cellulose microfibrils in Brachypodium and Arabidopsis cell walls exhibits H4-H6 polarization transfer curves that are indicative of a tg conformation, whereas surface cellulose chains exhibit slower H4-H6 polarization transfer that is best fit to the gt conformation. Joint constraints by the H4-H6 polarization transfer curves and 13C chemical shifts indicate that it is unlikely for interior cellulose to have a significant population of the gt and gg conformation mixed with the tg conformation, while surface cellulose may adopt a small percentage of the gg conformation. These results provide new constraints to the structure and matrix interactions of cellulose in plant cell walls, and represent the first direct determination of a torsion angle in an important noncrystalline carbohydrate polymer.\",\n \"corpus_id\": 4450726,\n \"score\": 2\n },\n {\n \"doc_id\": \"18781703\",\n \"title\": \"Spectral assignments and anisotropy data of cellulose I(alpha): 13C-NMR chemical shift data of cellulose I(alpha) determined by INADEQUATE and RAI techniques applied to uniformly 13C-labeled bacterial celluloses of different Gluconacetobacter xylinus strains.\",\n \"abstract\": \"Solid-state (13)C-NMR spectroscopy was used to characterize native cellulose pellicles from two strains of Gluconacetobacter xylinus (ATCC 53582, ATCC 23769), which had been statically cultivated in Hestrin-Schramm (HS) medium containing fully (13)C-labeled beta-D-glucose-U-(13)C(6) as the sole source of carbon. For both samples, the (13)C-NMR chemical shifts were completely assigned for each (13)C-labeled site of cellulose I(alpha) with the aid of 2D refocused INADEQUATE NMR. To determine the principal chemical shift tensor components, a pulse sequence based on the recoupling of anisotropy information (RAI) was applied at 10 kHz MAS. The detailed (13)C tensors of cellulose I(alpha) from different bacterial celluloses are thus available now for the first time, and these results have been compared with previously published data of nonenriched material and with theoretical predictions.\",\n \"corpus_id\": 43760876,\n \"score\": 1\n },\n {\n \"doc_id\": \"19133744\",\n \"title\": \"Characterizing slight structural disorder in solids by combined solid-state NMR and first principles calculations.\",\n \"abstract\": \"A general approach for structural interpretation of local disorder in partially ordered solids is proposed, combining high-resolution two-dimensional (2D) nuclear magnetic resonance (NMR) and first principles calculations. We show that small chemical shift variations of the order of a ppm can be interpreted in detailed structural terms with advanced density functional theory methods. Focusing on a model system of bisphosphinoamine, we demonstrate that the existence and the spatial range of small amplitude disorder can be probed using quantitative statistical analyses of 2D NMR line shapes obtained from through-space correlation experiments collected using variable mixing times. We show how low-energy vibration modes calculated from first principles can be conveniently used not as a cause of disorder but, instead, to generate a basis set of physically plausible local distortions to describe candidate static distributions of local geometries. Calculations of (31)P NMR isotropic chemical shifts are then used for the first time to simulate 2D correlation lineshapes associated with these distortions, which permit their evaluation as a potential source of disorder by comparison to experimental 2D cross-peaks between phosphorus sites. This new type of structural constraints allows the identification of changes in the bonding geometry that most likely contribute to the local structural disorder. We thus identify at least one type of structural deformation that is compatible with the experimental 2D NMR data and is also within the order of magnitude of the \\\"thermal ellipsoids\\\" associated with the uncertainties on the atomic positions of the X-ray diffraction structure.\",\n \"corpus_id\": 44816685,\n \"score\": 1\n },\n {\n \"doc_id\": \"19817435\",\n \"title\": \"Solid-state 13C NMR study of a composite of tobacco xyloglucan and Gluconacetobacter xylinus cellulose: molecular interactions between the component polysaccharides.\",\n \"abstract\": \"To investigate possible molecular interactions between xyloglucans (XGs) and cellulose in plant cell walls, a model composite was produced using cellulose from the bacterium Gluconacetobacter xylinus and XG from the walls of a tobacco cell-suspension culture that had been incubated with (13)C-labeled glucose. Solid-state (13)C NMR with cross-polarization (CP) and magic-angle spinning (MAS) was used in combination with proton spin-relaxation editing to separate signals from crystalline (rigid) and less rigid domains of the composite. Signals from XG were confined to subspectra of less rigid domains, with no detectable signals from XG attached to surfaces of cellulose crystallites. Signal displacements indicated XGs were more rigid than the mobile coil (twisted backbone) conformation expected for unattached XGs. Similar (13)C chemical shifts were observed in a single-pulse excitation experiment. The results were not compatible with extensive hydrogen bonding between XG and cellulose, but were consistent with a composite structure in which cellulose crystallites were embedded in a matrix of XG with a semirigid (straightened backbone) conformation, that is, a matrix that is partly ordered rather than amorphous.\",\n \"corpus_id\": 206868345,\n \"score\": 1\n },\n {\n \"doc_id\": \"21338135\",\n \"title\": \"High-temperature behavior of cellulose I.\",\n \"abstract\": \"We use molecular simulation to elucidate the structural behavior of small hydrated cellulose Iβ microfibrils heated to 227 °C (500 K) with two carbohydrate force fields. In contrast to the characteristic two-dimensional hydrogen-bonded layer sheets present in the cellulose Iβ crystal structure, we show that at high temperature a three-dimensional hydrogen bond network forms, made possible by hydroxymethyl groups changing conformation from trans-gauche (TG) to gauche-gauche (GG) in every second layer corresponding to \\\"center\\\" chains in cellulose Iβ and from TG to gauche-trans (GT) in the \\\"origin\\\" layer. The presence of a regular three-dimensional hydrogen bond network between neighboring sheets eliminates the possibility of twist, whereas two-dimensional hydrogen bonding allows for microfibril twist to occur. Structural features of this high-temperature phase as determined by molecular simulation may explain several experimental observations for which no detailed structural basis has been offered. This includes an explanation for the observed temperature and crystal size dependence for the extent of hydrogen/deuterium exchange, and diffraction patterns of cellulose at high temperature.\",\n \"corpus_id\": 39581325,\n \"score\": 1\n },\n {\n \"doc_id\": \"21563791\",\n \"title\": \"Natural-abundance solid-state 2H NMR spectroscopy at high magnetic field.\",\n \"abstract\": \"High-resolution solid-state (2)H NMR spectroscopy provides a method for measuring (1)H NMR chemical shifts in solids and is advantageous over the direct measurement of high-resolution solid-state (1)H NMR spectra, as it requires only the application of routine magic angle sample spinning (MAS) and routine (1)H decoupling methods, in contrast to the requirement for complex pulse sequences for homonuclear (1)H decoupling and ultrafast MAS in the case of high-resolution solid-state (1)H NMR. However, a significant obstacle to the routine application of high-resolution solid-state (2)H NMR is the very low natural abundance of (2)H, with the consequent problem of inherently low sensitivity. Here, we explore the feasibility of measuring (2)H MAS NMR spectra of various solids with natural isotopic abundances at high magnetic field (850 MHz), focusing on samples of amino acids, peptides, collagen, and various organic solids. The results show that high-resolution solid-state (2)H NMR can be used successfully to measure isotropic (1)H chemical shifts in favorable cases, particularly for mobile functional groups, such as methyl and -N(+)H(3) groups, and in some cases phenyl groups. Furthermore, we demonstrate that routine (2)H MAS NMR measurements can be exploited for assessing the relative dynamics of different functional groups in a molecule and for assessing whole-molecule motions in the solid state. The magnitude and field-dependence of second-order shifts due to the (2)H quadrupole interaction are also investigated, on the basis of analysis of simulated and experimental (1)H and (2)H MAS NMR spectra of fully deuterated and selectively deuterated samples of the α polymorph of glycine at two different magnetic field strengths.\",\n \"corpus_id\": 25181140,\n \"score\": 1\n },\n {\n \"doc_id\": \"21677972\",\n \"title\": \"Hydrogen bonding and chemical shift assignments in carbazole functionalized isocyanides from solid-state NMR and first-principles calculations.\",\n \"abstract\": \"Carbazole functionalized polyisocyanides are known to exhibit excellent electronic properties (E. Schwartz, et al., Chemistry of Materials, 2010, 22, 2597). The functionalities and properties of such materials crucially depend on the organization and stability of the polymer structure. We combine solid-state Nuclear Magnetic Resonance (NMR) experiments with first-principles calculations of isotropic chemical shifts, within the recently developed converse approach, to rationalize the origin of isotropic chemical shifts in the crystalline monomer l-isocyanoalanine 2-(9H-carbazol-9-yl) ethyl amide (monomer 1) and thereby gain insight into the structural organization of its polymer (polymer 2). The use of state-of-the-art solid-state NMR experiments combined with Density Functional Theory (DFT) based calculations allows an unambiguous assignment of all proton and carbon resonances of the monomer. We were able to identify the structure stabilising interactions in the crystal and understand the influence of the molecular packing in the crystal structure on the chemical shift data observed in the NMR spectra. Here the Nuclear Independent Chemical Shift (NICS) approach allows discriminating between 'physical' interactions amongst neighboring molecules such as ring-current effects and 'chemical' interactions such as hydrogen bonding. This analysis reveals that the isocyanide monomer is stabilized by multiple hydrogen bonds such as a bifurcated hydrogen bond involving -N-H, -C-H and O=C- moieties and Ar-H···C≡N- hydrogen bonding (Ar = aromatic group). Based on the geometrical arrangement it is postulated that the carbazole units are involved in the weak σ-π interactions giving rise to a Herringbone packing of the molecules. The chemical shift analysis of the polymer spectra readily establishes the existence of N-H···O=C hydrogen bonds despite the limited resolution exhibited by the polymer spectra. It is also elucidated that the relative arrangement of the carbazole units in the polymer differs significantly from that of the monomer.\",\n \"corpus_id\": 20518868,\n \"score\": 1\n },\n {\n \"doc_id\": \"22044314\",\n \"title\": \"Hydration and temperature dependence of 13C and 1H NMR spectra of the DMPC phospholipid membrane and complete resonance assignment of its crystalline state.\",\n \"abstract\": \"Inhomogeneous line broadening due to conformational distributions of molecules is one of the troublesome problems in solid-state NMR spectroscopy. The best possible way to avoid it is to crystallize the sample. Here, we present a highly resolved (13)C cross-polarization (CP) magic angle spinning (MAS) NMR spectrum of the highly ordered crystalline 1,2-dimyrystoyl-sn-glycero-3-phosphocholine (DMPC) and completely assigned it using two-dimensional (2D) solid-state NMR spectra, dipolar heteronuclear correlation (HETCOR) spectra, scalar heteronuclear J coupling based chemical shift correlation (MAS-J-HMQC) spectra, and Dipolar Assisted Rotational Resonance (DARR) spectra. A comparison between assigned chemical shift values by solid-state NMR in this study and the calculated chemical shift values for X-ray crystal DMPC structures shows good agreement, indicating that the two isomers in the crystalline DMPC take the same conformation as the X-ray crystal structure. The phase diagram of the low hydration level of DMPC (3 ≤ n(W) ≤ 12) determined by (1)H and (13)C NMR spectra indicates that DMPC takes a crystalline state only in a very narrow region around n(W) = 4 and T < 313 K. These findings provide us with conformational information on crystalline DMPC and the physical properties of DMPC at a low hydration level and can possibly help us obtain a highly resolved solid-state NMR spectrum of microcrystalline membrane-associated protein samples.\",\n \"corpus_id\": 24457741,\n \"score\": 1\n },\n {\n \"doc_id\": \"22129840\",\n \"title\": \"DFT study of (17)O, (1)H and (13)C NMR chemical shifts in two forms of native cellulose, I(α) and I(β).\",\n \"abstract\": \"This computational study is intended to shed light on the crystalline and molecular structure, together with the hydrogen bonding (H-bonding) differences between two forms of native cellulose. DFT calculations were carried out to characterize the (17)O, (1)H and (13)C nuclear magnetic resonance (NMR) parameters in cellulose I(α) and I(β) with the B3LYP functional employing the 6-311++G∗∗ and 6-31+G∗ basis sets. Geometry optimization revealed that the average HB length is shortened by 0.01-0.08Å when the chains are aligned, whereas the average bond angle increases by about 4-8° exhibiting the enhancement of HB strength. For the isolated cellotetramer chains, the isotropic (17)O-H chemical shifts were plotted as a function of HB length. Our results indicated that as the HB length in cellotetramer I(α) increases, the (17)O-H chemical shift isotropy increases, but this parameter changes in the opposite direction for the other structure. Moreover, B3LYP/6-311++G∗∗ calculations reveal that there is an acceptable correlation between the calculated (13)C chemical shifts of the two structures and their experimental values.\",\n \"corpus_id\": 9458598,\n \"score\": 1\n },\n {\n \"doc_id\": \"22163913\",\n \"title\": \"Sensing the structural differences in cellulose from apple and bacterial cell wall materials by Raman and FT-IR spectroscopy.\",\n \"abstract\": \"Raman and Fourier Transform Infrared (FT-IR) spectroscopy was used for assessment of structural differences of celluloses of various origins. Investigated celluloses were: bacterial celluloses cultured in presence of pectin and/or xyloglucan, as well as commercial celluloses and cellulose extracted from apple parenchyma. FT-IR spectra were used to estimate of the I(β) content, whereas Raman spectra were used to evaluate the degree of crystallinity of the cellulose. The crystallinity index (X(C)(RAMAN)%) varied from -25% for apple cellulose to 53% for microcrystalline commercial cellulose. Considering bacterial cellulose, addition of xyloglucan has an impact on the percentage content of cellulose I(β). However, addition of only xyloglucan or only pectins to pure bacterial cellulose both resulted in a slight decrease of crystallinity. However, culturing bacterial cellulose in the presence of mixtures of xyloglucan and pectins results in an increase of crystallinity. The results confirmed that the higher degree of crystallinity, the broader the peak around 913 cm(-1). Among all bacterial celluloses the bacterial cellulose cultured in presence of xyloglucan and pectin (BCPX) has the most similar structure to those observed in natural primary cell walls.\",\n \"corpus_id\": 16979107,\n \"score\": 1\n },\n {\n \"doc_id\": \"23774714\",\n \"title\": \"Determining hydrogen-bond interactions in spider silk with 1H-13C HETCOR fast MAS solid-state NMR and DFT proton chemical shift calculations.\",\n \"abstract\": \"Two-dimensional (2D) (1)H-(13)C heteronuclear correlation (HETCOR) solid-state NMR spectra collected with fast magic angle spinning (MAS) are used in conjunction with density functional theory (DFT) proton chemical shift calculations to determine the hydrogen-bonding strength for ordered β-sheet and disordered 310-helical structures in spider dragline silk. The hydrogen-bond strength is determined to be identical for both structures in spider silk with a 1.83-1.84 Å NH···OC hydrogen-bond distance.\",\n \"corpus_id\": 205840285,\n \"score\": 1\n },\n {\n \"doc_id\": \"24065828\",\n \"title\": \"Sensitivity-enhanced solid-state NMR detection of expansin's target in plant cell walls.\",\n \"abstract\": \"Structure determination of protein binding to noncrystalline macromolecular assemblies such as plant cell walls (CWs) poses a significant structural biology challenge. CWs are loosened during growth by expansin proteins, which weaken the noncovalent network formed by cellulose, hemicellulose, and pectins, but the CW target of expansins has remained elusive because of the minute amount of the protein required for activity and the complex nature of the CW. Using solid-state NMR spectroscopy, combined with sensitivity-enhancing dynamic nuclear polarization (DNP) and differential isotopic labeling of expansin and polysaccharides, we have now determined the functional binding target of expansin in the Arabidopsis thaliana CW. By transferring the electron polarization of a biradical dopant to the nuclei, DNP allowed selective detection of (13)C spin diffusion from trace concentrations of (13)C, (15)N-labeled expansin in the CW to nearby polysaccharides. From the spin diffusion data of wild-type and mutant expansins, we conclude that to loosen the CW, expansin binds highly specific cellulose domains enriched in xyloglucan, whereas more abundant binding to pectins is unrelated to activity. Molecular dynamics simulations indicate short (13)C-(13)C distances of 4-6 Å between a hydrophobic surface of the cellulose microfibril and an aromatic motif on the expansin surface, consistent with the observed NMR signals. DNP-enhanced 2D (13)C correlation spectra further reveal that the expansin-bound cellulose has altered conformation and is enriched in xyloglucan, thus providing unique insight into the mechanism of CW loosening. DNP-enhanced NMR provides a powerful, generalizable approach for investigating protein binding to complex macromolecular targets.\",\n \"corpus_id\": 21065255,\n \"score\": 1\n },\n {\n \"doc_id\": \"24760365\",\n \"title\": \"Probing crystal structure and mesoscale assembly of cellulose microfibrils in plant cell walls, tunicate tests, and bacterial films using vibrational sum frequency generation (SFG) spectroscopy.\",\n \"abstract\": \"This study reports that the noncentrosymmetry and phase synchronization requirements of the sum frequency generation (SFG) process can be used to distinguish the three-dimensional organization of crystalline cellulose distributed in amorphous matrices. Crystalline cellulose is produced as microfibrils with a few nanometer diameters by plants, tunicates, and bacteria. Crystalline cellulose microfibrils are embedded in wall matrix polymers and assembled into hierarchical structures that are precisely designed for specific biological and mechanical functions. The cellulose microfibril assemblies inside cell walls are extremely difficult to probe. The comparison of vibrational SFG spectra of uniaxially-aligned and disordered films of cellulose Iβ nanocrystals revealed that the spectral features cannot be fully explained with the crystallographic unit structure of cellulose. The overall SFG intensity, the alkyl peak shape, and the alkyl/hydroxyl intensity ratio are sensitive to the lateral packing and net directionality of the cellulose microfibrils within the SFG coherence length scale. It was also found that the OH SFG stretch peaks could be deconvoluted to find the polymorphic crystal structures of cellulose (Iα and Iβ). These findings were used to investigate the cellulose crystal structure and mesoscale cellulose microfibril packing in intact plant cell walls, tunicate tests, and bacterial films.\",\n \"corpus_id\": 38622688,\n \"score\": 1\n },\n {\n \"doc_id\": \"24846814\",\n \"title\": \"Effects of plant cell wall matrix polysaccharides on bacterial cellulose structure studied with vibrational sum frequency generation spectroscopy and X-ray diffraction.\",\n \"abstract\": \"The crystallinity, allomorph content, and mesoscale ordering of cellulose produced by Gluconacetobacter xylinus cultured with different plant cell wall matrix polysaccharides were studied with vibrational sum frequency generation (SFG) spectroscopy and X-ray diffraction (XRD). Crystallinity and ordering were assessed as the intensity of SFG signals in the CH/CH2 stretch vibration region (and confirmed by XRD), while Iα content was assessed by the relative intensity of the OH stretch vibration at 3240 cm(-1). A key finding is that the presence of xyloglucan in the culture medium greatly reduced Iα allomorph content but with a relatively small effect on cellulose crystallinity, whereas xylan resulted in a larger decrease in crystallinity with a relatively small decrease in the Iα fraction. Arabinoxylan and various pectins had much weaker effects on cellulose structure as assessed by SFG and XRD. Homogalacturonan with calcium ion reduced the SFG signal, evidently by changing the ordering of cellulose microfibrils. We propose that the distinct effects of matrix polysaccharides on cellulose crystal structure result, at least in part, from selective interactions of the backbone and side chains of matrix polysaccharides with cellulose chains during the formation of the microfibril.\",\n \"corpus_id\": 11759417,\n \"score\": 1\n },\n {\n \"doc_id\": \"25050643\",\n \"title\": \"Theoretical study of the structural stability of molecular chain sheet models of cellulose crystal allomorphs.\",\n \"abstract\": \"The structural stabilities of the molecular chain sheets constituting the crystal structures of the cellulose allomorphs Iα, Iβ, II, and IIII were investigated by density functional theory (DFT) optimization of the isolated chain sheet models with finite dimensions. The DFT-optimized chain sheet models of the two native cellulose crystals developed a right-handed twist with a similar amount of twisting. The DFT-optimized cellulose II (010) and (020) models twisted in opposite directions with right- and left-handed chirality, respectively. The cellulose IIII (1-10) model retained the initial flat structure after the DFT-optimization. The structural features of the DFT-optimized chain sheet models were reflected in the structures of the parent crystal models observed in solvated molecular dynamics (MD) simulations. The minor conformations of the hydroxymethyl groups proposed in the real crystal structures were detected in the MD crystal models and the DFT-optimized (010) model of cellulose II. The crystal chain packing and crystal conversions are interpreted in terms of principal chain sheet stacking.\",\n \"corpus_id\": 8674241,\n \"score\": 1\n },\n {\n \"doc_id\": \"25584993\",\n \"title\": \"Investigating albendazole desmotropes by solid-state NMR spectroscopy.\",\n \"abstract\": \"Characterization of the molecular structure and physicochemical solid-state properties of the solid forms of pharmaceutical compounds is a key requirement for successful commercialization as potential active ingredients in drug products. These properties can ultimately have a critical effect on the solubility and bioavailability of the final drug product. Here, the desmotropy of Albendazole forms I and II was investigated at the atomic level. Ultrafast magic angle spinning (MAS) solid-state nuclear magnetic resonance (NMR) spectroscopy, together with powder X-ray diffraction, thermal analysis, and Fourier transform infrared spectroscopy, were performed on polycrystalline samples of the two solids in order to fully characterize and distinguish the two forms. High-resolution one-dimensional (1)H, (13)C, and (15)N together with two-dimensional (1)H/(1)H single quantum-single quantum, (1)H/(1)H single quantum-double quantum, and (1)H/(13)C chemical shift correlation solid-state NMR experiments under MAS conditions were extensively used to decipher the intramolecular and intermolecular hydrogen bonding interactions present in both solid forms. These experiments enabled the unequivocal identification of the tautomers of each desmotrope. Our results also revealed that both solid forms may be described as dimeric structures, with different intermolecular hydrogen bonds connecting the tautomers in each dimer.\",\n \"corpus_id\": 10483551,\n \"score\": 1\n },\n {\n \"doc_id\": \"26036615\",\n \"title\": \"Cellulose-Pectin Spatial Contacts Are Inherent to Never-Dried Arabidopsis Primary Cell Walls: Evidence from Solid-State Nuclear Magnetic Resonance.\",\n \"abstract\": \"The structural role of pectins in plant primary cell walls is not yet well understood because of the complex and disordered nature of the cell wall polymers. We recently introduced multidimensional solid-state nuclear magnetic resonance spectroscopy to characterize the spatial proximities of wall polysaccharides. The data showed extensive cross peaks between pectins and cellulose in the primary wall of Arabidopsis (Arabidopsis thaliana), indicating subnanometer contacts between the two polysaccharides. This result was unexpected because stable pectin-cellulose interactions are not predicted by in vitro binding assays and prevailing cell wall models. To investigate whether the spatial contacts that give rise to the cross peaks are artifacts of sample preparation, we now compare never-dried Arabidopsis primary walls with dehydrated and rehydrated samples. One-dimensional (13)C spectra, two-dimensional (13)C-(13)C correlation spectra, water-polysaccharide correlation spectra, and dynamics data all indicate that the structure, mobility, and intermolecular contacts of the polysaccharides are indistinguishable between never-dried and rehydrated walls. Moreover, a partially depectinated cell wall in which 40% of homogalacturonan is extracted retains cellulose-pectin cross peaks, indicating that the cellulose-pectin contacts are not due to molecular crowding. The cross peaks are observed both at -20 °C and at ambient temperature, thus ruling out freezing as a cause of spatial contacts. These results indicate that rhamnogalacturonan I and a portion of homogalacturonan have significant interactions with cellulose microfibrils in the native primary wall. This pectin-cellulose association may be formed during wall biosynthesis and may involve pectin entrapment in or between cellulose microfibrils, which cannot be mimicked by in vitro binding assays.\",\n \"corpus_id\": 9464878,\n \"score\": 1\n },\n {\n \"doc_id\": \"26717549\",\n \"title\": \"Comparison of celery (Apium graveolens L.) collenchyma and parenchyma cell wall polysaccharides enabled by solid-state (13)C NMR.\",\n \"abstract\": \"Collenchyma cells with their thickened walls are one of specific mechanical support tissues for plants, while parenchyma cells are thin walled and serve multiple functions. The parenchyma tissue is what you enjoy eating, while collenchyma, because of its fibrous nature, is not so attractive. Celery is a useful model for comparing the cell walls (CWs) of the two cell types such as collenchyma and parenchyma. However, to date, the structural characteristics of collenchyma and parenchyma cell walls from the same plant have not been compared. Monosaccharide composition suggested the collenchyma cell walls contained less pectin but more hemicellulose in comparison to parenchyma. High-resolution solid-state NMR spectra of highly mobile pectins revealed that the arabinan signals were more evident in the collenchyma spectrum, while galactan showed a much stronger resonance in the parenchyma spectrum. In addition, methyl esterified and non-esterified galacturonic acid signals were observed in parenchyma CWs, but only the latter one appeared in the collenchyma. The ratio of cellulose surface/interior obtained from CP/MAS spectra for collenchyma suggested the cellulose microfibrils were ~2.4 nm, while in the parenchyma, these were somewhat larger. X-ray diffraction indicated the size of the cellulose microfibrils were the same for both types of CWs.\",\n \"corpus_id\": 25449914,\n \"score\": 1\n },\n {\n \"doc_id\": \"27474592\",\n \"title\": \"(13)C NMR assignments of regenerated cellulose from solid-state 2D NMR spectroscopy.\",\n \"abstract\": \"From the assignment of the solid-state (13)C NMR signals in the C4 region, distinct types of crystalline cellulose, cellulose at crystalline surfaces, and disordered cellulose can be identified and quantified. For regenerated cellulose, complete (13)C assignments of the other carbon regions have not previously been attainable, due to signal overlap. In this study, two-dimensional (2D) NMR correlation methods were used to resolve and assign (13)C signals for all carbon atoms in regenerated cellulose. (13)C-enriched bacterial nanocellulose was biosynthesized, dissolved, and coagulated as highly crystalline cellulose II. Specifically, four distinct (13)C signals were observed corresponding to conformationally different anhydroglucose units: two signals assigned to crystalline moieties and two signals assigned to non-crystalline species. The C1, C4 and C6 regions for cellulose II were fully examined by global spectral deconvolution, which yielded qualitative trends of the relative populations of the different cellulose moieties, as a function of wetting and drying treatments.\",\n \"corpus_id\": 206450513,\n \"score\": 1\n },\n {\n \"doc_id\": \"28619057\",\n \"title\": \"Polysaccharide compositions of collenchyma cell walls from celery (Apium graveolens L.) petioles.\",\n \"abstract\": \"BACKGROUND: Collenchyma serves as a mechanical support tissue for many herbaceous plants. Previous work based on solid-state NMR and immunomicroscopy suggested collenchyma cell walls (CWs) may have similar polysaccharide compositions to those commonly found in eudicotyledon parenchyma walls, but no detailed chemical analysis was available. In this study, compositions and structures of cell wall polysaccharides of peripheral collenchyma from celery petioles were investigated. RESULTS: This is the first detailed investigation of the cell wall composition of collenchyma from any plant. Celery petioles were found to elongate throughout their length during early growth, but as they matured elongation was increasingly confined to the upper region, until elongation ceased. Mature, fully elongated, petioles were divided into three equal segments, upper, middle and lower, and peripheral collenchyma strands isolated from each. Cell walls (CWs) were prepared from the strands, which also yielded a HEPES buffer soluble fraction. The CWs were sequentially extracted with CDTA, Na2CO3, 1 M KOH and 4 M KOH. Monosaccharide compositions of the CWs showed that pectin was the most abundant polysaccharide [with homogalacturonan (HG) more abundant than rhamnogalacturonan I (RG-I) and rhamnogalacturonan II (RG-II)], followed by cellulose, and other polysaccharides, mainly xyloglucans, with smaller amounts of heteroxylans and heteromannans. CWs from different segments had similar compositions, but those from the upper segments had slightly more pectin than those from the lower two segments. Further, the pectin in the CWs of the upper segment had a higher degree of methyl esterification than the other segments. In addition to the anticipated water-soluble pectins, the HEPES-soluble fractions surprisingly contained large amounts of heteroxylans. The CDTA and Na2CO3 fractions were rich in HG and RG-I, the 1 M KOH fraction had abundant heteroxylans, the 4 M KOH fraction was rich in xyloglucan and heteromannans, and cellulose was predominant in the final residue. The structures of the xyloglucans, heteroxylans and heteromannans were deduced from the linkage analysis and were similar to those present in most eudicotyledon parenchyma CWs. Cross polarization with magic angle spinning (CP/MAS) NMR spectroscopy showed no apparent difference in the rigid and semi-rigid polysaccharides in the CWs of the three segments. Single-pulse excitation with magic-angle spinning (SPE/MAS) NMR spectroscopy, which detects highly mobile polysaccharides, showed the presence of arabinan, the detailed structure of which varied among the cell walls from the three segments. CONCLUSIONS: Celery collenchyma CWs have similar polysaccharide compositions to most eudicotyledon parenchyma CWs. However, celery collenchyma CWs have much higher XG content than celery parenchyma CWs. The degree of methyl esterification of pectin and the structures of the arabinan side chains of RG-I show some variation in the collenchyma CWs from the different segments. Unexpectedly, the HEPES-soluble fraction contained a large amount of heteroxylans.\",\n \"corpus_id\": 24343520,\n \"score\": 1\n },\n {\n \"doc_id\": \"28674916\",\n \"title\": \"(2)H-(13)C correlation solid-state NMR for investigating dynamics and water accessibilities of proteins and carbohydrates.\",\n \"abstract\": \"Site-specific determination of molecular motion and water accessibility by indirect detection of (2)H NMR spectra has advantages over dipolar-coupling based techniques due to the large quadrupolar couplings and the ensuing high angular resolution. Recently, a Rotor Echo Short Pulse IRrAdiaTION mediated cross polarization ((RESPIRATION)CP) technique was developed, which allowed efficient transfer of (2)H magnetization to (13)C at moderate (2)H radiofrequency field strengths available on most commercial MAS probes. In this work, we investigate the (2)H-(13)C magnetization transfer characteristics of one-bond perdeuterated CD n spin systems and two-bond H/D exchanged C-(O)-D and C-(N)-D spin systems in carbohydrates and proteins. Our results show that multi-bond, broadband (2)H-(13)C polarization transfer can be achieved using (2)H radiofrequency fields of ~50 kHz, relatively short contact times of 1.3-1.7 ms, and with sufficiently high sensitivity to enable 2D (2)H-(13)C correlation experiments with undistorted (2)H spectra in the indirect dimension. To demonstrate the utility of this (2)H-(13)C technique for studying molecular motion, we show (2)H-(13)C correlation spectra of perdeuterated bacterial cellulose, whose surface glucan chains exhibit a motionally averaged C6 (2)H quadrupolar coupling that indicates fast trans-gauche isomerization about the C5-C6 bond. In comparison, the interior chains in the microfibril core are fully immobilized. Application of the (2)H-(13)C correlation experiment to H/D exchanged Arabidopsis primary cell walls show that the O-D quadrupolar spectra of the highest polysaccharide peaks can be fit to a two-component model, in which 74% of the spectral intensity, assigned to cellulose, has a near-rigid-limit coupling, while 26% of the intensity, assigned to matrix polysaccharides, has a weakened coupling of 50 kHz. The latter O-D quadrupolar order parameter of 0.22 is significantly smaller than previously reported C-D dipolar order parameters of 0.46-0.55 for pectins, suggesting that additional motions exist at the C-O bonds in the wall polysaccharides. (2)H-(13)C polarization transfer profiles are also compared between statistically deuterated and H/D exchanged GB1.\",\n \"corpus_id\": 10869643,\n \"score\": 1\n },\n {\n \"doc_id\": \"28759814\",\n \"title\": \"Evaluation of hydrogen bond networks in cellulose Iβ and II crystals using density functional theory and Car-Parrinello molecular dynamics.\",\n \"abstract\": \"Crystal models of cellulose Iβ and II, which contain various hydrogen bonding (HB) networks, were analyzed using density functional theory and Car-Parrinello molecular dynamics (CPMD) simulations. From the CPMD trajectories, the power spectra of the velocity correlation functions of hydroxyl groups involved in hydrogen bonds were calculated. For the Iβ allomorph, HB network A, which is dominant according to the neutron diffraction data, was stable, and the power spectrum represented the essential features of the experimental IR spectra. In contrast, network B, which is a minor structure, was unstable because its hydroxymethyl groups reoriented during the CPMD simulation, yielding a different crystal structure to that determined by experiments. For the II allomorph, a HB network A is proposed based on diffraction data, whereas molecular modeling identifies an alternative network B. Our simulations showed that the interaction energies of the cellulose II (B) model are slightly more favorable than model II(A). However, the evaluation of the free energy should be waited for the accurate determination from the energy point of view. For the IR calculation, cellulose II (B) model reproduces the spectra better than model II (A).\",\n \"corpus_id\": 13783281,\n \"score\": 1\n },\n {\n \"doc_id\": \"29565567\",\n \"title\": \"Hydrogen Bond Dynamics of Cellulose through Inelastic Neutron Scattering Spectroscopy.\",\n \"abstract\": \"This work explores the dynamics of hydrogen bond networks in cellulose through inelastic neutron scattering (INS) and periodic CASTEP calculations. Estimated spectra were based on the crystal structure of cellulose Iα and Iβ and replicate the INS spectrum of cellulose samples with remarkable similarity, allowing a reliable assignment of INS bands to vibrational modes of cellulose. Comparison of cellulose samples from varied sources, from bacterial to kraft pulp, allows the identification of characteristic INS bands, arising from C2-OH torsional motions, which easily identify which allomorph-Iα or Iβ-is prevalent. A high crystallinity index is revealed by the presence of well-defined INS bands associated with highly cooperative CH bending modes along the chain. Hydrating kraft cellulose samples clearly affects those INS bands related with the hydroxymethyl group, identified as the preferred binding site for water molecules. At high humidity content level, a significant proportion of the water molecules is aggregated in clusters within the amorphous cellulose domains. The formation of ice microcrystals leads to a partial disruption of the hydrogen-bond network, as can be concluded from the observed red-shift of the torsional OH vibrational modes. The full assignment and interpretation of cellulose's INS spectra herein provided is a sound basis for future use of INS spectroscopy in the characterization of functionalized cellulose fibers and composite materials.\",\n \"corpus_id\": 4700982,\n \"score\": 1\n },\n {\n \"doc_id\": \"18098151\",\n \"title\": \"Solid-state NMR studies and DFT calculations of flavonoids: baicalein, baicalin and wogonoside.\",\n \"abstract\": \"Three flavonoids of pharmaceutical importance-baicalein, baicalin, and wogonoside-were isolated from a Chinese medicinal plant Scutellaria baicalensis Georgi and studied by 13C NMR in solution and solid state. Two-dimensional (2D) NMR spectroscopy in the liquid phase and dipolar dephasing (DD) experiments in magic-angle spinning (MAS) spectra enabled the assignment of 13C resonances. The cross-polarization (CP) time constants T(CH) and relaxation times T(H) (1rho) were obtained from the variable-contact time experiments. The principal elements of the 13C chemical shift tensor were determined in the spectra recorded under slow sample spinning (2 kHz) using phase-adjusted spinning sideband (PASS)-2D NMR technique, and were verified by density functional theory gauge-independent atomic orbital (DFT GIAO) calculations of shielding constants. Analysis of the 13C delta(ii) and comparison with shielding parameters calculated for different conformers of compounds 1-3 enabled the selection of the most reliable geometry in the solid phase. In all three compounds, an intramolecular hydrogen bond C5--OH...=C4 is formed; the existence of baicalein and baicalin with 'anticlockwise' orientation of OH groups is more probable.\",\n \"corpus_id\": 44605780,\n \"score\": 0\n },\n {\n \"doc_id\": \"18523586\",\n \"title\": \"High-resolution 3D structure determination of kaliotoxin by solid-state NMR spectroscopy.\",\n \"abstract\": \"High-resolution solid-state NMR spectroscopy can provide structural information of proteins that cannot be studied by X-ray crystallography or solution NMR spectroscopy. Here we demonstrate that it is possible to determine a protein structure by solid-state NMR to a resolution comparable to that by solution NMR. Using an iterative assignment and structure calculation protocol, a large number of distance restraints was extracted from (1)H/(1)H mixing experiments recorded on a single uniformly labeled sample under magic angle spinning conditions. The calculated structure has a coordinate precision of 0.6 A and 1.3 A for the backbone and side chain heavy atoms, respectively, and deviates from the structure observed in solution. The approach is expected to be applicable to larger systems enabling the determination of high-resolution structures of amyloid or membrane proteins.\",\n \"corpus_id\": 1633957,\n \"score\": 0\n },\n {\n \"doc_id\": \"18980301\",\n \"title\": \"Investigation of silver-containing layered materials and their interactions with primary amines using solid-state 109Ag and 15N NMR spectroscopy and first principles calculations.\",\n \"abstract\": \"Silver-containing layered networks of the form [Ag(L)] (L = 4-pyridinesulfonate or p-toluenesulfonate) were treated with primary amines in different ratios. The structures of the parent supramolecular networks are well-known; however, their interactions with primary amines lead to the formation of new layered materials for which single-crystal X-ray structures cannot be obtained. Solid-state (109)Ag, (15)N, and (13)C cross-polarization magic-angle spinning (CP/MAS) NMR experiments, in combination with powder X-ray diffraction experiments and ab initio calculations, are utilized to investigate the interactions between the primary amines and the parent materials, and to propose structural models for the new materials. (109)Ag chemical shift (CS) tensor parameters are extremely sensitive to changes in silver environments; hence, (1)H-(109)Ag CP/MAS NMR experiments are used to distinguish and characterize silver sites. The combination of (109)Ag and (15)N NMR experiments on starting materials and samples prepared with both (15)N-labeled and unlabeled amines permits the accurate measurements of indirect (1)J((109)Ag,(15)N) and (1)J((109)Ag,(14)N) spin-spin coupling constants, providing further information on structure and bonding in these systems. First principles calculations of silver CS tensors and (1)J((109)Ag,(14)N) coupling constants in model complexes aid in formulating the proposed structural models for the new materials, which are largely comprised of layers of silver-diamine cations.\",\n \"corpus_id\": 24477410,\n \"score\": 0\n },\n {\n \"doc_id\": \"19177476\",\n \"title\": \"The structure of (SCN)(x): a study using molecular and solid-state density functional theory calculations.\",\n \"abstract\": \"A riddle solved! Despite its simple formula, the structure of the (SCN)(x) polymer has remained elusive since its first synthesis in 1929. From energetics as well as NMR chemical shifts, based on DFT calculations, we have strong evidence that it is indeed a tangle of linear chains, made up from N-linked S(2)C(2)N five-membered rings. Molecular fragments and crystal structures based on proposed structures for polythiocyanogen were studied by using molecular and solid-state electronic structure calculations at the density functional theory level. The energetics and chemical shifts from both types of calculations indicate that a planar N-linked chain consisting of 1,2,4-dithiazole five-membered rings with adjacent rings pointing in opposite directions is the most likely local structure of the (SCN)(x) polymer.\",\n \"corpus_id\": 7390333,\n \"score\": 0\n },\n {\n \"doc_id\": \"19331396\",\n \"title\": \"Solid state NMR study and density functional theory (DFT) calculations of structure and dynamics of poly(p-xylylenes).\",\n \"abstract\": \"High resolution solid state (13)C nuclear magnetic resonance (SS NMR) measurements were carried out on poly(p-xylylene) (PPX). The samples comprised vapor-deposited specimens as well as pure alpha and beta polymorphs of this polymer. The measurements were performed using cross-polarization and magic angle spinning (CP/MAS) techniques. Density functional theory gauge-including-atomic-orbital (DFT GIAO) calculations of NMR shielding parameters (13)C sigma(ii) were performed for the optimized geometry and structure of a xylylene trimer, acquired from the X-ray data, including intermolecular interactions. Two-dimensional phase adjusted spinning sideband (2D PASS) correlation was employed for the assignment of the values of the principal elements (13)C delta(ii) of the chemical shift tensor (CST). A comparative analysis of shielding (sigma(ii)) versus chemical shift (delta(ii)) parameters showed substantial differences between the molecular dynamics of alpha and beta polymorphs. This observation was further supported by the measurements of (13)C T(1) relaxation times and the analysis of cross-polarization kinetics. Frequency switched Lee-Goldburg heteronuclear correlation (FSLG HETCOR) for the (1)H-(13)C system was used in order to analyze molecular packing in both polymorphs. As a result of all of the above measurements, new insight into the mechanism of thermal phase transition from the alpha to the beta polymorph of poly(p-xylylene) is presented.\",\n \"corpus_id\": 30133585,\n \"score\": 0\n },\n {\n \"doc_id\": \"19663434\",\n \"title\": \"Conformational studies of poly(9,9-dialkylfluorene)s in solution using NMR spectroscopy and density functional theory calculations.\",\n \"abstract\": \"Relationships have been obtained between intermonomer torsional angle and NMR chemical shifts ((1)H and (13)C) for isolated chains of two of the most important poly(9,9-dialkylfluorenes), poly[9,9-bis(2-ethylhexyl)fluorene-2,7-diyl] (PF2/6) and the copolymer poly(9,9-dioctylfluorene-co-[2,1,3]benzothiadiazole-4,7-diyl) (F8BT), using DFT calculations. The correlations provide a model for NMR spectral data interpretation and the basis for analysis of conformational changes in poly(9,9-dialkylfluorene-2,7-diyl)s. The correlations obtained for PF2/6 indicate that the (13)C chemical shifts of the aromatic carbons close to the intermonomer connection (C1, C2, and C3) have minimum values at planar conformations (0 degrees and 180 degrees ) and maximum values at 90 degrees conformations. In contrast, the (1)H chemical shifts of the corresponding aromatic ortho protons (Ha and Hb) are greatest for planar conformations, and the minimum values are seen for 90 degrees conformations. For the F8BT copolymer, similar relationships are observed for the (1)H (Ha, Hb, and Hc) aromatic shifts. Considering the aromatic carbons of F8BT, the behavior of C2, C4, C5, and C6 is similar to that found for the PF2/6 carbons. However, C1 and C3 of the fluorene moiety behave differently with varying torsion angle. These are in close proximity to the fluorene-benzothiadiazole linkage and are markedly affected by interactions with the thiadiazole unit such that delta(C1) is a maximum for 180 degrees and a minimum for 0 degrees , whereas delta(C3) is a maximum for 0 degrees and minimum for 180 degrees. We have studied the (1)H and (13)C spectra of the two polymers at temperatures between -50 degrees C and +65 degrees C. The observed changes to higher or lower frequency in the aromatic resonances were analyzed using these theoretical relationships. Fluorescence studies on PF2/6 in chloroform solution suggest there are no significant interchain interactions under these conditions. This is supported by variable-temperature NMR results. Polymer-solvent and polymer intramolecular interactions were found to be present and influence all of the alkylic and one of the aromatic (1)H resonances (Hb). The detailed attribution of the (1)H and (13)C NMR spectra of the two polymers was made prior to the establishment of the relationships between torsion angle and NMR chemical shifts. This was carried out through DFT calculation of the (1)H and (13)C shielding constants of the monomers, coupled with distortionless enhancement by polarization transfer and heteronuclear correlation NMR spectra. Several DFT levels of calculation were tested for both optimization of structures and shielding constants calculation. The B3LYP/6-31G(d,p) method was found to perform well in both cases.\",\n \"corpus_id\": 15939891,\n \"score\": 0\n },\n {\n \"doc_id\": \"19900275\",\n \"title\": \"Characterisation of different polymorphs of tris(8-hydroxyquinolinato)aluminium(III) using solid-state NMR and DFT calculations.\",\n \"abstract\": \"BACKGROUND: Organic light emitting devices (OLED) are becoming important and characterisation of them, in terms of structure, charge distribution, and intermolecular interactions, is important. Tris(8-hydroxyquinolinato)-aluminium(III), known as Alq3, an organomettalic complex has become a reference material of great importance in OLED. It is important to elucidate the structural details of Alq3 in its various isomeric and solvated forms. Solid-state nuclear magnetic resonance (NMR) is a useful tool for this which can also complement the information obtained with X-ray diffraction studies. RESULTS: We report here 27Al one-dimensional (1D) and two-dimensional (2D) multiple-quantum magic-angle spinning (MQMAS) NMR studies of the meridional (alpha-phase) and the facial (delta-phase) isomeric forms of Alq3. Quadrupolar parameters are estimated from the 1D spectra under MAS and anisotropic slices of the 2D spectra and also calculated using DFT (density functional theory) quantum-chemical calculations. We have also studied solvated phase of Alq3 containing ethanol in its lattice. We show that both the XRD patterns and the quadrupolar parameters of the solvated phase are different from both the alpha-phase and the delta-phase, although the fluorescence emission shows no substantial difference between the alpha-phase and the solvated phase. Moreover, we have shown that after the removal of ethanol from the matrix the solvated Alq3 has similar XRD patterns and quadrupolar parameters to that of the alpha-phase. CONCLUSION: The 2D MQMAS experiments have shown that all the different modifications of Alq3 have 27Al in single unique crystallographic site. The quadrupolar parameters predicted using the DFT calculation under the isodensity polarisable continuum model resemble closely the experimentally obtained values. The solvated phase of Alq3 containing ethanol has structural difference from the alpha-phase of Alq3 (containing meridional isomer) from the solid-state NMR studies. Solid-state NMR can hence be used as an effective complementary tool to XRD for characterisation and structural elucidation.\",\n \"corpus_id\": 11159250,\n \"score\": 0\n },\n {\n \"doc_id\": \"20958031\",\n \"title\": \"High-resolution (19)F MAS NMR spectroscopy: structural disorder and unusual J couplings in a fluorinated hydroxy-silicate.\",\n \"abstract\": \"High-resolution (19)F magic angle spinning (MAS) NMR spectroscopy is used to study disorder and bonding in a crystalline solid. (19)F MAS NMR reveals four distinct F sites in a 50% fluorine-substituted deuterated hydrous magnesium silicate (clinohumite, 4Mg(2)SiO(4)·Mg(OD(1-x)F(x))(2) with x = 0.5), indicating extensive structural disorder. The four (19)F peaks can be assigned using density functional theory (DFT) calculations of NMR parameters for a number of structural models with a range of possible local F environments generated by F(-)/OH(-) substitution. These assignments are supported by two-dimensional (19)F double-quantum MAS NMR experiments that correlate F sites based on either spatial proximity (via dipolar couplings) or through-bond connectivity (via scalar, or J, couplings). The observation of (19)F-(19)F J couplings is unexpected as the fluorines coordinate Mg atoms and the Mg-F interaction is normally considered to be ionic in character (i.e., there is no formal F-Mg-F covalent bonding arrangement). However, DFT calculations predict significant (19)F-(19)F J couplings, and these are in good agreement with the splittings observed in a (19)F J-resolved MAS NMR experiment. The existence of these J couplings is discussed in relation to both the nature of bonding in the solid state and the occurrence of so-called \\\"through-space\\\" (19)F-(19)F J couplings in solution. Finally, we note that we have found similar structural disorder and spin-spin interactions in both synthetic and naturally occurring clinohumite samples.\",\n \"corpus_id\": 26079475,\n \"score\": 0\n },\n {\n \"doc_id\": \"21175136\",\n \"title\": \"Solid-state NMR and density functional theory studies of ionization states of thiamin.\",\n \"abstract\": \"Thiamin diphosphate (ThDP) is a key coenzyme in sugar metabolism. The 4'-aminopyrimidine ring of ThDP cycles through several ionization and tautomeric states during enzyme catalysis, but it is not fully understood which states are adopted during the individual steps of the catalytic cycle. Thiamin has been synthesized with labels selectively inserted into the C2 and C6' positions, as well as into the amino group, creating [C2, C6'-(13)C(2)] thiamin and [N4'-(15)N] thiamin. Magic-angle spinning (MAS) NMR spectroscopy has been employed to record the (13)C and (15)N chemical shift anisotropy (CSA) tensors for C2, C6', and N4' atoms. Our results indicate that the isotropic chemical shifts as well as the principal components of the (13)C and (15)N CSA tensors are very sensitive to the protonation states in these compounds and, therefore, permit differentiating between the two ionization states, 4-aminopyrimidine and 4-aminopyrimidinium. Using density functional theory (DFT), we have calculated the magnetic shielding anisotropy tensors of C2, C6', and N4' and found excellent agreement between the computed and the experimental tensors. Our findings indicate that MAS NMR spectroscopy in conjunction with DFT calculations is a sensitive probe of ionization states in the thiamin cofactor. The results of this study will serve as a guide for characterization of ionization and tautomeric states of thiamin in complexes with thiamin-dependent enzymes.\",\n \"corpus_id\": 32191231,\n \"score\": 0\n },\n {\n \"doc_id\": \"21384011\",\n \"title\": \"Multinuclear solid state NMR investigation of two polymorphic forms of ciprofloxacin-saccharinate.\",\n \"abstract\": \"Two polymorphic forms of a novel pharmaceutical compound, ciprofloxacin-saccharinate (CIP-SAC), are analyzed using one dimensional (1D) and two dimensional (2D) (1)H nuclear magnetic resonance (NMR) at fast magic angle spinning (MAS). Additionally (15)N spectroscopy and (1)H-(13)C correlation experiments were performed to complement our conclusions. The 1D (1)H NMR spectra of CIP and complexes reveal valuable information about the ionic bonding between ciprofloxacin and saccharine. Additionally, these spectra allow us to perform a clear characterization of each solid form, giving the number of molecules per unit cell in one of the polymorphs. From 2D (1)H-(1)H spectra obtained through double quantum correlations we can arrive at important conclusions about the hydrogen bonding, conformation, and intra and inter-molecular interactions present in these compounds. Comparing and contrasting the (1)H-(1)H correlation data obtained for both polymorphic forms and taking into account the single crystal structure data existing for the solid form CIP-SAC (II) was possible to extract some conclusions on the polymorph CIP-SAC (I) where no single crystal information is available. (1)H MAS NMR is shown to be an important tool in the field of polymorphism and for the characterization of multicomponent pharmaceutical compounds.\",\n \"corpus_id\": 205764252,\n \"score\": 0\n },\n {\n \"doc_id\": \"21846145\",\n \"title\": \"Solvation and crystal effects in bilirubin studied by NMR spectroscopy and density functional theory.\",\n \"abstract\": \"The open-chain tetrapyrrole compound bilirubin was investigated in chloroform and dimethyl sulfoxide solutions by liquid-state NMR and as solid by (1)H, (13)C, and (15)N magic-angle spinning (MAS) solid-state NMR spectroscopy. Density functional theory (DFT) calculations were performed to interpret the data, using the B3LYP exchange-correlation functional to optimize geometries and to compute NMR chemical shieldings by the gauge-including atomic orbital method. The dependence of geometries and chemical shieldings on the size of the basis sets was investigated for the reference molecules tetramethylsilane, NH(3), and H(2)O, and for bilirubin as a monomer and in clusters consisting of up to six molecules. In order to assess the intrinsic errors of the B3LYP approximation in calculating NMR shieldings, complete basis set estimates were obtained for the nuclear shielding values of the reference molecules. The experimental liquid-state NMR data of bilirubin are well reproduced by a monomeric bilirubin molecule using the 6-311+G(2d,p) basis set for geometry optimization and for calculating chemical shieldings. To simulate the bilirubin crystal, a hexameric model was required. It was constructed from geometry-optimized monomers using information from the X-ray structure of bilirubin to fix the monomeric entities in space and refined by partial optimization. Combining experimental (1)H-(13)C and (1)H-(15)N NMR correlation spectroscopy and density functional theory, almost complete sets of (1)H, (13)C, and (15)N chemical shift assignments were obtained for both liquid and solid states. It is shown that monomeric bilirubin in chloroform solution is formed by 3-vinyl anti conformers, while bilirubin crystals are formed by 3-vinyl syn conformers. This conformational change leads to characteristic differences between the liquid- and solid-state NMR resonances.\",\n \"corpus_id\": 5586220,\n \"score\": 0\n },\n {\n \"doc_id\": \"22225526\",\n \"title\": \"Multinuclear solid-state nuclear magnetic resonance and density functional theory characterization of interaction tensors in taurine.\",\n \"abstract\": \"A variety of experimental solid-state nuclear magnetic resonance (NMR) techniques has been used to characterize each of the elements in 2-aminoethane sulfonic acid (taurine). A combination of (15)N cross-polarization magic angle spinning (CPMAS), (14)N ultrawideline, and (14)N overtone experiments enabled a determination of the relative orientation of the nitrogen electric field gradient and chemical shift tensors. (17)O spectra recorded from an isotopically enriched taurine sample at multiple magnetic fields allowed the three nonequivalent oxygen sites to be distinguished, and NMR parameters calculated from a neutron diffraction structure using density functional theory allowed the assignment of the (17)O parameters to the correct crystallographic sites. This is the first time that a complete set of (17)O NMR tensors are reported for a sulfonate group. In combination with (1)H and (13)C MAS spectra, as well as a previously reported (33)S NMR study, this provides a very broad set of NMR data for this relatively simple organic molecule, making it a potentially useful structure on which to test DFT calculation methods (particularly for the quadrupolar nuclei (14)N, (17)O, and (33)S) or NMR crystallography approaches.\",\n \"corpus_id\": 26290723,\n \"score\": 0\n },\n {\n \"doc_id\": \"23464364\",\n \"title\": \"Protein structure determination with paramagnetic solid-state NMR spectroscopy.\",\n \"abstract\": \"Many structures of the proteins and protein assemblies that play central roles in fundamental biological processes and disease pathogenesis are not readily accessible via the conventional techniques of single-crystal X-ray diffraction and solution-state nuclear magnetic resonance (NMR). On the other hand, many of these challenging biological systems are suitable targets for atomic-level structural and dynamic analysis by magic-angle spinning (MAS) solid-state NMR spectroscopy, a technique that has far less stringent limitations on the molecular size and crystalline state. Over the past decade, major advances in instrumentation and methodology have prompted rapid growth in the field of biological solid-state NMR. However, despite this progress, one challenge for the elucidation of three-dimensional (3D) protein structures via conventional MAS NMR methods is the relative lack of long-distance data. Specifically, extracting unambiguous interatomic distance restraints larger than ∼5 Å from through-space magnetic dipole-dipole couplings among the protein (1)H, (13)C, and (15)N nuclei has proven to be a considerable challenge for researchers. It is possible to circumvent this problem by extending the structural studies to include several analogs of the protein of interest, intentionally modified to contain covalently attached paramagnetic tags at selected sites. In these paramagnetic proteins, the hyperfine couplings between the nuclei and unpaired electrons can manifest themselves in NMR spectra in the form of relaxation enhancements of the nuclear spins that depend on the electron-nucleus distance. These effects can be significant for nuclei located up to ∼20 Å away from the paramagnetic center. In this Account, we discuss MAS NMR structural studies of nitroxide and EDTA-Cu(2+) labeled variants of a model 56 amino acid globular protein, B1 immunoglobulin-binding domain of protein G (GB1), in the microcrystalline solid phase. We used a set of six EDTA-Cu(2+)-tagged GB1 mutants to rapidly determine the global protein fold in a de novo fashion. Remarkably, these studies required quantitative measurements of only approximately four or five backbone amide (15)N longitudinal paramagnetic relaxation enhancements per residue, in the complete absence of the usual internuclear distance restraints. Importantly, this paramagnetic solid-state NMR methodology is general and can be directly applied to larger proteins and protein complexes for which a significant fraction of the signals can be assigned in standard 2D and 3D MAS NMR chemical shift correlation spectra.\",\n \"corpus_id\": 14721048,\n \"score\": 0\n },\n {\n \"doc_id\": \"23738844\",\n \"title\": \"Sum-frequency-generation vibration spectroscopy and density functional theory calculations with dispersion corrections (DFT-D2) for cellulose Iα and Iβ.\",\n \"abstract\": \"Sum-frequency-generation (SFG) vibration spectroscopy selectively detects noncentrosymmetric vibrational modes in crystalline cellulose inside intact lignocellulose. However, SFG peak assignment in biomass samples is challenging due to the complexity of the SFG processes and the lack of reference SFG spectra from the two crystal forms synthesized in nature, cellulose Iα and Iβ. This paper compares SFG spectra of laterally aligned cellulose Iα and Iβ crystals with vibration frequencies calculated from density functional theory with dispersion corrections (DFT-D2). Two possible hydrogen-bond networks A and B ( Nishiyama et al. Biomacromolecules 2008 , 9 , 3133 ) were investigated for both polymorphs. From DFT-D2 calculations the energetically favorable structures for cellulose Iα and Iβ had CH2OH groups in tg conformations and network A hydrogen bonding. The calculated frequencies of C-H stretch modes agreed reasonably well with the peak positions observed with SFG and were localized vibrations; thus, peak assignments to specific alkyl groups were proposed. DFT-D2 calculations underestimated the distances between hydrogen-bonded oxygen atoms compared to the experimentally determined values; therefore, the OH stretching calculated frequencies were ~100 cm(-1) lower than observed. The SFG peak assignments through comparison with DFT-D2 calculations will guide the SFG analysis of the crystalline cellulose structure in plant cell walls and lignocellulose biomass.\",\n \"corpus_id\": 24349408,\n \"score\": 0\n },\n {\n \"doc_id\": \"23918278\",\n \"title\": \"Solid-state NMR analysis of a boron-containing pharmaceutical hydrochloride salt.\",\n \"abstract\": \"A novel crystalline form of the boron-containing antibacterial drug (S)-3-(aminomethyl)-7-(3-hydroxypropoxy)benzo[c] [1,2]oxaborol-1(3H)-ol hydrochloride is studied by solid-state nuclear magnetic resonance (SSNMR) and single-crystal X-ray diffraction techniques. After determination of the crystal structure by X-ray diffraction, SSNMR spectroscopy of this form is performed to obtain structural information using experimental approaches based on dipolar correlation, chemical shift analysis, and quadrupolar interaction analysis. 1H SSNMR experiments at 16.4 T using magic-angle spinning (MAS) and homonuclear dipolar decoupling, 2D SSNMR experiments based on (1)H–(13)C and (1)H–(11)B dipolar heteronuclear correlation, and density functional theory (DFT) calculations are combined in a novel approach to obtain a nearly complete assignment of the (1)H spectrum of this crystalline phase. (11)B and (35)Cl chemical shift and quadrupolar parameters are obtained using the analysis of MAS spectra and are found to be accurately reproduced using DFT calculations. NMR chemical shielding and electric field gradient parameters obtained using these methods are related to hydrogen-bonding trends in the crystal structure. The results illustrate the increasing capability of SSNMR techniques involving (1)H, (11)B, and (35)Cl SSNMR in the analysis of the crystal structure of a pharmaceutical compound containing covalently bonded boron.\",\n \"corpus_id\": 40929584,\n \"score\": 0\n },\n {\n \"doc_id\": \"23999926\",\n \"title\": \"Global fold of human cannabinoid type 2 receptor probed by solid-state 13C-, 15N-MAS NMR and molecular dynamics simulations.\",\n \"abstract\": \"The global fold of human cannabinoid type 2 (CB2 ) receptor in the agonist-bound active state in lipid bilayers was investigated by solid-state (13)C- and (15)N magic-angle spinning (MAS) NMR, in combination with chemical-shift prediction from a structural model of the receptor obtained by microsecond-long molecular dynamics (MD) simulations. Uniformly (13)C- and (15)N-labeled CB2 receptor was expressed in milligram quantities by bacterial fermentation, purified, and functionally reconstituted into liposomes. (13)C MAS NMR spectra were recorded without sensitivity enhancement for direct comparison of Cα, Cβ, and C=O bands of superimposed resonances with predictions from protein structures generated by MD. The experimental NMR spectra matched the calculated spectra reasonably well indicating agreement of the global fold of the protein between experiment and simulations. In particular, the (13) C chemical shift distribution of Cα resonances was shown to be very sensitive to both the primary amino acid sequence and the secondary structure of CB2. Thus the shape of the Cα band can be used as an indicator of CB2 global fold. The prediction from MD simulations indicated that upon receptor activation a rather limited number of amino acid residues, mainly located in the extracellular Loop 2 and the second half of intracellular Loop 3, change their chemical shifts significantly (≥ 1.5 ppm for carbons and ≥ 5.0 ppm for nitrogens). Simulated two-dimensional (13) Cα(i)-(13)C=O(i) and (13)C=O(i)-(15)NH(i + 1) dipolar-interaction correlation spectra provide guidance for selective amino acid labeling and signal assignment schemes to study the molecular mechanism of activation of CB2 by solid-state MAS NMR.\",\n \"corpus_id\": 25483523,\n \"score\": 0\n },\n {\n \"doc_id\": \"24516184\",\n \"title\": \"Density functional theory in the solid state.\",\n \"abstract\": \"Density functional theory (DFT) has been used in many fields of the physical sciences, but none so successfully as in the solid state. From its origins in condensed matter physics, it has expanded into materials science, high-pressure physics and mineralogy, solid-state chemistry and more, powering entire computational subdisciplines. Modern DFT simulation codes can calculate a vast range of structural, chemical, optical, spectroscopic, elastic, vibrational and thermodynamic phenomena. The ability to predict structure-property relationships has revolutionized experimental fields, such as vibrational and solid-state NMR spectroscopy, where it is the primary method to analyse and interpret experimental spectra. In semiconductor physics, great progress has been made in the electronic structure of bulk and defect states despite the severe challenges presented by the description of excited states. Studies are no longer restricted to known crystallographic structures. DFT is increasingly used as an exploratory tool for materials discovery and computational experiments, culminating in ex nihilo crystal structure prediction, which addresses the long-standing difficult problem of how to predict crystal structure polymorphs from nothing but a specified chemical composition. We present an overview of the capabilities of solid-state DFT simulations in all of these topics, illustrated with recent examples using the CASTEP computer program.\",\n \"corpus_id\": 7994033,\n \"score\": 0\n },\n {\n \"doc_id\": \"25133518\",\n \"title\": \"Solid-state NMR analysis of a complex crystalline phase of ronacaleret hydrochloride.\",\n \"abstract\": \"A crystalline phase of the pharmaceutical compound ronacaleret hydrochloride is studied by solid-state nuclear magnetic resonance (SSNMR) spectroscopy and single-crystal X-ray diffraction. The crystal structure is determined to contain two independent cationic molecules and chloride anions in the asymmetric unit, which combine with the covalent structure of the molecule to yield complex SSNMR spectra. Experimental approaches based on dipolar correlation, chemical shift tensor analysis, and quadrupolar interaction analysis are employed to obtain detailed information about this phase. Density functional theory (DFT) calculations are used to predict chemical shielding and electric field gradient (EFG) parameters for comparison with experiment. (1)H SSNMR experiments performed at 16.4 T using magic-angle spinning (MAS) and homonuclear dipolar decoupling provide information about hydrogen bonding and molecular connectivity that can be related to the crystal structure. (19)F and (13)C assignments for the Z' = 2 structure are obtained using DFT calculations, (19)F homonuclear dipolar correlation, and (13)C-(19)F heteronuclear dipolar correlation experiments. (35)Cl MAS experiments at 16.4 T observe two chlorine sites that are assigned using calculated chemical shielding and EFG parameters. SSNMR dipolar correlation experiments are used to extract (1)H-(13)C, (1)H-(15)N, (1)H-(19)F, (13)C-(19)F, and (1)H-(35)Cl through-space connectivity information for many positions of interest. The results allow for the evaluation of the performance of a suite of SSNMR experiments and computational approaches as applied to a complex but typical pharmaceutical solid phase.\",\n \"corpus_id\": 20647613,\n \"score\": 0\n },\n {\n \"doc_id\": \"25306191\",\n \"title\": \"On the crystal structure of the vaterite polymorph of CaCO3: a calcium-43 solid-state NMR and computational assessment.\",\n \"abstract\": \"The vaterite polymorph of CaCO3 has puzzled crystallographers for decades in part due to difficulties in obtaining single crystals. The multiple proposed structures for the vaterite polymorph of CaCO3 are assessed using a combined (43)Ca solid-state nuclear magnetic resonance (SSNMR) spectroscopic and computational approach. A combination of improved experimental and computational methods, along with a calibrated chemical shift scale and (43)Ca nuclear quadrupole moment, allow for improved insights relative to our earlier work (Bryce et al., J. Am. Chem. Soc. 2008, 130, 9282). Here, we synthesize a (43)Ca isotopically-enriched sample of vaterite and perform high-resolution quadrupolar SSNMR experiments including magic-angle spinning (MAS), double-rotation (DOR), and multiple-quantum (MQ) MAS experiments at magnetic field strengths of 9.4 and 21.1T. We identify one crystallographically unique Ca(2+) site in vaterite with a slight distribution in both chemical shifts and quadrupolar parameters. Both the experimental (43)Ca electric field gradient tensor and the isotropic chemical shift for vaterite are compared to those calculated with the gauge-including projector-augmented-wave (GIPAW) DFT method in an attempt to identify the model that best represents the crystal structure of vaterite. Simulations of (43)Ca DOR and MAS NMR spectra based on the NMR parameters computed for a total of 18 structural models for vaterite allow us to distinguish between these models. Among these 18, the P3221 and C2 structures provide simulated spectra and diffractograms in best agreement with all experimental data.\",\n \"corpus_id\": 23928342,\n \"score\": 0\n },\n {\n \"doc_id\": \"26114877\",\n \"title\": \"Terahertz Spectroscopy and Solid-State Density Functional Theory Calculations of Cyanobenzaldehyde Isomers.\",\n \"abstract\": \"Spectral signatures in the terahertz (THz) frequency region are mainly due to bulk vibrations of the molecules. These resonances are highly sensitive to the relative position of atoms in a molecule as well as the crystal packing arrangement. To understand the variation of THz resonances, THz spectra (2-10 THz) of three structural isomers: 2-, 3-, and 4-cyanobenzaldehyde have been studied. THz spectra obtained from Fourier transform infrared (FTIR) spectrometry of these isomers show that the resonances are distinctly different especially below 5 THz. For understanding the intermolecular interactions due to hydrogen bonds, four molecule cluster simulations of each of the isomers have been carried out using the B3LYP density functional with the 6-31G(d,p) basis set in Gaussian09 software and the compliance constants are obtained. However, to understand the exact reason behind the observed resonances, simulation of each isomer considering the full crystal structure is essential. The crystal structure of each isomer has been determined using X-ray diffraction (XRD) analysis for carrying out crystal structure simulations. Density functional theory (DFT) simulations using CRYSTAL14 software, utilizing the hybrid density functional B3LYP, have been carried out to understand the vibrational modes. The bond lengths and bond angles from the optimized structures are compared with the XRD results in terms of root-mean-square-deviation (RMSD) values. Very low RMSD values confirm the overall accuracy of the results. The simulations are able to predict most of the spectral features exhibited by the isomers. The results show that low frequency modes (<3 THz) are mediated through hydrogen bonds and are dominated by intermolecular vibrations.\",\n \"corpus_id\": 28110208,\n \"score\": 0\n },\n {\n \"doc_id\": \"26372719\",\n \"title\": \"Combining Nuclear Magnetic Resonance Spectroscopy and Density Functional Theory Calculations to Characterize Carvedilol Polymorphs.\",\n \"abstract\": \"The experiments of carvedilol form II, form III and hydrate by (13) C and (15) N cross-polarization magic-angle spinning (CP MAS) are reported. The GIPAW (gauge-including projector-augmented wave) method from DFT (density functional theory) calculations was used to simulate (13) C and (15) N chemical shifts. A very good agreement was found for the comparison between the global results of experimental and calculated nuclear magnetic resonance (NMR) chemical shifts for carvedilol polymorphs. This work aims a comprehensive understanding of carvedilol crystalline forms employing solution and solid-state NMR as well as DFT calculations. © 2015 Wiley Periodicals, Inc. and the American Pharmacists Association J Pharm Sci.\",\n \"corpus_id\": 5573445,\n \"score\": 0\n },\n {\n \"doc_id\": \"27018827\",\n \"title\": \"Molecular and electron-spin structures of a ring-shaped mixed-valence polyoxovanadate (IV, V) studied by (11)B and (23)Na solid-state NMR spectroscopy and DFT calculations.\",\n \"abstract\": \"(11)B and (23)Na solid-state nuclear magnetic resonance (NMR) spectra of ring-shaped paramagnetic crystals of H15[V7(IV)V5(V)B32O84Na4]·13H2O containing seven d(1) electrons from V(IV) were studied. Magic-angle-spinning (MAS) and multiple-quantum MAS NMR experiments were performed at moderate (9.4T) and ultrahigh magnetic fields (21.6T). The NMR parameters for quadrupole and isotropic chemical shift interactions were estimated by simulation of the NMR spectra and from relativistic density functional theory (DFT) calculations. Four Na ions incorporated into the framework were found to occupy four distinct sites with different populations. The DFT calculation showed that d(1) electrons with effectively one up-spin caused by strong antiferromagnetic interactions were delocalized over the 12V ions.\",\n \"corpus_id\": 205236529,\n \"score\": 0\n },\n {\n \"doc_id\": \"27891541\",\n \"title\": \"DFT calculations in the assignment of solid-state NMR and crystal structure elucidation of a lanthanum(iii) complex with dithiocarbamate and phenanthroline.\",\n \"abstract\": \"The molecular, crystal, and electronic structures as well as spectroscopic properties of a mononuclear heteroleptic lanthanum(iii) complex with diethyldithiocarbamate and 1,10-phenanthroline ligands (3 : 1) were studied by solid-state (13)C and (15)N cross-polarisation (CP) magic-angle-spinning (MAS) NMR, X-ray diffraction (XRD), and first principles density functional theory (DFT) calculations. A substantially different powder XRD pattern and (13)C and (15)N CP-MAS NMR spectra indicated that the title compound is not isostructural to the previously reported analogous rare earth complexes with the space group P21/n. Both (13)C and (15)N CP-MAS NMR revealed the presence of six structurally different dithiocarbamate groups in the asymmetric unit cell, implying a non-centrosymmetric packing arrangement of molecules. This was supported by single-crystal X-ray crystallography showing that the title compound crystallised in the triclinic space group P1[combining macron]. In addition, the crystal structure also revealed that one of the dithiocarbamate ligands has a conformational disorder. NMR chemical shift calculations employing the periodic gauge including projector augmented wave (GIPAW) approach supported the assignment of the experimental (13)C and (15)N NMR spectra. However, the best correspondences were obtained with the structure where the atomic positions in the X-ray unit cell were optimised at the DFT level. The roles of the scalar and spin-orbit relativistic effects on NMR shielding were investigated using the zeroth-order regular approximation (ZORA) method with the outcome that already the scalar relativistic level qualitatively reproduces the experimental chemical shifts. The electronic properties of the complex were evaluated based on the results of the natural bond orbital (NBO) and topology of the electron density analyses. Overall, we apply a multidisciplinary approach acquiring comprehensive information about the solid-state structure and the metal-ligand bonding of the heteroleptic lanthanum complex.\",\n \"corpus_id\": 38206398,\n \"score\": 0\n }\n]","isConversational":false}}},{"rowIdx":89,"cells":{"query":{"kind":"string","value":"{\n \"doc_id\": \"29674755\",\n \"title\": \"Characterizing metal-binding sites in proteins with X-ray crystallography.\",\n \"abstract\": \"Metals have crucial roles in many physiological, pathological, toxicological, pharmaceutical, and diagnostic processes. Proper handling of metal-containing macromolecule samples for structural studies is not trivial, and failure to handle them properly is often a source of irreproducibility caused by issues such as pH changes, incorporation of unexpected metals, or oxidization/reduction of the metal. This protocol outlines the guidelines and best practices for characterizing metal-binding sites in protein structures and alerts experimenters to potential pitfalls during the preparation and handling of metal-containing protein samples for X-ray crystallography studies. The protocol features strategies for controlling the sample pH and the metal oxidation state, recording X-ray fluorescence (XRF) spectra, and collecting diffraction data sets above and below the corresponding metal absorption edges. This protocol should allow experimenters to gather sufficient evidence to unambiguously determine the identity and location of the metal of interest, as well as to accurately characterize the coordinating ligands in the metal binding environment within the protein. Meticulous handling of metal-containing macromolecule samples as described in this protocol should enhance experimental reproducibility in biomedical sciences, especially in X-ray macromolecular crystallography. For most samples, the protocol can be completed within a period of 7-190 d, most of which (2-180 d) is devoted to growing the crystal. The protocol should be readily understandable to structural biologists, particularly protein crystallographers with an intermediate level of experience.\",\n \"corpus_id\": 5046084\n}"},"candidates":{"kind":"list like","value":[{"doc_id":"18004559","title":"X-ray absorption and diffraction studies of the metal binding sites in amyloid beta-peptide.","abstract":"A major source of neurodegeneration observed in Alzheimer's disease is believed to be caused by the toxicity from reactive oxygen species produced in the brain mediated by the A beta protein and mainly copper species. An atomic model of an amyloid beta-peptide (A beta) Cu2+ complex or at least the structure of the metal binding site is of great interest. Accurate information about the Cu-binding site of A beta protein can facilitate simulation of redox chemistry using high level quantum mechanics. Complementary X-ray diffraction and X-ray absorption techniques can be employed to obtain such accurate information. This review provides a blend of X-ray diffraction results on amyloid structures and selected works on A beta Cu2+ binding based on spectroscopic measurements with emphasis on the X-ray absorption technique.","corpus_id":32111603,"score":2},{"doc_id":"18034855","title":"Protein crystallography for non-crystallographers, or how to get the best (but not more) from published macromolecular structures.","abstract":"The number of macromolecular structures deposited in the Protein Data Bank now exceeds 45,000, with the vast majority determined using crystallographic methods. Thousands of studies describing such structures have been published in the scientific literature, and 14 Nobel prizes in chemistry or medicine have been awarded to protein crystallographers. As important as these structures are for understanding the processes that take place in living organisms and also for practical applications such as drug design, many non-crystallographers still have problems with critical evaluation of the structural literature data. This review attempts to provide a brief outline of technical aspects of crystallography and to explain the meaning of some parameters that should be evaluated by users of macromolecular structures in order to interpret, but not over-interpret, the information present in the coordinate files and in their description. A discussion of the extent of the information that can be gleaned from the coordinates of structures solved at different resolution, as well as problems and pitfalls encountered in structure determination and interpretation are also covered.","corpus_id":12525033,"score":2},{"doc_id":"18433638","title":"Time-resolved x-ray crystallography of heme proteins.","abstract":"Heme proteins, with their natural photosensitivity, are excellent systems for the application of time-resolved crystallographic methods. Ligand dissociation can be readily initiated by a short laser pulse with global structural changes probed at the atomic level by X-rays in real time. Third-generation synchrotrons provide 100-ps X-ray pulses of sufficient intensity for monitoring very fast processes. Successful application of such time-resolved crystallographic experiments requires that the structural changes being monitored are compatible with the crystal lattice. These techniques have recently permitted observing for the first time allosteric transitions in real time for a cooperative dimeric hemoglobin.","corpus_id":36149621,"score":2},{"doc_id":"18728313","title":"On-line optical and X-ray spectroscopies with crystallography: an integrated approach for determining metalloprotein structures in functionally well defined states.","abstract":"X-ray-induced redox changes can lead to incorrect assignments of the functional states of metals in metalloprotein crystals. The need for on-line monitoring of the status of metal ions (and other chromophores) during protein crystallography experiments is of growing importance with the use of intense synchrotron X-ray beams. Significant efforts are therefore being made worldwide to combine different spectroscopies in parallel with X-ray crystallographic data collection. Here the implementation and utilization of optical and X-ray absorption spectroscopies on the modern macromolecular crystallography (MX) beamline 10, at the SRS, Daresbury Laboratory, is described. This beamline is equipped with a dedicated monolithic energy-dispersive X-ray fluorescence detector, allowing X-ray absorption spectroscopy (XAS) measurements to be made in situ on the same crystal used to record the diffraction data. In addition, an optical microspectrophotometer has been incorporated on the beamline, thus facilitating combined MX, XAS and optical spectroscopic measurements. By uniting these techniques it is also possible to monitor the status of optically active and optically silent metal centres present in a crystal at the same time. This unique capability has been applied to observe the results of crystallographic data collection on crystals of nitrite reductase from Alcaligenes xylosoxidans, which contains both type-1 and type-2 Cu centres. It is found that the type-1 Cu centre photoreduces quickly, resulting in the loss of the 595 nm peak in the optical spectrum, while the type-2 Cu centre remains in the oxidized state over a much longer time period, for which independent confirmation is provided by XAS data as this centre has an optical spectrum which is barely detectable using microspectrophotometry. This example clearly demonstrates the importance of using two on-line methods, spectroscopy and XAS, for identifying well defined redox states of metalloproteins during crystallographic data collection.","corpus_id":20954052,"score":2},{"doc_id":"19240331","title":"Can soaked-in scavengers protect metalloprotein active sites from reduction during data collection?","abstract":"One of the first events taking place when a crystal of a metalloprotein is exposed to X-ray radiation is photoreduction of the metal centres. The oxidation state of a metal cannot always be determined from routine X-ray diffraction experiments alone, but it may have a crucial impact on the metal's environment and on the analysis of the structural data when considering the functional mechanism of a metalloenzyme. Here, UV-Vis microspectrophotometry is used to test the efficacy of selected scavengers in reducing the undesirable photoreduction of the iron and copper centres in myoglobin and azurin, respectively, and X-ray crystallography to assess their capacity of mitigating global and specific radiation damage effects. UV-Vis absorption spectra of native crystals, as well as those soaked in 18 different radioprotectants, show dramatic metal reduction occurring in the first 60 s of irradiation with an X-ray beam from a third-generation synchrotron source. Among the tested radioprotectants only potassium hexacyanoferrate(III) seems to be capable of partially mitigating the rate of metal photoreduction at the concentrations used, but not to a sufficient extent that would allow a complete data set to be recorded from a fully oxidized crystal. On the other hand, analysis of the X-ray crystallographic data confirms ascorbate as an efficient protecting agent against radiation damage, other than metal centre reduction, and suggests further testing of HEPES and 2,3-dichloro-1,4-naphtoquinone as potential scavengers.","corpus_id":25325140,"score":2},{"doc_id":"19488704","title":"Raman-assisted X-ray crystallography for the analysis of biomolecules.","abstract":"In this chapter, we describe Raman microspectrophotometry applied to crystals of biomolecules. Raman spectra collected in crystallo provide structural information highly complementary to X-ray diffraction, relate the crystalline state to the solution state, and allow the identification of ligand-bound or intermediate states of macromolecules. Nonresonant Raman spectroscopy is particularly suitable to the study of macromolecular crystals, and therefore applies to a wide range of noncolored crystalline proteins. Practical issues related to the investigation of crystals by Raman microspectrophotometry are reviewed, and the current limitations are highlighted.","corpus_id":21462449,"score":2},{"doc_id":"21942751","title":"Spectroscopic characterization of the metal-binding sites in the periplasmic metal-sensor domain of CnrX from Cupriavidus metallidurans CH34.","abstract":"CnrX, the dimeric metal sensor of the three-protein transmembrane signal transduction complex CnrYXH of Cupriavidus metallidurans CH34, contains one metal-binding site per monomer. Both Ni and Co elicit a biological response and bind the protein in a 3N2O1S coordination sphere with a nearly identical octahedral geometry as shown by the X-ray structure of CnrXs, the soluble domain of CnrX. However, in solution CnrXs is titrated by 4 Co-equiv and exhibits an unexpected intense band at 384 nm that was detected neither by single-crystal spectroscopy nor under anaerobiosis. The data from a combination of spectroscopic techniques (spectrophotometry, electron paramagnetic resonance, X-ray absorption spectroscopy) showed that two sites correspond to those identified by crystallography. The two extra binding sites accommodate Co(II) in an octahedral geometry in the absence of oxygen and are occupied in air by a mixture of low-spin Co(II) as well as EPR-silent Co(III). These extra sites, located at the N-terminus of the protein, are believed to participate to the formation of peroxo-bridged dimers. Accordingly, we hypothesize that the intense band at 384 nm relies on the formation of a binuclear μ-peroxo Co(III) complex. These metal binding sites are not physiologically relevant since they are not detected in full-length NccX, the closest homologue of CnrX. X-ray absorption spectroscopy demonstrates that NccX stabilizes Co(II) in two-binding sites similar to those characterized by crystallography in its soluble counterpart. Nevertheless, the original spectroscopic properties of the extra Co-binding sites are of interest because they are susceptible to be detected in other Co-bound proteins.","corpus_id":41113548,"score":2},{"doc_id":"22824156","title":"Metalloprotein active site structure determination: synergy between X-ray absorption spectroscopy and X-ray crystallography.","abstract":"Structures of metalloprotein active sites derived from X-ray crystallography frequently contain chemical anomalies such as unexpected atomic geometries or elongated bond-lengths. Such anomalies are expected from the known errors inherent in macromolecular crystallography (ca. 0.1-0.2Å) and from the lack of appropriate restraints for metal sites which are often without precedent in the small molecule structure literature. Here we review the potential of X-ray absorption spectroscopy to provide information and perspective which could aid in improving the accuracy of metalloprotein crystal structure solutions. We also review the potential problem areas in analysis of the extended X-ray absorption fine structure (EXAFS) and discuss the use of density functional theory as another possible source of geometrical restraints for crystal structure analysis of metalloprotein active sites.","corpus_id":41486973,"score":2},{"doc_id":"23093746","title":"X-ray absorption spectroscopy at a protein crystallography facility: the Canadian Light Source beamline 08B1-1.","abstract":"It is now possible to perform X-ray absorption spectroscopy (XAS) on metalloprotein crystals at the Canadian Macromolecular Crystallography Facility bend magnet (CMCF-BM) beamline (08B1-1) at the Canadian Light Source. The recent addition of a four-element fluorescence detector allows users to acquire data suitable for X-ray absorption near-edge structure and extended X-ray absorption fine-structure based studies by monitoring fluorescence. CMCF beamline users who wish to supplement their diffraction data with XAS can do so with virtually no additional sample preparation. XAS data collection is integrated with the established Mx Data Collector software package used to collect diffraction data. Mainstream XAS data-processing software packages are available for the users; assistance with data processing and interpretation by staff is also available upon request.","corpus_id":23215460,"score":2},{"doc_id":"23529438","title":"Analysis of Ca(2+)-binding sites in the MthK RCK domain by X-ray crystallography.","abstract":"Regulator of K(+) conductance (RCK) domains form a conserved class of ligand-binding domains that control the activity of a variety of prokaryotic and eukaryotic K(+) channels. Structural analysis of these domains by X-ray crystallography has provided insight toward mechanisms underlying ligand binding and channel gating, and thus the experimental strategies aimed at determining structures of liganded and unliganded forms of the domains may be useful in analysis of other ligand-binding domains. Here, we describe a basic strategy for crystallographic analysis of the RCK domain from the MthK channel, for determination of its Ca(2+)-bound structure.","corpus_id":10535094,"score":2},{"doc_id":"24356774","title":"Validation of metal-binding sites in macromolecular structures with the CheckMyMetal web server.","abstract":"Metals have vital roles in both the mechanism and architecture of biological macromolecules. Yet structures of metal-containing macromolecules in which metals are misidentified and/or suboptimally modeled are abundant in the Protein Data Bank (PDB). This shows the need for a diagnostic tool to identify and correct such modeling problems with metal-binding environments. The CheckMyMetal (CMM) web server (http://csgid.org/csgid/metal_sites/) is a sophisticated, user-friendly web-based method to evaluate metal-binding sites in macromolecular structures using parameters derived from 7,350 metal-binding sites observed in a benchmark data set of 2,304 high-resolution crystal structures. The protocol outlines how the CMM server can be used to detect geometric and other irregularities in the structures of metal-binding sites, as well as how it can alert researchers to potential errors in metal assignment. The protocol also gives practical guidelines for correcting problematic sites by modifying the metal-binding environment and/or redefining metal identity in the PDB file. Several examples where this has led to meaningful results are described in the ANTICIPATED RESULTS section. CMM was designed for a broad audience--biomedical researchers studying metal-containing proteins and nucleic acids--but it is equally well suited for structural biologists validating new structures during modeling or refinement. The CMM server takes the coordinates of a metal-containing macromolecule structure in the PDB format as input and responds within a few seconds for a typical protein structure with 2-5 metal sites and a few hundred amino acids.","corpus_id":195684158,"score":2},{"doc_id":"24639261","title":"X-ray crystallographic studies of metalloproteins.","abstract":"Many proteins require metals for their physiological function. In combination with spectroscopic characterizations, X-ray crystallography is a very powerful method to correlate the function of protein-bound metal sites with their structure. Due to their special X-ray scattering properties, specific metals may be located in metalloprotein structures and eventually used for phasing the diffracted X-rays by the method of Multi-wavelength Anomalous Dispersion (MAD). How this is done is the principle subject of this chapter. Attention is also given to the crystallographic characterization of different oxidation states of redox active metals and to the complication of structural changes that may be induced by X-ray irradiation of protein crystals.","corpus_id":6004528,"score":2},{"doc_id":"24701959","title":"Electrochemical X-ray fluorescence spectroscopy for trace heavy metal analysis: enhancing X-ray fluorescence detection capabilities by four orders of magnitude.","abstract":"The development of a novel analytical technique, electrochemical X-ray fluorescence (EC-XRF), is described and applied to the quantitative detection of heavy metals in solution, achieving sub-ppb limits of detection (LOD). In EC-XRF, electrochemical preconcentration of a species of interest onto the target electrode is achieved here by cathodic electrodeposition. Unambiguous elemental identification and quantification of metal concentration is then made using XRF. This simple electrochemical preconcentration step improves the LOD of energy dispersive XRF by over 4 orders of magnitude (for similar sample preparation time scales). Large area free-standing boron doped diamond grown using microwave plasma chemical vapor deposition techniques is found to be ideal as the electrode material for both electrodeposition and XRF due to its wide solvent window, transparency to the XRF beam, and ability to be produced in mechanically robust freestanding thin film form. During electrodeposition it is possible to vary both the deposition potential (Edep) and deposition time (tdep). For the metals Cu(2+) and Pb(2+) the highest detection sensitivities were found for Edep = -1.75 V and tdep (=) 4000 s with LODs of 0.05 and 0.04 ppb achieved, respectively. In mixed Cu(2+)/Pb(2+) solutions, EC-XRF shows that Cu(2+) deposition is unimpeded by Pb(2+), across a broad concentration range, but this is only true for Pb(2+) when both metals are present at low concentrations (10 nM), boding well for trace level measurements. In a dual mixed metal solution, EC-XRF can also be employed to either selectively deposit the metal which has the most positive formal reduction potential, E(0), or exhaustively deplete it from solution, enabling uninhibited detection of the metal with the more negative E(0).","corpus_id":206363086,"score":2},{"doc_id":"25945580","title":"Using support vector machines to improve elemental ion identification in macromolecular crystal structures.","abstract":"In the process of macromolecular model building, crystallographers must examine electron density for isolated atoms and differentiate sites containing structured solvent molecules from those containing elemental ions. This task requires specific knowledge of metal-binding chemistry and scattering properties and is prone to error. A method has previously been described to identify ions based on manually chosen criteria for a number of elements. Here, the use of support vector machines (SVMs) to automatically classify isolated atoms as either solvent or one of various ions is described. Two data sets of protein crystal structures, one containing manually curated structures deposited with anomalous diffraction data and another with automatically filtered, high-resolution structures, were constructed. On the manually curated data set, an SVM classifier was able to distinguish calcium from manganese, zinc, iron and nickel, as well as all five of these ions from water molecules, with a high degree of accuracy. Additionally, SVMs trained on the automatically curated set of high-resolution structures were able to successfully classify most common elemental ions in an independent validation test set. This method is readily extensible to other elemental ions and can also be used in conjunction with previous methods based on a priori expectations of the chemical environment and X-ray scattering.","corpus_id":14213127,"score":2},{"doc_id":"26740326","title":"UV-Visible Absorption Spectroscopy Enhanced X-ray Crystallography at Synchrotron and X-ray Free Electron Laser Sources.","abstract":"This review describes the use of single crystal UV-Visible Absorption micro-Spectrophotometry (UV-Vis AS) to enhance the design and execution of X-ray crystallography experiments for structural investigations of reaction intermediates of redox active and photosensitive proteins. Considerations for UV-Vis AS measurements at the synchrotron and associated instrumentation are described. UV-Vis AS is useful to verify the intermediate state of an enzyme and to monitor the progression of reactions within crystals. Radiation induced redox changes within protein crystals may be monitored to devise effective diffraction data collection strategies. An overview of the specific effects of radiation damage on macromolecular crystals is presented along with data collection strategies that minimize these effects by combining data from multiple crystals used at the synchrotron and with the X-ray free electron laser.","corpus_id":29851904,"score":2},{"doc_id":"26975689","title":"Metalloprotein Crystallography: More than a Structure.","abstract":"Metal ions and metallocofactors play important roles in a broad range of biochemical reactions. Accordingly, it has been estimated that as much as 25-50% of the proteome uses transition metal ions to carry out a variety of essential functions. The metal ions incorporated within metalloproteins fulfill functional roles based on chemical properties, the diversity of which arises as transition metals can adopt different redox states and geometries, dictated by the identity of the metal and the protein environment. The coupling of a metal ion with an organic framework in metallocofactors, such as heme and cobalamin, further expands the chemical functionality of metals in biology. The three-dimensional visualization of metal ions and complex metallocofactors within a protein scaffold is often a starting point for enzymology, highlighting the importance of structural characterization of metalloproteins. Metalloprotein crystallography, however, presents a number of implicit challenges including correctly incorporating the relevant metal or metallocofactor, maintaining the proper environment for the protein to be purified and crystallized (including providing anaerobic, cold, or aphotic environments), and being mindful of the possibility of X-ray induced damage to the proteins or incorporated metal ions. Nevertheless, the incorporated metals or metallocofactors also present unique advantages in metalloprotein crystallography. The significant resonance that metals undergo with X-ray photons at wavelengths used for protein crystallography and the rich electronic properties of metals, which provide intense and spectroscopically unique signatures, allow a metalloprotein crystallographer to use anomalous dispersion to determine phases for structure solution and to use simultaneous or parallel spectroscopic techniques on single crystals. These properties, coupled with the improved brightness of beamlines, the ability to tune the wavelength of the X-ray beam, the availability of advanced detectors, and the incorporation of spectroscopic equipment at a number of synchrotron beamlines, have yielded exciting developments in metalloprotein structure determination. Here we will present results on the advantageous uses of metals in metalloprotein crystallography, including using metallocofactors to obtain phasing information, using K-edge X-ray absorption spectroscopy to identify metals coordinated in metalloprotein crystals, and using UV-vis spectroscopy on crystals to probe the enzymatic activity of the crystallized protein.","corpus_id":14248206,"score":2},{"doc_id":"28291757","title":"CheckMyMetal: a macromolecular metal-binding validation tool.","abstract":"Metals are essential in many biological processes, and metal ions are modeled in roughly 40% of the macromolecular structures in the Protein Data Bank (PDB). However, a significant fraction of these structures contain poorly modeled metal-binding sites. CheckMyMetal (CMM) is an easy-to-use metal-binding site validation server for macromolecules that is freely available at http://csgid.org/csgid/metal_sites. The CMM server can detect incorrect metal assignments as well as geometrical and other irregularities in the metal-binding sites. Guidelines for metal-site modeling and validation in macromolecules are illustrated by several practical examples grouped by the type of metal. These examples show CMM users (and crystallographers in general) problems they may encounter during the modeling of a specific metal ion.","corpus_id":13636890,"score":2},{"doc_id":"28375143","title":"Data mining of iron(II) and iron(III) bond-valence parameters, and their relevance for macromolecular crystallography.","abstract":"The bond-valence model is a reliable way to validate assumed oxidation states based on structural data. It has successfully been employed for analyzing metal-binding sites in macromolecule structures. However, inconsistent results for heme-based structures suggest that some widely used bond-valence R0 parameters may need to be adjusted in certain cases. Given the large number of experimental crystal structures gathered since these initial parameters were determined and the similarity of binding sites in organic compounds and macromolecules, the Cambridge Structural Database (CSD) is a valuable resource for refining metal-organic bond-valence parameters. R0 bond-valence parameters for iron(II), iron(III) and other metals have been optimized based on an automated processing of all CSD crystal structures. Almost all R0 bond-valence parameters were reproduced, except for iron-nitrogen bonds, for which distinct R0 parameters were defined for two observed subpopulations, corresponding to low-spin and high-spin states, of iron in both oxidation states. The significance of this data-driven method for parameter discovery, and how the spin state affects the interpretation of heme-containing proteins and iron-binding sites in macromolecular structures, are discussed.","corpus_id":22455987,"score":2},{"doc_id":"28967006","title":"Principles and methods used to grow and optimize crystals of protein-metallodrug adducts, to determine metal binding sites and to assign metal ligands.","abstract":"The characterization of the interactions between biological macromolecules (proteins and nucleic acids) and metal-based drugs is a fundamental prerequisite for understanding their mechanisms of action. X-ray crystallography enables the structural analysis of such complexes with atomic level detail. However, this approach requires the preparation of highly diffracting single crystals, the measurement of diffraction patterns and the structural analysis and interpretation of macromolecule-metal interactions from electron density maps. In this review, we describe principles and methods used to grow and optimize crystals of protein-metallodrug adducts, to determine metal binding sites and to assign and validate metal ligands. Examples from the literature and experience in our own laboratory are provided and key challenges are described, notably crystallization and molecular model refinement against the X-ray diffraction data.","corpus_id":19820447,"score":2},{"doc_id":"29045784","title":"Metal Dependence of the Xylose Isomerase from Piromyces sp. E2 Explored by Activity Profiling and Protein Crystallography.","abstract":"Xylose isomerase from Piromyces sp. E2 (PirXI) can be used to equip Saccharomyces cerevisiae with the capacity to ferment xylose to ethanol. The biochemical properties and structure of the enzyme have not been described even though its metal content, catalytic parameters, and expression level are critical for rapid xylose utilization. We have isolated the enzyme after high-level expression in Escherichia coli, analyzed the metal dependence of its catalytic properties, and determined 12 crystal structures in the presence of different metals, substrates, and substrate analogues. The activity assays revealed that various bivalent metals can activate PirXI for xylose isomerization. Among these metals, Mn2+ is the most favorable for catalytic activity. Furthermore, the enzyme shows the highest affinity for Mn2+, which was established by measuring the activation constants (Kact) for different metals. Metal analysis of the purified enzyme showed that in vivo the enzyme binds a mixture of metals that is determined by metal availability as well as affinity, indicating that the native metal composition can influence activity. The crystal structures show the presence of an active site similar to that of other xylose isomerases, with a d-xylose binding site containing two tryptophans and a catalytic histidine, as well as two metal binding sites that are formed by carboxylate groups of conserved aspartates and glutamates. The binding positions and conformations of the metal-coordinating residues varied slightly for different metals, which is hypothesized to contribute to the observed metal dependence of the isomerase activity.","corpus_id":19522015,"score":2},{"doc_id":"19303027","title":"X-ray crystallography of chemical compounds.","abstract":"AIMS: Accurate knowledge of molecular structure is a prerequisite for rational drug design. This review examines the role of X-ray crystallography in providing the required structural information and advances in the field of X-ray crystallography that enhance or expand its role. MAIN METHODS: X-ray crystallography of new drugs candidates and intermediates can provide valuable information of new syntheses and parameters for quantitative structure activity relationships (QSAR). KEY FINDINGS: Crystallographic studies play a vital role in many disciplines including materials science, chemistry, pharmacology, and molecular biology. X-ray crystallography is the most comprehensive technique available to determine molecular structure. A requirement for the high accuracy of crystallographic structures is that a 'good crystal' must be found, and this is often the rate-limiting step. In the past three decades developments in detectors, increases in computer power, and powerful graphics capabilities have contributed to a dramatic increase in the number of materials characterized by X-ray crystallography. More recently the advent of high-throughput crystallization techniques has enhanced our ability to produce that one good crystal required for crystallographic analysis. SIGNIFICANCE: Continuing advances in all phases of a crystallographic study have expanded the ranges of samples which can be analyzes by X-ray crystallography to include larger molecules, smaller or weakly diffracting crystals, and twinned crystals.","corpus_id":206727089,"score":1},{"doc_id":"19322673","title":"Structures of proteins and cofactors: X-ray crystallography.","abstract":"Protein crystallography is the predominately used technique for the determination of the three-dimensional structures of proteins and other macromolecules. In this article, the methodology utilized for the measurement and analysis of the diffraction data from crystals is briefly reviewed. As examples of both the usefulness and difficulties of this technique, the determination of the structures of several photosynthetic pigment-protein complexes is described, namely, the reaction center from purple bacteria, photosystem I and photosystem II from cyanobacteria, the light-harvesting complex II from purple bacteria, and the FMO protein from green bacteria.","corpus_id":19069675,"score":1},{"doc_id":"20382997","title":"Temperature-dependent macromolecular X-ray crystallography.","abstract":"X-ray crystallography provides structural details of biological macromolecules. Whereas routine data are collected close to 100 K in order to mitigate radiation damage, more exotic temperature-controlled experiments in a broader temperature range from 15 K to room temperature can provide both dynamical and structural insights. Here, the dynamical behaviour of crystalline macromolecules and their surrounding solvent as a function of cryo-temperature is reviewed. Experimental strategies of kinetic crystallography are discussed that have allowed the generation and trapping of macromolecular intermediate states by combining reaction initiation in the crystalline state with appropriate temperature profiles. A particular focus is on recruiting X-ray-induced changes for reaction initiation, thus unveiling useful aspects of radiation damage, which otherwise has to be minimized in macromolecular crystallography.","corpus_id":14006498,"score":1},{"doc_id":"20694684","title":"X-ray crystallography in drug discovery.","abstract":"Macromolecular X-ray crystallography is an important and powerful technique in drug discovery, used by pharmaceutical companies in the discovery process of new medicines. The detailed analysis of crystal structures of protein-ligand complexes allows the study of the specific interactions of a particular drug with its protein target at the atomic level. It is used to design and improve drugs. The starting point of these studies is the preparation of suitable crystals of complexes with potential ligands, which can be achieved by using different strategies described in this chapter. In addition, an introduction to X-ray crystallography is given, highlighting the fundamental steps necessary to determine the three-dimensional structure of protein-ligand complexes, as well as some of the tools and criteria to validate crystal structures available in databases.","corpus_id":206673826,"score":1},{"doc_id":"20825181","title":"Structural comparisons of apo- and metalated three-stranded coiled coils clarify metal binding determinants in thiolate containing designed peptides.","abstract":"Over the past two decades, designed metallopeptides have held the promise for understanding a variety of fundamental questions in metallobiochemistry; however, these dreams have not yet been realized because of a lack of structural data to elaborate the protein scaffolds before metal complexation and the resultant metalated structures which ultimately exist. This is because there are few reports of structural characterization of such systems either in their metalated or nonmetalated forms and no examples where an apo structure and the corresponding metalated peptide assembly have both been defined by X-ray crystallography. Herein we present X-ray structures of two de novo designed parallel three-stranded coiled coils (designed using the heptad repeat (a → g)) CSL9C (CS = Coil Ser) and CSL19C in their nonmetalated forms, determined to 1.36 and 2.15 A resolutions, respectively. Leucines from either position 9 (a site) or 19 (d site) are replaced by cysteine to generate the constructs CSL9C and CSL19C, respectively, yielding thiol-rich pockets at the hydrophobic interior of these peptides, suitable to bind heavy metals such as As(III), Hg(II), Cd(II), and Pb(II). We use these structures to understand the inherent structural differences between a and d sites to clarify the basis of the observed differential spectroscopic behavior of metal binding in these types of peptides. Cys side chains of (CSL9C)(3) show alternate conformations and are partially preorganized for metal binding, whereas cysteines in (CSL19C)(3) are present as a single conformer. Zn(II) ions, which do not coordinate or influence Cys residues at the designed metal sites but are essential for forming X-ray quality crystals, are bound to His and Glu residues at the crystal packing interfaces of both structures. These \"apo\" structures are used to clarify the changes in metal site organization between metalated As(CSL9C)(3) and to speculate on the differential basis of Hg(II) binding in a versus d peptides. Thus, for the first time, one can establish general rules for heavy metal binding to Cys-rich sites in designed proteins which may provide insight for understanding how heavy metals bind to metallochaperones or metalloregulatory proteins.","corpus_id":34204911,"score":1},{"doc_id":"21041930","title":"Joint X-ray and neutron refinement with phenix.refine.","abstract":"Approximately 85% of the structures deposited in the Protein Data Bank have been solved using X-ray crystallography, making it the leading method for three-dimensional structure determination of macromolecules. One of the limitations of the method is that the typical data quality (resolution) does not allow the direct determination of H-atom positions. Most hydrogen positions can be inferred from the positions of other atoms and therefore can be readily included into the structure model as a priori knowledge. However, this may not be the case in biologically active sites of macromolecules, where the presence and position of hydrogen is crucial to the enzymatic mechanism. This makes the application of neutron crystallography in biology particularly important, as H atoms can be clearly located in experimental neutron scattering density maps. Without exception, when a neutron structure is determined the corresponding X-ray structure is also known, making it possible to derive the complete structure using both data sets. Here, the implementation of crystallographic structure-refinement procedures that include both X-ray and neutron data (separate or jointly) in the PHENIX system is described.","corpus_id":16124013,"score":1},{"doc_id":"21293373","title":"Femtosecond X-ray protein nanocrystallography.","abstract":"X-ray crystallography provides the vast majority of macromolecular structures, but the success of the method relies on growing crystals of sufficient size. In conventional measurements, the necessary increase in X-ray dose to record data from crystals that are too small leads to extensive damage before a diffraction signal can be recorded. It is particularly challenging to obtain large, well-diffracting crystals of membrane proteins, for which fewer than 300 unique structures have been determined despite their importance in all living cells. Here we present a method for structure determination where single-crystal X-ray diffraction 'snapshots' are collected from a fully hydrated stream of nanocrystals using femtosecond pulses from a hard-X-ray free-electron laser, the Linac Coherent Light Source. We prove this concept with nanocrystals of photosystem I, one of the largest membrane protein complexes. More than 3,000,000 diffraction patterns were collected in this study, and a three-dimensional data set was assembled from individual photosystem I nanocrystals (∼200 nm to 2 μm in size). We mitigate the problem of radiation damage in crystallography by using pulses briefer than the timescale of most damage processes. This offers a new approach to structure determination of macromolecules that do not yield crystals of sufficient size for studies using conventional radiation sources or are particularly sensitive to radiation damage.","corpus_id":1020650,"score":1},{"doc_id":"21304455","title":"Protein crystallization for X-ray crystallography.","abstract":"Using the three-dimensional structure of biological macromolecules to infer how they function is one of the most important fields of modern biology. The availability of atomic resolution structures provides a deep and unique understanding of protein function, and helps to unravel the inner workings of the living cell. To date, 86% of the Protein Data Bank (rcsb-PDB) entries are macromolecular structures that were determined using X-ray crystallography. To obtain crystals suitable for crystallographic studies, the macromolecule (e.g. protein, nucleic acid, protein-protein complex or protein-nucleic acid complex) must be purified to homogeneity, or as close as possible to homogeneity. The homogeneity of the preparation is a key factor in obtaining crystals that diffract to high resolution (Bergfors, 1999; McPherson, 1999). Crystallization requires bringing the macromolecule to supersaturation. The sample should therefore be concentrated to the highest possible concentration without causing aggregation or precipitation of the macromolecule (usually 2-50 mg/mL). Introducing the sample to precipitating agent can promote the nucleation of protein crystals in the solution, which can result in large three-dimensional crystals growing from the solution. There are two main techniques to obtain crystals: vapor diffusion and batch crystallization. In vapor diffusion, a drop containing a mixture of precipitant and protein solutions is sealed in a chamber with pure precipitant. Water vapor then diffuses out of the drop until the osmolarity of the drop and the precipitant are equal (Figure 1A). The dehydration of the drop causes a slow concentration of both protein and precipitant until equilibrium is achieved, ideally in the crystal nucleation zone of the phase diagram. The batch method relies on bringing the protein directly into the nucleation zone by mixing protein with the appropriate amount of precipitant (Figure 1B). This method is usually performed under a paraffin/mineral oil mixture to prevent the diffusion of water out of the drop. Here we will demonstrate two kinds of experimental setup for vapor diffusion, hanging drop and sitting drop, in addition to batch crystallization under oil.","corpus_id":11632900,"score":1},{"doc_id":"21376143","title":"Infrared protein crystallography.","abstract":"We consider the application of infrared spectroscopy to protein crystals, with particular emphasis on exploiting molecular orientation through polarization measurements on oriented single crystals. Infrared microscopes enable transmission measurements on individual crystals using either thermal or nonthermal sources, and can accommodate flow cells, used to measure spectral changes induced by exposure to soluble ligands, and cryostreams, used for measurements of flash-cooled crystals. Comparison of unpolarized infrared measurements on crystals and solutions probes the effects of crystallization and can enhance the value of the structural models refined from X-ray diffraction data by establishing solution conditions under which they are most relevant. Results on several proteins are consistent with similar equilibrium conformational distributions in crystal and solutions. However, the rates of conformational change are often perturbed. Infrared measurements also detect products generated by X-ray exposure, including CO(2). Crystals with favorable symmetry exhibit infrared dichroism that enhances the synergy with X-ray crystallography. Polarized infrared measurements on crystals can distinguish spectral contributions from chemically similar sites, identify hydrogen bonding partners, and, in opportune situations, determine three-dimensional orientations of molecular groups. This article is part of a Special Issue entitled: Protein Structure and Function in the Crystalline State.","corpus_id":37045533,"score":1},{"doc_id":"21833866","title":"X-ray crystallography.","abstract":"X-ray crystallography has been particularly important in the study of the enzyme nitrogenase, providing researchers with high-resolution structural models that have been essential to studying the enzyme's unique metal clusters and nucleotide-binding modes and protein interactions. While several important nitrogenase structures have already been determined using X-ray crystallography, the technique still holds great potential for future significant discoveries involving reaction intermediates and redox states of the enzyme's metal clusters. Thus, it is important to inform future nitrogenase researchers about the procedures for obtaining crystals of nitrogenase component proteins and their complexes and determining their structures. While nitrogenase component proteins from several bacteria have been crystallized, the majority of structures and those of highest resolution are of the nitrogenase proteins from the bacteria Azotobacter vinelandii. Therefore, the bulk of this chapter will focus on methods for crystallization and structure determination of nitrogenase component proteins from A. vinelandii.","corpus_id":104916134,"score":1},{"doc_id":"21949273","title":"ISPyB: an information management system for synchrotron macromolecular crystallography.","abstract":"MOTIVATION: Individual research groups now analyze thousands of samples per year at synchrotron macromolecular crystallography (MX) resources. The efficient management of experimental data is thus essential if the best possible experiments are to be performed and the best possible data used in downstream processes in structure determination pipelines. Information System for Protein crystallography Beamlines (ISPyB), a Laboratory Information Management System (LIMS) with an underlying data model allowing for the integration of analyses down-stream of the data collection experiment was developed to facilitate such data management. RESULTS: ISPyB is now a multisite, generic LIMS for synchrotron-based MX experiments. Its initial functionality has been enhanced to include improved sample tracking and reporting of experimental protocols, the direct ranking of the diffraction characteristics of individual samples and the archiving of raw data and results from ancillary experiments and post-experiment data processing protocols. This latter feature paves the way for ISPyB to play a central role in future macromolecular structure solution pipelines and validates the application of the approach used in ISPyB to other experimental techniques, such as biological solution Small Angle X-ray Scattering and spectroscopy, which have similar sample tracking and data handling requirements.","corpus_id":9383206,"score":1},{"doc_id":"22045560","title":"Crystallization of macromolecules.","abstract":"X-ray crystallography has evolved into a very powerful tool to determine the three-dimensional structure of macromolecules and macromolecular complexes. The major bottleneck in structure determination by X-ray crystallography is the preparation of suitable crystalline samples. This unit outlines steps for the crystallization of a macromolecule, starting with a purified, homogeneous sample. The first protocols describe preparation of the macromolecular sample (i.e., proteins, nucleic acids, and macromolecular complexes). The preparation and assessment of crystallization trials is then described, along with a protocol for confirming whether the crystals obtained are composed of macromolecule as opposed to a crystallization reagent. Next, the optimization of crystallization conditions is presented. Finally, protocols that facilitate the growth of larger crystals through seeding are described.","corpus_id":20703254,"score":1},{"doc_id":"23132076","title":"Determination of soluble and membrane protein structures by X-ray crystallography.","abstract":"X-ray crystallography is a technique used to determine the atomic-detail structure of a biological macromolecule. The method relies on the ability to generate a three-dimensional crystal of a highly purified protein or nucleic acid for diffraction by X-rays. The extent of scattering of X-rays by the crystal determines the accuracy of the resulting structural model. Unlike electrons, X-rays cannot be refocused after they have been scattered by their target. Thus, calculations are needed to reconstruct the image of the macromolecule that builds the crystal lattice. Tremendous advances over the past 60 years in recombinant expression and purification, crystal growth methods and equipment, X-ray sources, computer processing power, programs, and graphics have taken X-ray crystallography from a highly specialized field to one increasingly accessible to researchers in the biomedical sciences. In this chapter, we review the major concepts of macromolecular X-ray crystallography, focusing mainly on techniques for crystallizing soluble and membrane proteins, and provide a protocol for the crystallization of lysozyme as a model for the crystallization of other proteins.","corpus_id":29230067,"score":1},{"doc_id":"23729263","title":"Studying protein-ligand interactions using X-ray crystallography.","abstract":"X-ray crystallography is a powerful technique for studying protein-ligand interactions. Advances in techniques have meant that it is now possible to routinely determine the structures of ligand complexes in the majority of cases where crystallization conditions and protein structures are already known. Ligand soaking or cocrystallization, together with the potential use of molecular replacement, provides data for determining the structures of a protein in complex with ligands. Furthermore, advances in protein structure model building facilitate automatic ligand fitting to residual electron density in the protein-ligand complex.","corpus_id":41459476,"score":1},{"doc_id":"24372145","title":"The future of crystallography in drug discovery.","abstract":"INTRODUCTION: X-ray crystallography plays an important role in structure-based drug design (SBDD), and accurate analysis of crystal structures of target macromolecules and macromolecule-ligand complexes is critical at all stages. However, whereas there has been significant progress in improving methods of structural biology, particularly in X-ray crystallography, corresponding progress in the development of computational methods (such as in silico high-throughput screening) is still on the horizon. Crystal structures can be overinterpreted and thus bias hypotheses and follow-up experiments. As in any experimental science, the models of macromolecular structures derived from X-ray diffraction data have their limitations, which need to be critically evaluated and well understood for structure-based drug discovery. AREAS COVERED: This review describes how the validity, accuracy and precision of a protein or nucleic acid structure determined by X-ray crystallography can be evaluated from three different perspectives: i) the nature of the diffraction experiment; ii) the interpretation of an electron density map; and iii) the interpretation of the structural model in terms of function and mechanism. The strategies to optimally exploit a macromolecular structure are also discussed in the context of 'Big Data' analysis, biochemical experimental design and structure-based drug discovery. EXPERT OPINION: Although X-ray crystallography is one of the most detailed 'microscopes' available today for examining macromolecular structures, the authors would like to re-emphasize that such structures are only simplified models of the target macromolecules. The authors also wish to reinforce the idea that a structure should not be thought of as a set of precise coordinates but rather as a framework for generating hypotheses to be explored. Numerous biochemical and biophysical experiments, including new diffraction experiments, can and should be performed to verify or falsify these hypotheses. X-ray crystallography will find its future application in drug discovery by the development of specific tools that would allow realistic interpretation of the outcome coordinates and/or support testing of these hypotheses.","corpus_id":38488861,"score":1},{"doc_id":"24590727","title":"Screening Ligands by X-ray crystallography.","abstract":"X-ray crystallography is an invaluable technique in structure-based drug discovery, including fragment-based drug discovery, because it is the only technique that can provide a complete three dimensional readout of the interaction between the small molecule and its macromolecular target. X-ray diffraction (XRD) techniques can be employed as the sole method for conducting a screen of a fragment library, or it can be employed as the final technique in a screening campaign to confirm putative \"hit\" compounds identified by a variety of biochemical and/or biophysical screening techniques. Both approaches require an efficient technique to prepare dozens to hundreds of crystals for data collection, and a reproducible way to deliver ligands to the crystal. Here, a general method for screening cocktails of fragments is described. In cases where X-ray crystallography is employed as a method to verify putative hits, the cocktails of fragments described below would simply be replaced with single fragment solutions.","corpus_id":8218772,"score":1},{"doc_id":"24648090","title":"Protein structure validation and analysis with X-ray crystallography.","abstract":"X-ray crystallography is the main technique for the determination of protein structures. About 85 % of all protein structures known to date have been elucidated using X-ray crystallography. Knowledge of the three-dimensional structure of proteins can be used in various applications in biotechnology, biomedicine, drug design, and basic research and as a validation tool for protein modifications, ligand binding, and structural authenticity. Moreover, the requirement for pure, homogeneous, and stable protein solutions in crystallizations makes X-ray crystallography beneficial in other fields of protein research as well. Here, we describe the technique of X-ray protein crystallography and the steps involved for a successful three-dimensional crystal structure determination.","corpus_id":10634886,"score":1},{"doc_id":"25068843","title":"X-ray absorption spectroscopy systematics at the tungsten L-edge.","abstract":"A series of mononuclear six-coordinate tungsten compounds spanning formal oxidation states from 0 to +VI, largely in a ligand environment of inert chloride and/or phosphine, was interrogated by tungsten L-edge X-ray absorption spectroscopy. The L-edge spectra of this compound set, comprised of [W(0)(PMe3)6], [W(II)Cl2(PMePh2)4], [W(III)Cl2(dppe)2][PF6] (dppe = 1,2-bis(diphenylphosphino)ethane), [W(IV)Cl4(PMePh2)2], [W(V)(NPh)Cl3(PMe3)2], and [W(VI)Cl6], correlate with formal oxidation state and have usefulness as references for the interpretation of the L-edge spectra of tungsten compounds with redox-active ligands and ambiguous electronic structure descriptions. The utility of these spectra arises from the combined correlation of the estimated branching ratio of the L3,2-edges and the L1 rising-edge energy with metal Zeff, thereby permitting an assessment of effective metal oxidation state. An application of these reference spectra is illustrated by their use as backdrop for the L-edge X-ray absorption spectra of [W(IV)(mdt)2(CO)2] and [W(IV)(mdt)2(CN)2](2-) (mdt(2-) = 1,2-dimethylethene-1,2-dithiolate), which shows that both compounds are effectively W(IV) species even though the mdt ligands exist at different redox levels in the two compounds. Use of metal L-edge XAS to assess a compound of uncertain formulation requires: (1) Placement of that data within the context of spectra offered by unambiguous calibrant compounds, preferably with the same coordination number and similar metal ligand distances. Such spectra assist in defining upper and/or lower limits for metal Zeff in the species of interest. ( 2) Evaluation of that data in conjunction with information from other physical methods, especially ligand K-edge XAS. ( 3) Increased care in interpretation if strong π-acceptor ligands, particularly CO, or π-donor ligands are present. The electron-withdrawing/donating nature of these ligand types, combined with relatively short metal-ligand distances, exaggerate the difference between formal oxidation state and metal Zeff or, as in the case of [W(IV)(mdt)2(CO)2], exert the subtle effect of modulating the redox level of other ligands in the coordination sphere.","corpus_id":32116483,"score":1},{"doc_id":"26057665","title":"In meso in situ serial X-ray crystallography of soluble and membrane proteins.","abstract":"The lipid cubic phase (LCP) continues to grow in popularity as a medium in which to generate crystals of membrane (and soluble) proteins for high-resolution X-ray crystallographic structure determination. To date, the PDB includes 227 records attributed to the LCP or in meso method. Among the listings are some of the highest profile membrane proteins, including the β2-adrenoreceptor-Gs protein complex that figured in the award of the 2012 Nobel Prize in Chemistry to Lefkowitz and Kobilka. The most successful in meso protocol to date uses glass sandwich crystallization plates. Despite their many advantages, glass plates are challenging to harvest crystals from. However, performing in situ X-ray diffraction measurements with these plates is not practical. Here, an alternative approach is described that provides many of the advantages of glass plates and is compatible with high-throughput in situ measurements. The novel in meso in situ serial crystallography (IMISX) method introduced here has been demonstrated with AlgE and PepT (alginate and peptide transporters, respectively) as model integral membrane proteins and with lysozyme as a test soluble protein. Structures were solved by molecular replacement and by experimental phasing using bromine SAD and native sulfur SAD methods to resolutions ranging from 1.8 to 2.8 Å using single-digit microgram quantities of protein. That sulfur SAD phasing worked is testament to the exceptional quality of the IMISX diffraction data. The IMISX method is compatible with readily available, inexpensive materials and equipment, is simple to implement and is compatible with high-throughput in situ serial data collection at macromolecular crystallography synchrotron beamlines worldwide. Because of its simplicity and effectiveness, the IMISX approach is likely to supplant existing in meso crystallization protocols. It should prove particularly attractive in the area of ligand screening for drug discovery and development.","corpus_id":4943457,"score":1},{"doc_id":"26175905","title":"Sub-atomic resolution X-ray crystallography and neutron crystallography: promise, challenges and potential.","abstract":"The International Year of Crystallography saw the number of macromolecular structures deposited in the Protein Data Bank cross the 100000 mark, with more than 90000 of these provided by X-ray crystallography. The number of X-ray structures determined to sub-atomic resolution (i.e. ≤1 Å) has passed 600 and this is likely to continue to grow rapidly with diffraction-limited synchrotron radiation sources such as MAX-IV (Sweden) and Sirius (Brazil) under construction. A dozen X-ray structures have been deposited to ultra-high resolution (i.e. ≤0.7 Å), for which precise electron density can be exploited to obtain charge density and provide information on the bonding character of catalytic or electron transfer sites. Although the development of neutron macromolecular crystallography over the years has been far less pronounced, and its application much less widespread, the availability of new and improved instrumentation, combined with dedicated deuteration facilities, are beginning to transform the field. Of the 83 macromolecular structures deposited with neutron diffraction data, more than half (49/83, 59%) were released since 2010. Sub-mm(3) crystals are now regularly being used for data collection, structures have been determined to atomic resolution for a few small proteins, and much larger unit-cell systems (cell edges >100 Å) are being successfully studied. While some details relating to H-atom positions are tractable with X-ray crystallography at sub-atomic resolution, the mobility of certain H atoms precludes them from being located. In addition, highly polarized H atoms and protons (H(+)) remain invisible with X-rays. Moreover, the majority of X-ray structures are determined from cryo-cooled crystals at 100 K, and, although radiation damage can be strongly controlled, especially since the advent of shutterless fast detectors, and by using limited doses and crystal translation at micro-focus beams, radiation damage can still take place. Neutron crystallography therefore remains the only approach where diffraction data can be collected at room temperature without radiation damage issues and the only approach to locate mobile or highly polarized H atoms and protons. Here a review of the current status of sub-atomic X-ray and neutron macromolecular crystallography is given and future prospects for combined approaches are outlined. New results from two metalloproteins, copper nitrite reductase and cytochrome c', are also included, which illustrate the type of information that can be obtained from sub-atomic-resolution (∼0.8 Å) X-ray structures, while also highlighting the need for complementary neutron studies that can provide details of H atoms not provided by X-ray crystallography.","corpus_id":15471858,"score":1},{"doc_id":"26798817","title":"Time-resolved structural studies with serial crystallography: A new light on retinal proteins.","abstract":"Structural information of the different conformational states of the two prototypical light-sensitive membrane proteins, bacteriorhodopsin and rhodopsin, has been obtained in the past by X-ray cryo-crystallography and cryo-electron microscopy. However, these methods do not allow for the structure determination of most intermediate conformations. Recently, the potential of X-Ray Free Electron Lasers (X-FELs) for tracking the dynamics of light-triggered processes by pump-probe serial femtosecond crystallography has been demonstrated using 3D-micron-sized crystals. In addition, X-FELs provide new opportunities for protein 2D-crystal diffraction, which would allow to observe the course of conformational changes of membrane proteins in a close-to-physiological lipid bilayer environment. Here, we describe the strategies towards structural dynamic studies of retinal proteins at room temperature, using injector or fixed-target based serial femtosecond crystallography at X-FELs. Thanks to recent progress especially in sample delivery methods, serial crystallography is now also feasible at synchrotron X-ray sources, thus expanding the possibilities for time-resolved structure determination.","corpus_id":9158424,"score":1},{"doc_id":"27841751","title":"A public database of macromolecular diffraction experiments.","abstract":"The low reproducibility of published experimental results in many scientific disciplines has recently garnered negative attention in scientific journals and the general media. Public transparency, including the availability of `raw' experimental data, will help to address growing concerns regarding scientific integrity. Macromolecular X-ray crystallography has led the way in requiring the public dissemination of atomic coordinates and a wealth of experimental data, making the field one of the most reproducible in the biological sciences. However, there remains no mandate for public disclosure of the original diffraction data. The Integrated Resource for Reproducibility in Macromolecular Crystallography (IRRMC) has been developed to archive raw data from diffraction experiments and, equally importantly, to provide related metadata. Currently, the database of our resource contains data from 2920 macromolecular diffraction experiments (5767 data sets), accounting for around 3% of all depositions in the Protein Data Bank (PDB), with their corresponding partially curated metadata. IRRMC utilizes distributed storage implemented using a federated architecture of many independent storage servers, which provides both scalability and sustainability. The resource, which is accessible via the web portal at http://www.proteindiffraction.org, can be searched using various criteria. All data are available for unrestricted access and download. The resource serves as a proof of concept and demonstrates the feasibility of archiving raw diffraction data and associated metadata from X-ray crystallographic studies of biological macromolecules. The goal is to expand this resource and include data sets that failed to yield X-ray structures in order to facilitate collaborative efforts that will improve protein structure-determination methods and to ensure the availability of `orphan' data left behind for various reasons by individual investigators and/or extinct structural genomics projects.","corpus_id":25116696,"score":1},{"doc_id":"27896717","title":"A Practical Approach to Protein Crystallography.","abstract":"Macromolecular crystallography is a powerful tool for structural biology. The resolution of a protein crystal structure is becoming much easier than in the past, thanks to developments in computing, automation of crystallization techniques and high-flux synchrotron sources to collect diffraction datasets. The aim of this chapter is to provide practical procedures to determine a protein crystal structure, illustrating the new techniques, experimental methods, and software that have made protein crystallography a tool accessible to a larger scientific community. It is impossible to give more than a taste of what the X-ray crystallographic technique entails in one brief chapter and there are different ways to solve a protein structure. Since the number of structures available in the Protein Data Bank (PDB) is becoming ever larger (the protein data bank now contains more than 100,000 entries) and therefore the probability to find a good model to solve the structure is ever increasing, we focus our attention on the Molecular Replacement method. Indeed, whenever applicable, this method allows the resolution of macromolecular structures starting from a single data set and a search model downloaded from the PDB, with the aid only of computer work.","corpus_id":4969587,"score":1},{"doc_id":"28177310","title":"Combining X-ray and neutron crystallography with spectroscopy.","abstract":"X-ray protein crystallography has, through the determination of the three-dimensional structures of enzymes and their complexes, been essential to the understanding of biological chemistry. However, as X-rays are scattered by electrons, the technique has difficulty locating the presence and position of H atoms (and cannot locate H(+) ions), knowledge of which is often crucially important for the understanding of enzyme mechanism. Furthermore, X-ray irradiation, through photoelectronic effects, will perturb the redox state in the crystal. By using single-crystal spectrophotometry, reactions taking place in the crystal can be monitored, either to trap intermediates or follow photoreduction during X-ray data collection. By using neutron crystallography, the positions of H atoms can be located, as it is the nuclei rather than the electrons that scatter neutrons, and the scattering length is not determined by the atomic number. Combining the two techniques allows much greater insight into both reaction mechanism and X-ray-induced photoreduction.","corpus_id":15007429,"score":1},{"doc_id":"28342173","title":"Metal ions-binding T4 lysozyme as an intramolecular protein purification tag compatible with X-ray crystallography.","abstract":"Phage T4 lysozyme is a well folded and highly soluble protein that is widely used as an insertion tag to improve solubility and crystallization properties of poorly behaved recombinant proteins. It has been used in the fusion protein strategy to facilitate crystallization of various proteins including multiple G protein-coupled receptors, lipid kinases, or sterol binding proteins. Here, we present a structural and biochemical characterization of its novel, metal ions-binding mutant (mbT4L). We demonstrate that mbT4L can be used as a purification tag in the immobilized-metal affinity chromatography and that, in many respects, it is superior to the conventional hexahistidine tag. In addition, structural characterization of mbT4L suggests that mbT4L can be used as a purification tag compatible with X-ray crystallography.","corpus_id":37076861,"score":1},{"doc_id":"28572170","title":"New developments in crystallography: exploring its technology, methods and scope in the molecular biosciences.","abstract":"Since the Protein Data Bank (PDB) was founded in 1971, there are now over 120,000 depositions, the majority of which are from X-ray crystallography and 90% of those made use of synchrotron beamlines. At the Cambridge Structure Database (CSD), founded in 1965, there are more than 800,000 'small molecule' crystal structure depositions and a very large number of those are relevant in the biosciences as ligands or cofactors. The technology for crystal structure analysis is still developing rapidly both at synchrotrons and in home labs. Determination of the details of the hydrogen atoms in biological macromolecules is well served using neutrons as probe. Large multi-macromolecular complexes cause major challenges to crystallization; electrons as probes offer unique advantages here. Methods developments naturally accompany technology change, mainly incremental but some, such as the tuneability, intensity and collimation of synchrotron radiation, have effected radical changes in capability of biological crystallography. In the past few years, the X-ray laser has taken X-ray crystallography measurement times into the femtosecond range. In terms of applications many new discoveries have been made in the molecular biosciences. The scope of crystallographic techniques is indeed very wide. As examples, new insights into chemical catalysis of enzymes and relating ligand bound structures to thermodynamics have been gained but predictive power is seen as not yet achieved. Metal complexes are also an emerging theme for biomedicine applications. Our studies of coloration of live and cooked lobsters proved to be an unexpected favourite with the public and schoolchildren. More generally, public understanding of the biosciences and crystallography's role within the field have been greatly enhanced by the United Nations International Year of Crystallography coordinated by the International Union of Crystallography. This topical review describes each of these areas along with illustrative results to document the scope of each methodology.","corpus_id":3220623,"score":1},{"doc_id":"28653703","title":"Pitfalls in metal-organic framework crystallography: towards more accurate crystal structures.","abstract":"Single crystal X-ray diffraction (SC-XRD) is the principal method for determining the crystal structures of metal-organic frameworks (MOFs). This tutorial deals with the handling of MOF crystals and analysis of crystallographic data obtained from single-crystal X-ray diffraction, focusing on two features that are particularly important in MOF crystallography and have a large impact on the quality and reliability of the final crystal structures: (1) the treatment of pore-occupying entities (both in the physical crystals and in the crystallographic model) and (2) crystallographic twinning. Proper handling of samples and data will reduce the need for using solvent masking software (e.g. SQUEEZE) to obtain acceptable crystal structures. If SC-XRD is to retain its position as the definitive method of MOF structure determination, these issues must be addressed when a new MOF structure is determined and reported. The issues addressed in this review is also valid for other porous, crystalline solids such as porous organic cages, metal-organic polyhedra, covalent organic frameworks and zeotype materials.","corpus_id":3731050,"score":1},{"doc_id":"28695856","title":"Crystal structure of Yersinia pestis virulence factor YfeA reveals two polyspecific metal-binding sites.","abstract":"Gram-negative bacteria use siderophores, outer membrane receptors, inner membrane transporters and substrate-binding proteins (SBPs) to transport transition metals through the periplasm. The SBPs share a similar protein fold that has undergone significant structural evolution to communicate with a variety of differentially regulated transporters in the cell. In Yersinia pestis, the causative agent of plague, YfeA (YPO2439, y1897), an SBP, is important for full virulence during mammalian infection. To better understand the role of YfeA in infection, crystal structures were determined under several environmental conditions with respect to transition-metal levels. Energy-dispersive X-ray spectroscopy and anomalous X-ray scattering data show that YfeA is polyspecific and can alter its substrate specificity. In minimal-media experiments, YfeA crystals grown after iron supplementation showed a threefold increase in iron fluorescence emission over the iron fluorescence emission from YfeA crystals grown from nutrient-rich conditions, and YfeA crystals grown after manganese supplementation during overexpression showed a fivefold increase in manganese fluorescence emission over the manganese fluorescence emission from YfeA crystals grown from nutrient-rich conditions. In all experiments, the YfeA crystals produced the strongest fluorescence emission from zinc and could not be manipulated otherwise. Additionally, this report documents the discovery of a novel surface metal-binding site that prefers to chelate zinc but can also bind manganese. Flexibility across YfeA crystal forms in three loops and a helix near the buried metal-binding site suggest that a structural rearrangement is required for metal loading and unloading.","corpus_id":20248903,"score":1},{"doc_id":"28989710","title":"Protein microcrystallography using synchrotron radiation.","abstract":"The progress in X-ray microbeam applications using synchrotron radiation is beneficial to structure determination from macromolecular microcrystals such as small in meso crystals. However, the high intensity of microbeams causes severe radiation damage, which worsens both the statistical quality of diffraction data and their resolution, and in the worst cases results in the failure of structure determination. Even in the event of successful structure determination, site-specific damage can lead to the misinterpretation of structural features. In order to overcome this issue, technological developments in sample handling and delivery, data-collection strategy and data processing have been made. For a few crystals with dimensions of the order of 10 µm, an elegant two-step scanning strategy works well. For smaller samples, the development of a novel method to analyze multiple isomorphous microcrystals was motivated by the success of serial femtosecond crystallography with X-ray free-electron lasers. This method overcame the radiation-dose limit in diffraction data collection by using a sufficient number of crystals. Here, important technologies and the future prospects for microcrystallography are discussed.","corpus_id":30687709,"score":1},{"doc_id":"29353938","title":"Watching Proteins Function with Time-resolved X-ray Crystallography.","abstract":"Macromolecular crystallography was immensely successful in the last two decades. To a large degree this success resulted from use of powerful third generation synchrotron X-ray sources. An expansive database of more than 100,000 protein structures, of which many were determined at resolution better than 2 Å, is available today. With this achievement, the spotlight in structural biology is shifting from determination of static structures to elucidating dynamic aspects of protein function. A powerful tool for addressing these aspects is time-resolved crystallography, where a genuine biological function is triggered in the crystal with a goal of capturing molecules in action and determining protein kinetics and structures of intermediates (Schmidt et al., 2005a; Schmidt 2008; Neutze and Moffat, 2012; Šrajer 2014). In this approach, short and intense X-ray pulses are used to probe intermediates in real time and at room temperature, in an ongoing reaction that is initiated synchronously and rapidly in the crystal. Time-resolved macromolecular crystallography with 100 ps time resolution at synchrotron X-ray sources is in its mature phase today, particularly for studies of reversible, light-initiated reactions. The advent of the new free electron lasers for hard X-rays (XFELs; 5-20 keV), which provide exceptionally intense, femtosecond X-ray pulses, marks a new frontier for time-resolved crystallography. The exploration of ultra-fast events becomes possible in high-resolution structural detail, on sub-picosecond time scales (Tenboer et al., 2014; Barends et al., 2015; Pande et al., 2016). We review here state-of-the-art time-resolved crystallographic experiments both at synchrotrons and XFELs. We also outline challenges and further developments necessary to broaden the application of these methods to many important proteins and enzymes of biomedical relevance.","corpus_id":24074635,"score":1},{"doc_id":"29757285","title":"Microfluidic Chips for In Situ Crystal X-ray Diffraction and In Situ Dynamic Light Scattering for Serial Crystallography.","abstract":"This protocol describes fabricating microfluidic devices with low X-ray background optimized for goniometer based fixed target serial crystallography. The devices are patterned from epoxy glue using soft lithography and are suitable for in situ X-ray diffraction experiments at room temperature. The sample wells are lidded on both sides with polymeric polyimide foil windows that allow diffraction data collection with low X-ray background. This fabrication method is undemanding and inexpensive. After the sourcing of a SU-8 master wafer, all fabrication can be completed outside of a cleanroom in a typical research lab environment. The chip design and fabrication protocol utilize capillary valving to microfluidically split an aqueous reaction into defined nanoliter sized droplets. This loading mechanism avoids the sample loss from channel dead-volume and can easily be performed manually without using pumps or other equipment for fluid actuation. We describe how isolated nanoliter sized drops of protein solution can be monitored in situ by dynamic light scattering to control protein crystal nucleation and growth. After suitable crystals are grown, complete X-ray diffraction datasets can be collected using goniometer based in situ fixed target serial X-ray crystallography at room temperature. The protocol provides custom scripts to process diffraction datasets using a suite of software tools to solve and refine the protein crystal structure. This approach avoids the artefacts possibly induced during cryo-preservation or manual crystal handling in conventional crystallography experiments. We present and compare three protein structures that were solved using small crystals with dimensions of approximately 10-20 µm grown in chip. By crystallizing and diffracting in situ, handling and hence mechanical disturbances of fragile crystals is minimized. The protocol details how to fabricate a custom X-ray transparent microfluidic chip suitable for in situ serial crystallography. As almost every crystal can be used for diffraction data collection, these microfluidic chips are a very efficient crystal delivery method.","corpus_id":21662166,"score":1},{"doc_id":"20526948","title":"Assessment of occupational exposure to manganese and other metals in welding fumes by portable X-ray fluorescence spectrometer.","abstract":"Elemental analysis of welding fume samples can be done using several laboratory-based techniques. However, portable measurement techniques could offer several advantages. In this study, we sought to determine whether the portable X-ray fluorescence spectrometer (XRF) is suitable for analysis of five metals (manganese, iron, zinc, copper, and chromium) on 37-mm polytetrafluoroethylene filters. Using this filter fitted on a cyclone in line with a personal pump, gravimetric samples were collected from a group of boilermakers exposed to welding fumes. We assessed the assumption of uniform deposition of these metals on the filters, and the relationships between measurement results of each metal obtained from traditional laboratory-based XRF and the portable XRF. For all five metals of interest, repeated measurements with the portable XRF at the same filter area showed good consistency (reliability ratios are equal or close to 1.0 for almost all metals). The portable XRF readings taken from three different areas of each filter were not significantly different (p-values = 0.77 to 0.98). This suggested that the metal rich PM(2.5) deposits uniformly on the samples collected using this gravimetric method. For comparison of the two XRFs, the results from the portable XRF were well correlated and highly predictive of those from the laboratory XRF. The Spearman correlation coefficients were from 0.325 for chromium, to 0.995 for manganese and 0.998 for iron. The mean differences as a percent of the mean laboratory XRF readings were also small (<5%) for manganese, iron, and copper. The differences were greater for zinc and chromium, which were present at very low amounts in our samples and below the limits of detection of the portable XRF for many of the samples. These five metals were moderately to strongly correlated with the total fine particle fraction on filters (Spearman rho = 0.41 for zinc to 0.97 for iron). Such strong correlations and comparable results suggested that the portable XRF could be used as an effective and reliable tool for exposure assessment in many studies.","corpus_id":21130222,"score":0},{"doc_id":"21545119","title":"Discrete, solvent-free alkaline-earth metal cations: metal···fluorine interactions and ROP catalytic activity.","abstract":"Efficient protocols for the syntheses of well-defined, solvent-free cations of the large alkaline-earth (Ae) metals (Ca, Sr, Ba) and their smaller Zn and Mg analogues have been designed. The reaction of 2,4-di-tert-butyl-6-(morpholinomethyl)phenol ({LO(1)}H), 2-{[bis(2-methoxyethyl)amino]methyl}-4,6-di-tert-butylphenol ({LO(2)}H), 2-[(1,4,7,10-tetraoxa-13-azacyclopentadecan-13-yl)methyl]-4,6-di-tert-butylphenol ({LO(3)}H), and 2-[(1,4,7,10-tetraoxa-13-azacyclo-pentadecan-13-yl)methyl]-1,1,1,3,3,3-hexafluoropropan-2-ol ({RO(3)}H) with [H(OEt(2))(2)](+)[H(2)N{B(C(6)F(5))(3)}(2)](-) readily afforded the doubly acidic pro-ligands [{LO(1)}HH](+)[X](-) (1), [{LO(2)}HH](+)[X](-) (2), [{LO(3)}HH](+)[X](-) (3), and [{RO(3)}HH](+)[X](-) (4) ([X](-) = [H(2)N{B(C(6)F(5))(3)}(2)](-)). The addition of 2 to Ca[N(SiMe(3))(2)](2)(THF)(2) and Sr[N(SiMe(3))(2)](2)(THF)(2) yielded [{LO(2)}Ca(THF)(0.5)](+)[X](-) (5) and [{LO(2)}Sr(THF)](+)[X](-) (6), respectively. Alternatively, 5 could also be prepared upon treatment of {LO(2)}CaN(SiMe(3))(2) (7) with [H(OEt(2))(2)](+)[X](-). Complexes [{LO(3)}M](+)[X](-) (M = Zn, 8; Mg, 9; Ca, 10; Sr, 11; Ba, 12) and [{RO(3)}M](+)[X](-) (M = Zn, 13; Mg, 14; Ca, 15; Sr, 16; Ba, 17) were synthesized in high yields (70-90%) by reaction of 3 or 4 with the neutral precursors M[N(SiMe(3))(2)](2)(THF)(x) (M = Zn, Mg, x = 0; M = Ca, Sr, Ba, x = 2). All compounds were fully characterized by spectroscopic methods, and the solid-sate structures of compounds 1, 3, 7, 8, 13, 14, {15}(4)·3CD(2)Cl(2), {16}(4)·3CD(2)Cl(2), and {{17}(4)·EtOH}·3CD(2)Cl(2) were determined by X-ray diffraction crystallography. Whereas the complexes are monomeric in the case of Zn and Mg, they form bimetallic cations in the case of Ca, Sr and Ba; there is no contact between the metal and the weakly coordinating anion. In all metal complexes, the multidentate ligand is κ(6)-coordinated to the metal. Strong intramolecular M···F secondary interactions between the metal and F atoms from the ancillary ligands are observed in the structures of {15}(4)·3CD(2)Cl(2), {16}(4)·3CD(2)Cl(2), and {{17}(4)·EtOH}·3CD(2)Cl(2). VT (19)F{(1)H} NMR provided no direct evidence that these interactions are maintained in solution; nevertheless, significant Ae···F energies of stabilization of 25-26 (Ca, Ba) and 40 kcal·mol(-1) (Sr) were calculated by NBO analysis on DFT-optimized structures. The identity and integrity of the cationic complexes are preserved in solution in the presence of an excess of alcohol (BnOH, (i)PrOH) or L-lactide (L-LA). Efficient binary catalytic systems for the immortal ring-opening polymerization of L-LA (up to 3,000 equiv) are produced upon addition of an excess (5-50 equiv) of external protic nucleophilic agents (BnOH, (i)PrOH) to 8-12 or 13-17. PLLAs with M(n) up to 35,000 g·mol(-1) were produced in a very controlled fashion (M(w)/M(n) ≈ 1.10-1.20) and without epimerization. In each series of catalysts, the following order of catalytic activity was established: Mg ≪ Zn < Ca < Sr ≈ Ba; also, Ae complexes supported by the aryloxide ligand are more active than their parents supported by the fluorinated alkoxide ancillary, possibly owing to the presence of Ae···F interactions in the latter case. The rate law -d[L-LA]/dt = k(p)·[L-LA](1.0)·[16](1.0)·[BnOH](1.0) was established by NMR kinetic investigations, with the corresponding activation parameters ΔH(++) = 14.8(5) kcal·mol(-1) and ΔS(++) = -7.6(2.0) cal·K(-1)·mol(-1). DFT calculations indicated that the observed order of catalytic activity matches an increase of the L-LA coordination energy onto the cationic metal centers with parallel decrease of the positive metal charge.","corpus_id":21502229,"score":0},{"doc_id":"23252592","title":"Kinetic products in coordination networks: ab initio X-ray powder diffraction analysis.","abstract":"Porous coordination networks are materials that maintain their crystal structure as molecular \"guests\" enter and exit their pores. They are of great research interest with applications in areas such as catalysis, gas adsorption, proton conductivity, and drug release. As with zeolite preparation, the kinetic states in coordination network preparation play a crucial role in determining the final products. Controlling the kinetic state during self-assembly of coordination networks is a fundamental aspect of developing further functionalization of this class of materials. However, unlike for zeolites, there are few structural studies reporting the kinetic products made during self-assembly of coordination networks. Synthetic routes that produce the necessary selectivity are complex. The structural knowledge obtained from X-ray crystallography has been crucial for developing rational strategies for design of organic-inorganic hybrid networks. However, despite the explosive progress in the solid-state study of coordination networks during the last 15 years, researchers still do not understand many chemical reaction processes because of the difficulties in growing single crystals suitable for X-ray diffraction: Fast precipitation can lead to kinetic (metastable) products, but in microcrystalline form, unsuitable for single crystal X-ray analysis. X-ray powder diffraction (XRPD) routinely is used to check phase purity, crystallinity, and to monitor the stability of frameworks upon guest removal/inclusion under various conditions, but rarely is used for structure elucidation. Recent advances in structure determination of microcrystalline solids from ab initio XRPD have allowed three-dimensional structure determination when single crystals are not available. Thus, ab initio XRPD structure determination is becoming a powerful method for structure determination of microcrystalline solids, including porous coordination networks. Because of the great interest across scientific disciplines in coordination networks, especially porous coordination networks, the ability to determine crystal structures when the crystals are not suitable for single crystal X-ray analysis is of paramount importance. In this Account, we report the potential of kinetic control to synthesize new coordination networks and we describe ab initio XRPD structure determination to characterize these networks' crystal structures. We describe our recent work on selective instant synthesis to yield kinetically controlled porous coordination networks. We demonstrate that instant synthesis can selectively produce metastable networks that are not possible to synthesize by conventional solution chemistry. Using kinetic products, we provide mechanistic insights into thermally induced (573-723 K) (i.e., annealing method) structural transformations in porous coordination networks as well as examples of guest exchange/inclusion reactions. Finally, we describe a memory effect that allows the transfer of structural information from kinetic precursor structures to thermally stable structures through amorphous intermediate phases. We believe that ab initio XRPD structure determination will soon be used to investigate chemical processes that lead intrinsically to microcrystalline solids, which up to now have not been fully understood due to the unavailability of single crystals. For example, only recently have researchers used single-crystal X-ray diffraction to elucidate crystal-to-crystal chemical reactions taking place in the crystalline scaffold of coordination networks. The potential of ab initio X-ray powder diffraction analysis goes beyond single-crystal-to-single-crystal processes, potentially allowing members of this field to study intriguing in situ reactions, such as reactions within pores.","corpus_id":36488253,"score":0},{"doc_id":"23737050","title":"X-ray crystallography of viruses.","abstract":"For about 30 years X-ray crystallography has been by far the most powerful approach for determining virus structures at close to atomic resolutions. Information provided by these studies has deeply and extensively enriched and shaped our vision of the virus world. In turn, the ever increasing complexity and size of the virus structures being investigated have constituted a major driving force for methodological and conceptual developments in X-ray macromolecular crystallography. Landmarks of new virus structures determinations, such as the ones from the first animal viruses or from the first membrane-containing viruses, have often been associated to methodological breakthroughs in X-ray crystallography. In this chapter we present the common ground of proteins and virus crystallography with an emphasis in the peculiarities of virus studies. For example, the solution of the phase problem, a central issue in X-ray diffraction, has benefited enormously from the presence of non-crystallographic symmetry in virus crystals.","corpus_id":24255211,"score":0},{"doc_id":"23912807","title":"Macromolecular crowding: chemistry and physics meet biology (Ascona, Switzerland, 10-14 June 2012).","abstract":"More than 60 years of biochemical and biophysical studies have accustomed us to think of proteins as highly purified entities that act in isolation, more or less freely diffusing until they find their cognate partner to bind to. While in vitro experiments that reproduce these conditions largely remain the only way to investigate the intrinsic properties of molecules, this approach ignores an important factor: in their natural milieu , proteins are surrounded by several other molecules of different chemical nature, and this crowded environment can considerably modify their behaviour. About 40% of the cellular volume on average is occupied by all sorts of molecules. Furthermore, biological macromolecules live and operate in an extremely structured and complex environment within the cell (endoplasmic reticulum, Golgi apparatus, cytoskeletal structures, etc). Hence, to further complicate the picture, the interior of the cell is by no means a simply crowded medium, rather, a most crowded and confining one. In recent times, several approaches have been developed in the attempt to take into account important factors such as the ones mentioned above, at both theoretical and experimental levels, so that this field of research is now emerging as one of the most thriving in molecular and cell biology (see figure 1). [ Formula: see text] Figure 1. Left: number of articles containing the word 'crowding' as a keyword limited to the biological and chemical science domains (source: ISI Web of Science). The arrow flags the 2003 'EMBO Workshop on Biological Implications of Macromolecular Crowding' (Embo, 2012). Right: number of citations to articles containing the word 'crowding' limited to the same domains (bars) and an exponential regression curve (source: Elsevier Scopus). To promote the importance of molecular crowding and confinement and provide researchers active in this field an interdisciplinary forum for meeting and exchanging ideas, we recently organized an international conference held in Ascona from 10 to 14 June 2012. In the unique scenario of the Maggiore lake and absorbed in the magic atmosphere of the Centro Stefano Franscini (CSF) at Monte Verità, we enjoyed three-and-a-half days of intense and inspiring activity, where not only many of the most prominent scientists working on macromolecular crowding, but also experts in closely related fields such as colloids and soft matter presented their work. The meeting was intended and has been organized to bring theoreticians and experimentalists together in the attempt to promote an active dialogue. Moreover, we wanted different disciplines to be represented, notably physics and chemistry, besides biology, as cross-fertilization is proving an increasingly fundamental source of inspiration and advancement. This issue of Physical Biology (PB) features a selection of the oral contributions presented at the conference, expanded in the form of research or review articles. PB, one of the scientific journals of the Institute of Physics (IOP), is one of the most dynamic and lively forums active at the interface between biology on one side, and physics and mathematics on the other. As its mission is stated by IOP, PB 'focuses on research in which physics-based approaches lead to new insights into biological systems at all scales of space and time, and all levels of complexity'. For these reasons, and also in view of its high reputation and broad readership, PB appears to be the ideal place for disseminating the thriving pieces of research presented at the conference. We are extremely grateful to PB and its kind and efficient editorial staff who helped make this issue a great scientific follow-up to the conference. The opening lecture of the conference, the first of four day-opening keynote lectures, was given by Allen P Minton from NIH (USA), possibly the most influential among the pioneers in the field. He provided a lucid and well-thought-out overview of the concept of macromolecular crowding through an exhaustive chronological account of the major milestones. It is clear that the concept of excluded volume as a key factor remains central to the concept of molecular crowding. As a consequence, simple descriptive paradigms borrowed essentially from colloid physics may still provide useful tools to understand the subtle effects of crowding and confinement in living matter. The contiguity between crowding, colloids and soft matter further emerged as an important concept in the course of the conference in several theoretical lectures and a few experimental ones. Dave Thirumalai, from the University of Maryland (USA), one of the most active theoreticians in the field of theoretical biophysics, outlined scaling theories, concepts from colloid literature and different simulation techniques to describe scenarios for crowding-induced changes in the structure and dynamics of proteins and RNA. In particular, he showed the importance of the shape of crowding particles in affecting folding oligomerization of amyloidogenic peptides. Johannes Schöneberg, from IMPRS, Mathematics Institute (Germany), illustrated ReaDDy , a newly developed particle-based simulation software tool for reaction-diffusion dynamics, developed in the group of Frank Noe at EMPRS. He showed that ReaDDy makes it possible to bridge the gap between soft matter and molecular dynamics (MD) simulations on the one hand and particle-based stochastic reaction-diffusion simulations on the other. We asked Johannes to organize a tutorial session to lead interested participants into the package and 'get their hands wet' under the guidance of the developers. The tutorial session was indeed successful and the broad possibilities offered by the simulation toolkit appeared to be clear to the participants. Paolo De Los Rios, from the Ecole Polytechnique Fédérale de Lausanne (EPFL, Switzerland), examined the complexity of the effects caused by crowding conditions from the point of view of statistical physics. Starting from a modification of the well-known Smoluchowski approach to calculate the encounter rate of diffusion-limited reactions, he showed how more realistic situations accounting for crowding effects could be treated equally well on the same theoretical grounds. This talk marked an important point in the conference as it reinforced the idea that simple models of theoretical physics still have the power to provide inspiring results in spite of the intrinsic simplifications of such theoretical approaches. Along the same lines, Nicolas Dorsaz, from the University of Cambridge (UK), proposed an extension of the Smoluchowski framework that incorporates repulsive and attracting interactions between the reactants. This approach was illustrated by reaction rates obtained from event-driven Brownian dynamics and dynamical Monte Carlo simulations. Another striking example of the physical subtleties associated with modelling crowding effects was provided by Jeffrey Skolnick, from the Georgia Institute of Technology (USA). He examined the role of hydrodynamic interactions in the self-organization of biological assemblies in the presence of crowding. His results strongly suggest that hydrodynamic interactions greatly affect the kinetics of self-assembly reactions, so that including them in the picture appears crucial for understanding the dynamics of biological systems in vivo . Margareth Cheung, from the University of Houston (USA), emphasized that how the crowded environment inside a cell affects the structural conformation of a protein with a spherical shape is a vital question because the geometry of proteins and protein-protein complexes are far from globules in vivo . Her work demonstrates the malleability of 'native' proteins and implies that crowding-induced shape changes may be important for protein function and malfunction in vivo . Huan-Xiang Zhou, from the Florida State University (USA), focused on atomistic simulations of protein folding and binding under crowding conditions. His lab has developed a post-processing method that allows the atomistic representation of proteins in folding and binding processes under crowding. A comparison with experimental results was also presented. Other lecturers pointed out that there are still aspects not entirely explored in the effects of both crowding and confinement. As suggested in the talk by Gary Pielak, from the University of North Carolina (USA), the currently used synthetic crowding agents are far from being satisfactory in replicating naturally occurring effects associated with crowded environments. For example, non-specific binding seems to play a subtle role in the cell, as natural macromolecules can induce both stabilization and destabilization when used as crowders. It is indeed possible to fine-tune the effect of proteins, as crowders, on the stability of other proteins. Another aspect that became clear is that new, more powerful methods need to be developed to study the effect of crowding, but even more to compare crowding and confinement. Indeed, it appeared clear from the lecture by Pierandrea Temussi, from the University of Naples (Italy), that a reliable comparison of the effects of crowding and confinement on the stability of proteins can only be based on the measurement of the whole stability curve of the same protein. Controversial aspects do not pertain only to the influence of crowding on protein stability, but also to aggregation phenomena in natural fluids. Domenico Sanfelice, from NIMR (London, UK), reported an interesting case of the apparent influence of crowding on aggregation. Hen egg white, a possible natural medium to study macromolecules in crowded conditions can dramatically increase the aggregation kinetics of proteins with an inbuilt tendency to associate. By carefully dissecting the phenomenology, it was shown that only part of this effect is due to crowding, while another factor playing an important role is the interaction with proteins from the milieu . In other words, high-molecular-weight glycoproteins can act as efficient molecular seeds for aggregation. A special topic of great relevance in the conference appeared to be the direct study of crowding in living systems. Alan Verkman, from the University of California, San Francisco (USA), one of the world's leading scientific personalities in the field of experimental investigation of crowding and confinement, was invited to give the second plenary lecture devoted to the experimental study of crowding effects in vivo . In his keynote lecture, Dr Verkman led us on a wide and compelling tour, exploring the main experimental approaches to study molecular crowding in and around cells. After a thorough examination of methods such as fluorescence recovery after photo-bleaching, fluorescence correlation spectroscopy, photo-activation localization microscopy and stochastic reconstruction microscopy, he concluded that the general consensus emerging from experimental studies is that the notion of universally anomalous diffusion in and around cells as a consequence of molecular crowding may not be correct, and that the slowing of diffusion in cells is less marked than has been widely assumed and can be simply described through a five- to sixfold reduction of the normal diffusion coefficient. A Soranno, from the University of Zürich (Switzerland), described how, by employing FRET measurements, it is possible to quantify the effect of molecular crowding on the dimensions of the highly charged, intrinsically disordered protein human prothymosin alpha. For a large variety of polymeric crowders (PEG, PVP, Ficoll, Dextran, PVA, PAA), a collapse of the polypeptide chain is observed with increasing polymer size and polymer concentration. The largest extent of collapse is observed for polymer radii comparable to the dimensions of the protein, in agreement with theoretical considerations. For his contribution, A Soranno was awarded the CSF Award for the best contributed talk. In his most inspiring talk, Clifford Brangwynne, from Princeton University (USA), drew attention to very important objects, namely Ribonucleoprotein (RNP) bodies. These are non-membrane-bound macromolecular assemblies that form from the dynamic interactions of RNA and proteins. The assembly of RNP bodies may sensitively depend on the biophysical features of the surrounding cytoplasm, including the degree of crowding, transport coefficients and mechanical properties. This dependency may have important implications for the RNA processing reactions involved in fundamental biological processes such as developmental cell growth. Remarkably, Brangwynne showed how RNPs behave in the cell as liquid droplets, pointing to a possible entirely new means that the cell could use to control and fine-tune its internal processes, in fact, more than that, a completely unexplored, new state of organization of living matter, and a functional one. Giuseppe Zaccai, from Institut Laue Langevin, Grenoble (France), showed that protein dynamics is more sensitive than structure to environmental factors such as crowding, solvent, temperature or pressure. Furthermore, he convincingly explained how neutron scattering provides unique experimental data to underpin MD calculations in this context. Following up on environment-induced modulations of protein functional dynamics, Ruth Nussinov, from Tel Aviv University (Israel), addressed the important problem of whether cellular signals can travel long distances in a crowded environment. She proposed a model based on the evolution of at least three properties: a modular functional organization of the cellular network, sequences in some key regions of proteins, such as linkers or loops, and compact interactions between proteins, possibly favoured by a crowded environment. The workshop ended on a keynote lecture by Jean-Marie Lehn, from the Université de Strasbourg (France). Lehn, 1987 Nobel Laureate in chemistry, offered a 'supramolecular view' of the field of molecular interactions. Supramolecular chemistry explores the design of systems undergoing self-organization , i.e. systems capable of generating well-defined functional supramolecular architectures by self-assembling from their components, thus behaving as programmed chemical systems . Chemistry may therefore be considered an information science , the science of informed matter. Supramolecular chemistry is intrinsically a dynamic chemistry in view of the ability of the interactions connecting the molecular components of a supramolecular entity and the resulting ability of supramolecular species to exchange their constituents. The same holds for molecular chemistry when the molecular entity contains covalent bonds that may form and break reversibly, so as to allow a continuous change in constitution by the reorganization and exchange of building blocks. These features define a constitutional dynamic chemistry (CDC) on both the molecular and supramolecular levels. CDC takes advantage of dynamic constitutional diversity to allow variation and selection in response to either internal or external factors to achieve adaptation . The merging of the features-information and programmability, dynamics and reversibility, constitution and structural diversity-points towards the emergence of adaptive and evolutive chemistry . The whole workshop could have not taken place without the help of the Centro Stefano Franscini. The CSF is the congress centre of the Swiss Federal Institute of Technology of Zurich (ETH Zurich) and has been situated at Monte Verità since 1989. It is an ideal meeting point for all members of the international scientific community who wish to discuss the state-of-the-art and new challenges of any field of research. The CSF supports 20-25 international conferences every year and, since 2010, up to ten winter doctoral schools1. The competence and professionalism of the staff were at the same level of beauty and inspiring character as that of Monte Verità. A meeting of this sort, if successful, leaves the audience with more open questions than settled answers, and this was definitely the case for Crowding 2012. Excluded volume is clearly a fundamental concept that has allowed crowding, a very familiar concept in soft matter, to enter into the domain of biological sciences. However, the complexity of the biological milieu calls for more refined descriptions. What is the role of electrostatic and electrodynamic interactions? What is the role of hydrodynamics interactions? To what extent does the strong spatial inhomogeneity (clustering of molecules, cellular compartmentalization, etc) have to be taken into account? Or, more generally, what are the minimal elements that prove crucial to describe reactions within a cell? How does the diffusion proceed (diffusion, slow diffusion, sub-diffusion) given that the experimental evidences are still controversial? In conclusion, we knew that allowing scientists with very different backgrounds and ideas to mingle was a hazardous attempt. Despite that, the workshop turned out to be a very successful experiment, which was highly enjoyed both by the participants and the organizers. Discussions sparked regularly among ever-changing groups, comprising senior scientists and students, despite the rather tight schedule, adding to the sense of fulfilment ignited by the outstanding level of the presentations. Given the success of the meeting Crowding 2012, a new event has been organized and will take place on the same themes during fall 2013, this time in the beautiful scenery of the Loire valley in France. The workshop 'Macromolecular crowding effects in cell biology: models and experiments' will be held on the CNRS campus in Orléans, France, on 24-25 October 2013. More information can be found on the workshop website: http://dirac.cnrs-orleans.fr/∼piazza/. 1Source: www.csf.ethz.ch/","corpus_id":3008401,"score":0},{"doc_id":"25604506","title":"X-ray crystallography and its impact on understanding bacterial cell wall remodeling processes.","abstract":"The molecular structure of matter defines its properties and function. This is especially true for biological macromolecules such as proteins, which participate in virtually all biochemical processes. A three dimensional structural model of a protein is thus essential for the detailed understanding of its physiological function and the characterization of essential properties such as ligand binding and reaction mechanism. X-ray crystallography is a well-established technique that has been used for many years, but it is still by far the most widely used method for structure determination. A particular strength of this technique is the elucidation of atomic details of molecular interactions, thus providing an invaluable tool for a multitude of scientific projects ranging from the structural classification of macromolecules over the validation of enzymatic mechanisms or the understanding of host-pathogen interactions to structure-guided drug design. In the first part of this review, we describe essential methodological and practical aspects of X-ray crystallography. We provide some pointers that should allow researchers without a background in structural biology to assess the overall quality and reliability of a crystal structure. To highlight its potential, we then survey the impact X-ray crystallography has had on advancing an understanding of a class of enzymes that modify the bacterial cell wall. A substantial number of different bacterial amidase structures have been solved, mostly by X-ray crystallography. Comparison of these structures highlights conserved as well as divergent features. In combination with functional analyses, structural information on these enzymes has therefore proven to be a valuable template not only for understanding their mechanism of catalysis, but also for targeted interference with substrate binding.","corpus_id":205290612,"score":0},{"doc_id":"26671943","title":"Sample preparation of biological macromolecular assemblies for the determination of high-resolution structures by cryo-electron microscopy.","abstract":"Single particle cryo-EM has recently developed into a powerful tool to determine the 3D structure of macromolecular complexes at near-atomic resolution, which allows structural biologists to build atomic models of proteins. All technical aspects of cryo-EM technology have been considerably improved over the last two decades, including electron microscopic hardware, image processing software and the ever growing speed of computers. This leads to a more widespread use of the technique, and it can be anticipated that further automation of electron microscopes and image processing tools will soon fully shift the focus away from the technological aspects, onto biological questions that can be answered. In single particle cryo-EM, no crystals of a macromolecule are required. In contrast to X-ray crystallography, this significantly facilitates structure determination by cryo-EM. Nevertheless, a relatively high level of biochemical control is still essential to obtain high-resolution structures by cryo-EM, and it can be anticipated that the success of the cryo-EM technology goes hand in hand with further developments of sample purification and preparation techniques. This will allow routine high-resolution structure determination of the many macromolecular complexes of the cell that until now represent evasive targets for X-ray crystallographers. Here we discuss the various biochemical tools that are currently available and the existing sample purification and preparation techniques for cryo-EM grid preparation that are needed to obtain high-resolution images for structure determination.","corpus_id":23067203,"score":0},{"doc_id":"27077331","title":"The collection of MicroED data for macromolecular crystallography.","abstract":"The formation of large, well-ordered crystals for crystallographic experiments remains a crucial bottleneck to the structural understanding of many important biological systems. To help alleviate this problem in crystallography, we have developed the MicroED method for the collection of electron diffraction data from 3D microcrystals and nanocrystals of radiation-sensitive biological material. In this approach, liquid solutions containing protein microcrystals are deposited on carbon-coated electron microscopy grids and are vitrified by plunging them into liquid ethane. MicroED data are collected for each selected crystal using cryo-electron microscopy, in which the crystal is diffracted using very few electrons as the stage is continuously rotated. This protocol gives advice on how to identify microcrystals by light microscopy or by negative-stain electron microscopy in samples obtained from standard protein crystallization experiments. The protocol also includes information about custom-designed equipment for controlling crystal rotation and software for recording experimental parameters in diffraction image metadata. Identifying microcrystals, preparing samples and setting up the microscope for diffraction data collection take approximately half an hour for each step. Screening microcrystals for quality diffraction takes roughly an hour, and the collection of a single data set is ∼10 min in duration. Complete data sets and resulting high-resolution structures can be obtained from a single crystal or by merging data from multiple crystals.","corpus_id":24255876,"score":0},{"doc_id":"29588032","title":"Xenon-Protein Interactions: Characterization by X-Ray Crystallography and Hyper-CEST NMR.","abstract":"The physiological activity of xenon has long been recognized, though the exact nature of its interactions with biomolecules remains poorly understood. Xe is an inert noble gas, but can act as a general anesthetic, most likely by binding internal hydrophobic cavities within proteins. Understanding Xe-protein interactions, therefore, can provide crucial insight regarding the mechanism of Xe anesthesia and potentially other general anesthetic agents. Historically, Xe-protein interactions have been studied primarily through X-ray crystallography and nuclear magnetic resonance (NMR). In this chapter, we first describe our methods for preparing Xe derivatives of protein crystals and identifying Xe-binding sites. Second, we detail our procedure for 129Xe hyper-CEST NMR spectroscopy, a versatile NMR technique well suited for characterizing the weak, transient nature of Xe-protein interactions.","corpus_id":4385000,"score":0}],"string":"[\n {\n \"doc_id\": \"18004559\",\n \"title\": \"X-ray absorption and diffraction studies of the metal binding sites in amyloid beta-peptide.\",\n \"abstract\": \"A major source of neurodegeneration observed in Alzheimer's disease is believed to be caused by the toxicity from reactive oxygen species produced in the brain mediated by the A beta protein and mainly copper species. An atomic model of an amyloid beta-peptide (A beta) Cu2+ complex or at least the structure of the metal binding site is of great interest. Accurate information about the Cu-binding site of A beta protein can facilitate simulation of redox chemistry using high level quantum mechanics. Complementary X-ray diffraction and X-ray absorption techniques can be employed to obtain such accurate information. This review provides a blend of X-ray diffraction results on amyloid structures and selected works on A beta Cu2+ binding based on spectroscopic measurements with emphasis on the X-ray absorption technique.\",\n \"corpus_id\": 32111603,\n \"score\": 2\n },\n {\n \"doc_id\": \"18034855\",\n \"title\": \"Protein crystallography for non-crystallographers, or how to get the best (but not more) from published macromolecular structures.\",\n \"abstract\": \"The number of macromolecular structures deposited in the Protein Data Bank now exceeds 45,000, with the vast majority determined using crystallographic methods. Thousands of studies describing such structures have been published in the scientific literature, and 14 Nobel prizes in chemistry or medicine have been awarded to protein crystallographers. As important as these structures are for understanding the processes that take place in living organisms and also for practical applications such as drug design, many non-crystallographers still have problems with critical evaluation of the structural literature data. This review attempts to provide a brief outline of technical aspects of crystallography and to explain the meaning of some parameters that should be evaluated by users of macromolecular structures in order to interpret, but not over-interpret, the information present in the coordinate files and in their description. A discussion of the extent of the information that can be gleaned from the coordinates of structures solved at different resolution, as well as problems and pitfalls encountered in structure determination and interpretation are also covered.\",\n \"corpus_id\": 12525033,\n \"score\": 2\n },\n {\n \"doc_id\": \"18433638\",\n \"title\": \"Time-resolved x-ray crystallography of heme proteins.\",\n \"abstract\": \"Heme proteins, with their natural photosensitivity, are excellent systems for the application of time-resolved crystallographic methods. Ligand dissociation can be readily initiated by a short laser pulse with global structural changes probed at the atomic level by X-rays in real time. Third-generation synchrotrons provide 100-ps X-ray pulses of sufficient intensity for monitoring very fast processes. Successful application of such time-resolved crystallographic experiments requires that the structural changes being monitored are compatible with the crystal lattice. These techniques have recently permitted observing for the first time allosteric transitions in real time for a cooperative dimeric hemoglobin.\",\n \"corpus_id\": 36149621,\n \"score\": 2\n },\n {\n \"doc_id\": \"18728313\",\n \"title\": \"On-line optical and X-ray spectroscopies with crystallography: an integrated approach for determining metalloprotein structures in functionally well defined states.\",\n \"abstract\": \"X-ray-induced redox changes can lead to incorrect assignments of the functional states of metals in metalloprotein crystals. The need for on-line monitoring of the status of metal ions (and other chromophores) during protein crystallography experiments is of growing importance with the use of intense synchrotron X-ray beams. Significant efforts are therefore being made worldwide to combine different spectroscopies in parallel with X-ray crystallographic data collection. Here the implementation and utilization of optical and X-ray absorption spectroscopies on the modern macromolecular crystallography (MX) beamline 10, at the SRS, Daresbury Laboratory, is described. This beamline is equipped with a dedicated monolithic energy-dispersive X-ray fluorescence detector, allowing X-ray absorption spectroscopy (XAS) measurements to be made in situ on the same crystal used to record the diffraction data. In addition, an optical microspectrophotometer has been incorporated on the beamline, thus facilitating combined MX, XAS and optical spectroscopic measurements. By uniting these techniques it is also possible to monitor the status of optically active and optically silent metal centres present in a crystal at the same time. This unique capability has been applied to observe the results of crystallographic data collection on crystals of nitrite reductase from Alcaligenes xylosoxidans, which contains both type-1 and type-2 Cu centres. It is found that the type-1 Cu centre photoreduces quickly, resulting in the loss of the 595 nm peak in the optical spectrum, while the type-2 Cu centre remains in the oxidized state over a much longer time period, for which independent confirmation is provided by XAS data as this centre has an optical spectrum which is barely detectable using microspectrophotometry. This example clearly demonstrates the importance of using two on-line methods, spectroscopy and XAS, for identifying well defined redox states of metalloproteins during crystallographic data collection.\",\n \"corpus_id\": 20954052,\n \"score\": 2\n },\n {\n \"doc_id\": \"19240331\",\n \"title\": \"Can soaked-in scavengers protect metalloprotein active sites from reduction during data collection?\",\n \"abstract\": \"One of the first events taking place when a crystal of a metalloprotein is exposed to X-ray radiation is photoreduction of the metal centres. The oxidation state of a metal cannot always be determined from routine X-ray diffraction experiments alone, but it may have a crucial impact on the metal's environment and on the analysis of the structural data when considering the functional mechanism of a metalloenzyme. Here, UV-Vis microspectrophotometry is used to test the efficacy of selected scavengers in reducing the undesirable photoreduction of the iron and copper centres in myoglobin and azurin, respectively, and X-ray crystallography to assess their capacity of mitigating global and specific radiation damage effects. UV-Vis absorption spectra of native crystals, as well as those soaked in 18 different radioprotectants, show dramatic metal reduction occurring in the first 60 s of irradiation with an X-ray beam from a third-generation synchrotron source. Among the tested radioprotectants only potassium hexacyanoferrate(III) seems to be capable of partially mitigating the rate of metal photoreduction at the concentrations used, but not to a sufficient extent that would allow a complete data set to be recorded from a fully oxidized crystal. On the other hand, analysis of the X-ray crystallographic data confirms ascorbate as an efficient protecting agent against radiation damage, other than metal centre reduction, and suggests further testing of HEPES and 2,3-dichloro-1,4-naphtoquinone as potential scavengers.\",\n \"corpus_id\": 25325140,\n \"score\": 2\n },\n {\n \"doc_id\": \"19488704\",\n \"title\": \"Raman-assisted X-ray crystallography for the analysis of biomolecules.\",\n \"abstract\": \"In this chapter, we describe Raman microspectrophotometry applied to crystals of biomolecules. Raman spectra collected in crystallo provide structural information highly complementary to X-ray diffraction, relate the crystalline state to the solution state, and allow the identification of ligand-bound or intermediate states of macromolecules. Nonresonant Raman spectroscopy is particularly suitable to the study of macromolecular crystals, and therefore applies to a wide range of noncolored crystalline proteins. Practical issues related to the investigation of crystals by Raman microspectrophotometry are reviewed, and the current limitations are highlighted.\",\n \"corpus_id\": 21462449,\n \"score\": 2\n },\n {\n \"doc_id\": \"21942751\",\n \"title\": \"Spectroscopic characterization of the metal-binding sites in the periplasmic metal-sensor domain of CnrX from Cupriavidus metallidurans CH34.\",\n \"abstract\": \"CnrX, the dimeric metal sensor of the three-protein transmembrane signal transduction complex CnrYXH of Cupriavidus metallidurans CH34, contains one metal-binding site per monomer. Both Ni and Co elicit a biological response and bind the protein in a 3N2O1S coordination sphere with a nearly identical octahedral geometry as shown by the X-ray structure of CnrXs, the soluble domain of CnrX. However, in solution CnrXs is titrated by 4 Co-equiv and exhibits an unexpected intense band at 384 nm that was detected neither by single-crystal spectroscopy nor under anaerobiosis. The data from a combination of spectroscopic techniques (spectrophotometry, electron paramagnetic resonance, X-ray absorption spectroscopy) showed that two sites correspond to those identified by crystallography. The two extra binding sites accommodate Co(II) in an octahedral geometry in the absence of oxygen and are occupied in air by a mixture of low-spin Co(II) as well as EPR-silent Co(III). These extra sites, located at the N-terminus of the protein, are believed to participate to the formation of peroxo-bridged dimers. Accordingly, we hypothesize that the intense band at 384 nm relies on the formation of a binuclear μ-peroxo Co(III) complex. These metal binding sites are not physiologically relevant since they are not detected in full-length NccX, the closest homologue of CnrX. X-ray absorption spectroscopy demonstrates that NccX stabilizes Co(II) in two-binding sites similar to those characterized by crystallography in its soluble counterpart. Nevertheless, the original spectroscopic properties of the extra Co-binding sites are of interest because they are susceptible to be detected in other Co-bound proteins.\",\n \"corpus_id\": 41113548,\n \"score\": 2\n },\n {\n \"doc_id\": \"22824156\",\n \"title\": \"Metalloprotein active site structure determination: synergy between X-ray absorption spectroscopy and X-ray crystallography.\",\n \"abstract\": \"Structures of metalloprotein active sites derived from X-ray crystallography frequently contain chemical anomalies such as unexpected atomic geometries or elongated bond-lengths. Such anomalies are expected from the known errors inherent in macromolecular crystallography (ca. 0.1-0.2Å) and from the lack of appropriate restraints for metal sites which are often without precedent in the small molecule structure literature. Here we review the potential of X-ray absorption spectroscopy to provide information and perspective which could aid in improving the accuracy of metalloprotein crystal structure solutions. We also review the potential problem areas in analysis of the extended X-ray absorption fine structure (EXAFS) and discuss the use of density functional theory as another possible source of geometrical restraints for crystal structure analysis of metalloprotein active sites.\",\n \"corpus_id\": 41486973,\n \"score\": 2\n },\n {\n \"doc_id\": \"23093746\",\n \"title\": \"X-ray absorption spectroscopy at a protein crystallography facility: the Canadian Light Source beamline 08B1-1.\",\n \"abstract\": \"It is now possible to perform X-ray absorption spectroscopy (XAS) on metalloprotein crystals at the Canadian Macromolecular Crystallography Facility bend magnet (CMCF-BM) beamline (08B1-1) at the Canadian Light Source. The recent addition of a four-element fluorescence detector allows users to acquire data suitable for X-ray absorption near-edge structure and extended X-ray absorption fine-structure based studies by monitoring fluorescence. CMCF beamline users who wish to supplement their diffraction data with XAS can do so with virtually no additional sample preparation. XAS data collection is integrated with the established Mx Data Collector software package used to collect diffraction data. Mainstream XAS data-processing software packages are available for the users; assistance with data processing and interpretation by staff is also available upon request.\",\n \"corpus_id\": 23215460,\n \"score\": 2\n },\n {\n \"doc_id\": \"23529438\",\n \"title\": \"Analysis of Ca(2+)-binding sites in the MthK RCK domain by X-ray crystallography.\",\n \"abstract\": \"Regulator of K(+) conductance (RCK) domains form a conserved class of ligand-binding domains that control the activity of a variety of prokaryotic and eukaryotic K(+) channels. Structural analysis of these domains by X-ray crystallography has provided insight toward mechanisms underlying ligand binding and channel gating, and thus the experimental strategies aimed at determining structures of liganded and unliganded forms of the domains may be useful in analysis of other ligand-binding domains. Here, we describe a basic strategy for crystallographic analysis of the RCK domain from the MthK channel, for determination of its Ca(2+)-bound structure.\",\n \"corpus_id\": 10535094,\n \"score\": 2\n },\n {\n \"doc_id\": \"24356774\",\n \"title\": \"Validation of metal-binding sites in macromolecular structures with the CheckMyMetal web server.\",\n \"abstract\": \"Metals have vital roles in both the mechanism and architecture of biological macromolecules. Yet structures of metal-containing macromolecules in which metals are misidentified and/or suboptimally modeled are abundant in the Protein Data Bank (PDB). This shows the need for a diagnostic tool to identify and correct such modeling problems with metal-binding environments. The CheckMyMetal (CMM) web server (http://csgid.org/csgid/metal_sites/) is a sophisticated, user-friendly web-based method to evaluate metal-binding sites in macromolecular structures using parameters derived from 7,350 metal-binding sites observed in a benchmark data set of 2,304 high-resolution crystal structures. The protocol outlines how the CMM server can be used to detect geometric and other irregularities in the structures of metal-binding sites, as well as how it can alert researchers to potential errors in metal assignment. The protocol also gives practical guidelines for correcting problematic sites by modifying the metal-binding environment and/or redefining metal identity in the PDB file. Several examples where this has led to meaningful results are described in the ANTICIPATED RESULTS section. CMM was designed for a broad audience--biomedical researchers studying metal-containing proteins and nucleic acids--but it is equally well suited for structural biologists validating new structures during modeling or refinement. The CMM server takes the coordinates of a metal-containing macromolecule structure in the PDB format as input and responds within a few seconds for a typical protein structure with 2-5 metal sites and a few hundred amino acids.\",\n \"corpus_id\": 195684158,\n \"score\": 2\n },\n {\n \"doc_id\": \"24639261\",\n \"title\": \"X-ray crystallographic studies of metalloproteins.\",\n \"abstract\": \"Many proteins require metals for their physiological function. In combination with spectroscopic characterizations, X-ray crystallography is a very powerful method to correlate the function of protein-bound metal sites with their structure. Due to their special X-ray scattering properties, specific metals may be located in metalloprotein structures and eventually used for phasing the diffracted X-rays by the method of Multi-wavelength Anomalous Dispersion (MAD). How this is done is the principle subject of this chapter. Attention is also given to the crystallographic characterization of different oxidation states of redox active metals and to the complication of structural changes that may be induced by X-ray irradiation of protein crystals.\",\n \"corpus_id\": 6004528,\n \"score\": 2\n },\n {\n \"doc_id\": \"24701959\",\n \"title\": \"Electrochemical X-ray fluorescence spectroscopy for trace heavy metal analysis: enhancing X-ray fluorescence detection capabilities by four orders of magnitude.\",\n \"abstract\": \"The development of a novel analytical technique, electrochemical X-ray fluorescence (EC-XRF), is described and applied to the quantitative detection of heavy metals in solution, achieving sub-ppb limits of detection (LOD). In EC-XRF, electrochemical preconcentration of a species of interest onto the target electrode is achieved here by cathodic electrodeposition. Unambiguous elemental identification and quantification of metal concentration is then made using XRF. This simple electrochemical preconcentration step improves the LOD of energy dispersive XRF by over 4 orders of magnitude (for similar sample preparation time scales). Large area free-standing boron doped diamond grown using microwave plasma chemical vapor deposition techniques is found to be ideal as the electrode material for both electrodeposition and XRF due to its wide solvent window, transparency to the XRF beam, and ability to be produced in mechanically robust freestanding thin film form. During electrodeposition it is possible to vary both the deposition potential (Edep) and deposition time (tdep). For the metals Cu(2+) and Pb(2+) the highest detection sensitivities were found for Edep = -1.75 V and tdep (=) 4000 s with LODs of 0.05 and 0.04 ppb achieved, respectively. In mixed Cu(2+)/Pb(2+) solutions, EC-XRF shows that Cu(2+) deposition is unimpeded by Pb(2+), across a broad concentration range, but this is only true for Pb(2+) when both metals are present at low concentrations (10 nM), boding well for trace level measurements. In a dual mixed metal solution, EC-XRF can also be employed to either selectively deposit the metal which has the most positive formal reduction potential, E(0), or exhaustively deplete it from solution, enabling uninhibited detection of the metal with the more negative E(0).\",\n \"corpus_id\": 206363086,\n \"score\": 2\n },\n {\n \"doc_id\": \"25945580\",\n \"title\": \"Using support vector machines to improve elemental ion identification in macromolecular crystal structures.\",\n \"abstract\": \"In the process of macromolecular model building, crystallographers must examine electron density for isolated atoms and differentiate sites containing structured solvent molecules from those containing elemental ions. This task requires specific knowledge of metal-binding chemistry and scattering properties and is prone to error. A method has previously been described to identify ions based on manually chosen criteria for a number of elements. Here, the use of support vector machines (SVMs) to automatically classify isolated atoms as either solvent or one of various ions is described. Two data sets of protein crystal structures, one containing manually curated structures deposited with anomalous diffraction data and another with automatically filtered, high-resolution structures, were constructed. On the manually curated data set, an SVM classifier was able to distinguish calcium from manganese, zinc, iron and nickel, as well as all five of these ions from water molecules, with a high degree of accuracy. Additionally, SVMs trained on the automatically curated set of high-resolution structures were able to successfully classify most common elemental ions in an independent validation test set. This method is readily extensible to other elemental ions and can also be used in conjunction with previous methods based on a priori expectations of the chemical environment and X-ray scattering.\",\n \"corpus_id\": 14213127,\n \"score\": 2\n },\n {\n \"doc_id\": \"26740326\",\n \"title\": \"UV-Visible Absorption Spectroscopy Enhanced X-ray Crystallography at Synchrotron and X-ray Free Electron Laser Sources.\",\n \"abstract\": \"This review describes the use of single crystal UV-Visible Absorption micro-Spectrophotometry (UV-Vis AS) to enhance the design and execution of X-ray crystallography experiments for structural investigations of reaction intermediates of redox active and photosensitive proteins. Considerations for UV-Vis AS measurements at the synchrotron and associated instrumentation are described. UV-Vis AS is useful to verify the intermediate state of an enzyme and to monitor the progression of reactions within crystals. Radiation induced redox changes within protein crystals may be monitored to devise effective diffraction data collection strategies. An overview of the specific effects of radiation damage on macromolecular crystals is presented along with data collection strategies that minimize these effects by combining data from multiple crystals used at the synchrotron and with the X-ray free electron laser.\",\n \"corpus_id\": 29851904,\n \"score\": 2\n },\n {\n \"doc_id\": \"26975689\",\n \"title\": \"Metalloprotein Crystallography: More than a Structure.\",\n \"abstract\": \"Metal ions and metallocofactors play important roles in a broad range of biochemical reactions. Accordingly, it has been estimated that as much as 25-50% of the proteome uses transition metal ions to carry out a variety of essential functions. The metal ions incorporated within metalloproteins fulfill functional roles based on chemical properties, the diversity of which arises as transition metals can adopt different redox states and geometries, dictated by the identity of the metal and the protein environment. The coupling of a metal ion with an organic framework in metallocofactors, such as heme and cobalamin, further expands the chemical functionality of metals in biology. The three-dimensional visualization of metal ions and complex metallocofactors within a protein scaffold is often a starting point for enzymology, highlighting the importance of structural characterization of metalloproteins. Metalloprotein crystallography, however, presents a number of implicit challenges including correctly incorporating the relevant metal or metallocofactor, maintaining the proper environment for the protein to be purified and crystallized (including providing anaerobic, cold, or aphotic environments), and being mindful of the possibility of X-ray induced damage to the proteins or incorporated metal ions. Nevertheless, the incorporated metals or metallocofactors also present unique advantages in metalloprotein crystallography. The significant resonance that metals undergo with X-ray photons at wavelengths used for protein crystallography and the rich electronic properties of metals, which provide intense and spectroscopically unique signatures, allow a metalloprotein crystallographer to use anomalous dispersion to determine phases for structure solution and to use simultaneous or parallel spectroscopic techniques on single crystals. These properties, coupled with the improved brightness of beamlines, the ability to tune the wavelength of the X-ray beam, the availability of advanced detectors, and the incorporation of spectroscopic equipment at a number of synchrotron beamlines, have yielded exciting developments in metalloprotein structure determination. Here we will present results on the advantageous uses of metals in metalloprotein crystallography, including using metallocofactors to obtain phasing information, using K-edge X-ray absorption spectroscopy to identify metals coordinated in metalloprotein crystals, and using UV-vis spectroscopy on crystals to probe the enzymatic activity of the crystallized protein.\",\n \"corpus_id\": 14248206,\n \"score\": 2\n },\n {\n \"doc_id\": \"28291757\",\n \"title\": \"CheckMyMetal: a macromolecular metal-binding validation tool.\",\n \"abstract\": \"Metals are essential in many biological processes, and metal ions are modeled in roughly 40% of the macromolecular structures in the Protein Data Bank (PDB). However, a significant fraction of these structures contain poorly modeled metal-binding sites. CheckMyMetal (CMM) is an easy-to-use metal-binding site validation server for macromolecules that is freely available at http://csgid.org/csgid/metal_sites. The CMM server can detect incorrect metal assignments as well as geometrical and other irregularities in the metal-binding sites. Guidelines for metal-site modeling and validation in macromolecules are illustrated by several practical examples grouped by the type of metal. These examples show CMM users (and crystallographers in general) problems they may encounter during the modeling of a specific metal ion.\",\n \"corpus_id\": 13636890,\n \"score\": 2\n },\n {\n \"doc_id\": \"28375143\",\n \"title\": \"Data mining of iron(II) and iron(III) bond-valence parameters, and their relevance for macromolecular crystallography.\",\n \"abstract\": \"The bond-valence model is a reliable way to validate assumed oxidation states based on structural data. It has successfully been employed for analyzing metal-binding sites in macromolecule structures. However, inconsistent results for heme-based structures suggest that some widely used bond-valence R0 parameters may need to be adjusted in certain cases. Given the large number of experimental crystal structures gathered since these initial parameters were determined and the similarity of binding sites in organic compounds and macromolecules, the Cambridge Structural Database (CSD) is a valuable resource for refining metal-organic bond-valence parameters. R0 bond-valence parameters for iron(II), iron(III) and other metals have been optimized based on an automated processing of all CSD crystal structures. Almost all R0 bond-valence parameters were reproduced, except for iron-nitrogen bonds, for which distinct R0 parameters were defined for two observed subpopulations, corresponding to low-spin and high-spin states, of iron in both oxidation states. The significance of this data-driven method for parameter discovery, and how the spin state affects the interpretation of heme-containing proteins and iron-binding sites in macromolecular structures, are discussed.\",\n \"corpus_id\": 22455987,\n \"score\": 2\n },\n {\n \"doc_id\": \"28967006\",\n \"title\": \"Principles and methods used to grow and optimize crystals of protein-metallodrug adducts, to determine metal binding sites and to assign metal ligands.\",\n \"abstract\": \"The characterization of the interactions between biological macromolecules (proteins and nucleic acids) and metal-based drugs is a fundamental prerequisite for understanding their mechanisms of action. X-ray crystallography enables the structural analysis of such complexes with atomic level detail. However, this approach requires the preparation of highly diffracting single crystals, the measurement of diffraction patterns and the structural analysis and interpretation of macromolecule-metal interactions from electron density maps. In this review, we describe principles and methods used to grow and optimize crystals of protein-metallodrug adducts, to determine metal binding sites and to assign and validate metal ligands. Examples from the literature and experience in our own laboratory are provided and key challenges are described, notably crystallization and molecular model refinement against the X-ray diffraction data.\",\n \"corpus_id\": 19820447,\n \"score\": 2\n },\n {\n \"doc_id\": \"29045784\",\n \"title\": \"Metal Dependence of the Xylose Isomerase from Piromyces sp. E2 Explored by Activity Profiling and Protein Crystallography.\",\n \"abstract\": \"Xylose isomerase from Piromyces sp. E2 (PirXI) can be used to equip Saccharomyces cerevisiae with the capacity to ferment xylose to ethanol. The biochemical properties and structure of the enzyme have not been described even though its metal content, catalytic parameters, and expression level are critical for rapid xylose utilization. We have isolated the enzyme after high-level expression in Escherichia coli, analyzed the metal dependence of its catalytic properties, and determined 12 crystal structures in the presence of different metals, substrates, and substrate analogues. The activity assays revealed that various bivalent metals can activate PirXI for xylose isomerization. Among these metals, Mn2+ is the most favorable for catalytic activity. Furthermore, the enzyme shows the highest affinity for Mn2+, which was established by measuring the activation constants (Kact) for different metals. Metal analysis of the purified enzyme showed that in vivo the enzyme binds a mixture of metals that is determined by metal availability as well as affinity, indicating that the native metal composition can influence activity. The crystal structures show the presence of an active site similar to that of other xylose isomerases, with a d-xylose binding site containing two tryptophans and a catalytic histidine, as well as two metal binding sites that are formed by carboxylate groups of conserved aspartates and glutamates. The binding positions and conformations of the metal-coordinating residues varied slightly for different metals, which is hypothesized to contribute to the observed metal dependence of the isomerase activity.\",\n \"corpus_id\": 19522015,\n \"score\": 2\n },\n {\n \"doc_id\": \"19303027\",\n \"title\": \"X-ray crystallography of chemical compounds.\",\n \"abstract\": \"AIMS: Accurate knowledge of molecular structure is a prerequisite for rational drug design. This review examines the role of X-ray crystallography in providing the required structural information and advances in the field of X-ray crystallography that enhance or expand its role. MAIN METHODS: X-ray crystallography of new drugs candidates and intermediates can provide valuable information of new syntheses and parameters for quantitative structure activity relationships (QSAR). KEY FINDINGS: Crystallographic studies play a vital role in many disciplines including materials science, chemistry, pharmacology, and molecular biology. X-ray crystallography is the most comprehensive technique available to determine molecular structure. A requirement for the high accuracy of crystallographic structures is that a 'good crystal' must be found, and this is often the rate-limiting step. In the past three decades developments in detectors, increases in computer power, and powerful graphics capabilities have contributed to a dramatic increase in the number of materials characterized by X-ray crystallography. More recently the advent of high-throughput crystallization techniques has enhanced our ability to produce that one good crystal required for crystallographic analysis. SIGNIFICANCE: Continuing advances in all phases of a crystallographic study have expanded the ranges of samples which can be analyzes by X-ray crystallography to include larger molecules, smaller or weakly diffracting crystals, and twinned crystals.\",\n \"corpus_id\": 206727089,\n \"score\": 1\n },\n {\n \"doc_id\": \"19322673\",\n \"title\": \"Structures of proteins and cofactors: X-ray crystallography.\",\n \"abstract\": \"Protein crystallography is the predominately used technique for the determination of the three-dimensional structures of proteins and other macromolecules. In this article, the methodology utilized for the measurement and analysis of the diffraction data from crystals is briefly reviewed. As examples of both the usefulness and difficulties of this technique, the determination of the structures of several photosynthetic pigment-protein complexes is described, namely, the reaction center from purple bacteria, photosystem I and photosystem II from cyanobacteria, the light-harvesting complex II from purple bacteria, and the FMO protein from green bacteria.\",\n \"corpus_id\": 19069675,\n \"score\": 1\n },\n {\n \"doc_id\": \"20382997\",\n \"title\": \"Temperature-dependent macromolecular X-ray crystallography.\",\n \"abstract\": \"X-ray crystallography provides structural details of biological macromolecules. Whereas routine data are collected close to 100 K in order to mitigate radiation damage, more exotic temperature-controlled experiments in a broader temperature range from 15 K to room temperature can provide both dynamical and structural insights. Here, the dynamical behaviour of crystalline macromolecules and their surrounding solvent as a function of cryo-temperature is reviewed. Experimental strategies of kinetic crystallography are discussed that have allowed the generation and trapping of macromolecular intermediate states by combining reaction initiation in the crystalline state with appropriate temperature profiles. A particular focus is on recruiting X-ray-induced changes for reaction initiation, thus unveiling useful aspects of radiation damage, which otherwise has to be minimized in macromolecular crystallography.\",\n \"corpus_id\": 14006498,\n \"score\": 1\n },\n {\n \"doc_id\": \"20694684\",\n \"title\": \"X-ray crystallography in drug discovery.\",\n \"abstract\": \"Macromolecular X-ray crystallography is an important and powerful technique in drug discovery, used by pharmaceutical companies in the discovery process of new medicines. The detailed analysis of crystal structures of protein-ligand complexes allows the study of the specific interactions of a particular drug with its protein target at the atomic level. It is used to design and improve drugs. The starting point of these studies is the preparation of suitable crystals of complexes with potential ligands, which can be achieved by using different strategies described in this chapter. In addition, an introduction to X-ray crystallography is given, highlighting the fundamental steps necessary to determine the three-dimensional structure of protein-ligand complexes, as well as some of the tools and criteria to validate crystal structures available in databases.\",\n \"corpus_id\": 206673826,\n \"score\": 1\n },\n {\n \"doc_id\": \"20825181\",\n \"title\": \"Structural comparisons of apo- and metalated three-stranded coiled coils clarify metal binding determinants in thiolate containing designed peptides.\",\n \"abstract\": \"Over the past two decades, designed metallopeptides have held the promise for understanding a variety of fundamental questions in metallobiochemistry; however, these dreams have not yet been realized because of a lack of structural data to elaborate the protein scaffolds before metal complexation and the resultant metalated structures which ultimately exist. This is because there are few reports of structural characterization of such systems either in their metalated or nonmetalated forms and no examples where an apo structure and the corresponding metalated peptide assembly have both been defined by X-ray crystallography. Herein we present X-ray structures of two de novo designed parallel three-stranded coiled coils (designed using the heptad repeat (a → g)) CSL9C (CS = Coil Ser) and CSL19C in their nonmetalated forms, determined to 1.36 and 2.15 A resolutions, respectively. Leucines from either position 9 (a site) or 19 (d site) are replaced by cysteine to generate the constructs CSL9C and CSL19C, respectively, yielding thiol-rich pockets at the hydrophobic interior of these peptides, suitable to bind heavy metals such as As(III), Hg(II), Cd(II), and Pb(II). We use these structures to understand the inherent structural differences between a and d sites to clarify the basis of the observed differential spectroscopic behavior of metal binding in these types of peptides. Cys side chains of (CSL9C)(3) show alternate conformations and are partially preorganized for metal binding, whereas cysteines in (CSL19C)(3) are present as a single conformer. Zn(II) ions, which do not coordinate or influence Cys residues at the designed metal sites but are essential for forming X-ray quality crystals, are bound to His and Glu residues at the crystal packing interfaces of both structures. These \\\"apo\\\" structures are used to clarify the changes in metal site organization between metalated As(CSL9C)(3) and to speculate on the differential basis of Hg(II) binding in a versus d peptides. Thus, for the first time, one can establish general rules for heavy metal binding to Cys-rich sites in designed proteins which may provide insight for understanding how heavy metals bind to metallochaperones or metalloregulatory proteins.\",\n \"corpus_id\": 34204911,\n \"score\": 1\n },\n {\n \"doc_id\": \"21041930\",\n \"title\": \"Joint X-ray and neutron refinement with phenix.refine.\",\n \"abstract\": \"Approximately 85% of the structures deposited in the Protein Data Bank have been solved using X-ray crystallography, making it the leading method for three-dimensional structure determination of macromolecules. One of the limitations of the method is that the typical data quality (resolution) does not allow the direct determination of H-atom positions. Most hydrogen positions can be inferred from the positions of other atoms and therefore can be readily included into the structure model as a priori knowledge. However, this may not be the case in biologically active sites of macromolecules, where the presence and position of hydrogen is crucial to the enzymatic mechanism. This makes the application of neutron crystallography in biology particularly important, as H atoms can be clearly located in experimental neutron scattering density maps. Without exception, when a neutron structure is determined the corresponding X-ray structure is also known, making it possible to derive the complete structure using both data sets. Here, the implementation of crystallographic structure-refinement procedures that include both X-ray and neutron data (separate or jointly) in the PHENIX system is described.\",\n \"corpus_id\": 16124013,\n \"score\": 1\n },\n {\n \"doc_id\": \"21293373\",\n \"title\": \"Femtosecond X-ray protein nanocrystallography.\",\n \"abstract\": \"X-ray crystallography provides the vast majority of macromolecular structures, but the success of the method relies on growing crystals of sufficient size. In conventional measurements, the necessary increase in X-ray dose to record data from crystals that are too small leads to extensive damage before a diffraction signal can be recorded. It is particularly challenging to obtain large, well-diffracting crystals of membrane proteins, for which fewer than 300 unique structures have been determined despite their importance in all living cells. Here we present a method for structure determination where single-crystal X-ray diffraction 'snapshots' are collected from a fully hydrated stream of nanocrystals using femtosecond pulses from a hard-X-ray free-electron laser, the Linac Coherent Light Source. We prove this concept with nanocrystals of photosystem I, one of the largest membrane protein complexes. More than 3,000,000 diffraction patterns were collected in this study, and a three-dimensional data set was assembled from individual photosystem I nanocrystals (∼200 nm to 2 μm in size). We mitigate the problem of radiation damage in crystallography by using pulses briefer than the timescale of most damage processes. This offers a new approach to structure determination of macromolecules that do not yield crystals of sufficient size for studies using conventional radiation sources or are particularly sensitive to radiation damage.\",\n \"corpus_id\": 1020650,\n \"score\": 1\n },\n {\n \"doc_id\": \"21304455\",\n \"title\": \"Protein crystallization for X-ray crystallography.\",\n \"abstract\": \"Using the three-dimensional structure of biological macromolecules to infer how they function is one of the most important fields of modern biology. The availability of atomic resolution structures provides a deep and unique understanding of protein function, and helps to unravel the inner workings of the living cell. To date, 86% of the Protein Data Bank (rcsb-PDB) entries are macromolecular structures that were determined using X-ray crystallography. To obtain crystals suitable for crystallographic studies, the macromolecule (e.g. protein, nucleic acid, protein-protein complex or protein-nucleic acid complex) must be purified to homogeneity, or as close as possible to homogeneity. The homogeneity of the preparation is a key factor in obtaining crystals that diffract to high resolution (Bergfors, 1999; McPherson, 1999). Crystallization requires bringing the macromolecule to supersaturation. The sample should therefore be concentrated to the highest possible concentration without causing aggregation or precipitation of the macromolecule (usually 2-50 mg/mL). Introducing the sample to precipitating agent can promote the nucleation of protein crystals in the solution, which can result in large three-dimensional crystals growing from the solution. There are two main techniques to obtain crystals: vapor diffusion and batch crystallization. In vapor diffusion, a drop containing a mixture of precipitant and protein solutions is sealed in a chamber with pure precipitant. Water vapor then diffuses out of the drop until the osmolarity of the drop and the precipitant are equal (Figure 1A). The dehydration of the drop causes a slow concentration of both protein and precipitant until equilibrium is achieved, ideally in the crystal nucleation zone of the phase diagram. The batch method relies on bringing the protein directly into the nucleation zone by mixing protein with the appropriate amount of precipitant (Figure 1B). This method is usually performed under a paraffin/mineral oil mixture to prevent the diffusion of water out of the drop. Here we will demonstrate two kinds of experimental setup for vapor diffusion, hanging drop and sitting drop, in addition to batch crystallization under oil.\",\n \"corpus_id\": 11632900,\n \"score\": 1\n },\n {\n \"doc_id\": \"21376143\",\n \"title\": \"Infrared protein crystallography.\",\n \"abstract\": \"We consider the application of infrared spectroscopy to protein crystals, with particular emphasis on exploiting molecular orientation through polarization measurements on oriented single crystals. Infrared microscopes enable transmission measurements on individual crystals using either thermal or nonthermal sources, and can accommodate flow cells, used to measure spectral changes induced by exposure to soluble ligands, and cryostreams, used for measurements of flash-cooled crystals. Comparison of unpolarized infrared measurements on crystals and solutions probes the effects of crystallization and can enhance the value of the structural models refined from X-ray diffraction data by establishing solution conditions under which they are most relevant. Results on several proteins are consistent with similar equilibrium conformational distributions in crystal and solutions. However, the rates of conformational change are often perturbed. Infrared measurements also detect products generated by X-ray exposure, including CO(2). Crystals with favorable symmetry exhibit infrared dichroism that enhances the synergy with X-ray crystallography. Polarized infrared measurements on crystals can distinguish spectral contributions from chemically similar sites, identify hydrogen bonding partners, and, in opportune situations, determine three-dimensional orientations of molecular groups. This article is part of a Special Issue entitled: Protein Structure and Function in the Crystalline State.\",\n \"corpus_id\": 37045533,\n \"score\": 1\n },\n {\n \"doc_id\": \"21833866\",\n \"title\": \"X-ray crystallography.\",\n \"abstract\": \"X-ray crystallography has been particularly important in the study of the enzyme nitrogenase, providing researchers with high-resolution structural models that have been essential to studying the enzyme's unique metal clusters and nucleotide-binding modes and protein interactions. While several important nitrogenase structures have already been determined using X-ray crystallography, the technique still holds great potential for future significant discoveries involving reaction intermediates and redox states of the enzyme's metal clusters. Thus, it is important to inform future nitrogenase researchers about the procedures for obtaining crystals of nitrogenase component proteins and their complexes and determining their structures. While nitrogenase component proteins from several bacteria have been crystallized, the majority of structures and those of highest resolution are of the nitrogenase proteins from the bacteria Azotobacter vinelandii. Therefore, the bulk of this chapter will focus on methods for crystallization and structure determination of nitrogenase component proteins from A. vinelandii.\",\n \"corpus_id\": 104916134,\n \"score\": 1\n },\n {\n \"doc_id\": \"21949273\",\n \"title\": \"ISPyB: an information management system for synchrotron macromolecular crystallography.\",\n \"abstract\": \"MOTIVATION: Individual research groups now analyze thousands of samples per year at synchrotron macromolecular crystallography (MX) resources. The efficient management of experimental data is thus essential if the best possible experiments are to be performed and the best possible data used in downstream processes in structure determination pipelines. Information System for Protein crystallography Beamlines (ISPyB), a Laboratory Information Management System (LIMS) with an underlying data model allowing for the integration of analyses down-stream of the data collection experiment was developed to facilitate such data management. RESULTS: ISPyB is now a multisite, generic LIMS for synchrotron-based MX experiments. Its initial functionality has been enhanced to include improved sample tracking and reporting of experimental protocols, the direct ranking of the diffraction characteristics of individual samples and the archiving of raw data and results from ancillary experiments and post-experiment data processing protocols. This latter feature paves the way for ISPyB to play a central role in future macromolecular structure solution pipelines and validates the application of the approach used in ISPyB to other experimental techniques, such as biological solution Small Angle X-ray Scattering and spectroscopy, which have similar sample tracking and data handling requirements.\",\n \"corpus_id\": 9383206,\n \"score\": 1\n },\n {\n \"doc_id\": \"22045560\",\n \"title\": \"Crystallization of macromolecules.\",\n \"abstract\": \"X-ray crystallography has evolved into a very powerful tool to determine the three-dimensional structure of macromolecules and macromolecular complexes. The major bottleneck in structure determination by X-ray crystallography is the preparation of suitable crystalline samples. This unit outlines steps for the crystallization of a macromolecule, starting with a purified, homogeneous sample. The first protocols describe preparation of the macromolecular sample (i.e., proteins, nucleic acids, and macromolecular complexes). The preparation and assessment of crystallization trials is then described, along with a protocol for confirming whether the crystals obtained are composed of macromolecule as opposed to a crystallization reagent. Next, the optimization of crystallization conditions is presented. Finally, protocols that facilitate the growth of larger crystals through seeding are described.\",\n \"corpus_id\": 20703254,\n \"score\": 1\n },\n {\n \"doc_id\": \"23132076\",\n \"title\": \"Determination of soluble and membrane protein structures by X-ray crystallography.\",\n \"abstract\": \"X-ray crystallography is a technique used to determine the atomic-detail structure of a biological macromolecule. The method relies on the ability to generate a three-dimensional crystal of a highly purified protein or nucleic acid for diffraction by X-rays. The extent of scattering of X-rays by the crystal determines the accuracy of the resulting structural model. Unlike electrons, X-rays cannot be refocused after they have been scattered by their target. Thus, calculations are needed to reconstruct the image of the macromolecule that builds the crystal lattice. Tremendous advances over the past 60 years in recombinant expression and purification, crystal growth methods and equipment, X-ray sources, computer processing power, programs, and graphics have taken X-ray crystallography from a highly specialized field to one increasingly accessible to researchers in the biomedical sciences. In this chapter, we review the major concepts of macromolecular X-ray crystallography, focusing mainly on techniques for crystallizing soluble and membrane proteins, and provide a protocol for the crystallization of lysozyme as a model for the crystallization of other proteins.\",\n \"corpus_id\": 29230067,\n \"score\": 1\n },\n {\n \"doc_id\": \"23729263\",\n \"title\": \"Studying protein-ligand interactions using X-ray crystallography.\",\n \"abstract\": \"X-ray crystallography is a powerful technique for studying protein-ligand interactions. Advances in techniques have meant that it is now possible to routinely determine the structures of ligand complexes in the majority of cases where crystallization conditions and protein structures are already known. Ligand soaking or cocrystallization, together with the potential use of molecular replacement, provides data for determining the structures of a protein in complex with ligands. Furthermore, advances in protein structure model building facilitate automatic ligand fitting to residual electron density in the protein-ligand complex.\",\n \"corpus_id\": 41459476,\n \"score\": 1\n },\n {\n \"doc_id\": \"24372145\",\n \"title\": \"The future of crystallography in drug discovery.\",\n \"abstract\": \"INTRODUCTION: X-ray crystallography plays an important role in structure-based drug design (SBDD), and accurate analysis of crystal structures of target macromolecules and macromolecule-ligand complexes is critical at all stages. However, whereas there has been significant progress in improving methods of structural biology, particularly in X-ray crystallography, corresponding progress in the development of computational methods (such as in silico high-throughput screening) is still on the horizon. Crystal structures can be overinterpreted and thus bias hypotheses and follow-up experiments. As in any experimental science, the models of macromolecular structures derived from X-ray diffraction data have their limitations, which need to be critically evaluated and well understood for structure-based drug discovery. AREAS COVERED: This review describes how the validity, accuracy and precision of a protein or nucleic acid structure determined by X-ray crystallography can be evaluated from three different perspectives: i) the nature of the diffraction experiment; ii) the interpretation of an electron density map; and iii) the interpretation of the structural model in terms of function and mechanism. The strategies to optimally exploit a macromolecular structure are also discussed in the context of 'Big Data' analysis, biochemical experimental design and structure-based drug discovery. EXPERT OPINION: Although X-ray crystallography is one of the most detailed 'microscopes' available today for examining macromolecular structures, the authors would like to re-emphasize that such structures are only simplified models of the target macromolecules. The authors also wish to reinforce the idea that a structure should not be thought of as a set of precise coordinates but rather as a framework for generating hypotheses to be explored. Numerous biochemical and biophysical experiments, including new diffraction experiments, can and should be performed to verify or falsify these hypotheses. X-ray crystallography will find its future application in drug discovery by the development of specific tools that would allow realistic interpretation of the outcome coordinates and/or support testing of these hypotheses.\",\n \"corpus_id\": 38488861,\n \"score\": 1\n },\n {\n \"doc_id\": \"24590727\",\n \"title\": \"Screening Ligands by X-ray crystallography.\",\n \"abstract\": \"X-ray crystallography is an invaluable technique in structure-based drug discovery, including fragment-based drug discovery, because it is the only technique that can provide a complete three dimensional readout of the interaction between the small molecule and its macromolecular target. X-ray diffraction (XRD) techniques can be employed as the sole method for conducting a screen of a fragment library, or it can be employed as the final technique in a screening campaign to confirm putative \\\"hit\\\" compounds identified by a variety of biochemical and/or biophysical screening techniques. Both approaches require an efficient technique to prepare dozens to hundreds of crystals for data collection, and a reproducible way to deliver ligands to the crystal. Here, a general method for screening cocktails of fragments is described. In cases where X-ray crystallography is employed as a method to verify putative hits, the cocktails of fragments described below would simply be replaced with single fragment solutions.\",\n \"corpus_id\": 8218772,\n \"score\": 1\n },\n {\n \"doc_id\": \"24648090\",\n \"title\": \"Protein structure validation and analysis with X-ray crystallography.\",\n \"abstract\": \"X-ray crystallography is the main technique for the determination of protein structures. About 85 % of all protein structures known to date have been elucidated using X-ray crystallography. Knowledge of the three-dimensional structure of proteins can be used in various applications in biotechnology, biomedicine, drug design, and basic research and as a validation tool for protein modifications, ligand binding, and structural authenticity. Moreover, the requirement for pure, homogeneous, and stable protein solutions in crystallizations makes X-ray crystallography beneficial in other fields of protein research as well. Here, we describe the technique of X-ray protein crystallography and the steps involved for a successful three-dimensional crystal structure determination.\",\n \"corpus_id\": 10634886,\n \"score\": 1\n },\n {\n \"doc_id\": \"25068843\",\n \"title\": \"X-ray absorption spectroscopy systematics at the tungsten L-edge.\",\n \"abstract\": \"A series of mononuclear six-coordinate tungsten compounds spanning formal oxidation states from 0 to +VI, largely in a ligand environment of inert chloride and/or phosphine, was interrogated by tungsten L-edge X-ray absorption spectroscopy. The L-edge spectra of this compound set, comprised of [W(0)(PMe3)6], [W(II)Cl2(PMePh2)4], [W(III)Cl2(dppe)2][PF6] (dppe = 1,2-bis(diphenylphosphino)ethane), [W(IV)Cl4(PMePh2)2], [W(V)(NPh)Cl3(PMe3)2], and [W(VI)Cl6], correlate with formal oxidation state and have usefulness as references for the interpretation of the L-edge spectra of tungsten compounds with redox-active ligands and ambiguous electronic structure descriptions. The utility of these spectra arises from the combined correlation of the estimated branching ratio of the L3,2-edges and the L1 rising-edge energy with metal Zeff, thereby permitting an assessment of effective metal oxidation state. An application of these reference spectra is illustrated by their use as backdrop for the L-edge X-ray absorption spectra of [W(IV)(mdt)2(CO)2] and [W(IV)(mdt)2(CN)2](2-) (mdt(2-) = 1,2-dimethylethene-1,2-dithiolate), which shows that both compounds are effectively W(IV) species even though the mdt ligands exist at different redox levels in the two compounds. Use of metal L-edge XAS to assess a compound of uncertain formulation requires: (1) Placement of that data within the context of spectra offered by unambiguous calibrant compounds, preferably with the same coordination number and similar metal ligand distances. Such spectra assist in defining upper and/or lower limits for metal Zeff in the species of interest. ( 2) Evaluation of that data in conjunction with information from other physical methods, especially ligand K-edge XAS. ( 3) Increased care in interpretation if strong π-acceptor ligands, particularly CO, or π-donor ligands are present. The electron-withdrawing/donating nature of these ligand types, combined with relatively short metal-ligand distances, exaggerate the difference between formal oxidation state and metal Zeff or, as in the case of [W(IV)(mdt)2(CO)2], exert the subtle effect of modulating the redox level of other ligands in the coordination sphere.\",\n \"corpus_id\": 32116483,\n \"score\": 1\n },\n {\n \"doc_id\": \"26057665\",\n \"title\": \"In meso in situ serial X-ray crystallography of soluble and membrane proteins.\",\n \"abstract\": \"The lipid cubic phase (LCP) continues to grow in popularity as a medium in which to generate crystals of membrane (and soluble) proteins for high-resolution X-ray crystallographic structure determination. To date, the PDB includes 227 records attributed to the LCP or in meso method. Among the listings are some of the highest profile membrane proteins, including the β2-adrenoreceptor-Gs protein complex that figured in the award of the 2012 Nobel Prize in Chemistry to Lefkowitz and Kobilka. The most successful in meso protocol to date uses glass sandwich crystallization plates. Despite their many advantages, glass plates are challenging to harvest crystals from. However, performing in situ X-ray diffraction measurements with these plates is not practical. Here, an alternative approach is described that provides many of the advantages of glass plates and is compatible with high-throughput in situ measurements. The novel in meso in situ serial crystallography (IMISX) method introduced here has been demonstrated with AlgE and PepT (alginate and peptide transporters, respectively) as model integral membrane proteins and with lysozyme as a test soluble protein. Structures were solved by molecular replacement and by experimental phasing using bromine SAD and native sulfur SAD methods to resolutions ranging from 1.8 to 2.8 Å using single-digit microgram quantities of protein. That sulfur SAD phasing worked is testament to the exceptional quality of the IMISX diffraction data. The IMISX method is compatible with readily available, inexpensive materials and equipment, is simple to implement and is compatible with high-throughput in situ serial data collection at macromolecular crystallography synchrotron beamlines worldwide. Because of its simplicity and effectiveness, the IMISX approach is likely to supplant existing in meso crystallization protocols. It should prove particularly attractive in the area of ligand screening for drug discovery and development.\",\n \"corpus_id\": 4943457,\n \"score\": 1\n },\n {\n \"doc_id\": \"26175905\",\n \"title\": \"Sub-atomic resolution X-ray crystallography and neutron crystallography: promise, challenges and potential.\",\n \"abstract\": \"The International Year of Crystallography saw the number of macromolecular structures deposited in the Protein Data Bank cross the 100000 mark, with more than 90000 of these provided by X-ray crystallography. The number of X-ray structures determined to sub-atomic resolution (i.e. ≤1 Å) has passed 600 and this is likely to continue to grow rapidly with diffraction-limited synchrotron radiation sources such as MAX-IV (Sweden) and Sirius (Brazil) under construction. A dozen X-ray structures have been deposited to ultra-high resolution (i.e. ≤0.7 Å), for which precise electron density can be exploited to obtain charge density and provide information on the bonding character of catalytic or electron transfer sites. Although the development of neutron macromolecular crystallography over the years has been far less pronounced, and its application much less widespread, the availability of new and improved instrumentation, combined with dedicated deuteration facilities, are beginning to transform the field. Of the 83 macromolecular structures deposited with neutron diffraction data, more than half (49/83, 59%) were released since 2010. Sub-mm(3) crystals are now regularly being used for data collection, structures have been determined to atomic resolution for a few small proteins, and much larger unit-cell systems (cell edges >100 Å) are being successfully studied. While some details relating to H-atom positions are tractable with X-ray crystallography at sub-atomic resolution, the mobility of certain H atoms precludes them from being located. In addition, highly polarized H atoms and protons (H(+)) remain invisible with X-rays. Moreover, the majority of X-ray structures are determined from cryo-cooled crystals at 100 K, and, although radiation damage can be strongly controlled, especially since the advent of shutterless fast detectors, and by using limited doses and crystal translation at micro-focus beams, radiation damage can still take place. Neutron crystallography therefore remains the only approach where diffraction data can be collected at room temperature without radiation damage issues and the only approach to locate mobile or highly polarized H atoms and protons. Here a review of the current status of sub-atomic X-ray and neutron macromolecular crystallography is given and future prospects for combined approaches are outlined. New results from two metalloproteins, copper nitrite reductase and cytochrome c', are also included, which illustrate the type of information that can be obtained from sub-atomic-resolution (∼0.8 Å) X-ray structures, while also highlighting the need for complementary neutron studies that can provide details of H atoms not provided by X-ray crystallography.\",\n \"corpus_id\": 15471858,\n \"score\": 1\n },\n {\n \"doc_id\": \"26798817\",\n \"title\": \"Time-resolved structural studies with serial crystallography: A new light on retinal proteins.\",\n \"abstract\": \"Structural information of the different conformational states of the two prototypical light-sensitive membrane proteins, bacteriorhodopsin and rhodopsin, has been obtained in the past by X-ray cryo-crystallography and cryo-electron microscopy. However, these methods do not allow for the structure determination of most intermediate conformations. Recently, the potential of X-Ray Free Electron Lasers (X-FELs) for tracking the dynamics of light-triggered processes by pump-probe serial femtosecond crystallography has been demonstrated using 3D-micron-sized crystals. In addition, X-FELs provide new opportunities for protein 2D-crystal diffraction, which would allow to observe the course of conformational changes of membrane proteins in a close-to-physiological lipid bilayer environment. Here, we describe the strategies towards structural dynamic studies of retinal proteins at room temperature, using injector or fixed-target based serial femtosecond crystallography at X-FELs. Thanks to recent progress especially in sample delivery methods, serial crystallography is now also feasible at synchrotron X-ray sources, thus expanding the possibilities for time-resolved structure determination.\",\n \"corpus_id\": 9158424,\n \"score\": 1\n },\n {\n \"doc_id\": \"27841751\",\n \"title\": \"A public database of macromolecular diffraction experiments.\",\n \"abstract\": \"The low reproducibility of published experimental results in many scientific disciplines has recently garnered negative attention in scientific journals and the general media. Public transparency, including the availability of `raw' experimental data, will help to address growing concerns regarding scientific integrity. Macromolecular X-ray crystallography has led the way in requiring the public dissemination of atomic coordinates and a wealth of experimental data, making the field one of the most reproducible in the biological sciences. However, there remains no mandate for public disclosure of the original diffraction data. The Integrated Resource for Reproducibility in Macromolecular Crystallography (IRRMC) has been developed to archive raw data from diffraction experiments and, equally importantly, to provide related metadata. Currently, the database of our resource contains data from 2920 macromolecular diffraction experiments (5767 data sets), accounting for around 3% of all depositions in the Protein Data Bank (PDB), with their corresponding partially curated metadata. IRRMC utilizes distributed storage implemented using a federated architecture of many independent storage servers, which provides both scalability and sustainability. The resource, which is accessible via the web portal at http://www.proteindiffraction.org, can be searched using various criteria. All data are available for unrestricted access and download. The resource serves as a proof of concept and demonstrates the feasibility of archiving raw diffraction data and associated metadata from X-ray crystallographic studies of biological macromolecules. The goal is to expand this resource and include data sets that failed to yield X-ray structures in order to facilitate collaborative efforts that will improve protein structure-determination methods and to ensure the availability of `orphan' data left behind for various reasons by individual investigators and/or extinct structural genomics projects.\",\n \"corpus_id\": 25116696,\n \"score\": 1\n },\n {\n \"doc_id\": \"27896717\",\n \"title\": \"A Practical Approach to Protein Crystallography.\",\n \"abstract\": \"Macromolecular crystallography is a powerful tool for structural biology. The resolution of a protein crystal structure is becoming much easier than in the past, thanks to developments in computing, automation of crystallization techniques and high-flux synchrotron sources to collect diffraction datasets. The aim of this chapter is to provide practical procedures to determine a protein crystal structure, illustrating the new techniques, experimental methods, and software that have made protein crystallography a tool accessible to a larger scientific community. It is impossible to give more than a taste of what the X-ray crystallographic technique entails in one brief chapter and there are different ways to solve a protein structure. Since the number of structures available in the Protein Data Bank (PDB) is becoming ever larger (the protein data bank now contains more than 100,000 entries) and therefore the probability to find a good model to solve the structure is ever increasing, we focus our attention on the Molecular Replacement method. Indeed, whenever applicable, this method allows the resolution of macromolecular structures starting from a single data set and a search model downloaded from the PDB, with the aid only of computer work.\",\n \"corpus_id\": 4969587,\n \"score\": 1\n },\n {\n \"doc_id\": \"28177310\",\n \"title\": \"Combining X-ray and neutron crystallography with spectroscopy.\",\n \"abstract\": \"X-ray protein crystallography has, through the determination of the three-dimensional structures of enzymes and their complexes, been essential to the understanding of biological chemistry. However, as X-rays are scattered by electrons, the technique has difficulty locating the presence and position of H atoms (and cannot locate H(+) ions), knowledge of which is often crucially important for the understanding of enzyme mechanism. Furthermore, X-ray irradiation, through photoelectronic effects, will perturb the redox state in the crystal. By using single-crystal spectrophotometry, reactions taking place in the crystal can be monitored, either to trap intermediates or follow photoreduction during X-ray data collection. By using neutron crystallography, the positions of H atoms can be located, as it is the nuclei rather than the electrons that scatter neutrons, and the scattering length is not determined by the atomic number. Combining the two techniques allows much greater insight into both reaction mechanism and X-ray-induced photoreduction.\",\n \"corpus_id\": 15007429,\n \"score\": 1\n },\n {\n \"doc_id\": \"28342173\",\n \"title\": \"Metal ions-binding T4 lysozyme as an intramolecular protein purification tag compatible with X-ray crystallography.\",\n \"abstract\": \"Phage T4 lysozyme is a well folded and highly soluble protein that is widely used as an insertion tag to improve solubility and crystallization properties of poorly behaved recombinant proteins. It has been used in the fusion protein strategy to facilitate crystallization of various proteins including multiple G protein-coupled receptors, lipid kinases, or sterol binding proteins. Here, we present a structural and biochemical characterization of its novel, metal ions-binding mutant (mbT4L). We demonstrate that mbT4L can be used as a purification tag in the immobilized-metal affinity chromatography and that, in many respects, it is superior to the conventional hexahistidine tag. In addition, structural characterization of mbT4L suggests that mbT4L can be used as a purification tag compatible with X-ray crystallography.\",\n \"corpus_id\": 37076861,\n \"score\": 1\n },\n {\n \"doc_id\": \"28572170\",\n \"title\": \"New developments in crystallography: exploring its technology, methods and scope in the molecular biosciences.\",\n \"abstract\": \"Since the Protein Data Bank (PDB) was founded in 1971, there are now over 120,000 depositions, the majority of which are from X-ray crystallography and 90% of those made use of synchrotron beamlines. At the Cambridge Structure Database (CSD), founded in 1965, there are more than 800,000 'small molecule' crystal structure depositions and a very large number of those are relevant in the biosciences as ligands or cofactors. The technology for crystal structure analysis is still developing rapidly both at synchrotrons and in home labs. Determination of the details of the hydrogen atoms in biological macromolecules is well served using neutrons as probe. Large multi-macromolecular complexes cause major challenges to crystallization; electrons as probes offer unique advantages here. Methods developments naturally accompany technology change, mainly incremental but some, such as the tuneability, intensity and collimation of synchrotron radiation, have effected radical changes in capability of biological crystallography. In the past few years, the X-ray laser has taken X-ray crystallography measurement times into the femtosecond range. In terms of applications many new discoveries have been made in the molecular biosciences. The scope of crystallographic techniques is indeed very wide. As examples, new insights into chemical catalysis of enzymes and relating ligand bound structures to thermodynamics have been gained but predictive power is seen as not yet achieved. Metal complexes are also an emerging theme for biomedicine applications. Our studies of coloration of live and cooked lobsters proved to be an unexpected favourite with the public and schoolchildren. More generally, public understanding of the biosciences and crystallography's role within the field have been greatly enhanced by the United Nations International Year of Crystallography coordinated by the International Union of Crystallography. This topical review describes each of these areas along with illustrative results to document the scope of each methodology.\",\n \"corpus_id\": 3220623,\n \"score\": 1\n },\n {\n \"doc_id\": \"28653703\",\n \"title\": \"Pitfalls in metal-organic framework crystallography: towards more accurate crystal structures.\",\n \"abstract\": \"Single crystal X-ray diffraction (SC-XRD) is the principal method for determining the crystal structures of metal-organic frameworks (MOFs). This tutorial deals with the handling of MOF crystals and analysis of crystallographic data obtained from single-crystal X-ray diffraction, focusing on two features that are particularly important in MOF crystallography and have a large impact on the quality and reliability of the final crystal structures: (1) the treatment of pore-occupying entities (both in the physical crystals and in the crystallographic model) and (2) crystallographic twinning. Proper handling of samples and data will reduce the need for using solvent masking software (e.g. SQUEEZE) to obtain acceptable crystal structures. If SC-XRD is to retain its position as the definitive method of MOF structure determination, these issues must be addressed when a new MOF structure is determined and reported. The issues addressed in this review is also valid for other porous, crystalline solids such as porous organic cages, metal-organic polyhedra, covalent organic frameworks and zeotype materials.\",\n \"corpus_id\": 3731050,\n \"score\": 1\n },\n {\n \"doc_id\": \"28695856\",\n \"title\": \"Crystal structure of Yersinia pestis virulence factor YfeA reveals two polyspecific metal-binding sites.\",\n \"abstract\": \"Gram-negative bacteria use siderophores, outer membrane receptors, inner membrane transporters and substrate-binding proteins (SBPs) to transport transition metals through the periplasm. The SBPs share a similar protein fold that has undergone significant structural evolution to communicate with a variety of differentially regulated transporters in the cell. In Yersinia pestis, the causative agent of plague, YfeA (YPO2439, y1897), an SBP, is important for full virulence during mammalian infection. To better understand the role of YfeA in infection, crystal structures were determined under several environmental conditions with respect to transition-metal levels. Energy-dispersive X-ray spectroscopy and anomalous X-ray scattering data show that YfeA is polyspecific and can alter its substrate specificity. In minimal-media experiments, YfeA crystals grown after iron supplementation showed a threefold increase in iron fluorescence emission over the iron fluorescence emission from YfeA crystals grown from nutrient-rich conditions, and YfeA crystals grown after manganese supplementation during overexpression showed a fivefold increase in manganese fluorescence emission over the manganese fluorescence emission from YfeA crystals grown from nutrient-rich conditions. In all experiments, the YfeA crystals produced the strongest fluorescence emission from zinc and could not be manipulated otherwise. Additionally, this report documents the discovery of a novel surface metal-binding site that prefers to chelate zinc but can also bind manganese. Flexibility across YfeA crystal forms in three loops and a helix near the buried metal-binding site suggest that a structural rearrangement is required for metal loading and unloading.\",\n \"corpus_id\": 20248903,\n \"score\": 1\n },\n {\n \"doc_id\": \"28989710\",\n \"title\": \"Protein microcrystallography using synchrotron radiation.\",\n \"abstract\": \"The progress in X-ray microbeam applications using synchrotron radiation is beneficial to structure determination from macromolecular microcrystals such as small in meso crystals. However, the high intensity of microbeams causes severe radiation damage, which worsens both the statistical quality of diffraction data and their resolution, and in the worst cases results in the failure of structure determination. Even in the event of successful structure determination, site-specific damage can lead to the misinterpretation of structural features. In order to overcome this issue, technological developments in sample handling and delivery, data-collection strategy and data processing have been made. For a few crystals with dimensions of the order of 10 µm, an elegant two-step scanning strategy works well. For smaller samples, the development of a novel method to analyze multiple isomorphous microcrystals was motivated by the success of serial femtosecond crystallography with X-ray free-electron lasers. This method overcame the radiation-dose limit in diffraction data collection by using a sufficient number of crystals. Here, important technologies and the future prospects for microcrystallography are discussed.\",\n \"corpus_id\": 30687709,\n \"score\": 1\n },\n {\n \"doc_id\": \"29353938\",\n \"title\": \"Watching Proteins Function with Time-resolved X-ray Crystallography.\",\n \"abstract\": \"Macromolecular crystallography was immensely successful in the last two decades. To a large degree this success resulted from use of powerful third generation synchrotron X-ray sources. An expansive database of more than 100,000 protein structures, of which many were determined at resolution better than 2 Å, is available today. With this achievement, the spotlight in structural biology is shifting from determination of static structures to elucidating dynamic aspects of protein function. A powerful tool for addressing these aspects is time-resolved crystallography, where a genuine biological function is triggered in the crystal with a goal of capturing molecules in action and determining protein kinetics and structures of intermediates (Schmidt et al., 2005a; Schmidt 2008; Neutze and Moffat, 2012; Šrajer 2014). In this approach, short and intense X-ray pulses are used to probe intermediates in real time and at room temperature, in an ongoing reaction that is initiated synchronously and rapidly in the crystal. Time-resolved macromolecular crystallography with 100 ps time resolution at synchrotron X-ray sources is in its mature phase today, particularly for studies of reversible, light-initiated reactions. The advent of the new free electron lasers for hard X-rays (XFELs; 5-20 keV), which provide exceptionally intense, femtosecond X-ray pulses, marks a new frontier for time-resolved crystallography. The exploration of ultra-fast events becomes possible in high-resolution structural detail, on sub-picosecond time scales (Tenboer et al., 2014; Barends et al., 2015; Pande et al., 2016). We review here state-of-the-art time-resolved crystallographic experiments both at synchrotrons and XFELs. We also outline challenges and further developments necessary to broaden the application of these methods to many important proteins and enzymes of biomedical relevance.\",\n \"corpus_id\": 24074635,\n \"score\": 1\n },\n {\n \"doc_id\": \"29757285\",\n \"title\": \"Microfluidic Chips for In Situ Crystal X-ray Diffraction and In Situ Dynamic Light Scattering for Serial Crystallography.\",\n \"abstract\": \"This protocol describes fabricating microfluidic devices with low X-ray background optimized for goniometer based fixed target serial crystallography. The devices are patterned from epoxy glue using soft lithography and are suitable for in situ X-ray diffraction experiments at room temperature. The sample wells are lidded on both sides with polymeric polyimide foil windows that allow diffraction data collection with low X-ray background. This fabrication method is undemanding and inexpensive. After the sourcing of a SU-8 master wafer, all fabrication can be completed outside of a cleanroom in a typical research lab environment. The chip design and fabrication protocol utilize capillary valving to microfluidically split an aqueous reaction into defined nanoliter sized droplets. This loading mechanism avoids the sample loss from channel dead-volume and can easily be performed manually without using pumps or other equipment for fluid actuation. We describe how isolated nanoliter sized drops of protein solution can be monitored in situ by dynamic light scattering to control protein crystal nucleation and growth. After suitable crystals are grown, complete X-ray diffraction datasets can be collected using goniometer based in situ fixed target serial X-ray crystallography at room temperature. The protocol provides custom scripts to process diffraction datasets using a suite of software tools to solve and refine the protein crystal structure. This approach avoids the artefacts possibly induced during cryo-preservation or manual crystal handling in conventional crystallography experiments. We present and compare three protein structures that were solved using small crystals with dimensions of approximately 10-20 µm grown in chip. By crystallizing and diffracting in situ, handling and hence mechanical disturbances of fragile crystals is minimized. The protocol details how to fabricate a custom X-ray transparent microfluidic chip suitable for in situ serial crystallography. As almost every crystal can be used for diffraction data collection, these microfluidic chips are a very efficient crystal delivery method.\",\n \"corpus_id\": 21662166,\n \"score\": 1\n },\n {\n \"doc_id\": \"20526948\",\n \"title\": \"Assessment of occupational exposure to manganese and other metals in welding fumes by portable X-ray fluorescence spectrometer.\",\n \"abstract\": \"Elemental analysis of welding fume samples can be done using several laboratory-based techniques. However, portable measurement techniques could offer several advantages. In this study, we sought to determine whether the portable X-ray fluorescence spectrometer (XRF) is suitable for analysis of five metals (manganese, iron, zinc, copper, and chromium) on 37-mm polytetrafluoroethylene filters. Using this filter fitted on a cyclone in line with a personal pump, gravimetric samples were collected from a group of boilermakers exposed to welding fumes. We assessed the assumption of uniform deposition of these metals on the filters, and the relationships between measurement results of each metal obtained from traditional laboratory-based XRF and the portable XRF. For all five metals of interest, repeated measurements with the portable XRF at the same filter area showed good consistency (reliability ratios are equal or close to 1.0 for almost all metals). The portable XRF readings taken from three different areas of each filter were not significantly different (p-values = 0.77 to 0.98). This suggested that the metal rich PM(2.5) deposits uniformly on the samples collected using this gravimetric method. For comparison of the two XRFs, the results from the portable XRF were well correlated and highly predictive of those from the laboratory XRF. The Spearman correlation coefficients were from 0.325 for chromium, to 0.995 for manganese and 0.998 for iron. The mean differences as a percent of the mean laboratory XRF readings were also small (<5%) for manganese, iron, and copper. The differences were greater for zinc and chromium, which were present at very low amounts in our samples and below the limits of detection of the portable XRF for many of the samples. These five metals were moderately to strongly correlated with the total fine particle fraction on filters (Spearman rho = 0.41 for zinc to 0.97 for iron). Such strong correlations and comparable results suggested that the portable XRF could be used as an effective and reliable tool for exposure assessment in many studies.\",\n \"corpus_id\": 21130222,\n \"score\": 0\n },\n {\n \"doc_id\": \"21545119\",\n \"title\": \"Discrete, solvent-free alkaline-earth metal cations: metal···fluorine interactions and ROP catalytic activity.\",\n \"abstract\": \"Efficient protocols for the syntheses of well-defined, solvent-free cations of the large alkaline-earth (Ae) metals (Ca, Sr, Ba) and their smaller Zn and Mg analogues have been designed. The reaction of 2,4-di-tert-butyl-6-(morpholinomethyl)phenol ({LO(1)}H), 2-{[bis(2-methoxyethyl)amino]methyl}-4,6-di-tert-butylphenol ({LO(2)}H), 2-[(1,4,7,10-tetraoxa-13-azacyclopentadecan-13-yl)methyl]-4,6-di-tert-butylphenol ({LO(3)}H), and 2-[(1,4,7,10-tetraoxa-13-azacyclo-pentadecan-13-yl)methyl]-1,1,1,3,3,3-hexafluoropropan-2-ol ({RO(3)}H) with [H(OEt(2))(2)](+)[H(2)N{B(C(6)F(5))(3)}(2)](-) readily afforded the doubly acidic pro-ligands [{LO(1)}HH](+)[X](-) (1), [{LO(2)}HH](+)[X](-) (2), [{LO(3)}HH](+)[X](-) (3), and [{RO(3)}HH](+)[X](-) (4) ([X](-) = [H(2)N{B(C(6)F(5))(3)}(2)](-)). The addition of 2 to Ca[N(SiMe(3))(2)](2)(THF)(2) and Sr[N(SiMe(3))(2)](2)(THF)(2) yielded [{LO(2)}Ca(THF)(0.5)](+)[X](-) (5) and [{LO(2)}Sr(THF)](+)[X](-) (6), respectively. Alternatively, 5 could also be prepared upon treatment of {LO(2)}CaN(SiMe(3))(2) (7) with [H(OEt(2))(2)](+)[X](-). Complexes [{LO(3)}M](+)[X](-) (M = Zn, 8; Mg, 9; Ca, 10; Sr, 11; Ba, 12) and [{RO(3)}M](+)[X](-) (M = Zn, 13; Mg, 14; Ca, 15; Sr, 16; Ba, 17) were synthesized in high yields (70-90%) by reaction of 3 or 4 with the neutral precursors M[N(SiMe(3))(2)](2)(THF)(x) (M = Zn, Mg, x = 0; M = Ca, Sr, Ba, x = 2). All compounds were fully characterized by spectroscopic methods, and the solid-sate structures of compounds 1, 3, 7, 8, 13, 14, {15}(4)·3CD(2)Cl(2), {16}(4)·3CD(2)Cl(2), and {{17}(4)·EtOH}·3CD(2)Cl(2) were determined by X-ray diffraction crystallography. Whereas the complexes are monomeric in the case of Zn and Mg, they form bimetallic cations in the case of Ca, Sr and Ba; there is no contact between the metal and the weakly coordinating anion. In all metal complexes, the multidentate ligand is κ(6)-coordinated to the metal. Strong intramolecular M···F secondary interactions between the metal and F atoms from the ancillary ligands are observed in the structures of {15}(4)·3CD(2)Cl(2), {16}(4)·3CD(2)Cl(2), and {{17}(4)·EtOH}·3CD(2)Cl(2). VT (19)F{(1)H} NMR provided no direct evidence that these interactions are maintained in solution; nevertheless, significant Ae···F energies of stabilization of 25-26 (Ca, Ba) and 40 kcal·mol(-1) (Sr) were calculated by NBO analysis on DFT-optimized structures. The identity and integrity of the cationic complexes are preserved in solution in the presence of an excess of alcohol (BnOH, (i)PrOH) or L-lactide (L-LA). Efficient binary catalytic systems for the immortal ring-opening polymerization of L-LA (up to 3,000 equiv) are produced upon addition of an excess (5-50 equiv) of external protic nucleophilic agents (BnOH, (i)PrOH) to 8-12 or 13-17. PLLAs with M(n) up to 35,000 g·mol(-1) were produced in a very controlled fashion (M(w)/M(n) ≈ 1.10-1.20) and without epimerization. In each series of catalysts, the following order of catalytic activity was established: Mg ≪ Zn < Ca < Sr ≈ Ba; also, Ae complexes supported by the aryloxide ligand are more active than their parents supported by the fluorinated alkoxide ancillary, possibly owing to the presence of Ae···F interactions in the latter case. The rate law -d[L-LA]/dt = k(p)·[L-LA](1.0)·[16](1.0)·[BnOH](1.0) was established by NMR kinetic investigations, with the corresponding activation parameters ΔH(++) = 14.8(5) kcal·mol(-1) and ΔS(++) = -7.6(2.0) cal·K(-1)·mol(-1). DFT calculations indicated that the observed order of catalytic activity matches an increase of the L-LA coordination energy onto the cationic metal centers with parallel decrease of the positive metal charge.\",\n \"corpus_id\": 21502229,\n \"score\": 0\n },\n {\n \"doc_id\": \"23252592\",\n \"title\": \"Kinetic products in coordination networks: ab initio X-ray powder diffraction analysis.\",\n \"abstract\": \"Porous coordination networks are materials that maintain their crystal structure as molecular \\\"guests\\\" enter and exit their pores. They are of great research interest with applications in areas such as catalysis, gas adsorption, proton conductivity, and drug release. As with zeolite preparation, the kinetic states in coordination network preparation play a crucial role in determining the final products. Controlling the kinetic state during self-assembly of coordination networks is a fundamental aspect of developing further functionalization of this class of materials. However, unlike for zeolites, there are few structural studies reporting the kinetic products made during self-assembly of coordination networks. Synthetic routes that produce the necessary selectivity are complex. The structural knowledge obtained from X-ray crystallography has been crucial for developing rational strategies for design of organic-inorganic hybrid networks. However, despite the explosive progress in the solid-state study of coordination networks during the last 15 years, researchers still do not understand many chemical reaction processes because of the difficulties in growing single crystals suitable for X-ray diffraction: Fast precipitation can lead to kinetic (metastable) products, but in microcrystalline form, unsuitable for single crystal X-ray analysis. X-ray powder diffraction (XRPD) routinely is used to check phase purity, crystallinity, and to monitor the stability of frameworks upon guest removal/inclusion under various conditions, but rarely is used for structure elucidation. Recent advances in structure determination of microcrystalline solids from ab initio XRPD have allowed three-dimensional structure determination when single crystals are not available. Thus, ab initio XRPD structure determination is becoming a powerful method for structure determination of microcrystalline solids, including porous coordination networks. Because of the great interest across scientific disciplines in coordination networks, especially porous coordination networks, the ability to determine crystal structures when the crystals are not suitable for single crystal X-ray analysis is of paramount importance. In this Account, we report the potential of kinetic control to synthesize new coordination networks and we describe ab initio XRPD structure determination to characterize these networks' crystal structures. We describe our recent work on selective instant synthesis to yield kinetically controlled porous coordination networks. We demonstrate that instant synthesis can selectively produce metastable networks that are not possible to synthesize by conventional solution chemistry. Using kinetic products, we provide mechanistic insights into thermally induced (573-723 K) (i.e., annealing method) structural transformations in porous coordination networks as well as examples of guest exchange/inclusion reactions. Finally, we describe a memory effect that allows the transfer of structural information from kinetic precursor structures to thermally stable structures through amorphous intermediate phases. We believe that ab initio XRPD structure determination will soon be used to investigate chemical processes that lead intrinsically to microcrystalline solids, which up to now have not been fully understood due to the unavailability of single crystals. For example, only recently have researchers used single-crystal X-ray diffraction to elucidate crystal-to-crystal chemical reactions taking place in the crystalline scaffold of coordination networks. The potential of ab initio X-ray powder diffraction analysis goes beyond single-crystal-to-single-crystal processes, potentially allowing members of this field to study intriguing in situ reactions, such as reactions within pores.\",\n \"corpus_id\": 36488253,\n \"score\": 0\n },\n {\n \"doc_id\": \"23737050\",\n \"title\": \"X-ray crystallography of viruses.\",\n \"abstract\": \"For about 30 years X-ray crystallography has been by far the most powerful approach for determining virus structures at close to atomic resolutions. Information provided by these studies has deeply and extensively enriched and shaped our vision of the virus world. In turn, the ever increasing complexity and size of the virus structures being investigated have constituted a major driving force for methodological and conceptual developments in X-ray macromolecular crystallography. Landmarks of new virus structures determinations, such as the ones from the first animal viruses or from the first membrane-containing viruses, have often been associated to methodological breakthroughs in X-ray crystallography. In this chapter we present the common ground of proteins and virus crystallography with an emphasis in the peculiarities of virus studies. For example, the solution of the phase problem, a central issue in X-ray diffraction, has benefited enormously from the presence of non-crystallographic symmetry in virus crystals.\",\n \"corpus_id\": 24255211,\n \"score\": 0\n },\n {\n \"doc_id\": \"23912807\",\n \"title\": \"Macromolecular crowding: chemistry and physics meet biology (Ascona, Switzerland, 10-14 June 2012).\",\n \"abstract\": \"More than 60 years of biochemical and biophysical studies have accustomed us to think of proteins as highly purified entities that act in isolation, more or less freely diffusing until they find their cognate partner to bind to. While in vitro experiments that reproduce these conditions largely remain the only way to investigate the intrinsic properties of molecules, this approach ignores an important factor: in their natural milieu , proteins are surrounded by several other molecules of different chemical nature, and this crowded environment can considerably modify their behaviour. About 40% of the cellular volume on average is occupied by all sorts of molecules. Furthermore, biological macromolecules live and operate in an extremely structured and complex environment within the cell (endoplasmic reticulum, Golgi apparatus, cytoskeletal structures, etc). Hence, to further complicate the picture, the interior of the cell is by no means a simply crowded medium, rather, a most crowded and confining one. In recent times, several approaches have been developed in the attempt to take into account important factors such as the ones mentioned above, at both theoretical and experimental levels, so that this field of research is now emerging as one of the most thriving in molecular and cell biology (see figure 1). [ Formula: see text] Figure 1. Left: number of articles containing the word 'crowding' as a keyword limited to the biological and chemical science domains (source: ISI Web of Science). The arrow flags the 2003 'EMBO Workshop on Biological Implications of Macromolecular Crowding' (Embo, 2012). Right: number of citations to articles containing the word 'crowding' limited to the same domains (bars) and an exponential regression curve (source: Elsevier Scopus). To promote the importance of molecular crowding and confinement and provide researchers active in this field an interdisciplinary forum for meeting and exchanging ideas, we recently organized an international conference held in Ascona from 10 to 14 June 2012. In the unique scenario of the Maggiore lake and absorbed in the magic atmosphere of the Centro Stefano Franscini (CSF) at Monte Verità, we enjoyed three-and-a-half days of intense and inspiring activity, where not only many of the most prominent scientists working on macromolecular crowding, but also experts in closely related fields such as colloids and soft matter presented their work. The meeting was intended and has been organized to bring theoreticians and experimentalists together in the attempt to promote an active dialogue. Moreover, we wanted different disciplines to be represented, notably physics and chemistry, besides biology, as cross-fertilization is proving an increasingly fundamental source of inspiration and advancement. This issue of Physical Biology (PB) features a selection of the oral contributions presented at the conference, expanded in the form of research or review articles. PB, one of the scientific journals of the Institute of Physics (IOP), is one of the most dynamic and lively forums active at the interface between biology on one side, and physics and mathematics on the other. As its mission is stated by IOP, PB 'focuses on research in which physics-based approaches lead to new insights into biological systems at all scales of space and time, and all levels of complexity'. For these reasons, and also in view of its high reputation and broad readership, PB appears to be the ideal place for disseminating the thriving pieces of research presented at the conference. We are extremely grateful to PB and its kind and efficient editorial staff who helped make this issue a great scientific follow-up to the conference. The opening lecture of the conference, the first of four day-opening keynote lectures, was given by Allen P Minton from NIH (USA), possibly the most influential among the pioneers in the field. He provided a lucid and well-thought-out overview of the concept of macromolecular crowding through an exhaustive chronological account of the major milestones. It is clear that the concept of excluded volume as a key factor remains central to the concept of molecular crowding. As a consequence, simple descriptive paradigms borrowed essentially from colloid physics may still provide useful tools to understand the subtle effects of crowding and confinement in living matter. The contiguity between crowding, colloids and soft matter further emerged as an important concept in the course of the conference in several theoretical lectures and a few experimental ones. Dave Thirumalai, from the University of Maryland (USA), one of the most active theoreticians in the field of theoretical biophysics, outlined scaling theories, concepts from colloid literature and different simulation techniques to describe scenarios for crowding-induced changes in the structure and dynamics of proteins and RNA. In particular, he showed the importance of the shape of crowding particles in affecting folding oligomerization of amyloidogenic peptides. Johannes Schöneberg, from IMPRS, Mathematics Institute (Germany), illustrated ReaDDy , a newly developed particle-based simulation software tool for reaction-diffusion dynamics, developed in the group of Frank Noe at EMPRS. He showed that ReaDDy makes it possible to bridge the gap between soft matter and molecular dynamics (MD) simulations on the one hand and particle-based stochastic reaction-diffusion simulations on the other. We asked Johannes to organize a tutorial session to lead interested participants into the package and 'get their hands wet' under the guidance of the developers. The tutorial session was indeed successful and the broad possibilities offered by the simulation toolkit appeared to be clear to the participants. Paolo De Los Rios, from the Ecole Polytechnique Fédérale de Lausanne (EPFL, Switzerland), examined the complexity of the effects caused by crowding conditions from the point of view of statistical physics. Starting from a modification of the well-known Smoluchowski approach to calculate the encounter rate of diffusion-limited reactions, he showed how more realistic situations accounting for crowding effects could be treated equally well on the same theoretical grounds. This talk marked an important point in the conference as it reinforced the idea that simple models of theoretical physics still have the power to provide inspiring results in spite of the intrinsic simplifications of such theoretical approaches. Along the same lines, Nicolas Dorsaz, from the University of Cambridge (UK), proposed an extension of the Smoluchowski framework that incorporates repulsive and attracting interactions between the reactants. This approach was illustrated by reaction rates obtained from event-driven Brownian dynamics and dynamical Monte Carlo simulations. Another striking example of the physical subtleties associated with modelling crowding effects was provided by Jeffrey Skolnick, from the Georgia Institute of Technology (USA). He examined the role of hydrodynamic interactions in the self-organization of biological assemblies in the presence of crowding. His results strongly suggest that hydrodynamic interactions greatly affect the kinetics of self-assembly reactions, so that including them in the picture appears crucial for understanding the dynamics of biological systems in vivo . Margareth Cheung, from the University of Houston (USA), emphasized that how the crowded environment inside a cell affects the structural conformation of a protein with a spherical shape is a vital question because the geometry of proteins and protein-protein complexes are far from globules in vivo . Her work demonstrates the malleability of 'native' proteins and implies that crowding-induced shape changes may be important for protein function and malfunction in vivo . Huan-Xiang Zhou, from the Florida State University (USA), focused on atomistic simulations of protein folding and binding under crowding conditions. His lab has developed a post-processing method that allows the atomistic representation of proteins in folding and binding processes under crowding. A comparison with experimental results was also presented. Other lecturers pointed out that there are still aspects not entirely explored in the effects of both crowding and confinement. As suggested in the talk by Gary Pielak, from the University of North Carolina (USA), the currently used synthetic crowding agents are far from being satisfactory in replicating naturally occurring effects associated with crowded environments. For example, non-specific binding seems to play a subtle role in the cell, as natural macromolecules can induce both stabilization and destabilization when used as crowders. It is indeed possible to fine-tune the effect of proteins, as crowders, on the stability of other proteins. Another aspect that became clear is that new, more powerful methods need to be developed to study the effect of crowding, but even more to compare crowding and confinement. Indeed, it appeared clear from the lecture by Pierandrea Temussi, from the University of Naples (Italy), that a reliable comparison of the effects of crowding and confinement on the stability of proteins can only be based on the measurement of the whole stability curve of the same protein. Controversial aspects do not pertain only to the influence of crowding on protein stability, but also to aggregation phenomena in natural fluids. Domenico Sanfelice, from NIMR (London, UK), reported an interesting case of the apparent influence of crowding on aggregation. Hen egg white, a possible natural medium to study macromolecules in crowded conditions can dramatically increase the aggregation kinetics of proteins with an inbuilt tendency to associate. By carefully dissecting the phenomenology, it was shown that only part of this effect is due to crowding, while another factor playing an important role is the interaction with proteins from the milieu . In other words, high-molecular-weight glycoproteins can act as efficient molecular seeds for aggregation. A special topic of great relevance in the conference appeared to be the direct study of crowding in living systems. Alan Verkman, from the University of California, San Francisco (USA), one of the world's leading scientific personalities in the field of experimental investigation of crowding and confinement, was invited to give the second plenary lecture devoted to the experimental study of crowding effects in vivo . In his keynote lecture, Dr Verkman led us on a wide and compelling tour, exploring the main experimental approaches to study molecular crowding in and around cells. After a thorough examination of methods such as fluorescence recovery after photo-bleaching, fluorescence correlation spectroscopy, photo-activation localization microscopy and stochastic reconstruction microscopy, he concluded that the general consensus emerging from experimental studies is that the notion of universally anomalous diffusion in and around cells as a consequence of molecular crowding may not be correct, and that the slowing of diffusion in cells is less marked than has been widely assumed and can be simply described through a five- to sixfold reduction of the normal diffusion coefficient. A Soranno, from the University of Zürich (Switzerland), described how, by employing FRET measurements, it is possible to quantify the effect of molecular crowding on the dimensions of the highly charged, intrinsically disordered protein human prothymosin alpha. For a large variety of polymeric crowders (PEG, PVP, Ficoll, Dextran, PVA, PAA), a collapse of the polypeptide chain is observed with increasing polymer size and polymer concentration. The largest extent of collapse is observed for polymer radii comparable to the dimensions of the protein, in agreement with theoretical considerations. For his contribution, A Soranno was awarded the CSF Award for the best contributed talk. In his most inspiring talk, Clifford Brangwynne, from Princeton University (USA), drew attention to very important objects, namely Ribonucleoprotein (RNP) bodies. These are non-membrane-bound macromolecular assemblies that form from the dynamic interactions of RNA and proteins. The assembly of RNP bodies may sensitively depend on the biophysical features of the surrounding cytoplasm, including the degree of crowding, transport coefficients and mechanical properties. This dependency may have important implications for the RNA processing reactions involved in fundamental biological processes such as developmental cell growth. Remarkably, Brangwynne showed how RNPs behave in the cell as liquid droplets, pointing to a possible entirely new means that the cell could use to control and fine-tune its internal processes, in fact, more than that, a completely unexplored, new state of organization of living matter, and a functional one. Giuseppe Zaccai, from Institut Laue Langevin, Grenoble (France), showed that protein dynamics is more sensitive than structure to environmental factors such as crowding, solvent, temperature or pressure. Furthermore, he convincingly explained how neutron scattering provides unique experimental data to underpin MD calculations in this context. Following up on environment-induced modulations of protein functional dynamics, Ruth Nussinov, from Tel Aviv University (Israel), addressed the important problem of whether cellular signals can travel long distances in a crowded environment. She proposed a model based on the evolution of at least three properties: a modular functional organization of the cellular network, sequences in some key regions of proteins, such as linkers or loops, and compact interactions between proteins, possibly favoured by a crowded environment. The workshop ended on a keynote lecture by Jean-Marie Lehn, from the Université de Strasbourg (France). Lehn, 1987 Nobel Laureate in chemistry, offered a 'supramolecular view' of the field of molecular interactions. Supramolecular chemistry explores the design of systems undergoing self-organization , i.e. systems capable of generating well-defined functional supramolecular architectures by self-assembling from their components, thus behaving as programmed chemical systems . Chemistry may therefore be considered an information science , the science of informed matter. Supramolecular chemistry is intrinsically a dynamic chemistry in view of the ability of the interactions connecting the molecular components of a supramolecular entity and the resulting ability of supramolecular species to exchange their constituents. The same holds for molecular chemistry when the molecular entity contains covalent bonds that may form and break reversibly, so as to allow a continuous change in constitution by the reorganization and exchange of building blocks. These features define a constitutional dynamic chemistry (CDC) on both the molecular and supramolecular levels. CDC takes advantage of dynamic constitutional diversity to allow variation and selection in response to either internal or external factors to achieve adaptation . The merging of the features-information and programmability, dynamics and reversibility, constitution and structural diversity-points towards the emergence of adaptive and evolutive chemistry . The whole workshop could have not taken place without the help of the Centro Stefano Franscini. The CSF is the congress centre of the Swiss Federal Institute of Technology of Zurich (ETH Zurich) and has been situated at Monte Verità since 1989. It is an ideal meeting point for all members of the international scientific community who wish to discuss the state-of-the-art and new challenges of any field of research. The CSF supports 20-25 international conferences every year and, since 2010, up to ten winter doctoral schools1. The competence and professionalism of the staff were at the same level of beauty and inspiring character as that of Monte Verità. A meeting of this sort, if successful, leaves the audience with more open questions than settled answers, and this was definitely the case for Crowding 2012. Excluded volume is clearly a fundamental concept that has allowed crowding, a very familiar concept in soft matter, to enter into the domain of biological sciences. However, the complexity of the biological milieu calls for more refined descriptions. What is the role of electrostatic and electrodynamic interactions? What is the role of hydrodynamics interactions? To what extent does the strong spatial inhomogeneity (clustering of molecules, cellular compartmentalization, etc) have to be taken into account? Or, more generally, what are the minimal elements that prove crucial to describe reactions within a cell? How does the diffusion proceed (diffusion, slow diffusion, sub-diffusion) given that the experimental evidences are still controversial? In conclusion, we knew that allowing scientists with very different backgrounds and ideas to mingle was a hazardous attempt. Despite that, the workshop turned out to be a very successful experiment, which was highly enjoyed both by the participants and the organizers. Discussions sparked regularly among ever-changing groups, comprising senior scientists and students, despite the rather tight schedule, adding to the sense of fulfilment ignited by the outstanding level of the presentations. Given the success of the meeting Crowding 2012, a new event has been organized and will take place on the same themes during fall 2013, this time in the beautiful scenery of the Loire valley in France. The workshop 'Macromolecular crowding effects in cell biology: models and experiments' will be held on the CNRS campus in Orléans, France, on 24-25 October 2013. More information can be found on the workshop website: http://dirac.cnrs-orleans.fr/∼piazza/. 1Source: www.csf.ethz.ch/\",\n \"corpus_id\": 3008401,\n \"score\": 0\n },\n {\n \"doc_id\": \"25604506\",\n \"title\": \"X-ray crystallography and its impact on understanding bacterial cell wall remodeling processes.\",\n \"abstract\": \"The molecular structure of matter defines its properties and function. This is especially true for biological macromolecules such as proteins, which participate in virtually all biochemical processes. A three dimensional structural model of a protein is thus essential for the detailed understanding of its physiological function and the characterization of essential properties such as ligand binding and reaction mechanism. X-ray crystallography is a well-established technique that has been used for many years, but it is still by far the most widely used method for structure determination. A particular strength of this technique is the elucidation of atomic details of molecular interactions, thus providing an invaluable tool for a multitude of scientific projects ranging from the structural classification of macromolecules over the validation of enzymatic mechanisms or the understanding of host-pathogen interactions to structure-guided drug design. In the first part of this review, we describe essential methodological and practical aspects of X-ray crystallography. We provide some pointers that should allow researchers without a background in structural biology to assess the overall quality and reliability of a crystal structure. To highlight its potential, we then survey the impact X-ray crystallography has had on advancing an understanding of a class of enzymes that modify the bacterial cell wall. A substantial number of different bacterial amidase structures have been solved, mostly by X-ray crystallography. Comparison of these structures highlights conserved as well as divergent features. In combination with functional analyses, structural information on these enzymes has therefore proven to be a valuable template not only for understanding their mechanism of catalysis, but also for targeted interference with substrate binding.\",\n \"corpus_id\": 205290612,\n \"score\": 0\n },\n {\n \"doc_id\": \"26671943\",\n \"title\": \"Sample preparation of biological macromolecular assemblies for the determination of high-resolution structures by cryo-electron microscopy.\",\n \"abstract\": \"Single particle cryo-EM has recently developed into a powerful tool to determine the 3D structure of macromolecular complexes at near-atomic resolution, which allows structural biologists to build atomic models of proteins. All technical aspects of cryo-EM technology have been considerably improved over the last two decades, including electron microscopic hardware, image processing software and the ever growing speed of computers. This leads to a more widespread use of the technique, and it can be anticipated that further automation of electron microscopes and image processing tools will soon fully shift the focus away from the technological aspects, onto biological questions that can be answered. In single particle cryo-EM, no crystals of a macromolecule are required. In contrast to X-ray crystallography, this significantly facilitates structure determination by cryo-EM. Nevertheless, a relatively high level of biochemical control is still essential to obtain high-resolution structures by cryo-EM, and it can be anticipated that the success of the cryo-EM technology goes hand in hand with further developments of sample purification and preparation techniques. This will allow routine high-resolution structure determination of the many macromolecular complexes of the cell that until now represent evasive targets for X-ray crystallographers. Here we discuss the various biochemical tools that are currently available and the existing sample purification and preparation techniques for cryo-EM grid preparation that are needed to obtain high-resolution images for structure determination.\",\n \"corpus_id\": 23067203,\n \"score\": 0\n },\n {\n \"doc_id\": \"27077331\",\n \"title\": \"The collection of MicroED data for macromolecular crystallography.\",\n \"abstract\": \"The formation of large, well-ordered crystals for crystallographic experiments remains a crucial bottleneck to the structural understanding of many important biological systems. To help alleviate this problem in crystallography, we have developed the MicroED method for the collection of electron diffraction data from 3D microcrystals and nanocrystals of radiation-sensitive biological material. In this approach, liquid solutions containing protein microcrystals are deposited on carbon-coated electron microscopy grids and are vitrified by plunging them into liquid ethane. MicroED data are collected for each selected crystal using cryo-electron microscopy, in which the crystal is diffracted using very few electrons as the stage is continuously rotated. This protocol gives advice on how to identify microcrystals by light microscopy or by negative-stain electron microscopy in samples obtained from standard protein crystallization experiments. The protocol also includes information about custom-designed equipment for controlling crystal rotation and software for recording experimental parameters in diffraction image metadata. Identifying microcrystals, preparing samples and setting up the microscope for diffraction data collection take approximately half an hour for each step. Screening microcrystals for quality diffraction takes roughly an hour, and the collection of a single data set is ∼10 min in duration. Complete data sets and resulting high-resolution structures can be obtained from a single crystal or by merging data from multiple crystals.\",\n \"corpus_id\": 24255876,\n \"score\": 0\n },\n {\n \"doc_id\": \"29588032\",\n \"title\": \"Xenon-Protein Interactions: Characterization by X-Ray Crystallography and Hyper-CEST NMR.\",\n \"abstract\": \"The physiological activity of xenon has long been recognized, though the exact nature of its interactions with biomolecules remains poorly understood. Xe is an inert noble gas, but can act as a general anesthetic, most likely by binding internal hydrophobic cavities within proteins. Understanding Xe-protein interactions, therefore, can provide crucial insight regarding the mechanism of Xe anesthesia and potentially other general anesthetic agents. Historically, Xe-protein interactions have been studied primarily through X-ray crystallography and nuclear magnetic resonance (NMR). In this chapter, we first describe our methods for preparing Xe derivatives of protein crystals and identifying Xe-binding sites. Second, we detail our procedure for 129Xe hyper-CEST NMR spectroscopy, a versatile NMR technique well suited for characterizing the weak, transient nature of Xe-protein interactions.\",\n \"corpus_id\": 4385000,\n \"score\": 0\n }\n]","isConversational":false}}},{"rowIdx":90,"cells":{"query":{"kind":"string","value":"{\n \"doc_id\": \"26390853\",\n \"title\": \"Cryo-EM and the elucidation of new macromolecular structures: Random Conical Tilt revisited.\",\n \"abstract\": \"Cryo-Electron Microscopy (cryo-EM) of macromolecular complexes is a fundamental structural biology technique which is expanding at a very fast pace. Key to its success in elucidating the three-dimensional structure of a macromolecular complex, especially of small and non-symmetric ones, is the ability to start from a low resolution map, which is subsequently refined with the actual images collected at the microscope. There are several methods to produce this first structure. Among them, Random Conical Tilt (RCT) plays a prominent role due to its unbiased nature (it can create an initial model based on experimental measurements). In this article, we revise the fundamental mathematical expressions supporting RCT, providing new expressions handling all key geometrical parameters without the need of intermediate operations, leading to improved automation and overall reliability, essential for the success of cryo-EM when analyzing new complexes. We show that the here proposed RCT workflow based on the new formulation performs very well in practical cases, requiring very few image pairs (as low as 13 image pairs in one of our examples) to obtain relevant 3D maps.\",\n \"corpus_id\": 13916472\n}"},"candidates":{"kind":"list like","value":[{"doc_id":"20888964","title":"The orthogonal tilt reconstruction method.","abstract":"Generating reliable initial models for novel asymmetric molecules, particularly heterogeneous ones, remains a major challenge in cryo-electron microscopy. Geometric reconstruction methods, relying on the ability to tilt the microscope stage to obtain two or more views of each molecule, are arguably the most robust for these types of samples as they generate independent reconstructions for each characteristic view obtained. Random Conical Tilt (RCT) is the classic geometric reconstruction method. Pairs of images are collected at high tilt (around 50°) and 0°. The latter are used to sort the data into characteristic views of the molecule and the former are used for their reconstruction. RCT's greatest strength is its ability to generate structures regardless of the number of orientations adopted by the sample on the support. Its major drawback stems from the limited tilt of the microscope stage; this results in an incomplete sampling of the structure in Fourier space and artifacts in its real space representation. Orthogonal Tilt Reconstruction (OTR), a modification of this data collection strategy, results in fully sampled structures. It relies on collecting data at -45° and +45° and treating the tilt pairs as equivalent to the ideal 0°/90° that cannot be collected directly in the microscope. OTR requires a sample that adopts a large number of orientations on the support. Here, the RCT and OTR methods are reviewed and their performances with a biological test sample are compared. The steps required to apply OTR are also discussed.","corpus_id":25782305,"score":2},{"doc_id":"21536134","title":"Validation of the orthogonal tilt reconstruction method with a biological test sample.","abstract":"Electron microscopy of frozen-hydrated samples (cryo-EM) can yield high resolution structures of macromolecular complexes by accurately determining the orientation of large numbers of experimental views of the sample relative to an existing 3D model. The \"initial model problem\", the challenge of obtaining these orientations ab initio, remains a major bottleneck in determining the structure of novel macromolecules, chiefly those lacking internal symmetry. We previously proposed a method for the generation of initial models--orthogonal tilt reconstruction (OTR)--that bypasses limitations inherent to the other two existing methods, random conical tilt (RCT) and angular reconstitution (AR). Here we present a validation of OTR with a biological test sample whose structure was previously solved by RCT: the complex between the yeast exosome and the subunit Rrp44. We show that, as originally demonstrated with synthetic data, OTR generates initial models that do not exhibit the \"missing cone\" artifacts associated with RCT and show an isotropic distribution of information when compared with the known structure. This eliminates the need for further user intervention to solve these artifacts and makes OTR ideal for automation and the analysis of heterogeneous samples. With the former in mind, we propose a set of simple quantitative criteria that can be used, in combination, to select from a large set of initial reconstructions a subset that can be used as reliable references for refinement to higher resolution.","corpus_id":24370377,"score":2},{"doc_id":"23142631","title":"Automated correlation of single particle tilt pairs for Random Conical Tilt and Orthogonal Tilt Reconstructions.","abstract":"One of the major methodological challenges in single particle electron microscopy is obtaining initial reconstructions which represent the structural heterogeneity of the dataset. Random Conical Tilt and Orthogonal Tilt Reconstruction techniques in combination with 3D alignment and classification can be used to obtain initial low-resolution reconstructions which represent the full range of structural heterogeneity of the dataset. In order to achieve statistical significance, however, a large number of 3D reconstructions, and, in turn, a large number of tilted image pairs are required. The extraction of single particle tilted image pairs from micrographs can be tedious and time-consuming, as it requires intensive user input even for semi-automated approaches. To overcome the bottleneck of manual selection of a large number of tilt pairs, we developed an algorithm for the correlation of single particle images from tilted image pairs in a fully automated and user-independent manner. The algorithm reliably correlates correct pairs even from noisy micrographs. We further demonstrate the applicability of the algorithm by using it to obtain initial references both from negative stain and unstained cryo datasets.","corpus_id":32528253,"score":2},{"doc_id":"19767196","title":"Exploring conformational modes of macromolecular assemblies by multiparticle cryo-EM.","abstract":"Single particle cryo-electron microscopy (cryo-EM) is a technique aimed at structure determination of large macromolecular complexes in their unconstrained, physiological conditions. The power of the method has been demonstrated in selected studies where for highly symmetric molecules the resolution attained permitted backbone tracing. However, most molecular complexes appear to exhibit intrinsic conformational variability necessary to perform their functions. Therefore, it is now increasingly recognized that sample heterogeneity constitutes a major methodological challenge for cryo-EM. To overcome it dedicated experimental and particularly computational multiparticle approaches have been developed. Their applications point to the future of cryo-EM as an experimental method uniquely suited to visualize the conformational modes of large macromolecular complexes and machines.","corpus_id":39306886,"score":1},{"doc_id":"21490573","title":"Single particle electron microscopy reconstruction of the exosome complex using the random conical tilt method.","abstract":"Single particle electron microscopy (EM) reconstruction has recently become a popular tool to get the three-dimensional (3D) structure of large macromolecular complexes. Compared to X-ray crystallography, it has some unique advantages. First, single particle EM reconstruction does not need to crystallize the protein sample, which is the bottleneck in X-ray crystallography, especially for large macromolecular complexes. Secondly, it does not need large amounts of protein samples. Compared with milligrams of proteins necessary for crystallization, single particle EM reconstruction only needs several micro-liters of protein solution at nano-molar concentrations, using the negative staining EM method. However, despite a few macromolecular assemblies with high symmetry, single particle EM is limited at relatively low resolution (lower than 1 nm resolution) for many specimens especially those without symmetry. This technique is also limited by the size of the molecules under study, i.e. 100 kDa for negatively stained specimens and 300 kDa for frozen-hydrated specimens in general. For a new sample of unknown structure, we generally use a heavy metal solution to embed the molecules by negative staining. The specimen is then examined in a transmission electron microscope to take two-dimensional (2D) micrographs of the molecules. Ideally, the protein molecules have a homogeneous 3D structure but exhibit different orientations in the micrographs. These micrographs are digitized and processed in computers as \"single particles\". Using two-dimensional alignment and classification techniques, homogenous molecules in the same views are clustered into classes. Their averages enhance the signal of the molecule's 2D shapes. After we assign the particles with the proper relative orientation (Euler angles), we will be able to reconstruct the 2D particle images into a 3D virtual volume. In single particle 3D reconstruction, an essential step is to correctly assign the proper orientation of each single particle. There are several methods to assign the view for each particle, including the angular reconstitution(1) and random conical tilt (RCT) method(2). In this protocol, we describe our practice in getting the 3D reconstruction of yeast exosome complex using negative staining EM and RCT. It should be noted that our protocol of electron microscopy and image processing follows the basic principle of RCT but is not the only way to perform the method. We first describe how to embed the protein sample into a layer of Uranyl-Formate with a thickness comparable to the protein size, using a holey carbon grid covered with a layer of continuous thin carbon film. Then the specimen is inserted into a transmission electron microscope to collect untilted (0-degree) and tilted (55-degree) pairs of micrographs that will be used later for processing and obtaining an initial 3D model of the yeast exosome. To this end, we perform RCT and then refine the initial 3D model by using the projection matching refinement method(3).","corpus_id":45189809,"score":1},{"doc_id":"23674685","title":"Cross-validation in cryo-EM-based structural modeling.","abstract":"Single-particle cryo-EM is a powerful approach to determine the structure of large macromolecules and assemblies thereof in many cases at subnanometer resolution. It has become popular to refine or flexibly fit atomic models into density maps derived from cryo-EM experiments. These density maps are typically significantly lower in resolution than electron density maps obtained from X-ray diffraction experiments, such that the number of parameters that need to be determined is much larger than the number of experimental observables. Overfitting and misinterpretation of the density, thus, become a serious problem. For diffraction data, a cross-validation approach was introduced almost 20 y ago; however, no such approach has been described yet for structure refinement against cryo-EM density maps, although the overfitting problem is, because of the lower resolution, significantly larger. We present a cross-validation approach for real-space refinement against cryo-EM density maps in analogy to cross-validation typically used in crystallography. Our approach is able to detect overfitting and allows for optimizing the choice of restraints used in the refinement. The approach is shown on three protein structures with simulated data and experimental data of the rotavirus double-layer particle. Because cross-validation requires splitting the dataset into at least two independent sets, we further present an approach to quantify correlations between the structure factor sets. This analysis is also helpful for other cross-validation applications, such as refinements against diffraction data or 3D reconstructions of cryo-EM density maps.","corpus_id":205256350,"score":1},{"doc_id":"25839831","title":"SubspaceEM: A fast maximum-a-posteriori algorithm for cryo-EM single particle reconstruction.","abstract":"Single particle reconstruction methods based on the maximum-likelihood principle and the expectation-maximization (E-M) algorithm are popular because of their ability to produce high resolution structures. However, these algorithms are computationally very expensive, requiring a network of computational servers. To overcome this computational bottleneck, we propose a new mathematical framework for accelerating maximum-likelihood reconstructions. The speedup is by orders of magnitude and the proposed algorithm produces similar quality reconstructions compared to the standard maximum-likelihood formulation. Our approach uses subspace approximations of the cryo-electron microscopy (cryo-EM) data and projection images, greatly reducing the number of image transformations and comparisons that are computed. Experiments using simulated and actual cryo-EM data show that speedup in overall execution time compared to traditional maximum-likelihood reconstruction reaches factors of over 300.","corpus_id":17850477,"score":1},{"doc_id":"27313000","title":"Implementation of a cryo-electron tomography tilt-scheme optimized for high resolution subtomogram averaging.","abstract":"Cryo-electron tomography (cryoET) allows 3D structural information to be obtained from cells and other biological samples in their close-to-native state. In combination with subtomogram averaging, detailed structures of repeating features can be resolved. CryoET data is collected as a series of images of the sample from different tilt angles; this is performed by physically rotating the sample in the microscope between each image. The angles at which the images are collected, and the order in which they are collected, together are called the tilt-scheme. Here we describe a \"dose-symmetric tilt-scheme\" that begins at low tilt and then alternates between increasingly positive and negative tilts. This tilt-scheme maximizes the amount of high-resolution information maintained in the tomogram for subsequent subtomogram averaging, and may also be advantageous for other applications. We describe implementation of the tilt-scheme in combination with further data-collection refinements including setting thresholds on acceptable drift and improving focus accuracy. Requirements for microscope set-up are introduced, and a macro is provided which automates the application of the tilt-scheme within SerialEM.","corpus_id":3910770,"score":1},{"doc_id":"27800126","title":"Cryo-electron Microscopy Analysis of Structurally Heterogeneous Macromolecular Complexes.","abstract":"Cryo-electron microscopy (cryo-EM) has for a long time been a technique of choice for determining structure of large and flexible macromolecular complexes that were difficult to study by other experimental techniques such as X-ray crystallography or nuclear magnetic resonance. However, a fast development of instruments and software for cryo-EM in the last decade has allowed that a large range of complexes can be studied by cryo-EM, and that their structures can be obtained at near-atomic resolution, including the structures of small complexes (e.g., membrane proteins) whose size was earlier an obstacle to cryo-EM. Image analysis to identify multiple coexisting structures in the same specimen (multiconformation reconstruction) is now routinely done both to solve structures at near-atomic resolution and to study conformational dynamics. Methods for multiconformation reconstruction and latest examples of their applications are the focus of this review.","corpus_id":15780788,"score":1},{"doc_id":"18274535","title":"Visualization of macromolecular complexes using cryo-electron microscopy with FEI Tecnai transmission electron microscopes.","abstract":"This protocol details the steps used for visualizing the frozen-hydrated grids as prepared following the accompanying protocol entitled 'Preparation of macromolecular complexes for visualization using cryo-electron microscopy.' This protocol describes how to transfer the grid to the microscope using a standard cryo-transfer holder or, alternatively, using a cryo-cartridge loading system, and how to collect low-dose data using an FEI Tecnai transmission electron microscope. This protocol also summarizes and compares the various options that are available in data collection for three-dimensional (3D) single-particle reconstruction. These options include microscope settings, choice of detectors and data collection strategies both in situations where a 3D reference is available and in the absence of such a reference (random-conical and common lines).","corpus_id":10724478,"score":0},{"doc_id":"20541504","title":"An approach for de novo structure determination of dynamic molecular assemblies by electron cryomicroscopy.","abstract":"Single-particle electron cryomicroscopy is a powerful method for three-dimensional (3D) structure determination of macromolecular assemblies. Here we address the challenge of determining a 3D structure in the absence of reference models. The 3D structures are determined by alignment and weighted averaging of densities obtained by native cryo random conical tilt (RCT) reconstructions including consideration of missing data. Our weighted averaging scheme (wRCT) offers advantages for potentially heterogeneous 3D densities of low signal-to-noise ratios. Sets of aligned RCT structures can also be analyzed by multivariate statistical analysis (MSA) to provide insights into snapshots of the assemblies. The approach is used to compute 3D structures of the Escherichia coli 70S ribosome and the human U4/U6.U5 tri-snRNP under vitrified unstained cryo conditions, and to visualize by 3D MSA the L7/L12 stalk of the 70S ribosome and states of tri-snRNP. The approach thus combines de novo 3D structure determination with an analysis of compositional and conformational heterogeneity.","corpus_id":261333,"score":0},{"doc_id":"20869255","title":"Obtaining high-resolution images of biological macromolecules by using a cryo-electron microscope with a liquid-helium cooled stage.","abstract":"To obtain high-resolution images of biological macromolecules, a cryo-electron microscope (cryo-EM) is useful to preserve the hydrated state of the molecules. In addition, the cryo-conditions reduce some of the electron radiation damage, although averaging is necessary to obtain the molecular resolution from biological macromolecules. For the averaging, the three reconstruction methods of electron crystallography, helical reconstruction, and single particle analysis facilitate the determination of the atomic models. Here we describe suitable techniques for high-resolution imaging in these three different methods, based on our experiences using cryo-EM with a liquid-helium cooled stage. Irradiation damage by the electron beam is the most serious problem in the structural analysis of a biological specimen, and we clearly show that further reduction of the specimen temperature, from liquid nitrogen to liquid helium temperature, improves the cryo-protection factor by at least two-fold for both glucose-embedded and frozen-hydrated specimens. We review the image processing, and then discuss the future prospects of cryo-EM.","corpus_id":31986896,"score":0},{"doc_id":"20885381","title":"Cryo-EM of macromolecular assemblies at near-atomic resolution.","abstract":"With single-particle electron cryomicroscopy (cryo-EM), it is possible to visualize large, macromolecular assemblies in near-native states. Although subnanometer resolutions have been routinely achieved for many specimens, state of the art cryo-EM has pushed to near-atomic (3.3-4.6 Å) resolutions. At these resolutions, it is now possible to construct reliable atomic models directly from the cryo-EM density map. In this study, we describe our recently developed protocols for performing the three-dimensional reconstruction and modeling of Mm-cpn, a group II chaperonin, determined to 4.3 Å resolution. This protocol, utilizing the software tools EMAN, Gorgon and Coot, can be adapted for use with nearly all specimens imaged with cryo-EM that target beyond 5 Å resolution. Additionally, the feature recognition and computational modeling tools can be applied to any near-atomic resolution density maps, including those from X-ray crystallography.","corpus_id":34769448,"score":0},{"doc_id":"20887855","title":"GraFix: stabilization of fragile macromolecular complexes for single particle cryo-EM.","abstract":"Here, we review the GraFix (Gradient Fixation) method to purify and stabilize macromolecular complexes for single particle cryo-electron microscopy (cryo-EM). During GraFix, macromolecules undergo a weak, intramolecular chemical cross-linking while being purified by density gradient ultracentrifugation. GraFix-stabilized particles can be used directly for negative-stain cryo-EM or, after a brief buffer-exchange step, for unstained cryo-EM. This highly reproducible method has proved to dramatically reduce problems in heterogeneity due to particle dissociation during EM grid preparation. Additionally, there is often an appreciable increase in particles binding to the carbon support film. This and the fact that binding times can be drastically increased, with no apparent disruption of the native structures of the macromolecules, makes GraFix a method of choice when preparing low-abundance complexes for cryo-EM. The higher sample quality following GraFix purification is evident when examining raw images, which usually present a low background of fragmented particles, good particle dispersion, and high-contrast, well-defined particles. Setting up the GraFix method is straightforward, and the resulting improvement in sample homogeneity has been beneficial in successfully obtaining the 3D structures of numerous macromolecular complexes by cryo-EM in the past few years.","corpus_id":30501335,"score":0},{"doc_id":"21089695","title":"[A review of automatic particle recognition in Cryo-EM images].","abstract":"Advances in cryo-electron microscopy (Cryo-EM) and single-particle reconstruction have led to increasingly high resolutions of macromolecular three-dimensional reconstruction. However, for keeping up the continuing improvements in resolution, it is necessary to increase the number of particles included in performing reconstructions. Manual selection of particles, even assisted by computer, is a bottleneck of single-particle reconstruction. Cryo-EM image has low signal-to-noise ratio and low contrast, which leads to difficulty in particle picking. Various approaches have been developed to address the problem of automatic particle. This paper describes the application of template-based method, edge based method, feature-based method, neural network, DoG-based and simulated annealing approach in particle picking. The characteristics of various approaches are discussed, and the future development is presented.","corpus_id":38932072,"score":0},{"doc_id":"21296162","title":"Modeling protein structure at near atomic resolutions with Gorgon.","abstract":"Electron cryo-microscopy (cryo-EM) has played an increasingly important role in elucidating the structure and function of macromolecular assemblies in near native solution conditions. Typically, however, only non-atomic resolution reconstructions have been obtained for these large complexes, necessitating computational tools for integrating and extracting structural details. With recent advances in cryo-EM, maps at near-atomic resolutions have been achieved for several macromolecular assemblies from which models have been manually constructed. In this work, we describe a new interactive modeling toolkit called Gorgon targeted at intermediate to near-atomic resolution density maps (10-3.5 Å), particularly from cryo-EM. Gorgon's de novo modeling procedure couples sequence-based secondary structure prediction with feature detection and geometric modeling techniques to generate initial protein backbone models. Beyond model building, Gorgon is an extensible interactive visualization platform with a variety of computational tools for annotating a wide variety of 3D volumes. Examples from cryo-EM maps of Rotavirus and Rice Dwarf Virus are used to demonstrate its applicability to modeling protein structure.","corpus_id":330872,"score":0},{"doc_id":"21336521","title":"Almost lost in translation. Cryo-EM of a dynamic macromolecular complex: the ribosome.","abstract":"Ribosomes are dynamic biological machines that perform numerous tasks during translation, the biosynthesis of proteins. Translocation, the movement of transfer RNAs (tRNAs) and messenger RNA (mRNA) to progress in the reading frame of codons in the mRNA, takes place after the addition of each amino acid. This process involves large ribosome conformational changes, where tRNAs proceed through intermediate states. The structural characterization of these translocation intermediates has remained elusive. Cryo-electron microscopy (cryo-EM) produces three-dimensional averages, and translocating ribosomes poise distinct conformational states, and hence, structurally heterogeneous populations. During the last decade, the quest for visualization of translocation intermediates has progressed together with the development of classification tools in cryo-EM. Some of these new tools have recently been tested in ribosomal translocation, uncovering a clearer picture of the process. This success goes along with the latest advances in cryo-EM and illustrates how the technique offers multiple possibilities for studying macromolecular complexes engaged in dynamic reactions.","corpus_id":26027815,"score":0},{"doc_id":"21385038","title":"A blind deconvolution approach for improving the resolution of cryo-EM density maps.","abstract":"Cryo-electron microscopy (cryo-EM) plays an increasingly prominent role in structure elucidation of macromolecular assemblies. Advances in experimental instrumentation and computational power have spawned numerous cryo-EM studies of large biomolecular complexes resulting in the reconstruction of three-dimensional density maps at intermediate and low resolution. In this resolution range, identification and interpretation of structural elements and modeling of biomolecular structure with atomic detail becomes problematic. In this article, we present a novel algorithm that enhances the resolution of intermediate- and low-resolution density maps. Our underlying assumption is to model the low-resolution density map as a blurred and possibly noise-corrupted version of an unknown high-resolution map that we seek to recover by deconvolution. By exploiting the nonnegativity of both the high-resolution map and blur kernel, we derive multiplicative updates reminiscent of those used in nonnegative matrix factorization. Our framework allows for easy incorporation of additional prior knowledge such as smoothness and sparseness, on both the sharpened density map and the blur kernel. A probabilistic formulation enables us to derive updates for the hyperparameters; therefore, our approach has no parameter that needs adjustment. We apply the algorithm to simulated three-dimensional electron microscopic data. We show that our method provides better resolved density maps when compared with B-factor sharpening, especially in the presence of noise. Moreover, our method can use additional information provided by homologous structures, which helps to improve the resolution even further.","corpus_id":206154292,"score":0},{"doc_id":"21845206","title":"Near-atomic-resolution cryo-EM for molecular virology.","abstract":"Electron cryo-microscopy (cryo-EM) is a technique in structural biology that is widely used to solve the three-dimensional structures of macromolecular assemblies, close to their biological and solution conditions. Recent improvements in cryo-EM and single-particle reconstruction methodologies have led to the determination of several virus structures at near-atomic resolution (3.3 - 4.6 Å). These cryo-EM structures not only resolve the Cα backbones and side-chain densities of viral capsid proteins, but also suggest functional roles that the protein domains and some key amino acid residues play. This paper reviews the recent advances in near-atomic-resolution cryo-EM for probing the mechanisms of virus assembly and morphogenesis.","corpus_id":13880338,"score":0},{"doc_id":"21860371","title":"Structure of HIV-1 capsid assemblies by cryo-electron microscopy and iterative helical real-space reconstruction.","abstract":"Cryo-electron microscopy (cryo-EM), combined with image processing, is an increasingly powerful tool for structure determination of macromolecular protein complexes and assemblies. In fact, single particle electron microscopy and two-dimensional (2D) electron crystallography have become relatively routine methodologies and a large number of structures have been solved using these methods. At the same time, image processing and three-dimensional (3D) reconstruction of helical objects has rapidly developed, especially, the iterative helical real-space reconstruction (IHRSR) method, which uses single particle analysis tools in conjunction with helical symmetry. Many biological entities function in filamentous or helical forms, including actin filaments, microtubules, amyloid fibers, tobacco mosaic viruses, and bacteria flagella, and, because a 3D density map of a helical entity can be attained from a single projection image, compared to the many images required for 3D reconstruction of a non-helical object, with the IHRSR method, structural analysis of such flexible and disordered helical assemblies is now attainable. In this video article, we provide detailed protocols for obtaining a 3D density map of a helical protein assembly (HIV-1 capsid is our example), including protocols for cryo-EM specimen preparation, low dose data collection by cryo-EM, indexing of helical diffraction patterns, and image processing and 3D reconstruction using IHRSR. Compared to other techniques, cryo-EM offers optimal specimen preservation under near native conditions. Samples are embedded in a thin layer of vitreous ice, by rapid freezing, and imaged in electron microscopes at liquid nitrogen temperature, under low dose conditions to minimize the radiation damage. Sample images are obtained under near native conditions at the expense of low signal and low contrast in the recorded micrographs. Fortunately, the process of helical reconstruction has largely been automated, with the exception of indexing the helical diffraction pattern. Here, we describe an approach to index helical structure and determine helical symmetries (helical parameters) from digitized micrographs, an essential step for 3D helical reconstruction. Briefly, we obtain an initial 3D density map by applying the IHRSR method. This initial map is then iteratively refined by introducing constraints for the alignment parameters of each segment, thus controlling their degrees of freedom. Further improvement is achieved by correcting for the contrast transfer function (CTF) of the electron microscope (amplitude and phase correction) and by optimizing the helical symmetry of the assembly.","corpus_id":8398013,"score":0},{"doc_id":"22100448","title":"A Bayesian view on cryo-EM structure determination.","abstract":"Three-dimensional (3D) structure determination by single-particle analysis of cryo-electron microscopy (cryo-EM) images requires many parameters to be determined from extremely noisy data. This makes the method prone to overfitting, that is, when structures describe noise rather than signal, in particular near their resolution limit where noise levels are highest. Cryo-EM structures are typically filtered using ad hoc procedures to prevent overfitting, but the tuning of arbitrary parameters may lead to subjectivity in the results. I describe a Bayesian interpretation of cryo-EM structure determination, where smoothness in the reconstructed density is imposed through a Gaussian prior in the Fourier domain. The statistical framework dictates how data and prior knowledge should be combined, so that the optimal 3D linear filter is obtained without the need for arbitrariness and objective resolution estimates may be obtained. Application to experimental data indicates that the statistical approach yields more reliable structures than existing methods and is capable of detecting smaller classes in data sets that contain multiple different structures.","corpus_id":5427936,"score":0},{"doc_id":"22291925","title":"IPET and FETR: experimental approach for studying molecular structure dynamics by cryo-electron tomography of a single-molecule structure.","abstract":"The dynamic personalities and structural heterogeneity of proteins are essential for proper functioning. Structural determination of dynamic/heterogeneous proteins is limited by conventional approaches of X-ray and electron microscopy (EM) of single-particle reconstruction that require an average from thousands to millions different molecules. Cryo-electron tomography (cryoET) is an approach to determine three-dimensional (3D) reconstruction of a single and unique biological object such as bacteria and cells, by imaging the object from a series of tilting angles. However, cconventional reconstruction methods use large-size whole-micrographs that are limited by reconstruction resolution (lower than 20 Å), especially for small and low-symmetric molecule (<400 kDa). In this study, we demonstrated the adverse effects from image distortion and the measuring tilt-errors (including tilt-axis and tilt-angle errors) both play a major role in limiting the reconstruction resolution. Therefore, we developed a \"focused electron tomography reconstruction\" (FETR) algorithm to improve the resolution by decreasing the reconstructing image size so that it contains only a single-instance protein. FETR can tolerate certain levels of image-distortion and measuring tilt-errors, and can also precisely determine the translational parameters via an iterative refinement process that contains a series of automatically generated dynamic filters and masks. To describe this method, a set of simulated cryoET images was employed; to validate this approach, the real experimental images from negative-staining and cryoET were used. Since this approach can obtain the structure of a single-instance molecule/particle, we named it individual-particle electron tomography (IPET) as a new robust strategy/approach that does not require a pre-given initial model, class averaging of multiple molecules or an extended ordered lattice, but can tolerate small tilt-errors for high-resolution single \"snapshot\" molecule structure determination. Thus, FETR/IPET provides a completely new opportunity for a single-molecule structure determination, and could be used to study the dynamic character and equilibrium fluctuation of macromolecules.","corpus_id":4807732,"score":0},{"doc_id":"23181775","title":"Cryo-electron microscopy--a primer for the non-microscopist.","abstract":"Cryo-electron microscopy (cryo-EM) is increasingly becoming a mainstream technology for studying the architecture of cells, viruses and protein assemblies at molecular resolution. Recent developments in microscope design and imaging hardware, paired with enhanced image processing and automation capabilities, are poised to further advance the effectiveness of cryo-EM methods. These developments promise to increase the speed and extent of automation, and to improve the resolutions that may be achieved, making this technology useful to determine a wide variety of biological structures. Additionally, established modalities for structure determination, such as X-ray crystallography and nuclear magnetic resonance spectroscopy, are being routinely integrated with cryo-EM density maps to achieve atomic-resolution models of complex, dynamic molecular assemblies. In this review, which is directed towards readers who are not experts in cryo-EM methodology, we provide an overview of emerging themes in the application of this technology to investigate diverse questions in biology and medicine. We discuss the ways in which these methods are being used to study structures of macromolecular assemblies that range in size from whole cells to small proteins. Finally, we include a description of how the structural information obtained by cryo-EM is deposited and archived in a publicly accessible database.","corpus_id":205132714,"score":0},{"doc_id":"23217682","title":"Protein secondary structure determination by constrained single-particle cryo-electron tomography.","abstract":"Cryo-electron microscopy (cryo-EM) is a powerful technique for 3D structure determination of protein complexes by averaging information from individual molecular images. The resolutions that can be achieved with single-particle cryo-EM are frequently limited by inaccuracies in assigning molecular orientations based solely on 2D projection images. Tomographic data collection schemes, however, provide powerful constraints that can be used to more accurately determine molecular orientations necessary for 3D reconstruction. Here, we propose \"constrained single-particle tomography\" as a general strategy for 3D structure determination in cryo-EM. A key component of our approach is the effective use of images recorded in tilt series to extract high-resolution information and correct for the contrast transfer function. By incorporating geometric constraints into the refinement to improve orientational accuracy of images, we reduce model bias and overrefinement artifacts and demonstrate that protein structures can be determined at resolutions of ∼8 Å starting from low-dose tomographic tilt series.","corpus_id":13791074,"score":0},{"doc_id":"23416197","title":"Consensus among multiple approaches as a reliability measure for flexible fitting into cryo-EM data.","abstract":"Cryo-electron microscopy (cryo-EM) can provide low-resolution density maps of large macromolecular assemblies. As the number of structures deposited in the Protein Data Bank by fitting a high-resolution structure into a low-resolution cryo-EM map is increasing, there is a need to revise the protocols and improve the measures for fitting. A recent study suggested using a combination of multiple automated flexible fitting approaches to improve the interpretation of cryo-EM data. The current work further explores the use of multiple approaches by validating this \"consensus\" fitting approach and deriving a local reliability measure. Here four different flexible fitting approaches are applied for fitting an initial structure into a simulated density map of known target structure from a dataset of proteins. It is found that the models produced from different approaches often have a consensus in conformation and are also near to the target structure, whereas cases not showing consensus are away from the target. A high correlation is also observed between the RMSF profiles calculated with respect to the average and the target structures, which indicates that the relation between consensus and accuracy can also be extended to a per-residue level. Therefore, the RMSF among the fitted models is proposed as a local reliability measure, which can be used to assess the reliability of the fit at specific regions. Hence, we encourage the community to use consensus flexible fitting with different methods to report on local reliability of the resulting models and improve the interpretation of cryo-EM data.","corpus_id":12214200,"score":0},{"doc_id":"23707684","title":"Validation of cryo-EM structure of IP₃R1 channel.","abstract":"About a decade ago, three electron cryomicroscopy (cryo-EM) single-particle reconstructions of IP3R1 were reported at low resolution. It was disturbing that these structures bore little similarity to one another, even at the level of quaternary structure. Recently, we published an improved structure of IP3R1 at ∼1 nm resolution. However, this structure did not bear any resemblance to any of the three previously published structures, leading to the question of why the structure should be considered more reliable than the original three. Here, we apply several methods, including class-average/map comparisons, tilt-pair validation, and use of multiple refinement software packages, to give strong evidence for the reliability of our recent structure. The map resolution and feature resolvability are assessed with the gold standard criterion. This approach is generally applicable to assessing the validity of cryo-EM maps of other molecular machines.","corpus_id":9719520,"score":0},{"doc_id":"23737049","title":"Conventional electron microscopy, cryo-electron microscopy and cryo-electron tomography of viruses.","abstract":"Electron microscopy (EM) techniques have been crucial for understanding the structure of biological specimens such as cells, tissues and macromolecular assemblies. Viruses and related viral assemblies are ideal targets for structural studies that help to define essential biological functions. Whereas conventional EM methods use chemical fixation, dehydration, and staining of the specimens, cryo-electron microscopy (cryo-EM) preserves the native hydrated state. Combined with image processing and three-dimensional reconstruction techniques, cryo-EM provides 3D maps of these macromolecular complexes from projection images, at subnanometer to near-atomic resolutions. Cryo-EM is also a major technique in structural biology for dynamic studies of functional complexes, which are often unstable, flexible, scarce or transient in their native environments. As a tool, cryo-EM complements high-resolution techniques such as X-ray diffraction and NMR spectroscopy; these synergistic hybrid approaches provide important new information. Three-dimensional cryo-electron tomography goes further, and allows the study of viruses not only in their physiological state, but also in their natural environment in the cell, thereby bridging structural studies at the molecular and cellular levels.","corpus_id":38844770,"score":0},{"doc_id":"23931142","title":"PRIME: probabilistic initial 3D model generation for single-particle cryo-electron microscopy.","abstract":"Low-dose electron microscopy of cryo-preserved individual biomolecules (single-particle cryo-EM) is a powerful tool for obtaining information about the structure and dynamics of large macromolecular assemblies. Acquiring images with low dose reduces radiation damage, preserves atomic structural details, but results in low signal-to-noise ratio of the individual images. The projection directions of the two-dimensional images are random and unknown. The grand challenge is to achieve the precise three-dimensional (3D) alignment of many (tens of thousands to millions) noisy projection images, which may then be combined to obtain a faithful 3D map. An accurate initial 3D model is critical for obtaining the precise 3D alignment required for high-resolution (<10 Å) map reconstruction. We report a method (PRIME) that, in a single step and without prior structural knowledge, can generate an accurate initial 3D map directly from the noisy images.","corpus_id":12087592,"score":0},{"doc_id":"24161732","title":"Optimod--an automated approach for constructing and optimizing initial models for single-particle electron microscopy.","abstract":"Single-particle cryo-electron microscopy is now well established as a technique for the structural characterization of large macromolecules and macromolecular complexes. The raw data is very noisy and consists of two-dimensional projections, from which the 3D biological object must be reconstructed. The 3D object depends upon knowledge of proper angular orientations assigned to the 2D projection images. Numerous algorithms have been developed for determining relative angular orientations between 2D images, but the transition from 2D to 3D remains challenging and can result in erroneous and conflicting results. Here we describe a general, automated procedure, called OptiMod, for reconstructing and optimizing 3D models using common-lines methodologies. OptiMod approximates orientation angles and reconstructs independent maps from 2D class averages. It then iterates the procedure, while considering each map as a raw solution that needs to be compared with other possible outcomes. We incorporate procedures for 3D alignment, clustering, and refinement to optimize each map, as well as standard scoring metrics to facilitate the selection of the optimal model. We also show that small angle tilt-pair data can be included as one of the scoring metrics to improve the selection of the optimal initial model, and also to provide a validation check. The overall approach is demonstrated using two experimental cryo-EM data sets--the 80S ribosome that represents a relatively straightforward case for ab initio reconstruction, and the Tf-TfR complex that represents a challenging case in that it has previously been shown to provide multiple equally plausible solutions to the initial model problem.","corpus_id":36681249,"score":0},{"doc_id":"24390311","title":"High-resolution cryo-electron microscopy on macromolecular complexes and cell organelles.","abstract":"Cryo-electron microscopy techniques and computational 3-D reconstruction of macromolecular assemblies are tightly linked tools in modern structural biology. This symbiosis has produced vast amounts of detailed information on the structure and function of biological macromolecules. Typically, one of two fundamentally different strategies is used depending on the specimens and their environment. A: 3-D reconstruction based on repetitive and structurally identical unit cells that allow for averaging, and B: tomographic 3-D reconstructions where tilt-series between approximately ± 60 and ± 70° at small angular increments are collected from highly complex and flexible structures that are beyond averaging procedures, at least during the first round of 3-D reconstruction. Strategies of group A are averaging-based procedures and collect large number of 2-D projections at different angles that are computationally aligned, averaged together, and back-projected in 3-D space to reach a most complete 3-D dataset with high resolution, today often down to atomic detail. Evidently, success relies on structurally repetitive particles and an aligning procedure that unambiguously determines the angular relationship of all 2-D projections with respect to each other. The alignment procedure of small particles may rely on their packing into a regular array such as a 2-D crystal, an icosahedral (viral) particle, or a helical assembly. Critically important for cryo-methods, each particle will only be exposed once to the electron beam, making these procedures optimal for highest-resolution studies where beam-induced damage is a significant concern. In contrast, tomographic 3-D reconstruction procedures (group B) do not rely on averaging, but collect an entire dataset from the very same structure of interest. Data acquisition requires collecting a large series of tilted projections at angular increments of 1-2° or less and a tilt range of ± 60° or more. Accordingly, tomographic data collection exposes its specimens to a large electron dose, which is particularly problematic for frozen-hydrated samples. Currently, cryo-electron tomography is a rapidly emerging technology, on one end driven by the newest developments of hardware such as super-stabile microscopy stages as well as the latest generation of direct electron detectors and cameras. On the other end, success also strongly depends on new software developments on all kinds of fronts such as tilt-series alignment and back-projection procedures that are all adapted to the very low-dose and therefore very noisy primary data. Here, we will review the status quo of cryo-electron microscopy and discuss the future of cellular cryo-electron tomography from data collection to data analysis, CTF-correction of tilt-series, post-tomographic sub-volume averaging, and 3-D particle classification. We will also discuss the pros and cons of plunge freezing of cellular specimens to vitrified sectioning procedures and their suitability for post-tomographic volume averaging despite multiple artifacts that may distort specimens to some degree.","corpus_id":13894885,"score":0},{"doc_id":"25544475","title":"How cryo-EM is revolutionizing structural biology.","abstract":"For many years, structure determination of biological macromolecules by cryo-electron microscopy (cryo-EM) was limited to large complexes or low-resolution models. With recent advances in electron detection and image processing, the resolution by cryo-EM is now beginning to rival X-ray crystallography. A new generation of electron detectors record images with unprecedented quality, while new image-processing tools correct for sample movements and classify images according to different structural states. Combined, these advances yield density maps with sufficient detail to deduce the atomic structure for a range of specimens. Here, we review the recent advances and illustrate the exciting new opportunities that they offer to structural biology research.","corpus_id":19727349,"score":0},{"doc_id":"25707802","title":"Structure of the E. coli ribosome-EF-Tu complex at <3 Å resolution by Cs-corrected cryo-EM.","abstract":"Single particle electron cryomicroscopy (cryo-EM) has recently made significant progress in high-resolution structure determination of macromolecular complexes due to improvements in electron microscopic instrumentation and computational image analysis. However, cryo-EM structures can be highly non-uniform in local resolution and all structures available to date have been limited to resolutions above 3 Å. Here we present the cryo-EM structure of the 70S ribosome from Escherichia coli in complex with elongation factor Tu, aminoacyl-tRNA and the antibiotic kirromycin at 2.65-2.9 Å resolution using spherical aberration (Cs)-corrected cryo-EM. Overall, the cryo-EM reconstruction at 2.9 Å resolution is comparable to the best-resolved X-ray structure of the E. coli 70S ribosome (2.8 Å), but provides more detailed information (2.65 Å) at the functionally important ribosomal core. The cryo-EM map elucidates for the first time the structure of all 35 rRNA modifications in the bacterial ribosome, explaining their roles in fine-tuning ribosome structure and function and modulating the action of antibiotics. We also obtained atomic models for flexible parts of the ribosome such as ribosomal proteins L9 and L31. The refined cryo-EM-based model presents the currently most complete high-resolution structure of the E. coli ribosome, which demonstrates the power of cryo-EM in structure determination of large and dynamic macromolecular complexes.","corpus_id":4395954,"score":0},{"doc_id":"25747402","title":"Cryogenic electron microscopy and single-particle analysis.","abstract":"About 20 years ago, the first three-dimensional (3D) reconstructions at subnanometer (<10-Å) resolution of an icosahedral virus assembly were obtained by cryogenic electron microscopy (cryo-EM) and single-particle analysis. Since then, thousands of structures have been determined to resolutions ranging from 30 Å to near atomic (<4 Å). Almost overnight, the recent development of direct electron detectors and the attendant improvement in analysis software have advanced the technology considerably. Near-atomic-resolution reconstructions can now be obtained, not only for megadalton macromolecular complexes or highly symmetrical assemblies but also for proteins of only a few hundred kilodaltons. We discuss the developments that led to this breakthrough in high-resolution structure determination by cryo-EM and point to challenges that lie ahead.","corpus_id":37880033,"score":0},{"doc_id":"25894285","title":"Cryo-electron microscopy for structural biology: current status and future perspectives.","abstract":"Recently, significant technical breakthroughs in both hardware equipment and software algorithms have enabled cryo-electron microscopy (cryo-EM) to become one of the most important techniques in biological structural analysis. The technical aspects of cryo-EM define its unique advantages and the direction of development. As a rapidly emerging field, cryo-EM has benefitted from highly interdisciplinary research efforts. Here we review the current status of cryo-EM in the context of structural biology and discuss the technical challenges. It may eventually merge structural and cell biology at multiple scales.","corpus_id":1728363,"score":0},{"doc_id":"25955078","title":"Cryo-electron microscopy and the amazing race to atomic resolution.","abstract":"Cryo-electron microscopy (cryo-EM), the structural analysis of samples embedded in vitreous ice, is a powerful approach for determining three-dimensional (3D) structures of biological specimens. Over the past two decades, this technique has been used to successfully calculate subnanometer (<10 Å) resolution and, in some cases, near-atomic resolution structures of highly symmetrical and stable complexes such as icosahedral viruses and ribosomes, as well as samples that form ordered two-dimensional or helical arrays. However, determining high-resolution 3D structures of smaller, less symmetrical, and dynamic samples remains a significant challenge. The recent development of electron microscopes with automated data collection capabilities and robust direct electron detection cameras, as well as new powerful image processing algorithms, has dramatically expanded the number of biological macromolecules amenable for study using cryo-EM. In addition, these new technological and computational developments have been used to successfully determine <5 Å resolution 3D structures of samples, such as membrane proteins and complexes with either low or no symmetry, that traditionally were not considered promising candidates for high-resolution cryo-EM. With these exciting new advances, cryo-EM is now on pace to determine atomic resolution 3D structures.","corpus_id":5180848,"score":0},{"doc_id":"26000851","title":"Cryo-EM: A Unique Tool for the Visualization of Macromolecular Complexity.","abstract":"3D cryo-electron microscopy (cryo-EM) is an expanding structural biology technique that has recently undergone a quantum leap progression in its achievable resolution and its applicability to the study of challenging biological systems. Because crystallization is not required, only small amounts of sample are needed, and because images can be classified in a computer, the technique has the potential to deal with compositional and conformational mixtures. Therefore, cryo-EM can be used to investigate complete and fully functional macromolecular complexes in different functional states, providing a richness of biological insight. In this review, we underlie some of the principles behind the cryo-EM methodology of single particle analysis and discuss some recent results of its application to challenging systems of paramount biological importance. We place special emphasis on new methodological developments that are leading to an explosion of new studies, many of which are reaching resolutions that could only be dreamed of just a couple of years ago.","corpus_id":40789821,"score":0},{"doc_id":"26068751","title":"Using Molecular Simulation to Model High-Resolution Cryo-EM Reconstructions.","abstract":"An explosion of new data from high-resolution cryo-electron microscopy (cryo-EM) studies has produced a large number of data sets for many species of ribosomes in various functional states over the past few years. While many methods exist to produce structural models for lower resolution cryo-EM reconstructions, high-resolution reconstructions are often modeled using crystallographic techniques and extensive manual intervention. Here, we present an automated fitting technique for high-resolution cryo-EM data sets that produces all-atom models highly consistent with the EM density. Using a molecular dynamics approach, atomic positions are optimized with a potential that includes the cross-correlation coefficient between the structural model and the cryo-EM electron density, as well as a biasing potential preserving the stereochemistry and secondary structure of the biomolecule. Specifically, we use a hybrid structure-based/ab initio molecular dynamics potential to extend molecular dynamics fitting. In addition, we find that simulated annealing integration, as opposed to straightforward molecular dynamics integration, significantly improves performance. We obtain atomistic models of the human ribosome consistent with high-resolution cryo-EM reconstructions of the human ribosome. Automated methods such as these have the potential to produce atomistic models for a large number of ribosome complexes simultaneously that can be subsequently refined manually.","corpus_id":27340829,"score":0},{"doc_id":"26456135","title":"In Situ Cryo-Electron Tomography: A Post-Reductionist Approach to Structural Biology.","abstract":"Cryo-electron tomography is a powerful technique that can faithfully image the native cellular environment at nanometer resolution. Unlike many other imaging approaches, cryo-electron tomography provides a label-free method of detecting biological structures, relying on the intrinsic contrast of frozen cellular material for direct identification of macromolecules. Recent advances in sample preparation, detector technology, and phase plate imaging have enabled the structural characterization of protein complexes within intact cells. Here, we review these technical developments and outline a detailed computational workflow for in situ structural analysis. Two recent studies are described to illustrate how this workflow can be adapted to examine both known and unknown cellular complexes. The stage is now set to realize the promise of visual proteomics-a complete structural description of the cell's native molecular landscape.","corpus_id":206214810,"score":0},{"doc_id":"26611544","title":"Single-particle cryo-electron microscopy of macromolecular complexes.","abstract":"Recent technological breakthroughs in image acquisition have enabled single-particle cryo-electron microscopy (cryo-EM) to achieve near-atomic resolution structural information for biological complexes. The improvements in image quality coupled with powerful computational methods for sorting distinct particle populations now also allow the determination of compositional and conformational ensembles, thereby providing key insights into macromolecular function. However, the inherent instability and dynamic nature of biological assemblies remain a tremendous challenge that often requires tailored approaches for successful implementation of the methodology. Here, we briefly describe the fundamentals of single-particle cryo-EM with an emphasis on covering the breadth of techniques and approaches, including low- and high-resolution methods, aiming to illustrate specific steps that are crucial for obtaining structural information by this method.","corpus_id":4928921,"score":0},{"doc_id":"26638773","title":"Cryo electron microscopy to determine the structure of macromolecular complexes.","abstract":"Cryo-electron microscopy (cryo-EM) is a structural molecular and cellular biology technique that has experienced major advances in recent years. Technological developments in image recording as well as in processing software make it possible to obtain three-dimensional reconstructions of macromolecular assemblies at near-atomic resolution that were formerly obtained only by X-ray crystallography or NMR spectroscopy. In parallel, cryo-electron tomography has also benefitted from these technological advances, so that visualization of irregular complexes, organelles or whole cells with their molecular machines in situ has reached subnanometre resolution. Cryo-EM can therefore address a broad range of biological questions. The aim of this review is to provide a brief overview of the principles and current state of the cryo-EM field.","corpus_id":4981550,"score":0},{"doc_id":"26671943","title":"Sample preparation of biological macromolecular assemblies for the determination of high-resolution structures by cryo-electron microscopy.","abstract":"Single particle cryo-EM has recently developed into a powerful tool to determine the 3D structure of macromolecular complexes at near-atomic resolution, which allows structural biologists to build atomic models of proteins. All technical aspects of cryo-EM technology have been considerably improved over the last two decades, including electron microscopic hardware, image processing software and the ever growing speed of computers. This leads to a more widespread use of the technique, and it can be anticipated that further automation of electron microscopes and image processing tools will soon fully shift the focus away from the technological aspects, onto biological questions that can be answered. In single particle cryo-EM, no crystals of a macromolecule are required. In contrast to X-ray crystallography, this significantly facilitates structure determination by cryo-EM. Nevertheless, a relatively high level of biochemical control is still essential to obtain high-resolution structures by cryo-EM, and it can be anticipated that the success of the cryo-EM technology goes hand in hand with further developments of sample purification and preparation techniques. This will allow routine high-resolution structure determination of the many macromolecular complexes of the cell that until now represent evasive targets for X-ray crystallographers. Here we discuss the various biochemical tools that are currently available and the existing sample purification and preparation techniques for cryo-EM grid preparation that are needed to obtain high-resolution images for structure determination.","corpus_id":23067203,"score":0},{"doc_id":"26787742","title":"Cellular structural biology as revealed by cryo-electron tomography.","abstract":"Understanding the function of cellular machines requires a thorough analysis of the structural elements that underline their function. Electron microscopy (EM) has been pivotal in providing information about cellular ultrastructure, as well as macromolecular organization. Biological materials can be physically fixed by vitrification and imaged with cryo-electron tomography (cryo-ET) in a close-to-native condition. Using this technique, one can acquire three-dimensional (3D) information about the macromolecular architecture of cells, depict unique cellular states and reconstruct molecular networks. Technical advances over the last few years, such as improved sample preparation and electron detection methods, have been instrumental in obtaining data with unprecedented structural details. This presents an exciting opportunity to explore the molecular architecture of both individual cells and multicellular organisms at nanometer to subnanometer resolution. In this Commentary, we focus on the recent developments and in situ applications of cryo-ET to cell and structural biology.","corpus_id":2543759,"score":0},{"doc_id":"26931652","title":"An introduction to sample preparation and imaging by cryo-electron microscopy for structural biology.","abstract":"Transmission electron microscopy (EM) is a versatile technique that can be used to image biological specimens ranging from intact eukaryotic cells to individual proteins >150kDa. There are several strategies for preparing samples for imaging by EM, including negative staining and cryogenic freezing. In the last few years, cryo-EM has undergone a 'resolution revolution', owing to both advances in imaging hardware, image processing software, and improvements in sample preparation, leading to growing number of researchers using cryo-EM as a research tool. However, cryo-EM is still a rapidly growing field, with unique challenges. Here, we summarise considerations for imaging of a range of specimens from macromolecular complexes to cells using EM.","corpus_id":3562560,"score":0},{"doc_id":"27280059","title":"Comparison of an Atomic Model and Its Cryo-EM Image at the Central Axis of a Helix.","abstract":"Cryo-electron microscopy (cryo-EM) is an important biophysical technique that produces three-dimensional (3D) density maps at different resolutions. Because more and more models are being produced from cryo-EM density maps, validation of the models is becoming important. We propose a method for measuring local agreement between a model and the density map using the central axis of the helix. This method was tested using 19 helices from cryo-EM density maps between 5.5 Å and 7.2 Å resolution and 94 helices from simulated density maps. This method distinguished most of the well-fitting helices, although challenges exist for shorter helices.","corpus_id":23795543,"score":0},{"doc_id":"27572731","title":"Refinement of Atomic Structures Against cryo-EM Maps.","abstract":"This review describes some of the methods for atomic structure refinement (fitting) against medium/high-resolution single-particle cryo-EM reconstructed maps. Some of the tools developed for macromolecular X-ray crystal structure analysis, especially those encapsulating prior chemical and structural information can be transferred directly for fitting into cryo-EM maps. However, despite the similarities, there are significant differences between data produced by these two techniques; therefore, different likelihood functions linking the data and model must be used in cryo-EM and crystallographic refinement. Although tools described in this review are mostly designed for medium/high-resolution maps, if maps have sufficiently good quality, then these tools can also be used at moderately low resolution, as shown in one example. In addition, the use of several popular crystallographic methods is strongly discouraged in cryo-EM refinement, such as 2Fo-Fc maps, solvent flattening, and feature-enhanced maps (FEMs) for visualization and model (re)building. Two problems in the cryo-EM field are overclaiming resolution and severe map oversharpening. Both of these should be avoided; if data of higher resolution than the signal are used, then overfitting of model parameters into the noise is unavoidable, and if maps are oversharpened, then at least parts of the maps might become very noisy and ultimately uninterpretable. Both of these may result in suboptimal and even misleading atomic models.","corpus_id":3568888,"score":0},{"doc_id":"27572734","title":"High-Resolution Macromolecular Structure Determination by MicroED, a cryo-EM Method.","abstract":"Microelectron diffraction (MicroED) is a new cryo-electron microscopy (cryo-EM) method capable of determining macromolecular structures at atomic resolution from vanishingly small 3D crystals. MicroED promises to solve atomic resolution structures from even the tiniest of crystals, less than a few hundred nanometers thick. MicroED complements frontier advances in crystallography and represents part of the rebirth of cryo-EM that is making macromolecular structure determination more accessible for all. Here we review the concept and practice of MicroED, for both the electron microscopist and crystallographer. Where other reviews have addressed specific details of the technique (Hattne et al., 2015; Shi et al., 2016; Shi, Nannenga, Iadanza, & Gonen, 2013), we aim to provide context and highlight important features that should be considered when performing a MicroED experiment.","corpus_id":205165728,"score":0},{"doc_id":"27669148","title":"Automated structure refinement of macromolecular assemblies from cryo-EM maps using Rosetta.","abstract":"Cryo-EM has revealed the structures of many challenging yet exciting macromolecular assemblies at near-atomic resolution (3-4.5Å), providing biological phenomena with molecular descriptions. However, at these resolutions, accurately positioning individual atoms remains challenging and error-prone. Manually refining thousands of amino acids - typical in a macromolecular assembly - is tedious and time-consuming. We present an automated method that can improve the atomic details in models that are manually built in near-atomic-resolution cryo-EM maps. Applying the method to three systems recently solved by cryo-EM, we are able to improve model geometry while maintaining the fit-to-density. Backbone placement errors are automatically detected and corrected, and the refinement shows a large radius of convergence. The results demonstrate that the method is amenable to structures with symmetry, of very large size, and containing RNA as well as covalently bound ligands. The method should streamline the cryo-EM structure determination process, providing accurate and unbiased atomic structure interpretation of such maps.","corpus_id":1186306,"score":0},{"doc_id":"27685097","title":"Resolving macromolecular structures from electron cryo-tomography data using subtomogram averaging in RELION.","abstract":"Electron cryo-tomography (cryo-ET) is a technique that is used to produce 3D pictures (tomograms) of complex objects such as asymmetric viruses, cellular organelles or whole cells from a series of tilted electron cryo-microscopy (cryo-EM) images. Averaging of macromolecular complexes found within tomograms is known as subtomogram averaging, and this technique allows structure determination of macromolecular complexes in situ. Subtomogram averaging is also gaining in popularity for the calculation of initial models for single-particle analysis. We describe herein a protocol for subtomogram averaging from cryo-ET data using the RELION software (http://www2.mrc-lmb.cam.ac.uk/relion). RELION was originally developed for cryo-EM single-particle analysis, and the subtomogram averaging approach presented in this protocol has been implemented in the existing workflow for single-particle analysis so that users may conveniently tap into existing capabilities of the RELION software. We describe how to calculate 3D models for the contrast transfer function (CTF) that describe the transfer of information in the imaging process, and we illustrate the results of classification and subtomogram averaging refinement for cryo-ET data of purified hepatitis B capsid particles and Saccharomyces cerevisiae 80S ribosomes. Using the steps described in this protocol, along with the troubleshooting and optimization guidelines, high-resolution maps can be obtained in which secondary structure elements are resolved subtomogram.","corpus_id":19321982,"score":0},{"doc_id":"28132494","title":"Introduction to high-resolution cryo-electron microscopy.","abstract":"Wprowadzenie do wysokorozdzielczej kriogenicznej mikroskopii elektronowej. For many years two techniques have dominated structural biology - X-ray crystallography and NMR spectroscopy. Traditional cryo-electron microscopy of biological macromolecules produced macromolecular reconstructions at resolution limited to 6-10 Å. Recent development of transmission electron microscopes, in particular the development of direct electron detectors, and continuous improvements in the available software, have led to the \"resolution revolution\" in cryo-EM. It is now possible to routinely obtain near-atomic-resolution 3D maps of intact biological macromolecules as small as ~100 kDa. Thus, cryo-EM is now becoming the method of choice for structural analysis of many complex assemblies that are unsuitable for structure determination by other methods.","corpus_id":1205060,"score":0},{"doc_id":"28165473","title":"cryoSPARC: algorithms for rapid unsupervised cryo-EM structure determination.","abstract":"Single-particle electron cryomicroscopy (cryo-EM) is a powerful method for determining the structures of biological macromolecules. With automated microscopes, cryo-EM data can often be obtained in a few days. However, processing cryo-EM image data to reveal heterogeneity in the protein structure and to refine 3D maps to high resolution frequently becomes a severe bottleneck, requiring expert intervention, prior structural knowledge, and weeks of calculations on expensive computer clusters. Here we show that stochastic gradient descent (SGD) and branch-and-bound maximum likelihood optimization algorithms permit the major steps in cryo-EM structure determination to be performed in hours or minutes on an inexpensive desktop computer. Furthermore, SGD with Bayesian marginalization allows ab initio 3D classification, enabling automated analysis and discovery of unexpected structures without bias from a reference map. These algorithms are combined in a user-friendly computer program named cryoSPARC (http://www.cryosparc.com).","corpus_id":-1,"score":0},{"doc_id":"28368275","title":"Cryo-electron microscopy and X-ray crystallography: complementary approaches to structural biology and drug discovery.","abstract":"The invention of the electron microscope has greatly enhanced the view scientists have of small structural details. Since its implementation, this technology has undergone considerable evolution and the resolution that can be obtained for biological objects has been extended. In addition, the latest generation of cryo-electron microscopes equipped with direct electron detectors and software for the automated collection of images, in combination with the use of advanced image-analysis methods, has dramatically improved the performance of this technique in terms of resolution. While calculating a sub-10 Å resolution structure was an accomplishment less than a decade ago, it is now common to generate structures at sub-5 Å resolution and even better. It is becoming possible to relatively quickly obtain high-resolution structures of biological molecules, in particular large ones (>500 kDa) which, in some cases, have resisted more conventional methods such as X-ray crystallography or nuclear magnetic resonance (NMR). Such newly resolved structures may, for the first time, shed light on the precise mechanisms that are essential for cellular physiological processes. The ability to attain atomic resolution may support the development of new drugs that target these proteins, allowing medicinal chemists to understand the intimacy of the relationship between their molecules and targets. In addition, recent developments in cryo-electron microscopy combined with image analysis can provide unique information on the conformational variability of macromolecular complexes. Conformational flexibility of macromolecular complexes can be investigated using cryo-electron microscopy and multiconformation reconstruction methods. However, the biochemical quality of the sample remains the major bottleneck to routine cryo-electron microscopy-based determination of structures at very high resolution.","corpus_id":2588079,"score":0},{"doc_id":"28646653","title":"Cryo-EM: beyond the microscope.","abstract":"The pace at which cryo-EM is being adopted as a mainstream tool in structural biology has continued unabated over the past year. Initial successes in obtaining near-atomic resolution structures with cryo-EM were enabled to a large extent by advances in microscope and detector technology. Here, we review some of the complementary technical improvements that are helping sustain the cryo-EM revolution. We highlight advances in image processing that permit high resolution structure determination even in the presence of structural and conformational heterogeneity. We also review selected examples where biochemical strategies for membrane protein stabilization facilitate cryo-EM structure determination, and discuss emerging approaches for further improving the preparation of reliable plunge-frozen specimens.","corpus_id":205063574,"score":0},{"doc_id":"28667626","title":"Structural Analysis of Protein Complexes by Cryo Electron Microscopy.","abstract":"Structural studies of biocomplexes using single-particle cryo-electron microscopy (cryo-EM) is now a well-established technique in structural biology and has become competitive with X-ray crystallography. The latest advances in EM enable us to determine structures of protein complexes at 3-5 Å resolution for an extremely broad range of sizes from ~200 kDa up to hundreds of megadaltons (Bartesaghi et al., Science 348(6239):1147-1151, 2051; Bai et al., Nature 525(7568):212-217, 2015; Vinothkumar et al., Nature 515(7525):80-84, 2014; Grigorieff and Harrison, Curr Opin Struct Biol 21(2):265-273, 2011). The majority of biocomplexes comprise a number of different components and are not amenable to crystallisation. Secretion systems are typical examples of such multi-protein complexes, and structural studies of them are extremely challenging. The only feasible approach to revealing their spatial organisation and functional modification is cryo-EM. The development of systems for digital registration of images and algorithms for the fast and efficient processing of recorded images and subsequent analysis facilitated the determination of structures at near-atomic resolution. In this review we will describe sample preparation for cryo-EM, how data are collected by new detectors, and the logistics of image analysis through the basic steps required for reconstructions of both small and large biological complexes and their refinement to nearly atomic resolution. The processing workflow is illustrated using examples of EM analysis of a Type IV Secretion System.","corpus_id":4322690,"score":0},{"doc_id":"28949136","title":"Iterative Molecular Dynamics-Rosetta Membrane Protein Structure Refinement Guided by Cryo-EM Densities.","abstract":"Knowing atomistic details of proteins is essential not only for the understanding of protein function but also for the development of drugs. Experimental methods such as X-ray crystallography, NMR, and cryo-electron microscopy (cryo-EM) are the preferred forms of protein structure determination and have achieved great success over the most recent decades. Computational methods may be an alternative when experimental techniques fail. However, computational methods are severely limited when it comes to predicting larger macromolecule structures with little sequence similarity to known structures. The incorporation of experimental restraints in computational methods is becoming increasingly important to more reliably predict protein structure. One such experimental input used in structure prediction and refinement is cryo-EM densities. Recent advances in cryo-EM have arguably revolutionized the field of structural biology. Our previously developed cryo-EM-guided Rosetta-MD protocol has shown great promise in the refinement of soluble protein structures. In this study, we extended cryo-EM density-guided iterative Rosetta-MD to membrane proteins. We also improved the methodology in general by picking models based on a combination of their score and fit-to-density during the Rosetta model selection. By doing so, we have been able to pick models superior to those with the previous selection based on Rosetta score only and we have been able to further improve our previously refined models of soluble proteins. The method was tested with five membrane spanning protein structures. By applying density-guided Rosetta-MD iteratively we were able to refine the predicted structures of these membrane proteins to atomic resolutions. We also showed that the resolution of the density maps determines the improvement and quality of the refined models. By incorporating high-resolution density maps (∼4 Å), we were able to more significantly improve the quality of the models than when medium-resolution maps (6.9 Å) were used. Beginning from an average starting structure root mean square deviation (RMSD) to native of 4.66 Å, our protocol was able to refine the structures to bring the average refined structure RMSD to 1.66 Å when 4 Å density maps were used. The protocol also successfully refined the HIV-1 CTD guided by an experimental 5 Å density map.","corpus_id":25509155,"score":0},{"doc_id":"28989723","title":"Single-particle cryo-EM using alignment by classification (ABC): the structure of Lumbricus terrestris haemoglobin.","abstract":"Single-particle cryogenic electron microscopy (cryo-EM) can now yield near-atomic resolution structures of biological complexes. However, the reference-based alignment algorithms commonly used in cryo-EM suffer from reference bias, limiting their applicability (also known as the 'Einstein from random noise' problem). Low-dose cryo-EM therefore requires robust and objective approaches to reveal the structural information contained in the extremely noisy data, especially when dealing with small structures. A reference-free pipeline is presented for obtaining near-atomic resolution three-dimensional reconstructions from heterogeneous ('four-dimensional') cryo-EM data sets. The methodologies integrated in this pipeline include a posteriori camera correction, movie-based full-data-set contrast transfer function determination, movie-alignment algorithms, (Fourier-space) multivariate statistical data compression and unsupervised classification, 'random-startup' three-dimensional reconstructions, four-dimensional structural refinements and Fourier shell correlation criteria for evaluating anisotropic resolution. The procedures exclusively use information emerging from the data set itself, without external 'starting models'. Euler-angle assignments are performed by angular reconstitution rather than by the inherently slower projection-matching approaches. The comprehensive 'ABC-4D' pipeline is based on the two-dimensional reference-free 'alignment by classification' (ABC) approach, where similar images in similar orientations are grouped by unsupervised classification. Some fundamental differences between X-ray crystallography versus single-particle cryo-EM data collection and data processing are discussed. The structure of the giant haemoglobin from Lumbricus terrestris at a global resolution of ∼3.8 Å is presented as an example of the use of the ABC-4D procedure.","corpus_id":6151708,"score":0},{"doc_id":"29080436","title":"Combining cryo-electron microscopy (cryo-EM) and cross-linking mass spectrometry (CX-MS) for structural elucidation of large protein assemblies.","abstract":"Determining the structures of, and gaining insight into, the function of large protein complexes at the molecular or atomic level has become a key part of modern structural biology. Electron cryo-microscopy (cryo-EM) can solve structures of highly dynamic macromolecular complexes that are not feasible with other structural techniques like X-ray of crystallized proteins (protein complexes) or nuclear magnetic resonance (NMR) spectroscopy of proteins (protein complexes) in solution. To resolve the regions that are less well defined in cryo-EM images, cross-linking coupled with mass spectrometry (CX-MS) provides valuable information on the proximity between amino-acid residues as distance constraints for homology or de novo modelling. The CX-MS strategy involves covalent linkage, with chemical cross-linkers, of residues close to each other in three-dimensional space and identifying these connections by mass spectrometry. In this article, we summarise the advances of CX-MS and its integration with cryo-EM for structural reconstruction. We further evaluate a number of important examples of structure determination that followed this combinatorial strategy.","corpus_id":3535945,"score":0},{"doc_id":"29214692","title":"Cryo-EM Revolutionizes the Structure Determination of Biomolecules.","abstract":"Freeze frame: The Nobel Prize in Chemistry 2017 was jointly awarded to Jacques Dubochet, Joachim Frank, and Richard Henderson for \"developing cryo-electron microscopy (cryo-EM) for the high-resolution structure determination of biomolecules in solution\". This Highlight describes how the field of cryo-EM developed from the first transmission electron microscope in 1931 to the sophisticated technique of today.","corpus_id":2614386,"score":0},{"doc_id":"29337113","title":"Volta phase plate data collection facilitates image processing and cryo-EM structure determination.","abstract":"A current bottleneck in structure determination of macromolecular complexes by cryo electron microscopy (cryo-EM) is the large amount of data needed to obtain high-resolution 3D reconstructions, including through sorting into different conformations and compositions with advanced image processing. Additionally, it may be difficult to visualize small ligands that bind in sub-stoichiometric levels. Volta phase plates (VPP) introduce a phase shift in the contrast transfer and drastically increase the contrast of the recorded low-dose cryo-EM images while preserving high frequency information. Here we present a comparative study to address the behavior of different data sets during image processing and quantify important parameters during structure refinement. The automated data collection was done from the same human ribosome sample either as a conventional defocus range dataset or with a Volta phase plate close to focus (cfVPP) or with a small defocus (dfVPP). The analysis of image processing parameters shows that dfVPP data behave more robustly during cryo-EM structure refinement because particle alignments, Euler angle assignments and 2D & 3D classifications behave more stably and converge faster. In particular, less particle images are required to reach the same resolution in the 3D reconstructions. Finally, we find that defocus range data collection is also applicable to VPP. This study shows that data processing and cryo-EM map interpretation, including atomic model refinement, are facilitated significantly by performing VPP cryo-EM, which will have an important impact on structural biology.","corpus_id":21655197,"score":0},{"doc_id":"29429092","title":"Use of Cryo-EM to Study the Structure of Chemoreceptor Arrays In Vivo.","abstract":"Cryo-electron microscopy (cryo-EM) allows the imaging of intact macromolecular complexes in the context of whole cells. The biological samples for cryo-EM are kept in a near-native state by flash freezing, without the need for any additional sample preparation or fixation steps. Since transmission electron microscopy only generates 2D projections of the samples, the specimen has to be tilted in order to recover its 3D structural information. This is done by collecting images of the sample with various tilt angles in respect to the electron beam. The acquired tilt series can then be computationally back-projected. This technique is called electron cryotomography (ECT), and has been instrumental in unraveling the architecture of chemoreceptor arrays. Here we describe the method of visualizing in vivo bacterial chemoreceptor arrays in three main steps: immobilization of bacterial cells on EM grids by plunge-freezing; 2D image acquisition in tilt series; and 3D tomogram reconstruction.","corpus_id":46874692,"score":0},{"doc_id":"29656089","title":"Microbiology catches the cryo-EM bug.","abstract":"Over the past few years, the advances in technology and methods that have revolutionized cryo-EM are allowing for key insights in a variety of areas in biology, and microbiology is no exception. A wide range of important macromolecular assemblies in prokaryotic and eukaryotic cells, as well as intact viruses, have now become accessible to investigation by new methods in 3D electron microscopy. We focus here on selected examples that illustrate this breadth, and review the application of methods in single particle cryo-EM and cryo-electron tomography to progress in the structural biology of CRISPR systems, visualization of small molecule drugs in membrane proteins, in situ visualization of bacterial nanomachines, and the analysis of antigen-antibody interactions to drive vaccine design.","corpus_id":4891845,"score":0}],"string":"[\n {\n \"doc_id\": \"20888964\",\n \"title\": \"The orthogonal tilt reconstruction method.\",\n \"abstract\": \"Generating reliable initial models for novel asymmetric molecules, particularly heterogeneous ones, remains a major challenge in cryo-electron microscopy. Geometric reconstruction methods, relying on the ability to tilt the microscope stage to obtain two or more views of each molecule, are arguably the most robust for these types of samples as they generate independent reconstructions for each characteristic view obtained. Random Conical Tilt (RCT) is the classic geometric reconstruction method. Pairs of images are collected at high tilt (around 50°) and 0°. The latter are used to sort the data into characteristic views of the molecule and the former are used for their reconstruction. RCT's greatest strength is its ability to generate structures regardless of the number of orientations adopted by the sample on the support. Its major drawback stems from the limited tilt of the microscope stage; this results in an incomplete sampling of the structure in Fourier space and artifacts in its real space representation. Orthogonal Tilt Reconstruction (OTR), a modification of this data collection strategy, results in fully sampled structures. It relies on collecting data at -45° and +45° and treating the tilt pairs as equivalent to the ideal 0°/90° that cannot be collected directly in the microscope. OTR requires a sample that adopts a large number of orientations on the support. Here, the RCT and OTR methods are reviewed and their performances with a biological test sample are compared. The steps required to apply OTR are also discussed.\",\n \"corpus_id\": 25782305,\n \"score\": 2\n },\n {\n \"doc_id\": \"21536134\",\n \"title\": \"Validation of the orthogonal tilt reconstruction method with a biological test sample.\",\n \"abstract\": \"Electron microscopy of frozen-hydrated samples (cryo-EM) can yield high resolution structures of macromolecular complexes by accurately determining the orientation of large numbers of experimental views of the sample relative to an existing 3D model. The \\\"initial model problem\\\", the challenge of obtaining these orientations ab initio, remains a major bottleneck in determining the structure of novel macromolecules, chiefly those lacking internal symmetry. We previously proposed a method for the generation of initial models--orthogonal tilt reconstruction (OTR)--that bypasses limitations inherent to the other two existing methods, random conical tilt (RCT) and angular reconstitution (AR). Here we present a validation of OTR with a biological test sample whose structure was previously solved by RCT: the complex between the yeast exosome and the subunit Rrp44. We show that, as originally demonstrated with synthetic data, OTR generates initial models that do not exhibit the \\\"missing cone\\\" artifacts associated with RCT and show an isotropic distribution of information when compared with the known structure. This eliminates the need for further user intervention to solve these artifacts and makes OTR ideal for automation and the analysis of heterogeneous samples. With the former in mind, we propose a set of simple quantitative criteria that can be used, in combination, to select from a large set of initial reconstructions a subset that can be used as reliable references for refinement to higher resolution.\",\n \"corpus_id\": 24370377,\n \"score\": 2\n },\n {\n \"doc_id\": \"23142631\",\n \"title\": \"Automated correlation of single particle tilt pairs for Random Conical Tilt and Orthogonal Tilt Reconstructions.\",\n \"abstract\": \"One of the major methodological challenges in single particle electron microscopy is obtaining initial reconstructions which represent the structural heterogeneity of the dataset. Random Conical Tilt and Orthogonal Tilt Reconstruction techniques in combination with 3D alignment and classification can be used to obtain initial low-resolution reconstructions which represent the full range of structural heterogeneity of the dataset. In order to achieve statistical significance, however, a large number of 3D reconstructions, and, in turn, a large number of tilted image pairs are required. The extraction of single particle tilted image pairs from micrographs can be tedious and time-consuming, as it requires intensive user input even for semi-automated approaches. To overcome the bottleneck of manual selection of a large number of tilt pairs, we developed an algorithm for the correlation of single particle images from tilted image pairs in a fully automated and user-independent manner. The algorithm reliably correlates correct pairs even from noisy micrographs. We further demonstrate the applicability of the algorithm by using it to obtain initial references both from negative stain and unstained cryo datasets.\",\n \"corpus_id\": 32528253,\n \"score\": 2\n },\n {\n \"doc_id\": \"19767196\",\n \"title\": \"Exploring conformational modes of macromolecular assemblies by multiparticle cryo-EM.\",\n \"abstract\": \"Single particle cryo-electron microscopy (cryo-EM) is a technique aimed at structure determination of large macromolecular complexes in their unconstrained, physiological conditions. The power of the method has been demonstrated in selected studies where for highly symmetric molecules the resolution attained permitted backbone tracing. However, most molecular complexes appear to exhibit intrinsic conformational variability necessary to perform their functions. Therefore, it is now increasingly recognized that sample heterogeneity constitutes a major methodological challenge for cryo-EM. To overcome it dedicated experimental and particularly computational multiparticle approaches have been developed. Their applications point to the future of cryo-EM as an experimental method uniquely suited to visualize the conformational modes of large macromolecular complexes and machines.\",\n \"corpus_id\": 39306886,\n \"score\": 1\n },\n {\n \"doc_id\": \"21490573\",\n \"title\": \"Single particle electron microscopy reconstruction of the exosome complex using the random conical tilt method.\",\n \"abstract\": \"Single particle electron microscopy (EM) reconstruction has recently become a popular tool to get the three-dimensional (3D) structure of large macromolecular complexes. Compared to X-ray crystallography, it has some unique advantages. First, single particle EM reconstruction does not need to crystallize the protein sample, which is the bottleneck in X-ray crystallography, especially for large macromolecular complexes. Secondly, it does not need large amounts of protein samples. Compared with milligrams of proteins necessary for crystallization, single particle EM reconstruction only needs several micro-liters of protein solution at nano-molar concentrations, using the negative staining EM method. However, despite a few macromolecular assemblies with high symmetry, single particle EM is limited at relatively low resolution (lower than 1 nm resolution) for many specimens especially those without symmetry. This technique is also limited by the size of the molecules under study, i.e. 100 kDa for negatively stained specimens and 300 kDa for frozen-hydrated specimens in general. For a new sample of unknown structure, we generally use a heavy metal solution to embed the molecules by negative staining. The specimen is then examined in a transmission electron microscope to take two-dimensional (2D) micrographs of the molecules. Ideally, the protein molecules have a homogeneous 3D structure but exhibit different orientations in the micrographs. These micrographs are digitized and processed in computers as \\\"single particles\\\". Using two-dimensional alignment and classification techniques, homogenous molecules in the same views are clustered into classes. Their averages enhance the signal of the molecule's 2D shapes. After we assign the particles with the proper relative orientation (Euler angles), we will be able to reconstruct the 2D particle images into a 3D virtual volume. In single particle 3D reconstruction, an essential step is to correctly assign the proper orientation of each single particle. There are several methods to assign the view for each particle, including the angular reconstitution(1) and random conical tilt (RCT) method(2). In this protocol, we describe our practice in getting the 3D reconstruction of yeast exosome complex using negative staining EM and RCT. It should be noted that our protocol of electron microscopy and image processing follows the basic principle of RCT but is not the only way to perform the method. We first describe how to embed the protein sample into a layer of Uranyl-Formate with a thickness comparable to the protein size, using a holey carbon grid covered with a layer of continuous thin carbon film. Then the specimen is inserted into a transmission electron microscope to collect untilted (0-degree) and tilted (55-degree) pairs of micrographs that will be used later for processing and obtaining an initial 3D model of the yeast exosome. To this end, we perform RCT and then refine the initial 3D model by using the projection matching refinement method(3).\",\n \"corpus_id\": 45189809,\n \"score\": 1\n },\n {\n \"doc_id\": \"23674685\",\n \"title\": \"Cross-validation in cryo-EM-based structural modeling.\",\n \"abstract\": \"Single-particle cryo-EM is a powerful approach to determine the structure of large macromolecules and assemblies thereof in many cases at subnanometer resolution. It has become popular to refine or flexibly fit atomic models into density maps derived from cryo-EM experiments. These density maps are typically significantly lower in resolution than electron density maps obtained from X-ray diffraction experiments, such that the number of parameters that need to be determined is much larger than the number of experimental observables. Overfitting and misinterpretation of the density, thus, become a serious problem. For diffraction data, a cross-validation approach was introduced almost 20 y ago; however, no such approach has been described yet for structure refinement against cryo-EM density maps, although the overfitting problem is, because of the lower resolution, significantly larger. We present a cross-validation approach for real-space refinement against cryo-EM density maps in analogy to cross-validation typically used in crystallography. Our approach is able to detect overfitting and allows for optimizing the choice of restraints used in the refinement. The approach is shown on three protein structures with simulated data and experimental data of the rotavirus double-layer particle. Because cross-validation requires splitting the dataset into at least two independent sets, we further present an approach to quantify correlations between the structure factor sets. This analysis is also helpful for other cross-validation applications, such as refinements against diffraction data or 3D reconstructions of cryo-EM density maps.\",\n \"corpus_id\": 205256350,\n \"score\": 1\n },\n {\n \"doc_id\": \"25839831\",\n \"title\": \"SubspaceEM: A fast maximum-a-posteriori algorithm for cryo-EM single particle reconstruction.\",\n \"abstract\": \"Single particle reconstruction methods based on the maximum-likelihood principle and the expectation-maximization (E-M) algorithm are popular because of their ability to produce high resolution structures. However, these algorithms are computationally very expensive, requiring a network of computational servers. To overcome this computational bottleneck, we propose a new mathematical framework for accelerating maximum-likelihood reconstructions. The speedup is by orders of magnitude and the proposed algorithm produces similar quality reconstructions compared to the standard maximum-likelihood formulation. Our approach uses subspace approximations of the cryo-electron microscopy (cryo-EM) data and projection images, greatly reducing the number of image transformations and comparisons that are computed. Experiments using simulated and actual cryo-EM data show that speedup in overall execution time compared to traditional maximum-likelihood reconstruction reaches factors of over 300.\",\n \"corpus_id\": 17850477,\n \"score\": 1\n },\n {\n \"doc_id\": \"27313000\",\n \"title\": \"Implementation of a cryo-electron tomography tilt-scheme optimized for high resolution subtomogram averaging.\",\n \"abstract\": \"Cryo-electron tomography (cryoET) allows 3D structural information to be obtained from cells and other biological samples in their close-to-native state. In combination with subtomogram averaging, detailed structures of repeating features can be resolved. CryoET data is collected as a series of images of the sample from different tilt angles; this is performed by physically rotating the sample in the microscope between each image. The angles at which the images are collected, and the order in which they are collected, together are called the tilt-scheme. Here we describe a \\\"dose-symmetric tilt-scheme\\\" that begins at low tilt and then alternates between increasingly positive and negative tilts. This tilt-scheme maximizes the amount of high-resolution information maintained in the tomogram for subsequent subtomogram averaging, and may also be advantageous for other applications. We describe implementation of the tilt-scheme in combination with further data-collection refinements including setting thresholds on acceptable drift and improving focus accuracy. Requirements for microscope set-up are introduced, and a macro is provided which automates the application of the tilt-scheme within SerialEM.\",\n \"corpus_id\": 3910770,\n \"score\": 1\n },\n {\n \"doc_id\": \"27800126\",\n \"title\": \"Cryo-electron Microscopy Analysis of Structurally Heterogeneous Macromolecular Complexes.\",\n \"abstract\": \"Cryo-electron microscopy (cryo-EM) has for a long time been a technique of choice for determining structure of large and flexible macromolecular complexes that were difficult to study by other experimental techniques such as X-ray crystallography or nuclear magnetic resonance. However, a fast development of instruments and software for cryo-EM in the last decade has allowed that a large range of complexes can be studied by cryo-EM, and that their structures can be obtained at near-atomic resolution, including the structures of small complexes (e.g., membrane proteins) whose size was earlier an obstacle to cryo-EM. Image analysis to identify multiple coexisting structures in the same specimen (multiconformation reconstruction) is now routinely done both to solve structures at near-atomic resolution and to study conformational dynamics. Methods for multiconformation reconstruction and latest examples of their applications are the focus of this review.\",\n \"corpus_id\": 15780788,\n \"score\": 1\n },\n {\n \"doc_id\": \"18274535\",\n \"title\": \"Visualization of macromolecular complexes using cryo-electron microscopy with FEI Tecnai transmission electron microscopes.\",\n \"abstract\": \"This protocol details the steps used for visualizing the frozen-hydrated grids as prepared following the accompanying protocol entitled 'Preparation of macromolecular complexes for visualization using cryo-electron microscopy.' This protocol describes how to transfer the grid to the microscope using a standard cryo-transfer holder or, alternatively, using a cryo-cartridge loading system, and how to collect low-dose data using an FEI Tecnai transmission electron microscope. This protocol also summarizes and compares the various options that are available in data collection for three-dimensional (3D) single-particle reconstruction. These options include microscope settings, choice of detectors and data collection strategies both in situations where a 3D reference is available and in the absence of such a reference (random-conical and common lines).\",\n \"corpus_id\": 10724478,\n \"score\": 0\n },\n {\n \"doc_id\": \"20541504\",\n \"title\": \"An approach for de novo structure determination of dynamic molecular assemblies by electron cryomicroscopy.\",\n \"abstract\": \"Single-particle electron cryomicroscopy is a powerful method for three-dimensional (3D) structure determination of macromolecular assemblies. Here we address the challenge of determining a 3D structure in the absence of reference models. The 3D structures are determined by alignment and weighted averaging of densities obtained by native cryo random conical tilt (RCT) reconstructions including consideration of missing data. Our weighted averaging scheme (wRCT) offers advantages for potentially heterogeneous 3D densities of low signal-to-noise ratios. Sets of aligned RCT structures can also be analyzed by multivariate statistical analysis (MSA) to provide insights into snapshots of the assemblies. The approach is used to compute 3D structures of the Escherichia coli 70S ribosome and the human U4/U6.U5 tri-snRNP under vitrified unstained cryo conditions, and to visualize by 3D MSA the L7/L12 stalk of the 70S ribosome and states of tri-snRNP. The approach thus combines de novo 3D structure determination with an analysis of compositional and conformational heterogeneity.\",\n \"corpus_id\": 261333,\n \"score\": 0\n },\n {\n \"doc_id\": \"20869255\",\n \"title\": \"Obtaining high-resolution images of biological macromolecules by using a cryo-electron microscope with a liquid-helium cooled stage.\",\n \"abstract\": \"To obtain high-resolution images of biological macromolecules, a cryo-electron microscope (cryo-EM) is useful to preserve the hydrated state of the molecules. In addition, the cryo-conditions reduce some of the electron radiation damage, although averaging is necessary to obtain the molecular resolution from biological macromolecules. For the averaging, the three reconstruction methods of electron crystallography, helical reconstruction, and single particle analysis facilitate the determination of the atomic models. Here we describe suitable techniques for high-resolution imaging in these three different methods, based on our experiences using cryo-EM with a liquid-helium cooled stage. Irradiation damage by the electron beam is the most serious problem in the structural analysis of a biological specimen, and we clearly show that further reduction of the specimen temperature, from liquid nitrogen to liquid helium temperature, improves the cryo-protection factor by at least two-fold for both glucose-embedded and frozen-hydrated specimens. We review the image processing, and then discuss the future prospects of cryo-EM.\",\n \"corpus_id\": 31986896,\n \"score\": 0\n },\n {\n \"doc_id\": \"20885381\",\n \"title\": \"Cryo-EM of macromolecular assemblies at near-atomic resolution.\",\n \"abstract\": \"With single-particle electron cryomicroscopy (cryo-EM), it is possible to visualize large, macromolecular assemblies in near-native states. Although subnanometer resolutions have been routinely achieved for many specimens, state of the art cryo-EM has pushed to near-atomic (3.3-4.6 Å) resolutions. At these resolutions, it is now possible to construct reliable atomic models directly from the cryo-EM density map. In this study, we describe our recently developed protocols for performing the three-dimensional reconstruction and modeling of Mm-cpn, a group II chaperonin, determined to 4.3 Å resolution. This protocol, utilizing the software tools EMAN, Gorgon and Coot, can be adapted for use with nearly all specimens imaged with cryo-EM that target beyond 5 Å resolution. Additionally, the feature recognition and computational modeling tools can be applied to any near-atomic resolution density maps, including those from X-ray crystallography.\",\n \"corpus_id\": 34769448,\n \"score\": 0\n },\n {\n \"doc_id\": \"20887855\",\n \"title\": \"GraFix: stabilization of fragile macromolecular complexes for single particle cryo-EM.\",\n \"abstract\": \"Here, we review the GraFix (Gradient Fixation) method to purify and stabilize macromolecular complexes for single particle cryo-electron microscopy (cryo-EM). During GraFix, macromolecules undergo a weak, intramolecular chemical cross-linking while being purified by density gradient ultracentrifugation. GraFix-stabilized particles can be used directly for negative-stain cryo-EM or, after a brief buffer-exchange step, for unstained cryo-EM. This highly reproducible method has proved to dramatically reduce problems in heterogeneity due to particle dissociation during EM grid preparation. Additionally, there is often an appreciable increase in particles binding to the carbon support film. This and the fact that binding times can be drastically increased, with no apparent disruption of the native structures of the macromolecules, makes GraFix a method of choice when preparing low-abundance complexes for cryo-EM. The higher sample quality following GraFix purification is evident when examining raw images, which usually present a low background of fragmented particles, good particle dispersion, and high-contrast, well-defined particles. Setting up the GraFix method is straightforward, and the resulting improvement in sample homogeneity has been beneficial in successfully obtaining the 3D structures of numerous macromolecular complexes by cryo-EM in the past few years.\",\n \"corpus_id\": 30501335,\n \"score\": 0\n },\n {\n \"doc_id\": \"21089695\",\n \"title\": \"[A review of automatic particle recognition in Cryo-EM images].\",\n \"abstract\": \"Advances in cryo-electron microscopy (Cryo-EM) and single-particle reconstruction have led to increasingly high resolutions of macromolecular three-dimensional reconstruction. However, for keeping up the continuing improvements in resolution, it is necessary to increase the number of particles included in performing reconstructions. Manual selection of particles, even assisted by computer, is a bottleneck of single-particle reconstruction. Cryo-EM image has low signal-to-noise ratio and low contrast, which leads to difficulty in particle picking. Various approaches have been developed to address the problem of automatic particle. This paper describes the application of template-based method, edge based method, feature-based method, neural network, DoG-based and simulated annealing approach in particle picking. The characteristics of various approaches are discussed, and the future development is presented.\",\n \"corpus_id\": 38932072,\n \"score\": 0\n },\n {\n \"doc_id\": \"21296162\",\n \"title\": \"Modeling protein structure at near atomic resolutions with Gorgon.\",\n \"abstract\": \"Electron cryo-microscopy (cryo-EM) has played an increasingly important role in elucidating the structure and function of macromolecular assemblies in near native solution conditions. Typically, however, only non-atomic resolution reconstructions have been obtained for these large complexes, necessitating computational tools for integrating and extracting structural details. With recent advances in cryo-EM, maps at near-atomic resolutions have been achieved for several macromolecular assemblies from which models have been manually constructed. In this work, we describe a new interactive modeling toolkit called Gorgon targeted at intermediate to near-atomic resolution density maps (10-3.5 Å), particularly from cryo-EM. Gorgon's de novo modeling procedure couples sequence-based secondary structure prediction with feature detection and geometric modeling techniques to generate initial protein backbone models. Beyond model building, Gorgon is an extensible interactive visualization platform with a variety of computational tools for annotating a wide variety of 3D volumes. Examples from cryo-EM maps of Rotavirus and Rice Dwarf Virus are used to demonstrate its applicability to modeling protein structure.\",\n \"corpus_id\": 330872,\n \"score\": 0\n },\n {\n \"doc_id\": \"21336521\",\n \"title\": \"Almost lost in translation. Cryo-EM of a dynamic macromolecular complex: the ribosome.\",\n \"abstract\": \"Ribosomes are dynamic biological machines that perform numerous tasks during translation, the biosynthesis of proteins. Translocation, the movement of transfer RNAs (tRNAs) and messenger RNA (mRNA) to progress in the reading frame of codons in the mRNA, takes place after the addition of each amino acid. This process involves large ribosome conformational changes, where tRNAs proceed through intermediate states. The structural characterization of these translocation intermediates has remained elusive. Cryo-electron microscopy (cryo-EM) produces three-dimensional averages, and translocating ribosomes poise distinct conformational states, and hence, structurally heterogeneous populations. During the last decade, the quest for visualization of translocation intermediates has progressed together with the development of classification tools in cryo-EM. Some of these new tools have recently been tested in ribosomal translocation, uncovering a clearer picture of the process. This success goes along with the latest advances in cryo-EM and illustrates how the technique offers multiple possibilities for studying macromolecular complexes engaged in dynamic reactions.\",\n \"corpus_id\": 26027815,\n \"score\": 0\n },\n {\n \"doc_id\": \"21385038\",\n \"title\": \"A blind deconvolution approach for improving the resolution of cryo-EM density maps.\",\n \"abstract\": \"Cryo-electron microscopy (cryo-EM) plays an increasingly prominent role in structure elucidation of macromolecular assemblies. Advances in experimental instrumentation and computational power have spawned numerous cryo-EM studies of large biomolecular complexes resulting in the reconstruction of three-dimensional density maps at intermediate and low resolution. In this resolution range, identification and interpretation of structural elements and modeling of biomolecular structure with atomic detail becomes problematic. In this article, we present a novel algorithm that enhances the resolution of intermediate- and low-resolution density maps. Our underlying assumption is to model the low-resolution density map as a blurred and possibly noise-corrupted version of an unknown high-resolution map that we seek to recover by deconvolution. By exploiting the nonnegativity of both the high-resolution map and blur kernel, we derive multiplicative updates reminiscent of those used in nonnegative matrix factorization. Our framework allows for easy incorporation of additional prior knowledge such as smoothness and sparseness, on both the sharpened density map and the blur kernel. A probabilistic formulation enables us to derive updates for the hyperparameters; therefore, our approach has no parameter that needs adjustment. We apply the algorithm to simulated three-dimensional electron microscopic data. We show that our method provides better resolved density maps when compared with B-factor sharpening, especially in the presence of noise. Moreover, our method can use additional information provided by homologous structures, which helps to improve the resolution even further.\",\n \"corpus_id\": 206154292,\n \"score\": 0\n },\n {\n \"doc_id\": \"21845206\",\n \"title\": \"Near-atomic-resolution cryo-EM for molecular virology.\",\n \"abstract\": \"Electron cryo-microscopy (cryo-EM) is a technique in structural biology that is widely used to solve the three-dimensional structures of macromolecular assemblies, close to their biological and solution conditions. Recent improvements in cryo-EM and single-particle reconstruction methodologies have led to the determination of several virus structures at near-atomic resolution (3.3 - 4.6 Å). These cryo-EM structures not only resolve the Cα backbones and side-chain densities of viral capsid proteins, but also suggest functional roles that the protein domains and some key amino acid residues play. This paper reviews the recent advances in near-atomic-resolution cryo-EM for probing the mechanisms of virus assembly and morphogenesis.\",\n \"corpus_id\": 13880338,\n \"score\": 0\n },\n {\n \"doc_id\": \"21860371\",\n \"title\": \"Structure of HIV-1 capsid assemblies by cryo-electron microscopy and iterative helical real-space reconstruction.\",\n \"abstract\": \"Cryo-electron microscopy (cryo-EM), combined with image processing, is an increasingly powerful tool for structure determination of macromolecular protein complexes and assemblies. In fact, single particle electron microscopy and two-dimensional (2D) electron crystallography have become relatively routine methodologies and a large number of structures have been solved using these methods. At the same time, image processing and three-dimensional (3D) reconstruction of helical objects has rapidly developed, especially, the iterative helical real-space reconstruction (IHRSR) method, which uses single particle analysis tools in conjunction with helical symmetry. Many biological entities function in filamentous or helical forms, including actin filaments, microtubules, amyloid fibers, tobacco mosaic viruses, and bacteria flagella, and, because a 3D density map of a helical entity can be attained from a single projection image, compared to the many images required for 3D reconstruction of a non-helical object, with the IHRSR method, structural analysis of such flexible and disordered helical assemblies is now attainable. In this video article, we provide detailed protocols for obtaining a 3D density map of a helical protein assembly (HIV-1 capsid is our example), including protocols for cryo-EM specimen preparation, low dose data collection by cryo-EM, indexing of helical diffraction patterns, and image processing and 3D reconstruction using IHRSR. Compared to other techniques, cryo-EM offers optimal specimen preservation under near native conditions. Samples are embedded in a thin layer of vitreous ice, by rapid freezing, and imaged in electron microscopes at liquid nitrogen temperature, under low dose conditions to minimize the radiation damage. Sample images are obtained under near native conditions at the expense of low signal and low contrast in the recorded micrographs. Fortunately, the process of helical reconstruction has largely been automated, with the exception of indexing the helical diffraction pattern. Here, we describe an approach to index helical structure and determine helical symmetries (helical parameters) from digitized micrographs, an essential step for 3D helical reconstruction. Briefly, we obtain an initial 3D density map by applying the IHRSR method. This initial map is then iteratively refined by introducing constraints for the alignment parameters of each segment, thus controlling their degrees of freedom. Further improvement is achieved by correcting for the contrast transfer function (CTF) of the electron microscope (amplitude and phase correction) and by optimizing the helical symmetry of the assembly.\",\n \"corpus_id\": 8398013,\n \"score\": 0\n },\n {\n \"doc_id\": \"22100448\",\n \"title\": \"A Bayesian view on cryo-EM structure determination.\",\n \"abstract\": \"Three-dimensional (3D) structure determination by single-particle analysis of cryo-electron microscopy (cryo-EM) images requires many parameters to be determined from extremely noisy data. This makes the method prone to overfitting, that is, when structures describe noise rather than signal, in particular near their resolution limit where noise levels are highest. Cryo-EM structures are typically filtered using ad hoc procedures to prevent overfitting, but the tuning of arbitrary parameters may lead to subjectivity in the results. I describe a Bayesian interpretation of cryo-EM structure determination, where smoothness in the reconstructed density is imposed through a Gaussian prior in the Fourier domain. The statistical framework dictates how data and prior knowledge should be combined, so that the optimal 3D linear filter is obtained without the need for arbitrariness and objective resolution estimates may be obtained. Application to experimental data indicates that the statistical approach yields more reliable structures than existing methods and is capable of detecting smaller classes in data sets that contain multiple different structures.\",\n \"corpus_id\": 5427936,\n \"score\": 0\n },\n {\n \"doc_id\": \"22291925\",\n \"title\": \"IPET and FETR: experimental approach for studying molecular structure dynamics by cryo-electron tomography of a single-molecule structure.\",\n \"abstract\": \"The dynamic personalities and structural heterogeneity of proteins are essential for proper functioning. Structural determination of dynamic/heterogeneous proteins is limited by conventional approaches of X-ray and electron microscopy (EM) of single-particle reconstruction that require an average from thousands to millions different molecules. Cryo-electron tomography (cryoET) is an approach to determine three-dimensional (3D) reconstruction of a single and unique biological object such as bacteria and cells, by imaging the object from a series of tilting angles. However, cconventional reconstruction methods use large-size whole-micrographs that are limited by reconstruction resolution (lower than 20 Å), especially for small and low-symmetric molecule (<400 kDa). In this study, we demonstrated the adverse effects from image distortion and the measuring tilt-errors (including tilt-axis and tilt-angle errors) both play a major role in limiting the reconstruction resolution. Therefore, we developed a \\\"focused electron tomography reconstruction\\\" (FETR) algorithm to improve the resolution by decreasing the reconstructing image size so that it contains only a single-instance protein. FETR can tolerate certain levels of image-distortion and measuring tilt-errors, and can also precisely determine the translational parameters via an iterative refinement process that contains a series of automatically generated dynamic filters and masks. To describe this method, a set of simulated cryoET images was employed; to validate this approach, the real experimental images from negative-staining and cryoET were used. Since this approach can obtain the structure of a single-instance molecule/particle, we named it individual-particle electron tomography (IPET) as a new robust strategy/approach that does not require a pre-given initial model, class averaging of multiple molecules or an extended ordered lattice, but can tolerate small tilt-errors for high-resolution single \\\"snapshot\\\" molecule structure determination. Thus, FETR/IPET provides a completely new opportunity for a single-molecule structure determination, and could be used to study the dynamic character and equilibrium fluctuation of macromolecules.\",\n \"corpus_id\": 4807732,\n \"score\": 0\n },\n {\n \"doc_id\": \"23181775\",\n \"title\": \"Cryo-electron microscopy--a primer for the non-microscopist.\",\n \"abstract\": \"Cryo-electron microscopy (cryo-EM) is increasingly becoming a mainstream technology for studying the architecture of cells, viruses and protein assemblies at molecular resolution. Recent developments in microscope design and imaging hardware, paired with enhanced image processing and automation capabilities, are poised to further advance the effectiveness of cryo-EM methods. These developments promise to increase the speed and extent of automation, and to improve the resolutions that may be achieved, making this technology useful to determine a wide variety of biological structures. Additionally, established modalities for structure determination, such as X-ray crystallography and nuclear magnetic resonance spectroscopy, are being routinely integrated with cryo-EM density maps to achieve atomic-resolution models of complex, dynamic molecular assemblies. In this review, which is directed towards readers who are not experts in cryo-EM methodology, we provide an overview of emerging themes in the application of this technology to investigate diverse questions in biology and medicine. We discuss the ways in which these methods are being used to study structures of macromolecular assemblies that range in size from whole cells to small proteins. Finally, we include a description of how the structural information obtained by cryo-EM is deposited and archived in a publicly accessible database.\",\n \"corpus_id\": 205132714,\n \"score\": 0\n },\n {\n \"doc_id\": \"23217682\",\n \"title\": \"Protein secondary structure determination by constrained single-particle cryo-electron tomography.\",\n \"abstract\": \"Cryo-electron microscopy (cryo-EM) is a powerful technique for 3D structure determination of protein complexes by averaging information from individual molecular images. The resolutions that can be achieved with single-particle cryo-EM are frequently limited by inaccuracies in assigning molecular orientations based solely on 2D projection images. Tomographic data collection schemes, however, provide powerful constraints that can be used to more accurately determine molecular orientations necessary for 3D reconstruction. Here, we propose \\\"constrained single-particle tomography\\\" as a general strategy for 3D structure determination in cryo-EM. A key component of our approach is the effective use of images recorded in tilt series to extract high-resolution information and correct for the contrast transfer function. By incorporating geometric constraints into the refinement to improve orientational accuracy of images, we reduce model bias and overrefinement artifacts and demonstrate that protein structures can be determined at resolutions of ∼8 Å starting from low-dose tomographic tilt series.\",\n \"corpus_id\": 13791074,\n \"score\": 0\n },\n {\n \"doc_id\": \"23416197\",\n \"title\": \"Consensus among multiple approaches as a reliability measure for flexible fitting into cryo-EM data.\",\n \"abstract\": \"Cryo-electron microscopy (cryo-EM) can provide low-resolution density maps of large macromolecular assemblies. As the number of structures deposited in the Protein Data Bank by fitting a high-resolution structure into a low-resolution cryo-EM map is increasing, there is a need to revise the protocols and improve the measures for fitting. A recent study suggested using a combination of multiple automated flexible fitting approaches to improve the interpretation of cryo-EM data. The current work further explores the use of multiple approaches by validating this \\\"consensus\\\" fitting approach and deriving a local reliability measure. Here four different flexible fitting approaches are applied for fitting an initial structure into a simulated density map of known target structure from a dataset of proteins. It is found that the models produced from different approaches often have a consensus in conformation and are also near to the target structure, whereas cases not showing consensus are away from the target. A high correlation is also observed between the RMSF profiles calculated with respect to the average and the target structures, which indicates that the relation between consensus and accuracy can also be extended to a per-residue level. Therefore, the RMSF among the fitted models is proposed as a local reliability measure, which can be used to assess the reliability of the fit at specific regions. Hence, we encourage the community to use consensus flexible fitting with different methods to report on local reliability of the resulting models and improve the interpretation of cryo-EM data.\",\n \"corpus_id\": 12214200,\n \"score\": 0\n },\n {\n \"doc_id\": \"23707684\",\n \"title\": \"Validation of cryo-EM structure of IP₃R1 channel.\",\n \"abstract\": \"About a decade ago, three electron cryomicroscopy (cryo-EM) single-particle reconstructions of IP3R1 were reported at low resolution. It was disturbing that these structures bore little similarity to one another, even at the level of quaternary structure. Recently, we published an improved structure of IP3R1 at ∼1 nm resolution. However, this structure did not bear any resemblance to any of the three previously published structures, leading to the question of why the structure should be considered more reliable than the original three. Here, we apply several methods, including class-average/map comparisons, tilt-pair validation, and use of multiple refinement software packages, to give strong evidence for the reliability of our recent structure. The map resolution and feature resolvability are assessed with the gold standard criterion. This approach is generally applicable to assessing the validity of cryo-EM maps of other molecular machines.\",\n \"corpus_id\": 9719520,\n \"score\": 0\n },\n {\n \"doc_id\": \"23737049\",\n \"title\": \"Conventional electron microscopy, cryo-electron microscopy and cryo-electron tomography of viruses.\",\n \"abstract\": \"Electron microscopy (EM) techniques have been crucial for understanding the structure of biological specimens such as cells, tissues and macromolecular assemblies. Viruses and related viral assemblies are ideal targets for structural studies that help to define essential biological functions. Whereas conventional EM methods use chemical fixation, dehydration, and staining of the specimens, cryo-electron microscopy (cryo-EM) preserves the native hydrated state. Combined with image processing and three-dimensional reconstruction techniques, cryo-EM provides 3D maps of these macromolecular complexes from projection images, at subnanometer to near-atomic resolutions. Cryo-EM is also a major technique in structural biology for dynamic studies of functional complexes, which are often unstable, flexible, scarce or transient in their native environments. As a tool, cryo-EM complements high-resolution techniques such as X-ray diffraction and NMR spectroscopy; these synergistic hybrid approaches provide important new information. Three-dimensional cryo-electron tomography goes further, and allows the study of viruses not only in their physiological state, but also in their natural environment in the cell, thereby bridging structural studies at the molecular and cellular levels.\",\n \"corpus_id\": 38844770,\n \"score\": 0\n },\n {\n \"doc_id\": \"23931142\",\n \"title\": \"PRIME: probabilistic initial 3D model generation for single-particle cryo-electron microscopy.\",\n \"abstract\": \"Low-dose electron microscopy of cryo-preserved individual biomolecules (single-particle cryo-EM) is a powerful tool for obtaining information about the structure and dynamics of large macromolecular assemblies. Acquiring images with low dose reduces radiation damage, preserves atomic structural details, but results in low signal-to-noise ratio of the individual images. The projection directions of the two-dimensional images are random and unknown. The grand challenge is to achieve the precise three-dimensional (3D) alignment of many (tens of thousands to millions) noisy projection images, which may then be combined to obtain a faithful 3D map. An accurate initial 3D model is critical for obtaining the precise 3D alignment required for high-resolution (<10 Å) map reconstruction. We report a method (PRIME) that, in a single step and without prior structural knowledge, can generate an accurate initial 3D map directly from the noisy images.\",\n \"corpus_id\": 12087592,\n \"score\": 0\n },\n {\n \"doc_id\": \"24161732\",\n \"title\": \"Optimod--an automated approach for constructing and optimizing initial models for single-particle electron microscopy.\",\n \"abstract\": \"Single-particle cryo-electron microscopy is now well established as a technique for the structural characterization of large macromolecules and macromolecular complexes. The raw data is very noisy and consists of two-dimensional projections, from which the 3D biological object must be reconstructed. The 3D object depends upon knowledge of proper angular orientations assigned to the 2D projection images. Numerous algorithms have been developed for determining relative angular orientations between 2D images, but the transition from 2D to 3D remains challenging and can result in erroneous and conflicting results. Here we describe a general, automated procedure, called OptiMod, for reconstructing and optimizing 3D models using common-lines methodologies. OptiMod approximates orientation angles and reconstructs independent maps from 2D class averages. It then iterates the procedure, while considering each map as a raw solution that needs to be compared with other possible outcomes. We incorporate procedures for 3D alignment, clustering, and refinement to optimize each map, as well as standard scoring metrics to facilitate the selection of the optimal model. We also show that small angle tilt-pair data can be included as one of the scoring metrics to improve the selection of the optimal initial model, and also to provide a validation check. The overall approach is demonstrated using two experimental cryo-EM data sets--the 80S ribosome that represents a relatively straightforward case for ab initio reconstruction, and the Tf-TfR complex that represents a challenging case in that it has previously been shown to provide multiple equally plausible solutions to the initial model problem.\",\n \"corpus_id\": 36681249,\n \"score\": 0\n },\n {\n \"doc_id\": \"24390311\",\n \"title\": \"High-resolution cryo-electron microscopy on macromolecular complexes and cell organelles.\",\n \"abstract\": \"Cryo-electron microscopy techniques and computational 3-D reconstruction of macromolecular assemblies are tightly linked tools in modern structural biology. This symbiosis has produced vast amounts of detailed information on the structure and function of biological macromolecules. Typically, one of two fundamentally different strategies is used depending on the specimens and their environment. A: 3-D reconstruction based on repetitive and structurally identical unit cells that allow for averaging, and B: tomographic 3-D reconstructions where tilt-series between approximately ± 60 and ± 70° at small angular increments are collected from highly complex and flexible structures that are beyond averaging procedures, at least during the first round of 3-D reconstruction. Strategies of group A are averaging-based procedures and collect large number of 2-D projections at different angles that are computationally aligned, averaged together, and back-projected in 3-D space to reach a most complete 3-D dataset with high resolution, today often down to atomic detail. Evidently, success relies on structurally repetitive particles and an aligning procedure that unambiguously determines the angular relationship of all 2-D projections with respect to each other. The alignment procedure of small particles may rely on their packing into a regular array such as a 2-D crystal, an icosahedral (viral) particle, or a helical assembly. Critically important for cryo-methods, each particle will only be exposed once to the electron beam, making these procedures optimal for highest-resolution studies where beam-induced damage is a significant concern. In contrast, tomographic 3-D reconstruction procedures (group B) do not rely on averaging, but collect an entire dataset from the very same structure of interest. Data acquisition requires collecting a large series of tilted projections at angular increments of 1-2° or less and a tilt range of ± 60° or more. Accordingly, tomographic data collection exposes its specimens to a large electron dose, which is particularly problematic for frozen-hydrated samples. Currently, cryo-electron tomography is a rapidly emerging technology, on one end driven by the newest developments of hardware such as super-stabile microscopy stages as well as the latest generation of direct electron detectors and cameras. On the other end, success also strongly depends on new software developments on all kinds of fronts such as tilt-series alignment and back-projection procedures that are all adapted to the very low-dose and therefore very noisy primary data. Here, we will review the status quo of cryo-electron microscopy and discuss the future of cellular cryo-electron tomography from data collection to data analysis, CTF-correction of tilt-series, post-tomographic sub-volume averaging, and 3-D particle classification. We will also discuss the pros and cons of plunge freezing of cellular specimens to vitrified sectioning procedures and their suitability for post-tomographic volume averaging despite multiple artifacts that may distort specimens to some degree.\",\n \"corpus_id\": 13894885,\n \"score\": 0\n },\n {\n \"doc_id\": \"25544475\",\n \"title\": \"How cryo-EM is revolutionizing structural biology.\",\n \"abstract\": \"For many years, structure determination of biological macromolecules by cryo-electron microscopy (cryo-EM) was limited to large complexes or low-resolution models. With recent advances in electron detection and image processing, the resolution by cryo-EM is now beginning to rival X-ray crystallography. A new generation of electron detectors record images with unprecedented quality, while new image-processing tools correct for sample movements and classify images according to different structural states. Combined, these advances yield density maps with sufficient detail to deduce the atomic structure for a range of specimens. Here, we review the recent advances and illustrate the exciting new opportunities that they offer to structural biology research.\",\n \"corpus_id\": 19727349,\n \"score\": 0\n },\n {\n \"doc_id\": \"25707802\",\n \"title\": \"Structure of the E. coli ribosome-EF-Tu complex at <3 Å resolution by Cs-corrected cryo-EM.\",\n \"abstract\": \"Single particle electron cryomicroscopy (cryo-EM) has recently made significant progress in high-resolution structure determination of macromolecular complexes due to improvements in electron microscopic instrumentation and computational image analysis. However, cryo-EM structures can be highly non-uniform in local resolution and all structures available to date have been limited to resolutions above 3 Å. Here we present the cryo-EM structure of the 70S ribosome from Escherichia coli in complex with elongation factor Tu, aminoacyl-tRNA and the antibiotic kirromycin at 2.65-2.9 Å resolution using spherical aberration (Cs)-corrected cryo-EM. Overall, the cryo-EM reconstruction at 2.9 Å resolution is comparable to the best-resolved X-ray structure of the E. coli 70S ribosome (2.8 Å), but provides more detailed information (2.65 Å) at the functionally important ribosomal core. The cryo-EM map elucidates for the first time the structure of all 35 rRNA modifications in the bacterial ribosome, explaining their roles in fine-tuning ribosome structure and function and modulating the action of antibiotics. We also obtained atomic models for flexible parts of the ribosome such as ribosomal proteins L9 and L31. The refined cryo-EM-based model presents the currently most complete high-resolution structure of the E. coli ribosome, which demonstrates the power of cryo-EM in structure determination of large and dynamic macromolecular complexes.\",\n \"corpus_id\": 4395954,\n \"score\": 0\n },\n {\n \"doc_id\": \"25747402\",\n \"title\": \"Cryogenic electron microscopy and single-particle analysis.\",\n \"abstract\": \"About 20 years ago, the first three-dimensional (3D) reconstructions at subnanometer (<10-Å) resolution of an icosahedral virus assembly were obtained by cryogenic electron microscopy (cryo-EM) and single-particle analysis. Since then, thousands of structures have been determined to resolutions ranging from 30 Å to near atomic (<4 Å). Almost overnight, the recent development of direct electron detectors and the attendant improvement in analysis software have advanced the technology considerably. Near-atomic-resolution reconstructions can now be obtained, not only for megadalton macromolecular complexes or highly symmetrical assemblies but also for proteins of only a few hundred kilodaltons. We discuss the developments that led to this breakthrough in high-resolution structure determination by cryo-EM and point to challenges that lie ahead.\",\n \"corpus_id\": 37880033,\n \"score\": 0\n },\n {\n \"doc_id\": \"25894285\",\n \"title\": \"Cryo-electron microscopy for structural biology: current status and future perspectives.\",\n \"abstract\": \"Recently, significant technical breakthroughs in both hardware equipment and software algorithms have enabled cryo-electron microscopy (cryo-EM) to become one of the most important techniques in biological structural analysis. The technical aspects of cryo-EM define its unique advantages and the direction of development. As a rapidly emerging field, cryo-EM has benefitted from highly interdisciplinary research efforts. Here we review the current status of cryo-EM in the context of structural biology and discuss the technical challenges. It may eventually merge structural and cell biology at multiple scales.\",\n \"corpus_id\": 1728363,\n \"score\": 0\n },\n {\n \"doc_id\": \"25955078\",\n \"title\": \"Cryo-electron microscopy and the amazing race to atomic resolution.\",\n \"abstract\": \"Cryo-electron microscopy (cryo-EM), the structural analysis of samples embedded in vitreous ice, is a powerful approach for determining three-dimensional (3D) structures of biological specimens. Over the past two decades, this technique has been used to successfully calculate subnanometer (<10 Å) resolution and, in some cases, near-atomic resolution structures of highly symmetrical and stable complexes such as icosahedral viruses and ribosomes, as well as samples that form ordered two-dimensional or helical arrays. However, determining high-resolution 3D structures of smaller, less symmetrical, and dynamic samples remains a significant challenge. The recent development of electron microscopes with automated data collection capabilities and robust direct electron detection cameras, as well as new powerful image processing algorithms, has dramatically expanded the number of biological macromolecules amenable for study using cryo-EM. In addition, these new technological and computational developments have been used to successfully determine <5 Å resolution 3D structures of samples, such as membrane proteins and complexes with either low or no symmetry, that traditionally were not considered promising candidates for high-resolution cryo-EM. With these exciting new advances, cryo-EM is now on pace to determine atomic resolution 3D structures.\",\n \"corpus_id\": 5180848,\n \"score\": 0\n },\n {\n \"doc_id\": \"26000851\",\n \"title\": \"Cryo-EM: A Unique Tool for the Visualization of Macromolecular Complexity.\",\n \"abstract\": \"3D cryo-electron microscopy (cryo-EM) is an expanding structural biology technique that has recently undergone a quantum leap progression in its achievable resolution and its applicability to the study of challenging biological systems. Because crystallization is not required, only small amounts of sample are needed, and because images can be classified in a computer, the technique has the potential to deal with compositional and conformational mixtures. Therefore, cryo-EM can be used to investigate complete and fully functional macromolecular complexes in different functional states, providing a richness of biological insight. In this review, we underlie some of the principles behind the cryo-EM methodology of single particle analysis and discuss some recent results of its application to challenging systems of paramount biological importance. We place special emphasis on new methodological developments that are leading to an explosion of new studies, many of which are reaching resolutions that could only be dreamed of just a couple of years ago.\",\n \"corpus_id\": 40789821,\n \"score\": 0\n },\n {\n \"doc_id\": \"26068751\",\n \"title\": \"Using Molecular Simulation to Model High-Resolution Cryo-EM Reconstructions.\",\n \"abstract\": \"An explosion of new data from high-resolution cryo-electron microscopy (cryo-EM) studies has produced a large number of data sets for many species of ribosomes in various functional states over the past few years. While many methods exist to produce structural models for lower resolution cryo-EM reconstructions, high-resolution reconstructions are often modeled using crystallographic techniques and extensive manual intervention. Here, we present an automated fitting technique for high-resolution cryo-EM data sets that produces all-atom models highly consistent with the EM density. Using a molecular dynamics approach, atomic positions are optimized with a potential that includes the cross-correlation coefficient between the structural model and the cryo-EM electron density, as well as a biasing potential preserving the stereochemistry and secondary structure of the biomolecule. Specifically, we use a hybrid structure-based/ab initio molecular dynamics potential to extend molecular dynamics fitting. In addition, we find that simulated annealing integration, as opposed to straightforward molecular dynamics integration, significantly improves performance. We obtain atomistic models of the human ribosome consistent with high-resolution cryo-EM reconstructions of the human ribosome. Automated methods such as these have the potential to produce atomistic models for a large number of ribosome complexes simultaneously that can be subsequently refined manually.\",\n \"corpus_id\": 27340829,\n \"score\": 0\n },\n {\n \"doc_id\": \"26456135\",\n \"title\": \"In Situ Cryo-Electron Tomography: A Post-Reductionist Approach to Structural Biology.\",\n \"abstract\": \"Cryo-electron tomography is a powerful technique that can faithfully image the native cellular environment at nanometer resolution. Unlike many other imaging approaches, cryo-electron tomography provides a label-free method of detecting biological structures, relying on the intrinsic contrast of frozen cellular material for direct identification of macromolecules. Recent advances in sample preparation, detector technology, and phase plate imaging have enabled the structural characterization of protein complexes within intact cells. Here, we review these technical developments and outline a detailed computational workflow for in situ structural analysis. Two recent studies are described to illustrate how this workflow can be adapted to examine both known and unknown cellular complexes. The stage is now set to realize the promise of visual proteomics-a complete structural description of the cell's native molecular landscape.\",\n \"corpus_id\": 206214810,\n \"score\": 0\n },\n {\n \"doc_id\": \"26611544\",\n \"title\": \"Single-particle cryo-electron microscopy of macromolecular complexes.\",\n \"abstract\": \"Recent technological breakthroughs in image acquisition have enabled single-particle cryo-electron microscopy (cryo-EM) to achieve near-atomic resolution structural information for biological complexes. The improvements in image quality coupled with powerful computational methods for sorting distinct particle populations now also allow the determination of compositional and conformational ensembles, thereby providing key insights into macromolecular function. However, the inherent instability and dynamic nature of biological assemblies remain a tremendous challenge that often requires tailored approaches for successful implementation of the methodology. Here, we briefly describe the fundamentals of single-particle cryo-EM with an emphasis on covering the breadth of techniques and approaches, including low- and high-resolution methods, aiming to illustrate specific steps that are crucial for obtaining structural information by this method.\",\n \"corpus_id\": 4928921,\n \"score\": 0\n },\n {\n \"doc_id\": \"26638773\",\n \"title\": \"Cryo electron microscopy to determine the structure of macromolecular complexes.\",\n \"abstract\": \"Cryo-electron microscopy (cryo-EM) is a structural molecular and cellular biology technique that has experienced major advances in recent years. Technological developments in image recording as well as in processing software make it possible to obtain three-dimensional reconstructions of macromolecular assemblies at near-atomic resolution that were formerly obtained only by X-ray crystallography or NMR spectroscopy. In parallel, cryo-electron tomography has also benefitted from these technological advances, so that visualization of irregular complexes, organelles or whole cells with their molecular machines in situ has reached subnanometre resolution. Cryo-EM can therefore address a broad range of biological questions. The aim of this review is to provide a brief overview of the principles and current state of the cryo-EM field.\",\n \"corpus_id\": 4981550,\n \"score\": 0\n },\n {\n \"doc_id\": \"26671943\",\n \"title\": \"Sample preparation of biological macromolecular assemblies for the determination of high-resolution structures by cryo-electron microscopy.\",\n \"abstract\": \"Single particle cryo-EM has recently developed into a powerful tool to determine the 3D structure of macromolecular complexes at near-atomic resolution, which allows structural biologists to build atomic models of proteins. All technical aspects of cryo-EM technology have been considerably improved over the last two decades, including electron microscopic hardware, image processing software and the ever growing speed of computers. This leads to a more widespread use of the technique, and it can be anticipated that further automation of electron microscopes and image processing tools will soon fully shift the focus away from the technological aspects, onto biological questions that can be answered. In single particle cryo-EM, no crystals of a macromolecule are required. In contrast to X-ray crystallography, this significantly facilitates structure determination by cryo-EM. Nevertheless, a relatively high level of biochemical control is still essential to obtain high-resolution structures by cryo-EM, and it can be anticipated that the success of the cryo-EM technology goes hand in hand with further developments of sample purification and preparation techniques. This will allow routine high-resolution structure determination of the many macromolecular complexes of the cell that until now represent evasive targets for X-ray crystallographers. Here we discuss the various biochemical tools that are currently available and the existing sample purification and preparation techniques for cryo-EM grid preparation that are needed to obtain high-resolution images for structure determination.\",\n \"corpus_id\": 23067203,\n \"score\": 0\n },\n {\n \"doc_id\": \"26787742\",\n \"title\": \"Cellular structural biology as revealed by cryo-electron tomography.\",\n \"abstract\": \"Understanding the function of cellular machines requires a thorough analysis of the structural elements that underline their function. Electron microscopy (EM) has been pivotal in providing information about cellular ultrastructure, as well as macromolecular organization. Biological materials can be physically fixed by vitrification and imaged with cryo-electron tomography (cryo-ET) in a close-to-native condition. Using this technique, one can acquire three-dimensional (3D) information about the macromolecular architecture of cells, depict unique cellular states and reconstruct molecular networks. Technical advances over the last few years, such as improved sample preparation and electron detection methods, have been instrumental in obtaining data with unprecedented structural details. This presents an exciting opportunity to explore the molecular architecture of both individual cells and multicellular organisms at nanometer to subnanometer resolution. In this Commentary, we focus on the recent developments and in situ applications of cryo-ET to cell and structural biology.\",\n \"corpus_id\": 2543759,\n \"score\": 0\n },\n {\n \"doc_id\": \"26931652\",\n \"title\": \"An introduction to sample preparation and imaging by cryo-electron microscopy for structural biology.\",\n \"abstract\": \"Transmission electron microscopy (EM) is a versatile technique that can be used to image biological specimens ranging from intact eukaryotic cells to individual proteins >150kDa. There are several strategies for preparing samples for imaging by EM, including negative staining and cryogenic freezing. In the last few years, cryo-EM has undergone a 'resolution revolution', owing to both advances in imaging hardware, image processing software, and improvements in sample preparation, leading to growing number of researchers using cryo-EM as a research tool. However, cryo-EM is still a rapidly growing field, with unique challenges. Here, we summarise considerations for imaging of a range of specimens from macromolecular complexes to cells using EM.\",\n \"corpus_id\": 3562560,\n \"score\": 0\n },\n {\n \"doc_id\": \"27280059\",\n \"title\": \"Comparison of an Atomic Model and Its Cryo-EM Image at the Central Axis of a Helix.\",\n \"abstract\": \"Cryo-electron microscopy (cryo-EM) is an important biophysical technique that produces three-dimensional (3D) density maps at different resolutions. Because more and more models are being produced from cryo-EM density maps, validation of the models is becoming important. We propose a method for measuring local agreement between a model and the density map using the central axis of the helix. This method was tested using 19 helices from cryo-EM density maps between 5.5 Å and 7.2 Å resolution and 94 helices from simulated density maps. This method distinguished most of the well-fitting helices, although challenges exist for shorter helices.\",\n \"corpus_id\": 23795543,\n \"score\": 0\n },\n {\n \"doc_id\": \"27572731\",\n \"title\": \"Refinement of Atomic Structures Against cryo-EM Maps.\",\n \"abstract\": \"This review describes some of the methods for atomic structure refinement (fitting) against medium/high-resolution single-particle cryo-EM reconstructed maps. Some of the tools developed for macromolecular X-ray crystal structure analysis, especially those encapsulating prior chemical and structural information can be transferred directly for fitting into cryo-EM maps. However, despite the similarities, there are significant differences between data produced by these two techniques; therefore, different likelihood functions linking the data and model must be used in cryo-EM and crystallographic refinement. Although tools described in this review are mostly designed for medium/high-resolution maps, if maps have sufficiently good quality, then these tools can also be used at moderately low resolution, as shown in one example. In addition, the use of several popular crystallographic methods is strongly discouraged in cryo-EM refinement, such as 2Fo-Fc maps, solvent flattening, and feature-enhanced maps (FEMs) for visualization and model (re)building. Two problems in the cryo-EM field are overclaiming resolution and severe map oversharpening. Both of these should be avoided; if data of higher resolution than the signal are used, then overfitting of model parameters into the noise is unavoidable, and if maps are oversharpened, then at least parts of the maps might become very noisy and ultimately uninterpretable. Both of these may result in suboptimal and even misleading atomic models.\",\n \"corpus_id\": 3568888,\n \"score\": 0\n },\n {\n \"doc_id\": \"27572734\",\n \"title\": \"High-Resolution Macromolecular Structure Determination by MicroED, a cryo-EM Method.\",\n \"abstract\": \"Microelectron diffraction (MicroED) is a new cryo-electron microscopy (cryo-EM) method capable of determining macromolecular structures at atomic resolution from vanishingly small 3D crystals. MicroED promises to solve atomic resolution structures from even the tiniest of crystals, less than a few hundred nanometers thick. MicroED complements frontier advances in crystallography and represents part of the rebirth of cryo-EM that is making macromolecular structure determination more accessible for all. Here we review the concept and practice of MicroED, for both the electron microscopist and crystallographer. Where other reviews have addressed specific details of the technique (Hattne et al., 2015; Shi et al., 2016; Shi, Nannenga, Iadanza, & Gonen, 2013), we aim to provide context and highlight important features that should be considered when performing a MicroED experiment.\",\n \"corpus_id\": 205165728,\n \"score\": 0\n },\n {\n \"doc_id\": \"27669148\",\n \"title\": \"Automated structure refinement of macromolecular assemblies from cryo-EM maps using Rosetta.\",\n \"abstract\": \"Cryo-EM has revealed the structures of many challenging yet exciting macromolecular assemblies at near-atomic resolution (3-4.5Å), providing biological phenomena with molecular descriptions. However, at these resolutions, accurately positioning individual atoms remains challenging and error-prone. Manually refining thousands of amino acids - typical in a macromolecular assembly - is tedious and time-consuming. We present an automated method that can improve the atomic details in models that are manually built in near-atomic-resolution cryo-EM maps. Applying the method to three systems recently solved by cryo-EM, we are able to improve model geometry while maintaining the fit-to-density. Backbone placement errors are automatically detected and corrected, and the refinement shows a large radius of convergence. The results demonstrate that the method is amenable to structures with symmetry, of very large size, and containing RNA as well as covalently bound ligands. The method should streamline the cryo-EM structure determination process, providing accurate and unbiased atomic structure interpretation of such maps.\",\n \"corpus_id\": 1186306,\n \"score\": 0\n },\n {\n \"doc_id\": \"27685097\",\n \"title\": \"Resolving macromolecular structures from electron cryo-tomography data using subtomogram averaging in RELION.\",\n \"abstract\": \"Electron cryo-tomography (cryo-ET) is a technique that is used to produce 3D pictures (tomograms) of complex objects such as asymmetric viruses, cellular organelles or whole cells from a series of tilted electron cryo-microscopy (cryo-EM) images. Averaging of macromolecular complexes found within tomograms is known as subtomogram averaging, and this technique allows structure determination of macromolecular complexes in situ. Subtomogram averaging is also gaining in popularity for the calculation of initial models for single-particle analysis. We describe herein a protocol for subtomogram averaging from cryo-ET data using the RELION software (http://www2.mrc-lmb.cam.ac.uk/relion). RELION was originally developed for cryo-EM single-particle analysis, and the subtomogram averaging approach presented in this protocol has been implemented in the existing workflow for single-particle analysis so that users may conveniently tap into existing capabilities of the RELION software. We describe how to calculate 3D models for the contrast transfer function (CTF) that describe the transfer of information in the imaging process, and we illustrate the results of classification and subtomogram averaging refinement for cryo-ET data of purified hepatitis B capsid particles and Saccharomyces cerevisiae 80S ribosomes. Using the steps described in this protocol, along with the troubleshooting and optimization guidelines, high-resolution maps can be obtained in which secondary structure elements are resolved subtomogram.\",\n \"corpus_id\": 19321982,\n \"score\": 0\n },\n {\n \"doc_id\": \"28132494\",\n \"title\": \"Introduction to high-resolution cryo-electron microscopy.\",\n \"abstract\": \"Wprowadzenie do wysokorozdzielczej kriogenicznej mikroskopii elektronowej. For many years two techniques have dominated structural biology - X-ray crystallography and NMR spectroscopy. Traditional cryo-electron microscopy of biological macromolecules produced macromolecular reconstructions at resolution limited to 6-10 Å. Recent development of transmission electron microscopes, in particular the development of direct electron detectors, and continuous improvements in the available software, have led to the \\\"resolution revolution\\\" in cryo-EM. It is now possible to routinely obtain near-atomic-resolution 3D maps of intact biological macromolecules as small as ~100 kDa. Thus, cryo-EM is now becoming the method of choice for structural analysis of many complex assemblies that are unsuitable for structure determination by other methods.\",\n \"corpus_id\": 1205060,\n \"score\": 0\n },\n {\n \"doc_id\": \"28165473\",\n \"title\": \"cryoSPARC: algorithms for rapid unsupervised cryo-EM structure determination.\",\n \"abstract\": \"Single-particle electron cryomicroscopy (cryo-EM) is a powerful method for determining the structures of biological macromolecules. With automated microscopes, cryo-EM data can often be obtained in a few days. However, processing cryo-EM image data to reveal heterogeneity in the protein structure and to refine 3D maps to high resolution frequently becomes a severe bottleneck, requiring expert intervention, prior structural knowledge, and weeks of calculations on expensive computer clusters. Here we show that stochastic gradient descent (SGD) and branch-and-bound maximum likelihood optimization algorithms permit the major steps in cryo-EM structure determination to be performed in hours or minutes on an inexpensive desktop computer. Furthermore, SGD with Bayesian marginalization allows ab initio 3D classification, enabling automated analysis and discovery of unexpected structures without bias from a reference map. These algorithms are combined in a user-friendly computer program named cryoSPARC (http://www.cryosparc.com).\",\n \"corpus_id\": -1,\n \"score\": 0\n },\n {\n \"doc_id\": \"28368275\",\n \"title\": \"Cryo-electron microscopy and X-ray crystallography: complementary approaches to structural biology and drug discovery.\",\n \"abstract\": \"The invention of the electron microscope has greatly enhanced the view scientists have of small structural details. Since its implementation, this technology has undergone considerable evolution and the resolution that can be obtained for biological objects has been extended. In addition, the latest generation of cryo-electron microscopes equipped with direct electron detectors and software for the automated collection of images, in combination with the use of advanced image-analysis methods, has dramatically improved the performance of this technique in terms of resolution. While calculating a sub-10 Å resolution structure was an accomplishment less than a decade ago, it is now common to generate structures at sub-5 Å resolution and even better. It is becoming possible to relatively quickly obtain high-resolution structures of biological molecules, in particular large ones (>500 kDa) which, in some cases, have resisted more conventional methods such as X-ray crystallography or nuclear magnetic resonance (NMR). Such newly resolved structures may, for the first time, shed light on the precise mechanisms that are essential for cellular physiological processes. The ability to attain atomic resolution may support the development of new drugs that target these proteins, allowing medicinal chemists to understand the intimacy of the relationship between their molecules and targets. In addition, recent developments in cryo-electron microscopy combined with image analysis can provide unique information on the conformational variability of macromolecular complexes. Conformational flexibility of macromolecular complexes can be investigated using cryo-electron microscopy and multiconformation reconstruction methods. However, the biochemical quality of the sample remains the major bottleneck to routine cryo-electron microscopy-based determination of structures at very high resolution.\",\n \"corpus_id\": 2588079,\n \"score\": 0\n },\n {\n \"doc_id\": \"28646653\",\n \"title\": \"Cryo-EM: beyond the microscope.\",\n \"abstract\": \"The pace at which cryo-EM is being adopted as a mainstream tool in structural biology has continued unabated over the past year. Initial successes in obtaining near-atomic resolution structures with cryo-EM were enabled to a large extent by advances in microscope and detector technology. Here, we review some of the complementary technical improvements that are helping sustain the cryo-EM revolution. We highlight advances in image processing that permit high resolution structure determination even in the presence of structural and conformational heterogeneity. We also review selected examples where biochemical strategies for membrane protein stabilization facilitate cryo-EM structure determination, and discuss emerging approaches for further improving the preparation of reliable plunge-frozen specimens.\",\n \"corpus_id\": 205063574,\n \"score\": 0\n },\n {\n \"doc_id\": \"28667626\",\n \"title\": \"Structural Analysis of Protein Complexes by Cryo Electron Microscopy.\",\n \"abstract\": \"Structural studies of biocomplexes using single-particle cryo-electron microscopy (cryo-EM) is now a well-established technique in structural biology and has become competitive with X-ray crystallography. The latest advances in EM enable us to determine structures of protein complexes at 3-5 Å resolution for an extremely broad range of sizes from ~200 kDa up to hundreds of megadaltons (Bartesaghi et al., Science 348(6239):1147-1151, 2051; Bai et al., Nature 525(7568):212-217, 2015; Vinothkumar et al., Nature 515(7525):80-84, 2014; Grigorieff and Harrison, Curr Opin Struct Biol 21(2):265-273, 2011). The majority of biocomplexes comprise a number of different components and are not amenable to crystallisation. Secretion systems are typical examples of such multi-protein complexes, and structural studies of them are extremely challenging. The only feasible approach to revealing their spatial organisation and functional modification is cryo-EM. The development of systems for digital registration of images and algorithms for the fast and efficient processing of recorded images and subsequent analysis facilitated the determination of structures at near-atomic resolution. In this review we will describe sample preparation for cryo-EM, how data are collected by new detectors, and the logistics of image analysis through the basic steps required for reconstructions of both small and large biological complexes and their refinement to nearly atomic resolution. The processing workflow is illustrated using examples of EM analysis of a Type IV Secretion System.\",\n \"corpus_id\": 4322690,\n \"score\": 0\n },\n {\n \"doc_id\": \"28949136\",\n \"title\": \"Iterative Molecular Dynamics-Rosetta Membrane Protein Structure Refinement Guided by Cryo-EM Densities.\",\n \"abstract\": \"Knowing atomistic details of proteins is essential not only for the understanding of protein function but also for the development of drugs. Experimental methods such as X-ray crystallography, NMR, and cryo-electron microscopy (cryo-EM) are the preferred forms of protein structure determination and have achieved great success over the most recent decades. Computational methods may be an alternative when experimental techniques fail. However, computational methods are severely limited when it comes to predicting larger macromolecule structures with little sequence similarity to known structures. The incorporation of experimental restraints in computational methods is becoming increasingly important to more reliably predict protein structure. One such experimental input used in structure prediction and refinement is cryo-EM densities. Recent advances in cryo-EM have arguably revolutionized the field of structural biology. Our previously developed cryo-EM-guided Rosetta-MD protocol has shown great promise in the refinement of soluble protein structures. In this study, we extended cryo-EM density-guided iterative Rosetta-MD to membrane proteins. We also improved the methodology in general by picking models based on a combination of their score and fit-to-density during the Rosetta model selection. By doing so, we have been able to pick models superior to those with the previous selection based on Rosetta score only and we have been able to further improve our previously refined models of soluble proteins. The method was tested with five membrane spanning protein structures. By applying density-guided Rosetta-MD iteratively we were able to refine the predicted structures of these membrane proteins to atomic resolutions. We also showed that the resolution of the density maps determines the improvement and quality of the refined models. By incorporating high-resolution density maps (∼4 Å), we were able to more significantly improve the quality of the models than when medium-resolution maps (6.9 Å) were used. Beginning from an average starting structure root mean square deviation (RMSD) to native of 4.66 Å, our protocol was able to refine the structures to bring the average refined structure RMSD to 1.66 Å when 4 Å density maps were used. The protocol also successfully refined the HIV-1 CTD guided by an experimental 5 Å density map.\",\n \"corpus_id\": 25509155,\n \"score\": 0\n },\n {\n \"doc_id\": \"28989723\",\n \"title\": \"Single-particle cryo-EM using alignment by classification (ABC): the structure of Lumbricus terrestris haemoglobin.\",\n \"abstract\": \"Single-particle cryogenic electron microscopy (cryo-EM) can now yield near-atomic resolution structures of biological complexes. However, the reference-based alignment algorithms commonly used in cryo-EM suffer from reference bias, limiting their applicability (also known as the 'Einstein from random noise' problem). Low-dose cryo-EM therefore requires robust and objective approaches to reveal the structural information contained in the extremely noisy data, especially when dealing with small structures. A reference-free pipeline is presented for obtaining near-atomic resolution three-dimensional reconstructions from heterogeneous ('four-dimensional') cryo-EM data sets. The methodologies integrated in this pipeline include a posteriori camera correction, movie-based full-data-set contrast transfer function determination, movie-alignment algorithms, (Fourier-space) multivariate statistical data compression and unsupervised classification, 'random-startup' three-dimensional reconstructions, four-dimensional structural refinements and Fourier shell correlation criteria for evaluating anisotropic resolution. The procedures exclusively use information emerging from the data set itself, without external 'starting models'. Euler-angle assignments are performed by angular reconstitution rather than by the inherently slower projection-matching approaches. The comprehensive 'ABC-4D' pipeline is based on the two-dimensional reference-free 'alignment by classification' (ABC) approach, where similar images in similar orientations are grouped by unsupervised classification. Some fundamental differences between X-ray crystallography versus single-particle cryo-EM data collection and data processing are discussed. The structure of the giant haemoglobin from Lumbricus terrestris at a global resolution of ∼3.8 Å is presented as an example of the use of the ABC-4D procedure.\",\n \"corpus_id\": 6151708,\n \"score\": 0\n },\n {\n \"doc_id\": \"29080436\",\n \"title\": \"Combining cryo-electron microscopy (cryo-EM) and cross-linking mass spectrometry (CX-MS) for structural elucidation of large protein assemblies.\",\n \"abstract\": \"Determining the structures of, and gaining insight into, the function of large protein complexes at the molecular or atomic level has become a key part of modern structural biology. Electron cryo-microscopy (cryo-EM) can solve structures of highly dynamic macromolecular complexes that are not feasible with other structural techniques like X-ray of crystallized proteins (protein complexes) or nuclear magnetic resonance (NMR) spectroscopy of proteins (protein complexes) in solution. To resolve the regions that are less well defined in cryo-EM images, cross-linking coupled with mass spectrometry (CX-MS) provides valuable information on the proximity between amino-acid residues as distance constraints for homology or de novo modelling. The CX-MS strategy involves covalent linkage, with chemical cross-linkers, of residues close to each other in three-dimensional space and identifying these connections by mass spectrometry. In this article, we summarise the advances of CX-MS and its integration with cryo-EM for structural reconstruction. We further evaluate a number of important examples of structure determination that followed this combinatorial strategy.\",\n \"corpus_id\": 3535945,\n \"score\": 0\n },\n {\n \"doc_id\": \"29214692\",\n \"title\": \"Cryo-EM Revolutionizes the Structure Determination of Biomolecules.\",\n \"abstract\": \"Freeze frame: The Nobel Prize in Chemistry 2017 was jointly awarded to Jacques Dubochet, Joachim Frank, and Richard Henderson for \\\"developing cryo-electron microscopy (cryo-EM) for the high-resolution structure determination of biomolecules in solution\\\". This Highlight describes how the field of cryo-EM developed from the first transmission electron microscope in 1931 to the sophisticated technique of today.\",\n \"corpus_id\": 2614386,\n \"score\": 0\n },\n {\n \"doc_id\": \"29337113\",\n \"title\": \"Volta phase plate data collection facilitates image processing and cryo-EM structure determination.\",\n \"abstract\": \"A current bottleneck in structure determination of macromolecular complexes by cryo electron microscopy (cryo-EM) is the large amount of data needed to obtain high-resolution 3D reconstructions, including through sorting into different conformations and compositions with advanced image processing. Additionally, it may be difficult to visualize small ligands that bind in sub-stoichiometric levels. Volta phase plates (VPP) introduce a phase shift in the contrast transfer and drastically increase the contrast of the recorded low-dose cryo-EM images while preserving high frequency information. Here we present a comparative study to address the behavior of different data sets during image processing and quantify important parameters during structure refinement. The automated data collection was done from the same human ribosome sample either as a conventional defocus range dataset or with a Volta phase plate close to focus (cfVPP) or with a small defocus (dfVPP). The analysis of image processing parameters shows that dfVPP data behave more robustly during cryo-EM structure refinement because particle alignments, Euler angle assignments and 2D & 3D classifications behave more stably and converge faster. In particular, less particle images are required to reach the same resolution in the 3D reconstructions. Finally, we find that defocus range data collection is also applicable to VPP. This study shows that data processing and cryo-EM map interpretation, including atomic model refinement, are facilitated significantly by performing VPP cryo-EM, which will have an important impact on structural biology.\",\n \"corpus_id\": 21655197,\n \"score\": 0\n },\n {\n \"doc_id\": \"29429092\",\n \"title\": \"Use of Cryo-EM to Study the Structure of Chemoreceptor Arrays In Vivo.\",\n \"abstract\": \"Cryo-electron microscopy (cryo-EM) allows the imaging of intact macromolecular complexes in the context of whole cells. The biological samples for cryo-EM are kept in a near-native state by flash freezing, without the need for any additional sample preparation or fixation steps. Since transmission electron microscopy only generates 2D projections of the samples, the specimen has to be tilted in order to recover its 3D structural information. This is done by collecting images of the sample with various tilt angles in respect to the electron beam. The acquired tilt series can then be computationally back-projected. This technique is called electron cryotomography (ECT), and has been instrumental in unraveling the architecture of chemoreceptor arrays. Here we describe the method of visualizing in vivo bacterial chemoreceptor arrays in three main steps: immobilization of bacterial cells on EM grids by plunge-freezing; 2D image acquisition in tilt series; and 3D tomogram reconstruction.\",\n \"corpus_id\": 46874692,\n \"score\": 0\n },\n {\n \"doc_id\": \"29656089\",\n \"title\": \"Microbiology catches the cryo-EM bug.\",\n \"abstract\": \"Over the past few years, the advances in technology and methods that have revolutionized cryo-EM are allowing for key insights in a variety of areas in biology, and microbiology is no exception. A wide range of important macromolecular assemblies in prokaryotic and eukaryotic cells, as well as intact viruses, have now become accessible to investigation by new methods in 3D electron microscopy. We focus here on selected examples that illustrate this breadth, and review the application of methods in single particle cryo-EM and cryo-electron tomography to progress in the structural biology of CRISPR systems, visualization of small molecule drugs in membrane proteins, in situ visualization of bacterial nanomachines, and the analysis of antigen-antibody interactions to drive vaccine design.\",\n \"corpus_id\": 4891845,\n \"score\": 0\n }\n]","isConversational":false}}},{"rowIdx":91,"cells":{"query":{"kind":"string","value":"{\n \"doc_id\": \"26094203\",\n \"title\": \"A fast iterative convolution weighting approach for gridding-based direct Fourier three-dimensional reconstruction with correction for the contrast transfer function.\",\n \"abstract\": \"We describe a fast and accurate method for the reconstruction of macromolecular complexes from a set of projections. Direct Fourier inversion (in which the Fourier Slice Theorem plays a central role) is a solution for dealing with this inverse problem. Unfortunately, the set of projections provides a non-equidistantly sampled version of the macromolecule Fourier transform in the single particle field (and, therefore, a direct Fourier inversion) may not be an optimal solution. In this paper, we introduce a gridding-based direct Fourier method for the three-dimensional reconstruction approach that uses a weighting technique to compute a uniform sampled Fourier transform. Moreover, the contrast transfer function of the microscope, which is a limiting factor in pursuing a high resolution reconstruction, is corrected by the algorithm. Parallelization of this algorithm, both on threads and on multiple CPU's, makes the process of three-dimensional reconstruction even faster. The experimental results show that our proposed gridding-based direct Fourier reconstruction is slightly more accurate than similar existing methods and presents a lower computational complexity both in terms of time and memory, thereby allowing its use on larger volumes. The algorithm is fully implemented in the open-source Xmipp package and is downloadable from http://xmipp.cnb.csic.es.\",\n \"corpus_id\": 205524467\n}"},"candidates":{"kind":"list like","value":[{"doc_id":"18499351","title":"Cryo-EM image alignment based on nonuniform fast Fourier transform.","abstract":"In single particle analysis, two-dimensional (2-D) alignment is a fundamental step intended to put into register various particle projections of biological macromolecules collected at the electron microscope. The efficiency and quality of three-dimensional (3-D) structure reconstruction largely depends on the computational speed and alignment accuracy of this crucial step. In order to improve the performance of alignment, we introduce a new method that takes advantage of the highly accurate interpolation scheme based on the gridding method, a version of the nonuniform fast Fourier transform, and utilizes a multi-dimensional optimization algorithm for the refinement of the orientation parameters. Using simulated data, we demonstrate that by using less than half of the sample points and taking twice the runtime, our new 2-D alignment method achieves dramatically better alignment accuracy than that based on quadratic interpolation. We also apply our method to image to volume registration, the key step in the single particle EM structure refinement protocol. We find that in this case the accuracy of the method not only surpasses the accuracy of the commonly used real-space implementation, but results are achieved in much shorter time, making gridding-based alignment a perfect candidate for efficient structure determination in single particle analysis.","corpus_id":25736312,"score":2},{"doc_id":"18692361","title":"Evaluation of a new gridding method for fully 3D direct Fourier PET reconstruction based on a two-plane geometry.","abstract":"This study investigated how the choice of fixed planes for the representation of the projection data of a cylindrical positron emission tomography (PET) scanner simplifies the frequency interpolation required by the 3D Fourier slice theorem (3D-FST). A new gridding algorithm based on a two-plane geometry and requiring only 1D interpolations in the Fourier domain was compared with the direct implementation of the 3D-FST. We show that the use of two orthogonal planes leads to signal to noise ratios similar to those achieved with the 3D-FST algorithm from projection data acquired with up to two times more count rates, while the resolution remains similar.","corpus_id":19761761,"score":2},{"doc_id":"20888956","title":"Fundamentals of three-dimensional reconstruction from projections.","abstract":"Three-dimensional (3D) reconstruction of an object mass density from the set of its 2D line projections lies at a core of both single-particle reconstruction technique and electron tomography. Both techniques utilize electron microscope to collect a set of projections of either multiple objects representing in principle the same macromolecular complex in an isolated form, or a subcellular structure isolated in situ. Therefore, the goal of macromolecular electron microscopy is to invert the projection transformation to recover the distribution of the mass density of the original object. The problem is interesting in that in its discrete form it is ill-posed and not invertible. Various algorithms have been proposed to cope with the practical difficulties of this inversion problem and their differ widely in terms of their robustness with respect to noise in the data, completeness of the collected projection dataset, errors in projections orientation parameters, abilities to efficiently handle large datasets, and other obstacles typically encountered in molecular electron microscopy. Here, we review the theoretical foundations of 3D reconstruction from line projections followed by an overview of reconstruction algorithms routinely used in practice of electron microscopy.","corpus_id":23406418,"score":2},{"doc_id":"24326216","title":"Iterative reconstruction of cryo-electron tomograms using nonuniform fast Fourier transforms.","abstract":"Algorithms for three-dimensional (3D) reconstruction of objects based on their projections are essential in various biological and medical imaging modalities. In cryo-electron tomography (CET) a major challenge for reconstruction is the limited range of projection angles, which manifests itself as a \"missing wedge\" of data in Fourier space making the reconstruction problem ill-posed. Here, we apply an iterative reconstruction method that makes use of nonuniform fast Fourier transform (NUFFT) to the reconstruction of cryo-electron tomograms. According to several measures the reconstructions are superior to those obtained using conventional methods, most notably weighted backprojection. Most importantly, we show that it is possible to fill in partially the unsampled region in Fourier space with meaningful information without making assumptions about the data or applying prior knowledge. As a consequence, particles of known structure can be localized with higher confidence in cryotomograms and subtomogram averaging yields higher resolution densities.","corpus_id":5514970,"score":2},{"doc_id":"27410628","title":"Fast gridding projectors for analytical and iterative tomographic reconstruction of differential phase contrast data.","abstract":"This paper introduces new gridding projectors designed to efficiently perform analytical and iterative tomographic reconstruction, when the forward model is represented by the derivative of the Radon transform. This inverse problem is tightly connected with an emerging X-ray tube- and synchrotron-based imaging technique: differential phase contrast based on a grating interferometer. This study shows, that the proposed projectors, compared to space-based implementations of the same operators, yield high quality analytical and iterative reconstructions, while improving the computational efficiency by few orders of magnitude.","corpus_id":7129985,"score":2},{"doc_id":"27661946","title":"Precise and fast spatial-frequency analysis using the iterative local Fourier transform.","abstract":"The use of the discrete Fourier transform has decreased since the introduction of the fast Fourier transform (fFT), which is a numerically efficient computing process. This paper presents the iterative local Fourier transform (ilFT), a set of new processing algorithms that iteratively apply the discrete Fourier transform within a local and optimal frequency domain. The new technique achieves 2<sup>10</sup> times higher frequency resolution than the fFT within a comparable computation time. The method's superb computing efficiency, high resolution, spectrum zoom-in capability, and overall performance are evaluated and compared to other advanced high-resolution Fourier transform techniques, such as the fFT combined with several fitting methods. The effectiveness of the ilFT is demonstrated through the data analysis of a set of Talbot self-images (1280 × 1024 pixels) obtained with an experimental setup using grating in a diverging beam produced by a coherent point source.","corpus_id":4980403,"score":2},{"doc_id":"29312997","title":"A Survey of the Use of Iterative Reconstruction Algorithms in Electron Microscopy.","abstract":"One of the key steps in Electron Microscopy is the tomographic reconstruction of a three-dimensional (3D) map of the specimen being studied from a set of two-dimensional (2D) projections acquired at the microscope. This tomographic reconstruction may be performed with different reconstruction algorithms that can be grouped into several large families: direct Fourier inversion methods, back-projection methods, Radon methods, or iterative algorithms. In this review, we focus on the latter family of algorithms, explaining the mathematical rationale behind the different algorithms in this family as they have been introduced in the field of Electron Microscopy. We cover their use in Single Particle Analysis (SPA) as well as in Electron Tomography (ET).","corpus_id":26646474,"score":2},{"doc_id":"18390350","title":"Accelerating the nonequispaced fast Fourier transform on commodity graphics hardware.","abstract":"We present a fast parallel algorithm to compute the nonequispaced fast Fourier transform on commodity graphics hardware (the GPU). We focus particularly on a novel implementation of the convolution step in the transform as it was previously its most time consuming part. We describe the performance for two common sample distributions in medical imaging (radial and spiral trajectories), and for different convolution kernels as these parameters all influence the speed of the algorithm. The GPU-accelerated convolution is up to 85 times faster as our reference, the open source NFFT library on a state-of-the-art 64 bit CPU. The accuracy of the proposed GPU implementation was quantitatively evaluated at the various settings. To illustrate the applicability of the transform in medical imaging, in which it is also known as gridding, we look specifically at non-Cartesian magnetic resonance imaging and reconstruct both a numerical phantom and an in vivo cardiac image.","corpus_id":206747049,"score":1},{"doc_id":"18672425","title":"Rotate-and-slant projector for fast LOR-based fully-3-D iterative PET reconstruction.","abstract":"One of the greatest challenges facing iterative fully-3-D positron emission tomography (PET) reconstruction is the issue of long reconstruction times due to the large number of measurements for 3-D mode as compared to 2-D mode. A rotate-and-slant projector has been developed that takes advantage of symmetries in the geometry to compute volumetric projections to multiple oblique sinograms in a computationally efficient manner. It is based upon the 2-D rotation-based projector using the three-pass method of shears, and it conserves the 2-D rotator computations for multiple projections to each oblique sinogram set. The projector is equally applicable to both conventional evenly-spaced projections and unevenly-spaced line-of-response (LOR) data. The LOR-based version models the location and orientation of the individual LORs (i.e., the arc-correction), providing an ordinary Poisson reconstruction framework. The projector was implemented in C with several optimizations for speed, exploiting the vertical symmetry of the oblique projection process, depth compression, and array indexing schemes which maximize serial memory access. The new projector was evaluated and compared to ray-driven and distance-driven projectors using both analytical and experimental phantoms, and fully-3-D iterative reconstructions with each projector were also compared to Fourier rebinning with 2-D iterative reconstruction. In terms of spatial resolution, contrast, and background noise measures, 3-D LOR-based iterative reconstruction with the rotate-and-slant projector performed as well as or better than the other methods. Total processing times, measured on a single cpu Linux workstation, were approximately 10x faster for the rotate-and-slant projector than for the other 3-D projectors studied. The new projector provided four iterations fully-3-D ordered-subsets reconstruction in as little as 15 s--approximately the same time as FORE + 2-D reconstruction. We conclude that the rotate-and-slant projector is a viable option for fully-3-D PET, offering quality statistical reconstruction in times only marginally slower than 2-D or rebinning methods.","corpus_id":8142165,"score":1},{"doc_id":"19131666","title":"Fast 3D iterative image reconstruction for SPECT with rotating slat collimators.","abstract":"As an alternative to the use of traditional parallel hole collimators, SPECT imaging can be performed using rotating slat collimators. While maintaining the spatial resolution, a gain in image quality could be expected from the higher photon collection efficiency of this type of collimator. However, the use of iterative methods to do fully three-dimensional (3D) reconstruction is computationally much more expensive and furthermore involves slow convergence compared to a classical SPECT reconstruction. It has been proposed to do 3D reconstruction by splitting the system matrix into two separate matrices, forcing the reconstruction to first estimate the sinograms from the rotating slat SPECT data before estimating the image. While alleviating the computational load by one order of magnitude, this split matrix approach would result in fast computation of the projections in an iterative algorithm, but does not solve the problem of slow convergence. There is thus a need for an algorithm which speeds up convergence while maintaining image quality for rotating slat collimated SPECT cameras. Therefore, we developed a reconstruction algorithm based on the split matrix approach which allows both a fast calculation of the forward and backward projection and a fast convergence. In this work, an algorithm of the maximum likelihood expectation maximization (MLEM) type, obtained from a split system matrix MLEM reconstruction, is proposed as a reconstruction method for rotating slat collimated SPECT data. Here, we compare this new algorithm to the conventional split system matrix MLEM method and to a gold standard fully 3D MLEM reconstruction algorithm on the basis of computational load, convergence and contrast-to-noise. Furthermore, ordered subsets expectation maximization (OSEM) implementations of these three algorithms are compared. Calculation of computational load and convergence for the different algorithms shows a speedup for the new method of 38 and 426 compared to the split matrix MLEM approach and the fully 3D MLEM respectively and a speedup of 16 and 21 compared to the split matrix OSEM and the fully 3D OSEM respectively. A contrast-to-noise study based on simulated data shows that our new approach has comparable accuracy as the fully 3D reconstruction method. The algorithm developed in this study allows iterative image reconstruction of rotating slat collimated SPECT data with equal image quality in a comparable amount of computation time as a classical SPECT reconstruction.","corpus_id":41250680,"score":1},{"doc_id":"20009184","title":"A fast and pragmatic approach for scatter correction in flat-detector CT using elliptic modeling and iterative optimization.","abstract":"Scattered radiation is a major source of artifacts in flat detector computed tomography (FDCT) due to the increased irradiated volumes. We propose a fast projection-based algorithm for correction of scatter artifacts. The presented algorithm combines a convolution method to determine the spatial distribution of the scatter intensity distribution with an object-size-dependent scaling of the scatter intensity distributions using a priori information generated by Monte Carlo simulations. A projection-based (PBSE) and an image-based (IBSE) strategy for size estimation of the scanned object are presented. Both strategies provide good correction and comparable results; the faster PBSE strategy is recommended. Even with such a fast and simple algorithm that in the PBSE variant does not rely on reconstructed volumes or scatter measurements, it is possible to provide a reasonable scatter correction even for truncated scans. For both simulations and measurements, scatter artifacts were significantly reduced and the algorithm showed stable behavior in the z-direction. For simulated voxelized head, hip and thorax phantoms, a figure of merit Q of 0.82, 0.76 and 0.77 was reached, respectively (Q = 0 for uncorrected, Q = 1 for ideal). For a water phantom with 15 cm diameter, for example, a cupping reduction from 10.8% down to 2.1% was achieved. The performance of the correction method has limitations in the case of measurements using non-ideal detectors, intensity calibration, etc. An iterative approach to overcome most of these limitations was proposed. This approach is based on root finding of a cupping metric and may be useful for other scatter correction methods as well. By this optimization, cupping of the measured water phantom was further reduced down to 0.9%. The algorithm was evaluated on a commercial system including truncated and non-homogeneous clinically relevant objects.","corpus_id":10988988,"score":1},{"doc_id":"20236843","title":"Gridding and fast Fourier transformation on non-uniformly sparse sampled multidimensional NMR data.","abstract":"For multidimensional NMR method, indirect dimensional non-uniform sparse sampling can dramatically shorten acquisition time of the experiments. However, the non-uniformly sampled NMR data cannot be processed directly using fast Fourier transform (FFT). We show that the non-uniformly sampled NMR data can be reconstructed to Cartesian grid with the gridding method that has been wide applied in MRI, and sequentially be processed using FFT. The proposed gridding-FFT (GFFT) method increases the processing speed sharply compared with the previously proposed non-uniform Fourier Transform, and may speed up application of the non-uniform sparse sampling approaches.","corpus_id":31422311,"score":1},{"doc_id":"20578028","title":"Iterative image reconstruction for PROPELLER-MRI using the nonuniform fast fourier transform.","abstract":"PURPOSE: To investigate an iterative image reconstruction algorithm using the nonuniform fast Fourier transform (NUFFT) for PROPELLER (Periodically Rotated Overlapping ParallEL Lines with Enhanced Reconstruction) MRI. MATERIALS AND METHODS: Numerical simulations, as well as experiments on a phantom and a healthy human subject were used to evaluate the performance of the iterative image reconstruction algorithm for PROPELLER, and compare it with that of conventional gridding. The trade-off between spatial resolution, signal to noise ratio, and image artifacts, was investigated for different values of the regularization parameter. The performance of the iterative image reconstruction algorithm in the presence of motion was also evaluated. RESULTS: It was demonstrated that, for a certain range of values of the regularization parameter, iterative reconstruction produced images with significantly increased signal to noise ratio, reduced artifacts, for similar spatial resolution, compared with gridding. Furthermore, the ability to reduce the effects of motion in PROPELLER-MRI was maintained when using the iterative reconstruction approach. CONCLUSION: An iterative image reconstruction technique based on the NUFFT was investigated for PROPELLER MRI. For a certain range of values of the regularization parameter, the new reconstruction technique may provide PROPELLER images with improved image quality compared with conventional gridding.","corpus_id":22676783,"score":1},{"doc_id":"21144688","title":"Non-Iterative Regularized reconstruction Algorithm for Non-CartesiAn MRI: NIRVANA.","abstract":"We introduce a novel noniterative algorithm for the fast and accurate reconstruction of nonuniformly sampled MRI data. The proposed scheme derives the reconstructed image as the nonuniform inverse Fourier transform of a compensated dataset. We derive each sample in the compensated dataset as a weighted linear combination of a few measured k-space samples. The specific k-space samples and the weights involved in the linear combination are derived such that the reconstruction error is minimized. The computational complexity of the proposed scheme is comparable to that of gridding. At the same time, it provides significantly improved accuracy and is considerably more robust to noise and undersampling. The advantages of the proposed scheme makes it ideally suited for the fast reconstruction of large multidimensional datasets, which routinely arise in applications such as f-MRI and MR spectroscopy. The comparisons with state-of-the-art algorithms on numerical phantoms and MRI data clearly demonstrate the performance improvement.","corpus_id":18085059,"score":1},{"doc_id":"21740865","title":"A fast algorithm for computing and correcting the CTF for tilted, thick specimens in TEM.","abstract":"Today, the resolution in phase-contrast cryo-electron tomography is for a significant part limited by the contrast transfer function (CTF) of the microscope. The CTF is a function of defocus and thus varies spatially as a result of the tilting of the specimen and the finite specimen thickness. Models that include spatial dependencies have not been adopted in daily practice because of their high computational complexity. Here we present an algorithm which reduces the processing time for computing the 'tilted' CTF by more than a factor 100. Our implementation of the full 3D CTF has a processing time on the order of a Radon transform of a full tilt-series. We derive and validate an expression for the damping envelope function describing the loss of resolution due to specimen thickness. Using simulations we quantify the effects of specimen thickness on the accuracy of various forward models. We study the influence of spatially varying CTF correction and subsequent tomographic reconstruction by simulation and present a new approach for space-variant phase-flipping. We show that our CTF correction strategies are successful in increasing the resolution after tomographic reconstruction.","corpus_id":7298961,"score":1},{"doc_id":"21859004","title":"A fast forward projection using multithreads for multirays on GPUs in medical image reconstruction.","abstract":"PURPOSE: Iterative reconstruction techniques hold great potential to mitigate the effects of data noise and/or incompleteness, and hence can facilitate the patient dose reduction. However, they are not suitable for routine clinical practice due to their long reconstruction times. In this work, the authors accelerated the computations by fully taking advantage of the highly parallel computational power on single and multiple graphics processing units (GPUs). In particular, the forward projection algorithm, which is not included in the close-form formulas, will be accelerated and optimized by using GPU here. METHODS: The main contribution is a novel forward projection algorithm that uses multithreads to handle the computations associated with a bunch of adjacent rays simultaneously. The proposed algorithm is free of divergence and bank conflict on GPU, and benefits from data locality and data reuse. It achieves the efficiency particularly by (i) employing a tiled algorithm with three-level parallelization, (ii) optimizing thread block size, (iii) maximizing data reuse on constant memory and shared memory, and (iv) exploiting built-in texture memory interpolation capability to increase efficiency. In addition, to accelerate the iterative algorithms and the Feldkamp-Davis-Kress (FDK) algorithm on GPU, the authors apply batched fast Fourier transform (FFT) to expedite filtering process in FDK and utilize projection bundling parallelism during backprojection to shorten the execution times in FDK and the expectation-maximization (EM). RESULTS: Numerical experiments conducted on an NVIDIA Tesla C1060 GPU demonstrated the superiority of the proposed algorithms in computational time saving. The forward projection, filtering, and backprojection times for generating a volume image of 512 x 512 x 512 with 360 projection data of 512 x 512 using one GPU are about 4.13, 0.65, and 2.47 s (including distance weighting), respectively. In particular, the proposed forward projection algorithm is ray-driven and its paralleli-zation strategy evolves from single-thread-for-single-ray (38.56 s), multithreads-for-single-ray (26.05 s), to multithreads-for-multirays (4.13 s). For the voxel-driven backprojection, the use of texture memory reduces the reconstruction time from 4.95 to 3.35 s. By applying the projection bundle technique, the computation time is further reduced to 2.47 s. When employing multiple GPUs, near-perfect speedups were observed as the number of GPUs increases. For example, by using four GPUs, the time for the forward projection, filtering, and backprojection are further reduced to 1.11, 0.18, and 0.66 s. The results obtained by GPU-based algorithms are virtually indistinguishable with those by CPU. CONCLUSIONS: The authors have proposed a highly optimized GPU-based forward projection algorithm, as well as the GPU-based FDK and expectation-maximization reconstruction algorithms. Our compute unified device architecture (CUDA) codes provide the exceedingly fast forward projection and backprojection that outperform those using the shading languages, cell broadband engine architecture and previous CUDA implementations. The reconstruction times in the FDK and the EM algorithms were considerably shortened, and thus can facilitate their routine usage in a variety of applications such as image quality improvement and dose reduction.","corpus_id":7931248,"score":1},{"doc_id":"21860371","title":"Structure of HIV-1 capsid assemblies by cryo-electron microscopy and iterative helical real-space reconstruction.","abstract":"Cryo-electron microscopy (cryo-EM), combined with image processing, is an increasingly powerful tool for structure determination of macromolecular protein complexes and assemblies. In fact, single particle electron microscopy and two-dimensional (2D) electron crystallography have become relatively routine methodologies and a large number of structures have been solved using these methods. At the same time, image processing and three-dimensional (3D) reconstruction of helical objects has rapidly developed, especially, the iterative helical real-space reconstruction (IHRSR) method, which uses single particle analysis tools in conjunction with helical symmetry. Many biological entities function in filamentous or helical forms, including actin filaments, microtubules, amyloid fibers, tobacco mosaic viruses, and bacteria flagella, and, because a 3D density map of a helical entity can be attained from a single projection image, compared to the many images required for 3D reconstruction of a non-helical object, with the IHRSR method, structural analysis of such flexible and disordered helical assemblies is now attainable. In this video article, we provide detailed protocols for obtaining a 3D density map of a helical protein assembly (HIV-1 capsid is our example), including protocols for cryo-EM specimen preparation, low dose data collection by cryo-EM, indexing of helical diffraction patterns, and image processing and 3D reconstruction using IHRSR. Compared to other techniques, cryo-EM offers optimal specimen preservation under near native conditions. Samples are embedded in a thin layer of vitreous ice, by rapid freezing, and imaged in electron microscopes at liquid nitrogen temperature, under low dose conditions to minimize the radiation damage. Sample images are obtained under near native conditions at the expense of low signal and low contrast in the recorded micrographs. Fortunately, the process of helical reconstruction has largely been automated, with the exception of indexing the helical diffraction pattern. Here, we describe an approach to index helical structure and determine helical symmetries (helical parameters) from digitized micrographs, an essential step for 3D helical reconstruction. Briefly, we obtain an initial 3D density map by applying the IHRSR method. This initial map is then iteratively refined by introducing constraints for the alignment parameters of each segment, thus controlling their degrees of freedom. Further improvement is achieved by correcting for the contrast transfer function (CTF) of the electron microscope (amplitude and phase correction) and by optimizing the helical symmetry of the assembly.","corpus_id":8398013,"score":1},{"doc_id":"22274272","title":"Selection of convolution kernel in non-uniform fast Fourier transform for Fourier domain optical coherence tomography.","abstract":"Gridding based non-uniform fast Fourier transform (NUFFT) has recently been shown as an efficient method of processing non-linearly sampled data from Fourier-domain optical coherence tomography (FD-OCT). This method requires selecting design parameters, such as kernel function type, oversampling ratio and kernel width, to balance between computational complexity and accuracy. The Kaiser-Bessel (KB) and Gaussian kernels have been used independently on the NUFFT algorithm for FD-OCT. This paper compares the reconstruction error and speed for the optimization of these design parameters and justifies particular kernel choice for FD-OCT applications. It is found that for on-the-fly computation of the kernel function, the simpler Gaussian function offers a better accuracy-speed tradeoff. The KB kernel, however, is a better choice in the pre-computed kernel mode of NUFFT, in which the processing speed is no longer dependent on the kernel function type. Finally, the algorithm is used to reconstruct in-vivo images of a human finger at a camera limited 50k A-line/s.","corpus_id":207320571,"score":1},{"doc_id":"22759428","title":"High-performance blob-based iterative three-dimensional reconstruction in electron tomography using multi-GPUs.","abstract":"BACKGROUND: Three-dimensional (3D) reconstruction in electron tomography (ET) has emerged as a leading technique to elucidate the molecular structures of complex biological specimens. Blob-based iterative methods are advantageous reconstruction methods for 3D reconstruction in ET, but demand huge computational costs. Multiple graphic processing units (multi-GPUs) offer an affordable platform to meet these demands. However, a synchronous communication scheme between multi-GPUs leads to idle GPU time, and a weighted matrix involved in iterative methods cannot be loaded into GPUs especially for large images due to the limited available memory of GPUs. RESULTS: In this paper we propose a multilevel parallel strategy combined with an asynchronous communication scheme and a blob-ELLR data structure to efficiently perform blob-based iterative reconstructions on multi-GPUs. The asynchronous communication scheme is used to minimize the idle GPU time so as to asynchronously overlap communications with computations. The blob-ELLR data structure only needs nearly 1/16 of the storage space in comparison with ELLPACK-R (ELLR) data structure and yields significant acceleration. CONCLUSIONS: Experimental results indicate that the multilevel parallel scheme combined with the asynchronous communication scheme and the blob-ELLR data structure allows efficient implementations of 3D reconstruction in ET on multi-GPUs.","corpus_id":1777063,"score":1},{"doc_id":"22898698","title":"A CUDA-based reverse gridding algorithm for MR reconstruction.","abstract":"MR raw data collected using non-Cartesian method can be transformed on Cartesian grids by traditional gridding algorithm (GA) and reconstructed by Fourier transform. However, its runtime complexity is O(K×N(2)), where resolution of raw data is N×N and size of convolution window (CW) is K. And it involves a large number of matrix calculation including modulus, addition, multiplication and convolution. Therefore, a Compute Unified Device Architecture (CUDA)-based algorithm is proposed to improve the reconstruction efficiency of PROPELLER (a globally recognized non-Cartesian sampling method). Experiment shows a write-write conflict among multiple CUDA threads. This induces an inconsistent result when synchronously convoluting multiple k-space data onto the same grid. To overcome this problem, a reverse gridding algorithm (RGA) was developed. Different from the method of generating a grid window for each trajectory as in traditional GA, RGA calculates a trajectory window for each grid. This is what \"reverse\" means. For each k-space point in the CW, contribution is cumulated to this grid. Although this algorithm can be easily extended to reconstruct other non-Cartesian sampled raw data, we only implement it based on PROPELLER. Experiment illustrates that this CUDA-based RGA has successfully solved the write-write conflict and its reconstruction speed is 7.5 times higher than that of traditional GA.","corpus_id":22143791,"score":1},{"doc_id":"23464329","title":"Radiation dose reduction in medical x-ray CT via Fourier-based iterative reconstruction.","abstract":"PURPOSE: A Fourier-based iterative reconstruction technique, termed Equally Sloped Tomography (EST), is developed in conjunction with advanced mathematical regularization to investigate radiation dose reduction in x-ray CT. The method is experimentally implemented on fan-beam CT and evaluated as a function of imaging dose on a series of image quality phantoms and anonymous pediatric patient data sets. Numerical simulation experiments are also performed to explore the extension of EST to helical cone-beam geometry. METHODS: EST is a Fourier based iterative algorithm, which iterates back and forth between real and Fourier space utilizing the algebraically exact pseudopolar fast Fourier transform (PPFFT). In each iteration, physical constraints and mathematical regularization are applied in real space, while the measured data are enforced in Fourier space. The algorithm is automatically terminated when a proposed termination criterion is met. Experimentally, fan-beam projections were acquired by the Siemens z-flying focal spot technology, and subsequently interleaved and rebinned to a pseudopolar grid. Image quality phantoms were scanned at systematically varied mAs settings, reconstructed by EST and conventional reconstruction methods such as filtered back projection (FBP), and quantified using metrics including resolution, signal-to-noise ratios (SNRs), and contrast-to-noise ratios (CNRs). Pediatric data sets were reconstructed at their original acquisition settings and additionally simulated to lower dose settings for comparison and evaluation of the potential for radiation dose reduction. Numerical experiments were conducted to quantify EST and other iterative methods in terms of image quality and computation time. The extension of EST to helical cone-beam CT was implemented by using the advanced single-slice rebinning (ASSR) method. RESULTS: Based on the phantom and pediatric patient fan-beam CT data, it is demonstrated that EST reconstructions with the lowest scanner flux setting of 39 mAs produce comparable image quality, resolution, and contrast relative to FBP with the 140 mAs flux setting. Compared to the algebraic reconstruction technique and the expectation maximization statistical reconstruction algorithm, a significant reduction in computation time is achieved with EST. Finally, numerical experiments on helical cone-beam CT data suggest that the combination of EST and ASSR produces reconstructions with higher image quality and lower noise than the Feldkamp Davis and Kress (FDK) method and the conventional ASSR approach. CONCLUSIONS: A Fourier-based iterative method has been applied to the reconstruction of fan-bean CT data with reduced x-ray fluence. This method incorporates advantageous features in both real and Fourier space iterative schemes: using a fast and algebraically exact method to calculate forward projection, enforcing the measured data in Fourier space, and applying physical constraints and flexible regularization in real space. Our results suggest that EST can be utilized for radiation dose reduction in x-ray CT via the readily implementable technique of lowering mAs settings. Numerical experiments further indicate that EST requires less computation time than several other iterative algorithms and can, in principle, be extended to helical cone-beam geometry in combination with the ASSR method.","corpus_id":13455029,"score":1},{"doc_id":"25080112","title":"Fan beam image reconstruction with generalized Fourier slice theorem.","abstract":"For parallel beam geometry the Fourier reconstruction works via the Fourier slice theorem (or central slice theorem, projection slice theorem). For fan beam situation, Fourier slice can be extended to a generalized Fourier slice theorem (GFST) for fan-beam image reconstruction. We have briefly introduced this method in a conference. This paper reintroduces the GFST method for fan beam geometry in details. The GFST method can be described as following: the Fourier plane is filled by adding up the contributions from all fanbeam projections individually; thereby the values in the Fourier plane are directly calculated for Cartesian coordinates such avoiding the interpolation from polar to Cartesian coordinates in the Fourier domain; inverse fast Fourier transform is applied to the image in Fourier plane and leads to a reconstructed image in spacial domain. The reconstructed image is compared between the result of the GFST method and the result from the filtered backprojection (FBP) method. The major differences of the GFST and the FBP methods are: (1) The interpolation process are at different data sets. The interpolation of the GFST method is at projection data. The interpolation of the FBP method is at filtered projection data. ( 2) The filtering process are done in different places. The filtering process of the GFST is at Fourier domain. The filtering process of the FBP method is the ramp filter which is done at projections. The resolution of ramp filter is variable with different location but the filter in the Fourier domain lead to resolution invariable with location. One advantage of the GFST method over the FBP method is in short scan situation, an exact solution can be obtained with the GFST method, but it can not be obtained with the FBP method. The calculation of both the GFST and the FBP methods are at O(N<formula>^3</formula>), where N is the number of pixel in one dimension.","corpus_id":23386700,"score":1},{"doc_id":"25176282","title":"Fast reconstruction of 3D volumes from 2D CT projection data with GPUs.","abstract":"BACKGROUND: Biomedical image reconstruction applications require producing high fidelity images in or close to real-time. We have implemented reconstruction of three dimensional conebeam computed tomography(CBCT) with two dimensional projections. The algorithm takes slices of the target, weights and filters them to backproject the data, then creates the final 3D volume. We have implemented the algorithm using several hardware and software approaches and taken advantage of different types of parallelism in modern processors. The two hardware platforms used are a Central Processing Unit (CPU) and a heterogeneous system with a combination of CPU and GPU. On the CPU we implement serial MATLAB, parallel MATLAB, C and parallel C with OpenMP extensions. These codes are compared against the heterogeneous versions written in CUDA-C and OpenCL. FINDINGS: Our results show that GPUs are particularly well suited to accelerating CBCT. Relative performance was evaluated on a mathematical phantom as well as on mouse data. Speedups of up to 200x are observed by using an AMD GPU compared to a parallel version in C with OpenMP constructs. CONCLUSIONS: In this paper, we have implemented the Feldkamp-Davis-Kress algorithm, compatible with Fessler's image reconstruction toolbox and tested it on different hardware platforms including CPU and a combination of CPU and GPU. Both NVIDIA and AMD GPUs have been used for performance evaluation. GPUs provide significant speedup over the parallel CPU version.","corpus_id":10756187,"score":1},{"doc_id":"25436931","title":"Atomic resolution tomography reconstruction of tilt series based on a GPU accelerated hybrid input-output algorithm using polar Fourier transform.","abstract":"Advances in diffraction and transmission electron microscopy (TEM) have greatly improved the prospect of three-dimensional (3D) structure reconstruction from two-dimensional (2D) images or diffraction patterns recorded in a tilt series at atomic resolution. Here, we report a new graphics processing unit (GPU) accelerated iterative transformation algorithm (ITA) based on polar fast Fourier transform for reconstructing 3D structure from 2D diffraction patterns. The algorithm also applies to image tilt series by calculating diffraction patterns from the recorded images using the projection-slice theorem. A gold icosahedral nanoparticle of 309 atoms is used as the model to test the feasibility, performance and robustness of the developed algorithm using simulations. Atomic resolution in 3D is achieved for the 309 atoms Au nanoparticle using 75 diffraction patterns covering 150° rotation. The capability demonstrated here provides an opportunity to uncover the 3D structure of small objects of nanometers in size by electron diffraction.","corpus_id":10994340,"score":1},{"doc_id":"25807565","title":"Fast Volume Reconstruction From Motion Corrupted Stacks of 2D Slices.","abstract":"Capturing an enclosing volume of moving subjects and organs using fast individual image slice acquisition has shown promise in dealing with motion artefacts. Motion between slice acquisitions results in spatial inconsistencies that can be resolved by slice-to-volume reconstruction (SVR) methods to provide high quality 3D image data. Existing algorithms are, however, typically very slow, specialised to specific applications and rely on approximations, which impedes their potential clinical use. In this paper, we present a fast multi-GPU accelerated framework for slice-to-volume reconstruction. It is based on optimised 2D/3D registration, super-resolution with automatic outlier rejection and an additional (optional) intensity bias correction. We introduce a novel and fully automatic procedure for selecting the image stack with least motion to serve as an initial registration target. We evaluate the proposed method using artificial motion corrupted phantom data as well as clinical data, including tracked freehand ultrasound of the liver and fetal Magnetic Resonance Imaging. We achieve speed-up factors greater than 30 compared to a single CPU system and greater than 10 compared to currently available state-of-the-art multi-core CPU methods. We ensure high reconstruction accuracy by exact computation of the point-spread function for every input data point, which has not previously been possible due to computational limitations. Our framework and its implementation is scalable for available computational infrastructures and tests show a speed-up factor of 1.70 for each additional GPU. This paves the way for the online application of image based reconstruction methods during clinical examinations. The source code for the proposed approach is publicly available.","corpus_id":424951,"score":1},{"doc_id":"27046874","title":"Direct Fourier Inversion Reconstruction Algorithm for Computed Laminography.","abstract":"Synchrotron radiation computed laminography (CL) was developed to complement the conventional computed tomography as a non-destructive 3D imaging method for the inspection of flat thin objects. Recent progress in hardware at synchrotron sources allows one to record internal evolution of specimens at the micrometer scale and sub-second range but also requires increased reconstruction speed to follow structural changes online. A 3D image of the sample interior is usually reconstructed by the well-established filtered backprojection (FBP) approach. Despite of a great success in the reduction of reconstruction time via parallel computations, the FBP algorithm still remains a time-consuming procedure. A promising way to significantly shorten computation time is to directly perform backprojection in frequency domain (a direct Fourier inversion approach). The corresponding algorithms are rarely considered in the literature because of a poor performance or inferior reconstruction quality resulted from inaccurate interpolation in Fourier domain. In this paper, we derive a Fourier-based reconstruction equation designed for the CL scanning geometry. Furthermore, we outline the translation of the continuous solution to a discrete version, which utilizes 3D sinc interpolation. A projection resampling technique allowing for the reduction of the expensive interpolation to its 1D version is proposed. A series of numerical experiments confirms that the resulting image quality is well comparable with the FBP approach while reconstruction time is drastically reduced.","corpus_id":16942536,"score":1},{"doc_id":"28086901","title":"GPU accelerated voxel-driven forward projection for iterative reconstruction of cone-beam CT.","abstract":"BACKGROUND: For cone-beam computed tomography (CBCT), which has been playing an important role in clinical applications, iterative reconstruction algorithms are able to provide advantageous image qualities over the classical FDK. However, the computational speed of iterative reconstruction is a notable issue for CBCT, of which the forward projection calculation is one of the most time-consuming components. METHOD AND RESULTS: In this study, the cone-beam forward projection problem using the voxel-driven model is analysed, and a GPU-based acceleration method for CBCT forward projection is proposed with the method rationale and implementation workflow detailed as well. For method validation and evaluation, computational simulations are performed, and the calculation times of different methods are collected. Compared with the benchmark CPU processing time, the proposed method performs effectively in handling the inter-thread interference problem, and an acceleration ratio as high as more than 100 is achieved compared to a single-threaded CPU implementation. CONCLUSION: The voxel-driven forward projection calculation for CBCT is highly paralleled by the proposed method, and we believe it will serve as a critical module to develop iterative reconstruction and correction methods for CBCT imaging.","corpus_id":16168638,"score":1},{"doc_id":"28248347","title":"Three-dimensional optoacoustic reconstruction using fast sparse representation.","abstract":"Optoacoustic tomography based on insufficient spatial sampling of ultrasound waves leads to loss of contrast and artifacts on the reconstructed images. Compared to reconstructions based on L2-norm regularization, sparsity-based reconstructions may improve contrast and reduce image artifacts but at a high computational cost, which has so far limited their use to 2D optoacoustic tomography. Here we propose a fast, sparsity-based reconstruction algorithm for 3D optoacoustic tomography, based on gradient descent with Barzilai-Borwein line search (L1-GDBB). Using simulations and experiments, we show that the L1-GDBB offers fourfold faster reconstruction than the previously reported L1-norm regularized reconstruction based on gradient descent with backtracking line search. Moreover, the new algorithm provides higher-quality images with fewer artifacts than the L2-norm regularized reconstruction and the back-projection reconstruction.","corpus_id":46740925,"score":1},{"doc_id":"28463289","title":"Comparative study of fully three-dimensional reconstruction algorithms for lens-free microscopy.","abstract":"We propose a three-dimensional (3D) imaging platform based on lens-free microscopy to perform multiangle acquisitions on 3D cell cultures embedded in extracellular matrices. Lens-free microscopy acquisitions present some inherent issues such as the lack of phase information on the sensor plane and a limited angular coverage. We developed and compared three different algorithms based on the Fourier diffraction theorem to obtain fully 3D reconstructions. These algorithms present an increasing complexity associated with a better reconstruction quality. Two of them are based on a regularized inverse problem approach. To compare the reconstruction methods in terms of artefact reduction, signal-to-noise ratio, and computation time, we tested them on two experimental datasets: an endothelial cell culture and a prostate cell culture grown in a 3D extracellular matrix with large reconstructed volumes up to ∼5 mm<sup>3</sup> with a resolution sufficient to resolve isolated single cells. The lens-free reconstructions compare well with standard microscopy.","corpus_id":46771637,"score":1},{"doc_id":"28788711","title":"Iterative wave-front reconstruction in the Fourier domain.","abstract":"The use of Fourier methods in wave-front reconstruction can significantly reduce the computation time for large telescopes with a high number of degrees of freedom. However, Fourier algorithms for discrete data require a rectangular data set which conform to specific boundary requirements, whereas wave-front sensor data is typically defined over a circular domain (the telescope pupil). Here we present an iterative Gerchberg routine modified for the purposes of discrete wave-front reconstruction which adapts the measurement data (wave-front sensor slopes) for Fourier analysis, fulfilling the requirements of the fast Fourier transform (FFT) and providing accurate reconstruction. The routine is used in the adaptation step only and can be coupled to any other Wiener-like or least-squares method. We compare simulations using this method with previous Fourier methods and show an increase in performance in terms of Strehl ratio and a reduction in noise propagation for a 40×40 SPHERE-like adaptive optics system. For closed loop operation with minimal iterations the Gerchberg method provides an improvement in Strehl, from 95.4% to 96.9% in K-band. This corresponds to ~ 40 nm improvement in rms, and avoids the high spatial frequency errors present in other methods, providing an increase in contrast towards the edge of the correctable band.","corpus_id":46802255,"score":1},{"doc_id":"18756356","title":"Three-dimensional SPECT reconstruction with transmission-dependent scatter correction.","abstract":"OBJECTIVE: The quality of single-photon emission computed tomography (SPECT) imaging is hampered by attenuation, collimator blurring, and scatter. Correction for all of these three factors is required for accurate reconstruction, but unfortunately, reconstruction-based compensation often leads to clinically unacceptable long reconstruction times. Especially, efficient scatter correction has proved to be difficult to achieve. The objective of this article was to extend the well-known transmission-dependent convolution subtraction (TDCS) scatter-correction approach into a rapid reconstruction-based scatter-compensation method and to include it into a fast 3D reconstruction algorithm with attenuation and collimator-blurring corrections. METHODS: Ordered subsets expectation maximization algorithm with attenuation, collimator blurring, and accelerated transmission-dependent scatter compensation were implemented. The new reconstruction method was compared with TDCS-based scatter correction and with one other transmission-dependent scatter-correction method using Monte Carlo simulated projection data of (99m)Tc-ECD and (123)I-FP-CIT brain studies. RESULTS: The new reconstruction-based scatter compensation outperformed the other two scatter-correction methods in terms of quantitative accuracy and contrast measured with normalized mean-squared error, gray-to-white matter and striatum-to-background ratios, and also in visual quality. Highest accuracy was achieved when all the corrections (i.e., attenuation, collimator blurring, and scatter) were applied. CONCLUSIONS: The developed 3D reconstruction algorithm with transmission-dependent scatter compensation is a promising alternative to accurate and efficient SPECT reconstruction.","corpus_id":31484937,"score":0},{"doc_id":"19081053","title":"Heterogeneity of large macromolecular complexes revealed by 3D cryo-EM variance analysis.","abstract":"Macromolecular structure determination by cryo-electron microscopy (EM) and single-particle analysis are based on the assumption that imaged molecules have identical structure. With the increased size of processed data sets, it becomes apparent that many complexes coexist in a mixture of conformational states or contain flexible regions. We describe an implementation of the bootstrap resampling technique that yields estimates of voxel-by-voxel variance of a structure reconstructed from the set of its projections. We introduce a highly efficient reconstruction algorithm that is based on direct Fourier inversion and that incorporates correction for the transfer function of the microscope, thus extending the resolution limits of variance estimation. We also describe a validation method to determine the number of resampled volumes required to achieve stable estimate of the variance. The proposed bootstrap method was applied to a data set of 70S ribosome complexed with tRNA and the elongation factor G. The proposed method of variance estimation opens new possibilities for single-particle analysis, by extending applicability of the technique to heterogeneous data sets of macromolecules and to complexes with significant conformational variability.","corpus_id":205258900,"score":0},{"doc_id":"19321015","title":"Error analysis in the determination of the electron microscopical contrast transfer function parameters from experimental power Spectra.","abstract":"BACKGROUND: The transmission electron microscope is used to acquire structural information of macromolecular complexes. However, as any other imaging device, it introduces optical aberrations that must be corrected if high-resolution structural information is to be obtained. The set of all aberrations are usually modeled in Fourier space by the so-called Contrast Transfer Function (CTF). Before correcting for the CTF, we must first estimate it from the electron micrographs. This is usually done by estimating a number of parameters specifying a theoretical model of the CTF. This estimation is performed by minimizing some error measure between the theoretical Power Spectrum Density (PSD) and the experimentally observed PSD. The high noise present in the micrographs, the possible local minima of the error function for estimating the CTF parameters, and the cross-talking between CTF parameters may cause errors in the estimated CTF parameters. RESULTS: In this paper, we explore the effect of these estimation errors on the theoretical CTF. For the CTF model proposed in 1 we show which are the most sensitive CTF parameters as well as the most sensitive background parameters. Moreover, we provide a methodology to reveal the internal structure of the CTF model (which parameters influence in which parameters) and to estimate the accuracy of each model parameter. Finally, we explore the effect of the variability in the detection of the CTF for CTF phase and amplitude correction. CONCLUSION: We show that the estimation errors for the CTF detection methodology proposed in 1 does not show a significant deterioration of the CTF correction capabilities of subsequent algorithms. All together, the methodology described in this paper constitutes a powerful tool for the quantitative analysis of CTF models that can be applied to other models different from the one analyzed here.","corpus_id":2395327,"score":0},{"doc_id":"19651555","title":"Fast parallel approach for 2-D DHT-based real-valued discrete Gabor transform.","abstract":"Two-dimensional fast Gabor transform algorithms are useful for real-time applications due to the high computational complexity of the traditional 2-D complex-valued discrete Gabor transform (CDGT). This paper presents two block time-recursive algorithms for 2-D DHT-based real-valued discrete Gabor transform (RDGT) and its inverse transform and develops a fast parallel approach for the implementation of the two algorithms. The computational complexity of the proposed parallel approach is analyzed and compared with that of the existing 2-D CDGT algorithms. The results indicate that the proposed parallel approach is attractive for real time image processing.","corpus_id":18330870,"score":0},{"doc_id":"20163916","title":"A novel approximation method of CTF amplitude correction for 3D single particle reconstruction.","abstract":"The typical resolution of three-dimensional reconstruction by cryo-EM single particle analysis is now being pushed up to and beyond the nanometer scale. Correction of the contrast transfer function (CTF) of electron microscopic images is essential for achieving such a high resolution. Various correction methods exist and are employed in popular reconstruction software packages. Here, we present a novel approximation method that corrects the amplitude modulation introduced by the contrast transfer function by convoluting the images with a piecewise continuous function. Our new approach can easily be implemented and incorporated into other packages. The implemented method yielded higher resolution reconstructions with data sets from both highly symmetric and asymmetric structures. It is an efficient alternative correction method that allows quick convergence of the 3D reconstruction and has a high tolerance for noisy images, thus easing a bottleneck in practical reconstruction of macromolecules.","corpus_id":24159841,"score":0},{"doc_id":"20647619","title":"Electrical impedance tomography reconstruction for three-dimensional imaging of the prostate.","abstract":"Transrectal electrical impedance tomography (TREIT) has been proposed as an adjunct modality for enhancing standard clinical ultrasound (US) imaging of the prostate. The proposed TREIT probe has an array of electrodes adhered to the surface of a cylindrical US probe that is introduced inside of the imaging volume. Reconstructing TREIT images in the open-domain geometry established with this technique poses additional challenges to those encountered with closed-domain geometries, present in more conventional EIT systems, because of the rapidly decaying current densities at increasing distances from the probe surface. We developed a finite element method (FEM)-based dual-mesh reconstruction algorithm which employs an interpolation scheme for linking a fine forward mesh with a coarse grid of pixels, used for conductivity estimation. Simulation studies using the developed algorithm demonstrate the feasibility of imaging moderately contrasting inclusions at distances of three times the probe radius from the probe surface and at multiple angles about the probe's axis. The large, dense FEM meshes used here require significant computational effort. We have optimized our reconstruction algorithm with multi-core processing hardware and efficient parallelized computational software packages to achieve a speedup of 9.3 times when compared to a more traditional Matlab-based, single CPU solution. The simulation findings and computational optimization provide a state-of-the-art reconstruction platform for use in further evaluating transrectal electrical impedance tomography.","corpus_id":10451680,"score":0},{"doc_id":"20835366","title":"The Fast Multipole Method and Fourier Convolution for the Solution of Acoustic Scattering on Regular Volumetric Grids.","abstract":"The fast multipole method (FMM) is applied to the solution of large-scale, three-dimensional acoustic scattering problems involving inhomogeneous objects defined on a regular grid. The grid arrangement is especially well suited to applications in which the scattering geometry is not known a priori and is reconstructed on a regular grid using iterative inverse scattering algorithms or other imaging techniques. The regular structure of unknown scattering elements facilitates a dramatic reduction in the amount of storage and computation required for the FMM, both of which scale linearly with the number of scattering elements. In particular, the use of fast Fourier transforms to compute Green's function convolutions required for neighboring interactions lowers the often-significant cost of finest-level FMM computations and helps mitigate the dependence of FMM cost on finest-level box size. Numerical results demonstrate the efficiency of the composite method as the number of scattering elements in each finest-level box is increased.","corpus_id":32823989,"score":0},{"doc_id":"21922018","title":"Mapping iterative medical imaging algorithm on cell accelerator.","abstract":"Algebraic reconstruction techniques require about half the number of projections as that of Fourier backprojection methods, which makes these methods safer in terms of required radiation dose. Algebraic reconstruction technique (ART) and its variant OS-SART (ordered subset simultaneous ART) are techniques that provide faster convergence with comparatively good image quality. However, the prohibitively long processing time of these techniques prevents their adoption in commercial CT machines. Parallel computing is one solution to this problem. With the advent of heterogeneous multicore architectures that exploit data parallel applications, medical imaging algorithms such as OS-SART can be studied to produce increased performance. In this paper, we map OS-SART on cell broadband engine (Cell BE). We effectively use the architectural features of Cell BE to provide an efficient mapping. The Cell BE consists of one powerPC processor element (PPE) and eight SIMD coprocessors known as synergetic processor elements (SPEs). The limited memory storage on each of the SPEs makes the mapping challenging. Therefore, we present optimization techniques to efficiently map the algorithm on the Cell BE for improved performance over CPU version. We compare the performance of our proposed algorithm on Cell BE to that of Sun Fire ×4600, a shared memory machine. The Cell BE is five times faster than AMD Opteron dual-core processor. The speedup of the algorithm on Cell BE increases with the increase in the number of SPEs. We also experiment with various parameters, such as number of subsets, number of processing elements, and number of DMA transfers between main memory and local memory, that impact the performance of the algorithm.","corpus_id":10532111,"score":0},{"doc_id":"22149859","title":"Fully 3D list-mode time-of-flight PET image reconstruction on GPUs using CUDA.","abstract":"PURPOSE: List-mode processing is an efficient way of dealing with the sparse nature of positron emission tomography (PET) data sets and is the processing method of choice for time-of-flight (ToF) PET image reconstruction. However, the massive amount of computation involved in forward projection and backprojection limits the application of list-mode reconstruction in practice, and makes it challenging to incorporate accurate system modeling. METHODS: The authors present a novel formulation for computing line projection operations on graphics processing units (GPUs) using the compute unified device architecture (CUDA) framework, and apply the formulation to list-mode ordered-subsets expectation maximization (OSEM) image reconstruction. Our method overcomes well-known GPU challenges such as divergence of compute threads, limited bandwidth of global memory, and limited size of shared memory, while exploiting GPU capabilities such as fast access to shared memory and efficient linear interpolation of texture memory. Execution time comparison and image quality analysis of the GPU-CUDA method and the central processing unit (CPU) method are performed on several data sets acquired on a preclinical scanner and a clinical ToF scanner. RESULTS: When applied to line projection operations for non-ToF list-mode PET, this new GPU-CUDA method is >200 times faster than a single-threaded reference CPU implementation. For ToF reconstruction, we exploit a ToF-specific optimization to improve the efficiency of our parallel processing method, resulting in GPU reconstruction >300 times faster than the CPU counterpart. For a typical whole-body scan with 75 × 75 × 26 image matrix, 40.7 million LORs, 33 subsets, and 3 iterations, the overall processing time is 7.7 s for GPU and 42 min for a single-threaded CPU. Image quality and accuracy are preserved for multiple imaging configurations and reconstruction parameters, with normalized root mean squared (RMS) deviation less than 1% between CPU and GPU-generated images for all cases. CONCLUSIONS: A list-mode ToF OSEM library was developed on the GPU-CUDA platform. Our studies show that the GPU reformulation is considerably faster than a single-threaded reference CPU method especially for ToF processing, while producing virtually identical images. This new method can be easily adapted to enable more advanced algorithms for high resolution PET reconstruction based on additional information such as depth of interaction (DoI), photon energy, and point spread functions (PSFs).","corpus_id":1870700,"score":0},{"doc_id":"22331404","title":"Application of iterative soft thresholding for fast reconstruction of NMR data non-uniformly sampled with multidimensional Poisson Gap scheduling.","abstract":"The fast Fourier transformation has been the gold standard for transforming data from time to frequency domain in many spectroscopic methods, including NMR. While reliable, it has as a drawback that it requires a grid of uniformly sampled data points. This needs very long measuring times for sampling in multidimensional experiments in all indirect dimensions uniformly and even does not allow reaching optimal evolution times that would match the resolution power of modern high-field instruments. Thus, many alternative sampling and transformation schemes have been proposed. Their common challenges are the suppression of the artifacts due to the non-uniformity of the sampling schedules, the preservation of the relative signal amplitudes, and the computing time needed for spectra reconstruction. Here we present a fast implementation of the Iterative Soft Thresholding approach (istHMS) that can reconstruct high-resolution non-uniformly sampled NMR data up to four dimensions within a few hours and make routine reconstruction of high-resolution NUS 3D and 4D spectra convenient. We include a graphical user interface for generating sampling schedules with the Poisson-Gap method and an estimation of optimal evolution times based on molecular properties. The performance of the approach is demonstrated with the reconstruction of non-uniformly sampled medium and high-resolution 3D and 4D protein spectra acquired with sampling densities as low as 0.8%. The method presented here facilitates acquisition, reconstruction and use of multidimensional NMR spectra at otherwise unreachable spectral resolution in indirect dimensions.","corpus_id":20831382,"score":0},{"doc_id":"22752128","title":"Recovering missing slices of the discrete Fourier transform using Ghosts.","abstract":"The discrete Fourier transform (DFT) underpins the solution to many inverse problems commonly possessing missing or unmeasured frequency information. This incomplete coverage of the Fourier space always produces systematic artifacts called Ghosts. In this paper, a fast and exact method for deconvolving cyclic artifacts caused by missing slices of the DFT using redundant image regions is presented. The slices discussed here originate from the exact partitioning of the Discrete Fourier Transform (DFT) space, under the projective Discrete Radon Transform, called the discrete Fourier slice theorem. The method has a computational complexity of O(n log(2) n) (for an n=N×N image) and is constructed from a new cyclic theory of Ghosts. This theory is also shown to unify several aspects of work done on Ghosts over the past three decades. This paper concludes with an application to fast, exact, non-iterative image reconstruction from a highly asymmetric set of rational angle projections that give rise to sets of sparse slices within the DFT.","corpus_id":2317098,"score":0},{"doc_id":"23165973","title":"Fast direct fourier reconstruction of radial and PROPELLER MRI data using the chirp transform algorithm on graphics hardware.","abstract":"PURPOSE: To develop and test a new algorithm for fast direct Fourier transform (DrFT) reconstruction of MR data on non-Cartesian trajectories composed of lines with equally spaced points. THEORY AND METHODS: The DrFT, which is normally used as a reference in evaluating the accuracy of other reconstruction methods, can reconstruct images directly from non-Cartesian MR data without interpolation. However, DrFT reconstruction involves substantially intensive computation, which makes the DrFT impractical for clinical routine applications. In this article, the Chirp transform algorithm was introduced to accelerate the DrFT reconstruction of radial and Periodically Rotated Overlapping ParallEL Lines with Enhanced Reconstruction (PROPELLER) MRI data located on the trajectories that are composed of lines with equally spaced points. The performance of the proposed Chirp transform algorithm-DrFT algorithm was evaluated by using simulation and in vivo MRI data. RESULTS: After implementing the algorithm on a graphics processing unit, the proposed Chirp transform algorithm-DrFT algorithm achieved an acceleration of approximately one order of magnitude, and the speed-up factor was further increased to approximately three orders of magnitude compared with the traditional single-thread DrFT reconstruction. CONCLUSION: Implementation the Chirp transform algorithm-DrFT algorithm on the graphics processing unit can efficiently calculate the DrFT reconstruction of the radial and PROPELLER MRI data.","corpus_id":206282080,"score":0},{"doc_id":"23201934","title":"Three-dimensional reconstruction of particle holograms: a fast and accurate multiscale approach.","abstract":"In-line digital holography is an imaging technique that is being increasingly used for studying three-dimensional flows. It has been previously shown that very accurate reconstructions of objects could be achieved with the use of an inverse problem framework. Such approaches, however, suffer from higher computational times compared to less accurate conventional reconstructions based on hologram backpropagation. To overcome this computational issue, we propose a coarse-to-fine multiscale approach to strongly reduce the algorithm complexity. We illustrate that an accuracy comparable to that of state-of-the-art methods can be reached while accelerating parameter-space scanning.","corpus_id":42428028,"score":0},{"doc_id":"23261401","title":"FASTDEF: fast defocus and astigmatism estimation for high-throughput transmission electron microscopy.","abstract":"In this work we present a fast and automated algorithm for estimating the contrast transfer function (CTF) of a transmission electron microscope. The approach is very suitable for High Throughput work because: (a) it does not require any initial defocus estimation, (b) it is almost an order of magnitude faster than existing approaches, (c) it opens the way to well-defined extensions to the estimation of higher order aberrations, at the same time that provides defocus and astigmatism estimations comparable in accuracy to well established methods, such as Xmipp and CTFFIND3 approaches. The new algorithm is based on obtaining the wrapped modulating phase of the power spectra density pattern by the use of a quadrature filter. This phase is further unwrapped in order to obtain the continuous and smooth absolute phase map; then a Zernike polynomial fitting is performed and the defocus and astigmatism parameters are determined. While the method does not require an initial estimation of the defocus parameters or any non-linear optimization procedure, these approaches can be used if further refinement is desired. Results of the CTF estimation method are presented for standard negative stained images, cryo-electron microscopy images in the absence of carbon support, as well as micrographs with only ice. Additionally, we have also tested the proposed method with micrographs acquired from tilted and untilted samples, obtaining good results. The algorithm is freely available as a part of the Xmipp package [http://xmipp.cnb.csic.es].","corpus_id":9415778,"score":0},{"doc_id":"23387778","title":"Accelerating image reconstruction in three-dimensional optoacoustic tomography on graphics processing units.","abstract":"PURPOSE: Optoacoustic tomography (OAT) is inherently a three-dimensional (3D) inverse problem. However, most studies of OAT image reconstruction still employ two-dimensional imaging models. One important reason is because 3D image reconstruction is computationally burdensome. The aim of this work is to accelerate existing image reconstruction algorithms for 3D OAT by use of parallel programming techniques. METHODS: Parallelization strategies are proposed to accelerate a filtered backprojection (FBP) algorithm and two different pairs of projection/backprojection operations that correspond to two different numerical imaging models. The algorithms are designed to fully exploit the parallel computing power of graphics processing units (GPUs). In order to evaluate the parallelization strategies for the projection/backprojection pairs, an iterative image reconstruction algorithm is implemented. Computer simulation and experimental studies are conducted to investigate the computational efficiency and numerical accuracy of the developed algorithms. RESULTS: The GPU implementations improve the computational efficiency by factors of 1000, 125, and 250 for the FBP algorithm and the two pairs of projection/backprojection operators, respectively. Accurate images are reconstructed by use of the FBP and iterative image reconstruction algorithms from both computer-simulated and experimental data. CONCLUSIONS: Parallelization strategies for 3D OAT image reconstruction are proposed for the first time. These GPU-based implementations significantly reduce the computational time for 3D image reconstruction, complementing our earlier work on 3D OAT iterative image reconstruction.","corpus_id":24053409,"score":0},{"doc_id":"23482123","title":"Fast iterative reconstruction of differential phase contrast X-ray tomograms.","abstract":"Differential phase-contrast is a recent technique in the context of X-ray imaging. In order to reduce the specimen's exposure time, we propose a new iterative algorithm that can achieve the same quality as FBP-type methods, while using substantially fewer angular views. Our approach is based on 1) a novel spline-based discretization of the forward model and 2) an iterative reconstruction algorithm using the alternating direction method of multipliers. Our experimental results on real data suggest that the method allows to reduce the number of required views by at least a factor of four.","corpus_id":12511920,"score":0},{"doc_id":"23933392","title":"Particle quality assessment and sorting for automatic and semiautomatic particle-picking techniques.","abstract":"Three-dimensional reconstruction of biological specimens using electron microscopy by single particle methodologies requires the identification and extraction of the imaged particles from the acquired micrographs. Automatic and semiautomatic particle selection approaches can localize these particles, minimizing the user interaction, but at the cost of selecting a non-negligible number of incorrect particles, which can corrupt the final three-dimensional reconstruction. In this work, we present a novel particle quality assessment and sorting method that can separate most erroneously picked particles from correct ones. The proposed method is based on multivariate statistical analysis of a particle set that has been picked previously using any automatic or manual approach. The new method uses different sets of particle descriptors, which are morphology-based, histogram-based and signal to noise analysis based. We have tested our proposed algorithm with experimental data obtaining very satisfactory results. The algorithm is freely available as a part of the Xmipp 3.0 package [http://xmipp.cnb.csic.es].","corpus_id":7094288,"score":0},{"doc_id":"23958728","title":"A pattern matching approach to the automatic selection of particles from low-contrast electron micrographs.","abstract":"MOTIVATION: Structural information of macromolecular complexes provides key insights into the way they carry out their biological functions. Achieving high-resolution structural details with electron microscopy requires the identification of a large number (up to hundreds of thousands) of single particles from electron micrographs, which is a laborious task if it has to be manually done and constitutes a hurdle towards high-throughput. Automatic particle selection in micrographs is far from being settled and new and more robust algorithms are required to reduce the number of false positives and false negatives. RESULTS: In this article, we introduce an automatic particle picker that learns from the user the kind of particles he is interested in. Particle candidates are quickly and robustly classified as particles or non-particles. A number of new discriminative shape-related features as well as some statistical description of the image grey intensities are used to train two support vector machine classifiers. Experimental results demonstrate that the proposed method: (i) has a considerably low computational complexity and (ii) provides results better or comparable with previously reported methods at a fraction of their computing time. AVAILABILITY: The algorithm is fully implemented in the open-source Xmipp package and downloadable from http://xmipp.cnb.csic.es.","corpus_id":11199882,"score":0},{"doc_id":"24075951","title":"Xmipp 3.0: an improved software suite for image processing in electron microscopy.","abstract":"Xmipp is a specialized software package for image processing in electron microscopy, and that is mainly focused on 3D reconstruction of macromolecules through single-particles analysis. In this article we present Xmipp 3.0, a major release which introduces several improvements and new developments over the previous version. A central improvement is the concept of a project that stores the entire processing workflow from data import to final results. It is now possible to monitor, reproduce and restart all computing tasks as well as graphically explore the complete set of interrelated tasks associated to a given project. Other graphical tools have also been improved such as data visualization, particle picking and parameter \"wizards\" that allow the visual selection of some key parameters. Many standard image formats are transparently supported for input/output from all programs. Additionally, results have been standardized, facilitating the interoperation between different Xmipp programs. Finally, as a result of a large code refactoring, the underlying C++ libraries are better suited for future developments and all code has been optimized. Xmipp is an open-source package that is freely available for download from: http://xmipp.cnb.csic.es.","corpus_id":14314008,"score":0},{"doc_id":"24228274","title":"Efficient volume reconstruction for parallel-beam computed laminography by filtered backprojection on multi-core clusters.","abstract":"Computed laminography (CL) was developed to use X-rays from synchrotron sources for high-resolution imaging of the internal structure of a flat specimen from a series of 2-D projection images. The projections are acquired by irradiation of the sample under different rotation angles where the object rotation axis is inclined with respect to the beam direction. This yields for laterally extended objects a more uniform average transmitted intensity during sample rotation compared with computed tomography (CT). The reconstruction problem of CL cannot be reduced to a data-efficient 2-D case (as for parallel-beam CT) since each single slice perpendicular to the rotation axis requires a 2-D region on the detector as input data for all projection directions. This paper describes a computationally efficient reconstruction procedure based on filtered backprojection (FBP) adapted to the CL acquisition geometry. From the Fourier slice theorem, we derive a framework for analytic image reconstruction and outline implementation details of the generic FBP algorithm. Different approaches reducing the reconstruction time by means of parallel and distributed computations are considered and evaluated.","corpus_id":41159872,"score":0},{"doc_id":"24710398","title":"Fast space-varying convolution using matrix source coding with applications to camera stray light reduction.","abstract":"Many imaging applications require the implementation of space-varying convolution for accurate restoration and reconstruction of images. Here, we use the term space-varying convolution to refer to linear operators whose impulse response has slow spatial variation. In addition, these space-varying convolution operators are often dense, so direct implementation of the convolution operator is typically computationally impractical. One such example is the problem of stray light reduction in digital cameras, which requires the implementation of a dense space-varying deconvolution operator. However, other inverse problems, such as iterative tomographic reconstruction, can also depend on the implementation of dense space-varying convolution. While space-invariant convolution can be efficiently implemented with the fast Fourier transform, this approach does not work for space-varying operators. So direct convolution is often the only option for implementing space-varying convolution. In this paper, we develop a general approach to the efficient implementation of space-varying convolution, and demonstrate its use in the application of stray light reduction. Our approach, which we call matrix source coding, is based on lossy source coding of the dense space-varying convolution matrix. Importantly, by coding the transformation matrix, we not only reduce the memory required to store it; we also dramatically reduce the computation required to implement matrix-vector products. Our algorithm is able to reduce computation by approximately factoring the dense space-varying convolution operator into a product of sparse transforms. Experimental results show that our method can dramatically reduce the computation required for stray light reduction while maintaining high accuracy.","corpus_id":14385528,"score":0},{"doc_id":"24974203","title":"Efficient initial volume determination from electron microscopy images of single particles.","abstract":"MOTIVATION: Structural information of macromolecular complexes provides key insights into the way they carry out their biological functions. The reconstruction process leading to the final 3D map requires an approximate initial model. Generation of an initial model is still an open and challenging problem in single-particle analysis. RESULTS: We present a fast and efficient approach to obtain a reliable, low-resolution estimation of the 3D structure of a macromolecule, without any a priori knowledge, addressing the well-known issue of initial volume estimation in the field of single-particle analysis. The input of the algorithm is a set of class average images obtained from individual projections of a biological object at random and unknown orientations by transmission electron microscopy micrographs. The proposed method is based on an initial non-lineal dimensionality reduction approach, which allows to automatically selecting representative small sets of class average images capturing the most of the structural information of the particle under study. These reduced sets are then used to generate volumes from random orientation assignments. The best volume is determined from these guesses using a random sample consensus (RANSAC) approach. We have tested our proposed algorithm, which we will term 3D-RANSAC, with simulated and experimental data, obtaining satisfactory results under the low signal-to-noise conditions typical of cryo-electron microscopy. AVAILABILITY: The algorithm is freely available as part of the Xmipp 3.1 package [http://xmipp.cnb.csic.es]. CONTACT: jvargas@cnb.csic.es SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.","corpus_id":8183036,"score":0},{"doc_id":"25069768","title":"Geometric correction method for 3D in-line X-ray phase contrast image reconstruction.","abstract":"BACKGROUND: Mechanical system with imperfect or misalignment of X-ray phase contrast imaging (XPCI) components causes projection data misplaced, and thus result in the reconstructed slice images of computed tomography (CT) blurred or with edge artifacts. So the features of biological microstructures to be investigated are destroyed unexpectedly, and the spatial resolution of XPCI image is decreased. It makes data correction an essential pre-processing step for CT reconstruction of XPCI. METHODS: To remove unexpected blurs and edge artifacts, a mathematics model for in-line XPCI is built by considering primary geometric parameters which include a rotation angle and a shift variant in this paper. Optimal geometric parameters are achieved by finding the solution of a maximization problem. And an iterative approach is employed to solve the maximization problem by using a two-step scheme which includes performing a composite geometric transformation and then following a linear regression process. After applying the geometric transformation with optimal parameters to projection data, standard filtered back-projection algorithm is used to reconstruct CT slice images. RESULTS: Numerical experiments were carried out on both synthetic and real in-line XPCI datasets. Experimental results demonstrate that the proposed method improves CT image quality by removing both blurring and edge artifacts at the same time compared to existing correction methods. CONCLUSIONS: The method proposed in this paper provides an effective projection data correction scheme and significantly improves the image quality by removing both blurring and edge artifacts at the same time for in-line XPCI. It is easy to implement and can also be extended to other XPCI techniques.","corpus_id":11752183,"score":0},{"doc_id":"25268657","title":"Hybrid Electron Microscopy Normal Mode Analysis graphical interface and protocol.","abstract":"This article presents an integral graphical interface to the Hybrid Electron Microscopy Normal Mode Analysis (HEMNMA) approach that was developed for capturing continuous motions of large macromolecular complexes from single-particle EM images. HEMNMA was shown to be a good approach to analyze multiple conformations of a macromolecular complex but it could not be widely used in the EM field due to a lack of an integral interface. In particular, its use required switching among different software sources as well as selecting modes for image analysis was difficult without the graphical interface. The graphical interface was thus developed to simplify the practical use of HEMNMA. It is implemented in the open-source software package Xmipp 3.1 (http://xmipp.cnb.csic.es) and only a small part of it relies on MATLAB that is accessible through the main interface. Such integration provides the user with an easy way to perform the analysis of macromolecular dynamics and forms a direct connection to the single-particle reconstruction process. A step-by-step HEMNMA protocol with the graphical interface is given in full details in Supplementary material. The graphical interface will be useful to experimentalists who are interested in studies of continuous conformational changes of macromolecular complexes beyond the modeling of continuous heterogeneity in single particle reconstruction.","corpus_id":13918346,"score":0},{"doc_id":"25304701","title":"Iterative reconstruction: how it works, how to apply it.","abstract":"Computed tomography acquires X-ray projection data from multiple angles though an object to generate a tomographic rendition of its attenuation characteristics. Filtered back projection is a fast, closed analytical solution to the reconstruction process, whereby all projections are equally weighted, but is prone to deliver inadequate image quality when the dose levels are reduced. Iterative reconstruction is an algorithmic method that uses statistical and geometric models to variably weight the image data in a process that can be solved iteratively to independently reduce noise and preserve resolution and image quality. Applications of this technology in a clinical setting can result in lower dose on the order of 20-40% compared to a standard filtered back projection reconstruction for most exams. A carefully planned implementation strategy and methodological approach is necessary to achieve the goals of lower dose with uncompromised image quality.","corpus_id":22095801,"score":0},{"doc_id":"25637660","title":"A statistical approach to the initial volume problem in Single Particle Analysis by Electron Microscopy.","abstract":"Cryo Electron Microscopy is a powerful Structural Biology technique, allowing the elucidation of the three-dimensional structure of biological macromolecules. In particular, the structural study of purified macromolecules -often referred as Single Particle Analysis(SPA)- is normally performed through an iterative process that needs a first estimation of the three-dimensional structure that is progressively refined using experimental data. It is well-known the local optimisation nature of this refinement, so that the initial choice of this first structure may substantially change the final result. Computational algorithms aiming to providing this first structure already exist. However, the question is far from settled and more robust algorithms are still needed so that the refinement process can be performed with sufficient guarantees. In this article we present a new algorithm that addresses the initial volume problem in SPA by setting it in a Weighted Least Squares framework and calculating the weights through a statistical approach based on the cumulative density function of different image similarity measures. We show that the new algorithm is significantly more robust than other state-of-the-art algorithms currently in use in the field. The algorithm is available as part of the software suite Xmipp (http://xmipp.cnb.csic.es) and Scipion (http://scipion.cnb.csic.es) under the name \"Significant\".","corpus_id":15342000,"score":0},{"doc_id":"25866499","title":"High Performance GPU-Based Fourier Volume Rendering.","abstract":"Fourier volume rendering (FVR) is a significant visualization technique that has been used widely in digital radiography. As a result of its 𝒪(N (2)logN) time complexity, it provides a faster alternative to spatial domain volume rendering algorithms that are 𝒪(N (3)) computationally complex. Relying on the Fourier projection-slice theorem, this technique operates on the spectral representation of a 3D volume instead of processing its spatial representation to generate attenuation-only projections that look like X-ray radiographs. Due to the rapid evolution of its underlying architecture, the graphics processing unit (GPU) became an attractive competent platform that can deliver giant computational raw power compared to the central processing unit (CPU) on a per-dollar-basis. The introduction of the compute unified device architecture (CUDA) technology enables embarrassingly-parallel algorithms to run efficiently on CUDA-capable GPU architectures. In this work, a high performance GPU-accelerated implementation of the FVR pipeline on CUDA-enabled GPUs is presented. This proposed implementation can achieve a speed-up of 117x compared to a single-threaded hybrid implementation that uses the CPU and GPU together by taking advantage of executing the rendering pipeline entirely on recent GPU architectures.","corpus_id":1954769,"score":0},{"doc_id":"26776541","title":"Efficient methods for implementation of multi-level nonrigid mass-preserving image registration on GPUs and multi-threaded CPUs.","abstract":"BACKGROUND AND OBJECTIVE: Faster and more accurate methods for registration of images are important for research involved in conducting population-based studies that utilize medical imaging, as well as improvements for use in clinical applications. We present a novel computation- and memory-efficient multi-level method on graphics processing units (GPU) for performing registration of two computed tomography (CT) volumetric lung images. METHODS: We developed a computation- and memory-efficient Diffeomorphic Multi-level B-Spline Transform Composite (DMTC) method to implement nonrigid mass-preserving registration of two CT lung images on GPU. The framework consists of a hierarchy of B-Spline control grids of increasing resolution. A similarity criterion known as the sum of squared tissue volume difference (SSTVD) was adopted to preserve lung tissue mass. The use of SSTVD consists of the calculation of the tissue volume, the Jacobian, and their derivatives, which makes its implementation on GPU challenging due to memory constraints. The use of the DMTC method enabled reduced computation and memory storage of variables with minimal communication between GPU and Central Processing Unit (CPU) due to ability to pre-compute values. The method was assessed on six healthy human subjects. RESULTS: Resultant GPU-generated displacement fields were compared against the previously validated CPU counterpart fields, showing good agreement with an average normalized root mean square error (nRMS) of 0.044±0.015. Runtime and performance speedup are compared between single-threaded CPU, multi-threaded CPU, and GPU algorithms. Best performance speedup occurs at the highest resolution in the GPU implementation for the SSTVD cost and cost gradient computations, with a speedup of 112 times that of the single-threaded CPU version and 11 times over the twelve-threaded version when considering average time per iteration using a Nvidia Tesla K20X GPU. CONCLUSIONS: The proposed GPU-based DMTC method outperforms its multi-threaded CPU version in terms of runtime. Total registration time reduced runtime to 2.9min on the GPU version, compared to 12.8min on twelve-threaded CPU version and 112.5min on a single-threaded CPU. Furthermore, the GPU implementation discussed in this work can be adapted for use of other cost functions that require calculation of the first derivatives.","corpus_id":10051304,"score":0},{"doc_id":"28590565","title":"Three-dimensional MR reconstruction of high-contrast magnetic susceptibility by the variational born iterative method based on the magnetic field volume integral equation.","abstract":"PURPOSE: To provide high-quality and high-contrast magnetic susceptibility mapping, a 3D MR reconstruction method for magnetic susceptibility based on the magnetic field volume integral equation with the variational Born iterative method (VBIM) is developed. METHODS: Three-dimensional magnetic susceptibility is reconstructed from the positive rotating magnetic field component H1+ of the radiofrequency field acquired by B1 mapping. The stabilized biconjugate gradient fast Fourier transform (BCGS-FFT) method is implemented in the forward problem to solve for the magnetic field, and the conjugate gradient fast Fourier transform method is implemented in the inverse problem to reconstruct the magnetic susceptibility distribution. RESULTS: Numerical results demonstrated that good effectiveness and high accuracy can be achieved for both the forward solver of the stabilized biconjugate gradient fast Fourier transform method and the inverse solver of the VBIM method. The method proved to be robust under noise contamination. Moreover, the magnetic susceptibilities with much higher contrasts than that of the non-full wave methods can also be efficiently reconstructed. CONCLUSIONS: The proposed method can reconstruct the magnetic susceptibility of not only human head, but also other human tissues or materials such as magnetic contrast agents with high magnetic susceptibilities. It has promising applications in high-contrast magnetic susceptibility mapping. Magn Reson Med, 2017. © 2017 International Society for Magnetic Resonance in Medicine.","corpus_id":21847798,"score":0}],"string":"[\n {\n \"doc_id\": \"18499351\",\n \"title\": \"Cryo-EM image alignment based on nonuniform fast Fourier transform.\",\n \"abstract\": \"In single particle analysis, two-dimensional (2-D) alignment is a fundamental step intended to put into register various particle projections of biological macromolecules collected at the electron microscope. The efficiency and quality of three-dimensional (3-D) structure reconstruction largely depends on the computational speed and alignment accuracy of this crucial step. In order to improve the performance of alignment, we introduce a new method that takes advantage of the highly accurate interpolation scheme based on the gridding method, a version of the nonuniform fast Fourier transform, and utilizes a multi-dimensional optimization algorithm for the refinement of the orientation parameters. Using simulated data, we demonstrate that by using less than half of the sample points and taking twice the runtime, our new 2-D alignment method achieves dramatically better alignment accuracy than that based on quadratic interpolation. We also apply our method to image to volume registration, the key step in the single particle EM structure refinement protocol. We find that in this case the accuracy of the method not only surpasses the accuracy of the commonly used real-space implementation, but results are achieved in much shorter time, making gridding-based alignment a perfect candidate for efficient structure determination in single particle analysis.\",\n \"corpus_id\": 25736312,\n \"score\": 2\n },\n {\n \"doc_id\": \"18692361\",\n \"title\": \"Evaluation of a new gridding method for fully 3D direct Fourier PET reconstruction based on a two-plane geometry.\",\n \"abstract\": \"This study investigated how the choice of fixed planes for the representation of the projection data of a cylindrical positron emission tomography (PET) scanner simplifies the frequency interpolation required by the 3D Fourier slice theorem (3D-FST). A new gridding algorithm based on a two-plane geometry and requiring only 1D interpolations in the Fourier domain was compared with the direct implementation of the 3D-FST. We show that the use of two orthogonal planes leads to signal to noise ratios similar to those achieved with the 3D-FST algorithm from projection data acquired with up to two times more count rates, while the resolution remains similar.\",\n \"corpus_id\": 19761761,\n \"score\": 2\n },\n {\n \"doc_id\": \"20888956\",\n \"title\": \"Fundamentals of three-dimensional reconstruction from projections.\",\n \"abstract\": \"Three-dimensional (3D) reconstruction of an object mass density from the set of its 2D line projections lies at a core of both single-particle reconstruction technique and electron tomography. Both techniques utilize electron microscope to collect a set of projections of either multiple objects representing in principle the same macromolecular complex in an isolated form, or a subcellular structure isolated in situ. Therefore, the goal of macromolecular electron microscopy is to invert the projection transformation to recover the distribution of the mass density of the original object. The problem is interesting in that in its discrete form it is ill-posed and not invertible. Various algorithms have been proposed to cope with the practical difficulties of this inversion problem and their differ widely in terms of their robustness with respect to noise in the data, completeness of the collected projection dataset, errors in projections orientation parameters, abilities to efficiently handle large datasets, and other obstacles typically encountered in molecular electron microscopy. Here, we review the theoretical foundations of 3D reconstruction from line projections followed by an overview of reconstruction algorithms routinely used in practice of electron microscopy.\",\n \"corpus_id\": 23406418,\n \"score\": 2\n },\n {\n \"doc_id\": \"24326216\",\n \"title\": \"Iterative reconstruction of cryo-electron tomograms using nonuniform fast Fourier transforms.\",\n \"abstract\": \"Algorithms for three-dimensional (3D) reconstruction of objects based on their projections are essential in various biological and medical imaging modalities. In cryo-electron tomography (CET) a major challenge for reconstruction is the limited range of projection angles, which manifests itself as a \\\"missing wedge\\\" of data in Fourier space making the reconstruction problem ill-posed. Here, we apply an iterative reconstruction method that makes use of nonuniform fast Fourier transform (NUFFT) to the reconstruction of cryo-electron tomograms. According to several measures the reconstructions are superior to those obtained using conventional methods, most notably weighted backprojection. Most importantly, we show that it is possible to fill in partially the unsampled region in Fourier space with meaningful information without making assumptions about the data or applying prior knowledge. As a consequence, particles of known structure can be localized with higher confidence in cryotomograms and subtomogram averaging yields higher resolution densities.\",\n \"corpus_id\": 5514970,\n \"score\": 2\n },\n {\n \"doc_id\": \"27410628\",\n \"title\": \"Fast gridding projectors for analytical and iterative tomographic reconstruction of differential phase contrast data.\",\n \"abstract\": \"This paper introduces new gridding projectors designed to efficiently perform analytical and iterative tomographic reconstruction, when the forward model is represented by the derivative of the Radon transform. This inverse problem is tightly connected with an emerging X-ray tube- and synchrotron-based imaging technique: differential phase contrast based on a grating interferometer. This study shows, that the proposed projectors, compared to space-based implementations of the same operators, yield high quality analytical and iterative reconstructions, while improving the computational efficiency by few orders of magnitude.\",\n \"corpus_id\": 7129985,\n \"score\": 2\n },\n {\n \"doc_id\": \"27661946\",\n \"title\": \"Precise and fast spatial-frequency analysis using the iterative local Fourier transform.\",\n \"abstract\": \"The use of the discrete Fourier transform has decreased since the introduction of the fast Fourier transform (fFT), which is a numerically efficient computing process. This paper presents the iterative local Fourier transform (ilFT), a set of new processing algorithms that iteratively apply the discrete Fourier transform within a local and optimal frequency domain. The new technique achieves 2<sup>10</sup> times higher frequency resolution than the fFT within a comparable computation time. The method's superb computing efficiency, high resolution, spectrum zoom-in capability, and overall performance are evaluated and compared to other advanced high-resolution Fourier transform techniques, such as the fFT combined with several fitting methods. The effectiveness of the ilFT is demonstrated through the data analysis of a set of Talbot self-images (1280 × 1024 pixels) obtained with an experimental setup using grating in a diverging beam produced by a coherent point source.\",\n \"corpus_id\": 4980403,\n \"score\": 2\n },\n {\n \"doc_id\": \"29312997\",\n \"title\": \"A Survey of the Use of Iterative Reconstruction Algorithms in Electron Microscopy.\",\n \"abstract\": \"One of the key steps in Electron Microscopy is the tomographic reconstruction of a three-dimensional (3D) map of the specimen being studied from a set of two-dimensional (2D) projections acquired at the microscope. This tomographic reconstruction may be performed with different reconstruction algorithms that can be grouped into several large families: direct Fourier inversion methods, back-projection methods, Radon methods, or iterative algorithms. In this review, we focus on the latter family of algorithms, explaining the mathematical rationale behind the different algorithms in this family as they have been introduced in the field of Electron Microscopy. We cover their use in Single Particle Analysis (SPA) as well as in Electron Tomography (ET).\",\n \"corpus_id\": 26646474,\n \"score\": 2\n },\n {\n \"doc_id\": \"18390350\",\n \"title\": \"Accelerating the nonequispaced fast Fourier transform on commodity graphics hardware.\",\n \"abstract\": \"We present a fast parallel algorithm to compute the nonequispaced fast Fourier transform on commodity graphics hardware (the GPU). We focus particularly on a novel implementation of the convolution step in the transform as it was previously its most time consuming part. We describe the performance for two common sample distributions in medical imaging (radial and spiral trajectories), and for different convolution kernels as these parameters all influence the speed of the algorithm. The GPU-accelerated convolution is up to 85 times faster as our reference, the open source NFFT library on a state-of-the-art 64 bit CPU. The accuracy of the proposed GPU implementation was quantitatively evaluated at the various settings. To illustrate the applicability of the transform in medical imaging, in which it is also known as gridding, we look specifically at non-Cartesian magnetic resonance imaging and reconstruct both a numerical phantom and an in vivo cardiac image.\",\n \"corpus_id\": 206747049,\n \"score\": 1\n },\n {\n \"doc_id\": \"18672425\",\n \"title\": \"Rotate-and-slant projector for fast LOR-based fully-3-D iterative PET reconstruction.\",\n \"abstract\": \"One of the greatest challenges facing iterative fully-3-D positron emission tomography (PET) reconstruction is the issue of long reconstruction times due to the large number of measurements for 3-D mode as compared to 2-D mode. A rotate-and-slant projector has been developed that takes advantage of symmetries in the geometry to compute volumetric projections to multiple oblique sinograms in a computationally efficient manner. It is based upon the 2-D rotation-based projector using the three-pass method of shears, and it conserves the 2-D rotator computations for multiple projections to each oblique sinogram set. The projector is equally applicable to both conventional evenly-spaced projections and unevenly-spaced line-of-response (LOR) data. The LOR-based version models the location and orientation of the individual LORs (i.e., the arc-correction), providing an ordinary Poisson reconstruction framework. The projector was implemented in C with several optimizations for speed, exploiting the vertical symmetry of the oblique projection process, depth compression, and array indexing schemes which maximize serial memory access. The new projector was evaluated and compared to ray-driven and distance-driven projectors using both analytical and experimental phantoms, and fully-3-D iterative reconstructions with each projector were also compared to Fourier rebinning with 2-D iterative reconstruction. In terms of spatial resolution, contrast, and background noise measures, 3-D LOR-based iterative reconstruction with the rotate-and-slant projector performed as well as or better than the other methods. Total processing times, measured on a single cpu Linux workstation, were approximately 10x faster for the rotate-and-slant projector than for the other 3-D projectors studied. The new projector provided four iterations fully-3-D ordered-subsets reconstruction in as little as 15 s--approximately the same time as FORE + 2-D reconstruction. We conclude that the rotate-and-slant projector is a viable option for fully-3-D PET, offering quality statistical reconstruction in times only marginally slower than 2-D or rebinning methods.\",\n \"corpus_id\": 8142165,\n \"score\": 1\n },\n {\n \"doc_id\": \"19131666\",\n \"title\": \"Fast 3D iterative image reconstruction for SPECT with rotating slat collimators.\",\n \"abstract\": \"As an alternative to the use of traditional parallel hole collimators, SPECT imaging can be performed using rotating slat collimators. While maintaining the spatial resolution, a gain in image quality could be expected from the higher photon collection efficiency of this type of collimator. However, the use of iterative methods to do fully three-dimensional (3D) reconstruction is computationally much more expensive and furthermore involves slow convergence compared to a classical SPECT reconstruction. It has been proposed to do 3D reconstruction by splitting the system matrix into two separate matrices, forcing the reconstruction to first estimate the sinograms from the rotating slat SPECT data before estimating the image. While alleviating the computational load by one order of magnitude, this split matrix approach would result in fast computation of the projections in an iterative algorithm, but does not solve the problem of slow convergence. There is thus a need for an algorithm which speeds up convergence while maintaining image quality for rotating slat collimated SPECT cameras. Therefore, we developed a reconstruction algorithm based on the split matrix approach which allows both a fast calculation of the forward and backward projection and a fast convergence. In this work, an algorithm of the maximum likelihood expectation maximization (MLEM) type, obtained from a split system matrix MLEM reconstruction, is proposed as a reconstruction method for rotating slat collimated SPECT data. Here, we compare this new algorithm to the conventional split system matrix MLEM method and to a gold standard fully 3D MLEM reconstruction algorithm on the basis of computational load, convergence and contrast-to-noise. Furthermore, ordered subsets expectation maximization (OSEM) implementations of these three algorithms are compared. Calculation of computational load and convergence for the different algorithms shows a speedup for the new method of 38 and 426 compared to the split matrix MLEM approach and the fully 3D MLEM respectively and a speedup of 16 and 21 compared to the split matrix OSEM and the fully 3D OSEM respectively. A contrast-to-noise study based on simulated data shows that our new approach has comparable accuracy as the fully 3D reconstruction method. The algorithm developed in this study allows iterative image reconstruction of rotating slat collimated SPECT data with equal image quality in a comparable amount of computation time as a classical SPECT reconstruction.\",\n \"corpus_id\": 41250680,\n \"score\": 1\n },\n {\n \"doc_id\": \"20009184\",\n \"title\": \"A fast and pragmatic approach for scatter correction in flat-detector CT using elliptic modeling and iterative optimization.\",\n \"abstract\": \"Scattered radiation is a major source of artifacts in flat detector computed tomography (FDCT) due to the increased irradiated volumes. We propose a fast projection-based algorithm for correction of scatter artifacts. The presented algorithm combines a convolution method to determine the spatial distribution of the scatter intensity distribution with an object-size-dependent scaling of the scatter intensity distributions using a priori information generated by Monte Carlo simulations. A projection-based (PBSE) and an image-based (IBSE) strategy for size estimation of the scanned object are presented. Both strategies provide good correction and comparable results; the faster PBSE strategy is recommended. Even with such a fast and simple algorithm that in the PBSE variant does not rely on reconstructed volumes or scatter measurements, it is possible to provide a reasonable scatter correction even for truncated scans. For both simulations and measurements, scatter artifacts were significantly reduced and the algorithm showed stable behavior in the z-direction. For simulated voxelized head, hip and thorax phantoms, a figure of merit Q of 0.82, 0.76 and 0.77 was reached, respectively (Q = 0 for uncorrected, Q = 1 for ideal). For a water phantom with 15 cm diameter, for example, a cupping reduction from 10.8% down to 2.1% was achieved. The performance of the correction method has limitations in the case of measurements using non-ideal detectors, intensity calibration, etc. An iterative approach to overcome most of these limitations was proposed. This approach is based on root finding of a cupping metric and may be useful for other scatter correction methods as well. By this optimization, cupping of the measured water phantom was further reduced down to 0.9%. The algorithm was evaluated on a commercial system including truncated and non-homogeneous clinically relevant objects.\",\n \"corpus_id\": 10988988,\n \"score\": 1\n },\n {\n \"doc_id\": \"20236843\",\n \"title\": \"Gridding and fast Fourier transformation on non-uniformly sparse sampled multidimensional NMR data.\",\n \"abstract\": \"For multidimensional NMR method, indirect dimensional non-uniform sparse sampling can dramatically shorten acquisition time of the experiments. However, the non-uniformly sampled NMR data cannot be processed directly using fast Fourier transform (FFT). We show that the non-uniformly sampled NMR data can be reconstructed to Cartesian grid with the gridding method that has been wide applied in MRI, and sequentially be processed using FFT. The proposed gridding-FFT (GFFT) method increases the processing speed sharply compared with the previously proposed non-uniform Fourier Transform, and may speed up application of the non-uniform sparse sampling approaches.\",\n \"corpus_id\": 31422311,\n \"score\": 1\n },\n {\n \"doc_id\": \"20578028\",\n \"title\": \"Iterative image reconstruction for PROPELLER-MRI using the nonuniform fast fourier transform.\",\n \"abstract\": \"PURPOSE: To investigate an iterative image reconstruction algorithm using the nonuniform fast Fourier transform (NUFFT) for PROPELLER (Periodically Rotated Overlapping ParallEL Lines with Enhanced Reconstruction) MRI. MATERIALS AND METHODS: Numerical simulations, as well as experiments on a phantom and a healthy human subject were used to evaluate the performance of the iterative image reconstruction algorithm for PROPELLER, and compare it with that of conventional gridding. The trade-off between spatial resolution, signal to noise ratio, and image artifacts, was investigated for different values of the regularization parameter. The performance of the iterative image reconstruction algorithm in the presence of motion was also evaluated. RESULTS: It was demonstrated that, for a certain range of values of the regularization parameter, iterative reconstruction produced images with significantly increased signal to noise ratio, reduced artifacts, for similar spatial resolution, compared with gridding. Furthermore, the ability to reduce the effects of motion in PROPELLER-MRI was maintained when using the iterative reconstruction approach. CONCLUSION: An iterative image reconstruction technique based on the NUFFT was investigated for PROPELLER MRI. For a certain range of values of the regularization parameter, the new reconstruction technique may provide PROPELLER images with improved image quality compared with conventional gridding.\",\n \"corpus_id\": 22676783,\n \"score\": 1\n },\n {\n \"doc_id\": \"21144688\",\n \"title\": \"Non-Iterative Regularized reconstruction Algorithm for Non-CartesiAn MRI: NIRVANA.\",\n \"abstract\": \"We introduce a novel noniterative algorithm for the fast and accurate reconstruction of nonuniformly sampled MRI data. The proposed scheme derives the reconstructed image as the nonuniform inverse Fourier transform of a compensated dataset. We derive each sample in the compensated dataset as a weighted linear combination of a few measured k-space samples. The specific k-space samples and the weights involved in the linear combination are derived such that the reconstruction error is minimized. The computational complexity of the proposed scheme is comparable to that of gridding. At the same time, it provides significantly improved accuracy and is considerably more robust to noise and undersampling. The advantages of the proposed scheme makes it ideally suited for the fast reconstruction of large multidimensional datasets, which routinely arise in applications such as f-MRI and MR spectroscopy. The comparisons with state-of-the-art algorithms on numerical phantoms and MRI data clearly demonstrate the performance improvement.\",\n \"corpus_id\": 18085059,\n \"score\": 1\n },\n {\n \"doc_id\": \"21740865\",\n \"title\": \"A fast algorithm for computing and correcting the CTF for tilted, thick specimens in TEM.\",\n \"abstract\": \"Today, the resolution in phase-contrast cryo-electron tomography is for a significant part limited by the contrast transfer function (CTF) of the microscope. The CTF is a function of defocus and thus varies spatially as a result of the tilting of the specimen and the finite specimen thickness. Models that include spatial dependencies have not been adopted in daily practice because of their high computational complexity. Here we present an algorithm which reduces the processing time for computing the 'tilted' CTF by more than a factor 100. Our implementation of the full 3D CTF has a processing time on the order of a Radon transform of a full tilt-series. We derive and validate an expression for the damping envelope function describing the loss of resolution due to specimen thickness. Using simulations we quantify the effects of specimen thickness on the accuracy of various forward models. We study the influence of spatially varying CTF correction and subsequent tomographic reconstruction by simulation and present a new approach for space-variant phase-flipping. We show that our CTF correction strategies are successful in increasing the resolution after tomographic reconstruction.\",\n \"corpus_id\": 7298961,\n \"score\": 1\n },\n {\n \"doc_id\": \"21859004\",\n \"title\": \"A fast forward projection using multithreads for multirays on GPUs in medical image reconstruction.\",\n \"abstract\": \"PURPOSE: Iterative reconstruction techniques hold great potential to mitigate the effects of data noise and/or incompleteness, and hence can facilitate the patient dose reduction. However, they are not suitable for routine clinical practice due to their long reconstruction times. In this work, the authors accelerated the computations by fully taking advantage of the highly parallel computational power on single and multiple graphics processing units (GPUs). In particular, the forward projection algorithm, which is not included in the close-form formulas, will be accelerated and optimized by using GPU here. METHODS: The main contribution is a novel forward projection algorithm that uses multithreads to handle the computations associated with a bunch of adjacent rays simultaneously. The proposed algorithm is free of divergence and bank conflict on GPU, and benefits from data locality and data reuse. It achieves the efficiency particularly by (i) employing a tiled algorithm with three-level parallelization, (ii) optimizing thread block size, (iii) maximizing data reuse on constant memory and shared memory, and (iv) exploiting built-in texture memory interpolation capability to increase efficiency. In addition, to accelerate the iterative algorithms and the Feldkamp-Davis-Kress (FDK) algorithm on GPU, the authors apply batched fast Fourier transform (FFT) to expedite filtering process in FDK and utilize projection bundling parallelism during backprojection to shorten the execution times in FDK and the expectation-maximization (EM). RESULTS: Numerical experiments conducted on an NVIDIA Tesla C1060 GPU demonstrated the superiority of the proposed algorithms in computational time saving. The forward projection, filtering, and backprojection times for generating a volume image of 512 x 512 x 512 with 360 projection data of 512 x 512 using one GPU are about 4.13, 0.65, and 2.47 s (including distance weighting), respectively. In particular, the proposed forward projection algorithm is ray-driven and its paralleli-zation strategy evolves from single-thread-for-single-ray (38.56 s), multithreads-for-single-ray (26.05 s), to multithreads-for-multirays (4.13 s). For the voxel-driven backprojection, the use of texture memory reduces the reconstruction time from 4.95 to 3.35 s. By applying the projection bundle technique, the computation time is further reduced to 2.47 s. When employing multiple GPUs, near-perfect speedups were observed as the number of GPUs increases. For example, by using four GPUs, the time for the forward projection, filtering, and backprojection are further reduced to 1.11, 0.18, and 0.66 s. The results obtained by GPU-based algorithms are virtually indistinguishable with those by CPU. CONCLUSIONS: The authors have proposed a highly optimized GPU-based forward projection algorithm, as well as the GPU-based FDK and expectation-maximization reconstruction algorithms. Our compute unified device architecture (CUDA) codes provide the exceedingly fast forward projection and backprojection that outperform those using the shading languages, cell broadband engine architecture and previous CUDA implementations. The reconstruction times in the FDK and the EM algorithms were considerably shortened, and thus can facilitate their routine usage in a variety of applications such as image quality improvement and dose reduction.\",\n \"corpus_id\": 7931248,\n \"score\": 1\n },\n {\n \"doc_id\": \"21860371\",\n \"title\": \"Structure of HIV-1 capsid assemblies by cryo-electron microscopy and iterative helical real-space reconstruction.\",\n \"abstract\": \"Cryo-electron microscopy (cryo-EM), combined with image processing, is an increasingly powerful tool for structure determination of macromolecular protein complexes and assemblies. In fact, single particle electron microscopy and two-dimensional (2D) electron crystallography have become relatively routine methodologies and a large number of structures have been solved using these methods. At the same time, image processing and three-dimensional (3D) reconstruction of helical objects has rapidly developed, especially, the iterative helical real-space reconstruction (IHRSR) method, which uses single particle analysis tools in conjunction with helical symmetry. Many biological entities function in filamentous or helical forms, including actin filaments, microtubules, amyloid fibers, tobacco mosaic viruses, and bacteria flagella, and, because a 3D density map of a helical entity can be attained from a single projection image, compared to the many images required for 3D reconstruction of a non-helical object, with the IHRSR method, structural analysis of such flexible and disordered helical assemblies is now attainable. In this video article, we provide detailed protocols for obtaining a 3D density map of a helical protein assembly (HIV-1 capsid is our example), including protocols for cryo-EM specimen preparation, low dose data collection by cryo-EM, indexing of helical diffraction patterns, and image processing and 3D reconstruction using IHRSR. Compared to other techniques, cryo-EM offers optimal specimen preservation under near native conditions. Samples are embedded in a thin layer of vitreous ice, by rapid freezing, and imaged in electron microscopes at liquid nitrogen temperature, under low dose conditions to minimize the radiation damage. Sample images are obtained under near native conditions at the expense of low signal and low contrast in the recorded micrographs. Fortunately, the process of helical reconstruction has largely been automated, with the exception of indexing the helical diffraction pattern. Here, we describe an approach to index helical structure and determine helical symmetries (helical parameters) from digitized micrographs, an essential step for 3D helical reconstruction. Briefly, we obtain an initial 3D density map by applying the IHRSR method. This initial map is then iteratively refined by introducing constraints for the alignment parameters of each segment, thus controlling their degrees of freedom. Further improvement is achieved by correcting for the contrast transfer function (CTF) of the electron microscope (amplitude and phase correction) and by optimizing the helical symmetry of the assembly.\",\n \"corpus_id\": 8398013,\n \"score\": 1\n },\n {\n \"doc_id\": \"22274272\",\n \"title\": \"Selection of convolution kernel in non-uniform fast Fourier transform for Fourier domain optical coherence tomography.\",\n \"abstract\": \"Gridding based non-uniform fast Fourier transform (NUFFT) has recently been shown as an efficient method of processing non-linearly sampled data from Fourier-domain optical coherence tomography (FD-OCT). This method requires selecting design parameters, such as kernel function type, oversampling ratio and kernel width, to balance between computational complexity and accuracy. The Kaiser-Bessel (KB) and Gaussian kernels have been used independently on the NUFFT algorithm for FD-OCT. This paper compares the reconstruction error and speed for the optimization of these design parameters and justifies particular kernel choice for FD-OCT applications. It is found that for on-the-fly computation of the kernel function, the simpler Gaussian function offers a better accuracy-speed tradeoff. The KB kernel, however, is a better choice in the pre-computed kernel mode of NUFFT, in which the processing speed is no longer dependent on the kernel function type. Finally, the algorithm is used to reconstruct in-vivo images of a human finger at a camera limited 50k A-line/s.\",\n \"corpus_id\": 207320571,\n \"score\": 1\n },\n {\n \"doc_id\": \"22759428\",\n \"title\": \"High-performance blob-based iterative three-dimensional reconstruction in electron tomography using multi-GPUs.\",\n \"abstract\": \"BACKGROUND: Three-dimensional (3D) reconstruction in electron tomography (ET) has emerged as a leading technique to elucidate the molecular structures of complex biological specimens. Blob-based iterative methods are advantageous reconstruction methods for 3D reconstruction in ET, but demand huge computational costs. Multiple graphic processing units (multi-GPUs) offer an affordable platform to meet these demands. However, a synchronous communication scheme between multi-GPUs leads to idle GPU time, and a weighted matrix involved in iterative methods cannot be loaded into GPUs especially for large images due to the limited available memory of GPUs. RESULTS: In this paper we propose a multilevel parallel strategy combined with an asynchronous communication scheme and a blob-ELLR data structure to efficiently perform blob-based iterative reconstructions on multi-GPUs. The asynchronous communication scheme is used to minimize the idle GPU time so as to asynchronously overlap communications with computations. The blob-ELLR data structure only needs nearly 1/16 of the storage space in comparison with ELLPACK-R (ELLR) data structure and yields significant acceleration. CONCLUSIONS: Experimental results indicate that the multilevel parallel scheme combined with the asynchronous communication scheme and the blob-ELLR data structure allows efficient implementations of 3D reconstruction in ET on multi-GPUs.\",\n \"corpus_id\": 1777063,\n \"score\": 1\n },\n {\n \"doc_id\": \"22898698\",\n \"title\": \"A CUDA-based reverse gridding algorithm for MR reconstruction.\",\n \"abstract\": \"MR raw data collected using non-Cartesian method can be transformed on Cartesian grids by traditional gridding algorithm (GA) and reconstructed by Fourier transform. However, its runtime complexity is O(K×N(2)), where resolution of raw data is N×N and size of convolution window (CW) is K. And it involves a large number of matrix calculation including modulus, addition, multiplication and convolution. Therefore, a Compute Unified Device Architecture (CUDA)-based algorithm is proposed to improve the reconstruction efficiency of PROPELLER (a globally recognized non-Cartesian sampling method). Experiment shows a write-write conflict among multiple CUDA threads. This induces an inconsistent result when synchronously convoluting multiple k-space data onto the same grid. To overcome this problem, a reverse gridding algorithm (RGA) was developed. Different from the method of generating a grid window for each trajectory as in traditional GA, RGA calculates a trajectory window for each grid. This is what \\\"reverse\\\" means. For each k-space point in the CW, contribution is cumulated to this grid. Although this algorithm can be easily extended to reconstruct other non-Cartesian sampled raw data, we only implement it based on PROPELLER. Experiment illustrates that this CUDA-based RGA has successfully solved the write-write conflict and its reconstruction speed is 7.5 times higher than that of traditional GA.\",\n \"corpus_id\": 22143791,\n \"score\": 1\n },\n {\n \"doc_id\": \"23464329\",\n \"title\": \"Radiation dose reduction in medical x-ray CT via Fourier-based iterative reconstruction.\",\n \"abstract\": \"PURPOSE: A Fourier-based iterative reconstruction technique, termed Equally Sloped Tomography (EST), is developed in conjunction with advanced mathematical regularization to investigate radiation dose reduction in x-ray CT. The method is experimentally implemented on fan-beam CT and evaluated as a function of imaging dose on a series of image quality phantoms and anonymous pediatric patient data sets. Numerical simulation experiments are also performed to explore the extension of EST to helical cone-beam geometry. METHODS: EST is a Fourier based iterative algorithm, which iterates back and forth between real and Fourier space utilizing the algebraically exact pseudopolar fast Fourier transform (PPFFT). In each iteration, physical constraints and mathematical regularization are applied in real space, while the measured data are enforced in Fourier space. The algorithm is automatically terminated when a proposed termination criterion is met. Experimentally, fan-beam projections were acquired by the Siemens z-flying focal spot technology, and subsequently interleaved and rebinned to a pseudopolar grid. Image quality phantoms were scanned at systematically varied mAs settings, reconstructed by EST and conventional reconstruction methods such as filtered back projection (FBP), and quantified using metrics including resolution, signal-to-noise ratios (SNRs), and contrast-to-noise ratios (CNRs). Pediatric data sets were reconstructed at their original acquisition settings and additionally simulated to lower dose settings for comparison and evaluation of the potential for radiation dose reduction. Numerical experiments were conducted to quantify EST and other iterative methods in terms of image quality and computation time. The extension of EST to helical cone-beam CT was implemented by using the advanced single-slice rebinning (ASSR) method. RESULTS: Based on the phantom and pediatric patient fan-beam CT data, it is demonstrated that EST reconstructions with the lowest scanner flux setting of 39 mAs produce comparable image quality, resolution, and contrast relative to FBP with the 140 mAs flux setting. Compared to the algebraic reconstruction technique and the expectation maximization statistical reconstruction algorithm, a significant reduction in computation time is achieved with EST. Finally, numerical experiments on helical cone-beam CT data suggest that the combination of EST and ASSR produces reconstructions with higher image quality and lower noise than the Feldkamp Davis and Kress (FDK) method and the conventional ASSR approach. CONCLUSIONS: A Fourier-based iterative method has been applied to the reconstruction of fan-bean CT data with reduced x-ray fluence. This method incorporates advantageous features in both real and Fourier space iterative schemes: using a fast and algebraically exact method to calculate forward projection, enforcing the measured data in Fourier space, and applying physical constraints and flexible regularization in real space. Our results suggest that EST can be utilized for radiation dose reduction in x-ray CT via the readily implementable technique of lowering mAs settings. Numerical experiments further indicate that EST requires less computation time than several other iterative algorithms and can, in principle, be extended to helical cone-beam geometry in combination with the ASSR method.\",\n \"corpus_id\": 13455029,\n \"score\": 1\n },\n {\n \"doc_id\": \"25080112\",\n \"title\": \"Fan beam image reconstruction with generalized Fourier slice theorem.\",\n \"abstract\": \"For parallel beam geometry the Fourier reconstruction works via the Fourier slice theorem (or central slice theorem, projection slice theorem). For fan beam situation, Fourier slice can be extended to a generalized Fourier slice theorem (GFST) for fan-beam image reconstruction. We have briefly introduced this method in a conference. This paper reintroduces the GFST method for fan beam geometry in details. The GFST method can be described as following: the Fourier plane is filled by adding up the contributions from all fanbeam projections individually; thereby the values in the Fourier plane are directly calculated for Cartesian coordinates such avoiding the interpolation from polar to Cartesian coordinates in the Fourier domain; inverse fast Fourier transform is applied to the image in Fourier plane and leads to a reconstructed image in spacial domain. The reconstructed image is compared between the result of the GFST method and the result from the filtered backprojection (FBP) method. The major differences of the GFST and the FBP methods are: (1) The interpolation process are at different data sets. The interpolation of the GFST method is at projection data. The interpolation of the FBP method is at filtered projection data. ( 2) The filtering process are done in different places. The filtering process of the GFST is at Fourier domain. The filtering process of the FBP method is the ramp filter which is done at projections. The resolution of ramp filter is variable with different location but the filter in the Fourier domain lead to resolution invariable with location. One advantage of the GFST method over the FBP method is in short scan situation, an exact solution can be obtained with the GFST method, but it can not be obtained with the FBP method. The calculation of both the GFST and the FBP methods are at O(N<formula>^3</formula>), where N is the number of pixel in one dimension.\",\n \"corpus_id\": 23386700,\n \"score\": 1\n },\n {\n \"doc_id\": \"25176282\",\n \"title\": \"Fast reconstruction of 3D volumes from 2D CT projection data with GPUs.\",\n \"abstract\": \"BACKGROUND: Biomedical image reconstruction applications require producing high fidelity images in or close to real-time. We have implemented reconstruction of three dimensional conebeam computed tomography(CBCT) with two dimensional projections. The algorithm takes slices of the target, weights and filters them to backproject the data, then creates the final 3D volume. We have implemented the algorithm using several hardware and software approaches and taken advantage of different types of parallelism in modern processors. The two hardware platforms used are a Central Processing Unit (CPU) and a heterogeneous system with a combination of CPU and GPU. On the CPU we implement serial MATLAB, parallel MATLAB, C and parallel C with OpenMP extensions. These codes are compared against the heterogeneous versions written in CUDA-C and OpenCL. FINDINGS: Our results show that GPUs are particularly well suited to accelerating CBCT. Relative performance was evaluated on a mathematical phantom as well as on mouse data. Speedups of up to 200x are observed by using an AMD GPU compared to a parallel version in C with OpenMP constructs. CONCLUSIONS: In this paper, we have implemented the Feldkamp-Davis-Kress algorithm, compatible with Fessler's image reconstruction toolbox and tested it on different hardware platforms including CPU and a combination of CPU and GPU. Both NVIDIA and AMD GPUs have been used for performance evaluation. GPUs provide significant speedup over the parallel CPU version.\",\n \"corpus_id\": 10756187,\n \"score\": 1\n },\n {\n \"doc_id\": \"25436931\",\n \"title\": \"Atomic resolution tomography reconstruction of tilt series based on a GPU accelerated hybrid input-output algorithm using polar Fourier transform.\",\n \"abstract\": \"Advances in diffraction and transmission electron microscopy (TEM) have greatly improved the prospect of three-dimensional (3D) structure reconstruction from two-dimensional (2D) images or diffraction patterns recorded in a tilt series at atomic resolution. Here, we report a new graphics processing unit (GPU) accelerated iterative transformation algorithm (ITA) based on polar fast Fourier transform for reconstructing 3D structure from 2D diffraction patterns. The algorithm also applies to image tilt series by calculating diffraction patterns from the recorded images using the projection-slice theorem. A gold icosahedral nanoparticle of 309 atoms is used as the model to test the feasibility, performance and robustness of the developed algorithm using simulations. Atomic resolution in 3D is achieved for the 309 atoms Au nanoparticle using 75 diffraction patterns covering 150° rotation. The capability demonstrated here provides an opportunity to uncover the 3D structure of small objects of nanometers in size by electron diffraction.\",\n \"corpus_id\": 10994340,\n \"score\": 1\n },\n {\n \"doc_id\": \"25807565\",\n \"title\": \"Fast Volume Reconstruction From Motion Corrupted Stacks of 2D Slices.\",\n \"abstract\": \"Capturing an enclosing volume of moving subjects and organs using fast individual image slice acquisition has shown promise in dealing with motion artefacts. Motion between slice acquisitions results in spatial inconsistencies that can be resolved by slice-to-volume reconstruction (SVR) methods to provide high quality 3D image data. Existing algorithms are, however, typically very slow, specialised to specific applications and rely on approximations, which impedes their potential clinical use. In this paper, we present a fast multi-GPU accelerated framework for slice-to-volume reconstruction. It is based on optimised 2D/3D registration, super-resolution with automatic outlier rejection and an additional (optional) intensity bias correction. We introduce a novel and fully automatic procedure for selecting the image stack with least motion to serve as an initial registration target. We evaluate the proposed method using artificial motion corrupted phantom data as well as clinical data, including tracked freehand ultrasound of the liver and fetal Magnetic Resonance Imaging. We achieve speed-up factors greater than 30 compared to a single CPU system and greater than 10 compared to currently available state-of-the-art multi-core CPU methods. We ensure high reconstruction accuracy by exact computation of the point-spread function for every input data point, which has not previously been possible due to computational limitations. Our framework and its implementation is scalable for available computational infrastructures and tests show a speed-up factor of 1.70 for each additional GPU. This paves the way for the online application of image based reconstruction methods during clinical examinations. The source code for the proposed approach is publicly available.\",\n \"corpus_id\": 424951,\n \"score\": 1\n },\n {\n \"doc_id\": \"27046874\",\n \"title\": \"Direct Fourier Inversion Reconstruction Algorithm for Computed Laminography.\",\n \"abstract\": \"Synchrotron radiation computed laminography (CL) was developed to complement the conventional computed tomography as a non-destructive 3D imaging method for the inspection of flat thin objects. Recent progress in hardware at synchrotron sources allows one to record internal evolution of specimens at the micrometer scale and sub-second range but also requires increased reconstruction speed to follow structural changes online. A 3D image of the sample interior is usually reconstructed by the well-established filtered backprojection (FBP) approach. Despite of a great success in the reduction of reconstruction time via parallel computations, the FBP algorithm still remains a time-consuming procedure. A promising way to significantly shorten computation time is to directly perform backprojection in frequency domain (a direct Fourier inversion approach). The corresponding algorithms are rarely considered in the literature because of a poor performance or inferior reconstruction quality resulted from inaccurate interpolation in Fourier domain. In this paper, we derive a Fourier-based reconstruction equation designed for the CL scanning geometry. Furthermore, we outline the translation of the continuous solution to a discrete version, which utilizes 3D sinc interpolation. A projection resampling technique allowing for the reduction of the expensive interpolation to its 1D version is proposed. A series of numerical experiments confirms that the resulting image quality is well comparable with the FBP approach while reconstruction time is drastically reduced.\",\n \"corpus_id\": 16942536,\n \"score\": 1\n },\n {\n \"doc_id\": \"28086901\",\n \"title\": \"GPU accelerated voxel-driven forward projection for iterative reconstruction of cone-beam CT.\",\n \"abstract\": \"BACKGROUND: For cone-beam computed tomography (CBCT), which has been playing an important role in clinical applications, iterative reconstruction algorithms are able to provide advantageous image qualities over the classical FDK. However, the computational speed of iterative reconstruction is a notable issue for CBCT, of which the forward projection calculation is one of the most time-consuming components. METHOD AND RESULTS: In this study, the cone-beam forward projection problem using the voxel-driven model is analysed, and a GPU-based acceleration method for CBCT forward projection is proposed with the method rationale and implementation workflow detailed as well. For method validation and evaluation, computational simulations are performed, and the calculation times of different methods are collected. Compared with the benchmark CPU processing time, the proposed method performs effectively in handling the inter-thread interference problem, and an acceleration ratio as high as more than 100 is achieved compared to a single-threaded CPU implementation. CONCLUSION: The voxel-driven forward projection calculation for CBCT is highly paralleled by the proposed method, and we believe it will serve as a critical module to develop iterative reconstruction and correction methods for CBCT imaging.\",\n \"corpus_id\": 16168638,\n \"score\": 1\n },\n {\n \"doc_id\": \"28248347\",\n \"title\": \"Three-dimensional optoacoustic reconstruction using fast sparse representation.\",\n \"abstract\": \"Optoacoustic tomography based on insufficient spatial sampling of ultrasound waves leads to loss of contrast and artifacts on the reconstructed images. Compared to reconstructions based on L2-norm regularization, sparsity-based reconstructions may improve contrast and reduce image artifacts but at a high computational cost, which has so far limited their use to 2D optoacoustic tomography. Here we propose a fast, sparsity-based reconstruction algorithm for 3D optoacoustic tomography, based on gradient descent with Barzilai-Borwein line search (L1-GDBB). Using simulations and experiments, we show that the L1-GDBB offers fourfold faster reconstruction than the previously reported L1-norm regularized reconstruction based on gradient descent with backtracking line search. Moreover, the new algorithm provides higher-quality images with fewer artifacts than the L2-norm regularized reconstruction and the back-projection reconstruction.\",\n \"corpus_id\": 46740925,\n \"score\": 1\n },\n {\n \"doc_id\": \"28463289\",\n \"title\": \"Comparative study of fully three-dimensional reconstruction algorithms for lens-free microscopy.\",\n \"abstract\": \"We propose a three-dimensional (3D) imaging platform based on lens-free microscopy to perform multiangle acquisitions on 3D cell cultures embedded in extracellular matrices. Lens-free microscopy acquisitions present some inherent issues such as the lack of phase information on the sensor plane and a limited angular coverage. We developed and compared three different algorithms based on the Fourier diffraction theorem to obtain fully 3D reconstructions. These algorithms present an increasing complexity associated with a better reconstruction quality. Two of them are based on a regularized inverse problem approach. To compare the reconstruction methods in terms of artefact reduction, signal-to-noise ratio, and computation time, we tested them on two experimental datasets: an endothelial cell culture and a prostate cell culture grown in a 3D extracellular matrix with large reconstructed volumes up to ∼5 mm<sup>3</sup> with a resolution sufficient to resolve isolated single cells. The lens-free reconstructions compare well with standard microscopy.\",\n \"corpus_id\": 46771637,\n \"score\": 1\n },\n {\n \"doc_id\": \"28788711\",\n \"title\": \"Iterative wave-front reconstruction in the Fourier domain.\",\n \"abstract\": \"The use of Fourier methods in wave-front reconstruction can significantly reduce the computation time for large telescopes with a high number of degrees of freedom. However, Fourier algorithms for discrete data require a rectangular data set which conform to specific boundary requirements, whereas wave-front sensor data is typically defined over a circular domain (the telescope pupil). Here we present an iterative Gerchberg routine modified for the purposes of discrete wave-front reconstruction which adapts the measurement data (wave-front sensor slopes) for Fourier analysis, fulfilling the requirements of the fast Fourier transform (FFT) and providing accurate reconstruction. The routine is used in the adaptation step only and can be coupled to any other Wiener-like or least-squares method. We compare simulations using this method with previous Fourier methods and show an increase in performance in terms of Strehl ratio and a reduction in noise propagation for a 40×40 SPHERE-like adaptive optics system. For closed loop operation with minimal iterations the Gerchberg method provides an improvement in Strehl, from 95.4% to 96.9% in K-band. This corresponds to ~ 40 nm improvement in rms, and avoids the high spatial frequency errors present in other methods, providing an increase in contrast towards the edge of the correctable band.\",\n \"corpus_id\": 46802255,\n \"score\": 1\n },\n {\n \"doc_id\": \"18756356\",\n \"title\": \"Three-dimensional SPECT reconstruction with transmission-dependent scatter correction.\",\n \"abstract\": \"OBJECTIVE: The quality of single-photon emission computed tomography (SPECT) imaging is hampered by attenuation, collimator blurring, and scatter. Correction for all of these three factors is required for accurate reconstruction, but unfortunately, reconstruction-based compensation often leads to clinically unacceptable long reconstruction times. Especially, efficient scatter correction has proved to be difficult to achieve. The objective of this article was to extend the well-known transmission-dependent convolution subtraction (TDCS) scatter-correction approach into a rapid reconstruction-based scatter-compensation method and to include it into a fast 3D reconstruction algorithm with attenuation and collimator-blurring corrections. METHODS: Ordered subsets expectation maximization algorithm with attenuation, collimator blurring, and accelerated transmission-dependent scatter compensation were implemented. The new reconstruction method was compared with TDCS-based scatter correction and with one other transmission-dependent scatter-correction method using Monte Carlo simulated projection data of (99m)Tc-ECD and (123)I-FP-CIT brain studies. RESULTS: The new reconstruction-based scatter compensation outperformed the other two scatter-correction methods in terms of quantitative accuracy and contrast measured with normalized mean-squared error, gray-to-white matter and striatum-to-background ratios, and also in visual quality. Highest accuracy was achieved when all the corrections (i.e., attenuation, collimator blurring, and scatter) were applied. CONCLUSIONS: The developed 3D reconstruction algorithm with transmission-dependent scatter compensation is a promising alternative to accurate and efficient SPECT reconstruction.\",\n \"corpus_id\": 31484937,\n \"score\": 0\n },\n {\n \"doc_id\": \"19081053\",\n \"title\": \"Heterogeneity of large macromolecular complexes revealed by 3D cryo-EM variance analysis.\",\n \"abstract\": \"Macromolecular structure determination by cryo-electron microscopy (EM) and single-particle analysis are based on the assumption that imaged molecules have identical structure. With the increased size of processed data sets, it becomes apparent that many complexes coexist in a mixture of conformational states or contain flexible regions. We describe an implementation of the bootstrap resampling technique that yields estimates of voxel-by-voxel variance of a structure reconstructed from the set of its projections. We introduce a highly efficient reconstruction algorithm that is based on direct Fourier inversion and that incorporates correction for the transfer function of the microscope, thus extending the resolution limits of variance estimation. We also describe a validation method to determine the number of resampled volumes required to achieve stable estimate of the variance. The proposed bootstrap method was applied to a data set of 70S ribosome complexed with tRNA and the elongation factor G. The proposed method of variance estimation opens new possibilities for single-particle analysis, by extending applicability of the technique to heterogeneous data sets of macromolecules and to complexes with significant conformational variability.\",\n \"corpus_id\": 205258900,\n \"score\": 0\n },\n {\n \"doc_id\": \"19321015\",\n \"title\": \"Error analysis in the determination of the electron microscopical contrast transfer function parameters from experimental power Spectra.\",\n \"abstract\": \"BACKGROUND: The transmission electron microscope is used to acquire structural information of macromolecular complexes. However, as any other imaging device, it introduces optical aberrations that must be corrected if high-resolution structural information is to be obtained. The set of all aberrations are usually modeled in Fourier space by the so-called Contrast Transfer Function (CTF). Before correcting for the CTF, we must first estimate it from the electron micrographs. This is usually done by estimating a number of parameters specifying a theoretical model of the CTF. This estimation is performed by minimizing some error measure between the theoretical Power Spectrum Density (PSD) and the experimentally observed PSD. The high noise present in the micrographs, the possible local minima of the error function for estimating the CTF parameters, and the cross-talking between CTF parameters may cause errors in the estimated CTF parameters. RESULTS: In this paper, we explore the effect of these estimation errors on the theoretical CTF. For the CTF model proposed in 1 we show which are the most sensitive CTF parameters as well as the most sensitive background parameters. Moreover, we provide a methodology to reveal the internal structure of the CTF model (which parameters influence in which parameters) and to estimate the accuracy of each model parameter. Finally, we explore the effect of the variability in the detection of the CTF for CTF phase and amplitude correction. CONCLUSION: We show that the estimation errors for the CTF detection methodology proposed in 1 does not show a significant deterioration of the CTF correction capabilities of subsequent algorithms. All together, the methodology described in this paper constitutes a powerful tool for the quantitative analysis of CTF models that can be applied to other models different from the one analyzed here.\",\n \"corpus_id\": 2395327,\n \"score\": 0\n },\n {\n \"doc_id\": \"19651555\",\n \"title\": \"Fast parallel approach for 2-D DHT-based real-valued discrete Gabor transform.\",\n \"abstract\": \"Two-dimensional fast Gabor transform algorithms are useful for real-time applications due to the high computational complexity of the traditional 2-D complex-valued discrete Gabor transform (CDGT). This paper presents two block time-recursive algorithms for 2-D DHT-based real-valued discrete Gabor transform (RDGT) and its inverse transform and develops a fast parallel approach for the implementation of the two algorithms. The computational complexity of the proposed parallel approach is analyzed and compared with that of the existing 2-D CDGT algorithms. The results indicate that the proposed parallel approach is attractive for real time image processing.\",\n \"corpus_id\": 18330870,\n \"score\": 0\n },\n {\n \"doc_id\": \"20163916\",\n \"title\": \"A novel approximation method of CTF amplitude correction for 3D single particle reconstruction.\",\n \"abstract\": \"The typical resolution of three-dimensional reconstruction by cryo-EM single particle analysis is now being pushed up to and beyond the nanometer scale. Correction of the contrast transfer function (CTF) of electron microscopic images is essential for achieving such a high resolution. Various correction methods exist and are employed in popular reconstruction software packages. Here, we present a novel approximation method that corrects the amplitude modulation introduced by the contrast transfer function by convoluting the images with a piecewise continuous function. Our new approach can easily be implemented and incorporated into other packages. The implemented method yielded higher resolution reconstructions with data sets from both highly symmetric and asymmetric structures. It is an efficient alternative correction method that allows quick convergence of the 3D reconstruction and has a high tolerance for noisy images, thus easing a bottleneck in practical reconstruction of macromolecules.\",\n \"corpus_id\": 24159841,\n \"score\": 0\n },\n {\n \"doc_id\": \"20647619\",\n \"title\": \"Electrical impedance tomography reconstruction for three-dimensional imaging of the prostate.\",\n \"abstract\": \"Transrectal electrical impedance tomography (TREIT) has been proposed as an adjunct modality for enhancing standard clinical ultrasound (US) imaging of the prostate. The proposed TREIT probe has an array of electrodes adhered to the surface of a cylindrical US probe that is introduced inside of the imaging volume. Reconstructing TREIT images in the open-domain geometry established with this technique poses additional challenges to those encountered with closed-domain geometries, present in more conventional EIT systems, because of the rapidly decaying current densities at increasing distances from the probe surface. We developed a finite element method (FEM)-based dual-mesh reconstruction algorithm which employs an interpolation scheme for linking a fine forward mesh with a coarse grid of pixels, used for conductivity estimation. Simulation studies using the developed algorithm demonstrate the feasibility of imaging moderately contrasting inclusions at distances of three times the probe radius from the probe surface and at multiple angles about the probe's axis. The large, dense FEM meshes used here require significant computational effort. We have optimized our reconstruction algorithm with multi-core processing hardware and efficient parallelized computational software packages to achieve a speedup of 9.3 times when compared to a more traditional Matlab-based, single CPU solution. The simulation findings and computational optimization provide a state-of-the-art reconstruction platform for use in further evaluating transrectal electrical impedance tomography.\",\n \"corpus_id\": 10451680,\n \"score\": 0\n },\n {\n \"doc_id\": \"20835366\",\n \"title\": \"The Fast Multipole Method and Fourier Convolution for the Solution of Acoustic Scattering on Regular Volumetric Grids.\",\n \"abstract\": \"The fast multipole method (FMM) is applied to the solution of large-scale, three-dimensional acoustic scattering problems involving inhomogeneous objects defined on a regular grid. The grid arrangement is especially well suited to applications in which the scattering geometry is not known a priori and is reconstructed on a regular grid using iterative inverse scattering algorithms or other imaging techniques. The regular structure of unknown scattering elements facilitates a dramatic reduction in the amount of storage and computation required for the FMM, both of which scale linearly with the number of scattering elements. In particular, the use of fast Fourier transforms to compute Green's function convolutions required for neighboring interactions lowers the often-significant cost of finest-level FMM computations and helps mitigate the dependence of FMM cost on finest-level box size. Numerical results demonstrate the efficiency of the composite method as the number of scattering elements in each finest-level box is increased.\",\n \"corpus_id\": 32823989,\n \"score\": 0\n },\n {\n \"doc_id\": \"21922018\",\n \"title\": \"Mapping iterative medical imaging algorithm on cell accelerator.\",\n \"abstract\": \"Algebraic reconstruction techniques require about half the number of projections as that of Fourier backprojection methods, which makes these methods safer in terms of required radiation dose. Algebraic reconstruction technique (ART) and its variant OS-SART (ordered subset simultaneous ART) are techniques that provide faster convergence with comparatively good image quality. However, the prohibitively long processing time of these techniques prevents their adoption in commercial CT machines. Parallel computing is one solution to this problem. With the advent of heterogeneous multicore architectures that exploit data parallel applications, medical imaging algorithms such as OS-SART can be studied to produce increased performance. In this paper, we map OS-SART on cell broadband engine (Cell BE). We effectively use the architectural features of Cell BE to provide an efficient mapping. The Cell BE consists of one powerPC processor element (PPE) and eight SIMD coprocessors known as synergetic processor elements (SPEs). The limited memory storage on each of the SPEs makes the mapping challenging. Therefore, we present optimization techniques to efficiently map the algorithm on the Cell BE for improved performance over CPU version. We compare the performance of our proposed algorithm on Cell BE to that of Sun Fire ×4600, a shared memory machine. The Cell BE is five times faster than AMD Opteron dual-core processor. The speedup of the algorithm on Cell BE increases with the increase in the number of SPEs. We also experiment with various parameters, such as number of subsets, number of processing elements, and number of DMA transfers between main memory and local memory, that impact the performance of the algorithm.\",\n \"corpus_id\": 10532111,\n \"score\": 0\n },\n {\n \"doc_id\": \"22149859\",\n \"title\": \"Fully 3D list-mode time-of-flight PET image reconstruction on GPUs using CUDA.\",\n \"abstract\": \"PURPOSE: List-mode processing is an efficient way of dealing with the sparse nature of positron emission tomography (PET) data sets and is the processing method of choice for time-of-flight (ToF) PET image reconstruction. However, the massive amount of computation involved in forward projection and backprojection limits the application of list-mode reconstruction in practice, and makes it challenging to incorporate accurate system modeling. METHODS: The authors present a novel formulation for computing line projection operations on graphics processing units (GPUs) using the compute unified device architecture (CUDA) framework, and apply the formulation to list-mode ordered-subsets expectation maximization (OSEM) image reconstruction. Our method overcomes well-known GPU challenges such as divergence of compute threads, limited bandwidth of global memory, and limited size of shared memory, while exploiting GPU capabilities such as fast access to shared memory and efficient linear interpolation of texture memory. Execution time comparison and image quality analysis of the GPU-CUDA method and the central processing unit (CPU) method are performed on several data sets acquired on a preclinical scanner and a clinical ToF scanner. RESULTS: When applied to line projection operations for non-ToF list-mode PET, this new GPU-CUDA method is >200 times faster than a single-threaded reference CPU implementation. For ToF reconstruction, we exploit a ToF-specific optimization to improve the efficiency of our parallel processing method, resulting in GPU reconstruction >300 times faster than the CPU counterpart. For a typical whole-body scan with 75 × 75 × 26 image matrix, 40.7 million LORs, 33 subsets, and 3 iterations, the overall processing time is 7.7 s for GPU and 42 min for a single-threaded CPU. Image quality and accuracy are preserved for multiple imaging configurations and reconstruction parameters, with normalized root mean squared (RMS) deviation less than 1% between CPU and GPU-generated images for all cases. CONCLUSIONS: A list-mode ToF OSEM library was developed on the GPU-CUDA platform. Our studies show that the GPU reformulation is considerably faster than a single-threaded reference CPU method especially for ToF processing, while producing virtually identical images. This new method can be easily adapted to enable more advanced algorithms for high resolution PET reconstruction based on additional information such as depth of interaction (DoI), photon energy, and point spread functions (PSFs).\",\n \"corpus_id\": 1870700,\n \"score\": 0\n },\n {\n \"doc_id\": \"22331404\",\n \"title\": \"Application of iterative soft thresholding for fast reconstruction of NMR data non-uniformly sampled with multidimensional Poisson Gap scheduling.\",\n \"abstract\": \"The fast Fourier transformation has been the gold standard for transforming data from time to frequency domain in many spectroscopic methods, including NMR. While reliable, it has as a drawback that it requires a grid of uniformly sampled data points. This needs very long measuring times for sampling in multidimensional experiments in all indirect dimensions uniformly and even does not allow reaching optimal evolution times that would match the resolution power of modern high-field instruments. Thus, many alternative sampling and transformation schemes have been proposed. Their common challenges are the suppression of the artifacts due to the non-uniformity of the sampling schedules, the preservation of the relative signal amplitudes, and the computing time needed for spectra reconstruction. Here we present a fast implementation of the Iterative Soft Thresholding approach (istHMS) that can reconstruct high-resolution non-uniformly sampled NMR data up to four dimensions within a few hours and make routine reconstruction of high-resolution NUS 3D and 4D spectra convenient. We include a graphical user interface for generating sampling schedules with the Poisson-Gap method and an estimation of optimal evolution times based on molecular properties. The performance of the approach is demonstrated with the reconstruction of non-uniformly sampled medium and high-resolution 3D and 4D protein spectra acquired with sampling densities as low as 0.8%. The method presented here facilitates acquisition, reconstruction and use of multidimensional NMR spectra at otherwise unreachable spectral resolution in indirect dimensions.\",\n \"corpus_id\": 20831382,\n \"score\": 0\n },\n {\n \"doc_id\": \"22752128\",\n \"title\": \"Recovering missing slices of the discrete Fourier transform using Ghosts.\",\n \"abstract\": \"The discrete Fourier transform (DFT) underpins the solution to many inverse problems commonly possessing missing or unmeasured frequency information. This incomplete coverage of the Fourier space always produces systematic artifacts called Ghosts. In this paper, a fast and exact method for deconvolving cyclic artifacts caused by missing slices of the DFT using redundant image regions is presented. The slices discussed here originate from the exact partitioning of the Discrete Fourier Transform (DFT) space, under the projective Discrete Radon Transform, called the discrete Fourier slice theorem. The method has a computational complexity of O(n log(2) n) (for an n=N×N image) and is constructed from a new cyclic theory of Ghosts. This theory is also shown to unify several aspects of work done on Ghosts over the past three decades. This paper concludes with an application to fast, exact, non-iterative image reconstruction from a highly asymmetric set of rational angle projections that give rise to sets of sparse slices within the DFT.\",\n \"corpus_id\": 2317098,\n \"score\": 0\n },\n {\n \"doc_id\": \"23165973\",\n \"title\": \"Fast direct fourier reconstruction of radial and PROPELLER MRI data using the chirp transform algorithm on graphics hardware.\",\n \"abstract\": \"PURPOSE: To develop and test a new algorithm for fast direct Fourier transform (DrFT) reconstruction of MR data on non-Cartesian trajectories composed of lines with equally spaced points. THEORY AND METHODS: The DrFT, which is normally used as a reference in evaluating the accuracy of other reconstruction methods, can reconstruct images directly from non-Cartesian MR data without interpolation. However, DrFT reconstruction involves substantially intensive computation, which makes the DrFT impractical for clinical routine applications. In this article, the Chirp transform algorithm was introduced to accelerate the DrFT reconstruction of radial and Periodically Rotated Overlapping ParallEL Lines with Enhanced Reconstruction (PROPELLER) MRI data located on the trajectories that are composed of lines with equally spaced points. The performance of the proposed Chirp transform algorithm-DrFT algorithm was evaluated by using simulation and in vivo MRI data. RESULTS: After implementing the algorithm on a graphics processing unit, the proposed Chirp transform algorithm-DrFT algorithm achieved an acceleration of approximately one order of magnitude, and the speed-up factor was further increased to approximately three orders of magnitude compared with the traditional single-thread DrFT reconstruction. CONCLUSION: Implementation the Chirp transform algorithm-DrFT algorithm on the graphics processing unit can efficiently calculate the DrFT reconstruction of the radial and PROPELLER MRI data.\",\n \"corpus_id\": 206282080,\n \"score\": 0\n },\n {\n \"doc_id\": \"23201934\",\n \"title\": \"Three-dimensional reconstruction of particle holograms: a fast and accurate multiscale approach.\",\n \"abstract\": \"In-line digital holography is an imaging technique that is being increasingly used for studying three-dimensional flows. It has been previously shown that very accurate reconstructions of objects could be achieved with the use of an inverse problem framework. Such approaches, however, suffer from higher computational times compared to less accurate conventional reconstructions based on hologram backpropagation. To overcome this computational issue, we propose a coarse-to-fine multiscale approach to strongly reduce the algorithm complexity. We illustrate that an accuracy comparable to that of state-of-the-art methods can be reached while accelerating parameter-space scanning.\",\n \"corpus_id\": 42428028,\n \"score\": 0\n },\n {\n \"doc_id\": \"23261401\",\n \"title\": \"FASTDEF: fast defocus and astigmatism estimation for high-throughput transmission electron microscopy.\",\n \"abstract\": \"In this work we present a fast and automated algorithm for estimating the contrast transfer function (CTF) of a transmission electron microscope. The approach is very suitable for High Throughput work because: (a) it does not require any initial defocus estimation, (b) it is almost an order of magnitude faster than existing approaches, (c) it opens the way to well-defined extensions to the estimation of higher order aberrations, at the same time that provides defocus and astigmatism estimations comparable in accuracy to well established methods, such as Xmipp and CTFFIND3 approaches. The new algorithm is based on obtaining the wrapped modulating phase of the power spectra density pattern by the use of a quadrature filter. This phase is further unwrapped in order to obtain the continuous and smooth absolute phase map; then a Zernike polynomial fitting is performed and the defocus and astigmatism parameters are determined. While the method does not require an initial estimation of the defocus parameters or any non-linear optimization procedure, these approaches can be used if further refinement is desired. Results of the CTF estimation method are presented for standard negative stained images, cryo-electron microscopy images in the absence of carbon support, as well as micrographs with only ice. Additionally, we have also tested the proposed method with micrographs acquired from tilted and untilted samples, obtaining good results. The algorithm is freely available as a part of the Xmipp package [http://xmipp.cnb.csic.es].\",\n \"corpus_id\": 9415778,\n \"score\": 0\n },\n {\n \"doc_id\": \"23387778\",\n \"title\": \"Accelerating image reconstruction in three-dimensional optoacoustic tomography on graphics processing units.\",\n \"abstract\": \"PURPOSE: Optoacoustic tomography (OAT) is inherently a three-dimensional (3D) inverse problem. However, most studies of OAT image reconstruction still employ two-dimensional imaging models. One important reason is because 3D image reconstruction is computationally burdensome. The aim of this work is to accelerate existing image reconstruction algorithms for 3D OAT by use of parallel programming techniques. METHODS: Parallelization strategies are proposed to accelerate a filtered backprojection (FBP) algorithm and two different pairs of projection/backprojection operations that correspond to two different numerical imaging models. The algorithms are designed to fully exploit the parallel computing power of graphics processing units (GPUs). In order to evaluate the parallelization strategies for the projection/backprojection pairs, an iterative image reconstruction algorithm is implemented. Computer simulation and experimental studies are conducted to investigate the computational efficiency and numerical accuracy of the developed algorithms. RESULTS: The GPU implementations improve the computational efficiency by factors of 1000, 125, and 250 for the FBP algorithm and the two pairs of projection/backprojection operators, respectively. Accurate images are reconstructed by use of the FBP and iterative image reconstruction algorithms from both computer-simulated and experimental data. CONCLUSIONS: Parallelization strategies for 3D OAT image reconstruction are proposed for the first time. These GPU-based implementations significantly reduce the computational time for 3D image reconstruction, complementing our earlier work on 3D OAT iterative image reconstruction.\",\n \"corpus_id\": 24053409,\n \"score\": 0\n },\n {\n \"doc_id\": \"23482123\",\n \"title\": \"Fast iterative reconstruction of differential phase contrast X-ray tomograms.\",\n \"abstract\": \"Differential phase-contrast is a recent technique in the context of X-ray imaging. In order to reduce the specimen's exposure time, we propose a new iterative algorithm that can achieve the same quality as FBP-type methods, while using substantially fewer angular views. Our approach is based on 1) a novel spline-based discretization of the forward model and 2) an iterative reconstruction algorithm using the alternating direction method of multipliers. Our experimental results on real data suggest that the method allows to reduce the number of required views by at least a factor of four.\",\n \"corpus_id\": 12511920,\n \"score\": 0\n },\n {\n \"doc_id\": \"23933392\",\n \"title\": \"Particle quality assessment and sorting for automatic and semiautomatic particle-picking techniques.\",\n \"abstract\": \"Three-dimensional reconstruction of biological specimens using electron microscopy by single particle methodologies requires the identification and extraction of the imaged particles from the acquired micrographs. Automatic and semiautomatic particle selection approaches can localize these particles, minimizing the user interaction, but at the cost of selecting a non-negligible number of incorrect particles, which can corrupt the final three-dimensional reconstruction. In this work, we present a novel particle quality assessment and sorting method that can separate most erroneously picked particles from correct ones. The proposed method is based on multivariate statistical analysis of a particle set that has been picked previously using any automatic or manual approach. The new method uses different sets of particle descriptors, which are morphology-based, histogram-based and signal to noise analysis based. We have tested our proposed algorithm with experimental data obtaining very satisfactory results. The algorithm is freely available as a part of the Xmipp 3.0 package [http://xmipp.cnb.csic.es].\",\n \"corpus_id\": 7094288,\n \"score\": 0\n },\n {\n \"doc_id\": \"23958728\",\n \"title\": \"A pattern matching approach to the automatic selection of particles from low-contrast electron micrographs.\",\n \"abstract\": \"MOTIVATION: Structural information of macromolecular complexes provides key insights into the way they carry out their biological functions. Achieving high-resolution structural details with electron microscopy requires the identification of a large number (up to hundreds of thousands) of single particles from electron micrographs, which is a laborious task if it has to be manually done and constitutes a hurdle towards high-throughput. Automatic particle selection in micrographs is far from being settled and new and more robust algorithms are required to reduce the number of false positives and false negatives. RESULTS: In this article, we introduce an automatic particle picker that learns from the user the kind of particles he is interested in. Particle candidates are quickly and robustly classified as particles or non-particles. A number of new discriminative shape-related features as well as some statistical description of the image grey intensities are used to train two support vector machine classifiers. Experimental results demonstrate that the proposed method: (i) has a considerably low computational complexity and (ii) provides results better or comparable with previously reported methods at a fraction of their computing time. AVAILABILITY: The algorithm is fully implemented in the open-source Xmipp package and downloadable from http://xmipp.cnb.csic.es.\",\n \"corpus_id\": 11199882,\n \"score\": 0\n },\n {\n \"doc_id\": \"24075951\",\n \"title\": \"Xmipp 3.0: an improved software suite for image processing in electron microscopy.\",\n \"abstract\": \"Xmipp is a specialized software package for image processing in electron microscopy, and that is mainly focused on 3D reconstruction of macromolecules through single-particles analysis. In this article we present Xmipp 3.0, a major release which introduces several improvements and new developments over the previous version. A central improvement is the concept of a project that stores the entire processing workflow from data import to final results. It is now possible to monitor, reproduce and restart all computing tasks as well as graphically explore the complete set of interrelated tasks associated to a given project. Other graphical tools have also been improved such as data visualization, particle picking and parameter \\\"wizards\\\" that allow the visual selection of some key parameters. Many standard image formats are transparently supported for input/output from all programs. Additionally, results have been standardized, facilitating the interoperation between different Xmipp programs. Finally, as a result of a large code refactoring, the underlying C++ libraries are better suited for future developments and all code has been optimized. Xmipp is an open-source package that is freely available for download from: http://xmipp.cnb.csic.es.\",\n \"corpus_id\": 14314008,\n \"score\": 0\n },\n {\n \"doc_id\": \"24228274\",\n \"title\": \"Efficient volume reconstruction for parallel-beam computed laminography by filtered backprojection on multi-core clusters.\",\n \"abstract\": \"Computed laminography (CL) was developed to use X-rays from synchrotron sources for high-resolution imaging of the internal structure of a flat specimen from a series of 2-D projection images. The projections are acquired by irradiation of the sample under different rotation angles where the object rotation axis is inclined with respect to the beam direction. This yields for laterally extended objects a more uniform average transmitted intensity during sample rotation compared with computed tomography (CT). The reconstruction problem of CL cannot be reduced to a data-efficient 2-D case (as for parallel-beam CT) since each single slice perpendicular to the rotation axis requires a 2-D region on the detector as input data for all projection directions. This paper describes a computationally efficient reconstruction procedure based on filtered backprojection (FBP) adapted to the CL acquisition geometry. From the Fourier slice theorem, we derive a framework for analytic image reconstruction and outline implementation details of the generic FBP algorithm. Different approaches reducing the reconstruction time by means of parallel and distributed computations are considered and evaluated.\",\n \"corpus_id\": 41159872,\n \"score\": 0\n },\n {\n \"doc_id\": \"24710398\",\n \"title\": \"Fast space-varying convolution using matrix source coding with applications to camera stray light reduction.\",\n \"abstract\": \"Many imaging applications require the implementation of space-varying convolution for accurate restoration and reconstruction of images. Here, we use the term space-varying convolution to refer to linear operators whose impulse response has slow spatial variation. In addition, these space-varying convolution operators are often dense, so direct implementation of the convolution operator is typically computationally impractical. One such example is the problem of stray light reduction in digital cameras, which requires the implementation of a dense space-varying deconvolution operator. However, other inverse problems, such as iterative tomographic reconstruction, can also depend on the implementation of dense space-varying convolution. While space-invariant convolution can be efficiently implemented with the fast Fourier transform, this approach does not work for space-varying operators. So direct convolution is often the only option for implementing space-varying convolution. In this paper, we develop a general approach to the efficient implementation of space-varying convolution, and demonstrate its use in the application of stray light reduction. Our approach, which we call matrix source coding, is based on lossy source coding of the dense space-varying convolution matrix. Importantly, by coding the transformation matrix, we not only reduce the memory required to store it; we also dramatically reduce the computation required to implement matrix-vector products. Our algorithm is able to reduce computation by approximately factoring the dense space-varying convolution operator into a product of sparse transforms. Experimental results show that our method can dramatically reduce the computation required for stray light reduction while maintaining high accuracy.\",\n \"corpus_id\": 14385528,\n \"score\": 0\n },\n {\n \"doc_id\": \"24974203\",\n \"title\": \"Efficient initial volume determination from electron microscopy images of single particles.\",\n \"abstract\": \"MOTIVATION: Structural information of macromolecular complexes provides key insights into the way they carry out their biological functions. The reconstruction process leading to the final 3D map requires an approximate initial model. Generation of an initial model is still an open and challenging problem in single-particle analysis. RESULTS: We present a fast and efficient approach to obtain a reliable, low-resolution estimation of the 3D structure of a macromolecule, without any a priori knowledge, addressing the well-known issue of initial volume estimation in the field of single-particle analysis. The input of the algorithm is a set of class average images obtained from individual projections of a biological object at random and unknown orientations by transmission electron microscopy micrographs. The proposed method is based on an initial non-lineal dimensionality reduction approach, which allows to automatically selecting representative small sets of class average images capturing the most of the structural information of the particle under study. These reduced sets are then used to generate volumes from random orientation assignments. The best volume is determined from these guesses using a random sample consensus (RANSAC) approach. We have tested our proposed algorithm, which we will term 3D-RANSAC, with simulated and experimental data, obtaining satisfactory results under the low signal-to-noise conditions typical of cryo-electron microscopy. AVAILABILITY: The algorithm is freely available as part of the Xmipp 3.1 package [http://xmipp.cnb.csic.es]. CONTACT: jvargas@cnb.csic.es SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.\",\n \"corpus_id\": 8183036,\n \"score\": 0\n },\n {\n \"doc_id\": \"25069768\",\n \"title\": \"Geometric correction method for 3D in-line X-ray phase contrast image reconstruction.\",\n \"abstract\": \"BACKGROUND: Mechanical system with imperfect or misalignment of X-ray phase contrast imaging (XPCI) components causes projection data misplaced, and thus result in the reconstructed slice images of computed tomography (CT) blurred or with edge artifacts. So the features of biological microstructures to be investigated are destroyed unexpectedly, and the spatial resolution of XPCI image is decreased. It makes data correction an essential pre-processing step for CT reconstruction of XPCI. METHODS: To remove unexpected blurs and edge artifacts, a mathematics model for in-line XPCI is built by considering primary geometric parameters which include a rotation angle and a shift variant in this paper. Optimal geometric parameters are achieved by finding the solution of a maximization problem. And an iterative approach is employed to solve the maximization problem by using a two-step scheme which includes performing a composite geometric transformation and then following a linear regression process. After applying the geometric transformation with optimal parameters to projection data, standard filtered back-projection algorithm is used to reconstruct CT slice images. RESULTS: Numerical experiments were carried out on both synthetic and real in-line XPCI datasets. Experimental results demonstrate that the proposed method improves CT image quality by removing both blurring and edge artifacts at the same time compared to existing correction methods. CONCLUSIONS: The method proposed in this paper provides an effective projection data correction scheme and significantly improves the image quality by removing both blurring and edge artifacts at the same time for in-line XPCI. It is easy to implement and can also be extended to other XPCI techniques.\",\n \"corpus_id\": 11752183,\n \"score\": 0\n },\n {\n \"doc_id\": \"25268657\",\n \"title\": \"Hybrid Electron Microscopy Normal Mode Analysis graphical interface and protocol.\",\n \"abstract\": \"This article presents an integral graphical interface to the Hybrid Electron Microscopy Normal Mode Analysis (HEMNMA) approach that was developed for capturing continuous motions of large macromolecular complexes from single-particle EM images. HEMNMA was shown to be a good approach to analyze multiple conformations of a macromolecular complex but it could not be widely used in the EM field due to a lack of an integral interface. In particular, its use required switching among different software sources as well as selecting modes for image analysis was difficult without the graphical interface. The graphical interface was thus developed to simplify the practical use of HEMNMA. It is implemented in the open-source software package Xmipp 3.1 (http://xmipp.cnb.csic.es) and only a small part of it relies on MATLAB that is accessible through the main interface. Such integration provides the user with an easy way to perform the analysis of macromolecular dynamics and forms a direct connection to the single-particle reconstruction process. A step-by-step HEMNMA protocol with the graphical interface is given in full details in Supplementary material. The graphical interface will be useful to experimentalists who are interested in studies of continuous conformational changes of macromolecular complexes beyond the modeling of continuous heterogeneity in single particle reconstruction.\",\n \"corpus_id\": 13918346,\n \"score\": 0\n },\n {\n \"doc_id\": \"25304701\",\n \"title\": \"Iterative reconstruction: how it works, how to apply it.\",\n \"abstract\": \"Computed tomography acquires X-ray projection data from multiple angles though an object to generate a tomographic rendition of its attenuation characteristics. Filtered back projection is a fast, closed analytical solution to the reconstruction process, whereby all projections are equally weighted, but is prone to deliver inadequate image quality when the dose levels are reduced. Iterative reconstruction is an algorithmic method that uses statistical and geometric models to variably weight the image data in a process that can be solved iteratively to independently reduce noise and preserve resolution and image quality. Applications of this technology in a clinical setting can result in lower dose on the order of 20-40% compared to a standard filtered back projection reconstruction for most exams. A carefully planned implementation strategy and methodological approach is necessary to achieve the goals of lower dose with uncompromised image quality.\",\n \"corpus_id\": 22095801,\n \"score\": 0\n },\n {\n \"doc_id\": \"25637660\",\n \"title\": \"A statistical approach to the initial volume problem in Single Particle Analysis by Electron Microscopy.\",\n \"abstract\": \"Cryo Electron Microscopy is a powerful Structural Biology technique, allowing the elucidation of the three-dimensional structure of biological macromolecules. In particular, the structural study of purified macromolecules -often referred as Single Particle Analysis(SPA)- is normally performed through an iterative process that needs a first estimation of the three-dimensional structure that is progressively refined using experimental data. It is well-known the local optimisation nature of this refinement, so that the initial choice of this first structure may substantially change the final result. Computational algorithms aiming to providing this first structure already exist. However, the question is far from settled and more robust algorithms are still needed so that the refinement process can be performed with sufficient guarantees. In this article we present a new algorithm that addresses the initial volume problem in SPA by setting it in a Weighted Least Squares framework and calculating the weights through a statistical approach based on the cumulative density function of different image similarity measures. We show that the new algorithm is significantly more robust than other state-of-the-art algorithms currently in use in the field. The algorithm is available as part of the software suite Xmipp (http://xmipp.cnb.csic.es) and Scipion (http://scipion.cnb.csic.es) under the name \\\"Significant\\\".\",\n \"corpus_id\": 15342000,\n \"score\": 0\n },\n {\n \"doc_id\": \"25866499\",\n \"title\": \"High Performance GPU-Based Fourier Volume Rendering.\",\n \"abstract\": \"Fourier volume rendering (FVR) is a significant visualization technique that has been used widely in digital radiography. As a result of its 𝒪(N (2)logN) time complexity, it provides a faster alternative to spatial domain volume rendering algorithms that are 𝒪(N (3)) computationally complex. Relying on the Fourier projection-slice theorem, this technique operates on the spectral representation of a 3D volume instead of processing its spatial representation to generate attenuation-only projections that look like X-ray radiographs. Due to the rapid evolution of its underlying architecture, the graphics processing unit (GPU) became an attractive competent platform that can deliver giant computational raw power compared to the central processing unit (CPU) on a per-dollar-basis. The introduction of the compute unified device architecture (CUDA) technology enables embarrassingly-parallel algorithms to run efficiently on CUDA-capable GPU architectures. In this work, a high performance GPU-accelerated implementation of the FVR pipeline on CUDA-enabled GPUs is presented. This proposed implementation can achieve a speed-up of 117x compared to a single-threaded hybrid implementation that uses the CPU and GPU together by taking advantage of executing the rendering pipeline entirely on recent GPU architectures.\",\n \"corpus_id\": 1954769,\n \"score\": 0\n },\n {\n \"doc_id\": \"26776541\",\n \"title\": \"Efficient methods for implementation of multi-level nonrigid mass-preserving image registration on GPUs and multi-threaded CPUs.\",\n \"abstract\": \"BACKGROUND AND OBJECTIVE: Faster and more accurate methods for registration of images are important for research involved in conducting population-based studies that utilize medical imaging, as well as improvements for use in clinical applications. We present a novel computation- and memory-efficient multi-level method on graphics processing units (GPU) for performing registration of two computed tomography (CT) volumetric lung images. METHODS: We developed a computation- and memory-efficient Diffeomorphic Multi-level B-Spline Transform Composite (DMTC) method to implement nonrigid mass-preserving registration of two CT lung images on GPU. The framework consists of a hierarchy of B-Spline control grids of increasing resolution. A similarity criterion known as the sum of squared tissue volume difference (SSTVD) was adopted to preserve lung tissue mass. The use of SSTVD consists of the calculation of the tissue volume, the Jacobian, and their derivatives, which makes its implementation on GPU challenging due to memory constraints. The use of the DMTC method enabled reduced computation and memory storage of variables with minimal communication between GPU and Central Processing Unit (CPU) due to ability to pre-compute values. The method was assessed on six healthy human subjects. RESULTS: Resultant GPU-generated displacement fields were compared against the previously validated CPU counterpart fields, showing good agreement with an average normalized root mean square error (nRMS) of 0.044±0.015. Runtime and performance speedup are compared between single-threaded CPU, multi-threaded CPU, and GPU algorithms. Best performance speedup occurs at the highest resolution in the GPU implementation for the SSTVD cost and cost gradient computations, with a speedup of 112 times that of the single-threaded CPU version and 11 times over the twelve-threaded version when considering average time per iteration using a Nvidia Tesla K20X GPU. CONCLUSIONS: The proposed GPU-based DMTC method outperforms its multi-threaded CPU version in terms of runtime. Total registration time reduced runtime to 2.9min on the GPU version, compared to 12.8min on twelve-threaded CPU version and 112.5min on a single-threaded CPU. Furthermore, the GPU implementation discussed in this work can be adapted for use of other cost functions that require calculation of the first derivatives.\",\n \"corpus_id\": 10051304,\n \"score\": 0\n },\n {\n \"doc_id\": \"28590565\",\n \"title\": \"Three-dimensional MR reconstruction of high-contrast magnetic susceptibility by the variational born iterative method based on the magnetic field volume integral equation.\",\n \"abstract\": \"PURPOSE: To provide high-quality and high-contrast magnetic susceptibility mapping, a 3D MR reconstruction method for magnetic susceptibility based on the magnetic field volume integral equation with the variational Born iterative method (VBIM) is developed. METHODS: Three-dimensional magnetic susceptibility is reconstructed from the positive rotating magnetic field component H1+ of the radiofrequency field acquired by B1 mapping. The stabilized biconjugate gradient fast Fourier transform (BCGS-FFT) method is implemented in the forward problem to solve for the magnetic field, and the conjugate gradient fast Fourier transform method is implemented in the inverse problem to reconstruct the magnetic susceptibility distribution. RESULTS: Numerical results demonstrated that good effectiveness and high accuracy can be achieved for both the forward solver of the stabilized biconjugate gradient fast Fourier transform method and the inverse solver of the VBIM method. The method proved to be robust under noise contamination. Moreover, the magnetic susceptibilities with much higher contrasts than that of the non-full wave methods can also be efficiently reconstructed. CONCLUSIONS: The proposed method can reconstruct the magnetic susceptibility of not only human head, but also other human tissues or materials such as magnetic contrast agents with high magnetic susceptibilities. It has promising applications in high-contrast magnetic susceptibility mapping. Magn Reson Med, 2017. © 2017 International Society for Magnetic Resonance in Medicine.\",\n \"corpus_id\": 21847798,\n \"score\": 0\n }\n]","isConversational":false}}},{"rowIdx":92,"cells":{"query":{"kind":"string","value":"{\n \"doc_id\": \"25681631\",\n \"title\": \"Alignment of direct detection device micrographs using a robust Optical Flow approach.\",\n \"abstract\": \"The introduction of direct detection devices in cryo-EM has shown that specimens present beam-induced motion (BIM). Consequently, in this work, we develop a BIM correction method at the image level, resulting in an integrated image in which the in-plane BIM blurring is compensated prior to particle picking. The methodology is based on a robust Optical Flow (OF) approach that can efficiently correct for local movements in a rapid manner. The OF works particularly well if the BIM pattern presents a substantial degree of local movements, which occurs in our data sets for Falcon II data. However, for those cases in which the BIM pattern corresponds to global movements, we have found it advantageous to first run a global motion correction approach and to subsequently apply OF. Additionally, spatial analysis of the Optical Flow allows for quantitative analysis of the BIM pattern. The software that incorporates the new approach is available in XMIPP (http://xmipp.cnb.csic.es).\",\n \"corpus_id\": 16383699\n}"},"candidates":{"kind":"list like","value":[{"doc_id":"22155955","title":"Locally oriented optical flow computation.","abstract":"This paper proposes the use of an adaptive locally oriented coordinate frame when calculating an optical flow field. The coordinate frame is aligned with the least curvature direction in a local window about each pixel. This has advantages to both fitting the flow field to the image data and in imposing smoothness constraints between neighboring pixels. In terms of fitting, robustness is obtained to a wider variety of image motions due to the extra invariance provided by the coordinate frame. Smoothness constraints are naturally propagated along image boundaries which often correspond to motion boundaries. In addition, moving objects can be efficiently segmented in the least curvature direction. We show experimentally the benefits of the method and demonstrate robustness to fast rotational motion, such as what often occurs in human motion.","corpus_id":16414857,"score":2},{"doc_id":"23022349","title":"Movies of ice-embedded particles enhance resolution in electron cryo-microscopy.","abstract":"Low-dose images obtained by electron cryo-microscopy (cryo-EM) are often affected by blurring caused by sample motion during electron beam exposure, degrading signal especially at high resolution. We show here that we can align frames of movies, recorded with a direct electron detector during beam exposure of rotavirus double-layered particles, thereby greatly reducing image blurring caused by beam-induced motion and sample stage instabilities. This procedure increases the efficiency of cryo-EM imaging and enhances the resolution obtained in three-dimensional reconstructions of the particle. Using movies in this way is generally applicable to all cryo-EM samples and should also improve the performance of midrange electron microscopes that may have limited mechanical stability and beam coherence.","corpus_id":15260039,"score":2},{"doc_id":"23254656","title":"Non-rigid image registration to reduce beam-induced blurring of cryo-electron microscopy images.","abstract":"The typical dose used to record cryo-electron microscopy images from vitrified biological specimens is so high that radiation-induced structural alterations are bound to occur during data acquisition. Integration of all scattered electrons into one image can lead to significant blurring, particularly if the data are collected from an unsupported thin layer of ice suspended over the holes of a support film. Here, the dose has been fractioned and exposure series have been acquired in order to study beam-induced specimen movements under low dose conditions, prior to bubbling. Gold particles were added to the protein sample as fiducial markers. These were automatically localized and tracked throughout the exposure series and showed correlated motions within small patches, with larger amplitudes of motion vectors at the start of a series compared with the end of each series. A non-rigid scheme was used to register all images within each exposure series, using natural neighbor interpolation with the gold particles as anchor points. The procedure increases the contrast and resolution of the examined macromolecules.","corpus_id":15509596,"score":2},{"doc_id":"23644547","title":"Electron counting and beam-induced motion correction enable near-atomic-resolution single-particle cryo-EM.","abstract":"In recent work with large high-symmetry viruses, single-particle electron cryomicroscopy (cryo-EM) has achieved the determination of near-atomic-resolution structures by allowing direct fitting of atomic models into experimental density maps. However, achieving this goal with smaller particles of lower symmetry remains challenging. Using a newly developed single electron-counting detector, we confirmed that electron beam-induced motion substantially degrades resolution, and we showed that the combination of rapid readout and nearly noiseless electron counting allow image blurring to be corrected to subpixel accuracy, restoring intrinsic image information to high resolution (Thon rings visible to ∼3 Å). Using this approach, we determined a 3.3-Å-resolution structure of an ∼700-kDa protein with D7 symmetry, the Thermoplasma acidophilum 20S proteasome, showing clear side-chain density. Our method greatly enhances image quality and data acquisition efficiency-key bottlenecks in applying near-atomic-resolution cryo-EM to a broad range of protein samples.","corpus_id":2313269,"score":2},{"doc_id":"25020094","title":"Robust optical flow integration.","abstract":"We analyze the problem of how to correctly construct dense point trajectories from optical flow fields. First, we show that simple Euler integration is unavoidably inaccurate, no matter how good is the optical flow estimator. Then, an inverse integration scheme is analyzed which is more robust to bias and input noise and shows better stability properties. Our contribution is threefold: 1) a theoretical analysis that demonstrates why and in what sense inverse integration is more accurate; 2) a rich experimental validation both on synthetic and real (image) data; and 3) an algorithm for approximate online inverse integration. This new technique is precious whether one is trying to propagate information densely available on a reference frame to the other frames in the sequence or, conversely, to assign information densely over each frame by pulling it from the reference.","corpus_id":15285720,"score":2},{"doc_id":"25122622","title":"Beam-induced motion correction for sub-megadalton cryo-EM particles.","abstract":"In electron cryo-microscopy (cryo-EM), the electron beam that is used for imaging also causes the sample to move. This motion blurs the images and limits the resolution attainable by single-particle analysis. In a previous Research article (Bai et al., 2013) we showed that correcting for this motion by processing movies from fast direct-electron detectors allowed structure determination to near-atomic resolution from 35,000 ribosome particles. In this Research advance article, we show that an improved movie processing algorithm is applicable to a much wider range of specimens. The new algorithm estimates straight movement tracks by considering multiple particles that are close to each other in the field of view, and models the fall-off of high-resolution information content by radiation damage in a dose-dependent manner. Application of the new algorithm to four data sets illustrates its potential for significantly improving cryo-EM structures, even for particles that are smaller than 200 kDa.","corpus_id":12574480,"score":2},{"doc_id":"26296328","title":"Alignment of cryo-EM movies of individual particles by optimization of image translations.","abstract":"Direct detector device (DDD) cameras have revolutionized single particle electron cryomicroscopy (cryo-EM). In addition to an improved camera detective quantum efficiency, acquisition of DDD movies allows for correction of movement of the specimen, due to both instabilities in the microscope specimen stage and electron beam-induced movement. Unlike specimen stage drift, beam-induced movement is not always homogeneous within an image. Local correlation in the trajectories of nearby particles suggests that beam-induced motion is due to deformation of the ice layer. Algorithms have already been described that can correct movement for large regions of frames and for >1MDa protein particles. Another algorithm allows individual <1MDa protein particle trajectories to be estimated, but requires rolling averages to be calculated from frames and fits linear trajectories for particles. Here we describe an algorithm that allows for individual <1MDa particle images to be aligned without frame averaging or linear trajectories. The algorithm maximizes the overall correlation of the shifted frames with the sum of the shifted frames. The optimum in this single objective function is found efficiently by making use of analytically calculated derivatives of the function. To smooth estimates of particle trajectories, rapid changes in particle positions between frames are penalized in the objective function and weighted averaging of nearby trajectories ensures local correlation in trajectories. This individual particle motion correction, in combination with weighting of Fourier components to account for increasing radiation damage in later frames, can be used to improve 3-D maps from single particle cryo-EM.","corpus_id":17501197,"score":2},{"doc_id":"27016144","title":"Methods to account for movement and flexibility in cryo-EM data processing.","abstract":"Recent advances in direct electron detectors and improved CMOS cameras have been accompanied by the development of a range of software to take advantage of the data they produce. In particular they allow for the correction of two types of motion in cryo electron microscopy samples: motion correction for movements of the sample particles in the ice, and differential masking to account for heterogeneity caused by flexibility within protein complexes. Here we provide several scripts that allow users to move between RELION and standalone motion correction and centring programs. We then compare the computational cost and improvements in data quality with each program. We also describe our masking procedures to account for conformational flexibility. For the different elements of this study we have used three samples; a high symmetry virus, flexible protein complex (∼1MDa) and a relatively small protein complex (∼550kDa), to benchmark four widely available motion correction packages. Using these as test cases we demonstrate how motion correction and differential masking, as well as an additional particle re-centring protocol can improve final reconstructions when used within the RELION image-processing package.","corpus_id":3557048,"score":2},{"doc_id":"27016284","title":"Alignment algorithms and per-particle CTF correction for single particle cryo-electron tomography.","abstract":"Single particle cryo-electron tomography (cryoSPT) extracts features from cryo-electron tomograms, followed by 3D classification, alignment and averaging to generate improved 3D density maps of such features. Robust methods to correct for the contrast transfer function (CTF) of the electron microscope are necessary for cryoSPT to reach its resolution potential. Many factors can make CTF correction for cryoSPT challenging, such as lack of eucentricity of the specimen stage, inherent low dose per image, specimen charging, beam-induced specimen motions, and defocus gradients resulting both from specimen tilting and from unpredictable ice thickness variations. Current CTF correction methods for cryoET make at least one of the following assumptions: that the defocus at the center of the image is the same across the images of a tiltseries, that the particles all lie at the same Z-height in the embedding ice, and/or that the specimen, the cryo-electron microscopy (cryoEM) grid and/or the carbon support are flat. These experimental conditions are not always met. We have developed a CTF correction algorithm for cryoSPT without making any of the aforementioned assumptions. We also introduce speed and accuracy improvements and a higher degree of automation to the subtomogram averaging algorithms available in EMAN2. Using motion-corrected images of isolated virus particles as a benchmark specimen, recorded with a DE20 direct detection camera, we show that our CTF correction and subtomogram alignment routines can yield subtomogram averages close to 4/5 Nyquist frequency of the detector under our experimental conditions.","corpus_id":3934913,"score":2},{"doc_id":"27572722","title":"Specimen Behavior in the Electron Beam.","abstract":"It has long been known that cryo-EM specimens are severely damaged by a level of electron exposure that is much lower than what is needed to obtain high-resolution images from single macromolecules. Perhaps less well appreciated in the cryo-EM literature, the vitreous ice in which samples are suspended is equally sensitivity to radiation damage. This chapter provides a review of several fundamental topics such as inelastic scattering of electrons, radiation chemistry, and radiation biology, which-together-can help one to understand why radiation damage occurs so \"easily.\" This chapter also addresses the issue of beam-induced motion that occurs at even lower levels of electron exposure. While specimen charging may be a contributor to this motion, it is argued that both radiation-induced relief of preexisting stress and damage-induced generation of additional stress may be the dominant causes of radiation-induced movement.","corpus_id":3580735,"score":2},{"doc_id":"18054249","title":"Applications of direct detection device in transmission electron microscopy.","abstract":"A prototype direct detection device (DDD) camera system has shown great promise in improving both the spatial resolution and the signal to noise ratio for electron microscopy at 120-400 keV beam energies (Xuong et al., 2007. Methods in Cell Biology, 79, 721-739). Without the need for a resolution-limiting scintillation screen as in the charge coupled device (CCD), the DDD camera can outperform CCD based systems in terms of spatial resolution, due to its small pixel size (5 microm). In this paper, the modulation transfer function (MTF) of the DDD prototype is measured and compared with the specifications of commercial scientific CCD camera systems. Combining the fast speed of the DDD with image mosaic techniques, fast wide-area imaging is now possible. In this paper, the first large area mosaic image and the first tomography dataset from the DDD camera are presented, along with an image processing algorithm to correct the specimen drift utilizing the fast readout of the DDD system.","corpus_id":46631247,"score":1},{"doc_id":"19378279","title":"Optical flow approaches to the identification of brain dynamics.","abstract":"The superior temporal resolution of magneto- and electroencephalography (MEEG) provides unique insight into the dynamics of brain function. The analysis of the spatial dimensions of MEEG recordings can take a multiplicity of approaches: from the original scalp recordings to the identification of their generators through localizing or imaging techniques. Overall, both MEEG native or imaging data may be considered as multidimensional structures with potentially dense information contents. Quantitative analysis of the spatiotemporal flow of information conveyed by MEEG begins with a feature-extraction problem, thereby leading to improved insight in the multidimensional structure of brain dynamics. In this contribution, we approach this endeavor by suggesting that brain dynamic features from local through global spatial scales may be identified using the previously-introduced technique of surface-based optical flow. We illustrate this assertion by the quantitative analysis of time-resolved sequences of brain activity through the identification of episodes of relative topographical stability. In that respect, we revisit the concept of brain microstates with a new approach and distinct operational hypotheses. Local dynamic features from a variety of brain systems may also be explored through this methodology, as illustrated by experimental data on fast responses in the visual system as revealed by MEEG source imaging.","corpus_id":19140799,"score":1},{"doc_id":"21575566","title":"Reaching the information limit in cryo-EM of biological macromolecules: experimental aspects.","abstract":"Although cryo-electron microscopy (cryo-EM) of biological macromolecules has made important advances in the past few years, the level of current technical performance is still well below what the physics of electron scattering would allow. It should be possible, for example, to use cryo-EM to solve protein structures at atomic resolution for particle sizes well below 80 kDa, but currently this has been achieved only for particles at least 10 times larger than that. In this review, we first examine some of the reasons for this large gap in performance. We then give an overview of work that is currently in progress to 1), improve the signal/noise ratio for area detectors; 2), improve the signal transfer between the scattered electrons and the corresponding images; and 3), reduce the extent to which beam-induced movement causes a steep fall-off of signal at high resolution. In each case, there is substantial reason to think that cryo-EM can indeed be made to approach the estimated physical limits.","corpus_id":19832292,"score":1},{"doc_id":"22167624","title":"Bayesian inference of models and hyperparameters for robust optical-flow estimation.","abstract":"Selecting optimal models and hyperparameters is crucial for accurate optical-flow estimation. This paper provides a solution to the problem in a generic Bayesian framework. The method is based on a conditional model linking the image intensity function, the unknown velocity field, hyperparameters, and the prior and likelihood motion models. Inference is performed on each of the three levels of this so-defined hierarchical model by maximization of marginalized a posteriori probability distribution functions. In particular, the first level is used to achieve motion estimation in a classical a posteriori scheme. By marginalizing out the motion variable, the second level enables to infer regularization coefficients and hyperparameters of non-Gaussian M-estimators commonly used in robust statistics. The last level of the hierarchy is used for selection of the likelihood and prior motion models conditioned to the image data. The method is evaluated on image sequences of fluid flows and from the \"Middlebury\" database. Experiments prove that applying the proposed inference strategy yields better results than manually tuning smoothing parameters or discontinuity preserving cost functions of the state-of-the-art methods.","corpus_id":260973284,"score":1},{"doc_id":"23454482","title":"Automatic post-picking using MAPPOS improves particle image detection from cryo-EM micrographs.","abstract":"Cryo-electron microscopy (cryo-EM) studies using single particle reconstruction are extensively used to reveal structural information on macromolecular complexes. Aiming at the highest achievable resolution, state of the art electron microscopes automatically acquire thousands of high-quality micrographs. Particles are detected on and boxed out from each micrograph using fully- or semi-automated approaches. However, the obtained particles still require laborious manual post-picking classification, which is one major bottleneck for single particle analysis of large datasets. We introduce MAPPOS, a supervised post-picking strategy for the classification of boxed particle images, as additional strategy adding to the already efficient automated particle picking routines. MAPPOS employs machine learning techniques to train a robust classifier from a small number of characteristic image features. In order to accurately quantify the performance of MAPPOS we used simulated particle and non-particle images. In addition, we verified our method by applying it to an experimental cryo-EM dataset and comparing the results to the manual classification of the same dataset. Comparisons between MAPPOS and manual post-picking classification by several human experts demonstrated that merely a few hundred sample images are sufficient for MAPPOS to classify an entire dataset with a human-like performance. MAPPOS was shown to greatly accelerate the throughput of large datasets by reducing the manual workload by orders of magnitude while maintaining a reliable identification of non-particle images.","corpus_id":9789870,"score":1},{"doc_id":"23711417","title":"Image formation modeling in cryo-electron microscopy.","abstract":"Accurate modeling of image formation in cryo-electron microscopy is an important requirement for quantitative image interpretation and optimization of the data acquisition strategy. Here we present a forward model that accounts for the specimen's scattering properties, microscope optics, and detector response. The specimen interaction potential is calculated with the isolated atom superposition approximation (IASA) and extended with the influences of solvent's dielectric and ionic properties as well as the molecular electrostatic distribution. We account for an effective charge redistribution via the Poisson-Boltzmann approach and find that the IASA-based potential forms the dominant part of the interaction potential, as the contribution of the redistribution is less than 10%. The electron wave is propagated through the specimen by a multislice approach and the influence of the optics is included via the contrast transfer function. We incorporate the detective quantum efficiency of the camera due to the difference between signal and noise transfer characteristics, instead of using only the modulation transfer function. The full model was validated against experimental images of 20S proteasome, hemoglobin, and GroEL. The simulations adequately predict the effects of phase contrast, changes due to the integrated electron flux, thickness, inelastic scattering, detective quantum efficiency and acceleration voltage. We suggest that beam-induced specimen movements are relevant in the experiments whereas the influence of the solvent amorphousness can be neglected. All simulation parameters are based on physical principles and, when necessary, experimentally determined.","corpus_id":14817435,"score":1},{"doc_id":"24075951","title":"Xmipp 3.0: an improved software suite for image processing in electron microscopy.","abstract":"Xmipp is a specialized software package for image processing in electron microscopy, and that is mainly focused on 3D reconstruction of macromolecules through single-particles analysis. In this article we present Xmipp 3.0, a major release which introduces several improvements and new developments over the previous version. A central improvement is the concept of a project that stores the entire processing workflow from data import to final results. It is now possible to monitor, reproduce and restart all computing tasks as well as graphically explore the complete set of interrelated tasks associated to a given project. Other graphical tools have also been improved such as data visualization, particle picking and parameter \"wizards\" that allow the visual selection of some key parameters. Many standard image formats are transparently supported for input/output from all programs. Additionally, results have been standardized, facilitating the interoperation between different Xmipp programs. Finally, as a result of a large code refactoring, the underlying C++ libraries are better suited for future developments and all code has been optimized. Xmipp is an open-source package that is freely available for download from: http://xmipp.cnb.csic.es.","corpus_id":14314008,"score":1},{"doc_id":"26087140","title":"Description and comparison of algorithms for correcting anisotropic magnification in cryo-EM images.","abstract":"Single particle electron cryomicroscopy (cryo-EM) allows for structures of proteins and protein complexes to be determined from images of non-crystalline specimens. Cryo-EM data analysis requires electron microscope images of randomly oriented ice-embedded protein particles to be rotated and translated to allow for coherent averaging when calculating three-dimensional (3D) structures. Rotation of 2D images is usually done with the assumption that the magnification of the electron microscope is the same in all directions. However, due to electron optical aberrations, this condition is not met with some electron microscopes when used with the settings necessary for cryo-EM with a direct detector device (DDD) camera. Correction of images by linear interpolation in real space has allowed high-resolution structures to be calculated from cryo-EM images for symmetric particles. Here we describe and compare a simple real space method, a simple Fourier space method, and a somewhat more sophisticated Fourier space method to correct images for a measured anisotropy in magnification. Further, anisotropic magnification causes contrast transfer function (CTF) parameters estimated from image power spectra to have an apparent systematic astigmatism. To address this problem we develop an approach to adjust CTF parameters measured from distorted images so that they can be used with corrected images. The effect of anisotropic magnification on CTF parameters provides a simple way of detecting magnification anisotropy in cryo-EM datasets.","corpus_id":6082134,"score":1},{"doc_id":"26671944","title":"Automated data collection in single particle electron microscopy.","abstract":"Automated data collection is an integral part of modern workflows in single particle electron microscopy (EM) research. This review surveys the software packages available for automated single particle EM data collection. The degree of automation at each stage of data collection is evaluated, and the capabilities of the software packages are described. Finally, future trends in automation are discussed.","corpus_id":9154059,"score":1},{"doc_id":"27572725","title":"Processing of Cryo-EM Movie Data.","abstract":"Direct detector device (DDD) cameras dramatically enhance the capabilities of electron cryomicroscopy (cryo-EM) due to their improved detective quantum efficiency (DQE) relative to other detectors. DDDs use semiconductor technology that allows micrographs to be recorded as movies rather than integrated individual exposures. Movies from DDDs improve cryo-EM in another, more surprising, way. DDD movies revealed beam-induced specimen movement as a major source of image degradation and provide a way to partially correct the problem by aligning frames or regions of frames to account for this specimen movement. In this chapter, we use a self-consistent mathematical notation to explain, compare, and contrast several of the most popular existing algorithms for computationally correcting specimen movement in DDD movies. We conclude by discussing future developments in algorithms for processing DDD movies that would extend the capabilities of cryo-EM even further.","corpus_id":3572644,"score":1},{"doc_id":"28600243","title":"Robust Non-Local TV-L1 Optical Flow Estimation with Occlusion Detection.","abstract":"In this paper, we propose a robust non-local TV-L1 optical flow method with occlusion detection to address the problem of weak robustness of optical flow estimation with motion occlusion. Firstly, a TV-L1 form for flow estimation is defined using a combination of the brightness constancy and gradient constancy assumptions in the data term and by varying the weight under the Charbonnier function in the smoothing term. Secondly, to handle the potential risk of the outlier in the flow field, a general non-local term is added in the TV-L1 optical flow model to engender the typical non-local TV-L1 form. Thirdly, an occlusion detection method based on triangulation is presented to detect the occlusion regions of the sequence. The proposed non-local TV-L1 optical flow model is performed in a linearizing iterative scheme using improved median filtering and a coarse-to-fine computing strategy. The results of the complex experiment indicate that the proposed method can overcome the significant influence of non-rigid motion, motion occlusion, and large displacement motion. Results of experiments comparing the proposed method and existing state-of-the-art methods by respectively using Middlebury and MPI Sintel database test sequences show that the proposed method has higher accuracy and better robustness.","corpus_id":195671907,"score":1},{"doc_id":"18443909","title":"Design of MEMS devices with optical apertures for the detection of transparent biological cells.","abstract":"This paper provides a novel technique to detect transparent biological living cells trapped in a microfluidic MEMS device by optical diffraction. The device essentially consists of an optical aperture or an aperture array patterned in metal layer and a microfluidic chamber positioned above the center of the aperture. When the cells in the chamber are illuminated through the aperture, the far-field diffraction pattern can be recorded by a CCD camera or a photodetector array. This diffraction pattern uniquely corresponds to the sizes, positions, and intrinsic optical properties of the aperture, cells, and the microfluidic chamber materials, so any unknown but relevant parameter is able to be extrapolated when all other parameters are fixed or identified. This paper describes in detail the designs of various microfluidic chambers and apertures for this application, and the development of a complete set of software for the analysis of the cells' optical properties. Compared with other currently available methods for the detection of transparent living cells, this method has the advantages of simple device structure, easy to manipulate, able to simultaneously detect several cells of different species, as well as providing accurate and sensitive results. Besides the detection of living cells, this technique can also be used to detect or characterize other transparent or low optical absorption particles, such as polymer spheres or insoluble droplets, inside an aqueous solution.","corpus_id":25085132,"score":0},{"doc_id":"18672433","title":"Respiratory motion correction in 3-D PET data with advanced optical flow algorithms.","abstract":"The problem of motion is well known in positron emission tomography (PET) studies. The PET images are formed over an elongated period of time. As the patients cannot hold breath during the PET acquisition, spatial blurring and motion artifacts are the natural result. These may lead to wrong quantification of the radioactive uptake. We present a solution to this problem by respiratory-gating the PET data and correcting the PET images for motion with optical flow algorithms. The algorithm is based on the combined local and global optical flow algorithm with modifications to allow for discontinuity preservation across organ boundaries and for application to 3-D volume sets. The superiority of the algorithm over previous work is demonstrated on software phantom and real patient data.","corpus_id":22147460,"score":0},{"doc_id":"19717361","title":"An optical flow-based approach to robust face recognition under expression variations.","abstract":"Face recognition is one of the most intensively studied topics in computer vision and pattern recognition, but few are focused on how to robustly recognize faces with expressions under the restriction of one single training sample per class. A constrained optical flow algorithm, which combines the advantages of the unambiguous correspondence of feature point labeling and the flexible representation of optical flow computation, has been developed for face recognition from expressional face images. In this paper, we propose an integrated face recognition system that is robust against facial expressions by combining information from the computed intraperson optical flow and the synthesized face image in a probabilistic framework. Our experimental results show that the proposed system improves the accuracy of face recognition from expressional face images.","corpus_id":18194254,"score":0},{"doc_id":"20117216","title":"Alignator: a GPU powered software package for robust fiducial-less alignment of cryo tilt-series.","abstract":"The robust alignment of tilt-series collected for cryo-electron tomography in the absence of fiducial markers, is a problem that, especially for tilt-series of vitreous sections, still represents a significant challenge. Here we present a complete software package that implements a cross-correlation-based procedure that tracks similar image features that are present in several micrographs and explores them implicitly as substitutes for fiducials like gold beads and quantum dots. The added value compared to previous approaches, is that the algorithm explores a huge number of random positions, which are tracked on several micrographs, while being able to identify trace failures, using a cross-validation procedure based on the 3D marker model of the tilt-series. Furthermore, this method allows the reliable identification of areas which behave as a rigid body during the tilt-series and hence addresses specific difficulties for the alignment of vitreous sections, by correcting practical caveats. The resulting alignments can attain sub-pixel precision at the local level and is able to yield a substantial number of usable tilt-series (around 60%). In principle, the algorithm has the potential to run in a fully automated fashion, and could be used to align any tilt-series directly from the microscope. Finally, we have significantly improved the user interface and implemented the source code on the graphics processing unit (GPU) to accelerate the computations.","corpus_id":23038314,"score":0},{"doc_id":"20356853","title":"Automated specimen search in cryo-TEM observation with DIFF-defocus imaging.","abstract":"We have developed an automated specimen search algorithm for cryo-electron microscopy imaging of ice-embedded single particles suspended across regularly spaced holes. To maximize the particle visibility under a low electron exposure rate condition, specimen searching is carried out in diffraction mode. However, images in diffraction mode contain significant pincushion distortion, making it difficult to computationally predict the locations of the regularly spaced holes. We have implemented a distortion-correction mechanism to restore the primitive distortion-free image and a correlation-based algorithm to accurately determine the periodicity of the holes. A stage-shift method to optimize positional reproducibility is also implemented. Addition of our algorithms to the JADAS software for automated transmission electron microscopy data acquisition has significantly improved the accuracy of specimen search.","corpus_id":262442938,"score":0},{"doc_id":"20409993","title":"Robust processing of optical flow of fluids.","abstract":"This paper proposes a new approach, coupling physical models and image estimation techniques, for modelling the movement of fluids. The fluid flow is characterized by turbulent movement and dynamically changing patterns which poses challenges to existing optical flow estimation methods. The proposed methodology, which relies on Navier-Stokes equations, is used for processing fluid optical flow by using a succession of stages such as advection, diffusion and mass conservation. A robust diffusion step jointly considering the local data geometry and its statistics is embedded in the proposed framework. The diffusion kernel is Gaussian with the covariance matrix defined by the local second derivatives. Such an anisotropic kernel is able to implicitly detect changes in the vector field orientation and to diffuse accordingly. A new approach is developed for detecting fluid flow structures such as vortices. The proposed methodology is applied on artificially generated vector fields as well as on various image sequences.","corpus_id":239581,"score":0},{"doc_id":"20637414","title":"Ab initio structure determination from electron microscopic images of single molecules coexisting in different functional states.","abstract":"We have developed methods for ab initio three-dimensional (3D) structure determination from projection images of randomly oriented single molecules coexisting in multiple functional states, to aid the study of complex samples of macromolecules and nanoparticles by electron microscopy (EM). New algorithms for the determination of relative 3D orientations and conformational state assignment of single-molecule projection images are combined with well-established techniques for alignment and statistical image analysis. We describe how the methodology arrives at homogeneous groups of images aligned in 3D and discuss application to experimental EM data sets of the Escherichia coli ribosome and yeast RNA polymerase II.","corpus_id":37167871,"score":0},{"doc_id":"21089695","title":"[A review of automatic particle recognition in Cryo-EM images].","abstract":"Advances in cryo-electron microscopy (Cryo-EM) and single-particle reconstruction have led to increasingly high resolutions of macromolecular three-dimensional reconstruction. However, for keeping up the continuing improvements in resolution, it is necessary to increase the number of particles included in performing reconstructions. Manual selection of particles, even assisted by computer, is a bottleneck of single-particle reconstruction. Cryo-EM image has low signal-to-noise ratio and low contrast, which leads to difficulty in particle picking. Various approaches have been developed to address the problem of automatic particle. This paper describes the application of template-based method, edge based method, feature-based method, neural network, DoG-based and simulated annealing approach in particle picking. The characteristics of various approaches are discussed, and the future development is presented.","corpus_id":38932072,"score":0},{"doc_id":"21266556","title":"Flow velocity vector fields by ultrasound particle imaging velocimetry: in vitro comparison with optical flow velocimetry.","abstract":"OBJECTIVES: We performed an in vitro study to assess the precision and accuracy of particle imaging velocimetry (PIV) data acquired using a clinically available portable ultrasound system via comparison with stereo optical PIV. METHODS: The performance of ultrasound PIV was compared with optical PIV on a benchmark problem involving vortical flow with a substantial out-of-plane velocity component. Optical PIV is capable of stereo image acquisition, thus measuring out-of-plane velocity components. This allowed us to quantify the accuracy of ultrasound PIV, which is limited to in-plane acquisition. The system performance was assessed by considering the instantaneous velocity fields without extracting velocity profiles by spatial averaging. RESULTS: Within the 2-dimensional correlation window, using 7 time-averaged frames, the vector fields were found to have correlations of 0.867 in the direction along the ultrasound beam and 0.738 in the perpendicular direction. Out-of-plane motion of greater than 20% of the in-plane vector magnitude was found to increase the SD by 11% for the vectors parallel to the ultrasound beam direction and 8.6% for the vectors perpendicular to the beam. CONCLUSIONS: The results show a close correlation and agreement of individual velocity vectors generated by ultrasound PIV compared with optical PIV. Most of the measurement distortions were caused by out-of-plane velocity components.","corpus_id":25965900,"score":0},{"doc_id":"21279198","title":"Hydrodynamic optical alignment for microflow cytometry.","abstract":"A microfabricated flow cytometer has been developed that is capable of detecting nearly all of the microparticles in an aqueous suspension. Current design allows for integrated coupling between an optical fiber-based detection system and the particle stream via hydrodynamic focusing. By adjusting the relative flow-rates at the auxiliary inputs of the focusing manifold, the particle stream can be steered out-of-plane relative to the illuminating laser, and similarly the particle stream can be squeezed or expanded. The microfabricated device was constructed in polydimethylsiloxane with cross-sectional microfluidic dimensions of 125 µm×125 µm. Using the present device and method, fluorescent microparticles in aqueous solution were counted at an absolute counting efficiency of 91±4%. The coefficient of variation of the fluorescence pulse-heights for far-red fluorescent microparticles was 15%. The device exhibited a linear response to fluorescence intensity calibration microparticles as shown by comparison with a commercial cytometer instrument.","corpus_id":20847181,"score":0},{"doc_id":"21978037","title":"Evaluation of a 3D local multiresolution algorithm for the correction of partial volume effects in positron emission tomography.","abstract":"PURPOSE: Partial volume effects (PVEs) are consequences of the limited spatial resolution in emission tomography leading to underestimation of uptake in tissues of size similar to the point spread function (PSF) of the scanner as well as activity spillover between adjacent structures. Among PVE correction methodologies, a voxel-wise mutual multiresolution analysis (MMA) was recently introduced. MMA is based on the extraction and transformation of high resolution details from an anatomical image (MR/CT) and their subsequent incorporation into a low-resolution PET image using wavelet decompositions. Although this method allows creating PVE corrected images, it is based on a 2D global correlation model, which may introduce artifacts in regions where no significant correlation exists between anatomical and functional details. METHODS: A new model was designed to overcome these two issues (2D only and global correlation) using a 3D wavelet decomposition process combined with a local analysis. The algorithm was evaluated on synthetic, simulated and patient images, and its performance was compared to the original approach as well as the geometric transfer matrix (GTM) method. RESULTS: Quantitative performance was similar to the 2D global model and GTM in correlated cases. In cases where mismatches between anatomical and functional information were present, the new model outperformed the 2D global approach, avoiding artifacts and significantly improving quality of the corrected images and their quantitative accuracy. CONCLUSIONS: A new 3D local model was proposed for a voxel-wise PVE correction based on the original mutual multiresolution analysis approach. Its evaluation demonstrated an improved and more robust qualitative and quantitative accuracy compared to the original MMA methodology, particularly in the absence of full correlation between anatomical and functional information.","corpus_id":19007461,"score":0},{"doc_id":"22231171","title":"Alignment of 3-D optical coherence tomography scans to correct eye movement using a particle filtering.","abstract":"Eye movement artifacts occurring during 3-D optical coherence tomography (OCT) scanning is a well-recognized problem that may adversely affect image analysis and interpretation. A particle filtering algorithm is presented in this paper to correct motion in a 3-D dataset by considering eye movement as a target tracking problem in a dynamic system. The proposed particle filtering algorithm is an independent 3-D alignment approach, which does not rely on any reference image. 3-D OCT data is considered as a dynamic system, while the location of each A-scan is represented by the state space. A particle set is used to approximate the probability density of the state in the dynamic system. The state of the system is updated frame by frame to detect A-scan movement. The proposed method was applied on both simulated data for objective evaluation and experimental data for subjective evaluation. The sensitivity and specificity of the x-movement detection were 98.85% and 99.43%, respectively, in the simulated data. For the experimental data (74 3-D OCT images), all the images were improved after z-alignment, while 81.1% images were improved after x-alignment. The proposed algorithm is an efficient way to align 3-D OCT volume data and correct the eye movement without using references.","corpus_id":32665239,"score":0},{"doc_id":"22363510","title":"RAMTaB: robust alignment of multi-tag bioimages.","abstract":"BACKGROUND: In recent years, new microscopic imaging techniques have evolved to allow us to visualize several different proteins (or other biomolecules) in a visual field. Analysis of protein co-localization becomes viable because molecules can interact only when they are located close to each other. We present a novel approach to align images in a multi-tag fluorescence image stack. The proposed approach is applicable to multi-tag bioimaging systems which (a) acquire fluorescence images by sequential staining and (b) simultaneously capture a phase contrast image corresponding to each of the fluorescence images. To the best of our knowledge, there is no existing method in the literature, which addresses simultaneous registration of multi-tag bioimages and selection of the reference image in order to maximize the overall overlap between the images. METHODOLOGY/PRINCIPAL FINDINGS: We employ a block-based method for registration, which yields a confidence measure to indicate the accuracy of our registration results. We derive a shift metric in order to select the Reference Image with Maximal Overlap (RIMO), in turn minimizing the total amount of non-overlapping signal for a given number of tags. Experimental results show that the Robust Alignment of Multi-Tag Bioimages (RAMTaB) framework is robust to variations in contrast and illumination, yields sub-pixel accuracy, and successfully selects the reference image resulting in maximum overlap. The registration results are also shown to significantly improve any follow-up protein co-localization studies. CONCLUSIONS: For the discovery of protein complexes and of functional protein networks within a cell, alignment of the tag images in a multi-tag fluorescence image stack is a key pre-processing step. The proposed framework is shown to produce accurate alignment results on both real and synthetic data. Our future work will use the aligned multi-channel fluorescence image data for normal and diseased tissue specimens to analyze molecular co-expression patterns and functional protein networks.","corpus_id":2098029,"score":0},{"doc_id":"22393363","title":"Path curvature discrimination: dependence on gaze direction and optical flow speed.","abstract":"Many experimental approaches to the control of steering rely on the tangent point (TP) as major source of information. The TP is a good candidate to control self-motion. It corresponds to a singular and salient point in the subject's visual field, and its location depends on the road geometry, the direction of self-motion relative to the road and the position of the driver on the road. However, the particular status of the TP in the optical flow, as a local minimum of flow speed, has often been left aside. We therefore assume that the TP is actually an optimal location in the dynamic optical array to perceive a change in the trajectory curvature. In this study, we evaluated the ability of human observers to detect variations in their path curvature from optical flow patterns, as a function of their gaze direction in a virtual environment. We simulated curvilinear self-motion parallel to a ground plane. Using random-dot optic flow stimuli of brief duration and a two-alternative forced-choice adaptive procedure, we determined path curvature discrimination thresholds, as a function of gaze direction. The discrimination thresholds are minimal for a gaze directed toward a local minimum of optical flow speed. A model based on Weber fraction of the foveal velocities (ΔV/V) correctly predicts the relationship between experimental thresholds and local flow velocities. This model was also tested for an optical flow computation integrating larger circular areas in central vision. Averaging the flow over five degrees leads to an even better fit of the model to experimental thresholds. We also found that the minimal optical flow speed direction corresponds to a maximal sensitivity of the visual system, as predicted by our model. The spontaneous gazing strategies observed during driving might thus correspond to an optimal selection of relevant information in the optical flow field.","corpus_id":8739397,"score":0},{"doc_id":"22411045","title":"Robust real-time-constrained estimation of respiratory motion for interventional MRI on mobile organs.","abstract":"Real-time magnetic resonance imaging is a promising tool for image-guided interventions. For applications such as thermotherapy on moving organs, a precise image-based compensation of motion is required in real time to allow quantitative analysis, retrocontrol of the interventional device, or determination of the therapy endpoint. Reduced field-of-view imaging represents a promising way to improve spatial and/or temporal resolution. However, it introduces new challenges for target motion estimation, since structures near the target may appear transiently due to the respiratory motion and the limited spatial coverage. In this paper, a new image-based motion estimation method is proposed combining a global motion estimation with a novel optical flow approach extending the initial Horn and Schunck (H&S) method by an additional regularization term. This term integrates the displacement of physiological landmarks into the variational formulation of the optical flow problem. This allowed for a better control of the optical flow in presence of transient structures. The method was compared to the same registration pipeline employing the H&S approach on a synthetic dataset and in vivo image sequences. Compared to the H&S approach, a significant improvement (p<0.05) of the Dice's similarity criterion computed between the reference and the registered organ positions was achieved.","corpus_id":14830896,"score":0},{"doc_id":"23242263","title":"Fast and robust optical flow for time-lapse microscopy using super-voxels.","abstract":"MOTIVATION: Optical flow is a key method used for quantitative motion estimation of biological structures in light microscopy. It has also been used as a key module in segmentation and tracking systems and is considered a mature technology in the field of computer vision. However, most of the research focused on 2D natural images, which are small in size and rich in edges and texture information. In contrast, 3D time-lapse recordings of biological specimens comprise up to several terabytes of image data and often exhibit complex object dynamics as well as blurring due to the point-spread-function of the microscope. Thus, new approaches to optical flow are required to improve performance for such data. RESULTS: We solve optical flow in large 3D time-lapse microscopy datasets by defining a Markov random field (MRF) over super-voxels in the foreground and applying motion smoothness constraints between super-voxels instead of voxel-wise. This model is tailored to the specific characteristics of light microscopy datasets: super-voxels help registration in textureless areas, the MRF over super-voxels efficiently propagates motion information between neighboring cells and the background subtraction and super-voxels reduce the dimensionality of the problem by an order of magnitude. We validate our approach on large 3D time-lapse datasets of Drosophila and zebrafish development by analyzing cell motion patterns. We show that our approach is, on average, 10 × faster than commonly used optical flow implementations in the Insight Tool-Kit (ITK) and reduces the average flow end point error by 50% in regions with complex dynamic processes, such as cell divisions. AVAILABILITY: Source code freely available in the Software section at http://janelia.org/lab/keller-lab.","corpus_id":9589582,"score":0},{"doc_id":"23261401","title":"FASTDEF: fast defocus and astigmatism estimation for high-throughput transmission electron microscopy.","abstract":"In this work we present a fast and automated algorithm for estimating the contrast transfer function (CTF) of a transmission electron microscope. The approach is very suitable for High Throughput work because: (a) it does not require any initial defocus estimation, (b) it is almost an order of magnitude faster than existing approaches, (c) it opens the way to well-defined extensions to the estimation of higher order aberrations, at the same time that provides defocus and astigmatism estimations comparable in accuracy to well established methods, such as Xmipp and CTFFIND3 approaches. The new algorithm is based on obtaining the wrapped modulating phase of the power spectra density pattern by the use of a quadrature filter. This phase is further unwrapped in order to obtain the continuous and smooth absolute phase map; then a Zernike polynomial fitting is performed and the defocus and astigmatism parameters are determined. While the method does not require an initial estimation of the defocus parameters or any non-linear optimization procedure, these approaches can be used if further refinement is desired. Results of the CTF estimation method are presented for standard negative stained images, cryo-electron microscopy images in the absence of carbon support, as well as micrographs with only ice. Additionally, we have also tested the proposed method with micrographs acquired from tilted and untilted samples, obtaining good results. The algorithm is freely available as a part of the Xmipp package [http://xmipp.cnb.csic.es].","corpus_id":9415778,"score":0},{"doc_id":"23523719","title":"Fast and accurate reference-free alignment of subtomograms.","abstract":"In cryoelectron tomography alignment and averaging of subtomograms, each dnepicting the same macromolecule, improves the resolution compared to the individual subtomogram. Major challenges of subtomogram alignment are noise enhancement due to overfitting, the bias of an initial reference in the iterative alignment process, and the computational cost of processing increasingly large amounts of data. Here, we propose an efficient and accurate alignment algorithm via a generalized convolution theorem, which allows computation of a constrained correlation function using spherical harmonics. This formulation increases computational speed of rotational matching dramatically compared to rotation search in Cartesian space without sacrificing accuracy in contrast to other spherical harmonic based approaches. Using this sampling method, a reference-free alignment procedure is proposed to tackle reference bias and overfitting, which also includes contrast transfer function correction by Wiener filtering. Application of the method to simulated data allowed us to obtain resolutions near the ground truth. For two experimental datasets, ribosomes from yeast lysate and purified 20S proteasomes, we achieved reconstructions of approximately 20Å and 16Å, respectively. The software is ready-to-use and made public to the community.","corpus_id":26641993,"score":0},{"doc_id":"23537496","title":"3D imaging of flow patterns in an internally-pumped microfluidic device: redox magnetohydrodynamics and electrochemically-generated density gradients.","abstract":"Redox magnetohydrodynamics (MHD) is a promising technique for developing new electrochemical-based microfluidic flow devices with unique capabilities, such as easily switching flow direction and adjusting flow speeds and flow patterns as well as avoiding bubble formation. However, a detailed description of all the forces involved and predicting flow patterns in confined geometries is lacking. In addition to redox-MHD, density gradients caused by the redox reactions also play important roles. Flow in these devices with small fluid volumes has mainly been characterized by following microbead motion by optical microscopy either by particle tracking velocimetry (PTV) or by processing the microbead images by particle image velocimetry (PIV) software. This approach has limitations in spatial resolution and dimensionality. Here we use fluorescence correlation spectroscopy (FCS) to quantitatively and accurately measure flow speeds and patterns in the ~5-50 μm/s range in redox-MHD-based microfluidic devices, from which 3D flow maps are obtained with a spatial resolution down to 2 μm. The 2 μm spatial resolution flow speeds map revealed detailed flow profiles during redox-MHD in which the velocity increases linearly from above the electrode and reaches a plateau across the center of the cell. By combining FCS and video-microscopy (with PTV and PIV processing approaches), we are able to quantify a vertical flow of ~10 μm/s above the electrodes as a result of density gradients caused by the redox reactions and follow convection flow patterns. Overall, combining FCS, PIV, and PTV analysis of redox-MHD is a powerful combination to more thoroughly characterize the underlying forces in these promising microfluidic devices.","corpus_id":44437844,"score":0},{"doc_id":"23613042","title":"Optical flow estimation for flame detection in videos.","abstract":"Computational vision-based flame detection has drawn significant attention in the past decade with camera surveillance systems becoming ubiquitous. Whereas many discriminating features, such as color, shape, texture, etc., have been employed in the literature, this paper proposes a set of motion features based on motion estimators. The key idea consists of exploiting the difference between the turbulent, fast, fire motion, and the structured, rigid motion of other objects. Since classical optical flow methods do not model the characteristics of fire motion (e.g., non-smoothness of motion, non-constancy of intensity), two optical flow methods are specifically designed for the fire detection task: optimal mass transport models fire with dynamic texture, while a data-driven optical flow scheme models saturated flames. Then, characteristic features related to the flow magnitudes and directions are computed from the flow fields to discriminate between fire and non-fire motion. The proposed features are tested on a large video database to demonstrate their practical usefulness. Moreover, a novel evaluation method is proposed by fire simulations that allow for a controlled environment to analyze parameter influences, such as flame saturation, spatial resolution, frame rate, and random noise.","corpus_id":11840275,"score":0},{"doc_id":"23799696","title":"A decoupled approach to illumination-robust optical flow estimation.","abstract":"Despite continuous improvements in optical flow in the last three decades, the ability for optical flow algorithms to handle illumination variation is still an unsolved challenge. To improve the ability to interpret apparent object motion in video containing illumination variation, an illumination-robust optical flow method is designed. This method decouples brightness into reflectance and illumination components using a stochastic technique; reflectance is given higher weight to ensure robustness against illumination, which is suppressed. Illumination experiments using the Middlebury and University of Oulu databases demonstrate the decoupled method's improvement when compared with state-of-the-art. In addition, a novel technique is implemented to visualize optical flow output, which is especially useful to compare different optical flow methods in the absence of the ground truth.","corpus_id":6269043,"score":0},{"doc_id":"23933392","title":"Particle quality assessment and sorting for automatic and semiautomatic particle-picking techniques.","abstract":"Three-dimensional reconstruction of biological specimens using electron microscopy by single particle methodologies requires the identification and extraction of the imaged particles from the acquired micrographs. Automatic and semiautomatic particle selection approaches can localize these particles, minimizing the user interaction, but at the cost of selecting a non-negligible number of incorrect particles, which can corrupt the final three-dimensional reconstruction. In this work, we present a novel particle quality assessment and sorting method that can separate most erroneously picked particles from correct ones. The proposed method is based on multivariate statistical analysis of a particle set that has been picked previously using any automatic or manual approach. The new method uses different sets of particle descriptors, which are morphology-based, histogram-based and signal to noise analysis based. We have tested our proposed algorithm with experimental data obtaining very satisfactory results. The algorithm is freely available as a part of the Xmipp 3.0 package [http://xmipp.cnb.csic.es].","corpus_id":7094288,"score":0},{"doc_id":"23958728","title":"A pattern matching approach to the automatic selection of particles from low-contrast electron micrographs.","abstract":"MOTIVATION: Structural information of macromolecular complexes provides key insights into the way they carry out their biological functions. Achieving high-resolution structural details with electron microscopy requires the identification of a large number (up to hundreds of thousands) of single particles from electron micrographs, which is a laborious task if it has to be manually done and constitutes a hurdle towards high-throughput. Automatic particle selection in micrographs is far from being settled and new and more robust algorithms are required to reduce the number of false positives and false negatives. RESULTS: In this article, we introduce an automatic particle picker that learns from the user the kind of particles he is interested in. Particle candidates are quickly and robustly classified as particles or non-particles. A number of new discriminative shape-related features as well as some statistical description of the image grey intensities are used to train two support vector machine classifiers. Experimental results demonstrate that the proposed method: (i) has a considerably low computational complexity and (ii) provides results better or comparable with previously reported methods at a fraction of their computing time. AVAILABILITY: The algorithm is fully implemented in the open-source Xmipp package and downloadable from http://xmipp.cnb.csic.es.","corpus_id":11199882,"score":0},{"doc_id":"24213166","title":"Quantifying the local resolution of cryo-EM density maps.","abstract":"We propose a definition of local resolution for three-dimensional electron cryo-microscopy (cryo-EM) density maps that uses local sinusoidal features. Our algorithm has no free parameters and is applicable to other imaging modalities, including tomography. By evaluating the local resolution of single-particle reconstructions and subtomogram averages for four example data sets, we report variable resolution across a 4- to 40-Å range.","corpus_id":13250075,"score":0},{"doc_id":"24269484","title":"Fabrication of carbon films with ∼ 500nm holes for cryo-EM with a direct detector device.","abstract":"Single particle electron cryomicroscopy (cryo-EM) is often performed using EM grids coated with a perforated or holey layer of amorphous carbon. Regular arrays of holes enable efficient cryo-EM data collection and several methods for the production of micropatterned holey-carbon film coated grids have been described. However, a new generation of direct detector device (DDD) electron microscope cameras can benefit from hole diameters that are smaller than currently available. Here we extend a previously proposed method involving soft lithography with a poly(dimethylsiloxane) (PDMS) stamp for the production of holey-carbon film coated EM grids. By incorporating electron-beam (e-beam) lithography and modifying the procedure, we are able to produce low-cost high-quality holey-carbon film coated EM grids with ∼500nm holes spaced 4μm apart centre-to-centre. We demonstrate that these grids can be used for cryo-EM. Furthermore, we show that by applying image shifts to obtain movies of the carbon regions beside the holes after imaging the holes, the contrast transfer function (CTF) parameters needed for calculation of high-resolution cryo-EM maps with a DDD can be obtained efficiently.","corpus_id":32465812,"score":0},{"doc_id":"24569482","title":"Atomic model of the F420-reducing [NiFe] hydrogenase by electron cryo-microscopy using a direct electron detector.","abstract":"The introduction of direct electron detectors with higher detective quantum efficiency and fast read-out marks the beginning of a new era in electron cryo-microscopy. Using the FEI Falcon II direct electron detector in video mode, we have reconstructed a map at 3.36 Å resolution of the 1.2 MDa F420-reducing hydrogenase (Frh) from methanogenic archaea from only 320,000 asymmetric units. Videos frames were aligned by a combination of image and particle alignment procedures to overcome the effects of beam-induced motion. The reconstructed density map shows all secondary structure as well as clear side chain densities for most residues. The full coordination of all cofactors in the electron transfer chain (a [NiFe] center, four [4Fe4S] clusters and an FAD) is clearly visible along with a well-defined substrate access channel. From the rigidity of the complex we conclude that catalysis is diffusion-limited and does not depend on protein flexibility or conformational changes. DOI: http://dx.doi.org/10.7554/eLife.01963.001.","corpus_id":16176308,"score":0},{"doc_id":"24751405","title":"Cortical responses to optic flow and motion contrast across patterns and speeds.","abstract":"Motion provides animals with fast and robust cues for navigation and object detection. In the first case, stereotyped patterns of optic flow inform a moving observer about the direction and speed of its own movement. In the case of object detection, regional differences in motion allow for the segmentation of figures from their background, even in the absence of color or shading cues. Previous research has investigated human electrophysiological responses to global motion across speeds, but only focused upon one type of optic flow pattern. Here, we compared steady-state visual evoked potential (SSVEP) responses across patterns and speeds, both for optic flow and for motion-defined figure patterns, to assess the extent to which the processes are pattern-general or pattern-specific. For optic flow, pattern and speed effects on response amplitudes varied substantially across channels, suggesting pattern-specific processing at slow speeds and pattern-general activity at fast speeds. Responses for coherence- and direction-defined figures were comparatively more uniform, with similar response profiles and spatial distributions. Self- and object-motion patterns activate some of the same circuits, but these data suggest differential sensitivity: not only across the two classes of motion, but also across the patterns within each class, and across speeds. Thus, the results demonstrate that cortical processing of global motion is complex and activates a distributed network.","corpus_id":18185547,"score":0},{"doc_id":"25268657","title":"Hybrid Electron Microscopy Normal Mode Analysis graphical interface and protocol.","abstract":"This article presents an integral graphical interface to the Hybrid Electron Microscopy Normal Mode Analysis (HEMNMA) approach that was developed for capturing continuous motions of large macromolecular complexes from single-particle EM images. HEMNMA was shown to be a good approach to analyze multiple conformations of a macromolecular complex but it could not be widely used in the EM field due to a lack of an integral interface. In particular, its use required switching among different software sources as well as selecting modes for image analysis was difficult without the graphical interface. The graphical interface was thus developed to simplify the practical use of HEMNMA. It is implemented in the open-source software package Xmipp 3.1 (http://xmipp.cnb.csic.es) and only a small part of it relies on MATLAB that is accessible through the main interface. Such integration provides the user with an easy way to perform the analysis of macromolecular dynamics and forms a direct connection to the single-particle reconstruction process. A step-by-step HEMNMA protocol with the graphical interface is given in full details in Supplementary material. The graphical interface will be useful to experimentalists who are interested in studies of continuous conformational changes of macromolecular complexes beyond the modeling of continuous heterogeneity in single particle reconstruction.","corpus_id":13918346,"score":0},{"doc_id":"25528571","title":"Seeing tobacco mosaic virus through direct electron detectors.","abstract":"With the introduction of direct electron detectors (DED) to the field of electron cryo-microscopy, a wave of atomic-resolution structures has become available. As the new detectors still require comparative characterization, we have used tobacco mosaic virus (TMV) as a test specimen to study the quality of 3D image reconstructions from data recorded on the two direct electron detector cameras, K2 Summit and Falcon II. Using DED movie frames, we explored related image-processing aspects and compared the performance of micrograph-based and segment-based motion correction approaches. In addition, we investigated the effect of dose deposition on the atomic-resolution structure of TMV and show that radiation damage affects negative carboxyl chains first in a side-chain specific manner. Finally, using 450,000 asymmetric units and limiting the effects of radiation damage, we determined a high-resolution cryo-EM map at 3.35Å resolution. Here, we provide a comparative case study of highly ordered TMV recorded on different direct electron detectors to establish recording and processing conditions that enable structure determination up to 3.2Å in resolution using cryo-EM.","corpus_id":20499036,"score":0},{"doc_id":"25570703","title":"Robust estimation for class averaging in cryo-EM Single Particle Reconstruction.","abstract":"Single Particle Reconstruction (SPR) for Cryogenic Electron Microscopy (cryo-EM) aligns and averages the images extracted from micrographs to improve the Signal-to-Noise ratio (SNR). Outliers compromise the fidelity of the averaging. We propose a robust cross-correlation-like w-estimator for combating the effect of outliers on the average images in cryo-EM. The estimator accounts for the natural variation of signal contrast among the images and eliminates the need for a threshold for outlier rejection. We show that the influence function of our estimator is asymptotically bounded. Evaluations of the estimator on simulated and real cryo-EM images show good performance in the presence of outliers.","corpus_id":8996078,"score":0},{"doc_id":"25637660","title":"A statistical approach to the initial volume problem in Single Particle Analysis by Electron Microscopy.","abstract":"Cryo Electron Microscopy is a powerful Structural Biology technique, allowing the elucidation of the three-dimensional structure of biological macromolecules. In particular, the structural study of purified macromolecules -often referred as Single Particle Analysis(SPA)- is normally performed through an iterative process that needs a first estimation of the three-dimensional structure that is progressively refined using experimental data. It is well-known the local optimisation nature of this refinement, so that the initial choice of this first structure may substantially change the final result. Computational algorithms aiming to providing this first structure already exist. However, the question is far from settled and more robust algorithms are still needed so that the refinement process can be performed with sufficient guarantees. In this article we present a new algorithm that addresses the initial volume problem in SPA by setting it in a Weighted Least Squares framework and calculating the weights through a statistical approach based on the cumulative density function of different image similarity measures. We show that the new algorithm is significantly more robust than other state-of-the-art algorithms currently in use in the field. The algorithm is available as part of the software suite Xmipp (http://xmipp.cnb.csic.es) and Scipion (http://scipion.cnb.csic.es) under the name \"Significant\".","corpus_id":15342000,"score":0},{"doc_id":"25941470","title":"On event-based optical flow detection.","abstract":"Event-based sensing, i.e., the asynchronous detection of luminance changes, promises low-energy, high dynamic range, and sparse sensing. This stands in contrast to whole image frame-wise acquisition by standard cameras. Here, we systematically investigate the implications of event-based sensing in the context of visual motion, or flow, estimation. Starting from a common theoretical foundation, we discuss different principal approaches for optical flow detection ranging from gradient-based methods over plane-fitting to filter based methods and identify strengths and weaknesses of each class. Gradient-based methods for local motion integration are shown to suffer from the sparse encoding in address-event representations (AER). Approaches exploiting the local plane like structure of the event cloud, on the other hand, are shown to be well suited. Within this class, filter based approaches are shown to define a proper detection scheme which can also deal with the problem of representing multiple motions at a single location (motion transparency). A novel biologically inspired efficient motion detector is proposed, analyzed and experimentally validated. Furthermore, a stage of surround normalization is incorporated. Together with the filtering this defines a canonical circuit for motion feature detection. The theoretical analysis shows that such an integrated circuit reduces motion ambiguity in addition to decorrelating the representation of motion related activations.","corpus_id":16638035,"score":0},{"doc_id":"25955078","title":"Cryo-electron microscopy and the amazing race to atomic resolution.","abstract":"Cryo-electron microscopy (cryo-EM), the structural analysis of samples embedded in vitreous ice, is a powerful approach for determining three-dimensional (3D) structures of biological specimens. Over the past two decades, this technique has been used to successfully calculate subnanometer (<10 Å) resolution and, in some cases, near-atomic resolution structures of highly symmetrical and stable complexes such as icosahedral viruses and ribosomes, as well as samples that form ordered two-dimensional or helical arrays. However, determining high-resolution 3D structures of smaller, less symmetrical, and dynamic samples remains a significant challenge. The recent development of electron microscopes with automated data collection capabilities and robust direct electron detection cameras, as well as new powerful image processing algorithms, has dramatically expanded the number of biological macromolecules amenable for study using cryo-EM. In addition, these new technological and computational developments have been used to successfully determine <5 Å resolution 3D structures of samples, such as membrane proteins and complexes with either low or no symmetry, that traditionally were not considered promising candidates for high-resolution cryo-EM. With these exciting new advances, cryo-EM is now on pace to determine atomic resolution 3D structures.","corpus_id":5180848,"score":0},{"doc_id":"27893394","title":"A Robust and Efficient Approach to License Plate Detection.","abstract":"This paper presents a robust and efficient method for license plate detection with the purpose of accurately localizing vehicle license plates from complex scenes in real time. A simple yet effective image downscaling method is first proposed to substantially accelerate license plate localization without sacrificing detection performance compared with that achieved using the original image. Furthermore, a novel line density filter approach is proposed to extract candidate regions, thereby significantly reducing the area to be analyzed for license plate localization. Moreover, a cascaded license plate classifier based on linear support vector machines using color saliency features is introduced to identify the true license plate from among the candidate regions. For performance evaluation, a data set consisting of 3977 images captured from diverse scenes under different conditions is also presented. Extensive experiments on the widely used Caltech license plate data set and our newly introduced data set demonstrate that the proposed approach substantially outperforms state-of-the-art methods in terms of both detection accuracy and run-time efficiency, increasing the detection ratio from 91.09% to 96.62% while decreasing the run time from 672 to 42 ms for processing an image with a resolution of 1082×728 . The executable code and our collected data set are publicly available.","corpus_id":17045780,"score":0},{"doc_id":"28109158","title":"Using the Volta phase plate with defocus for cryo-EM single particle analysis.","abstract":"Previously, we reported an in-focus data acquisition method for cryo-EM single-particle analysis with the Volta phase plate (Danev and Baumeister, 2016). Here, we extend the technique to include a small amount of defocus which enables contrast transfer function measurement and correction. This hybrid approach simplifies the experiment and increases the data acquisition speed. It also removes the resolution limit inherent to the in-focus method thus allowing 3D reconstructions with resolutions better than 3 Å.","corpus_id":7467768,"score":0},{"doc_id":"28732461","title":"A deep convolutional neural network approach to single-particle recognition in cryo-electron microscopy.","abstract":"BACKGROUND: Single-particle cryo-electron microscopy (cryo-EM) has become a mainstream tool for the structural determination of biological macromolecular complexes. However, high-resolution cryo-EM reconstruction often requires hundreds of thousands of single-particle images. Particle extraction from experimental micrographs thus can be laborious and presents a major practical bottleneck in cryo-EM structural determination. Existing computational methods for particle picking often use low-resolution templates for particle matching, making them susceptible to reference-dependent bias. It is critical to develop a highly efficient template-free method for the automatic recognition of particle images from cryo-EM micrographs. RESULTS: We developed a deep learning-based algorithmic framework, DeepEM, for single-particle recognition from noisy cryo-EM micrographs, enabling automated particle picking, selection and verification in an integrated fashion. The kernel of DeepEM is built upon a convolutional neural network (CNN) composed of eight layers, which can be recursively trained to be highly \"knowledgeable\". Our approach exhibits an improved performance and accuracy when tested on the standard KLH dataset. Application of DeepEM to several challenging experimental cryo-EM datasets demonstrated its ability to avoid the selection of un-wanted particles and non-particles even when true particles contain fewer features. CONCLUSIONS: The DeepEM methodology, derived from a deep CNN, allows automated particle extraction from raw cryo-EM micrographs in the absence of a template. It demonstrates an improved performance, objectivity and accuracy. Application of this novel method is expected to free the labor involved in single-particle verification, significantly improving the efficiency of cryo-EM data processing.","corpus_id":9763578,"score":0},{"doc_id":"29352317","title":"Optic flow detection is not influenced by visual-vestibular congruency.","abstract":"Optic flow patterns generated by self-motion relative to the stationary environment result in congruent visual-vestibular self-motion signals. Incongruent signals can arise due to object motion, vestibular dysfunction, or artificial stimulation, which are less common. Hence, we are predominantly exposed to congruent rather than incongruent visual-vestibular stimulation. If the brain takes advantage of this probabilistic association, we expect observers to be more sensitive to visual optic flow that is congruent with ongoing vestibular stimulation. We tested this expectation by measuring the motion coherence threshold, which is the percentage of signal versus noise dots, necessary to detect an optic flow pattern. Observers seated on a hexapod motion platform in front of a screen experienced two sequential intervals. One interval contained optic flow with a given motion coherence and the other contained noise dots only. Observers had to indicate which interval contained the optic flow pattern. The motion coherence threshold was measured for detection of laminar and radial optic flow during leftward/rightward and fore/aft linear self-motion, respectively. We observed no dependence of coherence thresholds on vestibular congruency for either radial or laminar optic flow. Prior studies using similar methods reported both decreases and increases in coherence thresholds in response to congruent vestibular stimulation; our results do not confirm either of these prior reports. While methodological differences may explain the diversity of results, another possibility is that motion coherence thresholds are mediated by neural populations that are either not modulated by vestibular stimulation or that are modulated in a manner that does not depend on congruency.","corpus_id":3587693,"score":0},{"doc_id":"29400760","title":"Alignment of sensor arrays in optical instruments using a geometric approach.","abstract":"Alignment of sensor arrays in optical instruments is critical to maximize the instrument's performance. While many commercial systems use standardized mounting threads for alignment, custom systems require specialized equipment and alignment procedures. These alignment procedures can be time-consuming, dependent on operator experience, and have low repeatability. Furthermore, each alignment solution must be considered on a case-by-case basis, leading to additional time and resource cost. Here I present a method to align a sensor array using geometric analysis. By imaging a grid pattern of dots, I show that it is possible to calculate the misalignment for a sensor in five degrees of freedom simultaneously. I first test the approach by simulating different cases of misalignment using Zemax before applying the method to experimentally acquired data of sensor misalignment for an echelle spectrograph. The results show that the algorithm effectively quantifies misalignment in five degrees of freedom for an F/5 imaging system, accurate to within ±0.87 deg in rotation and ±0.86 μm in translation. Furthermore, the results suggest that the method can also be applied to non-imaging systems with a small penalty to precision. This general approach can potentially improve the alignment of sensor arrays in custom instruments by offering an accurate, quantitative approach to calculating misalignment in five degrees of freedom simultaneously.","corpus_id":46861650,"score":0},{"doc_id":"29607548","title":"Motion-robust sub-millimeter isotropic diffusion imaging through motion corrected generalized slice dithered enhanced resolution (MC-gSlider) acquisition.","abstract":"PURPOSE: To develop an efficient MR technique for ultra-high resolution diffusion MRI (dMRI) in the presence of motion. METHODS: gSlider is an SNR-efficient high-resolution dMRI acquisition technique. However, subject motion is inevitable during a prolonged scan for high spatial resolution, leading to potential image artifacts and blurring. In this study, an integrated technique termed Motion Corrected gSlider (MC-gSlider) is proposed to obtain high-quality, high-resolution dMRI in the presence of large in-plane and through-plane motion. A motion-aware reconstruction with spatially adaptive regularization is developed to optimize the conditioning of the image reconstruction under difficult through-plane motion cases. In addition, an approach for intra-volume motion estimation and correction is proposed to achieve motion correction at high temporal resolution. RESULTS: Theoretical SNR and resolution analysis validated the efficiency of MC-gSlider with regularization, and aided in selection of reconstruction parameters. Simulations and in vivo experiments further demonstrated the ability of MC-gSlider to mitigate motion artifacts and recover detailed brain structures for dMRI at 860 μm isotropic resolution in the presence of motion with various ranges. CONCLUSION: MC-gSlider provides motion-robust, high-resolution dMRI with a temporal motion correction sensitivity of 2 s, allowing for the recovery of fine detailed brain structures in the presence of large subject movements.","corpus_id":4663910,"score":0}],"string":"[\n {\n \"doc_id\": \"22155955\",\n \"title\": \"Locally oriented optical flow computation.\",\n \"abstract\": \"This paper proposes the use of an adaptive locally oriented coordinate frame when calculating an optical flow field. The coordinate frame is aligned with the least curvature direction in a local window about each pixel. This has advantages to both fitting the flow field to the image data and in imposing smoothness constraints between neighboring pixels. In terms of fitting, robustness is obtained to a wider variety of image motions due to the extra invariance provided by the coordinate frame. Smoothness constraints are naturally propagated along image boundaries which often correspond to motion boundaries. In addition, moving objects can be efficiently segmented in the least curvature direction. We show experimentally the benefits of the method and demonstrate robustness to fast rotational motion, such as what often occurs in human motion.\",\n \"corpus_id\": 16414857,\n \"score\": 2\n },\n {\n \"doc_id\": \"23022349\",\n \"title\": \"Movies of ice-embedded particles enhance resolution in electron cryo-microscopy.\",\n \"abstract\": \"Low-dose images obtained by electron cryo-microscopy (cryo-EM) are often affected by blurring caused by sample motion during electron beam exposure, degrading signal especially at high resolution. We show here that we can align frames of movies, recorded with a direct electron detector during beam exposure of rotavirus double-layered particles, thereby greatly reducing image blurring caused by beam-induced motion and sample stage instabilities. This procedure increases the efficiency of cryo-EM imaging and enhances the resolution obtained in three-dimensional reconstructions of the particle. Using movies in this way is generally applicable to all cryo-EM samples and should also improve the performance of midrange electron microscopes that may have limited mechanical stability and beam coherence.\",\n \"corpus_id\": 15260039,\n \"score\": 2\n },\n {\n \"doc_id\": \"23254656\",\n \"title\": \"Non-rigid image registration to reduce beam-induced blurring of cryo-electron microscopy images.\",\n \"abstract\": \"The typical dose used to record cryo-electron microscopy images from vitrified biological specimens is so high that radiation-induced structural alterations are bound to occur during data acquisition. Integration of all scattered electrons into one image can lead to significant blurring, particularly if the data are collected from an unsupported thin layer of ice suspended over the holes of a support film. Here, the dose has been fractioned and exposure series have been acquired in order to study beam-induced specimen movements under low dose conditions, prior to bubbling. Gold particles were added to the protein sample as fiducial markers. These were automatically localized and tracked throughout the exposure series and showed correlated motions within small patches, with larger amplitudes of motion vectors at the start of a series compared with the end of each series. A non-rigid scheme was used to register all images within each exposure series, using natural neighbor interpolation with the gold particles as anchor points. The procedure increases the contrast and resolution of the examined macromolecules.\",\n \"corpus_id\": 15509596,\n \"score\": 2\n },\n {\n \"doc_id\": \"23644547\",\n \"title\": \"Electron counting and beam-induced motion correction enable near-atomic-resolution single-particle cryo-EM.\",\n \"abstract\": \"In recent work with large high-symmetry viruses, single-particle electron cryomicroscopy (cryo-EM) has achieved the determination of near-atomic-resolution structures by allowing direct fitting of atomic models into experimental density maps. However, achieving this goal with smaller particles of lower symmetry remains challenging. Using a newly developed single electron-counting detector, we confirmed that electron beam-induced motion substantially degrades resolution, and we showed that the combination of rapid readout and nearly noiseless electron counting allow image blurring to be corrected to subpixel accuracy, restoring intrinsic image information to high resolution (Thon rings visible to ∼3 Å). Using this approach, we determined a 3.3-Å-resolution structure of an ∼700-kDa protein with D7 symmetry, the Thermoplasma acidophilum 20S proteasome, showing clear side-chain density. Our method greatly enhances image quality and data acquisition efficiency-key bottlenecks in applying near-atomic-resolution cryo-EM to a broad range of protein samples.\",\n \"corpus_id\": 2313269,\n \"score\": 2\n },\n {\n \"doc_id\": \"25020094\",\n \"title\": \"Robust optical flow integration.\",\n \"abstract\": \"We analyze the problem of how to correctly construct dense point trajectories from optical flow fields. First, we show that simple Euler integration is unavoidably inaccurate, no matter how good is the optical flow estimator. Then, an inverse integration scheme is analyzed which is more robust to bias and input noise and shows better stability properties. Our contribution is threefold: 1) a theoretical analysis that demonstrates why and in what sense inverse integration is more accurate; 2) a rich experimental validation both on synthetic and real (image) data; and 3) an algorithm for approximate online inverse integration. This new technique is precious whether one is trying to propagate information densely available on a reference frame to the other frames in the sequence or, conversely, to assign information densely over each frame by pulling it from the reference.\",\n \"corpus_id\": 15285720,\n \"score\": 2\n },\n {\n \"doc_id\": \"25122622\",\n \"title\": \"Beam-induced motion correction for sub-megadalton cryo-EM particles.\",\n \"abstract\": \"In electron cryo-microscopy (cryo-EM), the electron beam that is used for imaging also causes the sample to move. This motion blurs the images and limits the resolution attainable by single-particle analysis. In a previous Research article (Bai et al., 2013) we showed that correcting for this motion by processing movies from fast direct-electron detectors allowed structure determination to near-atomic resolution from 35,000 ribosome particles. In this Research advance article, we show that an improved movie processing algorithm is applicable to a much wider range of specimens. The new algorithm estimates straight movement tracks by considering multiple particles that are close to each other in the field of view, and models the fall-off of high-resolution information content by radiation damage in a dose-dependent manner. Application of the new algorithm to four data sets illustrates its potential for significantly improving cryo-EM structures, even for particles that are smaller than 200 kDa.\",\n \"corpus_id\": 12574480,\n \"score\": 2\n },\n {\n \"doc_id\": \"26296328\",\n \"title\": \"Alignment of cryo-EM movies of individual particles by optimization of image translations.\",\n \"abstract\": \"Direct detector device (DDD) cameras have revolutionized single particle electron cryomicroscopy (cryo-EM). In addition to an improved camera detective quantum efficiency, acquisition of DDD movies allows for correction of movement of the specimen, due to both instabilities in the microscope specimen stage and electron beam-induced movement. Unlike specimen stage drift, beam-induced movement is not always homogeneous within an image. Local correlation in the trajectories of nearby particles suggests that beam-induced motion is due to deformation of the ice layer. Algorithms have already been described that can correct movement for large regions of frames and for >1MDa protein particles. Another algorithm allows individual <1MDa protein particle trajectories to be estimated, but requires rolling averages to be calculated from frames and fits linear trajectories for particles. Here we describe an algorithm that allows for individual <1MDa particle images to be aligned without frame averaging or linear trajectories. The algorithm maximizes the overall correlation of the shifted frames with the sum of the shifted frames. The optimum in this single objective function is found efficiently by making use of analytically calculated derivatives of the function. To smooth estimates of particle trajectories, rapid changes in particle positions between frames are penalized in the objective function and weighted averaging of nearby trajectories ensures local correlation in trajectories. This individual particle motion correction, in combination with weighting of Fourier components to account for increasing radiation damage in later frames, can be used to improve 3-D maps from single particle cryo-EM.\",\n \"corpus_id\": 17501197,\n \"score\": 2\n },\n {\n \"doc_id\": \"27016144\",\n \"title\": \"Methods to account for movement and flexibility in cryo-EM data processing.\",\n \"abstract\": \"Recent advances in direct electron detectors and improved CMOS cameras have been accompanied by the development of a range of software to take advantage of the data they produce. In particular they allow for the correction of two types of motion in cryo electron microscopy samples: motion correction for movements of the sample particles in the ice, and differential masking to account for heterogeneity caused by flexibility within protein complexes. Here we provide several scripts that allow users to move between RELION and standalone motion correction and centring programs. We then compare the computational cost and improvements in data quality with each program. We also describe our masking procedures to account for conformational flexibility. For the different elements of this study we have used three samples; a high symmetry virus, flexible protein complex (∼1MDa) and a relatively small protein complex (∼550kDa), to benchmark four widely available motion correction packages. Using these as test cases we demonstrate how motion correction and differential masking, as well as an additional particle re-centring protocol can improve final reconstructions when used within the RELION image-processing package.\",\n \"corpus_id\": 3557048,\n \"score\": 2\n },\n {\n \"doc_id\": \"27016284\",\n \"title\": \"Alignment algorithms and per-particle CTF correction for single particle cryo-electron tomography.\",\n \"abstract\": \"Single particle cryo-electron tomography (cryoSPT) extracts features from cryo-electron tomograms, followed by 3D classification, alignment and averaging to generate improved 3D density maps of such features. Robust methods to correct for the contrast transfer function (CTF) of the electron microscope are necessary for cryoSPT to reach its resolution potential. Many factors can make CTF correction for cryoSPT challenging, such as lack of eucentricity of the specimen stage, inherent low dose per image, specimen charging, beam-induced specimen motions, and defocus gradients resulting both from specimen tilting and from unpredictable ice thickness variations. Current CTF correction methods for cryoET make at least one of the following assumptions: that the defocus at the center of the image is the same across the images of a tiltseries, that the particles all lie at the same Z-height in the embedding ice, and/or that the specimen, the cryo-electron microscopy (cryoEM) grid and/or the carbon support are flat. These experimental conditions are not always met. We have developed a CTF correction algorithm for cryoSPT without making any of the aforementioned assumptions. We also introduce speed and accuracy improvements and a higher degree of automation to the subtomogram averaging algorithms available in EMAN2. Using motion-corrected images of isolated virus particles as a benchmark specimen, recorded with a DE20 direct detection camera, we show that our CTF correction and subtomogram alignment routines can yield subtomogram averages close to 4/5 Nyquist frequency of the detector under our experimental conditions.\",\n \"corpus_id\": 3934913,\n \"score\": 2\n },\n {\n \"doc_id\": \"27572722\",\n \"title\": \"Specimen Behavior in the Electron Beam.\",\n \"abstract\": \"It has long been known that cryo-EM specimens are severely damaged by a level of electron exposure that is much lower than what is needed to obtain high-resolution images from single macromolecules. Perhaps less well appreciated in the cryo-EM literature, the vitreous ice in which samples are suspended is equally sensitivity to radiation damage. This chapter provides a review of several fundamental topics such as inelastic scattering of electrons, radiation chemistry, and radiation biology, which-together-can help one to understand why radiation damage occurs so \\\"easily.\\\" This chapter also addresses the issue of beam-induced motion that occurs at even lower levels of electron exposure. While specimen charging may be a contributor to this motion, it is argued that both radiation-induced relief of preexisting stress and damage-induced generation of additional stress may be the dominant causes of radiation-induced movement.\",\n \"corpus_id\": 3580735,\n \"score\": 2\n },\n {\n \"doc_id\": \"18054249\",\n \"title\": \"Applications of direct detection device in transmission electron microscopy.\",\n \"abstract\": \"A prototype direct detection device (DDD) camera system has shown great promise in improving both the spatial resolution and the signal to noise ratio for electron microscopy at 120-400 keV beam energies (Xuong et al., 2007. Methods in Cell Biology, 79, 721-739). Without the need for a resolution-limiting scintillation screen as in the charge coupled device (CCD), the DDD camera can outperform CCD based systems in terms of spatial resolution, due to its small pixel size (5 microm). In this paper, the modulation transfer function (MTF) of the DDD prototype is measured and compared with the specifications of commercial scientific CCD camera systems. Combining the fast speed of the DDD with image mosaic techniques, fast wide-area imaging is now possible. In this paper, the first large area mosaic image and the first tomography dataset from the DDD camera are presented, along with an image processing algorithm to correct the specimen drift utilizing the fast readout of the DDD system.\",\n \"corpus_id\": 46631247,\n \"score\": 1\n },\n {\n \"doc_id\": \"19378279\",\n \"title\": \"Optical flow approaches to the identification of brain dynamics.\",\n \"abstract\": \"The superior temporal resolution of magneto- and electroencephalography (MEEG) provides unique insight into the dynamics of brain function. The analysis of the spatial dimensions of MEEG recordings can take a multiplicity of approaches: from the original scalp recordings to the identification of their generators through localizing or imaging techniques. Overall, both MEEG native or imaging data may be considered as multidimensional structures with potentially dense information contents. Quantitative analysis of the spatiotemporal flow of information conveyed by MEEG begins with a feature-extraction problem, thereby leading to improved insight in the multidimensional structure of brain dynamics. In this contribution, we approach this endeavor by suggesting that brain dynamic features from local through global spatial scales may be identified using the previously-introduced technique of surface-based optical flow. We illustrate this assertion by the quantitative analysis of time-resolved sequences of brain activity through the identification of episodes of relative topographical stability. In that respect, we revisit the concept of brain microstates with a new approach and distinct operational hypotheses. Local dynamic features from a variety of brain systems may also be explored through this methodology, as illustrated by experimental data on fast responses in the visual system as revealed by MEEG source imaging.\",\n \"corpus_id\": 19140799,\n \"score\": 1\n },\n {\n \"doc_id\": \"21575566\",\n \"title\": \"Reaching the information limit in cryo-EM of biological macromolecules: experimental aspects.\",\n \"abstract\": \"Although cryo-electron microscopy (cryo-EM) of biological macromolecules has made important advances in the past few years, the level of current technical performance is still well below what the physics of electron scattering would allow. It should be possible, for example, to use cryo-EM to solve protein structures at atomic resolution for particle sizes well below 80 kDa, but currently this has been achieved only for particles at least 10 times larger than that. In this review, we first examine some of the reasons for this large gap in performance. We then give an overview of work that is currently in progress to 1), improve the signal/noise ratio for area detectors; 2), improve the signal transfer between the scattered electrons and the corresponding images; and 3), reduce the extent to which beam-induced movement causes a steep fall-off of signal at high resolution. In each case, there is substantial reason to think that cryo-EM can indeed be made to approach the estimated physical limits.\",\n \"corpus_id\": 19832292,\n \"score\": 1\n },\n {\n \"doc_id\": \"22167624\",\n \"title\": \"Bayesian inference of models and hyperparameters for robust optical-flow estimation.\",\n \"abstract\": \"Selecting optimal models and hyperparameters is crucial for accurate optical-flow estimation. This paper provides a solution to the problem in a generic Bayesian framework. The method is based on a conditional model linking the image intensity function, the unknown velocity field, hyperparameters, and the prior and likelihood motion models. Inference is performed on each of the three levels of this so-defined hierarchical model by maximization of marginalized a posteriori probability distribution functions. In particular, the first level is used to achieve motion estimation in a classical a posteriori scheme. By marginalizing out the motion variable, the second level enables to infer regularization coefficients and hyperparameters of non-Gaussian M-estimators commonly used in robust statistics. The last level of the hierarchy is used for selection of the likelihood and prior motion models conditioned to the image data. The method is evaluated on image sequences of fluid flows and from the \\\"Middlebury\\\" database. Experiments prove that applying the proposed inference strategy yields better results than manually tuning smoothing parameters or discontinuity preserving cost functions of the state-of-the-art methods.\",\n \"corpus_id\": 260973284,\n \"score\": 1\n },\n {\n \"doc_id\": \"23454482\",\n \"title\": \"Automatic post-picking using MAPPOS improves particle image detection from cryo-EM micrographs.\",\n \"abstract\": \"Cryo-electron microscopy (cryo-EM) studies using single particle reconstruction are extensively used to reveal structural information on macromolecular complexes. Aiming at the highest achievable resolution, state of the art electron microscopes automatically acquire thousands of high-quality micrographs. Particles are detected on and boxed out from each micrograph using fully- or semi-automated approaches. However, the obtained particles still require laborious manual post-picking classification, which is one major bottleneck for single particle analysis of large datasets. We introduce MAPPOS, a supervised post-picking strategy for the classification of boxed particle images, as additional strategy adding to the already efficient automated particle picking routines. MAPPOS employs machine learning techniques to train a robust classifier from a small number of characteristic image features. In order to accurately quantify the performance of MAPPOS we used simulated particle and non-particle images. In addition, we verified our method by applying it to an experimental cryo-EM dataset and comparing the results to the manual classification of the same dataset. Comparisons between MAPPOS and manual post-picking classification by several human experts demonstrated that merely a few hundred sample images are sufficient for MAPPOS to classify an entire dataset with a human-like performance. MAPPOS was shown to greatly accelerate the throughput of large datasets by reducing the manual workload by orders of magnitude while maintaining a reliable identification of non-particle images.\",\n \"corpus_id\": 9789870,\n \"score\": 1\n },\n {\n \"doc_id\": \"23711417\",\n \"title\": \"Image formation modeling in cryo-electron microscopy.\",\n \"abstract\": \"Accurate modeling of image formation in cryo-electron microscopy is an important requirement for quantitative image interpretation and optimization of the data acquisition strategy. Here we present a forward model that accounts for the specimen's scattering properties, microscope optics, and detector response. The specimen interaction potential is calculated with the isolated atom superposition approximation (IASA) and extended with the influences of solvent's dielectric and ionic properties as well as the molecular electrostatic distribution. We account for an effective charge redistribution via the Poisson-Boltzmann approach and find that the IASA-based potential forms the dominant part of the interaction potential, as the contribution of the redistribution is less than 10%. The electron wave is propagated through the specimen by a multislice approach and the influence of the optics is included via the contrast transfer function. We incorporate the detective quantum efficiency of the camera due to the difference between signal and noise transfer characteristics, instead of using only the modulation transfer function. The full model was validated against experimental images of 20S proteasome, hemoglobin, and GroEL. The simulations adequately predict the effects of phase contrast, changes due to the integrated electron flux, thickness, inelastic scattering, detective quantum efficiency and acceleration voltage. We suggest that beam-induced specimen movements are relevant in the experiments whereas the influence of the solvent amorphousness can be neglected. All simulation parameters are based on physical principles and, when necessary, experimentally determined.\",\n \"corpus_id\": 14817435,\n \"score\": 1\n },\n {\n \"doc_id\": \"24075951\",\n \"title\": \"Xmipp 3.0: an improved software suite for image processing in electron microscopy.\",\n \"abstract\": \"Xmipp is a specialized software package for image processing in electron microscopy, and that is mainly focused on 3D reconstruction of macromolecules through single-particles analysis. In this article we present Xmipp 3.0, a major release which introduces several improvements and new developments over the previous version. A central improvement is the concept of a project that stores the entire processing workflow from data import to final results. It is now possible to monitor, reproduce and restart all computing tasks as well as graphically explore the complete set of interrelated tasks associated to a given project. Other graphical tools have also been improved such as data visualization, particle picking and parameter \\\"wizards\\\" that allow the visual selection of some key parameters. Many standard image formats are transparently supported for input/output from all programs. Additionally, results have been standardized, facilitating the interoperation between different Xmipp programs. Finally, as a result of a large code refactoring, the underlying C++ libraries are better suited for future developments and all code has been optimized. Xmipp is an open-source package that is freely available for download from: http://xmipp.cnb.csic.es.\",\n \"corpus_id\": 14314008,\n \"score\": 1\n },\n {\n \"doc_id\": \"26087140\",\n \"title\": \"Description and comparison of algorithms for correcting anisotropic magnification in cryo-EM images.\",\n \"abstract\": \"Single particle electron cryomicroscopy (cryo-EM) allows for structures of proteins and protein complexes to be determined from images of non-crystalline specimens. Cryo-EM data analysis requires electron microscope images of randomly oriented ice-embedded protein particles to be rotated and translated to allow for coherent averaging when calculating three-dimensional (3D) structures. Rotation of 2D images is usually done with the assumption that the magnification of the electron microscope is the same in all directions. However, due to electron optical aberrations, this condition is not met with some electron microscopes when used with the settings necessary for cryo-EM with a direct detector device (DDD) camera. Correction of images by linear interpolation in real space has allowed high-resolution structures to be calculated from cryo-EM images for symmetric particles. Here we describe and compare a simple real space method, a simple Fourier space method, and a somewhat more sophisticated Fourier space method to correct images for a measured anisotropy in magnification. Further, anisotropic magnification causes contrast transfer function (CTF) parameters estimated from image power spectra to have an apparent systematic astigmatism. To address this problem we develop an approach to adjust CTF parameters measured from distorted images so that they can be used with corrected images. The effect of anisotropic magnification on CTF parameters provides a simple way of detecting magnification anisotropy in cryo-EM datasets.\",\n \"corpus_id\": 6082134,\n \"score\": 1\n },\n {\n \"doc_id\": \"26671944\",\n \"title\": \"Automated data collection in single particle electron microscopy.\",\n \"abstract\": \"Automated data collection is an integral part of modern workflows in single particle electron microscopy (EM) research. This review surveys the software packages available for automated single particle EM data collection. The degree of automation at each stage of data collection is evaluated, and the capabilities of the software packages are described. Finally, future trends in automation are discussed.\",\n \"corpus_id\": 9154059,\n \"score\": 1\n },\n {\n \"doc_id\": \"27572725\",\n \"title\": \"Processing of Cryo-EM Movie Data.\",\n \"abstract\": \"Direct detector device (DDD) cameras dramatically enhance the capabilities of electron cryomicroscopy (cryo-EM) due to their improved detective quantum efficiency (DQE) relative to other detectors. DDDs use semiconductor technology that allows micrographs to be recorded as movies rather than integrated individual exposures. Movies from DDDs improve cryo-EM in another, more surprising, way. DDD movies revealed beam-induced specimen movement as a major source of image degradation and provide a way to partially correct the problem by aligning frames or regions of frames to account for this specimen movement. In this chapter, we use a self-consistent mathematical notation to explain, compare, and contrast several of the most popular existing algorithms for computationally correcting specimen movement in DDD movies. We conclude by discussing future developments in algorithms for processing DDD movies that would extend the capabilities of cryo-EM even further.\",\n \"corpus_id\": 3572644,\n \"score\": 1\n },\n {\n \"doc_id\": \"28600243\",\n \"title\": \"Robust Non-Local TV-L1 Optical Flow Estimation with Occlusion Detection.\",\n \"abstract\": \"In this paper, we propose a robust non-local TV-L1 optical flow method with occlusion detection to address the problem of weak robustness of optical flow estimation with motion occlusion. Firstly, a TV-L1 form for flow estimation is defined using a combination of the brightness constancy and gradient constancy assumptions in the data term and by varying the weight under the Charbonnier function in the smoothing term. Secondly, to handle the potential risk of the outlier in the flow field, a general non-local term is added in the TV-L1 optical flow model to engender the typical non-local TV-L1 form. Thirdly, an occlusion detection method based on triangulation is presented to detect the occlusion regions of the sequence. The proposed non-local TV-L1 optical flow model is performed in a linearizing iterative scheme using improved median filtering and a coarse-to-fine computing strategy. The results of the complex experiment indicate that the proposed method can overcome the significant influence of non-rigid motion, motion occlusion, and large displacement motion. Results of experiments comparing the proposed method and existing state-of-the-art methods by respectively using Middlebury and MPI Sintel database test sequences show that the proposed method has higher accuracy and better robustness.\",\n \"corpus_id\": 195671907,\n \"score\": 1\n },\n {\n \"doc_id\": \"18443909\",\n \"title\": \"Design of MEMS devices with optical apertures for the detection of transparent biological cells.\",\n \"abstract\": \"This paper provides a novel technique to detect transparent biological living cells trapped in a microfluidic MEMS device by optical diffraction. The device essentially consists of an optical aperture or an aperture array patterned in metal layer and a microfluidic chamber positioned above the center of the aperture. When the cells in the chamber are illuminated through the aperture, the far-field diffraction pattern can be recorded by a CCD camera or a photodetector array. This diffraction pattern uniquely corresponds to the sizes, positions, and intrinsic optical properties of the aperture, cells, and the microfluidic chamber materials, so any unknown but relevant parameter is able to be extrapolated when all other parameters are fixed or identified. This paper describes in detail the designs of various microfluidic chambers and apertures for this application, and the development of a complete set of software for the analysis of the cells' optical properties. Compared with other currently available methods for the detection of transparent living cells, this method has the advantages of simple device structure, easy to manipulate, able to simultaneously detect several cells of different species, as well as providing accurate and sensitive results. Besides the detection of living cells, this technique can also be used to detect or characterize other transparent or low optical absorption particles, such as polymer spheres or insoluble droplets, inside an aqueous solution.\",\n \"corpus_id\": 25085132,\n \"score\": 0\n },\n {\n \"doc_id\": \"18672433\",\n \"title\": \"Respiratory motion correction in 3-D PET data with advanced optical flow algorithms.\",\n \"abstract\": \"The problem of motion is well known in positron emission tomography (PET) studies. The PET images are formed over an elongated period of time. As the patients cannot hold breath during the PET acquisition, spatial blurring and motion artifacts are the natural result. These may lead to wrong quantification of the radioactive uptake. We present a solution to this problem by respiratory-gating the PET data and correcting the PET images for motion with optical flow algorithms. The algorithm is based on the combined local and global optical flow algorithm with modifications to allow for discontinuity preservation across organ boundaries and for application to 3-D volume sets. The superiority of the algorithm over previous work is demonstrated on software phantom and real patient data.\",\n \"corpus_id\": 22147460,\n \"score\": 0\n },\n {\n \"doc_id\": \"19717361\",\n \"title\": \"An optical flow-based approach to robust face recognition under expression variations.\",\n \"abstract\": \"Face recognition is one of the most intensively studied topics in computer vision and pattern recognition, but few are focused on how to robustly recognize faces with expressions under the restriction of one single training sample per class. A constrained optical flow algorithm, which combines the advantages of the unambiguous correspondence of feature point labeling and the flexible representation of optical flow computation, has been developed for face recognition from expressional face images. In this paper, we propose an integrated face recognition system that is robust against facial expressions by combining information from the computed intraperson optical flow and the synthesized face image in a probabilistic framework. Our experimental results show that the proposed system improves the accuracy of face recognition from expressional face images.\",\n \"corpus_id\": 18194254,\n \"score\": 0\n },\n {\n \"doc_id\": \"20117216\",\n \"title\": \"Alignator: a GPU powered software package for robust fiducial-less alignment of cryo tilt-series.\",\n \"abstract\": \"The robust alignment of tilt-series collected for cryo-electron tomography in the absence of fiducial markers, is a problem that, especially for tilt-series of vitreous sections, still represents a significant challenge. Here we present a complete software package that implements a cross-correlation-based procedure that tracks similar image features that are present in several micrographs and explores them implicitly as substitutes for fiducials like gold beads and quantum dots. The added value compared to previous approaches, is that the algorithm explores a huge number of random positions, which are tracked on several micrographs, while being able to identify trace failures, using a cross-validation procedure based on the 3D marker model of the tilt-series. Furthermore, this method allows the reliable identification of areas which behave as a rigid body during the tilt-series and hence addresses specific difficulties for the alignment of vitreous sections, by correcting practical caveats. The resulting alignments can attain sub-pixel precision at the local level and is able to yield a substantial number of usable tilt-series (around 60%). In principle, the algorithm has the potential to run in a fully automated fashion, and could be used to align any tilt-series directly from the microscope. Finally, we have significantly improved the user interface and implemented the source code on the graphics processing unit (GPU) to accelerate the computations.\",\n \"corpus_id\": 23038314,\n \"score\": 0\n },\n {\n \"doc_id\": \"20356853\",\n \"title\": \"Automated specimen search in cryo-TEM observation with DIFF-defocus imaging.\",\n \"abstract\": \"We have developed an automated specimen search algorithm for cryo-electron microscopy imaging of ice-embedded single particles suspended across regularly spaced holes. To maximize the particle visibility under a low electron exposure rate condition, specimen searching is carried out in diffraction mode. However, images in diffraction mode contain significant pincushion distortion, making it difficult to computationally predict the locations of the regularly spaced holes. We have implemented a distortion-correction mechanism to restore the primitive distortion-free image and a correlation-based algorithm to accurately determine the periodicity of the holes. A stage-shift method to optimize positional reproducibility is also implemented. Addition of our algorithms to the JADAS software for automated transmission electron microscopy data acquisition has significantly improved the accuracy of specimen search.\",\n \"corpus_id\": 262442938,\n \"score\": 0\n },\n {\n \"doc_id\": \"20409993\",\n \"title\": \"Robust processing of optical flow of fluids.\",\n \"abstract\": \"This paper proposes a new approach, coupling physical models and image estimation techniques, for modelling the movement of fluids. The fluid flow is characterized by turbulent movement and dynamically changing patterns which poses challenges to existing optical flow estimation methods. The proposed methodology, which relies on Navier-Stokes equations, is used for processing fluid optical flow by using a succession of stages such as advection, diffusion and mass conservation. A robust diffusion step jointly considering the local data geometry and its statistics is embedded in the proposed framework. The diffusion kernel is Gaussian with the covariance matrix defined by the local second derivatives. Such an anisotropic kernel is able to implicitly detect changes in the vector field orientation and to diffuse accordingly. A new approach is developed for detecting fluid flow structures such as vortices. The proposed methodology is applied on artificially generated vector fields as well as on various image sequences.\",\n \"corpus_id\": 239581,\n \"score\": 0\n },\n {\n \"doc_id\": \"20637414\",\n \"title\": \"Ab initio structure determination from electron microscopic images of single molecules coexisting in different functional states.\",\n \"abstract\": \"We have developed methods for ab initio three-dimensional (3D) structure determination from projection images of randomly oriented single molecules coexisting in multiple functional states, to aid the study of complex samples of macromolecules and nanoparticles by electron microscopy (EM). New algorithms for the determination of relative 3D orientations and conformational state assignment of single-molecule projection images are combined with well-established techniques for alignment and statistical image analysis. We describe how the methodology arrives at homogeneous groups of images aligned in 3D and discuss application to experimental EM data sets of the Escherichia coli ribosome and yeast RNA polymerase II.\",\n \"corpus_id\": 37167871,\n \"score\": 0\n },\n {\n \"doc_id\": \"21089695\",\n \"title\": \"[A review of automatic particle recognition in Cryo-EM images].\",\n \"abstract\": \"Advances in cryo-electron microscopy (Cryo-EM) and single-particle reconstruction have led to increasingly high resolutions of macromolecular three-dimensional reconstruction. However, for keeping up the continuing improvements in resolution, it is necessary to increase the number of particles included in performing reconstructions. Manual selection of particles, even assisted by computer, is a bottleneck of single-particle reconstruction. Cryo-EM image has low signal-to-noise ratio and low contrast, which leads to difficulty in particle picking. Various approaches have been developed to address the problem of automatic particle. This paper describes the application of template-based method, edge based method, feature-based method, neural network, DoG-based and simulated annealing approach in particle picking. The characteristics of various approaches are discussed, and the future development is presented.\",\n \"corpus_id\": 38932072,\n \"score\": 0\n },\n {\n \"doc_id\": \"21266556\",\n \"title\": \"Flow velocity vector fields by ultrasound particle imaging velocimetry: in vitro comparison with optical flow velocimetry.\",\n \"abstract\": \"OBJECTIVES: We performed an in vitro study to assess the precision and accuracy of particle imaging velocimetry (PIV) data acquired using a clinically available portable ultrasound system via comparison with stereo optical PIV. METHODS: The performance of ultrasound PIV was compared with optical PIV on a benchmark problem involving vortical flow with a substantial out-of-plane velocity component. Optical PIV is capable of stereo image acquisition, thus measuring out-of-plane velocity components. This allowed us to quantify the accuracy of ultrasound PIV, which is limited to in-plane acquisition. The system performance was assessed by considering the instantaneous velocity fields without extracting velocity profiles by spatial averaging. RESULTS: Within the 2-dimensional correlation window, using 7 time-averaged frames, the vector fields were found to have correlations of 0.867 in the direction along the ultrasound beam and 0.738 in the perpendicular direction. Out-of-plane motion of greater than 20% of the in-plane vector magnitude was found to increase the SD by 11% for the vectors parallel to the ultrasound beam direction and 8.6% for the vectors perpendicular to the beam. CONCLUSIONS: The results show a close correlation and agreement of individual velocity vectors generated by ultrasound PIV compared with optical PIV. Most of the measurement distortions were caused by out-of-plane velocity components.\",\n \"corpus_id\": 25965900,\n \"score\": 0\n },\n {\n \"doc_id\": \"21279198\",\n \"title\": \"Hydrodynamic optical alignment for microflow cytometry.\",\n \"abstract\": \"A microfabricated flow cytometer has been developed that is capable of detecting nearly all of the microparticles in an aqueous suspension. Current design allows for integrated coupling between an optical fiber-based detection system and the particle stream via hydrodynamic focusing. By adjusting the relative flow-rates at the auxiliary inputs of the focusing manifold, the particle stream can be steered out-of-plane relative to the illuminating laser, and similarly the particle stream can be squeezed or expanded. The microfabricated device was constructed in polydimethylsiloxane with cross-sectional microfluidic dimensions of 125 µm×125 µm. Using the present device and method, fluorescent microparticles in aqueous solution were counted at an absolute counting efficiency of 91±4%. The coefficient of variation of the fluorescence pulse-heights for far-red fluorescent microparticles was 15%. The device exhibited a linear response to fluorescence intensity calibration microparticles as shown by comparison with a commercial cytometer instrument.\",\n \"corpus_id\": 20847181,\n \"score\": 0\n },\n {\n \"doc_id\": \"21978037\",\n \"title\": \"Evaluation of a 3D local multiresolution algorithm for the correction of partial volume effects in positron emission tomography.\",\n \"abstract\": \"PURPOSE: Partial volume effects (PVEs) are consequences of the limited spatial resolution in emission tomography leading to underestimation of uptake in tissues of size similar to the point spread function (PSF) of the scanner as well as activity spillover between adjacent structures. Among PVE correction methodologies, a voxel-wise mutual multiresolution analysis (MMA) was recently introduced. MMA is based on the extraction and transformation of high resolution details from an anatomical image (MR/CT) and their subsequent incorporation into a low-resolution PET image using wavelet decompositions. Although this method allows creating PVE corrected images, it is based on a 2D global correlation model, which may introduce artifacts in regions where no significant correlation exists between anatomical and functional details. METHODS: A new model was designed to overcome these two issues (2D only and global correlation) using a 3D wavelet decomposition process combined with a local analysis. The algorithm was evaluated on synthetic, simulated and patient images, and its performance was compared to the original approach as well as the geometric transfer matrix (GTM) method. RESULTS: Quantitative performance was similar to the 2D global model and GTM in correlated cases. In cases where mismatches between anatomical and functional information were present, the new model outperformed the 2D global approach, avoiding artifacts and significantly improving quality of the corrected images and their quantitative accuracy. CONCLUSIONS: A new 3D local model was proposed for a voxel-wise PVE correction based on the original mutual multiresolution analysis approach. Its evaluation demonstrated an improved and more robust qualitative and quantitative accuracy compared to the original MMA methodology, particularly in the absence of full correlation between anatomical and functional information.\",\n \"corpus_id\": 19007461,\n \"score\": 0\n },\n {\n \"doc_id\": \"22231171\",\n \"title\": \"Alignment of 3-D optical coherence tomography scans to correct eye movement using a particle filtering.\",\n \"abstract\": \"Eye movement artifacts occurring during 3-D optical coherence tomography (OCT) scanning is a well-recognized problem that may adversely affect image analysis and interpretation. A particle filtering algorithm is presented in this paper to correct motion in a 3-D dataset by considering eye movement as a target tracking problem in a dynamic system. The proposed particle filtering algorithm is an independent 3-D alignment approach, which does not rely on any reference image. 3-D OCT data is considered as a dynamic system, while the location of each A-scan is represented by the state space. A particle set is used to approximate the probability density of the state in the dynamic system. The state of the system is updated frame by frame to detect A-scan movement. The proposed method was applied on both simulated data for objective evaluation and experimental data for subjective evaluation. The sensitivity and specificity of the x-movement detection were 98.85% and 99.43%, respectively, in the simulated data. For the experimental data (74 3-D OCT images), all the images were improved after z-alignment, while 81.1% images were improved after x-alignment. The proposed algorithm is an efficient way to align 3-D OCT volume data and correct the eye movement without using references.\",\n \"corpus_id\": 32665239,\n \"score\": 0\n },\n {\n \"doc_id\": \"22363510\",\n \"title\": \"RAMTaB: robust alignment of multi-tag bioimages.\",\n \"abstract\": \"BACKGROUND: In recent years, new microscopic imaging techniques have evolved to allow us to visualize several different proteins (or other biomolecules) in a visual field. Analysis of protein co-localization becomes viable because molecules can interact only when they are located close to each other. We present a novel approach to align images in a multi-tag fluorescence image stack. The proposed approach is applicable to multi-tag bioimaging systems which (a) acquire fluorescence images by sequential staining and (b) simultaneously capture a phase contrast image corresponding to each of the fluorescence images. To the best of our knowledge, there is no existing method in the literature, which addresses simultaneous registration of multi-tag bioimages and selection of the reference image in order to maximize the overall overlap between the images. METHODOLOGY/PRINCIPAL FINDINGS: We employ a block-based method for registration, which yields a confidence measure to indicate the accuracy of our registration results. We derive a shift metric in order to select the Reference Image with Maximal Overlap (RIMO), in turn minimizing the total amount of non-overlapping signal for a given number of tags. Experimental results show that the Robust Alignment of Multi-Tag Bioimages (RAMTaB) framework is robust to variations in contrast and illumination, yields sub-pixel accuracy, and successfully selects the reference image resulting in maximum overlap. The registration results are also shown to significantly improve any follow-up protein co-localization studies. CONCLUSIONS: For the discovery of protein complexes and of functional protein networks within a cell, alignment of the tag images in a multi-tag fluorescence image stack is a key pre-processing step. The proposed framework is shown to produce accurate alignment results on both real and synthetic data. Our future work will use the aligned multi-channel fluorescence image data for normal and diseased tissue specimens to analyze molecular co-expression patterns and functional protein networks.\",\n \"corpus_id\": 2098029,\n \"score\": 0\n },\n {\n \"doc_id\": \"22393363\",\n \"title\": \"Path curvature discrimination: dependence on gaze direction and optical flow speed.\",\n \"abstract\": \"Many experimental approaches to the control of steering rely on the tangent point (TP) as major source of information. The TP is a good candidate to control self-motion. It corresponds to a singular and salient point in the subject's visual field, and its location depends on the road geometry, the direction of self-motion relative to the road and the position of the driver on the road. However, the particular status of the TP in the optical flow, as a local minimum of flow speed, has often been left aside. We therefore assume that the TP is actually an optimal location in the dynamic optical array to perceive a change in the trajectory curvature. In this study, we evaluated the ability of human observers to detect variations in their path curvature from optical flow patterns, as a function of their gaze direction in a virtual environment. We simulated curvilinear self-motion parallel to a ground plane. Using random-dot optic flow stimuli of brief duration and a two-alternative forced-choice adaptive procedure, we determined path curvature discrimination thresholds, as a function of gaze direction. The discrimination thresholds are minimal for a gaze directed toward a local minimum of optical flow speed. A model based on Weber fraction of the foveal velocities (ΔV/V) correctly predicts the relationship between experimental thresholds and local flow velocities. This model was also tested for an optical flow computation integrating larger circular areas in central vision. Averaging the flow over five degrees leads to an even better fit of the model to experimental thresholds. We also found that the minimal optical flow speed direction corresponds to a maximal sensitivity of the visual system, as predicted by our model. The spontaneous gazing strategies observed during driving might thus correspond to an optimal selection of relevant information in the optical flow field.\",\n \"corpus_id\": 8739397,\n \"score\": 0\n },\n {\n \"doc_id\": \"22411045\",\n \"title\": \"Robust real-time-constrained estimation of respiratory motion for interventional MRI on mobile organs.\",\n \"abstract\": \"Real-time magnetic resonance imaging is a promising tool for image-guided interventions. For applications such as thermotherapy on moving organs, a precise image-based compensation of motion is required in real time to allow quantitative analysis, retrocontrol of the interventional device, or determination of the therapy endpoint. Reduced field-of-view imaging represents a promising way to improve spatial and/or temporal resolution. However, it introduces new challenges for target motion estimation, since structures near the target may appear transiently due to the respiratory motion and the limited spatial coverage. In this paper, a new image-based motion estimation method is proposed combining a global motion estimation with a novel optical flow approach extending the initial Horn and Schunck (H&S) method by an additional regularization term. This term integrates the displacement of physiological landmarks into the variational formulation of the optical flow problem. This allowed for a better control of the optical flow in presence of transient structures. The method was compared to the same registration pipeline employing the H&S approach on a synthetic dataset and in vivo image sequences. Compared to the H&S approach, a significant improvement (p<0.05) of the Dice's similarity criterion computed between the reference and the registered organ positions was achieved.\",\n \"corpus_id\": 14830896,\n \"score\": 0\n },\n {\n \"doc_id\": \"23242263\",\n \"title\": \"Fast and robust optical flow for time-lapse microscopy using super-voxels.\",\n \"abstract\": \"MOTIVATION: Optical flow is a key method used for quantitative motion estimation of biological structures in light microscopy. It has also been used as a key module in segmentation and tracking systems and is considered a mature technology in the field of computer vision. However, most of the research focused on 2D natural images, which are small in size and rich in edges and texture information. In contrast, 3D time-lapse recordings of biological specimens comprise up to several terabytes of image data and often exhibit complex object dynamics as well as blurring due to the point-spread-function of the microscope. Thus, new approaches to optical flow are required to improve performance for such data. RESULTS: We solve optical flow in large 3D time-lapse microscopy datasets by defining a Markov random field (MRF) over super-voxels in the foreground and applying motion smoothness constraints between super-voxels instead of voxel-wise. This model is tailored to the specific characteristics of light microscopy datasets: super-voxels help registration in textureless areas, the MRF over super-voxels efficiently propagates motion information between neighboring cells and the background subtraction and super-voxels reduce the dimensionality of the problem by an order of magnitude. We validate our approach on large 3D time-lapse datasets of Drosophila and zebrafish development by analyzing cell motion patterns. We show that our approach is, on average, 10 × faster than commonly used optical flow implementations in the Insight Tool-Kit (ITK) and reduces the average flow end point error by 50% in regions with complex dynamic processes, such as cell divisions. AVAILABILITY: Source code freely available in the Software section at http://janelia.org/lab/keller-lab.\",\n \"corpus_id\": 9589582,\n \"score\": 0\n },\n {\n \"doc_id\": \"23261401\",\n \"title\": \"FASTDEF: fast defocus and astigmatism estimation for high-throughput transmission electron microscopy.\",\n \"abstract\": \"In this work we present a fast and automated algorithm for estimating the contrast transfer function (CTF) of a transmission electron microscope. The approach is very suitable for High Throughput work because: (a) it does not require any initial defocus estimation, (b) it is almost an order of magnitude faster than existing approaches, (c) it opens the way to well-defined extensions to the estimation of higher order aberrations, at the same time that provides defocus and astigmatism estimations comparable in accuracy to well established methods, such as Xmipp and CTFFIND3 approaches. The new algorithm is based on obtaining the wrapped modulating phase of the power spectra density pattern by the use of a quadrature filter. This phase is further unwrapped in order to obtain the continuous and smooth absolute phase map; then a Zernike polynomial fitting is performed and the defocus and astigmatism parameters are determined. While the method does not require an initial estimation of the defocus parameters or any non-linear optimization procedure, these approaches can be used if further refinement is desired. Results of the CTF estimation method are presented for standard negative stained images, cryo-electron microscopy images in the absence of carbon support, as well as micrographs with only ice. Additionally, we have also tested the proposed method with micrographs acquired from tilted and untilted samples, obtaining good results. The algorithm is freely available as a part of the Xmipp package [http://xmipp.cnb.csic.es].\",\n \"corpus_id\": 9415778,\n \"score\": 0\n },\n {\n \"doc_id\": \"23523719\",\n \"title\": \"Fast and accurate reference-free alignment of subtomograms.\",\n \"abstract\": \"In cryoelectron tomography alignment and averaging of subtomograms, each dnepicting the same macromolecule, improves the resolution compared to the individual subtomogram. Major challenges of subtomogram alignment are noise enhancement due to overfitting, the bias of an initial reference in the iterative alignment process, and the computational cost of processing increasingly large amounts of data. Here, we propose an efficient and accurate alignment algorithm via a generalized convolution theorem, which allows computation of a constrained correlation function using spherical harmonics. This formulation increases computational speed of rotational matching dramatically compared to rotation search in Cartesian space without sacrificing accuracy in contrast to other spherical harmonic based approaches. Using this sampling method, a reference-free alignment procedure is proposed to tackle reference bias and overfitting, which also includes contrast transfer function correction by Wiener filtering. Application of the method to simulated data allowed us to obtain resolutions near the ground truth. For two experimental datasets, ribosomes from yeast lysate and purified 20S proteasomes, we achieved reconstructions of approximately 20Å and 16Å, respectively. The software is ready-to-use and made public to the community.\",\n \"corpus_id\": 26641993,\n \"score\": 0\n },\n {\n \"doc_id\": \"23537496\",\n \"title\": \"3D imaging of flow patterns in an internally-pumped microfluidic device: redox magnetohydrodynamics and electrochemically-generated density gradients.\",\n \"abstract\": \"Redox magnetohydrodynamics (MHD) is a promising technique for developing new electrochemical-based microfluidic flow devices with unique capabilities, such as easily switching flow direction and adjusting flow speeds and flow patterns as well as avoiding bubble formation. However, a detailed description of all the forces involved and predicting flow patterns in confined geometries is lacking. In addition to redox-MHD, density gradients caused by the redox reactions also play important roles. Flow in these devices with small fluid volumes has mainly been characterized by following microbead motion by optical microscopy either by particle tracking velocimetry (PTV) or by processing the microbead images by particle image velocimetry (PIV) software. This approach has limitations in spatial resolution and dimensionality. Here we use fluorescence correlation spectroscopy (FCS) to quantitatively and accurately measure flow speeds and patterns in the ~5-50 μm/s range in redox-MHD-based microfluidic devices, from which 3D flow maps are obtained with a spatial resolution down to 2 μm. The 2 μm spatial resolution flow speeds map revealed detailed flow profiles during redox-MHD in which the velocity increases linearly from above the electrode and reaches a plateau across the center of the cell. By combining FCS and video-microscopy (with PTV and PIV processing approaches), we are able to quantify a vertical flow of ~10 μm/s above the electrodes as a result of density gradients caused by the redox reactions and follow convection flow patterns. Overall, combining FCS, PIV, and PTV analysis of redox-MHD is a powerful combination to more thoroughly characterize the underlying forces in these promising microfluidic devices.\",\n \"corpus_id\": 44437844,\n \"score\": 0\n },\n {\n \"doc_id\": \"23613042\",\n \"title\": \"Optical flow estimation for flame detection in videos.\",\n \"abstract\": \"Computational vision-based flame detection has drawn significant attention in the past decade with camera surveillance systems becoming ubiquitous. Whereas many discriminating features, such as color, shape, texture, etc., have been employed in the literature, this paper proposes a set of motion features based on motion estimators. The key idea consists of exploiting the difference between the turbulent, fast, fire motion, and the structured, rigid motion of other objects. Since classical optical flow methods do not model the characteristics of fire motion (e.g., non-smoothness of motion, non-constancy of intensity), two optical flow methods are specifically designed for the fire detection task: optimal mass transport models fire with dynamic texture, while a data-driven optical flow scheme models saturated flames. Then, characteristic features related to the flow magnitudes and directions are computed from the flow fields to discriminate between fire and non-fire motion. The proposed features are tested on a large video database to demonstrate their practical usefulness. Moreover, a novel evaluation method is proposed by fire simulations that allow for a controlled environment to analyze parameter influences, such as flame saturation, spatial resolution, frame rate, and random noise.\",\n \"corpus_id\": 11840275,\n \"score\": 0\n },\n {\n \"doc_id\": \"23799696\",\n \"title\": \"A decoupled approach to illumination-robust optical flow estimation.\",\n \"abstract\": \"Despite continuous improvements in optical flow in the last three decades, the ability for optical flow algorithms to handle illumination variation is still an unsolved challenge. To improve the ability to interpret apparent object motion in video containing illumination variation, an illumination-robust optical flow method is designed. This method decouples brightness into reflectance and illumination components using a stochastic technique; reflectance is given higher weight to ensure robustness against illumination, which is suppressed. Illumination experiments using the Middlebury and University of Oulu databases demonstrate the decoupled method's improvement when compared with state-of-the-art. In addition, a novel technique is implemented to visualize optical flow output, which is especially useful to compare different optical flow methods in the absence of the ground truth.\",\n \"corpus_id\": 6269043,\n \"score\": 0\n },\n {\n \"doc_id\": \"23933392\",\n \"title\": \"Particle quality assessment and sorting for automatic and semiautomatic particle-picking techniques.\",\n \"abstract\": \"Three-dimensional reconstruction of biological specimens using electron microscopy by single particle methodologies requires the identification and extraction of the imaged particles from the acquired micrographs. Automatic and semiautomatic particle selection approaches can localize these particles, minimizing the user interaction, but at the cost of selecting a non-negligible number of incorrect particles, which can corrupt the final three-dimensional reconstruction. In this work, we present a novel particle quality assessment and sorting method that can separate most erroneously picked particles from correct ones. The proposed method is based on multivariate statistical analysis of a particle set that has been picked previously using any automatic or manual approach. The new method uses different sets of particle descriptors, which are morphology-based, histogram-based and signal to noise analysis based. We have tested our proposed algorithm with experimental data obtaining very satisfactory results. The algorithm is freely available as a part of the Xmipp 3.0 package [http://xmipp.cnb.csic.es].\",\n \"corpus_id\": 7094288,\n \"score\": 0\n },\n {\n \"doc_id\": \"23958728\",\n \"title\": \"A pattern matching approach to the automatic selection of particles from low-contrast electron micrographs.\",\n \"abstract\": \"MOTIVATION: Structural information of macromolecular complexes provides key insights into the way they carry out their biological functions. Achieving high-resolution structural details with electron microscopy requires the identification of a large number (up to hundreds of thousands) of single particles from electron micrographs, which is a laborious task if it has to be manually done and constitutes a hurdle towards high-throughput. Automatic particle selection in micrographs is far from being settled and new and more robust algorithms are required to reduce the number of false positives and false negatives. RESULTS: In this article, we introduce an automatic particle picker that learns from the user the kind of particles he is interested in. Particle candidates are quickly and robustly classified as particles or non-particles. A number of new discriminative shape-related features as well as some statistical description of the image grey intensities are used to train two support vector machine classifiers. Experimental results demonstrate that the proposed method: (i) has a considerably low computational complexity and (ii) provides results better or comparable with previously reported methods at a fraction of their computing time. AVAILABILITY: The algorithm is fully implemented in the open-source Xmipp package and downloadable from http://xmipp.cnb.csic.es.\",\n \"corpus_id\": 11199882,\n \"score\": 0\n },\n {\n \"doc_id\": \"24213166\",\n \"title\": \"Quantifying the local resolution of cryo-EM density maps.\",\n \"abstract\": \"We propose a definition of local resolution for three-dimensional electron cryo-microscopy (cryo-EM) density maps that uses local sinusoidal features. Our algorithm has no free parameters and is applicable to other imaging modalities, including tomography. By evaluating the local resolution of single-particle reconstructions and subtomogram averages for four example data sets, we report variable resolution across a 4- to 40-Å range.\",\n \"corpus_id\": 13250075,\n \"score\": 0\n },\n {\n \"doc_id\": \"24269484\",\n \"title\": \"Fabrication of carbon films with ∼ 500nm holes for cryo-EM with a direct detector device.\",\n \"abstract\": \"Single particle electron cryomicroscopy (cryo-EM) is often performed using EM grids coated with a perforated or holey layer of amorphous carbon. Regular arrays of holes enable efficient cryo-EM data collection and several methods for the production of micropatterned holey-carbon film coated grids have been described. However, a new generation of direct detector device (DDD) electron microscope cameras can benefit from hole diameters that are smaller than currently available. Here we extend a previously proposed method involving soft lithography with a poly(dimethylsiloxane) (PDMS) stamp for the production of holey-carbon film coated EM grids. By incorporating electron-beam (e-beam) lithography and modifying the procedure, we are able to produce low-cost high-quality holey-carbon film coated EM grids with ∼500nm holes spaced 4μm apart centre-to-centre. We demonstrate that these grids can be used for cryo-EM. Furthermore, we show that by applying image shifts to obtain movies of the carbon regions beside the holes after imaging the holes, the contrast transfer function (CTF) parameters needed for calculation of high-resolution cryo-EM maps with a DDD can be obtained efficiently.\",\n \"corpus_id\": 32465812,\n \"score\": 0\n },\n {\n \"doc_id\": \"24569482\",\n \"title\": \"Atomic model of the F420-reducing [NiFe] hydrogenase by electron cryo-microscopy using a direct electron detector.\",\n \"abstract\": \"The introduction of direct electron detectors with higher detective quantum efficiency and fast read-out marks the beginning of a new era in electron cryo-microscopy. Using the FEI Falcon II direct electron detector in video mode, we have reconstructed a map at 3.36 Å resolution of the 1.2 MDa F420-reducing hydrogenase (Frh) from methanogenic archaea from only 320,000 asymmetric units. Videos frames were aligned by a combination of image and particle alignment procedures to overcome the effects of beam-induced motion. The reconstructed density map shows all secondary structure as well as clear side chain densities for most residues. The full coordination of all cofactors in the electron transfer chain (a [NiFe] center, four [4Fe4S] clusters and an FAD) is clearly visible along with a well-defined substrate access channel. From the rigidity of the complex we conclude that catalysis is diffusion-limited and does not depend on protein flexibility or conformational changes. DOI: http://dx.doi.org/10.7554/eLife.01963.001.\",\n \"corpus_id\": 16176308,\n \"score\": 0\n },\n {\n \"doc_id\": \"24751405\",\n \"title\": \"Cortical responses to optic flow and motion contrast across patterns and speeds.\",\n \"abstract\": \"Motion provides animals with fast and robust cues for navigation and object detection. In the first case, stereotyped patterns of optic flow inform a moving observer about the direction and speed of its own movement. In the case of object detection, regional differences in motion allow for the segmentation of figures from their background, even in the absence of color or shading cues. Previous research has investigated human electrophysiological responses to global motion across speeds, but only focused upon one type of optic flow pattern. Here, we compared steady-state visual evoked potential (SSVEP) responses across patterns and speeds, both for optic flow and for motion-defined figure patterns, to assess the extent to which the processes are pattern-general or pattern-specific. For optic flow, pattern and speed effects on response amplitudes varied substantially across channels, suggesting pattern-specific processing at slow speeds and pattern-general activity at fast speeds. Responses for coherence- and direction-defined figures were comparatively more uniform, with similar response profiles and spatial distributions. Self- and object-motion patterns activate some of the same circuits, but these data suggest differential sensitivity: not only across the two classes of motion, but also across the patterns within each class, and across speeds. Thus, the results demonstrate that cortical processing of global motion is complex and activates a distributed network.\",\n \"corpus_id\": 18185547,\n \"score\": 0\n },\n {\n \"doc_id\": \"25268657\",\n \"title\": \"Hybrid Electron Microscopy Normal Mode Analysis graphical interface and protocol.\",\n \"abstract\": \"This article presents an integral graphical interface to the Hybrid Electron Microscopy Normal Mode Analysis (HEMNMA) approach that was developed for capturing continuous motions of large macromolecular complexes from single-particle EM images. HEMNMA was shown to be a good approach to analyze multiple conformations of a macromolecular complex but it could not be widely used in the EM field due to a lack of an integral interface. In particular, its use required switching among different software sources as well as selecting modes for image analysis was difficult without the graphical interface. The graphical interface was thus developed to simplify the practical use of HEMNMA. It is implemented in the open-source software package Xmipp 3.1 (http://xmipp.cnb.csic.es) and only a small part of it relies on MATLAB that is accessible through the main interface. Such integration provides the user with an easy way to perform the analysis of macromolecular dynamics and forms a direct connection to the single-particle reconstruction process. A step-by-step HEMNMA protocol with the graphical interface is given in full details in Supplementary material. The graphical interface will be useful to experimentalists who are interested in studies of continuous conformational changes of macromolecular complexes beyond the modeling of continuous heterogeneity in single particle reconstruction.\",\n \"corpus_id\": 13918346,\n \"score\": 0\n },\n {\n \"doc_id\": \"25528571\",\n \"title\": \"Seeing tobacco mosaic virus through direct electron detectors.\",\n \"abstract\": \"With the introduction of direct electron detectors (DED) to the field of electron cryo-microscopy, a wave of atomic-resolution structures has become available. As the new detectors still require comparative characterization, we have used tobacco mosaic virus (TMV) as a test specimen to study the quality of 3D image reconstructions from data recorded on the two direct electron detector cameras, K2 Summit and Falcon II. Using DED movie frames, we explored related image-processing aspects and compared the performance of micrograph-based and segment-based motion correction approaches. In addition, we investigated the effect of dose deposition on the atomic-resolution structure of TMV and show that radiation damage affects negative carboxyl chains first in a side-chain specific manner. Finally, using 450,000 asymmetric units and limiting the effects of radiation damage, we determined a high-resolution cryo-EM map at 3.35Å resolution. Here, we provide a comparative case study of highly ordered TMV recorded on different direct electron detectors to establish recording and processing conditions that enable structure determination up to 3.2Å in resolution using cryo-EM.\",\n \"corpus_id\": 20499036,\n \"score\": 0\n },\n {\n \"doc_id\": \"25570703\",\n \"title\": \"Robust estimation for class averaging in cryo-EM Single Particle Reconstruction.\",\n \"abstract\": \"Single Particle Reconstruction (SPR) for Cryogenic Electron Microscopy (cryo-EM) aligns and averages the images extracted from micrographs to improve the Signal-to-Noise ratio (SNR). Outliers compromise the fidelity of the averaging. We propose a robust cross-correlation-like w-estimator for combating the effect of outliers on the average images in cryo-EM. The estimator accounts for the natural variation of signal contrast among the images and eliminates the need for a threshold for outlier rejection. We show that the influence function of our estimator is asymptotically bounded. Evaluations of the estimator on simulated and real cryo-EM images show good performance in the presence of outliers.\",\n \"corpus_id\": 8996078,\n \"score\": 0\n },\n {\n \"doc_id\": \"25637660\",\n \"title\": \"A statistical approach to the initial volume problem in Single Particle Analysis by Electron Microscopy.\",\n \"abstract\": \"Cryo Electron Microscopy is a powerful Structural Biology technique, allowing the elucidation of the three-dimensional structure of biological macromolecules. In particular, the structural study of purified macromolecules -often referred as Single Particle Analysis(SPA)- is normally performed through an iterative process that needs a first estimation of the three-dimensional structure that is progressively refined using experimental data. It is well-known the local optimisation nature of this refinement, so that the initial choice of this first structure may substantially change the final result. Computational algorithms aiming to providing this first structure already exist. However, the question is far from settled and more robust algorithms are still needed so that the refinement process can be performed with sufficient guarantees. In this article we present a new algorithm that addresses the initial volume problem in SPA by setting it in a Weighted Least Squares framework and calculating the weights through a statistical approach based on the cumulative density function of different image similarity measures. We show that the new algorithm is significantly more robust than other state-of-the-art algorithms currently in use in the field. The algorithm is available as part of the software suite Xmipp (http://xmipp.cnb.csic.es) and Scipion (http://scipion.cnb.csic.es) under the name \\\"Significant\\\".\",\n \"corpus_id\": 15342000,\n \"score\": 0\n },\n {\n \"doc_id\": \"25941470\",\n \"title\": \"On event-based optical flow detection.\",\n \"abstract\": \"Event-based sensing, i.e., the asynchronous detection of luminance changes, promises low-energy, high dynamic range, and sparse sensing. This stands in contrast to whole image frame-wise acquisition by standard cameras. Here, we systematically investigate the implications of event-based sensing in the context of visual motion, or flow, estimation. Starting from a common theoretical foundation, we discuss different principal approaches for optical flow detection ranging from gradient-based methods over plane-fitting to filter based methods and identify strengths and weaknesses of each class. Gradient-based methods for local motion integration are shown to suffer from the sparse encoding in address-event representations (AER). Approaches exploiting the local plane like structure of the event cloud, on the other hand, are shown to be well suited. Within this class, filter based approaches are shown to define a proper detection scheme which can also deal with the problem of representing multiple motions at a single location (motion transparency). A novel biologically inspired efficient motion detector is proposed, analyzed and experimentally validated. Furthermore, a stage of surround normalization is incorporated. Together with the filtering this defines a canonical circuit for motion feature detection. The theoretical analysis shows that such an integrated circuit reduces motion ambiguity in addition to decorrelating the representation of motion related activations.\",\n \"corpus_id\": 16638035,\n \"score\": 0\n },\n {\n \"doc_id\": \"25955078\",\n \"title\": \"Cryo-electron microscopy and the amazing race to atomic resolution.\",\n \"abstract\": \"Cryo-electron microscopy (cryo-EM), the structural analysis of samples embedded in vitreous ice, is a powerful approach for determining three-dimensional (3D) structures of biological specimens. Over the past two decades, this technique has been used to successfully calculate subnanometer (<10 Å) resolution and, in some cases, near-atomic resolution structures of highly symmetrical and stable complexes such as icosahedral viruses and ribosomes, as well as samples that form ordered two-dimensional or helical arrays. However, determining high-resolution 3D structures of smaller, less symmetrical, and dynamic samples remains a significant challenge. The recent development of electron microscopes with automated data collection capabilities and robust direct electron detection cameras, as well as new powerful image processing algorithms, has dramatically expanded the number of biological macromolecules amenable for study using cryo-EM. In addition, these new technological and computational developments have been used to successfully determine <5 Å resolution 3D structures of samples, such as membrane proteins and complexes with either low or no symmetry, that traditionally were not considered promising candidates for high-resolution cryo-EM. With these exciting new advances, cryo-EM is now on pace to determine atomic resolution 3D structures.\",\n \"corpus_id\": 5180848,\n \"score\": 0\n },\n {\n \"doc_id\": \"27893394\",\n \"title\": \"A Robust and Efficient Approach to License Plate Detection.\",\n \"abstract\": \"This paper presents a robust and efficient method for license plate detection with the purpose of accurately localizing vehicle license plates from complex scenes in real time. A simple yet effective image downscaling method is first proposed to substantially accelerate license plate localization without sacrificing detection performance compared with that achieved using the original image. Furthermore, a novel line density filter approach is proposed to extract candidate regions, thereby significantly reducing the area to be analyzed for license plate localization. Moreover, a cascaded license plate classifier based on linear support vector machines using color saliency features is introduced to identify the true license plate from among the candidate regions. For performance evaluation, a data set consisting of 3977 images captured from diverse scenes under different conditions is also presented. Extensive experiments on the widely used Caltech license plate data set and our newly introduced data set demonstrate that the proposed approach substantially outperforms state-of-the-art methods in terms of both detection accuracy and run-time efficiency, increasing the detection ratio from 91.09% to 96.62% while decreasing the run time from 672 to 42 ms for processing an image with a resolution of 1082×728 . The executable code and our collected data set are publicly available.\",\n \"corpus_id\": 17045780,\n \"score\": 0\n },\n {\n \"doc_id\": \"28109158\",\n \"title\": \"Using the Volta phase plate with defocus for cryo-EM single particle analysis.\",\n \"abstract\": \"Previously, we reported an in-focus data acquisition method for cryo-EM single-particle analysis with the Volta phase plate (Danev and Baumeister, 2016). Here, we extend the technique to include a small amount of defocus which enables contrast transfer function measurement and correction. This hybrid approach simplifies the experiment and increases the data acquisition speed. It also removes the resolution limit inherent to the in-focus method thus allowing 3D reconstructions with resolutions better than 3 Å.\",\n \"corpus_id\": 7467768,\n \"score\": 0\n },\n {\n \"doc_id\": \"28732461\",\n \"title\": \"A deep convolutional neural network approach to single-particle recognition in cryo-electron microscopy.\",\n \"abstract\": \"BACKGROUND: Single-particle cryo-electron microscopy (cryo-EM) has become a mainstream tool for the structural determination of biological macromolecular complexes. However, high-resolution cryo-EM reconstruction often requires hundreds of thousands of single-particle images. Particle extraction from experimental micrographs thus can be laborious and presents a major practical bottleneck in cryo-EM structural determination. Existing computational methods for particle picking often use low-resolution templates for particle matching, making them susceptible to reference-dependent bias. It is critical to develop a highly efficient template-free method for the automatic recognition of particle images from cryo-EM micrographs. RESULTS: We developed a deep learning-based algorithmic framework, DeepEM, for single-particle recognition from noisy cryo-EM micrographs, enabling automated particle picking, selection and verification in an integrated fashion. The kernel of DeepEM is built upon a convolutional neural network (CNN) composed of eight layers, which can be recursively trained to be highly \\\"knowledgeable\\\". Our approach exhibits an improved performance and accuracy when tested on the standard KLH dataset. Application of DeepEM to several challenging experimental cryo-EM datasets demonstrated its ability to avoid the selection of un-wanted particles and non-particles even when true particles contain fewer features. CONCLUSIONS: The DeepEM methodology, derived from a deep CNN, allows automated particle extraction from raw cryo-EM micrographs in the absence of a template. It demonstrates an improved performance, objectivity and accuracy. Application of this novel method is expected to free the labor involved in single-particle verification, significantly improving the efficiency of cryo-EM data processing.\",\n \"corpus_id\": 9763578,\n \"score\": 0\n },\n {\n \"doc_id\": \"29352317\",\n \"title\": \"Optic flow detection is not influenced by visual-vestibular congruency.\",\n \"abstract\": \"Optic flow patterns generated by self-motion relative to the stationary environment result in congruent visual-vestibular self-motion signals. Incongruent signals can arise due to object motion, vestibular dysfunction, or artificial stimulation, which are less common. Hence, we are predominantly exposed to congruent rather than incongruent visual-vestibular stimulation. If the brain takes advantage of this probabilistic association, we expect observers to be more sensitive to visual optic flow that is congruent with ongoing vestibular stimulation. We tested this expectation by measuring the motion coherence threshold, which is the percentage of signal versus noise dots, necessary to detect an optic flow pattern. Observers seated on a hexapod motion platform in front of a screen experienced two sequential intervals. One interval contained optic flow with a given motion coherence and the other contained noise dots only. Observers had to indicate which interval contained the optic flow pattern. The motion coherence threshold was measured for detection of laminar and radial optic flow during leftward/rightward and fore/aft linear self-motion, respectively. We observed no dependence of coherence thresholds on vestibular congruency for either radial or laminar optic flow. Prior studies using similar methods reported both decreases and increases in coherence thresholds in response to congruent vestibular stimulation; our results do not confirm either of these prior reports. While methodological differences may explain the diversity of results, another possibility is that motion coherence thresholds are mediated by neural populations that are either not modulated by vestibular stimulation or that are modulated in a manner that does not depend on congruency.\",\n \"corpus_id\": 3587693,\n \"score\": 0\n },\n {\n \"doc_id\": \"29400760\",\n \"title\": \"Alignment of sensor arrays in optical instruments using a geometric approach.\",\n \"abstract\": \"Alignment of sensor arrays in optical instruments is critical to maximize the instrument's performance. While many commercial systems use standardized mounting threads for alignment, custom systems require specialized equipment and alignment procedures. These alignment procedures can be time-consuming, dependent on operator experience, and have low repeatability. Furthermore, each alignment solution must be considered on a case-by-case basis, leading to additional time and resource cost. Here I present a method to align a sensor array using geometric analysis. By imaging a grid pattern of dots, I show that it is possible to calculate the misalignment for a sensor in five degrees of freedom simultaneously. I first test the approach by simulating different cases of misalignment using Zemax before applying the method to experimentally acquired data of sensor misalignment for an echelle spectrograph. The results show that the algorithm effectively quantifies misalignment in five degrees of freedom for an F/5 imaging system, accurate to within ±0.87 deg in rotation and ±0.86 μm in translation. Furthermore, the results suggest that the method can also be applied to non-imaging systems with a small penalty to precision. This general approach can potentially improve the alignment of sensor arrays in custom instruments by offering an accurate, quantitative approach to calculating misalignment in five degrees of freedom simultaneously.\",\n \"corpus_id\": 46861650,\n \"score\": 0\n },\n {\n \"doc_id\": \"29607548\",\n \"title\": \"Motion-robust sub-millimeter isotropic diffusion imaging through motion corrected generalized slice dithered enhanced resolution (MC-gSlider) acquisition.\",\n \"abstract\": \"PURPOSE: To develop an efficient MR technique for ultra-high resolution diffusion MRI (dMRI) in the presence of motion. METHODS: gSlider is an SNR-efficient high-resolution dMRI acquisition technique. However, subject motion is inevitable during a prolonged scan for high spatial resolution, leading to potential image artifacts and blurring. In this study, an integrated technique termed Motion Corrected gSlider (MC-gSlider) is proposed to obtain high-quality, high-resolution dMRI in the presence of large in-plane and through-plane motion. A motion-aware reconstruction with spatially adaptive regularization is developed to optimize the conditioning of the image reconstruction under difficult through-plane motion cases. In addition, an approach for intra-volume motion estimation and correction is proposed to achieve motion correction at high temporal resolution. RESULTS: Theoretical SNR and resolution analysis validated the efficiency of MC-gSlider with regularization, and aided in selection of reconstruction parameters. Simulations and in vivo experiments further demonstrated the ability of MC-gSlider to mitigate motion artifacts and recover detailed brain structures for dMRI at 860 μm isotropic resolution in the presence of motion with various ranges. CONCLUSION: MC-gSlider provides motion-robust, high-resolution dMRI with a temporal motion correction sensitivity of 2 s, allowing for the recovery of fine detailed brain structures in the presence of large subject movements.\",\n \"corpus_id\": 4663910,\n \"score\": 0\n }\n]","isConversational":false}}},{"rowIdx":93,"cells":{"query":{"kind":"string","value":"{\n \"doc_id\": \"27701049\",\n \"title\": \"Soluble curcumin amalgamated chitosan microspheres augmented drug delivery and cytotoxicity in colon cancer cells: In vitro and in vivo study.\",\n \"abstract\": \"In present investigation, initially curcumin was complexed with 2-HP-β-CD (curcumin-2-HP-β-CD-complex) in 1:1 ratio and later amalgamated with chitosan microspheres (curcumin-2-HP-β-CD-CMs) for selective delivery in colon only through oral route of administration. Various analytical, spectral and in-silico docking techniques revealed that the curcumin was deeply inserted in the 2-HP-β-CD cavity with apparent stability constant of 3.35×10(-3)M. Furthermore, the mean particle size of 6.8±2.6μm and +39.2±4.1mV surface charge of curcumin-2-HP-β-CD-complex-CMs in addition to encapsulation efficiency of about 79.8±6.3% exhibited that the tailored microspheres were optimum for colon delivery of curcumin. This was also demonstrated in dissolution testing and standard cell proliferation assay in which curcumin-2-HP-β-CD-complex-CMs exhibited maximum release in simulated colonic fluid (SCF, pH ∼7.0-8.0, almond emulsion-β-glucosidase) with improved therapeutic index in HT-29 cells. Consistently, curcumin-2-HP-β-CD-complex-CMs successively enhanced the colonic bio-distribution of curcumin by ∼8.36 folds as compared to curcumin suspension in preclinical pharmacokinetic studies. In conclusion, curcumin-2-HP-β-CD-complex-CMs warrant further in vivo tumor regression study to establish its therapeutic efficacy in experimental colon cancer.\",\n \"corpus_id\": 206888667\n}"},"candidates":{"kind":"list like","value":[{"doc_id":"18702170","title":"Uniform chitosan microspheres for potential application to colon-specific drug delivery.","abstract":"Uniform chitosan microspheres have been fabricated and weakly crosslinked for potential applications in colon-specific drug delivery. The effects of microsphere size, crosslinking density and electrostatic interactions between the drug and chitosan on drug release were studied, employing model drugs of different acidities. When the drug was basic, all chitosan spheres exhibited 100% release within 30 min. As the acidity of the drug increased, the release slowed down and depended on the crosslinking density and microsphere size. The release of weakly acidic drug was most suppressed for large spheres (35-38 microm), while the small spheres (23-25 microm) with higher crosslinking exhibited the most retention of highly acidic drug, indicating that they are a promising candidate for colon-specific delivery.","corpus_id":20307098,"score":2},{"doc_id":"19491009","title":"Nanoparticle encapsulation improves oral bioavailability of curcumin by at least 9-fold when compared to curcumin administered with piperine as absorption enhancer.","abstract":"Curcumin, a derived product from common spice turmeric that is safe and beneficial in several aliments was formulated into biodegradable nanoparticles with a view to improve its oral bioavailability. The curcumin encapsulated nanoparticles prepared by emulsion technique were spherical in shape with particle size of 264nm (polydispersity index 0.31) and 76.9% entrapment at 15% loading. The curcumin encapsulated nanoparticles were able to withstand the International Conference on Harmonisation (ICH) accelerated stability test conditions for refrigerated products for the studied duration of 3 months. X-ray diffraction analysis revealed the amorphous nature of the encapsulated curcumin. The in vitro release was predominantly by diffusion phenomenon and followed Higuchi's release pattern. The in vivo pharmacokinetics revealed that curcumin entrapped nanoparticles demonstrate at least 9-fold increase in oral bioavailability when compared to curcumin administered with piperine as absorption enhancer. Together the results clearly indicate the promise of nanoparticles for oral delivery of poorly bioavailable molecules like curcumin.","corpus_id":24999453,"score":2},{"doc_id":"20201417","title":"Curcumin loaded pH-sensitive nanoparticles for the treatment of colon cancer.","abstract":"The investigation was aimed at designing pH-sensitive, polymeric nanoparticles of curcumin, a natural anti-cancer agent, for the treatment of colon cancer. The objective was to enhance the bioavailability of curcumin, simultaneously reducing the required dose through selective targeting to colon. Eudragit S100 was chosen to aid targeting since the polymer dissolves at colonic pH to result in selective colonic release of the entrapped drug. Solvent emulsion-evaporation technique was employed to formulate the nanoparticles. Various process parameters were optimized and the optimized formulation was evaluated for particle size distribution and encapsulation efficiency before subjecting to freeze-drying. The freeze dried product was characterized for particle size, drug content, DSC studies, particle morphology. Anti-cancer potential of the formulation was demonstrated by MTT assay in HT-29 cell line. Nanometric, homogeneous, spherical particles were obtained with encapsulation efficiency of 72%. Freeze-dried nanoparticles exhibited a negative surface charge, drug content of > 99% and presence of drug in amorphous form which may result in possible enhanced absorption. MTT assay demonstrated almost double inhibition of the cancerous cells by nanoparticles, as compared to curcumin alone, at the concentrations tested. Enhanced action may be attributed to size influenced improved cellular uptake, and may result in reduction of overall dose requirement. Results indicate the potential for in vivo studies to establish the clinical application of the formulation.","corpus_id":23272718,"score":2},{"doc_id":"20456930","title":"beta-Cyclodextrin-curcumin self-assembly enhances curcumin delivery in prostate cancer cells.","abstract":"Curcumin, a hydrophobic polyphenolic compound derived from the rhizome of the herb Curcuma longa, possesses a wide range of biological applications including cancer therapy. However, its prominent application in cancer treatment is limited due to sub-optimal pharmacokinetics and poor bioavailability at the tumor site. In order to improve its hydrophilic and drug delivery characteristics, we have developed a beta-cyclodextrin (CD) mediated curcumin drug delivery system via encapsulation technique. Curcumin encapsulation into the CD cavity was achieved by inclusion complex mechanism. Curcumin encapsulation efficiency was improved by increasing the ratio of curcumin to CD. The formations of CD-curcumin complexes were characterized by Fourier transform infrared (FTIR), differential scanning calorimetry (DSC), thermo-gravimetric analysis (TGA), scanning electron microscope (SEM), and transmission electron microscope (TEM) analyses. An optimized CD-curcumin complex (CD30) was evaluated for intracellular uptake and anti-cancer activity. Cell proliferation and clonogenic assays demonstrated that beta-cyclodextrin-curcumin self-assembly enhanced curcumin delivery and improved its therapeutic efficacy in prostate cancer cells compared to free curcumin.","corpus_id":8818892,"score":2},{"doc_id":"21722423","title":"Curcumin-loaded N,O-carboxymethyl chitosan nanoparticles for cancer drug delivery.","abstract":"Chitosan (CS) and its carboxymethyl derivatives are smart biopolymers that are non-toxic, biocompatible and biodegradable, and, hence, suitable for various biomedical applications, such as drug delivery, gene therapy and tissue engineering. Curcumin is a major chemotherapeutic agent with antioxidant, anti-inflammatory, anti-proliferative, anticancer and antimicrobial effects. However, the potential of curcumin as a chemotherapeutic agent is limited by its hydrophobicity and poor bioavailability. In this work, we developed a nanoformulation of curcumin in a carboxymethyl chitosan (CMC) derivative, N,O-carboxymethyl chitosan (N,O-CMC). The curcumin-loaded N,O-CMC (curcumin-N,O-CMC) nanoparticles were characterized using DLS, AFM, SEM, FT-IR and XRD. DLS studies revealed nanoparticles with a mean diameter of 150 ± 30 nm. AFM and SEM confirmed that the particles have a spherical morphology within the size range of 150 ± 30 nm. Curcumin was entrapped with in N,O-CMC nanopartcles with an efficiency of 80%. The in vitro drug-release profile was studied at different pH (7.4 and 4.5) at 37°C for different incubation periods with and without lysozyme. Cytotoxicity studies using MTT assay indicated that curcumin-N,O-CMC nanoparticles showed specific toxicity towards cancer cells and non-toxicity to normal cells. Cellular uptake of curcumin-N,O-CMC nanoparticles was analyzed by fluorescence microscopy and was reconfirmed by flow cytometry. Overall, these results indicate that like previously reported curcumin loaded O-CMC nanoparticles, N,O-CMC will also be an efficient nanocarrier for delivering curcumin to cancer cells.","corpus_id":23164152,"score":2},{"doc_id":"22047549","title":"Mucoadhesive bilayer buccal tablet of carvedilol-loaded chitosan microspheres: in vitro, pharmacokinetic and pharmacodynamic investigations.","abstract":"A multiple-unit system comprising mucoadhesive bilayer buccal tablets of carvedilol-loaded chitosan microspheres (CMs) was developed to improve bioavailability and therapeutic efficacy of carvedilol. Drug-loaded CMs were prepared by spray drying, evaluated for powder and particle characteristics, and optimized batch of CMs was compressed into bilayer buccal tablets using Carbopol. Tablets were evaluated for physicochemical parameters, in vitro drug release, in vivo pharmacokinetic and pharmacodynamic studies. Optimized formulation, CMT1 (CMT, chitosan microsphere tablet) showed maximum mucoadhesive force (50 ± 1.84 dyne/cm²), exhibited 73.08 ± 3.05% drug release and demonstrated zero-order kinetics with non-Fickian release mechanism. Pharmacokinetic studies in rabbits showed significantly higher C(max) (71.26 ± 6.45 ng/mL), AUC(0-10) (AUC, area under the curve 390.75 ± 5.23 ng/mL/h) and AUC(0-∞) (664.72 ng/mL/h) than carvedilol oral tablet. Pharmacodynamic studies confirmed reduction in mean arterial pressure, heart rate, body weight and triglyceride on administration of bilayer buccal tablet compared to oral carvedilol tablet. Multiple-unit system exhibited enhanced bioavailability and sustained release of carvedilol, indicating its improved therapeutic potential for the treatment of hypertension.","corpus_id":4375905,"score":2},{"doc_id":"22275831","title":"A novel folate-modified self-microemulsifying drug delivery system of curcumin for colon targeting.","abstract":"BACKGROUND: The objective of this study was to prepare, characterize, and evaluate a folate-modified self-microemulsifying drug delivery system (FSMEDDS) with the aim to improve the solubility of curcumin and its delivery to the colon, facilitating endocytosis of FSMEDDS mediated by folate receptors on colon cancer cells. METHODS: Ternary phase diagrams were constructed in order to obtain the most efficient self-emulsification region, and the formulation of curcumin-loaded SMEDDS was optimized by a simplex lattice experiment design. Then, three lipophilic folate derivatives (folate-polyethylene glycol-distearoylphosphatidylethanolamine, folate-polyethylene glycol-cholesteryl hemisuccinate, and folate-polyethylene glycol-cholesterol) used as a surfactant were added to curcumin-loaded SMEDDS formulations. An in situ colon perfusion method in rats was used to optimize the formulation of FSMEDDS. Curcumin-loaded FSMEDDS was then filled into colon-targeted capsules and the in vitro release was investigated. Cytotoxicity studies and cellular uptake studies was used in this research. RESULTS: The optimal formulation of FSMEDDS obtained with the established in situ colon perfusion method in rats was comprised of 57.5% Cremophor(®) EL, 32.5% Transcutol(®) HP, 10% Capryol™ 90, and a small amount of folate-polyethylene glycol-cholesteryl hemisuccinate (the weight ratio of folate materials to Cremophor EL was 1:100). The in vitro release results indicated that the obtained formulation of curcumin could reach the colon efficiently and release the drug immediately. Cellular uptake studies analyzed with fluorescence microscopy and flow cytometry indicated that the FSMEDDS formulation could efficiently bind with the folate receptors on the surface of positive folate receptors cell lines. In addition, FSMEDDS showed greater cytotoxicity than SMEDDS in the above two cells. CONCLUSION: FSMEDDS-filled colon-targeted capsules are a potential carrier for colon delivery of curcumin.","corpus_id":13908952,"score":2},{"doc_id":"22557928","title":"Preparation and in vitro/in vivo characterization of curcumin microspheres intended to treat colon cancer.","abstract":"OBJECTIVE: The objective of the present investigation was to prepare colon targeted curcumin microspheres using Eudragit S100 and evaluate the same for in vitro/in vivo properties. MATERIALS AND METHODS: A \"O/O solvent evaporation\" technique was used in the preparation of microspheres. The influence of various process variables including stirring speed, drug:polymer ratio and percentage of emulsifier on the fabrication were investigated and the formulation was optimized. Prepared microspheres were evaluated for in vitro and in vivo properties. Surface morphology, particle size, percentage drug entrapment, percentage yield, drug polymer interaction, in vitro drug release in simulated gastrointestinal transit conditions and stability were the in vitro parameters investigated. Using an optimized formulation, drug release into the systemic circulation and organ distribution were investigated as in vivo parameters. In vivo parameters were estimated in male albino rats. RESULTS: Curcumin microspheres of Eudragit S100 were successfully prepared using o/o solvent evaporation method. Microspheres prepared using 1:2 drug:polymer ratio, with a stirring speed of 1000 rpm, and using 1.0% w/v concentration of emulsifying agent was selected as an optimized formulation. The release studies with optimized formulation demonstrated that aqueous solubility of curcumin was enhanced by 8 times with the formulation. FTIR studies demonstrated no change in drug characteristics upon microsphere fabrication. The enhancement in solubility is thus due to the increase in the surface area of the drug substance and not due to a change of drug to a different physical state. This was further confirmed by scanning electron microsphere pictures. Drug release followed Korsmeyer and Peppas release model. Accelerated stability studies indicated that the drug is stable in the formulation for a period of atleast 14 weeks at room temperature. In vivo studies demonstrated a sustained drug release into the systemic circulation after oral administration of the formulation. Further, colon target was affectively achieved using the optimized formulation. Eudragit microspheres delivered most of their drug load (79.0%) to the colon, whereas with plain drug suspension only 28.0% of the total dose reached the target site. CONCLUSION: This study successfully developed curcumin microspheres that can be used effectively in the treatment of the colon cancer.","corpus_id":42879570,"score":2},{"doc_id":"23030405","title":"Native and β-cyclodextrin-enclosed curcumin: entrapment within liposomes and their in vitro cytotoxicity in lung and colon cancer.","abstract":"With a view to improving the solubility and delivery characteristics of poorly water-soluble drugs, we prepared β-cyclodextrin-curcumin (βCD-C) inclusion complexes (hydrophilic curcumin) and entrapped both native curcumin (hydrophobic) and the complexes separately into liposomes; these were then assessed for in vitro cytotoxicity in lung and colon cancer cell lines. Optimization of curcumin entrapment within βCD was achieved, with the resultant βCD-C complexes prepared by methanol reflux. Inclusion complexes were confirmed using UV spectroscopy, Fourier transform infrared spectroscopy (FT-IR) and X-ray diffraction. The water solubility of βCD-C complexes improved markedly (c.f. native curcumin) and successful entrapment of complexes into liposomes, prepared using a thin-film hydration approach, was also achieved. All the liposomal formulations were characterized for curcumin and βCD-C complex entrapment efficiency, particle size, polydispersity and stability at 2-8°C. Curcumin, βCD-C complex and their optimized liposomal formulations were evaluated for anticancer activity in lung (A-459) and colon (SW-620) cancer cell lines. All curcumin-containing formulations tested were effective in inhibiting cell proliferation, as determined via an MTT assay. The median effective dose (EC(50)) for all curcumin formulations was found to be in the low µM range for both lung and colon cancer cell lines tested. Our results confirm that βCD inclusion complexes of poorly water soluble drugs, such as curcumin can be entrapped within biocompatible vesicles such as liposomes, and this does not preclude their anticancer activity.","corpus_id":32953815,"score":2},{"doc_id":"23618291","title":"In vitro and in vivo evaluation of curcumin loaded lauroyl sulphated chitosan for enhancing oral bioavailability.","abstract":"Curcumin has been demonstrated as a potent anticancer agent but its clinical application has been limited by its poor aqueous solubility and bioavailability. Here we describe encapsulation of curcumin in the lauroyl sulphated chitosan with a view to improve its bioavailability. In vitro antioxidant activity of extract of curcumin loaded matrix was investigated and exhibited dose dependent radical scavenging and reducing activity. Cytotoxicity studies carried out with curcumin loaded carrier on C6 cell line and were found to be toxic. Its in vitro effects on proliferation using the C6 cell lines also studied and observed antiproliferation of C6 cell line. Plasma concentration of curcumin-time profiles from pharmacokinetic studies in rats after oral administration showed a 11.5-fold increased pharmacological availability of curcumin with encapsulated curcumin compared with native curcumin. Overall we demonstrate that the curcumin loaded matrix has shown a superior pharmacological availability in vivo over curcumin.","corpus_id":479446,"score":2},{"doc_id":"23990077","title":"Molecular inclusion complex of curcumin-β-cyclodextrin nanoparticle to enhance curcumin skin permeability from hydrophilic matrix gel.","abstract":"Curcumin (CUR) has various pharmacological effects, but its extensive first-pass metabolism and short elimination half-life limit its bioavailability. Therefore, transdermal application has become a potential alternative to delivery CUR. To increase CUR solubility for the development of a transparent homogenous gel and also enhance the permeation rate of CUR into the skin, β-cyclodextrin-curcumin nanoparticle complex (BCD-CUR-N) was developed. CUR encapsulation efficiency was increased by raising the percentage of CUR to BCD up to 20%. The mean particle size of the best CUR loading formula was 156 nm. All evaluation data using infrared spectroscopy, Raman spectroscopy, powder X-ray diffractometry, differential thermal analysis and scanning electron microscopy confirmed the successful formation of the inclusion complex. BCD-CUR-N increased the CUR dissolution rate of 10-fold (p < 0.01). In addition, the improvement of CUR permeability acrossed skin model tissue was observed in gel containing the BCD-CUR-N and was about 1.8-fold when compared with the free CUR gel (p < 0.01). Overall, CUR in the form of the BCD-CUR-N improved the solubility further on the penetration of CUR.","corpus_id":17581609,"score":2},{"doc_id":"24299818","title":"Telmisartan complex augments solubility, dissolution and drug delivery in prostate cancer cells.","abstract":"Telmisartan (TEL) requires superior bioavailability in cancer cell compartments. To meet these challenges, we have synthesized a 2-HP-β-CD-TEL complex with stability constant (Kc) of 2.39 × 10(-3)mM. The absence in the FTIR spectrum of 2-HP-β-CD-TEL complex of the characteristic peaks of TEL at 1,699 cm(-1) (carboxylic acid) and 741 and 756 cm(-1) (1,2-disubstituted benzene ring vibrations), is indicative of the encapsulation of TEL in the 2-HP-β-CD cavity. DSC and PXRD also confirmed the synthesis and amorphous structure of complex. The interaction of TEL with 2-HP-β-CD was examined by NMR and 2D-ROESY which affirms the encapsulation of TEL in the 2-HP-β-CD cavity in at least two orientations with equal binding energies. The complex also exhibited its superiority in both in vitro release and cytotoxicity experiments on prostate cancer, PC-3 cells as compared to free drug. These data warrant an in depth in vivo to scale-up the technology for the management of prostate cancer.","corpus_id":30910521,"score":2},{"doc_id":"24698148","title":"Curcumin-cyclodextrin encapsulated chitosan nanoconjugates with enhanced solubility and cell cytotoxicity.","abstract":"Curcumin (CUR), a naturally derived anti-cancer cocktail is arguably the most widely studied neutraceutical. Despite a lot of promises, it is yet to reach the market as an active anti-cancer formulation. In the present study, we have prepared highly soluble (3 mg/ml) CUR-γ-hydroxypropyl cyclodextrin (CUR-CD) hollow spheres. CUR-CD hollow spheres were prepared by a novel and scalable spray drying method. CUR-CD was then encapsulated into positively charged biodegradable chitosan (CUR-CD-CS) nanoparticles. The CUR-CD-CS nanoparticles were characterised by TEM, SEM, DLS, drug loading and in vitro release. We tested the efficacy of these CUR-CD-CS nanoparticles in SCC25 cell lines using MTT assay and investigated its cellular uptake mechanism. We also studied Oligo DNA loading in CUR-CD-CS nanoparticles and its delivery via confocal imaging and FACS analysis. Our results demonstrated that CUR-CD-CS nanoparticles showed superior in vitro release performance and higher cytotoxicity in SCC25 cell line amongst all tested formulations. The cytotoxicity results were corroborated by cell cycle analysis and apoptosis test, showing nearly 100% apoptotic cell death in the case of CUR-CD-CS nanoparticles. Compared to CS nanoparticles, CS-CD nanoformulation showed higher cellular delivery of Cy3-Oligo DNA which was tested quantitatively using flowcytometry analysis, indicating that CD not only enhanced CUR solubility but also boosted the cellular uptake. Our study shows that rationally designed bio-degradable natural biomaterials have great potential as next generation nano-carriers for hydrophobic drug delivery such as CUR with potential of dual drug-gene delivery.","corpus_id":21250009,"score":2},{"doc_id":"24758141","title":"pH triggered delivery of curcumin from Eudragit-coated chitosan microspheres for inflammatory bowel disease: characterization and pharmacodynamic evaluation.","abstract":"OBJECTIVE: This investigation deals with the development and evaluation (in vitro and in vivo) of pH triggered Eudragit-coated chitosan microspheres of curcumin (CUR) for treating ulcerative colitis. METHODS: CUR-loaded chitosan microspheres were initially prepared by emulsion cross linking method followed by coating with Eudragit S-100. The pharmacodynamics of the developed formulation was analyzed in mice by acetic acid induced colitis model. RESULTS: The developed microspheres were of uniform spherical shape with high entrapment efficiency. CUR-chitosan microspheres showed less intense peaks compared to free CUR confirming inclusion of drug within microspheres as revealed by X-ray diffractogram. Uncoated CUR-chitosan microspheres exhibited burst release within initial 4 h while microspheres coated with Eudragit S-100 prevented premature release of CUR and showed controlled release up to 12 h following Higuchi model. In vivo organ biodistribution study showed negligible amount of CUR in stomach and small intestine confirming integrity of microsphere in upper gastrointestinal tract (GIT). In vivo study revealed significant reduction in severity and extent of colonic damage with CUR-loaded microspheres as compared to pure CUR which was further confirmed by histopathological study. CONCLUSION: In vitro and in vivo studies proved the developed formulations as a promising system for pH-dependent delivery of drug to colon in ulcerative colitis.","corpus_id":13310404,"score":2},{"doc_id":"25511809","title":"Effects of the Preparation Method on the Formation of True Nimodipine SBE-β-CD/HP-β-CD Inclusion Complexes and Their Dissolution Rates Enhancement.","abstract":"The aims of this study were to enhance the solubility and dissolution rate of nimodipine (ND) by preparing the inclusion complexes of ND with sulfobutylether-b-cyclodextrin (SBE-β-CD) and 2-hydroxypropyl-b-cyclodextrin (HP-β-CD) and to study the effect of the preparation method on the in vitro dissolution profile in different media (0.1 N HCl pH 1.2, phosphate buffer pH 7.4, and distilled water). Thus, the inclusion complexes were prepared by kneading, coprecipitation, and freeze-drying methods. Phase solubility studies were conducted to characterize the complexes in the liquid state. The inclusion complexes in the solid state were investigated with differential scanning calorimetry (DSC), X-ray diffractometry (X-RD), and Fourier transform infrared spectroscopy (FT-IR). Stable complexes of ND/SBE-β-CD and ND/HP-β-CD were formed in distilled water in a 1:1 stoichiometric inclusion complex as indicated by an AL-type diagram. The apparent stability constants (Ks) were 1334.4 and 464.1 M(-1) for ND/SBE-β-CD and ND/HP-β-CD, respectively. The water-solubility of ND was significantly increased in an average of 22- and 8-fold for SBE-β-CD and HP-β-CD, respectively. DSC results showed the formation of true inclusion complexes between the drug and both SBE-β-CD and HP-β-CD prepared by the kneading method. In contrast, crystalline drug was detectable in all other products. The dissolution studies showed that all the products exhibited higher dissolution rate than those of the physical mixtures and ND alone, in all mediums. However, the kneading complexes displayed the maximum dissolution rate in comparison with drug and other complexes, confirming the influence of the preparation method on the physicochemical properties of the products.","corpus_id":14844305,"score":2},{"doc_id":"26170159","title":"Cost-effective alternative to nano-encapsulation: Amorphous curcumin-chitosan nanoparticle complex exhibiting high payload and supersaturation generation.","abstract":"While the wide-ranging therapeutic activities of curcumin have been well established, its successful delivery to realize its true therapeutic potentials faces a major challenge due to its low oral bioavailability. Even though nano-encapsulation has been widely demonstrated to be effective in enhancing the bioavailability of curcumin, it is not without drawbacks (i.e. low payload and costly preparation). Herein we present a cost-effective bioavailability enhancement strategy of curcumin in the form of amorphous curcumin-chitosan nanoparticle complex (or curcumin nanoplex in short) exhibiting a high payload (>80%). The curcumin nanoplex was prepared by a simple yet highly efficient drug-polysaccharide complexation method that required only mixing of the curcumin and chitosan solutions under ambient condition. The effects of (1) pH and (2) charge ratio of chitosan to curcumin on the (i) physical characteristics of the nanoplex (i.e. size, colloidal stability and payload), (ii) complexation efficiency, and (iii) production yield were investigated from which the optimal preparation condition was determined. The nanoplex formation was found to favor low acidic pH and charge ratio below unity. At the optimal condition (i.e. pH 4.4. and charge ratio=0.8), stable curcumin nanoplex (≈260nm) was prepared at >90% complexation efficiency and ≈50% production yield. The amorphous state stability, colloidal stability, and in vitro non-cytotoxicity of the nanoplex were successfully established. The curcumin nanoplex produced prolonged supersaturation (3h) in the presence of hydroxypropyl methylcellulose (HPMC) at five times of the saturation solubility of curcumin. In addition, curcumin released from the nanoplex exhibited improved chemical stability owed to the presence of chitosan. Both results (i.e. high supersaturation and improved chemical stability) bode well for the ability of the curcumin nanoplex to enhance the bioavailability of curcumin clinically.","corpus_id":44681741,"score":2},{"doc_id":"26394122","title":"In vitro cytotoxicity and in vivo efficacy of 5-fluorouracil-loaded enteric-coated PEG-crosslinked chitosan microspheres in colorectal cancer therapy in rats.","abstract":"PURPOSE: Microspheres of chitosan (CS) crosslinked with polyethylene glycol (PEG) were prepared by emulsion crosslinking followed by solvent evaporation technique. The formulations were characterized and subjected to in vitro and in vivo tests to assess cell growth, changes in cell morphology and activities by 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide (MTT) assay on human HT-29 colon cancer cell lines. METHODS: In vivo activity was evaluated for dimethyl hydrazine-induced colorectal cancer in albino male Wistar rats. Biochemical and histological parameters were evaluated to understand their effectiveness for colon cancer therapy. RESULTS: The 5-FU immediate release (IR) formulations suspended in sodium carboxymethyl cellulose (SCMC) produced an immediate cytotoxic effect, whereas microspheres inhibited the proliferation of tumor cells to induce apoptosis over an extended time. Minimum inhibitory concentration (IC50) values for both standard plain 5-FU and 5-FU-loaded microspheres were, respectively, 5.00 ± 0.004 µg/mL and 165 ± 1.9 µg/mL which showed the improved safety profile of the microsphere formulation. Tissue distribution showed high concentration of 5-FU in colon that was higher than IC50 required to stop the growth or death of colon cancer cells from the colonic dysplasia in Duke's Stage A. Significant reduction in tumor volume and multiplicity was observed with increased levels of liver enzymes in animals when treated with standard 5-FU formulation compared to 5-FU-loaded microspheres. Elevated levels of serum albumin, creatinine, leukocytopenia and thrombocytopenia were observed in animals for the standard 5-FU formulation. CONCLUSION: The PEG-crosslinked CS microspheres of this study slowly released 5-FU up to 24 h to colonic region and enhanced the antitumor activity.","corpus_id":45975018,"score":2},{"doc_id":"26678861","title":"Optimization of chitosan nanoparticles for colon tumors using experimental design methodology.","abstract":"Purpose Colon-specific drug delivery systems (CDDS) can improve the bio-availability of drugs through the oral route. A novel formulation for oral administration using ligand coupled chitosan nanoparticles bearing 5-Flurouracil (5FU) encapsulated in enteric coated pellets has been investigated for CDDS. Method The effect of polymer concentration, drug concentration, stirring time and stirring speed on the encapsulation efficiency, and size of nanoparticles were evaluated. The best (or optimum) formulation was obtained by response surface methodology. Using the experimental data, analysis of variance has been carried out to evolve linear empirical models. Using a new methodology, polynomial models have been evolved and the parametric analysis has been carried out. In order to target nanoparticles to the hyaluronic acid (HA) receptors present on colon tumors, HA coupled nanoparticles were tested for their efficacy in vivo. The HA coupled nanoparticles were encapsulated in pellets and were enteric coated to release the drug in the colon. Results Drug release studies under conditions of mimicking stomach to colon transit have shown that the drug was protected from being released in the physiological environment of the stomach and small intestine. The relatively high local drug concentration with prolonged exposure time provides a potential to enhance anti-tumor efficacy with low systemic toxicity for the treatment of colon cancer. Conclusions Conclusively, HA coupled nanoparticles can be considered as the potential candidate for targeted drug delivery and are anticipated to be promising in the treatment of colorectal cancer.","corpus_id":23450589,"score":2},{"doc_id":"27582072","title":"Mucoadhesive Chitosan-Pectinate Nanoparticles for the Delivery of Curcumin to the Colon.","abstract":"In the present study, we report the properties of a mucoadhesive chitosan-pectinate nanoparticulate formulation able to retain its integrity in the milieu of the upper gastrointestinal tract and subsequently, mucoadhere and release curcumin in colon conditions. Using this system, we aimed to deliver curcumin to the colon for the possible management of colorectal cancer. The delivery system comprised of a chitosan-pectinate composite nanopolymeric with a z-average of 206.0 nm (±6.6 nm) and zeta potential of +32.8 mV (±0.5 mV) and encapsulation efficiency of 64%. The nanoparticles mucoadhesiveness was higher at alkaline pH compared to acidic pH. Furthermore, more than 80% release of curcumin was achieved in pectinase-enriched medium (pH 6.4) as opposed to negligible release in acidic and enzyme-restricted media at pH 6.8. SEM images of the nanoparticles after exposure to the various media indicate a retained matrix in acid media as opposed to a distorted/fragmented matrix in pectinase-enriched medium. The data strongly indicates that the system has the potential to be applied as a colon-targeted mucoadhesive curcumin delivery system for the possible treatment of colon cancer.","corpus_id":4730016,"score":2},{"doc_id":"28130133","title":"Inhalable bioresponsive chitosan microspheres of doxorubicin and soluble curcumin augmented drug delivery in lung cancer cells.","abstract":"In present investigation, doxorubicin (Dox) and soluble curcumin (Cur-2-HP-β-CD-complex) combination was simultaneously loaded in inhalable bioresponsive chitosan microspheres (Dox/Cur-2-HP-β-CD-complex-elastin-CMs) bearing a substrate-stimuli, elastin. The mean particle size and mean aerodynamic diameter of inhalable bioresponsive microspheres displayed noteworthy differences after incorporation of elastin. Moreover, combination of Dox and soluble curcumin was molecularly dispersed in microspheres matrix as substantiated by a range of spectral techniques. Inhalable bioresponsive microspheres released astonishingly higher amount of Dox in presence of elastase enzyme at pH∼5.5 in comparison to pH∼7.4. However, the release of soluble curcumin from tailored bioresponsive microspheres in presence of elastase enzyme was independent of pH. Consistently, inhalable bioresponsive microspheres exhibited outstandingly lower IC50 of 3.4-μM in comparison to 6.5-μM of inhalable drug loaded microspheres (Dox/Cur-2-HP-β-CD-complex-CMs) bearing no elastin, against A549, non-small cell lung cancer cells. The superior therapeutic profile of inhalable bioresponsive microspheres may be attributed to enhanced drug release and consequently augmented drug exposure to A549 cells expressing elastase enzyme. In this way, stimuli triggered drug release from tailored inhalable bioresponsive microspheres boosted the phenomena of apoptosis in A549 cells. In conclusion, Dox/Cur-2-HP-β-CD-complex-elastin-CMs warrant further in-vivo tumor regression study to prove its therapeutic efficacy.","corpus_id":205191838,"score":2},{"doc_id":"28891961","title":"Visible Light-Cured Glycol Chitosan Hydrogel Containing a Beta-Cyclodextrin-Curcumin Inclusion Complex Improves Wound Healing In Vivo.","abstract":"Scarless wound healing is ideal for patients suffering from soft tissue defects. In this study, we prepared a novel wet dressing (β-CD-ic-CUR/GC) based on the visible light-cured glycol chitosan (GC) hydrogel and inclusion complex between beta-cyclodextrin (β-CD) and curcumin (CUR). We also evaluated its efficacy in the acceleration of wound healing as compared to that of CUR-loaded GC (CUR/GC). The conjugation of glycidyl methacrylate (GM) to GC for photo-curing was confirmed by ¹H-NMR measurement, and the photo-cured GC hydrogel was characterized by the analyses of rheology, swelling ratio, SEM and degradation rate. After visible light irradiation, the surface/cross-sectional morphologies and storage (G')/loss (G'') moduli revealed the formation of hydrogel with interconnected porosity. The dressing β-CD-ic-CUR/GC exhibited a controlled release of 90% CUR in a sustained manner for 30 days. On the other hand, CUR/GC showed CUR release of 16%. β-CD acted as an excipient in improving the water-solubility of CUR and affected the release behavior of CUR. The in vivo animal tests including measurement of the remaining unhealed wound area and histological analyses showed that β-CD-ic-CUR/GC may have potential as a wet dressing agent to enhance soft tissue recovery in open fractures.","corpus_id":22452956,"score":2},{"doc_id":"29110292","title":"Development of Chitosan-Based pH-Sensitive Polymeric Micelles Containing Curcumin for Colon-Targeted Drug Delivery.","abstract":"pH-sensitive N-naphthyl-N,O-succinyl chitosan (NSCS) and N-octyl-N,O-succinyl chitosan (OSCS) polymeric micelles carriers have been developed to incorporate curcumin (CUR) for colon-targeted drug delivery. The physical entrapment methods (dialysis, co-solvent evaporation, dropping, and O/W emulsion) were applied. The CUR-loaded micelles prepared by the dialysis method presented the highest loading capacity. Increasing initial amount of CUR from 5 to 40 wt% to polymer resulted in the increase in loading capacity of the polymeric micelles. Among the hydrophobic cores, there were no significant differences in the loading capacity of CUR-loaded micelles. The particle sizes of all CUR-loaded micelles were in the range of 120-338 nm. The morphology of the micelles changed after being contacted with medium with different pH values, confirming the pH-responsive properties of the micelles. The release characteristics of curcumin from all CUR-loaded micelles were pH-dependent. The percent cumulative release of curcumin from all CUR-loaded micelles in simulated gastric fluid (SGF) was limited to about 20%. However, the release amount was significantly increased after contacted with simulated intestinal fluid (SIF) (50-55%) and simulated colonic fluid (SCF) (60-70%). The released amount in SIF and SCF was significantly greater than the release of CUR from CUR powder. CUR-loaded NSCS exhibited the highest anti-cancer activity against HT-29 colorectal cancer cells. The stability studies indicated that all CUR-loaded micelles were stable for at least 90 days. Therefore, the colon targeted, pH-sensitive NSCS micelles may have potential to be a prospective candidate for curcumin delivery to the colon.","corpus_id":4444547,"score":2},{"doc_id":"18289808","title":"Nanoparticles of quaternized chitosan derivatives as a carrier for colon delivery of insulin: ex vivo and in vivo studies.","abstract":"The aim of the present study was to develop insulin nanoparticulate systems by using chitosan (CS), triethylchitosan (TEC) and dimethyl-ethylchitosan (DMEC, a new quaternized derivative of chitosan) for colon delivery. The nanoparticles were prepared by the polyelectrolyte complexation (PEC) method. Particle size distribution, zeta potential and polydispersity index of the nanoparticles were determined using dynamic light scattering technique. Transmission electron microscopy (TEM) was also used to observe the morphology of the nanoparticles. It was found that the nanoparticles carried positive charges and showed a size distribution in the range of 170-270 nm with spherical morphology and smooth surface structure. The amount of insulin loaded into the nanoparticles was determined by measuring the association efficiency and also the content of insulin in the nanoparticles. Insulin loading was found to be more than 80% for all of the nanoparticles. In vitro release studies showed a small burst effect at the beginning and then a sustained release characteristic for 5h. Ex vivo investigations revealed better insulin transport across the colon membrane of rats for nanoparticles made with quaternized derivatives than those made of chitosan. In vivo studies in rats have showed enhanced colon absorption of insulin by using these nanoparticles compared to free insulin in diabetic rats. The insulin absorption from the rat's colon was evaluated by its hypoglycemic effect.","corpus_id":19580041,"score":1},{"doc_id":"18523891","title":"Mucoadhesive microspheres for gastroretentive delivery of acyclovir: in vitro and in vivo evaluation.","abstract":"The aim of the present investigation was to evaluate the potential use of mucoadhesive microspheres for gastroretentive delivery of acyclovir. Chitosan, thiolated chitosan, Carbopol 71G and Methocel K15M were used as mucoadhesive polymers. Microsphere formulations were prepared using emulsion-chemical crosslinking technique and evaluated in vitro, ex-vivo and in-vivo. Gelatin capsules containing drug powder showed complete dissolution (90.5 +/- 3.6%) in 1 h. The release of drug was prolonged to 12 h (78.8 +/- 3.9) when incorporated into mucoadhesive microspheres. The poor bioavailability of acyclovir is attributed to short retention of its dosage form at the absorption sites (in upper gastrointestinal tract to duodenum and jejunum). The results of mucoadhesion study showed better retention of thiolated chitosan microspheres (8.0 +/- 0.8 h) in duodenal and jejunum regions of intestine. The results of qualitative and quantitative GI distribution study also showed significant higher retention of mucoadhesive microspheres in upper GI tract. Pharmacokinetic study revealed that administration of mucoadhesive microspheres could maintain measurable plasma concentration of acyclovir through 24 h, as compared to 5 h after its administration in solution form. Thiolated chitosan microsphere showed superiority over the other formulations as observed with nearly 4.0-fold higher AUC(0-24) value (1,090 +/- 51 ng h/ml) in comparison to drug solution (281 +/- 28 ng h/ml). Overall, the result indicated prolonged delivery with significant improvement in oral bioavailability of acyclovir from mucoadhesive microspheres due to enhanced retention in the upper GI tract.","corpus_id":22185592,"score":1},{"doc_id":"18591810","title":"Study on colon-specific 5-Fu pH-enzyme Di-dependent chitosan microspheres.","abstract":"Colon-specific drug delivery systems (CDDS) can improve the bioavailability of drug through the oral route. A novel formulation for oral administration using pH-enzyme Di-dependent chitosan mcirospheres (MS) and 5-Fu as a model drug has been investigated for colon-specific drug delivery by the emulsification/chemical cross-linking and coating technique, respectively. The influence of polymer concentration, ratio of drug to polymer, the amount of crosslinking agent and the stirring speed on the encapsulation efficiency, particle size in microspheres were evaluated. The best formulation was optimized by an orthogonal design. Drug release studies under conditions mimicking stomach to colon transit have shown that the drug was protected from being released in the physiological environment of the stomach and small intestine. The plasma concentrations of 5-Fu after oral administration of coated chitosan MS to rats were determined and compared with that of 5-Fu solution. The in vivo pharmacokinetics study of 5-Fu loaded pH-enzyme Di-dependent chitosan MS showed sustained plasma 5-Fu concentration-time profile. The in vitro release correlated well with the pharmacokinetics profile. The results clearly demonstrated that the pH-enzyme Di-dependent chitosan MS is potential system for colon-specific drug delivery of 5-Fu.","corpus_id":6062522,"score":1},{"doc_id":"18855198","title":"In vitro evaluation of chondroitin sulphate-chitosan microspheres as carrier for the delivery of proteins.","abstract":"A novel formulation based on chondroitin sulphate/chitosan microspheres (CS/CH) has been investigated for oral delivery of macromolecules using ovalbumin as the model protein (OVA). The microspheres were prepared by a new emulsion-complex coacervation method. Physico-chemical properties of the polymers constituting microparticulate matrix were investigated by IR, DSC, TGA and X-ray diffraction analyses. In vitro tests were performed to evaluate the drug delivery system degradation and the protein release under conditions simulating the intestinal fluids. The ability of colonic enzymes to degrade the microparticulate systems was simulated employing the chondroitinase ABC enzyme. Results showed that the different CS/CH compositions influenced both microparticles stability and the protein release rate. Only the microspheres composed by 1:1 chondroitin sulphate-chitosan ratio achieved an OVA release profile suitable to a possible colon targeting. These microspheres released approximately 30% of ovalbumin encapsulated in 24 h in the different aqueous media tested, while they released 100% of protein in the presence of chondroitinase. The preliminary results demonstrated that chondroitin sulphate-chitosan microspheres can be a suitable delivery system for protein drug envisaged to oral administration.","corpus_id":1200540,"score":1},{"doc_id":"20136490","title":"Ondansetron-loaded chitosan microspheres for nasal antiemetic drug delivery: an alternative approach to oral and parenteral routes.","abstract":"BACKGROUND: The aim of this study was to develop chitosan microspheres for nasal delivery of ondansetron hydrochloride (OND). METHOD: Microspheres were prepared with spray-drying method using glutaraldehyde as the crosslinking agent. Microspheres were characterized in terms of morphology, particle size, zeta potential, production yield, drug content, encapsulation efficiency, and in vitro drug release. RESULTS: All microspheres were spherical in shape with smooth surface and positively charged. Microspheres had also high encapsulation efficiency and the suitable particle size for nasal administration. In vitro studies indicated that all crosslinked microspheres had a significant burst effect, and sustained drug release pattern was observed until 24 hours following burst drug release. Nasal absorption of OND from crosslinked chitosan microspheres was evaluated in rats, and pharmacokinetic parameters of OND calculated from nasal microsphere administration were compared with those of both nasal and parenteral administration of aqueous solutions of OND. In vivo data also supported that OND-loaded microspheres were also able to attain a sustained plasma profile and significantly larger area under the curve values with respect to nasal aqueous solution of OND. CONCLUSION: Based on in vitro and in vivo data, it could be concluded that crosslinked chitosan microspheres are considered as a nasal delivery system of OND.","corpus_id":23543784,"score":1},{"doc_id":"20535630","title":"Eudragit S-100 entrapped chitosan microspheres of valdecoxib for colon cancer.","abstract":"COX-2 inhibitors have demonstrated beneficial effects in colorectal cancer. The purpose of this study was to prepare and evaluate the colon specific microspheres of COX-2 inhibitors using valdecoxib as a model drug. Mucoadhesive core microspheres were prepared using chitosan as polymer and entrapped within Eudragit S 100 for colon targeting. FTIR spectrum of selected, coated microspheres showed peaks of valdecoxib at 3377, 3250, 1334 and 1155 cm(-1). XRD showed amorphous character and DSC showed depressed broad endotherm of valdecoxib at 169.07 degrees C, which may be attributed to dilution effect by the amorphous polymer. The coated microspheres were spherical with an average size of 90 mum. Storage of the microspheres at 40 degrees C/75% relative humidity for 6 months indicated no significant drug degradation. The coated microspheres did neither release the drug in acidic pH of stomach (pH 1.2) nor in small intestinal pH between 5 to 6.8, and the release started at pH 7.4, indicting perfect colonic delivery. The coated microspheres pretreated with phosphate buffer pH 7.4 for 30 min, when applied to mucosal surface of freshly excised goat colon, showed good mucoadhesion. The drug release at pH 7.4 and good mucoadhesive property of the microspheres make the system ideal for colonic delivery.","corpus_id":20799285,"score":1},{"doc_id":"20735299","title":"Chitosan microspheres of aceclofenac: in vitro and in vivo evaluation.","abstract":"The objective of this investigation was to achieve controlled drug release of Aceclofenac (ACE) microspheres and to minimize local side-effects in the gastrointestinal tract (GIT). Sustained release chitosan microspheres containing ACE were prepared using double-emulsion solvent evaporation method (O/W/O). Chitosan microspheres were prepared by varying drug to polymer ratio (1:3, 1:4, 1:5 and 1:6). Microspheres were characterized for morphology, swelling behavior, mucoadhesive properties, FTIR and DSC study, drug loading efficiency, in vitro release, release kinetics, and in vivo study was performed on rat model. ACE-loaded microspheres were successfully prepared having production yield, 57-70% w/w. Drug encapsulation efficiency was ranging from 53-72% w/w, Scanning electron microscopy (SEM) revealed particle size of microspheres was between 39 and 55 mum. FTIR spectra and DSC thermograms demonstrated no interaction between drug and polymer. The in vitro release profiles of drug from chitosan microspheres showed sustained-release pattern of the drug in phosphate buffer, pH 6.8. In vitro release data showed correlation (r2 > 0.98), good fit with Higuchi/Korsmeyer-Peppas models, and exhibited Fickian diffusion. ACE microspheres demonstrated controlled delivery of aceclofenac and apparently, no G.I.T. erosion was noticed.","corpus_id":22750407,"score":1},{"doc_id":"20848388","title":"Formulation and evaluation of chitosan microspheres of aceclofenac for colon-targeted drug delivery.","abstract":"The objective of this investigation was to develop novel colon specific drug delivery. Aceclofenac, a NSAID, was successfully encapsulated into chitosan microspheres. Various formulations were prepared by varying the ratio of chitosan, span-85 and stirring speed and the amount of glutaraldehyde. The SEM study showed that microspheres have smooth surfaces. Microspheres were characterised by Fourier transform infrared (FTIR) spectroscopy and differential scanning calorimetry (DSC) to confirm the absence of chemical interactions between drug and polymer and to know the formation of microspheres structure. The microspheres were evaluated for particle size, encapsulation efficiency, drug loading capacity, mucoadhesion studies, stability studies, in vitro and in vivo drug release studies. Particle sizes, as measured by the laser light scattering technique, were of an average size in the range 41-80 µm. The swelling index was in the range 0.37-0.82 and the entrapment efficiency range was 51-75% for all the formulations. The optimised batch ACM(13) released 83.6% at 8 h and 104% at 24 h in SCF containing rat caecal content. Eudragit coated chitosan microspheres prevented the release of the aceclofenac in the physiological environment of the stomach and small intestine and released 95.9±0.34% in the colon. With regard to release kinetics, the data were best fitted with the Higuchi model and showed zero order release with non-Fickian diffusion mechanism. The in vivo findings suggest that aceclofenac microspheres exhibit a prolonged effect of aceclofenac in rats and produce a significant anti-inflammatory effect. The findings of the present study conclusively state that chitosan microspheres are promising for colon targeting of aceclofenac to synchronise with chronobiological symptoms of rheumatoid arthritis.","corpus_id":22430281,"score":1},{"doc_id":"20933083","title":"Preparation and evaluation of alginate-chitosan microspheres for oral delivery of insulin.","abstract":"The alginate-chitosan microspheres with narrow size distribution were prepared by membrane emulsification technique in combination with ion (Ca(2+)) and polymer (chitosan) solidification. The preparation procedure was observed, and the physical properties (particle size distribution, surface morphology, chitosan distribution, zeta potential) of the microspheres were characterized. Subsequently, the microspheres were employed to load model peptide of insulin. The effect of loading ways on the loading efficiency and immunological activity of insulin were investigated. It was shown that the higher loading efficiency (56.7%) and remarkable activity maintenance (99.4%) were obtained when the insulin was loaded during the chitosan solidification process (Method B). Afterward, the release profile in vitro for the optimal insulin-loaded microspheres was investigated. Under the pH conditions of gastrointestinal environment, only 32% of insulin released during the simulated transit time of drug (2 h in the stomach and 4 h in the intestinal). While under the pH condition of blood environment, insulin release was stable and sustained for a long time (14 days). Furthermore, the chemical stability of insulin released from the microspheres was well preserved after they were treated with the simulated gastric fluid containing pepsin for 2 h. Finally, the blood glucose level of diabetic rats could be effectively reduced and stably kept for a long time (∼60 h) after oral administration of the insulin-loaded alginate-chitosan microspheres. Therefore, the alginate-chitosan microspheres were found to be promising vectors showing a good efficiency in oral administration of protein or peptide drugs.","corpus_id":19310111,"score":1},{"doc_id":"21168477","title":"Preparation and evaluation of zinc-pectin-chitosan composite particles for drug delivery to the colon: role of chitosan in modifying in vitro and in vivo drug release.","abstract":"Zinc-pectin-chitosan composite microparticles were designed and developed as colon-specific carrier. Resveratrol was used as model drug due to its potential activity on colon diseases. Formulations were produced by varying different formulation parameters (cross-linking pH, chitosan concentration, cross-linking time, molecular weight of chitosan, and drug concentration). Single-step formulation technique was compared with multi-step technique. Effect of these parameters was investigated on shape, size, weight, weight loss (WL), moisture content (MC), encapsulation efficiency (EE), drug loading (L), and drug release pattern of the microparticles. The formulation conditions were optimized from the drug release study. In vivo pharmacokinetics of the zinc-pectinate particles was compared with the zinc-pectin-chitosan composite particles in rats. Formulations were spherical with 920.48-1107.56 μm size, 21.19-24.27 mg weight of 50 particles, 89.83-94.34% WL, 8.31-13.25% MC, 96.95-98.85% EE, and 17.82-48.31% L. Formulation parameters showed significant influence on drug release pattern from the formulations. Formulation prepared at pH 1.5, 1% chitosan, 120 min cross-linking time, and pectin:drug at 3:1 ratio demonstrated colon-specific drug release. Microparticles were stable at 4 °C and room temperature. Pharmacokinetic study indicated in vivo colon-specific drug release from the zinc-pectin-chitosan composite particles only.","corpus_id":21222772,"score":1},{"doc_id":"21194900","title":"Colon specific chitosan microspheres for chronotherapy of chronic stable angina.","abstract":"In the present work, chitosan microspheres with a mean diameter between 6.32 μm and 9.44 μm, were produced by emulsion cross-linking of chitosan, and tested for chronotherapy of chronic stable angina. Aiming at developing a suitable colon specific strategy, diltiazem hydrochloride (DTZ) was encapsulated in the microspheres, following Eudragit S-100 coating by solvent evaporation technique, exploiting the advantages of microbiological properties of chitosan and pH dependent solubility of Eudragit S-100. Different microsphere formulations were prepared varying the ratio DTZ:chitosan (1:2 to 1:10), stirring speed (1000-2000 rpm), and the concentration of emulsifier Span 80 (0.5-1.5% (w/v)). The effect of these variables on the particle size and encapsulation parameters (production yield (PY), loading capacity (LC), encapsulation efficiency (EE)) was evaluated to develop an optimized formulation. In vitro release study of non-coated chitosan microspheres in simulated gastrointestinal (GI) fluid exhibited a burst release pattern in the first hour, whereas Eudragit S-100 coating allowed producing systems of controlled release diffusion fitting to the Higuchi model, and thus suitable for colon-specific drug delivery. DSC analysis indicated that DTZ was dispersed within the microspheres matrix. Scanning electron microscopy revealed that the microspheres were spherical and had a smooth surface. Chitosan biodegradability was proven by the enhanced release rate of DTZ in presence of rat caecal contents.","corpus_id":22854209,"score":1},{"doc_id":"21431353","title":"Sustained release optimized formulation of anastrozole-loaded chitosan microspheres: in vitro and in vivo evaluation.","abstract":"The purpose of this study was to develop sustained release formulation of anastrozole-loaded chitosan microspheres for treatment of breast cancer. Chitosan microspheres cross-linked with two different cross-linking agents viz, tripolyphosphate (TPP) and glutaraldehyde (GA) were prepared using single emulsion (w/o) method. A reverse phase HPLC method was developed and used for quantification of drug in microspheres and rat plasma. Influence of cross-linking agents on the properties of chitosan microspheres was extensively investigated. Formulations were characterized for encapsulation efficiency (EE), compatibility of drug with excipients, particle size, surface morphology, swelling capacity, erosion and drug release profile in phosphate buffer pH 7.4. EE varied from 30.4 ± 1.2 to 69.2 ± 3.2% and mean particle size distribution ranged from 72.5 ± 0.5 to 157.9 ± 1.5 μm. SEM analysis revealed smooth and spherical nature of microspheres. TPP microspheres exhibited higher swelling capacity, percentage erosion and drug release compared to GA microspheres. Release of anastrozole (ANS) was rapid up to 4 h followed by slow release status. FTIR analysis revealed no chemical interaction between drug and polymer. DSC analysis indicated ANS trapped in the microspheres existed in amorphous form in polymer matrix. The highest correlation coefficients (R (2)) were obtained for Higuchi model, suggesting a diffusion controlled mechanism. There was significant difference in the pharmacokinetic parameters (AUC(0-∞), Kel and t(1/2)) when ANS was formulated in the form of microspheres compared to pure drug. This may be attributed to slow release rate of ANS from chitosan microspheres and was detectable in rat plasma up to 48 h which correlates well with the in vitro release data.","corpus_id":25829231,"score":1},{"doc_id":"21699389","title":"Inclusion complex of colchicine in hydroxypropyl-β-cyclodextrin tenders better solubility and improved pharmacokinetics.","abstract":"CONTEXT: Colchicine (CLC) causes cell death by destabilizing the tubulin unit. However, it ionizes at physiological pH resultant low bioavailability and therapeutic efficacy. OBJECTIVES: We have attempted to augment the bioavailability of CLC by fabricating the inclusion complex with hydroxypropyl-β-cyclodextrin (HP-β-CD). MATERIALS AND METHODS: CLC-HP-β-CD inclusion complex was prepared and evaluated with Fourier-transform infrared spectroscopy, differential scanning calorimetry, powder X-ray diffractometry, scanning electron microscopy, (1)H nuclear magnetic resonance ((1)H NMR) spectroscopy and rotating frame overhauser enhancement spectroscopy (ROESY). Oral bioavailability of CLC-HP-β-CD inclusion complex was analyzed using high performance liquid chromatography method. RESULTS AND DISCUSSION: Our phase-solubility data indicated the formation of a stable complex with K(c) ~0.31 mM(-1) at pH 7.4. (1)H NMR ascertains that NHCOCH(3) moiety of CLC enters in the HP-β-CD cavity and deshielded the H-3 and H-5 protons. ROESY also correlates the H(f) and H(g) of CLC with H-3 and H-5 protons of HP-β-CD and indicates that H(f) and H(g) protons of CLC are present either as cis and/or trans form in CLC-HP-β-CD inclusion complex. Pharmacokinetic studies showed a 1.82-fold increase in absolute bioavailability of CLC upon complexation. CONCLUSION: CLC-HP-β-CD inclusion complex may potentially be used as a viable formulation of CLC.","corpus_id":23636364,"score":1},{"doc_id":"21824069","title":"Eudragit® S100 coated calcium pectinate microspheres of curcumin for colon targeting.","abstract":"Currently, colon-specific drug delivery systems have been investigated for drugs that can exert their bioactivities in the colon. In this study, Eudragit® S100 coated calcium pectinate microsphere, a pH-dependent and enzyme-dependent system, as colon-specific delivery carrier for curcumin was investigated. Curcumin-loaded calcium pectinate microspheres were prepared by emulsification-linkage method, and the preparation technology was optimised by uniform experimental design. The morphology of microspheres was observed under scanning electron microscopy. Interactions between drug and polymers were investigated with differential scanning calorimetry (DSC) and X-ray diffraction. In vitro drug release studies were performed in simulated colonic fluid in the presence of Pectinex Ultra SP-L or 1% (w/v) rat caecal content, and the results indicated that the release of curcumin was significantly increased in the presence of 1% (w/v) rat caecal contents. It could be concluded that Eudragit® S100 coated calcium pectinate microsphere was a potential carrier for colon delivery of curcumin.","corpus_id":12225404,"score":1},{"doc_id":"21864681","title":"Quality by design approach for developing chitosan-Ca-alginate microspheres for colon delivery of celecoxib-hydroxypropyl-β-cyclodextrin-PVP complex.","abstract":"The aim of the present work was to develop a new multiparticulate system, designed for colon-specific delivery of celecoxib for both systemic (in chronotherapic treatment of arthritis) and local (in prophylaxis of colon carcinogenesis) therapy. The system simultaneously benefits from ternary complexation with hydroxypropyl-β-cyclodextrin and PVP (polyvinylpyrrolidone), to increase drug solubility, and vectorization in chitosan-Ca-alginate microspheres, to exploit the colon-specific carrier properties of these polymers. Statistical experimental design was employed to investigate the combined effect of four formulation variables, i.e., % of alginate, CaCl₂, and chitosan and time of cross-linking on microsphere entrapment efficiency (EE%) and drug amount released after 4h in colonic medium, considered as the responses to be optimized. Design of experiment was used in the context of Quality by Design, which requires a multivariate approach for understanding the multifactorial relationships among formulation parameters. Doehlert design allowed for defining a design space, which revealed that variations of the considered factors had in most cases an opposite influence on the responses. Desirability function was used to attain simultaneous optimization of both responses. The desired goals were achieved for both systemic and local use of celecoxib. Experimental values obtained from the optimized formulations were in both cases very close to the predicted values, thus confirming the validity of the generated mathematical model. These results demonstrated the effectiveness of the proposed jointed use of drug cyclodextrin complexation and chitosan-Ca-alginate microsphere vectorization, as well as the usefulness of the multivariate approach for the preparation of colon-targeted celecoxib microspheres with optimized properties.","corpus_id":22446904,"score":1},{"doc_id":"22139691","title":"Controlled release chitosan microspheres of mirtazapine: in vitro and in vivo evaluation.","abstract":"The purpose of the study was to formulate and evaluate controlled release chitosan microspheres of mirtazapine (MTZ) to improve the bioavailability by altering the pharmacokinetic profiles of the drug. Chitosan microspheres were prepared to prolong the release of the drug into the systemic circulation. Microspheres were prepared by a single water in oil (w/o) emulsion technique varying the chitosan/drug ratio, stirring speed and concentration of the crosslinking agent (glutaraldehyde). Drug-polymer compatibility studies were carried out using fourier transform infrared spectroscopy (FT-IR) and differential scanning calorimetry (DSC). The microspheres were evaluated for encapsulation efficiency, particle size, surface morphology, swelling index, in vitro release, as well as erosion and in vivo studies in rats. The FT-IR and DSC studies revealed no interaction between drug and polymer. The encapsulation efficiency of different formulation varied from 53 ± 1.2% to 78 ± 1.5%. The mean particle size of the optimized formulation F-14 was 106.4 ± 0.5 μm. Surface morphology revealed that chitosan microspheres were discrete and spherical in shape with a porous surface. The release of MTZ from chitosan microspheres was rapid up to 4 h, and then it was continuously and slowly released up to 48 h. Optimized formulation (F-14) was found to be stable under accelerated storage conditions based on International Conference on Harmonisation guidelines. Pharmacokinetic studies revealed that the optimized formulation showed significant increases in systemic exposure (AUC = 177.70 ± 7.39 μg·h/mL), half-life (4.72 ± 0.46 h) and reduced clearance (0.009 ± 0.0001 L/h) compared to pure drug administration. Hence, the present study demonstrates that controlled release formulation of MTZ microspheres using chitosan can improve pharmacokinetic profiles of MTZ.","corpus_id":26979488,"score":1},{"doc_id":"22944438","title":"Investigation of inclusion complex of cilnidipine with hydroxypropyl-β-cyclodextrin.","abstract":"The objective of this study was to improve the water-solubility and photostability of cilnidipine by complexing it with hydroxypropyl-β-cyclodextrin (HP-β-CD or HP-beta-CD). The interactions of cilnidipine and HP-β-CD were characterized by ultra violet-visible (UV/VIS) spectroscopy, differential scanning calorimetry (DSC), powder X-ray diffraction (PXRD), Fourier transformation-infrared (FT-IR) spectroscopy and (1)H nuclear magnetic resonance ((1)H NMR) spectroscopy to verify the formation of cilnidipine-HP-β-CD complex inclusion. Moreover, the binding sites in the HP-β-CD structure were also tracked through (1)H NMR spectroscopy analysis. All the characterization information proved the formation of cilnidipine-HP-β-CD inclusion complex, and the results demonstrated the superiority of the inclusion complex in dissolution rates and photostability; in addition, the apparent solubility of cilnidipine was increased more than 10,000-fold in the presence of HP-β-CD. The stability constant (1:1) was found to be 50,116 M(-1), suggesting a high tendency of the drug to enter the HP-β-CD cavity. These results identified the cilnidipine-HP-β-CD inclusion complex as an effective new approach to design a novel formulation for pharmaceutical application.","corpus_id":39906702,"score":1},{"doc_id":"23524117","title":"Development and evaluation of a novel phytosome-loaded chitosan microsphere system for curcumin delivery.","abstract":"In this study, we developed a novel drug delivery system, curcumin-phytosome-loaded chitosan microspheres (Cur-PS-CMs) by combining polymer- and lipid-based delivery systems. Curcumin exhibits poor water-solubility and is rapidly eliminated from the body. We aimed to use our novel delivery system to improve the bioavailability and prolong the retention time of curcumin in the body. The Cur-PS-CMs were produced by encapsulating curcumin-phytosomes (Cur-PSs) in chitosan microspheres using ionotropic gelation. The final microsphere was spherical, with a mean particle size of 23.21 ± 6.72 μm and drug loading efficiency of 2.67 ± 0.23%. Differential scanning calorimetry and Fourier transform infrared spectroscopy demonstrated that the integrity of the phytosomes was preserved within the polymeric matrix of the microspheres. The in vitro release rate of curcumin from the Cur-PS-CMs was slower than that from curcumin-loaded chitosan microspheres (Cur-CMs) in pH 1.0, 4.0, 6.8, and 7.4. Pharmacokinetic studies in rats dosed with Cur-PS-CMs showed a 1.67- and a 1.07-fold increase in absorption of curcumin compared with Cur-PSs and Cur-CMs, respectively. The half-life of curcumin orally administration of Cur-PS-CMs (3.16 h) was longer than those of Cur-PSs (1.73 h) and Cur-CMs (2.34h). These results indicated that the new Cur-PS-CMs system combined the advantages of chitosan microspheres and phytosomes, which had better effects of promoting oral absorption and prolonging retention time of curcumin than single Cur-PSs or Cur-CMs. Therefore, the PS-CMs may be used as a sustained delivery system for lipophilic compounds with poor water-solubility and low oral bioavailability.","corpus_id":43675599,"score":1},{"doc_id":"24312757","title":"Hollow microspheres for gastroretentive floating- pulsatile drug delivery: preparation and in vitro evaluation.","abstract":"PURPOSE: A multiparticular floating-pulsatile drug delivery system was developed for time and site specific drug release of piroxicam. A blend of floating and pulsatile principles of drug delivery system would have the advantage that a drug can be released in the upper GI tract after a definite time period. METHODS: Hollow microspheres were prepared by the emulsion solvent diffusion method using Eudragit S as an enteric acrylic polymer with piroxicam at various polymer/drug ratios in a mixture of dichloromethane and ethanol. Developed formulations were evaluated for yield, encapsulation efficiency, particle size, shape, apparent density, buoyancy studies and dissolution studies. RESULTS: The obtained microballoons were spherical with no major surface irregularity and mean particle size ranging from 250 to 380 for different batches. Formulations show a slight amount of relaese ranging from 0.7 to 11% in acidic medium (SGF) with complete release of drug in simulated intestinal fluid (SIF) in less than 3 h. Encapsulation efficiency of different formulations varied from 90 to 98%. The optimum loading amount of drug in the particles was found to impart suitable floatable properties to the microballoons. With increasing polymer/drug ratio, buancy of the microballoons increases accompanied by simultaneous reduction of apparent particle density. CONCLUSION: A pulsatile release of piroxicam was demonstrated by a simple drug delivery system which could be useful in chronopharmacotherapy of rheumatoid arthritis.","corpus_id":23662412,"score":1},{"doc_id":"24360896","title":"Electrosprayed 4-carboxybenzenesulfonamide-chitosan microspheres for acetazolamide delivery.","abstract":"4-Carboxybenzensulfonamide-chitosan (4-CBS-chitosan) microspheres were prepared by electrospraying with acetazolamide (ACZ) as a model drug. The obtained 4-CBS-chitosan microspheres with or without ACZ-loading were characterized by Fourier transform infrared spectroscopy, differential scanning colorimetry, scanning electron microscopy and particle size analyses. The crystalline form and the stability of ACZ in a basic solution was determined using X-ray single crystal analysis. 4-CBS-chitosan had 90% encapsulation efficiency for ACZ compared to 47% of encapsulation efficiency (EE) obtained from native chitosan, forming 3.1 μm diameter microspheres with a low polydispersity index (0.4). After an initial burst release (58% in 5 min), ACZ-loaded 4-CBS-chitosan gave a sustained release of ACZ (∼ 100% over 3h) in simulated gastric fluid (0.1N HCl; pH 1.2), which was better than that seen for the release from ACZ-loaded chitosan (44% over 1.5h). Thus, 4-CBS-chitosan microspheres are a possible drug carrier in acidic conditions, such as at the gastric mucosal wall.","corpus_id":205182720,"score":1},{"doc_id":"24577314","title":"Docetaxel-loaded chitosan microspheres as a lung targeted drug delivery system: in vitro and in vivo evaluation.","abstract":"The aim of this study was to prepare docetaxel-loaded chitosan microspheres and to evaluate their in vitro and in vivo characteristics. Glutaraldehyde crosslinked microspheres were prepared using a water-in-oil emulsification method, and characterized in terms of the morphological examination, particle size distribution, encapsulation ratio, drug-loading coefficient and in vitro release. Pharmacokinetics and biodistribution studies were used to evaluate that microspheres have more advantage than the conventional formulations. The emulsion crosslinking method was simple to prepare microspheres and easy to scale up. The formed microspheres were spherical in shape, with a smooth surface and the size was uniform (9.6 ± 0.8 µm); the encapsulation efficiency and drug loading of prepared microspheres were 88.1% ± 3.5% and 18.7% ± 1.2%, respectively. In vitro release indicated that the DTX microspheres had a well-sustained release efficacy and in vivo studies showed that the microspheres were found to release the drug to a maximum extent in the target tissue (lung). The prepared microspheres were found to possess suitable physico-chemical properties and the particle size range. The sustained release of DTX from microspheres revealed its applicability as drug delivery system to minimize the exposure of healthy tissues while increasing the accumulation of therapeutic drug in target sites.","corpus_id":880929,"score":1},{"doc_id":"24815764","title":"In vitro combinatorial anticancer effects of 5-fluorouracil and curcumin loaded N,O-carboxymethyl chitosan nanoparticles toward colon cancer and in vivo pharmacokinetic studies.","abstract":"Colon cancer is the third most leading causes of death due to cancer worldwide and the chemo drug 5-fluorouracil's (5-FU) applicability is limited due to its non-specificity, low bioavailability and overdose. The efficacy of 5-FU in colon cancer chemo treatment could be improved by nanoencapsulation and combinatorial approach. In the present study curcumin (CUR), a known anticancer phytochemical, was used in combination with 5-FU and the work focuses on the development of a combinatorial nanomedicine based on 5-FU and CUR in N,O-carboxymethyl chitosan nanoparticles (N,O-CMC NPs). The developed 5-FU-N,O-CMC NPs and CUR-N,O-CMC NPs were found to be blood compatible. The in vitro drug release profile in pH 4.5 and 7.4 showed a sustained release profile over a period of 4 days. The combined exposure of the nanoformulations in colon cancer cells (HT 29) proved the enhanced anticancer effects. In addition, the in vivo pharmacokinetic data in mouse model revealed the improved plasma concentrations of 5-FU and CUR which prolonged up to 72 h unlike the bare drugs. In conclusion, the 5-FU and CUR released from the N,O-CMC NPs produced enhanced anticancer effects in vitro and improved plasma concentrations under in vivo conditions.","corpus_id":34471849,"score":1},{"doc_id":"24937382","title":"Preparation oral levofloxacin colon-specific microspheres delivery: in vitro and in vivo studies.","abstract":"The aim of this study was to prepare levofloxacin-loaded chitosan microspheres and to evaluate their in vitro and in vivo characteristics. Glutaraldehyde-crosslinked microspheres were prepared using a spray-drying method, and characterized in terms of the morphological examination, particle size distribution, entrapment efficiency, drug loading and in vitro release. Pharmacokinetics and colon biodistribution studies were used to evaluate that microspheres have more advantage than the conventional formulations. The surface morphology of the freeze-dried microspheres were smooth, discrete with a regular spherical to near-spherical shape. Size of the microspheres after freeze-drying was 4.96 ± 0.76 μm and well-distributed. The zeta potential of microspheres was -29.3 ± 2.1 mV. An average drug loading of 9.3 ± 0.4% and encapsulation efficiency of 81.1 ± 4.7% of levofloxacin microspheres were obtained with the optimized preparation parameters. The cumulative release rate of levofloxacin microspheres was followed by a sustained release and fitted for classic Higuchi kinetic model. In vivo studies showed that chitosan microspheres are thought to have the potential to maintain levofloxacin concentration within target ranges for a long time, decreasing side effects caused by concentration fluctuation, ensuring the efficiency of treatment and improving patient compliance by reducing dosing frequency. It also does not cause any harmful or toxic effect in colon and rectum as evaluated by histopathologic studies.","corpus_id":207519100,"score":1},{"doc_id":"25350222","title":"Cyclodextrin complexes of reduced bromonoscapine in guar gum microspheres enhance colonic drug delivery.","abstract":"Here, we report improved solubility and enhanced colonic delivery of reduced bromonoscapine (Red-Br-Nos), a cyclic ether brominated analogue of noscapine, upon encapsulation of its cyclodextrin (CD) complexes in bioresponsive guar gum microspheres (GGM). Phase-solubility analysis suggested that Red-Br-Nos complexed with β-CD and methyl-β-CD in a 1:1 stoichiometry, with a stability constant (Kc) of 2.29 × 10(3) M(-1) and 4.27 × 10(3) M(-1). Fourier transforms infrared spectroscopy indicated entrance of an O-CH₂ or OCH₃-C₆H₄-OCH₃ moiety of Red-Br-Nos in the β-CD or methyl-β-CD cavity. Furthermore, the cage complex of Red-Br-Nos with β-CD and methyl-β-CD was validated by several spectral techniques. Rotating frame Overhauser enhancement spectroscopy revealed that the Ha proton of the OCH₃-C₆H₄-OCH₃ moiety was closer to the H₅ proton of β-CD and the H₃ proton of the methyl-β-CD cavity. The solubility of Red-Br-Nos in phosphate buffer saline (PBS, pH ∼ 7.4) was improved by ∼10.7-fold and ∼21.2-fold when mixed with β-CD and methyl-β-CD, respectively. This increase in solubility led to a favorable decline in the IC₅₀ by ∼2-fold and ∼3-fold for Red-Br-Nos-β-CD-GGM and Red-Br-Nos-methyl-β-CD-GGM formulations respectively, compared to free Red-Br-Nos-β-CD and Red-Br-Nos-methyl-β-CD in human colon HT-29 cells. GGM-bearing drug complex formulations were found to be highly cytotoxic to the HT-29 cell line and further effective with simultaneous continuous release of Red-Br-Nos from microspheres. This is the first study to showing the preparation of drug-complex loaded GGMS for colon delivery of Red-Br-Nos that warrants preclinical assessment for the effective management of colon cancer.","corpus_id":26317129,"score":1},{"doc_id":"25709403","title":"Development of lovastatin-loaded poly(lactic acid) microspheres for sustained oral delivery: in vitro and ex vivo evaluation.","abstract":"BACKGROUND: A novel lovastatin (LVT)-loaded poly(lactic acid) microsphere suitable for oral administration was developed in this study, and in vitro and in vivo characteristics were evaluated. METHODS: The designed microspheres were obtained by an improved emulsion-solvent evaporation method. The morphological examination, particle size, encapsulation ratio, drug loading, and in vitro release were characterized. Pharmacokinetics studies were used to show that microspheres possess more advantages than the conventional formulations. RESULTS: By using the emulsion-solvent evaporation method, it was simple to prepare microspheres and easy to scale up production. The morphology of formed microspheres showed a spherical shape with a smooth surface, without any particle aggregation. Mean size of the microspheres was 2.65±0.69 μm; the encapsulation efficiency was 92.5%±3.6%, and drug loading was 16.7%±2.1%. In vitro release indicated that the LVT microspheres had a well-sustained release efficacy, and ex vivo studies showed that after LVT was loaded to microspheres, the area under the plasma concentration-time curve from zero to the last measurable plasma concentration point and the extrapolation to time infinity increased significantly, which represented 2.63-fold and 2.49-fold increases, respectively, compared to suspensions. The rate of ex vivo clearance was significantly reduced. CONCLUSION: This research proved that poly(lactic acid) microspheres can significantly prolong the drug circulation time in vivo and can also significantly increase the relative bioavailability of the drug.","corpus_id":16717565,"score":1},{"doc_id":"26047885","title":"Wheat germ agglutinin anchored chitosan microspheres of reduced brominated derivative of noscapine ameliorated acute inflammation in experimental colitis.","abstract":"Reduced brominated derivative of noscapine (Red-Br-Nos, EM012), has potent anti-inflammatory property. However, physicochemical limitations of Red-Br-Nos like low aqueous solubility (0.43×10(-3) g/mL), high lipophilicity (logP∼2.94) and ionization at acidic pH greatly encumber the scale-up of oral drug delivery systems for the management of colitis. Therefore, in present investigation, chitosan microspheres bearing Red-Br-Nos (CTS-MS-Red-Br-Nos) were prepared by emulsion polymerization method and later coated with wheat germ agglutinin (WGA-CTS-MS-Red-Br-Nos) to boost the bioadhesive property. The mean particle size and zeta-potential of CTS-MS-Red-Br-Nos were measured to be 10.5±5.4 μm and 8.1±2.2 mV, significantly (P<0.05) lesser than, 30.2±3.2 μm and 19.2±2.3 mV of WGA-CTS-MS-Red-Br-Nos. Furthermore, various spectral techniques like SEM, FT-IR, DSC and PXRD substantiated that Red-Br-Nos was molecularly dispersed in tailored microspheres in amorphous state. Surface bioadhesive property of WGA-CTS-MS-Red-Br-Nos promoted the affinity toward colon mucin cells in simulated colonic fluid (SCF, pH∼7.2). In vitro release studies carried out on WGA-CTS-MS-Red-Br-Nos and CTS-MS-Red-Br-Nos indicated that SCF with colitis milieu (pH∼4.7) favored the controlled release of Red-Br-Nos, owing to solubilization at acidic pH. Consistently, in vivo investigation also demonstrated the utility of WGA-CTS-MS-Red-Br-Nos, which remarkably attenuated the DSS encouraged neutrophil infiltration, myeloperoxidase activity, and pro-inflammatory cytokine production in C57BL6J mice, as compared to CTS-MS-Red-Br-Nos and Red-Br-Nos suspension. The noteworthy anti-inflammatory activity of WGA-CTS-MS-Red-Br-Nos against acute colitis may be attributed to enhanced drug delivery, affinity and utmost drug exposure at inflamed mucosal layers of colon. In conclusion, WGA-CTS-MS-Red-Br-Nos warrants further in-depth in vitro and in vivo investigations to scale-up the technology for clinical translation.","corpus_id":25736954,"score":1},{"doc_id":"26530807","title":"In vitro cytotoxicity and in vivo efficacy of 5-fluorouracil-loaded enteric-coated PEG-cross-linked chitosan microspheres in colorectal cancer therapy in rats.","abstract":"PURPOSE: Microspheres of chitosan (CS) cross-linked with polyethylene glycol (PEG) were prepared by emulsion-cross-linking followed by the solvent evaporation technique. The formulations were characterized and subjected to in vitro and in vivo tests to assess cell growth, changes in cell morphology, and activities by 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide (MTT) assay on human HT-29 colon cancer cell-lines. METHODS: In vivo activity was evaluated for dimethyl hydrazine-induced colorectal cancer in albino male Wistar rats. Biochemical and histological parameters were evaluated to understand their effectiveness for colon cancer therapy. RESULTS: The 5-FU immediate release (IR) formulations suspended in SCMC produced an immediate cytotoxic effect, whereas microspheres inhibited proliferation of tumor cells to induce apoptosis over an extended time. Minimum inhibitory concentration (IC50) values for both standard plain 5-FU and 5-FU-loaded microspheres were respectively 5.00 ± 0.004 µg/mL and 165 ± 1.9 µg/mL which showed the improved safety profile of the microsphere formulation. Tissue distribution showed high concentration of 5-FU in colon that was higher than IC50 value required to stop the growth or death of colon cancer cells from the colonic dysplasia in Duke's stage A. Significant reduction in tumor volume and multiplicity was observed with increased levels of liver enzymes in animals when treated with standard 5-FU formulation compared with 5-FU loaded microspheres. Elevated levels of serum albumin, creatinine, leukocytopenia, and thrombocytopenia were observed in animals for the standard 5-FU formulation. CONCLUSION: The PEG cross-linked CS microspheres of this study slowly released 5-FU up to 24 h to colonic region and enhanced the antitumor activity.","corpus_id":1343189,"score":1},{"doc_id":"26674842","title":"Budesonide-hydroxypropyl-β-cyclodextrin inclusion complex in binary poloxamer 407/403 system for ulcerative colitis treatment: A physico-chemical study from micelles to hydrogels.","abstract":"Budesonide (BUD) is a glucocorticoid widely used for the treatment of ulcerative colitis. In this work, we propose the study of the system BUD-HP-β-CD inclusion complex incorporated into PL 407 and PL407-PL403 thermoreversible hydrogels, considering physico-chemical and pharmaceutical aspects. Complexation between BUD and HP-β-CD was confirmed by phase solubility studies (1:1 stoichiometry, Kc=8662.8M(-1)), DSC, FTIR and microscopy analyzes. BUD solubility in simulated upper and lower colon fluids was improved in a dependence of HP-β-CD and PL 407 or PL407-PL403 association. Micellar hydrodynamic diameter studies showed the interaction between HP-β-CD and PL blocks, as well as the reorganization of the micellar system in the presence of BUD and its inclusion complex. Micellization temperature (Tm) was not shifted, but sol-gel phase transition studies showed that in the presence of BUD, HP-β-CD or BUD:HP-β-CD complex, the association PL407-PL403 favored the gel formation close to the physiological temperature. Physico-chemical and in vitro release assays studies revealed no competitive displacement of BUD from the HP-β-CD cavity evoked by PL407 or PL407-PL403 addition. These findings point out the BUD-HP-β-CD in PL-based hydrogels as strategies for future investigations on development of new pharmaceutical formulations for the treatment of ulcerative colitis.","corpus_id":24897673,"score":1},{"doc_id":"26838831","title":"Vincristine sulfate loaded dextran microspheres amalgamated with thermosensitive gel offered sustained release and enhanced cytotoxicity in THP-1, human leukemia cells: In vitro and in vivo study.","abstract":"Vincristine sulfate (VCS) is a drug of choice for the treatment of childhood and adult acute lymphocytic leukemia, Hodgkin's, non-Hodgkin's lymphoma as well as solid tumors including sarcomas. However, poor biopharmaceutical and pharmacokinetic traits of VCS like short serum half-life (12 min), high dosing frequency (1.4 mg/m(2) per week for 4 weeks) and extensive protein binding (75%) limit the clinical potential of VCS in cancer therapy. In present investigation, injectable vincristine sulfate loaded dextran microspheres (VCS-Dextran-MSs) were prepared and amalgamated with chitosan-β-glycerophosphate gel (VCS-Dextran-MSs-Gel) to surmount the biopharmaceutical and pharmacokinetic limitations of VCS that consequently induced synergistic sustained release pattern of the drug. Particle size and zeta-potential of VCS-Dextran-MSs were measured to be 6.8 ± 2.4 μm and -18.3 ± 0.11 mV along with the encapsulation efficiency of about 60.4 ± 4.5%. Furthermore, VCS-Dextran-MSs and VCS-Dextran-MSs-Gel exhibited slow release pattern and 94.7% and 95.8% of the drug was released in 72 h and 720 h, respectively. Results from cell viability assay and pharmacokinetic as well as histopathological analysis in mice indicated that VCS-Dextran-MSs-Gel offers superior therapeutic potential and higher AUClast than VCS-Dextran-MSs and drug solution. In conclusion, VCS-Dextran-MSs-Gel warrants further preclinical tumor growth study to scale up the technology.","corpus_id":21125458,"score":1},{"doc_id":"27427699","title":"Synthesis and Characterization of Curcumin-Functionalized HP-β-CD-Modified GoldMag Nanoparticles as Drug Delivery Agents.","abstract":"Curcumin, a polyphenol extracted from turmeric (Curcuma longa), has emerged as a potent multimodal cancer-preventing agent. It may attenuate the spread of cancer and render chemotherapy more effective. However, curcumin is neither well absorbed nor well retained in the blood, resulting in low efficacy. In an attempt to enhance the potency and to improve the bioavailability of curcumin, new delivery agents, hydroxypropyl-beta-cyclodextrin (HP-β-CD)-modified GoldMag nanoparticles (CD-GMNs) were designed and synthesized to incorporate curcumin. The CD-GMNs were characterized by Fourier Transform Infrared Spectroscopy (FT-IR), Thermo-gravimetric Analysis (TGA), X-ray Diffraction (XRD), Dynamic Light Scattering measurements (DLS), Transmission Electron Microscopy (TEM) and Vibrating Sample Magnetometer (VSM) analyses. For the magnetic carrier of CD-GMNs, the content of HP-β-CD was 26.9 wt%. CD-GMNs have a saturation magnetization of 22.7 emu/g with an average hydrodynamic diameter of 80 nm. The curcumin loading, encapsulation efficiency and releasing properties in vitro were also investigated. The results showed that the drug encapsulation ratio was 88% and the maximum curcumin loading capacity of CD-GMNs was 660 μg/5 mg. In vitro drug release studies showed a controlled and pH-sensitive curcumin release over a period of one week. Collectively, our data suggest that HP-β-CD-modified GoldMag nanoparticles can be considered to form a promising delivery system for curcumin to tumor sites. Targeting can be achieved by the combined effects of the application of an external magnetic field and the effect on drug release of lower pH values often found in the tumor microenvironment.","corpus_id":39016998,"score":1},{"doc_id":"27451026","title":"Molecular modeling and cytotoxicity of diffractaic acid: HP-β-CD inclusion complex encapsulated in microspheres.","abstract":"In this pioneer study, 2-hydroxypropyl-β-cyclodextrin (HP-β-CD) was used to improve the solubility of the diffractaic acid (DA) via inclusion complex (DA:HP-β-CD). Subsequently, DA:HP-β-CD was incorporated into poly-ε-caprolactone (PCL) microspheres (DA:HP-β-CD-MS). Microspheres containing DA (DA-MS) or DA:HP-β-CD (DA:HP-β-CD-MS) were prepared using the multiple W/O/W emulsion-solvent evaporation technique. The phase-solubility diagram of DA in HP-β-CD (10-50mM) showed an AL type curve with a stability constant K1:1=821M(-1). (1)H NMR, FTIR, X-ray diffraction and thermal analysis showed changes in the molecular environment of DA in DA:HP-β-CD. The molecular modeling approach suggests a guest-host complex formation between the carboxylic moiety of both DA and the host (HP-β-CD). The mean particle size of the microspheres were ∅DA-MS=5.23±1.65μm and ∅DA:HP-β-CD-MS=4.11±1.39μm, respectively. The zeta potential values of the microspheres were ζDA-MS=-7.85±0.32mV and ζDA:HP-β-CD-MS=-6.93±0.46mV. Moreover, the encapsulation of DA:HP-β-CD into microspheres resulted in a more slower release (k2=0.042±0.001; r(2)=0.996) when compared with DA-MS (k2=0.183±0.005; r(2)=0.996). The encapsulation of DA or DA:HP-β-CD into microspheres reduced the cytotoxicity of DA (IC50=43.29μM) against Vero cells (IC50 of DA-MS=108.48μM and IC50 of DA:HP-β-CD-MS=142.63μM).","corpus_id":32403983,"score":1},{"doc_id":"27770878","title":"Cationic cyclodextrin/alginate chitosan nanoflowers as 5-fluorouracil drug delivery system.","abstract":"Cyclodextrins (CDs) have widely been used as component of drug delivery systems. However unmodified cyclodextrins are associated with cytotoxicity and poor water solubility thus limiting their use in pharmaceutical industry. The cationic-β-cyclodextrin (Cat-β-CD) polymer cores were synthesized using β-CD, epichlorohydrin and choline chloride via a one-step polycondensation process. The main aim of this study was to synthesize hierarchical nanoflowers composed of cationic-β-CD as polymeric core along with alginate and chitosan \"petals\" (Cat-β-CD/Alg-Chi nanoflowers) as carriers for oral delivery of 5-Fluorouracil (5-FU) via an ionic-gelation technique. The drug loading capacity, particle size, zeta potential and surface morphology of the synthesized nanoflowers were determined. The prepared nanoflowers were formed with an average size of 300nm and a zeta potential of +9.90mV with good encapsulation efficiency of up to 77.3%. In vitro release of 5-FU from the loaded nanoflowers showed controlled and sustained release compared to the inclusion complex alone. Cat-β-CD/Alg-Chi nanoflowers were assessed against L929 cells and found to be effectively inhibiting the growth of L929 cells in a concentration dependent manner.","corpus_id":40572649,"score":1},{"doc_id":"29023400","title":"Electrostatic Self-Assembled Chitosan-Pectin Nano- and Microparticles for Insulin Delivery.","abstract":"A polyelectrolyte complex system of chitosan-pectin nano- and microparticles was developed to encapsulate the hormone insulin. The aim of this work was to obtain small particles for oral insulin delivery without chemical crosslinkers based on natural and biodegradable polysaccharides. The nano- and microparticles were developed using chitosans (with different degrees of acetylation: 15.0% and 28.8%) and pectin solutions at various charge ratios (n⁺/n- given by the chitosan/pectin mass ratio) and total charge. Nano- and microparticles were characterized regarding particle size, zeta potential, production yield, encapsulation efficiency, stability in different media, transmission electron microscopy and cytotoxicity assays using Caco-2 cells. The insulin release was evaluated in vitro in simulated gastric and intestinal media. Small-sized particles (~240-~1900 nm) with a maximum production yield of ~34.0% were obtained. The highest encapsulation efficiency (~62.0%) of the system was observed at a charge ratio (n⁺/n-) 5.00. The system was stable in various media, particularly in simulated gastric fluid (pH 1.2). Transmission electron microscopy (TEM) analysis showed spherical shape particles when insulin was added to the system. In simulated intestinal fluid (pH 6.8), controlled insulin release occurred over 2 h. In vitro tests indicated that the proposed system presents potential as a drug delivery for oral administration of bioactive peptides.","corpus_id":13096792,"score":1},{"doc_id":"23547762","title":"Budesonide/cyclodextrin complex-loaded lyophilized microparticles for intranasal application.","abstract":"OBJECTIVE: Lyophilized microparticles composed of budesonide (BDS), hydroxypropyl-β-cyclodextrin (HP-β-CD), and hydroxypropylmethylcellulose (HPMC) or sodium carboxymethylcellulose (CMC-Na) were developed for intranasal delivery and their characteristics were evaluated. MATERIALS AND METHODS: The particle size and morphology were assessed by mean diameter measurement and scanning electron microscopy (SEM) image, respectively. The solid-state of products was tested by X-ray powder diffraction (XRPD), Fourier transform infrared spectroscopy (FT-IR) and differential scanning calorimetry (DSC). In vitro drug release and cytotoxicity to the primary human nasal epithelial (HNE) cells were also evaluated. RESULTS AND DISCUSSION: Lyophilized microparticles exhibited vanishment of crystallinity of drug in XRPD analysis, the enfeeblement of carbonyl (C=O) stretching bands of carboxyl group in BDS in FT-IR spectra and the disappearance of endothermic peak of drug in the results of DSC study. Based on the results of solid-state studies, BDS was existed as an amorphous form in the lyophilized microparticles. CD complexation enhanced drug solubility and release rate, and HPMC or CMC-Na also improved drug dissolution rates. Cytotoxicity of developed microparticles to the HNE cells was measured and their safety to HNE cell was identified. CONCLUSION: Developed microparticles can efficiently deliver insoluble drug, such as BDS, to the nasal epithelium and thus it may improve therapeutic efficacy in the respiratory tract.","corpus_id":24134475,"score":0},{"doc_id":"24732397","title":"Bleomycin sulphate loaded nanostructured lipid particles augment oral bioavailability, cytotoxicity and apoptosis in cervical cancer cells.","abstract":"In present investigation, bleomycin sulphate loaded nanostructured lipid particles (BLM-NLPs) were constructed to enhance the oral bioavailability by overwhelming the first pass hepatic metabolism. The particles size and nanoencapsulation efficiency of BLM-NLPs were measured to be 17.4±5.4nm and 45.3±3.4%, respectively. Our studies indicated that the drug was molecularly dispersed in the lipid nanocoacervates, with amorphous geometry, without altering the chemical structure, as ascertained by spectral studies. The nanoformulation, BLM-NLPs was analyzed for dissolution testing, cytotoxicity, apoptosis and cellular uptake in human cervical cancer cell line, HeLa cells. BLM-NLPs released the drug with first order kinetic in simulated intestinal fluid (pH∼6.8±0.1), characterized by initial burst and followed by slow release. Further, an enhanced cytotoxicity (∼5.6 fold lower IC50), improved intracellular concentration (∼4.38 fold) and greater degree of apoptosis was induced by BLM-NLPs in HeLa cells, as compared to BLM alone. Moreover, BLM-NLPs also showed dose-dependent internalization, as evinced by cellular uptake study. The in vivo study indicated a significantly (P<0.0001) smaller elimination rate constant (KE), volume of distribution (Vd) and clearance rate (CLTotal) for BLM-NLPs, as compared to BLM solution in post-oral administrations. This clearly depicts the retention and stability of tailored nanoformulation in intestinal absorption pathway. In addition, our nanoformulation, BLM-NLPs documented significantly (P<0.0001)∼3.4 fold (66.20±2.57%) higher bioavailability than BLM solution (19.56±0.79%). In conclusion, our in vitro and in vivo results warrant the safety, efficacy and potency of tailored nanoformulation in clinical settings.","corpus_id":26734681,"score":0},{"doc_id":"27473308","title":"Modified-chitosan nanoparticles: Novel drug delivery systems improve oral bioavailability of doxorubicin.","abstract":"The efficacy of most anticancer drugs is highly limited in vivo due mainly to poor pharmacokinetics behavior including poor bioavailability after extravascular administration. We have developed novel chitosan-modified polymeric nanoparticles for oral as well as i.v. administration. Nanoparticles were developed utilizing the double emulsion solvent evaporation technique for sustained delivery of various anticancer drugs. Chitosan diacetate (CDA) and chitosan triacetate (CTA) polymers were previously modified in our laboratory and used as novel matrix. Nanoparticles, loaded with various anticancer drugs, were characterized for particle size using dynamic light scattering as well as transmission electron microscopy and net surface charge using dynamic light scattering. Particles size was below 100nm in diameter and zeta potential ranged - (25-30). Encapsulation efficiency of anticancer drugs varied considerably and was dependent on the physicochemical characteristics of the encapsulated drug. However, chitosan triacetate nanoparticles showed relatively higher encapsulation efficiency than chitosan diacetate nanoparticles. In vitro release of encapsulated drugs was sustained over a period of 14days. Nanoparticles enhanced cellular accumulation of encapsulated drugs, compared to the free drugs, in vitro in MCF-7 and Caco-II tumor cell lines. In conclusion, diacetate and triacetate chitosan are novel polymers that can be used to formulate nanoparticles which efficiently encapsulated anticancer drugs, and sustained the release and enhanced tumor cellular uptake of these drugs. Further, chitosan triacetate nanoparticles enhanced oral bioavailability of doxorubicin. CDA and CTA nanoparticles can be used to efficiently deliver anticancer drugs and improve their in vivo profile.","corpus_id":23682785,"score":0},{"doc_id":"27660413","title":"Preparation of novel pirfenidone microspheres for lung-targeted delivery: in vitro and in vivo study.","abstract":"The aim of this study was to develop and characterize pirfenidone (PF)-loaded chitosan microspheres for lung targeting. The microspheres were prepared using the emulsion-solvent evaporation method and characterized by assessing morphology, particle size, and zeta potential. The microspheres had a spherical nature with highly smooth and integrated surfaces. The particle size of microspheres was 4.6±0.3 µm, and the zeta potential was 20.3±1.4 mV. The in vitro release results indicated that the obtained formulation of PF could reach the state of sustained release with a biphasic drug release pattern. It was observed that there was no significant difference in both the percentage of entrapment efficiency and that of drug release before and after the stability study. In vivo, the calculated relative bioavailability indicated greater pulmonary absorption of PF when it was encapsulated in microspheres. According to histopathological studies, no histological change occurred to the rat lung after the administration of PF-loaded chitosan microspheres.","corpus_id":14856065,"score":0},{"doc_id":"28424979","title":"Studies on Core-Shell Nanocapsules of Felodipine: In Vitro-In Vivo Evaluations.","abstract":"The present study aimed for in vitro-in vivo-in silico simulation studies of experimentally designed (3(2)-factorial) Capmul PG-8-cored, Eudragit RSPO-Lutrol F 127 nanocapsules to ferry felodipine using GastroPlus™. The in silico parameter sensitivity analysis for pharmacokinetic parameters was initially assessed to justify the preparation of felodipine-loaded nanocapsules (FLNs) with enhanced solubility to overcome the bioavailability issues of felodipine. The overall integrated desirability ranged between 0.8187 and 0.9488 for three optimized FLNs when analyzed for mean particle size, zeta potential, encapsulation efficiency, and in vitro dissolution parameters. The morphological evaluation (SEM, TEM, and AFM) demonstrated spherical nanoparticles (200-300 nm). Validated LC-MS/MS analysis demonstrated enhanced relative bioavailability (13.37-fold) of optimized FLN as compared to suspension. The simulated regional absorption of the FLN presented significant absorption from the cecum (26.3%) and ascending colon (20.1%) with overall absorption of 67.4% from the GIT tract. Furthermore, in vitro-in vivo correlation demonstrated the Wagner-Nelson method as the preferred model as compared to mechanistic and numerical deconvolution on the basis of least mean absolute prediction error, least standard error of prediction, least mean absolute error, and maximum correlation coefficient (r (2) = 0.920). The study demonstrated enhanced oral absorption of felodipine-loaded nanocapsules, and GastroPlus™ was found to be an efficient simulation tool for in vitro-in vivo-in silico simulations.","corpus_id":13660276,"score":0}],"string":"[\n {\n \"doc_id\": \"18702170\",\n \"title\": \"Uniform chitosan microspheres for potential application to colon-specific drug delivery.\",\n \"abstract\": \"Uniform chitosan microspheres have been fabricated and weakly crosslinked for potential applications in colon-specific drug delivery. The effects of microsphere size, crosslinking density and electrostatic interactions between the drug and chitosan on drug release were studied, employing model drugs of different acidities. When the drug was basic, all chitosan spheres exhibited 100% release within 30 min. As the acidity of the drug increased, the release slowed down and depended on the crosslinking density and microsphere size. The release of weakly acidic drug was most suppressed for large spheres (35-38 microm), while the small spheres (23-25 microm) with higher crosslinking exhibited the most retention of highly acidic drug, indicating that they are a promising candidate for colon-specific delivery.\",\n \"corpus_id\": 20307098,\n \"score\": 2\n },\n {\n \"doc_id\": \"19491009\",\n \"title\": \"Nanoparticle encapsulation improves oral bioavailability of curcumin by at least 9-fold when compared to curcumin administered with piperine as absorption enhancer.\",\n \"abstract\": \"Curcumin, a derived product from common spice turmeric that is safe and beneficial in several aliments was formulated into biodegradable nanoparticles with a view to improve its oral bioavailability. The curcumin encapsulated nanoparticles prepared by emulsion technique were spherical in shape with particle size of 264nm (polydispersity index 0.31) and 76.9% entrapment at 15% loading. The curcumin encapsulated nanoparticles were able to withstand the International Conference on Harmonisation (ICH) accelerated stability test conditions for refrigerated products for the studied duration of 3 months. X-ray diffraction analysis revealed the amorphous nature of the encapsulated curcumin. The in vitro release was predominantly by diffusion phenomenon and followed Higuchi's release pattern. The in vivo pharmacokinetics revealed that curcumin entrapped nanoparticles demonstrate at least 9-fold increase in oral bioavailability when compared to curcumin administered with piperine as absorption enhancer. Together the results clearly indicate the promise of nanoparticles for oral delivery of poorly bioavailable molecules like curcumin.\",\n \"corpus_id\": 24999453,\n \"score\": 2\n },\n {\n \"doc_id\": \"20201417\",\n \"title\": \"Curcumin loaded pH-sensitive nanoparticles for the treatment of colon cancer.\",\n \"abstract\": \"The investigation was aimed at designing pH-sensitive, polymeric nanoparticles of curcumin, a natural anti-cancer agent, for the treatment of colon cancer. The objective was to enhance the bioavailability of curcumin, simultaneously reducing the required dose through selective targeting to colon. Eudragit S100 was chosen to aid targeting since the polymer dissolves at colonic pH to result in selective colonic release of the entrapped drug. Solvent emulsion-evaporation technique was employed to formulate the nanoparticles. Various process parameters were optimized and the optimized formulation was evaluated for particle size distribution and encapsulation efficiency before subjecting to freeze-drying. The freeze dried product was characterized for particle size, drug content, DSC studies, particle morphology. Anti-cancer potential of the formulation was demonstrated by MTT assay in HT-29 cell line. Nanometric, homogeneous, spherical particles were obtained with encapsulation efficiency of 72%. Freeze-dried nanoparticles exhibited a negative surface charge, drug content of > 99% and presence of drug in amorphous form which may result in possible enhanced absorption. MTT assay demonstrated almost double inhibition of the cancerous cells by nanoparticles, as compared to curcumin alone, at the concentrations tested. Enhanced action may be attributed to size influenced improved cellular uptake, and may result in reduction of overall dose requirement. Results indicate the potential for in vivo studies to establish the clinical application of the formulation.\",\n \"corpus_id\": 23272718,\n \"score\": 2\n },\n {\n \"doc_id\": \"20456930\",\n \"title\": \"beta-Cyclodextrin-curcumin self-assembly enhances curcumin delivery in prostate cancer cells.\",\n \"abstract\": \"Curcumin, a hydrophobic polyphenolic compound derived from the rhizome of the herb Curcuma longa, possesses a wide range of biological applications including cancer therapy. However, its prominent application in cancer treatment is limited due to sub-optimal pharmacokinetics and poor bioavailability at the tumor site. In order to improve its hydrophilic and drug delivery characteristics, we have developed a beta-cyclodextrin (CD) mediated curcumin drug delivery system via encapsulation technique. Curcumin encapsulation into the CD cavity was achieved by inclusion complex mechanism. Curcumin encapsulation efficiency was improved by increasing the ratio of curcumin to CD. The formations of CD-curcumin complexes were characterized by Fourier transform infrared (FTIR), differential scanning calorimetry (DSC), thermo-gravimetric analysis (TGA), scanning electron microscope (SEM), and transmission electron microscope (TEM) analyses. An optimized CD-curcumin complex (CD30) was evaluated for intracellular uptake and anti-cancer activity. Cell proliferation and clonogenic assays demonstrated that beta-cyclodextrin-curcumin self-assembly enhanced curcumin delivery and improved its therapeutic efficacy in prostate cancer cells compared to free curcumin.\",\n \"corpus_id\": 8818892,\n \"score\": 2\n },\n {\n \"doc_id\": \"21722423\",\n \"title\": \"Curcumin-loaded N,O-carboxymethyl chitosan nanoparticles for cancer drug delivery.\",\n \"abstract\": \"Chitosan (CS) and its carboxymethyl derivatives are smart biopolymers that are non-toxic, biocompatible and biodegradable, and, hence, suitable for various biomedical applications, such as drug delivery, gene therapy and tissue engineering. Curcumin is a major chemotherapeutic agent with antioxidant, anti-inflammatory, anti-proliferative, anticancer and antimicrobial effects. However, the potential of curcumin as a chemotherapeutic agent is limited by its hydrophobicity and poor bioavailability. In this work, we developed a nanoformulation of curcumin in a carboxymethyl chitosan (CMC) derivative, N,O-carboxymethyl chitosan (N,O-CMC). The curcumin-loaded N,O-CMC (curcumin-N,O-CMC) nanoparticles were characterized using DLS, AFM, SEM, FT-IR and XRD. DLS studies revealed nanoparticles with a mean diameter of 150 ± 30 nm. AFM and SEM confirmed that the particles have a spherical morphology within the size range of 150 ± 30 nm. Curcumin was entrapped with in N,O-CMC nanopartcles with an efficiency of 80%. The in vitro drug-release profile was studied at different pH (7.4 and 4.5) at 37°C for different incubation periods with and without lysozyme. Cytotoxicity studies using MTT assay indicated that curcumin-N,O-CMC nanoparticles showed specific toxicity towards cancer cells and non-toxicity to normal cells. Cellular uptake of curcumin-N,O-CMC nanoparticles was analyzed by fluorescence microscopy and was reconfirmed by flow cytometry. Overall, these results indicate that like previously reported curcumin loaded O-CMC nanoparticles, N,O-CMC will also be an efficient nanocarrier for delivering curcumin to cancer cells.\",\n \"corpus_id\": 23164152,\n \"score\": 2\n },\n {\n \"doc_id\": \"22047549\",\n \"title\": \"Mucoadhesive bilayer buccal tablet of carvedilol-loaded chitosan microspheres: in vitro, pharmacokinetic and pharmacodynamic investigations.\",\n \"abstract\": \"A multiple-unit system comprising mucoadhesive bilayer buccal tablets of carvedilol-loaded chitosan microspheres (CMs) was developed to improve bioavailability and therapeutic efficacy of carvedilol. Drug-loaded CMs were prepared by spray drying, evaluated for powder and particle characteristics, and optimized batch of CMs was compressed into bilayer buccal tablets using Carbopol. Tablets were evaluated for physicochemical parameters, in vitro drug release, in vivo pharmacokinetic and pharmacodynamic studies. Optimized formulation, CMT1 (CMT, chitosan microsphere tablet) showed maximum mucoadhesive force (50 ± 1.84 dyne/cm²), exhibited 73.08 ± 3.05% drug release and demonstrated zero-order kinetics with non-Fickian release mechanism. Pharmacokinetic studies in rabbits showed significantly higher C(max) (71.26 ± 6.45 ng/mL), AUC(0-10) (AUC, area under the curve 390.75 ± 5.23 ng/mL/h) and AUC(0-∞) (664.72 ng/mL/h) than carvedilol oral tablet. Pharmacodynamic studies confirmed reduction in mean arterial pressure, heart rate, body weight and triglyceride on administration of bilayer buccal tablet compared to oral carvedilol tablet. Multiple-unit system exhibited enhanced bioavailability and sustained release of carvedilol, indicating its improved therapeutic potential for the treatment of hypertension.\",\n \"corpus_id\": 4375905,\n \"score\": 2\n },\n {\n \"doc_id\": \"22275831\",\n \"title\": \"A novel folate-modified self-microemulsifying drug delivery system of curcumin for colon targeting.\",\n \"abstract\": \"BACKGROUND: The objective of this study was to prepare, characterize, and evaluate a folate-modified self-microemulsifying drug delivery system (FSMEDDS) with the aim to improve the solubility of curcumin and its delivery to the colon, facilitating endocytosis of FSMEDDS mediated by folate receptors on colon cancer cells. METHODS: Ternary phase diagrams were constructed in order to obtain the most efficient self-emulsification region, and the formulation of curcumin-loaded SMEDDS was optimized by a simplex lattice experiment design. Then, three lipophilic folate derivatives (folate-polyethylene glycol-distearoylphosphatidylethanolamine, folate-polyethylene glycol-cholesteryl hemisuccinate, and folate-polyethylene glycol-cholesterol) used as a surfactant were added to curcumin-loaded SMEDDS formulations. An in situ colon perfusion method in rats was used to optimize the formulation of FSMEDDS. Curcumin-loaded FSMEDDS was then filled into colon-targeted capsules and the in vitro release was investigated. Cytotoxicity studies and cellular uptake studies was used in this research. RESULTS: The optimal formulation of FSMEDDS obtained with the established in situ colon perfusion method in rats was comprised of 57.5% Cremophor(®) EL, 32.5% Transcutol(®) HP, 10% Capryol™ 90, and a small amount of folate-polyethylene glycol-cholesteryl hemisuccinate (the weight ratio of folate materials to Cremophor EL was 1:100). The in vitro release results indicated that the obtained formulation of curcumin could reach the colon efficiently and release the drug immediately. Cellular uptake studies analyzed with fluorescence microscopy and flow cytometry indicated that the FSMEDDS formulation could efficiently bind with the folate receptors on the surface of positive folate receptors cell lines. In addition, FSMEDDS showed greater cytotoxicity than SMEDDS in the above two cells. CONCLUSION: FSMEDDS-filled colon-targeted capsules are a potential carrier for colon delivery of curcumin.\",\n \"corpus_id\": 13908952,\n \"score\": 2\n },\n {\n \"doc_id\": \"22557928\",\n \"title\": \"Preparation and in vitro/in vivo characterization of curcumin microspheres intended to treat colon cancer.\",\n \"abstract\": \"OBJECTIVE: The objective of the present investigation was to prepare colon targeted curcumin microspheres using Eudragit S100 and evaluate the same for in vitro/in vivo properties. MATERIALS AND METHODS: A \\\"O/O solvent evaporation\\\" technique was used in the preparation of microspheres. The influence of various process variables including stirring speed, drug:polymer ratio and percentage of emulsifier on the fabrication were investigated and the formulation was optimized. Prepared microspheres were evaluated for in vitro and in vivo properties. Surface morphology, particle size, percentage drug entrapment, percentage yield, drug polymer interaction, in vitro drug release in simulated gastrointestinal transit conditions and stability were the in vitro parameters investigated. Using an optimized formulation, drug release into the systemic circulation and organ distribution were investigated as in vivo parameters. In vivo parameters were estimated in male albino rats. RESULTS: Curcumin microspheres of Eudragit S100 were successfully prepared using o/o solvent evaporation method. Microspheres prepared using 1:2 drug:polymer ratio, with a stirring speed of 1000 rpm, and using 1.0% w/v concentration of emulsifying agent was selected as an optimized formulation. The release studies with optimized formulation demonstrated that aqueous solubility of curcumin was enhanced by 8 times with the formulation. FTIR studies demonstrated no change in drug characteristics upon microsphere fabrication. The enhancement in solubility is thus due to the increase in the surface area of the drug substance and not due to a change of drug to a different physical state. This was further confirmed by scanning electron microsphere pictures. Drug release followed Korsmeyer and Peppas release model. Accelerated stability studies indicated that the drug is stable in the formulation for a period of atleast 14 weeks at room temperature. In vivo studies demonstrated a sustained drug release into the systemic circulation after oral administration of the formulation. Further, colon target was affectively achieved using the optimized formulation. Eudragit microspheres delivered most of their drug load (79.0%) to the colon, whereas with plain drug suspension only 28.0% of the total dose reached the target site. CONCLUSION: This study successfully developed curcumin microspheres that can be used effectively in the treatment of the colon cancer.\",\n \"corpus_id\": 42879570,\n \"score\": 2\n },\n {\n \"doc_id\": \"23030405\",\n \"title\": \"Native and β-cyclodextrin-enclosed curcumin: entrapment within liposomes and their in vitro cytotoxicity in lung and colon cancer.\",\n \"abstract\": \"With a view to improving the solubility and delivery characteristics of poorly water-soluble drugs, we prepared β-cyclodextrin-curcumin (βCD-C) inclusion complexes (hydrophilic curcumin) and entrapped both native curcumin (hydrophobic) and the complexes separately into liposomes; these were then assessed for in vitro cytotoxicity in lung and colon cancer cell lines. Optimization of curcumin entrapment within βCD was achieved, with the resultant βCD-C complexes prepared by methanol reflux. Inclusion complexes were confirmed using UV spectroscopy, Fourier transform infrared spectroscopy (FT-IR) and X-ray diffraction. The water solubility of βCD-C complexes improved markedly (c.f. native curcumin) and successful entrapment of complexes into liposomes, prepared using a thin-film hydration approach, was also achieved. All the liposomal formulations were characterized for curcumin and βCD-C complex entrapment efficiency, particle size, polydispersity and stability at 2-8°C. Curcumin, βCD-C complex and their optimized liposomal formulations were evaluated for anticancer activity in lung (A-459) and colon (SW-620) cancer cell lines. All curcumin-containing formulations tested were effective in inhibiting cell proliferation, as determined via an MTT assay. The median effective dose (EC(50)) for all curcumin formulations was found to be in the low µM range for both lung and colon cancer cell lines tested. Our results confirm that βCD inclusion complexes of poorly water soluble drugs, such as curcumin can be entrapped within biocompatible vesicles such as liposomes, and this does not preclude their anticancer activity.\",\n \"corpus_id\": 32953815,\n \"score\": 2\n },\n {\n \"doc_id\": \"23618291\",\n \"title\": \"In vitro and in vivo evaluation of curcumin loaded lauroyl sulphated chitosan for enhancing oral bioavailability.\",\n \"abstract\": \"Curcumin has been demonstrated as a potent anticancer agent but its clinical application has been limited by its poor aqueous solubility and bioavailability. Here we describe encapsulation of curcumin in the lauroyl sulphated chitosan with a view to improve its bioavailability. In vitro antioxidant activity of extract of curcumin loaded matrix was investigated and exhibited dose dependent radical scavenging and reducing activity. Cytotoxicity studies carried out with curcumin loaded carrier on C6 cell line and were found to be toxic. Its in vitro effects on proliferation using the C6 cell lines also studied and observed antiproliferation of C6 cell line. Plasma concentration of curcumin-time profiles from pharmacokinetic studies in rats after oral administration showed a 11.5-fold increased pharmacological availability of curcumin with encapsulated curcumin compared with native curcumin. Overall we demonstrate that the curcumin loaded matrix has shown a superior pharmacological availability in vivo over curcumin.\",\n \"corpus_id\": 479446,\n \"score\": 2\n },\n {\n \"doc_id\": \"23990077\",\n \"title\": \"Molecular inclusion complex of curcumin-β-cyclodextrin nanoparticle to enhance curcumin skin permeability from hydrophilic matrix gel.\",\n \"abstract\": \"Curcumin (CUR) has various pharmacological effects, but its extensive first-pass metabolism and short elimination half-life limit its bioavailability. Therefore, transdermal application has become a potential alternative to delivery CUR. To increase CUR solubility for the development of a transparent homogenous gel and also enhance the permeation rate of CUR into the skin, β-cyclodextrin-curcumin nanoparticle complex (BCD-CUR-N) was developed. CUR encapsulation efficiency was increased by raising the percentage of CUR to BCD up to 20%. The mean particle size of the best CUR loading formula was 156 nm. All evaluation data using infrared spectroscopy, Raman spectroscopy, powder X-ray diffractometry, differential thermal analysis and scanning electron microscopy confirmed the successful formation of the inclusion complex. BCD-CUR-N increased the CUR dissolution rate of 10-fold (p < 0.01). In addition, the improvement of CUR permeability acrossed skin model tissue was observed in gel containing the BCD-CUR-N and was about 1.8-fold when compared with the free CUR gel (p < 0.01). Overall, CUR in the form of the BCD-CUR-N improved the solubility further on the penetration of CUR.\",\n \"corpus_id\": 17581609,\n \"score\": 2\n },\n {\n \"doc_id\": \"24299818\",\n \"title\": \"Telmisartan complex augments solubility, dissolution and drug delivery in prostate cancer cells.\",\n \"abstract\": \"Telmisartan (TEL) requires superior bioavailability in cancer cell compartments. To meet these challenges, we have synthesized a 2-HP-β-CD-TEL complex with stability constant (Kc) of 2.39 × 10(-3)mM. The absence in the FTIR spectrum of 2-HP-β-CD-TEL complex of the characteristic peaks of TEL at 1,699 cm(-1) (carboxylic acid) and 741 and 756 cm(-1) (1,2-disubstituted benzene ring vibrations), is indicative of the encapsulation of TEL in the 2-HP-β-CD cavity. DSC and PXRD also confirmed the synthesis and amorphous structure of complex. The interaction of TEL with 2-HP-β-CD was examined by NMR and 2D-ROESY which affirms the encapsulation of TEL in the 2-HP-β-CD cavity in at least two orientations with equal binding energies. The complex also exhibited its superiority in both in vitro release and cytotoxicity experiments on prostate cancer, PC-3 cells as compared to free drug. These data warrant an in depth in vivo to scale-up the technology for the management of prostate cancer.\",\n \"corpus_id\": 30910521,\n \"score\": 2\n },\n {\n \"doc_id\": \"24698148\",\n \"title\": \"Curcumin-cyclodextrin encapsulated chitosan nanoconjugates with enhanced solubility and cell cytotoxicity.\",\n \"abstract\": \"Curcumin (CUR), a naturally derived anti-cancer cocktail is arguably the most widely studied neutraceutical. Despite a lot of promises, it is yet to reach the market as an active anti-cancer formulation. In the present study, we have prepared highly soluble (3 mg/ml) CUR-γ-hydroxypropyl cyclodextrin (CUR-CD) hollow spheres. CUR-CD hollow spheres were prepared by a novel and scalable spray drying method. CUR-CD was then encapsulated into positively charged biodegradable chitosan (CUR-CD-CS) nanoparticles. The CUR-CD-CS nanoparticles were characterised by TEM, SEM, DLS, drug loading and in vitro release. We tested the efficacy of these CUR-CD-CS nanoparticles in SCC25 cell lines using MTT assay and investigated its cellular uptake mechanism. We also studied Oligo DNA loading in CUR-CD-CS nanoparticles and its delivery via confocal imaging and FACS analysis. Our results demonstrated that CUR-CD-CS nanoparticles showed superior in vitro release performance and higher cytotoxicity in SCC25 cell line amongst all tested formulations. The cytotoxicity results were corroborated by cell cycle analysis and apoptosis test, showing nearly 100% apoptotic cell death in the case of CUR-CD-CS nanoparticles. Compared to CS nanoparticles, CS-CD nanoformulation showed higher cellular delivery of Cy3-Oligo DNA which was tested quantitatively using flowcytometry analysis, indicating that CD not only enhanced CUR solubility but also boosted the cellular uptake. Our study shows that rationally designed bio-degradable natural biomaterials have great potential as next generation nano-carriers for hydrophobic drug delivery such as CUR with potential of dual drug-gene delivery.\",\n \"corpus_id\": 21250009,\n \"score\": 2\n },\n {\n \"doc_id\": \"24758141\",\n \"title\": \"pH triggered delivery of curcumin from Eudragit-coated chitosan microspheres for inflammatory bowel disease: characterization and pharmacodynamic evaluation.\",\n \"abstract\": \"OBJECTIVE: This investigation deals with the development and evaluation (in vitro and in vivo) of pH triggered Eudragit-coated chitosan microspheres of curcumin (CUR) for treating ulcerative colitis. METHODS: CUR-loaded chitosan microspheres were initially prepared by emulsion cross linking method followed by coating with Eudragit S-100. The pharmacodynamics of the developed formulation was analyzed in mice by acetic acid induced colitis model. RESULTS: The developed microspheres were of uniform spherical shape with high entrapment efficiency. CUR-chitosan microspheres showed less intense peaks compared to free CUR confirming inclusion of drug within microspheres as revealed by X-ray diffractogram. Uncoated CUR-chitosan microspheres exhibited burst release within initial 4 h while microspheres coated with Eudragit S-100 prevented premature release of CUR and showed controlled release up to 12 h following Higuchi model. In vivo organ biodistribution study showed negligible amount of CUR in stomach and small intestine confirming integrity of microsphere in upper gastrointestinal tract (GIT). In vivo study revealed significant reduction in severity and extent of colonic damage with CUR-loaded microspheres as compared to pure CUR which was further confirmed by histopathological study. CONCLUSION: In vitro and in vivo studies proved the developed formulations as a promising system for pH-dependent delivery of drug to colon in ulcerative colitis.\",\n \"corpus_id\": 13310404,\n \"score\": 2\n },\n {\n \"doc_id\": \"25511809\",\n \"title\": \"Effects of the Preparation Method on the Formation of True Nimodipine SBE-β-CD/HP-β-CD Inclusion Complexes and Their Dissolution Rates Enhancement.\",\n \"abstract\": \"The aims of this study were to enhance the solubility and dissolution rate of nimodipine (ND) by preparing the inclusion complexes of ND with sulfobutylether-b-cyclodextrin (SBE-β-CD) and 2-hydroxypropyl-b-cyclodextrin (HP-β-CD) and to study the effect of the preparation method on the in vitro dissolution profile in different media (0.1 N HCl pH 1.2, phosphate buffer pH 7.4, and distilled water). Thus, the inclusion complexes were prepared by kneading, coprecipitation, and freeze-drying methods. Phase solubility studies were conducted to characterize the complexes in the liquid state. The inclusion complexes in the solid state were investigated with differential scanning calorimetry (DSC), X-ray diffractometry (X-RD), and Fourier transform infrared spectroscopy (FT-IR). Stable complexes of ND/SBE-β-CD and ND/HP-β-CD were formed in distilled water in a 1:1 stoichiometric inclusion complex as indicated by an AL-type diagram. The apparent stability constants (Ks) were 1334.4 and 464.1 M(-1) for ND/SBE-β-CD and ND/HP-β-CD, respectively. The water-solubility of ND was significantly increased in an average of 22- and 8-fold for SBE-β-CD and HP-β-CD, respectively. DSC results showed the formation of true inclusion complexes between the drug and both SBE-β-CD and HP-β-CD prepared by the kneading method. In contrast, crystalline drug was detectable in all other products. The dissolution studies showed that all the products exhibited higher dissolution rate than those of the physical mixtures and ND alone, in all mediums. However, the kneading complexes displayed the maximum dissolution rate in comparison with drug and other complexes, confirming the influence of the preparation method on the physicochemical properties of the products.\",\n \"corpus_id\": 14844305,\n \"score\": 2\n },\n {\n \"doc_id\": \"26170159\",\n \"title\": \"Cost-effective alternative to nano-encapsulation: Amorphous curcumin-chitosan nanoparticle complex exhibiting high payload and supersaturation generation.\",\n \"abstract\": \"While the wide-ranging therapeutic activities of curcumin have been well established, its successful delivery to realize its true therapeutic potentials faces a major challenge due to its low oral bioavailability. Even though nano-encapsulation has been widely demonstrated to be effective in enhancing the bioavailability of curcumin, it is not without drawbacks (i.e. low payload and costly preparation). Herein we present a cost-effective bioavailability enhancement strategy of curcumin in the form of amorphous curcumin-chitosan nanoparticle complex (or curcumin nanoplex in short) exhibiting a high payload (>80%). The curcumin nanoplex was prepared by a simple yet highly efficient drug-polysaccharide complexation method that required only mixing of the curcumin and chitosan solutions under ambient condition. The effects of (1) pH and (2) charge ratio of chitosan to curcumin on the (i) physical characteristics of the nanoplex (i.e. size, colloidal stability and payload), (ii) complexation efficiency, and (iii) production yield were investigated from which the optimal preparation condition was determined. The nanoplex formation was found to favor low acidic pH and charge ratio below unity. At the optimal condition (i.e. pH 4.4. and charge ratio=0.8), stable curcumin nanoplex (≈260nm) was prepared at >90% complexation efficiency and ≈50% production yield. The amorphous state stability, colloidal stability, and in vitro non-cytotoxicity of the nanoplex were successfully established. The curcumin nanoplex produced prolonged supersaturation (3h) in the presence of hydroxypropyl methylcellulose (HPMC) at five times of the saturation solubility of curcumin. In addition, curcumin released from the nanoplex exhibited improved chemical stability owed to the presence of chitosan. Both results (i.e. high supersaturation and improved chemical stability) bode well for the ability of the curcumin nanoplex to enhance the bioavailability of curcumin clinically.\",\n \"corpus_id\": 44681741,\n \"score\": 2\n },\n {\n \"doc_id\": \"26394122\",\n \"title\": \"In vitro cytotoxicity and in vivo efficacy of 5-fluorouracil-loaded enteric-coated PEG-crosslinked chitosan microspheres in colorectal cancer therapy in rats.\",\n \"abstract\": \"PURPOSE: Microspheres of chitosan (CS) crosslinked with polyethylene glycol (PEG) were prepared by emulsion crosslinking followed by solvent evaporation technique. The formulations were characterized and subjected to in vitro and in vivo tests to assess cell growth, changes in cell morphology and activities by 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide (MTT) assay on human HT-29 colon cancer cell lines. METHODS: In vivo activity was evaluated for dimethyl hydrazine-induced colorectal cancer in albino male Wistar rats. Biochemical and histological parameters were evaluated to understand their effectiveness for colon cancer therapy. RESULTS: The 5-FU immediate release (IR) formulations suspended in sodium carboxymethyl cellulose (SCMC) produced an immediate cytotoxic effect, whereas microspheres inhibited the proliferation of tumor cells to induce apoptosis over an extended time. Minimum inhibitory concentration (IC50) values for both standard plain 5-FU and 5-FU-loaded microspheres were, respectively, 5.00 ± 0.004 µg/mL and 165 ± 1.9 µg/mL which showed the improved safety profile of the microsphere formulation. Tissue distribution showed high concentration of 5-FU in colon that was higher than IC50 required to stop the growth or death of colon cancer cells from the colonic dysplasia in Duke's Stage A. Significant reduction in tumor volume and multiplicity was observed with increased levels of liver enzymes in animals when treated with standard 5-FU formulation compared to 5-FU-loaded microspheres. Elevated levels of serum albumin, creatinine, leukocytopenia and thrombocytopenia were observed in animals for the standard 5-FU formulation. CONCLUSION: The PEG-crosslinked CS microspheres of this study slowly released 5-FU up to 24 h to colonic region and enhanced the antitumor activity.\",\n \"corpus_id\": 45975018,\n \"score\": 2\n },\n {\n \"doc_id\": \"26678861\",\n \"title\": \"Optimization of chitosan nanoparticles for colon tumors using experimental design methodology.\",\n \"abstract\": \"Purpose Colon-specific drug delivery systems (CDDS) can improve the bio-availability of drugs through the oral route. A novel formulation for oral administration using ligand coupled chitosan nanoparticles bearing 5-Flurouracil (5FU) encapsulated in enteric coated pellets has been investigated for CDDS. Method The effect of polymer concentration, drug concentration, stirring time and stirring speed on the encapsulation efficiency, and size of nanoparticles were evaluated. The best (or optimum) formulation was obtained by response surface methodology. Using the experimental data, analysis of variance has been carried out to evolve linear empirical models. Using a new methodology, polynomial models have been evolved and the parametric analysis has been carried out. In order to target nanoparticles to the hyaluronic acid (HA) receptors present on colon tumors, HA coupled nanoparticles were tested for their efficacy in vivo. The HA coupled nanoparticles were encapsulated in pellets and were enteric coated to release the drug in the colon. Results Drug release studies under conditions of mimicking stomach to colon transit have shown that the drug was protected from being released in the physiological environment of the stomach and small intestine. The relatively high local drug concentration with prolonged exposure time provides a potential to enhance anti-tumor efficacy with low systemic toxicity for the treatment of colon cancer. Conclusions Conclusively, HA coupled nanoparticles can be considered as the potential candidate for targeted drug delivery and are anticipated to be promising in the treatment of colorectal cancer.\",\n \"corpus_id\": 23450589,\n \"score\": 2\n },\n {\n \"doc_id\": \"27582072\",\n \"title\": \"Mucoadhesive Chitosan-Pectinate Nanoparticles for the Delivery of Curcumin to the Colon.\",\n \"abstract\": \"In the present study, we report the properties of a mucoadhesive chitosan-pectinate nanoparticulate formulation able to retain its integrity in the milieu of the upper gastrointestinal tract and subsequently, mucoadhere and release curcumin in colon conditions. Using this system, we aimed to deliver curcumin to the colon for the possible management of colorectal cancer. The delivery system comprised of a chitosan-pectinate composite nanopolymeric with a z-average of 206.0 nm (±6.6 nm) and zeta potential of +32.8 mV (±0.5 mV) and encapsulation efficiency of 64%. The nanoparticles mucoadhesiveness was higher at alkaline pH compared to acidic pH. Furthermore, more than 80% release of curcumin was achieved in pectinase-enriched medium (pH 6.4) as opposed to negligible release in acidic and enzyme-restricted media at pH 6.8. SEM images of the nanoparticles after exposure to the various media indicate a retained matrix in acid media as opposed to a distorted/fragmented matrix in pectinase-enriched medium. The data strongly indicates that the system has the potential to be applied as a colon-targeted mucoadhesive curcumin delivery system for the possible treatment of colon cancer.\",\n \"corpus_id\": 4730016,\n \"score\": 2\n },\n {\n \"doc_id\": \"28130133\",\n \"title\": \"Inhalable bioresponsive chitosan microspheres of doxorubicin and soluble curcumin augmented drug delivery in lung cancer cells.\",\n \"abstract\": \"In present investigation, doxorubicin (Dox) and soluble curcumin (Cur-2-HP-β-CD-complex) combination was simultaneously loaded in inhalable bioresponsive chitosan microspheres (Dox/Cur-2-HP-β-CD-complex-elastin-CMs) bearing a substrate-stimuli, elastin. The mean particle size and mean aerodynamic diameter of inhalable bioresponsive microspheres displayed noteworthy differences after incorporation of elastin. Moreover, combination of Dox and soluble curcumin was molecularly dispersed in microspheres matrix as substantiated by a range of spectral techniques. Inhalable bioresponsive microspheres released astonishingly higher amount of Dox in presence of elastase enzyme at pH∼5.5 in comparison to pH∼7.4. However, the release of soluble curcumin from tailored bioresponsive microspheres in presence of elastase enzyme was independent of pH. Consistently, inhalable bioresponsive microspheres exhibited outstandingly lower IC50 of 3.4-μM in comparison to 6.5-μM of inhalable drug loaded microspheres (Dox/Cur-2-HP-β-CD-complex-CMs) bearing no elastin, against A549, non-small cell lung cancer cells. The superior therapeutic profile of inhalable bioresponsive microspheres may be attributed to enhanced drug release and consequently augmented drug exposure to A549 cells expressing elastase enzyme. In this way, stimuli triggered drug release from tailored inhalable bioresponsive microspheres boosted the phenomena of apoptosis in A549 cells. In conclusion, Dox/Cur-2-HP-β-CD-complex-elastin-CMs warrant further in-vivo tumor regression study to prove its therapeutic efficacy.\",\n \"corpus_id\": 205191838,\n \"score\": 2\n },\n {\n \"doc_id\": \"28891961\",\n \"title\": \"Visible Light-Cured Glycol Chitosan Hydrogel Containing a Beta-Cyclodextrin-Curcumin Inclusion Complex Improves Wound Healing In Vivo.\",\n \"abstract\": \"Scarless wound healing is ideal for patients suffering from soft tissue defects. In this study, we prepared a novel wet dressing (β-CD-ic-CUR/GC) based on the visible light-cured glycol chitosan (GC) hydrogel and inclusion complex between beta-cyclodextrin (β-CD) and curcumin (CUR). We also evaluated its efficacy in the acceleration of wound healing as compared to that of CUR-loaded GC (CUR/GC). The conjugation of glycidyl methacrylate (GM) to GC for photo-curing was confirmed by ¹H-NMR measurement, and the photo-cured GC hydrogel was characterized by the analyses of rheology, swelling ratio, SEM and degradation rate. After visible light irradiation, the surface/cross-sectional morphologies and storage (G')/loss (G'') moduli revealed the formation of hydrogel with interconnected porosity. The dressing β-CD-ic-CUR/GC exhibited a controlled release of 90% CUR in a sustained manner for 30 days. On the other hand, CUR/GC showed CUR release of 16%. β-CD acted as an excipient in improving the water-solubility of CUR and affected the release behavior of CUR. The in vivo animal tests including measurement of the remaining unhealed wound area and histological analyses showed that β-CD-ic-CUR/GC may have potential as a wet dressing agent to enhance soft tissue recovery in open fractures.\",\n \"corpus_id\": 22452956,\n \"score\": 2\n },\n {\n \"doc_id\": \"29110292\",\n \"title\": \"Development of Chitosan-Based pH-Sensitive Polymeric Micelles Containing Curcumin for Colon-Targeted Drug Delivery.\",\n \"abstract\": \"pH-sensitive N-naphthyl-N,O-succinyl chitosan (NSCS) and N-octyl-N,O-succinyl chitosan (OSCS) polymeric micelles carriers have been developed to incorporate curcumin (CUR) for colon-targeted drug delivery. The physical entrapment methods (dialysis, co-solvent evaporation, dropping, and O/W emulsion) were applied. The CUR-loaded micelles prepared by the dialysis method presented the highest loading capacity. Increasing initial amount of CUR from 5 to 40 wt% to polymer resulted in the increase in loading capacity of the polymeric micelles. Among the hydrophobic cores, there were no significant differences in the loading capacity of CUR-loaded micelles. The particle sizes of all CUR-loaded micelles were in the range of 120-338 nm. The morphology of the micelles changed after being contacted with medium with different pH values, confirming the pH-responsive properties of the micelles. The release characteristics of curcumin from all CUR-loaded micelles were pH-dependent. The percent cumulative release of curcumin from all CUR-loaded micelles in simulated gastric fluid (SGF) was limited to about 20%. However, the release amount was significantly increased after contacted with simulated intestinal fluid (SIF) (50-55%) and simulated colonic fluid (SCF) (60-70%). The released amount in SIF and SCF was significantly greater than the release of CUR from CUR powder. CUR-loaded NSCS exhibited the highest anti-cancer activity against HT-29 colorectal cancer cells. The stability studies indicated that all CUR-loaded micelles were stable for at least 90 days. Therefore, the colon targeted, pH-sensitive NSCS micelles may have potential to be a prospective candidate for curcumin delivery to the colon.\",\n \"corpus_id\": 4444547,\n \"score\": 2\n },\n {\n \"doc_id\": \"18289808\",\n \"title\": \"Nanoparticles of quaternized chitosan derivatives as a carrier for colon delivery of insulin: ex vivo and in vivo studies.\",\n \"abstract\": \"The aim of the present study was to develop insulin nanoparticulate systems by using chitosan (CS), triethylchitosan (TEC) and dimethyl-ethylchitosan (DMEC, a new quaternized derivative of chitosan) for colon delivery. The nanoparticles were prepared by the polyelectrolyte complexation (PEC) method. Particle size distribution, zeta potential and polydispersity index of the nanoparticles were determined using dynamic light scattering technique. Transmission electron microscopy (TEM) was also used to observe the morphology of the nanoparticles. It was found that the nanoparticles carried positive charges and showed a size distribution in the range of 170-270 nm with spherical morphology and smooth surface structure. The amount of insulin loaded into the nanoparticles was determined by measuring the association efficiency and also the content of insulin in the nanoparticles. Insulin loading was found to be more than 80% for all of the nanoparticles. In vitro release studies showed a small burst effect at the beginning and then a sustained release characteristic for 5h. Ex vivo investigations revealed better insulin transport across the colon membrane of rats for nanoparticles made with quaternized derivatives than those made of chitosan. In vivo studies in rats have showed enhanced colon absorption of insulin by using these nanoparticles compared to free insulin in diabetic rats. The insulin absorption from the rat's colon was evaluated by its hypoglycemic effect.\",\n \"corpus_id\": 19580041,\n \"score\": 1\n },\n {\n \"doc_id\": \"18523891\",\n \"title\": \"Mucoadhesive microspheres for gastroretentive delivery of acyclovir: in vitro and in vivo evaluation.\",\n \"abstract\": \"The aim of the present investigation was to evaluate the potential use of mucoadhesive microspheres for gastroretentive delivery of acyclovir. Chitosan, thiolated chitosan, Carbopol 71G and Methocel K15M were used as mucoadhesive polymers. Microsphere formulations were prepared using emulsion-chemical crosslinking technique and evaluated in vitro, ex-vivo and in-vivo. Gelatin capsules containing drug powder showed complete dissolution (90.5 +/- 3.6%) in 1 h. The release of drug was prolonged to 12 h (78.8 +/- 3.9) when incorporated into mucoadhesive microspheres. The poor bioavailability of acyclovir is attributed to short retention of its dosage form at the absorption sites (in upper gastrointestinal tract to duodenum and jejunum). The results of mucoadhesion study showed better retention of thiolated chitosan microspheres (8.0 +/- 0.8 h) in duodenal and jejunum regions of intestine. The results of qualitative and quantitative GI distribution study also showed significant higher retention of mucoadhesive microspheres in upper GI tract. Pharmacokinetic study revealed that administration of mucoadhesive microspheres could maintain measurable plasma concentration of acyclovir through 24 h, as compared to 5 h after its administration in solution form. Thiolated chitosan microsphere showed superiority over the other formulations as observed with nearly 4.0-fold higher AUC(0-24) value (1,090 +/- 51 ng h/ml) in comparison to drug solution (281 +/- 28 ng h/ml). Overall, the result indicated prolonged delivery with significant improvement in oral bioavailability of acyclovir from mucoadhesive microspheres due to enhanced retention in the upper GI tract.\",\n \"corpus_id\": 22185592,\n \"score\": 1\n },\n {\n \"doc_id\": \"18591810\",\n \"title\": \"Study on colon-specific 5-Fu pH-enzyme Di-dependent chitosan microspheres.\",\n \"abstract\": \"Colon-specific drug delivery systems (CDDS) can improve the bioavailability of drug through the oral route. A novel formulation for oral administration using pH-enzyme Di-dependent chitosan mcirospheres (MS) and 5-Fu as a model drug has been investigated for colon-specific drug delivery by the emulsification/chemical cross-linking and coating technique, respectively. The influence of polymer concentration, ratio of drug to polymer, the amount of crosslinking agent and the stirring speed on the encapsulation efficiency, particle size in microspheres were evaluated. The best formulation was optimized by an orthogonal design. Drug release studies under conditions mimicking stomach to colon transit have shown that the drug was protected from being released in the physiological environment of the stomach and small intestine. The plasma concentrations of 5-Fu after oral administration of coated chitosan MS to rats were determined and compared with that of 5-Fu solution. The in vivo pharmacokinetics study of 5-Fu loaded pH-enzyme Di-dependent chitosan MS showed sustained plasma 5-Fu concentration-time profile. The in vitro release correlated well with the pharmacokinetics profile. The results clearly demonstrated that the pH-enzyme Di-dependent chitosan MS is potential system for colon-specific drug delivery of 5-Fu.\",\n \"corpus_id\": 6062522,\n \"score\": 1\n },\n {\n \"doc_id\": \"18855198\",\n \"title\": \"In vitro evaluation of chondroitin sulphate-chitosan microspheres as carrier for the delivery of proteins.\",\n \"abstract\": \"A novel formulation based on chondroitin sulphate/chitosan microspheres (CS/CH) has been investigated for oral delivery of macromolecules using ovalbumin as the model protein (OVA). The microspheres were prepared by a new emulsion-complex coacervation method. Physico-chemical properties of the polymers constituting microparticulate matrix were investigated by IR, DSC, TGA and X-ray diffraction analyses. In vitro tests were performed to evaluate the drug delivery system degradation and the protein release under conditions simulating the intestinal fluids. The ability of colonic enzymes to degrade the microparticulate systems was simulated employing the chondroitinase ABC enzyme. Results showed that the different CS/CH compositions influenced both microparticles stability and the protein release rate. Only the microspheres composed by 1:1 chondroitin sulphate-chitosan ratio achieved an OVA release profile suitable to a possible colon targeting. These microspheres released approximately 30% of ovalbumin encapsulated in 24 h in the different aqueous media tested, while they released 100% of protein in the presence of chondroitinase. The preliminary results demonstrated that chondroitin sulphate-chitosan microspheres can be a suitable delivery system for protein drug envisaged to oral administration.\",\n \"corpus_id\": 1200540,\n \"score\": 1\n },\n {\n \"doc_id\": \"20136490\",\n \"title\": \"Ondansetron-loaded chitosan microspheres for nasal antiemetic drug delivery: an alternative approach to oral and parenteral routes.\",\n \"abstract\": \"BACKGROUND: The aim of this study was to develop chitosan microspheres for nasal delivery of ondansetron hydrochloride (OND). METHOD: Microspheres were prepared with spray-drying method using glutaraldehyde as the crosslinking agent. Microspheres were characterized in terms of morphology, particle size, zeta potential, production yield, drug content, encapsulation efficiency, and in vitro drug release. RESULTS: All microspheres were spherical in shape with smooth surface and positively charged. Microspheres had also high encapsulation efficiency and the suitable particle size for nasal administration. In vitro studies indicated that all crosslinked microspheres had a significant burst effect, and sustained drug release pattern was observed until 24 hours following burst drug release. Nasal absorption of OND from crosslinked chitosan microspheres was evaluated in rats, and pharmacokinetic parameters of OND calculated from nasal microsphere administration were compared with those of both nasal and parenteral administration of aqueous solutions of OND. In vivo data also supported that OND-loaded microspheres were also able to attain a sustained plasma profile and significantly larger area under the curve values with respect to nasal aqueous solution of OND. CONCLUSION: Based on in vitro and in vivo data, it could be concluded that crosslinked chitosan microspheres are considered as a nasal delivery system of OND.\",\n \"corpus_id\": 23543784,\n \"score\": 1\n },\n {\n \"doc_id\": \"20535630\",\n \"title\": \"Eudragit S-100 entrapped chitosan microspheres of valdecoxib for colon cancer.\",\n \"abstract\": \"COX-2 inhibitors have demonstrated beneficial effects in colorectal cancer. The purpose of this study was to prepare and evaluate the colon specific microspheres of COX-2 inhibitors using valdecoxib as a model drug. Mucoadhesive core microspheres were prepared using chitosan as polymer and entrapped within Eudragit S 100 for colon targeting. FTIR spectrum of selected, coated microspheres showed peaks of valdecoxib at 3377, 3250, 1334 and 1155 cm(-1). XRD showed amorphous character and DSC showed depressed broad endotherm of valdecoxib at 169.07 degrees C, which may be attributed to dilution effect by the amorphous polymer. The coated microspheres were spherical with an average size of 90 mum. Storage of the microspheres at 40 degrees C/75% relative humidity for 6 months indicated no significant drug degradation. The coated microspheres did neither release the drug in acidic pH of stomach (pH 1.2) nor in small intestinal pH between 5 to 6.8, and the release started at pH 7.4, indicting perfect colonic delivery. The coated microspheres pretreated with phosphate buffer pH 7.4 for 30 min, when applied to mucosal surface of freshly excised goat colon, showed good mucoadhesion. The drug release at pH 7.4 and good mucoadhesive property of the microspheres make the system ideal for colonic delivery.\",\n \"corpus_id\": 20799285,\n \"score\": 1\n },\n {\n \"doc_id\": \"20735299\",\n \"title\": \"Chitosan microspheres of aceclofenac: in vitro and in vivo evaluation.\",\n \"abstract\": \"The objective of this investigation was to achieve controlled drug release of Aceclofenac (ACE) microspheres and to minimize local side-effects in the gastrointestinal tract (GIT). Sustained release chitosan microspheres containing ACE were prepared using double-emulsion solvent evaporation method (O/W/O). Chitosan microspheres were prepared by varying drug to polymer ratio (1:3, 1:4, 1:5 and 1:6). Microspheres were characterized for morphology, swelling behavior, mucoadhesive properties, FTIR and DSC study, drug loading efficiency, in vitro release, release kinetics, and in vivo study was performed on rat model. ACE-loaded microspheres were successfully prepared having production yield, 57-70% w/w. Drug encapsulation efficiency was ranging from 53-72% w/w, Scanning electron microscopy (SEM) revealed particle size of microspheres was between 39 and 55 mum. FTIR spectra and DSC thermograms demonstrated no interaction between drug and polymer. The in vitro release profiles of drug from chitosan microspheres showed sustained-release pattern of the drug in phosphate buffer, pH 6.8. In vitro release data showed correlation (r2 > 0.98), good fit with Higuchi/Korsmeyer-Peppas models, and exhibited Fickian diffusion. ACE microspheres demonstrated controlled delivery of aceclofenac and apparently, no G.I.T. erosion was noticed.\",\n \"corpus_id\": 22750407,\n \"score\": 1\n },\n {\n \"doc_id\": \"20848388\",\n \"title\": \"Formulation and evaluation of chitosan microspheres of aceclofenac for colon-targeted drug delivery.\",\n \"abstract\": \"The objective of this investigation was to develop novel colon specific drug delivery. Aceclofenac, a NSAID, was successfully encapsulated into chitosan microspheres. Various formulations were prepared by varying the ratio of chitosan, span-85 and stirring speed and the amount of glutaraldehyde. The SEM study showed that microspheres have smooth surfaces. Microspheres were characterised by Fourier transform infrared (FTIR) spectroscopy and differential scanning calorimetry (DSC) to confirm the absence of chemical interactions between drug and polymer and to know the formation of microspheres structure. The microspheres were evaluated for particle size, encapsulation efficiency, drug loading capacity, mucoadhesion studies, stability studies, in vitro and in vivo drug release studies. Particle sizes, as measured by the laser light scattering technique, were of an average size in the range 41-80 µm. The swelling index was in the range 0.37-0.82 and the entrapment efficiency range was 51-75% for all the formulations. The optimised batch ACM(13) released 83.6% at 8 h and 104% at 24 h in SCF containing rat caecal content. Eudragit coated chitosan microspheres prevented the release of the aceclofenac in the physiological environment of the stomach and small intestine and released 95.9±0.34% in the colon. With regard to release kinetics, the data were best fitted with the Higuchi model and showed zero order release with non-Fickian diffusion mechanism. The in vivo findings suggest that aceclofenac microspheres exhibit a prolonged effect of aceclofenac in rats and produce a significant anti-inflammatory effect. The findings of the present study conclusively state that chitosan microspheres are promising for colon targeting of aceclofenac to synchronise with chronobiological symptoms of rheumatoid arthritis.\",\n \"corpus_id\": 22430281,\n \"score\": 1\n },\n {\n \"doc_id\": \"20933083\",\n \"title\": \"Preparation and evaluation of alginate-chitosan microspheres for oral delivery of insulin.\",\n \"abstract\": \"The alginate-chitosan microspheres with narrow size distribution were prepared by membrane emulsification technique in combination with ion (Ca(2+)) and polymer (chitosan) solidification. The preparation procedure was observed, and the physical properties (particle size distribution, surface morphology, chitosan distribution, zeta potential) of the microspheres were characterized. Subsequently, the microspheres were employed to load model peptide of insulin. The effect of loading ways on the loading efficiency and immunological activity of insulin were investigated. It was shown that the higher loading efficiency (56.7%) and remarkable activity maintenance (99.4%) were obtained when the insulin was loaded during the chitosan solidification process (Method B). Afterward, the release profile in vitro for the optimal insulin-loaded microspheres was investigated. Under the pH conditions of gastrointestinal environment, only 32% of insulin released during the simulated transit time of drug (2 h in the stomach and 4 h in the intestinal). While under the pH condition of blood environment, insulin release was stable and sustained for a long time (14 days). Furthermore, the chemical stability of insulin released from the microspheres was well preserved after they were treated with the simulated gastric fluid containing pepsin for 2 h. Finally, the blood glucose level of diabetic rats could be effectively reduced and stably kept for a long time (∼60 h) after oral administration of the insulin-loaded alginate-chitosan microspheres. Therefore, the alginate-chitosan microspheres were found to be promising vectors showing a good efficiency in oral administration of protein or peptide drugs.\",\n \"corpus_id\": 19310111,\n \"score\": 1\n },\n {\n \"doc_id\": \"21168477\",\n \"title\": \"Preparation and evaluation of zinc-pectin-chitosan composite particles for drug delivery to the colon: role of chitosan in modifying in vitro and in vivo drug release.\",\n \"abstract\": \"Zinc-pectin-chitosan composite microparticles were designed and developed as colon-specific carrier. Resveratrol was used as model drug due to its potential activity on colon diseases. Formulations were produced by varying different formulation parameters (cross-linking pH, chitosan concentration, cross-linking time, molecular weight of chitosan, and drug concentration). Single-step formulation technique was compared with multi-step technique. Effect of these parameters was investigated on shape, size, weight, weight loss (WL), moisture content (MC), encapsulation efficiency (EE), drug loading (L), and drug release pattern of the microparticles. The formulation conditions were optimized from the drug release study. In vivo pharmacokinetics of the zinc-pectinate particles was compared with the zinc-pectin-chitosan composite particles in rats. Formulations were spherical with 920.48-1107.56 μm size, 21.19-24.27 mg weight of 50 particles, 89.83-94.34% WL, 8.31-13.25% MC, 96.95-98.85% EE, and 17.82-48.31% L. Formulation parameters showed significant influence on drug release pattern from the formulations. Formulation prepared at pH 1.5, 1% chitosan, 120 min cross-linking time, and pectin:drug at 3:1 ratio demonstrated colon-specific drug release. Microparticles were stable at 4 °C and room temperature. Pharmacokinetic study indicated in vivo colon-specific drug release from the zinc-pectin-chitosan composite particles only.\",\n \"corpus_id\": 21222772,\n \"score\": 1\n },\n {\n \"doc_id\": \"21194900\",\n \"title\": \"Colon specific chitosan microspheres for chronotherapy of chronic stable angina.\",\n \"abstract\": \"In the present work, chitosan microspheres with a mean diameter between 6.32 μm and 9.44 μm, were produced by emulsion cross-linking of chitosan, and tested for chronotherapy of chronic stable angina. Aiming at developing a suitable colon specific strategy, diltiazem hydrochloride (DTZ) was encapsulated in the microspheres, following Eudragit S-100 coating by solvent evaporation technique, exploiting the advantages of microbiological properties of chitosan and pH dependent solubility of Eudragit S-100. Different microsphere formulations were prepared varying the ratio DTZ:chitosan (1:2 to 1:10), stirring speed (1000-2000 rpm), and the concentration of emulsifier Span 80 (0.5-1.5% (w/v)). The effect of these variables on the particle size and encapsulation parameters (production yield (PY), loading capacity (LC), encapsulation efficiency (EE)) was evaluated to develop an optimized formulation. In vitro release study of non-coated chitosan microspheres in simulated gastrointestinal (GI) fluid exhibited a burst release pattern in the first hour, whereas Eudragit S-100 coating allowed producing systems of controlled release diffusion fitting to the Higuchi model, and thus suitable for colon-specific drug delivery. DSC analysis indicated that DTZ was dispersed within the microspheres matrix. Scanning electron microscopy revealed that the microspheres were spherical and had a smooth surface. Chitosan biodegradability was proven by the enhanced release rate of DTZ in presence of rat caecal contents.\",\n \"corpus_id\": 22854209,\n \"score\": 1\n },\n {\n \"doc_id\": \"21431353\",\n \"title\": \"Sustained release optimized formulation of anastrozole-loaded chitosan microspheres: in vitro and in vivo evaluation.\",\n \"abstract\": \"The purpose of this study was to develop sustained release formulation of anastrozole-loaded chitosan microspheres for treatment of breast cancer. Chitosan microspheres cross-linked with two different cross-linking agents viz, tripolyphosphate (TPP) and glutaraldehyde (GA) were prepared using single emulsion (w/o) method. A reverse phase HPLC method was developed and used for quantification of drug in microspheres and rat plasma. Influence of cross-linking agents on the properties of chitosan microspheres was extensively investigated. Formulations were characterized for encapsulation efficiency (EE), compatibility of drug with excipients, particle size, surface morphology, swelling capacity, erosion and drug release profile in phosphate buffer pH 7.4. EE varied from 30.4 ± 1.2 to 69.2 ± 3.2% and mean particle size distribution ranged from 72.5 ± 0.5 to 157.9 ± 1.5 μm. SEM analysis revealed smooth and spherical nature of microspheres. TPP microspheres exhibited higher swelling capacity, percentage erosion and drug release compared to GA microspheres. Release of anastrozole (ANS) was rapid up to 4 h followed by slow release status. FTIR analysis revealed no chemical interaction between drug and polymer. DSC analysis indicated ANS trapped in the microspheres existed in amorphous form in polymer matrix. The highest correlation coefficients (R (2)) were obtained for Higuchi model, suggesting a diffusion controlled mechanism. There was significant difference in the pharmacokinetic parameters (AUC(0-∞), Kel and t(1/2)) when ANS was formulated in the form of microspheres compared to pure drug. This may be attributed to slow release rate of ANS from chitosan microspheres and was detectable in rat plasma up to 48 h which correlates well with the in vitro release data.\",\n \"corpus_id\": 25829231,\n \"score\": 1\n },\n {\n \"doc_id\": \"21699389\",\n \"title\": \"Inclusion complex of colchicine in hydroxypropyl-β-cyclodextrin tenders better solubility and improved pharmacokinetics.\",\n \"abstract\": \"CONTEXT: Colchicine (CLC) causes cell death by destabilizing the tubulin unit. However, it ionizes at physiological pH resultant low bioavailability and therapeutic efficacy. OBJECTIVES: We have attempted to augment the bioavailability of CLC by fabricating the inclusion complex with hydroxypropyl-β-cyclodextrin (HP-β-CD). MATERIALS AND METHODS: CLC-HP-β-CD inclusion complex was prepared and evaluated with Fourier-transform infrared spectroscopy, differential scanning calorimetry, powder X-ray diffractometry, scanning electron microscopy, (1)H nuclear magnetic resonance ((1)H NMR) spectroscopy and rotating frame overhauser enhancement spectroscopy (ROESY). Oral bioavailability of CLC-HP-β-CD inclusion complex was analyzed using high performance liquid chromatography method. RESULTS AND DISCUSSION: Our phase-solubility data indicated the formation of a stable complex with K(c) ~0.31 mM(-1) at pH 7.4. (1)H NMR ascertains that NHCOCH(3) moiety of CLC enters in the HP-β-CD cavity and deshielded the H-3 and H-5 protons. ROESY also correlates the H(f) and H(g) of CLC with H-3 and H-5 protons of HP-β-CD and indicates that H(f) and H(g) protons of CLC are present either as cis and/or trans form in CLC-HP-β-CD inclusion complex. Pharmacokinetic studies showed a 1.82-fold increase in absolute bioavailability of CLC upon complexation. CONCLUSION: CLC-HP-β-CD inclusion complex may potentially be used as a viable formulation of CLC.\",\n \"corpus_id\": 23636364,\n \"score\": 1\n },\n {\n \"doc_id\": \"21824069\",\n \"title\": \"Eudragit® S100 coated calcium pectinate microspheres of curcumin for colon targeting.\",\n \"abstract\": \"Currently, colon-specific drug delivery systems have been investigated for drugs that can exert their bioactivities in the colon. In this study, Eudragit® S100 coated calcium pectinate microsphere, a pH-dependent and enzyme-dependent system, as colon-specific delivery carrier for curcumin was investigated. Curcumin-loaded calcium pectinate microspheres were prepared by emulsification-linkage method, and the preparation technology was optimised by uniform experimental design. The morphology of microspheres was observed under scanning electron microscopy. Interactions between drug and polymers were investigated with differential scanning calorimetry (DSC) and X-ray diffraction. In vitro drug release studies were performed in simulated colonic fluid in the presence of Pectinex Ultra SP-L or 1% (w/v) rat caecal content, and the results indicated that the release of curcumin was significantly increased in the presence of 1% (w/v) rat caecal contents. It could be concluded that Eudragit® S100 coated calcium pectinate microsphere was a potential carrier for colon delivery of curcumin.\",\n \"corpus_id\": 12225404,\n \"score\": 1\n },\n {\n \"doc_id\": \"21864681\",\n \"title\": \"Quality by design approach for developing chitosan-Ca-alginate microspheres for colon delivery of celecoxib-hydroxypropyl-β-cyclodextrin-PVP complex.\",\n \"abstract\": \"The aim of the present work was to develop a new multiparticulate system, designed for colon-specific delivery of celecoxib for both systemic (in chronotherapic treatment of arthritis) and local (in prophylaxis of colon carcinogenesis) therapy. The system simultaneously benefits from ternary complexation with hydroxypropyl-β-cyclodextrin and PVP (polyvinylpyrrolidone), to increase drug solubility, and vectorization in chitosan-Ca-alginate microspheres, to exploit the colon-specific carrier properties of these polymers. Statistical experimental design was employed to investigate the combined effect of four formulation variables, i.e., % of alginate, CaCl₂, and chitosan and time of cross-linking on microsphere entrapment efficiency (EE%) and drug amount released after 4h in colonic medium, considered as the responses to be optimized. Design of experiment was used in the context of Quality by Design, which requires a multivariate approach for understanding the multifactorial relationships among formulation parameters. Doehlert design allowed for defining a design space, which revealed that variations of the considered factors had in most cases an opposite influence on the responses. Desirability function was used to attain simultaneous optimization of both responses. The desired goals were achieved for both systemic and local use of celecoxib. Experimental values obtained from the optimized formulations were in both cases very close to the predicted values, thus confirming the validity of the generated mathematical model. These results demonstrated the effectiveness of the proposed jointed use of drug cyclodextrin complexation and chitosan-Ca-alginate microsphere vectorization, as well as the usefulness of the multivariate approach for the preparation of colon-targeted celecoxib microspheres with optimized properties.\",\n \"corpus_id\": 22446904,\n \"score\": 1\n },\n {\n \"doc_id\": \"22139691\",\n \"title\": \"Controlled release chitosan microspheres of mirtazapine: in vitro and in vivo evaluation.\",\n \"abstract\": \"The purpose of the study was to formulate and evaluate controlled release chitosan microspheres of mirtazapine (MTZ) to improve the bioavailability by altering the pharmacokinetic profiles of the drug. Chitosan microspheres were prepared to prolong the release of the drug into the systemic circulation. Microspheres were prepared by a single water in oil (w/o) emulsion technique varying the chitosan/drug ratio, stirring speed and concentration of the crosslinking agent (glutaraldehyde). Drug-polymer compatibility studies were carried out using fourier transform infrared spectroscopy (FT-IR) and differential scanning calorimetry (DSC). The microspheres were evaluated for encapsulation efficiency, particle size, surface morphology, swelling index, in vitro release, as well as erosion and in vivo studies in rats. The FT-IR and DSC studies revealed no interaction between drug and polymer. The encapsulation efficiency of different formulation varied from 53 ± 1.2% to 78 ± 1.5%. The mean particle size of the optimized formulation F-14 was 106.4 ± 0.5 μm. Surface morphology revealed that chitosan microspheres were discrete and spherical in shape with a porous surface. The release of MTZ from chitosan microspheres was rapid up to 4 h, and then it was continuously and slowly released up to 48 h. Optimized formulation (F-14) was found to be stable under accelerated storage conditions based on International Conference on Harmonisation guidelines. Pharmacokinetic studies revealed that the optimized formulation showed significant increases in systemic exposure (AUC = 177.70 ± 7.39 μg·h/mL), half-life (4.72 ± 0.46 h) and reduced clearance (0.009 ± 0.0001 L/h) compared to pure drug administration. Hence, the present study demonstrates that controlled release formulation of MTZ microspheres using chitosan can improve pharmacokinetic profiles of MTZ.\",\n \"corpus_id\": 26979488,\n \"score\": 1\n },\n {\n \"doc_id\": \"22944438\",\n \"title\": \"Investigation of inclusion complex of cilnidipine with hydroxypropyl-β-cyclodextrin.\",\n \"abstract\": \"The objective of this study was to improve the water-solubility and photostability of cilnidipine by complexing it with hydroxypropyl-β-cyclodextrin (HP-β-CD or HP-beta-CD). The interactions of cilnidipine and HP-β-CD were characterized by ultra violet-visible (UV/VIS) spectroscopy, differential scanning calorimetry (DSC), powder X-ray diffraction (PXRD), Fourier transformation-infrared (FT-IR) spectroscopy and (1)H nuclear magnetic resonance ((1)H NMR) spectroscopy to verify the formation of cilnidipine-HP-β-CD complex inclusion. Moreover, the binding sites in the HP-β-CD structure were also tracked through (1)H NMR spectroscopy analysis. All the characterization information proved the formation of cilnidipine-HP-β-CD inclusion complex, and the results demonstrated the superiority of the inclusion complex in dissolution rates and photostability; in addition, the apparent solubility of cilnidipine was increased more than 10,000-fold in the presence of HP-β-CD. The stability constant (1:1) was found to be 50,116 M(-1), suggesting a high tendency of the drug to enter the HP-β-CD cavity. These results identified the cilnidipine-HP-β-CD inclusion complex as an effective new approach to design a novel formulation for pharmaceutical application.\",\n \"corpus_id\": 39906702,\n \"score\": 1\n },\n {\n \"doc_id\": \"23524117\",\n \"title\": \"Development and evaluation of a novel phytosome-loaded chitosan microsphere system for curcumin delivery.\",\n \"abstract\": \"In this study, we developed a novel drug delivery system, curcumin-phytosome-loaded chitosan microspheres (Cur-PS-CMs) by combining polymer- and lipid-based delivery systems. Curcumin exhibits poor water-solubility and is rapidly eliminated from the body. We aimed to use our novel delivery system to improve the bioavailability and prolong the retention time of curcumin in the body. The Cur-PS-CMs were produced by encapsulating curcumin-phytosomes (Cur-PSs) in chitosan microspheres using ionotropic gelation. The final microsphere was spherical, with a mean particle size of 23.21 ± 6.72 μm and drug loading efficiency of 2.67 ± 0.23%. Differential scanning calorimetry and Fourier transform infrared spectroscopy demonstrated that the integrity of the phytosomes was preserved within the polymeric matrix of the microspheres. The in vitro release rate of curcumin from the Cur-PS-CMs was slower than that from curcumin-loaded chitosan microspheres (Cur-CMs) in pH 1.0, 4.0, 6.8, and 7.4. Pharmacokinetic studies in rats dosed with Cur-PS-CMs showed a 1.67- and a 1.07-fold increase in absorption of curcumin compared with Cur-PSs and Cur-CMs, respectively. The half-life of curcumin orally administration of Cur-PS-CMs (3.16 h) was longer than those of Cur-PSs (1.73 h) and Cur-CMs (2.34h). These results indicated that the new Cur-PS-CMs system combined the advantages of chitosan microspheres and phytosomes, which had better effects of promoting oral absorption and prolonging retention time of curcumin than single Cur-PSs or Cur-CMs. Therefore, the PS-CMs may be used as a sustained delivery system for lipophilic compounds with poor water-solubility and low oral bioavailability.\",\n \"corpus_id\": 43675599,\n \"score\": 1\n },\n {\n \"doc_id\": \"24312757\",\n \"title\": \"Hollow microspheres for gastroretentive floating- pulsatile drug delivery: preparation and in vitro evaluation.\",\n \"abstract\": \"PURPOSE: A multiparticular floating-pulsatile drug delivery system was developed for time and site specific drug release of piroxicam. A blend of floating and pulsatile principles of drug delivery system would have the advantage that a drug can be released in the upper GI tract after a definite time period. METHODS: Hollow microspheres were prepared by the emulsion solvent diffusion method using Eudragit S as an enteric acrylic polymer with piroxicam at various polymer/drug ratios in a mixture of dichloromethane and ethanol. Developed formulations were evaluated for yield, encapsulation efficiency, particle size, shape, apparent density, buoyancy studies and dissolution studies. RESULTS: The obtained microballoons were spherical with no major surface irregularity and mean particle size ranging from 250 to 380 for different batches. Formulations show a slight amount of relaese ranging from 0.7 to 11% in acidic medium (SGF) with complete release of drug in simulated intestinal fluid (SIF) in less than 3 h. Encapsulation efficiency of different formulations varied from 90 to 98%. The optimum loading amount of drug in the particles was found to impart suitable floatable properties to the microballoons. With increasing polymer/drug ratio, buancy of the microballoons increases accompanied by simultaneous reduction of apparent particle density. CONCLUSION: A pulsatile release of piroxicam was demonstrated by a simple drug delivery system which could be useful in chronopharmacotherapy of rheumatoid arthritis.\",\n \"corpus_id\": 23662412,\n \"score\": 1\n },\n {\n \"doc_id\": \"24360896\",\n \"title\": \"Electrosprayed 4-carboxybenzenesulfonamide-chitosan microspheres for acetazolamide delivery.\",\n \"abstract\": \"4-Carboxybenzensulfonamide-chitosan (4-CBS-chitosan) microspheres were prepared by electrospraying with acetazolamide (ACZ) as a model drug. The obtained 4-CBS-chitosan microspheres with or without ACZ-loading were characterized by Fourier transform infrared spectroscopy, differential scanning colorimetry, scanning electron microscopy and particle size analyses. The crystalline form and the stability of ACZ in a basic solution was determined using X-ray single crystal analysis. 4-CBS-chitosan had 90% encapsulation efficiency for ACZ compared to 47% of encapsulation efficiency (EE) obtained from native chitosan, forming 3.1 μm diameter microspheres with a low polydispersity index (0.4). After an initial burst release (58% in 5 min), ACZ-loaded 4-CBS-chitosan gave a sustained release of ACZ (∼ 100% over 3h) in simulated gastric fluid (0.1N HCl; pH 1.2), which was better than that seen for the release from ACZ-loaded chitosan (44% over 1.5h). Thus, 4-CBS-chitosan microspheres are a possible drug carrier in acidic conditions, such as at the gastric mucosal wall.\",\n \"corpus_id\": 205182720,\n \"score\": 1\n },\n {\n \"doc_id\": \"24577314\",\n \"title\": \"Docetaxel-loaded chitosan microspheres as a lung targeted drug delivery system: in vitro and in vivo evaluation.\",\n \"abstract\": \"The aim of this study was to prepare docetaxel-loaded chitosan microspheres and to evaluate their in vitro and in vivo characteristics. Glutaraldehyde crosslinked microspheres were prepared using a water-in-oil emulsification method, and characterized in terms of the morphological examination, particle size distribution, encapsulation ratio, drug-loading coefficient and in vitro release. Pharmacokinetics and biodistribution studies were used to evaluate that microspheres have more advantage than the conventional formulations. The emulsion crosslinking method was simple to prepare microspheres and easy to scale up. The formed microspheres were spherical in shape, with a smooth surface and the size was uniform (9.6 ± 0.8 µm); the encapsulation efficiency and drug loading of prepared microspheres were 88.1% ± 3.5% and 18.7% ± 1.2%, respectively. In vitro release indicated that the DTX microspheres had a well-sustained release efficacy and in vivo studies showed that the microspheres were found to release the drug to a maximum extent in the target tissue (lung). The prepared microspheres were found to possess suitable physico-chemical properties and the particle size range. The sustained release of DTX from microspheres revealed its applicability as drug delivery system to minimize the exposure of healthy tissues while increasing the accumulation of therapeutic drug in target sites.\",\n \"corpus_id\": 880929,\n \"score\": 1\n },\n {\n \"doc_id\": \"24815764\",\n \"title\": \"In vitro combinatorial anticancer effects of 5-fluorouracil and curcumin loaded N,O-carboxymethyl chitosan nanoparticles toward colon cancer and in vivo pharmacokinetic studies.\",\n \"abstract\": \"Colon cancer is the third most leading causes of death due to cancer worldwide and the chemo drug 5-fluorouracil's (5-FU) applicability is limited due to its non-specificity, low bioavailability and overdose. The efficacy of 5-FU in colon cancer chemo treatment could be improved by nanoencapsulation and combinatorial approach. In the present study curcumin (CUR), a known anticancer phytochemical, was used in combination with 5-FU and the work focuses on the development of a combinatorial nanomedicine based on 5-FU and CUR in N,O-carboxymethyl chitosan nanoparticles (N,O-CMC NPs). The developed 5-FU-N,O-CMC NPs and CUR-N,O-CMC NPs were found to be blood compatible. The in vitro drug release profile in pH 4.5 and 7.4 showed a sustained release profile over a period of 4 days. The combined exposure of the nanoformulations in colon cancer cells (HT 29) proved the enhanced anticancer effects. In addition, the in vivo pharmacokinetic data in mouse model revealed the improved plasma concentrations of 5-FU and CUR which prolonged up to 72 h unlike the bare drugs. In conclusion, the 5-FU and CUR released from the N,O-CMC NPs produced enhanced anticancer effects in vitro and improved plasma concentrations under in vivo conditions.\",\n \"corpus_id\": 34471849,\n \"score\": 1\n },\n {\n \"doc_id\": \"24937382\",\n \"title\": \"Preparation oral levofloxacin colon-specific microspheres delivery: in vitro and in vivo studies.\",\n \"abstract\": \"The aim of this study was to prepare levofloxacin-loaded chitosan microspheres and to evaluate their in vitro and in vivo characteristics. Glutaraldehyde-crosslinked microspheres were prepared using a spray-drying method, and characterized in terms of the morphological examination, particle size distribution, entrapment efficiency, drug loading and in vitro release. Pharmacokinetics and colon biodistribution studies were used to evaluate that microspheres have more advantage than the conventional formulations. The surface morphology of the freeze-dried microspheres were smooth, discrete with a regular spherical to near-spherical shape. Size of the microspheres after freeze-drying was 4.96 ± 0.76 μm and well-distributed. The zeta potential of microspheres was -29.3 ± 2.1 mV. An average drug loading of 9.3 ± 0.4% and encapsulation efficiency of 81.1 ± 4.7% of levofloxacin microspheres were obtained with the optimized preparation parameters. The cumulative release rate of levofloxacin microspheres was followed by a sustained release and fitted for classic Higuchi kinetic model. In vivo studies showed that chitosan microspheres are thought to have the potential to maintain levofloxacin concentration within target ranges for a long time, decreasing side effects caused by concentration fluctuation, ensuring the efficiency of treatment and improving patient compliance by reducing dosing frequency. It also does not cause any harmful or toxic effect in colon and rectum as evaluated by histopathologic studies.\",\n \"corpus_id\": 207519100,\n \"score\": 1\n },\n {\n \"doc_id\": \"25350222\",\n \"title\": \"Cyclodextrin complexes of reduced bromonoscapine in guar gum microspheres enhance colonic drug delivery.\",\n \"abstract\": \"Here, we report improved solubility and enhanced colonic delivery of reduced bromonoscapine (Red-Br-Nos), a cyclic ether brominated analogue of noscapine, upon encapsulation of its cyclodextrin (CD) complexes in bioresponsive guar gum microspheres (GGM). Phase-solubility analysis suggested that Red-Br-Nos complexed with β-CD and methyl-β-CD in a 1:1 stoichiometry, with a stability constant (Kc) of 2.29 × 10(3) M(-1) and 4.27 × 10(3) M(-1). Fourier transforms infrared spectroscopy indicated entrance of an O-CH₂ or OCH₃-C₆H₄-OCH₃ moiety of Red-Br-Nos in the β-CD or methyl-β-CD cavity. Furthermore, the cage complex of Red-Br-Nos with β-CD and methyl-β-CD was validated by several spectral techniques. Rotating frame Overhauser enhancement spectroscopy revealed that the Ha proton of the OCH₃-C₆H₄-OCH₃ moiety was closer to the H₅ proton of β-CD and the H₃ proton of the methyl-β-CD cavity. The solubility of Red-Br-Nos in phosphate buffer saline (PBS, pH ∼ 7.4) was improved by ∼10.7-fold and ∼21.2-fold when mixed with β-CD and methyl-β-CD, respectively. This increase in solubility led to a favorable decline in the IC₅₀ by ∼2-fold and ∼3-fold for Red-Br-Nos-β-CD-GGM and Red-Br-Nos-methyl-β-CD-GGM formulations respectively, compared to free Red-Br-Nos-β-CD and Red-Br-Nos-methyl-β-CD in human colon HT-29 cells. GGM-bearing drug complex formulations were found to be highly cytotoxic to the HT-29 cell line and further effective with simultaneous continuous release of Red-Br-Nos from microspheres. This is the first study to showing the preparation of drug-complex loaded GGMS for colon delivery of Red-Br-Nos that warrants preclinical assessment for the effective management of colon cancer.\",\n \"corpus_id\": 26317129,\n \"score\": 1\n },\n {\n \"doc_id\": \"25709403\",\n \"title\": \"Development of lovastatin-loaded poly(lactic acid) microspheres for sustained oral delivery: in vitro and ex vivo evaluation.\",\n \"abstract\": \"BACKGROUND: A novel lovastatin (LVT)-loaded poly(lactic acid) microsphere suitable for oral administration was developed in this study, and in vitro and in vivo characteristics were evaluated. METHODS: The designed microspheres were obtained by an improved emulsion-solvent evaporation method. The morphological examination, particle size, encapsulation ratio, drug loading, and in vitro release were characterized. Pharmacokinetics studies were used to show that microspheres possess more advantages than the conventional formulations. RESULTS: By using the emulsion-solvent evaporation method, it was simple to prepare microspheres and easy to scale up production. The morphology of formed microspheres showed a spherical shape with a smooth surface, without any particle aggregation. Mean size of the microspheres was 2.65±0.69 μm; the encapsulation efficiency was 92.5%±3.6%, and drug loading was 16.7%±2.1%. In vitro release indicated that the LVT microspheres had a well-sustained release efficacy, and ex vivo studies showed that after LVT was loaded to microspheres, the area under the plasma concentration-time curve from zero to the last measurable plasma concentration point and the extrapolation to time infinity increased significantly, which represented 2.63-fold and 2.49-fold increases, respectively, compared to suspensions. The rate of ex vivo clearance was significantly reduced. CONCLUSION: This research proved that poly(lactic acid) microspheres can significantly prolong the drug circulation time in vivo and can also significantly increase the relative bioavailability of the drug.\",\n \"corpus_id\": 16717565,\n \"score\": 1\n },\n {\n \"doc_id\": \"26047885\",\n \"title\": \"Wheat germ agglutinin anchored chitosan microspheres of reduced brominated derivative of noscapine ameliorated acute inflammation in experimental colitis.\",\n \"abstract\": \"Reduced brominated derivative of noscapine (Red-Br-Nos, EM012), has potent anti-inflammatory property. However, physicochemical limitations of Red-Br-Nos like low aqueous solubility (0.43×10(-3) g/mL), high lipophilicity (logP∼2.94) and ionization at acidic pH greatly encumber the scale-up of oral drug delivery systems for the management of colitis. Therefore, in present investigation, chitosan microspheres bearing Red-Br-Nos (CTS-MS-Red-Br-Nos) were prepared by emulsion polymerization method and later coated with wheat germ agglutinin (WGA-CTS-MS-Red-Br-Nos) to boost the bioadhesive property. The mean particle size and zeta-potential of CTS-MS-Red-Br-Nos were measured to be 10.5±5.4 μm and 8.1±2.2 mV, significantly (P<0.05) lesser than, 30.2±3.2 μm and 19.2±2.3 mV of WGA-CTS-MS-Red-Br-Nos. Furthermore, various spectral techniques like SEM, FT-IR, DSC and PXRD substantiated that Red-Br-Nos was molecularly dispersed in tailored microspheres in amorphous state. Surface bioadhesive property of WGA-CTS-MS-Red-Br-Nos promoted the affinity toward colon mucin cells in simulated colonic fluid (SCF, pH∼7.2). In vitro release studies carried out on WGA-CTS-MS-Red-Br-Nos and CTS-MS-Red-Br-Nos indicated that SCF with colitis milieu (pH∼4.7) favored the controlled release of Red-Br-Nos, owing to solubilization at acidic pH. Consistently, in vivo investigation also demonstrated the utility of WGA-CTS-MS-Red-Br-Nos, which remarkably attenuated the DSS encouraged neutrophil infiltration, myeloperoxidase activity, and pro-inflammatory cytokine production in C57BL6J mice, as compared to CTS-MS-Red-Br-Nos and Red-Br-Nos suspension. The noteworthy anti-inflammatory activity of WGA-CTS-MS-Red-Br-Nos against acute colitis may be attributed to enhanced drug delivery, affinity and utmost drug exposure at inflamed mucosal layers of colon. In conclusion, WGA-CTS-MS-Red-Br-Nos warrants further in-depth in vitro and in vivo investigations to scale-up the technology for clinical translation.\",\n \"corpus_id\": 25736954,\n \"score\": 1\n },\n {\n \"doc_id\": \"26530807\",\n \"title\": \"In vitro cytotoxicity and in vivo efficacy of 5-fluorouracil-loaded enteric-coated PEG-cross-linked chitosan microspheres in colorectal cancer therapy in rats.\",\n \"abstract\": \"PURPOSE: Microspheres of chitosan (CS) cross-linked with polyethylene glycol (PEG) were prepared by emulsion-cross-linking followed by the solvent evaporation technique. The formulations were characterized and subjected to in vitro and in vivo tests to assess cell growth, changes in cell morphology, and activities by 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide (MTT) assay on human HT-29 colon cancer cell-lines. METHODS: In vivo activity was evaluated for dimethyl hydrazine-induced colorectal cancer in albino male Wistar rats. Biochemical and histological parameters were evaluated to understand their effectiveness for colon cancer therapy. RESULTS: The 5-FU immediate release (IR) formulations suspended in SCMC produced an immediate cytotoxic effect, whereas microspheres inhibited proliferation of tumor cells to induce apoptosis over an extended time. Minimum inhibitory concentration (IC50) values for both standard plain 5-FU and 5-FU-loaded microspheres were respectively 5.00 ± 0.004 µg/mL and 165 ± 1.9 µg/mL which showed the improved safety profile of the microsphere formulation. Tissue distribution showed high concentration of 5-FU in colon that was higher than IC50 value required to stop the growth or death of colon cancer cells from the colonic dysplasia in Duke's stage A. Significant reduction in tumor volume and multiplicity was observed with increased levels of liver enzymes in animals when treated with standard 5-FU formulation compared with 5-FU loaded microspheres. Elevated levels of serum albumin, creatinine, leukocytopenia, and thrombocytopenia were observed in animals for the standard 5-FU formulation. CONCLUSION: The PEG cross-linked CS microspheres of this study slowly released 5-FU up to 24 h to colonic region and enhanced the antitumor activity.\",\n \"corpus_id\": 1343189,\n \"score\": 1\n },\n {\n \"doc_id\": \"26674842\",\n \"title\": \"Budesonide-hydroxypropyl-β-cyclodextrin inclusion complex in binary poloxamer 407/403 system for ulcerative colitis treatment: A physico-chemical study from micelles to hydrogels.\",\n \"abstract\": \"Budesonide (BUD) is a glucocorticoid widely used for the treatment of ulcerative colitis. In this work, we propose the study of the system BUD-HP-β-CD inclusion complex incorporated into PL 407 and PL407-PL403 thermoreversible hydrogels, considering physico-chemical and pharmaceutical aspects. Complexation between BUD and HP-β-CD was confirmed by phase solubility studies (1:1 stoichiometry, Kc=8662.8M(-1)), DSC, FTIR and microscopy analyzes. BUD solubility in simulated upper and lower colon fluids was improved in a dependence of HP-β-CD and PL 407 or PL407-PL403 association. Micellar hydrodynamic diameter studies showed the interaction between HP-β-CD and PL blocks, as well as the reorganization of the micellar system in the presence of BUD and its inclusion complex. Micellization temperature (Tm) was not shifted, but sol-gel phase transition studies showed that in the presence of BUD, HP-β-CD or BUD:HP-β-CD complex, the association PL407-PL403 favored the gel formation close to the physiological temperature. Physico-chemical and in vitro release assays studies revealed no competitive displacement of BUD from the HP-β-CD cavity evoked by PL407 or PL407-PL403 addition. These findings point out the BUD-HP-β-CD in PL-based hydrogels as strategies for future investigations on development of new pharmaceutical formulations for the treatment of ulcerative colitis.\",\n \"corpus_id\": 24897673,\n \"score\": 1\n },\n {\n \"doc_id\": \"26838831\",\n \"title\": \"Vincristine sulfate loaded dextran microspheres amalgamated with thermosensitive gel offered sustained release and enhanced cytotoxicity in THP-1, human leukemia cells: In vitro and in vivo study.\",\n \"abstract\": \"Vincristine sulfate (VCS) is a drug of choice for the treatment of childhood and adult acute lymphocytic leukemia, Hodgkin's, non-Hodgkin's lymphoma as well as solid tumors including sarcomas. However, poor biopharmaceutical and pharmacokinetic traits of VCS like short serum half-life (12 min), high dosing frequency (1.4 mg/m(2) per week for 4 weeks) and extensive protein binding (75%) limit the clinical potential of VCS in cancer therapy. In present investigation, injectable vincristine sulfate loaded dextran microspheres (VCS-Dextran-MSs) were prepared and amalgamated with chitosan-β-glycerophosphate gel (VCS-Dextran-MSs-Gel) to surmount the biopharmaceutical and pharmacokinetic limitations of VCS that consequently induced synergistic sustained release pattern of the drug. Particle size and zeta-potential of VCS-Dextran-MSs were measured to be 6.8 ± 2.4 μm and -18.3 ± 0.11 mV along with the encapsulation efficiency of about 60.4 ± 4.5%. Furthermore, VCS-Dextran-MSs and VCS-Dextran-MSs-Gel exhibited slow release pattern and 94.7% and 95.8% of the drug was released in 72 h and 720 h, respectively. Results from cell viability assay and pharmacokinetic as well as histopathological analysis in mice indicated that VCS-Dextran-MSs-Gel offers superior therapeutic potential and higher AUClast than VCS-Dextran-MSs and drug solution. In conclusion, VCS-Dextran-MSs-Gel warrants further preclinical tumor growth study to scale up the technology.\",\n \"corpus_id\": 21125458,\n \"score\": 1\n },\n {\n \"doc_id\": \"27427699\",\n \"title\": \"Synthesis and Characterization of Curcumin-Functionalized HP-β-CD-Modified GoldMag Nanoparticles as Drug Delivery Agents.\",\n \"abstract\": \"Curcumin, a polyphenol extracted from turmeric (Curcuma longa), has emerged as a potent multimodal cancer-preventing agent. It may attenuate the spread of cancer and render chemotherapy more effective. However, curcumin is neither well absorbed nor well retained in the blood, resulting in low efficacy. In an attempt to enhance the potency and to improve the bioavailability of curcumin, new delivery agents, hydroxypropyl-beta-cyclodextrin (HP-β-CD)-modified GoldMag nanoparticles (CD-GMNs) were designed and synthesized to incorporate curcumin. The CD-GMNs were characterized by Fourier Transform Infrared Spectroscopy (FT-IR), Thermo-gravimetric Analysis (TGA), X-ray Diffraction (XRD), Dynamic Light Scattering measurements (DLS), Transmission Electron Microscopy (TEM) and Vibrating Sample Magnetometer (VSM) analyses. For the magnetic carrier of CD-GMNs, the content of HP-β-CD was 26.9 wt%. CD-GMNs have a saturation magnetization of 22.7 emu/g with an average hydrodynamic diameter of 80 nm. The curcumin loading, encapsulation efficiency and releasing properties in vitro were also investigated. The results showed that the drug encapsulation ratio was 88% and the maximum curcumin loading capacity of CD-GMNs was 660 μg/5 mg. In vitro drug release studies showed a controlled and pH-sensitive curcumin release over a period of one week. Collectively, our data suggest that HP-β-CD-modified GoldMag nanoparticles can be considered to form a promising delivery system for curcumin to tumor sites. Targeting can be achieved by the combined effects of the application of an external magnetic field and the effect on drug release of lower pH values often found in the tumor microenvironment.\",\n \"corpus_id\": 39016998,\n \"score\": 1\n },\n {\n \"doc_id\": \"27451026\",\n \"title\": \"Molecular modeling and cytotoxicity of diffractaic acid: HP-β-CD inclusion complex encapsulated in microspheres.\",\n \"abstract\": \"In this pioneer study, 2-hydroxypropyl-β-cyclodextrin (HP-β-CD) was used to improve the solubility of the diffractaic acid (DA) via inclusion complex (DA:HP-β-CD). Subsequently, DA:HP-β-CD was incorporated into poly-ε-caprolactone (PCL) microspheres (DA:HP-β-CD-MS). Microspheres containing DA (DA-MS) or DA:HP-β-CD (DA:HP-β-CD-MS) were prepared using the multiple W/O/W emulsion-solvent evaporation technique. The phase-solubility diagram of DA in HP-β-CD (10-50mM) showed an AL type curve with a stability constant K1:1=821M(-1). (1)H NMR, FTIR, X-ray diffraction and thermal analysis showed changes in the molecular environment of DA in DA:HP-β-CD. The molecular modeling approach suggests a guest-host complex formation between the carboxylic moiety of both DA and the host (HP-β-CD). The mean particle size of the microspheres were ∅DA-MS=5.23±1.65μm and ∅DA:HP-β-CD-MS=4.11±1.39μm, respectively. The zeta potential values of the microspheres were ζDA-MS=-7.85±0.32mV and ζDA:HP-β-CD-MS=-6.93±0.46mV. Moreover, the encapsulation of DA:HP-β-CD into microspheres resulted in a more slower release (k2=0.042±0.001; r(2)=0.996) when compared with DA-MS (k2=0.183±0.005; r(2)=0.996). The encapsulation of DA or DA:HP-β-CD into microspheres reduced the cytotoxicity of DA (IC50=43.29μM) against Vero cells (IC50 of DA-MS=108.48μM and IC50 of DA:HP-β-CD-MS=142.63μM).\",\n \"corpus_id\": 32403983,\n \"score\": 1\n },\n {\n \"doc_id\": \"27770878\",\n \"title\": \"Cationic cyclodextrin/alginate chitosan nanoflowers as 5-fluorouracil drug delivery system.\",\n \"abstract\": \"Cyclodextrins (CDs) have widely been used as component of drug delivery systems. However unmodified cyclodextrins are associated with cytotoxicity and poor water solubility thus limiting their use in pharmaceutical industry. The cationic-β-cyclodextrin (Cat-β-CD) polymer cores were synthesized using β-CD, epichlorohydrin and choline chloride via a one-step polycondensation process. The main aim of this study was to synthesize hierarchical nanoflowers composed of cationic-β-CD as polymeric core along with alginate and chitosan \\\"petals\\\" (Cat-β-CD/Alg-Chi nanoflowers) as carriers for oral delivery of 5-Fluorouracil (5-FU) via an ionic-gelation technique. The drug loading capacity, particle size, zeta potential and surface morphology of the synthesized nanoflowers were determined. The prepared nanoflowers were formed with an average size of 300nm and a zeta potential of +9.90mV with good encapsulation efficiency of up to 77.3%. In vitro release of 5-FU from the loaded nanoflowers showed controlled and sustained release compared to the inclusion complex alone. Cat-β-CD/Alg-Chi nanoflowers were assessed against L929 cells and found to be effectively inhibiting the growth of L929 cells in a concentration dependent manner.\",\n \"corpus_id\": 40572649,\n \"score\": 1\n },\n {\n \"doc_id\": \"29023400\",\n \"title\": \"Electrostatic Self-Assembled Chitosan-Pectin Nano- and Microparticles for Insulin Delivery.\",\n \"abstract\": \"A polyelectrolyte complex system of chitosan-pectin nano- and microparticles was developed to encapsulate the hormone insulin. The aim of this work was to obtain small particles for oral insulin delivery without chemical crosslinkers based on natural and biodegradable polysaccharides. The nano- and microparticles were developed using chitosans (with different degrees of acetylation: 15.0% and 28.8%) and pectin solutions at various charge ratios (n⁺/n- given by the chitosan/pectin mass ratio) and total charge. Nano- and microparticles were characterized regarding particle size, zeta potential, production yield, encapsulation efficiency, stability in different media, transmission electron microscopy and cytotoxicity assays using Caco-2 cells. The insulin release was evaluated in vitro in simulated gastric and intestinal media. Small-sized particles (~240-~1900 nm) with a maximum production yield of ~34.0% were obtained. The highest encapsulation efficiency (~62.0%) of the system was observed at a charge ratio (n⁺/n-) 5.00. The system was stable in various media, particularly in simulated gastric fluid (pH 1.2). Transmission electron microscopy (TEM) analysis showed spherical shape particles when insulin was added to the system. In simulated intestinal fluid (pH 6.8), controlled insulin release occurred over 2 h. In vitro tests indicated that the proposed system presents potential as a drug delivery for oral administration of bioactive peptides.\",\n \"corpus_id\": 13096792,\n \"score\": 1\n },\n {\n \"doc_id\": \"23547762\",\n \"title\": \"Budesonide/cyclodextrin complex-loaded lyophilized microparticles for intranasal application.\",\n \"abstract\": \"OBJECTIVE: Lyophilized microparticles composed of budesonide (BDS), hydroxypropyl-β-cyclodextrin (HP-β-CD), and hydroxypropylmethylcellulose (HPMC) or sodium carboxymethylcellulose (CMC-Na) were developed for intranasal delivery and their characteristics were evaluated. MATERIALS AND METHODS: The particle size and morphology were assessed by mean diameter measurement and scanning electron microscopy (SEM) image, respectively. The solid-state of products was tested by X-ray powder diffraction (XRPD), Fourier transform infrared spectroscopy (FT-IR) and differential scanning calorimetry (DSC). In vitro drug release and cytotoxicity to the primary human nasal epithelial (HNE) cells were also evaluated. RESULTS AND DISCUSSION: Lyophilized microparticles exhibited vanishment of crystallinity of drug in XRPD analysis, the enfeeblement of carbonyl (C=O) stretching bands of carboxyl group in BDS in FT-IR spectra and the disappearance of endothermic peak of drug in the results of DSC study. Based on the results of solid-state studies, BDS was existed as an amorphous form in the lyophilized microparticles. CD complexation enhanced drug solubility and release rate, and HPMC or CMC-Na also improved drug dissolution rates. Cytotoxicity of developed microparticles to the HNE cells was measured and their safety to HNE cell was identified. CONCLUSION: Developed microparticles can efficiently deliver insoluble drug, such as BDS, to the nasal epithelium and thus it may improve therapeutic efficacy in the respiratory tract.\",\n \"corpus_id\": 24134475,\n \"score\": 0\n },\n {\n \"doc_id\": \"24732397\",\n \"title\": \"Bleomycin sulphate loaded nanostructured lipid particles augment oral bioavailability, cytotoxicity and apoptosis in cervical cancer cells.\",\n \"abstract\": \"In present investigation, bleomycin sulphate loaded nanostructured lipid particles (BLM-NLPs) were constructed to enhance the oral bioavailability by overwhelming the first pass hepatic metabolism. The particles size and nanoencapsulation efficiency of BLM-NLPs were measured to be 17.4±5.4nm and 45.3±3.4%, respectively. Our studies indicated that the drug was molecularly dispersed in the lipid nanocoacervates, with amorphous geometry, without altering the chemical structure, as ascertained by spectral studies. The nanoformulation, BLM-NLPs was analyzed for dissolution testing, cytotoxicity, apoptosis and cellular uptake in human cervical cancer cell line, HeLa cells. BLM-NLPs released the drug with first order kinetic in simulated intestinal fluid (pH∼6.8±0.1), characterized by initial burst and followed by slow release. Further, an enhanced cytotoxicity (∼5.6 fold lower IC50), improved intracellular concentration (∼4.38 fold) and greater degree of apoptosis was induced by BLM-NLPs in HeLa cells, as compared to BLM alone. Moreover, BLM-NLPs also showed dose-dependent internalization, as evinced by cellular uptake study. The in vivo study indicated a significantly (P<0.0001) smaller elimination rate constant (KE), volume of distribution (Vd) and clearance rate (CLTotal) for BLM-NLPs, as compared to BLM solution in post-oral administrations. This clearly depicts the retention and stability of tailored nanoformulation in intestinal absorption pathway. In addition, our nanoformulation, BLM-NLPs documented significantly (P<0.0001)∼3.4 fold (66.20±2.57%) higher bioavailability than BLM solution (19.56±0.79%). In conclusion, our in vitro and in vivo results warrant the safety, efficacy and potency of tailored nanoformulation in clinical settings.\",\n \"corpus_id\": 26734681,\n \"score\": 0\n },\n {\n \"doc_id\": \"27473308\",\n \"title\": \"Modified-chitosan nanoparticles: Novel drug delivery systems improve oral bioavailability of doxorubicin.\",\n \"abstract\": \"The efficacy of most anticancer drugs is highly limited in vivo due mainly to poor pharmacokinetics behavior including poor bioavailability after extravascular administration. We have developed novel chitosan-modified polymeric nanoparticles for oral as well as i.v. administration. Nanoparticles were developed utilizing the double emulsion solvent evaporation technique for sustained delivery of various anticancer drugs. Chitosan diacetate (CDA) and chitosan triacetate (CTA) polymers were previously modified in our laboratory and used as novel matrix. Nanoparticles, loaded with various anticancer drugs, were characterized for particle size using dynamic light scattering as well as transmission electron microscopy and net surface charge using dynamic light scattering. Particles size was below 100nm in diameter and zeta potential ranged - (25-30). Encapsulation efficiency of anticancer drugs varied considerably and was dependent on the physicochemical characteristics of the encapsulated drug. However, chitosan triacetate nanoparticles showed relatively higher encapsulation efficiency than chitosan diacetate nanoparticles. In vitro release of encapsulated drugs was sustained over a period of 14days. Nanoparticles enhanced cellular accumulation of encapsulated drugs, compared to the free drugs, in vitro in MCF-7 and Caco-II tumor cell lines. In conclusion, diacetate and triacetate chitosan are novel polymers that can be used to formulate nanoparticles which efficiently encapsulated anticancer drugs, and sustained the release and enhanced tumor cellular uptake of these drugs. Further, chitosan triacetate nanoparticles enhanced oral bioavailability of doxorubicin. CDA and CTA nanoparticles can be used to efficiently deliver anticancer drugs and improve their in vivo profile.\",\n \"corpus_id\": 23682785,\n \"score\": 0\n },\n {\n \"doc_id\": \"27660413\",\n \"title\": \"Preparation of novel pirfenidone microspheres for lung-targeted delivery: in vitro and in vivo study.\",\n \"abstract\": \"The aim of this study was to develop and characterize pirfenidone (PF)-loaded chitosan microspheres for lung targeting. The microspheres were prepared using the emulsion-solvent evaporation method and characterized by assessing morphology, particle size, and zeta potential. The microspheres had a spherical nature with highly smooth and integrated surfaces. The particle size of microspheres was 4.6±0.3 µm, and the zeta potential was 20.3±1.4 mV. The in vitro release results indicated that the obtained formulation of PF could reach the state of sustained release with a biphasic drug release pattern. It was observed that there was no significant difference in both the percentage of entrapment efficiency and that of drug release before and after the stability study. In vivo, the calculated relative bioavailability indicated greater pulmonary absorption of PF when it was encapsulated in microspheres. According to histopathological studies, no histological change occurred to the rat lung after the administration of PF-loaded chitosan microspheres.\",\n \"corpus_id\": 14856065,\n \"score\": 0\n },\n {\n \"doc_id\": \"28424979\",\n \"title\": \"Studies on Core-Shell Nanocapsules of Felodipine: In Vitro-In Vivo Evaluations.\",\n \"abstract\": \"The present study aimed for in vitro-in vivo-in silico simulation studies of experimentally designed (3(2)-factorial) Capmul PG-8-cored, Eudragit RSPO-Lutrol F 127 nanocapsules to ferry felodipine using GastroPlus™. The in silico parameter sensitivity analysis for pharmacokinetic parameters was initially assessed to justify the preparation of felodipine-loaded nanocapsules (FLNs) with enhanced solubility to overcome the bioavailability issues of felodipine. The overall integrated desirability ranged between 0.8187 and 0.9488 for three optimized FLNs when analyzed for mean particle size, zeta potential, encapsulation efficiency, and in vitro dissolution parameters. The morphological evaluation (SEM, TEM, and AFM) demonstrated spherical nanoparticles (200-300 nm). Validated LC-MS/MS analysis demonstrated enhanced relative bioavailability (13.37-fold) of optimized FLN as compared to suspension. The simulated regional absorption of the FLN presented significant absorption from the cecum (26.3%) and ascending colon (20.1%) with overall absorption of 67.4% from the GIT tract. Furthermore, in vitro-in vivo correlation demonstrated the Wagner-Nelson method as the preferred model as compared to mechanistic and numerical deconvolution on the basis of least mean absolute prediction error, least standard error of prediction, least mean absolute error, and maximum correlation coefficient (r (2) = 0.920). The study demonstrated enhanced oral absorption of felodipine-loaded nanocapsules, and GastroPlus™ was found to be an efficient simulation tool for in vitro-in vivo-in silico simulations.\",\n \"corpus_id\": 13660276,\n \"score\": 0\n }\n]","isConversational":false}}},{"rowIdx":94,"cells":{"query":{"kind":"string","value":"{\n \"doc_id\": \"29483539\",\n \"title\": \"Genome sequencing and analysis of Alcaligenes faecalis subsp. phenolicus MB207.\",\n \"abstract\": \"Bacteria within the genus Alcaligenes, exhibit diverse properties but remain largely unexplored at genome scale. To shed light on the genome structure, heterogeneity and traits of Alcaligenes species, the genome of a tannery effluent isolated Alcaligenes faecalis subsp. phenolicus MB207 was sequenced and assembled. The genome was compared to the whole genome sequences of genus Alcaligenes present in the National Centre for Biotechnology Information database. Core, pan and species specific gene sequences i.e. singletons were identified. Members of this genus did not portray exceptional genetic heterogeneity or conservation and out of 5,166 protein coding genes from pooled genome dataset, 2429 (47.01%) contributed to the core, 1193 (23.09%) to singletons and 1544 (29.88%) to accessory genome. Secondary metabolite forming apparatus, antibiotic production and resistance was also profiled. Alcaligenes faecalis subsp. phenolicus MB207 genome consisted of a copious amount of bioremediation genes i.e. metal tolerance and xenobiotic degrading genes. This study marks this strain as a prospective eco-friendly bacterium with numerous benefits for the environment related research. Availability of the whole genome sequence heralds an opportunity for researchers to explore enzymes and apparatus for sustainable environmental clean-up as well as important compounds/substance production.\",\n \"corpus_id\": 3525349\n}"},"candidates":{"kind":"list like","value":[{"doc_id":"20843356","title":"Pan-genome sequence analysis using Panseq: an online tool for the rapid analysis of core and accessory genomic regions.","abstract":"BACKGROUND: The pan-genome of a bacterial species consists of a core and an accessory gene pool. The accessory genome is thought to be an important source of genetic variability in bacterial populations and is gained through lateral gene transfer, allowing subpopulations of bacteria to better adapt to specific niches. Low-cost and high-throughput sequencing platforms have created an exponential increase in genome sequence data and an opportunity to study the pan-genomes of many bacterial species. In this study, we describe a new online pan-genome sequence analysis program, Panseq. RESULTS: Panseq was used to identify Escherichia coli O157:H7 and E. coli K-12 genomic islands. Within a population of 60 E. coli O157:H7 strains, the existence of 65 accessory genomic regions identified by Panseq analysis was confirmed by PCR. The accessory genome and binary presence/absence data, and core genome and single nucleotide polymorphisms (SNPs) of six L. monocytogenes strains were extracted with Panseq and hierarchically clustered and visualized. The nucleotide core and binary accessory data were also used to construct maximum parsimony (MP) trees, which were compared to the MP tree generated by multi-locus sequence typing (MLST). The topology of the accessory and core trees was identical but differed from the tree produced using seven MLST loci. The Loci Selector module found the most variable and discriminatory combinations of four loci within a 100 loci set among 10 strains in 1 s, compared to the 449 s required to exhaustively search for all possible combinations; it also found the most discriminatory 20 loci from a 96 loci E. coli O157:H7 SNP dataset. CONCLUSION: Panseq determines the core and accessory regions among a collection of genomic sequences based on user-defined parameters. It readily extracts regions unique to a genome or group of genomes, identifies SNPs within shared core genomic regions, constructs files for use in phylogeny programs based on both the presence/absence of accessory regions and SNPs within core regions and produces a graphical overview of the output. Panseq also includes a loci selector that calculates the most variable and discriminatory loci among sets of accessory loci or core gene SNPs. AVAILABILITY: Panseq is freely available online at http://76.70.11.198/panseq. Panseq is written in Perl.","corpus_id":7253201,"score":2},{"doc_id":"22933773","title":"Draft genome sequence of Alcaligenes faecalis subsp. faecalis NCIB 8687 (CCUG 2071).","abstract":"Alcaligenes faecalis subsp. faecalis NCIB 8687, the betaproteobacterium from which arsenite oxidase had its structure solved and the first \"arsenate gene island\" identified, provided a draft genome of 3.9 Mb in 186 contigs (with the largest 15 comprising 90% of the total) for this opportunistic pathogen species.","corpus_id":29801219,"score":2},{"doc_id":"23469352","title":"Genome Sequence of Alcaligenes sp. Strain HPC1271.","abstract":"We report a draft genome sequence of Alcaligenes sp. strain HPC1271, which demonstrates antimicrobial activity against multidrug-resistant bacteria. Antibiotic production by Alcaligenes has not been frequently reported, and hence, the availability of the genome sequence should enable us to explore new antibiotic-producing gene clusters.","corpus_id":11290688,"score":2},{"doc_id":"25540337","title":"A Newly Sequenced Alcaligenes faecalis Strain: Implications for Novel Temporal Symbiotic Relationships.","abstract":"We report here the draft genome sequence of Alcaligenes faecalis strain MOR02, a bacterium that is able to colonize nematodes in a temporary fashion and kill insects for their own benefit. The availability of the genome should enable us to explain these phenotypes.","corpus_id":9640421,"score":2},{"doc_id":"25667924","title":"Identification of a new Alcaligenes faecalis strain MOR02 and assessment of its toxicity and pathogenicity to insects.","abstract":"We report the isolation of a bacterium from Galleria mellonella larva and its identification using genome sequencing and phylogenomic analysis. This bacterium was named Alcaligenes faecalis strain MOR02. Microscopic analyses revealed that the bacteria are located in the esophagus and intestine of the nematodes Steinernema feltiae, S. carpocapsae, and H. bacteriophora. Using G. mellonella larvae as a model, when the larvae were injected with 24,000 CFU in their hemocoel, more than 96% mortality was achieved after 24 h. Additionally, toxicity assays determined that 1 μg of supernatant extract from A. faecalis MOR02 killed more than 70% G. mellonella larvae 96 h after injection. A correlation of experimental data with sequence genome analyses was also performed. We discovered genes that encode proteins and enzymes that are related to pathogenicity, toxicity, and host/environment interactions that may be responsible for the observed phenotypic characteristics. Our data demonstrates that the bacteria are able to use different strategies to colonize nematodes and kill insects to their own benefit. However, there remains an extensive group of unidentified microorganisms that could be participating in the infection process. Additionally, a nematode-bacterium association could be established probably as a strategy of dispersion and colonization.","corpus_id":14987232,"score":2},{"doc_id":"26238381","title":"A heavy-metal tolerant novel bacterium, Alcaligenes pakistanensis sp. nov., isolated from industrial effluent in Pakistan.","abstract":"Two strains, NCCP-650(T) and NCCP-667, were isolated from industrial effluent and their taxonomic positions were investigated using a polyphasic taxonomic approach. The strains were found to be Gram-stain negative, strictly aerobic, motile short rods, which are tolerant to heavy-metals (Cr(+2), As(+2), Pb(+2) and Cu(+2)). Cells were observed to grow at a temperature range of 10-37 °C (optimal 25-33 °C), pH range of 5.5-10.0 (optimal 6.5-7.5) and can tolerate 0-7 % NaCl (w/v) (optimum 0-1 %) in tryptic soya agar medium. Sequencing of the 16S rRNA gene and two housekeeping genes, gyrB and nirK, of the isolated strains revealed that both strains belong to the Betaproteobacteria showing highest sequence similarities with members of the genus Alcaligenes. The chemotaxonomic data [major quinones as Q-8; predominant cellular fatty acids as summed features 3 (C16 :1 ω7c/iso-C15 :0 2OH) and C16:0 followed by Summed features 2 (iso-C16 :1 I/C14 :0 3OH), C17:0 Cyclo and C18:1 ω7c; major polar lipids as diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine and one unidentified aminolipid] also supported the affiliation of the isolated strains with the genus Alcaligenes. DNA-DNA hybridizations between the two strains and with closely related type strains of species of the genus Alcaligenes confirmed that both isolates belong to a single novel species within the genus Alcaligenes. On the basis of phylogenetic analyses, physiological, biochemical characteristics and DNA-DNA hybridization, the isolated strains can be differentiated from established Alcaligenes species and thus represent a novel species, for which the name Alcaligenes pakistanensis sp. nov. is proposed with the type strain NCCP-650(T) (=LMG 28368(T) = KCTC42083(T) = JCM 30216(T)).","corpus_id":3126732,"score":2},{"doc_id":"26656226","title":"The complete genome sequence of Alcaligenes faecalis ZD02, a novel potential bionematocide.","abstract":"Root-knot nematodes (RKNs) can infect almost all crops, and result in huge economic losses in agriculture. There is no effective and environmentally safe means available to control RKNs. Alcaligenes faecalis ZD02 isolated from free living nematode Caenorhabditis elegans cadavers shows toxicity against RKN Meloidogyne incognita, that makes this strain to be a good bionematicide candidate for controlling of RKNs. Here, we firstly report the complete genome of A. faecalis ZD02 and describe its features. Additionally, we found two potential virulence factors in this genome, which play important roles for the nematocidal activity of A. faecalis ZD02.","corpus_id":29559758,"score":2},{"doc_id":"26941148","title":"Draft Genome Sequence of Alcaligenes faecalis Strain IITR89, an Indole-Oxidizing Bacterium.","abstract":"We report the draft genome sequence of Alcaligenes faecalis strain IITR89, a bacterium able to form indigo by utilizing indole as the sole carbon source. The Alcaligenes species is increasingly reported for biodegradation of diverse toxicants and thus complete sequencing may provide insight into biodegradation capabilities and other phenotypes.","corpus_id":36381041,"score":2},{"doc_id":"27056227","title":"The Genome Sequence of Alcaligenes faecalis NBIB-017 Contains Genes with Potentially High Activities against Erwinia carotovora.","abstract":"Alcaligenes faecalisNBIB-017, a Gram-negative bacterium, was isolated from soil in China. Here, we provide the complete genome sequence of this bacterium, which possesses a high number of genes encoding antibacterial factors, including proteins and small molecular peptides.","corpus_id":1240255,"score":2},{"doc_id":"27071527","title":"BPGA- an ultra-fast pan-genome analysis pipeline.","abstract":"Recent advances in ultra-high-throughput sequencing technology and metagenomics have led to a paradigm shift in microbial genomics from few genome comparisons to large-scale pan-genome studies at different scales of phylogenetic resolution. Pan-genome studies provide a framework for estimating the genomic diversity of the dataset, determining core (conserved), accessory (dispensable) and unique (strain-specific) gene pool of a species, tracing horizontal gene-flux across strains and providing insight into species evolution. The existing pan genome software tools suffer from various limitations like limited datasets, difficult installation/requirements, inadequate functional features etc. Here we present an ultra-fast computational pipeline BPGA (Bacterial Pan Genome Analysis tool) with seven functional modules. In addition to the routine pan genome analyses, BPGA introduces a number of novel features for downstream analyses like core/pan/MLST (Multi Locus Sequence Typing) phylogeny, exclusive presence/absence of genes in specific strains, subset analysis, atypical G + C content analysis and KEGG &COG mapping of core, accessory and unique genes. Other notable features include minimum running prerequisites, freedom to select the gene clustering method, ultra-fast execution, user friendly command line interface and high-quality graphics outputs. The performance of BPGA has been evaluated using a dataset of complete genome sequences of 28 Streptococcus pyogenes strains.","corpus_id":17374766,"score":2},{"doc_id":"27959788","title":"Alcaligenes endophyticus sp. nov., isolated from roots of Ammodendron bifolium.","abstract":"A Gram-stain-negative, rod-shaped, motile bacterium, designated AER10T, was isolated from the roots of Ammodendron bifolium collected from Takeermohuer desert in Xinjiang Uygur Autonomous Region, northwestern China. Growth was found to occur from 10 to 45 °C, at pH 5.0-9.0, and could tolerate up to 10 % (w/v) NaCl. 16S rRNA gene sequence result indicated that the strain AER10T belongs to the genus Alcaligenes and was closely related to Alcaligenes aquatilis (98.4 %), Alcaligenes faecalissubsp. parafaecalis (98.4 %), Alcaligenes faecalissubsp. faecalis (98.1 %) and Alcaligenes faecalissubsp. phenolicus (97.9 %). However, the DNA-DNA hybridization values between the strain AER10T and the above strains were less than the threshold value (below 70 %) for the delineation of genomic species. The DNA G+C content was 53.3 mol%. Ubiquinone-8 (Q-8) was the only quinone system present. The major fatty acids were summed feature 8 (C18 : 1ω7c, 25 %), C16 : 0 (24.2 %), summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c, 19.3 %) and cyclo-C17 : 0 (10.5 %). The polar lipid profile of the strain AER10T consists of diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, phosphatidylserine, two unidentified aminolipids and five unknown polar lipids. On the basis of the evidence presented in this study, strain AER10T is a representative of a novel species in the genus Alcaligenes, for which the name Alcaligenes endophyticus sp. nov. is proposed. The type strain is AER10T (=DSM 100498T=KCTC 42688T).","corpus_id":2751070,"score":2},{"doc_id":"28708280","title":"Biodegradation of ochratoxin A by Alcaligenes faecalis isolated from soil.","abstract":"AIMS: The aim of this study is to report on the hydrolytic action of Alcaligenes faecalis isolated from soil samples and its ability to degrade ochratoxin A. METHODS AND RESULTS: An A. faecalis strain was identified and characterized by employing both a phenotypic analysis and 16S rDNA sequence analysis. The results show that this strain could degrade ochratoxin A efficiently but could not use it as a sole carbon source. Ochratoxin α was confirmed as a degradation product in the intracellular extract of A. faecalis using UPLC-MS/MS. Our results suggest that the biodegradation of ochratoxin A by the A. faecalis strain occurs through the hydrolysis of the ochratoxin A amide bond by a putative peptidase. This is the first report to date on the degradation of ochratoxin A by A. faecalis. CONCLUSION: The A. faecalis strain is presumably a suitable candidate for use in the biodegradation of ochratoxin A. SIGNIFICANCE AND IMPACT OF THE STUDY: Ochratoxin A, which is produced by some filamentous fungi, severely impacts human and animal health by contaminating several types of food and feed. Our study contributes to the identification of the function of A. faecalis 0D-1, which is capable of producing hydrolytic enzyme(s) to biodegrade ochratoxin A into nontoxic ochratoxin α, to minimize the risk associated with ochratoxin A exposure.","corpus_id":9524096,"score":2},{"doc_id":"29192081","title":"Draft Genome Sequence of Alcaligenes faecalis BDB4, a Polyaromatic Hydrocarbon-Degrading Bacterium Isolated from Crude Oil-Contaminated Soil.","abstract":"Alcaligenes fecalis BDB4 was isolated from crude oil-contaminated soil in India. The genome sequence of A. faecalis BDB4 revealed the presence of important genes required for polyaromatic hydrocarbon (PAH) metabolism and other associated functions, such as chemotaxis, membrane transport, and biofilm formation, giving insight into the complete PAH mineralization potential of this bacterium.","corpus_id":7712392,"score":2},{"doc_id":"29623398","title":"Complete Genome Sequence of Alcaligenes Faecalis Strain JQ135, a Bacterium Capable of Efficiently Degrading Nicotinic Acid.","abstract":"Nicotinic acid (NA), known as vitamin B3, is ubiquitous in nature and plays an important role in living organisms. The microbial catabolism of NA is highly diverse. However, the NA degradation by Alcaligenes faecalis strains has been poorly investigated. In this study, we report the complete genome sequence of A. faecalis JQ135 (4.08 Mbp) and several essential genes for NA degradation. This genome sequence will facilitate to elucidate the molecular metabolism of NA and advance the potential biotechnological applications of A. faecalis strains.","corpus_id":4603499,"score":2},{"doc_id":"19376856","title":"Comparison of the complete genome sequences of Bifidobacterium animalis subsp. lactis DSM 10140 and Bl-04.","abstract":"Bifidobacteria are important members of the human gut flora, especially in infants. Comparative genomic analysis of two Bifidobacterium animalis subsp. lactis strains revealed evolution by internal deletion of consecutive spacer-repeat units within a novel clustered regularly interspaced short palindromic repeat locus, which represented the largest differential content between the two genomes. Additionally, 47 single nucleotide polymorphisms were identified, consisting primarily of nonsynonymous mutations, indicating positive selection and/or recent divergence. A particular nonsynonymous mutation in a putative glucose transporter was linked to a negative phenotypic effect on the ability of the variant to catabolize glucose, consistent with a modification in the predicted protein transmembrane topology. Comparative genome sequence analysis of three Bifidobacterium species provided a core genome set of 1,117 orthologs complemented by a pan-genome of 2,445 genes. The genome sequences of the intestinal bacterium B. animalis subsp. lactis provide insights into rapid genome evolution and the genetic basis for adaptation to the human gut environment, notably with regard to catabolism of dietary carbohydrates, resistance to bile and acid, and interaction with the intestinal epithelium. The high degree of genome conservation observed between the two strains in terms of size, organization, and sequence is indicative of a genomically monomorphic subspecies and explains the inability to differentiate the strains by standard techniques such as pulsed-field gel electrophoresis.","corpus_id":17711655,"score":1},{"doc_id":"19684310","title":"Paenalcaligenes hominis gen. nov., sp. nov., a new member of the family Alcaligenaceae.","abstract":"A beige-pigmented bacterium (strain CCUG 53761A(T)) was isolated from human blood from an 85-year-old man in Göteborg, Sweden. Comparative analysis of 16S rRNA gene sequences showed that this bacterium displayed <95 % similarity to all described species of the genera of the family Alcaligenaceae. It grouped within the radiation of the genus Alcaligenes, but showed only 93.0-94.8 % similarity to type strains of members of this genus (Alcaligenes faecalis subsp. parafaecalis, 94.8 %; Alcaligenes faecalis subsp. faecalis, 94.2 %; Alcaligenes faecalis subsp. phenolicus, 93.4 %). This discrimination was supported by chemotaxonomic differences. The polyamine pattern consisted of the predominant compound putrescine, moderate amounts of spermidine and minor to trace amounts of spermine and cadaverine; 2-hydroxyputrescine was not detectable. The quinone system was ubiquinone Q-8 with minor amounts of Q-7. The polar lipid profile was composed of the major lipids diphosphatidylglycerol and phosphatidylethanolamine and moderate amounts of phosphatidylglycerol and an unknown phospholipid; minor lipids were also detected. The fatty acid profile, with large amounts of C(16 : 0) and C(17 : 0) cyclo and the absence of C(12 : 0) 2-OH as hydroxylated fatty acid, also differed significantly from those reported for Alcaligenes species. On the basis of these data, it is proposed that strain CCUG 53761A(T) represents a novel genus and species, for which the name Paenalcaligenes hominis gen. nov., sp. nov. is proposed. The type strain of Paenalcaligenes hominis is CCUG 53761A(T) =CCM 7698(T).","corpus_id":19810955,"score":1},{"doc_id":"19696499","title":"The genus burkholderia: analysis of 56 genomic sequences.","abstract":"The genus Burkholderia consists of a number of very diverse species, both in terms of lifestyle (which varies from category B pathogens to apathogenic soil bacteria and plant colonizers) and their genetic contents. We have used 56 publicly available genomes to explore the genomic diversity within this genus, including genome sequences that are not completely finished, but are available from the NCBI database. Defining the pan- and core genomes of species results in insights in the conserved and variable fraction of genomes, and can verify (or question) historic, taxonomic groupings. We find only several hundred genes that are conserved across all Burkholderia genomes, whilst there are more than 40,000 gene families in the Burkholderia pan-genome. A BLAST matrix visualizes the fraction of conserved genes in pairwise comparisons. A BLAST atlas shows which genes are actually conserved in a number of genomes, located and visualized with reference to a chosen genome. Genomic islands are common in many Burkholderia genomes, and most of these can be readily visualized by DNA structural properties of the chromosome. Trees that are based on relatedness of gene family content yield different results depending on what genes are analyzed. Some of the differences can be explained by errors in incomplete genome sequences, but, as our data illustrate, the outcome of phylogenetic trees depends on the type of genes that are analyzed.","corpus_id":35213378,"score":1},{"doc_id":"21264216","title":"Complete sequencing and pan-genomic analysis of Lactobacillus delbrueckii subsp. bulgaricus reveal its genetic basis for industrial yogurt production.","abstract":"Lactobacillus delbrueckii subsp. bulgaricus (Lb. bulgaricus) is an important species of Lactic Acid Bacteria (LAB) used for cheese and yogurt fermentation. The genome of Lb. bulgaricus 2038, an industrial strain mainly used for yogurt production, was completely sequenced and compared against the other two ATCC collection strains of the same subspecies. Specific physiological properties of strain 2038, such as lysine biosynthesis, formate production, aspartate-related carbon-skeleton intermediate metabolism, unique EPS synthesis and efficient DNA restriction/modification systems, are all different from those of the collection strains that might benefit the industrial production of yogurt. Other common features shared by Lb. bulgaricus strains, such as efficient protocooperation with Streptococcus thermophilus and lactate production as well as well-equipped stress tolerance mechanisms may account for it being selected originally for yogurt fermentation industry. Multiple lines of evidence suggested that Lb. bulgaricus 2038 was genetically closer to the common ancestor of the subspecies than the other two sequenced collection strains, probably due to a strict industrial maintenance process for strain 2038 that might have halted its genome decay and sustained a gene network suitable for large scale yogurt production.","corpus_id":18997941,"score":1},{"doc_id":"21764529","title":"Everything at once: comparative analysis of the genomes of bacterial pathogens.","abstract":"The sum of unique genes in all genomes of a bacterial species is referred to as the pan-genome and is comprised of variably absent or present accessory genes and universally present core genes. The accessory genome is an important source of genetic variability in bacterial populations, allowing sub-populations of bacteria to better adapt to specific niches. Such subgroups may themselves have a relatively stable core genome that may influence host preference, virulence, or an association with specific disease syndromes. The core genome provides a useful means of phylogenetic reconstruction as well as contributing to phenotypic heterogeneity. Variation within the pan-genome forms the basis of comparative genotyping techniques, which have evolved alongside technology. Current high-throughput sequencing platforms have created an unprecedented opportunity for comparisons among multiple, closely related genomes. The computer algorithms and software for such comparisons continue to evolve and promise exciting advances in the world of bacterial comparative genomics. We review genotyping techniques based upon phenotypic traits, both core and accessory genomes, and look at some of the software programs currently available to perform whole-genome comparative analyses.","corpus_id":11909593,"score":1},{"doc_id":"22863143","title":"Comparative analysis of the Oenococcus oeni pan genome reveals genetic diversity in industrially-relevant pathways.","abstract":"BACKGROUND: Oenococcus oeni, a member of the lactic acid bacteria, is one of a limited number of microorganisms that not only survive, but actively proliferate in wine. It is also unusual as, unlike the majority of bacteria present in wine, it is beneficial to wine quality rather than causing spoilage. These benefits are realised primarily through catalysing malolactic fermentation, but also through imparting other positive sensory properties. However, many of these industrially-important secondary attributes have been shown to be strain-dependent and their genetic basis it yet to be determined. RESULTS: In order to investigate the scale and scope of genetic variation in O. oeni, we have performed whole-genome sequencing on eleven strains of this bacterium, bringing the total number of strains for which genome sequences are available to fourteen. While any single strain of O. oeni was shown to contain around 1800 protein-coding genes, in-depth comparative annotation based on genomic synteny and protein orthology identified over 2800 orthologous open reading frames that comprise the pan genome of this species, and less than 1200 genes that make up the conserved genomic core present in all of the strains. The expansion of the pan genome relative to the coding potential of individual strains was shown to be due to the varied presence and location of multiple distinct bacteriophage sequences and also in various metabolic functions with potential impacts on the industrial performance of this species, including cell wall exopolysaccharide biosynthesis, sugar transport and utilisation and amino acid biosynthesis. CONCLUSIONS: By providing a large cohort of sequenced strains, this study provides a broad insight into the genetic variation present within O. oeni. This data is vital to understanding and harnessing the phenotypic variation present in this economically-important species.","corpus_id":5870427,"score":1},{"doc_id":"22958348","title":"Complete genome sequence of Saccharothrix espanaensis DSM 44229(T) and comparison to the other completely sequenced Pseudonocardiaceae.","abstract":"BACKGROUND: The genus Saccharothrix is a representative of the family Pseudonocardiaceae, known to include producer strains of a wide variety of potent antibiotics. Saccharothrix espanaensis produces both saccharomicins A and B of the promising new class of heptadecaglycoside antibiotics, active against both bacteria and yeast. RESULTS: To better assess its capabilities, the complete genome sequence of S. espanaensis was established. With a size of 9,360,653 bp, coding for 8,501 genes, it stands alongside other Pseudonocardiaceae with large genomes. Besides a predicted core genome of 810 genes shared in the family, S. espanaensis has a large number of accessory genes: 2,967 singletons when compared to the family, of which 1,292 have no clear orthologs in the RefSeq database. The genome analysis revealed the presence of 26 biosynthetic gene clusters potentially encoding secondary metabolites. Among them, the cluster coding for the saccharomicins could be identified. CONCLUSION: S. espanaensis is the first completely sequenced species of the genus Saccharothrix. The genome discloses the cluster responsible for the biosynthesis of the saccharomicins, the largest oligosaccharide antibiotic currently identified. Moreover, the genome revealed 25 additional putative secondary metabolite gene clusters further suggesting the strain's potential for natural product synthesis.","corpus_id":5593930,"score":1},{"doc_id":"23626695","title":"Comparative genomic analysis of the genus Nocardiopsis provides new insights into its genetic mechanisms of environmental adaptability.","abstract":"The genus Nocardiopsis, a widespread group in phylum Actinobacteria, has received much attention owing to its ecological versatility, pathogenicity, and ability to produce a rich array of bioactive metabolites. Its high environmental adaptability might be attributable to its genome dynamics, which can be estimated through comparative genomic analysis targeting microorganisms with close phylogenetic relationships but different phenotypes. To shed light on speciation, gene content evolution, and environmental adaptation in these unique actinobacteria, we sequenced draft genomes for 16 representative species of the genus and compared them with that of the type species N. dassonvillei subsp. dassonvillei DSM 43111(T). The core genome of 1,993 orthologous and paralogous gene clusters was identified, and the pan-genomic reservoir was found not only to accommodate more than 22,000 genes, but also to be open. The top ten paralogous genes in terms of copy number could be referred to three functional categories: transcription regulators, transporters, and synthases related to bioactive metabolites. Based on phylogenomic reconstruction, we inferred past evolutionary events, such as gene gains and losses, and identified a list of clade-specific genes implicated in environmental adaptation. These results provided insights into the genetic causes of environmental adaptability in this cosmopolitan actinobacterial group and the contributions made by its inherent features, including genome dynamics and the constituents of core and accessory proteins.","corpus_id":13863929,"score":1},{"doc_id":"24069314","title":"Comparative genome analysis of Enterobacter cloacae.","abstract":"The Enterobacter cloacae species includes an extremely diverse group of bacteria that are associated with plants, soil and humans. Publication of the complete genome sequence of the plant growth-promoting endophytic E. cloacae subsp. cloacae ENHKU01 provided an opportunity to perform the first comparative genome analysis between strains of this dynamic species. Examination of the pan-genome of E. cloacae showed that the conserved core genome retains the general physiological and survival genes of the species, while genomic factors in plasmids and variable regions determine the virulence of the human pathogenic E. cloacae strain; additionally, the diversity of fimbriae contributes to variation in colonization and host determination of different E. cloacae strains. Comparative genome analysis further illustrated that E. cloacae strains possess multiple mechanisms for antagonistic action against other microorganisms, which involve the production of siderophores and various antimicrobial compounds, such as bacteriocins, chitinases and antibiotic resistance proteins. The presence of Type VI secretion systems is expected to provide further fitness advantages for E. cloacae in microbial competition, thus allowing it to survive in different environments. Competition assays were performed to support our observations in genomic analysis, where E. cloacae subsp. cloacae ENHKU01 demonstrated antagonistic activities against a wide range of plant pathogenic fungal and bacterial species.","corpus_id":18067744,"score":1},{"doc_id":"25119988","title":"Genome analysis of Bacillus amyloliquefaciens Subsp. plantarum UCMB5113: a rhizobacterium that improves plant growth and stress management.","abstract":"The Bacillus amyloliquefaciens subsp. plantarum strain UCMB5113 is a Gram-positive rhizobacterium that can colonize plant roots and stimulate plant growth and defense based on unknown mechanisms. This reinforcement of plants may provide protection to various forms of biotic and abiotic stress. To determine the genetic traits involved in the mechanism of plant-bacteria association, the genome sequence of UCMB5113 was obtained by assembling paired-end Illumina reads. The assembled chromosome of 3,889,532 bp was predicted to encode 3,656 proteins. Genes that potentially contribute to plant growth promotion such as indole-3-acetic acid (IAA) biosynthesis, acetoin synthesis and siderophore production were identified. Moreover, annotation identified putative genes responsible for non-ribosomal synthesis of secondary metabolites and genes supporting environment fitness of UCMB5113 including drug and metal resistance. A large number of genes encoding a diverse set of secretory proteins, enzymes of primary and secondary metabolism and carbohydrate active enzymes were found which reflect a high capacity to degrade various rhizosphere macromolecules. Additionally, many predicted membrane transporters provides the bacterium with efficient uptake capabilities of several nutrients. Although, UCMB5113 has the possibility to produce antibiotics and biosurfactants, the protective effect of plants to pathogens seems to be indirect and due to priming of plant induced systemic resistance. The availability of the genome enables identification of genes and their function underpinning beneficial interactions of UCMB5113 with plants.","corpus_id":16610459,"score":1},{"doc_id":"25218520","title":"De novo assembly of soybean wild relatives for pan-genome analysis of diversity and agronomic traits.","abstract":"Wild relatives of crops are an important source of genetic diversity for agriculture, but their gene repertoire remains largely unexplored. We report the establishment and analysis of a pan-genome of Glycine soja, the wild relative of cultivated soybean Glycine max, by sequencing and de novo assembly of seven phylogenetically and geographically representative accessions. Intergenomic comparisons identified lineage-specific genes and genes with copy number variation or large-effect mutations, some of which show evidence of positive selection and may contribute to variation of agronomic traits such as biotic resistance, seed composition, flowering and maturity time, organ size and final biomass. Approximately 80% of the pan-genome was present in all seven accessions (core), whereas the rest was dispensable and exhibited greater variation than the core genome, perhaps reflecting a role in adaptation to diverse environments. This work will facilitate the harnessing of untapped genetic diversity from wild soybean for enhancement of elite cultivars.","corpus_id":5360362,"score":1},{"doc_id":"25280501","title":"Comparative and genetic analysis of the four sequenced Paenibacillus polymyxa genomes reveals a diverse metabolism and conservation of genes relevant to plant-growth promotion and competitiveness.","abstract":"BACKGROUND: Members of the genus Paenibacillus are important plant growth-promoting rhizobacteria that can serve as bio-reactors. Paenibacillus polymyxa promotes the growth of a variety of economically important crops. Our lab recently completed the genome sequence of Paenibacillus polymyxa CR1. As of January 2014, four P. polymyxa genomes have been completely sequenced but no comparative genomic analyses have been reported. RESULTS: Here we report the comparative and genetic analyses of four sequenced P. polymyxa genomes, which revealed a significantly conserved core genome. Complex metabolic pathways and regulatory networks were highly conserved and allow P. polymyxa to rapidly respond to dynamic environmental cues. Genes responsible for phytohormone synthesis, phosphate solubilization, iron acquisition, transcriptional regulation, σ-factors, stress responses, transporters and biomass degradation were well conserved, indicating an intimate association with plant hosts and the rhizosphere niche. In addition, genes responsible for antimicrobial resistance and non-ribosomal peptide/polyketide synthesis are present in both the core and accessory genome of each strain. Comparative analyses also reveal variations in the accessory genome, including large plasmids present in strains M1 and SC2. Furthermore, a considerable number of strain-specific genes and genomic islands are irregularly distributed throughout each genome. Although a variety of plant-growth promoting traits are encoded by all strains, only P. polymyxa CR1 encodes the unique nitrogen fixation cluster found in other Paenibacillus sp. CONCLUSIONS: Our study revealed that genomic loci relevant to host interaction and ecological fitness are highly conserved within the P. polymyxa genomes analysed, despite variations in the accessory genome. This work suggets that plant-growth promotion by P. polymyxa is mediated largely through phytohormone production, increased nutrient availability and bio-control mechanisms. This study provides an in-depth understanding of the genome architecture of this species, thus facilitating future genetic engineering and applications in agriculture, industry and medicine. Furthermore, this study highlights the current gap in our understanding of complex plant biomass metabolism in Gram-positive bacteria.","corpus_id":13428819,"score":1},{"doc_id":"25649186","title":"Whole genome sequence and comparative genomic analysis of multidrug-resistant Staphylococcus capitis subsp. urealyticus strain LNZR-1.","abstract":"BACKGROUND: Staphylococcus capitis is an emerging opportunistic pathogen of humans, and found as a colonizer of the human gut. Here, we report a case of S. capitis subsp. urealyticus infection. The strain LNZR-1 was isolated from the blood culture of a patient with sigmoid colon cancer. It was found to be resistant to some important antibiotics, such as linezolid, a highly effective antimicrobial against clinically important Staphylococci pathogens. However, data on the genetic resistance mechanisms in S. capitis subsp. urealyticus are only sparsely available. RESULTS: The draft genome of S. capitis subsp. urealyticus strain LNZR-1 was sequenced by using next-generation sequencing technologies. Sequence data assembly revealed a genome size of 2,595,865 bp with a G + C content of 32.67%. Genome annotation revealed the presence of antibiotic resistance genes conferring resistance against some of the tested antibiotics as well as non-tested antibiotics. The genome also possesses a lot of genes that may be related to multidrug resistance. Whole genome comparison of the LNZR-1 with five other S. capitis strains showed that some functional regions are highly homologous between the six assemblies made herein. The LNZR-1 genome has high similarity with the genomes of the strains VCU116 and CR01, although some short stretches present in the genomes of strains VCU116 and CR01 were absent in the strain LNZR-1. CONCLUSIONS: The presence of a plethora of genes responsible for antibiotic resistance suggests that strain LNZR-1 could present a potential threat to human health. The comparative genomic analysis of S. capitis strains presented in this study is important for better understanding of multidrug resistance in S. capitis.","corpus_id":17109673,"score":1},{"doc_id":"26354704","title":"Biodegradation of nicosulfuron by a novel Alcaligenes faecalis strain ZWS11.","abstract":"A bacterial strain ZWS11 was isolated from sulfonylurea herbicide-contaminated farmland soil and identified as a potential nicosulfuron-degrading bacterium. Based on morphological and physicochemical characterization of the bacterium and phylogenetic analysis of the 16S rRNA sequence, strain ZWS11 was identified as Alcaligenes faecalis. The effects of the initial concentration of nicosulfuron, inoculation volume, and medium pH on degradation of nicosulfuron were investigated. Strain ZWS11 could degrade 80.56% of the initial nicosulfuron supplemented at 500.0mg/L under the conditions of pH7.0, 180r/min and 30°C after incubation for 6days. Strain ZWS11 was also capable of degrading rimsulfuron, tribenuron-methyl and thifensulfuron-methyl. Four metabolites from biodegradation of nicosulfuron were identified, which were 2-aminosulfonyl-N, N-dimethylnicotinamide (M1), 4, 6-dihydroxypyrimidine (M2), 2-amino-4, 6-dimethoxypyrimidine (M3) and 2-(1-(4,6-dimethoxy-pyrimidin-2-yl)-ureido)-N,N-dimethyl-nicotinamide (M4). Among the metabolites detected, M2 was reported for the first time. Possible biodegradation pathways of nicosulfuron by strain ZWS11 were proposed. The degradation proceeded mainly via cleavage of the sulfonylurea bridge, O-dealkylation, and contraction of the sulfonylurea bridge by elimination of a sulfur dioxide group. The results provide valuable information for degradation of nicosulfuron in contaminated environments.","corpus_id":22220531,"score":1},{"doc_id":"26964309","title":"[Extraction, Purification and Identification of a Dexamethasone-degrading Enzymes Generated by Pseudomonas Alcaligenes].","abstract":"In this research a strain of isolated Pseudomonas alcaligenes which causes degradation of dexamethasone was acclimated further and its proteins of every position in the bacterium were separated by the osmotic shock method. The separated intracellular proteins which had the highest enzyme activity were extracted by the salting out with ammonium sulfate and were purified with the cation exchange chromatography and gel chromatography. The purified proteins which was active to cause degradation of dexamethasone had been detected were cut with enzyme and were analyzed with mass spectrometry. The results showed that the degradation rate to dexamethasone by acclimated Pseudomonas alcaligenes were increased from 23.63% to 52.84%. The degrading enzymes were located mainly in the intracellular of the bacteria and its molecular weight was about 41 kD. The specific activity of the purified degrading enzymes were achieved to 1.02 U x mg(-1). Its 5-peptide amino acid sequences were consistent with some sequences of the isovaleryl-CoA dehydrogenase. The protein enzyme may be a new kind degrading enzyme of steroidal compounds. Our experimental results provided new strategies for cleanup of dexamethasone in water environment with microbial bioremediation technique.","corpus_id":25343637,"score":1},{"doc_id":"27006628","title":"Inside the Pan-genome - Methods and Software Overview.","abstract":"The number of genomes that have been deposited in databases has increased exponentially after the advent of Next-Generation Sequencing (NGS), which produces high-throughput sequence data; this circumstance has demanded the development of new bioinformatics software and the creation of new areas, such as comparative genomics. In comparative genomics, the genetic content of an organism is compared against other organisms, which helps in the prediction of gene function and coding region sequences, identification of evolutionary events and determination of phylogenetic relationships. However, expanding comparative genomics to a large number of related bacteria, we can infer their lifestyles, gene repertoires and minimal genome size. In this context, a powerful approach called Pan-genome has been initiated and developed. This approach involves the genomic comparison of different strains of the same species, or even genus. Its main goal is to establish the total number of non-redundant genes that are present in a determined dataset. Pan-genome consists of three parts: core genome; accessory or dispensable genome; and species-specific or strain-specific genes. Furthermore, pan-genome is considered to be \"open\" as long as new genes are added significantly to the total repertoire for each new additional genome and \"closed\" when the newly added genomes cannot be inferred to significantly increase the total repertoire of the genes. To perform all of the required calculations, a substantial amount of software has been developed, based on orthologous and paralogous gene identification.","corpus_id":13310059,"score":1},{"doc_id":"27107724","title":"Genome sequence of Roseivirga sp. strain D-25 and its potential applications from the genomic aspect.","abstract":"Roseivirga sp. strain D-25 is an aerobic marine bacterium isolated from seawater collected from Desaru beach, Malaysia. To date, the genus Roseivirga consists of only four species with no genome sequence reported. Here, we present the genome sequence of Roseivirga sp. strain D-25 (=KCTC 42709=DSM 101709), with a genome size of approximately 4.08Mbp and G+C content of 39.18%. Genome sequence analysis of strain D-25 revealed the presence of genes related to petroleum hydrocarbon degradation, 2,4,6-trinitrotoluene detoxification, heavy metals bioremediation and production of carotenoids, which shed light on the potential application of this strain.","corpus_id":43583837,"score":1},{"doc_id":"27591845","title":"Keratinase production and biodegradation of polluted secondary chicken feather wastes by a newly isolated multi heavy metal tolerant bacterium-Alcaligenes sp. AQ05-001.","abstract":"Biodegradation of agricultural wastes, generated annually from poultry farms and slaughterhouses, can solve the pollution problem and at the same time yield valuable degradation products. But these wastes also constitute environmental nuisance, especially in Malaysia where their illegal disposal on heavy metal contaminated soils poses a serious biodegradation issue as feather tends to accumulate heavy metals from the surrounding environment. Further, continuous use of feather wastes as cheap biosorbent material for the removal of heavy metals from effluents has contributed to the rising amount of polluted feathers, which has necessitated the search for heavy metal-tolerant feather degrading strains. Isolation, characterization and application of a novel heavy metal-tolerant feather-degrading bacterium, identified by 16S RNA sequencing as Alcaligenes sp. AQ05-001 in degradation of heavy metal polluted recalcitrant agricultural wastes, have been reported. Physico-cultural conditions influencing its activities were studied using one-factor-at-a-time and a statistical optimisation approach. Complete degradation of 5 g/L feather was achieved with pH 8, 2% inoculum at 27 °C and incubation period of 36 h. The medium optimisation after the response surface methodology (RSM) resulted in a 10-fold increase in keratinase production (88.4 U/mL) over the initial 8.85 U/mL when supplemented with 0.5% (w/v) sucrose, 0.15% (w/v) ammonium bicarbonate, 0.3% (w/v) skim milk, and 0.01% (w/v) urea. Under optimum conditions, the bacterium was able to degrade heavy metal polluted feathers completely and produced valuable keratinase and protein-rich hydrolysates. About 83% of the feathers polluted with a mixture of highly toxic metals were degraded with high keratinase activities. The heavy metal tolerance ability of this bacterium can be harnessed not only in keratinase production but also in the bioremediation of heavy metal-polluted feather wastes.","corpus_id":12304281,"score":1},{"doc_id":"27712915","title":"Comparative genomics unravels metabolic differences at the species and/or strain level and extremely acidic environmental adaptation of ten bacteria belonging to the genus Acidithiobacillus.","abstract":"Members of the Acidithiobacillus genus are widely found in extreme environments characterized by low pH and high concentrations of toxic substances, thus it is necessary to identify the cellular mechanisms needed to cope with these harsh conditions. Pan-genome analysis of ten bacteria belonging to the genus Acidithiobacillus suggested the existence of core genome, most of which were assigned to the metabolism-associated genes. Additionally, the unique genes of Acidithiobacillus ferrooxidans were much less than those of other species. A large proportion of Acidithiobacillus ferrivorans-specific genes were mapped especially to metabolism-related genes, indicating that diverse metabolic pathways might confer an advantage for adaptation to local environmental conditions. Analyses of functional metabolisms revealed the differences of carbon metabolism, nitrogen metabolism, and sulfur metabolism at the species and/or strain level. The findings also showed that Acidithiobacillus spp. harbored specific adaptive mechanisms for thriving under extreme environments. The genus Acidithiobacillus had the genetic potential to resist and metabolize toxic substances such as heavy metals and organic solvents. Comparison across species and/or strains of Acidithiobacillus populations provided a deeper appreciation of metabolic differences and environmental adaptation, as well as highlighting the importance of cellular mechanisms that maintain the basal physiological functions under complex acidic environmental conditions.","corpus_id":33986159,"score":1},{"doc_id":"27924153","title":"Genome sequence of a commensal bacterium, Enterococcus faecalis CBA7120, isolated from a Korean fecal sample.","abstract":"BACKGROUND: Enterococcus faecalis, the type strain of the genus Enterococcus, is not only a commensal bacterium in the gastrointestinal tract in vertebrates and invertebrates, but also causes serious disease as an opportunistic pathogen. To date, genome sequences have been published for over four hundred E. faecalis strains; however, pathogenicity of these microbes remains complicated. To increase our knowledge of E. faecalis virulence factors, we isolated strain CBA7120 from the feces of an 81-year-old female from the Republic of Korea and performed a comparative genomic analysis. RESULTS: The genome sequence of E. faecalis CBA7120 is 3,134,087 bp in length, with a G + C content of 37.35 mol%, and is comprised of four contigs with an N50 value of 2,922,046 bp. The genome showed high similarity with other strains of E. faecalis, including OG1RF, T13, 12107 and T20, based on OrthoANI values. Strain CBA7120 contains 374 pan-genome orthologous groups (POGs) as singletons, including \"Phages, Prophages, Transposable elements, Plasmids,\" \"Carbohydrates,\" \"DNA metabolism,\" and \"Virulence, Disease and Defense\" subsystems. Genes related to multidrug resistance efflux pumps were annotated in the genome. CONCLUSIONS: The comparative genomic analysis of E. faecalis strains presented in this study was performed using a variety of analysis methods and will facilitate future identification of hypothetical proteins.","corpus_id":14391886,"score":1},{"doc_id":"28095778","title":"The pangenome of (Antarctic) Pseudoalteromonas bacteria: evolutionary and functional insights.","abstract":"BACKGROUND: Pseudoalteromonas is a genus of ubiquitous marine bacteria used as model organisms to study the biological mechanisms involved in the adaptation to cold conditions. A remarkable feature shared by these bacteria is their ability to produce secondary metabolites with a strong antimicrobial and antitumor activity. Despite their biotechnological relevance, representatives of this genus are still lacking (with few exceptions) an extensive genomic characterization, including features involved in the evolution of secondary metabolites production. Indeed, biotechnological applications would greatly benefit from such analysis. RESULTS: Here, we analyzed the genomes of 38 strains belonging to different Pseudoalteromonas species and isolated from diverse ecological niches, including extreme ones (i.e. Antarctica). These sequences were used to reconstruct the largest Pseudoalteromonas pangenome computed so far, including also the two main groups of Pseudoalteromonas strains (pigmented and not pigmented strains). The downstream analyses were conducted to describe the genomic diversity, both at genus and group levels. This allowed highlighting a remarkable genomic heterogeneity, even for closely related strains. We drafted all the main evolutionary steps that led to the current structure and gene content of Pseudoalteromonas representatives. These, most likely, included an extensive genome reduction and a strong contribution of Horizontal Gene Transfer (HGT), which affected biotechnologically relevant gene sets and occurred in a strain-specific fashion. Furthermore, this study also identified the genomic determinants related to some of the most interesting features of the Pseudoalteromonas representatives, such as the production of secondary metabolites, the adaptation to cold temperatures and the resistance to abiotic compounds. CONCLUSIONS: This study poses the bases for a comprehensive understanding of the evolutionary trajectories followed in time by this peculiar bacterial genus and for a focused exploitation of their biotechnological potential.","corpus_id":10133785,"score":1},{"doc_id":"28229046","title":"Genome sequence of three Psychrobacter sp. strains with potential applications in bioremediation.","abstract":"To date, the genus Psychrobacter consists of 37 recognized species isolated from different sources, however they are more frequently found in cold and other non-polar environments of low water activity. Some strains belonging to the genus have shown different enzymatic activities with potential applications in bioremediation or food industry. In the present study, the whole genome sequences of three Psychrobacter-like strains (C 20.9, Cmf 22.2 and Rd 27.2) isolated from reared clams in Galicia (Spain) are described. The sequenced genomes resulted in an assembly size of 3,143,782 bp for C 20.9 isolate, 3,168,467 bp for Cmf 22.2 isolate and 3,028,386 bp for Rd 27.2 isolate. Among the identified coding sequences of the genomes, mercury detoxification and biogeochemistry genes were found, as well as genes related to heavy metals and antibiotic resistance. Also virulence-related features were identified such as the siderophore vibrioferrin or an aerobactin-like siderophore. The phylogenetic analysis of the 16S rRNA gene suggested that these strains may represent novel species of the Psychrobacter genus. The genome sequences of the Psychrobacter sp. strains have been deposited at DDBJ/EMBL/GenBank under the accession numbers MRYA00000000 (Cmf 22.2), MRYB00000000 (Rd 27.2) and MRYC00000000 (C 20.9), and the sequences could be found at the site https://www.ncbi.nlm.nih.gov/bioproject/PRJNA353858.","corpus_id":16800392,"score":1},{"doc_id":"28352091","title":"Genome sequencing and analysis of Talaromyces pinophilus provide insights into biotechnological applications.","abstract":"Species from the genus Talaromyces produce useful biomass-degrading enzymes and secondary metabolites. However, these enzymes and secondary metabolites are still poorly understood and have not been explored in depth because of a lack of comprehensive genetic information. Here, we report a 36.51-megabase genome assembly of Talaromyces pinophilus strain 1-95, with coverage of nine scaffolds of eight chromosomes with telomeric repeats at their ends and circular mitochondrial DNA. In total, 13,472 protein-coding genes were predicted. Of these, 803 were annotated to encode enzymes that act on carbohydrates, including 39 cellulose-degrading and 24 starch-degrading enzymes. In addition, 68 secondary metabolism gene clusters were identified, mainly including T1 polyketide synthase genes and nonribosomal peptide synthase genes. Comparative genomic analyses revealed that T. pinophilus 1-95 harbors more biomass-degrading enzymes and secondary metabolites than other related filamentous fungi. The prediction of the T. pinophilus 1-95 secretome indicated that approximately 50% of the biomass-degrading enzymes are secreted into the extracellular environment. These results expanded our genetic knowledge of the biomass-degrading enzyme system of T. pinophilus and its biosynthesis of secondary metabolites, facilitating the cultivation of T. pinophilus for high production of useful products.","corpus_id":4104057,"score":1},{"doc_id":"28619812","title":"Draft Genome Sequences of Six Enterococcus faecalis Strains Isolated from Malaysian Clinical and Environmental Origins.","abstract":"Enterococcus faecalis is known to cause a variety of nosocomial infections, including urinary tract infections. Antibiotic resistance and virulence properties in this species are of public concern. The draft genome sequences of six E. faecalis strains isolated from clinical and environmental sources in Malaysia are presented here.","corpus_id":22798684,"score":1},{"doc_id":"28848020","title":"Genomic Characterization of VIM Metallo-β-Lactamase-Producing Alcaligenes faecalis from Gaza, Palestine.","abstract":"Carbapenemase-producing Gram-negative bacteria (CP-GNB) have increasingly spread worldwide, and different families of carbapenemases have been identified in various bacterial species. Here, we report the identification of five VIM metallo-β-lactamase-producing Alcaligenes faecalis isolates associated with a small outbreak in a large hospital in Gaza, Palestine. Next-generation sequencing analysis showed blaVIM-2 is harbored by a chromosomal genomic island among three strains, while blaVIM-4 is carried by a novel plasmid in two strains.","corpus_id":13785179,"score":1},{"doc_id":"28848520","title":"Genome Sequencing Reveals the Potential of Achromobacter sp. HZ01 for Bioremediation.","abstract":"Petroleum pollution is a severe environmental issue. Comprehensively revealing the genetic backgrounds of hydrocarbon-degrading microorganisms contributes to developing effective methods for bioremediation of crude oil-polluted environments. Marine bacterium Achromobacter sp. HZ01 is capable of degrading hydrocarbons and producing biosurfactants. In this study, the draft genome (5.5 Mbp) of strain HZ01 has been obtained by Illumina sequencing, containing 5,162 predicted genes. Genome annotation shows that \"amino acid metabolism\" is the most abundant metabolic pathway. Strain HZ01 is not capable of using some common carbohydrates as the sole carbon sources, which is due to that it contains few genes associated with carbohydrate transport and lacks some important enzymes related to glycometabolism. It contains abundant proteins directly related to petroleum hydrocarbon degradation. AlkB hydroxylase and its homologs were not identified. It harbors a complete enzyme system of terminal oxidation pathway for n-alkane degradation, which may be initiated by cytochrome P450. The enzymes involved in the catechol pathway are relatively complete for the degradation of aromatic compounds. This bacterium lacks several essential enzymes for methane oxidation, and Baeyer-Villiger monooxygenase involved in the subterminal oxidation pathway and cycloalkane degradation was not identified. These results suggest that strain HZ01 degrades n-alkanes via the terminal oxidation pathway, degrades aromatic compounds primarily via the catechol pathway and cannot perform methane oxidation or cycloalkane degradation. Additionally, strain HZ01 possesses abundant genes related to the metabolism of secondary metabolites, including some genes involved in biosurfactant (such as glycolipids and lipopeptides) synthesis. The genome analysis also reveals its genetic basis for nitrogen metabolism, antibiotic resistance, regulatory responses to environmental changes, cell motility, and material transport. The obtained genome data provide us with a better understanding of hydrocarbon-degrading bacteria, which may contribute to the future design of rational strategies for bioremediation of petroleum-polluted marine environments.","corpus_id":10604795,"score":1},{"doc_id":"29479501","title":"Comparative genomic analysis of a new tellurite-resistant Psychrobacter strain isolated from the Antarctic Peninsula.","abstract":"The Psychrobacter genus is a cosmopolitan and diverse group of aerobic, cold-adapted, Gram-negative bacteria exhibiting biotechnological potential for low-temperature applications including bioremediation. Here, we present the draft genome sequence of a bacterium from the Psychrobacter genus isolated from a sediment sample from King George Island, Antarctica (3,490,622 bp; 18 scaffolds; G + C = 42.76%). Using phylogenetic analysis, biochemical properties and scanning electron microscopy the bacterium was identified as Psychrobacter glacincola BNF20, making it the first genome sequence reported for this species. P. glacincola BNF20 showed high tellurite (MIC 2.3 mM) and chromate (MIC 6.0 mM) resistance, respectively. Genome-wide nucleotide identity comparisons revealed that P. glacincola BNF20 is highly similar (>90%) to other uncharacterized Psychrobacter spp. such as JCM18903, JCM18902, and P11F6. Bayesian multi-locus phylogenetic analysis showed that P. glacincola BNF20 belongs to a polyphyletic clade with other bacteria isolated from polar regions. A high number of genes related to metal(loid) resistance were found, including tellurite resistance genetic determinants located in two contigs: Contig LIQB01000002.1 exhibited five ter genes, each showing putative promoter sequences (terACDEZ), whereas contig LIQB1000003.2 showed a variant of the terZ gene. Finally, investigating the presence and taxonomic distribution of ter genes in the NCBI's RefSeq bacterial database (5,398 genomes, as January 2017), revealed that 2,623 (48.59%) genomes showed at least one ter gene. At the family level, most (68.7%) genomes harbored one ter gene and 15.6% exhibited five (including P. glacincola BNF20). Overall, our results highlight the diverse nature (genetic and geographic diversity) of the Psychrobacter genus, provide insights into potential mechanisms of metal resistance, and exemplify the benefits of sampling remote locations for prospecting new molecular determinants.","corpus_id":3528059,"score":1},{"doc_id":"18720850","title":"[Isolation and characterization of a new glyphosate-resistant strain from extremely polluted environment].","abstract":"OBJECTIVE: To isolate and characterize a glyphosate-resistant strain from extremely polluted environment. METHODS: A glyphosate-resistant strain was isolated from extremely polluted soil taking glyphosate as the selection pressure. Its glyphosate resistance, growth optimal pH and antibiotic sensitivity were detected. Its morphology, cultural characteristics, physiological and biochemical properties, chemotaxonomy and 16S rDNA sequences were studied. Based on these results, the strain was identified according to the ninth edition of Bergey's manual of determinative bacteriology. RESULTS: The isolate was named SL06500. It could grow in M9 minimal medium containing up to 500 mmol/L glyphosate. The cell growth optimal pH of SL06500 was 4.0. It was resistant to ampicillin, kanamycin, tetracycline and chloromycetin. The 16S rDNA of SL06500 was amplified by PCR and sequenced. Compared with the published nucleotide sequence of 16S rDNA in NCBI (National Center for Biotechnology Information), SL06500 showed high identity with Achromobacter and Alcaligenes. Based on morphological, physiological and biochemical characteristics, the strain was identified as Alcaligenes xylosoxidans subsp.xylosoxidans SL06500 according to the ninth edition of Bergey's manual of determinative bacteriology. CONCLUSION: Strain SL06500 is worthy to be studied because of its high glyphosate resistance.","corpus_id":10164170,"score":0},{"doc_id":"23138713","title":"Extrachromosomal genetic elements in Micrococcus.","abstract":"Micrococci are Gram-positive G + C-rich, nonmotile, nonspore-forming actinomycetous bacteria. Micrococcus comprises ten members, with Micrococcus luteus being the type species. Representatives of the genus play important roles in the biodegradation of xenobiotics, bioremediation processes, production of biotechnologically important enzymes or bioactive compounds, as test strains in biological assays for lysozyme and antibiotics, and as infective agents in immunocompromised humans. The first description of plasmids dates back approximately 28 years, when several extrachromosomal elements ranging in size from 1.5 to 30.2 kb were found in Micrococcus luteus. Up to the present, a number of circular plasmids conferring antibiotic resistance, the ability to degrade aromatic compounds, and osmotolerance are known, as well as cryptic elements with unidentified functions. Here, we review the Micrococcus extrachromosomal traits reported thus far including phages and the only quite recently described large linear extrachromosomal genetic elements, termed linear plasmids, which range in size from 75 kb (pJD12) to 110 kb (pLMA1) and which confer putative advantageous capabilities, such as antibiotic or heavy metal resistances (inferred from sequence analyses and curing experiments). The role of the extrachromosomal elements for the frequently proven ecological and biotechnological versatility of the genus will be addressed as well as their potential for the development and use as genetic tools.","corpus_id":5623260,"score":0},{"doc_id":"23350846","title":"Genome sequence reveals that Pseudomonas fluorescens F113 possesses a large and diverse array of systems for rhizosphere function and host interaction.","abstract":"BACKGROUND: Pseudomonas fluorescens F113 is a plant growth-promoting rhizobacterium (PGPR) isolated from the sugar-beet rhizosphere. This bacterium has been extensively studied as a model strain for genetic regulation of secondary metabolite production in P. fluorescens, as a candidate biocontrol agent against phytopathogens, and as a heterologous host for expression of genes with biotechnological application. The F113 genome sequence and annotation has been recently reported. RESULTS: Comparative analysis of 50 genome sequences of strains belonging to the P. fluorescens group has revealed the existence of five distinct subgroups. F113 belongs to subgroup I, which is mostly composed of strains classified as P. brassicacearum. The core genome of these five strains is highly conserved and represents approximately 76% of the protein-coding genes in any given genome. Despite this strong conservation, F113 also contains a large number of unique protein-coding genes that encode traits potentially involved in the rhizocompetence of this strain. These features include protein coding genes required for denitrification, diterpenoids catabolism, motility and chemotaxis, protein secretion and production of antimicrobial compounds and insect toxins. CONCLUSIONS: The genome of P. fluorescens F113 is composed of numerous protein-coding genes, not usually found together in previously sequenced genomes, which are potentially decisive during the colonisation of the rhizosphere and/or interaction with other soil organisms. This includes genes encoding proteins involved in the production of a second flagellar apparatus, the use of abietic acid as a growth substrate, the complete denitrification pathway, the possible production of a macrolide antibiotic and the assembly of multiple protein secretion systems.","corpus_id":-1,"score":0},{"doc_id":"23524352","title":"Genome sequencing identifies Listeria fleischmannii subsp. coloradonensis subsp. nov., isolated from a ranch.","abstract":"Twenty Listeria-like isolates were obtained from environmental samples collected on a cattle ranch in northern Colorado; all of these isolates were found to share an identical partial sigB sequence, suggesting close relatedness. The isolates were similar to members of the genus Listeria in that they were Gram-stain-positive, short rods, oxidase-negative and catalase-positive; the isolates were similar to Listeria fleischmannii because they were non-motile at 25 °C. 16S rRNA gene sequencing for representative isolates and whole genome sequencing for one isolate was performed. The genome of the type strain of Listeria fleischmannii (strain LU2006-1(T)) was also sequenced. The draft genomes were very similar in size and the average MUMmer nucleotide identity across 91% of the genomes was 95.16%. Genome sequence data were used to design primers for a six-gene multi-locus sequence analysis (MLSA) scheme. Phylogenies based on (i) the near-complete 16S rRNA gene, (ii) 31 core genes and (iii) six housekeeping genes illustrated the close relationship of these Listeria-like isolates to Listeria fleischmannii LU2006-1(T). Sufficient genetic divergence of the Listeria-like isolates from the type strain of Listeria fleischmannii and differing phenotypic characteristics warrant these isolates to be classified as members of a distinct infraspecific taxon, for which the name Listeria fleischmannii subsp. coloradonensis subsp. nov. is proposed. The type strain is TTU M1-001(T) ( =BAA-2414(T) =DSM 25391(T)). The isolates of Listeria fleischmannii subsp. coloradonensis subsp. nov. differ from the nominate subspecies by the inability to utilize melezitose, turanose and sucrose, and the ability to utilize inositol. The results also demonstrate the utility of whole genome sequencing to facilitate identification of novel taxa within a well-described genus. The genomes of both subspecies of Listeria fleischmannii contained putative enhancin genes; the Listeria fleischmannii subsp. coloradonensis subsp. nov. genome also encoded a putative mosquitocidal toxin. The presence of these genes suggests possible adaptation to an insect host, and further studies are needed to probe niche adaptation of Listeria fleischmannii.","corpus_id":206178335,"score":0},{"doc_id":"23977017","title":"Whole genome duplication and enrichment of metal cation transporters revealed by de novo genome sequencing of extremely halotolerant black yeast Hortaea werneckii.","abstract":"Hortaea werneckii, ascomycetous yeast from the order Capnodiales, shows an exceptional adaptability to osmotically stressful conditions. To investigate this unusual phenotype we obtained a draft genomic sequence of a H. werneckii strain isolated from hypersaline water of solar saltern. Two of its most striking characteristics that may be associated with a halotolerant lifestyle are the large genetic redundancy and the expansion of genes encoding metal cation transporters. Although no sexual state of H. werneckii has yet been described, a mating locus with characteristics of heterothallic fungi was found. The total assembly size of the genome is 51.6 Mb, larger than most phylogenetically related fungi, coding for almost twice the usual number of predicted genes (23333). The genome appears to have experienced a relatively recent whole genome duplication, and contains two highly identical gene copies of almost every protein. This is consistent with some previous studies that reported increases in genomic DNA content triggered by exposure to salt stress. In hypersaline conditions transmembrane ion transport is of utmost importance. The analysis of predicted metal cation transporters showed that most types of transporters experienced several gene duplications at various points during their evolution. Consequently they are present in much higher numbers than expected. The resulting diversity of transporters presents interesting biotechnological opportunities for improvement of halotolerance of salt-sensitive species. The involvement of plasma P-type H⁺ ATPases in adaptation to different concentrations of salt was indicated by their salt dependent transcription. This was not the case with vacuolar H⁺ ATPases, which were transcribed constitutively. The availability of this genomic sequence is expected to promote the research of H. werneckii. Studying its extreme halotolerance will not only contribute to our understanding of life in hypersaline environments, but should also identify targets for improving the salt- and osmotolerance of economically important plants and microorganisms.","corpus_id":4089447,"score":0},{"doc_id":"24628867","title":"Genome sequence of type strain of Staphylococcus aureus subsp. aureus.","abstract":"BACKGROUND: Staphylococcus aureus is a pathogen that causes food poisoning and community-associated infection with antibiotic resistance. This species is an indigenous intestinal microbe found in infants and not found in adult intestine. The relatively small genome size and rapid evolution of antibiotic resistance genes in the species have been drawing an increasing attention in public health. To extend our understanding of the species and use the genome data for comparative genomic studies, we sequenced the type strain of S. aureus subsp. aureus DSM 20231T. RESULTS: Seventeen contigs were generated using hybrid assembly of sequences derived from the Roche 454 and Illumina systems. The length of the genome sequence was 2,902,619 bases with a G + C content of 32.8%. Among the 2,550 annotated CDSs, 44 CDSs were annotated to antibiotic resistance genes and 13 CDSs were related to methicillin resistance. It is interesting to note that this strain was first isolated in 1884 before methicillin was generally used on patients. CONCLUSIONS: The present study analyzed the genome sequence of S. aureus subsp. aureus type strain as the reference sequence for comparative genomic analyses of clinical isolates. Methicillin resistance genes found in the genome indicate the presence of antibiotic resistance mechanism prior to the usage of antibiotics. Further comparative genomic studies of methicillin-resistant strains based on this reference genome would help to understand the evolution of resistance mechanism and dissemination of resistance genes.","corpus_id":-1,"score":0},{"doc_id":"24800692","title":"Complete genome sequencing and comparative analysis of the linezolid-resistant Enterococcus faecalis strain DENG1.","abstract":"Genome level analysis of bacterial strains provides information on genetic composition and resistance mechanisms to clinically relevant antibiotics. To date, whole genome characterization of linezolid-resistant Enterococcus faecalis isolated in the clinic is lacking. In this study, we report the entire genome sequence, genomic characteristics and virulence factors of a pathogenic E. faecalis strain, DENG1. Our results showed considerable differences in genomic characteristics and virulence factors compared with other E. faecalis strains (V583 and OG1RF). The genome of this LZD-resistant E. faecalis strain can be used as a reference to study the mechanism of LZD resistance and the phylogenetic relationship of E. faecalis strains worldwide.","corpus_id":2366159,"score":0},{"doc_id":"24803570","title":"Comparative genomic analysis of malaria mosquito vector-associated novel pathogen Elizabethkingia anophelis.","abstract":"Acquisition of Elizabethkingia infections in intensive care units (ICUs) has risen in the past decade. Treatment of Elizabethkingia infections is challenging due to the lack of effective therapeutic regimens, leading to a high mortality rate. Elizabethkingia infections have long been attributed to Elizabethkingia meningoseptica. Recently, we used whole-genome sequencing to reveal that E. anophelis is the pathogenic agent for an Elizabethkingia outbreak at two ICUs. We performed comparative genomic analysis of seven hospital-isolated E. anophelis strains with five available Elizabethkingia spp. genomes deposited in the National Center for Biotechnology Information Database. A pan-genomic approach was applied to identify the core- and pan-genome for the Elizabethkingia genus. We showed that unlike the hospital-isolated pathogen E. meningoseptica ATCC 12535 strain, the hospital-isolated E. anophelis strains have genome content and organization similar to the E. anophelis Ag1 and R26 strains isolated from the midgut microbiota of the malaria mosquito vector Anopheles gambiae. Both the core- and accessory genomes of Elizabethkingia spp. possess genes conferring antibiotic resistance and virulence. Our study highlights that E. anophelis is an emerging bacterial pathogen for hospital environments.","corpus_id":12285885,"score":0},{"doc_id":"25825433","title":"Genome Modification in Enterococcus faecalis OG1RF Assessed by Bisulfite Sequencing and Single-Molecule Real-Time Sequencing.","abstract":"UNLABELLED: Enterococcus faecalis is a Gram-positive bacterium that natively colonizes the human gastrointestinal tract and opportunistically causes life-threatening infections. Multidrug-resistant (MDR) E. faecalis strains have emerged, reducing treatment options for these infections. MDR E. faecalis strains have large genomes containing mobile genetic elements (MGEs) that harbor genes for antibiotic resistance and virulence determinants. Bacteria commonly possess genome defense mechanisms to block MGE acquisition, and we hypothesize that these mechanisms have been compromised in MDR E. faecalis. In restriction-modification (R-M) defense, the bacterial genome is methylated at cytosine (C) or adenine (A) residues by a methyltransferase (MTase), such that nonself DNA can be distinguished from self DNA. A cognate restriction endonuclease digests improperly modified nonself DNA. Little is known about R-M in E. faecalis. Here, we use genome resequencing to identify DNA modifications occurring in the oral isolate OG1RF. OG1RF has one of the smallest E. faecalis genomes sequenced to date and possesses few MGEs. Single-molecule real-time (SMRT) and bisulfite sequencing revealed that OG1RF has global 5-methylcytosine (m5C) methylation at 5'-GCWGC-3' motifs. A type II R-M system confers the m5C modification, and disruption of this system impacts OG1RF electrotransformability and conjugative transfer of an antibiotic resistance plasmid. A second DNA MTase was poorly expressed under laboratory conditions but conferred global N(4)-methylcytosine (m4C) methylation at 5'-CCGG-3' motifs when expressed in Escherichia coli. Based on our results, we conclude that R-M can act as a barrier to MGE acquisition and likely influences antibiotic resistance gene dissemination in the E. faecalis species. IMPORTANCE: The horizontal transfer of antibiotic resistance genes among bacteria is a critical public health concern. Enterococcus faecalis is an opportunistic pathogen that causes life-threatening infections in humans. Multidrug resistance acquired by horizontal gene transfer limits treatment options for these infections. In this study, we used innovative DNA sequencing methodologies to investigate how a model strain of E. faecalis discriminates its own DNA from foreign DNA, i.e., self versus nonself discrimination. We also assess the role of an E. faecalis genome modification system in modulating conjugative transfer of an antibiotic resistance plasmid. These results are significant because they demonstrate that differential genome modification impacts horizontal gene transfer frequencies in E. faecalis.","corpus_id":539901,"score":0},{"doc_id":"26203344","title":"Genome sequences of copper resistant and sensitive Enterococcus faecalis strains isolated from copper-fed pigs in Denmark.","abstract":"Six strains of Enterococcus faecalis (S1, S12, S17, S18, S19 and S32) were isolated from copper fed pigs in Denmark. These Gram-positive bacteria within the genus Enterococcus are able to survive a variety of physical and chemical challenges by the acquisition of diverse genetic elements. The genome of strains S1, S12, S17, S18, S19 and S32 contained 2,615, 2,769, 2,625, 2,804, 2,853 and 2,935 protein-coding genes, with 41, 42, 27, 42, 32 and 44 genes encoding antibiotic and metal resistance, respectively. Differences between Cu resistant and sensitive E. faecalis strains, and possible co-transfer of Cu and antibiotic resistance determinants were detected through comparative genome analysis.","corpus_id":15997608,"score":0},{"doc_id":"27090021","title":"Complete genome sequence of Enterococcus faecalis LD33, a bacteriocin-producing strain.","abstract":"Enterococcus faecalis LD33 strain was originally isolated from traditional naturally fermented cream in Inner Mongolia of China. Its complete genome sequence was carried out using the Illumina Hiseq and the PacBio RSII platform. The genome only has a circular chromosome and a GC content of 37.58%. Other core information shown in the genome sequencing results further insight on this bacterium's genetic elements for bacteriocin production and the genes related to respiratory chain.","corpus_id":1569677,"score":0},{"doc_id":"27189997","title":"Antibiotic Resistance, Core-Genome and Protein Expression in IncHI1 Plasmids in Salmonella Typhimurium.","abstract":"Conjugative plasmids from the IncHI1 incompatibility group play an important role in transferring antibiotic resistance in Salmonella Typhimurium. However, knowledge of their genome structure or gene expression is limited. In this study, we determined the complete nucleotide sequences of four IncHI1 plasmids transferring resistance to antibiotics by two different next generation sequencing protocols and protein expression by mass spectrometry. Sequence data including additional 11 IncHI1 plasmids from GenBank were used for the definition of the IncHI1 plasmid core-genome and pan-genome. The core-genome consisted of approximately 123 kbp and 122 genes while the total pan-genome represented approximately 600 kbp. When the core-genome sequences were used for multiple alignments, the 15 tested IncHI1 plasmids were separated into two main lineages. GC content in core-genome genes was around 46% and 50% in accessory genome genes. A multidrug resistance region present in all 4 sequenced plasmids extended over 20 kbp and, except for tet(B), the genes responsible for antibiotic resistance were those with the highest GC content. IncHI1 plasmids therefore represent replicons that evolved in low GC content bacteria. From their original host, they spread to Salmonella and during this spread these plasmids acquired multiple accessory genes including those coding for antibiotic resistance. Antibiotic-resistance genes belonged to genes with the highest level of expression and were constitutively expressed even in the absence of antibiotics. This is the likely mechanism that facilitates host cell survival when antibiotics suddenly emerge in the environment.","corpus_id":6646506,"score":0},{"doc_id":"27303749","title":"CRISPR-Cas and Restriction-Modification Act Additively against Conjugative Antibiotic Resistance Plasmid Transfer in Enterococcus faecalis.","abstract":"Enterococcus faecalis is an opportunistic pathogen and a leading cause of nosocomial infections. Conjugative pheromone-responsive plasmids are narrow-host-range mobile genetic elements (MGEs) that are rapid disseminators of antibiotic resistance in the faecalis species. Clustered regularly interspaced short palindromic repeat (CRISPR)-Cas and restriction-modification confer acquired and innate immunity, respectively, against MGE acquisition in bacteria. Most multidrug-resistant E. faecalis isolates lack CRISPR-Cas and possess an orphan locus lacking cas genes, CRISPR2, that is of unknown function. Little is known about restriction-modification defense in E. faecalis. Here, we explore the hypothesis that multidrug-resistant E. faecalis strains are immunocompromised. We assessed MGE acquisition by E. faecalis T11, a strain closely related to the multidrug-resistant hospital isolate V583 but which lacks the ~620 kb of horizontally acquired genome content that characterizes V583. T11 possesses the E. faecalis CRISPR3-cas locus and a predicted restriction-modification system, neither of which occurs in V583. We demonstrate that CRISPR-Cas and restriction-modification together confer a 4-log reduction in acquisition of the pheromone-responsive plasmid pAM714 in biofilm matings. Additionally, we show that the orphan CRISPR2 locus is functional for genome defense against another pheromone-responsive plasmid, pCF10, only in the presence of cas9 derived from the E. faecalis CRISPR1-cas locus, which most multidrug-resistant E. faecalis isolates lack. Overall, our work demonstrated that the loss of only two loci led to a dramatic reduction in genome defense against a clinically relevant MGE, highlighting the critical importance of the E. faecalis accessory genome in modulating horizontal gene transfer. Our results rationalize the development of antimicrobial strategies that capitalize upon the immunocompromised status of multidrug-resistant E. faecalis. IMPORTANCE Enterococcus faecalis is a bacterium that normally inhabits the gastrointestinal tracts of humans and other animals. Although these bacteria are members of our native gut flora, they can cause life-threatening infections in hospitalized patients. Antibiotic resistance genes appear to be readily shared among high-risk E. faecalis strains, and multidrug resistance in these bacteria limits treatment options for infections. Here, we find that CRISPR-Cas and restriction-modification systems, which function as adaptive and innate immune systems in bacteria, significantly impact the spread of antibiotic resistance genes in E. faecalis populations. The loss of these systems in high-risk E. faecalis suggests that they are immunocompromised, a tradeoff that allows them to readily acquire new genes and adapt to new antibiotics.","corpus_id":24766913,"score":0},{"doc_id":"27688323","title":"Genome Sequence of Klebsiella quasipneumoniae subsp. similipneumoniae MB373, an Effective Bioremediator.","abstract":"Klebsiella quasipneumoniae subsp. similipneumoniae MB373 was isolated from effluent of the Hattar Industrial Estate, Haripur, Pakistan. K. quasipneumoniae subsp. similipneumoniae has few cultivated/characterized members so far. Whole-genome sequencing revealed its potential for metal and toxin resistance, which further elucidated various enzymatic processes for the degradation of xenobiotics, illuminating its bioremediation applications.","corpus_id":17576857,"score":0},{"doc_id":"27785154","title":"Whole genome sequencing uncovers a novel IND-16 metallo-β-lactamase from an extensively drug-resistant Chryseobacterium indologenes strain J31.","abstract":"BACKGROUND: Chryseobacterium indologenes is an emerging opportunistic pathogen in hospital-acquired infection, which is intrinsically resistant to most antimicrobial agents against gram-negative bacteria. In the purpose of extending our understanding of the resistance mechanism of C. indologenes, we sequenced and analyzed the genome of an extensively antibiotic resistant C. indologenes strain, isolated from a Chinese prostate cancer patient. We also investigated the presence of antibiotic resistance genes, particularly metallo-β-lactamase (MBL) genes, and performed a comparative genomic analysis with other Chryseobacterium species. RESULTS: 16s rRNA sequencing indicated the isolate belongs to C. indologenes. We assembled a total of 1095M bp clean-filtered reads into 171 contigs by de novo assembly. The draft genome of C. indologenes J31 consisted of 5,830,795 bp with a GC content of 36.9 %. RAST analysis revealed the genome contained 5196 coding sequences (CDSs), 28 rRNAs, 81 tRNAs and 114 pseudogenes. We detected 90 antibiotic resistance genes from different drug classes in the whole genome. Notably, a novel blaIND allele blaIND-16 was identified, which shared 99 % identity with blaIND-8 and blaIND-10. By comparing strain J31 genome to the closely four related neighbors in the genus Chryseobacterium, we identified 2634 conserved genes, and 1449 unique genes. CONCLUSIONS: In this study, we described the whole genome sequence of C. indologenes strain J31. Numerous resistance determinants were detected in the genome and might be responsible for the extensively antibiotic resistance of this strain. Comparative genomic analysis revealed the presence of considerable strain-specific genes which would contribute to the distinctive characteristics of strain J31. Our study provides the insight of the multidrug resistance mechanism in genus Chryseobacterium.","corpus_id":18850120,"score":0},{"doc_id":"27795252","title":"Draft Genome Sequence of Enterococcus faecalis Strain F165 Isolated from a Urinary Tract Infection.","abstract":"We report here a draft genome sequence of Enterococcus faecalis strain F165 isolated from a urine specimen in South Brazil. The genome size was 3,049,734 bp, with a G+C content of 37.38%, and genes related to antimicrobial resistance and adherence were found in the strain. These findings are consistent with pathogenesis of E. faecalis species.","corpus_id":6389485,"score":0},{"doc_id":"28302789","title":"Draft Genome Sequences of 11 Lactococcus lactis subsp. cremoris Strains.","abstract":"The lactic acid bacterium Lactococcus lactis is widely used for the fermentation of dairy products. Here, we present the draft genome sequences of 11 L. lactis subsp. cremoris strains isolated from different environments.","corpus_id":33491517,"score":0},{"doc_id":"28377746","title":"Genome-Guided Insights into the Plant Growth Promotion Capabilities of the Physiologically Versatile Bacillus aryabhattai Strain AB211.","abstract":"Bacillus aryabhattai AB211 is a plant growth promoting, Gram-positive firmicute, isolated from the rhizosphere of tea (Camellia sinensis), one of the oldest perennial crops and a major non-alcoholic beverage widely consumed all over the world. The whole genome of B. aryabhattai AB211 was sequenced, annotated and evaluated with special focus on genomic elements related to plant microbe interaction. It's genome sequence reveals the presence of a 5,403,026 bp chromosome. A total of 5226 putative protein-coding sequences, 16 rRNA, 120 tRNA, 8 ncRNAs, 58 non-protein coding genes, and 11 prophage regions were identified. Genome sequence comparisons between strain AB211 and other related environmental strains of B. aryabhattai, identified about 3558 genes conserved among all B. aryabhattai genomes analyzed. Most of the common genes involved in plant growth promotion activities were found to be present within core genes of all the genomes used for comparison, illustrating possible common plant growth promoting traits shared among all the strains of B. aryabhattai. Besides the core genes, some genes were exclusively identified in the genome of strain AB211. Functional annotation of the genes predicted in the strain AB211 revealed the presence of genes responsible for mineral phosphate solubilization, siderophores, acetoin, butanediol, exopolysaccharides, flagella biosynthesis, surface attachment/biofilm formation, and indole acetic acid production, most of which were experimentally verified in the present study. Genome analysis and experimental evidence suggested that AB211 has robust central carbohydrate metabolism implying that this bacterium can efficiently utilize the root exudates and other organic materials as an energy source. Genes for the production of peroxidases, catalases, and superoxide dismutases, that confer resistance to oxidative stresses in plants were identified in AB211 genome. Besides these, genes for heat shock tolerance, cold shock tolerance, glycine-betaine production, and antibiotic/heavy metal resistance that enable bacteria to survive biotic/abiotic stress were also identified. Based on the genome sequence information and experimental evidence as presented in this study, strain AB211 appears to be metabolically diverse and exhibits tremendous potential as a plant growth promoting bacterium.","corpus_id":6341115,"score":0},{"doc_id":"29152584","title":"Large-Scale Bioinformatics Analysis of Bacillus Genomes Uncovers Conserved Roles of Natural Products in Bacterial Physiology.","abstract":"Bacteria possess an amazing capacity to synthesize a diverse range of structurally complex, bioactive natural products known as specialized (or secondary) metabolites. Many of these specialized metabolites are used as clinical therapeutics, while others have important ecological roles in microbial communities. The biosynthetic gene clusters (BGCs) that generate these metabolites can be identified in bacterial genome sequences using their highly conserved genetic features. We analyzed an unprecedented 1,566 bacterial genomes from Bacillus species and identified nearly 20,000 BGCs. By comparing these BGCs to one another as well as a curated set of known specialized metabolite BGCs, we discovered that the majority of Bacillus natural products are comprised of a small set of highly conserved, well-distributed, known natural product compounds. Most of these metabolites have important roles influencing the physiology and development of Bacillus species. We identified, in addition to these characterized compounds, many unique, weakly conserved BGCs scattered across the genus that are predicted to encode unknown natural products. Many of these \"singleton\" BGCs appear to have been acquired via horizontal gene transfer. Based on this large-scale characterization of metabolite production in the Bacilli, we go on to connect the alkylpyrones, natural products that are highly conserved but previously biologically uncharacterized, to a role in Bacillus physiology: inhibiting spore development. IMPORTANCEBacilli are capable of producing a diverse array of specialized metabolites, many of which have gained attention for their roles as signals that affect bacterial physiology and development. Up to this point, however, the Bacillus genus's metabolic capacity has been underexplored. We undertook a deep genomic analysis of 1,566 Bacillus genomes to understand the full spectrum of metabolites that this bacterial group can make. We discovered that the majority of the specialized metabolites produced by Bacillus species are highly conserved, known compounds with important signaling roles in the physiology and development of this bacterium. Additionally, there is significant unique biosynthetic machinery distributed across the genus that might lead to new, unknown metabolites with diverse biological functions. Inspired by the findings of our genomic analysis, we speculate that the highly conserved alkylpyrones might have an important biological activity within this genus. We go on to validate this prediction by demonstrating that these natural products are developmental signals in Bacillus and act by inhibiting sporulation.","corpus_id":9881959,"score":0}],"string":"[\n {\n \"doc_id\": \"20843356\",\n \"title\": \"Pan-genome sequence analysis using Panseq: an online tool for the rapid analysis of core and accessory genomic regions.\",\n \"abstract\": \"BACKGROUND: The pan-genome of a bacterial species consists of a core and an accessory gene pool. The accessory genome is thought to be an important source of genetic variability in bacterial populations and is gained through lateral gene transfer, allowing subpopulations of bacteria to better adapt to specific niches. Low-cost and high-throughput sequencing platforms have created an exponential increase in genome sequence data and an opportunity to study the pan-genomes of many bacterial species. In this study, we describe a new online pan-genome sequence analysis program, Panseq. RESULTS: Panseq was used to identify Escherichia coli O157:H7 and E. coli K-12 genomic islands. Within a population of 60 E. coli O157:H7 strains, the existence of 65 accessory genomic regions identified by Panseq analysis was confirmed by PCR. The accessory genome and binary presence/absence data, and core genome and single nucleotide polymorphisms (SNPs) of six L. monocytogenes strains were extracted with Panseq and hierarchically clustered and visualized. The nucleotide core and binary accessory data were also used to construct maximum parsimony (MP) trees, which were compared to the MP tree generated by multi-locus sequence typing (MLST). The topology of the accessory and core trees was identical but differed from the tree produced using seven MLST loci. The Loci Selector module found the most variable and discriminatory combinations of four loci within a 100 loci set among 10 strains in 1 s, compared to the 449 s required to exhaustively search for all possible combinations; it also found the most discriminatory 20 loci from a 96 loci E. coli O157:H7 SNP dataset. CONCLUSION: Panseq determines the core and accessory regions among a collection of genomic sequences based on user-defined parameters. It readily extracts regions unique to a genome or group of genomes, identifies SNPs within shared core genomic regions, constructs files for use in phylogeny programs based on both the presence/absence of accessory regions and SNPs within core regions and produces a graphical overview of the output. Panseq also includes a loci selector that calculates the most variable and discriminatory loci among sets of accessory loci or core gene SNPs. AVAILABILITY: Panseq is freely available online at http://76.70.11.198/panseq. Panseq is written in Perl.\",\n \"corpus_id\": 7253201,\n \"score\": 2\n },\n {\n \"doc_id\": \"22933773\",\n \"title\": \"Draft genome sequence of Alcaligenes faecalis subsp. faecalis NCIB 8687 (CCUG 2071).\",\n \"abstract\": \"Alcaligenes faecalis subsp. faecalis NCIB 8687, the betaproteobacterium from which arsenite oxidase had its structure solved and the first \\\"arsenate gene island\\\" identified, provided a draft genome of 3.9 Mb in 186 contigs (with the largest 15 comprising 90% of the total) for this opportunistic pathogen species.\",\n \"corpus_id\": 29801219,\n \"score\": 2\n },\n {\n \"doc_id\": \"23469352\",\n \"title\": \"Genome Sequence of Alcaligenes sp. Strain HPC1271.\",\n \"abstract\": \"We report a draft genome sequence of Alcaligenes sp. strain HPC1271, which demonstrates antimicrobial activity against multidrug-resistant bacteria. Antibiotic production by Alcaligenes has not been frequently reported, and hence, the availability of the genome sequence should enable us to explore new antibiotic-producing gene clusters.\",\n \"corpus_id\": 11290688,\n \"score\": 2\n },\n {\n \"doc_id\": \"25540337\",\n \"title\": \"A Newly Sequenced Alcaligenes faecalis Strain: Implications for Novel Temporal Symbiotic Relationships.\",\n \"abstract\": \"We report here the draft genome sequence of Alcaligenes faecalis strain MOR02, a bacterium that is able to colonize nematodes in a temporary fashion and kill insects for their own benefit. The availability of the genome should enable us to explain these phenotypes.\",\n \"corpus_id\": 9640421,\n \"score\": 2\n },\n {\n \"doc_id\": \"25667924\",\n \"title\": \"Identification of a new Alcaligenes faecalis strain MOR02 and assessment of its toxicity and pathogenicity to insects.\",\n \"abstract\": \"We report the isolation of a bacterium from Galleria mellonella larva and its identification using genome sequencing and phylogenomic analysis. This bacterium was named Alcaligenes faecalis strain MOR02. Microscopic analyses revealed that the bacteria are located in the esophagus and intestine of the nematodes Steinernema feltiae, S. carpocapsae, and H. bacteriophora. Using G. mellonella larvae as a model, when the larvae were injected with 24,000 CFU in their hemocoel, more than 96% mortality was achieved after 24 h. Additionally, toxicity assays determined that 1 μg of supernatant extract from A. faecalis MOR02 killed more than 70% G. mellonella larvae 96 h after injection. A correlation of experimental data with sequence genome analyses was also performed. We discovered genes that encode proteins and enzymes that are related to pathogenicity, toxicity, and host/environment interactions that may be responsible for the observed phenotypic characteristics. Our data demonstrates that the bacteria are able to use different strategies to colonize nematodes and kill insects to their own benefit. However, there remains an extensive group of unidentified microorganisms that could be participating in the infection process. Additionally, a nematode-bacterium association could be established probably as a strategy of dispersion and colonization.\",\n \"corpus_id\": 14987232,\n \"score\": 2\n },\n {\n \"doc_id\": \"26238381\",\n \"title\": \"A heavy-metal tolerant novel bacterium, Alcaligenes pakistanensis sp. nov., isolated from industrial effluent in Pakistan.\",\n \"abstract\": \"Two strains, NCCP-650(T) and NCCP-667, were isolated from industrial effluent and their taxonomic positions were investigated using a polyphasic taxonomic approach. The strains were found to be Gram-stain negative, strictly aerobic, motile short rods, which are tolerant to heavy-metals (Cr(+2), As(+2), Pb(+2) and Cu(+2)). Cells were observed to grow at a temperature range of 10-37 °C (optimal 25-33 °C), pH range of 5.5-10.0 (optimal 6.5-7.5) and can tolerate 0-7 % NaCl (w/v) (optimum 0-1 %) in tryptic soya agar medium. Sequencing of the 16S rRNA gene and two housekeeping genes, gyrB and nirK, of the isolated strains revealed that both strains belong to the Betaproteobacteria showing highest sequence similarities with members of the genus Alcaligenes. The chemotaxonomic data [major quinones as Q-8; predominant cellular fatty acids as summed features 3 (C16 :1 ω7c/iso-C15 :0 2OH) and C16:0 followed by Summed features 2 (iso-C16 :1 I/C14 :0 3OH), C17:0 Cyclo and C18:1 ω7c; major polar lipids as diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine and one unidentified aminolipid] also supported the affiliation of the isolated strains with the genus Alcaligenes. DNA-DNA hybridizations between the two strains and with closely related type strains of species of the genus Alcaligenes confirmed that both isolates belong to a single novel species within the genus Alcaligenes. On the basis of phylogenetic analyses, physiological, biochemical characteristics and DNA-DNA hybridization, the isolated strains can be differentiated from established Alcaligenes species and thus represent a novel species, for which the name Alcaligenes pakistanensis sp. nov. is proposed with the type strain NCCP-650(T) (=LMG 28368(T) = KCTC42083(T) = JCM 30216(T)).\",\n \"corpus_id\": 3126732,\n \"score\": 2\n },\n {\n \"doc_id\": \"26656226\",\n \"title\": \"The complete genome sequence of Alcaligenes faecalis ZD02, a novel potential bionematocide.\",\n \"abstract\": \"Root-knot nematodes (RKNs) can infect almost all crops, and result in huge economic losses in agriculture. There is no effective and environmentally safe means available to control RKNs. Alcaligenes faecalis ZD02 isolated from free living nematode Caenorhabditis elegans cadavers shows toxicity against RKN Meloidogyne incognita, that makes this strain to be a good bionematicide candidate for controlling of RKNs. Here, we firstly report the complete genome of A. faecalis ZD02 and describe its features. Additionally, we found two potential virulence factors in this genome, which play important roles for the nematocidal activity of A. faecalis ZD02.\",\n \"corpus_id\": 29559758,\n \"score\": 2\n },\n {\n \"doc_id\": \"26941148\",\n \"title\": \"Draft Genome Sequence of Alcaligenes faecalis Strain IITR89, an Indole-Oxidizing Bacterium.\",\n \"abstract\": \"We report the draft genome sequence of Alcaligenes faecalis strain IITR89, a bacterium able to form indigo by utilizing indole as the sole carbon source. The Alcaligenes species is increasingly reported for biodegradation of diverse toxicants and thus complete sequencing may provide insight into biodegradation capabilities and other phenotypes.\",\n \"corpus_id\": 36381041,\n \"score\": 2\n },\n {\n \"doc_id\": \"27056227\",\n \"title\": \"The Genome Sequence of Alcaligenes faecalis NBIB-017 Contains Genes with Potentially High Activities against Erwinia carotovora.\",\n \"abstract\": \"Alcaligenes faecalisNBIB-017, a Gram-negative bacterium, was isolated from soil in China. Here, we provide the complete genome sequence of this bacterium, which possesses a high number of genes encoding antibacterial factors, including proteins and small molecular peptides.\",\n \"corpus_id\": 1240255,\n \"score\": 2\n },\n {\n \"doc_id\": \"27071527\",\n \"title\": \"BPGA- an ultra-fast pan-genome analysis pipeline.\",\n \"abstract\": \"Recent advances in ultra-high-throughput sequencing technology and metagenomics have led to a paradigm shift in microbial genomics from few genome comparisons to large-scale pan-genome studies at different scales of phylogenetic resolution. Pan-genome studies provide a framework for estimating the genomic diversity of the dataset, determining core (conserved), accessory (dispensable) and unique (strain-specific) gene pool of a species, tracing horizontal gene-flux across strains and providing insight into species evolution. The existing pan genome software tools suffer from various limitations like limited datasets, difficult installation/requirements, inadequate functional features etc. Here we present an ultra-fast computational pipeline BPGA (Bacterial Pan Genome Analysis tool) with seven functional modules. In addition to the routine pan genome analyses, BPGA introduces a number of novel features for downstream analyses like core/pan/MLST (Multi Locus Sequence Typing) phylogeny, exclusive presence/absence of genes in specific strains, subset analysis, atypical G + C content analysis and KEGG &COG mapping of core, accessory and unique genes. Other notable features include minimum running prerequisites, freedom to select the gene clustering method, ultra-fast execution, user friendly command line interface and high-quality graphics outputs. The performance of BPGA has been evaluated using a dataset of complete genome sequences of 28 Streptococcus pyogenes strains.\",\n \"corpus_id\": 17374766,\n \"score\": 2\n },\n {\n \"doc_id\": \"27959788\",\n \"title\": \"Alcaligenes endophyticus sp. nov., isolated from roots of Ammodendron bifolium.\",\n \"abstract\": \"A Gram-stain-negative, rod-shaped, motile bacterium, designated AER10T, was isolated from the roots of Ammodendron bifolium collected from Takeermohuer desert in Xinjiang Uygur Autonomous Region, northwestern China. Growth was found to occur from 10 to 45 °C, at pH 5.0-9.0, and could tolerate up to 10 % (w/v) NaCl. 16S rRNA gene sequence result indicated that the strain AER10T belongs to the genus Alcaligenes and was closely related to Alcaligenes aquatilis (98.4 %), Alcaligenes faecalissubsp. parafaecalis (98.4 %), Alcaligenes faecalissubsp. faecalis (98.1 %) and Alcaligenes faecalissubsp. phenolicus (97.9 %). However, the DNA-DNA hybridization values between the strain AER10T and the above strains were less than the threshold value (below 70 %) for the delineation of genomic species. The DNA G+C content was 53.3 mol%. Ubiquinone-8 (Q-8) was the only quinone system present. The major fatty acids were summed feature 8 (C18 : 1ω7c, 25 %), C16 : 0 (24.2 %), summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c, 19.3 %) and cyclo-C17 : 0 (10.5 %). The polar lipid profile of the strain AER10T consists of diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, phosphatidylserine, two unidentified aminolipids and five unknown polar lipids. On the basis of the evidence presented in this study, strain AER10T is a representative of a novel species in the genus Alcaligenes, for which the name Alcaligenes endophyticus sp. nov. is proposed. The type strain is AER10T (=DSM 100498T=KCTC 42688T).\",\n \"corpus_id\": 2751070,\n \"score\": 2\n },\n {\n \"doc_id\": \"28708280\",\n \"title\": \"Biodegradation of ochratoxin A by Alcaligenes faecalis isolated from soil.\",\n \"abstract\": \"AIMS: The aim of this study is to report on the hydrolytic action of Alcaligenes faecalis isolated from soil samples and its ability to degrade ochratoxin A. METHODS AND RESULTS: An A. faecalis strain was identified and characterized by employing both a phenotypic analysis and 16S rDNA sequence analysis. The results show that this strain could degrade ochratoxin A efficiently but could not use it as a sole carbon source. Ochratoxin α was confirmed as a degradation product in the intracellular extract of A. faecalis using UPLC-MS/MS. Our results suggest that the biodegradation of ochratoxin A by the A. faecalis strain occurs through the hydrolysis of the ochratoxin A amide bond by a putative peptidase. This is the first report to date on the degradation of ochratoxin A by A. faecalis. CONCLUSION: The A. faecalis strain is presumably a suitable candidate for use in the biodegradation of ochratoxin A. SIGNIFICANCE AND IMPACT OF THE STUDY: Ochratoxin A, which is produced by some filamentous fungi, severely impacts human and animal health by contaminating several types of food and feed. Our study contributes to the identification of the function of A. faecalis 0D-1, which is capable of producing hydrolytic enzyme(s) to biodegrade ochratoxin A into nontoxic ochratoxin α, to minimize the risk associated with ochratoxin A exposure.\",\n \"corpus_id\": 9524096,\n \"score\": 2\n },\n {\n \"doc_id\": \"29192081\",\n \"title\": \"Draft Genome Sequence of Alcaligenes faecalis BDB4, a Polyaromatic Hydrocarbon-Degrading Bacterium Isolated from Crude Oil-Contaminated Soil.\",\n \"abstract\": \"Alcaligenes fecalis BDB4 was isolated from crude oil-contaminated soil in India. The genome sequence of A. faecalis BDB4 revealed the presence of important genes required for polyaromatic hydrocarbon (PAH) metabolism and other associated functions, such as chemotaxis, membrane transport, and biofilm formation, giving insight into the complete PAH mineralization potential of this bacterium.\",\n \"corpus_id\": 7712392,\n \"score\": 2\n },\n {\n \"doc_id\": \"29623398\",\n \"title\": \"Complete Genome Sequence of Alcaligenes Faecalis Strain JQ135, a Bacterium Capable of Efficiently Degrading Nicotinic Acid.\",\n \"abstract\": \"Nicotinic acid (NA), known as vitamin B3, is ubiquitous in nature and plays an important role in living organisms. The microbial catabolism of NA is highly diverse. However, the NA degradation by Alcaligenes faecalis strains has been poorly investigated. In this study, we report the complete genome sequence of A. faecalis JQ135 (4.08 Mbp) and several essential genes for NA degradation. This genome sequence will facilitate to elucidate the molecular metabolism of NA and advance the potential biotechnological applications of A. faecalis strains.\",\n \"corpus_id\": 4603499,\n \"score\": 2\n },\n {\n \"doc_id\": \"19376856\",\n \"title\": \"Comparison of the complete genome sequences of Bifidobacterium animalis subsp. lactis DSM 10140 and Bl-04.\",\n \"abstract\": \"Bifidobacteria are important members of the human gut flora, especially in infants. Comparative genomic analysis of two Bifidobacterium animalis subsp. lactis strains revealed evolution by internal deletion of consecutive spacer-repeat units within a novel clustered regularly interspaced short palindromic repeat locus, which represented the largest differential content between the two genomes. Additionally, 47 single nucleotide polymorphisms were identified, consisting primarily of nonsynonymous mutations, indicating positive selection and/or recent divergence. A particular nonsynonymous mutation in a putative glucose transporter was linked to a negative phenotypic effect on the ability of the variant to catabolize glucose, consistent with a modification in the predicted protein transmembrane topology. Comparative genome sequence analysis of three Bifidobacterium species provided a core genome set of 1,117 orthologs complemented by a pan-genome of 2,445 genes. The genome sequences of the intestinal bacterium B. animalis subsp. lactis provide insights into rapid genome evolution and the genetic basis for adaptation to the human gut environment, notably with regard to catabolism of dietary carbohydrates, resistance to bile and acid, and interaction with the intestinal epithelium. The high degree of genome conservation observed between the two strains in terms of size, organization, and sequence is indicative of a genomically monomorphic subspecies and explains the inability to differentiate the strains by standard techniques such as pulsed-field gel electrophoresis.\",\n \"corpus_id\": 17711655,\n \"score\": 1\n },\n {\n \"doc_id\": \"19684310\",\n \"title\": \"Paenalcaligenes hominis gen. nov., sp. nov., a new member of the family Alcaligenaceae.\",\n \"abstract\": \"A beige-pigmented bacterium (strain CCUG 53761A(T)) was isolated from human blood from an 85-year-old man in Göteborg, Sweden. Comparative analysis of 16S rRNA gene sequences showed that this bacterium displayed <95 % similarity to all described species of the genera of the family Alcaligenaceae. It grouped within the radiation of the genus Alcaligenes, but showed only 93.0-94.8 % similarity to type strains of members of this genus (Alcaligenes faecalis subsp. parafaecalis, 94.8 %; Alcaligenes faecalis subsp. faecalis, 94.2 %; Alcaligenes faecalis subsp. phenolicus, 93.4 %). This discrimination was supported by chemotaxonomic differences. The polyamine pattern consisted of the predominant compound putrescine, moderate amounts of spermidine and minor to trace amounts of spermine and cadaverine; 2-hydroxyputrescine was not detectable. The quinone system was ubiquinone Q-8 with minor amounts of Q-7. The polar lipid profile was composed of the major lipids diphosphatidylglycerol and phosphatidylethanolamine and moderate amounts of phosphatidylglycerol and an unknown phospholipid; minor lipids were also detected. The fatty acid profile, with large amounts of C(16 : 0) and C(17 : 0) cyclo and the absence of C(12 : 0) 2-OH as hydroxylated fatty acid, also differed significantly from those reported for Alcaligenes species. On the basis of these data, it is proposed that strain CCUG 53761A(T) represents a novel genus and species, for which the name Paenalcaligenes hominis gen. nov., sp. nov. is proposed. The type strain of Paenalcaligenes hominis is CCUG 53761A(T) =CCM 7698(T).\",\n \"corpus_id\": 19810955,\n \"score\": 1\n },\n {\n \"doc_id\": \"19696499\",\n \"title\": \"The genus burkholderia: analysis of 56 genomic sequences.\",\n \"abstract\": \"The genus Burkholderia consists of a number of very diverse species, both in terms of lifestyle (which varies from category B pathogens to apathogenic soil bacteria and plant colonizers) and their genetic contents. We have used 56 publicly available genomes to explore the genomic diversity within this genus, including genome sequences that are not completely finished, but are available from the NCBI database. Defining the pan- and core genomes of species results in insights in the conserved and variable fraction of genomes, and can verify (or question) historic, taxonomic groupings. We find only several hundred genes that are conserved across all Burkholderia genomes, whilst there are more than 40,000 gene families in the Burkholderia pan-genome. A BLAST matrix visualizes the fraction of conserved genes in pairwise comparisons. A BLAST atlas shows which genes are actually conserved in a number of genomes, located and visualized with reference to a chosen genome. Genomic islands are common in many Burkholderia genomes, and most of these can be readily visualized by DNA structural properties of the chromosome. Trees that are based on relatedness of gene family content yield different results depending on what genes are analyzed. Some of the differences can be explained by errors in incomplete genome sequences, but, as our data illustrate, the outcome of phylogenetic trees depends on the type of genes that are analyzed.\",\n \"corpus_id\": 35213378,\n \"score\": 1\n },\n {\n \"doc_id\": \"21264216\",\n \"title\": \"Complete sequencing and pan-genomic analysis of Lactobacillus delbrueckii subsp. bulgaricus reveal its genetic basis for industrial yogurt production.\",\n \"abstract\": \"Lactobacillus delbrueckii subsp. bulgaricus (Lb. bulgaricus) is an important species of Lactic Acid Bacteria (LAB) used for cheese and yogurt fermentation. The genome of Lb. bulgaricus 2038, an industrial strain mainly used for yogurt production, was completely sequenced and compared against the other two ATCC collection strains of the same subspecies. Specific physiological properties of strain 2038, such as lysine biosynthesis, formate production, aspartate-related carbon-skeleton intermediate metabolism, unique EPS synthesis and efficient DNA restriction/modification systems, are all different from those of the collection strains that might benefit the industrial production of yogurt. Other common features shared by Lb. bulgaricus strains, such as efficient protocooperation with Streptococcus thermophilus and lactate production as well as well-equipped stress tolerance mechanisms may account for it being selected originally for yogurt fermentation industry. Multiple lines of evidence suggested that Lb. bulgaricus 2038 was genetically closer to the common ancestor of the subspecies than the other two sequenced collection strains, probably due to a strict industrial maintenance process for strain 2038 that might have halted its genome decay and sustained a gene network suitable for large scale yogurt production.\",\n \"corpus_id\": 18997941,\n \"score\": 1\n },\n {\n \"doc_id\": \"21764529\",\n \"title\": \"Everything at once: comparative analysis of the genomes of bacterial pathogens.\",\n \"abstract\": \"The sum of unique genes in all genomes of a bacterial species is referred to as the pan-genome and is comprised of variably absent or present accessory genes and universally present core genes. The accessory genome is an important source of genetic variability in bacterial populations, allowing sub-populations of bacteria to better adapt to specific niches. Such subgroups may themselves have a relatively stable core genome that may influence host preference, virulence, or an association with specific disease syndromes. The core genome provides a useful means of phylogenetic reconstruction as well as contributing to phenotypic heterogeneity. Variation within the pan-genome forms the basis of comparative genotyping techniques, which have evolved alongside technology. Current high-throughput sequencing platforms have created an unprecedented opportunity for comparisons among multiple, closely related genomes. The computer algorithms and software for such comparisons continue to evolve and promise exciting advances in the world of bacterial comparative genomics. We review genotyping techniques based upon phenotypic traits, both core and accessory genomes, and look at some of the software programs currently available to perform whole-genome comparative analyses.\",\n \"corpus_id\": 11909593,\n \"score\": 1\n },\n {\n \"doc_id\": \"22863143\",\n \"title\": \"Comparative analysis of the Oenococcus oeni pan genome reveals genetic diversity in industrially-relevant pathways.\",\n \"abstract\": \"BACKGROUND: Oenococcus oeni, a member of the lactic acid bacteria, is one of a limited number of microorganisms that not only survive, but actively proliferate in wine. It is also unusual as, unlike the majority of bacteria present in wine, it is beneficial to wine quality rather than causing spoilage. These benefits are realised primarily through catalysing malolactic fermentation, but also through imparting other positive sensory properties. However, many of these industrially-important secondary attributes have been shown to be strain-dependent and their genetic basis it yet to be determined. RESULTS: In order to investigate the scale and scope of genetic variation in O. oeni, we have performed whole-genome sequencing on eleven strains of this bacterium, bringing the total number of strains for which genome sequences are available to fourteen. While any single strain of O. oeni was shown to contain around 1800 protein-coding genes, in-depth comparative annotation based on genomic synteny and protein orthology identified over 2800 orthologous open reading frames that comprise the pan genome of this species, and less than 1200 genes that make up the conserved genomic core present in all of the strains. The expansion of the pan genome relative to the coding potential of individual strains was shown to be due to the varied presence and location of multiple distinct bacteriophage sequences and also in various metabolic functions with potential impacts on the industrial performance of this species, including cell wall exopolysaccharide biosynthesis, sugar transport and utilisation and amino acid biosynthesis. CONCLUSIONS: By providing a large cohort of sequenced strains, this study provides a broad insight into the genetic variation present within O. oeni. This data is vital to understanding and harnessing the phenotypic variation present in this economically-important species.\",\n \"corpus_id\": 5870427,\n \"score\": 1\n },\n {\n \"doc_id\": \"22958348\",\n \"title\": \"Complete genome sequence of Saccharothrix espanaensis DSM 44229(T) and comparison to the other completely sequenced Pseudonocardiaceae.\",\n \"abstract\": \"BACKGROUND: The genus Saccharothrix is a representative of the family Pseudonocardiaceae, known to include producer strains of a wide variety of potent antibiotics. Saccharothrix espanaensis produces both saccharomicins A and B of the promising new class of heptadecaglycoside antibiotics, active against both bacteria and yeast. RESULTS: To better assess its capabilities, the complete genome sequence of S. espanaensis was established. With a size of 9,360,653 bp, coding for 8,501 genes, it stands alongside other Pseudonocardiaceae with large genomes. Besides a predicted core genome of 810 genes shared in the family, S. espanaensis has a large number of accessory genes: 2,967 singletons when compared to the family, of which 1,292 have no clear orthologs in the RefSeq database. The genome analysis revealed the presence of 26 biosynthetic gene clusters potentially encoding secondary metabolites. Among them, the cluster coding for the saccharomicins could be identified. CONCLUSION: S. espanaensis is the first completely sequenced species of the genus Saccharothrix. The genome discloses the cluster responsible for the biosynthesis of the saccharomicins, the largest oligosaccharide antibiotic currently identified. Moreover, the genome revealed 25 additional putative secondary metabolite gene clusters further suggesting the strain's potential for natural product synthesis.\",\n \"corpus_id\": 5593930,\n \"score\": 1\n },\n {\n \"doc_id\": \"23626695\",\n \"title\": \"Comparative genomic analysis of the genus Nocardiopsis provides new insights into its genetic mechanisms of environmental adaptability.\",\n \"abstract\": \"The genus Nocardiopsis, a widespread group in phylum Actinobacteria, has received much attention owing to its ecological versatility, pathogenicity, and ability to produce a rich array of bioactive metabolites. Its high environmental adaptability might be attributable to its genome dynamics, which can be estimated through comparative genomic analysis targeting microorganisms with close phylogenetic relationships but different phenotypes. To shed light on speciation, gene content evolution, and environmental adaptation in these unique actinobacteria, we sequenced draft genomes for 16 representative species of the genus and compared them with that of the type species N. dassonvillei subsp. dassonvillei DSM 43111(T). The core genome of 1,993 orthologous and paralogous gene clusters was identified, and the pan-genomic reservoir was found not only to accommodate more than 22,000 genes, but also to be open. The top ten paralogous genes in terms of copy number could be referred to three functional categories: transcription regulators, transporters, and synthases related to bioactive metabolites. Based on phylogenomic reconstruction, we inferred past evolutionary events, such as gene gains and losses, and identified a list of clade-specific genes implicated in environmental adaptation. These results provided insights into the genetic causes of environmental adaptability in this cosmopolitan actinobacterial group and the contributions made by its inherent features, including genome dynamics and the constituents of core and accessory proteins.\",\n \"corpus_id\": 13863929,\n \"score\": 1\n },\n {\n \"doc_id\": \"24069314\",\n \"title\": \"Comparative genome analysis of Enterobacter cloacae.\",\n \"abstract\": \"The Enterobacter cloacae species includes an extremely diverse group of bacteria that are associated with plants, soil and humans. Publication of the complete genome sequence of the plant growth-promoting endophytic E. cloacae subsp. cloacae ENHKU01 provided an opportunity to perform the first comparative genome analysis between strains of this dynamic species. Examination of the pan-genome of E. cloacae showed that the conserved core genome retains the general physiological and survival genes of the species, while genomic factors in plasmids and variable regions determine the virulence of the human pathogenic E. cloacae strain; additionally, the diversity of fimbriae contributes to variation in colonization and host determination of different E. cloacae strains. Comparative genome analysis further illustrated that E. cloacae strains possess multiple mechanisms for antagonistic action against other microorganisms, which involve the production of siderophores and various antimicrobial compounds, such as bacteriocins, chitinases and antibiotic resistance proteins. The presence of Type VI secretion systems is expected to provide further fitness advantages for E. cloacae in microbial competition, thus allowing it to survive in different environments. Competition assays were performed to support our observations in genomic analysis, where E. cloacae subsp. cloacae ENHKU01 demonstrated antagonistic activities against a wide range of plant pathogenic fungal and bacterial species.\",\n \"corpus_id\": 18067744,\n \"score\": 1\n },\n {\n \"doc_id\": \"25119988\",\n \"title\": \"Genome analysis of Bacillus amyloliquefaciens Subsp. plantarum UCMB5113: a rhizobacterium that improves plant growth and stress management.\",\n \"abstract\": \"The Bacillus amyloliquefaciens subsp. plantarum strain UCMB5113 is a Gram-positive rhizobacterium that can colonize plant roots and stimulate plant growth and defense based on unknown mechanisms. This reinforcement of plants may provide protection to various forms of biotic and abiotic stress. To determine the genetic traits involved in the mechanism of plant-bacteria association, the genome sequence of UCMB5113 was obtained by assembling paired-end Illumina reads. The assembled chromosome of 3,889,532 bp was predicted to encode 3,656 proteins. Genes that potentially contribute to plant growth promotion such as indole-3-acetic acid (IAA) biosynthesis, acetoin synthesis and siderophore production were identified. Moreover, annotation identified putative genes responsible for non-ribosomal synthesis of secondary metabolites and genes supporting environment fitness of UCMB5113 including drug and metal resistance. A large number of genes encoding a diverse set of secretory proteins, enzymes of primary and secondary metabolism and carbohydrate active enzymes were found which reflect a high capacity to degrade various rhizosphere macromolecules. Additionally, many predicted membrane transporters provides the bacterium with efficient uptake capabilities of several nutrients. Although, UCMB5113 has the possibility to produce antibiotics and biosurfactants, the protective effect of plants to pathogens seems to be indirect and due to priming of plant induced systemic resistance. The availability of the genome enables identification of genes and their function underpinning beneficial interactions of UCMB5113 with plants.\",\n \"corpus_id\": 16610459,\n \"score\": 1\n },\n {\n \"doc_id\": \"25218520\",\n \"title\": \"De novo assembly of soybean wild relatives for pan-genome analysis of diversity and agronomic traits.\",\n \"abstract\": \"Wild relatives of crops are an important source of genetic diversity for agriculture, but their gene repertoire remains largely unexplored. We report the establishment and analysis of a pan-genome of Glycine soja, the wild relative of cultivated soybean Glycine max, by sequencing and de novo assembly of seven phylogenetically and geographically representative accessions. Intergenomic comparisons identified lineage-specific genes and genes with copy number variation or large-effect mutations, some of which show evidence of positive selection and may contribute to variation of agronomic traits such as biotic resistance, seed composition, flowering and maturity time, organ size and final biomass. Approximately 80% of the pan-genome was present in all seven accessions (core), whereas the rest was dispensable and exhibited greater variation than the core genome, perhaps reflecting a role in adaptation to diverse environments. This work will facilitate the harnessing of untapped genetic diversity from wild soybean for enhancement of elite cultivars.\",\n \"corpus_id\": 5360362,\n \"score\": 1\n },\n {\n \"doc_id\": \"25280501\",\n \"title\": \"Comparative and genetic analysis of the four sequenced Paenibacillus polymyxa genomes reveals a diverse metabolism and conservation of genes relevant to plant-growth promotion and competitiveness.\",\n \"abstract\": \"BACKGROUND: Members of the genus Paenibacillus are important plant growth-promoting rhizobacteria that can serve as bio-reactors. Paenibacillus polymyxa promotes the growth of a variety of economically important crops. Our lab recently completed the genome sequence of Paenibacillus polymyxa CR1. As of January 2014, four P. polymyxa genomes have been completely sequenced but no comparative genomic analyses have been reported. RESULTS: Here we report the comparative and genetic analyses of four sequenced P. polymyxa genomes, which revealed a significantly conserved core genome. Complex metabolic pathways and regulatory networks were highly conserved and allow P. polymyxa to rapidly respond to dynamic environmental cues. Genes responsible for phytohormone synthesis, phosphate solubilization, iron acquisition, transcriptional regulation, σ-factors, stress responses, transporters and biomass degradation were well conserved, indicating an intimate association with plant hosts and the rhizosphere niche. In addition, genes responsible for antimicrobial resistance and non-ribosomal peptide/polyketide synthesis are present in both the core and accessory genome of each strain. Comparative analyses also reveal variations in the accessory genome, including large plasmids present in strains M1 and SC2. Furthermore, a considerable number of strain-specific genes and genomic islands are irregularly distributed throughout each genome. Although a variety of plant-growth promoting traits are encoded by all strains, only P. polymyxa CR1 encodes the unique nitrogen fixation cluster found in other Paenibacillus sp. CONCLUSIONS: Our study revealed that genomic loci relevant to host interaction and ecological fitness are highly conserved within the P. polymyxa genomes analysed, despite variations in the accessory genome. This work suggets that plant-growth promotion by P. polymyxa is mediated largely through phytohormone production, increased nutrient availability and bio-control mechanisms. This study provides an in-depth understanding of the genome architecture of this species, thus facilitating future genetic engineering and applications in agriculture, industry and medicine. Furthermore, this study highlights the current gap in our understanding of complex plant biomass metabolism in Gram-positive bacteria.\",\n \"corpus_id\": 13428819,\n \"score\": 1\n },\n {\n \"doc_id\": \"25649186\",\n \"title\": \"Whole genome sequence and comparative genomic analysis of multidrug-resistant Staphylococcus capitis subsp. urealyticus strain LNZR-1.\",\n \"abstract\": \"BACKGROUND: Staphylococcus capitis is an emerging opportunistic pathogen of humans, and found as a colonizer of the human gut. Here, we report a case of S. capitis subsp. urealyticus infection. The strain LNZR-1 was isolated from the blood culture of a patient with sigmoid colon cancer. It was found to be resistant to some important antibiotics, such as linezolid, a highly effective antimicrobial against clinically important Staphylococci pathogens. However, data on the genetic resistance mechanisms in S. capitis subsp. urealyticus are only sparsely available. RESULTS: The draft genome of S. capitis subsp. urealyticus strain LNZR-1 was sequenced by using next-generation sequencing technologies. Sequence data assembly revealed a genome size of 2,595,865 bp with a G + C content of 32.67%. Genome annotation revealed the presence of antibiotic resistance genes conferring resistance against some of the tested antibiotics as well as non-tested antibiotics. The genome also possesses a lot of genes that may be related to multidrug resistance. Whole genome comparison of the LNZR-1 with five other S. capitis strains showed that some functional regions are highly homologous between the six assemblies made herein. The LNZR-1 genome has high similarity with the genomes of the strains VCU116 and CR01, although some short stretches present in the genomes of strains VCU116 and CR01 were absent in the strain LNZR-1. CONCLUSIONS: The presence of a plethora of genes responsible for antibiotic resistance suggests that strain LNZR-1 could present a potential threat to human health. The comparative genomic analysis of S. capitis strains presented in this study is important for better understanding of multidrug resistance in S. capitis.\",\n \"corpus_id\": 17109673,\n \"score\": 1\n },\n {\n \"doc_id\": \"26354704\",\n \"title\": \"Biodegradation of nicosulfuron by a novel Alcaligenes faecalis strain ZWS11.\",\n \"abstract\": \"A bacterial strain ZWS11 was isolated from sulfonylurea herbicide-contaminated farmland soil and identified as a potential nicosulfuron-degrading bacterium. Based on morphological and physicochemical characterization of the bacterium and phylogenetic analysis of the 16S rRNA sequence, strain ZWS11 was identified as Alcaligenes faecalis. The effects of the initial concentration of nicosulfuron, inoculation volume, and medium pH on degradation of nicosulfuron were investigated. Strain ZWS11 could degrade 80.56% of the initial nicosulfuron supplemented at 500.0mg/L under the conditions of pH7.0, 180r/min and 30°C after incubation for 6days. Strain ZWS11 was also capable of degrading rimsulfuron, tribenuron-methyl and thifensulfuron-methyl. Four metabolites from biodegradation of nicosulfuron were identified, which were 2-aminosulfonyl-N, N-dimethylnicotinamide (M1), 4, 6-dihydroxypyrimidine (M2), 2-amino-4, 6-dimethoxypyrimidine (M3) and 2-(1-(4,6-dimethoxy-pyrimidin-2-yl)-ureido)-N,N-dimethyl-nicotinamide (M4). Among the metabolites detected, M2 was reported for the first time. Possible biodegradation pathways of nicosulfuron by strain ZWS11 were proposed. The degradation proceeded mainly via cleavage of the sulfonylurea bridge, O-dealkylation, and contraction of the sulfonylurea bridge by elimination of a sulfur dioxide group. The results provide valuable information for degradation of nicosulfuron in contaminated environments.\",\n \"corpus_id\": 22220531,\n \"score\": 1\n },\n {\n \"doc_id\": \"26964309\",\n \"title\": \"[Extraction, Purification and Identification of a Dexamethasone-degrading Enzymes Generated by Pseudomonas Alcaligenes].\",\n \"abstract\": \"In this research a strain of isolated Pseudomonas alcaligenes which causes degradation of dexamethasone was acclimated further and its proteins of every position in the bacterium were separated by the osmotic shock method. The separated intracellular proteins which had the highest enzyme activity were extracted by the salting out with ammonium sulfate and were purified with the cation exchange chromatography and gel chromatography. The purified proteins which was active to cause degradation of dexamethasone had been detected were cut with enzyme and were analyzed with mass spectrometry. The results showed that the degradation rate to dexamethasone by acclimated Pseudomonas alcaligenes were increased from 23.63% to 52.84%. The degrading enzymes were located mainly in the intracellular of the bacteria and its molecular weight was about 41 kD. The specific activity of the purified degrading enzymes were achieved to 1.02 U x mg(-1). Its 5-peptide amino acid sequences were consistent with some sequences of the isovaleryl-CoA dehydrogenase. The protein enzyme may be a new kind degrading enzyme of steroidal compounds. Our experimental results provided new strategies for cleanup of dexamethasone in water environment with microbial bioremediation technique.\",\n \"corpus_id\": 25343637,\n \"score\": 1\n },\n {\n \"doc_id\": \"27006628\",\n \"title\": \"Inside the Pan-genome - Methods and Software Overview.\",\n \"abstract\": \"The number of genomes that have been deposited in databases has increased exponentially after the advent of Next-Generation Sequencing (NGS), which produces high-throughput sequence data; this circumstance has demanded the development of new bioinformatics software and the creation of new areas, such as comparative genomics. In comparative genomics, the genetic content of an organism is compared against other organisms, which helps in the prediction of gene function and coding region sequences, identification of evolutionary events and determination of phylogenetic relationships. However, expanding comparative genomics to a large number of related bacteria, we can infer their lifestyles, gene repertoires and minimal genome size. In this context, a powerful approach called Pan-genome has been initiated and developed. This approach involves the genomic comparison of different strains of the same species, or even genus. Its main goal is to establish the total number of non-redundant genes that are present in a determined dataset. Pan-genome consists of three parts: core genome; accessory or dispensable genome; and species-specific or strain-specific genes. Furthermore, pan-genome is considered to be \\\"open\\\" as long as new genes are added significantly to the total repertoire for each new additional genome and \\\"closed\\\" when the newly added genomes cannot be inferred to significantly increase the total repertoire of the genes. To perform all of the required calculations, a substantial amount of software has been developed, based on orthologous and paralogous gene identification.\",\n \"corpus_id\": 13310059,\n \"score\": 1\n },\n {\n \"doc_id\": \"27107724\",\n \"title\": \"Genome sequence of Roseivirga sp. strain D-25 and its potential applications from the genomic aspect.\",\n \"abstract\": \"Roseivirga sp. strain D-25 is an aerobic marine bacterium isolated from seawater collected from Desaru beach, Malaysia. To date, the genus Roseivirga consists of only four species with no genome sequence reported. Here, we present the genome sequence of Roseivirga sp. strain D-25 (=KCTC 42709=DSM 101709), with a genome size of approximately 4.08Mbp and G+C content of 39.18%. Genome sequence analysis of strain D-25 revealed the presence of genes related to petroleum hydrocarbon degradation, 2,4,6-trinitrotoluene detoxification, heavy metals bioremediation and production of carotenoids, which shed light on the potential application of this strain.\",\n \"corpus_id\": 43583837,\n \"score\": 1\n },\n {\n \"doc_id\": \"27591845\",\n \"title\": \"Keratinase production and biodegradation of polluted secondary chicken feather wastes by a newly isolated multi heavy metal tolerant bacterium-Alcaligenes sp. AQ05-001.\",\n \"abstract\": \"Biodegradation of agricultural wastes, generated annually from poultry farms and slaughterhouses, can solve the pollution problem and at the same time yield valuable degradation products. But these wastes also constitute environmental nuisance, especially in Malaysia where their illegal disposal on heavy metal contaminated soils poses a serious biodegradation issue as feather tends to accumulate heavy metals from the surrounding environment. Further, continuous use of feather wastes as cheap biosorbent material for the removal of heavy metals from effluents has contributed to the rising amount of polluted feathers, which has necessitated the search for heavy metal-tolerant feather degrading strains. Isolation, characterization and application of a novel heavy metal-tolerant feather-degrading bacterium, identified by 16S RNA sequencing as Alcaligenes sp. AQ05-001 in degradation of heavy metal polluted recalcitrant agricultural wastes, have been reported. Physico-cultural conditions influencing its activities were studied using one-factor-at-a-time and a statistical optimisation approach. Complete degradation of 5 g/L feather was achieved with pH 8, 2% inoculum at 27 °C and incubation period of 36 h. The medium optimisation after the response surface methodology (RSM) resulted in a 10-fold increase in keratinase production (88.4 U/mL) over the initial 8.85 U/mL when supplemented with 0.5% (w/v) sucrose, 0.15% (w/v) ammonium bicarbonate, 0.3% (w/v) skim milk, and 0.01% (w/v) urea. Under optimum conditions, the bacterium was able to degrade heavy metal polluted feathers completely and produced valuable keratinase and protein-rich hydrolysates. About 83% of the feathers polluted with a mixture of highly toxic metals were degraded with high keratinase activities. The heavy metal tolerance ability of this bacterium can be harnessed not only in keratinase production but also in the bioremediation of heavy metal-polluted feather wastes.\",\n \"corpus_id\": 12304281,\n \"score\": 1\n },\n {\n \"doc_id\": \"27712915\",\n \"title\": \"Comparative genomics unravels metabolic differences at the species and/or strain level and extremely acidic environmental adaptation of ten bacteria belonging to the genus Acidithiobacillus.\",\n \"abstract\": \"Members of the Acidithiobacillus genus are widely found in extreme environments characterized by low pH and high concentrations of toxic substances, thus it is necessary to identify the cellular mechanisms needed to cope with these harsh conditions. Pan-genome analysis of ten bacteria belonging to the genus Acidithiobacillus suggested the existence of core genome, most of which were assigned to the metabolism-associated genes. Additionally, the unique genes of Acidithiobacillus ferrooxidans were much less than those of other species. A large proportion of Acidithiobacillus ferrivorans-specific genes were mapped especially to metabolism-related genes, indicating that diverse metabolic pathways might confer an advantage for adaptation to local environmental conditions. Analyses of functional metabolisms revealed the differences of carbon metabolism, nitrogen metabolism, and sulfur metabolism at the species and/or strain level. The findings also showed that Acidithiobacillus spp. harbored specific adaptive mechanisms for thriving under extreme environments. The genus Acidithiobacillus had the genetic potential to resist and metabolize toxic substances such as heavy metals and organic solvents. Comparison across species and/or strains of Acidithiobacillus populations provided a deeper appreciation of metabolic differences and environmental adaptation, as well as highlighting the importance of cellular mechanisms that maintain the basal physiological functions under complex acidic environmental conditions.\",\n \"corpus_id\": 33986159,\n \"score\": 1\n },\n {\n \"doc_id\": \"27924153\",\n \"title\": \"Genome sequence of a commensal bacterium, Enterococcus faecalis CBA7120, isolated from a Korean fecal sample.\",\n \"abstract\": \"BACKGROUND: Enterococcus faecalis, the type strain of the genus Enterococcus, is not only a commensal bacterium in the gastrointestinal tract in vertebrates and invertebrates, but also causes serious disease as an opportunistic pathogen. To date, genome sequences have been published for over four hundred E. faecalis strains; however, pathogenicity of these microbes remains complicated. To increase our knowledge of E. faecalis virulence factors, we isolated strain CBA7120 from the feces of an 81-year-old female from the Republic of Korea and performed a comparative genomic analysis. RESULTS: The genome sequence of E. faecalis CBA7120 is 3,134,087 bp in length, with a G + C content of 37.35 mol%, and is comprised of four contigs with an N50 value of 2,922,046 bp. The genome showed high similarity with other strains of E. faecalis, including OG1RF, T13, 12107 and T20, based on OrthoANI values. Strain CBA7120 contains 374 pan-genome orthologous groups (POGs) as singletons, including \\\"Phages, Prophages, Transposable elements, Plasmids,\\\" \\\"Carbohydrates,\\\" \\\"DNA metabolism,\\\" and \\\"Virulence, Disease and Defense\\\" subsystems. Genes related to multidrug resistance efflux pumps were annotated in the genome. CONCLUSIONS: The comparative genomic analysis of E. faecalis strains presented in this study was performed using a variety of analysis methods and will facilitate future identification of hypothetical proteins.\",\n \"corpus_id\": 14391886,\n \"score\": 1\n },\n {\n \"doc_id\": \"28095778\",\n \"title\": \"The pangenome of (Antarctic) Pseudoalteromonas bacteria: evolutionary and functional insights.\",\n \"abstract\": \"BACKGROUND: Pseudoalteromonas is a genus of ubiquitous marine bacteria used as model organisms to study the biological mechanisms involved in the adaptation to cold conditions. A remarkable feature shared by these bacteria is their ability to produce secondary metabolites with a strong antimicrobial and antitumor activity. Despite their biotechnological relevance, representatives of this genus are still lacking (with few exceptions) an extensive genomic characterization, including features involved in the evolution of secondary metabolites production. Indeed, biotechnological applications would greatly benefit from such analysis. RESULTS: Here, we analyzed the genomes of 38 strains belonging to different Pseudoalteromonas species and isolated from diverse ecological niches, including extreme ones (i.e. Antarctica). These sequences were used to reconstruct the largest Pseudoalteromonas pangenome computed so far, including also the two main groups of Pseudoalteromonas strains (pigmented and not pigmented strains). The downstream analyses were conducted to describe the genomic diversity, both at genus and group levels. This allowed highlighting a remarkable genomic heterogeneity, even for closely related strains. We drafted all the main evolutionary steps that led to the current structure and gene content of Pseudoalteromonas representatives. These, most likely, included an extensive genome reduction and a strong contribution of Horizontal Gene Transfer (HGT), which affected biotechnologically relevant gene sets and occurred in a strain-specific fashion. Furthermore, this study also identified the genomic determinants related to some of the most interesting features of the Pseudoalteromonas representatives, such as the production of secondary metabolites, the adaptation to cold temperatures and the resistance to abiotic compounds. CONCLUSIONS: This study poses the bases for a comprehensive understanding of the evolutionary trajectories followed in time by this peculiar bacterial genus and for a focused exploitation of their biotechnological potential.\",\n \"corpus_id\": 10133785,\n \"score\": 1\n },\n {\n \"doc_id\": \"28229046\",\n \"title\": \"Genome sequence of three Psychrobacter sp. strains with potential applications in bioremediation.\",\n \"abstract\": \"To date, the genus Psychrobacter consists of 37 recognized species isolated from different sources, however they are more frequently found in cold and other non-polar environments of low water activity. Some strains belonging to the genus have shown different enzymatic activities with potential applications in bioremediation or food industry. In the present study, the whole genome sequences of three Psychrobacter-like strains (C 20.9, Cmf 22.2 and Rd 27.2) isolated from reared clams in Galicia (Spain) are described. The sequenced genomes resulted in an assembly size of 3,143,782 bp for C 20.9 isolate, 3,168,467 bp for Cmf 22.2 isolate and 3,028,386 bp for Rd 27.2 isolate. Among the identified coding sequences of the genomes, mercury detoxification and biogeochemistry genes were found, as well as genes related to heavy metals and antibiotic resistance. Also virulence-related features were identified such as the siderophore vibrioferrin or an aerobactin-like siderophore. The phylogenetic analysis of the 16S rRNA gene suggested that these strains may represent novel species of the Psychrobacter genus. The genome sequences of the Psychrobacter sp. strains have been deposited at DDBJ/EMBL/GenBank under the accession numbers MRYA00000000 (Cmf 22.2), MRYB00000000 (Rd 27.2) and MRYC00000000 (C 20.9), and the sequences could be found at the site https://www.ncbi.nlm.nih.gov/bioproject/PRJNA353858.\",\n \"corpus_id\": 16800392,\n \"score\": 1\n },\n {\n \"doc_id\": \"28352091\",\n \"title\": \"Genome sequencing and analysis of Talaromyces pinophilus provide insights into biotechnological applications.\",\n \"abstract\": \"Species from the genus Talaromyces produce useful biomass-degrading enzymes and secondary metabolites. However, these enzymes and secondary metabolites are still poorly understood and have not been explored in depth because of a lack of comprehensive genetic information. Here, we report a 36.51-megabase genome assembly of Talaromyces pinophilus strain 1-95, with coverage of nine scaffolds of eight chromosomes with telomeric repeats at their ends and circular mitochondrial DNA. In total, 13,472 protein-coding genes were predicted. Of these, 803 were annotated to encode enzymes that act on carbohydrates, including 39 cellulose-degrading and 24 starch-degrading enzymes. In addition, 68 secondary metabolism gene clusters were identified, mainly including T1 polyketide synthase genes and nonribosomal peptide synthase genes. Comparative genomic analyses revealed that T. pinophilus 1-95 harbors more biomass-degrading enzymes and secondary metabolites than other related filamentous fungi. The prediction of the T. pinophilus 1-95 secretome indicated that approximately 50% of the biomass-degrading enzymes are secreted into the extracellular environment. These results expanded our genetic knowledge of the biomass-degrading enzyme system of T. pinophilus and its biosynthesis of secondary metabolites, facilitating the cultivation of T. pinophilus for high production of useful products.\",\n \"corpus_id\": 4104057,\n \"score\": 1\n },\n {\n \"doc_id\": \"28619812\",\n \"title\": \"Draft Genome Sequences of Six Enterococcus faecalis Strains Isolated from Malaysian Clinical and Environmental Origins.\",\n \"abstract\": \"Enterococcus faecalis is known to cause a variety of nosocomial infections, including urinary tract infections. Antibiotic resistance and virulence properties in this species are of public concern. The draft genome sequences of six E. faecalis strains isolated from clinical and environmental sources in Malaysia are presented here.\",\n \"corpus_id\": 22798684,\n \"score\": 1\n },\n {\n \"doc_id\": \"28848020\",\n \"title\": \"Genomic Characterization of VIM Metallo-β-Lactamase-Producing Alcaligenes faecalis from Gaza, Palestine.\",\n \"abstract\": \"Carbapenemase-producing Gram-negative bacteria (CP-GNB) have increasingly spread worldwide, and different families of carbapenemases have been identified in various bacterial species. Here, we report the identification of five VIM metallo-β-lactamase-producing Alcaligenes faecalis isolates associated with a small outbreak in a large hospital in Gaza, Palestine. Next-generation sequencing analysis showed blaVIM-2 is harbored by a chromosomal genomic island among three strains, while blaVIM-4 is carried by a novel plasmid in two strains.\",\n \"corpus_id\": 13785179,\n \"score\": 1\n },\n {\n \"doc_id\": \"28848520\",\n \"title\": \"Genome Sequencing Reveals the Potential of Achromobacter sp. HZ01 for Bioremediation.\",\n \"abstract\": \"Petroleum pollution is a severe environmental issue. Comprehensively revealing the genetic backgrounds of hydrocarbon-degrading microorganisms contributes to developing effective methods for bioremediation of crude oil-polluted environments. Marine bacterium Achromobacter sp. HZ01 is capable of degrading hydrocarbons and producing biosurfactants. In this study, the draft genome (5.5 Mbp) of strain HZ01 has been obtained by Illumina sequencing, containing 5,162 predicted genes. Genome annotation shows that \\\"amino acid metabolism\\\" is the most abundant metabolic pathway. Strain HZ01 is not capable of using some common carbohydrates as the sole carbon sources, which is due to that it contains few genes associated with carbohydrate transport and lacks some important enzymes related to glycometabolism. It contains abundant proteins directly related to petroleum hydrocarbon degradation. AlkB hydroxylase and its homologs were not identified. It harbors a complete enzyme system of terminal oxidation pathway for n-alkane degradation, which may be initiated by cytochrome P450. The enzymes involved in the catechol pathway are relatively complete for the degradation of aromatic compounds. This bacterium lacks several essential enzymes for methane oxidation, and Baeyer-Villiger monooxygenase involved in the subterminal oxidation pathway and cycloalkane degradation was not identified. These results suggest that strain HZ01 degrades n-alkanes via the terminal oxidation pathway, degrades aromatic compounds primarily via the catechol pathway and cannot perform methane oxidation or cycloalkane degradation. Additionally, strain HZ01 possesses abundant genes related to the metabolism of secondary metabolites, including some genes involved in biosurfactant (such as glycolipids and lipopeptides) synthesis. The genome analysis also reveals its genetic basis for nitrogen metabolism, antibiotic resistance, regulatory responses to environmental changes, cell motility, and material transport. The obtained genome data provide us with a better understanding of hydrocarbon-degrading bacteria, which may contribute to the future design of rational strategies for bioremediation of petroleum-polluted marine environments.\",\n \"corpus_id\": 10604795,\n \"score\": 1\n },\n {\n \"doc_id\": \"29479501\",\n \"title\": \"Comparative genomic analysis of a new tellurite-resistant Psychrobacter strain isolated from the Antarctic Peninsula.\",\n \"abstract\": \"The Psychrobacter genus is a cosmopolitan and diverse group of aerobic, cold-adapted, Gram-negative bacteria exhibiting biotechnological potential for low-temperature applications including bioremediation. Here, we present the draft genome sequence of a bacterium from the Psychrobacter genus isolated from a sediment sample from King George Island, Antarctica (3,490,622 bp; 18 scaffolds; G + C = 42.76%). Using phylogenetic analysis, biochemical properties and scanning electron microscopy the bacterium was identified as Psychrobacter glacincola BNF20, making it the first genome sequence reported for this species. P. glacincola BNF20 showed high tellurite (MIC 2.3 mM) and chromate (MIC 6.0 mM) resistance, respectively. Genome-wide nucleotide identity comparisons revealed that P. glacincola BNF20 is highly similar (>90%) to other uncharacterized Psychrobacter spp. such as JCM18903, JCM18902, and P11F6. Bayesian multi-locus phylogenetic analysis showed that P. glacincola BNF20 belongs to a polyphyletic clade with other bacteria isolated from polar regions. A high number of genes related to metal(loid) resistance were found, including tellurite resistance genetic determinants located in two contigs: Contig LIQB01000002.1 exhibited five ter genes, each showing putative promoter sequences (terACDEZ), whereas contig LIQB1000003.2 showed a variant of the terZ gene. Finally, investigating the presence and taxonomic distribution of ter genes in the NCBI's RefSeq bacterial database (5,398 genomes, as January 2017), revealed that 2,623 (48.59%) genomes showed at least one ter gene. At the family level, most (68.7%) genomes harbored one ter gene and 15.6% exhibited five (including P. glacincola BNF20). Overall, our results highlight the diverse nature (genetic and geographic diversity) of the Psychrobacter genus, provide insights into potential mechanisms of metal resistance, and exemplify the benefits of sampling remote locations for prospecting new molecular determinants.\",\n \"corpus_id\": 3528059,\n \"score\": 1\n },\n {\n \"doc_id\": \"18720850\",\n \"title\": \"[Isolation and characterization of a new glyphosate-resistant strain from extremely polluted environment].\",\n \"abstract\": \"OBJECTIVE: To isolate and characterize a glyphosate-resistant strain from extremely polluted environment. METHODS: A glyphosate-resistant strain was isolated from extremely polluted soil taking glyphosate as the selection pressure. Its glyphosate resistance, growth optimal pH and antibiotic sensitivity were detected. Its morphology, cultural characteristics, physiological and biochemical properties, chemotaxonomy and 16S rDNA sequences were studied. Based on these results, the strain was identified according to the ninth edition of Bergey's manual of determinative bacteriology. RESULTS: The isolate was named SL06500. It could grow in M9 minimal medium containing up to 500 mmol/L glyphosate. The cell growth optimal pH of SL06500 was 4.0. It was resistant to ampicillin, kanamycin, tetracycline and chloromycetin. The 16S rDNA of SL06500 was amplified by PCR and sequenced. Compared with the published nucleotide sequence of 16S rDNA in NCBI (National Center for Biotechnology Information), SL06500 showed high identity with Achromobacter and Alcaligenes. Based on morphological, physiological and biochemical characteristics, the strain was identified as Alcaligenes xylosoxidans subsp.xylosoxidans SL06500 according to the ninth edition of Bergey's manual of determinative bacteriology. CONCLUSION: Strain SL06500 is worthy to be studied because of its high glyphosate resistance.\",\n \"corpus_id\": 10164170,\n \"score\": 0\n },\n {\n \"doc_id\": \"23138713\",\n \"title\": \"Extrachromosomal genetic elements in Micrococcus.\",\n \"abstract\": \"Micrococci are Gram-positive G + C-rich, nonmotile, nonspore-forming actinomycetous bacteria. Micrococcus comprises ten members, with Micrococcus luteus being the type species. Representatives of the genus play important roles in the biodegradation of xenobiotics, bioremediation processes, production of biotechnologically important enzymes or bioactive compounds, as test strains in biological assays for lysozyme and antibiotics, and as infective agents in immunocompromised humans. The first description of plasmids dates back approximately 28 years, when several extrachromosomal elements ranging in size from 1.5 to 30.2 kb were found in Micrococcus luteus. Up to the present, a number of circular plasmids conferring antibiotic resistance, the ability to degrade aromatic compounds, and osmotolerance are known, as well as cryptic elements with unidentified functions. Here, we review the Micrococcus extrachromosomal traits reported thus far including phages and the only quite recently described large linear extrachromosomal genetic elements, termed linear plasmids, which range in size from 75 kb (pJD12) to 110 kb (pLMA1) and which confer putative advantageous capabilities, such as antibiotic or heavy metal resistances (inferred from sequence analyses and curing experiments). The role of the extrachromosomal elements for the frequently proven ecological and biotechnological versatility of the genus will be addressed as well as their potential for the development and use as genetic tools.\",\n \"corpus_id\": 5623260,\n \"score\": 0\n },\n {\n \"doc_id\": \"23350846\",\n \"title\": \"Genome sequence reveals that Pseudomonas fluorescens F113 possesses a large and diverse array of systems for rhizosphere function and host interaction.\",\n \"abstract\": \"BACKGROUND: Pseudomonas fluorescens F113 is a plant growth-promoting rhizobacterium (PGPR) isolated from the sugar-beet rhizosphere. This bacterium has been extensively studied as a model strain for genetic regulation of secondary metabolite production in P. fluorescens, as a candidate biocontrol agent against phytopathogens, and as a heterologous host for expression of genes with biotechnological application. The F113 genome sequence and annotation has been recently reported. RESULTS: Comparative analysis of 50 genome sequences of strains belonging to the P. fluorescens group has revealed the existence of five distinct subgroups. F113 belongs to subgroup I, which is mostly composed of strains classified as P. brassicacearum. The core genome of these five strains is highly conserved and represents approximately 76% of the protein-coding genes in any given genome. Despite this strong conservation, F113 also contains a large number of unique protein-coding genes that encode traits potentially involved in the rhizocompetence of this strain. These features include protein coding genes required for denitrification, diterpenoids catabolism, motility and chemotaxis, protein secretion and production of antimicrobial compounds and insect toxins. CONCLUSIONS: The genome of P. fluorescens F113 is composed of numerous protein-coding genes, not usually found together in previously sequenced genomes, which are potentially decisive during the colonisation of the rhizosphere and/or interaction with other soil organisms. This includes genes encoding proteins involved in the production of a second flagellar apparatus, the use of abietic acid as a growth substrate, the complete denitrification pathway, the possible production of a macrolide antibiotic and the assembly of multiple protein secretion systems.\",\n \"corpus_id\": -1,\n \"score\": 0\n },\n {\n \"doc_id\": \"23524352\",\n \"title\": \"Genome sequencing identifies Listeria fleischmannii subsp. coloradonensis subsp. nov., isolated from a ranch.\",\n \"abstract\": \"Twenty Listeria-like isolates were obtained from environmental samples collected on a cattle ranch in northern Colorado; all of these isolates were found to share an identical partial sigB sequence, suggesting close relatedness. The isolates were similar to members of the genus Listeria in that they were Gram-stain-positive, short rods, oxidase-negative and catalase-positive; the isolates were similar to Listeria fleischmannii because they were non-motile at 25 °C. 16S rRNA gene sequencing for representative isolates and whole genome sequencing for one isolate was performed. The genome of the type strain of Listeria fleischmannii (strain LU2006-1(T)) was also sequenced. The draft genomes were very similar in size and the average MUMmer nucleotide identity across 91% of the genomes was 95.16%. Genome sequence data were used to design primers for a six-gene multi-locus sequence analysis (MLSA) scheme. Phylogenies based on (i) the near-complete 16S rRNA gene, (ii) 31 core genes and (iii) six housekeeping genes illustrated the close relationship of these Listeria-like isolates to Listeria fleischmannii LU2006-1(T). Sufficient genetic divergence of the Listeria-like isolates from the type strain of Listeria fleischmannii and differing phenotypic characteristics warrant these isolates to be classified as members of a distinct infraspecific taxon, for which the name Listeria fleischmannii subsp. coloradonensis subsp. nov. is proposed. The type strain is TTU M1-001(T) ( =BAA-2414(T) =DSM 25391(T)). The isolates of Listeria fleischmannii subsp. coloradonensis subsp. nov. differ from the nominate subspecies by the inability to utilize melezitose, turanose and sucrose, and the ability to utilize inositol. The results also demonstrate the utility of whole genome sequencing to facilitate identification of novel taxa within a well-described genus. The genomes of both subspecies of Listeria fleischmannii contained putative enhancin genes; the Listeria fleischmannii subsp. coloradonensis subsp. nov. genome also encoded a putative mosquitocidal toxin. The presence of these genes suggests possible adaptation to an insect host, and further studies are needed to probe niche adaptation of Listeria fleischmannii.\",\n \"corpus_id\": 206178335,\n \"score\": 0\n },\n {\n \"doc_id\": \"23977017\",\n \"title\": \"Whole genome duplication and enrichment of metal cation transporters revealed by de novo genome sequencing of extremely halotolerant black yeast Hortaea werneckii.\",\n \"abstract\": \"Hortaea werneckii, ascomycetous yeast from the order Capnodiales, shows an exceptional adaptability to osmotically stressful conditions. To investigate this unusual phenotype we obtained a draft genomic sequence of a H. werneckii strain isolated from hypersaline water of solar saltern. Two of its most striking characteristics that may be associated with a halotolerant lifestyle are the large genetic redundancy and the expansion of genes encoding metal cation transporters. Although no sexual state of H. werneckii has yet been described, a mating locus with characteristics of heterothallic fungi was found. The total assembly size of the genome is 51.6 Mb, larger than most phylogenetically related fungi, coding for almost twice the usual number of predicted genes (23333). The genome appears to have experienced a relatively recent whole genome duplication, and contains two highly identical gene copies of almost every protein. This is consistent with some previous studies that reported increases in genomic DNA content triggered by exposure to salt stress. In hypersaline conditions transmembrane ion transport is of utmost importance. The analysis of predicted metal cation transporters showed that most types of transporters experienced several gene duplications at various points during their evolution. Consequently they are present in much higher numbers than expected. The resulting diversity of transporters presents interesting biotechnological opportunities for improvement of halotolerance of salt-sensitive species. The involvement of plasma P-type H⁺ ATPases in adaptation to different concentrations of salt was indicated by their salt dependent transcription. This was not the case with vacuolar H⁺ ATPases, which were transcribed constitutively. The availability of this genomic sequence is expected to promote the research of H. werneckii. Studying its extreme halotolerance will not only contribute to our understanding of life in hypersaline environments, but should also identify targets for improving the salt- and osmotolerance of economically important plants and microorganisms.\",\n \"corpus_id\": 4089447,\n \"score\": 0\n },\n {\n \"doc_id\": \"24628867\",\n \"title\": \"Genome sequence of type strain of Staphylococcus aureus subsp. aureus.\",\n \"abstract\": \"BACKGROUND: Staphylococcus aureus is a pathogen that causes food poisoning and community-associated infection with antibiotic resistance. This species is an indigenous intestinal microbe found in infants and not found in adult intestine. The relatively small genome size and rapid evolution of antibiotic resistance genes in the species have been drawing an increasing attention in public health. To extend our understanding of the species and use the genome data for comparative genomic studies, we sequenced the type strain of S. aureus subsp. aureus DSM 20231T. RESULTS: Seventeen contigs were generated using hybrid assembly of sequences derived from the Roche 454 and Illumina systems. The length of the genome sequence was 2,902,619 bases with a G + C content of 32.8%. Among the 2,550 annotated CDSs, 44 CDSs were annotated to antibiotic resistance genes and 13 CDSs were related to methicillin resistance. It is interesting to note that this strain was first isolated in 1884 before methicillin was generally used on patients. CONCLUSIONS: The present study analyzed the genome sequence of S. aureus subsp. aureus type strain as the reference sequence for comparative genomic analyses of clinical isolates. Methicillin resistance genes found in the genome indicate the presence of antibiotic resistance mechanism prior to the usage of antibiotics. Further comparative genomic studies of methicillin-resistant strains based on this reference genome would help to understand the evolution of resistance mechanism and dissemination of resistance genes.\",\n \"corpus_id\": -1,\n \"score\": 0\n },\n {\n \"doc_id\": \"24800692\",\n \"title\": \"Complete genome sequencing and comparative analysis of the linezolid-resistant Enterococcus faecalis strain DENG1.\",\n \"abstract\": \"Genome level analysis of bacterial strains provides information on genetic composition and resistance mechanisms to clinically relevant antibiotics. To date, whole genome characterization of linezolid-resistant Enterococcus faecalis isolated in the clinic is lacking. In this study, we report the entire genome sequence, genomic characteristics and virulence factors of a pathogenic E. faecalis strain, DENG1. Our results showed considerable differences in genomic characteristics and virulence factors compared with other E. faecalis strains (V583 and OG1RF). The genome of this LZD-resistant E. faecalis strain can be used as a reference to study the mechanism of LZD resistance and the phylogenetic relationship of E. faecalis strains worldwide.\",\n \"corpus_id\": 2366159,\n \"score\": 0\n },\n {\n \"doc_id\": \"24803570\",\n \"title\": \"Comparative genomic analysis of malaria mosquito vector-associated novel pathogen Elizabethkingia anophelis.\",\n \"abstract\": \"Acquisition of Elizabethkingia infections in intensive care units (ICUs) has risen in the past decade. Treatment of Elizabethkingia infections is challenging due to the lack of effective therapeutic regimens, leading to a high mortality rate. Elizabethkingia infections have long been attributed to Elizabethkingia meningoseptica. Recently, we used whole-genome sequencing to reveal that E. anophelis is the pathogenic agent for an Elizabethkingia outbreak at two ICUs. We performed comparative genomic analysis of seven hospital-isolated E. anophelis strains with five available Elizabethkingia spp. genomes deposited in the National Center for Biotechnology Information Database. A pan-genomic approach was applied to identify the core- and pan-genome for the Elizabethkingia genus. We showed that unlike the hospital-isolated pathogen E. meningoseptica ATCC 12535 strain, the hospital-isolated E. anophelis strains have genome content and organization similar to the E. anophelis Ag1 and R26 strains isolated from the midgut microbiota of the malaria mosquito vector Anopheles gambiae. Both the core- and accessory genomes of Elizabethkingia spp. possess genes conferring antibiotic resistance and virulence. Our study highlights that E. anophelis is an emerging bacterial pathogen for hospital environments.\",\n \"corpus_id\": 12285885,\n \"score\": 0\n },\n {\n \"doc_id\": \"25825433\",\n \"title\": \"Genome Modification in Enterococcus faecalis OG1RF Assessed by Bisulfite Sequencing and Single-Molecule Real-Time Sequencing.\",\n \"abstract\": \"UNLABELLED: Enterococcus faecalis is a Gram-positive bacterium that natively colonizes the human gastrointestinal tract and opportunistically causes life-threatening infections. Multidrug-resistant (MDR) E. faecalis strains have emerged, reducing treatment options for these infections. MDR E. faecalis strains have large genomes containing mobile genetic elements (MGEs) that harbor genes for antibiotic resistance and virulence determinants. Bacteria commonly possess genome defense mechanisms to block MGE acquisition, and we hypothesize that these mechanisms have been compromised in MDR E. faecalis. In restriction-modification (R-M) defense, the bacterial genome is methylated at cytosine (C) or adenine (A) residues by a methyltransferase (MTase), such that nonself DNA can be distinguished from self DNA. A cognate restriction endonuclease digests improperly modified nonself DNA. Little is known about R-M in E. faecalis. Here, we use genome resequencing to identify DNA modifications occurring in the oral isolate OG1RF. OG1RF has one of the smallest E. faecalis genomes sequenced to date and possesses few MGEs. Single-molecule real-time (SMRT) and bisulfite sequencing revealed that OG1RF has global 5-methylcytosine (m5C) methylation at 5'-GCWGC-3' motifs. A type II R-M system confers the m5C modification, and disruption of this system impacts OG1RF electrotransformability and conjugative transfer of an antibiotic resistance plasmid. A second DNA MTase was poorly expressed under laboratory conditions but conferred global N(4)-methylcytosine (m4C) methylation at 5'-CCGG-3' motifs when expressed in Escherichia coli. Based on our results, we conclude that R-M can act as a barrier to MGE acquisition and likely influences antibiotic resistance gene dissemination in the E. faecalis species. IMPORTANCE: The horizontal transfer of antibiotic resistance genes among bacteria is a critical public health concern. Enterococcus faecalis is an opportunistic pathogen that causes life-threatening infections in humans. Multidrug resistance acquired by horizontal gene transfer limits treatment options for these infections. In this study, we used innovative DNA sequencing methodologies to investigate how a model strain of E. faecalis discriminates its own DNA from foreign DNA, i.e., self versus nonself discrimination. We also assess the role of an E. faecalis genome modification system in modulating conjugative transfer of an antibiotic resistance plasmid. These results are significant because they demonstrate that differential genome modification impacts horizontal gene transfer frequencies in E. faecalis.\",\n \"corpus_id\": 539901,\n \"score\": 0\n },\n {\n \"doc_id\": \"26203344\",\n \"title\": \"Genome sequences of copper resistant and sensitive Enterococcus faecalis strains isolated from copper-fed pigs in Denmark.\",\n \"abstract\": \"Six strains of Enterococcus faecalis (S1, S12, S17, S18, S19 and S32) were isolated from copper fed pigs in Denmark. These Gram-positive bacteria within the genus Enterococcus are able to survive a variety of physical and chemical challenges by the acquisition of diverse genetic elements. The genome of strains S1, S12, S17, S18, S19 and S32 contained 2,615, 2,769, 2,625, 2,804, 2,853 and 2,935 protein-coding genes, with 41, 42, 27, 42, 32 and 44 genes encoding antibiotic and metal resistance, respectively. Differences between Cu resistant and sensitive E. faecalis strains, and possible co-transfer of Cu and antibiotic resistance determinants were detected through comparative genome analysis.\",\n \"corpus_id\": 15997608,\n \"score\": 0\n },\n {\n \"doc_id\": \"27090021\",\n \"title\": \"Complete genome sequence of Enterococcus faecalis LD33, a bacteriocin-producing strain.\",\n \"abstract\": \"Enterococcus faecalis LD33 strain was originally isolated from traditional naturally fermented cream in Inner Mongolia of China. Its complete genome sequence was carried out using the Illumina Hiseq and the PacBio RSII platform. The genome only has a circular chromosome and a GC content of 37.58%. Other core information shown in the genome sequencing results further insight on this bacterium's genetic elements for bacteriocin production and the genes related to respiratory chain.\",\n \"corpus_id\": 1569677,\n \"score\": 0\n },\n {\n \"doc_id\": \"27189997\",\n \"title\": \"Antibiotic Resistance, Core-Genome and Protein Expression in IncHI1 Plasmids in Salmonella Typhimurium.\",\n \"abstract\": \"Conjugative plasmids from the IncHI1 incompatibility group play an important role in transferring antibiotic resistance in Salmonella Typhimurium. However, knowledge of their genome structure or gene expression is limited. In this study, we determined the complete nucleotide sequences of four IncHI1 plasmids transferring resistance to antibiotics by two different next generation sequencing protocols and protein expression by mass spectrometry. Sequence data including additional 11 IncHI1 plasmids from GenBank were used for the definition of the IncHI1 plasmid core-genome and pan-genome. The core-genome consisted of approximately 123 kbp and 122 genes while the total pan-genome represented approximately 600 kbp. When the core-genome sequences were used for multiple alignments, the 15 tested IncHI1 plasmids were separated into two main lineages. GC content in core-genome genes was around 46% and 50% in accessory genome genes. A multidrug resistance region present in all 4 sequenced plasmids extended over 20 kbp and, except for tet(B), the genes responsible for antibiotic resistance were those with the highest GC content. IncHI1 plasmids therefore represent replicons that evolved in low GC content bacteria. From their original host, they spread to Salmonella and during this spread these plasmids acquired multiple accessory genes including those coding for antibiotic resistance. Antibiotic-resistance genes belonged to genes with the highest level of expression and were constitutively expressed even in the absence of antibiotics. This is the likely mechanism that facilitates host cell survival when antibiotics suddenly emerge in the environment.\",\n \"corpus_id\": 6646506,\n \"score\": 0\n },\n {\n \"doc_id\": \"27303749\",\n \"title\": \"CRISPR-Cas and Restriction-Modification Act Additively against Conjugative Antibiotic Resistance Plasmid Transfer in Enterococcus faecalis.\",\n \"abstract\": \"Enterococcus faecalis is an opportunistic pathogen and a leading cause of nosocomial infections. Conjugative pheromone-responsive plasmids are narrow-host-range mobile genetic elements (MGEs) that are rapid disseminators of antibiotic resistance in the faecalis species. Clustered regularly interspaced short palindromic repeat (CRISPR)-Cas and restriction-modification confer acquired and innate immunity, respectively, against MGE acquisition in bacteria. Most multidrug-resistant E. faecalis isolates lack CRISPR-Cas and possess an orphan locus lacking cas genes, CRISPR2, that is of unknown function. Little is known about restriction-modification defense in E. faecalis. Here, we explore the hypothesis that multidrug-resistant E. faecalis strains are immunocompromised. We assessed MGE acquisition by E. faecalis T11, a strain closely related to the multidrug-resistant hospital isolate V583 but which lacks the ~620 kb of horizontally acquired genome content that characterizes V583. T11 possesses the E. faecalis CRISPR3-cas locus and a predicted restriction-modification system, neither of which occurs in V583. We demonstrate that CRISPR-Cas and restriction-modification together confer a 4-log reduction in acquisition of the pheromone-responsive plasmid pAM714 in biofilm matings. Additionally, we show that the orphan CRISPR2 locus is functional for genome defense against another pheromone-responsive plasmid, pCF10, only in the presence of cas9 derived from the E. faecalis CRISPR1-cas locus, which most multidrug-resistant E. faecalis isolates lack. Overall, our work demonstrated that the loss of only two loci led to a dramatic reduction in genome defense against a clinically relevant MGE, highlighting the critical importance of the E. faecalis accessory genome in modulating horizontal gene transfer. Our results rationalize the development of antimicrobial strategies that capitalize upon the immunocompromised status of multidrug-resistant E. faecalis. IMPORTANCE Enterococcus faecalis is a bacterium that normally inhabits the gastrointestinal tracts of humans and other animals. Although these bacteria are members of our native gut flora, they can cause life-threatening infections in hospitalized patients. Antibiotic resistance genes appear to be readily shared among high-risk E. faecalis strains, and multidrug resistance in these bacteria limits treatment options for infections. Here, we find that CRISPR-Cas and restriction-modification systems, which function as adaptive and innate immune systems in bacteria, significantly impact the spread of antibiotic resistance genes in E. faecalis populations. The loss of these systems in high-risk E. faecalis suggests that they are immunocompromised, a tradeoff that allows them to readily acquire new genes and adapt to new antibiotics.\",\n \"corpus_id\": 24766913,\n \"score\": 0\n },\n {\n \"doc_id\": \"27688323\",\n \"title\": \"Genome Sequence of Klebsiella quasipneumoniae subsp. similipneumoniae MB373, an Effective Bioremediator.\",\n \"abstract\": \"Klebsiella quasipneumoniae subsp. similipneumoniae MB373 was isolated from effluent of the Hattar Industrial Estate, Haripur, Pakistan. K. quasipneumoniae subsp. similipneumoniae has few cultivated/characterized members so far. Whole-genome sequencing revealed its potential for metal and toxin resistance, which further elucidated various enzymatic processes for the degradation of xenobiotics, illuminating its bioremediation applications.\",\n \"corpus_id\": 17576857,\n \"score\": 0\n },\n {\n \"doc_id\": \"27785154\",\n \"title\": \"Whole genome sequencing uncovers a novel IND-16 metallo-β-lactamase from an extensively drug-resistant Chryseobacterium indologenes strain J31.\",\n \"abstract\": \"BACKGROUND: Chryseobacterium indologenes is an emerging opportunistic pathogen in hospital-acquired infection, which is intrinsically resistant to most antimicrobial agents against gram-negative bacteria. In the purpose of extending our understanding of the resistance mechanism of C. indologenes, we sequenced and analyzed the genome of an extensively antibiotic resistant C. indologenes strain, isolated from a Chinese prostate cancer patient. We also investigated the presence of antibiotic resistance genes, particularly metallo-β-lactamase (MBL) genes, and performed a comparative genomic analysis with other Chryseobacterium species. RESULTS: 16s rRNA sequencing indicated the isolate belongs to C. indologenes. We assembled a total of 1095M bp clean-filtered reads into 171 contigs by de novo assembly. The draft genome of C. indologenes J31 consisted of 5,830,795 bp with a GC content of 36.9 %. RAST analysis revealed the genome contained 5196 coding sequences (CDSs), 28 rRNAs, 81 tRNAs and 114 pseudogenes. We detected 90 antibiotic resistance genes from different drug classes in the whole genome. Notably, a novel blaIND allele blaIND-16 was identified, which shared 99 % identity with blaIND-8 and blaIND-10. By comparing strain J31 genome to the closely four related neighbors in the genus Chryseobacterium, we identified 2634 conserved genes, and 1449 unique genes. CONCLUSIONS: In this study, we described the whole genome sequence of C. indologenes strain J31. Numerous resistance determinants were detected in the genome and might be responsible for the extensively antibiotic resistance of this strain. Comparative genomic analysis revealed the presence of considerable strain-specific genes which would contribute to the distinctive characteristics of strain J31. Our study provides the insight of the multidrug resistance mechanism in genus Chryseobacterium.\",\n \"corpus_id\": 18850120,\n \"score\": 0\n },\n {\n \"doc_id\": \"27795252\",\n \"title\": \"Draft Genome Sequence of Enterococcus faecalis Strain F165 Isolated from a Urinary Tract Infection.\",\n \"abstract\": \"We report here a draft genome sequence of Enterococcus faecalis strain F165 isolated from a urine specimen in South Brazil. The genome size was 3,049,734 bp, with a G+C content of 37.38%, and genes related to antimicrobial resistance and adherence were found in the strain. These findings are consistent with pathogenesis of E. faecalis species.\",\n \"corpus_id\": 6389485,\n \"score\": 0\n },\n {\n \"doc_id\": \"28302789\",\n \"title\": \"Draft Genome Sequences of 11 Lactococcus lactis subsp. cremoris Strains.\",\n \"abstract\": \"The lactic acid bacterium Lactococcus lactis is widely used for the fermentation of dairy products. Here, we present the draft genome sequences of 11 L. lactis subsp. cremoris strains isolated from different environments.\",\n \"corpus_id\": 33491517,\n \"score\": 0\n },\n {\n \"doc_id\": \"28377746\",\n \"title\": \"Genome-Guided Insights into the Plant Growth Promotion Capabilities of the Physiologically Versatile Bacillus aryabhattai Strain AB211.\",\n \"abstract\": \"Bacillus aryabhattai AB211 is a plant growth promoting, Gram-positive firmicute, isolated from the rhizosphere of tea (Camellia sinensis), one of the oldest perennial crops and a major non-alcoholic beverage widely consumed all over the world. The whole genome of B. aryabhattai AB211 was sequenced, annotated and evaluated with special focus on genomic elements related to plant microbe interaction. It's genome sequence reveals the presence of a 5,403,026 bp chromosome. A total of 5226 putative protein-coding sequences, 16 rRNA, 120 tRNA, 8 ncRNAs, 58 non-protein coding genes, and 11 prophage regions were identified. Genome sequence comparisons between strain AB211 and other related environmental strains of B. aryabhattai, identified about 3558 genes conserved among all B. aryabhattai genomes analyzed. Most of the common genes involved in plant growth promotion activities were found to be present within core genes of all the genomes used for comparison, illustrating possible common plant growth promoting traits shared among all the strains of B. aryabhattai. Besides the core genes, some genes were exclusively identified in the genome of strain AB211. Functional annotation of the genes predicted in the strain AB211 revealed the presence of genes responsible for mineral phosphate solubilization, siderophores, acetoin, butanediol, exopolysaccharides, flagella biosynthesis, surface attachment/biofilm formation, and indole acetic acid production, most of which were experimentally verified in the present study. Genome analysis and experimental evidence suggested that AB211 has robust central carbohydrate metabolism implying that this bacterium can efficiently utilize the root exudates and other organic materials as an energy source. Genes for the production of peroxidases, catalases, and superoxide dismutases, that confer resistance to oxidative stresses in plants were identified in AB211 genome. Besides these, genes for heat shock tolerance, cold shock tolerance, glycine-betaine production, and antibiotic/heavy metal resistance that enable bacteria to survive biotic/abiotic stress were also identified. Based on the genome sequence information and experimental evidence as presented in this study, strain AB211 appears to be metabolically diverse and exhibits tremendous potential as a plant growth promoting bacterium.\",\n \"corpus_id\": 6341115,\n \"score\": 0\n },\n {\n \"doc_id\": \"29152584\",\n \"title\": \"Large-Scale Bioinformatics Analysis of Bacillus Genomes Uncovers Conserved Roles of Natural Products in Bacterial Physiology.\",\n \"abstract\": \"Bacteria possess an amazing capacity to synthesize a diverse range of structurally complex, bioactive natural products known as specialized (or secondary) metabolites. Many of these specialized metabolites are used as clinical therapeutics, while others have important ecological roles in microbial communities. The biosynthetic gene clusters (BGCs) that generate these metabolites can be identified in bacterial genome sequences using their highly conserved genetic features. We analyzed an unprecedented 1,566 bacterial genomes from Bacillus species and identified nearly 20,000 BGCs. By comparing these BGCs to one another as well as a curated set of known specialized metabolite BGCs, we discovered that the majority of Bacillus natural products are comprised of a small set of highly conserved, well-distributed, known natural product compounds. Most of these metabolites have important roles influencing the physiology and development of Bacillus species. We identified, in addition to these characterized compounds, many unique, weakly conserved BGCs scattered across the genus that are predicted to encode unknown natural products. Many of these \\\"singleton\\\" BGCs appear to have been acquired via horizontal gene transfer. Based on this large-scale characterization of metabolite production in the Bacilli, we go on to connect the alkylpyrones, natural products that are highly conserved but previously biologically uncharacterized, to a role in Bacillus physiology: inhibiting spore development. IMPORTANCEBacilli are capable of producing a diverse array of specialized metabolites, many of which have gained attention for their roles as signals that affect bacterial physiology and development. Up to this point, however, the Bacillus genus's metabolic capacity has been underexplored. We undertook a deep genomic analysis of 1,566 Bacillus genomes to understand the full spectrum of metabolites that this bacterial group can make. We discovered that the majority of the specialized metabolites produced by Bacillus species are highly conserved, known compounds with important signaling roles in the physiology and development of this bacterium. Additionally, there is significant unique biosynthetic machinery distributed across the genus that might lead to new, unknown metabolites with diverse biological functions. Inspired by the findings of our genomic analysis, we speculate that the highly conserved alkylpyrones might have an important biological activity within this genus. We go on to validate this prediction by demonstrating that these natural products are developmental signals in Bacillus and act by inhibiting sporulation.\",\n \"corpus_id\": 9881959,\n \"score\": 0\n }\n]","isConversational":false}}},{"rowIdx":95,"cells":{"query":{"kind":"string","value":"{\n \"doc_id\": \"27618775\",\n \"title\": \"Prediction of post translation modifications at the contact site between Anaplasma phagocytophilum and human host during autophagosome induction using a bioinformatic approach.\",\n \"abstract\": \"Autophagy is crucial for maintaining physiological homeostasis, but its role in infectious diseases is not yet adequately understood. The binding of Anaplasma translocated substrate-1 (ATS1) to the human Beclin1 (BECN1) protein is responsible for the modulation of autophagy pathway. ATS1-BECN1 is a novel type of interaction that facilitates Anaplasma phagocytophilum proliferation, leading to intracellular infection via autophagosome induction and segregation from the lysosome. Currently, there is no report of post translational modifications (PTMs) of BECN1 or cross-talk required for ATS-BECN1 complex formation. Prediction/modeling of the cross-talk between phosphorylation and other PTMs (O-β-glycosylation, sumoylation, methylation and palmitoylation) has been attempted in this study, which might be responsible for regulating function after the interaction of ATS1 with BECN1. PTMs were predicted computationally and mapped onto the interface of the docked ATS1-BECN1 complex. Results show that BECN1 phosphorylation at five residues (Thr91, Ser93, Ser96, Thr141 and Ser234), the interplay with O-β-glycosylation at three sites (Thr91, Ser93 and Ser96) with ATS1 may be crucial for attachment and, hence, infection. No other PTM site at the BECN1 interface was predicted to associate with ATS1. These findings may have significant clinical implications for understanding the etiology of Anaplasma infection and for therapeutic studies.\",\n \"corpus_id\": 24715586\n}"},"candidates":{"kind":"list like","value":[{"doc_id":"17979984","title":"Subversion of cellular autophagy by Anaplasma phagocytophilum.","abstract":"Anaplasma phagocytophilum, the causative agent of human granulocytic anaplasmosis, is an obligatory intracellular pathogen. After entry into host cells, the bacterium is diverted from the endosomal pathway and replicates in a membrane-bound compartment devoid of endosomal or lysosomal markers. Here, we show that several hallmarks of early autophagosomes can be identified in A. phagocytophilum replicative inclusions, including a double-lipid bilayer membrane and colocalization with GFP-tagged LC3 and Beclin 1, the human homologues of Saccharomyces cerevisiae autophagy-related proteins Atg8 and Atg6 respectively. While the membrane-associated form of LC3, LC3-II, increased during A. phagocytophilum infection, A. phagocytophilum-containing inclusions enveloped with punctate GFP-LC3 did not colocalize with a lysosomal marker. Stimulation of autophagy by rapamycin favoured A. phagocytophilum infection. Inhibition of the autophagosomal pathway by 3-methyladenine did not inhibit A. phagocytophilum internalization, but reversibly arrested its growth. Although autophagy is considered part of the innate immune system that clears a variety of intracellular pathogens, our study implies that A. phagocytophilum subverts this system to establish itself in an early autophagosome-like compartment segregated from lysosomes to facilitate its proliferation.","corpus_id":37080350,"score":2},{"doc_id":"18286469","title":"MAPRes: an efficient method to analyze protein sequence around post-translational modification sites.","abstract":"Functional switches are often regulated by dynamic protein modifications. Assessing protein functions, in vivo, and their functional switches remains still a great challenge in this age of development. An alternative methodology based on in silico procedures may facilitate assessing the multifunctionality of proteins and, in addition, allow predicting functions of those proteins that exhibit their functionality through transitory modifications. Extensive research is ongoing to predict the sequence of protein modification sites and analyze their dynamic nature. This study reports the analysis performed on phosphorylation, Phospho. ELM (version 3.0) and glycosylation, OGlycBase (version 6.0) data for mining association patterns utilizing a newly developed algorithm, MAPRes. This method, MAPRes (Mining Association Patterns among preferred amino acid residues in the vicinity of amino acids targeted for post-translational modifications), is based on mining association among significantly preferred amino acids of neighboring sequence environment and modification sites themselves. Association patterns arrived at by association pattern/rule mining were in significant conformity with the results of different approaches. However, attempts to analyze substrate sequence environment of phosphorylation sites catalyzed for Tyr kinases and the sequence data for O-GlcNAc modification were not successful, due to the limited data available. Using the MAPRes algorithm for developing an association among PTM site with its vicinal amino acids is a valid method with many potential uses: this is indeed the first method ever to apply the association pattern mining technique to protein post-translational modification data.","corpus_id":40979012,"score":2},{"doc_id":"19549291","title":"A comprehensive resource for integrating and displaying protein post-translational modifications.","abstract":"BACKGROUND: Protein Post-Translational Modification (PTM) plays an essential role in cellular control mechanisms that adjust protein physical and chemical properties, folding, conformation, stability and activity, thus also altering protein function. FINDINGS: dbPTM (version 1.0), which was developed previously, aimed on a comprehensive collection of protein post-translational modifications. In this update version (dbPTM2.0), we developed a PTM database towards an expert system of protein post-translational modifications. The database comprehensively collects experimental and predictive protein PTM sites. In addition, dbPTM2.0 was extended to a knowledge base comprising the modified sites, solvent accessibility of substrate, protein secondary and tertiary structures, protein domains, protein intrinsic disorder region, and protein variations. Moreover, this work compiles a benchmark to construct evaluation datasets for computational study to identifying PTM sites, such as phosphorylated sites, glycosylated sites, acetylated sites and methylated sites. CONCLUSION: The current release not only provides the sequence-based information, but also annotates the structure-based information for protein post-translational modification. The interface is also designed to facilitate the access to the resource. This effective database is now freely accessible at http://dbPTM.mbc.nctu.edu.tw/.","corpus_id":2505660,"score":2},{"doc_id":"20670295","title":"Type IV secretion in the obligatory intracellular bacterium Anaplasma phagocytophilum.","abstract":"Anaplasma phagocytophilum is an obligatory intracellular bacterium that infects neutrophils, the primary host defence cells. Consequent effects of infection on host cells result in a potentially fatal systemic disease called human granulocytic anaplasmosis. Despite ongoing reductive genome evolution and deletion of most genes for intermediary metabolism and amino acid biosynthesis, Anaplasma has also experienced expansion of genes encoding several components of the type IV secretion (T4S) apparatus. Two A. phagocytophilum T4S effector molecules are currently known; Anaplasma translocated substrate 1 (Ats-1) and ankyrin repeat domain-containing protein A (AnkA) have C-terminal positively charged amino acid residues that are recognized by the T4S coupling protein, VirD4. AnkA and Ats-1 contain eukaryotic protein motifs and are uniquely evolved in the family Anaplasmataceae; Ats-1 contains a mitochondria-targeting signal. They are abundantly produced and secreted into the host cytoplasm, are not toxic to host cells, and manipulate host cell processes to aid in the infection process. At the cellular level, the two effectors have distinct subcellular localization and signalling in host cells. Thus in this obligatory intracellular pathogen, the T4S system has evolved as a host-subversive survival factor.","corpus_id":7712782,"score":2},{"doc_id":"20674646","title":"Post-translational modification by SUMO.","abstract":"Post-translational modifications (PTMs) are chemical alterations to a protein following translation, regulating stability and function. Reversible phosphorylation is an example of an important and well studied PTM involved in a number of cellular processes. SUMOylation is another PTM known to modify a large number of proteins and plays a role in various cellular processes including: cell cycle regulation, gene transcription, differentiation and cellular localisation. Therefore, understanding the role of SUMOylation in cell biology may allow the development of more efficient models, important in streamlining the drug discovery process. This review will focus on protein SUMOylation and its role in stem cell and somatic cell biology.","corpus_id":10830819,"score":2},{"doc_id":"21053365","title":"CREB in long-term potentiation in hippocampus: role of post-translational modifications-studies In silico.","abstract":"The multifunctionality of proteins is dictated by post-translational modifications (PTMs) which involve the attachment of small functional groups such as phosphate and acetate, as well as carbohydrate moieties. These functional groups make the protein perform various functions in different environments. PTMs play a crucial role in memory and learning. Phosphorylation of synaptic proteins and transcription factors regulate the generation and storage of memory. Among these is the cAMP-regulated element binding protein CREB that regulates CRE containing genes like c-fos. Both phosphorylation and acetylation control the function of CREB as a transcription factor. CREB is also susceptible to O-GlcNAc modification, which inhibits its activity. O-GlcNAc modification occurs on the same or neighboring Ser/Thr residues akin to phosphorylation. An interplay between these modifications was shown to operate in nuclear and cytoplasmic proteins. In this study computational methods were utilized to predict different modification sites in CREB. These in silico results suggest that phosphorylation, O-GlcNAc modification and acetylation modulate the transcriptional activity of CREB and thus dictate its contribution to synaptic plasticity.","corpus_id":27770274,"score":2},{"doc_id":"21617949","title":"Role of post translational modifications and novel crosstalk between phosphorylation and O-beta-GlcNAc modifications in human claudin-1, -3 and -4.","abstract":"The precise characterization of post translational modifications (PTMs) is important for the understanding of protein regulatory mechanisms and their role in disease. However, experimental studies on PTMs, especially with multifunctional proteins are difficult to follow and investigate. Bioinformatic tools are therefore helpful in predicting key protein modifications. To study the role of PTMs in claudin proteins, specifically claudin-1, -3 and -4 in the onset or progression of human cancers, we performed an in silico study of various PTMs and investigated their interplay. Given that the activity of claudins is known to be influenced by two types of PTMs, specifically palmitoylation and kinase- dependent phosphorylation, we predicted two conserved regions in the topological domains of claudin-1, -3 and -4 as potential palmitoylation sites. Furthermore, conserved phosphorylation residues, which may be targets for kinases and can alter claudin's ability to maintain the integrity of tight junctions, were identified. To our knowledge, this is the first report to suggest O-glycosylation of claudin proteins, as well as a potential novel interplay between phosphorylation and O-glycosylation at Yin Yang sites. Thus, our findings may facilitate the production of anti-cancer drugs, and suggest that novel therapeutic strategies should target post translational events.","corpus_id":6333545,"score":2},{"doc_id":"22212234","title":"Subversion of NPC1 pathway of cholesterol transport by Anaplasma phagocytophilum.","abstract":"Intracellular cholesterol amounts, distribution and traffic are tightly regulated to maintain the healthy eukaryotic cell function. However, how intracellular pathogens that require cholesterol, interact with the host cholesterol homeostasis and traffic is not well understood. Anaplasma phagocytophilum is an obligatory intracellular and cholesterol-robbing bacterium, which causes human granulocytic anaplasmosis. Here we found that a subset of cholesterol-binding membrane protein, Niemann-Pick type C1 (NPC1)-bearing vesicles devoid of lysosomal markers were upregulated in HL-60 cells infected with A. phagocytophilum, and trafficked to live bacterial inclusions. The NPC1 localization to A. phagocytophilum inclusions was abolished by low-density lipoprotein (LDL)-derived cholesterol traffic inhibitor U18666A. Studies using NPC1 siRNA and the cell line with cholesterol traffic defect demonstrated that the NPC1 function is required for bacterial cholesterol acquisition and infection. Furthermore, trans-Golgi network-specific soluble N-ethylmaleimide-sensitive factor attachment protein receptors, vesicle-associated membrane protein (VAMP4) and syntaxin 16, which are associated with NPC1 and LDL-derived cholesterol vesicular transport were recruited to A. phagocytophilum inclusions, and VAMP4 was required for bacteria infection. Taken together, A. phagocytophilum is the first example of a pathogen that subverts the NPC1 pathway of intracellular cholesterol transport and homeostasis for bacterial inclusion membrane biogenesis and cholesterol capture.","corpus_id":43726533,"score":2},{"doc_id":"22708570","title":"Prediction of lysine post-translational modifications using bioinformatic tools.","abstract":"Our understanding of the importance of lysine post-translational modifications in mediating protein function has led to a significant improvement in the experimental tools aimed at characterizing their existence. Nevertheless, it remains likely that at present we have only experimentally detected a small fraction of all lysine modification sites across the commonly studied proteomes. As a result, online computational tools aimed at predicting lysine modification sites have the potential to provide valuable insight to researchers developing hypotheses regarding these modifications. This chapter discusses the metrics and procedures used to assess predictive tools and surveys 11 online computational tools aimed at the prediction of the four most widely studied lysine post-translational modifications (acetylation, methylation, SUMOylation and ubiquitination). Analyses using unbiased testing data sets suggest that nine of the 11 lysine post-translational modification tools perform no better than random, or have false-positive rates which make them unusable by the experimental biologist, despite self-reported sensitivity and specificity values to the contrary. The implications of these findings for those using and creating lysine post-translational modification software are discussed.","corpus_id":25292764,"score":2},{"doc_id":"23197835","title":"Autophagosomes induced by a bacterial Beclin 1 binding protein facilitate obligatory intracellular infection.","abstract":"Autophagy, a cytoplasmic catabolic process, plays a critical role in defense against intracellular infection. In turn, evasion or inhibition of autophagy has emerged as an important virulence factor for intracellular pathogens. However, Anaplasma phagocytophilum, the obligatory intracellular bacterium that causes human granulocytic anaplasmosis, replicates in the membrane-bound compartment resembling early autophagosome. Here, we found that Anaplasma translocated substrate 1 (Ats-1), a type IV secretion effector, binds Beclin 1, a subunit of the class III PI3K and Atg14L, and it nucleates autophagosomes with markers of omegasomes, double FYVE-containing protein 1, Atg14L, and LC3. Ats-1 autophagy induction did not activate the starvation signaling pathway of mammalian target of rapamycin. These autophagy proteins were also localized to the Anaplasma inclusion. Ectopically expressed Ats-1 targeted the Anaplasma inclusions and enhanced infection, whereas host cytoplasmic delivery of anti-Ats-1 or Beclin 1 depletion by siRNA suppressed the infection; beclin 1 heterozygous-deficient mice were resistant to Anaplasma infection. Furthermore, Anaplasma growth arrest by the class III PI3K inhibitor 3-methyladenine was alleviated by essential amino acid supplementation. Thus, Anaplasma actively induces autophagy by secreting Ats-1 that hijacks the Beclin 1-Atg14L autophagy initiation pathway likely to acquire host nutrients for its growth.","corpus_id":11691354,"score":2},{"doc_id":"23387271","title":"[Bioinformatic analysis of potential post-translational modification sites of the human O6-methylguanine-DNA methyltransferase (MGMT) protein].","abstract":"Using in silico analysis a number of potential sites for post-translational modifications has been revealed within the human O6-methylguanine-DNA methyltransferase (MGMT) protein. In particular these were the acetylation of Gly3 residue in the N-terminus of protein and internal residues Lys132 and Lys135; Arg166 residue methylation; Lys63 SUMOylation and ubiquitination of Lys31, Lys39, Lys49, Lys63, Lys67, Lys135, Lys156, Lys196, Lys209. Also it has been predicted 16 novel potential phosphorylation sites of serine residues (positions 13, 124, 144, 182, 183, 190, 215, 216 and 230), tyrosine residues (positions 100 and 189) and threonine residues (positions 23, 69, 94, 126 and 229), as well as five binding sites for kinases and other proteins (Serl3 with 14-3-3, Val21 and Ile172 with D-domain, Pro78 and Pro111 with SH3-domain, Pro111 with MAPK3). Some kinases predicted by the authors are known as partners of the MGMT protein, that confirms the probability of modification of the given sites. Potential sites require further experimental confirmation of modifications and investigation of their influence on stability and DNA-repair activity of this protein.","corpus_id":26535998,"score":2},{"doc_id":"23388398","title":"Ats-1: a novel bacterial molecule that links autophagy to bacterial nutrition.","abstract":"Obligatory intracellular life style and a small number of genes for biosynthesis and metabolism necessitate the Gram-negative bacterium, Anaplasma phagocytophilum, to depend on the host cell for nutrients. A. phagocytophilum resides in a membrane-bound inclusion, and secretes a protein, Ats-1 (Anaplasma translocated substrate-1), into the host cell cytoplasm. Ats-1 binds BECN1, a protein critical for autophagy nucleation, and induces autophagosome formation. The autophagosomes traffic to, and fuse with, A. phagocytophilum inclusions, delivering autophagic cargo into the inclusions, which can serve as nutrients for bacterial growth. This finding demonstrates that A. phagocytophilum subverts host cell autophagic machinery to facilitate infection by secreting a BECN1-binding molecule.","corpus_id":207508030,"score":2},{"doc_id":"24556839","title":"Post-translational modifications of intermediate filament proteins: mechanisms and functions.","abstract":"Intermediate filaments (IFs) are cytoskeletal and nucleoskeletal structures that provide mechanical and stress-coping resilience to cells, contribute to subcellular and tissue-specific biological functions, and facilitate intracellular communication. IFs, including nuclear lamins and those in the cytoplasm (keratins, vimentin, desmin, neurofilaments and glial fibrillary acidic protein, among others), are functionally regulated by post-translational modifications (PTMs). Proteomic advances highlight the enormous complexity and regulatory potential of IF protein PTMs, which include phosphorylation, glycosylation, sumoylation, acetylation and prenylation, with novel modifications becoming increasingly appreciated. Future studies will need to characterize their on-off mechanisms, crosstalk and utility as biomarkers and targets for diseases involving the IF cytoskeleton.","corpus_id":28089575,"score":2},{"doc_id":"25120100","title":"In-silico analysis of claudin-5 reveals novel putative sites for post-translational modifications: Insights into potential molecular determinants of blood-brain barrier breach during HIV-1 infiltration.","abstract":"The blood-brain barrier (BBB) poses a huge challenge and is a serious issue in deciphering the pathophysiology of central nervous system disorders. Endothelial tight junctions play an essential role in maintaining the integrity of the BBB. Post-translational modifications (PTMs) in endothelial tight junction proteins are known to cause deleterious functional impairment and possible disruptions in BBB integrity. PTMs in tight junction proteins play an important role in human immunodeficiency virus type 1 (HIV-1) entry through the BBB. Human claudin-5 is one of the highly expressed brain endothelial tight junction protein and various PTMs in claudin-5 are expected to aid HIV-1 in crossing the BBB. A precise characterization of PTMs in claudin-5 is important for understanding its role in HIV-1 brain infiltration. In this study, we have examined post-translational crosstalk between phosphorylation, O-glycosylation, palmitoylation and methylation sites in claudin-5, which could alter claudin-5's ability to maintain BBB integrity. To the best of our knowledge, this is the first report on claudin-5 protein that suggests a novel interplay between potential PTM sites. PTMs of predicted residues in claudin-5, suggested in this study, can serve as compelling targets for potential therapeutic agents against HIV-1 induced neuropathogenesis. Further site-specific experimental studies in this aspect are highly recommended.","corpus_id":10115867,"score":2},{"doc_id":"25365205","title":"Regulation of autophagy by protein post-translational modification.","abstract":"Autophagy is a lysosome-mediated intracellular protein degradation process that involves about 38 autophagy-related genes as well as key signaling pathways that sense cellular metabolic and redox status, and has an important role in quality control of macromolecules and organelles. As with other major cellular pathways, autophagy proteins are subjected to regulatory post-translational modification. Phosphorylation is so far the most intensively studied post-translational modification in the autophagy process, followed by ubiquitination and acetylation. An interesting and new area is also now emerging, which appears to complement these more traditional mechanisms, and includes O-GlcNAcylation and redox regulation at thiol residues. Identification of the full spectrum of post-translational modifications of autophagy proteins, and determination of their impact on autophagy will be crucial for a better understanding of autophagy regulation, its deficits in diseases, and how to exploit this process for disease therapies.","corpus_id":35552001,"score":2},{"doc_id":"25484070","title":"Posttranslational modification of autophagy-related proteins in macroautophagy.","abstract":"Macroautophagy is an intracellular catabolic process involved in the formation of multiple membrane structures ranging from phagophores to autophagosomes and autolysosomes. Dysfunction of macroautophagy is implicated in both physiological and pathological conditions. To date, 38 autophagy-related (ATG) genes have been identified as controlling these complicated membrane dynamics during macroautophagy in yeast; approximately half of these genes are clearly conserved up to human, and there are additional genes whose products function in autophagy in higher eukaryotes that are not found in yeast. The function of the ATG proteins, in particular their ability to interact with a number of macroautophagic regulators, is modulated by posttranslational modifications (PTMs) such as phosphorylation, glycosylation, ubiquitination, acetylation, lipidation, and proteolysis. In this review, we summarize our current knowledge of the role of ATG protein PTMs and their functional relevance in macroautophagy. Unraveling how these PTMs regulate ATG protein function during macroautophagy will not only reveal fundamental mechanistic insights into the regulatory process, but also provide new therapeutic targets for the treatment of autophagy-associated diseases.","corpus_id":32079965,"score":2},{"doc_id":"25605461","title":"Systematic characterization and prediction of post-translational modification cross-talk.","abstract":"Post-translational modification (PTM)(1) plays an important role in regulating the functions of proteins. PTMs of multiple residues on one protein may work together to determine a functional outcome, which is known as PTM cross-talk. Identification of PTM cross-talks is an emerging theme in proteomics and has elicited great interest, but their properties remain to be systematically characterized. To this end, we collected 193 PTM cross-talk pairs in 77 human proteins from the literature and then tested location preference and co-evolution at the residue and modification levels. We found that cross-talk events preferentially occurred among nearby PTM sites, especially in disordered protein regions, and cross-talk pairs tended to co-evolve. Given the properties of PTM cross-talk pairs, a naïve Bayes classifier integrating different features was built to predict cross-talks for pairwise combination of PTM sites. By using a 10-fold cross-validation, the integrated prediction model showed an area under the receiver operating characteristic (ROC) curve of 0.833, superior to using any individual feature alone. The prediction performance was also demonstrated to be robust to the biases in the collected PTM cross-talk pairs. The integrated approach has the potential for large-scale prioritization of PTM cross-talk candidates for functional validation and was implemented as a web server available at http://bioinfo.bjmu.edu.cn/ptm-x/.","corpus_id":25404416,"score":2},{"doc_id":"26344496","title":"A novel method for predicting post-translational modifications on serine and threonine sites by using site-modification network profiles.","abstract":"Post-translational modifications (PTMs) regulate many aspects of biological behaviours including protein-protein interactions and cellular processes. Identification of PTM sites is helpful for understanding the PTM regulatory mechanisms. The PTMs on serine and threonine sites include phosphorylation, O-linked glycosylation and acetylation. Although a lot of computational approaches have been developed for PTM site prediction, currently most of them generate the predictive models by employing only local sequence information and few of them consider the relationship between different PTMs. In this paper, by adopting the site-modification network (SMNet) profiles that efficiently incorporate in situ PTM information, we develop a novel method to predict PTM sites on serine and threonine. PTM data are collected from various PTM databases and the SMNet is built to reflect the relationship between multiple PTMs, from which SMNet profiles are extracted to train predictive models based on SVM. Performance analysis of the SVM models shows that the SMNet profiles play an important role in accurately predicting PTM sites on serine and threonine. Furthermore, the proposed method is compared with existing PTM prediction approaches. The results from 10-fold cross-validation demonstrate that the proposed method with SMNet profiles performs remarkably better than existing methods, suggesting the power of SMNet profiles in identifying PTM sites.","corpus_id":205973316,"score":2},{"doc_id":"27174170","title":"A homology-based pipeline for global prediction of post-translational modification sites.","abstract":"The pathways of protein post-translational modifications (PTMs) have been shown to play particularly important roles for almost any biological process. Identification of PTM substrates along with information on the exact sites is fundamental for fully understanding or controlling biological processes. Alternative computational strategies would help to annotate PTMs in a high-throughput manner. Traditional algorithms are suited for identifying the common organisms and tissues that have a complete PTM atlas or extensive experimental data. While annotation of rare PTMs in most organisms is a clear challenge. In this work, to this end we have developed a novel homology-based pipeline named PTMProber that allows identification of potential modification sites for most of the proteomes lacking PTMs data. Cross-promotion E-value (CPE) as stringent benchmark has been used in our pipeline to evaluate homology to known modification sites. Independent-validation tests show that PTMProber achieves over 58.8% recall with high precision by CPE benchmark. Comparisons with other machine-learning tools show that PTMProber pipeline performs better on general predictions. In addition, we developed a web-based tool to integrate this pipeline at http://bioinfo.ncu.edu.cn/PTMProber/index.aspx. In addition to pre-constructed prediction models of PTM, the website provides an extensional functionality to allow users to customize models.","corpus_id":205697208,"score":2},{"doc_id":"27367363","title":"DAPPLE 2: a Tool for the Homology-Based Prediction of Post-Translational Modification Sites.","abstract":"The post-translational modification of proteins is critical for regulating their function. Although many post-translational modification sites have been experimentally determined, particularly in certain model organisms, experimental knowledge of these sites is severely lacking for many species. Thus, it is important to be able to predict sites of post-translational modification in such species. Previously, we described DAPPLE, a tool that facilitates the homology-based prediction of one particular post-translational modification, phosphorylation, in an organism of interest using known phosphorylation sites from other organisms. Here, we describe DAPPLE 2, which expands and improves upon DAPPLE in three major ways. First, it predicts sites for many post-translational modifications (20 different types) using data from several sources (15 online databases). Second, it has the ability to make predictions approximately 2-7 times faster than DAPPLE depending on the database size and the organism of interest. Third, it simplifies and accelerates the process of selecting predicted sites of interest by categorizing them based on gene ontology terms, keywords, and signaling pathways. We show that DAPPLE 2 can successfully predict known human post-translational modification sites using, as input, known sites from species that are either closely (e.g., mouse) or distantly (e.g., yeast) related to humans. DAPPLE 2 can be accessed at http://saphire.usask.ca/saphire/dapple2 .","corpus_id":24513686,"score":2},{"doc_id":"27414988","title":"Conformational flexibility of BECN1: Essential to its key role in autophagy and beyond.","abstract":"BECN1 (Beclin 1), a highly conserved eukaryotic protein, is a key regulator of autophagy, a cellular homeostasis pathway, and also participates in vacuolar protein sorting, endocytic trafficking, and apoptosis. BECN1 is important for embryonic development, the innate immune response, tumor suppression, and protection against neurodegenerative disorders, diabetes, and heart disease. BECN1 mediates autophagy as a core component of the class III phosphatidylinositol 3-kinase complexes. However, the exact mechanism by which it regulates the activity of these complexes, or mediates its other diverse functions is unclear. BECN1 interacts with several diverse protein partners, perhaps serving as a scaffold or interaction hub for autophagy. Based on extensive structural, biophysical and bioinformatics analyses, BECN1 consists of an intrinsically disordered region (IDR), which includes a BH3 homology domain (BH3D); a flexible helical domain (FHD); a coiled-coil domain (CCD); and a β-α-repeated autophagy-specific domain (BARAD). Each of these BECN1 domains mediates multiple diverse interactions that involve concomitant conformational changes. Thus, BECN1 conformational flexibility likely plays a key role in facilitating diverse protein interactions. Further, BECN1 conformation and interactions are also modulated by numerous post-translational modifications. A better structure-based understanding of the interplay between different BECN1 conformational and binding states, and the impact of post-translational modifications will be essential to elucidating the mechanism of its multiple biological roles.","corpus_id":206393147,"score":2},{"doc_id":"27534850","title":"A machine learning strategy for predicting localization of post-translational modification sites in protein-protein interacting regions.","abstract":"BACKGROUND: One very important functional domain of proteins is the protein-protein interacting region (PPIR), which forms the binding interface between interacting polypeptide chains. Post-translational modifications (PTMs) that occur in the PPIR can either interfere with or facilitate the interaction between proteins. The ability to predict whether sites of protein modifications are inside or outside of PPIRs would be useful in further elucidating the regulatory mechanisms by which modifications of specific proteins regulate their cellular functions. RESULTS: Using two of the comprehensive databases for protein-protein interaction and protein modification site data (PDB and PhosphoSitePlus, respectively), we created new databases that map PTMs to their locations inside or outside of PPIRs. The mapped PTMs represented only 5 % of all known PTMs. Thus, in order to predict localization within or outside of PPIRs for the vast majority of PTMs, a machine learning strategy was used to generate predictive models from these mapped databases. For the three mapped PTM databases which had sufficient numbers of modification sites for generating models (acetylation, phosphorylation, and ubiquitylation), the resulting models yielded high overall predictive performance as judged by a combined performance score (CPS). Among the multiple properties of amino acids that were used in the classification tasks, hydrophobicity was found to contribute substantially to the performance of the final predictive models. Compared to the other classifiers we also evaluated, the SVM provided the best performance overall. CONCLUSIONS: These models are the first to predict whether PTMs are located inside or outside of PPIRs, as demonstrated by their high predictive performance. The models and data presented here should be useful in prioritizing both known and newly identified PTMs for further studies to determine the functional relationship between specific PTMs and protein-protein interactions. The implemented R package is available online ( http://sysbio.chula.ac.th/PtmPPIR ).","corpus_id":15910362,"score":2},{"doc_id":"28356000","title":"New Achievements in Bioinformatics Prediction of Post Translational Modification of Proteins.","abstract":"Post translational modification (PTM) is one of the critical levels in regulation of gene expression that determines the fate of proteins after translation in eukaryotic cells. Since the detection of PTM sites in proteins is useful for diagnosis and prevention of diseases, numerous web-tool predictors are introduced to predict various types of PTMs. In this paper, an attempt is made to summarize a number of server predictors for the prediction of PTM sites.","corpus_id":38700278,"score":2},{"doc_id":"28458782","title":"Protein post-translational modifications: In silico prediction tools and molecular modeling.","abstract":"Post-translational modifications (PTMs) occur in almost all proteins and play an important role in numerous biological processes by significantly affecting proteins' structure and dynamics. Several computational approaches have been developed to study PTMs (e.g., phosphorylation, sumoylation or palmitoylation) showing the importance of these techniques in predicting modified sites that can be further investigated with experimental approaches. In this review, we summarize some of the available online platforms and their contribution in the study of PTMs. Moreover, we discuss the emerging capabilities of molecular modeling and simulation that are able to complement these bioinformatics methods, providing deeper molecular insights into the biological function of post-translational modified proteins.","corpus_id":6342639,"score":2},{"doc_id":"28462053","title":"Prediction of post-translational modification sites using multiple kernel support vector machine.","abstract":"Protein post-translational modification (PTM) is an important mechanism that is involved in the regulation of protein function. Considering the high-cost and labor-intensive of experimental identification, many computational prediction methods are currently available for the prediction of PTM sites by using protein local sequence information in the context of conserved motif. Here we proposed a novel computational method by using the combination of multiple kernel support vector machines (SVM) for predicting PTM sites including phosphorylation, O-linked glycosylation, acetylation, sulfation and nitration. To largely make use of local sequence information and site-modification relationships, we developed a local sequence kernel and Gaussian interaction profile kernel, respectively. Multiple kernels were further combined to train SVM for efficiently leveraging kernel information to boost predictive performance. We compared the proposed method with existing PTM prediction methods. The experimental results revealed that the proposed method performed comparable or better performance than the existing prediction methods, suggesting the feasibility of the developed kernels and the usefulness of the proposed method in PTM sites prediction.","corpus_id":268578,"score":2},{"doc_id":"29185708","title":"The Autophagy-Related Beclin-1 Protein Requires the Coiled-Coil and BARA Domains To Form a Homodimer with Submicromolar Affinity.","abstract":"Beclin-1 (BECN1) is an essential component of macroautophagy. This process is a highly conserved survival mechanism that recycles damaged cellular components or pathogens by encasing them in a bilayer vesicle that fuses with a lysosome to allow degradation of the vesicular contents. Mutations or altered expression profiles of BECN1 have been linked to various cancers and neurodegenerative diseases. Viruses, including HIV and herpes simplex virus 1 (HSV-1), are also known to specifically target BECN1 as a means of evading host defense mechanisms. Autophagy is regulated by the interaction between BECN1 and Bcl-2, a pro-survival protein in the apoptotic pathway that stabilizes the BECN1 homodimer. Disruption of the homodimer by phosphorylation or competitive binding promotes autophagy through an unknown mechanism. We report here the first recombinant synthesis (3-5 mg/L in an Escherichia coli culture) and characterization of full-length, human BECN1. Our analysis reveals that full-length BECN1 exists as a soluble homodimer (KD ∼ 0.45 μM) that interacts with Bcl-2 (KD = 4.3 ± 1.2 μM) and binds to lipid membranes. Dimerization is proposed to be mediated by a coiled-coil region of BECN1. A construct lacking the C-terminal BARA domain but including the coiled-coil region exhibits a homodimer KD 3.5-fold weaker than that of full-length BECN1, indicating that both the BARA domain and the coiled-coil region of BECN1 contribute to dimer formation. Using site-directed mutagenesis, we show that residues at the C-terminus of the coiled-coil region previously shown to interact with the BARA domain play a key role in dimerization and mutations weaken the interface by ∼5-fold.","corpus_id":206518010,"score":2},{"doc_id":"20174550","title":"Anaplasma phagocytophilum Ats-1 is imported into host cell mitochondria and interferes with apoptosis induction.","abstract":"Anaplasma phagocytophilum, the causative agent of human granulocytic anaplasmosis, infects human neutrophils and inhibits mitochondria-mediated apoptosis. Bacterial factors involved in this process are unknown. In the present study, we screened a genomic DNA library of A. phagocytophilum for effectors of the type IV secretion system by a bacterial two-hybrid system, using A. phagocytophilum VirD4 as bait. A hypothetical protein was identified as a putative effector, hereby named Anaplasmatranslocated substrate 1 (Ats-1). Using triple immunofluorescence labeling and Western blot analysis of infected cells, including human neutrophils, we determined that Ats-1 is abundantly expressed by A. phagocytophilum, translocated across the inclusion membrane, localized in the host cell mitochondria, and cleaved. Ectopically expressed Ats-1 targeted mitochondria in an N-terminal 17 residue-dependent manner, localized in matrix or at the inner membrane, and was cleaved as native protein, which required residues 55-57. In vitro-translated Ats-1 was imported in a receptor-dependent manner into isolated mitochondria. Ats-1 inhibited etoposide-induced cytochrome c release from mitochondria, PARP cleavage, and apoptosis in mammalian cells, as well as Bax-induced yeast apoptosis. Ats-1(55-57) had significantly reduced anti-apoptotic activity. Bax redistribution was inhibited in both etoposide-induced and Bax-induced apoptosis by Ats-1. Taken together, Ats-1 is the first example of a bacterial protein that traverses five membranes and prevents apoptosis at the mitochondria.","corpus_id":6867624,"score":1},{"doc_id":"20559548","title":"Regulation of amyloid precursor protein processing by the Beclin 1 complex.","abstract":"Autophagy is an intracellular degradation pathway that functions in protein and organelle turnover in response to starvation and cellular stress. Autophagy is initiated by the formation of a complex containing Beclin 1 (BECN1) and its binding partner Phosphoinositide-3-kinase, class 3 (PIK3C3). Recently, BECN1 deficiency was shown to enhance the pathology of a mouse model of Alzheimer Disease (AD). However, the mechanism by which BECN1 or autophagy mediate these effects are unknown. Here, we report that the levels of Amyloid precursor protein (APP) and its metabolites can be reduced through autophagy activation, indicating that they are a substrate for autophagy. Furthermore, we find that knockdown of Becn1 in cell culture increases the levels of APP and its metabolites. Accumulation of APP and APP C-terminal fragments (APP-CTF) are accompanied by impaired autophagosomal clearance. Pharmacological inhibition of autophagosomal-lysosomal degradation causes a comparable accumulation of APP and APP-metabolites in autophagosomes. Becn1 reduction in cell culture leads to lower levels of its binding partner Pik3c3 and increased presence of Microtubule-associated protein 1, light chain 3 (LC3). Overexpression of Becn1, on the other hand, reduces cellular APP levels. In line with these observations, we detected less BECN1 and PIK3C3 but more LC3 protein in brains of AD patients. We conclude that BECN1 regulates APP processing and turnover. BECN1 is involved in autophagy initiation and autophagosome clearance. Accordingly, BECN1 deficiency disrupts cellular autophagy and autophagosomal-lysosomal degradation and alters APP metabolism. Together, our findings suggest that autophagy and the BECN1-PIK3C3 complex regulate APP processing and play an important role in AD pathology.","corpus_id":1915839,"score":1},{"doc_id":"22164248","title":"Bioinformatic analysis and post-translational modification crosstalk prediction of lysine acetylation.","abstract":"Recent proteomics studies suggest high abundance and a much wider role for lysine acetylation (K-Ac) in cellular functions. Nevertheless, cross influence between K-Ac and other post-translational modifications (PTMs) has not been carefully examined. Here, we used a variety of bioinformatics tools to analyze several available K-Ac datasets. Using gene ontology databases, we demonstrate that K-Ac sites are found in all cellular compartments. KEGG analysis indicates that the K-Ac sites are found on proteins responsible for a diverse and wide array of vital cellular functions. Domain structure prediction shows that K-Ac sites are found throughout a wide variety of protein domains, including those in heat shock proteins and those involved in cell cycle functions and DNA repair. Secondary structure prediction proves that K-Ac sites are preferentially found in ordered structures such as alpha helices and beta sheets. Finally, by mutating K-Ac sites in silico and predicting the effect on nearby phosphorylation sites, we demonstrate that the majority of lysine acetylation sites have the potential to impact protein phosphorylation, methylation, and ubiquitination status. Our work validates earlier smaller-scale studies on the acetylome and demonstrates the importance of PTM crosstalk for regulation of cellular function.","corpus_id":8934622,"score":1},{"doc_id":"22438791","title":"Post-translational modifications of nuclear receptors and human disease.","abstract":"Nuclear receptors (NR) impact a myriad of physiological processes including homeostasis, reproduction, development, and metabolism. NRs are regulated by post-translational modifications (PTM) that markedly impact receptor function. Recent studies have identified NR PTMs that are involved in the onset and progression of human diseases, including cancer. The majority of evidence linking NR PTMs with disease has been demonstrated for phosphorylation, acetylation and sumoylation of androgen receptor (AR), estrogen receptor α (ERα), glucocorticoid receptor (GR) and peroxisome proliferator activated receptor γ (PPARγ). Phosphorylation of AR has been associated with hormone refractory prostate cancer and decreased disease-specific survival. AR acetylation and sumoylation increased growth of prostate cancer tumor models. AR phosphorylation reduced the toxicity of the expanded polyglutamine AR in Kennedy's Disease as a consequence of reduced ligand binding. A comprehensive evaluation of ERα phosphorylation in breast cancer revealed several sites associated with better clinical outcome to tamoxifen therapy, whereas other phosphorylation sites were associated with poorer clinical outcome. ERα acetylation and sumoylation may also have predictive value for breast cancer. GR phosphorylation and acetylation impact GR responsiveness to glucocorticoids that are used as anti-inflammatory drugs. PPARγ phosphorylation can regulate the balance between growth and differentiation in adipose tissue that is linked to obesity and insulin resistance. Sumoylation of PPARγ is linked to repression of inflammatory genes important in patients with inflammatory diseases. NR PTMs provide an additional measure of NR function that can be used as both biomarkers of disease progression, and predictive markers for patient response to NR-directed treatments.","corpus_id":3651263,"score":1},{"doc_id":"22494029","title":"Post-translational modification of human heat shock factors and their functions: a recent update by proteomic approach.","abstract":"Heat shock factors (HSFs) are vital for modulating stress and heat shock-related gene expression in cells. The activity of HSFs is controlled largely by post-translational modifications (PTMs). For example, basal phosphorylation of HSF1 on three serine sites suppresses the heat shock response, and hyperphosphorylation of HSF1 on several other serine and threonine sites by stress-activated kinases results in its activation, while acetylation on K80 inhibits its DNA-binding ability. Sumoylation of HSF2 on K82 regulates its DNA-binding ability, whereas sumoylation of HSF4B on K293 represses its transcriptional activity. With the advancement of proteomic technology, novel PTM sites on various HSFs have been identified with the use of tandem mass spectrometry (MS/MS), but the functions of many of these PTMs are still unclear. Yet, it should be noted that the discovery of these novel PTM sites provided the necessary evidence for the existence of these PTM marks in vivo. Followed by subsequent functional analysis, this would ultimately lead to a better understanding of these PTM marks. MS/MS-based proteomic approach is becoming a gold standard in PTM validation in the field of life science. Here, the recent literature of all known PTMs reported on human HSFs and the resulting functions will be discussed.","corpus_id":23588597,"score":1},{"doc_id":"22770978","title":"The inside and out of dystroglycan post-translational modification.","abstract":"In neuromuscular systems dystroglycan provides a vital link between laminin in the extracellular matrix and dystrophin in the membrane cytoskeleton. The integrity of this link is maintained and regulated by post-translational modifications of dystroglycan that have effects both inside and outside the cell. Glycosylation of α-dystroglycan is crucial for its link to laminin and phosphorylation of β-dystroglycan on tyrosine regulates its association with intracellular binding partners. This short review focuses on some of the recent developments in our understanding of the role of these post-translational modification in regulating dystroglycan function, and how new knowledge of signalling through the laminin-dystroglycan axis is leading to hope for treatment for some neuromuscular diseases associated with this adhesion complex.","corpus_id":36373326,"score":1},{"doc_id":"23505349","title":"Dual coordination of post translational modifications in human protein networks.","abstract":"Post-translational modifications (PTMs) regulate protein activity, stability and interaction profiles and are critical for cellular functioning. Further regulation is gained through PTM interplay whereby modifications modulate the occurrence of other PTMs or act in combination. Integration of global acetylation, ubiquitination and tyrosine or serine/threonine phosphorylation datasets with protein interaction data identified hundreds of protein complexes that selectively accumulate each PTM, indicating coordinated targeting of specific molecular functions. A second layer of PTM coordination exists in these complexes, mediated by PTM integration (PTMi) spots. PTMi spots represent very dense modification patterns in disordered protein regions and showed an equally high mutation rate as functional protein domains in cancer, inferring equivocal importance for cellular functioning. Systematic PTMi spot identification highlighted more than 300 candidate proteins for combinatorial PTM regulation. This study reveals two global PTM coordination mechanisms and emphasizes dataset integration as requisite in proteomic PTM studies to better predict modification impact on cellular signaling.","corpus_id":2072269,"score":1},{"doc_id":"25308709","title":"The Anaplasma phagocytophilum effector AmpA hijacks host cell SUMOylation.","abstract":"SUMOylation, the covalent attachment of a member of the small ubiquitin-like modifier (SUMO) family of proteins to lysines in target substrates, is an essential post-translational modification in eukaryotes. Microbial manipulation of SUMOylation recently emerged as a key virulence strategy for viruses and facultative intracellular bacteria, the latter of which have only been shown to deploy effectors that negatively regulate SUMOylation. Here, we demonstrate that the obligate intracellular bacterium, Anaplasma phagocytophilum, utilizes an effector, AmpA (A. phagocytophilum post-translationally modified protein A) that becomes SUMOylated in host cells and this is important for the pathogen's survival. We previously discovered that AmpA (formerly APH1387) localizes to the A. phagocytophilum-occupied vacuolar membrane (AVM). Algorithmic prediction analyses denoted AmpA as a candidate for SUMOylation. We verified this phenomenon using a SUMO affinity matrix to precipitate both native AmpA and ectopically expressed green fluorescent protein (GFP)-tagged AmpA. SUMOylation of AmpA was lysine dependent, as SUMO affinity beads failed to precipitate a GFP-AmpA protein when its lysine residues were substituted with arginine. Ectopically expressed and endogenous AmpA were poly-SUMOylated, which was consistent with the observation that AmpA colocalizes with SUMO2/3 at the AVM. Only late during the infection cycle did AmpA colocalize with SUMO1, which terminally caps poly-SUMO2/3 chains. AmpA was also detected in the cytosol of infected host cells, further supporting its secretion and likely participation in interactions that aid pathogen survival. Indeed, whereas siRNA-mediated knockdown of Ubc9 - a necessary enzyme for SUMOylation - slightly bolstered A. phagocytophilum infection, pharmacologically inhibiting SUMOylation in infected cells significantly reduced the bacterial load. Ectopically expressed GFP-AmpA served as a competitive agonist against native AmpA in infected cells, while lysine-deficient GFP-AmpA was less effective, implying that modification of AmpA lysines is important for infection. Collectively, these data show that AmpA becomes directly SUMOylated during infection, representing a novel tactic for A. phagocytophilum survival.","corpus_id":8692466,"score":1},{"doc_id":"27046249","title":"The BECN1 N-terminal domain is intrinsically disordered.","abstract":"BECN1/Beclin 1 has a critical role in the early stages of autophagosome formation. Recently, structures of its central and C-terminal domains were reported, however, little structural information is available on the N-terminal domain, comprising a third of the protein. This lack of structural information largely stems from the inability to produce this region in a purified form. Here, we describe the expression and purification of the N-terminal domain of BECN1 (residues 1 to 150) and detailed biophysical characterization, including NMR spectroscopy. Combined, our studies demonstrated at the atomic level that the BECN1 N-terminal domain is intrinsically disordered, and apart from the BH3 subdomain, remains disordered following interaction with a binding partner, BCL2L1/BCL-XL. In addition, the BH3 domain α-helix induced upon interaction with BCL2L1 reverts to a disordered state when the complex is dissociated by exposure to a competitive inhibitor. No significant interactions between N- and C-terminal domains were detected.","corpus_id":23545910,"score":1},{"doc_id":"27147466","title":"The role of post-translational modifications in hearing and deafness.","abstract":"Post-translational modifications (PTMs) are key molecular events that modify proteins after their synthesis and modulate their ultimate functional properties by affecting their stability, localisation, interaction potential or activity. These chemical changes expand the size of the proteome adding diversity to the molecular pathways governing the biological outcome of cells. PTMs are, thus, crucial in regulating a variety of cellular processes such as apoptosis, proliferation and differentiation and have been shown to be instrumental during embryonic development. In addition, alterations in protein PTMs have been implicated in the pathogenesis of many human diseases, including deafness. In this review, we summarize the recent progress made in understanding the roles of PTMs during cochlear development, with particular emphasis on the enzymes driving protein phosphorylation, acetylation, methylation, glycosylation, ubiquitination and SUMOylation. We also discuss how these enzymes may contribute to hearing impairment and deafness.","corpus_id":657737,"score":1},{"doc_id":"27383850","title":"Identification of BECN1 and ATG14 Coiled-Coil Interface Residues That Are Important for Starvation-Induced Autophagy.","abstract":"Autophagy, an essential eukaryotic homeostasis pathway, allows the sequestration of unwanted, damaged, or harmful cytoplasmic components in vesicles called autophagosomes, permitting subsequent lysosomal degradation and nutrient recycling. Autophagosome nucleation is mediated by class III phosphatidylinositol-3-kinase complexes that include two key autophagy proteins, BECN1/Beclin 1 and ATG14/BARKOR, which form parallel heterodimers via their coiled-coil domains (CCDs). Here we present the 1.46 Å X-ray crystal structure of the antiparallel, human BECN1 CCD homodimer, which represents BECN1 oligomerization outside the autophagosome nucleation complex. We use circular dichroism and small-angle X-ray scattering (SAXS) to show that the ATG14 CCD is significantly disordered but becomes more helical in the BECN1:ATG14 heterodimer, although it is less well-folded than the BECN1 CCD homodimer. SAXS also indicates that the BECN1:ATG14 heterodimer is more curved than other BECN1-containing CCD dimers, which has important implications for the structure of the autophagosome nucleation complex. A model of the BECN1:ATG14 CCD heterodimer that agrees well with the SAXS data shows that BECN1 residues at the homodimer interface are also responsible for heterodimerization, allowing us to identify ATG14 interface residues. Finally, we verify the role of BECN1 and ATG14 interface residues in binding by assessing the impact of point mutations of these residues on co-immunoprecipitation of the partner and demonstrate that these mutations abrogate starvation-induced upregulation of autophagy but do not impact basal autophagy. Thus, this research provides insights into structures of the BECN1 CCD homodimer and the BECN1:ATG14 CCD heterodimer and identifies interface residues that are important for BECN1:ATG14 heterodimerization and for autophagy.","corpus_id":20237132,"score":1},{"doc_id":"27438764","title":"Post-Translational Modification Control of Innate Immunity.","abstract":"A coordinated balance between the positive and negative regulation of pattern-recognition receptor (PRR)-initiated innate inflammatory responses is required to ensure the most favorable outcome for the host. Post-translational modifications (PTMs) of innate sensors and downstream signaling molecules influence their activity and function by inducing their covalent linkage to new functional groups. PTMs including phosphorylation and polyubiquitination have been shown to potently regulate innate inflammatory responses through the activation, cellular translocation, and interaction of innate receptors, adaptors, and downstream signaling molecules in response to infectious and dangerous signals. Other PTMs such as methylation, acetylation, SUMOylation, and succinylation are increasingly implicated in the regulation of innate immunity and inflammation. In this review, we focus on the roles of PTMs in controlling PRR-triggered innate immunity and inflammatory responses. The emerging roles of PTMs in the pathogenesis and potential treatment of infectious and inflammatory immune diseases are also discussed.","corpus_id":5572066,"score":1},{"doc_id":"27713867","title":"Anaplasma phagocytophilum APH0032 Is Exposed on the Cytosolic Face of the Pathogen-Occupied Vacuole and Co-opts Host Cell SUMOylation.","abstract":"Anaplasma phagocytophilum, a member of the family Anaplasmataceae and the obligate intracellular bacterium that causes granulocytic anaplasmosis, resides in a host cell-derived vacuole. Bacterial proteins that localize to the A. phagocytophilum-occupied vacuole membrane (AVM) are critical host-pathogen interfaces. Of the few bacterial AVM proteins that have been identified, the domains responsible for AVM localization and the host cell pathways that they co-opt are poorly defined. APH0032 is an effector that is expressed and localizes to the AVM late during the infection cycle. Herein, the APH0032 domain that is essential for associating with host cell membranes was mapped. Immunofluorescent labeling of infected cells that had been differentially permeabilized confirmed that APH0032 is exposed on the AVM's cytosolic face, signifying its potential to interface with host cell processes. SUMOylation is the covalent attachment of a member of the small ubiquitin-like modifier (SUMO) family of proteins to lysines in target substrates. Previous work from our laboratory determined that SUMOylation is important for A. phagocytophilum survival and that SUMOylated proteins decorate the AVM. Algorithmic prediction analyses identified APH0032 as a candidate for SUMOylation. Endogenous APH0032 was precipitated from infected cells using a SUMO affinity matrix, confirming that the effector co-opts SUMOylation during infection. APH0032 pronouncedly colocalized with SUMO1, but not SUMO2/3 moieties on the AVM. Ectopic expression of APH0032 in A. phagocytophilum infected host cells significantly boosted the bacterial load. This study delineates the first domain of any Anaplasmataceae protein that is essential for associating with the pathogen-occupied vacuole membrane, demonstrates the importance of APH0032 to infection, and identifies it as the second A. phagocytophilum effector that co-opts SUMOylation, thus underscoring the relevance of this post-translational modification to infection.","corpus_id":13655642,"score":1},{"doc_id":"28368777","title":"PINK1 and BECN1 relocalize at mitochondria-associated membranes during mitophagy and promote ER-mitochondria tethering and autophagosome formation.","abstract":"Mitophagy is a highly specialized process to remove dysfunctional or superfluous mitochondria through the macroautophagy/autophagy pathway, aimed at protecting cells from the damage of disordered mitochondrial metabolism and apoptosis induction. PINK1, a neuroprotective protein mutated in autosomal recessive Parkinson disease, has been implicated in the activation of mitophagy by selectively accumulating on depolarized mitochondria, and promoting PARK2/Parkin translocation to them. While these steps have been characterized in depth, less is known about the process and site of autophagosome formation upon mitophagic stimuli. A previous study reported that, in starvation-induced autophagy, the proautophagic protein BECN1/Beclin1 (which we previously showed to interact with PINK1) relocalizes at specific regions of contact between the endoplasmic reticulum (ER) and mitochondria called mitochondria-associated membranes (MAM), from which the autophagosome originates. Here we show that, following mitophagic stimuli, autophagosomes also form at MAM; moreover, endogenous PINK1 and BECN1 were both found to relocalize at MAM, where they promoted the enhancement of ER-mitochondria contact sites and the formation of omegasomes, that represent autophagosome precursors. PARK2 was also enhanced at MAM following mitophagy induction. However, PINK1 silencing impaired BECN1 enrichment at MAM independently of PARK2, suggesting a novel role for PINK1 in regulating mitophagy. MAM have been recently implicated in many key cellular events. In this light, the observed prevalent localization of PINK1 at MAM may well explain other neuroprotective activities of this protein, such as modulation of mitochondrial calcium levels, mitochondrial dynamics, and apoptosis.","corpus_id":205899700,"score":1},{"doc_id":"28408866","title":"Post-translational Modifications and Protein Quality Control in Motor Neuron and Polyglutamine Diseases.","abstract":"Neurodegenerative diseases, including motor neuron and polyglutamine (polyQ) diseases, are a broad class of neurological disorders. These diseases are characterized by neuronal dysfunction and death, and by the accumulation of toxic aggregation-prone proteins in the forms of inclusions and micro-aggregates. Protein quality control is a cellular mechanism to reduce the burden of accumulation of misfolded proteins, a function that results from the coordinated actions of chaperones and degradation systems, such as the ubiquitin-proteasome system (UPS) and autophagy-lysosomal degradation system. The rate of turnover, aggregation and degradation of the disease-causing proteins is modulated by post-translational modifications (PTMs), such as phosphorylation, arginine methylation, palmitoylation, acetylation, SUMOylation, ubiquitination, and proteolytic cleavage. Here, we describe how PTMs of proteins linked to motor neuron and polyQ diseases can either enhance or suppress protein quality control check and protein aggregation and degradation. The identification of molecular strategies targeting these modifications may offer novel avenues for the treatment of these yet incurable diseases.","corpus_id":18837748,"score":1},{"doc_id":"28798234","title":"Structural transitions in conserved, ordered Beclin 1 domains essential to regulating autophagy.","abstract":"Beclin 1 (BECN1) is a key regulator of autophagy, a critical catabolic homeostasis pathway that involves the sequestration of cytoplasmic components by multilayered vesicles called autophagosomes, followed by lysosomal fusion and degradation. BECN1 is a core component of class III phosphatidylinositol-3-kinase complexes responsible for autophagosome nucleation. Without heterologous binding partners, BECN1 forms an antiparallel homodimer via its coiled-coil domain (CCD). However, the last 16 CCD residues, composing an overlap helix (OH), have been crystallized in two mutually exclusive states: either as part of the CCD or packed against the C-terminal lower case β-α-repeated, autophagy-specific domain (BARAD). Here, using circular dichroism (CD) spectroscopy, isothermal titration calorimetry (ITC), and small-angle X-ray scattering (SAXS), we show that in the homodimeric state, the OH transitions between these two different packing states, with the predominant state comprising the OH packed against the BARAD, contrary to expectations based on known BECN1 interactions with heterologous partners. We confirmed this observation by comparing the impact of mutating four residues that mediate packing of the OH against both the CCD and BARAD on structure and stability of the CCD, the OH+BARAD, and the two-domain CCD-BARAD. Lastly, we used cellular assays demonstrating that mutation of these OH-interface residues abrogates starvation-induced up-regulation of autophagy, but does not affect basal autophagy. In summary, we have identified a BECN1 helical region that transitions between packing as part of either one of two conserved domains, i.e. the CCD or the BARAD. Our findings have important implications for the relative stability of autophagy-inactive and autophagy-active BECN1 complexes.","corpus_id":24318140,"score":1},{"doc_id":"28876241","title":"Structural insights into the interaction of the conserved mammalian proteins GAPR-1 and Beclin 1, a key autophagy protein.","abstract":"Mammalian Golgi-associated plant pathogenesis-related protein 1 (GAPR-1) is a negative autophagy regulator that binds Beclin 1, a key component of the autophagosome nucleation complex. Beclin 1 residues 267-284 are required for binding GAPR-1. Here, sequence analyses, structural modeling, mutagenesis combined with pull-down assays, X-ray crystal structure determination and small-angle X-ray scattering were used to investigate the Beclin 1-GAPR-1 interaction. Five conserved residues line an equatorial GAPR-1 surface groove that is large enough to bind a peptide. A model of a peptide comprising Beclin 1 residues 267-284 docked onto GAPR-1, built using the CABS-dock server, indicates that this peptide binds to this GAPR-1 groove. Mutation of the five conserved residues lining this groove, H54A/E86A/G102K/H103A/N138G, abrogates Beclin 1 binding. The 1.27 Å resolution X-ray crystal structure of this pentad mutant GAPR-1 was determined. Comparison with the wild-type (WT) GAPR-1 structure shows that the equatorial groove of the pentad mutant is shallower and more positively charged, and therefore may not efficiently bind Beclin 1 residues 267-284, which include many hydrophobic residues. Both WT and pentad mutant GAPR-1 crystallize as dimers, and in each case the equatorial groove of one subunit is partially occluded by the other subunit, indicating that dimeric GAPR-1 is unlikely to bind Beclin 1. SAXS analysis of WT and pentad mutant GAPR-1 indicates that in solution the WT forms monomers, while the pentad mutant is primarily dimeric. Thus, changes in the structure of the equatorial groove combined with the improved dimerization of pentad mutant GAPR-1 are likely to abrogate binding to Beclin 1.","corpus_id":25331239,"score":1},{"doc_id":"29099291","title":"Post-translational modifications: How to modulate Rab7 functions.","abstract":"The small GTPase Rab7 is the main regulator of membrane trafficking at late endosomes. This small GTPase regulates endosome-to-trans Golgi Network trafficking of sorting receptors, membrane fusion of late endosomes to lysosomes, and autophagosomes to lysosomes during autophagy. Rab7, like all Rab GTPases, binds downstream effectors coordinating several divergent pathways. How cells regulate these interactions and downstream functions is not well understood. Recent evidence suggests that Rab7 function can be modulated by the combination of several post-translational modifications that facilitate interactions with one effector while preventing binding to another one. In this review, we discuss recent data on how phosphorylation, palmitoylation and ubiquitination modulate the ability of this small GTPase to orchestrate membrane trafficking at the late endosomes.","corpus_id":35798382,"score":1},{"doc_id":"29157087","title":"THANATOS: an integrative data resource of proteins and post-translational modifications in the regulation of autophagy.","abstract":"Macroautophagy/autophagy is a highly conserved process for degrading cytoplasmic contents, determines cell survival or death, and regulates the cellular homeostasis. Besides ATG proteins, numerous regulators together with various post-translational modifications (PTMs) are also involved in autophagy. In this work, we collected 4,237 experimentally identified proteins regulated in autophagy and cell death pathways from the literature. Then we computationally identified potential orthologs of known proteins, and developed a comprehensive database of The Autophagy, Necrosis, ApopTosis OrchestratorS (THANATOS, http://thanatos.biocuckoo.org ), containing 191,543 proteins potentially associated with autophagy and cell death pathways in 164 eukaryotes. We performed an evolutionary analysis of ATG genes, and observed that ATGs required for the autophagosome formation are highly conserved across eukaryotes. Further analyses revealed that known cancer genes and drug targets were overrepresented in human autophagy proteins, which were significantly associated in a number of signaling pathways and human diseases. By reconstructing a human kinase-substrate phosphorylation network for ATG proteins, our results confirmed that phosphorylation play a critical role in regulating autophagy. In total, we mapped 65,015 known sites of 11 types of PTMs to collected proteins, and revealed that all types of PTM substrates were enriched in human autophagy. In addition, we observed multiple types of PTM regulators such as protein kinases and ubiquitin E3 ligases or adaptors were significantly associated with human autophagy, and again the results emphasized the importance of PTM regulations in autophagy. We anticipated THANATOS can be a useful resource for further studies.","corpus_id":36543837,"score":1},{"doc_id":"29322920","title":"Investigation and identification of functional post-translational modification sites associated with drug binding and protein-protein interactions.","abstract":"BACKGROUND: Protein post-translational modification (PTM) plays an essential role in various cellular processes that modulates the physical and chemical properties, folding, conformation, stability and activity of proteins, thereby modifying the functions of proteins. The improved throughput of mass spectrometry (MS) or MS/MS technology has not only brought about a surge in proteome-scale studies, but also contributed to a fruitful list of identified PTMs. However, with the increase in the number of identified PTMs, perhaps the more crucial question is what kind of biological mechanisms these PTMs are involved in. This is particularly important in light of the fact that most protein-based pharmaceuticals deliver their therapeutic effects through some form of PTM. Yet, our understanding is still limited with respect to the local effects and frequency of PTM sites near pharmaceutical binding sites and the interfaces of protein-protein interaction (PPI). Understanding PTM's function is critical to our ability to manipulate the biological mechanisms of protein. RESULTS: In this study, to understand the regulation of protein functions by PTMs, we mapped 25,835 PTM sites to proteins with available three-dimensional (3D) structural information in the Protein Data Bank (PDB), including 1785 modified PTM sites on the 3D structure. Based on the acquired structural PTM sites, we proposed to use five properties for the structural characterization of PTM substrate sites: the spatial composition of amino acids, residues and side-chain orientations surrounding the PTM substrate sites, as well as the secondary structure, division of acidity and alkaline residues, and solvent-accessible surface area. We further mapped the structural PTM sites to the structures of drug binding and PPI sites, identifying a total of 1917 PTM sites that may affect PPI and 3951 PTM sites associated with drug-target binding. An integrated analytical platform (CruxPTM), with a variety of methods and online molecular docking tools for exploring the structural characteristics of PTMs, is presented. In addition, all tertiary structures of PTM sites on proteins can be visualized using the JSmol program. CONCLUSION: Resolving the function of PTM sites is important for understanding the role that proteins play in biological mechanisms. Our work attempted to delineate the structural correlation between PTM sites and PPI or drug-target binding. CurxPTM could help scientists narrow the scope of their PTM research and enhance the efficiency of PTM identification in the face of big proteome data. CruxPTM is now available at http://csb.cse.yzu.edu.tw/CruxPTM/ .","corpus_id":1953914,"score":1},{"doc_id":"29536364","title":"Role and Function of the Type IV Secretion System in Anaplasma and Ehrlichia Species.","abstract":"The obligatory intracellular pathogens Anaplasma phagocytophilum and Ehrlichia chaffeensis proliferate within membrane-bound vacuoles of human leukocytes and cause potentially fatal emerging infectious diseases. Despite the reductive genome evolution in this group of bacteria, genes encoding the type IV secretion system (T4SS), which is homologous to the VirB/VirD4 system of the plant pathogen Agrobacterium tumefaciens, have been expanded and are highly expressed in A. phagocytophilum and E. chaffeensis in human cells. Of six T4SS effector proteins identified in them, roles and functions have been described so far only for ankyrin repeat domain-containing protein A (AnkA), Anaplasma translocated substrate 1 (Ats-1), and Ehrlichia translocated factor 1 (Etf-1, ECH0825). These effectors are abundantly produced and secreted into the host cytoplasm during infection, but not toxic to host cells. They contain eukaryotic protein motifs or organelle localization signals and have distinct subcellular localization, target to specific host cell molecules to promote infection. Ats-1 and Etf-1 are orthologous proteins, subvert two important innate immune mechanisms against intracellular infection, cellular apoptosis and autophagy, and manipulate autophagy to gain nutrients from host cells. Although Ats-1 and Etf-1 have similar functions and roles in obligatory intracellular infection, they are specifically adapted to the distinct membrane-bound intracellular niche of A. phagocytophilum and E. chaffeensis, respectively. Ectopic expression of these effectors enhances respective bacterial infection, whereas intracellular delivery of antibodies against these effectors or targeted knockdown of the effector with antisense peptide nucleic acid significantly impairs bacterial infection. Thus, both T4SSs have evolved as important survival and nutritional virulence mechanism in these obligatory intracellular bacteria. Future studies on the functions of Anaplasma and Ehrlichia T4SS effector molecules and signaling pathways will undoubtedly advance our understanding of the complex interplay between obligatory intracellular pathogens and their hosts. Such data can be applied toward the treatment and control of anaplasmosis and ehrlichiosis.","corpus_id":3834894,"score":1},{"doc_id":"20600793","title":"Anaplasma phagocytophilum APH_0032 is expressed late during infection and localizes to the pathogen-occupied vacuolar membrane.","abstract":"Anaplasma phagocytophilum infects neutrophils and myeloid, endothelial, and tick cell lines to reside within a host cell-derived vacuole that is indispensible for its survival. Here, we identify APH_0032 as an Anaplasma-derived protein that associates with the A. phagocytophilum-occupied vacuolar membrane (AVM). APH_0032 is a 66.1 kDa acidic protein that electrophoretically migrates with an apparent molecular weight of 130 kDa. It contains a predicted transmembrane domain and tandemly arranged direct repeats that comprise 46% of the protein. APH_0032 is undetectable on Anaplasma organisms bound to the surfaces of HL-60 cells, but is detected on the AVM and surfaces of intravacuolar bacteria beginning 24 h post-infection. APH_0032 localizes to the AVM in HL-60, THP-1, HMEC-1, and ISE6 cells. APH_0032, along with APH_1387, which encodes a confirmed AVM protein, is transcribed during A. phagocytophilum infection of tick salivary glands and murine neutrophils. APH_0032 localizes to the AVM in neutrophils recovered from infected mice. The Legionella pneumophila Dot/IcM type IV secretion system (T4SS) can heterologously secrete a CyaA-tagged version of the A. phagocytophilum VirB/D T4SS effector, AnkA, but fails to secrete CyaA-tagged APH_0032 or APH_1387. These data confirm APH_0032 as an Anaplasma-derived AVM protein and hint that neither it nor APH_1387 are T4SS effectors.","corpus_id":13536895,"score":0},{"doc_id":"23071137","title":"Anaplasma phagocytophilum Asp14 is an invasin that interacts with mammalian host cells via its C terminus to facilitate infection.","abstract":"Anaplasma phagocytophilum, a member of the family Anaplasmataceae, is the tick-transmitted obligate intracellular bacterium that causes human granulocytic anaplasmosis. The life cycle of A. phagocytophilum is biphasic, transitioning between the noninfectious reticulate cell (RC) and infectious dense-cored (DC) forms. We analyzed the bacterium's DC surface proteome by selective biotinylation of surface proteins, NeutrAvidin affinity purification, and mass spectrometry. Transcriptional profiling of selected outer membrane protein candidates over the course of infection revealed that aph_0248 (designated asp14 [14-kDa A. phagocytophilum surface protein]) expression was upregulated the most during A. phagocytophilum cellular invasion. asp14 transcription was induced during transmission feeding of A. phagocytophilum-infected ticks on mice and was upregulated when the bacterium engaged its receptor, P-selectin glycoprotein ligand 1. Asp14 localized to the A. phagocytophilum surface and was expressed during in vivo infection. Treating DC organisms with Asp14 antiserum or preincubating mammalian host cells with glutathione S-transferase (GST)-Asp14 significantly inhibited infection of host cells. Moreover, preincubating host cells with GST-tagged forms of both Asp14 and outer membrane protein A, another A. phagocytophilum invasin, pronouncedly reduced infection relative to treatment with either protein alone. The Asp14 domain that is sufficient for cellular adherence and invasion lies within the C-terminal 12 to 24 amino acids and is conserved among other Anaplasma and Ehrlichia species. These results identify Asp14 as an A. phagocytophilum surface protein that is critical for infection, delineate its invasion domain, and demonstrate the potential of targeting Asp14 in concert with OmpA for protecting against infection by A. phagocytophilum and other Anaplasmataceae pathogens.","corpus_id":12767334,"score":0},{"doc_id":"23727157","title":"Autophagosome formation--the role of ULK1 and Beclin1-PI3KC3 complexes in setting the stage.","abstract":"Autophagy is a conserved and highly regulated degradative membrane trafficking pathway, maintaining energy homeostasis and protein synthesis during nutrient stress. Our understanding of how the autophagy machinery is regulated has expanded greatly over recent years. The ULK and Beclin1-PI3KC3 complexes are key signaling complexes required for autophagosome formation. The nutrient and energy sensors mTORC1 and AMPK signal directly to the ULK complex and affect its activity. Formation and activation of distinct Beclin1-PI3KC3 complexes produces PI3P, a signaling lipid required for the recruitment of autophagy effectors. In this review we discuss how the mammalian ULK1 and Beclin1 complexes are controlled by post-translational modifications and protein-protein interactions and we highlight data linking these complexes together.","corpus_id":22757669,"score":0},{"doc_id":"24840982","title":"Unconventional post-translational modifications in immunological signaling.","abstract":"The activity of a cell is governed by the signals it receives from the extracellular milieu, which are 'translated' into the appropriate biological output, such as activation, survival, proliferation, migration or differentiation. Signaling pathways are responsible for converting environmental cues into discrete intracellular events. The alteration of existing proteins by post-translational modification (PTM) is a key feature of signal-transduction pathways that allows the modulation of protein function. Research into PTMs has long been dominated by the investigation of protein phosphorylation; other PTMs, such as methylation of lysine and arginine residues, acetylation, and nitrosylation of thiol groups and tyrosine residues, have received comparatively little attention. This Review aims to present an overview of these PTMs, with an emphasis on their role in cells of the immune system.","corpus_id":10016852,"score":0},{"doc_id":"25172281","title":"Investigating interference with apoptosis induction by bacterial proteins.","abstract":"The modulation of host cell apoptosis by bacterial pathogens is critical for their intracellular survival. Several intracellular bacteria achieve this by secreting proteins that interact with apoptosis pathways to inhibit host cell apoptosis. Anaplasma phagocytophilum, which causes human granulocytic anaplasmosis, is such bacterium. The protein Ats-1, translocated from A. phagocytophilum by the bacterial type IV secretion system, localizes to host cell mitochondria, and interferes with apoptosis induction. In this chapter, we present a protocol applied to investigate an anti-apoptotic effect of Ats-1.","corpus_id":40331983,"score":0},{"doc_id":"26351162","title":"[Post-translational modification (PTM) bioinformatics in China: progresses and perspectives].","abstract":"Post-translational modifications (PTMs) are essential for regulating conformational changes, activities and functions of proteins, and are involved in almost all cellular pathways and processes. Identification of protein PTMs is the basis for understanding cellular and molecular mechanisms. In contrast with labor-intensive and time-consuming experiments, the PTM prediction using various bioinformatics approaches can provide accurate, convenient, and efficient strategies and generate valuable information for further experimental consideration. In this review, we summarize the current progresses made by Chineses bioinformaticians in the field of PTM Bioinformatics, including the design and improvement of computational algorithms for predicting PTM substrates and sites, design and maintenance of online and offline tools, establishment of PTM-related databases and resources, and bioinformatics analysis of PTM proteomics data. Through comparing similar studies in China and other countries, we demonstrate both advantages and limitations of current PTM bioinformatics as well as perspectives for future studies in China.","corpus_id":37715772,"score":0},{"doc_id":"26424601","title":"Integrated Metabolomics, Transcriptomics and Proteomics Identifies Metabolic Pathways Affected by Anaplasma phagocytophilum Infection in Tick Cells.","abstract":"Anaplasma phagocytophilum is an emerging zoonotic pathogen that causes human granulocytic anaplasmosis. These intracellular bacteria establish infection by affecting cell function in both the vertebrate host and the tick vector, Ixodes scapularis. Previous studies have characterized the tick transcriptome and proteome in response to A. phagocytophilum infection. However, in the postgenomic era, the integration of omics datasets through a systems biology approach allows network-based analyses to describe the complexity and functionality of biological systems such as host-pathogen interactions and the discovery of new targets for prevention and control of infectious diseases. This study reports the first systems biology integration of metabolomics, transcriptomics, and proteomics data to characterize essential metabolic pathways involved in the tick response to A. phagocytophilum infection. The ISE6 tick cells used in this study constitute a model for hemocytes involved in pathogen infection and immune response. The results showed that infection affected protein processing in endoplasmic reticulum and glucose metabolic pathways in tick cells. These results supported tick-Anaplasma co-evolution by providing new evidence of how tick cells limit pathogen infection, while the pathogen benefits from the tick cell response to establish infection. Additionally, ticks benefit from A. phagocytophilum infection by increasing survival while pathogens guarantee transmission. The results suggested that A. phagocytophilum induces protein misfolding to limit the tick cell response and facilitate infection but requires protein degradation to prevent ER stress and cell apoptosis to survive in infected cells. Additionally, A. phagocytophilum may benefit from the tick cell's ability to limit bacterial infection through PEPCK inhibition leading to decreased glucose metabolism, which also results in the inhibition of cell apoptosis that increases infection of tick cells. These results support the use of this experimental approach to systematically identify cell pathways and molecular mechanisms involved in tick-pathogen interactions. Data are available via ProteomeXchange with identifier PXD002181.","corpus_id":27973649,"score":0},{"doc_id":"26636486","title":"GADD45A inhibits autophagy by regulating the interaction between BECN1 and PIK3C3.","abstract":"GADD45A is a TP53-regulated and DNA damage-inducible tumor suppressor protein, which regulates cell cycle arrest, apoptosis, and DNA repair, and inhibits tumor growth and angiogenesis. However, the function of GADD45A in autophagy remains unknown. In this report, we demonstrate that GADD45A plays an important role in regulating the process of autophagy. GADD45A is able to decrease LC3-II expression and numbers of autophagosomes in mouse tissues and different cancer cell lines. Using bafilomycin A1 treatment, we have observed that GADD45A regulates autophagosome initiation. Likely, GADD45A inhibition of autophagy is through its influence on the interaction between BECN1 and PIK3C3. Immunoprecipitation and GST affinity isolation assays exhibit that GADD45A directly interacts with BECN1, and in turn dissociates the BECN1-PIK3C3 complex. Furthermore, we have mapped the 71 to 81 amino acids of the GADD45A protein that are necessary for the GADD45A interaction with BECN1. Knockdown of BECN1 can abolish autophagy alterations induced by GADD45A. Taken together, these findings provide the novel evidence that GADD45A inhibits autophagy via impairing the BECN1-PIK3C3 complex formation.","corpus_id":32849119,"score":0},{"doc_id":"26714841","title":"Disturbed flow-induced endothelial pro-atherogenic signaling via regulating post-translational modifications and epigenetic events.","abstract":"SIGNIFICANCE: Hemodynamic shear stress, the frictional force exerted onto the vascular endothelial cell (EC) surface, influences vascular EC functions. Atherosclerotic plaque formation in the endothelium is known to be site-specific: disturbed blood flow (d-flow) formed at the lesser curvature of the aortic arch and branch points promotes plaque formation, and steady laminar flow (s-flow) at the greater curvature is athero-protective. Recent Advances: Posttranslational modifications (PTMs), including phosphorylation and SUMOylation, and epigenetic events, including DNA methylation and histone modifications, provide a new perspective on the pathogenesis of atherosclerosis, elucidating how gene expression is altered by d-flow. Activation of PKCζ and p90RSK, SUMOylation of ERK5 and p53, and DNA hypermethylation are uniquely induced by d-flow, but not by s-flow. CRITICAL ISSUES: Extensive crosstalk has been observed among the phosphorylation, SUMOylation, acetylation, and methylation PTMs, as well as among epigenetic events along the cascade of d-flow-induced signaling, from the top (mechanosensory systems) to the bottom (epigenetic events). In addition, PKCζ activation plays a role in regulating SUMOylation-related enzymes of PIAS4, p90RSK activation plays a role in regulating SUMOylation-related enzymes of SENP2, and DNA methyltransferase, SUMOylation may play a role in d-flow signaling. FUTURE DIRECTIONS: Although possible contributions of DNA events such as histone modification and the epigenetic and cytosolic events of PTMs in d-flow signaling have become clearer, determining the interplay of each PTM and epigenetic event will provide a new paradigm to elucidate the difference between d-flow and s-flow and lead to novel therapeutic interventions to inhibit plaque formation.","corpus_id":3740884,"score":0},{"doc_id":"27541856","title":"Ehrlichia secretes Etf-1 to induce autophagy and capture nutrients for its growth through RAB5 and class III phosphatidylinositol 3-kinase.","abstract":"Ehrlichia chaffeensis is an obligatory intracellular bacterium that causes a potentially fatal emerging zoonosis, human monocytic ehrlichiosis. E. chaffeensis has a limited capacity for biosynthesis and metabolism and thus depends mostly on host-synthesized nutrients for growth. Although the host cell cytoplasm is rich with these nutrients, as E. chaffeensis is confined within the early endosome-like membrane-bound compartment, only host nutrients that enter the compartment can be used by this bacterium. How this occurs is unknown. We found that ehrlichial replication depended on autophagy induction involving class III phosphatidylinositol 3-kinase (PtdIns3K) activity, BECN1 (Beclin 1), and ATG5 (autophagy-related 5). Ehrlichia acquired host cell preincorporated amino acids in a class III PtdIns3K-dependent manner and ehrlichial growth was enhanced by treatment with rapamycin, an autophagy inducer. Moreover, ATG5 and RAB5A/B/C were routed to ehrlichial inclusions. RAB5A/B/C siRNA knockdown, or overexpression of a RAB5-specific GTPase-activating protein or dominant-negative RAB5A inhibited ehrlichial infection, indicating the critical role of GTP-bound RAB5 during infection. Both native and ectopically expressed ehrlichial type IV secretion effector protein, Etf-1, bound RAB5 and the autophagy-initiating class III PtdIns3K complex, PIK3C3/VPS34, and BECN1, and homed to ehrlichial inclusions. Ectopically expressed Etf-1 activated class III PtdIns3K as in E. chaffeensis infection and induced autophagosome formation, cleared an aggregation-prone mutant huntingtin protein in a class III PtdIns3K-dependent manner, and enhanced ehrlichial proliferation. These data support the notion that E. chaffeensis secretes Etf-1 to induce autophagy to repurpose the host cytoplasm and capture nutrients for its growth through RAB5 and class III PtdIns3K, while avoiding autolysosomal killing.","corpus_id":11826101,"score":0},{"doc_id":"27715386","title":"BECN1/Beclin 1 sorts cell-surface APP/amyloid β precursor protein for lysosomal degradation.","abstract":"The regulation of plasma membrane (PM)-localized transmembrane protein/receptor trafficking has critical implications for cell signaling, metabolism and survival. In this study, we investigated the role of BECN1 (Beclin 1) in the degradative trafficking of PM-associated APP (amyloid β precursor protein), whose metabolism to amyloid-β, an essential event in Alzheimer disease, is dependent on divergent PM trafficking pathways. We report a novel interaction between PM-associated APP and BECN1 that recruits macroautophagy/endosomal regulatory proteins PIK3C3 and UVRAG. We found that BECN1 promotes surface APP internalization and sorting predominantly to endosomes and endolysosomes. BECN1 also promotes the targeting of a smaller fraction of internalized APP to LC3-positive phagophores, suggesting a role for BECN1-dependent PM macroautophagy in APP degradation. Furthermore, BECN1 facilitates lysosomal degradation of surface APP and reduces the secretion of APP metabolites (soluble ectodomains, sAPP). The association between APP and BECN1 is dependent on the evolutionarily conserved domain (ECD) of BECN1 (amino acids 267-337). Deletion of a BECN1 ECD subregion (amino acids 285-299) did not impair BECN1- PIK3C3 interaction, PtdIns3K function or macroautophagy, but was sufficient to impair the APP-BECN1 interaction and BECN1's effects on surface APP internalization and degradation, resulting in increased secretion of sAPPs. Interestingly, both the BECN1-APP association and BECN1-dependent APP endocytosis and degradative trafficking were negatively regulated by active AKT. Our results further implicate phosphorylation of the BECN1 Ser295 residue in the inhibition of APP degradation by AKT. Our studies reveal a novel function for BECN1 in the sorting of a plasma membrane protein for endolysosomal and macroautophagic degradation.","corpus_id":27028372,"score":0},{"doc_id":"28085066","title":"Mutation-Structure-Function Relationship Based Integrated Strategy Reveals the Potential Impact of Deleterious Missense Mutations in Autophagy Related Proteins on Hepatocellular Carcinoma (HCC): A Comprehensive Informatics Approach.","abstract":"Autophagy, an evolutionary conserved multifaceted lysosome-mediated bulk degradation system, plays a vital role in liver pathologies including hepatocellular carcinoma (HCC). Post-translational modifications (PTMs) and genetic variations in autophagy components have emerged as significant determinants of autophagy related proteins. Identification of a comprehensive spectrum of genetic variations and PTMs of autophagy related proteins and their impact at molecular level will greatly expand our understanding of autophagy based regulation. In this study, we attempted to identify high risk missense mutations that are highly damaging to the structure as well as function of autophagy related proteins including LC3A, LC3B, BECN1 and SCD1. Number of putative structural and functional residues, including several sites that undergo PTMs were also identified. In total, 16 high-risk SNPs in LC3A, 18 in LC3B, 40 in BECN1 and 43 in SCD1 were prioritized. Out of these, 2 in LC3A (K49A, K51A), 1 in LC3B (S92C), 6 in BECN1 (S113R, R292C, R292H, Y338C, S346Y, Y352H) and 6 in SCD1 (Y41C, Y55D, R131W, R135Q, R135W, Y151C) coincide with potential PTM sites. Our integrated analysis found LC3B Y113C, BECN1 I403T, SCD1 R126S and SCD1 Y218C as highly deleterious HCC-associated mutations. This study is the first extensive in silico mutational analysis of the LC3A, LC3B, BECN1 and SCD1 proteins. We hope that the observed results will be a valuable resource for in-depth mechanistic insight into future investigations of pathological missense SNPs using an integrated computational platform.","corpus_id":2362616,"score":0},{"doc_id":"28129024","title":"BECN1-dependent CASP2 incomplete autophagy induction by binding to rabies virus phosphoprotein.","abstract":"Autophagy is an essential component of host immunity and used by viruses for survival. However, the autophagy signaling pathways involved in virus replication are poorly documented. Here, we observed that rabies virus (RABV) infection triggered intracellular autophagosome accumulation and results in incomplete autophagy by inhibiting autophagy flux. Subsequently, we found that RABV infection induced the reduction of CASP2/caspase 2 and the activation of AMP-activated protein kinase (AMPK)-AKT-MTOR (mechanistic target of rapamycin) and AMPK-MAPK (mitogen-activated protein kinase) pathways. Further investigation revealed that BECN1/Beclin 1 binding to viral phosphoprotein (P) induced an incomplete autophagy via activating the pathways CASP2-AMPK-AKT-MTOR and CASP2-AMPK-MAPK by decreasing CASP2. Taken together, our data first reveals a crosstalk of BECN1 and CASP2-dependent autophagy pathways by RABV infection.","corpus_id":18186807,"score":0}],"string":"[\n {\n \"doc_id\": \"17979984\",\n \"title\": \"Subversion of cellular autophagy by Anaplasma phagocytophilum.\",\n \"abstract\": \"Anaplasma phagocytophilum, the causative agent of human granulocytic anaplasmosis, is an obligatory intracellular pathogen. After entry into host cells, the bacterium is diverted from the endosomal pathway and replicates in a membrane-bound compartment devoid of endosomal or lysosomal markers. Here, we show that several hallmarks of early autophagosomes can be identified in A. phagocytophilum replicative inclusions, including a double-lipid bilayer membrane and colocalization with GFP-tagged LC3 and Beclin 1, the human homologues of Saccharomyces cerevisiae autophagy-related proteins Atg8 and Atg6 respectively. While the membrane-associated form of LC3, LC3-II, increased during A. phagocytophilum infection, A. phagocytophilum-containing inclusions enveloped with punctate GFP-LC3 did not colocalize with a lysosomal marker. Stimulation of autophagy by rapamycin favoured A. phagocytophilum infection. Inhibition of the autophagosomal pathway by 3-methyladenine did not inhibit A. phagocytophilum internalization, but reversibly arrested its growth. Although autophagy is considered part of the innate immune system that clears a variety of intracellular pathogens, our study implies that A. phagocytophilum subverts this system to establish itself in an early autophagosome-like compartment segregated from lysosomes to facilitate its proliferation.\",\n \"corpus_id\": 37080350,\n \"score\": 2\n },\n {\n \"doc_id\": \"18286469\",\n \"title\": \"MAPRes: an efficient method to analyze protein sequence around post-translational modification sites.\",\n \"abstract\": \"Functional switches are often regulated by dynamic protein modifications. Assessing protein functions, in vivo, and their functional switches remains still a great challenge in this age of development. An alternative methodology based on in silico procedures may facilitate assessing the multifunctionality of proteins and, in addition, allow predicting functions of those proteins that exhibit their functionality through transitory modifications. Extensive research is ongoing to predict the sequence of protein modification sites and analyze their dynamic nature. This study reports the analysis performed on phosphorylation, Phospho. ELM (version 3.0) and glycosylation, OGlycBase (version 6.0) data for mining association patterns utilizing a newly developed algorithm, MAPRes. This method, MAPRes (Mining Association Patterns among preferred amino acid residues in the vicinity of amino acids targeted for post-translational modifications), is based on mining association among significantly preferred amino acids of neighboring sequence environment and modification sites themselves. Association patterns arrived at by association pattern/rule mining were in significant conformity with the results of different approaches. However, attempts to analyze substrate sequence environment of phosphorylation sites catalyzed for Tyr kinases and the sequence data for O-GlcNAc modification were not successful, due to the limited data available. Using the MAPRes algorithm for developing an association among PTM site with its vicinal amino acids is a valid method with many potential uses: this is indeed the first method ever to apply the association pattern mining technique to protein post-translational modification data.\",\n \"corpus_id\": 40979012,\n \"score\": 2\n },\n {\n \"doc_id\": \"19549291\",\n \"title\": \"A comprehensive resource for integrating and displaying protein post-translational modifications.\",\n \"abstract\": \"BACKGROUND: Protein Post-Translational Modification (PTM) plays an essential role in cellular control mechanisms that adjust protein physical and chemical properties, folding, conformation, stability and activity, thus also altering protein function. FINDINGS: dbPTM (version 1.0), which was developed previously, aimed on a comprehensive collection of protein post-translational modifications. In this update version (dbPTM2.0), we developed a PTM database towards an expert system of protein post-translational modifications. The database comprehensively collects experimental and predictive protein PTM sites. In addition, dbPTM2.0 was extended to a knowledge base comprising the modified sites, solvent accessibility of substrate, protein secondary and tertiary structures, protein domains, protein intrinsic disorder region, and protein variations. Moreover, this work compiles a benchmark to construct evaluation datasets for computational study to identifying PTM sites, such as phosphorylated sites, glycosylated sites, acetylated sites and methylated sites. CONCLUSION: The current release not only provides the sequence-based information, but also annotates the structure-based information for protein post-translational modification. The interface is also designed to facilitate the access to the resource. This effective database is now freely accessible at http://dbPTM.mbc.nctu.edu.tw/.\",\n \"corpus_id\": 2505660,\n \"score\": 2\n },\n {\n \"doc_id\": \"20670295\",\n \"title\": \"Type IV secretion in the obligatory intracellular bacterium Anaplasma phagocytophilum.\",\n \"abstract\": \"Anaplasma phagocytophilum is an obligatory intracellular bacterium that infects neutrophils, the primary host defence cells. Consequent effects of infection on host cells result in a potentially fatal systemic disease called human granulocytic anaplasmosis. Despite ongoing reductive genome evolution and deletion of most genes for intermediary metabolism and amino acid biosynthesis, Anaplasma has also experienced expansion of genes encoding several components of the type IV secretion (T4S) apparatus. Two A. phagocytophilum T4S effector molecules are currently known; Anaplasma translocated substrate 1 (Ats-1) and ankyrin repeat domain-containing protein A (AnkA) have C-terminal positively charged amino acid residues that are recognized by the T4S coupling protein, VirD4. AnkA and Ats-1 contain eukaryotic protein motifs and are uniquely evolved in the family Anaplasmataceae; Ats-1 contains a mitochondria-targeting signal. They are abundantly produced and secreted into the host cytoplasm, are not toxic to host cells, and manipulate host cell processes to aid in the infection process. At the cellular level, the two effectors have distinct subcellular localization and signalling in host cells. Thus in this obligatory intracellular pathogen, the T4S system has evolved as a host-subversive survival factor.\",\n \"corpus_id\": 7712782,\n \"score\": 2\n },\n {\n \"doc_id\": \"20674646\",\n \"title\": \"Post-translational modification by SUMO.\",\n \"abstract\": \"Post-translational modifications (PTMs) are chemical alterations to a protein following translation, regulating stability and function. Reversible phosphorylation is an example of an important and well studied PTM involved in a number of cellular processes. SUMOylation is another PTM known to modify a large number of proteins and plays a role in various cellular processes including: cell cycle regulation, gene transcription, differentiation and cellular localisation. Therefore, understanding the role of SUMOylation in cell biology may allow the development of more efficient models, important in streamlining the drug discovery process. This review will focus on protein SUMOylation and its role in stem cell and somatic cell biology.\",\n \"corpus_id\": 10830819,\n \"score\": 2\n },\n {\n \"doc_id\": \"21053365\",\n \"title\": \"CREB in long-term potentiation in hippocampus: role of post-translational modifications-studies In silico.\",\n \"abstract\": \"The multifunctionality of proteins is dictated by post-translational modifications (PTMs) which involve the attachment of small functional groups such as phosphate and acetate, as well as carbohydrate moieties. These functional groups make the protein perform various functions in different environments. PTMs play a crucial role in memory and learning. Phosphorylation of synaptic proteins and transcription factors regulate the generation and storage of memory. Among these is the cAMP-regulated element binding protein CREB that regulates CRE containing genes like c-fos. Both phosphorylation and acetylation control the function of CREB as a transcription factor. CREB is also susceptible to O-GlcNAc modification, which inhibits its activity. O-GlcNAc modification occurs on the same or neighboring Ser/Thr residues akin to phosphorylation. An interplay between these modifications was shown to operate in nuclear and cytoplasmic proteins. In this study computational methods were utilized to predict different modification sites in CREB. These in silico results suggest that phosphorylation, O-GlcNAc modification and acetylation modulate the transcriptional activity of CREB and thus dictate its contribution to synaptic plasticity.\",\n \"corpus_id\": 27770274,\n \"score\": 2\n },\n {\n \"doc_id\": \"21617949\",\n \"title\": \"Role of post translational modifications and novel crosstalk between phosphorylation and O-beta-GlcNAc modifications in human claudin-1, -3 and -4.\",\n \"abstract\": \"The precise characterization of post translational modifications (PTMs) is important for the understanding of protein regulatory mechanisms and their role in disease. However, experimental studies on PTMs, especially with multifunctional proteins are difficult to follow and investigate. Bioinformatic tools are therefore helpful in predicting key protein modifications. To study the role of PTMs in claudin proteins, specifically claudin-1, -3 and -4 in the onset or progression of human cancers, we performed an in silico study of various PTMs and investigated their interplay. Given that the activity of claudins is known to be influenced by two types of PTMs, specifically palmitoylation and kinase- dependent phosphorylation, we predicted two conserved regions in the topological domains of claudin-1, -3 and -4 as potential palmitoylation sites. Furthermore, conserved phosphorylation residues, which may be targets for kinases and can alter claudin's ability to maintain the integrity of tight junctions, were identified. To our knowledge, this is the first report to suggest O-glycosylation of claudin proteins, as well as a potential novel interplay between phosphorylation and O-glycosylation at Yin Yang sites. Thus, our findings may facilitate the production of anti-cancer drugs, and suggest that novel therapeutic strategies should target post translational events.\",\n \"corpus_id\": 6333545,\n \"score\": 2\n },\n {\n \"doc_id\": \"22212234\",\n \"title\": \"Subversion of NPC1 pathway of cholesterol transport by Anaplasma phagocytophilum.\",\n \"abstract\": \"Intracellular cholesterol amounts, distribution and traffic are tightly regulated to maintain the healthy eukaryotic cell function. However, how intracellular pathogens that require cholesterol, interact with the host cholesterol homeostasis and traffic is not well understood. Anaplasma phagocytophilum is an obligatory intracellular and cholesterol-robbing bacterium, which causes human granulocytic anaplasmosis. Here we found that a subset of cholesterol-binding membrane protein, Niemann-Pick type C1 (NPC1)-bearing vesicles devoid of lysosomal markers were upregulated in HL-60 cells infected with A. phagocytophilum, and trafficked to live bacterial inclusions. The NPC1 localization to A. phagocytophilum inclusions was abolished by low-density lipoprotein (LDL)-derived cholesterol traffic inhibitor U18666A. Studies using NPC1 siRNA and the cell line with cholesterol traffic defect demonstrated that the NPC1 function is required for bacterial cholesterol acquisition and infection. Furthermore, trans-Golgi network-specific soluble N-ethylmaleimide-sensitive factor attachment protein receptors, vesicle-associated membrane protein (VAMP4) and syntaxin 16, which are associated with NPC1 and LDL-derived cholesterol vesicular transport were recruited to A. phagocytophilum inclusions, and VAMP4 was required for bacteria infection. Taken together, A. phagocytophilum is the first example of a pathogen that subverts the NPC1 pathway of intracellular cholesterol transport and homeostasis for bacterial inclusion membrane biogenesis and cholesterol capture.\",\n \"corpus_id\": 43726533,\n \"score\": 2\n },\n {\n \"doc_id\": \"22708570\",\n \"title\": \"Prediction of lysine post-translational modifications using bioinformatic tools.\",\n \"abstract\": \"Our understanding of the importance of lysine post-translational modifications in mediating protein function has led to a significant improvement in the experimental tools aimed at characterizing their existence. Nevertheless, it remains likely that at present we have only experimentally detected a small fraction of all lysine modification sites across the commonly studied proteomes. As a result, online computational tools aimed at predicting lysine modification sites have the potential to provide valuable insight to researchers developing hypotheses regarding these modifications. This chapter discusses the metrics and procedures used to assess predictive tools and surveys 11 online computational tools aimed at the prediction of the four most widely studied lysine post-translational modifications (acetylation, methylation, SUMOylation and ubiquitination). Analyses using unbiased testing data sets suggest that nine of the 11 lysine post-translational modification tools perform no better than random, or have false-positive rates which make them unusable by the experimental biologist, despite self-reported sensitivity and specificity values to the contrary. The implications of these findings for those using and creating lysine post-translational modification software are discussed.\",\n \"corpus_id\": 25292764,\n \"score\": 2\n },\n {\n \"doc_id\": \"23197835\",\n \"title\": \"Autophagosomes induced by a bacterial Beclin 1 binding protein facilitate obligatory intracellular infection.\",\n \"abstract\": \"Autophagy, a cytoplasmic catabolic process, plays a critical role in defense against intracellular infection. In turn, evasion or inhibition of autophagy has emerged as an important virulence factor for intracellular pathogens. However, Anaplasma phagocytophilum, the obligatory intracellular bacterium that causes human granulocytic anaplasmosis, replicates in the membrane-bound compartment resembling early autophagosome. Here, we found that Anaplasma translocated substrate 1 (Ats-1), a type IV secretion effector, binds Beclin 1, a subunit of the class III PI3K and Atg14L, and it nucleates autophagosomes with markers of omegasomes, double FYVE-containing protein 1, Atg14L, and LC3. Ats-1 autophagy induction did not activate the starvation signaling pathway of mammalian target of rapamycin. These autophagy proteins were also localized to the Anaplasma inclusion. Ectopically expressed Ats-1 targeted the Anaplasma inclusions and enhanced infection, whereas host cytoplasmic delivery of anti-Ats-1 or Beclin 1 depletion by siRNA suppressed the infection; beclin 1 heterozygous-deficient mice were resistant to Anaplasma infection. Furthermore, Anaplasma growth arrest by the class III PI3K inhibitor 3-methyladenine was alleviated by essential amino acid supplementation. Thus, Anaplasma actively induces autophagy by secreting Ats-1 that hijacks the Beclin 1-Atg14L autophagy initiation pathway likely to acquire host nutrients for its growth.\",\n \"corpus_id\": 11691354,\n \"score\": 2\n },\n {\n \"doc_id\": \"23387271\",\n \"title\": \"[Bioinformatic analysis of potential post-translational modification sites of the human O6-methylguanine-DNA methyltransferase (MGMT) protein].\",\n \"abstract\": \"Using in silico analysis a number of potential sites for post-translational modifications has been revealed within the human O6-methylguanine-DNA methyltransferase (MGMT) protein. In particular these were the acetylation of Gly3 residue in the N-terminus of protein and internal residues Lys132 and Lys135; Arg166 residue methylation; Lys63 SUMOylation and ubiquitination of Lys31, Lys39, Lys49, Lys63, Lys67, Lys135, Lys156, Lys196, Lys209. Also it has been predicted 16 novel potential phosphorylation sites of serine residues (positions 13, 124, 144, 182, 183, 190, 215, 216 and 230), tyrosine residues (positions 100 and 189) and threonine residues (positions 23, 69, 94, 126 and 229), as well as five binding sites for kinases and other proteins (Serl3 with 14-3-3, Val21 and Ile172 with D-domain, Pro78 and Pro111 with SH3-domain, Pro111 with MAPK3). Some kinases predicted by the authors are known as partners of the MGMT protein, that confirms the probability of modification of the given sites. Potential sites require further experimental confirmation of modifications and investigation of their influence on stability and DNA-repair activity of this protein.\",\n \"corpus_id\": 26535998,\n \"score\": 2\n },\n {\n \"doc_id\": \"23388398\",\n \"title\": \"Ats-1: a novel bacterial molecule that links autophagy to bacterial nutrition.\",\n \"abstract\": \"Obligatory intracellular life style and a small number of genes for biosynthesis and metabolism necessitate the Gram-negative bacterium, Anaplasma phagocytophilum, to depend on the host cell for nutrients. A. phagocytophilum resides in a membrane-bound inclusion, and secretes a protein, Ats-1 (Anaplasma translocated substrate-1), into the host cell cytoplasm. Ats-1 binds BECN1, a protein critical for autophagy nucleation, and induces autophagosome formation. The autophagosomes traffic to, and fuse with, A. phagocytophilum inclusions, delivering autophagic cargo into the inclusions, which can serve as nutrients for bacterial growth. This finding demonstrates that A. phagocytophilum subverts host cell autophagic machinery to facilitate infection by secreting a BECN1-binding molecule.\",\n \"corpus_id\": 207508030,\n \"score\": 2\n },\n {\n \"doc_id\": \"24556839\",\n \"title\": \"Post-translational modifications of intermediate filament proteins: mechanisms and functions.\",\n \"abstract\": \"Intermediate filaments (IFs) are cytoskeletal and nucleoskeletal structures that provide mechanical and stress-coping resilience to cells, contribute to subcellular and tissue-specific biological functions, and facilitate intracellular communication. IFs, including nuclear lamins and those in the cytoplasm (keratins, vimentin, desmin, neurofilaments and glial fibrillary acidic protein, among others), are functionally regulated by post-translational modifications (PTMs). Proteomic advances highlight the enormous complexity and regulatory potential of IF protein PTMs, which include phosphorylation, glycosylation, sumoylation, acetylation and prenylation, with novel modifications becoming increasingly appreciated. Future studies will need to characterize their on-off mechanisms, crosstalk and utility as biomarkers and targets for diseases involving the IF cytoskeleton.\",\n \"corpus_id\": 28089575,\n \"score\": 2\n },\n {\n \"doc_id\": \"25120100\",\n \"title\": \"In-silico analysis of claudin-5 reveals novel putative sites for post-translational modifications: Insights into potential molecular determinants of blood-brain barrier breach during HIV-1 infiltration.\",\n \"abstract\": \"The blood-brain barrier (BBB) poses a huge challenge and is a serious issue in deciphering the pathophysiology of central nervous system disorders. Endothelial tight junctions play an essential role in maintaining the integrity of the BBB. Post-translational modifications (PTMs) in endothelial tight junction proteins are known to cause deleterious functional impairment and possible disruptions in BBB integrity. PTMs in tight junction proteins play an important role in human immunodeficiency virus type 1 (HIV-1) entry through the BBB. Human claudin-5 is one of the highly expressed brain endothelial tight junction protein and various PTMs in claudin-5 are expected to aid HIV-1 in crossing the BBB. A precise characterization of PTMs in claudin-5 is important for understanding its role in HIV-1 brain infiltration. In this study, we have examined post-translational crosstalk between phosphorylation, O-glycosylation, palmitoylation and methylation sites in claudin-5, which could alter claudin-5's ability to maintain BBB integrity. To the best of our knowledge, this is the first report on claudin-5 protein that suggests a novel interplay between potential PTM sites. PTMs of predicted residues in claudin-5, suggested in this study, can serve as compelling targets for potential therapeutic agents against HIV-1 induced neuropathogenesis. Further site-specific experimental studies in this aspect are highly recommended.\",\n \"corpus_id\": 10115867,\n \"score\": 2\n },\n {\n \"doc_id\": \"25365205\",\n \"title\": \"Regulation of autophagy by protein post-translational modification.\",\n \"abstract\": \"Autophagy is a lysosome-mediated intracellular protein degradation process that involves about 38 autophagy-related genes as well as key signaling pathways that sense cellular metabolic and redox status, and has an important role in quality control of macromolecules and organelles. As with other major cellular pathways, autophagy proteins are subjected to regulatory post-translational modification. Phosphorylation is so far the most intensively studied post-translational modification in the autophagy process, followed by ubiquitination and acetylation. An interesting and new area is also now emerging, which appears to complement these more traditional mechanisms, and includes O-GlcNAcylation and redox regulation at thiol residues. Identification of the full spectrum of post-translational modifications of autophagy proteins, and determination of their impact on autophagy will be crucial for a better understanding of autophagy regulation, its deficits in diseases, and how to exploit this process for disease therapies.\",\n \"corpus_id\": 35552001,\n \"score\": 2\n },\n {\n \"doc_id\": \"25484070\",\n \"title\": \"Posttranslational modification of autophagy-related proteins in macroautophagy.\",\n \"abstract\": \"Macroautophagy is an intracellular catabolic process involved in the formation of multiple membrane structures ranging from phagophores to autophagosomes and autolysosomes. Dysfunction of macroautophagy is implicated in both physiological and pathological conditions. To date, 38 autophagy-related (ATG) genes have been identified as controlling these complicated membrane dynamics during macroautophagy in yeast; approximately half of these genes are clearly conserved up to human, and there are additional genes whose products function in autophagy in higher eukaryotes that are not found in yeast. The function of the ATG proteins, in particular their ability to interact with a number of macroautophagic regulators, is modulated by posttranslational modifications (PTMs) such as phosphorylation, glycosylation, ubiquitination, acetylation, lipidation, and proteolysis. In this review, we summarize our current knowledge of the role of ATG protein PTMs and their functional relevance in macroautophagy. Unraveling how these PTMs regulate ATG protein function during macroautophagy will not only reveal fundamental mechanistic insights into the regulatory process, but also provide new therapeutic targets for the treatment of autophagy-associated diseases.\",\n \"corpus_id\": 32079965,\n \"score\": 2\n },\n {\n \"doc_id\": \"25605461\",\n \"title\": \"Systematic characterization and prediction of post-translational modification cross-talk.\",\n \"abstract\": \"Post-translational modification (PTM)(1) plays an important role in regulating the functions of proteins. PTMs of multiple residues on one protein may work together to determine a functional outcome, which is known as PTM cross-talk. Identification of PTM cross-talks is an emerging theme in proteomics and has elicited great interest, but their properties remain to be systematically characterized. To this end, we collected 193 PTM cross-talk pairs in 77 human proteins from the literature and then tested location preference and co-evolution at the residue and modification levels. We found that cross-talk events preferentially occurred among nearby PTM sites, especially in disordered protein regions, and cross-talk pairs tended to co-evolve. Given the properties of PTM cross-talk pairs, a naïve Bayes classifier integrating different features was built to predict cross-talks for pairwise combination of PTM sites. By using a 10-fold cross-validation, the integrated prediction model showed an area under the receiver operating characteristic (ROC) curve of 0.833, superior to using any individual feature alone. The prediction performance was also demonstrated to be robust to the biases in the collected PTM cross-talk pairs. The integrated approach has the potential for large-scale prioritization of PTM cross-talk candidates for functional validation and was implemented as a web server available at http://bioinfo.bjmu.edu.cn/ptm-x/.\",\n \"corpus_id\": 25404416,\n \"score\": 2\n },\n {\n \"doc_id\": \"26344496\",\n \"title\": \"A novel method for predicting post-translational modifications on serine and threonine sites by using site-modification network profiles.\",\n \"abstract\": \"Post-translational modifications (PTMs) regulate many aspects of biological behaviours including protein-protein interactions and cellular processes. Identification of PTM sites is helpful for understanding the PTM regulatory mechanisms. The PTMs on serine and threonine sites include phosphorylation, O-linked glycosylation and acetylation. Although a lot of computational approaches have been developed for PTM site prediction, currently most of them generate the predictive models by employing only local sequence information and few of them consider the relationship between different PTMs. In this paper, by adopting the site-modification network (SMNet) profiles that efficiently incorporate in situ PTM information, we develop a novel method to predict PTM sites on serine and threonine. PTM data are collected from various PTM databases and the SMNet is built to reflect the relationship between multiple PTMs, from which SMNet profiles are extracted to train predictive models based on SVM. Performance analysis of the SVM models shows that the SMNet profiles play an important role in accurately predicting PTM sites on serine and threonine. Furthermore, the proposed method is compared with existing PTM prediction approaches. The results from 10-fold cross-validation demonstrate that the proposed method with SMNet profiles performs remarkably better than existing methods, suggesting the power of SMNet profiles in identifying PTM sites.\",\n \"corpus_id\": 205973316,\n \"score\": 2\n },\n {\n \"doc_id\": \"27174170\",\n \"title\": \"A homology-based pipeline for global prediction of post-translational modification sites.\",\n \"abstract\": \"The pathways of protein post-translational modifications (PTMs) have been shown to play particularly important roles for almost any biological process. Identification of PTM substrates along with information on the exact sites is fundamental for fully understanding or controlling biological processes. Alternative computational strategies would help to annotate PTMs in a high-throughput manner. Traditional algorithms are suited for identifying the common organisms and tissues that have a complete PTM atlas or extensive experimental data. While annotation of rare PTMs in most organisms is a clear challenge. In this work, to this end we have developed a novel homology-based pipeline named PTMProber that allows identification of potential modification sites for most of the proteomes lacking PTMs data. Cross-promotion E-value (CPE) as stringent benchmark has been used in our pipeline to evaluate homology to known modification sites. Independent-validation tests show that PTMProber achieves over 58.8% recall with high precision by CPE benchmark. Comparisons with other machine-learning tools show that PTMProber pipeline performs better on general predictions. In addition, we developed a web-based tool to integrate this pipeline at http://bioinfo.ncu.edu.cn/PTMProber/index.aspx. In addition to pre-constructed prediction models of PTM, the website provides an extensional functionality to allow users to customize models.\",\n \"corpus_id\": 205697208,\n \"score\": 2\n },\n {\n \"doc_id\": \"27367363\",\n \"title\": \"DAPPLE 2: a Tool for the Homology-Based Prediction of Post-Translational Modification Sites.\",\n \"abstract\": \"The post-translational modification of proteins is critical for regulating their function. Although many post-translational modification sites have been experimentally determined, particularly in certain model organisms, experimental knowledge of these sites is severely lacking for many species. Thus, it is important to be able to predict sites of post-translational modification in such species. Previously, we described DAPPLE, a tool that facilitates the homology-based prediction of one particular post-translational modification, phosphorylation, in an organism of interest using known phosphorylation sites from other organisms. Here, we describe DAPPLE 2, which expands and improves upon DAPPLE in three major ways. First, it predicts sites for many post-translational modifications (20 different types) using data from several sources (15 online databases). Second, it has the ability to make predictions approximately 2-7 times faster than DAPPLE depending on the database size and the organism of interest. Third, it simplifies and accelerates the process of selecting predicted sites of interest by categorizing them based on gene ontology terms, keywords, and signaling pathways. We show that DAPPLE 2 can successfully predict known human post-translational modification sites using, as input, known sites from species that are either closely (e.g., mouse) or distantly (e.g., yeast) related to humans. DAPPLE 2 can be accessed at http://saphire.usask.ca/saphire/dapple2 .\",\n \"corpus_id\": 24513686,\n \"score\": 2\n },\n {\n \"doc_id\": \"27414988\",\n \"title\": \"Conformational flexibility of BECN1: Essential to its key role in autophagy and beyond.\",\n \"abstract\": \"BECN1 (Beclin 1), a highly conserved eukaryotic protein, is a key regulator of autophagy, a cellular homeostasis pathway, and also participates in vacuolar protein sorting, endocytic trafficking, and apoptosis. BECN1 is important for embryonic development, the innate immune response, tumor suppression, and protection against neurodegenerative disorders, diabetes, and heart disease. BECN1 mediates autophagy as a core component of the class III phosphatidylinositol 3-kinase complexes. However, the exact mechanism by which it regulates the activity of these complexes, or mediates its other diverse functions is unclear. BECN1 interacts with several diverse protein partners, perhaps serving as a scaffold or interaction hub for autophagy. Based on extensive structural, biophysical and bioinformatics analyses, BECN1 consists of an intrinsically disordered region (IDR), which includes a BH3 homology domain (BH3D); a flexible helical domain (FHD); a coiled-coil domain (CCD); and a β-α-repeated autophagy-specific domain (BARAD). Each of these BECN1 domains mediates multiple diverse interactions that involve concomitant conformational changes. Thus, BECN1 conformational flexibility likely plays a key role in facilitating diverse protein interactions. Further, BECN1 conformation and interactions are also modulated by numerous post-translational modifications. A better structure-based understanding of the interplay between different BECN1 conformational and binding states, and the impact of post-translational modifications will be essential to elucidating the mechanism of its multiple biological roles.\",\n \"corpus_id\": 206393147,\n \"score\": 2\n },\n {\n \"doc_id\": \"27534850\",\n \"title\": \"A machine learning strategy for predicting localization of post-translational modification sites in protein-protein interacting regions.\",\n \"abstract\": \"BACKGROUND: One very important functional domain of proteins is the protein-protein interacting region (PPIR), which forms the binding interface between interacting polypeptide chains. Post-translational modifications (PTMs) that occur in the PPIR can either interfere with or facilitate the interaction between proteins. The ability to predict whether sites of protein modifications are inside or outside of PPIRs would be useful in further elucidating the regulatory mechanisms by which modifications of specific proteins regulate their cellular functions. RESULTS: Using two of the comprehensive databases for protein-protein interaction and protein modification site data (PDB and PhosphoSitePlus, respectively), we created new databases that map PTMs to their locations inside or outside of PPIRs. The mapped PTMs represented only 5 % of all known PTMs. Thus, in order to predict localization within or outside of PPIRs for the vast majority of PTMs, a machine learning strategy was used to generate predictive models from these mapped databases. For the three mapped PTM databases which had sufficient numbers of modification sites for generating models (acetylation, phosphorylation, and ubiquitylation), the resulting models yielded high overall predictive performance as judged by a combined performance score (CPS). Among the multiple properties of amino acids that were used in the classification tasks, hydrophobicity was found to contribute substantially to the performance of the final predictive models. Compared to the other classifiers we also evaluated, the SVM provided the best performance overall. CONCLUSIONS: These models are the first to predict whether PTMs are located inside or outside of PPIRs, as demonstrated by their high predictive performance. The models and data presented here should be useful in prioritizing both known and newly identified PTMs for further studies to determine the functional relationship between specific PTMs and protein-protein interactions. The implemented R package is available online ( http://sysbio.chula.ac.th/PtmPPIR ).\",\n \"corpus_id\": 15910362,\n \"score\": 2\n },\n {\n \"doc_id\": \"28356000\",\n \"title\": \"New Achievements in Bioinformatics Prediction of Post Translational Modification of Proteins.\",\n \"abstract\": \"Post translational modification (PTM) is one of the critical levels in regulation of gene expression that determines the fate of proteins after translation in eukaryotic cells. Since the detection of PTM sites in proteins is useful for diagnosis and prevention of diseases, numerous web-tool predictors are introduced to predict various types of PTMs. In this paper, an attempt is made to summarize a number of server predictors for the prediction of PTM sites.\",\n \"corpus_id\": 38700278,\n \"score\": 2\n },\n {\n \"doc_id\": \"28458782\",\n \"title\": \"Protein post-translational modifications: In silico prediction tools and molecular modeling.\",\n \"abstract\": \"Post-translational modifications (PTMs) occur in almost all proteins and play an important role in numerous biological processes by significantly affecting proteins' structure and dynamics. Several computational approaches have been developed to study PTMs (e.g., phosphorylation, sumoylation or palmitoylation) showing the importance of these techniques in predicting modified sites that can be further investigated with experimental approaches. In this review, we summarize some of the available online platforms and their contribution in the study of PTMs. Moreover, we discuss the emerging capabilities of molecular modeling and simulation that are able to complement these bioinformatics methods, providing deeper molecular insights into the biological function of post-translational modified proteins.\",\n \"corpus_id\": 6342639,\n \"score\": 2\n },\n {\n \"doc_id\": \"28462053\",\n \"title\": \"Prediction of post-translational modification sites using multiple kernel support vector machine.\",\n \"abstract\": \"Protein post-translational modification (PTM) is an important mechanism that is involved in the regulation of protein function. Considering the high-cost and labor-intensive of experimental identification, many computational prediction methods are currently available for the prediction of PTM sites by using protein local sequence information in the context of conserved motif. Here we proposed a novel computational method by using the combination of multiple kernel support vector machines (SVM) for predicting PTM sites including phosphorylation, O-linked glycosylation, acetylation, sulfation and nitration. To largely make use of local sequence information and site-modification relationships, we developed a local sequence kernel and Gaussian interaction profile kernel, respectively. Multiple kernels were further combined to train SVM for efficiently leveraging kernel information to boost predictive performance. We compared the proposed method with existing PTM prediction methods. The experimental results revealed that the proposed method performed comparable or better performance than the existing prediction methods, suggesting the feasibility of the developed kernels and the usefulness of the proposed method in PTM sites prediction.\",\n \"corpus_id\": 268578,\n \"score\": 2\n },\n {\n \"doc_id\": \"29185708\",\n \"title\": \"The Autophagy-Related Beclin-1 Protein Requires the Coiled-Coil and BARA Domains To Form a Homodimer with Submicromolar Affinity.\",\n \"abstract\": \"Beclin-1 (BECN1) is an essential component of macroautophagy. This process is a highly conserved survival mechanism that recycles damaged cellular components or pathogens by encasing them in a bilayer vesicle that fuses with a lysosome to allow degradation of the vesicular contents. Mutations or altered expression profiles of BECN1 have been linked to various cancers and neurodegenerative diseases. Viruses, including HIV and herpes simplex virus 1 (HSV-1), are also known to specifically target BECN1 as a means of evading host defense mechanisms. Autophagy is regulated by the interaction between BECN1 and Bcl-2, a pro-survival protein in the apoptotic pathway that stabilizes the BECN1 homodimer. Disruption of the homodimer by phosphorylation or competitive binding promotes autophagy through an unknown mechanism. We report here the first recombinant synthesis (3-5 mg/L in an Escherichia coli culture) and characterization of full-length, human BECN1. Our analysis reveals that full-length BECN1 exists as a soluble homodimer (KD ∼ 0.45 μM) that interacts with Bcl-2 (KD = 4.3 ± 1.2 μM) and binds to lipid membranes. Dimerization is proposed to be mediated by a coiled-coil region of BECN1. A construct lacking the C-terminal BARA domain but including the coiled-coil region exhibits a homodimer KD 3.5-fold weaker than that of full-length BECN1, indicating that both the BARA domain and the coiled-coil region of BECN1 contribute to dimer formation. Using site-directed mutagenesis, we show that residues at the C-terminus of the coiled-coil region previously shown to interact with the BARA domain play a key role in dimerization and mutations weaken the interface by ∼5-fold.\",\n \"corpus_id\": 206518010,\n \"score\": 2\n },\n {\n \"doc_id\": \"20174550\",\n \"title\": \"Anaplasma phagocytophilum Ats-1 is imported into host cell mitochondria and interferes with apoptosis induction.\",\n \"abstract\": \"Anaplasma phagocytophilum, the causative agent of human granulocytic anaplasmosis, infects human neutrophils and inhibits mitochondria-mediated apoptosis. Bacterial factors involved in this process are unknown. In the present study, we screened a genomic DNA library of A. phagocytophilum for effectors of the type IV secretion system by a bacterial two-hybrid system, using A. phagocytophilum VirD4 as bait. A hypothetical protein was identified as a putative effector, hereby named Anaplasmatranslocated substrate 1 (Ats-1). Using triple immunofluorescence labeling and Western blot analysis of infected cells, including human neutrophils, we determined that Ats-1 is abundantly expressed by A. phagocytophilum, translocated across the inclusion membrane, localized in the host cell mitochondria, and cleaved. Ectopically expressed Ats-1 targeted mitochondria in an N-terminal 17 residue-dependent manner, localized in matrix or at the inner membrane, and was cleaved as native protein, which required residues 55-57. In vitro-translated Ats-1 was imported in a receptor-dependent manner into isolated mitochondria. Ats-1 inhibited etoposide-induced cytochrome c release from mitochondria, PARP cleavage, and apoptosis in mammalian cells, as well as Bax-induced yeast apoptosis. Ats-1(55-57) had significantly reduced anti-apoptotic activity. Bax redistribution was inhibited in both etoposide-induced and Bax-induced apoptosis by Ats-1. Taken together, Ats-1 is the first example of a bacterial protein that traverses five membranes and prevents apoptosis at the mitochondria.\",\n \"corpus_id\": 6867624,\n \"score\": 1\n },\n {\n \"doc_id\": \"20559548\",\n \"title\": \"Regulation of amyloid precursor protein processing by the Beclin 1 complex.\",\n \"abstract\": \"Autophagy is an intracellular degradation pathway that functions in protein and organelle turnover in response to starvation and cellular stress. Autophagy is initiated by the formation of a complex containing Beclin 1 (BECN1) and its binding partner Phosphoinositide-3-kinase, class 3 (PIK3C3). Recently, BECN1 deficiency was shown to enhance the pathology of a mouse model of Alzheimer Disease (AD). However, the mechanism by which BECN1 or autophagy mediate these effects are unknown. Here, we report that the levels of Amyloid precursor protein (APP) and its metabolites can be reduced through autophagy activation, indicating that they are a substrate for autophagy. Furthermore, we find that knockdown of Becn1 in cell culture increases the levels of APP and its metabolites. Accumulation of APP and APP C-terminal fragments (APP-CTF) are accompanied by impaired autophagosomal clearance. Pharmacological inhibition of autophagosomal-lysosomal degradation causes a comparable accumulation of APP and APP-metabolites in autophagosomes. Becn1 reduction in cell culture leads to lower levels of its binding partner Pik3c3 and increased presence of Microtubule-associated protein 1, light chain 3 (LC3). Overexpression of Becn1, on the other hand, reduces cellular APP levels. In line with these observations, we detected less BECN1 and PIK3C3 but more LC3 protein in brains of AD patients. We conclude that BECN1 regulates APP processing and turnover. BECN1 is involved in autophagy initiation and autophagosome clearance. Accordingly, BECN1 deficiency disrupts cellular autophagy and autophagosomal-lysosomal degradation and alters APP metabolism. Together, our findings suggest that autophagy and the BECN1-PIK3C3 complex regulate APP processing and play an important role in AD pathology.\",\n \"corpus_id\": 1915839,\n \"score\": 1\n },\n {\n \"doc_id\": \"22164248\",\n \"title\": \"Bioinformatic analysis and post-translational modification crosstalk prediction of lysine acetylation.\",\n \"abstract\": \"Recent proteomics studies suggest high abundance and a much wider role for lysine acetylation (K-Ac) in cellular functions. Nevertheless, cross influence between K-Ac and other post-translational modifications (PTMs) has not been carefully examined. Here, we used a variety of bioinformatics tools to analyze several available K-Ac datasets. Using gene ontology databases, we demonstrate that K-Ac sites are found in all cellular compartments. KEGG analysis indicates that the K-Ac sites are found on proteins responsible for a diverse and wide array of vital cellular functions. Domain structure prediction shows that K-Ac sites are found throughout a wide variety of protein domains, including those in heat shock proteins and those involved in cell cycle functions and DNA repair. Secondary structure prediction proves that K-Ac sites are preferentially found in ordered structures such as alpha helices and beta sheets. Finally, by mutating K-Ac sites in silico and predicting the effect on nearby phosphorylation sites, we demonstrate that the majority of lysine acetylation sites have the potential to impact protein phosphorylation, methylation, and ubiquitination status. Our work validates earlier smaller-scale studies on the acetylome and demonstrates the importance of PTM crosstalk for regulation of cellular function.\",\n \"corpus_id\": 8934622,\n \"score\": 1\n },\n {\n \"doc_id\": \"22438791\",\n \"title\": \"Post-translational modifications of nuclear receptors and human disease.\",\n \"abstract\": \"Nuclear receptors (NR) impact a myriad of physiological processes including homeostasis, reproduction, development, and metabolism. NRs are regulated by post-translational modifications (PTM) that markedly impact receptor function. Recent studies have identified NR PTMs that are involved in the onset and progression of human diseases, including cancer. The majority of evidence linking NR PTMs with disease has been demonstrated for phosphorylation, acetylation and sumoylation of androgen receptor (AR), estrogen receptor α (ERα), glucocorticoid receptor (GR) and peroxisome proliferator activated receptor γ (PPARγ). Phosphorylation of AR has been associated with hormone refractory prostate cancer and decreased disease-specific survival. AR acetylation and sumoylation increased growth of prostate cancer tumor models. AR phosphorylation reduced the toxicity of the expanded polyglutamine AR in Kennedy's Disease as a consequence of reduced ligand binding. A comprehensive evaluation of ERα phosphorylation in breast cancer revealed several sites associated with better clinical outcome to tamoxifen therapy, whereas other phosphorylation sites were associated with poorer clinical outcome. ERα acetylation and sumoylation may also have predictive value for breast cancer. GR phosphorylation and acetylation impact GR responsiveness to glucocorticoids that are used as anti-inflammatory drugs. PPARγ phosphorylation can regulate the balance between growth and differentiation in adipose tissue that is linked to obesity and insulin resistance. Sumoylation of PPARγ is linked to repression of inflammatory genes important in patients with inflammatory diseases. NR PTMs provide an additional measure of NR function that can be used as both biomarkers of disease progression, and predictive markers for patient response to NR-directed treatments.\",\n \"corpus_id\": 3651263,\n \"score\": 1\n },\n {\n \"doc_id\": \"22494029\",\n \"title\": \"Post-translational modification of human heat shock factors and their functions: a recent update by proteomic approach.\",\n \"abstract\": \"Heat shock factors (HSFs) are vital for modulating stress and heat shock-related gene expression in cells. The activity of HSFs is controlled largely by post-translational modifications (PTMs). For example, basal phosphorylation of HSF1 on three serine sites suppresses the heat shock response, and hyperphosphorylation of HSF1 on several other serine and threonine sites by stress-activated kinases results in its activation, while acetylation on K80 inhibits its DNA-binding ability. Sumoylation of HSF2 on K82 regulates its DNA-binding ability, whereas sumoylation of HSF4B on K293 represses its transcriptional activity. With the advancement of proteomic technology, novel PTM sites on various HSFs have been identified with the use of tandem mass spectrometry (MS/MS), but the functions of many of these PTMs are still unclear. Yet, it should be noted that the discovery of these novel PTM sites provided the necessary evidence for the existence of these PTM marks in vivo. Followed by subsequent functional analysis, this would ultimately lead to a better understanding of these PTM marks. MS/MS-based proteomic approach is becoming a gold standard in PTM validation in the field of life science. Here, the recent literature of all known PTMs reported on human HSFs and the resulting functions will be discussed.\",\n \"corpus_id\": 23588597,\n \"score\": 1\n },\n {\n \"doc_id\": \"22770978\",\n \"title\": \"The inside and out of dystroglycan post-translational modification.\",\n \"abstract\": \"In neuromuscular systems dystroglycan provides a vital link between laminin in the extracellular matrix and dystrophin in the membrane cytoskeleton. The integrity of this link is maintained and regulated by post-translational modifications of dystroglycan that have effects both inside and outside the cell. Glycosylation of α-dystroglycan is crucial for its link to laminin and phosphorylation of β-dystroglycan on tyrosine regulates its association with intracellular binding partners. This short review focuses on some of the recent developments in our understanding of the role of these post-translational modification in regulating dystroglycan function, and how new knowledge of signalling through the laminin-dystroglycan axis is leading to hope for treatment for some neuromuscular diseases associated with this adhesion complex.\",\n \"corpus_id\": 36373326,\n \"score\": 1\n },\n {\n \"doc_id\": \"23505349\",\n \"title\": \"Dual coordination of post translational modifications in human protein networks.\",\n \"abstract\": \"Post-translational modifications (PTMs) regulate protein activity, stability and interaction profiles and are critical for cellular functioning. Further regulation is gained through PTM interplay whereby modifications modulate the occurrence of other PTMs or act in combination. Integration of global acetylation, ubiquitination and tyrosine or serine/threonine phosphorylation datasets with protein interaction data identified hundreds of protein complexes that selectively accumulate each PTM, indicating coordinated targeting of specific molecular functions. A second layer of PTM coordination exists in these complexes, mediated by PTM integration (PTMi) spots. PTMi spots represent very dense modification patterns in disordered protein regions and showed an equally high mutation rate as functional protein domains in cancer, inferring equivocal importance for cellular functioning. Systematic PTMi spot identification highlighted more than 300 candidate proteins for combinatorial PTM regulation. This study reveals two global PTM coordination mechanisms and emphasizes dataset integration as requisite in proteomic PTM studies to better predict modification impact on cellular signaling.\",\n \"corpus_id\": 2072269,\n \"score\": 1\n },\n {\n \"doc_id\": \"25308709\",\n \"title\": \"The Anaplasma phagocytophilum effector AmpA hijacks host cell SUMOylation.\",\n \"abstract\": \"SUMOylation, the covalent attachment of a member of the small ubiquitin-like modifier (SUMO) family of proteins to lysines in target substrates, is an essential post-translational modification in eukaryotes. Microbial manipulation of SUMOylation recently emerged as a key virulence strategy for viruses and facultative intracellular bacteria, the latter of which have only been shown to deploy effectors that negatively regulate SUMOylation. Here, we demonstrate that the obligate intracellular bacterium, Anaplasma phagocytophilum, utilizes an effector, AmpA (A. phagocytophilum post-translationally modified protein A) that becomes SUMOylated in host cells and this is important for the pathogen's survival. We previously discovered that AmpA (formerly APH1387) localizes to the A. phagocytophilum-occupied vacuolar membrane (AVM). Algorithmic prediction analyses denoted AmpA as a candidate for SUMOylation. We verified this phenomenon using a SUMO affinity matrix to precipitate both native AmpA and ectopically expressed green fluorescent protein (GFP)-tagged AmpA. SUMOylation of AmpA was lysine dependent, as SUMO affinity beads failed to precipitate a GFP-AmpA protein when its lysine residues were substituted with arginine. Ectopically expressed and endogenous AmpA were poly-SUMOylated, which was consistent with the observation that AmpA colocalizes with SUMO2/3 at the AVM. Only late during the infection cycle did AmpA colocalize with SUMO1, which terminally caps poly-SUMO2/3 chains. AmpA was also detected in the cytosol of infected host cells, further supporting its secretion and likely participation in interactions that aid pathogen survival. Indeed, whereas siRNA-mediated knockdown of Ubc9 - a necessary enzyme for SUMOylation - slightly bolstered A. phagocytophilum infection, pharmacologically inhibiting SUMOylation in infected cells significantly reduced the bacterial load. Ectopically expressed GFP-AmpA served as a competitive agonist against native AmpA in infected cells, while lysine-deficient GFP-AmpA was less effective, implying that modification of AmpA lysines is important for infection. Collectively, these data show that AmpA becomes directly SUMOylated during infection, representing a novel tactic for A. phagocytophilum survival.\",\n \"corpus_id\": 8692466,\n \"score\": 1\n },\n {\n \"doc_id\": \"27046249\",\n \"title\": \"The BECN1 N-terminal domain is intrinsically disordered.\",\n \"abstract\": \"BECN1/Beclin 1 has a critical role in the early stages of autophagosome formation. Recently, structures of its central and C-terminal domains were reported, however, little structural information is available on the N-terminal domain, comprising a third of the protein. This lack of structural information largely stems from the inability to produce this region in a purified form. Here, we describe the expression and purification of the N-terminal domain of BECN1 (residues 1 to 150) and detailed biophysical characterization, including NMR spectroscopy. Combined, our studies demonstrated at the atomic level that the BECN1 N-terminal domain is intrinsically disordered, and apart from the BH3 subdomain, remains disordered following interaction with a binding partner, BCL2L1/BCL-XL. In addition, the BH3 domain α-helix induced upon interaction with BCL2L1 reverts to a disordered state when the complex is dissociated by exposure to a competitive inhibitor. No significant interactions between N- and C-terminal domains were detected.\",\n \"corpus_id\": 23545910,\n \"score\": 1\n },\n {\n \"doc_id\": \"27147466\",\n \"title\": \"The role of post-translational modifications in hearing and deafness.\",\n \"abstract\": \"Post-translational modifications (PTMs) are key molecular events that modify proteins after their synthesis and modulate their ultimate functional properties by affecting their stability, localisation, interaction potential or activity. These chemical changes expand the size of the proteome adding diversity to the molecular pathways governing the biological outcome of cells. PTMs are, thus, crucial in regulating a variety of cellular processes such as apoptosis, proliferation and differentiation and have been shown to be instrumental during embryonic development. In addition, alterations in protein PTMs have been implicated in the pathogenesis of many human diseases, including deafness. In this review, we summarize the recent progress made in understanding the roles of PTMs during cochlear development, with particular emphasis on the enzymes driving protein phosphorylation, acetylation, methylation, glycosylation, ubiquitination and SUMOylation. We also discuss how these enzymes may contribute to hearing impairment and deafness.\",\n \"corpus_id\": 657737,\n \"score\": 1\n },\n {\n \"doc_id\": \"27383850\",\n \"title\": \"Identification of BECN1 and ATG14 Coiled-Coil Interface Residues That Are Important for Starvation-Induced Autophagy.\",\n \"abstract\": \"Autophagy, an essential eukaryotic homeostasis pathway, allows the sequestration of unwanted, damaged, or harmful cytoplasmic components in vesicles called autophagosomes, permitting subsequent lysosomal degradation and nutrient recycling. Autophagosome nucleation is mediated by class III phosphatidylinositol-3-kinase complexes that include two key autophagy proteins, BECN1/Beclin 1 and ATG14/BARKOR, which form parallel heterodimers via their coiled-coil domains (CCDs). Here we present the 1.46 Å X-ray crystal structure of the antiparallel, human BECN1 CCD homodimer, which represents BECN1 oligomerization outside the autophagosome nucleation complex. We use circular dichroism and small-angle X-ray scattering (SAXS) to show that the ATG14 CCD is significantly disordered but becomes more helical in the BECN1:ATG14 heterodimer, although it is less well-folded than the BECN1 CCD homodimer. SAXS also indicates that the BECN1:ATG14 heterodimer is more curved than other BECN1-containing CCD dimers, which has important implications for the structure of the autophagosome nucleation complex. A model of the BECN1:ATG14 CCD heterodimer that agrees well with the SAXS data shows that BECN1 residues at the homodimer interface are also responsible for heterodimerization, allowing us to identify ATG14 interface residues. Finally, we verify the role of BECN1 and ATG14 interface residues in binding by assessing the impact of point mutations of these residues on co-immunoprecipitation of the partner and demonstrate that these mutations abrogate starvation-induced upregulation of autophagy but do not impact basal autophagy. Thus, this research provides insights into structures of the BECN1 CCD homodimer and the BECN1:ATG14 CCD heterodimer and identifies interface residues that are important for BECN1:ATG14 heterodimerization and for autophagy.\",\n \"corpus_id\": 20237132,\n \"score\": 1\n },\n {\n \"doc_id\": \"27438764\",\n \"title\": \"Post-Translational Modification Control of Innate Immunity.\",\n \"abstract\": \"A coordinated balance between the positive and negative regulation of pattern-recognition receptor (PRR)-initiated innate inflammatory responses is required to ensure the most favorable outcome for the host. Post-translational modifications (PTMs) of innate sensors and downstream signaling molecules influence their activity and function by inducing their covalent linkage to new functional groups. PTMs including phosphorylation and polyubiquitination have been shown to potently regulate innate inflammatory responses through the activation, cellular translocation, and interaction of innate receptors, adaptors, and downstream signaling molecules in response to infectious and dangerous signals. Other PTMs such as methylation, acetylation, SUMOylation, and succinylation are increasingly implicated in the regulation of innate immunity and inflammation. In this review, we focus on the roles of PTMs in controlling PRR-triggered innate immunity and inflammatory responses. The emerging roles of PTMs in the pathogenesis and potential treatment of infectious and inflammatory immune diseases are also discussed.\",\n \"corpus_id\": 5572066,\n \"score\": 1\n },\n {\n \"doc_id\": \"27713867\",\n \"title\": \"Anaplasma phagocytophilum APH0032 Is Exposed on the Cytosolic Face of the Pathogen-Occupied Vacuole and Co-opts Host Cell SUMOylation.\",\n \"abstract\": \"Anaplasma phagocytophilum, a member of the family Anaplasmataceae and the obligate intracellular bacterium that causes granulocytic anaplasmosis, resides in a host cell-derived vacuole. Bacterial proteins that localize to the A. phagocytophilum-occupied vacuole membrane (AVM) are critical host-pathogen interfaces. Of the few bacterial AVM proteins that have been identified, the domains responsible for AVM localization and the host cell pathways that they co-opt are poorly defined. APH0032 is an effector that is expressed and localizes to the AVM late during the infection cycle. Herein, the APH0032 domain that is essential for associating with host cell membranes was mapped. Immunofluorescent labeling of infected cells that had been differentially permeabilized confirmed that APH0032 is exposed on the AVM's cytosolic face, signifying its potential to interface with host cell processes. SUMOylation is the covalent attachment of a member of the small ubiquitin-like modifier (SUMO) family of proteins to lysines in target substrates. Previous work from our laboratory determined that SUMOylation is important for A. phagocytophilum survival and that SUMOylated proteins decorate the AVM. Algorithmic prediction analyses identified APH0032 as a candidate for SUMOylation. Endogenous APH0032 was precipitated from infected cells using a SUMO affinity matrix, confirming that the effector co-opts SUMOylation during infection. APH0032 pronouncedly colocalized with SUMO1, but not SUMO2/3 moieties on the AVM. Ectopic expression of APH0032 in A. phagocytophilum infected host cells significantly boosted the bacterial load. This study delineates the first domain of any Anaplasmataceae protein that is essential for associating with the pathogen-occupied vacuole membrane, demonstrates the importance of APH0032 to infection, and identifies it as the second A. phagocytophilum effector that co-opts SUMOylation, thus underscoring the relevance of this post-translational modification to infection.\",\n \"corpus_id\": 13655642,\n \"score\": 1\n },\n {\n \"doc_id\": \"28368777\",\n \"title\": \"PINK1 and BECN1 relocalize at mitochondria-associated membranes during mitophagy and promote ER-mitochondria tethering and autophagosome formation.\",\n \"abstract\": \"Mitophagy is a highly specialized process to remove dysfunctional or superfluous mitochondria through the macroautophagy/autophagy pathway, aimed at protecting cells from the damage of disordered mitochondrial metabolism and apoptosis induction. PINK1, a neuroprotective protein mutated in autosomal recessive Parkinson disease, has been implicated in the activation of mitophagy by selectively accumulating on depolarized mitochondria, and promoting PARK2/Parkin translocation to them. While these steps have been characterized in depth, less is known about the process and site of autophagosome formation upon mitophagic stimuli. A previous study reported that, in starvation-induced autophagy, the proautophagic protein BECN1/Beclin1 (which we previously showed to interact with PINK1) relocalizes at specific regions of contact between the endoplasmic reticulum (ER) and mitochondria called mitochondria-associated membranes (MAM), from which the autophagosome originates. Here we show that, following mitophagic stimuli, autophagosomes also form at MAM; moreover, endogenous PINK1 and BECN1 were both found to relocalize at MAM, where they promoted the enhancement of ER-mitochondria contact sites and the formation of omegasomes, that represent autophagosome precursors. PARK2 was also enhanced at MAM following mitophagy induction. However, PINK1 silencing impaired BECN1 enrichment at MAM independently of PARK2, suggesting a novel role for PINK1 in regulating mitophagy. MAM have been recently implicated in many key cellular events. In this light, the observed prevalent localization of PINK1 at MAM may well explain other neuroprotective activities of this protein, such as modulation of mitochondrial calcium levels, mitochondrial dynamics, and apoptosis.\",\n \"corpus_id\": 205899700,\n \"score\": 1\n },\n {\n \"doc_id\": \"28408866\",\n \"title\": \"Post-translational Modifications and Protein Quality Control in Motor Neuron and Polyglutamine Diseases.\",\n \"abstract\": \"Neurodegenerative diseases, including motor neuron and polyglutamine (polyQ) diseases, are a broad class of neurological disorders. These diseases are characterized by neuronal dysfunction and death, and by the accumulation of toxic aggregation-prone proteins in the forms of inclusions and micro-aggregates. Protein quality control is a cellular mechanism to reduce the burden of accumulation of misfolded proteins, a function that results from the coordinated actions of chaperones and degradation systems, such as the ubiquitin-proteasome system (UPS) and autophagy-lysosomal degradation system. The rate of turnover, aggregation and degradation of the disease-causing proteins is modulated by post-translational modifications (PTMs), such as phosphorylation, arginine methylation, palmitoylation, acetylation, SUMOylation, ubiquitination, and proteolytic cleavage. Here, we describe how PTMs of proteins linked to motor neuron and polyQ diseases can either enhance or suppress protein quality control check and protein aggregation and degradation. The identification of molecular strategies targeting these modifications may offer novel avenues for the treatment of these yet incurable diseases.\",\n \"corpus_id\": 18837748,\n \"score\": 1\n },\n {\n \"doc_id\": \"28798234\",\n \"title\": \"Structural transitions in conserved, ordered Beclin 1 domains essential to regulating autophagy.\",\n \"abstract\": \"Beclin 1 (BECN1) is a key regulator of autophagy, a critical catabolic homeostasis pathway that involves the sequestration of cytoplasmic components by multilayered vesicles called autophagosomes, followed by lysosomal fusion and degradation. BECN1 is a core component of class III phosphatidylinositol-3-kinase complexes responsible for autophagosome nucleation. Without heterologous binding partners, BECN1 forms an antiparallel homodimer via its coiled-coil domain (CCD). However, the last 16 CCD residues, composing an overlap helix (OH), have been crystallized in two mutually exclusive states: either as part of the CCD or packed against the C-terminal lower case β-α-repeated, autophagy-specific domain (BARAD). Here, using circular dichroism (CD) spectroscopy, isothermal titration calorimetry (ITC), and small-angle X-ray scattering (SAXS), we show that in the homodimeric state, the OH transitions between these two different packing states, with the predominant state comprising the OH packed against the BARAD, contrary to expectations based on known BECN1 interactions with heterologous partners. We confirmed this observation by comparing the impact of mutating four residues that mediate packing of the OH against both the CCD and BARAD on structure and stability of the CCD, the OH+BARAD, and the two-domain CCD-BARAD. Lastly, we used cellular assays demonstrating that mutation of these OH-interface residues abrogates starvation-induced up-regulation of autophagy, but does not affect basal autophagy. In summary, we have identified a BECN1 helical region that transitions between packing as part of either one of two conserved domains, i.e. the CCD or the BARAD. Our findings have important implications for the relative stability of autophagy-inactive and autophagy-active BECN1 complexes.\",\n \"corpus_id\": 24318140,\n \"score\": 1\n },\n {\n \"doc_id\": \"28876241\",\n \"title\": \"Structural insights into the interaction of the conserved mammalian proteins GAPR-1 and Beclin 1, a key autophagy protein.\",\n \"abstract\": \"Mammalian Golgi-associated plant pathogenesis-related protein 1 (GAPR-1) is a negative autophagy regulator that binds Beclin 1, a key component of the autophagosome nucleation complex. Beclin 1 residues 267-284 are required for binding GAPR-1. Here, sequence analyses, structural modeling, mutagenesis combined with pull-down assays, X-ray crystal structure determination and small-angle X-ray scattering were used to investigate the Beclin 1-GAPR-1 interaction. Five conserved residues line an equatorial GAPR-1 surface groove that is large enough to bind a peptide. A model of a peptide comprising Beclin 1 residues 267-284 docked onto GAPR-1, built using the CABS-dock server, indicates that this peptide binds to this GAPR-1 groove. Mutation of the five conserved residues lining this groove, H54A/E86A/G102K/H103A/N138G, abrogates Beclin 1 binding. The 1.27 Å resolution X-ray crystal structure of this pentad mutant GAPR-1 was determined. Comparison with the wild-type (WT) GAPR-1 structure shows that the equatorial groove of the pentad mutant is shallower and more positively charged, and therefore may not efficiently bind Beclin 1 residues 267-284, which include many hydrophobic residues. Both WT and pentad mutant GAPR-1 crystallize as dimers, and in each case the equatorial groove of one subunit is partially occluded by the other subunit, indicating that dimeric GAPR-1 is unlikely to bind Beclin 1. SAXS analysis of WT and pentad mutant GAPR-1 indicates that in solution the WT forms monomers, while the pentad mutant is primarily dimeric. Thus, changes in the structure of the equatorial groove combined with the improved dimerization of pentad mutant GAPR-1 are likely to abrogate binding to Beclin 1.\",\n \"corpus_id\": 25331239,\n \"score\": 1\n },\n {\n \"doc_id\": \"29099291\",\n \"title\": \"Post-translational modifications: How to modulate Rab7 functions.\",\n \"abstract\": \"The small GTPase Rab7 is the main regulator of membrane trafficking at late endosomes. This small GTPase regulates endosome-to-trans Golgi Network trafficking of sorting receptors, membrane fusion of late endosomes to lysosomes, and autophagosomes to lysosomes during autophagy. Rab7, like all Rab GTPases, binds downstream effectors coordinating several divergent pathways. How cells regulate these interactions and downstream functions is not well understood. Recent evidence suggests that Rab7 function can be modulated by the combination of several post-translational modifications that facilitate interactions with one effector while preventing binding to another one. In this review, we discuss recent data on how phosphorylation, palmitoylation and ubiquitination modulate the ability of this small GTPase to orchestrate membrane trafficking at the late endosomes.\",\n \"corpus_id\": 35798382,\n \"score\": 1\n },\n {\n \"doc_id\": \"29157087\",\n \"title\": \"THANATOS: an integrative data resource of proteins and post-translational modifications in the regulation of autophagy.\",\n \"abstract\": \"Macroautophagy/autophagy is a highly conserved process for degrading cytoplasmic contents, determines cell survival or death, and regulates the cellular homeostasis. Besides ATG proteins, numerous regulators together with various post-translational modifications (PTMs) are also involved in autophagy. In this work, we collected 4,237 experimentally identified proteins regulated in autophagy and cell death pathways from the literature. Then we computationally identified potential orthologs of known proteins, and developed a comprehensive database of The Autophagy, Necrosis, ApopTosis OrchestratorS (THANATOS, http://thanatos.biocuckoo.org ), containing 191,543 proteins potentially associated with autophagy and cell death pathways in 164 eukaryotes. We performed an evolutionary analysis of ATG genes, and observed that ATGs required for the autophagosome formation are highly conserved across eukaryotes. Further analyses revealed that known cancer genes and drug targets were overrepresented in human autophagy proteins, which were significantly associated in a number of signaling pathways and human diseases. By reconstructing a human kinase-substrate phosphorylation network for ATG proteins, our results confirmed that phosphorylation play a critical role in regulating autophagy. In total, we mapped 65,015 known sites of 11 types of PTMs to collected proteins, and revealed that all types of PTM substrates were enriched in human autophagy. In addition, we observed multiple types of PTM regulators such as protein kinases and ubiquitin E3 ligases or adaptors were significantly associated with human autophagy, and again the results emphasized the importance of PTM regulations in autophagy. We anticipated THANATOS can be a useful resource for further studies.\",\n \"corpus_id\": 36543837,\n \"score\": 1\n },\n {\n \"doc_id\": \"29322920\",\n \"title\": \"Investigation and identification of functional post-translational modification sites associated with drug binding and protein-protein interactions.\",\n \"abstract\": \"BACKGROUND: Protein post-translational modification (PTM) plays an essential role in various cellular processes that modulates the physical and chemical properties, folding, conformation, stability and activity of proteins, thereby modifying the functions of proteins. The improved throughput of mass spectrometry (MS) or MS/MS technology has not only brought about a surge in proteome-scale studies, but also contributed to a fruitful list of identified PTMs. However, with the increase in the number of identified PTMs, perhaps the more crucial question is what kind of biological mechanisms these PTMs are involved in. This is particularly important in light of the fact that most protein-based pharmaceuticals deliver their therapeutic effects through some form of PTM. Yet, our understanding is still limited with respect to the local effects and frequency of PTM sites near pharmaceutical binding sites and the interfaces of protein-protein interaction (PPI). Understanding PTM's function is critical to our ability to manipulate the biological mechanisms of protein. RESULTS: In this study, to understand the regulation of protein functions by PTMs, we mapped 25,835 PTM sites to proteins with available three-dimensional (3D) structural information in the Protein Data Bank (PDB), including 1785 modified PTM sites on the 3D structure. Based on the acquired structural PTM sites, we proposed to use five properties for the structural characterization of PTM substrate sites: the spatial composition of amino acids, residues and side-chain orientations surrounding the PTM substrate sites, as well as the secondary structure, division of acidity and alkaline residues, and solvent-accessible surface area. We further mapped the structural PTM sites to the structures of drug binding and PPI sites, identifying a total of 1917 PTM sites that may affect PPI and 3951 PTM sites associated with drug-target binding. An integrated analytical platform (CruxPTM), with a variety of methods and online molecular docking tools for exploring the structural characteristics of PTMs, is presented. In addition, all tertiary structures of PTM sites on proteins can be visualized using the JSmol program. CONCLUSION: Resolving the function of PTM sites is important for understanding the role that proteins play in biological mechanisms. Our work attempted to delineate the structural correlation between PTM sites and PPI or drug-target binding. CurxPTM could help scientists narrow the scope of their PTM research and enhance the efficiency of PTM identification in the face of big proteome data. CruxPTM is now available at http://csb.cse.yzu.edu.tw/CruxPTM/ .\",\n \"corpus_id\": 1953914,\n \"score\": 1\n },\n {\n \"doc_id\": \"29536364\",\n \"title\": \"Role and Function of the Type IV Secretion System in Anaplasma and Ehrlichia Species.\",\n \"abstract\": \"The obligatory intracellular pathogens Anaplasma phagocytophilum and Ehrlichia chaffeensis proliferate within membrane-bound vacuoles of human leukocytes and cause potentially fatal emerging infectious diseases. Despite the reductive genome evolution in this group of bacteria, genes encoding the type IV secretion system (T4SS), which is homologous to the VirB/VirD4 system of the plant pathogen Agrobacterium tumefaciens, have been expanded and are highly expressed in A. phagocytophilum and E. chaffeensis in human cells. Of six T4SS effector proteins identified in them, roles and functions have been described so far only for ankyrin repeat domain-containing protein A (AnkA), Anaplasma translocated substrate 1 (Ats-1), and Ehrlichia translocated factor 1 (Etf-1, ECH0825). These effectors are abundantly produced and secreted into the host cytoplasm during infection, but not toxic to host cells. They contain eukaryotic protein motifs or organelle localization signals and have distinct subcellular localization, target to specific host cell molecules to promote infection. Ats-1 and Etf-1 are orthologous proteins, subvert two important innate immune mechanisms against intracellular infection, cellular apoptosis and autophagy, and manipulate autophagy to gain nutrients from host cells. Although Ats-1 and Etf-1 have similar functions and roles in obligatory intracellular infection, they are specifically adapted to the distinct membrane-bound intracellular niche of A. phagocytophilum and E. chaffeensis, respectively. Ectopic expression of these effectors enhances respective bacterial infection, whereas intracellular delivery of antibodies against these effectors or targeted knockdown of the effector with antisense peptide nucleic acid significantly impairs bacterial infection. Thus, both T4SSs have evolved as important survival and nutritional virulence mechanism in these obligatory intracellular bacteria. Future studies on the functions of Anaplasma and Ehrlichia T4SS effector molecules and signaling pathways will undoubtedly advance our understanding of the complex interplay between obligatory intracellular pathogens and their hosts. Such data can be applied toward the treatment and control of anaplasmosis and ehrlichiosis.\",\n \"corpus_id\": 3834894,\n \"score\": 1\n },\n {\n \"doc_id\": \"20600793\",\n \"title\": \"Anaplasma phagocytophilum APH_0032 is expressed late during infection and localizes to the pathogen-occupied vacuolar membrane.\",\n \"abstract\": \"Anaplasma phagocytophilum infects neutrophils and myeloid, endothelial, and tick cell lines to reside within a host cell-derived vacuole that is indispensible for its survival. Here, we identify APH_0032 as an Anaplasma-derived protein that associates with the A. phagocytophilum-occupied vacuolar membrane (AVM). APH_0032 is a 66.1 kDa acidic protein that electrophoretically migrates with an apparent molecular weight of 130 kDa. It contains a predicted transmembrane domain and tandemly arranged direct repeats that comprise 46% of the protein. APH_0032 is undetectable on Anaplasma organisms bound to the surfaces of HL-60 cells, but is detected on the AVM and surfaces of intravacuolar bacteria beginning 24 h post-infection. APH_0032 localizes to the AVM in HL-60, THP-1, HMEC-1, and ISE6 cells. APH_0032, along with APH_1387, which encodes a confirmed AVM protein, is transcribed during A. phagocytophilum infection of tick salivary glands and murine neutrophils. APH_0032 localizes to the AVM in neutrophils recovered from infected mice. The Legionella pneumophila Dot/IcM type IV secretion system (T4SS) can heterologously secrete a CyaA-tagged version of the A. phagocytophilum VirB/D T4SS effector, AnkA, but fails to secrete CyaA-tagged APH_0032 or APH_1387. These data confirm APH_0032 as an Anaplasma-derived AVM protein and hint that neither it nor APH_1387 are T4SS effectors.\",\n \"corpus_id\": 13536895,\n \"score\": 0\n },\n {\n \"doc_id\": \"23071137\",\n \"title\": \"Anaplasma phagocytophilum Asp14 is an invasin that interacts with mammalian host cells via its C terminus to facilitate infection.\",\n \"abstract\": \"Anaplasma phagocytophilum, a member of the family Anaplasmataceae, is the tick-transmitted obligate intracellular bacterium that causes human granulocytic anaplasmosis. The life cycle of A. phagocytophilum is biphasic, transitioning between the noninfectious reticulate cell (RC) and infectious dense-cored (DC) forms. We analyzed the bacterium's DC surface proteome by selective biotinylation of surface proteins, NeutrAvidin affinity purification, and mass spectrometry. Transcriptional profiling of selected outer membrane protein candidates over the course of infection revealed that aph_0248 (designated asp14 [14-kDa A. phagocytophilum surface protein]) expression was upregulated the most during A. phagocytophilum cellular invasion. asp14 transcription was induced during transmission feeding of A. phagocytophilum-infected ticks on mice and was upregulated when the bacterium engaged its receptor, P-selectin glycoprotein ligand 1. Asp14 localized to the A. phagocytophilum surface and was expressed during in vivo infection. Treating DC organisms with Asp14 antiserum or preincubating mammalian host cells with glutathione S-transferase (GST)-Asp14 significantly inhibited infection of host cells. Moreover, preincubating host cells with GST-tagged forms of both Asp14 and outer membrane protein A, another A. phagocytophilum invasin, pronouncedly reduced infection relative to treatment with either protein alone. The Asp14 domain that is sufficient for cellular adherence and invasion lies within the C-terminal 12 to 24 amino acids and is conserved among other Anaplasma and Ehrlichia species. These results identify Asp14 as an A. phagocytophilum surface protein that is critical for infection, delineate its invasion domain, and demonstrate the potential of targeting Asp14 in concert with OmpA for protecting against infection by A. phagocytophilum and other Anaplasmataceae pathogens.\",\n \"corpus_id\": 12767334,\n \"score\": 0\n },\n {\n \"doc_id\": \"23727157\",\n \"title\": \"Autophagosome formation--the role of ULK1 and Beclin1-PI3KC3 complexes in setting the stage.\",\n \"abstract\": \"Autophagy is a conserved and highly regulated degradative membrane trafficking pathway, maintaining energy homeostasis and protein synthesis during nutrient stress. Our understanding of how the autophagy machinery is regulated has expanded greatly over recent years. The ULK and Beclin1-PI3KC3 complexes are key signaling complexes required for autophagosome formation. The nutrient and energy sensors mTORC1 and AMPK signal directly to the ULK complex and affect its activity. Formation and activation of distinct Beclin1-PI3KC3 complexes produces PI3P, a signaling lipid required for the recruitment of autophagy effectors. In this review we discuss how the mammalian ULK1 and Beclin1 complexes are controlled by post-translational modifications and protein-protein interactions and we highlight data linking these complexes together.\",\n \"corpus_id\": 22757669,\n \"score\": 0\n },\n {\n \"doc_id\": \"24840982\",\n \"title\": \"Unconventional post-translational modifications in immunological signaling.\",\n \"abstract\": \"The activity of a cell is governed by the signals it receives from the extracellular milieu, which are 'translated' into the appropriate biological output, such as activation, survival, proliferation, migration or differentiation. Signaling pathways are responsible for converting environmental cues into discrete intracellular events. The alteration of existing proteins by post-translational modification (PTM) is a key feature of signal-transduction pathways that allows the modulation of protein function. Research into PTMs has long been dominated by the investigation of protein phosphorylation; other PTMs, such as methylation of lysine and arginine residues, acetylation, and nitrosylation of thiol groups and tyrosine residues, have received comparatively little attention. This Review aims to present an overview of these PTMs, with an emphasis on their role in cells of the immune system.\",\n \"corpus_id\": 10016852,\n \"score\": 0\n },\n {\n \"doc_id\": \"25172281\",\n \"title\": \"Investigating interference with apoptosis induction by bacterial proteins.\",\n \"abstract\": \"The modulation of host cell apoptosis by bacterial pathogens is critical for their intracellular survival. Several intracellular bacteria achieve this by secreting proteins that interact with apoptosis pathways to inhibit host cell apoptosis. Anaplasma phagocytophilum, which causes human granulocytic anaplasmosis, is such bacterium. The protein Ats-1, translocated from A. phagocytophilum by the bacterial type IV secretion system, localizes to host cell mitochondria, and interferes with apoptosis induction. In this chapter, we present a protocol applied to investigate an anti-apoptotic effect of Ats-1.\",\n \"corpus_id\": 40331983,\n \"score\": 0\n },\n {\n \"doc_id\": \"26351162\",\n \"title\": \"[Post-translational modification (PTM) bioinformatics in China: progresses and perspectives].\",\n \"abstract\": \"Post-translational modifications (PTMs) are essential for regulating conformational changes, activities and functions of proteins, and are involved in almost all cellular pathways and processes. Identification of protein PTMs is the basis for understanding cellular and molecular mechanisms. In contrast with labor-intensive and time-consuming experiments, the PTM prediction using various bioinformatics approaches can provide accurate, convenient, and efficient strategies and generate valuable information for further experimental consideration. In this review, we summarize the current progresses made by Chineses bioinformaticians in the field of PTM Bioinformatics, including the design and improvement of computational algorithms for predicting PTM substrates and sites, design and maintenance of online and offline tools, establishment of PTM-related databases and resources, and bioinformatics analysis of PTM proteomics data. Through comparing similar studies in China and other countries, we demonstrate both advantages and limitations of current PTM bioinformatics as well as perspectives for future studies in China.\",\n \"corpus_id\": 37715772,\n \"score\": 0\n },\n {\n \"doc_id\": \"26424601\",\n \"title\": \"Integrated Metabolomics, Transcriptomics and Proteomics Identifies Metabolic Pathways Affected by Anaplasma phagocytophilum Infection in Tick Cells.\",\n \"abstract\": \"Anaplasma phagocytophilum is an emerging zoonotic pathogen that causes human granulocytic anaplasmosis. These intracellular bacteria establish infection by affecting cell function in both the vertebrate host and the tick vector, Ixodes scapularis. Previous studies have characterized the tick transcriptome and proteome in response to A. phagocytophilum infection. However, in the postgenomic era, the integration of omics datasets through a systems biology approach allows network-based analyses to describe the complexity and functionality of biological systems such as host-pathogen interactions and the discovery of new targets for prevention and control of infectious diseases. This study reports the first systems biology integration of metabolomics, transcriptomics, and proteomics data to characterize essential metabolic pathways involved in the tick response to A. phagocytophilum infection. The ISE6 tick cells used in this study constitute a model for hemocytes involved in pathogen infection and immune response. The results showed that infection affected protein processing in endoplasmic reticulum and glucose metabolic pathways in tick cells. These results supported tick-Anaplasma co-evolution by providing new evidence of how tick cells limit pathogen infection, while the pathogen benefits from the tick cell response to establish infection. Additionally, ticks benefit from A. phagocytophilum infection by increasing survival while pathogens guarantee transmission. The results suggested that A. phagocytophilum induces protein misfolding to limit the tick cell response and facilitate infection but requires protein degradation to prevent ER stress and cell apoptosis to survive in infected cells. Additionally, A. phagocytophilum may benefit from the tick cell's ability to limit bacterial infection through PEPCK inhibition leading to decreased glucose metabolism, which also results in the inhibition of cell apoptosis that increases infection of tick cells. These results support the use of this experimental approach to systematically identify cell pathways and molecular mechanisms involved in tick-pathogen interactions. Data are available via ProteomeXchange with identifier PXD002181.\",\n \"corpus_id\": 27973649,\n \"score\": 0\n },\n {\n \"doc_id\": \"26636486\",\n \"title\": \"GADD45A inhibits autophagy by regulating the interaction between BECN1 and PIK3C3.\",\n \"abstract\": \"GADD45A is a TP53-regulated and DNA damage-inducible tumor suppressor protein, which regulates cell cycle arrest, apoptosis, and DNA repair, and inhibits tumor growth and angiogenesis. However, the function of GADD45A in autophagy remains unknown. In this report, we demonstrate that GADD45A plays an important role in regulating the process of autophagy. GADD45A is able to decrease LC3-II expression and numbers of autophagosomes in mouse tissues and different cancer cell lines. Using bafilomycin A1 treatment, we have observed that GADD45A regulates autophagosome initiation. Likely, GADD45A inhibition of autophagy is through its influence on the interaction between BECN1 and PIK3C3. Immunoprecipitation and GST affinity isolation assays exhibit that GADD45A directly interacts with BECN1, and in turn dissociates the BECN1-PIK3C3 complex. Furthermore, we have mapped the 71 to 81 amino acids of the GADD45A protein that are necessary for the GADD45A interaction with BECN1. Knockdown of BECN1 can abolish autophagy alterations induced by GADD45A. Taken together, these findings provide the novel evidence that GADD45A inhibits autophagy via impairing the BECN1-PIK3C3 complex formation.\",\n \"corpus_id\": 32849119,\n \"score\": 0\n },\n {\n \"doc_id\": \"26714841\",\n \"title\": \"Disturbed flow-induced endothelial pro-atherogenic signaling via regulating post-translational modifications and epigenetic events.\",\n \"abstract\": \"SIGNIFICANCE: Hemodynamic shear stress, the frictional force exerted onto the vascular endothelial cell (EC) surface, influences vascular EC functions. Atherosclerotic plaque formation in the endothelium is known to be site-specific: disturbed blood flow (d-flow) formed at the lesser curvature of the aortic arch and branch points promotes plaque formation, and steady laminar flow (s-flow) at the greater curvature is athero-protective. Recent Advances: Posttranslational modifications (PTMs), including phosphorylation and SUMOylation, and epigenetic events, including DNA methylation and histone modifications, provide a new perspective on the pathogenesis of atherosclerosis, elucidating how gene expression is altered by d-flow. Activation of PKCζ and p90RSK, SUMOylation of ERK5 and p53, and DNA hypermethylation are uniquely induced by d-flow, but not by s-flow. CRITICAL ISSUES: Extensive crosstalk has been observed among the phosphorylation, SUMOylation, acetylation, and methylation PTMs, as well as among epigenetic events along the cascade of d-flow-induced signaling, from the top (mechanosensory systems) to the bottom (epigenetic events). In addition, PKCζ activation plays a role in regulating SUMOylation-related enzymes of PIAS4, p90RSK activation plays a role in regulating SUMOylation-related enzymes of SENP2, and DNA methyltransferase, SUMOylation may play a role in d-flow signaling. FUTURE DIRECTIONS: Although possible contributions of DNA events such as histone modification and the epigenetic and cytosolic events of PTMs in d-flow signaling have become clearer, determining the interplay of each PTM and epigenetic event will provide a new paradigm to elucidate the difference between d-flow and s-flow and lead to novel therapeutic interventions to inhibit plaque formation.\",\n \"corpus_id\": 3740884,\n \"score\": 0\n },\n {\n \"doc_id\": \"27541856\",\n \"title\": \"Ehrlichia secretes Etf-1 to induce autophagy and capture nutrients for its growth through RAB5 and class III phosphatidylinositol 3-kinase.\",\n \"abstract\": \"Ehrlichia chaffeensis is an obligatory intracellular bacterium that causes a potentially fatal emerging zoonosis, human monocytic ehrlichiosis. E. chaffeensis has a limited capacity for biosynthesis and metabolism and thus depends mostly on host-synthesized nutrients for growth. Although the host cell cytoplasm is rich with these nutrients, as E. chaffeensis is confined within the early endosome-like membrane-bound compartment, only host nutrients that enter the compartment can be used by this bacterium. How this occurs is unknown. We found that ehrlichial replication depended on autophagy induction involving class III phosphatidylinositol 3-kinase (PtdIns3K) activity, BECN1 (Beclin 1), and ATG5 (autophagy-related 5). Ehrlichia acquired host cell preincorporated amino acids in a class III PtdIns3K-dependent manner and ehrlichial growth was enhanced by treatment with rapamycin, an autophagy inducer. Moreover, ATG5 and RAB5A/B/C were routed to ehrlichial inclusions. RAB5A/B/C siRNA knockdown, or overexpression of a RAB5-specific GTPase-activating protein or dominant-negative RAB5A inhibited ehrlichial infection, indicating the critical role of GTP-bound RAB5 during infection. Both native and ectopically expressed ehrlichial type IV secretion effector protein, Etf-1, bound RAB5 and the autophagy-initiating class III PtdIns3K complex, PIK3C3/VPS34, and BECN1, and homed to ehrlichial inclusions. Ectopically expressed Etf-1 activated class III PtdIns3K as in E. chaffeensis infection and induced autophagosome formation, cleared an aggregation-prone mutant huntingtin protein in a class III PtdIns3K-dependent manner, and enhanced ehrlichial proliferation. These data support the notion that E. chaffeensis secretes Etf-1 to induce autophagy to repurpose the host cytoplasm and capture nutrients for its growth through RAB5 and class III PtdIns3K, while avoiding autolysosomal killing.\",\n \"corpus_id\": 11826101,\n \"score\": 0\n },\n {\n \"doc_id\": \"27715386\",\n \"title\": \"BECN1/Beclin 1 sorts cell-surface APP/amyloid β precursor protein for lysosomal degradation.\",\n \"abstract\": \"The regulation of plasma membrane (PM)-localized transmembrane protein/receptor trafficking has critical implications for cell signaling, metabolism and survival. In this study, we investigated the role of BECN1 (Beclin 1) in the degradative trafficking of PM-associated APP (amyloid β precursor protein), whose metabolism to amyloid-β, an essential event in Alzheimer disease, is dependent on divergent PM trafficking pathways. We report a novel interaction between PM-associated APP and BECN1 that recruits macroautophagy/endosomal regulatory proteins PIK3C3 and UVRAG. We found that BECN1 promotes surface APP internalization and sorting predominantly to endosomes and endolysosomes. BECN1 also promotes the targeting of a smaller fraction of internalized APP to LC3-positive phagophores, suggesting a role for BECN1-dependent PM macroautophagy in APP degradation. Furthermore, BECN1 facilitates lysosomal degradation of surface APP and reduces the secretion of APP metabolites (soluble ectodomains, sAPP). The association between APP and BECN1 is dependent on the evolutionarily conserved domain (ECD) of BECN1 (amino acids 267-337). Deletion of a BECN1 ECD subregion (amino acids 285-299) did not impair BECN1- PIK3C3 interaction, PtdIns3K function or macroautophagy, but was sufficient to impair the APP-BECN1 interaction and BECN1's effects on surface APP internalization and degradation, resulting in increased secretion of sAPPs. Interestingly, both the BECN1-APP association and BECN1-dependent APP endocytosis and degradative trafficking were negatively regulated by active AKT. Our results further implicate phosphorylation of the BECN1 Ser295 residue in the inhibition of APP degradation by AKT. Our studies reveal a novel function for BECN1 in the sorting of a plasma membrane protein for endolysosomal and macroautophagic degradation.\",\n \"corpus_id\": 27028372,\n \"score\": 0\n },\n {\n \"doc_id\": \"28085066\",\n \"title\": \"Mutation-Structure-Function Relationship Based Integrated Strategy Reveals the Potential Impact of Deleterious Missense Mutations in Autophagy Related Proteins on Hepatocellular Carcinoma (HCC): A Comprehensive Informatics Approach.\",\n \"abstract\": \"Autophagy, an evolutionary conserved multifaceted lysosome-mediated bulk degradation system, plays a vital role in liver pathologies including hepatocellular carcinoma (HCC). Post-translational modifications (PTMs) and genetic variations in autophagy components have emerged as significant determinants of autophagy related proteins. Identification of a comprehensive spectrum of genetic variations and PTMs of autophagy related proteins and their impact at molecular level will greatly expand our understanding of autophagy based regulation. In this study, we attempted to identify high risk missense mutations that are highly damaging to the structure as well as function of autophagy related proteins including LC3A, LC3B, BECN1 and SCD1. Number of putative structural and functional residues, including several sites that undergo PTMs were also identified. In total, 16 high-risk SNPs in LC3A, 18 in LC3B, 40 in BECN1 and 43 in SCD1 were prioritized. Out of these, 2 in LC3A (K49A, K51A), 1 in LC3B (S92C), 6 in BECN1 (S113R, R292C, R292H, Y338C, S346Y, Y352H) and 6 in SCD1 (Y41C, Y55D, R131W, R135Q, R135W, Y151C) coincide with potential PTM sites. Our integrated analysis found LC3B Y113C, BECN1 I403T, SCD1 R126S and SCD1 Y218C as highly deleterious HCC-associated mutations. This study is the first extensive in silico mutational analysis of the LC3A, LC3B, BECN1 and SCD1 proteins. We hope that the observed results will be a valuable resource for in-depth mechanistic insight into future investigations of pathological missense SNPs using an integrated computational platform.\",\n \"corpus_id\": 2362616,\n \"score\": 0\n },\n {\n \"doc_id\": \"28129024\",\n \"title\": \"BECN1-dependent CASP2 incomplete autophagy induction by binding to rabies virus phosphoprotein.\",\n \"abstract\": \"Autophagy is an essential component of host immunity and used by viruses for survival. However, the autophagy signaling pathways involved in virus replication are poorly documented. Here, we observed that rabies virus (RABV) infection triggered intracellular autophagosome accumulation and results in incomplete autophagy by inhibiting autophagy flux. Subsequently, we found that RABV infection induced the reduction of CASP2/caspase 2 and the activation of AMP-activated protein kinase (AMPK)-AKT-MTOR (mechanistic target of rapamycin) and AMPK-MAPK (mitogen-activated protein kinase) pathways. Further investigation revealed that BECN1/Beclin 1 binding to viral phosphoprotein (P) induced an incomplete autophagy via activating the pathways CASP2-AMPK-AKT-MTOR and CASP2-AMPK-MAPK by decreasing CASP2. Taken together, our data first reveals a crosstalk of BECN1 and CASP2-dependent autophagy pathways by RABV infection.\",\n \"corpus_id\": 18186807,\n \"score\": 0\n }\n]","isConversational":false}}},{"rowIdx":96,"cells":{"query":{"kind":"string","value":"{\n \"doc_id\": \"28153749\",\n \"title\": \"Energy landscape of a GSTP1 polymorph linked with cytological function decay in response to chemical stressors.\",\n \"abstract\": \"Gene polymorphisms lead to varied structure and functional properties. A single nucleotide polymorphism (SNP) i.e. Ile105Val (rs1695) in glutathione S-transferase P1 (GSTP1) gene influences cytological toxicity and modulates the risk to occupational diseases. Apart from this, cancer, neuropathy, NOx, SOx and ozone mediated respiratory function decline including lung inflammation, asthma, allergy etc., have been reported in people with this missense mutation. Here, the functional properties of rs1695 polymorph are revisited through a computational approach. Changes incurred by GSTP1 antioxidant protein as a result of alteration in its sequence, have been studied through docking followed by Poisson-Boltzmann electrostatic equation interpretation, grid and coulombic energy profile mapping for protein polymorphs with DelPhi. Molecular docking simulation of variant and wild type (WT) protein was carried out with eight FDA approved compounds that target GSTP1 for treatment of various diseases. This was to observe binding pattern variation upon mutation induction. Grid, reaction field and coulombic energy calculation of WT and mutated polymorph, complexed with and without these moieties was then attempted. Alteration in conformation and energy was observed in apo- and holo- form of GSTP1 and their ligand-bound complexes as a result of this mutation. This study is a demo of appraising gene-environment interaction based deleteriousness through molecular docking and dynamics simulation approach.\",\n \"corpus_id\": 2901952\n}"},"candidates":{"kind":"list like","value":[{"doc_id":"18335111","title":"Glutathione S-transferase P1, maternal smoking, and asthma in children: a haplotype-based analysis.","abstract":"BACKGROUND: Glutathione S-transferase P1 (GSTP1) plays a role in a spectrum of respiratory diseases; however, the effects of sequence variation across the entire locus in asthma pathogenesis have yet to be determined. OBJECTIVES: This study was designed to investigate whether sequence variations in the GSTP1 coding and promoter regions are associated with asthma and wheezing outcomes and to determine whether variants affect susceptibility to maternal smoking. METHODS: Four haplotype tagging SNPs were selected that accounted for 83% of the common haplotypic variation in GSTP1. The associations of GSTP1 variants with asthma and wheezing were assessed among white children in the Children's Health Study (CHS). RESULTS: The Ile105Val allele and a SNP in the upstream promoter region (SNP1: rs6591255, putative transcription factor 1 binding site) were associated with asthma and wheezing outcomes, an association observed in two cohorts of the CHS recruited in different years. Haplotypes that included both the promoter SNP (i.e., rs6591255) and the 105 Val variant were associated with an increased risk for asthma in non-Hispanic whites. Using SNP- and haplotype-based approaches, the effect of maternal smoking on wheezing was largest in children with the Ile105Val allele. CONCLUSIONS: Variants in both the promoter and coding regions of the GSTP1 locus may contribute to the occurrence of childhood asthma and wheezing and may increase susceptibility to adverse effects of tobacco-smoke exposure.","corpus_id":15505921,"score":2},{"doc_id":"18559526","title":"Glutathione s-transferase p1: gene sequence variation and functional genomic studies.","abstract":"Glutathione S-transferase P1 (GSTP1) is of importance for cancer research because of its role in detoxifying carcinogens, activating antineoplastic prodrugs, metabolizing chemotherapeutic agents, and its involvement in cell cycle and apoptosis regulation. Two common GSTP1 genetic polymorphisms have been studied extensively. However, the full range of GSTP1 genetic variation has not been systematically characterized in the absence of disease pathology. We set out to identify common GSTP1 polymorphisms in four ethnic groups, followed by functional genomic studies. All exons, splice junctions, and the 5'-flanking region of GSTP1 were resequenced using 60 DNA samples each from four ethnic groups. The 35 single-nucleotide polymorphisms (SNP) identified included six nonsynonymous SNPs and 17 previously unreported polymorphisms. GSTP1 variant allozymes were then expressed in COS-1 cells, and five displayed significantly altered levels of enzyme activity. One decreased to 22% of the wild-type (WT) activity. Four variant allozymes had K(m) values that differed significantly from that of the WT, and five showed altered levels of immunoreactive protein compared with WT, with a significant correlation (r = 0.79, P < 0.007) between levels of immunoreactive protein and enzyme activity in these samples. In the Mexican American population, five linked SNPs were significantly associated with GSTP1 mRNA expression, one of which was found by electrophoretic mobility shift assay to alter protein binding. These studies have identified functionally significant genetic variation, in addition to the two frequently studied GSTP1 nonsynonymous SNPs, that may influence GSTP1's contribution to carcinogen and drug metabolism, and possibly disease pathogenesis and/or drug response.","corpus_id":15355135,"score":2},{"doc_id":"18988661","title":"Glutathione-S-transferase (GST) P1, GSTM1, exercise, ozone and asthma incidence in school children.","abstract":"BACKGROUND: Because asthma has been associated with exercise and ozone exposure, an association likely mediated by oxidative stress, we hypothesised that glutathione-S-transferase (GST)P1, GSTM1, exercise and ozone exposure have interrelated effects on the pathogenesis of asthma. METHODS: Associations of the well characterised null variant of GSTM1 and four single nucleotide polymorphisms (SNPs) that characterised common variation in the GSTP1 locus with new onset asthma in a cohort of 1610 school children were examined. Children's exercise and ozone exposure were classified using participation in team sports and community annual average ozone levels, respectively. RESULTS: A two SNP model involving putatively functional variants (rs6591255, rs1695 (Ile105Va)) best captured the association between GSTP1 and asthma. The risk of asthma was lower for those with the Val allele of Ile105Val (hazard ratio (HR) 0.60, 95% CI 0.4 to 0.8) and higher for the variant allele of rs6591255 (HR 1.40, 95% CI 1.1 to 1.9). The risk of asthma increased with level of exercise among ile(105) homozygotes but not among those with at least one val(105) allele (interaction p value = 0.02). The risk was highest among ile(105) homozygotes who participated in >or=3 sports in the high ozone communities (HR 6.15, 95% CI 2.2 to 7.4). GSTM1 null was independently associated with an increased risk of asthma and showed little variation with air pollution or GSTP1 genotype. These results were consistent in two independent fourth grade cohorts recruited in 1993 and 1996. CONCLUSION: Children who inherit a val(105) variant allele may be protected from the increased risk of asthma associated with exercise, especially in high ozone communities. GSTM1 null genotype was associated with an increased risk of asthma.","corpus_id":23179993,"score":2},{"doc_id":"19240225","title":"Meta- and pooled analysis of GSTP1 polymorphism and lung cancer: a HuGE-GSEC review.","abstract":"Lung cancer is the most common cancer worldwide. Polymorphisms in genes associated with carcinogen metabolism may modulate risk of disease. Glutathione S-transferase pi (GSTP1) detoxifies polycyclic aromatic hydrocarbons found in cigarette smoke and is the most highly expressed glutathione S-transferase in lung tissue. A polymorphism in the GSTP1 gene, an A-to-G transition in exon 5 (Ile105Val, 313A --> 313G), results in lower activity among individuals who carry the valine allele. The authors present a meta- and a pooled analysis of case-control studies that examined the association between this polymorphism in GSTP1 and lung cancer risk (27 studies, 8,322 cases and 8,844 controls and 15 studies, 4,282 cases and 5,032 controls, respectively). Overall, the meta-analysis found no significant association between lung cancer risk and the GSTP1 exon 5 polymorphism. In the pooled analysis, there was an overall association (odds ratio = 1.11, 95% confidence interval: 1.03, 1.21) between lung cancer and carriage of the GSTP1 Val/Val or Ile/Val genotype compared with those carrying the Ile/Ile genotype. Increased risk varied by histologic type in Asians. There appears to be evidence for interaction between amount of smoking, the GSTP1 exon 5 polymorphism, and risk of lung cancer in whites.","corpus_id":-1,"score":2},{"doc_id":"19403501","title":"In utero smoke exposure, glutathione S-transferase P1 haplotypes, and respiratory illness-related absence among schoolchildren.","abstract":"BACKGROUND: The GSTP1 Ile105Val variant and secondhand tobacco smoke exposure have been independently associated with acute respiratory illness; however, susceptibility to in utero and secondhand tobacco smoke has yet to be examined in relation to variation across the GSTP1 locus. OBJECTIVE: The purpose of this work was to determine whether variation across the GSTP1 locus is associated with respiratory illness-related school absences and to determine whether this relationship varies by in utero and secondhand tobacco smoke exposure. METHODS: Tobacco smoke exposure status, incident respiratory-related school absence records, and DNA samples was ascertained for 1132 Hispanic and non-Hispanic white elementary school children as part of the Children's Health Study. RESULTS: Four GSTP1 single-nucleotide polymorphisms were selected that accounted for 93% of the variation across the locus. Individual single-nucleotide polymorphism analyses showed a protective effect for the minor alleles in single-nucleotide polymorphisms 1 (rs6591255), 3 (GSTP1 Ile105Val: rs1695), and 4 (rs749174) for respiratory illness. The haplotype, which includes a minor allele for single-nucleotide polymorphisms 1, 3, and 4 (h1011), was associated with a decreased risk of respiratory illness. The protective effect of GSTP1 variants was lost among individuals exposed to in utero and secondhand tobacco smoke. CONCLUSIONS: A common GSTP1 haplotype, which includes the functional Ile105Val polymorphism, was associated with respiratory-related school absences. The protection afforded by this haplotype was lost in children exposed to involuntary tobacco smoke. The paradigm of loss of genetic protection among those exposed to tobacco smoke has clinical and public health implications that warrant broader consideration in research and practice.","corpus_id":45920598,"score":2},{"doc_id":"20858151","title":"The role of GSTP1 polymorphisms and tobacco smoke exposure in children with acute asthma.","abstract":"BACKGROUND: The glutathione S-transferase enzymes (GSTs) play an important role in the detoxification of environmental tobacco smoke (ETS), which contributes to airway inflammation, a key component of asthma. Genetic variation in GST genes may influence individuals' ability to detoxify environmental pollutants. OBJECTIVE: To examine the role of polymorphisms in GSTP1 (Ile105Val and Ala114Val), alone and in combination with ETS exposure, on atopy and asthma severity. METHODS: GSTP1 Ile105Val and Ala114Val were genotyped and ETS exposure was assessed by parental questionnaire, which was validated by urinary cotinine measurements. Associations between ETS exposure, GSTP1 polymorphisms, and their interaction on atopy and asthma severity were investigated. RESULTS: For the functional GSTP1 105 SNP, those with the Ile/Ile genotype had odds for atopy of 2.77 (p = .054) when assessed by genotype alone, which increased to 9.02 (p = .050) when ETS was included, relative to individuals with other genotypes. Likewise, compared to children with other GSTP1 114 genotypes, those with Ala/Ala genotype had a 5.47-fold (p = .002) increased risk of atopy (p = .020) when assessed by genotype alone, increasing to 9.17-fold when ETS was included. The 105 Ile/Ile individuals all had the AA (105 Ile/Ile and 114 Ala/Ala) haplotype group; therefore, the odds for atopy were the same. Individuals without any *C haplotype (105 Val and 114 Val allele) who were exposed to ETS had a 9.17-fold increased risk of atopy when compared with individuals with at least one *C haplotype and not exposed to ETS (p = .020). CONCLUSION: There were significant interactions between GSTP1 SNPs, atopy, and ETS exposure in this cohort.","corpus_id":21167211,"score":2},{"doc_id":"21128213","title":"GSTP1 Ile105Val polymorphism in astrocytomas and glioblastomas.","abstract":"Glutathione S-transferases (GSTs) constitute a superfamily of ubiquitous multifunctional enzymes that are involved in the cellular detoxification of a large number of endogenous and exogenous chemical agents that have electrophilic functional groups. People who have deficiencies in this family of genes are at increased risk of developing some types of tumors. We examined GSTP1 Ile105Val polymorphism using PCR-RFLP in 80 astrocytoma and glioblastoma samples. Patients who had the Val allele of the GSTP1 Ile105Val polymorphism had an increased risk of tumor development (odds ratio = 8.60; 95% confidence interval = 4.74-17.87; P < 0.001). Overall survival of patients did not differ significantly. We suggest that GSTP1 Ile105Val polymorphisms are involved in susceptibility to developing astrocytomas and glioblastomas.","corpus_id":16092935,"score":2},{"doc_id":"22052985","title":"Glutathione S-transferase P1 c.313A > G polymorphism could be useful in the prediction of doxorubicin response in breast cancer patients.","abstract":"BACKGROUND: Identification of predicting factors for anthracyclines-based chemotherapy remains a clinical challenge. Glutathione S-transferase (GSTs) enzymes detoxify chemotherapy drugs and their metabolites. Several polymorphisms in GST genes result in reduced or no activity of the enzymes. Specifically, GSTM1 and GSTT1 genes are polymorphically deleted, the polymorphism GSTP1 c.313A>G (rs1695) determines the amino acid substitution Ile105Val, where the Val-containing enzyme has reduced activity. Also, GSTA1*B allele has reduced levels of GSTA1 enzyme. Several polymorphisms in GSTs have been associated with differences in survival for cancer patients treated with chemotherapy. PATIENTS AND METHODS: We genotyped a total of five polymorphisms in GSTM1, GSTT1, GSTP1 and GSTA1 genes in 159 patients with locally advanced breast cancer, treated with single-agent doxorubicin or docetaxel (Taxotere). Gene expression microarrays were performed in 67 breast tumor samples. We correlate this data with treatment outcome. RESULTS: In multivariate analysis, patients homozygous GG for GSTP1 c.313A>G SNP had a lower risk of chemoresistance when treated with doxorubicin (odds ratio 0.106; confidence interval 0.012-0.898; P=0.040). No association was found in the docetaxel arm. Also, we found that GSTP1 expression varied significantly among breast cancer molecular subtypes. CONCLUSIONS: GSTP1 may constitute another tool contributing to individualized anthracycline-based therapy.","corpus_id":1516136,"score":2},{"doc_id":"22339038","title":"Evaluation of glutathione S-transferase P1 polymorphisms (Ile105Val and Ala114Val) in patients with small cell lung cancer.","abstract":"AIMS: Glutathione S-transferase P1 (GSTP1) plays an important role in cellular protection against oxidative stress and toxic chemicals. Polymorphisms within GSTP1 are associated with alterations in enzyme activity, which may lead to development of lung disease and cancer. In this study, we aimed to investigate the GSTP1 Ile105Val and Ala114Val polymorphisms in patients with small cell lung cancer (SCLC). PATIENTS/METHODS: GSTP1 Ile105Val polymorphism in exon 5 and GSTP1 Ala114Val polymorphism in exon 6 were determined by using polymerase chain reaction-restriction fragment length polymorphism techniques in 89 patients with SCLC and 108 control patients with chronic obstructive pulmonary disease (COPD). Genotype frequencies and cigarette smoking intensities were compared among SCLC and COPD patients. RESULTS: There were significantly less SCLC patients with variant exon 6 genotypes than COPD patients (7.9% vs. 20.4%, p=0.007), while the number of patients with variant exon 5 genotypes were comparable among groups. SCLC and COPD patients with variant exon 6 genotype showed trends toward exhibiting reduced cigarette consumption. CONCLUSIONS: The variant GSTP1 exon 6 genotype might be conferring protection against SCLC development. Whether this effect is associated with exposure to cigarette smoking needs to be clarified.","corpus_id":39810015,"score":2},{"doc_id":"22783438","title":"Correlation of CYP1A1, GSTP1 and GSTM1 gene polymorphisms and lung cancer risk among smokers.","abstract":"Lung cancer is the leading cause of cancer mortality worldwide and tobacco smoking has been established as its biggest risk factor. Cigarette smoke contains several carcinogens. Most of them need to be activated by phase I enzymes, such as cytochrome P450 (CYP), while phase II enzymes, such as glutathione S-transferases are responsible for the detoxification of activated forms. The present study aimed to determine the role of CYP1A1, GSTP1 and GSTM1 gene polymorphisms in smoking-related lung cancer risk. It also aimed to investigate the association of the above polymorphisms with clinicopathological parameters, as well as their effect on survival. One hundred newly diagnosed lung cancer patients with advanced disease and 125 healthy controls with a smoking history participated in the study. The participants were screened for the presence of the following polymorphisms: MspI (CYP1A1), Ile105Val (GSTP1) and GSTM1 deletion. The above polymorphisms were also examined with regards to gender, age, histological type and survival. GSTP1 Ile/Val and GSTM1-null genotypes were associated with increased lung cancer risk and the presence of the combination of the three non-wild-type genotypes increases susceptibility to lung cancer (OR 3.328, 95% CI=1.681-6.587, p=0.001). In the non-small cell lung cancer group, the GSTP1 homozygous variant was significantly associated with increased lung cancer risk (p=0.008) and shorter survival. The results of this study suggest that the GSTP1 Ile/Val genotype and GSTM1 deletion contribute to increased lung cancer susceptibility. Moreover, GSTP1 Val/Val genotype is associated with increased lung cancer risk and shorter survival in non-small cell lung cancer patients.","corpus_id":6761337,"score":2},{"doc_id":"23811488","title":"GSTP1 Ile105Val polymorphism and colorectal cancer risk: an updated analysis.","abstract":"BACKGROUND: Many studies have investigated the association between the Glutathione S transferase-P1 (GSTP1) Ile105Val polymorphism and colorectal cancer (CRC) susceptibility, but the results were conflicting. The aim of this study is to quantitatively summarize the relationship between this polymorphism and CRC risk. METHODS: Two investigators independently searched the Medline, Embase, China National Knowledge Infrastructure (CNKI) and Chinese Biomedicine databases for studies published before December 2012. Summary odds ratios (ORs) and 95% confidence intervals (95% CIs) for GSTP1 polymorphism and CRC were calculated in a fixed-effects model (the Mantel-Haenszel method) and a random-effects model (the DerSimonian and Laird method) when appropriate. RESULTS: This meta-analysis included 29 case-control studies, which included 8160 CRC cases and 10,450 controls. Overall, the variant genotypes (ValVal and IleVal) of the Ile105Val were not associated with CRC risk when compared with the wild-type IleIle homozygote. Similarly, no associations were found in the dominant and recessive models. When stratifying for ethnicity, source of controls, study sample size and genotyping methods, no evidence of significant association was observed in any subgroup, except among those studies taking others as genotyping methods (recessive model, OR=0.71, 95%CI=0.52-0.96). Limiting the analysis to the studies within Hardy-Weinberg equilibrium, the results were persistent and robust. No publication bias was found in the present study. CONCLUSION: This updated meta-analysis suggests that the GSTP1 Ile105Val polymorphism may not be associated with CRC risk, while the observed decrease in risk of CRC may be due to small-study bias.","corpus_id":19737051,"score":2},{"doc_id":"27366093","title":"Association between GSTP1 Ile105Val polymorphism and urinary system cancer risk: evidence from 51 studies.","abstract":"The GSTP1 gene plays an important role in detoxification of carcinogens. GSTP1 gene polymorphisms may alter the susceptibility of urinary system cancer. Numerous studies have been performed to investigate the association between GSTP1 Ile105Val (rs1695 A>G) polymorphism and urinary system cancer risk. Nevertheless, the results remain controversial and only prostate cancer and bladder cancer are covered. We identified eligible studies from PubMed, Elsevier, and three equivalent Chinese databases including the Chinese National Knowledge Infrastructure, Wanfang, and Weipu. Pooled odds ratios and 95% confidence intervals were used to assess the strength of the association between GSTP1 Ile105Val polymorphism and urinary system cancer risk. In total, 11,762 cases and 15,150 controls from 51 studies were included in the final meta-analysis. The pooled results from all included studies showed a statistically significant association between GSTP1 Ile105Val polymorphism and urinary system cancer. In the subgroup analyses, the GSTP1 Ile105Val polymorphism was found to be significantly associated with prostate cancer risk and also a risk factor for urinary system cancer among Asians. In conclusion, our meta-analysis indicated that GSTP1 Ile105Val polymorphism was associated with urinary system cancer susceptibility, which needs to be validated by more rigorous data from further large-scale population studies with different ethnicities.","corpus_id":-1,"score":2},{"doc_id":"28844589","title":"Impact of CYP1A1, GSTP1 and XRCC1 genes polymorphisms on toxicity and response to chemotherapy in childhood acute lymphoblastic leukemia.","abstract":"BACKGROUND: Acute lymphoblastic leukemia (ALL) is the most common childhood malignancy. The interindividual genetic variations in drug metabolizing enzymes and DNA repair genes influence the efficacy and toxicity of numerous chemotherapeutic drugs affecting the treatment outcome. AIM OF THE WORK: The aim of the study was to investigate the impact of drug metabolizing CYP1, GSTP1 and DNA repair (XRCC1) genes polymorphisms on the toxicity and response to chemotherapy in childhood ALL. PATIENTS AND METHODOLOGY: Ninety seven ALL pediatric patients were genotyped for CYP1A1, GSTP1 ILe105Val and XRCC1 Arg194Tryp single nucleotide polymorphisms (SNPs) using PCR-RFLP. RESULTS: No statistically significant differences were observed between the wild and variant (homozygous and heterozygous) genotypes of the polymorphisms studied in CYP1A1, GSTP1 or XRCC1 genes regarding age, total leukocyte count, immunophenotyping, cytogenetic or risk group. The SNPs in CYP1A1, GSTP1 and XRCC1 genes did not show significant association with complete remission (CR) rate, overall survival (OS) or event free survival (EFS). However, XRCC1 Arg194Trp SNP was associated with higher drug toxicity; carriers of variant genotypes (CT and TT) had a significantly higher frequency of myelosuppression compared to those with the wild CC genotype (21/43[48.8%]) compared to (14/54[25.9%]) (p=0.020). The analysis of the combined effect of studied SNPs did not show any significant association with patient outcome. CONCLUSION: Our study reported a significant association between the DNA repair gene polymorphism and myelosuppression in childhood ALL patients. Adjustment of the dose of chemotherapeutic agents according to XRCC1 Arg194Trp polymorphism may improve outcome in cases with risk of toxicity.","corpus_id":206261373,"score":2},{"doc_id":"29285015","title":"Evaluation of glutathione S-transferase P1 (GSTP1) Ile105Val polymorphism and susceptibility to type 2 diabetes mellitus, a meta-analysis.","abstract":"It is well established that type 2 diabetes mellitus (T2DM) is associated with oxidative stress and glutathione S-transferases (GSTs) protect cells against oxidative stress. The missense substitution Ile105Val (rs1695) of the glutathione S-transferase P1 (GSTP1, OMIM: 134660) results from an A/G base substitution at nucleotide 313. Many studies have evaluated the correlation between the rs1695 polymorphism and T2DM, but the results remain inconclusive. The aim of the present meta-analysis was to investigate the association between GSTP1 Ile105Val polymorphism and the susceptibility risk of T2DM. Eligible studies (published before August 2017) were identified in several databases. The heterogeneity between studies was evaluated with the chi-square based Q test and the I2 test. The strengths of the association were assessed by pooled odds ratios (ORs) and the corresponding 95 % confidence interval (95 % CI) using either a fixed or random-effects models. Eighteen studies documenting a total of 2595 T2DM cases and 2888 controls were included in this meta-analysis. In the overall analysis there was no significant association between the rs1695 polymorphism and the risk of T2DM. The subgroup analyses stratified by ethnicity, publication year and sample size did not reveal significant association between the study polymorphism and the risk of T2DM and any sources contributing to the substantial heterogeneity between studies. The present meta-analysis suggested that there was significant heterogeneity between studies. Considering some limi tations of our meta-analysis, further large-scale studies should be done to reach a more comprehensive understanding.","corpus_id":23222476,"score":2},{"doc_id":"18188076","title":"The influence of genetic polymorphisms of GSTP1 on the development of asbestosis.","abstract":"OBJECTIVE: Genetic factors play an important role in the development of asbestosis. The aim of this study was to investigate whether genetic polymorphisms of glutathione S-transferase (GST) P1 represent a risk factor for this disease. METHODS: The study population included 262 workers with asbestosis and 265 matched controls. Information on cumulative asbestos exposure was available. A real-time PCR based on the 5' nuclease assay was designed for the analysis of GSTP1 Ile105Val and Ala114Val polymorphisms. RESULTS: Asbestosis was associated with GSTP1 genotype coding for an enzyme with high conjugation capacity versus genotypes resulting in intermediate and low enzyme activity (odds ratio = 1.49, confidence interval = 1.06-2.10). CONCLUSIONS: The key finding of the study was that GSTP1 genotype coding for an enzyme with high conjugation capacity significantly increases the risk of developing asbestosis.","corpus_id":20637263,"score":1},{"doc_id":"18505928","title":"Identification and functional characterization of the human glutathione S-transferase P1 gene as a novel transcriptional target of the p53 tumor suppressor gene.","abstract":"The glutathione S-transferase P1 (GSTP1) is involved in multiple cellular functions, including phase II metabolism, stress response, signaling, and apoptosis. The mechanisms underlying the significantly high GSTP1 expression in many human tumors are, however, currently not well understood. We report here that the GSTP1 gene is a heretofore unrecognized downstream transcriptional target of the tumor suppressor p53. We identified a p53-binding motif comprising two consecutive half-sites located in intron 4 of the GSTP1 gene and is highly homologous to consensus p53-binding motifs in other p53-responsive genes. Using a combination of electrophoretic mobility shift assay and DNase I footprinting analyses, we showed that wild-type p53 protein binds to the GSTP1 p53 motif and luciferase reporter assays showed the motif to be transcriptionally functional in human tumor cells. In a temperature-sensitive p53-mutant cells, levels of both p21/WAF1 and GSTP1 gene transcripts increased time dependently when cells were switched from the inactive mutant state to the wild-type p53 state. Small interfering RNA-mediated reduction of p53 expression resulted in a specific decrease in GSTP1 expression and in tumor cells with mutated p53; adenovirally mediated expression of wild-type p53 increased GSTP1 expression significantly. In a panel of early-passage brain tumor cultures from patients, high levels of GSTP1 transcripts and protein were associated with wild-type p53 and, conversely, low GSTP1 levels with mutant p53. p53 expression knockdown by small interfering RNA increased cisplatin sensitivity. The ability of wild-type p53 to transcriptionally activate the human GSTP1 gene defines a novel mechanism of protecting the genome and, potentially, of tumor drug resistance.","corpus_id":23871030,"score":1},{"doc_id":"18787219","title":"Glutathione transferase P1: an endogenous inhibitor of allergic responses in a mouse model of asthma.","abstract":"RATIONALE: Although epidemiological studies have linked asthma susceptibility and severity to polymorphisms in human glutathione transferase Pi (GSTP) 1, there is no direct evidence for a functional involvement of GSTP1 in processes that are pathognomic of asthma. OBJECTIVES: To examine the role of GSTP1 in modulating the development of allergic airways disease. METHODS: Allergic airways disease was induced in wild-type (WT) and Gstp-null mice employing both acute and chronic models. Eosinophilia, goblet cells, and remodeling were quantified by histological assessment; respiratory function was determined using invasive methods. ELISA was used to evaluate Th2 cytokines, eotaxin, and phospho-c-Jun. Gstp1/2 expression was quantified by reverse transcriptase-polymerase chain reaction. MEASUREMENTS AND MAIN RESULTS: Compared with allergic WT mice, eosinophilia, goblet cell hyperplasia, airway remodeling, lung resistance, and IL-5 were enhanced in allergic Gstp-null mice. However, the protective efficacy of GSTP1 was mouse-strain dependent, and associated with inherent variation in expression of Gstp1. Although elevated levels of phospho-c-Jun were detected in Gstp-null mice, treatment of WT mice with a GSTP/c-Jun N-terminal kinase (JNK) inhibitory peptide enhanced phospho-c-Jun and significantly attenuated allergic responses. CONCLUSIONS: GSTP1 attenuates the severity of allergic airways disease. However, the efficacy of GSTP1 correlated with mouse strain-dependent variation in Gstp1 expression. Although GSTP1 attenuated c-Jun phosphorylation, treatment with a GSTP/JNK inhibitory peptide revealed an inverse relationship between c-Jun phosphorylation and allergic responses, indicating that the mechanism by which GSTP attenuates allergic responses is not dependent on the JNK/c-Jun axis. Our data, together with epidemiological evidence, suggest variation in expression and/or function of this protein is an important determinant in asthma pathophysiology.","corpus_id":41707355,"score":1},{"doc_id":"19568750","title":"MRP2 and GSTP1 polymorphisms and chemotherapy response in advanced non-small cell lung cancer.","abstract":"PURPOSE: The level of drug metabolism and drug transport is correlated with the sensitivity of cancer cells towards platinum-based chemotherapy. We hypothesize that genetic polymorphisms in metabolising enzymes gene GSTP1 (glutathione S-transferase P1), and MRP2 (multidrug resistance-associated protein 2) (ABCC2), which result in inter-individual differences in metabolism and drug disposition, may predict clinical response to platinum agents in advanced non-small cell lung cancer (NSCLC) patients. METHODS: Totally 113 patients with advanced NSCLC were routinely treated with platinum-based chemotherapy, and clinical response was evaluated after four cycles. MRP2 C-24T (-24C>T), MRP2 Val417Ile (1249G>A), MRP2 Ile1324Ile (3972C>T), and GSTP1 Ile105Val (342A>G) genotype were determined by gene-chip method (a 3-D (three dimensions) polyacrylamide gel-based DNA microarray method) using DNA samples isolated from peripheral blood collected before treatment. Pearson Chi-square test and Fisher's exact test were performed to measure the differences of the chemotherapeutic efficacy among variant genotype. The odds ratios and 95% confidence intervals were computed by logistic regression. RESULTS: The C-->T change of MRP2 C-24T and the A-->G change of GSTP1 Ile105Val polymorphism significantly increased platinum-based chemotherapy response. CONCLUSION: The polymorphic status of MRP2 C-24T and GSTP1 Ile105Val might be the predictive markers for the treatment response of advanced NSCLC patients. The DNA microarray-based method is accurate, high throughput and inexpensive, suitable for single-nucleotide polymorphism genotyping in a large number of individuals.","corpus_id":10702244,"score":1},{"doc_id":"20210814","title":"Interaction between early maternal smoking and variants in TNF and GSTP1 in childhood wheezing.","abstract":"BACKGROUND: Children exposed to tobacco smoke early in life have a higher risk of wheeze. Individual susceptibility may depend on genetic factors. OBJECTIVE: We studied whether variations in single nucleotide polymorphisms (SNPs) in the TNF, glutathione S transferase P1 (GSTP1) and beta2-adrenoreceptor (ADRB2) genes modify the effect of early maternal smoking on the development of childhood asthma, wheeze and allergic sensitization. METHODS: In the Swedish prospective birth cohort BAMSE (Children, Allergy, Milieu, Stockholm, Epidemiological Survey) (n=4089), data collection included questionnaires to measure tobacco smoke exposure and clinical outcomes up to age 4 and medical examinations with blood sampling for specific IgE measurements and genotyping. We defined early maternal smoking as daily smoking by the mother during pregnancy and/or postnatally. We investigated five TNF, six GSTP1 and three ADRB2 SNPs in 982 selected wheezers and non-wheezers. RESULTS: An interaction with early maternal smoking was found for three TNF SNPs (-857C/T, Intron 1, Intron 3) with respect to early wheeze (up to 2 years of age). For example, the odds ratio (OR) for developing early wheeze related to early maternal smoking was 2.4 [95% confidence interval (CI) 1.6-3.7] in children with a wild-type CC homozygote genotype of the TNF-857 SNP, while no tobacco-related risk was seen in children carrying the rare T allele. A clear dose response was observed in children with the CC genotype, with an OR of 1.3 (95% CI 1.1-1.5) per each additional pack per week smoked by the mother during pregnancy. A suggestive interaction with early maternal smoking was also seen for three GSTP1 SNPs (Intron 5, Intron 6 and Ile105Val) with respect to transient wheeze, but not for ADRB2 and wheeze phenotypes. No effect modifications were observed for allergic sensitization. CONCLUSION: Our results suggest that the risk of early childhood wheeze associated with early maternal smoking may be modified by TNF and GSTP1 polymorphisms.","corpus_id":205274695,"score":1},{"doc_id":"20840864","title":"Polymorphism in glutathione S-transferase P1 is associated with susceptibility to Plasmodium vivax malaria compared to P. falciparum and upregulates the GST level during malarial infection.","abstract":"Glutathione S-transferase P1 (GSTP1) is a member of the GST superfamily, which has well-established multiple roles in various infectious and parasitic diseases. The genetic regulation of GSTP1 has been extensively studied. Thus, its biological significance and disease association prompted us to investigate the role of GSTP1 polymorphisms in Plasmodium-mediated pathogenesis in infected humans. The genotypic distribution of Ile105Val in Plasmodium vivax infection was observed to be significant and strongly associated (OR=4.5) with the progression of pathology, whereas in P. falciparum infection no significant association was observed compared to healthy subjects. Interestingly, we observed significant elevation of GST in vivax infection, with both genotypes Ile105Val and Val105Val, compared to healthy subjects, whereas in P. falciparum infection we found marginally elevated GST levels of mutated genotypes but significantly depleted compared to healthy subjects. Further, during vivax and falciparum infection overall significant elevations of glutathione, glutathione peroxidase, and GST levels were observed. Expression of both GSTP1 mRNA and protein was significantly upregulated during vivax infection compared to falciparum infection and both were significantly upregulated compared to the levels in healthy subjects as well. These studies suggest that GSTP1 polymorphism is involved in the pathogenesis of malaria and it may serve as a valuable molecular marker, possessing a promising rationale for diagnostic potential in assessing disease progression during clinical malaria.","corpus_id":207547055,"score":1},{"doc_id":"20922139","title":"GST (GSTM1, GSTT1, and GSTP1) polymorphisms in the genetic susceptibility of Turkish patients to cervical cancer.","abstract":"OBJECTIVE: This work investigates the role of glutathione S-transferase M1 (GSTM1), glutathione S-transferase T1 (GSTT1), and glutathione S-transferase P1 (GSTP1) enzymes and polymorphisms, which are found in phase II detoxification reactions in the development of cervical cancer. METHODS: This study was conducted with 46 patients diagnosed with cervical cancer and 52 people with no cancer history. Multiplex PCR methods were used to evaluate the GSTM1 and GSTT1 gene polymorphism. However, the GSTP1 (Ile105Val) gene polymorphism was studied using a PCR-RFLP method. The patient and control groups were compared using a chi-square test with p<0.05. RESULTS: In the patient group, statistical significance was determined for gravidity (p=0.03), parity (p=0.01), and the number of living children (p=0.01) compared to the control group. The gene frequency of GSTM1, GSTT1, and GSTP1 polymorphisms was evaluated. We observed that GSTM1 and GSTT1 null genotype frequencies were 54.3% and 32.6% respectively, while GSTP1 (Ile/Val), (Ile/Ile), (Val/Val) genotype frequencies were 52%, 44%, and 4%, respectively, in the cervical cancer patients. No statistical variation was determined between the control and patient groups in terms of GSTM1, GSTT1, and GSTP1 polymorphisms (p>0.05). CONCLUSION: Our results demonstrate that GSTT1, GSTM1, and GSTP1 polymorphisms are not associated with cervical cancer in Turkish patients.","corpus_id":34933820,"score":1},{"doc_id":"20979931","title":"Associations between oxaliplatin-induced peripheral neuropathy and polymorphisms of the ERCC1 and GSTP1 genes.","abstract":"OBJECTIVE: Oxaliplatin-induced chronic neuropathy is cumulative and dose-limiting; reliable predictors and determination of the mechanism of this toxic effect are needed. METHODS: We retrospectively studied 51 Japanese adults with colorectal cancer who had received oxaliplatin-based chemotherapy to explore the pharmacogenetic association between oxaliplatin-induced neuropathy and polymorphisms of the excision repair cross-complementation Group 1 (ERCC1) and glutathione-S-transferases pi 1 (GSTP1) genes. RESULTS: For the ERCC1 C118T polymorphism, Grade 1 chronic neuropathy developed earlier in patients with C/T and T/T genotypes (median number of treatment cycles at onset = 6) than in those with the reference C/C genotype (7 cycles; p = 0.0162 by the generalized Wilcoxon test). For the GSTP1 Ile105Val polymorphism, chronic neuropathy developed earlier in patients with the reference Ile/Ile genotype (6 cycles) than in those with Ile/Val and Val/Val genotypes (9 cycles; p = 0.0321). ERCC1 C118T and GSTP1 Ile105Val polymorphisms were not significantly associated with an increased risk of developing Grade 2 or more severe chronic neuropathy. CONCLUSIONS: Our results suggest that ERCC1, C118T and GSTP1 Ile105Val polymorphisms are more strongly related to the time until onset of neuropathy than to the grade of neuropathy. Most likely these polymorphisms influence patients' sensitivity to neuropathy.","corpus_id":11629487,"score":1},{"doc_id":"21091064","title":"Exploring the landscape of protein-ligand interaction energy using probabilistic approach.","abstract":"Analysis of protein/small molecule interactions is crucial in the discovery of new drug candidates and lead structure optimization. Small biomolecules (ligands) are highly flexible and may adopt numerous conformations upon binding to the protein. Using computer simulations instead of sophisticated laboratory procedures may significantly reduce cost of some stages of drug development. Inspired by probabilistic path planning in robotics, stochastic roadmap methodology can be regarded as a very interesting approach to effective sampling of ligand conformational space around a protein molecule. Protein-ligand interactions are divided into two parts: electrostatics, modeled by the Poisson-Boltzmann equation, and van der Waals interactions, represented by the Lennard-Jones potential. The results are promising; it can be shown that locations of binding sites predicted by the simulation are in agreement with those revealed by experimental x-ray crystallography of protein-ligand complexes. We wanted to extend our knowledge beyond the current molecular modeling tools to arrive at a better understanding of the ligand-binding process. To this end, we investigated a two-level model of protein-ligand interaction and sampling of ligand conformational space covering the entire surface of protein target.","corpus_id":35188846,"score":1},{"doc_id":"21608983","title":"Free-energy landscapes of protein domain movements upon ligand binding.","abstract":"The conformation and functions of proteins are closely linked, and many proteins undergo conformational changes upon ligand binding. The X-ray crystallographic studies have revealed conformational differences in proteins between the liganded and unliganded states. Currently, the conformational transitions that originate in the ligand binding are explained on the basis of two representative models, the induced-fit and preexisting equilibrium dynamics models. However, the actual dynamics of the proteins remain ambiguous. Though these two models are the extreme ones, it is important to understand the difference between these two, particularly in structural biology and medicinal chemistry studies. Here, we clarified the difference in the mechanisms responsible for the conformational changes induced in two proteins upon ligand binding by examining computationally determined free-energy profiles of the apo- and holoproteins. The lysine/arginine/ornithine-binding protein and maltose/maltodextrin-binding protein were chosen as the target proteins, and the energy profiles were generated by a molecular simulation approach. Our results revealed that fluctuations in the apo state and protein-ligand interactions both play important roles in conformational transition, and the mechanism is highly influenced by the fluctuations in the apo state, which are unique to a particular structure.","corpus_id":12513402,"score":1},{"doc_id":"22180037","title":"Genetic polymorphism of the glutathione-S-transferase P1 gene (GSTP1) and susceptibility to prostate cancer in the Kashmiri population.","abstract":"Glutathione-S-transferase P1 (GSTP1) is a critical enzyme of the phase II detoxification pathway. One of the common functional polymorphisms of GSTP1 is A→G at nucleotide 313, which results in an amino acid substitution (Ile105Val) at the substrate binding site of GSTP1 and reduces catalytic activity of GSTP1. To investigate the GSTP1 Ile105Val genotype frequency in prostate cancer cases in the Kashmiri population, we designed a case-control study, in which 50 prostate cancer cases and 45 benign prostate hyperplasia cases were studied for GSTP1 Ile105Val polymorphism, compared to 80 controls taken from the general population, employing the PCR-RFLP technique. We found the frequency of the three different genotypes of GSTP1 Ile105Val in our ethnic Kashmir population, i.e., Ile/Ile, Ile/Val and Val/Val, to be 52.4, 33.3 and 14.3% among prostate cancer cases, 48.5, 37.5 and 14% among benign prostate hyperplasia cases and 73.8, 21.3 and 5% in the control population, respectively. There was a significant association between the GSTP1 Ile/Val genotype and the advanced age group among the cases. We conclude that GSTP1 Ile/Val polymorphism is involved in the risk of prostate cancer development in our population.","corpus_id":38386494,"score":1},{"doc_id":"22251241","title":"Role of glutathione S-transferases in melanoma susceptibility: association with GSTP1 rs1695 polymorphism.","abstract":"BACKGROUND: Glutathione S-transferases (GSTs) GSTM1, GSTT1 and GSTP1 are multifunctional enzymes involved in the detoxification of a wide range of reactive oxygen species produced during melanin synthesis and oxidative stress processes. OBJECTIVES: Single nucleotide polymorphisms (SNPs) in GSTP1 and copy number variants in GSTM1 and GSTT1 may be candidate low-penetrance variants with a role in susceptibility to malignant melanoma (MM). METHODS: In this case-control study, 562 Spanish patients with sporadic MM and 338 cancer-free control subjects were included, and the role of polymorphisms in these GST genes was investigated. Genotypes were established by quantitative real-time polymerase chain reaction for GSTM1 and GSTT1 while TaqMan probes were used to genotype GSTP1 SNPs. RESULTS: The GSTP1 polymorphism rs1695, which encodes the amino acid change p.Ile105Val, was individually associated with MM [odds ratio (OR): 1·32, 95% confidence interval (CI): 1·06-1·63]. Furthermore, individuals carrying one or two MC1R nonsynonymous changes and GSTP1 rs1695 rare allele had an increased risk of developing MM (OR: 3·34, 95% CI: 1·42-8·09 and OR: 20·42, 95% CI: 2·80-417·42, respectively). CONCLUSIONS: This is the first time that the GSTP1 rs1695 polymorphism is reported to be associated with MM. In addition, this study is one of the largest GST polymorphism studies undertaken in the Spanish population and the first time that copy number variants have been scrutinized in relation to MM.","corpus_id":26123505,"score":1},{"doc_id":"22812193","title":"Lack of association between GSTM1, GSTP1, and GSTT1 gene polymorphisms and asthma in adult patients from Rome, central Italy.","abstract":"BACKGROUND: Asthma is a complex multifactorial disease that is not yet fully understood. Oxidative stress due to an imbalance between the oxidative forces and the antioxidant defense systems has been implicated in asthma pathogenesis. However, much debate still surrounds the key genetic factors involved in the development of this disease. Candidate genes include the glutathione S-transferases (GSTs). In particular, mu, pi, and theta classes of GSTs play an important role in regulating inflammatory responses. However, few and contradictory data are available on the association between asthma development and GST gene polymorphisms (GSTM1, GSTP1, and GST1). OBJECTIVE: To investigate whether GSTM1, GSTT1, and GSTP1 polymorphisms are associated with asthma development. METHODS: We recruited 200 unrelated healthy individuals and 199 asthmatic patients from Rome in Central Italy. Genotyping of GSTMI and GSTT1 genes was performed by a multiplex polymerase chain reaction (PCR) while the GSTP1 polymorphism (rs1695) was determined using PCR-restriction fragment length polymorphism analysis. RESULTS: Our results suggest that the GST polymorphisms analyzed are not associated with asthma, confirming the uncertain role of GST genes in the development of asthma. CONCLUSIONS: Oxidative stress is certainly involved in the development of asthma, and GSTs may therefore influence asthma risk, although, as our results show, their role in pathogenesis remains to be elucidated. Future studies should focus on the interactions of GST genes with the environment and other antioxidant genes to shed light on the role of GSTs in asthma.","corpus_id":2367056,"score":1},{"doc_id":"22938488","title":"The GSTP1 Ile105Val polymorphism is not associated with susceptibility to colorectal cancer.","abstract":"The glutathione S transferase (GST) family is a major part of cellular defense mechanisms against endogenous and exogenous substances, many of which have carcinogenic potential. Alteration in the expression level or structure of the glutathione-S-transferase (GST) enzymes may lead to inadequate detoxification of potential carcinogens and consequently contribute to cancer development. A member of the glutathione-S-transferase (GST) family, GSTP1, is an attractive candidate for involvement in susceptibility to carcinogen-associated colorectal cancer. An A>G transition in exon 5 resulting in an Ile105Val amino acid substitution has been identified which alters catalytic efficiency. The present study investigated the possible impact of Ile105Val GSTP1 polymorphism on susceptibility to colorectal cancer. in Jordan We examined 90 tissue samples previously diagnosed with colorectal carcinoma, and 56 non-cancerous colon tissues. DNA was extracted from paraffin embedded tissues and the status of the GSTP1 polymorphism was determined using a polymerase chain reaction restriction fragment length polymorphism (RFLP) method. No statistically significant differences were found between colorectal cancer cases and controls for the GSTP1 Ile/Ile, Ile/Val and Val/Val genotypes. The glutathione S-transferase polymorphism was not associated with risk in colorectal cancer cases in Jordan stratified by age, sex, site, grade or tumor stage. In conclusion, the GSTP1 Ile105Val polymorphism is unlikely to affect the risk of colorectal cancer.","corpus_id":14665063,"score":1},{"doc_id":"23025812","title":"Modulation of a ligand's energy landscape and kinetics by the chemical environment.","abstract":"Understanding how the chemical environment modulates the predominant conformations and kinetics of flexible molecules is a core interest of biochemistry and a prerequisite for the rational design of synthetic catalysts. This study combines molecular dynamics simulation and Markov state models (MSMs) to a systematic computational strategy for investigating the effect of the chemical environment of a molecule on its conformations and kinetics. MSMs allow quantities to be computed that are otherwise difficult to access, such as the metastable sets, their free energies, and the relaxation time scales related to the rare transitions between metastable states. Additionally, MSMs are useful to identify observables that may act as sensors for the conformational or binding state of the molecule, thus guiding the design of experiments. In the present study, the conformation dynamics of UDP-GlcNAc are studied in vacuum, water, water + Mg(2+), and in the protein UDP-GlcNAc 2-epimerase. It is found that addition of Mg(2+) significantly affects the conformational stability, thermodynamics, and kinetics of UDP-GlcNAc. In particular, the slowest structural process, puckering of the GlcNAc sugar, depends on the overall conformation of UDP-GlcNAc and may thus act as a sensor of whether Mg(2+) is bound or not. Interestingly, transferring the molecule from vacuum to water makes the protein-binding conformations UDP-GlcNAc first accessible, while adding Mg(2+) further stabilizes them by specifically associating to binding-competent conformations. While Mg(2+) is not cocrystallized in the UDP-GlcNAc 2-epimerase complex, the selectively stabilized Mg(2+)/UDP-GlcNAc complex may be a template for the bound state, and Mg(2+) may accompany the binding-competent ligand conformation to the binding pocket. This serves as a possible explanation of the enhanced epimerization rate in the presence of Mg(2+). This role of Mg(2+) has previously not been described and opens the question whether \"binding co-factors\" may be a concept of general relevance for protein-ligand binding.","corpus_id":23245271,"score":1},{"doc_id":"23077566","title":"Interaction between GSTP1 Val allele and H. pylori infection, smoking and alcohol consumption and risk of gastric cancer among the Chinese population.","abstract":"Glutathione S-transferase P1 (GSTP1) is a critical enzyme in the phase II detoxification pathway. One of the common functional polymorphisms of GSTP1 is A→G at nucleotide 313, which results in an amino acid substitution (Ile105Val) at the substrate binding site and reduced catalytic activity. We evaluated the interaction between GSTP1 Val allele and Helicobacter pylori infection, smoking and alcohol consumption, increasing the risk of gastric cancer among the Chinese population. Information on potential gastric cancer risk factors and blood specimens were collected from 618 incident gastric cancer cases and 1,830 non-cancer controls between March 2002 and December 2011 in Liaoning Province, China. GSTP1 Ile105Val was genotyped by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry and polymerase chain reaction-restriction fragment length polymorphism. Serum levels of anti-H. pylori IgG were measured by ELISA. Odds ratio (OR) and 95% confidence interval (CI) were calculated using multivariate logistic regression, adjusted by sex and age. The risk of gastric cancer was significantly elevated in patients with the GSTP1 Val/Val genotype (adjusted OR = 3.324; 95% CI = 1.790-6.172). An elevated risk of gastric cancer was observed in patients with H. pylori infection, smoking, or alcohol consumption, and together with the GSTP1 Ile/Val +Val/Val genotype (OR = 3.696; 95% CI = 2.475-5.521; OR = 1.638; 95% CI = 1.044-2.571; OR = 1.641; 95% CI = 0.983-2.739, respectively) (p<0.05). The GSTP1 Val allele shows an interaction with smoking, alcohol consumption, and especially H. pylori infection for increasing the risk of gastric cancer. These findings could demonstrate new pathophysiological pathways for the development of gastric cancer.","corpus_id":16222411,"score":1},{"doc_id":"23471163","title":"Glutathione S-transferase P1 Ile105Val polymorphism and oral cancer risk: a meta-analysis.","abstract":"Objective The glutathione S-transferase P1 (GSTP1) gene has been suggested to play an important role in the pathogenesis of oral cancer. However, the results have been inconsistent. In this study, we performed a meta-analysis to clarify the association of GSTP1 Ile105Val polymorphisms with oral cancer risk. Methods Published literature from PubMed and EMBASE were retrieved. Pooled odds ratio (OR) with 95% confidence interval (CI) was calculated using fixed- or random-effects model. Results 13 studies (1803 oral cancer cases and 2998 controls) for GSTP1 Ile105Val polymorphism were included in the meta-analysis. The results indicated that there was no significant association between GSTP1 Ile105Val polymorphism and oral cancer in the overall population (OR=1.30, 95%CI=0.92-1.38, I(2)=48.0%, p for heterogeneity=0.027). Further subgroup analysis by ethnicity suggested that GSTP1 Ile105Val polymorphism was significantly associated with oral cancer only in East Asians (OR=1.64, 95%CI=1.16-2.31, I(2)=0.0%, p for heterogeneity=0.525), but not in Caucasians (OR=1.16, 95%CI=0.73-1.82, I(2)=7.5%, p for heterogeneity=0.299), Africans (OR=1.10, 95%CI=0.37-3.28), South Asians (OR=1.20, 95%CI=0.69-2.08, I(2)=74.3%, p for heterogeneity=0.021) and mixed population (OR=0.91, 95%CI=0.70-1.20, I(2)=39.7%, p for heterogeneity=0.174). Conclusions The present meta-analysis has limited evidence to support the association of GSTP1 Ile105Val polymorphism with HCC risk in the overall population. However, GSTP1 Ile105Val polymorphism might be associated with risk of oral cancer in East Asians.","corpus_id":6893153,"score":1},{"doc_id":"23494181","title":"Association between the GSTP1 Ile105Val polymorphism and prostate cancer risk: a systematic review and meta-analysis.","abstract":"Many studies have reported the role of glutathione S-transferase P1 (GSTP1) Ile105Val polymorphism with prostate cancer (PCa) risk. However, these studies have yielded conflicting results. Hence, we performed this meta-analysis to investigate the association between GSTP1 Ile105Val polymorphism and PCa in different inheritance models. A total of 13 eligible studies were pooled into this meta-analysis. There was significant association between the GSTP1 Ile158Val variant genotypes and PCa for Ile/Ile vs Val/Val comparison [odds ratio (OR) =0.705; I (2) =63.7 %; 95 % confidence interval (95 % CI) = 0.508-0.977], Ile/Val vs Val/Val comparison (OR=0.736; I (2) =8.0 %; 95 % CI=0.613-0.883), and dominant model (OR=0.712; I (2) =45.5 %; 95 % CI=0.555-0.913). However, no associations were detected for other genetic models. In the stratified analysis by ethnicity, significant associations between GSTP1 Ile105Val polymorphism and PCa risk were also found among Caucasians (Ile/Ile vs Val/Val comparison OR=0.818, I (2) =0.0 %, 95 % CI=0.681-0.982; Ile/Val vs Val/Val comparison OR=0.779, I (2) =0.0 %, 95 % CI=0.651-0.933; and dominant model OR=0.794, I (2) =0.0 %, 95 % CI=0.670-0.941), while there were no associations found for other genetic models. However, no associations were found in Asians and African-Americans for all genetic models when stratified by ethnicity. In conclusion, our meta-analysis indicates that GSTP1 Ile105Val polymorphisms contributed to the PCa susceptibility. However, a study with the larger sample size is needed to further evaluate gene-environment interaction on GSTP1 Ile105Val polymorphisms and PCa risk.","corpus_id":768191,"score":1},{"doc_id":"23604281","title":"Genetic polymorphisms of ERCC1‑118, XRCC1‑399 and GSTP1‑105 are associated with the clinical outcome of gastric cancer patients receiving oxaliplatin‑based adjuvant chemotherapy.","abstract":"The aim of the present study was to determine whether specific molecular parameters may serve as predictors of treatment outcomes and toxicity of oxaliplatin (OXA)‑based chemotherapy, which is used as an adjuvant treatment in resected gastric cancer. All gastric cancer patients examined in the study received an OXA/5‑fluorouracil chemotherapeutic regimen. Genetic polymorphisms of certain platinum‑related genes were determined by the TaqMan 5' nuclease assay and direct sequencing. Relapse‑free survival (RFS), overall survival (OS) and toxicity were evaluated according to each genotype. Following adjustment for the most relevant clinical variables, excision repair cross‑complimentary group 1 (ERCC1)‑118 and X-ray repair cross-complementing protein 1 (XRCC1‑399) demonstrated significant predictive value for RFS and OS. We also demonstrated that carrying at least one variant XRCC1 Arg399Gln or glutathione S-transferase π 1 (GSTP1) Ile105Val allele significantly increased the risk of any grade 3 or 4 hematological toxicity. In particular, carrying at least one variant GSTP1 Ile105Val allele was also significantly correlated with an increased risk of grade 3 or 4 gastrointestinal toxicity and neurotoxicity. Our data suggested that gastric cancer patients harboring ERCC1‑118 C/C and XRCC1‑399 A/G or A/A genotypes may benefit from receiving OXA‑based adjuvant chemotherapy, and carrying at least one variant XRCC1 Arg399Gln or GSTP1 Ile105Val allele may contribute to the occurrence of adverse drug effects associated with OXA‑based chemotherapy.","corpus_id":207562730,"score":1},{"doc_id":"23765758","title":"Quantitative assessment of the association between GSTP1 gene Ile105Val polymorphism and susceptibility to hepatocellular carcinoma.","abstract":"Glutathione S-transferase P1 (GSTP1) gene Ile105Val polymorphism has been suggested to be involved in the development of cancer. However, the results from the studies regarding the association between GSTP1 Ile105Val polymorphism and hepatocellular carcinoma risk have been inconsistent. Thus, we performed a meta-analysis to investigate the association. Published literature from PubMed, Chinese Biomedical Literature, and Wanfang databases was searched for eligible publications. Pooled odds ratios (ORs) with 95 % confidence intervals (95 %CIs) were calculated using random- or fixed-effects model. Six studies with a total of 1,843 participants were finally included into this meta-analysis. The results suggested there was no association between GSTP1 Ile105Val polymorphism and hepatocellular carcinoma risk under all genetic models (for ValVal vs. IleIle, OR = 0.79, 95 %CI 0.48-1.29, P = 0.341; for IleVal vs. IleIle, OR = 1.05, 95 %CI 0.84-1.30, P = 0.678; for the dominant model, OR = 0.91, 95 %CI 0.68-1.20, P = 0.498; and for the recessive model, OR = 0.76, 95 %CI 0.47-1.24, P = 0.269). Subgroup analyses by ethnicity showed there was also no association between GSTP1 Ile105Val polymorphism and hepatocellular carcinoma risk in Asians under all genetic models (All P values were more than 0.05), but GSTP1 Ile105Val polymorphism was associated with decreased risk of hepatocellular carcinoma in European under the recessive model (ValVal vs. IleVal/IleIle) (OR = 0.44, 95 %CI 0.20-0.98, P = 0.044). In conclusion, the meta-analysis suggests that there is little evidence for the association between GSTP1 Ile105Val polymorphism and hepatocellular carcinoma risk. However, more well-designed studies are needed to further assess this association.","corpus_id":14562467,"score":1},{"doc_id":"23812950","title":"Pharmacogenetic influence of GST polymorphisms on anthracycline-based chemotherapy responses and toxicity in breast cancer patients: a multi-analytical approach.","abstract":"BACKGROUND AND OBJECTIVE: Chemotherapeutic drug treatment outcomes are genetically determined. Polymorphisms in genes encoding phase II drug metabolizing enzyme glutathione-S-transferase (GST) can possibly predict treatment outcomes, and can be of prognostic significance in breast cancer patients. The aim of this study was to determine the role of genetic variations in GST in predicting response to, and toxicity of, anthracycline-based chemotherapy in breast cancer patients. METHOD: Two hundred and seven patients treated with anthracycline-based chemotherapy were genotyped for GSTM1 and GSTT1 deletion polymorphisms, and GSTP1 Ile105Val (rs1695), by polymerase chain reaction (PCR)/ PCR-restriction fragment length polymorphism (RFLP). Genetic variations were correlated with tumor response to neo-adjuvant chemotherapy (NACT) in 100 patients, and with chemo-toxicity in 207 who received adjuvant chemotherapy or NACT, using Chi-square and logistic regression. Higher order gene-gene interactions with treatment outcomes were characterized by multifactor dimensionality reduction (MDR) analysis. RESULTS: In single-locus analysis, Ile/Val and Ile/Val+Val/Val genotypes of the GSTP1 Ile105Val (rs1695) polymorphism reached statistical significance with grade 2-4 anemia (P=0.019, P=0.027). On performing gene-gene interaction analysis, GSTM1 null-GSTP1 Ile/Val was significantly associated with response to NACT (P=0.032). On evaluating higher order gene-gene interaction models by MDR analysis, GSTM1 and GSTP1 Ile105Val; GSTM1 and GSTT1; and GSTT1 and GSTP1 Ile105Val showed significant association with treatment response, grade 2-4 anemia, and dose delay/reduction due to neutropenia (P=0.046, P=0.027, P=0.026), respectively. CONCLUSION: Multi-analytical strategies may serve as a better tool for characterization of pharmacogenetic-based breast cancer treatment outcomes.","corpus_id":17256907,"score":1},{"doc_id":"23975366","title":"Association between GSTP1 Ile105Val polymorphism and glioma risk: a systematic review and meta-analysis.","abstract":"Glutathione S-transferase P1 (GSTP1) gene Ile105Val polymorphism has been suggested to be involved in the development of glioma. However, the results from the studies regarding the association between GSTP1 Ile105Val polymorphism and glioma risk have been inconsistent. Thus, we performed a meta-analysis to investigate this association. Pooled odds ratios (ORs) with 95% confidence intervals (95%CIs) were calculated using random or fixed effects model. Nine studies with 2,078 cases and 3,970 controls were finally included into this meta-analysis. The results suggested there was no association between GSTP1 Ile105Val polymorphism and glioma risk under recessive model (OR = 1.138, 95%CI = 0.966-1.341, Pheterogeneity = 0.088, P = 0.123). Subgroup analyses by ethnicity showed there was also no association between GSTP1 Ile105Val polymorphism and glioma risk in mixed populations under recessive model (OR = 1.199, 95%CI = 0.928-1.549, Pheterogeneity = 0.060, P = 0.166) and Caucasian populations (OR = 1.097, 95%CI = 0.885-1.360, Pheterogeneity = 0.186, P = 0.398). In conclusion, the meta-analysis suggests that there is no association between GSTP1 Ile105Val polymorphism and glioma risk. However, more well-designed and larger studies are needed to further assess this association.","corpus_id":8205798,"score":1},{"doc_id":"23977100","title":"GSTP1 Ile105Val polymorphism and prostate cancer risk: evidence from a meta-analysis.","abstract":"BACKGROUND: Glutathione S-transferase P1 (GSTP1) is thought to be involved in the detoxification of reactive carcinogen metabolites. Numerous epidemiological studies have evaluated the association of GSTP1 Ile105Val polymorphism with the risk of prostate cancer. However, the results remain inconclusive. To derive a more precise estimation, a meta-analysis was performed. METHODOLOGY/PRINCIPAL FINDINGS: A comprehensive search was conducted to identify the eligible studies. We used odds ratios (ORs) with 95% confidence intervals (CIs) to assess the strength of the relationship. The overall association was not significant (Val/Val vs. Ile/Ile OR = 1.06, 95% CI = 0.90-1.25, P = 0.50; Val/Val vs. Val/Ile+Ile/Ile: OR = 1.07, 95% CI = 0.91-1.25, P = 0.44). In subgroup analyses by ethnicity and prostate cancer grade, the similar results were observed. However, in stratified analysis by clinical stage, we found a significant association with low-stage prostate cancer (Val/Val vs. Ile/Ile: OR = 2.70, 95% CI = 1.73-4.22, P<0.001; Val/Val vs. Val/Ile+Ile/Ile: OR = 2.14, 95% CI = 1.38-3.33, P = 0.001). Moreover, there was no statistically significant evidence of multiplicative interactions neither between the GSTP1 Ile105Val polymorphism and GSTM1, nor between smoking status and GSTP1 on prostate cancer risk. CONCLUSIONS: This meta-analysis showed that GSTP1 Ile105Val polymorphism might not be significantly associated with overall prostate cancer risk. Further stratified analyses showed a significant association with low-stage prostate cancer.","corpus_id":6911263,"score":1},{"doc_id":"25008867","title":"Pharmacogenetic association between GSTP1 genetic polymorphism and febrile neutropenia in Japanese patients with early breast cancer.","abstract":"BACKGROUND: Genetic risk factors for febrile neutropenia (FN), the major adverse event of perioperative chemotherapy for early breast cancer, remain unclear. METHODS: This study retrospectively explored pharmacogenetic associations of single nucleotide polymorphisms (SNPs) of the uridine glucuronosyltransferase 2B7 (UGT2B7, rs7668258), glutathione-S-transferase pi 1 (GSTP1, rs1695), and microcephalin 1 (MCPH1, rs2916733) genes with chemotherapy-related adverse events in 102 Japanese women who received epirubicin and cyclophosphamide as perioperative chemotherapy for early breast cancer. RESULTS: The allele frequencies for all of the SNPs were in concordance with the Hap-Map data of Japanese individuals. Among the 24 patients who had FN at least once during all courses of chemotherapy, 23 had the A/A genotype, and 1 had the A/G genotype of the GSTP1 polymorphism (rs1695, P = 0.001); 23 of the 70 patients with the A/A genotype had FN, as compared with only 1 of the 32 patients with the A/G and G/G genotypes. The genotype distributions of the UGT2B7 and MCPH1 polymorphisms did not differ between the patients who had FN or grade 3/4 neutropenia and those who did not. CONCLUSION: Among Japanese women who received epirubicin and cyclophosphamide as perioperative chemotherapy for early breast cancer, those with the A/A genotype of the GSTP1 polymorphism (rs1695) were more likely to have FN.","corpus_id":20647725,"score":1},{"doc_id":"25515186","title":"GSTM1, GSTP1, and GSTT1 genetic variability in Turkish and worldwide populations.","abstract":"OBJECTIVE: Glutathione S-transferase (GST) variants have been widely investigated to better understand their role in several pathologic conditions. To our knowledge, no data about these genetic polymorphisms within the Turkish population are currently available. The aim of this study was to analyze GSTM1 positive/null, GSTT1 positive/null, GSTP1*I105V (rs1695), and GSTP1*A114V (rs1138272) variants in the general Turkish population, to provide information about its genetic diversity, and predisposition to GST-related diseases. METHODS: Genotyping was performed in 500 Turkish individuals using the Sequenom MassARRAY platform. A comparative analysis was executed using the data from the HapMap and Human Genome Diversity Projects (HGDP). Sequence variation was deeply explored using the Phase 1 data of the 1,000 Genomes Project. RESULTS: The variability of GSTM1, GSTT1, and GSTP1 polymorphisms in the Turkish population was similar to that observed in Central Asian, European, and Middle Eastern populations. The high linkage disequilibrium between GSTP1*I105V and GSTP1*A114V in these populations may have a confounding effect on GSTP1 genetic association studies. In analyzing GSTM1, GSTT1, and GSTP1 sequence variation, we observed other common functional variants that may be candidates for associated studies of diseases related to GST genes (e.g., cancer, cardiovascular disease, and allergy). CONCLUSIONS: This study provides novel data about GSTM1 positive/null, GSTT1 positive/null, GSTP1*I105V, and GSTP1*A114V variants in the Turkish population, and other functional variants that may affect GSTM1, GSTT1, and GSTP1 functions among worldwide populations. This information can assist in the design of future genetic association studies investigating oxidative stress-related diseases.","corpus_id":25339892,"score":1},{"doc_id":"25775823","title":"[Role of gene polymorphisms of phase II of xenobiotic biotransformation from glutathione-S-transferase and N-acetyltransferase families in susceptibility to lung cancer among Mayak workers].","abstract":"An association between polymorphous (allelic) gene variants of phase II of enzymatic xenobiotic biotransformation (EXB) of multigene families of glutathione-S-transferase (GSTs) GSTM1*0, GSTT1*0, GSTP1*B Ile105Val, and N-acetyltransferase (NAT) NAT2*6 590G>A, NAT2*5 481C>T, as well as lung cancer in Mayak workers exposed occupationally to prolonged external γ-rays and internal α-radiation from incorporated 239Pu was studied. Analysis of the population frequency of genotypes and alleles of the studied genes in the cohort of Mayak workers revealed their compliance with the Hardy-Weinberg principle and with the corresponding frequency in the European population. The study was based on the case-control method. A case-group consisted of 49 Mayal workers with a verified diagnosis of lung cancer. The mean total absorbed dose from external γ-rays at the moment of diagnostics was 1.03 Gy; the mean total absorbed dose from internal α-radiation from incorporated 239Pu to lung was 0.35 Gy. Control consisted of 172 Mayak workers matched by the year of birth, gender, and age at the moment of employment at one of the main facilities with no lung cancer registered within the study period. No increase in the relative risk of lung cancer (odds ratio, OR) was revealed among the individuals with deletion variants of genes GSTM1*0 and GSTT1*0 (pp genotype, complete absence of gene products) as compared to the individuals with ww or wp genotype, which was determined in total for these genes (normal or partly decreased gene activity). An increase in OR of lung cancer in 1.849 times (p = 0.239) and in 2.439 times (p = 0.075) was found in the carriers with a complete absence of the product of genes GSTP1*B and NAT2*6 590G>A, correspondingly (pp genotype). A statistically significant decrease in OR of lung cancer was found in the wp genotype carriers of gene GSTP1*B (OR = 0.50, p = 0.041). Three variants of paired combinations of gene alleles were established in the carriers with a statistically significant increase in OR of lung cancer (ww GSTP1*B + pp GSTM1*0; ww GSTP1*B + pp NAT2*6 590G>A; pp GSTP1*B + pp NAT2*5 481C>T), and one combination in the carriers with a statistically significant decrease in OR of lung cancer (wp GSTP1*B and ww +wp GSTT1*0).","corpus_id":24492777,"score":1},{"doc_id":"26044055","title":"Association of glutathione S-transferase pi (GSTP1) Ile105Val polymorphism with the risk of skin cancer: a meta-analysis.","abstract":"Numerous epidemiological studies have evaluated the association of Glutathione S-transferase P1 (GSTP1) Ile105Val polymorphism with the risk of skin cancer. However, the results remain inconclusive. To derive a more precise estimation of the association between the GSTP1 Ile105Val polymorphism and skin cancer risk, a meta-analysis was performed. A comprehensive search was conducted to identify the eligible studies. We used odds ratios (ORs) with 95 % confidence intervals (CIs) to assess the association of GSTP1 Ile105Val polymorphism with skin cancer risk. Thirteen case-control studies in nine articles, which included a total of 1504 cases and 2243 controls. Overall, we found that GSTP1 Ile105Val polymorphism was not associated with skin cancer risk. Furthermore, subgroup analysis by histological types showed that GSTP1 Ile105Val polymorphism was associated with risks of malignant melanoma under the dominant model (Val/Val + Val/Ile vs. Ile/Ile: OR 1.230, 95 % CI 1.017-1.488, P = 0.033). However, lack of association between GSTP1 Ile105Val polymorphism and BCC and SCC risk in all genetic models. Our meta-analysis suggested that the GSTP1 Ile105Val polymorphism might be associated with increased risk of malignant melanoma in Caucasian population.","corpus_id":28856268,"score":1},{"doc_id":"26046522","title":"Modifying Role of GSTP1 Polymorphism on the Association between Tea Fluoride Exposure and the Brick-Tea Type Fluorosis.","abstract":"BACKGROUND: Brick tea type fluorosis is a public health concern in the north-west area of China. The association between SNPs of genes influencing bone mass and fluorosis has attracted attention, but the association of SNPs with the risk of brick-tea type of fluorosis has not been reported. OBJECTIVE: To investigate the modifying roles of GSTP1 rs1695 polymorphisms on this association. METHODS: A cross-sectional study was conducted. Brick-tea water was tested by the standard of GB1996-2005 (China). Urinary fluoride was tested by the standard of WS/T 89-2006 (China). Skeletal fluorosis was diagnosed by X-ray, the part we scheduled was forearm, shank, and pelvic, then diagnosed the skeletal fluorosis by the standard of WS/192-2008 (China). Gene polymorphism was tested by Sequenom MassARRAY system. RESULT: The prevalence rate in different ethnical participants was different: Tibetan individuals had the highest prevalence rate of skeletal fluorosis. There were significant differences in genotype frequencies of GSTP1 Rs1695 among different ethnical participants (p<0.001): Tibetan, Mongolian and Han subjects with homozygous wild type (GSTP1-AA) genotype were numerically higher than Kazakh and Russian subjects (p<0.001). Compared to Tibetan participants who carried homozygous A allele of GSTP1 Rs1695, Tibetan participants who carried G allele had a significantly decreased risk of skeletal fluorosis (OR = 0.558 [95% CI, 0.326-0.955]). For Kazakh participants, a decreased risk of skeletal fluorosis among carriers of the G allele was limited to non high-loaded fluoride status (OR = 0. 166 [95% CI, 0.035-0.780] vs. OR = 1.478 [95% CI, 0.866-2.552] in participants with high-loaded fluoride status). Neither SNP-IF nor SNP-age for GSTP1 Rs1695 was observed. CONCLUSION: The prevalence rate of the brick tea type fluorosis might have ethnic difference. For Tibetan individuals, who had the highest prevalence rate, G allele of GSTP1 Rs1695 might be a protective factor for brick tea type skeletal fluorosis.","corpus_id":25352523,"score":1},{"doc_id":"26345972","title":"Association of GSTP1 and XRCC1 gene polymorphisms with clinical outcomes of patients with advanced non-small cell lung cancer.","abstract":"We investigated the association between the polymorphisms GSTP1 rs1695 and XRCC1 rs1799782 and rs25487 and the clinical outcome of patients with non-small cell lung cancer (NSCLC) receiving cisplatin-based chemotherapy. Genotyping of GSTP1 rs1695 and XRCC1 rs1799782, and rs25487 was conducted by polymerase chain reaction-restriction fragment length polymorphism analysis. By conditional logistic regression analysis, patients carrying the GG genotype of GSTP1 rs1695 and the AA genotype of XRCC1 rs25487 were found to be more highly associated with response to chemotherapy than were those carrying the AA genotype; the ORs (95%CIs) were 0.13 (0.04-0.37) and 3.37 (1.44-8.53), respectively. Presence of the GG genotype of GSTP1 rs1695 and the GA and AA genotypes of XRCC1 rs25487 was associated with overall survival of NSCLC, and the hazards ratios (95%CI) were 4.35 (1.40-17.92), 0.53 (0.31-0.91), and 0.39 (0.18-0.83), respectively. The results of our study suggest that the GSTP1 rs1695 and XRCC1 rs25487 polymorphisms might affect the clinical outcome of patients with advanced NSCLC receiving cisplatin-based chemotherapy.","corpus_id":33404211,"score":1},{"doc_id":"26823821","title":"Role of GSTP1 Ile105Val and XRCC1 Arg194Trp, Arg280His and Arg399Gln gene polymorphisms in the clinical outcome of advanced non-small cell lung cancer.","abstract":"We conducted a study to investigate the association between the clinical outcome and GSTP1 Ile105Val and XRCC1 Arg194Trp, Arg280His and Arg399Gln gene polymorphisms in advanced NSCLC patients with cisplatin-based chemotherapy. Between January 2010 and December 2012, a total of 206 patients with advanced NSCLC were histopathologically confirmed were included into analysis. By logistic regression analysis, individuals carrying the AG and GG genotypes of GSTP1 Ile105Val were associated with better response to chemotherapy when compared with the AA genotype, and the adjusted Ors (95% CI) were 2.06 (1.10-3.86) and 4.89 (1.52-18.33), respectively. The TT genotype of XRCC1 Arg194Trp was correlated with better response to chemotherapy compared to the CC genotype, and the adjusted OR (95% CI) was 3.23 (1.20-9.30). By Cox Hazard Proportional Model, the GG genotype of GSTP1 Ile105Val and the TT genotype of XRCC1 Arg194Trp were found to be associated with lower risk of death from all causes when compared with the wide-type genotype, and the adjusted HRs (95% CI) were 0.05 (0.01-0.18) and 0.20 (0.07-0.62), respectively. Moreover, individuals carrying both the G/A+G/G genotype of GSTP1 Ile105Val and the G/A+A/A of XRCC1 Arg194Trp were associated with heavy greater CR+PR response to chemotherapy (OR=2.98, 95% CI=1.39-6.42), and also correlated with longer overall survival of advanced NSCLC (HR=0.19, 95% CI=0.05-0.61). In conclusion, we found that the GSTP1 Ile105Val and XRCC1 Arg194Trp were associated with better response to chemotherapy and longer survival of advanced NSCLC, compared to the wide-type genotype.","corpus_id":24341152,"score":1},{"doc_id":"27299594","title":"GSTM1 and GSTP1 Genetic Polymorphisms and Their Associations With Acute Lymphoblastic Leukemia Susceptibility in a Jordanian Population.","abstract":"The genetic variations between different individuals in the xenobiotic detoxifying enzyme activity were shown to change susceptibility to acute lymphoblastic leukemia (ALL). The current study aimed to assess the association of GSTM1 and GSTP1 genetic polymorphisms with the susceptibility of ALL. This case-control study (N=264) involved 88 Jordanian ALL children and 176 healthy controls from an ethnically homogenous Jordanian children population. The polymerase chain reaction assay was used to genotype GSTM1 (null/present) and the polymerase chain reaction-restriction fragment length polymorphism technique was also applied to detect the genetic polymorphisms of GSTP1 (Ile105Val) at the rs1695 position. The biallelic analysis revealed that there was no association between GSTM1 double-null genotype and ALL (P=0.57). However, there was a strong association between GSTP1 (Ile105Val) polymorphism genotypes and alleles within GSTP1 gene and ALL (P=0.00049 and 0.000044, respectively). A combination between GSTM1 double-null genotype and rs1695 also showed an association with ALL (P=0.042). This study showed that the rs1695 single nucleotide polymorphism within the GSTP1 gene is strongly implicated in ALL among Jordanian children with ALL. These results indicate that genetic variants of GSTP1 gene influence the risk of developing ALL in the Jordanian children of Arab ancestry.","corpus_id":42283380,"score":1},{"doc_id":"27323109","title":"GSTP1 Ile105Val and XRCC1 Arg399Gln gene polymorphisms contribute to the clinical outcome of patients with advanced non-small cell lung cancer.","abstract":"Glutathione S-transferase P1 (GSTP1) and X-ray repair cross-complementing group 1 (XRCC1) genetic variations may in-fluence the efficacy of chemotherapy in various cancers. We investi-gated the possible roles of GSTP1 Ile105Val and XRCC1 Arg194Trp, and Arg399Gln gene polymorphisms in the prognosis of advanced non-small cell lung carcinoma (NSCLC) patients with cisplatin-based chemotherapy. Between January 2010 and December 2012, this study consecutively recruited 141 patients with advanced NSCLC from the First People's Hospital of Yunnan Province. Logistic regression analy-sis showed that individuals carrying the GG genotype were associated with a better response to chemotherapy than those with the wide-type genotype, with an adjusted odds ratio (95% confidence interval, CI) of 4.07 (1.06-25.06). Moreover, we observed that the AA genotype of XRCC1 Arg399Gln was correlated with a greater complete response + partial response to chemotherapy than that with the GG genotype (odds ratio = 2.71, 95%CI = 1.13-10.08). Based on the Cox hazard proportional model, the GG genotype of GSTP1 Ile105Val was found to be associated with a lower risk of death from all causes as compared to that with the AA genotype (hazard ratio = 0.07, 95%CI = 0.01-0.34). In summary, we suggest that GSTP1 Ile105Val and XRCC1 Arg399Gln polymorphisms could influence the response to chemotherapy and sur-vival of advanced NSCLC.","corpus_id":26046816,"score":1},{"doc_id":"27349566","title":"NQO1 rs1800566 polymorph is more prone to NOx induced lung injury: Endorsing deleterious functionality through informatics approach.","abstract":"Gene-environment interaction studies have led to the identification of genetic mutations in individuals with increased susceptibility to pollution related diseases. rs1800566 polymorphism of NQO1, leading to P187S missense mutation in the transcribed antioxidant protein, causes individuals carrying this mutation more prone to NO2 induced lung inflammatory injury. Here, we report significant structural and functional changes incurred by NQO1 antioxidant protein as a result of alteration in its nucleotide (C609T) and hence, protein sequence. Detailed insights were obtained regarding the prospective impact of this mutation on the structural stability of normal and mutated NQO1 protein, using a myriad of bioinformatic tools and webservers. Structure analysis showed no significant change at secondary level. A change in the native backbone conformation was observed due to formation of a hydrogen bond. Hydrophobicity and phosphorylation properties, decisive factors for functioning and stability of NQO1 were considerably influenced by P187S mutation. Computational study of the properties of a polymorph linked with NOx induced lung injury sheds light on the molecular basis of this polymorphism and endorses previous findings, reported by the scientists working in this domain.","corpus_id":205026478,"score":1},{"doc_id":"27561723","title":"Asthma and rhinitis have different genetic profiles for IL13, IL17A and GSTP1 polymorphisms.","abstract":"BACKGROUND: Asthma and rhinitis have a complex etiology, depending on multiple genetic and environmental risk factors. An increasing number of susceptibility genes are currently being identified, but the majority of reported associations have not been consistently replicated across populations of different genetic backgrounds. PURPOSE: To evaluate whether polymorphisms of IL4R (rs1805015), IL13 (rs20541), IL17A (rs2275913) and GSTP1 (rs1695) genes are associated with rhinitis and/or asthma in adults of Portuguese ancestry. METHODS: 192 unrelated healthy individuals and 232 patients, 83 with rhinitis and 149 with asthma, were studied. All polymorphisms were detected by real time polymerase chain reaction (PCR) using TaqMan assays. RESULTS: Comparing to controls, significant association with asthma was observed for GSTP1 rs1695 AA genotype (odds ratio (OR) - 1.96; 95% CI - 1.18 to 3.25; p=0.010). The association sustains for allergic asthma (OR - 2.17; 95% CI - 1.23 to 3.80; p=0.007). IL13 rs20541 GG genotype was associated with less susceptibility to asthma (OR - 0.55, 95% CI - 0.33 to 0.94, p=0.028). Among patients, IL17A rs2275913 AA genotype was less associated with asthma than with rhinitis (OR - 0.20; 95% CI of 0.07 to 0.56; p=0.002). A similar association was found for IL13 rs20541 GG genotype (OR - 0.48; 95% CI of 0.25 to 0.93; p=0.031). There were no significant differences in the distribution of allelic and genotypic frequencies between patients and controls for the IL4R polymorphism' analyzed. CONCLUSION: These results support the existence of a significant association between GSTP1 rs1695 and IL13 rs20541 SNPs, with susceptibility to asthma, in the population studied. Different genotype profiles of IL17A and IL13 genes seem to influence the clinical pattern of disease expression mainly confined to the upper airways, as rhinitis, or including the lower airways, as asthma.","corpus_id":29603910,"score":1},{"doc_id":"28062686","title":"GSTP1 c.313A>G polymorphism in Russian and Polish athletes.","abstract":"The GSTP1 gene encodes glutathione S-transferase P1, which is a member of the glutathione S-transferases (GSTs), a family of enzymes playing an important role in detoxification and in the antioxidant defense system. There is some evidence indicating that GSTP1 c.313A>G polymorphism may be beneficial for exercise performance. Therefore, we decided to verify the association between the frequency of GSTP1 c.313A>G variants, physical performance, and athletes' status in two cohorts: in a group of Russian athletes (n = 507) and in an independent population of Polish athletes (n = 510) in a replication study. The initial association study conducted with the Russian athletes revealed that the frequency of the minor G allele was significantly higher in all athletes than in controls; that was confirmed in the replication study of Polish athletes. In the combined cohort, the differences between athletes (n = 1017) and controls (n = 1246) were even more pronounced (32.7 vs 25.0%, P < 0.0001). Our findings emphasize that the G allele of the GSTP1 gene c.313A>G single nucleotide polymorphism is associated with improved endurance performance. These observations could support the hypothesis that the GSTP1 G allele may improve exercise performance by better elimination of exercise-induced ROS.","corpus_id":207620914,"score":1},{"doc_id":"28739440","title":"Genetic Variation in GSTP1, Lung Function, Risk of Lung Cancer, and Mortality.","abstract":"INTRODUCTION: Glutathione S-transferase pi 1 metabolizes carcinogens from tobacco smoke in the lung. We tested whether genetically altered glutathione S-transferase pi 1 activity affects lung function and risk for tobacco-related cancer and mortality in the general population. METHODS: We genotyped 66,069 individuals from the white general population for two common functional variants in the glutathione S-transferase pi 1 gene (GSTP1)-amino acid isoleucine 105 changed to a valine (Ile105Val) and amino acid alanine 114 changed to a valine (Ala114Val)-and recorded lung function, lung cancer, tobacco-related cancer, and death as outcomes. RESULTS: Lung function was increased stepwise with the Ile105Val genotype overall (p < 0.01) and among smokers separately (p < 0.01). Adjusted hazard ratios for lung cancer, tobacco-related cancer, and death were reduced stepwise with the Ile105Val genotype (p < 0.02): Ile105Val homozygotes and heterozygotes versus noncarriers had hazard ratios for lung cancer of 0.64 (0.47-0.89) and 0.93 (0.78-1.11), for tobacco-related cancer of 0.74 (0.60-0.92) and 0.92 (0.81-1.04), and hazard ratios for death of 0.87 (0.80-0.95) and 0.94 (0.89-0.99), respectively. Population prevented fractions of lung cancer, tobacco-related cancer, and death due to Ile105Val homozygosity were 4%, 3% and 2%, respectively. The Ala114Val genotype was associated with reduced mortality (p < 0.01) but not with lung function, lung cancer, or tobacco-related cancer. CONCLUSION: GSTP1 Ile105Val was associated with increased lung function, reduced risk for lung cancer and tobacco-related cancer, and reduced all-cause mortality in the general population.","corpus_id":43062062,"score":1},{"doc_id":"28770488","title":"Identification and characterization of functional single nucleotide polymorphisms (SNPs) in Axin 1 gene: a molecular dynamics approach.","abstract":"Wnt signaling pathway has been reported to play crucial role in intestinal crypt formation and deregulation of this pathway is responsible for colorectal cancer initiation and progression. Axin 1, a scaffold protein, play pivotal role in the regulation of Wnt/β-catenin signaling pathway and has been found to be mutated in several cancers; primarily in colon cancer. Considering its crucial role, a structural and functional analysis of missense mutations in Axin 1 gene was performed in this study. Initially, one hundred non-synonymous single nucleotide polymorphisms in the coding regions of Axin 1 gene were selected for in silico analysis. Six variants (G820S, G856S, E830K, L811V, L847V, and R767C) were predicted to be deleterious by combinatorial prediction. Further investigation of structural attributes confirmed two highly deleterious single nucleotide polymorphisms (G820S and G856S). Molecular dynamics simulation demonstrated variation in different structural attributes between native and two highly deleterious Axin 1 mutant models. Finally, docking analysis showed variation in binding affinity of mutant Axin 1 proteins with two destruction complex members, GSK3β and adenomatous polyposis. The results collectively showed the deleterious effect of the above predicted single nucleotide polymorphisms on the Axin 1 protein structure and could prove to be an adjunct in the disease genotype-phenotype correlation studies.","corpus_id":3995844,"score":1},{"doc_id":"29046813","title":"Single nucleotide polymorphisms and microsatellites in the canine glutathione S-transferase pi 1 (GSTP1) gene promoter.","abstract":"BACKGROUND: Genetic polymorphisms within the glutathione S-transferase P1 (GSTP1) gene affect the elimination of toxic xenobiotics by the GSTP1 enzyme. In dogs, exposure to environmental chemicals that may be GSTP1 substrates is associated with cancer. The objectives of this study were to investigate the genetic variability in the GSTP1 promoter in a diverse population of 278 purebred dogs, compare the incidence of any variants found between breeds, and predict their effects on gene expression. To provide information on ancestral alleles, a number of wolves, coyotes, and foxes were also sequenced. RESULTS: Fifteen single nucleotide polymorphisms (SNPs) and two microsatellites were discovered. Three of these loci were only polymorphic in dogs while three other SNPs were unique to wolves and coyotes. The major allele at c.-46 is T in dogs but is C in the wild canids. The c.-185 delT variant was unique to dogs. The microsatellite located in the 5' untranslated region (5'UTR) was a highly polymorphic GCC tandem repeat, consisting of simple and compound alleles that varied in size from 10 to 22-repeat units. The most common alleles consisted of 11, 16, and 17-repeats. The 11-repeat allele was found in 10% of dogs but not in the other canids. Unequal recombination and replication slippage between similar and distinct alleles may be the mechanism for the multiple microsatellites observed. Twenty-eight haplotypes were constructed in the dog, and an additional 8 were observed in wolves and coyotes. While the most common haplotype acrossbreeds was the wild-type *1A(17), other prevalent haplotypes included *3A(11) in Greyhounds, *6A(16) in Labrador Retrievers, *9A(16) in Golden Retrievers, and *8A(19) in Standard Poodles. Boxers and Siberian Huskies exhibited minimal haplotypic diversity. Compared to the simple 16*1 allele, the compound 16*2 allele (found in 12% of dogs) may interfere with transcription factor binding and/or the stability of the GSTP1 transcript. CONCLUSIONS: Dogs and other canids exhibit extensive variation in the GSTP1 promoter. Genetic polymorphisms within distinct haplotypes prevalent in certain breeds can affect GSTP1 expression and carcinogen detoxification, and thus may be useful as genetic markers for cancer in dogs.","corpus_id":19386679,"score":1},{"doc_id":"29476931","title":"Vitamin D receptor (VDR) non-synonymous single nucleotide polymorphisms (nsSNPs) affect the calcitriol drug response - A theoretical insight.","abstract":"Pharmacogenetics and pharmacogenomics have become presumptive with advancements in next-generation sequencing technology. In complex diseases, distinguishing the feasibility of pathogenic and neutral disease-causing variants is a time consuming and expensive process. Recent drug research and development processes mainly rely on the relationship between the genotype and phenotype through Single nucleotide polymorphisms (SNPs). The SNPs play an indispensable role in elucidating the individual's vulnerability to disease and drug response. The understanding of the interplay between these leads to the establishment of personalized medicine. In order to address this issue, we developed a computational pipeline of vitamin D receptor (VDR) for SNP centered study by application of elegant molecular docking and molecular dynamics simulation approaches. In a few SNPs the volume of the binding cavities has increased in mutant structures when compared to the wild type, indicating a weakening in interaction (699.1 Å3 in wild type Vs. 738.8 in Leu230Val, 820.7 Å3 in Arg247Leu). This also differently reflected in the H-bond interactions and binding free energies -169.93 kcal/mol (wild type) Vs -156.43 kcal/mol (R154W), -105.49 kcal/mol (R274L) in Leu230Val and Arg247Leu respectively. Although we could not find noteworthy changes in the binding free energies and binding pocket in the remaining mutations, the H-bond interactions made these SNPs deleterious. Thus, we further analyzed the H-bond interactions and distances using molecular dynamics (MD) simulation studies.","corpus_id":3523623,"score":1},{"doc_id":"18950218","title":"Multiple protonation equilibria in electrostatics of protein-protein binding.","abstract":"All proteins contain groups capable of exchanging protons with their environment. We present here an approach, based on a rigorous thermodynamic cycle and the partition functions for energy levels characterizing protonation states of the associating proteins and their complex, to compute the electrostatic pH-dependent contribution to the free energy of protein-protein binding. The computed electrostatic binding free energies include the pH of the solution as the variable of state, mutual \"polarization\" of associating proteins reflected as changes in the distribution of their protonation states upon binding and fluctuations between available protonation states. The only fixed property of both proteins is the conformation; the structure of the monomers is kept in the same conformation as they have in the complex structure. As a reference, we use the electrostatic binding free energies obtained from the traditional Poisson-Boltzmann model, computed for a single macromolecular conformation fixed in a given protonation state, appropriate for given solution conditions. The new approach was tested for 12 protein-protein complexes. It is shown that explicit inclusion of protonation degrees of freedom might lead to a substantially different estimation of the electrostatic contribution to the binding free energy than that based on the traditional Poisson-Boltzmann model. This has important implications for the balancing of different contributions to the energetics of protein-protein binding and other related problems, for example, the choice of protein models for Brownian dynamics simulations of their association. Our procedure can be generalized to include conformational degrees of freedom by combining it with molecular dynamics simulations at constant pH. Unfortunately, in practice, a prohibitive factor is an enormous requirement for computer time and power. However, there may be some hope for solving this problem by combining existing constant pH molecular dynamics algorithms with so-called accelerated molecular dynamics algorithms.","corpus_id":25347971,"score":0},{"doc_id":"20526737","title":"Glutathione S-transferase P1 Ile105Val polymorphism and breast cancer risk: a meta-analysis involving 34,658 subjects.","abstract":"Glutathione S-transferase P1 (GSTP1) is involved in a wide range of detoxifying reactions. Any alteration in the structure, function, or expression of GSTP1 gene may alter the ability of a cell to inactivate carcinogens or mutagens, and thus modify an individual's risk to cancer. Previous epidemiological studies on the potential association between GSTP1 Ile105Val polymorphism and breast cancer risk have produced inconsistent results. In order to drive a more precise estimation of this association, we performed a meta-analysis of 30 published case-control studies including 15,901 cases and 18,757 controls. Crude odds ratios (ORs) with 95% confidence intervals (CIs) were used to assess the strength of the association. The results of this meta-analysis showed that GSTP1 Ile105Val polymorphism was not associated with breast cancer susceptibility in overall population. However, in subgroup analysis by ethnicity, we found a significant association among Asian population (for Val/Val vs. Ile/Ile: OR 1.27, 95% CI 1.02-1.83; for the recessive model Val/Val vs. Ile/Ile + Ile/Val: OR 1.42, 95% CI 1.20-1.69). When stratified by study design, significantly elevated susceptibility to breast cancer was found among hospital-based studies (for Val/Val vs. Ile/Ile: OR 1.38, 95% CI 1.16-1.63; for recessive model Val/Val vs. Ile/Val + Ile/Ile: OR 1.31, 95% CI 1.12-1.55; for dominant model: Val/Val + Ile/Val vs. Ile/Ile: OR 1.10, 95% CI 1.02-1.19). In conclusion, our meta-analysis suggests that GSTP1 Ile105Val polymorphism may increase susceptibility to breast cancer in Asian population.","corpus_id":22096713,"score":0},{"doc_id":"20964430","title":"Vibrational Stark effect spectroscopy at the interface of Ras and Rap1A bound to the Ras binding domain of RalGDS reveals an electrostatic mechanism for protein-protein interaction.","abstract":"Electrostatic fields at the interface of the Ras binding domain of the protein Ral guanine nucleotide dissociation stimulator (RalGDS) with the structurally analogous GTPases Ras and Rap1A were measured with vibrational Stark effect (VSE) spectroscopy. Eleven residues on the surface of RalGDS that participate in this protein-protein interaction were systematically mutated to cysteine and subsequently converted to cyanocysteine in order to introduce a nitrile VSE probe in the form of the thiocyanate (SCN) functional group. The measured SCN absorption energy on the monomeric protein was compared with solvent-accessible surface area (SASA) calculations and solutions to the Poisson-Boltzmann equation using Boltzmann-weighted structural snapshots from molecular dynamics simulations. We found a weak negative correlation between SASA and measured absorption energy, indicating that water exposure of protein surface amino acids can be estimated from experimental measurement of the magnitude of the thiocyanate absorption energy. We found no correlation between calculated field and measured absorption energy. These results highlight the complex structural and electrostatic nature of the protein-water interface. The SCN-labeled RalGDS was incubated with either wild-type Ras or wild-type Rap1A, and the formation of the docked complex was confirmed by measurement of the dissociation constant of the interaction. The change in absorption energy of the thiocyanate functional group due to complex formation was related to the change in electrostatic field experienced by the nitrile functional group when the protein-protein interface forms. At some locations, the nitrile experiences the same shift in field when bound to Ras and Rap1A, but at others, the change in field is dramatically different. These differences identify residues on the surface of RalGDS that direct the specificity of RalGDS binding to its in vivo binding partner, Rap1A, through an electrostatic mechanism.","corpus_id":5333542,"score":0},{"doc_id":"21669193","title":"GSTP1 mRNA expression in human circulating blood leukocytes is associated with GSTP1 genetic polymorphism.","abstract":"OBJECTIVES: We explored association between GSTP1 Ile(105)Val (rs1695) polymorphism and GSTP1 mRNA expression in circulating blood leukocytes. DESIGN AND METHODS: GSTP1 transcripts level and polymorphism were determined by Real-Time PCR in 51 bladder cancer and 90 healthy men. RESULTS: Individuals with at least one GSTP1 Val(105) variant allele possessed higher GSTP1 mRNA level in blood leukocytes compared to GSTP1 Ile(105)Ile carriers. CONCLUSIONS: GSTP1 Ile(105)Val gene polymorphism influences its expression in blood, regardless of cancer disease.","corpus_id":20177747,"score":0},{"doc_id":"24786234","title":"HapMap-based study on the association between MPO and GSTP1 gene polymorphisms and lung cancer susceptibility in Chinese Han population.","abstract":"AIM: Myeloperoxidase (MPO) and glutathione S-transferase pi 1 (GSTP1) are important carcinogen-metabolizing enzymes. The aim of this study was to investigate the association between the common polymorphisms of MPO and GSTP1 genes and lung cancer risk in Chinese Han population. METHODS: A total of 266 subjects with lung cancer and 307 controls without personal history of the disease were recruited in this case control study. The tagSNPs approach was used to assess the common polymorphisms of MOP and GSTP1 genes and lung cancer risk according to the disequilibrium information from the HapMap project. The tagSNP rs7208693 was selected as the polymorphism site for MPO, while the haplotype-tagging SNPs rs1695, rs4891, rs762803 and rs749174 were selected as the polymorphism sites for GSTP1. The gene polymorphisms were confirmed using real-time PCR, cloning and sequencing. RESULTS: The four GSTP1 haplotype-tagging SNPs rs1695, rs4891, rs762803 and rs749174, but not the MPO tagSNP rs7208693, exhibited an association with lung cancer susceptibility in smokers in the overall population and in the studied subgroups. When Phase 2 software was used to reconstruct the haplotype for GSTP1, the haplotype CACA (rs749174+rs1695 + rs762803+rs4891) exhibited an increased risk of lung cancer among smokers (adjust odds ratio 1.53; 95%CI 1.04-2.25, P=0.033). Furthermore, diplotype analyses demonstrated that the significant association between the risk haplotype and lung cancer. The risk haplotypes co-segregated with one or more biologically functional polymorphisms and corresponded to a recessive inheritance model. CONCLUSION: The common polymorphisms of the GSTP1 gene may be the candidates for SNP markers for lung cancer susceptibility in Chinese Han population.","corpus_id":12842717,"score":0},{"doc_id":"26621436","title":"Origins of Resistance Conferred by the R292K Neuraminidase Mutation via Molecular Dynamics and Free Energy Calculations.","abstract":"Point mutations in the influenza virus enzyme neuraminidase (NA) have been reported that lead to dramatic loss of activity for known NA inhibitors including the FDA approved sialic acid mimics zanamivir and oseltamivir. A more complete understanding of the molecular basis for such resistance is a critical component toward development of improved next-generation drugs. In this study, we have used explicit solvent all-atom molecular dynamics simulations, free energy calculations (MM-GBSA), and residue-based decomposition to model binding of four ligands with NA from influenza virus subtype N9. The goal is to elucidate which structural and energetic properties change as a result of a mutation at position R292K. Computed binding free energies show strong correlation with experiment (r(2) = 0.76), and an examination of individual energy components reveal that changes in intermolecular Coulombic terms (ΔEcoul) best describe the variation in affinity with structure (r(2) = 0.93). H-bond populations also parallel the experimental ordering (r = -0.96, r(2) = 0.86) reinforcing the view that electrostatics modulate binding in this system. Notably, in every case, the simulation results correctly predict that loss of binding occurs as a result of the R292K mutation. Per-residue binding footprints reveal that changes in ΔΔEcoul for R292K-wildtype at position 292 parallel the change in experimental fold resistance energies (ΔΔGR292K-WT) with S03 < S00 < S02 < S01. The footprints also reveal that the most potent ligands have (1) less reliance on R292 for intrinsic affinity, (2) enhanced binding via residues E119, E227, and E277, and (3) flatter ΔEcoul and ΔH-bond profiles. Improved resistance for S03 appears to be a function of the ligand's larger guanidinium group which leads to an increased affinity for wildtype NA while at the same time a reduction in favorable interactions localized to R292. Overall, the computational results significantly enhance experimental observations through quantification of specific interactions which govern molecular recognition along the N9-ligand binding interface.","corpus_id":16772843,"score":0},{"doc_id":"29434449","title":"Impact of SNP-SNP interactions of DNA repair gene ERCC5 and metabolic gene GSTP1 on gastric cancer/atrophic gastritis risk in a Chinese population.","abstract":"AIM: To investigate the interactions of the DNA repair gene excision repair cross complementing group 5 (ERCC5) and the metabolic gene glutathione S-transferase pi 1 (GSTP1) and their effects on atrophic gastritis (AG) and gastric cancer (GC) risk. METHODS: Seven ERCC5 single nucleotide polymorphisms (SNPs) (rs1047768, rs2094258, rs2228959, rs4150291, rs4150383, rs751402, and rs873601) and GSTP1 SNP rs1695 were detected using the Sequenom MassARRAY platform in 450 GC patients, 634 AG cases, and 621 healthy control subjects in a Chinese population. RESULTS: Two pairwise combinations (ERCC5 rs2094258 and rs873601 with GSTP1 rs1695) influenced AG risk (Pinteraction = 0.008 and 0.043, respectively), and the ERCC5 rs2094258-GSTP1 rs1695 SNP pair demonstrated an antagonistic effect, while ERCC5 rs873601-GSTP1 rs1695 showed a synergistic effect on AG risk OR = 0.51 and 1.79, respectively). No pairwise combinations were observed in relation to GC risk. There were no cumulative effects among the pairwise interactions (ERCC5 rs2094258 and rs873601 with GSTP1 rs1695) on AG susceptibility (Ptrend > 0.05). When the modification effect of Helicobacter pylori (H. pylori) infection was evaluated, the cumulative effect of one of the aforementioned pairwise interactions (ERCC5 rs873601-GSTP1 rs1695) was associated with an increased AG risk in the case of negative H. pylori status (Ptrend = 0.043). CONCLUSION: There is a multifarious interaction between the DNA repair gene ERCC5 SNPs (rs2094258 and rs873601) and the metabolic gene GSTP1 rs1695, which may form the basis for various inter-individual susceptibilities to AG.","corpus_id":24058752,"score":0}],"string":"[\n {\n \"doc_id\": \"18335111\",\n \"title\": \"Glutathione S-transferase P1, maternal smoking, and asthma in children: a haplotype-based analysis.\",\n \"abstract\": \"BACKGROUND: Glutathione S-transferase P1 (GSTP1) plays a role in a spectrum of respiratory diseases; however, the effects of sequence variation across the entire locus in asthma pathogenesis have yet to be determined. OBJECTIVES: This study was designed to investigate whether sequence variations in the GSTP1 coding and promoter regions are associated with asthma and wheezing outcomes and to determine whether variants affect susceptibility to maternal smoking. METHODS: Four haplotype tagging SNPs were selected that accounted for 83% of the common haplotypic variation in GSTP1. The associations of GSTP1 variants with asthma and wheezing were assessed among white children in the Children's Health Study (CHS). RESULTS: The Ile105Val allele and a SNP in the upstream promoter region (SNP1: rs6591255, putative transcription factor 1 binding site) were associated with asthma and wheezing outcomes, an association observed in two cohorts of the CHS recruited in different years. Haplotypes that included both the promoter SNP (i.e., rs6591255) and the 105 Val variant were associated with an increased risk for asthma in non-Hispanic whites. Using SNP- and haplotype-based approaches, the effect of maternal smoking on wheezing was largest in children with the Ile105Val allele. CONCLUSIONS: Variants in both the promoter and coding regions of the GSTP1 locus may contribute to the occurrence of childhood asthma and wheezing and may increase susceptibility to adverse effects of tobacco-smoke exposure.\",\n \"corpus_id\": 15505921,\n \"score\": 2\n },\n {\n \"doc_id\": \"18559526\",\n \"title\": \"Glutathione s-transferase p1: gene sequence variation and functional genomic studies.\",\n \"abstract\": \"Glutathione S-transferase P1 (GSTP1) is of importance for cancer research because of its role in detoxifying carcinogens, activating antineoplastic prodrugs, metabolizing chemotherapeutic agents, and its involvement in cell cycle and apoptosis regulation. Two common GSTP1 genetic polymorphisms have been studied extensively. However, the full range of GSTP1 genetic variation has not been systematically characterized in the absence of disease pathology. We set out to identify common GSTP1 polymorphisms in four ethnic groups, followed by functional genomic studies. All exons, splice junctions, and the 5'-flanking region of GSTP1 were resequenced using 60 DNA samples each from four ethnic groups. The 35 single-nucleotide polymorphisms (SNP) identified included six nonsynonymous SNPs and 17 previously unreported polymorphisms. GSTP1 variant allozymes were then expressed in COS-1 cells, and five displayed significantly altered levels of enzyme activity. One decreased to 22% of the wild-type (WT) activity. Four variant allozymes had K(m) values that differed significantly from that of the WT, and five showed altered levels of immunoreactive protein compared with WT, with a significant correlation (r = 0.79, P < 0.007) between levels of immunoreactive protein and enzyme activity in these samples. In the Mexican American population, five linked SNPs were significantly associated with GSTP1 mRNA expression, one of which was found by electrophoretic mobility shift assay to alter protein binding. These studies have identified functionally significant genetic variation, in addition to the two frequently studied GSTP1 nonsynonymous SNPs, that may influence GSTP1's contribution to carcinogen and drug metabolism, and possibly disease pathogenesis and/or drug response.\",\n \"corpus_id\": 15355135,\n \"score\": 2\n },\n {\n \"doc_id\": \"18988661\",\n \"title\": \"Glutathione-S-transferase (GST) P1, GSTM1, exercise, ozone and asthma incidence in school children.\",\n \"abstract\": \"BACKGROUND: Because asthma has been associated with exercise and ozone exposure, an association likely mediated by oxidative stress, we hypothesised that glutathione-S-transferase (GST)P1, GSTM1, exercise and ozone exposure have interrelated effects on the pathogenesis of asthma. METHODS: Associations of the well characterised null variant of GSTM1 and four single nucleotide polymorphisms (SNPs) that characterised common variation in the GSTP1 locus with new onset asthma in a cohort of 1610 school children were examined. Children's exercise and ozone exposure were classified using participation in team sports and community annual average ozone levels, respectively. RESULTS: A two SNP model involving putatively functional variants (rs6591255, rs1695 (Ile105Va)) best captured the association between GSTP1 and asthma. The risk of asthma was lower for those with the Val allele of Ile105Val (hazard ratio (HR) 0.60, 95% CI 0.4 to 0.8) and higher for the variant allele of rs6591255 (HR 1.40, 95% CI 1.1 to 1.9). The risk of asthma increased with level of exercise among ile(105) homozygotes but not among those with at least one val(105) allele (interaction p value = 0.02). The risk was highest among ile(105) homozygotes who participated in >or=3 sports in the high ozone communities (HR 6.15, 95% CI 2.2 to 7.4). GSTM1 null was independently associated with an increased risk of asthma and showed little variation with air pollution or GSTP1 genotype. These results were consistent in two independent fourth grade cohorts recruited in 1993 and 1996. CONCLUSION: Children who inherit a val(105) variant allele may be protected from the increased risk of asthma associated with exercise, especially in high ozone communities. GSTM1 null genotype was associated with an increased risk of asthma.\",\n \"corpus_id\": 23179993,\n \"score\": 2\n },\n {\n \"doc_id\": \"19240225\",\n \"title\": \"Meta- and pooled analysis of GSTP1 polymorphism and lung cancer: a HuGE-GSEC review.\",\n \"abstract\": \"Lung cancer is the most common cancer worldwide. Polymorphisms in genes associated with carcinogen metabolism may modulate risk of disease. Glutathione S-transferase pi (GSTP1) detoxifies polycyclic aromatic hydrocarbons found in cigarette smoke and is the most highly expressed glutathione S-transferase in lung tissue. A polymorphism in the GSTP1 gene, an A-to-G transition in exon 5 (Ile105Val, 313A --> 313G), results in lower activity among individuals who carry the valine allele. The authors present a meta- and a pooled analysis of case-control studies that examined the association between this polymorphism in GSTP1 and lung cancer risk (27 studies, 8,322 cases and 8,844 controls and 15 studies, 4,282 cases and 5,032 controls, respectively). Overall, the meta-analysis found no significant association between lung cancer risk and the GSTP1 exon 5 polymorphism. In the pooled analysis, there was an overall association (odds ratio = 1.11, 95% confidence interval: 1.03, 1.21) between lung cancer and carriage of the GSTP1 Val/Val or Ile/Val genotype compared with those carrying the Ile/Ile genotype. Increased risk varied by histologic type in Asians. There appears to be evidence for interaction between amount of smoking, the GSTP1 exon 5 polymorphism, and risk of lung cancer in whites.\",\n \"corpus_id\": -1,\n \"score\": 2\n },\n {\n \"doc_id\": \"19403501\",\n \"title\": \"In utero smoke exposure, glutathione S-transferase P1 haplotypes, and respiratory illness-related absence among schoolchildren.\",\n \"abstract\": \"BACKGROUND: The GSTP1 Ile105Val variant and secondhand tobacco smoke exposure have been independently associated with acute respiratory illness; however, susceptibility to in utero and secondhand tobacco smoke has yet to be examined in relation to variation across the GSTP1 locus. OBJECTIVE: The purpose of this work was to determine whether variation across the GSTP1 locus is associated with respiratory illness-related school absences and to determine whether this relationship varies by in utero and secondhand tobacco smoke exposure. METHODS: Tobacco smoke exposure status, incident respiratory-related school absence records, and DNA samples was ascertained for 1132 Hispanic and non-Hispanic white elementary school children as part of the Children's Health Study. RESULTS: Four GSTP1 single-nucleotide polymorphisms were selected that accounted for 93% of the variation across the locus. Individual single-nucleotide polymorphism analyses showed a protective effect for the minor alleles in single-nucleotide polymorphisms 1 (rs6591255), 3 (GSTP1 Ile105Val: rs1695), and 4 (rs749174) for respiratory illness. The haplotype, which includes a minor allele for single-nucleotide polymorphisms 1, 3, and 4 (h1011), was associated with a decreased risk of respiratory illness. The protective effect of GSTP1 variants was lost among individuals exposed to in utero and secondhand tobacco smoke. CONCLUSIONS: A common GSTP1 haplotype, which includes the functional Ile105Val polymorphism, was associated with respiratory-related school absences. The protection afforded by this haplotype was lost in children exposed to involuntary tobacco smoke. The paradigm of loss of genetic protection among those exposed to tobacco smoke has clinical and public health implications that warrant broader consideration in research and practice.\",\n \"corpus_id\": 45920598,\n \"score\": 2\n },\n {\n \"doc_id\": \"20858151\",\n \"title\": \"The role of GSTP1 polymorphisms and tobacco smoke exposure in children with acute asthma.\",\n \"abstract\": \"BACKGROUND: The glutathione S-transferase enzymes (GSTs) play an important role in the detoxification of environmental tobacco smoke (ETS), which contributes to airway inflammation, a key component of asthma. Genetic variation in GST genes may influence individuals' ability to detoxify environmental pollutants. OBJECTIVE: To examine the role of polymorphisms in GSTP1 (Ile105Val and Ala114Val), alone and in combination with ETS exposure, on atopy and asthma severity. METHODS: GSTP1 Ile105Val and Ala114Val were genotyped and ETS exposure was assessed by parental questionnaire, which was validated by urinary cotinine measurements. Associations between ETS exposure, GSTP1 polymorphisms, and their interaction on atopy and asthma severity were investigated. RESULTS: For the functional GSTP1 105 SNP, those with the Ile/Ile genotype had odds for atopy of 2.77 (p = .054) when assessed by genotype alone, which increased to 9.02 (p = .050) when ETS was included, relative to individuals with other genotypes. Likewise, compared to children with other GSTP1 114 genotypes, those with Ala/Ala genotype had a 5.47-fold (p = .002) increased risk of atopy (p = .020) when assessed by genotype alone, increasing to 9.17-fold when ETS was included. The 105 Ile/Ile individuals all had the AA (105 Ile/Ile and 114 Ala/Ala) haplotype group; therefore, the odds for atopy were the same. Individuals without any *C haplotype (105 Val and 114 Val allele) who were exposed to ETS had a 9.17-fold increased risk of atopy when compared with individuals with at least one *C haplotype and not exposed to ETS (p = .020). CONCLUSION: There were significant interactions between GSTP1 SNPs, atopy, and ETS exposure in this cohort.\",\n \"corpus_id\": 21167211,\n \"score\": 2\n },\n {\n \"doc_id\": \"21128213\",\n \"title\": \"GSTP1 Ile105Val polymorphism in astrocytomas and glioblastomas.\",\n \"abstract\": \"Glutathione S-transferases (GSTs) constitute a superfamily of ubiquitous multifunctional enzymes that are involved in the cellular detoxification of a large number of endogenous and exogenous chemical agents that have electrophilic functional groups. People who have deficiencies in this family of genes are at increased risk of developing some types of tumors. We examined GSTP1 Ile105Val polymorphism using PCR-RFLP in 80 astrocytoma and glioblastoma samples. Patients who had the Val allele of the GSTP1 Ile105Val polymorphism had an increased risk of tumor development (odds ratio = 8.60; 95% confidence interval = 4.74-17.87; P < 0.001). Overall survival of patients did not differ significantly. We suggest that GSTP1 Ile105Val polymorphisms are involved in susceptibility to developing astrocytomas and glioblastomas.\",\n \"corpus_id\": 16092935,\n \"score\": 2\n },\n {\n \"doc_id\": \"22052985\",\n \"title\": \"Glutathione S-transferase P1 c.313A > G polymorphism could be useful in the prediction of doxorubicin response in breast cancer patients.\",\n \"abstract\": \"BACKGROUND: Identification of predicting factors for anthracyclines-based chemotherapy remains a clinical challenge. Glutathione S-transferase (GSTs) enzymes detoxify chemotherapy drugs and their metabolites. Several polymorphisms in GST genes result in reduced or no activity of the enzymes. Specifically, GSTM1 and GSTT1 genes are polymorphically deleted, the polymorphism GSTP1 c.313A>G (rs1695) determines the amino acid substitution Ile105Val, where the Val-containing enzyme has reduced activity. Also, GSTA1*B allele has reduced levels of GSTA1 enzyme. Several polymorphisms in GSTs have been associated with differences in survival for cancer patients treated with chemotherapy. PATIENTS AND METHODS: We genotyped a total of five polymorphisms in GSTM1, GSTT1, GSTP1 and GSTA1 genes in 159 patients with locally advanced breast cancer, treated with single-agent doxorubicin or docetaxel (Taxotere). Gene expression microarrays were performed in 67 breast tumor samples. We correlate this data with treatment outcome. RESULTS: In multivariate analysis, patients homozygous GG for GSTP1 c.313A>G SNP had a lower risk of chemoresistance when treated with doxorubicin (odds ratio 0.106; confidence interval 0.012-0.898; P=0.040). No association was found in the docetaxel arm. Also, we found that GSTP1 expression varied significantly among breast cancer molecular subtypes. CONCLUSIONS: GSTP1 may constitute another tool contributing to individualized anthracycline-based therapy.\",\n \"corpus_id\": 1516136,\n \"score\": 2\n },\n {\n \"doc_id\": \"22339038\",\n \"title\": \"Evaluation of glutathione S-transferase P1 polymorphisms (Ile105Val and Ala114Val) in patients with small cell lung cancer.\",\n \"abstract\": \"AIMS: Glutathione S-transferase P1 (GSTP1) plays an important role in cellular protection against oxidative stress and toxic chemicals. Polymorphisms within GSTP1 are associated with alterations in enzyme activity, which may lead to development of lung disease and cancer. In this study, we aimed to investigate the GSTP1 Ile105Val and Ala114Val polymorphisms in patients with small cell lung cancer (SCLC). PATIENTS/METHODS: GSTP1 Ile105Val polymorphism in exon 5 and GSTP1 Ala114Val polymorphism in exon 6 were determined by using polymerase chain reaction-restriction fragment length polymorphism techniques in 89 patients with SCLC and 108 control patients with chronic obstructive pulmonary disease (COPD). Genotype frequencies and cigarette smoking intensities were compared among SCLC and COPD patients. RESULTS: There were significantly less SCLC patients with variant exon 6 genotypes than COPD patients (7.9% vs. 20.4%, p=0.007), while the number of patients with variant exon 5 genotypes were comparable among groups. SCLC and COPD patients with variant exon 6 genotype showed trends toward exhibiting reduced cigarette consumption. CONCLUSIONS: The variant GSTP1 exon 6 genotype might be conferring protection against SCLC development. Whether this effect is associated with exposure to cigarette smoking needs to be clarified.\",\n \"corpus_id\": 39810015,\n \"score\": 2\n },\n {\n \"doc_id\": \"22783438\",\n \"title\": \"Correlation of CYP1A1, GSTP1 and GSTM1 gene polymorphisms and lung cancer risk among smokers.\",\n \"abstract\": \"Lung cancer is the leading cause of cancer mortality worldwide and tobacco smoking has been established as its biggest risk factor. Cigarette smoke contains several carcinogens. Most of them need to be activated by phase I enzymes, such as cytochrome P450 (CYP), while phase II enzymes, such as glutathione S-transferases are responsible for the detoxification of activated forms. The present study aimed to determine the role of CYP1A1, GSTP1 and GSTM1 gene polymorphisms in smoking-related lung cancer risk. It also aimed to investigate the association of the above polymorphisms with clinicopathological parameters, as well as their effect on survival. One hundred newly diagnosed lung cancer patients with advanced disease and 125 healthy controls with a smoking history participated in the study. The participants were screened for the presence of the following polymorphisms: MspI (CYP1A1), Ile105Val (GSTP1) and GSTM1 deletion. The above polymorphisms were also examined with regards to gender, age, histological type and survival. GSTP1 Ile/Val and GSTM1-null genotypes were associated with increased lung cancer risk and the presence of the combination of the three non-wild-type genotypes increases susceptibility to lung cancer (OR 3.328, 95% CI=1.681-6.587, p=0.001). In the non-small cell lung cancer group, the GSTP1 homozygous variant was significantly associated with increased lung cancer risk (p=0.008) and shorter survival. The results of this study suggest that the GSTP1 Ile/Val genotype and GSTM1 deletion contribute to increased lung cancer susceptibility. Moreover, GSTP1 Val/Val genotype is associated with increased lung cancer risk and shorter survival in non-small cell lung cancer patients.\",\n \"corpus_id\": 6761337,\n \"score\": 2\n },\n {\n \"doc_id\": \"23811488\",\n \"title\": \"GSTP1 Ile105Val polymorphism and colorectal cancer risk: an updated analysis.\",\n \"abstract\": \"BACKGROUND: Many studies have investigated the association between the Glutathione S transferase-P1 (GSTP1) Ile105Val polymorphism and colorectal cancer (CRC) susceptibility, but the results were conflicting. The aim of this study is to quantitatively summarize the relationship between this polymorphism and CRC risk. METHODS: Two investigators independently searched the Medline, Embase, China National Knowledge Infrastructure (CNKI) and Chinese Biomedicine databases for studies published before December 2012. Summary odds ratios (ORs) and 95% confidence intervals (95% CIs) for GSTP1 polymorphism and CRC were calculated in a fixed-effects model (the Mantel-Haenszel method) and a random-effects model (the DerSimonian and Laird method) when appropriate. RESULTS: This meta-analysis included 29 case-control studies, which included 8160 CRC cases and 10,450 controls. Overall, the variant genotypes (ValVal and IleVal) of the Ile105Val were not associated with CRC risk when compared with the wild-type IleIle homozygote. Similarly, no associations were found in the dominant and recessive models. When stratifying for ethnicity, source of controls, study sample size and genotyping methods, no evidence of significant association was observed in any subgroup, except among those studies taking others as genotyping methods (recessive model, OR=0.71, 95%CI=0.52-0.96). Limiting the analysis to the studies within Hardy-Weinberg equilibrium, the results were persistent and robust. No publication bias was found in the present study. CONCLUSION: This updated meta-analysis suggests that the GSTP1 Ile105Val polymorphism may not be associated with CRC risk, while the observed decrease in risk of CRC may be due to small-study bias.\",\n \"corpus_id\": 19737051,\n \"score\": 2\n },\n {\n \"doc_id\": \"27366093\",\n \"title\": \"Association between GSTP1 Ile105Val polymorphism and urinary system cancer risk: evidence from 51 studies.\",\n \"abstract\": \"The GSTP1 gene plays an important role in detoxification of carcinogens. GSTP1 gene polymorphisms may alter the susceptibility of urinary system cancer. Numerous studies have been performed to investigate the association between GSTP1 Ile105Val (rs1695 A>G) polymorphism and urinary system cancer risk. Nevertheless, the results remain controversial and only prostate cancer and bladder cancer are covered. We identified eligible studies from PubMed, Elsevier, and three equivalent Chinese databases including the Chinese National Knowledge Infrastructure, Wanfang, and Weipu. Pooled odds ratios and 95% confidence intervals were used to assess the strength of the association between GSTP1 Ile105Val polymorphism and urinary system cancer risk. In total, 11,762 cases and 15,150 controls from 51 studies were included in the final meta-analysis. The pooled results from all included studies showed a statistically significant association between GSTP1 Ile105Val polymorphism and urinary system cancer. In the subgroup analyses, the GSTP1 Ile105Val polymorphism was found to be significantly associated with prostate cancer risk and also a risk factor for urinary system cancer among Asians. In conclusion, our meta-analysis indicated that GSTP1 Ile105Val polymorphism was associated with urinary system cancer susceptibility, which needs to be validated by more rigorous data from further large-scale population studies with different ethnicities.\",\n \"corpus_id\": -1,\n \"score\": 2\n },\n {\n \"doc_id\": \"28844589\",\n \"title\": \"Impact of CYP1A1, GSTP1 and XRCC1 genes polymorphisms on toxicity and response to chemotherapy in childhood acute lymphoblastic leukemia.\",\n \"abstract\": \"BACKGROUND: Acute lymphoblastic leukemia (ALL) is the most common childhood malignancy. The interindividual genetic variations in drug metabolizing enzymes and DNA repair genes influence the efficacy and toxicity of numerous chemotherapeutic drugs affecting the treatment outcome. AIM OF THE WORK: The aim of the study was to investigate the impact of drug metabolizing CYP1, GSTP1 and DNA repair (XRCC1) genes polymorphisms on the toxicity and response to chemotherapy in childhood ALL. PATIENTS AND METHODOLOGY: Ninety seven ALL pediatric patients were genotyped for CYP1A1, GSTP1 ILe105Val and XRCC1 Arg194Tryp single nucleotide polymorphisms (SNPs) using PCR-RFLP. RESULTS: No statistically significant differences were observed between the wild and variant (homozygous and heterozygous) genotypes of the polymorphisms studied in CYP1A1, GSTP1 or XRCC1 genes regarding age, total leukocyte count, immunophenotyping, cytogenetic or risk group. The SNPs in CYP1A1, GSTP1 and XRCC1 genes did not show significant association with complete remission (CR) rate, overall survival (OS) or event free survival (EFS). However, XRCC1 Arg194Trp SNP was associated with higher drug toxicity; carriers of variant genotypes (CT and TT) had a significantly higher frequency of myelosuppression compared to those with the wild CC genotype (21/43[48.8%]) compared to (14/54[25.9%]) (p=0.020). The analysis of the combined effect of studied SNPs did not show any significant association with patient outcome. CONCLUSION: Our study reported a significant association between the DNA repair gene polymorphism and myelosuppression in childhood ALL patients. Adjustment of the dose of chemotherapeutic agents according to XRCC1 Arg194Trp polymorphism may improve outcome in cases with risk of toxicity.\",\n \"corpus_id\": 206261373,\n \"score\": 2\n },\n {\n \"doc_id\": \"29285015\",\n \"title\": \"Evaluation of glutathione S-transferase P1 (GSTP1) Ile105Val polymorphism and susceptibility to type 2 diabetes mellitus, a meta-analysis.\",\n \"abstract\": \"It is well established that type 2 diabetes mellitus (T2DM) is associated with oxidative stress and glutathione S-transferases (GSTs) protect cells against oxidative stress. The missense substitution Ile105Val (rs1695) of the glutathione S-transferase P1 (GSTP1, OMIM: 134660) results from an A/G base substitution at nucleotide 313. Many studies have evaluated the correlation between the rs1695 polymorphism and T2DM, but the results remain inconclusive. The aim of the present meta-analysis was to investigate the association between GSTP1 Ile105Val polymorphism and the susceptibility risk of T2DM. Eligible studies (published before August 2017) were identified in several databases. The heterogeneity between studies was evaluated with the chi-square based Q test and the I2 test. The strengths of the association were assessed by pooled odds ratios (ORs) and the corresponding 95 % confidence interval (95 % CI) using either a fixed or random-effects models. Eighteen studies documenting a total of 2595 T2DM cases and 2888 controls were included in this meta-analysis. In the overall analysis there was no significant association between the rs1695 polymorphism and the risk of T2DM. The subgroup analyses stratified by ethnicity, publication year and sample size did not reveal significant association between the study polymorphism and the risk of T2DM and any sources contributing to the substantial heterogeneity between studies. The present meta-analysis suggested that there was significant heterogeneity between studies. Considering some limi tations of our meta-analysis, further large-scale studies should be done to reach a more comprehensive understanding.\",\n \"corpus_id\": 23222476,\n \"score\": 2\n },\n {\n \"doc_id\": \"18188076\",\n \"title\": \"The influence of genetic polymorphisms of GSTP1 on the development of asbestosis.\",\n \"abstract\": \"OBJECTIVE: Genetic factors play an important role in the development of asbestosis. The aim of this study was to investigate whether genetic polymorphisms of glutathione S-transferase (GST) P1 represent a risk factor for this disease. METHODS: The study population included 262 workers with asbestosis and 265 matched controls. Information on cumulative asbestos exposure was available. A real-time PCR based on the 5' nuclease assay was designed for the analysis of GSTP1 Ile105Val and Ala114Val polymorphisms. RESULTS: Asbestosis was associated with GSTP1 genotype coding for an enzyme with high conjugation capacity versus genotypes resulting in intermediate and low enzyme activity (odds ratio = 1.49, confidence interval = 1.06-2.10). CONCLUSIONS: The key finding of the study was that GSTP1 genotype coding for an enzyme with high conjugation capacity significantly increases the risk of developing asbestosis.\",\n \"corpus_id\": 20637263,\n \"score\": 1\n },\n {\n \"doc_id\": \"18505928\",\n \"title\": \"Identification and functional characterization of the human glutathione S-transferase P1 gene as a novel transcriptional target of the p53 tumor suppressor gene.\",\n \"abstract\": \"The glutathione S-transferase P1 (GSTP1) is involved in multiple cellular functions, including phase II metabolism, stress response, signaling, and apoptosis. The mechanisms underlying the significantly high GSTP1 expression in many human tumors are, however, currently not well understood. We report here that the GSTP1 gene is a heretofore unrecognized downstream transcriptional target of the tumor suppressor p53. We identified a p53-binding motif comprising two consecutive half-sites located in intron 4 of the GSTP1 gene and is highly homologous to consensus p53-binding motifs in other p53-responsive genes. Using a combination of electrophoretic mobility shift assay and DNase I footprinting analyses, we showed that wild-type p53 protein binds to the GSTP1 p53 motif and luciferase reporter assays showed the motif to be transcriptionally functional in human tumor cells. In a temperature-sensitive p53-mutant cells, levels of both p21/WAF1 and GSTP1 gene transcripts increased time dependently when cells were switched from the inactive mutant state to the wild-type p53 state. Small interfering RNA-mediated reduction of p53 expression resulted in a specific decrease in GSTP1 expression and in tumor cells with mutated p53; adenovirally mediated expression of wild-type p53 increased GSTP1 expression significantly. In a panel of early-passage brain tumor cultures from patients, high levels of GSTP1 transcripts and protein were associated with wild-type p53 and, conversely, low GSTP1 levels with mutant p53. p53 expression knockdown by small interfering RNA increased cisplatin sensitivity. The ability of wild-type p53 to transcriptionally activate the human GSTP1 gene defines a novel mechanism of protecting the genome and, potentially, of tumor drug resistance.\",\n \"corpus_id\": 23871030,\n \"score\": 1\n },\n {\n \"doc_id\": \"18787219\",\n \"title\": \"Glutathione transferase P1: an endogenous inhibitor of allergic responses in a mouse model of asthma.\",\n \"abstract\": \"RATIONALE: Although epidemiological studies have linked asthma susceptibility and severity to polymorphisms in human glutathione transferase Pi (GSTP) 1, there is no direct evidence for a functional involvement of GSTP1 in processes that are pathognomic of asthma. OBJECTIVES: To examine the role of GSTP1 in modulating the development of allergic airways disease. METHODS: Allergic airways disease was induced in wild-type (WT) and Gstp-null mice employing both acute and chronic models. Eosinophilia, goblet cells, and remodeling were quantified by histological assessment; respiratory function was determined using invasive methods. ELISA was used to evaluate Th2 cytokines, eotaxin, and phospho-c-Jun. Gstp1/2 expression was quantified by reverse transcriptase-polymerase chain reaction. MEASUREMENTS AND MAIN RESULTS: Compared with allergic WT mice, eosinophilia, goblet cell hyperplasia, airway remodeling, lung resistance, and IL-5 were enhanced in allergic Gstp-null mice. However, the protective efficacy of GSTP1 was mouse-strain dependent, and associated with inherent variation in expression of Gstp1. Although elevated levels of phospho-c-Jun were detected in Gstp-null mice, treatment of WT mice with a GSTP/c-Jun N-terminal kinase (JNK) inhibitory peptide enhanced phospho-c-Jun and significantly attenuated allergic responses. CONCLUSIONS: GSTP1 attenuates the severity of allergic airways disease. However, the efficacy of GSTP1 correlated with mouse strain-dependent variation in Gstp1 expression. Although GSTP1 attenuated c-Jun phosphorylation, treatment with a GSTP/JNK inhibitory peptide revealed an inverse relationship between c-Jun phosphorylation and allergic responses, indicating that the mechanism by which GSTP attenuates allergic responses is not dependent on the JNK/c-Jun axis. Our data, together with epidemiological evidence, suggest variation in expression and/or function of this protein is an important determinant in asthma pathophysiology.\",\n \"corpus_id\": 41707355,\n \"score\": 1\n },\n {\n \"doc_id\": \"19568750\",\n \"title\": \"MRP2 and GSTP1 polymorphisms and chemotherapy response in advanced non-small cell lung cancer.\",\n \"abstract\": \"PURPOSE: The level of drug metabolism and drug transport is correlated with the sensitivity of cancer cells towards platinum-based chemotherapy. We hypothesize that genetic polymorphisms in metabolising enzymes gene GSTP1 (glutathione S-transferase P1), and MRP2 (multidrug resistance-associated protein 2) (ABCC2), which result in inter-individual differences in metabolism and drug disposition, may predict clinical response to platinum agents in advanced non-small cell lung cancer (NSCLC) patients. METHODS: Totally 113 patients with advanced NSCLC were routinely treated with platinum-based chemotherapy, and clinical response was evaluated after four cycles. MRP2 C-24T (-24C>T), MRP2 Val417Ile (1249G>A), MRP2 Ile1324Ile (3972C>T), and GSTP1 Ile105Val (342A>G) genotype were determined by gene-chip method (a 3-D (three dimensions) polyacrylamide gel-based DNA microarray method) using DNA samples isolated from peripheral blood collected before treatment. Pearson Chi-square test and Fisher's exact test were performed to measure the differences of the chemotherapeutic efficacy among variant genotype. The odds ratios and 95% confidence intervals were computed by logistic regression. RESULTS: The C-->T change of MRP2 C-24T and the A-->G change of GSTP1 Ile105Val polymorphism significantly increased platinum-based chemotherapy response. CONCLUSION: The polymorphic status of MRP2 C-24T and GSTP1 Ile105Val might be the predictive markers for the treatment response of advanced NSCLC patients. The DNA microarray-based method is accurate, high throughput and inexpensive, suitable for single-nucleotide polymorphism genotyping in a large number of individuals.\",\n \"corpus_id\": 10702244,\n \"score\": 1\n },\n {\n \"doc_id\": \"20210814\",\n \"title\": \"Interaction between early maternal smoking and variants in TNF and GSTP1 in childhood wheezing.\",\n \"abstract\": \"BACKGROUND: Children exposed to tobacco smoke early in life have a higher risk of wheeze. Individual susceptibility may depend on genetic factors. OBJECTIVE: We studied whether variations in single nucleotide polymorphisms (SNPs) in the TNF, glutathione S transferase P1 (GSTP1) and beta2-adrenoreceptor (ADRB2) genes modify the effect of early maternal smoking on the development of childhood asthma, wheeze and allergic sensitization. METHODS: In the Swedish prospective birth cohort BAMSE (Children, Allergy, Milieu, Stockholm, Epidemiological Survey) (n=4089), data collection included questionnaires to measure tobacco smoke exposure and clinical outcomes up to age 4 and medical examinations with blood sampling for specific IgE measurements and genotyping. We defined early maternal smoking as daily smoking by the mother during pregnancy and/or postnatally. We investigated five TNF, six GSTP1 and three ADRB2 SNPs in 982 selected wheezers and non-wheezers. RESULTS: An interaction with early maternal smoking was found for three TNF SNPs (-857C/T, Intron 1, Intron 3) with respect to early wheeze (up to 2 years of age). For example, the odds ratio (OR) for developing early wheeze related to early maternal smoking was 2.4 [95% confidence interval (CI) 1.6-3.7] in children with a wild-type CC homozygote genotype of the TNF-857 SNP, while no tobacco-related risk was seen in children carrying the rare T allele. A clear dose response was observed in children with the CC genotype, with an OR of 1.3 (95% CI 1.1-1.5) per each additional pack per week smoked by the mother during pregnancy. A suggestive interaction with early maternal smoking was also seen for three GSTP1 SNPs (Intron 5, Intron 6 and Ile105Val) with respect to transient wheeze, but not for ADRB2 and wheeze phenotypes. No effect modifications were observed for allergic sensitization. CONCLUSION: Our results suggest that the risk of early childhood wheeze associated with early maternal smoking may be modified by TNF and GSTP1 polymorphisms.\",\n \"corpus_id\": 205274695,\n \"score\": 1\n },\n {\n \"doc_id\": \"20840864\",\n \"title\": \"Polymorphism in glutathione S-transferase P1 is associated with susceptibility to Plasmodium vivax malaria compared to P. falciparum and upregulates the GST level during malarial infection.\",\n \"abstract\": \"Glutathione S-transferase P1 (GSTP1) is a member of the GST superfamily, which has well-established multiple roles in various infectious and parasitic diseases. The genetic regulation of GSTP1 has been extensively studied. Thus, its biological significance and disease association prompted us to investigate the role of GSTP1 polymorphisms in Plasmodium-mediated pathogenesis in infected humans. The genotypic distribution of Ile105Val in Plasmodium vivax infection was observed to be significant and strongly associated (OR=4.5) with the progression of pathology, whereas in P. falciparum infection no significant association was observed compared to healthy subjects. Interestingly, we observed significant elevation of GST in vivax infection, with both genotypes Ile105Val and Val105Val, compared to healthy subjects, whereas in P. falciparum infection we found marginally elevated GST levels of mutated genotypes but significantly depleted compared to healthy subjects. Further, during vivax and falciparum infection overall significant elevations of glutathione, glutathione peroxidase, and GST levels were observed. Expression of both GSTP1 mRNA and protein was significantly upregulated during vivax infection compared to falciparum infection and both were significantly upregulated compared to the levels in healthy subjects as well. These studies suggest that GSTP1 polymorphism is involved in the pathogenesis of malaria and it may serve as a valuable molecular marker, possessing a promising rationale for diagnostic potential in assessing disease progression during clinical malaria.\",\n \"corpus_id\": 207547055,\n \"score\": 1\n },\n {\n \"doc_id\": \"20922139\",\n \"title\": \"GST (GSTM1, GSTT1, and GSTP1) polymorphisms in the genetic susceptibility of Turkish patients to cervical cancer.\",\n \"abstract\": \"OBJECTIVE: This work investigates the role of glutathione S-transferase M1 (GSTM1), glutathione S-transferase T1 (GSTT1), and glutathione S-transferase P1 (GSTP1) enzymes and polymorphisms, which are found in phase II detoxification reactions in the development of cervical cancer. METHODS: This study was conducted with 46 patients diagnosed with cervical cancer and 52 people with no cancer history. Multiplex PCR methods were used to evaluate the GSTM1 and GSTT1 gene polymorphism. However, the GSTP1 (Ile105Val) gene polymorphism was studied using a PCR-RFLP method. The patient and control groups were compared using a chi-square test with p<0.05. RESULTS: In the patient group, statistical significance was determined for gravidity (p=0.03), parity (p=0.01), and the number of living children (p=0.01) compared to the control group. The gene frequency of GSTM1, GSTT1, and GSTP1 polymorphisms was evaluated. We observed that GSTM1 and GSTT1 null genotype frequencies were 54.3% and 32.6% respectively, while GSTP1 (Ile/Val), (Ile/Ile), (Val/Val) genotype frequencies were 52%, 44%, and 4%, respectively, in the cervical cancer patients. No statistical variation was determined between the control and patient groups in terms of GSTM1, GSTT1, and GSTP1 polymorphisms (p>0.05). CONCLUSION: Our results demonstrate that GSTT1, GSTM1, and GSTP1 polymorphisms are not associated with cervical cancer in Turkish patients.\",\n \"corpus_id\": 34933820,\n \"score\": 1\n },\n {\n \"doc_id\": \"20979931\",\n \"title\": \"Associations between oxaliplatin-induced peripheral neuropathy and polymorphisms of the ERCC1 and GSTP1 genes.\",\n \"abstract\": \"OBJECTIVE: Oxaliplatin-induced chronic neuropathy is cumulative and dose-limiting; reliable predictors and determination of the mechanism of this toxic effect are needed. METHODS: We retrospectively studied 51 Japanese adults with colorectal cancer who had received oxaliplatin-based chemotherapy to explore the pharmacogenetic association between oxaliplatin-induced neuropathy and polymorphisms of the excision repair cross-complementation Group 1 (ERCC1) and glutathione-S-transferases pi 1 (GSTP1) genes. RESULTS: For the ERCC1 C118T polymorphism, Grade 1 chronic neuropathy developed earlier in patients with C/T and T/T genotypes (median number of treatment cycles at onset = 6) than in those with the reference C/C genotype (7 cycles; p = 0.0162 by the generalized Wilcoxon test). For the GSTP1 Ile105Val polymorphism, chronic neuropathy developed earlier in patients with the reference Ile/Ile genotype (6 cycles) than in those with Ile/Val and Val/Val genotypes (9 cycles; p = 0.0321). ERCC1 C118T and GSTP1 Ile105Val polymorphisms were not significantly associated with an increased risk of developing Grade 2 or more severe chronic neuropathy. CONCLUSIONS: Our results suggest that ERCC1, C118T and GSTP1 Ile105Val polymorphisms are more strongly related to the time until onset of neuropathy than to the grade of neuropathy. Most likely these polymorphisms influence patients' sensitivity to neuropathy.\",\n \"corpus_id\": 11629487,\n \"score\": 1\n },\n {\n \"doc_id\": \"21091064\",\n \"title\": \"Exploring the landscape of protein-ligand interaction energy using probabilistic approach.\",\n \"abstract\": \"Analysis of protein/small molecule interactions is crucial in the discovery of new drug candidates and lead structure optimization. Small biomolecules (ligands) are highly flexible and may adopt numerous conformations upon binding to the protein. Using computer simulations instead of sophisticated laboratory procedures may significantly reduce cost of some stages of drug development. Inspired by probabilistic path planning in robotics, stochastic roadmap methodology can be regarded as a very interesting approach to effective sampling of ligand conformational space around a protein molecule. Protein-ligand interactions are divided into two parts: electrostatics, modeled by the Poisson-Boltzmann equation, and van der Waals interactions, represented by the Lennard-Jones potential. The results are promising; it can be shown that locations of binding sites predicted by the simulation are in agreement with those revealed by experimental x-ray crystallography of protein-ligand complexes. We wanted to extend our knowledge beyond the current molecular modeling tools to arrive at a better understanding of the ligand-binding process. To this end, we investigated a two-level model of protein-ligand interaction and sampling of ligand conformational space covering the entire surface of protein target.\",\n \"corpus_id\": 35188846,\n \"score\": 1\n },\n {\n \"doc_id\": \"21608983\",\n \"title\": \"Free-energy landscapes of protein domain movements upon ligand binding.\",\n \"abstract\": \"The conformation and functions of proteins are closely linked, and many proteins undergo conformational changes upon ligand binding. The X-ray crystallographic studies have revealed conformational differences in proteins between the liganded and unliganded states. Currently, the conformational transitions that originate in the ligand binding are explained on the basis of two representative models, the induced-fit and preexisting equilibrium dynamics models. However, the actual dynamics of the proteins remain ambiguous. Though these two models are the extreme ones, it is important to understand the difference between these two, particularly in structural biology and medicinal chemistry studies. Here, we clarified the difference in the mechanisms responsible for the conformational changes induced in two proteins upon ligand binding by examining computationally determined free-energy profiles of the apo- and holoproteins. The lysine/arginine/ornithine-binding protein and maltose/maltodextrin-binding protein were chosen as the target proteins, and the energy profiles were generated by a molecular simulation approach. Our results revealed that fluctuations in the apo state and protein-ligand interactions both play important roles in conformational transition, and the mechanism is highly influenced by the fluctuations in the apo state, which are unique to a particular structure.\",\n \"corpus_id\": 12513402,\n \"score\": 1\n },\n {\n \"doc_id\": \"22180037\",\n \"title\": \"Genetic polymorphism of the glutathione-S-transferase P1 gene (GSTP1) and susceptibility to prostate cancer in the Kashmiri population.\",\n \"abstract\": \"Glutathione-S-transferase P1 (GSTP1) is a critical enzyme of the phase II detoxification pathway. One of the common functional polymorphisms of GSTP1 is A→G at nucleotide 313, which results in an amino acid substitution (Ile105Val) at the substrate binding site of GSTP1 and reduces catalytic activity of GSTP1. To investigate the GSTP1 Ile105Val genotype frequency in prostate cancer cases in the Kashmiri population, we designed a case-control study, in which 50 prostate cancer cases and 45 benign prostate hyperplasia cases were studied for GSTP1 Ile105Val polymorphism, compared to 80 controls taken from the general population, employing the PCR-RFLP technique. We found the frequency of the three different genotypes of GSTP1 Ile105Val in our ethnic Kashmir population, i.e., Ile/Ile, Ile/Val and Val/Val, to be 52.4, 33.3 and 14.3% among prostate cancer cases, 48.5, 37.5 and 14% among benign prostate hyperplasia cases and 73.8, 21.3 and 5% in the control population, respectively. There was a significant association between the GSTP1 Ile/Val genotype and the advanced age group among the cases. We conclude that GSTP1 Ile/Val polymorphism is involved in the risk of prostate cancer development in our population.\",\n \"corpus_id\": 38386494,\n \"score\": 1\n },\n {\n \"doc_id\": \"22251241\",\n \"title\": \"Role of glutathione S-transferases in melanoma susceptibility: association with GSTP1 rs1695 polymorphism.\",\n \"abstract\": \"BACKGROUND: Glutathione S-transferases (GSTs) GSTM1, GSTT1 and GSTP1 are multifunctional enzymes involved in the detoxification of a wide range of reactive oxygen species produced during melanin synthesis and oxidative stress processes. OBJECTIVES: Single nucleotide polymorphisms (SNPs) in GSTP1 and copy number variants in GSTM1 and GSTT1 may be candidate low-penetrance variants with a role in susceptibility to malignant melanoma (MM). METHODS: In this case-control study, 562 Spanish patients with sporadic MM and 338 cancer-free control subjects were included, and the role of polymorphisms in these GST genes was investigated. Genotypes were established by quantitative real-time polymerase chain reaction for GSTM1 and GSTT1 while TaqMan probes were used to genotype GSTP1 SNPs. RESULTS: The GSTP1 polymorphism rs1695, which encodes the amino acid change p.Ile105Val, was individually associated with MM [odds ratio (OR): 1·32, 95% confidence interval (CI): 1·06-1·63]. Furthermore, individuals carrying one or two MC1R nonsynonymous changes and GSTP1 rs1695 rare allele had an increased risk of developing MM (OR: 3·34, 95% CI: 1·42-8·09 and OR: 20·42, 95% CI: 2·80-417·42, respectively). CONCLUSIONS: This is the first time that the GSTP1 rs1695 polymorphism is reported to be associated with MM. In addition, this study is one of the largest GST polymorphism studies undertaken in the Spanish population and the first time that copy number variants have been scrutinized in relation to MM.\",\n \"corpus_id\": 26123505,\n \"score\": 1\n },\n {\n \"doc_id\": \"22812193\",\n \"title\": \"Lack of association between GSTM1, GSTP1, and GSTT1 gene polymorphisms and asthma in adult patients from Rome, central Italy.\",\n \"abstract\": \"BACKGROUND: Asthma is a complex multifactorial disease that is not yet fully understood. Oxidative stress due to an imbalance between the oxidative forces and the antioxidant defense systems has been implicated in asthma pathogenesis. However, much debate still surrounds the key genetic factors involved in the development of this disease. Candidate genes include the glutathione S-transferases (GSTs). In particular, mu, pi, and theta classes of GSTs play an important role in regulating inflammatory responses. However, few and contradictory data are available on the association between asthma development and GST gene polymorphisms (GSTM1, GSTP1, and GST1). OBJECTIVE: To investigate whether GSTM1, GSTT1, and GSTP1 polymorphisms are associated with asthma development. METHODS: We recruited 200 unrelated healthy individuals and 199 asthmatic patients from Rome in Central Italy. Genotyping of GSTMI and GSTT1 genes was performed by a multiplex polymerase chain reaction (PCR) while the GSTP1 polymorphism (rs1695) was determined using PCR-restriction fragment length polymorphism analysis. RESULTS: Our results suggest that the GST polymorphisms analyzed are not associated with asthma, confirming the uncertain role of GST genes in the development of asthma. CONCLUSIONS: Oxidative stress is certainly involved in the development of asthma, and GSTs may therefore influence asthma risk, although, as our results show, their role in pathogenesis remains to be elucidated. Future studies should focus on the interactions of GST genes with the environment and other antioxidant genes to shed light on the role of GSTs in asthma.\",\n \"corpus_id\": 2367056,\n \"score\": 1\n },\n {\n \"doc_id\": \"22938488\",\n \"title\": \"The GSTP1 Ile105Val polymorphism is not associated with susceptibility to colorectal cancer.\",\n \"abstract\": \"The glutathione S transferase (GST) family is a major part of cellular defense mechanisms against endogenous and exogenous substances, many of which have carcinogenic potential. Alteration in the expression level or structure of the glutathione-S-transferase (GST) enzymes may lead to inadequate detoxification of potential carcinogens and consequently contribute to cancer development. A member of the glutathione-S-transferase (GST) family, GSTP1, is an attractive candidate for involvement in susceptibility to carcinogen-associated colorectal cancer. An A>G transition in exon 5 resulting in an Ile105Val amino acid substitution has been identified which alters catalytic efficiency. The present study investigated the possible impact of Ile105Val GSTP1 polymorphism on susceptibility to colorectal cancer. in Jordan We examined 90 tissue samples previously diagnosed with colorectal carcinoma, and 56 non-cancerous colon tissues. DNA was extracted from paraffin embedded tissues and the status of the GSTP1 polymorphism was determined using a polymerase chain reaction restriction fragment length polymorphism (RFLP) method. No statistically significant differences were found between colorectal cancer cases and controls for the GSTP1 Ile/Ile, Ile/Val and Val/Val genotypes. The glutathione S-transferase polymorphism was not associated with risk in colorectal cancer cases in Jordan stratified by age, sex, site, grade or tumor stage. In conclusion, the GSTP1 Ile105Val polymorphism is unlikely to affect the risk of colorectal cancer.\",\n \"corpus_id\": 14665063,\n \"score\": 1\n },\n {\n \"doc_id\": \"23025812\",\n \"title\": \"Modulation of a ligand's energy landscape and kinetics by the chemical environment.\",\n \"abstract\": \"Understanding how the chemical environment modulates the predominant conformations and kinetics of flexible molecules is a core interest of biochemistry and a prerequisite for the rational design of synthetic catalysts. This study combines molecular dynamics simulation and Markov state models (MSMs) to a systematic computational strategy for investigating the effect of the chemical environment of a molecule on its conformations and kinetics. MSMs allow quantities to be computed that are otherwise difficult to access, such as the metastable sets, their free energies, and the relaxation time scales related to the rare transitions between metastable states. Additionally, MSMs are useful to identify observables that may act as sensors for the conformational or binding state of the molecule, thus guiding the design of experiments. In the present study, the conformation dynamics of UDP-GlcNAc are studied in vacuum, water, water + Mg(2+), and in the protein UDP-GlcNAc 2-epimerase. It is found that addition of Mg(2+) significantly affects the conformational stability, thermodynamics, and kinetics of UDP-GlcNAc. In particular, the slowest structural process, puckering of the GlcNAc sugar, depends on the overall conformation of UDP-GlcNAc and may thus act as a sensor of whether Mg(2+) is bound or not. Interestingly, transferring the molecule from vacuum to water makes the protein-binding conformations UDP-GlcNAc first accessible, while adding Mg(2+) further stabilizes them by specifically associating to binding-competent conformations. While Mg(2+) is not cocrystallized in the UDP-GlcNAc 2-epimerase complex, the selectively stabilized Mg(2+)/UDP-GlcNAc complex may be a template for the bound state, and Mg(2+) may accompany the binding-competent ligand conformation to the binding pocket. This serves as a possible explanation of the enhanced epimerization rate in the presence of Mg(2+). This role of Mg(2+) has previously not been described and opens the question whether \\\"binding co-factors\\\" may be a concept of general relevance for protein-ligand binding.\",\n \"corpus_id\": 23245271,\n \"score\": 1\n },\n {\n \"doc_id\": \"23077566\",\n \"title\": \"Interaction between GSTP1 Val allele and H. pylori infection, smoking and alcohol consumption and risk of gastric cancer among the Chinese population.\",\n \"abstract\": \"Glutathione S-transferase P1 (GSTP1) is a critical enzyme in the phase II detoxification pathway. One of the common functional polymorphisms of GSTP1 is A→G at nucleotide 313, which results in an amino acid substitution (Ile105Val) at the substrate binding site and reduced catalytic activity. We evaluated the interaction between GSTP1 Val allele and Helicobacter pylori infection, smoking and alcohol consumption, increasing the risk of gastric cancer among the Chinese population. Information on potential gastric cancer risk factors and blood specimens were collected from 618 incident gastric cancer cases and 1,830 non-cancer controls between March 2002 and December 2011 in Liaoning Province, China. GSTP1 Ile105Val was genotyped by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry and polymerase chain reaction-restriction fragment length polymorphism. Serum levels of anti-H. pylori IgG were measured by ELISA. Odds ratio (OR) and 95% confidence interval (CI) were calculated using multivariate logistic regression, adjusted by sex and age. The risk of gastric cancer was significantly elevated in patients with the GSTP1 Val/Val genotype (adjusted OR = 3.324; 95% CI = 1.790-6.172). An elevated risk of gastric cancer was observed in patients with H. pylori infection, smoking, or alcohol consumption, and together with the GSTP1 Ile/Val +Val/Val genotype (OR = 3.696; 95% CI = 2.475-5.521; OR = 1.638; 95% CI = 1.044-2.571; OR = 1.641; 95% CI = 0.983-2.739, respectively) (p<0.05). The GSTP1 Val allele shows an interaction with smoking, alcohol consumption, and especially H. pylori infection for increasing the risk of gastric cancer. These findings could demonstrate new pathophysiological pathways for the development of gastric cancer.\",\n \"corpus_id\": 16222411,\n \"score\": 1\n },\n {\n \"doc_id\": \"23471163\",\n \"title\": \"Glutathione S-transferase P1 Ile105Val polymorphism and oral cancer risk: a meta-analysis.\",\n \"abstract\": \"Objective The glutathione S-transferase P1 (GSTP1) gene has been suggested to play an important role in the pathogenesis of oral cancer. However, the results have been inconsistent. In this study, we performed a meta-analysis to clarify the association of GSTP1 Ile105Val polymorphisms with oral cancer risk. Methods Published literature from PubMed and EMBASE were retrieved. Pooled odds ratio (OR) with 95% confidence interval (CI) was calculated using fixed- or random-effects model. Results 13 studies (1803 oral cancer cases and 2998 controls) for GSTP1 Ile105Val polymorphism were included in the meta-analysis. The results indicated that there was no significant association between GSTP1 Ile105Val polymorphism and oral cancer in the overall population (OR=1.30, 95%CI=0.92-1.38, I(2)=48.0%, p for heterogeneity=0.027). Further subgroup analysis by ethnicity suggested that GSTP1 Ile105Val polymorphism was significantly associated with oral cancer only in East Asians (OR=1.64, 95%CI=1.16-2.31, I(2)=0.0%, p for heterogeneity=0.525), but not in Caucasians (OR=1.16, 95%CI=0.73-1.82, I(2)=7.5%, p for heterogeneity=0.299), Africans (OR=1.10, 95%CI=0.37-3.28), South Asians (OR=1.20, 95%CI=0.69-2.08, I(2)=74.3%, p for heterogeneity=0.021) and mixed population (OR=0.91, 95%CI=0.70-1.20, I(2)=39.7%, p for heterogeneity=0.174). Conclusions The present meta-analysis has limited evidence to support the association of GSTP1 Ile105Val polymorphism with HCC risk in the overall population. However, GSTP1 Ile105Val polymorphism might be associated with risk of oral cancer in East Asians.\",\n \"corpus_id\": 6893153,\n \"score\": 1\n },\n {\n \"doc_id\": \"23494181\",\n \"title\": \"Association between the GSTP1 Ile105Val polymorphism and prostate cancer risk: a systematic review and meta-analysis.\",\n \"abstract\": \"Many studies have reported the role of glutathione S-transferase P1 (GSTP1) Ile105Val polymorphism with prostate cancer (PCa) risk. However, these studies have yielded conflicting results. Hence, we performed this meta-analysis to investigate the association between GSTP1 Ile105Val polymorphism and PCa in different inheritance models. A total of 13 eligible studies were pooled into this meta-analysis. There was significant association between the GSTP1 Ile158Val variant genotypes and PCa for Ile/Ile vs Val/Val comparison [odds ratio (OR) =0.705; I (2) =63.7 %; 95 % confidence interval (95 % CI) = 0.508-0.977], Ile/Val vs Val/Val comparison (OR=0.736; I (2) =8.0 %; 95 % CI=0.613-0.883), and dominant model (OR=0.712; I (2) =45.5 %; 95 % CI=0.555-0.913). However, no associations were detected for other genetic models. In the stratified analysis by ethnicity, significant associations between GSTP1 Ile105Val polymorphism and PCa risk were also found among Caucasians (Ile/Ile vs Val/Val comparison OR=0.818, I (2) =0.0 %, 95 % CI=0.681-0.982; Ile/Val vs Val/Val comparison OR=0.779, I (2) =0.0 %, 95 % CI=0.651-0.933; and dominant model OR=0.794, I (2) =0.0 %, 95 % CI=0.670-0.941), while there were no associations found for other genetic models. However, no associations were found in Asians and African-Americans for all genetic models when stratified by ethnicity. In conclusion, our meta-analysis indicates that GSTP1 Ile105Val polymorphisms contributed to the PCa susceptibility. However, a study with the larger sample size is needed to further evaluate gene-environment interaction on GSTP1 Ile105Val polymorphisms and PCa risk.\",\n \"corpus_id\": 768191,\n \"score\": 1\n },\n {\n \"doc_id\": \"23604281\",\n \"title\": \"Genetic polymorphisms of ERCC1‑118, XRCC1‑399 and GSTP1‑105 are associated with the clinical outcome of gastric cancer patients receiving oxaliplatin‑based adjuvant chemotherapy.\",\n \"abstract\": \"The aim of the present study was to determine whether specific molecular parameters may serve as predictors of treatment outcomes and toxicity of oxaliplatin (OXA)‑based chemotherapy, which is used as an adjuvant treatment in resected gastric cancer. All gastric cancer patients examined in the study received an OXA/5‑fluorouracil chemotherapeutic regimen. Genetic polymorphisms of certain platinum‑related genes were determined by the TaqMan 5' nuclease assay and direct sequencing. Relapse‑free survival (RFS), overall survival (OS) and toxicity were evaluated according to each genotype. Following adjustment for the most relevant clinical variables, excision repair cross‑complimentary group 1 (ERCC1)‑118 and X-ray repair cross-complementing protein 1 (XRCC1‑399) demonstrated significant predictive value for RFS and OS. We also demonstrated that carrying at least one variant XRCC1 Arg399Gln or glutathione S-transferase π 1 (GSTP1) Ile105Val allele significantly increased the risk of any grade 3 or 4 hematological toxicity. In particular, carrying at least one variant GSTP1 Ile105Val allele was also significantly correlated with an increased risk of grade 3 or 4 gastrointestinal toxicity and neurotoxicity. Our data suggested that gastric cancer patients harboring ERCC1‑118 C/C and XRCC1‑399 A/G or A/A genotypes may benefit from receiving OXA‑based adjuvant chemotherapy, and carrying at least one variant XRCC1 Arg399Gln or GSTP1 Ile105Val allele may contribute to the occurrence of adverse drug effects associated with OXA‑based chemotherapy.\",\n \"corpus_id\": 207562730,\n \"score\": 1\n },\n {\n \"doc_id\": \"23765758\",\n \"title\": \"Quantitative assessment of the association between GSTP1 gene Ile105Val polymorphism and susceptibility to hepatocellular carcinoma.\",\n \"abstract\": \"Glutathione S-transferase P1 (GSTP1) gene Ile105Val polymorphism has been suggested to be involved in the development of cancer. However, the results from the studies regarding the association between GSTP1 Ile105Val polymorphism and hepatocellular carcinoma risk have been inconsistent. Thus, we performed a meta-analysis to investigate the association. Published literature from PubMed, Chinese Biomedical Literature, and Wanfang databases was searched for eligible publications. Pooled odds ratios (ORs) with 95 % confidence intervals (95 %CIs) were calculated using random- or fixed-effects model. Six studies with a total of 1,843 participants were finally included into this meta-analysis. The results suggested there was no association between GSTP1 Ile105Val polymorphism and hepatocellular carcinoma risk under all genetic models (for ValVal vs. IleIle, OR = 0.79, 95 %CI 0.48-1.29, P = 0.341; for IleVal vs. IleIle, OR = 1.05, 95 %CI 0.84-1.30, P = 0.678; for the dominant model, OR = 0.91, 95 %CI 0.68-1.20, P = 0.498; and for the recessive model, OR = 0.76, 95 %CI 0.47-1.24, P = 0.269). Subgroup analyses by ethnicity showed there was also no association between GSTP1 Ile105Val polymorphism and hepatocellular carcinoma risk in Asians under all genetic models (All P values were more than 0.05), but GSTP1 Ile105Val polymorphism was associated with decreased risk of hepatocellular carcinoma in European under the recessive model (ValVal vs. IleVal/IleIle) (OR = 0.44, 95 %CI 0.20-0.98, P = 0.044). In conclusion, the meta-analysis suggests that there is little evidence for the association between GSTP1 Ile105Val polymorphism and hepatocellular carcinoma risk. However, more well-designed studies are needed to further assess this association.\",\n \"corpus_id\": 14562467,\n \"score\": 1\n },\n {\n \"doc_id\": \"23812950\",\n \"title\": \"Pharmacogenetic influence of GST polymorphisms on anthracycline-based chemotherapy responses and toxicity in breast cancer patients: a multi-analytical approach.\",\n \"abstract\": \"BACKGROUND AND OBJECTIVE: Chemotherapeutic drug treatment outcomes are genetically determined. Polymorphisms in genes encoding phase II drug metabolizing enzyme glutathione-S-transferase (GST) can possibly predict treatment outcomes, and can be of prognostic significance in breast cancer patients. The aim of this study was to determine the role of genetic variations in GST in predicting response to, and toxicity of, anthracycline-based chemotherapy in breast cancer patients. METHOD: Two hundred and seven patients treated with anthracycline-based chemotherapy were genotyped for GSTM1 and GSTT1 deletion polymorphisms, and GSTP1 Ile105Val (rs1695), by polymerase chain reaction (PCR)/ PCR-restriction fragment length polymorphism (RFLP). Genetic variations were correlated with tumor response to neo-adjuvant chemotherapy (NACT) in 100 patients, and with chemo-toxicity in 207 who received adjuvant chemotherapy or NACT, using Chi-square and logistic regression. Higher order gene-gene interactions with treatment outcomes were characterized by multifactor dimensionality reduction (MDR) analysis. RESULTS: In single-locus analysis, Ile/Val and Ile/Val+Val/Val genotypes of the GSTP1 Ile105Val (rs1695) polymorphism reached statistical significance with grade 2-4 anemia (P=0.019, P=0.027). On performing gene-gene interaction analysis, GSTM1 null-GSTP1 Ile/Val was significantly associated with response to NACT (P=0.032). On evaluating higher order gene-gene interaction models by MDR analysis, GSTM1 and GSTP1 Ile105Val; GSTM1 and GSTT1; and GSTT1 and GSTP1 Ile105Val showed significant association with treatment response, grade 2-4 anemia, and dose delay/reduction due to neutropenia (P=0.046, P=0.027, P=0.026), respectively. CONCLUSION: Multi-analytical strategies may serve as a better tool for characterization of pharmacogenetic-based breast cancer treatment outcomes.\",\n \"corpus_id\": 17256907,\n \"score\": 1\n },\n {\n \"doc_id\": \"23975366\",\n \"title\": \"Association between GSTP1 Ile105Val polymorphism and glioma risk: a systematic review and meta-analysis.\",\n \"abstract\": \"Glutathione S-transferase P1 (GSTP1) gene Ile105Val polymorphism has been suggested to be involved in the development of glioma. However, the results from the studies regarding the association between GSTP1 Ile105Val polymorphism and glioma risk have been inconsistent. Thus, we performed a meta-analysis to investigate this association. Pooled odds ratios (ORs) with 95% confidence intervals (95%CIs) were calculated using random or fixed effects model. Nine studies with 2,078 cases and 3,970 controls were finally included into this meta-analysis. The results suggested there was no association between GSTP1 Ile105Val polymorphism and glioma risk under recessive model (OR = 1.138, 95%CI = 0.966-1.341, Pheterogeneity = 0.088, P = 0.123). Subgroup analyses by ethnicity showed there was also no association between GSTP1 Ile105Val polymorphism and glioma risk in mixed populations under recessive model (OR = 1.199, 95%CI = 0.928-1.549, Pheterogeneity = 0.060, P = 0.166) and Caucasian populations (OR = 1.097, 95%CI = 0.885-1.360, Pheterogeneity = 0.186, P = 0.398). In conclusion, the meta-analysis suggests that there is no association between GSTP1 Ile105Val polymorphism and glioma risk. However, more well-designed and larger studies are needed to further assess this association.\",\n \"corpus_id\": 8205798,\n \"score\": 1\n },\n {\n \"doc_id\": \"23977100\",\n \"title\": \"GSTP1 Ile105Val polymorphism and prostate cancer risk: evidence from a meta-analysis.\",\n \"abstract\": \"BACKGROUND: Glutathione S-transferase P1 (GSTP1) is thought to be involved in the detoxification of reactive carcinogen metabolites. Numerous epidemiological studies have evaluated the association of GSTP1 Ile105Val polymorphism with the risk of prostate cancer. However, the results remain inconclusive. To derive a more precise estimation, a meta-analysis was performed. METHODOLOGY/PRINCIPAL FINDINGS: A comprehensive search was conducted to identify the eligible studies. We used odds ratios (ORs) with 95% confidence intervals (CIs) to assess the strength of the relationship. The overall association was not significant (Val/Val vs. Ile/Ile OR = 1.06, 95% CI = 0.90-1.25, P = 0.50; Val/Val vs. Val/Ile+Ile/Ile: OR = 1.07, 95% CI = 0.91-1.25, P = 0.44). In subgroup analyses by ethnicity and prostate cancer grade, the similar results were observed. However, in stratified analysis by clinical stage, we found a significant association with low-stage prostate cancer (Val/Val vs. Ile/Ile: OR = 2.70, 95% CI = 1.73-4.22, P<0.001; Val/Val vs. Val/Ile+Ile/Ile: OR = 2.14, 95% CI = 1.38-3.33, P = 0.001). Moreover, there was no statistically significant evidence of multiplicative interactions neither between the GSTP1 Ile105Val polymorphism and GSTM1, nor between smoking status and GSTP1 on prostate cancer risk. CONCLUSIONS: This meta-analysis showed that GSTP1 Ile105Val polymorphism might not be significantly associated with overall prostate cancer risk. Further stratified analyses showed a significant association with low-stage prostate cancer.\",\n \"corpus_id\": 6911263,\n \"score\": 1\n },\n {\n \"doc_id\": \"25008867\",\n \"title\": \"Pharmacogenetic association between GSTP1 genetic polymorphism and febrile neutropenia in Japanese patients with early breast cancer.\",\n \"abstract\": \"BACKGROUND: Genetic risk factors for febrile neutropenia (FN), the major adverse event of perioperative chemotherapy for early breast cancer, remain unclear. METHODS: This study retrospectively explored pharmacogenetic associations of single nucleotide polymorphisms (SNPs) of the uridine glucuronosyltransferase 2B7 (UGT2B7, rs7668258), glutathione-S-transferase pi 1 (GSTP1, rs1695), and microcephalin 1 (MCPH1, rs2916733) genes with chemotherapy-related adverse events in 102 Japanese women who received epirubicin and cyclophosphamide as perioperative chemotherapy for early breast cancer. RESULTS: The allele frequencies for all of the SNPs were in concordance with the Hap-Map data of Japanese individuals. Among the 24 patients who had FN at least once during all courses of chemotherapy, 23 had the A/A genotype, and 1 had the A/G genotype of the GSTP1 polymorphism (rs1695, P = 0.001); 23 of the 70 patients with the A/A genotype had FN, as compared with only 1 of the 32 patients with the A/G and G/G genotypes. The genotype distributions of the UGT2B7 and MCPH1 polymorphisms did not differ between the patients who had FN or grade 3/4 neutropenia and those who did not. CONCLUSION: Among Japanese women who received epirubicin and cyclophosphamide as perioperative chemotherapy for early breast cancer, those with the A/A genotype of the GSTP1 polymorphism (rs1695) were more likely to have FN.\",\n \"corpus_id\": 20647725,\n \"score\": 1\n },\n {\n \"doc_id\": \"25515186\",\n \"title\": \"GSTM1, GSTP1, and GSTT1 genetic variability in Turkish and worldwide populations.\",\n \"abstract\": \"OBJECTIVE: Glutathione S-transferase (GST) variants have been widely investigated to better understand their role in several pathologic conditions. To our knowledge, no data about these genetic polymorphisms within the Turkish population are currently available. The aim of this study was to analyze GSTM1 positive/null, GSTT1 positive/null, GSTP1*I105V (rs1695), and GSTP1*A114V (rs1138272) variants in the general Turkish population, to provide information about its genetic diversity, and predisposition to GST-related diseases. METHODS: Genotyping was performed in 500 Turkish individuals using the Sequenom MassARRAY platform. A comparative analysis was executed using the data from the HapMap and Human Genome Diversity Projects (HGDP). Sequence variation was deeply explored using the Phase 1 data of the 1,000 Genomes Project. RESULTS: The variability of GSTM1, GSTT1, and GSTP1 polymorphisms in the Turkish population was similar to that observed in Central Asian, European, and Middle Eastern populations. The high linkage disequilibrium between GSTP1*I105V and GSTP1*A114V in these populations may have a confounding effect on GSTP1 genetic association studies. In analyzing GSTM1, GSTT1, and GSTP1 sequence variation, we observed other common functional variants that may be candidates for associated studies of diseases related to GST genes (e.g., cancer, cardiovascular disease, and allergy). CONCLUSIONS: This study provides novel data about GSTM1 positive/null, GSTT1 positive/null, GSTP1*I105V, and GSTP1*A114V variants in the Turkish population, and other functional variants that may affect GSTM1, GSTT1, and GSTP1 functions among worldwide populations. This information can assist in the design of future genetic association studies investigating oxidative stress-related diseases.\",\n \"corpus_id\": 25339892,\n \"score\": 1\n },\n {\n \"doc_id\": \"25775823\",\n \"title\": \"[Role of gene polymorphisms of phase II of xenobiotic biotransformation from glutathione-S-transferase and N-acetyltransferase families in susceptibility to lung cancer among Mayak workers].\",\n \"abstract\": \"An association between polymorphous (allelic) gene variants of phase II of enzymatic xenobiotic biotransformation (EXB) of multigene families of glutathione-S-transferase (GSTs) GSTM1*0, GSTT1*0, GSTP1*B Ile105Val, and N-acetyltransferase (NAT) NAT2*6 590G>A, NAT2*5 481C>T, as well as lung cancer in Mayak workers exposed occupationally to prolonged external γ-rays and internal α-radiation from incorporated 239Pu was studied. Analysis of the population frequency of genotypes and alleles of the studied genes in the cohort of Mayak workers revealed their compliance with the Hardy-Weinberg principle and with the corresponding frequency in the European population. The study was based on the case-control method. A case-group consisted of 49 Mayal workers with a verified diagnosis of lung cancer. The mean total absorbed dose from external γ-rays at the moment of diagnostics was 1.03 Gy; the mean total absorbed dose from internal α-radiation from incorporated 239Pu to lung was 0.35 Gy. Control consisted of 172 Mayak workers matched by the year of birth, gender, and age at the moment of employment at one of the main facilities with no lung cancer registered within the study period. No increase in the relative risk of lung cancer (odds ratio, OR) was revealed among the individuals with deletion variants of genes GSTM1*0 and GSTT1*0 (pp genotype, complete absence of gene products) as compared to the individuals with ww or wp genotype, which was determined in total for these genes (normal or partly decreased gene activity). An increase in OR of lung cancer in 1.849 times (p = 0.239) and in 2.439 times (p = 0.075) was found in the carriers with a complete absence of the product of genes GSTP1*B and NAT2*6 590G>A, correspondingly (pp genotype). A statistically significant decrease in OR of lung cancer was found in the wp genotype carriers of gene GSTP1*B (OR = 0.50, p = 0.041). Three variants of paired combinations of gene alleles were established in the carriers with a statistically significant increase in OR of lung cancer (ww GSTP1*B + pp GSTM1*0; ww GSTP1*B + pp NAT2*6 590G>A; pp GSTP1*B + pp NAT2*5 481C>T), and one combination in the carriers with a statistically significant decrease in OR of lung cancer (wp GSTP1*B and ww +wp GSTT1*0).\",\n \"corpus_id\": 24492777,\n \"score\": 1\n },\n {\n \"doc_id\": \"26044055\",\n \"title\": \"Association of glutathione S-transferase pi (GSTP1) Ile105Val polymorphism with the risk of skin cancer: a meta-analysis.\",\n \"abstract\": \"Numerous epidemiological studies have evaluated the association of Glutathione S-transferase P1 (GSTP1) Ile105Val polymorphism with the risk of skin cancer. However, the results remain inconclusive. To derive a more precise estimation of the association between the GSTP1 Ile105Val polymorphism and skin cancer risk, a meta-analysis was performed. A comprehensive search was conducted to identify the eligible studies. We used odds ratios (ORs) with 95 % confidence intervals (CIs) to assess the association of GSTP1 Ile105Val polymorphism with skin cancer risk. Thirteen case-control studies in nine articles, which included a total of 1504 cases and 2243 controls. Overall, we found that GSTP1 Ile105Val polymorphism was not associated with skin cancer risk. Furthermore, subgroup analysis by histological types showed that GSTP1 Ile105Val polymorphism was associated with risks of malignant melanoma under the dominant model (Val/Val + Val/Ile vs. Ile/Ile: OR 1.230, 95 % CI 1.017-1.488, P = 0.033). However, lack of association between GSTP1 Ile105Val polymorphism and BCC and SCC risk in all genetic models. Our meta-analysis suggested that the GSTP1 Ile105Val polymorphism might be associated with increased risk of malignant melanoma in Caucasian population.\",\n \"corpus_id\": 28856268,\n \"score\": 1\n },\n {\n \"doc_id\": \"26046522\",\n \"title\": \"Modifying Role of GSTP1 Polymorphism on the Association between Tea Fluoride Exposure and the Brick-Tea Type Fluorosis.\",\n \"abstract\": \"BACKGROUND: Brick tea type fluorosis is a public health concern in the north-west area of China. The association between SNPs of genes influencing bone mass and fluorosis has attracted attention, but the association of SNPs with the risk of brick-tea type of fluorosis has not been reported. OBJECTIVE: To investigate the modifying roles of GSTP1 rs1695 polymorphisms on this association. METHODS: A cross-sectional study was conducted. Brick-tea water was tested by the standard of GB1996-2005 (China). Urinary fluoride was tested by the standard of WS/T 89-2006 (China). Skeletal fluorosis was diagnosed by X-ray, the part we scheduled was forearm, shank, and pelvic, then diagnosed the skeletal fluorosis by the standard of WS/192-2008 (China). Gene polymorphism was tested by Sequenom MassARRAY system. RESULT: The prevalence rate in different ethnical participants was different: Tibetan individuals had the highest prevalence rate of skeletal fluorosis. There were significant differences in genotype frequencies of GSTP1 Rs1695 among different ethnical participants (p<0.001): Tibetan, Mongolian and Han subjects with homozygous wild type (GSTP1-AA) genotype were numerically higher than Kazakh and Russian subjects (p<0.001). Compared to Tibetan participants who carried homozygous A allele of GSTP1 Rs1695, Tibetan participants who carried G allele had a significantly decreased risk of skeletal fluorosis (OR = 0.558 [95% CI, 0.326-0.955]). For Kazakh participants, a decreased risk of skeletal fluorosis among carriers of the G allele was limited to non high-loaded fluoride status (OR = 0. 166 [95% CI, 0.035-0.780] vs. OR = 1.478 [95% CI, 0.866-2.552] in participants with high-loaded fluoride status). Neither SNP-IF nor SNP-age for GSTP1 Rs1695 was observed. CONCLUSION: The prevalence rate of the brick tea type fluorosis might have ethnic difference. For Tibetan individuals, who had the highest prevalence rate, G allele of GSTP1 Rs1695 might be a protective factor for brick tea type skeletal fluorosis.\",\n \"corpus_id\": 25352523,\n \"score\": 1\n },\n {\n \"doc_id\": \"26345972\",\n \"title\": \"Association of GSTP1 and XRCC1 gene polymorphisms with clinical outcomes of patients with advanced non-small cell lung cancer.\",\n \"abstract\": \"We investigated the association between the polymorphisms GSTP1 rs1695 and XRCC1 rs1799782 and rs25487 and the clinical outcome of patients with non-small cell lung cancer (NSCLC) receiving cisplatin-based chemotherapy. Genotyping of GSTP1 rs1695 and XRCC1 rs1799782, and rs25487 was conducted by polymerase chain reaction-restriction fragment length polymorphism analysis. By conditional logistic regression analysis, patients carrying the GG genotype of GSTP1 rs1695 and the AA genotype of XRCC1 rs25487 were found to be more highly associated with response to chemotherapy than were those carrying the AA genotype; the ORs (95%CIs) were 0.13 (0.04-0.37) and 3.37 (1.44-8.53), respectively. Presence of the GG genotype of GSTP1 rs1695 and the GA and AA genotypes of XRCC1 rs25487 was associated with overall survival of NSCLC, and the hazards ratios (95%CI) were 4.35 (1.40-17.92), 0.53 (0.31-0.91), and 0.39 (0.18-0.83), respectively. The results of our study suggest that the GSTP1 rs1695 and XRCC1 rs25487 polymorphisms might affect the clinical outcome of patients with advanced NSCLC receiving cisplatin-based chemotherapy.\",\n \"corpus_id\": 33404211,\n \"score\": 1\n },\n {\n \"doc_id\": \"26823821\",\n \"title\": \"Role of GSTP1 Ile105Val and XRCC1 Arg194Trp, Arg280His and Arg399Gln gene polymorphisms in the clinical outcome of advanced non-small cell lung cancer.\",\n \"abstract\": \"We conducted a study to investigate the association between the clinical outcome and GSTP1 Ile105Val and XRCC1 Arg194Trp, Arg280His and Arg399Gln gene polymorphisms in advanced NSCLC patients with cisplatin-based chemotherapy. Between January 2010 and December 2012, a total of 206 patients with advanced NSCLC were histopathologically confirmed were included into analysis. By logistic regression analysis, individuals carrying the AG and GG genotypes of GSTP1 Ile105Val were associated with better response to chemotherapy when compared with the AA genotype, and the adjusted Ors (95% CI) were 2.06 (1.10-3.86) and 4.89 (1.52-18.33), respectively. The TT genotype of XRCC1 Arg194Trp was correlated with better response to chemotherapy compared to the CC genotype, and the adjusted OR (95% CI) was 3.23 (1.20-9.30). By Cox Hazard Proportional Model, the GG genotype of GSTP1 Ile105Val and the TT genotype of XRCC1 Arg194Trp were found to be associated with lower risk of death from all causes when compared with the wide-type genotype, and the adjusted HRs (95% CI) were 0.05 (0.01-0.18) and 0.20 (0.07-0.62), respectively. Moreover, individuals carrying both the G/A+G/G genotype of GSTP1 Ile105Val and the G/A+A/A of XRCC1 Arg194Trp were associated with heavy greater CR+PR response to chemotherapy (OR=2.98, 95% CI=1.39-6.42), and also correlated with longer overall survival of advanced NSCLC (HR=0.19, 95% CI=0.05-0.61). In conclusion, we found that the GSTP1 Ile105Val and XRCC1 Arg194Trp were associated with better response to chemotherapy and longer survival of advanced NSCLC, compared to the wide-type genotype.\",\n \"corpus_id\": 24341152,\n \"score\": 1\n },\n {\n \"doc_id\": \"27299594\",\n \"title\": \"GSTM1 and GSTP1 Genetic Polymorphisms and Their Associations With Acute Lymphoblastic Leukemia Susceptibility in a Jordanian Population.\",\n \"abstract\": \"The genetic variations between different individuals in the xenobiotic detoxifying enzyme activity were shown to change susceptibility to acute lymphoblastic leukemia (ALL). The current study aimed to assess the association of GSTM1 and GSTP1 genetic polymorphisms with the susceptibility of ALL. This case-control study (N=264) involved 88 Jordanian ALL children and 176 healthy controls from an ethnically homogenous Jordanian children population. The polymerase chain reaction assay was used to genotype GSTM1 (null/present) and the polymerase chain reaction-restriction fragment length polymorphism technique was also applied to detect the genetic polymorphisms of GSTP1 (Ile105Val) at the rs1695 position. The biallelic analysis revealed that there was no association between GSTM1 double-null genotype and ALL (P=0.57). However, there was a strong association between GSTP1 (Ile105Val) polymorphism genotypes and alleles within GSTP1 gene and ALL (P=0.00049 and 0.000044, respectively). A combination between GSTM1 double-null genotype and rs1695 also showed an association with ALL (P=0.042). This study showed that the rs1695 single nucleotide polymorphism within the GSTP1 gene is strongly implicated in ALL among Jordanian children with ALL. These results indicate that genetic variants of GSTP1 gene influence the risk of developing ALL in the Jordanian children of Arab ancestry.\",\n \"corpus_id\": 42283380,\n \"score\": 1\n },\n {\n \"doc_id\": \"27323109\",\n \"title\": \"GSTP1 Ile105Val and XRCC1 Arg399Gln gene polymorphisms contribute to the clinical outcome of patients with advanced non-small cell lung cancer.\",\n \"abstract\": \"Glutathione S-transferase P1 (GSTP1) and X-ray repair cross-complementing group 1 (XRCC1) genetic variations may in-fluence the efficacy of chemotherapy in various cancers. We investi-gated the possible roles of GSTP1 Ile105Val and XRCC1 Arg194Trp, and Arg399Gln gene polymorphisms in the prognosis of advanced non-small cell lung carcinoma (NSCLC) patients with cisplatin-based chemotherapy. Between January 2010 and December 2012, this study consecutively recruited 141 patients with advanced NSCLC from the First People's Hospital of Yunnan Province. Logistic regression analy-sis showed that individuals carrying the GG genotype were associated with a better response to chemotherapy than those with the wide-type genotype, with an adjusted odds ratio (95% confidence interval, CI) of 4.07 (1.06-25.06). Moreover, we observed that the AA genotype of XRCC1 Arg399Gln was correlated with a greater complete response + partial response to chemotherapy than that with the GG genotype (odds ratio = 2.71, 95%CI = 1.13-10.08). Based on the Cox hazard proportional model, the GG genotype of GSTP1 Ile105Val was found to be associated with a lower risk of death from all causes as compared to that with the AA genotype (hazard ratio = 0.07, 95%CI = 0.01-0.34). In summary, we suggest that GSTP1 Ile105Val and XRCC1 Arg399Gln polymorphisms could influence the response to chemotherapy and sur-vival of advanced NSCLC.\",\n \"corpus_id\": 26046816,\n \"score\": 1\n },\n {\n \"doc_id\": \"27349566\",\n \"title\": \"NQO1 rs1800566 polymorph is more prone to NOx induced lung injury: Endorsing deleterious functionality through informatics approach.\",\n \"abstract\": \"Gene-environment interaction studies have led to the identification of genetic mutations in individuals with increased susceptibility to pollution related diseases. rs1800566 polymorphism of NQO1, leading to P187S missense mutation in the transcribed antioxidant protein, causes individuals carrying this mutation more prone to NO2 induced lung inflammatory injury. Here, we report significant structural and functional changes incurred by NQO1 antioxidant protein as a result of alteration in its nucleotide (C609T) and hence, protein sequence. Detailed insights were obtained regarding the prospective impact of this mutation on the structural stability of normal and mutated NQO1 protein, using a myriad of bioinformatic tools and webservers. Structure analysis showed no significant change at secondary level. A change in the native backbone conformation was observed due to formation of a hydrogen bond. Hydrophobicity and phosphorylation properties, decisive factors for functioning and stability of NQO1 were considerably influenced by P187S mutation. Computational study of the properties of a polymorph linked with NOx induced lung injury sheds light on the molecular basis of this polymorphism and endorses previous findings, reported by the scientists working in this domain.\",\n \"corpus_id\": 205026478,\n \"score\": 1\n },\n {\n \"doc_id\": \"27561723\",\n \"title\": \"Asthma and rhinitis have different genetic profiles for IL13, IL17A and GSTP1 polymorphisms.\",\n \"abstract\": \"BACKGROUND: Asthma and rhinitis have a complex etiology, depending on multiple genetic and environmental risk factors. An increasing number of susceptibility genes are currently being identified, but the majority of reported associations have not been consistently replicated across populations of different genetic backgrounds. PURPOSE: To evaluate whether polymorphisms of IL4R (rs1805015), IL13 (rs20541), IL17A (rs2275913) and GSTP1 (rs1695) genes are associated with rhinitis and/or asthma in adults of Portuguese ancestry. METHODS: 192 unrelated healthy individuals and 232 patients, 83 with rhinitis and 149 with asthma, were studied. All polymorphisms were detected by real time polymerase chain reaction (PCR) using TaqMan assays. RESULTS: Comparing to controls, significant association with asthma was observed for GSTP1 rs1695 AA genotype (odds ratio (OR) - 1.96; 95% CI - 1.18 to 3.25; p=0.010). The association sustains for allergic asthma (OR - 2.17; 95% CI - 1.23 to 3.80; p=0.007). IL13 rs20541 GG genotype was associated with less susceptibility to asthma (OR - 0.55, 95% CI - 0.33 to 0.94, p=0.028). Among patients, IL17A rs2275913 AA genotype was less associated with asthma than with rhinitis (OR - 0.20; 95% CI of 0.07 to 0.56; p=0.002). A similar association was found for IL13 rs20541 GG genotype (OR - 0.48; 95% CI of 0.25 to 0.93; p=0.031). There were no significant differences in the distribution of allelic and genotypic frequencies between patients and controls for the IL4R polymorphism' analyzed. CONCLUSION: These results support the existence of a significant association between GSTP1 rs1695 and IL13 rs20541 SNPs, with susceptibility to asthma, in the population studied. Different genotype profiles of IL17A and IL13 genes seem to influence the clinical pattern of disease expression mainly confined to the upper airways, as rhinitis, or including the lower airways, as asthma.\",\n \"corpus_id\": 29603910,\n \"score\": 1\n },\n {\n \"doc_id\": \"28062686\",\n \"title\": \"GSTP1 c.313A>G polymorphism in Russian and Polish athletes.\",\n \"abstract\": \"The GSTP1 gene encodes glutathione S-transferase P1, which is a member of the glutathione S-transferases (GSTs), a family of enzymes playing an important role in detoxification and in the antioxidant defense system. There is some evidence indicating that GSTP1 c.313A>G polymorphism may be beneficial for exercise performance. Therefore, we decided to verify the association between the frequency of GSTP1 c.313A>G variants, physical performance, and athletes' status in two cohorts: in a group of Russian athletes (n = 507) and in an independent population of Polish athletes (n = 510) in a replication study. The initial association study conducted with the Russian athletes revealed that the frequency of the minor G allele was significantly higher in all athletes than in controls; that was confirmed in the replication study of Polish athletes. In the combined cohort, the differences between athletes (n = 1017) and controls (n = 1246) were even more pronounced (32.7 vs 25.0%, P < 0.0001). Our findings emphasize that the G allele of the GSTP1 gene c.313A>G single nucleotide polymorphism is associated with improved endurance performance. These observations could support the hypothesis that the GSTP1 G allele may improve exercise performance by better elimination of exercise-induced ROS.\",\n \"corpus_id\": 207620914,\n \"score\": 1\n },\n {\n \"doc_id\": \"28739440\",\n \"title\": \"Genetic Variation in GSTP1, Lung Function, Risk of Lung Cancer, and Mortality.\",\n \"abstract\": \"INTRODUCTION: Glutathione S-transferase pi 1 metabolizes carcinogens from tobacco smoke in the lung. We tested whether genetically altered glutathione S-transferase pi 1 activity affects lung function and risk for tobacco-related cancer and mortality in the general population. METHODS: We genotyped 66,069 individuals from the white general population for two common functional variants in the glutathione S-transferase pi 1 gene (GSTP1)-amino acid isoleucine 105 changed to a valine (Ile105Val) and amino acid alanine 114 changed to a valine (Ala114Val)-and recorded lung function, lung cancer, tobacco-related cancer, and death as outcomes. RESULTS: Lung function was increased stepwise with the Ile105Val genotype overall (p < 0.01) and among smokers separately (p < 0.01). Adjusted hazard ratios for lung cancer, tobacco-related cancer, and death were reduced stepwise with the Ile105Val genotype (p < 0.02): Ile105Val homozygotes and heterozygotes versus noncarriers had hazard ratios for lung cancer of 0.64 (0.47-0.89) and 0.93 (0.78-1.11), for tobacco-related cancer of 0.74 (0.60-0.92) and 0.92 (0.81-1.04), and hazard ratios for death of 0.87 (0.80-0.95) and 0.94 (0.89-0.99), respectively. Population prevented fractions of lung cancer, tobacco-related cancer, and death due to Ile105Val homozygosity were 4%, 3% and 2%, respectively. The Ala114Val genotype was associated with reduced mortality (p < 0.01) but not with lung function, lung cancer, or tobacco-related cancer. CONCLUSION: GSTP1 Ile105Val was associated with increased lung function, reduced risk for lung cancer and tobacco-related cancer, and reduced all-cause mortality in the general population.\",\n \"corpus_id\": 43062062,\n \"score\": 1\n },\n {\n \"doc_id\": \"28770488\",\n \"title\": \"Identification and characterization of functional single nucleotide polymorphisms (SNPs) in Axin 1 gene: a molecular dynamics approach.\",\n \"abstract\": \"Wnt signaling pathway has been reported to play crucial role in intestinal crypt formation and deregulation of this pathway is responsible for colorectal cancer initiation and progression. Axin 1, a scaffold protein, play pivotal role in the regulation of Wnt/β-catenin signaling pathway and has been found to be mutated in several cancers; primarily in colon cancer. Considering its crucial role, a structural and functional analysis of missense mutations in Axin 1 gene was performed in this study. Initially, one hundred non-synonymous single nucleotide polymorphisms in the coding regions of Axin 1 gene were selected for in silico analysis. Six variants (G820S, G856S, E830K, L811V, L847V, and R767C) were predicted to be deleterious by combinatorial prediction. Further investigation of structural attributes confirmed two highly deleterious single nucleotide polymorphisms (G820S and G856S). Molecular dynamics simulation demonstrated variation in different structural attributes between native and two highly deleterious Axin 1 mutant models. Finally, docking analysis showed variation in binding affinity of mutant Axin 1 proteins with two destruction complex members, GSK3β and adenomatous polyposis. The results collectively showed the deleterious effect of the above predicted single nucleotide polymorphisms on the Axin 1 protein structure and could prove to be an adjunct in the disease genotype-phenotype correlation studies.\",\n \"corpus_id\": 3995844,\n \"score\": 1\n },\n {\n \"doc_id\": \"29046813\",\n \"title\": \"Single nucleotide polymorphisms and microsatellites in the canine glutathione S-transferase pi 1 (GSTP1) gene promoter.\",\n \"abstract\": \"BACKGROUND: Genetic polymorphisms within the glutathione S-transferase P1 (GSTP1) gene affect the elimination of toxic xenobiotics by the GSTP1 enzyme. In dogs, exposure to environmental chemicals that may be GSTP1 substrates is associated with cancer. The objectives of this study were to investigate the genetic variability in the GSTP1 promoter in a diverse population of 278 purebred dogs, compare the incidence of any variants found between breeds, and predict their effects on gene expression. To provide information on ancestral alleles, a number of wolves, coyotes, and foxes were also sequenced. RESULTS: Fifteen single nucleotide polymorphisms (SNPs) and two microsatellites were discovered. Three of these loci were only polymorphic in dogs while three other SNPs were unique to wolves and coyotes. The major allele at c.-46 is T in dogs but is C in the wild canids. The c.-185 delT variant was unique to dogs. The microsatellite located in the 5' untranslated region (5'UTR) was a highly polymorphic GCC tandem repeat, consisting of simple and compound alleles that varied in size from 10 to 22-repeat units. The most common alleles consisted of 11, 16, and 17-repeats. The 11-repeat allele was found in 10% of dogs but not in the other canids. Unequal recombination and replication slippage between similar and distinct alleles may be the mechanism for the multiple microsatellites observed. Twenty-eight haplotypes were constructed in the dog, and an additional 8 were observed in wolves and coyotes. While the most common haplotype acrossbreeds was the wild-type *1A(17), other prevalent haplotypes included *3A(11) in Greyhounds, *6A(16) in Labrador Retrievers, *9A(16) in Golden Retrievers, and *8A(19) in Standard Poodles. Boxers and Siberian Huskies exhibited minimal haplotypic diversity. Compared to the simple 16*1 allele, the compound 16*2 allele (found in 12% of dogs) may interfere with transcription factor binding and/or the stability of the GSTP1 transcript. CONCLUSIONS: Dogs and other canids exhibit extensive variation in the GSTP1 promoter. Genetic polymorphisms within distinct haplotypes prevalent in certain breeds can affect GSTP1 expression and carcinogen detoxification, and thus may be useful as genetic markers for cancer in dogs.\",\n \"corpus_id\": 19386679,\n \"score\": 1\n },\n {\n \"doc_id\": \"29476931\",\n \"title\": \"Vitamin D receptor (VDR) non-synonymous single nucleotide polymorphisms (nsSNPs) affect the calcitriol drug response - A theoretical insight.\",\n \"abstract\": \"Pharmacogenetics and pharmacogenomics have become presumptive with advancements in next-generation sequencing technology. In complex diseases, distinguishing the feasibility of pathogenic and neutral disease-causing variants is a time consuming and expensive process. Recent drug research and development processes mainly rely on the relationship between the genotype and phenotype through Single nucleotide polymorphisms (SNPs). The SNPs play an indispensable role in elucidating the individual's vulnerability to disease and drug response. The understanding of the interplay between these leads to the establishment of personalized medicine. In order to address this issue, we developed a computational pipeline of vitamin D receptor (VDR) for SNP centered study by application of elegant molecular docking and molecular dynamics simulation approaches. In a few SNPs the volume of the binding cavities has increased in mutant structures when compared to the wild type, indicating a weakening in interaction (699.1 Å3 in wild type Vs. 738.8 in Leu230Val, 820.7 Å3 in Arg247Leu). This also differently reflected in the H-bond interactions and binding free energies -169.93 kcal/mol (wild type) Vs -156.43 kcal/mol (R154W), -105.49 kcal/mol (R274L) in Leu230Val and Arg247Leu respectively. Although we could not find noteworthy changes in the binding free energies and binding pocket in the remaining mutations, the H-bond interactions made these SNPs deleterious. Thus, we further analyzed the H-bond interactions and distances using molecular dynamics (MD) simulation studies.\",\n \"corpus_id\": 3523623,\n \"score\": 1\n },\n {\n \"doc_id\": \"18950218\",\n \"title\": \"Multiple protonation equilibria in electrostatics of protein-protein binding.\",\n \"abstract\": \"All proteins contain groups capable of exchanging protons with their environment. We present here an approach, based on a rigorous thermodynamic cycle and the partition functions for energy levels characterizing protonation states of the associating proteins and their complex, to compute the electrostatic pH-dependent contribution to the free energy of protein-protein binding. The computed electrostatic binding free energies include the pH of the solution as the variable of state, mutual \\\"polarization\\\" of associating proteins reflected as changes in the distribution of their protonation states upon binding and fluctuations between available protonation states. The only fixed property of both proteins is the conformation; the structure of the monomers is kept in the same conformation as they have in the complex structure. As a reference, we use the electrostatic binding free energies obtained from the traditional Poisson-Boltzmann model, computed for a single macromolecular conformation fixed in a given protonation state, appropriate for given solution conditions. The new approach was tested for 12 protein-protein complexes. It is shown that explicit inclusion of protonation degrees of freedom might lead to a substantially different estimation of the electrostatic contribution to the binding free energy than that based on the traditional Poisson-Boltzmann model. This has important implications for the balancing of different contributions to the energetics of protein-protein binding and other related problems, for example, the choice of protein models for Brownian dynamics simulations of their association. Our procedure can be generalized to include conformational degrees of freedom by combining it with molecular dynamics simulations at constant pH. Unfortunately, in practice, a prohibitive factor is an enormous requirement for computer time and power. However, there may be some hope for solving this problem by combining existing constant pH molecular dynamics algorithms with so-called accelerated molecular dynamics algorithms.\",\n \"corpus_id\": 25347971,\n \"score\": 0\n },\n {\n \"doc_id\": \"20526737\",\n \"title\": \"Glutathione S-transferase P1 Ile105Val polymorphism and breast cancer risk: a meta-analysis involving 34,658 subjects.\",\n \"abstract\": \"Glutathione S-transferase P1 (GSTP1) is involved in a wide range of detoxifying reactions. Any alteration in the structure, function, or expression of GSTP1 gene may alter the ability of a cell to inactivate carcinogens or mutagens, and thus modify an individual's risk to cancer. Previous epidemiological studies on the potential association between GSTP1 Ile105Val polymorphism and breast cancer risk have produced inconsistent results. In order to drive a more precise estimation of this association, we performed a meta-analysis of 30 published case-control studies including 15,901 cases and 18,757 controls. Crude odds ratios (ORs) with 95% confidence intervals (CIs) were used to assess the strength of the association. The results of this meta-analysis showed that GSTP1 Ile105Val polymorphism was not associated with breast cancer susceptibility in overall population. However, in subgroup analysis by ethnicity, we found a significant association among Asian population (for Val/Val vs. Ile/Ile: OR 1.27, 95% CI 1.02-1.83; for the recessive model Val/Val vs. Ile/Ile + Ile/Val: OR 1.42, 95% CI 1.20-1.69). When stratified by study design, significantly elevated susceptibility to breast cancer was found among hospital-based studies (for Val/Val vs. Ile/Ile: OR 1.38, 95% CI 1.16-1.63; for recessive model Val/Val vs. Ile/Val + Ile/Ile: OR 1.31, 95% CI 1.12-1.55; for dominant model: Val/Val + Ile/Val vs. Ile/Ile: OR 1.10, 95% CI 1.02-1.19). In conclusion, our meta-analysis suggests that GSTP1 Ile105Val polymorphism may increase susceptibility to breast cancer in Asian population.\",\n \"corpus_id\": 22096713,\n \"score\": 0\n },\n {\n \"doc_id\": \"20964430\",\n \"title\": \"Vibrational Stark effect spectroscopy at the interface of Ras and Rap1A bound to the Ras binding domain of RalGDS reveals an electrostatic mechanism for protein-protein interaction.\",\n \"abstract\": \"Electrostatic fields at the interface of the Ras binding domain of the protein Ral guanine nucleotide dissociation stimulator (RalGDS) with the structurally analogous GTPases Ras and Rap1A were measured with vibrational Stark effect (VSE) spectroscopy. Eleven residues on the surface of RalGDS that participate in this protein-protein interaction were systematically mutated to cysteine and subsequently converted to cyanocysteine in order to introduce a nitrile VSE probe in the form of the thiocyanate (SCN) functional group. The measured SCN absorption energy on the monomeric protein was compared with solvent-accessible surface area (SASA) calculations and solutions to the Poisson-Boltzmann equation using Boltzmann-weighted structural snapshots from molecular dynamics simulations. We found a weak negative correlation between SASA and measured absorption energy, indicating that water exposure of protein surface amino acids can be estimated from experimental measurement of the magnitude of the thiocyanate absorption energy. We found no correlation between calculated field and measured absorption energy. These results highlight the complex structural and electrostatic nature of the protein-water interface. The SCN-labeled RalGDS was incubated with either wild-type Ras or wild-type Rap1A, and the formation of the docked complex was confirmed by measurement of the dissociation constant of the interaction. The change in absorption energy of the thiocyanate functional group due to complex formation was related to the change in electrostatic field experienced by the nitrile functional group when the protein-protein interface forms. At some locations, the nitrile experiences the same shift in field when bound to Ras and Rap1A, but at others, the change in field is dramatically different. These differences identify residues on the surface of RalGDS that direct the specificity of RalGDS binding to its in vivo binding partner, Rap1A, through an electrostatic mechanism.\",\n \"corpus_id\": 5333542,\n \"score\": 0\n },\n {\n \"doc_id\": \"21669193\",\n \"title\": \"GSTP1 mRNA expression in human circulating blood leukocytes is associated with GSTP1 genetic polymorphism.\",\n \"abstract\": \"OBJECTIVES: We explored association between GSTP1 Ile(105)Val (rs1695) polymorphism and GSTP1 mRNA expression in circulating blood leukocytes. DESIGN AND METHODS: GSTP1 transcripts level and polymorphism were determined by Real-Time PCR in 51 bladder cancer and 90 healthy men. RESULTS: Individuals with at least one GSTP1 Val(105) variant allele possessed higher GSTP1 mRNA level in blood leukocytes compared to GSTP1 Ile(105)Ile carriers. CONCLUSIONS: GSTP1 Ile(105)Val gene polymorphism influences its expression in blood, regardless of cancer disease.\",\n \"corpus_id\": 20177747,\n \"score\": 0\n },\n {\n \"doc_id\": \"24786234\",\n \"title\": \"HapMap-based study on the association between MPO and GSTP1 gene polymorphisms and lung cancer susceptibility in Chinese Han population.\",\n \"abstract\": \"AIM: Myeloperoxidase (MPO) and glutathione S-transferase pi 1 (GSTP1) are important carcinogen-metabolizing enzymes. The aim of this study was to investigate the association between the common polymorphisms of MPO and GSTP1 genes and lung cancer risk in Chinese Han population. METHODS: A total of 266 subjects with lung cancer and 307 controls without personal history of the disease were recruited in this case control study. The tagSNPs approach was used to assess the common polymorphisms of MOP and GSTP1 genes and lung cancer risk according to the disequilibrium information from the HapMap project. The tagSNP rs7208693 was selected as the polymorphism site for MPO, while the haplotype-tagging SNPs rs1695, rs4891, rs762803 and rs749174 were selected as the polymorphism sites for GSTP1. The gene polymorphisms were confirmed using real-time PCR, cloning and sequencing. RESULTS: The four GSTP1 haplotype-tagging SNPs rs1695, rs4891, rs762803 and rs749174, but not the MPO tagSNP rs7208693, exhibited an association with lung cancer susceptibility in smokers in the overall population and in the studied subgroups. When Phase 2 software was used to reconstruct the haplotype for GSTP1, the haplotype CACA (rs749174+rs1695 + rs762803+rs4891) exhibited an increased risk of lung cancer among smokers (adjust odds ratio 1.53; 95%CI 1.04-2.25, P=0.033). Furthermore, diplotype analyses demonstrated that the significant association between the risk haplotype and lung cancer. The risk haplotypes co-segregated with one or more biologically functional polymorphisms and corresponded to a recessive inheritance model. CONCLUSION: The common polymorphisms of the GSTP1 gene may be the candidates for SNP markers for lung cancer susceptibility in Chinese Han population.\",\n \"corpus_id\": 12842717,\n \"score\": 0\n },\n {\n \"doc_id\": \"26621436\",\n \"title\": \"Origins of Resistance Conferred by the R292K Neuraminidase Mutation via Molecular Dynamics and Free Energy Calculations.\",\n \"abstract\": \"Point mutations in the influenza virus enzyme neuraminidase (NA) have been reported that lead to dramatic loss of activity for known NA inhibitors including the FDA approved sialic acid mimics zanamivir and oseltamivir. A more complete understanding of the molecular basis for such resistance is a critical component toward development of improved next-generation drugs. In this study, we have used explicit solvent all-atom molecular dynamics simulations, free energy calculations (MM-GBSA), and residue-based decomposition to model binding of four ligands with NA from influenza virus subtype N9. The goal is to elucidate which structural and energetic properties change as a result of a mutation at position R292K. Computed binding free energies show strong correlation with experiment (r(2) = 0.76), and an examination of individual energy components reveal that changes in intermolecular Coulombic terms (ΔEcoul) best describe the variation in affinity with structure (r(2) = 0.93). H-bond populations also parallel the experimental ordering (r = -0.96, r(2) = 0.86) reinforcing the view that electrostatics modulate binding in this system. Notably, in every case, the simulation results correctly predict that loss of binding occurs as a result of the R292K mutation. Per-residue binding footprints reveal that changes in ΔΔEcoul for R292K-wildtype at position 292 parallel the change in experimental fold resistance energies (ΔΔGR292K-WT) with S03 < S00 < S02 < S01. The footprints also reveal that the most potent ligands have (1) less reliance on R292 for intrinsic affinity, (2) enhanced binding via residues E119, E227, and E277, and (3) flatter ΔEcoul and ΔH-bond profiles. Improved resistance for S03 appears to be a function of the ligand's larger guanidinium group which leads to an increased affinity for wildtype NA while at the same time a reduction in favorable interactions localized to R292. Overall, the computational results significantly enhance experimental observations through quantification of specific interactions which govern molecular recognition along the N9-ligand binding interface.\",\n \"corpus_id\": 16772843,\n \"score\": 0\n },\n {\n \"doc_id\": \"29434449\",\n \"title\": \"Impact of SNP-SNP interactions of DNA repair gene ERCC5 and metabolic gene GSTP1 on gastric cancer/atrophic gastritis risk in a Chinese population.\",\n \"abstract\": \"AIM: To investigate the interactions of the DNA repair gene excision repair cross complementing group 5 (ERCC5) and the metabolic gene glutathione S-transferase pi 1 (GSTP1) and their effects on atrophic gastritis (AG) and gastric cancer (GC) risk. METHODS: Seven ERCC5 single nucleotide polymorphisms (SNPs) (rs1047768, rs2094258, rs2228959, rs4150291, rs4150383, rs751402, and rs873601) and GSTP1 SNP rs1695 were detected using the Sequenom MassARRAY platform in 450 GC patients, 634 AG cases, and 621 healthy control subjects in a Chinese population. RESULTS: Two pairwise combinations (ERCC5 rs2094258 and rs873601 with GSTP1 rs1695) influenced AG risk (Pinteraction = 0.008 and 0.043, respectively), and the ERCC5 rs2094258-GSTP1 rs1695 SNP pair demonstrated an antagonistic effect, while ERCC5 rs873601-GSTP1 rs1695 showed a synergistic effect on AG risk OR = 0.51 and 1.79, respectively). No pairwise combinations were observed in relation to GC risk. There were no cumulative effects among the pairwise interactions (ERCC5 rs2094258 and rs873601 with GSTP1 rs1695) on AG susceptibility (Ptrend > 0.05). When the modification effect of Helicobacter pylori (H. pylori) infection was evaluated, the cumulative effect of one of the aforementioned pairwise interactions (ERCC5 rs873601-GSTP1 rs1695) was associated with an increased AG risk in the case of negative H. pylori status (Ptrend = 0.043). CONCLUSION: There is a multifarious interaction between the DNA repair gene ERCC5 SNPs (rs2094258 and rs873601) and the metabolic gene GSTP1 rs1695, which may form the basis for various inter-individual susceptibilities to AG.\",\n \"corpus_id\": 24058752,\n \"score\": 0\n }\n]","isConversational":false}}},{"rowIdx":97,"cells":{"query":{"kind":"string","value":"{\n \"doc_id\": \"26445296\",\n \"title\": \"Survey of compound microsatellites in multiple Lactobacillus genomes.\",\n \"abstract\": \"Distinct simple sequence repeats with 2 or more individual microsatellites joined together or lying adjacent to each other are identified as compound microsatellites. Investigation of such composite microsatellites in the genomes of genus Lactobacillus was the aim of this study. In silico inspection of microsatellite clustering in genomes of 14 Lactobacillus species revealed a wealth of compound microsatellites. All of the mined compound microsatellites were imperfect, were composed of variant motifs, and increased in all genomes, with maximum distance (dMAX) increments of 10 to 50. The majority of these repeats were present in the coding regions. A correlation of microsatellite to compound microsatellite density was detected. The difference established in compound microsatellite division among eukaryotes, Escherichia coli, and lactobacilli is suggestive of diverse genomic features and elementary distinction between creation and fixation methods of compound microsatellites among these organisms.\",\n \"corpus_id\": 9813476\n}"},"candidates":{"kind":"list like","value":[{"doc_id":"17947328","title":"UgMicroSatdb: database for mining microsatellites from unigenes.","abstract":"Microsatellites, also known as simple sequence repeats (SSRs) or short tandem repeats (STRs), have extensively been exploited as molecular markers for diverse applications. Recently, their role in gene regulation and genome evolution has also been discussed widely. We have developed UgMicroSatdb (Unigene MicroSatellite database), a web-based relational database of microsatellites present in unigene sequences covering 80 genomes. UgMicroSatdb allows microsatellite search using multiple parameters like microsatellite type (simple perfect, compound perfect and imperfect), repeat unit length (mono- to hexa-nucleotide), repeat number, microsatellite length and repeat sequence class. Microsatellites can also be retrieved by specifying EST, cDNA, CDS identity or by using Gene Index, GenBank, UniGene IDs. The database also provides information about trinucleotide repeats encoding various amino acids. Such codon repeats can be searched by specifying characteristics of coded amino acids like charge (basic, acidic or neutral), polarity (polar or non-polar), and their hydrophobic or hydrophilic nature. The nucleotide sequences of the target UniGenes are also provided to facilitate primer designing for PCR amplification of the desired microsatellite. UgMicroSatdb is available at http://ipu.ac.in/usbt/UgMicroSatdb.htm.","corpus_id":5530971,"score":2},{"doc_id":"18191346","title":"Distribution and evolution of short tandem repeats in closely related bacterial genomes.","abstract":"Simultaneous identification and comparison of perfect and imperfect microsatellites within a genome is a valuable tool both to overcome the lack of a consensus definition of SSRs and to assess repeat history. Detailed analysis of the overall distribution of perfect and imperfect microsatellites in closely related bacterial taxa is expected to give new insight into the evolution of prokaryotic genomes. We have performed a genome-wide analysis of microsatellite distribution in four Escherichia coli and seven Chlamydial strains. Chlamydial strains generally have a higher density of SSRs and show greater intra-group differences of SSR distribution patterns than E. coli genomes. In most investigated genomes the distribution of the total lengths of matching perfect and imperfect trinucleotide repeats are highly similar, with the notable exception of C. muridarum. Closely related strains show more similar repeat distribution patterns than strains separated by a longer divergence time. The discrepancy between the preferred classes of perfect and imperfect repeats in C. muridarum implies accelerated evolution of SSRs in this particular strain. Our results suggest that microsatellites, although considerably less abundant than in eukaryotic genomes, may nevertheless play an important role in the evolution of prokaryotic genomes and several gene families.","corpus_id":25919969,"score":2},{"doc_id":"19091106","title":"Survey of microsatellite clustering in eight fully sequenced species sheds light on the origin of compound microsatellites.","abstract":"BACKGROUND: Compound microsatellites are a special variation of microsatellites in which two or more individual microsatellites are found directly adjacent to each other. Until now, such composite microsatellites have not been investigated in a comprehensive manner. RESULTS: Our in silico survey of microsatellite clustering in genomes of Homo sapiens, Maccaca mulatta, Mus musculus, Rattus norvegicus, Ornithorhynchus anatinus, Gallus gallus, Danio rerio and Drosophila melanogaster revealed an unexpected high abundance of compound microsatellites. About 4 - 25% of all microsatellites could be categorized as compound microsatellites. Compound microsatellites are approximately 15 times more frequent than expected under the assumption of a random distribution of microsatellites. Interestingly, microsatellites do not only tend to cluster but the adjacent repeat types of compound microsatellites have very similar motifs: in most cases (>90%) these motifs differ only by a single mutation (base substitution or indel). We propose that the majority of the compound microsatellites originates by duplication of imperfections in a microsatellite tract. This process occurs mostly at the end of a microsatellite, leading to a new repeat type and a potential microsatellite repeat track. CONCLUSION: Our findings suggest a more dynamic picture of microsatellite evolution than previously believed. Imperfections within microsatellites might not only cause the \"death\" of microsatellites they might also result in their \"birth\".","corpus_id":10330376,"score":2},{"doc_id":"21382371","title":"Compound microsatellites in complete Escherichia coli genomes.","abstract":"Compound microsatellites consisting of two or more repeats in close proximity have been found in eukaryotic genomes. So far such compound microsatellites have not been investigated in any prokaryotic genomes. We have therefore examined compound microsatellites in 22 complete genomes of Escherichia coli, which is one of the ideal model organisms to analyze the nature and evolution of prokaryotic compound microsatellites. Our results indicated that about 1.75-2.85% of all microsatellites could be accounted as compound microsatellites with very low complexity, and most compound microsatellites were composed of very different motifs. Compound microsatellites were significantly overrepresented in all surveyed genomes. These results were dramatically different from those in eukaryotes. We discussed the possible reasons for the observed divergence.","corpus_id":30630965,"score":2},{"doc_id":"21723421","title":"Microsatellite is an important component of complete hepatitis C virus genomes.","abstract":"Microsatellites are common and play diverse roles in eukaryotic and prokaryotic genomes. However, to our knowledge, microsatellite distribution remains largely enigmatic in viruses yet is crucial for understanding instability of viral genomes. We have therefore, examined microsatellite distribution in 54 complete genomes of Hepatitis C virus (HCV) from six genotypes, showing microsatellites were an important component of HCV genomes. Our results showed, in all analyzed HCV genomes, genome size and GC content had a weak influence on number, relative abundance and relative density of microsatellites, respectively. For each HCV genome, mono-, di- and trinucleotide repeats were very predominant, whereas other types of repeats rarely occurred. Our results revealed that the occurrence of microsatellites was significantly less than higher prokaryotes and eukaryotes and that all identified microsatellites were very short. The discovery of microsatellites in HCV genomes may become useful for population genetic, evolutionary analysis and strain (isolate) identification.","corpus_id":24505985,"score":2},{"doc_id":"21920415","title":"Microsatellites in different Potyvirus genomes: survey and analysis.","abstract":"Simple sequence repeats (SSRs) have been extensively used for various genetic and evolutionary studies in eukaryotic and prokaryotic organisms, while few relevant researches have been made in viruses. The Potyvirus is a fine system to study roles and evolution of SSRs in viruses. The densities, relative abundances, compositions and evolutionary inferences of SSRs in 45 different Potyvirus genomes have been analyzed in this study. Results showed that the densities and relative abundances of SSRs are similar in all those Potyvirus genomes. The number of SSRs decreases with an increase in the length of repeat unit. Dinucleotide repeats are the most abundant and followed by trinucleotide repeats, and the numbers of tetra-, penta- and hexanucleotide repeats are very small. Repeats of AC/CA, AG/GA and AAG/GAA predominate, whereas repeats of CG/GC, ATA and CAC are rare. The genome sizes of the Potyvirus species have little influence on the total number and relative abundance of SSRs. Our study suggested that the variety of SSRs may be related to the genome diversity of Potyvirus. Maybe Potyvirus and HIV genomes have the similar evolution mode and parallel evolution level.","corpus_id":27870850,"score":2},{"doc_id":"22659082","title":"Differential distribution of compound microsatellites in various Human Immunodeficiency Virus Type 1 complete genomes.","abstract":"Compound microsatellites consist of two or more individual microsatellites, and may originate from dynamic mutations or imperfection of microsatellites. Previous studies have found microsatellites were present in 81 completed Human Immunodeficiency Virus Type 1 (HIV-1) genomes, suggesting compound microsatellites may exist in viral genomes. However, up to now, compound microsatellites have not been analyzed in any viral genomes. We identified and characterized 238 compound microsatellites in 81 completed HIV-1 genomes. About 0-24.24% of all microsatellites could be categorized as compound microsatellites. Compound microsatellite distribution is very different in two aspects between diverse HIV-1 genomes. First, the number and motifs of compound microsatellites are variable between surveyed genomes. Second, the relative abundance and relative density of compound microsatellites exhibit very significant differences between these surveyed genomes, respectively. The relative abundance and relative density of compound microsatellites were weakly correlated with genome size and microsatellite density. We observed a more dynamic picture of compound microsatellites than previously reported in eukaryotes. This might be attributed to the lack of proofreading in HIV-1 genomes, as it has been demonstrated that the loss of polymerase proofreading activity can greatly enhance the mutation rate of microsatellites.","corpus_id":23283489,"score":2},{"doc_id":"22903752","title":"Differential distribution and occurrence of simple sequence repeats in diverse geminivirus genomes.","abstract":"Microsatellites are tandem repeat sequences with repeat unit of one to six base pairs. Although, microsatellites have been studied in eukaryotes as well as prokaryotes, information on their occurrence on virus genomes is limited. We examined microsatellite distribution in 263 complete geminivirus genomes. Results indicated microsatellites to be an important component of geminiviral genomes. For each geminiviral genome, mono- and dinucleotide repeats were found to be highly predominant. Occurrence of microsatellites within geminiviral genome is significantly lesser than organisms with higher genome sizes and their number decreased with an increase in the length of repeat unit. Repeats of AT/TA, GT/TG, CT/TC, CTT/TTC, and GAA/AAG occurred with high frequency, whereas CG/GC, CGA/AGC, AAC/CAA, and GCT/TCG repeats had rare incidence. Interesting observation related to differential distribution of simple sequence repeats in genomic components of begomoviruses has been noted. We discussed the possible reasons for the observed divergence. To our knowledge, this is the first analysis of microsatellites occurring in any ssDNA viral genome for such purposes and represents a general approach for analysis of other viral genomes. The presence of microsatellites in geminiviral genomes may be used to obtain information regarding viral genetic diversity, evolution, and strain (isolate) identification.","corpus_id":18742651,"score":2},{"doc_id":"23524008","title":"Occurrence and analysis of imperfect microsatellites in diverse potyvirus genomes.","abstract":"Simple sequence repeats (SSRs) or microsatellites are known to exhibit ubiquitous across all kingdoms of life including viruses. However, imperfections in simple sequence repeats have been analyzed in genomes of human, Escherichia coli and Human Immunodeficiency virus. The assessment of compound microsatellites in plant viral genomes is yet to be studied. Potyviruses severely affect crop plant growth and reduce economic yield in diverse cropping systems worldwide. Hence, we analyze the nature and distribution of compound microsatellites present in complete genome of 45 potyvirus species. The results indicate that compound microsatellites accounted for about 0% to 15.15% of all microsatellites and have low complexity as compared to that of prokaryotic genomes. Overall, 14% of compound microsatellites were of similar motifs and such motif duplications were observed for CA, TA and AG repeats. Among all 45 potyvirus genomes analyzed, SSR couple (AG)-x-(AC) was found to be the most abundant one. Hence it is apparent that in contrast to eukaryotes, majority of compound microsatellites in potyviruses were composed of variant motifs. We also highlight the relative frequency of different classes of compound microsatellites as well as their patterns of distribution and correlate with biology of potyviruses. Further characterization of such variation is important for elucidating the origin, mutational processes, and structure of these widely used, but incompletely understood sequences.","corpus_id":31193256,"score":2},{"doc_id":"23981776","title":"In-silico analysis of simple and imperfect microsatellites in diverse tobamovirus genomes.","abstract":"An in-silico analysis of simple sequence repeats (SSRs) in 30 species of tobamoviruses was done. SSRs (mono to hexa) were present with variant frequency across species. Compound microsatellites, primarily of variant motifs accounted for up to 11.43% of the SSRs. Motif duplications were observed for A, T, AT, and ACA repeats. (AG)-(TC) was the most prevalent SSR-couple. SSRs were differentially localized in the coding region with ~54% on the 128 kDa protein while 20.37% was exclusive to 186 kDa protein. Characterization of such variations is important for elucidating the origin, sequence variations, and structure of these widely used, but incompletely understood sequences.","corpus_id":9379152,"score":2},{"doc_id":"24291012","title":"Genome-wide scan for analysis of simple and imperfect microsatellites in diverse carlaviruses.","abstract":"An exhaustive compilation and analysis of incidence, distribution and variation of simple sequence repeats (SSRs) in viruses are required to understand the evolution and functional aspects of repetitive sequences. Present study focuses on the analysis of SSRs in 32 species of carlaviruses. The full length genome sequences were assessed from NCBI (http://www.ncbi.nlm.nih.-gov/) and analyzed using IMEx software. Variance in incidence of SSRs was observed, independent of genome size. Though the conversion of SSRs to imperfect microsatellite or compound SSR is low; compound microsatellites constituted by variant motifs accounted for up to 12.5% of the SSRs. Mononucleotide A/T is most prevalent followed by dinucleotide GT/TG and trinucleotide AAG/GAA in these genomes. The SSR and cSSR are predominantly localized to the coding region RDRP (RNA dependent RNA polymerase) and ORF-6 (open reading frame). The relative frequency of different classes of simple and compound microsatellites has been highlighted in accordance with the biology of carlavirus. Characterization of such variations would be pivotal for deciphering the enigma of these widely used, but incompletely understood sequences.","corpus_id":206883351,"score":2},{"doc_id":"24434368","title":"Incidence, complexity and diversity of simple sequence repeats across potexvirus genomes.","abstract":"An in-silico analysis of simple sequence repeats (SSRs) in genomes of 32 species of potexviruses was performed wherein a total of 691 SSRs and 33 cSSRs were observed. Though SSRs were present in all the studied genomes their incident frequency ranged from 11 to 30 per genome. Further, 10 potexvirus genomes possessed no cSSRs when extracted at a dMAX of 10 and wherein present, the highest frequency was 3. SSR and cSSR incidence, relative density and relative abundance were non-significantly correlated with genome size and GC content suggesting an ongoing evolutionary and adaptive phase of the virus species. SSRs present primarily ranged from mono- to tri-nucleotide repeat motifs with a greatly skewed distribution across the coding and non-coding regions. Present work is an effort for the undergoing compilation and analysis of incidence, distribution and variation of the viral repeat sequences to understand their evolutionary and functional relevance.","corpus_id":26944643,"score":2},{"doc_id":"24662441","title":"Frequency and distribution of simple and compound microsatellites in forty-eight Human papillomavirus (HPV) genomes.","abstract":"Simple sequence repeats (SSRs) are tandem-repeated sequences ubiquitously present but differentially distributed across genomes. Present study is a systematic analysis for incidence, composition and complexity of different microsatellites in 48 representative Human papillomavirus (HPV) genomes. The analysis revealed a total of 1868 SSRs and 120 cSSRs. However, four genomes (HPV-60, HPV-92, HPV-112 and HPV-136) lacked any cSSR content; while HPV-31 accounted for a maximum of 10 cSSRs. An overall increase in cSSR% with higher dMAX was observed. The SSRs and cSSRs were prevalent in coding regions. Poly(A/T) repeats were significantly more abundant than poly(G/C) repeats possibly due to high (A/T) content of the HPV genomes. Further, higher prevalence of di-nucleotide repeats over tri-nucleotide repeats may be attributed to instability of former because of higher slippage rate. An in-depth study of the satellite sequences would provide an insight into the imperfections and evolution of microsatellites.","corpus_id":23676984,"score":2},{"doc_id":"25172209","title":"The analysis of microsatellites and compound microsatellites in 56 complete genomes of Herpesvirales.","abstract":"Simple sequence repeats (SSRs), or microsatellites, are special DNA/RNA sequences with repeated unit of 1-6 bp. The genomes of Herpesvirales have many repeating structures, which is an excellent system to study the evolution and roles of microsatellites and compound microsatellites in viruses. Therefore, 56 genomes of Herpesvirales were selected and the occurrence, composition and complexity of different repeats were investigated in the genomes. A total of 63,939 microsatellites and 5825 compound microsatellites were extracted from 56 genomes. It found that GC content has a significant strong correlation with both the counts of microsatellites (CM) and the counts of compound microsatellites (CCM). However, genome size has a moderate correlation only with CM and almost no correlation with CCM. The compound microsatellites occurring in genic regions are obviously more than that in intergenic regions. In general, the number of compound microsatellite decreases with the increase of complexity (C) (the count of individual microsatellites being part of a compound microsatellite) and the complexity hardly exceeds C=4. The vast majority of compound microsatellites exist in intergenic regions, when C≥10. The distributions of SSRs tend to be organism-specific rather than host-specific in herpesvirus genomes. The diversity of microsatellites and compound microsatellites may be helpful for a better understanding of the viral genetic diversity, genotyping, and evolutionary biology in herpesviruses genomes.","corpus_id":24338625,"score":2},{"doc_id":"25241644","title":"Genome wide survey of microsatellites in ssDNA viruses infecting vertebrates.","abstract":"Microsatellites or Simple Sequence Repeats (SSRs) are tandem iterations of one to six base pairs, non-randomly distributed throughout prokaryotic and eukaryotic genomes. Limited knowledge is available about distribution of microsatellites in single stranded DNA (ssDNA) viruses, particularly vertebrate infecting viruses. We studied microsatellite distribution in 118 ssDNA virus genomes belonging to three families of vertebrate infecting viruses namely Circoviridae, Parvoviridae, and Anelloviridae, and found that microsatellites constitute an important component of these virus genomes. Mononucleotide repeats were predominant followed by dinucleotide and trinucleotide repeats. A strong positive relationship existed between number of mononucleotide repeats and genome size among all the three virus families. A similar relationship existed for the occurrence of DTTPH (di-, tri-, tetra-, penta- and hexa-nucleotide) repeats in the families Anelloviridae and Parvoviridae only. Relative abundance and relative density of mononucleotide repeats showed a strong positive relationship with genome size in Circoviridae and Parvoviridae. However, in the case of DTTPH repeats, these features showed a strong relationship with genome size in Circoviridae only. On the other hand, relative microsatellite abundance and relative density of mononucleotide repeats were negatively correlated with GC content (%) in Parvoviridae genomes. On the basis of available annotations, our analysis revealed maximum occurrence of mononucleotide as well as DTTPH repeats in the coding regions of these virus genomes. Interestingly, after normalizing the length of the coding and non-coding regions of each virus genome, we found relative density of microsatellites much higher in the non-coding regions. We understand that the present study will help in the better characterization of the stability, genome organization and evolution of these virus classes and may provide useful leads to decipher the etiopathogenesis of these viruses.","corpus_id":35009787,"score":2},{"doc_id":"25606453","title":"In- silico exploration of thirty alphavirus genomes for analysis of the simple sequence repeats.","abstract":"The compilation of simple sequence repeats (SSRs) in viruses and its analysis with reference to incidence, distribution and variation would be instrumental in understanding the functional and evolutionary aspects of repeat sequences. Present study encompasses the analysis of SSRs across 30 species of alphaviruses. The full length genome sequences, assessed from NCBI were used for extraction and analysis of repeat sequences using IMEx software. The repeats of different motif sizes (mono- to penta-nucleotide) observed therein exhibited variable incidence across the species. Expectedly, mononucleotide A/T was the most prevalent followed by dinucleotide AG/GA and trinucleotide AAG/GAA in these genomes. The conversion of SSRs to imperfect microsatellite or compound microsatellite (cSSR) is low. cSSR, primarily constituted by variant motifs accounted for up to 12.5% of the SSRs. Interestingly, seven species lacked cSSR in their genomes. However, the SSR and cSSR are predominantly localized to the coding region ORFs for non structural protein and structural proteins. The relative frequencies of different classes of simple and compound microsatellites within and across genomes have been highlighted.","corpus_id":14395507,"score":2},{"doc_id":"25817404","title":"Potential linkage between compound microsatellites and recombination in geminiviruses: Evidence from comparative analysis.","abstract":"The compound microsatellites consist of two or more individual microsatellites, originate from mutation or imperfection in simple repeat sequences. The reports on systematic analysis of the occurrence, size and density of compound microsatellite (cSSR) types are very rare. Our study indicates that cSSRs are clustered at specific regions in the begomovirus genomes. cSSRs were overrepresented in majority of begomovirus genomes indicating that they might have some functional significance. Further, non-random distribution pattern of cSSR in begomovirus genomes was significantly correlated with the recombination breakpoint positions in the genome. The analysis of cSSR regions in the viral genome indicates the presence of stem loop (hairpin) secondary structure. The significance of these findings in biology of geminiviruses is discussed based on our present understanding of recombination and repetitive DNA. To our knowledge, this is the first analysis suggesting the possible association between recombination and microsatellites in any viral genome.","corpus_id":42111704,"score":2},{"doc_id":"26410414","title":"Comparative analysis of microsatellites and compound microsatellites in T4-like viruses.","abstract":"Microsatellites or simple sequence repeats (SSRs) are known to present ubiquitously in genomes of eukaryotes and prokaryotes, as well as viruses. A comprehensive analysis of microsatellites and compound microsatellites (CM) was performed for 67 T4-like bacteriophage genomes. We found that the number of repeats was generally proportional to the size of the genome. CM were more abundant in genic regions, while their relative abundance was higher in intergenic regions. Meanwhile, the number of CM rapidly decreased with the increase of complexity but gradually increased with higher dMAX (maximum distance between any two adjacent microsatellites). (A)n/(T)n, (AT)n/(TA)n and (AAG)n were the most abundant repeats of mono-, di- and trinucleotide microsatellites, respectively. The number of microsatellites in reference sequences was significantly lower than that in corresponding random sequences. This result was mainly attributed to mono- and dinucleotide repeats which hardly exceeded 6bp in T4-like viruses. These observations may be helpful to understand the distribution of microsatellites and viral genetic diversity in T4-like viruses.","corpus_id":13609230,"score":2},{"doc_id":"27030027","title":"Identification of common, unique and polymorphic microsatellites among 73 cyanobacterial genomes.","abstract":"Microsatellites also known as Simple Sequence Repeats are short tandem repeats of 1-6 nucleotides. These repeats are found in coding as well as non-coding regions of both prokaryotic and eukaryotic genomes and play a significant role in the study of gene regulation, genetic mapping, DNA fingerprinting and evolutionary studies. The availability of 73 complete genome sequences of cyanobacteria enabled us to mine and statistically analyze microsatellites in these genomes. The cyanobacterial microsatellites identified through bioinformatics analysis were stored in a user-friendly database named CyanoSat, which is an efficient data representation and query system designed using ASP.net. The information in CyanoSat comprises of perfect, imperfect and compound microsatellites found in coding, non-coding and coding-non-coding regions. Moreover, it contains PCR primers with 200 nucleotides long flanking region. The mined cyanobacterial microsatellites can be freely accessed at www.compubio.in/CyanoSat/home.aspx. In addition to this 82 polymorphic, 13,866 unique and 2390 common microsatellites were also detected. These microsatellites will be useful in strain identification and genetic diversity studies of cyanobacteria.","corpus_id":29784366,"score":2},{"doc_id":"27650818","title":"Genome-wide In Silico Analysis, Characterization and Identification of Microsatellites in Spodoptera littoralis Multiple nucleopolyhedrovirus (SpliMNPV).","abstract":"In this study, we undertook a survey to analyze the distribution and frequency of microsatellites or Simple Sequence Repeats (SSRs) in Spodoptera littoralis multiple nucleopolyhedrovirus (SpliMNPV) genome (isolate AN-1956). Out of the 55 microsatellite motifs, identified in the SpliMNPV-AN1956 genome using in silico analysis (inclusive of mono-, di-, tri- and hexa-nucleotide repeats), 39 were found to be distributed within coding regions (cSSRs), whereas 16 were observed to lie within intergenic or noncoding regions. Among the 39 motifs located in coding regions, 21 were located in annotated functional genes whilst 18 were identified in unknown functional genes (hypothetical proteins). Among the identified motifs, trinucleotide (80%) repeats were found to be the most abundant followed by dinucleotide (13%), mononucleotide (5%) and hexanucleotide (2%) repeats. The 39 motifs located within coding regions were further validated in vitro by using PCR analysis, while the 21 motifs located within known functional genes (15 genes) were characterized using nucleotide sequencing. A comparison of the sequence analysis data of the 21 sequenced cSSRs with the published sequences is presented. Finally, the developed SSR markers of the 39 motifs were further mapped/localized onto the SpliMNPV-AN1956 genome. In conclusion, the SSR markers specific to SpliMNPV, developed in this study, could be a useful tool for the identification of isolates and analysis of genetic diversity and viral evolutionary status.","corpus_id":10889483,"score":2},{"doc_id":"18022767","title":"Structural families of genomic microsatellites.","abstract":"We present an analysis of tandem repeats of short sequence motifs (microsatellites) in twelve eukaryotes for which a large part of the genome has been sequenced and assembled. The pattern of motif abundance varies significantly in different species, but it is very similar in different chromosomes of the same species. The most abundant repeats can be classified in two main families. The first family has a rigid conformation, with purines in one strand and pyrimidines in the complementary strand, mainly A(n)/T(n) and (AG)(n)/(CT)(n). The second family has alternating, flexible sequences, such as (AT)(n), (AC)(n) and related sequences. In the pluricellular organisms the relative frequency of both families is rather constant. These observations indicate that microsatellites have structural information and may be involved in the organization of chromatin fibers and in chromosome architecture in general. An additional intriguing finding is the absence of microsatellites with sequences which appear to be forbidden, such as (AATT)(n).","corpus_id":40137722,"score":1},{"doc_id":"18560170","title":"Eucalyptus microsatellites mined in silico: survey and evaluation.","abstract":"Eucalyptus is an important short rotation pulpy woody plant, grown widely in the tropics. Recently, many genomic programmes are underway leading to the accumulation of voluminous genomic and expressed sequence tag sequences in public databases. These sequences can be utilized for analysis of simple sequence repeats (SSRs) and single nucleotide polymorphism (SNPs) available in the transcribed genes. In this study, in silico analysis of 15,285 sequences representing partial and full-length mRNA from Eucalyptus species for their use in developing SSRs or microsatellites were carried out. A total of 875 EST-SSRs were identified from 772 SSR containing ESTs. Motif size of 6 for dinucleotide and 5 for trinucleotide, tetranucleotide, and pentanucleotides were considered in locating the microsatellites. The average frequency of identified SSRs was 12.9%. The dinucleotide repeats were the most abundant among the dinucleotide, trinucleotide and tetranucleotide motifs and accounted for 50.9% of the Eucalyptus genome. Primer designing analysis showed that 571 sequences with SSRs had sufficient flanking regions for polymerase chain reaction (PCR) primer synthesis. Evaluation of the usefulness of the SSRs showed that EST-derived SSRs can generate polymorphic markers as all the primers showed allelic diversity among the 16 provenances of E. tereticornis.","corpus_id":26092757,"score":1},{"doc_id":"18928198","title":"In silico analysis of microsatellites in organellar genomes of major cereals for understanding their phylogenetic relationships.","abstract":"Microsatellites are abundant across prokaryotic and eukaryotic genomes. However, comparative analysis of microsatellites in the organellar genomes of plants and their utility in understanding phylogeny has not been reported. The purpose of this study was to understand the organization of microsatellites in the coding and non-coding regions of organellar genomes of major cereals viz., rice, wheat, maize and sorghum. About 5.8-14.3% of mitochondrial and 30.5-43.2% of chloroplast microsatellites were observed in the coding regions. About 83.8-86.8% of known mitochondrial genes had at least one microsatellite while this value ranged from 78.6-82.9% among the chloroplast genomes. Dinucleotide repeats were the most abundant in the coding and non-coding regions of the mitochondrial genome while mononucleotides were predominant in chloroplast genomes. Maize harbored more repeats in the mitochondrial genome, which could be due to the larger size of genome. A phylogenetic analysis based on mitochondrial and chloroplast genomic microsatellites revealed that rice and sorghum were closer to each other, while wheat was the farthest and this corroborated with the earlier reported phylogenies based on nuclear genome co-linearity and chloroplast gene-based analysis.","corpus_id":22851127,"score":1},{"doc_id":"19146945","title":"Consensus features of microsatellite distribution: microsatellite contents are universally correlated with recombination rates and are preferentially depressed by centromeres in multicellular eukaryotic genomes.","abstract":"Microsatellite DNA is highly polymorphic and informative, which makes its distribution pattern and its associations very valuable for marker applications and genomic research in evolution. Using computational and statistical approaches, based on database technology, we have demonstrated that microsatellite content is consistently and significantly 2 to 5 fold lower than the average chromosomal level in the centromeric and pericentromeric regions of the chromosomes of two plant species, Arabidopsis thaliana and Oryza sativa. We conducted a path coefficient analysis to compare the direct effect of microsatellites (from mono-nucleotide through to penta-nucleotide repeats) on recombination rates. The results revealed that tri- and penta-nucleotide microsatellites significantly influence recombination rates. In the human genome, tri-, tetra- and mono-nucleotide microsatellites, in decreasing order, make significant direct contributions to recombination rates, according to DECODE, GENTHON, and MARSHFIELD averages. Path coefficient analysis in rice and human genomes of the impact of di-nucleotide microsatellites of different motifs on recombination rates indicate that motifs with either A or T have an effect, resulting in increased recombination rates for microsatellites with motifs consisting of 50% A or T, such as AG, TC, CA, TG. Conversely, microsatellites with motifs consisting of only A & T or G & C, such as AT, TA, GC or CG, have decreased recombination rates. The extremely low microsatellite content in centromeric and pericentromeric regions, as well as the quantitative association of microsatellite sequences with the recombination rate at the genome level, suggests that purifying selection in genome evolution creates a balance between genomic polymorphisms and the biological function of sequences in a genome.","corpus_id":27350196,"score":1},{"doc_id":"19273135","title":"Genomic features of Lactobacillus species.","abstract":"As member of the lactic acid bacteria (LAB), the genus Lactobacillus represents a diverse number of species that play significant roles in the biopreservation of foods and commensals common within the human gastrointestinal (GI) tract. Certain species of Lactobacillus, particularly those of human origin, have been used as probiotic bacteria due to their health-promoting effects. A recent explosion of genomic information on lactobacilli has expanded our knowledge of metabolic capabilities and key gene features that are predicted to play important roles in niche adaptation and function. This review provides an overview of probiotic-related genome features and functional genomic studies that have linked genes to traits. Interspecies heterogeneity and niche-specialized adaptation among lactobacilli, as revealed by comparative genome analysis, are also discussed.","corpus_id":24769565,"score":1},{"doc_id":"19484264","title":"Genome-wide analysis of conservation and divergence of microsatellites in rice.","abstract":"Studies on microsatellite distribution and divergence in related genomes contribute towards understanding of genome evolution in eukaryotes. Despite the availability of whole genome sequences of four rice genomes, occurrence and significance of microsatellites in the rice genome has remained a relatively unexplored area of research. We have aligned genomes of two rice subspecies i.e. indica and japonica to understand the trends of microsatellite conservation and divergence in the rice genome. Nearly 62% of the indica microsatellites were also found in the japonica genome. Occurrence of microsatellites showed a negative association with that of retrotransposons. Microsatellites repeat unit length and sequence showed direct influence on the microsatellite locus length. Further, microsatellite allele length was also influenced by the sequence characteristics of the neighbouring regions. CCG repeats were most conserved microsatellite sequences across the different syntenic regions in the two rice genomes and often showed association with CpG islands. Our study suggested that microsatellite distribution is not only governed by a balance between replication slippage and point mutations as proposed earlier, but also by the microsatellite motif sequence and characteristics of microsatellite neighbouring regions in the genome. Thus, this study is likely to prove an important reference for understanding the process of microsatellite evolution and dynamics in the two rice subspecies.","corpus_id":6305878,"score":1},{"doc_id":"20130749","title":"Microsatellites in Brassica unigenes: relative abundance, marker design, and use in comparative physical mapping and genome analysis.","abstract":"